Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 106 of 198
Found at i:33953832 original size:98 final size:98
Alignment explanation
Indices: 33953662--33953905 Score: 301
Period size: 98 Copynumber: 2.5 Consensus size: 98
33953652 ACTCAATATC
* * * **
33953662 TGAATAAGATGGGCCACTAGTAGGGCATATTAGTTGCTAACCAGATTGGTAGATGTGAAAGACCA
1 TGAATAAGATGGGCCACTGGTAGGGCATGTTAGTTGCTAACTAGATTGACAGATGTGAAAGACCA
* *
33953727 CTGGTAAGGCATGTTAGTTGCTAACCAGATGGG
66 CTAGTAAGACATGTTAGTTGCTAACCAGATGGG
* * **
33953760 TGAATAAAATGGGTCACTGGTAGGGCATGTTAGGTT-CTAACTAGATTGACAGATGTGAAAGATG
1 TGAATAAGATGGGCCACTGGTAGGGCATGTTA-GTTGCTAACTAGATTGACAGATGTGAAAGACC
* *
33953824 ACTAGTAAGACTTGTTAGTTGCTAACTAGATGGG
65 ACTAGTAAGACATGTTAGTTGCTAACCAGATGGG
* * * * * *
33953858 TAAATAAGGTAGACCATTGGTAGGGTATGTTAGTTGCTAACTAGATTG
1 TGAATAAGATGGGCCACTGGTAGGGCATGTTAGTTGCTAACTAGATTG
33953906 GTGTGAGCGC
Statistics
Matches: 123, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
97 3 0.02
98 117 0.95
99 3 0.02
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (98 bp):
TGAATAAGATGGGCCACTGGTAGGGCATGTTAGTTGCTAACTAGATTGACAGATGTGAAAGACCA
CTAGTAAGACATGTTAGTTGCTAACCAGATGGG
Found at i:33962841 original size:23 final size:20
Alignment explanation
Indices: 33962789--33962842 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 20
33962779 TGATCTATAC
33962789 TAATAATAATAAGAAAATAAA
1 TAATAA-AATAAGAAAATAAA
* *
33962810 GAATTAAATCAAGAGAAATCAAA
1 TAATAAAAT-AAGA-AAAT-AAA
33962833 TAATAAAATA
1 TAATAAAATA
33962843 TATATCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
20 3 0.12
21 8 0.31
22 5 0.19
23 10 0.38
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (20 bp):
TAATAAAATAAGAAAATAAA
Found at i:33969646 original size:22 final size:23
Alignment explanation
Indices: 33969614--33969661 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
33969604 GCATATTTCT
* *
33969614 TTTTTATTTTTAGTTTAG-TTTG
1 TTTTTAATTTTAATTTAGTTTTG
*
33969636 TTTTTAATTTTAATTTTGTTTTG
1 TTTTTAATTTTAATTTAGTTTTG
33969659 TTT
1 TTT
33969662 AGTTTGCTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.75
Consensus pattern (23 bp):
TTTTTAATTTTAATTTAGTTTTG
Found at i:33970788 original size:19 final size:19
Alignment explanation
Indices: 33970764--33970802 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
33970754 TTATCTATCG
33970764 TAATA-TAAGATTTGATTAT
1 TAATATTAAGATTT-ATTAT
*
33970783 TAATATTTAGATTTATTAT
1 TAATATTAAGATTTATTAT
33970802 T
1 T
33970803 GTAAAGAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TAATATTAAGATTTATTAT
Found at i:33991198 original size:45 final size:44
Alignment explanation
Indices: 33991029--33991218 Score: 173
Period size: 45 Copynumber: 4.2 Consensus size: 44
33991019 TATGGACTCT
* * * * * * **
33991029 TACATGCGGACTCGTAGAAGAAGATTAATGGATATGGCAGGCTCA
1 TACATGCGAATTCATAGAAGAATATTTATAGATATGG-AGATTCA
* ***
33991074 TACATGCGGATTCATAGAAGAATATTTATAGATACCACAGATTCA
1 TACATGCGAATTCATAGAAGAATATTTATAGATA-TGGAGATTCA
* * *
33991119 TATATGCAAAATCATAGAAGAATATTTATAGATATGGTAGATTCA
1 TACATGCGAATTCATAGAAGAATATTTATAGATATGG-AGATTCA
* * *
33991164 TACATGCGAATTCATAGAAAAATATTCATAGATATAGGGGATTCA
1 TACATGCGAATTCATAGAAGAATATTTATAGATAT-GGAGATTCA
*
33991209 TACATACGAA
1 TACATGCGAA
33991219 CTCTGTTGCA
Statistics
Matches: 118, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
45 116 0.98
46 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (44 bp):
TACATGCGAATTCATAGAAGAATATTTATAGATATGGAGATTCA
Found at i:33998864 original size:13 final size:13
Alignment explanation
Indices: 33998846--33998871 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
33998836 CTATCATCCA
33998846 CTATCTCATAAAT
1 CTATCTCATAAAT
33998859 CTATCTCATAAAT
1 CTATCTCATAAAT
33998872 GGGATATTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
CTATCTCATAAAT
Found at i:34004409 original size:31 final size:29
Alignment explanation
Indices: 34004374--34004432 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
34004364 AGAGGTGGGA
34004374 TGGGAAGG-GAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAGGAGAAT-AAA-TTTT-GGGGAAAAG
*
34004405 TGGGAGGGAGAATAAATTTTGGGGAAAA
1 TGGGAAGGAGAATAAATTTTGGGGAAAA
34004433 ATAAAAGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 8 0.31
30 4 0.15
31 10 0.38
32 4 0.15
ACGTcount: A:0.41, C:0.00, G:0.39, T:0.20
Consensus pattern (29 bp):
TGGGAAGGAGAATAAATTTTGGGGAAAAG
Found at i:34005467 original size:59 final size:60
Alignment explanation
Indices: 34005375--34005501 Score: 220
Period size: 59 Copynumber: 2.1 Consensus size: 60
34005365 AAATGTAGAA
* *
34005375 AAGGGGGGACTTTTGTTTTTTTTTGAAATGGGTATCCAAACCTATTGAAACCTTTGTAAC
1 AAGGGGGGACTTTTGTTTTTTTTTGAAATGGGTATACAAACCGATTGAAACCTTTGTAAC
34005435 AAGGGGGGACTTTTG-TTTTTTTTGAAATGGGTATACAAACCGATTGAAACCTTTGTAAC
1 AAGGGGGGACTTTTGTTTTTTTTTGAAATGGGTATACAAACCGATTGAAACCTTTGTAAC
*
34005494 GAGGGGGG
1 AAGGGGGG
34005502 TTTTTTTTTT
Statistics
Matches: 64, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
59 49 0.77
60 15 0.23
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (60 bp):
AAGGGGGGACTTTTGTTTTTTTTTGAAATGGGTATACAAACCGATTGAAACCTTTGTAAC
Found at i:34006324 original size:18 final size:17
Alignment explanation
Indices: 34006263--34006344 Score: 67
Period size: 18 Copynumber: 4.6 Consensus size: 17
34006253 TTTAGCAATC
34006263 TTATTATTTTGTTTATTA
1 TTATTATTTT-TTTATTA
*** *
34006281 TT-TTAACGTATTATTA
1 TTATTATTTTTTTATTA
*
34006297 TTTATCATTTTTGTTATTA
1 -TTATTATTTTT-TTATTA
*
34006316 TTATTATTTATTTATTTA
1 TTATTATTTTTTTA-TTA
34006334 TTATTATTTTT
1 TTATTATTTTT
34006345 AACTTTAAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
16 6 0.12
17 9 0.19
18 27 0.56
19 6 0.12
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (17 bp):
TTATTATTTTTTTATTA
Found at i:34006351 original size:18 final size:18
Alignment explanation
Indices: 34006313--34006351 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
34006303 ATTTTTGTTA
*
34006313 TTATTATTATTTATTTAT
1 TTATTATTATTTATTAAT
34006331 TTATTATTATTT-TTAACT
1 TTATTATTATTTATTAA-T
34006349 TTA
1 TTA
34006352 AAATTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTATTATTTATTAAT
Found at i:34006478 original size:12 final size:11
Alignment explanation
Indices: 34006461--34006514 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 11
34006451 CACGTATTTT
34006461 TTTATATA-TA
1 TTTATATATTA
34006471 TATT-TATATTA
1 T-TTATATATTA
34006482 TTTTATATATTA
1 -TTTATATATTA
34006494 TTTAT-TATTA
1 TTTATATATTA
34006504 TTT-T-TATTA
1 TTTATATATTA
34006513 TT
1 TT
34006515 CTTATTTTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
9 8 0.20
10 13 0.32
11 11 0.28
12 8 0.20
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATATATTA
Found at i:34006480 original size:22 final size:22
Alignment explanation
Indices: 34006455--34006514 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
34006445 TATATACACG
34006455 TATTTTTTTATATATATATTTA-
1 TATTTTTTTATATAT-TATTTAT
*
34006477 TATTATTTTATATATTATTTAT
1 TATTTTTTTATATATTATTTAT
34006499 TATTATTTTTAT-TATT
1 TATT-TTTTTATATATT
34006515 CTTATTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 6 0.18
22 22 0.65
23 6 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTTTTTATATATTATTTAT
Found at i:34006490 original size:18 final size:19
Alignment explanation
Indices: 34006467--34006502 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
34006457 TTTTTTTATA
34006467 TATATATT-TATATTATTT
1 TATATATTATATATTATTT
*
34006485 TATATATTATTTATTATT
1 TATATATTATATATTATT
34006503 ATTTTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TATATATTATATATTATTT
Found at i:34012260 original size:44 final size:44
Alignment explanation
Indices: 34012192--34012628 Score: 209
Period size: 44 Copynumber: 10.0 Consensus size: 44
34012182 TAGATCGCAT
* * * *
34012192 CAGATTGAGGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCAAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* *
34012236 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCAAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * * * * * *
34012280 CGGATTAAAACCAAG-GATCTTATCTCTCT-AAAGTTACAGTAGAG
1 CAGATT-GAAGCAAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * * * * *
34012324 TAGATTGCA-CCAG--GTCTTATTTCCCTGAGATTACAGTGGAA
1 CAGATTGAAGCAAGTAATCTTATCTCCCTGAGATTACAGTGGAG
** * *
34012365 CAGACCGAAG-AATTTCAGATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCAA-GT-A-ATCTTATCTCCCTGAGATTACAGTGGAG
* ** * *
34012411 TAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTATAGTGGAG
1 CAGATTGAAGCAAGTAATCTTATCTCCCTGAGATTACAGTGGAG
* * * * *
34012455 CGGATTGAAACCAAG-GATCTTATCTCTCTGA-AGTTACAGTAGAG
1 CAGATTG-AAGCAAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG
* * * * * * * * *
34012499 TAGATCGCA-CCAG--GTCTTATTTCCCTAAGATAACAGTGGAA
1 CAGATTGAAGCAAGTAATCTTATCTCCCTGAGATTACAGTGGAG
** * * * **
34012540 CAGACCGAAG-AATTTCAGATCTTATCTCCTTGAG-TTATAGTAAAG
1 CAGATTGAAGCAA-GT-A-ATCTTATCTCCCTGAGATTACAGTGGAG
* * *
34012585 CAGATTGAAGCTACTAATCCTATCTCCCTGA-AGTTACAGTGGAG
1 CAGATTGAAGCAAGTAATCTTATCTCCCTGAGA-TTACAGTGGAG
34012629 TGGAATAAAA
Statistics
Matches: 282, Mismatches: 89, Indels: 44
0.68 0.21 0.11
Matches are distributed among these distances:
41 51 0.18
42 9 0.03
43 18 0.06
44 134 0.48
45 25 0.09
46 45 0.16
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
CAGATTGAAGCAAGTAATCTTATCTCCCTGAGATTACAGTGGAG
Found at i:34012499 original size:175 final size:175
Alignment explanation
Indices: 34012208--34012639 Score: 697
Period size: 175 Copynumber: 2.5 Consensus size: 175
34012198 GAGGCCAGAA
34012208 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
*
34012273 AGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATTGCACCAGG
66 AGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAGG
* *
34012338 TCTTATTTCCCTGAGATTACAGTGGAACAGACCGAAGAATTTCAG
131 TCTTATTTCCCTAAGATAACAGTGGAACAGACCGAAGAATTTCAG
* * *
34012383 ATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTGGTAATCCTATCTCCCTGAGATTAT
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
* *
34012448 AGTGGAGCGGATTGAAACCAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCACCAGG
66 AGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAGG
34012513 TCTTATTTCCCTAAGATAACAGTGGAACAGACCGAAGAATTTCAG
131 TCTTATTTCCCTAAGATAACAGTGGAACAGACCGAAGAATTTCAG
* * *** *
34012558 ATCTTATCTCCTTGAG-TTATAGTAAAGCAGATTGAAGCTACTAATCCTATCTCCCTGA-AGTTA
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGA-TTA
* *
34012621 CAGTGGAGTGGAATAAAAC
65 CAGTGGAGCGGATTAAAAC
34012640 GATGAATCAT
Statistics
Matches: 236, Mismatches: 20, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
173 1 0.00
174 53 0.22
175 182 0.77
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (175 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTAC
AGTGGAGCGGATTAAAACCAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCACCAGG
TCTTATTTCCCTAAGATAACAGTGGAACAGACCGAAGAATTTCAG
Found at i:34014205 original size:3 final size:3
Alignment explanation
Indices: 34014199--34014250 Score: 50
Period size: 3 Copynumber: 16.3 Consensus size: 3
34014189 TATTTTAACG
* * *
34014199 TAT TAT TATT TAT CAT TTT TGT TAT TAT TAT TAT TATT TATT TAT TAT
1 TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT
34014247 TAT T
1 TAT T
34014251 TTTAACTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
3 32 0.76
4 10 0.24
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:34014484 original size:12 final size:13
Alignment explanation
Indices: 34014459--34014496 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
34014449 NNNNNNTATT
34014459 TTATATATTATTTA
1 TTAT-TATTATTTA
34014473 TTATTATT-TTTA
1 TTATTATTATTTA
*
34014485 TTATTCTTATTT
1 TTATTATTATTT
34014497 TCATAACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 11 0.50
13 7 0.32
14 4 0.18
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTATTATTTA
Found at i:34014524 original size:2 final size:2
Alignment explanation
Indices: 34014517--34014545 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34014507 TATACACATT
34014517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34014546 TTCATTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34017453 original size:12 final size:12
Alignment explanation
Indices: 34017435--34017464 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34017425 CCTCACACGC
34017435 CCGTGTGCTAGG
1 CCGTGTGCTAGG
*
34017447 TCGTGTGCTAGG
1 CCGTGTGCTAGG
34017459 CCGTGT
1 CCGTGT
34017465 AACAGCCTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.23, G:0.40, T:0.30
Consensus pattern (12 bp):
CCGTGTGCTAGG
Found at i:34018755 original size:24 final size:25
Alignment explanation
Indices: 34018673--34018783 Score: 104
Period size: 25 Copynumber: 4.5 Consensus size: 25
34018663 ATGAGCTATT
* * *
34018673 AATCGGTATGCTCTCAGGAGTTGTA-
1 AATCGGTAAGCTCTCACGAGCTG-AC
* *
34018698 AATCGATAAGCTCAT-ACGAGCTGAG
1 AATCGGTAAGCTC-TCACGAGCTGAC
34018723 AATCGGTAAGCTCTCACGAGCTG-C
1 AATCGGTAAGCTCTCACGAGCTGAC
*
34018747 AATCGGTAAGCTCTTACGAGCT-AC
1 AATCGGTAAGCTCTCACGAGCTGAC
* *
34018771 TATCAGTAAGCTC
1 AATCGGTAAGCTC
34018784 ATACAACCTG
Statistics
Matches: 73, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
24 35 0.48
25 37 0.51
26 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (25 bp):
AATCGGTAAGCTCTCACGAGCTGAC
Found at i:34020729 original size:21 final size:21
Alignment explanation
Indices: 34020703--34020742 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
34020693 TTACACCACA
34020703 TTGTGGATAAACCACTCATCG
1 TTGTGGATAAACCACTCATCG
34020724 TTGTGGATAAACCACTCAT
1 TTGTGGATAAACCACTCAT
34020743 AATAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (21 bp):
TTGTGGATAAACCACTCATCG
Found at i:34030576 original size:14 final size:14
Alignment explanation
Indices: 34030552--34030593 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
34030542 AATCAAAGTC
*
34030552 AAAAT-AAAAAATG
1 AAAATGAAAAAAGG
34030565 AAAATGAAAAAAGG
1 AAAATGAAAAAAGG
34030579 AAAATGAAAAAAGG
1 AAAATGAAAAAAGG
34030593 A
1 A
34030594 GAGGCCAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATGAAAAAAGG
Found at i:34031387 original size:15 final size:15
Alignment explanation
Indices: 34031367--34031410 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
34031357 TCGAGTCAAA
34031367 AAAAAGTGAAAAATG
1 AAAAAGTGAAAAATG
*
34031382 AAAAAGTG-AAAACG
1 AAAAAGTGAAAAATG
*
34031396 AAAAA-TAAAAAATG
1 AAAAAGTGAAAAATG
34031410 A
1 A
34031411 TGAAAGAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 1 0.04
14 16 0.64
15 8 0.32
ACGTcount: A:0.70, C:0.02, G:0.16, T:0.11
Consensus pattern (15 bp):
AAAAAGTGAAAAATG
Found at i:34033267 original size:31 final size:31
Alignment explanation
Indices: 34033217--34033282 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
34033207 GATCGCATCC
* * * * *
34033217 GATCTTATCTCTCTGAAGTTGCAGTGGAGCA
1 GATCCTATCTCCCTAAAGTTACAGTAGAGCA
*
34033248 GATCCTATCTCCCTAAAGTTACAGTAGAGCG
1 GATCCTATCTCCCTAAAGTTACAGTAGAGCA
34033279 GATC
1 GATC
34033283 AAAATGATGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (31 bp):
GATCCTATCTCCCTAAAGTTACAGTAGAGCA
Found at i:34042127 original size:19 final size:20
Alignment explanation
Indices: 34042071--34042127 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 20
34042061 CTAGATGTAG
34042071 TTTAAAATATTATAAAAA-A
1 TTTAAAATATTATAAAAATA
* *
34042090 TTTAAAATGTTGTAAAAATA
1 TTTAAAATATTATAAAAATA
34042110 -TTATAAAT-TTATAAAAAT
1 TTTA-AAATATTATAAAAAT
34042128 TATCGATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 28 0.85
20 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (20 bp):
TTTAAAATATTATAAAAATA
Found at i:34042354 original size:2 final size:2
Alignment explanation
Indices: 34042347--34042378 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34042337 CAAATTATCA
34042347 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
34042379 TAAGAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34042865 original size:16 final size:16
Alignment explanation
Indices: 34042852--34042886 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
34042842 TCAAATTTGA
34042852 ATTTTCTTATATTTAG
1 ATTTTCTTATATTTAG
* *
34042868 ATTTTCTTAGATTCAG
1 ATTTTCTTATATTTAG
34042884 ATT
1 ATT
34042887 ATTACATGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (16 bp):
ATTTTCTTATATTTAG
Found at i:34068013 original size:104 final size:96
Alignment explanation
Indices: 34067754--34067975 Score: 279
Period size: 93 Copynumber: 2.3 Consensus size: 96
34067744 GATATTTTTA
* * * * * * **
34067754 TTTTTAAGAAAAAATCAATTAAATTAGGGTTTAAGGTTACTTGAGTAATTTAATTA-AAA-AATT
1 TTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTAATTAAATTAATTATAAATTTTT
* * *
34067817 -AAAAATAAAATTCGGGTTTAGAGTTAAGGG
66 AAAAAATTAGATTAGGGTTTAGAGTTAAGGG
*
34067847 TTTTTAAGGAAAAATTAAATAAATTAGGGTTTAGGGTTACTTAATTAAATTAATTATAAATTTTT
1 TTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTAATTAAATTAATTATAAATTTTT
* *
34067912 AAAAAATTAGATTAGGGTTTAGTGTTTAGGG
66 AAAAAATTAGATTAGGGTTTAGAGTTAAGGG
*
34067943 TTTTTAAGTAAAAACTCAAATAAATTAGGGTTT
1 TTTTTAAGGAAAAA-TCAAATAAATTAGGGTTT
34067976 GGGATTTAGG
Statistics
Matches: 109, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
93 49 0.45
94 3 0.03
95 2 0.02
96 38 0.35
97 17 0.16
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.39
Consensus pattern (96 bp):
TTTTTAAGGAAAAATCAAATAAATTAGGGTTTAGGGTTACTTAATTAAATTAATTATAAATTTTT
AAAAAATTAGATTAGGGTTTAGAGTTAAGGG
Found at i:34068239 original size:126 final size:126
Alignment explanation
Indices: 34068014--34068304 Score: 485
Period size: 126 Copynumber: 2.3 Consensus size: 126
34068004 TTGTTAATTT
* * * *
34068014 AAAGAAGCTCCCACGTGGACACGCTTTCGCTACAATAGCTCCTGAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGAC
* *
34068079 GTTTCTGAGTAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCA-ATAGTACTG
66 GTTTCTGAGCAAATAGTATCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGA-AGTACTG
* *
34068140 AAAGAAGCTCCCATGTGGACGCGCTTTTGCTACAGTAGCTCTTAAAAAAATAATTTCGAGTAGAC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGAC
*
34068205 GTTTTTGAGCAAATAGTATCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
66 GTTTCTGAGCAAATAGTATCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
34068266 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGC
1 AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGC
34068305 GCATGTTTGG
Statistics
Matches: 154, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
126 153 0.99
127 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (126 bp):
AAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTAAAAAAATAATTTCGAGTAGAC
GTTTCTGAGCAAATAGTATCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTG
Found at i:34072027 original size:18 final size:18
Alignment explanation
Indices: 34072000--34072037 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
34071990 GAAAAAGAAA
* *
34072000 ACATATAAGGGTTAGGAT
1 ACATAAAAGGGCTAGGAT
34072018 ACATAAAAGGGCTAGGAT
1 ACATAAAAGGGCTAGGAT
34072036 AC
1 AC
34072038 GCACCTGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (18 bp):
ACATAAAAGGGCTAGGAT
Found at i:34072162 original size:30 final size:30
Alignment explanation
Indices: 34072110--34072171 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
34072100 TGACTGTGTC
* * *
34072110 GGTGCTGTTGCTGAGCCTGGTGATTGTATG
1 GGTGCTGATGATGAGCCGGGTGATTGTATG
* *
34072140 GGTGCTGATGATGGGCCGGGTGATTGTCTG
1 GGTGCTGATGATGAGCCGGGTGATTGTATG
34072170 GG
1 GG
34072172 CCACGTTGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.10, C:0.13, G:0.45, T:0.32
Consensus pattern (30 bp):
GGTGCTGATGATGAGCCGGGTGATTGTATG
Found at i:34072695 original size:7 final size:7
Alignment explanation
Indices: 34072685--34072724 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
34072675 TTATATACAT
34072685 AATACTA
1 AATACTA
34072692 AATACTA
1 AATACTA
34072699 AATACTA
1 AATACTA
34072706 AATACTA
1 AATACTA
34072713 AATACTA
1 AATACTA
34072720 AATAC
1 AATAC
34072725 CAATTGACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:34073869 original size:27 final size:29
Alignment explanation
Indices: 34073832--34073892 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
34073822 TTTAAAAAAA
*
34073832 TTAAAAATAA-T-AAAATTTAAAACTTTT
1 TTAAAAATAATTAAAAAATTAAAACTTTT
* *
34073859 TTAAAAGTAATTAAAAAATTAAAGCTTTT
1 TTAAAAATAATTAAAAAATTAAAACTTTT
34073888 TTAAA
1 TTAAA
34073893 TAGGAATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 9 0.31
28 1 0.03
29 19 0.66
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (29 bp):
TTAAAAATAATTAAAAAATTAAAACTTTT
Found at i:34073908 original size:11 final size:11
Alignment explanation
Indices: 34073894--34073925 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
34073884 TTTTTTAAAT
34073894 AGGAATTTGAG
1 AGGAATTTGAG
34073905 AGGAATTTGAG
1 AGGAATTTGAG
34073916 AGGAATTTGA
1 AGGAATTTGA
34073926 TAGAATATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (11 bp):
AGGAATTTGAG
Found at i:34073919 original size:22 final size:22
Alignment explanation
Indices: 34073894--34073949 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
34073884 TTTTTTAAAT
34073894 AGGAATTTGAGAGGAAT-TTGAG
1 AGGAATTTGAGAGGAATATT-AG
*
34073916 AGGAATTTGATA-GAATATTAG
1 AGGAATTTGAGAGGAATATTAG
34073937 AGAGAA-TTGAGAG
1 AG-GAATTTGAGAG
34073950 AAAGCATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.27
Consensus pattern (22 bp):
AGGAATTTGAGAGGAATATTAG
Found at i:34079286 original size:52 final size:51
Alignment explanation
Indices: 34079161--34079287 Score: 150
Period size: 52 Copynumber: 2.4 Consensus size: 51
34079151 TTGAATTTTA
* * *
34079161 AAAACTCTTTTAAATAATAATTTAAATTCTATTTAATTATCTTTTTATTTTTT
1 AAAACTCTTTTAAATAATAATTTAAATTATATTTAATTATCTATTTA--TTCT
* *
34079214 GAAACTCTTTTAAATAATAATAATTAAATTATGTTTTAATTAT-TATTTA-TCT
1 AAAACTCTTTTAAATAATAAT--TTAAATTAT-ATTTAATTATCTATTTATTCT
34079266 AAAACTCTTTTAAATAATAATT
1 AAAACTCTTTTAAATAATAATT
34079288 ATATCTAAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
50 1 0.02
52 22 0.34
53 20 0.31
55 13 0.20
56 9 0.14
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (51 bp):
AAAACTCTTTTAAATAATAATTTAAATTATATTTAATTATCTATTTATTCT
Found at i:34079298 original size:28 final size:28
Alignment explanation
Indices: 34079215--34079316 Score: 117
Period size: 28 Copynumber: 3.8 Consensus size: 28
34079205 TTATTTTTTG
34079215 AAACTCTTTTAAATAATAA-TA-AT-TA
1 AAACTCTTTTAAATAATAATTATATCTA
* * *
34079240 AATTA-TGTTTT-AATTATTATT-TATCTA
1 AA--ACTCTTTTAAATAATAATTATATCTA
34079267 AAACTCTTTTAAATAATAATTATATCTA
1 AAACTCTTTTAAATAATAATTATATCTA
34079295 AAACTCTTTTAAATAATAATTA
1 AAACTCTTTTAAATAATAATTA
34079317 AATTCTATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
25 9 0.14
26 13 0.21
27 13 0.21
28 28 0.44
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (28 bp):
AAACTCTTTTAAATAATAATTATATCTA
Found at i:34079474 original size:95 final size:94
Alignment explanation
Indices: 34079295--34079476 Score: 246
Period size: 95 Copynumber: 1.9 Consensus size: 94
34079285 ATTATATCTA
* * *
34079295 AAACTCTTTTAAATAATAATTAAATTCTATTTCTTTTATCTGATAAGAAATGTATCAAATCCTTT
1 AAACTCTTTTAAATAATAATTAAATTATATTTCTCTTATCTGATAAGAAATATATCAAATCCTTT
* *
34079360 TGATTTTGAATTTTAATTATTATTTATTTG
66 T-ATTATCAATTTTAATTATTATTTATTTG
34079390 AAACTCTTTTAAATAATAATTAAATTATATTT-TCTTATCTGATAATG-AATATATCAAATCCTA
1 AAACTCTTTTAAATAATAATTAAATTATATTTCTCTTATCTGATAA-GAAATATATCAAATCCT-
**
34079453 TTT-TTATCTCTTTT-ATTATTATTT
64 TTTATTATCAATTTTAATTATTATTT
34079477 TCGAATTTAA
Statistics
Matches: 78, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
92 10 0.13
93 7 0.09
94 26 0.33
95 35 0.45
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.51
Consensus pattern (94 bp):
AAACTCTTTTAAATAATAATTAAATTATATTTCTCTTATCTGATAAGAAATATATCAAATCCTTT
TATTATCAATTTTAATTATTATTTATTTG
Found at i:34090557 original size:13 final size:12
Alignment explanation
Indices: 34090540--34090581 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
34090530 GTGTTGTCGA
34090540 AAAATACTTTTG
1 AAAATACTTTTG
34090552 AGAAATACTTTTG
1 A-AAATACTTTTG
*
34090565 AAAAGTGCTTTTG
1 AAAA-TACTTTTG
34090578 AAAA
1 AAAA
34090582 ATTTGAGTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 4 0.15
13 23 0.85
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (12 bp):
AAAATACTTTTG
Found at i:34096888 original size:25 final size:23
Alignment explanation
Indices: 34096849--34096895 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
34096839 TTGATTGAGA
*
34096849 AATTTATAGATTTTCATTATTTT
1 AATTTATAGATTTTCATAATTTT
34096872 AATTTAATAGAATTTTCATAATTT
1 AATTT-ATAG-ATTTTCATAATTT
34096896 GCTTTGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 4 0.19
25 12 0.57
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.55
Consensus pattern (23 bp):
AATTTATAGATTTTCATAATTTT
Found at i:34098541 original size:2 final size:2
Alignment explanation
Indices: 34098529--34098572 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
34098519 ATAAGAAATC
34098529 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34098570 AT A
1 AT A
34098573 ATAAATAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34102062 original size:101 final size:101
Alignment explanation
Indices: 34101882--34102121 Score: 417
Period size: 101 Copynumber: 2.4 Consensus size: 101
34101872 AATTCGTCCT
* *
34101882 TTACATTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAACCCAGCTATGGT
*
34101947 CTTACATATAAACACTGTCATGGTCCAACCATGGTC
66 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
* * * *
34101983 TTACGTTCATAGTGCTAGAACTCAGTTATGGTCTTATCATCAGAATGCCATAACCTAGCTATGGT
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAACCCAGCTATGGT
34102048 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
66 CTTACATATAAACACTGCCATGGTCCAACCATGGTC
34102084 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATC
34102122 CGTCAATTCA
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 129 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (101 bp):
TTACGTTCATAGTGCCATAACCCAGTTATGGTCTTATCATCAGAATGCCATAACCCAGCTATGGT
CTTACATATAAACACTGCCATGGTCCAACCATGGTC
Found at i:34102115 original size:33 final size:33
Alignment explanation
Indices: 34101882--34102119 Score: 129
Period size: 33 Copynumber: 7.1 Consensus size: 33
34101872 AATTCGTCCT
*
34101882 TTACATTCATAGTGCCATAACCCAGTTATGGTC
1 TTACATTCATAGTGCCATAACCCAGCTATGGTC
* * *
34101915 TTATCA-TCAGAATGCCATAGCCCAGCTATGGTC
1 TTA-CATTCATAGTGCCATAACCCAGCTATGGTC
* * * * *** * *
34101948 TTACATATAAACACTGTCATGGTCCAACCATGGTC
1 TTACAT-T-CATAGTGCCATAACCCAGCTATGGTC
* * * * *
34101983 TTACGTTCATAGTGCTAGAACTCAGTTATGGTC
1 TTACATTCATAGTGCCATAACCCAGCTATGGTC
* * *
34102016 TTATCA-TCAGAATGCCATAACCTAGCTATGGTC
1 TTA-CATTCATAGTGCCATAACCCAGCTATGGTC
* * * *** * *
34102049 TTACATATAAACACTGCCATGGTCCAACCATGGTC
1 TTACAT-T-CATAGTGCCATAACCCAGCTATGGTC
* *
34102084 TTACGTTCATAGTGCCATAACCCAGTTATGGTC
1 TTACATTCATAGTGCCATAACCCAGCTATGGTC
34102117 TTA
1 TTA
34102120 TCCGTCAATT
Statistics
Matches: 144, Mismatches: 53, Indels: 16
0.68 0.25 0.08
Matches are distributed among these distances:
32 4 0.03
33 88 0.61
34 7 0.05
35 45 0.31
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (33 bp):
TTACATTCATAGTGCCATAACCCAGCTATGGTC
Found at i:34102997 original size:19 final size:20
Alignment explanation
Indices: 34102959--34102997 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
34102949 AGAAATTCTA
*
34102959 TTAAATTCAATTTGTCTTAT
1 TTAAATTCAATTTATCTTAT
*
34102979 TTAATTTCAATTTAT-TTAT
1 TTAAATTCAATTTATCTTAT
34102998 CATTTTGCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.59
Consensus pattern (20 bp):
TTAAATTCAATTTATCTTAT
Found at i:34112614 original size:2 final size:2
Alignment explanation
Indices: 34112607--34112631 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34112597 CGAATATGTT
34112607 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
34112632 TTATCTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34117685 original size:38 final size:38
Alignment explanation
Indices: 34117599--34117677 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 38
34117589 CAGATCCAAT
*
34117599 TCAAAAA-AAAAAGAAGAAAAAAATCAAAAAATCAAAA
1 TCAAAAACAAAAAGAAGAAAAAAATAAAAAAATCAAAA
34117636 TCAAAAACAAAAAGAAGAAAAAAA-AAGAAAAATCAAAA
1 TCAAAAACAAAAAGAAGAAAAAAATAA-AAAAATCAAAA
34117674 TCAA
1 TCAA
34117678 GGTCAAAATG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
37 8 0.21
38 31 0.79
ACGTcount: A:0.77, C:0.09, G:0.06, T:0.08
Consensus pattern (38 bp):
TCAAAAACAAAAAGAAGAAAAAAATAAAAAAATCAAAA
Found at i:34120062 original size:87 final size:87
Alignment explanation
Indices: 34119916--34120193 Score: 398
Period size: 87 Copynumber: 3.2 Consensus size: 87
34119906 CAAACCAGTG
* * * *
34119916 AAGATAGCAGATCTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAAATAAAGCCTTGCCTCCA
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACACAGCCTTGCCTCCC
*
34119981 TCGGTTGCAGTGGAGCTGGTTA
66 TCGGTTGCAGTGGAGCAGGTTA
*
34120003 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAAACACAGCCTTGCCTCCC
1 AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACACAGCCTTGCCTCCC
* *
34120068 CCGGTTGCAGTGAAGCAGGTTA
66 TCGGTTGCAGTGGAGCAGGTTA
* *
34120090 AAGATAGCAGATCTTGCCTTCCTGCGA-TAACAGCGAAGCAGATCGAAGATAC-CAGCCTTACCT
1 AAGATAGCAGATCTTGCCTTCCTGC-ATTGACAGCGAAGCAGATCGAA-A-ACACAGCCTTGCCT
* *
34120153 CCCTCGATTGCGGTGGAGCAGGTTA
63 CCCTCGGTTGCAGTGGAGCAGGTTA
*
34120178 AAGATAGTAGATCTTG
1 AAGATAGCAGATCTTG
34120194 TCCCTAAGCA
Statistics
Matches: 172, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
87 122 0.71
88 48 0.28
89 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (87 bp):
AAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACACAGCCTTGCCTCCC
TCGGTTGCAGTGGAGCAGGTTA
Found at i:34120064 original size:43 final size:43
Alignment explanation
Indices: 34119928--34120148 Score: 116
Period size: 45 Copynumber: 5.1 Consensus size: 43
34119918 GATAGCAGAT
* * *
34119928 CTTGCCTTTCTGCATTGACAGCGAAGCAGATCGAAAATAAAGC
1 CTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAAATACAGC
* * * * * *
34119971 CTTGCC-TCCAT-CGGTTG-CAGTGGAGCTGGT-TAAAGATAGCAGAT
1 CTTGCCTTCC-TGC-ATTGACAGTGAAGCAGATCGAAA-ATA-CAG-C
*
34120015 CTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAAACACAGC
1 CTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAAATACAGC
** * * * *
34120058 CTTGCC-TCCCCCGGTTG-CAGTGAAGCAGGT-TAAAGATAGCAGAT
1 CTTGCCTTCCTGC-ATTGACAGTGAAGCAGATCGAAA-ATA-CAG-C
* * *
34120102 CTTGCCTTCCTGCGA-TAACAGCGAAGCAGATCGAAGATACCAGC
1 CTTGCCTTCCTGC-ATTGACAGTGAAGCAGATCGAAAATA-CAGC
34120146 CTT
1 CTT
34120149 ACCTCCCTCG
Statistics
Matches: 129, Mismatches: 33, Indels: 31
0.67 0.17 0.16
Matches are distributed among these distances:
41 6 0.05
42 33 0.26
43 24 0.19
44 23 0.18
45 38 0.29
46 5 0.04
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (43 bp):
CTTGCCTTCCTGCATTGACAGTGAAGCAGATCGAAAATACAGC
Found at i:34120139 original size:45 final size:45
Alignment explanation
Indices: 34120003--34120140 Score: 122
Period size: 45 Copynumber: 3.1 Consensus size: 45
34119993 GAGCTGGTTA
*
34120003 AAGATAGCAGATCTTGCCTTCCTGC-ATTGACAGTGAAGCAGATCG
1 AAGATAGCAGATCTTGCCTTCCTGCGA-TAACAGTGAAGCAGATCG
* * * ** * ** * **
34120048 AAAACA-CAG-CCTTGCC-TCCCCCGGTTGCAGTGAAGCAGGTTA
1 AAGATAGCAGATCTTGCCTTCCTGCGATAACAGTGAAGCAGATCG
*
34120090 AAGATAGCAGATCTTGCCTTCCTGCGATAACAGCGAAGCAGATCG
1 AAGATAGCAGATCTTGCCTTCCTGCGATAACAGTGAAGCAGATCG
34120135 AAGATA
1 AAGATA
34120141 CCAGCCTTAC
Statistics
Matches: 66, Mismatches: 23, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
42 21 0.32
43 9 0.14
44 9 0.14
45 27 0.41
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (45 bp):
AAGATAGCAGATCTTGCCTTCCTGCGATAACAGTGAAGCAGATCG
Found at i:34120638 original size:44 final size:44
Alignment explanation
Indices: 34120530--34120691 Score: 125
Period size: 44 Copynumber: 3.7 Consensus size: 44
34120520 AAGCAGGTCT
*
34120530 TATC-CCCTGAAGTTGCAGT-GAGGCAGATCGAAGAAGTAAATCT
1 TATCTCCCTGAAGTTGCAGTGGA-GCAGATCGAAGAAGTAAATCC
* * * **
34120573 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCG-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGAAGTA-AATCC
* ** ** * *
34120617 TATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAGTAA-TAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAG-AAGTAAATCC
* * *
34120661 TATCTCTCTGAAGTTGCAATAGAGCAGATCG
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATCG
34120692 CATCAAGTCT
Statistics
Matches: 90, Mismatches: 24, Indels: 9
0.73 0.20 0.07
Matches are distributed among these distances:
43 5 0.06
44 82 0.91
45 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATCGAAGAAGTAAATCC
Found at i:34122382 original size:2 final size:2
Alignment explanation
Indices: 34122375--34122405 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
34122365 CGAATATGTT
34122375 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34122406 TATCCTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34126601 original size:110 final size:111
Alignment explanation
Indices: 34126297--34126641 Score: 515
Period size: 106 Copynumber: 3.2 Consensus size: 111
34126287 GAAAAATTAA
* * * *
34126297 TTTTTTTTT-ACTTTTTTCGTATACTAATACCTGCTATTGACACGAAAAAAGTAAAAAAAAAATT
1 TTTTTTTTTAACTTTTTTAGTATACTGATACCTTCTTTTGACACGAAAAAAGTAAAAAAAAAATT
*
34126361 CCCACAAAAAAGGTGGTGCCTGCCATTGGCAGGCCACCA-C--AA-
66 CCCACAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAT
* * *
34126403 TTTTTTTTTAA-TTTTTTAGTATATTGATACATTCTTTTGACACGAAAAATGTAAAAAAAAAATT
1 TTTTTTTTTAACTTTTTTAGTATACTGATACCTTCTTTTGACACGAAAAAAGTAAAAAAAAAATT
34126467 CCCACAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAT
66 CCCACAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAT
*
34126513 TTTTTTTTTAACTTTTTTAGTATACTGATACCTTCTTTTGACATGAAAAAAGTAAAAAAAAAATT
1 TTTTTTTTTAACTTTTTTAGTATACTGATACCTTCTTTTGACACGAAAAAAGTAAAAAAAAAATT
**
34126578 ATCAC-AAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAATT
66 CCCACAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAA-T
*
34126624 TTCTTTTTTTTACTTTTT
1 TT-TTTTTTTAACTTTTT
34126642 CTCTTATTCT
Statistics
Matches: 216, Mismatches: 15, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
106 93 0.43
107 2 0.01
109 2 0.01
110 50 0.23
111 55 0.25
112 14 0.06
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (111 bp):
TTTTTTTTTAACTTTTTTAGTATACTGATACCTTCTTTTGACACGAAAAAAGTAAAAAAAAAATT
CCCACAAAAAAGGTGGTGCCGGCCATTGGCAGGCCACCACCAAAAT
Found at i:34127183 original size:19 final size:19
Alignment explanation
Indices: 34127161--34127217 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
34127151 TTTTATTTAA
34127161 TTTTTCTAAATTTATAAAT
1 TTTTTCTAAATTTATAAAT
* ** *
34127180 TTTTTTTATTTTTATCAAT
1 TTTTTCTAAATTTATAAAT
* *
34127199 TTTTCTCAAAATTGATAAA
1 TTTT-TCTAAATTTATAAA
34127218 AAATTAAATT
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTCTAAATTTATAAAT
Found at i:34127199 original size:27 final size:28
Alignment explanation
Indices: 34127142--34127201 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
34127132 TTAAAAAATT
* *
34127142 ATTTTAACTTTTTATTTAATTTTTCTAA
1 ATTTTAAATTTTTATTTAATTTTTATAA
*
34127170 ATTTATAAATTTTT-TTT-ATTTTTATCA
1 ATTT-TAAATTTTTATTTAATTTTTATAA
34127197 ATTTT
1 ATTTT
34127202 TCTCAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 1 0.04
27 12 0.43
28 7 0.25
29 8 0.29
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (28 bp):
ATTTTAAATTTTTATTTAATTTTTATAA
Found at i:34128119 original size:28 final size:28
Alignment explanation
Indices: 34128065--34128119 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
34128055 ACAAAAAATT
* **
34128065 AAATTAAGAAGTAAAATAATTTTTTATA
1 AAATTAAGAAGTAAAATAAATCATTATA
34128093 AAATT-AGAATGTAAAATAAATCATTAT
1 AAATTAAGAA-GTAAAATAAATCATTAT
34128120 TATTTGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (28 bp):
AAATTAAGAAGTAAAATAAATCATTATA
Found at i:34134845 original size:46 final size:46
Alignment explanation
Indices: 34134778--34134954 Score: 264
Period size: 46 Copynumber: 3.8 Consensus size: 46
34134768 AGTGTGGAAC
*
34134778 GTAGGTTTGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
34134824 GTAGGTATGGTATTTCAGTAAAGAAAACCATATTGAGTTGTGAGAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* * * * *
34134870 GTAGGTATGGTATTTTACTAACGAAAACCGTACTGAGTTGCGAAAA
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
* *
34134916 GTAGATATGGTATTTCAGTGAAGAAAACCATACTGAGTT
1 GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
34134955 ATACCATTGT
Statistics
Matches: 115, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 115 1.00
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAA
Found at i:34139738 original size:25 final size:25
Alignment explanation
Indices: 34139684--34139763 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
34139674 AGATTACTTG
*
34139684 GAAAGACTTTGTGGC-TAATCT-TATA
1 GAAAGCCTTTGTGGCGT-AT-TATATA
* *
34139709 AAAAGCCTTTGTGGCGTATTATCTA
1 GAAAGCCTTTGTGGCGTATTATATA
* *
34139734 GAAAGCCTTTGTGGTGTATTGTATA
1 GAAAGCCTTTGTGGCGTATTATATA
34139759 GAAAG
1 GAAAG
34139764 ACTGTATGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 1 0.02
25 44 0.96
26 1 0.02
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (25 bp):
GAAAGCCTTTGTGGCGTATTATATA
Found at i:34142150 original size:94 final size:92
Alignment explanation
Indices: 34141987--34142213 Score: 330
Period size: 94 Copynumber: 2.4 Consensus size: 92
34141977 AGGTGTAAAT
* *
34141987 AGCCCTCAAACTTTTTAAAAGCAAAAAGCAATTAAGCCCTTGCTCTTTTTTTTTGCACTCAATTG
1 AGCCCTCAAACTTTTT-CAA--AAAAAGCAATTAAGCCCCTGCTCTTTTTTTTTGCACTCAATTG
34142052 GGTACATGAACTT-TCAAAATGCATAAAAAA
63 GGTACATGAA-TTGTCAAAATGCATAAAAAA
*
34142082 GGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTGCTTTTTTTTTTGCACTCAATTGG
1 AGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCT-C-TTTTTTTTTGCACTCAATTGG
*
34142147 GTACTTGAATTGTCAAAATGCATAAAAAA
64 GTACATGAATTGTCAAAATGCATAAAAAA
* **
34142176 AACCCTCAAAAATTTTCAAAAAAAGCAATTAAGCCCCT
1 AGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCT
34142214 ATTTTTTTTG
Statistics
Matches: 121, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
92 21 0.17
93 3 0.02
94 82 0.68
95 15 0.12
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.30
Consensus pattern (92 bp):
AGCCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTCTTTTTTTTTGCACTCAATTGGGT
ACATGAATTGTCAAAATGCATAAAAAA
Found at i:34142397 original size:27 final size:29
Alignment explanation
Indices: 34142358--34142429 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
34142348 ACATGTGATA
34142358 AAAAATTAT-AAAAAATA-AAA-ATCAAT
1 AAAAATTATAAAAAAATATAAACATCAAT
* *
34142384 AAAAATTATAAAAAAATATTAAACTTTAAT
1 AAAAATTATAAAAAAATA-TAAACATCAAT
34142414 AAAAA-TATAAAAAAAT
1 AAAAATTATAAAAAAAT
34142430 TATTTAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.22
27 8 0.20
29 14 0.35
30 9 0.22
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (29 bp):
AAAAATTATAAAAAAATATAAACATCAAT
Found at i:34142785 original size:40 final size:39
Alignment explanation
Indices: 34142741--34142825 Score: 95
Period size: 40 Copynumber: 2.2 Consensus size: 39
34142731 CTCTTTACCT
34142741 TTTTTAATCAT-TTTCT-TATGAATTTATAAATTTTTATA-TA
1 TTTTTAAT-ATATTTCTATAT-AATTTAT-AATTTTT-TACTA
* *
34142781 TTTTTTATATATTTCTATATATTTTATAATTTTTTACTA
1 TTTTTAATATATTTCTATATAATTTATAATTTTTTACTA
34142820 TTTTTA
1 TTTTTA
34142826 TAAAATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
38 2 0.05
39 16 0.41
40 18 0.46
41 3 0.08
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (39 bp):
TTTTTAATATATTTCTATATAATTTATAATTTTTTACTA
Found at i:34142787 original size:11 final size:10
Alignment explanation
Indices: 34142763--34142866 Score: 74
Period size: 10 Copynumber: 10.6 Consensus size: 10
34142753 TTCTTATGAA
*
34142763 TTTATAAATT
1 TTTATATATT
34142773 TTTATATATTT
1 TTTATATA-TT
34142784 TTTATATATT
1 TTTATATATT
*
34142794 TCTATATA-T
1 TTTATATATT
34142803 TTTATA-ATT
1 TTTATATATT
34142812 TTT-TACTATT
1 TTTATA-TATT
* *
34142822 TTTATAAAAT
1 TTTATATATT
* *
34142832 TTTACA-ACT
1 TTTATATATT
34142841 TTTATA-ATCT
1 TTTATATAT-T
* *
34142851 TTTCTATGTT
1 TTTATATATT
34142861 TTTATA
1 TTTATA
34142867 AAAATTAAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
8 3 0.04
9 18 0.24
10 41 0.55
11 13 0.17
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTATATATT
Found at i:34142787 original size:21 final size:20
Alignment explanation
Indices: 34142763--34142868 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 20
34142753 TTCTTATGAA
34142763 TTTATAAATTTTTATATATTT
1 TTTATAAATTTTTATATA-TT
* *
34142784 TTTATATATTTCTATATA-T
1 TTTATAAATTTTTATATATT
34142803 TTTAT-AATTTTT-TACTATT
1 TTTATAAATTTTTATA-TATT
* * *
34142822 TTTATAAAATTTTACA-ACT
1 TTTATAAATTTTTATATATT
* *
34142841 TTTAT-AATCTTTTCTATGTT
1 TTTATAAAT-TTTTATATATT
34142861 TTTATAAA
1 TTTATAAA
34142869 AATTAAATAT
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
17 2 0.03
18 9 0.14
19 24 0.36
20 12 0.18
21 19 0.29
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (20 bp):
TTTATAAATTTTTATATATT
Found at i:34142788 original size:29 final size:29
Alignment explanation
Indices: 34142741--34142835 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
34142731 CTCTTTACCT
34142741 TTTTTA-ATCATTTTCTTATGA-ATTTATAAA
1 TTTTTATAT-ATTTT-TTAT-ATATTTATAAA
* *
34142771 TTTTTATATATTTTTTATATATTTCTATA
1 TTTTTATATATTTTTTATATATTTATAAA
*
34142800 TATTTTATA-ATTTTTTACTATTTTTATAAA
1 T-TTTTATATATTTTTTA-TATATTTATAAA
*
34142830 ATTTTA
1 TTTTTA
34142836 CAACTTTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
28 1 0.02
29 25 0.45
30 27 0.49
31 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (29 bp):
TTTTTATATATTTTTTATATATTTATAAA
Found at i:34142898 original size:28 final size:27
Alignment explanation
Indices: 34142851--34142908 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
34142841 TTTATAATCT
*
34142851 TTTCTATGTTTTTATAAAAATTAAATA
1 TTTCTATATTTTTATAAAAATTAAATA
* *
34142878 TTTCTTATATTTTTATTAAAATTTAATA
1 TTTC-TATATTTTTATAAAAATTAAATA
34142906 TTT
1 TTT
34142909 TGTATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTCTATATTTTTATAAAAATTAAATA
Found at i:34142914 original size:28 final size:27
Alignment explanation
Indices: 34142845--34142923 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 27
34142835 ACAACTTTTA
* * *
34142845 TAATCTTTTCTATGTTTTTATAAAAATT
1 TAATATTTT-TATATTTTTATTAAAATT
*
34142873 AAATATTTCTTATATTTTTATTAAAATT
1 TAATATTT-TTATATTTTTATTAAAATT
*
34142901 TAATATTTTGTATAAATTTTATT
1 TAATATTTT-TAT-ATTTTTATT
34142924 GATTTTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 1 0.02
28 32 0.76
29 9 0.21
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.58
Consensus pattern (27 bp):
TAATATTTTTATATTTTTATTAAAATT
Found at i:34143187 original size:85 final size:83
Alignment explanation
Indices: 34143069--34143255 Score: 248
Period size: 84 Copynumber: 2.2 Consensus size: 83
34143059 TGCATTTTGA
* *
34143069 CAATTGAGTGCAAAAAAAAGGGTTTAATTGCTTTTTTGAAAAAGTTTAAGGGCATTTTTGATGCA
1 CAATTAAGTGCAAAAAAAAGGGCTTAATTGCTTTTTTGAAAAAGTTTAAGGGCATTTTT-ATGCA
**
34143134 TTTTGGCAGTTCAAGTACC
65 TTTTGAAAGTTCAAGTACC
* ** * *
34143153 CAATTAAGTGCAAAAAAAGGGGGCTTAATTGCTTTTTTGAAAACTTTTGAGGGCCTTTTTATGCA
1 CAATTAAGTGCAAAAAAA-AGGGCTTAATTGCTTTTTTGAAAAAGTTTAAGGGCATTTTTATGCA
**
34143218 TTTTGAAAGTTCAAGTGTC
65 TTTTGAAAGTTCAAGTACC
*
34143237 CAATTAAGTGCAGAAAAAA
1 CAATTAAGTGCAAAAAAAA
34143256 TCAGGGGCTT
Statistics
Matches: 89, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
84 54 0.61
85 35 0.39
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (83 bp):
CAATTAAGTGCAAAAAAAAGGGCTTAATTGCTTTTTTGAAAAAGTTTAAGGGCATTTTTATGCAT
TTTGAAAGTTCAAGTACC
Found at i:34143274 original size:85 final size:84
Alignment explanation
Indices: 34143069--34143276 Score: 231
Period size: 84 Copynumber: 2.4 Consensus size: 84
34143059 TGCATTTTGA
* * *
34143069 CAATTGAGTGCAAAAAAAA-GGGTTTAATTGCTTTTTTGAAAAAGTTTAAGGGCATTTTTGATGC
1 CAATTAAGTGCAAAAAAAAGGGGCTTAACT-CTTTTTTGAAAAAGTTTAAGGGCATTTTTGATGC
**
34143133 ATTTTGGCAGTTCAAGTACC
65 ATTTTGAAAGTTCAAGTACC
* * ** * *
34143153 CAATTAAGTGCAAAAAAAGGGGGCTTAATTGCTTTTTTGAAAACTTTTGAGGGCCTTTTT-ATGC
1 CAATTAAGTGCAAAAAAAAGGGGCTTAACT-CTTTTTTGAAAAAGTTTAAGGGCATTTTTGATGC
**
34143217 ATTTTGAAAGTTCAAGTGTC
65 ATTTTGAAAGTTCAAGTACC
*
34143237 CAATTAAGTGCAGAAAAAATCAGGGGCTTAACTTTTTTTT
1 CAATTAAGTGCA-AAAAAA--AGGGGCTTAACTCTTTTTT
34143277 CTTTAAATTT
Statistics
Matches: 106, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
84 49 0.46
85 41 0.39
86 6 0.06
87 10 0.09
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.36
Consensus pattern (84 bp):
CAATTAAGTGCAAAAAAAAGGGGCTTAACTCTTTTTTGAAAAAGTTTAAGGGCATTTTTGATGCA
TTTTGAAAGTTCAAGTACC
Found at i:34146865 original size:18 final size:18
Alignment explanation
Indices: 34146842--34146879 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
34146832 GCATACTTCA
*
34146842 AACAACATATGTTCGCAT
1 AACAACATAGGTTCGCAT
34146860 AACAACATAGGTTCGCAT
1 AACAACATAGGTTCGCAT
34146878 AA
1 AA
34146880 TGGGTTCGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (18 bp):
AACAACATAGGTTCGCAT
Found at i:34151725 original size:14 final size:15
Alignment explanation
Indices: 34151699--34151731 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
34151689 TGCCAAACTG
*
34151699 GGAAGGACCTTATGT
1 GGAAGGACCTTATCT
34151714 GGAAGG-CCTTATCT
1 GGAAGGACCTTATCT
34151728 GGAA
1 GGAA
34151732 AAGCGTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.24
Consensus pattern (15 bp):
GGAAGGACCTTATCT
Found at i:34153199 original size:89 final size:89
Alignment explanation
Indices: 34153054--34153589 Score: 768
Period size: 89 Copynumber: 6.0 Consensus size: 89
34153044 GTGAAGATAG
* *
34153054 CAGCCTTGCCTTCCTATACTGATAGCGGAGCAGACTGAAGATAGCAGAT-TTAGCCTTCCTATAC
1 CAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTT-GCCTTCCTATAC
*
34153118 TGACGGCGAAGCAGATCGAAGACAC
65 TGACAGCGAAGCAGATCGAAGACAC
* * **
34153143 CAGCCTTGCCTTCCTGTACTGGCAGCGGAGAAGACTGAAGATAGCAGATCTTGCCTTCCTGCACT
1 CAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTATACT
* * *
34153208 GACAACGAAGCAGATCAAAAACAC
66 GACAGCGAAGCAGATCGAAGACAC
** * *
34153232 CAGCCTTGCCTTCCTGTACTGACAGAAGAGCAGACTGAATATAGCAGATCTTGCCTTCCTGTACT
1 CAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTATACT
*
34153297 GACAGCGAAGCAGATCTAAGACAC
66 GACAGCGAAGCAGATCGAAGACAC
*
34153321 CAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAATATAGCAGATCTTGCCTTCCTATACT
1 CAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTATACT
* *
34153386 GATAGCGAAGCAGATCTAAGACAC
66 GACAGCGAAGCAGATCGAAGACAC
* * * * * *
34153410 CAGCCTTGCCTTCCTGTACTGATAGCAGAACAGACTGAATATAGCAGATCTTACCTTCCTATATT
1 CAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTATACT
34153475 GACAGCGAAGCAGATCGAAGACAC
66 GACAGCGAAGCAGATCGAAGACAC
* * * * * *
34153499 CAGCCTTGCCTTCTTATACTGACAGCGGAGCAGACTGAAGATAGCAGATTTTGCTTTCATGTACT
1 CAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTATACT
* *
34153564 GGCAGCGAAGCAGATCGAAAACAC
66 GACAGCGAAGCAGATCGAAGACAC
34153588 CA
1 CA
34153590 TAGTTTGCAA
Statistics
Matches: 402, Mismatches: 44, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
89 400 1.00
90 2 0.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (89 bp):
CAGCCTTGCCTTCCTGTACTGACAGCGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTATACT
GACAGCGAAGCAGATCGAAGACAC
Found at i:34153781 original size:44 final size:44
Alignment explanation
Indices: 34153719--34153832 Score: 144
Period size: 44 Copynumber: 2.6 Consensus size: 44
34153709 TATCAAATTT
* *
34153719 TATCTCTCTGAAGTTGCAGTAGAGCAAGTTGAAG-TAGCAAAC-C
1 TATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATA-CAAACTC
* *
34153762 TTATC-CCCATGAAGTTGCAGTGGGGCAAGTTGAAGATACAAATTC
1 -TATCTCCC-TGAAGTTGCAGTGGAGCAAGTTGAAGATACAAACTC
34153807 TATCTCCCTGAAGTTGCAGTGGAGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCA
34153833 GATTAAAACT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
43 2 0.03
44 53 0.87
45 6 0.10
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAAGTTGAAGATACAAACTC
Found at i:34154637 original size:24 final size:24
Alignment explanation
Indices: 34154610--34154656 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
34154600 AAACCCTCTT
*
34154610 TTTA-GTGTTTTTATTTAAAAAAAA
1 TTTACGTGTTTCT-TTTAAAAAAAA
34154634 TTTACTGTGTTTCTTTTAAAAAA
1 TTTAC-GTGTTTCTTTTAAAAAA
34154657 TATCTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 9 0.45
26 7 0.35
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (24 bp):
TTTACGTGTTTCTTTTAAAAAAAA
Found at i:34167682 original size:23 final size:23
Alignment explanation
Indices: 34167652--34167698 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
34167642 CTTTAGGGTC
34167652 CTCATTTTCAACTGTTGGTTCGT
1 CTCATTTTCAACTGTTGGTTCGT
34167675 CTCATTTTCAACTGTTGGTTCGT
1 CTCATTTTCAACTGTTGGTTCGT
34167698 C
1 C
34167699 CATGTTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.47
Consensus pattern (23 bp):
CTCATTTTCAACTGTTGGTTCGT
Found at i:34169451 original size:14 final size:15
Alignment explanation
Indices: 34169432--34169464 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
34169422 TTAATATTTT
34169432 AATTAAACTAA-TTA
1 AATTAAACTAACTTA
34169446 AATT-AACTAACTTA
1 AATTAAACTAACTTA
34169460 AATTA
1 AATTA
34169465 CCCTAATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTAAACTAACTTA
Found at i:34175604 original size:22 final size:21
Alignment explanation
Indices: 34175578--34175683 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 21
34175568 TACACATATG
34175578 ATCACATAACATTCAAGCATGT
1 ATCACATAACATTCAAGCAT-T
* *
34175600 ATCACA-ATAC--TC-A-TATA
1 ATCACATA-ACATTCAAGCATT
34175617 ATCACATAACATTCAAGCATAT
1 ATCACATAACATTCAAGCAT-T
* *
34175639 ATCACA-ATAC--TC-A-TATA
1 ATCACATA-ACATTCAAGCATT
34175656 ATCACATAACATTCAAGCATAT
1 ATCACATAACATTCAAGCAT-T
34175678 ATCACA
1 ATCACA
34175684 ATACTCAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 28
0.63 0.08 0.29
Matches are distributed among these distances:
17 16 0.26
18 6 0.10
19 6 0.10
20 6 0.10
21 6 0.10
22 22 0.35
ACGTcount: A:0.45, C:0.24, G:0.04, T:0.27
Consensus pattern (21 bp):
ATCACATAACATTCAAGCATT
Found at i:34175622 original size:17 final size:17
Alignment explanation
Indices: 34175600--34175661 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
34175590 TCAAGCATGT
34175600 ATCACAATACTCATATA
1 ATCACAATACTCATATA
*
34175617 ATCAC-ATAACATTCAAGCATA
1 ATCACAAT-AC--TC-A-TATA
34175638 TATCACAATACTCATATA
1 -ATCACAATACTCATATA
34175656 ATCACA
1 ATCACA
34175662 TAACATTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
16 2 0.06
17 13 0.36
18 3 0.08
19 3 0.08
20 3 0.08
21 3 0.08
22 7 0.19
23 2 0.06
ACGTcount: A:0.47, C:0.24, G:0.02, T:0.27
Consensus pattern (17 bp):
ATCACAATACTCATATA
Found at i:34175688 original size:39 final size:39
Alignment explanation
Indices: 34175514--34175690 Score: 282
Period size: 39 Copynumber: 4.5 Consensus size: 39
34175504 ATTCACTTTT
* * * *
34175514 AAGCATATATCACATTACACATATAATAACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * *
34175553 AAGCATATATCATAATACACATATGATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
34175592 AAGCATGTATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
34175631 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
34175670 AAGCATATATCACAATACTCA
1 AAGCATATATCACAATACTCA
34175691 AAAACATGTT
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 128 1.00
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.28
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:34186515 original size:26 final size:27
Alignment explanation
Indices: 34186449--34186515 Score: 111
Period size: 26 Copynumber: 2.6 Consensus size: 27
34186439 AAAAATAAAA
34186449 ATTTACCAAAATAT-TATAACTTTTTT
1 ATTTACCAAAATATATATAACTTTTTT
*
34186475 ATTTACCAAAATATATA-AATTTTTTT
1 ATTTACCAAAATATATATAACTTTTTT
34186501 ATTTACCAAAATATA
1 ATTTACCAAAATATA
34186516 CAAAAACCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 37 0.95
27 2 0.05
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTTACCAAAATATATATAACTTTTTT
Found at i:34186614 original size:27 final size:27
Alignment explanation
Indices: 34186584--34186677 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 27
34186574 CGCCAATGGG
* *
34186584 ATTGGGGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAATGGTGCCAAAACC
**
34186611 ATTGGCGGCACCAATGGTGCCAATGCC
1 ATTGGCGGCACCAATGGTGCCAAAACC
* *
34186638 ATTGGCGGCACCAATGGTGCC-ATACTA
1 ATTGGCGGCACCAATGGTGCCAAAAC-C
34186665 ATTGGCGGCACCA
1 ATTGGCGGCACCA
34186678 CTCGTATTAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
26 3 0.05
27 57 0.95
ACGTcount: A:0.27, C:0.28, G:0.29, T:0.17
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAACC
Found at i:34186657 original size:54 final size:54
Alignment explanation
Indices: 34186575--34186677 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
34186565 AACTGGTCAC
** * *
34186575 GCCAATGGGATTGGGGGCACCAAAGGTGCCAAAAC-CATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAAAGGTGCC-AAACTAATTGGCGGCACCAATGGT
* *
34186629 GCCAATGCCATTGGCGGCACCAATGGTGCCATACTAATTGGCGGCACCA
1 GCCAATGCCATTGGCGGCACCAAAGGTGCCAAACTAATTGGCGGCACCA
34186678 CTCGTATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 3 0.07
54 39 0.93
ACGTcount: A:0.26, C:0.27, G:0.30, T:0.17
Consensus pattern (54 bp):
GCCAATGCCATTGGCGGCACCAAAGGTGCCAAACTAATTGGCGGCACCAATGGT
Found at i:34186841 original size:10 final size:10
Alignment explanation
Indices: 34186826--34186851 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
34186816 TTGTTGTTAT
34186826 TATTTTGTAA
1 TATTTTGTAA
34186836 TATTTTGTAA
1 TATTTTGTAA
34186846 TATTTT
1 TATTTT
34186852 TTGTTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (10 bp):
TATTTTGTAA
Found at i:34187159 original size:26 final size:26
Alignment explanation
Indices: 34187130--34187182 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
34187120 TTTTAGTGTG
*
34187130 TATTATTTTGAGTATAAAATTATTAA
1 TATTATTTTGAGTATAAAATTAATAA
34187156 TATTATTTTGAGTATAAAATTAATAA
1 TATTATTTTGAGTATAAAATTAATAA
34187182 T
1 T
34187183 TTTAGTGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (26 bp):
TATTATTTTGAGTATAAAATTAATAA
Found at i:34187205 original size:12 final size:12
Alignment explanation
Indices: 34187188--34187218 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
34187178 ATAATTTTAG
34187188 TGTGTATTATTT
1 TGTGTATTATTT
34187200 TGTGTATTATTT
1 TGTGTATTATTT
*
34187212 TGAGTAT
1 TGTGTAT
34187219 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:34187817 original size:18 final size:18
Alignment explanation
Indices: 34187774--34187818 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
34187764 TTGACATGGT
*
34187774 TGGTGGTGAAGAAAAAGG
1 TGGTGGCGAAGAAAAAGG
** *
34187792 TGCCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAAAAGG
34187810 TGGTGGCGA
1 TGGTGGCGA
34187819 TATGAAGAGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.09, G:0.47, T:0.13
Consensus pattern (18 bp):
TGGTGGCGAAGAAAAAGG
Found at i:34193652 original size:4 final size:4
Alignment explanation
Indices: 34193630--34193703 Score: 62
Period size: 4 Copynumber: 18.5 Consensus size: 4
34193620 TCTCCTTTCC
* * * *
34193630 CTTT CTTT CCTT C-TT -TTT CTTT CTTCC CTCT CATTT CTTC CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTT-T CTTT C-TTT CTTT CTTT CTTT
* *
34193678 CTCT CTTT CTTT CTTT CTTT CCTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CT
34193704 CCTTCTGCCC
Statistics
Matches: 55, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
3 4 0.07
4 46 0.84
5 5 0.09
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (4 bp):
CTTT
Found at i:34194002 original size:3 final size:3
Alignment explanation
Indices: 34193994--34194055 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
34193984 ATATAAAGTG
34193994 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
34194042 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
34194056 ACTACCTCTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:34194533 original size:31 final size:30
Alignment explanation
Indices: 34194468--34194534 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
34194458 GCCTAGTATT
* * *
34194468 TTAAATAAAATTTTTGAATAGTTTATTGAT
1 TTAAATAAAACTTTTGAATAGTTTAATGAC
*
34194498 TTAAATAAAAACTTTTGAATAGTTTAATGGC
1 TTAAAT-AAAACTTTTGAATAGTTTAATGAC
34194529 TTAAAT
1 TTAAAT
34194535 TGAAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (30 bp):
TTAAATAAAACTTTTGAATAGTTTAATGAC
Found at i:34196087 original size:29 final size:29
Alignment explanation
Indices: 34196047--34196119 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
34196037 ACAATATTGA
34196047 ATAGTT-GAGTGACCATTTTGTAACTTTTT-
1 ATAGTTAG-GTGACCATTTTGTAA-TTTTTC
**
34196076 ATAGTTTTGTGACCATTTTGTAATTTTTC
1 ATAGTTAGGTGACCATTTTGTAATTTTTC
34196105 ATAGTTAGGTGACCA
1 ATAGTTAGGTGACCA
34196120 AAAAAGAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
28 5 0.13
29 34 0.87
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.47
Consensus pattern (29 bp):
ATAGTTAGGTGACCATTTTGTAATTTTTC
Found at i:34196387 original size:59 final size:60
Alignment explanation
Indices: 34196277--34196427 Score: 177
Period size: 59 Copynumber: 2.5 Consensus size: 60
34196267 TTTCATTTTT
* * * *
34196277 ATGACCAAAAAAGGCAAATTTA--AATAGTTGAGTAACTATTTTGTAACTTTTCATAATTTA
1 ATGACCAAAAAA-G-AAATTTACTAATAATTGAGTAACTATTTTATAAATTTTCATAATTAA
*
34196337 ATGACCAAAAAAGAAATTTACTAATAATT-AGTGACTATTTTATAAATTTTCATAATTAA
1 ATGACCAAAAAAGAAATTTACTAATAATTGAGTAACTATTTTATAAATTTTCATAATTAA
*
34196396 AT-AGCCAAAAAA-AAGTTTTACTAATAATTGAG
1 ATGA-CCAAAAAAGAA-ATTTACTAATAATTGAG
34196428 AAAGTGTAGC
Statistics
Matches: 80, Mismatches: 6, Indels: 10
0.83 0.06 0.10
Matches are distributed among these distances:
58 10 0.12
59 50 0.62
60 20 0.25
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.35
Consensus pattern (60 bp):
ATGACCAAAAAAGAAATTTACTAATAATTGAGTAACTATTTTATAAATTTTCATAATTAA
Found at i:34210074 original size:19 final size:17
Alignment explanation
Indices: 34210052--34210085 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
34210042 TATTTAATAT
34210052 ATATATTTGATTAAAAA
1 ATATATTTGATTAAAAA
34210069 ATATATTTGATTAAAAA
1 ATATATTTGATTAAAAA
34210086 TTTAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATATATTTGATTAAAAA
Found at i:34210468 original size:15 final size:15
Alignment explanation
Indices: 34210445--34210494 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
34210435 TTATGTCAAT
*
34210445 AATTATTAAAAGTTCAA
1 AATT-TTAAAA-TTAAA
34210462 AA-TTTAAAATTAAA
1 AATTTTAAAATTAAA
*
34210476 AATTTTAAAAATAAA
1 AATTTTAAAATTAAA
34210491 AATT
1 AATT
34210495 ATTTAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 6 0.20
15 21 0.70
16 1 0.03
17 2 0.07
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
AATTTTAAAATTAAA
Found at i:34210503 original size:16 final size:16
Alignment explanation
Indices: 34210463--34210503 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
34210453 AAAGTTCAAA
34210463 ATTTAAAATTAAAAATT
1 ATTTAAAA-TAAAAATT
*
34210480 -TTAAAAATAAAAATT
1 ATTTAAAATAAAAATT
34210495 ATTTAAAAT
1 ATTTAAAAT
34210504 CTATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTAAAATAAAAATT
Found at i:34211398 original size:11 final size:11
Alignment explanation
Indices: 34211384--34211449 Score: 61
Period size: 11 Copynumber: 6.3 Consensus size: 11
34211374 TTTTTTTAAA
34211384 TTTAAAATATT
1 TTTAAAATATT
34211395 TTTAAAATACTT
1 TTTAAAATA-TT
*
34211407 TTT-ATA-ATT
1 TTTAAAATATT
*
34211416 TTT---ATAAT
1 TTTAAAATATT
34211424 TTTAAAATATT
1 TTTAAAATATT
34211435 TTTAAAATACTT
1 TTTAAAATA-TT
34211447 TTT
1 TTT
34211450 TTAATTTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
7 1 0.02
8 5 0.11
9 5 0.11
10 1 0.02
11 24 0.52
12 10 0.22
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (11 bp):
TTTAAAATATT
Found at i:34211408 original size:29 final size:27
Alignment explanation
Indices: 34211376--34211440 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 27
34211366 TTTTTAATTT
*
34211376 TTTTTAAATTTAAAATATTTTTAAAATA
1 TTTTTAAATTT-AAATAATTTTAAAATA
**
34211404 CTTTTTATAATTTTTATAATTTTAAAATA
1 -TTTTTA-AATTTAAATAATTTTAAAATA
34211433 TTTTTAAA
1 TTTTTAAA
34211441 ATACTTTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 6 0.19
29 19 0.59
30 5 0.16
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTTAAATTTAAATAATTTTAAAATA
Found at i:34211428 original size:40 final size:40
Alignment explanation
Indices: 34211364--34211463 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 40
34211354 AATATATTTA
*
34211364 TTTTTTTAATTTTTTTTAAATTTAAAATATTTTTAAAATAC
1 TTTTTTTAA-TTTTTATAAATTTAAAATATTTTTAAAATAC
* *
34211405 TTTTTATAATTTTTATAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTAATTTTTATAAATTTAAAATATTTTTAAAATAC
34211445 TTTTTTTAATTTTTA-AAAT
1 TTTTTTTAATTTTTATAAAT
34211464 AAATTTTTGG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
39 3 0.06
40 43 0.80
41 8 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (40 bp):
TTTTTTTAATTTTTATAAATTTAAAATATTTTTAAAATAC
Found at i:34211470 original size:21 final size:21
Alignment explanation
Indices: 34211432--34211471 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34211422 ATTTTAAAAT
**
34211432 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
34211453 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
34211472 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:34211478 original size:22 final size:20
Alignment explanation
Indices: 34211431--34211485 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 20
34211421 AATTTTAAAA
* *
34211431 TATTTTTAAAATACTTTTTT
1 TATTTTTAAAATAATTTTTG
34211451 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAAT-AATTTTT-G
34211474 TATTTATTAAAA
1 TATTT-TTAAAA
34211486 AATGGGCCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.38
22 10 0.34
23 7 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTTAAAATAATTTTTG
Found at i:34211945 original size:33 final size:30
Alignment explanation
Indices: 34211908--34211971 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 30
34211898 TAATGAAAAC
* *
34211908 TAAATTTATTATTATATTGAATGACTAAAATAT
1 TAAATTTATGATAATATT-AATGA--AAAATAT
*
34211941 TAAATTTCTGATAATATTAATGAAAAATAT
1 TAAATTTATGATAATATTAATGAAAAATAT
34211971 T
1 T
34211972 TTAAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 8 0.29
32 5 0.18
33 15 0.54
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (30 bp):
TAAATTTATGATAATATTAATGAAAAATAT
Found at i:34213594 original size:15 final size:15
Alignment explanation
Indices: 34213551--34213594 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
34213541 TTTTATTTTG
*
34213551 TAATTAATATAAACA
1 TAATTAATATAAATA
**
34213566 TAATTTTTAT-AATA
1 TAATTAATATAAATA
34213580 TAATTAATATAAATA
1 TAATTAATATAAATA
34213595 CAATACAATG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATTAATATAAATA
Found at i:34214091 original size:27 final size:27
Alignment explanation
Indices: 34214043--34214143 Score: 130
Period size: 27 Copynumber: 3.7 Consensus size: 27
34214033 TCAGTTTATC
*
34214043 ACCACAAAAGGCTATCCTTTCATAATTT
1 ACCAC-AAAGGCTATTCTTTCATAATTT
** * * *
34214071 GTCACAAATGTTATTCTTTCATAATTC
1 ACCACAAAGGCTATTCTTTCATAATTT
34214098 ACCACAAAGGCTATTCTTTCATAATTT
1 ACCACAAAGGCTATTCTTTCATAATTT
*
34214125 ACCACAAAGGCTATCCTTT
1 ACCACAAAGGCTATTCTTT
34214144 ACTGTTGTGT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
27 58 0.95
28 3 0.05
ACGTcount: A:0.33, C:0.24, G:0.08, T:0.36
Consensus pattern (27 bp):
ACCACAAAGGCTATTCTTTCATAATTT
Found at i:34215696 original size:18 final size:18
Alignment explanation
Indices: 34215675--34215715 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
34215665 GGCAGAAATC
* * *
34215675 GAGAGCAAATCAGAGAAA
1 GAGAGAAAATAAGAAAAA
34215693 GAGAGAAAATAAGAAAAA
1 GAGAGAAAATAAGAAAAA
34215711 GAGAG
1 GAGAG
34215716 GATTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.61, C:0.05, G:0.29, T:0.05
Consensus pattern (18 bp):
GAGAGAAAATAAGAAAAA
Found at i:34217384 original size:39 final size:40
Alignment explanation
Indices: 34217271--34217421 Score: 209
Period size: 39 Copynumber: 3.8 Consensus size: 40
34217261 CGTTTGGACA
* * ** *
34217271 AAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTCAACAT
1 AAAAGCGCCGCTAAAAATCGAGCATTAGCGGCGCT-TTCAG
* *
34217312 AAAA-CGCCGCCAAAGATCGAGCATTAGCGGCGCTTTCAG
1 AAAAGCGCCGCTAAAAATCGAGCATTAGCGGCGCTTTCAG
34217351 AAAAGCGCCGCTAAAAAT-GAGCATTAGCGGCGCTTTCAG
1 AAAAGCGCCGCTAAAAATCGAGCATTAGCGGCGCTTTCAG
34217390 AAAAGCGCCGCTAAAAAT-GAGCATTAGCGGCG
1 AAAAGCGCCGCTAAAAATCGAGCATTAGCGGCG
34217422 TTTTTTCAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
39 59 0.58
40 38 0.38
41 4 0.04
ACGTcount: A:0.36, C:0.25, G:0.24, T:0.15
Consensus pattern (40 bp):
AAAAGCGCCGCTAAAAATCGAGCATTAGCGGCGCTTTCAG
Found at i:34217446 original size:79 final size:79
Alignment explanation
Indices: 34217269--34217446 Score: 209
Period size: 79 Copynumber: 2.2 Consensus size: 79
34217259 GGCGTTTGGA
* * *
34217269 CAAAAAACGCCACTAAAAATCGAGCATTAGCGGCGCTCAACATAAAACGCCGCCAAAGATCGAGC
1 CAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTCAACAGAAAACGCCGCCAAAAATCGAGC
34217334 ATTAGCGGCGCTTT
66 ATTAGCGGCGCTTT
* ** *
34217348 CAGAAAAGCGCCGCTAAAAAT-GAGCATTAGCGGCGCT-TTCAGAAAAGCGCCGCTAAAAAT-GA
1 CA-AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTCAACAGAAAA-CGCCGCCAAAAATCGA
*
34217410 GCATTAGCGGCGTTTTTT
64 GCATTAGCGGCG--CTTT
* *
34217428 CAAAAAACACCGCAAAAAA
1 CAAAAAACGCCGCTAAAAA
34217447 CCTAAGCCCA
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
78 20 0.24
79 43 0.51
80 21 0.25
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (79 bp):
CAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTCAACAGAAAACGCCGCCAAAAATCGAGC
ATTAGCGGCGCTTT
Found at i:34217540 original size:41 final size:41
Alignment explanation
Indices: 34217484--34217676 Score: 237
Period size: 41 Copynumber: 4.7 Consensus size: 41
34217474 CCATTTGGGG
* * *
34217484 CTTTAGCGACATTTTTTCAAAAGCGCCGCTAATGCTCTAG-C
1 CTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTC-AGAC
* *
34217525 TTTTAGCGGCG-TTTTTAATAAAGCGTCGCTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTTAA-AAAGCGCCGCTAATGCTCAGAC
*
34217566 CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGAC
1 CTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGAC
** **
34217607 CTTTAGCGGCGTTTTCGAAAAAGCGCCGCTAATGCTCAGGG
1 CTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGAC
* * *
34217648 CTTTAGTGGCGCTTTTCAAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTTAAAAAGCGCCGC
34217677 AAAAACATTT
Statistics
Matches: 134, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
40 8 0.06
41 120 0.90
42 6 0.04
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.29
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGAC
Found at i:34218598 original size:7 final size:7
Alignment explanation
Indices: 34218584--34218626 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
34218574 ATTGTAAAAG
34218584 AGGGGTT
1 AGGGGTT
*
34218591 ATGGGTT
1 AGGGGTT
*
34218598 AAGGGTT
1 AGGGGTT
*
34218605 AGAGGTT
1 AGGGGTT
34218612 AGGGGTT
1 AGGGGTT
34218619 AGGGGTT
1 AGGGGTT
34218626 A
1 A
34218627 CGAGTTTATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.21, C:0.00, G:0.49, T:0.30
Consensus pattern (7 bp):
AGGGGTT
Found at i:34218612 original size:21 final size:22
Alignment explanation
Indices: 34218587--34218636 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
34218577 GTAAAAGAGG
34218587 GGTTATGGGTTAAGGGTTA-GA
1 GGTTATGGGTTAAGGGTTACGA
* *
34218608 GGTTAGGGGTTAGGGGTTACGA
1 GGTTATGGGTTAAGGGTTACGA
*
34218630 GTTTATG
1 GGTTATG
34218637 TTTTATGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.20, C:0.02, G:0.44, T:0.34
Consensus pattern (22 bp):
GGTTATGGGTTAAGGGTTACGA
Found at i:34218975 original size:14 final size:14
Alignment explanation
Indices: 34218958--34218995 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
34218948 ATAAAAATCC
34218958 AGTTTATAAAAAAT
1 AGTTTATAAAAAAT
34218972 AG-TTATAAAAAAT
1 AGTTTATAAAAAAT
*
34218985 ATTTTATAAAA
1 AGTTTATAAAA
34218996 TCACATAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (14 bp):
AGTTTATAAAAAAT
Found at i:34222616 original size:43 final size:43
Alignment explanation
Indices: 34222508--34222820 Score: 326
Period size: 43 Copynumber: 7.3 Consensus size: 43
34222498 AAGTCATGTT
* *** * * *
34222508 TTTAGTGGCGTTTGTCAAAAAAGCGCCGCTAAAAGTCAT-CT-
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * * * * *
34222549 TTATAGTGGCGTTTGTTGTAGAAGCGTCGCTAAAGGTCATGATC
1 TT-TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
** * * **
34222593 TTTAGCGGCGTTTGTGCTAGAAGCGCCGCTAAAGAT-TATGACC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCT-TGGTC
*
34222636 TTTAGCGGCGTTTGTGGGACAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
34222679 TTCAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAAGTCTTCGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
34222722 TTTTGCGGCGTTTGTGGGAAATGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
34222765 TTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
34222808 TTTAGCAGCGTTT
1 TTTAGCGGCGTTT
34222821 TTTTCTAAAA
Statistics
Matches: 231, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
41 2 0.01
42 31 0.13
43 195 0.84
44 3 0.01
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:34227326 original size:32 final size:32
Alignment explanation
Indices: 34227283--34227347 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
34227273 GCTATATCCC
34227283 TCCTCCAATCGGGTACATGT-C-AATGGCATAAG
1 TCCTCCAATC-GG-ACATGTGCAAATGGCATAAG
* *
34227315 TCCTCCGATCGGATATGTGCAAATGGCATAAG
1 TCCTCCAATCGGACATGTGCAAATGGCATAAG
34227347 T
1 T
34227348 AACGTTGACC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 3 0.10
32 21 0.72
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (32 bp):
TCCTCCAATCGGACATGTGCAAATGGCATAAG
Found at i:34228357 original size:20 final size:20
Alignment explanation
Indices: 34228328--34228367 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
34228318 GGACTAAATT
*
34228328 GAAAAGATTTAAAATTTATG
1 GAAAAAATTTAAAATTTATG
* *
34228348 GAAAAAATTTGAATTTTATG
1 GAAAAAATTTAAAATTTATG
34228368 AAAGACATGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (20 bp):
GAAAAAATTTAAAATTTATG
Found at i:34228896 original size:24 final size:24
Alignment explanation
Indices: 34228869--34228966 Score: 81
Period size: 24 Copynumber: 4.0 Consensus size: 24
34228859 AGCGTCCCGT
*
34228869 TATTAACTCTCATGAGCATCCTGA
1 TATTAGCTCTCATGAGCATCCTGA
* * *
34228893 TATTGGCTCTCTTGAGCTTCCTGA
1 TATTAGCTCTCATGAGCATCCTGA
* * * *
34228917 TGTATGGCTCTCATGAGC-TTCTCGT
1 TAT-TAGCTCTCATGAGCATCCT-GA
* *
34228942 TATTAGCTCTTATGAGCATCTTGA
1 TATTAGCTCTCATGAGCATCCTGA
34228966 T
1 T
34228967 TTGGTTGTGA
Statistics
Matches: 57, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
24 39 0.68
25 18 0.32
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.40
Consensus pattern (24 bp):
TATTAGCTCTCATGAGCATCCTGA
Found at i:34228933 original size:25 final size:24
Alignment explanation
Indices: 34228875--34228937 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
34228865 CCGTTATTAA
*
34228875 CTCTCATGAGCATCCTGATATTGG
1 CTCTCATGAGCTTCCTGATATTGG
* *
34228899 CTCTCTTGAGCTTCCTGATGTATGG
1 CTCTCATGAGCTTCCTGATAT-TGG
34228924 CTCTCATGAGCTTC
1 CTCTCATGAGCTTC
34228938 TCGTTATTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 18 0.53
25 16 0.47
ACGTcount: A:0.16, C:0.27, G:0.21, T:0.37
Consensus pattern (24 bp):
CTCTCATGAGCTTCCTGATATTGG
Found at i:34229056 original size:25 final size:25
Alignment explanation
Indices: 34229028--34229100 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 25
34229018 CCCGATATAT
*
34229028 GGCTCTCCGGAGCTTCCTGATTAAA
1 GGCTCTCCAGAGCTTCCTGATTAAA
* *
34229053 GGCTCTCGCATGAGCTTCCTAATTAAT
1 GGCTCTC-CA-GAGCTTCCTGATTAAA
* *
34229080 GGCTCCCCAGAGCTTTCTGAT
1 GGCTCTCCAGAGCTTCCTGAT
34229101 AATTATCTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
25 17 0.43
26 3 0.08
27 20 0.50
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.30
Consensus pattern (25 bp):
GGCTCTCCAGAGCTTCCTGATTAAA
Found at i:34229151 original size:25 final size:25
Alignment explanation
Indices: 34229112--34229181 Score: 77
Period size: 25 Copynumber: 2.8 Consensus size: 25
34229102 ATTATCTCGT
* *
34229112 AAGAGCTTTCTGTTACATGGCTCAC
1 AAGAGCTTCCCGTTACATGGCTCAC
* * * *
34229137 ATGAGCTTCCCGTTATATGGTTCAG
1 AAGAGCTTCCCGTTACATGGCTCAC
34229162 AAGAGCTTCCCGTTTACATG
1 AAGAGCTTCCCG-TTACATG
34229182 TTTGTATAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 30 0.83
26 6 0.17
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (25 bp):
AAGAGCTTCCCGTTACATGGCTCAC
Found at i:34238364 original size:18 final size:17
Alignment explanation
Indices: 34238338--34238372 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
34238328 AATATTAAGA
*
34238338 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
34238355 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
34238373 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:34238592 original size:44 final size:45
Alignment explanation
Indices: 34238529--34238626 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 45
34238519 CTATTACACC
*
34238529 TCCATTCCATTCAACCAAACACA-AGAA-TACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAT
* *
34238573 TCCATTACATTCAACCAAACAATTGAATTGCTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
* *
34238618 ACCAATACA
1 TCCATTACA
34238627 GCGAACCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
43 1 0.02
44 23 0.49
45 23 0.49
ACGTcount: A:0.37, C:0.30, G:0.05, T:0.29
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
Found at i:34241875 original size:15 final size:15
Alignment explanation
Indices: 34241854--34241884 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
34241844 TGATTTTGTC
34241854 AAAAAAAAGAATCTAT
1 AAAAAAAA-AATCTAT
34241870 AAAAAAAAAATCTAT
1 AAAAAAAAAATCTAT
34241885 CCATTCTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.19
Consensus pattern (15 bp):
AAAAAAAAAATCTAT
Found at i:34241897 original size:2 final size:2
Alignment explanation
Indices: 34241892--34241930 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
34241882 TATCCATTCT
34241892 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34241931 GACTAGTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:34242057 original size:34 final size:35
Alignment explanation
Indices: 34241995--34242074 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 35
34241985 GCCTTTTTTA
* *
34241995 ATATTATTATTTTTAAATGAAAATTTTATATATGAT
1 ATATTATT-TTTTAAAATGAAAATTTTATATATAAT
**
34242031 ATATTATTTTTTAAAATTTAAA-TTTATATATAAT
1 ATATTATTTTTTAAAATGAAAATTTTATATATAAT
34242065 ATA-TATTTTT
1 ATATTATTTTT
34242075 CACTTGTGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
33 7 0.17
34 14 0.35
35 11 0.28
36 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (35 bp):
ATATTATTTTTTAAAATGAAAATTTTATATATAAT
Found at i:34248244 original size:101 final size:99
Alignment explanation
Indices: 34248096--34248285 Score: 240
Period size: 101 Copynumber: 1.9 Consensus size: 99
34248086 CCTTTTGTGC
* ** * **
34248096 CATAGTCCAACTATGGTCTTACACATGCATTGCCATGGCTCTGCCATGGTCTTATATTTGTAGTA
1 CATAGTCCAACTATGGTCTTACACATACATTGCCATGGCTCAACCATGGTCTTACATTCATAGTA
*
34248161 TCATAACCCAGTTATGGTCTTATCATCAGAATGT
66 CCATAACCCAGTTATGGTCTTATCATCAGAATGT
* *
34248195 CATA-TCCAAACTATGGTCTTACATATAAACATTGCCATGG-TCCAACCATGGTCTTACGTTCAT
1 CATAGTCC-AACTATGGTCTTACACAT--ACATTGCCATGGCT-CAACCATGGTCTTACATTCAT
*
34248258 AGTGCCATAACCCAGTTATGGTCTTATC
62 AGTACCATAACCCAGTTATGGTCTTATC
34248286 CGTCAATTCA
Statistics
Matches: 77, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
98 3 0.04
99 21 0.27
100 1 0.01
101 52 0.68
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.34
Consensus pattern (99 bp):
CATAGTCCAACTATGGTCTTACACATACATTGCCATGGCTCAACCATGGTCTTACATTCATAGTA
CCATAACCCAGTTATGGTCTTATCATCAGAATGT
Done.