Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008075.1 Hibiscus syriacus cultivar Beakdansim tig00110577_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: 1947163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 10
Found at i:603642 original size:3 final size:3
Alignment explanation
Indices: 603634--603697 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
603624 GCTCCAGCTC
603634 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
603682 GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG G
603698 GTTTTGATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:616971 original size:2 final size:2
Alignment explanation
Indices: 616964--616998 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
616954 TTATTAGAAT
616964 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
616999 CAATAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:618049 original size:20 final size:20
Alignment explanation
Indices: 618026--618085 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
618016 TTTGAGTTTC
618026 TATTTAAATTTAATTATAAA
1 TATTTAAATTTAATTATAAA
618046 TATTTATAA--T-ATTATGAAA
1 TATTTA-AATTTAATTAT-AAA
*
618065 TTATTTAATTTTAATT-TAAA
1 -TATTTAAATTTAATTATAAA
618085 T
1 T
618086 GATATTCTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 13
0.70 0.02 0.28
Matches are distributed among these distances:
18 5 0.15
19 6 0.18
20 15 0.45
21 4 0.12
22 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TATTTAAATTTAATTATAAA
Found at i:620234 original size:20 final size:20
Alignment explanation
Indices: 620209--620270 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
620199 ATCTATTATC
620209 AACTAATTACCTATTTTGTT
1 AACTAATTACCTATTTTGTT
* *
620229 AACT-A--A-CT-TTATTATC
1 AACTAATTACCTATT-TTGTT
*
620245 AACTAATTACCTATTCTGTT
1 AACTAATTACCTATTTTGTT
620265 AACTAA
1 AACTAA
620271 CTTATAAGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 12
0.65 0.10 0.25
Matches are distributed among these distances:
15 2 0.06
16 9 0.29
17 2 0.06
19 2 0.06
20 14 0.45
21 2 0.06
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.44
Consensus pattern (20 bp):
AACTAATTACCTATTTTGTT
Found at i:620249 original size:36 final size:36
Alignment explanation
Indices: 620202--620273 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
620192 AAATACAATC
*
620202 TATTATCAACTAATTACCTATTTTGTTAACTAACTT
1 TATTATCAACTAATTACCTATTCTGTTAACTAACTT
620238 TATTATCAACTAATTACCTATTCTGTTAACTAACTT
1 TATTATCAACTAATTACCTATTCTGTTAACTAACTT
620274 ATAAGTACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.33, C:0.18, G:0.03, T:0.46
Consensus pattern (36 bp):
TATTATCAACTAATTACCTATTCTGTTAACTAACTT
Found at i:620404 original size:40 final size:40
Alignment explanation
Indices: 620360--620451 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
620350 TTTATCTTTT
* * **
620360 AATACTTCGACATCTCGA-TTCTTCCTTCTTATTGAGGCGG
1 AATACTTTGACATCTC-ACTTCTTCCATCTTATAAAGGCGG
*
620400 AATACTTTGACATCTCACTTCTTCCATCTTATAAAGGTGG
1 AATACTTTGACATCTCACTTCTTCCATCTTATAAAGGCGG
620440 AATACTTTGACA
1 AATACTTTGACA
620452 CCGGTCAATC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.02
40 45 0.98
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (40 bp):
AATACTTTGACATCTCACTTCTTCCATCTTATAAAGGCGG
Found at i:622881 original size:14 final size:14
Alignment explanation
Indices: 622862--622892 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
622852 ATGGCGGCTG
622862 AGGAAATTAGGGTT
1 AGGAAATTAGGGTT
622876 AGGAAATTAGGGTT
1 AGGAAATTAGGGTT
622890 AGG
1 AGG
622893 TTTAATCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.39, T:0.26
Consensus pattern (14 bp):
AGGAAATTAGGGTT
Found at i:622992 original size:3 final size:3
Alignment explanation
Indices: 622984--623086 Score: 188
Period size: 3 Copynumber: 34.3 Consensus size: 3
622974 TAATGTATAT
*
622984 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
623032 TAA TAT TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
623080 TAA TAA T
1 TAA TAA T
623087 GGATAAAAAA
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:623649 original size:113 final size:113
Alignment explanation
Indices: 623403--624154 Score: 1155
Period size: 113 Copynumber: 6.6 Consensus size: 113
623393 AGAATTATGC
* * * * *
623403 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
623468 TATGAAC-TTCTCTGGAAAAGATAATCCATCAATTGATGAATTCAAGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGACTCAGGT
623515 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
623580 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGACTCAGGT
623628 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
623693 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGACTCAGGT
623741 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
623806 TATGAACTTTCTCTGGAAAGGCTGATCCATCAAATGATGGACTCAGGT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGACTCAGGT
*
623854 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * **
623919 TATGAACTTTCTCTGGAAAAGATAATCCATCAAGTGATAGATTTAAGCA
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGA-CTCAGGT
623968 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**** * * * * * **
624033 TATGAACTCGAACTGGAAAAAATAATCCATCAAGTGATAGATTTAAGCA
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGA-CTCAGGT
624082 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
624147 TATGAACT
66 TATGAACT
624155 CGAACTGGAA
Statistics
Matches: 610, Mismatches: 28, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
112 67 0.11
113 359 0.59
114 184 0.30
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGGACTCAGGT
Found at i:625075 original size:84 final size:84
Alignment explanation
Indices: 624916--625143 Score: 397
Period size: 84 Copynumber: 2.7 Consensus size: 84
624906 GTAGTTCTTA
*
624916 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT-AGCAAATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCAAATTCATCTTCCA
624980 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
624999 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCAAATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCAAATTCATCTTCCA
*
625064 AATTCAGTGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
* * *
625083 CCAAATCAGATCAGATAACTCAAAGAACACTTTCAGAAAATGCTATTG-GTAAATTCATCTT
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCAAATTCATCTT
625144 TCAGTTAATG
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
83 58 0.42
84 81 0.58
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGAGCAAATTCATCTTCCA
AATTCAATGATTGGTTCTG
Found at i:626300 original size:21 final size:21
Alignment explanation
Indices: 626274--626325 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
626264 CCTTGACCCC
*
626274 CTTTTTCTTTT-TTCCTTTTTT
1 CTTTTT-TTTTCTCCCTTTTTT
626295 CTTTTTTTTTCTCCCTTTTTT
1 CTTTTTTTTTCTCCCTTTTTT
626316 -TTGTTTTTTT
1 CTT-TTTTTTT
626326 AAGCATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (21 bp):
CTTTTTTTTTCTCCCTTTTTT
Found at i:639012 original size:14 final size:14
Alignment explanation
Indices: 638993--639023 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
638983 ATGGCGGCTG
638993 AGGAAATTAGGGTT
1 AGGAAATTAGGGTT
639007 AGGAAATTAGGGTT
1 AGGAAATTAGGGTT
639021 AGG
1 AGG
639024 TTTAATCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.39, T:0.26
Consensus pattern (14 bp):
AGGAAATTAGGGTT
Found at i:639128 original size:3 final size:3
Alignment explanation
Indices: 639120--639262 Score: 286
Period size: 3 Copynumber: 47.7 Consensus size: 3
639110 AATGTATATT
639120 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
639168 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
639216 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
639263 TGGATAAAAA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 140 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:651826 original size:13 final size:13
Alignment explanation
Indices: 651808--651863 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
651798 ATTATAATTA
651808 TATTTTT-TATTT
1 TATTTTTATATTT
651820 GTATTTTTATATTT
1 -TATTTTTATATTT
*
651834 TATTATTAT-TTT
1 TATTTTTATATTT
* **
651846 AATTGATATATTT
1 TATTTTTATATTT
651859 TATTT
1 TATTT
651864 ATAATAATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
12 9 0.26
13 21 0.60
14 5 0.14
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (13 bp):
TATTTTTATATTT
Found at i:651839 original size:31 final size:33
Alignment explanation
Indices: 651799--651880 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 33
651789 TTTATTATGA
*
651799 TTATAATTATATTTTTTATTTG-TAT-TTTTAT
1 TTATAATTATATTTTTTAATTGATATATTTTAT
* *
651830 ATT-TTATTAT-TATTTTAATTGATATATTTTAT
1 -TTATAATTATATTTTTTAATTGATATATTTTAT
*
651862 TTATAATAATATTTTTTAA
1 TTATAATTATATTTTTTAA
651881 AAATTTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
30 9 0.22
31 11 0.28
32 13 0.32
33 7 0.17
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (33 bp):
TTATAATTATATTTTTTAATTGATATATTTTAT
Found at i:656696 original size:2 final size:2
Alignment explanation
Indices: 656689--656730 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
656679 ATTGTTTTTC
656689 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
656731 GTGTGTGTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:668911 original size:15 final size:15
Alignment explanation
Indices: 668893--668926 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
668883 AAATCGAAGA
668893 ATATTAAAAATGATC
1 ATATTAAAAATGATC
668908 ATATTAAAAATGATC
1 ATATTAAAAATGATC
668923 ATAT
1 ATAT
668927 CTTTCAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
ATATTAAAAATGATC
Found at i:669221 original size:14 final size:14
Alignment explanation
Indices: 669202--669240 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
669192 GGTTCTAATT
*
669202 TAAATTTAGTTTAA
1 TAAATTTAATTTAA
669216 TAAATTTAATTTAA
1 TAAATTTAATTTAA
669230 TAAATTTAATT
1 TAAATTTAATT
669241 CTCTAATCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (14 bp):
TAAATTTAATTTAA
Found at i:676632 original size:13 final size:13
Alignment explanation
Indices: 676632--676680 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
676622 CCGTTGACCC
*
676632 GACCCGACCAGTT
1 GACCCGACCCGTT
676645 GACCCGACCCGATT
1 GACCCGACCCG-TT
676659 -ACCCGACCCGTT
1 GACCCGACCCGTT
*
676671 GACTCGACCC
1 GACCCGACCC
676681 AACCCGTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.20, C:0.45, G:0.20, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:676633 original size:18 final size:18
Alignment explanation
Indices: 676610--676656 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
676600 ACCGGTCACA
*
676610 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCAGTTG
676628 ACCCGACCCGACCAGTTG
1 ACCCGACCCGACCAGTTG
676646 ACCCGACCCGA
1 ACCCGACCCGA
676657 TTACCCGACC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.09
Consensus pattern (18 bp):
ACCCGACCCGACCAGTTG
Found at i:676680 original size:18 final size:18
Alignment explanation
Indices: 676659--676699 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
676649 CGACCCGATT
*
676659 ACCCGACCCGTTGACTCG
1 ACCCGACCCGTTGACCCG
* *
676677 ACCCAACCCGTTGTCCCG
1 ACCCGACCCGTTGACCCG
676695 ACCCG
1 ACCCG
676700 TTGACCGTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.49, G:0.20, T:0.15
Consensus pattern (18 bp):
ACCCGACCCGTTGACCCG
Found at i:676680 original size:31 final size:31
Alignment explanation
Indices: 676613--676704 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
676603 GGTCACAACC
*** *
676613 CGACCCGACCCGTTGACCCGACCCGACCAGT
1 CGACCCGACCCGTTGACCCGACCCGTTGACT
*
676644 TGACCCGACCCGATT-ACCCGACCCGTTGACT
1 CGACCCGACCCG-TTGACCCGACCCGTTGACT
* *
676675 CGACCCAACCCGTTGTCCCGACCCGTTGAC
1 CGACCCGACCCGTTGACCCGACCCGTTGAC
676705 CGTTGACCCG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
30 2 0.04
31 47 0.92
32 2 0.04
ACGTcount: A:0.18, C:0.46, G:0.21, T:0.15
Consensus pattern (31 bp):
CGACCCGACCCGTTGACCCGACCCGTTGACT
Found at i:676705 original size:8 final size:8
Alignment explanation
Indices: 676694--676737 Score: 56
Period size: 7 Copynumber: 5.5 Consensus size: 8
676684 CCGTTGTCCC
676694 GACCCGTT
1 GACCCGTT
676702 GA-CCGTT
1 GACCCGTT
676709 GACCCGTT
1 GACCCGTT
676717 GA-CCGTT
1 GACCCGTT
676724 GACCACTGTT
1 GACC-C-GTT
676734 GACC
1 GACC
676738 AAAATTTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
7 14 0.44
8 10 0.31
9 1 0.03
10 7 0.22
ACGTcount: A:0.16, C:0.34, G:0.25, T:0.25
Consensus pattern (8 bp):
GACCCGTT
Found at i:676714 original size:15 final size:15
Alignment explanation
Indices: 676694--676737 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 15
676684 CCGTTGTCCC
676694 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
676709 GACCCGTTGACCGTT
1 GACCCGTTGACCGTT
676724 GACCACTGTTGACC
1 GACC-C-GTTGACC
676738 AAAATTTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 19 0.70
16 1 0.04
17 7 0.26
ACGTcount: A:0.16, C:0.34, G:0.25, T:0.25
Consensus pattern (15 bp):
GACCCGTTGACCGTT
Found at i:679292 original size:24 final size:24
Alignment explanation
Indices: 679174--679289 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
679164 TTCGATTTGA
679174 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
* *
679198 ATTCTGATATGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
679222 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
679246 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
679270 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
679290 CTGATTTATA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.01
24 80 0.98
25 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:681410 original size:18 final size:18
Alignment explanation
Indices: 681387--681474 Score: 107
Period size: 18 Copynumber: 5.2 Consensus size: 18
681377 ACCGGTCACA
681387 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
681405 ACCCGACCCGACCAGTTG
1 ACCCGACCCGACCCGTTG
681423 ACCCGACCCGACCCGATT-
1 ACCCGACCCGACCCG-TTG
681441 -----ACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
681454 ACTCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
681472 ACC
1 ACC
681475 GTTGACCGGC
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
12 2 0.03
13 10 0.17
18 46 0.77
19 2 0.03
ACGTcount: A:0.19, C:0.48, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:681445 original size:31 final size:31
Alignment explanation
Indices: 681410--681468 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
681400 CGTTGACCCG
681410 ACCCGACCAGTTGACCCGACCCGACCCGATT
1 ACCCGACCAGTTGACCCGACCCGACCCGATT
* *
681441 ACCCGACCCGTTGACTCGACCCGACCCG
1 ACCCGACCAGTTGACCCGACCCGACCCG
681469 TTGACCGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.12
Consensus pattern (31 bp):
ACCCGACCAGTTGACCCGACCCGACCCGATT
Found at i:681474 original size:13 final size:14
Alignment explanation
Indices: 681427--681464 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
681417 CAGTTGACCC
681427 GACCCGACCCGATT
1 GACCCGACCCGATT
681441 -ACCCGACCCG-TT
1 GACCCGACCCGATT
*
681453 GACTCGACCCGA
1 GACCCGACCCGA
681465 CCCGTTGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 2 0.10
13 19 0.90
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.13
Consensus pattern (14 bp):
GACCCGACCCGATT
Found at i:684055 original size:24 final size:24
Alignment explanation
Indices: 683937--684052 Score: 171
Period size: 24 Copynumber: 4.8 Consensus size: 24
683927 TTCGATTTGA
683937 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
*
683961 ATTCTGATCTGATA-TCTGACATAG
1 ATTCTGATCTGATACT-TGACATGG
*
683985 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
*
684009 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATCTGATACTTGACATGG
* *
684033 ATTTTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
684053 CTGATTTATA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 82 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:689251 original size:16 final size:17
Alignment explanation
Indices: 689232--689266 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
689222 AATAAATTAT
689232 AATAAAAAGT-ATTTTA
1 AATAAAAAGTAATTTTA
*
689248 AATATAAAGTAATTTTA
1 AATAAAAAGTAATTTTA
689265 AA
1 AA
689267 ATTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (17 bp):
AATAAAAAGTAATTTTA
Found at i:701369 original size:18 final size:18
Alignment explanation
Indices: 701330--701371 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
701320 TAATACTAAC
*
701330 GTTACAAGAACCTACAAT
1 GTTACAAGAACCTACAAG
*
701348 GTTACAAGAACCTACAGG
1 GTTACAAGAACCTACAAG
701366 GTTACA
1 GTTACA
701372 CCCTAGAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (18 bp):
GTTACAAGAACCTACAAG
Found at i:704378 original size:53 final size:55
Alignment explanation
Indices: 704310--704465 Score: 190
Period size: 53 Copynumber: 2.8 Consensus size: 55
704300 TATGGTCGTT
* * * *
704310 CCCACCATCTACACTAGCTATACTTTAGTGCAGTCCCGAATATGACACAT-A-TA
1 CCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAATATGACACATAAGTA
* *
704363 CCCACCATATGCACTAGTTATACTTTAGTGCAATCCCAAATATGACACATAAGGTCGTG
1 CCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAATATGACACATAA----GTA
* *
704422 CCCATCATATGCACTAGTTATACTTTAATGCAATCCCGAATATG
1 CCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAATATG
704466 CAGCATGCTG
Statistics
Matches: 88, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
53 45 0.51
54 1 0.01
59 42 0.48
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (55 bp):
CCCACCATATGCACTAGTTATACTTTAGTGCAATCCCGAATATGACACATAAGTA
Found at i:704464 original size:59 final size:59
Alignment explanation
Indices: 704276--704465 Score: 223
Period size: 59 Copynumber: 3.3 Consensus size: 59
704266 ACATGCACCG
* * * * * *
704276 TAGTGCTAA-CCCGAGTATGACACATATGGTCGTTCCCACCATCTACACTAGCTATACTT
1 TAGTGC-AATCCCGAATATGACACATAAGGTCGTACCCACCATATGCACTAGTTATACTT
*
704335 TAGTGCAGTCCCGAATATGACACAT-A-----TACCCACCATATGCACTAGTTATACTT
1 TAGTGCAATCCCGAATATGACACATAAGGTCGTACCCACCATATGCACTAGTTATACTT
* * *
704388 TAGTGCAATCCCAAATATGACACATAAGGTCGTGCCCATCATATGCACTAGTTATACTT
1 TAGTGCAATCCCGAATATGACACATAAGGTCGTACCCACCATATGCACTAGTTATACTT
*
704447 TAATGCAATCCCGAATATG
1 TAGTGCAATCCCGAATATG
704466 CAGCATGCTG
Statistics
Matches: 111, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
53 46 0.41
54 1 0.01
58 1 0.01
59 63 0.57
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (59 bp):
TAGTGCAATCCCGAATATGACACATAAGGTCGTACCCACCATATGCACTAGTTATACTT
Found at i:707184 original size:29 final size:31
Alignment explanation
Indices: 707108--707185 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
707098 CTTATTAAAA
* *
707108 TTACACTTTAGTCCCTAAACTTTTCTAAAGT
1 TTACATTTTAGTCACTAAACTTTTCTAAAGT
* *
707139 TTATATTTTAG-CTACTAAAC-TTTC-AAATT
1 TTACATTTTAGTC-ACTAAACTTTTCTAAAGT
*
707168 TTACATTTTCGTCACTAA
1 TTACATTTTAGTCACTAA
707186 CCAAAATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 18 0.46
30 6 0.15
31 15 0.38
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (31 bp):
TTACATTTTAGTCACTAAACTTTTCTAAAGT
Found at i:717805 original size:7 final size:7
Alignment explanation
Indices: 717793--717883 Score: 71
Period size: 7 Copynumber: 13.4 Consensus size: 7
717783 TAGATTACAT
717793 CCTAAAC
1 CCTAAAC
717800 CCTAAAC
1 CCTAAAC
717807 CC--AAC
1 CCTAAAC
717812 CCTAAAC
1 CCTAAAC
**
717819 TATAAAC
1 CCTAAAC
717826 CCTAAAC
1 CCTAAAC
** *
717833 TATAAAT
1 CCTAAAC
*
717840 CATAAAC
1 CCTAAAC
*
717847 CCTAATC
1 CCTAAAC
*
717854 ACTAAA-
1 CCTAAAC
*
717860 TCTAAAC
1 CCTAAAC
717867 CCTAAAC
1 CCTAAAC
*
717874 TCTAAAC
1 CCTAAAC
717881 CCT
1 CCT
717884 TAATCCGATT
Statistics
Matches: 64, Mismatches: 17, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
5 5 0.08
6 5 0.08
7 54 0.84
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (7 bp):
CCTAAAC
Found at i:717828 original size:14 final size:14
Alignment explanation
Indices: 717794--717883 Score: 87
Period size: 14 Copynumber: 6.6 Consensus size: 14
717784 AGATTACATC
717794 CTAAACCCTAAAC-
1 CTAAACCCTAAACT
*
717807 C-CAACCCTAAACT
1 CTAAACCCTAAACT
*
717820 ATAAACCCTAAACT
1 CTAAACCCTAAACT
* * * *
717834 ATAAATCATAAACC
1 CTAAACCCTAAACT
* *
717848 CTAATCACTAAA-T
1 CTAAACCCTAAACT
717861 CTAAACCCTAAACT
1 CTAAACCCTAAACT
717875 CTAAACCCT
1 CTAAACCCT
717884 TAATCCGATT
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
12 10 0.17
13 11 0.18
14 39 0.65
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAAACCCTAAACT
Found at i:717867 original size:20 final size:21
Alignment explanation
Indices: 717820--717879 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
717810 ACCCTAAACT
717820 ATAAACCCTAAACTATAAATC
1 ATAAACCCTAAACTATAAATC
*
717841 ATAAACCCTAATC-ACTAAATC
1 ATAAACCCTAAACTA-TAAATC
*
717862 -TAAACCCTAAACTCTAAA
1 ATAAACCCTAAACTATAAA
717880 CCCTTAATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAAACCCTAAACTATAAATC
Found at i:717966 original size:7 final size:7
Alignment explanation
Indices: 717954--718048 Score: 66
Period size: 7 Copynumber: 13.6 Consensus size: 7
717944 GTTAGATTAC
717954 ACCCTAA
1 ACCCTAA
717961 ACCCTAA
1 ACCCTAA
*
717968 ACTCTAA
1 ACCCTAA
**
717975 AATCTAA
1 ACCCTAA
**
717982 ACTATAA
1 ACCCTAA
**
717989 ACTATAA
1 ACCCTAA
*
717996 ACCATAA
1 ACCCTAA
*
718003 ATCCTAA
1 ACCCTAA
*
718010 A-TCTCAA
1 ACCCT-AA
718017 ACCCTAA
1 ACCCTAA
*
718024 ACCTTAA
1 ACCCTAA
*
718031 GCCCTAA
1 ACCCTAA
718038 ACCCTAA
1 ACCCTAA
718045 ACCC
1 ACCC
718049 GATTATATGA
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
6 2 0.03
7 69 0.95
8 2 0.03
ACGTcount: A:0.45, C:0.33, G:0.01, T:0.21
Consensus pattern (7 bp):
ACCCTAA
Found at i:721023 original size:15 final size:15
Alignment explanation
Indices: 721003--721034 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
720993 TCAATGTTTC
*
721003 TAACTAGTACCAAAA
1 TAACTAATACCAAAA
721018 TAACTAATACCAAAA
1 TAACTAATACCAAAA
721033 TA
1 TA
721035 TTTTGCTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.19, G:0.03, T:0.22
Consensus pattern (15 bp):
TAACTAATACCAAAA
Found at i:723991 original size:15 final size:14
Alignment explanation
Indices: 723965--724011 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
723955 AAAATCAATC
723965 ATTTATTTAATATT
1 ATTTATTTAATATT
723979 ATTTATGTTAATATT
1 ATTTAT-TTAATATT
*
723994 A-TTATTAAAATATT
1 ATTTATT-TAATATT
724008 ATTT
1 ATTT
724012 CTATACTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.03
14 17 0.59
15 11 0.38
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:724288 original size:22 final size:22
Alignment explanation
Indices: 724262--724314 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
724252 ATATAAGATC
* *
724262 ATATATTATTATAATATTAAAA
1 ATATAATACTATAATATTAAAA
*
724284 ATATAATACTATATTATTAAAA
1 ATATAATACTATAATATTAAAA
*
724306 TTATTAATA
1 ATA-TAATA
724315 AATATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAATACTATAATATTAAAA
Found at i:724299 original size:30 final size:33
Alignment explanation
Indices: 724247--724320 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
724237 GTTACTAAAA
*
724247 TAAAAATATAAGATCATATATTATTATAA-TAT
1 TAAAAATATAAGATCATATATTATTAAAATTAT
*
724279 TAAAAATATAATA-C-TATATTATTAAAATTAT
1 TAAAAATATAAGATCATATATTATTAAAATTAT
724310 TAATAAATATA
1 TAA-AAATATA
724321 TTTTACATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 12 0.32
31 7 0.18
32 19 0.50
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (33 bp):
TAAAAATATAAGATCATATATTATTAAAATTAT
Found at i:724319 original size:22 final size:22
Alignment explanation
Indices: 724276--724319 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
724266 ATTATTATAA
*
724276 TATTAAAAATATAATACTATAT
1 TATTAAAAATATAATACAATAT
*
724298 TATTAAAATTATTAATA-AATAT
1 TATTAAAAATA-TAATACAATAT
724320 ATTTTACATA
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:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATACAATAT
Found at i:726036 original size:9 final size:10
Alignment explanation
Indices: 726010--726038 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
726000 GTATAAGCAT
726010 AAATTAATAA
1 AAATTAATAA
726020 AAATTAATAA
1 AAATTAATAA
726030 AAA-TAATAA
1 AAATTAATAA
726039 TATGTGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
AAATTAATAA
Found at i:726297 original size:27 final size:27
Alignment explanation
Indices: 726278--726332 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
726268 AAACTCAAAT
*
726278 TAAAATTAAATCAATCCAAATTAAACA
1 TAAAATTAAATCAATCCAAATCAAACA
* * *
726305 TAAATTTAAATCAATTCAAATTAAACA
1 TAAAATTAAATCAATCCAAATCAAACA
726332 T
1 T
726333 TGTTTATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (27 bp):
TAAAATTAAATCAATCCAAATCAAACA
Found at i:727064 original size:18 final size:18
Alignment explanation
Indices: 727041--727086 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
727031 AATATTAAAA
*
727041 TGTTTGATATACAGTTAT
1 TGTTTGATATACAATTAT
727059 TGTTTGATATACAATTAT
1 TGTTTGATATACAATTAT
727077 TGTTTGATAT
1 TGTTTGATAT
727087 GTTTGAGTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.52
Consensus pattern (18 bp):
TGTTTGATATACAATTAT
Found at i:729273 original size:24 final size:22
Alignment explanation
Indices: 729233--729309 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
729223 ATGCAATTAA
729233 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
729252 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
729275 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
729296 TGCATCGATGCACT
1 TGCATCGATGCACT
729310 TCAAAGGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:730595 original size:30 final size:29
Alignment explanation
Indices: 730512--730596 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
730502 TATGAGATAT
* * * * *
730512 ATGAA-TACGAAATGATATGAAAATTTAT
1 ATGAACTACGAGATTATATGAATATGTAA
* * *
730540 ATGAACTACGTGATTACATGTATATGTAA
1 ATGAACTACGAGATTATATGAATATGTAA
*
730569 ATGAAGCTACGAGTTTATATGAATATGT
1 ATGAA-CTACGAGATTATATGAATATGT
730597 GATCTGTTTA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
28 5 0.12
29 20 0.47
30 18 0.42
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.34
Consensus pattern (29 bp):
ATGAACTACGAGATTATATGAATATGTAA
Found at i:730864 original size:23 final size:23
Alignment explanation
Indices: 730831--730882 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
730821 CATCTTATAT
*
730831 GGCACTACGGTGTATTTCTACGC
1 GGCACTACGGTGTAATTCTACGC
* *
730854 GGCACTTCGGTGTAATTCTACGT
1 GGCACTACGGTGTAATTCTACGC
730877 GGCACT
1 GGCACT
730883 CCAGTGCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.31
Consensus pattern (23 bp):
GGCACTACGGTGTAATTCTACGC
Found at i:732141 original size:19 final size:19
Alignment explanation
Indices: 732117--732157 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
732107 TTTGTAATGG
732117 ATTCACCCTTTTTGACTAA
1 ATTCACCCTTTTTGACTAA
732136 ATTCACCCTTTTTGACTAA
1 ATTCACCCTTTTTGACTAA
732155 ATT
1 ATT
732158 AACAAGTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.24, G:0.05, T:0.44
Consensus pattern (19 bp):
ATTCACCCTTTTTGACTAA
Found at i:732771 original size:198 final size:198
Alignment explanation
Indices: 732386--732795 Score: 601
Period size: 198 Copynumber: 2.1 Consensus size: 198
732376 CGGTTTTGAG
* * * * ** * * *
732386 CTATTACTTTAATGTAATAGGTTTCGAAATTTCAAGTATTGATACTTTATATATGTGCATCTATA
1 CTATTACTTAAAAGTAACAGGTTTCGAAATTCCAAGTATCAATACTTTACACATGT-CATCGATA
* *
732451 CATTTTGCATGCAAATTGTTTGAGAAACATACTGGAATAAAAATATCGATACCTATATAAAAGTA
65 CATTTTGCATGCAAATTATTTGAGAAACATACTGGAATAAAAATATCCATACCTATATAAAAGTA
* *
732516 TCGATACTTGGTATTTACGCCTATTATCATTATACCAGTAGACTTTTATCATTTACATTGTTAAT
130 TCGATACTTGGTATTTACGCCTATTATCATTATACCAGTAAACTTTTACCATTTACATTGTTAAT
732581 TTAC
195 TTAC
732585 CTATTACTTAAAAGTAACAGGTTTCGAAATTCCAAGTATCAATACTTTACACATGT-ATCGATAC
1 CTATTACTTAAAAGTAACAGGTTTCGAAATTCCAAGTATCAATACTTTACACATGTCATCGATAC
**
732649 ATTTTGCGA-GCAAATTATTTGAGAAACATGTTGGAATAAAAGA-ATCCATACCTATATACAAAG
66 ATTTTGC-ATGCAAATTATTTGAGAAACATACTGGAATAAAA-ATATCCATACCTATATA-AAAG
* *
732712 TATCGATACTTGGTATTTACGCCTATTATCATTATACTAGTAAACTTTTACCGTTTACATTGTTA
128 TATCGATACTTGGTATTTACGCCTATTATCATTATACCAGTAAACTTTTACCATTTACATTGTTA
732777 ATTTAC
193 ATTTAC
*
732783 CTATTACCTAAAA
1 CTATTACTTAAAA
732796 TTATATAATG
Statistics
Matches: 190, Mismatches: 18, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
197 57 0.30
198 85 0.45
199 48 0.25
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (198 bp):
CTATTACTTAAAAGTAACAGGTTTCGAAATTCCAAGTATCAATACTTTACACATGTCATCGATAC
ATTTTGCATGCAAATTATTTGAGAAACATACTGGAATAAAAATATCCATACCTATATAAAAGTAT
CGATACTTGGTATTTACGCCTATTATCATTATACCAGTAAACTTTTACCATTTACATTGTTAATT
TAC
Found at i:734269 original size:197 final size:197
Alignment explanation
Indices: 733916--734412 Score: 671
Period size: 197 Copynumber: 2.5 Consensus size: 197
733906 TTTTCATTTA
* *
733916 TTTTAAATTCCTAAAGTACCGATACTGTGGTACATATACTTAT-AAAGTATCAATAC---TTTCA
1 TTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCA
* * * * * *
733977 ACAATTTCGGTAGCGCTTTACTGATTTTTTCAAATTGAAACCAGTTTTGTCAATTTTCAACCTGT
66 ACAATTTCGGTAGCTCTTTACCGATTTTTTCAAATTGAAACCAGTTTTGCCAAATTTAAACATGT
* ** * * *
734042 TATATTGTCATGTATCGATACACGTGTCTAAGGTATCGATATTTTATAGGTGCTATTATTGCAAT
131 TATATTGTCATGTATCGATACACATGTCTAAGACATCAATACTTTATAGCTGCTATTATTGCAAT
734107 TC
196 TC
*
734109 TTTTAAATTCCTAAAGTACCGATACTTTGATACATATACTTATAAAAGTATCGATACAAATTTCA
1 TTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCA
* * * * *
734174 ATC-ATTACGGCAGCTCTTTACCAATTTTTTCAAATTGAAATCGGTTTTGCCAAATTTAAACATG
66 A-CAATTTCGGTAGCTCTTTACCGATTTTTTCAAATTGAAACCAGTTTTGCCAAATTTAAACATG
* * * *
734238 TTATATTGTCATGTATTGATACATATGTCTAAGACATCAATACTTTATAGCTGTTTTTATTGCAA
130 TTATATTGTCATGTATCGATACACATGTCTAAGACATCAATACTTTATAGCTGCTATTATTGCAA
734303 TTC
195 TTC
* ** * *
734306 TTTTAAATTCATAAAGTACATATACTTTGGTACATATAATTATAAACGTATCGATACAAATTTCA
1 TTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCA
* *
734371 ACAATTTCGGTAGTTCTTTACCGATTTTGTCAAATTGAAACC
66 ACAATTTCGGTAGCTCTTTACCGATTTTTTCAAATTGAAACC
734413 TGATATATTG
Statistics
Matches: 262, Mismatches: 36, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
193 41 0.16
194 12 0.05
196 1 0.00
197 207 0.79
198 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (197 bp):
TTTTAAATTCCTAAAGTACCGATACTTTGGTACATATACTTATAAAAGTATCGATACAAATTTCA
ACAATTTCGGTAGCTCTTTACCGATTTTTTCAAATTGAAACCAGTTTTGCCAAATTTAAACATGT
TATATTGTCATGTATCGATACACATGTCTAAGACATCAATACTTTATAGCTGCTATTATTGCAAT
TC
Found at i:734488 original size:176 final size:177
Alignment explanation
Indices: 734218--734588 Score: 523
Period size: 176 Copynumber: 2.1 Consensus size: 177
734208 TTGAAATCGG
* * * * * *
734218 TTTTGCCAAATTTAAACATGTTATATTGTCATGTATTGATACATATGTCTAAGACATCAATACTT
1 TTTTGTCAAATTGAAACATGATATATTGTCATGCATCGATACATATGTATAAGACATCAATACTT
* * * *
734283 TATAGCTGTTTTTATTGCAATTCTTTTAAATTCATAAAGTACAT-ATACTTTGGTACATATAATT
66 TATAGCCGCTATTATTGCAATTATTTTAAATTCATAAAGTAC-TGATACTTTGGTACATATAATT
*
734347 ATAAACGTATCGATACAAATTTCAACAATTTCGGTAGT-TCTTTACCGA
130 ATAAACGTATCGATACAAATTTCAACAATTTCGATA-TCTCTTTACCGA
* ** *
734395 TTTTGTCAAATTGAAACCTGATATATTGTCATGCATCGATACATATGTATAAGGTATCGATAC-T
1 TTTTGTCAAATTGAAACATGATATATTGTCATGCATCGATACATATGTATAAGACATCAATACTT
* * *
734459 TATAGCCGCTATTATTGCAATTATTTTAAATTCCTACAGTACTGATACTTTGGTACATATACTTA
66 TATAGCCGCTATTATTGCAATTATTTTAAATTCATAAAGTACTGATACTTTGGTACATATAATTA
* *
734524 TAAATGTATCGATACAAATTTCAACAATTTCGATATCTCTTTACCGG
131 TAAACGTATCGATACAAATTTCAACAATTTCGATATCTCTTTACCGA
734571 TTTTGTCAAATTGAAACA
1 TTTTGTCAAATTGAAACA
734589 GTTTTGTCAA
Statistics
Matches: 171, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
175 2 0.01
176 116 0.68
177 53 0.31
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (177 bp):
TTTTGTCAAATTGAAACATGATATATTGTCATGCATCGATACATATGTATAAGACATCAATACTT
TATAGCCGCTATTATTGCAATTATTTTAAATTCATAAAGTACTGATACTTTGGTACATATAATTA
TAAACGTATCGATACAAATTTCAACAATTTCGATATCTCTTTACCGA
Found at i:734614 original size:20 final size:20
Alignment explanation
Indices: 734566--734622 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
734556 ATATCTCTTT
*
734566 ACCGGTTTTGTCAAA-TTGA
1 ACCGGTTTTGTCAAATTTCA
* *
734585 AACAGTTTTGTCAAATTTCA
1 ACCGGTTTTGTCAAATTTCA
734605 ACCGGTTTTGTC-AATTTC
1 ACCGGTTTTGTCAAATTTC
734623 CAATCAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (20 bp):
ACCGGTTTTGTCAAATTTCA
Found at i:734641 original size:39 final size:39
Alignment explanation
Indices: 734566--734642 Score: 93
Period size: 39 Copynumber: 2.0 Consensus size: 39
734556 ATATCTCTTT
* *
734566 ACCGGTTTTGTCAAATTGAAACAGTTTTGTCAAATTTCA
1 ACCGGTTTTGTCAAATTCAAACAATTTTGTCAAATTTCA
* * *
734605 ACCGGTTTTGTCAATTTCCAATCAATTTTG-CCAATTTC
1 ACCGGTTTTGTCAAATT-CAAACAATTTTGTCAAATTTC
734643 GTTACCTGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 23 0.72
40 9 0.28
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (39 bp):
ACCGGTTTTGTCAAATTCAAACAATTTTGTCAAATTTCA
Found at i:737416 original size:21 final size:21
Alignment explanation
Indices: 737392--737465 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
737382 GCGTTGCATT
737392 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
737413 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
*
737433 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
737454 TCGCGTTGCGAT
1 TCGCGTTGCGAT
737466 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:737441 original size:20 final size:20
Alignment explanation
Indices: 737413--737545 Score: 135
Period size: 20 Copynumber: 6.6 Consensus size: 20
737403 TAGTTGAAAA
737413 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* * ** **
737433 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
737454 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
* * *
737474 TCGCGTTGCGATAGTCTACA-G
1 TCGCGTTGCGAT--TTTCCATT
737495 TCGCGTTGC-ATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
737514 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
737534 TCGCGTTGCGAT
1 TCGCGTTGCGAT
737546 AGTCTACAGT
Statistics
Matches: 90, Mismatches: 18, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
18 4 0.04
19 9 0.10
20 50 0.56
21 23 0.26
22 4 0.04
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:737445 original size:41 final size:41
Alignment explanation
Indices: 737388--737525 Score: 217
Period size: 41 Copynumber: 3.4 Consensus size: 41
737378 TATCGCGTTG
737388 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
737429 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
* *
737470 CATTTCGCGTTGCGATAGTCT-ACAGTCGCGTTGC-ATTTTC
1 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTC
737510 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
737526 TTTCCATTTC
Statistics
Matches: 90, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
40 21 0.23
41 68 0.76
42 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:737525 original size:60 final size:62
Alignment explanation
Indices: 737454--737573 Score: 208
Period size: 60 Copynumber: 2.0 Consensus size: 62
737444 TAGTTGAAAA
*
737454 TCGCGTTGCGATTTTTCATTTCGCGTTGCGATAGTCTACAGTCG-CGTTGC-ATTTTCCATT
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCATT
*
737514 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCA
1 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCA
737574 AATTCGTTGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
60 42 0.75
61 6 0.11
62 8 0.14
ACGTcount: A:0.13, C:0.23, G:0.23, T:0.41
Consensus pattern (62 bp):
TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTCGTCGTTGCGATTTTCCATT
Found at i:737536 original size:101 final size:101
Alignment explanation
Indices: 737413--737596 Score: 266
Period size: 101 Copynumber: 1.8 Consensus size: 101
737403 TAGTTGAAAA
* *
737413 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGT-TGAAAATCG-CGTTGCGATTTTTC-ATTT
1 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCT-AAAATCGTCGTTGCGATTTTCCAAATT
737475 CGCGTTGCGATAGTCTACAGTCGCGTTGCATTTTCCATT
65 --CGTTGCGATAGTCTACAGTCGCGTTGCATTTTCCATT
* * * *
737514 TCGCGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATTC
1 TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAATTC
737579 GTTGCGATAGTCTACAGT
66 GTTGCGATAGTCTACAGT
737597 TAAAGATTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
101 57 0.77
102 14 0.19
103 3 0.04
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (101 bp):
TCGCGTTGCGATTTTCCATTTCGCATTGCGATAGTCTAAAATCGTCGTTGCGATTTTCCAAATTC
GTTGCGATAGTCTACAGTCGCGTTGCATTTTCCATT
Found at i:737565 original size:22 final size:21
Alignment explanation
Indices: 737537--737597 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 21
737527 TTCCATTTCG
737537 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTT-T
* * **
737559 CGTTGCGAT--TTTCCAAATT
1 CGTTGCGATAGTCTACAGTTT
737578 CGTTGCGATAGTCTACAGTT
1 CGTTGCGATAGTCTACAGTT
737598 AAAGATTTTG
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
19 10 0.34
20 5 0.17
21 5 0.17
22 9 0.31
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTTT
Found at i:737592 original size:41 final size:41
Alignment explanation
Indices: 737517--737597 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
737507 TTCCATTTCG
*
737517 CGTTGCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAATTC-CGTTGCGATAGTCTACAGTTGT
737559 CGTTGCGATTTTCCAAATT-CGTTGCGATAGTCTACAGTT
1 CGTTGCGATTTTCC-AATTCCGTTGCGATAGTCTACAGTT
737598 AAAGATTTTG
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 20 0.54
42 14 0.38
43 3 0.08
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAATTCCGTTGCGATAGTCTACAGTTGT
Found at i:737752 original size:19 final size:19
Alignment explanation
Indices: 737728--737793 Score: 51
Period size: 19 Copynumber: 3.3 Consensus size: 19
737718 TTAACTATCA
737728 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * **
737747 CAACGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
* *
737769 CAACAAATTTGAAAAATCG
1 CAACGAATTTGGAAAATCG
737788 CAACGA
1 CAACGA
737794 CAACTGTCGA
Statistics
Matches: 33, Mismatches: 11, Indels: 6
0.66 0.22 0.12
Matches are distributed among these distances:
19 17 0.52
20 2 0.06
21 2 0.06
22 12 0.36
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:737770 original size:22 final size:22
Alignment explanation
Indices: 737743--737814 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
737733 AATTTGGAAA
737743 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* **
737765 ATCGCAAC-A-AA-T-TTGAAAA
1 ATCGCAACGACAACTGTAG-ACT
*
737784 ATCGCAACGACAACTGTCGACT
1 ATCGCAACGACAACTGTAGACT
737806 ATCGCAACG
1 ATCGCAACG
737815 CGAAATGGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 2 0.05
19 10 0.26
20 3 0.08
21 3 0.08
22 19 0.49
23 2 0.05
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:737778 original size:41 final size:41
Alignment explanation
Indices: 737721--737813 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
737711 TCTTTTTTTA
* * *
737721 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACAAATTTGAAAAATCGCAACGACAACTGTAG
*
737762 ACTATCGCAACAAATTTGAAAAATCGCAACGACAACTGTCG
1 ACTATCGCAACAAATTTGAAAAATCGCAACGACAACTGTAG
737803 ACTATCGCAAC
1 ACTATCGCAAC
737814 GCGAAATGGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.41, C:0.25, G:0.15, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACAAATTTGAAAAATCGCAACGACAACTGTAG
Found at i:737866 original size:21 final size:21
Alignment explanation
Indices: 737803--737866 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
737793 ACAACTGTCG
*
737803 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
737824 A-AATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
737844 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
737865 AC
1 AC
737867 ACGAATTTGC
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:737918 original size:20 final size:20
Alignment explanation
Indices: 737895--738000 Score: 63
Period size: 20 Copynumber: 5.2 Consensus size: 20
737885 AGATCGCGTT
737895 GCGATTTCAACTATCGCAAC
1 GCGATTTCAACTATCGCAAC
* ** *
737915 GCGAAATGGAA-AATCGCAAC
1 GCG-ATTTCAACTATCGCAAC
*
737935 GCGATCTCCAACTATCGCAAC
1 GCGAT-TTCAACTATCGCAAC
* * * *
737956 GCGAAATTGAA-AAACGCAAC
1 GCG-ATTTCAACTATCGCAAC
* *
737976 GCGATTTTAAACTATCGCAAT
1 GCGA-TTTCAACTATCGCAAC
737997 GCGA
1 GCGA
738001 AATGCAACGT
Statistics
Matches: 62, Mismatches: 18, Indels: 11
0.68 0.20 0.12
Matches are distributed among these distances:
19 2 0.03
20 31 0.50
21 28 0.45
22 1 0.02
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
GCGATTTCAACTATCGCAAC
Found at i:737952 original size:41 final size:41
Alignment explanation
Indices: 737902--738004 Score: 152
Period size: 41 Copynumber: 2.5 Consensus size: 41
737892 GTTGCGATTT
*
737902 CAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTC
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* * *
737943 CAACTATCGCAACGCGAAATTGAAAAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
* *
737984 AAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
738005 CAACGTGAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.17
Consensus pattern (41 bp):
CAACTATCGCAACGCGAAATGGAAAAACGCAACGCGATCTC
Found at i:741122 original size:3 final size:3
Alignment explanation
Indices: 741116--741148 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
741106 TAAGCTTATT
741116 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
741149 TACGCTGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:743601 original size:26 final size:26
Alignment explanation
Indices: 743565--743617 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
743555 CACTGCCTTC
*
743565 CGATATACATGTTCTACTCGTAATAA
1 CGATATACATGTTCTACTCATAATAA
743591 CGATATACATGTTCTACTCATAATAA
1 CGATATACATGTTCTACTCATAATAA
743617 C
1 C
743618 ATACACTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (26 bp):
CGATATACATGTTCTACTCATAATAA
Found at i:744231 original size:19 final size:19
Alignment explanation
Indices: 744187--744229 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
744177 TGCAATATAC
744187 GATTTTATTTGATATTGAT
1 GATTTTATTTGATATTGAT
744206 GATTTTATTTGATATTGAT
1 GATTTTATTTGATATTGAT
744225 -ATTTT
1 GATTTT
744230 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (19 bp):
GATTTTATTTGATATTGAT
Found at i:745906 original size:41 final size:41
Alignment explanation
Indices: 745849--745928 Score: 151
Period size: 41 Copynumber: 2.0 Consensus size: 41
745839 TGAAGGAAAT
745849 TGTAGTTGTTGTTGAAGGAAATTTGTTTCTTATAATGTTGG
1 TGTAGTTGTTGTTGAAGGAAATTTGTTTCTTATAATGTTGG
*
745890 TGTAGTTGTTGTTGAAGGAAATTTTTTTCTTATAATGTT
1 TGTAGTTGTTGTTGAAGGAAATTTGTTTCTTATAATGTT
745929 TCTTATAGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.23, C:0.03, G:0.24, T:0.51
Consensus pattern (41 bp):
TGTAGTTGTTGTTGAAGGAAATTTGTTTCTTATAATGTTGG
Found at i:746739 original size:27 final size:27
Alignment explanation
Indices: 746709--746769 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
746699 TGTTGACAGT
* **
746709 GGTGTTGAAGCAGGGGGTGTACAAAGA
1 GGTGGTGAAGCAGGGGGTCAACAAAGA
** *
746736 GGTGGTGTTGCATGGGGTCAACAAAGA
1 GGTGGTGAAGCAGGGGGTCAACAAAGA
746763 GGTGGTG
1 GGTGGTG
746770 TTAAAGCAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.46, T:0.21
Consensus pattern (27 bp):
GGTGGTGAAGCAGGGGGTCAACAAAGA
Found at i:747992 original size:29 final size:30
Alignment explanation
Indices: 747904--747992 Score: 110
Period size: 30 Copynumber: 3.0 Consensus size: 30
747894 ACAAACTGGC
* *
747904 CCCGGGACAAAGGTTGGGCACTAAATT-GAA
1 CCCGAGACAAAGGTTAGGCACTAAATTAG-A
*
747934 CCCGAGACAAAGGTTAGGCACTAAACTAGA
1 CCCGAGACAAAGGTTAGGCACTAAATTAGA
**
747964 CTTGAGACAAA-GTTAGGCACTAAATTAGA
1 CCCGAGACAAAGGTTAGGCACTAAATTAGA
747993 AAACAATTGG
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.33
30 34 0.65
31 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.18
Consensus pattern (30 bp):
CCCGAGACAAAGGTTAGGCACTAAATTAGA
Found at i:749126 original size:56 final size:57
Alignment explanation
Indices: 748973--749143 Score: 265
Period size: 57 Copynumber: 3.0 Consensus size: 57
748963 AGTTTGAATA
* * * *
748973 ACCTAAAAATATCAATATAGGTAACAATTAATAAGCAAAATAATTTAATCAACATGC
1 ACCTAAAAATATCAATATAGTTAATAGTTAATAAACAAAATAATTTAATCAACATGC
749030 ACCTAAAAATATCAATATAGTTAATAGTTAATTAAA-AAAATAATTTAATCAACATGC
1 ACCTAAAAATATCAATATAGTTAATAGTTAA-TAAACAAAATAATTTAATCAACATGC
* *
749087 ACCT-AAAATATTAATATAATTAATAGTTAATAAACAAAATAATTTAATCAACATGC
1 ACCTAAAAATATCAATATAGTTAATAGTTAATAAACAAAATAATTTAATCAACATGC
749143 A
1 A
749144 AAAAAATAAA
Statistics
Matches: 106, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
55 4 0.04
56 46 0.43
57 53 0.50
58 3 0.03
ACGTcount: A:0.53, C:0.12, G:0.05, T:0.30
Consensus pattern (57 bp):
ACCTAAAAATATCAATATAGTTAATAGTTAATAAACAAAATAATTTAATCAACATGC
Found at i:762147 original size:15 final size:15
Alignment explanation
Indices: 762109--762148 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
762099 TACATGGAGC
*
762109 GATGAAGAAGGTTCT
1 GATGAAGAGGGTTCT
762124 GATGAAGAGGGTTCT
1 GATGAAGAGGGTTCT
762139 GATGAAGAGG
1 GATGAAGAGG
762149 AACAAGAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.40, T:0.23
Consensus pattern (15 bp):
GATGAAGAGGGTTCT
Found at i:768503 original size:19 final size:20
Alignment explanation
Indices: 768479--768518 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
768469 GAGAAGTGTA
*
768479 AAATGTTTTA-AAGGGGGAG
1 AAATGTTATAGAAGGGGGAG
768498 AAATGTTATAGTAAGGGGGAG
1 AAATGTTATAG-AAGGGGGAG
768519 TAATTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.25
Consensus pattern (20 bp):
AAATGTTATAGAAGGGGGAG
Found at i:772507 original size:26 final size:27
Alignment explanation
Indices: 772460--772515 Score: 96
Period size: 26 Copynumber: 2.1 Consensus size: 27
772450 AAAGATGAAG
*
772460 TAAAATAAGGTTTTTTTGAAAGTTATA
1 TAAAATAAGGTTTTTTTAAAAGTTATA
772487 TAAAATAA-GTTTTTTTAAAAGTTATA
1 TAAAATAAGGTTTTTTTAAAAGTTATA
772513 TAA
1 TAA
772516 GTGTTGACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (27 bp):
TAAAATAAGGTTTTTTTAAAAGTTATA
Found at i:790511 original size:3 final size:3
Alignment explanation
Indices: 790505--790551 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
790495 ATTTTTGTTT
790505 TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
790550 TT
1 TT
790552 TACAAACAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:790533 original size:22 final size:21
Alignment explanation
Indices: 790507--790549 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
790497 TTTTGTTTTT
790507 ATTATTATTATTATTATTATTA
1 ATTATTATTATTATTA-TATTA
790529 ATTATTATTATTATTATATTA
1 ATTATTATTATTATTATATTA
790550 TTTACAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATTATTATTATTATTATATTA
Found at i:790594 original size:26 final size:26
Alignment explanation
Indices: 790558--790612 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
790548 TATTTACAAA
* * *
790558 CAGTTACAAACCAAACTGGACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
790584 CAGTTACAAACAAAACAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
790610 CAG
1 CAG
790613 ACCAACCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.33, G:0.18, T:0.09
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGGCC
Found at i:791928 original size:15 final size:15
Alignment explanation
Indices: 791908--791978 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
791898 ATCCATTAGT
791908 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
791923 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
791937 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
*
791953 TTTTATTTTATTATTAC
1 TTTTA--ATATTATTAC
*
791970 GTTTAATAT
1 TTTTAATAT
791979 ATGTTTAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
14 5 0.12
15 21 0.49
16 9 0.21
17 8 0.19
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:792025 original size:20 final size:22
Alignment explanation
Indices: 791937--792025 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 22
791927 AATTTCTTTC
791937 ATTTTAATTATTA-TTATT-TT
1 ATTTTAATTATTACTTATTATT
*
791957 ATTTT-ATTATTACGTT-TAATAT
1 ATTTTAATTATTAC-TTATTAT-T
*
791979 ATGTTTAGATTATTATCTTCATGATT
1 AT-TTTA-ATTATTA-CTT-ATTATT
792005 ATTTT-ATTATTA-TTATTATT
1 ATTTTAATTATTACTTATTATT
792025 A
1 A
792026 AGTTATATAA
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
19 7 0.12
20 12 0.21
21 5 0.09
22 3 0.05
23 10 0.18
25 12 0.21
26 4 0.07
27 3 0.05
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTTAATTATTACTTATTATT
Found at i:792045 original size:14 final size:15
Alignment explanation
Indices: 792028--792060 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
792018 TATTATTAAG
792028 TTATATAA-ATATAT
1 TTATATAATATATAT
*
792042 TTATATAATATTTAT
1 TTATATAATATATAT
792057 TTAT
1 TTAT
792061 TCTTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:792789 original size:18 final size:18
Alignment explanation
Indices: 792768--792835 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 18
792758 TTTTATATAC
792768 TTATTATTTTCATAATAT
1 TTATTATTTTCATAATAT
792786 TTATATATTTTCTTATTAATAT
1 TTAT-TATTTTC--A-TAATAT
* *
792808 TTCATTATTTGCA-AGTATT
1 TT-ATTATTTTCATAATA-T
792827 TTATTATTT
1 TTATTATTT
792836 ATTTTTCTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
18 14 0.33
19 10 0.24
20 1 0.02
21 1 0.02
22 14 0.33
23 2 0.05
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATTATTTTCATAATAT
Found at i:797442 original size:20 final size:20
Alignment explanation
Indices: 797395--797442 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
797385 CTCATCCAGC
*
797395 AAAGAAAGAAGAAGAAAAAA
1 AAAGAAAAAAGAAGAAAAAA
* *
797415 AAACAAAAAAGAAGAAGAAA
1 AAAGAAAAAAGAAGAAAAAA
*
797435 AAGGAAAA
1 AAAGAAAA
797443 TTGAATCAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAGAAGAAAAAA
Found at i:799920 original size:114 final size:114
Alignment explanation
Indices: 799720--799936 Score: 344
Period size: 114 Copynumber: 1.9 Consensus size: 114
799710 CGTTCTCGTA
* * *
799720 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTTGG
1 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTAAGTTATCTGATCTAGTTCGG
* * * *
799785 TATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCATG
66 TAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCATG
* *
799834 GTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTAGTTCGG
1 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTAAGTTATCTGATCTAGTTCGG
*
799899 TAGGAACCACAGAACCAATCATTGGAATTAAAAGATGA
66 TAGGAACCACAAAACCAATCATTGGAATTAAAAGATGA
799937 GCTGCATGAT
Statistics
Matches: 93, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 93 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (114 bp):
GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTAAGTTATCTGATCTAGTTCGG
TAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCATG
Found at i:801923 original size:54 final size:54
Alignment explanation
Indices: 801837--801948 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
801827 CAATGATTGA
***
801837 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
* *
801891 GAACATCTGAGCATAAGCCACAGGAAAA-GATGAATGCACTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACA-AAAAAGGATGAATGCACTGTCAAATGTTTTAC
801945 GAAC
1 GAAC
801949 CTGTTATTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 48 0.92
55 4 0.08
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.22
Consensus pattern (54 bp):
GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
Found at i:802345 original size:22 final size:22
Alignment explanation
Indices: 802316--802370 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
802306 ATCTACACTC
*
802316 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
802338 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
802360 TTCAAAGATGA
1 TTCAAAGATGA
802371 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:803151 original size:76 final size:76
Alignment explanation
Indices: 803053--803768 Score: 1261
Period size: 76 Copynumber: 9.4 Consensus size: 76
803043 TATTTCCCAT
*
803053 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
803118 GCCTTCGGGTC
66 GCCTTCGGGTC
803129 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
803194 ACCTTCGGGTC
66 GCCTTCGGGTC
803205 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
803270 ACCTTCGGGTC
66 GCCTTCGGGTC
*
803281 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
803346 GCCTTCGGGTC
66 GCCTTCGGGTC
*
803357 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
803422 GCCTTCGGGTC
66 GCCTTCGGGTC
* * *
803433 ATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCCTCAGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
803498 GCCTTCGGGTC
66 GCCTTCGGGTC
803509 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
803574 GCCTTCGGGTC
66 GCCTTCGGGTC
*
803585 ATCTATAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
* *
803650 ACCGTCGGGTC
66 GCCTTCGGGTC
* * *
803661 ATCTGTAAGTCCTGCAGTGCATGATGTTTCAAAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTC
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTC---CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
803726 AAAGCCTTAGGGTC
63 AAAGCCTTCGGGTC
*
803740 ATCTGTAAGTCCTGCAGTGCATGATGTTT
1 ATCTGTAAGTCCTTCAGTGCATGATGTTT
803769 TTAAGACATC
Statistics
Matches: 618, Mismatches: 19, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
76 548 0.89
79 70 0.11
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTCGGGTC
Found at i:803929 original size:3 final size:3
Alignment explanation
Indices: 803906--803970 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
803896 CACTAATTTT
* * *
803906 TTA TTT TTA TTT TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
*
803952 ATA TTA TTA TTA -TA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
803971 TACAAACAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.92
4 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:804013 original size:26 final size:26
Alignment explanation
Indices: 803977--804031 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
803967 TATTTACAAA
* * *
803977 CAGTTACAAACCAAACTGGACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
804003 CAGTTACAAACAAAACAGAACCGGCC
1 CAGTTACAAACAAAACAGAACCGGCC
804029 CAG
1 CAG
804032 ACCAACCAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.40, C:0.33, G:0.18, T:0.09
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCGGCC
Found at i:805311 original size:15 final size:15
Alignment explanation
Indices: 805291--805361 Score: 56
Period size: 15 Copynumber: 4.6 Consensus size: 15
805281 ATCCATTAGT
805291 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
805306 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
805320 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
*
805336 TTTTATTTTATTATTAC
1 TTTTA--ATATTATTAC
*
805353 GTTTAATAT
1 TTTTAATAT
805362 ATGTTTAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
14 5 0.12
15 21 0.49
16 9 0.21
17 8 0.19
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:805408 original size:20 final size:22
Alignment explanation
Indices: 805320--805408 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 22
805310 AATTTCTTTC
805320 ATTTTAATTATTA-TTATT-TT
1 ATTTTAATTATTACTTATTATT
*
805340 ATTTT-ATTATTACGTT-TAATAT
1 ATTTTAATTATTAC-TTATTAT-T
*
805362 ATGTTTAGATTATTATCTTCATGATT
1 AT-TTTA-ATTATTA-CTT-ATTATT
805388 ATTTT-ATTATTA-TTATTATT
1 ATTTTAATTATTACTTATTATT
805408 A
1 A
805409 AGTTATATAA
Statistics
Matches: 56, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
19 7 0.12
20 12 0.21
21 5 0.09
22 3 0.05
23 10 0.18
25 12 0.21
26 4 0.07
27 3 0.05
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTTAATTATTACTTATTATT
Found at i:805428 original size:14 final size:15
Alignment explanation
Indices: 805411--805443 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
805401 TATTATTAAG
805411 TTATATAA-ATATAT
1 TTATATAATATATAT
*
805425 TTATATAATATTTAT
1 TTATATAATATATAT
805440 TTAT
1 TTAT
805444 TCTTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:806170 original size:18 final size:18
Alignment explanation
Indices: 806149--806216 Score: 57
Period size: 18 Copynumber: 3.5 Consensus size: 18
806139 TTTTATATAC
806149 TTATTATTTTCATAATAT
1 TTATTATTTTCATAATAT
806167 TTATATATTTTCTTATTAATAT
1 TTAT-TATTTTC--A-TAATAT
* *
806189 TTCATTATTTGCA-AGTATT
1 TT-ATTATTTTCATAATA-T
806208 TTATTATTT
1 TTATTATTT
806217 ATTTTTCTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
18 14 0.33
19 10 0.24
20 1 0.02
21 1 0.02
22 14 0.33
23 2 0.05
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (18 bp):
TTATTATTTTCATAATAT
Found at i:813261 original size:114 final size:114
Alignment explanation
Indices: 813061--813277 Score: 353
Period size: 114 Copynumber: 1.9 Consensus size: 114
813051 CGTTCTCGTA
* *
813061 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTGATCTGGTTTGG
1 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTAAGTTATCTGATCTGGTTCGG
* * * *
813126 TATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCATG
66 TAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCATG
* *
813175 GTAGAAATAAGGAGGCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTCGG
1 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTAAGTTATCTGATCTGGTTCGG
*
813240 TAGGAACCACAGAACCAATCATTGGAATTAAAAGATGA
66 TAGGAACCACAAAACCAATCATTGGAATTAAAAGATGA
813278 GCTGCATGAT
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 94 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (114 bp):
GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTATTCTTTAAGTTATCTGATCTGGTTCGG
TAGGAACCACAAAACCAATCATTGGAATTAAAAGATGAATTTGCTCATG
Found at i:815669 original size:22 final size:22
Alignment explanation
Indices: 815640--815694 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
815630 ATCTACACTC
*
815640 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
*
815662 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
815684 TTCAAAGATGA
1 TTCAAAGATGA
815695 AAACTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:816457 original size:76 final size:76
Alignment explanation
Indices: 816375--817166 Score: 1415
Period size: 76 Copynumber: 10.4 Consensus size: 76
816365 CTATTTCCCA
816375 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
816440 AGCCTTCGGGT
66 AGCCTTCGGGT
*
816451 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCTGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
816516 AACCTTCGGGT
66 AGCCTTCGGGT
816527 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
816592 AACCTTCGGGT
66 AGCCTTCGGGT
*
816603 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
816668 AGCCTTCGGGT
66 AGCCTTCGGGT
816679 CATCTGTAAG-CCATTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 CATCTGTAAGTCC-TTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
816743 AAGCCTTCGGGT
65 AAGCCTTCGGGT
* *
816755 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
816820 AGCCTTCGGGT
66 AGCCTTCGGGT
* *
816831 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
816896 AGCCTTCGGGT
66 AGCCTTCGGGT
816907 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
816972 AGCCTTCGGGT
66 AGCCTTCGGGT
*
816983 CATCTGTAAGTCCTTCAGTGCATGCTGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
817048 AACCGTCGGGT
66 AGCCTTCGGGT
* *
817059 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAAAACCTTCGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
*
817124 AAAGCCTTAGGGT
64 AAAGCCTTCGGGT
*
817137 CATCTGTAAGTCCTGCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
817167 TTAAGACATC
Statistics
Matches: 693, Mismatches: 19, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
75 2 0.00
76 619 0.89
77 2 0.00
78 70 0.10
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTCGGGT
Found at i:817330 original size:12 final size:12
Alignment explanation
Indices: 817315--817348 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
817305 TTTAATTTTG
817315 TTTTTATTATTA
1 TTTTTATTATTA
817327 TTTTTATTATTA
1 TTTTTATTATTA
*
817339 -TATTATTATT
1 TTTTTATTATT
817349 TACAAACAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:817407 original size:26 final size:26
Alignment explanation
Indices: 817355--817409 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
817345 TATTTACAAA
* * * * *
817355 CAGTTACAAACCAAACTGGATCGGCC
1 CAGTTACAAACAAAACAGAACCAGCC
817381 CAGTTACAAACAAAACAGAACCAGCC
1 CAGTTACAAACAAAACAGAACCAGCC
817407 CAG
1 CAG
817410 ACCAACCAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.31, G:0.16, T:0.11
Consensus pattern (26 bp):
CAGTTACAAACAAAACAGAACCAGCC
Found at i:818726 original size:15 final size:15
Alignment explanation
Indices: 818706--818755 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
818696 ATCCATTAGT
818706 TTTTAATATTATTAC
1 TTTTAATATTATTAC
* *
818721 TTTTAAT-TTCTTTC
1 TTTTAATATTATTAC
818735 ATTTTAATTATTATTA-
1 -TTTTAA-TATTATTAC
818751 TTTTA
1 TTTTA
818756 TTTTAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 5 0.18
15 18 0.64
16 1 0.04
17 4 0.14
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAATATTATTAC
Found at i:818843 original size:14 final size:15
Alignment explanation
Indices: 818826--818858 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
818816 TAATATTAAG
818826 TTATATAA-ATATAT
1 TTATATAATATATAT
*
818840 TTATATAATATTTAT
1 TTATATAATATATAT
818855 TTAT
1 TTAT
818859 TCTTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATAATATATAT
Found at i:820102 original size:15 final size:15
Alignment explanation
Indices: 820084--820139 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
820074 TAACCGGTTT
820084 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
820099 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
820116 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
820131 CGATTTTAA
1 CGGTTTTAA
820140 TATTATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:820112 original size:17 final size:17
Alignment explanation
Indices: 820087--820137 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
820077 CCGGTTTCGG
820087 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
820104 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
820119 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
820136 TT
1 TT
820138 AATATTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:821318 original size:32 final size:33
Alignment explanation
Indices: 821222--821320 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
821212 AACTCAACAT
* * *
821222 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
821255 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
821288 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
821320 A
1 A
821321 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:821339 original size:21 final size:21
Alignment explanation
Indices: 821315--821356 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
821305 ACTTCAAGTT
821315 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
821336 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
821357 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:828825 original size:18 final size:19
Alignment explanation
Indices: 828799--828834 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
828789 TTATTTAAAC
828799 AAAACAATATAAA-AAAAT
1 AAAACAATATAAATAAAAT
*
828817 AAAATAATATAAATAAAA
1 AAAACAATATAAATAAAA
828835 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAACAATATAAATAAAAT
Found at i:832481 original size:2 final size:2
Alignment explanation
Indices: 832474--832502 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
832464 CACAAAATTA
832474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
832503 ATTAATAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:834770 original size:56 final size:56
Alignment explanation
Indices: 834703--834812 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
834693 AATCATTTTT
*
834703 GTTTTTATTTAATTAAGAAGTGTCATCTTAAGTTAATTATCACTAACAACAGTTTC
1 GTTTTTATTTAATTAAGAAGTGTCATATTAAGTTAATTATCACTAACAACAGTTTC
*
834759 GTTTTTATTTAATTAAGAAGTGTCATATTGAGTTAATTATCACTAACAACAGTT
1 GTTTTTATTTAATTAAGAAGTGTCATATTAAGTTAATTATCACTAACAACAGTT
834813 AAATATTTTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.43
Consensus pattern (56 bp):
GTTTTTATTTAATTAAGAAGTGTCATATTAAGTTAATTATCACTAACAACAGTTTC
Found at i:835032 original size:21 final size:20
Alignment explanation
Indices: 835008--835075 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
834998 GATTCGCAAC
835008 GCGATAGTCGAAGTTCGCATT
1 GCGATAGTCGAAGTTCGC-TT
* * *
835029 GCGATTTATTCCAAATTCG-TT
1 GCGA--TAGTCGAAGTTCGCTT
*
835050 GCGATAGGCGAAGTTCGCGTT
1 GCGATAGTCGAAGTTCGC-TT
835071 GCGAT
1 GCGAT
835076 TCATTCCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
19 9 0.25
21 17 0.47
23 10 0.28
ACGTcount: A:0.22, C:0.19, G:0.28, T:0.31
Consensus pattern (20 bp):
GCGATAGTCGAAGTTCGCTT
Found at i:835062 original size:42 final size:42
Alignment explanation
Indices: 835008--835098 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
834998 GATTCGCAAC
* *
835008 GCGATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
*
835050 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
835092 GCGATAG
1 GCGATAG
835099 TCCAAATATT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (42 bp):
GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAAATTCGTT
Found at i:835091 original size:21 final size:20
Alignment explanation
Indices: 835027--835105 Score: 63
Period size: 21 Copynumber: 3.9 Consensus size: 20
835017 GAAGTTCGCA
835027 TTGCGATTTATTCCAAATTCG
1 TTGCGA-TTATTCCAAATTCG
** * *
835048 TTGCGA-TAGGCGAAGTTCGCG
1 TTGCGATTATTCCAAATT--CG
835069 TTGCGATTCATTCCAAATTCG
1 TTGCGATT-ATTCCAAATTCG
*
835090 TTGCGA-TAGTCCAAAT
1 TTGCGATTATTCCAAAT
835106 ATTGCATTTG
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
19 15 0.33
20 1 0.02
21 22 0.49
22 1 0.02
23 6 0.13
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (20 bp):
TTGCGATTATTCCAAATTCG
Found at i:835104 original size:19 final size:19
Alignment explanation
Indices: 835038--835105 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 19
835028 TGCGATTTAT
835038 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * * *
835057 GCGAAGTTCGCGTTGCGATTCAT
1 TCCAAATT--CGTTGCGA-T-AG
835080 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
835099 TCCAAAT
1 TCCAAAT
835106 ATTGCATTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 13 0.35
20 1 0.03
21 16 0.43
22 1 0.03
23 6 0.16
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:835191 original size:6 final size:6
Alignment explanation
Indices: 835176--835208 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
835166 GACACGTATT
*
835176 ACCACG ACCACA ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
835209 CGAGACAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.36, C:0.52, G:0.12, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:835924 original size:6 final size:6
Alignment explanation
Indices: 835893--835933 Score: 54
Period size: 5 Copynumber: 7.5 Consensus size: 6
835883 TCCCGTCCCG
835893 GGTCGT -GTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
835934 AATACGTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 18 0.55
6 15 0.45
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:842200 original size:21 final size:21
Alignment explanation
Indices: 842137--842206 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
842127 GGGAATCGAC
**
842137 CCCCCCATGAGGGAACCGATT
1 CCCCCCACAAGGGAACCGATT
***
842158 CCCCCTTTGAAGGGGAACCGATT
1 CCCCC-CACAA-GGGAACCGATT
* *
842181 CCCCCCACAAGGGAATCGATA
1 CCCCCCACAAGGGAACCGATT
842202 CCCCC
1 CCCCC
842207 TGGGGTTCTG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
21 19 0.50
22 3 0.08
23 16 0.42
ACGTcount: A:0.24, C:0.40, G:0.21, T:0.14
Consensus pattern (21 bp):
CCCCCCACAAGGGAACCGATT
Found at i:844457 original size:19 final size:19
Alignment explanation
Indices: 844433--844472 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
844423 GTGTTTTAAG
844433 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
844452 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
844471 TG
1 TG
844473 GGAGAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (19 bp):
TGTGTTTTAAAATGATAAA
Found at i:846110 original size:27 final size:26
Alignment explanation
Indices: 846037--846145 Score: 95
Period size: 27 Copynumber: 4.3 Consensus size: 26
846027 TTAAATTCAT
846037 AATATTTTA-TA-TATA-TTATCTTAAA
1 AATATTTTATTATTA-ACTTAT-TTAAA
*
846062 AACA-TTTA-TATTAACTTA-TTAAA
1 AATATTTTATTATTAACTTATTTAAA
*
846085 TATATTTTATTATTAACTTAATTTAAA
1 AATATTTTATTATTAACTT-ATTTAAA
* **
846112 AATATTTTATTTTTATTTTCATTTAAA
1 AATATTTTATTATTAACTT-ATTTAAA
846139 AATATTT
1 AATATTT
846146 ATTTTATGTT
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
23 7 0.10
24 11 0.16
25 17 0.24
26 1 0.01
27 34 0.49
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (26 bp):
AATATTTTATTATTAACTTATTTAAA
Found at i:846162 original size:27 final size:27
Alignment explanation
Indices: 846080--846163 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
846070 TATTAACTTA
* * *
846080 TTAAATATATTTTATTATTAACTT-AAT
1 TTAAAAATATTTTATT-TTTATTTAAAT
**
846107 TTAAAAATATTTTATTTTTATTTTCAT
1 TTAAAAATATTTTATTTTTATTTAAAT
846134 TTAAAAATA-TTTA-TTTTATGTTAAAAT
1 TTAAAAATATTTTATTTTTAT-TT-AAAT
846161 TTA
1 TTA
846164 TTTAAAAGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
25 6 0.12
26 11 0.23
27 31 0.65
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.57
Consensus pattern (27 bp):
TTAAAAATATTTTATTTTTATTTAAAT
Done.