Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001129.1 Hibiscus syriacus cultivar Beakdansim tig00002237_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: 21326069
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 41 of 89
Found at i:9084414 original size:9 final size:8
Alignment explanation
Indices: 9084370--9084453 Score: 50
Period size: 9 Copynumber: 10.2 Consensus size: 8
9084360 TTGTTGTTAA
9084370 TATTAT-T
1 TATTATAT
*
9084377 TATATATGT
1 TAT-TATAT
9084386 TATTATTAT
1 TATTA-TAT
*
9084395 CA-TATTAT
1 TATTA-TAT
9084403 TATTACTAT
1 TATTA-TAT
9084412 TATTA-AT
1 TATTATAT
* *
9084419 TA-CATGT
1 TATTATAT
9084426 TATTATAT
1 TATTATAT
9084434 TATTAATAT
1 TATT-ATAT
9084443 TATTATTAT
1 TATTA-TAT
9084452 TA
1 TA
9084454 AATAATATTA
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
6 1 0.02
7 10 0.16
8 20 0.33
9 30 0.49
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (8 bp):
TATTATAT
Found at i:9086749 original size:35 final size:36
Alignment explanation
Indices: 9086681--9086750 Score: 97
Period size: 35 Copynumber: 1.9 Consensus size: 36
9086671 AAGAACGAAG
*
9086681 AAAAAAATGGAGAAGAGAAAAAAGAATGCCAGAAAGA
1 AAAAAAAT-GAGAAGAGAAAAAAGAACGCCAGAAAGA
* *
9086718 AAAAAAAT-AGAAGAGAAAAAGGAACGGCAGAAA
1 AAAAAAATGAGAAGAGAAAAAAGAACGCCAGAAA
9086751 TTAAATGAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 22 0.73
37 8 0.27
ACGTcount: A:0.66, C:0.06, G:0.24, T:0.04
Consensus pattern (36 bp):
AAAAAAATGAGAAGAGAAAAAAGAACGCCAGAAAGA
Found at i:9086798 original size:2 final size:2
Alignment explanation
Indices: 9086791--9086854 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
9086781 CCTAAATAAC
9086791 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9086833 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
9086855 GGGATGACAT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9087440 original size:17 final size:17
Alignment explanation
Indices: 9087397--9087448 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
9087387 GTTACAGTAG
*
9087397 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
9087414 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
9087429 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
9087446 AAA
1 AAA
9087449 TTTGTCCAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:9087809 original size:16 final size:16
Alignment explanation
Indices: 9087790--9087822 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9087780 AATTTATCGA
*
9087790 TAAATTAATAACTTTC
1 TAAATTAATAAATTTC
9087806 TAAATTAATAAATTTC
1 TAAATTAATAAATTTC
9087822 T
1 T
9087823 CCGGTCCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTAATAAATTTC
Found at i:9088677 original size:91 final size:92
Alignment explanation
Indices: 9088481--9088691 Score: 338
Period size: 92 Copynumber: 2.3 Consensus size: 92
9088471 ATATAACTCT
* *
9088481 TCATACGGAGGTGACGAGTCTATTAAAAATACTATTTTATAAAAAAAATGAAAATAAATTTTATA
1 TCATGCGGAGGTGACGAGTCCATTAAAAATACTATTTTATAAAAAAAATGAAAATAAATTTTATA
9088546 AATATTAAATAAATTAGGTGGAACTTC
66 AATATTAAATAAATTAGGTGGAACTTC
9088573 TCATGCGGAGGTGACGAGTCCATTAAAAATACTATTTTATAAAAAAAATGAAAATAAA-TTTATA
1 TCATGCGGAGGTGACGAGTCCATTAAAAATACTATTTTATAAAAAAAATGAAAATAAATTTTATA
9088637 AATATTAAA-AATATTAGGTGGAACTTC
66 AATATTAAATAA-ATTAGGTGGAACTTC
* *
9088664 TCATATC-GAGGTGACGAGTTCCTTTAAA
1 TCAT-GCGGAGGTGACGAG-TCCATTAAA
9088692 TTAAAAATAC
Statistics
Matches: 112, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
90 2 0.02
91 45 0.40
92 65 0.58
ACGTcount: A:0.44, C:0.09, G:0.15, T:0.32
Consensus pattern (92 bp):
TCATGCGGAGGTGACGAGTCCATTAAAAATACTATTTTATAAAAAAAATGAAAATAAATTTTATA
AATATTAAATAAATTAGGTGGAACTTC
Found at i:9089621 original size:22 final size:21
Alignment explanation
Indices: 9089591--9089637 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
9089581 TTTCACTTGA
*
9089591 TTTTTTTTTAAATTTATAATT
1 TTTTTTTTTAAATTTACAATT
* *
9089612 TTTTTATTTTCACTTTACAATT
1 TTTTT-TTTTAAATTTACAATT
9089634 TTTT
1 TTTT
9089638 ATAAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTTTTAAATTTACAATT
Found at i:9091021 original size:23 final size:23
Alignment explanation
Indices: 9090995--9091057 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
9090985 ACTTTGATGT
*
9090995 TGAATCATTCAATACTGTTTTGC
1 TGAATCATTCAACACTGTTTTGC
* *
9091018 TGAATCATTCAACATTGTTTTGT
1 TGAATCATTCAACACTGTTTTGC
* *
9091041 TGAATCAGTCAGCACTG
1 TGAATCATTCAACACTG
9091058 AATCATTCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (23 bp):
TGAATCATTCAACACTGTTTTGC
Found at i:9103329 original size:23 final size:23
Alignment explanation
Indices: 9103299--9103384 Score: 91
Period size: 23 Copynumber: 3.7 Consensus size: 23
9103289 GAGTCGAGGG
9103299 TTCTACGTGATCCTTCGGGACAA
1 TTCTACGTGATCCTTCGGGACAA
* * * *
9103322 TTCTACGTGTTTCTTCGAGACAT
1 TTCTACGTGATCCTTCGGGACAA
* *
9103345 TTCTACGCGATCCTTCGGGATAA
1 TTCTACGTGATCCTTCGGGACAA
* * *
9103368 TACTATGTGGTCCTTCG
1 TTCTACGTGATCCTTCG
9103385 ATACATTTTA
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (23 bp):
TTCTACGTGATCCTTCGGGACAA
Found at i:9103357 original size:46 final size:46
Alignment explanation
Indices: 9103299--9103392 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 46
9103289 GAGTCGAGGG
* * * *
9103299 TTCTACGTGATCCTTCGGGACAATTCTACGTGTTTCTTCGAGACAT
1 TTCTACGCGATCCTTCGGGACAATACTACGTGGTCCTTCGAGACAT
* * *
9103345 TTCTACGCGATCCTTCGGGATAATACTATGTGGTCCTTCGATACAT
1 TTCTACGCGATCCTTCGGGACAATACTACGTGGTCCTTCGAGACAT
9103391 TT
1 TT
9103393 TATGTGGTAC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.37
Consensus pattern (46 bp):
TTCTACGCGATCCTTCGGGACAATACTACGTGGTCCTTCGAGACAT
Found at i:9104045 original size:23 final size:20
Alignment explanation
Indices: 9104019--9104066 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 20
9104009 ATTAAAATAT
9104019 AAATAAATTCCATAAATACATTA
1 AAATAAATT-CA-AAATA-ATTA
9104042 AAAT--ATTCAAAATAATTA
1 AAATAAATTCAAAATAATTA
9104060 AAATAAA
1 AAATAAA
9104067 ATATTAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 3 0.13
21 3 0.13
23 4 0.17
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.29
Consensus pattern (20 bp):
AAATAAATTCAAAATAATTA
Found at i:9104172 original size:19 final size:19
Alignment explanation
Indices: 9104150--9104198 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
9104140 TCTCAAAAAT
9104150 CATAATAATCAATAAAAGA
1 CATAATAATCAATAAAAGA
9104169 CATAATAATCAATAAAAGA
1 CATAATAATCAATAAAAGA
9104188 CATAATAATCA
1 CATAATAATCA
9104199 TTTAACATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.61, C:0.12, G:0.04, T:0.22
Consensus pattern (19 bp):
CATAATAATCAATAAAAGA
Found at i:9107866 original size:257 final size:257
Alignment explanation
Indices: 9107404--9107870 Score: 844
Period size: 257 Copynumber: 1.8 Consensus size: 257
9107394 AATCAATAAC
* * * *
9107404 ACATAGCCTTAGAATATCTTCAAGTACTTGAATGGTACGCTCATACTGATCATCCGTTTATGTAT
1 ACATACCCTTAGAATATCTTCAAGTACGTGAATGGTACGCTCAGACTGACCATCCGTTTATGTAT
*
9107469 GAACATCAGTGCTAAAGTTCAGTCGAGTCCCTAAAGCTTCGTGTAGAGTCTTCCAAAATCTCGAA
66 GAACATCAGTGCTAAAGTTCAGTCGAGTCCCTAAAGCTTCGTGCAGAGTCTTCCAAAATCTCGAA
*
9107534 GTAAACCACAGGTCTCTGTCAGAAACTATCGATACAGGTACTCCATGTAATCGTACAATCTCCCT
131 GTAAACCACAGGTCTCTATCAGAAACTATCGATACAGGTACTCCATGTAATCGTACAATCTCCCT
9107599 GATGAATAACTCAACATACTTATCCATCGAATAATCCTCTCAAATTGGAATAAAGTGTGTGA
196 GATGAATAACTCAACATACTTATCCATCGAATAATCCTCTCAAATTGGAATAAAGTGTGTGA
9107661 ACATACCCTTAGAATATCTTCAAGTACGTGAATGGTACGCTCAGACTGACCATCCGTTTATGTAT
1 ACATACCCTTAGAATATCTTCAAGTACGTGAATGGTACGCTCAGACTGACCATCCGTTTATGTAT
* *
9107726 GAACATCAGTGCTAAAGTTTAGTCGAGTCCTTAAAGCTTCGTGCAGAGTCTTCCAAAATCTCGAA
66 GAACATCAGTGCTAAAGTTCAGTCGAGTCCCTAAAGCTTCGTGCAGAGTCTTCCAAAATCTCGAA
* *
9107791 GTAAACCTCGGGTCTCTATCAGAAACTATCGATACAGGTACTCCATGTAATCGTACAATCTCCCT
131 GTAAACCACAGGTCTCTATCAGAAACTATCGATACAGGTACTCCATGTAATCGTACAATCTCCCT
9107856 GATGAATAACTCAAC
196 GATGAATAACTCAAC
9107871 TGGAATAAAG
Statistics
Matches: 200, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
257 200 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (257 bp):
ACATACCCTTAGAATATCTTCAAGTACGTGAATGGTACGCTCAGACTGACCATCCGTTTATGTAT
GAACATCAGTGCTAAAGTTCAGTCGAGTCCCTAAAGCTTCGTGCAGAGTCTTCCAAAATCTCGAA
GTAAACCACAGGTCTCTATCAGAAACTATCGATACAGGTACTCCATGTAATCGTACAATCTCCCT
GATGAATAACTCAACATACTTATCCATCGAATAATCCTCTCAAATTGGAATAAAGTGTGTGA
Found at i:9108781 original size:20 final size:20
Alignment explanation
Indices: 9108756--9108794 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9108746 TTTTCAAGGG
9108756 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
9108776 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
9108795 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:9108871 original size:26 final size:26
Alignment explanation
Indices: 9108841--9108910 Score: 113
Period size: 26 Copynumber: 2.7 Consensus size: 26
9108831 TGCACATACC
**
9108841 ATGCATCGATGCACTCAGTGTGTTTG
1 ATGCATCGATGCACTCAGTGCATTTG
*
9108867 ATGCATCAATGCACTCAGTGCATTTG
1 ATGCATCGATGCACTCAGTGCATTTG
9108893 ATGCATCGATGCACTCAG
1 ATGCATCGATGCACTCAG
9108911 ACTTTTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (26 bp):
ATGCATCGATGCACTCAGTGCATTTG
Found at i:9117514 original size:20 final size:20
Alignment explanation
Indices: 9117489--9117527 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9117479 TTTTCAAGGG
9117489 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
9117509 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
9117528 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:9125503 original size:20 final size:20
Alignment explanation
Indices: 9125478--9125516 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
9125468 TTTTCAAGGG
9125478 CATGCACCGATGCACCAATC
1 CATGCACCGATGCACCAATC
* *
9125498 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
9125517 TAATTTCTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.31, C:0.33, G:0.15, T:0.21
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:9125593 original size:45 final size:46
Alignment explanation
Indices: 9125534--9125622 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 46
9125524 TTGAACATCA
* *
9125534 AATGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTC
1 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
* *
9125579 AATGTATTTGATGCATCGATGCACAAGACTATGCATCGATGCAC
1 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCAC
9125623 AGACGCTCTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.56
46 17 0.44
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (46 bp):
AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
Found at i:9131839 original size:8 final size:8
Alignment explanation
Indices: 9131799--9131865 Score: 51
Period size: 8 Copynumber: 9.2 Consensus size: 8
9131789 AGTGTCATTT
9131799 TTATATTTA
1 TTATA-TTA
9131808 TTATA-TA
1 TTATATTA
9131815 --ATATT-
1 TTATATTA
9131820 TT-TATTA
1 TTATATTA
9131827 TTATATTA
1 TTATATTA
*
9131835 ATATATTA
1 TTATATTA
9131843 TTATA-TA
1 TTATATTA
9131850 -T-TATTA
1 TTATATTA
*
9131856 CTATATTA
1 TTATATTA
9131864 TT
1 TT
9131866 TTTACAAATG
Statistics
Matches: 47, Mismatches: 3, Indels: 17
0.70 0.04 0.25
Matches are distributed among these distances:
5 5 0.11
6 8 0.17
7 7 0.15
8 22 0.47
9 5 0.11
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATTA
Found at i:9131860 original size:21 final size:19
Alignment explanation
Indices: 9131805--9131865 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
9131795 ATTTTTATAT
*
9131805 TTATTATA-TAATATTTTTA
1 TTATTATATTAATA-TATTA
9131824 TTATTATATTAATATATTA
1 TTATTATATTAATATATTA
*
9131843 TTATATATTATTACTATATTA
1 TTAT-TA-TATTAATATATTA
9131864 TT
1 TT
9131866 TTTACAAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.43
20 7 0.19
21 14 0.38
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTATATTAATATATTA
Found at i:9134060 original size:46 final size:48
Alignment explanation
Indices: 9133973--9134062 Score: 121
Period size: 46 Copynumber: 1.9 Consensus size: 48
9133963 GTTATTTTAT
* * * * *
9133973 TTTTTTCATATAAAGGCATGCGAACTAGAAATCATGTGGTTAGGTTTG
1 TTTTTCCAAATAAAGGCATGCGAACTAAAAAACATGAGGTTAGGTTTG
9134021 TTTTTCCAAATAAA-GCATG-GAACTAAAAAACATGAGGTTAGG
1 TTTTTCCAAATAAAGGCATGCGAACTAAAAAACATGAGGTTAGG
9134063 ATGTATATAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 20 0.54
47 5 0.14
48 12 0.32
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (48 bp):
TTTTTCCAAATAAAGGCATGCGAACTAAAAAACATGAGGTTAGGTTTG
Found at i:9140221 original size:34 final size:35
Alignment explanation
Indices: 9140173--9140448 Score: 206
Period size: 36 Copynumber: 7.6 Consensus size: 35
9140163 AAATCTGATA
* *
9140173 TTCATGGAAGAGTAGTGAAG-TTCATCA-TCTAGCC
1 TTCACGGAAGAGTAGTGAAGATTCATCATTC-AACC
*
9140207 TTCACGGAAGAGTAGTGAAG-TTCATCATTCAATC
1 TTCACGGAAGAGTAGTGAAGATTCATCATTCAACC
* * * **
9140241 TTCACGGAAAAGTAGTGAAGAAATAAAAATTCAACC
1 TTCACGGAAGAGTAGTGAAG-ATTCATCATTCAACC
* *
9140277 TTCACGGAAGAGTAGTGAAGAAATGT-A-AATTCAGCC
1 TTCACGGAAGAGTAGTGAAG--AT-TCATCATTCAACC
* *
9140313 TTCACGGAAGAGTAGTGAAGCAAATCATTTGCAAATCATCCAGCC
1 TTCACGGAAGAGTAGTGAAG------A-TT-C--ATCATTCAACC
9140358 TTCACGGAAGAGTAGTGAAG-TTCATCATTCAACC
1 TTCACGGAAGAGTAGTGAAGATTCATCATTCAACC
* *
9140392 TTCACGGAAGAGTAGTGAAGAAATACA-AATTCAACC
1 TTCACGGAAGAGTAGTGAAG--ATTCATCATTCAACC
**
9140428 TTCACTAAAGAGTAGTGAAGA
1 TTCACGGAAGAGTAGTGAAGA
9140449 AATGAAAATT
Statistics
Matches: 202, Mismatches: 22, Indels: 36
0.78 0.08 0.14
Matches are distributed among these distances:
34 77 0.38
35 2 0.01
36 83 0.41
37 8 0.04
38 1 0.00
40 2 0.01
41 1 0.00
44 1 0.00
45 27 0.13
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (35 bp):
TTCACGGAAGAGTAGTGAAGATTCATCATTCAACC
Found at i:9140280 original size:36 final size:36
Alignment explanation
Indices: 9140205--9140488 Score: 252
Period size: 36 Copynumber: 7.7 Consensus size: 36
9140195 CATCATCTAG
* * **
9140205 CCTTCACGGAAGAGTAGTGAAG--TTCATCATTCAA
1 CCTTCACGGAAGAGTAGTGAAGAAATAAAAATTCAA
* *
9140239 TCTTCACGGAAAAGTAGTGAAGAAATAAAAATTCAA
1 CCTTCACGGAAGAGTAGTGAAGAAATAAAAATTCAA
** *
9140275 CCTTCACGGAAGAGTAGTGAAGAAATGTAAATTCAG
1 CCTTCACGGAAGAGTAGTGAAGAAATAAAAATTCAA
* *
9140311 CCTTCACGGAAGAGTAGTGAAGCAAATCATTTGCAAATCATCCAG
1 CCTTCACGGAAGAGTAGTGAAG-AAAT-A-----AAA--ATTCAA
* * **
9140356 CCTTCACGGAAGAGTAGTGAAG--TTCATCATTCAA
1 CCTTCACGGAAGAGTAGTGAAGAAATAAAAATTCAA
*
9140390 CCTTCACGGAAGAGTAGTGAAGAAATACAAATTCAA
1 CCTTCACGGAAGAGTAGTGAAGAAATAAAAATTCAA
** * *
9140426 CCTTCACTAAAGAGTAGTGAAGAAATGAAAATTCAG
1 CCTTCACGGAAGAGTAGTGAAGAAATAAAAATTCAA
* *
9140462 CCATCACGAAAGAGTAGTGAAGCAAAT
1 CCTTCACGGAAGAGTAGTGAAG-AAAT
9140489 CATTTATAAA
Statistics
Matches: 204, Mismatches: 32, Indels: 25
0.78 0.12 0.10
Matches are distributed among these distances:
34 46 0.23
36 120 0.59
37 8 0.04
42 1 0.00
43 2 0.01
45 27 0.13
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.22
Consensus pattern (36 bp):
CCTTCACGGAAGAGTAGTGAAGAAATAAAAATTCAA
Found at i:9140475 original size:151 final size:151
Alignment explanation
Indices: 9140196--9140530 Score: 544
Period size: 151 Copynumber: 2.2 Consensus size: 151
9140186 AGTGAAGTTC
* *
9140196 ATCATCTAGCCTTCACGGAAGAGTAGTGAAGTTCATCATTCAATCTTCACGGAAAAGTAGTGAAG
1 ATCATCCAGCCTTCACGGAAGAGTAGTGAAGTTCATCATTCAACCTTCACGGAAAAGTAGTGAAG
* * * *
9140261 AAATAAAAATTCAACCTTCACGGAAGAGTAGTGAAGAAATGTAAATTCAGCCTTCACGGAAGAGT
66 AAATAAAAATTCAACCTTCACGAAAGAGTAGTGAAGAAATGAAAATTCAGCCATCACGAAAGAGT
*
9140326 AGTGAAGCAAATCATTTGCAA
131 AGTGAAGCAAATCATTTACAA
*
9140347 ATCATCCAGCCTTCACGGAAGAGTAGTGAAGTTCATCATTCAACCTTCACGGAAGAGTAGTGAAG
1 ATCATCCAGCCTTCACGGAAGAGTAGTGAAGTTCATCATTCAACCTTCACGGAAAAGTAGTGAAG
* *
9140412 AAATACAAATTCAACCTTCACTAAAGAGTAGTGAAGAAATGAAAATTCAGCCATCACGAAAGAGT
66 AAATAAAAATTCAACCTTCACGAAAGAGTAGTGAAGAAATGAAAATTCAGCCATCACGAAAGAGT
*
9140477 AGTGAAGCAAATCATTTATAA
131 AGTGAAGCAAATCATTTACAA
*
9140498 ATCATCTTCAGTCTTCACGGAAGAGTAGTGAAG
1 ATCATC--CAGCCTTCACGGAAGAGTAGTGAAG
9140531 CAAGAGCATG
Statistics
Matches: 170, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
151 146 0.86
153 24 0.14
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (151 bp):
ATCATCCAGCCTTCACGGAAGAGTAGTGAAGTTCATCATTCAACCTTCACGGAAAAGTAGTGAAG
AAATAAAAATTCAACCTTCACGAAAGAGTAGTGAAGAAATGAAAATTCAGCCATCACGAAAGAGT
AGTGAAGCAAATCATTTACAA
Found at i:9140730 original size:16 final size:16
Alignment explanation
Indices: 9140709--9140770 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
9140699 GTGTCGTTTT
9140709 TATATTTATTATATAA
1 TATATTTATTATATAA
*
9140725 TATATTTATTATTATAT
1 TATATTTATTA-TATAA
*
9140742 TAATATACTATTATAT-A
1 T-ATAT-TTATTATATAA
9140759 T-TA-TTATTATAT
1 TATATTTATTATAT
9140771 TATTGTTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
13 8 0.21
15 2 0.05
16 11 0.28
17 6 0.15
18 7 0.18
19 5 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (16 bp):
TATATTTATTATATAA
Found at i:9140756 original size:8 final size:7
Alignment explanation
Indices: 9140715--9140770 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
9140705 TTTTTATATT
9140715 TATTATA
1 TATTATA
*
9140722 TAATATA
1 TATTATA
9140729 T-TTAT-
1 TATTATA
9140734 TATTATA
1 TATTATA
*
9140741 TTAATATA
1 -TATTATA
9140749 CTATTATA
1 -TATTATA
9140757 TATTAT-
1 TATTATA
9140763 TATTATA
1 TATTATA
9140770 T
1 T
9140771 TATTGTTACA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
5 1 0.03
6 13 0.32
7 14 0.35
8 12 0.30
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (7 bp):
TATTATA
Found at i:9142729 original size:31 final size:31
Alignment explanation
Indices: 9142693--9142752 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
9142683 AACTTAAAAG
* *
9142693 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
9142724 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
9142753 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:9142848 original size:22 final size:22
Alignment explanation
Indices: 9142779--9142839 Score: 122
Period size: 22 Copynumber: 2.8 Consensus size: 22
9142769 TAAATTATTT
9142779 AAATAAATCAATCCATATTTTA
1 AAATAAATCAATCCATATTTTA
9142801 AAATAAATCAATCCATATTTTA
1 AAATAAATCAATCCATATTTTA
9142823 AAATAAATCAATCCATA
1 AAATAAATCAATCCATA
9142840 CTAATAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATAAATCAATCCATATTTTA
Found at i:9142892 original size:80 final size:80
Alignment explanation
Indices: 9142801--9143190 Score: 393
Period size: 80 Copynumber: 4.8 Consensus size: 80
9142791 CCATATTTTA
9142801 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAT
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAT
9142866 TTCATACAACTACAAT
66 TTCATA-AACTACAAT
* * *
9142882 -AATAAATCAATCCATATTTTAAAATAAATCAGTTCATACTAATAAATTATTTAAAATAAATCAA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAT
* *** *
9142946 TCCATATTTTAAAAT
66 TTCATAAACTACAAT
* * * *
9142961 AAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAC-AACTACAA-TA-AT-AAA
1 AAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAATCCATACTAA-TA-AATTATTTAAAA
* * *
9143022 TCAATCCATATT-TTAAAATA-AAT
58 TAAAT-CAT-TTCATAAACTACAAT
* ** **
9143045 CAATTCATACTAATAAAT-TATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 AAATAAAT-C-AATCCATAT-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
9143109 CATTTCATACAACTACAAT
63 CATTTCATA-AACTACAAT
*
9143128 -AATAAATCAATCCATATTTTAAAATAAATCAATCCACACTAATAAATTATTTAAAATAAATCA
1 AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCA
9143191 ATCCATGTTT
Statistics
Matches: 253, Mismatches: 35, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
79 7 0.03
80 155 0.61
81 11 0.04
82 18 0.07
83 3 0.01
84 19 0.08
85 11 0.04
86 27 0.11
87 2 0.01
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (80 bp):
AAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAT
TTCATAAACTACAAT
Found at i:9142919 original size:48 final size:51
Alignment explanation
Indices: 9142766--9143430 Score: 215
Period size: 54 Copynumber: 12.4 Consensus size: 51
9142756 ACAACTACAA
* *
9142766 TAATAAATTATTTAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA-
1 TAATAAA-TA-TTAAATAAATCAATCCATATTTTAAAATAAATCAGTTCATAC
** * * * *
9142818 TTTTAAA-A-TAAATCAATCCATACTAATAAATTATTTAAAATAAATCATTTCATAC
1 TAATAAATATTAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAGTTCATAC
*
9142873 -AACTACA-A-T-AATAAATCAATCCATATTTTAAAATAAATCAGTTCATAC
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAGTTCATAC
* *
9142921 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAGTTCATAC
* ** * *
9142975 TAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAA-TA-TT-AAATAAATCAATCCAT---ATTTTAA-AATAAATCAGTTCATAC
** * * * *
9143032 TTTTAAA-A-TAAATCAATTC-ATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATATTAAAT-AAATCAAT-C-CAT--A-T-TTTAAAATAAATCAGTTCATAC
* * * ** * *
9143087 TAATAAATTATTTAAAATAAATCATTTCATACAACTACAATAATAAATCAATCCATA-
1 TAATAAA-TA-TT-AAATAAATCAATCCAT---ATTTTAA-AATAAATCAGTTCATAC
** * * * * *
9143144 TTTTAAA-A-TAAATCAATCCACA-CTAATAAATTATTTAAAATAAATCAATCCAT-G
1 TAATAAATATTAAATAAAT-CA-ATC-CAT--A-T-TTTAAAATAAATCAGTTCATAC
** * * * *
9143198 TTTTAAA-A-TAAATCAATCAATACTAATAAATTATTTAAAATAAATCAATCCATAC
1 TAATAAATATTAAATAAATCAAT-C-CAT--A-T-TTTAAAATAAATCAGTTCATAC
* *
9143253 -AACTACA-A-T-AATAAATCAATCCATATTTTAAAATAAATCA-ATCGATAC
1 TAA-TAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAGTTC-ATAC
* * *
9143301 TAATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATCAATCCATAC
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAGTTCATAC
* *
9143355 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
1 TAATAAA-TA-TT-AAATAAATCAATCCATATTTTAAAATAAATCAGTTCATAC
9143409 TAATAAATTATTTAAAATAAAT
1 TAATAAA-TA-TT-AAATAAAT
9143431 TATTTTAAAA
Statistics
Matches: 500, Mismatches: 61, Indels: 102
0.75 0.09 0.15
Matches are distributed among these distances:
47 1 0.00
48 56 0.11
49 7 0.01
50 7 0.01
52 26 0.05
53 18 0.04
54 297 0.59
55 24 0.05
57 18 0.04
58 34 0.07
59 7 0.01
60 5 0.01
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.34
Consensus pattern (51 bp):
TAATAAATATTAAATAAATCAATCCATATTTTAAAATAAATCAGTTCATAC
Found at i:9142948 original size:134 final size:134
Alignment explanation
Indices: 9142797--9143085 Score: 551
Period size: 134 Copynumber: 2.2 Consensus size: 134
9142787 CAATCCATAT
9142797 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
* * *
9142862 TCATTTCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAGTTCATACTAATAA
66 TCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAA
9142927 ATTA
131 ATTA
9142931 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
1 TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
9142996 TCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAA
66 TCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAA
9143061 ATTA
131 ATTA
9143065 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
9143086 CTAATAAATT
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 152 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (134 bp):
TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAA
TCAATCCATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAA
ATTA
Found at i:9142957 original size:22 final size:22
Alignment explanation
Indices: 9142931--9142973 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
9142921 TAATAAATTA
9142931 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
9142953 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
9142974 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:9142982 original size:22 final size:22
Alignment explanation
Indices: 9142933--9142981 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
9142923 ATAAATTATT
**
9142933 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
9142955 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
9142978 TAAA
1 TAAA
9142982 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:9143020 original size:112 final size:112
Alignment explanation
Indices: 9142904--9143430 Score: 446
Period size: 112 Copynumber: 4.8 Consensus size: 112
9142894 CATATTTTAA
* *
9142904 AATAAATCAGTTCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
1 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
9142969 CCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
66 CCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
* * * * * *
9143016 AATAAATCAATCCATATTTTAAAATAAATCAATTCATACT-AATAAAT---TA-TTTAAAATAAA
1 AATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAA
* *
9143076 TCAATCCATACTAATAAATTATTTAAAATAAATCATTTCATACAACTACAAT
61 TCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
* * ** * * *
9143128 AATAAATCAATCCATATTTTAAAATAAATCAATCCACACT-AATAAAT---TA-TTTAAAATAAA
1 AATAAATCAATCCATA--CT--AATAAAT-TATTTAAAATAAATCAATCCATATTTTAAAATAAA
* ** * * * *
9143188 TCAATCCAT-GTTTTAAA--A--T-AAATCAATCAATACTAATA-AATTATTTAA-
61 TCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C-CATACAACTA--CAAT
*
9143236 AATAAATCAATCCATAC-AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAA
1 AATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAA
* * * **
9143294 TCGATACTAATAAATTATTTAAAATAAATCAAT-C-TA-TATTTTAA-
65 TCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
9143338 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
1 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
9143403 CCATACTAATAAATTATTTAAAATAAAT
66 CCATACTAATAAATTATTTAAAATAAAT
9143431 TATTTTAAAA
Statistics
Matches: 351, Mismatches: 36, Indels: 60
0.79 0.08 0.13
Matches are distributed among these distances:
97 2 0.01
98 6 0.02
101 3 0.01
102 42 0.12
103 9 0.03
104 9 0.03
105 1 0.00
106 11 0.03
107 6 0.02
108 90 0.26
109 3 0.01
111 5 0.01
112 142 0.40
113 2 0.01
114 1 0.00
116 13 0.04
117 6 0.02
ACGTcount: A:0.52, C:0.13, G:0.01, T:0.34
Consensus pattern (112 bp):
AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
CCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAAT
Found at i:9143059 original size:18 final size:18
Alignment explanation
Indices: 9143038--9143094 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
9143028 CATATTTTAA
9143038 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
* *
9143056 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
*
9143070 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
9143088 AATAAAT
1 AATAAAT
9143095 TATTTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
17 5 0.17
18 14 0.47
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:9143154 original size:134 final size:132
Alignment explanation
Indices: 9143016--9143385 Score: 432
Period size: 134 Copynumber: 2.8 Consensus size: 132
9143006 CAACTACAAT
* *
9143016 AATAAATCAATCCATATTTTAAAATAAATCAATT-CATACTAATAAAT-TATTTAAAATAAATCA
1 AATAAATCAATCCATA-TATAAAATAAAT-AATTAAATA--AATAAATATATTTAAAATAAATCA
* *
9143079 ATCCATACTAATAAATTATTTAAAATAAATCATTTCATACAACTACAATAATAAATCAATCCATA
62 ATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATA
9143144 TTTTAA
127 TTTTAA
* * * * *
9143150 AATAAATCAATCCACA-CT--AATAAATTATTTAAAATAAATCAATCCATGTTTTAAAATAAATC
1 AATAAATCAATCCATATATAAAATAAA-TAATT-AAATAAATAAAT--AT-ATTTAAAATAAATC
*
9143212 AATCAATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCAT
61 AATCCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCAT
9143277 ATTTTAA
126 ATTTTAA
* * * *
9143284 AATAAATCAATCGATA-CT--AATAAATTATTTAAAATAAATCAATCTATATTTTAAAATAAATC
1 AATAAATCAATCCATATATAAAATAAA-TAATT-AAATAAAT-AA-ATATA-TTTAAAATAAATC
9143346 AATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
61 AATCCATACTAATAAATTATTTAAAATAAATCAATCCATA
9143386 TTTTAAAATA
Statistics
Matches: 211, Mismatches: 15, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
130 15 0.07
131 1 0.00
132 4 0.02
133 1 0.00
134 188 0.89
135 1 0.00
136 1 0.00
ACGTcount: A:0.52, C:0.14, G:0.01, T:0.34
Consensus pattern (132 bp):
AATAAATCAATCCATATATAAAATAAATAATTAAATAAATAAATATATTTAAAATAAATCAATCC
ATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATTTT
AA
Found at i:9143320 original size:54 final size:54
Alignment explanation
Indices: 9143262--9143430 Score: 320
Period size: 54 Copynumber: 3.1 Consensus size: 54
9143252 CAACTACAAT
*
9143262 AATAAATCAATCCATATTTTAAAATAAATCAATCGATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
9143316 AATAAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
9143370 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
9143424 AATAAAT
1 AATAAAT
9143431 TATTTTAAAA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 112 1.00
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.36
Consensus pattern (54 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:9143362 original size:22 final size:22
Alignment explanation
Indices: 9143313--9143361 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
9143303 ATAAATTATT
* **
9143313 TAAAATAAATCAATCTATATTT
1 TAAAATAAATCAATCCATATAA
9143335 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
9143358 TAAA
1 TAAA
9143362 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:9143391 original size:22 final size:22
Alignment explanation
Indices: 9143365--9143465 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
9143355 TAATAAATTA
9143365 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
9143387 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
9143410 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
9143434 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
9143456 TTTATAATAA
1 TTTAAAATAA
9143466 TTTATTTTAA
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
22 33 0.56
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:9143439 original size:15 final size:15
Alignment explanation
Indices: 9143410--9143542 Score: 169
Period size: 15 Copynumber: 8.5 Consensus size: 15
9143400 AATCCATACT
9143410 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
9143424 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
9143439 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
9143461 AATAATTTATTTTAA
1 AATAAATTATTTTAA
9143476 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
9143491 AATAAATTATTTTAT
1 AATAAATTATTTTAA
9143506 AATAAATTATTTTAA
1 AATAAATTATTTTAA
9143521 AATAAATTATTTTAA
1 AATAAATTATTTTAA
9143536 AATAAAT
1 AATAAAT
9143543 AACCTTATTA
Statistics
Matches: 105, Mismatches: 6, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
14 9 0.09
15 79 0.75
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:9143452 original size:69 final size:67
Alignment explanation
Indices: 9143356--9143512 Score: 210
Period size: 69 Copynumber: 2.3 Consensus size: 67
9143346 AATCCATACT
*
9143356 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAAT-AATCAAT-CATA-AAATAAATTAT
9143419 TTTAA
63 TTTAA
* ** **
9143424 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATCATAAAATAAATTATTTT
9143489 AA
66 AA
*
9143491 AATAAATTATTTTATAATAAAT
1 AATAAATTATTTTAAAATAAAT
9143513 TATTTTAAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
66 9 0.11
67 28 0.35
68 14 0.17
69 29 0.36
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATCATAAAATAAATTATTTT
AA
Found at i:9143504 original size:45 final size:46
Alignment explanation
Indices: 9143384--9143542 Score: 196
Period size: 45 Copynumber: 3.3 Consensus size: 46
9143374 AATCAATCCA
* **
9143384 TATTTTAAAATAAATCAATCCATACTAATAAATTA-TTTAAAATAAAT
1 TATTTTAAAATAAATCTAT-TTTA-TAATAAATTATTTTAAAATAAAT
*
9143431 TATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAAAAT--A--AAT-C-TATTTTATAATAAATTATTTTAAAATAAAT
9143483 TATTTTAAAATAAAT-TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTAAAATAAATCTATTTTATAATAAATTATTTTAAAATAAAT
9143528 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
9143543 AACCTTATTA
Statistics
Matches: 100, Mismatches: 5, Indels: 16
0.83 0.04 0.13
Matches are distributed among these distances:
45 44 0.44
47 11 0.11
48 3 0.03
49 1 0.01
50 1 0.01
51 12 0.12
52 26 0.26
53 2 0.02
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (46 bp):
TATTTTAAAATAAATCTATTTTATAATAAATTATTTTAAAATAAAT
Found at i:9145286 original size:14 final size:15
Alignment explanation
Indices: 9145269--9145306 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
9145259 GTGTTAGAGT
9145269 TTAAGGTTTAAGCG-
1 TTAAGGTTTAAGCGA
*
9145283 TTAAGGTTT-AGGGA
1 TTAAGGTTTAAGCGA
9145297 TTAAGGTTTA
1 TTAAGGTTTA
9145307 TGATTTAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 18 0.86
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (15 bp):
TTAAGGTTTAAGCGA
Found at i:9150713 original size:18 final size:18
Alignment explanation
Indices: 9150690--9150760 Score: 106
Period size: 18 Copynumber: 3.9 Consensus size: 18
9150680 ACTGAAAATT
*
9150690 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
9150708 TGTCCCGAAGGACTACTA
1 TGTCCCGAAGGACCACTA
*
9150726 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
9150744 TGTCCCGAATGACCACT
1 TGTCCCGAAGGACCACT
9150761 TATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:9151455 original size:20 final size:19
Alignment explanation
Indices: 9151430--9151494 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
9151420 TTTCAAAGAT
9151430 GGTATCGATATTGTCCTTAA
1 GGTATCGATATTGTCCTT-A
*
9151450 GGTATCGATA---CCCTT-
1 GGTATCGATATTGTCCTTA
*
9151465 GGTATCGATATTGTTCTTCA
1 GGTATCGATATTGTCCTT-A
9151485 GGTATCGATA
1 GGTATCGATA
9151495 CCTCATGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
15 10 0.27
17 4 0.11
18 3 0.08
20 20 0.54
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (19 bp):
GGTATCGATATTGTCCTTA
Found at i:9151470 original size:35 final size:35
Alignment explanation
Indices: 9151429--9151496 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
9151419 GTTTCAAAGA
9151429 TGGTATCGATATTGTCCTTAAGGTATCGATACCCT
1 TGGTATCGATATTGTCCTTAAGGTATCGATACCCT
* *
9151464 TGGTATCGATATTGTTCTTCAGGTATCGATACC
1 TGGTATCGATATTGTCCTTAAGGTATCGATACC
9151497 TCATGAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (35 bp):
TGGTATCGATATTGTCCTTAAGGTATCGATACCCT
Found at i:9156972 original size:11 final size:11
Alignment explanation
Indices: 9156956--9156985 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
9156946 TGTAACACCC
9156956 CCAACCCGTAT
1 CCAACCCGTAT
9156967 CCAACCCGTAT
1 CCAACCCGTAT
9156978 CCAACCCG
1 CCAACCCG
9156986 GATAGGAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.27, C:0.50, G:0.10, T:0.13
Consensus pattern (11 bp):
CCAACCCGTAT
Found at i:9158282 original size:20 final size:20
Alignment explanation
Indices: 9158257--9158356 Score: 67
Period size: 20 Copynumber: 5.5 Consensus size: 20
9158247 TTTCAAATAT
9158257 GGTATCGATATTGTTCTTTA
1 GGTATCGATATTGTTCTTTA
* * *
9158277 GGTATCGGTA----CCCTT-
1 GGTATCGATATTGTTCTTTA
9158292 GGTATCGATATTGTTCTTTA
1 GGTATCGATATTGTTCTTTA
* * *
9158312 GGTATCGGTA----CCCTT-
1 GGTATCGATATTGTTCTTTA
*
9158327 GGTATCGATATTGTTCTTCA
1 GGTATCGATATTGTTCTTTA
9158347 GGTATCGATA
1 GGTATCGATA
9158357 CCTCATGAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 20
0.63 0.14 0.22
Matches are distributed among these distances:
15 18 0.32
16 6 0.11
19 5 0.09
20 28 0.49
ACGTcount: A:0.19, C:0.16, G:0.23, T:0.42
Consensus pattern (20 bp):
GGTATCGATATTGTTCTTTA
Found at i:9158296 original size:35 final size:35
Alignment explanation
Indices: 9158256--9158358 Score: 188
Period size: 35 Copynumber: 2.9 Consensus size: 35
9158246 GTTTCAAATA
9158256 TGGTATCGATATTGTTCTTTAGGTATCGGTACCCT
1 TGGTATCGATATTGTTCTTTAGGTATCGGTACCCT
9158291 TGGTATCGATATTGTTCTTTAGGTATCGGTACCCT
1 TGGTATCGATATTGTTCTTTAGGTATCGGTACCCT
* *
9158326 TGGTATCGATATTGTTCTTCAGGTATCGATACC
1 TGGTATCGATATTGTTCTTTAGGTATCGGTACC
9158359 TCATGAATTC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.18, C:0.17, G:0.22, T:0.42
Consensus pattern (35 bp):
TGGTATCGATATTGTTCTTTAGGTATCGGTACCCT
Found at i:9159354 original size:26 final size:26
Alignment explanation
Indices: 9159325--9159377 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
9159315 CATTAAATTT
*
9159325 CATTTTATTTATGACATCCTTTCATG
1 CATTTTATTTATGACATCCTTCCATG
*
9159351 CATTTTATTTATGGCATCCTTCCATG
1 CATTTTATTTATGACATCCTTCCATG
9159377 C
1 C
9159378 CAATAATGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.21, C:0.23, G:0.09, T:0.47
Consensus pattern (26 bp):
CATTTTATTTATGACATCCTTCCATG
Found at i:9159853 original size:19 final size:19
Alignment explanation
Indices: 9159779--9159854 Score: 55
Period size: 19 Copynumber: 3.8 Consensus size: 19
9159769 ATTTCTGACT
* *
9159779 CTATAGTATCGATACCCCTA
1 CTATGGTATCGATA-CTCTA
* *
9159799 CCATGGTATCGATACTATTATA
1 CTATGGTATCGATAC---TCTA
*
9159821 CTATGGT-GCTGATACTCTA
1 CTATGGTATC-GATACTCTA
9159840 CTATGGTATCGATAC
1 CTATGGTATCGATAC
9159855 CATTTTTGCA
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
19 16 0.37
20 13 0.30
21 1 0.02
22 13 0.30
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (19 bp):
CTATGGTATCGATACTCTA
Found at i:9166204 original size:20 final size:20
Alignment explanation
Indices: 9166179--9166218 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
9166169 TTTGGGTTTG
* *
9166179 AGTATCGATATTGGATGAAC
1 AGTATCGATACTGAATGAAC
9166199 AGTATCGATACTGAATGAAC
1 AGTATCGATACTGAATGAAC
9166219 TAAGATGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTGAATGAAC
Found at i:9173110 original size:31 final size:31
Alignment explanation
Indices: 9173072--9173144 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
9173062 AAAATATTTT
* *
9173072 AAATTTGTGATGGAATATGTGGACCCATCAC
1 AAATTTGTGACGGAATATGAGGACCCATCAC
* *
9173103 AAATTTGTGACGGAATATGAGGATCCGTCAC
1 AAATTTGTGACGGAATATGAGGACCCATCAC
*
9173134 AAATTTCTGAC
1 AAATTTGTGAC
9173145 AGATTCACCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (31 bp):
AAATTTGTGACGGAATATGAGGACCCATCAC
Found at i:9173161 original size:31 final size:31
Alignment explanation
Indices: 9173126--9173198 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
9173116 AATATGAGGA
*
9173126 TCCGTCACAAATTTCTGACAGATT-CACCTAT
1 TCCGTCACAAATTTCTGAC-GATTCCACATAT
* *
9173157 TCCGTCACAAATTTCTGACGGTTCCACATGT
1 TCCGTCACAAATTTCTGACGATTCCACATAT
9173188 TCCGTCACAAA
1 TCCGTCACAAA
9173199 ATTTAGAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 3 0.08
31 35 0.92
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.30
Consensus pattern (31 bp):
TCCGTCACAAATTTCTGACGATTCCACATAT
Found at i:9173809 original size:18 final size:18
Alignment explanation
Indices: 9173786--9173821 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9173776 TATTATTATT
*
9173786 ATCTAATTTTTTAAATTA
1 ATCTAATTATTTAAATTA
*
9173804 ATCTAATTATTTGAATTA
1 ATCTAATTATTTAAATTA
9173822 TATTATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.53
Consensus pattern (18 bp):
ATCTAATTATTTAAATTA
Found at i:9174076 original size:2 final size:2
Alignment explanation
Indices: 9174071--9174147 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
9174061 TATATTATTT
9174071 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
9174113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9174148 TCCGACGAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9178468 original size:8 final size:8
Alignment explanation
Indices: 9178455--9178495 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
9178445 CTCATTTTCA
9178455 GAGAATTT
1 GAGAATTT
9178463 GAGAATTT
1 GAGAATTT
*
9178471 -AGAGTTT
1 GAGAATTT
*
9178478 GGGAATTT
1 GAGAATTT
9178486 GAGAATTT
1 GAGAATTT
9178494 GA
1 GA
9178496 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:9178794 original size:128 final size:128
Alignment explanation
Indices: 9178566--9179191 Score: 1243
Period size: 128 Copynumber: 4.9 Consensus size: 128
9178556 TAATCGGAGT
*
9178566 ACTATTCACATGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
9178631 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
9178694 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
9178759 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
9178822 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
9178887 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
9178950 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
9179015 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
9179078 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
9179143 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCA
9179192 GTAAATCAGG
Statistics
Matches: 497, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 497 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
Found at i:9179332 original size:23 final size:23
Alignment explanation
Indices: 9179284--9179338 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
9179274 TGAAGTTTGA
* * *
9179284 ATAAATTAAATAAAATGTTATGG
1 ATAAATTGAATAAAATGTGAAGG
9179307 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGAATAAAATGTGAAG-G
*
9179330 ATAAGTTGA
1 ATAAATTGA
9179339 TTGTGACATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 8 0.30
23 19 0.70
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (23 bp):
ATAAATTGAATAAAATGTGAAGG
Found at i:9179656 original size:33 final size:33
Alignment explanation
Indices: 9179595--9179694 Score: 128
Period size: 34 Copynumber: 3.0 Consensus size: 33
9179585 AAATTTAATG
*
9179595 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTT-GAATAATATAATTTATATTTTAAAT
* * * *
9179629 TTAAATTTGAATAATATTATTTTTATTTTTATT
1 TTAAATTTGAATAATATAATTTATATTTTAAAT
*
9179662 TTAAATTTTGAATAATATAATTTGTATTTTAAA
1 TTAAA-TTTGAATAATATAATTTATATTTTAAA
9179695 AACATTTATC
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 25 0.45
34 31 0.55
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (33 bp):
TTAAATTTGAATAATATAATTTATATTTTAAAT
Found at i:9180293 original size:21 final size:21
Alignment explanation
Indices: 9180213--9180306 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
9180203 TATGGTATAA
*
9180213 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
9180234 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
9180255 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
9180276 AACCCTGCGGGCTCGGAATAT
1 AACCCTGCGGGCTAGGAATGT
9180297 AACCCTGCGG
1 AACCCTGCGG
9180307 AGATGGCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 3 0.04
21 62 0.91
22 3 0.04
ACGTcount: A:0.21, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:9180317 original size:21 final size:21
Alignment explanation
Indices: 9180269--9180319 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
9180259 TGGCGGGCTA
* *
9180269 GGAATGTAACCCTGCGGGCTC
1 GGAATATAACCCTGCGGGATC
9180290 GGAATATAACCCTGCGGAGAT-
1 GGAATATAACCCTGCGG-GATC
*
9180311 GGCATATAA
1 GGAATATAA
9180320 ACTGGTGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
GGAATATAACCCTGCGGGATC
Found at i:9180334 original size:21 final size:21
Alignment explanation
Indices: 9180310--9180357 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
9180300 CCTGCGGAGA
*
9180310 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
9180331 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
9180352 GGGCAT
1 TGGCAT
9180358 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:9182102 original size:33 final size:30
Alignment explanation
Indices: 9182065--9182151 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 30
9182055 AAAAAAAAAA
9182065 AAAAAAATAATAATATATAAATATTATTTTAAT
1 AAAAAAATAATAATATATAAATA-TA--TTAAT
* *
9182098 AAAAAAATAATATTTACATAAATATATTAAT
1 AAAAAAATAATA-ATATATAAATATATTAAT
*
9182129 ATAAAAAATAATAACTATTTAAA
1 A-AAAAAATAATAA-TATATAAA
9182152 AAAATACTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
31 6 0.13
32 17 0.37
33 14 0.30
34 9 0.20
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (30 bp):
AAAAAAATAATAATATATAAATATATTAAT
Found at i:9182125 original size:36 final size:33
Alignment explanation
Indices: 9182063--9182174 Score: 91
Period size: 34 Copynumber: 3.3 Consensus size: 33
9182053 GCAAAAAAAA
* * * *
9182063 AAAAAAAAATAATA-ATATATAAATATTATTTT
1 AAAAAAAAATAATATTTACATAAATATTAATAT
9182095 AATAAAAAAATAATATTTACATAAATATATTAATAT
1 AA-AAAAAAATAATATTTACAT-AA-ATATTAATAT
* * * * *
9182131 AAAAAATAATAACTATTTAAAAAAATACTAACAT
1 AAAAAAAAATAA-TATTTACATAAATATTAATAT
*
9182165 AAAAATAAAT
1 AAAAAAAAAT
9182175 TTCTTACCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
32 2 0.03
33 12 0.19
34 20 0.31
35 13 0.20
36 17 0.27
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (33 bp):
AAAAAAAAATAATATTTACATAAATATTAATAT
Found at i:9182140 original size:32 final size:32
Alignment explanation
Indices: 9182065--9182142 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 32
9182055 AAAAAAAAAA
*
9182065 AAAAAAATAATAATATATAAATATTATTTTAAT
1 AAAAAAATAATAATACATAAATATTA-TTTAAT
*
9182098 AAAAAAATAATATTTACATAAATA-TA-TTAAT
1 AAAAAAATAATA-ATACATAAATATTATTTAAT
9182129 ATAAAAAATAATAA
1 A-AAAAAATAATAA
9182143 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
31 6 0.15
32 11 0.28
33 14 0.35
34 9 0.22
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (32 bp):
AAAAAAATAATAATACATAAATATTATTTAAT
Found at i:9183998 original size:20 final size:21
Alignment explanation
Indices: 9183973--9184021 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
9183963 GACCAACAAA
*
9183973 TTCGCAACGCGA-ATTCCAAT
1 TTCGCAACGCCAGATTCCAAT
*
9183993 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCCAGATTCCAAT
9184013 TTCGCAACG
1 TTCGCAACG
9184022 GATGTAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.27
Consensus pattern (21 bp):
TTCGCAACGCCAGATTCCAAT
Found at i:9184069 original size:20 final size:20
Alignment explanation
Indices: 9184046--9184121 Score: 107
Period size: 20 Copynumber: 3.8 Consensus size: 20
9184036 TGCGATTTTC
*
9184046 CAAATTCGGAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
* *
9184066 CAAATTCGGAACGCGAAAGT
1 CAAATTCGCAACGCGATAGT
**
9184086 CAAATTAACAACGCGATAGT
1 CAAATTCGCAACGCGATAGT
9184106 CAAATTCGCAACGCGA
1 CAAATTCGCAACGCGA
9184122 ATTTGTAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
CAAATTCGCAACGCGATAGT
Found at i:9184144 original size:19 final size:19
Alignment explanation
Indices: 9184105--9184175 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
9184095 AACGCGATAG
*
9184105 TCAAATTCGCAACGCGAATT
1 TCAAATTCGCAAC-TGAATT
*
9184125 TGTAAA-TCGCAACTGAATT
1 T-CAAATTCGCAACTGAATT
9184144 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
9184163 TCAAATTCGCAAC
1 TCAAATTCGCAAC
9184176 AGGTTTTAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
18 3 0.07
19 32 0.70
20 8 0.17
21 3 0.07
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:9185111 original size:24 final size:24
Alignment explanation
Indices: 9185084--9185137 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
9185074 GTATTCGAAA
9185084 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
9185108 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
9185132 TTTGAT
1 TTTGAT
9185138 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:9187421 original size:12 final size:12
Alignment explanation
Indices: 9187399--9187434 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
9187389 AAGCAAAAGG
*
9187399 AAATCAAAATCA
1 AAATCACAATCA
*
9187411 AAATCGCAATCA
1 AAATCACAATCA
9187423 AAATCACAATCA
1 AAATCACAATCA
9187435 CCTTTTGGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.58, C:0.22, G:0.03, T:0.17
Consensus pattern (12 bp):
AAATCACAATCA
Found at i:9187769 original size:20 final size:20
Alignment explanation
Indices: 9187744--9187793 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
9187734 GAAATAAGCA
9187744 TTGCAAATTTGACTATCACG
1 TTGCAAATTTGACTATCACG
* *
9187764 TTGCAAATTTGACTTTCGCG
1 TTGCAAATTTGACTATCACG
*
9187784 TTGCGAATTT
1 TTGCAAATTT
9187794 ACCTTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (20 bp):
TTGCAAATTTGACTATCACG
Found at i:9187884 original size:25 final size:25
Alignment explanation
Indices: 9187856--9187907 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
9187846 AACAAATCAA
*
9187856 TTAAACATTATTGTGGGTACATTAT
1 TTAAACATTATTATGGGTACATTAT
* *
9187881 TTAAACATTGTTATGGGTATATTAT
1 TTAAACATTATTATGGGTACATTAT
9187906 TT
1 TT
9187908 GGAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (25 bp):
TTAAACATTATTATGGGTACATTAT
Found at i:9188685 original size:39 final size:39
Alignment explanation
Indices: 9188642--9188728 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
9188632 TCCGATGCTC
9188642 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
9188681 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
9188720 ATCAAAATC
1 ATCAAAATC
9188729 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:9189135 original size:47 final size:49
Alignment explanation
Indices: 9189028--9189126 Score: 139
Period size: 52 Copynumber: 2.0 Consensus size: 49
9189018 TTTAGAAACA
*
9189028 ACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTT
1 ACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTT
*
9189080 ACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTT
1 ACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTT
9189127 CCTCATCAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
47 17 0.38
48 3 0.07
52 25 0.56
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.32
Consensus pattern (49 bp):
ACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTT
Found at i:9190559 original size:21 final size:21
Alignment explanation
Indices: 9190535--9190630 Score: 97
Period size: 21 Copynumber: 4.6 Consensus size: 21
9190525 GGTGGGACCA
*
9190535 CTTGAACGATGACAGGGGCCT
1 CTTGAACGATGAGAGGGGCCT
* * *
9190556 CTTGAACGGTGGGAGGGGCTT
1 CTTGAACGATGAGAGGGGCCT
*
9190577 CTTCG-ATGATGAGAGGGGCCT
1 CTT-GAACGATGAGAGGGGCCT
*
9190598 CTTGAACGAT-AGGAGGCGCCT
1 CTTGAACGATGA-GAGGGGCCT
*
9190619 CTTGAATGATGA
1 CTTGAACGATGA
9190631 TAGGTGCACC
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
20 2 0.03
21 56 0.93
22 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (21 bp):
CTTGAACGATGAGAGGGGCCT
Found at i:9190613 original size:42 final size:42
Alignment explanation
Indices: 9190535--9190630 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
9190525 GGTGGGACCA
* * * * *
9190535 CTTGAACGATGACAGGGGCCTCTTGAACGGTGGGAGGGGCTT
1 CTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
*
9190577 CTTCG-ATGATGAGAGGGGCCTCTTGAACGATAGGAGGCGCCT
1 CTT-GAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
9190619 CTTGAATGATGA
1 CTTGAATGATGA
9190631 TAGGTGCACC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.02
42 44 0.96
43 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.23
Consensus pattern (42 bp):
CTTGAATGATGACAGGGGCCTCTTGAACGATAGGAGGCGCCT
Found at i:9193263 original size:40 final size:39
Alignment explanation
Indices: 9193218--9193318 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 39
9193208 GCGTAAAAAC
9193218 ATTTGACTTTCGCGTTGCGAATTTGACTATC-GCGTTGCG
1 ATTTGACTTTCGCGTTGCGAATTTGACT-TCTGCGTTGCG
* * *
9193257 AATTTGACTATCGTGTTGCGAATTTGACTTCTGTGTTGCG
1 -ATTTGACTTTCGCGTTGCGAATTTGACTTCTGCGTTGCG
*
9193297 ATTT-ACAAATTCGCGTTGCGAA
1 ATTTGAC--TTTCGCGTTGCGAA
9193319 ATTGGAAACT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
38 2 0.04
39 6 0.12
40 44 0.85
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.39
Consensus pattern (39 bp):
ATTTGACTTTCGCGTTGCGAATTTGACTTCTGCGTTGCG
Found at i:9193297 original size:20 final size:20
Alignment explanation
Indices: 9193218--9193285 Score: 118
Period size: 20 Copynumber: 3.4 Consensus size: 20
9193208 GCGTAAAAAC
*
9193218 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
9193238 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
*
9193258 ATTTGACTATCGTGTTGCGA
1 ATTTGACTATCGCGTTGCGA
9193278 ATTTGACT
1 ATTTGACT
9193286 TCTGTGTTGC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:9193354 original size:20 final size:20
Alignment explanation
Indices: 9193304--9193358 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
9193294 GCGATTTACA
9193304 AATTCGCGTTGCGAAATTGG
1 AATTCGCGTTGCGAAATTGG
* *
9193324 AA-ACTGGGTTGCGAAATTGG
1 AATTC-GCGTTGCGAAATTGG
*
9193344 AATTCGTGTTGCGAA
1 AATTCGCGTTGCGAA
9193359 TTTGTTGGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (20 bp):
AATTCGCGTTGCGAAATTGG
Found at i:9195243 original size:21 final size:20
Alignment explanation
Indices: 9195213--9195254 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
9195203 AATAATGATT
* *
9195213 ATTTTTTTAATATTTCATAA
1 ATTTTTTTAAAAATTCATAA
9195233 ATTTATTTTAAAAATTCATAA
1 ATTT-TTTTAAAAATTCATAA
9195254 A
1 A
9195255 AAAGTAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTTTTTAAAAATTCATAA
Found at i:9195320 original size:15 final size:15
Alignment explanation
Indices: 9195300--9195350 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
9195290 TTTCGAAAAA
9195300 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
9195315 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
9195330 CGAATTACTGGAATT
1 TGAATTACTGGAATT
9195345 TGAATT
1 TGAATT
9195351 TTGAAAAATG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.37, C:0.08, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:9195378 original size:20 final size:20
Alignment explanation
Indices: 9195355--9195398 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
9195345 TGAATTTTGA
9195355 AAAATGAATTACATTTCTGG
1 AAAATGAATTACATTTCTGG
*
9195375 AAAATGAATTATATTTCTGG
1 AAAATGAATTACATTTCTGG
9195395 AAAA
1 AAAA
9195399 CATCTGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (20 bp):
AAAATGAATTACATTTCTGG
Found at i:9195736 original size:24 final size:23
Alignment explanation
Indices: 9195701--9195848 Score: 68
Period size: 25 Copynumber: 6.0 Consensus size: 23
9195691 CTTACTAAAA
* *
9195701 TATTATTAAATATATAAATATAT
1 TATTATTAAATAAAAAAATATAT
9195724 TATTAATTAAATAAAAAAATTTATTAT
1 TATT-ATTAAATAAAAAAA--TA-TAT
* *
9195751 ATATTATAAAATAAAAAATAATATCT
1 -TATTATTAAAT-AAAAA-AATATAT
* ***
9195777 TATTATTTAATATAATTGAT-TA-
1 TATTATTAAATA-AAAAAATATAT
* *
9195799 TATTATTAAAATAAAATATTATAT
1 TATTATT-AAATAAAAAAATATAT
*
9195823 ATATTA-TAAATATTAATAAATATAT
1 -TATTATTAAATA--AAAAAATATAT
9195848 T
1 T
9195849 TAAATATTTT
Statistics
Matches: 94, Mismatches: 17, Indels: 27
0.68 0.12 0.20
Matches are distributed among these distances:
22 11 0.12
23 16 0.17
24 17 0.18
25 24 0.26
26 4 0.04
27 11 0.12
28 9 0.10
29 2 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (23 bp):
TATTATTAAATAAAAAAATATAT
Found at i:9195737 original size:20 final size:19
Alignment explanation
Indices: 9195696--9195739 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
9195686 AATATCTTAC
*
9195696 TAAAATATTATTAAATATA
1 TAAAATATTATTAAATAAA
*
9195715 TAAATATATTATTAATTAAA
1 TAAA-ATATTATTAAATAAA
9195735 TAAAA
1 TAAAA
9195740 AAATTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAAATATTATTAAATAAA
Found at i:9195791 original size:27 final size:25
Alignment explanation
Indices: 9195716--9195791 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 25
9195706 TTAAATATAT
*
9195716 AAATATATTATTAATTAAAT-AAAA
1 AAATATATTATTATTTAAATAAAAA
*
9195740 AAATTTATTATATATTATAAAATAAAAA
1 AAATATATTAT-TATT-T-AAATAAAAA
*
9195768 ATAATATCTTATTATTTAATATAA
1 A-AATATATTATTATTTAA-ATAA
9195792 TTGATTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
24 10 0.24
25 3 0.07
26 3 0.07
27 9 0.21
28 9 0.21
29 8 0.19
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATATATTATTATTTAAATAAAAA
Found at i:9195825 original size:25 final size:25
Alignment explanation
Indices: 9195700--9195829 Score: 78
Period size: 25 Copynumber: 5.3 Consensus size: 25
9195690 TCTTACTAAA
9195700 ATATTATTAAATATATAAATA-TAT-T
1 ATATTATTAAA-ATA-AAATATTATAT
* *
9195725 AT-TAATT-AAATAAAAAAATTTATTAT
1 ATATTATTAAAAT-AAAATA-TTA-TAT
* *
9195751 ATATTA-TAAAATAAAAAATAATAT
1 ATATTATTAAAATAAAATATTATAT
* * * *
9195775 CTTATTATT-TAATATAAT-TGAT-T
1 -ATATTATTAAAATAAAATATTATAT
9195798 ATATTATTAAAATAAAATATTATAT
1 ATATTATTAAAATAAAATATTATAT
9195823 ATATTAT
1 ATATTAT
9195830 AAATATTAAT
Statistics
Matches: 80, Mismatches: 13, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
22 13 0.16
23 11 0.14
24 15 0.19
25 24 0.30
26 11 0.14
27 6 0.08
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (25 bp):
ATATTATTAAAATAAAATATTATAT
Found at i:9195828 original size:9 final size:9
Alignment explanation
Indices: 9195812--9195856 Score: 54
Period size: 9 Copynumber: 4.8 Consensus size: 9
9195802 TATTAAAATA
9195812 AAATATTAT
1 AAATATTAT
*
9195821 ATATATTAT
1 AAATATTAT
9195830 AAATATTAAT
1 AAATATT-AT
*
9195840 AAATATATTT
1 AAATAT-TAT
9195850 AAATATT
1 AAATATT
9195857 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
9 15 0.48
10 15 0.48
11 1 0.03
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AAATATTAT
Found at i:9195842 original size:29 final size:29
Alignment explanation
Indices: 9195808--9195869 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
9195798 ATATTATTAA
*
9195808 AATAAA-ATATTATATATATTATAAAT-ATT
1 AATAAATATATT-TAAATATT-TAAATAATT
*
9195837 AATAAATATATTTAAATATTTTAATAATT
1 AATAAATATATTTAAATATTTAAATAATT
9195866 AATA
1 AATA
9195870 TTTGATGAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 4 0.14
29 20 0.69
30 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AATAAATATATTTAAATATTTAAATAATT
Found at i:9196058 original size:19 final size:18
Alignment explanation
Indices: 9196030--9196082 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
9196020 CTGTTACTAG
* *
9196030 GAAAATGAATTACGTTCTT
1 GAAAACGAATTACGTTC-C
9196049 GAAAACGAATTACGTTCC
1 GAAAACGAATTACGTTCC
9196067 GAAAAACGAATTACGT
1 G-AAAACGAATTACGT
9196083 GTAACAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.03
19 30 0.97
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (18 bp):
GAAAACGAATTACGTTCC
Found at i:9196793 original size:14 final size:13
Alignment explanation
Indices: 9196771--9196814 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
9196761 ATTTTATATA
9196771 TTAATTATAATCC
1 TTAATTATAATCC
9196784 TTATATTATAAAT-C
1 TTA-ATTAT-AATCC
*
9196798 TTAATTATAATCG
1 TTAATTATAATCC
9196811 TTAA
1 TTAA
9196815 ATTAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 3 0.11
13 12 0.44
14 9 0.33
15 3 0.11
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (13 bp):
TTAATTATAATCC
Found at i:9197085 original size:19 final size:18
Alignment explanation
Indices: 9197063--9197117 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
9197053 ATTTTATTTA
9197063 AGAATTTAGAGGAAAATTG
1 AGAATTTAGAGG-AAATTG
* *
9197082 AGAAATTTTG-GGAAGTTG
1 AG-AATTTAGAGGAAATTG
9197100 AGAATTTAGAGGGAAATT
1 AGAATTTAGA-GGAAATT
9197118 AGTGGGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
17 6 0.21
18 7 0.24
19 10 0.34
20 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (18 bp):
AGAATTTAGAGGAAATTG
Found at i:9197432 original size:9 final size:9
Alignment explanation
Indices: 9197420--9197465 Score: 62
Period size: 9 Copynumber: 5.3 Consensus size: 9
9197410 CATCTTTGTA
9197420 TTATTTAAT
1 TTATTTAAT
9197429 TTATTTAAT
1 TTATTTAAT
9197438 TTATTTAAT
1 TTATTTAAT
9197447 TTCA--T-AT
1 TT-ATTTAAT
9197454 TTATTTAAT
1 TTATTTAAT
9197463 TTA
1 TTA
9197466 GTCCTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 1 0.03
7 4 0.12
8 2 0.06
9 25 0.76
10 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (9 bp):
TTATTTAAT
Found at i:9198260 original size:20 final size:20
Alignment explanation
Indices: 9198225--9198285 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
9198215 GGAGTGAAAA
9198225 AAAAGAGGATAAGAAAGAAGAG
1 AAAAGAGG--AAGAAAGAAGAG
*
9198247 AAAAGAGGAAGAAATAAGAG
1 AAAAGAGGAAGAAAGAAGAG
*
9198267 AAAAGAGAAAGAAAGAAGA
1 AAAAGAGGAAGAAAGAAGA
9198286 AGAAGAGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 28 0.78
22 8 0.22
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (20 bp):
AAAAGAGGAAGAAAGAAGAG
Found at i:9198284 original size:27 final size:27
Alignment explanation
Indices: 9198233--9198294 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
9198223 AAAAAAGAGG
*
9198233 ATAAGA-AAGAAGAGAAAAGAGGAAGAA
1 ATAAGAGAAGAAGAGAAAAGAAGAAG-A
9198260 ATAAGAGAA-AAGAG-AAAGAAAGAAGA
1 ATAAGAGAAGAAGAGAAAAG-AAGAAGA
*
9198286 AGAAGAGAA
1 ATAAGAGAA
9198295 TCTCAGTTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 13 0.42
27 16 0.52
28 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (27 bp):
ATAAGAGAAGAAGAGAAAAGAAGAAGA
Found at i:9198653 original size:20 final size:17
Alignment explanation
Indices: 9198610--9198644 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
9198600 TACTTAGTAG
9198610 ATTAA-TTTTATAATAA
1 ATTAATTTTTATAATAA
9198626 ATTAATTTTTATAATAA
1 ATTAATTTTTATAATAA
9198643 AT
1 AT
9198645 GTGATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAATTTTTATAATAA
Found at i:9198838 original size:17 final size:18
Alignment explanation
Indices: 9198811--9198844 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
9198801 AACAACATCT
9198811 TTATGTGTTATTAAATTA
1 TTATGTGTTATTAAATTA
9198829 TTAT-TGTTATTAAATT
1 TTATGTGTTATTAAATT
9198845 TTGTTGTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (18 bp):
TTATGTGTTATTAAATTA
Found at i:9198976 original size:20 final size:21
Alignment explanation
Indices: 9198935--9198986 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
9198925 AGAGATGGTG
*
9198935 TTATTATTATTTAATAAAATA
1 TTATAATTATTTAATAAAATA
*
9198956 TTATAATTATTT-ATTAAATA
1 TTATAATTATTTAATAAAATA
*
9198976 TTATAAATATT
1 TTATAATTATT
9198987 AATGTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TTATAATTATTTAATAAAATA
Found at i:9200017 original size:14 final size:14
Alignment explanation
Indices: 9199990--9200042 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
9199980 ATTATACTAT
9199990 TTAATTTAATTTAAA
1 TTAATTT-ATTTAAA
*
9200005 TTAATTTATTTAAC
1 TTAATTTATTTAAA
*
9200019 TTCATTTATTT--A
1 TTAATTTATTTAAA
*
9200031 TTGATTTATTTA
1 TTAATTTATTTA
9200043 TATTTATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.30
14 16 0.48
15 7 0.21
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (14 bp):
TTAATTTATTTAAA
Found at i:9202026 original size:37 final size:37
Alignment explanation
Indices: 9201984--9202067 Score: 105
Period size: 37 Copynumber: 2.3 Consensus size: 37
9201974 TTAATCTTCT
* * * * * *
9201984 TTGCAATTGTTTCTGCTTCTTGTATCGATTTTTTGAA
1 TTGCAATTGCTTCTGCTCCCTATATCAATTTTATGAA
9202021 TTGCAATTGCTTCTGCTCCCTATATCAATTTTATGAA
1 TTGCAATTGCTTCTGCTCCCTATATCAATTTTATGAA
*
9202058 TTACAATTGC
1 TTGCAATTGC
9202068 CCTGATTTCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (37 bp):
TTGCAATTGCTTCTGCTCCCTATATCAATTTTATGAA
Found at i:9203064 original size:70 final size:70
Alignment explanation
Indices: 9202913--9203052 Score: 174
Period size: 70 Copynumber: 2.0 Consensus size: 70
9202903 CTAGTAGTAG
* * * * *
9202913 GATAATTATATTC-TTTTGAATATTTCAAATTAATATATCTTTGTTATATATTTAACTTTAAATA
1 GATAATTATA-TCGTTTTGAATATTTCAAATTAAAAGATATCTATTATATATTTAACTTTAAATA
*
9202977 TTAAAA
65 TCAAAA
* * * *
9202983 GATAATTATATCGTTTTGAATATTTCAAATTAAAAGATATCTATTATCTCTTTAAGTTTGAATAT
1 GATAATTATATCGTTTTGAATATTTCAAATTAAAAGATATCTATTATATATTTAACTTTAAATAT
9203048 CAAAA
66 CAAAA
9203053 TGTATCTATA
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
69 2 0.03
70 57 0.97
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.46
Consensus pattern (70 bp):
GATAATTATATCGTTTTGAATATTTCAAATTAAAAGATATCTATTATATATTTAACTTTAAATAT
CAAAA
Found at i:9203295 original size:2 final size:2
Alignment explanation
Indices: 9203288--9203325 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
9203278 TTTACTTTGT
*
9203288 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9203326 ATAATAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9205207 original size:43 final size:43
Alignment explanation
Indices: 9205160--9205257 Score: 110
Period size: 43 Copynumber: 2.2 Consensus size: 43
9205150 TTTTTCTCTG
9205160 TATAATTGAATCTCTTAATTATTTTTAATATT-A-TTTTTATATT
1 TATAATTGAAT-TCTTAATTATTTTTAAT-TTCACTTTTTATATT
* * * *
9205203 TATAATTCAGGTTCTTAATTTTTTTTAATTTCACTTTTTTTTATT
1 TATAATTGA-ATTCTTAATTATTTTTAATTTCAC-TTTTTATATT
9205248 TATAATTGAA
1 TATAATTGAA
9205258 CCCTCTAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
42 2 0.04
43 25 0.56
44 1 0.02
45 17 0.38
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (43 bp):
TATAATTGAATTCTTAATTATTTTTAATTTCACTTTTTATATT
Found at i:9205369 original size:43 final size:43
Alignment explanation
Indices: 9205223--9205740 Score: 379
Period size: 43 Copynumber: 12.1 Consensus size: 43
9205213 GTTCTTAATT
* **
9205223 TTTTTTAATTTCACTTTTTTTTATTTATAATTG-A-ACCCTCTAA
1 TTTTTTAATCTCACTTTTTACT-TTTATAATTGAAGACCC-CTAA
* * * * ** * *
9205266 CTTTTCAATCCCACATTTT-CTTTTATAATTG-AGGTCCTTAG
1 TTTTTTAATCTCACTTTTTACTTTTATAATTGAAGACCCCTAA
* * * **
9205307 TTTTTCCAATATCA-TTTTTACCTTTATAATTGAAG-CCTTTAA
1 TTTTT-TAATCTCACTTTTTACTTTTATAATTGAAGACCCCTAA
* *
9205349 TTTTTTAATCTCACTTTTTTACTTTTATAATTG-AGATCTCTAA
1 TTTTTTAATCTCAC-TTTTTACTTTTATAATTGAAGACCCCTAA
* *
9205392 TTTTTTCAATC-CATCTTTTTACTTTTATAATTG-AGACCCTTGA
1 TTTTTT-AATCTCA-CTTTTTACTTTTATAATTGAAGACCCCTAA
* * *
9205435 TTTTTTCAATCTCACCTTCTAGTTTTATAATTGAA-ACCCCTAA
1 TTTTTT-AATCTCACTTTTTACTTTTATAATTGAAGACCCCTAA
* *
9205478 TTTTTTTAATCTCACTTTTTACTTTTATAATTG-AGACCTCTAGC
1 -TTTTTTAATCTCACTTTTTACTTTTATAATTGAAGACCCCTA-A
** *
9205522 TTTTCCAATCTCACTTTTTACTTTTATAATTGAA-TCCCCTAA
1 TTTTTTAATCTCACTTTTTACTTTTATAATTGAAGACCCCTAA
**
9205564 TTTTTTAATCTCACTTTTTTTA-TCTTTATAATTG-AGGTCCCTAA
1 TTTTTTAATCTCAC--TTTTTACT-TTTATAATTGAAGACCCCTAA
* *
9205608 TTTTTTCAATCTCACTTTCTACCTTTATAATTGAAG-CCCCTAA
1 TTTTTT-AATCTCACTTTTTACTTTTATAATTGAAGACCCCTAA
* * * * * *
9205651 TTTTTGTAACCTCAATTTTTACCTTTATAATTGAGGA-CTCAAA
1 TTTTT-TAATCTCACTTTTTACTTTTATAATTGAAGACCCCTAA
* * * *
9205694 TATTTTCAATC-CAAATTTTTTACTTTTATAATT-TAGGCCCCTAA
1 T-TTTTTAATCTC--ACTTTTTACTTTTATAATTGAAGACCCCTAA
9205738 TTT
1 TTT
9205741 AATCAATTTT
Statistics
Matches: 383, Mismatches: 64, Indels: 56
0.76 0.13 0.11
Matches are distributed among these distances:
41 27 0.07
42 45 0.12
43 231 0.60
44 72 0.19
45 8 0.02
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.50
Consensus pattern (43 bp):
TTTTTTAATCTCACTTTTTACTTTTATAATTGAAGACCCCTAA
Found at i:9205483 original size:129 final size:124
Alignment explanation
Indices: 9205223--9205740 Score: 438
Period size: 130 Copynumber: 4.0 Consensus size: 124
9205213 GTTCTTAATT
* ** * *
9205223 TTTTTTAATTTCACTTTTTTTTATTTATAATTGA-ACCCTCTAACTTTTCAATCCCACATTTT-C
1 TTTTTTAATCTCACTTTTTACT-TTTATAATTGAGA-CCTCTAATTTTTCAAT-CCACTTTTTAC
** * * * **
9205286 TTTTATAATTGAGGTCCTTAGTTTTTCCAATATCA-TTTTTACCTTTATAATTGAAGCCTTTAA
63 TTTTATAATTGAGACCCTTA-TTTTTTCAATCTCACTTTTTA-TTTTATAATTGAAGCCCCTAA
*
9205349 TTTTTTAATCTCACTTTTTTACTTTTATAATTGAGATCTCTAATTTTTTCAATCCATCTTTTTAC
1 TTTTTTAATCTCAC-TTTTTACTTTTATAATTGAGACCTCTAA-TTTTTCAATCCA-CTTTTTAC
* * *
9205414 TTTTATAATTGAGACCCTTGATTTTTTCAATCTCACCTTCTAGTTTTATAATTGAAACCCCTAA
63 TTTTATAATTGAGACCCTT-ATTTTTTCAATCTCACTTTTTA-TTTTATAATTGAAGCCCCTAA
* *
9205478 TTTTTTTAATCTCACTTTTTACTTTTATAATTGAGACCTCTAGCTTTTCCAATCTCACTTTTTAC
1 -TTTTTTAATCTCACTTTTTACTTTTATAATTGAGACCTCTA-ATTTTTCAATC-CACTTTTTAC
* * *
9205543 TTTTATAATTGA-ATCCCCTAATTTTTT-AATCTCACTTTTTTTATCTTTATAATTGAGGTCCCT
63 TTTTATAATTGAGA--CCCTTATTTTTTCAATCTCAC--TTTTTAT-TTTATAATTGAAGCCCCT
9205606 AA
123 AA
* * * * * *
9205608 TTTTTTCAATCTCACTTTCTACCTTTATAATTGA-AGCCCCTAATTTTTGTAACCTCAATTTTTA
1 TTTTTT-AATCTCACTTTTTACTTTTATAATTGAGA-CCTCTAATTTTT-CAATC-CACTTTTTA
* * ** * * * *
9205672 CCTTTATAATTGAGGACTCAAATATTTTCAATC-CAAATTTTTTACTTTTATAATTTAGGCCCCT
62 CTTTTATAATTGA-GACCCTTATTTTTTCAATCTC--ACTTTTTA-TTTTATAATTGAAGCCCCT
9205736 AA
123 AA
9205738 TTT
1 TTT
9205741 AATCAATTTT
Statistics
Matches: 327, Mismatches: 41, Indels: 44
0.79 0.10 0.11
Matches are distributed among these distances:
126 33 0.10
127 20 0.06
128 39 0.12
129 96 0.29
130 132 0.40
131 5 0.02
132 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.50
Consensus pattern (124 bp):
TTTTTTAATCTCACTTTTTACTTTTATAATTGAGACCTCTAATTTTTCAATCCACTTTTTACTTT
TATAATTGAGACCCTTATTTTTTCAATCTCACTTTTTATTTTATAATTGAAGCCCCTAA
Found at i:9205508 original size:21 final size:21
Alignment explanation
Indices: 9205479--9205551 Score: 51
Period size: 21 Copynumber: 3.4 Consensus size: 21
9205469 AACCCCTAAT
*
9205479 TTTTTTAATCTCACTTTTTAC
1 TTTTATAATCTCACTTTTTAC
* * *
9205500 TTTTATAAT-TGAGAC-CTCTAGC
1 TTTTATAATCT--CACTTTTTA-C
**
9205522 TTTTCCAATCTCACTTTTTAC
1 TTTTATAATCTCACTTTTTAC
9205543 TTTTATAAT
1 TTTTATAAT
9205552 TGAATCCCCT
Statistics
Matches: 36, Mismatches: 11, Indels: 10
0.63 0.19 0.18
Matches are distributed among these distances:
20 1 0.03
21 21 0.58
22 13 0.36
23 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTATAATCTCACTTTTTAC
Found at i:9205637 original size:173 final size:172
Alignment explanation
Indices: 9205223--9205740 Score: 524
Period size: 173 Copynumber: 3.0 Consensus size: 172
9205213 GTTCTTAATT
* * * *
9205223 TTTTTTAATTTCACTTTTTTT-TATTTATAATTGA-ACCCTCTAA-CTTTTCAATCCCACATTT-
1 TTTTTTAATCTCACTTTTTTTATCTTTATAATTGAGA-CC-CTAATTTTTTCAATCTCAC-TTTC
* * * * * * *
9205284 T-CTTTTATAATTGAGGTCCTTAGTTTTTCCAATATCATTTTTACCTTTATAATTGA-AGCCTTT
63 TACTTTTATAATTGAAGCCCCTAATTTTTCTAATCTCATTTTTACCTTTATAATTGAGAGCCTCT
** *
9205347 AATTTTTTAATCTCACTTTTTTACTTTTATAATTGAGATCTCTAA
128 AATTTTCCAATCTCACTTTTTTACTTTTATAATTGAGATCCCTAA
* * *
9205392 TTTTTTCAATC-CA-TCTTTTTA-CTTTTATAATTGAGACCCTTGATTTTTTCAATCTCACCTTC
1 TTTTTT-AATCTCACTTTTTTTATC-TTTATAATTGAGACCC-TAATTTTTTCAATCTCACTTTC
* * * *
9205454 TAGTTTTATAATTGAAACCCCTAATTTTTTTAATCTCACTTTTTACTTTTATAATTGAGA-CCTC
63 TACTTTTATAATTGAAGCCCCTAATTTTTCTAATCTCA-TTTTTACCTTTATAATTGAGAGCCTC
*
9205518 TAGCTTTTCCAATCTCAC-TTTTTACTTTTATAATTGA-ATCCCCTAA
127 TA-ATTTTCCAATCTCACTTTTTTACTTTTATAATTGAGAT-CCCTAA
*
9205564 TTTTTTAATCTCACTTTTTTTATCTTTATAATTGAGGTCCCTAATTTTTTCAATCTCACTTTCTA
1 TTTTTTAATCTCACTTTTTTTATCTTTATAATTGA-GACCCTAATTTTTTCAATCTCACTTTCTA
* * * * *
9205629 CCTTTATAATTGAAGCCCCTAATTTTTGTAACCTCAATTTTTACCTTTATAATTGAG-GACTCAA
65 CTTTTATAATTGAAGCCCCTAATTTTTCTAATCTC-ATTTTTACCTTTATAATTGAGAGCCTCTA
* * * **
9205693 ATATTTTCAATC-CAAATTTTTTACTTTTATAATTTAGGCCCCTAA
129 AT-TTTCCAATCTC-ACTTTTTTACTTTTATAATTGAGATCCCTAA
9205738 TTT
1 TTT
9205741 AATCAATTTT
Statistics
Matches: 287, Mismatches: 40, Indels: 39
0.78 0.11 0.11
Matches are distributed among these distances:
168 7 0.02
169 25 0.09
170 17 0.06
171 33 0.11
172 57 0.20
173 115 0.40
174 33 0.11
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.50
Consensus pattern (172 bp):
TTTTTTAATCTCACTTTTTTTATCTTTATAATTGAGACCCTAATTTTTTCAATCTCACTTTCTAC
TTTTATAATTGAAGCCCCTAATTTTTCTAATCTCATTTTTACCTTTATAATTGAGAGCCTCTAAT
TTTCCAATCTCACTTTTTTACTTTTATAATTGAGATCCCTAA
Found at i:9209295 original size:19 final size:19
Alignment explanation
Indices: 9209262--9209298 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
9209252 ATGATCAACA
*
9209262 AAATCGCAATACGATCTCT
1 AAATCGCAACACGATCTCT
*
9209281 AAATCGCAACGCGATCTC
1 AAATCGCAACACGATCTC
9209299 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACACGATCTCT
Found at i:9210052 original size:20 final size:20
Alignment explanation
Indices: 9210027--9210071 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9210017 AAAATTGCAA
*
9210027 GCGATAGTCAAATTCGCGTT
1 GCGATAATCAAATTCGCGTT
** *
9210047 GCGATAATCATTTTCGTGTT
1 GCGATAATCAAATTCGCGTT
9210067 GCGAT
1 GCGAT
9210072 TTTCATTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (20 bp):
GCGATAATCAAATTCGCGTT
Found at i:9210077 original size:20 final size:20
Alignment explanation
Indices: 9210039--9210094 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
9210029 GATAGTCAAA
* **
9210039 TTCGCGTTGCGATAATCATT
1 TTCGTGTTGCGATTTTCATT
9210059 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
9210079 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
9210095 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:9210101 original size:20 final size:20
Alignment explanation
Indices: 9210058--9210101 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
9210048 CGATAATCAT
* *
9210058 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
9210078 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
9210098 TTTC
1 TTTC
9210102 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:9212037 original size:20 final size:20
Alignment explanation
Indices: 9212014--9212077 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
9212004 GAAACTTAAA
9212014 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
9212034 ATCGCAA--C---AATGACT
1 ATCGCAACGCGAAAATGACT
**
9212049 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
9212069 ATCGCAACG
1 ATCGCAACG
9212078 GGATAATCGC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 14 0.38
17 1 0.03
18 1 0.03
20 21 0.57
ACGTcount: A:0.36, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:9212047 original size:15 final size:15
Alignment explanation
Indices: 9212027--9212056 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
9212017 GCAACGCGAA
9212027 AATGACTATCGCAAC
1 AATGACTATCGCAAC
9212042 AATGACTATCGCAAC
1 AATGACTATCGCAAC
9212057 GCGAATTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (15 bp):
AATGACTATCGCAAC
Found at i:9212169 original size:33 final size:33
Alignment explanation
Indices: 9212127--9212199 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
9212117 TAAATTCGCA
* * *
9212127 TTGCGATTTTCATTTTGTATTGCGATTTTCACG
1 TTGCGATTTTCATTTCGCATTGCGATTATCACG
* *
9212160 TTGCGATTTTTATTTCGCATTGCGATTATCCCG
1 TTGCGATTTTCATTTCGCATTGCGATTATCACG
9212193 TTGCGAT
1 TTGCGAT
9212200 AGTCAAATTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.15, C:0.18, G:0.19, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTATCACG
Found at i:9212216 original size:20 final size:20
Alignment explanation
Indices: 9212191--9212239 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
9212181 GCGATTATCC
9212191 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
9212211 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
9212231 CATTGCGAT
1 CGTTGCGAT
9212240 TTTAAGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:9212846 original size:42 final size:42
Alignment explanation
Indices: 9212756--9212867 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
9212746 CTGTCATCGT
* *
9212756 TCAAGAGG-CCTCTCCTATCGTTCAAGAGGCCCCTATCATCCC
1 TCAAGAGGTCC-CTCCCACCGTTCAAGAGGCCCCTATCATCCC
* * * **
9212798 TCAAGA-GTCCCCTCCCACTGTTCAAGAGGCCCCTGTTATCGT
1 TCAAGAGGT-CCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
* *
9212840 TGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCAAGAGGTCCCTCCCACCGTTCAAGAG
9212868 CCCGATTCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
41 1 0.02
42 52 0.91
43 4 0.07
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (42 bp):
TCAAGAGGTCCCTCCCACCGTTCAAGAGGCCCCTATCATCCC
Found at i:9214263 original size:14 final size:14
Alignment explanation
Indices: 9214221--9214257 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
9214211 GCTTGTTTAA
*
9214221 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
9214235 TTGATTTGTAAAAT
1 TTGATTTGTAAAAT
9214249 TTGATTTGT
1 TTGATTTGT
9214258 TTAATTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:9214265 original size:27 final size:28
Alignment explanation
Indices: 9214221--9214273 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
9214211 GCTTGTTTAA
*
9214221 TTGATTTGTAAAAGTTGATTTGTAAAAT
1 TTGATTTGTAAAAGTTGATGTGTAAAAT
**
9214249 TTGATTTGTTTAA-TTGATGTGTAAA
1 TTGATTTGTAAAAGTTGATGTGTAAA
9214274 TAATTCTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (28 bp):
TTGATTTGTAAAAGTTGATGTGTAAAAT
Found at i:9214595 original size:20 final size:20
Alignment explanation
Indices: 9214433--9214602 Score: 165
Period size: 20 Copynumber: 8.8 Consensus size: 20
9214423 GCGATTTTCA
* * *
9214433 CGTTGCGAAAGT-TAATTGG
1 CGTTGCGATAGTCAAATTCG
*
9214452 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
* * *
9214472 CGTTGCAATAGTAAAATTCC
1 CGTTGCGATAGTCAAATTCG
* *
9214492 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
9214512 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
9214532 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
9214552 AGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
9214566 CGTTGAGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
9214586 TGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
9214603 GAATGTGTAA
Statistics
Matches: 124, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
14 10 0.08
16 1 0.01
18 1 0.01
19 11 0.09
20 101 0.81
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:9217104 original size:24 final size:24
Alignment explanation
Indices: 9217070--9217123 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
9217060 CTGAAACATC
9217070 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
*
9217094 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
9217118 ATCAAA
1 ATCAAA
9217124 TTTCGAATAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Done.