Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 38
Found at i:3211303 original size:41 final size:40
Alignment explanation
Indices: 3211209--3211307 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 40
3211199 AAATGCTGCC
* * *
3211209 AAAGACTCGTACTTTAGTGGCGTTTTATACAAACGCCACT
1 AAAGACTTGTACTTTAGTGGCGTTTTATACAAACACCAAT
* * *
3211249 ATATA-TTCATACTTTAGTGGCGTTTTTATACAAACACCAAT
1 AAAGACTT-GTACTTTAGTGGCG-TTTTATACAAACACCAAT
3211290 AAAGACTTGTACTTTAGT
1 AAAGACTTGTACTTTAGT
3211308 TGCATTTGTG
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
39 1 0.02
40 16 0.34
41 28 0.60
42 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.35
Consensus pattern (40 bp):
AAAGACTTGTACTTTAGTGGCGTTTTATACAAACACCAAT
Found at i:3212992 original size:22 final size:22
Alignment explanation
Indices: 3212952--3212993 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3212942 TTTCCACCGG
* **
3212952 AAGTTGGTAGCAAGTTGGCAAC
1 AAGTTGGTAGAAAAATGGCAAC
3212974 AAGTTGGTAGAAAAATGGCA
1 AAGTTGGTAGAAAAATGGCA
3212994 TGGTAAAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.31, T:0.21
Consensus pattern (22 bp):
AAGTTGGTAGAAAAATGGCAAC
Found at i:3219608 original size:21 final size:21
Alignment explanation
Indices: 3219583--3219631 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
3219573 TAAACTTTGA
*
3219583 TTTATTGTTATGAATTTCAAG
1 TTTATTGTTATGAATGTCAAG
*
3219604 TTTATTGTTATGGATGTCAAG
1 TTTATTGTTATGAATGTCAAG
3219625 TTTATTG
1 TTTATTG
3219632 GATAATGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.04, G:0.18, T:0.53
Consensus pattern (21 bp):
TTTATTGTTATGAATGTCAAG
Found at i:3220025 original size:41 final size:41
Alignment explanation
Indices: 3219965--3220047 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
3219955 AAATAGCAGT
3219965 GTTTGGAAAAAATGCCGTTAAATATCATAACCTTTAACGGC
1 GTTTGGAAAAAATGCCGTTAAATATCATAACCTTTAACGGC
* * * *
3220006 GTTTGTAAAAAATGTCGTTAAATATCATTACCTTTAGCGGC
1 GTTTGGAAAAAATGCCGTTAAATATCATAACCTTTAACGGC
3220047 G
1 G
3220048 CTTTCTGCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Consensus pattern (41 bp):
GTTTGGAAAAAATGCCGTTAAATATCATAACCTTTAACGGC
Found at i:3230804 original size:2 final size:2
Alignment explanation
Indices: 3230797--3230823 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3230787 CCGTAATTCC
3230797 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
3230824 AACATAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3232646 original size:27 final size:27
Alignment explanation
Indices: 3232580--3232681 Score: 86
Period size: 27 Copynumber: 3.7 Consensus size: 27
3232570 TAAATAAATT
*
3232580 TTAATAATAAAATATATATTTTTAATTGAAA
1 TTAATAAT-AAA-A-ATATTTTTAATT-AAG
* *
3232611 ATAAAAAT-AAAATATTTTTAAATTAAG
1 TTAATAATAAAAATATTTTT-AATTAAG
* *
3232638 TTAATAAT-AAAATGTATTTAA-TAAG
1 TTAATAATAAAAATATTTTTAATTAAG
3232663 TTAAT-ATAAAAATATTTTT
1 TTAATAATAAAAATATTTTT
3232682 TACGTTAATA
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
24 2 0.03
25 18 0.30
26 2 0.03
27 25 0.42
28 5 0.08
29 2 0.03
31 6 0.10
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
TTAATAATAAAAATATTTTTAATTAAG
Found at i:3235390 original size:14 final size:14
Alignment explanation
Indices: 3235371--3235402 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3235361 TAGTATAGAT
3235371 GGAGATAGCAAGGA
1 GGAGATAGCAAGGA
3235385 GGAGATAGCAAGGA
1 GGAGATAGCAAGGA
3235399 GGAG
1 GGAG
3235403 CAAGCCTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.06, G:0.47, T:0.06
Consensus pattern (14 bp):
GGAGATAGCAAGGA
Found at i:3236376 original size:17 final size:17
Alignment explanation
Indices: 3236354--3236393 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3236344 GATAGGAATT
3236354 AAACTAGTTCATTCATC
1 AAACTAGTTCATTCATC
* *
3236371 AAACTAGTTCATTTATT
1 AAACTAGTTCATTCATC
3236388 AAACTA
1 AAACTA
3236394 ACTCTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (17 bp):
AAACTAGTTCATTCATC
Found at i:3236787 original size:6 final size:6
Alignment explanation
Indices: 3236775--3236809 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3236765 ACTTCAAATC
* *
3236775 CATCCA TATCCA TATCCA CATCCA CATCCA CATCC
1 CATCCA CATCCA CATCCA CATCCA CATCCA CATCC
3236810 TTTTCATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.46, G:0.00, T:0.23
Consensus pattern (6 bp):
CATCCA
Found at i:3237339 original size:16 final size:17
Alignment explanation
Indices: 3237299--3237349 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 17
3237289 TAATGCATAT
*
3237299 ATATTATTAATAAATTAA
1 ATATTATT-TTAAATTAA
*
3237317 ATTTTATTTTAAA-TAA
1 ATATTATTTTAAATTAA
3237333 ATATTATTTTATAATTA
1 ATATTATTTTA-AATTA
3237350 TCTTATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
16 13 0.46
17 6 0.21
18 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATTATTTTAAATTAA
Found at i:3240230 original size:16 final size:16
Alignment explanation
Indices: 3240209--3240240 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3240199 TTAACGTTAT
3240209 TTTAAAATTAAATTAA
1 TTTAAAATTAAATTAA
*
3240225 TTTAAATTTAAATTAA
1 TTTAAAATTAAATTAA
3240241 ATTTTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAATTAAATTAA
Found at i:3258939 original size:123 final size:123
Alignment explanation
Indices: 3258657--3258927 Score: 334
Period size: 123 Copynumber: 2.2 Consensus size: 123
3258647 AAAGAAACTA
* * * * * * * *
3258657 AGTCGTAGAACGATCTTACTCCTTTCTTTGAAGGAAGCTAAGTCGTAATTCGGATGATTCGCTCA
1 AGTCATAGGACGATCTTACTCCTTTCTCTGAAGGACGCTAAATCGTAATTAGGATGATCCCCTCA
*
3258722 TTTCCATGAAGGATGTTAAATCCGGAGATGATCTTACTCTTTCCTCTGAAAAATTTTG
66 TTTCCATGAAGGATGTTAAATCCGGAGATGATCTCACTCTTTCCTCTGAAAAATTTTG
*
3258780 AGTCAT-GGAAAGATCTTACTCCTTTCTCTGAAGGACGCTAAATCGTAATTTAGG-TGATCCCCT
1 AGTCATAGG-ACGATCTTACTCCTTTCTCTGAAGGACGCTAAATCGTAA-TTAGGATGATCCCCT
* * * * * *
3258843 CCTTTCCCTTAAGGATGTTAAATCTGGTGATGATCTCACTCTTTTCC-CTGAAATATGTTT-
64 CATTTCCATGAAGGATGTTAAATCCGGAGATGATCTCACTC-TTTCCTCTGAAAAAT-TTTG
3258903 AGTCATAGGACGATCTTACTCCTTT
1 AGTCATAGGACGATCTTACTCCTTT
3258928 TCCTAAAGGA
Statistics
Matches: 126, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
122 1 0.01
123 111 0.88
124 14 0.11
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (123 bp):
AGTCATAGGACGATCTTACTCCTTTCTCTGAAGGACGCTAAATCGTAATTAGGATGATCCCCTCA
TTTCCATGAAGGATGTTAAATCCGGAGATGATCTCACTCTTTCCTCTGAAAAATTTTG
Found at i:3258960 original size:123 final size:123
Alignment explanation
Indices: 3258728--3258989 Score: 302
Period size: 123 Copynumber: 2.1 Consensus size: 123
3258718 CTCATTTCCA
*
3258728 TGAAGGATGTTAAATCCGGAGATGATCTTACTCTTTCCTCTGAAAAATTTTGAGTCATGGAAAGA
1 TGAAGGATGTTAAATCCGGAGATGATCTCACTCTTTCCTCTGAAAAATTTTGAGTCATGGAAAGA
* * * * *
3258793 TCTTACTCCTTTCTCTGAAGGACGCTAAATCGTAATTTAGGTGATCCCCTCCTTTC-CC
66 TCTTACTCCTTTCTCTAAAGGACGCTAAATCATAATTTAAGTGATCCACT-CATTCACC
* * * *
3258851 TTAAGGATGTTAAATCTGGTGATGATCTCACTCTTTTCC-CTGAAATATGTTT-AGTCATAGG-A
1 TGAAGGATGTTAAATCCGGAGATGATCTCACTC-TTTCCTCTGAAAAAT-TTTGAGTCAT-GGAA
* * *
3258913 CGATCTTACTCCTTT-TCCTAAAGGACGTTAAGTCAT-ATTTCAAGTGATCCACTCATTCACC
63 AGATCTTACTCCTTTCT-CTAAAGGACGCTAAATCATAATTT-AAGTGATCCACTCATTCACC
*
3258974 TGAAGGATGTTGAATC
1 TGAAGGATGTTAAATC
3258990 GTGATTCGGG
Statistics
Matches: 118, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
122 9 0.08
123 99 0.84
124 10 0.08
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.35
Consensus pattern (123 bp):
TGAAGGATGTTAAATCCGGAGATGATCTCACTCTTTCCTCTGAAAAATTTTGAGTCATGGAAAGA
TCTTACTCCTTTCTCTAAAGGACGCTAAATCATAATTTAAGTGATCCACTCATTCACC
Found at i:3259025 original size:166 final size:166
Alignment explanation
Indices: 3258832--3259202 Score: 440
Period size: 166 Copynumber: 2.2 Consensus size: 166
3258822 TCGTAATTTA
* * * * ** *
3258832 GGTGATCCCCTCCTTTCCCTTAAGGATGTTAAATCTGGTGATGATCTCACTCTTTTCCCTGAAAT
1 GGTGATCCACTCATTTCCCTAAAGGATGCTAAATCTGGTGACAATCTCACTCTTTTCCCTGAAAG
* * * **
3258897 ATGTTTAGTCATAGGACGATCTTACTCCTTTTCCTAAAGGACGTTAAGTCATATTTCAAGTGATC
66 ATATTGAGTCATAGGACGATCTTACTCCTTTCCCTAAAGGACGTTAAGTCATATTTCAAGCAATC
*
3258962 CAC-TCATTCACCTGAAGGATGTTGAATCGTGATTCG
131 CACTTCATTCA-CTGAAGAATGTTGAATCGTGATTCG
* *
3258998 GGTGATCCACTCATTTCCCTAAAGGATGCTGAATCTGGTGACAATCTCACTCTTTTCCTTGAAAG
1 GGTGATCCACTCATTTCCCTAAAGGATGCTAAATCTGGTGACAATCTCACTCTTTTCCCTGAAAG
* * * * ***
3259063 ATATTGAGTCATAGGATGATCTTACTCCTTTCCCTGAAGGATGTTAAGTCGTATTTTGGGCAATC
66 ATATTGAGTCATAGGACGATCTTACTCCTTTCCCTAAAGGACGTTAAGTCATATTTCAAGCAATC
* *
3259128 CACTTCTTTCACTGAAGAATGTTGAATTGTGATTCG
131 CACTTCATTCACTGAAGAATGTTGAATCGTGATTCG
* *** * *
3259164 GGTGGTTTGCTCCTTTTCC-AGAAGGATGCTAAATCTGGT
1 GGTGATCCACTCATTTCCCTA-AAGGATGCTAAATCTGGT
3259203 TCGGGCGATC
Statistics
Matches: 172, Mismatches: 31, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
165 1 0.01
166 165 0.96
167 6 0.03
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (166 bp):
GGTGATCCACTCATTTCCCTAAAGGATGCTAAATCTGGTGACAATCTCACTCTTTTCCCTGAAAG
ATATTGAGTCATAGGACGATCTTACTCCTTTCCCTAAAGGACGTTAAGTCATATTTCAAGCAATC
CACTTCATTCACTGAAGAATGTTGAATCGTGATTCG
Found at i:3259241 original size:42 final size:42
Alignment explanation
Indices: 3258956--3259283 Score: 138
Period size: 43 Copynumber: 7.8 Consensus size: 42
3258946 CATATTTCAA
*
3258956 GTGATCCACTCA-TTCACCTGAAGGATGTTGAATCGTGATTCGG
1 GTGATCCACTCATTTC-CCTGAAGGATGTTGAATC-TGGTTCGG
* *
3258999 GTGATCCACTCATTTCCCTAAAGGATGCTGAATCTGG-T--G
1 GTGATCCACTCATTTCCCTGAAGGATGTTGAATCTGGTTCGG
*** * * * * * * *
3259038 ACAATCTCACTCTTTTCCTTGAAAGATATTGAGTC---ATAGG
1 GTGATC-CACTCATTTCCCTGAAGGATGTTGAATCTGGTTCGG
* * * ** *
3259078 ATGATCTTACTCCTTTCCCTGAAGGATGTT-AAGTCGTATTTTGG
1 GTGATC-CACTCATTTCCCTGAAGGATGTTGAA-TC-TGGTTCGG
** * *
3259122 GCAATCCACTTC-TTTCACTGAAGAATGTTGAAT-TGTGATTCGG
1 GTGATCCAC-TCATTTCCCTGAAGGATGTTGAATCTG-G-TTCGG
* *** * * * * *
3259165 GTGGTTTGCTCCTTTTCCAGAAGGATGCTAAATCTGGTTCGG
1 GTGATCCACTCATTTCCCTGAAGGATGTTGAATCTGGTTCGG
* * *
3259207 GCGATCCACTCATTTCCCTGAAGGATGTTGAATCTAGTGT-AG
1 GTGATCCACTCATTTCCCTGAAGGATGTTGAATCTGGT-TCGG
* * * *
3259249 GTGATCAACTCCTTTTCCTGAAGGATATTGAATCT
1 GTGATCCACTCATTTCCCTGAAGGATGTTGAATCT
3259284 TATGATGACT
Statistics
Matches: 207, Mismatches: 61, Indels: 35
0.68 0.20 0.12
Matches are distributed among these distances:
38 1 0.00
39 5 0.02
40 47 0.23
41 2 0.01
42 67 0.32
43 70 0.34
44 15 0.07
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (42 bp):
GTGATCCACTCATTTCCCTGAAGGATGTTGAATCTGGTTCGG
Found at i:3261533 original size:24 final size:23
Alignment explanation
Indices: 3261504--3261569 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
3261494 ACTTGATCTG
* *
3261504 TTTTCTTTCTTTTTTGTTTTTTGT
1 TTTTCTTTCTTTTTTGCTTTCT-T
3261528 TTTTCTCTT-TTTTTTGCTTTCTT
1 TTTTCT-TTCTTTTTTGCTTTCTT
*
3261551 TTTTC-TTCTTTTTTTCTTT
1 TTTTCTTTCTTTTTTGCTTT
3261570 GTGTTCTCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 2 0.05
22 10 0.27
23 6 0.16
24 17 0.46
25 2 0.05
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (23 bp):
TTTTCTTTCTTTTTTGCTTTCTT
Found at i:3261564 original size:11 final size:10
Alignment explanation
Indices: 3261504--3261569 Score: 62
Period size: 11 Copynumber: 6.2 Consensus size: 10
3261494 ACTTGATCTG
*
3261504 TTTTCTTTCT
1 TTTTTTTTCT
3261514 TTTTTGTTT-T
1 TTTTT-TTTCT
3261524 TTGTTTTTCTCT
1 TT-TTTTT-TCT
*
3261536 TTTTTTTGCT
1 TTTTTTTTCT
3261546 TTCTTTTTTCT
1 TT-TTTTTTCT
3261557 TCTTTTTTTCT
1 T-TTTTTTTCT
3261568 TT
1 TT
3261570 GTGTTCTCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
10 14 0.30
11 29 0.62
12 4 0.09
ACGTcount: A:0.00, C:0.14, G:0.05, T:0.82
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:3273594 original size:961 final size:961
Alignment explanation
Indices: 3271726--3273645 Score: 3795
Period size: 961 Copynumber: 2.0 Consensus size: 961
3271716 AATTTTACAC
3271726 TTGAGTAAGGATTAAAAATGACATTTGAAGATTTGGAGTAATATTTTGATATTCGAATAATTATA
1 TTGAGTAAGGATTAAAAATGACATTTGAAGATTTGGAGTAATATTTTGATATTCGAATAATTATA
3271791 TCGAATATAATTAGAAAATCTTTTTGGAAAATCTTAAAATTCATTTAACTTAATTTGTTGTATCG
66 TCGAATATAATTAGAAAATCTTTTTGGAAAATCTTAAAATTCATTTAACTTAATTTGTTGTATCG
3271856 AAATATCAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAA
131 AAATATCAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAA
3271921 GATTTTATTTTGAAATCAAGTTTGAAATTACTCCCCCTTACTCTAACACTTCTCCCCTTTAAAAC
196 GATTTTATTTTGAAATCAAGTTTGAAATTACTCCCCCTTACTCTAACACTTCTCCCCTTTAAAAC
3271986 ACTTTTAACATTTCTCCCCCTTTTGTTAAATCAAAAAGACTTTTAAAAGATATTAAAAAAGGTTT
261 ACTTTTAACATTTCTCCCCCTTTTGTTAAATCAAAAAGACTTTTAAAAGATATTAAAAAAGGTTT
3272051 TGAAATCATTCAGCCAACTGATTATATATAGATAAATAGCTTAAGCTGCTAAGATCACAATCAAG
326 TGAAATCATTCAGCCAACTGATTATATATAGATAAATAGCTTAAGCTGCTAAGATCACAATCAAG
3272116 AGAAACATTAGCCATTAGTTTCATAATCAATATTCATAAACATGTAATGAATAATTGGTCATATA
391 AGAAACATTAGCCATTAGTTTCATAATCAATATTCATAAACATGTAATGAATAATTGGTCATATA
3272181 TGTCTACAGATGATGTAAATGATGTAATAAGGAATAAATTTAACCACCCATATATAGAAATATAA
456 TGTCTACAGATGATGTAAATGATGTAATAAGGAATAAATTTAACCACCCATATATAGAAATATAA
3272246 GTTCAAACCATCCATAAATCCAAACAAATTCAAAGTCAACCAATCCACAAATTCAAACATTCCAA
521 GTTCAAACCATCCATAAATCCAAACAAATTCAAAGTCAACCAATCCACAAATTCAAACATTCCAA
3272311 AATATTCAAAATGTTAAAACAATAAGTTTGAAGTTTTGATCCAATAAAGCTAAACAAGAACAGAG
586 AATATTCAAAATGTTAAAACAATAAGTTTGAAGTTTTGATCCAATAAAGCTAAACAAGAACAGAG
3272376 CCTAATCGTCCATCGGTGCATCAGGGGGAGATAAATGTGACCAAATATTGGTCACATCACGTGAA
651 CCTAATCGTCCATCGGTGCATCAGGGGGAGATAAATGTGACCAAATATTGGTCACATCACGTGAA
3272441 AGAGCATCGACCCTTTCATCCAACGAATCAAAACGACGATTCATCATTTCGGTGGTAGCAGTCAG
716 AGAGCATCGACCCTTTCATCCAACGAATCAAAACGACGATTCATCATTTCGGTGGTAGCAGTCAG
3272506 ATTGGAATCGATAGATGCAAGCCTCAAATCAATGTTCTCCATAAAAGATCAGAAGTATGGAGGCA
781 ATTGGAATCGATAGATGCAAGCCTCAAATCAATGTTCTCCATAAAAGATCAGAAGTATGGAGGCA
3272571 TTTGATACTCAGGACGAGGTTGTTCCTCTGGAGGTGCTTGTTCCTCGTGCTGCTCCGGCTCATTG
846 TTTGATACTCAGGACGAGGTTGTTCCTCTGGAGGTGCTTGTTCCTCGTGCTGCTCCGGCTCATTG
3272636 TCAGAGTCGTCTTCTTCCGGAGGTCGCTCACCGGTACGAACCCAAAGACAT
911 TCAGAGTCGTCTTCTTCCGGAGGTCGCTCACCGGTACGAACCCAAAGACAT
3272687 TTGAGTAAGGATTAAAAATGACATTTGAAGATTTGGAGTAATATTTTGATATTCGAATAATTATA
1 TTGAGTAAGGATTAAAAATGACATTTGAAGATTTGGAGTAATATTTTGATATTCGAATAATTATA
3272752 TCGAATATAATTAGAAAATCTTTTTGGAAAATCTTAAAATTCATTTAACTTAATTTGTTGTATCG
66 TCGAATATAATTAGAAAATCTTTTTGGAAAATCTTAAAATTCATTTAACTTAATTTGTTGTATCG
3272817 AAATATCAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAA
131 AAATATCAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAA
3272882 GATTTTATTTTGAAATCAAGTTTGAAATTACTCCCCCTTACTCTAACACTTCTCCCCTTTAAAAC
196 GATTTTATTTTGAAATCAAGTTTGAAATTACTCCCCCTTACTCTAACACTTCTCCCCTTTAAAAC
3272947 ACTTTTAACATTTCTCCCCCTTTTGTTAAATCAAAAAGACTTTTAAAAGATATTAAAAAAGGTTT
261 ACTTTTAACATTTCTCCCCCTTTTGTTAAATCAAAAAGACTTTTAAAAGATATTAAAAAAGGTTT
3273012 TGAAATCATTCAGCCAACTGATTATATATAGATAAATAGCTTAAGCTGCTAAGATCACAATCAAG
326 TGAAATCATTCAGCCAACTGATTATATATAGATAAATAGCTTAAGCTGCTAAGATCACAATCAAG
*
3273077 AGAAACGTTAGCCATTAGTTTCATAATCAATATTCATAAACATGTAATGAATAATTGGTCATATA
391 AGAAACATTAGCCATTAGTTTCATAATCAATATTCATAAACATGTAATGAATAATTGGTCATATA
3273142 TGTCTACAGATGATGTAAATGATGTAATAAGGAATAAATTTAACCACCCATATATAGAAATATAA
456 TGTCTACAGATGATGTAAATGATGTAATAAGGAATAAATTTAACCACCCATATATAGAAATATAA
3273207 GTTCAAACCATCCATAAATCCAAACAAATTCAAAGTCAACCAATCCACAAATTCAAACATTCCAA
521 GTTCAAACCATCCATAAATCCAAACAAATTCAAAGTCAACCAATCCACAAATTCAAACATTCCAA
3273272 AATATTCAAAATGTTAAAACAATAAGTTTGAAGTTTTGATCCAATAAAGCTAAACAAGAACAGAG
586 AATATTCAAAATGTTAAAACAATAAGTTTGAAGTTTTGATCCAATAAAGCTAAACAAGAACAGAG
3273337 CCTAATCGTCCATCGGTGCATCAGGGGGAGATAAATGTGACCAAATATTGGTCACATCACGTGAA
651 CCTAATCGTCCATCGGTGCATCAGGGGGAGATAAATGTGACCAAATATTGGTCACATCACGTGAA
*
3273402 AGAGCATCGACCCTTTCATCCAACGAATCAAAACGACGATTCATCGTTTCGGTGGTAGCAGTCAG
716 AGAGCATCGACCCTTTCATCCAACGAATCAAAACGACGATTCATCATTTCGGTGGTAGCAGTCAG
3273467 ATTGGAATCGATAGATGCAAGCCTCAAATCAATGTTCTCCATAAAAGATCAGAAGTATGGAGGCA
781 ATTGGAATCGATAGATGCAAGCCTCAAATCAATGTTCTCCATAAAAGATCAGAAGTATGGAGGCA
*
3273532 TTTGATACTCAGGACGAGGTTGTTCCTCTGGAGGTGCTTGTTCCTCGTGCTGCTCTGGCTCATTG
846 TTTGATACTCAGGACGAGGTTGTTCCTCTGGAGGTGCTTGTTCCTCGTGCTGCTCCGGCTCATTG
* *
3273597 TCAGAGTCGTCTTCTTCTGGAGGTTGCTCACCGGTACGAACCCAAAGAC
911 TCAGAGTCGTCTTCTTCCGGAGGTCGCTCACCGGTACGAACCCAAAGAC
3273646 CAGTTTCTTC
Statistics
Matches: 954, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
961 954 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (961 bp):
TTGAGTAAGGATTAAAAATGACATTTGAAGATTTGGAGTAATATTTTGATATTCGAATAATTATA
TCGAATATAATTAGAAAATCTTTTTGGAAAATCTTAAAATTCATTTAACTTAATTTGTTGTATCG
AAATATCAAAATGTTTTCAACAATCTCCCCCTTTTTGATATAACAAAACATTTTAGTAATTTTAA
GATTTTATTTTGAAATCAAGTTTGAAATTACTCCCCCTTACTCTAACACTTCTCCCCTTTAAAAC
ACTTTTAACATTTCTCCCCCTTTTGTTAAATCAAAAAGACTTTTAAAAGATATTAAAAAAGGTTT
TGAAATCATTCAGCCAACTGATTATATATAGATAAATAGCTTAAGCTGCTAAGATCACAATCAAG
AGAAACATTAGCCATTAGTTTCATAATCAATATTCATAAACATGTAATGAATAATTGGTCATATA
TGTCTACAGATGATGTAAATGATGTAATAAGGAATAAATTTAACCACCCATATATAGAAATATAA
GTTCAAACCATCCATAAATCCAAACAAATTCAAAGTCAACCAATCCACAAATTCAAACATTCCAA
AATATTCAAAATGTTAAAACAATAAGTTTGAAGTTTTGATCCAATAAAGCTAAACAAGAACAGAG
CCTAATCGTCCATCGGTGCATCAGGGGGAGATAAATGTGACCAAATATTGGTCACATCACGTGAA
AGAGCATCGACCCTTTCATCCAACGAATCAAAACGACGATTCATCATTTCGGTGGTAGCAGTCAG
ATTGGAATCGATAGATGCAAGCCTCAAATCAATGTTCTCCATAAAAGATCAGAAGTATGGAGGCA
TTTGATACTCAGGACGAGGTTGTTCCTCTGGAGGTGCTTGTTCCTCGTGCTGCTCCGGCTCATTG
TCAGAGTCGTCTTCTTCCGGAGGTCGCTCACCGGTACGAACCCAAAGACAT
Found at i:3274941 original size:21 final size:21
Alignment explanation
Indices: 3274882--3274940 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3274872 AGAACCCCAG
*
3274882 AGGGGTATCAATTCCCCTACA
1 AGGGGTATCGATTCCCCTACA
* * *
3274903 AGGGGAATCGGTTCCCCTTCA
1 AGGGGTATCGATTCCCCTACA
3274924 AGGGGGTATCGATTCCC
1 A-GGGGTATCGATTCCC
3274941 TCTGCACTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (21 bp):
AGGGGTATCGATTCCCCTACA
Found at i:3282878 original size:13 final size:13
Alignment explanation
Indices: 3282862--3282898 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3282852 GCGCAATGTG
*
3282862 CGTCAAAAATGCA
1 CGTCATAAATGCA
3282875 CGTCATAAATGCA
1 CGTCATAAATGCA
*
3282888 TGTCATAAATG
1 CGTCATAAATG
3282899 TGTTTCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (13 bp):
CGTCATAAATGCA
Found at i:3283690 original size:3 final size:3
Alignment explanation
Indices: 3283682--3283716 Score: 52
Period size: 3 Copynumber: 11.0 Consensus size: 3
3283672 CAAAATGTAA
3283682 AAT AAT AAT AAT AAT AAT AAT AGAT AAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT -AAT AAT AAT
3283717 TTATAAACTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 25 0.83
4 4 0.13
5 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3284052 original size:42 final size:43
Alignment explanation
Indices: 3283996--3284087 Score: 116
Period size: 42 Copynumber: 2.2 Consensus size: 43
3283986 TATATAAATG
* *
3283996 CCGCT-AAAGACTTGTACTTTAACGGTGTTTTAAGCACAAACA
1 CCGCTAAAAGACTTGTACTTTAACGGCGTTTAAAGCACAAACA
** *
3284038 CCGCTAAAAG-CTTGTACTTTAGTGGCGTTTAAAGCACAAACG
1 CCGCTAAAAGACTTGTACTTTAACGGCGTTTAAAGCACAAACA
*
3284080 CCACTAAA
1 CCGCTAAA
3284088 TATTATACTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 39 0.91
43 4 0.09
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (43 bp):
CCGCTAAAAGACTTGTACTTTAACGGCGTTTAAAGCACAAACA
Found at i:3284097 original size:41 final size:40
Alignment explanation
Indices: 3284024--3284131 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 40
3284014 TTAACGGTGT
* * *
3284024 TTTAAGCACAAACACCGCTAAA-AGCTTGTACTTTAGTGGCG
1 TTTAAGCACAAACGCCACTAAATA--TTATACTTTAGTGGCG
*
3284065 TTTAAAGCACAAACGCCACTAAATATTATACTTTAGTGGTG
1 TTT-AAGCACAAACGCCACTAAATATTATACTTTAGTGGCG
** * *
3284106 TTTGGGTACAAACGCCGCTAAATATT
1 TTTAAGCACAAACGCCACTAAATATT
3284132 TAGGTGGTGT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
40 19 0.33
41 20 0.35
42 17 0.30
43 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (40 bp):
TTTAAGCACAAACGCCACTAAATATTATACTTTAGTGGCG
Found at i:3284603 original size:22 final size:22
Alignment explanation
Indices: 3284590--3284655 Score: 132
Period size: 22 Copynumber: 3.0 Consensus size: 22
3284580 TATATTTTAG
3284590 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3284612 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3284634 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
3284656 AATTTATTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:3284714 original size:31 final size:31
Alignment explanation
Indices: 3284679--3284737 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
3284669 AGTTGTATGG
* *
3284679 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAATATTGCAAAACTAAA
3284710 ATTATTTAAATTTCAATATTGCAAAACT
1 ATTATTTAAATTTCAATATTGCAAAACT
3284738 CTTTTAAGTT
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:0.44, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTCAATATTGCAAAACTAAA
Found at i:3284890 original size:23 final size:23
Alignment explanation
Indices: 3284860--3284950 Score: 155
Period size: 23 Copynumber: 4.0 Consensus size: 23
3284850 CTTCTGCTGC
3284860 AGATGCCTGCAGATGTGGTCCGT
1 AGATGCCTGCAGATGTGGTCCGT
3284883 AGATGCCTGCAGATGTGGTCCGT
1 AGATGCCTGCAGATGTGGTCCGT
*
3284906 AGATTCCTGCAGATGTGGTCCGT
1 AGATGCCTGCAGATGTGGTCCGT
* *
3284929 AGATTCCTGCAGATGTAGTCCG
1 AGATGCCTGCAGATGTGGTCCG
3284951 CATACTGCAG
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 66 1.00
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (23 bp):
AGATGCCTGCAGATGTGGTCCGT
Found at i:3287918 original size:19 final size:19
Alignment explanation
Indices: 3287891--3287927 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3287881 ATGACCAATA
3287891 AAATCGCAATGCGATCTCT
1 AAATCGCAATGCGATCTCT
*
3287910 AAATTGCAATGCGATCTC
1 AAATCGCAATGCGATCTC
3287928 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (19 bp):
AAATCGCAATGCGATCTCT
Found at i:3287998 original size:41 final size:41
Alignment explanation
Indices: 3287953--3288049 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 41
3287943 GTTTCCAGAT
* *
3287953 TCGCAACGCGATTTTGACTATTGCAACGCAATAATACATAA
1 TCGCAACGCGATTTTGACTATCGCAACGCAATAATACAAAA
* ***
3287994 TCGCAACGCGATTCTGACTATCGCGTTGCAATAATACAAAA
1 TCGCAACGCGATTTTGACTATCGCAACGCAATAATACAAAA
*
3288035 TCGCAATGCGATTTT
1 TCGCAACGCGATTTT
3288050 CAAAGCGTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (41 bp):
TCGCAACGCGATTTTGACTATCGCAACGCAATAATACAAAA
Found at i:3288222 original size:22 final size:22
Alignment explanation
Indices: 3288192--3288239 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
3288182 CTACGGCGAC
*
3288192 ATCCGTCCCCATCTCCGACAAA
1 ATCCATCCCCATCTCCGACAAA
*
3288214 ATCCATCCCCATCTCCGACGAA
1 ATCCATCCCCATCTCCGACAAA
3288236 ATCC
1 ATCC
3288240 GTCTATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.46, G:0.08, T:0.19
Consensus pattern (22 bp):
ATCCATCCCCATCTCCGACAAA
Found at i:3288625 original size:14 final size:14
Alignment explanation
Indices: 3288606--3288645 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
3288596 ACGCGAAATG
*
3288606 AAAATCGCAATGAC
1 AAAATCGCAACGAC
3288620 AAAATCGCAACGAC
1 AAAATCGCAACGAC
3288634 AAAATCGCAACG
1 AAAATCGCAACG
3288646 CCATTTTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.50, C:0.25, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:3288748 original size:20 final size:20
Alignment explanation
Indices: 3288655--3288750 Score: 113
Period size: 20 Copynumber: 4.8 Consensus size: 20
3288645 GCCATTTTAG
3288655 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
** *
3288674 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATTTTCAT
* **
3288694 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATTTTCAT
*
3288714 TTCCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
3288734 TTTCGTGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
3288751 AAGTTTCAGA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 17 0.26
20 49 0.74
ACGTcount: A:0.14, C:0.20, G:0.23, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:3288757 original size:20 final size:20
Alignment explanation
Indices: 3288720--3288757 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3288710 TCATTTCCGC
* *
3288720 GTTGCGATTTTCATTTTCGT
1 GTTGCGATTTTAAGTTTCGT
3288740 GTTGCGATTTTAAGTTTC
1 GTTGCGATTTTAAGTTTC
3288758 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTAAGTTTCGT
Found at i:3290679 original size:20 final size:20
Alignment explanation
Indices: 3290656--3290704 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
3290646 GAAACTTAAA
3290656 ATCGCAACGCGGAA-ATGACT
1 ATCGCAACGC-GAATATGACT
*
3290676 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAATATGACT
3290696 ATCGCAACG
1 ATCGCAACG
3290705 GGATAATCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:3290733 original size:33 final size:34
Alignment explanation
Indices: 3290696--3290770 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
3290686 GAATTTGACT
*
3290696 ATCGCAACGGGATAATCGTAATGCG-AAATAAAA
1 ATCGCAACGGGAAAATCGTAATGCGAAAATAAAA
* *
3290729 ATCGCAACGTGAAAATCGTAATGCGAAAATGAAA
1 ATCGCAACGGGAAAATCGTAATGCGAAAATAAAA
3290763 ATCGCAAC
1 ATCGCAAC
3290771 TGCGATTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 23 0.61
34 15 0.39
ACGTcount: A:0.45, C:0.17, G:0.20, T:0.17
Consensus pattern (34 bp):
ATCGCAACGGGAAAATCGTAATGCGAAAATAAAA
Found at i:3290843 original size:20 final size:20
Alignment explanation
Indices: 3290783--3290850 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
3290773 CGATTATCTT
* **
3290783 GTTGCGATAGTCAAATTCGC
1 GTTGCAATAGTCATTTTCGC
* * * *
3290803 GATGCGATAGTCGTTTCCGC
1 GTTGCAATAGTCATTTTCGC
3290823 GTTGCAATAGTCATTTTCGC
1 GTTGCAATAGTCATTTTCGC
3290843 GTTGCAAT
1 GTTGCAAT
3290851 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (20 bp):
GTTGCAATAGTCATTTTCGC
Found at i:3290860 original size:20 final size:20
Alignment explanation
Indices: 3290837--3290877 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3290827 CAATAGTCAT
3290837 TTTCGCGTTGCAATTTTAAG
1 TTTCGCGTTGCAATTTTAAG
* *
3290857 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCAATTTTAAG
3290877 T
1 T
3290878 CTCAGAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.12, G:0.22, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCAATTTTAAG
Found at i:3291469 original size:21 final size:21
Alignment explanation
Indices: 3291361--3291478 Score: 87
Period size: 21 Copynumber: 5.6 Consensus size: 21
3291351 ACTCACCTGT
3291361 CATCGTTCAAGAGG-CCTCTCC
1 CATCGTTCAAGAGGTCC-CTCC
* * **
3291382 TATCGTTCAAGAGGCCCCTAA
1 CATCGTTCAAGAGGTCCCTCC
** *
3291403 CATCCCTCAAGA-GTCCCCTTC
1 CATCGTTCAAGAGGT-CCCTCC
* * **
3291424 CACCGTTCAAGAGGTCCTTGT
1 CATCGTTCAAGAGGTCCCTCC
*
3291445 CATCGTTGAAGAGGTCCCTCC
1 CATCGTTCAAGAGGTCCCTCC
*
3291466 CATCATTCAAGAG
1 CATCGTTCAAGAG
3291479 CCCGAAGCAC
Statistics
Matches: 72, Mismatches: 22, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
20 1 0.01
21 67 0.93
22 4 0.06
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.25
Consensus pattern (21 bp):
CATCGTTCAAGAGGTCCCTCC
Found at i:3293062 original size:20 final size:20
Alignment explanation
Indices: 3293015--3293065 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
3293005 ACGCTAAACT
* *
3293015 CAAAATCACAATGCGAAAGT
1 CAAAATCGCAATGCGAAAGC
*
3293035 CAAAATCGCAATGTGAAAGC
1 CAAAATCGCAATGCGAAAGC
3293055 CAAAATCGCAA
1 CAAAATCGCAA
3293066 CACGAAAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.22, G:0.16, T:0.14
Consensus pattern (20 bp):
CAAAATCGCAATGCGAAAGC
Found at i:3293072 original size:20 final size:20
Alignment explanation
Indices: 3293028--3293073 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3293018 AATCACAATG
* **
3293028 CGAAAGTCAAAATCGCAATG
1 CGAAAGCCAAAATCGCAACA
*
3293048 TGAAAGCCAAAATCGCAACA
1 CGAAAGCCAAAATCGCAACA
3293068 CGAAAG
1 CGAAAG
3293074 TAAATTCGCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.11
Consensus pattern (20 bp):
CGAAAGCCAAAATCGCAACA
Found at i:3293141 original size:20 final size:20
Alignment explanation
Indices: 3293116--3293266 Score: 179
Period size: 20 Copynumber: 7.8 Consensus size: 20
3293106 GCGATTTTCT
*
3293116 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
3293136 CGTTGCAATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
* *
3293156 CTTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
3293170 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
3293190 CGTTGCTATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
3293210 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3293230 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
3293250 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
3293267 GAATGTGTAA
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 12 0.11
16 1 0.01
18 1 0.01
20 99 0.88
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:3293159 original size:54 final size:54
Alignment explanation
Indices: 3293075--3293218 Score: 182
Period size: 54 Copynumber: 2.7 Consensus size: 54
3293065 ACACGAAAGT
* ** * *
3293075 AAATTCGCGTTGTGATAGTCTAATACGCTTTGCGATTTTCT-CGTTGCGATAGTC
1 AAATTCCCGTTGCAATAGTCAAATTCGCTTTGCGATTTT-TGCGTTGCGATAGTC
*
3293129 AAATTCCCGTTGCAATAGTCAAATTTGCTTTGCGATTTTTGCGTTGCGATAGTC
1 AAATTCCCGTTGCAATAGTCAAATTCGCTTTGCGATTTTTGCGTTGCGATAGTC
* * * *
3293183 ATATTCGCGTTGCTATAGTCAAATTCGCGTTGCGAT
1 AAATTCCCGTTGCAATAGTCAAATTCGCTTTGCGAT
3293219 AGTCAAATTC
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 77 0.99
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (54 bp):
AAATTCCCGTTGCAATAGTCAAATTCGCTTTGCGATTTTTGCGTTGCGATAGTC
Found at i:3293460 original size:18 final size:18
Alignment explanation
Indices: 3293437--3293471 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3293427 AAGCCGGTTG
*
3293437 TGATTAGGATTTTGATTT
1 TGATTACGATTTTGATTT
3293455 TGATTACGATTTTGATT
1 TGATTACGATTTTGATT
3293472 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.03, G:0.20, T:0.54
Consensus pattern (18 bp):
TGATTACGATTTTGATTT
Found at i:3296501 original size:20 final size:20
Alignment explanation
Indices: 3296476--3296543 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
3296466 GAAATTCAGT
* *
3296476 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGA
*
3296496 GTTGCGATAGTCAGAATCGT
1 GTTGCGATAGTCAGAATCGA
3296516 GTTGCGATAGTCAGAATCGA
1 GTTGCGATAGTCAGAATCGA
3296536 GTTGCGAT
1 GTTGCGAT
3296544 TATGTATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGA
Found at i:3296598 original size:21 final size:21
Alignment explanation
Indices: 3296531--3296606 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
3296521 GATAGTCAGA
*
3296531 ATCGAGTTGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
* * **
3296552 ATCTCGTTGC-AATA-GTCAGA
1 ATCGCGTTGCGATTATGT-ATT
*
3296572 ATCGCGATGCGATTATGTATT
1 ATCGCGTTGCGATTATGTATT
3296593 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
3296607 TACATATTCG
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 2 0.05
20 12 0.29
21 25 0.61
22 2 0.05
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (21 bp):
ATCGCGTTGCGATTATGTATT
Found at i:3296626 original size:41 final size:42
Alignment explanation
Indices: 3296484--3296602 Score: 140
Period size: 41 Copynumber: 2.9 Consensus size: 42
3296474 GTGTTGCGAC
** * *
3296484 AGTCAGAATCGCG-TTGCGA-TA-GTCAGAATCGTGTTGCGAT
1 AGTCAGAATCGCGATTGCGATTATGT-ATTATCGCGTTGCAAT
* *
3296524 AGTCAGAATCGAG-TTGCGATTATGTATTATCTCGTTGCAAT
1 AGTCAGAATCGCGATTGCGATTATGTATTATCGCGTTGCAAT
3296565 AGTCAGAATCGCGA-TGCGATTATGTATTATCGCGTTGC
1 AGTCAGAATCGCGATTGCGATTATGTATTATCGCGTTGC
3296603 GATTTACATA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
40 18 0.26
41 48 0.71
42 2 0.03
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (42 bp):
AGTCAGAATCGCGATTGCGATTATGTATTATCGCGTTGCAAT
Found at i:3296645 original size:21 final size:21
Alignment explanation
Indices: 3296621--3296667 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3296611 TATTCGCATT
*
3296621 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCGAAAATCGCAAC
* * *
3296642 GCGAATTTGGAAAATCGCAAT
1 GCGATTTTCGAAAATCGCAAC
3296663 GCGAT
1 GCGAT
3296668 AGTCAAAATC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GCGATTTTCGAAAATCGCAAC
Found at i:3296724 original size:20 final size:19
Alignment explanation
Indices: 3296701--3296746 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3296691 GGAAACTGAT
*
3296701 TTGCGATACTAGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
3296721 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
3296740 TTGCGAT
1 TTGCGAT
3296747 TTTGTTGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:3296734 original size:19 final size:19
Alignment explanation
Indices: 3296710--3296748 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3296700 TTTGCGATAC
*
3296710 TAGAGATCGCGTTGCGATT
1 TAGAGATCGCATTGCGATT
3296729 TAGAGATCGCATTGCGATT
1 TAGAGATCGCATTGCGATT
3296748 T
1 T
3296749 TGTTGGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (19 bp):
TAGAGATCGCATTGCGATT
Found at i:3297883 original size:2 final size:2
Alignment explanation
Indices: 3297876--3297915 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3297866 AGGTGATGCC
3297876 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3297916 TTGTTGGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3301134 original size:23 final size:21
Alignment explanation
Indices: 3301096--3301138 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3301086 TTAAAATATT
*
3301096 ATAAAAAAAAAGAAAAGAAAG
1 ATAAAAAAAAAAAAAAGAAAG
3301117 ATAAAAAAAATATAAAAAGAAA
1 ATAAAAAAAA-A-AAAAAGAAA
3301139 AGTAAAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 1 0.05
23 8 0.42
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (21 bp):
ATAAAAAAAAAAAAAAGAAAG
Found at i:3304270 original size:197 final size:197
Alignment explanation
Indices: 3303935--3304328 Score: 788
Period size: 197 Copynumber: 2.0 Consensus size: 197
3303925 TACAATGAAG
3303935 GCACCAGCAACATCAATAGTAGCAAGTGTATTGCTATTTCCCAGAGAAAAATGACCAGCCATTCC
1 GCACCAGCAACATCAATAGTAGCAAGTGTATTGCTATTTCCCAGAGAAAAATGACCAGCCATTCC
3304000 CAAGTAGTAAAGTCCTGCAATCTAAGAGAACAAAATACTGACATTAGTGCAGAAAGCTGTTACTT
66 CAAGTAGTAAAGTCCTGCAATCTAAGAGAACAAAATACTGACATTAGTGCAGAAAGCTGTTACTT
3304065 ATTTAAAGAGTTCTTAAAAGCAATTTCACATCTGTTCAACTTACTTCTATACCAATATAAGAATA
131 ATTTAAAGAGTTCTTAAAAGCAATTTCACATCTGTTCAACTTACTTCTATACCAATATAAGAATA
3304130 GC
196 GC
3304132 GCACCAGCAACATCAATAGTAGCAAGTGTATTGCTATTTCCCAGAGAAAAATGACCAGCCATTCC
1 GCACCAGCAACATCAATAGTAGCAAGTGTATTGCTATTTCCCAGAGAAAAATGACCAGCCATTCC
3304197 CAAGTAGTAAAGTCCTGCAATCTAAGAGAACAAAATACTGACATTAGTGCAGAAAGCTGTTACTT
66 CAAGTAGTAAAGTCCTGCAATCTAAGAGAACAAAATACTGACATTAGTGCAGAAAGCTGTTACTT
3304262 ATTTAAAGAGTTCTTAAAAGCAATTTCACATCTGTTCAACTTACTTCTATACCAATATAAGAATA
131 ATTTAAAGAGTTCTTAAAAGCAATTTCACATCTGTTCAACTTACTTCTATACCAATATAAGAATA
3304327 GC
196 GC
3304329 TGCTTTCAAG
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 197 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (197 bp):
GCACCAGCAACATCAATAGTAGCAAGTGTATTGCTATTTCCCAGAGAAAAATGACCAGCCATTCC
CAAGTAGTAAAGTCCTGCAATCTAAGAGAACAAAATACTGACATTAGTGCAGAAAGCTGTTACTT
ATTTAAAGAGTTCTTAAAAGCAATTTCACATCTGTTCAACTTACTTCTATACCAATATAAGAATA
GC
Found at i:3306677 original size:9 final size:9
Alignment explanation
Indices: 3306663--3306687 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3306653 ATAATGTCCA
3306663 CCATTTCCC
1 CCATTTCCC
3306672 CCATTTCCC
1 CCATTTCCC
3306681 CCATTTC
1 CCATTTC
3306688 ATTCAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.52, G:0.00, T:0.36
Consensus pattern (9 bp):
CCATTTCCC
Found at i:3308125 original size:21 final size:20
Alignment explanation
Indices: 3308101--3308142 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
3308091 ATATATTGTA
*
3308101 TTTAATGTAGGATATTACATT
1 TTTAATGTAGGAGATTA-ATT
3308122 TTTAATGTAGGAGATTAATT
1 TTTAATGTAGGAGATTAATT
3308142 T
1 T
3308143 ACATATCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (20 bp):
TTTAATGTAGGAGATTAATT
Found at i:3311352 original size:4 final size:4
Alignment explanation
Indices: 3311343--3311373 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
3311333 CGCCAATTAT
3311343 AATA AATA AATA AATA AATA AAGTA AATA AA
1 AATA AATA AATA AATA AATA AA-TA AATA AA
3311374 CTGAGAGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:3314257 original size:159 final size:157
Alignment explanation
Indices: 3313994--3314370 Score: 435
Period size: 159 Copynumber: 2.4 Consensus size: 157
3313984 TGTGGTTTAT
* * ** * *
3313994 GAGCATGTGGTTCAAATTTGATAAAAAAAATGACTTAAAATAAATCACAAATTGAAGGAATAAGG
1 GAGCATGTGG-TCCAATTTGGTAAAAAAAATGACTTAAAATAAATGGCGAATTGAAGAAAT-AGG
* ** *
3314059 AGATTATGAAAAATTGAAGGATTAAACTGAAAAATAAAAAATTTGTTATAAAAAAC-AGGAACTT
64 AGATTATGAAAAATTGAAGGACTAAACTGAAAAATAAAAAAAGTATTAT-AAAAACGAGGAA-TT
*
3314123 -AAAGTACACATTTATTCTACTATGCTATAG
127 GAAAGTACACATGTATTCTACTATGCTATAG
** *
3314153 GAGCATGTGGCTCCAATTTGGTAAAAAATGTGACTTAAAATAAATGGTGAATTGAAGAAATA-GA
1 GAGCATGTGG-TCCAATTTGGTAAAAAAAATGACTTAAAATAAATGGCGAATTGAAGAAATAGGA
*
3314217 GATTATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAAAAAGTATTATAAAAACGAGGAATTG
65 GATTATGAAAAATTGAAGGACTAAACTGAAAAAT--AAAAAAAGTATTATAAAAACGAGGAATTG
* *
3314282 AAAGTACACATGTATTCTACTATGGTTTAG
128 AAAGTACACATGTATTCTACTATGCTATAG
* * * *
3314312 GAGCACGTGGTTC---TTGGTAAAAAAAATAGACTTAAAATGAA-GGAGGAATTGAAGAAATA
1 GAGCATGTGGTCCAATTTGGTAAAAAAAAT-GACTTAAAATAAATGG-CGAATTGAAGAAATA
3314371 ATGAAGTCAA
Statistics
Matches: 188, Mismatches: 24, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
155 14 0.07
156 26 0.14
157 34 0.18
158 11 0.06
159 103 0.55
ACGTcount: A:0.47, C:0.07, G:0.19, T:0.27
Consensus pattern (157 bp):
GAGCATGTGGTCCAATTTGGTAAAAAAAATGACTTAAAATAAATGGCGAATTGAAGAAATAGGAG
ATTATGAAAAATTGAAGGACTAAACTGAAAAATAAAAAAAGTATTATAAAAACGAGGAATTGAAA
GTACACATGTATTCTACTATGCTATAG
Found at i:3324833 original size:42 final size:42
Alignment explanation
Indices: 3324753--3324833 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
3324743 CGTTTTAGCC
* ** *
3324753 CAAATACCACAATATAGTGGTACTTTAGTGGCATTTATATCA
1 CAAACACCACAATATAGTGGTAAATTAGTGGCACTTATATCA
* *
3324795 CAAACACCGCAATATAGTGGTAAATTAGTGGCGCTTATA
1 CAAACACCACAATATAGTGGTAAATTAGTGGCACTTATA
3324834 CCTCAAATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (42 bp):
CAAACACCACAATATAGTGGTAAATTAGTGGCACTTATATCA
Found at i:3334377 original size:21 final size:21
Alignment explanation
Indices: 3334352--3334411 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
3334342 GCAGAGAGAG
*
3334352 CAGCAACGAGAGAAGCATTGGA
1 CAGCAACGAGAGAAGCAAT-GA
3334374 -AGCAGA-GAGAGAAGCAATGA
1 CAGCA-ACGAGAGAAGCAATGA
3334394 CAG-AACAGAGAGAAGCAA
1 CAGCAAC-GAGAGAAGCAA
3334412 CGGCAACACA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
19 1 0.03
20 3 0.09
21 28 0.85
22 1 0.03
ACGTcount: A:0.48, C:0.15, G:0.32, T:0.05
Consensus pattern (21 bp):
CAGCAACGAGAGAAGCAATGA
Found at i:3334387 original size:12 final size:11
Alignment explanation
Indices: 3334330--3334411 Score: 50
Period size: 12 Copynumber: 7.6 Consensus size: 11
3334320 AGTCAAAAAT
3334330 GAAGCAAG-G-
1 GAAGCAAGAGA
3334339 GAAGCAGAGAGA
1 GAAGCA-AGAGA
*
3334351 GCAGCAACGAGA
1 GAAGCAA-GAGA
**
3334363 GAAGC-ATTG-
1 GAAGCAAGAGA
3334372 GAAGCAGAGAGA
1 GAAGCA-AGAGA
*
3334384 GAAGCAATGACA
1 GAAGCAA-GAGA
3334396 GAA-C-AGAGA
1 GAAGCAAGAGA
3334405 GAAGCAA
1 GAAGCAA
3334412 CGGCAACACA
Statistics
Matches: 55, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
9 17 0.31
10 5 0.09
11 8 0.15
12 25 0.45
ACGTcount: A:0.48, C:0.13, G:0.35, T:0.04
Consensus pattern (11 bp):
GAAGCAAGAGA
Found at i:3334409 original size:33 final size:33
Alignment explanation
Indices: 3334330--3334410 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 33
3334320 AGTCAAAAAT
* *
3334330 GAAGCA-AGGGAAGCAGAGAGAGCAGCAACGAGA
1 GAAGCAGA-GGAAGCAGAGAGAGAAGCAACGACA
** *
3334363 GAAGCATTGGAAGCAGAGAGAGAAGCAATGACA
1 GAAGCAGAGGAAGCAGAGAGAGAAGCAACGACA
3334396 GAA-CAGAGAGAAGCA
1 GAAGCAGAG-GAAGCA
3334411 ACGGCAACAC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.08
33 37 0.93
ACGTcount: A:0.47, C:0.14, G:0.36, T:0.04
Consensus pattern (33 bp):
GAAGCAGAGGAAGCAGAGAGAGAAGCAACGACA
Found at i:3334422 original size:21 final size:21
Alignment explanation
Indices: 3334379--3334431 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
3334369 TTGGAAGCAG
*
3334379 AGAGAGAAGCAATGACAGAAC
1 AGAGAGAAGCAACGACAGAAC
*
3334400 AGAGAGAAGCAACGGCA-ACAC
1 AGAGAGAAGCAACGACAGA-AC
3334421 AGAGAGAAGCA
1 AGAGAGAAGCA
3334432 GCATATTAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.51, C:0.17, G:0.30, T:0.02
Consensus pattern (21 bp):
AGAGAGAAGCAACGACAGAAC
Found at i:3334879 original size:43 final size:43
Alignment explanation
Indices: 3334813--3334912 Score: 132
Period size: 43 Copynumber: 2.3 Consensus size: 43
3334803 TATATCCTCA
*
3334813 AAACGCCGCAATAGGTAGTGATATATAGCGACATTTGT-TCAAT
1 AAACGCCGCAATAGATAGTGATATATAGCGACATTTGTCT-AAT
* * *
3334856 AAACGCCGCAATAGAT-GTCGATATTTAGCGGCATTTGTCTTAT
1 AAACGCCGCAATAGATAGT-GATATATAGCGACATTTGTCTAAT
3334899 AAACGCCGCAATAG
1 AAACGCCGCAATAG
3334913 GTGTTAGTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
42 2 0.04
43 48 0.94
44 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAATAGATAGTGATATATAGCGACATTTGTCTAAT
Found at i:3340731 original size:222 final size:221
Alignment explanation
Indices: 3340345--3340787 Score: 877
Period size: 222 Copynumber: 2.0 Consensus size: 221
3340335 TCAATTTATA
3340345 TGGTATCAATATTGTTCTTCATGTATCGACATCTAATCCAACAAATGAATAATTTTAAGTTTGGG
1 TGGTATCAATATTGTTCTTCATGTATCGACATCTAATCCAACAAATGAATAATTTTAAGTTTGGG
3340410 AATCACTCTAAAACCCTCCCAAACACTTTAATTTAAACCTAAGTTGATTCCTACGGCTCATGGGG
66 AATCACTCTAAAACCCTCCCAAACACTTTAATTTAAACCTAAGTTGATTCCTACGGCTCATGGGG
3340475 TAACATGGGGGCATCTAGCATCATAAAACACATGGTCAACAATAATTTCTTCATCTAAAGTCATA
131 TAACATGGGGGCATCTAGCATCATAAAACACATGGTCAACAATAATTTCTTCATCT-AAGTCATA
3340540 AATCATGCATAACACTCGATATATCTT
195 AATCATGCATAACACTCGATATATCTT
3340567 TGGTATCAATATTGTTCTTCATGTATCGACATCTAATCCAACAAATGAATAATTTTAAGTTTGGG
1 TGGTATCAATATTGTTCTTCATGTATCGACATCTAATCCAACAAATGAATAATTTTAAGTTTGGG
3340632 AATCACTCTAAAACCCTCCCAAACACTTTAATTTAAACCTAAGTTGATTCCTACGGCTCATGGGG
66 AATCACTCTAAAACCCTCCCAAACACTTTAATTTAAACCTAAGTTGATTCCTACGGCTCATGGGG
3340697 TAACATGGGGGCATCTAGCATCATAAAACACATGGTCAACAATAATTTCTTCATCTAAGTCATAA
131 TAACATGGGGGCATCTAGCATCATAAAACACATGGTCAACAATAATTTCTTCATCTAAGTCATAA
3340762 ATCATGCATAACACTCGATATATCTT
196 ATCATGCATAACACTCGATATATCTT
3340788 ACAATGCTAG
Statistics
Matches: 221, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
221 35 0.16
222 186 0.84
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (221 bp):
TGGTATCAATATTGTTCTTCATGTATCGACATCTAATCCAACAAATGAATAATTTTAAGTTTGGG
AATCACTCTAAAACCCTCCCAAACACTTTAATTTAAACCTAAGTTGATTCCTACGGCTCATGGGG
TAACATGGGGGCATCTAGCATCATAAAACACATGGTCAACAATAATTTCTTCATCTAAGTCATAA
ATCATGCATAACACTCGATATATCTT
Found at i:3342604 original size:16 final size:16
Alignment explanation
Indices: 3342583--3342613 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3342573 TTTATGTTTC
3342583 AATTAAGGCTAGTATT
1 AATTAAGGCTAGTATT
3342599 AATTAAGGCTAGTAT
1 AATTAAGGCTAGTAT
3342614 CGACACATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (16 bp):
AATTAAGGCTAGTATT
Found at i:3345731 original size:20 final size:22
Alignment explanation
Indices: 3345688--3345738 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
3345678 CGAGGATCAA
*
3345688 TATCGGTACTGATAGATGGAGG
1 TATCGATACTGATAGATGGAGG
*
3345710 TATCGATACTGA-A-ATGGGGG
1 TATCGATACTGATAGATGGAGG
*
3345730 TATCAATAC
1 TATCGATAC
3345739 CAAGGGTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 14 0.54
21 1 0.04
22 11 0.42
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.27
Consensus pattern (22 bp):
TATCGATACTGATAGATGGAGG
Found at i:3351426 original size:23 final size:23
Alignment explanation
Indices: 3351393--3351502 Score: 76
Period size: 23 Copynumber: 4.8 Consensus size: 23
3351383 GTCTAGGGTT
*
3351393 CTATGTGGTCCTTCGGGACAAAC
1 CTATATGGTCCTTCGGGACAAAC
* * *
3351416 CTCTATGGTCCTTTGGGACAATC
1 CTATATGGTCCTTCGGGACAAAC
* ** * *
3351439 CTATGTGGTCCTTTAGTACAATC
1 CTATATGGTCCTTCGGGACAAAC
* * * *
3351462 CTATGTGGTCATTTGGGACAAAA
1 CTATATGGTCCTTCGGGACAAAC
* **
3351485 TTATATGGTTTTTCGGGA
1 CTATATGGTCCTTCGGGA
3351503 TAAATATGTG
Statistics
Matches: 69, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (23 bp):
CTATATGGTCCTTCGGGACAAAC
Found at i:3351471 original size:46 final size:46
Alignment explanation
Indices: 3351393--3351482 Score: 117
Period size: 46 Copynumber: 2.0 Consensus size: 46
3351383 GTCTAGGGTT
* * *
3351393 CTATGTGGTCCTTCGGGACAAACCTCTATGGTCCTTTGGGACAATC
1 CTATGTGGTCCTTCAGGACAAACCTATATGGTCATTTGGGACAATC
* * * *
3351439 CTATGTGGTCCTTTAGTACAATCCTATGTGGTCATTTGGGACAA
1 CTATGTGGTCCTTCAGGACAAACCTATATGGTCATTTGGGACAA
3351483 AATTATATGG
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.33
Consensus pattern (46 bp):
CTATGTGGTCCTTCAGGACAAACCTATATGGTCATTTGGGACAATC
Found at i:3358421 original size:23 final size:23
Alignment explanation
Indices: 3358372--3358422 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3358362 GGGTTCTATG
*
3358372 TGGTCCTTCGGGACAAACCTGTG
1 TGGTCCTTCGGGACAAACCTGTA
* *
3358395 TGGTCCTTCGGGACAATCCTTTA
1 TGGTCCTTCGGGACAAACCTGTA
3358418 TGGTC
1 TGGTC
3358423 ATTCAGGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (23 bp):
TGGTCCTTCGGGACAAACCTGTA
Found at i:3358851 original size:16 final size:16
Alignment explanation
Indices: 3358830--3358860 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3358820 AAATTGTTGG
3358830 CATGTACTACAAGTTA
1 CATGTACTACAAGTTA
3358846 CATGTACTACAAGTT
1 CATGTACTACAAGTT
3358861 TAAATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (16 bp):
CATGTACTACAAGTTA
Found at i:3360318 original size:53 final size:53
Alignment explanation
Indices: 3360260--3360363 Score: 145
Period size: 53 Copynumber: 2.0 Consensus size: 53
3360250 CACAATTAAC
* * * *
3360260 CAACACAAGATATGCAAAATAAAAATATTATAGAAGAGTATCAAGTCTCAAAT
1 CAACACAAGATATGCAAAATAAAAATATCACACAAGAGTATCAAATCTCAAAT
* * *
3360313 CAACACAAGATGTTCAAATTAAAAATATCACACAAGAGTATCAAATCTCAA
1 CAACACAAGATATGCAAAATAAAAATATCACACAAGAGTATCAAATCTCAA
3360364 CAACGCAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.22
Consensus pattern (53 bp):
CAACACAAGATATGCAAAATAAAAATATCACACAAGAGTATCAAATCTCAAAT
Found at i:3360438 original size:64 final size:65
Alignment explanation
Indices: 3360309--3360440 Score: 176
Period size: 64 Copynumber: 2.0 Consensus size: 65
3360299 ATCAAGTCTC
* * *
3360309 AAATCAACACAAGATGTTCAAATTAAAAATATCACACAAGAGTATCAAATCTCAACAACGCAATA
1 AAATCAACACAAGATGTTCAAAATAAAAATACCACACAAGAGTATCAAATCTCAACAACACAATA
* * * * * *
3360374 AAATCAACACAATATGTTTAAAAT-AAAATACCACACAAGAGTATCAAGTCTTAACCACATAATA
1 AAATCAACACAAGATGTTCAAAATAAAAATACCACACAAGAGTATCAAATCTCAACAACACAATA
3360438 AAA
1 AAA
3360441 GAGATAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
64 37 0.64
65 21 0.36
ACGTcount: A:0.53, C:0.19, G:0.07, T:0.21
Consensus pattern (65 bp):
AAATCAACACAAGATGTTCAAAATAAAAATACCACACAAGAGTATCAAATCTCAACAACACAATA
Found at i:3360861 original size:20 final size:21
Alignment explanation
Indices: 3360818--3360861 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
3360808 CTCGGAATGT
*
3360818 TAAAAAAATTAACATTTCATG
1 TAAAAAAATTAACATTTCAGG
* *
3360839 TAAAAAAA-TAATATTTTAGG
1 TAAAAAAATTAACATTTCAGG
3360859 TAA
1 TAA
3360862 TTTTTTTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (21 bp):
TAAAAAAATTAACATTTCAGG
Found at i:3361116 original size:81 final size:80
Alignment explanation
Indices: 3360995--3361289 Score: 223
Period size: 81 Copynumber: 3.5 Consensus size: 80
3360985 CGGTAAAAAA
* * * * * * *
3360995 TTACATAAAACATTATTATTTCTATC-GAAATGTTATTATTGGGCGCTTCACCGGAAATGTTAAC
1 TTACCTAAAACATTATTTTTTATACCGGAAATGTTAATATTGGACGCTTTACCGGAAATGTTAAC
*
3361059 ATATCTGATAAAGTG
66 ATATCTGATAAAGAG
* * * * *
3361074 TTATCTAAAACATTATTGTTTTATACCGGAAATGTTAATATTGAACACTTTACTTGAAAATGTTA
1 TTACCTAAAACATTATT-TTTTATACCGGAAATGTTAATATTGGACGCTTTAC-CGGAAATGTT-
* *
3361139 AAAAACATTAATATTTCTGATAAAAAA
63 ---AAC----ATA--TCTGATAAAGAG
* * * * *
3361166 TTACCTAAAACATTATTATTTATACTGAAAATGTTATTATTGGACGCTTTATCGGAAATGTTTAA
1 TTACCTAAAACATTATTTTTTATACCGGAAATGTTAATATTGGACGCTTTACCGGAAATG-TTAA
* * *
3361231 CATATCCGGTAAAGCG
65 CATATCTGATAAAGAG
* * * *
3361247 CTACCTAAAACATTATTTTTTTTACTGGAAATGTTGATATTGG
1 TTACCTAAAACATTATTTTTTATACCGGAAATGTTAATATTGG
3361290 GAAAATTACC
Statistics
Matches: 166, Mismatches: 36, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
79 15 0.09
80 6 0.04
81 64 0.39
82 8 0.05
83 3 0.02
86 3 0.02
87 3 0.02
90 9 0.05
91 30 0.18
92 25 0.15
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (80 bp):
TTACCTAAAACATTATTTTTTATACCGGAAATGTTAATATTGGACGCTTTACCGGAAATGTTAAC
ATATCTGATAAAGAG
Found at i:3361336 original size:171 final size:170
Alignment explanation
Indices: 3360981--3361337 Score: 454
Period size: 171 Copynumber: 2.1 Consensus size: 170
3360971 AAACATTTGT
* *
3360981 TTTTCGGTAAAAAATTACATAAAACATTATTATTTCTATCGAAATGTTATTATTGGGCGCTTCAC
1 TTTT-GGTAAAAAATTACATAAAACATTATTATTTATATCGAAATGTTATTATTGGACGCTTCAC
* * * *
3361046 CGGAAATGTTAACATATCTGATAAAGTGTTATCTAAAACATTATTGTTTTATACCGGAAATGTTA
65 CGGAAATGTTAACATATCCGATAAAGCGCTACCTAAAACATTATTGTTTTATACCGGAAATGTTA
* * *
3361111 ATATTGAACACTTTACTTGAAAATGTTAAAAAACATTAATA
130 ATATTGAACACATTACTCGAAAATGTTAAAAAACATTAACA
* * *
3361152 TTTCTGATAAAAAATTACCTAAAACATTATTATTTATA-CTGAAAATGTTATTATTGGACGCTTT
1 TTT-TGGTAAAAAATTACATAAAACATTATTATTTATATC-G-AAATGTTATTATTGGACGCTTC
* * * *
3361216 ATCGGAAATGTTTAACATATCCGGTAAAGCGCTACCTAAAACATTATT-TTTTTTACTGGAAATG
63 ACCGGAAATG-TTAACATATCCGATAAAGCGCTACCTAAAACATTATTGTTTTATACCGGAAATG
*
3361280 TTGATATTGGGAA-A-ATTAC-CGAAAATGTTAAAAAACATTAACA
127 TTAATATT--GAACACATTACTCGAAAATGTTAAAAAACATTAACA
3361323 TTTTAGGTAAAAAAT
1 TTTT-GGTAAAAAAT
3361338 AATGTTTTAG
Statistics
Matches: 161, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
170 2 0.01
171 68 0.42
172 55 0.34
173 33 0.20
174 3 0.02
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (170 bp):
TTTTGGTAAAAAATTACATAAAACATTATTATTTATATCGAAATGTTATTATTGGACGCTTCACC
GGAAATGTTAACATATCCGATAAAGCGCTACCTAAAACATTATTGTTTTATACCGGAAATGTTAA
TATTGAACACATTACTCGAAAATGTTAAAAAACATTAACA
Found at i:3361429 original size:21 final size:21
Alignment explanation
Indices: 3361400--3361439 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3361390 GGTAAAAAAT
*
3361400 TACCTAAAACATTATTATTTC
1 TACCGAAAACATTATTATTTC
**
3361421 TACCGAAAATGTTATTATT
1 TACCGAAAACATTATTATT
3361440 GGACGCTTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
TACCGAAAACATTATTATTTC
Found at i:3361570 original size:233 final size:232
Alignment explanation
Indices: 3361129--3362814 Score: 2114
Period size: 234 Copynumber: 7.1 Consensus size: 232
3361119 CACTTTACTT
* * * * *
3361129 GAAAATGTT-AAAAAACATTAATATTTCTGATAAAAAATTACCTAAAACATTATTATTTATACTG
1 GAAAATGTTAAAAAAATATTAACATTTCTGGTAAAAAATTACCTAAAACATTATTATTTCTACCG
* * *
3361193 AAAATGTTATTATTGGACGCTTTATCGGAAATGTTTAACATATCCGGTAAAGCGCTACCTAAAAC
66 AAAATGTTATTATTGGGCGCTTTACCGGAAATG-TTAACATATCCGATAAAGCGCTACCTAAAAC
* * * * * ** *
3361258 ATTATTTTTTTTACTGGAAATGTTGATATTGGGAAAATTACCGAAAATGTTAAAAAACATTAACA
130 ATTATTTTTTCTACCGAAAATGTTAATATTGGGCACTTTACCGGAAATGTTAAAAAACATTAACA
3361323 TTTTAGGT-AAAAAATAATGTTTTAGGTAATTTTTTACC
195 -TTTAGGTAAAAAAATAATGTTTTAGGTAATTTTTTACC
*
3361361 GAAAATGTTAAAAAAATATTAATATTTCTGGTAAAAAATTACCTAAAACATTATTATTTCTACCG
1 GAAAATGTTAAAAAAATATTAACATTTCTGGTAAAAAATTACCTAAAACATTATTATTTCTACCG
* *
3361426 AAAATGTTATTATTGGACGCTTCACCGGAAATGTTAACATATCCGATAAAGCGCTACCTAAAACA
66 AAAATGTTATTATTGGGCGCTTTACCGGAAATGTTAACATATCCGATAAAGCGCTACCTAAAACA
* *
3361491 TTATTATTTT-TACCGAAAATGTTAATATTGGGCACTTTAACGAAAATGTTAAAAAACATTAACA
131 TTATT-TTTTCTACCGAAAATGTTAATATTGGGCACTTTACCGGAAATGTTAAAAAACATTAACA
*
3361555 TTCTAGGTAAAAAAATAATGTTTTAGATAATTTTTTACC
195 TT-TAGGTAAAAAAATAATGTTTTAGGTAATTTTTTACC
* *
3361594 GAAATTGTTAAAAAAATATTAACATTTCCGGTAAAAATAAATTACCTAAAACATTATTATTTCTA
1 GAAAATGTTAAAAAAATATTAACATTTCTGGT--AAA-AAATTACCTAAAACATTATTATTTCTA
* * * *
3361659 TCGGAAATGTTATTATTGGGCGCTTTACCGGAAATGTTTAACATATACGGTAAAGCGCTACCTAA
63 CCGAAAATGTTATTATTGGGCGCTTTACCGGAAATG-TTAACATATCCGATAAAGCGCTACCTAA
*
3361724 AACATTATTTTTTCTACCGAAAATGTTAATATTGGGCACCTTACCGGAAATGTTAAAAAACATTA
127 AACATTATTTTTTCTACCGAAAATGTTAATATTGGGCACTTTACCGGAAATGTTAAAAAACATTA
* *
3361789 ACATTTTAGGTAAAAAAATAATGTTTCAGGTAATTTTTTAAC
192 ACA-TTTAGGTAAAAAAATAATGTTTTAGGTAATTTTTTACC
*
3361831 GAAAATGTT-AAAAAATATTAACATTTCAGGTAAAAACTATTAACATTTCCGGTAAAAAAAATTA
1 GAAAATGTTAAAAAAATATTAACATTTCTGGTAAAAA--ATT---A---CC--------------
* *
3361895 CCTAAAACATTATTATTTCTACCGAAAATGTTATTATTGGGCGTTTTACTGGAAATGTTAACATA
44 --TAAAACATTATTATTTCTACCGAAAATGTTATTATTGGGCGCTTTACCGGAAATGTTAACATA
* * * * **
3361960 TTCAATAAAACGCTACCTAAAACATTATTTTTTCTA-CTAGAAATGTTAATATTGAACACTTTAC
107 TCCGATAAAGCGCTACCTAAAACATTATTTTTTCTACCGA-AAATGTTAATATTGGGCACTTTAC
*
3362024 CGGAATTGTTAAAAAACATTAACATTTCAGGT-AAAAAATAATGTTTTA-GTAATTTTTTACC
171 CGGAAATGTTAAAAAACATTAACATTT-AGGTAAAAAAATAATGTTTTAGGTAATTTTTTACC
* * *
3362085 GAAAATGTTAAAACAATATTGACATTT-TCGGTAAAAAAATTACCTAAAACATTATTATTTCTAT
1 GAAAATGTTAAAAAAATATTAACATTTCT-GGT-AAAAAATTACCTAAAACATTATTATTTCTAC
* * ***
3362149 C-AGAAATATTATTATTGGGCGCTTTACCGGAAATGTTTAACATATCCGGTAAAATACTACCTAA
64 CGA-AAATGTTATTATTGGGCGCTTTACCGGAAATG-TTAACATATCCGATAAAGCGCTACCTAA
*
3362213 AACATTATTTTTTTTCTACCGAAAATGTTAATATTGGGCCCTTTACCGGAAATGTT-AAAAACAT
127 AACATTA--TTTTTTCTACCGAAAATGTTAATATTGGGCACTTTACCGGAAATGTTAAAAAACAT
*
3362277 TAACATTTAAGGT-AAAAATTAATGTTTTAGGTAATTTTTTACC
190 TAACATTT-AGGTAAAAAAATAATGTTTTAGGTAATTTTTTACC
* * *
3362320 GAAAATGTTAAAAAAATATTAACATTTCCGGTAAAAAATTACCTAAATCATTATTATTTCAACCG
1 GAAAATGTTAAAAAAATATTAACATTTCTGGTAAAAAATTACCTAAAACATTATTATTTCTACCG
** ** *
3362385 AAAATGTTATTATTGGGCGCTTTACTAGAAATGTTAACATATTAGATAAAGAGCTACCTAAAACA
66 AAAATGTTATTATTGGGCGCTTTACCGGAAATGTTAACATATCCGATAAAGCGCTACCTAAAACA
* * ** *
3362450 TTATTTTTTCTA-CTAGAAATATTAATATTGGGCACTTTATGGGAATTGTTAAAAAACATTAACA
131 TTATTTTTTCTACCGA-AAATGTTAATATTGGGCACTTTACCGGAAATGTTAAAAAACATTAACA
*
3362514 TTTCAGGTAAAAAAAATAATGTTTTAGGTAATATTTTACC
195 TTT-AGGT-AAAAAAATAATGTTTTAGGTAATTTTTTACC
* *
3362554 GAAAATGTTAAAAAAATATTAACATTTCTGGTAAAAACTTACCTAAAACATTATTATTTCTATCG
1 GAAAATGTTAAAAAAATATTAACATTTCTGGTAAAAAATTACCTAAAACATTATTATTTCTACCG
* * *
3362619 GAAATGTTATTATTAGGCACTTTACCGG--A----AACATATCCGATAAAGCGCTACCTAAAACA
66 AAAATGTTATTATTGGGCGCTTTACCGGAAATGTTAACATATCCGATAAAGCGCTACCTAAAACA
* * * * * *
3362678 TTATTTTTTTCTACCGGAAATATTAATATTTGACACTTTACCAGAAATGTTAAAAAACATTAATA
131 TTA-TTTTTTCTACCGAAAATGTTAATATTGGGCACTTTACCGGAAATGTTAAAAAACATTAACA
3362743 TTTTAGGTAAAAAAAATAATGTTTTAGGTAATTTTTTACC
195 -TTTAGGT-AAAAAAATAATGTTTTAGGTAATTTTTTACC
*
3362783 GAAAATGTT-AAAAAATATTGACATTTCTGGTA
1 GAAAATGTTAAAAAAATATTAACATTTCTGGTA
3362815 GCGTCTTTCC
Statistics
Matches: 1286, Mismatches: 114, Indels: 112
0.85 0.08 0.07
Matches are distributed among these distances:
228 52 0.04
229 94 0.07
230 6 0.00
231 41 0.03
232 167 0.13
233 205 0.16
234 207 0.16
235 87 0.07
236 86 0.07
237 127 0.10
238 3 0.00
241 2 0.00
248 2 0.00
251 1 0.00
254 24 0.02
255 38 0.03
256 93 0.07
257 51 0.04
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (232 bp):
GAAAATGTTAAAAAAATATTAACATTTCTGGTAAAAAATTACCTAAAACATTATTATTTCTACCG
AAAATGTTATTATTGGGCGCTTTACCGGAAATGTTAACATATCCGATAAAGCGCTACCTAAAACA
TTATTTTTTCTACCGAAAATGTTAATATTGGGCACTTTACCGGAAATGTTAAAAAACATTAACAT
TTAGGTAAAAAAATAATGTTTTAGGTAATTTTTTACC
Found at i:3361730 original size:469 final size:468
Alignment explanation
Indices: 3361129--3362814 Score: 2275
Period size: 469 Copynumber: 3.6 Consensus size: 468
3361119 CACTTTACTT
* * * * *
3361129 GAAAATGTT-AAAAAACATTAATATTTCTGAT-AAAAAATTACCTAAAACATTATTATTTATA-C
1 GAAAATGTTAAAAAAATATTAACATTTCCGGTAAAAAAATTACCTAAAACATTATTATTTCTATC
* * *
3361191 TGAAAATGTTATTATTGGACGCTTTATCGGAAATGTTTAACATATCCGGTAAAGCGCTACCTAAA
66 -GGAAATGTTATTATTGGGCGCTTTACCGGAAATGTTTAACATATCCGGTAAAGCGCTACCTAAA
* * * **
3361256 ACATTATTTTTTT-TACTGGAAATGTTGATATTGGGAAAATTACCGAAAATGTTAAAAAACATTA
130 ACATTATTTTTTTCTACCGAAAATGTTAATATTGGGAACTTTACCGAAAATGTTAAAAAACATTA
*
3361320 ACATTTTAGGT-AAAAAATAATGTTTTAGGTAATTTTTTACCGAAAATGTTAAAAAAATATTAAT
195 ACATTTTAGGTAAAAAAATAATGTTTTAGGTAATTTTTTACCGAAAATGTTAAAAAAATATTAAC
* * *
3361384 ATTTCTGGTAAAAAATTACCTAAAACATTATTATTTCTACCGAAAATGTTATTATTGGACGCTTC
260 ATTTCCGGTAAAAAATTACCTAAAACATTATTATTTCTACCGAAAATGTTATTATTGGGCGCTTT
* * *
3361449 ACCGGAAATGTTAACATATCCGATAAAGCGCTACCTAAAACATTATTATTTT-TAC-CGAAAATG
325 ACTGGAAATGTTAACATATTCGATAAAGCGCTACCTAAAACATTATT-TTTTCTACTAG-AAATG
* *
3361512 TTAATATTGGGCACTTTAACGAAAATGTTAAAAAACATTAACA-TTCTAGGTAAAAAAATAATGT
388 TTAATATTGGGCACTTTAACGGAATTGTTAAAAAACATTAACATTTC-AGGTAAAAAAATAATGT
3361576 TTTAGATAATTTTTTACC
452 TTTAG-TAATTTTTTACC
*
3361594 GAAATTGTTAAAAAAATATTAACATTTCCGGTAAAAATAAATTACCTAAAACATTATTATTTCTA
1 GAAAATGTTAAAAAAATATTAACATTTCCGGT-AAAA-AAATTACCTAAAACATTATTATTTCTA
*
3361659 TCGGAAATGTTATTATTGGGCGCTTTACCGGAAATGTTTAACATATACGGTAAAGCGCTACCTAA
64 TCGGAAATGTTATTATTGGGCGCTTTACCGGAAATGTTTAACATATCCGGTAAAGCGCTACCTAA
* * *
3361724 AACATTA-TTTTTTCTACCGAAAATGTTAATATTGGGCACCTTACCGGAAATGTTAAAAAACATT
129 AACATTATTTTTTTCTACCGAAAATGTTAATATTGGGAACTTTACCGAAAATGTTAAAAAACATT
* *
3361788 AACATTTTAGGTAAAAAAATAATGTTTCAGGTAATTTTTTAACGAAAATGTTAAAAAATATTAAC
194 AACATTTTAGGTAAAAAAATAATGTTTTAGGTAATTTTTTACCGAAAATG----------TT---
3361853 ATTTCAGGTAAAAACTATTAACATTTCCGGTAAAAAAAATTACCTAAAACATTATTATTTCTACC
246 A----A---AAAAA-TATTAACATTTCCGGT--AAAAAATTACCTAAAACATTATTATTTCTACC
* * *
3361918 GAAAATGTTATTATTGGGCGTTTTACTGGAAATGTTAACATATTCAATAAAACGCTACCTAAAAC
301 GAAAATGTTATTATTGGGCGCTTTACTGGAAATGTTAACATATTCGATAAAGCGCTACCTAAAAC
** *
3361983 ATTATTTTTTCTACTAGAAATGTTAATATTGAACACTTTACCGGAATTGTTAAAAAACATTAACA
366 ATTATTTTTTCTACTAGAAATGTTAATATTGGGCACTTTAACGGAATTGTTAAAAAACATTAACA
3362048 TTTCAGGT-AAAAAATAATGTTTTAGTAATTTTTTACC
431 TTTCAGGTAAAAAAATAATGTTTTAGTAATTTTTTACC
* * *
3362085 GAAAATGTTAAAACAATATTGACATTTTCGGTAAAAAAATTACCTAAAACATTATTATTTCTATC
1 GAAAATGTTAAAAAAATATTAACATTTCCGGTAAAAAAATTACCTAAAACATTATTATTTCTATC
* * ***
3362150 AGAAATATTATTATTGGGCGCTTTACCGGAAATGTTTAACATATCCGGTAAAATACTACCTAAAA
66 GGAAATGTTATTATTGGGCGCTTTACCGGAAATGTTTAACATATCCGGTAAAGCGCTACCTAAAA
** *
3362215 CATTATTTTTTTTCTACCGAAAATGTTAATATTGGGCCCTTTACCGGAAATGTT-AAAAACATTA
131 CATTA-TTTTTTTCTACCGAAAATGTTAATATTGGGAACTTTACCGAAAATGTTAAAAAACATTA
* *
3362279 ACATTTAAGGT-AAAAATTAATGTTTTAGGTAATTTTTTACCGAAAATGTTAAAAAAATATTAAC
195 ACATTTTAGGTAAAAAAATAATGTTTTAGGTAATTTTTTACCGAAAATGTTAAAAAAATATTAAC
* *
3362343 ATTTCCGGTAAAAAATTACCTAAATCATTATTATTTCAACCGAAAATGTTATTATTGGGCGCTTT
260 ATTTCCGGTAAAAAATTACCTAAAACATTATTATTTCTACCGAAAATGTTATTATTGGGCGCTTT
* * * *
3362408 ACTAGAAATGTTAACATATTAGATAAAGAGCTACCTAAAACATTATTTTTTCTACTAGAAATATT
325 ACTGGAAATGTTAACATATTCGATAAAGCGCTACCTAAAACATTATTTTTTCTACTAGAAATGTT
**
3362473 AATATTGGGCACTTTATGGGAATTGTTAAAAAACATTAACATTTCAGGTAAAAAAAATAATGTTT
390 AATATTGGGCACTTTAACGGAATTGTTAAAAAACATTAACATTTCAGGT-AAAAAAATAATGTTT
*
3362538 TAGGTAATATTTTACC
454 TA-GTAATTTTTTACC
* *
3362554 GAAAATGTTAAAAAAATATTAACATTTCTGGT-AAAAACTTACCTAAAACATTATTATTTCTATC
1 GAAAATGTTAAAAAAATATTAACATTTCCGGTAAAAAAATTACCTAAAACATTATTATTTCTATC
* * *
3362618 GGAAATGTTATTATTAGGCACTTTACCGG--A-----AACATATCCGATAAAGCGCTACCTAAAA
66 GGAAATGTTATTATTGGGCGCTTTACCGGAAATGTTTAACATATCCGGTAAAGCGCTACCTAAAA
* * *
3362676 CATTATTTTTTTCTACCGGAAATATTAATATT-TGACACTTTACC-AGAAATGTTAAAAAACATT
131 CATTATTTTTTTCTACCGAAAATGTTAATATTGGGA-ACTTTACCGA-AAATGTTAAAAAACATT
* *
3362739 AATATTTTAGGTAAAAAAAATAATGTTTTAGGTAATTTTTTACCGAAAATGTT-AAAAAATATTG
194 AACATTTTAGGT-AAAAAAATAATGTTTTAGGTAATTTTTTACCGAAAATGTTAAAAAAATATTA
*
3362803 ACATTTCTGGTA
258 ACATTTCCGGTA
3362815 GCGTCTTTCC
Statistics
Matches: 1090, Mismatches: 88, Indels: 89
0.86 0.07 0.07
Matches are distributed among these distances:
459 1 0.00
460 39 0.04
461 48 0.04
462 21 0.02
463 38 0.03
465 8 0.01
466 176 0.16
468 97 0.09
469 192 0.18
470 36 0.03
472 1 0.00
476 1 0.00
479 2 0.00
480 2 0.00
483 1 0.00
487 1 0.00
489 127 0.12
490 29 0.03
491 99 0.09
492 21 0.02
493 146 0.13
494 4 0.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.36
Consensus pattern (468 bp):
GAAAATGTTAAAAAAATATTAACATTTCCGGTAAAAAAATTACCTAAAACATTATTATTTCTATC
GGAAATGTTATTATTGGGCGCTTTACCGGAAATGTTTAACATATCCGGTAAAGCGCTACCTAAAA
CATTATTTTTTTCTACCGAAAATGTTAATATTGGGAACTTTACCGAAAATGTTAAAAAACATTAA
CATTTTAGGTAAAAAAATAATGTTTTAGGTAATTTTTTACCGAAAATGTTAAAAAAATATTAACA
TTTCCGGTAAAAAATTACCTAAAACATTATTATTTCTACCGAAAATGTTATTATTGGGCGCTTTA
CTGGAAATGTTAACATATTCGATAAAGCGCTACCTAAAACATTATTTTTTCTACTAGAAATGTTA
ATATTGGGCACTTTAACGGAATTGTTAAAAAACATTAACATTTCAGGTAAAAAAATAATGTTTTA
GTAATTTTTTACC
Found at i:3361888 original size:23 final size:22
Alignment explanation
Indices: 3361839--3361894 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
3361829 ACGAAAATGT
3361839 TAAAAAATATTAACATTTCAGG
1 TAAAAAATATTAACATTTCAGG
* *
3361861 TAAAAACTATTAACATTTCCGG
1 TAAAAAATATTAACATTTCAGG
*
3361883 TAAAAAAAATTA
1 TAAAAAATATTA
3361895 CCTAAAACAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.52, C:0.11, G:0.07, T:0.30
Consensus pattern (22 bp):
TAAAAAATATTAACATTTCAGG
Found at i:3361922 original size:21 final size:21
Alignment explanation
Indices: 3361893--3361932 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3361883 TAAAAAAAAT
*
3361893 TACCTAAAACATTATTATTTC
1 TACCGAAAACATTATTATTTC
**
3361914 TACCGAAAATGTTATTATT
1 TACCGAAAACATTATTATT
3361933 GGGCGTTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.42
Consensus pattern (21 bp):
TACCGAAAACATTATTATTTC
Found at i:3362756 original size:22 final size:21
Alignment explanation
Indices: 3362728--3362773 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3362718 CCAGAAATGT
*
3362728 TAAAAAACATTAATATTTTAGG
1 TAAAAAA-AATAATATTTTAGG
*
3362750 TAAAAAAAATAATGTTTTAGG
1 TAAAAAAAATAATATTTTAGG
3362771 TAA
1 TAA
3362774 TTTTTTACCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (21 bp):
TAAAAAAAATAATATTTTAGG
Found at i:3364134 original size:34 final size:33
Alignment explanation
Indices: 3364086--3364183 Score: 101
Period size: 34 Copynumber: 2.9 Consensus size: 33
3364076 AATGAATTTA
*
3364086 ATAGATATTATTTTAATATTTAAATTTAAACAAAT
1 ATAGATA-TCTTTTAATATTTAAATTTAAA-AAAT
* *
3364121 AATA-ATATCTTTTAAT-TTGAAATATTCAAAAGAT
1 -ATAGATATCTTTTAATATTTAAAT-TT-AAAAAAT
*
3364155 ATAGATATCTTTTAATATTTAAACTTAAA
1 ATAGATATCTTTTAATATTTAAATTTAAA
3364184 TAGATATTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
33 12 0.23
34 27 0.51
35 11 0.21
36 3 0.06
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (33 bp):
ATAGATATCTTTTAATATTTAAATTTAAAAAAT
Found at i:3364212 original size:63 final size:63
Alignment explanation
Indices: 3364130--3364252 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
3364120 TAATAATATC
* *
3364130 TTTTAATTTGAAATATTCAAAA-GATATAGA-TATCTTTTAATATTTAAACTTAAATAGATATTA
1 TTTTAATTTAAAATATTCAAAATGATATA-ATTATC-TTTAATATTCAAACTTAAATAGATATTA
* *
3364193 TTTTATTTTAAAATATTCAAAATGATATAATTATCTTTAATATTCAAAGTTAAATAGATA
1 TTTTAATTTAAAATATTCAAAATGATATAATTATCTTTAATATTCAAACTTAAATAGATA
3364253 ATAAATATCG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
63 44 0.81
64 10 0.19
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (63 bp):
TTTTAATTTAAAATATTCAAAATGATATAATTATCTTTAATATTCAAACTTAAATAGATATTA
Found at i:3366953 original size:3 final size:3
Alignment explanation
Indices: 3366947--3366979 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3366937 TTTCTTCTCT
3366947 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
3366980 GAGTGAGGAG
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:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:3381700 original size:143 final size:144
Alignment explanation
Indices: 3381428--3381715 Score: 560
Period size: 143 Copynumber: 2.0 Consensus size: 144
3381418 CAAAGAGTAA
3381428 TTGAAGTTATATATATAAATATTCTATGGTGATAGAGGGACATGTGGTTCAAATTCGATAAAAAA
1 TTGAAGTTATATATATAAATATTCTATGGTGATAGAGGGACATGTGGTTCAAATTCGATAAAAAA
3381493 TAGACTTAAAACGAATGTGGAATTGAAAATAATATATGCAAAACTAAGAAACTAAATTGAAAAAA
66 TAGACTTAAAACGAATGTGGAATTGAAAATAATATATGCAAAACTAAGAAACTAAATTGAAAAAA
3381558 AAAAG-TGAATTTT
131 AAAAGATGAATTTT
3381571 TTGAAGTTATATATATAAATATTCTATGGTGATAGAGGGACATGTGGTTCAAATTCGATAAAAAA
1 TTGAAGTTATATATATAAATATTCTATGGTGATAGAGGGACATGTGGTTCAAATTCGATAAAAAA
3381636 TAGACTTAAAACGAATGTGGAATTGAAAATATATATATGCAAAACTAAGAAACTAAATTGAAAAA
66 TAGACTTAAAACGAATGTGGAATTGAAAATA-ATATATGCAAAACTAAGAAACTAAATTGAAAAA
3381701 AAAAAGATGAATTTT
130 AAAAAGATGAATTTT
3381716 GTTGTCTGAA
Statistics
Matches: 143, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
143 96 0.67
144 39 0.27
145 8 0.06
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.30
Consensus pattern (144 bp):
TTGAAGTTATATATATAAATATTCTATGGTGATAGAGGGACATGTGGTTCAAATTCGATAAAAAA
TAGACTTAAAACGAATGTGGAATTGAAAATAATATATGCAAAACTAAGAAACTAAATTGAAAAAA
AAAAGATGAATTTT
Found at i:3382149 original size:36 final size:36
Alignment explanation
Indices: 3382107--3382183 Score: 136
Period size: 36 Copynumber: 2.1 Consensus size: 36
3382097 TGAAACAAAA
*
3382107 GAAAATAAAATATTGAAATGAATATCAAAATTAATT
1 GAAAATAAAATATTGAAACGAATATCAAAATTAATT
*
3382143 GAAAATAAAATATTGAAACGAATATTAAAATTAATT
1 GAAAATAAAATATTGAAACGAATATCAAAATTAATT
3382179 GAAAA
1 GAAAA
3382184 AGTTCAACGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.60, C:0.03, G:0.09, T:0.29
Consensus pattern (36 bp):
GAAAATAAAATATTGAAACGAATATCAAAATTAATT
Found at i:3382244 original size:12 final size:11
Alignment explanation
Indices: 3382220--3382287 Score: 59
Period size: 11 Copynumber: 6.1 Consensus size: 11
3382210 ACAATACAAT
3382220 TAATATAAATA
1 TAATATAAATA
*
3382231 TAATTATAATTA
1 TAA-TATAAATA
*
3382243 TAATAT-AACA
1 TAATATAAATA
*
3382253 TAACA-AAATAAA
1 TAATATAAAT--A
*
3382265 TAATACAAATA
1 TAATATAAATA
3382276 TAATATAAATA
1 TAATATAAATA
3382287 T
1 T
3382288 TTTAATATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
10 8 0.18
11 18 0.40
12 15 0.33
13 4 0.09
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATATAAATA
Found at i:3383255 original size:21 final size:20
Alignment explanation
Indices: 3383231--3383292 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 20
3383221 GAAAATAAAG
3383231 TAAATAAAACTTAATATCATC
1 TAAAT-AAACTTAATATCATC
*
3383252 TAAAT--A-TT-AT-TCA-G
1 TAAATAAACTTAATATCATC
3383266 TAAATAACACTTAATATCATC
1 TAAATAA-ACTTAATATCATC
3383287 TAAATA
1 TAAATA
3383293 TTTTAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 14
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.16
15 3 0.09
16 2 0.06
17 3 0.09
18 3 0.09
19 2 0.06
20 3 0.09
21 11 0.34
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (20 bp):
TAAATAAACTTAATATCATC
Found at i:3385834 original size:13 final size:13
Alignment explanation
Indices: 3385818--3385859 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
3385808 TTGATCGATT
3385818 TTGACCCGACCCG
1 TTGACCCGACCCG
3385831 TTGACCCGACCC-
1 TTGACCCGACCCG
3385843 --GACCCGACCCG
1 TTGACCCGACCCG
3385854 TTGACC
1 TTGACC
3385860 GTTGATCGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.38
13 16 0.62
ACGTcount: A:0.17, C:0.48, G:0.21, T:0.14
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:3385909 original size:29 final size:29
Alignment explanation
Indices: 3385867--3385972 Score: 160
Period size: 29 Copynumber: 3.7 Consensus size: 29
3385857 ACCGTTGATC
3385867 GGGTGCTATTTTGGGAATTAATTCAAAAT
1 GGGTGCTATTTTGGGAATTAATTCAAAAT
* *
3385896 GGGTGTTATTTTGGGAAATAATTCAAAAT
1 GGGTGCTATTTTGGGAATTAATTCAAAAT
3385925 GGGTGCTATTTTGGGAATTAATTCAAAA-
1 GGGTGCTATTTTGGGAATTAATTCAAAAT
** *
3385953 AAGTGCTATTTTGGTAATTA
1 GGGTGCTATTTTGGGAATTA
3385973 TTAAAAAAAG
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 17 0.24
29 53 0.76
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.39
Consensus pattern (29 bp):
GGGTGCTATTTTGGGAATTAATTCAAAAT
Found at i:3386732 original size:24 final size:24
Alignment explanation
Indices: 3386698--3386818 Score: 134
Period size: 24 Copynumber: 5.0 Consensus size: 24
3386688 TGAATAGTTA
3386698 TCTGATATGATACTTGACCTGAAT
1 TCTGATATGATACTTGACCTGAAT
* * *
3386722 TTTGATATGATACTTGACATGGAT
1 TCTGATATGATACTTGACCTGAAT
* * *
3386746 TCTGATCTGTTACCTGACCTGAAT
1 TCTGATATGATACTTGACCTGAAT
* * *
3386770 TTTGATATGATACTTGACATGGAT
1 TCTGATATGATACTTGACCTGAAT
* * *
3386794 TCTGATATGTTACCTGACCTAAAT
1 TCTGATATGATACTTGACCTGAAT
3386818 T
1 T
3386819 ATGTTTTAAT
Statistics
Matches: 76, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (24 bp):
TCTGATATGATACTTGACCTGAAT
Found at i:3386769 original size:48 final size:48
Alignment explanation
Indices: 3386698--3386818 Score: 206
Period size: 48 Copynumber: 2.5 Consensus size: 48
3386688 TGAATAGTTA
* *
3386698 TCTGATATGATACTTGACCTGAATTTTGATATGATACTTGACATGGAT
1 TCTGATATGTTACCTGACCTGAATTTTGATATGATACTTGACATGGAT
*
3386746 TCTGATCTGTTACCTGACCTGAATTTTGATATGATACTTGACATGGAT
1 TCTGATATGTTACCTGACCTGAATTTTGATATGATACTTGACATGGAT
*
3386794 TCTGATATGTTACCTGACCTAAATT
1 TCTGATATGTTACCTGACCTGAATT
3386819 ATGTTTTAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 68 1.00
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (48 bp):
TCTGATATGTTACCTGACCTGAATTTTGATATGATACTTGACATGGAT
Found at i:3395160 original size:13 final size:13
Alignment explanation
Indices: 3395142--3395166 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3395132 TTGACCAGTT
3395142 TTGACCCGACCCG
1 TTGACCCGACCCG
3395155 TTGACCCGACCC
1 TTGACCCGACCC
3395167 AACCGTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.20, T:0.16
Consensus pattern (13 bp):
TTGACCCGACCCG
Found at i:3395287 original size:29 final size:29
Alignment explanation
Indices: 3395179--3395265 Score: 156
Period size: 29 Copynumber: 3.0 Consensus size: 29
3395169 CCGTTGACCA
* *
3395179 GGTGCTATTTTGGGAATTAATTTGAAATA
1 GGTGCTATTTTGGGAATTAATTCGAAATG
3395208 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
3395237 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
3395266 TGTTTTATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.29, C:0.06, G:0.26, T:0.39
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATG
Found at i:3395302 original size:58 final size:58
Alignment explanation
Indices: 3395179--3395305 Score: 141
Period size: 58 Copynumber: 2.2 Consensus size: 58
3395169 CCGTTGACCA
* ** *
3395179 GGTGCTATTTTGGGAATTAATTTGAAATAGGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATAGGTGCTATTTTGGGAATTAATTAAAAAAG
** ***
3395237 GGTGCTATTTTGGGAATTAATTCGAAAT-GTGTTTTATTTTTTTAATTAATTAAAAAAAG
1 GGTGCTATTTTGGGAATTAATTCGAAATAG-GTGCTATTTTGGGAATTAATT-AAAAAAG
3395296 GG-GCTATTTT
1 GGTGCTATTTT
3395306 AGTAATTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
57 1 0.02
58 51 0.88
59 6 0.10
ACGTcount: A:0.30, C:0.05, G:0.22, T:0.43
Consensus pattern (58 bp):
GGTGCTATTTTGGGAATTAATTCGAAATAGGTGCTATTTTGGGAATTAATTAAAAAAG
Found at i:3395331 original size:28 final size:29
Alignment explanation
Indices: 3395270--3395332 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
3395260 GAAATGTGTT
**
3395270 TTATTTTTTTAATTAATTAAAAAAAGGGG
1 TTATTTTAGTAATTAATTAAAAAAAGGGG
*
3395299 CTATTTTAGTAATT-ATT-AAAAAAGGGTG
1 TTATTTTAGTAATTAATTAAAAAAAGGG-G
3395327 TTATTT
1 TTATTT
3395333 CTGTAAAATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 9 0.31
28 9 0.31
29 11 0.38
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (29 bp):
TTATTTTAGTAATTAATTAAAAAAAGGGG
Found at i:3395338 original size:28 final size:28
Alignment explanation
Indices: 3395274--3395338 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
3395264 TGTGTTTTAT
* *
3395274 TTTTTTAATTAATTAAAAAAAGGGGCTA
1 TTTTGTAATTAATTAAAAAAAGGGGTTA
3395302 TTTTAGTAATT-ATT-AAAAAAGGGTGTTA
1 TTTT-GTAATTAATTAAAAAAAGGG-GTTA
3395330 TTTCTGTAA
1 TTT-TGTAA
3395339 AATGGTTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 9 0.28
28 17 0.53
29 6 0.19
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.43
Consensus pattern (28 bp):
TTTTGTAATTAATTAAAAAAAGGGGTTA
Found at i:3396056 original size:24 final size:24
Alignment explanation
Indices: 3396027--3396147 Score: 134
Period size: 24 Copynumber: 5.0 Consensus size: 24
3396017 TGAATAATTA
3396027 TCTGATATGATACTTGACCTGAAT
1 TCTGATATGATACTTGACCTGAAT
* * *
3396051 TTTGATATGATACTTGACATGGAT
1 TCTGATATGATACTTGACCTGAAT
* * *
3396075 TCTGATCTGTTACCTGACCTGAAT
1 TCTGATATGATACTTGACCTGAAT
* * *
3396099 TTTGATATGATACTTGACATGGAT
1 TCTGATATGATACTTGACCTGAAT
* * *
3396123 TCTGATCTGTTACCTGACCTGAAT
1 TCTGATATGATACTTGACCTGAAT
3396147 T
1 T
3396148 ATGTTTTAAT
Statistics
Matches: 76, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (24 bp):
TCTGATATGATACTTGACCTGAAT
Found at i:3396098 original size:48 final size:48
Alignment explanation
Indices: 3396027--3396147 Score: 215
Period size: 48 Copynumber: 2.5 Consensus size: 48
3396017 TGAATAATTA
* * *
3396027 TCTGATATGATACTTGACCTGAATTTTGATATGATACTTGACATGGAT
1 TCTGATCTGTTACCTGACCTGAATTTTGATATGATACTTGACATGGAT
3396075 TCTGATCTGTTACCTGACCTGAATTTTGATATGATACTTGACATGGAT
1 TCTGATCTGTTACCTGACCTGAATTTTGATATGATACTTGACATGGAT
3396123 TCTGATCTGTTACCTGACCTGAATT
1 TCTGATCTGTTACCTGACCTGAATT
3396148 ATGTTTTAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (48 bp):
TCTGATCTGTTACCTGACCTGAATTTTGATATGATACTTGACATGGAT
Found at i:3397097 original size:6 final size:6
Alignment explanation
Indices: 3397087--3397139 Score: 97
Period size: 6 Copynumber: 8.8 Consensus size: 6
3397077 GGCTTAGATT
*
3397087 CTCTCT CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC
3397135 CTCTC
1 CTCTC
3397140 ATTCTCATTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (6 bp):
CTCTCC
Found at i:3400541 original size:14 final size:14
Alignment explanation
Indices: 3400522--3400561 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3400512 TCAAAAGGTA
3400522 AAATATAATTAAAT
1 AAATATAATTAAAT
3400536 AAATATAATATAAAT
1 AAATATAAT-TAAAT
*
3400551 -AATTTAATTAA
1 AAATATAATTAA
3400562 TTATTTACCC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 3 0.12
14 16 0.67
15 5 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATATAATTAAAT
Found at i:3404963 original size:23 final size:23
Alignment explanation
Indices: 3404932--3405010 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
3404922 CCTGTCTGCC
* * * *
3404932 CGACTTGACTCGTCTACCCAACT
1 CGACCTGACCCGTCTGCCCGACT
*
3404955 CGACCTGACCCGTTTGCCCGACT
1 CGACCTGACCCGTCTGCCCGACT
* *
3404978 CGACCCGACCCATCTGCCCGACT
1 CGACCTGACCCGTCTGCCCGACT
*
3405001 CGACCCGACC
1 CGACCTGACC
3405011 ACTTGGTCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.18, C:0.47, G:0.18, T:0.18
Consensus pattern (23 bp):
CGACCTGACCCGTCTGCCCGACT
Found at i:3405847 original size:49 final size:48
Alignment explanation
Indices: 3405783--3405879 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 48
3405773 TCAGACTTTT
3405783 CGCAAAGCACTTAGGTTAGTCTTTTGCTATGAAAAAAAAATTATTCTAA
1 CGCAAAGCACTTAGGTTAGTCTTTTGCTATG-AAAAAAAATTATTCTAA
3405832 CGCAAAGCACTTAGGTTAGTCTTTTGCTATGAAAAAAAATTATTCTAA
1 CGCAAAGCACTTAGGTTAGTCTTTTGCTATGAAAAAAAATTATTCTAA
3405880 GTCTGGAATG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 17 0.35
49 31 0.65
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (48 bp):
CGCAAAGCACTTAGGTTAGTCTTTTGCTATGAAAAAAAATTATTCTAA
Found at i:3407493 original size:18 final size:20
Alignment explanation
Indices: 3407457--3407493 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3407447 GTACTTATGT
3407457 TTTGTCAAGGCATCAAATTA
1 TTTGTCAAGGCATCAAATTA
3407477 TTTGTCAA-GCA-CAAATT
1 TTTGTCAAGGCATCAAATT
3407494 CTACTTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (20 bp):
TTTGTCAAGGCATCAAATTA
Found at i:3430387 original size:14 final size:15
Alignment explanation
Indices: 3430353--3430393 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
3430343 AGTCCAATCA
3430353 CTGAGTCAACTCAGC
1 CTGAGTCAACTCAGC
* *
3430368 CTGAGTCAAC-CCGT
1 CTGAGTCAACTCAGC
3430382 CTGAGTCAACTC
1 CTGAGTCAACTC
3430394 GATCTAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (15 bp):
CTGAGTCAACTCAGC
Found at i:3432886 original size:24 final size:24
Alignment explanation
Indices: 3432859--3432991 Score: 142
Period size: 24 Copynumber: 5.5 Consensus size: 24
3432849 TATATCAAAA
* * *
3432859 ATCAAATCATAATTCACGTCAAGT
1 ATCAGATCATAATCCAGGTCAAGT
* * *
3432883 ATCATATCAAAATCTAGGTCAAGT
1 ATCAGATCATAATCCAGGTCAAGT
* *
3432907 AACAGATCAGAATCCAGGTCAAGT
1 ATCAGATCATAATCCAGGTCAAGT
*
3432931 ATCAGATCATAATCCATGTC-AGAT
1 ATCAGATCATAATCCAGGTCAAG-T
* * *
3432955 ATCATATCAGAATCCATGTCAAGT
1 ATCAGATCATAATCCAGGTCAAGT
3432979 ATCAGATCATAAT
1 ATCAGATCATAAT
3432992 TCAAATAAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
23 2 0.02
24 87 0.96
25 2 0.02
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.27
Consensus pattern (24 bp):
ATCAGATCATAATCCAGGTCAAGT
Found at i:3433007 original size:72 final size:72
Alignment explanation
Indices: 3432855--3433009 Score: 168
Period size: 72 Copynumber: 2.2 Consensus size: 72
3432845 CGGATATATC
* * *
3432855 AAAAATCAAATCATAATTCACGTCAAGTATCATATCAAAATCTAGGTCAAGTAACAGATCAGAAT
1 AAAAATCAGATCATAATCCACGTCAAGTATCATATCAAAATCCAGGTCAAGTAACAGATCAGAAT
** *
3432920 CCAGGTC
66 CCAAATA
** * * * * *
3432927 AAGTATCAGATCATAATCCATGTC-AGATATCATATCAGAATCCATGTCAAGTATCAGATCATAA
1 AAAAATCAGATCATAATCCACGTCAAG-TATCATATCAAAATCCAGGTCAAGTAACAGATCAGAA
*
3432991 TTCAAATA
65 TCCAAATA
3432999 AAAAATCAGAT
1 AAAAATCAGAT
3433010 AAAATTTTCA
Statistics
Matches: 66, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
71 2 0.03
72 64 0.97
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.26
Consensus pattern (72 bp):
AAAAATCAGATCATAATCCACGTCAAGTATCATATCAAAATCCAGGTCAAGTAACAGATCAGAAT
CCAAATA
Found at i:3439319 original size:21 final size:21
Alignment explanation
Indices: 3439293--3439333 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3439283 AACTGAAATA
3439293 ATAGTGGCAATGCCTTTATTC
1 ATAGTGGCAATGCCTTTATTC
3439314 ATAGTGGCAATGCCTTTATT
1 ATAGTGGCAATGCCTTTATT
3439334 GAATAAAGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (21 bp):
ATAGTGGCAATGCCTTTATTC
Found at i:3441644 original size:2 final size:2
Alignment explanation
Indices: 3441639--3441758 Score: 85
Period size: 2 Copynumber: 62.0 Consensus size: 2
3441629 GAAAAAAATA
*
3441639 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AGT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * * *
3441680 AA ACT AT AT AT AT AA ACT AT AT TT AC AT -T AT AA ACT AT AT A-
1 AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT
*
3441721 AT -T AT -T AT AA AT -T AT AT AT AT AT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3441759 TATTCAAAGT
Statistics
Matches: 92, Mismatches: 14, Indels: 24
0.71 0.11 0.18
Matches are distributed among these distances:
1 8 0.09
2 81 0.88
3 3 0.03
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3441729 original size:9 final size:11
Alignment explanation
Indices: 3441723--3441761 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
3441713 ACTATATAAT
*
3441723 TATTATAAAT-
1 TATTATATATA
3441733 TATATATATATA
1 TAT-TATATATA
3441745 TATTATATATA
1 TATTATATATA
3441756 TATTAT
1 TATTAT
3441762 TCAAAGTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 3 0.12
11 20 0.77
12 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATTATATATA
Found at i:3441751 original size:13 final size:13
Alignment explanation
Indices: 3441639--3441761 Score: 79
Period size: 13 Copynumber: 10.0 Consensus size: 13
3441629 GAAAAAAATA
3441639 ATATATATA-TAT
1 ATATATATATTAT
3441651 ATATATATA-TAT
1 ATATATATATTAT
3441663 A-ATATA-AGTT-T
1 ATATATATA-TTAT
* *
3441674 ATATATAAACTAT
1 ATATATATATTAT
* *
3441687 ATATATAAACTAT
1 ATATATATATTAT
*
3441700 AT-T-TACATTAT
1 ATATATATATTAT
*
3441711 AAACTATATAATTAT
1 ATA-TATAT-ATTAT
3441726 -TATA-A-ATTAT
1 ATATATATATTAT
3441736 ATATATATA-TATT
1 ATATATATATTA-T
3441749 ATATATATATTAT
1 ATATATATATTAT
3441762 TCAAAGTGAG
Statistics
Matches: 91, Mismatches: 6, Indels: 27
0.73 0.05 0.22
Matches are distributed among these distances:
10 6 0.07
11 18 0.20
12 25 0.27
13 32 0.35
14 5 0.05
15 5 0.05
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:3442119 original size:4 final size:4
Alignment explanation
Indices: 3442110--3442160 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
3442100 TTTAATTTTC
* * * *
3442110 TATG TATG TATG TATG TATG CATG TATG CATG TATG CATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
3442158 TAT
1 TAT
3442161 AAACTAGATA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (4 bp):
TATG
Found at i:3442123 original size:8 final size:8
Alignment explanation
Indices: 3442110--3442160 Score: 84
Period size: 8 Copynumber: 6.4 Consensus size: 8
3442100 TTTAATTTTC
*
3442110 TATGTATG
1 TATGCATG
*
3442118 TATGTATG
1 TATGCATG
3442126 TATGCATG
1 TATGCATG
3442134 TATGCATG
1 TATGCATG
3442142 TATGCATG
1 TATGCATG
3442150 TATGCATG
1 TATGCATG
3442158 TAT
1 TAT
3442161 AAACTAGATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 42 1.00
ACGTcount: A:0.25, C:0.08, G:0.24, T:0.43
Consensus pattern (8 bp):
TATGCATG
Found at i:3442437 original size:2 final size:2
Alignment explanation
Indices: 3442387--3442428 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3442377 ATAAACCATG
3442387 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
3442429 AACTATATAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3442527 original size:49 final size:49
Alignment explanation
Indices: 3442426--3442530 Score: 122
Period size: 49 Copynumber: 2.1 Consensus size: 49
3442416 ATATATATAT
* ** ***
3442426 ATAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACACTGTGC
1 ATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACACTAACC
* *
3442475 ATAAACTATATAAAGT-AATAAAGTATATAGTTTATATAAACCCTAAACC
1 ATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACACT-AACC
3442524 ATAAACT
1 ATAAACT
3442531 TACCATAAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
48 23 0.49
49 24 0.51
ACGTcount: A:0.49, C:0.11, G:0.08, T:0.32
Consensus pattern (49 bp):
ATAAACTATATAAAGTAAATAAAGTATATAGTTTATAGAAACACTAACC
Found at i:3442876 original size:15 final size:14
Alignment explanation
Indices: 3442858--3442900 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
3442848 TTAATCATGT
*
3442858 TTTATATAATTTTCA
1 TTTAAATAATTTT-A
3442873 TTTAAATAATTTTA
1 TTTAAATAATTTTA
3442887 -TTAAATAATTTTA
1 TTTAAATAATTTTA
3442900 T
1 T
3442901 ATATTATGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 13 0.50
14 1 0.04
15 12 0.46
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTAAATAATTTTA
Found at i:3442953 original size:19 final size:19
Alignment explanation
Indices: 3442929--3442983 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
3442919 CCATGAATAG
3442929 TATATATAAACTATATATA
1 TATATATAAACTATATATA
3442948 TATATAT-AACATATATATA
1 TATATATAAAC-TATATATA
*
3442967 TATATTTAAACTATATA
1 TATATATAAACTATATA
3442984 AAGTAAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 3 0.09
19 27 0.82
20 3 0.09
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
TATATATAAACTATATATA
Found at i:3442983 original size:2 final size:2
Alignment explanation
Indices: 3442929--3442971 Score: 52
Period size: 2 Copynumber: 21.5 Consensus size: 2
3442919 CCATGAATAG
* *
3442929 TA TA TA TA AA CTA TA TA TA TA TA TA TA -A CA 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
3442971 T
1 T
3442972 TTAAACTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
1 1 0.03
2 34 0.94
3 1 0.03
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:3443020 original size:7 final size:7
Alignment explanation
Indices: 3443010--3443102 Score: 87
Period size: 7 Copynumber: 13.3 Consensus size: 7
3443000 TAGTTTATAG
3443010 AAACCCT
1 AAACCCT
3443017 AAACCCT
1 AAACCCT
*
3443024 AAACCAT
1 AAACCCT
3443031 AAACCCT
1 AAACCCT
* *
3443038 AAATCAT
1 AAACCCT
3443045 AAACCCT
1 AAACCCT
3443052 AAACCCT
1 AAACCCT
**
3443059 AAACTTT
1 AAACCCT
*
3443066 AAACCAT
1 AAACCCT
***
3443073 AAATAAT
1 AAACCCT
*
3443080 AACCCCT
1 AAACCCT
*
3443087 AAACCAT
1 AAACCCT
3443094 AAACCCT
1 AAACCCT
3443101 AA
1 AA
3443103 TATAAATGGA
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 67 1.00
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.18
Consensus pattern (7 bp):
AAACCCT
Found at i:3443036 original size:21 final size:21
Alignment explanation
Indices: 3443010--3443102 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
3443000 TAGTTTATAG
3443010 AAACCCTAAACCCTAAACCAT
1 AAACCCTAAACCCTAAACCAT
* * *
3443031 AAACCCTAAATCATAAACCCT
1 AAACCCTAAACCCTAAACCAT
**
3443052 AAACCCTAAACTTTAAACCAT
1 AAACCCTAAACCCTAAACCAT
*** *
3443073 AAATAATAACCCCTAAACCAT
1 AAACCCTAAACCCTAAACCAT
3443094 AAACCCTAA
1 AAACCCTAA
3443103 TATAAATGGA
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 56 1.00
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.18
Consensus pattern (21 bp):
AAACCCTAAACCCTAAACCAT
Found at i:3443413 original size:536 final size:539
Alignment explanation
Indices: 3442393--3443426 Score: 1501
Period size: 536 Copynumber: 1.9 Consensus size: 539
3442383 CATGTATATA
* *
3442393 TATATATATATATATATATATATATATATATATATAAACTATATAAAGTAAATTACTTATATAGT
1 TATATATATATATATATACATATATATATATATATAAACTATATAAAGTAAATTAATTATATAGT
* * **
3442458 TTATAGAAACACTGTGCATAAACTATATAAAGTAATAAAGTATATAGTTTATATAAACCCTAAAC
66 TTATAGAAACAC---GCATAAAC-ACATAAAGCAATAAACCATATA---TATATAAACCCTAAAC
* *
3442523 CATAAACTTACCATAAATACTAAACCATAAACCATAAACCCTAATATAAATAGACTAGTACTAAT
124 CATAAACTTACCATAAATAATAAACCATAAACCATAAACCCTAATATAAATAGACTAGCACTAAT
* * *
3442588 GCATATATATTTGTAATAAAAGAGTGTGCTTATGTATTGGGCCTATGTAAACTAATATAAATGGA
189 GCATATATATTTGCAATAAAAGAGTGGGCTTATGTATTGGACCTATGTAAACTAATATAAATGGA
* * * * * *
3442653 CTAGTACTATTGGAAATGGACTTATATTTGGGTTTTATTATTACTTATTCATAACAACGAAATAT
254 CTAGCACTAATGCAAATGGACTTATATTTGGATTTTATTATTACTTATTCATAACAACAAAATAA
3442718 ATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAAT
319 ATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAAT
* *
3442783 ACGGCATATACTACTATTTATGAACCATAAAATATGCAATGTGATACTAATTATTGAATACCTAA
384 A-GACATATACTACTATTTATGAACCATAAAATATGCAATGTGATACTAATTATTGAAAACCTAA
*
3442848 TTAATCATGTTTTATATAATTTTCATTTAAATAATTTTATTAAATAATTTTATATATTATGTATG
448 TTAATCATGTTTTATATAATTTACATTTAAATAATTTTATTAAATAATTTTATATATTATGTATG
3442913 CATAAACCATGAATAGTATATATAAAC
513 CATAAACCATGAATAGTATATATAAAC
*
3442940 TATATATATATATATA-ACATATATATATATATTTAAACTATATAAAGTAAATTAATTATATAGT
1 TATATATATATATATATACATATATATATATATATAAACTATATAAAGTAAATTAATTATATAGT
* * * *
3443004 TTATAGAAAC-C-C-TAAAC-CCTAAA-CCATAAACCCTA-A-ATCATAAACCCTAAACCCTAAA
66 TTATAGAAACACGCATAAACACATAAAGCAATAAACCATATATAT-ATAAACCCTAAACCATAAA
* * *
3443062 CTTTAAACCATAAATAATAACCCCTAAACCATAAACCCTAATATAAATGGACTAGCACTAATGCA
130 C-TT--ACCATAAATAATAAACCATAAACCATAAACCCTAATATAAATAGACTAGCACTAATGCA
*
3443127 TATATATTTGCAATAAAAGAGTGGGCTTATGTATTGGACCTATGTAAACTAATGTAAATGGACTA
192 TATATATTTGCAATAAAAGAGTGGGCTTATGTATTGGACCTATGTAAACTAATATAAATGGACTA
* * *
3443192 GCACTAATGCAAATGGACTTATTTTTTGATTTTATTATTACTTATTCATAACAATAAAATAAATG
257 GCACTAATGCAAATGGACTTATATTTGGATTTTATTATTACTTATTCATAACAACAAAATAAATG
* * *
3443257 GGTTGTTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATTAAATTAAT-GA
322 GGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATAGA
* * ** *
3443321 CATGTACTACTATTTATGAACCATATAATATGCAATGTGACATTGTAATTATTTAAAACCTAATT
387 CATATACTACTATTTATGAACCATAAAATATGCAATGTG--ATACTAATTATTGAAAACCTAATT
* *
3443386 AATCATGTTTTATTTAATTTACATTTAAATAGTTTTATTAA
450 AATCATGTTTTATATAATTTACATTTAAATAATTTTATTAA
3443427 TTTTATTAAA
Statistics
Matches: 439, Mismatches: 42, Indels: 23
0.87 0.08 0.05
Matches are distributed among these distances:
532 2 0.00
533 19 0.04
534 40 0.09
536 289 0.66
537 7 0.02
538 4 0.01
540 5 0.01
541 1 0.00
545 1 0.00
546 55 0.13
547 16 0.04
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (539 bp):
TATATATATATATATATACATATATATATATATATAAACTATATAAAGTAAATTAATTATATAGT
TTATAGAAACACGCATAAACACATAAAGCAATAAACCATATATATATAAACCCTAAACCATAAAC
TTACCATAAATAATAAACCATAAACCATAAACCCTAATATAAATAGACTAGCACTAATGCATATA
TATTTGCAATAAAAGAGTGGGCTTATGTATTGGACCTATGTAAACTAATATAAATGGACTAGCAC
TAATGCAAATGGACTTATATTTGGATTTTATTATTACTTATTCATAACAACAAAATAAATGGGCT
ATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATAGACATA
TACTACTATTTATGAACCATAAAATATGCAATGTGATACTAATTATTGAAAACCTAATTAATCAT
GTTTTATATAATTTACATTTAAATAATTTTATTAAATAATTTTATATATTATGTATGCATAAACC
ATGAATAGTATATATAAAC
Found at i:3443438 original size:22 final size:24
Alignment explanation
Indices: 3443392--3443445 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
3443382 AATTAATCAT
3443392 GTTTTATTTAATTTACATTTAAATA
1 GTTTTA-TTAATTTACATTTAAATA
*
3443417 GTTTTATTAATTT-TA-TTAAATA
1 GTTTTATTAATTTACATTTAAATA
*
3443439 ATTTTAT
1 GTTTTAT
3443446 AGAAACCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 13 0.48
23 1 0.04
24 7 0.26
25 6 0.22
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (24 bp):
GTTTTATTAATTTACATTTAAATA
Done.