Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 70 of 276
Found at i:21596659 original size:24 final size:25
Alignment explanation
Indices: 21596626--21596677 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
21596616 TTTCAATCAA
* *
21596626 AATAATTTCAATCA-ATA-TAAATTC
1 AATAAATTC-ATCACATACTAAAATC
21596650 AATAAATTCATCACATACTAAAATC
1 AATAAATTCATCACATACTAAAATC
21596675 AAT
1 AAT
21596678 CTATTTCAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 11 0.46
25 9 0.38
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (25 bp):
AATAAATTCATCACATACTAAAATC
Found at i:21597924 original size:13 final size:13
Alignment explanation
Indices: 21597906--21597933 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21597896 CCTCTTTTTA
21597906 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
21597919 TTCTTTTGTTTCT
1 TTCTTTTGTTTCT
21597932 TT
1 TT
21597934 TATATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (13 bp):
TTCTTTTGTTTCT
Found at i:21600846 original size:23 final size:25
Alignment explanation
Indices: 21600815--21600867 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
21600805 AAGGGAAAAA
*
21600815 AAATATTATATACATATAA-AATTT
1 AAATATTATACACATATAATAATTT
**
21600839 AAAT-TTATACGTATATAATAATTT
1 AAATATTATACACATATAATAATTT
21600863 AAATA
1 AAATA
21600868 AAAAATAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATATTATACACATATAATAATTT
Found at i:21602551 original size:18 final size:18
Alignment explanation
Indices: 21602528--21602588 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
21602518 GTAAAGGATA
21602528 TTAAATTTTCACATATGT
1 TTAAATTTTCACATATGT
* * *
21602546 TTAAATATT-A-GTGTGGAT
1 TTAAATTTTCACATAT-G-T
21602564 ATTAAATTTTCACATATGT
1 -TTAAATTTTCACATATGT
21602583 TTAAAT
1 TTAAAT
21602589 ATTAGTGTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
16 2 0.06
17 2 0.06
18 15 0.47
19 9 0.28
20 2 0.06
21 2 0.06
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (18 bp):
TTAAATTTTCACATATGT
Found at i:21602573 original size:37 final size:37
Alignment explanation
Indices: 21602523--21602596 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
21602513 CATTGGTAAA
21602523 GGATATTAAATTTTCACATATGTTTAAATATTAGTGT
1 GGATATTAAATTTTCACATATGTTTAAATATTAGTGT
21602560 GGATATTAAATTTTCACATATGTTTAAATATTAGTGT
1 GGATATTAAATTTTCACATATGTTTAAATATTAGTGT
21602597 ATCTTTATCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (37 bp):
GGATATTAAATTTTCACATATGTTTAAATATTAGTGT
Found at i:21603570 original size:12 final size:12
Alignment explanation
Indices: 21603553--21603577 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21603543 AATAAATAAA
21603553 TGAAATGTATTT
1 TGAAATGTATTT
21603565 TGAAATGTATTT
1 TGAAATGTATTT
21603577 T
1 T
21603578 ATTAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TGAAATGTATTT
Found at i:21604121 original size:16 final size:16
Alignment explanation
Indices: 21604100--21604132 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21604090 TAAAAGATTA
21604100 AAAGTAA-ATGATATAC
1 AAAGTAATAT-ATATAC
21604116 AAAGTAATATATATAC
1 AAAGTAATATATATAC
21604132 A
1 A
21604133 TGAAAAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (16 bp):
AAAGTAATATATATAC
Found at i:21605881 original size:40 final size:40
Alignment explanation
Indices: 21605753--21605966 Score: 94
Period size: 42 Copynumber: 5.2 Consensus size: 40
21605743 CCGCTATTCT
* *
21605753 TTAGGGGAGATCTGTATTTTCTAGCATGTTACCCTACTGC
1 TTAGGGGAGATCCGTATTTTCTAGCCTGTTACCCTACTGC
** * * * * * **
21605793 TTA-GGGAGTTAAGGCTTATTGTCTTCGATCTGCT-CCACTACTAT
1 TTAGGGGAG---ATCCGTATTTTC-TAG-CCTGTTACC-CTACTGC
21605837 TTAGGGGAGATCCGTATTTTCTAGCCTGTTACCCTACTGC
1 TTAGGGGAGATCCGTATTTTCTAGCCTGTTACCCTACTGC
** * * * * * **
21605877 TTA-GGGAGTTAAGGCTTACTTTCTTTGATCTGCT-CCGCTACTAT
1 TTAGGGGAG---ATCCGTATTTTC-TAG-CCTGTTACC-CTACTGC
* *
21605921 TTAGGGGAGATCTGTATTTTCTAGCCTCTTACCCTACTGC
1 TTAGGGGAGATCCGTATTTTCTAGCCTGTTACCCTACTGC
21605961 TTAGGG
1 TTAGGG
21605967 AGTTAACGCT
Statistics
Matches: 118, Mismatches: 40, Indels: 32
0.62 0.21 0.17
Matches are distributed among these distances:
39 10 0.08
40 29 0.25
41 8 0.07
42 30 0.25
43 8 0.07
44 23 0.19
45 10 0.08
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (40 bp):
TTAGGGGAGATCCGTATTTTCTAGCCTGTTACCCTACTGC
Found at i:21606184 original size:255 final size:253
Alignment explanation
Indices: 21605564--21606316 Score: 918
Period size: 250 Copynumber: 3.0 Consensus size: 253
21605554 TAGAAACTCG
* *** * * *
21605564 TCTTCAATTTGCTCCACTACTATTTAGGGGAGATTTTTATCTTCTA-ACTGGTTACCCTACTATT
1 TCTTCAATCTGCTCCACTACTATTTAGGGGAGATCCGTATTTTCTAGCCT-GTTACCCTACTACT
* **
21605628 TAGGGAGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTGTTTAGGAAAGATCTGTATTTTCT
65 TAGGGAGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCT
** * * * *
21605693 AGCCTGTTACCCTACTGCTTAGGGAGTTAAGGCTTATTGTCTTT-A-CTGCTCCGCTATTCTTTA
130 AGCCTGTTACCCTACTGCTTAGGGAGTTAA-GCTTGCTGTCTTTGATCTGTTCCACTACTGTTTA
* * *
21605756 GGGGAGATCTGTA--TTTTCTAGCATGTTACCCTACTGCTTAGGGAGTTAAGGCTTATTG
194 GGGGAGATCTGTATTTTTTCTAGCATGTCACCCTACTGCTTAGGGAGTTAAGGCTTACTA
* *
21605814 TCTTCGATCTGCTCCACTACTATTTAGGGGAGATCCGTATTTTCTAGCCTGTTACCCTACTGCTT
1 TCTTCAATCTGCTCCACTACTATTTAGGGGAGATCCGTATTTTCTAGCCTGTTACCCTACTACTT
* * *
21605879 AGGGAGTTAAGGCTTACTTTCTTTGATCTGCTCCGCTACTATTTAGGGGAGATCTGTATTTTCTA
66 AGGGAGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCTA
* *
21605944 GCCTCTTACCCTACTGCTTAGGGAGTTAACGCTTGCTGACTTTGATCTGTTCCACTACTGTTTAG
131 GCCTGTTACCCTACTGCTTAGGGAGTTAA-GCTTGCTGTCTTTGATCTGTTCCACTACTGTTTAG
* * * *
21606009 GGGAGATCTGTATTTTTTTTAGTC-TGTCACCCTACTGTTTAGGGGGTTAAGGCTTGCTA
195 GGGAGATCTGTATTTTTTCTAG-CATGTCACCCTACTGCTTAGGGAGTTAAGGCTTACTA
* * * * *
21606068 TCTTCAATCTGTTCCAC-ACTGTTTAGGGGAGATCTGTATTTTTTTTAGCCTGTTACCCTAATAC
1 TCTTCAATCTGCTCCACTACTATTTAGGGGAGATCCGTA--TTTTCTAGCCTGTTACCCTACTAC
* * * *
21606132 TTAGGGAGTTAAAGCTTGCTGACTTCGATCTACTCCACTACTATTTAGGGGAGATCTGTATTTTC
64 TTAGGGAGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTC
* * *
21606197 TA-ACTGGTTACCCTACTGCTTAGGGAGTTAAGACCTGCTGTCTTCGATCTGTTCCACTACTGTT
129 TAGCCT-GTTACCCTACTGCTTAGGGAGTTAAG-CTTGCTGTCTTTGATCTGTTCCACTACTGTT
* * * *
21606261 TAGGGGAGATC--TATATTTTC-ATGCCTGTTACCCTGCTGCTTA-GGAGGTTAAGGCTT
192 TAGGGGAGATCTGTATTTTTTCTA-GCATGTCACCCTACTGCTTAGGGA-GTTAAGGCTT
21606317 GTTGTCTTGA
Statistics
Matches: 434, Mismatches: 56, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
250 150 0.35
251 3 0.01
252 31 0.07
253 51 0.12
254 54 0.12
255 145 0.33
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.39
Consensus pattern (253 bp):
TCTTCAATCTGCTCCACTACTATTTAGGGGAGATCCGTATTTTCTAGCCTGTTACCCTACTACTT
AGGGAGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCTA
GCCTGTTACCCTACTGCTTAGGGAGTTAAGCTTGCTGTCTTTGATCTGTTCCACTACTGTTTAGG
GGAGATCTGTATTTTTTCTAGCATGTCACCCTACTGCTTAGGGAGTTAAGGCTTACTA
Found at i:21606209 original size:339 final size:334
Alignment explanation
Indices: 21605563--21606317 Score: 935
Period size: 339 Copynumber: 2.2 Consensus size: 334
21605553 ATAGAAACTC
* * * * * * **
21605563 GTCTTCAATTTGCTCCACTACTATTTAGGGGAGATTTTTATCTTCTA-ACTGGTTACCCTACTAT
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTATATTTTCTAGCCT-GTTACCCTACTGC
* *
21605627 TTAGGGAGTTAAGGCTTACTGTCTTCGATCTGCTCCACTACTGTTTAGGAAAGATCTGTATTTTC
65 TTAGGGAGTTAAGGCTTGCTGACTTCGATCTGCTCCACTACTGTTTAGGAAAGATCTGTATTTTC
* * * * * *
21605692 TAGCCTGTTACCCTACTGCTTAGGGAGTTAAGGCTTATTGTCTTTACTGCTCCGCTATTCTTTAG
130 TAGCCTGTCACCCTACTGCTTAGGGAGTTAAGGCTTACTATCTTAACTGCTCCACTACTCTTTAG
* * * * *
21605757 GGGAGATCTGTATTTTCTAGCATGTTACCCTACTGCTTAGGGAGTTAAGGCTTATTGTCTTCGAT
195 GGGAGATCTGTATTTTCTAGCATGTTACCCTAATACTTAGGGAGTTAAAGCTTACTGACTTCGAT
* *
21605822 CTGCTCCACTACTATTTAGGGGAGATCCGTATTTTCTAGCCTGTTACCCTACTGCTTAGGGAGTT
260 CTACTCCACTACTATTTAGGGGAGATCCGTATTTTCTAGACTGTTACCCTACTGCTTAGGGAGTT
* *
21605887 AAGGCTTACT
325 AAGACCTACT
* * * * *
21605897 TTCTTTGATCTGCTCCGCTACTATTTAGGGGAGATCTGTATTTTCTAGCCTCTTACCCTACTGCT
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTATATTTTCTAGCCTGTTACCCTACTGCT
* * * **
21605962 TAGGGAGTTAACGCTTGCTGACTTTGATCTGTTCCACTACTGTTTAGGGGAGATCTGTATTTTTT
66 TAGGGAGTTAAGGCTTGCTGACTTCGATCTGCTCCACTACTGTTTAGGAAAGATCTGTA--TTTT
* * * * * * *
21606027 TTAGTCTGTCACCCTACTGTTTAGGGGGTTAAGGCTTGCTATCTTCAATCTGTTCCAC-ACTGTT
129 CTAGCCTGTCACCCTACTGCTTAGGGAGTTAAGGCTTACTATCTT-AA-CTGCTCCACTACTCTT
* * *
21606091 TAGGGGAGATCTGTATTTTTTTTAGCCTGTTACCCTAATACTTAGGGAGTTAAAGCTTGCTGACT
192 TAGGGGAGATCTGTA--TTTTCTAGCATGTTACCCTAATACTTAGGGAGTTAAAGCTTACTGACT
*
21606156 TCGATCTACTCCACTACTATTTAGGGGAGATCTGTATTTTCTA-ACTGGTTACCCTACTGCTTAG
255 TCGATCTACTCCACTACTATTTAGGGGAGATCCGTATTTTCTAGACT-GTTACCCTACTGCTTAG
*
21606220 GGAGTTAAGACCTGCT
319 GGAGTTAAGACCTACT
* * *
21606236 GTCTTCGATCTGTTCCACTACTGTTTAGGGGAGATCTATATTTTC-ATGCCTGTTACCCTGCTGC
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTATATTTTCTA-GCCTGTTACCCTACTGC
21606300 TTA-GGAGGTTAAGGCTTG
65 TTAGGGA-GTTAAGGCTTG
21606318 TTGTCTTGAC
Statistics
Matches: 356, Mismatches: 55, Indels: 15
0.84 0.13 0.04
Matches are distributed among these distances:
334 102 0.29
335 2 0.01
336 41 0.12
337 20 0.06
338 13 0.04
339 178 0.50
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (334 bp):
GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTATATTTTCTAGCCTGTTACCCTACTGCT
TAGGGAGTTAAGGCTTGCTGACTTCGATCTGCTCCACTACTGTTTAGGAAAGATCTGTATTTTCT
AGCCTGTCACCCTACTGCTTAGGGAGTTAAGGCTTACTATCTTAACTGCTCCACTACTCTTTAGG
GGAGATCTGTATTTTCTAGCATGTTACCCTAATACTTAGGGAGTTAAAGCTTACTGACTTCGATC
TACTCCACTACTATTTAGGGGAGATCCGTATTTTCTAGACTGTTACCCTACTGCTTAGGGAGTTA
AGACCTACT
Found at i:21606323 original size:84 final size:84
Alignment explanation
Indices: 21605563--21606324 Score: 908
Period size: 84 Copynumber: 9.1 Consensus size: 84
21605553 ATAGAAACTC
* * * * * * **
21605563 GTCTTCAATTTGCTCCACTACTATTTAGGGGAGATTTTTATCTTCTA-ACTGGTTACCCTACTAT
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCTAGCCT-GTTACCCTACTGC
*
21605627 TTAGGGAGTTAAGGCTTACT
65 TTAGGGAGTTAAGGCTTGCT
* **
21605647 GTCTTCGATCTGCTCCACTACTGTTTAGGAAAGATCTGTATTTTCTAGCCTGTTACCCTACTGCT
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCTAGCCTGTTACCCTACTGCT
**
21605712 TAGGGAGTTAAGGCTTATT
66 TAGGGAGTTAAGGCTTGCT
* * * * *
21605731 GTCTT-TA-CTGCTCCGCTATTCTTTAGGGGAGATCTGTATTTTCTAGCATGTTACCCTACTGCT
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCTAGCCTGTTACCCTACTGCT
**
21605794 TAGGGAGTTAAGGCTTATT
66 TAGGGAGTTAAGGCTTGCT
*
21605813 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCCGTATTTTCTAGCCTGTTACCCTACTGCT
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCTAGCCTGTTACCCTACTGCT
*
21605878 TAGGGAGTTAAGGCTTACT
66 TAGGGAGTTAAGGCTTGCT
* * * *
21605897 TTCTTTGATCTGCTCCGCTACTATTTAGGGGAGATCTGTATTTTCTAGCCTCTTACCCTACTGCT
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCTAGCCTGTTACCCTACTGCT
*
21605962 TAGGGAGTTAACGCTTGCT
66 TAGGGAGTTAAGGCTTGCT
* * * * * * *
21605981 GACTTTGATCTGTTCCACTACTGTTTAGGGGAGATCTGTATTTTTTTTAGTCTGTCACCCTACTG
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTA--TTTTCTAGCCTGTTACCCTACTG
* *
21606046 TTTAGGGGGTTAAGGCTTGCT
64 CTTAGGGAGTTAAGGCTTGCT
* * * * * * *
21606067 ATCTTCAATCTGTTCCAC-ACTGTTTAGGGGAGATCTGTATTTTTTTTAGCCTGTTACCCTAATA
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTA--TTTTCTAGCCTGTTACCCTACTG
*
21606131 CTTAGGGAGTTAAAGCTTGCT
64 CTTAGGGAGTTAAGGCTTGCT
* * *
21606152 GACTTCGATCTACTCCACTACTATTTAGGGGAGATCTGTATTTTCTA-ACTGGTTACCCTACTGC
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCTAGCCT-GTTACCCTACTGC
* *
21606216 TTAGGGAGTTAAGACCTGCT
65 TTAGGGAGTTAAGGCTTGCT
* * * *
21606236 GTCTTCGATCTGTTCCACTACTGTTTAGGGGAGATCTATATTTTC-ATGCCTGTTACCCTGCTGC
1 GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCTA-GCCTGTTACCCTACTGC
*
21606300 TTA-GGAGGTTAAGGCTTGTT
65 TTAGGGA-GTTAAGGCTTGCT
21606320 GTCTT
1 GTCTT
21606325 GACCGATGCC
Statistics
Matches: 589, Mismatches: 79, Indels: 20
0.86 0.11 0.03
Matches are distributed among these distances:
82 74 0.13
83 8 0.01
84 359 0.61
85 77 0.13
86 71 0.12
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (84 bp):
GTCTTCGATCTGCTCCACTACTATTTAGGGGAGATCTGTATTTTCTAGCCTGTTACCCTACTGCT
TAGGGAGTTAAGGCTTGCT
Found at i:21612405 original size:46 final size:46
Alignment explanation
Indices: 21612335--21612426 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
21612325 CTTATTTATC
* * *
21612335 TTTGACATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTT
1 TTTGACATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTT
* * *
21612381 TTTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1 TTTGACATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTT
21612427 CATATCAGAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (46 bp):
TTTGACATGATGCCATAGTATCTTTCAACCATGGTCTTACACATTT
Found at i:21614531 original size:11 final size:11
Alignment explanation
Indices: 21614515--21614549 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
21614505 ATATATATTA
21614515 AATAAAATAAT
1 AATAAAATAAT
21614526 AATAAAATAAT
1 AATAAAATAAT
21614537 AATAAAATAAT
1 AATAAAATAAT
21614548 AA
1 AA
21614550 AATATCAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:21614852 original size:29 final size:31
Alignment explanation
Indices: 21614811--21614871 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
21614801 TAAAATATTG
* *
21614811 CACTATTAGTCCTTCAAATTTTTA-TATTTA
1 CACTATTAATCCTTCAAATTTTGAGTATTTA
21614841 CACT-TTAATCCTTCAAATTTTGAGTATTTA
1 CACTATTAATCCTTCAAATTTTGAGTATTTA
21614871 C
1 C
21614872 TCATGGGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.48
Consensus pattern (31 bp):
CACTATTAATCCTTCAAATTTTGAGTATTTA
Found at i:21629567 original size:6 final size:6
Alignment explanation
Indices: 21629556--21629589 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
21629546 ACAATTTTTG
21629556 AAATCT AAATCT AAATCT AAATCT AAATTCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAA-TCT AAA
21629590 ATTTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:21632326 original size:32 final size:32
Alignment explanation
Indices: 21632254--21632413 Score: 203
Period size: 32 Copynumber: 4.9 Consensus size: 32
21632244 TAACCTCAGT
**
21632254 GGAATGGACAAAACCAACATATTGATTGACCTTAAT
1 GGAATGGACAAAACCAACATATTG---G-CCTTAGC
*
21632290 GGAATGGACAAAACCAACACATTGGCCTTAGC
1 GGAATGGACAAAACCAACATATTGGCCTTAGC
** **
21632322 GGAATGGACAAAATGAACATGCTGGCCTTAGC
1 GGAATGGACAAAACCAACATATTGGCCTTAGC
*
21632354 GGAATGGACAAAATCAACATATTGGCCTTAGC
1 GGAATGGACAAAACCAACATATTGGCCTTAGC
*
21632386 GGAATGAACAAAACCAACATATTGGCCT
1 GGAATGGACAAAACCAACATATTGGCCT
21632414 CAACTTACTC
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
32 87 0.78
33 1 0.01
36 23 0.21
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (32 bp):
GGAATGGACAAAACCAACATATTGGCCTTAGC
Found at i:21638718 original size:104 final size:104
Alignment explanation
Indices: 21638538--21638746 Score: 382
Period size: 104 Copynumber: 2.0 Consensus size: 104
21638528 CAAAATTATG
*
21638538 CAAGGTGACCATCGTAAACAGTCCCTCAATTTTGGTCACCTTCAGTTTTGATATTTTGTACGAAT
1 CAAGGTGACCATCGTAAACAGTCCCTCAACTTTGGTCACCTTCAGTTTTGATATTTTGTACGAAT
*
21638603 CTTTGTGTAATTGTTTTTGTAAATTACAATTTGAAGCTA
66 CTTTGTGTAATTGCTTTTGTAAATTACAATTTGAAGCTA
**
21638642 CAAGGTGACCATCGTAAACAGTCCCTCAACTTTGGTCACCTTCAGTTTTGATATTTTGTTTGAAT
1 CAAGGTGACCATCGTAAACAGTCCCTCAACTTTGGTCACCTTCAGTTTTGATATTTTGTACGAAT
21638707 CTTTGTGTAATTGCTTTTGTAAATTACAATTTGAAGCTA
66 CTTTGTGTAATTGCTTTTGTAAATTACAATTTGAAGCTA
21638746 C
1 C
21638747 TAAAAAGTCA
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.40
Consensus pattern (104 bp):
CAAGGTGACCATCGTAAACAGTCCCTCAACTTTGGTCACCTTCAGTTTTGATATTTTGTACGAAT
CTTTGTGTAATTGCTTTTGTAAATTACAATTTGAAGCTA
Found at i:21641490 original size:30 final size:31
Alignment explanation
Indices: 21641431--21641494 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
21641421 ACTTAACAAG
21641431 CAAATGCTTCTAAAATAATAAAAAAAATTAA
1 CAAATGCTTCTAAAATAATAAAAAAAATTAA
*
21641462 CAAATGCCTT-TAAAATAAT-AAGAAAATTAA
1 CAAATG-CTTCTAAAATAATAAAAAAAATTAA
21641492 CAA
1 CAA
21641495 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 13 0.42
31 15 0.48
32 3 0.10
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (31 bp):
CAAATGCTTCTAAAATAATAAAAAAAATTAA
Found at i:21643539 original size:6 final size:6
Alignment explanation
Indices: 21643528--21643552 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
21643518 TTAGCCTTTA
21643528 ATATTT ATATTT ATATTT ATATTT A
1 ATATTT ATATTT ATATTT ATATTT A
21643553 ATGACAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:21650807 original size:11 final size:11
Alignment explanation
Indices: 21650791--21650815 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
21650781 TTTTTTAGAG
21650791 AATGAAGCAAA
1 AATGAAGCAAA
21650802 AATGAAGCAAA
1 AATGAAGCAAA
21650813 AAT
1 AAT
21650816 AAAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.08, G:0.16, T:0.12
Consensus pattern (11 bp):
AATGAAGCAAA
Found at i:21651353 original size:43 final size:43
Alignment explanation
Indices: 21651298--21651455 Score: 210
Period size: 43 Copynumber: 3.7 Consensus size: 43
21651288 GGTCCCTACA
* * * **
21651298 TTATATATTTCAAACTATTATATCTTATTTATTTTGAAATTGC
1 TTATATACTTCAAACTATTATATATTATTTCTTTTGAAATTAT
*
21651341 TTATATACTTCAAACTATTATATTTTATTTCTTTTGAAATTAT
1 TTATATACTTCAAACTATTATATATTATTTCTTTTGAAATTAT
* * *
21651384 TTATATGCTTTAAACTTTTATATATTATTTCTTTTGAAATTAT
1 TTATATACTTCAAACTATTATATATTATTTCTTTTGAAATTAT
* *
21651427 TTATATACTTTAAA-TTTTATATATTATTT
1 TTATATACTTCAAACTATTATATATTATTT
21651456 TGGATTATTT
Statistics
Matches: 105, Mismatches: 10, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
42 15 0.14
43 90 0.86
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (43 bp):
TTATATACTTCAAACTATTATATATTATTTCTTTTGAAATTAT
Found at i:21651441 original size:18 final size:18
Alignment explanation
Indices: 21651420--21651471 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
21651410 ATTTCTTTTG
21651420 AAATTATTTATATACTTT
1 AAATTATTTATATACTTT
*
21651438 AAATT-TTATATATTATTTT
1 AAATTATT-TATA-TACTTT
**
21651457 GGATTATTTATATAC
1 AAATTATTTATATAC
21651472 ATATGTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
17 2 0.07
18 11 0.41
19 12 0.44
20 2 0.07
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (18 bp):
AAATTATTTATATACTTT
Found at i:21651626 original size:25 final size:25
Alignment explanation
Indices: 21651573--21651632 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
21651563 ATGTTAAACC
*
21651573 ATTTTATATATTATCTATTTTACGT
1 ATTTTATATATTATCTATTGTACGT
* *
21651598 -TTTTATATGTTATTTTATTGTAC-T
1 ATTTTATATATTA-TCTATTGTACGT
21651622 ATTTTATATAT
1 ATTTTATATAT
21651633 GTGAATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.63
Consensus pattern (25 bp):
ATTTTATATATTATCTATTGTACGT
Found at i:21651904 original size:17 final size:19
Alignment explanation
Indices: 21651862--21651906 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
21651852 ATTTTGTATA
*
21651862 TTATTTTTTTTAAGATCTC
1 TTATTTATTTTAAGATCTC
21651881 TCT-TTTATTTT-AGAT-TC
1 T-TATTTATTTTAAGATCTC
21651898 TTATTTATT
1 TTATTTATT
21651907 ATTTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
16 1 0.04
17 9 0.39
18 4 0.17
19 8 0.35
20 1 0.04
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.67
Consensus pattern (19 bp):
TTATTTATTTTAAGATCTC
Found at i:21651930 original size:25 final size:24
Alignment explanation
Indices: 21651897--21651944 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
21651887 ATTTTAGATT
21651897 CTTATTTA-TTATTTTTAAAATTGA
1 CTTATTTATTTA-TTTTAAAATTGA
21651921 CTTATATTATTTATTTTAAAATTG
1 CTTAT-TTATTTATTTTAAAATTG
21651945 TTTTATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.23
25 14 0.64
26 3 0.14
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (24 bp):
CTTATTTATTTATTTTAAAATTGA
Found at i:21653783 original size:49 final size:48
Alignment explanation
Indices: 21653703--21653806 Score: 115
Period size: 49 Copynumber: 2.1 Consensus size: 48
21653693 ATAAAAATCG
* * * *
21653703 TAAAATTTTATAAATTTTTTATAAACATATAAAAATATAG-AAA-AATATA
1 TAAAATTTTATAAAGTTGTAAGAAACATATAAAAA-AT-GTAAAGAA-ATA
21653752 TAAAATTTTATAAAGTTGTAAGAAA-ATTATAAAAAATGTAAAGAAATA
1 TAAAATTTTATAAAGTTGTAAGAAACA-TATAAAAAATGTAAAGAAATA
21653800 TAAAATT
1 TAAAATT
21653807 CATAAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
47 1 0.02
48 16 0.33
49 31 0.65
ACGTcount: A:0.58, C:0.01, G:0.06, T:0.36
Consensus pattern (48 bp):
TAAAATTTTATAAAGTTGTAAGAAACATATAAAAAATGTAAAGAAATA
Found at i:21654067 original size:9 final size:9
Alignment explanation
Indices: 21654053--21654142 Score: 53
Period size: 9 Copynumber: 9.9 Consensus size: 9
21654043 TAAAAAAAAT
21654053 TAATTTTTA
1 TAATTTTTA
21654062 TAA-TTTTA
1 TAATTTTTA
21654070 -AATTTTTTTA
1 TAA--TTTTTA
21654080 TAA-TTTTA
1 TAATTTTTA
* *
21654088 TTAAAATTTAA
1 -T-AATTTTTA
21654099 TAATTTTTA
1 TAATTTTTA
*
21654108 TAACTTTTA
1 TAATTTTTA
**
21654117 TTGTTTTT-
1 TAATTTTTA
*
21654125 TATTTTTTTA
1 TA-ATTTTTA
21654135 TAATTTTT
1 TAATTTTT
21654143 TTACCACCTG
Statistics
Matches: 62, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
7 2 0.03
8 11 0.18
9 33 0.53
10 10 0.16
11 6 0.10
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (9 bp):
TAATTTTTA
Found at i:21654086 original size:10 final size:10
Alignment explanation
Indices: 21654056--21654143 Score: 50
Period size: 10 Copynumber: 9.5 Consensus size: 10
21654046 AAAAAATTAA
21654056 TTTTTATAA-
1 TTTTTATAAT
21654065 -TTTTA-AATT
1 TTTTTATAA-T
21654074 TTTTTATAAT
1 TTTTTATAAT
21654084 TTTATTA-AA-
1 TTT-TTATAAT
* *
21654093 ATTTAATAA-
1 TTTTTATAAT
21654102 TTTTTATAA-
1 TTTTTATAAT
* **
21654111 CTTTTATTGT
1 TTTTTATAAT
21654121 TTTTTAT--T
1 TTTTTATAAT
21654129 TTTTTATAAT
1 TTTTTATAAT
21654139 TTTTT
1 TTTTT
21654144 TACCACCTGT
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
7 2 0.03
8 15 0.24
9 17 0.27
10 23 0.37
11 5 0.08
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:21654141 original size:18 final size:18
Alignment explanation
Indices: 21654055--21654143 Score: 63
Period size: 18 Copynumber: 4.9 Consensus size: 18
21654045 AAAAAAATTA
**
21654055 ATTTTTATAATTTTAAAT
1 ATTTTTATAATTTTTTAT
* *
21654073 TTTTTTATAATTTTATTAA
1 ATTTTTATAATTTT-TTAT
* *
21654092 AATTTAATAA-TTTTTAT
1 ATTTTTATAATTTTTTAT
* **
21654109 AACTTTTATTGTTTTTTAT
1 -ATTTTTATAATTTTTTAT
*
21654128 TTTTTTATAATTTTTT
1 ATTTTTATAATTTTTT
21654144 TACCACCTGT
Statistics
Matches: 52, Mismatches: 16, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
17 3 0.06
18 34 0.65
19 15 0.29
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (18 bp):
ATTTTTATAATTTTTTAT
Found at i:21656861 original size:8 final size:8
Alignment explanation
Indices: 21656848--21656878 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
21656838 ATTTAAGTAA
21656848 ATATTATT
1 ATATTATT
21656856 ATATTATT
1 ATATTATT
21656864 ATATTATT
1 ATATTATT
21656872 ATATTAT
1 ATATTAT
21656879 ATTAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATATTATT
Found at i:21657056 original size:13 final size:13
Alignment explanation
Indices: 21657038--21657089 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
21657028 TAAATGAACA
*
21657038 AAAGAAACAAAAG
1 AAAGAAAAAAAAG
21657051 AAAGAAAAAAAAG
1 AAAGAAAAAAAAG
* *
21657064 AAAGAACAGAATAG
1 AAAGAA-AAAAAAG
21657078 AAACGAAAAAAA
1 AAA-GAAAAAAA
21657090 CAGGGTAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 18 0.56
14 11 0.34
15 3 0.09
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:21657062 original size:22 final size:23
Alignment explanation
Indices: 21657037--21657080 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
21657027 ATAAATGAAC
21657037 AAAAGAAACAAAAGAA-AGAAAA
1 AAAAGAAACAAAAGAATAGAAAA
* *
21657059 AAAAGAAAGAACAGAATAGAAA
1 AAAAGAAACAAAAGAATAGAAA
21657081 CGAAAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAGAAACAAAAGAATAGAAAA
Found at i:21657123 original size:17 final size:15
Alignment explanation
Indices: 21657101--21657134 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
21657091 AGGGTAGAAA
21657101 GAAAGAAAGGAAAAAGG
1 GAAAGAAA-G-AAAAGG
21657118 GAAAGAAAGAAAAGG
1 GAAAGAAAGAAAAGG
21657133 GA
1 GA
21657135 GAAATTAGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
16 1 0.06
17 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
GAAAGAAAGAAAAGG
Found at i:21657131 original size:9 final size:9
Alignment explanation
Indices: 21657037--21657131 Score: 52
Period size: 9 Copynumber: 10.6 Consensus size: 9
21657027 ATAAATGAAC
*
21657037 AAAAGAAAC
1 AAAAGAAAG
21657046 AAAAGAAAG
1 AAAAGAAAG
*
21657055 AAAAAAAAG
1 AAAAGAAAG
21657064 -AAAGAACAG
1 AAAAGAA-AG
*
21657073 AATAGAAACG
1 AAAAGAAA-G
*
21657083 AAAAAAACAG
1 AAAAGAA-AG
***
21657093 GGTAGAAAG
1 AAAAGAAAG
21657102 -AAAGAAAG
1 AAAAGAAAG
* *
21657110 GAAA-AAGG
1 AAAAGAAAG
*
21657118 GAAAGAAAG
1 AAAAGAAAG
21657127 AAAAG
1 AAAAG
21657132 GGAGAAATTA
Statistics
Matches: 65, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
8 18 0.28
9 31 0.48
10 15 0.23
11 1 0.02
ACGTcount: A:0.71, C:0.04, G:0.23, T:0.02
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:21657138 original size:17 final size:18
Alignment explanation
Indices: 21657100--21657138 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
21657090 CAGGGTAGAA
21657100 AGAAAGAAAGGAAAAAGG
1 AGAAAGAAAGGAAAAAGG
*
21657118 -GAAAGAAA-GAAAAGGG
1 AGAAAGAAAGGAAAAAGG
21657134 AGAAA
1 AGAAA
21657139 TTAGGGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGAAAGAAAGGAAAAAGG
Found at i:21658035 original size:40 final size:39
Alignment explanation
Indices: 21657971--21658085 Score: 151
Period size: 40 Copynumber: 2.9 Consensus size: 39
21657961 CCTTCTCGAG
* *
21657971 AATTAAAAGTGAATAGGATCTATTCTTGATTCACTAAAAGA
1 AATT-AAAGTGAATAGGATTTATTCCTGATTCACTAAAA-A
* *
21658012 AATTAAAGTGAATAAGATTTATTCCTGATTCACTAGAAA
1 AATTAAAGTGAATAGGATTTATTCCTGATTCACTAAAAA
*
21658051 TATATAAAGTGAATAGGATTT-TTCCTGATTCACTA
1 AAT-TAAAGTGAATAGGATTTATTCCTGATTCACTA
21658086 TGGTAACTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
39 17 0.25
40 46 0.69
41 4 0.06
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.35
Consensus pattern (39 bp):
AATTAAAGTGAATAGGATTTATTCCTGATTCACTAAAAA
Found at i:21658102 original size:39 final size:36
Alignment explanation
Indices: 21657971--21658111 Score: 129
Period size: 40 Copynumber: 3.6 Consensus size: 36
21657961 CCTTCTCGAG
* *
21657971 AATTAAAAGTGAATAGGATCTATTCTTGATTCACTAAAAGA
1 AATT-AAAGTGAATAGGAT-TTTTCCTGATTCACT---AGA
*
21658012 AATTAAAGTGAATAAGATTTATTCCTGATTCACTAGAA
1 AATTAAAGTGAATAGGATTT-TTCCTGATTCACTAG-A
21658050 ATATATAAAGTGAATAGGATTTTTCCTGATTCACTATGGTA
1 A-AT-TAAAGTGAATAGGATTTTTCCTGATTCACTA--G-A
* *
21658091 ACTTAAGGTGAATAGGATTTT
1 AATTAAAGTGAATAGGATTTT
21658112 CCCTAAAATG
Statistics
Matches: 87, Mismatches: 7, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
37 2 0.02
38 2 0.02
39 34 0.39
40 42 0.48
41 7 0.08
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.35
Consensus pattern (36 bp):
AATTAAAGTGAATAGGATTTTTCCTGATTCACTAGA
Found at i:21659767 original size:42 final size:42
Alignment explanation
Indices: 21659704--21659813 Score: 145
Period size: 42 Copynumber: 2.6 Consensus size: 42
21659694 CATAATTCAA
* * * *
21659704 CTATGATCTTATACATCTTCACATAAT-GATGTCATAGCCCAG
1 CTATGGTCTTACACATATTCACAT-ATCGATGCCATAGCCCAG
21659746 CTATGGTCTTACACATATTCACATATCGATGCCATAGCCCAG
1 CTATGGTCTTACACATATTCACATATCGATGCCATAGCCCAG
21659788 CTATGGTCTTACACGA-A-TCACATATC
1 CTATGGTCTTACAC-ATATTCACATATC
21659814 TCACTGATGC
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
41 11 0.18
42 50 0.81
43 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (42 bp):
CTATGGTCTTACACATATTCACATATCGATGCCATAGCCCAG
Found at i:21659879 original size:48 final size:47
Alignment explanation
Indices: 21659772--21659965 Score: 194
Period size: 48 Copynumber: 4.0 Consensus size: 47
21659762 ATTCACATAT
* * * * *
21659772 CGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC
* * *
21659818 TGATGCCATATCCCAGATATGGTCTTATACAGTTAGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTATACAG-AAGCACATATCACAC
21659866 CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATAATCACATCTCTC
1 CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACAT-ATCACA-----C
* * *
21659919 CGATGCCATAGCCCA-ACTATGGTCTTATACGGAAATCACATATCACA
1 CGATGCCATATCCCAGA-TATGGTCTTATACAG-AAGCACATATCACA
21659966 TGTTGCCATG
Statistics
Matches: 124, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
46 26 0.21
47 7 0.06
48 48 0.39
52 1 0.01
53 35 0.28
54 7 0.06
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.26
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTATACAGAAGCACATATCACAC
Found at i:21659962 original size:101 final size:102
Alignment explanation
Indices: 21659803--21660095 Score: 274
Period size: 103 Copynumber: 2.9 Consensus size: 102
21659793 GTCTTACACG
* * * ** * *
21659803 AATCACATATCTCACTGATGCCATATCCCAGA-TATGGTCTTATACAGTTAGCATATATCACACC
1 AATCACATCTCTC-C-GATGCCATAGCCCA-ACTATGGTCTTATACGGAAATCACATATCACA-C
*
21659867 GATGCCAT-ATCCCAGA-TATGGTCTTATACAG-AA-GC-ACAT
62 GATGCCATGAT-CCA-ACCATGGTCTT-TACAGCAATGCGACAT
* *
21659906 AATCACATCTCTCCGATGCCATAGCCCAACTATGGTCTTATACGGAAATCACATATCACATGTTG
1 AATCACATCTCTCCGATGCCATAGCCCAACTATGGTCTTATACGGAAATCACATATCACACGATG
* * * * * *
21659971 CCATGGTCCAACCATGGTCTTTTCCGTCAATTCGTCTT
66 CCATGATCCAACCATGGTCTTTACAG-CAATGCGACAT
** * * *
21660009 AGCCACATCTCTCCGATGCCATAGCCTAACTATGGTCTTATACGGAAATCACATATCACATGTTG
1 AATCACATCTCTCCGATGCCATAGCCCAACTATGGTCTTATACGGAAATCACATATCACACGATG
*
21660074 CCATGGTCCAACCATGGTCTTT
66 CCATGATCCAACCATGGTCTTT
21660096 TTCGTCAATT
Statistics
Matches: 164, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
99 4 0.02
100 19 0.12
101 41 0.25
102 2 0.01
103 98 0.60
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (102 bp):
AATCACATCTCTCCGATGCCATAGCCCAACTATGGTCTTATACGGAAATCACATATCACACGATG
CCATGATCCAACCATGGTCTTTACAGCAATGCGACAT
Found at i:21659982 original size:47 final size:47
Alignment explanation
Indices: 21659922--21660094 Score: 132
Period size: 47 Copynumber: 3.5 Consensus size: 47
21659912 ATCTCTCCGA
* * *
21659922 TGCCATAGCCCAACTATGGTCTTATACGGAAATCACATATCACATGT
1 TGCCATGGTCCAACCATGGTCTTATACGGAAATCACATATCACATGT
* * * * * * * *
21659969 TGCCATGGTCCAACCATGGTCTTTTCCGTCAATTCGTCTTAGCCACATCT
1 TGCCATGGTCCAACCATGGTCTTATACG-GAAATC-ACATA-TCACATGT
* *
21660019 CT-CCGATGCCATAGCCTAACTATGGTCTTATACGGAAATCACATATCACATGT
1 -TGCC-ATG--GT--CC-AACCATGGTCTTATACGGAAATCACATATCACATGT
21660072 TGCCATGGTCCAACCATGGTCTT
1 TGCCATGGTCCAACCATGGTCTT
21660095 TTTCGTCAAT
Statistics
Matches: 92, Mismatches: 23, Indels: 22
0.67 0.17 0.16
Matches are distributed among these distances:
47 34 0.37
48 6 0.07
49 3 0.03
50 9 0.10
51 4 0.04
52 4 0.04
53 9 0.10
54 3 0.03
55 6 0.07
56 14 0.15
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.30
Consensus pattern (47 bp):
TGCCATGGTCCAACCATGGTCTTATACGGAAATCACATATCACATGT
Found at i:21660029 original size:103 final size:103
Alignment explanation
Indices: 21659909--21660117 Score: 400
Period size: 103 Copynumber: 2.0 Consensus size: 103
21659899 AGCACATAAT
21659909 CACATCTCTCCGATGCCATAGCCCAACTATGGTCTTATACGGAAATCACATATCACATGTTGCCA
1 CACATCTCTCCGATGCCATAGCCCAACTATGGTCTTATACGGAAATCACATATCACATGTTGCCA
21659974 TGGTCCAACCATGGTCTTTTCCGTCAATTCGTCTTAGC
66 TGGTCCAACCATGGTCTTTTCCGTCAATTCGTCTTAGC
*
21660012 CACATCTCTCCGATGCCATAGCCTAACTATGGTCTTATACGGAAATCACATATCACATGTTGCCA
1 CACATCTCTCCGATGCCATAGCCCAACTATGGTCTTATACGGAAATCACATATCACATGTTGCCA
*
21660077 TGGTCCAACCATGGTCTTTTTCGTCAATTCGTCTTAGC
66 TGGTCCAACCATGGTCTTTTCCGTCAATTCGTCTTAGC
21660115 CAC
1 CAC
21660118 TGAACGAAAG
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.31
Consensus pattern (103 bp):
CACATCTCTCCGATGCCATAGCCCAACTATGGTCTTATACGGAAATCACATATCACATGTTGCCA
TGGTCCAACCATGGTCTTTTCCGTCAATTCGTCTTAGC
Found at i:21661684 original size:10 final size:10
Alignment explanation
Indices: 21661669--21661700 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
21661659 TAGCTGATGA
21661669 AAATGAAGAG
1 AAATGAAGAG
21661679 AAATGAAGAG
1 AAATGAAGAG
*
21661689 AATTGAAGAG
1 AAATGAAGAG
21661699 AA
1 AA
21661701 TTCTAGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.12
Consensus pattern (10 bp):
AAATGAAGAG
Found at i:21662335 original size:73 final size:73
Alignment explanation
Indices: 21662247--21662385 Score: 208
Period size: 73 Copynumber: 1.9 Consensus size: 73
21662237 GGAATAACTT
* * * *
21662247 TTTATTGGTTTGTGTAAACCATGACAGGTGTTAGACTATCGAGACT-TACTTGAAAATATAAATT
1 TTTATTGGTTGGTGTAAACCATGACACGTGTTAGACTATCAAGA-TATACTTGAAAAAATAAATT
21662311 AGATTCCTC
65 AGATTCCTC
**
21662320 TTTATTGGTTGGTGTAAACCATGACACGTGTTAGGTTATCAAGATATACTTGAAAAAATAAATTA
1 TTTATTGGTTGGTGTAAACCATGACACGTGTTAGACTATCAAGATATACTTGAAAAAATAAATTA
21662385 G
66 G
21662386 TTGATAGTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 1 0.02
73 58 0.98
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.36
Consensus pattern (73 bp):
TTTATTGGTTGGTGTAAACCATGACACGTGTTAGACTATCAAGATATACTTGAAAAAATAAATTA
GATTCCTC
Found at i:21667340 original size:105 final size:105
Alignment explanation
Indices: 21667167--21667478 Score: 376
Period size: 105 Copynumber: 3.0 Consensus size: 105
21667157 ACCCAAAAAT
* * * ** *
21667167 AATACATGCAGATACACAAATATGCAAAACAAAGTGTATAAAAGCTATAAGTCTATTTTATTAT-
1 AATACATGGAGATACACAAATATGCAAAACAAAGTATATAAAA-CTATGAGTCTACATCATTATA
21667231 ACCTTGGGAAAAAGAGCCCTGCAATCACCACAATTAGTCCA
65 ACCTTGGGAAAAAGAGCCCTGCAATCACCACAATTAGTCCA
* * * *
21667272 AATACATGGAGATACACAATTATGCAAAGCAAAGTATACAAAACTATGAGCCTACATCATTATAA
1 AATACATGGAGATACACAAATATGCAAAACAAAGTATATAAAACTATGAGTCTACATCATTATAA
* * * * ** *
21667337 CCTTGGAAAAAAGATCCATGCAATCGCCACAAAGAATCCA
66 CCTTGGGAAAAAGAGCCCTGCAATCACCACAATTAGTCCA
* * *
21667377 AATTCATGGAGATACACAAATATGCAAAACAAAGGATATAAAACTATTGAGTCTGCA-CTATTAT
1 AATACATGGAGATACACAAATATGCAAAACAAAGTATATAAAACTA-TGAGTCTACATC-ATTAT
* **
21667441 AACCTTGGGGAAAAGAGCCCTGCAGCCACCACAATTAG
64 AACCTTGGGAAAAAGAGCCCTGCAATCACCACAATTAG
21667479 GGGAGAAGAA
Statistics
Matches: 170, Mismatches: 34, Indels: 5
0.81 0.16 0.02
Matches are distributed among these distances:
104 15 0.09
105 114 0.67
106 41 0.24
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (105 bp):
AATACATGGAGATACACAAATATGCAAAACAAAGTATATAAAACTATGAGTCTACATCATTATAA
CCTTGGGAAAAAGAGCCCTGCAATCACCACAATTAGTCCA
Found at i:21668936 original size:12 final size:12
Alignment explanation
Indices: 21668919--21668943 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21668909 TTATTTTTTT
21668919 ATTAAAATATTA
1 ATTAAAATATTA
21668931 ATTAAAATATTA
1 ATTAAAATATTA
21668943 A
1 A
21668944 ATTTTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTAAAATATTA
Found at i:21670069 original size:15 final size:15
Alignment explanation
Indices: 21670049--21670079 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
21670039 AGCAATAACT
21670049 ATGGTTGCACATTAG
1 ATGGTTGCACATTAG
21670064 ATGGTTGCACATTAG
1 ATGGTTGCACATTAG
21670079 A
1 A
21670080 AGGCACCAAG
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:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (15 bp):
ATGGTTGCACATTAG
Found at i:21688104 original size:127 final size:127
Alignment explanation
Indices: 21687878--21688135 Score: 408
Period size: 127 Copynumber: 2.0 Consensus size: 127
21687868 TAAAAGGGAT
*
21687878 GAAACTTAAAAGGGAAACCTGATTATTTAGACAAACGAAAGAACGAAACCCAACACATTAGGGCA
1 GAAACTTAAAAGGGAAACCTGATTATTTAAACAAACGAAAGAACGAAACCCAACACATTAGGGCA
* * * * *
21687943 CGATCTCTTGAATTTCTAAGCATCAAACATCGCCTTTGTTTCATGGTTTAGAAAATGAGGAC
66 CGATCCCTCGAATTTCTAAACATCAAACATCGCCTTTGTTTCAAGGTTTAGAAAACGAGGAC
* *** *
21688005 GAAACTTTAAAGGGAAGTTTGATTATTTAAACAAACGAAAGATCGAAACCCAACACATTAGGGCA
1 GAAACTTAAAAGGGAAACCTGATTATTTAAACAAACGAAAGAACGAAACCCAACACATTAGGGCA
*
21688070 CGATCCCTCGAATTTCTAAACATCAAACATCGCCTTTGTTTCAAGGTTTAGAAAACGCGGAC
66 CGATCCCTCGAATTTCTAAACATCAAACATCGCCTTTGTTTCAAGGTTTAGAAAACGAGGAC
21688132 GAAA
1 GAAA
21688136 TTCTAAAAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
127 119 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (127 bp):
GAAACTTAAAAGGGAAACCTGATTATTTAAACAAACGAAAGAACGAAACCCAACACATTAGGGCA
CGATCCCTCGAATTTCTAAACATCAAACATCGCCTTTGTTTCAAGGTTTAGAAAACGAGGAC
Found at i:21688219 original size:128 final size:127
Alignment explanation
Indices: 21687897--21688227 Score: 382
Period size: 127 Copynumber: 2.6 Consensus size: 127
21687887 AAGGGAAACC
* * *
21687897 TGATTATTTAGACAAACGAAAGAA-CGAAACCCAACACATTAGGGCACGATCTCTTGAATTTCTA
1 TGATCATTTAAACAAACGAAA-AATCGAAACCCAACACATTAGGGCACGATCTCTCGAATTTCTA
* * * *
21687961 AGCATCAAACATCGCCTTTGTTTCATGGTTTAGAAAATGAGGACGAAACTTTAAAGGGAAGTT
65 AACATCAAACATCGCCTTTGTTTCAAGGTTTAGAAAACGAGGACGAAACTTTAAAAGGAAGTT
* * *
21688024 TGATTATTTAAACAAACGAAAGATCGAAACCCAACACATTAGGGCACGATCCCTCGAATTTCTAA
1 TGATCATTTAAACAAACGAAAAATCGAAACCCAACACATTAGGGCACGATCTCTCGAATTTCTAA
*
21688089 ACATCAAACATCGCCTTTGTTTCAAGGTTTAGAAAACGCGGACGAAA-TTCTAAAA--AAGGTGT
66 ACATCAAACATCGCCTTTGTTTCAAGGTTTAGAAAACGAGGACGAAACTT-TAAAAGGAA-GT-T
* * *** * * * * * *
21688151 TTAGTCGTTTGGTCAAACGAAAAATCGAAACACAGCACATTAGAGCACGATTTCGCGAATTTCCA
1 TGA-TCATTTAAACAAACGAAAAATCGAAACCCAACACATTAGGGCACGATCTCTCGAATTTCTA
*
21688216 AACATGAAACAT
65 AACATCAAACAT
21688228 TACCTTGTTC
Statistics
Matches: 175, Mismatches: 24, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
125 2 0.01
126 5 0.03
127 109 0.62
128 59 0.34
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (127 bp):
TGATCATTTAAACAAACGAAAAATCGAAACCCAACACATTAGGGCACGATCTCTCGAATTTCTAA
ACATCAAACATCGCCTTTGTTTCAAGGTTTAGAAAACGAGGACGAAACTTTAAAAGGAAGTT
Found at i:21688837 original size:3 final size:3
Alignment explanation
Indices: 21688829--21688864 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
21688819 AGTAATATCG
21688829 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
21688865 TAAAAAAAAC
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:21690412 original size:29 final size:29
Alignment explanation
Indices: 21690350--21690424 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 29
21690340 TAAAATATAT
21690350 TTAAAACAA-ATATTAAAACAAGAAACAAA
1 TTAAAA-AATATATTAAAACAAGAAACAAA
* *
21690379 -TAAAAAATATATTAAAACAATACACAAA
1 TTAAAAAATATATTAAAACAAGAAACAAA
*
21690407 TTAAAAAATATAATAAAA
1 TTAAAAAATATATTAAAA
21690425 ATTGATTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
27 2 0.05
28 23 0.56
29 16 0.39
ACGTcount: A:0.69, C:0.08, G:0.01, T:0.21
Consensus pattern (29 bp):
TTAAAAAATATATTAAAACAAGAAACAAA
Found at i:21690483 original size:12 final size:12
Alignment explanation
Indices: 21690405--21690484 Score: 51
Period size: 12 Copynumber: 6.9 Consensus size: 12
21690395 ACAATACACA
21690405 AATTAAAAAATAT
1 AATT-AAAAATAT
21690418 AA-TAAAAAT-T
1 AATTAAAAATAT
* * * *
21690428 GATT-ATATTAA
1 AATTAAAAATAT
21690439 AATT-AAAATAT
1 AATTAAAAATAT
* *
21690450 AAATATAAATAT
1 AATTAAAAATAT
* *
21690462 AAATATAAATAT
1 AATTAAAAATAT
21690474 AATTAAAAATA
1 AATTAAAAATA
21690485 AAAAATATAT
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
10 5 0.10
11 17 0.33
12 28 0.54
13 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (12 bp):
AATTAAAAATAT
Found at i:21690483 original size:18 final size:18
Alignment explanation
Indices: 21690439--21690484 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
21690429 ATTATATTAA
21690439 AATT-AAAATATAAATAT
1 AATTAAAAATATAAATAT
* *
21690456 AAATATAAATATAAATAT
1 AATTAAAAATATAAATAT
21690474 AATTAAAAATA
1 AATTAAAAATA
21690485 AAAAATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AATTAAAAATATAAATAT
Found at i:21690488 original size:6 final size:6
Alignment explanation
Indices: 21690444--21690475 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
21690434 ATTAAAATTA
21690444 AAATAT AAATAT AAATAT AAATAT AAATAT AA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AA
21690476 TTAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATAT
Found at i:21702993 original size:21 final size:21
Alignment explanation
Indices: 21702967--21703007 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
21702957 AGACAAGCAA
* *
21702967 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
21702988 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
21703008 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:21704940 original size:16 final size:16
Alignment explanation
Indices: 21704907--21704940 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
21704897 GGAGATTGTT
* *
21704907 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
21704923 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
21704939 AA
1 AA
21704941 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:21707273 original size:24 final size:23
Alignment explanation
Indices: 21707215--21707275 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
21707205 CGATACGTAT
*
21707215 ATATATAACTTTAAAAATTATAAA
1 ATATATAA-TTTAATAATTATAAA
* *
21707239 A-ATATATTTTAATAATATGTAAA
1 ATATATAATTTAATAAT-TATAAA
21707262 ATATATAATTTAAT
1 ATATATAATTTAAT
21707276 TCTCGATCCT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
22 8 0.26
23 11 0.35
24 12 0.39
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATATAATTTAATAATTATAAA
Found at i:21712659 original size:2 final size:2
Alignment explanation
Indices: 21712652--21712679 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21712642 AAAATTAATT
21712652 TA 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 TA
21712680 AAAGAAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21715743 original size:13 final size:13
Alignment explanation
Indices: 21715721--21715754 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
21715711 TGATAGTTTG
21715721 GTATGAATTTATAT
1 GTATG-ATTTATAT
*
21715735 GTATGATTTGTAT
1 GTATGATTTATAT
21715748 GTATGAT
1 GTATGAT
21715755 GTGCTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (13 bp):
GTATGATTTATAT
Found at i:21716206 original size:16 final size:17
Alignment explanation
Indices: 21716182--21716215 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
21716172 TGTTTTCACA
21716182 TGGCCAAGTCA-AATTG
1 TGGCCAAGTCAGAATTG
*
21716198 TGGCTAAGTCAGAATTG
1 TGGCCAAGTCAGAATTG
21716215 T
1 T
21716216 CTACAGGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (17 bp):
TGGCCAAGTCAGAATTG
Found at i:21719069 original size:46 final size:46
Alignment explanation
Indices: 21719002--21719233 Score: 340
Period size: 46 Copynumber: 5.0 Consensus size: 46
21718992 AGTGTGCTTT
21719002 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* * *
21719048 TGACATGAAATGAATAAGACCATGGTTGAAAGATACGATAGCAACG
1 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* *
21719094 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGACAACG
1 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
**
21719140 TGACATGAAATGAACGAGACCATGGTTGAAAGATACCATGGCAACA
1 TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
* * * * *
21719186 TGACA-GAAAGTGAGTAAGACCATAGTTGAAAGACACTATGGCATCA
1 TGACATGAAA-TGAATAAGACCATGGTTGAAAGATACCATGGCAACA
21719232 TG
1 TG
21719234 TCTAAGATAA
Statistics
Matches: 168, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 164 0.98
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.19
Consensus pattern (46 bp):
TGACATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
Found at i:21719374 original size:26 final size:26
Alignment explanation
Indices: 21719317--21719366 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
21719307 TCAAATGATG
* *
21719317 AATGGTTTTATGAATTGGTTATACAA
1 AATGGTTGTATGAAGTGGTTATACAA
21719343 AATGGTTGTATGAAGT-GTT-TACAA
1 AATGGTTGTATGAAGTGGTTATACAA
21719367 GAATTGGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 3 0.14
26 14 0.64
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (26 bp):
AATGGTTGTATGAAGTGGTTATACAA
Found at i:21732183 original size:27 final size:26
Alignment explanation
Indices: 21732146--21732257 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
21732136 AGCATGGCTG
* *
21732146 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
21732172 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
21732200 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
21732227 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
21732254 CCAG
1 CCAG
21732258 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:21732238 original size:54 final size:54
Alignment explanation
Indices: 21732146--21732257 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
21732136 AGCATGGCTG
* *
21732146 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
21732200 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
21732254 CCAG
1 CCAG
21732258 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:21741984 original size:27 final size:26
Alignment explanation
Indices: 21741949--21742060 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
21741939 AGCATGGCTG
* *
21741949 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
21741975 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
21742003 CCAGAACAGAAATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
21742030 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
21742057 CCAG
1 CCAG
21742061 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 53 0.70
28 17 0.22
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:21742041 original size:54 final size:54
Alignment explanation
Indices: 21741949--21742060 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
21741939 AGCATGGCTG
* *
21741949 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
21742003 CCAGAACAGAAATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAGAAA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
21742057 CCAG
1 CCAG
21742061 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (54 bp):
CCAGAACAGAAAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:21742204 original size:25 final size:24
Alignment explanation
Indices: 21742159--21742209 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
21742149 TCAGACAAAA
* *
21742159 TTAACCCTAGGGTATATTGGTCAT
1 TTAAACCTAGGGTATATTGGTAAT
21742183 TTAAACCTAGGGGTATCA-TGGTAAT
1 TTAAACCTA-GGGTAT-ATTGGTAAT
21742208 TT
1 TT
21742210 CCCATACATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.35
25 14 0.61
26 1 0.04
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.37
Consensus pattern (24 bp):
TTAAACCTAGGGTATATTGGTAAT
Found at i:21745155 original size:44 final size:45
Alignment explanation
Indices: 21745107--21745192 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 45
21745097 GAATTATTCT
21745107 TGTCTCC-AAGTCCATA-TATAATATGGACTTACATGGCTCAATCC
1 TGTCTCCAAAG-CCATATTATAATATGGACTTACATGGCTCAATCC
*
21745151 TGTCTCCAAAGCCATATTTCTAATATGGACTTACATGGCTCA
1 TGTCTCCAAAGCCATA-TTATAATATGGACTTACATGGCTCA
21745193 TTTCTGTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
44 12 0.32
45 3 0.08
46 23 0.61
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (45 bp):
TGTCTCCAAAGCCATATTATAATATGGACTTACATGGCTCAATCC
Found at i:21754931 original size:25 final size:25
Alignment explanation
Indices: 21754903--21754951 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
21754893 TTAGCGTCAA
21754903 TGAGTGATAGCTCCGAGCTTATGTT
1 TGAGTGATAGCTCCGAGCTTATGTT
21754928 TGAGTGATAGCTCCGAGCTTATGT
1 TGAGTGATAGCTCCGAGCTTATGT
21754952 CCGAGTGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (25 bp):
TGAGTGATAGCTCCGAGCTTATGTT
Found at i:21754957 original size:25 final size:25
Alignment explanation
Indices: 21754904--21754958 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
21754894 TAGCGTCAAT
**
21754904 GAGTGATAGCTCCGAGCTTATGTTT
1 GAGTGATAGCTCCGAGCTTATGTCC
21754929 GAGTGATAGCTCCGAGCTTATGTCC
1 GAGTGATAGCTCCGAGCTTATGTCC
21754954 GAGTG
1 GAGTG
21754959 GATGCTAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (25 bp):
GAGTGATAGCTCCGAGCTTATGTCC
Found at i:21756654 original size:26 final size:26
Alignment explanation
Indices: 21756625--21756707 Score: 157
Period size: 26 Copynumber: 3.2 Consensus size: 26
21756615 TGATACAAAT
21756625 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
21756651 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21756677 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
21756703 TGATA
1 TGATA
21756708 GGAATTTCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:21763984 original size:30 final size:30
Alignment explanation
Indices: 21763928--21764011 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
21763918 ATCAATAAAA
* *
21763928 ATTATAAAATATAGAAAATATTTAAAATTT
1 ATTAGAAAATATAAAAAATATTTAAAATTT
* **
21763958 ATTAGAAAATA-AAAAAATGTTCTAAAAACT
1 ATTAGAAAATATAAAAAATATT-TAAAATTT
*
21763988 ATTTAAAAAATATAAAAAAATATT
1 A-TTAGAAAATAT-AAAAAATATT
21764012 CCTTTTCCCA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 8 0.19
30 17 0.40
31 9 0.21
33 9 0.21
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (30 bp):
ATTAGAAAATATAAAAAATATTTAAAATTT
Found at i:21767361 original size:15 final size:15
Alignment explanation
Indices: 21767341--21767369 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
21767331 TCTTTTGTTT
21767341 TTATTATTATAACTA
1 TTATTATTATAACTA
21767356 TTATTATTATAACT
1 TTATTATTATAACT
21767370 TAATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TTATTATTATAACTA
Found at i:21773228 original size:14 final size:15
Alignment explanation
Indices: 21773202--21773233 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
21773192 ATATATATAT
21773202 ATAAAATGGAATCCA
1 ATAAAATGGAATCCA
21773217 ATAAAA-GGAATCCA
1 ATAAAATGGAATCCA
21773231 ATA
1 ATA
21773234 CTTAAATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (15 bp):
ATAAAATGGAATCCA
Found at i:21781916 original size:30 final size:30
Alignment explanation
Indices: 21781882--21781983 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
21781872 TTAAAAATAA
*
21781882 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-CT
* *
21781912 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTCT
* * *
21781942 AAATTTCACTTAGACCCCTAAACCTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTC-TCT
21781972 AAATTTCATTTT
1 AAATTTCATTTT
21781984 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
30 59 0.97
31 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.04, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTCT
Found at i:21783347 original size:16 final size:16
Alignment explanation
Indices: 21783299--21783347 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
21783289 TTTCTTTCTA
*
21783299 AAAAAATCGTGTTTTC
1 AAAAATTCGTGTTTTC
21783315 AAAAATTTCCGTG-TTTC
1 AAAAA-TT-CGTGTTTTC
21783332 AAAAATTCGTGTTTTC
1 AAAAATTCGTGTTTTC
21783348 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 10 0.34
18 4 0.14
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (16 bp):
AAAAATTCGTGTTTTC
Found at i:21783390 original size:9 final size:9
Alignment explanation
Indices: 21783376--21783409 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
21783366 TCGTGCTTCA
21783376 AAAAAAAAT
1 AAAAAAAAT
21783385 AAAAAAAAT
1 AAAAAAAAT
21783394 --AAAAAAT
1 AAAAAAAAT
21783401 AAAAAAAAT
1 AAAAAAAAT
21783410 TCTCGTGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
9 16 0.70
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:21783397 original size:16 final size:16
Alignment explanation
Indices: 21783378--21783409 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21783368 GTGCTTCAAA
21783378 AAAAAATAAAAAAAAT
1 AAAAAATAAAAAAAAT
21783394 AAAAAATAAAAAAAAT
1 AAAAAATAAAAAAAAT
21783410 TCTCGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:21783494 original size:18 final size:18
Alignment explanation
Indices: 21783473--21783993 Score: 301
Period size: 18 Copynumber: 30.0 Consensus size: 18
21783463 AAATTTAGTG
21783473 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
21783491 TTTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
21783509 TCTTT-GTGTTTTCAAAAA
1 T-TTTCGTGTTTTCAAAAA
* * *
21783527 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
** *
21783544 TTTTCGTGTTTTCCCCAAT
1 TTTTCGTGTTTT-CAAAAA
*
21783563 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
21783580 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
21783598 TCTTT-GTGTTTTCAAAAA
1 T-TTTCGTGTTTTCAAAAA
* * *
21783616 TTCTGGCG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
**
21783633 TTTTCGTGTTTAAAAAAAA
1 TTTTCGTGTTT-TCAAAAA
* *
21783652 TTTACGTGTTTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
21783670 TTTTCGTG-TTTCACAAA
1 TTTTCGTGTTTTCAAAAA
*
21783687 TTCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
21783705 -CTCCAGTG-TTTC-AAAG
1 TTTTC-GTGTTTTCAAAAA
* *
21783721 TTTCCATGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* * **
21783739 TTCTCGCGTTTAAAAAAA
1 TTTTCGTGTTTTCAAAAA
**
21783757 AATTCGTG-TTTCAAAATA
1 TTTTCGTGTTTTCAAAA-A
* **
21783775 TTCTCG-CATTTC---AA
1 TTTTCGTGTTTTCAAAAA
**
21783789 TTTT--TGTTTT-TTAAA
1 TTTTCGTGTTTTCAAAAA
21783804 ---TCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
* *
21783818 ATGTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
*
21783835 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
21783852 TTTTCCTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
**
21783869 TTCCCGTG-TTTCAAAAAAAA
1 TTTTCGTGTTTTC---AAAAA
* *
21783889 ATGTCGTGTTTT-AAGAAA
1 TTTTCGTGTTTTCAA-AAA
* *
21783907 ATTTCGTTTTTTCTAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
21783926 TTTTCGTG-TTTCTAAAA
1 TTTTCGTGTTTTCAAAAA
*
21783943 TTTTCGTG-TTT-ACAAA
1 TTTTCGTGTTTTCAAAAA
* *
21783959 TTCTCGTGTTTTGAAAAA
1 TTTTCGTGTTTTCAAAAA
*
21783977 TTCTCGTGTTTT-AAAAA
1 TTTTCGTGTTTTCAAAAA
21783994 AAAACTTTCG
Statistics
Matches: 389, Mismatches: 75, Indels: 79
0.72 0.14 0.15
Matches are distributed among these distances:
12 1 0.00
13 6 0.02
14 9 0.02
15 3 0.01
16 21 0.05
17 138 0.35
18 156 0.40
19 40 0.10
20 12 0.03
21 3 0.01
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:21783591 original size:107 final size:106
Alignment explanation
Indices: 21783476--21783756 Score: 315
Period size: 107 Copynumber: 2.6 Consensus size: 106
21783466 TTTAGTGTTT
* * *
21783476 TCGTGTTTTCAAAAAT-TTTCGTGTTTTCAAAAATCTTTGTG-TTTTCAAAAATTCTGGCGTTT-
1 TCGTGTTTTCAAAAATCTTT-GTGTTTTCAAAAAT-TCTG-GCGTTTCAAAAATTCTCGCGTTTA
* * * *
21783538 CAAAAATTTTCGTGTTTTCCCCAATTTTTCGTGTTTCACAAATTC
63 AAAAAATTTACGTGTTTT-CACAAATTTTCGTGTTTCACAAATTC
* *
21783583 TCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTTCAAAAATTTTCGTGTTTAAAA
1 TCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTTCAAAAATTCTCGCGTTT-AAA
21783648 AAAATTTACGTGTTTTCACAAATTTTCGTGTTTCACAAATTC
65 AAAATTTACGTGTTTTCACAAATTTTCGTGTTTCACAAATTC
** ** *
21783690 TCGTGTTTTCAAAAA-CTCCAGTG-TTTCAAAGTTTCCAT-G-TTTTCAAAAATTCTCGCGTTTA
1 TCGTGTTTTCAAAAATCT-TTGTGTTTTCAAAAATT-C-TGGCGTTTCAAAAATTCTCGCGTTTA
21783751 AAAAAA
63 AAAAAA
21783757 AATTCGTGTT
Statistics
Matches: 151, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
105 8 0.05
106 49 0.32
107 74 0.49
108 20 0.13
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.43
Consensus pattern (106 bp):
TCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTTCAAAAATTCTCGCGTTTAAAA
AAATTTACGTGTTTTCACAAATTTTCGTGTTTCACAAATTC
Found at i:21783625 original size:89 final size:90
Alignment explanation
Indices: 21783473--21783704 Score: 335
Period size: 89 Copynumber: 2.6 Consensus size: 90
21783463 AAATTTAGTG
*
21783473 TTTTCGTGTTTTCAAAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTT
1 TTTTCGTGTTTTCACAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTT
***** *
21783538 CAAAAATTTTCGTGTTTTCCCCAAT
66 CAAAAATTTTCGTGTTTAAAAAAAA
*
21783563 TTTTCGTG-TTTCACAAATTCTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTT
1 TTTTCGTGTTTTCACAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTT
21783627 CAAAAATTTTCGTGTTTAAAAAAAA
66 CAAAAATTTTCGTGTTTAAAAAAAA
* * *
21783652 TTTACGTGTTTTCACAAATTTTCGTG-TTTCACAAAT-TCTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCACAAATTTTCGTGTTTTCAAAAATCT-TTGTGTTTTCAAAAA
21783705 CTCCAGTGTT
Statistics
Matches: 128, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
88 1 0.01
89 103 0.80
90 24 0.19
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (90 bp):
TTTTCGTGTTTTCACAAATTTTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGGCGTTT
CAAAAATTTTCGTGTTTAAAAAAAA
Found at i:21783643 original size:17 final size:17
Alignment explanation
Indices: 21783473--21783993 Score: 276
Period size: 17 Copynumber: 30.0 Consensus size: 17
21783463 AAATTTAGTG
21783473 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
21783491 TTTTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
21783509 TCTTT-GTGTTTTCAAAAA
1 T-TTTCGTG-TTTCAAAAA
* * *
21783527 TTCTGGCGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
** *
21783544 TTTTCGTGTTTTCCCCAAT
1 TTTTCGTG-TTT-CAAAAA
*
21783563 TTTTCGTGTTTCACAAA
1 TTTTCGTGTTTCAAAAA
*
21783580 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
21783598 TCTTT-GTGTTTTCAAAAA
1 T-TTTCGTG-TTTCAAAAA
* * *
21783616 TTCTGGCGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
*
21783633 TTTTCGTGTTTAAAAAAAA
1 TTTTCGTGTTT--CAAAAA
* *
21783652 TTTACGTGTTTTCACAAA
1 TTTTCGTG-TTTCAAAAA
*
21783670 TTTTCGTGTTTCACAAA
1 TTTTCGTGTTTCAAAAA
*
21783687 TTCTCGTGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
21783705 -CTCCAGTGTTTC-AAAG
1 TTTTC-GTGTTTCAAAAA
* *
21783721 TTTCCATGTTTTCAAAAA
1 TTTTCGTG-TTTCAAAAA
* * *
21783739 TTCTCGCGTTTAAAAAAA
1 TTTTCGTGTTT-CAAAAA
**
21783757 AATTCGTGTTTCAAAATA
1 TTTTCGTGTTTCAAAA-A
* **
21783775 TTCTCGCATTTC---AA
1 TTTTCGTGTTTCAAAAA
***
21783789 TTTT--TGTTTTTTAAA
1 TTTTCGTGTTTCAAAAA
21783804 ---TCGTGTTTCAAAAA
1 TTTTCGTGTTTCAAAAA
* * *
21783818 ATGTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
*
21783835 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
* *
21783852 TTTTCCTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
**
21783869 TTCCCGTGTTTCAAAAAAAA
1 TTTTCGTGTTTC---AAAAA
* * *
21783889 ATGTCGTGTTTTAAGAAA
1 TTTTCGTGTTTCAA-AAA
* *
21783907 ATTTCGTTTTTTCTAAAAA
1 TTTTCG-TGTTTC-AAAAA
*
21783926 TTTTCGTGTTTCTAAAA
1 TTTTCGTGTTTCAAAAA
*
21783943 TTTTCGTGTTT-ACAAA
1 TTTTCGTGTTTCAAAAA
* *
21783959 TTCTCGTGTTTTGAAAAA
1 TTTTCGTG-TTTCAAAAA
* *
21783977 TTCTCGTGTTTTAAAAA
1 TTTTCGTGTTTCAAAAA
21783994 AAAACTTTCG
Statistics
Matches: 389, Mismatches: 81, Indels: 67
0.72 0.15 0.12
Matches are distributed among these distances:
12 4 0.01
14 12 0.03
15 3 0.01
16 15 0.04
17 157 0.40
18 140 0.36
19 40 0.10
20 18 0.05
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (17 bp):
TTTTCGTGTTTCAAAAA
Found at i:21783766 original size:52 final size:51
Alignment explanation
Indices: 21783569--21783773 Score: 151
Period size: 53 Copynumber: 3.9 Consensus size: 51
21783559 CAATTTTTCG
* ** ** * * **
21783569 TGTTTCACAAATTCTCGTGTTTTCAAAAATCTTTGTGTTTTCAAAAATTCTGG
1 TGTTTCAAAAATTCTCGTGTTTAAAAAAAAATTCGTG-TTTCAAAATTTC-CA
* * * * *
21783622 CGTTTCAAAAATTTTCGTGTTTAAAAAAAATTTACGTGTTTTCACAAATTTTCG
1 TGTTTCAAAAATTCTCGTGTTTAAAAAAAAATT-CGTG-TTTCA-AAATTTCCA
* ** * * *
21783676 TGTTTCACAAATTCTCGTGTTT-TCAAAAACTCCAGTGTTTCAAAGTTTCCA
1 TGTTTCAAAAATTCTCGTGTTTAAAAAAAAATTC-GTGTTTCAAAATTTCCA
*
21783727 TGTTTTCAAAAATTCTCGCGTTTAAAAAAAAATTCGTGTTTCAAAAT
1 TG-TTTCAAAAATTCTCGTGTTTAAAAAAAAATTCGTGTTTCAAAAT
21783774 ATTCTCGCAT
Statistics
Matches: 119, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
51 8 0.07
52 35 0.29
53 42 0.35
54 29 0.24
55 5 0.04
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (51 bp):
TGTTTCAAAAATTCTCGTGTTTAAAAAAAAATTCGTGTTTCAAAATTTCCA
Found at i:21784007 original size:91 final size:90
Alignment explanation
Indices: 21783804--21783995 Score: 241
Period size: 91 Copynumber: 2.2 Consensus size: 90
21783794 GTTTTTTAAA
* * *
21783804 TCGTG-TTTCAAAAAATGTCG-TGTTT-TAAAAATTTTCGTGTTTCTAAAATTTTCCTGTTTTAA
1 TCGTGTTTTAAAAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTTCCTGTTTTAA
*
21783866 AAATTCCCGTGTTTCAAAAAAAAATG
66 AAATTCCCGTGTTT-AAAAAAAAATC
* * *
21783892 TCGTGTTTTAAGAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTTCGTG-TTTAC
1 TCGTGTTTTAAAAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTTCCTGTTTTAA
* ** *
21783956 AAATTCTCGTGTTT-TGAAAAATTC
66 AAATTCCCGTGTTTAAAAAAAAATC
21783980 TCGTGTTTTAAAAAAA
1 TCGTGTTTTAAAAAAA
21783996 AACTTTCGTT
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
88 26 0.29
89 12 0.13
90 21 0.24
91 30 0.34
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (90 bp):
TCGTGTTTTAAAAAAATTTCGTTTTTTCTAAAAATTTTCGTGTTTCTAAAATTTTCCTGTTTTAA
AAATTCCCGTGTTTAAAAAAAAATC
Found at i:21795993 original size:123 final size:123
Alignment explanation
Indices: 21795767--21796009 Score: 353
Period size: 122 Copynumber: 2.0 Consensus size: 123
21795757 AGGAAAATCA
* *
21795767 ACTCATATCACGAGAGGTGAGTTGAGCCTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGC
1 ACTCATATCACGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGC
* *
21795832 GAGAAGTGAGTTGAGCCTCGGGGCACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
**
21795890 ACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTC-AAAATCAACTCATATTGC
1 ACTCATATCACGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGC
* * ** * * *
21795954 TAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTTAATTTCTGTTGTTAAA
66 GAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGTATTTTTAGTTTATGTT-TTAAA
21796010 AAAAAATCAA
Statistics
Matches: 106, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
122 59 0.56
123 47 0.44
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (123 bp):
ACTCATATCACGAGAGGTGAGTTAAGCCTTTTAATTTATGTTTTTCAAAAATCAACTCATATTGC
GAGAAGTGAGTTGAGCCTCAGGACACGCCAAGGTATTTTTAGTTTATGTTTTAAATTG
Found at i:21796134 original size:72 final size:72
Alignment explanation
Indices: 21795922--21796374 Score: 559
Period size: 72 Copynumber: 6.2 Consensus size: 72
21795912 TAAGCCTTTT
* * ** *
21795922 AATTTATGTTTTTCAAAA-TCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
*
21795986 GTAATTTT
65 GTAATTTC
* * *
21795994 AATTTCTGTTGTTAAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCT
1 AATTTCTGTT-TT---CAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCT
21796059 GAGGTAATTTC
62 GAGGTAATTTC
* *
21796070 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTCAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGG
21796135 TAATTTC
66 TAATTTC
* *
21796142 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACAAGTTGAGG
1 AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGG
*
21796207 TATTTTC
66 TAATTTC
** *
21796214 AATTTCTGCTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATACTTAG
1 AATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAG
21796279 GT-ATTGTC
65 GTAATT-TC
* * * ** * *
21796287 AATTTTTTGTATGTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCT
1 AA-TTTCTG--T-TTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCT
*
21796352 GAGGTATTTTC
62 GAGGTAATTTC
*
21796363 CATTTCTGTTTT
1 AATTTCTGTTTT
21796375 TCAATTTATG
Statistics
Matches: 339, Mismatches: 31, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
71 2 0.01
72 146 0.43
73 59 0.17
74 5 0.01
75 12 0.04
76 113 0.33
77 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (72 bp):
AATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGCTGAGG
TAATTTC
Found at i:21796552 original size:14 final size:14
Alignment explanation
Indices: 21796533--21796567 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
21796523 CGCTGAGGTA
21796533 TTTTCAATTTCTGG
1 TTTTCAATTTCTGG
*
21796547 TTTTCAATTTCTGT
1 TTTTCAATTTCTGG
21796561 TTTTCAA
1 TTTTCAA
21796568 AAATCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGG
Found at i:21796557 original size:89 final size:87
Alignment explanation
Indices: 21796300--21796640 Score: 474
Period size: 86 Copynumber: 3.9 Consensus size: 87
21796290 TTTTTGTATG
* * *
21796300 TTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACATGCTGAGGTATTTTCCA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
* *
21796365 TTTCTGTTTTTCAATTTATG-T
66 TTTCTGGTTTTCAATTTCTGTT
* *
21796386 TTTCAAAAATCAATTCATATTG-GAAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCA
1 TTTCAAAAATCAACTCATATTGCG-AGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCA
**
21796450 ATTTCTACTTTTCAATTTCTGTT
65 ATTTCTGGTTTTCAATTTCTGTT
* *
21796473 TTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-TGGCTCACACGCTGAGGTATTTT
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTT
21796537 CAATTTCTGGTTTTCAATTTCTGTT
63 CAATTTCTGGTTTTCAATTTCTGTT
* * * *
21796562 TTTCAAAAATCGACTCATATTGCGAGAGGAGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAA
1 TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
21796627 TTTCT-GTTTGTCAA
66 TTTCTGGTTT-TCAA
21796641 AAATTAACTC
Statistics
Matches: 228, Mismatches: 19, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
85 1 0.00
86 81 0.36
87 66 0.29
88 1 0.00
89 77 0.34
90 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (87 bp):
TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
TTTCTGGTTTTCAATTTCTGTT
Found at i:21796669 original size:73 final size:73
Alignment explanation
Indices: 21796548--21796704 Score: 253
Period size: 73 Copynumber: 2.2 Consensus size: 73
21796538 AATTTCTGGT
* *
21796548 TTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGAGAGTTGAGCCTC-GGGACACG
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCAGGG-CACG
21796612 CTGAGGTAA
65 CTGAGGTAA
* *
21796621 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCAGGGCACGC
*
21796686 TGAGGTAT
66 TGAGGTAA
21796694 TTTCAATTTCT
1 TTTCAATTTCT
21796705 ACTTTTCAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
73 75 0.96
74 3 0.04
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (73 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCAGGGCACGC
TGAGGTAA
Found at i:21796740 original size:160 final size:160
Alignment explanation
Indices: 21796459--21796762 Score: 484
Period size: 160 Copynumber: 1.9 Consensus size: 160
21796449 AATTTCTACT
* *
21796459 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACAC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTAGG--CACAC
** *
21796524 GCTGAGGTATTTTCAATTTCTGGTTTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGA
64 GCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGA
*
21796589 GGAGAGTTGAGCCTCGGGACACGCTGAGGTAA
129 GGAGAGCTGAGCCTCGGGACACGCTGAGGTAA
* * *
21796621 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GCACG
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-AGGCACACG
21796685 CTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAG
65 CTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAG
*
21796750 GTGAGCTGAGCCT
130 GAGAGCTGAGCCT
21796763 TTTAATTTTT
Statistics
Matches: 131, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
160 77 0.59
162 52 0.40
163 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (160 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTAGGCACACGC
TGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGG
AGAGCTGAGCCTCGGGACACGCTGAGGTAA
Found at i:21796981 original size:14 final size:14
Alignment explanation
Indices: 21796962--21796996 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
21796952 CGCTGAGGTA
21796962 TTTTCAATTTCTGG
1 TTTTCAATTTCTGG
*
21796976 TTTTCAATTTCTGT
1 TTTTCAATTTCTGG
21796990 TTTTCAA
1 TTTTCAA
21796997 AAATCGACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.17, C:0.14, G:0.09, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTGG
Found at i:21796992 original size:89 final size:86
Alignment explanation
Indices: 21796845--21797069 Score: 317
Period size: 89 Copynumber: 2.6 Consensus size: 86
21796835 AAAGAGAGGT
* *
21796845 GAGTTGAGCCTCAGG-GCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAA
1 GAGTTGAGCCTC-GGCACACGCTGAGGTATTTTCAATTTCT-GTTTTCAATTTCTGTTTTTCAAA
*
21796909 AATCAACTCATATTGCGAGAAGT
64 AATCAACTCATATTGCGAGAAGA
*
21796932 GAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAATTTCTGGTTTTCAATTTCTGTTTTTCAA
1 GAGTTGAGCCTCGG--CACACGCTGAGGTATTTTCAATTTCT-GTTTTCAATTTCTGTTTTTCAA
* *
21796997 AAATCGACTCATATTGCGAGAGGA
63 AAATCAACTCATATTGCGAGAAGA
* *
21797021 GAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAA
1 GAGTTGAGCCTCGGCACACGCTGAGGTATTTTCAATTTCTGTTT-TCAA
21797070 AAATTAACTC
Statistics
Matches: 124, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
86 6 0.05
87 39 0.31
89 79 0.64
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.36
Consensus pattern (86 bp):
GAGTTGAGCCTCGGCACACGCTGAGGTATTTTCAATTTCTGTTTTCAATTTCTGTTTTTCAAAAA
TCAACTCATATTGCGAGAAGA
Found at i:21797098 original size:73 final size:73
Alignment explanation
Indices: 21796977--21797133 Score: 253
Period size: 73 Copynumber: 2.2 Consensus size: 73
21796967 AATTTCTGGT
* *
21796977 TTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGAGAGTTGAGCCTC-GGGACACG
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCAGGG-CACG
21797041 CTGAGGTAA
65 CTGAGGTAA
* *
21797050 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCAGGGCACGC
*
21797115 TGAGGTAT
66 TGAGGTAA
21797123 TTTCAATTTCT
1 TTTCAATTTCT
21797134 ACTTTTCAAT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
73 75 0.96
74 3 0.04
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (73 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGAGAGTTGAGCCTCAGGGCACGC
TGAGGTAA
Found at i:21797169 original size:160 final size:160
Alignment explanation
Indices: 21796888--21797191 Score: 484
Period size: 160 Copynumber: 1.9 Consensus size: 160
21796878 AATTTCTACT
* *
21796888 TTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACAC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTAGG--CACAC
** *
21796953 GCTGAGGTATTTTCAATTTCTGGTTTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGA
64 GCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGA
*
21797018 GGAGAGTTGAGCCTCGGGACACGCTGAGGTAA
129 GGAGAGCTGAGCCTCGGGACACGCTGAGGTAA
* * *
21797050 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-GCACG
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT-AGGCACACG
21797114 CTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAG
65 CTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAG
*
21797179 GTGAGCTGAGCCT
130 GAGAGCTGAGCCT
21797192 TTTAATTTTT
Statistics
Matches: 131, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
160 77 0.59
162 52 0.40
163 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (160 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTAGGCACACGC
TGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGG
AGAGCTGAGCCTCGGGACACGCTGAGGTAA
Found at i:21797209 original size:429 final size:429
Alignment explanation
Indices: 21796410--21797250 Score: 1682
Period size: 429 Copynumber: 2.0 Consensus size: 429
21796400 TCATATTGGA
21796410 AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTT
1 AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTT
21796475 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAA
66 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAA
21796540 TTTCTGGTTTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGAGAGTTGAGCCTCG
131 TTTCTGGTTTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGAGAGTTGAGCCTCG
21796605 GGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTT
196 GGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTT
21796670 GAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAA
261 GAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAA
21796735 CTCATATTGCGAGAGGTGAGCTGAGCCTTTTAATTTTTATTTTTCAAAAAAACCAACTCATATTG
326 CTCATATTGCGAGAGGTGAGCTGAGCCTTTTAATTTTTATTTTTCAAAAAAACCAACTCATATTG
21796800 CGAGAGGTGAGTTGAGCCTTTTTCTATTTTTCAAAAAAG
391 CGAGAGGTGAGTTGAGCCTTTTTCTATTTTTCAAAAAAG
21796839 AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTT
1 AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTT
21796904 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAA
66 TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAA
21796969 TTTCTGGTTTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGAGAGTTGAGCCTCG
131 TTTCTGGTTTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGAGAGTTGAGCCTCG
21797034 GGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTT
196 GGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTT
21797099 GAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAA
261 GAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAA
21797164 CTCATATTGCGAGAGGTGAGCTGAGCCTTTTAATTTTTATTTTTCAAAAAAACCAACTCATATTG
326 CTCATATTGCGAGAGGTGAGCTGAGCCTTTTAATTTTTATTTTTCAAAAAAACCAACTCATATTG
21797229 CGAGAGGTGAGTTGAGCCTTTT
391 CGAGAGGTGAGTTGAGCCTTTT
21797251 GCAAATTCTG
Statistics
Matches: 412, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
429 412 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (429 bp):
AGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTT
TCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGCTCACACGCTGAGGTATTTTCAA
TTTCTGGTTTTCAATTTCTGTTTTTCAAAAATCGACTCATATTGCGAGAGGAGAGTTGAGCCTCG
GGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTT
GAGCCTCAGGGCACGCTGAGGTATTTTCAATTTCTACTTTTCAATTTCTGTTTTTCAAAAATCAA
CTCATATTGCGAGAGGTGAGCTGAGCCTTTTAATTTTTATTTTTCAAAAAAACCAACTCATATTG
CGAGAGGTGAGTTGAGCCTTTTTCTATTTTTCAAAAAAG
Found at i:21797295 original size:55 final size:54
Alignment explanation
Indices: 21797135--21797303 Score: 232
Period size: 55 Copynumber: 3.1 Consensus size: 54
21797125 TCAATTTCTA
*
21797135 CTTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGC
1 CTTTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
21797190 CTTTT-AATTTTTATTTTTCAAAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCT-GTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* *
21797246 CTTTTGCAAATTCTGTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
21797301 CTT
1 CTT
21797304 GGCTCACGTG
Statistics
Matches: 100, Mismatches: 9, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
54 11 0.11
55 41 0.41
56 38 0.38
57 5 0.05
58 5 0.05
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (54 bp):
CTTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:21797614 original size:30 final size:30
Alignment explanation
Indices: 21797580--21797681 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
21797570 TTAAAAATAA
*
21797580 AAATTGCATTTTGACCCCTAAACTTT-TCCT
1 AAATTTCATTTTGACCCCTAAACTTTCT-CT
* *
21797610 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCTCT
* * *
21797640 AAATTTCACTTAGACCCCTAAACCTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTC-TCT
21797670 AAATTTCATTTT
1 AAATTTCATTTT
21797682 AATCCTAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
30 59 0.97
31 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.04, T:0.43
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCTCT
Found at i:21798947 original size:93 final size:93
Alignment explanation
Indices: 21798805--21798992 Score: 367
Period size: 93 Copynumber: 2.0 Consensus size: 93
21798795 TTAAATTGAA
*
21798805 TTAATTTAACACTAATTCGATAGTTTCATCGCCATATCGGGGTGAATATCATCGATTTGTGTTAA
1 TTAATTTAACACTAATTCGATAGTTTCATCGCCATATCAGGGTGAATATCATCGATTTGTGTTAA
21798870 ATACAGTATTTTTAAAGAAAAATCGTTT
66 ATACAGTATTTTTAAAGAAAAATCGTTT
21798898 TTAATTTAACACTAATTCGATAGTTTCATCGCCATATCAGGGTGAATATCATCGATTTGTGTTAA
1 TTAATTTAACACTAATTCGATAGTTTCATCGCCATATCAGGGTGAATATCATCGATTTGTGTTAA
21798963 ATACAGTATTTTTAAAGAAAAATCGTTT
66 ATACAGTATTTTTAAAGAAAAATCGTTT
21798991 TT
1 TT
21798993 TTAAAAAAAA
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (93 bp):
TTAATTTAACACTAATTCGATAGTTTCATCGCCATATCAGGGTGAATATCATCGATTTGTGTTAA
ATACAGTATTTTTAAAGAAAAATCGTTT
Found at i:21799140 original size:16 final size:16
Alignment explanation
Indices: 21799092--21799140 Score: 64
Period size: 16 Copynumber: 3.0 Consensus size: 16
21799082 TTTCTTTCTA
*
21799092 AAAAAATCGTGTTTTC
1 AAAAATTCGTGTTTTC
21799108 AAAAATTTCCGTG-TTTC
1 AAAAA-TT-CGTGTTTTC
21799125 AAAAATTCGTGTTTTC
1 AAAAATTCGTGTTTTC
21799141 GTGTTTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 10 0.34
18 4 0.14
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (16 bp):
AAAAATTCGTGTTTTC
Found at i:21803020 original size:48 final size:48
Alignment explanation
Indices: 21802936--21803793 Score: 1608
Period size: 48 Copynumber: 17.9 Consensus size: 48
21802926 GGGTTATCTT
* * * * *
21802936 TGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21802984 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
* * *
21803032 TGATCCCATGTAAGACCATATTTGGGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803080 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803128 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803176 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803224 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803272 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803320 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803368 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803416 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803464 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803512 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803560 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803608 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803656 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
21803704 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
* * * *
21803752 TGATCCCATGTAAGACCATATTTGGGATATGGCATTGGCATC
1 TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATC
21803794 TTACTATGTT
Statistics
Matches: 795, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 795 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (48 bp):
TGATCCCATGTAAAACCATATCTGAGATATGACATTGGCATCGATATG
Found at i:21805874 original size:72 final size:72
Alignment explanation
Indices: 21805743--21805883 Score: 219
Period size: 72 Copynumber: 2.0 Consensus size: 72
21805733 CGCTAAATCC
* * * *
21805743 ACAACCATCACATCCTTTGGATTAGTCACCGACTCTTTAAAACGGACCTTCTTAGTACTCGAATT
1 ACAACCATCACATCCTTTAGATTAGTCACCGACTCCTTAAAACGGACATTCTTAGTACTCGAATC
21805808 AGCAGGA
66 AGCAGGA
* * *
21805815 ACAACCATCACATCCTTTAGATTAGTCACCGACTCCTTAAAATGGACATTTTTATTACTCGAATC
1 ACAACCATCACATCCTTTAGATTAGTCACCGACTCCTTAAAACGGACATTCTTAGTACTCGAATC
21805880 AGCA
66 AGCA
21805884 AGAGGGTTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (72 bp):
ACAACCATCACATCCTTTAGATTAGTCACCGACTCCTTAAAACGGACATTCTTAGTACTCGAATC
AGCAGGA
Found at i:21806420 original size:3 final size:3
Alignment explanation
Indices: 21806412--21806458 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
21806402 ATAACAAAGA
21806412 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
21806459 AAGAAGAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:21806871 original size:23 final size:23
Alignment explanation
Indices: 21806841--21806886 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
21806831 TTACTTGCCA
21806841 TGGTCAAAAGTGATGAGAAGCTT
1 TGGTCAAAAGTGATGAGAAGCTT
21806864 TGGTCAAAAGTGATGAGAAGCTT
1 TGGTCAAAAGTGATGAGAAGCTT
21806887 GGGTAAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.30, T:0.26
Consensus pattern (23 bp):
TGGTCAAAAGTGATGAGAAGCTT
Found at i:21807111 original size:3 final size:3
Alignment explanation
Indices: 21807096--21807167 Score: 119
Period size: 3 Copynumber: 24.3 Consensus size: 3
21807086 CCTTTATTTC
*
21807096 TCT TCT CCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
21807144 TCT TCT TCT TCT TTT TC- TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
21807168 AAACCATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 2 0.03
3 62 0.97
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:21814538 original size:59 final size:59
Alignment explanation
Indices: 21814444--21814558 Score: 178
Period size: 59 Copynumber: 1.9 Consensus size: 59
21814434 TTTTAAAAAA
* *
21814444 CTAACTTGGACAAAAAAAAGTTCAAGCCCTAATGTGAGAACAGTTGCCAAATTCATGGC
1 CTAACTTGGACAAAAAAAAGTTCAAACCCTAATGTGAGAAAAGTTGCCAAATTCATGGC
* *
21814503 CTAACTTGGACAAAAAAAAAGTTCAAACCCT-ATGTGTGAAAAGTTGCCAAGTTCAT
1 CTAACTTGGAC-AAAAAAAAGTTCAAACCCTAATGTGAGAAAAGTTGCCAAATTCAT
21814559 TTAATTTCTT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 33 0.65
60 18 0.35
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (59 bp):
CTAACTTGGACAAAAAAAAGTTCAAACCCTAATGTGAGAAAAGTTGCCAAATTCATGGC
Found at i:21815823 original size:7 final size:7
Alignment explanation
Indices: 21815811--21815836 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21815801 AGAAATTAGA
21815811 TTAAATT
1 TTAAATT
21815818 TTAAATT
1 TTAAATT
21815825 TTAAATT
1 TTAAATT
21815832 TTAAA
1 TTAAA
21815837 ACATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (7 bp):
TTAAATT
Found at i:21818035 original size:31 final size:31
Alignment explanation
Indices: 21818000--21818063 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
21817990 AAAATTACAA
*
21818000 AAGTTACTAAATTATTAAAAAGT-TTTCATTT
1 AAGTTACTAAACTATTAAAAAGTATTT-ATTT
* *
21818031 AAGTTATTAAACTCTTAAAAAGTATTTATTT
1 AAGTTACTAAACTATTAAAAAGTATTTATTT
21818062 AA
1 AA
21818064 ATCATTGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (31 bp):
AAGTTACTAAACTATTAAAAAGTATTTATTT
Found at i:21818655 original size:15 final size:15
Alignment explanation
Indices: 21818632--21818663 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21818622 TTATTTAAGT
21818632 TATAAATAAATATTA
1 TATAAATAAATATTA
*
21818647 TATATATAAATATTA
1 TATAAATAAATATTA
21818662 TA
1 TA
21818664 ATTATTAACC
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TATAAATAAATATTA
Found at i:21818695 original size:3 final size:3
Alignment explanation
Indices: 21818689--21818732 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
21818679 TATGGTTTTA
21818689 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
21818733 AATAAAGTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:21819285 original size:6 final size:6
Alignment explanation
Indices: 21819254--21819297 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
21819244 AGAAGCAGGG
* * *
21819254 AAGAAA AAGAGA AAGAAA AAGGAA AAGAAA AATAAA AGAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A-AGAAA A
21819298 CTAGGGATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:21821653 original size:26 final size:26
Alignment explanation
Indices: 21821601--21821653 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
21821591 TTTACAGTTT
*
21821601 TACCCCTAGGAGATAAATTATCGAAA
1 TACCCCTAGGAGATAAATTACCGAAA
* *
21821627 TACCCCTAGG-GTTAAATTGACCTAAA
1 TACCCCTAGGAGATAAATT-ACCGAAA
21821653 T
1 T
21821654 GCATGTTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGAGATAAATTACCGAAA
Found at i:21822990 original size:21 final size:21
Alignment explanation
Indices: 21822945--21822990 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
21822935 CGTATTTGAG
* *
21822945 GCACCTCGTGTGTCGCATCAG
1 GCACCTCGTGTGTAGCATCAA
**
21822966 GCACCTCGTGTGTAGTTTCAA
1 GCACCTCGTGTGTAGCATCAA
21822987 GCAC
1 GCAC
21822991 TTATGTGTCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.30, G:0.26, T:0.26
Consensus pattern (21 bp):
GCACCTCGTGTGTAGCATCAA
Found at i:21823057 original size:8 final size:8
Alignment explanation
Indices: 21823044--21823084 Score: 73
Period size: 8 Copynumber: 5.1 Consensus size: 8
21823034 CAATGTGCTT
21823044 TGAATCCG
1 TGAATCCG
21823052 TGAATCCG
1 TGAATCCG
*
21823060 TGAATCTG
1 TGAATCCG
21823068 TGAATCCG
1 TGAATCCG
21823076 TGAATCCG
1 TGAATCCG
21823084 T
1 T
21823085 CAAAGTCTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (8 bp):
TGAATCCG
Found at i:21826478 original size:48 final size:48
Alignment explanation
Indices: 21826423--21826518 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
21826413 CTCGTATGGG
21826423 GTGGCTTAGGTCGTGTTAGAGTCTGCTAAATAGACACAGCCGTGTGGT
1 GTGGCTTAGGTCGTGTTAGAGTCTGCTAAATAGACACAGCCGTGTGGT
* * * *
21826471 GTGGCTTAGGTCGTGTTATAGTCTGTTAAATAGACACGGGCGTGTGGT
1 GTGGCTTAGGTCGTGTTAGAGTCTGCTAAATAGACACAGCCGTGTGGT
21826519 CTACCCGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.20, C:0.15, G:0.34, T:0.31
Consensus pattern (48 bp):
GTGGCTTAGGTCGTGTTAGAGTCTGCTAAATAGACACAGCCGTGTGGT
Found at i:21828762 original size:5 final size:5
Alignment explanation
Indices: 21828752--21828780 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
21828742 TTAAGTAATA
21828752 TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATA
21828781 ATAATAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:21829748 original size:44 final size:44
Alignment explanation
Indices: 21829683--21829774 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 44
21829673 TGTTTAGGGA
* * *
21829683 TACTTCGACCTTGAGTCGATGAGGCACTATAAGTGTCGTACTGT
1 TACTTCGACCTTAAGTCGATGAGGCACCATAAGTGTCGTACTGC
* * **
21829727 TACTTCGACTTTAAGTTGATGAGGCACCATGTGTGTCGTACTGC
1 TACTTCGACCTTAAGTCGATGAGGCACCATAAGTGTCGTACTGC
21829771 TACT
1 TACT
21829775 GTTACATCGG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.34
Consensus pattern (44 bp):
TACTTCGACCTTAAGTCGATGAGGCACCATAAGTGTCGTACTGC
Found at i:21840024 original size:31 final size:31
Alignment explanation
Indices: 21839924--21840027 Score: 136
Period size: 31 Copynumber: 3.4 Consensus size: 31
21839914 TCATGCTCAG
*
21839924 TTGCTTTATGTAATAATGTCTGTAGTACTGT
1 TTGCTTTATGTGATAATGTCTGTAGTACTGT
* * **
21839955 CTGTTTTATGTGATAATGTCTGTAGTACTAC
1 TTGCTTTATGTGATAATGTCTGTAGTACTGT
* *
21839986 TTGCTTTATGTGATAATGTCTATAGTATTGT
1 TTGCTTTATGTGATAATGTCTGTAGTACTGT
*
21840017 TTACTTTATGT
1 TTGCTTTATGT
21840028 ATTAATATCT
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.22, C:0.10, G:0.18, T:0.50
Consensus pattern (31 bp):
TTGCTTTATGTGATAATGTCTGTAGTACTGT
Found at i:21842264 original size:7 final size:7
Alignment explanation
Indices: 21842254--21842278 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21842244 TTATAAAATT
21842254 TAAAAGG
1 TAAAAGG
21842261 TAAAAGG
1 TAAAAGG
21842268 TAAAAGG
1 TAAAAGG
21842275 TAAA
1 TAAA
21842279 GGATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (7 bp):
TAAAAGG
Found at i:21842362 original size:8 final size:9
Alignment explanation
Indices: 21842339--21842364 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
21842329 TTTATCTAAT
21842339 CATTTTTCA
1 CATTTTTCA
21842348 CATTTTTCA
1 CATTTTTCA
21842357 CATTTTTC
1 CATTTTTC
21842365 TTGTTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (9 bp):
CATTTTTCA
Found at i:21842468 original size:17 final size:16
Alignment explanation
Indices: 21842437--21842475 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
21842427 AAATCTATAA
21842437 AAATATTAATTTTTAAT
1 AAAT-TTAATTTTTAAT
*
21842454 TAATTTAATTTTTTAAT
1 AAATTTAA-TTTTTAAT
21842471 AAATT
1 AAATT
21842476 ATCAAACTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AAATTTAATTTTTAAT
Done.