Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008343.1 Hibiscus syriacus cultivar Beakdansim tig00111070_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: 738381
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:347115 original size:113 final size:110
Alignment explanation
Indices: 346975--347251 Score: 424
Period size: 113 Copynumber: 2.5 Consensus size: 110
346965 TCAAATCATT
* *
346975 ATTATTA-AATCATTATTAT-AATGATTATTATAATGATTATTATTAAATCATTATTATAATGAT
1 ATTATTATAAT-ATTATTATAAATCATTATTATAATGATTATTATCAAATCATTATTATAATGAT
347038 TATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATC
65 TATTATCAAATCATTACTAAATCATCAAATCATTAAATA-TTAAATC
347085 ATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTATTATAATGA
1 ATTATTATAAT-ATTATTA-TAAATCATTATTATAATGATTATTATCAAATCATTATTATAATGA
347150 TTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAATTC
64 TTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAA-TC
*
347198 ATTATTA-AAT-TTATTATTAAATC---ATTATAATGATTATTATCAAATCATTTTTAT
1 ATTATTATAATATTATTA-TAAATCATTATTATAATGATTATTATCAAATCATTATTAT
347252 GGTTAATTGA
Statistics
Matches: 158, Mismatches: 5, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
107 30 0.19
110 19 0.12
111 10 0.06
112 9 0.06
113 90 0.57
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (110 bp):
ATTATTATAATATTATTATAAATCATTATTATAATGATTATTATCAAATCATTATTATAATGATT
ATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAATC
Found at i:347205 original size:12 final size:12
Alignment explanation
Indices: 347188--347225 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
347178 AATCATTAAA
347188 TATTAAATTCAT
1 TATTAAATTCAT
*
347200 TATTAAATTTAT
1 TATTAAATTCAT
347212 TATTAAA-TCAT
1 TATTAAATTCAT
347223 TAT
1 TAT
347226 AATGATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 6 0.25
12 18 0.75
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:347441 original size:17 final size:18
Alignment explanation
Indices: 347421--347509 Score: 65
Period size: 18 Copynumber: 4.8 Consensus size: 18
347411 TATTAGTAAA
347421 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
347438 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
* *
347456 ACTAATATTACTATCAAATAA-T
1 TC-ATTATTA-T-T--AATAATT
* * *
347478 TAAATATTAATAATAATT
1 TCATTATTATTAATAATT
*
347496 TCATTATTACTAAT
1 TCATTATTATTAAT
347510 CATTACTATC
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
17 16 0.28
18 19 0.33
19 7 0.12
20 1 0.02
21 8 0.14
22 1 0.02
23 5 0.09
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:350816 original size:17 final size:17
Alignment explanation
Indices: 350761--350822 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
350751 ACAATATAAA
*
350761 TTAAACAAAATATTTTT
1 TTAAACACAATATTTTT
* *
350778 TTAAAACAACACTAAATATTT
1 TT-AAAC-ACA--ATATTTTT
350799 TTAAACACAATATTTTT
1 TTAAACACAATATTTTT
350816 TTAAACA
1 TTAAACA
350823 GAAATTATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 15 0.42
18 4 0.11
19 5 0.14
20 4 0.11
21 8 0.22
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAACACAATATTTTT
Found at i:351354 original size:21 final size:21
Alignment explanation
Indices: 351321--351369 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
351311 AATATAATAT
351321 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
351342 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
351363 ATTAACT
1 A-TAACT
351370 AGATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:351834 original size:65 final size:65
Alignment explanation
Indices: 351764--351902 Score: 206
Period size: 65 Copynumber: 2.1 Consensus size: 65
351754 TGCAGCTACG
* * * *
351764 GATGCAGGAATCTCCCAGCTATGGATGAAACGTATGCATGAGTGATATGGTTAAAGCTTGGTCGT
1 GATGCAGGAATCTCCCAGCTATGGATGAAACGCATGCATGAGGGATAGGGTTAAAGCTTGGGCGT
* **
351829 GATGCAGGAATCTCCCAGCTATGGATGCAACGCATGCATGAGGGATAGGGTTAAATTTTGGGCGT
1 GATGCAGGAATCTCCCAGCTATGGATGAAACGCATGCATGAGGGATAGGGTTAAAGCTTGGGCGT
*
351894 GGTGCAGGA
1 GATGCAGGA
351903 CTCCACAGCT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (65 bp):
GATGCAGGAATCTCCCAGCTATGGATGAAACGCATGCATGAGGGATAGGGTTAAAGCTTGGGCGT
Found at i:351957 original size:29 final size:30
Alignment explanation
Indices: 351915--351974 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
351905 CCACAGCTTG
*
351915 GTCGCCGGGACTCCATGGCGACCTAC-CAT
1 GTCGCCGGGACTCCACGGCGACCTACACAT
351944 GTCGCCGGGACTCCACGGCGACCTACACAT
1 GTCGCCGGGACTCCACGGCGACCTACACAT
351974 G
1 G
351975 CAGCTCCCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.18, C:0.38, G:0.28, T:0.15
Consensus pattern (30 bp):
GTCGCCGGGACTCCACGGCGACCTACACAT
Found at i:352017 original size:16 final size:16
Alignment explanation
Indices: 351993--352045 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
351983 GCTCTTTGGT
* *
351993 CACCGATCTCCCCTTG
1 CACCAATCTCCCCATG
352009 CACCAATCTCCCCATG
1 CACCAATCTCCCCATG
*
352025 CATGCACGATCTCCCCATG
1 CA--C-CAATCTCCCCATG
352044 CA
1 CA
352046 TGCACTGATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 16 0.52
18 1 0.03
19 14 0.45
ACGTcount: A:0.21, C:0.47, G:0.11, T:0.21
Consensus pattern (16 bp):
CACCAATCTCCCCATG
Found at i:352038 original size:19 final size:20
Alignment explanation
Indices: 352014--352060 Score: 87
Period size: 19 Copynumber: 2.4 Consensus size: 20
352004 CCTTGCACCA
352014 ATCTCCCCATGCATGCAC-G
1 ATCTCCCCATGCATGCACTG
352033 ATCTCCCCATGCATGCACTG
1 ATCTCCCCATGCATGCACTG
352053 ATCTCCCC
1 ATCTCCCC
352061 CCACCCATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.19, C:0.45, G:0.13, T:0.23
Consensus pattern (20 bp):
ATCTCCCCATGCATGCACTG
Found at i:352121 original size:29 final size:29
Alignment explanation
Indices: 352105--352184 Score: 151
Period size: 29 Copynumber: 2.8 Consensus size: 29
352095 GTCGCCCCGA
352105 GTGCATGGCGACCTCCTTGGTCGTTGGGC
1 GTGCATGGCGACCTCCTTGGTCGTTGGGC
352134 GTGCATGGCGACCTCCTTGGTCGTTGGGC
1 GTGCATGGCGACCTCCTTGGTCGTTGGGC
*
352163 GTGCATGGCGACCTCTTTGGTC
1 GTGCATGGCGACCTCCTTGGTC
352185 ACTGTAGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.07, C:0.28, G:0.36, T:0.29
Consensus pattern (29 bp):
GTGCATGGCGACCTCCTTGGTCGTTGGGC
Found at i:352916 original size:218 final size:218
Alignment explanation
Indices: 352538--352974 Score: 811
Period size: 218 Copynumber: 2.0 Consensus size: 218
352528 CGCTCCTAAT
*
352538 CCTTGTCGAAGTGAAGTGGCTCCTTTGCTTAGCCTCAGCACAGTTCGTTGATCTCTGCACTCCGG
1 CCTTGTCGAAGTGAAGTGGCTCCTTTGCTTAGCCTCAGCACAGTTCGGTGATCTCTGCACTCCGG
*
352603 TTGATTGTCGGTTTGCTCCTTCGATTTCAGGCTGCGTCTTTGCGTCCTATTTCTCTGCTACTCCT
66 TTGATTGTCGGTTAGCTCCTTCGATTTCAGGCTGCGTCTTTGCGTCCTATTTCTCTGCTACTCCT
352668 TGTTTGGCTCTTCGTTTTTCAAATCTGGTGAGATCGCTCCTTTACTGCTCTCGGTTGTTTTGGCA
131 TGTTTGGCTCTTCGTTTTTCAAATCTGGTGAGATCGCTCCTTTACTGCTCTCGGTTGTTTTGGCA
352733 TACTGTTTTTCAATTTACGGTTA
196 TACTGTTTTTCAATTTACGGTTA
* * *
352756 CCTTGTCGAAGTGAAGTGGCTCCTTTGCTTGGCCTCAGCACAGTTTGGTGATCTCTGCACTCTGG
1 CCTTGTCGAAGTGAAGTGGCTCCTTTGCTTAGCCTCAGCACAGTTCGGTGATCTCTGCACTCCGG
*
352821 TTGATTGTCGGTTAGCTCCTTCGATTTCAGGCTGCGTCTTTGCGTCCTGTTTCTCTGCTACTCCT
66 TTGATTGTCGGTTAGCTCCTTCGATTTCAGGCTGCGTCTTTGCGTCCTATTTCTCTGCTACTCCT
*
352886 TGTTTGGCTCTTTGTTTTTCAAATCTGGTGAGATCGCTCCTTTACTGCTCTCGGTTGTTTTGGCA
131 TGTTTGGCTCTTCGTTTTTCAAATCTGGTGAGATCGCTCCTTTACTGCTCTCGGTTGTTTTGGCA
352951 TACTGTTTTTCAATTTACGGTTA
196 TACTGTTTTTCAATTTACGGTTA
352974 C
1 C
352975 TTCTCTCCGT
Statistics
Matches: 212, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
218 212 1.00
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (218 bp):
CCTTGTCGAAGTGAAGTGGCTCCTTTGCTTAGCCTCAGCACAGTTCGGTGATCTCTGCACTCCGG
TTGATTGTCGGTTAGCTCCTTCGATTTCAGGCTGCGTCTTTGCGTCCTATTTCTCTGCTACTCCT
TGTTTGGCTCTTCGTTTTTCAAATCTGGTGAGATCGCTCCTTTACTGCTCTCGGTTGTTTTGGCA
TACTGTTTTTCAATTTACGGTTA
Found at i:369704 original size:61 final size:61
Alignment explanation
Indices: 369577--369696 Score: 159
Period size: 61 Copynumber: 2.0 Consensus size: 61
369567 CATCAAGCGT
* * **
369577 GCCTTCCCTGGGTTTTCGTCTGAGCTGGCGCCACGTGGGTAAAGCACGAATCACCATCCAA
1 GCCTTCCCTGGGTTTTCGTCCGAGCTGACGCCACGTGGAAAAAGCACGAATCACCATCCAA
* * * **
369638 GCCTTCCCTGGGTTTTCGTCCGATCTGACGCCATGTGGAAAAAGCGCGGGTCACCATCC
1 GCCTTCCCTGGGTTTTCGTCCGAGCTGACGCCACGTGGAAAAAGCACGAATCACCATCC
369697 GCTCCTTCGT
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.18, C:0.32, G:0.27, T:0.23
Consensus pattern (61 bp):
GCCTTCCCTGGGTTTTCGTCCGAGCTGACGCCACGTGGAAAAAGCACGAATCACCATCCAA
Found at i:369862 original size:13 final size:13
Alignment explanation
Indices: 369844--369869 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
369834 TTTCACATTC
369844 TTCCTTCTATCAA
1 TTCCTTCTATCAA
369857 TTCCTTCTATCAA
1 TTCCTTCTATCAA
369870 GCTAAGTAGA
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:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
TTCCTTCTATCAA
Found at i:370436 original size:21 final size:21
Alignment explanation
Indices: 370410--370501 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 21
370400 ACCTTACGGC
370410 GGTGGCATTTAAACC-GGCTGT
1 GGTGGCATTT-AACCTGGCTGT
* * *
370431 GGTGGCATCTGAA-ATGGTTGT
1 GGTGGCAT-TTAACCTGGCTGT
* *
370452 GGTGGCGTTTGACCTGGCTGT
1 GGTGGCATTTAACCTGGCTGT
** *
370473 GGTGGTGTTTGACCTGGCTGT
1 GGTGGCATTTAACCTGGCTGT
370494 GGTGGCAT
1 GGTGGCAT
370502 CTGAAACATC
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
20 2 0.04
21 54 0.95
22 1 0.02
ACGTcount: A:0.12, C:0.15, G:0.40, T:0.33
Consensus pattern (21 bp):
GGTGGCATTTAACCTGGCTGT
Found at i:370477 original size:24 final size:21
Alignment explanation
Indices: 370449--370498 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
370439 CTGAAATGGT
*
370449 TGTGGTGGCGTTTGACCTGGC
1 TGTGGTGGTGTTTGACCTGGC
370470 TGTGGTGGTGTTTGACCTGGC
1 TGTGGTGGTGTTTGACCTGGC
370491 TGTGGTGG
1 TGTGGTGG
370499 CATCTGAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.04, C:0.14, G:0.46, T:0.36
Consensus pattern (21 bp):
TGTGGTGGTGTTTGACCTGGC
Found at i:372620 original size:50 final size:50
Alignment explanation
Indices: 372525--372624 Score: 123
Period size: 50 Copynumber: 2.0 Consensus size: 50
372515 ATTTGTCGTG
* * *
372525 TGGCGCCAGCTCAGACGAAAACCTAGGGAAGGCGCAGATGGTGATCCGCA
1 TGGCACCAGCTCAGACGAAAACCCAGGGAAGGCGCAGATGATGATCCGCA
* *
372575 TGGCACCAGCTC-GAACGAAAACCCAGGGAATGCGC-GCTTGATGATCCGCA
1 TGGCACCAGCTCAG-ACGAAAACCCAGGGAAGGCGCAG-ATGATGATCCGCA
372625 CCTTCTGTCC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
49 2 0.05
50 41 0.95
ACGTcount: A:0.28, C:0.28, G:0.31, T:0.13
Consensus pattern (50 bp):
TGGCACCAGCTCAGACGAAAACCCAGGGAAGGCGCAGATGATGATCCGCA
Found at i:373237 original size:13 final size:13
Alignment explanation
Indices: 373219--373314 Score: 50
Period size: 13 Copynumber: 8.0 Consensus size: 13
373209 TAAATTATAT
373219 TATAATAAATAAA
1 TATAATAAATAAA
373232 TATAAT-AAT--A
1 TATAATAAATAAA
*
373242 T-TAATTAAT-AA
1 TATAATAAATAAA
* *
373253 TATTAATTATTAAA
1 TA-TAATAAATAAA
*
373267 TGTAATAAAT-AA
1 TATAATAAATAAA
373279 T-TAA-AAATATAA
1 TATAATAAATA-AA
*
373291 -A-AATATATAAA
1 TATAATAAATAAA
*
373302 TATAATAATTAAA
1 TATAATAAATAAA
373315 ATAGATATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
9 4 0.06
10 9 0.14
11 9 0.14
12 13 0.20
13 27 0.42
14 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (13 bp):
TATAATAAATAAA
Found at i:373239 original size:16 final size:16
Alignment explanation
Indices: 373215--373310 Score: 57
Period size: 16 Copynumber: 5.6 Consensus size: 16
373205 GAAATAAATT
*
373215 ATATTATAATAAATAA
1 ATATAATAATAAATAA
*
373231 ATATAATAATATTAATTA
1 ATATAATAATA--AATAA
* * *
373249 ATAATATTAATTATTAA
1 AT-ATAATAATAAATAA
* *
373266 ATGTAATAAATAATTAAAA
1 ATATAAT-AATAA--ATAA
* *
373285 ATATAAAAATATATAA
1 ATATAATAATAAATAA
373301 ATATAATAAT
1 ATATAATAAT
373311 TAAAATAGAT
Statistics
Matches: 58, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
16 25 0.43
17 9 0.16
18 10 0.17
19 14 0.24
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (16 bp):
ATATAATAATAAATAA
Found at i:373302 original size:35 final size:36
Alignment explanation
Indices: 373222--373310 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 36
373212 ATTATATTAT
* * *
373222 AATAAATAAATATAATAATATTAATTAATAATATTA
1 AATATATAAATATAATAATATTAATTAAAAATATAA
* *
373258 ATTAT-TAAATGTAATAA-A-TAATTAAAAATATAAA
1 AATATATAAATATAATAATATTAATTAAAAATAT-AA
373292 AATATATAAATATAATAAT
1 AATATATAAATATAATAAT
373311 TAAAATAGAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
33 12 0.28
34 6 0.14
35 22 0.51
36 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (36 bp):
AATATATAAATATAATAATATTAATTAAAAATATAA
Found at i:377733 original size:21 final size:22
Alignment explanation
Indices: 377703--377744 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
377693 CATATATTTT
*
377703 TTAAATAAATATTATAATAAAG
1 TTAAATAAATAATATAATAAAG
*
377725 TTAAA-AAATAATATTATAAA
1 TTAAATAAATAATATAATAAA
377745 AAATTTTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
TTAAATAAATAATATAATAAAG
Found at i:379414 original size:22 final size:21
Alignment explanation
Indices: 379383--379423 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
379373 CGAACCGAAA
379383 AACCTGAACCGTTAAAAAACCCG
1 AACCTGAACCG--AAAAAACCCG
379406 AACC-GAACCGAAAAAACC
1 AACCTGAACCGAAAAAACC
379424 GGTTTCGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
22 6 0.33
23 4 0.22
ACGTcount: A:0.49, C:0.32, G:0.12, T:0.07
Consensus pattern (21 bp):
AACCTGAACCGAAAAAACCCG
Found at i:384678 original size:37 final size:36
Alignment explanation
Indices: 384619--384738 Score: 172
Period size: 35 Copynumber: 3.3 Consensus size: 36
384609 ATCCCATTAT
* * *
384619 CATTTTTC-AACAAACATCTACCAAACTTTAAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTT-GAAAAC
*
384655 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
384691 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
384726 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
384739 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 35 0.46
36 13 0.17
37 28 0.37
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:384694 original size:21 final size:21
Alignment explanation
Indices: 384670--384730 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
384660 TTCAAAGAAA
384670 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
384691 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
384705 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
384726 CATTT
1 CATTT
384731 TTTCAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:384747 original size:35 final size:36
Alignment explanation
Indices: 384621--384765 Score: 133
Period size: 35 Copynumber: 4.1 Consensus size: 36
384611 CCCATTATCA
* *
384621 TTTTTCAACA-AACA-TCTACCAAACTTTAAAAAAC-T
1 TTTTTCAA-AGAACAGT-TACCAAACTTTGAAAACCAT
*
384656 ATTTTTCAAAGAAACATTTACCAAACTTTGAAAACCA-
1 -TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
*
384693 -TTTTCAAAGAAACATTTACCAAACTTTGAAAACCAT
1 TTTTTCAAAG-AACAGTTACCAAACTTTGAAAACCAT
***
384729 TTTTTCAAAG-TTGGTTACCAAAC-TTGAAAACCAT
1 TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
384763 TTT
1 TTT
384766 AATAATTTTA
Statistics
Matches: 97, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
34 14 0.14
35 45 0.46
36 8 0.08
37 29 0.30
38 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (36 bp):
TTTTTCAAAGAACAGTTACCAAACTTTGAAAACCAT
Found at i:392953 original size:14 final size:14
Alignment explanation
Indices: 392934--392963 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
392924 AAAATCAATT
*
392934 TCGAGTTATTCTAG
1 TCGAGTTATTCGAG
392948 TCGAGTTATTCGAG
1 TCGAGTTATTCGAG
392962 TC
1 TC
392964 CTAATTATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (14 bp):
TCGAGTTATTCGAG
Found at i:397432 original size:40 final size:40
Alignment explanation
Indices: 397377--397452 Score: 134
Period size: 40 Copynumber: 1.9 Consensus size: 40
397367 CACAATACAA
*
397377 TTTCAAATGCCTTTTTGACCATTTCAAAATCCTATAACAC
1 TTTCAAATGCATTTTTGACCATTTCAAAATCCTATAACAC
*
397417 TTTCTAATGCATTTTTGACCATTTCAAAATCCTATA
1 TTTCAAATGCATTTTTGACCATTTCAAAATCCTATA
397453 TGTATAGTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (40 bp):
TTTCAAATGCATTTTTGACCATTTCAAAATCCTATAACAC
Found at i:397617 original size:19 final size:19
Alignment explanation
Indices: 397582--397621 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
397572 AAAAAATTAT
397582 AAATTTCATATATTTTTGAA
1 AAATTTCATATATTTTT-AA
*
397602 AAATTTCTTA-ATTTTTAA
1 AAATTTCATATATTTTTAA
397620 AA
1 AA
397622 TTAATTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 6 0.32
20 9 0.47
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (19 bp):
AAATTTCATATATTTTTAA
Found at i:397627 original size:13 final size:14
Alignment explanation
Indices: 397609--397638 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
397599 GAAAAATTTC
397609 TTAATT-TTTAAAA
1 TTAATTGTTTAAAA
397622 TTAATTGTTTAAAA
1 TTAATTGTTTAAAA
397636 TTA
1 TTA
397639 TAAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
TTAATTGTTTAAAA
Found at i:398326 original size:2 final size:2
Alignment explanation
Indices: 398319--398355 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
398309 ACATATTAAA
398319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
398356 CAATGTATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:398482 original size:3 final size:3
Alignment explanation
Indices: 398465--398517 Score: 88
Period size: 3 Copynumber: 17.3 Consensus size: 3
398455 AATTTATTGG
*
398465 TAT TAT TTT TCAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
398511 TAT TAT T
1 TAT TAT T
398518 GAAGAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 45 0.96
4 2 0.04
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:405104 original size:18 final size:17
Alignment explanation
Indices: 405081--405118 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
405071 TTAAAATGTT
*
405081 ATAAATATAAATAATTAA
1 ATAAATAAAAATAA-TAA
405099 ATAAATAAAAATAATAA
1 ATAAATAAAAATAATAA
405116 ATA
1 ATA
405119 TTAATGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAATAAAAATAATAA
Found at i:406009 original size:2 final size:2
Alignment explanation
Indices: 406002--406028 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
405992 ATATAAAATA
406002 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
406029 ATCGGGGCGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:412222 original size:41 final size:41
Alignment explanation
Indices: 412175--412278 Score: 163
Period size: 41 Copynumber: 2.5 Consensus size: 41
412165 GTGTTGACAA
* * *
412175 TTGCATGGCATTCTAGATGGCATCCATCAATTGTTGAAATT
1 TTGCATGGCATTCTAGATGACAACCAGCAATTGTTGAAATT
* *
412216 TTGCATGGCATTCTAGATGATAACTAGCAATTGTTGAAATT
1 TTGCATGGCATTCTAGATGACAACCAGCAATTGTTGAAATT
412257 TTGCATGGCATTCTAGATGACA
1 TTGCATGGCATTCTAGATGACA
412279 GCAAGTGGAT
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (41 bp):
TTGCATGGCATTCTAGATGACAACCAGCAATTGTTGAAATT
Found at i:416778 original size:41 final size:41
Alignment explanation
Indices: 416726--416832 Score: 162
Period size: 41 Copynumber: 2.6 Consensus size: 41
416716 TTGTTGACAA
* *
416726 TTGCATAGCATTCTAGATGTCAGCCATCAATTGTTGAAATT
1 TTGCATGGCATTCTAGATGTCAGCCAGCAATTGTTGAAATT
*
416767 TTGCATGGCATTCTAGATGAT-AGCTAGCAATTGTTGAAATT
1 TTGCATGGCATTCTAGATG-TCAGCCAGCAATTGTTGAAATT
*
416808 TTGCATGGCATTCTAGATGGCAGCC
1 TTGCATGGCATTCTAGATGTCAGCC
416833 GATGGATGTA
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
41 58 0.98
42 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (41 bp):
TTGCATGGCATTCTAGATGTCAGCCAGCAATTGTTGAAATT
Found at i:417624 original size:78 final size:78
Alignment explanation
Indices: 417495--417651 Score: 278
Period size: 78 Copynumber: 2.0 Consensus size: 78
417485 GATAAAGAAG
* *
417495 AGCCCCAACCATACTCTAATATGACTGAGCATCAACCAACGGAGACCAGCATCCTAGACCAACTT
1 AGCCCCAACCACACTCTAATATGACTGAGCATCAACCAACAGAGACCAGCATCCTAGACCAACTT
417560 TGGTGTGACAACC
66 TGGTGTGACAACC
* *
417573 AGCCCCAACCACACTCTAATATGACTGAGCATCAACCAACAGAGACCAGCATCTTGGACCAACTT
1 AGCCCCAACCACACTCTAATATGACTGAGCATCAACCAACAGAGACCAGCATCCTAGACCAACTT
417638 TGGTGTGACAACC
66 TGGTGTGACAACC
417651 A
1 A
417652 TGAGAGTGAA
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.18
Consensus pattern (78 bp):
AGCCCCAACCACACTCTAATATGACTGAGCATCAACCAACAGAGACCAGCATCCTAGACCAACTT
TGGTGTGACAACC
Found at i:419430 original size:20 final size:20
Alignment explanation
Indices: 419394--419433 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
419384 ATTTAGAGTG
**
419394 GTTCGACTTTCTCAACCAAA
1 GTTCGACTTTCAAAACCAAA
419414 GTTCGACTTTCAAAACCAAA
1 GTTCGACTTTCAAAACCAAA
419434 ATCTACGTCC
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:0.35, C:0.28, G:0.10, T:0.28
Consensus pattern (20 bp):
GTTCGACTTTCAAAACCAAA
Found at i:420033 original size:21 final size:21
Alignment explanation
Indices: 419988--420085 Score: 103
Period size: 20 Copynumber: 4.7 Consensus size: 21
419978 ATTATAACAT
*
419988 GGGGGTATCGGTACCTCCTGAGG
1 GGGGGTATCGGTACCT-CT-TGG
*
420011 GGGGGTATCAGTACCTCTTGG
1 GGGGGTATCGGTACCTCTTGG
*
420032 GGGGGTATCGGTACCTCCT-G
1 GGGGGTATCGGTACCTCTTGG
*
420052 GGGGGTATCGGTATCTCCTT--
1 GGGGGTATCGGTACCT-CTTGG
*
420072 AGGGGTATCGGTAC
1 GGGGGTATCGGTAC
420086 TCTCCGAGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
20 28 0.42
21 21 0.32
22 2 0.03
23 15 0.23
ACGTcount: A:0.13, C:0.20, G:0.40, T:0.27
Consensus pattern (21 bp):
GGGGGTATCGGTACCTCTTGG
Found at i:425169 original size:85 final size:85
Alignment explanation
Indices: 425022--425186 Score: 217
Period size: 85 Copynumber: 1.9 Consensus size: 85
425012 TACAATCACA
* *
425022 ACACACGAATGTGTGTCATCTTCATTTATGACGGGGGTTTCAATGACACACAATGTAAGTCATAG
1 ACACACAAATGTGTGTCATCTTCATTTATGACGGGGGTTTCAATGACACACAATGTAAGTCATAA
*
425087 ATGTGTGTCATAAATTTATG
66 ATGTGCGTCATAAATTTATG
* * * * *
425107 ACACACAAATGTGTGTCATCTTCATTTATGTCGGGGGCTTT-AATGTCGCGCAATG-AGCGTCAT
1 ACACACAAATGTGTGTCATCTTCATTTATGACGGGGG-TTTCAATGACACACAATGTA-AGTCAT
*
425170 AAATGTGCGTCGTAAAT
64 AAATGTGCGTCATAAAT
425187 GTGTCATAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 1 0.01
85 65 0.94
86 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (85 bp):
ACACACAAATGTGTGTCATCTTCATTTATGACGGGGGTTTCAATGACACACAATGTAAGTCATAA
ATGTGCGTCATAAATTTATG
Found at i:425179 original size:13 final size:13
Alignment explanation
Indices: 425158--425220 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
425148 AATGTCGCGC
*
425158 AATGAGCGTCATA
1 AATGCGCGTCATA
* *
425171 AATGTGCGTCGTA
1 AATGCGCGTCATA
*
425184 AAT--GTGTCATA
1 AATGCGCGTCATA
* *
425195 AATGCGTGTTATA
1 AATGCGCGTCATA
425208 AATGCGCGTCATA
1 AATGCGCGTCATA
425221 TATTTATGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
11 9 0.22
13 32 0.78
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:425910 original size:3 final size:3
Alignment explanation
Indices: 425878--425952 Score: 102
Period size: 3 Copynumber: 25.7 Consensus size: 3
425868 AAAAACAGAT
* *
425878 GAA GAA -AA G-A GAA -AA CGAA GAA GCA TAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA
425921 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
425953 GATGAGTTTT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 6 0.09
3 56 0.88
4 2 0.03
ACGTcount: A:0.65, C:0.03, G:0.31, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:440286 original size:4 final size:4
Alignment explanation
Indices: 440277--440302 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
440267 AATAAACTAA
440277 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
440303 TCATTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:440389 original size:31 final size:31
Alignment explanation
Indices: 440330--440417 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 31
440320 TATAGTTATT
* * *
440330 TTAATTATTAAATTTTTTAAA--ATTATAAA
1 TTAATCATTAAATTTATAAAATTATTATAAA
440359 TTAATCATTAAATTTATAAAATTATTATAAA
1 TTAATCATTAAATTTATAAAATTATTATAAA
** *
440390 ACAATCATTGTAATATTATAATAATTAT
1 TTAATCATT-AAAT-TTATAA-AATTAT
440418 AAAATATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
29 18 0.38
31 15 0.31
32 3 0.06
33 6 0.12
34 6 0.12
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (31 bp):
TTAATCATTAAATTTATAAAATTATTATAAA
Found at i:440519 original size:3 final size:3
Alignment explanation
Indices: 440511--440545 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
440501 AATATTGAGC
440511 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
440546 CAGAATTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:440769 original size:2 final size:2
Alignment explanation
Indices: 440762--440815 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
440752 AATATACGTT
440762 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
440804 TA TA TA TA TA TA
1 TA TA TA TA TA TA
440816 CTAGGGCTGG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:441029 original size:2 final size:2
Alignment explanation
Indices: 441017--441069 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
441007 TTATCTAACC
441017 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
441058 AT AT AT AT AT AT
1 AT AT AT AT AT AT
441070 TCTTTCATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:442465 original size:23 final size:23
Alignment explanation
Indices: 442400--442531 Score: 143
Period size: 23 Copynumber: 5.9 Consensus size: 23
442390 CAGCTCGTAA
*
442400 TTTGCACCGAAGTGTCACATA--
1 TTTGCACCGAAGTGCCACATAGG
*
442421 ATTGTC-CCGAA-TGACCACATAGG
1 TTTG-CACCGAAGTG-CCACATAGG
*
442444 TTTGCACCAAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACATAGG
442467 TTTGCACCGAAGTGCCACATAGG
1 TTTGCACCGAAGTGCCACATAGG
*
442490 TTTGCATCGAAGTGCCACATA--
1 TTTGCACCGAAGTGCCACATAGG
*
442511 TTTGTC-CCGAAGTACCACATA
1 TTTG-CACCGAAGTGCCACATA
442532 ATTATCCCGG
Statistics
Matches: 96, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
20 2 0.02
21 31 0.32
22 3 0.03
23 58 0.60
24 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (23 bp):
TTTGCACCGAAGTGCCACATAGG
Found at i:442494 original size:46 final size:44
Alignment explanation
Indices: 442400--442531 Score: 160
Period size: 44 Copynumber: 3.0 Consensus size: 44
442390 CAGCTCGTAA
* * *
442400 TTTGCACCGAAGTGTCACATAATTGTCCCGAA-TGACCACATAGG
1 TTTGCACCAAAGTGCCACATATTTGTCCCGAAGTG-CCACATAGG
442444 TTTGCACCAAAGTGCCACATAGGTTTG-CACCGAAGTGCCACATAGG
1 TTTGCACCAAAGTGCCACATA--TTTGTC-CCGAAGTGCCACATAGG
* * *
442490 TTTGCATCGAAGTGCCACATATTTGTCCCGAAGTACCACATA
1 TTTGCACCAAAGTGCCACATATTTGTCCCGAAGTGCCACATA
442532 ATTATCCCGG
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
44 37 0.48
45 2 0.03
46 36 0.47
47 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (44 bp):
TTTGCACCAAAGTGCCACATATTTGTCCCGAAGTGCCACATAGG
Found at i:442548 original size:21 final size:21
Alignment explanation
Indices: 442504--442553 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
442494 CATCGAAGTG
* * *
442504 CCACATATTTGTCCCGAAGTA
1 CCACATAATTATCCCGAAGGA
*
442525 CCACATAATTATCCCGGAGGA
1 CCACATAATTATCCCGAAGGA
442546 CCACATAA
1 CCACATAA
442554 AACCCTCGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.30, G:0.14, T:0.22
Consensus pattern (21 bp):
CCACATAATTATCCCGAAGGA
Found at i:445043 original size:13 final size:13
Alignment explanation
Indices: 445010--445058 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
445000 GCTCGAGCTG
*
445010 AGTCAACTCTCTA
1 AGTCAACTCACTA
* *
445023 AGTTAACTCACTG
1 AGTCAACTCACTA
*
445036 AGTCAACTCGACCA
1 AGTCAACTC-ACTA
445050 AGTCAACTC
1 AGTCAACTC
445059 GAATAGAGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.33, C:0.31, G:0.12, T:0.24
Consensus pattern (13 bp):
AGTCAACTCACTA
Found at i:447613 original size:390 final size:390
Alignment explanation
Indices: 446894--447678 Score: 1184
Period size: 390 Copynumber: 2.0 Consensus size: 390
446884 ACTATGGCTA
446894 CATGATGTGTGTTCTTTGGTTACATGTTTTCATTGGAAAATATAATCGTTCTTGATTTATGGATC
1 CATGATGTGTGTTCTTTGGTTACATGTTTTCATTGGAAAATATAATCGTTCTTGATTTATGGATC
* * *
446959 ATGAAATCTACTATTTACTGTATGAATTAATTATTGGGATACTGTCTGGGTAGGATTCTGGAGTA
66 ATGAAATCTACTATTTACTATATGAATTAATTATCGGGATACTGTCTGAGTAGGATTCTGGAGTA
* * * *
447024 TGAAGGTTCAGTTCTGATCAAGCTGATAATTCCTTATGGACCTAAGTTATTCATTGGGTAGGCTC
131 TGAAGGTTCAGCTCTGATCAAGCTGACAATTCCTTAAGGACCTAAGGTATTCATTGGGTAGGCTC
* * * * * * *
447089 TAAGGCCCCAAAGTACTCCCTTAGTATGGGGATTGTATTTTGTTGTACGGATGGAGGGCGTTTAT
196 AAAGGCCCCAAAGCACTCCCTTAGTATGGGGACTGTATTTTGTTATACGAACGAAGGGCGTTTAT
* * * * *
447154 GTGATTTAAATAACTAAATTGTCATTATTAAAACATATATTATATTATGATTTTAATATTAAAGT
261 ATGATTTAAAAAACTAAATTGTCATTATTAAAACATATACTAGATCATGATTTTAATATTAAAGT
* * * * * *
447219 TACTACTCAATCTGATTTCTACTGGATATTGTATGGTTAGGAGTCTGGAGTACGGAGGTTCAGCT
326 TACTACTCAATCTGATTTATACTAGATACTATATGGGTAGGAGTCTGGAGTACAGAGGTTCAGCT
*
447284 CATGATGTGTGTTCTTTGGTTATATGTTTTCATTGGAAAATATAATCGTTACTT-ATTTATGGAT
1 CATGATGTGTGTTCTTTGGTTACATGTTTTCATTGGAAAATATAATCGTT-CTTGATTTATGGAT
* * *
447348 CATGAAATCTACTATTTACTATATGAATTGATTATCGGGATACTGTTTGAGTAGGATTTTGGAGT
65 CATGAAATCTACTATTTACTATATGAATTAATTATCGGGATACTGTCTGAGTAGGATTCTGGAGT
*
447413 AT-AGAGGTT-AGGCTCTGATCAAGCTGACAATTCCTTAAGGACCTAAGGTATTCCTTGGGTAGG
130 ATGA-AGGTTCA-GCTCTGATCAAGCTGACAATTCCTTAAGGACCTAAGGTATTCATTGGGTAGG
* * *
447476 CTCAAAGGCCCCAAGGCACTCCCTTAGTAT-GGGACTGTATTTTGTTATATGAACGAAGGGTGTT
193 CTCAAAGGCCCCAAAGCACTCCCTTAGTATGGGGACTGTATTTTGTTATACGAACGAAGGGCGTT
* *
447540 TATATGATTTAAAAAACTAAATTTTCATTATTAAAACATTTTACTAGATCATGATTTTAATATTA
258 TATATGATTTAAAAAACTAAATTGTCATTATTAAAACA-TATACTAGATCATGATTTTAATATTA
447605 AAGTTACTACTCAATCTGATTTATACTAGATACTATATGGGTAGGAGTCTGGAGTACAGAGGTTC
322 AAGTTACTACTCAATCTGATTTATACTAGATACTATATGGGTAGGAGTCTGGAGTACAGAGGTTC
447670 AGCT
387 AGCT
447674 C-TGAT
1 CATGAT
447679 CAAACTGGTA
Statistics
Matches: 356, Mismatches: 35, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
389 68 0.19
390 285 0.80
391 3 0.01
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (390 bp):
CATGATGTGTGTTCTTTGGTTACATGTTTTCATTGGAAAATATAATCGTTCTTGATTTATGGATC
ATGAAATCTACTATTTACTATATGAATTAATTATCGGGATACTGTCTGAGTAGGATTCTGGAGTA
TGAAGGTTCAGCTCTGATCAAGCTGACAATTCCTTAAGGACCTAAGGTATTCATTGGGTAGGCTC
AAAGGCCCCAAAGCACTCCCTTAGTATGGGGACTGTATTTTGTTATACGAACGAAGGGCGTTTAT
ATGATTTAAAAAACTAAATTGTCATTATTAAAACATATACTAGATCATGATTTTAATATTAAAGT
TACTACTCAATCTGATTTATACTAGATACTATATGGGTAGGAGTCTGGAGTACAGAGGTTCAGCT
Found at i:452896 original size:16 final size:16
Alignment explanation
Indices: 452875--452910 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
452865 AGGAAATCTA
452875 TGATTTACCATATACC
1 TGATTTACCATATACC
452891 TGATTTACCATATACC
1 TGATTTACCATATACC
452907 TGAT
1 TGAT
452911 GACCTATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (16 bp):
TGATTTACCATATACC
Found at i:459950 original size:41 final size:41
Alignment explanation
Indices: 459904--460101 Score: 326
Period size: 41 Copynumber: 4.8 Consensus size: 41
459894 ATCGCAAATT
* *
459904 CGATTTTCCATTTCGCGTCACGATAGTTGAAAATCACGTTG
1 CGATTTTCCATTTCGCGTCGCGATAGTTGAAAATCGCGTTG
* *
459945 TGATTTTCCATTTCGCGAT-GCGATAGTTGACAATCGCGTTG
1 CGATTTTCCATTTCGCG-TCGCGATAGTTGAAAATCGCGTTG
459986 CGATTTTCCATTTCGCGTCGCGATAGTTGAAAATCGCGTTG
1 CGATTTTCCATTTCGCGTCGCGATAGTTGAAAATCGCGTTG
*
460027 CGATTTTCCATTTCGCGTCGCGATAGTTGAAAATCGCGTTA
1 CGATTTTCCATTTCGCGTCGCGATAGTTGAAAATCGCGTTG
*
460068 CGATTTTCCATTTCGCGTTGCGATAGTTGAAAAT
1 CGATTTTCCATTTCGCGTCGCGATAGTTGAAAAT
460102 ATATTTGAGA
Statistics
Matches: 147, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
40 1 0.01
41 145 0.99
42 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (41 bp):
CGATTTTCCATTTCGCGTCGCGATAGTTGAAAATCGCGTTG
Found at i:460003 original size:20 final size:20
Alignment explanation
Indices: 459940--460091 Score: 99
Period size: 20 Copynumber: 7.5 Consensus size: 20
459930 TTGAAAATCA
*
459940 CGTTGTGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* ** *
459960 CGATGCGATAGTTGACA-ATCG
1 CGTTGCGAT--TTTCCATTTCG
459981 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * ** **
460001 CGTCGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCATTTCG
460022 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
* * ** **
460042 CGTCGCGATAGTTGAAAATCG
1 CGTTGCGAT-TTTCCATTTCG
*
460063 CGTTACGATTTTCCATTTCG
1 CGTTGCGATTTTCCATTTCG
460083 CGTTGCGAT
1 CGTTGCGAT
460092 AGTTGAAAAT
Statistics
Matches: 92, Mismatches: 35, Indels: 10
0.67 0.26 0.07
Matches are distributed among these distances:
19 4 0.04
20 46 0.50
21 38 0.41
22 4 0.04
ACGTcount: A:0.18, C:0.22, G:0.24, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTTCCATTTCG
Found at i:463142 original size:20 final size:20
Alignment explanation
Indices: 463117--463164 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
463107 TTCACTATGG
*
463117 TATTGATACTTGAAGAACAA
1 TATTGATACTCGAAGAACAA
463137 TATTGATACTCGAAGAACAA
1 TATTGATACTCGAAGAACAA
*
463157 TATAGATA
1 TATTGATA
463165 ATGTTCATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (20 bp):
TATTGATACTCGAAGAACAA
Found at i:464216 original size:10 final size:10
Alignment explanation
Indices: 464203--464240 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
464193 TAATAATTTC
464203 TAAAAATATA
1 TAAAAATATA
464213 TAAAAATATA
1 TAAAAATATA
*
464223 T-AAAATTTA
1 TAAAAATATA
464232 TAAATAATA
1 TAAA-AATA
464241 ATATTTGTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.33
10 13 0.54
11 3 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
TAAAAATATA
Found at i:464275 original size:47 final size:48
Alignment explanation
Indices: 464200--464293 Score: 113
Period size: 47 Copynumber: 2.0 Consensus size: 48
464190 TTTTAATAAT
* * *
464200 TTCTAAAAATATATAAAAATATATAAAATTTATAA-ATAATAATATTTG
1 TTCTAAAAATATATAAAAATATAAAAAATATAAAACATAA-AATATTTG
*
464248 TTCT-AAAAT-TATGAAAATTATAAAAAATATAAAACATAAAATATTT
1 TTCTAAAAATATAT-AAAAATATAAAAAATATAAAACATAAAATATTT
464294 TAAGAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
46 3 0.08
47 29 0.73
48 8 0.20
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.37
Consensus pattern (48 bp):
TTCTAAAAATATATAAAAATATAAAAAATATAAAACATAAAATATTTG
Found at i:468135 original size:2 final size:2
Alignment explanation
Indices: 468128--468153 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
468118 ATCAACCTTG
468128 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
468154 TTTTTGACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:474111 original size:56 final size:58
Alignment explanation
Indices: 474050--474159 Score: 134
Period size: 56 Copynumber: 1.9 Consensus size: 58
474040 ATAATTTCTG
* *
474050 TTTTCATATATATAATTTTAAAAT-AAAATACTTTATATT-TTTTTACAATTATAATA
1 TTTTCATAAAAATAATTTTAAAATAAAAATACTTTATATTATTTTTACAATTATAATA
* ** * * *
474106 TTTTCATAAAAATTATTTTTTAATAAAAATATTTTTTATTATTTTTATAATTAT
1 TTTTCATAAAAATAATTTTAAAATAAAAATACTTTATATTATTTTTACAATTAT
474160 TTATAGTATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
56 19 0.43
57 13 0.30
58 12 0.27
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (58 bp):
TTTTCATAAAAATAATTTTAAAATAAAAATACTTTATATTATTTTTACAATTATAATA
Found at i:474126 original size:17 final size:16
Alignment explanation
Indices: 474106--474143 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
474096 AATTATAATA
*
474106 TTTTCATAAAAATTATT
1 TTTTAATAAAAA-TATT
474123 TTTTAATAAAAATATT
1 TTTTAATAAAAATATT
474139 TTTTA
1 TTTTA
474144 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTAATAAAAATATT
Found at i:487306 original size:7 final size:8
Alignment explanation
Indices: 487289--487313 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
487279 CCCACTATAC
487289 TTTTAATT
1 TTTTAATT
487297 TTTTAATT
1 TTTTAATT
487305 TTTTAATT
1 TTTTAATT
487313 T
1 T
487314 ATTCATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTAATT
Found at i:489984 original size:23 final size:23
Alignment explanation
Indices: 489935--489984 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
489925 ACCATTTTTG
**
489935 AATTCTTGTCAATCATACGACTG
1 AATTCTTGTCAATCATACGACCA
489958 AATTCTTGTCAATCATACCG-CCA
1 AATTCTTGTCAATCATA-CGACCA
489981 AATT
1 AATT
489985 ATTTAAATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 22 0.92
24 2 0.08
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.34
Consensus pattern (23 bp):
AATTCTTGTCAATCATACGACCA
Found at i:492233 original size:23 final size:21
Alignment explanation
Indices: 492183--492237 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
492173 AAACTTAATC
492183 AAATAA-ATAAAAAACAAAAA
1 AAATAACATAAAAAACAAAAA
* *
492203 ACATAACATAAAAAATAAAACA
1 AAATAACATAAAAAACAAAA-A
492225 AAATAAACATAAA
1 AAAT-AACATAAA
492238 TATCAGGATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 5 0.17
21 12 0.41
22 4 0.14
23 8 0.28
ACGTcount: A:0.78, C:0.09, G:0.00, T:0.13
Consensus pattern (21 bp):
AAATAACATAAAAAACAAAAA
Found at i:494394 original size:23 final size:23
Alignment explanation
Indices: 494363--494426 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 23
494353 GCTATATAAT
* * **
494363 TATAGTATATAACATAGTATGTA
1 TATATTATATAACATAATACATA
*
494386 TATATTATATAAAATAATACATA
1 TATATTATATAACATAATACATA
* *
494409 TACATTATATACCATAAT
1 TATATTATATAACATAAT
494427 TAATAACACA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.39
Consensus pattern (23 bp):
TATATTATATAACATAATACATA
Found at i:495885 original size:5 final size:5
Alignment explanation
Indices: 495875--495914 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
495865 GTTTGGGTAT
* *
495875 TTGGG TTGGG TTGGT TTGGG TTGGG TTGGT TTGGG TTGGG
1 TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG TTGGG
495915 CTTGAGGCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.55, T:0.45
Consensus pattern (5 bp):
TTGGG
Found at i:495894 original size:15 final size:15
Alignment explanation
Indices: 495874--495914 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
495864 GGTTTGGGTA
495874 TTTGGGTTGGGTTGG
1 TTTGGGTTGGGTTGG
495889 TTTGGGTTGGGTTGG
1 TTTGGGTTGGGTTGG
495904 TTTGGGTTGGG
1 TTTGGGTTGGG
495915 CTTGAGGCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.54, T:0.46
Consensus pattern (15 bp):
TTTGGGTTGGGTTGG
Found at i:497249 original size:20 final size:21
Alignment explanation
Indices: 497205--497256 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
497195 AGGGCTCTCG
*
497205 GTATCGATACT-AACCTTTGA
1 GTATCGATACTCAACCTTGGA
*
497225 GTATCGATACTCCACCTTGGA
1 GTATCGATACTCAACCTTGGA
*
497246 -TATCAATACTC
1 GTATCGATACTC
497257 TACAGTTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 21 0.75
21 7 0.25
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (21 bp):
GTATCGATACTCAACCTTGGA
Found at i:497887 original size:2 final size:2
Alignment explanation
Indices: 497880--497922 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
497870 AAACATAGTA
497880 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
497922 A
1 A
497923 CAACTTATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:499212 original size:12 final size:12
Alignment explanation
Indices: 499173--499213 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
499163 TCCAAAAGCT
499173 TCCAAATTG--C
1 TCCAAATTGATC
*
499183 TCCAAATTGATA
1 TCCAAATTGATC
*
499195 TGCAAATTGATC
1 TCCAAATTGATC
499207 TCCAAAT
1 TCCAAAT
499214 CACATAGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (12 bp):
TCCAAATTGATC
Found at i:504574 original size:11 final size:11
Alignment explanation
Indices: 504558--504597 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
504548 GGTTAACATT
504558 AAAAAAAAAGA
1 AAAAAAAAAGA
*
504569 AAAAAAAAATA
1 AAAAAAAAAGA
504580 AAAAAACAAAGA
1 AAAAAA-AAAGA
504592 AGAAAA
1 A-AAAA
504598 GGGTATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 16 0.64
12 5 0.20
13 4 0.16
ACGTcount: A:0.88, C:0.03, G:0.07, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:506511 original size:183 final size:179
Alignment explanation
Indices: 506182--506512 Score: 443
Period size: 183 Copynumber: 1.8 Consensus size: 179
506172 TATTACGAAT
* *
506182 TTAGTACCTAAAATTTTGATTTCTTTCAAAATCATACCTAAAATTTAATTTTTATTTTATTTTAG
1 TTAGTACCTAAAATTTCGATTTCTTTAAAAATCATACCTAAAATTTAATTTTTATTTTATTTTAG
** * *
506247 TACCATATTTAAAATTTAATTTTGAAAGTAAAATTGAAAGTTTAGGTACTAAAACGGACAAAACT
66 TACCATATTTAAAATTTAATTTTGAAAACAAAATTAAAAGTTTAGGTACTAAAACGGACAAAACG
* ** *
506312 TATAGTTTATGTACTAAACGCATTAAGTTATTAGGGTATATTATGCAAA
131 GATAGCATAGGTACTAAACGCATTAAGTTATTAGGGTATATTATGCAAA
* * * *
506361 TTAGTACCTAAACTTTCGGTTT-TTTAAAAATCATACTTAAAGTTTAA-TTTT-TTTTATTTTAG
1 TTAGTACCTAAAATTTCGATTTCTTTAAAAATCATACCTAAAATTTAATTTTTATTTTATTTTAG
*
506423 TACCATGTTTAAAATTTAACGTTAAATATTGAAAACAAAATTAAAAGTTTAGGTACTAAAACGGA
66 TACCATATTTAAAATTTAA---T---T-TTGAAAACAAAATTAAAAGTTTAGGTACTAAAACGGA
506488 CAAAACGGATAGCATAGGTACTAAA
124 CAAAACGGATAGCATAGGTACTAAA
506513 TGTATTAAAT
Statistics
Matches: 130, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
176 29 0.22
177 4 0.03
178 22 0.17
179 20 0.15
182 1 0.01
183 54 0.42
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (179 bp):
TTAGTACCTAAAATTTCGATTTCTTTAAAAATCATACCTAAAATTTAATTTTTATTTTATTTTAG
TACCATATTTAAAATTTAATTTTGAAAACAAAATTAAAAGTTTAGGTACTAAAACGGACAAAACG
GATAGCATAGGTACTAAACGCATTAAGTTATTAGGGTATATTATGCAAA
Found at i:507540 original size:7 final size:7
Alignment explanation
Indices: 507528--507586 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
507518 TAACGTTCTT
507528 TTTTTTC
1 TTTTTTC
507535 TTTTTTAC
1 TTTTTT-C
*
507543 -ATTTTC
1 TTTTTTC
507549 TTTTTTC
1 TTTTTTC
*
507556 TTTTTTA
1 TTTTTTC
* *
507563 TATTTTA
1 TTTTTTC
*
507570 TATTTTC
1 TTTTTTC
507577 TTTTTT-
1 TTTTTTC
507583 TTTT
1 TTTT
507587 CACATTTTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
6 5 0.11
7 38 0.86
8 1 0.02
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:507554 original size:21 final size:21
Alignment explanation
Indices: 507528--507582 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
507518 TAACGTTCTT
*
507528 TTTTTTCTTTTTTACATTTTC
1 TTTTTTCTTTTTTACATTTTA
*
507549 TTTTTTCTTTTTTATATTTTA
1 TTTTTTCTTTTTTACATTTTA
*
507570 TATTTTCTTTTTT
1 TTTTTTCTTTTTT
507583 TTTTCACATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.11, C:0.09, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTTCTTTTTTACATTTTA
Found at i:507568 original size:28 final size:27
Alignment explanation
Indices: 507526--507586 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
507516 AATAACGTTC
* *
507526 TTTTTTTTCTTTTTTACATTTTCTTTT
1 TTTTTTTTATATTTTACATTTTCTTTT
*
507553 TTCTTTTTTATATTTTATATTTTCTTTT
1 TT-TTTTTTATATTTTACATTTTCTTTT
507581 TTTTTT
1 TTTTTT
507587 CACATTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (27 bp):
TTTTTTTTATATTTTACATTTTCTTTT
Found at i:513706 original size:23 final size:22
Alignment explanation
Indices: 513655--513731 Score: 93
Period size: 23 Copynumber: 3.5 Consensus size: 22
513645 CAGAACCCTC
* * *
513655 AGGGGGTATCGATTCCCCTGT-
1 AGGGGGAATCGGTTCCCCTTTA
513676 AGGGGGAATCGGTTCCCCTTTAA
1 AGGGGGAATCGGTTCCCCTTT-A
*
513699 AGGGGGAATCGGTTCCCCTTCA
1 AGGGGGAATCGGTTCCCCTTTA
*
513721 AGGGGGTATCG
1 AGGGGGAATCG
513732 ATTATCTCTG
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
21 18 0.37
22 11 0.22
23 20 0.41
ACGTcount: A:0.18, C:0.22, G:0.35, T:0.25
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTTTA
Found at i:517591 original size:22 final size:21
Alignment explanation
Indices: 517549--517588 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
517539 GAGTTTGATT
*
517549 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
517570 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
517589 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:521599 original size:20 final size:20
Alignment explanation
Indices: 521574--521617 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
521564 GTTTGTCATG
521574 GGTGACAAGGTATTTCTTAA
1 GGTGACAAGGTATTTCTTAA
521594 GGTGACAAGGTATTTCTTAA
1 GGTGACAAGGTATTTCTTAA
521614 GGTG
1 GGTG
521618 TCTCAGTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.09, G:0.30, T:0.34
Consensus pattern (20 bp):
GGTGACAAGGTATTTCTTAA
Found at i:524886 original size:20 final size:21
Alignment explanation
Indices: 524848--524886 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
524838 ACTTATTTGT
**
524848 TTGAAATATTTATGTAAAACG
1 TTGAAATATTTATCAAAAACG
524869 TTGAAAT-TTTATCAAAAA
1 TTGAAATATTTATCAAAAA
524887 AAATTCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (21 bp):
TTGAAATATTTATCAAAAACG
Found at i:535862 original size:3 final size:3
Alignment explanation
Indices: 535854--535910 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
535844 ACTATATACA
* * *
535854 TAT TAT TAT TAGT TATT TAT TAT TAC TAT TAT TAT TAT TAT TGT TAG
1 TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
535901 TAT TTT TAT T
1 TAT TAT TAT T
535911 TACATGTTAC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:541817 original size:18 final size:18
Alignment explanation
Indices: 541768--541848 Score: 83
Period size: 18 Copynumber: 4.3 Consensus size: 18
541758 GGTCTACGCT
* *
541768 GTCCTTCGGGACACAGTG
1 GTCCTTCAGGACATAGTG
541786 GTCCTTC-GGAACATAGTG
1 GTCCTTCAGG-ACATAGTG
541804 GTCCTTCAGGACATATTTAGTG
1 GTCCTTCAGGAC--A--TAGTG
*
541826 GTTCTTCAGGACATAGTG
1 GTCCTTCAGGACATAGTG
541844 GTCCT
1 GTCCT
541849 CTGGGAAAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
17 2 0.04
18 32 0.59
19 2 0.04
20 2 0.04
22 16 0.30
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (18 bp):
GTCCTTCAGGACATAGTG
Found at i:541827 original size:22 final size:22
Alignment explanation
Indices: 541799--541840 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
541789 CTTCGGAACA
541799 TAGTGGTCCTTCAGGACATATT
1 TAGTGGTCCTTCAGGACATATT
*
541821 TAGTGGTTCTTCAGGACATA
1 TAGTGGTCCTTCAGGACATA
541841 GTGGTCCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.36
Consensus pattern (22 bp):
TAGTGGTCCTTCAGGACATATT
Found at i:543735 original size:20 final size:20
Alignment explanation
Indices: 543689--543737 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
543679 ATTGACTGAG
543689 CTGACATCATTATCTTAAGT
1 CTGACATCATTATCTTAAGT
* * *
543709 CTCACATCGTTATCTTAGGT
1 CTGACATCATTATCTTAAGT
*
543729 TTGACATCA
1 CTGACATCA
543738 ATATTAATGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (20 bp):
CTGACATCATTATCTTAAGT
Found at i:545245 original size:33 final size:33
Alignment explanation
Indices: 545203--545268 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
545193 AACAGGAATC
545203 AAACAATCAGACTTACTTTAGTAAATCGAAAAT
1 AAACAATCAGACTTACTTTAGTAAATCGAAAAT
*
545236 AAACAATCAGGCTTACTTTAGTAAATCGAAAAT
1 AAACAATCAGACTTACTTTAGTAAATCGAAAAT
545269 CAGACTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.47, C:0.15, G:0.11, T:0.27
Consensus pattern (33 bp):
AAACAATCAGACTTACTTTAGTAAATCGAAAAT
Found at i:553872 original size:188 final size:188
Alignment explanation
Indices: 553549--553908 Score: 522
Period size: 188 Copynumber: 1.9 Consensus size: 188
553539 AAACTAACAC
* *
553549 AAATTCACAGAAAATCTAGTAAAACAACAGCACGAGGCATGAACCACAAATCAATATTACTAAAT
1 AAATTCACAGAAAAACTAGTAAAACAACAGCACGAAGCATGAACCACAAATCAATATTACTAAAT
* * * * *
553614 CTGTAATGAGAACTAAAATAGAAACACAAACAAGCACTTCGCCAAGATTTTAACAAGTTCACACA
66 CTGTAATGAGAACCAAAATAGAAACACAAACAAGAACTTAGACAAGATTTTAACAAGTTCAAACA
* **
553679 AACAAAAGCAAATCAAGTATTTCTATAAACATAACAAAAATATATTGAGAACTAATGT
131 AACAAAAGCAAATCAAATACCTCTATAAACATAACAAAAATATATTGAGAACTAATGT
** * * * *
553737 AAATTCACAGAAAAACTTTTAAAATAACATCATGAAGCATGAACCACAAATCAATATTATTAAAT
1 AAATTCACAGAAAAACTAGTAAAACAACAGCACGAAGCATGAACCACAAATCAATATTACTAAAT
* * *
553802 CTGTAATGAGAACCAAAATAGAAACACAAACAAGAACTTAGACATGTTTTTAACAAGTTCAAATA
66 CTGTAATGAGAACCAAAATAGAAACACAAACAAGAACTTAGACAAGATTTTAACAAGTTCAAACA
** *
553867 AACAAAAGCGGATCAAATACCTCTATAAACATAACAATAATA
131 AACAAAAGCAAATCAAATACCTCTATAAACATAACAAAAATA
553909 GAAAAAGAAG
Statistics
Matches: 150, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
188 150 1.00
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (188 bp):
AAATTCACAGAAAAACTAGTAAAACAACAGCACGAAGCATGAACCACAAATCAATATTACTAAAT
CTGTAATGAGAACCAAAATAGAAACACAAACAAGAACTTAGACAAGATTTTAACAAGTTCAAACA
AACAAAAGCAAATCAAATACCTCTATAAACATAACAAAAATATATTGAGAACTAATGT
Found at i:555293 original size:32 final size:33
Alignment explanation
Indices: 555257--555326 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
555247 GAAATATCTA
* * * *
555257 GTATCAATATTTAGTAT-AATATTGTATATGTG
1 GTATCAATATCTACTATCAATATTGTACATGCG
555289 GTATCAATATCTACTATCAATATTGTACATGCG
1 GTATCAATATCTACTATCAATATTGTACATGCG
555322 GTATC
1 GTATC
555327 GATACCAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 15 0.45
33 18 0.55
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.41
Consensus pattern (33 bp):
GTATCAATATCTACTATCAATATTGTACATGCG
Found at i:556059 original size:31 final size:30
Alignment explanation
Indices: 555990--556091 Score: 79
Period size: 28 Copynumber: 3.5 Consensus size: 30
555980 TTCATTTAAA
* *
555990 CACCTAAA-CTATTTTTTGGTCAAATTATG
1 CACCTAAAGTTATTTTTTGGTCAAATTAGG
* *
556019 TACCCAAAGTTATCTTTTTGGTCAACA-TAGG
1 CACCTAAAGTTAT-TTTTTGGTCAA-ATTAGG
* * *
556050 CACCTAAAG-TATTTTAT-GTAAAAATAGG
1 CACCTAAAGTTATTTTTTGGTCAAATTAGG
*
556078 TACCTAAAG-TATTT
1 CACCTAAAGTTATTT
556092 AAACTTTTTC
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
27 1 0.02
28 21 0.35
29 10 0.17
30 6 0.10
31 21 0.35
32 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (30 bp):
CACCTAAAGTTATTTTTTGGTCAAATTAGG
Found at i:556769 original size:20 final size:22
Alignment explanation
Indices: 556736--556776 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
556726 ATATTAATGT
556736 TAAAAAATATTAATATTTTAAA
1 TAAAAAATATTAATATTTTAAA
556758 TAAAAAA-A-TAATATTTTAA
1 TAAAAAATATTAATATTTTAA
556777 GTATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAAAAATATTAATATTTTAAA
Found at i:560187 original size:18 final size:17
Alignment explanation
Indices: 560133--560181 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
560123 TTGGACCCTT
* *
560133 AGTGCATCGGTGCACTCTT
1 AGTGCATCGATGCA-TC-A
560152 AGTGCATCGATGCATCA
1 AGTGCATCGATGCATCA
560169 AGTGCATTCGATG
1 AGTGCA-TCGATG
560182 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:562999 original size:43 final size:43
Alignment explanation
Indices: 562932--563023 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 43
562922 GGCCTTGTGA
* * *
562932 ATCGATGCACATTCAAGGCGTGCATCGGTGCACCT-TTATGGTGT
1 ATCGATACACATTCAAGGCATGCATCGATGCA-CTGTTA-GGTGT
562976 ATCGATACACATTCAAGG-ATGCATCGATGCACTGTTAGGTGT
1 ATCGATACACATTCAAGGCATGCATCGATGCACTGTTAGGTGT
563018 ATCGAT
1 ATCGAT
563024 GCATGAAGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 13 0.30
43 14 0.32
44 17 0.39
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (43 bp):
ATCGATACACATTCAAGGCATGCATCGATGCACTGTTAGGTGT
Found at i:568876 original size:45 final size:46
Alignment explanation
Indices: 568812--568919 Score: 148
Period size: 45 Copynumber: 2.4 Consensus size: 46
568802 CGGTGCACTA
* *
568812 AGAGTGCATCAATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
*
568857 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCC
**
568903 TCAGTGCATCGATGCAT
1 AGAGTGCATCGATGCAT
568920 GGTATGTGCA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
45 30 0.54
46 23 0.41
47 3 0.05
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.29
Consensus pattern (46 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAAGCC
Found at i:568994 original size:65 final size:63
Alignment explanation
Indices: 568860--568985 Score: 166
Period size: 65 Copynumber: 2.0 Consensus size: 63
568850 AATAGCCAGA
568860 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGTAT
* **
568925 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATCTAAT-TCATGGTGCATCGATGCATGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG
568986 ATTGGTGCAC
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
62 3 0.05
63 3 0.05
64 21 0.38
65 28 0.51
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTAT
Found at i:571033 original size:32 final size:32
Alignment explanation
Indices: 570987--571056 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
570977 ACAAATTCTT
570987 AAAAAATGTATTTTTCTTAAAGTGAATTAGAC
1 AAAAAATGTATTTTTCTTAAAGTGAATTAGAC
* * *
571019 AAAAAATGTCTTTTTCTTAAAGTGAGTTGGAC
1 AAAAAATGTATTTTTCTTAAAGTGAATTAGAC
571051 AAAAAA
1 AAAAAA
571057 AAATGAGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.34
Consensus pattern (32 bp):
AAAAAATGTATTTTTCTTAAAGTGAATTAGAC
Found at i:578067 original size:18 final size:19
Alignment explanation
Indices: 578026--578064 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
578016 TTGGTTCACA
578026 GAATGTAAGATTACCAGTGG
1 GAATGTAAGATTACCAG-GG
*
578046 GAATGTAAGATTGCCAGGG
1 GAATGTAAGATTACCAGGG
578065 AATAGGATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 2 0.11
20 16 0.89
ACGTcount: A:0.33, C:0.10, G:0.33, T:0.23
Consensus pattern (19 bp):
GAATGTAAGATTACCAGGG
Found at i:578551 original size:15 final size:15
Alignment explanation
Indices: 578531--578560 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
578521 GTAAATGAGA
578531 TTTAGGGATTTTATT
1 TTTAGGGATTTTATT
578546 TTTAGGGATTTTATT
1 TTTAGGGATTTTATT
578561 CGAATTGGAA
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:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (15 bp):
TTTAGGGATTTTATT
Found at i:583770 original size:31 final size:32
Alignment explanation
Indices: 583697--583790 Score: 120
Period size: 32 Copynumber: 3.0 Consensus size: 32
583687 CCCAAATGAC
* * *
583697 CTATGCATTTGTCCCGAAGGACATAGGTAACA
1 CTATCCATATGTCCCAAAGGACATAGGTAACA
*
583729 CTGTCCATATGTCCCAAAGGACATAGGTAA-A
1 CTATCCATATGTCCCAAAGGACATAGGTAACA
*
583760 CTATCCATATGTCTCGAAA-GACATAGGTAAC
1 CTATCCATATGTC-CCAAAGGACATAGGTAAC
583791 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
31 24 0.44
32 30 0.56
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.24
Consensus pattern (32 bp):
CTATCCATATGTCCCAAAGGACATAGGTAACA
Found at i:593024 original size:2 final size:2
Alignment explanation
Indices: 593017--593058 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
593007 ACGTCAATTC
593017 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
593059 CATCTCTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:597758 original size:55 final size:55
Alignment explanation
Indices: 597674--597815 Score: 221
Period size: 55 Copynumber: 2.6 Consensus size: 55
597664 ATACTTGGGA
*
597674 GTATCGATACACTCCCCAGTGTACCGATACACAAATAACACTCGATGTTTTGAGG
1 GTATCGATACACTCCTCAGTGTACCGATACACAAATAACACTCGATGTTTTGAGG
* ** *
597729 GTATCGATACACTCCTCAGTGTACCGATACATAAATGGCATTCGATGTTTTGAGG
1 GTATCGATACACTCCTCAGTGTACCGATACACAAATAACACTCGATGTTTTGAGG
* *
597784 GTATCGATACACTTCTCAGTGTATCGATACAC
1 GTATCGATACACTCCTCAGTGTACCGATACAC
597816 TTTGAACATC
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 79 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (55 bp):
GTATCGATACACTCCTCAGTGTACCGATACACAAATAACACTCGATGTTTTGAGG
Found at i:602568 original size:79 final size:80
Alignment explanation
Indices: 602398--602568 Score: 211
Period size: 80 Copynumber: 2.1 Consensus size: 80
602388 ATCGAAAATA
* * * * * *
602398 TTAATAATATTTTAATATTTTTAGTAAAACGTTACCTAAAATAATATTTTTTTCTAATGAAAATG
1 TTAA-AATA-TTTAACATTTTTAATAAAACGCTACCTAAAACAATATTTTTTTCTAATAAAAATA
602463 TTAATATTAGACGCTAC
64 TTAATATTAGACGCTAC
* * *
602480 CTAAAATATTTAACATTTTTAATAAAACGCTACTTAAAACATTATTTTTTT-TACA-AAAAATAT
1 TTAAAATATTTAACATTTTTAATAAAACGCTACCTAAAACAATATTTTTTTCTA-ATAAAAATAT
*
602543 TAATATTAGACGTTAC
65 TAATATTAGACGCTAC
602559 TTAAAATATT
1 TTAAAATATT
602569 ATTTTTTCTA
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
79 32 0.42
80 38 0.49
81 4 0.05
82 3 0.04
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.43
Consensus pattern (80 bp):
TTAAAATATTTAACATTTTTAATAAAACGCTACCTAAAACAATATTTTTTTCTAATAAAAATATT
AATATTAGACGCTAC
Found at i:602633 original size:20 final size:20
Alignment explanation
Indices: 602586--602634 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
602576 CTATCTAAAA
*
602586 TTAAATAACAAAATTAACAT
1 TTAAATAACAAAAATAACAT
*
602606 TTATAATAA-AAAAATAATATT
1 TTA-AATAACAAAAATAACA-T
602627 TTAAATAA
1 TTAAATAA
602635 TACTATACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAAATAACAAAAATAACAT
Found at i:603102 original size:21 final size:21
Alignment explanation
Indices: 603059--603103 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
603049 TATCACATTA
**
603059 CGATTTTCCAAATTAGCGTTG
1 CGATTTTCCAAATTAGCAATG
* *
603080 CGATTTTCCTAATTCGCAATG
1 CGATTTTCCAAATTAGCAATG
603101 CGA
1 CGA
603104 ATACGTAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (21 bp):
CGATTTTCCAAATTAGCAATG
Found at i:603118 original size:20 final size:20
Alignment explanation
Indices: 603093--603145 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
603083 TTTTCCTAAT
603093 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
603113 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
603133 TCGCAATGCGAAT
1 TCGCAATGCGAAT
603146 CTGACTATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:603155 original size:20 final size:20
Alignment explanation
Indices: 603132--603198 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
603122 GAATACGTAA
* *
603132 ATCGCAATGCGAATCTGACT
1 ATCGCAACGCGATTCTGACT
*
603152 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
603172 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
603192 ATCGCAA
1 ATCGCAA
603199 TACTGAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:603156 original size:40 final size:41
Alignment explanation
Indices: 603112--603206 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 41
603102 GAATACGTAA
*
603112 ATCGCAATACGAATAC-GTA-AATCGCAATGCGAATCTGACT
1 ATCGCAATACGAATACTG-ACAATCGCAACGCGAATCTGACT
* * *
603152 ATCGC-A-ACGAGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAATACGA-ATACTGACAATCGCAACGCGAATCTGACT
603192 ATCGCAATACTGAAT
1 ATCGCAATAC-GAAT
603207 TTCAAATTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
38 4 0.09
39 5 0.11
40 29 0.64
41 1 0.02
42 4 0.09
43 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (41 bp):
ATCGCAATACGAATACTGACAATCGCAACGCGAATCTGACT
Found at i:604067 original size:24 final size:24
Alignment explanation
Indices: 604040--604093 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
604030 GTATTCGAAA
604040 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
604064 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
604088 TTTGAT
1 TTTGAT
604094 GATTTTCAGA
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:606534 original size:20 final size:20
Alignment explanation
Indices: 606509--606601 Score: 143
Period size: 20 Copynumber: 4.7 Consensus size: 20
606499 ACATTTATTC
606509 GACTATCGCAACGC-GAATAT
1 GACTATCGCAACGCGGAA-AT
* *
606529 GACTATTGCAACACGGAAAT
1 GACTATCGCAACGCGGAAAT
*
606549 GACTATCGCAACGCGGAATT
1 GACTATCGCAACGCGGAAAT
606569 GACTATCGCAACGCGGAAAT
1 GACTATCGCAACGCGGAAAT
606589 GACTATCGCAACG
1 GACTATCGCAACG
606602 AGAGAATCGC
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 63 0.95
21 3 0.05
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (20 bp):
GACTATCGCAACGCGGAAAT
Found at i:606623 original size:33 final size:33
Alignment explanation
Indices: 606573--606668 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
606563 GGAATTGACT
**
606573 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGC-GAAATGAAAATCGCAACGAGAGA
* *
606607 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
606640 ATCGCAACGCGAAAATGAAAATCGCAACG
1 ATCGCAACGCG-AAATGAAAATCGCAACG
606669 CGAATTTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:606741 original size:34 final size:33
Alignment explanation
Indices: 606683--606779 Score: 131
Period size: 34 Copynumber: 2.8 Consensus size: 33
606673 TTTAGTTTCA
*
606683 CGTTGTGATTTTCATTTTCGCATTGCGATTCTCTT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTC-T
606718 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
606751 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
606780 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
33 16 0.28
34 28 0.49
35 13 0.23
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:606896 original size:14 final size:14
Alignment explanation
Indices: 606877--606913 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
606867 CATCAATTAA
606877 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
606891 ACAAATCATCTTTT
1 ACAAATCAACATTT
606905 ACAAATCAA
1 ACAAATCAA
606914 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:608403 original size:42 final size:42
Alignment explanation
Indices: 608296--608406 Score: 111
Period size: 42 Copynumber: 2.6 Consensus size: 42
608286 TCTAGAATGT
* *
608296 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGTGGCCTCTTGAACGA
* * ** *
608338 TGGGAGGGGACTCTTGAGGGATGATA-TAGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGT-GGCCTCTTGAACGA
608380 TAGGG-GAGGCCTCTTGAACGATGACAG
1 T-GGGAGAGGCCTCTTGAACGATGACAG
608407 GTGAGTCGGG
Statistics
Matches: 54, Mismatches: 11, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
41 1 0.02
42 48 0.89
43 5 0.09
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGTGGCCTCTTGAACGA
Found at i:608910 original size:20 final size:20
Alignment explanation
Indices: 608887--608998 Score: 163
Period size: 20 Copynumber: 5.6 Consensus size: 20
608877 GAAACTTAAA
608887 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
608907 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
608927 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
608947 ATCGCAATGC-AAATTTAACT
1 ATCGCAATGCGAAA-ATGACT
**
608967 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
608987 ATCGCAATGCGA
1 ATCGCAATGCGA
608999 TTTTTATTTC
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
19 3 0.04
20 79 0.94
21 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:609078 original size:20 final size:20
Alignment explanation
Indices: 609024--609162 Score: 108
Period size: 20 Copynumber: 7.6 Consensus size: 20
609014 GCGATTCTTT
**
609024 CATTGCGATAGTCAAATTCG
1 CATTGCGATAGTCATTTTCG
609044 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
609064 CATTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
* *
609084 CGTTGCGCT--T--TTGTT-G
1 CATTGCGATAGTCATT-TTCG
**
609100 --TTGCGATTTTCA-TTTCG
1 CATTGCGATAGTCATTTTCG
*
609117 CATTGCGAT--TC--TCTCG
1 CATTGCGATAGTCATTTTCG
609133 --TTGCGATAGTCATTTTCG
1 CATTGCGATAGTCATTTTCG
609151 CATTGCGATAGT
1 CATTGCGATAGT
609163 AAACTATTCT
Statistics
Matches: 98, Mismatches: 7, Indels: 28
0.74 0.05 0.21
Matches are distributed among these distances:
14 13 0.13
16 12 0.12
17 6 0.06
18 5 0.05
19 7 0.07
20 55 0.56
ACGTcount: A:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (20 bp):
CATTGCGATAGTCATTTTCG
Found at i:609123 original size:33 final size:34
Alignment explanation
Indices: 609005--609159 Score: 141
Period size: 34 Copynumber: 4.4 Consensus size: 34
608995 GCGATTTTTA
* * *
609005 TTTCGCATTGCGATTCTTTCATTGCGATAGTCAA
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
* *
609039 ATTCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGAT--TC--TCTCG--TTGCGATAGTCAT
* * * * * **
609079 TTTCGCGTTGCGCTTTTGTTGTTGCGATTTTCA-
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
609112 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
609146 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
609160 AGTAAACTAT
Statistics
Matches: 96, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
33 26 0.27
34 37 0.39
36 5 0.05
38 5 0.05
40 23 0.24
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.43
Consensus pattern (34 bp):
TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
Found at i:611081 original size:20 final size:20
Alignment explanation
Indices: 611058--611167 Score: 78
Period size: 20 Copynumber: 5.5 Consensus size: 20
611048 TCTGAAACTT
*
611058 AAAATTGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
611078 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
611098 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * **
611118 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** *
611138 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
611157 AAAATCACAAC
1 AAAATCGCAAC
611168 GACAGAATCG
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 11 0.14
20 68 0.86
ACGTcount: A:0.44, C:0.23, G:0.16, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:611530 original size:22 final size:22
Alignment explanation
Indices: 611505--611580 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
611495 TGACCGTGAA
611505 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGCCGGAGATGGAGAC
* **
611527 TGATATCGTTGGAGAT-GAGAAC
1 TGATTTCGCCGGAGATGGAG-AC
* *
611549 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGCCGGAGATGGAGAC
* *
611571 GGATGTCGCC
1 TGATTTCGCC
611581 TTAGAGAGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 3 0.07
22 38 0.88
23 2 0.05
ACGTcount: A:0.22, C:0.16, G:0.37, T:0.25
Consensus pattern (22 bp):
TGATTTCGCCGGAGATGGAGAC
Found at i:611791 original size:20 final size:20
Alignment explanation
Indices: 611768--611840 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
611758 CGATAGTCAG
*
611768 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
611788 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
611808 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
611828 ATTCGCATTGCGA
1 ATTCGCATTGCGA
611841 ATTAGGAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:611861 original size:21 final size:21
Alignment explanation
Indices: 611837--611882 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
611827 TATTCGCATT
611837 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
611858 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
611879 GCGA
1 GCGA
611883 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:624819 original size:16 final size:16
Alignment explanation
Indices: 624800--624830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
624790 TTTAAAGTTT
624800 AAATAAAATAAATAAA
1 AAATAAAATAAATAAA
*
624816 AAATAAAATCAATAA
1 AAATAAAATAAATAA
624831 TATTTTCTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (16 bp):
AAATAAAATAAATAAA
Found at i:635700 original size:37 final size:37
Alignment explanation
Indices: 635652--635976 Score: 234
Period size: 37 Copynumber: 8.7 Consensus size: 37
635642 ATAAATTTCC
*
635652 AAAATGCTTTTAAAAACTATATATTATACATGTTTTTA
1 AAAATG-TTTTAAAAACTATATATTATATATGTTTTTA
* * * *
635690 AAAACGTTTTAAAAACT-T-TATAATATATATTTTCA
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
* * * * *
635725 GAAACGGTTTAAAAATTATATATTATATATATTTTT-
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
* * *
635761 AAAATGTTTTTCAAAAATTATATAATATTTAAATG-TTTTA
1 AAAATG-TTTT-AAAAACTATAT-AT-TATATATGTTTTTA
*** * * * *
635801 AAAA-AAATTCAAAACAATATATTATATAAGTTTTCA
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
* *
635837 AAAATGATTTTAAAAACTATATATTATATATATCTTCT-
1 AAAATG-TTTTAAAAACTATATATTATATATGT-TTTTA
* *
635875 AAAATGTTTTAAAAACTATATACTATATA-GTTTTCA
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
* * ** *
635911 AAAATATTTTTAAAACTATATATTATATA-CATTTTC
1 AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
*
635947 AAAATGTTTTCAAAAATTATGTATATTATA
1 AAAATGTTTT-AAAAACTA--TATATTATA
635977 AGTATTTTCA
Statistics
Matches: 223, Mismatches: 49, Indels: 29
0.74 0.16 0.10
Matches are distributed among these distances:
35 34 0.15
36 55 0.25
37 64 0.29
38 44 0.20
39 17 0.08
40 9 0.04
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATATTATATATGTTTTTA
Found at i:635737 original size:35 final size:36
Alignment explanation
Indices: 635660--635759 Score: 105
Period size: 35 Copynumber: 2.8 Consensus size: 36
635650 CCAAAATGCT
* * * * * *
635660 TTTAAAAACTATATATTATACATGTTTTTAAAAACGT
1 TTTAAAAATTATATA-TATATATATTTTCAGAAACGG
635697 TTTAAAAACTT-TATA-ATATATATTTTCAGAAACGG
1 TTTAAAAA-TTATATATATATATATTTTCAGAAACGG
635732 TTTAAAAATTATATATTATATATATTTT
1 TTTAAAAATTATATA-TATATATATTTT
635760 TAAAATGTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
34 2 0.04
35 27 0.51
37 23 0.43
38 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (36 bp):
TTTAAAAATTATATATATATATATTTTCAGAAACGG
Found at i:635805 original size:29 final size:31
Alignment explanation
Indices: 635746--635806 Score: 81
Period size: 29 Copynumber: 2.0 Consensus size: 31
635736 AAAATTATAT
* **
635746 ATTATATATATTTTTAAAATGTTTTTCAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
635777 ATTATATA-ATATTT-AAATGTTTTAAAAAA
1 ATTATATATATATTTAAAATGTTTTAAAAAA
635806 A
1 A
635807 ATTCAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 14 0.52
30 5 0.19
31 8 0.30
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTATATATATATTTAAAATGTTTTAAAAAA
Found at i:635937 original size:73 final size:72
Alignment explanation
Indices: 635617--635976 Score: 278
Period size: 75 Copynumber: 4.9 Consensus size: 72
635607 ATATATATAT
* * * * *
635617 AAATATTTTCAAAAA-AATGTAATATATAAATTTCCAAAATGCTTTTAAAAACTATATATTATAC
1 AAATATTTT-AAAAACTATATATTATATAAATTTTCAAAATG-TTTTAAAAACTATATATTATAT
*
635681 ATGTTTTTAA
64 A-GTTTTCAA
** * * * * *
635691 AAACGTTTTAAAAACT-T-TATAATATATATTTTCAGAAACGGTTTAAAAATTATATATTATATA
1 AAATATTTTAAAAACTATATATTATATAAATTTTCA-AAATGTTTTAAAAACTATATATTATATA
**
635754 -TATTTTTA
65 GT-TTTCAA
* * * * * **** * *
635762 AAATGTTTTTCAAAAATTATATAATATTTAAATGTTTTAAAAAAAATTCAAAACAATATATTATA
1 AAAT-ATTTT-AAAAACTATATATTATATAAAT-TTTCAAAATGTTTTAAAAACTATATATTATA
635827 TAAGTTTTCAA
63 T-AGTTTTCAA
* * *
635838 AAATGATTTTAAAAACTATATATTATATATATCTTCTAAAATGTTTTAAAAACTATATACTATAT
1 AAAT-ATTTTAAAAACTATATATTATATAAATTTTC-AAAATGTTTTAAAAACTATATATTATAT
635903 AGTTTTCAA
64 AGTTTTCAA
* * *
635912 AAATATTTTTAAAACTATATATTATATACATTTTCAAAATGTTTTCAAAAATTATGTATATTATA
1 AAATATTTTAAAAACTATATATTATATAAATTTTCAAAATGTTTT-AAAAACTA--TATATTATA
635977 AGTATTTTCA
Statistics
Matches: 224, Mismatches: 48, Indels: 27
0.75 0.16 0.09
Matches are distributed among these distances:
70 1 0.00
71 8 0.04
72 47 0.21
73 51 0.23
74 23 0.10
75 75 0.33
76 18 0.08
77 1 0.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (72 bp):
AAATATTTTAAAAACTATATATTATATAAATTTTCAAAATGTTTTAAAAACTATATATTATATAG
TTTTCAA
Done.