Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007956.1 Hibiscus syriacus cultivar Beakdansim tig00110383_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: 3102597
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 14
Found at i:428163 original size:27 final size:29
Alignment explanation
Indices: 427983--428188 Score: 158
Period size: 29 Copynumber: 7.3 Consensus size: 29
427973 TTTAACTTAT
* * * *
427983 AAATATATTTATTTAGTGAAGATAATAATA
1 AAATATATTTA-TAAGTTAAAATAAGAATA
*
428013 AAATATTTTTAT-A-TTAAAATAAGAATA
1 AAATATATTTATAAGTTAAAATAAGAATA
* * * *
428040 AAATAGATTTATAAGTTAAGACAAAAATA
1 AAATATATTTATAAGTTAAAATAAGAATA
* *
428069 AAATATATTT-TCAACTTTAAATAAGAATA
1 AAATATATTTAT-AAGTTAAAATAAGAATA
* * *
428098 AAATATAGTTT-TAAGTGAATATAATAA-A
1 AAATATA-TTTATAAGTTAAAATAAGAATA
* *
428126 AAATATTTTTAT-A-TTAAAATTAGAATA
1 AAATATATTTATAAGTTAAAATAAGAATA
* * *
428153 AAATAGATTTATAAGTTAAGACAA-AATA
1 AAATATATTTATAAGTTAAAATAAGAATA
428181 AAATATAT
1 AAATATAT
428189 CTTTGAAAGT
Statistics
Matches: 137, Mismatches: 31, Indels: 18
0.74 0.17 0.10
Matches are distributed among these distances:
26 8 0.06
27 36 0.26
28 23 0.17
29 56 0.41
30 14 0.10
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.36
Consensus pattern (29 bp):
AAATATATTTATAAGTTAAAATAAGAATA
Found at i:428184 original size:55 final size:55
Alignment explanation
Indices: 428009--428186 Score: 227
Period size: 55 Copynumber: 3.2 Consensus size: 55
427999 TGAAGATAAT
428009 AATAAAATATTTTTATATTAAAATAAGAATAAAATAGATTTATAAGTTAAGACAAA
1 AATAAAATATTTTTATATTAAAATAAGAATAAAATAGATTTATAAGTTAAGAC-AA
* * * * *
428065 AATAAAATATATTTTCA-ACTTTAAATAAGAATAAAATATAGTTT-TAAGTGAATATAA
1 AATAAAATAT-TTTT-ATA-TTAAAATAAGAATAAAATAGA-TTTATAAGTTAAGACAA
*
428122 TAA-AAAATATTTTTATATTAAAATTAGAATAAAATAGATTTATAAGTTAAGACAA
1 -AATAAAATATTTTTATATTAAAATAAGAATAAAATAGATTTATAAGTTAAGACAA
428177 AATAAAATAT
1 AATAAAATAT
428187 ATCTTTGAAA
Statistics
Matches: 103, Mismatches: 11, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
54 5 0.05
55 36 0.35
56 15 0.15
57 14 0.14
58 30 0.29
59 3 0.03
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (55 bp):
AATAAAATATTTTTATATTAAAATAAGAATAAAATAGATTTATAAGTTAAGACAA
Found at i:429000 original size:23 final size:26
Alignment explanation
Indices: 428974--429026 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 26
428964 TTTCCACTAG
*
428974 TTAATATAA-TTATTT-TTA-AAATA
1 TTAAAATAATTTATTTATTATAAATA
428997 TTAAAATAATTTATTTATTATTAAATA
1 TTAAAATAATTTATTTATTA-TAAATA
429024 TTA
1 TTA
429027 CTTTTATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 8 0.32
24 6 0.24
25 3 0.12
27 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAAAATAATTTATTTATTATAAATA
Found at i:429098 original size:31 final size:29
Alignment explanation
Indices: 429030--429099 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
429020 AATATTACTT
*
429030 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
429060 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
429093 TTATATT
1 TTATATT
429100 AATTATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:429181 original size:23 final size:23
Alignment explanation
Indices: 429132--429182 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
429122 GTGCTATATT
**
429132 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
429155 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
429178 ATATT
1 ATATT
429183 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:429238 original size:19 final size:19
Alignment explanation
Indices: 429170--429250 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
429160 TTAAATATCT
429170 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
429189 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
429208 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
429228 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
429246 -TATTA
1 TTATTA
429251 TTTCTATGAA
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:431577 original size:18 final size:18
Alignment explanation
Indices: 431554--431590 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
431544 ACACCGTCAA
431554 AACCCGCGGGCTAAACGG
1 AACCCGCGGGCTAAACGG
*
431572 AACCCGTGGGCTAAACGG
1 AACCCGCGGGCTAAACGG
431590 A
1 A
431591 CGGGTAGCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.32, T:0.08
Consensus pattern (18 bp):
AACCCGCGGGCTAAACGG
Found at i:432106 original size:3 final size:3
Alignment explanation
Indices: 432098--432128 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
432088 TTAAAGAATA
432098 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
432129 TAATTCTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:432610 original size:18 final size:18
Alignment explanation
Indices: 432587--432631 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
432577 ATAGTCGGAG
432587 GAGAAGAAGAACGGCGAA
1 GAGAAGAAGAACGGCGAA
*
432605 GAGAAGAAGAACGGCGAG
1 GAGAAGAAGAACGGCGAA
432623 GAG-AGAAGA
1 GAGAAGAAGA
432632 GATTGGGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.49, C:0.09, G:0.42, T:0.00
Consensus pattern (18 bp):
GAGAAGAAGAACGGCGAA
Found at i:446023 original size:26 final size:25
Alignment explanation
Indices: 445986--446034 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 25
445976 ATATTCTATC
445986 TAAAAAATTATTTTAGTATTTTTATTA
1 TAAAAAATTATTTTA--ATTTTTATTA
446013 TAAAAAA-TATTTTAATTTTTAT
1 TAAAAAATTATTTTAATTTTTAT
446035 ATATTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.36
26 7 0.32
27 7 0.32
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
TAAAAAATTATTTTAATTTTTATTA
Found at i:455437 original size:20 final size:20
Alignment explanation
Indices: 455412--455451 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
455402 ATAAGGATAT
455412 TAATTAACTTTTTGAAACCA
1 TAATTAACTTTTTGAAACCA
455432 TAATTAACTTTTTGAAACCA
1 TAATTAACTTTTTGAAACCA
455452 AAATGATCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (20 bp):
TAATTAACTTTTTGAAACCA
Found at i:456087 original size:17 final size:17
Alignment explanation
Indices: 456067--456114 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
456057 AAAATTTAAA
*
456067 AATTCAAAAATATATTT
1 AATTCAAAATTATATTT
* *
456084 AATTTAAAATTCTA-TT
1 AATTCAAAATTATATTT
*
456100 ATTTCAAAATTATAT
1 AATTCAAAATTATAT
456115 AAAAAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTCAAAATTATATTT
Found at i:456349 original size:20 final size:21
Alignment explanation
Indices: 456326--456366 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
456316 TATTATATGT
**
456326 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
456346 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
456367 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:457308 original size:12 final size:12
Alignment explanation
Indices: 457291--457328 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
457281 TCTTCTCAGT
457291 TCTCTGTTTCTG
1 TCTCTGTTTCTG
*
457303 TCTCTG--TCTC
1 TCTCTGTTTCTG
457313 TCTCTGTTTCTG
1 TCTCTGTTTCTG
457325 TCTC
1 TCTC
457329 CCTTTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.00, C:0.32, G:0.13, T:0.55
Consensus pattern (12 bp):
TCTCTGTTTCTG
Found at i:457814 original size:3 final size:3
Alignment explanation
Indices: 457806--457904 Score: 171
Period size: 3 Copynumber: 32.7 Consensus size: 3
457796 TTAATATATT
457806 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* *
457852 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
457900 TAA TA
1 TAA TA
457905 TGGATAAAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
3 88 0.97
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:458905 original size:112 final size:113
Alignment explanation
Indices: 458218--459421 Score: 1731
Period size: 113 Copynumber: 10.7 Consensus size: 113
458208 ATAGAATTAT
* * * *
458218 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * * *
458283 CTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAA
63 CTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
458334 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
458399 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
*
458447 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
458512 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
*
458560 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
458625 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
* * *
458673 GTAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
458738 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
* *
458786 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
458850 ATTATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTC-G
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
* * *
458897 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * *
458961 CATTATGAACTTTCTCTGGAAATGTTAATCCATCAAGTGATGAATTC-G
65 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
* * *
459009 AGCAAAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
** * * *
459073 CATTATGAACTTTCTCTGGAAAAAATAATTCATCAAGTGATGAATTCAG
65 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
* *
459122 GGAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** * ** * *** * *
459186 ATTATGAACTCTAACTGGCACTGCTGATCCACCGGGTGATGAATTTAA
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
* * *
459234 GCAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * *
459299 ATTATGAACTTTCTCTGGAAATGCTGATCCATCGAATGATGGATT-TG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
*
459346 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 -GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
*
459411 CATTATAAACT
65 CATTATGAACT
459422 CGACCTGGAA
Statistics
Matches: 1014, Mismatches: 69, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
111 1 0.00
112 408 0.40
113 555 0.55
116 50 0.05
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAG
Found at i:459883 original size:22 final size:22
Alignment explanation
Indices: 459858--459912 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
459848 GATAAAGCTT
*
459858 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
459880 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
459902 TCATCTTTGAA
1 TCATCTTTGAA
459913 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:461488 original size:36 final size:34
Alignment explanation
Indices: 461448--461521 Score: 78
Period size: 35 Copynumber: 2.1 Consensus size: 34
461438 TGTTACTTCT
461448 TATTG-AGATGAACCTCCAAGAATGCCCAAATATTC
1 TATTGCAG-TGAACCTCCAA-AATGCCCAAATATTC
* * * *
461483 ATATTGCTGTGAGCCTTCAAAATGCCCTAATATTC
1 -TATTGCAGTGAACCTCCAAAATGCCCAAATATTC
461518 TATT
1 TATT
461522 TCTGGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
34 4 0.12
35 14 0.42
36 14 0.42
37 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (34 bp):
TATTGCAGTGAACCTCCAAAATGCCCAAATATTC
Found at i:462519 original size:84 final size:84
Alignment explanation
Indices: 462378--462601 Score: 421
Period size: 84 Copynumber: 2.7 Consensus size: 84
462368 ATTTTTACCA
* *
462378 AACCAGATCAAATAACTCAAAGAATACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
462443 TCAATGATTGGTTCCGTCC
66 TCAATGATTGGTTCCGTCC
462462 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
462527 TCAATGATTGGTTCCGTCC
66 TCAATGATTGGTTCCGTCC
*
462546 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCAT
462602 TTTTCAGTTA
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 137 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (84 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCACATTCATCTTCTAAAT
TCAATGATTGGTTCCGTCC
Found at i:464839 original size:6 final size:6
Alignment explanation
Indices: 464825--464869 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
464815 CTTTATTCGA
* *
464825 TTTTCC TTTTTC TTTTT- TTTTTC TTTTTC TTCTTC TTCTTTC TTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TT-TTTC TTT
464870 GCTGGATGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 5 0.15
6 24 0.71
7 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:464850 original size:17 final size:19
Alignment explanation
Indices: 464825--464869 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
464815 CTTTATTCGA
*
464825 TTTTCCTTTTTCTT-TT-T
1 TTTTTCTTTTTCTTCTTCT
464842 TTTTTCTTTTTCTTCTTCT
1 TTTTTCTTTTTCTTCTTCT
*
464861 TCTTTCTTT
1 TTTTTCTTT
464870 GCTGGATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.54
18 2 0.08
19 9 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTTCTTCTTCT
Found at i:467992 original size:14 final size:14
Alignment explanation
Indices: 467959--468010 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
467949 TATGACATAA
* *
467959 AAATGCAAAGATGCC
1 AAATGTAAAAATG-C
* *
467974 AAATGTAGATATGC
1 AAATGTAAAAATGC
*
467988 AAATGTAAAAATGT
1 AAATGTAAAAATGC
468002 AAATGTAAA
1 AAATGTAAA
468011 TTATTTAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (14 bp):
AAATGTAAAAATGC
Found at i:470095 original size:17 final size:17
Alignment explanation
Indices: 470075--470122 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
470065 AAAATTTAAA
*
470075 AATTCAAAAATATATTT
1 AATTCAAAATTATATTT
* *
470092 AATTTAAAATTCTA-TT
1 AATTCAAAATTATATTT
*
470108 ATTTCAAAATTATAT
1 AATTCAAAATTATAT
470123 AAAAAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTCAAAATTATATTT
Found at i:470357 original size:20 final size:21
Alignment explanation
Indices: 470334--470374 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
470324 TATTATATGT
**
470334 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
470354 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
470375 TAAAAATATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:471318 original size:16 final size:16
Alignment explanation
Indices: 471297--471328 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
471287 TCTTCTCAAT
471297 TCTCTGTTTCTGTCTC
1 TCTCTGTTTCTGTCTC
471313 TCTCTGTTTCTGTCTC
1 TCTCTGTTTCTGTCTC
471329 CCTTTTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.12, T:0.56
Consensus pattern (16 bp):
TCTCTGTTTCTGTCTC
Found at i:471805 original size:3 final size:3
Alignment explanation
Indices: 471799--471902 Score: 190
Period size: 3 Copynumber: 34.7 Consensus size: 3
471789 ATTATGTATT
471799 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
471847 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
471895 TAA TAA TA
1 TAA TAA TA
471903 TGGATAAAAA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 97 1.00
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:474241 original size:2 final size:2
Alignment explanation
Indices: 474236--474263 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
474226 ACAACCATTT
474236 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
474264 ATTGATATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:474955 original size:20 final size:21
Alignment explanation
Indices: 474922--474963 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
474912 GCATACCAAC
*
474922 TTTTGTCTTAAAAATGATTTT
1 TTTTCTCTTAAAAATGATTTT
*
474943 TTTTCTCTT-AAAATTATTTT
1 TTTTCTCTTAAAAATGATTTT
474963 T
1 T
474964 AAAAGATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTCTCTTAAAAATGATTTT
Found at i:479574 original size:31 final size:31
Alignment explanation
Indices: 479538--479596 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
479528 AACTTAAAAG
* *
479538 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
479569 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
479597 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:479647 original size:22 final size:22
Alignment explanation
Indices: 479621--479663 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
479611 TAATAAATTA
479621 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
479643 TTTAAAATAAATCAATTCATA
1 TTTAAAATAAATCAATCCATA
479664 CTAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:479672 original size:22 final size:22
Alignment explanation
Indices: 479623--479671 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
479613 ATAAATTATT
**
479623 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
479645 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
479668 TAAA
1 TAAA
479672 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:479675 original size:54 final size:54
Alignment explanation
Indices: 479611--479973 Score: 381
Period size: 54 Copynumber: 6.6 Consensus size: 54
479601 ACAACTACAA
*
479611 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* ** * ** * *
479665 TAATAAATTATTTAAAATAAATAAATTAATACAACTACAATAATAAATCAATCTATGC
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCCATAC
* *
479723 TAATAAATTATTTAAAACAAATCAATTCATATTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
* **
479777 TAATAAATTATTTAAAATAAATCAATTCATACATCTACAATAATAAATCAATCCATA-
1 TAATAAATTATTTAAAATAAATCAATCCAT--AT-TTTAA-AATAAATCAATCCATAC
** * ** * * * **
479834 TTTTAAAATAAAT-CAATCTATTCTAATAAAT-TATTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAAT-AAATC-AATCCATAT-TTTAAAATAAATCAATCCATAC
*
479889 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
479943 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAATAAATCAATCCATA
479974 CAACTACAAT
Statistics
Matches: 252, Mismatches: 44, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
54 144 0.57
55 20 0.08
56 8 0.03
57 18 0.07
58 62 0.25
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATAC
Found at i:479681 original size:32 final size:32
Alignment explanation
Indices: 479643--479808 Score: 134
Period size: 32 Copynumber: 5.7 Consensus size: 32
479633 CAATCCATAT
479643 TTTAAAATAAATCAATTCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
* * *
479675 TTTAAAATAAATAAATTAATAC-AACTACA--A
1 TTTAAAATAAATCAATTCATACTAA-TAAATTA
*
479705 --T--AATAAATCAA-TCTATGCTAATAAATTA
1 TTTAAAATAAATCAATTC-ATACTAATAAATTA
*
479733 TTTAAAACAAATCAA-T--T-C--AT--A-T-
1 TTTAAAATAAATCAATTCATACTAATAAATTA
*
479755 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATTCATACTAATAAATTA
479787 TTTAAAATAAATCAATTCATAC
1 TTTAAAATAAATCAATTCATAC
479809 ATCTACAATA
Statistics
Matches: 104, Mismatches: 11, Indels: 38
0.68 0.07 0.25
Matches are distributed among these distances:
22 14 0.13
23 1 0.01
24 1 0.01
25 2 0.02
26 18 0.17
27 2 0.02
28 5 0.05
29 1 0.01
30 3 0.03
31 3 0.03
32 54 0.52
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATTCATACTAATAAATTA
Found at i:479687 original size:18 final size:18
Alignment explanation
Indices: 479612--479692 Score: 55
Period size: 22 Copynumber: 4.5 Consensus size: 18
479602 CAACTACAAT
479612 AATAAATTATTTAAAATA
1 AATAAATTATTTAAAATA
*
479630 AATCAATCCATATTTTAAAATA
1 AATAAAT---TA-TTTAAAATA
* *
479652 AATCAATTCA--T--ACT-
1 AATAAATT-ATTTAAAATA
479666 AATAAATTATTTAAAATA
1 AATAAATTATTTAAAATA
479684 AATAAATTA
1 AATAAATTA
479693 ATACAACTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 20
0.67 0.05 0.27
Matches are distributed among these distances:
13 1 0.02
14 7 0.14
15 3 0.06
17 3 0.06
18 15 0.31
19 1 0.02
20 1 0.02
21 2 0.04
22 16 0.33
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAAATTATTTAAAATA
Found at i:479745 original size:112 final size:111
Alignment explanation
Indices: 479611--479973 Score: 439
Period size: 112 Copynumber: 3.3 Consensus size: 111
479601 ACAACTACAA
* *
479611 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTAT
1 TAATAAATTATTTAAAACAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* *
479676 TTAAAATAAATAAATTAATACAACTACAATAATAAATCAATCTATGC
66 TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCTAT-C
*
479723 TAATAAATTATTTAAAACAAATCAATTCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAACAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
* * *
479788 TTAAAATAAATCAATTCATACATCTACAATAATAAATCAATCCATA
66 TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCTATC
** * ** * * * * **
479834 TTTTAAAATAAATCAATCTATTCTAATAAAT-TATTTAAAATAAATCAATCCATACTAATAAATT
1 TAATAAATTATTTAAAACAAATC-AATCCATAT-TTTAAAATAAATCAATCCATACTAATAAATT
* * **
479898 ATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCTATAC
64 ATTTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCTAT-C
*
479943 TAATAAATTATTTAAAATAAATCAATCCATA
1 TAATAAATTATTTAAAACAAATCAATCCATA
479974 CAACTACAAT
Statistics
Matches: 209, Mismatches: 38, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
108 19 0.09
109 16 0.08
111 15 0.07
112 159 0.76
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (111 bp):
TAATAAATTATTTAAAACAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
TTAAAATAAATCAATTCATACAACTACAATAATAAATCAATCTATC
Found at i:479759 original size:22 final size:22
Alignment explanation
Indices: 479733--479775 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
479723 TAATAAATTA
*
479733 TTTAAAACAAATCAATTCATAT
1 TTTAAAACAAATCAATCCATAT
*
479755 TTTAAAATAAATCAATCCATA
1 TTTAAAACAAATCAATCCATA
479776 CTAATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAACAAATCAATCCATAT
Found at i:479861 original size:18 final size:20
Alignment explanation
Indices: 479817--479864 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
479807 ACATCTACAA
*
479817 TAATAAATCAATCCATATTT
1 TAATAAATCAATCCATATTC
479837 TAAAATAAATCAAT-C-TATTC
1 T--AATAAATCAATCCATATTC
479857 TAATAAAT
1 TAATAAAT
479865 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.28
20 6 0.24
21 1 0.04
22 11 0.44
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (20 bp):
TAATAAATCAATCCATATTC
Found at i:479864 original size:22 final size:22
Alignment explanation
Indices: 479785--479851 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 22
479775 ACTAATAAAT
*
479785 TATTT-AAAATAAATCAATTCA
1 TATTTAAAAATAAATCAATCCA
*
479806 TACATCTACAATAATAAATCAATCCA
1 T--ATTTA-AA-AATAAATCAATCCA
*
479832 TATTTTAAAATAAATCAATC
1 TATTTAAAAATAAATCAATC
479852 TATTCTAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
21 1 0.03
22 12 0.32
23 5 0.14
24 3 0.08
25 2 0.05
26 14 0.38
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (22 bp):
TATTTAAAAATAAATCAATCCA
Found at i:479874 original size:32 final size:32
Alignment explanation
Indices: 479835--479974 Score: 183
Period size: 32 Copynumber: 4.7 Consensus size: 32
479825 CAATCCATAT
*
479835 TTTAAAATAAATCAATCTATTCTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
479867 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
479899 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
479921 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
479953 TTTAAAATAAATCAATCCATAC
1 TTTAAAATAAATCAATCTATAC
479975 AACTACAATA
Statistics
Matches: 95, Mismatches: 3, Indels: 20
0.81 0.03 0.17
Matches are distributed among these distances:
22 17 0.18
23 1 0.01
24 1 0.01
26 3 0.03
28 3 0.03
30 1 0.01
31 1 0.01
32 68 0.72
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:479950 original size:22 final size:22
Alignment explanation
Indices: 479901--479949 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
479891 ATAAATTATT
**
479901 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
479923 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCCATA-TAA
479946 TAAA
1 TAAA
479950 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:479983 original size:166 final size:164
Alignment explanation
Indices: 479706--480047 Score: 569
Period size: 166 Copynumber: 2.1 Consensus size: 164
479696 CAACTACAAT
* * *
479706 AATAAATCAATCTATGCTAATAAATTATTTAAAACAAATCAATTCATATTTTAAAATAAATCAAT
1 AATAAATCAATCCATACTAATAAATTATTTAAAACAAATCAATCCATATTTTAAAATAAATCAAT
* *
479771 CCATACTAATAAATTATTTAAAATAAATCAATTCATACATCTACAATAATAAATCAATCCATATT
66 CCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATT
479836 TT-AAAATAAATCAATCTATTCTAATAAATTATTTAA
131 TTAAAAATAAATCAATC-A--CTAATAAATTATTTAA
*
479872 AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT
1 AATAAATCAATCCATACTAATAAATTATTTAAAACAAATCAATCCATATTTTAAAATAAATCAAT
*
479937 CTATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATT
66 CCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATT
* *
480002 TTAAAAATAAATTAATCACTACTAAATTATTTAA
131 TTAAAAATAAATCAATCACTAATAAATTATTTAA
480036 AATAAATCAATC
1 AATAAATCAATC
480048 ATTTTAAAAA
Statistics
Matches: 166, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
164 27 0.16
166 126 0.76
167 13 0.08
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (164 bp):
AATAAATCAATCCATACTAATAAATTATTTAAAACAAATCAATCCATATTTTAAAATAAATCAAT
CCATACTAATAAATTATTTAAAATAAATCAATCCATACAACTACAATAATAAATCAATCCATATT
TTAAAAATAAATCAATCACTAATAAATTATTTAA
Found at i:480104 original size:22 final size:22
Alignment explanation
Indices: 480031--480118 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 22
480021 TACTAAATTA
480031 TTTAAAATAAATCAAT-C--AT
1 TTTAAAATAAATCAATCCATAT
480050 TTTAAAA-AAA-CAAATCAACACTATT
1 TTTAAAATAAATC-AATC--CA-TA-T
480075 ATTTAAAATAAATCAATCCATAT
1 -TTTAAAATAAATCAATCCATAT
480098 TTTAAAAT-AATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
480119 AAATTTTAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
17 1 0.02
18 6 0.10
19 7 0.12
21 14 0.24
22 8 0.14
23 1 0.02
24 3 0.05
25 3 0.05
26 7 0.12
27 7 0.12
28 1 0.02
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:480186 original size:15 final size:14
Alignment explanation
Indices: 480169--480219 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
480159 AATAATATTT
480169 AAATAAATATTTTA
1 AAATAAATATTTTA
* *
480183 TAA-AATTATTTTA
1 AAATAAATATTTTA
*
480196 AAACAAATTATTTTA
1 AAATAAA-TATTTTA
480211 AAATAAATA
1 AAATAAATA
480220 ACCTTATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 11 0.37
14 6 0.20
15 13 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATAAATATTTTA
Found at i:485242 original size:7 final size:7
Alignment explanation
Indices: 485232--485258 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
485222 TGGTTCATGG
485232 TCCACTC
1 TCCACTC
485239 TCCACTC
1 TCCACTC
485246 TCCACTC
1 TCCACTC
485253 TCCACT
1 TCCACT
485259 GGCCTAGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.56, G:0.00, T:0.30
Consensus pattern (7 bp):
TCCACTC
Found at i:489727 original size:18 final size:19
Alignment explanation
Indices: 489704--489748 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
489694 CCCAGTAATC
*
489704 TTATTCC-CTGATAATCTT
1 TTATTCCACTGAAAATCTT
489722 TTATTCTCACTGAAAATCTT
1 TTATTC-CACTGAAAATCTT
489742 TTATTCC
1 TTATTCC
489749 TACTAGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 6 0.25
19 2 0.08
20 16 0.67
ACGTcount: A:0.24, C:0.22, G:0.04, T:0.49
Consensus pattern (19 bp):
TTATTCCACTGAAAATCTT
Found at i:508309 original size:12 final size:12
Alignment explanation
Indices: 508292--508316 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
508282 TGCTTTTTTT
508292 CATATATAACCA
1 CATATATAACCA
508304 CATATATAACCA
1 CATATATAACCA
508316 C
1 C
508317 CTCCAACTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (12 bp):
CATATATAACCA
Found at i:510710 original size:4 final size:4
Alignment explanation
Indices: 510693--510724 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
510683 CTTATATGCA
510693 TATT TATGT TATT TATT TATT TATT TATT TAT
1 TATT TAT-T TATT TATT TATT TATT TATT TAT
510725 AATTTTGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:512733 original size:17 final size:17
Alignment explanation
Indices: 512708--512758 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
512698 AATTTGTCTG
*
512708 AAATTTAAAAATAATAA
1 AAATCTAAAAATAATAA
*
512725 AAATCTAAATAAT-ATTA
1 AAATCTAAA-AATAATAA
*
512742 AAGTCATAAAAATAATA
1 AAATC-TAAAAATAATA
512759 TTTAATTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (17 bp):
AAATCTAAAAATAATAA
Found at i:526947 original size:29 final size:30
Alignment explanation
Indices: 526878--526936 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
526868 AATTTAAGGT
526878 AAAATGGTTTTTGGACTAGAATTGAATTTAC
1 AAAAT-GTTTTTGGACTAGAATTGAATTTAC
*
526909 AAAATGTTTTTGGACT-TAATTGAATTTA
1 AAAATGTTTTTGGACTAGAATTGAATTTA
526937 TTCAATGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.42
Consensus pattern (30 bp):
AAAATGTTTTTGGACTAGAATTGAATTTAC
Found at i:527042 original size:21 final size:20
Alignment explanation
Indices: 527016--527114 Score: 119
Period size: 21 Copynumber: 4.8 Consensus size: 20
527006 AGGGTGTCAA
527016 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
527037 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
527058 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
527079 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
*
527100 AATGCATCCATGCAC
1 AGTGCATCCATGCAC
527115 TCAAACACCG
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 36 0.52
22 13 0.19
23 3 0.04
ACGTcount: A:0.23, C:0.36, G:0.19, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:527160 original size:20 final size:20
Alignment explanation
Indices: 527135--527187 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
527125 AATGCAATTA
* *
527135 GTGCATCGATGCATTCTTCT
1 GTGCATCGATGCATCCTGCT
527155 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTGCT
*
527175 GTGCATCCATGCA
1 GTGCATCGATGCA
527188 CGAAGGCTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.28, G:0.23, T:0.32
Consensus pattern (20 bp):
GTGCATCGATGCATCCTGCT
Found at i:539276 original size:17 final size:20
Alignment explanation
Indices: 539254--539299 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
539244 ATCCTTTCTA
*
539254 TTTTTTGTAT-TTATTATAC
1 TTTTTAGTATCTTATTATAC
539273 TTTTTAGTATCTTATTATAC
1 TTTTTAGTATCTTATTATAC
539293 TCTTTTA
1 T-TTTTA
539300 TATAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTTAGTATCTTATTATAC
Found at i:539336 original size:16 final size:16
Alignment explanation
Indices: 539315--539346 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
539305 ATATATTTGT
*
539315 TTATTTATTATTATTA
1 TTATTTATTATCATTA
539331 TTATTTATTATCATTA
1 TTATTTATTATCATTA
539347 ACGTGTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTATTATCATTA
Found at i:539432 original size:2 final size:2
Alignment explanation
Indices: 539427--539471 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
539417 TTTTTTATTT
539427 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
539469 TA T
1 TA T
539472 TAGTTTTTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:543634 original size:95 final size:95
Alignment explanation
Indices: 543522--543703 Score: 294
Period size: 95 Copynumber: 1.9 Consensus size: 95
543512 ATATTATTTA
* *
543522 TATACAATAAAGCTTGAGTTTTCCATCT-AGAGCAATTGGTTAAACGCCCCAGCTTTATGGATAA
1 TATACAATAAAGCTTGAGCTGTCCATCTAAG-GCAATTGGTTAAACGCCCCAGCTTTATGGATAA
* *
543586 TATTCAGCTAGCCTGATAAAGGTGATTATAC
65 GATTCAGCTAACCTGATAAAGGTGATTATAC
* *
543617 TATACAATAAAGCTTGAGCTGTCCCTCTAAGGCAATTGGTTAAACGCCCCGGCTTTATGGATAAG
1 TATACAATAAAGCTTGAGCTGTCCATCTAAGGCAATTGGTTAAACGCCCCAGCTTTATGGATAAG
543682 ATTCAGCTAACCTGATAAAGGT
66 ATTCAGCTAACCTGATAAAGGT
543704 ATTTACATAC
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 78 0.98
96 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (95 bp):
TATACAATAAAGCTTGAGCTGTCCATCTAAGGCAATTGGTTAAACGCCCCAGCTTTATGGATAAG
ATTCAGCTAACCTGATAAAGGTGATTATAC
Found at i:545212 original size:99 final size:98
Alignment explanation
Indices: 545037--545240 Score: 309
Period size: 99 Copynumber: 2.1 Consensus size: 98
545027 AGGGGCTTCC
* *
545037 CAATTTCAGAACCAATTTCAACTTCACAGCGAATGATATTGGACCCAAGACAACACAAGCTCAAC
1 CAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAAC
*
545102 TTCACGACGAAGGGGCGACTGATTGTCAAAAAA
66 TTCACGACGAAGGGGCGACTGACTGTCAAAAAA
** * *
545135 CAACTTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGCACAAGCTCAA
1 CAA-TTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAA
* * *
545200 CTTCACGGCGAAGGGGCGGCTGACTGTCAACAAA
65 CTTCACGACGAAGGGGCGACTGACTGTCAAAAAA
545234 CAATTTC
1 CAATTTC
545241 CCAGTTCCAG
Statistics
Matches: 95, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
98 7 0.07
99 88 0.93
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (98 bp):
CAATTTCAGAACCAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAACACAAGCTCAAC
TTCACGACGAAGGGGCGACTGACTGTCAAAAAA
Found at i:545929 original size:84 final size:84
Alignment explanation
Indices: 545762--545917 Score: 188
Period size: 84 Copynumber: 1.9 Consensus size: 84
545752 GGTATATCGT
* * * * * *
545762 TTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCGACCAAAGACCTTCGAGTTTGATTCCGC
1 TTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACCAAAGACCTTCAAGTTCGATTCCAC
545827 TTAGCTCCAAGGCATATCA
66 TTAGCTCCAAGGCATATCA
* * * * *
545846 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCGAATACCTTTCAAGTTCGA-TCCA
1 TTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACCAAAGACC-TTCAAGTTCGATTCCA
*
545910 TTTAGCTC
65 CTTAGCTC
545918 GAGGGCTTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
84 50 0.85
85 9 0.15
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (84 bp):
TTTGCAGCATAACTCAAGGCGAGAAGGGCTATCTGCCAACCAAAGACCTTCAAGTTCGATTCCAC
TTAGCTCCAAGGCATATCA
Found at i:547578 original size:17 final size:20
Alignment explanation
Indices: 547556--547601 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
547546 CCTTTCTGTT
*
547556 TTTTTTGTAT-TTATTATAC
1 TTTTTAGTATCTTATTATAC
547575 TTTTTAGTATCTTATTATAC
1 TTTTTAGTATCTTATTATAC
547595 TCTTTTA
1 T-TTTTA
547602 CATAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 9 0.38
20 10 0.42
21 5 0.21
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (20 bp):
TTTTTAGTATCTTATTATAC
Found at i:547628 original size:3 final size:3
Alignment explanation
Indices: 547620--547656 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
547610 TACTGTTTAT
*
547620 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
547657 ACGTGTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:547738 original size:2 final size:2
Alignment explanation
Indices: 547733--547795 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
547723 TATGTTTTTT
547733 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
547775 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
547796 TTTAGTTTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:547903 original size:3 final size:3
Alignment explanation
Indices: 547895--547935 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
547885 TATCTATGTT
547895 TTA TTA TTA TTA TTA TTA TTA TATA TT- TTA TATA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA TT
547936 TCATTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 4 0.12
3 24 0.71
4 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:547909 original size:9 final size:8
Alignment explanation
Indices: 547893--547945 Score: 52
Period size: 9 Copynumber: 5.9 Consensus size: 8
547883 TTTATCTATG
547893 TTTTATTA
1 TTTTATTA
547901 TTATTATTA
1 TT-TTATTA
547910 TTATTATATA
1 TT-TTAT-TA
547920 TTTTATATA
1 TTTTAT-TA
547929 TTTTATTTCA
1 TTTTA-TT-A
547939 TTTTATT
1 TTTTATT
547946 TTGTGATCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
8 2 0.05
9 28 0.68
10 11 0.27
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTATTA
Found at i:555245 original size:2 final size:2
Alignment explanation
Indices: 555238--555268 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
555228 CAGTTATTAA
555238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
555269 ATTTTGTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:556489 original size:31 final size:31
Alignment explanation
Indices: 556400--556503 Score: 95
Period size: 31 Copynumber: 3.4 Consensus size: 31
556390 GGGTTTGAGA
* *
556400 GCCTA-CCTAAGAAAGTTCTCAGGGCCAC-GAG
1 GCCTATCC-AAGAAAGATCTCAGGGCCGCAG-G
* * *
556431 GCATATCCAAGAAAAATCTCGGGGCCGCAGG
1 GCCTATCCAAGAAAGATCTCAGGGCCGCAGG
* * *
556462 GCCTATCCAAGAAAGGTCTCAGAGCCGCAGA
1 GCCTATCCAAGAAAGATCTCAGGGCCGCAGG
*
556493 GCCTACCCAAG
1 GCCTATCCAAG
556504 GGCCGTCTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
31 56 0.95
32 3 0.05
ACGTcount: A:0.31, C:0.30, G:0.26, T:0.13
Consensus pattern (31 bp):
GCCTATCCAAGAAAGATCTCAGGGCCGCAGG
Found at i:557373 original size:31 final size:31
Alignment explanation
Indices: 557335--557618 Score: 532
Period size: 31 Copynumber: 9.2 Consensus size: 31
557325 GGTCACAATA
557335 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
* *
557366 TAGACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
557397 TAAACTGTTCATATATGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
557428 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
557459 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
557490 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
557521 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
557552 TAAACTGTTCATATGTGCCTTTAAACATATG
1 TAAACTGTTCATATGTGCCTTTAAACATATG
*
557583 TAAACTGTTCATATGTGCCTTTAAACATATA
1 TAAACTGTTCATATGTGCCTTTAAACATATG
557614 TAAAC
1 TAAAC
557619 CCTCGACTCT
Statistics
Matches: 246, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 246 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (31 bp):
TAAACTGTTCATATGTGCCTTTAAACATATG
Found at i:558234 original size:64 final size:63
Alignment explanation
Indices: 558128--558304 Score: 203
Period size: 64 Copynumber: 2.8 Consensus size: 63
558118 TAATGAAGGT
* * ** ** * **
558128 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGTATTCGATGT-GTCACTATTAATGGG
* *
558192 ATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGTATTCGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGTATTCGATGTGTCACTATTAATGGG
*
558256 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGTATTCGATGT
558305 CTTTATTTTA
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
63 3 0.03
64 94 0.97
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGATTGTATTCGATGTGTCACTATTAATGGG
Found at i:559038 original size:23 final size:23
Alignment explanation
Indices: 559012--559057 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
559002 CACCACAGCT
*
559012 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
559035 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
559058 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:559298 original size:151 final size:149
Alignment explanation
Indices: 559024--559341 Score: 575
Period size: 151 Copynumber: 2.1 Consensus size: 149
559014 TATAATTGCA
559024 CCGAAGTG-CCACGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCACGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
*
559088 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTT
65 TTCCTTAAGAATAATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTT
559153 CCACAGAATATATATATATATC
130 CCACAG-A-ATATATATATATC
*
559175 CCGAAGGACCACGTAGAATTGCACCGTAGTGGCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCACGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
559240 TCCTTAAGAATAATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
66 TCCTTAAGAATAATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
559305 CACAGAATATATATATATC
131 CACAGAATATATATATATC
*
559324 CCGAAGGACCGCGTAGAA
1 CCGAAGGACCACGTAGAA
559342 CCCTCGACTC
Statistics
Matches: 163, Mismatches: 3, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
149 30 0.18
150 2 0.01
151 131 0.80
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCACGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATAATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTC
CACAGAATATATATATATC
Found at i:564245 original size:23 final size:23
Alignment explanation
Indices: 564219--564264 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
564209 CACCACAGCT
*
564219 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
564242 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
564265 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:564481 original size:149 final size:149
Alignment explanation
Indices: 564242--564546 Score: 592
Period size: 149 Copynumber: 2.0 Consensus size: 149
564232 CGAAGTGCCA
564242 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
564307 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
564372 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
564391 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
564456 AATATATATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
564521 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
564540 CGTAGAA
1 CGTAGAA
564547 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
AATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:569775 original size:21 final size:21
Alignment explanation
Indices: 569749--569802 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
569739 TTACCCTTGA
*
569749 TGCATCGGTGCACCTTGAATG
1 TGCATCGATGCACCTTGAATG
569770 TGCATCGATGCACCTTGAATG
1 TGCATCGATGCACCTTGAATG
569791 TGCATCGATGCA
1 TGCATCGATGCA
569803 TATAGCCCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCACCTTGAATG
Found at i:571172 original size:31 final size:30
Alignment explanation
Indices: 571130--571192 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
571120 AAAAATAGCA
*
571130 AGGGGCAAATTATAGTTTAAAGCCAAAATT
1 AGGGGCAAATTATAGTTCAAAGCCAAAATT
* *
571160 AGGGGTCAAATTATGGTTCAAAGCCAAAGTT
1 AGGGG-CAAATTATAGTTCAAAGCCAAAATT
571191 AG
1 AG
571193 AAGCTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (30 bp):
AGGGGCAAATTATAGTTCAAAGCCAAAATT
Found at i:571202 original size:31 final size:31
Alignment explanation
Indices: 571135--571202 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
571125 TAGCAAGGGG
* * *
571135 CAAATTATAGTTTAAAGCCAAAATTAGGGGT
1 CAAATTATAGTTCAAAGCCAAAATTAGAGCT
* *
571166 CAAATTATGGTTCAAAGCCAAAGTTAGAAGCT
1 CAAATTATAGTTCAAAGCCAAAATTAG-AGCT
571198 -AAATT
1 CAAATT
571203 TTACCCAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.28
Consensus pattern (31 bp):
CAAATTATAGTTCAAAGCCAAAATTAGAGCT
Found at i:572108 original size:13 final size:13
Alignment explanation
Indices: 572090--572114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
572080 AGTTGAACAG
572090 TCTTCATATGCAA
1 TCTTCATATGCAA
572103 TCTTCATATGCA
1 TCTTCATATGCA
572115 CGTCTGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (13 bp):
TCTTCATATGCAA
Found at i:576452 original size:27 final size:27
Alignment explanation
Indices: 576400--576455 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
576390 CCACCATCAC
* *
576400 CACTTTGAACTTGAAACTTCATAGCAT
1 CACTTTGAACTTGAAACTCCACAGCAT
576427 CACTTTGAACTTGAAAGC-CCACAGCAT
1 CACTTTGAACTTGAAA-CTCCACAGCAT
576454 CA
1 CA
576456 AGATCTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (27 bp):
CACTTTGAACTTGAAACTCCACAGCAT
Found at i:578308 original size:22 final size:22
Alignment explanation
Indices: 578275--578316 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
578265 TTAATTTATA
578275 AAATGTTAAATTATAAATTACT
1 AAATGTTAAATTATAAATTACT
578297 AAATG-TATAATTATAAATTA
1 AAATGTTA-AATTATAAATTA
578317 ATTAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.40
Consensus pattern (22 bp):
AAATGTTAAATTATAAATTACT
Found at i:578328 original size:23 final size:23
Alignment explanation
Indices: 578283--578346 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
578273 TAAAATGTTA
* **
578283 AATTATAAATT-ACTAAATGTAT
1 AATTATAAATTAATTAAAAATAT
578305 AATTATAAATTAATTAAAAATAT
1 AATTATAAATTAATTAAAAATAT
* * *
578328 AAATGTAATTTAATTAAAA
1 AATTATAAATTAATTAAAA
578347 TAAAATATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
22 11 0.31
23 24 0.69
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (23 bp):
AATTATAAATTAATTAAAAATAT
Found at i:585932 original size:3 final size:3
Alignment explanation
Indices: 585926--585980 Score: 92
Period size: 3 Copynumber: 17.7 Consensus size: 3
585916 GTAGTAGTAG
585926 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
585972 TAA TTAA TA
1 TAA -TAA TA
585981 TTTTTGGTTC
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:587733 original size:28 final size:28
Alignment explanation
Indices: 587703--587756 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
587693 TTAAACCCCT
*
587703 TTTTATCT-CATCCCTATCTTTTCTCAC
1 TTTTATCTAAATCCCTATCTTTTCTCAC
*
587730 TTTTATCTAAATCCTTATCTTTTCTCA
1 TTTTATCTAAATCCCTATCTTTTCTCA
587757 TCCTTATCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.19, C:0.28, G:0.00, T:0.54
Consensus pattern (28 bp):
TTTTATCTAAATCCCTATCTTTTCTCAC
Found at i:587763 original size:28 final size:28
Alignment explanation
Indices: 587712--587770 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
587702 TTTTTATCTC
* *
587712 ATCCCTATCTTTTCTCACTTTTATCTAA
1 ATCCCTATCTTTTCTCACTCTTATCCAA
*
587740 ATCCTTATCTTTTCTCA-TCCTTATCCAA
1 ATCCCTATCTTTTCTCACT-CTTATCCAA
587768 ATC
1 ATC
587771 TAAATCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (28 bp):
ATCCCTATCTTTTCTCACTCTTATCCAA
Found at i:594766 original size:20 final size:20
Alignment explanation
Indices: 594741--594784 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
594731 CGTAGGGGCC
594741 GAACCTATTCGATTCTAATT
1 GAACCTATTCGATTCTAATT
594761 GAACCTATTCGATTCTAATT
1 GAACCTATTCGATTCTAATT
594781 GAAC
1 GAAC
594785 AAGTTCTTCA
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:0.32, C:0.20, G:0.11, T:0.36
Consensus pattern (20 bp):
GAACCTATTCGATTCTAATT
Found at i:596565 original size:15 final size:15
Alignment explanation
Indices: 596560--596596 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
596550 AGAAAAAACC
596560 AGAAAAAACACAAAA
1 AGAAAAAACACAAAA
596575 AGAAAAAACACAAAA
1 AGAAAAAACACAAAA
596590 AGAAAAA
1 AGAAAAA
596597 GAAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (15 bp):
AGAAAAAACACAAAA
Found at i:596604 original size:15 final size:15
Alignment explanation
Indices: 596560--596606 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
596550 AGAAAAAACC
*
596560 AGAAAAAACACAAAA
1 AGAAAAAACAAAAAA
*
596575 AGAAAAAACACAAAA
1 AGAAAAAACAAAAAA
*
596590 AG-AAAAAGAAAAAA
1 AGAAAAAACAAAAAA
596604 AGA
1 AGA
596607 GGTAATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.81, C:0.09, G:0.11, T:0.00
Consensus pattern (15 bp):
AGAAAAAACAAAAAA
Found at i:597362 original size:22 final size:23
Alignment explanation
Indices: 597326--597369 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
597316 CGTGGTGTTG
597326 AGTCAGCACCTTCTAGAAGGTCC
1 AGTCAGCACCTTCTAGAAGGTCC
*
597349 AGTCAG-AGCTTCTAGAAGGTC
1 AGTCAGCACCTTCTAGAAGGTC
597370 GAATGGGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
AGTCAGCACCTTCTAGAAGGTCC
Found at i:597575 original size:21 final size:20
Alignment explanation
Indices: 597551--597589 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
597541 TTGCTTTGAG
597551 TTTTATAAAAGTTTCCTTTTA
1 TTTT-TAAAAGTTTCCTTTTA
* *
597572 TTTTTCAAAGTTTTCTTT
1 TTTTTAAAAGTTTCCTTT
597590 GTTTGTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.23, C:0.10, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTTAAAAGTTTCCTTTTA
Found at i:603125 original size:24 final size:24
Alignment explanation
Indices: 603098--603153 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
603088 TAGAAGTTCG
603098 ATTGAAGCCTAAAACTTGAGCTCA
1 ATTGAAGCCTAAAACTTGAGCTCA
*
603122 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAACTTGAGCTCA
603146 ATTGAAGC
1 ATTGAAGC
603154 GAAAGAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (24 bp):
ATTGAAGCCTAAAACTTGAGCTCA
Found at i:604836 original size:188 final size:177
Alignment explanation
Indices: 604637--604982 Score: 505
Period size: 188 Copynumber: 1.9 Consensus size: 177
604627 AACTAAACCC
*
604637 AAATCATTTAAAACTCAATTAATAATTTAAGATTCT-ATATCTTTTAAACCTAAATCAATATTAA
1 AAATCATTTAAAACTCAATTAATAATTTAAGA-TCTAATAACTTTTAAACCTAAATCAATATTAA
*
604701 TTAATTAAAAAATTTATATACAATTTTTATTTTATAATTATATATTATTTAAATTAATTGTAAAC
65 TTAATTAAAAAATTTATATA-AA-----ATTTTAT-ATT-TATATTATTTAAATTAATTATAAAC
*
604766 TGTTTTTTCTGAATTAAAAAAATATTAAATATATTATATATAACATATAGGTTCAACTT
122 TATTTTTT-TGAATT-AAAAAATATTAAAT-TATTATATATAACATATAGGTTCAACTT
* *
604825 AAATTATTTAAAACTCAATTAATAATTTAAGATCTAATAACTTTTAAATCTAAATCAATATTAAT
1 AAATCATTTAAAACTCAATTAATAATTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAAT
604890 TAATTAAAAAATTTATATAAAATTTTATATTTATATTATTTAAATTAATTATAAACTATTTTTTT
66 TAATTAAAAAATTTATATAAAATTTTATATTTATATTATTTAAATTAATTATAAACTATTTTTTT
* * *
604955 GAATTATAAAATATTTAATTTTTATATA
131 GAATTAAAAAATATTAAATTATTATATA
604983 AATTATAAAA
Statistics
Matches: 149, Mismatches: 8, Indels: 13
0.88 0.05 0.08
Matches are distributed among these distances:
177 8 0.05
178 12 0.08
179 6 0.04
180 31 0.21
181 3 0.02
182 7 0.05
187 5 0.03
188 77 0.52
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (177 bp):
AAATCATTTAAAACTCAATTAATAATTTAAGATCTAATAACTTTTAAACCTAAATCAATATTAAT
TAATTAAAAAATTTATATAAAATTTTATATTTATATTATTTAAATTAATTATAAACTATTTTTTT
GAATTAAAAAATATTAAATTATTATATATAACATATAGGTTCAACTT
Found at i:610331 original size:14 final size:14
Alignment explanation
Indices: 610299--610332 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
610289 GATTTCTATG
*
610299 TAGGGAATTATTTG
1 TAGGGAATTATTTA
*
610313 CAGGGAATTATTTA
1 TAGGGAATTATTTA
610327 TAGGGA
1 TAGGGA
610333 TTACTCCCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.35
Consensus pattern (14 bp):
TAGGGAATTATTTA
Found at i:614619 original size:24 final size:24
Alignment explanation
Indices: 614572--614639 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
614562 TATGATTATT
*
614572 TTTTTAATAATAATAATAATAATA
1 TTTTTAATAATAATAATAAAAATA
*
614596 TTTTTAATTAATAA-ATTAAAAATA
1 TTTTTAA-TAATAATAATAAAAATA
*
614620 TTTTCTAA-AAAAATAATAAA
1 TTTT-TAATAATAATAATAAA
614640 GTAATCCCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
23 4 0.11
24 24 0.65
25 9 0.24
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTTAATAATAATAATAAAAATA
Found at i:614894 original size:15 final size:17
Alignment explanation
Indices: 614869--614908 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
614859 ATTTAAATTT
*
614869 TATTAAAAAAAATATAAA
1 TATTAAAAATAATA-AAA
*
614887 AATTAAAAATAATAAAA
1 TATTAAAAATAATAAAA
614904 TATTA
1 TATTA
614909 TATTTTCTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
TATTAAAAATAATAAAA
Found at i:616459 original size:23 final size:23
Alignment explanation
Indices: 616429--616473 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
616419 ACGATTCGTC
616429 GGTTAATTGCAGCACCTACCGTT
1 GGTTAATTGCAGCACCTACCGTT
616452 GGTTAATTGCAGCACCTACCGT
1 GGTTAATTGCAGCACCTACCGT
616474 ACAACAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (23 bp):
GGTTAATTGCAGCACCTACCGTT
Found at i:621763 original size:37 final size:37
Alignment explanation
Indices: 621713--621784 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
621703 ATAAGAACAT
*
621713 ATCTTTTGAAATCAAACTTCAAATTTTTAAAACTTCA
1 ATCTTTCGAAATCAAACTTCAAATTTTTAAAACTTCA
*
621750 ATCTTTCGAAATCAAACTTTAAATTTTTAAAACTT
1 ATCTTTCGAAATCAAACTTCAAATTTTTAAAACTT
621785 TCATTTTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (37 bp):
ATCTTTCGAAATCAAACTTCAAATTTTTAAAACTTCA
Found at i:621869 original size:173 final size:172
Alignment explanation
Indices: 621574--621892 Score: 577
Period size: 173 Copynumber: 1.8 Consensus size: 172
621564 CCTTGAAGTT
* *
621574 TTCAATCTTTTGAAATCAAACTTCAAATTTTTAAAACTTTTATTTTAGTCACTAACCCTTATTTT
1 TTCAATCTTTCGAAATCAAACTTCAAATTTTTAAAACTTTCATTTTAGTCACTAACCCTTATTTT
621639 GGGATATTACAAATCTCCCCTCCTTTTAAGAAAATTTGTCCTCGAATTTTCATTGCACATACCGA
66 GGGATATTACAAATCTCCCCTCCTTTTAAGAAAATTTGTCCTCGAATTTTCATTGCACATACCGA
621704 TAAGAACATATCTTTTGAAATCAAACTTCAAATTTTTAAAAC
131 TAAGAACATATCTTTTGAAATCAAACTTCAAATTTTTAAAAC
* *
621746 TTCAATCTTTCGAAATCAAACTTTAAATTTTTAAAACTTTCATTTTAGTCACTAACCCTTTTTTT
1 TTCAATCTTTCGAAATCAAACTTCAAATTTTTAAAACTTTCATTTTAGTCACTAACCC-TTATTT
621811 TGGGATATTACAAATCTCCCCTCCTTTTAAGAAAATTTGTCCTCGAAATTTT-ATTGCACATACC
65 TGGGATATTACAAATCTCCCCTCCTTTTAAGAAAATTTGTCCTCG-AATTTTCATTGCACATACC
621875 GATAAGAACATATCTTTT
129 GATAAGAACATATCTTTT
621893 AATATTCTCA
Statistics
Matches: 141, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
172 55 0.39
173 80 0.57
174 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.40
Consensus pattern (172 bp):
TTCAATCTTTCGAAATCAAACTTCAAATTTTTAAAACTTTCATTTTAGTCACTAACCCTTATTTT
GGGATATTACAAATCTCCCCTCCTTTTAAGAAAATTTGTCCTCGAATTTTCATTGCACATACCGA
TAAGAACATATCTTTTGAAATCAAACTTCAAATTTTTAAAAC
Found at i:624666 original size:20 final size:20
Alignment explanation
Indices: 624643--624685 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
624633 TATCCCGAAA
*
624643 GACCTCTATATTTCCTGAAG
1 GACCTCTATATGTCCTGAAG
*
624663 GACCTCTGTATGTCCTGAAG
1 GACCTCTATATGTCCTGAAG
624683 GAC
1 GAC
624686 TGATGAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (20 bp):
GACCTCTATATGTCCTGAAG
Found at i:627556 original size:24 final size:24
Alignment explanation
Indices: 627524--627572 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
627514 CCCTTCAAGG
627524 TAAGATTGAAAACAAATTCAGATT
1 TAAGATTGAAAACAAATTCAGATT
* *
627548 TAAGCTTGAAAACATATTCAGATT
1 TAAGATTGAAAACAAATTCAGATT
627572 T
1 T
627573 CATTCTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (24 bp):
TAAGATTGAAAACAAATTCAGATT
Found at i:627626 original size:19 final size:19
Alignment explanation
Indices: 627602--627638 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
627592 GAGATTTATA
627602 AAAGTTTTCCTTT-TTTTTC
1 AAAGTTTT-CTTTATTTTTC
627621 AAAGTTTTCTTTATTTTT
1 AAAGTTTTCTTTATTTTT
627639 TTTATTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.19, C:0.11, G:0.05, T:0.65
Consensus pattern (19 bp):
AAAGTTTTCTTTATTTTTC
Found at i:627637 original size:18 final size:19
Alignment explanation
Indices: 627602--627637 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
627592 GAGATTTATA
*
627602 AAAGTTTTCCTTTTTTTTC
1 AAAGTTTTCCTTTATTTTC
627621 AAAGTTTT-CTTTATTTT
1 AAAGTTTTCCTTTATTTT
627638 TTTTATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.64
Consensus pattern (19 bp):
AAAGTTTTCCTTTATTTTC
Found at i:627670 original size:28 final size:28
Alignment explanation
Indices: 627606--627670 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
627596 TTTATAAAAG
627606 TTTTC-CTTT-TTTTTCAAAGTTTTCTT
1 TTTTCTCTTTATTTTTCAAAGTTTTCTT
*
627632 TATTT-TTTTTATTTTTCAAAGTTTTCTT
1 T-TTTCTCTTTATTTTTCAAAGTTTTCTT
627660 TTTTCTCTTTA
1 TTTTCTCTTTA
627671 AATTGAGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 1 0.03
27 9 0.27
28 23 0.70
ACGTcount: A:0.14, C:0.12, G:0.03, T:0.71
Consensus pattern (28 bp):
TTTTCTCTTTATTTTTCAAAGTTTTCTT
Found at i:628063 original size:16 final size:17
Alignment explanation
Indices: 628032--628065 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
628022 ATTTAAAATC
*
628032 CCCTATTTTATTCTCAT
1 CCCTATCTTATTCTCAT
628049 CCCTATCTT-TTCTCAT
1 CCCTATCTTATTCTCAT
628065 C
1 C
628066 TTTATCCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (17 bp):
CCCTATCTTATTCTCAT
Found at i:628106 original size:28 final size:28
Alignment explanation
Indices: 628051--628106 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
628041 ATTCTCATCC
628051 CTATCTTTTCTCATCTTTATCCAAATCT
1 CTATCTTTTCTCATCTTTATCCAAATCT
*
628079 CTATCTTTTCTCATCTTTATCCAGATCT
1 CTATCTTTTCTCATCTTTATCCAAATCT
628107 AAAATCAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.20, C:0.29, G:0.02, T:0.50
Consensus pattern (28 bp):
CTATCTTTTCTCATCTTTATCCAAATCT
Found at i:645371 original size:15 final size:15
Alignment explanation
Indices: 645351--645379 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
645341 TTCATAGGGA
645351 AAAAAGAAAACGTCT
1 AAAAAGAAAACGTCT
645366 AAAAAGAAAACGTC
1 AAAAAGAAAACGTC
645380 AAAGAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.10
Consensus pattern (15 bp):
AAAAAGAAAACGTCT
Found at i:645390 original size:15 final size:15
Alignment explanation
Indices: 645357--645405 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
645347 GGGAAAAAAG
*
645357 AAAACGTCTAAA-AAG
1 AAAACGTC-AAAGAAT
645372 AAAACGTCAAAGAAT
1 AAAACGTCAAAGAAT
*
645387 AAAACTTCAAAGAAT
1 AAAACGTCAAAGAAT
645402 AAAA
1 AAAA
645406 AAGAAAGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 3 0.10
15 28 0.90
ACGTcount: A:0.63, C:0.12, G:0.10, T:0.14
Consensus pattern (15 bp):
AAAACGTCAAAGAAT
Found at i:649274 original size:45 final size:42
Alignment explanation
Indices: 649224--649370 Score: 122
Period size: 45 Copynumber: 3.3 Consensus size: 42
649214 ACTTGTTGAA
*
649224 AAAGAAGAGGAGAAAGGAGAAGGGACACCGAAGATGGAAAAAGAG
1 AAAGAAAAGGAGAAAGGAGAAGGGACACCGAAGA-GG-AAAA-AG
649269 AAAGAAAAGGAATAGGGTAAAGGAGAAGGGACACCGTAA-AGG--AAA-
1 AAAGAAAAGG---A--G-AAAGGAGAAGGGACACCG-AAGAGGAAAAAG
* *
649314 AAAGAAGAGGAGAAAGAAGAAGGGACACCGAAGAGGGAAGGAAAG
1 AAAGAAAAGGAGAAAGGAGAAGGGACACCGAAGA-GGAA--AAAG
649359 AAAGAAAAGGAG
1 AAAGAAAAGGAG
649371 GAATGAACAC
Statistics
Matches: 84, Mismatches: 4, Indels: 28
0.72 0.03 0.24
Matches are distributed among these distances:
38 2 0.02
39 18 0.21
40 3 0.04
42 1 0.01
44 3 0.04
45 29 0.35
46 1 0.01
47 2 0.02
48 1 0.01
50 3 0.04
51 19 0.23
52 2 0.02
ACGTcount: A:0.54, C:0.06, G:0.37, T:0.03
Consensus pattern (42 bp):
AAAGAAAAGGAGAAAGGAGAAGGGACACCGAAGAGGAAAAAG
Found at i:651299 original size:2 final size:2
Alignment explanation
Indices: 651292--651406 Score: 189
Period size: 2 Copynumber: 58.5 Consensus size: 2
651282 TTAATCTACA
651292 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
* *
651334 AT AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT TT AT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
651374 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
651407 ATTTATGAAA
Statistics
Matches: 105, Mismatches: 6, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
1 2 0.02
2 103 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:651558 original size:85 final size:84
Alignment explanation
Indices: 651466--651730 Score: 352
Period size: 85 Copynumber: 3.1 Consensus size: 84
651456 GACGTGTGCA
* * * * * *
651466 TCAATGACACGTAATGTAAGTCATATATGTATGCCATAAATTTATGACACACAAATGTATGTCAA
1 TCAATGACACGCAATGTAAGTCATACATGTGTGTCATAAATTTATGACGCACAAATGTGTGTC-A
*
651531 GC-AGATTTATGACGGGGGCT
65 TCTA-ATTTATGACGGGGGCT
* **
651551 TCAATGACGCGCAATGTAAGTCATACATACGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
1 TCAATGACACGCAATGTAAGTCATACATGTGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
651616 CTTAATTTATGACGGGGGCT
66 C-TAATTTATGACGGGGGCT
* * *
651636 TCAATGACGCGCAATGTAATTCATACATGTGTGTCATAAATTTATGATGCACAAATGTGTGTCAT
1 TCAATGACACGCAATGTAAGTCATACATGTGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
*
651701 CTTAATTTATGACGGGAGCT
66 C-TAATTTATGACGGGGGCT
*
651721 TTAATGACAC
1 TCAATGACAC
651731 TCAAAGAACG
Statistics
Matches: 161, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
84 2 0.01
85 158 0.98
86 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.31
Consensus pattern (84 bp):
TCAATGACACGCAATGTAAGTCATACATGTGTGTCATAAATTTATGACGCACAAATGTGTGTCAT
CTAATTTATGACGGGGGCT
Found at i:652121 original size:43 final size:44
Alignment explanation
Indices: 652063--652149 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
652053 GAAAGCTTGC
* *
652063 CCAACTTGTGCACATGGGAT-ATTCATCTTTGGTTAGCAAGTTG
1 CCAACTTGAGCACATGGGATAATTCATCCTTGGTTAGCAAGTTG
*
652106 CCAACTTGAGCACATGGGATAATTCATCCTTGGTTGGCAAGTTG
1 CCAACTTGAGCACATGGGATAATTCATCCTTGGTTAGCAAGTTG
652150 ACAAGTTGTG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 19 0.47
44 21 0.52
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (44 bp):
CCAACTTGAGCACATGGGATAATTCATCCTTGGTTAGCAAGTTG
Found at i:656502 original size:43 final size:43
Alignment explanation
Indices: 656405--656504 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
656395 GCATATTGGC
* * * *
656405 AAGTTGGCAAGTAGCCAACTTGTGCACATGGGATATTCATCCT
1 AAGTTGACAAGTTGCCAACTTGAGCACATGGGATAATCATCCT
*
656448 TAGTT-AGCAAGTTGCCAACTTGAGCACATGGGATAATCATCCT
1 AAGTTGA-CAAGTTGCCAACTTGAGCACATGGGATAATCATCCT
656491 AAGTTGACAAGTTG
1 AAGTTGACAAGTTG
656505 TGCAAGTGGC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 48 0.98
44 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (43 bp):
AAGTTGACAAGTTGCCAACTTGAGCACATGGGATAATCATCCT
Found at i:662187 original size:5 final size:5
Alignment explanation
Indices: 662179--662203 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
662169 AGAAGAAAAG
662179 GAAAT GAAAT GAAAT GAAAT GAAAT
1 GAAAT GAAAT GAAAT GAAAT GAAAT
662204 AATAAGCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
GAAAT
Found at i:668160 original size:3 final size:3
Alignment explanation
Indices: 668152--668183 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
668142 TGTTCAATCA
668152 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
668184 ACAGACAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:669748 original size:51 final size:51
Alignment explanation
Indices: 669672--669777 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
669662 TTGGAAGATT
669672 CGAACTAAGGCCAATAGGATGGTGATCATAGGCAGAGATGGGCATGAGACC
1 CGAACTAAGGCCAATAGGATGGTGATCATAGGCAGAGATGGGCATGAGACC
669723 CGAACTAAGGCCAATAGGATGGTGATCATAGGCAGAGATGGGCATGAGACC
1 CGAACTAAGGCCAATAGGATGGTGATCATAGGCAGAGATGGGCATGAGACC
669774 CGAA
1 CGAA
669778 TCCGACGGGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.34, C:0.18, G:0.33, T:0.15
Consensus pattern (51 bp):
CGAACTAAGGCCAATAGGATGGTGATCATAGGCAGAGATGGGCATGAGACC
Found at i:670221 original size:32 final size:32
Alignment explanation
Indices: 670180--670244 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
670170 TTTACAATAT
**
670180 TTTTTTATATATCCTGTCATTCTTAATGAAAG
1 TTTTTTATATATCCTCACATTCTTAATGAAAG
670212 TTTTTTATATATCCTCACATTCTTAATGAAAG
1 TTTTTTATATATCCTCACATTCTTAATGAAAG
670244 T
1 T
670245 AAAAAATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (32 bp):
TTTTTTATATATCCTCACATTCTTAATGAAAG
Found at i:678396 original size:20 final size:20
Alignment explanation
Indices: 678373--678432 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
678363 CACAGTTTCA
*
678373 GAATTAGCAACTCGAATTTG
1 GAATTCGCAACTCGAATTTG
* * *
678393 GAATTCGCAACACAGAA-GTC
1 GAATTCGCAACTC-GAATTTG
678413 GAATTCGCAACTCGAATTTG
1 GAATTCGCAACTCGAATTTG
678433 ACAATTTCGC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
19 3 0.10
20 25 0.81
21 3 0.10
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (20 bp):
GAATTCGCAACTCGAATTTG
Found at i:679080 original size:20 final size:20
Alignment explanation
Indices: 679057--679094 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
679047 CTCGAAAATG
* *
679057 AAATTTGAGTTGCGAATTCA
1 AAATTCGAGTTCCGAATTCA
679077 AAATTCGAGTTCCGAATT
1 AAATTCGAGTTCCGAATT
679095 TTATTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (20 bp):
AAATTCGAGTTCCGAATTCA
Found at i:679116 original size:14 final size:14
Alignment explanation
Indices: 679097--679130 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
679087 TCCGAATTTT
679097 ATTTTCGAGTTGCG
1 ATTTTCGAGTTGCG
*
679111 ATTTTCGTGTTGCG
1 ATTTTCGAGTTGCG
*
679125 AATTTC
1 ATTTTC
679131 ATTTTCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTTTCGAGTTGCG
Found at i:679156 original size:33 final size:34
Alignment explanation
Indices: 679080--679169 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 34
679070 GAATTCAAAA
* * * *
679080 TTCGAGTTCCGAATTTTATTTTCGAGTTGCGATT
1 TTCGAGTTGCGAATTTCATTTTCAAATTGCGATT
*
679114 TTCGTGTTGCGAATTTCATTTTCAAATT-CGATT
1 TTCGAGTTGCGAATTTCATTTTCAAATTGCGATT
679147 TTCGAGTTGCGAATTTCATTTTC
1 TTCGAGTTGCGAATTTCATTTTC
679170 TTGAAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.48
Consensus pattern (34 bp):
TTCGAGTTGCGAATTTCATTTTCAAATTGCGATT
Found at i:680584 original size:42 final size:42
Alignment explanation
Indices: 680515--680642 Score: 159
Period size: 42 Copynumber: 3.0 Consensus size: 42
680505 CCCCACTTTT
* * *
680515 TCATCAAGTCGATTCTCCAATTCGACACCGAGATCTATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
* * *
680557 TCCTTGAGTCGATTCTCCACTTTGACACCGAGATCCATCACC
1 TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
* * *
680599 TCATCGAG-CTGATTCTACACATCAACACCGAGATCCATCACC
1 TCATCGAGTC-GATTCTCCACTTCGACACCGAGATCCATCACC
680641 TC
1 TC
680643 TAGCCAACTC
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 1 0.01
42 72 0.99
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.26
Consensus pattern (42 bp):
TCATCGAGTCGATTCTCCACTTCGACACCGAGATCCATCACC
Found at i:680671 original size:39 final size:41
Alignment explanation
Indices: 680580--680680 Score: 116
Period size: 39 Copynumber: 2.5 Consensus size: 41
680570 TCTCCACTTT
** *
680580 GACACCGAGATCCATCACCTCATCGAGCTGATTCTACACATC
1 GACACCGAGATCCATCACCTCATC-AGCCAACTCTACACATC
* *
680622 AACACCGAGATCCATCACCTC-T-AGCCAACTCTACACCTC
1 GACACCGAGATCCATCACCTCATCAGCCAACTCTACACATC
* *
680661 GACACTGAGATTCATCACCT
1 GACACCGAGATCCATCACCT
680681 ATTCCATCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 30 0.59
41 1 0.02
42 20 0.39
ACGTcount: A:0.30, C:0.38, G:0.12, T:0.21
Consensus pattern (41 bp):
GACACCGAGATCCATCACCTCATCAGCCAACTCTACACATC
Found at i:680806 original size:21 final size:21
Alignment explanation
Indices: 680780--680907 Score: 159
Period size: 21 Copynumber: 6.1 Consensus size: 21
680770 ACCTCCACGA
*
680780 GATGAGTTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
680801 GATGAGGTCGGTGATTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
680822 GGTGAGGTAGTTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* **
680843 GGTGA-CAATGGTGCTTTACGT
1 GATGAGGTA-GGTGCTTTACGT
680864 GATGAGGTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
*
680885 GATGAGGTGGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
680906 GA
1 GA
680908 GATTGTTTCA
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
20 1 0.01
21 89 0.98
22 1 0.01
ACGTcount: A:0.18, C:0.10, G:0.38, T:0.34
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:681286 original size:21 final size:21
Alignment explanation
Indices: 681226--681400 Score: 126
Period size: 21 Copynumber: 8.3 Consensus size: 21
681216 GAATGAGTCT
* * *
681226 GATCCATCTACCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* *
681247 GATCCACATCCCATTGTTCAG
1 GATCCACCTCCCATCGTTCAG
* *
681268 GATTCACCTCTCATCGTTCCA-
1 GATCCACCTCCCATCGTT-CAG
* *
681289 GAGGCC-CCTCCCATCATTCAG
1 GA-TCCACCTCCCATCGTTCAG
* *
681310 GATCCACCTCTCATTGTTCCA-
1 GATCCACCTCCCATCGTT-CAG
* *
681331 GAGGCC-CCTCCCATCGTTTAG
1 GA-TCCACCTCCCATCGTTCAG
*
681352 AATCCACCTCCCATCGTTCAG
1 GATCCACCTCCCATCGTTCAG
* *
681373 GATCCACC-CCGCATCATTCAA
1 GATCCACCTCC-CATCGTTCAG
681394 GATCCAC
1 GATCCAC
681401 ATTCCATTCT
Statistics
Matches: 120, Mismatches: 25, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
20 9 0.08
21 104 0.87
22 7 0.06
ACGTcount: A:0.22, C:0.38, G:0.14, T:0.26
Consensus pattern (21 bp):
GATCCACCTCCCATCGTTCAG
Found at i:681318 original size:42 final size:42
Alignment explanation
Indices: 681263--681370 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 42
681253 CATCCCATTG
*
681263 TTCAGGATTCACCTCTCATCGTTCCAGAGGCCCCTCCCATCA
1 TTCAGGATCCACCTCTCATCGTTCCAGAGGCCCCTCCCATCA
* *
681305 TTCAGGATCCACCTCTCATTGTTCCAGAGGCCCCTCCCATCG
1 TTCAGGATCCACCTCTCATCGTTCCAGAGGCCCCTCCCATCA
* * *
681347 TTTAGAATCCACCTCCCATCGTTC
1 TTCAGGATCCACCTCTCATCGTTC
681371 AGGATCCACC
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.19, C:0.40, G:0.14, T:0.28
Consensus pattern (42 bp):
TTCAGGATCCACCTCTCATCGTTCCAGAGGCCCCTCCCATCA
Done.