Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 30
Found at i:903660 original size:23 final size:23
Alignment explanation
Indices: 903630--903677 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
903620 TTCCATGGAC
903630 GAGCCACACCTTAAGCATCCTAT
1 GAGCCACACCTTAAGCATCCTAT
903653 GAGCCACACCTTAAGCATCCTAT
1 GAGCCACACCTTAAGCATCCTAT
903676 GA
1 GA
903678 CCCCCATGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (23 bp):
GAGCCACACCTTAAGCATCCTAT
Found at i:904610 original size:11 final size:12
Alignment explanation
Indices: 904588--904625 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
904578 TTTCGAGTGC
904588 AAAAAGAA-AAG
1 AAAAAGAAGAAG
904599 AAAAA-AAGAAG
1 AAAAAGAAGAAG
*
904610 AAAAAGTAGAAG
1 AAAAAGAAGAAG
904622 AAAA
1 AAAA
904626 GTTGCAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 2 0.08
11 13 0.54
12 9 0.38
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (12 bp):
AAAAAGAAGAAG
Found at i:908721 original size:9 final size:9
Alignment explanation
Indices: 908619--908804 Score: 65
Period size: 9 Copynumber: 20.1 Consensus size: 9
908609 ACCTTCTTTA
908619 TTTTTTATT
1 TTTTTTATT
908628 TTTTTATATT
1 TTTTT-TATT
* *
908638 CTATTTCATT
1 -TTTTTTATT
*
908648 TTTTTCATT
1 TTTTTTATT
*
908657 TTTTCTT-TC
1 TTTT-TTATT
*
908666 TTTTTTATA
1 TTTTTTATT
*
908675 TTTGTTA-T
1 TTTTTTATT
* *
908683 TCTCTTATT
1 TTTTTTATT
* *
908692 TTTATTAGT
1 TTTTTTATT
**
908701 TTTTGGA--
1 TTTTTTATT
*
908708 CTTTTTATT
1 TTTTTTATT
908717 TTTTTTATT
1 TTTTTTATT
*
908726 TTTTTCAATT
1 TTTTT-TATT
*
908736 TATTTTTTTT
1 T-TTTTTATT
* *
908746 ATTTTTTCTC
1 -TTTTTTATT
** *
908756 TGGTTTATG
1 TTTTTTATT
908765 TTTTTTATT
1 TTTTTTATT
908774 ATTTTATTATT
1 -TTTT-TTATT
*
908785 ATTTTTATT
1 TTTTTTATT
*
908794 TGTTTTGATT
1 T-TTTTTATT
908804 T
1 T
908805 ATTATTTTAC
Statistics
Matches: 129, Mismatches: 35, Indels: 25
0.68 0.19 0.13
Matches are distributed among these distances:
7 4 0.03
8 7 0.05
9 69 0.53
10 35 0.27
11 14 0.11
ACGTcount: A:0.15, C:0.06, G:0.05, T:0.75
Consensus pattern (9 bp):
TTTTTTATT
Found at i:908737 original size:23 final size:22
Alignment explanation
Indices: 908711--908844 Score: 92
Period size: 26 Copynumber: 5.7 Consensus size: 22
908701 TTTTGGACTT
*
908711 TTTATTTTTTTTATTTTTTTCAA
1 TTTATTTTTTTTATTTTTTT-GA
*
908734 TTTATTTTTTTTATTTTTTCTCTGG
1 TTTATTTTTTTTA-TTTTT-T-TGA
* *
908759 TTTATGTTTTTTATTATTTT-A
1 TTTATTTTTTTTATTTTTTTGA
*
908780 -TTATTATTTTTATTTGTTTTGA
1 TTTATTTTTTTTATTT-TTTTGA
* *
908802 TTTATTATTTTACTATTCATTTTTTA
1 TTTATT-TTTT-TTATT--TTTTTGA
908828 TTTATTATTTATTTATT
1 TTTATT-TTT-TTTATT
908845 ACTTTTGTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
20 12 0.14
21 4 0.05
22 2 0.02
23 19 0.22
24 12 0.14
25 17 0.19
26 20 0.23
27 2 0.02
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (22 bp):
TTTATTTTTTTTATTTTTTTGA
Found at i:908762 original size:25 final size:23
Alignment explanation
Indices: 908711--908812 Score: 86
Period size: 23 Copynumber: 4.5 Consensus size: 23
908701 TTTTGGACTT
908711 TTTATTTTTTTTATTTTTTTCAA
1 TTTATTTTTTTTATTTTTTTCAA
**
908734 TTTATTTTTTTTATTTTTTCTCTGG
1 TTTATTTTTTTTATTTTTT-TC-AA
* *
908759 TTTATGTTTTTTATTATTTT--A
1 TTTATTTTTTTTATTTTTTTCAA
* *
908780 -TTATTATTTTTATTTGTTTT-GA
1 TTTATTTTTTTTATTT-TTTTCAA
*
908802 TTTATTATTTT
1 TTTATTTTTTT
908813 ACTATTCATT
Statistics
Matches: 66, Mismatches: 8, Indels: 10
0.79 0.10 0.12
Matches are distributed among these distances:
20 12 0.18
21 4 0.06
22 1 0.02
23 29 0.44
24 3 0.05
25 17 0.26
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (23 bp):
TTTATTTTTTTTATTTTTTTCAA
Found at i:908773 original size:90 final size:95
Alignment explanation
Indices: 908615--908787 Score: 212
Period size: 90 Copynumber: 1.9 Consensus size: 95
908605 TTTAACCTTC
* * **
908615 TTTATTTTTTATTTTTTTATATTCTATTTCATTTTTTTCATTTTTTCTTTCTTTTTTATATTTGT
1 TTTATTTTTTATTATTTTATATTCAATTTCATTTTTTTCATTTTTTC-TTCTGGTTTATATTTGT
* *
908680 TATTCTCTTATTTTTATTAGTTTTTGGACTT
65 TATTATCTTATTATTATTAGTTTTTGGACTT
* * *
908711 TTTATTTTTT-TTATTTT-T-TTCAATTT-ATTTTTTTTATTTTTTC-TCTGGTTTATGTTTTTT
1 TTTATTTTTTATTATTTTATATTCAATTTCATTTTTTTCATTTTTTCTTCTGGTTTATATTTGTT
*
908771 ATTATTTTATTATTATT
66 ATTATCTTATTATTATT
908788 TTTATTTGTT
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
90 27 0.40
92 16 0.24
93 7 0.10
94 1 0.01
95 6 0.09
96 10 0.15
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.75
Consensus pattern (95 bp):
TTTATTTTTTATTATTTTATATTCAATTTCATTTTTTTCATTTTTTCTTCTGGTTTATATTTGTT
ATTATCTTATTATTATTAGTTTTTGGACTT
Found at i:908829 original size:11 final size:10
Alignment explanation
Indices: 908709--908840 Score: 51
Period size: 9 Copynumber: 12.8 Consensus size: 10
908699 GTTTTTGGAC
908709 TTTTTATT-T
1 TTTTTATTAT
908718 TTTTTATT-T
1 TTTTTATTAT
*
908727 TTTTCAATTTAT
1 TTTT-TA-TTAT
908739 TTTTT-TTAT
1 TTTTTATTAT
* *
908748 TTTTT-CTCT
1 TTTTTATTAT
** *
908757 GGTTTA-TGT
1 TTTTTATTAT
908766 TTTTTATTAT
1 TTTTTATTAT
908776 TTTATTATTA-
1 TTT-TTATTAT
*
908786 TTTTTATTTGTT
1 TTTTTA-TT-AT
908798 TTGATTTATTAT
1 TT--TTTATTAT
*
908810 TTTACTATTCAT
1 TTT-TTATT-AT
908822 TTTTTATTTAT
1 TTTTTA-TTAT
*
908833 TATTTATT
1 TTTTTATT
908841 TATTACTTTT
Statistics
Matches: 94, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
9 36 0.38
10 14 0.15
11 21 0.22
12 17 0.18
13 2 0.02
14 4 0.04
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (10 bp):
TTTTTATTAT
Found at i:908841 original size:11 final size:11
Alignment explanation
Indices: 908768--908845 Score: 52
Period size: 11 Copynumber: 6.6 Consensus size: 11
908758 GTTTATGTTT
908768 TTTATTATTT-
1 TTTATTATTTA
908778 TATTATTATTTTTA
1 T-TTATTA--TTTA
* *
908792 TTTGTT-TTGA
1 TTTATTATTTA
908802 TTTATTATTTTA
1 TTTATTA-TTTA
*
908814 CTATTCATTTTTTA
1 -T-TT-ATTATTTA
908828 TTTATTATTTA
1 TTTATTATTTA
908839 TTTATTA
1 TTTATTA
908846 CTTTTGTATC
Statistics
Matches: 53, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
10 9 0.17
11 20 0.38
12 5 0.09
13 9 0.17
14 7 0.13
15 3 0.06
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:912585 original size:36 final size:37
Alignment explanation
Indices: 912537--912610 Score: 123
Period size: 36 Copynumber: 2.0 Consensus size: 37
912527 CAAAAAAAAG
* *
912537 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AAA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACTAAA
912573 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACTAAA
1 TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACTAAA
912610 T
1 T
912611 CTTTGAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 31 0.89
37 4 0.11
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (37 bp):
TTTTATCTCTCTTGAGACAGTTTCCCTTGAAACTAAA
Found at i:912733 original size:36 final size:36
Alignment explanation
Indices: 912613--912852 Score: 156
Period size: 36 Copynumber: 6.8 Consensus size: 36
912603 AACTAAATCT
* **
912613 TTGA-ATATGTTTTCCTTGAAACAAATTTCGTCTCCC
1 TTGAGATA-GTTTCCCTTGAAACAAATTTTATCTCCC
* * ** * * * *
912649 TTGAGACAATTTCTTTTGGAACTAAGTTTTGTCTCTC
1 TTGAGATAGTTTCCCTTGAAAC-AAATTTTATCTCCC
* *
912686 TTGAGACAGTTTCCCTTGAAACAAATTTTATCTCAC
1 TTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
912722 TTGAGATAGTTTCCCTTGAAACAAA----ATCT---
1 TTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
* *
912751 TTGA-ATATGTTTTCCTTGAAACAAATTTCATCTCCC
1 TTGAGATA-GTTTCCCTTGAAACAAATTTTATCTCCC
* ** * * * *
912787 TTGATATAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 TTGAGATAGTTTCCCTTGAAAC-AAATTTTATCTCCC
* * *
912824 TTGAGACAGTTTCTCTTGAAACAATTTTT
1 TTGAGATAGTTTCCCTTGAAACAAATTTT
912853 TTCTTTCTTG
Statistics
Matches: 161, Mismatches: 31, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
28 3 0.02
29 20 0.12
32 4 0.02
33 4 0.02
36 68 0.42
37 62 0.39
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.42
Consensus pattern (36 bp):
TTGAGATAGTTTCCCTTGAAACAAATTTTATCTCCC
Found at i:912758 original size:138 final size:138
Alignment explanation
Indices: 912534--912941 Score: 597
Period size: 138 Copynumber: 2.9 Consensus size: 138
912524 ACTCAAAAAA
912534 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCC
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCC
*
912599 TTGAAACTAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTT
66 TTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTT
912664 TTGGAACT
131 TTGGAACT
* * *
912672 AAGTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTATCTCACTTGAGATAGTTTCCC
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCC
* * * *
912737 TTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCATCTCCCTTGATATAGTTTCTT
66 TTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTT
912802 TTGGAACT
131 TTGGAACT
* * * *
912810 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAATTTTTTTCTTTCTTGAGACAATTTCTC
1 AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTC-C
* * * *
912875 TTTG-AACACCAATCTTTGAATATG-TTTCTCTTGAGAAAAAAAATTT-GCCTCCCTTGAGACAA
65 CTTGAAACA-AAATCTTTGAATATGTTTTC-CTT--G-AAACAAATTTCGTCTCCCTTGAGACAA
912937 TTTCT
125 TTTCT
912942 CTTGAAACAC
Statistics
Matches: 241, Mismatches: 23, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
138 194 0.80
139 21 0.09
141 17 0.07
142 9 0.04
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (138 bp):
AAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTATCTCTCTTGAGACAGTTTCCC
TTGAAACAAAATCTTTGAATATGTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAATTTCTT
TTGGAACT
Found at i:912836 original size:37 final size:36
Alignment explanation
Indices: 912766--912880 Score: 104
Period size: 37 Copynumber: 3.1 Consensus size: 36
912756 TATGTTTTCC
* ** * * *
912766 TTGAAACAAATTTCATCTCCCTTGATATAGTTTCTT
1 TTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTT
* *
912802 TTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTC
1 TTGAAAC-AAGTTTTGTCTCTCTTGAGACAGTTTCTT
* * * *
912839 TTGAAACAATTTTTTTCTTTCTTGAGACAATTTCTCT
1 TTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCT-T
912876 TTGAA
1 TTGAA
912881 CACCAATCTT
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
36 30 0.48
37 33 0.52
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.46
Consensus pattern (36 bp):
TTGAAACAAGTTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:912864 original size:36 final size:37
Alignment explanation
Indices: 912794--912876 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 37
912784 CCCTTGATAT
* *
912794 AGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGAC
1 AGTTTCTCTTGAAACTAAGTTTTGTCTCTCTTGAGAC
* * *
912831 AGTTTCTCTTGAAAC-AATTTTTTTCTTTCTTGAGAC
1 AGTTTCTCTTGAAACTAAGTTTTGTCTCTCTTGAGAC
*
912867 AATTTCTCTT
1 AGTTTCTCTT
912877 TGAACACCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 27 0.68
37 13 0.32
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.49
Consensus pattern (37 bp):
AGTTTCTCTTGAAACTAAGTTTTGTCTCTCTTGAGAC
Found at i:914787 original size:8 final size:8
Alignment explanation
Indices: 914774--914801 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
914764 GTTATGAACC
914774 ATATATTT
1 ATATATTT
914782 ATATATTT
1 ATATATTT
914790 ATATATTT
1 ATATATTT
914798 ATAT
1 ATAT
914802 CTTATATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
ATATATTT
Found at i:916703 original size:17 final size:17
Alignment explanation
Indices: 916681--916714 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
916671 TATCCTTCCC
916681 CTATACCATAACCATTT
1 CTATACCATAACCATTT
*
916698 CTATACCCTAACCATTT
1 CTATACCATAACCATTT
916715 TTTTTAAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (17 bp):
CTATACCATAACCATTT
Found at i:942638 original size:26 final size:24
Alignment explanation
Indices: 942609--942671 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
942599 TTATTTAATT
942609 ATAATATTATATTATTAGAA-ATATTA
1 ATAATA-TATATT-TTA-AATATATTA
*
942635 ATAA-ATATATTTTAAATATTTTA
1 ATAATATATATTTTAAATATATTA
942658 ATAAT-TAATATTTT
1 ATAATAT-ATATTTT
942672 GATTAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 13 0.39
24 13 0.39
25 1 0.03
26 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATAATATATATTTTAAATATATTA
Found at i:961195 original size:21 final size:22
Alignment explanation
Indices: 961170--961216 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
961160 CAACATCACC
961170 ACCATTAG-CATTTCATCATCA
1 ACCATTAGCCATTTCATCATCA
*
961191 ACCA-TCGCCATTTCATCATCA
1 ACCATTAGCCATTTCATCATCA
961212 ACCAT
1 ACCAT
961217 CATCAACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.32, C:0.34, G:0.04, T:0.30
Consensus pattern (22 bp):
ACCATTAGCCATTTCATCATCA
Found at i:961217 original size:21 final size:21
Alignment explanation
Indices: 961178--961217 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
961168 CCACCATTAG
961178 CATTTCATCATCAACCATCGC
1 CATTTCATCATCAACCATCGC
961199 CATTTCATCATCAACCATC
1 CATTTCATCATCAACCATC
961218 ATCAACATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.38, G:0.03, T:0.30
Consensus pattern (21 bp):
CATTTCATCATCAACCATCGC
Found at i:961318 original size:25 final size:24
Alignment explanation
Indices: 961284--961334 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
961274 TCAATCTTTA
* * *
961284 TTTTATTTTATTTTTTTCTATTTC
1 TTTTATTTTATTATTATCCATTTC
961308 TTTTACTTTTATTATTATCCATTTC
1 TTTTA-TTTTATTATTATCCATTTC
961333 TT
1 TT
961335 AAACCTATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 5 0.22
25 18 0.78
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTATTTTATTATTATCCATTTC
Found at i:966141 original size:23 final size:23
Alignment explanation
Indices: 966095--966136 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
966085 CATTAGAGTG
966095 CAAAGAAAAAAGAAAAAGAAATT
1 CAAAGAAAAAAGAAAAAGAAATT
966118 CAAA-AAAAAAG-AAAAGAAA
1 CAAAGAAAAAAGAAAAAGAAA
966137 GATTCCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 8 0.42
22 7 0.37
23 4 0.21
ACGTcount: A:0.79, C:0.05, G:0.12, T:0.05
Consensus pattern (23 bp):
CAAAGAAAAAAGAAAAAGAAATT
Found at i:972344 original size:3 final size:3
Alignment explanation
Indices: 972276--972327 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
972266 TTAAATAATA
*
972276 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
972320 TAT TAT TA
1 TAT TAT TA
972328 ATACTAATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:974132 original size:10 final size:10
Alignment explanation
Indices: 974117--974144 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
974107 TTATTATTTT
974117 TTTTATTTCA
1 TTTTATTTCA
974127 TTTTATTTCA
1 TTTTATTTCA
974137 TTTTATTT
1 TTTTATTT
974145 TTTTCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTATTTCA
Found at i:974145 original size:26 final size:26
Alignment explanation
Indices: 974087--974146 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
974077 GTTCCTTTTC
*
974087 TTATATTTATTTCATTTAGTTTATTA
1 TTATTTTTATTTCATTTAGTTTATTA
*
974113 TTTTTTTTATTTCATTTTA-TTTCATT-
1 TTATTTTTATTTCA-TTTAGTTT-ATTA
974139 TTATTTTT
1 TTATTTTT
974147 TTCCTTTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 22 0.76
27 7 0.24
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (26 bp):
TTATTTTTATTTCATTTAGTTTATTA
Found at i:974149 original size:24 final size:24
Alignment explanation
Indices: 974110--974173 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 24
974100 ATTTAGTTTA
974110 TTATTTT-TTTTATTTCATTTT-AT
1 TTATTTTATTTT-TTTCATTTTGAT
*
974133 TTCATTTTATTTTTTTCCTTTTGAT
1 TT-ATTTTATTTTTTTCATTTTGAT
*
974158 TTATTTAATGTTTTTT
1 TTATTTTAT-TTTTTT
974174 ACTTTCTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 2 0.06
24 19 0.54
25 14 0.40
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (24 bp):
TTATTTTATTTTTTTCATTTTGAT
Found at i:974159 original size:15 final size:15
Alignment explanation
Indices: 974087--974145 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
974077 GTTCCTTTTC
974087 TTATATTTATTTCA-T
1 TTAT-TTTATTTCATT
*
974102 TTAGTTTA-TT-ATT
1 TTATTTTATTTCATT
974115 TT-TTTTATTTCATT
1 TTATTTTATTTCATT
* *
974129 TTATTTCATTTTATT
1 TTATTTTATTTCATT
974144 TT
1 TT
974146 TTTCCTTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
12 5 0.14
13 7 0.19
14 9 0.25
15 15 0.42
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (15 bp):
TTATTTTATTTCATT
Found at i:975309 original size:17 final size:17
Alignment explanation
Indices: 975289--975321 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
975279 CTCACTAACC
*
975289 CTTTTATTTTTTGTTCT
1 CTTTTATTTTGTGTTCT
975306 CTTTTATTTTGTGTTC
1 CTTTTATTTTGTGTTC
975322 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.73
Consensus pattern (17 bp):
CTTTTATTTTGTGTTCT
Found at i:978116 original size:106 final size:106
Alignment explanation
Indices: 977931--979094 Score: 1943
Period size: 106 Copynumber: 11.0 Consensus size: 106
977921 TTGTTCGAGT
977931 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
977996 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
*
978037 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
978102 ATGGACCGCTGGTTGTCAACAAACAACTTTTCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
*
978143 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
978208 AGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
*
978249 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
978314 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* * *
978355 GCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCATGTTCAACTTCACAACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
978420 AGGGACCGCTGGTTGTCAACAAACAATTTCCCAATATTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT-TTCAGA
* * *
978462 GCCAATTTCAACTTCACAGCGAATGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
978527 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* * *
978568 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACAATGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
978633 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
*
978674 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
978739 AGCGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
*
978780 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
978845 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* *
978886 GCCAATTTCAACTTCACAGCAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
978951 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
* * * * * *
978992 GTCAATTTCAACTTCATAGCAAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGATGA
1 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* *
979057 AGGGACCGCTGGTTGTCAATAAACAACTT-TCAACTTCA
66 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCA
979095 CGATGAAGGA
Statistics
Matches: 1002, Mismatches: 55, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
105 7 0.01
106 896 0.89
107 99 0.10
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (106 bp):
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGA
Found at i:978940 original size:531 final size:530
Alignment explanation
Indices: 977931--979087 Score: 2026
Period size: 531 Copynumber: 2.2 Consensus size: 530
977921 TTGTTCGAGT
*
977931 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
977996 AGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATCAGAGCCAATTTCAACTTCACAACGAAG
66 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAG
*
978061 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAATGGACCGCTGGTTGTCAACAAAC
131 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAAC
* * *
978126 AACTTTTCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
196 AACTTCTCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
*
978191 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATT
261 GTTCAACTTCACGACGAAGCGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATT
978256 TCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGAAGGGACC
326 TCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGAAGGGACC
* * *
978321 GCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTA
391 GCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTA
*
978386 GACTCCAGACAACGCATGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
456 GACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
978451 CAATATTCAGA
521 CAAT-TTCAGA
* *
978462 GCCAATTTCAACTTCACAGCGAATGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGA
1 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
*
978527 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
66 AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAG
* *
978592 GATATTGGACTCCAGACAACGCATGTTCAACTTCACAATGAAGGGACCGCTGGTTGTCAACAAAC
131 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAAC
*
978657 AACTTCTCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAA
196 AACTTCTCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
*
978722 GTTCAACTTCACGACGAAGCGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATT
261 GTTCAACTTCACGACGAAGCGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATT
978787 TCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGAAGGGACC
326 TCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGAAGGGACC
* * *
978852 GCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTG
391 GCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTA
* *
978917 GACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
456 GACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
978982 CAATTTCAGA
521 CAATTTCAGA
* * * * *
978992 GTCAATTTCAACTTCATAGCAAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGATGA
1 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
979057 AGGGACCGCTGGTTGTCAATAAACAACTTTC
66 AGGGACCGCTGGTTGTCAATAAACAA-TTTC
979088 AACTTCACGA
Statistics
Matches: 593, Mismatches: 32, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
530 90 0.15
531 503 0.85
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (530 bp):
GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
AGGGACCGCTGGTTGTCAATAAACAATTTCCCAATATCAGAGCCAATTTCAACTTCACAACGAAG
GATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAAC
AACTTCTCAATATCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
GTTCAACTTCACGACGAAGCGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATT
TCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCAAGTTCAACTTCACGACGAAGGGACC
GCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTA
GACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
CAATTTCAGA
Found at i:979252 original size:84 final size:84
Alignment explanation
Indices: 979129--979317 Score: 261
Period size: 84 Copynumber: 2.2 Consensus size: 84
979119 AGGCTATCTG
* * *
979129 CCAAAGACCCCCGAGTTCGATTACGCTCAACTCTAAGGCACATCATTTGCAGCATAACTTAAGTC
1 CCAAAGACCTCCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
979194 GAGAAGGGTTATCTTCCAA
66 GAGAAGGGCTATCTGCCAA
* * * * * *
979213 CCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCGAGGCACATCATTTGCAGCATAGCTTAAGTT
1 CCAAAGACCTCCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
979278 GAGAAGGGCTATCTGCCAA
66 GAGAAGGGCTATCTGCCAA
*
979297 CCAAAGACCTGACGAGTTCGA
1 CCAAAGACCT-CCGAGTTCGA
979318 TTTCATTCAG
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
84 83 0.91
85 8 0.09
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.23
Consensus pattern (84 bp):
CCAAAGACCTCCGAGTTCGACTACGCTCAACTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
GAGAAGGGCTATCTGCCAA
Found at i:979557 original size:3 final size:3
Alignment explanation
Indices: 979546--979614 Score: 79
Period size: 3 Copynumber: 23.3 Consensus size: 3
979536 TTAAATAATA
*
979546 TAT TA- TAT TAT TAT TAT TAT TAT AAT TACT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
* * *
979590 TAT TAT TAA TAC TAT TAA TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
979615 TTTGCAGGCT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:981399 original size:14 final size:14
Alignment explanation
Indices: 981361--981455 Score: 56
Period size: 14 Copynumber: 6.9 Consensus size: 14
981351 TTTTCTTATA
**
981361 TTTATTTCATTTAG
1 TTTATTTCATTTTT
981375 TTTA-TT-ATTTTT
1 TTTATTTCATTTTT
981387 TTTATTTCATTTTAT
1 TTTATTTCATTTT-T
* *
981402 TTT-TTTCCTTTTGA
1 TTTATTTCATTTT-T
* *
981416 TTTATTTAATGTTT
1 TTTATTTCATTTTT
*
981430 TTTACTTTC-TTTAT
1 TTTA-TTTCATTTTT
*
981444 TTTCTTT-ATTTT
1 TTTATTTCATTTT
981456 CTTATTATTA
Statistics
Matches: 61, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
12 8 0.13
13 10 0.16
14 30 0.49
15 13 0.21
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (14 bp):
TTTATTTCATTTTT
Found at i:981430 original size:24 final size:25
Alignment explanation
Indices: 981385--981431 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
981375 TTTATTATTT
* * *
981385 TTTTTATTTCATTTTATTTTTTTCC
1 TTTTGATTTCATTTAATGTTTTTCC
981410 TTTTGATTT-ATTTAATGTTTTT
1 TTTTGATTTCATTTAATGTTTTT
981432 TACTTTCTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.15, C:0.06, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTGATTTCATTTAATGTTTTTCC
Found at i:981430 original size:25 final size:25
Alignment explanation
Indices: 981385--981437 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
981375 TTTATTATTT
* * *
981385 TTTTTATTTCATTTTATTTTTTTCC
1 TTTTGATTTCATTTAATTTTTTTAC
981410 TTTTGATTT-ATTTAATGTTTTTTAC
1 TTTTGATTTCATTTAAT-TTTTTTAC
981435 TTT
1 TTT
981438 CTTTATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.25
25 18 0.75
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTTGATTTCATTTAATTTTTTTAC
Found at i:990875 original size:21 final size:20
Alignment explanation
Indices: 990846--990887 Score: 50
Period size: 19 Copynumber: 2.0 Consensus size: 20
990836 AATGCCAGCG
*
990846 GCAAGAATATAAAGTGAAAATT
1 GCAAGAATAGAAA--GAAAATT
990868 GCAA-AATAGAAAGAAAATT
1 GCAAGAATAGAAAGAAAATT
990887 G
1 G
990888 TGATAGGACA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.42
21 7 0.37
22 4 0.21
ACGTcount: A:0.57, C:0.05, G:0.19, T:0.19
Consensus pattern (20 bp):
GCAAGAATAGAAAGAAAATT
Found at i:991741 original size:38 final size:37
Alignment explanation
Indices: 991657--991796 Score: 118
Period size: 36 Copynumber: 3.9 Consensus size: 37
991647 CGAATATAGC
991657 TTTTG-AAA-ATATAAAGTATATAGTTTTTAAAGTAT
1 TTTTGAAAACATATAAAGTATATAGTTTTTAAAGTAT
991692 TTTTGAAAACATATAATA-TATATAGTTTTTAAAACG-A-
1 TTTTGAAAACATATAA-AGTATATAGTTTTT-AAA-GTAT
* * * * *
991729 TTTTGAAAAACATAT--AGCATGTGGTTTTTAAAAATAA
1 TTTTG-AAAACATATAAAGTATATAGTTTTT-AAAGTAT
*
991766 TCTTGAAAACATAT--AGTATATAGTTTTTAAA
1 TTTTGAAAACATATAAAGTATATAGTTTTTAAA
991797 ATAACAATTA
Statistics
Matches: 88, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
35 9 0.10
36 37 0.42
37 27 0.31
38 14 0.16
39 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (37 bp):
TTTTGAAAACATATAAAGTATATAGTTTTTAAAGTAT
Found at i:991861 original size:34 final size:34
Alignment explanation
Indices: 991822--991892 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
991812 AACGTACATT
**
991822 TTTAAAAAATGTATAATATATGGTTTTTAAAACA
1 TTTAAAAAACATATAATATATGGTTTTTAAAACA
* *
991856 TTTAAAAAACATATGATATATGGTTTTTAAAATA
1 TTTAAAAAACATATAATATATGGTTTTTAAAACA
991890 TTT
1 TTT
991893 TTTTTTGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (34 bp):
TTTAAAAAACATATAATATATGGTTTTTAAAACA
Found at i:991982 original size:41 final size:40
Alignment explanation
Indices: 991906--991999 Score: 129
Period size: 39 Copynumber: 2.4 Consensus size: 40
991896 TTTGAAAACA
991906 TATAGTTTT-AAAAAACAATTCTTTTTAAAACATATATAT
1 TATAGTTTTGAAAAAACAATTCTTTTTAAAACATATATAT
* *
991945 TATGGTTTTGAAAAAA-AATTCTTTTTAAAGCATATATATAT
1 TATAGTTTTGAAAAAACAATTCTTTTTAAA--ACATATATAT
*
991986 TATAGTTTCGAAAA
1 TATAGTTTTGAAAA
992000 TAATTTTCGA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
39 21 0.44
40 6 0.12
41 21 0.44
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (40 bp):
TATAGTTTTGAAAAAACAATTCTTTTTAAAACATATATAT
Found at i:993149 original size:6 final size:7
Alignment explanation
Indices: 993140--993189 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 7
993130 CCTTTTTTTC
993140 ATTA-AT
1 ATTATAT
993146 ATTATAT
1 ATTATAT
993153 A-TATAT
1 ATTATAT
993159 A-TATAT
1 ATTATAT
993165 ATATATAT
1 AT-TATAT
993173 ATATATAT
1 AT-TATAT
*
993181 ATTACAT
1 ATTATAT
993188 AT
1 AT
993190 CTTATCTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
6 16 0.40
7 9 0.22
8 15 0.38
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (7 bp):
ATTATAT
Found at i:993153 original size:2 final size:2
Alignment explanation
Indices: 993144--993182 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
993134 TTTTTCATTA
993144 AT AT -T 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
993183 TACATATCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:993271 original size:2 final size:2
Alignment explanation
Indices: 993264--993312 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
993254 TACGTAAATT
993264 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
*
993306 TG TA TA T
1 TA TA TA T
993313 GTATCTACCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:993680 original size:20 final size:20
Alignment explanation
Indices: 993631--993683 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 20
993621 GCACAAAAAG
*
993631 TTTT-TATGAATAGTACTGA
1 TTTTGTATGAATAGTACCGA
*
993650 -ATTGT-TGAATAGTACCGA
1 TTTTGTATGAATAGTACCGA
993668 TTTTGTATGAATAGTA
1 TTTTGTATGAATAGTA
993684 TTGATATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 14 0.50
19 5 0.18
20 9 0.32
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (20 bp):
TTTTGTATGAATAGTACCGA
Found at i:993693 original size:20 final size:20
Alignment explanation
Indices: 993635--993698 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
993625 AAAAAGTTTT
993635 TATGAATAGTACTGA-ATTG
1 TATGAATAGTACTGATATTG
* *
993654 T-TGAATAGTACCGATTTTG
1 TATGAATAGTACTGATATTG
*
993673 TATGAATAGTATTGATATTG
1 TATGAATAGTACTGATATTG
*
993693 TGTGAA
1 TATGAA
993699 CATTAGTATC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 12 0.32
19 5 0.14
20 20 0.54
ACGTcount: A:0.33, C:0.05, G:0.22, T:0.41
Consensus pattern (20 bp):
TATGAATAGTACTGATATTG
Found at i:993726 original size:21 final size:21
Alignment explanation
Indices: 993695--993745 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
993685 TGATATTGTG
*
993695 TGAACATTAGTATCGATACCA
1 TGAACAGTAGTATCGATACCA
*
993716 TGAATAGTAGTATCGATACCA
1 TGAACAGTAGTATCGATACCA
993737 TGAACAGTA
1 TGAACAGTA
993746 TCGATGCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (21 bp):
TGAACAGTAGTATCGATACCA
Found at i:993824 original size:21 final size:21
Alignment explanation
Indices: 993798--993846 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
993788 GCTACATTAG
*
993798 TATCGATACCATGAATAGTAA
1 TATCGATACCATGAACAGTAA
* *
993819 TATCGATACCGTGAACAGTAG
1 TATCGATACCATGAACAGTAA
993840 TATCGAT
1 TATCGAT
993847 GCTATCAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (21 bp):
TATCGATACCATGAACAGTAA
Found at i:993913 original size:21 final size:21
Alignment explanation
Indices: 993884--993942 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
993874 AAATATTACA
*
993884 AAGGTAGTAGCGATACTCATTG
1 AAGG-AGTACCGATACTCATTG
993906 AAGGAGTACCGATACTCATTG
1 AAGGAGTACCGATACTCATTG
* *
993927 AAGGATTACCGGTACT
1 AAGGAGTACCGATACT
993943 ACTTGTTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 30 0.88
22 4 0.12
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (21 bp):
AAGGAGTACCGATACTCATTG
Found at i:996251 original size:23 final size:23
Alignment explanation
Indices: 996223--996291 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
996213 ACTTTTTATA
*
996223 TGGCACTTCGGTGCATTTCTATG
1 TGGCACTTCGGTGCATTTCTACG
*
996246 CT-GCACTTCGGTGTATTTCTACG
1 -TGGCACTTCGGTGCATTTCTACG
*
996269 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
996292 AGCTGTTGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.14, C:0.23, G:0.25, T:0.38
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:1000524 original size:21 final size:21
Alignment explanation
Indices: 1000477--1000527 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1000467 GGGTCTACGT
* * *
1000477 GGTCCTTCGGGACATATATGT
1 GGTCCTTTGGAACATATATGC
**
1000498 AATCCTTTGGAACATATATGC
1 GGTCCTTTGGAACATATATGC
1000519 GGTCCTTTG
1 GGTCCTTTG
1000528 AGACACGTAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
GGTCCTTTGGAACATATATGC
Found at i:1000659 original size:23 final size:23
Alignment explanation
Indices: 1000604--1000662 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
1000594 ACATTTTATA
* *
1000604 TGGCACTTCAGTGCATTTCTACG
1 TGGCACTTCGGTGCACTTCTACG
*
1000627 TGGCACTTCGGTGCACTTCTATG
1 TGGCACTTCGGTGCACTTCTACG
1000650 TGGCACTTCGGTG
1 TGGCACTTCGGTG
1000663 TATATATACG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.14, C:0.25, G:0.27, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGTGCACTTCTACG
Found at i:1001733 original size:19 final size:20
Alignment explanation
Indices: 1001709--1001756 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1001699 AATGATTTTC
* * *
1001709 TTTTGAAAGCTAAAATG-GA
1 TTTTGAAAACCAAAATGAAA
1001728 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATGAAA
1001748 TTTTGAAAA
1 TTTTGAAAA
1001757 ATGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (20 bp):
TTTTGAAAACCAAAATGAAA
Found at i:1002858 original size:20 final size:19
Alignment explanation
Indices: 1002799--1002863 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
1002789 TTTTTTATGG
1002799 ATAGTATCG-TACTGTGTGA
1 ATAGTATCGATACT-TGTGA
* *
1002818 ATAATACCGATA-TTGAATGA
1 ATAGTATCGATACTTG--TGA
1002838 ATAGTATCGATACTATGTGA
1 ATAGTATCGATACT-TGTGA
*
1002858 ACAGTA
1 ATAGTA
1002864 GTATCAATAC
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
18 2 0.06
19 8 0.22
20 23 0.64
21 1 0.03
22 2 0.06
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (19 bp):
ATAGTATCGATACTTGTGA
Found at i:1004044 original size:19 final size:19
Alignment explanation
Indices: 1004007--1004044 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1003997 CTCAAATAGG
*
1004007 CATTCACATATATATTAAA
1 CATTCACATATATAATAAA
1004026 CATTCA-ATATATACATAAA
1 CATTCACATATATA-ATAAA
1004045 AAAATTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (19 bp):
CATTCACATATATAATAAA
Found at i:1009591 original size:16 final size:17
Alignment explanation
Indices: 1009553--1009593 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1009543 ATATTTATAT
* *
1009553 TATAAATTTTGAGTAGA
1 TATAAAATTTGAGTAAA
1009570 TA-AAAATTTGA-TAAA
1 TATAAAATTTGAGTAAA
1009585 TATAAAATT
1 TATAAAATT
1009594 AAAATAGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 5 0.24
16 14 0.67
17 2 0.10
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (17 bp):
TATAAAATTTGAGTAAA
Found at i:1012197 original size:22 final size:22
Alignment explanation
Indices: 1012134--1012198 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
1012124 CGTGAGTATT
1012134 CTTTATAAAATTAAGGCTTAAA
1 CTTTATAAAATTAAGGCTTAAA
** **
1012156 CTAAAT-AAAGGAA--CTTAAA
1 CTTTATAAAATTAAGGCTTAAA
1012175 CTTTATAAAATTAAGGCTTAAA
1 CTTTATAAAATTAAGGCTTAAA
1012197 CT
1 CT
1012199 AAAAAAGTAC
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
19 10 0.31
20 5 0.16
21 5 0.16
22 12 0.38
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (22 bp):
CTTTATAAAATTAAGGCTTAAA
Found at i:1015812 original size:90 final size:91
Alignment explanation
Indices: 1015698--1015865 Score: 248
Period size: 91 Copynumber: 1.9 Consensus size: 91
1015688 GGACGACACT
* * ** *
1015698 GCTCATACGTGATGAAGAGGTCTGGTCGTC-TAAGGGTGGATGATAACTCGGTTCCTACGTGATG
1 GCTCATACGTGATGAAGAGGTCTGGCCATCTTAAGGAAGGATGATAACACGGTTCCTACGTGATG
1015762 AGGACGACTGGTTGGTGGATGACATG
66 AGGACGACTGGTTGGTGGATGACATG
* * *
1015788 GCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGTGATG
1 GCTCATACGTGATGAAGAGGTCTGGCCATCTTAAGGAAGGATGATAACACGGTTCCTACGTGATG
*
1015853 AGGACGGCTGGTT
66 AGGACGACTGGTT
1015866 ATCTAGGGGT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 27 0.40
91 41 0.60
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.27
Consensus pattern (91 bp):
GCTCATACGTGATGAAGAGGTCTGGCCATCTTAAGGAAGGATGATAACACGGTTCCTACGTGATG
AGGACGACTGGTTGGTGGATGACATG
Found at i:1015890 original size:43 final size:43
Alignment explanation
Indices: 1015834--1016028 Score: 193
Period size: 43 Copynumber: 4.5 Consensus size: 43
1015824 AAGGGTGATA
1015834 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGGGTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGGGTG
* ***
1015877 ACCCGGTTCCTACGTGATGAGGAAATCTGG---TC-AGGGGATG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGGG-TG
* * * ** * *
1015917 ACACGGCTCATACGTGATGAAGA-GGTCTGGCCATCTAAAGGTGATA
1 ACACGGTTCCTACGTGATGAGGACGG-CTGGTTATCT--AGG-GGTG
*
1015963 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTG
1 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGGGTG
*
1016006 ACCCGGTTCCTACGTGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
1016029 AATCTGGCCA
Statistics
Matches: 121, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
39 5 0.04
40 27 0.22
43 52 0.43
44 2 0.02
46 32 0.26
47 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (43 bp):
ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGGGTG
Found at i:1015946 original size:40 final size:42
Alignment explanation
Indices: 1015824--1016151 Score: 210
Period size: 40 Copynumber: 7.7 Consensus size: 42
1015814 CATCTTTAGG
* * *
1015824 AAGGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATC
1 AAGGG-GATGACACGGTTCCTACGTGATGAGGA-GATCTGG--CTC
* * *
1015869 TAGGGG-TGACCCGGTTCCTACGTGATGAGGAAATCTGG-TC
1 AAGGGGATGACACGGTTCCTACGTGATGAGGAGATCTGGCTC
* * * *
1015909 -AGGGGATGACACGGCTCATACGTGATGAAGAGGTCTGGCCATC
1 AAGGGGATGACACGGTTCCTACGTGATGAGGAGATCTGG-C-TC
* * * *
1015952 TAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATC
1 --AAGGGGATGACACGGTTCCTACGTGATGAGGA-GATCTGG--CTC
* *
1015998 TAA-GGG-TGACCCGGTTCCTACGTGATGAGGAAATCTGGC-C
1 -AAGGGGATGACACGGTTCCTACGTGATGAGGAGATCTGGCTC
* * * *
1016038 -AGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATC
1 AAGGGGATGACACGGTTCCTACGTGATGAGGAGATCTGG-C-TC
* * *
1016081 TAAAGGTGATAACACGGCTCCTACGTGATGAGGAGATCTGG-TC
1 --AAGGGGATGACACGGTTCCTACGTGATGAGGAGATCTGGCTC
* *
1016124 -TGGGGATGACACGGTTCCTACATGATGA
1 AAGGGGATGACACGGTTCCTACGTGATGA
1016152 AGACGGATGG
Statistics
Matches: 222, Mismatches: 42, Indels: 43
0.72 0.14 0.14
Matches are distributed among these distances:
38 1 0.00
39 8 0.04
40 78 0.35
41 1 0.00
43 59 0.27
44 3 0.01
45 6 0.03
46 65 0.29
47 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.23
Consensus pattern (42 bp):
AAGGGGATGACACGGTTCCTACGTGATGAGGAGATCTGGCTC
Found at i:1016020 original size:129 final size:129
Alignment explanation
Indices: 1015746--1016114 Score: 598
Period size: 129 Copynumber: 2.8 Consensus size: 129
1015736 GATGATAACT
* * *
1015746 CGGTTCCTACGTGATGAGGACGA-CTGGT-TGGTGGATGACATGGCTCATACGTGATGAAGAGTT
1 CGGTTCCTACGTGATGAGGA-AATCTGGTCAGG-GGATGACACGGCTCATACGTGATGAAGAGTT
*
1015809 CTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAGGG
64 CTGGCCATC--TA--AA-GGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGG
1015874 GTGACC
124 GTGACC
*
1015880 CGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGATGACACGGCTCATACGTGATGAAGAGGTCT
1 CGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGATGACACGGCTCATACGTGATGAAGAGTTCT
1015945 GGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACC
66 GGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACC
*
1016009 CGGTTCCTACGTGATGAGGAAATCTGGCCAGGGGATGACACGGCTCATACGTGATGAAGAGTTCT
1 CGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGATGACACGGCTCATACGTGATGAAGAGTTCT
*
1016074 GGCCATCTAAAGGTGATAACACGGCTCCTACGTGATGAGGA
66 GGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGA
1016115 GATCTGGTCT
Statistics
Matches: 225, Mismatches: 8, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
129 155 0.69
130 2 0.01
132 2 0.01
133 1 0.00
134 63 0.28
135 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (129 bp):
CGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGATGACACGGCTCATACGTGATGAAGAGTTCT
GGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACC
Found at i:1016129 original size:86 final size:86
Alignment explanation
Indices: 1015685--1016154 Score: 293
Period size: 86 Copynumber: 5.4 Consensus size: 86
1015675 TGTTGGTTGT
* * * * * * *
1015685 TGGGGACGACACTGCTCATACGTGATGAAGAGGTCTGGTCGTCTAAGGGTGGATGATAACTCGGT
1 TGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAA---AGG-TGATAACACGGT
1015750 TCCTACGTGATGAGGACGA-CTGGT-
62 TCCTACGTGATGAGGA-GATCTGGTC
*
1015774 TGGTGGATGACATGGCTCATACGTGATGAAGAGTTCTGGCCATCTTTAGGAAGGGTGATAACACG
1 TGG-GGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATC--TA--AA-GGTGATAACACG
*
1015839 GTTCCTACGTGATGAGGACG-GCTGGTTATC
60 GTTCCTACGTGATGAGGA-GATCTGG---TC
* * * * ** * * * *
1015869 TAGGGG-TGACCCGGTTCCTACGTGATGAGGAAATCTGG---TC---AGGGGATGACACGGCTCA
1 T-GGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCC
* *
1015927 TACGTGATGAAGAGGTCTGGCCATC
65 TACGTGATGAGGAGATCTGG---TC
* * * * * * ** * *
1015952 TAAAGGTGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-AAGG-G-TGACCCGGT
1 T---GGGGATGACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAAAGGTGATAACACGGT
* *
1016013 TCCTACGTGATGAGGAAATCTGGCC
62 TCCTACGTGATGAGGAGATCTGGTC
* *
1016038 AGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGCTCCT
1 TGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCT
1016103 ACGTGATGAGGAGATCTGGTC
66 ACGTGATGAGGAGATCTGGTC
* * *
1016124 TGGGGATGACACGGTTCCTACATGATGAAGA
1 TGGGGATGACACGGCTCATACGTGATGAAGA
1016155 CGGATGGCCA
Statistics
Matches: 302, Mismatches: 53, Indels: 55
0.74 0.13 0.13
Matches are distributed among these distances:
82 2 0.01
83 66 0.22
84 5 0.02
85 5 0.02
86 84 0.28
89 31 0.10
90 35 0.12
91 38 0.13
92 4 0.01
94 27 0.09
95 3 0.01
96 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (86 bp):
TGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCT
ACGTGATGAGGAGATCTGGTC
Found at i:1016220 original size:28 final size:28
Alignment explanation
Indices: 1016180--1016242 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
1016170 AGGAGTTATG
* *
1016180 GTTTCAAGAGAAACCA-AATTAAAGATTT
1 GTTTCAAAAGAAA-CAGAATCAAAGATTT
*
1016208 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGAATCAAAGATTT
1016236 GTTTCAA
1 GTTTCAA
1016243 GAAAACAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGAATCAAAGATTT
Found at i:1016271 original size:30 final size:28
Alignment explanation
Indices: 1016200--1016275 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
1016190 AAACCAAATT
1016200 AAAGATTTGTTTCAAAAGAAACAGACTC
1 AAAGATTTGTTTCAAAAGAAACAGACTC
*
1016228 AAAGATTTGTTTCAAGA-AAACA-AGCTC
1 AAAGATTTGTTTCAAAAGAAACAGA-CTC
1016255 AAAGATAATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
1016276 CAACTGTCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.02
27 14 0.34
28 16 0.39
29 1 0.02
30 9 0.22
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAGACTC
Found at i:1016466 original size:66 final size:65
Alignment explanation
Indices: 1016277--1016466 Score: 154
Period size: 66 Copynumber: 2.9 Consensus size: 65
1016267 TTTCAAAAGC
** ** *
1016277 AACTGTCTCGAAAGAGACAAAATTCATTTCAAATGAAAC-AACTCAAAAGATG-ACGTTTAAAGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACGATTTC-AAAGATGTATGTTTAAAGG
1016340 GA
64 GA
* * ** * * * * * *
1016342 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGG-AACG-TTCTCAAATATCTGTGTTTCATG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACGATT-TCAAAGATGTATGTTTAAAG
1016405 GGA
63 GGA
*
1016408 AACTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACGATTTCAAAGATGTTTGTTT
1 AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACGATTTCAAAGATGTATGTTT
1016467 TGTTTCATGG
Statistics
Matches: 94, Mismatches: 23, Indels: 15
0.71 0.17 0.11
Matches are distributed among these distances:
64 2 0.02
65 35 0.37
66 55 0.59
67 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (65 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACGATTTCAAAGATGTATGTTTAAAGGGA
Found at i:1016925 original size:40 final size:40
Alignment explanation
Indices: 1016881--1016960 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
1016871 GTTTTAATAG
1016881 AAACGATCTCAAA-GATGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACGATCTCAAATG-TGGGTA-TTTTCAAAAGAAATTGTCT
*
1016921 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAATTGTCT
1016961 CGAGAGACAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 4 0.11
40 32 0.86
41 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACGATCTCAAATGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:1017049 original size:65 final size:64
Alignment explanation
Indices: 1016942--1017067 Score: 180
Period size: 65 Copynumber: 2.0 Consensus size: 64
1016932 AATGTGGGTA
* * * *
1016942 TTTTCAAAAGAAGTTGTCTCGAGAGACAATATTTTGTTTCAAAGGAAACAAACTCAAAGATTTT
1 TTTTCAAAAGAAATTGTCTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTT
* * *
1017006 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTC-TCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
1017068 GGATCACATC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
64 17 0.31
65 37 0.69
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTT
Found at i:1017315 original size:64 final size:64
Alignment explanation
Indices: 1017235--1017460 Score: 258
Period size: 67 Copynumber: 3.5 Consensus size: 64
1017225 ATGAACATAT
** * * * * * *
1017235 TCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGA
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCAA-AGAAACAAA
*
1017298 T
64 C
* *
1017299 TCAAAGATTTTTTTCAAAAGAAATTATCTTAAGATAGACAAAATTTTGTTTCCAAAGAAACAAAC
1 TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAAAC
*
1017364 TCAAAGATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGA-TTTT-TTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAA
1017429 AC
63 AC
*
1017431 TCAAAGATTTTTTTCAAAAAGAAACAATCT
1 TCAAAGATTTTTTTC-AAAAGAAACTATCT
1017461 CAAAGATTTT
Statistics
Matches: 140, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
63 1 0.01
64 40 0.29
65 18 0.13
66 23 0.16
67 58 0.41
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.31
Consensus pattern (64 bp):
TCAAAGATTTTTTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCAAAGAAACAAAC
Found at i:1017356 original size:37 final size:36
Alignment explanation
Indices: 1017300--1017426 Score: 106
Period size: 37 Copynumber: 3.6 Consensus size: 36
1017290 GAAACAGATT
*
1017300 CAAAGATTTT-TTTCAAAAGAAATTATCTTAAGATAGA
1 CAAA-ATTTTGTTTCAAAAGAAACTATCTTAAGA-AGA
* * * *
1017337 CAAAATTTTGTTTCCAAAGAAACAAAC-TCA-AAG-
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAGAAGA
* *
1017370 ---ATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGA
1 CAAAATTTTGTTTCAAAAGAAACTATCTTAAGA-AGA
*
1017404 CAAAATTTTGTTTCCAAAGAAAC
1 CAAAATTTTGTTTCAAAAGAAAC
1017427 AAACTCAAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 19 0.28
31 2 0.03
32 1 0.01
33 2 0.03
34 2 0.03
35 1 0.01
36 7 0.10
37 34 0.50
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (36 bp):
CAAAATTTTGTTTCAAAAGAAACTATCTTAAGAAGA
Found at i:1017643 original size:29 final size:28
Alignment explanation
Indices: 1017575--1017793 Score: 261
Period size: 27 Copynumber: 7.9 Consensus size: 28
1017565 AAATAAATAG
*
1017575 ACTCAAAGA--TTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
* * *
1017600 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTTTTTCAAGAGAAACAA
* * * *
1017629 ACTCCAAGATTTTTATTCAAAAGGAGCAA
1 ACTCAAAGATTTTT-TTCAAGAGAAACAA
*
1017658 ACTCAAAGATTTTTTT-AAGAGGAACAA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
*
1017685 ACTCAAAGA-TTTTTTCCAGAGAAACAA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
* *
1017712 ACTCAAAGCTTTTTTTTCAAGAGAAACTA
1 ACTCAAAG-ATTTTTTTCAAGAGAAACAA
1017741 ACTCAAAGA-TTTTTTCAAGAGAAACAA
1 ACTCAAAGATTTTTTTCAAGAGAAACAA
1017768 ACTCAAAGATTTTTTTCAAGAGAAAC
1 ACTCAAAGATTTTTTTCAAGAGAAAC
1017794 TGTCTCAAGA
Statistics
Matches: 170, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
25 9 0.05
26 6 0.04
27 61 0.36
28 34 0.20
29 60 0.35
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.28
Consensus pattern (28 bp):
ACTCAAAGATTTTTTTCAAGAGAAACAA
Found at i:1017665 original size:83 final size:83
Alignment explanation
Indices: 1017561--1017793 Score: 272
Period size: 83 Copynumber: 2.8 Consensus size: 83
1017551 AAAACTTTGT
* * * * *
1017561 TTCAAAATAAATAGACTCAAAGA-TTTTTCAAAAGAAAC-AACTCAAAGATATTTATTCAAAAGG
1 TTCAAAAGAAACAAACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAGAT-TTT-TTCAAAAGA
*
1017624 AACAAACTCCAAGATTTTTA
64 AACAAACTCAAAGATTTTTA
* * * * * *
1017644 TTCAAAAGGAGCAAACTCAAAGATTTTTTTAAGAGGAACAAACTCAAAGATTTTTTCCAGAGAAA
1 TTCAAAAGAAACAAACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAGATTTTTTCAAAAGAAA
* *
1017709 CAAACTCAAAGCTTTTTT
66 CAAACTCAAAGATTTTTA
* * *
1017727 TTCAAGAGAAACTAACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAGATTTTTTTCAAGAGAA
1 TTCAAAAGAAACAAACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAGA-TTTTTTCAAAAGAA
1017792 AC
65 AC
1017794 TGTCTCAAGA
Statistics
Matches: 126, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
83 85 0.67
84 30 0.24
85 11 0.09
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (83 bp):
TTCAAAAGAAACAAACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAGATTTTTTCAAAAGAAA
CAAACTCAAAGATTTTTA
Found at i:1017687 original size:56 final size:55
Alignment explanation
Indices: 1017575--1017789 Score: 274
Period size: 56 Copynumber: 3.9 Consensus size: 55
1017565 AAATAAATAG
* * *
1017575 ACTCAAAGA-TTTTTCAAAAGAAAC-AACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAGAT-TTTTTTCAAGAGGAACAA
* * * *
1017629 ACTCCAAGATTTTTATTCAAAAGGAGCAAACTCAAAGATTTTTTT-AAGAGGAACAA
1 ACTCAAAGA-TTTT-TTCAAGAGAAACAAACTCAAAGATTTTTTTCAAGAGGAACAA
* * * *
1017685 ACTCAAAGATTTTTTCCAGAGAAACAAACTCAAAGCTTTTTTTTCAAGAGAAACTA
1 ACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAG-ATTTTTTTCAAGAGGAACAA
1017741 ACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAGATTTTTTTCAAGAG
1 ACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAGATTTTTTTCAAGAG
1017790 AAACTGTCTC
Statistics
Matches: 140, Mismatches: 15, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
54 26 0.19
55 24 0.17
56 64 0.46
57 15 0.11
58 11 0.08
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (55 bp):
ACTCAAAGATTTTTTCAAGAGAAACAAACTCAAAGATTTTTTTCAAGAGGAACAA
Found at i:1018084 original size:34 final size:36
Alignment explanation
Indices: 1018037--1018127 Score: 107
Period size: 35 Copynumber: 2.6 Consensus size: 36
1018027 AGAAAATGAT
*
1018037 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA
1 GTCTCAAGCGAGACAAAATTTGTCTTTAGAGAAATA
** * *
1018071 GTCTCAAATGAGAC-AAATTTGTTTTTAGAGAAATT
1 GTCTCAAGCGAGACAAAATTTGTCTTTAGAGAAATA
*
1018106 GTCTCAAGCGAGACAAAGTTTG
1 GTCTCAAGCGAGACAAAATTTG
1018128 AGAAAACGAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
33 7 0.15
34 16 0.35
35 17 0.37
36 6 0.13
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (36 bp):
GTCTCAAGCGAGACAAAATTTGTCTTTAGAGAAATA
Found at i:1018257 original size:36 final size:35
Alignment explanation
Indices: 1018217--1018334 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 35
1018207 AGTGAGGCGG
1018217 AATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAACGAGACAA
* *
1018253 AATTTGTTTTT-AGAAAGCTGTCTCAATCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAACGAGACAA
** *
1018288 AATTTGCTTTGAAAGAAATTGTCTCAAGCGAGACAAA
1 AATTTG-TTTTTAAGAAATTGTCTCAAACGAGAC-AA
1018325 AATTTGTTTT
1 AATTTGTTTT
1018335 AAAATTCTCA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
34 5 0.07
35 22 0.31
36 31 0.44
37 13 0.18
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAACGAGACAA
Found at i:1018890 original size:4 final size:4
Alignment explanation
Indices: 1018881--1018925 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
1018871 TTTATGTATC
1018881 ATGT ATGT ATG- -TGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1018925 A
1 A
1018926 CTTTTCTCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 4 0.11
4 33 0.89
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:1018897 original size:10 final size:10
Alignment explanation
Indices: 1018882--1018924 Score: 68
Period size: 10 Copynumber: 4.1 Consensus size: 10
1018872 TTATGTATCA
1018882 TGTATGTATG
1 TGTATGTATG
1018892 TGTATGTATG
1 TGTATGTATG
1018902 TGTATGTATG
1 TGTATGTATG
1018912 TATGTATGTATG
1 --TGTATGTATG
1018924 T
1 T
1018925 ACTTTTCTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 21 0.68
12 10 0.32
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (10 bp):
TGTATGTATG
Found at i:1018900 original size:14 final size:14
Alignment explanation
Indices: 1018881--1018920 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1018871 TTTATGTATC
1018881 ATGTATGTATGTGT
1 ATGTATGTATGTGT
* *
1018895 ATGTATGTGTATGT
1 ATGTATGTATGTGT
1018909 ATGTATGTATGT
1 ATGTATGTATGT
1018921 ATGTACTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (14 bp):
ATGTATGTATGTGT
Found at i:1020147 original size:17 final size:16
Alignment explanation
Indices: 1020121--1020155 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1020111 TTTCACTTTG
*
1020121 TTTCTTTCTCTTTGCT
1 TTTCTTTCTCTTCGCT
1020137 TTTCTTTTCTCTTCGCT
1 TTTC-TTTCTCTTCGCT
1020154 TT
1 TT
1020156 AATATGATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.00, C:0.26, G:0.06, T:0.69
Consensus pattern (16 bp):
TTTCTTTCTCTTCGCT
Found at i:1026700 original size:3 final size:3
Alignment explanation
Indices: 1026692--1026749 Score: 73
Period size: 3 Copynumber: 18.3 Consensus size: 3
1026682 ATTAATAAAC
1026692 ATA ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA A-A TATA TATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA -ATA -AT-A
1026740 ATA ATA ATA A
1 ATA ATA ATA A
1026750 AAAAGACCCG
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 1 0.02
3 40 0.78
4 9 0.18
5 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1027846 original size:16 final size:16
Alignment explanation
Indices: 1027825--1027856 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1027815 TTGGGAAGAA
1027825 TTTTCCCATAATAAAT
1 TTTTCCCATAATAAAT
1027841 TTTTCCCATAATAAAT
1 TTTTCCCATAATAAAT
1027857 GTTGCCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTTCCCATAATAAAT
Found at i:1027864 original size:16 final size:16
Alignment explanation
Indices: 1027829--1027864 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1027819 GAAGAATTTT
* *
1027829 CCCATAATAAATTTTT
1 CCCATAATAAATGTTG
1027845 CCCATAATAAATGTTG
1 CCCATAATAAATGTTG
1027861 CCCA
1 CCCA
1027865 AACGCCTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (16 bp):
CCCATAATAAATGTTG
Found at i:1028221 original size:14 final size:14
Alignment explanation
Indices: 1028202--1028229 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1028192 ACTTGAATTT
1028202 TTCAAAAGAGTAAG
1 TTCAAAAGAGTAAG
1028216 TTCAAAAGAGTAAG
1 TTCAAAAGAGTAAG
1028230 AAGTAATTAT
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:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
TTCAAAAGAGTAAG
Found at i:1031289 original size:185 final size:184
Alignment explanation
Indices: 1030852--1031404 Score: 871
Period size: 185 Copynumber: 3.0 Consensus size: 184
1030842 AACCGAAATT
* * ** *
1030852 AAATTTTAAATATATTATATATAACATATTAATTTAGCTCAAACTATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTTAACTCAAACTATTTAAAACTCAATTAATAA
* *
1030917 TTTAAGATCTAATAATTTTTAAACCTAAATCAATATTAATTAATT-AAAAATTTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
1030981 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAA
131 TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAA
* * *
1031035 AAATATTAAATATATTATATATAGCATATG-GACTTAACCCAAACCATTTAAAACTCAATTAATA
1 AAATATTAAATATATTATATATAACATATGAG-CTTAACTCAAACTATTTAAAACTCAATTAATA
* *
1031099 ATTTAAGATCCAATAACTTTTAAACCTAAAACAATATTAATTAATTAAAAAAATTATATAAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
*
1031164 TTTATATTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAA
* * * *
1031219 AATATATTAAATATATTATATATAATATATGAGCTCAACTCAAATTATTTAAAACCCAATTAATA
1 AA-ATATTAAATATATTATATATAACATATGAGCTTAACTCAAACTATTTAAAACTCAATTAATA
* *
1031284 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATT
* *
1031349 TTTATTTTATAATTATATATTATTTAAATTAATTATAAAC--TTTTTTGAATTAA
130 TTTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAA
1031402 AAA
1 AAA
1031405 ACATTTAATT
Statistics
Matches: 339, Mismatches: 27, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
182 1 0.00
183 112 0.33
184 73 0.22
185 152 0.45
186 1 0.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGAGCTTAACTCAAACTATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATATAAAATTT
TTATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTTAATTAA
Found at i:1031401 original size:21 final size:20
Alignment explanation
Indices: 1031358--1031401 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1031348 TTTTATTTTA
*
1031358 TAATTATATATTATTTAAAT
1 TAATTATAAATTATTTAAAT
* *
1031378 TAATTATAAACTTTTTTGAAT
1 TAATTATAAA-TTATTTAAAT
1031399 TAA
1 TAA
1031402 AAAACATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (20 bp):
TAATTATAAATTATTTAAAT
Found at i:1031987 original size:27 final size:27
Alignment explanation
Indices: 1031957--1032008 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1031947 TCATAAAACT
* *
1031957 TAATATTA-TTATTTTTAAAATATTAAA
1 TAAT-TTATTTATTATTAAAAAATTAAA
1031984 TAATTTATTTATTATTAAAAAATTA
1 TAATTTATTTATTATTAAAAAATTA
1032009 TTTTTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.14
27 19 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TAATTTATTTATTATTAAAAAATTAAA
Found at i:1031999 original size:19 final size:17
Alignment explanation
Indices: 1031977--1032015 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1031967 ATTTTTAAAA
*
1031977 TATTAAATAATTTATTTAT
1 TATTAAA-AAATTATTT-T
1031996 TATTAAAAAATTATTTT
1 TATTAAAAAATTATTTT
1032013 TAT
1 TAT
1032016 AATTTTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 8 0.42
19 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAAAAAATTATTTT
Found at i:1032081 original size:26 final size:27
Alignment explanation
Indices: 1032031--1032081 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
1032021 TATTAATAAA
* *
1032031 AATAAAAATATTGATATATTTTATTGC
1 AATAAAAATATTGATAAATTATATTGC
1032058 AATAAAAATATT-ATAAATTATATT
1 AATAAAAATATTGATAAATTATATT
1032082 AATTATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (27 bp):
AATAAAAATATTGATAAATTATATTGC
Found at i:1032161 original size:23 final size:23
Alignment explanation
Indices: 1032112--1032162 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1032102 CTGTTATATT
**
1032112 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
1032135 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1032158 ATATT
1 ATATT
1032163 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1032358 original size:22 final size:23
Alignment explanation
Indices: 1032330--1032376 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1032320 TTGATTATTT
1032330 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
1032352 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
1032375 TA
1 TA
1032377 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:1032381 original size:22 final size:22
Alignment explanation
Indices: 1032338--1032381 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1032328 TTTATTATAA
*
1032338 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
1032360 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
1032382 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:1039550 original size:29 final size:29
Alignment explanation
Indices: 1039511--1039688 Score: 146
Period size: 29 Copynumber: 6.1 Consensus size: 29
1039501 ATGGGATTTG
* *
1039511 ATCCCCATCCTGGTTCTGCATGAGATTAT
1 ATCCCCGTCCTGATTCTGCATGAGATTAT
* *
1039540 ATCCTCGTCCT-AGTTCTGCA-CAGGATT-T
1 ATCCCCGTCCTGA-TTCTGCATGA-GATTAT
*** * *
1039568 GATCCAAATCTTGATTTTGCATGAGATTAT
1 -ATCCCCGTCCTGATTCTGCATGAGATTAT
* ** * * *
1039598 ATCTCTATCCTAATTCTACATGGGATTAT
1 ATCCCCGTCCTGATTCTGCATGAGATTAT
1039627 ATCCCCGTCCTGATTCTGCATGAGATTAT
1 ATCCCCGTCCTGATTCTGCATGAGATTAT
* * *
1039656 ATCCCCGTCCTGATTCTACACGGGATTAT
1 ATCCCCGTCCTGATTCTGCATGAGATTAT
1039685 ATCC
1 ATCC
1039689 ACATTCTGAT
Statistics
Matches: 116, Mismatches: 27, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
28 2 0.02
29 111 0.96
30 3 0.03
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (29 bp):
ATCCCCGTCCTGATTCTGCATGAGATTAT
Found at i:1039594 original size:58 final size:58
Alignment explanation
Indices: 1039504--1039701 Score: 204
Period size: 58 Copynumber: 3.4 Consensus size: 58
1039494 ATTTTGTATG
* * *
1039504 GGATTTGATCCCCATCCTGGTTCTGCATGAGATTATATCCTCGTCCTAGTTCTGCACA
1 GGATTTGATCCCCATCCTGATTCTGCATGAGATTATATCCTCGTCCTAATTCTACACA
** * * * **
1039562 GGATTTGATCCAAATCTTGATTTTGCATGAGATTATAT-CTCTATCCTAATTCTACATG
1 GGATTTGATCCCCATCCTGATTCTGCATGAGATTATATCCTC-GTCCTAATTCTACACA
* * * *
1039620 GGATTAT-ATCCCCGTCCTGATTCTGCATGAGATTATATCCCCGTCCTGATTCTACACG
1 GGATT-TGATCCCCATCCTGATTCTGCATGAGATTATATCCTCGTCCTAATTCTACACA
* *
1039678 GGATTAT-ATCCACATTCTGATTCT
1 GGATT-TGATCCCCATCCTGATTCT
1039702 ACATAGGATC
Statistics
Matches: 115, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
57 3 0.03
58 109 0.95
59 3 0.03
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (58 bp):
GGATTTGATCCCCATCCTGATTCTGCATGAGATTATATCCTCGTCCTAATTCTACACA
Found at i:1039697 original size:29 final size:29
Alignment explanation
Indices: 1039587--1039710 Score: 140
Period size: 29 Copynumber: 4.3 Consensus size: 29
1039577 CTTGATTTTG
* * ** *
1039587 CATGAGATTATATCTCTATCCTAATTCTA
1 CATGGGATTATATCCCCGTCCTGATTCTA
*
1039616 CATGGGATTATATCCCCGTCCTGATTCTG
1 CATGGGATTATATCCCCGTCCTGATTCTA
*
1039645 CATGAGATTATATCCCCGTCCTGATTCTA
1 CATGGGATTATATCCCCGTCCTGATTCTA
* * * *
1039674 CACGGGATTATATCCACATTCTGATTCTA
1 CATGGGATTATATCCCCGTCCTGATTCTA
*
1039703 CATAGGAT
1 CATGGGAT
1039711 CTTTTATGGA
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 80 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (29 bp):
CATGGGATTATATCCCCGTCCTGATTCTA
Found at i:1042719 original size:135 final size:134
Alignment explanation
Indices: 1042451--1042716 Score: 311
Period size: 135 Copynumber: 2.0 Consensus size: 134
1042441 TTCATTTTAG
* * ** * * * *
1042451 AAACTTTTTAGTGATATATCACTTCAATTTAGTGTTATATCATACCATTGAATGTTTTTTTTACT
1 AAACTTTTCAGTGATATATCACTTCAATTCAAAGATATATCAGACCATTGAATGTGTTTTTGACT
* * * * ** * *
1042516 TGTTTCTCTTTGATGAAAAACGTTATTTTCTCAAATTATTTAATACACAATGACAATCACTTCAT
66 TGTTTCCCTTTAATGAAAAAAGTCATTTTCTCAAACCATTTAATACACAATGACAATAAATT-AT
1042581 TTCAT
130 TTCAT
* *
1042586 AAACTTTTCAGTGATATATCACTTCAATTCAAAGATATATCAGGCCATTGAATGATGTTTTTGGC
1 AAACTTTTCAGTGATATATCACTTCAATTCAAAGATATATCAGACCATTGAATG-TGTTTTTGAC
* *
1042651 TTGTTTCCCTTTAATGAAAAAAAGTCATTTTTTCAGACCATTTAATACACAATGACAA-AAA-TA
65 TTGTTTCCCTTTAATG-AAAAAAGTCATTTTCTCAAACCATTTAATACACAATGACAATAAATTA
1042714 TTT
129 TTT
1042717 TCAGTGAAAT
Statistics
Matches: 109, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
134 4 0.04
135 48 0.44
136 22 0.20
137 35 0.32
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (134 bp):
AAACTTTTCAGTGATATATCACTTCAATTCAAAGATATATCAGACCATTGAATGTGTTTTTGACT
TGTTTCCCTTTAATGAAAAAAGTCATTTTCTCAAACCATTTAATACACAATGACAATAAATTATT
TCAT
Found at i:1043501 original size:17 final size:17
Alignment explanation
Indices: 1043455--1043493 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1043445 TTATATTTAA
1043455 TTTCTAATAAAATATAT
1 TTTCTAATAAAATATAT
1043472 TTTCTAATAAAATATAT
1 TTTCTAATAAAATATAT
1043489 TTTCT
1 TTTCT
1043494 TATGAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTCTAATAAAATATAT
Found at i:1043721 original size:6 final size:6
Alignment explanation
Indices: 1043710--1043764 Score: 110
Period size: 6 Copynumber: 9.2 Consensus size: 6
1043700 CAGAGAGCAG
1043710 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA
1043758 CTAAAA C
1 CTAAAA C
1043765 AGAGACCGAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.16
Consensus pattern (6 bp):
CTAAAA
Found at i:1050916 original size:33 final size:33
Alignment explanation
Indices: 1050825--1050933 Score: 114
Period size: 33 Copynumber: 3.3 Consensus size: 33
1050815 CTTGAACCTG
* *
1050825 CTGACTCGAATGATGGTTCTTCCCTTGGCTCTA
1 CTGACTCGAATGGTGGTACTTCCCTTGGCTCTA
* * **
1050858 ATGACTC-AACTGGTGATACCGCCCTTGGCTCTA
1 CTGACTCGAA-TGGTGGTACTTCCCTTGGCTCTA
*
1050891 CTGACTCGAATGGTGGTGCTTCCCTTGG-TCCTA
1 CTGACTCGAATGGTGGTACTTCCCTTGGCT-CTA
*
1050924 CTGATTCGAA
1 CTGACTCGAA
1050934 CAATAATGCT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
32 3 0.05
33 56 0.92
34 2 0.03
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (33 bp):
CTGACTCGAATGGTGGTACTTCCCTTGGCTCTA
Found at i:1054717 original size:28 final size:28
Alignment explanation
Indices: 1054677--1054736 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
1054667 TTCATATATC
* *
1054677 CAAAACAAGCGATAGAGAAAAGCAAATT
1 CAAAACAAACGATAGAGAAAAGCAAAAT
1054705 CAAAACAAACGATAGAGAAAAGCAAAAT
1 CAAAACAAACGATAGAGAAAAGCAAAAT
1054733 CAAA
1 CAAA
1054737 GGTTGATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (28 bp):
CAAAACAAACGATAGAGAAAAGCAAAAT
Found at i:1054749 original size:2 final size:2
Alignment explanation
Indices: 1054742--1054773 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1054732 TCAAAGGTTG
1054742 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
1054774 TATTTAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1055255 original size:3 final size:3
Alignment explanation
Indices: 1055247--1055275 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1055237 TTTTACCAAA
1055247 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1055276 AACCGATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1055615 original size:249 final size:249
Alignment explanation
Indices: 1055177--1055670 Score: 961
Period size: 249 Copynumber: 2.0 Consensus size: 249
1055167 TATGTTAATA
*
1055177 AAACCGGTAAAACGCCCAATAATAACAAAACGGGTGGAAATAATAATGTTTTAGGTAATTTTTTA
1 AAACCGGTAAAACGCCCAATAATAACAAAACGGGTGGAAATAATAATATTTTAGGTAATTTTTTA
1055242 CCAAAAATAATAATAATAATAATAATAATAATAAAACCGATAATACCTTTCCTTAGCCGTATATT
66 CCAAAAATAATAATAATAATAATAATAATAATAAAACCGATAATACCTTTCCTTAGCCGTATATT
1055307 AAGACCGCCATATGCGAGACTTCCTGATTAAGGTACTCCTACCTTGTTGATTGATTGTGGATATA
131 AAGACCGCCATATGCGAGACTTCCTGATTAAGGTACTCCTACCTTGTTGATTGATTGTGGATATA
1055372 GGAAGGAAGCAAAACAACATGCATAAGTGAATGAATCAAATAGATGGTTTGGTG
196 GGAAGGAAGCAAAACAACATGCATAAGTGAATGAATCAAATAGATGGTTTGGTG
1055426 AAACCGGTAAAACGCCCAATAATAACAAAACGGGTGGAAATAATAATATTTTAGGTAATTTTTTA
1 AAACCGGTAAAACGCCCAATAATAACAAAACGGGTGGAAATAATAATATTTTAGGTAATTTTTTA
* *
1055491 CCAAAAATATTATTAATAATAATAATAATAATAAAACCGATAATACCTTTCCTTAGCCGTATATT
66 CCAAAAATAATAATAATAATAATAATAATAATAAAACCGATAATACCTTTCCTTAGCCGTATATT
1055556 AAGACCGCCATATGCGAGACTTCCTGATTAAGGTACTCCTACCTTGTTGATTGATTGTGGATATA
131 AAGACCGCCATATGCGAGACTTCCTGATTAAGGTACTCCTACCTTGTTGATTGATTGTGGATATA
1055621 GGAAGGAAGCAAAACAACATGCATAAGTGAATGAATCAAATAGATGGTTT
196 GGAAGGAAGCAAAACAACATGCATAAGTGAATGAATCAAATAGATGGTTT
1055671 AGTGGTAGAT
Statistics
Matches: 242, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
249 242 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (249 bp):
AAACCGGTAAAACGCCCAATAATAACAAAACGGGTGGAAATAATAATATTTTAGGTAATTTTTTA
CCAAAAATAATAATAATAATAATAATAATAATAAAACCGATAATACCTTTCCTTAGCCGTATATT
AAGACCGCCATATGCGAGACTTCCTGATTAAGGTACTCCTACCTTGTTGATTGATTGTGGATATA
GGAAGGAAGCAAAACAACATGCATAAGTGAATGAATCAAATAGATGGTTTGGTG
Found at i:1059786 original size:11 final size:11
Alignment explanation
Indices: 1059770--1059794 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1059760 TTTTATTTCT
1059770 TTCACTTGCAC
1 TTCACTTGCAC
1059781 TTCACTTGCAC
1 TTCACTTGCAC
1059792 TTC
1 TTC
1059795 TTTTTGTATT
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:0.16, C:0.36, G:0.08, T:0.40
Consensus pattern (11 bp):
TTCACTTGCAC
Found at i:1063416 original size:23 final size:23
Alignment explanation
Indices: 1063390--1063434 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1063380 CACCACAGCT
*
1063390 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1063413 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1063435 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1063672 original size:149 final size:149
Alignment explanation
Indices: 1063402--1063716 Score: 553
Period size: 149 Copynumber: 2.1 Consensus size: 149
1063392 TATAATTGCA
1063402 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
*
1063466 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
65 GTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTT
1063531 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
*
1063551 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGACG
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAG
*
1063616 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTTTCCAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATACTAGGGATCA-AGTATGTGTCTTTCCAGACTTCACACATGTT
*
1063680 CCAAAGATTATACATATGTC
130 CCAAAGAATATACATATGTC
*
1063700 CCGAAGGATCGCGTAGA
1 CCGAAGGACCGCGTAGA
1063717 CCCTCGACTC
Statistics
Matches: 159, Mismatches: 5, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
148 1 0.01
149 157 0.99
150 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAG
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:1064623 original size:18 final size:18
Alignment explanation
Indices: 1064602--1064636 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1064592 TCCCATCTAG
1064602 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1064620 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1064637 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1065241 original size:21 final size:21
Alignment explanation
Indices: 1065217--1065261 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1065207 TGTTGTTCGT
* *
1065217 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1065238 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1065259 TTG
1 TTG
1065262 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1068540 original size:23 final size:23
Alignment explanation
Indices: 1068514--1068558 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1068504 CACCACAGCT
*
1068514 CGTATAATTGAACCGAAGTGCCG
1 CGTAGAATTGAACCGAAGTGCCG
* *
1068537 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGAACCGAAGTGCC
1068559 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGAACCGAAGTGCCG
Found at i:1069597 original size:18 final size:18
Alignment explanation
Indices: 1069576--1069610 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1069566 TCCCATCTAG
1069576 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
1069594 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
1069611 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:1070215 original size:21 final size:21
Alignment explanation
Indices: 1070191--1070235 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1070181 TGTTGTTCGT
* *
1070191 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1070212 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1070233 TTG
1 TTG
1070236 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1073801 original size:8 final size:8
Alignment explanation
Indices: 1073790--1073843 Score: 63
Period size: 8 Copynumber: 6.5 Consensus size: 8
1073780 TTTTGAAATC
1073790 TTTTTTCT
1 TTTTTTCT
1073798 TTTTCTTCT
1 TTTT-TTCT
*
1073807 TTTCTTCT
1 TTTTTTCT
*
1073815 TTTCTTCT
1 TTTTTTCT
*
1073823 TTTTGTCT
1 TTTTTTCT
1073831 TTTCTTTCT
1 TTT-TTTCT
1073840 TTTT
1 TTTT
1073844 GTACTCCAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
8 26 0.65
9 14 0.35
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTTCT
Found at i:1073809 original size:16 final size:15
Alignment explanation
Indices: 1073788--1073843 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 15
1073778 CTTTTTGAAA
1073788 TCTTTTTTCTTTTTCT
1 TCTTTTTTC-TTTTCT
1073804 TCTTTTCTTCTTTTCT
1 TCTTTT-TTCTTTTCT
1073820 TCTTTTTGTCTTTTCTT
1 TCTTTTT-TCTTTTC-T
1073837 TCTTTTT
1 TCTTTTT
1073844 GTACTCCAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.03
16 25 0.68
17 11 0.30
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (15 bp):
TCTTTTTTCTTTTCT
Found at i:1073815 original size:24 final size:24
Alignment explanation
Indices: 1073789--1073843 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
1073779 TTTTTGAAAT
*
1073789 CTTTTTTCTTTTTCTTCTTTTC-TT
1 CTTTTTTCTTTTT-GTCTTTTCTTT
1073813 CTTTTCTTCTTTTTGTCTTTTCTTT
1 CTTTT-TTCTTTTTGTCTTTTCTTT
1073838 CTTTTT
1 CTTTTT
1073844 GTACTCCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (24 bp):
CTTTTTTCTTTTTGTCTTTTCTTT
Found at i:1081678 original size:22 final size:22
Alignment explanation
Indices: 1081653--1081730 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
1081643 TACGAGTAGC
1081653 TAAATAATTATGACTAAAAATA
1 TAAATAATTATGACTAAAAATA
**
1081675 TAAACTACAAGGAAATTGA-TAAAATATA
1 TAAA-T--AA--TTA-TGACTAAAA-ATA
*
1081703 TAAATAATTATGACTAAATATA
1 TAAATAATTATGACTAAAAATA
1081725 TAAATA
1 TAAATA
1081731 TATAAATTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
22 16 0.37
23 6 0.14
25 4 0.09
27 7 0.16
28 10 0.23
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (22 bp):
TAAATAATTATGACTAAAAATA
Found at i:1089096 original size:18 final size:18
Alignment explanation
Indices: 1089061--1089096 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1089051 TCGGTAAAAA
*
1089061 TACATAACTTAATGAATG
1 TACATAACTTAATAAATG
*
1089079 TACATAACTTATTAAATG
1 TACATAACTTAATAAATG
1089097 AATGCATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (18 bp):
TACATAACTTAATAAATG
Found at i:1090327 original size:278 final size:278
Alignment explanation
Indices: 1089813--1090327 Score: 906
Period size: 278 Copynumber: 1.9 Consensus size: 278
1089803 TATAATATAA
*
1089813 GCTAAGTAATCAAAAAATATTAACTTTTCTATTAATGGTGTCATGTCATCAATTTAATAGAGATA
1 GCTAAGTAATCAAAAAATATTAACTTTTCTATTAATGGTGCCATGTCATCAATTTAATAGAGATA
1089878 ATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTTTGTTACAAATCAATAA
66 ATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTTTGTTACAAATCAATAA
*
1089943 TGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAACGAAACATACTCAAACATTA
131 TGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAACATACTCAAACATTA
* *
1090008 GTGACAACTTTTAATTAACCCACCTTCTTTATATACATTAGCGATTCCAGGATTGAGAAAGAAGC
196 GTGACAACTTTTAATTAACCCACATTCTCTATATACATTAGCGATTCCAGGATTGAGAAAGAAGC
1090073 AGCAAGTGATGGGATTCT
261 AGCAAGTGATGGGATTCT
1090091 GCTAAGTAAT-AAAAAATATTAACATTTTCTATTAATGGTGCCATGTCATCAATTTAATAGAGAT
1 GCTAAGTAATCAAAAAATATTAAC-TTTTCTATTAATGGTGCCATGTCATCAATTTAATAGAGAT
1090155 AATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTTTGTTACAAATCAATA
65 AATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTTTGTTACAAATCAATA
* * * **
1090220 ATTTTAATGATGAATTTATTACTTTTTAAAACTTTAGTGGAGAAAAAGAAATGTACTCAAACATT
130 ATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAACATACTCAAACATT
* * *
1090285 CGTGACAACTTTTAATTAACCCACATTCTCTCTATCCATTAGC
195 AGTGACAACTTTTAATTAACCCACATTCTCTATATACATTAGC
1090328 TTAATTGAGT
Statistics
Matches: 224, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
277 13 0.06
278 211 0.94
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (278 bp):
GCTAAGTAATCAAAAAATATTAACTTTTCTATTAATGGTGCCATGTCATCAATTTAATAGAGATA
ATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTTTGTTACAAATCAATAA
TGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAACATACTCAAACATTA
GTGACAACTTTTAATTAACCCACATTCTCTATATACATTAGCGATTCCAGGATTGAGAAAGAAGC
AGCAAGTGATGGGATTCT
Found at i:1091767 original size:278 final size:279
Alignment explanation
Indices: 1091256--1091771 Score: 865
Period size: 278 Copynumber: 1.9 Consensus size: 279
1091246 CATAATATAA
* *
1091256 GCTAAGTACTCAAAAAATATTAACTTTTTCTATTAATGGTGCCATGTCATCAATTTAACAGAGAT
1 GCTAAGTAATCAAAAAATATTAACATTTTCTATTAATGGTGCCATGTCATCAATTTAACAGAGAT
*
1091321 AATGGTGGAGTAACCATTTTATTATAAATAGATAACATTAGTAATTATTTTGTTACAAATGAATA
66 AATGGTGGAGTAACCATTTTATTATAAATAGATAACATTAGTAATTATTTTGTTACAAATCAATA
*
1091386 ATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAACGTACCCAAACATT
131 ATGTTAATGACAAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAACGTACCCAAACATT
* *
1091451 AGTGACGACTTTTAATTAACCCACCTTCTCTATATCCATTAGCGATTCTAGGATTGAGAAAGAAG
196 AGTGACAACTTTTAATTAACCCACATTCTCTATATCCATTAGCGATTCTAGGATTGAGAAAGAAG
1091516 CAGCAAGTGATGGGATTCT
261 CAGCAAGTGATGGGATTCT
* *
1091535 GCTAAGTAAT-AAAAAATATTAACATTTTCTATTAATGGTGCCATGTCATCAATTTAATATAGAT
1 GCTAAGTAATCAAAAAATATTAACATTTTCTATTAATGGTGCCATGTCATCAATTTAACAGAGAT
* *
1091599 AATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTTTGTTACAAATCAATA
66 AATGGTGGAGTAACCATTTTATTATAAATAGATAACATTAGTAATTATTTTGTTACAAATCAATA
* * * *
1091664 ATTTTAATGACAAATTTATTACTTTTTAAAACTTTAGTGGAGAAAAAGAAATGTACTCAAACA-T
131 ATGTTAATGACAAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAACGTACCCAAACATT
* *
1091728 ATGTGACAACTTTTAATTTACCCACATTCTCTCTATCCATTAGC
196 A-GTGACAACTTTTAATTAACCCACATTCTCTATATCCATTAGC
1091772 TTAATTGGAG
Statistics
Matches: 220, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
277 2 0.01
278 209 0.95
279 9 0.04
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (279 bp):
GCTAAGTAATCAAAAAATATTAACATTTTCTATTAATGGTGCCATGTCATCAATTTAACAGAGAT
AATGGTGGAGTAACCATTTTATTATAAATAGATAACATTAGTAATTATTTTGTTACAAATCAATA
ATGTTAATGACAAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAACGTACCCAAACATT
AGTGACAACTTTTAATTAACCCACATTCTCTATATCCATTAGCGATTCTAGGATTGAGAAAGAAG
CAGCAAGTGATGGGATTCT
Found at i:1092172 original size:723 final size:722
Alignment explanation
Indices: 1089604--1092985 Score: 6068
Period size: 722 Copynumber: 4.7 Consensus size: 722
1089594 GCTACTCCCC
* * * * * *
1089604 AGCTGAATTGAGTAGCCTAGCCAGCTCAAAAGTTCAGTTCAAGTTAGCTATGAACTCGGAGTGCA
1 AGCTTAATTGAGTAGCCTAGCTACCTCAAAAGTCCAGTTCAAGTCAGCTATGAGCTCGGAGTGCA
* * * *
1089669 GCTGACAACTTTTCTTCAAATTGATCATTAGCTTCCCTGAAGTTA-TCATAGTCATGTTCCCATA
66 ACTGGCAACTTTTCTTCAAATTGATCATTAGCTTCCCCGAAG-TAGTCCTAGTCATGTTCCCATA
*
1089733 GCTTTGGAGTCTATTTACTAGCTTAAGTCAGCTCCCAATATGTGGCTGCCTATGTACCTTCATAA
130 GCTTTGGACTCTATTTACTAGCTTAAGTCAGCTCCCAATATGTGGCTGCCTATGTACCTTCATAA
* *
1089798 TGAAATATAATATAAGCTAAGTAATCAAAAAATATTAA-CTTTTCTATTAATGGTGTCATGTCAT
195 TGAAACATAATATAAGCTAAGTAATCAAAAAATATTAACCTTTTCTATTAATGGTGCCATGTCAT
*
1089862 CAATTTAATAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTT
260 CAATTTAACAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTT
*
1089927 TGTTACAAATCAATAATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAACGAA
325 TGTTACAAATCAATAATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAA
* * *
1089992 ACATACTCAAACATTAGTGACAACTTTTAATTAACCCACCTTCTTTATATACATTAGCGATTCCA
390 ACGTACTCAAACATTAGTGACAACTTTTAATTAACCCACCTTCTCTATATCCATTAGCGATTCCA
1090057 GGATTGAGAAAGAAGCAGCAAGTGATGGGATTCTGCTAAGTAATAAAAAATATTAACATTTTCTA
455 GGATTGAGAAAGAAGCAGCAAGTGATGGGATTCTGCTAAGTAATAAAAAATATTAACATTTTCTA
1090122 TTAATGGTGCCATGTCATCAATTTAATAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGA
520 TTAATGGTGCCATGTCATCAATTTAATAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGA
*
1090187 TAACGTTAGTAATTATTTTGTTACAAATCAATAATTTTAATGATGAATTTATTACTTTTTAAAAC
585 TAACGTTAGTAATTATTTTGTTACAAATCAATAATTTTAATGACGAATTTATTACTTTTTAAAAC
*
1090252 TTTAGTGGAGAAAAAGAAATGTACTCAAACATTCGTGACAACTTTTAATTAACCCACATTCTCTC
650 TTTAGTGGAGAAAAAGAAATGTACTCAAACATTCGTGACAACTTTTAATTTACCCACATTCTCTC
1090317 TATCCATT
715 TATCCATT
*
1090325 AGCTTAATTGAGTAGCCTAGCTAGCTCAAAAGTCCAGTTCAAGTCAGCTATGAGCTCGGAGTGCA
1 AGCTTAATTGAGTAGCCTAGCTACCTCAAAAGTCCAGTTCAAGTCAGCTATGAGCTCGGAGTGCA
* *
1090390 ACTGGCAACTTTTCTTCAAATTGATCATTAGCTTCCCTGAAGTAGTCCTAATCATGTTCCCATAG
66 ACTGGCAACTTTTCTTCAAATTGATCATTAGCTTCCCCGAAGTAGTCCTAGTCATGTTCCCATAG
* ** * * *
1090455 CTTTGGACTATATTTACTAGAGTAAGTCAACTCCCAATATATGGTTGCCTATGTACCTTCATAAT
131 CTTTGGACTCTATTTACTAGCTTAAGTCAGCTCCCAATATGTGGCTGCCTATGTACCTTCATAAT
* * *
1090520 GAAACATAATATAAGATAAGTAATCAAAAAATATTAACTTTTTCTATTCATGGTGCCATGTCATC
196 GAAACATAATATAAGCTAAGTAATCAAAAAATATTAACCTTTTCTATTAATGGTGCCATGTCATC
*
1090585 AATTTAATAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTTT
261 AATTTAACAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTTT
1090650 GTTACAAATCAATAATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAA
326 GTTACAAATCAATAATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAA
*
1090715 CGTACTCAAACATTAGTGACAACTTTTAATTAACCCACCTTCTCTATATCTATTAGCGATTCCAG
391 CGTACTCAAACATTAGTGACAACTTTTAATTAACCCACCTTCTCTATATCCATTAGCGATTCCAG
1090780 GATTGAGAAAGAAGCAGCAAGTGATGGGATTCTGCTAAGTAATAAAAAATATTAACATTTTCTAT
456 GATTGAGAAAGAAGCAGCAAGTGATGGGATTCTGCTAAGTAATAAAAAATATTAACATTTTCTAT
1090845 TAATGGTGCCATGTCATCAATTTAATAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGAT
521 TAATGGTGCCATGTCATCAATTTAATAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGAT
*
1090910 ATCGTTAGTAATTATTTTGTTACAAATCAATAATTTTAATGACGAATTTATTACTTTTTAAAACT
586 AACGTTAGTAATTATTTTGTTACAAATCAATAATTTTAATGACGAATTTATTACTTTTTAAAACT
1090975 TTAGTGGAGAAAAAGAAATGTACTCAAACATTCGTGACAACTTTTAATTTACCCACATTCTCTCT
651 TTAGTGGAGAAAAAGAAATGTACTCAAACATTCGTGACAACTTTTAATTTACCCACATTCTCTCT
1091040 ATCCATT
716 ATCCATT
1091047 AGCTTAATTGAGTAGCCTAGCTACCTCAAAAGTCCAGTTCAAGTCAGCTATGAGCTCGGAGTGCA
1 AGCTTAATTGAGTAGCCTAGCTACCTCAAAAGTCCAGTTCAAGTCAGCTATGAGCTCGGAGTGCA
*
1091112 ACTGCCAACTTTTCTTCAAATTGATCATTAGCTTCCCCGAAGTAGTCCTAGTCATGTTCCCATAG
66 ACTGGCAACTTTTCTTCAAATTGATCATTAGCTTCCCCGAAGTAGTCCTAGTCATGTTCCCATAG
*
1091177 CTTTGGACTCTATTTACTAGCTTAAGTCAGCTCCCAATATGTGGTTGCCTATGTACCTTCATAAT
131 CTTTGGACTCTATTTACTAGCTTAAGTCAGCTCCCAATATGTGGCTGCCTATGTACCTTCATAAT
* *
1091242 GAAACATAATATAAGCTAAGTACTCAAAAAATATTAACTTTTTCTATTAATGGTGCCATGTCATC
196 GAAACATAATATAAGCTAAGTAATCAAAAAATATTAACCTTTTCTATTAATGGTGCCATGTCATC
* *
1091307 AATTTAACAGAGATAATGGTGGAGTAACCATTTTATTATAAATAGATAACATTAGTAATTATTTT
261 AATTTAACAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTTT
*
1091372 GTTACAAATGAATAATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAA
326 GTTACAAATCAATAATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAA
* * *
1091437 CGTACCCAAACATTAGTGACGACTTTTAATTAACCCACCTTCTCTATATCCATTAGCGATTCTAG
391 CGTACTCAAACATTAGTGACAACTTTTAATTAACCCACCTTCTCTATATCCATTAGCGATTCCAG
1091502 GATTGAGAAAGAAGCAGCAAGTGATGGGATTCTGCTAAGTAATAAAAAATATTAACATTTTCTAT
456 GATTGAGAAAGAAGCAGCAAGTGATGGGATTCTGCTAAGTAATAAAAAATATTAACATTTTCTAT
*
1091567 TAATGGTGCCATGTCATCAATTTAATATAGATAATGGTGGAGTAACCATTTTATTATAAATGGAT
521 TAATGGTGCCATGTCATCAATTTAATAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGAT
*
1091632 AACGTTAGTAATTATTTTGTTACAAATCAATAATTTTAATGACAAATTTATTACTTTTTAAAACT
586 AACGTTAGTAATTATTTTGTTACAAATCAATAATTTTAATGACGAATTTATTACTTTTTAAAACT
1091697 TTAGTGGAGAAAAAGAAATGTACTCAAACATAT-GTGACAACTTTTAATTTACCCACATTCTCTC
651 TTAGTGGAGAAAAAGAAATGTACTCAAACAT-TCGTGACAACTTTTAATTTACCCACATTCTCTC
1091761 TATCCATT
715 TATCCATT
1091769 AGCTTAATTGGAGTAGCCTAGCTACCTCAAAAGTCCAGTTCAAGTCAGCTATGAGCTCGGAGTGC
1 AGCTTAATT-GAGTAGCCTAGCTACCTCAAAAGTCCAGTTCAAGTCAGCTATGAGCTCGGAGTGC
*
1091834 AACTGGCAACTTTTCTTCAAATTGATCATTAGCTTCCCCAAAGTAGTCCTAGTCATGTTCCCATA
65 AACTGGCAACTTTTCTTCAAATTGATCATTAGCTTCCCCGAAGTAGTCCTAGTCATGTTCCCATA
1091899 GCTTTGGACTCTATTTACTAGCTTAAGTCAGCTCCCAATATGTGGCTGCCTATGTACCTTCATAA
130 GCTTTGGACTCTATTTACTAGCTTAAGTCAGCTCCCAATATGTGGCTGCCTATGTACCTTCATAA
1091964 TGAAACATAATATAAGCTAAGTAATCAAAAAATATTAACCTTTTCTATTAATGGTGCCATGTCAT
195 TGAAACATAATATAAGCTAAGTAATCAAAAAATATTAACCTTTTCTATTAATGGTGCCATGTCAT
1092029 CAATTTAACAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTT
260 CAATTTAACAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTT
* *
1092094 TGTTACAAATCAATAATGTTAATGATGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAG
325 TGTTACAAATCAATAATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAA
* * *
1092159 ATGTACTCAAACATTAGTGACGACTTTTAATTAACCCACCTTCTCTATATCCGTTAGCGATTCCA
390 ACGTACTCAAACATTAGTGACAACTTTTAATTAACCCACCTTCTCTATATCCATTAGCGATTCCA
*
1092224 GGATTGAGAAAGAAGCAGCAAGTGATGGGATTATGCTAAGTAATAAAAAATATTAACATTTTCTA
455 GGATTGAGAAAGAAGCAGCAAGTGATGGGATTCTGCTAAGTAATAAAAAATATTAACATTTTCTA
*
1092289 TTAATGGTGCCATGTCATCAATTTAATAGAAATAATGGTGGAGTAACCATTTTATTATAAATGGA
520 TTAATGGTGCCATGTCATCAATTTAATAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGA
1092354 TAACGTTAGTAATTATTTTGTTACAAATCAATAATTTTAATGACGAATTTATTACTTTTTAAAAC
585 TAACGTTAGTAATTATTTTGTTACAAATCAATAATTTTAATGACGAATTTATTACTTTTTAAAAC
*
1092419 TTTAGTGGAGAAAAAGAAATGTACTCAAATATTCGTGACAACTTTTAATTTACCCACATTCTCTC
650 TTTAGTGGAGAAAAAGAAATGTACTCAAACATTCGTGACAACTTTTAATTTACCCACATTCTCTC
1092484 TATCCATT
715 TATCCATT
1092492 AGCTTAATTGAGTAGCCTAGCTACCTCAAAAGTCCAGTTCAAGTCAGCTATGAGCTCGGAGTGCA
1 AGCTTAATTGAGTAGCCTAGCTACCTCAAAAGTCCAGTTCAAGTCAGCTATGAGCTCGGAGTGCA
* *
1092557 ACTGGAAACTTTTCTTCAAATTGATCATTAGCTTCCCCGAAGTAGTCCTAGTCATGTTCTCATAG
66 ACTGGCAACTTTTCTTCAAATTGATCATTAGCTTCCCCGAAGTAGTCCTAGTCATGTTCCCATAG
*
1092622 CTTTGGACTCTATTTACTAGCTTAAGTCAACTCCCAATATGTGGCTGCCTATGTACCTTCATAAT
131 CTTTGGACTCTATTTACTAGCTTAAGTCAGCTCCCAATATGTGGCTGCCTATGTACCTTCATAAT
* *
1092687 GAAACATAATATAAGCTAAGTAATAAAAAAAATATTAACCTTTTCTATTAATGGTTCCATGTCAT
196 GAAACATAATATAAGCTAAGTAAT-CAAAAAATATTAACCTTTTCTATTAATGGTGCCATGTCAT
* * * *
1092752 CAATTTAACAAAGATAATGGTGGAGTAACAATTTTATTATAAATGGATAACATTAATAATTATTT
260 CAATTTAACAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTT
*
1092817 TGTTACAAATCAATAATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAG
325 TGTTACAAATCAATAATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAA
* * * * *
1092882 ATGTACTCAAACATTAGTGACAACTTTTAATTAACCCACATTCTCTCTATCCGTTAGTGATTCCA
390 ACGTACTCAAACATTAGTGACAACTTTTAATTAACCCACCTTCTCTATATCCATTAGCGATTCCA
1092947 GGATTGAGAAAGAAGCAGCAAGTGATGGGATTCTGCTAA
455 GGATTGAGAAAGAAGCAGCAAGTGATGGGATTCTGCTAA
1092986 ATTTATTTGA
Statistics
Matches: 2568, Mismatches: 87, Indels: 10
0.96 0.03 0.00
Matches are distributed among these distances:
720 2 0.00
721 211 0.08
722 1391 0.54
723 964 0.38
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (722 bp):
AGCTTAATTGAGTAGCCTAGCTACCTCAAAAGTCCAGTTCAAGTCAGCTATGAGCTCGGAGTGCA
ACTGGCAACTTTTCTTCAAATTGATCATTAGCTTCCCCGAAGTAGTCCTAGTCATGTTCCCATAG
CTTTGGACTCTATTTACTAGCTTAAGTCAGCTCCCAATATGTGGCTGCCTATGTACCTTCATAAT
GAAACATAATATAAGCTAAGTAATCAAAAAATATTAACCTTTTCTATTAATGGTGCCATGTCATC
AATTTAACAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGATAACGTTAGTAATTATTTT
GTTACAAATCAATAATGTTAATGACGAATTTATTACTTTTTAAAACTTCAGTGGAGAAAAAGAAA
CGTACTCAAACATTAGTGACAACTTTTAATTAACCCACCTTCTCTATATCCATTAGCGATTCCAG
GATTGAGAAAGAAGCAGCAAGTGATGGGATTCTGCTAAGTAATAAAAAATATTAACATTTTCTAT
TAATGGTGCCATGTCATCAATTTAATAGAGATAATGGTGGAGTAACCATTTTATTATAAATGGAT
AACGTTAGTAATTATTTTGTTACAAATCAATAATTTTAATGACGAATTTATTACTTTTTAAAACT
TTAGTGGAGAAAAAGAAATGTACTCAAACATTCGTGACAACTTTTAATTTACCCACATTCTCTCT
ATCCATT
Found at i:1097745 original size:17 final size:15
Alignment explanation
Indices: 1097705--1097748 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 15
1097695 TTGCTGGAAA
1097705 TTTCTTTCTTTTTGGT
1 TTTCTTT-TTTTTGGT
*
1097721 TTTTTTTTTTTTGTGAT
1 TTTCTTTTTTTTG-G-T
1097738 TTTCTTTTTTT
1 TTTCTTTTTTT
1097749 GTTTTGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 7 0.29
17 11 0.46
ACGTcount: A:0.02, C:0.07, G:0.09, T:0.82
Consensus pattern (15 bp):
TTTCTTTTTTTTGGT
Found at i:1128551 original size:64 final size:67
Alignment explanation
Indices: 1128410--1128583 Score: 211
Period size: 65 Copynumber: 2.7 Consensus size: 67
1128400 CTGGGCAATG
* ** * *
1128410 TGCATCGATGCACA-TGTAGTGCATCGATGCAT---TAAATTTAAAAAGAAAACATCGAATAGGA
1 TGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCA-TTAAATA-CAAACATCGAATAGGA
1128471 TTTA
64 TTTA
1128475 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT-CC-CCATTAAATACAAACATCGAATAGGAT
1 TGCATCGATGCAT-AGTGTAGTGCATCGATGCATACCTCCATTAAATACAAACATCGAATAGGAT
1128536 TTA
65 TTA
*
1128539 TGCATCGATGCATGGTGTAGTGCATCGATGCATACCTCCATTAAA
1 TGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAA
1128584 AGATGAAAAT
Statistics
Matches: 95, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
63 1 0.01
64 33 0.35
65 48 0.51
66 5 0.05
67 8 0.08
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (67 bp):
TGCATCGATGCATAGTGTAGTGCATCGATGCATACCTCCATTAAATACAAACATCGAATAGGATT
TA
Found at i:1129257 original size:103 final size:103
Alignment explanation
Indices: 1129032--1129249 Score: 400
Period size: 103 Copynumber: 2.1 Consensus size: 103
1129022 GTAGAGGGTC
1129032 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATATGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATATGTGAGGTCTGGTGAGACACATAC
1129097 TTGATCCTTGACATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGACATATGTATATGATTCTTAAGGAATGA
* * *
1129135 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATATGTGAGGTCTGGTGAGACACATAC
*
1129200 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGACATATGTATATGATTCTTAAGGAATGA
1129238 TATGTGGTCCTT
1 TATGTGGTCCTT
1129250 ATGGACATTA
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATATGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGACATATGTATATGATTCTTAAGGAATGA
Found at i:1129299 original size:23 final size:23
Alignment explanation
Indices: 1129266--1129317 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
1129256 ATTATTATAT
1129266 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1129289 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
1129312 GGCACT
1 GGCACT
1129318 TAGGCGCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.31, G:0.27, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1129326 original size:23 final size:23
Alignment explanation
Indices: 1129277--1129328 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
1129267 GCACTACGGT
* *
1129277 GCAATTCTACGCGGCACTCCGGT
1 GCAATTCTACGCGGCACTCAGGC
* *
1129300 GCAATTCTACGTGGCACTTAGGC
1 GCAATTCTACGCGGCACTCAGGC
1129323 GCAATT
1 GCAATT
1129329 ATATGAGCTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GCAATTCTACGCGGCACTCAGGC
Found at i:1131138 original size:21 final size:21
Alignment explanation
Indices: 1131096--1131138 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1131086 TTTCTGGGCT
* * *
1131096 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1131117 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1131138 A
1 A
1131139 ACGAACCAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:1131210 original size:22 final size:22
Alignment explanation
Indices: 1131167--1131210 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1131157 AATGTCGTGG
*
1131167 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
1131189 GGGAACCGAT-CCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
1131211 AGAAATGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.32, C:0.34, G:0.27, T:0.07
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Done.