Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 140 of 144
Found at i:43346886 original size:24 final size:24
Alignment explanation
Indices: 43346859--43346907 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
43346849 CGTATATTTG
43346859 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
43346883 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
43346907 T
1 T
43346908 GTTATTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAAAGTTTATATAAAAATTAAT
Found at i:43346938 original size:219 final size:219
Alignment explanation
Indices: 43346559--43346996 Score: 860
Period size: 219 Copynumber: 2.0 Consensus size: 219
43346549 CAATTTGTTA
43346559 AAGTATGTTAAGAGAATTACTTTTTCTTTTTTAAGATTTAACACTCCTATGCGAACAAATATTAT
1 AAGTATGTTAAGAGAATTACTTTTTCTTTTTTAAGATTTAACACTCCTATGCGAACAAATATTAT
43346624 TTAACTCGTATATTTGTTAAAAGTTTATATAAAAATTAATTTAAAAGTTTATATAAAAATTAATT
66 TTAACTCGTATATTTGTTAAAAGTTTATATAAAAATTAATTTAAAAGTTTATATAAAAATTAATT
43346689 GTTATTTTGGTTATAATCATAAAGTTAATTGTGTTTCAAATTTTTATTATATATATATATATATA
131 GTTATTTTGGTTATAATCATAAAGTTAATTGTGTTTCAAATTTTTATTATATATATATATATATA
43346754 CATTCTTATAACTTAATTTATACG
196 CATTCTTATAACTTAATTTATACG
43346778 AAGTATGTTAAGAGAATTACTTTTTCTTTTTTAAGATTTAACACTCCTATGCGAA-AAGATATTA
1 AAGTATGTTAAGAGAATTACTTTTTCTTTTTTAAGATTTAACACTCCTATGCGAACAA-ATATTA
43346842 TTTAACTCGTATATTTGTTAAAAGTTTATATAAAAATTAATTTAAAAGTTTATATAAAAATTAAT
65 TTTAACTCGTATATTTGTTAAAAGTTTATATAAAAATTAATTTAAAAGTTTATATAAAAATTAAT
43346907 TGTTATTTTGGTTATAATCATAAAGTTAATTGTGTTTCAAATTTTTATTATATATATATATATAT
130 TGTTATTTTGGTTATAATCATAAAGTTAATTGTGTTTCAAATTTTTATTATATATATATATATAT
43346972 ACATTCTTATAACTTAATTTATACG
195 ACATTCTTATAACTTAATTTATACG
43346997 TGAGAGGGTA
Statistics
Matches: 218, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
218 2 0.01
219 216 0.99
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.46
Consensus pattern (219 bp):
AAGTATGTTAAGAGAATTACTTTTTCTTTTTTAAGATTTAACACTCCTATGCGAACAAATATTAT
TTAACTCGTATATTTGTTAAAAGTTTATATAAAAATTAATTTAAAAGTTTATATAAAAATTAATT
GTTATTTTGGTTATAATCATAAAGTTAATTGTGTTTCAAATTTTTATTATATATATATATATATA
CATTCTTATAACTTAATTTATACG
Found at i:43359637 original size:15 final size:15
Alignment explanation
Indices: 43359617--43359647 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
43359607 CTTTCGATCC
43359617 TTACGCTTCTTCTCT
1 TTACGCTTCTTCTCT
43359632 TTACGCTTCTTCTCT
1 TTACGCTTCTTCTCT
43359647 T
1 T
43359648 CATCTGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.32, G:0.06, T:0.55
Consensus pattern (15 bp):
TTACGCTTCTTCTCT
Found at i:43360949 original size:50 final size:50
Alignment explanation
Indices: 43360852--43360973 Score: 154
Period size: 50 Copynumber: 2.4 Consensus size: 50
43360842 GATGAGGGTG
* * * * *
43360852 GGACAATTTGCCACGTCGTGACGAGGAATCCCTTCACCAAGATGAGGCCA
1 GGACAGTTTGTCACGTCGTGACAAGGAATCCCATCACCAAGACGAGGCCA
* * *
43360902 GGACAGTTTGTCACGTCGTGACAAGGAATCCCATCATCACGACGAGGCCG
1 GGACAGTTTGTCACGTCGTGACAAGGAATCCCATCACCAAGACGAGGCCA
* *
43360952 GGATAGTTTGTCACATCGTGAC
1 GGACAGTTTGTCACGTCGTGAC
43360974 GAGAAACCCT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.20
Consensus pattern (50 bp):
GGACAGTTTGTCACGTCGTGACAAGGAATCCCATCACCAAGACGAGGCCA
Found at i:43361492 original size:19 final size:18
Alignment explanation
Indices: 43361459--43361494 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
43361449 TTATATTAGT
*
43361459 TAAACATGTTTAATTAAA
1 TAAACATGATTAATTAAA
43361477 TAAACTATGATTAATTAA
1 TAAAC-ATGATTAATTAA
43361495 TTTTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.39
Consensus pattern (18 bp):
TAAACATGATTAATTAAA
Found at i:43363530 original size:8 final size:8
Alignment explanation
Indices: 43363517--43363544 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
43363507 GTATTTATTA
43363517 TATTTTAT
1 TATTTTAT
43363525 TATTTTAT
1 TATTTTAT
43363533 TATTTTAT
1 TATTTTAT
43363541 TATT
1 TATT
43363545 CTGAATTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
TATTTTAT
Found at i:43372180 original size:28 final size:28
Alignment explanation
Indices: 43372121--43372180 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
43372111 TTGGTGTCGA
* *
43372121 TTTTGTATCATGTTTAAATTATCAGATC
1 TTTTGTATCATGTTTAAAGTATCAAATC
*
43372149 TTTTGTATCATGTTTAAAAGTAT-AAATT
1 TTTTGTATCATGTTT-AAAGTATCAAATC
43372177 TTTT
1 TTTT
43372181 TTTTGATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (28 bp):
TTTTGTATCATGTTTAAAGTATCAAATC
Found at i:43373387 original size:201 final size:201
Alignment explanation
Indices: 43373042--43373445 Score: 808
Period size: 201 Copynumber: 2.0 Consensus size: 201
43373032 TACTTAGAAA
43373042 ATTTCTGTTCAATAAAGAAAAAGTACTTGAAATTTTCTAGAATCATTTATAATGTATTTTGGCAC
1 ATTTCTGTTCAATAAAGAAAAAGTACTTGAAATTTTCTAGAATCATTTATAATGTATTTTGGCAC
43373107 ACTTAATGTGTGGATGAAAAAAAAATTAACAAATATATTTATAAAAAATTGATATAGAAACAATT
66 ACTTAATGTGTGGATGAAAAAAAAATTAACAAATATATTTATAAAAAATTGATATAGAAACAATT
43373172 GAGACTTTAATTGGAATGATAAATTTGAGACTTCAAAAGTTATGGTCTTTTGGGTTCAAATTCTA
131 GAGACTTTAATTGGAATGATAAATTTGAGACTTCAAAAGTTATGGTCTTTTGGGTTCAAATTCTA
43373237 TCTTAT
196 TCTTAT
43373243 ATTTCTGTTCAATAAAGAAAAAGTACTTGAAATTTTCTAGAATCATTTATAATGTATTTTGGCAC
1 ATTTCTGTTCAATAAAGAAAAAGTACTTGAAATTTTCTAGAATCATTTATAATGTATTTTGGCAC
43373308 ACTTAATGTGTGGATGAAAAAAAAATTAACAAATATATTTATAAAAAATTGATATAGAAACAATT
66 ACTTAATGTGTGGATGAAAAAAAAATTAACAAATATATTTATAAAAAATTGATATAGAAACAATT
43373373 GAGACTTTAATTGGAATGATAAATTTGAGACTTCAAAAGTTATGGTCTTTTGGGTTCAAATTCTA
131 GAGACTTTAATTGGAATGATAAATTTGAGACTTCAAAAGTTATGGTCTTTTGGGTTCAAATTCTA
43373438 TCTTAT
196 TCTTAT
43373444 AT
1 AT
43373446 GTATTTTTTT
Statistics
Matches: 203, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 203 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.37
Consensus pattern (201 bp):
ATTTCTGTTCAATAAAGAAAAAGTACTTGAAATTTTCTAGAATCATTTATAATGTATTTTGGCAC
ACTTAATGTGTGGATGAAAAAAAAATTAACAAATATATTTATAAAAAATTGATATAGAAACAATT
GAGACTTTAATTGGAATGATAAATTTGAGACTTCAAAAGTTATGGTCTTTTGGGTTCAAATTCTA
TCTTAT
Found at i:43375106 original size:13 final size:13
Alignment explanation
Indices: 43375090--43375123 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
43375080 ATTATTAATG
*
43375090 TAATTTATTATTT
1 TAATTAATTATTT
*
43375103 TAATAAATTATTT
1 TAATTAATTATTT
43375116 TAATTAAT
1 TAATTAAT
43375124 AAATTTTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATTAATTATTT
Found at i:43375141 original size:16 final size:16
Alignment explanation
Indices: 43375112--43375153 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
43375102 TTAATAAATT
*
43375112 ATTTTAATTAAT-A-A
1 ATTTTAAATAATAATA
43375126 ATTTTAAA-AATAATA
1 ATTTTAAATAATAATA
43375141 ATTTTAAATAATA
1 ATTTTAAATAATA
43375154 TGTTTCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.12
14 8 0.33
15 9 0.38
16 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTTTAAATAATAATA
Found at i:43375222 original size:34 final size:31
Alignment explanation
Indices: 43375162--43375229 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 31
43375152 TATGTTTCTT
* *
43375162 AATAATATTCAATTTCAATATTTTAATAATA
1 AATAATATTCAATTTAAATATATTAATAATA
43375193 AATAATTATTACAATTATAAATATATTAATAATA
1 AATAA-TATT-CAATT-TAAATATATTAATAATA
43375227 AAT
1 AAT
43375230 TGTTATAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 5 0.16
32 4 0.12
33 5 0.16
34 18 0.56
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (31 bp):
AATAATATTCAATTTAAATATATTAATAATA
Found at i:43375227 original size:15 final size:15
Alignment explanation
Indices: 43375178--43375229 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
43375168 ATTCAATTTC
*
43375178 AATATTTTAATAATA
1 AATATATTAATAATA
*
43375193 AATAATTATTACAATTATA
1 AAT-A-TATT--AATAATA
43375212 AATATATTAATAATA
1 AATATATTAATAATA
43375227 AAT
1 AAT
43375230 TGTTATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:43389711 original size:12 final size:12
Alignment explanation
Indices: 43389696--43389752 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
43389686 TCCCTCCTCT
*
43389696 CTTTCCTCTACC
1 CTTTCCTCCACC
* * *
43389708 CTTTCCACCGCT
1 CTTTCCTCCACC
*
43389720 CTTTCCTCCGCC
1 CTTTCCTCCACC
*
43389732 CTTTCCTCTACC
1 CTTTCCTCCACC
*
43389744 CCTTCCTCC
1 CTTTCCTCC
43389753 CTCCGTTCAC
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.05, C:0.54, G:0.04, T:0.37
Consensus pattern (12 bp):
CTTTCCTCCACC
Found at i:43392542 original size:25 final size:25
Alignment explanation
Indices: 43392508--43392555 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
43392498 TGTCAGCTAT
43392508 AGTTTAGGTTAGTAGCTTATGAACA
1 AGTTTAGGTTAGTAGCTTATGAACA
43392533 AGTTTAGGTTAGTAGCTTATGAA
1 AGTTTAGGTTAGTAGCTTATGAA
43392556 GATGATATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (25 bp):
AGTTTAGGTTAGTAGCTTATGAACA
Found at i:43393834 original size:104 final size:104
Alignment explanation
Indices: 43393428--43393827 Score: 777
Period size: 104 Copynumber: 3.9 Consensus size: 104
43393418 ATTTCATTAG
*
43393428 AAAAAA-AAAATTGTAAATGTTTCATAT-TGATGAAGAAGGTTATATAGCACCAAATTGTCCTAA
1 AAAAAACAAAAATGTAAATGTTTCATATGTGATGAAGAAGGTTATATAGCACCAAATTGTCCTAA
43393491 TAAGGGAAAAAGTGCAAGAAAAATTTCTAAAAAAATCTA
66 TAAGGGAAAAAGTGCAAGAAAAATTTCTAAAAAAATCTA
43393530 AAAAAACAAAAATGTAAATGTTTCATATGTGATGAAGAAGGTTATATAGCACCAAATTGTCCTAA
1 AAAAAACAAAAATGTAAATGTTTCATATGTGATGAAGAAGGTTATATAGCACCAAATTGTCCTAA
43393595 TAAGGGAAAAAGTGCAAGAAAAATTTCTAAAAAAATCTA
66 TAAGGGAAAAAGTGCAAGAAAAATTTCTAAAAAAATCTA
43393634 AAAAAACAAAAATGTAAATGTTTCATATGTGATGAAGAAGGTTATATAGCACCAAATTGTCCTAA
1 AAAAAACAAAAATGTAAATGTTTCATATGTGATGAAGAAGGTTATATAGCACCAAATTGTCCTAA
43393699 TAAGGGAAAAAGTGCAAGAAAAATTTCTAAAAAAATCTA
66 TAAGGGAAAAAGTGCAAGAAAAATTTCTAAAAAAATCTA
43393738 AAAAAACAAAAATGTAAATGTTTCATATGTGATGAAGAAGGTTATATAGCACCAAATTGTCCTAA
1 AAAAAACAAAAATGTAAATGTTTCATATGTGATGAAGAAGGTTATATAGCACCAAATTGTCCTAA
43393803 TAAGGGAAAAAGTGCAAGAAAAATT
66 TAAGGGAAAAAGTGCAAGAAAAATT
43393828 ATTAAAACAC
Statistics
Matches: 295, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
102 6 0.02
103 20 0.07
104 269 0.91
ACGTcount: A:0.50, C:0.09, G:0.16, T:0.25
Consensus pattern (104 bp):
AAAAAACAAAAATGTAAATGTTTCATATGTGATGAAGAAGGTTATATAGCACCAAATTGTCCTAA
TAAGGGAAAAAGTGCAAGAAAAATTTCTAAAAAAATCTA
Found at i:43394458 original size:15 final size:15
Alignment explanation
Indices: 43394438--43394466 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43394428 AGCCAAATTG
43394438 CTTTATATCTATTAA
1 CTTTATATCTATTAA
43394453 CTTTATATCTATTA
1 CTTTATATCTATTA
43394467 TAGATATTTT
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:0.31, C:0.14, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTTATATCTATTAA
Found at i:43395700 original size:15 final size:15
Alignment explanation
Indices: 43395680--43395709 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43395670 ACAAATTAAG
*
43395680 GAATTATTAGAAAAA
1 GAATTAATAGAAAAA
43395695 GAATTAATAGAAAAA
1 GAATTAATAGAAAAA
43395710 ACTAATAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (15 bp):
GAATTAATAGAAAAA
Found at i:43399508 original size:3 final size:3
Alignment explanation
Indices: 43399500--43399603 Score: 50
Period size: 3 Copynumber: 32.7 Consensus size: 3
43399490 AGAAAATGAC
* * * **
43399500 AAT AAT AAT AAT AAT ACT AAT AAC AAC AAT AAT AA- AGAT AGC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * *
43399545 AAT AAAT AA- AAA AAGT AAT AAAT AAGT ATGT GAAT AAAT AAC AAT AAT
1 AAT -AAT AAT AAT AA-T AAT -AAT AA-T A-AT -AAT -AAT AAT AAT AAT
43399593 AAT AAT AAT AA
1 AAT AAT AAT AA
43399604 AAGAAATAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
2 3 0.04
3 58 0.74
4 16 0.21
5 1 0.01
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:43399565 original size:16 final size:16
Alignment explanation
Indices: 43399544--43399619 Score: 59
Period size: 16 Copynumber: 4.8 Consensus size: 16
43399534 AAGATAGCAA
43399544 TAATAAATAAAAAAAG
1 TAATAAATAAAAAAAG
** *
43399560 TAATAAAT-AAGTATG
1 TAATAAATAAAAAAAG
*
43399575 TGAATAAATAACAATAA-
1 T-AATAAATAA-AAAAAG
*
43399592 TAAT-AATAATAAAAG
1 TAATAAATAAAAAAAG
*
43399607 AAATAAATAAAAA
1 TAATAAATAAAAA
43399620 TATAAACAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
14 3 0.07
15 13 0.28
16 25 0.54
17 2 0.04
18 3 0.07
ACGTcount: A:0.68, C:0.01, G:0.07, T:0.24
Consensus pattern (16 bp):
TAATAAATAAAAAAAG
Found at i:43401309 original size:49 final size:47
Alignment explanation
Indices: 43401069--43401697 Score: 324
Period size: 44 Copynumber: 13.6 Consensus size: 47
43401059 CTTCGATCCA
* * * * * *
43401069 CTCCAATGCAACCTCAGGGAAATAAAACTTGTA-GC--TTCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGGCTTTTCAATCTG
* * * * * *
43401113 TTCCGCTGCAACTCCAGGGAGGTGAGATTTGT--G-TCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGGCTTTTCAATCTG
* **** *
43401157 CTCCACTACAACTTCAGGGAGATAAGATTTGTTTAATTTT-AACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGGCTTTTCAATCTG
* * *
43401203 CACCACTACAACTTCAGGGAGATAAGGTTTGT-GGC-TTT-AATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGGCTTTTCAATCTG
* *
43401247 CTCCACTGTAACTTC-GGAGAGATAGGATTTGTAGGCTGTCTTCAATCTG
1 CTCCACTGCAACTTCAGG-GAGATAAGATTTGTAGGCT-T-TTCAATCTG
* * *
43401296 CTCCACTGCAACTTCAGAGAGATAAGATTTGTAGCCTATTTTCAATTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGGC--TTTTCAATCTG
** *
43401345 CTCCACTGCAACTTCAGGGAGATAAGATTTGTTTGATTTT-AA-CTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGGCTTTTCAATC-TG
* * * *
43401391 CTCCATTGCAACTTTAGGGAGATAAGATTTATAACTCGTAGC-TTT-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGT-A---G--GCTTTTCAATCTG
* * * * ** * * *
43401442 TTCCACTACAACTTCAGCGAAATAAGATCCGCTA-TC-TTT-AGTTTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGGCTTTTCAATCTG
* * * *
43401487 CTCCACTGCAACTTGAGGGAGATAAGACTTGTA-AC-TTT-AACCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGGCTTTTCAATCTG
* * * *
43401531 CTCCAATGCATCTTCAGGGAGATAAGGTTTGT-GAC--TTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGGCTTTTCAATCTG
* ** * * * * * * *
43401575 CTCCATTGCAACTTCAAAGAGATAAGATTCGCCATGATAACTTCGATATG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTG-TAGGCT--TTTCAATCTG
* * *
43401625 CTTCACTGCAACTTCAGGGAGATAAAATTTGT-GGC--TTCAATATG
1 CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGGCTTTTCAATCTG
* *
43401669 CTCCACTACAACTAT-AGGGAGGTAAGATT
1 CTCCACTGCAACT-TCAGGGAGATAAGATT
43401698 CGCCATAATG
Statistics
Matches: 447, Mismatches: 106, Indels: 64
0.72 0.17 0.10
Matches are distributed among these distances:
43 5 0.01
44 187 0.42
45 34 0.08
46 68 0.15
47 8 0.02
48 3 0.01
49 75 0.17
50 34 0.08
51 30 0.07
52 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (47 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTTGTAGGCTTTTCAATCTG
Found at i:43401681 original size:94 final size:94
Alignment explanation
Indices: 43401537--43401712 Score: 228
Period size: 94 Copynumber: 1.9 Consensus size: 94
43401527 CCTGCTCCAA
* ** * * *
43401537 TGCATCTTCAGGGAGATAAGGTTTGTGACTTCAATCTGCTCCATTGCAACT-TCAAAGAGATAAG
1 TGCAACTTCAGGGAGATAAAATTTGTGACTTCAATATGCTCCACTACAACTAT-AAAGAGATAAG
*
43401601 ATTCGCCATGATAACTTCGATATGCTTCAC
65 ATTCGCCATAATAACTTCGATATGCTTCAC
* ** *
43401631 TGCAACTTCAGGGAGATAAAATTTGTGGCTTCAATATGCTCCACTACAACTATAGGGAGGTAAGA
1 TGCAACTTCAGGGAGATAAAATTTGTGACTTCAATATGCTCCACTACAACTATAAAGAGATAAGA
*
43401696 TTCGCCATAATGACTTC
66 TTCGCCATAATAACTTC
43401713 AATCCATCCC
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
94 68 0.99
95 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (94 bp):
TGCAACTTCAGGGAGATAAAATTTGTGACTTCAATATGCTCCACTACAACTATAAAGAGATAAGA
TTCGCCATAATAACTTCGATATGCTTCAC
Found at i:43405757 original size:32 final size:33
Alignment explanation
Indices: 43405724--43405836 Score: 115
Period size: 32 Copynumber: 3.5 Consensus size: 33
43405714 TAGAGGAATA
*
43405724 TTGTTATCATTTAACAAAAATTAAAGTTGATAT
1 TTGTTATCATTTCACAAAAATTAAAGTTGATAT
* *
43405757 TTGTTATCACTTCAC-AAAATTGAAGTTG-TAAT
1 TTGTTATCATTTCACAAAAATTAAAGTTGAT-AT
* ** *
43405789 TTGTTACCATTTCAC-AAAATGGAAGCTGATAT
1 TTGTTATCATTTCACAAAAATTAAAGTTGATAT
* *
43405821 TTATCATCATTTCACA
1 TTGTTATCATTTCACA
43405837 TAACCACACG
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
31 1 0.01
32 52 0.78
33 14 0.21
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (33 bp):
TTGTTATCATTTCACAAAAATTAAAGTTGATAT
Found at i:43407095 original size:136 final size:136
Alignment explanation
Indices: 43406893--43407350 Score: 898
Period size: 136 Copynumber: 3.4 Consensus size: 136
43406883 TTAAAATTTT
43406893 GTGACCCAAATTCCTGTTAAATAAAATAAGAGATTGCTTGCAAGTCAAGTTAAACAAAATTTGTG
1 GTGACCCAAATTCCTGTTAAATAAAATAAGAGATTGCTTGCAAGTCAAGTTAAACAAAATTTGTG
*
43406958 TGTTCAATTTCTCAATTTCTTTCGCCATTTTTACTTGTTCGTTGCTTAACCTGGTCGATACCCAT
66 TGTTCAATTTCTCAATTTCTTTCGCCATTTTTACTTGTTCGTTGCTTAACCTGGTCGATCCCCAT
43407023 CAAGTG
131 CAAGTG
43407029 GTGACCCAAATTCCTGTTAAATAAAATAAGAGATTGCTTGCAAGTCAAGTTAAACAAAATTTGTG
1 GTGACCCAAATTCCTGTTAAATAAAATAAGAGATTGCTTGCAAGTCAAGTTAAACAAAATTTGTG
*
43407094 TGTTCAATTTCTCAATTTCTTTCGCTATTTTTACTTGTTCGTTGCTTAACCTGGTCGATCCCCAT
66 TGTTCAATTTCTCAATTTCTTTCGCCATTTTTACTTGTTCGTTGCTTAACCTGGTCGATCCCCAT
43407159 CAAGTG
131 CAAGTG
43407165 GTGACCCAAATTCCTGTTAAATAAAATAAGAGATTGCTTGCAAGTCAAGTTAAACAAAATTTGTG
1 GTGACCCAAATTCCTGTTAAATAAAATAAGAGATTGCTTGCAAGTCAAGTTAAACAAAATTTGTG
43407230 TGTTCAATTTCTCAATTTCTTTCGCCATTTTTACTTGTTCGTTGCTTAACCTGGTCGATCCCCAT
66 TGTTCAATTTCTCAATTTCTTTCGCCATTTTTACTTGTTCGTTGCTTAACCTGGTCGATCCCCAT
43407295 CAAGTG
131 CAAGTG
43407301 GTGACCCAAATTCCTGTTAAATAAAATAAGAGATTGCTTGCAAGTCAAGT
1 GTGACCCAAATTCCTGTTAAATAAAATAAGAGATTGCTTGCAAGTCAAGT
43407351 AAGAGATTGC
Statistics
Matches: 319, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 319 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (136 bp):
GTGACCCAAATTCCTGTTAAATAAAATAAGAGATTGCTTGCAAGTCAAGTTAAACAAAATTTGTG
TGTTCAATTTCTCAATTTCTTTCGCCATTTTTACTTGTTCGTTGCTTAACCTGGTCGATCCCCAT
CAAGTG
Found at i:43407357 original size:23 final size:23
Alignment explanation
Indices: 43407327--43407373 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
43407317 TTAAATAAAA
*
43407327 TAAGAGATTGCTTGCAAGTCAAG
1 TAAGAGATTGCTTACAAGTCAAG
43407350 TAAGAGATTGCTTACAAGTCAAG
1 TAAGAGATTGCTTACAAGTCAAG
43407373 T
1 T
43407374 TAAACAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (23 bp):
TAAGAGATTGCTTACAAGTCAAG
Found at i:43417412 original size:10 final size:10
Alignment explanation
Indices: 43417382--43417463 Score: 66
Period size: 10 Copynumber: 8.3 Consensus size: 10
43417372 CACATAAGCA
43417382 TTTAATTAATT
1 TTTAA-TAATT
*
43417393 TTT--TATTT
1 TTTAATAATT
*
43417401 TTTTATAATT
1 TTTAATAATT
43417411 TTTAATAATT
1 TTTAATAATT
43417421 TTTAATAA-T
1 TTTAATAATT
*
43417430 TTTAAT-TTT
1 TTTAATAATT
43417439 TTTAAAAATAATT
1 TTT---AATAATT
43417452 TTT-ATAATT
1 TTTAATAATT
43417461 TTT
1 TTT
43417464 CTGAATTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
8 7 0.12
9 20 0.34
10 21 0.36
11 3 0.05
12 3 0.05
13 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTAATAATT
Found at i:43417470 original size:10 final size:9
Alignment explanation
Indices: 43417400--43417482 Score: 53
Period size: 10 Copynumber: 8.7 Consensus size: 9
43417390 ATTTTTTATT
43417400 TTTTTATAA
1 TTTTTATAA
43417409 TTTTTAATAA
1 TTTTT-ATAA
43417419 TTTTTAATAA
1 TTTTT-ATAA
* *
43417429 TTTTAAT-T
1 TTTTTATAA
43417437 TTTTTAAAAATAA
1 TTTTT----ATAA
43417450 TTTTTATAA
1 TTTTTATAA
*
43417459 TTTTTCTGAA
1 TTTTTAT-AA
43417469 TTTTT-TAA
1 TTTTTATAA
*
43417477 ATTTTA
1 TTTTTA
43417483 AAAAATTAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
8 10 0.17
9 18 0.30
10 25 0.42
12 2 0.03
13 5 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:43426525 original size:6 final size:6
Alignment explanation
Indices: 43426514--43426540 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
43426504 TGCACAAAAA
43426514 AATTAT AATTAT AATTAT AATTAT AAT
1 AATTAT AATTAT AATTAT AATTAT AAT
43426541 AAAAACAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:43426754 original size:9 final size:9
Alignment explanation
Indices: 43426742--43426793 Score: 68
Period size: 9 Copynumber: 5.7 Consensus size: 9
43426732 TATTAAAAAC
43426742 GAGAGAGTT
1 GAGAGAGTT
*
43426751 GAGAGACTT
1 GAGAGAGTT
*
43426760 GAGAGGGTTT
1 GAGAGAG-TT
*
43426770 GAGAGAATT
1 GAGAGAGTT
43426779 GAGAGAGTT
1 GAGAGAGTT
43426788 GAGAGA
1 GAGAGA
43426794 ATGATGTGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
9 29 0.81
10 7 0.19
ACGTcount: A:0.35, C:0.02, G:0.42, T:0.21
Consensus pattern (9 bp):
GAGAGAGTT
Found at i:43426773 original size:19 final size:18
Alignment explanation
Indices: 43426742--43426795 Score: 81
Period size: 18 Copynumber: 2.9 Consensus size: 18
43426732 TATTAAAAAC
*
43426742 GAGAGAGTTGAGAGACTT
1 GAGAGAGTTGAGAGAATT
*
43426760 GAGAGGGTTTGAGAGAATT
1 GAGAGAG-TTGAGAGAATT
43426779 GAGAGAGTTGAGAGAAT
1 GAGAGAGTTGAGAGAAT
43426796 GATGTGAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.35, C:0.02, G:0.41, T:0.22
Consensus pattern (18 bp):
GAGAGAGTTGAGAGAATT
Found at i:43429012 original size:4 final size:4
Alignment explanation
Indices: 43429003--43429056 Score: 81
Period size: 4 Copynumber: 13.2 Consensus size: 4
43428993 CCTAGCAAGG
* *
43429003 TACA TACA TACA AACCA TGCA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TA-CA TACA TACA TACA TACA TACA TACA TACA TACA
43429052 TACA T
1 TACA T
43429057 GTACATATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
4 43 0.96
5 2 0.04
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:43432597 original size:18 final size:18
Alignment explanation
Indices: 43432563--43432617 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
43432553 TTTTTTAAAA
43432563 TATAAAT-TTTGGAATTT
1 TATAAATATTTGGAATTT
*
43432580 TATAAATATTTTGAATTT
1 TATAAATATTTGGAATTT
*
43432598 TAAAAATTATTTGGAATTT
1 TATAAA-TATTTGGAATTT
43432617 T
1 T
43432618 TTTTTTGTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 7 0.21
18 14 0.42
19 12 0.36
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TATAAATATTTGGAATTT
Found at i:43432733 original size:10 final size:10
Alignment explanation
Indices: 43432718--43432742 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
43432708 GTTACTCGAG
43432718 TTATTTGGAA
1 TTATTTGGAA
43432728 TTATTTGGAA
1 TTATTTGGAA
43432738 TTATT
1 TTATT
43432743 CGAGTTATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (10 bp):
TTATTTGGAA
Found at i:43436493 original size:17 final size:18
Alignment explanation
Indices: 43436471--43436512 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
43436461 GGATTTGACG
* *
43436471 TTTGACAAAC-TTTATGT
1 TTTGACAAACATTAAGGT
*
43436488 TTTGACGAACATTAAGGT
1 TTTGACAAACATTAAGGT
43436506 TTTGACA
1 TTTGACA
43436513 GACTCTTCTG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (18 bp):
TTTGACAAACATTAAGGT
Found at i:43442904 original size:28 final size:28
Alignment explanation
Indices: 43442873--43442944 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
43442863 TCAGTTTGCG
* *
43442873 ACAAAGGCTATTCTTTTCAGAGTTCACC
1 ACAAAGGTTATTCTTTTCAAAGTTCACC
**
43442901 ACAAAGGTTATTCTTTTCAAAGTTTGCC
1 ACAAAGGTTATTCTTTTCAAAGTTCACC
*
43442929 ACAATGGTTATTCTTT
1 ACAAAGGTTATTCTTT
43442945 ATTGTCGTGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (28 bp):
ACAAAGGTTATTCTTTTCAAAGTTCACC
Found at i:43445336 original size:20 final size:20
Alignment explanation
Indices: 43445311--43445358 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
43445301 TAAATTCTAA
* *
43445311 AAAGATAAATACATTTAATT
1 AAAGATAAATAAATATAATT
43445331 AAAGATAAATAAATATAATT
1 AAAGATAAATAAATATAATT
43445351 AAA-ATAAA
1 AAAGATAAA
43445359 ATCCTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
AAAGATAAATAAATATAATT
Found at i:43445402 original size:15 final size:15
Alignment explanation
Indices: 43445382--43445411 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43445372 ATAATCCTAA
*
43445382 TAATTATCTTAATAT
1 TAATTATCCTAATAT
43445397 TAATTATCCTAATAT
1 TAATTATCCTAATAT
43445412 AAATAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:43445422 original size:5 final size:5
Alignment explanation
Indices: 43445407--43445436 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
43445397 TAATTATCCT
43445407 AATATA AATAA AATAA AATAA AATAA AATA
1 AATA-A AATAA AATAA AATAA AATAA AATA
43445437 GAGTCTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AATAA
Found at i:43448876 original size:28 final size:28
Alignment explanation
Indices: 43448831--43448931 Score: 125
Period size: 28 Copynumber: 3.6 Consensus size: 28
43448821 TAAGAATTTT
*
43448831 CCACAAAGGC-ATCCTTTTCAGAGTTCG
1 CCACAAAGGCTATTCTTTTCAGAGTTCG
*
43448858 TCACACAA-GCTATTCTTTTCAGAGTTCG
1 CCACA-AAGGCTATTCTTTTCAGAGTTCG
* *
43448886 CCACAAAGGCTATTCTTTTCAGGGTTCC
1 CCACAAAGGCTATTCTTTTCAGAGTTCG
* *
43448914 CCACAAGGGCCATTCTTT
1 CCACAAAGGCTATTCTTT
43448932 ACTGTTGGGT
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
27 8 0.12
28 56 0.88
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.31
Consensus pattern (28 bp):
CCACAAAGGCTATTCTTTTCAGAGTTCG
Found at i:43455315 original size:16 final size:17
Alignment explanation
Indices: 43455277--43455319 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
43455267 GGTTTAAAAT
* *
43455277 TATTCTCAATAATTTAA
1 TATTTTCAATAATATAA
43455294 TA-TTTCAA-AATATAA
1 TATTTTCAATAATATAA
43455309 TATTTTCAATA
1 TATTTTCAATA
43455320 TGGATTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 3 0.14
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (17 bp):
TATTTTCAATAATATAA
Found at i:43458183 original size:24 final size:24
Alignment explanation
Indices: 43458119--43458201 Score: 87
Period size: 24 Copynumber: 3.3 Consensus size: 24
43458109 ATCTCTCTAA
*
43458119 AAAATCTAACCCTAGCCCATGGCCC
1 AAAA-CTAACCCTAACCCATGGCCC
* **
43458144 AAAA-TACAACAAAACCCATGGCCC
1 AAAACTA-ACCCTAACCCATGGCCC
43458168 AAAACTAACCCTAACCCAAATGGCCC
1 AAAACTAACCCTAACCC--ATGGCCC
43458194 AAAACTAA
1 AAAACTAA
43458202 ACCAATTTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
23 2 0.04
24 24 0.51
25 6 0.13
26 15 0.32
ACGTcount: A:0.45, C:0.35, G:0.08, T:0.12
Consensus pattern (24 bp):
AAAACTAACCCTAACCCATGGCCC
Found at i:43460978 original size:3 final size:3
Alignment explanation
Indices: 43460972--43461011 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
43460962 TTGTTCCCTT
43460972 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
43461012 ATACTTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43471613 original size:10 final size:10
Alignment explanation
Indices: 43471600--43471625 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
43471590 TTTTGGACTT
43471600 TTTTTGTTTA
1 TTTTTGTTTA
43471610 TTTTTGTTTA
1 TTTTTGTTTA
43471620 TTTTTG
1 TTTTTG
43471626 GGTTTTGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.12, T:0.81
Consensus pattern (10 bp):
TTTTTGTTTA
Found at i:43478448 original size:13 final size:13
Alignment explanation
Indices: 43478402--43478449 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
43478392 TTGGCAATGT
43478402 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
43478415 TTTTAAAAAGTGC
1 TTTTGAAAAGTGC
** *
43478428 CGTGGAAAAGTGC
1 TTTTGAAAAGTGC
43478441 TTTTGAAAA
1 TTTTGAAAA
43478450 TTTTGATTTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.33
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:43480869 original size:19 final size:18
Alignment explanation
Indices: 43480834--43480870 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
43480824 ATGATAATCT
*
43480834 TTTAAAAAATATTTAAAA
1 TTTAAAAAATATATAAAA
43480852 TTTAAAAAATCATATAAAA
1 TTTAAAAAAT-ATATAAAA
43480871 AGTTTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TTTAAAAAATATATAAAA
Found at i:43480876 original size:21 final size:18
Alignment explanation
Indices: 43480834--43480878 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
43480824 ATGATAATCT
*
43480834 TTTAAAAAATATTTAAAA
1 TTTAAAAAATATTAAAAA
43480852 TTTAAAAAATCATATAAAAA
1 TTTAAAAAAT-AT-TAAAAA
43480872 GTTTAAA
1 -TTTAAA
43480879 CATTTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.43
19 2 0.09
20 5 0.22
21 6 0.26
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
TTTAAAAAATATTAAAAA
Found at i:43480980 original size:13 final size:13
Alignment explanation
Indices: 43480945--43480982 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
43480935 GTTGGTTGAA
*
43480945 TAAATTAAATTTT
1 TAAAATAAATTTT
*
43480958 TAATAT-AATTTT
1 TAAAATAAATTTT
43480970 TAAAATAAATTTT
1 TAAAATAAATTTT
43480983 CAATTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TAAAATAAATTTT
Found at i:43481008 original size:19 final size:19
Alignment explanation
Indices: 43480986--43481025 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
43480976 AAATTTTCAA
*
43480986 TTTTAATATTATTGAGTTT
1 TTTTAATATTATTGACTTT
* *
43481005 TTTTAATTTTTTTGACTTT
1 TTTTAATATTATTGACTTT
43481024 TT
1 TT
43481026 ATGAGTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (19 bp):
TTTTAATATTATTGACTTT
Found at i:43484727 original size:45 final size:45
Alignment explanation
Indices: 43484676--43484766 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
43484666 CATACTTGCC
43484676 AAGGGATCTAAATTTCATCGATCATACAAGCAATATTGGGTGGAA
1 AAGGGATCTAAATTTCATCGATCATACAAGCAATATTGGGTGGAA
*
43484721 AAGGGATCTAAATTTCATCGATCATACAAGCAATATTGTGTGGAA
1 AAGGGATCTAAATTTCATCGATCATACAAGCAATATTGGGTGGAA
43484766 A
1 A
43484767 GAGTGAGTAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.27
Consensus pattern (45 bp):
AAGGGATCTAAATTTCATCGATCATACAAGCAATATTGGGTGGAA
Found at i:43490284 original size:30 final size:30
Alignment explanation
Indices: 43490248--43490306 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
43490238 TATGCCATAG
43490248 TTGAATGAATAATTTATTGTATAAAGATAT
1 TTGAATGAATAATTTATTGTATAAAGATAT
*
43490278 TTGAATGAATAATTTGTTGTATAAAGATA
1 TTGAATGAATAATTTATTGTATAAAGATA
43490307 CTTTTATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (30 bp):
TTGAATGAATAATTTATTGTATAAAGATAT
Found at i:43491612 original size:6 final size:6
Alignment explanation
Indices: 43491601--43491625 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43491591 TTCTAATAAC
43491601 CATCTT CATCTT CATCTT CATCTT C
1 CATCTT CATCTT CATCTT CATCTT C
43491626 TTCTCACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (6 bp):
CATCTT
Found at i:43494782 original size:69 final size:69
Alignment explanation
Indices: 43494611--43494775 Score: 312
Period size: 69 Copynumber: 2.4 Consensus size: 69
43494601 ATTTTTTCAG
* *
43494611 TTTAAAACTAAAATTATTATTTTATTTGGTGGAGAATGGTGCCACCACCTTTAGACTTTTTATTT
1 TTTAAAAATAAAATTATTATTTTATTTGGTGGAGAATGGTGCCAACACCTTTAGACTTTTTATTT
43494676 TTAA
66 TTAA
43494680 TTTAAAAATAAAATTATTATTTTATTTGGTGGAGAATGGTGCCAACACCTTTAGACTTTTTATTT
1 TTTAAAAATAAAATTATTATTTTATTTGGTGGAGAATGGTGCCAACACCTTTAGACTTTTTATTT
43494745 TTAA
66 TTAA
43494749 TTTAAAAATAAAATTATTATTTTATTT
1 TTTAAAAATAAAATTATTATTTTATTT
43494776 AATGGAGCCA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 94 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (69 bp):
TTTAAAAATAAAATTATTATTTTATTTGGTGGAGAATGGTGCCAACACCTTTAGACTTTTTATTT
TTAA
Found at i:43508227 original size:18 final size:17
Alignment explanation
Indices: 43508204--43508238 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
43508194 AATTTTAAAA
43508204 ATATATATTAAAAATTTT
1 ATATAT-TTAAAAATTTT
*
43508222 ATATATTTTAAAATTTT
1 ATATATTTAAAAATTTT
43508239 GAGAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATATTTAAAAATTTT
Found at i:43512747 original size:95 final size:95
Alignment explanation
Indices: 43512584--43512767 Score: 359
Period size: 95 Copynumber: 1.9 Consensus size: 95
43512574 CAGGCAGATG
43512584 TGCCGGATCGACTGAGGTGGGACAACCTACTTTGGTATATGCTGCACATTACCGTGAGGACCGAG
1 TGCCGGATCGACTGAGGTGGGACAACCTACTTTGGTATATGCTGCACATTACCGTGAGGACCGAG
43512649 ATGCTCCGGATGTCATTACGGGTACGCTTT
66 ATGCTCCGGATGTCATTACGGGTACGCTTT
43512679 TGCCGGATCGACTGAGGTGGGACAACCTACTTTGGTATATGCTGCACATTACCGTGAGGACCGAG
1 TGCCGGATCGACTGAGGTGGGACAACCTACTTTGGTATATGCTGCACATTACCGTGAGGACCGAG
*
43512744 ATGCTCTGGATGTCATTACGGGTA
66 ATGCTCCGGATGTCATTACGGGTA
43512768 TGTTTTTTAT
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 88 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (95 bp):
TGCCGGATCGACTGAGGTGGGACAACCTACTTTGGTATATGCTGCACATTACCGTGAGGACCGAG
ATGCTCCGGATGTCATTACGGGTACGCTTT
Found at i:43518964 original size:23 final size:23
Alignment explanation
Indices: 43518938--43518987 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
43518928 CCATTCACTT
*
43518938 TCAAACATTGTTTAAGGTTCAAA-
1 TCAAACA-TATTTAAGGTTCAAAC
*
43518961 TCAAGCATATTTAAGGTTCAAAC
1 TCAAACATATTTAAGGTTCAAAC
43518984 TCAA
1 TCAA
43518988 GAACATTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (23 bp):
TCAAACATATTTAAGGTTCAAAC
Found at i:43520761 original size:17 final size:17
Alignment explanation
Indices: 43520739--43520773 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
43520729 AAATTGAAAG
43520739 TAAGAATAGAGAAAATA
1 TAAGAATAGAGAAAATA
43520756 TAAGAATAGAGAAAATA
1 TAAGAATAGAGAAAATA
43520773 T
1 T
43520774 GTTAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (17 bp):
TAAGAATAGAGAAAATA
Found at i:43523481 original size:23 final size:24
Alignment explanation
Indices: 43523439--43523499 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 24
43523429 TTCTTTGAAA
*
43523439 ATAATAAAATCATAAATTAA-TAC
1 ATAATAAAATTATAAATTAACTAC
** *
43523462 ATAATAAAATTATATTTTAACTTC
1 ATAATAAAATTATAAATTAACTAC
*
43523486 TTAA-AAAATTATAA
1 ATAATAAAATTATAA
43523500 TTCAATTCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
23 26 0.84
24 5 0.16
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (24 bp):
ATAATAAAATTATAAATTAACTAC
Found at i:43523508 original size:22 final size:23
Alignment explanation
Indices: 43523467--43523509 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
43523457 AATACATAAT
* *
43523467 AAAATTATATTTTAACTTCTTAA
1 AAAATTATAATTCAACTTCTTAA
43523490 AAAATTATAATTCAA-TTCTT
1 AAAATTATAATTCAACTTCTT
43523510 CTTAATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATTATAATTCAACTTCTTAA
Found at i:43526466 original size:15 final size:15
Alignment explanation
Indices: 43526446--43526491 Score: 65
Period size: 15 Copynumber: 3.0 Consensus size: 15
43526436 ACTTCCACTG
*
43526446 GAATTAAAATGAAAT
1 GAATTAAATTGAAAT
*
43526461 GAATTAAATTGAATT
1 GAATTAAATTGAAAT
43526476 GAATTGAAATTGAAAT
1 GAATT-AAATTGAAAT
43526492 ATCAACCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.15, T:0.33
Consensus pattern (15 bp):
GAATTAAATTGAAAT
Found at i:43527866 original size:25 final size:26
Alignment explanation
Indices: 43527820--43527883 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
43527810 TTTAATTGTC
* * *
43527820 TTATTTTTATAATGAATTTGATATAA
1 TTATTTTTTTAATAAATCTGATATAA
*
43527846 TTATTTTTTTAA-AAATCTGATATGA
1 TTATTTTTTTAATAAATCTGATATAA
*
43527871 -GATTTTTTTAATA
1 TTATTTTTTTAATA
43527884 TTCCCAAGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 10 0.31
25 11 0.34
26 11 0.34
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.55
Consensus pattern (26 bp):
TTATTTTTTTAATAAATCTGATATAA
Found at i:43528377 original size:21 final size:21
Alignment explanation
Indices: 43528325--43528378 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
43528315 GTGGCCCTAA
*
43528325 ACATGGTCGTGTGGCTACTCT
1 ACATGCTCGTGTGGCTACTCT
* * *
43528346 ACATACCCGTGTGGTTACT-T
1 ACATGCTCGTGTGGCTACTCT
43528366 CACATGCTCGTGT
1 -ACATGCTCGTGT
43528379 ACAATTCGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (21 bp):
ACATGCTCGTGTGGCTACTCT
Found at i:43529005 original size:17 final size:18
Alignment explanation
Indices: 43528978--43529011 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
43528968 ATATTGTGAA
43528978 AAAATAAAATAAAGAAAT
1 AAAATAAAATAAAGAAAT
43528996 AAAA-AAAATAAAGAAA
1 AAAATAAAATAAAGAAA
43529012 CACACAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (18 bp):
AAAATAAAATAAAGAAAT
Found at i:43534682 original size:30 final size:30
Alignment explanation
Indices: 43534646--43534707 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
43534636 TGACCAAACC
* *
43534646 TTAGTTTCTCCTAGCTATGGAGTTTCGGGT
1 TTAGTTTCTCCTAGCTATAGAGTTTCAGGT
*
43534676 TTAGTTTCTCCTAGTTATAGAGTTTCAGGT
1 TTAGTTTCTCCTAGCTATAGAGTTTCAGGT
43534706 TT
1 TT
43534708 CTTTTTCTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.47
Consensus pattern (30 bp):
TTAGTTTCTCCTAGCTATAGAGTTTCAGGT
Found at i:43540532 original size:20 final size:20
Alignment explanation
Indices: 43540507--43540544 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
43540497 GTCAGTCCTA
* *
43540507 TAAATAGTGGGGTCAAATCG
1 TAAATAGTAGAGTCAAATCG
43540527 TAAATAGTAGAGTCAAAT
1 TAAATAGTAGAGTCAAAT
43540545 TATGAATAAT
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:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (20 bp):
TAAATAGTAGAGTCAAATCG
Found at i:43541105 original size:10 final size:10
Alignment explanation
Indices: 43541092--43541120 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
43541082 TACATATATC
43541092 TGACTTTAGG
1 TGACTTTAGG
43541102 TGACTTTAGG
1 TGACTTTAGG
43541112 TGACTTTAG
1 TGACTTTAG
43541121 ATGAGCGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41
Consensus pattern (10 bp):
TGACTTTAGG
Found at i:43544968 original size:16 final size:16
Alignment explanation
Indices: 43544947--43544977 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43544937 GATATTTTAA
43544947 TATATTATATTAATAT
1 TATATTATATTAATAT
*
43544963 TATATTATGTTAATA
1 TATATTATATTAATA
43544978 AAATAATAAA
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:43552080 original size:16 final size:16
Alignment explanation
Indices: 43552059--43552089 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43552049 GATATTTTAA
43552059 TATATTATATTAATAT
1 TATATTATATTAATAT
*
43552075 TATATTATGTTAATA
1 TATATTATATTAATA
43552090 AAATAATAAA
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:43552186 original size:12 final size:12
Alignment explanation
Indices: 43552169--43552199 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43552159 GAAGCAGGGG
43552169 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
43552181 AGAAAAAGGGAA
1 AGAAAAAGAGAA
43552193 AGAAAAA
1 AGAAAAA
43552200 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:43553887 original size:51 final size:51
Alignment explanation
Indices: 43553830--43553933 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
43553820 ATGAATGAAA
*
43553830 TTTTTAATCAATTTTGAATGATGTTATGATAGTTATTAAGTTAAAATTTTG
1 TTTTTAATCAATTTTGAATGATGCTATGATAGTTATTAAGTTAAAATTTTG
43553881 TTTTTAATCAATTTTGAATGATGCTATGATAGTTATTAAGTTAAAATTTTG
1 TTTTTAATCAATTTTGAATGATGCTATGATAGTTATTAAGTTAAAATTTTG
43553932 TT
1 TT
43553934 AATGATATAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.51
Consensus pattern (51 bp):
TTTTTAATCAATTTTGAATGATGCTATGATAGTTATTAAGTTAAAATTTTG
Found at i:43555486 original size:42 final size:42
Alignment explanation
Indices: 43555434--43555529 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 42
43555424 TATAATTATT
*
43555434 CACTGACTCAAAACCTGCTAGGGCC-AAGGCCTAATACAAATA
1 CACTGGCTCAAAACCTGCTA-GGCCTAAGGCCTAATACAAATA
* **
43555476 CACTGGCTCAAAGCCTGCTAGGCCTAAGGCCTTTTACAAATA
1 CACTGGCTCAAAACCTGCTAGGCCTAAGGCCTAATACAAATA
**
43555518 CACCAGCTCAAA
1 CACTGGCTCAAA
43555530 TTCTGCTTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 4 0.09
42 43 0.91
ACGTcount: A:0.34, C:0.30, G:0.17, T:0.19
Consensus pattern (42 bp):
CACTGGCTCAAAACCTGCTAGGCCTAAGGCCTAATACAAATA
Found at i:43560380 original size:91 final size:94
Alignment explanation
Indices: 43560215--43560477 Score: 293
Period size: 94 Copynumber: 2.8 Consensus size: 94
43560205 GGGTTAAGTT
* * * * * * * *
43560215 GCCGCTGCCATGTCCCAGACATGGTCTTACACTAGCTC-TCGTATATACATGCTGATGGATGTCC
1 GCCGATGCCATGTCCCAAACATCGTCTTACACTGGC-CATCATA-AT-GAGGCTGATGCATGTCC
43560279 CAGACATGTCTTACACTAGCACGAAACT-TA-
63 CAGACATGTCTTACACTAGCACGAAACTCTAC
* * *
43560309 GCCGATG-CATGTCCCAGACA-CGTCTTACACTGGCTATCATCATCGAGGCTGATGCATGTCCCA
1 GCCGATGCCATGTCCCAAACATCGTCTTACACTGGCCATCATAAT-GAGGCTGATGCATGTCCCA
* ** *
43560372 AACATGTCTTACACTAGCACTTATCTCTAC
65 GACATGTCTTACACTAGCACGAAACTCTAC
* * *
43560402 GCCGATGCCATGTCCCAAACATGGTTTTACACTGGCCATCATAATGTGGCTGATGCATGTCCCAG
1 GCCGATGCCATGTCCCAAACATCGTCTTACACTGGCCATCATAATGAGGCTGATGCATGTCCCAG
43560467 ACATGTCTTAC
66 ACATGTCTTAC
43560478 TTTAGCCCTG
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
91 40 0.28
92 17 0.12
93 20 0.14
94 47 0.33
95 19 0.13
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (94 bp):
GCCGATGCCATGTCCCAAACATCGTCTTACACTGGCCATCATAATGAGGCTGATGCATGTCCCAG
ACATGTCTTACACTAGCACGAAACTCTAC
Found at i:43560381 original size:47 final size:46
Alignment explanation
Indices: 43560312--43560477 Score: 174
Period size: 47 Copynumber: 3.5 Consensus size: 46
43560302 AAACTTAGCC
* *
43560312 GATGCATGTCCCAGACACGTCTTACACTGGCTATCATCATCGAGGCT
1 GATGCATGTCCCAAACATGTCTTACACTGGC-ATCATCATCGAGGCT
* * * * *
43560359 GATGCATGTCCCAAACATGTCTTACACTAGCACTTATC-TCTACGCC
1 GATGCATGTCCCAAACATGTCTTACACTGGCA-TCATCATCGAGGCT
* * *
43560405 GATGCCATGTCCCAAACATGGTTTTACACTGGCCATCATAAT-GTGGCT
1 GATG-CATGTCCCAAACAT-GTCTTACACTGG-CATCATCATCGAGGCT
*
43560453 GATGCATGTCCCAGACATGTCTTAC
1 GATGCATGTCCCAAACATGTCTTAC
43560478 TTTAGCCCTG
Statistics
Matches: 97, Mismatches: 17, Indels: 11
0.78 0.14 0.09
Matches are distributed among these distances:
46 16 0.16
47 59 0.61
48 19 0.20
49 3 0.03
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAAACATGTCTTACACTGGCATCATCATCGAGGCT
Found at i:43563723 original size:29 final size:29
Alignment explanation
Indices: 43563691--43563753 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
43563681 GAAAATCTGT
43563691 CAAATAAAGAATAAATGCGAAAAAATGGC
1 CAAATAAAGAATAAATGCGAAAAAATGGC
* * * *
43563720 CAAATAATGAATAAATGTGACAAAATTGC
1 CAAATAAAGAATAAATGCGAAAAAATGGC
43563749 CAAAT
1 CAAAT
43563754 CCCTTCAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.56, C:0.11, G:0.14, T:0.19
Consensus pattern (29 bp):
CAAATAAAGAATAAATGCGAAAAAATGGC
Found at i:43564459 original size:18 final size:17
Alignment explanation
Indices: 43564429--43564471 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
43564419 ATCGTTTCGA
* *
43564429 AGTTTTTAGAAAACCTT
1 AGTTTTTGGAAAACCTG
*
43564446 AGTTTTTGGTAAAATCTG
1 AGTTTTTGG-AAAACCTG
43564464 AGTTTTTG
1 AGTTTTTG
43564472 TCGAGTTCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.47
Consensus pattern (17 bp):
AGTTTTTGGAAAACCTG
Found at i:43564825 original size:35 final size:35
Alignment explanation
Indices: 43564754--43564828 Score: 107
Period size: 35 Copynumber: 2.1 Consensus size: 35
43564744 TTAGAATAAG
* *
43564754 ACAGATACAGATTCGGGCCTAAGCCCATTACCGAT
1 ACAGATACAGATTCAGGCCTAAGCCCATTACAGAT
*
43564789 ACAGATGCAGATTCAGGCCTAAGCCCATCT-CAGAT
1 ACAGATACAGATTCAGGCCTAAGCCCAT-TACAGAT
43564824 ACAGA
1 ACAGA
43564829 CATAGATGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 35 0.97
36 1 0.03
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (35 bp):
ACAGATACAGATTCAGGCCTAAGCCCATTACAGAT
Found at i:43575533 original size:10 final size:10
Alignment explanation
Indices: 43575518--43575577 Score: 68
Period size: 10 Copynumber: 6.0 Consensus size: 10
43575508 TAAATCTAAG
*
43575518 ATTTATTTTT
1 ATTTATCTTT
43575528 ATTTATCTTT
1 ATTTATCTTT
*
43575538 AATTATCTTT
1 ATTTATCTTT
* *
43575548 AATTACCTTT
1 ATTTATCTTT
43575558 ATTTAT-TTGT
1 ATTTATCTT-T
43575568 ATTTATCTTT
1 ATTTATCTTT
43575578 TAGAATTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
9 2 0.05
10 39 0.91
11 2 0.05
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.67
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:43594142 original size:13 final size:13
Alignment explanation
Indices: 43594124--43594161 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
43594114 ATGTACTTCA
43594124 TATTTGTTGTCAT
1 TATTTGTTGTCAT
43594137 TATTTGTTGTCAT
1 TATTTGTTGTCAT
43594150 TATTTGTT-TCAT
1 TATTTGTTGTCAT
43594162 ATGTCATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.16
13 21 0.84
ACGTcount: A:0.16, C:0.08, G:0.13, T:0.63
Consensus pattern (13 bp):
TATTTGTTGTCAT
Found at i:43594227 original size:25 final size:24
Alignment explanation
Indices: 43594173--43594229 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
43594163 TGTCATGTTA
*
43594173 ATAAATAATTTAAAATTATAAAAT
1 ATAAAAAATTTAAAATTATAAAAT
43594197 ATTAAAAAATTTAAAATTCA-AAGAAT
1 A-TAAAAAATTTAAAATT-ATAA-AAT
43594223 ATAAAAA
1 ATAAAAA
43594230 GTTCATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 1 0.03
25 23 0.79
26 5 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (24 bp):
ATAAAAAATTTAAAATTATAAAAT
Found at i:43594884 original size:26 final size:26
Alignment explanation
Indices: 43594851--43594911 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
43594841 AAAACATTTA
43594851 TTTTAAATTTAAAT-ATTTTTAATAAT
1 TTTTAAATTTAAATCA-TTTTAATAAT
43594877 TTTTAAATTTAAATCATTTTAATAAT
1 TTTTAAATTTAAATCATTTTAATAAT
*
43594903 TGTTAAATT
1 TTTTAAATT
43594912 ATAGTTTTGC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
26 32 0.97
27 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTTAAATTTAAATCATTTTAATAAT
Found at i:43594896 original size:16 final size:15
Alignment explanation
Indices: 43594849--43594898 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
43594839 TAAAAACATT
43594849 TATTTTAAATTTAAA
1 TATTTTAAATTTAAA
*
43594864 TATTTTTAA--T-AA
1 TATTTTAAATTTAAA
43594876 T-TTTTAAATTTAAA
1 TATTTTAAATTTAAA
43594890 TCATTTTAA
1 T-ATTTTAA
43594899 TAATTGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
11 6 0.21
12 3 0.11
13 2 0.07
14 3 0.11
15 8 0.29
16 6 0.21
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTTAAATTTAAA
Found at i:43596905 original size:38 final size:39
Alignment explanation
Indices: 43596848--43596949 Score: 100
Period size: 39 Copynumber: 2.6 Consensus size: 39
43596838 TTAGTGGCAT
* *
43596848 TAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCGAGC-C
1 TAGCGGCGC-TTTTAAAAAACGCCGCTATAGATCGACCAC
* * * *
43596887 TAGCGACGCTATTTAAAAAATGCCGCTGTAGGTCGACCAC
1 TAGCGGCGCT-TTTAAAAAACGCCGCTATAGATCGACCAC
* *
43596927 TAGCGGCAC-TTTGAAAAACGCCG
1 TAGCGGCGCTTTTAAAAAACGCCG
43596950 TAAAAAAATT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
38 13 0.25
39 30 0.59
40 8 0.16
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (39 bp):
TAGCGGCGCTTTTAAAAAACGCCGCTATAGATCGACCAC
Found at i:43597081 original size:40 final size:39
Alignment explanation
Indices: 43596997--43597104 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 39
43596987 GCTTTAGTGG
** *
43596997 CATTAGCAACGCTTTTTGAAAACGCCGCTATAGATCGAT
1 CATTAGCGGCGCTTTTTAAAAACGCCGCTATAGATCGAT
* *
43597036 CATTAGCGGCGCTTTTTAAAAAATGCCGCTATAGGTCGA-
1 CATTAGCGGCGCTTTTT-AAAAACGCCGCTATAGATCGAT
*
43597075 CTATTAGTGGCGCTTTTTGAAAAACGCCGC
1 C-ATTAGCGGCGCTTTTT-AAAAACGCCGC
43597105 AAAAAAATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
39 16 0.27
40 43 0.73
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (39 bp):
CATTAGCGGCGCTTTTTAAAAACGCCGCTATAGATCGAT
Found at i:43597155 original size:154 final size:153
Alignment explanation
Indices: 43596746--43597171 Score: 586
Period size: 152 Copynumber: 2.8 Consensus size: 153
43596736 GGCGTTTGGA
* * ** * * **
43596746 TAAAAAAAGCCGCTATAGATTAAGCATTAGCGGCGCTTTTTGAAAAATGCTACAAAAAAATTAAG
1 TAAAAAATGCCGCTATAGGTCGACCATTAGCGGCGCTTTTTGAAAAACGCCGCAAAAAAATTAAG
* *
43596811 CACAATGCTGTCGTTTTATGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTGAAAAACGCCGCTA
66 CACAATGCCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGCGACGCTTTTTG-AAAACGCCGCTA
43596876 TAGATCGAGCCTAGCGACGCTATT
130 TAGATCGAGCCTAGCGACGCTATT
* * * *
43596900 TAAAAAATGCCGCTGTAGGTCGACCACTAGCGGCAC--TTTGAAAAACGCCGTAAAAAAATTAAG
1 TAAAAAATGCCGCTATAGGTCGACCATTAGCGGCGCTTTTTGAAAAACGCCGCAAAAAAATTAAG
** * *
43596963 CACAACACCGTTGTTTTATGTTGAGCTTTAGTGGCATTAGCAACGCTTTTTGAAAACGCCGCTAT
66 CACAATGCCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGCGACGCTTTTTGAAAACGCCGCTAT
* * * *
43597028 AGATCGATCATTAGCGGCGCTTTT
131 AGATCGAGC-CTAGCGACGCTATT
* *
43597052 TAAAAAATGCCGCTATAGGTCGACTATTAGTGGCGCTTTTTGAAAAACGCCGCAAAAAAATTAAG
1 TAAAAAATGCCGCTATAGGTCGACCATTAGCGGCGCTTTTTGAAAAACGCCGCAAAAAAATTAAG
* *
43597117 CACAATGCCATCGTTTTATGTTTAGCTTTAGTGGCATTAGCGACGCTTTTTGAAA
66 CACAATGCCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGCGACGCTTTTTGAAA
43597172 TATTTATCAT
Statistics
Matches: 235, Mismatches: 34, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
151 21 0.09
152 111 0.47
154 103 0.44
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (153 bp):
TAAAAAATGCCGCTATAGGTCGACCATTAGCGGCGCTTTTTGAAAAACGCCGCAAAAAAATTAAG
CACAATGCCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGCGACGCTTTTTGAAAACGCCGCTAT
AGATCGAGCCTAGCGACGCTATT
Found at i:43597202 original size:7 final size:7
Alignment explanation
Indices: 43597187--43597312 Score: 76
Period size: 7 Copynumber: 17.7 Consensus size: 7
43597177 ATCATTATAT
*
43597187 TTTAGGG
1 TTTATGG
43597194 TTTATGG
1 TTTATGG
*
43597201 TTTAGGG
1 TTTATGG
*
43597208 TTTAAGG
1 TTTATGG
*
43597215 TTTAGGAG
1 TTTATG-G
43597223 TTACTAT--
1 TT--TATGG
*
43597230 TTTAAGG
1 TTTATGG
43597237 TTTATGG
1 TTTATGG
*
43597244 ATTATGGG
1 TTTAT-GG
*
43597252 TTTAGGG
1 TTTATGG
*
43597259 ATTATGG
1 TTTATGG
43597266 TTTATGG
1 TTTATGG
*
43597273 TTTAAGG
1 TTTATGG
* **
43597280 GTTGGGG
1 TTTATGG
*
43597287 TTTAAGG
1 TTTATGG
*
43597294 TTTAAGG
1 TTTATGG
43597301 TTTATGG
1 TTTATGG
43597308 TTTAT
1 TTTAT
43597313 ATCTTATAAT
Statistics
Matches: 92, Mismatches: 21, Indels: 12
0.74 0.17 0.10
Matches are distributed among these distances:
5 2 0.02
7 80 0.87
8 8 0.09
10 2 0.02
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.47
Consensus pattern (7 bp):
TTTATGG
Found at i:43597204 original size:14 final size:14
Alignment explanation
Indices: 43597187--43597312 Score: 87
Period size: 14 Copynumber: 8.9 Consensus size: 14
43597177 ATCATTATAT
43597187 TTTAGGGTTTATGG
1 TTTAGGGTTTATGG
*
43597201 TTTAGGGTTTAAGG
1 TTTAGGGTTTATGG
43597215 TTTAGGAGTTACTAT--
1 TTTAGG-GTT--TATGG
*
43597230 TTTAAGGTTTATGG
1 TTTAGGGTTTATGG
* *
43597244 ATTATGGGTTTAGGG
1 TTTA-GGGTTTATGG
* *
43597259 ATTATGGTTTATGG
1 TTTAGGGTTTATGG
**
43597273 TTTAAGGG-TTGGGG
1 TTT-AGGGTTTATGG
* *
43597287 TTTAAGGTTTAAGG
1 TTTAGGGTTTATGG
*
43597301 TTTATGGTTTAT
1 TTTAGGGTTTAT
43597313 ATCTTATAAT
Statistics
Matches: 87, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
12 3 0.03
13 3 0.03
14 56 0.64
15 23 0.26
17 2 0.02
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.47
Consensus pattern (14 bp):
TTTAGGGTTTATGG
Found at i:43597216 original size:21 final size:21
Alignment explanation
Indices: 43597187--43597311 Score: 101
Period size: 21 Copynumber: 5.9 Consensus size: 21
43597177 ATCATTATAT
*
43597187 TTTAGGGTTTATGGTTTAGGG
1 TTTAAGGTTTATGGTTTAGGG
* *
43597208 TTTAAGGTTTAGGAGTTACTA--T
1 TTTAAGGTTTATG-GTT--TAGGG
*
43597230 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGTTTATGGTTTA-GGG
* * *
43597252 TTTAGGGATTATGGTTTATGG
1 TTTAAGGTTTATGGTTTAGGG
* ** *
43597273 TTTAAGGGTTGGGGTTTAAGG
1 TTTAAGGTTTATGGTTTAGGG
43597294 TTTAAGGTTTATGGTTTA
1 TTTAAGGTTTATGGTTTA
43597312 TATCTTATAA
Statistics
Matches: 80, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.03
21 46 0.57
22 30 0.38
24 2 0.03
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (21 bp):
TTTAAGGTTTATGGTTTAGGG
Found at i:43597255 original size:15 final size:15
Alignment explanation
Indices: 43597235--43597282 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
43597225 ACTATTTTAA
43597235 GGTTTATGGATTATG
1 GGTTTATGGATTATG
*
43597250 GGTTTAGGGATTAT-
1 GGTTTATGGATTATG
* *
43597264 GGTTTATGGTTTAAG
1 GGTTTATGGATTATG
43597279 GGTT
1 GGTT
43597283 GGGGTTTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:43600955 original size:43 final size:43
Alignment explanation
Indices: 43600812--43601170 Score: 322
Period size: 43 Copynumber: 8.5 Consensus size: 43
43600802 ATTTTTTTAC
* * *
43600812 AAGGTCATGTTCTTTAGCAGCATTTGTGGGAAAAGCGCCGCTA
1 AAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTA
* * * * *
43600855 AAGGTCTAT-TT-TATAGTGGCATTTTTGGAAAAAGTGCCGCTA
1 AAGGTC-ATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTA
* * * **
43600897 AAGATC-TGTTTTATAGCGGCGTTTGTGGGAAAAGAGCCATTA
1 AAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTA
* * * *
43600939 AAGGTCATGTTCTATAGCTGCGATTGTGGG-AGAGCGCTGCTA
1 AAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTA
* * * * * *
43600981 AAGGTCATGTTCTATAGTGGGGTTTGTAGGAAAACCGTCTCTA
1 AAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTA
* * * ** *
43601024 AAAGTCATGTTCTATAGAGGCGTTTGTGGAAAAAATGCCACTA
1 AAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTA
43601067 AAGGTCA-----TATAGCGGCGTTTGTGGGAAAAGCGCCGCTA
1 AAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTA
* * * * *
43601105 AAAGTCATGTTCTATAGTGGCATTTATGGGAAAAGCGCTGCTA
1 AAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTA
* *
43601148 AATGTCATGTTTTATAGCGGCGT
1 AAGGTCATGTTCTATAGCGGCGT
43601171 GTTTCTATAT
Statistics
Matches: 249, Mismatches: 57, Indels: 20
0.76 0.17 0.06
Matches are distributed among these distances:
38 32 0.13
40 1 0.00
41 2 0.01
42 91 0.37
43 121 0.49
44 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (43 bp):
AAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAAGCGCCGCTA
Found at i:43601137 original size:124 final size:124
Alignment explanation
Indices: 43600834--43601170 Score: 364
Period size: 124 Copynumber: 2.7 Consensus size: 124
43600824 TTTAGCAGCA
* * * *
43600834 TTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-TT-TATAGTGGCATTTTTGGAAAAAGTGCCGCT-
1 TTTGTGGGAAAAGCGCCGCTAAAGGTC-ATGTTCTATAGTGGCATTTATGGGAAAAGCG-CTCTA
* * *
43600896 AAAGATC-TGTTTTATAGCGGCGTTTGTGGGAAAAGAGCCATTAAAGGTCATGTTCTATAGCTGC
64 AAAG-TCATGTTTTATAGCGGCGTTTGTGGGAAAAAAGCCACTAAAGGTCA---T-TATAGCGGC
43600960 G
124 G
* * * ** * * *
43600961 ATTGTGGG-AGAGCGCTGCTAAAGGTCATGTTCTATAGTGGGGTTTGTAGGAAAACCGTCTCTAA
1 TTTGTGGGAAAAGCGCCGCTAAAGGTCATGTTCTATAGTGGCATTTATGGGAAAAGCG-CTCTAA
* *
43601025 AAGTCATGTTCTATAGAGGCGTTTGT-GGAAAAAATGCCACTAAAGGTCA-TATAGCGGCG
65 AAGTCATGTTTTATAGCGGCGTTTGTGGGAAAAAA-GCCACTAAAGGTCATTATAGCGGCG
*
43601084 TTTGTGGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGTGGCATTTATGGGAAAAGCGCTGCTAA
1 TTTGTGGGAAAAGCGCCGCTAAAGGTCATGTTCTATAGTGGCATTTATGGGAAAAGCGCT-CTAA
*
43601149 ATGTCATGTTTTATAGCGGCGT
65 AAGTCATGTTTTATAGCGGCGT
43601171 GTTTCTATAT
Statistics
Matches: 174, Mismatches: 29, Indels: 17
0.79 0.13 0.08
Matches are distributed among these distances:
123 18 0.10
124 64 0.37
125 2 0.01
126 18 0.10
127 37 0.21
128 35 0.20
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (124 bp):
TTTGTGGGAAAAGCGCCGCTAAAGGTCATGTTCTATAGTGGCATTTATGGGAAAAGCGCTCTAAA
AGTCATGTTTTATAGCGGCGTTTGTGGGAAAAAAGCCACTAAAGGTCATTATAGCGGCG
Found at i:43601149 original size:81 final size:81
Alignment explanation
Indices: 43600834--43601155 Score: 258
Period size: 81 Copynumber: 3.9 Consensus size: 81
43600824 TTTAGCAGCA
* * *
43600834 TTTGTGGGAAAAGCGCCGCTAAAGGTCTAT-TT-TATAGTGGCATTTTTGGAAAAAGTGCCGCTA
1 TTTGTGGGAAAAGCGCCGCTAAAAGTC-ATGTTCTATAGTGGCATTTGTGGAAAAAGCGCCGCTA
**
43600897 AAGATCTGTTTTATAGCGGCG
65 AAG----GTCATATAGCGGCG
* ** * * * *
43600918 TTTGTGGGAAAAGAGCCATTAAAGGTCATGTTCTATAGCT-GCGA-TTGTGG-GAGAGCGCTGCT
1 TTTGTGGGAAAAGCGCCGCTAAAAGTCATGTTCTATAG-TGGC-ATTTGTGGAAAAAGCGCCGCT
* *
43600980 AAAGGTCATGTTCTATAGTGGGG
64 AAAGGTCA-----TATAGCGGCG
* * * * * * ** *
43601003 TTTGTAGGAAAACCGTCTCTAAAAGTCATGTTCTATAGAGGCGTTTGTGGAAAAAATGCCACTAA
1 TTTGTGGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGTGGCATTTGTGGAAAAAGCGCCGCTAA
43601068 AGGTCATATAGCGGCG
66 AGGTCATATAGCGGCG
* * *
43601084 TTTGTGGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGTGGCATTTATGGGAAAAGCGCTGCTAA
1 TTTGTGGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGTGGCATTTGTGGAAAAAGCGCCGCTAA
*
43601149 ATGTCAT
66 AGGTCAT
43601156 GTTTTATAGC
Statistics
Matches: 184, Mismatches: 42, Indels: 27
0.73 0.17 0.11
Matches are distributed among these distances:
80 2 0.01
81 67 0.36
83 2 0.01
84 38 0.21
85 59 0.32
86 16 0.09
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TTTGTGGGAAAAGCGCCGCTAAAAGTCATGTTCTATAGTGGCATTTGTGGAAAAAGCGCCGCTAA
AGGTCATATAGCGGCG
Found at i:43601534 original size:17 final size:18
Alignment explanation
Indices: 43601498--43601535 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43601488 CCCTCTTTTT
43601498 TTTCTCACTCAGAATTTA
1 TTTCTCACTCAGAATTTA
* *
43601516 TTTCTCTCTCA-ACTTTA
1 TTTCTCACTCAGAATTTA
43601533 TTT
1 TTT
43601536 ATTTATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.21, C:0.24, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTCACTCAGAATTTA
Found at i:43602348 original size:27 final size:27
Alignment explanation
Indices: 43602318--43602373 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
43602308 TGTTGGCAAC
* *
43602318 GTTGTTTAGGAAGATGTGTCAGGTGAT
1 GTTGTATAGGAAGATGTGTCAGGCGAT
* *
43602345 GTTGTATAGGGAGATGTGTCGGGCGAT
1 GTTGTATAGGAAGATGTGTCAGGCGAT
43602372 GT
1 GT
43602374 AACCACACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.05, G:0.41, T:0.34
Consensus pattern (27 bp):
GTTGTATAGGAAGATGTGTCAGGCGAT
Found at i:43605159 original size:19 final size:19
Alignment explanation
Indices: 43605137--43605176 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
43605127 TCAAATTAAA
*
43605137 ACCATTCGTGCCATCAAAC
1 ACCATTCGTACCATCAAAC
*
43605156 ACCATTTGTACCATCAAAC
1 ACCATTCGTACCATCAAAC
43605175 AC
1 AC
43605177 ATACCAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.35, G:0.07, T:0.23
Consensus pattern (19 bp):
ACCATTCGTACCATCAAAC
Found at i:43606311 original size:23 final size:21
Alignment explanation
Indices: 43606285--43606334 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
43606275 CGGTAAGCTC
*
43606285 CTCTTGAGCTGATAAACAGTAAG
1 CTCTTGAGCT-A-AAAAAGTAAG
43606308 CTCTATTGAGCTAAAAAAGTAAG
1 CTC--TTGAGCTAAAAAAGTAAG
43606331 CTCT
1 CTCT
43606335 AACGAGCTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 1 0.04
23 15 0.62
24 1 0.04
25 7 0.29
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (21 bp):
CTCTTGAGCTAAAAAAGTAAG
Found at i:43606335 original size:23 final size:24
Alignment explanation
Indices: 43606277--43606368 Score: 87
Period size: 24 Copynumber: 3.8 Consensus size: 24
43606267 GCCATGATCG
* *
43606277 GTAAGCTCCTCTTGAGCTGATAAACA
1 GTAAGCT-CTATTGAGCTGA-AAAAA
43606303 GTAAGCTCTATTGAGCT-AAAAAA
1 GTAAGCTCTATTGAGCTGAAAAAA
** * *
43606326 GTAAGCTCTAACGAGCTGAGAATA
1 GTAAGCTCTATTGAGCTGAAAAAA
**
43606350 GTAAGCTCTAACGAGCTGA
1 GTAAGCTCTATTGAGCTGA
43606369 TATATCGGTA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
23 19 0.32
24 24 0.41
25 9 0.15
26 7 0.12
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (24 bp):
GTAAGCTCTATTGAGCTGAAAAAA
Found at i:43606357 original size:24 final size:24
Alignment explanation
Indices: 43606290--43606368 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
43606280 AGCTCCTCTT
* **
43606290 GAGCTGATAAACAGTAAGCTCTATT
1 GAGCTGA-AAAAAGTAAGCTCTAAC
43606315 GAGCT-AAAAAAGTAAGCTCTAAC
1 GAGCTGAAAAAAGTAAGCTCTAAC
* *
43606338 GAGCTGAGAATAGTAAGCTCTAAC
1 GAGCTGAAAAAAGTAAGCTCTAAC
43606362 GAGCTGA
1 GAGCTGA
43606369 TATATCGGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
23 19 0.40
24 24 0.50
25 5 0.10
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (24 bp):
GAGCTGAAAAAAGTAAGCTCTAAC
Found at i:43613780 original size:48 final size:45
Alignment explanation
Indices: 43613674--43613785 Score: 120
Period size: 48 Copynumber: 2.4 Consensus size: 45
43613664 TCATGTTTGT
*
43613674 GAGCTAGTGTAAGACATGTCTGCGACATGCATCAGCCACATTATGA
1 GAGCTAGTGTAAGACATGTCTGCGACATGCATCAG-CAAATTATGA
* *
43613720 GAGCCAGTGTAAGACTATGTCTGGGACATGACATC-G-AAATTGAGATGA
1 GAGCTAGTGTAAGAC-ATGTCTGCGACATG-CATCAGCAAATT---ATGA
*
43613768 GTGCTAGTGTAAGACATG
1 GAGCTAGTGTAAGACATG
43613786 CATGCATCGG
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
45 4 0.07
46 14 0.25
47 17 0.30
48 21 0.38
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGCGACATGCATCAGCAAATTATGA
Found at i:43614517 original size:16 final size:16
Alignment explanation
Indices: 43614496--43614527 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43614486 AAGATGTATT
43614496 GTCATGGTTAAATGAA
1 GTCATGGTTAAATGAA
43614512 GTCATGGTTAAATGAA
1 GTCATGGTTAAATGAA
43614528 TGTCTATTTT
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:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (16 bp):
GTCATGGTTAAATGAA
Found at i:43620270 original size:26 final size:26
Alignment explanation
Indices: 43620241--43620290 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
43620231 TTGGGTGAAT
* * * *
43620241 TTTTTCTTCTTCTTCTTCTTTTTAAG
1 TTTTTATTCTGCTACTTATTTTTAAG
43620267 TTTTTATTCTGCTACTTATTTTTA
1 TTTTTATTCTGCTACTTATTTTTA
43620291 TTTCATTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.12, C:0.16, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTTTATTCTGCTACTTATTTTTAAG
Found at i:43621750 original size:91 final size:91
Alignment explanation
Indices: 43621616--43621930 Score: 425
Period size: 92 Copynumber: 3.4 Consensus size: 91
43621606 GGATGGCCAT
* * * * *
43621616 ATTGCATTATACCGCATGTACGTTAGCTACGCTACGTATCTTTGACTGAACTGGCAATTTACTAC
1 ATTGCACTGTACCACATGTACGTTAGCTACGCTACGTACCTTTGACTGAACTGGCAATTTACTGC
43621681 AACCTATCGATATAGCGGATTACCGC
66 AACCTATCGATATAGCGGATTACCGC
* *
43621707 ATTGCACTGTACCATATGTACGTTAGCTACGCTACGTACCTTTGACTGAACTGGCAGTTTTACTG
1 ATTGCACTGTACCACATGTACGTTAGCTACGCTACGTACCTTTGACTGAACTGGCA-ATTTACTG
* *
43621772 TAACCTATC-AGTATAGCGGATTACCGT
65 CAACCTATCGA-TATAGCGGATTACCGC
* * * * * * *
43621799 ATTGCACTGTACCGCATTTACGTTAGCTACGCTATGTACTTTTAACTGAACCGGCAATTTTATTG
1 ATTGCACTGTACCACATGTACGTTAGCTACGCTACGTACCTTTGACTGAACTGGCAA-TTTACTG
* *
43621864 CAACCTATCGGTATAGCTGATTACCGC
65 CAACCTATCGATATAGCGGATTACCGC
*
43621891 ATTGCACTGTACCACATGTACGTTAGCTACGCTATGTACC
1 ATTGCACTGTACCACATGTACGTTAGCTACGCTACGTACC
43621931 ACTATCTGAT
Statistics
Matches: 195, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
91 52 0.27
92 143 0.73
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (91 bp):
ATTGCACTGTACCACATGTACGTTAGCTACGCTACGTACCTTTGACTGAACTGGCAATTTACTGC
AACCTATCGATATAGCGGATTACCGC
Found at i:43621949 original size:184 final size:184
Alignment explanation
Indices: 43621601--43621956 Score: 493
Period size: 184 Copynumber: 1.9 Consensus size: 184
43621591 TAATATCGGC
* * *
43621601 ATAGCGGATGGCCATATTGCATTATACCGCATGTACGTTAGCTACGCTACGTATCTTTGACTGAA
1 ATAGCGGATGACCATATTGCACTATACCGCATGTACGTTAGCTACGCTACGTATCTTTAACTGAA
* *
43621666 CTGGCAATTTACTACAACCTATCGATATAGCGGATTACCGCATTGCACTGTACCATATGTACGTT
66 CCGGCAATTTACTACAACCTATCGATATAGCGGATTACCGCATTGCACTGTACCACATGTACGTT
** *
43621731 AGCTACGCTACGTACCTTTGACTGAACTGGCAGTTT-TACTGTAACCTATCAGT
131 AGCTACGCTACGTACCACTGACTGAACAGGCAGTTTATACTGTAACCTATCAGT
* * * * *
43621784 ATAGCGGATTACCGTATTGCACTGTACCGCATTTACGTTAGCTACGCTATGTA-CTTTTAACTGA
1 ATAGCGGATGACCATATTGCACTATACCGCATGTACGTTAGCTACGCTACGTATC-TTTAACTGA
* * * *
43621848 ACCGGCAATTTTATTGCAACCTATCGGTATAGCTGATTACCGCATTGCACTGTACCACATGTACG
65 ACCGGCAA-TTTACTACAACCTATCGATATAGCGGATTACCGCATTGCACTGTACCACATGTACG
* *
43621913 TTAGCTACGCTATGTACCACT-ATCTGATCAGGCAGTTTATACTG
129 TTAGCTACGCTACGTACCACTGA-CTGAACAGGCAGTTTATACTG
43621957 CATGTCTGTA
Statistics
Matches: 150, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
182 1 0.01
183 62 0.41
184 82 0.55
185 5 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (184 bp):
ATAGCGGATGACCATATTGCACTATACCGCATGTACGTTAGCTACGCTACGTATCTTTAACTGAA
CCGGCAATTTACTACAACCTATCGATATAGCGGATTACCGCATTGCACTGTACCACATGTACGTT
AGCTACGCTACGTACCACTGACTGAACAGGCAGTTTATACTGTAACCTATCAGT
Found at i:43629966 original size:17 final size:18
Alignment explanation
Indices: 43629929--43629972 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
43629919 AAGGCAAAGT
43629929 AATTTGGTATGAAATTTG
1 AATTTGGTATGAAATTTG
43629947 AATTTGGT-TGATAA-TTG
1 AATTTGGTATGA-AATTTG
43629964 AATTATGGT
1 AATT-TGGT
43629973 GTCGATGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (18 bp):
AATTTGGTATGAAATTTG
Found at i:43634563 original size:21 final size:21
Alignment explanation
Indices: 43634539--43634580 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
43634529 TATTTATCAC
43634539 AAAGACAAATGAAATAGTAAT
1 AAAGACAAATGAAATAGTAAT
43634560 AAAGACAAATGAAATAGTAAT
1 AAAGACAAATGAAATAGTAAT
43634581 TAAATATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (21 bp):
AAAGACAAATGAAATAGTAAT
Found at i:43638238 original size:90 final size:90
Alignment explanation
Indices: 43638080--43638245 Score: 212
Period size: 90 Copynumber: 1.8 Consensus size: 90
43638070 ATGCCAAAGC
* * * *
43638080 CATGTCCCTGACATGGTCTTACATGGGACTACATGTCGATGCCATATCCAAGATATGGTTCTATA
1 CATGTCCCAGACATGGTCTTACACGGGACTACATGTCGATGCCATATCCAAGACATGGTTCTACA
*
43638145 CGAAGTCTCATGTTGGTGCCGATGA
66 CGAAATCTCATGTTGGTGCCGATGA
* **
43638170 CATGTCCCAGACATGGTCTTACACGGGACCTCACAT-T-GATGCCATGTCTTAGACATGG-TCTT
1 CATGTCCCAGACATGGTCTTACACGGGA-CT-ACATGTCGATGCCATATCCAAGACATGGTTC-T
43638232 ACACGAAATCTCAT
63 ACACGAAATCTCAT
43638246 ATCAATGCCA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
89 2 0.03
90 56 0.86
91 3 0.05
92 4 0.06
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (90 bp):
CATGTCCCAGACATGGTCTTACACGGGACTACATGTCGATGCCATATCCAAGACATGGTTCTACA
CGAAATCTCATGTTGGTGCCGATGA
Found at i:43638254 original size:42 final size:42
Alignment explanation
Indices: 43638174--43638277 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 42
43638164 CGATGACATG
** ** *
43638174 TCCCAGACATGGTCTTACACGGGACCTCACATTGATGCCATG
1 TCCCAGACATGGTCTTACACGAAACCTCACATCAATGCCATA
** * *
43638216 TCTTAGACATGGTCTTACACGAAATCTCATATCAATGCCATA
1 TCCCAGACATGGTCTTACACGAAACCTCACATCAATGCCATA
*
43638258 TCCCAGATATGGTCTTACAC
1 TCCCAGACATGGTCTTACAC
43638278 TGGCATACAT
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAAACCTCACATCAATGCCATA
Found at i:43638323 original size:48 final size:48
Alignment explanation
Indices: 43638249--43638421 Score: 195
Period size: 48 Copynumber: 3.6 Consensus size: 48
43638239 ATCTCATATC
* * *
43638249 AATGCCATATCCCAGATATGGTCTTACACTGGCATACATAACAACGCA
1 AATGCCATGTCCCAGACATGGTCTTACACTGGCATACATATCAACGCA
* * *
43638297 AATGCCATGTCCCAGACATGGCCTTACACTGGCCCT-CATATCAACGCC
1 AATGCCATGTCCCAGACATGGTCTTACACTGG-CATACATATCAACGCA
* * * * * *
43638345 AATGCTATGTCCCACACATGATCTTACACTGGCACACATATCAACACT
1 AATGCCATGTCCCAGACATGGTCTTACACTGGCATACATATCAACGCA
* * *
43638393 GATGCCATGTCCTAGACGTGGTCTTACAC
1 AATGCCATGTCCCAGACATGGTCTTACAC
43638422 GGGATCTTAT
Statistics
Matches: 103, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.01
48 100 0.97
49 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (48 bp):
AATGCCATGTCCCAGACATGGTCTTACACTGGCATACATATCAACGCA
Found at i:43646840 original size:41 final size:42
Alignment explanation
Indices: 43646794--43646893 Score: 109
Period size: 41 Copynumber: 2.5 Consensus size: 42
43646784 TGACACATAT
** *
43646794 AACAAAATAATA-AGTAATACATACCATATTTAAATGTAATA
1 AACAAAATAATACACCAAAACATACCATATTTAAATGTAATA
* * *
43646835 AAC-AAATTATACCCCAAAAGATACCATATTTAAATGTAATA
1 AACAAAATAATACACCAAAACATACCATATTTAAATGTAATA
*
43646876 AAC-AAATTATAC-CCAAAA
1 AACAAAATAATACACCAAAA
43646894 GATTTGTTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
40 13 0.25
41 39 0.75
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (42 bp):
AACAAAATAATACACCAAAACATACCATATTTAAATGTAATA
Found at i:43647537 original size:42 final size:42
Alignment explanation
Indices: 43647431--43647543 Score: 145
Period size: 42 Copynumber: 2.7 Consensus size: 42
43647421 ATGCTATGTG
* * * * * *
43647431 CCAGACATGGTCTTACACGAGACCTCACATCCATGCCATGTC
1 CCAGACATGGTCTTACACGAAATCTCATATCAACGCCATATC
43647473 CCAGACATGGTCTTACACGAAATCTCATATCAACGCCATATC
1 CCAGACATGGTCTTACACGAAATCTCATATCAACGCCATATC
* * *
43647515 CCAGATATGGTCTTACATGAAATCACATA
1 CCAGACATGGTCTTACACGAAATCTCATA
43647544 CCGATGCTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (42 bp):
CCAGACATGGTCTTACACGAAATCTCATATCAACGCCATATC
Found at i:43647567 original size:132 final size:132
Alignment explanation
Indices: 43647334--43647577 Score: 285
Period size: 132 Copynumber: 1.8 Consensus size: 132
43647324 AATTCCAAAT
* ** * * *
43647334 CCATGTCCTCGACATGGTCTTACATGGGACTACATATCGATGCCATATCCCAGATATGGTCTTAT
1 CCATGTCCTCGACATGGTCTTACACGAAACTACATATCAACGCCATATCCCAGATATGGTCTTAC
* * ** * * * * *
43647399 ACGAAGCCTCATGTCGGTGCTTATGCTATGTGCCAGACATGGTCTTACACGAGACCTCACATCCA
66 ACGAAACCACATACCGATGCTGACGCCATATGCCAGACATGGTCTTACACGAGACCTCACATCCA
43647464 TG
131 TG
43647466 CCATGTCC-CAGACATGGTCTTACACGAAATCT-CATATCAACGCCATATCCCAGATATGGTCTT
1 CCATGTCCTC-GACATGGTCTTACACGAAA-CTACATATCAACGCCATATCCCAGATATGGTCTT
* * * *
43647529 ACATGAAATCACATACCGATGCTGACGCCATATTCCAGATATGGTCTTA
64 ACACGAAACCACATACCGATGCTGACGCCATATGCCAGACATGGTCTTA
43647578 TGCTGGCATA
Statistics
Matches: 91, Mismatches: 19, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
131 1 0.01
132 88 0.97
133 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (132 bp):
CCATGTCCTCGACATGGTCTTACACGAAACTACATATCAACGCCATATCCCAGATATGGTCTTAC
ACGAAACCACATACCGATGCTGACGCCATATGCCAGACATGGTCTTACACGAGACCTCACATCCA
TG
Found at i:43647652 original size:48 final size:48
Alignment explanation
Indices: 43647571--43647676 Score: 113
Period size: 48 Copynumber: 2.2 Consensus size: 48
43647561 TTCCAGATAT
** * * ** *
43647571 GGTCTTATGCTGGCATACATATCAGCGTGGATGCAATATCCCAAATAG
1 GGTCTTACACTGGCACACATATCAACGCCGATGCAATATCCCAAACAG
* * * *
43647619 GGTCTTACACTGGCACACATATCAACGCCGATGCCATGTCCCAGACAT
1 GGTCTTACACTGGCACACATATCAACGCCGATGCAATATCCCAAACAG
43647667 GGTCTTACAC
1 GGTCTTACAC
43647677 GGGATCTCAT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (48 bp):
GGTCTTACACTGGCACACATATCAACGCCGATGCAATATCCCAAACAG
Found at i:43662884 original size:11 final size:11
Alignment explanation
Indices: 43662868--43662892 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43662858 ATATGATATT
43662868 TTATTATTTTA
1 TTATTATTTTA
43662879 TTATTATTTTA
1 TTATTATTTTA
43662890 TTA
1 TTA
43662893 GTATATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:43666292 original size:28 final size:28
Alignment explanation
Indices: 43666252--43666306 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
43666242 ATTCATAACT
* *
43666252 ATTTTCAAACTTATTCAATGCTTATTAA
1 ATTTTCAAACTTAGTCAATACTTATTAA
43666280 ATTTTCAAACTTAGTCAATACTTATTA
1 ATTTTCAAACTTAGTCAATACTTATTA
43666307 GTGGCGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.04, T:0.45
Consensus pattern (28 bp):
ATTTTCAAACTTAGTCAATACTTATTAA
Found at i:43668822 original size:24 final size:25
Alignment explanation
Indices: 43668771--43668824 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
43668761 AAATCTAAGG
*
43668771 TTTCATTTTTCTTCCTCCTCTTTTT
1 TTTCATTTTTCTTCCTCCCCTTTTT
*
43668796 TTTC-TTTTTCTT-TTCCCCTTTTCT
1 TTTCATTTTTCTTCCTCCCCTTTT-T
43668820 TTTCA
1 TTTCA
43668825 ACAGAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 8 0.32
24 13 0.52
25 4 0.16
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTCATTTTTCTTCCTCCCCTTTTT
Found at i:43688720 original size:23 final size:23
Alignment explanation
Indices: 43688693--43688739 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
43688683 TTAAATTAAG
43688693 TAAAAAATAA-TATAAA-T-TTTA
1 TAAAAAA-AATTATAAAGTGTTTA
43688714 TAAAAAAAATTATAAAGTGTTTA
1 TAAAAAAAATTATAAAGTGTTTA
43688737 TAA
1 TAA
43688740 TTTGTTAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 2 0.09
21 13 0.57
22 1 0.04
23 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (23 bp):
TAAAAAAAATTATAAAGTGTTTA
Found at i:43689478 original size:20 final size:20
Alignment explanation
Indices: 43689414--43689478 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
43689404 AAATTAAATA
*
43689414 ATTGTATCTCTTGGATTAAT
1 ATTGTATCTCTTGGTTTAAT
* *
43689434 ATTGCAT-T-TT--TTCATAT
1 ATTGTATCTCTTGGTTTA-AT
43689451 AGTTGTATCTCTTGGTTTAAT
1 A-TTGTATCTCTTGGTTTAAT
43689472 ATTGTAT
1 ATTGTAT
43689479 TTTTTTTCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 12
0.67 0.10 0.24
Matches are distributed among these distances:
16 2 0.06
17 3 0.09
18 7 0.21
19 2 0.06
20 14 0.41
21 3 0.09
22 3 0.09
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.54
Consensus pattern (20 bp):
ATTGTATCTCTTGGTTTAAT
Found at i:43692828 original size:20 final size:20
Alignment explanation
Indices: 43692780--43692830 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
43692770 TAGAGTAGGA
*
43692780 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
* *
43692800 ATTTTGATACCTTAAGAAAT
1 ATATCGATACCTTAAGAAAT
*
43692820 GTATCGATACC
1 ATATCGATACC
43692831 GGACCGATAC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:43693178 original size:31 final size:31
Alignment explanation
Indices: 43693142--43693203 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
43693132 ATAGATTGCT
*
43693142 CCCCCT-TAATAAAAGTCATTTTAAATTTAAG
1 CCCCCTAT-ATAAAAATCATTTTAAATTTAAG
**
43693173 CCCCCTATATAAAAATCATTTTCTATTTAAG
1 CCCCCTATATAAAAATCATTTTAAATTTAAG
43693204 GCATAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (31 bp):
CCCCCTATATAAAAATCATTTTAAATTTAAG
Found at i:43706623 original size:25 final size:25
Alignment explanation
Indices: 43706595--43706647 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
43706585 GGTCAAACAA
43706595 AATACACCACAAAGGCATCATACAG
1 AATACACCACAAAGGCATCATACAG
** **
43706620 AATATGCTGCAAAGGCATCATACAG
1 AATACACCACAAAGGCATCATACAG
43706645 AAT
1 AAT
43706648 CATGTGTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.17
Consensus pattern (25 bp):
AATACACCACAAAGGCATCATACAG
Found at i:43709081 original size:28 final size:28
Alignment explanation
Indices: 43709050--43709261 Score: 212
Period size: 28 Copynumber: 7.6 Consensus size: 28
43709040 AGTCCCTGTG
*
43709050 GACTCTTTTTTGAAAGATAATTCATGCA
1 GACTCTTTCTTGAAAGATAATTCATGCA
*
43709078 GACTCTTTTTTGAAAGATAATTCATGCA
1 GACTCTTTCTTGAAAGATAATTCATGCA
* *
43709106 GACTCTTTCTTGAAAAATAATTCATGCG
1 GACTCTTTCTTGAAAGATAATTCATGCA
43709134 GACTCTTTCTTGAAAGATAATTCATGCA
1 GACTCTTTCTTGAAAGATAATTCATGCA
* * * * *
43709162 -AGCTCTTGCTTGAAAAATAATCCTTGTA
1 GA-CTCTTTCTTGAAAGATAATTCATGCA
* * * * **
43709190 AACTCTTGCTTGAAAGACAATTCAAGTG
1 GACTCTTTCTTGAAAGATAATTCATGCA
* * * * **
43709218 GACTCTTACTTGAATGATAGTCCATGTG
1 GACTCTTTCTTGAAAGATAATTCATGCA
43709246 GACTCTTTCTT-AAAGA
1 GACTCTTTCTTGAAAGA
43709262 ATAGTCCCTG
Statistics
Matches: 157, Mismatches: 25, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
27 5 0.03
28 151 0.96
29 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.36
Consensus pattern (28 bp):
GACTCTTTCTTGAAAGATAATTCATGCA
Found at i:43709268 original size:28 final size:29
Alignment explanation
Indices: 43709023--43709264 Score: 180
Period size: 28 Copynumber: 8.7 Consensus size: 29
43709013 GTTTATGCGA
* * * *
43709023 ACTCTTGCTTG-AAGAATAGTCCCTGTGG
1 ACTCTTTCTTGAAAGAATAATTCATGTGG
* **
43709051 ACTCTTTTTTGAAAG-ATAATTCATGCAG
1 ACTCTTTCTTGAAAGAATAATTCATGTGG
* **
43709079 ACTCTTTTTTGAAAG-ATAATTCATGCAG
1 ACTCTTTCTTGAAAGAATAATTCATGTGG
*
43709107 ACTCTTTCTTGAAA-AATAATTCATGCGG
1 ACTCTTTCTTGAAAGAATAATTCATGTGG
**
43709135 ACTCTTTCTTGAAAG-ATAATTCATG-CA
1 ACTCTTTCTTGAAAGAATAATTCATGTGG
* * * **
43709162 AGCTCTTGCTTGAAA-AATAATCCTTGTAA
1 A-CTCTTTCTTGAAAGAATAATTCATGTGG
* * *
43709191 ACTCTTGCTTGAAAG-ACAATTCAAGTGG
1 ACTCTTTCTTGAAAGAATAATTCATGTGG
* * * *
43709219 ACTCTTACTTGAATG-ATAGTCCATGTGG
1 ACTCTTTCTTGAAAGAATAATTCATGTGG
43709247 ACTCTTTCTT-AAAGAATA
1 ACTCTTTCTTGAAAGAATA
43709265 GTCCCTGCAT
Statistics
Matches: 177, Mismatches: 29, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
27 4 0.02
28 168 0.95
29 5 0.03
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (29 bp):
ACTCTTTCTTGAAAGAATAATTCATGTGG
Found at i:43719197 original size:27 final size:27
Alignment explanation
Indices: 43719118--43719224 Score: 115
Period size: 27 Copynumber: 4.0 Consensus size: 27
43719108 AAACATACAT
* * * *
43719118 CACATAGGGGTAAAACAGTCATCTTAA
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
43719145 CATAAAAGGGCAAAACAATCATTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
*
43719172 CACATAAGGGCAAAACAGTCACTTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * *
43719199 CTCATAAAGGCAAAATAGTCATTTTA
1 CACATAAGGGCAAAACAGTCATTTTA
43719225 TTAATTAAGA
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Done.