Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008283.1 Hibiscus syriacus cultivar Beakdansim tig00110945_pilon, whole genome shotgun sequence
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: 2862730
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 14
Found at i:2523007 original size:7 final size:7
Alignment explanation
Indices: 2522995--2523021 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2522985 TGGAGAGGAA
2522995 GAAGAGG
1 GAAGAGG
2523002 GAAGAGG
1 GAAGAGG
2523009 GAAGAGG
1 GAAGAGG
2523016 GAAGAG
1 GAAGAG
2523022 AGAAAGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (7 bp):
GAAGAGG
Found at i:2524068 original size:15 final size:16
Alignment explanation
Indices: 2524020--2524065 Score: 83
Period size: 16 Copynumber: 2.8 Consensus size: 16
2524010 TAACCGGTTT
2524020 CGGTTTAAAAAAAAAC
1 CGGTTTAAAAAAAAAC
2524036 CGGTTTAAAAAAAAAC
1 CGGTTTAAAAAAAAAC
2524052 CGGTTATAAAAAAA
1 CGGTT-TAAAAAAA
2524066 CCGATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.20
Consensus pattern (16 bp):
CGGTTTAAAAAAAAAC
Found at i:2524249 original size:21 final size:21
Alignment explanation
Indices: 2524224--2524276 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2524214 ACACTTAAGG
2524224 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
* *
2524245 AACCGATTCTCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
2524266 TACCGATTCCC
1 AACCGATTCCC
2524277 CCACGCTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:2524493 original size:13 final size:13
Alignment explanation
Indices: 2524472--2524526 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
2524462 AAGTTCGATA
*
2524472 AATTCAAATACTT
1 AATTGAAATACTT
2524485 AATTGAAATACTT
1 AATTGAAATACTT
* *
2524498 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
2524512 AATTGAAATACTT
1 AATTGAAATACTT
2524525 AA
1 AA
2524527 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:2524608 original size:32 final size:33
Alignment explanation
Indices: 2524512--2524610 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
2524502 AACTCAACAT
* * *
2524512 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2524545 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2524578 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
2524610 A
1 A
2524611 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:2524629 original size:21 final size:21
Alignment explanation
Indices: 2524605--2524644 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2524595 ACTTCAAGTT
2524605 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
2524626 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
2524645 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:2526965 original size:12 final size:12
Alignment explanation
Indices: 2526948--2526990 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
2526938 CGGATAAAAA
2526948 CGGTTTTTTAAC
1 CGGTTTTTTAAC
2526960 CGGTTTTTTTCAAAC
1 CGG-TTTTTT--AAC
*
2526975 CGGTTTTTTATC
1 CGGTTTTTTAAC
2526987 CGGT
1 CGGT
2526991 AAAAAAACCG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 6 0.22
14 6 0.22
15 6 0.22
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.49
Consensus pattern (12 bp):
CGGTTTTTTAAC
Found at i:2530315 original size:3 final size:3
Alignment explanation
Indices: 2530307--2530364 Score: 71
Period size: 3 Copynumber: 19.0 Consensus size: 3
2530297 TTTTTCAACC
* * *
2530307 ATT ATT ATT TTT ATT ATT ATT ATT ATT ATT AAT ATT ATT ATT ATAA
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T
*
2530353 AAT ATT ATT ATT
1 ATT ATT ATT ATT
2530365 TTTAAACCTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
3 45 0.98
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:2539934 original size:69 final size:69
Alignment explanation
Indices: 2539740--2539934 Score: 223
Period size: 69 Copynumber: 2.8 Consensus size: 69
2539730 TCTTAACATG
* * * *
2539740 GATCTTTCTTTCAATCAATTTTCTGGAAATATAT-CTG-TCCTTGAGAGTCTAACATCTCTTGAA
1 GATCTCTCTTCCAATCAATTTTCTGGAAATAT-TGATGCT-CTTAAGAGTCTAACATCTCTTGAA
2539803 ACATTA
64 ACATTA
** * * * ** * * *
2539809 TCTATCTATTCCAATCAACTTTCTATAAATATAGATGCTCTTAAAAGTCAAACATCTCTTGAAAC
1 GATCTCTCTTCCAATCAATTTTCTGGAAATATTGATGCTCTTAAGAGTCTAACATCTCTTGAAAC
2539874 ATTA
66 ATTA
*
2539878 GATCTCTCTTCCAATCAATTTTCTGGAAATATTGATGCTCTTAAGAGTCTAGCATCT
1 GATCTCTCTTCCAATCAATTTTCTGGAAATATTGATGCTCTTAAGAGTCTAACATCT
2539935 TTCCAAGACT
Statistics
Matches: 99, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
69 98 0.99
70 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.38
Consensus pattern (69 bp):
GATCTCTCTTCCAATCAATTTTCTGGAAATATTGATGCTCTTAAGAGTCTAACATCTCTTGAAAC
ATTA
Found at i:2544807 original size:18 final size:18
Alignment explanation
Indices: 2544777--2544818 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
2544767 TTAAAAAATA
2544777 ATATTAATATTTTATTTT
1 ATATTAATATTTTATTTT
2544795 ATATATAAT-TTTTATTTT
1 ATAT-TAATATTTTATTTT
2544813 ATATTA
1 ATATTA
2544819 TCAAATCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 2 0.09
18 17 0.74
19 4 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATATTAATATTTTATTTT
Found at i:2546776 original size:20 final size:22
Alignment explanation
Indices: 2546748--2546790 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
2546738 CAAGTAATCA
*
2546748 ATATTAAAGT-TAATTAA-ATT
1 ATATGAAAGTATAATTAATATT
2546768 ATATGAAAGTATAATTAATATT
1 ATATGAAAGTATAATTAATATT
2546790 A
1 A
2546791 ATAAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 7 0.35
22 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (22 bp):
ATATGAAAGTATAATTAATATT
Found at i:2557309 original size:69 final size:69
Alignment explanation
Indices: 2557197--2557391 Score: 198
Period size: 69 Copynumber: 2.8 Consensus size: 69
2557187 TCGCAACTTG
* * * ** *
2557197 GATCTTTCTTTCAATCAATTTTCTGGGAATATATC-TGTCCTTGAGGGTCTAACATCTCTT-AA-
1 GATCTTTCTTCCAATCAATTTTCTGGAAATATA-CATGTTCTTGAGAATCTAACATCTATTGAAG
2557259 AATAATA
65 AAT--TA
* * * *
2557266 GATCTCTCTTCCAGTCAATTTTCTGAAAATATACATGTTCTTGAGAATTTAACATCTATTGAAGA
1 GATCTTTCTTCCAATCAATTTTCTGGAAATATACATGTTCTTGAGAATCTAACATCTATTGAAGA
2557331 ATTA
66 ATTA
** * * * *
2557335 TTTCTTTCTTCCAATCAATTTTCTGGAAATATAGATGCTCTTAAGAATCTAGCATCT
1 GATCTTTCTTCCAATCAATTTTCTGGAAATATACATGTTCTTGAGAATCTAACATCT
2557392 CTCCGAGGAT
Statistics
Matches: 103, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
68 1 0.01
69 97 0.94
70 2 0.02
71 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (69 bp):
GATCTTTCTTCCAATCAATTTTCTGGAAATATACATGTTCTTGAGAATCTAACATCTATTGAAGA
ATTA
Found at i:2562640 original size:18 final size:18
Alignment explanation
Indices: 2562613--2562652 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2562603 TATGAGTTTC
2562613 GGGTTAACCCAAAATTCA
1 GGGTTAACCCAAAATTCA
*
2562631 GGGTTGACCCAAAATTCA
1 GGGTTAACCCAAAATTCA
2562649 GGGT
1 GGGT
2562653 ATTATAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (18 bp):
GGGTTAACCCAAAATTCA
Found at i:2563250 original size:20 final size:22
Alignment explanation
Indices: 2563221--2563261 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
2563211 TTAATAAATT
2563221 AAATAAATTTA-AA-ATTATAA
1 AAATAAATTTACAATATTATAA
*
2563241 AAATATATTTACAATATTATA
1 AAATAAATTTACAATATTATA
2563262 GCCATGGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATAAATTTACAATATTATAA
Found at i:2563390 original size:2 final size:2
Alignment explanation
Indices: 2563383--2563410 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2563373 ACTTATTTCA
2563383 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2563411 TTTGACAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2582680 original size:60 final size:60
Alignment explanation
Indices: 2582629--2582752 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
2582619 GATCTCTTGC
**
2582629 CTATAAAAT-ATTATTTTGTTGAGTAT-CTTAACTATTAATTGTTACAAAATGATCATCCGA
1 CTAT-AAATCATTATTTTGTTGAGT-TCCTTAACTATTAAAAGTTACAAAATGATCATCCGA
* ** * *
2582689 TTATATGTCATTGTTTTGTTGAGTTCCTTAACTATTAAAAGTTACAAAATGATCATCTGA
1 CTATAAATCATTATTTTGTTGAGTTCCTTAACTATTAAAAGTTACAAAATGATCATCCGA
2582749 CTAT
1 CTAT
2582753 TCATTATGTT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 3 0.06
60 51 0.94
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (60 bp):
CTATAAATCATTATTTTGTTGAGTTCCTTAACTATTAAAAGTTACAAAATGATCATCCGA
Found at i:2586202 original size:24 final size:26
Alignment explanation
Indices: 2586167--2586228 Score: 85
Period size: 24 Copynumber: 2.5 Consensus size: 26
2586157 TAATTTAAGC
*
2586167 AATA-TAAATATTGAAA-AAAAATT-
1 AATATTAAATATTAAAATAAAAATTA
2586190 AATATTAAATATTAAAATAAAAATTA
1 AATATTAAATATTAAAATAAAAATTA
2586216 AATTATTAAATAT
1 AA-TATTAAATAT
2586229 ATATATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 4 0.12
24 11 0.32
25 7 0.21
26 2 0.06
27 10 0.29
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AATATTAAATATTAAAATAAAAATTA
Found at i:2586834 original size:22 final size:22
Alignment explanation
Indices: 2586791--2586834 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2586781 ACTTTTAGTA
* *
2586791 ATTTAATTTTTTTATATTTTTT
1 ATTTAATTTTTTAATATATTTT
2586813 ATTTAATTTTTTGAATA-ATTTT
1 ATTTAATTTTTT-AATATATTTT
2586835 GTATTTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTAATTTTTTAATATATTTT
Found at i:2590976 original size:61 final size:60
Alignment explanation
Indices: 2590880--2591028 Score: 172
Period size: 61 Copynumber: 2.4 Consensus size: 60
2590870 GAAGTGCTTG
* * * * **
2590880 CACATAAGGTCGTCCTCACCTCATGCACTATGTTTACACTCTAGTGTTGACCCGGATATGA
1 CACATAAGGTCTTCC-CACCACCTGCACTAAGTTTACACTCTAGTACTGACCCGGATATGA
**
2590941 CACATAAGGTCATTCCCACCACCTGCACTAAGTTTACACTCTAGTACTGATTCGGATATGA
1 CACATAAGGTC-TTCCCACCACCTGCACTAAGTTTACACTCTAGTACTGACCCGGATATGA
* * *
2591002 CACATAAGATCGTGCCCACCATCTGCA
1 CACATAAGGTC-TTCCCACCACCTGCA
2591029 GCTACTGGGA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
61 72 0.96
62 3 0.04
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (60 bp):
CACATAAGGTCTTCCCACCACCTGCACTAAGTTTACACTCTAGTACTGACCCGGATATGA
Found at i:2591201 original size:22 final size:22
Alignment explanation
Indices: 2591170--2591213 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2591160 TGAAATAACT
*
2591170 TTCATAATAATCATTATATATA
1 TTCATAATAAACATTATATATA
*
2591192 TTCATGATAAACATTATATATA
1 TTCATAATAAACATTATATATA
2591214 ACAACCAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.43
Consensus pattern (22 bp):
TTCATAATAAACATTATATATA
Found at i:2595152 original size:21 final size:21
Alignment explanation
Indices: 2595126--2595166 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2595116 TTCAATTAAG
*
2595126 AATCAAGGAGCTTTACTTCAT
1 AATCAAGGAGCCTTACTTCAT
*
2595147 AATCAAGGCGCCTTACTTCA
1 AATCAAGGAGCCTTACTTCA
2595167 AAGCCATAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (21 bp):
AATCAAGGAGCCTTACTTCAT
Found at i:2607882 original size:59 final size:60
Alignment explanation
Indices: 2607741--2607906 Score: 156
Period size: 59 Copynumber: 2.8 Consensus size: 60
2607731 GCATTATAAG
* ** * * ** * *
2607741 TCCTCAAATTATGACTTCCATTCTAAATTAGTCTCTTAACTTTTGAACATTTTAATTTCA
1 TCCTCAAAATATGACACCCATTCTAAATTAGTCCCTAAACTTTTGAACATTCCAAATCCA
* * *
2607801 TCCTTAAACTATGACTCCCATTCTAAATTAGTCCCTAAAC-TTTGAACATTCCAAATCCA
1 TCCTCAAAATATGACACCCATTCTAAATTAGTCCCTAAACTTTTGAACATTCCAAATCCA
* * * * *
2607860 TTCTCAAAATATGACACTCATTCTATATT-GATCCATCAACTTTTGAA
1 TCCTCAAAATATGACACCCATTCTAAATTAG-TCCCTAAACTTTTGAA
2607907 TGTTCTAATT
Statistics
Matches: 87, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
58 1 0.01
59 45 0.52
60 41 0.47
ACGTcount: A:0.33, C:0.23, G:0.05, T:0.39
Consensus pattern (60 bp):
TCCTCAAAATATGACACCCATTCTAAATTAGTCCCTAAACTTTTGAACATTCCAAATCCA
Found at i:2615289 original size:21 final size:20
Alignment explanation
Indices: 2615265--2615312 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2615255 TCAAAGGACC
*
2615265 GATCCCTTTAACCAAAGGATA
1 GATCCCTTGAA-CAAAGGATA
*
2615286 GATCCCCTTGAA-AAAGGATT
1 GAT-CCCTTGAACAAAGGATA
2615306 GATCCCT
1 GATCCCT
2615313 AGGACAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 10 0.42
21 3 0.12
22 7 0.29
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
GATCCCTTGAACAAAGGATA
Found at i:2616639 original size:20 final size:21
Alignment explanation
Indices: 2616604--2616653 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
2616594 AAATGATTTT
2616604 CTTTTG-AAAGCAAAAATGGA
1 CTTTTGAAAAGCAAAAATGGA
*
2616624 -TTTTGAAAATCAAAAATGGA
1 CTTTTGAAAAGCAAAAATGGA
*
2616644 CTTTTCAAAA
1 CTTTTGAAAA
2616654 ATGATTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 5 0.19
20 13 0.50
21 8 0.31
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.30
Consensus pattern (21 bp):
CTTTTGAAAAGCAAAAATGGA
Found at i:2617360 original size:188 final size:188
Alignment explanation
Indices: 2617143--2617519 Score: 713
Period size: 188 Copynumber: 2.0 Consensus size: 188
2617133 GTTGTGATGA
2617143 ACATTTTGTAAAGTTTAAAGATTTTTTCATAAATGTGAATTCATCAAAATGAATTTTGGTCAAAA
1 ACATTTTGTAAAGTTTAAAGATTTTTTCATAAATGTGAATTCATCAAAATGAATTTTGGTCAAAA
2617208 TTCATTTTAATGCTTTGTTTTTACAATTTTTATTTTTTTGACCTTAATTTAAA-TTTATGCATGT
66 TTCATTTTAATGCTTTGTTTTTACAATTTTTA-TTTTTTGACCTTAATTTAAAGTTTATGCATGT
2617272 GACTTTATTGCCTATGATATCTCTCTAACAA-TGATGTCAATATTGAATGCATAACATT
130 GACTTTATTGCCTATGATATCTCTCTAACAATTGATGTCAATATTGAATGCATAACATT
2617330 ACATTTTGTAAAGTTTTAAAGATTTTTTCATAAATGTGAATTCATCAAAATGAATTTTGGTCAAA
1 ACATTTTGTAAAG-TTTAAAGATTTTTTCATAAATGTGAATTCATCAAAATGAATTTTGGTCAAA
2617395 ATTCATTTTAATGCTTTGTTTTTACAATTTTTATTTTTTGACCTTAATTTAAATGTTTATGCATG
65 ATTCATTTTAATGCTTTGTTTTTACAATTTTTATTTTTTGACCTTAATTTAAA-GTTTATGCATG
2617460 TGACTTTATTGCCTATGATATCTCTCTAACAATTGATGTCAATATTGAATGCATAACATT
129 TGACTTTATTGCCTATGATATCTCTCTAACAATTGATGTCAATATTGAATGCATAACATT
2617520 TTTGAAGTGC
Statistics
Matches: 186, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
187 33 0.18
188 84 0.45
189 42 0.23
190 27 0.15
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (188 bp):
ACATTTTGTAAAGTTTAAAGATTTTTTCATAAATGTGAATTCATCAAAATGAATTTTGGTCAAAA
TTCATTTTAATGCTTTGTTTTTACAATTTTTATTTTTTGACCTTAATTTAAAGTTTATGCATGTG
ACTTTATTGCCTATGATATCTCTCTAACAATTGATGTCAATATTGAATGCATAACATT
Found at i:2619205 original size:22 final size:21
Alignment explanation
Indices: 2619188--2619244 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
2619178 TTCTTTGGCT
2619188 CAAAGGATCGATCCCTTTGAC
1 CAAAGGATCGATCCCTTTGAC
*
2619209 CAAAGGATCGATCCCATTGA-
1 CAAAGGATCGATCCCTTTGAC
* *
2619229 AAAAGGATTGATCCCT
1 CAAAGGATCGATCCCT
2619245 CGAGGAAAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (21 bp):
CAAAGGATCGATCCCTTTGAC
Found at i:2621089 original size:18 final size:17
Alignment explanation
Indices: 2621063--2621101 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2621053 CTTGATTTTT
* *
2621063 TTTTGTTGAGTTTGAGTA
1 TTTTATTGAATTTGAG-A
2621081 TTTTATTGAATTTGAGA
1 TTTTATTGAATTTGAGA
2621098 TTTT
1 TTTT
2621102 GTCTTAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (17 bp):
TTTTATTGAATTTGAGA
Found at i:2624394 original size:16 final size:17
Alignment explanation
Indices: 2624373--2624406 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2624363 AGCAGGGGCG
*
2624373 GATGTACT-GGCCCCTA
1 GATGTACTAAGCCCCTA
2624389 GATGTACTAAGCCCCTA
1 GATGTACTAAGCCCCTA
2624406 G
1 G
2624407 GGGCCAGTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (17 bp):
GATGTACTAAGCCCCTA
Found at i:2624552 original size:21 final size:22
Alignment explanation
Indices: 2624526--2624570 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2624516 TTGAGTCGAG
*
2624526 TCAAGTAAAAAAAAT-GATTTT
1 TCAAGTAAAAAAAATCAATTTT
*
2624547 TCAAGTAAGAAAAATCAATTTT
1 TCAAGTAAAAAAAATCAATTTT
2624569 TC
1 TC
2624571 GAATCGAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (22 bp):
TCAAGTAAAAAAAATCAATTTT
Found at i:2625146 original size:46 final size:48
Alignment explanation
Indices: 2625079--2625175 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 48
2625069 TAAGAGAAAT
* *
2625079 TTGAGTTGACAAATGAAAAATAAAAA-AATTCATAT-TCTTCTTCTTC
1 TTGAGTTGACAAATAAAAAATAAAAAGAATTCACATGTCTTCTTCTTC
* * *
2625125 TTGAGTTGAGAATTAAAAAATAAAAAGTAATTCACGTGTCTTCTTCTTC
1 TTGAGTTGACAAATAAAAAATAAAAAG-AATTCACATGTCTTCTTCTTC
2625174 TT
1 TT
2625176 CTTCTAGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 23 0.53
48 7 0.16
49 13 0.30
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Consensus pattern (48 bp):
TTGAGTTGACAAATAAAAAATAAAAAGAATTCACATGTCTTCTTCTTC
Found at i:2629089 original size:73 final size:73
Alignment explanation
Indices: 2628970--2629176 Score: 414
Period size: 73 Copynumber: 2.8 Consensus size: 73
2628960 GTTAGAAATA
2628970 GATATTAAATCATTTTTACATATAGTTATTGTAGAAAATGTGGTTATAGAAGTACCTATTAATTA
1 GATATTAAATCATTTTTACATATAGTTATTGTAGAAAATGTGGTTATAGAAGTACCTATTAATTA
2629035 TTAATGTT
66 TTAATGTT
2629043 GATATTAAATCATTTTTACATATAGTTATTGTAGAAAATGTGGTTATAGAAGTACCTATTAATTA
1 GATATTAAATCATTTTTACATATAGTTATTGTAGAAAATGTGGTTATAGAAGTACCTATTAATTA
2629108 TTAATGTT
66 TTAATGTT
2629116 GATATTAAATCATTTTTACATATAGTTATTGTAGAAAATGTGGTTATAGAAGTACCTATTA
1 GATATTAAATCATTTTTACATATAGTTATTGTAGAAAATGTGGTTATAGAAGTACCTATTA
2629177 TTAATGTTGT
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 134 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (73 bp):
GATATTAAATCATTTTTACATATAGTTATTGTAGAAAATGTGGTTATAGAAGTACCTATTAATTA
TTAATGTT
Found at i:2632929 original size:2 final size:2
Alignment explanation
Indices: 2632922--2632949 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2632912 TTTATTGTTC
2632922 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2632950 CTGTTCTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2633345 original size:24 final size:24
Alignment explanation
Indices: 2633313--2633363 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
2633303 GCTTATCTTT
*
2633313 GGAGGAGGAAGAAGAAGAAGAGGA
1 GGAGGAGGAAGAAGAAGAAGAAGA
* *
2633337 GGAGGAGGAAGAGGGAGAAGAAGA
1 GGAGGAGGAAGAAGAAGAAGAAGA
2633361 GGA
1 GGA
2633364 AGAAGACACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (24 bp):
GGAGGAGGAAGAAGAAGAAGAAGA
Found at i:2633367 original size:9 final size:9
Alignment explanation
Indices: 2633314--2633369 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
2633304 CTTATCTTTG
*
2633314 GAGGAGGAA
1 GAGGAAGAA
*
2633323 GAAGAAGAA
1 GAGGAAGAA
* *
2633332 GAGGAGGAG
1 GAGGAAGAA
2633341 GAGGAAG-A
1 GAGGAAGAA
*
2633349 GGGAGAAGAA
1 GAG-GAAGAA
2633359 GAGGAAGAA
1 GAGGAAGAA
2633368 GA
1 GA
2633370 CACAAGTTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
8 2 0.06
9 31 0.86
10 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (9 bp):
GAGGAAGAA
Found at i:2643758 original size:14 final size:15
Alignment explanation
Indices: 2643739--2643806 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 15
2643729 GTACCTACCG
2643739 AATTAAAAAC-AAAA
1 AATTAAAAACAAAAA
*
2643753 AATTAAAAGCAAACAA
1 AATTAAAAACAAA-AA
*
2643769 AATT-AAAATAAAAA
1 AATTAAAAACAAAAA
* *
2643783 AATCAAAATCAAAATA
1 AATTAAAAACAAAA-A
2643799 AATTAAAA
1 AATTAAAA
2643807 CGGATATGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
14 14 0.33
15 15 0.35
16 14 0.33
ACGTcount: A:0.74, C:0.07, G:0.01, T:0.18
Consensus pattern (15 bp):
AATTAAAAACAAAAA
Found at i:2643775 original size:30 final size:30
Alignment explanation
Indices: 2643739--2643806 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
2643729 GTACCTACCG
*
2643739 AATTAAAA-ACAAAAAATTAAAAGCAAACA-A
1 AATTAAAATA-AAAAAATCAAAAGCAAA-ATA
*
2643769 AATTAAAATAAAAAAATCAAAATCAAAATA
1 AATTAAAATAAAAAAATCAAAAGCAAAATA
2643799 AATTAAAA
1 AATTAAAA
2643807 CGGATATGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 1 0.03
30 32 0.94
31 1 0.03
ACGTcount: A:0.74, C:0.07, G:0.01, T:0.18
Consensus pattern (30 bp):
AATTAAAATAAAAAAATCAAAAGCAAAATA
Found at i:2647928 original size:21 final size:21
Alignment explanation
Indices: 2647902--2647953 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
2647892 TTTTGAAATC
*
2647902 TTTCTTGGGAAGCTACTAATT
1 TTTCTTGGGAAGCGACTAATT
2647923 TTTCTT-GGAAGCGACTAATT
1 TTTCTTGGGAAGCGACTAATT
*
2647943 TCTCTTGGGAA
1 TTTCTTGGGAA
2647954 ATCGCCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.40
Consensus pattern (21 bp):
TTTCTTGGGAAGCGACTAATT
Found at i:2650987 original size:21 final size:21
Alignment explanation
Indices: 2650963--2651004 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2650953 CCAGAATGGG
*
2650963 GGGAATCGGTACCCCATCATA
1 GGGAATCGATACCCCATCATA
*
2650984 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCATCATA
2651005 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (21 bp):
GGGAATCGATACCCCATCATA
Found at i:2651194 original size:35 final size:34
Alignment explanation
Indices: 2651117--2651201 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
2651107 AAACCATGCA
*
2651117 GGGGGAATCTGTACCCGGGGAATCGATACCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
* *
2651151 GGGGGAATCTGTTCTCGGGGAATTGATACCCACTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCC-CTG
2651186 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
2651202 CCTGGACAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 28 0.61
35 18 0.39
ACGTcount: A:0.19, C:0.24, G:0.35, T:0.22
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:2652025 original size:23 final size:23
Alignment explanation
Indices: 2651960--2652025 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 23
2651950 CACCACAGCT
* *
2651960 CGTATAAATGCACCGAAGTACCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
2651983 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
2652006 CGTAGAAATGCACCGTAGTG
1 CGTAGAAATGCACCGAAGTG
2652026 TCATATAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.32, C:0.24, G:0.26, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2653853 original size:14 final size:14
Alignment explanation
Indices: 2653831--2653870 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
2653821 TCAAAGTAAC
*
2653831 TTGTCAATCATTCA
1 TTGTTAATCATTCA
2653845 TTGTTAATCATTCA
1 TTGTTAATCATTCA
2653859 TTGTTAATCATT
1 TTGTTAATCATT
2653871 TCACGTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (14 bp):
TTGTTAATCATTCA
Found at i:2654200 original size:14 final size:14
Alignment explanation
Indices: 2654181--2654212 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
2654171 TCCTTATATT
2654181 AATTTTAAGGAAAG
1 AATTTTAAGGAAAG
2654195 AATTTTAAGGAAAG
1 AATTTTAAGGAAAG
2654209 AATT
1 AATT
2654213 AATGTAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (14 bp):
AATTTTAAGGAAAG
Found at i:2659620 original size:16 final size:17
Alignment explanation
Indices: 2659593--2659625 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
2659583 AACAAACCCA
2659593 AAAACAAAAGACCCATT
1 AAAACAAAAGACCCATT
2659610 AAAAC-AAAGACCCATT
1 AAAACAAAAGACCCATT
2659626 TTTGGATTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.58, C:0.24, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAACAAAAGACCCATT
Found at i:2660407 original size:70 final size:66
Alignment explanation
Indices: 2660277--2660484 Score: 206
Period size: 70 Copynumber: 3.1 Consensus size: 66
2660267 TGAAAAATGA
* * * * * * *
2660277 ATCAATACTTTTGAATTTAAAAAATGAAAAATAAGAAAGATGCAAAATGT-TAATATTTTTCTAC
1 ATCAATACTTTCGAATTTAAAAAATGGAAAATGAG-AAGATGC-AAA-GTATCATAATTTTCCAA
*
2660341 AAGT
63 AAAT
* * *
2660345 GTCGATACTTTCGAATTTAAAAAAAATGGAAAATGAGAATGTTGCAAAGTATCGATAATTTTCCA
1 ATCAATACTTTCGAATTT--AAAAAATGGAAAATGAGAA-GATGCAAAGTATC-ATAATTTTCCA
2660410 AAAAT
62 AAAAT
*
2660415 ATCAATACTTTCAAATTTAAAAAATGG-AAATGAGAAGACTGCAAAGTATCA-AATTTTTCCAAA
1 ATCAATACTTTCGAATTTAAAAAATGGAAAATGAGAAGA-TGCAAAGTATCATAA-TTTTCCAAA
2660478 AAT
64 AAT
2660481 ATCA
1 ATCA
2660485 TAACATAAGT
Statistics
Matches: 118, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
65 2 0.02
66 18 0.15
67 20 0.17
68 26 0.22
69 6 0.05
70 46 0.39
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (66 bp):
ATCAATACTTTCGAATTTAAAAAATGGAAAATGAGAAGATGCAAAGTATCATAATTTTCCAAAAA
T
Found at i:2660726 original size:73 final size:73
Alignment explanation
Indices: 2660542--2660733 Score: 201
Period size: 73 Copynumber: 2.6 Consensus size: 73
2660532 ATGTAACGAT
* * * * **
2660542 ATTTTAACTATCGATCATTTTCATCAACTTTTTCAATATATAAAAGTATCAATCATTATTGCATA
1 ATTTTAAATTTCGATCA-TTTCTTCAACTTTTTCAATATTTAAAAGTATCAATCATTATAACATA
* *
2660607 AGTATCAAT
65 AATATCAAC
* * * *
2660616 ATTTTTAATTTTGA-CATTTTTATCAACTTTTACAATATTTAAAAGTATCAATCATTATAACATA
1 ATTTTAAATTTCGATCATTTCT-TCAACTTTTTCAATATTTAAAAGTATCAATCATTATAACATA
2660680 AATAT-AACC
65 AATATCAA-C
* *
2660689 ATTTTAAATTTCGATC-TTATCTTCAATTTTTTTAATATTTAAAAG
1 ATTTTAAATTTCGATCATT-TCTTCAACTTTTTCAATATTTAAAAG
2660734 ATTCGACCAT
Statistics
Matches: 96, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
72 5 0.05
73 78 0.81
74 13 0.14
ACGTcount: A:0.38, C:0.12, G:0.04, T:0.45
Consensus pattern (73 bp):
ATTTTAAATTTCGATCATTTCTTCAACTTTTTCAATATTTAAAAGTATCAATCATTATAACATAA
ATATCAAC
Found at i:2661272 original size:40 final size:42
Alignment explanation
Indices: 2661226--2661321 Score: 151
Period size: 40 Copynumber: 2.3 Consensus size: 42
2661216 CATATTCACA
* *
2661226 TTGCGATAGTCCAAGTTCGTGTTGTGA-TT-TTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
2661266 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
2661308 TTGCGATAGTCCAA
1 TTGCGATAGTCCAA
2661322 AATCGCAACG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 24 0.48
41 2 0.04
42 24 0.48
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:2661309 original size:21 final size:20
Alignment explanation
Indices: 2661246--2661314 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 20
2661236 CCAAGTTCGT
*
2661246 GTTGTGATT-TTCCAAATTC
1 GTTGCGATTATTCCAAATTC
* * *
2661265 GTTGCGA-TAGTCGAAGTTCGC
1 GTTGCGATTATTCCAAATT--C
2661286 GTTGCGATTTATTCCAAATTC
1 GTTGCGA-TTATTCCAAATTC
2661307 GTTGCGAT
1 GTTGCGAT
2661315 AGTCCAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
18 1 0.03
19 12 0.32
20 1 0.03
21 16 0.42
23 8 0.21
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.39
Consensus pattern (20 bp):
GTTGCGATTATTCCAAATTC
Found at i:2661865 original size:6 final size:6
Alignment explanation
Indices: 2661856--2661886 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
2661846 CGCCGCCGTC
*
2661856 TCGTGG TCGTAG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
2661887 AATACGTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.03, C:0.16, G:0.45, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:2662038 original size:42 final size:42
Alignment explanation
Indices: 2661979--2662279 Score: 520
Period size: 42 Copynumber: 7.3 Consensus size: 42
2661969 TGCGATTTTG
2661979 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
2662021 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
2662063 GACTATCGCAACAAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
2662105 GACTATCGCAACGAATTTGGAATAAATTGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
2662147 GACTATCGCAACGAATTTGGAAAAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2662189 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
2662229 GACTATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
2662269 GACTATCGCAA
1 GACTATCGCAA
2662280 TGCGAATATG
Statistics
Matches: 249, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
40 69 0.28
41 1 0.00
42 179 0.72
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:2662269 original size:21 final size:21
Alignment explanation
Indices: 2662002--2662285 Score: 151
Period size: 21 Copynumber: 13.7 Consensus size: 21
2661992 AATTTGGAAT
*
2662002 AAATCGCAACGCGAACTTCGA
1 AAATCGCAACGCGAACTTGGA
** * *
2662023 CTATCGCAA--CGAATTTGAAA
1 AAATCGCAACGCGAACTTG-GA
*
2662043 TAAATCGCAACGCGAACTTCGA
1 -AAATCGCAACGCGAACTTGGA
** *
2662065 CTATCGCAA--CAAACTTGGAA
1 AAATCGCAACGCGAACTTGG-A
*
2662085 TAAATCGCAACGCGAACTTCGA
1 -AAATCGCAACGCGAACTTGGA
** *
2662107 CTATCGCAA--CGAATTTGGAA
1 AAATCGCAACGCGAACTTGG-A
* *
2662127 TAAATTGCAACGCGAACTTCGA
1 -AAATCGCAACGCGAACTTGGA
** *
2662149 CTATCGCAA--CGAATTTGGAAA
1 AAATCGCAACGCGAACTTGG--A
*
2662170 AAATCGCAACGCGAACTTCGA
1 AAATCGCAACGCGAACTTGGA
** *
2662191 CTATCGCAA--CGAATTTGGA
1 AAATCGCAACGCGAACTTGGA
*
2662210 AAATCGCAACGCGAACTTCGA
1 AAATCGCAACGCGAACTTGGA
** *
2662231 CTATCGCAA--CGAATTTGGA
1 AAATCGCAACGCGAACTTGGA
2662250 AAATCGCAACGCGAACTTGGA
1 AAATCGCAACGCGAACTTGGA
** *
2662271 CTATCGCAATGCGAA
1 AAATCGCAACGCGAA
2662286 TATGTAAATC
Statistics
Matches: 189, Mismatches: 54, Indels: 40
0.67 0.19 0.14
Matches are distributed among these distances:
19 57 0.30
20 3 0.02
21 99 0.52
22 3 0.02
23 27 0.14
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (21 bp):
AAATCGCAACGCGAACTTGGA
Found at i:2662319 original size:21 final size:21
Alignment explanation
Indices: 2662294--2662346 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
2662284 AATATGTAAA
2662294 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
2662315 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
2662336 TCGCGTTGCGA
1 TCGCATTGCGA
2662347 ATCTGGAAAC
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:0.21, C:0.23, G:0.28, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:2662895 original size:148 final size:150
Alignment explanation
Indices: 2662705--2663047 Score: 406
Period size: 157 Copynumber: 2.2 Consensus size: 150
2662695 ATTTTTAGTA
* *
2662705 AAAAAAAAGTAGAAATTAAAGTTACATAGGTATTCTACTGTGGTATATGAGCA-TCCAA-TT-TA
1 AAAAAAAAG-AGAAATTGAAGTTACATAGGTATTCTACTGTGGTATATGAGCAGTCAAATTTGTA
* * *
2662767 AAAAAGGACCTAAAATAAATGTTGAATTGAAGAAATAAGAAAATTATGAAAAATTGAGGGACTAA
65 AAAAAGGACCTAAAATAAAGGATGAATTGAAGAAATAAGAAAATTATGAAAAATTAAGGGACTAA
2662832 ATTGAAAAAGAAAAAAATTATT
130 ATTGAAAAAGAAAAAAA-TATT
* * **
2662854 AAAAAAAAGAGGAATTGAAGTTATATAGGTATTCTGTTGTGGTATATGAGCATGTGGTTCAAATT
1 AAAAAAAAGAGAAATTGAAGTTACATAGGTATTCTACTGTGGTATATGAGCA----G-TCAAATT
** * * *
2662919 TGGTAAAAACTGACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATGAAAAATTAATGG
61 T-GTAAAAAAGGACCTAAAATAAAGGATGAATTGAAGAAATAAGAAAATTATGAAAAATTAAGGG
* *
2662984 ACTAAATTGAAAAATAAAAAAATGTT
125 ACTAAATTGAAAAAGAAAAAAATATT
* *
2663010 ATCAAAAAAGAGAAATTGAAAG-TACATATGTATTCTAC
1 A-AAAAAAAGAGAAATTG-AAGTTACATAGGTATTCTAC
2663048 GATGATTTAT
Statistics
Matches: 161, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
148 38 0.24
149 9 0.06
154 4 0.02
155 2 0.01
156 4 0.02
157 101 0.63
158 3 0.02
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (150 bp):
AAAAAAAAGAGAAATTGAAGTTACATAGGTATTCTACTGTGGTATATGAGCAGTCAAATTTGTAA
AAAAGGACCTAAAATAAAGGATGAATTGAAGAAATAAGAAAATTATGAAAAATTAAGGGACTAAA
TTGAAAAAGAAAAAAATATT
Found at i:2662968 original size:157 final size:158
Alignment explanation
Indices: 2662765--2663113 Score: 440
Period size: 157 Copynumber: 2.2 Consensus size: 158
2662755 GCATCCAATT
* * * *
2662765 TAAAAAA-GGACCTAAAATAAATGTTGAATTGAAGAAATAAGAAAATTATGAAAAATTGAGGGAC
1 TAAAAAATGGACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATTATGAAAAATTAAGGGAC
* * **
2662829 TAAATTGAAAAAGAAAAAAATTATTA-AAAAAAAGAGGAATTG-AAGTTATATAGGTATTCTGTT
66 TAAATTGAAAAAGAAAAAAA-TATTATAAAAAAAGAGAAATTGAAAG-TACATAGGTATTCT-AC
*
2662892 G-TGGTATATGAGCATGTGGTTC-AAATTTGG
128 GATGATATATGAGCATGTGG-TCAAAATTTGG
* * *
2662922 TAAAAACT-GACTTAAAATAAAGGATGAATTGAAGAAATAAGGAAATTATGAAAAATTAATGGAC
1 TAAAAAATGGACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATTATGAAAAATTAAGGGAC
* * * *
2662986 TAAATTGAAAAATAAAAAAATGTTATCAAAAAAGAGAAATTGAAAGTACATATGTATTCTACGAT
66 TAAATTGAAAAAGAAAAAAATATTATAAAAAAAGAGAAATTGAAAGTACATAGGTATTCTACGAT
*
2663051 GATTTATGAGCATGTGGTCAAAATTTGG
131 GATATATGAGCATGTGGTCAAAATTTGG
** *
2663079 TAAAAAATGGACTTAAAACGAAGGAGGAATTGAAG
1 TAAAAAATGGACTTAAAATAAAGGATGAATTGAAG
2663114 GGATAATGAA
Statistics
Matches: 165, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
156 7 0.04
157 132 0.80
158 26 0.16
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (158 bp):
TAAAAAATGGACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATTATGAAAAATTAAGGGAC
TAAATTGAAAAAGAAAAAAATATTATAAAAAAAGAGAAATTGAAAGTACATAGGTATTCTACGAT
GATATATGAGCATGTGGTCAAAATTTGG
Found at i:2665324 original size:35 final size:36
Alignment explanation
Indices: 2665240--2665326 Score: 124
Period size: 36 Copynumber: 2.4 Consensus size: 36
2665230 AAAACATCAA
2665240 CACTTCCGATTCAAGTCGAACGGAATGAAGCATCGG
1 CACTTCCGATTCAAGTCGAACGGAATGAAGCATCGG
*
2665276 CACTTCCGATTCAAGTCGAACGGAA-GAATGTATC-G
1 CACTTCCGATTCAAGTCGAACGGAATGAA-GCATCGG
* *
2665311 CACTTTCGTTTCAAGT
1 CACTTCCGATTCAAGT
2665327 GTTCGTCTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
35 18 0.38
36 29 0.62
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (36 bp):
CACTTCCGATTCAAGTCGAACGGAATGAAGCATCGG
Found at i:2670107 original size:31 final size:31
Alignment explanation
Indices: 2670072--2670133 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2670062 AAAACAATTG
* *
2670072 AACATGCTATGCATTGTCTAAATGCGAACCT
1 AACATGCTATGCATTATCTAAATGCAAACCT
* *
2670103 AACATGCTTTGCATTATCTGAATGCAAACCT
1 AACATGCTATGCATTATCTAAATGCAAACCT
2670134 GACTAGCATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (31 bp):
AACATGCTATGCATTATCTAAATGCAAACCT
Found at i:2671359 original size:19 final size:19
Alignment explanation
Indices: 2671318--2671358 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
2671308 GATATTGTCA
*
2671318 CCCTGAGTATCGATACTCC
1 CCCTGAGTATCAATACTCC
2671337 CCCTGTAGTATCAATACTCC
1 CCCTG-AGTATCAATACTCC
2671357 CC
1 CC
2671359 TTGGCACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.22, C:0.39, G:0.12, T:0.27
Consensus pattern (19 bp):
CCCTGAGTATCAATACTCC
Found at i:2683306 original size:17 final size:17
Alignment explanation
Indices: 2683284--2683317 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2683274 TTTACCGAAT
2683284 CAAAAAGATTATGGCAG
1 CAAAAAGATTATGGCAG
2683301 CAAAAAGATTATGGCAG
1 CAAAAAGATTATGGCAG
2683318 TTTTGTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.24, T:0.18
Consensus pattern (17 bp):
CAAAAAGATTATGGCAG
Found at i:2684528 original size:36 final size:33
Alignment explanation
Indices: 2684446--2684550 Score: 88
Period size: 36 Copynumber: 3.1 Consensus size: 33
2684436 AATACGAAAT
*
2684446 AAATAAACAACAT-AAAAAATAAAAAAATGATA
1 AAATAAACAAAATAAAAAAATAAAAAAATGATA
* ** *
2684478 AAGTAAAGGGAAATAAACAAAATAAATAGAATGATA
1 AAATAAA-CAAAATAAA-AAAATAAA-AAAATGATA
* * *
2684514 AAATAAACAAAA-ATAAAATATAAAAAAAGGATC
1 AAATAAACAAAATA-AAAAAATAAAAAAATGATA
2684547 AAAT
1 AAAT
2684551 TGAAGTAACC
Statistics
Matches: 56, Mismatches: 12, Indels: 9
0.73 0.16 0.12
Matches are distributed among these distances:
32 6 0.11
33 13 0.23
34 10 0.18
35 13 0.23
36 14 0.25
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (33 bp):
AAATAAACAAAATAAAAAAATAAAAAAATGATA
Found at i:2685860 original size:4 final size:4
Alignment explanation
Indices: 2685851--2685913 Score: 53
Period size: 4 Copynumber: 16.8 Consensus size: 4
2685841 ATAGACCTAA
* * * * *
2685851 AAAT AAAT AAAT AAAT AAAT AAAC GAGT AAAT -AAT -AAT AAA- CAAG
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
2685896 AAAT AAAT AAA- AAAT AAA
1 AAAT AAAT AAAT AAAT AAA
2685914 ATACTATATA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
3 11 0.23
4 36 0.77
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:2686043 original size:33 final size:31
Alignment explanation
Indices: 2685937--2686068 Score: 112
Period size: 33 Copynumber: 4.2 Consensus size: 31
2685927 TATATTTAAA
* *
2685937 AAAAATGTTTTAAAATTATA-TAT-A-TTTC
1 AAAAACGTTTTAAAACTATATTATAATTTTC
**
2685965 AAAAATATTTTCAAAACCATATACTATATAA-TTTC
1 AAAAACGTTTT-AAAA-C-TATA-T-TATAATTTTC
*
2686000 AAAAATGTTTTAAAACTATATGTTATAATTTTC
1 AAAAACGTTTTAAAACTATA--TTATAATTTTC
2686033 AAAAACGTTTTAAAACTATATTAT-ATGTTTC
1 AAAAACGTTTTAAAACTATATTATAAT-TTTC
2686064 AAAAA
1 AAAAA
2686069 AAAAATTTCA
Statistics
Matches: 89, Mismatches: 5, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
28 10 0.11
29 4 0.04
30 2 0.02
31 17 0.19
32 9 0.10
33 25 0.28
34 7 0.08
35 15 0.17
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (31 bp):
AAAAACGTTTTAAAACTATATTATAATTTTC
Found at i:2686152 original size:37 final size:38
Alignment explanation
Indices: 2685961--2686350 Score: 257
Period size: 36 Copynumber: 10.9 Consensus size: 38
2685951 ATTATATATA
* * *
2685961 TTTCAAAAAT-ATTTTCAAAACCATATACTATATAA--
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
*
2685996 TTTCAAAAATG-TTTT-AAAACTATAT-GT-TATAA-T
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
*
2686029 TTTCAAAAACG-TTTT-AAAAC--TATATTATAT--G-
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
** * * * *
2686060 TTTCAAAAAAAAAATTT--CAACTGTATATTATATAA-A
1 TTTC-AAAAATGATTTTAAAAACTATATATTATATAAGT
*
2686096 TTTC-AAAATGATTTT-AAAACTATTTATTATATAAGT
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
* * *
2686132 TTTC-AAAATGGTTTTAAAAACTATATA--ATATATGG
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
* * *
2686167 TTTCAAAAAT-ATCTTCAAAAACTATATAATATATATGT
1 TTTCAAAAATGAT-TTTAAAAACTATATATTATATAAGT
* * *
2686205 TTTCAAAAA-AACGTTTTCAAAACTATA-A-TATATATGT
1 TTTCAAAAATGA--TTTTAAAAACTATATATTATATAAGT
2686242 TTTCAAAAATG-TTTTCAAAAACTATATA-TATATAAGT
1 TTTCAAAAATGATTTT-AAAAACTATATATTATATAAGT
* *
2686279 TTTC-AAAATGATTTTCAAAATTATATATTATATATA-T
1 TTTCAAAAATGATTTTAAAAACTATATATTATATA-AGT
* * *
2686316 TTTCTAAAATGTCTTTTTTAAAACTATATATTATA
1 TTTCAAAAATG--ATTTTAAAAACTATATATTATA
2686351 GTTTTAAAAA
Statistics
Matches: 292, Mismatches: 32, Indels: 57
0.77 0.08 0.15
Matches are distributed among these distances:
31 7 0.02
32 14 0.05
33 26 0.09
34 27 0.09
35 44 0.15
36 62 0.21
37 56 0.19
38 25 0.09
39 11 0.04
40 20 0.07
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (38 bp):
TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
Found at i:2686246 original size:75 final size:74
Alignment explanation
Indices: 2686111--2686330 Score: 250
Period size: 75 Copynumber: 3.0 Consensus size: 74
2686101 AAATGATTTT
* * ** * *
2686111 AAAACTATTTATTATATAAGTTTTC-AAAATGGTTTTAAAAACTAT-ATAATATATGGTTTCAAA
1 AAAACTATATAATATATAAGTTTTCAAAAAAAGTTTTCAAAACTATAAT-ATATATGTTTTCAAA
*
2686174 AATATCTTCA
65 AATGTCTTCA
*
2686184 AAAACTATATAATATATATGTTTTCAAAAAAACGTTTTCAAAACTATAATATATATGTTTTCAAA
1 AAAACTATATAATATATAAGTTTTCAAAAAAA-GTTTTCAAAACTATAATATATATGTTTTCAAA
*
2686249 AATGTTTTCA
65 AATGTCTTCA
** * * *
2686259 AAAACTATAT-ATATATAAGTTTTCAAAATGA-TTTTCAAAATTATATATTATATATATTTTCTA
1 AAAACTATATAATATATAAGTTTTCAAAAAAAGTTTTCAAAACTATA-A-TATATATGTTTTCAA
2686322 AAATGTCTT
64 AAATGTCTT
2686331 TTTTAAAACT
Statistics
Matches: 126, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
72 13 0.10
73 23 0.18
74 43 0.34
75 45 0.36
76 2 0.02
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (74 bp):
AAAACTATATAATATATAAGTTTTCAAAAAAAGTTTTCAAAACTATAATATATATGTTTTCAAAA
ATGTCTTCA
Found at i:2686255 original size:12 final size:12
Alignment explanation
Indices: 2686238--2686262 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2686228 TATAATATAT
2686238 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2686250 ATGTTTTCAAAA
1 ATGTTTTCAAAA
2686262 A
1 A
2686263 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:2686311 original size:111 final size:110
Alignment explanation
Indices: 2686123--2686398 Score: 289
Period size: 111 Copynumber: 2.5 Consensus size: 110
2686113 AACTATTTAT
* * *
2686123 TATATAAGTTTTC-AAAATGGTTTTAAAAACTATATA-ATATATGGTTTCAAAAATATCTTCAAA
1 TATATATGTTTTCAAAAAT-GTTTTAAAAACTATATATATATAAGTTTTC-AAAATATCTTCAAA
*
2686186 AACTATATAATATATATGTTTTC-AAAAAAACGTTTTCAAAACTATAA
64 AACTATATAATATATATATTTTCTAAAAAAACGTTTTCAAAACTAT-A
*
2686233 TATATATGTTTTCAAAAATGTTTTCAAAAACTATATATATATAAGTTTTCAAAATGATTTTC-AA
1 TATATATGTTTTCAAAAATGTTTT-AAAAACTATATATATATAAGTTTTCAAAAT-ATCTTCAAA
* * *** * *
2686297 AATTATATATTATATATATTTTCTAAAATGTCTTTTTTAAAACTATA
64 AACTATATAATATATATATTTTCTAAAAAAACGTTTTCAAAACTATA
* * *
2686344 TAT-TATAGTTTT-AAAAA-CTATT-AAAACTATATATATATACGTAGTTTCAAAATAT
1 TATATAT-GTTTTCAAAAATGTTTTAAAAACTATATATATATAAGT--TTTCAAAATAT
2686399 GTATATATAA
Statistics
Matches: 143, Mismatches: 15, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
107 19 0.13
108 2 0.01
109 12 0.08
110 25 0.17
111 53 0.37
112 32 0.22
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (110 bp):
TATATATGTTTTCAAAAATGTTTTAAAAACTATATATATATAAGTTTTCAAAATATCTTCAAAAA
CTATATAATATATATATTTTCTAAAAAAACGTTTTCAAAACTATA
Found at i:2687451 original size:164 final size:164
Alignment explanation
Indices: 2687027--2688257 Score: 1762
Period size: 164 Copynumber: 7.4 Consensus size: 164
2687017 TGCCTCTGAA
* * * * *
2687027 CTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
1 CTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTG
* * * * ** * * *
2687092 CAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCT
65 TAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTC--T--TTGGCAGATAGCCCT
* * * * * * *
2687157 TCTAGACTTAAGTTGTGCTGCAAATGATATGTCCTCGAAG
126 TCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTAGGAG
* * * * *
2687197 CTGAGTGTAATCGAACTCGAAGGGGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATG
1 CTGAGCGTAGTCGAACTC-AA--AGGTC-TTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATG
* * * *
2687262 CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTT
62 CTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTT
* * * *
2687327 CTTGACTTAAGCTATCCTGCAAATGAGGTGCCTTGGAG
127 CTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAG
*
2687365 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGTCTTGAGTTATGCTGT
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
*
2687430 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCG
66 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
2687495 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAAG
131 ACTTAAGCTATTCTGCAAATGATGTGCCTAGG-AG
* * * *
2687530 CTGAGCGTAATCGAACTCGAAGGGGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATG
1 CTGAGCGTAGTCGAACTC-AA--AGGTC-TTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATG
* * * *
2687595 CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTT
62 CTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTT
* * * *
2687660 CTTGACTTAAGCTATTATGCAAATGAGGTGCCTTGGAG
127 CTCGACTTAAGCTATTCTGCAAATGATGTGCCTAGGAG
*
2687698 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGTCTTGAGTTATGCTGT
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
*
2687763 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCG
66 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
2687828 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAG
131 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAG
2687862 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
*
2687927 AAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
66 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
2687992 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAG
131 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAG
2688026 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
*
2688091 AAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
66 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
*
2688156 ACTTAAGCTATTCTGCAAATGATGTGCCTTGGAG
131 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAG
* * ** * * * * *
2688190 CTGAGCGTAGTCGAACTCGAAGGTC-TTGGTGGCAGGTAGCCCTTCTGGCCTTGAGTTAAGCTGC
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
2688254 AAAT
66 AAAT
2688258 AGTTTGTTTA
Statistics
Matches: 979, Mismatches: 74, Indels: 23
0.91 0.07 0.02
Matches are distributed among these distances:
163 35 0.04
164 600 0.61
165 27 0.03
166 2 0.00
167 4 0.00
168 45 0.05
169 163 0.17
170 18 0.02
171 2 0.00
173 83 0.08
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (164 bp):
CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAG
Found at i:2687670 original size:333 final size:332
Alignment explanation
Indices: 2687027--2688212 Score: 1912
Period size: 333 Copynumber: 3.6 Consensus size: 332
2687017 TGCCTCTGAA
* * * * *
2687027 CTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTG
1 CTGAGCGTAGTCGAACTCAAAGGTC-TTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTG
* * * * * * * *
2687092 CAAATGATGTGCCCTCGAAGCTGAGCGTAATCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCT
65 TAAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTC--T--TTGGCAGATAGCCCT
* * * * * * * *
2687157 TCTAGACTTAAGTTGTGCTGCAAATGATATGTCCTCGAAGCTGAGTGTAATCGAACTCGAAGGGG
126 TCTCGACTTAAGCTATTCTGCAAATGATGTG-CCTAGGAGCTGAGCGTAATCGAACTCGAAGGGG
2687222 GTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCT
190 GTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCT
*
2687287 GAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATCCTGCAAATG
255 GAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATG
2687352 AGGTGCCTTGGAG
320 AGGTGCCTTGGAG
*
2687365 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGTCTTGAGTTATGCTGT
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
2687430 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCG
66 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCG
2687495 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAAGCTGAGCGTAATCGAACTCGAAGGGGGTCTT
131 ACTTAAGCTATTCTGCAAATGATGTGCCTAGG-AGCTGAGCGTAATCGAACTCGAAGGGGGTCTT
2687560 TTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
195 TTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
*
2687625 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTATGCAAATGAGGTG
260 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGAGGTG
2687690 CCTTGGAG
325 CCTTGGAG
*
2687698 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGTCTTGAGTTATGCTGT
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
2687763 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCG
66 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCG
* *
2687828 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAGTCGAACTC-AA--AGGTC-TT
131 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAATCGAACTCGAAGGGGGTCTTT
* * * * *
2687889 TGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGT
196 TGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGT
* * * *
2687954 AATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGC
261 AATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGAGGTGC
*
2688019 CTAGGAG
326 CTTGGAG
2688026 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
1 CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
* *
2688091 AAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTGAGGGTCTTTGGCAGATAGCCCTTCTCG
66 AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCG
* *
2688156 ACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
131 ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAATCGAACTCGAAGG
2688213 TCTTGGTGGC
Statistics
Matches: 803, Mismatches: 41, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
328 306 0.38
329 6 0.01
331 2 0.00
332 23 0.03
333 368 0.46
335 1 0.00
337 75 0.09
338 22 0.03
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (332 bp):
CTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
AAATGATATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCG
ACTTAAGCTATTCTGCAAATGATGTGCCTAGGAGCTGAGCGTAATCGAACTCGAAGGGGGTCTTT
TGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGT
AATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGCTATTCTGCAAATGAGGTGC
CTTGGAG
Found at i:2691656 original size:21 final size:19
Alignment explanation
Indices: 2691609--2691648 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2691599 AGTTAATGTG
* *
2691609 AATGCAGAGAAAATAACAA
1 AATGCAAAGAAAATAAAAA
2691628 AATGCAAAGAAAATAAAAA
1 AATGCAAAGAAAATAAAAA
2691647 AA
1 AA
2691649 AATGCAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.10
Consensus pattern (19 bp):
AATGCAAAGAAAATAAAAA
Found at i:2695569 original size:22 final size:22
Alignment explanation
Indices: 2695539--2695589 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
2695529 GGCATGTGAA
*
2695539 ATTTATCCCGAATGACCTATGT
1 ATTTATCCCGAAAGACCTATGT
* *
2695561 ATTTGTCCCGAAAGACCTCTGT
1 ATTTATCCCGAAAGACCTATGT
2695583 ATATTAT
1 AT-TTAT
2695590 TTATGTCCCG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (22 bp):
ATTTATCCCGAAAGACCTATGT
Found at i:2697245 original size:31 final size:32
Alignment explanation
Indices: 2697173--2697246 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
2697163 TTACATGCGA
* ** * *
2697173 GCCTACCCAAGAAAATTCTTGGGGCCATAGTG
1 GCCTACCCAAGAAAAATCTCAGGGCCACAGAG
2697205 GCCTACCCAAGAAAAATCTCAGGGCCACAGAG
1 GCCTACCCAAGAAAAATCTCAGGGCCACAGAG
2697237 G-CTACCCAAG
1 GCCTACCCAAG
2697247 GGTCACCTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 9 0.24
32 28 0.76
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (32 bp):
GCCTACCCAAGAAAAATCTCAGGGCCACAGAG
Found at i:2697418 original size:12 final size:12
Alignment explanation
Indices: 2697388--2697444 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
2697378 ACAGAGATAT
*
2697388 CAGAAATCAGAA
1 CAGAAATCAGAG
* *
2697400 CATAAATTAGAG
1 CAGAAATCAGAG
* *
2697412 CAAAAATCAGAA
1 CAGAAATCAGAG
2697424 CAGAAATCAGAG
1 CAGAAATCAGAG
2697436 CAGAAATCA
1 CAGAAATCA
2697445 TATATAATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.56, C:0.16, G:0.16, T:0.12
Consensus pattern (12 bp):
CAGAAATCAGAG
Found at i:2697418 original size:24 final size:24
Alignment explanation
Indices: 2697391--2697444 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2697381 GAGATATCAG
* *
2697391 AAATCAGAACATAAATTAGAGCAA
1 AAATCAGAACAGAAATCAGAGCAA
*
2697415 AAATCAGAACAGAAATCAGAGCAG
1 AAATCAGAACAGAAATCAGAGCAA
2697439 AAATCA
1 AAATCA
2697445 TATATAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13
Consensus pattern (24 bp):
AAATCAGAACAGAAATCAGAGCAA
Found at i:2698960 original size:13 final size:13
Alignment explanation
Indices: 2698942--2698986 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
2698932 TTGACGTTTT
2698942 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
2698955 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
* *
2698968 AGTAAAGAGTCAAC
1 GGTCAA-AGTCAAC
2698982 GGTCA
1 GGTCA
2698987 CCGATCAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
13 17 0.63
14 10 0.37
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:2699053 original size:14 final size:14
Alignment explanation
Indices: 2699020--2699080 Score: 70
Period size: 14 Copynumber: 4.4 Consensus size: 14
2699010 CAACAGTCAA
* *
2699020 CGAGTTGACCCAGT
1 CGAGTTAACTCAGT
2699034 -GAGTTAACTCAGT
1 CGAGTTAACTCAGT
2699047 CGAGTTAACTCAGT
1 CGAGTTAACTCAGT
* *
2699061 GCGAGGTGACTCAGT
1 -CGAGTTAACTCAGT
2699076 CGAGT
1 CGAGT
2699081 CAGCGGGTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.28
14 17 0.43
15 12 0.30
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (14 bp):
CGAGTTAACTCAGT
Found at i:2699060 original size:27 final size:28
Alignment explanation
Indices: 2699020--2699080 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
2699010 CAACAGTCAA
* *
2699020 CGAGTTGACCCAGT-GAGTTAACTCAGT
1 CGAGTTAACCCAGTCGAGGTAACTCAGT
* *
2699047 CGAGTTAACTCAGTGCGAGGTGACTCAGT
1 CGAGTTAACCCAGT-CGAGGTAACTCAGT
2699076 CGAGT
1 CGAGT
2699081 CAGCGGGTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 12 0.43
29 16 0.57
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (28 bp):
CGAGTTAACCCAGTCGAGGTAACTCAGT
Found at i:2703714 original size:20 final size:21
Alignment explanation
Indices: 2703661--2703716 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
2703651 CTAAAAAGAA
2703661 AAATAATGAAAAAAAAGAAAAT
1 AAATAATG-AAAAAAAGAAAAT
* * *
2703683 AAATAA-GTAAAAAATAATAT
1 AAATAATGAAAAAAAGAAAAT
2703703 AAATAATGAAAAAA
1 AAATAATGAAAAAA
2703717 CTATATTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 16 0.55
21 7 0.24
22 6 0.21
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (21 bp):
AAATAATGAAAAAAAGAAAAT
Found at i:2703873 original size:37 final size:38
Alignment explanation
Indices: 2703813--2704137 Score: 287
Period size: 37 Copynumber: 8.6 Consensus size: 38
2703803 TTTCTTTTAA
* **
2703813 AAAACAATATATTATATATGTTTTCAAAAAATACTTTC
1 AAAACTATATATTATATATGTTTTCAAAAAATGTTTTC
*
2703851 -AAACTATATATTATATACGTTTTCAAAAAATGTTTTC
1 AAAACTATATATTATATATGTTTTCAAAAAATGTTTTC
*
2703888 AAAATTATATATTATATATG-TTTCAAAAAATGTTTTC
1 AAAACTATATATTATATATGTTTTCAAAAAATGTTTTC
* *
2703925 GAAACTATATATTATATACGTTTTC--AAAATGTTTTC
1 AAAACTATATATTATATATGTTTTCAAAAAATGTTTTC
* *
2703961 AAAAACTATATATTATGTATATGTTTTCAAAAACTATATTAT-
1 -AAAACTATATATTA--TATATGTTTTCAAAAA--ATGTTTTC
* * *
2704003 ATATA-TATATATATATATATATATTC--AAAATGTTTTC
1 A-AAACTATATAT-TATATATGTTTTCAAAAAATGTTTTC
* * *
2704040 AAAAACTATATATTATATATATGTTTTCAAAAACTATATT-
1 -AAAACTATATA-T-TATATATGTTTTCAAAAAATGTTTTC
* * *
2704080 -ATA-TATATATATATATATGTTTTC-GAAAATGTTCTC
1 AAAACTATATAT-TATATATGTTTTCAAAAAATGTTTTC
* *
2704116 AAAATTATATATTATATGTGTT
1 AAAACTATATATTATATATGTT
2704138 ATATGTATAT
Statistics
Matches: 235, Mismatches: 32, Indels: 41
0.76 0.10 0.13
Matches are distributed among these distances:
35 6 0.03
36 31 0.13
37 99 0.42
38 40 0.17
39 23 0.10
40 9 0.04
41 18 0.08
42 4 0.02
43 5 0.02
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (38 bp):
AAAACTATATATTATATATGTTTTCAAAAAATGTTTTC
Found at i:2703903 original size:75 final size:72
Alignment explanation
Indices: 2703807--2704137 Score: 330
Period size: 75 Copynumber: 4.4 Consensus size: 72
2703797 ATAAGTTTTC
* *
2703807 TTTTAAAAAACAATATATTATATATGTTTTCAAAAAATACTTTCAAACTATATAT-TATATACGT
1 TTTTCAAAAACTATATATTATATATGTTTTCAAAAAATA-TTT-AAA-TATATATATATATACGT
2703871 TTTCAAAAAATG
63 TTTC--AAAATG
* *
2703883 TTTTC-AAAATTATATATTATATATG-TTTCAAAAAATGTTTTCGAAACTATATAT-TATATACG
1 TTTTCAAAAACTATATATTATATATGTTTTCAAAAAAT-ATTT--AAA-TATATATATATATACG
2703945 TTTTCAAAATG
62 TTTTCAAAATG
2703956 TTTTCAAAAACTATATATTATGTATATGTTTTCAAAAACTATATTATATATATATATATATATAT
1 TTTTCAAAAACTATATATTA--TATATGTTTTCAAAAA--ATATT-TA-A-ATATATATATATAT
** *
2704021 ATATATTCAAAATG
59 ACGTTTTCAAAATG
* * *
2704035 TTTTCAAAAACTATATATTATATATATGTTTTCAAAAACTATATTATATATATATATATATATGT
1 TTTTCAAAAACTATATA-T-TATATATGTTTTCAAAAAATAT-TTAAATATATATATATATACGT
2704100 TTTCGAAAATG
63 TTTC-AAAATG
* * *
2704111 TTCTC-AAAATTATATATTATATGTGTT
1 TTTTCAAAAACTATATATTATATATGTT
2704138 ATATGTATAT
Statistics
Matches: 222, Mismatches: 17, Indels: 35
0.81 0.06 0.13
Matches are distributed among these distances:
73 20 0.09
74 28 0.13
75 72 0.32
76 20 0.09
77 15 0.07
78 11 0.05
79 53 0.24
80 1 0.00
81 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (72 bp):
TTTTCAAAAACTATATATTATATATGTTTTCAAAAAATATTTAAATATATATATATATACGTTTT
CAAAATG
Found at i:2703984 original size:28 final size:28
Alignment explanation
Indices: 2703953--2704091 Score: 148
Period size: 28 Copynumber: 5.1 Consensus size: 28
2703943 CGTTTTCAAA
*
2703953 ATGTTTTCAAAAACTATATATTATGTAT
1 ATGTTTTCAAAAACTATATATTATATAT
2703981 ATGTTTTCAAAAACTATAT-TATATATAT
1 ATGTTTTCAAAAACTATATAT-TATATAT
* * * *
2704009 AT-ATAT-ATATA-TATATATTCA-A-A-
1 ATGTTTTCAAAAACTATATATT-ATATAT
2704032 ATGTTTTCAAAAACTATATATTATATAT
1 ATGTTTTCAAAAACTATATATTATATAT
2704060 ATGTTTTCAAAAACTATATTATATATATAT
1 ATGTTTTCAAAAACTATA-TAT-TATATAT
2704090 AT
1 AT
2704092 ATATATGTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
23 2 0.02
24 3 0.03
25 11 0.12
26 14 0.15
27 4 0.04
28 45 0.49
29 3 0.03
30 9 0.10
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (28 bp):
ATGTTTTCAAAAACTATATATTATATAT
Found at i:2704007 original size:2 final size:2
Alignment explanation
Indices: 2703995--2704026 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2703985 TTTCAAAAAC
2703995 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2704027 TCAAAATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2704045 original size:79 final size:76
Alignment explanation
Indices: 2703807--2704130 Score: 321
Period size: 79 Copynumber: 4.3 Consensus size: 76
2703797 ATAAGTTTTC
* * *
2703807 TTTTAAAAAACAATATATTA-TATATGTTTTCAAAAA--ATACTT-TCAAACTATATAT-TATAT
1 TTTTCAAAAACTATATATTATTATATGTTTTCAAAAACTATA-TTAT-ATA-TATATATATATAT
*
2703867 ACGTTTTCAAAAAATG
63 ACATTTTC--AAAATG
* * * * ** *
2703883 TTTTC-AAAATTATATATTA-TATATG-TTTCAAAAAATGTTTTCGAAACTATATAT-TATATAC
1 TTTTCAAAAACTATATATTATTATATGTTTTCAAAAACTATATTATATA-TATATATATATATAC
*
2703944 GTTTTCAAAATG
65 ATTTTCAAAATG
*
2703956 TTTTCAAAAACTATATATTATGTATATGTTTTCAAAAACTATATTATATATATATATATATATAT
1 TTTTCAAAAACTATATATTAT-TATATGTTTTCAAAAACTATATTATATATATATATATATATAC
2704021 ATATATTCAAAATG
65 AT-T-TTCAAAATG
2704035 TTTTCAAAAACTATATATTATATATATGTTTTCAAAAACTATATTATATATATATATATATAT--
1 TTTTCAAAAACTATATATTAT-TATATGTTTTCAAAAACTATATTATATATATATATATATATAC
*
2704098 GTTTTCGAAAATG
65 ATTTTC-AAAATG
* *
2704111 TTCTC-AAAATTATATATTAT
1 TTTTCAAAAACTATATATTAT
2704131 ATGTGTTATA
Statistics
Matches: 218, Mismatches: 19, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
73 11 0.05
74 22 0.10
75 61 0.28
76 29 0.13
77 23 0.11
78 1 0.00
79 71 0.33
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.45
Consensus pattern (76 bp):
TTTTCAAAAACTATATATTATTATATGTTTTCAAAAACTATATTATATATATATATATATATACA
TTTTCAAAATG
Found at i:2704885 original size:202 final size:199
Alignment explanation
Indices: 2704552--2705054 Score: 548
Period size: 202 Copynumber: 2.5 Consensus size: 199
2704542 TCTTCTCAGA
* * * * * *
2704552 TTAAAGACCTC-GGTTTGAAAATTCAACCAGAAAGTAGCTCTTCGCTACTACGAAGCGGTTGATA
1 TTAAAGACATCAGG-TT-AAAATTCAACCGGAAAGTAGTTCTT-GCTGCTACCATGCGGTTGATA
* * * * * *
2704616 TGCCTTTGAGATGAATGGAATCGAACTCGAAAGTTTTTGTTGACAGATAACCCTTTTCGCATTGA
63 TGCCATCGAGCTGAATGGAATCGAACTCGAAAGTTTTTGTCGACAGATAACCCTTCTCACATTGA
* *
2704681 GCTATGA-TGTAAACT-AGGCTA-GGAGATAGCTCTCTATTGCTAAATCGCAGCCAACCTAGTTC
128 GCTA-CATTGTAAACTCA-GC-AGGGAGATAGCTCTCTATTGCTAAATCGCAGCCAACCTAGGTC
*
2704743 TTCTTCTTGGC
190 TTCTT-TTGAC
* *
2704754 TTAAAAGAC-TTAGGTATAAAATTCAACCGGTAAGTAGTTCATTGCTGCTACCATGCGGTTGATA
1 TT-AAAGACATCAGGT-TAAAATTCAACCGGAAAGTAGTTC-TTGCTGCTACCATGCGGTTGATA
* *
2704818 TGCCATCGAGCTGAATGGAATCGAACTCGAAAATTTTTGTCGACAGATAACCCTTCTCACCTTGA
63 TGCCATCGAGCTGAATGGAATCGAACTCGAAAGTTTTTGTCGACAGATAACCCTTCTCACATTGA
* * * * * *
2704883 GCTACATTGTAAATTCAGCAGGGAGATAGTTCTTTGTTGCTAAATTGTAGCCAACCTAGGTCTTC
128 GCTACATTGTAAACTCAGCAGGGAGATAGCTCTCTATTGCTAAATCGCAGCCAACCTAGGTCTTC
2704948 TTTTGAC
193 TTTTGAC
* * * * * * *
2704955 TTAAAGACATCAGGTTAAACTTTAACCGGAAAATAGTTCCTCGTTGCTATCATGCGGTTGATACG
1 TTAAAGACATCAGGTTAAAATTCAACCGGAAAGTAGTT-CTTGCTGCTACCATGCGGTTGATATG
* * * *
2705020 CCCTCAAGCTGAATAGAATCAAACTCGAAAGTTTT
65 CCATCGAGCTGAATGGAATCGAACTCGAAAGTTTT
2705055 GTTGATAGAT
Statistics
Matches: 254, Mismatches: 38, Indels: 20
0.81 0.12 0.06
Matches are distributed among these distances:
200 76 0.30
201 14 0.06
202 152 0.60
203 12 0.05
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (199 bp):
TTAAAGACATCAGGTTAAAATTCAACCGGAAAGTAGTTCTTGCTGCTACCATGCGGTTGATATGC
CATCGAGCTGAATGGAATCGAACTCGAAAGTTTTTGTCGACAGATAACCCTTCTCACATTGAGCT
ACATTGTAAACTCAGCAGGGAGATAGCTCTCTATTGCTAAATCGCAGCCAACCTAGGTCTTCTTT
TGAC
Found at i:2707076 original size:101 final size:103
Alignment explanation
Indices: 2706897--2707100 Score: 277
Period size: 101 Copynumber: 2.0 Consensus size: 103
2706887 TTATAATTTG
* * * * *
2706897 CCTTTATTAGGCTAGCTAAATCTTATCCATAATGTCGTGGTGTTTAACCAATTACTCTACAGAGA
1 CCTTTATCAGGCTAGCTAAATCTTATCCATAAAGTCGGGGTGATTAACAAATTACTCTACAGAGA
*
2706962 CAACTCAAGCTTTATTGTAT-ATAT-ATATTATAATCA
66 CAACTCAAACTTTATTGTATAATATAATATTATAATCA
* * * * *
2706998 CCTTTATCAGGCTAGCTGAATCTTATCCTTAAAGTCGGGGTGATTAACAAATTGCTCTAGAGGGA
1 CCTTTATCAGGCTAGCTAAATCTTATCCATAAAGTCGGGGTGATTAACAAATTACTCTACAGAGA
*
2707063 CAGCTCAAACTTTATTGTATACATATAATATTATAATC
66 CAACTCAAACTTTATTGTATA-ATATAATATTATAATC
2707101 TGGGTAAACG
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
101 73 0.83
103 4 0.05
104 11 0.12
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (103 bp):
CCTTTATCAGGCTAGCTAAATCTTATCCATAAAGTCGGGGTGATTAACAAATTACTCTACAGAGA
CAACTCAAACTTTATTGTATAATATAATATTATAATCA
Found at i:2708522 original size:23 final size:23
Alignment explanation
Indices: 2708496--2708540 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2708486 CACCACAGCT
*
2708496 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2708519 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2708541 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2708778 original size:149 final size:149
Alignment explanation
Indices: 2708508--2708822 Score: 596
Period size: 149 Copynumber: 2.1 Consensus size: 149
2708498 TATAATTGCA
*
2708508 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGAACCACATAGAA
2708572 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
2708637 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
2708657 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGAACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGAACCACATAGAAT
*
2708722 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
2708787 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
2708806 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
2708823 CCCTCGACTC
Statistics
Matches: 163, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 162 0.99
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGAACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:2709612 original size:18 final size:18
Alignment explanation
Indices: 2709591--2709625 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2709581 TCCCATCTAG
2709591 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
2709609 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
2709626 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:2710240 original size:21 final size:21
Alignment explanation
Indices: 2710210--2710254 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2710200 TCTTATTCGT
* *
2710210 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2710231 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2710252 TTG
1 TTG
2710255 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2713349 original size:23 final size:23
Alignment explanation
Indices: 2713323--2713367 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2713313 CACCACAGCT
*
2713323 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
2713346 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
2713368 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:2713605 original size:149 final size:149
Alignment explanation
Indices: 2713335--2713649 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
2713325 TATAATTGCA
* *
2713335 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGAACCACATAGAA
2713399 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
2713464 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
*
2713484 CCGAAGGACCGCGTAGAATTGCACCGTAATGCCATATAATGATGTCTATAAGAACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGAACCACATAGAAT
*
2713549 TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
2713614 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
2713633 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
2713650 CCCTCGACTC
Statistics
Matches: 161, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAATGCCATATAATGATGTCCATAAGAACCACATAGAAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:2714441 original size:18 final size:18
Alignment explanation
Indices: 2714420--2714454 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2714410 TCCCATCTAG
2714420 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
2714438 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
2714455 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:2718955 original size:22 final size:18
Alignment explanation
Indices: 2718910--2718953 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
2718900 ATAATCAAAG
2718910 ATAAATAATTAGAATCAA
1 ATAAATAATTAGAATCAA
2718928 ATAAATAATTAGAATCAA
1 ATAAATAATTAGAATCAA
2718946 ATAAATAA
1 ATAAATAA
2718954 ATTAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (18 bp):
ATAAATAATTAGAATCAA
Found at i:2719560 original size:15 final size:16
Alignment explanation
Indices: 2719542--2719574 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2719532 AAAAGAAATT
*
2719542 AAAAAGTTAAAA-TAA
1 AAAAAGATAAAATTAA
2719557 AAAAAGATAAAATTAA
1 AAAAAGATAAAATTAA
2719573 AA
1 AA
2719575 TAAATTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAAAGATAAAATTAA
Found at i:2720645 original size:35 final size:35
Alignment explanation
Indices: 2720600--2720681 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
2720590 TCAAAACTCT
* * *
2720600 TATATTTTATATGTTTT-CAAATTCATTTTAAAAAC
1 TATATATTATATGTTTTGAAAAAT-ATTTTAAAAAC
* * *
2720635 TATTTATTATAAGTTTTGAAAAATATTTTAAAAAT
1 TATATATTATATGTTTTGAAAAATATTTTAAAAAC
2720670 TATATATTATAT
1 TATATATTATAT
2720682 ATGCTTTCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 34 0.89
36 4 0.11
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (35 bp):
TATATATTATATGTTTTGAAAAATATTTTAAAAAC
Found at i:2720727 original size:37 final size:37
Alignment explanation
Indices: 2720686--2720854 Score: 202
Period size: 37 Copynumber: 4.6 Consensus size: 37
2720676 TTATATATGC
*
2720686 TTTC-AAACTATATATTATATACATTTTTAAAAAATGT
1 TTTCAAAACTATATATTATATAC-GTTTTAAAAAATGT
*
2720723 TTTCAAAAC--TATATTATATACGTTTCAAAAAATGT
1 TTTCAAAACTATATATTATATACGTTTTAAAAAATGT
* *
2720758 TTTCGAAACTATATATTATATACGTTTT-CAAAATGT
1 TTTCAAAACTATATATTATATACGTTTTAAAAAATGT
* ** **
2720794 TTTCAAAAATTATATATTATATATATTTTTTCAAAATGT
1 TTTC-AAAACTATATATTATATA-CGTTTTAAAAAATGT
2720833 TTTCAAAACTATATATTATATA
1 TTTCAAAACTATATATTATATA
2720855 TATGGTTTCA
Statistics
Matches: 116, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
35 20 0.17
36 23 0.20
37 36 0.31
38 25 0.22
39 12 0.10
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTCAAAACTATATATTATATACGTTTTAAAAAATGT
Found at i:2720734 original size:38 final size:37
Alignment explanation
Indices: 2720686--2720895 Score: 221
Period size: 38 Copynumber: 5.6 Consensus size: 37
2720676 TTATATATGC
*
2720686 TTTC-AAACTATATATTATATACATTTTTAAAAAATGT
1 TTTCAAAACTATATATTATATACATTTTT-CAAAATGT
* ***
2720723 TTTCAAAAC--TATATTATATACGTTTCAAAAAATGT
1 TTTCAAAACTATATATTATATACATTTTTCAAAATGT
* *
2720758 TTTCGAAACTATATATTATATAC-GTTTTCAAAATGT
1 TTTCAAAACTATATATTATATACATTTTTCAAAATGT
* *
2720794 TTTCAAAAATTATATATTATATATATTTTTTCAAAATGT
1 TTTC-AAAACTATATATTATATACA-TTTTTCAAAATGT
* * *
2720833 TTTCAAAACTATATATTATATATATGGTTTCAAAATAT
1 TTTCAAAACTATATATTATATACAT-TTTTCAAAATGT
2720871 TTTCAAAAACTATATTATATATATA
1 TTTC-AAAACTATA-TAT-TATATA
2720896 TATATATATG
Statistics
Matches: 148, Mismatches: 15, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
35 16 0.11
36 28 0.19
37 33 0.22
38 37 0.25
39 25 0.17
40 3 0.02
41 6 0.04
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTCAAAACTATATATTATATACATTTTTCAAAATGT
Found at i:2720901 original size:47 final size:47
Alignment explanation
Indices: 2720842--2720948 Score: 130
Period size: 47 Copynumber: 2.3 Consensus size: 47
2720832 TTTTCAAAAC
2720842 TATATATTATATATATGGTTTCAAAATAT-TT-TCAAAA-ACTATATTA
1 TATATATTATATATATGGTTTCAAAA-ATGTTCTCAAAATA-TATATTA
*
2720888 TATATATATATATATATGTTTTCAAAAATGTTCTCAAAATTATATATTA
1 TATATAT-TATATATATGGTTTCAAAAATGTTCTCAAAA-TATATATTA
* *
2720937 TATGTGTTATAT
1 TATATATTATAT
2720949 GTATATTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
46 9 0.17
47 20 0.38
48 11 0.21
49 12 0.23
50 1 0.02
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (47 bp):
TATATATTATATATATGGTTTCAAAAATGTTCTCAAAATATATATTA
Found at i:2721574 original size:17 final size:17
Alignment explanation
Indices: 2721552--2721586 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2721542 ATTTTTTTCC
2721552 TATTCTTCTTATTAATT
1 TATTCTTCTTATTAATT
* *
2721569 TATTCTTTTTATTTATT
1 TATTCTTCTTATTAATT
2721586 T
1 T
2721587 TGGAGAATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTCTTCTTATTAATT
Found at i:2723647 original size:20 final size:20
Alignment explanation
Indices: 2723622--2723757 Score: 71
Period size: 20 Copynumber: 6.7 Consensus size: 20
2723612 TGCGAAATAA
2723622 AATCGCAACGCGATATCCAG
1 AATCGCAACGCGATATCCAG
** *
2723642 AATCGCAAATCAAT-TCCCAG
1 AATCGCAACGCGATAT-CCAG
* **
2723662 AATCGCAACACGATTATGAAG
1 AATCGCAACGCGA-TATCCAG
* *
2723683 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATA-TCCAG
** * *
2723703 AATTCGCATTGCGATTTTCCAT
1 AA-TCGCAACGCGA-TATCCAG
* *
2723725 AATCGCAACGCGAATAT-GAA
1 AATCGCAACGCG-ATATCCAG
2723745 AATCGCAACGCGA
1 AATCGCAACGCGA
2723758 ACATATAAAT
Statistics
Matches: 88, Mismatches: 20, Indels: 17
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.02
20 42 0.48
21 39 0.44
22 5 0.06
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATATCCAG
Found at i:2723758 original size:20 final size:20
Alignment explanation
Indices: 2723725--2723999 Score: 134
Period size: 20 Copynumber: 13.7 Consensus size: 20
2723715 GATTTTCCAT
*
2723725 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
2723745 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
2723765 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
2723785 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
2723806 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* ** * *
2723827 AATCACAACGCCTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
2723847 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
2723867 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* * * *
2723887 AATTGCAATGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
2723907 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
2723927 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
2723948 AATCGCAACGTGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
2723968 AATCGCAACGCG-AT-CGATA
1 AATCGCAACGCGAATACGA-A
*
2723987 ATTCGCAACGCGA
1 AATCGCAACGCGA
2724000 TCTCCGGTAT
Statistics
Matches: 197, Mismatches: 43, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.01
19 18 0.09
20 128 0.65
21 50 0.25
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:2723888 original size:40 final size:40
Alignment explanation
Indices: 2723725--2724002 Score: 253
Period size: 40 Copynumber: 6.9 Consensus size: 40
2723715 GATTTTCCAT
* * * * *
2723725 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACATATA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATC-TGTA
* * * * *
2723765 AATCGCAACGCG-ATTC-TGACTATCGCAACGAGTATCCGTAA
1 AATCGCAACGAGAATACGT-A-AATCGCAACGCGTATCTGT-A
* * * *
2723806 AATCGCAACGACAATACGTAAAATCACAACGCCTATCCGTA
1 AATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTA
2723847 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTA
* * * *
2723887 AATTGCAATGAGAATACGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTA
* *
2723927 AATCGCAACGACAATACGTAAAATCGCAACGTGTATCTGTA
1 AATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTA
* *
2723968 AATCGCAACGCG-AT-CGATAATTCGCAACGCG-ATCT
1 AATCGCAACGAGAATACG-TAAATCGCAACGCGTATCT
2724003 CCGGTATCGC
Statistics
Matches: 196, Mismatches: 34, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
38 4 0.02
39 16 0.08
40 96 0.49
41 60 0.31
42 18 0.09
43 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTA
Found at i:2723993 original size:60 final size:60
Alignment explanation
Indices: 2723725--2723996 Score: 184
Period size: 60 Copynumber: 4.5 Consensus size: 60
2723715 GATTTTCCAT
* * * * *
2723725 AATCGCAACGCGAATATGAAAATCGCAACG-CGA-ACATATAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGTAAATCGCAACGACAATACGTA-AAATCGCAACGAGTA-TCGT-A
* * * * * **
2723784 CTATCGCAACGAGTATCCGTAAAATCGCAACGACAATACGTAAAATCACAACGCCTATCCGTA
1 -AATCGCAACGCGAATACGT-AAATCGCAACGACAATACGTAAAATCGCAACGAGTAT-CGTA
* * * * *
2723847 AATCGCAACGAGAATACGTAAATCGCAACG-C-GTATCTGT-AAATTGCAATGAGAATACGTA
1 AATCGCAACGCGAATACGTAAATCGCAACGACAATA-C-GTAAAATCGCAACGAGTAT-CGTA
* * * *
2723907 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGTGTATCTGTA
1 AATCGCAACGCGAATACGTAAATCGCAACGACAATACGTAAAATCGCAACGAGTATC-GTA
*
2723968 AATCGCAACGCG-AT-CGATAATTCGCAACG
1 AATCGCAACGCGAATACG-TAAATCGCAACG
2723997 CGATCTCCGG
Statistics
Matches: 167, Mismatches: 32, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
59 4 0.02
60 71 0.43
61 52 0.31
62 32 0.19
63 7 0.04
64 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGAATACGTAAATCGCAACGACAATACGTAAAATCGCAACGAGTATCGTA
Found at i:2724164 original size:14 final size:14
Alignment explanation
Indices: 2724145--2724171 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2724135 TCATTTGACT
2724145 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
2724159 ATCGCAACGCGAA
1 ATCGCAACGCGAA
2724172 TATGACTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.30, G:0.22, T:0.07
Consensus pattern (14 bp):
ATCGCAACGCGAAA
Found at i:2724184 original size:20 final size:20
Alignment explanation
Indices: 2724159--2724247 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
2724149 CAACGCGAAA
2724159 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
2724179 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
2724199 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
2724219 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
2724239 ATCGCAACG
1 ATCGCAACG
2724248 AGAGAATCAC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
20 59 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:2724276 original size:19 final size:19
Alignment explanation
Indices: 2724252--2724339 Score: 105
Period size: 19 Copynumber: 4.8 Consensus size: 19
2724242 GCAACGAGAG
*
2724252 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2724271 AATCACAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
2724290 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
2724304 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
2724324 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
2724340 TAGTTTCGCG
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
14 8 0.13
16 5 0.08
17 2 0.03
18 3 0.05
19 30 0.50
20 12 0.20
ACGTcount: A:0.48, C:0.17, G:0.19, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:2724295 original size:52 final size:53
Alignment explanation
Indices: 2724230--2724339 Score: 168
Period size: 52 Copynumber: 2.1 Consensus size: 53
2724220 TCGCAACGCG
**
2724230 GAAATGACTATCGCAACGAGAGAATCACAATGCG-AAATGAAAATCACAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGCGAAAATGAAAATCACAATGC
* * *
2724282 GAAATGAAAATCGCAACGAGTGAATCGCAATGCGAAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCACAATGCGAAAATGAAAATCACAATGC
2724335 GAAAT
1 GAAAT
2724340 TAGTTTCGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
52 30 0.58
53 22 0.42
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATGCGAAAATGAAAATCACAATGC
Found at i:2724405 original size:33 final size:33
Alignment explanation
Indices: 2724348--2724443 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
2724338 ATTAGTTTCG
*
2724348 CGTTGCAATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* * *
2724382 CGTTGTGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
2724415 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
2724444 AGTCTGTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 31 0.60
34 21 0.40
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:2724564 original size:14 final size:14
Alignment explanation
Indices: 2724545--2724581 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2724535 CATCAATTAA
2724545 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2724559 ACAAATCATCTTTT
1 ACAAATCAACATTT
2724573 ACAAATCAA
1 ACAAATCAA
2724582 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2725478 original size:14 final size:14
Alignment explanation
Indices: 2725459--2725486 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2725449 CACGTTTTTT
2725459 TAATATTTTTCTTC
1 TAATATTTTTCTTC
2725473 TAATATTTTTCTTC
1 TAATATTTTTCTTC
2725487 AATTTCCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (14 bp):
TAATATTTTTCTTC
Found at i:2725988 original size:21 final size:21
Alignment explanation
Indices: 2725959--2726059 Score: 87
Period size: 21 Copynumber: 4.8 Consensus size: 21
2725949 GGGAGGGACA
* *
2725959 TCTTCAACGATGACAGTGGCC
1 TCTTGAACGATGACAGGGGCC
* ** *
2725980 TCTTGAACGGTGGGAGGGGAC
1 TCTTGAACGATGACAGGGGCC
** *
2726001 TCTTGAGGGATGATAGGGGCC
1 TCTTGAACGATGACAGGGGCC
**
2726022 TCTTGAACGAT-AGGGGAGGCC
1 TCTTGAACGATGACAGG-GGCC
2726043 TCTTGAACGATGACAGG
1 TCTTGAACGATGACAGG
2726060 TGAGTCGGGC
Statistics
Matches: 60, Mismatches: 18, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 54 0.90
22 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
TCTTGAACGATGACAGGGGCC
Found at i:2726046 original size:42 final size:42
Alignment explanation
Indices: 2725967--2726059 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
2725957 CATCTTCAAC
* * *
2725967 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
2726009 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
2726051 GATGACAGG
1 GATGACAGG
2726060 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:2726562 original size:20 final size:19
Alignment explanation
Indices: 2726539--2726607 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
2726529 GAAACTTAAA
2726539 ATCGCAACGCGAAAATGACT
1 ATCGCAACGC-AAAATGACT
*
2726559 ATCGCAATGCAAAAATGACT
1 ATCGCAACGC-AAAATGACT
* *
2726579 ATCGCAATGCAAATTTGACT
1 ATCGCAACGCAAA-ATGACT
2726599 ATCGCAACG
1 ATCGCAACG
2726608 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 3 0.07
20 41 0.93
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (19 bp):
ATCGCAACGCAAAATGACT
Found at i:2726726 original size:19 final size:19
Alignment explanation
Indices: 2726650--2726758 Score: 69
Period size: 19 Copynumber: 5.7 Consensus size: 19
2726640 GCGATTATAG
* * **
2726650 TTTCGCGCTGCGATTTTTG
1 TTTCGCGTTGCGATATTCA
* *
2726669 TTTCGCGTTGTGATTTTCA
1 TTTCGCGTTGCGATATTCA
*
2726688 TTTCTCGTTGC-A-ATTCA
1 TTTCGCGTTGCGATATTCA
*
2726705 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATATTCA
* * *
2726724 TTTTTCACGTTGCGATTTTAA
1 --TTTCGCGTTGCGATATTCA
*
2726745 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
2726759 AAGTAAACTA
Statistics
Matches: 70, Mismatches: 16, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
17 14 0.20
18 2 0.03
19 28 0.40
20 11 0.16
21 15 0.21
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATATTCA
Found at i:2726975 original size:94 final size:94
Alignment explanation
Indices: 2726811--2727185 Score: 617
Period size: 94 Copynumber: 4.0 Consensus size: 94
2726801 TAGCATTATC
* * *
2726811 TCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACATAGTTTAGCA
1 TCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCA
*
2726876 TAATTGGCAGCAACCGAACAAATTTACTT
66 GAATTGGCAGCAACCGAACAAATTTACTT
* *
2726905 TCAACCAAAAGACAAAACAAAGATAAATACTAACTTCACAGTGTTAAAGAATACATAGTTTAGCA
1 TCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCA
2726970 GAATTGGCAGCAACCGAACAAATTTACTT
66 GAATTGGCAGCAACCGAACAAATTTACTT
* *
2726999 TTAACCAAAAGACAAAACAAAGACAAATACTAACTTCACATTGTTAAAGAATACACAGTTTAGCA
1 TCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCA
*
2727064 GAATTGGCAGCAACCGAATAAATTTAC-T
66 GAATTGGCAGCAACCGAACAAATTTACTT
*
2727092 TCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGTTTAGC
1 TCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
* * *
2727157 AGTATTGGAAGCAACCGAATAAATTTACT
65 AGAATTGGCAGCAACCGAACAAATTTACT
2727186 AAGCAATCTA
Statistics
Matches: 265, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 18 0.07
94 247 0.93
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.22
Consensus pattern (94 bp):
TCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCA
GAATTGGCAGCAACCGAACAAATTTACTT
Found at i:2728026 original size:21 final size:22
Alignment explanation
Indices: 2727984--2728026 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2727974 AATAACAAAC
*
2727984 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
2728006 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
2728027 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:2728908 original size:20 final size:20
Alignment explanation
Indices: 2728885--2728940 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
2728875 TGAAATGAAA
2728885 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
* * *
2728905 ATCGCAATGCGAAAATGACT
1 ATCGCAACGAGAGAATGACT
*
2728925 ATCGCAACAAGAGAAT
1 ATCGCAACGAGAGAAT
2728941 CGCAATGAGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:2728944 original size:14 final size:14
Alignment explanation
Indices: 2728925--2728960 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2728915 GAAAATGACT
2728925 ATCGCAACAAGAGA
1 ATCGCAACAAGAGA
**
2728939 ATCGCAATGAGAGA
1 ATCGCAACAAGAGA
2728953 ATCGCAAC
1 ATCGCAAC
2728961 GCGAAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACAAGAGA
Found at i:2728976 original size:19 final size:19
Alignment explanation
Indices: 2728952--2729016 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
2728942 GCAATGAGAG
*
2728952 AATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATGAA
*
2728971 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
2728985 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
2729004 AATCGCAATGCGA
1 AATCGCAACGCGA
2729017 TTTTGGTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 9 0.24
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.59
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:2728984 original size:33 final size:33
Alignment explanation
Indices: 2728938--2729011 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
2728928 GCAACAAGAG
* *
2728938 AATCGCAATGAGAGAATCGCAACGCGAAATTAA
1 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
2728971 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAACGCGAAATGAA
2729004 AATCGCAA
1 AATCGCAA
2729012 TGCGATTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAACGCGAAATGAA
Found at i:2729097 original size:40 final size:40
Alignment explanation
Indices: 2729039--2729130 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 40
2729029 GTTGCGATTA
**
2729039 TCTCGTTGCGATTTTCA-TTTCGCGTTGCGATTTTCATTT
1 TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCATTT
* *
2729078 CTCTCGTTGCGATAGTCATTTTTGTGTTGCGATTTTCATTT
1 -TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCATTT
2729119 TCAT-GTTGCGAT
1 TC-TCGTTGCGAT
2729131 TTTAAGTTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 25 0.54
41 21 0.46
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.50
Consensus pattern (40 bp):
TCTCGTTGCGATAGTCATTTTCGCGTTGCGATTTTCATTT
Found at i:2729131 original size:20 final size:20
Alignment explanation
Indices: 2729043--2729133 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
2729033 CGATTATCTC
*
2729043 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
2729062 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
** *
2729082 CGTTGCGATAGTCATTTTTGT
1 -GTTGCGATTTTCATTTTCGT
*
2729103 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
2729123 GTTGCGATTTT
1 GTTGCGATTTT
2729134 AAGTTTAGAA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
19 13 0.22
20 30 0.50
21 17 0.28
ACGTcount: A:0.12, C:0.16, G:0.20, T:0.52
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:2729716 original size:20 final size:20
Alignment explanation
Indices: 2729691--2729945 Score: 228
Period size: 20 Copynumber: 12.6 Consensus size: 20
2729681 CTTTAAAAAT
2729691 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
2729711 CGCGTTGCGATTTAACGTAT-
1 CGCGTTGCGATTT-ACGGATA
* *
2729731 TGTCGTTGTGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
2729752 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
2729772 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * * *
2729792 AGTGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
2729812 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2729832 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
2729854 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
2729873 CGCGTTGCGATTTTATGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
2729893 TGTCGTTGCGATTTAAGGATA
1 CG-CGTTGCGATTTACGGATA
*
2729914 CGCGTTACGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
2729935 CTCGTTGCGAT
1 CGCGTTGCGAT
2729946 AGTCAGAATC
Statistics
Matches: 183, Mismatches: 42, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.01
20 116 0.63
21 63 0.34
22 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Done.