Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007984.1 Hibiscus syriacus cultivar Beakdansim tig00110429_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12923621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 47 of 65
Found at i:9459472 original size:21 final size:21
Alignment explanation
Indices: 9459446--9459488 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
9459436 AGCAAAATTG
9459446 AATTTCAACAAATAATAACAA
1 AATTTCAACAAATAATAACAA
9459467 AATTTCAACAAATAATAACAA
1 AATTTCAACAAATAATAACAA
9459488 A
1 A
9459489 CATGTTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (21 bp):
AATTTCAACAAATAATAACAA
Found at i:9468967 original size:19 final size:19
Alignment explanation
Indices: 9468945--9468994 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 19
9468935 AACACGTAAG
9468945 AAATAATAAAATAT-AATAA
1 AAATAA-AAAATATGAATAA
*
9468964 AAATAAACAATATGAATAA
1 AAATAAAAAATATGAATAA
9468983 AATATTAAAAAA
1 AA-A-TAAAAAA
9468995 CAAAGACACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 6 0.23
19 13 0.50
20 1 0.04
21 6 0.23
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AAATAAAAAATATGAATAA
Found at i:9468968 original size:11 final size:10
Alignment explanation
Indices: 9468947--9468987 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
9468937 CACGTAAGAA
9468947 ATAATAAAAT
1 ATAATAAAAT
9468957 ATAATAAAA-
1 ATAATAAAAT
*
9468966 ATAA-ACAAT
1 ATAATAAAAT
9468975 ATGAATAAAAT
1 AT-AATAAAAT
9468986 AT
1 AT
9468988 TAAAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 3 0.12
9 6 0.23
10 11 0.42
11 6 0.23
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (10 bp):
ATAATAAAAT
Found at i:9469182 original size:10 final size:9
Alignment explanation
Indices: 9469165--9469199 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
9469155 TACATGATAT
9469165 TAAAAAAAA
1 TAAAAAAAA
9469174 TAGAAAAAAA
1 TA-AAAAAAA
9469184 TAAAAAAAA
1 TAAAAAAAA
9469193 GTAAAAA
1 -TAAAAA
9469200 TATAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 15 0.62
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:9469190 original size:18 final size:18
Alignment explanation
Indices: 9469167--9469204 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
9469157 CATGATATTA
9469167 AAAAAAATAG-AAAAAAAT
1 AAAAAAA-AGTAAAAAAAT
*
9469185 AAAAAAAAGTAAAAATAT
1 AAAAAAAAGTAAAAAAAT
9469203 AA
1 AA
9469205 TATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (18 bp):
AAAAAAAAGTAAAAAAAT
Found at i:9469222 original size:47 final size:46
Alignment explanation
Indices: 9469138--9469236 Score: 105
Period size: 47 Copynumber: 2.1 Consensus size: 46
9469128 GAATACTAAG
*
9469138 TAAAAAAAATAAAGATATACATGATATTAAAAAAAATAGAA-AAAAA
1 TAAAAAAAATAAAAATATACATGATATTAAAAAAAATA-AATAAAAA
* *
9469184 TAAAAAAAAGTAAAAATATA-AT-ATATATATATATAAATAAATAAAAA
1 TAAAAAAAA-TAAAAATATACATGATAT-TA-AAAAAAATAAATAAAAA
*
9469231 CAAAAA
1 TAAAAA
9469237 TAGAATATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
45 4 0.09
46 15 0.33
47 26 0.58
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.22
Consensus pattern (46 bp):
TAAAAAAAATAAAAATATACATGATATTAAAAAAAATAAATAAAAA
Found at i:9469265 original size:37 final size:38
Alignment explanation
Indices: 9469224--9469302 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 38
9469214 ATATAAATAA
9469224 ATAAAAAC-A-AAAATAGAATATTAAGAAAAAAATATAT
1 ATAAAAACGATAAAATAGAATATTAAG-AAAAAATATAT
*
9469261 ATAAAAACGTATAAAATATAATATTAAGAAAAAATATAT
1 ATAAAAACG-ATAAAATAGAATATTAAGAAAAAATATAT
9469300 ATA
1 ATA
9469303 CATAGTAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
37 8 0.21
39 15 0.39
40 15 0.39
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (38 bp):
ATAAAAACGATAAAATAGAATATTAAGAAAAAATATAT
Found at i:9469425 original size:15 final size:16
Alignment explanation
Indices: 9469402--9469435 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
9469392 AATATAGTAA
9469402 ATAAATAAAAAAA-AT
1 ATAAATAAAAAAATAT
*
9469417 ATAATTAAAAAAATAT
1 ATAAATAAAAAAATAT
9469433 ATA
1 ATA
9469436 TAGGGGACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAATAAAAAAATAT
Found at i:9469428 original size:14 final size:14
Alignment explanation
Indices: 9469400--9469433 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
9469390 GGAATATAGT
9469400 AAATA-AATAAAAA
1 AAATATAATAAAAA
*
9469413 AAATATAATTAAAA
1 AAATATAATAAAAA
9469427 AAATATA
1 AAATATA
9469434 TATAGGGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATATAATAAAAA
Found at i:9469899 original size:37 final size:36
Alignment explanation
Indices: 9469856--9469957 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 36
9469846 TTAGTAGAAC
9469856 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
9469893 GT-TATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 -TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
9469927 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
9469958 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
33 1 0.02
34 32 0.52
37 27 0.44
38 1 0.02
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.43
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:9470804 original size:105 final size:104
Alignment explanation
Indices: 9470505--9471029 Score: 720
Period size: 105 Copynumber: 5.0 Consensus size: 104
9470495 CATTGTTCCA
* * ** * *
9470505 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAATTGGGAAGTTG-TTGTTGACAAG
* * * *
9470570 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
9470611 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGAAC-CTGAA-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTG-GCTCTGAATTGGGAAGTTGTTGTTGACAAGC
9470671 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
9470711 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTGGGAAGTTGTTGTTGACAAGC
* *
9470776 AGTGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
9470816 AGTCTAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGGAAGTTGTTGTTGACAAGC
* *
9470881 TGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
9470921 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGGGAAGTTG-TTGTTGACAAG
* * *
9470986 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
9471027 AGT
1 AGT
9471030 GCCACGCTAT
Statistics
Matches: 378, Mismatches: 31, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
99 1 0.00
100 83 0.22
101 1 0.00
102 7 0.02
104 5 0.01
105 199 0.53
106 80 0.21
107 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (104 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGGGAAGTTGTTGTTGACAAGCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:9472879 original size:22 final size:22
Alignment explanation
Indices: 9472853--9472907 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
9472843 TTGTGTTTGG
*
9472853 TCAAAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
*
9472875 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
9472897 TCAAAGGTTTG
1 TCAAAGGTTTG
9472908 ATCGGGTAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.40
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:9473581 original size:22 final size:21
Alignment explanation
Indices: 9473533--9473581 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
9473523 TGATTTTTTC
9473533 TTCTTTTCTTTTTTGTTCTTG
1 TTCTTTTCTTTTTTGTTCTTG
9473554 TT-TTTTCCTTTTTTGCTTCTT-
1 TTCTTTT-CTTTTTTG-TTCTTG
9473575 TTCTTTT
1 TTCTTTT
9473582 TTGTTCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.16
21 12 0.48
22 9 0.36
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (21 bp):
TTCTTTTCTTTTTTGTTCTTG
Found at i:9473588 original size:15 final size:15
Alignment explanation
Indices: 9473526--9473589 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 15
9473516 TTCCTTTTGA
*
9473526 TTTTTTCTTCTTTTC
1 TTTTTTGTTCTTTTC
9473541 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTGTTC-----TTTT-C
9473562 TTTTTTGCTTCTTTTC
1 TTTTTTG-TTCTTTTC
9473578 TTTTTTGTTCTT
1 TTTTTTGTTCTT
9473590 GATTGAATCT
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
15 14 0.34
16 8 0.20
17 4 0.10
20 4 0.10
21 8 0.20
22 3 0.07
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (15 bp):
TTTTTTGTTCTTTTC
Found at i:9478172 original size:27 final size:26
Alignment explanation
Indices: 9478124--9478174 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
9478114 AATAATAAAT
*
9478124 AAAACAAGGAAAAAATAGAAAATAAC
1 AAAACAAGGAAAAAATAAAAAATAAC
* *
9478150 AAAACACGTAAAAAATAATAAAATA
1 AAAACAAGGAAAAAATAA-AAAATA
9478175 TAATAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.73, C:0.08, G:0.08, T:0.12
Consensus pattern (26 bp):
AAAACAAGGAAAAAATAAAAAATAAC
Found at i:9478182 original size:19 final size:19
Alignment explanation
Indices: 9478160--9478211 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
9478150 AAAACACGTA
9478160 AAAAATAATAAAATAT-AAT
1 AAAAATAA-AAAATATGAAT
*
9478179 AAAAATAAACAATATGAAT
1 AAAAATAAAAAATATGAAT
9478198 AAAATATTAAAAAA
1 AAAA-A-TAAAAAA
9478212 CAAAGACACC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.21
19 15 0.54
20 1 0.04
21 6 0.21
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATAAAAAATATGAAT
Found at i:9478438 original size:46 final size:43
Alignment explanation
Indices: 9478356--9478442 Score: 97
Period size: 46 Copynumber: 2.0 Consensus size: 43
9478346 GAATACTAAG
*
9478356 TAAAAAAATAAAGATATACATGATATTAAAAAAAATAGAAAAAA
1 TAAAAAAATAAAAATATACATGATATTAAAAAAAATA-AAAAAA
*
9478400 TAAAATAAAGTAAAAATATA-AT-ATATATATAAATAAATAAAAA
1 TAAAA-AAA-TAAAAATATACATGATAT-TA-AAAAAAATAAAAA
9478443 CAAAATAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
44 9 0.24
45 11 0.30
46 17 0.46
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.24
Consensus pattern (43 bp):
TAAAAAAATAAAAATATACATGATATTAAAAAAAATAAAAAAA
Found at i:9478595 original size:25 final size:25
Alignment explanation
Indices: 9478547--9478611 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
9478537 ACATCTAAAC
* *
9478547 ATATATATATATATATAATGATATAAG
1 ATATATATA-ATA-AAAATAATATAAG
*
9478574 ATATATATAATAAAAATAATATAAT
1 ATATATATAATAAAAATAATATAAG
*
9478599 ATAAATA-AATAAA
1 ATATATATAATAAA
9478612 TAAAAAACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 6 0.18
25 16 0.47
26 3 0.09
27 9 0.26
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (25 bp):
ATATATATAATAAAAATAATATAAG
Found at i:9478658 original size:15 final size:16
Alignment explanation
Indices: 9478635--9478668 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
9478625 AATATAGTAA
9478635 ATAAATAAAAAAA-AT
1 ATAAATAAAAAAATAT
*
9478650 ATAATTAAAAAAATAT
1 ATAAATAAAAAAATAT
9478666 ATA
1 ATA
9478669 TAAGGGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAATAAAAAAATAT
Found at i:9478661 original size:14 final size:14
Alignment explanation
Indices: 9478578--9478671 Score: 66
Period size: 14 Copynumber: 6.6 Consensus size: 14
9478568 TATAAGATAT
*
9478578 ATATAATAAAAATA
1 ATATAATAAAAAAA
*
9478592 ATATAATATAAATAA
1 ATATAATA-AAAAAA
*
9478607 ATA-AATAAAAAAC
1 ATATAATAAAAAAA
* * * **
9478620 AGAGGAATATAGTAA
1 ATA-TAATAAAAAAA
9478635 ATA-AATAAAAAAA
1 ATATAATAAAAAAA
*
9478648 ATATAATTAAAAAA
1 ATATAATAAAAAAA
9478662 ATATATATAA
1 ATATA-ATAA
9478672 GGGACAAAAT
Statistics
Matches: 60, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
13 16 0.27
14 26 0.43
15 18 0.30
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (14 bp):
ATATAATAAAAAAA
Found at i:9479115 original size:37 final size:35
Alignment explanation
Indices: 9479054--9479188 Score: 137
Period size: 37 Copynumber: 3.8 Consensus size: 35
9479044 GTGCTTGTGG
* * * * *
9479054 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAAGAGTTTAAATCTTAG-A-AAATTT
*
9479091 ATCCTATTTTTAAGAGTTTGAATCTTAGCAAAATGTT
1 ATCCTATTTTTAAGAGTTTAAATCTTAG-AAAAT-TT
* * *
9479128 ATCCTATTTTTAAGAGTTTGAATCCTA-AAATTTT
1 ATCCTATTTTTAAGAGTTTAAATCTTAGAAAATTT
*
9479162 ATCTTATTTTTAAGAGTTTAAATCTTA
1 ATCCTATTTTTAAGAGTTTAAATCTTA
9479189 ATAGGACGAA
Statistics
Matches: 85, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
34 26 0.31
35 4 0.05
36 3 0.04
37 52 0.61
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (35 bp):
ATCCTATTTTTAAGAGTTTAAATCTTAGAAAATTT
Found at i:9479164 original size:34 final size:35
Alignment explanation
Indices: 9479090--9479185 Score: 131
Period size: 34 Copynumber: 2.7 Consensus size: 35
9479080 AGTAGAACTC
*
9479090 TATCCTATTTTTAAGAGTTTGAATCTTAGCAAAATGT
1 TATCCTATTTTTAAGAGTTTGAATCCTA--AAAATGT
*
9479127 TATCCTATTTTTAAGAGTTTGAATCCT-AAAATTT
1 TATCCTATTTTTAAGAGTTTGAATCCTAAAAATGT
* *
9479161 TATCTTATTTTTAAGAGTTTAAATC
1 TATCCTATTTTTAAGAGTTTGAATC
9479186 TTAATAGGAC
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
34 29 0.53
37 26 0.47
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.47
Consensus pattern (35 bp):
TATCCTATTTTTAAGAGTTTGAATCCTAAAAATGT
Found at i:9479565 original size:2 final size:2
Alignment explanation
Indices: 9479560--9479607 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
9479550 ACACACACAC
9479560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9479602 AT AT AT
1 AT AT AT
9479608 TCGAGTATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9480840 original size:2 final size:2
Alignment explanation
Indices: 9480833--9480884 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
9480823 TCATTTACCC
9480833 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9480875 AT AT AT AT AT
1 AT AT AT AT AT
9480885 GTATGTATGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9482619 original size:2 final size:2
Alignment explanation
Indices: 9482612--9482637 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9482602 TGAGTATTTC
9482612 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
9482638 TCATGTGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9483597 original size:15 final size:14
Alignment explanation
Indices: 9483577--9483619 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
9483567 CTGATTTTCT
9483577 TAATTTTTAAAAAA
1 TAATTTTTAAAAAA
*
9483591 GTAATTTTGAAATAAA
1 -TAATTTTTAAA-AAA
9483607 T-ATTTTTAAAAAA
1 TAATTTTTAAAAAA
9483620 AATAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 3 0.12
14 8 0.32
15 11 0.44
16 3 0.12
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (14 bp):
TAATTTTTAAAAAA
Found at i:9484068 original size:18 final size:18
Alignment explanation
Indices: 9484026--9484068 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
9484016 AAAAACTGAG
*
9484026 TGATTTTAATAAAATATT
1 TGATTTTAATAAAATATC
*
9484044 TTATTTTAATAAAATA-C
1 TGATTTTAATAAAATATC
9484061 TGAGTTTT
1 TGA-TTTT
9484069 GGGGTCTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
TGATTTTAATAAAATATC
Found at i:9485152 original size:18 final size:17
Alignment explanation
Indices: 9485129--9485171 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
9485119 GAAACAAAAC
**
9485129 AATTAAAAACAAACTACT
1 AATTAAAAACAAAAGA-T
9485147 AATT-AAAACAAAAGAT
1 AATTAAAAACAAAAGAT
9485163 AATTAAAAA
1 AATTAAAAA
9485172 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 5 0.23
17 13 0.59
18 4 0.18
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.21
Consensus pattern (17 bp):
AATTAAAAACAAAAGAT
Found at i:9486462 original size:44 final size:43
Alignment explanation
Indices: 9486398--9486971 Score: 329
Period size: 44 Copynumber: 13.0 Consensus size: 43
9486388 ATCCATCTCA
* * * * *
9486398 TTCTGTGATGGAATCAAACAAGATATTGGTGTTGATCTACCTCC
1 TTCTGTGATAGAATCGAGCAA-ATATTGATGCTGATCTACCTCC
* * *
9486442 TTCTGTGATAGAATCGAACAAAAAGTTGACGCTGATCTAACC-CC
1 TTCTGTGATAGAATCGAGCAAATA-TTGATGCTGATCT-ACCTCC
* * * * *** * *
9486486 TTCTGCGATGGATTTGAGCGAAATAAAAATG-TCGATCCACTTCC
1 TTCTGTGATAGAATCGAGC-AAATATTGATGCT-GATCTACCTCC
* * * * * *
9486530 TTCTGTGATGGAATCGAACGAGATGTCGATGCTGAGCTACCTCC
1 TTCTGTGATAGAATCGAGC-AAATATTGATGCTGATCTACCTCC
* * * *
9486574 TTCTGTGATAGAATCGAGCAAAATGTTGTTTCTGATTTACCTCC
1 TTCTGTGATAGAATCGAGC-AAATATTGATGCTGATCTACCTCC
* * * * ** **
9486618 TTCTATGATAGAATCGAGCAAAAAGTTGACGATGATCTAATTTA
1 TTCTGTGATAGAATCGAGCAAATA-TTGATGCTGATCTACCTCC
* * *** * * *
9486662 TTCTGCGAT-GAATTTGAGCGAAATAAAAATG-TCAATCCACCTCA
1 TTCTGTGATAGAA-TCGAGC-AAATATTGATGCT-GATCTACCTCC
* *
9486706 TTCTGTGAT-GTAATCGAACAAGATGTCTG-TGCTGATCTACCTCC
1 TTCTGTGATAG-AATCGAGCAA-ATAT-TGATGCTGATCTACCTCC
* *
9486750 TTATGTGATAGAATCGAGCATAA-AGTTGATG-TCGATAC-AACTCC
1 TTCTGTGATAGAATCGAGCA-AATA-TTGATGCT-GAT-CTACCTCC
* * * * *
9486794 TTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCC
1 TTCTGTGATAGAATCGAGC-AAATATTGATGCTGATCTACCTCC
* *
9486838 TTCTGTGATAGAATCGAGCAAAATATTGGTACTGATCTACCTCC
1 TTCTGTGATAGAATCGAGC-AAATATTGATGCTGATCTACCTCC
* * * *
9486882 TTCTGTGATAGAATTGAGCAAAATATTGGTGCTGATTTACCTCA
1 TTCTGTGATAGAATCGAGC-AAATATTGATGCTGATCTACCTCC
* * * *
9486926 TTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCC
1 TTCTGTGATAGAATCGAGCAAATA-TTGATGCTGATCTACCTCC
9486970 TT
1 TT
9486972 TTGCGATGGA
Statistics
Matches: 400, Mismatches: 105, Indels: 50
0.72 0.19 0.09
Matches are distributed among these distances:
43 22 0.05
44 358 0.89
45 20 0.05
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (43 bp):
TTCTGTGATAGAATCGAGCAAATATTGATGCTGATCTACCTCC
Found at i:9486609 original size:132 final size:127
Alignment explanation
Indices: 9486345--9486601 Score: 327
Period size: 132 Copynumber: 2.0 Consensus size: 127
9486335 TGTTGATGAT
*
9486345 GCTGATCTAACTCCTTCTACGATGGATTTGAGAAAAAATGTAAATCCATCTCATTCTGTGATGGA
1 GCTGATCTAACCCCTTCTACGATGGATTTGAGAAAAAATGTAAATCCATCTCATTCTGTGATGGA
* * * *
9486410 ATCAAACAAGATATTGGTGTTGATCTACCTCCTTCTGTGATAGAATCGAACAAAAAGTTGAC
66 ATCAAACAAGATATCGATGCTGAGCTACCTCCTTCTGTGATAGAATCGAACAAAAAGTTGAC
* ** *
9486472 GCTGATCTAACCCCTTCTGCGATGGATTTGAGCGAAATAAAAATGTCGATCCA-CTTCCTTCTGT
1 GCTGATCTAACCCCTTCTACGATGGATTTGA--G--A-AAAAATGTAAATCCATC-TCATTCTGT
* * * * *
9486536 GATGGAATCGAACGAGATGTCGATGCTGAGCTACCTCCTTCTGTGATAGAATCGAGCAAAATGTT
60 GATGGAATCAAACAAGATATCGATGCTGAGCTACCTCCTTCTGTGATAGAATCGAACAAAAAGTT
9486601 G
125 G
9486602 TTTCTGATTT
Statistics
Matches: 110, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
127 29 0.26
129 1 0.01
131 2 0.02
132 78 0.71
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (127 bp):
GCTGATCTAACCCCTTCTACGATGGATTTGAGAAAAAATGTAAATCCATCTCATTCTGTGATGGA
ATCAAACAAGATATCGATGCTGAGCTACCTCCTTCTGTGATAGAATCGAACAAAAAGTTGAC
Found at i:9486666 original size:132 final size:131
Alignment explanation
Indices: 9486394--9486904 Score: 439
Period size: 132 Copynumber: 3.9 Consensus size: 131
9486384 GTAAATCCAT
* * * * * *
9486394 CTCATTCTGTGATGGAATCAAACAAGATATTGGTGTTGATCTACCTCCTTCTGTGATAGAATCGA
1 CTCATTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGA
* * * * * * ** *
9486459 ACAAAAAGTTG-ACGCTGATCTAACC-CCTTCTGCGATGGATTTGAGCGAAATAA--AAATGTCG
66 GCAAAATGTTGTA--CTGATCT-ACCTCCTTCTGTGATAGAATCGAGC-AAA-AAGTTGACGTCG
*
9486520 AT-CCA
126 ATACAA
* *
9486525 CTTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGAGCTACCTCCTTCTGTGATAGAATCG
1 C-TCATTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCG
* * *
9486590 AGCAAAATGTTGTTTCTGATTTACCTCCTTCTATGATAGAATCGAGCAAAAAGTTGACGAT-GAT
65 AGCAAAATGTTG-TACTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACG-TCGAT
9486654 -CTAA
128 AC-AA
* * * * * * **** * * *
9486658 TTTATTCTGCGAT-GAATTTGAGCGAAATAAAAATG-TCAATCCACCTCATTCTGTGAT-GTAAT
1 CTCATTCTGTGATGGAA-TCGAACGAGATGTCGATGCT-GATCTACCTCCTTCTGTGATAG-AAT
* * * * * *
9486720 CGAACAAGATGTCTGTGCTGATCTACCTCCTTATGTGATAGAATCGAGCATAAAGTTGATGTCGA
63 CGAGCAAAATGT-TGTACTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGTCGA
9486785 TACAA
127 TACAA
*
9486790 CTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGA
1 CTCATTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGA
* *
9486855 GCAAAATATTGGTACTGATCTACCTCCTTCTGTGATAGAATTGAGCAAAA
66 GCAAAATGTT-GTACTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAA
9486905 TATTGGTGCT
Statistics
Matches: 297, Mismatches: 65, Indels: 35
0.75 0.16 0.09
Matches are distributed among these distances:
130 2 0.01
131 14 0.05
132 271 0.91
133 10 0.03
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (131 bp):
CTCATTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGATAGAATCGA
GCAAAATGTTGTACTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGACGTCGATACA
A
Found at i:9486832 original size:176 final size:176
Alignment explanation
Indices: 9486438--9486812 Score: 522
Period size: 176 Copynumber: 2.1 Consensus size: 176
9486428 GTTGATCTAC
* *
9486438 CTCCTTCTGTGATAGAATCGAACAAAAAGTTGACGCTGATCTAACCCCTTCTGCGATGGATTTGA
1 CTCCTTCTGTGATAGAATCGAACAAAAAGTTGACGCTGATCTAACCCATTCTGCGATGAATTTGA
* * * *
9486503 GCGAAATAAAAATGTCGATCCACTTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGAGCT
66 GCGAAATAAAAATGTCAATCCACCTCATTCTGTGATGGAATCGAACAAGATGTCGATGCTGAGCT
* * ** *
9486568 ACCTCCTTCTGTGATAGAATCGAGCAAAATGTTGTTTCTGATTTAC
131 ACCTCCTTATGTGATAGAATCGAGCAAAATGTTGTGTCTGATACAA
* * * ***
9486614 CTCCTTCTATGATAGAATCGAGCAAAAAGTTGACGATGATCTAATTTATTCTGCGATGAATTTGA
1 CTCCTTCTGTGATAGAATCGAACAAAAAGTTGACGCTGATCTAACCCATTCTGCGATGAATTTGA
* *
9486679 GCGAAATAAAAATGTCAATCCACCTCATTCTGTGATGTAATCGAACAAGATGTCTG-TGCTGATC
66 GCGAAATAAAAATGTCAATCCACCTCATTCTGTGATGGAATCGAACAAGATGTC-GATGCTGAGC
9486743 TACCTCCTTATGTGATAGAATCGAGCATAAA-GTTGATGTC-GATACAA
130 TACCTCCTTATGTGATAGAATCGAGCA-AAATGTTG-TGTCTGATACAA
*
9486790 CTCCTTCTGTGATGGAATCGAAC
1 CTCCTTCTGTGATAGAATCGAAC
9486813 GAGATGTCGA
Statistics
Matches: 174, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
176 167 0.96
177 7 0.04
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (176 bp):
CTCCTTCTGTGATAGAATCGAACAAAAAGTTGACGCTGATCTAACCCATTCTGCGATGAATTTGA
GCGAAATAAAAATGTCAATCCACCTCATTCTGTGATGGAATCGAACAAGATGTCGATGCTGAGCT
ACCTCCTTATGTGATAGAATCGAGCAAAATGTTGTGTCTGATACAA
Found at i:9487770 original size:35 final size:35
Alignment explanation
Indices: 9487729--9487831 Score: 154
Period size: 35 Copynumber: 2.9 Consensus size: 35
9487719 ACATTTCTTC
9487729 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAAAAA
1 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAAAAA
***
9487764 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAACTCG
1 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAA-AAA
*
9487800 TTTCAAGGGAAACTGTCTCAAGAGAGA-AAAAA
1 TTTCAAGGGAAATTGTCTCAAGAGAGACAAAAA
9487832 TTTGTTTCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
35 36 0.58
36 26 0.42
ACGTcount: A:0.45, C:0.14, G:0.21, T:0.20
Consensus pattern (35 bp):
TTTCAAGGGAAATTGTCTCAAGAGAGACAAAAAAA
Found at i:9487898 original size:66 final size:67
Alignment explanation
Indices: 9487799--9487990 Score: 244
Period size: 68 Copynumber: 2.9 Consensus size: 67
9487789 GACAAAACTC
* * * * *
9487799 GTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGGAAAACGGTCTGAAAGATTTT
1 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAGTCTCAAAGATTTT
9487864 -T
66 GT
* * * *
9487865 GTTTCAAGAGAAATTATCTCAAGGGAGACAAAATTTGTTTCAAGAGAAAA-AATATTCAAAGATT
1 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAG-GAAAACAGT-CTCAAAGATT
9487929 TTGT
64 TTGT
* * *
9487933 GTTTCAAGAGAAATTGTCTCAAGCGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAA
1 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAGTCTCAA
9487991 GCGAGACAAA
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
66 40 0.37
67 23 0.21
68 44 0.41
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (67 bp):
GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACAGTCTCAAAGATTTT
GT
Found at i:9487909 original size:36 final size:36
Alignment explanation
Indices: 9487651--9488041 Score: 191
Period size: 36 Copynumber: 11.0 Consensus size: 36
9487641 ATAAAATTTC
* * *
9487651 TTGTTTCAAGGGAAAATTGTCTCAAGTGAGACGAAAT
1 TTGTTTCAAGAG-AAATTGTCTCAAGAGAGACAAAAT
* * * *** * * **
9487688 TGGTTTTAAGAAAAACCATCTCAAGTGAGATACATTT
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACA-AAAT
* *
9487725 CTTCTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA-
1 -TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
*** * *
9487761 AAATTTCAAGGGAAATTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
* * * *
9487797 TCGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAAT
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
** * **
9487833 TTGTTTCAAG-GAAAACGGTCT---GA-A-A-GATTT
1 TTGTTTCAAGAG-AAATTGTCTCAAGAGAGACAAAAT
* *
9487863 TTGTTTCAAGAGAAATTATCTCAAGGGAGACAAAAT
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
* * **
9487899 TTGTTTCAAGAGAAAAAATAT-TC-A-A-AG---ATTT
1 TTGTTTCAAGAG--AAATTGTCTCAAGAGAGACAAAAT
*
9487930 TGTGTTTCAAGAGAAATTGTCTCAAGCGAGACAAAAT
1 T-TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
* * *
9487967 TTGTTTCAAGGGAAACTGTCTCAAGCGAGACAAAATCT
1 TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA--T
* * * * *
9488005 TCTATTTCGAGATAAATTATCTCAAGCGAGACAAAAT
1 T-TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
9488042 CTTCTGTTTC
Statistics
Matches: 269, Mismatches: 61, Indels: 48
0.71 0.16 0.13
Matches are distributed among these distances:
30 23 0.09
31 7 0.03
32 13 0.05
33 3 0.01
34 5 0.02
35 34 0.13
36 109 0.41
37 17 0.06
38 30 0.11
39 28 0.10
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TTGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAAT
Found at i:9488039 original size:39 final size:39
Alignment explanation
Indices: 9487949--9488280 Score: 445
Period size: 39 Copynumber: 8.6 Consensus size: 39
9487939 AGAGAAATTG
* * *
9487949 TCTCAAGCGAGACAAAA--TT-TGTTTCAAGGGAAACTG
1 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
* * ** *
9487985 TCTCAAGCGAGACAAAATCTTCTATTTCGAGATAAATTA
1 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
*
9488024 TCTCAAGCGAGACAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
*
9488063 TCTTAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
* * *
9488102 TCTCATGCGAGATAAAATCTTCTATTTCGATGGAAACTA
1 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
* * *
9488141 TCTCAAGCGAGATAAAAGCTTTTGTTTCGAGGAAAACTA
1 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
* *
9488180 TCTAAAGCGAGATAAAATCTTTTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
** *
9488219 TCTCAAGAAAGATAAAATCTTTTGTTTCGAGGGAAACTA
1 TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
*
9488258 TCTCAAGCAAGATAAAATCTTCT
1 TCTCAAGCGAGATAAAATCTTCT
9488281 TTAAAAACAA
Statistics
Matches: 263, Mismatches: 30, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
36 17 0.06
38 2 0.01
39 244 0.93
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (39 bp):
TCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAACTA
Found at i:9488054 original size:20 final size:20
Alignment explanation
Indices: 9487992--9488054 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
9487982 CTGTCTCAAG
9487992 CGAGACAAAATCTTCTATTT
1 CGAGACAAAATCTTCTATTT
* **
9488012 CGAGA-TAAAT-TATCTCA-AG
1 CGAGACAAAATCT-TCT-ATTT
*
9488031 CGAGACAAAATCTTCTGTTT
1 CGAGACAAAATCTTCTATTT
9488051 CGAG
1 CGAG
9488055 GGAAACTATC
Statistics
Matches: 31, Mismatches: 7, Indels: 10
0.65 0.15 0.21
Matches are distributed among these distances:
18 1 0.03
19 12 0.39
20 17 0.55
21 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (20 bp):
CGAGACAAAATCTTCTATTT
Found at i:9488065 original size:22 final size:22
Alignment explanation
Indices: 9488040--9488104 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
9488030 GCGAGACAAA
9488040 ATCTTCTGTTTCGAGGGAAACT
1 ATCTTCTGTTTCGAGGGAAACT
** **
9488062 ATCTTAAG---CGAGATAAA--
1 ATCTTCTGTTTCGAGGGAAACT
9488079 ATCTTCTGTTTCGAGGGAAACT
1 ATCTTCTGTTTCGAGGGAAACT
9488101 ATCT
1 ATCT
9488105 CATGCGAGAT
Statistics
Matches: 30, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
17 6 0.20
19 7 0.23
20 7 0.23
22 10 0.33
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (22 bp):
ATCTTCTGTTTCGAGGGAAACT
Found at i:9494977 original size:31 final size:31
Alignment explanation
Indices: 9494939--9495078 Score: 226
Period size: 31 Copynumber: 4.5 Consensus size: 31
9494929 AGGGTTGAGA
*
9494939 GTTTACCTATGTTCTTCGTGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
9494970 GTTTACCTATGTTTTTCGGGATATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
9495001 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
9495032 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
9495063 GTTTACCTAGGTTCTT
1 GTTTACCTATGTTCTT
9495079 TGGAATCTAT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 100 1.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:9495079 original size:31 final size:31
Alignment explanation
Indices: 9494939--9495094 Score: 217
Period size: 31 Copynumber: 5.0 Consensus size: 31
9494929 AGGGTTGAGA
* *
9494939 GTTTACCTATGTTCTTCGTGACATATGGACT
1 GTTTACCTATGTTCTTTGGGACATATGGACT
* *
9494970 GTTTACCTATGTT-TTTCGGGATATATGAACT
1 GTTTACCTATGTTCTTT-GGGACATATGGACT
*
9495001 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTTGGGACATATGGACT
9495032 GTTTACCTATGTTCTTTGGGACATATGGACT
1 GTTTACCTATGTTCTTTGGGACATATGGACT
* *
9495063 GTTTACCTAGGTTCTTTGGAATC-TATGGACT
1 GTTTACCTATGTTCTTTGGGA-CATATGGACT
9495094 G
1 G
9495095 GTCTTTCGGG
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
30 2 0.02
31 107 0.96
32 3 0.03
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.42
Consensus pattern (31 bp):
GTTTACCTATGTTCTTTGGGACATATGGACT
Found at i:9497157 original size:30 final size:30
Alignment explanation
Indices: 9497121--9497192 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
9497111 CCCGAAGGAC
*
9497121 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
*
9497151 CTATCCAGAGGTCATAAAGATCCTTGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
9497181 CTGTCCATAGGT
1 CTATCCAGAGGT
9497193 TCCGAAGAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:9497217 original size:31 final size:31
Alignment explanation
Indices: 9497179--9497303 Score: 128
Period size: 31 Copynumber: 4.0 Consensus size: 31
9497169 GATCCTTGGC
* *
9497179 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
* ** *
9497210 AACTGTCCATATATTCCTTAGAACATACGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
9497241 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
9497272 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
9497304 TACTCTCGAC
Statistics
Matches: 75, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
30 3 0.04
31 46 0.61
32 23 0.31
33 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:9498578 original size:64 final size:64
Alignment explanation
Indices: 9498423--9498579 Score: 144
Period size: 64 Copynumber: 2.5 Consensus size: 64
9498413 CAATAAGGGT
* * ** *
9498423 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATACATTCGATGTTGTATTATTATTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATACATTCGATGTTCTATTATTAAAGAG
* * * * *
9498487 ATGCATCGATGCA-TGCCTTATGAATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATACATTCGATG-TTCTATTATTAAAG
9498548 AG
63 AG
9498550 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
9498580 ACACCTTCAA
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
63 3 0.04
64 60 0.81
65 11 0.15
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATACATTCGATGTTCTATTATTAAAGAG
Found at i:9503796 original size:31 final size:31
Alignment explanation
Indices: 9503674--9503798 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 31
9503664 GTCGAGAGTA
*
9503674 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTACGGAACATATGGACAG-TT
* * *
9503706 TACCTATG-TCTTTC-GAGACATATGGACAATA
1 TACCTATGTTC-TACGGA-ACATATGGACAGTT
*
9503737 TACCTATGTTCTAAGGAACATATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
* * *
9503768 TACCTAGGTTCTTCGGAACCTATGGACAGTT
1 TACCTATGTTCTACGGAACATATGGACAGTT
9503799 GCCAAGGATC
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
31 52 0.68
32 25 0.32
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (31 bp):
TACCTATGTTCTACGGAACATATGGACAGTT
Found at i:9503843 original size:30 final size:30
Alignment explanation
Indices: 9503785--9503856 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
9503775 GTTCTTCGGA
* * * *
9503785 ACCTATGGACAGTTGCCAAGGATCTTTATG
1 ACCTCTGGATAGTTACCAAGGATATTTATG
*
9503815 ACCTCTGGATAGTTACCGAGGATATTTATG
1 ACCTCTGGATAGTTACCAAGGATATTTATG
9503845 ACCTCTGGATAG
1 ACCTCTGGATAG
9503857 GTCCTTCGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (30 bp):
ACCTCTGGATAGTTACCAAGGATATTTATG
Found at i:9508244 original size:44 final size:44
Alignment explanation
Indices: 9508196--9508356 Score: 223
Period size: 44 Copynumber: 3.7 Consensus size: 44
9508186 GATCTATTTT
* * * * * * * *
9508196 CTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTAACTC
1 CTTCTGTGATAGAATCGAGCAAAATGTTGGTGTTGATCTACCTC
9508240 CTTCTGTGATAGAATCGAGCAAAATGTTGGTGTTGATCTACCTC
1 CTTCTGTGATAGAATCGAGCAAAATGTTGGTGTTGATCTACCTC
* *
9508284 ATTCTGTGATAGAATCGAGCAAAATGTTGGTGTTGATTTACCTC
1 CTTCTGTGATAGAATCGAGCAAAATGTTGGTGTTGATCTACCTC
*
9508328 CTTCTGTGATAGAATCGAGCAAAAAGTTG
1 CTTCTGTGATAGAATCGAGCAAAATGTTG
9508357 ACACTGATTC
Statistics
Matches: 105, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 105 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (44 bp):
CTTCTGTGATAGAATCGAGCAAAATGTTGGTGTTGATCTACCTC
Found at i:9508453 original size:44 final size:44
Alignment explanation
Indices: 9508405--9508489 Score: 71
Period size: 44 Copynumber: 1.9 Consensus size: 44
9508395 ATAAAAATTT
* * * * * * *
9508405 TGATCCACCTCATTCTGTGATGGAATCGATCGAGATGTCGGTGC
1 TGATCTACCTCATTCTGTGATAGAATCGAGCAAAATGTTGATGC
* * * *
9508449 TGATCTACCTCCTTTTGTAATAGAATCGAGCAAAAAGTTGA
1 TGATCTACCTCATTCTGTGATAGAATCGAGCAAAATGTTGA
9508490 ACAAGTTCTT
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
44 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (44 bp):
TGATCTACCTCATTCTGTGATAGAATCGAGCAAAATGTTGATGC
Found at i:9509243 original size:36 final size:36
Alignment explanation
Indices: 9509132--9509318 Score: 172
Period size: 36 Copynumber: 5.4 Consensus size: 36
9509122 ACATTTCTTC
* * * **
9509132 TTTCAAGTGAAATTGTCTCAAGAGAGTCAAAAAAAT-
1 TTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAATTTG
* * * * *
9509168 TTTCAAGGGAAATTGTCTCAAGAGAAACAAAACTCG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
9509204 TTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* * **
9509240 TTTCAAGGGAAACGGTCTC-A-A-AG---ATTTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
9509270 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
9509306 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
9509319 ATATTCAAAG
Statistics
Matches: 123, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
30 22 0.18
31 1 0.01
33 4 0.03
34 1 0.01
35 5 0.04
36 90 0.73
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.26
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:9509283 original size:66 final size:67
Alignment explanation
Indices: 9509203--9509396 Score: 223
Period size: 66 Copynumber: 2.9 Consensus size: 67
9509193 AACAAAACTC
* *
9509203 GTTTCAAGAGAAACTGTCTCAAGAGAGAGAAAATTTGTTTCAAGGGAAACGGT-CTCAAAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-ATACTCAAAGATTT
9509267 T-T
65 TGT
* * *
9509269 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACATATTCAAAGATTTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATACTCAAAGATTTT
9509334 GT
66 GT
* * * * * *
9509336 GTTTAAAAAGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGGGAAAC-TATCTCAA
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA--TT-TGTTTCAAGGGAAACATA-CTCAA
9509397 GCGAGATAAA
Statistics
Matches: 109, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
65 1 0.01
66 58 0.53
67 29 0.27
69 4 0.04
70 17 0.16
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (67 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACATACTCAAAGATTTT
GT
Found at i:9509389 original size:39 final size:39
Alignment explanation
Indices: 9509345--9509567 Score: 383
Period size: 39 Copynumber: 5.7 Consensus size: 39
9509335 TGTTTAAAAA
*
9509345 GAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGG
1 GAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGG
* *
9509384 GAAACTATCTCAAGCGAGATAAAATCTTATGTTTCGATG
1 GAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGG
9509423 GAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGG
1 GAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGG
* *
9509462 AAAACTATCTCAAGCGAGATAAAATCTTTTATTTCGAGG
1 GAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGG
**
9509501 GAAACTATCTCAAGAAAGATAAAATCTTTTGTTTCGAGG
1 GAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGG
9509540 GAAACTATCTCAAGCGAGATAAAATCTT
1 GAAACTATCTCAAGCGAGATAAAATCTT
9509568 CTTTAAAAAC
Statistics
Matches: 172, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 172 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (39 bp):
GAAACTATCTCAAGCGAGATAAAATCTTTTGTTTCGAGG
Found at i:9509663 original size:76 final size:76
Alignment explanation
Indices: 9509572--9509733 Score: 195
Period size: 76 Copynumber: 2.1 Consensus size: 76
9509562 AATCTTCTTT
* * *
9509572 AAAAACAATCTTGAGTAAAATGAAAT-ATCTTCTTTCGAGTGAAAA-TCGTCTCAAGCAAGACAA
1 AAAAACAATCCTGAGTAAAAT-AAATCATCTTCTTTCGAGTAAAAACT-ATCTCAAGCAAGACAA
*
9509635 ATAT-TGTTTTAAG
64 AT-TCTATTTTAAG
* * * **
9509648 AAAAACAATCCTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACTATCTCAAGTGAGACAAAT
1 AAAAACAATCCTGAGTAAAATAAATCATCTTCTTTCGAGTAAAAACTATCTCAAGCAAGACAAAT
9509713 TCTATTTTAAG
66 TCTATTTTAAG
9509724 AAAAACAATC
1 AAAAACAATC
9509734 TCAAGTGAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
75 5 0.07
76 68 0.92
77 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (76 bp):
AAAAACAATCCTGAGTAAAATAAATCATCTTCTTTCGAGTAAAAACTATCTCAAGCAAGACAAAT
TCTATTTTAAG
Found at i:9511915 original size:14 final size:15
Alignment explanation
Indices: 9511895--9511931 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
9511885 GCAAATGCAA
9511895 AGATGCAAAAATGGG
1 AGATGCAAAAATGGG
*
9511910 AG-TGC-AAAATGTG
1 AGATGCAAAAATGGG
9511923 AGATGCAAA
1 AGATGCAAA
9511932 TGCAACAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.47
14 6 0.32
15 4 0.21
ACGTcount: A:0.46, C:0.08, G:0.30, T:0.16
Consensus pattern (15 bp):
AGATGCAAAAATGGG
Found at i:9513557 original size:12 final size:11
Alignment explanation
Indices: 9513535--9513584 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
9513525 TTATAATTTA
9513535 TATTTAAAAAT
1 TATTTAAAAAT
9513546 TATTTAAAAAAT
1 TATTT-AAAAAT
*
9513558 T-GTTAAAAAT
1 TATTTAAAAAT
*
9513568 TA-TGAAAAAT
1 TATTTAAAAAT
*
9513578 AATTTAA
1 TATTTAA
9513585 TTAATATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
10 15 0.47
11 10 0.31
12 7 0.22
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (11 bp):
TATTTAAAAAT
Found at i:9513576 original size:22 final size:23
Alignment explanation
Indices: 9513538--9513581 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
9513528 TAATTTATAT
**
9513538 TTAAAAATTATTTAAAA-AATTG
1 TTAAAAATTATGAAAAATAATTG
9513560 TTAAAAATTATGAAAAATAATT
1 TTAAAAATTATGAAAAATAATT
9513582 TAATTAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.39
Consensus pattern (23 bp):
TTAAAAATTATGAAAAATAATTG
Found at i:9514913 original size:16 final size:17
Alignment explanation
Indices: 9514881--9514914 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9514871 TTTTATCCTT
*
9514881 TTTTAAAGTTTATATAA
1 TTTTAAAGTTAATATAA
9514898 TTTTAAA-TTAATATAA
1 TTTTAAAGTTAATATAA
9514914 T
1 T
9514915 ACTGAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTAAAGTTAATATAA
Found at i:9515624 original size:10 final size:10
Alignment explanation
Indices: 9515611--9515640 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
9515601 TTTTATTTTT
9515611 ATTATTATTA
1 ATTATTATTA
9515621 ATTATTATTA
1 ATTATTATTA
*
9515631 ACTATTATTA
1 ATTATTATTA
9515641 TTAATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTATTATTA
Found at i:9515627 original size:13 final size:14
Alignment explanation
Indices: 9515609--9515646 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
9515599 ATTTTTATTT
9515609 TTATTATT-ATTAA
1 TTATTATTAATTAA
*
9515622 TTATTATTAACT-A
1 TTATTATTAATTAA
9515635 TTATTATTAATT
1 TTATTATTAATT
9515647 TTACATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATTATTAATTAA
Found at i:9530196 original size:141 final size:141
Alignment explanation
Indices: 9529987--9530248 Score: 409
Period size: 141 Copynumber: 1.9 Consensus size: 141
9529977 TGACCAGATC
9529987 TCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCGAG
1 TCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCGAG
* ** *
9530052 TTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATCTACCCTTAG
66 TTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATCTACCCTTAG
9530117 ACGACCGGACT
131 ACGACCGGACT
* * *
9530128 TCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAATCAGCCGTCCTCATCACGTAGGAACCGA
1 TCCTCATCACGTAGGAG-AGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCGA
* * * *
9530192 GTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGAGCCGTGTCATC
65 GTTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
9530249 CCTTGACCAG
Statistics
Matches: 109, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
141 98 0.90
142 11 0.10
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (141 bp):
TCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCGAG
TTATCACCCTTCCTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATCTACCCTTAG
ACGACCGGACT
Found at i:9530491 original size:6 final size:6
Alignment explanation
Indices: 9530475--9530517 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
9530465 TGTCCGGGTC
* *
9530475 TTTTAT ATTTAT TTTTAT TTTTAT TTTTAT TTTTAT TATTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
9530518 AATTATTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:9530515 original size:3 final size:3
Alignment explanation
Indices: 9530483--9530541 Score: 55
Period size: 3 Copynumber: 19.0 Consensus size: 3
9530473 TCTTTTATAT
* * * *
9530483 TTA TTT TTA TTT TTA TTT TTA TTT TTA TTA TTA TTAA TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TT-A
*
9530530 CTA TTA TTA TTA
1 TTA TTA TTA TTA
9530542 ATTTTACATA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
3 39 0.89
4 5 0.11
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:9530523 original size:13 final size:14
Alignment explanation
Indices: 9530507--9530544 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
9530497 ATTTTTATTT
9530507 TTATTATT-ATTAA
1 TTATTATTAATTAA
*
9530520 TTATTATTAACT-A
1 TTATTATTAATTAA
9530533 TTATTATTAATT
1 TTATTATTAATT
9530545 TTACATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 20 0.91
14 2 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATTATTAATTAA
Found at i:9530524 original size:10 final size:10
Alignment explanation
Indices: 9530509--9530538 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
9530499 TTTTATTTTT
9530509 ATTATTATTA
1 ATTATTATTA
9530519 ATTATTATTA
1 ATTATTATTA
*
9530529 ACTATTATTA
1 ATTATTATTA
9530539 TTAATTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (10 bp):
ATTATTATTA
Found at i:9533352 original size:38 final size:38
Alignment explanation
Indices: 9533301--9533374 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
9533291 ATGTTTCATC
*
9533301 GAGTCGAGTCATAAAATTTAGAGTTATTTGAGTTGATT
1 GAGTCGAGTCATAAAATTTAGAATTATTTGAGTTGATT
*
9533339 GAGTCGATTCATAAAATTTAGAATTATTTGAGTTGA
1 GAGTCGAGTCATAAAATTTAGAATTATTTGAGTTGA
9533375 CGGGTCTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.39
Consensus pattern (38 bp):
GAGTCGAGTCATAAAATTTAGAATTATTTGAGTTGATT
Found at i:9534435 original size:229 final size:227
Alignment explanation
Indices: 9534035--9534483 Score: 801
Period size: 229 Copynumber: 2.0 Consensus size: 227
9534025 GTAAATTATC
* *
9534035 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
9534100 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
9534165 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
9534230 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
9534263 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
9534328 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-AT
* *
9534392 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
9534457 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
9534484 GCAGTTTTAC
Statistics
Matches: 212, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
228 43 0.20
229 169 0.80
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:9534572 original size:20 final size:19
Alignment explanation
Indices: 9534549--9534594 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
9534539 CGATATACCA
9534549 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
9534569 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
9534589 GGTAAA
1 GGTAAA
9534595 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:9534739 original size:20 final size:20
Alignment explanation
Indices: 9534716--9534763 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
9534706 CGATATAACA
*
9534716 GGTAAAATTATGATAAAACC
1 GGTAAAATAATGATAAAACC
*
9534736 GGTAACAA-AATGATAAAATC
1 GGTAA-AATAATGATAAAACC
9534756 GGTAAAAT
1 GGTAAAAT
9534764 GATACCGGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 20 0.83
21 2 0.08
ACGTcount: A:0.52, C:0.08, G:0.17, T:0.23
Consensus pattern (20 bp):
GGTAAAATAATGATAAAACC
Found at i:9537043 original size:21 final size:21
Alignment explanation
Indices: 9537000--9537060 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
9536990 CAATCAAGAA
* *
9537000 TCGAAGAGAAACTTGATCA-AG
1 TCGAAGAGAAACTCGA-GAGAG
*
9537021 TCGTAGAGAAACTCGAGAGAG
1 TCGAAGAGAAACTCGAGAGAG
* *
9537042 TCGAAGATACACTCGAGAG
1 TCGAAGAGAAACTCGAGAG
9537061 GAATAAGGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 1 0.03
21 32 0.97
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.16
Consensus pattern (21 bp):
TCGAAGAGAAACTCGAGAGAG
Found at i:9537136 original size:33 final size:33
Alignment explanation
Indices: 9537094--9537159 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
9537084 AAATAGATGG
*
9537094 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
9537127 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
9537160 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:9538990 original size:17 final size:19
Alignment explanation
Indices: 9538947--9538993 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
9538937 AATGTCGAGT
9538947 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
9538966 TAATTTTGTATACGA-TTA
1 TAATTTTGTATAAGATTTA
9538984 T-ATTTTGTAT
1 TAATTTTGTAT
9538994 GTGAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.33
18 4 0.15
19 14 0.52
ACGTcount: A:0.32, C:0.02, G:0.11, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:9540131 original size:196 final size:198
Alignment explanation
Indices: 9539112--9540163 Score: 2036
Period size: 198 Copynumber: 5.3 Consensus size: 198
9539102 CAATATGGCC
* *
9539112 AACAGGGTGCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCAATCCCAAAATCATCGAAC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAAC
*
9539177 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGA
65 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGA
9539242 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
130 GAATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAA
9539307 TGGAA
195 TGG-A
9539312 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
9539377 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
9539442 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
9539507 GGA
196 GGA
9539510 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
*
9539575 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
9539640 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
9539705 GGA
196 GGA
9539708 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
9539773 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
9539838 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
9539903 GGA
196 GGA
9539906 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
9539971 C-AAAGTATAATGTAATATGTAA-TTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
66 CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
9540034 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
131 AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
9540099 GGA
196 GGA
9540102 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
1 AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGA
9540164 TCCATATATA
Statistics
Matches: 847, Mismatches: 5, Indels: 4
0.99 0.01 0.00
Matches are distributed among these distances:
196 171 0.20
197 21 0.02
198 461 0.54
199 160 0.19
200 34 0.04
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (198 bp):
AACAAGGTGCACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACC
CAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTACACCGGTTTTATGAGAG
AATATGTCTAAATAATGTGTCGACACTAATATAGTTTGTGTCGATACTTTTTTCCCAGAATGAAT
GGA
Found at i:9540684 original size:3 final size:3
Alignment explanation
Indices: 9540676--9540747 Score: 72
Period size: 3 Copynumber: 24.0 Consensus size: 3
9540666 TCTTTTAACA
* * * ** * *
9540676 GAT GAT GAT GAT GAC GAT GAA GCT GGC GAT GAA GAT GAT GAC GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
9540724 GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT
9540748 CCAAACAAGT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:9542707 original size:365 final size:365
Alignment explanation
Indices: 9541946--9542823 Score: 1512
Period size: 365 Copynumber: 2.4 Consensus size: 365
9541936 CAAAGTTTTC
* * * *
9541946 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
9542011 AAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
* *
9542074 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCT
128 TATAACCGGTATAAAAATACCGGTTTTATGAGCAAATAGGTCTACAACCTATATCGACACTTTCT
9542139 AATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTG
193 AATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTG
9542204 TCGATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTA
258 TCGATT--AAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTA
*
9542269 TAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
321 TAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
9542314 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
9542379 AAAAAAGTGTCGACATTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
9542444 AA-CGGTATAAAAATACCGGTTTTATGAGCAAATAGGTCTACAACCTTTATCGACACTTTCTAAT
131 AACCGGTATAAAAATACCGGTTTTATGAGCAAATAGGTCTACAACCTATATCGACACTTTCTAAT
*
9542508 ATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
196 ATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
* * *
9542573 ACATT-TACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAA
261 --ATTAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAA
*
9542637 AAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
324 AAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
9542679 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
9542744 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
9542809 AACCGGTATAAAAAT
131 AACCGGTATAAAAAT
9542824 GTGTCGATAC
Statistics
Matches: 487, Mismatches: 18, Indels: 12
0.94 0.03 0.02
Matches are distributed among these distances:
365 226 0.46
366 135 0.28
367 47 0.10
368 76 0.16
370 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (365 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACCGGTTTTATGAGCAAATAGGTCTACAACCTATATCGACACTTTCTAAT
ATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
ATTAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAAA
ATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:9542729 original size:183 final size:183
Alignment explanation
Indices: 9541946--9542823 Score: 1514
Period size: 184 Copynumber: 4.8 Consensus size: 183
9541936 CAAAGTTTTC
* * * *
9541946 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGAAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
9542011 AAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
*
9542074 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
9542130 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
* *
9542195 AAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
66 AAAAAAGTGTCGACATT---TACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAA
*
9542258 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
9542314 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
9542379 AAAAAAGTGTCGACATTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
* *
9542444 AA-CGGTATAAAAATACCGGTTTTATGAGCAAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
9542496 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
*
9542561 AAAAAAGTGTCGACATTTACACATCGGAACCCATATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
*
9542626 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTTTATCG
131 AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
9542679 ACACTTTCTAATATTGTGTCGGTACTTTATGTTCAGATTGGAAGAAAAATGTGTCGATACCATTT
1 ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
9542744 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
66 AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
9542809 AACCGGTATAAAAAT
131 AACCGGTATAAAAAT
9542824 GTGTCGATAC
Statistics
Matches: 678, Mismatches: 13, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
182 178 0.26
183 240 0.35
184 257 0.38
186 3 0.00
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Consensus pattern (183 bp):
ACACTTTCTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTT
AAAAAAGTGTCGACATTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAAAATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:9542852 original size:22 final size:23
Alignment explanation
Indices: 9542819--9542861 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
9542809 AACCGGTATA
9542819 AAAATGTGTCGATACCTTTTTAT
1 AAAATGTGTCGATACCTTTTTAT
*
9542842 AAAA-GTGTCGATACTTTTTT
1 AAAATGTGTCGATACCTTTTT
9542862 CACTGTGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (23 bp):
AAAATGTGTCGATACCTTTTTAT
Found at i:9546014 original size:23 final size:23
Alignment explanation
Indices: 9545983--9546045 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
9545973 ATAGGTAAAC
*
9545983 ATATGATGTAATAGGTACCCCTT
1 ATATAATGTAATAGGTACCCCTT
* **
9546006 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTACCCCTT
9546029 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
9546046 GTGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTACCCCTT
Found at i:9546053 original size:23 final size:23
Alignment explanation
Indices: 9545983--9546055 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
9545973 ATAGGTAAAC
* * **
9545983 ATATGATGTAATAGGTACCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
9546006 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
9546029 ATATAATGTAATAGGTAGT-GGTT
1 ATATAATGTAATAGGTA-TCGGTT
9546052 ATAT
1 ATAT
9546056 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 43 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:9546444 original size:23 final size:23
Alignment explanation
Indices: 9546413--9546476 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
9546403 ATAGGTAAAC
*
9546413 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
9546436 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
9546459 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
9546477 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:9546483 original size:23 final size:23
Alignment explanation
Indices: 9546413--9546485 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
9546403 ATAGGTAAAC
* **
9546413 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
9546436 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
9546459 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
9546482 ATAT
1 ATAT
9546486 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:9547073 original size:18 final size:18
Alignment explanation
Indices: 9547052--9547088 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
9547042 GTAATTGGAG
9547052 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
9547070 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
9547088 T
1 T
9547089 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:9547096 original size:24 final size:24
Alignment explanation
Indices: 9547044--9547090 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
9547034 TTTCATATGT
* *
9547044 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
9547068 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
9547091 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:9547389 original size:39 final size:39
Alignment explanation
Indices: 9547346--9547432 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
9547336 TCCGATGCTC
*
9547346 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
*
9547385 ATCAAAATCCAAATCTCATATGATGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
9547424 ATCAAAATC
1 ATCAAAATC
9547433 TACAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:9547866 original size:23 final size:23
Alignment explanation
Indices: 9547835--9547898 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
9547825 ATAGGTAAAC
*
9547835 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
9547858 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
9547881 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
9547899 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:9547905 original size:23 final size:23
Alignment explanation
Indices: 9547835--9547907 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
9547825 ATAGGTAAAC
* **
9547835 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
*
9547858 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
9547881 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
9547904 ATAT
1 ATAT
9547908 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:9553580 original size:29 final size:29
Alignment explanation
Indices: 9553534--9553603 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 29
9553524 AGAGCCCTTA
* *
9553534 ATTTTTTT-TATTTATAATTAGGATCTCT
1 ATTTTTTTATAATTATAATTAGGACCTCT
*
9553562 ATTTTTTTATAATTGTAATTAGGACCTCT
1 ATTTTTTTATAATTATAATTAGGACCTCT
*
9553591 A-ATTTTTATAATT
1 ATTTTTTTATAATT
9553604 TCATAAGTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 19 0.51
29 18 0.49
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.57
Consensus pattern (29 bp):
ATTTTTTTATAATTATAATTAGGACCTCT
Found at i:9553596 original size:28 final size:29
Alignment explanation
Indices: 9553548--9553603 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
9553538 TTTTTATTTA
* *
9553548 TAATTAGGATCTCTATTTTTTTATAATTG
1 TAATTAGGACCTCTATATTTTTATAATTG
9553577 TAATTAGGACCTCTA-ATTTTTATAATT
1 TAATTAGGACCTCTATATTTTTATAATT
9553604 TCATAAGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (29 bp):
TAATTAGGACCTCTATATTTTTATAATTG
Found at i:9553703 original size:411 final size:409
Alignment explanation
Indices: 9552939--9553760 Score: 1348
Period size: 411 Copynumber: 2.0 Consensus size: 409
9552929 TTAATTACCA
9552939 CTTAAAGATTATTTGATATTTTTTATAAAAATAATTTGTTTTAATAAAACAAAATATTTAAAATT
1 CTTAAAGATTATTTGATATTTTTTATAAAAATAATTTGTTTTAATAAAACAAAATATTTAAAATT
* * *
9553004 ATAATGAAGATTACAACAATAACTATAAATTAAATATGTGATTGACATGTTTTTTATAATCATTG
66 ATAAAGAAAATTACAACAATAACTATAAATTAAATATGTGATTGACATGTTTTTTATAATAATTG
* *
9553069 ACACAAAGAATTATATATAAGGCCGGCACACTCTGAGCAACCGCTCAGGTCTCCTAATTTTTTTA
131 ACACAAAGAATTAGATACAAGGCCGGCACACTCTGAGCAACCGCTCAGGTCTCCTAATTTTTTTA
9553134 TTTATAATTAGAGTCTCAAATTTTTTATAATTATATTCAGGACCCTAATTTTTATAATTTCATAA
196 TTTATAATTAGAGTCTCAAATTTTTTATAATTATATTCAGGACCCTAATTTTTATAATTTCATAA
*
9553199 GTTTTTTAGTTTTTGATCATCTTTTTTCATTTCTCTTATTAATTATGTAATTTTGAATTAAATTT
261 GTTTTTTAGTTTTTGATCATCTTTCTTCATTTCTCTTATTAATTATGTAATTTTGAATTAAATTT
* *
9553264 AACCAATTTTTTTATATTTATGGTTAAGACCCTAATTTTTATAATTTCATAAAATATTTAGTTTT
326 AACCAATTTTTTTATATTTATAGTTAAGACCCTAATTTTTATAATTTCATAAAATATTTAGTTTG
**
9553329 TAACCCTCTTTTTTCATTT
391 TAACCCTAGTTTTTCATTT
*
9553348 CTTAAAGATTATTTGATATTTTTTATAAAAATAATTT-TTTTATTAAAACAAAATATTTAAAATT
1 CTTAAAGATTATTTGATATTTTTTATAAAAATAATTTGTTTTAATAAAACAAAATATTTAAAATT
* * *
9553412 GTAAAGAAAATTACAACAATAACTGTAAATTAAATTTGTGATTGACATGTTTTTTTATAATAATT
66 ATAAAGAAAATTACAACAATAACTATAAATTAAATATGTGATTGACATG-TTTTTTATAATAATT
* * * *
9553477 GACACAAAGAATTAGATACAAGGTCGGCACATTCTTAGTAACCGCTCAGAG-C-CCTTAATTTTT
130 GACACAAAGAATTAGATACAAGGCCGGCACACTCTGAGCAACCGCTCAG-GTCTCC-TAA-TTTT
* * *
9553540 TTTATTTATAATTAG-GATCTCTATTTTTTTATAATTGTAATT-AGGACCTCTAATTTTTATAAT
192 TTTATTTATAATTAGAG-TCTCAAATTTTTTATAATTAT-ATTCAGGACC-CTAATTTTTATAAT
9553603 TTCATAAGTTTTTTAGTTTTTGATCATCTTTCTTCATTTCTCTTATTAATTATGTAATTTTGAAT
254 TTCATAAGTTTTTTAGTTTTTGATCATCTTTCTTCATTTCTCTTATTAATTATGTAATTTTGAAT
*
9553668 TAAATTTAACCAATTTTTTTATATTTATAGTTAAGACCCTAATTTTTATAATTTCATAAAATGTT
319 TAAATTTAACCAATTTTTTTATATTTATAGTTAAGACCCTAATTTTTATAATTTCATAAAATATT
9553733 TAGTTTGTAACCCTAGTTTTTCATTT
384 TAGTTTGTAACCCTAGTTTTTCATTT
9553759 CT
1 CT
9553761 CTTATTTATT
Statistics
Matches: 384, Mismatches: 22, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
408 72 0.19
409 99 0.26
410 44 0.11
411 169 0.44
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.46
Consensus pattern (409 bp):
CTTAAAGATTATTTGATATTTTTTATAAAAATAATTTGTTTTAATAAAACAAAATATTTAAAATT
ATAAAGAAAATTACAACAATAACTATAAATTAAATATGTGATTGACATGTTTTTTATAATAATTG
ACACAAAGAATTAGATACAAGGCCGGCACACTCTGAGCAACCGCTCAGGTCTCCTAATTTTTTTA
TTTATAATTAGAGTCTCAAATTTTTTATAATTATATTCAGGACCCTAATTTTTATAATTTCATAA
GTTTTTTAGTTTTTGATCATCTTTCTTCATTTCTCTTATTAATTATGTAATTTTGAATTAAATTT
AACCAATTTTTTTATATTTATAGTTAAGACCCTAATTTTTATAATTTCATAAAATATTTAGTTTG
TAACCCTAGTTTTTCATTT
Found at i:9553710 original size:117 final size:119
Alignment explanation
Indices: 9553562--9553794 Score: 292
Period size: 117 Copynumber: 2.0 Consensus size: 119
9553552 TAGGATCTCT
* * ** * * * *
9553562 ATTTTTTTATAATTGTAATTAGGACCTCTAATTTTTATAATTTCATAAGTTTTTTAGTTTTTGAT
1 ATTTTTTTATAATTATAATTAAGACCTCTAATTTTTATAATTTCATAAAATGTTTAGTTTGTAAC
9553627 CAT-CTTTCTTCATTTCTCTTATTAATT-ATGTAATTTTGAATTAAATTTAACCA
66 CATACTTT-TTCATTTCTCTTATTAATTCATGTAATTTTGAATTAAATTTAACCA
* *
9553680 ATTTTTTTATATTTATAGTTAAGACC-CTAATTTTTATAATTTCATAAAATGTTTAGTTTGTAAC
1 ATTTTTTTATAATTATAATTAAGACCTCTAATTTTTATAATTTCATAAAATGTTTAGTTTGTAAC
* * * * * *
9553744 CCTAGTTTTTCATTTCTCTTATTTATTCATTTAATTTTGATTTATATTTAA
66 CATACTTTTTCATTTCTCTTATTAATTCATGTAATTTTGAATTAAATTTAA
9553795 TCATGTTTTT
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
117 52 0.54
118 45 0.46
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.55
Consensus pattern (119 bp):
ATTTTTTTATAATTATAATTAAGACCTCTAATTTTTATAATTTCATAAAATGTTTAGTTTGTAAC
CATACTTTTTCATTTCTCTTATTAATTCATGTAATTTTGAATTAAATTTAACCA
Found at i:9554275 original size:17 final size:17
Alignment explanation
Indices: 9554255--9554296 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
9554245 TCAACAAGCT
9554255 AACTATAAAAAAGATCA
1 AACTATAAAAAAGATCA
*
9554272 AACTAT-TAAAAGATCA
1 AACTATAAAAAAGATCA
*
9554288 CA-TATAAAA
1 AACTATAAAA
9554297 TTGTAAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 3 0.14
16 12 0.57
17 6 0.29
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.21
Consensus pattern (17 bp):
AACTATAAAAAAGATCA
Found at i:9555108 original size:3 final size:3
Alignment explanation
Indices: 9555100--9555157 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
9555090 ACAGTACTAC
*
9555100 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
9555148 ATT ATT ATT A
1 ATT ATT ATT A
9555158 AATCATAGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:9556853 original size:43 final size:43
Alignment explanation
Indices: 9556802--9557043 Score: 308
Period size: 43 Copynumber: 5.7 Consensus size: 43
9556792 TGAGAACAAA
* * * * *
9556802 AAACGTCGCAATAGGTCAAGATCTATCGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* *
9556845 AAACGTCGCAAAAGGTCGATATCAATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* *
9556888 AAACGCCG-AAAAGGTCGATATCTATTGCGGCGTTTTTGTAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* * * * *
9556930 GAACGCCTCAAAATGTCGATATCAATAGCGGCGTTTTTAGAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
* * *
9556973 AAACGCCGCAAAAGGTC-AGATCTATAGCGACGTTTTTGAAAC
1 AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
*
9557015 AAACGCCACAAAAGGTCGATATCTATAGC
1 AAACGCCGCAAAAGGTCGATATCTATAGC
9557044 AAATGTCAGA
Statistics
Matches: 171, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
42 73 0.43
43 98 0.57
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCGATATCTATAGCGGCGTTTTTGGAAC
Found at i:9556942 original size:85 final size:85
Alignment explanation
Indices: 9556802--9557043 Score: 324
Period size: 85 Copynumber: 2.8 Consensus size: 85
9556792 TGAGAACAAA
* * * * * *
9556802 AAACGTCGCAATAGGTCAAGATCTATCGCGGCGTTTTTGGAACAAACGTCGCAAAAGGTCGATAT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCGATAT
*
9556867 CAATAGCGGCGTTTTTGGAAC
65 CAATAGCGGCGTTTTTAGAAC
* * * * * *
9556888 AAACGCCG-AAAAGGTCGATATCTATTGCGGCGTTTTTGTAACGAACGCCTCAAAATGTCGATAT
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCGATAT
9556952 CAATAGCGGCGTTTTTAGAAC
65 CAATAGCGGCGTTTTTAGAAC
*
9556973 AAACGCCGCAAAAGGTCAGATCTATAGCGACGTTTTTGAAACAAACGCCACAAAAGGTCGATATC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCGATATC
*
9557038 TATAGC
66 AATAGC
9557044 AAATGTCAGA
Statistics
Matches: 136, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
85 121 0.89
86 15 0.11
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (85 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGAAACAAACGCCACAAAAGGTCGATATC
AATAGCGGCGTTTTTAGAAC
Found at i:9559939 original size:24 final size:24
Alignment explanation
Indices: 9559912--9559973 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
9559902 AGACAGTGAT
*
9559912 GACAATCATTATTGGAGATAGCAA
1 GACAATCATTATTGGAGACAGCAA
*
9559936 GACAATCATTATTGGAGACATCAA
1 GACAATCATTATTGGAGACAGCAA
9559960 GACAATCATTATTG
1 GACAATCATTATTG
9559974 AAAATAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (24 bp):
GACAATCATTATTGGAGACAGCAA
Found at i:9560332 original size:28 final size:28
Alignment explanation
Indices: 9560287--9560340 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
9560277 TTGTTTCACT
* *
9560287 GAAAACGTTTTTCGGAAAATG-AAATCTG
1 GAAAACGTTTTACAG-AAATGTAAATCTG
*
9560315 GAAAATGTTTTACAGAAATGTAAATC
1 GAAAACGTTTTACAGAAATGTAAATC
9560341 ATTTTCCAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.30
Consensus pattern (28 bp):
GAAAACGTTTTACAGAAATGTAAATCTG
Found at i:9560605 original size:15 final size:15
Alignment explanation
Indices: 9560585--9560613 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9560575 TACACTATTT
9560585 TAGGTTTATTTTATG
1 TAGGTTTATTTTATG
9560600 TAGGTTTATTTTAT
1 TAGGTTTATTTTAT
9560614 ATAATATTAA
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:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (15 bp):
TAGGTTTATTTTATG
Found at i:9562444 original size:33 final size:34
Alignment explanation
Indices: 9562406--9562476 Score: 90
Period size: 38 Copynumber: 2.0 Consensus size: 34
9562396 AAGAAACAGT
*
9562406 GAAGTT-TCGATGTGGAGCAAGGGACGGGAGAAG
1 GAAGTTATCAATGTGGAGCAAGGGACGGGAGAAG
9562439 GAAGTTCAGAATCAATGTGGAGCAAGGGACGGGAGAAG
1 GAAGTT----ATCAATGTGGAGCAAGGGACGGGAGAAG
9562477 CTGGAAAACG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 6 0.19
38 26 0.81
ACGTcount: A:0.34, C:0.10, G:0.42, T:0.14
Consensus pattern (34 bp):
GAAGTTATCAATGTGGAGCAAGGGACGGGAGAAG
Found at i:9562624 original size:14 final size:14
Alignment explanation
Indices: 9562605--9562642 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
9562595 GGAAAAGGTG
9562605 AAAATATTTTTCGT
1 AAAATATTTTTCGT
9562619 AAAATATTTTTCGT
1 AAAATATTTTTCGT
*
9562633 AAAATGTTTT
1 AAAATATTTT
9562643 CCCCAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (14 bp):
AAAATATTTTTCGT
Found at i:9563817 original size:42 final size:42
Alignment explanation
Indices: 9563686--9563825 Score: 142
Period size: 42 Copynumber: 3.4 Consensus size: 42
9563676 CTATTTGTAT
*
9563686 AAAAACGCCGCTAAATTA-ATACTCTATTGCGGCGTTTGTTGA
1 AAAAACGCCGCTAAATTACA-ACTCTATTGTGGCGTTTGTTGA
* * * ****
9563728 AAAAACGCCACTATAA--ACAACTATATTCTGGCGTTTGAACT
1 AAAAACGCCGCTA-AATTACAACTCTATTGTGGCGTTTGTTGA
* * *
9563769 ATAAACGTCGCTAAATTACCACTCTATTGTGGCGTTTGTTGA
1 AAAAACGCCGCTAAATTACAACTCTATTGTGGCGTTTGTTGA
9563811 AAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
9563826 GTAGTCTTTT
Statistics
Matches: 74, Mismatches: 20, Indels: 8
0.73 0.20 0.08
Matches are distributed among these distances:
40 2 0.03
41 26 0.35
42 44 0.59
43 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (42 bp):
AAAAACGCCGCTAAATTACAACTCTATTGTGGCGTTTGTTGA
Found at i:9564324 original size:11 final size:11
Alignment explanation
Indices: 9564308--9564333 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9564298 TGAGCTTAAA
9564308 ATATGTAATAT
1 ATATGTAATAT
9564319 ATATGTAATAT
1 ATATGTAATAT
9564330 ATAT
1 ATAT
9564334 AACATATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (11 bp):
ATATGTAATAT
Found at i:9570424 original size:35 final size:34
Alignment explanation
Indices: 9570358--9570445 Score: 133
Period size: 35 Copynumber: 2.5 Consensus size: 34
9570348 TAAATATATT
9570358 TATTATA-ATATTTCAAAATGTTTTAAAAACCATA
1 TATTATATAT-TTTCAAAATGTTTTAAAAACCATA
9570392 TATTATATATTTTCAAAATGTTTTTAAAAACCATA
1 TATTATATATTTTCAAAATG-TTTTAAAAACCATA
9570427 TATTATATAAGTTTTCAAA
1 TATTATAT-A-TTTTCAAA
9570446 TTATTTTTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
34 17 0.34
35 24 0.48
36 1 0.02
37 8 0.16
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (34 bp):
TATTATATATTTTCAAAATGTTTTAAAAACCATA
Found at i:9572472 original size:40 final size:40
Alignment explanation
Indices: 9572427--9572528 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
9572417 TTTTTTTATT
*
9572427 ATATATATATATATATTATAGTTTGCAAATGATTTTTGAA
1 ATATATATATATATATTATAGTTTGAAAATGATTTTTGAA
9572467 ATATATATATA-ATATATATAGTTTTGAAAATGATTTTTGAA
1 ATATATATATATATAT-TATAG-TTTGAAAATGATTTTTGAA
*
9572508 A-ATGTATATAT-TA-TATAGTTT
1 ATATATATATATATATTATAGTTT
9572529 TGGAATCATT
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
37 3 0.05
38 5 0.09
39 4 0.07
40 26 0.46
41 19 0.33
ACGTcount: A:0.41, C:0.01, G:0.10, T:0.48
Consensus pattern (40 bp):
ATATATATATATATATTATAGTTTGAAAATGATTTTTGAA
Found at i:9572476 original size:42 final size:42
Alignment explanation
Indices: 9572426--9572524 Score: 143
Period size: 41 Copynumber: 2.4 Consensus size: 42
9572416 TTTTTTTTAT
*
9572426 TATATATATATATATATTATAG-TTTGCAAATGATTTTTGAAA
1 TATATATATATATATA-TATAGTTTTGAAAATGATTTTTGAAA
9572468 TATATATATA-ATATATATAGTTTTGAAAATGATTTTTGAAA
1 TATATATATATATATATATAGTTTTGAAAATGATTTTTGAAA
*
9572509 -ATGTATATAT-TATATA
1 TATATATATATATATATA
9572525 GTTTTGGAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
40 19 0.36
41 24 0.45
42 10 0.19
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.47
Consensus pattern (42 bp):
TATATATATATATATATATAGTTTTGAAAATGATTTTTGAAA
Found at i:9572593 original size:35 final size:34
Alignment explanation
Indices: 9572535--9572759 Score: 171
Period size: 35 Copynumber: 6.5 Consensus size: 34
9572525 GTTTTGGAAT
9572535 CATTTTGAAAACTTATATAATATACGGTTTTTAAAAA
1 CATTTTGAAAAC-TATATAATATA-GGTTTTT-AAAA
9572572 CATTTTGAAAA-TATATAATATATGGTTTTTAAAA
1 CATTTTGAAAACTATATAATATA-GGTTTTTAAAA
**
9572606 CATTTTGAAAACTTATATAATATATATTTTTAAAA
1 CATTTTGAAAAC-TATATAATATAGGTTTTTAAAA
* * * *
9572641 CATTTTG--AA-TATAT-ATATATG-ATAT-ATA
1 CATTTTGAAAACTATATAATATAGGTTTTTAAAA
* *
9572669 -ATTTTGAAACATATATATAATATATAGTTTTTAAAA
1 CATTTTGAAA-A-CTATATAATATA-GGTTTTTAAAA
* *
9572705 CATTTTGAAAAAATATATATAATATATAG-TTTTAAAA
1 CATTTTG--AAAA-CTATATAATATA-GGTTTTTAAAA
* *
9572742 CATTTTTAAAAATATATA
1 CATTTTGAAAACTATATA
9572760 TAATATATAG
Statistics
Matches: 162, Mismatches: 12, Indels: 31
0.79 0.06 0.15
Matches are distributed among these distances:
27 6 0.04
28 2 0.01
29 3 0.02
30 7 0.04
31 5 0.03
32 5 0.03
33 7 0.04
34 23 0.14
35 40 0.25
36 13 0.08
37 31 0.19
38 17 0.10
39 3 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (34 bp):
CATTTTGAAAACTATATAATATAGGTTTTTAAAA
Found at i:9572682 original size:26 final size:27
Alignment explanation
Indices: 9572642--9572699 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
9572632 TTTTTAAAAC
* *
9572642 ATTTTGAATATATATATATGATATATA
1 ATTTTGAATACATATATATAATATATA
9572669 ATTTTGAA-ACATATATATAATATATA
1 ATTTTGAATACATATATATAATATATA
*
9572695 GTTTT
1 ATTTT
9572700 TAAAACATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (27 bp):
ATTTTGAATACATATATATAATATATA
Found at i:9572730 original size:38 final size:37
Alignment explanation
Indices: 9572669--9572772 Score: 174
Period size: 37 Copynumber: 2.8 Consensus size: 37
9572659 ATGATATATA
*
9572669 ATTTTGAAACATATATATAATATATAGTTTTTAAAAC
1 ATTTTGAAAAATATATATAATATATAGTTTTTAAAAC
9572706 ATTTTGAAAAAATATATATAATATATAG-TTTTAAAAC
1 ATTTTG-AAAAATATATATAATATATAGTTTTTAAAAC
*
9572743 ATTTTTAAAAATATATATAATATATAGTTT
1 ATTTTGAAAAATATATATAATATATAGTTT
9572773 AAAAATTATT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
36 21 0.33
37 22 0.35
38 20 0.32
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (37 bp):
ATTTTGAAAAATATATATAATATATAGTTTTTAAAAC
Found at i:9572767 original size:36 final size:36
Alignment explanation
Indices: 9572429--9572786 Score: 233
Period size: 36 Copynumber: 9.9 Consensus size: 36
9572419 TTTTTATTAT
* ** *
9572429 ATATATATATATATTATAGTTTGCAAATGATTTTTGAAAT
1 ATATATATA-ATA-TATAGTTT-TAAAACATTTTT-AAAA
* *
9572469 ATATATATAATATATATAGTTTTGAAAATGATTTTTGAAA
1 ATATATAT-A-ATATATAGTTTT-AAAA-CATTTTTAAAA
* * * * *
9572509 ATGTATATATTATATAGTTTTGGAATCATTTTGAAAA
1 ATATATATAATATATAGTTTT-AAAACATTTTTAAAA
* ** *
9572546 CT-TATATAATATACGGTTTTTAAAAACA-TTTT-GAA
1 ATATATATAATATATAG-TTTT-AAAACATTTTTAAAA
* *
9572581 A-ATATATAATATATGGTTTTTAAAACATTTTGAAAA
1 ATATATATAATATATAG-TTTTAAAACATTTTTAAAA
* * *
9572617 CT-TATATAATATATATTTTTAAAACA-TTTT--GA
1 ATATATATAATATATAGTTTTAAAACATTTTTAAAA
* * *
9572649 ATATATAT-ATATGATA----T-ATA-ATTTTGAAAC
1 ATATATATAATAT-ATAGTTTTAAAACATTTTTAAAA
*
9572679 ATATATATAATATATAGTTTTTAAAACATTTTGAAAAA
1 ATATATATAATATATAG-TTTTAAAACATTTT-TAAAA
9572717 ATATATATAATATATAGTTTTAAAACATTTTTAAAA
1 ATATATATAATATATAGTTTTAAAACATTTTTAAAA
* *
9572753 ATATATATAATATATAGTTTAAAAATTATTTTTA
1 ATATATATAATATATAGTTTTAAAA-CATTTTTA
9572787 TAATGATTTA
Statistics
Matches: 255, Mismatches: 40, Indels: 49
0.74 0.12 0.14
Matches are distributed among these distances:
27 1 0.00
28 5 0.02
29 1 0.00
30 11 0.04
31 4 0.02
32 6 0.02
33 8 0.03
34 9 0.04
35 34 0.13
36 58 0.23
37 43 0.17
38 34 0.13
39 1 0.00
40 28 0.11
41 12 0.05
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.45
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTAAAACATTTTTAAAA
Found at i:9574898 original size:27 final size:28
Alignment explanation
Indices: 9574868--9574927 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
9574858 ACTCAAAGAT
*
9574868 GATTTTGTT-AATAGAAACAAACTCAAA
1 GATTTTGTTCAAAAGAAACAAACTCAAA
* * * *
9574895 GATTTTTTTCAAAAGGAGCAGACTCAAA
1 GATTTTGTTCAAAAGAAACAAACTCAAA
9574923 GATTT
1 GATTT
9574928 GTTTCAAGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (28 bp):
GATTTTGTTCAAAAGAAACAAACTCAAA
Found at i:9574949 original size:28 final size:28
Alignment explanation
Indices: 9574883--9574941 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
9574873 TGTTAATAGA
* *
9574883 AACAAACTCAAAGATTTTTTTCAAAAGG
1 AACAGACTCAAAGATTTGTTTCAAAAGG
* *
9574911 AGCAGACTCAAAGATTTGTTTCAAGAGG
1 AACAGACTCAAAGATTTGTTTCAAAAGG
9574939 AAC
1 AAC
9574942 TGTCTCAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (28 bp):
AACAGACTCAAAGATTTGTTTCAAAAGG
Found at i:9575058 original size:64 final size:64
Alignment explanation
Indices: 9574891--9575059 Score: 182
Period size: 64 Copynumber: 2.6 Consensus size: 64
9574881 GAAACAAACT
* * * *
9574891 CAAAGATTTT-TTTCAAAAGGAGCAGACTCAAAGATTTGTTTCAAGAGGAACTGTCTCAAGAGAG
1 CAAA-ATTTTGTTTCAAAAGAAACAGACTCAAAGATTT-TTTCAAAAGAAACTGTCTCAAGAGAG
9574955 A
64 A
* * * * * *
9574956 CAAAA-ATCGTTTTAAGAA-AAACATACTCAAAGTTTTTTTTCAAAAGAAATTGTCTCAAGAGAG
1 CAAAATTTTGTTTCAA-AAGAAACAGACTCAAAG-ATTTTTTCAAAAGAAACTGTCTCAAGAGAG
9575019 A
64 A
*
9575020 CAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTT
1 CAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATTTTTT
9575060 TTTTGTTTCG
Statistics
Matches: 83, Mismatches: 16, Indels: 11
0.75 0.15 0.10
Matches are distributed among these distances:
63 1 0.01
64 54 0.65
65 28 0.34
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (64 bp):
CAAAATTTTGTTTCAAAAGAAACAGACTCAAAGATTTTTTCAAAAGAAACTGTCTCAAGAGAGA
Found at i:9575088 original size:34 final size:35
Alignment explanation
Indices: 9575025--9575093 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
9575015 AGAGACAAAA
9575025 TTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTT
1 TTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTT
*
9575060 TTTTGTTTCGAAAGAAACA-ACTCAAAGATTTTTT
1 TTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTT
9575094 CACAAAATTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 15 0.45
35 18 0.55
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (35 bp):
TTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTT
Found at i:9575115 original size:96 final size:100
Alignment explanation
Indices: 9574974--9575155 Score: 273
Period size: 96 Copynumber: 1.9 Consensus size: 100
9574964 GTTTTAAGAA
* * *
9574974 AAACATACTCAAAGTTTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAATTTTGTTTCCAAAG
1 AAACATACTCAAAGTATTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAAG
9575039 AAACAGACTCAAAGATTTTTTTTTTGTTTCGAAAG
66 AAACAGACTCAAAGATTTTTTTTTTGTTTCGAAAG
* *
9575074 AAACA-ACTCAAAG-ATTTTTTC-ACA-AAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAAT
1 AAACATACTCAAAGTATTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAAG
* *
9575135 AAATAGACTCAAATATTTTTT
66 AAACAGACTCAAAGATTTTTT
9575156 CACGAAATTG
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
96 53 0.71
97 2 0.03
98 7 0.09
99 8 0.11
100 5 0.07
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (100 bp):
AAACATACTCAAAGTATTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAAG
AAACAGACTCAAAGATTTTTTTTTTGTTTCGAAAG
Found at i:9575154 original size:61 final size:61
Alignment explanation
Indices: 9575061--9575224 Score: 247
Period size: 62 Copynumber: 2.7 Consensus size: 61
9575051 AGATTTTTTT
* *
9575061 TTTGTTTCGAAAGAAACAACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAAC
1 TTTGTTTCAAAAGAAACAACTCAAAGATTTTTTCACAAAATTGTCTCAAAAGAGACAAAAC
* * * *
9575122 TTTGTTTCAAAATAAATAGACTCAAATATTTTTTCACGAAATTGTCTCAAAAGAGACAAAAC
1 TTTGTTTCAAAAGAAACA-ACTCAAAGATTTTTTCACAAAATTGTCTCAAAAGAGACAAAAC
*
9575184 TTTGTTTCAAAAGAAACATACTCAAAGATTTTTTCTCAAAA
1 TTTGTTTCAAAAGAAACA-ACTCAAAGATTTTTTCACAAAA
9575225 GAAACAACTC
Statistics
Matches: 90, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
61 15 0.17
62 75 0.83
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.32
Consensus pattern (61 bp):
TTTGTTTCAAAAGAAACAACTCAAAGATTTTTTCACAAAATTGTCTCAAAAGAGACAAAAC
Found at i:9575235 original size:28 final size:28
Alignment explanation
Indices: 9575188--9575287 Score: 121
Period size: 28 Copynumber: 3.5 Consensus size: 28
9575178 CAAAACTTTG
*
9575188 TTTCAAAAGAAACATACTCAAAGATTTT
1 TTTCAAAAGAAACAGACTCAAAGATTTT
9575216 TTCTCAAAAGAAACA-ACTCAAAGATTTTTT
1 TT-TCAAAAGAAACAGACTCAAAGA--TTTT
* *
9575246 TTTCCAAAAGGAACAGACTCAAAGATTTG
1 TTT-CAAAAGAAACAGACTCAAAGATTTT
*
9575275 TTTCAAGAGAAAC
1 TTTCAAAAGAAAC
9575288 TGTCTTAAGA
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
28 19 0.30
29 19 0.30
30 16 0.25
31 9 0.14
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTT
Found at i:9575266 original size:31 final size:29
Alignment explanation
Indices: 9575190--9575278 Score: 117
Period size: 29 Copynumber: 3.0 Consensus size: 29
9575180 AAACTTTGTT
9575190 TCAAAAGAAACATACTCAAAGA-TTTTTTC
1 TCAAAAGAAACA-ACTCAAAGATTTTTTTC
*
9575219 TCAAAAGAAACAACTCAAAGATTTTTTTT
1 TCAAAAGAAACAACTCAAAGATTTTTTTC
* *
9575248 TCCAAAAGGAACAGACTCAAAGATTTGTTTC
1 T-CAAAAGAAACA-ACTCAAAGATTTTTTTC
9575279 AAGAGAAACT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
28 9 0.17
29 19 0.36
30 10 0.19
31 15 0.28
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (29 bp):
TCAAAAGAAACAACTCAAAGATTTTTTTC
Found at i:9575267 original size:158 final size:155
Alignment explanation
Indices: 9574880--9575246 Score: 413
Period size: 158 Copynumber: 2.3 Consensus size: 155
9574870 TTTTGTTAAT
* * * *
9574880 AGAAACAAACTCAAAGATTTTTTTCAAAAGGAGCAGACTCAAAGATTTGTTTCAAGAGGAACTGT
1 AGAAACAAACTCAAAGATTTTTTTCAAAAGAAACA-ACTCAAAGATTTTTTTCAAAAGGAACTGT
* * *
9574945 CTCAAGAGAGACAAAAATCGTTTTAAGAAAAACATACTCAAAGTTTTTTTTCAAAAGAAATTGTC
65 CTCAAGAGAGACAAAAATCGTTTCAAGAAAAACAGACTCAAAGTATTTTTTC-AAAGAAATTGTC
* * *
9575010 TCAAGAGAGACAAAATTTTGTTTCCAA
129 TCAAAAGAGACAAAACTTTGTTTCAAA
* * *
9575037 AGAAACAGACTCAAAGATTTTTTTTTTGTTTCGAAAGAAACAACTCAAAGA-TTTTTTCACAA--
1 AGAAACAAACTCAAAGA------TTTT-TTTCAAAAGAAACAACTCAAAGATTTTTTTCAAAAGG
* * * * *
9575099 AATTGTCTCAAGAGAGACAAAACTTTGTTTCAA-AATAAATAGACTCAAA-TATTTTTTC-ACGA
59 AACTGTCTCAAGAGAGACAAAA-ATCGTTTCAAGAA-AAACAGACTCAAAGTATTTTTTCAAAGA
9575161 AATTGTCTCAAAAGAGACAAAACTTTGTTTCAAA
122 AATTGTCTCAAAAGAGACAAAACTTTGTTTCAAA
*
9575195 AGAAACATACTCAAAGATTTTTTCTCAAAAGAAACAACTCAAAGATTTTTTT
1 AGAAACAAACTCAAAGATTTTTT-TCAAAAGAAACAACTCAAAGATTTTTTT
9575247 TTCCAAAAGG
Statistics
Matches: 179, Mismatches: 20, Indels: 26
0.80 0.09 0.12
Matches are distributed among these distances:
151 2 0.01
152 24 0.13
153 6 0.03
157 16 0.09
158 50 0.28
160 31 0.17
161 18 0.10
162 8 0.04
163 13 0.07
164 11 0.06
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (155 bp):
AGAAACAAACTCAAAGATTTTTTTCAAAAGAAACAACTCAAAGATTTTTTTCAAAAGGAACTGTC
TCAAGAGAGACAAAAATCGTTTCAAGAAAAACAGACTCAAAGTATTTTTTCAAAGAAATTGTCTC
AAAAGAGACAAAACTTTGTTTCAAA
Found at i:9575648 original size:105 final size:104
Alignment explanation
Indices: 9575496--9575755 Score: 423
Period size: 105 Copynumber: 2.5 Consensus size: 104
9575486 CAACAACTTT
*
9575496 GAAATTTGTATT-ATAAGGGAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAAAAACAA
1 GAAATTTGTATTCA-AAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAAAAACAA
* *
9575560 TTTCAAGTGAGATTAATTTTGTTTCATGTGAAGCAAATTC
65 TATCAAGTGAGATTAATTTTGTTTCAAGTGAAGCAAATTC
*
9575600 GAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAA
1 GAAATTTGTAT-TCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAAAAACAA
9575665 TATCAAGTGAGATTAATTTTGTTTCAAGTGAAGCAAATTC
65 TATCAAGTGAGATTAATTTTGTTTCAAGTGAAGCAAATTC
* * *
9575705 AAAATTTGTATATCAAAGGAAAAATGTCTAAAGCGAGACGAAGTTTGTTTT
1 GAAATTTGTAT-TCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTT
9575756 AAGATAAATT
Statistics
Matches: 146, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 11 0.08
105 134 0.92
106 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.31
Consensus pattern (104 bp):
GAAATTTGTATTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAAAAACAAT
ATCAAGTGAGATTAATTTTGTTTCAAGTGAAGCAAATTC
Found at i:9575813 original size:34 final size:33
Alignment explanation
Indices: 9575729--9575824 Score: 102
Period size: 34 Copynumber: 2.8 Consensus size: 33
9575719 AAAGGAAAAA
* * *
9575729 TGTCTAAAGCGAGACGAAGTTTGTTTTAAGATAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTT---ATAAAT
* * *
9575765 TGTCTTAAGTGAGACAACATTTGTTTTATAATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTATAA-AT
9575799 TGTCTCAAGCGAGACAAAATTTGTTT
1 TGTCTCAAGCGAGACAAAATTTGTTT
9575825 CAAGAAAAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 4 0.08
34 25 0.49
36 22 0.43
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (33 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTATAAAT
Found at i:9576141 original size:4 final size:4
Alignment explanation
Indices: 9576132--9576173 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
9576122 CTCATGTAAC
9576132 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT AT-T GATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT -ATGT ATGT
9576174 TTTCTCGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 2 0.06
3 1 0.03
4 30 0.88
5 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:9577367 original size:12 final size:11
Alignment explanation
Indices: 9577352--9577462 Score: 68
Period size: 10 Copynumber: 9.7 Consensus size: 11
9577342 TTCTTTGCTC
*
9577352 TTTTC-TTTAT
1 TTTTCTTTTTT
*
9577362 TTTT-TTATTT
1 TTTTCTTTTTT
9577372 TTTTC-TTTTT
1 TTTTCTTTTTT
*
9577382 CTTTCTGTTTGCTT
1 TTTTCT-TTT--TT
*
9577396 TTCTCTTTGTTT
1 TTTTCTTT-TTT
9577408 TTTTCTTTTTCT
1 TTTTCTTTTT-T
9577420 TTTTCTTTGCTCTT
1 TTTTCTTT--T-TT
*
9577434 TTTTCTTTTCT
1 TTTTCTTTTTT
*
9577445 TTTT-TTCTTT
1 TTTTCTTTTTT
9577455 TTTTCTTT
1 TTTTCTTT
9577463 GCTTCATTTC
Statistics
Matches: 78, Mismatches: 11, Indels: 23
0.70 0.10 0.21
Matches are distributed among these distances:
10 27 0.35
11 9 0.12
12 22 0.28
13 2 0.03
14 17 0.22
15 1 0.01
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:9577385 original size:31 final size:32
Alignment explanation
Indices: 9577339--9577455 Score: 94
Period size: 36 Copynumber: 3.5 Consensus size: 32
9577329 TGTTCTTTGC
*
9577339 TTTTTCTTTGCTCTTTTCTTT-ATTTTTTTATT
1 TTTTTCTTT-TTCTTTTCTTTGATTTTTTTATT
* * *
9577371 TTTTTCTTTTTCTTTCTGTTTGCTTTTCTCTTTGTT
1 TTTTTCTTTTTCTTT-TCTTTG-ATTT-T-TTTATT
* *
9577407 TTTTTCTTTTTCTTTTTCTTTGCTCTTTTTTCTT
1 TTTTTCTTTTTC-TTTTCTTTGAT-TTTTTTATT
*
9577441 TTCTT-TTTTTCTTTT
1 TTTTTCTTTTTCTTTT
9577456 TTTCTTTGCT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
31 5 0.07
32 17 0.24
33 6 0.09
34 12 0.17
35 3 0.04
36 24 0.34
37 3 0.04
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (32 bp):
TTTTTCTTTTTCTTTTCTTTGATTTTTTTATT
Found at i:9577397 original size:16 final size:13
Alignment explanation
Indices: 9577339--9577455 Score: 80
Period size: 14 Copynumber: 8.8 Consensus size: 13
9577329 TGTTCTTTGC
*
9577339 TTTTTC-TTTGCT
1 TTTTTCTTTTGTT
* *
9577351 CTTTTC-TTTATT
1 TTTTTCTTTTGTT
* *
9577363 TTTTTATTTTTTT
1 TTTTTCTTTTGTT
9577376 CTTTTTCTTTCTGTT
1 -TTTTTCTTT-TGTT
9577391 TGCTTTTCTCTTTGTT
1 T--TTTTCT-TTTGTT
*
9577407 TTTTTCTTTT-TC
1 TTTTTCTTTTGTT
9577419 TTTTTC-TTTGCTCT
1 TTTTTCTTTTG-T-T
*
9577433 TTTTTCTTTTCTT
1 TTTTTCTTTTGTT
9577446 TTTTTCTTTT
1 TTTTTCTTTT
9577456 TTTCTTTGCT
Statistics
Matches: 84, Mismatches: 11, Indels: 19
0.74 0.10 0.17
Matches are distributed among these distances:
11 3 0.04
12 20 0.24
13 20 0.24
14 22 0.26
15 6 0.07
16 11 0.13
17 2 0.02
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTTGTT
Done.