Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 37
Found at i:2708026 original size:17 final size:16
Alignment explanation
Indices: 2708004--2708041 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
2707994 TCAATTATTC
2708004 ATTTTTATTGTT-TTGTT
1 ATTTTTATT-TTATT-TT
2708021 ATTTTTATTTTATTTT
1 ATTTTTATTTTATTTT
2708037 ATTTT
1 ATTTT
2708042 ATTCAGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (16 bp):
ATTTTTATTTTATTTT
Found at i:2708788 original size:14 final size:14
Alignment explanation
Indices: 2708769--2708808 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2708759 AGATTGGTAT
2708769 AAACATAAATGAAC
1 AAACATAAATGAAC
* **
2708783 ACACATAAACAAAC
1 AAACATAAATGAAC
2708797 AAACATAAATGA
1 AAACATAAATGA
2708809 TCATAAATGA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.65, C:0.17, G:0.05, T:0.12
Consensus pattern (14 bp):
AAACATAAATGAAC
Found at i:2709212 original size:16 final size:16
Alignment explanation
Indices: 2709193--2709226 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2709183 TTCTCAATCG
2709193 ATAATTTAT-TTATATT
1 ATAA-TTATCTTATATT
2709209 ATAATTATCTTATATT
1 ATAATTATCTTATATT
2709225 AT
1 AT
2709227 TAAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
ATAATTATCTTATATT
Found at i:2709678 original size:51 final size:50
Alignment explanation
Indices: 2709586--2709698 Score: 129
Period size: 52 Copynumber: 2.2 Consensus size: 50
2709576 TAAGTATTTC
*
2709586 ATATTTTTCAAAATTTAAAAAATAAATATTATCCTCCTATTTTTCTAATCTAA
1 ATATTTTT--AAATTTAAAAAATAAATATTATCCTCATATTTTT-TAATCTAA
* * * * *
2709639 TTATTTTTAAATTATAAAAATTAAATCTTGTCCT-ATATTTTTTAATTTAA
1 ATATTTTTAAATT-TAAAAAATAAATATTATCCTCATATTTTTTAATCTAA
2709689 ATATTTTTAA
1 ATATTTTTAA
2709699 GTCTCTATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
50 16 0.31
51 12 0.23
52 17 0.33
53 7 0.13
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.50
Consensus pattern (50 bp):
ATATTTTTAAATTTAAAAAATAAATATTATCCTCATATTTTTTAATCTAA
Found at i:2713776 original size:9 final size:9
Alignment explanation
Indices: 2713762--2713787 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2713752 TCAGAGAATC
2713762 CTCCACCAT
1 CTCCACCAT
2713771 CTCCACCAT
1 CTCCACCAT
2713780 CTCCACCA
1 CTCCACCA
2713788 ACACAGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.58, G:0.00, T:0.19
Consensus pattern (9 bp):
CTCCACCAT
Found at i:2715741 original size:19 final size:19
Alignment explanation
Indices: 2715695--2715742 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2715685 AAAAAATGTT
2715695 ATAAA-AAAT-TATAATTA
1 ATAAATAAATATATAATTA
*
2715712 A-AATTATAATATATAATTA
1 ATAAATA-AATATATAATTA
2715731 ATAAATAAATAT
1 ATAAATAAATAT
2715743 CGATATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.08
17 2 0.08
18 3 0.12
19 14 0.56
20 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAATAAATATATAATTA
Found at i:2719223 original size:60 final size:60
Alignment explanation
Indices: 2719133--2719479 Score: 484
Period size: 60 Copynumber: 5.8 Consensus size: 60
2719123 AACACTTACA
* *
2719133 CTCCTCCATCTCTCCCCT-CACAGTCC-GAGAACCCTCCACCGTCTCCAACAACAACCTATC
1 CTCCTCCATCTC-CACCTGCACA-ACCGGAGAACCCTCCACCGTCTCCAACAACAACCTATC
* *
2719193 CTCCTCCATCTCCACCTGCACAACCGGAGAACCCTCCACCTTCTCCGACAACAACCTATC
1 CTCCTCCATCTCCACCTGCACAACCGGAGAACCCTCCACCGTCTCCAACAACAACCTATC
* * *
2719253 CTCCTCCATCGCCCCCTGCACAACCGGAGAACCCTCCACCTTCTCCAACAACAACCTATC
1 CTCCTCCATCTCCACCTGCACAACCGGAGAACCCTCCACCGTCTCCAACAACAACCTATC
* *
2719313 CTCCTCCATCTCCACCTGCACAATCGGAGAACCCTCCACCGTCTCCGACAACAACCTATC
1 CTCCTCCATCTCCACCTGCACAACCGGAGAACCCTCCACCGTCTCCAACAACAACCTATC
* * *
2719373 CTCCTCCATCTCCACCTGCACAATCAGAGAACCCTCCACCGTCTCCGACAACAACCTATC
1 CTCCTCCATCTCCACCTGCACAACCGGAGAACCCTCCACCGTCTCCAACAACAACCTATC
* * * * * *
2719433 CTCCTCCATCACCACCAT-CGCAATCAGAGAATCCTCCACCATCTCCA
1 CTCCTCCATCTCCACC-TGCACAACCGGAGAACCCTCCACCGTCTCCA
2719480 CCCACACAGC
Statistics
Matches: 266, Mismatches: 18, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
59 6 0.02
60 259 0.97
61 1 0.00
ACGTcount: A:0.25, C:0.48, G:0.08, T:0.18
Consensus pattern (60 bp):
CTCCTCCATCTCCACCTGCACAACCGGAGAACCCTCCACCGTCTCCAACAACAACCTATC
Found at i:2719379 original size:30 final size:30
Alignment explanation
Indices: 2719345--2719440 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
2719335 ATCGGAGAAC
2719345 CCTCCACCGTCTCCGACAACAACCTATCCT
1 CCTCCACCGTCTCCGACAACAACCTATCCT
* * * *
2719375 CCTCCATC-TCCACCTGCACAATCAGA--GA-AC-
1 CCTCCACCGT-CTCC-G-ACAA-CA-ACCTATCCT
2719405 CCTCCACCGTCTCCGACAACAACCTATCCT
1 CCTCCACCGTCTCCGACAACAACCTATCCT
2719435 CCTCCA
1 CCTCCA
2719441 TCACCACCAT
Statistics
Matches: 48, Mismatches: 8, Indels: 20
0.63 0.11 0.26
Matches are distributed among these distances:
26 1 0.02
27 2 0.04
28 5 0.10
29 3 0.06
30 26 0.54
31 3 0.06
32 5 0.10
33 2 0.04
34 1 0.02
ACGTcount: A:0.25, C:0.49, G:0.07, T:0.19
Consensus pattern (30 bp):
CCTCCACCGTCTCCGACAACAACCTATCCT
Found at i:2719418 original size:33 final size:33
Alignment explanation
Indices: 2719312--2719418 Score: 84
Period size: 33 Copynumber: 3.4 Consensus size: 33
2719302 AACAACCTAT
* *
2719312 CCTCCTCCATCTCCACCTGCACAATCGGAGAAC
1 CCTCCACCATCTCCACCTGCACAATCAGAGAAC
* ** *
2719345 CCTCCACCGTCT---CC-G-ACAA-CA-ACCTAT
1 CCTCCACCATCTCCACCTGCACAATCAGA-GAAC
*
2719372 CCTCCTCCATCTCCACCTGCACAATCAGAGAAC
1 CCTCCACCATCTCCACCTGCACAATCAGAGAAC
*
2719405 CCTCCACCGTCTCC
1 CCTCCACCATCTCC
2719419 GACAACAACC
Statistics
Matches: 53, Mismatches: 13, Indels: 16
0.65 0.16 0.20
Matches are distributed among these distances:
26 1 0.02
27 12 0.23
28 4 0.08
29 1 0.02
30 4 0.08
31 1 0.02
32 4 0.08
33 25 0.47
34 1 0.02
ACGTcount: A:0.23, C:0.49, G:0.09, T:0.19
Consensus pattern (33 bp):
CCTCCACCATCTCCACCTGCACAATCAGAGAAC
Found at i:2719471 original size:180 final size:180
Alignment explanation
Indices: 2719133--2719479 Score: 536
Period size: 180 Copynumber: 1.9 Consensus size: 180
2719123 AACACTTACA
* *
2719133 CTCCTCCATCTCTCCCCTCACAGTCCGAGAACCCTCCACCGTCTCCAACAACAACCTATCCTCCT
1 CTCCTCCATCTCTCACCTCACAATCCGAGAACCCTCCACCGTCTCCAACAACAACCTATCCTCCT
* *
2719198 CCATCTCCACCTGCACAACCGGAGAACCCTCCACCTTCTCCGACAACAACCTATCCTCCTCCATC
66 CCATCTCCACCTGCACAACCAGAGAACCCTCCACCGTCTCCGACAACAACCTATCCTCCTCCATC
* * * *
2719263 GCCCCCTGCACAACCGGAGAACCCTCCACCTTCTCCAACAACAACCTATC
131 ACCCCATGCACAACCAGAGAACCCTCCACCATCTCCAACAACAACCTATC
* *
2719313 CTCCTCCATCTC-CACCTGCACAATCGGAGAACCCTCCACCGTCTCCGACAACAACCTATCCTCC
1 CTCCTCCATCTCTCACCT-CACAATCCGAGAACCCTCCACCGTCTCCAACAACAACCTATCCTCC
*
2719377 TCCATCTCCACCTGCACAATCAGAGAACCCTCCACCGTCTCCGACAACAACCTATCCTCCTCCAT
65 TCCATCTCCACCTGCACAACCAGAGAACCCTCCACCGTCTCCGACAACAACCTATCCTCCTCCAT
* * *
2719442 CACCACCAT-CGCAATCAGAGAATCCTCCACCATCTCCA
130 CACC-CCATGCACAACCAGAGAACCCTCCACCATCTCCA
2719480 CCCACACAGC
Statistics
Matches: 151, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
179 4 0.03
180 144 0.95
181 3 0.02
ACGTcount: A:0.25, C:0.48, G:0.08, T:0.18
Consensus pattern (180 bp):
CTCCTCCATCTCTCACCTCACAATCCGAGAACCCTCCACCGTCTCCAACAACAACCTATCCTCCT
CCATCTCCACCTGCACAACCAGAGAACCCTCCACCGTCTCCGACAACAACCTATCCTCCTCCATC
ACCCCATGCACAACCAGAGAACCCTCCACCATCTCCAACAACAACCTATC
Found at i:2720837 original size:2 final size:2
Alignment explanation
Indices: 2720830--2720965 Score: 272
Period size: 2 Copynumber: 68.0 Consensus size: 2
2720820 ACATACATAC
2720830 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
2720872 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
2720914 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
2720956 AT AT AT AT AT
1 AT AT AT AT AT
2720966 CAAAACTCCA
Statistics
Matches: 134, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 134 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2721836 original size:19 final size:19
Alignment explanation
Indices: 2721815--2721850 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2721805 AATATATTTA
2721815 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
2721833 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
2721851 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:2723104 original size:3 final size:3
Alignment explanation
Indices: 2723096--2723222 Score: 191
Period size: 3 Copynumber: 41.7 Consensus size: 3
2723086 TTATTTATTA
*
2723096 AAT AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* **
2723143 ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2723191 AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2723223 AATGGATAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 106 0.95
4 6 0.05
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2723774 original size:113 final size:113
Alignment explanation
Indices: 2723519--2724239 Score: 1056
Period size: 113 Copynumber: 6.4 Consensus size: 113
2723509 GATATCAAAC
*
2723519 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * ** * * **
2723584 CATGAAATTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAGGCA
*
2723633 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * * *
2723698 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAGGCA
*
2723746 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * * *
2723811 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAGGCA
2723859 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
2723924 ATGAACTTTCTCTGGAAATGTTGATCCATC-AAGTGATGAATTCAAGCA
66 ATGAACTTTCTCTGGAAATGTTGATCCATCGAA-TGATGAATTCAGGCA
2723972 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
2724037 ATGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAGTG-A
66 ATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTC-AG-GCA
**
2724086 AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTATTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
** * * * *
2724150 ATGAACTCGAC-CTGGCAATGCTGATCCATCGAATGATTAATTCAAGCGA
66 ATGAACT-TTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAGGC-A
2724199 AAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCT
2724240 GGCAATGTTG
Statistics
Matches: 564, Mismatches: 36, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
111 1 0.00
112 3 0.01
113 488 0.87
114 71 0.13
115 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATGAATTCAGGCA
Found at i:2724261 original size:77 final size:77
Alignment explanation
Indices: 2724137--2724316 Score: 278
Period size: 77 Copynumber: 2.4 Consensus size: 77
2724127 TCTTCAGATG
** *
2724137 AGTTCTTCTCATTATGAA---C-TCGACCTGGCAATGCTGATCCATCGAATGATTAATTCAAGCG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
2724198 AAAAGTTGAACA
66 AAAAGTTGAACA
* *
2724210 AGTTCTTCTCATTATGAACTTCTTCTTCCTGGCAATGTTGATCCATTGAATGATGAATTCAAGCG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
2724275 AAAAGTTGAACA
66 AAAAGTTGAACA
*
2724287 AGTTCTTCTCATTATGAACTTATTCTTCCT
1 AGTTCTTCTCATTATGAACTTCTTCTTCCT
2724317 CTTTAGATAA
Statistics
Matches: 97, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
73 18 0.19
76 1 0.01
77 78 0.80
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (77 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
AAAAGTTGAACA
Found at i:2724312 original size:20 final size:21
Alignment explanation
Indices: 2724287--2724346 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 21
2724277 AAGTTGAACA
2724287 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
* *
2724308 A-TTCTTCCTCTTTA-G-A-TA
1 AGTTCTT-CTCATTATGAACTT
2724326 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
2724347 TTTCACTGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
18 8 0.27
19 7 0.23
20 7 0.23
21 8 0.27
ACGTcount: A:0.23, C:0.20, G:0.08, T:0.48
Consensus pattern (21 bp):
AGTTCTTCTCATTATGAACTT
Found at i:2724442 original size:117 final size:119
Alignment explanation
Indices: 2724281--2725265 Score: 421
Period size: 113 Copynumber: 8.5 Consensus size: 119
2724271 AGCGAAAAGT
* * *
2724281 TGAACAAGTTCTTCTCATTATGAACTTATTCTTCCTCTTTAGATAAGTTCTTCTCATTATGAACT
1 TGAACAAGTTCTTCTCAATATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC-
* * *
2724346 TTTTCACTGG-G-GATGATAATTTATCTCATTCTGTGAT-GTAATCATGC-AAAGGC
65 -TTTCACTGGAGTGATGATAATCTATCTCATTCCGTAATAG-AATCATGCAAAAGGC
** * *
2724399 TGAACAAGTTCTTCTC-GGATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTTTCATCATGAACT
1 TGAACAAGTTCTTCTCAATATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACT
* * * * * *
2724463 TTCTCTGGAAAAGTTGATGTTGATCTATCTCTTTCCGTAATAGAGTCATGCAAAAGGT
66 TTCACTGG---AG-TGATGATAATCTATCTCATTCCGTAATAGAATCATGCAAAAGGC
* *
2724521 TGAACAAGTTCTTCTCAATATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATG-ACA
1 TGAACAAGTTCTTCTCAATATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACT
* * * * * *
2724585 TTCTACCTGGCA---ATG-T--T-GATC-CA-TCGAGTGAT-GAATTGAAGCAAAAGGT
66 TTC-A-CTGG-AGTGATGATAATCTATCTCATTC-CGTAATAGAA-TCATGCAAAAGGC
* * * * *
2724634 TGAACAAATTCTTCTCATTATGAACTTATTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAGTTCTTCTCAATATGAACTTCTTCTTC-CTCTTCAGATAAGTTCTTCTCATTATGAAC
*** * * * * * * *
2724699 TCAAACTGGA---A--A-AGT-TGATC-CA-TCAAGTGATGGATTTGA-GCAAAAGGT
65 TTTCACTGGAGTGATGATAATCT-ATCTCATTC-CGTAATAGA-ATCATGCAAAAGGC
* * * *
2724747 TGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAGTTCTTCTCAATATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAAC
* * * * * * * *
2724812 TTTTACCTGGCA---ATGCTGATCCATC-GA----ATAAT-GAATTCAAGCGAAAA-GT
65 TTTCA-CTGG-AGTGATGATAATCTATCTCATTCCGTAATAGAA-TCATGC-AAAAGGC
* *
2724861 TGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAGTTCTTCTCAATATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAAC
* * *
2724926 TTTCTCTGGA---A--A-AGT-TGATC-CATT--G-AATGATGAATTCGA-GCAAAAGGT
65 TTTCACTGGAGTGATGATAATCT-ATCTCATTCCGTAAT-A-GAA-TC-ATGCAAAAGGC
* * * *
2724974 TGAATAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAGTTCTTCTCAATATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAAC
* * * * * * * *
2725039 -TTCTTCTGGA--AATGCTGATCCATC-GAAT--G--AT-GAATTCGA-GCAAAAGGT
65 TTTC-ACTGGAGTGATGATAATCTATCTCATTCCGTAATAGAA-TC-ATGCAAAAGGC
* * * * *
2725087 TGAATAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAGTTCTTCTCAATATGAACTTCTTCTTC-CTCTTCAGATAAGTTCTTCTCATTATGAAC
* * * * * * * * *
2725152 -TTCTTCTGGA--AATGCTGATCCATC-GAAT--G--AT-GAATTCAAGCAAAAGGT
65 TTTC-ACTGGAGTGATGATAATCTATCTCATTCCGTAATAGAA-TCATGCAAAAGGC
* * *
2725200 TGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TGAACAAGTTCTTCTCAATATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAAC
2725265 T
65 T
2725266 CTACAGATGA
Statistics
Matches: 739, Mismatches: 79, Indels: 102
0.80 0.09 0.11
Matches are distributed among these distances:
109 5 0.01
110 3 0.00
112 17 0.02
113 409 0.55
114 114 0.15
115 17 0.02
116 2 0.00
117 49 0.07
118 24 0.03
119 1 0.00
121 27 0.04
122 28 0.04
123 39 0.05
124 4 0.01
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (119 bp):
TGAACAAGTTCTTCTCAATATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACT
TTCACTGGAGTGATGATAATCTATCTCATTCCGTAATAGAATCATGCAAAAGGC
Found at i:2725118 original size:17 final size:17
Alignment explanation
Indices: 2725096--2725158 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
2725086 TTGAATAAGC
2725096 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
* *
2725113 TCTTCTTCATTCTTCAGATGAGT
1 TCTTC-TCATT-AT--GA--ACT
2725136 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
2725153 TCTTCT
1 TCTTCT
2725159 GGAAATGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
17 13 0.36
18 5 0.14
19 3 0.08
21 3 0.08
22 5 0.14
23 7 0.19
ACGTcount: A:0.19, C:0.24, G:0.08, T:0.49
Consensus pattern (17 bp):
TCTTCTCATTATGAACT
Found at i:2725264 original size:113 final size:113
Alignment explanation
Indices: 2724512--2725265 Score: 1108
Period size: 113 Copynumber: 6.7 Consensus size: 113
2724502 ATAGAGTCAT
*
2724512 GCAAAAGGTTGAACAAGTTCTTCTCAATATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * * *
2724576 ATTATG-ACATTCTACCTGGCAATGTTGATCCATCGAGTGATGAATTGAA
66 ATTATGAAC-TTCT-TCTGGAAATGCTGATCCATCGAATGATGAATTCAA
* * *
2724625 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
** * * * **
2724690 ATTATGAAC-TCAAACTGGAAAAGTTGATCCATC-AAGTGATGGATTTGA
66 ATTATGAACTTC-TTCTGGAAATGCTGATCCATCGAA-TGATGAATTCAA
* *
2724738 GCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
2724803 ATTATGAACTT-TTACCTGGCAATGCTGATCCATCGAATAATGAATTCAA
66 ATTATGAACTTCTT--CTGGAAATGCTGATCCATCGAATGATGAATTCAA
2724852 GCGAAAA-GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 GC-AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
2724916 CATTATGAACTT-TCTCTGGAAAAGTTGATCCATTGAATGATGAATTCGA
65 CATTATGAACTTCT-TCTGGAAATGCTGATCCATCGAATGATGAATTCAA
* *
2724965 GCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
2725030 ATTATGAACTTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCGA
66 ATTATGAACTTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
* * *
2725078 GCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2725143 ATTATGAACTTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
66 ATTATGAACTTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
*
2725191 GCAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
2725256 ATTATGAACT
66 ATTATGAACT
2725266 CTACAGATGA
Statistics
Matches: 586, Mismatches: 43, Indels: 24
0.90 0.07 0.04
Matches are distributed among these distances:
112 5 0.01
113 450 0.77
114 122 0.21
115 9 0.02
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTCTTCTGGAAATGCTGATCCATCGAATGATGAATTCAA
Found at i:2726050 original size:22 final size:22
Alignment explanation
Indices: 2726025--2726145 Score: 179
Period size: 22 Copynumber: 5.5 Consensus size: 22
2726015 AATAAAGCTT
*
2726025 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
2726047 TCATCTTTAAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
* *
2726069 TCATCTTTGAAGAGAGAATATA
1 TCATCTTTGAAAAGAGAATCTA
*
2726091 TCATCTTTGAAAACAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
2726113 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2726135 TCATCTTTGAA
1 TCATCTTTGAA
2726146 GAATGTAGAT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 87 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2727742 original size:37 final size:39
Alignment explanation
Indices: 2727686--2727786 Score: 118
Period size: 41 Copynumber: 2.6 Consensus size: 39
2727676 TATTTCTGAT
* * *
2727686 TGAAATGGGCCTTCAAGATGTCCCACA-GGGA-A-CTGTC
1 TGAAATGGGCTTTCGAGATG-CCCACATGGAACATCTGTC
*
2727723 TGAACTGGGCTTTCGAGATGCCCACATGGAACATTTCTGTC
1 TGAAATGGGCTTTCGAGATGCCCACATGGAACA--TCTGTC
2727764 TGAAATGGGCTTTCGAGATGCCC
1 TGAAATGGGCTTTCGAGATGCCC
2727787 CAATATTTGC
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
36 6 0.11
37 20 0.37
38 1 0.02
41 27 0.50
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (39 bp):
TGAAATGGGCTTTCGAGATGCCCACATGGAACATCTGTC
Found at i:2730924 original size:7 final size:7
Alignment explanation
Indices: 2730908--2730959 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
2730898 CTTGATTCAA
*
2730908 TTTTCCT
1 TTTTCTT
2730915 TTTTCTT
1 TTTTCTT
2730922 TTTTCTTTT
1 TTTTC--TT
2730931 TTTTCTT
1 TTTTCTT
2730938 CTTTT-TT
1 -TTTTCTT
2730945 TTTTCTT
1 TTTTCTT
*
2730952 CTTTCTT
1 TTTTCTT
2730959 T
1 T
2730960 GCTGGATGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
6 4 0.11
7 23 0.61
8 4 0.11
9 7 0.18
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTCTT
Found at i:2736559 original size:19 final size:19
Alignment explanation
Indices: 2736538--2736573 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2736528 AATATATTTA
2736538 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
2736556 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
2736574 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:2737826 original size:3 final size:3
Alignment explanation
Indices: 2737818--2737950 Score: 203
Period size: 3 Copynumber: 43.7 Consensus size: 3
2737808 TTATTTATTA
*
2737818 AAT AAT AAT AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT
* **
2737865 ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2737913 AAT AAT ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2737951 AATGGATAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
3 112 0.95
4 6 0.05
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:2749292 original size:28 final size:28
Alignment explanation
Indices: 2749241--2749314 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
2749231 TTTTGAACTT
* *
2749241 TGAAGCATTGAAGTTACTGAAAGAAATC
1 TGAAGTATTGAAGTTACTCAAAGAAATC
* * *
2749269 T-ATAGTATTGAAGTTACTCTAAGATATT
1 TGA-AGTATTGAAGTTACTCAAAGAAATC
*
2749297 TGAAGTCTTGAAGTTACT
1 TGAAGTATTGAAGTTACT
2749315 TATAAAATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
27 1 0.03
28 36 0.95
29 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.35
Consensus pattern (28 bp):
TGAAGTATTGAAGTTACTCAAAGAAATC
Found at i:2750059 original size:32 final size:33
Alignment explanation
Indices: 2750021--2750084 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2750011 TAGTTTCTTC
* *
2750021 ACCTGC-ATATTTTCCCCTGCAGCTT-CTAGCTT
1 ACCTGCAAAATTTTCCCCTACAG-TTCCTAGCTT
2750053 ACCTGCAAAATTTTCCCCTACAGTTCCTAGCT
1 ACCTGCAAAATTTTCCCCTACAGTTCCTAGCT
2750085 CTCATGCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 8 0.29
33 20 0.71
ACGTcount: A:0.20, C:0.34, G:0.11, T:0.34
Consensus pattern (33 bp):
ACCTGCAAAATTTTCCCCTACAGTTCCTAGCTT
Found at i:2750093 original size:33 final size:33
Alignment explanation
Indices: 2750029--2750093 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2750019 TCACCTGCAT
* *
2750029 ATTTTCCCCTGCAGCTTCTAGCTTACCTGCAAA
1 ATTTTCCCCTACAGCTTCTAGCTTACATGCAAA
2750062 ATTTTCCCCTACAG-TTCCTAGCTCT-CATGCAA
1 ATTTTCCCCTACAGCTT-CTAGCT-TACATGCAA
2750094 TTCCTTCACC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.07
33 25 0.89
34 1 0.04
ACGTcount: A:0.22, C:0.34, G:0.11, T:0.34
Consensus pattern (33 bp):
ATTTTCCCCTACAGCTTCTAGCTTACATGCAAA
Found at i:2751876 original size:22 final size:21
Alignment explanation
Indices: 2751824--2751884 Score: 104
Period size: 21 Copynumber: 2.9 Consensus size: 21
2751814 GATTTTTGGG
2751824 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
2751845 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
2751866 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
2751885 CTCAAGCGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
21 24 0.63
22 14 0.37
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:2753421 original size:23 final size:23
Alignment explanation
Indices: 2753388--2753455 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
2753378 ATTATTATAT
2753388 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2753411 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
** *
2753434 GGCACTTTGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
2753456 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2757600 original size:31 final size:31
Alignment explanation
Indices: 2757562--2757639 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 31
2757552 TCAAATGATC
*
2757562 GGGGACCATATTGCAAACAGACTAAATATTG
1 GGGGACCATATTGCAAACAAACTAAATATTG
* * *
2757593 GGGGACCATATTGTAAACAAATTAAATGTTG
1 GGGGACCATATTGCAAACAAACTAAATATTG
**
2757624 GGGGACTGTATTGCAA
1 GGGGACCATATTGCAA
2757640 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.26
Consensus pattern (31 bp):
GGGGACCATATTGCAAACAAACTAAATATTG
Found at i:2759456 original size:30 final size:30
Alignment explanation
Indices: 2759422--2759494 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
2759412 CCCGAAGGAC
2759422 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
2759452 CTATCCAGAGCTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
2759482 CTGTCCATAGGTC
1 CTATCCAGAGGTC
2759495 CCGAAGAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:2759596 original size:63 final size:62
Alignment explanation
Indices: 2759483--2759604 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 62
2759473 CCTCGGTAAC
* * *
2759483 TGTCCATAGGTCCCGAAGAACCTAGGTAAATTGTCCATATGTTCCTTAGAACATAGGTATAA
1 TGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTATAA
* *
2759545 TGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATAGGTA
1 TGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAGGTA
2759605 AACCCTCGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 1 0.02
62 22 0.42
63 30 0.57
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (62 bp):
TGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTATAA
Found at i:2759600 original size:32 final size:32
Alignment explanation
Indices: 2759480--2759606 Score: 136
Period size: 31 Copynumber: 4.0 Consensus size: 32
2759470 GATCCTCGGT
* * * *
2759480 AACTGTCCATAGGTCCCGAAGAACCTAGGT-A
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
* * *
2759511 AATTGTCCATATGTTCCTTAGAACATAGGTAT
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
*
2759543 AA-TGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTAA
2759574 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
2759606 A
1 A
2759607 CCCTCGACTC
Statistics
Matches: 79, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
30 4 0.05
31 46 0.58
32 25 0.32
33 4 0.05
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAA
Found at i:2764131 original size:30 final size:30
Alignment explanation
Indices: 2764097--2764169 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
2764087 CCCGAATGAC
2764097 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
2764127 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
2764157 CTGTCCATAGGTC
1 CTATCCAGAGGTC
2764170 CCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:2764193 original size:31 final size:31
Alignment explanation
Indices: 2764155--2764282 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
2764145 GATCCTCGGT
* *
2764155 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* **
2764186 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* * *
2764217 TATTGTCCATATGTCTCGAA-AGACATAGGTAA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* *
2764249 AACTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
2764280 AAC
1 AAC
2764283 CCTCGACTCT
Statistics
Matches: 78, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
30 1 0.01
31 52 0.67
32 24 0.31
33 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:2764263 original size:63 final size:62
Alignment explanation
Indices: 2764158--2764279 Score: 183
Period size: 63 Copynumber: 2.0 Consensus size: 62
2764148 CCTCGGTAAC
* *
2764158 TGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTATAT
1 TGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTATAT
* *
2764220 TGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTTCCGTAGAACATAGGTA
1 TGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCGTAGAACATAGGTA
2764280 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
61 1 0.02
62 22 0.41
63 31 0.57
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (62 bp):
TGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTATAT
Found at i:2766719 original size:6 final size:6
Alignment explanation
Indices: 2766710--2766748 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
2766700 ATTAAATTAA
2766710 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATT
2766749 AATCGGATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTAT
Found at i:2767566 original size:22 final size:21
Alignment explanation
Indices: 2767541--2767595 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 21
2767531 TATTTTGACT
2767541 AAATGTAGATATGATATATATA
1 AAATGTAGATATGATAT-TATA
2767563 AAAT-TAGA-AT-ATATTATA
1 AAATGTAGATATGATATTATA
*
2767581 AAATGTA-ATAGGATA
1 AAATGTAGATATGATA
2767596 AAAGTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 9 0.31
19 7 0.24
20 5 0.17
21 4 0.14
22 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.35
Consensus pattern (21 bp):
AAATGTAGATATGATATTATA
Found at i:2770502 original size:4 final size:4
Alignment explanation
Indices: 2770493--2770543 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
2770483 TTCACATGCC
2770493 AACA AACA AACA AACA AACA AACA AACA AACA AACA AACA AACA AACA
1 AACA AACA AACA AACA AACA AACA AACA AACA AACA AACA AACA AACA
2770541 AAC
1 AAC
2770544 CTCTTTATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:2772473 original size:2 final size:2
Alignment explanation
Indices: 2772466--2772517 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2772456 TTTTTATTTC
2772466 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
2772508 AT AT AT AT AT
1 AT AT AT AT AT
2772518 CTTTAATAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2773782 original size:13 final size:13
Alignment explanation
Indices: 2773764--2773805 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
2773754 ATTATTTATC
*
2773764 ATTAATAAATTTA
1 ATTAATAAATATA
2773777 ATTAAT-AATATA
1 ATTAATAAATATA
2773789 TATT-ATAAATATA
1 -ATTAATAAATATA
2773802 ATTA
1 ATTA
2773806 CTTTAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTAATAAATATA
Found at i:2775361 original size:17 final size:17
Alignment explanation
Indices: 2775341--2775381 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
2775331 ATAATTTATT
2775341 GAATTAAATTAAAATTA
1 GAATTAAATTAAAATTA
2775358 GAATTAAATTAAAATTA
1 GAATTAAATTAAAATTA
2775375 GAATTAA
1 GAATTAA
2775382 TTCAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (17 bp):
GAATTAAATTAAAATTA
Found at i:2776846 original size:3 final size:3
Alignment explanation
Indices: 2776838--2776883 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2776828 TCGAATACTT
2776838 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2776884 ACTAACCACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2778049 original size:17 final size:17
Alignment explanation
Indices: 2778027--2778072 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
2778017 GATCGAATGG
*
2778027 ACTCGACTCGAGCTCGA
1 ACTCGACTCGAGCTCAA
2778044 ACTCGACTCGAGCTCAA
1 ACTCGACTCGAGCTCAA
2778061 ACTCGACTCGAG
1 ACTCGACTCGAG
2778073 TTCTTAACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.26, C:0.35, G:0.22, T:0.17
Consensus pattern (17 bp):
ACTCGACTCGAGCTCAA
Found at i:2778192 original size:11 final size:11
Alignment explanation
Indices: 2778176--2778238 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
2778166 AAAATTATAT
2778176 TATTAAAAATA
1 TATTAAAAATA
2778187 TATTAAAAATA
1 TATTAAAAATA
* * ***
2778198 CACTATTGATA
1 TATTAAAAATA
2778209 -ATTATAAAAT-
1 TATTA-AAAATA
2778219 T-TTAAAAATA
1 TATTAAAAATA
2778229 TATTAAAAAT
1 TATTAAAAAT
2778239 TCTATAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:2778494 original size:17 final size:16
Alignment explanation
Indices: 2778472--2778532 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
2778462 GACAAATATT
2778472 TAATATATTTCTAATTA
1 TAATATATTT-TAATTA
*
2778489 TAATAT-TTTTAATAA
1 TAATATATTTTAATTA
2778504 CTAAT-TATTTTAAATTGA
1 -TAATATATTTT-AATT-A
*
2778522 TATTATATTTT
1 TAATATATTTT
2778533 GAGGTTTCGT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
15 6 0.17
16 11 0.31
17 12 0.33
18 7 0.19
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (16 bp):
TAATATATTTTAATTA
Found at i:2778678 original size:7 final size:7
Alignment explanation
Indices: 2778666--2778776 Score: 52
Period size: 7 Copynumber: 15.9 Consensus size: 7
2778656 TGCAATGAGC
2778666 CCTAAAT
1 CCTAAAT
*
2778673 CCTAAAC
1 CCTAAAT
2778680 CCTAAA-
1 CCTAAAT
*
2778686 CCACAAAT
1 CC-TAAAT
*
2778694 CCTAAAA
1 CCTAAAT
2778701 CCTTAAAT
1 CC-TAAAT
**
2778709 TATAAA-
1 CCTAAAT
2778715 CCTTAAA-
1 CC-TAAAT
2778722 CCTAAA-
1 CCTAAAT
2778728 CCATAAAT
1 CC-TAAAT
* *
2778736 CTTAAAC
1 CCTAAAT
*
2778743 CCTAAAC
1 CCTAAAT
2778750 CCTAAAT
1 CCTAAAT
*
2778757 ACTAAA-
1 CCTAAAT
*
2778763 CATTAAAT
1 C-CTAAAT
2778771 CCTAAA
1 CCTAAA
2778777 CCACAAACCC
Statistics
Matches: 79, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
6 8 0.10
7 63 0.80
8 8 0.10
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.23
Consensus pattern (7 bp):
CCTAAAT
Found at i:2778684 original size:14 final size:13
Alignment explanation
Indices: 2778666--2778819 Score: 87
Period size: 14 Copynumber: 11.2 Consensus size: 13
2778656 TGCAATGAGC
*
2778666 CCTAAATCCTAAA
1 CCTAAACCCTAAA
2778679 CCCTAAACCAC-AAA
1 -CCTAAACC-CTAAA
*
2778693 TCCTAAAACCTTAAA
1 -CCT-AAACCCTAAA
** *
2778708 TTATAAACCTTAAA
1 -CCTAAACCCTAAA
*
2778722 CCTAAACCATAAA
1 CCTAAACCCTAAA
*
2778735 TCTTAAACCCTAAA
1 -CCTAAACCCTAAA
**
2778749 CCCTAAATACTAAA
1 -CCTAAACCCTAAA
* *
2778763 CATTAAATCCTAAA
1 C-CTAAACCCTAAA
*
2778777 CCACAAACCCTAAA
1 CC-TAAACCCTAAA
*
2778791 CCATAAACCATAAA
1 CC-TAAACCCTAAA
2778805 CCTAAA-CCTAAA
1 CCTAAACCCTAAA
2778817 CCT
1 CCT
2778820 TACCTCTTAA
Statistics
Matches: 112, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
12 8 0.07
13 15 0.13
14 78 0.70
15 11 0.10
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.21
Consensus pattern (13 bp):
CCTAAACCCTAAA
Found at i:2778695 original size:21 final size:21
Alignment explanation
Indices: 2778669--2778818 Score: 85
Period size: 21 Copynumber: 6.9 Consensus size: 21
2778659 AATGAGCCCT
2778669 AAATCCTAAACCCTAAACCAC
1 AAATCCTAAACCCTAAACCAC
* ** *
2778690 AAATCCTAAAACCTTAAATTAT
1 AAATCCT-AAACCCTAAACCAC
*
2778712 AAA-CCTTAAA-CCTAAACCAT
1 AAATCC-TAAACCCTAAACCAC
*
2778732 AAATCTTAAACCCTAAACC-C
1 AAATCCTAAACCCTAAACCAC
*
2778752 TAAATACTAAACATTAAATCCTAAACCAC
1 -AAAT-C----C--TAAACCCTAAACCAC
* * *
2778781 AAACCCTAAACCATAAACCAT
1 AAATCCTAAACCCTAAACCAC
2778802 AAA-CCTAAA-CCTAAACC
1 AAATCCTAAACCCTAAACC
2778819 TTACCTCTTA
Statistics
Matches: 100, Mismatches: 16, Indels: 28
0.69 0.11 0.19
Matches are distributed among these distances:
19 7 0.07
20 20 0.20
21 40 0.40
22 15 0.15
23 1 0.01
27 1 0.01
28 15 0.15
29 1 0.01
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATCCTAAACCCTAAACCAC
Found at i:2778735 original size:27 final size:28
Alignment explanation
Indices: 2778698--2778841 Score: 91
Period size: 27 Copynumber: 5.0 Consensus size: 28
2778688 ACAAATCCTA
* *
2778698 AAACCTTAAAT-TATAAACCTTAAA-CCT
1 AAACCATAAATCT-TAAACCCTAAACCCT
2778725 AAACCATAAATCTTAAACCCTAAACCCT
1 AAACCATAAATCTTAAACCCTAAACCCT
*
2778753 AAATACTAAACATTAAATCCTAAACCAC-AAACCCT
1 -AA-AC----CA-TAAATCTTAAACC-CTAAACCCT
* *
2778788 AAACCATAAACCATAAA-CCTAAA-CCT
1 AAACCATAAATCTTAAACCCTAAACCCT
* ** *
2778814 AAACCTTACCTCTTAAACCCGAAACCCT
1 AAACCATAAATCTTAAACCCTAAACCCT
2778842 TAATTGTTAA
Statistics
Matches: 93, Mismatches: 11, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
26 16 0.17
27 29 0.31
28 16 0.17
29 4 0.04
30 2 0.02
33 2 0.02
34 4 0.04
35 19 0.20
36 1 0.01
ACGTcount: A:0.47, C:0.31, G:0.01, T:0.22
Consensus pattern (28 bp):
AAACCATAAATCTTAAACCCTAAACCCT
Found at i:2779608 original size:11 final size:11
Alignment explanation
Indices: 2779594--2779640 Score: 67
Period size: 11 Copynumber: 4.2 Consensus size: 11
2779584 CAGAATTGAA
2779594 CTTGAATCGAG
1 CTTGAATCGAG
2779605 CTTGAATCGAG
1 CTTGAATCGAG
2779616 CCTTGAATCGAG
1 -CTTGAATCGAG
* *
2779628 CTTCAATTGAG
1 CTTGAATCGAG
2779639 CT
1 CT
2779641 CTTAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (11 bp):
CTTGAATCGAG
Found at i:2779620 original size:23 final size:23
Alignment explanation
Indices: 2779594--2779639 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2779584 CAGAATTGAA
*
2779594 CTTGAATCGAGCTTGAATCGAGC
1 CTTGAATCGAGCTTCAATCGAGC
*
2779617 CTTGAATCGAGCTTCAATTGAGC
1 CTTGAATCGAGCTTCAATCGAGC
2779640 TCTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (23 bp):
CTTGAATCGAGCTTCAATCGAGC
Found at i:2779622 original size:12 final size:12
Alignment explanation
Indices: 2779594--2779628 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2779584 CAGAATTGAA
2779594 CTTGAATCGAG-
1 CTTGAATCGAGC
2779605 CTTGAATCGAGC
1 CTTGAATCGAGC
2779617 CTTGAATCGAGC
1 CTTGAATCGAGC
2779629 TTCAATTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 11 0.48
12 12 0.52
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (12 bp):
CTTGAATCGAGC
Found at i:2779666 original size:19 final size:19
Alignment explanation
Indices: 2779634--2779671 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2779624 CGAGCTTCAA
*
2779634 TTGAGCTCTTAAATTTTTG
1 TTGAGCTCTAAAATTTTTG
*
2779653 TTGAGTTCTAAAATTTTTG
1 TTGAGCTCTAAAATTTTTG
2779672 AGTTCGAGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.53
Consensus pattern (19 bp):
TTGAGCTCTAAAATTTTTG
Found at i:2780146 original size:30 final size:30
Alignment explanation
Indices: 2780112--2780183 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
2780102 CAGTTTTAAT
2780112 CGAATTAGTTCGGTTAAAACAGTTGACTAC
1 CGAATTAGTTCGGTTAAAACAGTTGACTAC
2780142 CGAATTAGTTCGGTTAAAACAGTTGACTAC
1 CGAATTAGTTCGGTTAAAACAGTTGACTAC
2780172 CGAATTAGTTCG
1 CGAATTAGTTCG
2780184 TTCGAAAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (30 bp):
CGAATTAGTTCGGTTAAAACAGTTGACTAC
Found at i:2780269 original size:2 final size:2
Alignment explanation
Indices: 2780262--2780331 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
2780252 AGTATTATGT
2780262 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2780304 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2780332 ATCGATTAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2786806 original size:77 final size:78
Alignment explanation
Indices: 2786661--2786825 Score: 287
Period size: 77 Copynumber: 2.1 Consensus size: 78
2786651 TGAATTAACA
* *
2786661 TAAATAATAATATAGTATGATACAATAGTTACATATTTAATCTCTAAAACTTGCATACTCTATTA
1 TAAATAATAATATAGTATGATACAATAGTTA-ATATTTAATCTCCAAAACTTGCATACTCTATGA
2786726 AATTAGACTTAATT
65 AATTAGACTTAATT
2786740 TAAATAATAATATAGTATGATACAATAGTT-ATATTTAATCTCCAAAACTTGCATACTCTATGAA
1 TAAATAATAATATAGTATGATACAATAGTTAATATTTAATCTCCAAAACTTGCATACTCTATGAA
2786804 ATTAGACTTAATT
66 ATTAGACTTAATT
2786817 TAAAATAAT
1 T-AAATAAT
2786826 TCAACTATTA
Statistics
Matches: 83, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
77 46 0.55
78 7 0.08
79 30 0.36
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (78 bp):
TAAATAATAATATAGTATGATACAATAGTTAATATTTAATCTCCAAAACTTGCATACTCTATGAA
ATTAGACTTAATT
Found at i:2788386 original size:21 final size:21
Alignment explanation
Indices: 2788360--2788404 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2788350 GATTTCTGGG
* *
2788360 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2788381 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2788402 CAA
1 CAA
2788405 ACGAACAACA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:2789796 original size:14 final size:14
Alignment explanation
Indices: 2789777--2789804 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2789767 GAAAAGAAGC
2789777 TATGTGATACGTGA
1 TATGTGATACGTGA
2789791 TATGTGATACGTGA
1 TATGTGATACGTGA
2789805 ATTACAAGTT
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:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:2790175 original size:149 final size:149
Alignment explanation
Indices: 2789905--2790368 Score: 876
Period size: 149 Copynumber: 3.1 Consensus size: 149
2789895 GAGTCGAGGG
2789905 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
2789970 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
2790035 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2790054 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
2790119 ACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
2790184 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
2790203 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
2790268 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
2790333 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
2790352 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
2790369 TGCAATTATA
Statistics
Matches: 308, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
148 1 0.00
149 307 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:2790369 original size:23 final size:23
Alignment explanation
Indices: 2790336--2790380 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2790326 ATCATTATAT
*
2790336 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
2790359 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
2790381 AGCTGTGGTG
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:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:2798416 original size:21 final size:21
Alignment explanation
Indices: 2798390--2798429 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2798380 CCCCCTTTGA
*
2798390 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2798411 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2798430 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2802433 original size:31 final size:30
Alignment explanation
Indices: 2802395--2802490 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
2802385 GTCAAAGAAC
2802395 TACCTATGTCTTTCGAGACATATGGACAGT
1 TACCTATGTCTTTCGAGACATATGGACAGT
*** *
2802425 ATACCTATGTTCTAAGGA-ACATATGGATAGTT
1 -TACCTATG-TCTTTCGAGACATATGGACAG-T
* * *
2802457 TACCTAGGT-TCTTCGGGACCTATGGACAGT
1 TACCTATGTCT-TTCGAGACATATGGACAGT
2802487 TACC
1 TACC
2802491 GAGGATCTTT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
29 1 0.02
30 7 0.14
31 36 0.72
32 6 0.12
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (30 bp):
TACCTATGTCTTTCGAGACATATGGACAGT
Found at i:2802507 original size:30 final size:30
Alignment explanation
Indices: 2802473--2802842 Score: 659
Period size: 30 Copynumber: 12.3 Consensus size: 30
2802463 GGTTCTTCGG
*
2802473 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
2802503 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
2802533 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
2802563 GACCTATGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
2802593 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
2802623 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
* *
2802653 GACCTCTGGATAGTTACTGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
2802683 GACCTCTGGACAGTTACCGTGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
2802713 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
*
2802743 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
2802773 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
2802803 GACCTCTGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGACAGTTACCGAGGATCTTTAT
2802833 GACCTCTGGA
1 GACCTCTGGA
2802843 TAGGTCCTTC
Statistics
Matches: 325, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 325 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
GACCTCTGGACAGTTACCGAGGATCTTTAT
Found at i:2808679 original size:29 final size:29
Alignment explanation
Indices: 2808629--2808685 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
2808619 AATCTACACT
*
2808629 TATAAGGTCGCCGGGATCACATGGCGACC
1 TATAAGGTCGCCGGCATCACATGGCGACC
2808658 TATAAGGTCGCCCGGCAT-ACATGGCGAC
1 TATAAGGTCG-CCGGCATCACATGGCGAC
2808686 TTCTATTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.25, C:0.28, G:0.30, T:0.18
Consensus pattern (29 bp):
TATAAGGTCGCCGGCATCACATGGCGACC
Found at i:2808832 original size:29 final size:29
Alignment explanation
Indices: 2808790--2808851 Score: 99
Period size: 29 Copynumber: 2.1 Consensus size: 29
2808780 AAGTGCAGCT
*
2808790 CCTATAAGGTCG-CCGGGATCACATGGCGA
1 CCTATAAGGTCGCCCGGCAT-ACATGGCGA
2808819 CCTATAAGGTCGCCCGGCATACATGGCGA
1 CCTATAAGGTCGCCCGGCATACATGGCGA
2808848 CCTA
1 CCTA
2808852 CATGAGATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (29 bp):
CCTATAAGGTCGCCCGGCATACATGGCGA
Found at i:2810039 original size:17 final size:16
Alignment explanation
Indices: 2809991--2810045 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
2809981 CGGGTCATTT
2809991 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* *
2810007 ACATGTCAGTTTAAAA
1 ACAGGTCAGGTTAAAA
* *
2810023 ACAGGTTAGGTTGAAA
1 ACAGGTCAGGTTAAAA
*
2810039 ACGGGTC
1 ACAGGTC
2810046 GGGTAATACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:2810641 original size:11 final size:11
Alignment explanation
Indices: 2810608--2810641 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2810598 AGACTCGAGA
*
2810608 CTCGATTCAAA
1 CTCGATTCAAG
*
2810619 CTCGATTTAAG
1 CTCGATTCAAG
2810630 CTCGATTCAAG
1 CTCGATTCAAG
2810641 C
1 C
2810642 ACAAGTGCTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (11 bp):
CTCGATTCAAG
Found at i:2812185 original size:28 final size:28
Alignment explanation
Indices: 2812153--2812208 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
2812143 AGAGGATTTA
2812153 ACTTAGACTAATCAATCTTACCCTGAGC
1 ACTTAGACTAATCAATCTTACCCTGAGC
2812181 ACTTAGACTAATCAATCTTACCCTGAGC
1 ACTTAGACTAATCAATCTTACCCTGAGC
2812209 CATTACATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.29, G:0.11, T:0.29
Consensus pattern (28 bp):
ACTTAGACTAATCAATCTTACCCTGAGC
Found at i:2815339 original size:79 final size:79
Alignment explanation
Indices: 2815254--2815420 Score: 280
Period size: 79 Copynumber: 2.1 Consensus size: 79
2815244 TGAATTAACA
*
2815254 TAAATAATAATATAGTACGATACAATAGTTACATATTTAATCTCCAAAACTTGCATACTCTATTA
1 TAAATAATAATATAGTACGATACAATAGTTACATATTTAATCTCCAAAACTTGCATACTCTATGA
*
2815319 AATTAGACTTAATT
66 AATTAAACTTAATT
* * *
2815333 TAAATAATAATATAGTATGATACGATAGTTACATATTTAATCTCCAGAACTTGCATACTCTATGA
1 TAAATAATAATATAGTACGATACAATAGTTACATATTTAATCTCCAAAACTTGCATACTCTATGA
2815398 AATTAAACTTAATT
66 AATTAAACTTAATT
2815412 TAAAATAAT
1 T-AAATAAT
2815421 TCAATTATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 75 0.91
80 7 0.09
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (79 bp):
TAAATAATAATATAGTACGATACAATAGTTACATATTTAATCTCCAAAACTTGCATACTCTATGA
AATTAAACTTAATT
Found at i:2817445 original size:12 final size:12
Alignment explanation
Indices: 2817428--2817453 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2817418 TAGAAAGAAT
2817428 AATAATAATAAA
1 AATAATAATAAA
2817440 AATAATAATAAA
1 AATAATAATAAA
2817452 AA
1 AA
2817454 ATGTTCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:2817592 original size:37 final size:37
Alignment explanation
Indices: 2817500--2817870 Score: 205
Period size: 37 Copynumber: 9.5 Consensus size: 37
2817490 ATTTTTTTAA
* * *
2817500 AAAAACTATATATTATACGTATTTTCAAAAACGTTTCA
1 AAAAACTATATATTATATGTATTTTCAAAAATGTTT-T
* **
2817538 AAAAACTATATAATATATGTATTTTTTAAAATGTTTT
1 AAAAACTATATATTATATGTATTTTCAAAAATGTTTT
** *
2817575 AAAAGTTATATATTATATATATTTTCAAAAATGTTTTTT
1 AAAAACTATATATTATATGTATTTTCAAAAATG--TTTT
* * ** *
2817614 AAAAAAAAAACCATATAACATATAAATGTTTTC-AAAATGTTTT
1 -----AAAAACTATAT-A-TTATATGTATTTTCAAAAATGTTTT
* **
2817657 CAAAACTATATATTATATAAATTTTCAAAAATGTTTT
1 AAAAACTATATATTATATGTATTTTCAAAAATGTTTT
* *
2817694 CAAAATTATATATTATATAAG-A-TTTCAAAAATGATTTT
1 AAAAACTATATATTATAT--GTATTTTCAAAAATG-TTTT
* * * * *
2817732 AAAAATTATATATTATCTATATTTTCTAAAACGTTTTTTTTTT
1 AAAAACTATATATTATATGTATTTTC-AAAA-----ATGTTTT
*
2817775 AAAAAAACTGTATATTATA--TAGTTTTCAAAAAATGTTTT
1 --AAAAACTATATATTATATGTA-TTTTC-AAAAATGTTTT
*
2817814 AAAAACTATATATTATATACGTATTTTCAAAGATCG-TTT
1 AAAAACTATATATTATAT--GTATTTTCAAAAAT-GTTTT
** *
2817853 GCAAACTATATAATATAT
1 AAAAACTATATATTATAT
2817871 ATATATGTAT
Statistics
Matches: 262, Mismatches: 42, Indels: 57
0.73 0.12 0.16
Matches are distributed among these distances:
36 10 0.04
37 83 0.32
38 65 0.25
39 36 0.14
40 6 0.02
41 2 0.01
43 10 0.04
44 18 0.07
45 21 0.08
46 11 0.04
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.43
Consensus pattern (37 bp):
AAAAACTATATATTATATGTATTTTCAAAAATGTTTT
Found at i:2817653 original size:11 final size:11
Alignment explanation
Indices: 2817637--2817661 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2817627 TATAACATAT
2817637 AAATGTTTTCA
1 AAATGTTTTCA
2817648 AAATGTTTTCA
1 AAATGTTTTCA
2817659 AAA
1 AAA
2817662 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:2817653 original size:82 final size:81
Alignment explanation
Indices: 2817537--2817693 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 81
2817527 AAAACGTTTC
* * ** * * *
2817537 AAAAAACTATATAATATATGTATTTTTTAAAATGTTTT-AAAAGTTATATATTATATATATTTTC
1 AAAAAACCATATAACATATAAATTTTTCAAAATGTTTTCAAAA-CTATATATTATATAAATTTTC
2817601 AAAAATGTTTTTTAAAA
65 AAAAATGTTTTTTAAAA
2817618 AAAAAACCATATAACATATAAATGTTTTCAAAATGTTTTCAAAACTATATATTATATAAATTTTC
1 AAAAAACCATATAACATATAAAT-TTTTCAAAATGTTTTCAAAACTATATATTATATAAATTTTC
2817683 AAAAATGTTTT
65 AAAAATGTTTT
2817694 CAAAATTATA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 19 0.28
82 44 0.66
83 4 0.06
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.43
Consensus pattern (81 bp):
AAAAAACCATATAACATATAAATTTTTCAAAATGTTTTCAAAACTATATATTATATAAATTTTCA
AAAATGTTTTTTAAAA
Found at i:2817863 original size:157 final size:157
Alignment explanation
Indices: 2817500--2817869 Score: 393
Period size: 157 Copynumber: 2.4 Consensus size: 157
2817490 ATTTTTTTAA
* *
2817500 AAAAACTATATA-T-TATACGTATTTTCAAAAACGTTTCAAAAAACTATATAATATATGTATTTT
1 AAAAACTATATATTATATACGTATTTTCAAAATCGTTTC--AAAACTATATAATATAAGTATTTT
** * *
2817563 TTAAAATGTTTTAAAAGTTATATATTATATATATTTTCAAAAATGTTTTTTAAAAAAAAAACCAT
64 CAAAAATGTTTTAAAAATTATATATTATATATATTTTCAAAAACGTTTTTTAAAAAAAAAACCAT
2817628 ATAACATATAAATGTTTTCAAAATGTTTT
129 ATAACATATAAATGTTTTCAAAATGTTTT
* * *
2817657 CAAAACTATATATTATATA--AATTTTCAAAAAT-GTTTTCAAAATTATATATTATATAAG-A-T
1 AAAAACTATATATTATATACGTATTTTC-AAAATCG-TTTCAAAACTATATA--ATATAAGTATT
* * ***
2817717 TTCAAAAATGATTTTAAAAATTATATATTATCTATATTTTCTAAAACGTTTTTTTTTTAAAAAAA
62 TTCAAAAATG-TTTTAAAAATTATATATTATATATATTTTCAAAAACG-TTTTTTAAAAAAAAAA
** * *
2817782 CTGTAT-A-TTATATA-GTTTTCAAAAAATGTTTT
125 CCATATAACATATAAATGTTTTC--AAAATGTTTT
2817814 AAAAACTATATATTATATACGTATTTTCAAAGATCGTTTGC-AAACTATATAATATA
1 AAAAACTATATATTATATACGTATTTTCAAA-ATCGTTT-CAAAACTATATAATATA
2817870 TATATATGTA
Statistics
Matches: 177, Mismatches: 21, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
155 6 0.03
156 24 0.14
157 86 0.49
158 35 0.20
159 24 0.14
160 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (157 bp):
AAAAACTATATATTATATACGTATTTTCAAAATCGTTTCAAAACTATATAATATAAGTATTTTCA
AAAATGTTTTAAAAATTATATATTATATATATTTTCAAAAACGTTTTTTAAAAAAAAAACCATAT
AACATATAAATGTTTTCAAAATGTTTT
Found at i:2818627 original size:84 final size:83
Alignment explanation
Indices: 2818519--2819280 Score: 603
Period size: 84 Copynumber: 9.2 Consensus size: 83
2818509 TCGGGGGTCT
* * *
2818519 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGT
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGATCGTAGT
* *
2818584 CAAACTCAAAAGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
* * * * * *
2818603 TTGGCAGACAACCCTCCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTCGT
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGATCGTAGT
*
2818668 CGAACTCGAAGGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
* ** * *
2818687 ATCACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGACCTCGAAGCTGAGT-GTA
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGA-TCGTA
* ** *
2818751 ATCGAACTC-GGGGTC----C
63 GTCGAACTCAAAGGTCTTTTG
* * *
2818767 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGT
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGAGCTGATCGTAGT
*
2818832 CAAACTCAAAGGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
* * * * * *
2818851 TTGGCAGACAACCCTCCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGATCGTAGT
*
2818916 CGAACTCGAAGGTCTTTTG
65 CGAACTCAAAGGTCTTTTG
* ** * *
2818935 GTCACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGACCTCGAAGCTGAGT-GTA
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGA-TCGTA
* ** *
2818999 ATCGAACTC-GGGGTC----C
63 GTCGAACTCAAAGGTCTTTTG
* * * *
2819015 TTGGCAGATAGCCCTTCTCA-ACTTAGGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGT-GT
1 TTGGCAGATAACCCTTCT-AGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGA-TCGT
* ***
2819078 AATCGAACTCGGGGGTCTTTTG
62 AGTCGAACTCAAAGGTCTTTTG
* ** * * * *
2819100 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGT-GTA
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTG-AGCTGA-TCGTA
* ***
2819164 ATCGAACTCGGGGGTC---T-
63 GTCGAACTCAAAGGTCTTTTG
* * * * *
2819181 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GAGCTGATCGTAGT
*
2819246 CGAACTCGAAGGTC--TTG
65 CGAACTCAAAGGTCTTTTG
* *
2819263 GTGGCAGATAGCCCTTCT
1 TTGGCAGATAACCCTTCT
2819281 GGCCTTGAGC
Statistics
Matches: 554, Mismatches: 98, Indels: 54
0.78 0.14 0.08
Matches are distributed among these distances:
78 1 0.00
79 18 0.03
80 133 0.24
81 45 0.08
82 18 0.03
83 4 0.01
84 227 0.41
85 108 0.19
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (83 bp):
TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGAGCTGATCGTAGTC
GAACTCAAAGGTCTTTTG
Found at i:2818893 original size:248 final size:247
Alignment explanation
Indices: 2818466--2819302 Score: 1128
Period size: 248 Copynumber: 3.4 Consensus size: 247
2818456 TGCCTTGAGC
* * * *
2818466 TATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACTCGGGGGTCTTTGGCAGATAGC
1 TATGCTGTAAATGATGTGACCTCGAAGCTGAGTGTAATCGAACTC-GGGGTCCTTGGCAGATAGC
*
2818531 CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCAAACTCAAAAG
65 CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCAAACTCAAAGG
*
2818596 TCTTTTGTTGGCAGACAACCCTCCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGA
130 TCTTTTGTTGGCAGACAACCCTCCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGA
*
2818661 GCGTCGTCGAACTCGAAGGTCTTTTGATCACAGATAACCCTTCTAGACTTAAGT
195 GCGTAGTCGAACTCGAAGGTCTTTTG-TCACAGATAACCCTTCTAGACTTAAGT
2818715 TATGCTGTAAATGATGTGACCTCGAAGCTGAGTGTAATCGAACTCGGGGTCCTTGGCAGATAGCC
1 TATGCTGTAAATGATGTGACCTCGAAGCTGAGTGTAATCGAACTCGGGGTCCTTGGCAGATAGCC
2818780 CTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCAAACTCAAAGGT
66 CTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCAAACTCAAAGGT
2818845 CTTTTGTTGGCAGACAACCCTCCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAG
131 CTTTTGTTGGCAGACAACCCTCCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAG
2818910 CGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGT
196 CGTAGTCGAACTCGAAGGTCTTTT-GTCACAGATAACCCTTCTAGACTTAAGT
2818963 TATGCTGTAAATGATGTGACCTCGAAGCTGAGTGTAATCGAACTCGGGGTCCTTGGCAGATAGCC
1 TATGCTGTAAATGATGTGACCTCGAAGCTGAGTGTAATCGAACTCGGGGTCCTTGGCAGATAGCC
* * * * * * ***
2819028 CTTCTCAACTTAGGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGT-GTAATCGAACTCGGGG
66 CTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGA-TCGTAGTCAAACTCAAAG
* ** * * * * * * * *
2819092 GTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCT
129 GTCTTTTGTTGGCAGACAACCCTCCTAGACTTAAGTTGTGCTGTAAATGATATG-CCTTGGAGCT
* * ** * * * *
2819157 GAGTGTAATCGAACTCGGGGGTC-TTTG--GCAGATAGCCCTTCTCGACTTAAGC
193 GAGCGTAGTCGAACTCGAAGGTCTTTTGTCACAGATAACCCTTCTAGACTTAAGT
* * * * * * * *
2819209 TATTCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTGGTGGCAGATA
1 TATGCTGTAAATGATGTGACCTCGAAGCTGAGTGTAATCGAACTCG-GGGTCCT--TGGCAGATA
* * *
2819273 GCCCTTCTGGCCTTGAGCTAAT-CTGCAAAT
63 GCCCTTCTCGACTTAAGCT-ATGCTGCAAAT
2819303 AGTTTGTTTA
Statistics
Matches: 532, Mismatches: 48, Indels: 17
0.89 0.08 0.03
Matches are distributed among these distances:
245 23 0.04
246 42 0.08
248 329 0.62
249 110 0.21
250 28 0.05
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.29
Consensus pattern (247 bp):
TATGCTGTAAATGATGTGACCTCGAAGCTGAGTGTAATCGAACTCGGGGTCCTTGGCAGATAGCC
CTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGATCGTAGTCAAACTCAAAGGT
CTTTTGTTGGCAGACAACCCTCCTAGACTTAAGTTGTGCTGTAAATGATATGCCTTGGAGCTGAG
CGTAGTCGAACTCGAAGGTCTTTTGTCACAGATAACCCTTCTAGACTTAAGT
Found at i:2824675 original size:38 final size:37
Alignment explanation
Indices: 2824632--2825001 Score: 122
Period size: 37 Copynumber: 9.5 Consensus size: 37
2824622 TATTTTTTTT
*
2824632 AAAACTATATATTATACGTATTTTCAAAAACGTTTCAA
1 AAAACTATATATTATATGTATTTTCAAAAACGTTT-AA
* ** * *
2824670 AAAACTATATAATATATGTATTTTTTAAAATGTTTTA
1 AAAACTATATATTATATGTATTTTCAAAAACGTTTAA
** * **
2824707 AAAGTTATATATTATATATATTTTCAAAAATATTTTTTTTAAAAAA
1 AAAACTATATATTATATGTATTTTC-AAAA-A---CGTTT----AA
* * ** * * **
2824753 AAAACCATATAACATATAAATGTTTTC-AAAATGTTTTC
1 AAAACTATAT-A-TTATATGTATTTTCAAAAACGTTTAA
** * **
2824791 AAAACTATATATTATATAAATTTTCAAAAATGTTTTC
1 AAAACTATATATTATATGTATTTTCAAAAACGTTTAA
* * *
2824828 AAAATTATATATTATATAAG-A-TTTCAAAAATGATTTTA
1 AAAACTATATATTATAT--GTATTTTCAAAAACG-TTTAA
* * * *
2824866 AAAATTATATATTATCTATATTTTCTAAAACGTTTATTTTATA
1 AAAACTATATATTATATGTATTTTCAAAAACG-----TTTA-A
* * *
2824909 AAAACTGTATATTATA--TAGTTTTCAAAAAATGTTTTA
1 AAAACTATATATTATATGTA-TTTTC-AAAAACGTTTAA
* *
2824946 AAAACTATATATTATATACGTATTTTCAAAGATCGTTT-G
1 AAAACTATATATTATAT--GTATTTTCAAA-AACGTTTAA
* *
2824985 CAAACTATATAATATAT
1 AAAACTATATATTATAT
2825002 ATATATGTAT
Statistics
Matches: 254, Mismatches: 49, Indels: 57
0.71 0.14 0.16
Matches are distributed among these distances:
36 10 0.04
37 77 0.30
38 75 0.30
39 19 0.07
40 10 0.04
41 4 0.02
42 16 0.06
43 19 0.07
45 1 0.00
46 11 0.04
47 1 0.00
48 11 0.04
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (37 bp):
AAAACTATATATTATATGTATTTTCAAAAACGTTTAA
Found at i:2824723 original size:37 final size:36
Alignment explanation
Indices: 2824628--2825001 Score: 128
Period size: 38 Copynumber: 9.6 Consensus size: 36
2824618 AAAATATTTT
*
2824628 TTTTAAAACTATATATTATACGTATTTTCAAAAACG
1 TTTTAAAACTATATATTATATGTATTTTCAAAAACG
* * ** *
2824664 TTTCAAAAAACTATATAATATATGTATTTTTTAAAATG
1 TTT--TAAAACTATATATTATATGTATTTTCAAAAACG
* * **
2824702 TTTTAAAAGTTATATATTATATATATTTTCAAAAATATTTT
1 TTTTAAAA-CTATATATTATATGTATTTTC-AAAA-A--CG
* * ** * *
2824743 TTTTAAAAAAAAAACCATATAACATATAAATGTTTTC-AAAATG
1 TTTT------AAAACTATAT-A-TTATATGTATTTTCAAAAACG
** *
2824786 TTTTCAAAACTATATATTATATAAATTTTCAAAAATG
1 TTTT-AAAACTATATATTATATGTATTTTCAAAAACG
* *
2824823 TTTTCAAAATTATATATTATATAAG-A-TTTCAAAAATG
1 TTTT-AAAACTATATATTATAT--GTATTTTCAAAAACG
* * * *
2824860 ATTTTAAAAATTATATATTATCTATATTTTCTAAAACG
1 -TTTT-AAAACTATATATTATATGTATTTTCAAAAACG
* *
2824898 TTTATTTTATAAAAACTGTATATTATA--TAGTTTTCAAAAAATG
1 -----TTT-T-AAAACTATATATTATATGTA-TTTTC-AAAAACG
*
2824941 TTTTAAAAACTATATATTATATACGTATTTTCAAAGATCG
1 TTTT-AAAACTATATATTATAT--GTATTTTCAAA-AACG
** *
2824981 TTTGCAAACTATATAATATAT
1 TTTTAAAACTATATATTATAT
2825002 ATATATGTAT
Statistics
Matches: 261, Mismatches: 44, Indels: 63
0.71 0.12 0.17
Matches are distributed among these distances:
36 17 0.07
37 74 0.28
38 75 0.29
39 19 0.07
40 10 0.04
41 9 0.03
42 8 0.03
43 25 0.10
45 1 0.00
46 7 0.03
47 5 0.02
48 11 0.04
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (36 bp):
TTTTAAAACTATATATTATATGTATTTTCAAAAACG
Found at i:2824756 original size:84 final size:84
Alignment explanation
Indices: 2824668--2824826 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 84
2824658 AAAACGTTTC
* * ** * * *
2824668 AAAAAACTATATAATATATGTAT-TTTTTAAAATGTTTT-AAAAGTTATATATTATATATATTTT
1 AAAAAACCATATAACATATAAATGTTTTCAAAATGTTTTCAAAA-CTATATATTATATAAATTTT
2824731 CAAAAATATTTTTTTTAAAA
65 CAAAAATATTTTTTTTAAAA
2824751 AAAAAACCATATAACATATAAATGTTTTCAAAATGTTTTCAAAACTATATATTATATAAATTTTC
1 AAAAAACCATATAACATATAAATGTTTTCAAAATGTTTTCAAAACTATATATTATATAAATTTTC
*
2824816 AAAAATGTTTT
66 AAAAATATTTT
2824827 CAAAATTATA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
83 19 0.29
84 43 0.65
85 4 0.06
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.44
Consensus pattern (84 bp):
AAAAAACCATATAACATATAAATGTTTTCAAAATGTTTTCAAAACTATATATTATATAAATTTTC
AAAAATATTTTTTTTAAAA
Found at i:2824786 original size:11 final size:11
Alignment explanation
Indices: 2824770--2824794 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2824760 TATAACATAT
2824770 AAATGTTTTCA
1 AAATGTTTTCA
2824781 AAATGTTTTCA
1 AAATGTTTTCA
2824792 AAA
1 AAA
2824795 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:2825003 original size:159 final size:157
Alignment explanation
Indices: 2824627--2825004 Score: 366
Period size: 159 Copynumber: 2.4 Consensus size: 157
2824617 AAAAATATTT
* * *
2824627 TTTTTAAAACTATATA-T-TATACGTATTTTCAAAAACGTTTCAAAAAACTATATAATATATGT-
1 TTTTAAAAACTATATATTATATACGTATTTTCAAAATCGTTTC---AAACTATATAATATATATA
* ** * * *
2824689 ATTTTTTAAAATGTTTTAAAAGTTATATATTATATATATTTTCAAAAATATTTTTTTTAAAAAAA
63 AATTTCAAAAATGTTTTAAAAATTATATATTATATATATTTTCAAAAACATTTATTTT--AAAAA
2824754 AAACCATATAACATATAAATGTTTTCAAAATG
126 AAACCATATAACATATAAATGTTTTCAAAATG
* * *
2824786 TTTTCAAAACTATATATTATATA--AATTTTCAAAAAT-GTTTTCAAAAT-TAT-ATATTATATA
1 TTTTAAAAACTATATATTATATACGTATTTTC-AAAATCG-TTTCAAACTATATAATA-TATATA
* * * *
2824846 AGATTTCAAAAATGATTTTAAAAATTATATATTATCTATATTTTCTAAAACGTTTATTTT-ATAA
63 A-ATTTCAAAAATG-TTTTAAAAATTATATATTATATATATTTTCAAAAACATTTATTTTAAAAA
** * *
2824910 AAACTGTAT-A-TTATATA-GTTTTCAAAAAATG
126 AAACCATATAACATATAAATGTTTTC--AAAATG
2824941 TTTTAAAAACTATATATTATATACGTATTTTCAAAGATCGTTTGCAAACTATATAATATATATA
1 TTTTAAAAACTATATATTATATACGTATTTTCAAA-ATCGTTT-CAAACTATATAATATATATA
2825005 TATGTATAAA
Statistics
Matches: 180, Mismatches: 22, Indels: 34
0.76 0.09 0.14
Matches are distributed among these distances:
153 6 0.03
154 5 0.03
155 32 0.18
156 20 0.11
157 16 0.09
158 15 0.08
159 70 0.39
160 12 0.07
161 4 0.02
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (157 bp):
TTTTAAAAACTATATATTATATACGTATTTTCAAAATCGTTTCAAACTATATAATATATATAAAT
TTCAAAAATGTTTTAAAAATTATATATTATATATATTTTCAAAAACATTTATTTTAAAAAAAACC
ATATAACATATAAATGTTTTCAAAATG
Found at i:2831729 original size:2 final size:2
Alignment explanation
Indices: 2831722--2831750 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2831712 ATATTATTAC
2831722 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2831751 AGTGATGACG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2832740 original size:22 final size:22
Alignment explanation
Indices: 2832715--2832766 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
2832705 GATGCCGAGA
2832715 TTGTGGAGGCTCACGCTATATG
1 TTGTGGAGGCTCACGCTATATG
2832737 TTGTGGAGGCTCACGCTATATG
1 TTGTGGAGGCTCACGCTATATG
2832759 TTGTGGAG
1 TTGTGGAG
2832767 TCCGCCTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.15, G:0.35, T:0.33
Consensus pattern (22 bp):
TTGTGGAGGCTCACGCTATATG
Found at i:2834532 original size:35 final size:35
Alignment explanation
Indices: 2834493--2834741 Score: 227
Period size: 35 Copynumber: 6.9 Consensus size: 35
2834483 TGAATAAGAA
2834493 GAACGAAAGGAAGCATAGCACTTTCGATTCAAGTT
1 GAACGAAAGGAAGCATAGCACTTTCGATTCAAGTT
* * *
2834528 GAACGAAATGAGGCAGAGCACTTTCGATTCAAGTT
1 GAACGAAAGGAAGCATAGCACTTTCGATTCAAGTT
* * * *
2834563 GAACGAAAGAAAGCAAAGCATTTTCGATTCTCGTATAAAGTA
1 GAACGAAAGGAAGCATAGCACTTTCGA-T-TC-----AAGTT
2834605 GAAC-AGAAGGAAGCATCA-CACTTTCGATTCAAGTT
1 GAACGA-AAGGAAGCAT-AGCACTTTCGATTCAAGTT
* *
2834640 GAAC-AGAAGGAAGCATTGCACTTTCGATTCAAGTA
1 GAACGA-AAGGAAGCATAGCACTTTCGATTCAAGTT
* * *
2834675 GAACGGAAGGAAGTATCA-CACTTTCGATTCAAGTC
1 GAACGAAAGGAAGCAT-AGCACTTTCGATTCAAGTT
* * * *
2834710 GAACGGAAGAAAGCATTGCACTTTAGATTCAA
1 GAACGAAAGGAAGCATAGCACTTTCGATTCAA
2834742 TTGTTCATCT
Statistics
Matches: 178, Mismatches: 23, Indels: 26
0.78 0.10 0.11
Matches are distributed among these distances:
35 146 0.82
36 1 0.01
37 2 0.01
40 2 0.01
41 2 0.01
42 24 0.13
43 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (35 bp):
GAACGAAAGGAAGCATAGCACTTTCGATTCAAGTT
Found at i:2834577 original size:70 final size:70
Alignment explanation
Indices: 2834493--2834741 Score: 252
Period size: 70 Copynumber: 3.5 Consensus size: 70
2834483 TGAATAAGAA
* * * * *
2834493 GAACGAAAGGAAGCATAGCACTTTCGATTCAAGTTGAACGAAATGAGGCA-GAGCACTTTCGATT
1 GAACGAAAGAAAGCATAGCACTTTCGATTCAAGTAGAACGAAAGGAAGCATCA-CACTTTCGATT
2834557 CAAGTT
65 CAAGTT
* *
2834563 GAACGAAAGAAAGCAAAGCATTTTCGATTCTCGTATAAAGTAGAAC-AGAAGGAAGCATCACACT
1 GAACGAAAGAAAGCATAGCACTTTCGA-T-TC-----AAGTAGAACGA-AAGGAAGCATCACACT
2834627 TTCGATTCAAGTT
58 TTCGATTCAAGTT
* * * *
2834640 GAAC-AGAAGGAAGCATTGCACTTTCGATTCAAGTAGAACGGAAGGAAGTATCACACTTTCGATT
1 GAACGA-AAGAAAGCATAGCACTTTCGATTCAAGTAGAACGAAAGGAAGCATCACACTTTCGATT
*
2834704 CAAGTC
65 CAAGTT
* * *
2834710 GAACGGAAGAAAGCATTGCACTTTAGATTCAA
1 GAACGAAAGAAAGCATAGCACTTTCGATTCAA
2834742 TTGTTCATCT
Statistics
Matches: 150, Mismatches: 17, Indels: 24
0.79 0.09 0.13
Matches are distributed among these distances:
70 88 0.59
71 1 0.01
72 2 0.01
75 2 0.01
76 3 0.02
77 53 0.35
78 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (70 bp):
GAACGAAAGAAAGCATAGCACTTTCGATTCAAGTAGAACGAAAGGAAGCATCACACTTTCGATTC
AAGTT
Found at i:2835642 original size:14 final size:16
Alignment explanation
Indices: 2835608--2835642 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
2835598 TCGAATTATA
2835608 ATATATAAATACAAAT
1 ATATATAAATACAAAT
2835624 ATATATAAATA-AAAT
1 ATATATAAATACAAAT
2835639 -TATA
1 ATATA
2835643 CTCGAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 4 0.21
16 11 0.58
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATATAAATACAAAT
Found at i:2836059 original size:21 final size:20
Alignment explanation
Indices: 2835973--2836129 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
2835963 AAATGACCAA
**
2835973 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
2835992 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
2836012 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
2836032 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * **
2836053 GAAAATCGCAATGCGATAGT
1 CAAAATCGCAACGCGATTTT
* **
2836073 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
2836093 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
2836114 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
2836130 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 9
0.73 0.20 0.06
Matches are distributed among these distances:
19 16 0.15
20 56 0.54
21 32 0.31
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:2836082 original size:41 final size:41
Alignment explanation
Indices: 2835973--2836129 Score: 126
Period size: 41 Copynumber: 3.9 Consensus size: 41
2835963 AAATGACCAA
* **
2835973 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGA-TCCC
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
* ** * *
2836012 CAGAATCGCAAATC-AGTTTCCAAAATCGCAACGCGATTCTT-
1 CAAAATCGCAACGCGAATAT-CAAAATCGCAACGCGATT-TTC
* * * **
2836053 GAAAATCGCAATGCG-ATAGTCAAATTCGCATTGCGATTTTC
1 CAAAATCGCAACGCGAATA-TCAAAATCGCAACGCGATTTTC
*
2836094 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATCAAAATCGCAACGCGA
2836130 ACACATAAAT
Statistics
Matches: 87, Mismatches: 23, Indels: 14
0.70 0.19 0.11
Matches are distributed among these distances:
38 1 0.01
39 12 0.14
40 17 0.20
41 53 0.61
42 4 0.05
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (41 bp):
CAAAATCGCAACGCGAATATCAAAATCGCAACGCGATTTTC
Found at i:2836158 original size:20 final size:20
Alignment explanation
Indices: 2836096--2836289 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
2836086 CGATTTTCCA
* ** *
2836096 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
2836116 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
2836136 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
2836156 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
2836176 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* *
2836196 AAATCGCAATGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
2836216 ATATCGCAACGCGTATCGGT
1 AAATCGCAACGCGTATCCGT
* * *
2836236 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
2836256 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
*
2836277 GAATCGCAACGCG
1 AAATCGCAACGCG
2836290 ATATTTAAAG
Statistics
Matches: 141, Mismatches: 28, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
19 2 0.01
20 121 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:2836181 original size:60 final size:60
Alignment explanation
Indices: 2836096--2836289 Score: 226
Period size: 60 Copynumber: 3.2 Consensus size: 60
2836086 CGATTTTCCA
* ** * *
2836096 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** * *
2836156 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGTGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
2836216 ATATCGCAACGCGTATCGGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
*
2836277 GAATCGCAACGCG
1 AAATCGCAACGCG
2836290 ATATTTAAAG
Statistics
Matches: 108, Mismatches: 25, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
60 79 0.73
61 29 0.27
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:2836711 original size:33 final size:33
Alignment explanation
Indices: 2836672--2836742 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
2836662 TTCACTTAGA
2836672 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
2836705 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
2836738 TTTCA
1 TTTCA
2836743 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:2836879 original size:41 final size:41
Alignment explanation
Indices: 2836821--2836898 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
2836811 TTGCAAAAGA
*
2836821 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
2836862 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
2836899 CGCAAAGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:2836895 original size:21 final size:21
Alignment explanation
Indices: 2836822--2836897 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
2836812 TGCAAAAGAG
*
2836822 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
2836843 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
2836863 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
2836884 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
2836898 TCGCAAAGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:2836901 original size:14 final size:14
Alignment explanation
Indices: 2836882--2836938 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2836872 GAGAAATGAA
2836882 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
2836896 AATCGCAAAGCGATATGAA
1 AATCGC-AA-CG--A-GAG
2836915 AATCGCAACGAGAG
1 AATCGCAACGAGAG
2836929 AATCGCAACG
1 AATCGCAACG
2836939 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 3 0.08
16 2 0.06
17 2 0.06
18 3 0.08
19 8 0.22
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:2836915 original size:33 final size:33
Alignment explanation
Indices: 2836877--2836941 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
2836867 AACGAGAGAA
2836877 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
*
2836910 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAAAGCGA
2836942 AACCAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAAAGCGAT
Found at i:2836950 original size:33 final size:33
Alignment explanation
Indices: 2836880--2836954 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
2836870 GAGAGAAATG
* **
2836880 AAAATCGCAACGAGAGAATCGCAAAGCGATATG
1 AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
*
2836913 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
2836946 AAAATCGCA
1 AAAATCGCA
2836955 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAAAGCGAAACC
Found at i:2836972 original size:19 final size:19
Alignment explanation
Indices: 2836950--2837047 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
2836940 GAAACCAAAA
*
2836950 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2836969 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
2836983 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2837002 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
2837016 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
2837035 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2837048 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2836991 original size:14 final size:14
Alignment explanation
Indices: 2836972--2837061 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
2836962 TTTCATTTCG
2836972 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2836986 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
2837005 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
2837019 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
2837038 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
2837052 CGTTGCGATT
1 CGTTGCGATT
2837062 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:2836997 original size:33 final size:33
Alignment explanation
Indices: 2836955--2837069 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
2836945 CAAAATCGCA
2836955 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2836988 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
2837021 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
2837054 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
2837070 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:2838921 original size:93 final size:93
Alignment explanation
Indices: 2838762--2839323 Score: 1074
Period size: 93 Copynumber: 6.1 Consensus size: 93
2838752 TAGATTGCTT
*
2838762 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2838827 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2838855 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2838920 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2838948 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2839013 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2839041 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2839106 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
2839134 AGTAAATTTGTTCGGTTACTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
2839199 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
2839226 AGTAAATTGTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATT-TGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
2839291 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
2839319 AGTAA
1 AGTAA
2839324 TGCAATCCAT
Statistics
Matches: 462, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 35 0.08
93 402 0.87
94 25 0.05
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:2839411 original size:19 final size:19
Alignment explanation
Indices: 2839371--2839499 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
2839361 TAGTTTACTT
* *
2839371 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
2839391 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
2839410 TCGCAACGCGAAATAAAAA
1 TCGCAACGCGAAACCAAAA
*
2839429 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
2839443 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
2839462 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
2839476 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
2839495 TCGCA
1 TCGCA
2839500 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:2839445 original size:33 final size:32
Alignment explanation
Indices: 2839407--2839499 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
2839397 CGCGAAACCA
**
2839407 AAATCGCAACGCGAAATAAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
2839439 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
2839472 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
2839500 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:2839497 original size:52 final size:52
Alignment explanation
Indices: 2839371--2839499 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 52
2839361 TAGTTTACTT
* **
2839371 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
*** *
2839423 TAAAAATCGC--AACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
2839476 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
2839500 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
51 3 0.05
52 47 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:2839517 original size:19 final size:19
Alignment explanation
Indices: 2839495--2839629 Score: 130
Period size: 19 Copynumber: 7.6 Consensus size: 19
2839485 GAAACCAAAA
*
2839495 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2839514 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
2839530 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
2839547 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
2839563 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
2839580 TCGCGTTGCGATTTT-AGTT
1 TCGCGTTGCGATTTTCA-TT
*
2839599 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
2839619 TCGTGTTGCGA
1 TCGCGTTGCGA
2839630 AAGTAAACTA
Statistics
Matches: 98, Mismatches: 6, Indels: 23
0.77 0.05 0.18
Matches are distributed among these distances:
14 15 0.15
16 11 0.11
17 11 0.11
18 1 0.01
19 46 0.47
20 14 0.14
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:2839536 original size:14 final size:14
Alignment explanation
Indices: 2839517--2839573 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
2839507 TTTCATTTCG
2839517 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
2839531 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
2839548 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
2839564 CGTTGCGATT
1 CGTTGCGATT
2839574 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:2839542 original size:33 final size:33
Alignment explanation
Indices: 2839500--2839592 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
2839490 CAAAATCGCA
*
2839500 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
2839533 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
2839566 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
2839593 TTAGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:2841568 original size:14 final size:14
Alignment explanation
Indices: 2841549--2841584 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2841539 ATTGTTTAAT
2841549 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
2841563 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
2841577 TGATTTGT
1 TGATTTGT
2841585 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:2841707 original size:19 final size:19
Alignment explanation
Indices: 2841691--2841788 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
2841681 AAAAATGACT
2841691 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2841710 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2841729 ATCGCAAT--G--A-GAGA
1 ATCGCAATGCGAAATGAAA
2841743 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2841762 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
2841782 ATCGCAA
1 ATCGCAA
2841789 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.15
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 40 0.56
20 16 0.23
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2841820 original size:53 final size:53
Alignment explanation
Indices: 2841691--2841806 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
2841681 AAAAATGACT
*
2841691 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
2841743 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
2841796 ATCGCAATGCG
1 ATCGCAATGCG
2841807 TTTATAATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:2841850 original size:33 final size:33
Alignment explanation
Indices: 2841813--2841965 Score: 159
Period size: 33 Copynumber: 4.5 Consensus size: 33
2841803 TGCGTTTATA
2841813 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
2841846 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
2841886 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
2841917 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
2841950 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
2841966 TTCATTTCGC
Statistics
Matches: 97, Mismatches: 12, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 52 0.54
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:2841859 original size:19 final size:19
Alignment explanation
Indices: 2841835--2842051 Score: 240
Period size: 19 Copynumber: 12.4 Consensus size: 19
2841825 GATTCTCTCG
2841835 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2841854 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2841873 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2841887 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2841906 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2841925 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2841939 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
2841958 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
2841977 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
2841991 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
2842011 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
2842025 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
2842044 TTGCGATT
1 TTGCGATT
2842052 GTAATTTCCG
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 29 0.17
16 23 0.14
17 20 0.12
18 3 0.02
19 82 0.49
20 12 0.07
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:2841870 original size:52 final size:52
Alignment explanation
Indices: 2841813--2842023 Score: 413
Period size: 52 Copynumber: 4.0 Consensus size: 52
2841803 TGCGTTTATA
2841813 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2841865 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2841917 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
2841969 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
2842022 AT
1 AT
2842024 GTTGGGATTT
Statistics
Matches: 158, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 141 0.89
53 17 0.11
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:2841995 original size:33 final size:33
Alignment explanation
Indices: 2841854--2842051 Score: 197
Period size: 33 Copynumber: 5.8 Consensus size: 33
2841844 TCATTTCGCA
2841854 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2841887 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
* * * * *
2841923 CATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCA
1 --TTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG
2841958 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
2841991 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
2842025 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
2842052 GTAATTTCCG
Statistics
Matches: 137, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.07
32 5 0.04
33 62 0.45
34 29 0.21
35 6 0.04
36 4 0.03
37 2 0.01
38 8 0.06
39 3 0.02
40 9 0.07
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:2844350 original size:12 final size:12
Alignment explanation
Indices: 2844333--2844357 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2844323 TCTTCGGGGA
2844333 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2844345 CTTTTTCTTCTT
1 CTTTTTCTTCTT
2844357 C
1 C
2844358 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:2844565 original size:24 final size:24
Alignment explanation
Indices: 2844531--2844577 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2844521 CTGAAACATC
2844531 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
2844555 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
2844578 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:2845288 original size:20 final size:20
Alignment explanation
Indices: 2845260--2845469 Score: 206
Period size: 20 Copynumber: 10.5 Consensus size: 20
2845250 AAATTTCAGT
* * *
2845260 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2845280 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
2845300 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
2845320 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
2845340 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
2845360 GTTGCGATATACGGAAACGC
1 GTTGCGATTTACGGATTCGC
** *
2845380 GTTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
2845400 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
2845420 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
2845440 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
2845460 GTTGCGATTT
1 GTTGCGATTT
2845470 TGGAAAATCG
Statistics
Matches: 162, Mismatches: 26, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 161 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:2845486 original size:21 final size:20
Alignment explanation
Indices: 2845436--2845533 Score: 79
Period size: 20 Copynumber: 4.8 Consensus size: 20
2845426 ATTTATGTGT
* * * *
2845436 TCGCGTTGCGATTTTCATAT
1 TCGCATTGCGATTTTGAAAA
*
2845456 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTT-GAAAA
* * **
2845477 TCGCAATGCGAATTTGACTA
1 TCGCATTGCGATTTTGAAAA
*
2845497 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTGAA-AA
*
2845518 TCGCGTTGCGATTTTG
1 TCGCATTGCGATTTTG
2845534 GAAACTGATT
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 32 0.52
21 29 0.48
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTTGAAAA
Found at i:2845509 original size:61 final size:60
Alignment explanation
Indices: 2845436--2845592 Score: 176
Period size: 61 Copynumber: 2.6 Consensus size: 60
2845426 ATTTATGTGT
*
2845436 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATCGCA-ATGCGAATT-TGACTA
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAAT-G-ATATGCG-ATTCTGACGA
* * * * * **
2845497 TCGCATTGCGATTTTCAAGAATCGCGTTGCGATTTTGGAAACTGATTTGCGATTCTGGGGA
1 TCGCGTTGCGATTTTC-ATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
*
2845558 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTG
2845593 TTGGTCATTT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.20
60 5 0.06
61 37 0.46
62 23 0.28
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (60 bp):
TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAATGATATGCGATTCTGACGA
Found at i:2845528 original size:41 final size:41
Alignment explanation
Indices: 2845436--2845592 Score: 110
Period size: 41 Copynumber: 3.9 Consensus size: 41
2845426 ATTTATGTGT
* * *
2845436 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
** *
2845477 TCGCAATGCGAATTTGACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGATTTTGA-TATTCGCATTGCGATTTTGCAA-AA
* * * ***
2845518 TCGCGTTGCGATTTTGGAAACT-G-ATTTGCGATTCTG-GGGA
1 TCGCGTTGCGATTTT-GATATTCGCA-TTGCGATTTTGCAAAA
* *
2845558 TCGCGTTGCGATTTTTAT-TTCGCGTTGCGATTTTG
1 TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTG
2845593 TTGGTCATTT
Statistics
Matches: 89, Mismatches: 19, Indels: 18
0.71 0.15 0.14
Matches are distributed among these distances:
38 1 0.01
39 12 0.13
40 19 0.21
41 52 0.58
42 5 0.06
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATTTTGATATTCGCATTGCGATTTTGCAAAA
Done.