Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 36 of 226
Found at i:15620589 original size:6 final size:6
Alignment explanation
Indices: 15620578--15620605 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
15620568 TATGTGCCGA
15620578 TTACTG TTACTG TTACTG TTACTG TTAC
1 TTACTG TTACTG TTACTG TTACTG TTAC
15620606 CGGTTCGGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (6 bp):
TTACTG
Found at i:15620635 original size:45 final size:45
Alignment explanation
Indices: 15620585--15620700 Score: 178
Period size: 45 Copynumber: 2.6 Consensus size: 45
15620575 CGATTACTGT
* *
15620585 TACTGTTACTGTTACTGTTACCGGTTCGGCACTTCGTGTGTCGAA
1 TACTGTTACTGTTACCGTTACCGATTCGGCACTTCGTGTGTCGAA
* * *
15620630 TACTGTTATTGTTACCGTCACCGATTCGGCACTTTGTGTGTCGAA
1 TACTGTTACTGTTACCGTTACCGATTCGGCACTTCGTGTGTCGAA
*
15620675 TACAGTTACTGTTACCGTTACCGATT
1 TACTGTTACTGTTACCGTTACCGATT
15620701 ACTGTTACTG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (45 bp):
TACTGTTACTGTTACCGTTACCGATTCGGCACTTCGTGTGTCGAA
Found at i:15620637 original size:51 final size:50
Alignment explanation
Indices: 15620557--15620697 Score: 141
Period size: 45 Copynumber: 2.9 Consensus size: 50
15620547 CCGGCTTACT
* * * * * *
15620557 GATTAGGCACTTATGTGCCGATTACTGTTACTGTTACTGTTACTGTTACC
1 GATTCGGCACTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGTCACC
*
15620607 GGTTCGGCACTTCGTGTGTCGAATACTGTTA----T--TGTTACCGTCACC
1 GATTCGGCACTT-GTGTGTCGAATACTGTTACTGTTACTGTTACCGTCACC
* *
15620652 GATTCGGCACTTTGTGTGTCGAATACAGTTACTGTTACCGTTACCG
1 GATTCGGCAC-TTGTGTGTCGAATACTGTTACTGTTACTGTTACCG
15620698 ATTACTGTTA
Statistics
Matches: 73, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
45 37 0.51
46 2 0.03
47 1 0.01
49 1 0.01
50 10 0.14
51 22 0.30
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (50 bp):
GATTCGGCACTTGTGTGTCGAATACTGTTACTGTTACTGTTACCGTCACC
Found at i:15632296 original size:29 final size:29
Alignment explanation
Indices: 15632254--15632320 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
15632244 GAAGAGGTAG
15632254 AGAACTTGTTCGTTGAGAGTTCGCGATGA
1 AGAACTTGTTCGTTGAGAGTTCGCGATGA
*
15632283 AGAACTTGTTCGTTGAGATTTCGCGATGA
1 AGAACTTGTTCGTTGAGAGTTCGCGATGA
15632312 AGAACTTGT
1 AGAACTTGT
15632321 GTCAAGGTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.33
Consensus pattern (29 bp):
AGAACTTGTTCGTTGAGAGTTCGCGATGA
Found at i:15649682 original size:18 final size:17
Alignment explanation
Indices: 15649655--15649690 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
15649645 TATATACAAT
15649655 TTAATCTCAAAAAACACA
1 TTAATCTC-AAAAACACA
*
15649673 TTAATGTCAAAAACACA
1 TTAATCTCAAAAACACA
15649690 T
1 T
15649691 CAAAACCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.25
Consensus pattern (17 bp):
TTAATCTCAAAAACACA
Found at i:15649749 original size:98 final size:99
Alignment explanation
Indices: 15649579--15649779 Score: 343
Period size: 98 Copynumber: 2.1 Consensus size: 99
15649569 CATTAATCGA
* * * *
15649579 GTCAAAAACACATCAAAACTAACCTAAATATGTGTCTAACTAATGTACCCTCATTGGTACCACAA
1 GTCAAAAACACATCAAAACCAACCTAAATATGTGCCGAACCAATGTACCCTCATTGGTACCACAA
15649644 TTATATACAATTTAATCTCAAAAAACACATTAAT
66 TTATATACAATTTAATCTCAAAAAACACATTAAT
15649678 GTCAAAAACACATCAAAACCAACCT-AATATGTGCCGAACCAATGTACCCTCATTGGTACCACAA
1 GTCAAAAACACATCAAAACCAACCTAAATATGTGCCGAACCAATGTACCCTCATTGGTACCACAA
*
15649742 TTATATACAATTTAATCTCAAAATACACATTAAT
66 TTATATACAATTTAATCTCAAAAAACACATTAAT
15649776 -TCAA
1 GTCAA
15649780 TTCATCAACT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 4 0.04
98 69 0.71
99 24 0.25
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (99 bp):
GTCAAAAACACATCAAAACCAACCTAAATATGTGCCGAACCAATGTACCCTCATTGGTACCACAA
TTATATACAATTTAATCTCAAAAAACACATTAAT
Found at i:15655390 original size:23 final size:23
Alignment explanation
Indices: 15655339--15655397 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
15655329 TAGCCTTTGA
* *
15655339 CCGAACGACAATGTATTTCATTC
1 CCGAACGATAGTGTATTTCATTC
**
15655362 TTGAACGATAGTGTATTTCATTC
1 CCGAACGATAGTGTATTTCATTC
15655385 CCGAACGAGTAGT
1 CCGAACGA-TAGT
15655398 CCCAGTAGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (23 bp):
CCGAACGATAGTGTATTTCATTC
Found at i:15665751 original size:12 final size:12
Alignment explanation
Indices: 15665734--15665758 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15665724 CAGCAGAAAG
15665734 GAGTGAAGAGAA
1 GAGTGAAGAGAA
15665746 GAGTGAAGAGAA
1 GAGTGAAGAGAA
15665758 G
1 G
15665759 GCATTTCAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.44, T:0.08
Consensus pattern (12 bp):
GAGTGAAGAGAA
Found at i:15674928 original size:21 final size:21
Alignment explanation
Indices: 15674888--15674929 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15674878 ATTTTTAATC
* *
15674888 TTTAAATTGATATCTGAATTT
1 TTTAAATTAATATCTAAATTT
*
15674909 TTTAAATTAATATTTAAATTT
1 TTTAAATTAATATCTAAATTT
15674930 ATTTCAATAT
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:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAAATTAATATCTAAATTT
Found at i:15674960 original size:52 final size:52
Alignment explanation
Indices: 15674863--15674961 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 52
15674853 AATATATCAT
* * * * * *
15674863 TTAATATTTAAATTTATTTTTAATCTTTAAATTGATATCTGAATTTTTTAAA
1 TTAATATTTAAATTTATTTTCAATATTTAAATTAAAATATAAATTTTTTAAA
*
15674915 TTAATATTTAAATTTA-TTTCAATATTTAAATTAAAATATAAAATTTT
1 TTAATATTTAAATTTATTTTCAATATTTAAATTAAAATATAAATTTTT
15674962 CAATTTTATA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
51 24 0.60
52 16 0.40
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (52 bp):
TTAATATTTAAATTTATTTTCAATATTTAAATTAAAATATAAATTTTTTAAA
Found at i:15682024 original size:31 final size:30
Alignment explanation
Indices: 15681986--15682092 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 30
15681976 TTAGGAAGTC
*
15681986 CTTATTTGAGCACTTTCAAAAAGGTCTGGCT
1 CTTATTTGAGCACTTTC-AAAAGGTTTGGCT
* * *
15682017 CTTATTTGAGCACTTCCCAAATGTTTTGGC-
1 CTTATTTGAGCACTT-TCAAAAGGTTTGGCT
* *
15682047 CATTACTTGAGCACTTT-GAAAGGTTTGGCT
1 C-TTATTTGAGCACTTTCAAAAGGTTTGGCT
15682077 -TTCATTTGAGCACTTT
1 CTT-ATTTGAGCACTTT
15682093 TGTAAAGGTT
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.03
29 21 0.34
30 1 0.02
31 37 0.60
32 1 0.02
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
CTTATTTGAGCACTTTCAAAAGGTTTGGCT
Found at i:15684787 original size:6 final size:6
Alignment explanation
Indices: 15684742--15684783 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
15684732 AAGCAGAGCT
* * *
15684742 GGCACT GGCACT GGCACC GGCACC GGCACC GGCACC AGCACC
1 GGCACC GGCACC GGCACC GGCACC GGCACC GGCACC GGCACC
15684784 AGCAAAGTGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.19, C:0.45, G:0.31, T:0.05
Consensus pattern (6 bp):
GGCACC
Found at i:15695072 original size:17 final size:18
Alignment explanation
Indices: 15695031--15695074 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
15695021 TTTATCAAAT
* *
15695031 AAATTATTAAAAATTTAT
1 AAATAATTAAAAATTTAA
15695049 AAA-AATTAAAAA-TTAA
1 AAATAATTAAAAATTTAA
15695065 AAATAATTAA
1 AAATAATTAA
15695075 GCTGATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 6 0.26
17 14 0.61
18 3 0.13
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATAATTAAAAATTTAA
Found at i:15696148 original size:32 final size:32
Alignment explanation
Indices: 15696110--15696170 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
15696100 TAATCAGTAT
*
15696110 GAGTTATCAAATTAAAATAATTAATTTATCAC
1 GAGTTATCAAATTAAAATAATCAATTTATCAC
* *
15696142 GAGTTATTAAATTAAAGTAATCAATTTAT
1 GAGTTATCAAATTAAAATAATCAATTTAT
15696171 AAATTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.39
Consensus pattern (32 bp):
GAGTTATCAAATTAAAATAATCAATTTATCAC
Found at i:15697457 original size:16 final size:17
Alignment explanation
Indices: 15697430--15697462 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
15697420 TTTGAGTACT
*
15697430 AAATTAAAAATATATAA
1 AAATTAAAAATAAATAA
15697447 AAATT-AAAATAAATAA
1 AAATTAAAAATAAATAA
15697463 TTTTTAAAAA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATTAAAAATAAATAA
Found at i:15700255 original size:16 final size:14
Alignment explanation
Indices: 15700232--15700282 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
15700222 CGAGAGGAAA
15700232 GAAAATTGGAAGGAT
1 GAAAATT-GAAGGAT
15700247 GAAAGATTGAAGGAT
1 GAAA-ATTGAAGGAT
*
15700262 AGAAAACTAGAAGGAT
1 -GAAAA-TTGAAGGAT
15700278 GAAAA
1 GAAAA
15700283 ACATAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
15 17 0.53
16 15 0.47
ACGTcount: A:0.53, C:0.02, G:0.29, T:0.16
Consensus pattern (14 bp):
GAAAATTGAAGGAT
Found at i:15706199 original size:2 final size:2
Alignment explanation
Indices: 15706192--15706217 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15706182 GCTTTCAGAA
15706192 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
15706218 GGTATTTTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15711282 original size:3 final size:3
Alignment explanation
Indices: 15711274--15711318 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
15711264 TTCCAAAGTA
15711274 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
15711319 TTTGAGAAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:15713604 original size:9 final size:9
Alignment explanation
Indices: 15713590--15713617 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
15713580 TAATTTGACA
15713590 TTTTTAAAT
1 TTTTTAAAT
15713599 TTTTTAAAT
1 TTTTTAAAT
15713608 TTTTTAAAT
1 TTTTTAAAT
15713617 T
1 T
15713618 AACTCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:15713700 original size:11 final size:11
Alignment explanation
Indices: 15713684--15713710 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
15713674 AAAAAATATC
15713684 AAATTAAATTA
1 AAATTAAATTA
15713695 AAATTAAATTA
1 AAATTAAATTA
15713706 AAATT
1 AAATT
15713711 CTAGTGAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAATTAAATTA
Found at i:15724451 original size:2 final size:2
Alignment explanation
Indices: 15724444--15724481 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
15724434 TTGTAACTTT
* *
15724444 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15724482 ATAAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:15724461 original size:12 final size:12
Alignment explanation
Indices: 15724444--15724481 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
15724434 TTGTAACTTT
*
15724444 TATATATATATA
1 TATATATATTTA
15724456 TATATATATTTA
1 TATATATATTTA
15724468 TATATATATTTA
1 TATATATATTTA
15724480 TA
1 TA
15724482 ATAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATATATTTA
Found at i:15726274 original size:17 final size:17
Alignment explanation
Indices: 15726248--15726281 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15726238 CAGGGGACGT
*
15726248 GTCAGCAAATCGCGTCC
1 GTCAGAAAATCGCGTCC
15726265 GTCAGAAAATCGCGTCC
1 GTCAGAAAATCGCGTCC
15726282 TCGTAGGCGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (17 bp):
GTCAGAAAATCGCGTCC
Found at i:15726687 original size:26 final size:26
Alignment explanation
Indices: 15726640--15726690 Score: 68
Period size: 28 Copynumber: 1.9 Consensus size: 26
15726630 GTTCCCAATG
*
15726640 TTTTTTTAAATTTTTATTTAAATTTGA
1 TTTTTTTAAAATTTTA-TTAAATTTGA
15726667 TTTTTTATAAAATTTTA-TAAATTT
1 TTTTTT-TAAAATTTTATTAAATTT
15726691 TAATGATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 6 0.27
28 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTTTTAAAATTTTATTAAATTTGA
Found at i:15726832 original size:61 final size:63
Alignment explanation
Indices: 15726736--15726866 Score: 153
Period size: 62 Copynumber: 2.1 Consensus size: 63
15726726 TGATTGAAGC
* * *
15726736 AATACAAAGTAGTATTTAAATATTAAACTGGT-AAAAATAAAATTTAATAACTGTAATATTTA
1 AATACAAAGTAGTATTTAAATATTAAACTGATAAAAAATAAAATTAAATAACTATAATATTTA
* * * * *
15726798 AATATAAA-TAGTATTTAAATATT-AATTAGATAAAAAATAAACTTAAATAATTATAATATCT-
1 AATACAAAGTAGTATTTAAATATTAAACT-GATAAAAAATAAAATTAAATAACTATAATATTTA
15726859 AATACAAA
1 AATACAAA
15726867 ACGAGCATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
60 3 0.05
61 24 0.41
62 31 0.53
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (63 bp):
AATACAAAGTAGTATTTAAATATTAAACTGATAAAAAATAAAATTAAATAACTATAATATTTA
Found at i:15737012 original size:3 final size:3
Alignment explanation
Indices: 15736925--15736993 Score: 129
Period size: 3 Copynumber: 23.0 Consensus size: 3
15736915 ATATATATAG
*
15736925 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15736973 TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
15736994 ATATAGCAGA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:15738905 original size:180 final size:177
Alignment explanation
Indices: 15738670--15739012 Score: 445
Period size: 180 Copynumber: 1.9 Consensus size: 177
15738660 ATTTACTCTC
* * * * * *
15738670 TTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTATCTCTAATCTACTTCACGCCAG
1 TTCGATCCACTTCGCCACCAATATAGGAAGACAAGACCTACTATCTCTAATCTACTTCACGCCAG
* * * * *
15738735 TACATGAAGACAAGATCTATTTTTTTCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATC
66 TACATGAAGACAAGATC---TGTTTTCTTCGACCTACTCCACCACCAATACAGGAAGACAAGATC
15738799 TGCTTTCTTGGATCTACTTCGCCACCAGTATGGGAAGATAAAATATGTATA
128 TG-TTTCTTGGATCTACTTCGCCACCAGTATGGGAAGATAAAATATGTATA
* * * *
15738850 TTCGATCCCCTTCGCTACCAATATAGGAAGACAAGACCTACTATCTTTGATCTACTTCACGCCAG
1 TTCGATCCACTTCGCCACCAATATAGGAAGACAAGACCTACTATCTCTAATCTACTTCACGCCAG
* * ** *
15738915 TACATGAAGACACGATCTGTTTTCTTCGACCTACTCCACCACCAGTATGGGGAGACAAGATCTGT
66 TACATGAAGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAATACAGGAAGACAAGATCTGT
* *
15738980 TTCTTTGATCTGCTTCGCCACCAGTATGGGAAG
131 TTCTTGGATCTACTTCGCCACCAGTATGGGAAG
15739013 GCAAGATCAG
Statistics
Matches: 140, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
177 50 0.36
178 19 0.14
180 71 0.51
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (177 bp):
TTCGATCCACTTCGCCACCAATATAGGAAGACAAGACCTACTATCTCTAATCTACTTCACGCCAG
TACATGAAGACAAGATCTGTTTTCTTCGACCTACTCCACCACCAATACAGGAAGACAAGATCTGT
TTCTTGGATCTACTTCGCCACCAGTATGGGAAGATAAAATATGTATA
Found at i:15738949 original size:44 final size:44
Alignment explanation
Indices: 15738535--15738949 Score: 251
Period size: 44 Copynumber: 9.3 Consensus size: 44
15738525 AAGACTCGTA
* *
15738535 TCTTCGATCTACTTCACTGCCACTACAGGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTT
* * **
15738580 TCTTCAATCTACTTCACGCTAATACATGAAGACAAGATCTATTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * * * * * *
15738624 TATTCAATCTGCTTTACGCCAATACATAAAGATAAGATTTACTC
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *** * *
15738668 TCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAG-TA
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCT-GCTT
* * **
15738713 TC-TCTAATCTACTTCACGCCAGTACATGAAGACAAGATCTATTTTTT
1 TCTTC-GATCTACTTCACGCCAATACATGAAGACAAGATC---TGCTT
15738760 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * *** * * * *
15738804 TCTTGGATCTACTTCGCCACCAGTATGGGAAGATAAAATATG-TA
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTT
* ** * * * * * * *
15738848 TATTCGATCCCCTTCGCTACCAATATAGGAAGACAAGACCTACTA
1 TCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGATCTGCTT
* * * *
15738893 TCTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
*
15738937 TCTTCGACCTACT
1 TCTTCGATCTACT
15738950 CCACCACCAG
Statistics
Matches: 276, Mismatches: 83, Indels: 23
0.72 0.22 0.06
Matches are distributed among these distances:
43 1 0.00
44 163 0.59
45 74 0.27
47 36 0.13
48 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
Found at i:15739002 original size:44 final size:44
Alignment explanation
Indices: 15738668--15739020 Score: 210
Period size: 44 Copynumber: 7.9 Consensus size: 44
15738658 AGATTTACTC
* *
15738668 TCTTCGATCTACTTCGCCACCAGTATGGGAAGGCAAGATCTAGTA
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT-GTT
* * * *** *
15738713 TC-TCTAATCTACTTC-ACGCCAGTACATGAAGACAAGATCTATTTTTT
1 TCTTC-GATCTACTTCGCCACCAGTATGGGAAGACAAGATC----TGTT
* * * ***
15738760 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-TT
* * * * *
15738804 TCTTGGATCTACTTCGCCACCAGTATGGGAAGATAAAATATGTA
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTT
* ** * * * * * *
15738848 TATTCGATCCCCTTCGCTACCAATATAGGAAGACAAGACCTACTA
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCT-GTT
* * * *** *
15738893 TCTTTGATCTACTTC-ACGCCAGTACATGAAGACACGATCTGTTT
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG-TT
* * * *
15738937 TCTTCGACCTACTCCACCACCAGTATGGGGAGACAAGATCTGTT
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTT
* * *
15738981 TCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATC
1 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATC
15739021 AGCTTTTTTC
Statistics
Matches: 231, Mismatches: 66, Indels: 23
0.72 0.21 0.07
Matches are distributed among these distances:
43 1 0.00
44 132 0.57
45 60 0.26
47 35 0.15
48 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGTT
Found at i:15739012 original size:133 final size:137
Alignment explanation
Indices: 15738760--15739081 Score: 355
Period size: 133 Copynumber: 2.4 Consensus size: 137
15738750 TCTATTTTTT
* * * * * * *
15738760 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTGGATCTACTTCGCCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGACCTACTCCACCACC
* *
15738825 AGTATGGGAAGATAAAATATGTATATTCGATCCCCTTCGCTACCAATATAGGAAGACAAGA-C-C
66 AGTATGGGAAGACAAAATATGTATATTCGATCCCCTTCGCCACCAATATAGGAAGACAAGATCAC
15738888 -TACT-A
131 TTACTGA
*
15738893 TCTTTGATCTACTTCACGCCAGTACATGAAGACACGATCTGTTTTCTTCGACCTACTCCACCACC
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGACCTACTCCACCACC
* * * * * * ** * * *
15738958 AGTATGGGGAGACAAGATCTGTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGGCAAGATCAG
66 AGTATGGGAAGACAAAATATGTATATTCGATCCCCTTCGCCACCAATATAGGAAGACAAGATCA-
*
15739023 CTTTTTTCTGA
130 C---TTACTGA
* * *
15739034 TCTCTGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTATCTT
1 TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
15739082 TCACCCTGCT
Statistics
Matches: 155, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
133 105 0.68
134 1 0.01
136 1 0.01
140 3 0.02
141 45 0.29
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (137 bp):
TCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGACCTACTCCACCACC
AGTATGGGAAGACAAAATATGTATATTCGATCCCCTTCGCCACCAATATAGGAAGACAAGATCAC
TTACTGA
Found at i:15742965 original size:25 final size:20
Alignment explanation
Indices: 15742907--15742966 Score: 111
Period size: 20 Copynumber: 3.0 Consensus size: 20
15742897 TAAAGGTCTT
15742907 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
15742927 TAATGCATATGATGCGATGC
1 TAATGCATATGATGCGATGC
*
15742947 TAATGCATATGATACGATGC
1 TAATGCATATGATGCGATGC
15742967 ATGAGGTGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (20 bp):
TAATGCATATGATGCGATGC
Found at i:15745417 original size:3 final size:3
Alignment explanation
Indices: 15745348--15745398 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
15745338 ATATATATAG
*
15745348 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15745396 TAA
1 TAA
15745399 ATATAGCAGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:15749012 original size:24 final size:22
Alignment explanation
Indices: 15748983--15749030 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
15748973 CCCGATTTTT
15748983 AATAAACACAAAAAAATATTTTAA
1 AATAAA-A-AAAAAAATATTTTAA
*
15749007 AATAAAAATAAAAATATTTTAA
1 AATAAAAAAAAAAATATTTTAA
15749029 AA
1 AA
15749031 GTATTTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 16 0.70
23 1 0.04
24 6 0.26
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (22 bp):
AATAAAAAAAAAAATATTTTAA
Found at i:15749037 original size:33 final size:34
Alignment explanation
Indices: 15748994--15749057 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
15748984 ATAAACACAA
15748994 AAAAATATTTTAAAA-TAAAAATAAAAATATTTT
1 AAAAATATTTTAAAATTAAAAATAAAAATATTTT
*
15749027 AAAAGTATTTTAAAATTAAAAATAAAAATAT
1 AAAAATATTTTAAAATTAAAAATAAAAATAT
15749058 ATTATTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 14 0.48
34 15 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (34 bp):
AAAAATATTTTAAAATTAAAAATAAAAATATTTT
Found at i:15755735 original size:58 final size:59
Alignment explanation
Indices: 15755640--15755758 Score: 195
Period size: 58 Copynumber: 2.0 Consensus size: 59
15755630 TTGTTGTTCA
15755640 AAAGTATTGTTGAGATAAAAAGCGCTTTTGGAACTATAATATTAAATGGG-CAATTTTT
1 AAAGTATTGTTGAGATAAAAAGCGCTTTTGGAACTATAATATTAAATGGGTCAATTTTT
* * * *
15755698 AAAGTATTGTTGATATAAAAAGCGCTTTTGGACCTATAATGTTAAATGGGTCATTTTTT
1 AAAGTATTGTTGAGATAAAAAGCGCTTTTGGAACTATAATATTAAATGGGTCAATTTTT
15755757 AA
1 AA
15755759 GTTAGAAGTA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
58 47 0.84
59 9 0.16
ACGTcount: A:0.36, C:0.08, G:0.18, T:0.38
Consensus pattern (59 bp):
AAAGTATTGTTGAGATAAAAAGCGCTTTTGGAACTATAATATTAAATGGGTCAATTTTT
Found at i:15766015 original size:61 final size:62
Alignment explanation
Indices: 15765902--15766020 Score: 179
Period size: 61 Copynumber: 1.9 Consensus size: 62
15765892 ACTATTTTAA
* *
15765902 TAAATTTAATTTAATATTTATCTTGATTAGTATTTTATACATTTAATATTAATATGAGATAT
1 TAAATTTAATTTAATATTTATCTTGAATAGTATTTTATACATTTAAAATTAATATGAGATAT
* *
15765964 TAAATTTGATTTAATATTTATCTT-AATAGTATTTTATTA-ATTTAAAATTAATGTGAG
1 TAAATTTAATTTAATATTTATCTTGAATAGTATTTTA-TACATTTAAAATTAATATGAG
15766021 TAATTTCAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
61 27 0.52
62 25 0.48
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.51
Consensus pattern (62 bp):
TAAATTTAATTTAATATTTATCTTGAATAGTATTTTATACATTTAAAATTAATATGAGATAT
Found at i:15769312 original size:6 final size:6
Alignment explanation
Indices: 15769301--15769325 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
15769291 CCTAACTGTT
15769301 CAAAGA CAAAGA CAAAGA CAAAGA C
1 CAAAGA CAAAGA CAAAGA CAAAGA C
15769326 GGGAGCTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.20, G:0.16, T:0.00
Consensus pattern (6 bp):
CAAAGA
Found at i:15776048 original size:21 final size:21
Alignment explanation
Indices: 15776024--15776068 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
15776014 GATCCAAGCT
*
15776024 CCAGATCTGCTTCCATTGATC
1 CCAGACCTGCTTCCATTGATC
15776045 CCAGACCTGCTTCCATTGATC
1 CCAGACCTGCTTCCATTGATC
15776066 CCA
1 CCA
15776069 ACTATAGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.38, G:0.13, T:0.29
Consensus pattern (21 bp):
CCAGACCTGCTTCCATTGATC
Found at i:15776100 original size:66 final size:66
Alignment explanation
Indices: 15775981--15776113 Score: 185
Period size: 66 Copynumber: 2.0 Consensus size: 66
15775971 TCCAAGCTCT
* * * *
15775981 AGACCTGCTTCCATCGATCCTAATTATAGAGCAGATCCAAGCTCCAGATCTGCTTCCATTGATCC
1 AGACCTGCTTCCATCGATCCCAACTATAGAGCAGATCCAAGCTCCAGAGCTGCTCCCATTGATCC
15776046 C
66 C
* * ** *
15776047 AGACCTGCTTCCATTGATCCCAACTATAGAGCGGATCCGGGCTCTAGAGCTGCTCCCATTGATCC
1 AGACCTGCTTCCATCGATCCCAACTATAGAGCAGATCCAAGCTCCAGAGCTGCTCCCATTGATCC
15776112 C
66 C
15776113 A
1 A
15776114 ATTATAGAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (66 bp):
AGACCTGCTTCCATCGATCCCAACTATAGAGCAGATCCAAGCTCCAGAGCTGCTCCCATTGATCC
C
Found at i:15776106 original size:45 final size:45
Alignment explanation
Indices: 15776051--15776213 Score: 220
Period size: 45 Copynumber: 3.6 Consensus size: 45
15776041 GATCCCAGAC
* * *
15776051 CTGCTTCCATTGATCCCAACTATAGAGCGGATCCGGGCTCTAGAG
1 CTGCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG
*
15776096 CTGCTCCCATTGATCCCAATTATAGAGTGGATCCGAGCTCTAGAG
1 CTGCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG
* * * * *
15776141 -TCGCTTCCATTGACCCCAATTATAGAGCGGATCCAAGCGCTAGAA
1 CT-GCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG
*
15776186 CTGCTCCGATTGATCCCAATTATAGAGC
1 CTGCTCCCATTGATCCCAATTATAGAGC
15776214 TGCTCCAGAG
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
44 1 0.01
45 101 0.98
46 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (45 bp):
CTGCTCCCATTGATCCCAATTATAGAGCGGATCCGAGCTCTAGAG
Found at i:15776687 original size:15 final size:15
Alignment explanation
Indices: 15776663--15776693 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
15776653 CAGCAATTTA
15776663 TAATCATATTTGAAC
1 TAATCATATTTGAAC
*
15776678 TAATCGTATTTGAAC
1 TAATCATATTTGAAC
15776693 T
1 T
15776694 GTGGATGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (15 bp):
TAATCATATTTGAAC
Found at i:15803190 original size:27 final size:26
Alignment explanation
Indices: 15803139--15803191 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
15803129 AGTAAAAAAC
*
15803139 TTTAAAATTCTATATAAAAGATTTTT
1 TTTAAAATTCTATATAAAACATTTTT
15803165 TTTAAAATTACTATATAAAAC-TTTTT
1 TTTAAAATT-CTATATAAAACATTTTT
15803191 T
1 T
15803192 ACTTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTAAAATTCTATATAAAACATTTTT
Found at i:15815526 original size:6 final size:6
Alignment explanation
Indices: 15815515--15815549 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
15815505 AGATAATTTA
15815515 ATATGT ATATGT ATATGT ATATGT ATATGT ATATG
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATG
15815550 CATGCATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (6 bp):
ATATGT
Found at i:15832394 original size:4 final size:4
Alignment explanation
Indices: 15832385--15832517 Score: 79
Period size: 4 Copynumber: 29.2 Consensus size: 4
15832375 CAGAAGGAGG
* *
15832385 GAAA GAAA GAAA GAAA TGAGAG GAAA GAAA GAAA GGAGAG GAAA GAAA
1 GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA GAAA -GA-AA GAAA GAAA
15832433 GAAAA TGAAA GGAAAA GAGAA GAAAA GGAAA GAAA GGAGAA GAAAA GGAGAA
1 G-AAA -GAAA -G-AAA GA-AA G-AAA -GAAA GAAA -GA-AA G-AAA -GA-AA
*
15832485 GAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA G
1 GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
15832518 GGAAAGGAGA
Statistics
Matches: 106, Mismatches: 7, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
3 3 0.03
4 52 0.49
5 37 0.35
6 14 0.13
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:15832412 original size:18 final size:18
Alignment explanation
Indices: 15832389--15832457 Score: 93
Period size: 18 Copynumber: 3.7 Consensus size: 18
15832379 AGGAGGGAAA
15832389 GAAAGAAAGAAATGAGAG
1 GAAAGAAAGAAATGAGAG
*
15832407 GAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAATGAGAG
*
15832425 GAAAGAAAGAAAATGAAAG
1 GAAAGAAAG-AAATGAGAG
15832444 GAAAAGAGAAGAAA
1 G-AAAGA-AAGAAA
15832458 AGGAAAGAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
18 26 0.58
19 8 0.18
20 8 0.18
21 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (18 bp):
GAAAGAAAGAAATGAGAG
Found at i:15832449 original size:6 final size:5
Alignment explanation
Indices: 15832426--15832504 Score: 52
Period size: 5 Copynumber: 15.4 Consensus size: 5
15832416 AAAGGAGAGG
* * * * *
15832426 AAAG- AAAGA AAATGA AAGGA AAAGA GAAGA AAAGG AAAGA AAGGA GAAGA
1 AAAGA AAAGA AAA-GA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
* * *
15832476 AAAGGA GAAGA GAAGA AAAAA GAAAGA AA
1 AAA-GA AAAGA AAAGA AAAGA -AAAGA AA
15832505 GAAGGAAAGA
Statistics
Matches: 57, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
4 4 0.07
5 41 0.72
6 12 0.21
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (5 bp):
AAAGA
Found at i:15832481 original size:11 final size:11
Alignment explanation
Indices: 15832431--15832486 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
15832421 AGAGGAAAGA
*
15832431 AAGAAAATGA-
1 AAGAAAAGGAG
15832441 AAGGAAAA-GAG
1 AA-GAAAAGGAG
15832452 AAGAAAAGGA-
1 AAGAAAAGGAG
15832462 AAG-AAAGGAG
1 AAGAAAAGGAG
15832472 AAGAAAAGGAG
1 AAGAAAAGGAG
15832483 AAGA
1 AAGA
15832487 GAAGAAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
9 6 0.15
10 15 0.37
11 20 0.49
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (11 bp):
AAGAAAAGGAG
Found at i:15832484 original size:31 final size:30
Alignment explanation
Indices: 15832407--15832572 Score: 98
Period size: 30 Copynumber: 5.5 Consensus size: 30
15832397 GAAATGAGAG
*
15832407 GAAA-GAAAG-AAAGGAG-AGGAAA-GAAA
1 GAAAGGAAAGAAAAGGAGAAGAAAAGGAAA
*
15832433 GAAAATGAAAGGAAAA-GAGAAGAAAAGGAAA
1 G-AAAGGAAA-GAAAAGGAGAAGAAAAGGAAA
*
15832464 GAAAGGAGAAGAAAAGGAGAAGAGAA-GAAA
1 GAAAGGA-AAGAAAAGGAGAAGAAAAGGAAA
*
15832494 -AAA-GAAAGAAAGAAGGA-AAGAAAGGGAAA
1 GAAAGGAAAG-AA-AAGGAGAAGAAAAGGAAA
* * * * *
15832523 GGAGAAGAGAAAAAAAAAGAAGAACAAGAGGGAA
1 -GA-AAG-G-AAAGAAAAGGAGAAGAAAAGGAAA
*
15832557 GAAAGGAAAAAAAAGG
1 GAAAGGAAAGAAAAGG
15832573 GAAAAATGTA
Statistics
Matches: 110, Mismatches: 12, Indels: 32
0.71 0.08 0.21
Matches are distributed among these distances:
26 1 0.01
27 6 0.05
28 13 0.12
29 16 0.15
30 31 0.28
31 18 0.16
32 5 0.05
33 6 0.05
34 11 0.10
35 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.01
Consensus pattern (30 bp):
GAAAGGAAAGAAAAGGAGAAGAAAAGGAAA
Found at i:15832530 original size:16 final size:14
Alignment explanation
Indices: 15832385--15832530 Score: 74
Period size: 14 Copynumber: 10.1 Consensus size: 14
15832375 CAGAAGGAGG
15832385 GAAAGAAA-GA-AA
1 GAAAGAAAGGAGAA
*
15832397 GAAATGAGAGGA-AA
1 GAAA-GAAAGGAGAA
*
15832411 GAAAGAAAGGAGAG
1 GAAAGAAAGGAGAA
*
15832425 GAAAGAAA-GAAAA
1 GAAAGAAAGGAGAA
*
15832438 TGAAAGGAAAAGAGAA
1 -GAAA-GAAAGGAGAA
15832454 GAAAAGGAAA-GA-AA
1 G-AAA-GAAAGGAGAA
15832468 GGAGAAGAAAAGGAGAA
1 -GA-AAG-AAAGGAGAA
**
15832485 GAGAAGAAAAAAGAAA
1 GA-AAGAAAGGAG-AA
15832501 GAAAG-AAGGA-AA
1 GAAAGAAAGGAGAA
15832513 GAAAGGGAAAGGAGAA
1 GAAA--GAAAGGAGAA
15832529 GA
1 GA
15832531 GAAAAAAAAA
Statistics
Matches: 107, Mismatches: 10, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
12 10 0.09
13 12 0.11
14 29 0.27
15 26 0.24
16 28 0.26
17 2 0.02
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (14 bp):
GAAAGAAAGGAGAA
Found at i:15832606 original size:19 final size:20
Alignment explanation
Indices: 15832582--15832620 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
15832572 GGAAAAATGT
15832582 AATTTTATTTATAA-ATTTG
1 AATTTTATTTATAATATTTG
* *
15832601 AATTTTTTTTGTAATATTTG
1 AATTTTATTTATAATATTTG
15832621 TGTGTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
AATTTTATTTATAATATTTG
Found at i:15840190 original size:62 final size:60
Alignment explanation
Indices: 15840058--15840190 Score: 144
Period size: 62 Copynumber: 2.1 Consensus size: 60
15840048 TTATACTCAA
* * ** *
15840058 AATAATACACAAAATAATATACACTAAAATTATTAAATTTATACTACGAATAATATTAAT
1 AATAATACTCAAAATAATACACACTAAAATTATTAAATTTATACTAAAAAAAATATTAAT
*
15840118 AATTTTATACTCAAAATAATACACACTAAAATTATT-AATTT-TACTAAAAAAAACTAACTATAA
1 AA--TAATACTCAAAATAATACACACTAAAATTATTAAATTTATACTAAAAAAAA-T-A-T-TAA
15840181 T
60 T
15840182 AATAATACT
1 AATAATACT
15840191 AATTTTTTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
60 11 0.18
61 6 0.10
62 36 0.60
63 1 0.02
64 6 0.10
ACGTcount: A:0.54, C:0.11, G:0.01, T:0.34
Consensus pattern (60 bp):
AATAATACTCAAAATAATACACACTAAAATTATTAAATTTATACTAAAAAAAATATTAAT
Found at i:15840325 original size:3 final size:3
Alignment explanation
Indices: 15840317--15840348 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
15840307 TCTTCATACT
15840317 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
15840349 TAATAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:15840442 original size:19 final size:21
Alignment explanation
Indices: 15840418--15840456 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
15840408 ACTAAAACAA
*
15840418 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
15840437 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
15840457 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:15840617 original size:27 final size:27
Alignment explanation
Indices: 15840579--15840654 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
15840569 GTAATACGAG
*
15840579 TGGTGCCGCCAATTAGTA-TGGCACCAT
1 TGGTGCCGCCAA-TAGCATTGGCACCAT
* *
15840606 TGGTGCCGCCAATGGCATTGGCACCGT
1 TGGTGCCGCCAATAGCATTGGCACCAT
* *
15840633 TGGTGCCGCCAACACCATTGGC
1 TGGTGCCGCCAATAGCATTGGC
15840655 GTGACCAGTA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 3 0.07
27 39 0.93
ACGTcount: A:0.18, C:0.30, G:0.29, T:0.22
Consensus pattern (27 bp):
TGGTGCCGCCAATAGCATTGGCACCAT
Found at i:15840731 original size:26 final size:26
Alignment explanation
Indices: 15840700--15840770 Score: 108
Period size: 26 Copynumber: 2.7 Consensus size: 26
15840690 TTGGTTTTGT
15840700 TTATATATTTTGGTAAATAAAAAAAAG
1 TTATATATTTTGGTAAAT-AAAAAAAG
15840727 -TATATATTTTGGTAAATAAAAAAAG
1 TTATATATTTTGGTAAATAAAAAAAG
*
15840752 TTGTAATATTTTGGTAAAT
1 TTAT-ATATTTTGGTAAAT
15840771 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 8 0.20
26 19 0.46
27 14 0.34
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.41
Consensus pattern (26 bp):
TTATATATTTTGGTAAATAAAAAAAG
Found at i:15847174 original size:46 final size:44
Alignment explanation
Indices: 15847073--15847434 Score: 380
Period size: 46 Copynumber: 8.6 Consensus size: 44
15847063 TACGTATGAT
*
15847073 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCTAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTA-GCTAC
15847116 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-A-GCTAC
*
15847162 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-A-GCTAC
15847208 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
15847244 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--TA---A-
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
15847280 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT--AGCTAC
*
15847326 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-TAG----
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
*
15847362 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT--AGCTAC
* * *
15847408 CACTTATCTCTTTATCTCTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
15847435 AGTACTCAAA
Statistics
Matches: 283, Mismatches: 12, Indels: 45
0.83 0.04 0.13
Matches are distributed among these distances:
36 92 0.33
38 5 0.02
39 1 0.00
40 5 0.02
41 1 0.00
42 5 0.02
43 11 0.04
44 10 0.04
45 21 0.07
46 132 0.47
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.36
Consensus pattern (44 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGCTAC
Found at i:15847248 original size:36 final size:36
Alignment explanation
Indices: 15847208--15847398 Score: 238
Period size: 36 Copynumber: 5.0 Consensus size: 36
15847198 CTAATGCTAC
*
15847208 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
15847244 CACTTATCACTTTTTCACTTGATCAGATAAGTATAA
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
15847280 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTTTCACTTGATCAGATAA--GTA--T--AG
* * *
15847322 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
*
15847362 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
15847398 C
1 C
15847399 TAAAGCTACC
Statistics
Matches: 137, Mismatches: 8, Indels: 20
0.83 0.05 0.12
Matches are distributed among these distances:
36 99 0.72
38 3 0.02
40 3 0.02
42 2 0.01
44 2 0.01
46 28 0.20
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTATAG
Found at i:15847330 original size:82 final size:82
Alignment explanation
Indices: 15847116--15847434 Score: 397
Period size: 82 Copynumber: 3.9 Consensus size: 82
15847106 GCTAGGCTAC
*
15847116 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
15847181 TGATCAGATAAGTGTAGCTAATGCTA
66 TGATCAGATAA--GTA--T-A----A
* *
15847207 CCACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG----CACTTATCACTTTTTCAC
1 -CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTC
15847262 TTGATCAGATAAGTATAA
65 TTGATCAGATAAGTATAA
*
15847280 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
* *
15847345 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAA
* * *
15847362 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCTCTTTATCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
15847427 TGATCAGA
66 TGATCAGA
15847435 AGTACTCAAA
Statistics
Matches: 207, Mismatches: 10, Indels: 30
0.84 0.04 0.12
Matches are distributed among these distances:
72 29 0.14
73 1 0.00
74 3 0.01
76 1 0.00
77 1 0.00
78 3 0.01
80 3 0.01
82 131 0.63
86 1 0.00
88 1 0.00
90 3 0.01
92 30 0.14
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (82 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATCAGATAAGTATAA
Found at i:15847370 original size:118 final size:118
Alignment explanation
Indices: 15847162--15847393 Score: 419
Period size: 118 Copynumber: 2.0 Consensus size: 118
15847152 CTAAGGCTAC
* *
15847162 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAATGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
15847227 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAA
66 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAA
* *
15847280 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
*
15847345 TGATCAGATAAGTGTAGCACTTATCACTTTTTCACTTGATCAGATAAGT
66 TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGT
15847394 GTAGCTAAAG
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 109 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.38
Consensus pattern (118 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
TGATCAGATAAGTATAGCACTTATCACTTTTTCACTTGATCAGATAAGTATAA
Found at i:15850351 original size:46 final size:46
Alignment explanation
Indices: 15850281--15850419 Score: 217
Period size: 46 Copynumber: 3.0 Consensus size: 46
15850271 ACAATGCTAT
*
15850281 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
* *
15850327 AACTCAATATGGTTTTCGTT-ACTGAAATATCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTC-TTCACTGAAATACCATACCTACGTTTCAC
* *
15850373 AACTCAGTATGGTTTTCTTCACTAAAATACCATACCTACGTTCCAC
1 AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
15850419 A
1 A
15850420 CTTTATCATG
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
45 2 0.02
46 80 0.95
47 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAATACCATACCTACGTTTCAC
Found at i:15855225 original size:111 final size:111
Alignment explanation
Indices: 15855031--15855254 Score: 439
Period size: 111 Copynumber: 2.0 Consensus size: 111
15855021 GATCACCTTG
15855031 AAAATAATTTTAGGTTTGCGAGATTTGAGAAAATAGGTCCGTGAGTCGGTTACGCACGAGGAAGG
1 AAAATAATTTTAGGTTTGCGAGATTTGAGAAAATAGGTCCGTGAGTCGGTTACGCACGAGGAAGG
15855096 GTTATCACCCTTGTAACGTCCAAAATTGGTACCGAATCGATTGTTT
66 GTTATCACCCTTGTAACGTCCAAAATTGGTACCGAATCGATTGTTT
15855142 AAAATAATTTTAGGTTTGCGAGATTTGAGAAAATAGGTCCGTGAGTCGGTTACGCACGAGGAAGG
1 AAAATAATTTTAGGTTTGCGAGATTTGAGAAAATAGGTCCGTGAGTCGGTTACGCACGAGGAAGG
*
15855207 GTTATCACCTTTGTAACGTCCAAAATTGGTACCGAATCGATTGTTT
66 GTTATCACCCTTGTAACGTCCAAAATTGGTACCGAATCGATTGTTT
15855253 AA
1 AA
15855255 TGTCTTAGTG
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 112 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (111 bp):
AAAATAATTTTAGGTTTGCGAGATTTGAGAAAATAGGTCCGTGAGTCGGTTACGCACGAGGAAGG
GTTATCACCCTTGTAACGTCCAAAATTGGTACCGAATCGATTGTTT
Found at i:15858061 original size:18 final size:17
Alignment explanation
Indices: 15858018--15858065 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
15858008 AAAAAATAAC
15858018 TTATTT-AAAAATATTT
1 TTATTTCAAAAATATTT
**
15858034 TTATCCCAAAAATATTTT
1 TTATTTCAAAAATA-TTT
15858052 TTATTTCAAAAATA
1 TTATTTCAAAAATA
15858066 CTTCTATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 4 0.15
17 7 0.27
18 15 0.58
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (17 bp):
TTATTTCAAAAATATTT
Found at i:15860590 original size:3 final size:3
Alignment explanation
Indices: 15860582--15860617 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
15860572 TCCTTCCATC
15860582 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
15860618 AGGTTTCTTT
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):
TAA
Found at i:15872859 original size:18 final size:18
Alignment explanation
Indices: 15872836--15872874 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
15872826 CCTAAATACT
15872836 CAAATTCATCAAAAATCC
1 CAAATTCATCAAAAATCC
15872854 CAAATTCATCAAAAATCC
1 CAAATTCATCAAAAATCC
15872872 CAA
1 CAA
15872875 GACAAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (18 bp):
CAAATTCATCAAAAATCC
Found at i:15883967 original size:2 final size:2
Alignment explanation
Indices: 15883960--15883991 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15883950 TTTTAAAGCA
15883960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15883992 TACACCCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15888385 original size:17 final size:15
Alignment explanation
Indices: 15888358--15888396 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
15888348 ATATAAGAAC
*
15888358 ATTTTATTATTAAATT
1 ATTTTAATATT-AATT
15888374 ATATTTAATATTAATT
1 AT-TTTAATATTAATT
15888390 ATTTTAA
1 ATTTTAA
15888397 ATTGTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 8 0.38
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTAATATTAATT
Found at i:15888599 original size:59 final size:59
Alignment explanation
Indices: 15888545--15888730 Score: 181
Period size: 59 Copynumber: 3.2 Consensus size: 59
15888535 ATTTTATTAA
15888545 ATCATATATTTTAATTAAAATATTTTTAATATTAATTACTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATTTTTAATATTAATTACTTCAAATTATATTTTATAGT
* * *** * * *
15888604 ATCATATATTATGATTTTAGCAAATTCATATAAGAATGTTGATTA-TT--AA-GA-ATTTTAT--
1 ATCATATATT-TTA-ATTA--AAA-T-AT-TTTTAATATTAATTACTTCAAATTATATTTTATAG
15888662 T
59 T
15888663 A-CATATATTTTAATTAAAATATTTTTAATATTAATTACTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATTTTTAATATTAATTACTTCAAATTATATTTTATAGT
15888721 ATCATATATT
1 ATCATATATT
15888731 ATGATTTTAG
Statistics
Matches: 96, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
51 10 0.10
52 4 0.04
53 1 0.01
54 5 0.05
55 1 0.01
56 10 0.10
57 2 0.02
58 10 0.10
59 20 0.21
60 2 0.02
61 10 0.10
62 1 0.01
63 5 0.05
64 1 0.01
65 4 0.04
66 10 0.10
ACGTcount: A:0.40, C:0.05, G:0.04, T:0.50
Consensus pattern (59 bp):
ATCATATATTTTAATTAAAATATTTTTAATATTAATTACTTCAAATTATATTTTATAGT
Found at i:15888772 original size:16 final size:15
Alignment explanation
Indices: 15888751--15888780 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
15888741 TAAATTCATA
15888751 TAAGAATTTTGATTAT
1 TAAGAATTTT-ATTAT
15888767 TAAGAATTTTATTA
1 TAAGAATTTTATTA
15888781 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (15 bp):
TAAGAATTTTATTAT
Found at i:15888788 original size:59 final size:60
Alignment explanation
Indices: 15888724--15888911 Score: 170
Period size: 61 Copynumber: 3.1 Consensus size: 60
15888714 TTATAGTATC
*
15888724 ATATATTATGATTTTAGTAAATTCATATAAGAATTTTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTAAGTAAATTCATATAAGAATTTTGATTATTAAGAATTTTATTAAA-T
* * * * * * * * * *
15888785 ATATATTTTAATTAAAATATATTTA-ATAATAATTATG-TTAAATT-A-TATTTTA-TAGTAT
1 ATATATTATGATTTAAGTAAATTCATATAAGAATTTTGATT--ATTAAGAATTTTATTA-AAT
* *
15888843 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 -ATATATTATGATTTAAGTAAATTCATATAAGAATTTTGATTATTAAGAATTTTATTAAA-T
15888905 ATATATT
1 ATATATT
15888912 TTAATTATAA
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 3 0.03
59 30 0.32
60 21 0.22
61 37 0.39
62 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (60 bp):
ATATATTATGATTTAAGTAAATTCATATAAGAATTTTGATTATTAAGAATTTTATTAAAT
Found at i:15888800 original size:18 final size:17
Alignment explanation
Indices: 15888772--15888806 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
15888762 ATTATTAAGA
*
15888772 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
15888789 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
15888807 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:15888943 original size:120 final size:120
Alignment explanation
Indices: 15888534--15888932 Score: 662
Period size: 120 Copynumber: 3.4 Consensus size: 120
15888524 AATTATTTTA
*
15888534 AATTTTATTAAATCATATATTTTAATTAAAATATTTTTAATATTAATTACTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTACTTCAAATTATATTTT
* *
15888599 ATAGTATCATATATTATGATTTTAGCAAATTCATATAAGAATGTTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
*
15888654 AATTTTATT--A-CATATATTTTAATTAAAATATTTTTAATATTAATTACTTCAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTACTTCAAATTATATTTT
*
15888716 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATTTTGATTATTAAG
66 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
* * *
15888771 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTA-TGTTAAATTATATTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTACT-TCAAATTATATTT
*
15888835 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
* *
15888891 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATA
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATA
15888933 ATTATTATGT
Statistics
Matches: 266, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
117 114 0.43
118 1 0.00
119 2 0.01
120 149 0.56
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTACTTCAAATTATATTTT
ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:15889186 original size:16 final size:16
Alignment explanation
Indices: 15889162--15889197 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
15889152 GATTTGCTAT
* *
15889162 TACACCTCTAATCTAA
1 TACAACTCTAATCCAA
15889178 TACAACTCTAATCCAA
1 TACAACTCTAATCCAA
15889194 TACA
1 TACA
15889198 GTAAACCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.28
Consensus pattern (16 bp):
TACAACTCTAATCCAA
Found at i:15902258 original size:2 final size:2
Alignment explanation
Indices: 15902251--15902279 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
15902241 ATAGCTGATA
15902251 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15902280 GCTTTTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15911786 original size:23 final size:23
Alignment explanation
Indices: 15911751--15911796 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
15911741 TAATTGATTT
15911751 TTTAATTAAATAAATTAAATAAA
1 TTTAATTAAATAAATTAAATAAA
** *
15911774 TTTAATTTTATAAATTAATTAAA
1 TTTAATTAAATAAATTAAATAAA
15911797 GGAAAATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAATTAAATAAATTAAATAAA
Found at i:15923634 original size:18 final size:17
Alignment explanation
Indices: 15923603--15923641 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
15923593 TTAGTTTGTA
*
15923603 ATTTTTTATATTATGTT
1 ATTTTTTATATTATGTG
*
15923620 ATTTTTATATGTTATGTG
1 ATTTTT-TATATTATGTG
15923638 ATTT
1 ATTT
15923642 ATAACACATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (17 bp):
ATTTTTTATATTATGTG
Found at i:15946673 original size:42 final size:42
Alignment explanation
Indices: 15946592--15946679 Score: 122
Period size: 42 Copynumber: 2.1 Consensus size: 42
15946582 GCGACAGCCT
* *
15946592 TGATGACGATCAACTCCAAGGCAGCGACAGCCGTAATGACGA
1 TGATGACGATCAACTCCAAAGCAGCGACAGCCATAATGACGA
* * * *
15946634 TGATGACGATCTACTCCAAAGCAGCGACAGGCATGATGACGG
1 TGATGACGATCAACTCCAAAGCAGCGACAGCCATAATGACGA
15946676 TGAT
1 TGAT
15946680 CATGATTGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.32, C:0.24, G:0.27, T:0.17
Consensus pattern (42 bp):
TGATGACGATCAACTCCAAAGCAGCGACAGCCATAATGACGA
Found at i:15949194 original size:27 final size:27
Alignment explanation
Indices: 15949159--15949236 Score: 92
Period size: 26 Copynumber: 3.0 Consensus size: 27
15949149 TAATTAATTC
*
15949159 ATCTCTTTTATCCTTATGATGTATTGT
1 ATCTCTTTTTTCCTTATGATGTATTGT
*
15949186 CT-TCTTTTTTCTCTTA-GTAT-TATT-T
1 ATCTCTTTTTTC-CTTATG-ATGTATTGT
15949211 ATCTCTTTTTTCCTTATGATGTATTG
1 ATCTCTTTTTTCCTTATGATGTATTG
15949237 ATTGTGTACT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
25 8 0.19
26 27 0.64
27 7 0.17
ACGTcount: A:0.15, C:0.15, G:0.09, T:0.60
Consensus pattern (27 bp):
ATCTCTTTTTTCCTTATGATGTATTGT
Found at i:15954394 original size:2 final size:2
Alignment explanation
Indices: 15954387--15954414 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15954377 GGCTCCTTAA
15954387 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
15954415 TTTTGGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:15957233 original size:17 final size:17
Alignment explanation
Indices: 15957193--15957234 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
15957183 TAAGTTGCAC
*
15957193 ATATCTTAGTGTTATTT
1 ATATATTAGTGTTATTT
*
15957210 ATTTATTAGTG-TATTT
1 ATATATTAGTGTTATTT
15957226 GATATATTA
1 -ATATATTA
15957235 TATTTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (17 bp):
ATATATTAGTGTTATTT
Found at i:15963863 original size:37 final size:37
Alignment explanation
Indices: 15963768--15963880 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 37
15963758 ATACACCAGT
* * *
15963768 TTGGCACCTAGTGCCTCATCAGATAATTCGAAGTAATAAA
1 TTGGCACCTAGTGCCTCATCGGTTAATCCGAAG---TAAA
* * ** *
15963808 TTGACACCCAGTATCTCATCGGTTAAACCGAAGTAAA
1 TTGGCACCTAGTGCCTCATCGGTTAATCCGAAGTAAA
*
15963845 TTGGCACCTAGTGCCTCATCGAATTAATCCGAAGTA
1 TTGGCACCTAGTGCCTCATCG-GTTAATCCGAAGTA
15963881 GTAAATTGAC
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
37 21 0.36
38 12 0.21
40 25 0.43
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.27
Consensus pattern (37 bp):
TTGGCACCTAGTGCCTCATCGGTTAATCCGAAGTAAA
Found at i:15963887 original size:41 final size:41
Alignment explanation
Indices: 15963772--15963905 Score: 127
Period size: 41 Copynumber: 3.4 Consensus size: 41
15963762 ACCAGTTTGG
* *
15963772 CACCTAGTGCCTCATC-AGA-TAATTCGAAGTAATAAATTGA
1 CACCTAGTGCCTCATCGA-ATTAATCCGAAGTAGTAAATTGA
* ** * * *
15963812 CACCCAGTATCTCATCG-GTTAAACCG-A--AGTAAATTGG
1 CACCTAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
15963849 CACCTAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCTAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
* *
15963890 CACATAGTGTCTCATC
1 CACCTAGTGCCTCATC
15963906 AACTCGAAGT
Statistics
Matches: 72, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
37 22 0.31
38 7 0.10
39 2 0.03
40 18 0.25
41 23 0.32
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (41 bp):
CACCTAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
Found at i:15964908 original size:2 final size:2
Alignment explanation
Indices: 15964897--15964953 Score: 70
Period size: 2 Copynumber: 31.0 Consensus size: 2
15964887 GTTTTATTAT
*
15964897 TA TA -A TA TA TA TA T- TT TA T- TA T- TA TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15964934 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
15964954 CTTATATGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
1 5 0.10
2 44 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:15964914 original size:22 final size:22
Alignment explanation
Indices: 15964888--15964953 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
15964878 ATTTTGTTTG
15964888 TTTTATTATTATAATATATATA
1 TTTTATTATTATAATATATATA
15964910 TTTTATTATTATAATATATATA
1 TTTTATTATTATAATATATATA
*
15964932 -TATA-TATATATATATATATATA
1 TTTTATTAT-TATA-ATATATATA
15964954 CTTATATGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
20 3 0.07
21 7 0.17
22 31 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTATTATTATAATATATATA
Found at i:15964959 original size:22 final size:21
Alignment explanation
Indices: 15964894--15964960 Score: 81
Period size: 19 Copynumber: 3.4 Consensus size: 21
15964884 TTTGTTTTAT
*
15964894 TATTATA-ATATATATAT-TT
1 TATTATATATATATATATATA
15964913 TATTAT-TATA-ATATATATA
1 TATTATATATATATATATATA
15964932 TA-TATATATATATATATATA
1 TATTATATATATATATATATA
15964952 TACTTATAT
1 TA-TTATAT
15964961 GTTAAGTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
18 9 0.22
19 16 0.39
20 11 0.27
22 5 0.12
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATATATATATATATATA
Found at i:15978537 original size:13 final size:13
Alignment explanation
Indices: 15978519--15978544 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15978509 TCAAACTTCT
15978519 ACAAAATCGTGTA
1 ACAAAATCGTGTA
15978532 ACAAAATCGTGTA
1 ACAAAATCGTGTA
15978545 GATTATTCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ACAAAATCGTGTA
Found at i:15982151 original size:18 final size:19
Alignment explanation
Indices: 15982130--15982171 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
15982120 GAAAATAAAA
15982130 ATAAATA-TAAAAATATTT
1 ATAAATATTAAAAATATTT
*
15982148 ATAAAAATTAAAAATATTT
1 ATAAATATTAAAAATATTT
15982167 A-AAAT
1 ATAAAT
15982172 TACAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAATATTAAAAATATTT
Found at i:15985472 original size:17 final size:17
Alignment explanation
Indices: 15985450--15985491 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
15985440 TTATATTTAA
15985450 TGTAATTTTAT-TATTT
1 TGTAATTTTATATATTT
*
15985466 TGATAA-TTTATATCTTT
1 TG-TAATTTTATATATTT
15985483 TGTAATTTT
1 TGTAATTTT
15985492 TAAAAGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.07, T:0.64
Consensus pattern (17 bp):
TGTAATTTTATATATTT
Found at i:15985879 original size:9 final size:9
Alignment explanation
Indices: 15985828--15986000 Score: 79
Period size: 9 Copynumber: 18.9 Consensus size: 9
15985818 ATTTTCTCAT
*
15985828 TAAAAATCA
1 TAAAAATTA
15985837 TAAAAATTTA
1 TAAAAA-TTA
**
15985847 TATAAACCTA
1 TA-AAAATTA
**
15985857 TAAAACCTA
1 TAAAAATTA
15985866 T-AAAATTA
1 TAAAAATTA
15985874 TAAAAACTTA
1 TAAAAA-TTA
15985884 TAATAAATTA
1 TAA-AAATTA
*
15985894 TACAAA-TA
1 TAAAAATTA
15985902 GTAAAAA-TA
1 -TAAAAATTA
15985911 -AAACATATTA
1 TAAA-A-ATTA
*
15985921 TAAATATT-
1 TAAAAATTA
**
15985929 TATCAATTA
1 TAAAAATTA
*
15985938 TAAATATTA
1 TAAAAATTA
* *
15985947 TAAAAAATC
1 TAAAAATTA
*
15985956 TAAAAA-TC
1 TAAAAATTA
*
15985964 TAATAATTA
1 TAAAAATTA
*
15985973 TCAATAATTA
1 T-AAAAATTA
*
15985983 TAAAACTTA
1 TAAAAATTA
15985992 TTAAAAATT
1 -TAAAAATT
15986001 CGAAACAAGT
Statistics
Matches: 128, Mismatches: 22, Indels: 27
0.72 0.12 0.15
Matches are distributed among these distances:
7 3 0.02
8 21 0.16
9 58 0.45
10 37 0.29
11 9 0.07
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.34
Consensus pattern (9 bp):
TAAAAATTA
Found at i:15987181 original size:23 final size:23
Alignment explanation
Indices: 15987148--15987191 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
15987138 AGGGTCAGTA
*
15987148 TTTTATAAAAATATAATAAAATGT
1 TTTTATAAAAATA-AAAAAAATGT
15987172 TTTTAT-AAAATAAAAAAAAT
1 TTTTATAAAAATAAAAAAAAT
15987192 ACATGATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTTATAAAAATAAAAAAAATGT
Found at i:15991895 original size:27 final size:27
Alignment explanation
Indices: 15991857--15991921 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
15991847 CAGATGCCAC
* **
15991857 AGGCTGCACCAAAGGTGCCTGTGGCAG
1 AGGCGGCACCAAAGGTGCCTGTCCCAG
* *
15991884 AGGCGGCACCAAATGTGCCTTTCCCAG
1 AGGCGGCACCAAAGGTGCCTGTCCCAG
15991911 AGGCGGCACCA
1 AGGCGGCACCA
15991922 CTCGTGTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.23, C:0.31, G:0.32, T:0.14
Consensus pattern (27 bp):
AGGCGGCACCAAAGGTGCCTGTCCCAG
Found at i:15992015 original size:10 final size:10
Alignment explanation
Indices: 15992000--15992037 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
15991990 AGGTGCTGCC
15992000 AGAAAAAGAG
1 AGAAAAAGAG
15992010 AGAAAAAGAG
1 AGAAAAAGAG
*
15992020 AGAAAGAGAAG
1 AGAAAAAG-AG
15992031 AGAAAAA
1 AGAAAAA
15992038 AAAGTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 17 0.68
11 8 0.32
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
AGAAAAAGAG
Found at i:15994437 original size:157 final size:154
Alignment explanation
Indices: 15994264--15995041 Score: 841
Period size: 157 Copynumber: 5.0 Consensus size: 154
15994254 CAAAAAAAAA
* * * * *
15994264 TTAGTAAAAAACCCTTATTTCGGCCATTTATTCGTACTATTTTCCCGAATTTTATTACTTTCAAT
1 TTAGAAAAAAACTCTTATTTCGGCCCTTTGTTCGTATTATTTTCCCGAATTTTATTACTTTCAAT
*
15994329 AAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGCTTGAAATTTAT
66 AAAAATAT-ATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAATTTAT
15994394 TAATTTAGTGTGTTTTTAAATAAAT
130 TAATTTAGTGTGTTTTTAAATAAAT
* * * * *
15994419 TTGAAAAAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCA
1 TT--AGAAAAAAACTCTTATTTCGGCCCTTTGTTCGTATTATTTTCCCGAATTTTATTACTTTCA
* * * *
15994484 ATAAAAATATATTATTTT-TGTATTTTATTATTTTATATTATTTCAGTAAATTTTGTTTGAAATA
64 ATAAAAATATA-TATTTTCT-AATTTTATTATTTTACATTATTTCAGTACATTATGTTTG-AA-A
* *
15994548 TTTGTATTAA-TTATTTCTGAATTTTTAAA-AAAT
125 -TT-TATTAATTTA-GTGTG--TTTTTAAATAAAT
* * *
15994581 TTAGTAAAAAACTCTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCC-ACATTTTATTACTTT--
1 TTAGAAAAAAACTCTTATTTCGGCCCTTTGTTCGTATTATTTTC-CCGA-ATTTTATTACTTTCA
* *
15994643 A-AAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTATATTATGTTTGAACTTT
64 ATAAAAATA-TATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAATTT
15994707 ATTAATTTAGTGTGTTTTTAAATAAAT
128 ATTAATTTAGTGTGTTTTTAAATAAAT
* * * * *
15994734 TT-TAAAAAAA-TCTTATTCCTGCCCTTTGCTCGTATTATTTTTCCGAATTTTATTACTTTCAAT
1 TTAGAAAAAAACTCTTATTTCGGCCCTTTGTTCGTATTATTTTCCCGAATTTTATTACTTTCAAT
* *
15994797 -AAAATATATTATTTTCGT-ATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATT
66 AAAAATATA-TATTTTC-TAATTTTATTATTTTACATTATTTCAGTACATTATGTTTG-AA-A-T
** * * *
15994860 TGTATTAATTATTTTTTAATTTTTAAA-AAAA
126 T-TATTAATT-TAGTGT-GTTTTTAAATAAAT
* * * *
15994891 TTAGTAAAAAACTCTTACTTCGACCCTTTGTTCGTATTTTTTTCTCC-ACATTTTATTACTTT--
1 TTAGAAAAAAACTCTTATTTCGGCCCTTTGTTCGTATTATTTTC-CCGA-ATTTTATTACTTTCA
* *
15994953 A-AAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTTAGTGCATTATGTTTGAAATTT
64 ATAAAAATA-TATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAATTT
15995017 ATTAATTTAGTGTGTTTTTTAAATA
128 ATTAATTTAGTGTG-TTTTTAAATA
15995042 TACCATTTTT
Statistics
Matches: 521, Mismatches: 64, Indels: 77
0.79 0.10 0.12
Matches are distributed among these distances:
150 15 0.03
151 29 0.06
152 63 0.12
153 20 0.04
154 18 0.03
155 11 0.02
156 11 0.02
157 116 0.22
158 112 0.21
159 33 0.06
160 55 0.11
161 24 0.05
162 6 0.01
163 8 0.02
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (154 bp):
TTAGAAAAAAACTCTTATTTCGGCCCTTTGTTCGTATTATTTTCCCGAATTTTATTACTTTCAAT
AAAAATATATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAATTTATT
AATTTAGTGTGTTTTTAAATAAAT
Found at i:15994897 original size:310 final size:313
Alignment explanation
Indices: 15994257--15995041 Score: 1283
Period size: 310 Copynumber: 2.5 Consensus size: 313
15994247 GCAATTTCAA
* * * * * *
15994257 AAAAAAATTAGTAAAAAACCCTTATTTCGGCCATTTATTCGTACTATTTTC-CCGA-ATTTTATT
1 AAAAAAATTAGTAAAAAACTCTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCC-ACATTTTATT
* *
15994320 ACTTTCAATAAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGCTT
65 ACTTT--A-AAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTT
15994385 GAAATTTATTAATTTAGTGTGTTTTTAAATAAATTTGAAAAAAAAAACCCTTATTCCTGCCCTTT
127 GAAATTTATTAATTTAGTGTGTTTTTAAATAAATTT--AAAAAAAAACCCTTATTCCTGCCCTTT
*
15994450 GCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTTGTATTTTATTAT
190 GCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTAT
15994515 TTTATATTATTTCAGTAAATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTT
255 TTTATATTATTTCAGTAAATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTT
*
15994574 AAAAAATTTAGTAAAAAACTCTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCCACATTTTATTA
1 AAAAAAATTAGTAAAAAACTCTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCCACATTTTATTA
* *
15994639 CTTTAAAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTATATTATGTTTGAAC
66 CTTTAAAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAA
* *
15994704 TTTATTAATTTAGTGTGTTTTTAAATAAATTT-TAAAAAAA-TCTTATTCCTGCCCTTTGCTCGT
131 TTTATTAATTTAGTGTGTTTTTAAATAAATTTAAAAAAAAACCCTTATTCCTGCCCTTTGCTCGT
*
15994767 ATTATTTTTCCGAATTTTATTACTTTCAAT-AAAATATATTATTTTCGTATTTTATTATTTTATA
196 ATTATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATA
* * *
15994831 TTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTTTTAATTTTT
261 TTATTTCAGTAAATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTT
*
15994884 AAAAAAATTAGTAAAAAACTCTTACTTCGACCCTTTGTTCGTATTTTTTTCTCCACATTTTATTA
1 AAAAAAATTAGTAAAAAACTCTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCCACATTTTATTA
* *
15994949 CTTTAAAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTTAGTGCATTATGTTTGAAA
66 CTTTAAAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAA
15995014 TTTATTAATTTAGTGTGTTTTTTAAATA
131 TTTATTAATTTAGTGTG-TTTTTAAATA
15995042 TACCATTTTT
Statistics
Matches: 441, Mismatches: 24, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
310 224 0.51
311 61 0.14
312 7 0.02
315 88 0.20
316 1 0.00
317 45 0.10
318 15 0.03
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.51
Consensus pattern (313 bp):
AAAAAAATTAGTAAAAAACTCTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCCACATTTTATTA
CTTTAAAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAA
TTTATTAATTTAGTGTGTTTTTAAATAAATTTAAAAAAAAACCCTTATTCCTGCCCTTTGCTCGT
ATTATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATA
TTATTTCAGTAAATTTTGTTTGAAATATTTGTATTAATTATTTCTGAATTTTT
Found at i:15995068 original size:158 final size:154
Alignment explanation
Indices: 15994312--15995041 Score: 690
Period size: 158 Copynumber: 4.7 Consensus size: 154
15994302 ATTTTCCCGA
*
15994312 ATTTTATTACTTTCAATAAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTCAGTACA
1 ATTTTATTACTTT--A-AAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTACA
* * * *
15994377 TTATGCTTGAAATTTATTAATTTAGTGTG-TTTTTAAATAAATTTGAAAAAAAAAACCCTTATT-
63 TTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAATTT-TAATAAAATA---TTATTA
* * *
15994440 CCT-GCCCTTTGCTCGTATTATTTTC-CCGA-
124 CTTCGCCCTTTGTTCGTATTTTTTTCTCC-AC
* *
15994469 ATTTTATTACTTTCAATAAAA-ATATATTATTTT-TGTATTTTATTATTTTATATTATTTCAGTA
1 ATTTTATTACTTT-AA-AAAATAT-TA-TATTTTCT-AATTTTATTATTTTACATTATTTCAGTA
* * * * * * * *
15994532 AATTTTGTTTGAAATATTTGTATTAA-TTATTTCTGAATTTTTAAA-AAA-TTTAGTAAAAAACT
61 CATTATGTTTG-AA-A-TT-TATTAATTTA-GTGTG-TTTTTTAAATAAATTTTAATAAAATATT
*
15994594 CTTACTTCGGCCCTTTGTTCGTATTTTTTTCTCCAC
120 ATTACTTC-GCCCTTTGTTCGTATTTTTTTCTCCAC
*
15994630 ATTTTATTACTTTAAAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTATATTA
1 ATTTTATTACTTTAAAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTA
* * * *
15994695 TGTTTGAACTTTATTAATTTAGTGTG-TTTTTAAATAAATTTTAAAAAAATCTTATT-CCT-GCC
66 TGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAATTTTAATAAAATATTATTACTTCGCC
* *
15994757 CTTTGCTCGTATTATTTTTC-CGA-
131 CTTTGTTCGTATT-TTTTTCTCCAC
*
15994780 ATTTTATTACTTTCAATAAAATA-TATTATTTTCGT-ATTTTATTATTTTATATTATTTCAGTAC
1 ATTTTATTACTTT-AA-AAAATATTA-TATTTTC-TAATTTTATTATTTTACATTATTTCAGTAC
* * * * * * * * *
15994843 ATTTTGTTTGAAATATTTGTATTAA-TTATTTTTTAATTTTTAAA-AAA-ATTAGTAAAAAACTC
62 ATTATGTTTG-AA-A-TT-TATTAATTTAGTGTGT--TTTTTAAATAAATTTTAATAAAATATTA
15994905 TTACTTCGACCCTTTGTTCGTATTTTTTTCTCCAC
121 TTACTTCG-CCCTTTGTTCGTATTTTTTTCTCCAC
* *
15994940 ATTTTATTACTTTAAAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTTAGTGCATTA
1 ATTTTATTACTTTAAAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTA
15995005 TGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATA
66 TGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATA
15995042 TACCATTTTT
Statistics
Matches: 474, Mismatches: 57, Indels: 87
0.77 0.09 0.14
Matches are distributed among these distances:
150 13 0.03
151 21 0.04
152 62 0.13
153 16 0.03
154 27 0.06
155 23 0.05
156 24 0.05
157 66 0.14
158 107 0.23
159 28 0.06
160 50 0.11
161 26 0.05
162 3 0.01
163 8 0.02
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (154 bp):
ATTTTATTACTTTAAAAAATATTATATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTA
TGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAATTTTAATAAAATATTATTACTTCGCC
CTTTGTTCGTATTTTTTTCTCCAC
Found at i:15995311 original size:20 final size:21
Alignment explanation
Indices: 15995288--15995400 Score: 78
Period size: 20 Copynumber: 5.6 Consensus size: 21
15995278 TTCTTCCCTC
*
15995288 TTCTTCTTCTTTTGTTTT-TT
1 TTCTTCTTCTTTCGTTTTCTT
*
15995308 TTCTTCTCCTTTCGTTTTCTT
1 TTCTTCTTCTTTCGTTTTCTT
* *
15995329 TCCTTCTT-TTTC-TTTCTTTCT
1 TTCTTCTTCTTTCGTTT-TCT-T
* * *
15995350 TTCCTCTCCTTTCCTTTTC-T
1 TTCTTCTTCTTTCGTTTTCTT
*
15995370 TTCTTTTTCTTTC--TTTC-T
1 TTCTTCTTCTTTCGTTTTCTT
*
15995388 TTCTTCTCCTTTC
1 TTCTTCTTCTTTC
15995401 CCTCTCATTC
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
18 16 0.22
19 3 0.04
20 33 0.45
21 14 0.19
22 5 0.07
23 3 0.04
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (21 bp):
TTCTTCTTCTTTCGTTTTCTT
Found at i:15995337 original size:38 final size:38
Alignment explanation
Indices: 15995291--15995401 Score: 129
Period size: 38 Copynumber: 2.8 Consensus size: 38
15995281 TTCCCTCTTC
*
15995291 TTCTTCTTTTGTT-TTT-TTTCTTCTCCTTTCGTTTTCT
1 TTCTTCTTTT-TTCTTTCTTTCTTCTCCTTTCCTTTTCT
*
15995328 TTCCTTCTTTTTCTTTCTTTCTTTCCTCTCCTTTCCTTTTCT
1 TT-CTTC--TTT-TTTCTTTCTTTCTTCTCCTTTCCTTTTCT
15995370 TTCTT-TTTCTTTCTTTCTTTCTTCTCCTTTCC
1 TTCTTCTTT-TTTCTTTCTTTCTTCTCCTTTCC
15995402 CTCTCATTCT
Statistics
Matches: 65, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
37 2 0.03
38 30 0.46
40 5 0.08
41 7 0.11
42 21 0.32
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (38 bp):
TTCTTCTTTTTTCTTTCTTTCTTCTCCTTTCCTTTTCT
Found at i:15995344 original size:4 final size:4
Alignment explanation
Indices: 15995323--15995392 Score: 58
Period size: 4 Copynumber: 17.5 Consensus size: 4
15995313 CTCCTTTCGT
* *
15995323 TTTC TTTC CTTC -TT- TTTC TTTC TTTC TTTCC TCTCC TTTCC TTTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C T-TTC TTT-C -TTTC
15995369 TTTC -TT- TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
15995393 CTCCTTTCCC
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
3 8 0.15
4 37 0.67
5 6 0.11
6 4 0.07
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:15995368 original size:42 final size:38
Alignment explanation
Indices: 15995307--15995401 Score: 136
Period size: 38 Copynumber: 2.4 Consensus size: 38
15995297 TTTTGTTTTT
*
15995307 TTTCTTCTCCTTTCGTTTTCTTTCCTTCTTTTTCTTTCTTTC
1 TTTCTTCTCCTTTCCTTTTC--T--TTCTTTTTCTTTCTTTC
*
15995349 TTTCCTCTCCTTTCCTTTTCTTTCTTTTTCTTTCTTTC
1 TTTCTTCTCCTTTCCTTTTCTTTCTTTTTCTTTCTTTC
15995387 TTTCTTCTCCTTTCC
1 TTTCTTCTCCTTTCC
15995402 CTCTCATTCT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
38 31 0.62
40 1 0.02
42 18 0.36
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.67
Consensus pattern (38 bp):
TTTCTTCTCCTTTCCTTTTCTTTCTTTTTCTTTCTTTC
Found at i:15995399 original size:10 final size:10
Alignment explanation
Indices: 15995288--15995400 Score: 67
Period size: 10 Copynumber: 11.3 Consensus size: 10
15995278 TTCTTCCCTC
15995288 TTCTTCTTCT
1 TTCTTCTTCT
* *
15995298 TT-TGTTTTTT
1 TTCT-TCTTCT
*
15995308 TTCTTCTCCT
1 TTCTTCTTCT
15995318 TTCGTT-TTCT
1 TTC-TTCTTCT
15995328 TTCCTTCTT-T
1 TT-CTTCTTCT
15995338 TTCTTTCTTTCT
1 TTC-TTC-TTCT
* *
15995350 TTCCTCTCCT
1 TTCTTCTTCT
15995360 TTCCTT-TTCT
1 TT-CTTCTTCT
*
15995370 TTCTTTTTCT
1 TTCTTCTTCT
15995380 TTC-T-TTCT
1 TTCTTCTTCT
*
15995388 TTCTTCTCCT
1 TTCTTCTTCT
15995398 TTC
1 TTC
15995401 CCTCTCATTC
Statistics
Matches: 80, Mismatches: 11, Indels: 24
0.70 0.10 0.21
Matches are distributed among these distances:
8 7 0.09
9 7 0.09
10 50 0.62
11 12 0.15
12 4 0.05
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:15995939 original size:22 final size:22
Alignment explanation
Indices: 15995895--15995953 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
15995885 ATGAATGTTG
*
15995895 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
15995919 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
*
15995941 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
15995954 GTATCATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
24 11 0.33
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:16000547 original size:46 final size:46
Alignment explanation
Indices: 16000446--16000720 Score: 410
Period size: 46 Copynumber: 6.0 Consensus size: 46
16000436 CATGGCAAAG
* * * *
16000446 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAA-CATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
* *
16000491 TGTGAAAAGTAGGTATGATGTTTCGGTAAAGAAAACCACACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
*
16000537 TGTTAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
* *
16000583 TGTGAAAAGTAGGTATGATGTTTCAGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
*
16000629 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
* * * *
16000675 TGTGAAAAGTAGGCATGGT-ATTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
16000720 T
1 T
16000721 ATAGCAATGT
Statistics
Matches: 210, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 54 0.26
46 156 0.74
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAACCATACTGAGT
Found at i:16001082 original size:3 final size:3
Alignment explanation
Indices: 16001074--16001116 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
16001064 GGTGTTACAG
16001074 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
16001117 ATATACACGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:16002514 original size:40 final size:40
Alignment explanation
Indices: 16002451--16002546 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 40
16002441 CAAACATGCT
*
16002451 CTTAGAAATTTTGGTAAAACCTTA-AATATTATGATAAATC
1 CTTAGAAATTTTAGTAAAACCTTAGAAT-TTATGATAAATC
* ** * * *
16002491 TTTAGAAATTTTAGTAACTCCTTAGAATTTTTGGTGAATC
1 CTTAGAAATTTTAGTAAAACCTTAGAATTTATGATAAATC
*
16002531 CTTAAAAATTTTAGTA
1 CTTAGAAATTTTAGTA
16002547 TTACCAAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
40 43 0.93
41 3 0.07
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (40 bp):
CTTAGAAATTTTAGTAAAACCTTAGAATTTATGATAAATC
Found at i:16002517 original size:20 final size:19
Alignment explanation
Indices: 16002487--16002546 Score: 66
Period size: 20 Copynumber: 3.1 Consensus size: 19
16002477 TATTATGATA
*
16002487 AATCTTTAGAAATTTTAGT
1 AATCCTTAGAAATTTTAGT
* *
16002506 AACTCCTTAGAATTTTTGGT
1 AA-TCCTTAGAAATTTTAGT
*
16002526 GAATCCTTAAAAATTTTAGT
1 -AATCCTTAGAAATTTTAGT
16002546 A
1 A
16002547 TTACCAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.09
20 28 0.85
21 2 0.06
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (19 bp):
AATCCTTAGAAATTTTAGT
Found at i:16008216 original size:6 final size:6
Alignment explanation
Indices: 16008185--16008233 Score: 62
Period size: 6 Copynumber: 7.8 Consensus size: 6
16008175 CCAAACACAC
* *
16008185 CAGTAAA CAGTAA TCAGTAA CGGTAA CAGTAA CAGTAA AAGTAA CAGTA
1 CAGT-AA CAGTAA -CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTA
16008234 TTCAACACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
6 27 0.73
7 10 0.27
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.18
Consensus pattern (6 bp):
CAGTAA
Found at i:16008264 original size:45 final size:46
Alignment explanation
Indices: 16008213--16008319 Score: 155
Period size: 46 Copynumber: 2.3 Consensus size: 46
16008203 AACGGTAACA
* *
16008213 GTAACAGTAAAAGTAACAGTA-TTCAACACACAAAGTGCTGAATCT-
1 GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAAT-TG
* *
16008258 GTAACAGTAACGGTAACAGTATTTCGACACACAAAGTGCCGAATTG
1 GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATTG
16008304 GTAACAGTAACAGTAA
1 GTAACAGTAACAGTAA
16008320 TCGGCACATA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
45 20 0.36
46 35 0.64
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (46 bp):
GTAACAGTAACAGTAACAGTATTTCAACACACAAAGTGCCGAATTG
Found at i:16010922 original size:20 final size:19
Alignment explanation
Indices: 16010874--16010923 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
16010864 TAACAGAAAT
*
16010874 TTATCCGTATCAACAGTAA
1 TTATCCATATCAACAGTAA
* *
16010893 CTTATACATATCAATAGTAA
1 -TTATCCATATCAACAGTAA
16010913 TTCATCCATAT
1 TT-ATCCATAT
16010924 AATTACATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (19 bp):
TTATCCATATCAACAGTAA
Found at i:16012260 original size:22 final size:22
Alignment explanation
Indices: 16012235--16012280 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
16012225 CATTTATCTT
*
16012235 AAACTCTAAACACTAAACCCTA
1 AAACCCTAAACACTAAACCCTA
*
16012257 AAACCCTAAACCCTAAACCCTA
1 AAACCCTAAACACTAAACCCTA
16012279 AA
1 AA
16012281 CCATAACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (22 bp):
AAACCCTAAACACTAAACCCTA
Found at i:16012262 original size:8 final size:7
Alignment explanation
Indices: 16012234--16012291 Score: 73
Period size: 7 Copynumber: 8.3 Consensus size: 7
16012224 GCATTTATCT
*
16012234 TAAACTC
1 TAAACCC
*
16012241 TAAACAC
1 TAAACCC
16012248 TAAACCC
1 TAAACCC
16012255 TAAAACCC
1 T-AAACCC
16012263 TAAACCC
1 TAAACCC
16012270 TAAACCC
1 TAAACCC
*
16012277 TAAACCA
1 TAAACCC
16012284 T-AACCC
1 TAAACCC
16012290 TA
1 TA
16012292 GTGACTTGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
6 5 0.11
7 33 0.73
8 7 0.16
ACGTcount: A:0.47, C:0.36, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:16012479 original size:36 final size:36
Alignment explanation
Indices: 16012432--16012503 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
16012422 AAGTAAATTC
*
16012432 ACATAACTAAAGTTTGATTCTATTGATACGAACTTA
1 ACATAACTAAAGTTCGATTCTATTGATACGAACTTA
16012468 ACATAACTAAAGTTCGATTCTATTGATACGAACTTA
1 ACATAACTAAAGTTCGATTCTATTGATACGAACTTA
16012504 CCTGGCTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (36 bp):
ACATAACTAAAGTTCGATTCTATTGATACGAACTTA
Found at i:16013440 original size:22 final size:22
Alignment explanation
Indices: 16013415--16013507 Score: 98
Period size: 22 Copynumber: 4.1 Consensus size: 22
16013405 TGCACTAATG
16013415 AACAGAGAGCA-TAGAAGTGCTA
1 AACAGAGAGCACT-GAAGTGCTA
*
16013437 AACAAAGAGCACTGAAGTGCTAA
1 AACAGAGAGCACTGAAGTGCT-A
* *
16013460 TAATCAGAGAGCACAGATGTGCTA
1 -AA-CAGAGAGCACTGAAGTGCTA
* *
16013484 ACCAGAGAGCACTGACGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
16013506 AA
1 AA
16013508 TATCAGAGAG
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
22 37 0.63
23 3 0.05
24 3 0.05
25 16 0.27
ACGTcount: A:0.42, C:0.18, G:0.25, T:0.15
Consensus pattern (22 bp):
AACAGAGAGCACTGAAGTGCTA
Found at i:16013481 original size:25 final size:24
Alignment explanation
Indices: 16013409--16013518 Score: 93
Period size: 22 Copynumber: 4.6 Consensus size: 24
16013399 TTATTATGCA
*
16013409 CTAATGAACAGAGAGCATAGAAGTG
1 CTAAT-AACAGAGAGCACAGAAGTG
* *
16013434 CT-A-AACAAAGAGCACTGAAGTG
1 CTAATAACAGAGAGCACAGAAGTG
*
16013456 CTAATAATCAGAGAGCACAGATGTG
1 CTAATAA-CAGAGAGCACAGAAGTG
* * *
16013481 CT-A-ACCAGAGAGCACTGACGTG
1 CTAATAACAGAGAGCACAGAAGTG
*
16013503 CTAAATATCAGAGAGC
1 CT-AATAACAGAGAGC
16013519 GCGCTAGAGT
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
22 35 0.51
23 2 0.03
24 5 0.07
25 27 0.39
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (24 bp):
CTAATAACAGAGAGCACAGAAGTG
Found at i:16013482 original size:47 final size:47
Alignment explanation
Indices: 16013409--16013518 Score: 143
Period size: 47 Copynumber: 2.3 Consensus size: 47
16013399 TTATTATGCA
*
16013409 CTAATGAA-CAGAGAGCATAGAAGTGCTAAACAAAGAGCACTGAAGTG
1 CTAAT-AATCAGAGAGCACAGAAGTGCTAAACAAAGAGCACTGAAGTG
* * * *
16013456 CTAATAATCAGAGAGCACAGATGTGCTAACCAGAGAGCACTGACGTG
1 CTAATAATCAGAGAGCACAGAAGTGCTAAACAAAGAGCACTGAAGTG
16013503 CTAA-ATATCAGAGAGC
1 CTAATA-ATCAGAGAGC
16013519 GCGCTAGAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
46 3 0.05
47 53 0.95
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (47 bp):
CTAATAATCAGAGAGCACAGAAGTGCTAAACAAAGAGCACTGAAGTG
Found at i:16014595 original size:5 final size:5
Alignment explanation
Indices: 16014577--16014662 Score: 81
Period size: 5 Copynumber: 17.0 Consensus size: 5
16014567 CTGTTGTTTT
*
16014577 ATATA ATAATA ATATA ATATA ATATA ATATT ATAATA ATATA ATATA ATA-A
1 ATATA AT-ATA ATATA ATATA ATATA ATATA AT-ATA ATATA ATATA ATATA
*
16014628 CATACTT AT-TA AT-TA AGTA-A ATATA ATATA ATATA
1 -ATA-TA ATATA ATATA A-TATA ATATA ATATA ATATA
16014663 TATTTTAAAT
Statistics
Matches: 69, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
4 9 0.13
5 49 0.71
6 11 0.16
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:16014601 original size:21 final size:22
Alignment explanation
Indices: 16014580--16014627 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
16014570 TTGTTTTATA
16014580 TAATAATAAT-ATAATATAATA
1 TAATAATAATAATAATATAATA
*
16014601 TAAT-ATTATAATAATATAATA
1 TAATAATAATAATAATATAATA
16014622 TAATAA
1 TAATAA
16014628 CATACTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 19 0.79
22 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATAATAATAATAATATAATA
Found at i:16014627 original size:8 final size:8
Alignment explanation
Indices: 16014582--16014621 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
16014572 GTTTTATATA
16014582 ATAATAAT
1 ATAATAAT
16014590 ATAATATAAT
1 AT-A-ATAAT
*
16014600 ATAATATT
1 ATAATAAT
16014608 ATAATAAT
1 ATAATAAT
16014616 ATAATA
1 ATAATA
16014622 TAATAACATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 19 0.68
9 2 0.07
10 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATAAT
Found at i:16017299 original size:21 final size:22
Alignment explanation
Indices: 16017273--16017323 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
16017263 TTATTTTCTA
16017273 AAACCACTTG-ACTTTAGGGAC
1 AAACCACTTGTACTTTAGGGAC
*
16017294 AAACCACTTGTACTTTCGGGAC
1 AAACCACTTGTACTTTAGGGAC
16017316 AAACCACT
1 AAACCACT
16017324 CGATTTCAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (22 bp):
AAACCACTTGTACTTTAGGGAC
Found at i:16018400 original size:2 final size:2
Alignment explanation
Indices: 16018393--16018436 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
16018383 TATTAAATTA
*
16018393 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16018435 AT
1 AT
16018437 CTATTCTATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16019650 original size:2 final size:2
Alignment explanation
Indices: 16019643--16019676 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
16019633 TGAATGGATG
16019643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16019677 GTGTGTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16020140 original size:2 final size:2
Alignment explanation
Indices: 16020133--16020177 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
16020123 TGGTCGGGTG
16020133 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16020175 AT A
1 AT A
16020178 AGTGATATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.