Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 119 of 135
Found at i:39713206 original size:117 final size:117
Alignment explanation
Indices: 39712953--39713206 Score: 332
Period size: 117 Copynumber: 2.2 Consensus size: 117
39712943 GTGTTGGAGT
* * * *
39712953 AGGTGCAGGTGGTGGTGGTGGTGTTGGGGTTGGTGGAGGTAGTGTTAGTGGAGGTGCAAGAGGAG
1 AGGTGCAGGTGGTGGTGGAGGTGTAGGGGTTGGTAGAGGTAGTGTTAGCGGAGGTGCAAGAGGAG
* *
39713018 GTGTTGGAGTAGGTGTAGGTGGTGGTGGTGGTGTTGGGGCTGGTGGAGGTGG
66 GTGTTGGAGTAGGTGCAGGTGGTGGTGGTGGTGGTGGGGCTGGTGGAGGTGG
* ** * * *
39713070 AGGAGCAGGTGCCGGTGGAGGTGCTAGGGG-TGGTAGAGGTGGTGTTGGCGGAGGTGCAGGAGGA
1 AGGTGCAGGTGGTGGTGGAGGTG-TAGGGGTTGGTAGAGGTAGTGTTAGCGGAGGTGCAAGAGGA
* *
39713134 GGTGTTGGAGTAGGTGCAGGTGGTGGTGGTGGTGGTGGTGTTGG-GGTAGGTGG
65 GGTGTTGGAGTAGGTGCAGGTGGTGGTGGTGGTGGTGGGGCTGGTGG-AGGTGG
* *
39713187 AGGTGGAGGTGGTGTTGGAG
1 AGGTGCAGGTGGTGGTGGAG
39713207 TAGGTGCAGG
Statistics
Matches: 116, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
116 2 0.02
117 109 0.94
118 5 0.04
ACGTcount: A:0.13, C:0.04, G:0.58, T:0.26
Consensus pattern (117 bp):
AGGTGCAGGTGGTGGTGGAGGTGTAGGGGTTGGTAGAGGTAGTGTTAGCGGAGGTGCAAGAGGAG
GTGTTGGAGTAGGTGCAGGTGGTGGTGGTGGTGGTGGGGCTGGTGGAGGTGG
Found at i:39713237 original size:63 final size:66
Alignment explanation
Indices: 39713127--39713302 Score: 234
Period size: 63 Copynumber: 2.7 Consensus size: 66
39713117 GCGGAGGTGC
* *
39713127 AGGAGGAGGTGTTGGAGTAGGTGCAGGTGGTGGTGGTGGTGGTGGTGTTGGGGTAGGTGGA-G-G
1 AGGAGGTGGTGTTGGAGTAGGTGCAGGTGGTAGTGGTGGTGGTGGTGTTGGGGTAGGTGGAGGAG
39713190 T
66 T
*
39713191 -GGAGGTGGTGTTGGAGTAGGTGCAGGTGGTAGTGGTGGTGGTGGTGTTGGGGTTGGTGGAGGAG
1 AGGAGGTGGTGTTGGAGTAGGTGCAGGTGGTAGTGGTGGTGGTGGTGTTGGGGTAGGTGGAGGAG
39713255 T
66 T
* * * * * *
39713256 AGGAGCTGGTGGTGGTGGAGGTGCTAGG-GGTAGTGGAGGTGCTGGTG
1 AGGAGGTGGTGTTGGAGTAGGTGC-AGGTGGTAGTGGTGGTGGTGGTG
39713303 GTGGTGCAGG
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
63 57 0.58
64 1 0.01
65 2 0.02
66 36 0.36
67 3 0.03
ACGTcount: A:0.12, C:0.03, G:0.59, T:0.27
Consensus pattern (66 bp):
AGGAGGTGGTGTTGGAGTAGGTGCAGGTGGTAGTGGTGGTGGTGGTGTTGGGGTAGGTGGAGGAG
T
Found at i:39713362 original size:96 final size:92
Alignment explanation
Indices: 39713226--39713447 Score: 256
Period size: 96 Copynumber: 2.4 Consensus size: 92
39713216 GTGGTAGTGG
* *
39713226 TGGTGGTGGTGTTGGGGTTGGTGGAGGAGTAGGA--GCTGGTGGTGGTGGAGGTGCTAGG-GGTA
1 TGGTGGTGGTGTTGGGGCTGGTGGAGGAGTAGGAGCGCTGGTGGTGGTGGAGGAGCT-GGAGGT-
* *
39713288 G-TGGAGGTGCTGGTG-GTGGTGCAGGTGT
64 GTTGGAGGTACTGGAGTG-GGTGCAGGTGT
* * * *
39713316 TGGTAGTGGTGTTGGAGCTGGTGGAGGAGTAGGAGCCGCTAATGGTGGTGGTGGTGGAGGTGGAG
1 TGGTGGTGGTGTTGGGGCTGGTGGAGGAGTAGGAG-CGC---TGGTGGTGGTGGAGGAGCTGGAG
39713381 GTGTTGGAGGTACTGGAGTGGGTGCAGGTGT
62 GTGTTGGAGGTACTGGAGTGGGTGCAGGTGT
* *
39713412 TGGTGGTGGTATTGGGGCTGGTGGAGGGGTAGGAGC
1 TGGTGGTGGTGTTGGGGCTGGTGGAGGAGTAGGAGC
39713448 TGGTGGAGGT
Statistics
Matches: 111, Mismatches: 12, Indels: 13
0.82 0.09 0.10
Matches are distributed among these distances:
90 31 0.28
93 2 0.02
95 4 0.04
96 73 0.66
97 1 0.01
ACGTcount: A:0.12, C:0.05, G:0.56, T:0.27
Consensus pattern (92 bp):
TGGTGGTGGTGTTGGGGCTGGTGGAGGAGTAGGAGCGCTGGTGGTGGTGGAGGAGCTGGAGGTGT
TGGAGGTACTGGAGTGGGTGCAGGTGT
Found at i:39713554 original size:18 final size:18
Alignment explanation
Indices: 39713412--39713554 Score: 55
Period size: 18 Copynumber: 8.3 Consensus size: 18
39713402 GTGCAGGTGT
* * *
39713412 TGGTGGTGGTATTGGGGC
1 TGGTGGAGGTGTTGGAGC
* *
39713430 TGGTGGAGGGGTAGGAGC
1 TGGTGGAGGTGTTGGAGC
39713448 TGGTGGA-G-G-T---GC
1 TGGTGGAGGTGTTGGAGC
* * *
39713460 AGGTGGAGGTGTTGCAAC
1 TGGTGGAGGTGTTGGAGC
* * *
39713478 AGGTGCAGGTGTTGGGGC
1 TGGTGGAGGTGTTGGAGC
* * *
39713496 TAGTGGAGGAGTAGGAGC
1 TGGTGGAGGTGTTGGAGC
* * ** * *
39713514 TGGTGGTGGCGCAGGTGG
1 TGGTGGAGGTGTTGGAGC
*
39713532 AGGTGGAGGTGTTGGAGC
1 TGGTGGAGGTGTTGGAGC
39713550 TGGTG
1 TGGTG
39713555 CAGATACTGG
Statistics
Matches: 87, Mismatches: 32, Indels: 12
0.66 0.24 0.09
Matches are distributed among these distances:
12 8 0.09
13 1 0.01
14 1 0.01
15 1 0.01
16 1 0.01
17 1 0.01
18 74 0.85
ACGTcount: A:0.14, C:0.08, G:0.55, T:0.23
Consensus pattern (18 bp):
TGGTGGAGGTGTTGGAGC
Found at i:39715523 original size:23 final size:22
Alignment explanation
Indices: 39715495--39715545 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
39715485 AAAGATATAT
*
39715495 ATAATTACTAAATATAAATAAAA
1 ATAATTACTAAAAATAAA-AAAA
**
39715518 ATAATTTTTTAAAAATAAAAAAA
1 ATAA-TTACTAAAAATAAAAAAA
39715541 ATAAT
1 ATAAT
39715546 ATGAGCGAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 12 0.50
24 11 0.46
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
ATAATTACTAAAAATAAAAAAA
Found at i:39719019 original size:16 final size:17
Alignment explanation
Indices: 39719000--39719032 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
39718990 AAATTTATTT
*
39719000 TTATATAAAAA-TAATA
1 TTATAAAAAAATTAATA
39719016 TTATAAAAAAATTAATA
1 TTATAAAAAAATTAATA
39719033 CGGGAGGGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TTATAAAAAAATTAATA
Found at i:39720575 original size:20 final size:20
Alignment explanation
Indices: 39720550--39720587 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39720540 GACAAGATTT
39720550 GTCCCATC-ACAAACATCCTC
1 GTCCCATCGA-AAACATCCTC
39720570 GTCCCATCGAAAACATCC
1 GTCCCATCGAAAACATCC
39720588 ACCCCATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.32, C:0.42, G:0.08, T:0.18
Consensus pattern (20 bp):
GTCCCATCGAAAACATCCTC
Found at i:39720780 original size:16 final size:16
Alignment explanation
Indices: 39720759--39720792 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
39720749 TCATATTCTC
39720759 TTCACTTTTTGTAACT
1 TTCACTTTTTGTAACT
39720775 TTCACTTTTTGTAACT
1 TTCACTTTTTGTAACT
39720791 TT
1 TT
39720793 GAACTTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (16 bp):
TTCACTTTTTGTAACT
Found at i:39720798 original size:17 final size:16
Alignment explanation
Indices: 39720762--39720799 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
39720752 TATTCTCTTC
*
39720762 ACTTTTTGTAACTTTC
1 ACTTTTTGTAACTTTA
39720778 ACTTTTTGTAACTTTGA
1 ACTTTTTGTAACTTT-A
39720795 ACTTT
1 ACTTT
39720800 CTAATTAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.21, C:0.16, G:0.08, T:0.55
Consensus pattern (16 bp):
ACTTTTTGTAACTTTA
Found at i:39721841 original size:57 final size:57
Alignment explanation
Indices: 39721770--39721881 Score: 190
Period size: 57 Copynumber: 2.0 Consensus size: 57
39721760 GAGATTATCC
**
39721770 AAAGGCAAAGTTGAGCAATTAATCCACCGAC-ATATAGATTGTTGGAGGACCAATTCT
1 AAAGGCAAAGTTGAGCAATTAATCCACCGACAAT-TAGATTCCTGGAGGACCAATTCT
39721827 AAAGGCAAAGTTGAGCAATTAATCCACCGACAATTAGATTCCTGGAGGACCAATT
1 AAAGGCAAAGTTGAGCAATTAATCCACCGACAATTAGATTCCTGGAGGACCAATT
39721882 TTAATTTATA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
57 50 0.96
58 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (57 bp):
AAAGGCAAAGTTGAGCAATTAATCCACCGACAATTAGATTCCTGGAGGACCAATTCT
Found at i:39722304 original size:19 final size:19
Alignment explanation
Indices: 39722282--39722318 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39722272 TAATTTGTTG
*
39722282 AATTTTTAATATTTTTACT
1 AATTTTTAATAATTTTACT
*
39722301 AATTTTTATTAATTTTAC
1 AATTTTTAATAATTTTAC
39722319 GTGGACAGGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTTTAATAATTTTACT
Found at i:39723964 original size:3 final size:3
Alignment explanation
Indices: 39723956--39723982 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39723946 CCAATTTGCT
39723956 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
39723983 AATCCTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39725024 original size:31 final size:31
Alignment explanation
Indices: 39724989--39725052 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
39724979 AAGTGATTAT
**
39724989 TAAATTATTC-AAAAGTTTTCATTTAAGTCAC
1 TAAATTATTCAAAAAAATTT-ATTTAAGTCAC
39725020 TAAATTATTCAAAAAAATTTATTTAAGTCAC
1 TAAATTATTCAAAAAAATTTATTTAAGTCAC
39725051 TA
1 TA
39725053 GATTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 23 0.77
32 7 0.23
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.41
Consensus pattern (31 bp):
TAAATTATTCAAAAAAATTTATTTAAGTCAC
Found at i:39728566 original size:17 final size:18
Alignment explanation
Indices: 39728538--39728571 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
39728528 TTTTCAATTG
39728538 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
39728556 TAATTAA-TTAAAATTT
1 TAATTAATTTAAAATTT
39728572 ATTTTCATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:39736027 original size:22 final size:21
Alignment explanation
Indices: 39736006--39736055 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
39735996 AATTTTTTTA
39736006 ATTTAAAAAATTCAAAAATTT
1 ATTTAAAAAATTCAAAAATTT
** *
39736027 ATTTTTAAAATTTAAAAA-TT
1 ATTTAAAAAATTCAAAAATTT
*
39736047 ATTTCAAAA
1 ATTTAAAAA
39736056 TTATAAATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTAAAAAATTCAAAAATTT
Found at i:39736048 original size:20 final size:21
Alignment explanation
Indices: 39736012--39736050 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39736002 TTTAATTTAA
39736012 AAAATTCAAAAATTTATTTTT
1 AAAATTCAAAAATTTATTTTT
*
39736033 AAAATTTAAAAA-TTATTT
1 AAAATTCAAAAATTTATTT
39736051 CAAAATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
AAAATTCAAAAATTTATTTTT
Found at i:39736062 original size:20 final size:21
Alignment explanation
Indices: 39736012--39736062 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
39736002 TTTAATTTAA
* *
39736012 AAAATTCAAAAATTTATTTTT
1 AAAATTTAAAAATTTATTTTC
39736033 AAAATTTAAAAA-TTA-TTTC
1 AAAATTTAAAAATTTATTTTC
39736052 AAAATTATAAA
1 AAAATT-TAAA
39736063 TAAATTAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 7 0.26
21 11 0.41
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATTTAAAAATTTATTTTC
Found at i:39738421 original size:16 final size:14
Alignment explanation
Indices: 39738391--39738420 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39738381 ATCTAATAAA
39738391 ACTGTAATCCACAC
1 ACTGTAATCCACAC
39738405 ACTGTAATCCACAC
1 ACTGTAATCCACAC
39738419 AC
1 AC
39738421 AGAAAATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.37, G:0.07, T:0.20
Consensus pattern (14 bp):
ACTGTAATCCACAC
Found at i:39738583 original size:2 final size:2
Alignment explanation
Indices: 39738576--39738610 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39738566 AGAAAAAGGA
39738576 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
39738611 CGGTAGCTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39740325 original size:16 final size:16
Alignment explanation
Indices: 39740304--39740364 Score: 77
Period size: 16 Copynumber: 3.8 Consensus size: 16
39740294 TTTGGTTCGC
*
39740304 TGTAATGAAATAGAGT
1 TGTAATGGAATAGAGT
* *
39740320 TGTAATGGAATAAAAT
1 TGTAATGGAATAGAGT
*
39740336 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGT
*
39740352 TGTAATAGAATAG
1 TGTAATGGAATAG
39740365 GGCTGTAATC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.44, C:0.02, G:0.25, T:0.30
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:39740369 original size:16 final size:16
Alignment explanation
Indices: 39740302--39740373 Score: 65
Period size: 16 Copynumber: 4.5 Consensus size: 16
39740292 TGTTTGGTTC
39740302 GCTGTAAT-GAAATAGA
1 GCTGTAATAG-AATAGA
* * *
39740318 GTTGTAATGGAATAAA
1 GCTGTAATAGAATAGA
** *
39740334 ATTGTAATGGAATAGA
1 GCTGTAATAGAATAGA
*
39740350 GCTGTAATAGAATAGG
1 GCTGTAATAGAATAGA
39740366 GCTGTAAT
1 GCTGTAAT
39740374 CGGTATTTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 46 0.98
17 1 0.02
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.29
Consensus pattern (16 bp):
GCTGTAATAGAATAGA
Found at i:39740372 original size:32 final size:32
Alignment explanation
Indices: 39740302--39740373 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
39740292 TGTTTGGTTC
* *
39740302 GCTGTAATGAAATAGAGTTGTAATGGAATAAA
1 GCTGTAATGAAATAGAGCTGTAATAGAATAAA
** * **
39740334 ATTGTAATGGAATAGAGCTGTAATAGAATAGG
1 GCTGTAATGAAATAGAGCTGTAATAGAATAAA
39740366 GCTGTAAT
1 GCTGTAAT
39740374 CGGTATTTCA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.29
Consensus pattern (32 bp):
GCTGTAATGAAATAGAGCTGTAATAGAATAAA
Found at i:39740595 original size:59 final size:58
Alignment explanation
Indices: 39740526--39740645 Score: 188
Period size: 57 Copynumber: 2.1 Consensus size: 58
39740516 AATGATTATC
*
39740526 ATTATTAAATATAATTTAATAAAAAATAATAAATAATTTAATTATA-TTTTAACATAATT
1 ATTATTAAATATAATTTAAT--AAAATAATAAATAATTTAATAATATTTTTAACATAATT
* *
39740585 ATTATTAAATATAATTTAATAAAATAATATATAATTTAATAATATTTTTAATATAATT
1 ATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAATATTTTTAACATAATT
39740643 ATT
1 ATT
39740646 GTTATTGTTA
Statistics
Matches: 57, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 22 0.39
58 15 0.26
59 20 0.35
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.47
Consensus pattern (58 bp):
ATTATTAAATATAATTTAATAAAATAATAAATAATTTAATAATATTTTTAACATAATT
Found at i:39740816 original size:22 final size:19
Alignment explanation
Indices: 39740771--39740824 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
39740761 CCTAATCGAA
39740771 AATAAT-AAAAAAATAAAG
1 AATAATAAAAAAAATAAAG
*
39740789 ACTAATAAAGAAAAATAAATG
1 AATAATAAA-AAAAATAAA-G
39740810 CAATAATAAATAAAA
1 -AATAATAAA-AAAA
39740825 CCATTAACTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 5 0.17
19 2 0.07
20 9 0.31
21 1 0.03
22 12 0.41
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (19 bp):
AATAATAAAAAAAATAAAG
Found at i:39746650 original size:16 final size:18
Alignment explanation
Indices: 39746624--39746657 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39746614 TTTATTATAT
39746624 TTCACTAATTAA-ACAAA
1 TTCACTAATTAACACAAA
39746641 TTCA-TAATTAACACAAA
1 TTCACTAATTAACACAAA
39746658 ATTTATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (18 bp):
TTCACTAATTAACACAAA
Found at i:39749946 original size:22 final size:23
Alignment explanation
Indices: 39749912--39749954 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
39749902 ACTTTATAAT
39749912 TTTTTATGATTAATTTAGTAACA
1 TTTTTATGATTAATTTAGTAACA
* *
39749935 TTTTTA-GTTTAATTTGGTAA
1 TTTTTATGATTAATTTAGTAA
39749955 ACTAATACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (23 bp):
TTTTTATGATTAATTTAGTAACA
Found at i:39772636 original size:31 final size:31
Alignment explanation
Indices: 39772592--39772652 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
39772582 ATAATCATTG
*
39772592 AATTAATCTAAAGTTTTCATTTAAGTCACTA
1 AATTAATCAAAAGTTTTCATTTAAGTCACTA
* *
39772623 AATTATTCAAAAGTTTTTATTTAAGTCACT
1 AATTAATCAAAAGTTTTCATTTAAGTCACT
39772653 GGACTCTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (31 bp):
AATTAATCAAAAGTTTTCATTTAAGTCACTA
Found at i:39777143 original size:1 final size:1
Alignment explanation
Indices: 39777137--39777161 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
39777127 TTTTATGATT
39777137 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
39777162 TTTCTCTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:39778089 original size:17 final size:16
Alignment explanation
Indices: 39778031--39778089 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
39778021 TTTATGTTTC
39778031 TATTTATATTATTGAAT
1 TATTTATATT-TTGAAT
*
39778048 TAAATTTTATATTTTGTAT
1 T--A-TTTATATTTTGAAT
39778067 TATTTATATTGTTGAAT
1 TATTTATATT-TTGAAT
*
39778084 TGTTTA
1 TATTTA
39778090 ATCATACTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 8 0.23
17 12 0.34
19 7 0.20
20 8 0.23
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (16 bp):
TATTTATATTTTGAAT
Found at i:39778251 original size:17 final size:17
Alignment explanation
Indices: 39778216--39778248 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39778206 TTATTAAAAA
39778216 AATATATTTTTACATTT
1 AATATATTTTTACATTT
39778233 AATATATTTTTA-ATTT
1 AATATATTTTTACATTT
39778249 TAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (17 bp):
AATATATTTTTACATTT
Found at i:39779130 original size:30 final size:29
Alignment explanation
Indices: 39779070--39779145 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
39779060 CGTATTCTTC
*
39779070 TAAAATTT-AAATTTGAATTTTTATACTTT
1 TAAATTTTAAAATTT-AATTTTTATACTTT
* * *
39779099 T-ATTTTTAAAAATTTAATTTTTCTATTTTT
1 TAAATTTT-AAAATTTAATTTTTATA-CTTT
39779129 TAAATTTTAAAATTTAA
1 TAAATTTTAAAATTTAA
39779146 ATTAACTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 4 0.11
29 10 0.26
30 19 0.50
31 5 0.13
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (29 bp):
TAAATTTTAAAATTTAATTTTTATACTTT
Found at i:39788084 original size:40 final size:40
Alignment explanation
Indices: 39788038--39788135 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
39788028 TTTGGTTGAA
*
39788038 AAATGCCACAAAGGGTAA-AACAATAGCGGCGTTTTTTCAT
1 AAATGCCACAAAAGGTAATAA-AATAGCGGCGTTTTTTCAT
* *
39788078 AAATGCCGCAAAAGGTAATGAAATAGCGGCGTTTTTTCAT
1 AAATGCCACAAAAGGTAATAAAATAGCGGCGTTTTTTCAT
* **
39788118 AAACGCCGTAAAAGGTAA
1 AAATGCCACAAAAGGTAA
39788136 AGTTATAGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 51 0.98
41 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.23
Consensus pattern (40 bp):
AAATGCCACAAAAGGTAATAAAATAGCGGCGTTTTTTCAT
Found at i:39788227 original size:41 final size:40
Alignment explanation
Indices: 39788159--39788333 Score: 172
Period size: 41 Copynumber: 4.3 Consensus size: 40
39788149 TTTAAAGAGA
* * * * * * *
39788159 AAACGCCGCTAATGCTCTGACCTTTAGCGGCGTTTTTGA-
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTTCAT
* *
39788198 AGAAGCGCCGCTAAAGGTCAGAGCATTAGCTGTGCTTTTTCAT
1 A-AA-CGCCGCTAAAGGTCAGAGCATTAGCGGCGC-TTTTCAT
* * * *
39788241 AAACGCTGCTAAAGATCAGAGCATTTGCGGCGCCTTATCAT
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCG-CTTTTCAT
*
39788282 AAATGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTTCCAT
1 AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTT-CAT
39788323 AAACGCCGCTA
1 AAACGCCGCTA
39788334 TTTTATTTAA
Statistics
Matches: 109, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
39 1 0.01
40 6 0.06
41 93 0.85
42 8 0.07
43 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
AAACGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTTTCAT
Found at i:39788588 original size:17 final size:17
Alignment explanation
Indices: 39788566--39788603 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
39788556 TTTATGAAAC
39788566 ATCATATTCAACTAACT
1 ATCATATTCAACTAACT
*
39788583 ATCATATTCCACTAACT
1 ATCATATTCAACTAACT
39788600 ATCA
1 ATCA
39788604 ATAAGAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.34
Consensus pattern (17 bp):
ATCATATTCAACTAACT
Found at i:39789504 original size:21 final size:20
Alignment explanation
Indices: 39789480--39789522 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
39789470 TTTAAATACA
39789480 TAATAATTT-AAATAATATTTT
1 TAATAATTTCAAAT-AT-TTTT
*
39789501 TAATTATTTCAAATATTTTT
1 TAATAATTTCAAATATTTTT
39789521 TA
1 TA
39789523 CCATCTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATAATTTCAAATATTTTT
Found at i:39789817 original size:41 final size:41
Alignment explanation
Indices: 39789771--39789855 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
39789761 ATTAGCGACG
* * * *
39789771 TTTATGGTAAAAACGCCGCTAAAAGTAAAGTAATAGCTGCA
1 TTTATGGGAAAAACGCCACTAAAAGTAAAGAAATAGCGGCA
*
39789812 TTTATGGGAAAAACGCCACTAAAAGTCAAGAAATAGCGGCA
1 TTTATGGGAAAAACGCCACTAAAAGTAAAGAAATAGCGGCA
39789853 TTT
1 TTT
39789856 TTCCATAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (41 bp):
TTTATGGGAAAAACGCCACTAAAAGTAAAGAAATAGCGGCA
Found at i:39789891 original size:42 final size:42
Alignment explanation
Indices: 39789843--39789960 Score: 123
Period size: 42 Copynumber: 2.8 Consensus size: 42
39789833 AAAGTCAAGA
*
39789843 AATAGCGGCATTTTTCCATAAACGCCGCAAAAGGT-ATAGAGC
1 AATAGCGGCGTTTTTCCATAAACGCCGCAAAAGGTCAT-GAGC
** * *
39789885 AATAGCGGCGTTTTTGTGA-AAACGCCGTAAAAGGTCCTGAGC
1 AATAGCGGCGTTTTT-CCATAAACGCCGCAAAAGGTCATGAGC
* * * *
39789927 ATTTGCGGCGTTTTTCCATAAACGTCGCTAAAGG
1 AATAGCGGCGTTTTTCCATAAACGCCGCAAAAGG
39789961 AATTGAAATA
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.02
42 58 0.95
43 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (42 bp):
AATAGCGGCGTTTTTCCATAAACGCCGCAAAAGGTCATGAGC
Found at i:39791835 original size:58 final size:58
Alignment explanation
Indices: 39791749--39791879 Score: 190
Period size: 58 Copynumber: 2.2 Consensus size: 58
39791739 ACTCGGGGGC
* * * *
39791749 AAAATGGTAGATTTTGGTGAAATTGGGGTTAAAAATGGGATTTAGGGGAGTTTGAGGGT
1 AAAATGGTA-ATTTTAGTGAAATCGGGGTTAAAAAGGGGATTTAGGGAAGTTTGAGGGT
* * *
39791808 GAAATGGTAATTTTAGTGAAATCGGGGTTTAAAAGGGGATTTAGGGAAGTTTGGGGGT
1 AAAATGGTAATTTTAGTGAAATCGGGGTTAAAAAGGGGATTTAGGGAAGTTTGAGGGT
39791866 AAAATGGTAATTTT
1 AAAATGGTAATTTT
39791880 TGAAAGTTTC
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
58 56 0.88
59 8 0.12
ACGTcount: A:0.31, C:0.01, G:0.35, T:0.33
Consensus pattern (58 bp):
AAAATGGTAATTTTAGTGAAATCGGGGTTAAAAAGGGGATTTAGGGAAGTTTGAGGGT
Found at i:39791968 original size:30 final size:31
Alignment explanation
Indices: 39791862--39792121 Score: 265
Period size: 30 Copynumber: 8.7 Consensus size: 31
39791852 GGAAGTTTGG
**
39791862 GGGT-AAAATGGTAATTTTT-G-AAAGTTTCG
1 GGGTCAAAAT-GTAATTTTTGGAAAAGTTTTA
* *
39791891 GGGTAAAAATGTAATTTTTGG-AAA-TTTTG
1 GGGTCAAAATGTAATTTTTGGAAAAGTTTTA
* *
39791920 GGGTCAAAATATGA-TTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTTGGAAAAGTTTTA
* *
39791950 GGGTTAAAATGT-ATTTTTGGAAAA-TTTTT
1 GGGTCAAAATGTAATTTTTGGAAAAGTTTTA
* *
39791979 GGAGTCAAAATATAATTTTTAG-AAAGTTTTA
1 GG-GTCAAAATGTAATTTTTGGAAAAGTTTTA
*
39792010 GGGTCAAAATATAA-TTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTTGGAAAAGTTTTA
* * *
39792040 GTGTCAAAATGTAATTTTTAG-AAAGTTTTG
1 GGGTCAAAATGTAATTTTTGGAAAAGTTTTA
* *
39792070 GGGTTAAAATGTAATTTTT-AAAAAGTTTTA
1 GGGTCAAAATGTAATTTTTGGAAAAGTTTTA
*
39792100 GGGTCAAAATATAATTTTTGGA
1 GGGTCAAAATGTAATTTTTGGA
39792122 CAATTTAGGG
Statistics
Matches: 195, Mismatches: 24, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
28 6 0.03
29 43 0.22
30 127 0.65
31 19 0.10
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (31 bp):
GGGTCAAAATGTAATTTTTGGAAAAGTTTTA
Found at i:39792030 original size:90 final size:90
Alignment explanation
Indices: 39791862--39792117 Score: 340
Period size: 90 Copynumber: 2.9 Consensus size: 90
39791852 GGAAGTTTGG
* * * * *
39791862 GGGT-AAAATGGTAATTTTT-GAAAGTTTCGGGGTAAAAATGTAATTTTTGGAAA-TTTTGGGGT
1 GGGTCAAAAT-GTAATTTTTAGAAAGTTTTGGAGTCAAAATGTAATTTTTAGAAAGTTTTAGGGT
*
39791924 CAAAATATGATTTTGGAAAAGTTTTA
65 CAAAATATAATTTTGGAAAAGTTTTA
* * * *
39791950 GGGTTAAAATGT-ATTTTTGGAAAATTTTTGGAGTCAAAATATAATTTTTAGAAAGTTTTAGGGT
1 GGGTCAAAATGTAATTTTTAG-AAAGTTTTGGAGTCAAAATGTAATTTTTAGAAAGTTTTAGGGT
39792014 CAAAATATAATTTTGGAAAAGTTTTA
65 CAAAATATAATTTTGGAAAAGTTTTA
* * * *
39792040 GTGTCAAAATGTAATTTTTAGAAAGTTTTGGGGTTAAAATGTAATTTTTAAAAAGTTTTAGGGTC
1 GGGTCAAAATGTAATTTTTAGAAAGTTTTGGAGTCAAAATGTAATTTTTAGAAAGTTTTAGGGTC
39792105 AAAATATAATTTT
66 AAAATATAATTTT
39792118 TGGACAATTT
Statistics
Matches: 147, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
87 6 0.04
88 7 0.05
89 32 0.22
90 95 0.65
91 7 0.05
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.41
Consensus pattern (90 bp):
GGGTCAAAATGTAATTTTTAGAAAGTTTTGGAGTCAAAATGTAATTTTTAGAAAGTTTTAGGGTC
AAAATATAATTTTGGAAAAGTTTTA
Found at i:39793228 original size:9 final size:9
Alignment explanation
Indices: 39793190--39793221 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
39793180 ATTACCATTG
*
39793190 TTATTAATA
1 TTATTGATA
39793199 TTATTGATA
1 TTATTGATA
39793208 TTATTGATA
1 TTATTGATA
39793217 TTATT
1 TTATT
39793222 ATTATTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (9 bp):
TTATTGATA
Found at i:39793931 original size:6 final size:6
Alignment explanation
Indices: 39793899--39793949 Score: 50
Period size: 6 Copynumber: 8.0 Consensus size: 6
39793889 GACATTGGAC
*
39793899 TTTTAA TTTTTAA TGTTTAGTA TTTTAA TTTTAA -TTTAA TTTTAA ATTTAA
1 TTTTAA -TTTTAA T-TTTA--A TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
39793950 AGTAAATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
5 5 0.13
6 18 0.46
7 10 0.26
8 4 0.10
9 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (6 bp):
TTTTAA
Found at i:39793938 original size:11 final size:12
Alignment explanation
Indices: 39793922--39793997 Score: 52
Period size: 11 Copynumber: 6.4 Consensus size: 12
39793912 TGTTTAGTAT
39793922 TTTAATTTT-AA
1 TTTAATTTTAAA
39793933 TTTAATTTTAAA
1 TTTAATTTTAAA
**
39793945 TTTAA-AGTAAA
1 TTTAATTTTAAA
*
39793956 TTTAAATAATTAAA
1 TTT-AAT-TTTAAA
*
39793970 TTTAAATTTAAGA
1 TTTAATTTTAA-A
*
39793983 --TAAATTTAAA
1 TTTAATTTTAAA
39793993 TTTAA
1 TTTAA
39793998 AAACAATTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
10 1 0.02
11 25 0.47
12 16 0.30
13 3 0.06
14 8 0.15
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:39793950 original size:6 final size:6
Alignment explanation
Indices: 39793920--39793998 Score: 74
Period size: 6 Copynumber: 13.2 Consensus size: 6
39793910 AATGTTTAGT
* * * *
39793920 ATTTTA ATTTTA ATTTAA TTTTAA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
39793969 ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA A
39793999 AACAATTTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.11
6 47 0.76
7 1 0.02
8 6 0.10
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:39793977 original size:31 final size:31
Alignment explanation
Indices: 39793934--39793993 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
39793924 TAATTTTAAT
*
39793934 TTAATTTTAAATTTAA-AGTAAATTTAAATAA
1 TTAAATTTAAATTTAAGA-TAAATTTAAATAA
39793965 TTAAATTTAAATTTAAGATAAATTTAAAT
1 TTAAATTTAAATTTAAGATAAATTTAAAT
39793994 TTAAAAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (31 bp):
TTAAATTTAAATTTAAGATAAATTTAAATAA
Found at i:39794005 original size:17 final size:17
Alignment explanation
Indices: 39793967--39794008 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
39793957 TTAAATAATT
*
39793967 AAATTTAAATTTAAGAT
1 AAATTTAAATTTAAGAA
39793984 AAATTTAAATTTAA-AA
1 AAATTTAAATTTAAGAA
39794000 ACAATTTAA
1 A-AATTTAA
39794009 CTCCAAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATTTAAATTTAAGAA
Found at i:39794371 original size:38 final size:37
Alignment explanation
Indices: 39794318--39794443 Score: 121
Period size: 38 Copynumber: 3.3 Consensus size: 37
39794308 TGCTATCCAA
*
39794318 CTTTACTTCAATTTCAAGAGGATGGGAAAAGATCTTG
1 CTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
* ** * **
39794355 CTCTTACTTCAATTTC-AGA-GATAAAGACGTGATATCCAG
1 CT-TTACTTCAATTTCAAGAGGAT-AGGA--AAAGATCTTG
39794394 CTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
1 CTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
39794431 CTTTTTACTTCAA
1 C--TTTACTTCAA
39794444 ATACTTGATA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
36 3 0.04
37 13 0.19
38 26 0.38
39 23 0.34
40 3 0.04
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (37 bp):
CTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
Found at i:39794422 original size:76 final size:76
Alignment explanation
Indices: 39794295--39795464 Score: 1503
Period size: 76 Copynumber: 15.8 Consensus size: 76
39794285 TGCTCTTTAG
* * *
39794295 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
39794360 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
39794371 AGAGATAAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCT-TT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
39794435 --TT--ACTTC
66 ACTTCAATTTC
* * * *
39794442 A-A-AT----ACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGG-AAAGATCTGGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
39794500 A---C---TT-
66 ACTTCAATTTC
* * *
39794504 -----TAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
39794564 ACTTCAATTTA
66 ACTTCAATTTC
* * *
39794575 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTGGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
39794640 ACTTCAATTTTC
66 ACTTCAA-TTTC
* * * * *
39794652 AGAGATGACGACTTGTTGTCCAACTCTACTTCAATTCCAAGGGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
39794717 ACTTCAATTTC
66 ACTTCAATTTC
* * * **
39794728 AGAGATAAAGGCGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATC-TG-GGTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
39794791 ACTTTAATTTTC
66 ACTTCAA-TTTC
* * * * * *
39794803 AGAGATGACGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAGAAGATCTTACTTTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
39794868 ACTTCAATTTA
66 ACTTCAATTTC
*
39794879 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGG-AAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
39794943 ACTTCAATTTC
66 ACTTCAATTTC
* * *
39794954 AGAGATAAAGACTTGTTATCTC-ACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCT
1 AGAGATAAAGACTTGTTATC-CAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCT
39795018 TACTTCAATTTC
65 TACTTCAATTTC
* *
39795030 AGAGATAATGACTTGTTATCCCACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
39795095 ACTTCAATTTC
66 ACTTCAATTTC
* *
39795106 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAGAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
39795171 ACTTCAATTTC
66 ACTTCAATTTC
* * *
39795182 AGAGATAAAGACTTGTTATCTC-ACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTACTCT
1 AGAGATAAAGACTTGTTATC-CAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCT
39795246 TACTTCAATTTC
65 TACTTCAATTTC
* * * *
39795258 AGAGATAATGACTTGTTATCCCACTCTACTTCAATTTCAAGAGGATAGGAAACGATGTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
39795323 ACTTCAATTTC
66 ACTTCAATTTC
* * *
39795334 AAAGATAATGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT--G---ACA--TTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
39795392 ACTTCAATTTC
66 ACTTCAATTTC
* * * * * *
39795403 AGAGATAAAGACGTGTTATCCAACTTTACTGCAATTTCAAGCGGATAGGAAAAAATTTTGCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCT
39795465 GTGGTCTGAT
Statistics
Matches: 978, Mismatches: 80, Indels: 72
0.87 0.07 0.06
Matches are distributed among these distances:
59 1 0.00
63 41 0.04
64 26 0.03
65 40 0.04
67 1 0.00
69 61 0.06
70 3 0.00
71 7 0.01
73 2 0.00
74 11 0.01
75 128 0.13
76 580 0.59
77 77 0.08
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTC
Found at i:39794465 original size:65 final size:64
Alignment explanation
Indices: 39794377--39794570 Score: 327
Period size: 63 Copynumber: 3.0 Consensus size: 64
39794367 TTTCAGAGAT
* *
39794377 AAAGACGTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTTTTTACTTC
1 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGC-TCTTACTTC
* * *
39794442 AAATACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGG-AAAGATCTGGCTCTTACTTT
1 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTC
39794505 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTC
1 AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTC
39794569 AA
1 AA
39794571 TTTAAGAGAT
Statistics
Matches: 120, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
63 49 0.41
64 30 0.25
65 41 0.34
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (64 bp):
AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTTACTTC
Found at i:39794643 original size:38 final size:37
Alignment explanation
Indices: 39794520--39795335 Score: 166
Period size: 38 Copynumber: 21.5 Consensus size: 37
39794510 CTTGATATCC
39794520 AGCT-TTACTTCAATTTCAAGAGGATAGGAAAAGATCT
1 AGCTCTTACTTCAATTTCAAG-GGATAGGAAAAGATCT
* * * *** *
39794557 TGCTCTTACTTCAATTT-AAGAGATAAAGACGTGTTATCC
1 AGCTCTTACTTCAATTTCAAGGGAT-AGGAAAAG--ATCT
*
39794596 AACTC-TACTTCAATTTCAAGCGGATAGGAAAAGATCT
1 AGCTCTTACTTCAATTTCAAG-GGATAGGAAAAGATCT
* * * *** * *
39794633 GGCTCTTACTTCAATTTTC-AGAGATGACGACTTGTTGTCC
1 AGCTCTTACTTCAA-TTTCAAGGGAT-AGGAAAAG--ATCT
* *
39794673 AACTC-TACTTCAATTCCAAGGGGATAGGAAAAGATCT
1 AGCTCTTACTTCAATTTCAA-GGGATAGGAAAAGATCT
* * *** *
39794710 TGCTCTTACTTCAATTTC-AGAGATAAAGG-CGTGTTATCC
1 AGCTCTTACTTCAATTTCAAGGGAT--AGGAAAAG--ATCT
*
39794749 AACTC-TACTTCAATTTCAAGCGGATAGGAAAAGATCT
1 AGCTCTTACTTCAATTTCAAG-GGATAGGAAAAGATCT
** * * * *** * *
39794786 -G-GGTTACTTTAATTTTC-AGAGATGACGACTTGTTGTCC
1 AGCTCTTACTTCAA-TTTCAAGGGAT-AGGAAAAG--ATCT
* *
39794824 AACTC-TACTTCAATTTCAAGAGGATAGGAGAAGATCTT
1 AGCTCTTACTTCAATTTCAAG-GGATAGGAAAAGATC-T
* * * *** * *
39794862 A-CTTTTACTTCAATTT-AAGAGATAAAGACTTGTTGTCC
1 AGCTCTTACTTCAATTTCAAGGGAT-AGGAAAAG--ATCT
*
39794900 AACTC-TACTTCAATTTCAAGAGGATAGG-AAAGATCT
1 AGCTCTTACTTCAATTTCAAG-GGATAGGAAAAGATCT
* * * ***
39794936 TGCTCTTACTTCAATTTC-AGAGATAAAGACTTGTTATCT
1 AGCTCTTACTTCAATTTCAAGGGAT-AGGAAAAG--ATCT
* *
39794975 CA-CTC-TACTTCAATTTCAAGAGGATAGGAAACGATGTT
1 -AGCTCTTACTTCAATTTCAAG-GGATAGGAAAAGAT-CT
* * *** *
39795013 A-CTCTTACTTCAATTTC-AGAGATAATGACTTGTTATCCC
1 AGCTCTTACTTCAATTTCAAGGGAT-AGGAAAAG--AT-CT
39795052 A-CTC-TACTTCAATTTCAAGAGGATAGGAAAAGATCT
1 AGCTCTTACTTCAATTTCAAG-GGATAGGAAAAGATCT
* * * *** * *
39795088 TGCTCTTACTTCAATTTC-AGAGATAAAGACTTGTTGTCC
1 AGCTCTTACTTCAATTTCAAGGGAT-AGGAAAAG--ATCT
* *
39795127 AACTC-TACTTCAATTTCAAGAGGATAGGAGAAGATCT
1 AGCTCTTACTTCAATTTCAAG-GGATAGGAAAAGATCT
* * * ***
39795164 TGCTCTTACTTCAATTTC-AGAGATAAAGACTTGTTATCT
1 AGCTCTTACTTCAATTTCAAGGGAT-AGGAAAAG--ATCT
* *
39795203 CA-CTC-TACTTCAATTTCAAGAGGATAGGAAACGATGTT
1 -AGCTCTTACTTCAATTTCAAG-GGATAGGAAAAGAT-CT
* * *** *
39795241 A-CTCTTACTTCAATTTC-AGAGATAATGACTTGTTATCCC
1 AGCTCTTACTTCAATTTCAAGGGAT-AGGAAAAG--AT-CT
* *
39795280 A-CTC-TACTTCAATTTCAAGAGGATAGGAAACGATGT
1 AGCTCTTACTTCAATTTCAAG-GGATAGGAAAAGATCT
*
39795316 TGCTCTTACTTCAATTTCAA
1 AGCTCTTACTTCAATTTCAA
39795336 AGATAATGAC
Statistics
Matches: 541, Mismatches: 162, Indels: 151
0.63 0.19 0.18
Matches are distributed among these distances:
35 6 0.01
36 45 0.08
37 108 0.20
38 224 0.41
39 122 0.23
40 36 0.07
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Consensus pattern (37 bp):
AGCTCTTACTTCAATTTCAAGGGATAGGAAAAGATCT
Found at i:39795426 original size:69 final size:69
Alignment explanation
Indices: 39795315--39795448 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 69
39795305 GGAAACGATG
* * *
39795315 TTGCTCTTACTTCAATTTCAAAGATAATGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGAT
1 TTGCTCTTACTTCAATTTCAAAGATAAAGACGTGTTATCCAACTCTACTGCAATTTCAAGAGGAT
39795380 GACA
66 GACA
* * *
39795384 TTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTTTACTGCAATTTCAAGCGGAT
1 TTGCTCTTACTTCAATTTCAAAGATAAAGACGTGTTATCCAACTCTACTGCAATTTCAAGAGGAT
39795449 AGGAAAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 59 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (69 bp):
TTGCTCTTACTTCAATTTCAAAGATAAAGACGTGTTATCCAACTCTACTGCAATTTCAAGAGGAT
GACA
Found at i:39807322 original size:58 final size:58
Alignment explanation
Indices: 39807216--39807352 Score: 184
Period size: 58 Copynumber: 2.3 Consensus size: 58
39807206 TTCGATACCC
* * * *
39807216 GAGGGCAAAATGGTAGATTTTGGTGAAATCGGGGTTAAAAATGAGATTTAGGGAAGTTT
1 GAGGGTAAAATGGTA-ATTTTAGTGAAATCGAGGTTAAAAAGGAGATTTAGGGAAGTTT
* * * *
39807275 GAGGGTGAAATGGTAATTTTAGTGAAATCGAGGTTTAAAAGGGGATTTATGGAAGTTT
1 GAGGGTAAAATGGTAATTTTAGTGAAATCGAGGTTAAAAAGGAGATTTAGGGAAGTTT
*
39807333 GGGGGTAAAATGGTAATTTT
1 GAGGGTAAAATGGTAATTTT
39807353 TGAAAGTTTC
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
58 55 0.81
59 13 0.19
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.31
Consensus pattern (58 bp):
GAGGGTAAAATGGTAATTTTAGTGAAATCGAGGTTAAAAAGGAGATTTAGGGAAGTTT
Found at i:39807620 original size:30 final size:29
Alignment explanation
Indices: 39807335--39807619 Score: 328
Period size: 30 Copynumber: 9.6 Consensus size: 29
39807325 GGAAGTTTGG
* *
39807335 GGGT-AAAATGGTAATTTTTGAAAG-TTTC
1 GGGTCAAAAT-GTAATTTTGGAAAGTTTTA
39807363 GAGGTCAAAATGTAATTTTGGAAA-TTTTA
1 G-GGTCAAAATGTAATTTTGGAAAGTTTTA
* *
39807392 GGGTCAAAATATGATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGG-AAAGTTTTA
39807422 GGGTCAAAATGTAATTTTGGAAGAGTTTTA
1 GGGTCAAAATGTAATTTTGGAA-AGTTTTA
* *
39807452 GGGTCAAAATATAATTTTTAGAAAGTTTTA
1 GGGTCAAAATGTAA-TTTTGGAAAGTTTTA
*
39807482 GGGTCAAAATATAATTTTGGAAAAGTTTT-
1 GGGTCAAAATGTAATTTTGG-AAAGTTTTA
* *
39807511 GAGGTCAAAATATAATTTTGGAAAAGTTTAA
1 G-GGTCAAAATGTAATTTTGG-AAAGTTTTA
* *
39807542 GGGTCAAAATGTGATTTTCAGAAAGTTTT-
1 GGGTCAAAATGTAATTTT-GGAAAGTTTTA
*
39807571 GAGGTCAAAATGTAATTTTTAGAAAGTTTTA
1 G-GGTCAAAATGTAA-TTTTGGAAAGTTTTA
39807602 GGGTCAAAATGTAATTTT
1 GGGTCAAAATGTAATTTT
39807620 TGGATAATTT
Statistics
Matches: 228, Mismatches: 15, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
28 18 0.08
29 35 0.15
30 161 0.71
31 14 0.06
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.38
Consensus pattern (29 bp):
GGGTCAAAATGTAATTTTGGAAAGTTTTA
Found at i:39808733 original size:9 final size:9
Alignment explanation
Indices: 39808695--39808726 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
39808685 ATTAACATTG
*
39808695 TTATTAATA
1 TTATTGATA
39808704 TTATTGATA
1 TTATTGATA
39808713 TTATTGATA
1 TTATTGATA
39808722 TTATT
1 TTATT
39808727 ATTATTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.59
Consensus pattern (9 bp):
TTATTGATA
Found at i:39809426 original size:6 final size:6
Alignment explanation
Indices: 39809394--39809442 Score: 62
Period size: 6 Copynumber: 7.5 Consensus size: 6
39809384 GACATTGGAC
39809394 TTTTAA TTTTTAA TGTTTAGTA TTTTAA TTTTAA TTTTAA TTTTAA TTT
1 TTTTAA -TTTTAA T-TTTA--A TTTTAA TTTTAA TTTTAA TTTTAA TTT
39809443 AAAGTAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 23 0.59
7 10 0.26
8 4 0.10
9 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (6 bp):
TTTTAA
Found at i:39809456 original size:6 final size:6
Alignment explanation
Indices: 39809415--39809503 Score: 71
Period size: 6 Copynumber: 15.2 Consensus size: 6
39809405 AATGTTTAGT
* * * * *
39809415 ATTTTA ATTTTA ATTTTA ATTTTA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
39809464 ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
39809504 ATCAATTTAA
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
4 5 0.07
5 7 0.10
6 53 0.74
7 1 0.01
8 6 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:39809473 original size:37 final size:37
Alignment explanation
Indices: 39809424--39809496 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
39809414 TATTTTAATT
* * **
39809424 TTAATTTTAATTTTAATTTAAA-GTAAATTTAAATAA
1 TTAAATTTAAATTTAAGATAAATGTAAATTTAAATAA
*
39809460 TTAAATTTAAATTTAAGATAAATTTAAATTTAAATAA
1 TTAAATTTAAATTTAAGATAAATGTAAATTTAAATAA
39809497 ATTTAAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
36 18 0.58
37 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (37 bp):
TTAAATTTAAATTTAAGATAAATGTAAATTTAAATAA
Found at i:39809505 original size:17 final size:16
Alignment explanation
Indices: 39809432--39809503 Score: 94
Period size: 17 Copynumber: 4.5 Consensus size: 16
39809422 TTTTAATTTT
*
39809432 AATTTTAATTTAAAGTA
1 AATTTAAATTTAAA-TA
*
39809449 AATTTAAA--TAATTA
1 AATTTAAATTTAAATA
39809463 AATTTAAATTTAAGATA
1 AATTTAAATTTAA-ATA
39809480 AATTTAAATTTAAATA
1 AATTTAAATTTAAATA
39809496 AATTTAAA
1 AATTTAAA
39809504 ATCAATTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 14 0.29
17 22 0.45
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:39809521 original size:27 final size:27
Alignment explanation
Indices: 39809467--39809521 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
39809457 TAATTAAATT
* **
39809467 TAAATTTAAGATAAATTTAAATTTAAA
1 TAAATTTAAAATAAATTTAAATCCAAA
* *
39809494 TAAATTTAAAATCAATTTAACTCCAAA
1 TAAATTTAAAATAAATTTAAATCCAAA
39809521 T
1 T
39809522 TAAAATAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCCAAA
Found at i:39811356 original size:8 final size:8
Alignment explanation
Indices: 39811343--39811418 Score: 62
Period size: 8 Copynumber: 8.6 Consensus size: 8
39811333 CAAATATTTA
39811343 ATTAAAAT
1 ATTAAAAT
39811351 ATTAAAAT
1 ATTAAAAT
39811359 ATTAAATTAT
1 ATTAAA--AT
39811369 ATTAAATAAAT
1 ATT--A-AAAT
*
39811380 ATTAAATT
1 ATTAAAAT
39811388 ATTAAAAT
1 ATTAAAAT
**
39811396 AGAACAAAT
1 ATTA-AAAT
39811405 ATTAAAAT
1 ATTAAAAT
39811413 AATTAA
1 -ATTAA
39811419 TTATTTAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
8 30 0.55
9 12 0.22
10 5 0.09
11 5 0.09
12 1 0.02
13 2 0.04
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.37
Consensus pattern (8 bp):
ATTAAAAT
Found at i:39811456 original size:119 final size:121
Alignment explanation
Indices: 39811255--39811725 Score: 806
Period size: 121 Copynumber: 3.9 Consensus size: 121
39811245 ATTAAAATAT
*
39811255 TAAATTATTAAATTATTAAAAAT-GAACAAATATTAAAATAAGTAATTATTTAATTAGTTATTTA
1 TAAA-TATTAAATTATTAAAAATAGAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTA
*
39811319 TTAAACCTTAAACTCAAATATTTAATT-AAAATATTAAAATATTAAATTATATTAAA
65 TTAAACCTTAAACCCAAATATTTAATTCAAAATATTAAAATATTAAATTATATTAAA
39811375 TAAATATTAAATTATT-AAAATAGAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTAT
1 TAAATATTAAATTATTAAAAATAGAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTAT
* *
39811439 TAAACCTTAAACCCAAATATTTAATT-AAAATATTAAATTATTCAATTATATTAAA
66 TAAACCTTAAACCCAAATATTTAATTCAAAATATTAAAATATTAAATTATATTAAA
* * *
39811494 TAAATATTAAATTATTAAAAATAGAAAAAATATTAAAATAATTAATTATCTAATTAATTATTTAT
1 TAAATATTAAATTATTAAAAATAGAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTAT
*
39811559 TAAACCTTAAACCCAAATATTTAATTCAAAATATTAAAATATTAAAATATATTAAA
66 TAAACCTTAAACCCAAATATTTAATTCAAAATATTAAAATATTAAATTATATTAAA
39811615 TAAATATTAAATTATTAAAAATAGAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTAT
1 TAAATATTAAATTATTAAAAATAGAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTAT
* * *
39811680 TAAACTTTAAATCCAAATATTTAATTCAAAATATTAAATTATTAAA
66 TAAACCTTAAACCCAAATATTTAATTCAAAATATTAAAATATTAAA
39811726 AATAGAACAA
Statistics
Matches: 332, Mismatches: 16, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
118 5 0.02
119 121 0.36
120 75 0.23
121 131 0.39
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (121 bp):
TAAATATTAAATTATTAAAAATAGAACAAATATTAAAATAATTAATTATTTAATTAGTTATTTAT
TAAACCTTAAACCCAAATATTTAATTCAAAATATTAAAATATTAAATTATATTAAA
Found at i:39811637 original size:21 final size:21
Alignment explanation
Indices: 39811595--39811633 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
39811585 CAAAATATTA
39811595 AAATATTAAAATATATTAAAT
1 AAATATTAAAATATATTAAAT
39811616 AAATATT-AAAT-TATTAAA
1 AAATATTAAAATATATTAAA
39811634 AATAGAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAATATTAAAATATATTAAAT
Found at i:39811719 original size:92 final size:91
Alignment explanation
Indices: 39811603--39811813 Score: 361
Period size: 92 Copynumber: 2.3 Consensus size: 91
39811593 TAAAATATTA
*
39811603 AAATATATTAAAT-AAATATTAAATTATTAAAAATAGAACAAATATTAAAATAATTAATTATTTA
1 AAATAT-TTAATTAAAATATTAAATTATTAAAAATAGAACAAATATTAAAATAATTAATTATTTA
* *
39811667 ATTAGTTATTTATTAAACTTTAAATCC
65 ATTAGTTATTTATTAAACCTTAAACCC
*
39811694 AAATATTTAATTCAAAATATTAAATTATTAAAAATAGAACAAATATTATAATAATTAATTATTTA
1 AAATATTTAATT-AAAATATTAAATTATTAAAAATAGAACAAATATTAAAATAATTAATTATTTA
39811759 ATTAGTTATTTATTAAACCTTAAACCC
65 ATTAGTTATTTATTAAACCTTAAACCC
39811786 AAATATTTAATTAAAATATTAAATTATT
1 AAATATTTAATTAAAATATTAAATTATT
39811814 CAATTATATT
Statistics
Matches: 114, Mismatches: 4, Indels: 4
0.93 0.03 0.03
Matches are distributed among these distances:
90 5 0.04
91 22 0.19
92 87 0.76
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (91 bp):
AAATATTTAATTAAAATATTAAATTATTAAAAATAGAACAAATATTAAAATAATTAATTATTTAA
TTAGTTATTTATTAAACCTTAAACCC
Found at i:39811870 original size:8 final size:8
Alignment explanation
Indices: 39811857--39811882 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39811847 ATAACAACCC
39811857 AAATATTT
1 AAATATTT
39811865 AAATATTT
1 AAATATTT
39811873 AAATATTT
1 AAATATTT
39811881 AA
1 AA
39811883 TTAGTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATATTT
Found at i:39811884 original size:123 final size:121
Alignment explanation
Indices: 39811708--39811944 Score: 345
Period size: 123 Copynumber: 1.9 Consensus size: 121
39811698 ATTTAATTCA
* *
39811708 AAATATTAAATTATTAAAAATAGAACAAATATTATAATAATTAATTATTTAATTAGTTATTTATT
1 AAATATTAAATTATTAAAAATACAACAAATATTATAATAATTAAATATTTAATTAGTTATTTATT
*
39811773 AAA-CCTTAAACCCAAATATTTAATT-AAAATATTAAATTATTCAATTATATTAAAT
66 AAATCC-TAAACACAAATATTTAATTCAAAATATTAAATTATTCAATTATATTAAAT
*
39811828 AAATATTAAATTATTAAAAATAACAACCCAAATATT-TAAATATTTAAATATTTAATTAGTTATT
1 AAATATTAAATTATTAAAAAT-ACAA--CAAATATTAT-AATAATTAAATATTTAATTAGTTATT
* * *
39811892 TATTAAATCCTAAACACAAATATTTAATTCAATATATTTAATTATTTAATTAT
62 TATTAAATCCTAAACACAAATATTTAATTCAAAATATTAAATTATTCAATTAT
39811945 TTGCAACTAT
Statistics
Matches: 104, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
120 21 0.20
121 3 0.03
122 1 0.01
123 57 0.55
124 22 0.21
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (121 bp):
AAATATTAAATTATTAAAAATACAACAAATATTATAATAATTAAATATTTAATTAGTTATTTATT
AAATCCTAAACACAAATATTTAATTCAAAATATTAAATTATTCAATTATATTAAAT
Found at i:39813974 original size:29 final size:28
Alignment explanation
Indices: 39813942--39814235 Score: 163
Period size: 29 Copynumber: 10.2 Consensus size: 28
39813932 CAAAAACAGG
39813942 ATTTTGGAAAGTTCGGGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGGGGGTAAAAT-GTA
* *
39813971 ATTTTCGTGAAA--TCGAGGGTAAAAATGAA
1 ATTTT-G-GAAAGTTCGGGGGT-AAAATGTA
*
39814000 ATTTTAGAAAGTTCGGGGGTAAAATGGTA
1 ATTTTGGAAAGTTCGGGGGTAAAAT-GTA
* *
39814029 ATTTTGGTGAAA--TCGGGGTTAAAAATGGA
1 ATTTT-G-GAAAGTTCGGGGGT-AAAATGTA
* *
39814058 ATTTTAGAAAGTTCAGGGGT-AAATGGTA
1 ATTTTGGAAAGTTCGGGGGTAAAAT-GTA
* *
39814086 ATTTTGGTGAAA--TCGGGGTTAAAAATGGA
1 ATTTT-G-GAAAGTTCGGGGGT-AAAATGTA
* * *** *
39814115 ATTTTTGAAAATTTAAGGTTAAAATGTA
1 ATTTTGGAAAGTTCGGGGGTAAAATGTA
*
39814143 ATTTTGGAAAAGTT-TGGGGTCAAAATGTA
1 ATTTTGG-AAAGTTCGGGGGT-AAAATGTA
** ** *
39814172 ATTTTTAAAAAGTTTTAGGGTTAAAATGTA
1 A-TTTTGGAAAG-TTCGGGGGTAAAATGTA
** *
39814202 ATTTTGGAAAAGTTTAGGGTTAAAATGTA
1 ATTTTGG-AAAGTTCGGGGGTAAAATGTA
39814231 ATTTT
1 ATTTT
39814236 CAAAAAGTTC
Statistics
Matches: 209, Mismatches: 32, Indels: 48
0.72 0.11 0.17
Matches are distributed among these distances:
27 16 0.08
28 34 0.16
29 109 0.52
30 38 0.18
31 12 0.06
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (28 bp):
ATTTTGGAAAGTTCGGGGGTAAAATGTA
Found at i:39814108 original size:57 final size:58
Alignment explanation
Indices: 39813899--39814124 Score: 316
Period size: 58 Copynumber: 3.9 Consensus size: 58
39813889 TGGATATCCA
* * * * *
39813899 GGGGCAAAATGGTAATTTTGGTCGAAAT-TGGGTCAAAAACAGG-ATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTGGT-GAAATCGGGGTTAAAAA-TGGAATTTTAGAAAGTTCG
* *
39813957 GGGGTAAAATGGTAATTTTCGTGAAATCGAGGG-TAAAAATGAAATTTTAGAAAGTTCG
1 GGGGTAAAATGGTAATTTTGGTGAAATCG-GGGTTAAAAATGGAATTTTAGAAAGTTCG
*
39814015 GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCA
1 GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCG
*
39814073 GGGGT-AAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTGAAA
1 GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAA
39814125 ATTTAAGGTT
Statistics
Matches: 153, Mismatches: 11, Indels: 9
0.88 0.06 0.05
Matches are distributed among these distances:
57 55 0.36
58 95 0.62
59 3 0.02
ACGTcount: A:0.35, C:0.05, G:0.30, T:0.30
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCG
Found at i:39814144 original size:57 final size:57
Alignment explanation
Indices: 39813897--39814149 Score: 289
Period size: 58 Copynumber: 4.4 Consensus size: 57
39813887 TTTGGATATC
* * * * *
39813897 CAGGGGCAAAATGGTAATTTTGGTCGAAAT-TGGGTCAAAAACAGG-ATTTTGGAAAGTT
1 CAGGGGTAAAATGGTAATTTTGGT-GAAATCGGGGT-AAAAA-TGGAATTTTAGAAAATT
* * * *
39813955 CGGGGGTAAAATGGTAATTTTCGTGAAATCGAGGGTAAAAATGAAATTTTAGAAAGTT
1 CAGGGGTAAAATGGTAATTTTGGTGAAATCG-GGGTAAAAATGGAATTTTAGAAAATT
* *
39814013 CGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTT
1 CAGGGGTAAAATGGTAATTTTGGTGAAATCGGGG-TAAAAATGGAATTTTAGAAAATT
*
39814071 CAGGGGT-AAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTGAAAATT
1 CAGGGGTAAAATGGTAATTTTGGTGAAATCGGGG-TAAAAATGGAATTTTAGAAAATT
* * *
39814128 TAAGGTTAAAAT-GTAATTTTGG
1 CAGGGGTAAAATGGTAATTTTGG
39814150 AAAAGTTTGG
Statistics
Matches: 175, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
57 71 0.41
58 100 0.57
59 4 0.02
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (57 bp):
CAGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTAAAAATGGAATTTTAGAAAATT
Found at i:39814200 original size:30 final size:29
Alignment explanation
Indices: 39814101--39814264 Score: 186
Period size: 29 Copynumber: 5.6 Consensus size: 29
39814091 GGTGAAATCG
* *
39814101 GGGTTAAAAATGGAATTTTTGAAAA-TTTA
1 GGGTT-AAAATGTAATTTTGGAAAAGTTTA
* *
39814130 AGGTTAAAATGTAATTTTGGAAAAGTTTG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
* **
39814159 GGGTCAAAATGTAATTTTTAAAAAGTTTTA
1 GGGTTAAAATGTAATTTTGGAAAAG-TTTA
39814189 GGGTTAAAATGTAATTTTGGAAAAGTTTA
1 GGGTTAAAATGTAATTTTGGAAAAGTTTA
**
39814218 GGGTTAAAATGTAATTTTCAAAAAGTTCTA
1 GGGTTAAAATGTAATTTTGGAAAAGTT-TA
* * *
39814248 GAGTCAAAATATAATTT
1 GGGTTAAAATGTAATTT
39814265 CAAAACAGTC
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
28 17 0.15
29 57 0.50
30 41 0.36
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTA
Found at i:39814206 original size:59 final size:59
Alignment explanation
Indices: 39814107--39814264 Score: 212
Period size: 59 Copynumber: 2.7 Consensus size: 59
39814097 ATCGGGGTTA
* * * *
39814107 AAAATGGAATTTTTGAAAA--TTTAAGGTTAAAATGTAATTTTGGAAAAGTTTGGGGTC
1 AAAATGTAATTTTTAAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGTC
*
39814164 AAAATGTAATTTTTAAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGTT
1 AAAATGTAATTTTTAAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGTC
* * * * *
39814223 AAAATGTAATTTTCAAAAAGTTCTAGAGTCAAAATATAATTT
1 AAAATGTAATTTTTAAAAAGTTTTAGGGTTAAAATGTAATTT
39814265 CAAAACAGTC
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
57 17 0.19
59 72 0.81
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (59 bp):
AAAATGTAATTTTTAAAAAGTTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAGGGTC
Found at i:39814279 original size:59 final size:59
Alignment explanation
Indices: 39814135--39814279 Score: 148
Period size: 59 Copynumber: 2.5 Consensus size: 59
39814125 ATTTAAGGTT
* ** * * * * * *
39814135 AAAATGTAATTTTGGAAAAGTTTGGGGTCAAAATGTAATTTTTAAAAAGTTTTAGGGTT
1 AAAATATAATTTTCAAAAAGTCTAGGGTCAAAATGTAATTTTCAAAAAGTTCTAGAGTC
* ** * *
39814194 AAAATGTAATTTTGGAAAAGTTTAGGGTTAAAATGTAATTTTCAAAAAGTTCTAGAGTC
1 AAAATATAATTTTCAAAAAGTCTAGGGTCAAAATGTAATTTTCAAAAAGTTCTAGAGTC
39814253 AAAATATAA-TTTCAAAACAGTCTAGGG
1 AAAATATAATTTTCAAAA-AGTCTAGGG
39814280 ACTTCCAGGG
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
58 6 0.08
59 69 0.92
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (59 bp):
AAAATATAATTTTCAAAAAGTCTAGGGTCAAAATGTAATTTTCAAAAAGTTCTAGAGTC
Found at i:39815959 original size:25 final size:24
Alignment explanation
Indices: 39815918--39815986 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 24
39815908 CAGATTCTTC
39815918 TTGGCAGC-GGCGGTGGCAGAGCTAGG
1 TTGG-AGCTGGCGGTGGCAGAG--AGG
*
39815944 -TGGAGCTGGCGATGGCAGGAGAGG
1 TTGGAGCTGGCGGTGGCA-GAGAGG
*
39815968 TTGGAGCTGGTGGTGGCAG
1 TTGGAGCTGGCGGTGGCAG
39815987 CAATCAGCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
24 7 0.19
25 27 0.73
26 3 0.08
ACGTcount: A:0.16, C:0.14, G:0.52, T:0.17
Consensus pattern (24 bp):
TTGGAGCTGGCGGTGGCAGAGAGG
Found at i:39816197 original size:17 final size:17
Alignment explanation
Indices: 39816171--39816296 Score: 127
Period size: 17 Copynumber: 7.6 Consensus size: 17
39816161 GGACATTTAT
39816171 TAAA-TTAAATTTATAA
1 TAAATTTAAATTTATAA
*
39816187 TAAATTTAAATTTATAT
1 TAAATTTAAATTTATAA
**
39816204 TAAATCCAAATTTA-AA
1 TAAATTTAAATTTATAA
39816220 TTAAATTTAAA-TT-TAA
1 -TAAATTTAAATTTATAA
* *
39816236 TAAATTTAGATTTAAAA
1 TAAATTTAAATTTATAA
* *
39816253 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTATAA
*
39816270 TAAATTTAATTTTGA-AA
1 TAAATTTAAATTT-ATAA
39816287 TAAATTTAAA
1 TAAATTTAAA
39816297 ATGGTTTGGT
Statistics
Matches: 93, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
15 9 0.10
16 11 0.12
17 72 0.77
18 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTATAA
Found at i:39816225 original size:11 final size:11
Alignment explanation
Indices: 39816170--39816296 Score: 77
Period size: 11 Copynumber: 11.5 Consensus size: 11
39816160 TGGACATTTA
39816170 TTAAATTAAAT
1 TTAAATTAAAT
39816181 TTATAA-TAAAT
1 TTA-AATTAAAT
*
39816192 TTAAATT-TAT
1 TTAAATTAAAT
*
39816202 ATTAAATCCAAAT
1 -TTAAAT-TAAAT
39816215 TTAAATTAAAT
1 TTAAATTAAAT
*
39816226 TTAAATTTAA-
1 TTAAATTAAAT
*
39816236 -TAAATTTAGAT
1 TTAAA-TTAAAT
*
39816247 TTAAAATAAAT
1 TTAAATTAAAT
*
39816258 TTAATTTTAAA-
1 TTAA-ATTAAAT
* *
39816269 ATAAATTTAATT
1 TTAAA-TTAAAT
39816281 TTGAAA-TAAAT
1 TT-AAATTAAAT
39816292 TTAAA
1 TTAAA
39816297 ATGGTTTGGT
Statistics
Matches: 88, Mismatches: 16, Indels: 25
0.68 0.12 0.19
Matches are distributed among these distances:
9 4 0.05
10 10 0.11
11 52 0.59
12 17 0.19
13 5 0.06
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:39816274 original size:66 final size:65
Alignment explanation
Indices: 39816165--39816296 Score: 158
Period size: 66 Copynumber: 2.0 Consensus size: 65
39816155 GCATTTGGAC
* * * *
39816165 ATTTATTAAATTAAATTTATAATAAATTTAAATTTATATTAAATCCAAATTT-AAATTAAATTTA
1 ATTTAATAAATTAAATTTAAAATAAATTTAAATTTAAAATAAATCCAAATTTGAAA-TAAATTTA
39816229 A
65 A
* * ** *
39816230 ATTTAATAAATTTAGATTTAAAATAAATTTAATTTTAAAATAAATTTAATTTTGAAATAAATTTA
1 ATTTAATAAA-TTAAATTTAAAATAAATTTAAATTTAAAATAAATCCAAATTTGAAATAAATTTA
39816295 A
65 A
39816296 A
1 A
39816297 ATGGTTTGGT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
65 9 0.16
66 44 0.79
67 3 0.05
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (65 bp):
ATTTAATAAATTAAATTTAAAATAAATTTAAATTTAAAATAAATCCAAATTTGAAATAAATTTAA
Found at i:39816741 original size:20 final size:20
Alignment explanation
Indices: 39816716--39816753 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
39816706 CTTTTTGTAT
*
39816716 CATTGTGGTATTGGATCTGC
1 CATTGTGGTATTAGATCTGC
39816736 CATTGTGGTATTAGATCT
1 CATTGTGGTATTAGATCT
39816754 TTCCCTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.26, T:0.42
Consensus pattern (20 bp):
CATTGTGGTATTAGATCTGC
Found at i:39816832 original size:100 final size:100
Alignment explanation
Indices: 39816686--39817472 Score: 996
Period size: 100 Copynumber: 7.9 Consensus size: 100
39816676 CCGGGTTCAT
* * * * * * *
39816686 CGTTGCGACTTAAACC-TTCCCTTTT-TGTATCATTGTGGTATTGGATCTGCCATTGTGGTATTA
1 CGTTGCGACTTAGACCTTTCCCTTTTCTGT-T-TTTGCGGTACTGGATCTGCCATTGCGATCTTA
39816749 GATCTTTCCCTTCATGCTTCTGAGGTACACGGTCCGC
64 GATCTTTCCCTTCATGCTTCTGAGGTACACGGTCCGC
*
39816786 CATTGCGACTTAGACCTTTCCCTTTTCTGTTTTTGCGGTACTGGATCTGCCATTGCGATCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTTCTGTTTTTGCGGTACTGGATCTGCCATTGCGATCTTAGA
* * ** *
39816851 TCTTTCCCTTCAAGCTTTTGAGGTACACAATCCAC
66 TCTTTCCCTTCATGCTTCTGAGGTACACGGTCCGC
* *
39816886 CGTTGCGACTTAGACCTTTCCC-TTTCGTGTTTTGGCGGTACTGGATCTGCCATTGCAATCTTAG
1 CGTTGCGACTTAGACCTTTCCCTTTTC-TGTTTTTGCGGTACTGGATCTGCCATTGCGATCTTAG
* * *
39816950 ATCTTTTCCTTCATGTTTCTGAGGTACACGGTCCGT
65 ATCTTTCCCTTCATGCTTCTGAGGTACACGGTCCGC
* * *
39816986 CGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTTCCGGTACTGGATCTGCCATTGTGATCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTTCTGTTTTTGCGGTACTGGATCTGCCATTGCGATCTTAGA
39817051 TCTTTCCCTTCATGCTTCTGAGGTACACGGTCCGC
66 TCTTTCCCTTCATGCTTCTGAGGTACACGGTCCGC
* * *
39817086 CGTTGCGACTTAGACCTTTCCCTTTTGTG-TTTTGACGGTACTGGATCTGTCATTGCGGTCTTAG
1 CGTTGCGACTTAGACCTTTCCCTTTTCTGTTTTTG-CGGTACTGGATCTGCCATTGCGATCTTAG
* *
39817150 ATCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCGT
65 ATCTTTCCCTT-CATGCTTCTGAGGTACACGGTCCGC
* * ** *
39817187 CGTTACGACTTAGACCTTTCCCTTTTCTGTTTTTACGGTACTGGATCCACCGTTGCGATCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTTCTGTTTTTGCGGTACTGGATCTGCCATTGCGATCTTAGA
* *
39817252 TCTTTCCCGTT-AT-ATT-TGAGGTACACGATCCGC
66 TCTTTCCC-TTCATGCTTCTGAGGTACACGGTCCGC
* * * * * * * *
39817285 CATTACGACTTAAACCTTTCCCTTTTTTGTTTTTGTGGTACTGGAT-TCGCCGTTGTGGTCTTAG
1 CGTTGCGACTTAGACCTTTCCCTTTTCTGTTTTTGCGGTACTGGATCT-GCCATTGCGATCTTAG
*
39817349 ATCTTTCCCTTCAATGCTTTTGAGGTACACGGTCCGC
65 ATCTTTCCCTTC-ATGCTTCTGAGGTACACGGTCCGC
* * * * * * *
39817386 CGTTGCGACTTAGATCTTTCCCTTTTGTGTTTTGGTGGTACTAGATCTGTCATTGCGGTCTTAGA
1 CGTTGCGACTTAGACCTTTCCCTTTTCTGTTTTTGCGGTACTGGATCTGCCATTGCGATCTTAGA
39817451 TCTTTCCCTTCCATGCTTCTGA
66 TCTTTCCCTT-CATGCTTCTGA
39817473 TGCTGAAACC
Statistics
Matches: 601, Mismatches: 71, Indels: 29
0.86 0.10 0.04
Matches are distributed among these distances:
97 2 0.00
98 78 0.13
99 12 0.02
100 314 0.52
101 184 0.31
102 11 0.02
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (100 bp):
CGTTGCGACTTAGACCTTTCCCTTTTCTGTTTTTGCGGTACTGGATCTGCCATTGCGATCTTAGA
TCTTTCCCTTCATGCTTCTGAGGTACACGGTCCGC
Found at i:39817375 original size:300 final size:300
Alignment explanation
Indices: 39816691--39817468 Score: 1104
Period size: 300 Copynumber: 2.6 Consensus size: 300
39816681 TTCATCGTTG
* * *
39816691 CGACTTAAACC-TTCCC-TTTTTGTATCATTGTGGTATTGGATCTGCCATTGTGGTATTAGATCT
1 CGACTTAAACCTTTCCCTTTTTTGT-T-TTTGTGGTACTGGATCTGCCATTGTGGTCTTAGATCT
* *
39816754 TTCCCTTCATGCTTCTGAGGTACACGGTCCGCCATTGCGACTTAGACCTTTCCCTTTTCTGTTTT
64 TTCCCTTCATGCTTCTGAGGTACACGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTG-TTT
* * *
39816819 TGCGGTACTGGATCTGCCATTGCGATCTTAGATCTTTCCCTT-CAAGCTTTTGAGGTACACAATC
128 TGCGGTACTGGATCTGTCATTGCGGTCTTAGATCTTTCCCTTCCATGCTTTTGAGGTACACAATC
* * **
39816883 CACCGTTGCGACTTAGACCTTTCCCTTTCGTGTTTTGGCGGTACTGGATCTGCCATTGCAATCTT
193 CACCGTTACGACTTAGACCTTTCCCTTTCGTGTTTTGACGGTACTGGATCCACCATTGCAATCTT
* * * * * *
39816948 AGATCTTTTCCTTCATGTTTCTGAGGTACACGGTCCGTCGTTG
258 AGATCTTTCCCTTCATGATTCTGAGGTACACGATCCGCCATTA
* * ** *
39816991 CGACTTAGACCTTTCCCTTTTGTGTTTTTCCGGTACTGGATCTGCCATTGTGATCTTAGATCTTT
1 CGACTTAAACCTTTCCCTTTTTTGTTTTTGTGGTACTGGATCTGCCATTGTGGTCTTAGATCTTT
39817056 CCCTTCATGCTTCTGAGGTACACGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTGA
66 CCCTTCATGCTTCTGAGGTACACGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTG-
** *
39817121 CGGTACTGGATCTGTCATTGCGGTCTTAGATCTTTCCCTTCCATGCTTTTGAGGTACACGGTCCG
130 CGGTACTGGATCTGTCATTGCGGTCTTAGATCTTTCCCTTCCATGCTTTTGAGGTACACAATCCA
* * * *
39817186 TCGTTACGACTTAGACCTTTCCCTTTTC-TGTTTTTACGGTACTGGATCCACCGTTGCGATCTTA
195 CCGTTACGACTTAGACCTTTCCC-TTTCGTGTTTTGACGGTACTGGATCCACCATTGCAATCTTA
39817250 GATCTTTCCCGTT-AT-ATT-TGAGGTACACGATCCGCCATTA
259 GATCTTTCCC-TTCATGATTCTGAGGTACACGATCCGCCATTA
*
39817290 CGACTTAAACCTTTCCCTTTTTTGTTTTTGTGGTACTGGAT-TCGCCGTTGTGGTCTTAGATCTT
1 CGACTTAAACCTTTCCCTTTTTTGTTTTTGTGGTACTGGATCT-GCCATTGTGGTCTTAGATCTT
* *
39817354 TCCCTTCAATGCTTTTGAGGTACACGGTCCGCCGTTGCGACTTAGATCTTTCCCTTTTGTGTTTT
65 TCCCTTC-ATGCTTCTGAGGTACACGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTGTTTT
* *
39817419 GGTGGTACTAGATCTGTCATTGCGGTCTTAGATCTTTCCCTTCCATGCTT
129 -GCGGTACTGGATCTGTCATTGCGGTCTTAGATCTTTCCCTTCCATGCTT
39817469 CTGATGCTGA
Statistics
Matches: 429, Mismatches: 40, Indels: 18
0.88 0.08 0.04
Matches are distributed among these distances:
298 1 0.00
299 86 0.20
300 241 0.56
301 89 0.21
302 12 0.03
ACGTcount: A:0.15, C:0.25, G:0.20, T:0.40
Consensus pattern (300 bp):
CGACTTAAACCTTTCCCTTTTTTGTTTTTGTGGTACTGGATCTGCCATTGTGGTCTTAGATCTTT
CCCTTCATGCTTCTGAGGTACACGGTCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTGTTTTGC
GGTACTGGATCTGTCATTGCGGTCTTAGATCTTTCCCTTCCATGCTTTTGAGGTACACAATCCAC
CGTTACGACTTAGACCTTTCCCTTTCGTGTTTTGACGGTACTGGATCCACCATTGCAATCTTAGA
TCTTTCCCTTCATGATTCTGAGGTACACGATCCGCCATTA
Found at i:39829112 original size:58 final size:57
Alignment explanation
Indices: 39829036--39829377 Score: 400
Period size: 58 Copynumber: 5.9 Consensus size: 57
39829026 TGGATACCCC
* * * * *
39829036 GGGGCAAAATGGTAATTTTGGTCGAAATTGGGTCAAAAATGGGATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTGGT-GAAATAGGGTTAAAAATGGAATTTTAGAAAGTTCG
* **
39829094 GGGGTAAAATGGTAATTTTGGTAAAATCGAGGG-TAAAAATGGCGTTTTAGAAAGTTCG
1 GGGGTAAAATGGTAATTTTGGTGAAAT--AGGGTTAAAAATGGAATTTTAGAAAGTTCG
* ** *
39829152 GGGGTAAAATGGTAACTTTGGTGAAATCAAAGTTAAAAATGGAATTTTAGAAAGTTTG
1 GGGGTAAAATGGTAATTTTGGTGAAAT-AGGGTTAAAAATGGAATTTTAGAAAGTTCG
* * *
39829210 GGGGTAAAATGGTAATTTTTGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCA
1 GGGGTAAAATGGTAATTTTGGTGAAATAG-GGTTAAAAATGGAATTTTAGAAAGTTCG
* * * *
39829268 AGGGTAAAATGGTAATTTTGGTGAAATCGATGTTAAAAATGGAATTTTAGAAAGTT-T
1 GGGGTAAAATGGTAATTTTGGTGAAATAG-GGTTAAAAATGGAATTTTAGAAAGTTCG
* * * *
39829325 GGGGTAAAATGATAATTTTGGTGAAATTGGGGTTAAAAATAGAATTTTTGAAA
1 GGGGTAAAATGGTAATTTTGGTGAAA-TAGGGTTAAAAATGGAATTTTAGAAA
39829378 ATTTAAGGTC
Statistics
Matches: 247, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
57 50 0.20
58 194 0.79
59 3 0.01
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.32
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTGGTGAAATAGGGTTAAAAATGGAATTTTAGAAAGTTCG
Found at i:39829217 original size:29 final size:29
Alignment explanation
Indices: 39829065--39829463 Score: 177
Period size: 29 Copynumber: 13.8 Consensus size: 29
39829055 GGTCGAAATT
* * *
39829065 GGGTCAAAAATGGGATTTTGGAAAGTTCGG
1 GGGT-AAAAATGGAATTTTAGAAAGTTCGA
* *
39829095 GGGT-AAAATGGTAATTTTGGTAAA-ATCGA
1 GGGTAAAAATGG-AATTTTAG-AAAGTTCGA
** *
39829124 GGGTAAAAATGGCGTTTTAGAAAGTTCGG
1 GGGTAAAAATGGAATTTTAGAAAGTTCGA
*
39829153 GGGT-AAAATGGTAACTTTGGT-GAAA--TCAA
1 GGGTAAAAATGG-AA-TTT--TAGAAAGTTCGA
* * * *
39829182 AGTTAAAAATGGAATTTTAGAAAGTTTGG
1 GGGTAAAAATGGAATTTTAGAAAGTTCGA
*
39829211 GGGT-AAAATGGTAATTTTTGTGAAA--TCGA
1 GGGTAAAAATGG-AA-TTTT-AGAAAGTTCGA
* *
39829240 GGTTAAAAATGGAATTTTAGAAAGTTCAA
1 GGGTAAAAATGGAATTTTAGAAAGTTCGA
*
39829269 GGGT-AAAATGGTAATTTTGGTGAAA--TCGA
1 GGGTAAAAATGG-AATTTT--AGAAAGTTCGA
* * *
39829298 TGTTAAAAATGGAATTTTAGAAAGTTTG-
1 GGGTAAAAATGGAATTTTAGAAAGTTCGA
* *
39829326 GGGT-AAAATGATAATTTTGGTGAAA-TT-G-
1 GGGTAAAAATG-GAATTTT--AGAAAGTTCGA
* * * *
39829354 GGGTTAAAAATAGAATTTTTGAAAATT-TA
1 GGG-TAAAAATGGAATTTTAGAAAGTTCGA
* * * **
39829383 AGGTCAAAATGTAATTTTAGAAAGTTTTA
1 GGGTAAAAATGGAATTTTAGAAAGTTCGA
* * * **
39829412 GGGTCAAAATGTAATTTTAGAAAATTTTA
1 GGGTAAAAATGGAATTTTAGAAAGTTCGA
* *
39829441 GGGTTAAAATGTAATTTTAGAAA
1 GGGTAAAAATGGAATTTTAGAAA
39829464 AATTTAGGGT
Statistics
Matches: 289, Mismatches: 48, Indels: 65
0.72 0.12 0.16
Matches are distributed among these distances:
26 1 0.00
27 23 0.08
28 70 0.24
29 131 0.45
30 51 0.18
31 12 0.04
32 1 0.00
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.33
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTAGAAAGTTCGA
Found at i:39829247 original size:116 final size:116
Alignment explanation
Indices: 39829070--39829377 Score: 447
Period size: 116 Copynumber: 2.7 Consensus size: 116
39829060 AAATTGGGTC
* * * * *
39829070 AAAAATGGGATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGGTAAAATCGAGGGTAAAAATG
1 AAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATG
** **
39829135 GCGTTTTAGAAAGTTCGGGGGTAAAATGGTAACTTTGGTGAAATCAAAGTT
66 GAATTTTAGAAAGTTCAAGGGTAAAATGGTAACTTTGGTGAAATCAAAGTT
*
39829186 AAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTTGTGAAATCGAGGTTAAAAATG
1 AAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATG
* * *
39829251 GAATTTTAGAAAGTTCAAGGGTAAAATGGTAATTTTGGTGAAATCGATGTT
66 GAATTTTAGAAAGTTCAAGGGTAAAATGGTAACTTTGGTGAAATCAAAGTT
* * * *
39829302 AAAAATGGAATTTTAGAAAGTTT-GGGGTAAAATGATAATTTTGGTGAAATTGGGGTTAAAAATA
1 AAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATG
*
39829366 GAATTTTTGAAA
66 GAATTTTAGAAA
39829378 ATTTAAGGTC
Statistics
Matches: 173, Mismatches: 19, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
115 47 0.27
116 126 0.73
ACGTcount: A:0.38, C:0.03, G:0.27, T:0.32
Consensus pattern (116 bp):
AAAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTGGTGAAATCGAGGTTAAAAATG
GAATTTTAGAAAGTTCAAGGGTAAAATGGTAACTTTGGTGAAATCAAAGTT
Found at i:39829464 original size:29 final size:29
Alignment explanation
Indices: 39829303--39829516 Score: 206
Period size: 29 Copynumber: 7.4 Consensus size: 29
39829293 ATCGATGTTA
* * *
39829303 AAAATGGAATTTTAG-AAAGTTT-GGGGT
1 AAAATGTAATTTTAGAAAATTTTAGGGTT
* * *
39829330 AAAATGATAATTTTGGTGAAA--TTGGGGTT
1 AAAATG-TAATTTTAG-AAAATTTTAGGGTT
* * *
39829359 AAAAATAG-AATTTTTGAAAA-TTTAAGGTC
1 -AAAAT-GTAATTTTAGAAAATTTTAGGGTT
* *
39829388 AAAATGTAATTTTAGAAAGTTTTAGGGTC
1 AAAATGTAATTTTAGAAAATTTTAGGGTT
39829417 AAAATGTAATTTTAGAAAATTTTAGGGTT
1 AAAATGTAATTTTAGAAAATTTTAGGGTT
* *
39829446 AAAATGTAATTTTAGAAAAATTTAGGGTC
1 AAAATGTAATTTTAGAAAATTTTAGGGTT
*
39829475 AAAATATAATTTTTAGAAAATTTTAGGGTT
1 AAAATGTAA-TTTTAGAAAATTTTAGGGTT
*
39829505 AAAACGTAATTT
1 AAAATGTAATTT
39829517 CAAGACAGTC
Statistics
Matches: 157, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
27 7 0.04
28 27 0.17
29 89 0.57
30 33 0.21
31 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTAGAAAATTTTAGGGTT
Found at i:39829468 original size:30 final size:29
Alignment explanation
Indices: 39829367--39829516 Score: 212
Period size: 29 Copynumber: 5.2 Consensus size: 29
39829357 TTAAAAATAG
* *
39829367 AATTTTTGAAAA-TTTAAGGTCAAAATGT
1 AATTTTAGAAAATTTTAGGGTCAAAATGT
*
39829395 AATTTTAGAAAGTTTTAGGGTCAAAATGT
1 AATTTTAGAAAATTTTAGGGTCAAAATGT
*
39829424 AATTTTAGAAAATTTTAGGGTTAAAATGT
1 AATTTTAGAAAATTTTAGGGTCAAAATGT
* *
39829453 AATTTTAGAAAAATTTAGGGTCAAAATAT
1 AATTTTAGAAAATTTTAGGGTCAAAATGT
* *
39829482 AATTTTTAGAAAATTTTAGGGTTAAAACGT
1 AA-TTTTAGAAAATTTTAGGGTCAAAATGT
39829512 AATTT
1 AATTT
39829517 CAAGACAGTC
Statistics
Matches: 108, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
28 10 0.09
29 73 0.68
30 25 0.23
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (29 bp):
AATTTTAGAAAATTTTAGGGTCAAAATGT
Found at i:39831132 original size:25 final size:26
Alignment explanation
Indices: 39831103--39831157 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
39831093 GCAGCGACGG
**
39831103 TGGCAAGGCTAGG-TGGAGCTGGTGA
1 TGGCAAGGAGAGGTTGGAGCTGGTGA
*
39831128 TGGC-AGGAGAGGTTGGAGCTGGTGG
1 TGGCAAGGAGAGGTTGGAGCTGGTGA
39831153 TGGCA
1 TGGCA
39831158 GCAATCAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.18, C:0.11, G:0.51, T:0.20
Consensus pattern (26 bp):
TGGCAAGGAGAGGTTGGAGCTGGTGA
Found at i:39831372 original size:17 final size:17
Alignment explanation
Indices: 39831350--39831469 Score: 104
Period size: 17 Copynumber: 7.2 Consensus size: 17
39831340 TTATTAAATA
*
39831350 AAATTTATAATAACTTT
1 AAATTTATAATAAATTT
* **
39831367 AAATTTATATTAAATCC
1 AAATTTATAATAAATTT
39831384 AAATTTA-AATTAAATTT
1 AAATTTATAA-TAAATTT
*
39831401 AAA-TT-TAATAAATTC
1 AAATTTATAATAAATTT
* *
39831416 AGATTTAAAATAAATTT
1 AAATTTATAATAAATTT
* *
39831433 AATTTTAAAATAAATTT
1 AAATTTATAATAAATTT
*
39831450 AATTTTGA-AATAAATTT
1 AAATTT-ATAATAAATTT
39831467 AAA
1 AAA
39831470 ATGGTTTGGT
Statistics
Matches: 84, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
15 8 0.10
16 7 0.08
17 68 0.81
18 1 0.01
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (17 bp):
AAATTTATAATAAATTT
Found at i:39831393 original size:6 final size:6
Alignment explanation
Indices: 39831364--39831469 Score: 59
Period size: 6 Copynumber: 19.0 Consensus size: 6
39831354 TTATAATAAC
* **
39831364 TTTAAA TTTATA -TTAAA TCCAAA TTTAAA -TTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * *
39831409 --TAAA TTCAGA TTTAAA -ATAAA TTTAAT TTTAAA -ATAAA TTTAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
39831453 TTTGAAA --TAAA TTTAAA
1 TTT-AAA TTTAAA TTTAAA
39831470 ATGGTTTGGT
Statistics
Matches: 72, Mismatches: 18, Indels: 20
0.65 0.16 0.18
Matches are distributed among these distances:
3 1 0.01
4 5 0.07
5 20 0.28
6 44 0.61
7 2 0.03
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:39831398 original size:11 final size:11
Alignment explanation
Indices: 39831343--39831469 Score: 59
Period size: 11 Copynumber: 11.5 Consensus size: 11
39831333 TGGATATTTA
*
39831343 TTAAATAAAAT
1 TTAAATTAAAT
*
39831354 TTATAA-TAACT
1 TTA-AATTAAAT
*
39831365 TTAAATT-TAT
1 TTAAATTAAAT
*
39831375 ATTAAATCCAAAT
1 -TTAAAT-TAAAT
39831388 TTAAATTAAAT
1 TTAAATTAAAT
*
39831399 TTAAATTTAA-
1 TTAAATTAAAT
*
39831409 -TAAATTCAGAT
1 TTAAATT-AAAT
*
39831420 TTAAAATAAAT
1 TTAAATTAAAT
*
39831431 TTAATTTTAAA-
1 TTAA-ATTAAAT
* *
39831442 ATAAATTTAATT
1 TTAAA-TTAAAT
39831454 TTGAAA-TAAAT
1 TT-AAATTAAAT
39831465 TTAAA
1 TTAAA
39831470 ATGGTTTGGT
Statistics
Matches: 85, Mismatches: 19, Indels: 25
0.66 0.15 0.19
Matches are distributed among these distances:
9 6 0.07
10 7 0.08
11 49 0.58
12 18 0.21
13 5 0.06
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (11 bp):
TTAAATTAAAT
Found at i:39836470 original size:15 final size:15
Alignment explanation
Indices: 39836450--39836482 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39836440 ATTTGAAGTT
*
39836450 ATTGGTTGGATTTGA
1 ATTGGTTAGATTTGA
39836465 ATTGGTTAGATTTGA
1 ATTGGTTAGATTTGA
39836480 ATT
1 ATT
39836483 TACAGGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (15 bp):
ATTGGTTAGATTTGA
Found at i:39836625 original size:43 final size:43
Alignment explanation
Indices: 39836550--39836728 Score: 202
Period size: 43 Copynumber: 4.2 Consensus size: 43
39836540 TCTGTTAATA
* * * *
39836550 TTAGCGGCGTTTGTGTGAAAAACGTCGCTAAAGAACATTATCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATTATCT
* * *
39836593 ATAGCGGCGTTTGTGGTAAAAGCGCCGTTAAAGACCATGT-TCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCAT-TATCT
* * *
39836636 TTATCGGCGTTTTTGGGGAAAGCGCCGCTAAAGACCA-TATTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATTA-TCT
* *
39836679 TTAGCGGCGTTTGTGGGGAAAGCGTCGCTAAAGACCATGT-TCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCAT-TATCT
39836722 TTAGCGG
1 TTAGCGG
39836729 TCTTTTTCCT
Statistics
Matches: 115, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
43 112 0.97
44 1 0.01
45 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATTATCT
Found at i:39836735 original size:86 final size:86
Alignment explanation
Indices: 39836550--39836728 Score: 234
Period size: 86 Copynumber: 2.1 Consensus size: 86
39836540 TCTGTTAATA
* * * * * *
39836550 TTAGCGGCGTTTGTGTGAAAAACGTCGCTAAAGAACATTATCTATAGCGGCGTTTGTGGTAAAAG
1 TTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGAACATTATCTATAGCGGCGTTTGTGGGAAAAG
*
39836615 CGCCGTTAAAGACCATGTTCT
66 CGCCGCTAAAGACCATGTTCT
* * * *
39836636 TTATCGGCGTTTTTGGGGAAAGCGCCGCTAAAGACCA-TATTCTTTAGCGGCGTTTGTGGGGAAA
1 TTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGAACATTA-TCTATAGCGGCGTTTGTGGGAAAA
*
39836700 GCGTCGCTAAAGACCATGTTCT
65 GCGCCGCTAAAGACCATGTTCT
39836722 TTAGCGG
1 TTAGCGG
39836729 TCTTTTTCCT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
85 2 0.03
86 77 0.97
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (86 bp):
TTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGAACATTATCTATAGCGGCGTTTGTGGGAAAAG
CGCCGCTAAAGACCATGTTCT
Found at i:39836768 original size:15 final size:15
Alignment explanation
Indices: 39836748--39836777 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39836738 TCATAAACGT
*
39836748 CGTTATTTTTAGCGG
1 CGTTATCTTTAGCGG
39836763 CGTTATCTTTAGCGG
1 CGTTATCTTTAGCGG
39836778 TATTTTTTGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.17, G:0.27, T:0.43
Consensus pattern (15 bp):
CGTTATCTTTAGCGG
Found at i:39852420 original size:21 final size:21
Alignment explanation
Indices: 39852364--39852421 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
39852354 AGATTCATGG
* *
39852364 TTGGGATTTAGAGTTTTATGT
1 TTGGGGTTTAGGGTTTTATGT
***
39852385 TTAAAGTTT-GAGGTTTTATGT
1 TTGGGGTTTAG-GGTTTTATGT
39852406 TTGGGGTTTAGGGTTT
1 TTGGGGTTTAGGGTTT
39852422 AGGGTTTTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
20 1 0.04
21 25 0.93
22 1 0.04
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (21 bp):
TTGGGGTTTAGGGTTTTATGT
Found at i:39853027 original size:13 final size:13
Alignment explanation
Indices: 39853009--39853038 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39852999 ACATTAAACT
*
39853009 CATTCTAAGGGCC
1 CATTCTAAAGGCC
39853022 CATTCTAAAGGCC
1 CATTCTAAAGGCC
39853035 CATT
1 CATT
39853039 TAGCATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (13 bp):
CATTCTAAAGGCC
Found at i:39860101 original size:29 final size:29
Alignment explanation
Indices: 39860059--39860120 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
39860049 GGTTCGTATA
*
39860059 GCATATAGGCTCGCATGTTCCTAGGGTTC
1 GCATATAGGCTCGCATGTTCCTAGAGTTC
39860088 GCATATAGGCTCGCATGTTCCTAGAGTTC
1 GCATATAGGCTCGCATGTTCCTAGAGTTC
39860117 GCAT
1 GCAT
39860121 GCATATAGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (29 bp):
GCATATAGGCTCGCATGTTCCTAGAGTTC
Found at i:39860148 original size:62 final size:63
Alignment explanation
Indices: 39860026--39860154 Score: 152
Period size: 62 Copynumber: 2.1 Consensus size: 63
39860016 TTCGCATAAT
* * * * ***
39860026 CATATAGGTTCACATGTACTTAGGGTTCGTATAGCATATAGGCTCGCATGTTCCTAGGGTTCG
1 CATATAGGCTCACATGTACCTAGAGTTCGCATAGCATATAGGCTCGCATAACCCTAGGGTTCG
* * * *
39860089 CATATAGGCTCGCATGTTCCTAGAGTTCGCAT-GCATATAGGTTCGCATAACCCTGGGGTTCG
1 CATATAGGCTCACATGTACCTAGAGTTCGCATAGCATATAGGCTCGCATAACCCTAGGGTTCG
39860151 CATA
1 CATA
39860155 CATACATGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
62 29 0.53
63 26 0.47
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (63 bp):
CATATAGGCTCACATGTACCTAGAGTTCGCATAGCATATAGGCTCGCATAACCCTAGGGTTCG
Found at i:39860215 original size:61 final size:61
Alignment explanation
Indices: 39860144--39860318 Score: 172
Period size: 61 Copynumber: 2.8 Consensus size: 61
39860134 CATAACCCTG
* * * * *
39860144 GGGTTCGCATACATACATGTTCGCATAAGCCTAGGGTTCACATACATACAGGCTTGCACTA
1 GGGTTCGCATACATACAAGCTCGCATAAGCCTAAGGTTCACAGACATAAAGGCTTGCACTA
* *
39860205 GGGTTCGCATACATACAAGCTCGCATAATCCTAAGGTTCGCAGACATAAAGGCTCACATAAGC-C
1 GGGTTCGCATACATACAAGCTCGCATAAGCCTAAGGTTCACAGACATAAAGGCT----T--GCAC
39860269 TA
60 TA
* * * * * *
39860271 GGGTTTGCATACATATAGGCTCGCATAATCCTAAGGTTCGCATACATA
1 GGGTTCGCATACATACAAGCTCGCATAAGCCTAAGGTTCACAGACATA
39860319 TAGGGTCGTA
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
61 47 0.48
65 1 0.01
66 47 0.48
67 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (61 bp):
GGGTTCGCATACATACAAGCTCGCATAAGCCTAAGGTTCACAGACATAAAGGCTTGCACTA
Found at i:39860232 original size:94 final size:94
Alignment explanation
Indices: 39860108--39860291 Score: 224
Period size: 94 Copynumber: 2.0 Consensus size: 94
39860098 TCGCATGTTC
* * * * ** * * * * *
39860108 CTAGAGTTCGCATGCATATAGGTTCGCATAACCCTGGGGTTCGCATACATACATGTTCGCATAAG
1 CTAGAGTTCGCATACATACAAGCTCGCATAACCCTAAGGTTCGCAGACATAAAGGCTCACATAAG
39860173 CCTAGGGTTCACATACATACAGGCTTGCA
66 CCTAGGGTTCACATACATACAGGCTTGCA
* *
39860202 CTAGGGTTCGCATACATACAAGCTCGCATAATCCTAAGGTTCGCAGACATAAAGGCTCACATAAG
1 CTAGAGTTCGCATACATACAAGCTCGCATAACCCTAAGGTTCGCAGACATAAAGGCTCACATAAG
** *
39860267 CCTAGGGTTTGCATACATATAGGCT
66 CCTAGGGTTCACATACATACAGGCT
39860292 CGCATAATCC
Statistics
Matches: 74, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
94 74 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.26
Consensus pattern (94 bp):
CTAGAGTTCGCATACATACAAGCTCGCATAACCCTAAGGTTCGCAGACATAAAGGCTCACATAAG
CCTAGGGTTCACATACATACAGGCTTGCA
Found at i:39860289 original size:17 final size:17
Alignment explanation
Indices: 39860269--39860324 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
39860259 CACATAAGCC
*
39860269 TAGGGTTTGCATACATA
1 TAGGGTTCGCATACATA
* *
39860286 TA-GGCTCGCATA-ATCC
1 TAGGGTTCGCATACAT-A
*
39860302 TAAGGTTCGCATACATA
1 TAGGGTTCGCATACATA
39860319 TAGGGT
1 TAGGGT
39860325 CGTATAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
15 2 0.07
16 10 0.33
17 16 0.53
18 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (17 bp):
TAGGGTTCGCATACATA
Found at i:39860319 original size:33 final size:33
Alignment explanation
Indices: 39860046--39860331 Score: 248
Period size: 33 Copynumber: 8.9 Consensus size: 33
39860036 CACATGTACT
* **
39860046 TAGGGTTCGTATAGCATATAGGCTCGCATGTTCC
1 TAGGGTTCGCATA-CATATAGGCTCGCATAATCC
**
39860080 TAGGGTTCG----CATATAGGCTCGCATGTTCC
1 TAGGGTTCGCATACATATAGGCTCGCATAATCC
* * * *
39860109 TAGAGTTCGCATGCATATAGGTTCGCATAACCC
1 TAGGGTTCGCATACATATAGGCTCGCATAATCC
* * * * *
39860142 TGGGGTTCGCATACATACATGTTCGCATAAGCC
1 TAGGGTTCGCATACATATAGGCTCGCATAATCC
* * *
39860175 TAGGGTTCACATACATACAGGCTTGC---A--C
1 TAGGGTTCGCATACATATAGGCTCGCATAATCC
* *
39860203 TAGGGTTCGCATACATACAAGCTCGCATAATCC
1 TAGGGTTCGCATACATATAGGCTCGCATAATCC
* * * * *
39860236 TAAGGTTCGCAGACATAAAGGCTCACATAAGCC
1 TAGGGTTCGCATACATATAGGCTCGCATAATCC
*
39860269 TAGGGTTTGCATACATATAGGCTCGCATAATCC
1 TAGGGTTCGCATACATATAGGCTCGCATAATCC
* * *
39860302 TAAGGTTCGCATACATATAGGGTCGTATAA
1 TAGGGTTCGCATACATATAGGCTCGCATAA
39860332 AATACATGGT
Statistics
Matches: 208, Mismatches: 35, Indels: 19
0.79 0.13 0.07
Matches are distributed among these distances:
28 24 0.12
29 28 0.13
30 1 0.00
31 1 0.00
33 145 0.70
34 9 0.04
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (33 bp):
TAGGGTTCGCATACATATAGGCTCGCATAATCC
Found at i:39866873 original size:35 final size:35
Alignment explanation
Indices: 39866827--39866902 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
39866817 AAGTTTTTCT
*
39866827 CTTGATTTGGATGTTTGGATATTAGACTCTTAAGC
1 CTTGAATTGGATGTTTGGATATTAGACTCTTAAGC
*
39866862 CTTGAATTGGATGTTTGGATATTAGTCTCTTAAGC
1 CTTGAATTGGATGTTTGGATATTAGACTCTTAAGC
39866897 CTTGAA
1 CTTGAA
39866903 GTGTTCTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.24, C:0.12, G:0.22, T:0.42
Consensus pattern (35 bp):
CTTGAATTGGATGTTTGGATATTAGACTCTTAAGC
Found at i:39870514 original size:21 final size:21
Alignment explanation
Indices: 39870485--39870526 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39870475 GTATTTTTGA
*
39870485 GTTTTAGATTCAAGATTTAAG
1 GTTTGAGATTCAAGATTTAAG
* *
39870506 GTTTGAGATTCATGGTTTAAG
1 GTTTGAGATTCAAGATTTAAG
39870527 ATAAAGAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.43
Consensus pattern (21 bp):
GTTTGAGATTCAAGATTTAAG
Found at i:39872176 original size:18 final size:18
Alignment explanation
Indices: 39872139--39872176 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
39872129 ATTAAATAAT
*
39872139 TTGAGTTATTTAGGTTAA
1 TTGAGTTATTTAGGTCAA
39872157 TTGAGTTATTT-GGATCAA
1 TTGAGTTATTTAGG-TCAA
39872175 TT
1 TT
39872177 TGAATAAAAA
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:0.26, C:0.03, G:0.21, T:0.50
Consensus pattern (18 bp):
TTGAGTTATTTAGGTCAA
Found at i:39873652 original size:17 final size:17
Alignment explanation
Indices: 39873625--39873692 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
39873615 ATAATTTAAT
39873625 TTTTAAA-TTAAATTTA
1 TTTTAAATTTAAATTTA
39873641 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
** * *
39873658 CATAAAATTTAAGTTTA
1 TTTTAAATTTAAATTTA
* *
39873675 TTATAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
39873692 T
1 T
39873693 AAATTAAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 7 0.17
17 34 0.83
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:39875512 original size:162 final size:163
Alignment explanation
Indices: 39875299--39875603 Score: 436
Period size: 162 Copynumber: 1.9 Consensus size: 163
39875289 ACCATAGACT
*
39875299 GCCACGTGTCACTATTTTGGTTTATTTATGCAAATGGTCCCTTATATTTTTAATTTATTTTAATT
1 GCCACGTGTCACTATTTTGGTTTATTTATGCAAATAGTCCCTTATATTTTTAATTTATTTTAATT
* * * * *
39875364 TAGTCCTT-AAATCAAGTTTTATTTAATTACAAAATTGACCCAAGAATTTTTCAAGATTTATAAA
66 TAAT-CTTCAAATCAACTTCTACTTAATTACAAAATTGACCCAAGAATTTTTCAAGATTTACAAA
39875428 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCC
130 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCC
* ** * *
39875462 GCCACGTGTCACT-TTTTGGTTTATTTATGTATCTAGT-CCTTGTCATTTTTAATTTGTTTTAAT
1 GCCACGTGTCACTATTTTGGTTTATTTATGCAAATAGTCCCTTAT-ATTTTTAATTTATTTTAAT
* * *
39875525 TTAATCTTCAAATCAACTTCTGCTTAATTACAAAATTGGCCCGAGAATTTTTCAAGATTTACAAA
65 TTAATCTTCAAATCAACTTCTACTTAATTACAAAATTGACCCAAGAATTTTTCAAGATTTACAAA
*
39875590 TTCATCCTTTGACT
130 TTAATCCTTTGACT
39875604 TCTGGATGCC
Statistics
Matches: 125, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
161 8 0.06
162 104 0.83
163 13 0.10
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.44
Consensus pattern (163 bp):
GCCACGTGTCACTATTTTGGTTTATTTATGCAAATAGTCCCTTATATTTTTAATTTATTTTAATT
TAATCTTCAAATCAACTTCTACTTAATTACAAAATTGACCCAAGAATTTTTCAAGATTTACAAAT
TAATCCTTTGACTGTTTGACTGCACCAGAGGCC
Found at i:39875718 original size:28 final size:27
Alignment explanation
Indices: 39875677--39875767 Score: 96
Period size: 29 Copynumber: 3.2 Consensus size: 27
39875667 GGACTGTCCA
39875677 AAAATTACCATTTTACCCCTAAACTTTCC
1 AAAATTACCATTTTA-CCC-AAACTTTCC
*
39875706 AAAATT-CCATTTTAACCCAGA-TTTCACC
1 AAAATTACCATTTT-ACCCAAACTTT--CC
*
39875734 AAAAATTACCATTTTACCCGAACTTTCC
1 -AAAATTACCATTTTACCCAAACTTTCC
39875762 AAAATT
1 AAAATT
39875768 CCTTTTTTAA
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
26 3 0.06
27 8 0.15
28 14 0.26
29 18 0.34
30 10 0.19
ACGTcount: A:0.37, C:0.27, G:0.02, T:0.33
Consensus pattern (27 bp):
AAAATTACCATTTTACCCAAACTTTCC
Found at i:39875738 original size:29 final size:29
Alignment explanation
Indices: 39875706--39875805 Score: 86
Period size: 30 Copynumber: 3.4 Consensus size: 29
39875696 TAAACTTTCC
39875706 AAAATTCCATTTTAACCCAGATTTCACCA
1 AAAATTCCATTTTAACCCAGATTTCACCA
39875735 AAAATTACCATTTT-ACCC-GAACTTT--CC-
1 AAAATT-CCATTTTAACCCAG-A-TTTCACCA
*
39875762 AAAATTCCTTTTTTAACCTCA-ATTTCACCA
1 AAAATTCC-ATTTTAACC-CAGATTTCACCA
*
39875792 AAAACTACCATTTT
1 AAAA-TTCCATTTT
39875806 TCCCTTGAAC
Statistics
Matches: 57, Mismatches: 3, Indels: 21
0.70 0.04 0.26
Matches are distributed among these distances:
26 2 0.04
27 13 0.23
28 7 0.12
29 14 0.25
30 18 0.32
31 3 0.05
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAATTCCATTTTAACCCAGATTTCACCA
Found at i:39875746 original size:58 final size:58
Alignment explanation
Indices: 39875674--39875892 Score: 261
Period size: 58 Copynumber: 3.8 Consensus size: 58
39875664 CCTGGACTGT
* *
39875674 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCAGATTTCA
1 CCAAAAACTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTAACCCAGATTTCA
* *
39875732 CCAAAAATTACCATTTTA-CCC-GAACTTTCCAAAATTCCTTTTTTAACCTCA-ATTTCA
1 CCAAAAACTACCATTTTACCCCTGAACTTTCCAAAATTCC-ATTTTAACC-CAGATTTCA
* * * *
39875789 CCAAAAACTACCATTTTTCCCTTGAACTTTCTAAAATT-CATTTTTAACCCCGATTTCA
1 CCAAAAACTACCATTTTACCCCTGAACTTTCCAAAATTCCA-TTTTAACCCAGATTTCA
* *
39875847 CAAAAAACTACCATTTTACCCCTGCAA--GTCCAAAATTACCATTTTA
1 CCAAAAACTACCATTTTACCCCTG-AACTTTCCAAAATT-CCATTTTA
39875893 CCCCCGGGTA
Statistics
Matches: 139, Mismatches: 13, Indels: 18
0.82 0.08 0.11
Matches are distributed among these distances:
56 16 0.12
57 42 0.30
58 63 0.45
59 18 0.13
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
CCAAAAACTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTAACCCAGATTTCA
Found at i:39875909 original size:115 final size:112
Alignment explanation
Indices: 39875673--39875897 Score: 240
Period size: 115 Copynumber: 2.0 Consensus size: 112
39875663 CCCTGGACTG
* *
39875673 TCCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCAGATTTCACCAAAA
1 TCCAAAAACTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCAGATTTCACAAAAA
* * * * *
39875738 ATTACCATTTTACCCGAACTTTCCAAAATTCCTTTTTTAACCTCAATT
66 ACTACCATTTTACCCGAAC-GTCCAAAATTCCTATTTTAACCCCAATA
* * * * *
39875786 TCACCAAAAACTACCATTTTTCCCTTGAACTTTCTAAAATT-CATTTTTAACCCCGATTTCACAA
1 T--CCAAAAACTACCATTTTACCCCTAAACTTTCCAAAATTCCA-TTTTAACCCAGATTTCACAA
*
39875850 AAAACTACCATTTTACCCCTGCAA-GTCCAAAATTACC-ATTTTACCCCC
63 AAAACTACCATTTTA-CCC-G-AACGTCCAAAATT-CCTATTTTAACCCC
39875898 GGGTATCCAA
Statistics
Matches: 93, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
113 1 0.01
114 2 0.02
115 65 0.70
116 20 0.22
117 3 0.03
118 2 0.02
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (112 bp):
TCCAAAAACTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCAGATTTCACAAAAA
ACTACCATTTTACCCGAACGTCCAAAATTCCTATTTTAACCCCAATA
Found at i:39875994 original size:15 final size:16
Alignment explanation
Indices: 39875974--39876018 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
39875964 TTATTTGCAC
39875974 TTGCATTTTATATT-T
1 TTGCATTTTATATTAT
*
39875989 TTGCATATTAT-TTAT
1 TTGCATTTTATATTAT
39876004 TTGC-TTATTATATTA
1 TTGCATT-TTATATTA
39876019 CTTCGTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 3 0.12
15 19 0.76
16 3 0.12
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (16 bp):
TTGCATTTTATATTAT
Found at i:39890798 original size:75 final size:76
Alignment explanation
Indices: 39890650--39891387 Score: 1148
Period size: 76 Copynumber: 9.8 Consensus size: 76
39890640 AGACCGTACT
* *
39890650 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGAT-ACTAAGTCTTTATCTCTGAAAT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC-AAGTCTTTATCTCTGAAAT
39890714 TGAAGTAAGAGC
65 TGAAGTAAGAGC
* *
39890726 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
39890790 GAAGTAAGAGC
66 GAAGTAAGAGC
* *
39890801 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
39890865 GAAGTAAGAGC
66 GAAGTAAGAGC
*
39890876 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
*
39890940 GAAGTAAGAAC
66 GAAGTAAGAGC
39890951 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACA-TCTTTATCTCTGAAAT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACA-AGTCTTTATCTCTGAAAT
*
39891014 TGAAGTAAGAAC
65 TGAAGTAAGAGC
* * * * *
39891026 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATATCAGGTCTTTGTCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
39891091 GAAGTAAGAGC
66 GAAGTAAGAGC
* * * *
39891102 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTGTCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
39891167 GAAGTAAGAGC
66 GAAGTAAGAGC
* * * *
39891178 AAGATCATTTCCTATCCTCTTGAAATTGAAATAAAGCTGGATATCAAGTCTTTATCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
*
39891243 GAAGTATGAGC
66 GAAGTAAGAGC
* *
39891254 AAGATCGTTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
39891319 GAAGTAAGAGC
66 GAAGTAAGAGC
* * *
39891330 AAGATCATTTCTTATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAG-CATTTATCTC
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTC-TTTATCTC
39891388 ACTAAAAGGG
Statistics
Matches: 626, Mismatches: 31, Indels: 10
0.94 0.05 0.01
Matches are distributed among these distances:
75 291 0.46
76 335 0.54
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Consensus pattern (76 bp):
AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
GAAGTAAGAGC
Found at i:39890878 original size:150 final size:151
Alignment explanation
Indices: 39890650--39891372 Score: 1148
Period size: 150 Copynumber: 4.8 Consensus size: 151
39890640 AGACCGTACT
* *
39890650 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGAT-ACTAAGTCTTTATCTCTGAAAT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC-AAGTCTTTATCTCTGAAAT
*
39890714 TGAAGTAAGAGCAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTA
65 TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTA
39890779 TCTCTGAAATTGAAGTAAGAGC
130 TCTCTGAAATTGAAGTAAGAGC
* *
39890801 AAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
39890865 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTAT
66 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTAT
*
39890930 CTCTGAAATTGAAGTAAGAAC
131 CTCTGAAATTGAAGTAAGAGC
39890951 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACA-TCTTTATCTCTGAAAT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACA-AGTCTTTATCTCTGAAAT
* * * * *
39891014 TGAAGTAAGAACAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAGAATTGGATATCAGGTCTTT
65 TGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAG-AGTGGATAACACGTCTTT
*
39891079 GTCTCTGAAATTGAAGTAAGAGC
129 ATCTCTGAAATTGAAGTAAGAGC
* * * *
39891102 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTGTCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
* * * *
39891167 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAATAAAGCTGGATATCAAGTCTTTA
66 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTA
*
39891232 TCTCTGAAATTGAAGTATGAGC
130 TCTCTGAAATTGAAGTAAGAGC
* *
39891254 AAGATCGTTTCCCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
1 AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
* *
39891319 GAAGTAAGAGCAAGATCATTTCTTATCCTCTTGAAATTGAAGTAAAGTTGGATA
66 GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAG-TGGATA
39891373 GCAAGCATTT
Statistics
Matches: 533, Mismatches: 33, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
150 212 0.40
151 110 0.21
152 211 0.40
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (151 bp):
AAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATT
GAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTAT
CTCTGAAATTGAAGTAAGAGC
Found at i:39892320 original size:17 final size:17
Alignment explanation
Indices: 39892293--39892360 Score: 75
Period size: 17 Copynumber: 4.1 Consensus size: 17
39892283 ATAATTTAAT
39892293 TTTTAAA-TTAAATTTA
1 TTTTAAATTTAAATTTA
39892309 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
** * *
39892326 CATAAAATTTAAGTTTA
1 TTTTAAATTTAAATTTA
* *
39892343 TTATAAATTTAAACTTA
1 TTTTAAATTTAAATTTA
39892360 T
1 T
39892361 AAATTAAATT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
16 7 0.17
17 34 0.83
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:39894050 original size:162 final size:163
Alignment explanation
Indices: 39893837--39894141 Score: 436
Period size: 162 Copynumber: 1.9 Consensus size: 163
39893827 ACCATAGACT
*
39893837 GCCACGTGTCACTATTTTGGTTTATTTATGCAAATGGTCCCTTATATTTTTAATTTATTTTAATT
1 GCCACGTGTCACTATTTTGGTTTATTTATGCAAATAGTCCCTTATATTTTTAATTTATTTTAATT
* * * * *
39893902 TAGTCCTT-AAATCAAGTTTTATTTAATTACAAAATTGACCCAAGAATTTTTCAAGATTTATAAA
66 TAAT-CTTCAAATCAACTTCTACTTAATTACAAAATTGACCCAAGAATTTTTCAAGATTTACAAA
39893966 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCC
130 TTAATCCTTTGACTGTTTGACTGCACCAGAGGCC
* ** * *
39894000 GCCACGTGTCACT-TTTTGGTTTATTTATGTATCTAGT-CCTTGTCATTTTTAATTTGTTTTAAT
1 GCCACGTGTCACTATTTTGGTTTATTTATGCAAATAGTCCCTTAT-ATTTTTAATTTATTTTAAT
* * *
39894063 TTAATCTTCAAATCAACTTCTGCTTAATTACAAAATTGGCCCGAGAATTTTTCAAGATTTACAAA
65 TTAATCTTCAAATCAACTTCTACTTAATTACAAAATTGACCCAAGAATTTTTCAAGATTTACAAA
*
39894128 TTCATCCTTTGACT
130 TTAATCCTTTGACT
39894142 TCTGGATGCC
Statistics
Matches: 125, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
161 8 0.06
162 104 0.83
163 13 0.10
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.44
Consensus pattern (163 bp):
GCCACGTGTCACTATTTTGGTTTATTTATGCAAATAGTCCCTTATATTTTTAATTTATTTTAATT
TAATCTTCAAATCAACTTCTACTTAATTACAAAATTGACCCAAGAATTTTTCAAGATTTACAAAT
TAATCCTTTGACTGTTTGACTGCACCAGAGGCC
Found at i:39894276 original size:29 final size:30
Alignment explanation
Indices: 39894212--39894345 Score: 97
Period size: 29 Copynumber: 4.6 Consensus size: 30
39894202 CCTGGACTGT
* *
39894212 CCAAAAATTACCATTTTACCCCTAAACTTT--
1 CCAAAAATTACCATTTTAACCC-AGA-TTTCA
39894242 CC-AAAATT-CCATTTTAACCCAGATTTCA
1 CCAAAAATTACCATTTTAACCCAGATTTCA
* * *
39894270 CCAAAAATTACGATTTTACCCCCGAACTTT--
1 CCAAAAATTACCATTTTAACCCAG-A-TTTCA
*
39894300 CC-AAAATT-CCTTTTTTAACCTCA-ATTTCA
1 CCAAAAATTACC-ATTTTAACC-CAGATTTCA
39894329 CCAAAAATTACCATTTT
1 CCAAAAATTACCATTTT
39894346 TCCCTTGAAC
Statistics
Matches: 82, Mismatches: 10, Indels: 24
0.71 0.09 0.21
Matches are distributed among these distances:
26 3 0.04
27 5 0.06
28 15 0.18
29 27 0.33
30 26 0.32
31 3 0.04
32 3 0.04
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.34
Consensus pattern (30 bp):
CCAAAAATTACCATTTTAACCCAGATTTCA
Found at i:39894286 original size:58 final size:58
Alignment explanation
Indices: 39894212--39894410 Score: 267
Period size: 58 Copynumber: 3.4 Consensus size: 58
39894202 CCTGGACTGT
*
39894212 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCAGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTAACCCAGATTTCA
* * *
39894270 CCAAAAATTACGATTTTACCCCCGAACTTTCCAAAATTCCTTTTTTAACCTCA-ATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCC-ATTTTAACC-CAGATTTCA
* * * *
39894329 CCAAAAATTACCATTTTTCCCTTGAACTTTCTAAAATT-CATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCA-TTTTAACCCAGATTTCA
* *
39894387 CAAAAAACTACCATTTTACCCCTG
1 CCAAAAATTACCATTTTACCCCTG
39894411 CAAGTCTAAA
Statistics
Matches: 122, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
57 1 0.01
58 72 0.59
59 47 0.39
60 2 0.02
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTAACCCAGATTTCA
Found at i:39894432 original size:58 final size:57
Alignment explanation
Indices: 39894212--39894438 Score: 242
Period size: 58 Copynumber: 3.9 Consensus size: 57
39894202 CCTGGACTGT
* * *
39894212 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCAGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAAC-TTCTAAAATTCCATTTTAACCCCGATTTCA
* * * * * *
39894270 CCAAAAATTACGATTTTACCCCCGAACTTTCCAAAATTCCTTTTTTAACCTCAATTTCA
1 CCAAAAATTACCATTTTACCCCTGAAC-TTCTAAAATTCC-ATTTTAACCCCGATTTCA
* *
39894329 CCAAAAATTACCATTTTTCCCTTGAACTTTCTAAAATT-CATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAAC-TTCTAAAATTCCA-TTTTAACCCCGATTTCA
* * * *
39894387 CAAAAAACTACCATTTTACCCCTGCAA-GTCTAAAATTACCATTTTACCCCCG
1 CCAAAAATTACCATTTTACCCCTG-AACTTCTAAAATT-CCATTTTAACCCCG
39894439 GGTATCCAAA
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
57 9 0.06
58 83 0.58
59 51 0.36
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (57 bp):
CCAAAAATTACCATTTTACCCCTGAACTTCTAAAATTCCATTTTAACCCCGATTTCA
Found at i:39909371 original size:16 final size:16
Alignment explanation
Indices: 39909346--39909380 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39909336 TAATCTAATT
*
39909346 TATTTGATATATTCAA
1 TATTTGATATATTAAA
*
39909362 TATTTTATATATTAAA
1 TATTTGATATATTAAA
39909378 TAT
1 TAT
39909381 ATTTTTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
TATTTGATATATTAAA
Found at i:39912668 original size:18 final size:18
Alignment explanation
Indices: 39912645--39912681 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
39912635 ATGTTCCAGT
39912645 TGGTACGCGTGATATTGA
1 TGGTACGCGTGATATTGA
39912663 TGGTACGCGTGATATTGA
1 TGGTACGCGTGATATTGA
39912681 T
1 T
39912682 ATAAAAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.32, T:0.35
Consensus pattern (18 bp):
TGGTACGCGTGATATTGA
Found at i:39912734 original size:31 final size:31
Alignment explanation
Indices: 39912696--39912772 Score: 154
Period size: 31 Copynumber: 2.5 Consensus size: 31
39912686 AAATGTGTTG
39912696 TTAGTCCTTGTACTTGTATAGAATTTAATAT
1 TTAGTCCTTGTACTTGTATAGAATTTAATAT
39912727 TTAGTCCTTGTACTTGTATAGAATTTAATAT
1 TTAGTCCTTGTACTTGTATAGAATTTAATAT
39912758 TTAGTCCTTGTACTT
1 TTAGTCCTTGTACTT
39912773 TAAACATTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (31 bp):
TTAGTCCTTGTACTTGTATAGAATTTAATAT
Found at i:39913197 original size:3 final size:3
Alignment explanation
Indices: 39913189--39913224 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
39913179 AGGAGTGTAA
39913189 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39913225 TAAGAAGTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.