Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 21 of 132
Found at i:6124492 original size:6 final size:6
Alignment explanation
Indices: 6124473--6124521 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
6124463 TTTATTTATT
6124473 TTCTCC TTCT-C TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC
1 TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC TTCTCC
6124520 TT
1 TT
6124522 TCCCCAACAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
5 5 0.12
6 37 0.88
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
TTCTCC
Found at i:6136212 original size:47 final size:47
Alignment explanation
Indices: 6136143--6136286 Score: 261
Period size: 47 Copynumber: 3.1 Consensus size: 47
6136133 AGTTTACTAA
* *
6136143 CCATTGTCTTAAATCCGAGGTATTTATTGGTAGGGCTTGTGTAATAC
1 CCATTGTTTTAAATCCGAGGTATCTATTGGTAGGGCTTGTGTAATAC
6136190 CCATTGTTTTAAATCCGAGGTATCTATTGGTAGGGCTTGTGTAATAC
1 CCATTGTTTTAAATCCGAGGTATCTATTGGTAGGGCTTGTGTAATAC
*
6136237 CCATTGTTTTAAATCCGAGGTATCTATTGGTGGGGCTTGTGTAATAC
1 CCATTGTTTTAAATCCGAGGTATCTATTGGTAGGGCTTGTGTAATAC
6136284 CCA
1 CCA
6136287 AGAGCCTCTA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 94 1.00
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.38
Consensus pattern (47 bp):
CCATTGTTTTAAATCCGAGGTATCTATTGGTAGGGCTTGTGTAATAC
Found at i:6138939 original size:24 final size:24
Alignment explanation
Indices: 6138907--6138954 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
6138897 ACTGGTTAAC
6138907 CATTCTGGGCTCATAAGAGCTAAT
1 CATTCTGGGCTCATAAGAGCTAAT
* **
6138931 CATTTTGGGCTCATGTGAGCTAAT
1 CATTCTGGGCTCATAAGAGCTAAT
6138955 GTTGTTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (24 bp):
CATTCTGGGCTCATAAGAGCTAAT
Found at i:6143215 original size:97 final size:97
Alignment explanation
Indices: 6143049--6143242 Score: 352
Period size: 97 Copynumber: 2.0 Consensus size: 97
6143039 TACAAAACCA
* *
6143049 TTAACCCAAAAAAATTAAACCCAAATACAAGCTCAATTACACCCTAGCCTAAACCCTAAACTAAG
1 TTAACCCAAAAAAATTAAACCCAAATACAAGCTCAATTACACCCTAACCTAAACCCTAAACTAAA
6143114 CCCAAATAACCCAACACCTAAAAATCAGCAAG
66 CCCAAATAACCCAACACCTAAAAATCAGCAAG
* *
6143146 TTAACCCAAAAATATTAAACCCAAATACAAGCTCAATTATACCCTAACCTAAACCCTAAACTAAA
1 TTAACCCAAAAAAATTAAACCCAAATACAAGCTCAATTACACCCTAACCTAAACCCTAAACTAAA
6143211 CCCAAATAACCCAACACCTAAAAATCAGCAAG
66 CCCAAATAACCCAACACCTAAAAATCAGCAAG
6143243 CCCTAAATTA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 93 1.00
ACGTcount: A:0.49, C:0.30, G:0.04, T:0.16
Consensus pattern (97 bp):
TTAACCCAAAAAAATTAAACCCAAATACAAGCTCAATTACACCCTAACCTAAACCCTAAACTAAA
CCCAAATAACCCAACACCTAAAAATCAGCAAG
Found at i:6143707 original size:23 final size:23
Alignment explanation
Indices: 6143664--6143707 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6143654 CCAAAAACAG
* *
6143664 TATTAATTGTATATTAAATAATA
1 TATTAATTATATAATAAATAATA
*
6143687 TATTAATTATATAATAGATAA
1 TATTAATTATATAATAAATAA
6143708 AAAATAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (23 bp):
TATTAATTATATAATAAATAATA
Found at i:6144661 original size:30 final size:30
Alignment explanation
Indices: 6144626--6145045 Score: 266
Period size: 30 Copynumber: 14.2 Consensus size: 30
6144616 ATTTTACCCA
* *
6144626 AAAATTACATTTTAACCCCCAAACCTTTCC
1 AAAATCACATTTTAACCCCCAAACTTTTCC
* * * * * *
6144656 AAAATTATATTTTGACCCCCTAGCTTTTCT
1 AAAATCACATTTTAACCCCCAAACTTTTCC
* * * *
6144686 AAAATTACA-TTTAGACCCTCGAACATTTT-T
1 AAAATCACATTTTA-ACCCCCAAAC-TTTTCC
* * * *
6144716 AAAATCACATTTTGACACTCAAACTTTT-T
1 AAAATCACATTTTAACCCCCAAACTTTTCC
* * * * * *
6144745 GAAATTATA-TTTGACCCCTAAACTTTTCA
1 AAAATCACATTTTAACCCCCAAACTTTTCC
* *
6144774 AAAATCACATTTTAACCCCTAAACTTTTCT
1 AAAATCACATTTTAACCCCCAAACTTTTCC
* **
6144804 AAAATCAAATTTTAACTTCCAAACTTTTCC
1 AAAATCACATTTTAACCCCCAAACTTTTCC
* ** *
6144834 AAAATCAAATTTTAACTTCCAAACTTTCCC
1 AAAATCACATTTTAACCCCCAAACTTTTCC
* *
6144864 AAAATCACATTTTTAACTCACAAACTTTTCC
1 AAAATCACA-TTTTAACCCCCAAACTTTTCC
* * *
6144895 AAAATCACATTTTGA-TCCTAAACTTTTCC
1 AAAATCACATTTTAACCCCCAAACTTTTCC
* * *
6144924 AAAATTACATTTTAACCCTCACA-TTTTCCC
1 AAAATCACATTTTAACCCCCAAACTTTT-CC
* *** *
6144954 AAAATCACATTTT-AGCCTTTAACTTTCCC
1 AAAATCACATTTTAACCCCCAAACTTTTCC
** * *
6144983 AAAGCCACATTTTGA-CCCTAAAC-TTTCC
1 AAAATCACATTTTAACCCCCAAACTTTTCC
* * *
6145011 TAAAATCACATTTTTA-CCTCAAACTTTTCA
1 -AAAATCACATTTTAACCCCCAAACTTTTCC
6145041 AAAAT
1 AAAAT
6145046 TATATATTGA
Statistics
Matches: 315, Mismatches: 63, Indels: 25
0.78 0.16 0.06
Matches are distributed among these distances:
28 19 0.06
29 96 0.30
30 166 0.53
31 34 0.11
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATCACATTTTAACCCCCAAACTTTTCC
Found at i:6145253 original size:25 final size:25
Alignment explanation
Indices: 6145208--6145258 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
6145198 TATTTTATCT
* *
6145208 TATGCTTAATTTTTGTATTTACTTA
1 TATGCTTAATTTTTCTATTTAATTA
6145233 TATGCTTAATTTTTCTATTTAATTA
1 TATGCTTAATTTTTCTATTTAATTA
6145258 T
1 T
6145259 GCCAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (25 bp):
TATGCTTAATTTTTCTATTTAATTA
Found at i:6148289 original size:20 final size:21
Alignment explanation
Indices: 6148254--6148296 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
6148244 CAGCAAATAA
6148254 TTTTAAAATTATTAAAATTATT
1 TTTTAAAATTATTAAAATT-TT
6148276 TTTTAAAA-TA-TAAAATTTT
1 TTTTAAAATTATTAAAATTTT
6148295 TT
1 TT
6148297 AAATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 7 0.33
21 2 0.10
22 8 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAAAATTATTAAAATTTT
Found at i:6148295 original size:17 final size:17
Alignment explanation
Indices: 6148273--6148321 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
6148263 TATTAAAATT
6148273 ATTTTTTAAAATATAAA
1 ATTTTTTAAAATATAAA
6148290 ATTTTTT-AAAT-T---
1 ATTTTTTAAAATATAAA
6148302 ATTTTTTAAAATATAAA
1 ATTTTTTAAAATATAAA
6148319 ATT
1 ATT
6148322 ATTAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
14 1 0.04
15 1 0.04
16 4 0.15
17 10 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTTAAAATATAAA
Found at i:6148308 original size:30 final size:29
Alignment explanation
Indices: 6148257--6148354 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 29
6148247 CAAATAATTT
6148257 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
* *
6148286 TAAAATTTTTTAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
**
6148315 TAAAATTATTAAAA--A-AATTTAAAATAA
1 TAAAATTATTAAAATTATTTTTTAAAAT-A
6148342 TAAAATTATTAAA
1 TAAAATTATTAAA
6148355 TAATTTTAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
26 8 0.13
27 15 0.24
29 39 0.63
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:6148345 original size:18 final size:19
Alignment explanation
Indices: 6148309--6148346 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
6148299 ATTATTTTTT
*
6148309 AAAATATAAAATTATTAAA
1 AAAATATAAAATTAATAAA
*
6148328 AAAATTTAAAA-TAATAAA
1 AAAATATAAAATTAATAAA
6148346 A
1 A
6148347 TTATTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATATAAAATTAATAAA
Found at i:6148359 original size:26 final size:26
Alignment explanation
Indices: 6148306--6148363 Score: 89
Period size: 27 Copynumber: 2.2 Consensus size: 26
6148296 TAAATTATTT
6148306 TTTAAAATATAAAATTATTAAAAAAA
1 TTTAAAATATAAAATTATTAAAAAAA
* *
6148332 TTTAAAATAATAAAATTATTAAATAAT
1 TTTAAAAT-ATAAAATTATTAAAAAAA
6148359 TTTAA
1 TTTAA
6148364 TTTTCAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTAAAATATAAAATTATTAAAAAAA
Found at i:6149263 original size:17 final size:18
Alignment explanation
Indices: 6149217--6149263 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
6149207 AAATAATTTT
*
6149217 AATAATTTTATATTTAAAA
1 AATAAATTTA-ATTTAAAA
6149236 AATTAAA-TTAATTT-AAA
1 AA-TAAATTTAATTTAAAA
6149253 AATAAATTTAA
1 AATAAATTTAA
6149264 AAATTTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 4 0.16
17 9 0.36
18 4 0.16
19 5 0.20
20 3 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAATTTAATTTAAAA
Found at i:6156062 original size:14 final size:16
Alignment explanation
Indices: 6156033--6156067 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
6156023 CAATAACTTC
6156033 TAAAAAAATACAAAAT
1 TAAAAAAATACAAAAT
6156049 TAAAAAAA-AC-AAAT
1 TAAAAAAATACAAAAT
6156063 TAAAA
1 TAAAA
6156068 TGTAAAGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 2 0.11
16 8 0.42
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (16 bp):
TAAAAAAATACAAAAT
Found at i:6158054 original size:158 final size:158
Alignment explanation
Indices: 6157761--6158083 Score: 486
Period size: 158 Copynumber: 2.0 Consensus size: 158
6157751 ATTTTGGGAT
*
6157761 TTACATGTTATATGGGTGCTAGTCTTAGATGCCCTACCGATGGCTAAGATCCGGCATATGTTGCG
1 TTACATGTTATATGGGTGCTAGTCTTAGATGCCCTACCGATGGCTAAGATCCGACATATGTTGCG
* * * *
6157826 GATTCTCCACAGCTCGTGTGAGCAGTATCGTGTAGCTTAATATCTCAACCCACAGCTCATGTGAG
66 GATTCTCCACAACTCGTATGAGCAGCATCGTGTAGCTTAACATCTCAACCCACAGCTCATGTGAG
*
6157891 CAGACCCACTTT-ACAGCTCGTGTGAGCA
131 CAGACCCA-TTTCACAGCTCATGTGAGCA
* * * *
6157919 TTACATGTTATATGGGTGTTGGTCTTAGATGCCCTACCGATGGCTGAGATCTGACATATGTTGCG
1 TTACATGTTATATGGGTGCTAGTCTTAGATGCCCTACCGATGGCTAAGATCCGACATATGTTGCG
* ** *
6157984 GATTCTCCACAACTTGTATGAGCAGCATCGTGTAGCTTAACATCTTGACCCATAGCTCATGTGAG
66 GATTCTCCACAACTCGTATGAGCAGCATCGTGTAGCTTAACATCTCAACCCACAGCTCATGTGAG
*
6158049 TAGACCCATTTCACAGCTCATGTGAGCA
131 CAGACCCATTTCACAGCTCATGTGAGCA
*
6158077 CTACATG
1 TTACATG
6158084 ATACAAAAAA
Statistics
Matches: 148, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
157 3 0.02
158 145 0.98
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (158 bp):
TTACATGTTATATGGGTGCTAGTCTTAGATGCCCTACCGATGGCTAAGATCCGACATATGTTGCG
GATTCTCCACAACTCGTATGAGCAGCATCGTGTAGCTTAACATCTCAACCCACAGCTCATGTGAG
CAGACCCATTTCACAGCTCATGTGAGCA
Found at i:6172398 original size:15 final size:16
Alignment explanation
Indices: 6172380--6172412 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
6172370 TTGGTATGAA
*
6172380 TTATTTT-TTTAAAAT
1 TTATTTTATATAAAAT
6172395 TTATTTTATATAAAAT
1 TTATTTTATATAAAAT
6172411 TT
1 TT
6172413 CAAAATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATTTTATATAAAAT
Found at i:6175445 original size:23 final size:23
Alignment explanation
Indices: 6175419--6175539 Score: 156
Period size: 23 Copynumber: 5.2 Consensus size: 23
6175409 ACACTAGCGC
6175419 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
6175442 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGATTAGCACTGTGT-GT
6175465 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
6175490 GCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCTGATTAGCACTGT-GTGT
*
6175513 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
6175536 GCTC
1 GCTC
6175540 AGTACTTTGT
Statistics
Matches: 86, Mismatches: 6, Indels: 12
0.83 0.06 0.12
Matches are distributed among these distances:
22 4 0.05
23 62 0.72
24 1 0.01
25 16 0.19
26 3 0.03
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:6175488 original size:48 final size:46
Alignment explanation
Indices: 6175419--6175539 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
6175409 ACACTAGCGC
* *
6175419 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTC-TCGT
1 GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGT-GT
*
6175465 GCTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTG--ATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
*
6175513 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCTGATTAGCACTGTGTGTGCTC
6175540 AGTACTTTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.12, C:0.26, G:0.23, T:0.40
Consensus pattern (46 bp):
GCTCTCTGATTAGCACTGTGTGTGCTCTCCGATTAGCACGTCGTGT
Found at i:6175568 original size:39 final size:39
Alignment explanation
Indices: 6175504--6175578 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
6175494 TCCGATTAGC
*
6175504 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
6175543 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
6175579 TCTATTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:6175573 original size:23 final size:23
Alignment explanation
Indices: 6175538--6175631 Score: 77
Period size: 23 Copynumber: 4.0 Consensus size: 23
6175528 CTTTGTGTGC
*
6175538 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* * *
6175561 TTAGCACTTTGTGTGCTCTCTAT
1 TCAGCACTTTGTGTACTCTCTGT
6175584 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
6175609 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
6175631 T
1 T
6175632 TGTTCCGTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.28
23 20 0.35
25 8 0.14
26 7 0.12
27 4 0.07
ACGTcount: A:0.13, C:0.26, G:0.18, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:6176946 original size:23 final size:23
Alignment explanation
Indices: 6176920--6176979 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
6176910 TTCGTGCTAT
*
6176920 TTCGTTTATCGTTCACGAACATG
1 TTCGTTTAACGTTCACGAACATG
*
6176943 TTCGTTTAACGTTCGCGAACATG
1 TTCGTTTAACGTTCACGAACATG
*
6176966 TTCGTTTAATGTTC
1 TTCGTTTAACGTTC
6176980 GTTTAACGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (23 bp):
TTCGTTTAACGTTCACGAACATG
Found at i:6176979 original size:11 final size:11
Alignment explanation
Indices: 6176940--6176991 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
6176930 GTTCACGAAC
6176940 ATGTTCGTTTA
1 ATGTTCGTTTA
* ***
6176951 ACGTTCGCGAA
1 ATGTTCGTTTA
6176962 CATGTTCGTTTA
1 -ATGTTCGTTTA
6176974 ATGTTCGTTTA
1 ATGTTCGTTTA
*
6176985 ACGTTCG
1 ATGTTCG
6176992 CGAACATGTT
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
11 24 0.77
12 7 0.23
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.42
Consensus pattern (11 bp):
ATGTTCGTTTA
Found at i:6176983 original size:34 final size:34
Alignment explanation
Indices: 6176940--6177007 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
6176930 GTTCACGAAC
6176940 ATGTTCGTTTAACGTTCGCGAACATGTTCGTTTA
1 ATGTTCGTTTAACGTTCGCGAACATGTTCGTTTA
6176974 ATGTTCGTTTAACGTTCGCGAACATGTTCGTTTA
1 ATGTTCGTTTAACGTTCGCGAACATGTTCGTTTA
6177008 TGCATTCACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (34 bp):
ATGTTCGTTTAACGTTCGCGAACATGTTCGTTTA
Found at i:6176984 original size:57 final size:58
Alignment explanation
Indices: 6176920--6177031 Score: 172
Period size: 57 Copynumber: 1.9 Consensus size: 58
6176910 TTCGTGCTAT
* * *
6176920 TTCGTTTATCGTTCACGAACATGTTCGTTTA-ACGTTCGCGAACATGTTCGTTTAATG
1 TTCGTTTAACGTTCACGAACATGTTCGTTTATACATTCACGAACATGTTCGTTTAATG
* *
6176977 TTCGTTTAACGTTCGCGAACATGTTCGTTTATGCATTCACGAACATGTTCGTTTA
1 TTCGTTTAACGTTCACGAACATGTTCGTTTATACATTCACGAACATGTTCGTTTA
6177032 TGCGTTCGTG
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
57 29 0.59
58 20 0.41
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (58 bp):
TTCGTTTAACGTTCACGAACATGTTCGTTTATACATTCACGAACATGTTCGTTTAATG
Found at i:6177024 original size:24 final size:24
Alignment explanation
Indices: 6176974--6177074 Score: 150
Period size: 24 Copynumber: 4.2 Consensus size: 24
6176964 TGTTCGTTTA
*
6176974 ATGTTCGTTTA-ACGTTCGCGAAC
1 ATGTTCGTTTATGCGTTCGCGAAC
* *
6176997 ATGTTCGTTTATGCATTCACGAAC
1 ATGTTCGTTTATGCGTTCGCGAAC
*
6177021 ATGTTCGTTTATGCGTTCGTGAAC
1 ATGTTCGTTTATGCGTTCGCGAAC
*
6177045 ATGTTCGTTTATGTGTTCGCGAAC
1 ATGTTCGTTTATGCGTTCGCGAAC
6177069 ATGTTC
1 ATGTTC
6177075 ATTTTTAACT
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
23 11 0.16
24 58 0.84
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (24 bp):
ATGTTCGTTTATGCGTTCGCGAAC
Found at i:6178756 original size:23 final size:23
Alignment explanation
Indices: 6178706--6178762 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
6178696 GATGGGTCTA
* ** *
6178706 ATAAATGAGCTTATAAACGGGCT
1 ATAAATGAGCTAATAAACGAACC
*
6178729 TTAAATGAGCTAATAAACGAACC
1 ATAAATGAGCTAATAAACGAACC
*
6178752 ATAAACGAGCT
1 ATAAATGAGCT
6178763 TGTTCGTGAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.23
Consensus pattern (23 bp):
ATAAATGAGCTAATAAACGAACC
Found at i:6179034 original size:79 final size:78
Alignment explanation
Indices: 6178939--6179222 Score: 354
Period size: 79 Copynumber: 3.6 Consensus size: 78
6178929 CACCCTTAGG
* *
6178939 CACCCAGTGCTTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTTGGATTAACCAACGATGT
1 CACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTTGGATTAACCAAC-ATAT
6179004 CCGTCAAATCCT-A
65 CCGTCAAATCCTGA
* * * * * * *
6179017 GCACCCAGTGCCTAGCGGATAAACTGCGATTGTGAACACATCTCTAGTTAGATTAACCAACAATA
1 -CACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTTGGATTAACCAAC-ATA
*
6179082 TCTGTCAAATCCTGA
64 TCCGTCAAATCCTGA
* ** *
6179097 CACCCAGTGCCTAGCGGAGAAACCATAAATGTAAGCCCAGCTCTAGTTGGATTAACCAACATTAT
1 CACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTTGGATTAACCAACA-TAT
*
6179162 CCGTCAAATCTTGA
65 CCGTCAAATCCTGA
* * * *
6179176 CACCCAATGCCTAGCGGATAAACCGCAAATATGTGCCCAGCACTAGT
1 CACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGT
6179223 CAGTTAAACT
Statistics
Matches: 171, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
78 1 0.01
79 169 0.99
80 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (78 bp):
CACCCAGTGCCTAGCGGATAAACCGCAAATGTGAGCCCAGCTCTAGTTGGATTAACCAACATATC
CGTCAAATCCTGA
Found at i:6184893 original size:28 final size:28
Alignment explanation
Indices: 6184858--6184915 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
6184848 ATCTATGCAT
* *
6184858 ACTTTCTTAATCCTTTGACAATGCATAC
1 ACTTTCTTAACCCGTTGACAATGCATAC
*
6184886 ACTTTCTTAACCCGTTGATAATGCATAC
1 ACTTTCTTAACCCGTTGACAATGCATAC
6184914 AC
1 AC
6184916 AACTTGCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (28 bp):
ACTTTCTTAACCCGTTGACAATGCATAC
Found at i:6186234 original size:14 final size:14
Alignment explanation
Indices: 6186217--6186247 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6186207 ATATTCAAAC
*
6186217 AATAATAATAAAAT
1 AATAACAATAAAAT
6186231 AATAACAATAAAAT
1 AATAACAATAAAAT
6186245 AAT
1 AAT
6186248 GAAATGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAACAATAAAAT
Found at i:6186239 original size:31 final size:28
Alignment explanation
Indices: 6186165--6186240 Score: 73
Period size: 31 Copynumber: 2.6 Consensus size: 28
6186155 TCAATACCTT
* *
6186165 TAAAATAGTAACAAAATTAACAATAAAA
1 TAAAATAATAACAATATTAACAATAAAA
*
6186193 TAAAA-ATTTATACAATATTCAAACAATAATAA
1 TAAAATA-ATA-ACAATATT--AACAATAA-AA
6186225 TAAAATAATAACAATA
1 TAAAATAATAACAATA
6186241 AAATAATGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 1 0.03
28 7 0.18
29 7 0.18
31 14 0.36
32 9 0.23
33 1 0.03
ACGTcount: A:0.64, C:0.08, G:0.01, T:0.26
Consensus pattern (28 bp):
TAAAATAATAACAATATTAACAATAAAA
Found at i:6193186 original size:9 final size:9
Alignment explanation
Indices: 6193172--6193212 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
6193162 GTTAAATTTT
*
6193172 ATAATTTAA
1 ATAATTCAA
6193181 ATAATTCAA
1 ATAATTCAA
**
6193190 ATAATTTGA
1 ATAATTCAA
6193199 ATAATTCAA
1 ATAATTCAA
6193208 ATAAT
1 ATAAT
6193213 ATATTGATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (9 bp):
ATAATTCAA
Found at i:6193219 original size:21 final size:18
Alignment explanation
Indices: 6193172--6193212 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
6193162 GTTAAATTTT
*
6193172 ATAATTTAAATAATTCAA
1 ATAATTTGAATAATTCAA
6193190 ATAATTTGAATAATTCAA
1 ATAATTTGAATAATTCAA
6193208 ATAAT
1 ATAAT
6193213 ATATTGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (18 bp):
ATAATTTGAATAATTCAA
Found at i:6212768 original size:23 final size:24
Alignment explanation
Indices: 6212717--6212768 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
6212707 TTGATAACAG
*
6212717 TAATTATAATTCTATTAAATTTGT
1 TAATTAAAATTCTATTAAATTTGT
*
6212741 T-ATTAAAATTTTA-TAAATATT-T
1 TAATTAAAATTCTATTAAAT-TTGT
6212763 TAATTA
1 TAATTA
6212769 TGTTGAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 7 0.29
23 16 0.67
24 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TAATTAAAATTCTATTAAATTTGT
Found at i:6217032 original size:18 final size:16
Alignment explanation
Indices: 6217009--6217043 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
6216999 ATATATATTT
6217009 ATTTATTTATTTATTTTA
1 ATTTATTT-TTT-TTTTA
6217027 ATTTATTTTTTTTTTA
1 ATTTATTTTTTTTTTA
6217043 A
1 A
6217044 AAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTATTTTTTTTTTA
Found at i:6217225 original size:21 final size:21
Alignment explanation
Indices: 6217186--6217225 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
6217176 TGTATATTTA
**
6217186 ATTTTAAATTTAATTTAATCT
1 ATTTTAAATTTAAAATAATCT
*
6217207 ATTTTTAATTTAAAATAAT
1 ATTTTAAATTTAAAATAAT
6217226 ATTATTTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTTTAAATTTAAAATAATCT
Found at i:6217237 original size:21 final size:21
Alignment explanation
Indices: 6217187--6217237 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
6217177 GTATATTTAA
**
6217187 TTTTAAATTTAATTTAATCTAT
1 TTTTAAATTTAAAATAA-CTAT
6217209 TTTT-AATTTAAAATAA-TAT
1 TTTTAAATTTAAAATAACTAT
6217228 TATTTAAATT
1 T-TTTAAATT
6217238 ATTGAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 4 0.16
20 3 0.12
21 14 0.56
22 4 0.16
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAAATTTAAAATAACTAT
Found at i:6217245 original size:19 final size:20
Alignment explanation
Indices: 6217223--6217275 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
6217213 AATTTAAAAT
* *
6217223 AATATTATTTAAAT-TATTG
1 AATATAATTAAAATGTATTG
6217242 AATATAATTAAAATGTATT-
1 AATATAATTAAAATGTATTG
*
6217261 AATTACAATTAAAAT
1 AA-TATAATTAAAAT
6217276 ATTTAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (20 bp):
AATATAATTAAAATGTATTG
Found at i:6225971 original size:18 final size:18
Alignment explanation
Indices: 6225939--6225986 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
6225929 GATTATATAT
* *
6225939 AAAATTA-TTAAAAAACTC
1 AAAATTATTTTAAAAA-TA
6225957 AAAATTATTTTAAAAATA
1 AAAATTATTTTAAAAATA
6225975 AAAAGTTATTTT
1 AAAA-TTATTTT
6225987 TCTTTTGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAATTATTTTAAAAATA
Found at i:6230398 original size:15 final size:17
Alignment explanation
Indices: 6230378--6230413 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6230368 ATAAATTATT
6230378 AAAAATA-T-ATATTTA
1 AAAAATATTAATATTTA
6230393 AAAAATATTAATATTTA
1 AAAAATATTAATATTTA
6230410 AAAA
1 AAAA
6230414 TTGCTTGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.37
16 1 0.05
17 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AAAAATATTAATATTTA
Found at i:6231567 original size:16 final size:17
Alignment explanation
Indices: 6231546--6231579 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6231536 AATTATATAA
6231546 ATAAAT-ATTAAAAAAT
1 ATAAATAATTAAAAAAT
*
6231562 ATAAATAATTTAAAAAT
1 ATAAATAATTAAAAAAT
6231579 A
1 A
6231580 AAAAATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAATAATTAAAAAAT
Found at i:6231575 original size:29 final size:29
Alignment explanation
Indices: 6231515--6231575 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
6231505 CTATTTAGAA
* * * *
6231515 AAATAAAGATTTAAATATCTAAATTATAT
1 AAATAAAGATTAAAAAATATAAATAATAT
* *
6231544 AAATAAATATTAAAAAATATAAATAATTT
1 AAATAAAGATTAAAAAATATAAATAATAT
6231573 AAA
1 AAA
6231576 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (29 bp):
AAATAAAGATTAAAAAATATAAATAATAT
Found at i:6231579 original size:17 final size:20
Alignment explanation
Indices: 6231526--6231577 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
6231516 AATAAAGATT
**
6231526 TAAATATCTAAATTATATAAA
1 TAAATAT-TAAAAAATATAAA
6231547 TAAATATTAAAAAATATAAA
1 TAAATATTAAAAAATATAAA
6231567 T-AAT-TTAAAAA
1 TAAATATTAAAAA
6231578 TAAAAAATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 7 0.24
19 3 0.10
20 12 0.41
21 7 0.24
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAATATTAAAAAATATAAA
Found at i:6234725 original size:17 final size:15
Alignment explanation
Indices: 6234685--6234716 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6234675 GGTATTCATT
*
6234685 TATTTTTATATAAAA
1 TATTTTTTTATAAAA
6234700 TATTTTTTTATAAAA
1 TATTTTTTTATAAAA
6234715 TA
1 TA
6234717 ATTCTTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTTTTTATAAAA
Found at i:6238781 original size:51 final size:51
Alignment explanation
Indices: 6238662--6238843 Score: 240
Period size: 51 Copynumber: 3.5 Consensus size: 51
6238652 TTTCATTTAA
* * ** * *
6238662 TACTCACGATGACA-TATAATCATCGGACCTCTTATTCTGTATAGGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TTAATCCATAAAGG-ATTCATT
* * * *
6238715 TACTCACGATAACACTGAGTCATCGGACCTTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
6238766 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
6238817 TACTCACGATGACACTTAGTCATCGGA
1 TACTCACGATGACACTTAGTCATCGGA
6238844 TTCATTTACT
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
51 80 0.70
52 8 0.07
53 25 0.22
54 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATT
Found at i:6238850 original size:33 final size:33
Alignment explanation
Indices: 6238808--6238873 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
6238798 AATCCATAAA
6238808 GGATTCATTTACTCACGATGACACTTAGTCATC
1 GGATTCATTTACTCACGATGACACTTAGTCATC
6238841 GGATTCATTTACTCACGATGACACTTAGTCATC
1 GGATTCATTTACTCACGATGACACTTAGTCATC
6238874 AGATCTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (33 bp):
GGATTCATTTACTCACGATGACACTTAGTCATC
Found at i:6252654 original size:11 final size:11
Alignment explanation
Indices: 6252632--6252661 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
6252622 AAACTAACCT
6252632 AATTTATTGTAA
1 AATTT-TTGTAA
6252644 AATTTTTGTAA
1 AATTTTTGTAA
6252655 AATTTTT
1 AATTTTT
6252662 AATTTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (11 bp):
AATTTTTGTAA
Found at i:6255259 original size:13 final size:11
Alignment explanation
Indices: 6255233--6255257 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6255223 AATTATGTGT
6255233 AAATTATATAA
1 AAATTATATAA
6255244 AAATTATATAA
1 AAATTATATAA
6255255 AAA
1 AAA
6255258 AAATTTATTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATTATATAA
Found at i:6257914 original size:20 final size:21
Alignment explanation
Indices: 6257880--6257926 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
6257870 AAATTAAGAG
*
6257880 TTATTTTTTTAATTTAATGTA
1 TTATTTATTTAATTTAATGTA
* *
6257901 TTATTTATTT-ATTTATTTTA
1 TTATTTATTTAATTTAATGTA
6257921 TTATTT
1 TTATTT
6257927 TTCACATGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TTATTTATTTAATTTAATGTA
Found at i:6259542 original size:2 final size:2
Alignment explanation
Indices: 6259524--6259579 Score: 62
Period size: 2 Copynumber: 28.0 Consensus size: 2
6259514 AATCATTCAC
* *
6259524 AT AT AT AC AT AT TT AT AT AT AT ACT -T AT A- ACT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT
6259566 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
6259580 TGTCTATAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
1 2 0.04
2 42 0.91
3 2 0.04
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6260075 original size:6 final size:6
Alignment explanation
Indices: 6260038--6260092 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
6260028 GTTTAAATTG
* * *
6260038 ATTTAA ATTT-A TTTTAA AATTAA ATTTGTAA ATTTAA ATTT-A CTTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA A-TT-TAA ATTTAA ATTTAA ATTTAA
6260086 ATTTAA A
1 ATTTAA A
6260093 CCTTGACCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
5 8 0.21
6 24 0.62
7 3 0.08
8 4 0.10
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:6261000 original size:24 final size:24
Alignment explanation
Indices: 6260956--6261001 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
6260946 AACAACACCT
*
6260956 AAAATAGAACAGATTTGAAGAACG
1 AAAATAAAACAGATTTGAAGAACG
*
6260980 AAAATAAAAGCAG-TTTTAAGAA
1 AAAATAAAA-CAGATTTGAAGAA
6261002 AAGGGAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.57, C:0.07, G:0.17, T:0.20
Consensus pattern (24 bp):
AAAATAAAACAGATTTGAAGAACG
Found at i:6261933 original size:29 final size:28
Alignment explanation
Indices: 6261880--6262132 Score: 215
Period size: 29 Copynumber: 8.7 Consensus size: 28
6261870 CCCTGAAGGT
* *
6261880 CCCTAAATTATCTAAAAATTACATTTTTA
1 CCCTAAATT-TCCAAAAATTCCATTTTTA
6261909 CCCCTAAATTTCCAAAAATTCCATTTTTGA
1 -CCCTAAATTTCCAAAAATTCCATTTTT-A
* * * *
6261939 CCTCAAAACTTCTAAAAATTACATTTTTA
1 CC-CTAAATTTCCAAAAATTCCATTTTTA
* *
6261968 CCCTCAAACTTCCAAAAATTCCATTTTGA
1 CCCT-AAATTTCCAAAAATTCCATTTTTA
* * * *
6261997 CCCAAAACTTCCAAAAATTACTTTTTTA
1 CCCTAAATTTCCAAAAATTCCATTTTTA
6262025 CCCTCAAATTTCCAAAAATTCCATTTTTGA
1 CCCT-AAATTTCCAAAAATTCCATTTTT-A
6262055 CCCTGAAACTTT-CAAAAATTACCA-TTTTA
1 CCCT-AAA-TTTCCAAAAATT-CCATTTTTA
* * * *
6262084 CCCCTAGATGTCCTAAAACTCCATTTTTGA
1 -CCCTAAATTTCCAAAAATTCCATTTTT-A
*
6262114 CCCGAAACTTT-CAAAAATT
1 CCCTAAA-TTTCCAAAAATT
6262133 ATCATTTTCC
Statistics
Matches: 183, Mismatches: 28, Indels: 25
0.78 0.12 0.11
Matches are distributed among these distances:
28 30 0.16
29 89 0.49
30 58 0.32
31 6 0.03
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.35
Consensus pattern (28 bp):
CCCTAAATTTCCAAAAATTCCATTTTTA
Found at i:6261982 original size:59 final size:58
Alignment explanation
Indices: 6261890--6262140 Score: 307
Period size: 59 Copynumber: 4.3 Consensus size: 58
6261880 CCCTAAATTA
6261890 TCTAAAAATTACATTTTTACCCCTAAATTTCCAAAAATTCCATTTTTGACCTCAAAACT
1 TCTAAAAATTACATTTTTACCCCTAAATTTCCAAAAATTCCATTTTTGACC-CAAAACT
*
6261949 TCTAAAAATTACATTTTTA-CCCTCAAACTTCCAAAAATTCCA-TTTTGACCCAAAACT
1 TCTAAAAATTACATTTTTACCCCT-AAATTTCCAAAAATTCCATTTTTGACCCAAAACT
* * *
6262006 TCCAAAAATTACTTTTTTA-CCCTCAAATTTCCAAAAATTCCATTTTTGACCCTGAAACT
1 TCTAAAAATTACATTTTTACCCCT-AAATTTCCAAAAATTCCATTTTTGACCC-AAAACT
* * * * *
6262065 T-TCAAAAATTACCA-TTTTACCCCTAGATGTCCTAAAACTCCATTTTTGACCCGAAACT
1 TCT-AAAAATTA-CATTTTTACCCCTAAATTTCCAAAAATTCCATTTTTGACCCAAAACT
6262123 T-TCAAAAATTATCATTTT
1 TCT-AAAAATTA-CATTTT
6262141 CCCCCCGAAT
Statistics
Matches: 173, Mismatches: 12, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
57 46 0.27
58 40 0.23
59 82 0.47
60 5 0.03
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (58 bp):
TCTAAAAATTACATTTTTACCCCTAAATTTCCAAAAATTCCATTTTTGACCCAAAACT
Found at i:6262107 original size:116 final size:117
Alignment explanation
Indices: 6261893--6262140 Score: 321
Period size: 116 Copynumber: 2.1 Consensus size: 117
6261883 TAAATTATCT
6261893 AAAAATTACATTTTTACCCCTAAATTTCCAAAAATTCCATTTTTGACCTCAAAACTTCTAAAAAT
1 AAAAATTACATTTTTACCCCTAAATTTCCAAAAATTCCATTTTTGACCTCAAAACTTCTAAAAAT
*
6261958 TACATTTTTACCCTCAAACTTCCAAAAATTCCA-TTTTGACCCAAAACTTCC
66 TACATTTTTACCCTCAAACTTCCAAAAACTCCATTTTTGACCCAAAACTTCC
* *
6262009 AAAAATTACTTTTTTA-CCCTCAAATTTCCAAAAATTCCATTTTTGACC-CTGAAACTT-TCAAA
1 AAAAATTACATTTTTACCCCT-AAATTTCCAAAAATTCCATTTTTGACCTC-AAAACTTCT-AAA
* * * *
6262071 AATTACCA-TTTTACCC-CTAGA-TGTCCTAAAACTCCATTTTTGACCCGAAACTTTC
63 AATTA-CATTTTTACCCTC-AAACT-TCCAAAAACTCCATTTTTGACCCAAAACTTCC
6262126 AAAAATTATCATTTT
1 AAAAATTA-CATTTT
6262141 CCCCCCGAAT
Statistics
Matches: 116, Mismatches: 8, Indels: 14
0.84 0.06 0.10
Matches are distributed among these distances:
115 8 0.07
116 77 0.66
117 26 0.22
118 5 0.04
ACGTcount: A:0.36, C:0.25, G:0.03, T:0.36
Consensus pattern (117 bp):
AAAAATTACATTTTTACCCCTAAATTTCCAAAAATTCCATTTTTGACCTCAAAACTTCTAAAAAT
TACATTTTTACCCTCAAACTTCCAAAAACTCCATTTTTGACCCAAAACTTCC
Found at i:6263890 original size:19 final size:20
Alignment explanation
Indices: 6263853--6263892 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
6263843 TAGGGTTTCC
*
6263853 CGAAAAAGTCAACTGGTCGA
1 CGAAAAAGTCAACTAGTCGA
6263873 CGAAAAAGTCAAC-AGTCGA
1 CGAAAAAGTCAACTAGTCGA
6263892 C
1 C
6263893 TGTCAATTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.42, C:0.23, G:0.23, T:0.12
Consensus pattern (20 bp):
CGAAAAAGTCAACTAGTCGA
Found at i:6274721 original size:13 final size:13
Alignment explanation
Indices: 6274695--6274759 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 13
6274685 GGTTTAGTAT
*
6274695 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
6274708 TGCTTTTTAAAAG
1 TGCTTTTGAAAAG
* *
6274721 TGATTTGGAAAAG
1 TGCTTTTGAAAAG
** *
6274734 TAATTTTAAAAAG
1 TGCTTTTGAAAAG
*
6274747 TACTTTT-AAAAG
1 TGCTTTTGAAAAG
6274759 T
1 T
6274760 TTGGTTTAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
12 6 0.14
13 37 0.86
ACGTcount: A:0.37, C:0.05, G:0.18, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:6274884 original size:19 final size:19
Alignment explanation
Indices: 6274842--6274882 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
6274832 ATGTGTTATA
*
6274842 AAATAATAAATAAATATTT
1 AAATAATAAATAAATAGTT
*
6274861 AAATAATAATTAAATTAGTT
1 AAATAATAAATAAA-TAGTT
6274881 AA
1 AA
6274883 TATTATGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAATAATAAATAAATAGTT
Found at i:6279882 original size:19 final size:20
Alignment explanation
Indices: 6279845--6279886 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
6279835 ATTTGGAGAA
*
6279845 AAGTATTTCAAAGGTGAAAT
1 AAGTATTTCAAAGGAGAAAT
*
6279865 AAGTATTT-GAAGGAGAAAT
1 AAGTATTTCAAAGGAGAAAT
6279884 AAG
1 AAG
6279887 AATAGTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (20 bp):
AAGTATTTCAAAGGAGAAAT
Found at i:6280341 original size:17 final size:17
Alignment explanation
Indices: 6280321--6280380 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
6280311 TTTTTCCCTT
6280321 TTTTTTTCTTTTTTCTC
1 TTTTTTTCTTTTTTCTC
*
6280338 TTTTGTTC--TTTTC-C
1 TTTTTTTCTTTTTTCTC
6280352 TTTTCTTTCTTTTTTCTC
1 TTTT-TTTCTTTTTTCTC
* *
6280370 CTTGTTTCTTT
1 TTTTTTTCTTT
6280381 CCCTTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
14 5 0.14
15 8 0.23
17 19 0.54
18 3 0.09
ACGTcount: A:0.00, C:0.20, G:0.03, T:0.77
Consensus pattern (17 bp):
TTTTTTTCTTTTTTCTC
Found at i:6280355 original size:22 final size:22
Alignment explanation
Indices: 6280319--6280368 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
6280309 TTTTTTTCCC
*
6280319 TTTTT-TTTT-CTTTTTTCTCT
1 TTTTTCTTTTCCTTTTCTCTCT
*
6280339 TTTGTTCTTTTCCTTTTCTTTCT
1 TTT-TTCTTTTCCTTTTCTCTCT
6280362 TTTTTCT
1 TTTTTCT
6280369 CCTTGTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 3 0.12
21 2 0.08
22 8 0.32
23 12 0.48
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTTCTTTTCCTTTTCTCTCT
Found at i:6280358 original size:19 final size:18
Alignment explanation
Indices: 6280308--6280372 Score: 50
Period size: 19 Copynumber: 3.7 Consensus size: 18
6280298 TGAATGAGAG
*
6280308 TTTT-TTTTCCCTTT-TT
1 TTTTCTTTTCCTTTTCTT
*
6280324 TTTTCTTTT--TTCTCTT
1 TTTTCTTTTCCTTTTCTT
6280340 TTGTTCTTTTCCTTTTCTT
1 TT-TTCTTTTCCTTTTCTT
6280359 TCTTT-TTTCTCCTT
1 T-TTTCTTT-TCCTT
6280373 GTTTCTTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
15 2 0.05
16 8 0.21
17 11 0.28
18 3 0.08
19 14 0.36
20 1 0.03
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTTCTTTTCCTTTTCTT
Found at i:6280375 original size:31 final size:33
Alignment explanation
Indices: 6280313--6280387 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
6280303 GAGAGTTTTT
* *
6280313 TTTCCCTTTTTTTTTCTTTTTTCTCTTTTG-TTC
1 TTTCCC-TTTTCTTTCTTTTTTCTCTCTTGTTTC
*
6280346 TTTTCCTTTTCTTTCTTTTTTCTC-CTTGTTTC
1 TTTCCCTTTTCTTTCTTTTTTCTCTCTTGTTTC
6280378 TTTCCCTTTT
1 TTTCCCTTTT
6280388 ATTTTTGCTG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 3 0.08
32 29 0.78
33 5 0.14
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (33 bp):
TTTCCCTTTTCTTTCTTTTTTCTCTCTTGTTTC
Found at i:6280607 original size:91 final size:90
Alignment explanation
Indices: 6280444--6280617 Score: 226
Period size: 91 Copynumber: 1.9 Consensus size: 90
6280434 GAAACTTTAA
* * * * *
6280444 CTTTTTGATGCATTTTGAAAGTTCAAGCACTAAATTGAGTGTCAAAAAAAAAGCAGTGACTTAAT
1 CTTTTTGATGCATTTTGAAAGTTCAAGCACCAAATTGAATGTAAAAAAAAAAGAAGAGACTTAAT
6280509 TGCTTTTTTTGAAAAAATTTAAGAAT
66 TG-TTTTTTTGAAAAAATTTAAGAAT
* * * * *
6280535 CTTTTTGATGCATTTTGACAGTTCAAGTACCCAATTGAATG-AAAAAAAAAATAAGAG-TTTAAT
1 CTTTTTGATGCATTTTGAAAGTTCAAGCACCAAATTGAATGTAAAAAAAAAAGAAGAGACTTAAT
6280598 TGATTTTTTTGAAAAAATTT
66 TG-TTTTTTTGAAAAAATTT
6280618 GAAAGCTTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
89 24 0.33
90 12 0.17
91 36 0.50
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (90 bp):
CTTTTTGATGCATTTTGAAAGTTCAAGCACCAAATTGAATGTAAAAAAAAAAGAAGAGACTTAAT
TGTTTTTTTGAAAAAATTTAAGAAT
Found at i:6281888 original size:2 final size:2
Alignment explanation
Indices: 6281881--6281916 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
6281871 AACATAACAA
6281881 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
6281917 GGAAAAGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6282135 original size:2 final size:2
Alignment explanation
Indices: 6282128--6282178 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
6282118 CAATCTTTTC
6282128 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
6282170 TA TA TA TA T
1 TA TA TA TA T
6282179 GCTATTTGTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6282545 original size:13 final size:13
Alignment explanation
Indices: 6282527--6282571 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
6282517 CGCTATATTA
6282527 AATTTTTTTATAT
1 AATTTTTTTATAT
6282540 AATTTTTTTGA-A-
1 AATTTTTTT-ATAT
*
6282552 AATATTTTTATAT
1 AATTTTTTTATAT
6282565 AATTTTT
1 AATTTTT
6282572 AAATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.04
12 9 0.33
13 16 0.59
14 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (13 bp):
AATTTTTTTATAT
Found at i:6282581 original size:25 final size:24
Alignment explanation
Indices: 6282526--6282579 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
6282516 CCGCTATATT
* *
6282526 AAATTTTTTTATATAATTTTTTTGA
1 AAATATTTTTATATAA-TTTTTTAA
6282551 AAATATTTTTATATAA-TTTTTAA
1 AAATATTTTTATATAATTTTTTAA
*
6282574 ATATAT
1 AAATAT
6282580 ATAATACATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
25 15 0.58
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
AAATATTTTTATATAATTTTTTAA
Found at i:6282728 original size:18 final size:18
Alignment explanation
Indices: 6282705--6282740 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
6282695 AAATGCCTCT
6282705 AAAATAATAATAAA-ATTA
1 AAAATAA-AATAAATATTA
6282723 AAAATAAAATAAATATTA
1 AAAATAAAATAAATATTA
6282741 TATAATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATAAAATAAATATTA
Found at i:6283570 original size:21 final size:21
Alignment explanation
Indices: 6283521--6283561 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6283511 AAATCTTATT
6283521 ATTA-ATAATTTTATAATATA
1 ATTATATAATTTTATAATATA
*
6283541 ATTATATAATTTTATTATATA
1 ATTATATAATTTTATAATATA
6283562 TTTTCATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTATATAATTTTATAATATA
Found at i:6291675 original size:3 final size:3
Alignment explanation
Indices: 6291651--6291694 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
6291641 AATAATATTT
*
6291651 TAA TAA AAA TAAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
6291695 TTTTGAAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:6300039 original size:201 final size:201
Alignment explanation
Indices: 6299694--6300095 Score: 795
Period size: 201 Copynumber: 2.0 Consensus size: 201
6299684 AAACATGAGC
6299694 ACAGTCAATGTGCCTATAACCAGCCTGCGAAACAATGGCATTATCAGAATACTCGATAGTTTTAA
1 ACAGTCAATGTGCCTATAACCAGCCTGCGAAACAATGGCATTATCAGAATACTCGATAGTTTTAA
6299759 GAGTAAGTCCCCTCACGGTATAAACTTGCAAAATAAGATTCATATCAAACTGAACTATATATGGG
66 GAGTAAGTCCCCTCACGGTATAAACTTGCAAAATAAGATTCATATCAAACTGAACTATATATGGG
6299824 GAAAGTTAAATCTTCTACTGCTGCAAAATGCCTCCCAAATCTGTTATGCCGGGAAAGTTAGAAGC
131 GAAAGTTAAATCTTCTACTGCTGCAAAATGCCTCCCAAATCTGTTATGCCGGGAAAGTTAGAAGC
6299889 AACTTT
196 AACTTT
*
6299895 ACAGTCAATGTGCCTATAACCAGTCTGCGAAACAATGGCATTATCAGAATACTCGATAGTTTTAA
1 ACAGTCAATGTGCCTATAACCAGCCTGCGAAACAATGGCATTATCAGAATACTCGATAGTTTTAA
6299960 GAGTAAGTCCCCTCACGGTATAAACTTGCAAAATAAGATTCATATCAAACTGAACTATATATGGG
66 GAGTAAGTCCCCTCACGGTATAAACTTGCAAAATAAGATTCATATCAAACTGAACTATATATGGG
6300025 GAAAGTTAAATCTTCTACTGCTGCAAAATGCCTCCCAAATCTGTTATGCCGGGAAAGTTAGAAGC
131 GAAAGTTAAATCTTCTACTGCTGCAAAATGCCTCCCAAATCTGTTATGCCGGGAAAGTTAGAAGC
6300090 AACTTT
196 AACTTT
6300096 CTGGGCTGAA
Statistics
Matches: 200, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 200 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.27
Consensus pattern (201 bp):
ACAGTCAATGTGCCTATAACCAGCCTGCGAAACAATGGCATTATCAGAATACTCGATAGTTTTAA
GAGTAAGTCCCCTCACGGTATAAACTTGCAAAATAAGATTCATATCAAACTGAACTATATATGGG
GAAAGTTAAATCTTCTACTGCTGCAAAATGCCTCCCAAATCTGTTATGCCGGGAAAGTTAGAAGC
AACTTT
Found at i:6300793 original size:19 final size:19
Alignment explanation
Indices: 6300765--6300812 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
6300755 TCCTTCTGGA
6300765 GACT-AGTTGGAGCTAACG
1 GACTGAGTTGGAGCTAACG
6300783 GACTGAGTTGGAGCTAACG
1 GACTGAGTTGGAGCTAACG
*
6300802 GACTGGGTTGG
1 GACTGAGTTGG
6300813 TATGGTCCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 4 0.14
19 24 0.86
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.23
Consensus pattern (19 bp):
GACTGAGTTGGAGCTAACG
Found at i:6301494 original size:34 final size:34
Alignment explanation
Indices: 6301456--6301523 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
6301446 CATCCCCTTT
6301456 TTACTCTTTTTTCCCCCTCACCACAAACAGATTC
1 TTACTCTTTTTTCCCCCTCACCACAAACAGATTC
6301490 TTACTCTTTTTTCCCCCTCACCACAAACAGATTC
1 TTACTCTTTTTTCCCCCTCACCACAAACAGATTC
6301524 GCTTTTCTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.38, G:0.03, T:0.35
Consensus pattern (34 bp):
TTACTCTTTTTTCCCCCTCACCACAAACAGATTC
Found at i:6305372 original size:7 final size:7
Alignment explanation
Indices: 6305360--6305395 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
6305350 TGGTGATCAC
6305360 ACGGTGG
1 ACGGTGG
6305367 ACGGTGG
1 ACGGTGG
6305374 ACGGTGG
1 ACGGTGG
6305381 ACGGTGG
1 ACGGTGG
6305388 ACGGTGG
1 ACGGTGG
6305395 A
1 A
6305396 GATTCGTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.56, T:0.14
Consensus pattern (7 bp):
ACGGTGG
Found at i:6306468 original size:4 final size:4
Alignment explanation
Indices: 6306459--6306484 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
6306449 CCAATTCCAT
6306459 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
6306485 ATTATTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:6306526 original size:4 final size:4
Alignment explanation
Indices: 6306519--6306559 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
6306509 TATAAAATAA
6306519 TATT TATTT TATT T-TAT TATT TATT TATT TATT TA-T TATT T
1 TATT TA-TT TATT TAT-T TATT TATT TATT TATT TATT TATT T
6306560 TATGAATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 4 0.12
4 24 0.73
5 5 0.15
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:6306531 original size:67 final size:68
Alignment explanation
Indices: 6306457--6306622 Score: 225
Period size: 67 Copynumber: 2.4 Consensus size: 68
6306447 ACCCAATTCC
6306457 ATTTTA-TTTATTTATTTATTTATTTATTATTATTTTTATGAACATAAATAAAT-A-TAAAATAA
1 ATTTTATTTTA-TTATTTATTTATTTATTATTA-TTTTATGAACATAAATAAATAAGTAAAATAA
*
6306519 TATTT
64 TATTA
*
6306524 ATTTTATTTTATTATTTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAATA
1 ATTTTATTTTATTATTTATTTATTTA-TTATTATTTTATGAACATAAATAAAT-AA-GTAAAATA
6306589 ATATTA
63 ATATTA
*
6306595 ATTTTGTTTTATTATTTA-TTA-TTATTAT
1 ATTTTATTTTATTATTTATTTATTTATTAT
6306623 AAATAAATAA
Statistics
Matches: 90, Mismatches: 3, Indels: 11
0.87 0.03 0.11
Matches are distributed among these distances:
67 40 0.44
68 14 0.16
69 4 0.04
70 3 0.03
71 29 0.32
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (68 bp):
ATTTTATTTTATTATTTATTTATTTATTATTATTTTATGAACATAAATAAATAAGTAAAATAATA
TTA
Found at i:6306580 original size:71 final size:71
Alignment explanation
Indices: 6306457--6306614 Score: 223
Period size: 71 Copynumber: 2.2 Consensus size: 71
6306447 ACCCAATTCC
*
6306457 ATTTTATTTATTTATTTATTTATTTATTATTATTTTTATGAACATAAATAAATATAAAATAATAT
1 ATTTTA-TTATTTATTTATTTATTTATTATTATTTATATGAACATAAATAAATATAAAATAATAT
*
6306522 TTATTTT
65 TAATTTT
*
6306529 ATTTTATTATTTATTTATTTATTTATTATT-TTATGAATAT-AA-ATAAATAAATGTAAAATAAT
1 ATTTTATTATTTATTTATTTATTTATTATTATT-T--ATATGAACATAAATAAATATAAAATAAT
6306591 ATTAATTTT
63 ATTAATTTT
*
6306600 GTTTTATTATTTATT
1 ATTTTATTATTTATT
6306615 ATTATTATAA
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
70 2 0.03
71 66 0.84
72 8 0.10
73 3 0.04
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.58
Consensus pattern (71 bp):
ATTTTATTATTTATTTATTTATTTATTATTATTTATATGAACATAAATAAATATAAAATAATATT
AATTTT
Found at i:6308987 original size:67 final size:62
Alignment explanation
Indices: 6308900--6309051 Score: 216
Period size: 67 Copynumber: 2.4 Consensus size: 62
6308890 TTATTTATTT
6308900 ATAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAT-A
1 ATAATAATAAATAAATAATAAAACAAAATTAATATTATTTT--A--TATTTA-TTATATTCATAA
6308964 AA
61 AA
* *
6308966 ATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTTATATTTATTATGTTCATAAAA
1 ATAAT-AATAAATAAATAATAAAACAAAATTAATATTATTTTATATTTATTATATTCATAAAA
6309029 ATAATAATAAATAAATAAATAAA
1 ATAATAATAAATAAAT-AATAAA
6309052 TAAAAATAAT
Statistics
Matches: 81, Mismatches: 2, Indels: 9
0.88 0.02 0.10
Matches are distributed among these distances:
62 20 0.25
63 20 0.25
65 1 0.01
66 5 0.06
67 35 0.43
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (62 bp):
ATAATAATAAATAAATAATAAAACAAAATTAATATTATTTTATATTTATTATATTCATAAAA
Found at i:6309013 original size:63 final size:64
Alignment explanation
Indices: 6308900--6309062 Score: 226
Period size: 62 Copynumber: 2.5 Consensus size: 64
6308890 TTATTTATTT
*
6308900 ATAATAATAAATAAATAATAAAACAAAATTAATATTATTTTACATTTATTTATTTATATTCAT-A
1 ATAATAATAAATAAATAATAAAATAAAATTAATATTATTTTA-A-TTATTTA-TTATATTCATAA
6308964 AA
63 AA
*
6308966 ATAATAAATAAATAAATAATAAAATAAAATTAATATTATTTT-A-TATTTATTATGTTCATAAAA
1 ATAAT-AATAAATAAATAATAAAATAAAATTAATATTATTTTAATTATTTATTATATTCATAAAA
*
6309029 ATAATAATAAATAAATAA-ATAAATAAAAATAATA
1 ATAATAATAAATAAATAATA-AAATAAAATTAATA
6309063 AGAAAAATGG
Statistics
Matches: 91, Mismatches: 3, Indels: 10
0.88 0.03 0.10
Matches are distributed among these distances:
61 1 0.01
62 35 0.38
63 14 0.15
65 1 0.01
66 5 0.05
67 35 0.38
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (64 bp):
ATAATAATAAATAAATAATAAAATAAAATTAATATTATTTTAATTATTTATTATATTCATAAAA
Found at i:6309070 original size:22 final size:22
Alignment explanation
Indices: 6309027--6309070 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
6309017 ATGTTCATAA
* *
6309027 AAATAATAATAAATAAATAAAT
1 AAATAAAAATAAATAAAAAAAT
6309049 AAATAAAAAT-AATAAGAAAAAT
1 AAATAAAAATAAATAA-AAAAAT
6309071 GGAATTGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATAAAAATAAATAAAAAAAT
Found at i:6309713 original size:80 final size:80
Alignment explanation
Indices: 6309668--6310521 Score: 1478
Period size: 80 Copynumber: 10.7 Consensus size: 80
6309658 CCTTTGGTTA
* * * *
6309668 GGGTAAAAGATTGGAT-TTCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATTTCTTTAA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
6309732 TCTGCCCCATGATCG
66 TCTGCCCCATGATCG
* *
6309747 GGGTAAAAGATCGGATGGTTTTCAATCTTGCCTTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
*
6309812 TCTGTCCCATGATCG
66 TCTGCCCCATGATCG
* *
6309827 GGGTAGAAGATCGGATGGTCTTCAATCTTGCCCTCTTGTTAGGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
6309892 TCTGCCCCATGATCG
66 TCTGCCCCATGATCG
6309907 GGGTAAAAGATCGGATGGTCTTCAATCTT-CCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
6309971 TCTGCCCCATGATCG
66 TCTGCCCCATGATCG
*
6309986 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGAATTTCTTCAA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
6310051 TCTGCCCCATGATCG
66 TCTGCCCCATGATCG
*
6310066 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
* *
6310131 TCTGTCCCATGATCA
66 TCTGCCCCATGATCG
6310146 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
*
6310211 TCTACCCCATGATCG
66 TCTGCCCCATGATCG
* * *
6310226 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGCTTAGGGTAAAATATTGGATTTCTTTAA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
*
6310291 TTTGCCCCATGATCG
66 TCTGCCCCATGATCG
*
6310306 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGCTTAGGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
6310371 TCTGCCCCATGATCG
66 TCTGCCCCATGATCG
*
6310386 GGGTAAAAGATCGGATGGTCTTCAATCTTACCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
*
6310451 TTTGCCCCATGATCG
66 TCTGCCCCATGATCG
* * *
6310466 GGGTAAAAGATCTGATGGTTTTCAATCTTGCCCTCTGGTGAGGGTAAAAGATTGGA
1 GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGA
6310522 GGTTGTAATT
Statistics
Matches: 735, Mismatches: 38, Indels: 3
0.95 0.05 0.00
Matches are distributed among these distances:
79 93 0.13
80 642 0.87
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (80 bp):
GGGTAAAAGATCGGATGGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATTTCTTCAA
TCTGCCCCATGATCG
Found at i:6310661 original size:50 final size:50
Alignment explanation
Indices: 6310607--6310752 Score: 211
Period size: 50 Copynumber: 2.9 Consensus size: 50
6310597 TTTAACTGAC
* * * * *
6310607 TGAGATTTGCCATTACAGCTTCATTCTGCCCCTCTACAGCTTTAGGTGTA
1 TGAGATTTGCCATTGCAGTTTCAATCTGCACCTCCACAGCTTTAGGTGTA
* *
6310657 TGAGATTTGACATTGCGGTTTCAATCTGCACCTCCACAGCTTTAGGTGTA
1 TGAGATTTGCCATTGCAGTTTCAATCTGCACCTCCACAGCTTTAGGTGTA
* *
6310707 TGAGATTTACCATTGCAGTTTCAATCTGCACCTCCACCGCTTTAGG
1 TGAGATTTGCCATTGCAGTTTCAATCTGCACCTCCACAGCTTTAGG
6310753 GGTAAAAGAT
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.34
Consensus pattern (50 bp):
TGAGATTTGCCATTGCAGTTTCAATCTGCACCTCCACAGCTTTAGGTGTA
Found at i:6311687 original size:6 final size:6
Alignment explanation
Indices: 6311676--6311755 Score: 58
Period size: 6 Copynumber: 12.7 Consensus size: 6
6311666 CGACCTCCCA
* *
6311676 TTTTTC TTTTTC TTTTCTTC TTTTTC CTTTTC TTTGTCTT TTTTTC TTTTTTC
1 TTTTTC TTTTTC -TTT-TTC TTTTTC TTTTTC TTT-T-TC TTTTTC -TTTTTC
6311729 TTTTT- TTAATTT- TTTTTC TTTTT- TTTT
1 TTTTTC TT--TTTC TTTTTC TTTTTC TTTT
6311756 GAAATTTCTT
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
5 9 0.15
6 27 0.44
7 19 0.31
8 7 0.11
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:6311698 original size:8 final size:7
Alignment explanation
Indices: 6311676--6311734 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
6311666 CGACCTCCCA
6311676 TTTTTC-
1 TTTTTCT
6311682 TTTTTCT
1 TTTTTCT
6311689 TTTCTTC-
1 TTT-TTCT
6311696 TTTTTC-
1 TTTTTCT
*
6311702 CTTTTC-
1 TTTTTCT
*
6311708 TTTGTCTT
1 TTTTTC-T
6311716 TTTTTCT
1 TTTTTCT
6311723 TTTTTCT
1 TTTTTCT
6311730 TTTTT
1 TTTTT
6311735 TAATTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
6 18 0.40
7 19 0.42
8 8 0.18
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:6311705 original size:15 final size:14
Alignment explanation
Indices: 6311679--6311753 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 14
6311669 CCTCCCATTT
6311679 TTCTTTTTCTTTTC
1 TTCTTTTTCTTTTC
*
6311693 TTCTTTTTC-CTT-
1 TTCTTTTTCTTTTC
* *
6311705 TTCTTTGTCTTTTT
1 TTCTTTTTCTTTTC
*
6311719 TTCTTTTTTCTTTTT
1 TTC-TTTTTCTTTTC
**
6311734 TTAATTTT-TTTTC
1 TTCTTTTTCTTTTC
6311747 TT-TTTTT
1 TTCTTTTT
6311754 TTGAAATTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
12 12 0.24
13 10 0.20
14 16 0.32
15 12 0.24
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.81
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:6311705 original size:21 final size:20
Alignment explanation
Indices: 6311676--6311732 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
6311666 CGACCTCCCA
6311676 TTTTT-CTTTTTCTTTTCTT
1 TTTTTCCTTTTTCTTTTCTT
6311695 CTTTTTCC-TTTTCTTTGTCTT
1 -TTTTTCCTTTTTCTTT-TCTT
*
6311716 TTTTTCTTTTTTCTTTT
1 TTTTTCCTTTTTCTTTT
6311733 TTTAATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 20 0.61
21 13 0.39
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTTCCTTTTTCTTTTCTT
Found at i:6311735 original size:8 final size:8
Alignment explanation
Indices: 6311682--6311753 Score: 58
Period size: 8 Copynumber: 8.6 Consensus size: 8
6311672 CCCATTTTTC
6311682 TTTTTCTT
1 TTTTTCTT
*
6311690 TTCTTCTT
1 TTTTTCTT
6311698 TTTCCTT-TT
1 TTT--TTCTT
*
6311707 CTTTGTCTT
1 -TTTTTCTT
6311716 TTTTTC-T
1 TTTTTCTT
6311723 TTTTTCTT
1 TTTTTCTT
*
6311731 TTTTTAATTT
1 TTTTT--CTT
6311741 TTTTTCTT
1 TTTTTCTT
6311749 TTTTT
1 TTTTT
6311754 TTGAAATTTC
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
7 7 0.14
8 28 0.55
9 4 0.08
10 12 0.24
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:6311742 original size:25 final size:26
Alignment explanation
Indices: 6311677--6311752 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 26
6311667 GACCTCCCAT
* * *
6311677 TTTTCTTTTTCTTTTCTTCTTTTTCC
1 TTTTCTTTATCTTTTTTTCTTTTTTC
*
6311703 TTTTCTTTGTCTTTTTTTCTTTTTTC
1 TTTTCTTTATCTTTTTTTCTTTTTTC
6311729 TTTT-TTTAAT-TTTTTTTCTTTTTT
1 TTTTCTTT-ATCTTTTTTTCTTTTTT
6311753 TTTGAAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
25 17 0.38
26 28 0.62
ACGTcount: A:0.03, C:0.14, G:0.01, T:0.82
Consensus pattern (26 bp):
TTTTCTTTATCTTTTTTTCTTTTTTC
Found at i:6311749 original size:33 final size:36
Alignment explanation
Indices: 6311688--6311753 Score: 93
Period size: 33 Copynumber: 1.9 Consensus size: 36
6311678 TTTCTTTTTC
**
6311688 TTTTCTTCTTTTTCCTTTTCTTTGTCTTTTTTTCTT
1 TTTTCTTCTTTTTAATTTTCTTTGTCTTTTTTTCTT
6311724 TTTTCTT-TTTTTAATTTT-TTT-TCTTTTTTT
1 TTTTCTTCTTTTTAATTTTCTTTGTCTTTTTTT
6311754 TTGAAATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 9 0.32
34 3 0.11
35 9 0.32
36 7 0.25
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.82
Consensus pattern (36 bp):
TTTTCTTCTTTTTAATTTTCTTTGTCTTTTTTTCTT
Found at i:6316795 original size:63 final size:65
Alignment explanation
Indices: 6316714--6316870 Score: 230
Period size: 67 Copynumber: 2.4 Consensus size: 65
6316704 GGATTTATTG
*
6316714 TTATTATTTTTATTTATTTATTATTATTTTTATGAACATAAATAAAT-A-TAAAATAATATTAAT
1 TTATT-TTATTATTTATTTATTATTATTTTTATGAACATAAATAAATAAGTAAAATAATATTAAT
6316777 T
65 T
*
6316778 TTATTTTATTATTTATTTATTTATTA-TTTTATGAATATAAATAAATAAATGTAAAATAATATTA
1 TTATTTTATTATTTATTTA-TTATTATTTTTATGAACATAAATAAAT-AA-GTAAAATAATATTA
6316842 ATT
63 ATT
*
6316845 TTGTTTTATTATTTATTTATTATTAT
1 TTATTTTATTATTTATTTATTATTAT
6316871 AAATTATACC
Statistics
Matches: 84, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
63 32 0.38
64 11 0.13
65 1 0.01
66 6 0.07
67 34 0.40
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (65 bp):
TTATTTTATTATTTATTTATTATTATTTTTATGAACATAAATAAATAAGTAAAATAATATTAATT
Found at i:6320620 original size:40 final size:40
Alignment explanation
Indices: 6320547--6320625 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
6320537 GAAACGCTGT
* * *
6320547 TGTGTGGTGGAGAAAATGAAAGGGAGGATGATGAAAAGTA
1 TGTGTGGTGGAGAAAATGAAAGGAAAGAGGATGAAAAGTA
* *
6320587 TGTGTGGTGGAGAAAATG-CAGTGAAAGAGGATGAGAAGT
1 TGTGTGGTGGAGAAAATGAAAG-GAAAGAGGATGAAAAGT
6320626 GGCTGTTTCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.38, C:0.01, G:0.41, T:0.20
Consensus pattern (40 bp):
TGTGTGGTGGAGAAAATGAAAGGAAAGAGGATGAAAAGTA
Found at i:6322747 original size:7 final size:7
Alignment explanation
Indices: 6322735--6322759 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
6322725 TTTTAGGGAC
6322735 TAAATTT
1 TAAATTT
6322742 TAAATTT
1 TAAATTT
6322749 TAAATTT
1 TAAATTT
6322756 TAAA
1 TAAA
6322760 AGAGTATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TAAATTT
Found at i:6334327 original size:16 final size:16
Alignment explanation
Indices: 6334315--6334359 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
6334305 GATTACAGCC
6334315 CTATTCCATTACAACT
1 CTATTCCATTACAACT
* *
6334331 CTATTTCATTATAACT
1 CTATTCCATTACAACT
6334347 CTATTCCATTACA
1 CTATTCCATTACA
6334360 GCGAACCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (16 bp):
CTATTCCATTACAACT
Found at i:6347101 original size:15 final size:16
Alignment explanation
Indices: 6347072--6347102 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6347062 ATCAATTTGA
6347072 TAAAATGTATAAATTT
1 TAAAATGTATAAATTT
6347088 TAAAATGT-TAAATTT
1 TAAAATGTATAAATTT
6347103 GTTATTAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TAAAATGTATAAATTT
Found at i:6371131 original size:71 final size:71
Alignment explanation
Indices: 6371011--6371163 Score: 216
Period size: 71 Copynumber: 2.2 Consensus size: 71
6371001 CATCTCTTGG
* * * * *
6371011 TTCTACCGATATAACCAATACTTCTATCAGTAGAGCAAATTCCAAAGAGCAAAGAAGTTGTGGCC
1 TTCTACCGATATAACCAAGACTTCTATCAGTAGAACAAACTCCAAAGAGCAAAGAAATTGTGACC
6371076 TGGGAC
66 TGGGAC
** * * *
6371082 TTCTACCGATATAATTAAGACTTTTATCGGTAGAACAAACTCCAGAGAGCAAAGAAATTGTGACC
1 TTCTACCGATATAACCAAGACTTCTATCAGTAGAACAAACTCCAAAGAGCAAAGAAATTGTGACC
6371147 TGGGAC
66 TGGGAC
6371153 TTCTACCGATA
1 TTCTACCGATA
6371164 CCTAGAAGGC
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (71 bp):
TTCTACCGATATAACCAAGACTTCTATCAGTAGAACAAACTCCAAAGAGCAAAGAAATTGTGACC
TGGGAC
Found at i:6373635 original size:21 final size:21
Alignment explanation
Indices: 6373595--6373636 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6373585 ATATAAAAAT
*
6373595 AAATTTATATTTTATCTCTAA
1 AAATTTATATTTAATCTCTAA
6373616 AAATTTATAGTTTAAT-TCTAA
1 AAATTTATA-TTTAATCTCTAA
6373637 CCCTCCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATTTATATTTAATCTCTAA
Found at i:6377349 original size:18 final size:18
Alignment explanation
Indices: 6377326--6377360 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6377316 GAAAATTTGT
6377326 AAAAATCAT-AATCAAATA
1 AAAAAT-ATAAATCAAATA
6377344 AAAAATATAAATCAAAT
1 AAAAATATAAATCAAAT
6377361 GTAAATGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAAATATAAATCAAATA
Found at i:6381927 original size:28 final size:28
Alignment explanation
Indices: 6381874--6382218 Score: 131
Period size: 29 Copynumber: 11.9 Consensus size: 28
6381864 ATAAACGATG
* *
6381874 AAATCGGGGTGAAAAATGGGACTTTTGGAT
1 AAATCGGGG-GTAAAAT-GGAATTTTGGAT
*
6381904 -ACTCGGGGGTAAAATGGTAATTTT-GAT
1 AAATCGGGGGTAAAATGG-AATTTTGGAT
*
6381931 AAAATCGGGGTTAAAATGGAATTTTGGA-
1 -AAATCGGGGGTAAAATGGAATTTTGGAT
* ** *
6381959 AAGTTTAGGGGTAAAATGGTGATTTTCGG-T
1 AA-ATCGGGGGTAAAATGG-AATTTT-GGAT
* * *
6381989 GAAATCGAGGTTAAAAATGGAATTTT--AA
1 -AAATCGGGGGT-AAAATGGAATTTTGGAT
6382017 AAGATTCGGGGGTAAAATGGTAATTTTTGG-T
1 AA-A-TCGGGGGTAAAATGG-AA-TTTTGGAT
* * *
6382048 GAAATTGGGGTTAAAATGGAATTTTAGA-
1 -AAATCGGGGGTAAAATGGAATTTTGGAT
* *
6382076 AGATTCGAGGGTAAAATGGTAATTTTCGG-T
1 A-AATCGGGGGTAAAATGG-AATTTT-GGAT
* * *
6382106 GAAATCGGGGTTAAAAATGG-ATTTT-TAA
1 -AAATCGGGGGT-AAAATGGAATTTTGGAT
* *
6382134 AAGATTCAGGGGT-AAATGGTAATTTTTGAT
1 AA-A-TCGGGGGTAAAATGG-AATTTTGGAT
* * *
6382164 GAAATCGGGGTTAAAAATGGATTTTTAGA-
1 -AAATCGGGGGT-AAAATGGAATTTTGGAT
* *
6382193 AGATTCAGGGGTAAAATGGTAATTTT
1 A-AATCGGGGGTAAAATGG-AATTTT
6382219 TAGAAGTTTT
Statistics
Matches: 234, Mismatches: 45, Indels: 73
0.66 0.13 0.21
Matches are distributed among these distances:
27 18 0.08
28 64 0.27
29 79 0.34
30 45 0.19
31 26 0.11
32 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (28 bp):
AAATCGGGGGTAAAATGGAATTTTGGAT
Found at i:6381939 original size:58 final size:58
Alignment explanation
Indices: 6381872--6382218 Score: 418
Period size: 58 Copynumber: 6.0 Consensus size: 58
6381862 TGATAAACGA
* * * * * * *
6381872 TGAAATCGGGGTGAAAAATGGGACTTTT-GGATACTCGGGGGTAAAATGGTAATTTTGA
1 TGAAATCGGGGTTAAAAAT-GGAATTTTAGAAGATTCAGGGGTAAAATGGTAATTTTGG
* * * *
6381930 TAAAATCGGGGTT-AAAATGGAATTTTGGAA-AGTTTAGGGGTAAAATGGTGATTTTCGG
1 TGAAATCGGGGTTAAAAATGGAATTTTAGAAGA-TTCAGGGGTAAAATGGTAATTTT-GG
* * *
6381988 TGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGGGGTAAAATGGTAA-TTTTGG
*
6382047 TGAAATTGGGGTT-AAAATGGAATTTTAGAAGATTC-GAGGGTAAAATGGTAATTTTCGG
1 TGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAG-GGGTAAAATGGTAATTTT-GG
* * *
6382105 TGAAATCGGGGTTAAAAATGGATTTTTAAAAGATTCAGGGGT-AAATGGTAATTTTTGA
1 TGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGGGGTAAAATGGTAA-TTTTGG
*
6382163 TGAAATCGGGGTTAAAAATGGATTTTTAGAAGATTCAGGGGTAAAATGGTAATTTT
1 TGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGGGGTAAAATGGTAATTTT
6382219 TAGAAGTTTT
Statistics
Matches: 253, Mismatches: 24, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
56 8 0.03
57 31 0.12
58 127 0.50
59 81 0.32
60 6 0.02
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.33
Consensus pattern (58 bp):
TGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGGGGTAAAATGGTAATTTTGG
Found at i:6382029 original size:59 final size:59
Alignment explanation
Indices: 6381909--6382218 Score: 425
Period size: 58 Copynumber: 5.3 Consensus size: 59
6381899 TGGATACTCG
* * * *
6381909 GGGGTAAAATGGTAATTTT-GATAAAATCGGGGTT-AAAATGGAATTTTGGAAAG-TTTA
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTT-AAAAGATTCA
* * *
6381966 GGGGTAAAATGGTGATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGATTCG
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
* * *
6382025 GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTT-AAAATGGAATTTTAGAAGATTC-
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
*
6382082 GAGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGATTTTTAAAAGATTCA
1 G-GGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
* * * *
6382142 GGGGT-AAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGATTTTTAGAAGATTCA
1 GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
6382200 GGGGTAAAATGGTAATTTT
1 GGGGTAAAATGGTAATTTT
6382219 TAGAAGTTTT
Statistics
Matches: 227, Mismatches: 19, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
57 19 0.08
58 124 0.55
59 83 0.37
60 1 0.00
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAAAAGATTCA
Found at i:6382101 original size:117 final size:117
Alignment explanation
Indices: 6381906--6382218 Score: 472
Period size: 117 Copynumber: 2.7 Consensus size: 117
6381896 TTTTGGATAC
* * * *
6381906 TCGGGGGTAAAATGGTAA-TTTTGATAAAATCGGGGTTAAAATGGAATTTTGGAAAGTTTAG-GG
1 TCGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAATGGAATTTTAG-AAGATTCGAGG
*
6381969 GTAAAATGGTGATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGAT
65 GTAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGAT
* *
6382022 TCGGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAATGGAATTTTAGAAGATTCGAGGG
1 TCGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAATGGAATTTTAGAAGATTCGAGGG
* *
6382087 TAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGATTTTTAAAAGAT
66 TAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGAT
* *
6382139 TCAGGGGT-AAATGGTAATTTTTGATGAAATCGGGGTTAAAAATGGATTTTTAGAAGATTC-AGG
1 TCGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTT-AAAATGGAATTTTAGAAGATTCGA-G
6382202 GGTAAAATGGTAATTTT
64 GGTAAAATGGTAATTTT
6382219 TAGAAGTTTT
Statistics
Matches: 180, Mismatches: 13, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
116 52 0.29
117 128 0.71
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (117 bp):
TCGGGGGTAAAATGGTAATTTTTGATGAAATCGGGGTTAAAATGGAATTTTAGAAGATTCGAGGG
TAAAATGGTAATTTTCGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAGAT
Found at i:6382233 original size:29 final size:28
Alignment explanation
Indices: 6382002--6382224 Score: 122
Period size: 30 Copynumber: 7.6 Consensus size: 28
6381992 ATCGAGGTTA
* * *
6382002 AAAATGGAATTTTAAAAGATTCGGGGGT
1 AAAATGGATTTTTAGAAGATTCAGGGGT
*
6382030 AAAATGGTAATTTTTGGTGAA-ATT--GGGGTT
1 AAAATGG--ATTTTT--AGAAGATTCAGGGG-T
*
6382060 AAAATGGAATTTTAGAAGATTC-GAGGGT
1 AAAATGGATTTTTAGAAGATTCAG-GGGT
* * ** *
6382088 AAAATGGTAATTTTCGGTGAAATC-GGGGTT
1 AAAATGG-ATTTTTAGAAG-ATTCAGGGG-T
*
6382118 AAAAATGGATTTTTAAAAGATTCAGGGGT
1 -AAAATGGATTTTTAGAAGATTCAGGGGT
6382147 -AAATGGTAATTTTTGATGAA-A-TC-GGGGTT
1 AAAATGG--ATTTTT-A-GAAGATTCAGGGG-T
6382176 AAAAATGGATTTTTAGAAGATTCAGGGGT
1 -AAAATGGATTTTTAGAAGATTCAGGGGT
6382205 AAAATGGTAATTTTTAGAAG
1 AAAATGG--ATTTTTAGAAG
6382225 TTTTAGGGTC
Statistics
Matches: 154, Mismatches: 16, Indels: 48
0.71 0.07 0.22
Matches are distributed among these distances:
26 3 0.02
27 12 0.08
28 34 0.22
29 40 0.26
30 45 0.29
31 18 0.12
32 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (28 bp):
AAAATGGATTTTTAGAAGATTCAGGGGT
Found at i:6382240 original size:30 final size:30
Alignment explanation
Indices: 6382002--6382224 Score: 153
Period size: 29 Copynumber: 7.7 Consensus size: 30
6381992 ATCGAGGTTA
* *
6382002 AAAATGG-AA-TTTTAAAAGATTCGGGGGT
1 AAAATGGTAATTTTTAGAAGATTCAGGGGT
*
6382030 AAAATGGTAATTTTTGGTGAA-ATT--GGGGTT
1 AAAATGGTAATTTTT--AGAAGATTCAGGGG-T
6382060 AAAATGG-AA-TTTTAGAAGATTC-GAGGGT
1 AAAATGGTAATTTTTAGAAGATTCAG-GGGT
6382088 AAAATGGTAATTTTCGGT-GAA-A-TC-GGGGTT
1 AAAATGGTAATTTT---TAGAAGATTCAGGGG-T
*
6382118 AAAAATGG--ATTTTTAAAAGATTCAGGGGT
1 -AAAATGGTAATTTTTAGAAGATTCAGGGGT
6382147 -AAATGGTAATTTTTGATGAA-A-TC-GGGGTT
1 AAAATGGTAATTTTT-A-GAAGATTCAGGGG-T
6382176 AAAAATGG--ATTTTTAGAAGATTCAGGGGT
1 -AAAATGGTAATTTTTAGAAGATTCAGGGGT
6382205 AAAATGGTAATTTTTAGAAG
1 AAAATGGTAATTTTTAGAAG
6382225 TTTTAGGGTC
Statistics
Matches: 159, Mismatches: 5, Indels: 60
0.71 0.02 0.27
Matches are distributed among these distances:
26 4 0.03
27 14 0.09
28 34 0.21
29 42 0.26
30 40 0.25
31 19 0.12
32 5 0.03
33 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.33
Consensus pattern (30 bp):
AAAATGGTAATTTTTAGAAGATTCAGGGGT
Found at i:6382523 original size:164 final size:164
Alignment explanation
Indices: 6382346--6382645 Score: 503
Period size: 164 Copynumber: 1.8 Consensus size: 164
6382336 TTGTAAATCT
*
6382346 TGAAAAATTCTTGGGCCAATTTTGTAATTAAATAAAAGTTAATTTGGGGATTAAATTAAAACAAA
1 TGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAGTTAATTTGGGGATTAAATTAAAACAAA
* *
6382411 TTAAAAATGAAAAGGACTAAATGCATAAATAAGCCAAAAAGTGACATGTGGCAG-CTCCTGGTAC
66 TTAAAAATGAAAAGGACTAAATGCATAAATAAGCCAAAAAATGACACGTGGCAGCCT-CTGGTAC
6382475 AGTCAAACAGTCAAAGGACTAATTTATAAAAACCA
130 AGTCAAACAGTCAAAGGACTAATTTATAAAAACCA
* *
6382510 TGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAGTTGATTTGGGGATTAAATTAAAATAAA
1 TGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAGTTAATTTGGGGATTAAATTAAAACAAA
** * *
6382575 TTAAAAATGTCAGGGACTAAATGCATAAATAATCCAAAAAATGACACGTGGCAGCCTCTGGTACA
66 TTAAAAATGAAAAGGACTAAATGCATAAATAAGCCAAAAAATGACACGTGGCAGCCTCTGGTACA
6382640 GTCAAA
131 GTCAAA
6382646 GGACTAAATT
Statistics
Matches: 126, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
164 124 0.98
165 2 0.02
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.26
Consensus pattern (164 bp):
TGAAAAATTCTTGGGCCAATTTCGTAATTAAATAAAAGTTAATTTGGGGATTAAATTAAAACAAA
TTAAAAATGAAAAGGACTAAATGCATAAATAAGCCAAAAAATGACACGTGGCAGCCTCTGGTACA
GTCAAACAGTCAAAGGACTAATTTATAAAAACCA
Found at i:6383243 original size:14 final size:14
Alignment explanation
Indices: 6383226--6383252 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6383216 TTTCTTTTAT
6383226 TCTTTTAATATTTC
1 TCTTTTAATATTTC
6383240 TCTTTTAATATTT
1 TCTTTTAATATTT
6383253 TCGTTCCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTTAATATTTC
Found at i:6383415 original size:15 final size:15
Alignment explanation
Indices: 6383395--6383432 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
6383385 TATAAAATAT
* *
6383395 TTATTATTATTACTG
1 TTATTATTATCACTA
6383410 TTATTATTATCACTA
1 TTATTATTATCACTA
6383425 TTATTATT
1 TTATTATT
6383433 GTTATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTATTATCACTA
Found at i:6383435 original size:24 final size:24
Alignment explanation
Indices: 6383399--6383454 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
6383389 AAATATTTAT
*
6383399 TATTATTACTGTTATT-ATTATCAC
1 TATTATTACTGTTATTAATGAT-AC
*
6383423 TATTATTATTGTTATTAATGATAC
1 TATTATTACTGTTATTAATGATAC
6383447 TATTATTA
1 TATTATTA
6383455 ACCATCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.55
Consensus pattern (24 bp):
TATTATTACTGTTATTAATGATAC
Found at i:6384153 original size:6 final size:6
Alignment explanation
Indices: 6384144--6384224 Score: 87
Period size: 6 Copynumber: 13.7 Consensus size: 6
6384134 ATTTTTATTC
* * *
6384144 AAATTT AAATTC AAA-GT AAATTT AAATAATT AAATTT AAATTT AAA-AT
1 AAATTT AAATTT AAATTT AAATTT AAAT--TT AAATTT AAATTT AAATTT
*
6384192 AAATTT AAATTT AAA-AT AAATTT AAATTT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
6384225 AAAATTAAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
5 11 0.18
6 45 0.73
8 6 0.10
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (6 bp):
AAATTT
Found at i:6384164 original size:17 final size:17
Alignment explanation
Indices: 6384144--6384233 Score: 116
Period size: 17 Copynumber: 5.5 Consensus size: 17
6384134 ATTTTTATTC
* *
6384144 AAATTTAAATTCAAAGT
1 AAATTTAAATTTAAAAT
*
6384161 AAATTTAAA--T-AATT
1 AAATTTAAATTTAAAAT
6384175 AAATTTAAATTTAAAAT
1 AAATTTAAATTTAAAAT
6384192 AAATTTAAATTTAAAAT
1 AAATTTAAATTTAAAAT
6384209 AAATTTAAATTT-AAAT
1 AAATTTAAATTTAAAAT
*
6384225 AAAATTAAA
1 AAATTTAAA
6384234 GATCAATTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
14 12 0.18
16 13 0.20
17 41 0.62
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (17 bp):
AAATTTAAATTTAAAAT
Found at i:6384194 original size:11 final size:12
Alignment explanation
Indices: 6384160--6384224 Score: 62
Period size: 11 Copynumber: 5.4 Consensus size: 12
6384150 AAATTCAAAG
6384160 TAAATTTAAATAA
1 TAAATTTAAAT-A
*
6384173 TTAAATTTAAATT
1 -TAAATTTAAATA
* *
6384186 TAAA-ATAAATT
1 TAAATTTAAATA
6384197 TAAATTTAAA-A
1 TAAATTTAAATA
*
6384208 TAAATTTAAATT
1 TAAATTTAAATA
6384220 TAAAT
1 TAAAT
6384225 AAAATTAAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
11 20 0.45
12 13 0.30
14 11 0.25
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAATTTAAATA
Found at i:6384229 original size:11 final size:12
Alignment explanation
Indices: 6384144--6384230 Score: 58
Period size: 11 Copynumber: 7.4 Consensus size: 12
6384134 ATTTTTATTC
*
6384144 AAATTTAAATTC
1 AAATTTAAATTA
*
6384156 AAA-GTAAATTTA
1 AAATTTAAA-TTA
* *
6384168 AATAATTAAATTT
1 AA-ATTTAAATTA
*
6384181 AAATTTAAAAT-
1 AAATTTAAATTA
6384192 AAATTTAAATTTA
1 AAATTTAAA-TTA
*
6384205 AAA--TAAATTT
1 AAATTTAAATTA
6384215 AAATTTAAA-TA
1 AAATTTAAATTA
6384226 AAATT
1 AAATT
6384231 AAAGATCAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
10 5 0.08
11 23 0.39
12 19 0.32
13 8 0.14
14 4 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (12 bp):
AAATTTAAATTA
Found at i:6384251 original size:28 final size:27
Alignment explanation
Indices: 6384171--6384252 Score: 67
Period size: 28 Copynumber: 2.9 Consensus size: 27
6384161 AAATTTAAAT
* *
6384171 AATTAAATTTAAATTTAAA-ATAAATTTAA
1 AATTAAA-ATAAATTTAAATCTAAA--TAA
* *
6384200 ATTTAAAATAAATTTAAATTTAAATAA
1 AATTAAAATAAATTTAAATCTAAATAA
* *
6384227 AATTAAAGATCAATTTAACTCTAAAT
1 AATTAAA-ATAAATTTAAATCTAAAT
6384253 TAAACGAAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 9 0.20
28 25 0.57
29 10 0.23
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (27 bp):
AATTAAAATAAATTTAAATCTAAATAA
Found at i:6384750 original size:76 final size:69
Alignment explanation
Indices: 6384588--6385147 Score: 685
Period size: 69 Copynumber: 7.9 Consensus size: 69
6384578 GGAAATGATC
* * * * *
6384588 TTGCTTTTATTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCATGAAGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
6384653 GACG
66 GACG
* *
6384657 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
6384722 AGGAAACGATG
66 --G--AC---G
* * *
6384733 TTACTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
6384798 GACG
66 GACG
* * * ** * *
6384802 TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAGTTTTACTTCAATTTCAAAAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
6384867 AGGAAACGATG
66 --G--AC---G
* * *
6384878 TTACTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
6384943 GACG
66 GACG
* * * *
6384947 TTGCTCTTACTTCAATTTCAGAGATAAAGGCGTGTTATCC-ATTCTACTTCAATTTCAAGCGGAC
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGA-
* *
6385011 TGGCA
65 TGACG
* *
6385016 TTTCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
6385080 GACG
66 GACG
* * *
6385084 TTGCTCTTACTTCAGTTTCAGAGATGAAGACGCGTTATCC-ACTCTACTTCAATTTCAAGCGGAT
1 TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
6385148 TGGCATTGAT
Statistics
Matches: 430, Mismatches: 46, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
68 84 0.20
69 215 0.50
71 2 0.00
72 4 0.01
73 4 0.01
74 2 0.00
76 119 0.28
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (69 bp):
TTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
GACG
Found at i:6384810 original size:145 final size:145
Alignment explanation
Indices: 6384531--6385147 Score: 867
Period size: 145 Copynumber: 4.3 Consensus size: 145
6384521 GCTCTTTAGG
* * * * * * * **
6384531 GAGATAAAGACTTTGCTATCCAACTTTACTTCAATTTCTAGAGGATAGGAAATGATCTTGCTTTT
1 GAGATAAAGAC-GTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCCT
* * * *
6384596 ATTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCATGAAGATGACGTTGC
65 ACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGC
6384661 TCTTACTTCAATTTCA
130 TCTTACTTCAATTTCA
*
6384677 GAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCCTA
1 GAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCCTA
*
6384742 CTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCT
66 CTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCT
6384807 CTTACTTCAATTTCA
131 CTTACTTCAATTTCA
* * ** * *
6384822 GAGATAAAGACTTGATATCCAGTTTTACTTCAATTTCAAAAGGATAGGAAACGATGTTACTCCTA
1 GAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCCTA
*
6384887 CTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCT
66 CTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCT
6384952 CTTACTTCAATTTCA
131 CTTACTTCAATTTCA
* * * *
6384967 GAGATAAAGGCGTGTTATCC-ATTCTACTTCAATTTCAAGCGGACT-GG---C-AT-TT-CTCTT
1 GAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGA-TAGGAAACGATGTTACTCCT
*
6385024 ACTTCAATTTCAGAGATGAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGGGGATGACGTTGC
65 ACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGC
*
6385088 TCTTACTTCAGTTTCA
130 TCTTACTTCAATTTCA
* * *
6385104 GAGATGAAGACGCGTTATCC-ACTCTACTTCAATTTCAAGCGGAT
1 GAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
6385148 TGGCATTGAT
Statistics
Matches: 433, Mismatches: 37, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
136 1 0.00
137 85 0.20
138 35 0.08
139 2 0.00
140 2 0.00
141 1 0.00
144 21 0.05
145 276 0.64
146 10 0.02
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (145 bp):
GAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCCTA
CTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAAGAGGATGACGTTGCT
CTTACTTCAATTTCA
Found at i:6397286 original size:28 final size:28
Alignment explanation
Indices: 6397233--6397695 Score: 271
Period size: 29 Copynumber: 15.9 Consensus size: 28
6397223 ATAAACGATG
* * *
6397233 AAATCGGGGTGAAAAATGGGACTTTTGGA
1 AAATCGGGG-GTAAAATGGTAATTTTGGA
* ** *
6397262 TACCCGGGGGTAAAATGGTAATTTTGATA
1 AAATCGGGGGTAAAATGGTAATTTTG-GA
* *
6397291 AAATCGGAGTTAAAATGG-AATTTTGGA
1 AAATCGGGGGTAAAATGGTAATTTTGGA
* * *
6397318 AAGTTCAGGGGTAAAATGGTGATTTTTGGTA
1 AA-ATCGGGGGTAAAATGGT-AATTTTGG-A
*
6397349 AAATCGGGGTTAAAAATGG-AATTTTGGA
1 AAATCGGGGGT-AAAATGGTAATTTTGGA
* *
6397377 AAGTTCGGGGGTAAAATGGTAATTTTGGTG
1 AA-ATCGGGGGTAAAATGGTAATTTTGG-A
* ** *
6397407 AAATCAGGATTAAAAATGG-AATTTT-AA
1 AAATCGGGGGT-AAAATGGTAATTTTGGA
*
6397434 AAGATTCGAGGGTAAAATGGTAATTTTCGGTA
1 AA-A-TCGGGGGTAAAATGGTAATTTT-GG-A
* * *
6397466 AAATCGAGGTTAAAAATGG-AATTTT-AA
1 AAATCGGGGGT-AAAATGGTAATTTTGGA
*
6397493 AAGATTCGGGGGTAAAATGGTAATTTTTGGTG
1 AA-A-TCGGGGGTAAAATGGTAA-TTTTGG-A
* *
6397525 AAATCGGGGTTAAAAATGG-AATTTTAGA
1 AAATCGGGGGT-AAAATGGTAATTTTGGA
* *
6397553 AAATTCGAGGGTAAAATGGTAATTTTCGGTG
1 AAA-TCGGGGGTAAAATGGTAATTTT-GG-A
** **
6397584 AAATCGGGTTTAAAAATGG--ATTTTTAA
1 AAATCGGGGGT-AAAATGGTAATTTTGGA
*
6397611 AAGATTCGGGGGTAAAATGGTAATTTTTGGTG
1 AA-A-TCGGGGGTAAAATGGTAA-TTTTGG-A
* * *
6397643 AAATCGGGGTTAAAATGG-ATTTTTAGA
1 AAATCGGGGGTAAAATGGTAATTTTGGA
*
6397670 AGATTCGGGGGTAAAATGGTAATTTT
1 A-AATCGGGGGTAAAATGGTAATTTT
6397696 CAGAAGTTTT
Statistics
Matches: 330, Mismatches: 67, Indels: 74
0.70 0.14 0.16
Matches are distributed among these distances:
27 11 0.03
28 97 0.29
29 105 0.32
30 69 0.21
31 41 0.12
32 7 0.02
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.32
Consensus pattern (28 bp):
AAATCGGGGGTAAAATGGTAATTTTGGA
Found at i:6397381 original size:59 final size:60
Alignment explanation
Indices: 6397231--6397695 Score: 587
Period size: 59 Copynumber: 8.0 Consensus size: 60
6397221 TGATAAACGA
* * * ** *
6397231 TGAAATCGGGGTGAAAAATGGGACTTTTGG--ATACCCGGGGGTAAAATGGTAA-TTTTGA
1 TGAAATCGGGGTTAAAAAT-GGAATTTTGGAAAGATTCGGGGGTAAAATGGTAATTTTTGG
* * * *
6397289 TAAAATCGGAGTT-AAAATGGAATTTTGGAAAG-TTCAGGGGTAAAATGGTGATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGATTCGGGGGTAAAATGGTAATTTTTGG
*
6397347 TAAAATCGGGGTTAAAAATGGAATTTTGGAAAG-TTCGGGGGTAAAATGGTAA-TTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGATTCGGGGGTAAAATGGTAATTTTTGG
* * * * *
6397405 TGAAATCAGGATTAAAAATGGAATTTT-AAAAGATTCGAGGGTAAAATGGTAATTTTCGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGATTCGGGGGTAAAATGGTAATTTTTGG
* * *
6397464 TAAAATCGAGGTTAAAAATGGAATTTT-AAAAGATTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGATTCGGGGGTAAAATGGTAATTTTTGG
* * *
6397523 TGAAATCGGGGTTAAAAATGGAATTTTAGAAA-ATTCGAGGGTAAAATGGTAATTTTCGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGATTCGGGGGTAAAATGGTAATTTTTGG
* **
6397582 TGAAATCGGGTTTAAAAATGG-ATTTTTAAAAGATTCGGGGGTAAAATGGTAATTTTTGG
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGATTCGGGGGTAAAATGGTAATTTTTGG
* *
6397641 TGAAATCGGGGTT-AAAATGGATTTTTAG-AAGATTCGGGGGTAAAATGGTAATTTT
1 TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGATTCGGGGGTAAAATGGTAATTTT
6397696 CAGAAGTTTT
Statistics
Matches: 359, Mismatches: 39, Indels: 18
0.86 0.09 0.04
Matches are distributed among these distances:
56 9 0.03
57 24 0.07
58 118 0.33
59 205 0.57
60 3 0.01
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (60 bp):
TGAAATCGGGGTTAAAAATGGAATTTTGGAAAGATTCGGGGGTAAAATGGTAATTTTTGG
Found at i:6398569 original size:14 final size:14
Alignment explanation
Indices: 6398552--6398578 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6398542 TTTCTTTTAT
6398552 TCTTTTAATATTTC
1 TCTTTTAATATTTC
6398566 TCTTTTAATATTT
1 TCTTTTAATATTT
6398579 TCGTTCCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (14 bp):
TCTTTTAATATTTC
Found at i:6398741 original size:15 final size:15
Alignment explanation
Indices: 6398721--6398758 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
6398711 TATAAAATAT
* *
6398721 TTATTATTATTACTG
1 TTATTATTATCACTA
6398736 TTATTATTATCACTA
1 TTATTATTATCACTA
6398751 TTATTATT
1 TTATTATT
6398759 GTTATTAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.61
Consensus pattern (15 bp):
TTATTATTATCACTA
Found at i:6398761 original size:24 final size:24
Alignment explanation
Indices: 6398725--6398780 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
6398715 AAATATTTAT
*
6398725 TATTATTACTGTTATT-ATTATCAC
1 TATTATTACTGTTATTAATGAT-AC
*
6398749 TATTATTATTGTTATTAATGATAC
1 TATTATTACTGTTATTAATGATAC
6398773 TATTATTA
1 TATTATTA
6398781 ACCATCATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.32, C:0.07, G:0.05, T:0.55
Consensus pattern (24 bp):
TATTATTACTGTTATTAATGATAC
Done.