Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 67 of 132
Found at i:18921240 original size:28 final size:28
Alignment explanation
Indices: 18921189--18921271 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 28
18921179 GAAGCGGAAG
* * * * *
18921189 GCTCAGATAGAGAAATGTTGTGATTTTA
1 GCTCAGATAAAGCAATATTCTGATTCTA
* * *
18921217 GCTCGGATAGAGCGATATTCTGATTCTA
1 GCTCAGATAAAGCAATATTCTGATTCTA
*
18921245 GCTCAGATAAAGCAATATTCTAATTCT
1 GCTCAGATAAAGCAATATTCTGATTCT
18921272 GGCTTGGGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (28 bp):
GCTCAGATAAAGCAATATTCTGATTCTA
Found at i:18921294 original size:28 final size:28
Alignment explanation
Indices: 18921263--18921519 Score: 214
Period size: 28 Copynumber: 9.2 Consensus size: 28
18921253 AAAGCAATAT
* * *
18921263 TCTAATTCTGGCTTGGGTAGATCATTAC
1 TCTATTTCTGGCTCGGGTAGAGCATTAC
* * **
18921291 TCTATTTCTTGCTCGGGTGGAGTGTTAC
1 TCTATTTCTGGCTCGGGTAGAGCATTAC
* *
18921319 TCT-TAATCTGGCTCGGGTAGAGCATTAT
1 TCTAT-TTCTGGCTCGGGTAGAGCATTAC
*
18921347 TCTATTTCTGGCTCAGGTAGAGCATTAC
1 TCTATTTCTGGCTCGGGTAGAGCATTAC
* * * *
18921375 TCTGAATT-TGGCTCGAGTAGAGAATTAT
1 TCT-ATTTCTGGCTCGGGTAGAGCATTAC
* **
18921403 TCTATTTCTAGCTCGGGTAGAGTGTTAC
1 TCTATTTCTGGCTCGGGTAGAGCATTAC
* * *
18921431 TCTAAATT-TGGCTTGGGTAGAGCATTAT
1 TCT-ATTTCTGGCTCGGGTAGAGCATTAC
* * *
18921459 TCTATTTTTGGCTCGGGTAGAGCGTTAT
1 TCTATTTCTGGCTCGGGTAGAGCATTAC
* * ** *
18921487 TCTATTTTTGGCTTGGAAAGAGCATTAT
1 TCTATTTCTGGCTCGGGTAGAGCATTAC
18921515 TCTAT
1 TCTAT
18921520 ATCTATGCTT
Statistics
Matches: 183, Mismatches: 40, Indels: 12
0.78 0.17 0.05
Matches are distributed among these distances:
27 7 0.04
28 169 0.92
29 7 0.04
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.40
Consensus pattern (28 bp):
TCTATTTCTGGCTCGGGTAGAGCATTAC
Found at i:18921355 original size:56 final size:56
Alignment explanation
Indices: 18921263--18921528 Score: 273
Period size: 56 Copynumber: 4.7 Consensus size: 56
18921253 AAAGCAATAT
* * * * * *
18921263 TCTAATTCTGGCTTGGGTAGATCATTACTCTATTTCTTGCTCGGGTGGAGTGTTAC
1 TCTAAATCTGGCTCGGGTAGAGCATTATTCTATTTCTTGCTCGGGTAGAGCGTTAC
* * * *
18921319 TCTTAATCTGGCTCGGGTAGAGCATTATTCTATTTCTGGCTCAGGTAGAGCATTAC
1 TCTAAATCTGGCTCGGGTAGAGCATTATTCTATTTCTTGCTCGGGTAGAGCGTTAC
* * * * * *
18921375 TCTGAATTTGGCTCGAGTAGAGAATTATTCTATTTCTAGCTCGGGTAGAGTGTTAC
1 TCTAAATCTGGCTCGGGTAGAGCATTATTCTATTTCTTGCTCGGGTAGAGCGTTAC
* * *
18921431 TCTAAATTTGGCTTGGGTAGAGCATTATTCTATTT-TTGGCTCGGGTAGAGCGTTAT
1 TCTAAATCTGGCTCGGGTAGAGCATTATTCTATTTCTT-GCTCGGGTAGAGCGTTAC
** * * ** *
18921487 TCTATTTTTGGCTTGGAAAGAGCATTATTCTATATCTATGCT
1 TCTAAATCTGGCTCGGGTAGAGCATTATTCTATTTCT-TGCT
18921529 TGAATGAGTT
Statistics
Matches: 177, Mismatches: 30, Indels: 5
0.83 0.14 0.02
Matches are distributed among these distances:
55 1 0.01
56 171 0.97
57 4 0.02
58 1 0.01
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.40
Consensus pattern (56 bp):
TCTAAATCTGGCTCGGGTAGAGCATTATTCTATTTCTTGCTCGGGTAGAGCGTTAC
Found at i:18921499 original size:112 final size:112
Alignment explanation
Indices: 18921217--18921481 Score: 320
Period size: 112 Copynumber: 2.4 Consensus size: 112
18921207 TGTGATTTTA
* * * * * * * *
18921217 GCTCGGATAGAGCGA-TATTCTGA-TTCTAGCTCAGATAAAGCAATATTCT-AATTCTGGCTTGG
1 GCTCGGGTAGAGC-ATTATTCT-ATTTCTGGCTCAGGTAGAGCATTACTCTGAATT-TGGCTCGA
** * * *
18921279 GTAGATCATTACTCTATTTCTTGCTCGGGTGGAGTGTTACTCTTAATCTG
63 GTAGAGAATTACTCTATTTCTAGCTCGGGTAGAGTGTTACTCTAAATCTG
18921329 GCTCGGGTAGAGCATTATTCTATTTCTGGCTCAGGTAGAGCATTACTCTGAATTTGGCTCGAGTA
1 GCTCGGGTAGAGCATTATTCTATTTCTGGCTCAGGTAGAGCATTACTCTGAATTTGGCTCGAGTA
* *
18921394 GAGAATTATTCTATTTCTAGCTCGGGTAGAGTGTTACTCTAAATTTG
66 GAGAATTACTCTATTTCTAGCTCGGGTAGAGTGTTACTCTAAATCTG
* * *
18921441 GCTTGGGTAGAGCATTATTCTATTTTTGGCTCGGGTAGAGC
1 GCTCGGGTAGAGCATTATTCTATTTCTGGCTCAGGTAGAGC
18921482 GTTATTCTAT
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
111 2 0.02
112 126 0.95
113 4 0.03
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.37
Consensus pattern (112 bp):
GCTCGGGTAGAGCATTATTCTATTTCTGGCTCAGGTAGAGCATTACTCTGAATTTGGCTCGAGTA
GAGAATTACTCTATTTCTAGCTCGGGTAGAGTGTTACTCTAAATCTG
Found at i:18929788 original size:51 final size:49
Alignment explanation
Indices: 18929715--18929810 Score: 129
Period size: 51 Copynumber: 1.9 Consensus size: 49
18929705 TGAAAATGAG
* * *
18929715 TTACTAATGCATGACTTTATTTAAGATGCAAACTTTAACTATCATGGGAA
1 TTACTAATGCATGACATAATTTAAGATGCAAA-TTTAACTAACATGGGAA
* *
18929765 TTACATAATGCATGGCATAATTTATGATGCAAATTTAACTAACATG
1 TTAC-TAATGCATGACATAATTTAAGATGCAAATTTAACTAACATG
18929811 AGAGTTGAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 16 0.40
51 24 0.60
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (49 bp):
TTACTAATGCATGACATAATTTAAGATGCAAATTTAACTAACATGGGAA
Found at i:18933893 original size:3 final size:3
Alignment explanation
Indices: 18933885--18933941 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
18933875 AAGATGAAAT
18933885 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18933933 ATA ATA ATA
1 ATA ATA ATA
18933942 TGGGATCCCC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18942245 original size:81 final size:80
Alignment explanation
Indices: 18942110--18942275 Score: 296
Period size: 81 Copynumber: 2.1 Consensus size: 80
18942100 AGAGTCTGTA
* *
18942110 GTCAGCTAGCTAGTTTGTTTACCACTCCTAAGAGTGATAGCCTTGTAGTGTTCTTTTCCCTTTGG
1 GTCAGCTAGCCAGTTTGTTTACCACTCCTAAGAGTGATAGCCTTGTAGTGTTCTTTTCCCTTCGG
18942175 ATTTGGATTTTTTTGT
66 ATTTGGA-TTTTTTGT
*
18942191 GTCAGCTCGCCAGTTTGTTTACCACTCCTAAGAGTGATAGCCTTGTAGTGTTCTTTTCCCTTCGG
1 GTCAGCTAGCCAGTTTGTTTACCACTCCTAAGAGTGATAGCCTTGTAGTGTTCTTTTCCCTTCGG
18942256 ATTTGGATTTTTTGT
66 ATTTGGATTTTTTGT
18942271 GTCAG
1 GTCAG
18942276 TAGATAGTGT
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
80 13 0.16
81 69 0.84
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (80 bp):
GTCAGCTAGCCAGTTTGTTTACCACTCCTAAGAGTGATAGCCTTGTAGTGTTCTTTTCCCTTCGG
ATTTGGATTTTTTGT
Found at i:18955710 original size:34 final size:34
Alignment explanation
Indices: 18955667--18955733 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
18955657 ATTTAGGGAG
*
18955667 AAAATATATGTCATTTGTAATACTATCACACCCT
1 AAAATATATGTCATTTGTAATACCATCACACCCT
18955701 AAAATATATGTCATTTGTAATACCATCACACCC
1 AAAATATATGTCATTTGTAATACCATCACACCC
18955734 CGAAACTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.39, C:0.22, G:0.06, T:0.33
Consensus pattern (34 bp):
AAAATATATGTCATTTGTAATACCATCACACCCT
Found at i:18964536 original size:52 final size:51
Alignment explanation
Indices: 18964480--18964779 Score: 408
Period size: 52 Copynumber: 5.8 Consensus size: 51
18964470 AATCAACAAG
*
18964480 GGATTCATATACTCACGATGACACCTAGTCATCAGACCTCTTAA-CTCGTAAA
1 GGATTCATATACTCACGATGACACTTAGTCATC-GACCTCTTAATC-CGTAAA
* *
18964532 GGATTCATATAGTCACGATGACACTTAGTCATCGGACGTCTTAATCCGTAAA
1 GGATTCATATACTCACGATGACACTTAGTCATC-GACCTCTTAATCCGTAAA
*
18964584 GGATTCATATACTCATGATGACACTTAGTCATCGGACCTCTTAATCCGTAAA
1 GGATTCATATACTCACGATGACACTTAGTCATC-GACCTCTTAATCCGTAAA
* * * **
18964636 GGATTCATATACTCACGATAACACTTAGTCATCAGATCTCTTATTCAATAAA
1 GGATTCATATACTCACGATGACACTTAGTCATC-GACCTCTTAATCCGTAAA
* *
18964688 GGATTC--ATACTCACGATGACACTTAGTCATCGAACATCTTAATCCATAAA
1 GGATTCATATACTCACGATGACACTTAGTCATCG-ACCTCTTAATCCGTAAA
*
18964738 GGATTCATATACTCACTATGACACTTAGTCATCGAACCTCTT
1 GGATTCATATACTCACGATGACACTTAGTCATCG-ACCTCTT
18964780 CGTTTATGGC
Statistics
Matches: 223, Mismatches: 21, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
49 1 0.00
50 43 0.19
52 178 0.80
53 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.30
Consensus pattern (51 bp):
GGATTCATATACTCACGATGACACTTAGTCATCGACCTCTTAATCCGTAAA
Found at i:18964613 original size:104 final size:103
Alignment explanation
Indices: 18964431--18964771 Score: 417
Period size: 104 Copynumber: 3.3 Consensus size: 103
18964421 TTTCACTTCG
* * * * *
18964431 TTCATATACTCAC-AGTGACACATAGCCACCGGA-C-CATATAATCAACAAGGGATTCATATACT
1 TTCATATACTCACGA-TGACACTTAGTCATCGGATCTC-T-TAATCAATAAAGGATTCATATACT
*
18964493 CACGATGACACCTAGTCATCAGACCTCTTAA-CTCGTAAAGGA
63 CACGATGACACTTAGTCATC-GACCTCTTAATC-CGTAAAGGA
* **
18964535 TTCATATAGTCACGATGACACTTAGTCATCGGA-CGTCTTAATCCGTAAAGGATTCATATACTCA
1 TTCATATACTCACGATGACACTTAGTCATCGGATC-TCTTAATCAATAAAGGATTCATATACTCA
*
18964599 TGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
65 CGATGACACTTAGTCATC-GACCTCTTAATCCGTAAAGGA
* * *
18964639 TTCATATACTCACGATAACACTTAGTCATCAGATCTCTTATTCAATAAAGGATTC--ATACTCAC
1 TTCATATACTCACGATGACACTTAGTCATCGGATCTCTTAATCAATAAAGGATTCATATACTCAC
* *
18964702 GATGACACTTAGTCATCGAACATCTTAATCCATAAAGGA
66 GATGACACTTAGTCATCG-ACCTCTTAATCCGTAAAGGA
*
18964741 TTCATATACTCACTATGACACTTAGTCATCG
1 TTCATATACTCACGATGACACTTAGTCATCG
18964772 AACCTCTTCG
Statistics
Matches: 208, Mismatches: 23, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
101 1 0.00
102 70 0.34
104 132 0.63
105 4 0.02
106 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (103 bp):
TTCATATACTCACGATGACACTTAGTCATCGGATCTCTTAATCAATAAAGGATTCATATACTCAC
GATGACACTTAGTCATCGACCTCTTAATCCGTAAAGGA
Found at i:18964764 original size:154 final size:155
Alignment explanation
Indices: 18964480--18964779 Score: 462
Period size: 154 Copynumber: 1.9 Consensus size: 155
18964470 AATCAACAAG
* * *
18964480 GGATTCATATACTCACGATGACACCTAGTCATCAGACCTCTTAACTCGTAAAGGATTCATATAGT
1 GGATTCATATACTCACGATAACACCTAGTCATCAGACCTCTTAACTCATAAAGGATTCA-ATACT
* * *
18964545 CACGATGACACTTAGTCATCGGACGTCTTAATCCGTAAAGGATTCATATACTCATGATGACACTT
65 CACGATGACACTTAGTCATCGAACATCTTAATCCATAAAGGATTCATATACTCATGATGACACTT
*
18964610 AGTCATCGGACCTCTTAATCCGTAAA
130 AGTCATCGAACCTCTTAATCCGTAAA
* * *
18964636 GGATTCATATACTCACGATAACACTTAGTCATCAGATCTCTT-ATTCAATAAAGGATTC-ATACT
1 GGATTCATATACTCACGATAACACCTAGTCATCAGACCTCTTAACTC-ATAAAGGATTCAATACT
18964699 CACGATGACACTTAGTCATCGAACATCTTAATCCATAAAGGATTCATATACTCACT-ATGACACT
65 CACGATGACACTTAGTCATCGAACATCTTAATCCATAAAGGATTCATATACTCA-TGATGACACT
18964763 TAGTCATCGAACCTCTT
129 TAGTCATCGAACCTCTT
18964780 CGTTTATGGC
Statistics
Matches: 132, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
154 79 0.60
155 4 0.03
156 49 0.37
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.30
Consensus pattern (155 bp):
GGATTCATATACTCACGATAACACCTAGTCATCAGACCTCTTAACTCATAAAGGATTCAATACTC
ACGATGACACTTAGTCATCGAACATCTTAATCCATAAAGGATTCATATACTCATGATGACACTTA
GTCATCGAACCTCTTAATCCGTAAA
Found at i:18976599 original size:17 final size:17
Alignment explanation
Indices: 18976573--18976611 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
18976563 TTAGCATTCT
18976573 TGCA-TTTTATTGTGC-C
1 TGCATTTTTATTGT-CAC
18976589 TGCATTTTTATTGTCAC
1 TGCATTTTTATTGTCAC
18976606 TGCATT
1 TGCATT
18976612 CATTTTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.15, C:0.18, G:0.15, T:0.51
Consensus pattern (17 bp):
TGCATTTTTATTGTCAC
Found at i:18984744 original size:52 final size:52
Alignment explanation
Indices: 18984657--18984955 Score: 411
Period size: 52 Copynumber: 5.8 Consensus size: 52
18984647 TTTGACTTTG
* * * * * ** *
18984657 TTCATATACTCACGGTGACACATAGCCACCAGACCT-TATAATCCACAAGGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCT-TAATCCGTAAAGGA
* * *
18984709 TTCATATACTCACGATGACACTTAGTCATCGGACCTTTTAATCCATAAAAGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
*
18984761 TTCATATATTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
* * *
18984813 TTCATATACTCACGATGACACTTAATCATCTGACCTCTTAATTCGTAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
* *
18984865 TTCATATACTCACAATGACACTTAGTCATCGGACCTCTTAATCCGTAAGGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
* *
18984917 TTCATATACTCACGATGACACTTAGCCATCGTACCTCTT
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTT
18984956 CGTTTATGGC
Statistics
Matches: 222, Mismatches: 24, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
52 221 1.00
53 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.29
Consensus pattern (52 bp):
TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGA
Found at i:19004085 original size:24 final size:25
Alignment explanation
Indices: 19004039--19004086 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
19004029 TCTTTCTTAC
19004039 TTAACTTTTTGTTTTTGCTAATTTGT
1 TTAACTTTTTGTTTTT-CTAATTTGT
19004065 TTAACTTTTCT-TTTTT-TAATTT
1 TTAACTTTT-TGTTTTTCTAATTT
19004087 TCTCTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 6 0.29
26 14 0.67
27 1 0.05
ACGTcount: A:0.17, C:0.08, G:0.06, T:0.69
Consensus pattern (25 bp):
TTAACTTTTTGTTTTTCTAATTTGT
Found at i:19009714 original size:20 final size:20
Alignment explanation
Indices: 19009671--19009714 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
19009661 TGTCAACGCA
*
19009671 TTTTTACATTTACTTTATCT
1 TTTTTACATTTACTTGATCT
*
19009691 TTTTTACTTTTACTTGATTCT
1 TTTTTACATTTACTTGA-TCT
19009712 TTT
1 TTT
19009715 AAGTCTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.16, C:0.14, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTTACATTTACTTGATCT
Found at i:19018674 original size:14 final size:16
Alignment explanation
Indices: 19018647--19018678 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
19018637 ATCGAGGAGA
19018647 AGAAGGAAGAAGAAAG
1 AGAAGGAAGAAGAAAG
19018663 AGAA-GAAG-AGAAAG
1 AGAAGGAAGAAGAAAG
19018677 AG
1 AG
19018679 GAAGTTCCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (16 bp):
AGAAGGAAGAAGAAAG
Found at i:19035937 original size:18 final size:18
Alignment explanation
Indices: 19035914--19035959 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
19035904 GATAAAATTA
*
19035914 TCGACGCAACTGT-CGATG
1 TCGACGCAAC-GTACAATG
19035932 TCGACGCAACGTACAATG
1 TCGACGCAACGTACAATG
*
19035950 TCGACACAAC
1 TCGACGCAAC
19035960 CTGATGTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 2 0.08
18 23 0.92
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.17
Consensus pattern (18 bp):
TCGACGCAACGTACAATG
Found at i:19039656 original size:11 final size:11
Alignment explanation
Indices: 19039640--19039664 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19039630 ATCTCAACTC
19039640 TTTTCTCTTTA
1 TTTTCTCTTTA
19039651 TTTTCTCTTTA
1 TTTTCTCTTTA
19039662 TTT
1 TTT
19039665 ATGCTTTTTG
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTCTCTTTA
Found at i:19046528 original size:17 final size:17
Alignment explanation
Indices: 19046506--19046542 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19046496 CTGTAGTATA
*
19046506 ATTGTCCCTACATTTTT
1 ATTGTCACTACATTTTT
*
19046523 ATTGTCACTGCATTTTT
1 ATTGTCACTACATTTTT
19046540 ATT
1 ATT
19046543 ATCGTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.19, G:0.08, T:0.54
Consensus pattern (17 bp):
ATTGTCACTACATTTTT
Found at i:19047161 original size:18 final size:20
Alignment explanation
Indices: 19047129--19047165 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
19047119 TTAGTCACAT
19047129 AAAAAAAGAGTAAAAGAAAG
1 AAAAAAAGAGTAAAAGAAAG
19047149 AAAAAAAG-G-AAAAGAAA
1 AAAAAAAGAGTAAAAGAAA
19047166 AAATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 1 0.06
20 8 0.47
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (20 bp):
AAAAAAAGAGTAAAAGAAAG
Found at i:19063047 original size:24 final size:23
Alignment explanation
Indices: 19063009--19063054 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
19062999 TAAAGGGTAG
* *
19063009 AAATTGTCAGTGCAAATGTAATAC
1 AAATTGTAAGAGCAAAT-TAATAC
19063033 AAATTGTAAGAGCAAATTAATA
1 AAATTGTAAGAGCAAATTAATA
19063055 AAAGATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.28
Consensus pattern (23 bp):
AAATTGTAAGAGCAAATTAATAC
Found at i:19065654 original size:15 final size:15
Alignment explanation
Indices: 19065634--19065684 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
19065624 AGCAATTCCT
19065634 TCTTCTTCTTCTTTC
1 TCTTCTTCTTCTTTC
19065649 TCTTCTT-TTCTTTC
1 TCTTCTTCTTCTTTC
*
19065663 T-TT-TTC-TCTTGC
1 TCTTCTTCTTCTTTC
19065675 TTCTTCTTCT
1 -TCTTCTTCT
19065685 ACTGTAATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
12 7 0.23
13 3 0.10
14 10 0.33
15 10 0.33
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (15 bp):
TCTTCTTCTTCTTTC
Found at i:19065681 original size:12 final size:11
Alignment explanation
Indices: 19065632--19065681 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
19065622 GGAGCAATTC
19065632 CTTCTTCTTCTT
1 CTTC-TCTTCTT
19065644 CTTTCTCTTCTT
1 C-TTCTCTTCTT
19065656 -TTCT-TTCTT
1 CTTCTCTTCTT
*
19065665 TTTCTCTTGCTT
1 CTTCTCTT-CTT
19065677 CTTCT
1 CTTCT
19065682 TCTACTGTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
9 5 0.15
10 8 0.24
11 2 0.06
12 15 0.45
13 3 0.09
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (11 bp):
CTTCTCTTCTT
Found at i:19076920 original size:17 final size:17
Alignment explanation
Indices: 19076898--19076935 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
19076888 AGTTTTCATA
*
19076898 CATTTTTATTGT-GTCTG
1 CATTTTAATTGTCGT-TG
19076915 CATTTTAATTGTCGTTG
1 CATTTTAATTGTCGTTG
19076932 CATT
1 CATT
19076936 CATTTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (17 bp):
CATTTTAATTGTCGTTG
Found at i:19089939 original size:20 final size:20
Alignment explanation
Indices: 19089899--19089939 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19089889 TAACATAACT
*
19089899 TAAACACTCTCAAATGATTC
1 TAAACACTCTCAAATCATTC
* *
19089919 TAAACTCTCTCAAATCCTTC
1 TAAACACTCTCAAATCATTC
19089939 T
1 T
19089940 CCCCCTCCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.34
Consensus pattern (20 bp):
TAAACACTCTCAAATCATTC
Found at i:19092342 original size:28 final size:29
Alignment explanation
Indices: 19092293--19092347 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 29
19092283 GGTTTAGCCA
19092293 AAAAGAGAGAAATGGTGAGAAATCAAAAAG
1 AAAAGAGAGAAATGGTGAGAAAT-AAAAAG
19092323 AAAAG-GA-AAATGAGT-AGAAATAAAA
1 AAAAGAGAGAAATG-GTGAGAAATAAAA
19092348 GAAGAGAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 4 0.17
28 11 0.46
29 4 0.17
30 5 0.21
ACGTcount: A:0.64, C:0.02, G:0.24, T:0.11
Consensus pattern (29 bp):
AAAAGAGAGAAATGGTGAGAAATAAAAAG
Found at i:19092864 original size:20 final size:20
Alignment explanation
Indices: 19092841--19092879 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19092831 TTAAATAGGT
*
19092841 TTAAGTAAAGTTAAAAATGG
1 TTAAGTAAACTTAAAAATGG
* *
19092861 TTAATTAAACTTAATAATG
1 TTAAGTAAACTTAAAAATG
19092880 AAAGTCATAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.36
Consensus pattern (20 bp):
TTAAGTAAACTTAAAAATGG
Found at i:19099667 original size:20 final size:20
Alignment explanation
Indices: 19099644--19099682 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19099634 TTAAATAGGT
*
19099644 TTAATAAAAGTTAAAAATGG
1 TTAATAAAACTTAAAAATGG
* *
19099664 TTAATTAAACTTAATAATG
1 TTAATAAAACTTAAAAATG
19099683 AAAGTCATGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (20 bp):
TTAATAAAACTTAAAAATGG
Found at i:19115784 original size:75 final size:76
Alignment explanation
Indices: 19115672--19115854 Score: 269
Period size: 75 Copynumber: 2.4 Consensus size: 76
19115662 ATTTTTTTAG
* * * *
19115672 ATTTTCTCATACTTTCTCTCTTTCCAAACACCCATGACTTTTTATTTTCTCATACTTTCCTTTCA
1 ATTTTCTCAGACTTTCTCACTTTCCAAACACCCATGACTTTTTATTTTCTCAGACTTTCCCTTCA
19115737 TTCATTCATAA
66 TTCATTCATAA
19115748 ATTTTCTCAGACTTTCTCAC-TTCCAAACACCCATGACTTTTTATTTTCTCAGACTTTCCCTTCA
1 ATTTTCTCAGACTTTCTCACTTTCCAAACACCCATGACTTTTTATTTTCTCAGACTTTCCCTTCA
* *
19115812 TTCCTTCATGA
66 TTCATTCATAA
* * **
19115823 ATTTTCTCAGGCTTTCTCCCTTTTTAAACACC
1 ATTTTCTCAGACTTTCTCACTTTCCAAACACC
19115855 TTTTTTCTTG
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
75 69 0.72
76 27 0.28
ACGTcount: A:0.21, C:0.30, G:0.04, T:0.45
Consensus pattern (76 bp):
ATTTTCTCAGACTTTCTCACTTTCCAAACACCCATGACTTTTTATTTTCTCAGACTTTCCCTTCA
TTCATTCATAA
Found at i:19116461 original size:4 final size:4
Alignment explanation
Indices: 19116452--19116489 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
19116442 AGACAACAAT
19116452 AATA AATA AATA AAT- AATA TAA-A AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA -AATA AATA AATA AATA AAT
19116490 GCAAATTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 5 0.16
4 24 0.77
5 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:19116502 original size:31 final size:27
Alignment explanation
Indices: 19116452--19116535 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 27
19116442 AGACAACAAT
19116452 AATAAATAAATAAATAATATAAAAATA
1 AATAAATAAATAAATAATATAAAAATA
*
19116479 AATAAATAAATGCAAATTGAATATCAAAATA
1 AATAAATAAAT--AAA-T-AATATAAAAATA
*
19116510 AATAAAATAATAAAAATAA-ATAAAAA
1 AAT-AAATAA-ATAAATAATATAAAAA
19116536 GGATTAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
27 11 0.23
28 6 0.12
29 5 0.10
30 2 0.04
31 17 0.35
32 6 0.12
33 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (27 bp):
AATAAATAAATAAATAATATAAAAATA
Found at i:19118476 original size:50 final size:50
Alignment explanation
Indices: 19118424--19118579 Score: 138
Period size: 50 Copynumber: 3.1 Consensus size: 50
19118414 GCTTTCCTAG
* *
19118424 CTTCAATCTGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTAGTAG
1 CTTCAATCTGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAA
** * * * * * *
19118474 CTTCGCT-TCATTCCACTGTAACTTCAGGGAG-ATTGAGATTCGCT-TCTGTAA
1 CTTCAATCTGA-CCCACTGCAACTTCAGGG-GTATAG-GATTTGATGT-TGTAA
* * *
19118525 CTTTAATCTGACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTTGTAA
1 CTTCAATCTGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAA
19118575 CTTCA
1 CTTCA
19118580 CTCCAATCCA
Statistics
Matches: 78, Mismatches: 21, Indels: 14
0.69 0.19 0.12
Matches are distributed among these distances:
49 2 0.03
50 41 0.53
51 33 0.42
52 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (50 bp):
CTTCAATCTGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTTGTAA
Found at i:19118606 original size:101 final size:101
Alignment explanation
Indices: 19118428--19119196 Score: 642
Period size: 101 Copynumber: 7.6 Consensus size: 101
19118418 TCCTAGCTTC
* * * * * * *
19118428 AATCTGACCCACTGCAACTTCAGGGGTATAGGATTTGATGTAGTAGCTTCGCTTCATTCCACTGT
1 AATCCGACCCACTGCAACTTCAGGGATATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTGC
* *
19118493 AACTTCAGGGAGATTGAGATTCGCTTCTGTAACTTT
66 AACTTCAAGGAGATTGAGATTCGCTTCCGTAACTTT
* * * * * *
19118529 AATCTGACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCACTCCAATCCATTGC
1 AATCCGACCCACTGCAACTTCAGGGATATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTGC
* * *
19118594 AACTACAAGGAGATTGAGATTAG-TTACCGT-AGTTCT
66 AACTTCAAGGAGATTGAGATTCGCTT-CCGTAACTT-T
* * * * * * * *
19118630 AATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTCATTCCAATCCATTGC
1 AATCCGACCCACTGCAACTTCAGGGATATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTGC
* *
19118695 AACTTCAAGGAGATTGAGATTC-TTTACCGT-AGTTCT
66 AACTTCAAGGAGATTGAGATTCGCTT-CCGTAACTT-T
* * * * * *
19118731 AATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTCACTCCATTCTACTGC
1 AATCCGACCCACTGCAACTTCAGGGATATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTGC
* * **
19118796 AATTTCAAGGAGATTGACATTCGCTTCTATAACTTT
66 AACTTCAAGGAGATTGAGATTCGCTTCCGTAACTTT
* * * * * *
19118832 AATCTGACCCACTACAGCTTCAAGGG-TATAAGATTTGATGTTGTAACTTCACTCCATTCCACTG
1 AATCCGACCCACTGCAACTTC-AGGGATATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTG
* * * * *
19118896 TAACTTCAGGGAGATTAAGATTC-ATTACCGT-AGTTCT
65 CAACTTCAAGGAGATTGAGATTCGCTT-CCGTAACTT-T
* * * * * * * * *
19118933 TATCCGATCCACTGTAATTTTAGGGATATAGGATTTTGTGTAGTAGCTTCACTCCATTCTACTGT
1 AATCCGACCCACTGCAACTTCAGGGATATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTGC
* * * *
19118998 AACTTCAAGAAGATTGAGA-TCTGC-TACATATCTTT
66 AACTTCAAGGAGATTGAGATTC-GCTTCCGTAACTTT
* * * * * *
19119033 AACCCGACCCATTGCAACTTTAAGGG-TATAGGATTTGGTTTTGTAACTTCACTCCATTCCATTG
1 AATCCGACCCACTGCAAC-TTCAGGGATATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTG
* * ** **
19119097 CAACTTCAAGAAGATTGAGATTC-ATTATAGTAGTTTT
65 CAACTTCAAGGAGATTGAGATTCGCTT-CCGTAACTTT
* * * * * * *
19119134 AATTCGATCCATTGTAACTTTAGGGATATAGGATTTGGTGTAGTAGCTTCACTCAATTCCACT
1 AATCCGACCCACTGCAACTTCAGGGATATAGGATTTGGTGTAGTAACTTCACTCCATTCCACT
19119197 ATATGTTTTG
Statistics
Matches: 544, Mismatches: 107, Indels: 34
0.79 0.16 0.05
Matches are distributed among these distances:
100 89 0.16
101 446 0.82
102 9 0.02
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (101 bp):
AATCCGACCCACTGCAACTTCAGGGATATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTGC
AACTTCAAGGAGATTGAGATTCGCTTCCGTAACTTT
Found at i:19118638 original size:51 final size:51
Alignment explanation
Indices: 19118581--19118752 Score: 163
Period size: 51 Copynumber: 3.4 Consensus size: 51
19118571 GTAACTTCAC
*
19118581 TCCAATCCATTGCAACTACAAGGAGATTGAGATTAGTTACCGTAGTTCTAA
1 TCCAATCCATTGCAACTTCAAGGAGATTGAGATTAGTTACCGTAGTTCTAA
* * * * * * * * *
19118632 TCCAATCCACTACAACTTCAGGGATATAGA-ATTTGGTGTA--ATAACTTC-AT
1 TCCAATCCATTGCAACTTCAAGGAGATTGAGA-TTAGT-TACCGT-AGTTCTAA
**
19118682 TCCAATCCATTGCAACTTCAAGGAGATTGAGATTCTTTACCGTAGTTCTAA
1 TCCAATCCATTGCAACTTCAAGGAGATTGAGATTAGTTACCGTAGTTCTAA
* *
19118733 TCCAATCCACTACAACTTCA
1 TCCAATCCATTGCAACTTCA
19118753 GGGATATAGA
Statistics
Matches: 92, Mismatches: 22, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
49 2 0.02
50 35 0.38
51 53 0.58
52 2 0.02
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.31
Consensus pattern (51 bp):
TCCAATCCATTGCAACTTCAAGGAGATTGAGATTAGTTACCGTAGTTCTAA
Found at i:19118650 original size:202 final size:201
Alignment explanation
Indices: 19118434--19119192 Score: 729
Period size: 202 Copynumber: 3.8 Consensus size: 201
19118424 CTTCAATCTG
* *
19118434 ACCCACTGCAACTTCAGGGGTATAGGATTTGATGTAGTAGCTTCGCTTCATTCCACTGTAACTTC
1 ACCCACTACAACTTCAGGGGTATAGGATTTGATGTAGTAACTTC-CTTCATTCCACTGTAACTTC
* * * * * *
19118499 AGGGAGATTGAGATTCGCTT-CTGTAACTT-TAATCTGACCCACTGCAACTTTAGGGGTATAGGA
65 AGGGAGATTGAGATTC-ATTACCGT-AGTTCTAATCCGATCCACTGCAACTTTAGGGATATAGGA
* * * * * *
19118562 TTTGGTGTTGTAACTTCACTCCAATCCATTGCAACTACAAGGAGATTGAGATTAG-TTACCGT-A
128 TTTGGTGTAGTAACTTCACTCCATTCTACTGCAACTTCAAGGAGATTGAGATTAGCTT-CCATAA
*
19118625 GTTCTAATCCA
192 CTT-TAATCCA
* * * * * * * * *
19118636 ATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTCATTCCAATCCATTGCAACTTC
1 ACCCACTACAACTTCAGGGGTATAGGATTTGATGTAGTAACTTCCTT-CATTCCACTGTAACTTC
* * * * * *
19118701 AAGGAGATTGAGATTCTTTACCGTAGTTCTAATCCAATCCACTACAACTTCAGGGATATAGAATT
65 AGGGAGATTGAGATTCATTACCGTAGTTCTAATCCGATCCACTGCAACTTTAGGGATATAGGATT
* * * * *
19118766 TGGTGTAATAACTTCACTCCATTCTACTGCAATTTCAAGGAGATTGACATTCGCTTCTATAACTT
130 TGGTGTAGTAACTTCACTCCATTCTACTGCAACTTCAAGGAGATTGAGATTAGCTTCCATAACTT
**
19118831 TAATCTG
195 TAATCCA
* * * * *
19118838 ACCCACTACAGCTTCAAGGGTATAAGATTTGATGTTGTAACTTCACTCCATTCCACTGTAACTTC
1 ACCCACTACAACTTCAGGGGTATAGGATTTGATGTAGTAACTTC-CTTCATTCCACTGTAACTTC
* * * *
19118903 AGGGAGATTAAGATTCATTACCGTAGTTCTTATCCGATCCACTGTAATTTTAGGGATATAGGATT
65 AGGGAGATTGAGATTCATTACCGTAGTTCTAATCCGATCCACTGCAACTTTAGGGATATAGGATT
* * * * * *
19118968 TTGTGTAGTAGCTTCACTCCATTCTACTGTAACTTCAAGAAGATTGAGATCT-GC-TACATATCT
130 TGGTGTAGTAACTTCACTCCATTCTACTGCAACTTCAAGGAGATTGAGAT-TAGCTTCCATAACT
* *
19119031 TTAACCCG
194 TTAATCCA
* * * * * * * * * *
19119039 ACCCATTGCAACTTTAAGGGTATAGGATTTGGTTTTGTAACTTCACTCCATTCCATTGCAACTTC
1 ACCCACTACAACTTCAGGGGTATAGGATTTGATGTAGTAACTTC-CTTCATTCCACTGTAACTTC
* * ** * * * *
19119104 AAGAAGATTGAGATTCATTATAGTAGTTTTAATTCGATCCATTGTAACTTTAGGGATATAGGATT
65 AGGGAGATTGAGATTCATTACCGTAGTTCTAATCCGATCCACTGCAACTTTAGGGATATAGGATT
* *
19119169 TGGTGTAGTAGCTTCACTCAATTC
130 TGGTGTAGTAACTTCACTCCATTC
19119193 CACTATATGT
Statistics
Matches: 457, Mismatches: 93, Indels: 15
0.81 0.16 0.03
Matches are distributed among these distances:
201 152 0.33
202 298 0.65
203 7 0.02
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (201 bp):
ACCCACTACAACTTCAGGGGTATAGGATTTGATGTAGTAACTTCCTTCATTCCACTGTAACTTCA
GGGAGATTGAGATTCATTACCGTAGTTCTAATCCGATCCACTGCAACTTTAGGGATATAGGATTT
GGTGTAGTAACTTCACTCCATTCTACTGCAACTTCAAGGAGATTGAGATTAGCTTCCATAACTTT
AATCCA
Found at i:19118698 original size:50 final size:50
Alignment explanation
Indices: 19118630--19118786 Score: 160
Period size: 50 Copynumber: 3.1 Consensus size: 50
19118620 CCGTAGTTCT
19118630 AATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTC
1 AATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTC
* * * * * * * *
19118680 ATTCCAATCCATTGCAACTTCAAGGAGATTGAGATTCT--T-TACCGT-AGTTC
1 AATCCAATCCACTACAACTTCAGGGATATAGA-ATT-TGGTGTA--ATAACTTC
19118730 TAATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTC
1 -AATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTC
*
19118781 ACTCCA
1 AATCCA
19118787 TTCTACTGCA
Statistics
Matches: 81, Mismatches: 17, Indels: 18
0.70 0.15 0.16
Matches are distributed among these distances:
49 3 0.04
50 40 0.49
51 35 0.43
52 3 0.04
ACGTcount: A:0.33, C:0.22, G:0.14, T:0.31
Consensus pattern (50 bp):
AATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTC
Found at i:19118836 original size:303 final size:301
Alignment explanation
Indices: 19118434--19119196 Score: 827
Period size: 303 Copynumber: 2.5 Consensus size: 301
19118424 CTTCAATCTG
* * * * *
19118434 ACCCACTGCAACTTCAGGGGTATAGGATTTGATGTAGTAGCTTCGCTTCATTCCACTGTAACTTC
1 ACCCACTGCAACTTCA-GGGTATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTGCAACTTC
* *
19118499 AGGGAGATTGAGATTCGCTTCTGTAACTTTAATCTGACCCACTGCAACTTTAGGGGTATAGGATT
65 AAGGAGATTGAGATTCGCTTCTATAACTTTAATCTGACCCACTGCAACTTTAGGGGTATAGGATT
* *
19118564 TGGTGTTGTAACTTCACTCCAATCCATTGCAACTACAAGGAGATTGAGATT-AGTTACCGTAGTT
130 TGGTGTTGTAACTTCACTCCAATCCACTGCAACTACAAGGAGATTAAGATTCA-TTACCGTAGTT
* *
19118628 CTAATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTCATTCCAATCCATT
194 CTAATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTCACTCCAATCCACT
* * * *
19118693 GCAACTTCAAGGAGATTGAGATTCT-TTACCGTAGT-TCTAATCCA
259 GCAACTTCAAGAAGATTGAGA-TCTGCTA-CATA-TCTCTAACCCA
* * * * * *
19118737 ATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTCACTCCATTCTACTGCAATTTC
1 ACCCACTGCAACTTCAGGG-TATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTGCAACTTC
* * * * * *
19118802 AAGGAGATTGACATTCGCTTCTATAACTTTAATCTGACCCACTACAGCTTCAAGGGTATAAGATT
65 AAGGAGATTGAGATTCGCTTCTATAACTTTAATCTGACCCACTGCAACTTTAGGGGTATAGGATT
* * * * *
19118867 TGATGTTGTAACTTCACTCCATTCCACTGTAACTTCAGGGAGATTAAGATTCATTACCGTAGTTC
130 TGGTGTTGTAACTTCACTCCAATCCACTGCAACTACAAGGAGATTAAGATTCATTACCGTAGTTC
* * ** * * * * * * * *
19118932 TTATCCGATCCACTGTAATTTTAGGGATATAGGATTTTGTGTAGTAGCTTCACTCCATTCTACTG
195 TAATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTCACTCCAATCCACTG
* * *
19118997 TAACTTCAAGAAGATTGAGATCTGCTACATATCTTTAACCCG
260 CAACTTCAAGAAGATTGAGATCTGCTACATATCTCTAACCCA
* * * * *
19119039 ACCCATTGCAACTTTAAGGGTATAGGATTTGGTTTTGTAACTTCACTCCATTCCATTGCAACTTC
1 ACCCACTGCAAC-TTCAGGGTATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTGCAACTTC
* * * ** * * * *
19119104 AAGAAGATTGAGATTC-ATTATAGTAGTTTTAAT-TCGATCCATTGTAACTTTAGGGATATAGGA
65 AAGGAGATTGAGATTCGCTTCTA-TAACTTTAATCT-GACCCACTGCAACTTTAGGGGTATAGGA
* *
19119167 TTTGGTGTAGTAGCTTCACT-CAATTCCACT
128 TTTGGTGTTGTAACTTCACTCCAA-TCCACT
19119197 ATATGTTTTG
Statistics
Matches: 375, Mismatches: 77, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
301 8 0.02
302 126 0.34
303 240 0.64
304 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (301 bp):
ACCCACTGCAACTTCAGGGTATAGGATTTGGTGTAGTAACTTCACTCCATTCCACTGCAACTTCA
AGGAGATTGAGATTCGCTTCTATAACTTTAATCTGACCCACTGCAACTTTAGGGGTATAGGATTT
GGTGTTGTAACTTCACTCCAATCCACTGCAACTACAAGGAGATTAAGATTCATTACCGTAGTTCT
AATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTCACTCCAATCCACTGC
AACTTCAAGAAGATTGAGATCTGCTACATATCTCTAACCCA
Found at i:19119215 original size:201 final size:200
Alignment explanation
Indices: 19118253--19119224 Score: 723
Period size: 202 Copynumber: 4.8 Consensus size: 200
19118243 CTTTAAAGAG
* * * *
19118253 ATAAAATTTGTTGTTGTAGCTTCACTCCATTCCACTT-CAACTTCAAGGAGATTGAGATTCGTTA
1 ATAAGATTTGATGTTGTAACTTCACTCCATTCCA-TTGCAACTTCAAGGAGATTGAGATTCATTA
* * * * * * * * * *
19118317 TCATGGTTTTAATCTGATCCGCTATAACTTTAGGGATATAAGATTTGGTTTTGTAGCTGCATCTT
65 CCGTAGTTTTAATCCGATCCACTGTAACTTTAGGGATATAGGATTTGGTGTAGTAGCTTCA-C-T
* * * * * * * * *
19118382 GCTTTGCTAC-A-ACTTT--AGAGAGA-TAAGCATTTGCT-TTCCTAGCTTCAATCTGACCCACT
128 CCATT-CTACTATA-TTTCAAG-GAGATTGAG-A-TTGCTACT-ATAACTTTAACCCGACCCACT
* *
19118441 GCAACTTCAGGGGT
187 ACAACTTCAAGGGT
* * * * * * * * *
19118455 ATAGGATTTGATGTAGTAGCTTCGCTTCATTCCACTGTAACTTCAGGGAGATTGAGATTCGCTT-
1 ATAAGATTTGATGTTGTAACTTCACTCCATTCCATTGCAACTTCAAGGAGATTGAGATTC-ATTA
* ** * * * * * *
19118519 CTGTAACTTTAATCTGACCCACTGCAACTTTAGGGGTATAGGATTTGGTGTTGTAACTTCACTCC
65 CCGTAGTTTTAATCCGATCCACTGTAACTTTAGGGATATAGGATTTGGTGTAGTAGCTTCACTCC
* * * * * * ** * * * *
19118584 AATCCATTGCA-ACTACAAGGAGATTGAGATTAGTTACCGT-AGTTCTAATCCAATCCACTACAA
130 ATTCTACT--ATATTTCAAGGAGATTGAGATT-GCTACTATAACTT-TAACCCGACCCACTACAA
19118647 CTTC-AGGG-
191 CTTCAAGGGT
* ** * * *
19118655 ATATAGAATTTGGTGTAATAACTTCATTCCAATCCATTGCAACTTCAAGGAGATTGAGATTCTTT
1 ATA-AG-ATTTGATGTTGTAACTTCACTCCATTCCATTGCAACTTCAAGGAGATTGAGATTCATT
* * ** * * * *
19118720 ACCGTAGTTCTAATCCAATCCACTACAACTTCAGGGATATAGAATTTGGTGTAATAACTTCACTC
64 ACCGTAGTTTTAATCCGATCCACTGTAACTTTAGGGATATAGGATTTGGTGTAGTAGCTTCACTC
* * * * *
19118785 CATTCTACTGCA-ATTTCAAGGAGATTGACATTCGCTTCTATAACTTTAATCTGACCCACTACAG
129 CATTCTACT--ATATTTCAAGGAGATTGAGATT-GCTACTATAACTTTAACCCGACCCACTACAA
19118849 CTTCAAGGGT
191 CTTCAAGGGT
* * * *
19118859 ATAAGATTTGATGTTGTAACTTCACTCCATTCCACTGTAACTTCAGGGAGATTAAGATTCATTAC
1 ATAAGATTTGATGTTGTAACTTCACTCCATTCCATTGCAACTTCAAGGAGATTGAGATTCATTAC
* *
19118924 CGTAGTTCTT-ATCCGATCCACTGTAATTTTAGGGATATAGGATTTTGTGTAGTAGCTTCACTCC
66 CGTAGTT-TTAATCCGATCCACTGTAACTTTAGGGATATAGGATTTGGTGTAGTAGCTTCACTCC
* * * * * *
19118988 ATTCTACTGTAACTTCAAGAAGATTGAGATCTGCTAC-ATATCTTTAACCCGACCCATTGCAACT
130 ATTCTACTAT-ATTTCAAGGAGATTGAGAT-TGCTACTATAACTTTAACCCGACCCACTACAACT
*
19119052 TTAAGGGT
193 TCAAGGGT
* * * * *
19119060 ATAGGATTTGGTTTTGTAACTTCACTCCATTCCATTGCAACTTCAAGAAGATTGAGATTCATTAT
1 ATAAGATTTGATGTTGTAACTTCACTCCATTCCATTGCAACTTCAAGGAGATTGAGATTCATTAC
* * * *
19119125 AGTAGTTTTAATTCGATCCATTGTAACTTTAGGGATATAGGATTTGGTGTAGTAGCTTCACTCAA
66 CGTAGTTTTAATCCGATCCACTGTAACTTTAGGGATATAGGATTTGGTGTAGTAGCTTCACTCCA
* ***
19119190 TTCCACTATATGTTTTGGGAGATTGAGATATGCTA
131 TTCTACTATAT-TTCAAGGAGATTGAGAT-TGCTA
19119225 TTGTTGTTTT
Statistics
Matches: 606, Mismatches: 141, Indels: 47
0.76 0.18 0.06
Matches are distributed among these distances:
199 2 0.00
200 9 0.01
201 178 0.29
202 396 0.65
203 18 0.03
204 3 0.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (200 bp):
ATAAGATTTGATGTTGTAACTTCACTCCATTCCATTGCAACTTCAAGGAGATTGAGATTCATTAC
CGTAGTTTTAATCCGATCCACTGTAACTTTAGGGATATAGGATTTGGTGTAGTAGCTTCACTCCA
TTCTACTATATTTCAAGGAGATTGAGATTGCTACTATAACTTTAACCCGACCCACTACAACTTCA
AGGGT
Found at i:19124714 original size:12 final size:12
Alignment explanation
Indices: 19124681--19124721 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
19124671 TATCTCAAAC
19124681 TTTTA-CTTTTA
1 TTTTATCTTTTA
*
19124692 TTTT-CCATTTTA
1 TTTTATC-TTTTA
19124704 TTTTATCTTTTA
1 TTTTATCTTTTA
19124716 TTTTAT
1 TTTTAT
19124722 GGTCTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 5 0.19
12 20 0.77
13 1 0.04
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATCTTTTA
Found at i:19136124 original size:13 final size:13
Alignment explanation
Indices: 19136106--19136130 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19136096 ATGGGGCCAA
19136106 TTTAGATTAATAC
1 TTTAGATTAATAC
19136119 TTTAGATTAATA
1 TTTAGATTAATA
19136131 TCCTTCACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTAGATTAATAC
Found at i:19139220 original size:12 final size:12
Alignment explanation
Indices: 19139187--19139227 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
19139177 CATCTCAAAC
19139187 TTTTA-CTTTTA
1 TTTTATCTTTTA
*
19139198 TTTT-CCATTTTA
1 TTTTATC-TTTTA
19139210 TTTTATCTTTTA
1 TTTTATCTTTTA
19139222 TTTTAT
1 TTTTAT
19139228 GTTCTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
11 5 0.19
12 20 0.77
13 1 0.04
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTATCTTTTA
Found at i:19142539 original size:15 final size:15
Alignment explanation
Indices: 19142496--19142533 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
19142486 TGTGAAGGAT
*
19142496 ATTAATCTAAAGT--
1 ATTAATCTAAACTAA
19142509 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
19142524 ATTAATCTAA
1 ATTAATCTAA
19142534 GTTAAAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:19165270 original size:12 final size:12
Alignment explanation
Indices: 19165253--19165283 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
19165243 TATAGAAACA
19165253 AAAATAAAAAAT
1 AAAATAAAAAAT
*
19165265 AAAATAACAAAT
1 AAAATAAAAAAT
19165277 AAAATAA
1 AAAATAA
19165284 TGATATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:19165436 original size:4 final size:4
Alignment explanation
Indices: 19165427--19165468 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
19165417 AGACAACAAT
*
19165427 AATA AATA AATA AATA AA-C AATA TAA-A AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA -AATA AATA AATA AATA AAT
19165469 GCAAATCGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 4 0.12
4 27 0.82
5 2 0.06
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:19165461 original size:27 final size:30
Alignment explanation
Indices: 19165427--19165505 Score: 101
Period size: 31 Copynumber: 2.7 Consensus size: 30
19165417 AGACAACAAT
19165427 AATAAATAAATAAAT-AAA-C-AATATAAA
1 AATAAATAAATAAATCAAATCGAATATAAA
*
19165454 AATAAATAAATAAATGCAAATCGAATATCAA
1 AATAAATAAATAAAT-CAAATCGAATATAAA
*
19165485 AATAAATAAAAAGAATCAAAT
1 AATAAATAAATA-AATCAAAT
19165506 TAAAAATAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 15 0.33
29 3 0.07
30 1 0.02
31 23 0.51
32 3 0.07
ACGTcount: A:0.68, C:0.06, G:0.04, T:0.22
Consensus pattern (30 bp):
AATAAATAAATAAATCAAATCGAATATAAA
Found at i:19174086 original size:17 final size:17
Alignment explanation
Indices: 19174051--19174088 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
19174041 GTTACTATTA
*
19174051 TTATTTTTTAATTTTAT
1 TTATTTTTTAATTTAAT
19174068 TTATTTTTTACA-TTAAT
1 TTATTTTTTA-ATTTAAT
19174085 TTAT
1 TTAT
19174089 GTAATTAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTATTTTTTAATTTAAT
Found at i:19176029 original size:13 final size:13
Alignment explanation
Indices: 19176011--19176074 Score: 76
Period size: 13 Copynumber: 4.9 Consensus size: 13
19176001 TAATCTAACA
*
19176011 TTTTCAAAAGTAC
1 TTTTCAAAAGCAC
*
19176024 TTTTCAAAATCAC
1 TTTTCAAAAGCAC
19176037 TTTTTC-AAAGCAC
1 -TTTTCAAAAGCAC
*
19176050 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
*
19176063 TTCTCAAAAGCA
1 TTTTCAAAAGCA
19176075 ATGCTAAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 4 0.09
13 34 0.79
14 5 0.12
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:19177202 original size:42 final size:41
Alignment explanation
Indices: 19177090--19177483 Score: 235
Period size: 41 Copynumber: 9.4 Consensus size: 41
19177080 AAAGGTAAAG
* * * * ***
19177090 CATTAGCGGCGCTTTTCCTAATGCGCCGCAAAAGGT-AAAT
1 CATTAGCGGCGCTTTACCCAAAGCGCCGCTAAAGGTCGGGT
*
19177130 CATTAGCGGCGC-TTACACAAAGCGCCGCTAAAGGTCGGGT
1 CATTAGCGGCGCTTTACCCAAAGCGCCGCTAAAGGTCGGGT
* **
19177170 CTTTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGACT
1 CATTAGCGGCGCTTTACCCA-AAGCGCCGCTAAAGGTCGGGT
* * * * *
19177212 CATTAGCGGCGC-TTAGACAAAAGCGCCACTAAAAGTCAGGT
1 CATTAGCGGCGCTTTA-CCCAAAGCGCCGCTAAAGGTCGGGT
* * * *
19177253 CATTAGCGGCTGGGTAGCGGCGCTTATCCAGAAGCGCCGCTAATGGTCTGGT
1 CATTA---GC---G--GC-GC-TTTACCCA-AAGCGCCGCTAAAGGTCGGGT
* * *
19177305 CATTAGCGGCGCTTCACCAAAAGCGCCGCTAAAAGT-GGAGT
1 CATTAGCGGCGCTTTACCCAAAGCGCCGCTAAAGGTCGG-GT
* * * **
19177346 CACTAGCGGTGC-TTACCCACAAACGCCGCTAAAGGTCGTAT
1 CATTAGCGGCGCTTTACCCA-AAGCGCCGCTAAAGGTCGGGT
* *** * *
19177387 CATTAGCGACGCTTATATAGAAAGCGCCGGTAAAGGTCAGGT
1 CATTAGCGGCGCTT-TACCCAAAGCGCCGCTAAAGGTCGGGT
* * ** *
19177429 TATTAGCGGCGCTTTTCTAATAAGCGCCGCTAAAGGT-GTG-
1 CATTAGCGGCGCTTTACCCA-AAGCGCCGCTAAAGGTCGGGT
19177469 CATTAGCGGCGCTTT
1 CATTAGCGGCGCTTT
19177484 TATATAAGCG
Statistics
Matches: 270, Mismatches: 62, Indels: 44
0.72 0.16 0.12
Matches are distributed among these distances:
39 18 0.07
40 44 0.16
41 83 0.31
42 81 0.30
43 5 0.02
44 4 0.01
46 1 0.00
47 1 0.00
49 4 0.01
50 2 0.01
51 2 0.01
52 25 0.09
ACGTcount: A:0.25, C:0.26, G:0.27, T:0.22
Consensus pattern (41 bp):
CATTAGCGGCGCTTTACCCAAAGCGCCGCTAAAGGTCGGGT
Found at i:19177232 original size:82 final size:82
Alignment explanation
Indices: 19177092--19177500 Score: 271
Period size: 82 Copynumber: 4.9 Consensus size: 82
19177082 AGGTAAAGCA
* * * * ** *
19177092 TTAGCGGCGCTTTTCCTA-ATGCGCCGCAAAAGGTAAATCATTAGCGGCGCTTACACAAAGCGCC
1 TTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGATCATTAGCGGCGCTTATACAAAGCGCC
* *
19177156 GCTAAAGGTCGGGTCT-
66 GCTAAAAGTCAGGTCTG
*
19177172 TTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGACTCATTAGCGGCGCTTAGACAAAAGCG
1 TTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGA-TCATTAGCGGCGCTTATAC-AAAGCG
*
19177237 CCACTAAAAGTCAGGTCATTAGCGG
64 CCGCTAAAAGTCAGGTC--T----G
* * * * *
19177262 CTGGGTAGCGGCGC-TTATCCAGAAGCGCCGCTAATGGTCTGGTCATTAGCGGCGCTTCA-CCAA
1 -T---TAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTC-GATCATTAGCGGCGCTT-ATAC-A
* *
19177325 AAGCGCCGCTAAAAGT-GGAGTC-A
59 AAGCGCCGCTAAAAGTCAG-GTCTG
* * * * *
19177348 CTAGCGGTGC-TTACCCACAAACGCCGCTAAAGGTCGTATCATTAGCGACGCTTATATAGAAAGC
1 TTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCG-ATCATTAGCGGCGC-T-TATACAAAGC
* * *
19177412 GCCGGTAAAGGTCAGGT-TA
63 GCCGCTAAAAGTCAGGTCTG
* ** * * *
19177431 TTAGCGGCGCTTTTCTAATAAGCGCCGCTAAAGGT-G-TGCATTAGCGGCGCTTTTATATAAGCG
1 TTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGAT-CATTAGCGGCGCTTATACA-AAGCG
19177494 CCGCTAA
64 CCGCTAA
19177501 TATATTTAAA
Statistics
Matches: 261, Mismatches: 42, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
80 20 0.08
81 29 0.11
82 70 0.27
83 49 0.19
84 21 0.08
85 1 0.00
91 1 0.00
92 1 0.00
93 58 0.22
94 11 0.04
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.22
Consensus pattern (82 bp):
TTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGATCATTAGCGGCGCTTATACAAAGCGCC
GCTAAAAGTCAGGTCTG
Found at i:19177306 original size:52 final size:52
Alignment explanation
Indices: 19177215--19177314 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 52
19177205 GTCGACTCAT
19177215 TAGCGGCGCTTAGACAAAAGCGCCACTAAAAGTCAGGTCATTAGCGGCTGGG
1 TAGCGGCGCTTAGACAAAAGCGCCACTAAAAGTCAGGTCATTAGCGGCTGGG
** * * ** *
19177267 TAGCGGCGCTTATCCAGAAGCGCCGCTAATGGTCTGGTCATTAGCGGC
1 TAGCGGCGCTTAGACAAAAGCGCCACTAAAAGTCAGGTCATTAGCGGC
19177315 GCTTCACCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.24, C:0.25, G:0.31, T:0.20
Consensus pattern (52 bp):
TAGCGGCGCTTAGACAAAAGCGCCACTAAAAGTCAGGTCATTAGCGGCTGGG
Found at i:19177353 original size:93 final size:94
Alignment explanation
Indices: 19177173--19177354 Score: 237
Period size: 93 Copynumber: 1.9 Consensus size: 94
19177163 GTCGGGTCTT
19177173 TAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGACTCATTAGCGGCGCTTAGACAAAAGCGC
1 TAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGACTCATTAGCGGCGCTTAGACAAAAGCGC
*
19177238 CACTAAAAGTCAGGTCATTAGCGGCTGGG
66 CACTAAAAGTCAGGTCACTAGCGGCTGGG
* * * * *
19177267 TAGCGGCGC-TTATCCAGAAGCGCCGCTAATGGTCTG-GTCATTAGCGGCGCTTCA-CCAAAAGC
1 TAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTC-GACTCATTAGCGGCGCTT-AGACAAAAGC
* *
19177329 GCCGCTAAAAGT-GGAGTCACTAGCGG
64 GCCACTAAAAGTCAG-GTCACTAGCGG
19177355 TGCTTACCCA
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
92 1 0.01
93 65 0.84
94 11 0.14
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (94 bp):
TAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGACTCATTAGCGGCGCTTAGACAAAAGCGC
CACTAAAAGTCAGGTCACTAGCGGCTGGG
Found at i:19177378 original size:134 final size:134
Alignment explanation
Indices: 19177133--19177378 Score: 327
Period size: 134 Copynumber: 1.8 Consensus size: 134
19177123 GGTAAATCAT
* * *
19177133 TAGCGGCGCTTACACAAAGCGCCGCTAAAGGTCGGGTCTTTAGCGGCGCTTTACCCACAAGCGCC
1 TAGCGGCGCTTACACAAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTCACCCAAAAGCGCC
* * *
19177198 GCTAAAGGTCGACTCATTAGCGGCGCTTAGACAAAAGCGCCACTAAAAGTCAGGTCATTAGCGGC
66 GCTAAAAGTCGACTCACTAGCGGCGCTTACACAAAAGCGCCACTAAAAGTCAGGTCATTAGCGGC
19177263 TGGG
131 TGGG
* *
19177267 TAGCGGCGCTTATC-CAGAAGCGCCGCTAATGGTCTGGTCATTAGCGGCGCTTCA-CCAAAAGCG
1 TAGCGGCGCTTA-CACA-AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTCACCCAAAAGCG
* * * * *
19177330 CCGCTAAAAGTGGAGTCACTAGCGGTGCTTACCCACAAA-CGCCGCTAAA
64 CCGCTAAAAGTCGACTCACTAGCGGCGCTTACACA-AAAGCGCCACTAAA
19177379 GGTCGTATCA
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
134 59 0.61
135 37 0.39
ACGTcount: A:0.26, C:0.28, G:0.27, T:0.19
Consensus pattern (134 bp):
TAGCGGCGCTTACACAAAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTCACCCAAAAGCGCC
GCTAAAAGTCGACTCACTAGCGGCGCTTACACAAAAGCGCCACTAAAAGTCAGGTCATTAGCGGC
TGGG
Found at i:19177499 original size:39 final size:40
Alignment explanation
Indices: 19177369--19177500 Score: 142
Period size: 42 Copynumber: 3.2 Consensus size: 40
19177359 TACCCACAAA
* * * *
19177369 CGCCGCTAAAGGTCGTATCATTAGCGACGCTTATATAGAAAG
1 CGCCGCTAAAGGTCGT-GCATTAGCGGCGCTTTTATA-TAAG
* * *
19177411 CGCCGGTAAAGGTCAG-GTTATTAGCGGCGCTTTTCTAATAAG
1 CGCCGCTAAAGGTC-GTG-CATTAGCGGCGCTTTTAT-ATAAG
19177453 CGCCGCTAAAGGT-GTGCATTAGCGGCGCTTTTATATAAG
1 CGCCGCTAAAGGTCGTGCATTAGCGGCGCTTTTATATAAG
19177492 CGCCGCTAA
1 CGCCGCTAA
19177501 TATATTTAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 11
0.78 0.10 0.11
Matches are distributed among these distances:
39 14 0.18
40 17 0.22
41 1 0.01
42 42 0.55
43 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CGCCGCTAAAGGTCGTGCATTAGCGGCGCTTTTATATAAG
Found at i:19177641 original size:26 final size:25
Alignment explanation
Indices: 19177593--19177657 Score: 96
Period size: 26 Copynumber: 2.6 Consensus size: 25
19177583 TCTGCATGCA
*
19177593 TCACCCCCAAATCACAGAACCCTCT
1 TCACCCCCAAATCGCAGAACCCTCT
19177618 TCACCCCCAAATCGCA-ATACCCCTCT
1 TCACCCCCAAATCGCAGA-A-CCCTCT
19177644 TCACCCCCAAATCG
1 TCACCCCCAAATCG
19177658 TTGAGCCCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
24 1 0.03
25 16 0.43
26 20 0.54
ACGTcount: A:0.29, C:0.49, G:0.05, T:0.17
Consensus pattern (25 bp):
TCACCCCCAAATCGCAGAACCCTCT
Found at i:19177666 original size:25 final size:25
Alignment explanation
Indices: 19177593--19177669 Score: 77
Period size: 25 Copynumber: 3.0 Consensus size: 25
19177583 TCTGCATGCA
*
19177593 TCACCCCCAAATC-ACAGAACCCTCT
1 TCACCCCCAAATCGA-TGAACCCTCT
*
19177618 TCACCCCCAAATCGCAAT-ACCCCTCT
1 TCACCCCCAAATCG--ATGAACCCTCT
* *
19177644 TCACCCCCAAATCGTTGAGCCCTCT
1 TCACCCCCAAATCGATGAACCCTCT
19177669 T
1 T
19177670 TTATTTCCCT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
24 1 0.02
25 21 0.48
26 21 0.48
28 1 0.02
ACGTcount: A:0.26, C:0.47, G:0.06, T:0.21
Consensus pattern (25 bp):
TCACCCCCAAATCGATGAACCCTCT
Found at i:19177788 original size:44 final size:44
Alignment explanation
Indices: 19177684--19177802 Score: 125
Period size: 44 Copynumber: 2.7 Consensus size: 44
19177674 TTCCCTCAGT
* * * *
19177684 CCGTTGCCTCTTCA-CCTGCAAAACCCACTTCTGTTCGCCTCACC
1 CCGTTCCCTCTTCACCCT-CAAAACCCGCTTCTCTTCCCCTCACC
* *
19177728 CCGTTCCCTCTTCACCCTCAAAACCGGCTTCTCTTCCCCTCACT
1 CCGTTCCCTCTTCACCCTCAAAACCCGCTTCTCTTCCCCTCACC
** * *
19177772 CCGTTCGGTCTTCACCC-CAGAACCTGCTTCT
1 CCGTTCCCTCTTCACCCTCAAAACCCGCTTCT
19177803 TCAGCCGATC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
43 12 0.19
44 49 0.77
45 3 0.05
ACGTcount: A:0.14, C:0.46, G:0.11, T:0.29
Consensus pattern (44 bp):
CCGTTCCCTCTTCACCCTCAAAACCCGCTTCTCTTCCCCTCACC
Found at i:19179658 original size:20 final size:22
Alignment explanation
Indices: 19179619--19179659 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
19179609 TTTTAATAAA
*
19179619 AAATATAAAATTATTAAATATT
1 AAATATAAAATTAATAAATATT
19179641 AAAT-TAAAA-TAATAAATAT
1 AAATATAAAATTAATAAATAT
19179660 ATGTTCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATATAAAATTAATAAATATT
Found at i:19179679 original size:8 final size:9
Alignment explanation
Indices: 19179666--19179958 Score: 83
Period size: 8 Copynumber: 34.3 Consensus size: 9
19179656 ATATATGTTC
19179666 TAATTAT-T
1 TAATTATAT
19179674 TAATTATAT
1 TAATTATAT
* *
19179683 TAAAGTA-AA
1 T-AATTATAT
19179692 TAATTATAT
1 TAATTATAT
19179701 TGAATTAAATATT
1 T-AATT--ATA-T
19179714 TAATTAT-T
1 TAATTATAT
19179722 TAATTATAT
1 TAATTATAT
19179731 TAAATTAAATATT
1 T-AATT--ATA-T
19179744 TAATTAT-T
1 TAATTATAT
19179752 TAATTATAT
1 TAATTATAT
* *
19179761 TAAAGTA-AA
1 T-AATTATAT
19179770 TAATTATAT
1 TAATTATAT
19179779 TAAGTTA-A-
1 TAA-TTATAT
*
19179787 -AA-GAT-T
1 TAATTATAT
19179793 TAATTAT-T
1 TAATTATAT
19179801 TAATTATAT
1 TAATTATAT
* *
19179810 TAAAGTA-AA
1 T-AATTATAT
19179819 TAATTATAT
1 TAATTATAT
19179828 TAAGTTA-A-
1 TAA-TTATAT
*
19179836 -AA-GAT-T
1 TAATTATAT
19179842 TAATTAT-T
1 TAATTATAT
*
19179850 TAATTATGT
1 TAATTATAT
* *
19179859 TAAAGTA-AA
1 T-AATTATAT
19179868 TAATTATAT
1 TAATTATAT
19179877 TAATT-TA-
1 TAATTATAT
*
19179884 -AA-GAT-T
1 TAATTATAT
19179890 TAATTAT-T
1 TAATTATAT
19179898 TAATTATAT
1 TAATTATAT
* *
19179907 TAAAGTA-AA
1 T-AATTATAT
19179916 TAATTATAT
1 TAATTATAT
19179925 TAAGTTA-A-
1 TAA-TTATAT
*
19179933 -AA-GAT-T
1 TAATTATAT
19179939 TAATTAT-T
1 TAATTATAT
19179947 TAATTATAT
1 TAATTATAT
19179956 TAA
1 TAA
19179959 AGTAAATAAT
Statistics
Matches: 212, Mismatches: 29, Indels: 87
0.65 0.09 0.27
Matches are distributed among these distances:
5 3 0.01
6 3 0.01
7 14 0.07
8 85 0.40
9 48 0.23
10 41 0.19
12 14 0.07
13 4 0.02
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (9 bp):
TAATTATAT
Found at i:19179692 original size:48 final size:49
Alignment explanation
Indices: 19179640--19179740 Score: 118
Period size: 48 Copynumber: 2.1 Consensus size: 49
19179630 TATTAAATAT
* *
19179640 TAAATTAA-AATAAT-AAATATATGTTCTAATTATTTAATTATATTAAAG
1 TAAATTAATAATAATGAAATAAATATT-TAATTATTTAATTATATTAAAG
* * * *
19179688 TAAA-TAATTATATTGAATTAAATATTTAATTATTTAATTATATTAAAT
1 TAAATTAATAATAATGAAATAAATATTTAATTATTTAATTATATTAAAG
19179736 TAAAT
1 TAAAT
19179741 ATTTAATTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
47 3 0.07
48 33 0.75
49 8 0.18
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (49 bp):
TAAATTAATAATAATGAAATAAATATTTAATTATTTAATTATATTAAAG
Found at i:19179726 original size:30 final size:30
Alignment explanation
Indices: 19179692--19180108 Score: 180
Period size: 31 Copynumber: 13.2 Consensus size: 30
19179682 TTAAAGTAAA
*
19179692 TAATTATATTGAATTAAATATTTAATTATT
1 TAATTATATTAAATTAAATATTTAATTATT
19179722 TAATTATATTAAATTAAATATTTAATTATT
1 TAATTATATTAAATTAAATATTTAATTATT
* * *
19179752 TAATTATATTAAAGTAAATAATTATATTAAGT
1 TAATTATATTAAATTAAATATTTA-ATT-ATT
* * * * **
19179784 TAA-AAGATTTAATTATTTAATTATATTAAAGTAAA
1 TAATTATA-TTAA--A-TTAA--ATATTTAATTATT
* *
19179819 TAATTATATTAAGTTAAAAGATTTAATTATT
1 TAATTATATTAAATT-AAATATTTAATTATT
* * *
19179850 TAATTATGTTAAAGTAAATAATTATATTAATT
1 TAATTATATTAAATTAAATATTTA-ATT-ATT
** * * **
19179882 TAAAGAT-TTAATTATTTAATTATATTAAAGTAAA
1 TAATTATATTAA--A-TTAA--ATATTTAATTATT
* *
19179916 TAATTATATTAAGTTAAAAGATTTAATTATT
1 TAATTATATTAAATT-AAATATTTAATTATT
* * * **
19179947 TAATTATATTAAAGTAAATAATTATATGAAAG
1 TAATTATATTAAATTAAATATTTA-AT-TATT
** * * **
19179979 TAAAGAT-TTAATTACTAAATTATATTAAAGTAAA
1 TAATTATATTAA--ATTAAA-TAT-TT-AATTATT
* *
19180013 TAATTATATTAAGTTAAAAGATTTAATTATT
1 TAATTATATTAAATT-AAATATTTAATTATT
* * *
19180044 TAATTATATTAAAGTAAATAATTATATTAAGT
1 TAATTATATTAAATTAAATATTTA-ATT-ATT
* *
19180076 TAA-AATATTTAATT--ATATTTAATTATT
1 TAATTATATTAAATTAAATATTTAATTATT
19180103 TAATTA
1 TAATTA
19180109 ATAAAAACAG
Statistics
Matches: 282, Mismatches: 74, Indels: 64
0.67 0.18 0.15
Matches are distributed among these distances:
27 5 0.02
28 4 0.01
29 6 0.02
30 72 0.26
31 87 0.31
32 34 0.12
33 13 0.05
34 22 0.08
35 24 0.09
36 10 0.04
37 5 0.02
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (30 bp):
TAATTATATTAAATTAAATATTTAATTATT
Found at i:19179809 original size:49 final size:49
Alignment explanation
Indices: 19179722--19180105 Score: 634
Period size: 49 Copynumber: 7.9 Consensus size: 49
19179712 TTTAATTATT
* *
19179722 TAATTATATTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAA
1 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
19179770 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
1 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
*
19179819 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATGTTAAAGTAAA
1 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
*
19179868 TAATTATATTAA-TTTAAAGATTTAATTATTTAATTATATTAAAGTAAA
1 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
19179916 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
1 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
* * *
19179965 TAATTATATGAAAG-T-AAAGATTTAATTACTAAATTATATTAAAGTAAA
1 TAATTATAT-TAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
19180013 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
1 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
*
19180062 TAATTATATTAAGTTAAAATATTTAATTATATTTAATTAT-TTAA
1 TAATTATATTAAGTTAAAAGATTTAA-T-TATTTAATTATATTAA
19180106 TTAATAAAAA
Statistics
Matches: 316, Mismatches: 13, Indels: 12
0.93 0.04 0.04
Matches are distributed among these distances:
47 3 0.01
48 101 0.32
49 193 0.61
50 8 0.03
51 11 0.03
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (49 bp):
TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAA
Found at i:19179885 original size:146 final size:145
Alignment explanation
Indices: 19179722--19180105 Score: 637
Period size: 146 Copynumber: 2.6 Consensus size: 145
19179712 TTTAATTATT
* *
19179722 TAATTATATTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAA
1 TAATTATATTAATTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAA
* * *
19179787 AAGATTTAATTATTTAATTATATTAAAGTAAATAATTATAT-TAAGTTAAAAGATTTAATTATTT
66 AAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATGAAAG-T-AAAGATTTAATTACTA
*
19179851 AATTATGTTAAAGTAAA
129 AATTATATTAAAGTAAA
19179868 TAATTATATTAATTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAA
1 TAATTATATTAATTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAA
19179933 AAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATGAAAGTAAAGATTTAATTACTAAA
66 AAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATGAAAGTAAAGATTTAATTACTAAA
19179998 TTATATTAAAGTAAA
131 TTATATTAAAGTAAA
*
19180013 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA
1 TAATTATATTAA-TTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA
*
19180078 AAATATTTAATTATATTTAATTAT-TTAA
65 AAAGATTTAA-T-TATTTAATTATATTAA
19180106 TTAATAAAAA
Statistics
Matches: 226, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
145 42 0.19
146 165 0.73
147 8 0.04
148 11 0.05
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (145 bp):
TAATTATATTAATTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAA
AAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATGAAAGTAAAGATTTAATTACTAAA
TTATATTAAAGTAAA
Found at i:19180090 original size:18 final size:17
Alignment explanation
Indices: 19180059--19180114 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
19180049 ATATTAAAGT
*
19180059 AAATAATTATATTAAGTTA
1 AAATATTTA-ATTAA-TTA
*
19180078 AAATATTTAATTATATTT
1 AAATATTTAATTA-ATTA
*
19180096 AATTATTTAATTAA-TA
1 AAATATTTAATTAATTA
19180112 AAA
1 AAA
19180115 ACAGCCCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.10
17 1 0.03
18 18 0.58
19 9 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AAATATTTAATTAATTA
Found at i:19180112 original size:97 final size:98
Alignment explanation
Indices: 19179722--19180105 Score: 634
Period size: 97 Copynumber: 3.9 Consensus size: 98
19179712 TTTAATTATT
* *
19179722 TAATTATATTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA
1 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA
19179786 AAAGATTTAATTATTTAATTATATTAAAGTAAA
66 AAAGATTTAATTATTTAATTATATTAAAGTAAA
* *
19179819 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATGTTAAAGTAAATAATTATATTAA-TTT
1 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA
19179883 AAAGATTTAATTATTTAATTATATTAAAGTAAA
66 AAAGATTTAATTATTTAATTATATTAAAGTAAA
*
19179916 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATGAAAG-T
1 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATAT-TAAGTT
* *
19179980 -AAAGATTTAATTACTAAATTATATTAAAGTAAA
65 AAAAGATTTAATTATTTAATTATATTAAAGTAAA
19180013 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA
1 TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA
*
19180078 AAATATTTAATTATATTTAATTAT-TTAA
66 AAAGATTTAA-T-TATTTAATTATATTAA
19180106 TTAATAAAAA
Statistics
Matches: 268, Mismatches: 12, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
96 3 0.01
97 196 0.73
98 55 0.21
99 5 0.02
100 9 0.03
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (98 bp):
TAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTA
AAAGATTTAATTATTTAATTATATTAAAGTAAA
Found at i:19185736 original size:66 final size:66
Alignment explanation
Indices: 19185630--19185786 Score: 217
Period size: 66 Copynumber: 2.4 Consensus size: 66
19185620 CAAATTGCTC
*
19185630 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
19185694 AA
65 AA
* ** *
19185696 AACTTAAAGAGGAGGTTGCATTGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
19185761 C
66 A
* * *
19185762 AACTTAAAGTGGAGGCAGCAGCGAG
1 AACTTAAAGAGGAGGCTGCAACGAG
19185787 GCAAGCGGAG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 1 0.01
66 78 0.99
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:19185798 original size:21 final size:21
Alignment explanation
Indices: 19185772--19185824 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
19185762 AACTTAAAGT
19185772 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
*
19185793 GGAGGCAGCAGCTAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
* *
19185814 GAAGGAAGCAG
1 GGAGGCAGCAG
19185825 AGGCTACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.45, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCAGCGAGGCAAGC
Found at i:19186177 original size:42 final size:42
Alignment explanation
Indices: 19186126--19186221 Score: 138
Period size: 43 Copynumber: 2.3 Consensus size: 42
19186116 CTGTTATATT
** *
19186126 AGCGGCGCTTTATCAAAAGCGCCGTTAAAGAACATGGCCTTC
1 AGCGGCGCTTTAGAAAAAGCGCCGCTAAAGAACATGGCCTTC
* *
19186168 AGCGACGCTTGTGGAAAAAGCGCCGCTAAAGAACATGGCCTTC
1 AGCGGCGCTT-TAGAAAAAGCGCCGCTAAAGAACATGGCCTTC
19186211 AGCGGCGCTTT
1 AGCGGCGCTTT
19186222 TTCGCATAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 10 0.21
43 37 0.79
ACGTcount: A:0.27, C:0.26, G:0.27, T:0.20
Consensus pattern (42 bp):
AGCGGCGCTTTAGAAAAAGCGCCGCTAAAGAACATGGCCTTC
Found at i:19188186 original size:19 final size:21
Alignment explanation
Indices: 19188162--19188215 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
19188152 ATACATGTAA
19188162 ATTTTTA-A-ATCAATTTAAT
1 ATTTTTATATATCAATTTAAT
*
19188181 ATTTTTATTATATCAATTTAAA
1 ATTTTTA-TATATCAATTTAAT
*
19188203 ATATTCTATATAT
1 AT-TTTTATATAT
19188216 TAATATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 7 0.24
21 1 0.03
22 17 0.59
23 4 0.14
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTTATATATCAATTTAAT
Found at i:19188342 original size:38 final size:38
Alignment explanation
Indices: 19188294--19188375 Score: 164
Period size: 38 Copynumber: 2.2 Consensus size: 38
19188284 ATTGATATGC
19188294 ATTATTTATATAAATAGATCGTAAAATATAATTGGTAA
1 ATTATTTATATAAATAGATCGTAAAATATAATTGGTAA
19188332 ATTATTTATATAAATAGATCGTAAAATATAATTGGTAA
1 ATTATTTATATAAATAGATCGTAAAATATAATTGGTAA
19188370 ATTATT
1 ATTATT
19188376 AAAATAGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.41
Consensus pattern (38 bp):
ATTATTTATATAAATAGATCGTAAAATATAATTGGTAA
Found at i:19190629 original size:25 final size:20
Alignment explanation
Indices: 19190580--19190621 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
19190570 TATCAAATAT
19190580 GATAAAATTACTACACTAGA
1 GATAAAATTACTACACTAGA
19190600 GATAAAATTACTACACTAGA
1 GATAAAATTACTACACTAGA
19190620 GA
1 GA
19190622 CACAATAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (20 bp):
GATAAAATTACTACACTAGA
Found at i:19190687 original size:17 final size:18
Alignment explanation
Indices: 19190662--19190695 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19190652 TTATCAAATA
*
19190662 ATTTTTATAATT-TCTAT
1 ATTTCTATAATTATCTAT
19190679 ATTTCTATAATTATCTA
1 ATTTCTATAATTATCTA
19190696 AAAAATCACG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTCTATAATTATCTAT
Found at i:19192571 original size:30 final size:30
Alignment explanation
Indices: 19192537--19192599 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
19192527 TGAATAGAAA
*
19192537 TGGAGCAATGAAATCATTTGGAAATGAATG
1 TGGAGCAATGAAACCATTTGGAAATGAATG
19192567 TGGAGCAATGAAACCATTTGGAAATGAATG
1 TGGAGCAATGAAACCATTTGGAAATGAATG
19192597 TGG
1 TGG
19192600 TTTTCTCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.29, T:0.25
Consensus pattern (30 bp):
TGGAGCAATGAAACCATTTGGAAATGAATG
Found at i:19210169 original size:40 final size:40
Alignment explanation
Indices: 19210113--19210202 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
19210103 TACAAATTTT
* * * * * *
19210113 TACACTAGCACGAAGCCTGTTAGGCACTAAGCCTGATCAA
1 TACACTGGCACAAAGCCTGCTAAGCACTAAGCCTAATAAA
*
19210153 TACACTGGCACAAAGCCTGCTAAGTACTAAGCCTAATAAA
1 TACACTGGCACAAAGCCTGCTAAGCACTAAGCCTAATAAA
*
19210193 TACACCGGCA
1 TACACTGGCA
19210203 GGCACAAGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.19
Consensus pattern (40 bp):
TACACTGGCACAAAGCCTGCTAAGCACTAAGCCTAATAAA
Found at i:19212448 original size:44 final size:44
Alignment explanation
Indices: 19212399--19212489 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
19212389 AATGACTTAC
19212399 ATGCATGAATAAAAGAAAGAACGAAGCTTGGAGATGTTGAAACT
1 ATGCATGAATAAAAGAAAGAACGAAGCTTGGAGATGTTGAAACT
19212443 ATGCATGAATAAAAGAAAGAACGAAGCTTGGAGATGTTGAAACT
1 ATGCATGAATAAAAGAAAGAACGAAGCTTGGAGATGTTGAAACT
19212487 ATG
1 ATG
19212490 AAGTTTAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.21
Consensus pattern (44 bp):
ATGCATGAATAAAAGAAAGAACGAAGCTTGGAGATGTTGAAACT
Found at i:19218233 original size:21 final size:21
Alignment explanation
Indices: 19218184--19218236 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
19218174 TTGTGATAGA
*
19218184 TCTACCAATACAAGTCATGCT
1 TCTACCGATACAAGTCATGCT
19218205 TCTACCGATACAAGTCATGCT
1 TCTACCGATACAAGTCATGCT
*
19218226 TCTGCCGATAC
1 TCTACCGATAC
19218237 TAAAAACTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTCATGCT
Found at i:19228714 original size:31 final size:29
Alignment explanation
Indices: 19228672--19228753 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 29
19228662 AAATTTTAAA
* *
19228672 TTAATAATGATAAAATTATATTTTAATCCTC
1 TTAAAAATGATAAAATTATAATTTAA-CC-C
19228703 TTAAAAATGATAAAAATT-TAATTTAACCC
1 TTAAAAATGAT-AAAATTATAATTTAACCC
*
19228732 TTCAAAAATGATAAAAATATAA
1 TT-AAAAATGATAAAATTATAA
19228754 ATTATTAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
29 8 0.18
30 14 0.31
31 17 0.38
32 6 0.13
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (29 bp):
TTAAAAATGATAAAATTATAATTTAACCC
Found at i:19228741 original size:30 final size:32
Alignment explanation
Indices: 19228672--19228753 Score: 102
Period size: 30 Copynumber: 2.7 Consensus size: 32
19228662 AAATTTTAAA
* *
19228672 TTAATAATGAT-AAAATTATATTTTAATCCTC
1 TTAAAAATGATAAAAATTATAATTTAATCCTC
19228703 TTAAAAATGATAAAAATT-TAATTTAA-CC-C
1 TTAAAAATGATAAAAATTATAATTTAATCCTC
19228732 TTCAAAAATGATAAAAA-TATAA
1 TT-AAAAATGATAAAAATTATAA
19228754 ATTATTAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
29 4 0.09
30 19 0.41
31 17 0.37
32 6 0.13
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (32 bp):
TTAAAAATGATAAAAATTATAATTTAATCCTC
Found at i:19229916 original size:17 final size:18
Alignment explanation
Indices: 19229894--19229938 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
19229884 ATAGTTATAC
19229894 TTAATATTATTTAAAT-T
1 TTAATATTATTTAAATAT
*
19229911 TTAATA-TATTCAAATAT
1 TTAATATTATTTAAATAT
19229928 TT-ATATTATTT
1 TTAATATTATTT
19229939 TTCATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (18 bp):
TTAATATTATTTAAATAT
Found at i:19231769 original size:15 final size:16
Alignment explanation
Indices: 19231749--19231781 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19231739 GAAAAAAACA
*
19231749 AATTCAATCAATT-TT
1 AATTCAATAAATTATT
19231764 AATTCAATAAATTATT
1 AATTCAATAAATTATT
19231780 AA
1 AA
19231782 AAATTTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTCAATAAATTATT
Found at i:19232814 original size:11 final size:11
Alignment explanation
Indices: 19232795--19232827 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
19232785 TTAGGATATT
19232795 ATTTATATTTA
1 ATTTATATTTA
*
19232806 ATTTGTATTTA
1 ATTTATATTTA
19232817 ATTTATATTTA
1 ATTTATATTTA
19232828 TCTTTTTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATTTATATTTA
Found at i:19232855 original size:14 final size:14
Alignment explanation
Indices: 19232818--19232847 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19232808 TTGTATTTAA
*
19232818 TTTATATTTATCTT
1 TTTAGATTTATCTT
19232832 TTTAGATTTATCTT
1 TTTAGATTTATCTT
19232846 TT
1 TT
19232848 AGAGTTTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTAGATTTATCTT
Found at i:19236678 original size:18 final size:18
Alignment explanation
Indices: 19236655--19236689 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19236645 AATTTTGATC
19236655 AAATAAATT-AAATTAATT
1 AAAT-AATTAAAATTAATT
19236673 AAATAATTAAAATTAAT
1 AAATAATTAAAATTAAT
19236690 AGGATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATAATTAAAATTAATT
Found at i:19242490 original size:4 final size:4
Alignment explanation
Indices: 19242477--19242507 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
19242467 GTGATATATG
19242477 TGTT TG-T TGTT TGTT TGTT TGTT TGTT TGTT
1 TGTT TGTT TGTT TGTT TGTT TGTT TGTT TGTT
19242508 CATGCATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.00, C:0.00, G:0.26, T:0.74
Consensus pattern (4 bp):
TGTT
Found at i:19249212 original size:82 final size:82
Alignment explanation
Indices: 19249075--19249249 Score: 314
Period size: 82 Copynumber: 2.1 Consensus size: 82
19249065 TGGGTTCCTC
* *
19249075 CGATGGCTGAGTCTTCGTATATGTTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCGAGAGTTA
1 CGATGGCTGAGTCTTCGCATATGTTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCGAGAGTGA
19249140 GAAATTCTGGACCGTAT
66 GAAATTCTGGACCGTAT
*
19249157 CGATGGCTGAGTCTTCGCATATGTTGTGGATTCTCATCAGCTTGTGTGAGCAGCATCGAGAGTGA
1 CGATGGCTGAGTCTTCGCATATGTTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCGAGAGTGA
19249222 GAAATTCTGGACCGTAT
66 GAAATTCTGGACCGTAT
*
19249239 CGATGGTTGAG
1 CGATGGCTGAG
19249250 ACTTAGCTTG
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 89 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.31
Consensus pattern (82 bp):
CGATGGCTGAGTCTTCGCATATGTTGCGGATTCTCATCAGCTTGTGTGAGCAGCATCGAGAGTGA
GAAATTCTGGACCGTAT
Found at i:19252419 original size:6 final size:6
Alignment explanation
Indices: 19252408--19252446 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
19252398 TTTAGGATAT
*
19252408 TATTTA TATTTA -ATTTG TATTTA -ATTTA TATTTA TATTT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTT
19252447 TTAGATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 9 0.31
6 20 0.69
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:19252428 original size:11 final size:11
Alignment explanation
Indices: 19252409--19252446 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
19252399 TTAGGATATT
19252409 ATTTATATTTA
1 ATTTATATTTA
*
19252420 ATTTGTATTTA
1 ATTTATATTTA
19252431 ATTTATATTTA
1 ATTTATATTTA
19252442 TATTT
1 -ATTT
19252447 TTAGATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 20 0.83
12 4 0.17
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (11 bp):
ATTTATATTTA
Found at i:19252430 original size:17 final size:17
Alignment explanation
Indices: 19252408--19252446 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
19252398 TTTAGGATAT
*
19252408 TATTTATATTTAATTTG
1 TATTTATATTTAATTTA
19252425 TATTTA-ATTTATATTTA
1 TATTTATATTTA-ATTTA
19252442 TATTT
1 TATTT
19252447 TTAGATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TATTTATATTTAATTTA
Found at i:19256351 original size:19 final size:20
Alignment explanation
Indices: 19256311--19256352 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
19256301 ATGAGCTATC
19256311 AAATAAGGAAACAAAGACTA
1 AAATAAGGAAACAAAGACTA
19256331 AAATAAGGAAACAAA-ACTA
1 AAATAAGGAAACAAAGACTA
19256350 AAA
1 AAA
19256353 GGAATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.69, C:0.10, G:0.12, T:0.10
Consensus pattern (20 bp):
AAATAAGGAAACAAAGACTA
Found at i:19257874 original size:20 final size:21
Alignment explanation
Indices: 19257837--19257875 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19257827 AAACCGAGTA
*
19257837 TCACTGAGTTAGAAAATGCAG
1 TCACTAAGTTAGAAAATGCAG
19257858 TCACTAAGTTA-AAAATGC
1 TCACTAAGTTAGAAAATGC
19257876 TAAAAATGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (21 bp):
TCACTAAGTTAGAAAATGCAG
Found at i:19271020 original size:18 final size:15
Alignment explanation
Indices: 19270988--19271016 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19270978 CTGCACTATG
19270988 CTTCTTCTTCCTCCT
1 CTTCTTCTTCCTCCT
19271003 CTTCTTC-TCCTCCT
1 CTTCTTCTTCCTCCT
19271017 TCCTGCGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (15 bp):
CTTCTTCTTCCTCCT
Found at i:19291644 original size:52 final size:52
Alignment explanation
Indices: 19291559--19291693 Score: 207
Period size: 52 Copynumber: 2.6 Consensus size: 52
19291549 ATTTCATTTA
* * * *
19291559 ATACTCACGATGACACATAGTCATCAGATCTCATAATTCGTAAAGGATTCCT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
19291611 ATACTCACGATGACACAAAGTCGTCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
19291663 ATACTCACGATAACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
19291694 TTTTCATTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:19302822 original size:21 final size:21
Alignment explanation
Indices: 19302798--19302847 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
19302788 CAACTTCTAT
*
19302798 CGATTCAAGTATCCTAACTAC
1 CGATACAAGTATCCTAACTAC
19302819 CGATACAAGTATCCTAACTAC
1 CGATACAAGTATCCTAACTAC
19302840 CGATACAA
1 CGATACAA
19302848 CCCATGTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.24
Consensus pattern (21 bp):
CGATACAAGTATCCTAACTAC
Found at i:19303513 original size:60 final size:59
Alignment explanation
Indices: 19303401--19303611 Score: 175
Period size: 52 Copynumber: 3.8 Consensus size: 59
19303391 CAACTCGCAT
* * *
19303401 TTTATACTCACGATGACATAGAGTCATCGGACCT-TTAATCCAT-AATGGGATTCATTTCA
1 TTTATACTCACGATGACACACAGTCATCGGACCTCTTAATCCGTAAAT--GATTCATTTCA
* *
19303460 TTTAATACTCACGATGACACATAGTCATCGGACCTCTTGATCCGTAAATG----A-TTCA
1 TTT-ATACTCACGATGACACACAGTCATCGGACCTCTTAATCCGTAAATGATTCATTTCA
* * *
19303515 --TATACTCACGATGACACACAGTCATCGGACTTCATAATCCGTAAA-G---GA-TTCA
1 TTTATACTCACGATGACACACAGTCATCGGACCTCTTAATCCGTAAATGATTCATTTCA
* * * *
19303567 --TATACTCACGATGACACATAGTCATCAGACCTCATAATTCGTAAA
1 TTTATACTCACGATGACACACAGTCATCGGACCTCTTAATCCGTAAA
19303612 GGATCCACAT
Statistics
Matches: 136, Mismatches: 12, Indels: 15
0.83 0.07 0.09
Matches are distributed among these distances:
51 1 0.01
52 86 0.63
53 1 0.01
55 4 0.03
56 1 0.01
59 3 0.02
60 30 0.22
61 7 0.05
62 3 0.02
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (59 bp):
TTTATACTCACGATGACACACAGTCATCGGACCTCTTAATCCGTAAATGATTCATTTCA
Found at i:19303538 original size:52 final size:52
Alignment explanation
Indices: 19303464--19303650 Score: 266
Period size: 52 Copynumber: 3.6 Consensus size: 52
19303454 ATTTCATTTA
* * *
19303464 ATACTCACGATGACACATAGTCATCGGACCTCTTGATCCGTAAATGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
19303516 ATACTCACGATGACACACAGTCATCGGACTTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
19303568 ATACTCACGATGACACATAGTCATCAGACCTCATAATTCGTAAAGGATCCAC
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* **
19303620 ATACTCACAAAAACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
19303651 TTTTCATTTA
Statistics
Matches: 120, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 120 1.00
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:19306320 original size:13 final size:13
Alignment explanation
Indices: 19306302--19306326 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19306292 TATAAGGAAA
19306302 CAAAAATAAAGGG
1 CAAAAATAAAGGG
19306315 CAAAAATAAAGG
1 CAAAAATAAAGG
19306327 AATTTAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (13 bp):
CAAAAATAAAGGG
Found at i:19316390 original size:17 final size:17
Alignment explanation
Indices: 19316370--19316417 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
19316360 CACATTCCCT
*
19316370 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTGAA
* * *
19316387 TTGTCACTGCATCTGCA
1 TTGTCATTGCATTTGAA
19316404 TTGTCATTGCATTT
1 TTGTCATTGCATTT
19316418 CCATGTATCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (17 bp):
TTGTCATTGCATTTGAA
Found at i:19322420 original size:83 final size:83
Alignment explanation
Indices: 19322272--19322434 Score: 263
Period size: 83 Copynumber: 2.0 Consensus size: 83
19322262 ATTGGCTAAT
*
19322272 TGTCACGTGTAAAATAATATTGCAATCGCAAATGTGCAAGTGTACACAACACAAGTAATAGAGTG
1 TGTCACGTGTAAAATAATATTGCAATCGCAAATGTGCAAGTGTACACAACACAAGTAATACAGTG
19322337 ATAAGTAAAGTATCGTAC
66 ATAAGTAAAGTATCGTAC
* * * ***
19322355 TGTCGCGTGTAAAATAATATTGCGATCGCAAATGTGCAAGTGTACGCAATGTAAGTAATACAGTG
1 TGTCACGTGTAAAATAATATTGCAATCGCAAATGTGCAAGTGTACACAACACAAGTAATACAGTG
19322420 ATAAGTAAAGTATCG
66 ATAAGTAAAGTATCG
19322435 ATCCCACAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (83 bp):
TGTCACGTGTAAAATAATATTGCAATCGCAAATGTGCAAGTGTACACAACACAAGTAATACAGTG
ATAAGTAAAGTATCGTAC
Found at i:19364725 original size:18 final size:18
Alignment explanation
Indices: 19364702--19364747 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
19364692 AATTCAAAAG
19364702 AAATAATTTGTACAT-ACA
1 AAATAATTTGT-CATAACA
* *
19364720 AAATAA-ATGTGATAACA
1 AAATAATTTGTCATAACA
19364737 AAATAATTTGT
1 AAATAATTTGT
19364748 GTTATCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 9 0.39
ACGTcount: A:0.52, C:0.07, G:0.09, T:0.33
Consensus pattern (18 bp):
AAATAATTTGTCATAACA
Found at i:19367529 original size:16 final size:16
Alignment explanation
Indices: 19367510--19367550 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
19367500 AAAGAAAAAG
*
19367510 AAAGAAAAAAATGTTA
1 AAAGAAAAAAATGTAA
**
19367526 AAAGAAAAATGTGTAA
1 AAAGAAAAAAATGTAA
19367542 AAAGAAAAA
1 AAAGAAAAA
19367551 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (16 bp):
AAAGAAAAAAATGTAA
Found at i:19367535 original size:14 final size:16
Alignment explanation
Indices: 19367516--19367551 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
19367506 AAAGAAAGAA
19367516 AAAAATGT-T-AAAAG
1 AAAAATGTGTAAAAAG
19367530 AAAAATGTGTAAAAAG
1 AAAAATGTGTAAAAAG
19367546 AAAAAT
1 AAAAAT
19367552 ATTTTTTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 11 0.55
ACGTcount: A:0.67, C:0.00, G:0.14, T:0.19
Consensus pattern (16 bp):
AAAAATGTGTAAAAAG
Found at i:19374717 original size:29 final size:29
Alignment explanation
Indices: 19374675--19374735 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
19374665 ATTTATAGCT
*
19374675 ATGAACAACTTAAAACTGGAACTTCATTA
1 ATGAACAACTTAAAACTGGAACTTCATCA
19374704 ATGAACAACTTAAAACTGGAACTTCATCA
1 ATGAACAACTTAAAACTGGAACTTCATCA
19374733 ATG
1 ATG
19374736 TTAGTATCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.26
Consensus pattern (29 bp):
ATGAACAACTTAAAACTGGAACTTCATCA
Found at i:19374802 original size:13 final size:13
Alignment explanation
Indices: 19374784--19374816 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
19374774 TTTCAGCAAT
*
19374784 TTTTTCTTTTTTC
1 TTTTTCTTTCTTC
19374797 TTTTTCTTTCTTC
1 TTTTTCTTTCTTC
19374810 TTTTTCT
1 TTTTTCT
19374817 CATTTATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTCTTTCTTC
Found at i:19389014 original size:20 final size:21
Alignment explanation
Indices: 19388978--19389016 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19388968 ATTTTTGTTA
*
19388978 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
19388999 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
19389017 AATTCCTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:19395628 original size:62 final size:62
Alignment explanation
Indices: 19395541--19395719 Score: 218
Period size: 62 Copynumber: 2.9 Consensus size: 62
19395531 AATTCACATC
* * *
19395541 TAATAACTCACAATGACATAGAGTCATCGGACCTTAAATCTGTAATAGGATTCATTTCCCATT
1 TAAT-ACTCACGATGACACAAAGTCATCGGACCTTAAATCTGTAATAGGATTCATTTCCCATT
* * * * *
19395604 TAATAGTCACGATGACACAAAGTCATCGAACCTTTAATTCT-TAATAGGATCCATTTCTCATT
1 TAATACTCACGATGACACAAAGTCATCGGACC-TTAAATCTGTAATAGGATTCATTTCCCATT
* * *
19395666 TAATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAA-AGGATTCAT
1 TAATACTCACGATGACACAAAGTCATCGGACCTTA-AATCTGTAATAGGATTCAT
19395720 ATACTCATGA
Statistics
Matches: 98, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
61 2 0.02
62 82 0.84
63 14 0.14
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.31
Consensus pattern (62 bp):
TAATACTCACGATGACACAAAGTCATCGGACCTTAAATCTGTAATAGGATTCATTTCCCATT
Found at i:19395746 original size:52 final size:52
Alignment explanation
Indices: 19395668--19395854 Score: 338
Period size: 52 Copynumber: 3.6 Consensus size: 52
19395658 TTCTCATTTA
19395668 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
19395720 ATACTCATGATGATACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
19395772 ATATTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
19395824 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
19395855 TTTTCATTTA
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 127 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:19398570 original size:7 final size:7
Alignment explanation
Indices: 19398558--19398583 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
19398548 TCATTTCATT
19398558 TTCTTTC
1 TTCTTTC
19398565 TTCTTTC
1 TTCTTTC
19398572 TTCTTTC
1 TTCTTTC
19398579 TTCTT
1 TTCTT
19398584 CACATGGCAC
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:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTTC
Found at i:19400268 original size:21 final size:19
Alignment explanation
Indices: 19400244--19400295 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
19400234 AGAGTTTTTG
19400244 GTATCGGTAGATGCATGACTT
1 GTATCGGTAGAT-CAT-ACTT
*
19400265 GTATCGGTGGAATCATACTT
1 GTATCGGTAG-ATCATACTT
19400285 GTATCGGTAGA
1 GTATCGGTAGA
19400296 GCTAGCACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 13 0.46
21 12 0.43
22 2 0.07
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (19 bp):
GTATCGGTAGATCATACTT
Found at i:19405809 original size:7 final size:7
Alignment explanation
Indices: 19405797--19405829 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
19405787 TCATTTCATT
19405797 TTCTTTC
1 TTCTTTC
19405804 TTCTTTC
1 TTCTTTC
19405811 TTCTTTC
1 TTCTTTC
19405818 TTCTTTC
1 TTCTTTC
19405825 TTCTT
1 TTCTT
19405830 CACATGGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTTC
Found at i:19407531 original size:21 final size:19
Alignment explanation
Indices: 19407505--19407557 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 19
19407495 GGAGTTTTTG
*
19407505 GTATCGGTAGATGCATAACTT
1 GTATCGATAGAT-CAT-ACTT
19407526 GTATCGATAGAAATCATACTT
1 GTATCGATAG--ATCATACTT
19407547 GTATCGATAGA
1 GTATCGATAGA
19407558 GCTAGCACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 1 0.03
21 23 0.79
22 3 0.10
23 2 0.07
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (19 bp):
GTATCGATAGATCATACTT
Found at i:19417782 original size:30 final size:30
Alignment explanation
Indices: 19417748--19417815 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
19417738 TAGAAATATA
* *
19417748 ATTTTTAAATAATTAAATTAAAATTTTATT
1 ATTTTTAAAGAATTAAAATAAAATTTTATT
*
19417778 ATTTTTAAAGAATTAAAATATAATTTTATT
1 ATTTTTAAAGAATTAAAATAAAATTTTATT
19417808 -TTTATTAA
1 ATTT-TTAA
19417816 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 3 0.09
30 31 0.91
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
ATTTTTAAAGAATTAAAATAAAATTTTATT
Found at i:19418334 original size:23 final size:22
Alignment explanation
Indices: 19418291--19418333 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
19418281 CCAACTTAGT
19418291 ATTTGATCTTAACATTTTTTTA
1 ATTTGATCTTAACATTTTTTTA
19418313 ATTTGATACTTAA-ATTTTTTT
1 ATTTGAT-CTTAACATTTTTTT
19418334 TGGATTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTGATCTTAACATTTTTTTA
Found at i:19418585 original size:29 final size:28
Alignment explanation
Indices: 19418526--19418654 Score: 120
Period size: 29 Copynumber: 4.5 Consensus size: 28
19418516 TTAAAAAAAT
* *
19418526 TTTAAGTATCAAATTAAAAAAATAATCAAA
1 TTTAAATATCAAATTAAAAAAAT--TTAAA
* *
19418556 TTTAGATATTAAATTAAAAAAATTTTAAA
1 TTTAAATATCAAATTAAAAAAA-TTTAAA
*
19418585 TTTAAGTATCAAATTAAATCAAAA---AAA
1 TTTAAATATCAAATTAAA--AAAATTTAAA
*
19418612 TTTAAATATCAAATTAAAAAAATGTTAAG
1 TTTAAATATCAAATTAAAAAAAT-TTAAA
*
19418641 TTTAAATATTAAAT
1 TTTAAATATCAAAT
19418655 ATTATATTAA
Statistics
Matches: 82, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
25 4 0.05
27 20 0.24
29 34 0.41
30 19 0.23
31 5 0.06
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (28 bp):
TTTAAATATCAAATTAAAAAAATTTAAA
Found at i:19418632 original size:56 final size:58
Alignment explanation
Indices: 19418526--19418654 Score: 163
Period size: 56 Copynumber: 2.2 Consensus size: 58
19418516 TTAAAAAAAT
* * *
19418526 TTTAAGTATCAAATTAAAAAAATAATCAAATTTAGATATTAAATTAAAAAAATTTTAAA
1 TTTAAGTATCAAATTAAAAAAATAA-CAAATTTAAATATCAAATTAAAAAAATGTTAAA
** *
19418585 TTTAAGTATCAAATTAAATCAA-AA-AAATTTAAATATCAAATTAAAAAAATGTTAAG
1 TTTAAGTATCAAATTAAAAAAATAACAAATTTAAATATCAAATTAAAAAAATGTTAAA
* *
19418641 TTTAAATATTAAAT
1 TTTAAGTATCAAAT
19418655 ATTATATTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
56 40 0.65
58 2 0.03
59 20 0.32
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (58 bp):
TTTAAGTATCAAATTAAAAAAATAACAAATTTAAATATCAAATTAAAAAAATGTTAAA
Found at i:19418647 original size:22 final size:22
Alignment explanation
Indices: 19418597--19418647 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
19418587 TAAGTATCAA
19418597 ATTAAATCAAAAAAATTTAAAT
1 ATTAAATCAAAAAAATTTAAAT
* * *
19418619 ATCAAATTAAAAAAATGTTAAGT
1 ATTAAATCAAAAAAAT-TTAAAT
19418642 -TTAAAT
1 ATTAAAT
19418648 ATTAAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (22 bp):
ATTAAATCAAAAAAATTTAAAT
Found at i:19418669 original size:25 final size:24
Alignment explanation
Indices: 19418622--19418691 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
19418612 TTTAAATATC
* * * *
19418622 AAATTAAAAAAATGTTAAGTTTA-
1 AAATTAAATATATATTAAATTTAT
19418645 AATATTAAATATTATATTAAATTTAT
1 AA-ATTAAATA-TATATTAAATTTAT
* *
19418671 AAATTAATTATATAGTAAATT
1 AAATTAAATATATATTAAATT
19418692 ATCTTCTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
23 2 0.05
24 17 0.45
25 17 0.45
26 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
AAATTAAATATATATTAAATTTAT
Found at i:19421421 original size:12 final size:12
Alignment explanation
Indices: 19421404--19421430 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19421394 TATTGGAAGA
19421404 AGATGCAGATGG
1 AGATGCAGATGG
19421416 AGATGCAGATGG
1 AGATGCAGATGG
19421428 AGA
1 AGA
19421431 AGGAGAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.41, T:0.15
Consensus pattern (12 bp):
AGATGCAGATGG
Found at i:19422072 original size:30 final size:30
Alignment explanation
Indices: 19422013--19422072 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
19422003 ATTTAAATGA
* * *
19422013 AAAATTTTAATTATTTATAAAGATGATTTT
1 AAAATTTTAATTAATTAGAAAGATAATTTT
19422043 AAAATTTTAATTAATTACGAAA-ATAATTTT
1 AAAATTTTAATTAATTA-GAAAGATAATTTT
19422073 TTTTTGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (30 bp):
AAAATTTTAATTAATTAGAAAGATAATTTT
Found at i:19423452 original size:16 final size:18
Alignment explanation
Indices: 19423422--19423464 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
19423412 TACGAAGCAA
*
19423422 ATATAATTTGAAATAAA-
1 ATATTATTTGAAATAAAT
*
19423439 AT-TTATTTGTAATAAAT
1 ATATTATTTGAAATAAAT
19423456 ATATTATTT
1 ATATTATTT
19423465 TTCAAATTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 12 0.55
17 4 0.18
18 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
ATATTATTTGAAATAAAT
Found at i:19425223 original size:19 final size:19
Alignment explanation
Indices: 19425199--19425235 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
19425189 TAAGATACAA
19425199 TATTTTT-ATTAGTTTTTTC
1 TATTTTTAATTA-TTTTTTC
19425218 TATTTTTAATTATTTTTT
1 TATTTTTAATTATTTTTT
19425236 ACAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (19 bp):
TATTTTTAATTATTTTTTC
Found at i:19425255 original size:36 final size:38
Alignment explanation
Indices: 19425214--19425290 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 38
19425204 TTATTAGTTT
*
19425214 TTTCT-ATTTTTAATTATTTTTT-ACAATA-TTTTACAA
1 TTTCTAATTTTT-ATAATTTTTTGACAATATTTTTACAA
* *
19425250 TTTCTAATTTTTATAATTTTTTGATAGTATTTTTACAA
1 TTTCTAATTTTTATAATTTTTTGACAATATTTTTACAA
19425288 TTT
1 TTT
19425291 TTAAAAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 14 0.40
37 10 0.29
38 11 0.31
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (38 bp):
TTTCTAATTTTTATAATTTTTTGACAATATTTTTACAA
Done.