Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 301 of 325
Found at i:95700715 original size:73 final size:72
Alignment explanation
Indices: 95700594--95700758 Score: 244
Period size: 73 Copynumber: 2.3 Consensus size: 72
95700584 AAAGCAGAAA
* * *
95700594 TTGAAAAACAGAAATT-AAAATACCTCGGCGTGCCCGAGGCTCAGCTCACCTCTCGCAATATGAG
1 TTGAAAAGCA-AAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAG
95700658 TTGA-TTT
65 TTGATTTT
* *
95700665 TTGAAAAGCATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
1 TTGAAAAGCA-AAATTGAAAATACCTCAGCGTG-CCCGAGGCTCAACTCACCTCTCGCAATATGA
95700730 GTTGATTTT
64 GTTGATTTT
95700739 TTGAAAAGCAAAATTGAAAA
1 TTGAAAAGCAAAATTGAAAA
95700759 AACGAAATTA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
71 14 0.17
72 14 0.17
73 43 0.51
74 13 0.15
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (72 bp):
TTGAAAAGCAAAATTGAAAATACCTCAGCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTTT
Found at i:95701685 original size:5 final size:5
Alignment explanation
Indices: 95701675--95701704 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
95701665 TGATCCTCTC
95701675 TCTTT TCTTT TCTTT TCTTT TCTTT T-TTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
95701705 AATATGCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:95707766 original size:16 final size:15
Alignment explanation
Indices: 95707740--95707774 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
95707730 TGATGTGAAT
95707740 AATATAAAATATTAA
1 AATATAAAATATTAA
*
95707755 AATATCAAAATATTAG
1 AATAT-AAAATATTAA
95707771 AATA
1 AATA
95707775 ATAATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (15 bp):
AATATAAAATATTAA
Found at i:95707953 original size:24 final size:24
Alignment explanation
Indices: 95707926--95708017 Score: 93
Period size: 25 Copynumber: 3.9 Consensus size: 24
95707916 GTGATAATAT
* *
95707926 TAAAAATATGTACATAATATAGTG
1 TAAAAATATATACATAATATAATG
*
95707950 TAAAAAATACATACATAATATAAT-
1 T-AAAAATATATACATAATATAATG
*
95707974 T-AAAATATATACATAAGATAACATG
1 TAAAAATATATACATAATAT-A-ATG
95707999 TAAAAATATAT--ATAATATA
1 TAAAAATATATACATAATATA
95708018 GTATTAAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
22 16 0.28
23 2 0.04
24 10 0.18
25 20 0.35
26 9 0.16
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (24 bp):
TAAAAATATATACATAATATAATG
Found at i:95708105 original size:18 final size:19
Alignment explanation
Indices: 95708063--95708107 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
95708053 AGAATATACC
95708063 TAAT-ATATTAAAAGAATA
1 TAATAATATTAAAAGAATA
*
95708081 TATATAATATTAAGA-AATA
1 TA-ATAATATTAAAAGAATA
95708100 TAATAATA
1 TAATAATA
95708108 ACAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 8 0.33
20 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (19 bp):
TAATAATATTAAAAGAATA
Found at i:95708614 original size:18 final size:18
Alignment explanation
Indices: 95708591--95708644 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
95708581 ATAAGTGGTG
95708591 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
*
95708609 GT-G-G--AGT-AGG-TA
1 GTGGAGCAAGTGTGGCTA
95708621 GTGGAGCAAGTGTGGCTA
1 GTGGAGCAAGTGTGGCTA
95708639 GTGGAG
1 GTGGAG
95708645 TTGGTGGTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 4 0.14
13 3 0.11
14 4 0.14
16 4 0.14
17 3 0.11
18 10 0.36
ACGTcount: A:0.22, C:0.07, G:0.48, T:0.22
Consensus pattern (18 bp):
GTGGAGCAAGTGTGGCTA
Found at i:95708627 original size:30 final size:30
Alignment explanation
Indices: 95708586--95708684 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
95708576 TAGGTATAAG
95708586 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
* *
95708616 AGGTAGTGGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
*
95708646 TGGTGGTAGAGCAAGTGTGGCTAGTGGAGT
1 TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
95708676 TGGTGGTGG
1 TGGTGGTGG
95708685 CAAAGGCTAG
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.18, C:0.06, G:0.49, T:0.26
Consensus pattern (30 bp):
TGGTGGTGGAGCAAGTGTGGCTAGTGGAGT
Found at i:95709179 original size:14 final size:15
Alignment explanation
Indices: 95709144--95709181 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
95709134 TACAATATTC
*
95709144 AAATAATAACAATTA
1 AAATAGTAACAATTA
95709159 AAATAGTAACAA-TA
1 AAATAGTAACAATTA
*
95709173 TAATAGTAA
1 AAATAGTAA
95709182 AATGACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (15 bp):
AAATAGTAACAATTA
Found at i:95711491 original size:16 final size:16
Alignment explanation
Indices: 95711472--95711541 Score: 104
Period size: 16 Copynumber: 4.4 Consensus size: 16
95711462 TTTGGTTCGC
* *
95711472 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
95711488 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
95711504 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
95711520 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
95711536 TGTAAT
1 TGTAAT
95711542 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:95711574 original size:45 final size:44
Alignment explanation
Indices: 95711520--95711614 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
95711510 GGAATAGAGG
*
95711520 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
95711565 TGTAATGGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
95711609 TGTAAT
1 TGTAAT
95711615 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:95711795 original size:18 final size:17
Alignment explanation
Indices: 95711774--95711808 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
95711764 TTATTATTAA
*
95711774 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
95711792 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
95711809 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:95723158 original size:20 final size:20
Alignment explanation
Indices: 95723117--95723159 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
95723107 AAAGTAAACC
**
95723117 AAATTTTTTTTAAAATTTTA
1 AAATTTTTTTTAAAATGATA
95723137 AAATTTCTTTTTAAAA-GATA
1 AAATTT-TTTTTAAAATGATA
95723157 AAA
1 AAA
95723160 GGTGTTGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (20 bp):
AAATTTTTTTTAAAATGATA
Found at i:95724205 original size:10 final size:11
Alignment explanation
Indices: 95724160--95724205 Score: 60
Period size: 10 Copynumber: 4.4 Consensus size: 11
95724150 AAATAATAGC
95724160 AAAACAATAAA
1 AAAACAATAAA
* *
95724171 AAAA-AGTAAC
1 AAAACAATAAA
95724181 AAAACAATAAA
1 AAAACAATAAA
95724192 AAAACAA-AAA
1 AAAACAATAAA
95724202 AAAA
1 AAAA
95724206 TCTTACACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
10 15 0.50
11 15 0.50
ACGTcount: A:0.83, C:0.09, G:0.02, T:0.07
Consensus pattern (11 bp):
AAAACAATAAA
Found at i:95724205 original size:21 final size:21
Alignment explanation
Indices: 95724160--95724205 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
95724150 AAATAATAGC
* *
95724160 AAAACAATAAAAAAAAGTAAC
1 AAAACAATAAAAAAAAGAAAA
95724181 AAAACAATAAAAAAACA-AAAA
1 AAAACAATAAAAAAA-AGAAAA
95724202 AAAA
1 AAAA
95724206 TCTTACACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.83, C:0.09, G:0.02, T:0.07
Consensus pattern (21 bp):
AAAACAATAAAAAAAAGAAAA
Found at i:95726967 original size:24 final size:25
Alignment explanation
Indices: 95726935--95726991 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 25
95726925 TGATGTGTTC
*
95726935 AAGTCGATTAAGCCGATTGTAA-AA
1 AAGTCGATTAAGCCAATTGTAAGAA
95726959 AAGTCGATTAAGCCAATTGTAAGAA
1 AAGTCGATTAAGCCAATTGTAAGAA
95726984 AA-TCGATT
1 AAGTCGATT
95726992 GAACAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.26
Consensus pattern (25 bp):
AAGTCGATTAAGCCAATTGTAAGAA
Found at i:95728863 original size:43 final size:43
Alignment explanation
Indices: 95728803--95728989 Score: 275
Period size: 43 Copynumber: 4.3 Consensus size: 43
95728793 AATGCTGCTA
*
95728803 AAAAAACGCCGCTAAAGACCAGGACTTTTAGCTGCACTTATAT
1 AAAAAACGCCGCTAAAGACCAGGACTTTTAGCAGCACTTATAT
* * * *
95728846 AAAAAATGCCGCTAAAGACCAGGACTTATAGCGGCGCTTATAT
1 AAAAAACGCCGCTAAAGACCAGGACTTTTAGCAGCACTTATAT
* *
95728889 AAAAAACGCCGCTAAAGACCAGGACTTTTAGCAGCACTTTTCT
1 AAAAAACGCCGCTAAAGACCAGGACTTTTAGCAGCACTTATAT
* * *
95728932 AAAAAACGCCGCTAAAGACCAGGACTTTTAGCAGCGCTTTTTT
1 AAAAAACGCCGCTAAAGACCAGGACTTTTAGCAGCACTTATAT
*
95728975 AAAAAACGCCACTAA
1 AAAAAACGCCGCTAA
95728990 TTTGTCCAGT
Statistics
Matches: 131, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 131 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (43 bp):
AAAAAACGCCGCTAAAGACCAGGACTTTTAGCAGCACTTATAT
Found at i:95729306 original size:21 final size:21
Alignment explanation
Indices: 95729282--95729329 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
95729272 TTCTGTTCTG
95729282 CTCCGCCTCCCTCGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
* *
95729303 CTCCACTTCCCTCGCTGCTGC
1 CTCCGCCTCCCTCGCTGCTGC
95729324 CTCCGC
1 CTCCGC
95729330 TCTAAGTTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.02, C:0.56, G:0.17, T:0.25
Consensus pattern (21 bp):
CTCCGCCTCCCTCGCTGCTGC
Found at i:95734889 original size:9 final size:9
Alignment explanation
Indices: 95734875--95735041 Score: 145
Period size: 9 Copynumber: 17.6 Consensus size: 9
95734865 ATGTATTAGT
95734875 TAAGTTATG
1 TAAGTTATG
95734884 TAAGTTGTTATG
1 TAA---GTTATG
* *
95734896 TACGTTAAG
1 TAAGTTATG
*
95734905 TGAGTTATG
1 TAAGTTATG
*
95734914 TAAATTATG
1 TAAGTTATG
95734923 TAAGTTATG
1 TAAGTTATG
*
95734932 TGAGTTATG
1 TAAGTTATG
95734941 TAAGTTGTTATG
1 TAA---GTTATG
*
95734953 TAAATTATG
1 TAAGTTATG
95734962 TAAGTTATG
1 TAAGTTATG
*
95734971 TGAGTTATG
1 TAAGTTATG
95734980 TAAGTTGTTATG
1 TAA---GTTATG
*
95734992 TAAATTATG
1 TAAGTTATG
*
95735001 TAAGTTATA
1 TAAGTTATG
*
95735010 TGAGTTATG
1 TAAGTTATG
95735019 TAAGTTATG
1 TAAGTTATG
* *
95735028 TAATTTATT
1 TAAGTTATG
95735037 TAAGT
1 TAAGT
95735042 AATGATCAAT
Statistics
Matches: 126, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
9 100 0.79
12 26 0.21
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:95734941 original size:57 final size:56
Alignment explanation
Indices: 95734875--95735041 Score: 185
Period size: 57 Copynumber: 2.9 Consensus size: 56
95734865 ATGTATTAGT
* *
95734875 TAAGTTATGTAAGTTGTTATGTACGTTAAGTGAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGTTATGTA-GTTATGTAAGTTATGTAAATTATGTAAGTTATG
* * * *
95734932 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTTGTTATG
1 TAAGTTATGTAAGTTGTTATGT-AGTTATGTAAGTTATGTAAATTATGTAA---GTTATG
* * * *
95734992 TAAATTATGTAAGTT-ATATG-AGTTATGTAAGTTATGTAATTTATTTAAGT
1 TAAGTTATGTAAGTTGTTATGTAGTTATGTAAGTTATGTAAATTATGTAAGT
95735042 AATGATCAAT
Statistics
Matches: 93, Mismatches: 13, Indels: 11
0.79 0.11 0.09
Matches are distributed among these distances:
54 2 0.02
57 67 0.72
58 1 0.01
59 4 0.04
60 19 0.20
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.46
Consensus pattern (56 bp):
TAAGTTATGTAAGTTGTTATGTAGTTATGTAAGTTATGTAAATTATGTAAGTTATG
Found at i:95735024 original size:39 final size:39
Alignment explanation
Indices: 95734908--95735024 Score: 225
Period size: 39 Copynumber: 3.0 Consensus size: 39
95734898 CGTTAAGTGA
95734908 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
1 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
95734947 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
1 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
*
95734986 GTTATGTAAATTATGTAAGTTATATGAGTTATGTAAGTT
1 GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
95735025 ATGTAATTTA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (39 bp):
GTTATGTAAATTATGTAAGTTATGTGAGTTATGTAAGTT
Found at i:95735025 original size:48 final size:48
Alignment explanation
Indices: 95734875--95735030 Score: 179
Period size: 48 Copynumber: 3.2 Consensus size: 48
95734865 ATGTATTAGT
* * * *
95734875 TAAGTTATGTAAGTTGTTATGTACGTTAAGTGAGTTATGTAAATTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAGTTATG
* * * * *
95734923 TAAGTTATGTGAGTTATGTAAGT-TGTTATGTAAATTATGTAAGTTATG
1 TAAGTTATGTAAGTTGT-TATGTAAGTTATGTAAGTTATGTAAGTTATG
* * * *
95734971 TGAGTTATGTAAGTTGTTATGTAAATTATGTAAGTTATATGAGTTATG
1 TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAGTTATG
95735019 TAAGTTATGTAA
1 TAAGTTATGTAA
95735031 TTTATTTAAG
Statistics
Matches: 88, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
47 4 0.05
48 80 0.91
49 4 0.05
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (48 bp):
TAAGTTATGTAAGTTGTTATGTAAGTTATGTAAGTTATGTAAGTTATG
Found at i:95738116 original size:19 final size:19
Alignment explanation
Indices: 95738092--95738129 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
95738082 GGTCGTCCAC
*
95738092 TCGGAGTCTTCAACGGCAG
1 TCGGAGCCTTCAACGGCAG
95738111 TCGGAGCCTTCAACGGCAG
1 TCGGAGCCTTCAACGGCAG
95738130 AAGGATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.32, T:0.18
Consensus pattern (19 bp):
TCGGAGCCTTCAACGGCAG
Found at i:95738186 original size:19 final size:20
Alignment explanation
Indices: 95738147--95738198 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
95738137 TTTCGATTTT
* *
95738147 GATTCGGGGAAATATTTAGG
1 GATTAGGGGAAATAGTTAGG
95738167 GATTAGGGGAAA-AGTTAGG
1 GATTAGGGGAAATAGTTAGG
*
95738186 GATTTGGGGAAAT
1 GATTAGGGGAAAT
95738199 TTGGGTGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.33, C:0.02, G:0.38, T:0.27
Consensus pattern (20 bp):
GATTAGGGGAAATAGTTAGG
Found at i:95739313 original size:14 final size:15
Alignment explanation
Indices: 95739281--95739317 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
95739271 GAAATTTATT
95739281 TTTAGGGTTTACAAA
1 TTTAGGGTTTACAAA
*
95739296 TTTAGGGTTTA-TAA
1 TTTAGGGTTTACAAA
95739310 TTTAGGGT
1 TTTAGGGT
95739318 AGAAGTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.46
Consensus pattern (15 bp):
TTTAGGGTTTACAAA
Found at i:95739523 original size:29 final size:29
Alignment explanation
Indices: 95739490--95739545 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
95739480 AGAGTTTAGA
*
95739490 TCATGGGTTATGATTTAGGGGTTAGGCGG
1 TCATGGGTTATGATTTAAGGGTTAGGCGG
95739519 TCATGGGTTATGATTTAAGGGTTAGGC
1 TCATGGGTTATGATTTAAGGGTTAGGC
95739546 TTCATATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.20, C:0.07, G:0.38, T:0.36
Consensus pattern (29 bp):
TCATGGGTTATGATTTAAGGGTTAGGCGG
Found at i:95740294 original size:41 final size:41
Alignment explanation
Indices: 95740123--95740277 Score: 222
Period size: 41 Copynumber: 3.8 Consensus size: 41
95740113 GGACCTAAAG
* *
95740123 CGCCACTATAT-CTCAGTTTTTTGCGGCGTTTTGCATGAAAA
1 CGCCACTAT-TGCTCAGTTTTTAGCGGCGTTTTGCACGAAAA
*
95740164 CGCCACTATTACTCAGTTTTTAGCGGCGTTTTGCACGAAAA
1 CGCCACTATTGCTCAGTTTTTAGCGGCGTTTTGCACGAAAA
* * *
95740205 CGCCACAATTGCTCAATTTTTAGTGGCGTTTTGCACGAAAA
1 CGCCACTATTGCTCAGTTTTTAGCGGCGTTTTGCACGAAAA
* *
95740246 AGCCACTATTGCTCAGTTTTTAGTGGCGTTTT
1 CGCCACTATTGCTCAGTTTTTAGCGGCGTTTT
95740278 TCATTCAAAC
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 1 0.01
41 103 0.99
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.35
Consensus pattern (41 bp):
CGCCACTATTGCTCAGTTTTTAGCGGCGTTTTGCACGAAAA
Found at i:95749185 original size:35 final size:35
Alignment explanation
Indices: 95749135--95749266 Score: 124
Period size: 35 Copynumber: 3.6 Consensus size: 35
95749125 TCAAAATTAT
* *
95749135 TATCGTCGGTATATCCGACTAGCACTAGGTGCAAA
1 TATCGTTGGTATATCCAACTAGCACTAGGTGCAAA
* *
95749170 TATCGTTGGTTTATCCAACTAG-AGCTGGGCT-CACTATTA
1 TATCGTTGGTATATCCAACTAGCA-CTAGG-TGCA--A--A
* *
95749209 TTATCGTTGGTATATCCGACTAGCACTTGGTGCAAA
1 -TATCGTTGGTATATCCAACTAGCACTAGGTGCAAA
*
95749245 TATCGTTGGTTTATCCAACTAG
1 TATCGTTGGTATATCCAACTAG
95749267 AGCTGGGCTC
Statistics
Matches: 79, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
34 1 0.01
35 45 0.57
36 2 0.03
37 1 0.01
38 1 0.01
39 2 0.03
40 26 0.33
41 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.33
Consensus pattern (35 bp):
TATCGTTGGTATATCCAACTAGCACTAGGTGCAAA
Found at i:95749216 original size:40 final size:38
Alignment explanation
Indices: 95749102--95749313 Score: 138
Period size: 40 Copynumber: 5.6 Consensus size: 38
95749092 AAATATCATA
* * * *
95749102 GGTTTATCCAACTAAATCTGGGCTCAAAATTATTATCGTC
1 GGTTTATCCAACTAGAGCTGGGCTC-ACATTA-TATCGTT
* * *
95749142 GGTATATCCGACTAGCA-CTAGG-TGCA-A--ATATCGTT
1 GGTTTATCCAACTAG-AGCTGGGCT-CACATTATATCGTT
95749177 GGTTTATCCAACTAGAGCTGGGCTCACTATTATTATCGTT
1 GGTTTATCCAACTAGAGCTGGGCTCAC-ATTA-TATCGTT
* * *
95749217 GGTATATCCGACTAGCA-CTTGG-TGCA-A--ATATCGTT
1 GGTTTATCCAACTAG-AGCTGGGCT-CACATTATATCGTT
95749252 GGTTTATCCAACTAGAGCTGGGCTCACATTCAATATCGTT
1 GGTTTATCCAACTAGAGCTGGGCTCACATT--ATATCGTT
* ** *
95749292 GGTTAATCTGACTAGCGCTGGG
1 GGTTTATCCAACTAGAGCTGGG
95749314 TGCAAACTTC
Statistics
Matches: 136, Mismatches: 18, Indels: 36
0.72 0.09 0.19
Matches are distributed among these distances:
34 2 0.01
35 51 0.38
36 5 0.04
37 1 0.01
38 2 0.01
39 4 0.03
40 69 0.51
41 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (38 bp):
GGTTTATCCAACTAGAGCTGGGCTCACATTATATCGTT
Found at i:95749278 original size:75 final size:74
Alignment explanation
Indices: 95749090--95749319 Score: 318
Period size: 75 Copynumber: 3.1 Consensus size: 74
95749080 AGTGCTGCGC
* * * * * *
95749090 GCAAATATCATAGGTTTATCCAACTAAATCTGGGCTCAAAATTATTATCGTCGGTATATCCGACT
1 GCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTC-ACATTATTATCGTTGGTATATCCGACT
95749155 AGCACTAGGT
65 AGCACTAGGT
95749165 GCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACTATTATTATCGTTGGTATATCCGACT
1 GCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCAC-ATTATTATCGTTGGTATATCCGACT
*
95749230 AGCACTTGGT
65 AGCACTAGGT
* *
95749240 GCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACATTCAATATCGTTGGT-TAATCTGAC
1 GCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACATT-ATTATCGTTGGTAT-ATCCGAC
* *
95749304 TAGCGCTGGGT
64 TAGCACTAGGT
95749315 GCAAA
1 GCAAA
95749320 CTTCTCTACG
Statistics
Matches: 141, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
74 5 0.04
75 136 0.96
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (74 bp):
GCAAATATCGTTGGTTTATCCAACTAGAGCTGGGCTCACATTATTATCGTTGGTATATCCGACTA
GCACTAGGT
Found at i:95751219 original size:31 final size:31
Alignment explanation
Indices: 95751184--95751245 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
95751174 ATCCAACCAA
* *
95751184 GAACATAACTTACCATTTCAATGCGTAACAT
1 GAACATAACCTACCATTTCAATGCATAACAT
* *
95751215 GAACATAACCTATCTTTTCAATGCATAACAT
1 GAACATAACCTACCATTTCAATGCATAACAT
95751246 TAAAATTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.31
Consensus pattern (31 bp):
GAACATAACCTACCATTTCAATGCATAACAT
Found at i:95753362 original size:51 final size:51
Alignment explanation
Indices: 95753222--95753363 Score: 171
Period size: 51 Copynumber: 2.8 Consensus size: 51
95753212 CGGATGCCCG
* *
95753222 GTGGCCTGCACATAGTACCACCCTTGT-AGTCAAAGCTACCTTCTTCACAAA
1 GTGGCCTGCACATAGTACCACACTTGTGA-TCAAAGCTATCTTCTTCACAAA
* * * *
95753273 GTGGCCTTCACATAGTACCACACTTGTGACCAGAGCTATCTT-TTACACATA
1 GTGGCCTGCACATAGTACCACACTTGTGATCAAAGCTATCTTCTT-CACAAA
* * *
95753324 GTGGCCTGCACTTAGTACCACACATGTGATCGAAGCTATC
1 GTGGCCTGCACATAGTACCACACTTGTGATCAAAGCTATC
95753364 AGGTATGCAT
Statistics
Matches: 77, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
50 2 0.03
51 74 0.96
52 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.27
Consensus pattern (51 bp):
GTGGCCTGCACATAGTACCACACTTGTGATCAAAGCTATCTTCTTCACAAA
Found at i:95756380 original size:65 final size:64
Alignment explanation
Indices: 95756303--95756423 Score: 181
Period size: 65 Copynumber: 1.9 Consensus size: 64
95756293 CAGTGTGAGC
* * *
95756303 TGTAAAGTTGCGAGCCTGTTGAAGACAATGAGCCAAATGTGCGAG-CTATCAAAGTGTACGAGCC
1 TGTAAAGTTGCGAGCATGTTAAAGACAATAAG-CAAA-GTGCGAGCCTATCAAAGTGTACGAGCC
95756367 T
64 T
*
95756368 TGTAAAGTTGCGAGCATGTTAAAGATAATAAGCAAAGTGCGAGCCTATCAAAGTGT
1 TGTAAAGTTGCGAGCATGTTAAAGACAATAAGCAAAGTGCGAGCCTATCAAAGTGT
95756424 GAGCCTATCG
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
63 7 0.14
64 16 0.31
65 28 0.55
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (64 bp):
TGTAAAGTTGCGAGCATGTTAAAGACAATAAGCAAAGTGCGAGCCTATCAAAGTGTACGAGCCT
Found at i:95756421 original size:16 final size:16
Alignment explanation
Indices: 95756400--95756432 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
95756390 AGATAATAAG
95756400 CAAAGTGCGAGCCTAT
1 CAAAGTGCGAGCCTAT
*
95756416 CAAAGTGTGAGCCTAT
1 CAAAGTGCGAGCCTAT
95756432 C
1 C
95756433 GAATTGCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.21
Consensus pattern (16 bp):
CAAAGTGCGAGCCTAT
Found at i:95757807 original size:25 final size:26
Alignment explanation
Indices: 95757773--95757825 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
95757763 AGTTATTTTG
95757773 TTTTGTTTACTTTGTTATTACAAACT
1 TTTTGTTTACTTTGTTATTACAAACT
* *
95757799 TTTTG-TTACTTTTTTATTACAAGCT
1 TTTTGTTTACTTTGTTATTACAAACT
95757824 TT
1 TT
95757826 GTAACTAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (26 bp):
TTTTGTTTACTTTGTTATTACAAACT
Found at i:95762079 original size:29 final size:29
Alignment explanation
Indices: 95762037--95762098 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
95762027 TTTAAGGTTT
*
95762037 AATTTGATATCTAAAGTTAATTTTGATCC
1 AATTAGATATCTAAAGTTAATTTTGATCC
* *
95762066 AATTAGATATCTAAAGTTTATTTTGGTCC
1 AATTAGATATCTAAAGTTAATTTTGATCC
95762095 AATT
1 AATT
95762099 TGAACTATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.10, G:0.11, T:0.45
Consensus pattern (29 bp):
AATTAGATATCTAAAGTTAATTTTGATCC
Found at i:95763704 original size:11 final size:11
Alignment explanation
Indices: 95763690--95763727 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
95763680 TATAAATTTC
95763690 TAAAATATTAT
1 TAAAATATTAT
95763701 T-AAATATTAT
1 TAAAATATTAT
* *
95763711 AAAAATATTAA
1 TAAAATATTAT
95763722 TAAAAT
1 TAAAAT
95763728 TAATAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAATATTAT
Found at i:95763707 original size:10 final size:10
Alignment explanation
Indices: 95763692--95763734 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
95763682 TAAATTTCTA
*
95763692 AAATATTATT
1 AAATATTAAT
*
95763702 AAATATTATAA
1 AAATATTA-AT
95763713 AAATATTAAT
1 AAATATTAAT
95763723 AAA-ATTAAT
1 AAATATTAAT
95763732 AAA
1 AAA
95763735 AACCATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 9 0.31
10 12 0.41
11 8 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATATTAAT
Found at i:95763716 original size:21 final size:21
Alignment explanation
Indices: 95763691--95763736 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
95763681 ATAAATTTCT
*
95763691 AAAATATTATTAAATATT-ATA
1 AAAATATTAATAAA-ATTAATA
95763712 AAAATATTAATAAAATTAATA
1 AAAATATTAATAAAATTAATA
95763733 AAAA
1 AAAA
95763737 CCATTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAATATTAATAAAATTAATA
Found at i:95763900 original size:24 final size:23
Alignment explanation
Indices: 95763872--95763918 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
95763862 AATTAATTAG
95763872 AAATTTAATATTTTTAAAAAAATT
1 AAATTT-ATATTTTTAAAAAAATT
* * *
95763896 AAATTTTTATTTTTTAAATAATT
1 AAATTTATATTTTTAAAAAAATT
95763919 TTGAAACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AAATTTATATTTTTAAAAAAATT
Found at i:95765511 original size:39 final size:39
Alignment explanation
Indices: 95765468--95765547 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
95765458 TGTTTTCGTT
* *
95765468 GTGGTTGTCACAATTATTGTAGAATTGCCTACTTTCACA
1 GTGGTTGTCACAATTATTGTAGAAGTGCCCACTTTCACA
95765507 GTGGTTGTCACAATTATTGTAGAAGTGCCCACTTTCACA
1 GTGGTTGTCACAATTATTGTAGAAGTGCCCACTTTCACA
95765546 GT
1 GT
95765548 CACGTCTGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (39 bp):
GTGGTTGTCACAATTATTGTAGAAGTGCCCACTTTCACA
Found at i:95772997 original size:2 final size:2
Alignment explanation
Indices: 95772986--95773021 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
95772976 GCGATCCCTT
95772986 TC TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
95773022 TTTTTAAACG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:95774352 original size:3 final size:3
Alignment explanation
Indices: 95774344--95774378 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
95774334 TTAAAACAGA
95774344 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
95774379 ATATTATCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:95786498 original size:15 final size:14
Alignment explanation
Indices: 95786478--95786508 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
95786468 TACTGCCTCC
95786478 ATTATTTAATTTCTT
1 ATTATTTAATTT-TT
95786493 ATTATTTAATTTTT
1 ATTATTTAATTTTT
95786507 AT
1 AT
95786509 ATCATATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTATTTAATTTTT
Found at i:95802339 original size:32 final size:32
Alignment explanation
Indices: 95802298--95802360 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
95802288 CGAGTGTTGT
95802298 TTATAATTCACAAAAATAAGGGTAAATTGTAA
1 TTATAATTCACAAAAATAAGGGTAAATTGTAA
95802330 TTATAATTCACAAAAATAAGGGTAAATTGTA
1 TTATAATTCACAAAAATAAGGGTAAATTGTA
95802361 CAATTTGTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.49, C:0.06, G:0.13, T:0.32
Consensus pattern (32 bp):
TTATAATTCACAAAAATAAGGGTAAATTGTAA
Found at i:95803755 original size:34 final size:33
Alignment explanation
Indices: 95803716--95803893 Score: 138
Period size: 34 Copynumber: 5.5 Consensus size: 33
95803706 TAAACATATA
*
95803716 AACAATCGATTTAAAAGAAGCAGTATTCTAACAT
1 AACAATCGATTTAAAAGAAGCAATATTC-AACAT
* ** * *
95803750 AACAATCAATTTAAACA-AATAAATAATCGAC-T
1 AACAATCGATTTAAA-AGAAGCAATATTCAACAT
*
95803782 CAA-AA--GA---AAAAGAAGCAATATTCCACCAT
1 -AACAATCGATTTAAAAGAAGCAATATT-CAACAT
*
95803811 AACAATCGATTTAAAAGAAGCAATATTCCACCAT
1 AACAATCGATTTAAAAGAAGCAATATT-CAACAT
* * *
95803845 AACAATCGATTTAAAAGAAACAGTATTACAGCAT
1 AACAATCGATTTAAAAGAAGCAATATT-CAACAT
*
95803879 GACAATCGATTTAAA
1 AACAATCGATTTAAA
95803894 CATACAAACA
Statistics
Matches: 116, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
26 1 0.01
27 10 0.09
28 4 0.03
29 3 0.03
30 1 0.01
31 2 0.02
32 3 0.03
33 4 0.03
34 87 0.75
35 1 0.01
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.23
Consensus pattern (33 bp):
AACAATCGATTTAAAAGAAGCAATATTCAACAT
Found at i:95804720 original size:23 final size:21
Alignment explanation
Indices: 95804686--95804729 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
95804676 ATATTATTAT
* *
95804686 TATTTTTTCCTTTAATTTTTC
1 TATTTTTTCCTTCAACTTTTC
95804707 TATTTTTTACCCTTCAACTTTTC
1 TATTTTTT--CCTTCAACTTTTC
95804730 CTTACACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
23 11 0.58
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (21 bp):
TATTTTTTCCTTCAACTTTTC
Found at i:95806005 original size:6 final size:6
Alignment explanation
Indices: 95805994--95806039 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
95805984 CTAGGGTGGA
*
95805994 AAAATG AAAATG AAAAATG AAAAAG AGAGAATG AAAATG AAAATG A
1 AAAATG AAAATG -AAAATG AAAATG A-A-AATG AAAATG AAAATG A
95806040 TCTATAAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 23 0.66
7 8 0.23
8 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.13
Consensus pattern (6 bp):
AAAATG
Found at i:95813267 original size:16 final size:16
Alignment explanation
Indices: 95813246--95813312 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
95813236 ATTTTTACAC
95813246 AAATAATATA-AAAAAT
1 AAATAAT-TACAAAAAT
95813262 AAATAATTACAAAAAT
1 AAATAATTACAAAAAT
* * *
95813278 GAGACAAGTA-AAAAAT
1 -AAATAATTACAAAAAT
95813294 ---TAATTACAAAAAT
1 AAATAATTACAAAAAT
95813307 AAATAA
1 AAATAA
95813313 AATAAACAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
12 4 0.10
13 6 0.15
15 2 0.05
16 22 0.55
17 6 0.15
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (16 bp):
AAATAATTACAAAAAT
Found at i:95813318 original size:29 final size:28
Alignment explanation
Indices: 95813240--95813318 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 28
95813230 CACATGATTT
* *
95813240 TTACACAAATAATATAAAA-AATAAATAA
1 TTACAAAAATAA-ATAAAATAAAAAATAA
* * *
95813268 TTACAAAAATGAGA-CAAGTAAAAAATTAA
1 TTACAAAAAT-AAATAAAATAAAAAA-TAA
95813297 TTACAAAAATAAATAAAATAAA
1 TTACAAAAATAAATAAAATAAA
95813319 CAGTTTTTGC
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
27 2 0.05
28 17 0.44
29 20 0.51
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (28 bp):
TTACAAAAATAAATAAAATAAAAAATAA
Found at i:95814666 original size:27 final size:26
Alignment explanation
Indices: 95814635--95814695 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
95814625 TTTTTGTATC
95814635 TTTGAAAACATTTCA-TCTTTCTCAACA
1 TTTGAAAACATTT-AGT-TTTCTCAACA
* *
95814662 TTTGAGAATATTTAGTTTTCTCAACA
1 TTTGAAAACATTTAGTTTTCTCAACA
95814688 TTTGAAAA
1 TTTGAAAA
95814696 TTAGAGAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.43
Consensus pattern (26 bp):
TTTGAAAACATTTAGTTTTCTCAACA
Found at i:95815148 original size:13 final size:14
Alignment explanation
Indices: 95815130--95815162 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
95815120 TTCAGTTTAC
*
95815130 TTATTTTTTGTA-A
1 TTATTTTTTATATA
95815143 TTATTTTTTATATA
1 TTATTTTTTATATA
95815157 TTATTT
1 TTATTT
95815163 GCGTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TTATTTTTTATATA
Found at i:95815908 original size:17 final size:17
Alignment explanation
Indices: 95815886--95815923 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
95815876 AAAATGACAC
95815886 ACATAGACATTTTAGGT
1 ACATAGACATTTTAGGT
95815903 ACATAGACATTTTAGGT
1 ACATAGACATTTTAGGT
95815920 ACAT
1 ACAT
95815924 GCCATTACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (17 bp):
ACATAGACATTTTAGGT
Found at i:95816442 original size:18 final size:18
Alignment explanation
Indices: 95816411--95816475 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
95816401 TATCAATATC
*
95816411 ATTCAGTAATAATCA-TT
1 ATTCAGTAACAATCAGTT
* *
95816428 TTCTCAGTAGCAATCAGTT
1 AT-TCAGTAACAATCAGTT
*
95816447 ATTCAGTAACAATCAATT
1 ATTCAGTAACAATCAGTT
*
95816465 ATTCAATAACA
1 ATTCAGTAACA
95816476 GTTAGTCGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
17 1 0.03
18 35 0.90
19 3 0.08
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (18 bp):
ATTCAGTAACAATCAGTT
Found at i:95816849 original size:24 final size:24
Alignment explanation
Indices: 95816803--95816859 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
95816793 AATAGGGTAT
*
95816803 TCAATTCACTTTTAATTTTATCAA
1 TCAATTCACTTTTAATTTAATCAA
*
95816827 TCAATTTACATTTTAA-TTAATCACA
1 TCAATTCAC-TTTTAATTTAATCA-A
*
95816852 TAAATTCA
1 TCAATTCA
95816860 TAATTCAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.46
Consensus pattern (24 bp):
TCAATTCACTTTTAATTTAATCAA
Found at i:95817845 original size:17 final size:15
Alignment explanation
Indices: 95817817--95817850 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
95817807 TCACTATTTC
95817817 TCCCTTTTCTTTCTT
1 TCCCTTTTCTTTCTT
95817832 TCCCTTTTTCCTTTCTT
1 TCCC-TTTT-CTTTCTT
95817849 TC
1 TC
95817851 TTTCTCCCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (15 bp):
TCCCTTTTCTTTCTT
Found at i:95818700 original size:26 final size:25
Alignment explanation
Indices: 95818663--95818719 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
95818653 GTGTTCTTGG
*
95818663 TTCTTTTTTATTTT-TATTTAGTTTTT
1 TTCTTTTGTATTTTCT-TTTA-TTTTT
95818689 TTCTTTTGTATTTTCTTTTATTTTT
1 TTCTTTTGTATTTTCTTTTATTTTT
95818714 TTCTTT
1 TTCTTT
95818720 CTCTTCGCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 11 0.38
26 17 0.59
27 1 0.03
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.81
Consensus pattern (25 bp):
TTCTTTTGTATTTTCTTTTATTTTT
Found at i:95818702 original size:13 final size:13
Alignment explanation
Indices: 95818663--95818719 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
95818653 GTGTTCTTGG
*
95818663 TTCTTTTTTATTT
1 TTCTTTTGTATTT
* * *
95818676 TTATTTAGTTTTT
1 TTCTTTTGTATTT
95818689 TTCTTTTGTA-TT
1 TTCTTTTGTATTT
* *
95818701 TTCTTTTATTTTT
1 TTCTTTTGTATTT
95818714 TTCTTT
1 TTCTTT
95818720 CTCTTCGCGA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
12 10 0.29
13 24 0.71
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.81
Consensus pattern (13 bp):
TTCTTTTGTATTT
Found at i:95818702 original size:25 final size:26
Alignment explanation
Indices: 95818663--95818719 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
95818653 GTGTTCTTGG
*
95818663 TTCTTTTTTATTTTT-ATTTAGTTTTT
1 TTCTTTTGTATTTTTCATTTA-TTTTT
*
95818689 TTCTTTTGTA-TTTTCTTTTATTTTT
1 TTCTTTTGTATTTTTCATTTATTTTT
95818714 TTCTTT
1 TTCTTT
95818720 CTCTTCGCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.54
26 13 0.46
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.81
Consensus pattern (26 bp):
TTCTTTTGTATTTTTCATTTATTTTT
Found at i:95818715 original size:20 final size:18
Alignment explanation
Indices: 95818663--95818715 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
95818653 GTGTTCTTGG
*
95818663 TTCTTTTTTATTTTTATT
1 TTCTTTTTTTTTTTTATT
**
95818681 TAGTTTTTTTCTTTTGTATT
1 TTCTTTTTTT-TTTT-TATT
*
95818701 TTCTTTTATTTTTTT
1 TTCTTTTTTTTTTTT
95818716 CTTTCTCTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
18 8 0.30
19 8 0.30
20 11 0.41
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (18 bp):
TTCTTTTTTTTTTTTATT
Found at i:95819415 original size:62 final size:62
Alignment explanation
Indices: 95819318--95819445 Score: 247
Period size: 62 Copynumber: 2.1 Consensus size: 62
95819308 TATTATCTCA
95819318 TTTAGTCCCTGCTACTTTCAGCGCACCGCAATTTGGTCCTTTGATTTTATTTTATTTCTATT
1 TTTAGTCCCTGCTACTTTCAGCGCACCGCAATTTGGTCCTTTGATTTTATTTTATTTCTATT
*
95819380 TTTAGTCCCTGCTACTTTCAGCGGACCGCAATTTGGTCCTTTGATTTTATTTTATTTCTATT
1 TTTAGTCCCTGCTACTTTCAGCGCACCGCAATTTGGTCCTTTGATTTTATTTTATTTCTATT
95819442 TTTA
1 TTTA
95819446 CCCCAAAACC
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.16, C:0.21, G:0.13, T:0.49
Consensus pattern (62 bp):
TTTAGTCCCTGCTACTTTCAGCGCACCGCAATTTGGTCCTTTGATTTTATTTTATTTCTATT
Found at i:95819771 original size:3 final size:3
Alignment explanation
Indices: 95819765--95819847 Score: 62
Period size: 3 Copynumber: 27.7 Consensus size: 3
95819755 CATCATCATC
* * * *
95819765 ATT ATT ATT GA-T ATT ATT ATT ATT ATT ATT ATT GTT ACTT TTT GTC
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
* * * *
95819811 ACT ATT GTC ATT ATT A-T ATT ATT ACT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
95819848 ACTTATATTC
Statistics
Matches: 61, Mismatches: 15, Indels: 8
0.73 0.18 0.10
Matches are distributed among these distances:
2 3 0.05
3 55 0.90
4 3 0.05
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:95821842 original size:3 final size:3
Alignment explanation
Indices: 95821834--95821864 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
95821824 TTAACTTATT
95821834 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
95821865 CTAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:95825952 original size:13 final size:14
Alignment explanation
Indices: 95825931--95825969 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
95825921 AAAATATTTC
95825931 TCAAAAACACTTTT
1 TCAAAAACACTTTT
*
95825945 TC-ATAACA-TTTT
1 TCAAAAACACTTTT
95825957 TCAAAAACACTTT
1 TCAAAAACACTTT
95825970 ATAAAAGCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 5 0.24
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (14 bp):
TCAAAAACACTTTT
Found at i:95827136 original size:13 final size:13
Alignment explanation
Indices: 95827120--95827161 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
95827110 TTAGTATTAT
95827120 TTTTTAACAAGTG
1 TTTTTAACAAGTG
95827133 -TTTTAA-AAGTG
1 TTTTTAACAAGTG
* *
95827144 TTTTTGACAAATG
1 TTTTTAACAAGTG
95827157 TTTTT
1 TTTTT
95827162 GATAAATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 5 0.20
12 11 0.44
13 9 0.36
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (13 bp):
TTTTTAACAAGTG
Found at i:95827478 original size:21 final size:22
Alignment explanation
Indices: 95827435--95827490 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
95827425 AAACTATGTT
* *
95827435 TTAAATATTT-AAATATAATTA
1 TTAAATATTTGTAATATAAATA
95827456 TTAAATATTTGTAAT-TAAATA
1 TTAAATATTTGTAATATAAATA
*
95827477 TTAATATAGTTGTA
1 TTAA-ATATTTGTA
95827491 TTATTTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TTAAATATTTGTAATATAAATA
Found at i:95832237 original size:17 final size:17
Alignment explanation
Indices: 95832215--95832281 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
95832205 TTTGGAATTT
95832215 ATTTTTAAATTTTTATA
1 ATTTTTAAATTTTTATA
****
95832232 ATTTTTAAAAAAATATA
1 ATTTTTAAATTTTTATA
95832249 ATTTTTAGAATTTTTATAA
1 ATTTTTA-AATTTTTAT-A
*
95832268 ATATTTTGAATTTT
1 AT-TTTTAAATTTT
95832282 AAAACTTATT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
17 20 0.53
18 5 0.13
19 9 0.24
20 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (17 bp):
ATTTTTAAATTTTTATA
Found at i:95832310 original size:20 final size:19
Alignment explanation
Indices: 95832251--95832316 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 19
95832241 AAAATATAAT
95832251 TTTTAGAATTTTTATAAA-TA
1 TTTT-GAATTTTTA-AAATTA
95832271 TTTTGAA-TTTTAAAACTTA
1 TTTTGAATTTTTAAAA-TTA
95832290 TTTTGAATTTTTGAAAATTA
1 TTTTGAATTTTT-AAAATTA
95832310 TTTTGAA
1 TTTTGAA
95832317 CTATTTTGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.07
18 5 0.12
19 12 0.29
20 18 0.43
21 4 0.10
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.55
Consensus pattern (19 bp):
TTTTGAATTTTTAAAATTA
Found at i:95832791 original size:42 final size:39
Alignment explanation
Indices: 95832745--95832854 Score: 142
Period size: 36 Copynumber: 2.9 Consensus size: 39
95832735 TAAAACTTTA
95832745 AAAAAAGAATATATATGTATATAAATTGAAAATAAAAAACAT
1 AAAAAA-AATATATATG--TATAAATTGAAAATAAAAAACAT
95832787 --AAAAAATA-ATATGTATAAATTGAAAATAAAAAACAT
1 AAAAAAAATATATATGTATAAATTGAAAATAAAAAACAT
*
95832823 --AAAAAATA-ATATGTATAATTTGAAAATAAAAA
1 AAAAAAAATATATATGTATAAATTGAAAATAAAAA
95832855 TATCAAATTT
Statistics
Matches: 67, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
36 54 0.81
38 5 0.07
39 4 0.06
40 4 0.06
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.26
Consensus pattern (39 bp):
AAAAAAAATATATATGTATAAATTGAAAATAAAAAACAT
Found at i:95832808 original size:36 final size:36
Alignment explanation
Indices: 95832764--95832854 Score: 173
Period size: 36 Copynumber: 2.5 Consensus size: 36
95832754 TATATATGTA
95832764 TATAAATTGAAAATAAAAAACATAAAAAATAATATG
1 TATAAATTGAAAATAAAAAACATAAAAAATAATATG
95832800 TATAAATTGAAAATAAAAAACATAAAAAATAATATG
1 TATAAATTGAAAATAAAAAACATAAAAAATAATATG
*
95832836 TATAATTTGAAAATAAAAA
1 TATAAATTGAAAATAAAAA
95832855 TATCAAATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.26
Consensus pattern (36 bp):
TATAAATTGAAAATAAAAAACATAAAAAATAATATG
Found at i:95832814 original size:20 final size:20
Alignment explanation
Indices: 95832789--95832851 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
95832779 AAAAACATAA
95832789 AAAATAATATGTATAAATTG
1 AAAATAATATGTATAAATTG
**
95832809 AAAATAA-A---A-AACATAA
1 AAAATAATATGTATAA-ATTG
*
95832825 AAAATAATATGTATAATTTG
1 AAAATAATATGTATAAATTG
95832845 AAAATAA
1 AAAATAA
95832852 AAATATCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 12
0.65 0.10 0.24
Matches are distributed among these distances:
15 2 0.06
16 10 0.31
17 1 0.03
19 1 0.03
20 16 0.50
21 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (20 bp):
AAAATAATATGTATAAATTG
Found at i:95833153 original size:23 final size:24
Alignment explanation
Indices: 95833108--95833160 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
95833098 AAAAAAATTA
* *
95833108 AATTTTATTTATTTGTATATTTTT
1 AATTTTATTTAGTTATATATTTTT
95833132 AATTTTATTT-GTTATATATTTTT
1 AATTTTATTTAGTTATATATTTTT
95833155 AGATTT
1 A-ATTT
95833161 AAATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (24 bp):
AATTTTATTTAGTTATATATTTTT
Found at i:95833680 original size:142 final size:144
Alignment explanation
Indices: 95833434--95833696 Score: 343
Period size: 142 Copynumber: 1.8 Consensus size: 144
95833424 TGTGTCAGTG
* * * *
95833434 TAGGGACTAATTTATGCAATGGATGCCAATCTTAGGGACCACTATGACCCCAAAAAAAAAAGTTT
1 TAGGGACCAATTTATGCAACGGATGCCAACCTTAGGGACCAATATGACCCC-AAAAAAAAAGTTT
* * *
95833499 AGGGGCCAATGTGAGAAAAGCTGCATAGTTTAGGGGCCAATCTGTATATTAAGCCTTAAAAAAAC
65 AGGAGCCAATGTGAGAAAAGCTGCATAGTTTAGGAGCCAATCTATATATTAAGCCTTAAAAAAAC
95833564 TAACGGTGTTAACCA
130 TAACGGTGTTAACCA
* * * * *
95833579 TAGGGACCGATTTATGTAACGGATGCCAACCTTAGGGACCAATGTGA-TCC-AAAAAAATGTTTA
1 TAGGGACCAATTTATGCAACGGATGCCAACCTTAGGGACCAATATGACCCCAAAAAAAAAGTTTA
* * * *
95833642 GGAGCTAATTTGAGAAAAGTTGCCA-AGTTTAGGAGCCAATCTATATTTTAAGCCT
66 GGAGCCAATGTGAGAAAAGCTG-CATAGTTTAGGAGCCAATCTATATATTAAGCCT
95833697 AAGTTTTATA
Statistics
Matches: 101, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
142 57 0.56
143 2 0.02
144 2 0.02
145 40 0.40
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.26
Consensus pattern (144 bp):
TAGGGACCAATTTATGCAACGGATGCCAACCTTAGGGACCAATATGACCCCAAAAAAAAAGTTTA
GGAGCCAATGTGAGAAAAGCTGCATAGTTTAGGAGCCAATCTATATATTAAGCCTTAAAAAAACT
AACGGTGTTAACCA
Found at i:95835488 original size:8 final size:8
Alignment explanation
Indices: 95835455--95835505 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
95835445 AAATTTTAAT
*
95835455 TTTAATTA
1 TTTAAATA
95835463 TATTAAATA
1 T-TTAAATA
* *
95835472 ATT-ATTA
1 TTTAAATA
*
95835479 TTTACATA
1 TTTAAATA
95835487 TTTAAATA
1 TTTAAATA
95835495 TTTAAATA
1 TTTAAATA
95835503 TTT
1 TTT
95835506 TTATATTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
7 5 0.15
8 23 0.68
9 6 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (8 bp):
TTTAAATA
Found at i:95835511 original size:16 final size:16
Alignment explanation
Indices: 95835461--95835512 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
95835451 TAATTTTAAT
*
95835461 TATA-TTAAATAATTA
1 TATATTTAAATATTTA
*
95835476 T-TATTTACATATTTA
1 TATATTTAAATATTTA
* *
95835491 AATATTTAAATATTTT
1 TATATTTAAATATTTA
95835507 TATATT
1 TATATT
95835513 ATATATACAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 2 0.07
15 10 0.34
16 17 0.59
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
TATATTTAAATATTTA
Found at i:95836634 original size:23 final size:24
Alignment explanation
Indices: 95836590--95836635 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
95836580 AATATGTATA
* **
95836590 ATAATATCATAAAATATTATTAAC
1 ATAATATCAGAAAATACAATTAAC
95836614 ATAATAT-AGAAAATACAATTAA
1 ATAATATCAGAAAATACAATTAA
95836636 ACATGCTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (24 bp):
ATAATATCAGAAAATACAATTAAC
Found at i:95836828 original size:21 final size:20
Alignment explanation
Indices: 95836799--95836838 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
95836789 TTAAAAAATA
95836799 TATTTATATATAA-TATATAG
1 TATTTATATA-AATTATATAG
95836819 TATTTAATATAAATTATATA
1 TATTT-ATATAAATTATATA
95836839 AAAATAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTTATATAAATTATATAG
Found at i:95843067 original size:12 final size:13
Alignment explanation
Indices: 95843050--95843082 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
95843040 TGACGATTTT
95843050 AAAAAAAAAAT-A
1 AAAAAAAAAATGA
*
95843062 AAAAAAAATATGA
1 AAAAAAAAAATGA
95843075 AAAAAAAA
1 AAAAAAAA
95843083 TCAAATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.88, C:0.00, G:0.03, T:0.09
Consensus pattern (13 bp):
AAAAAAAAAATGA
Found at i:95843083 original size:13 final size:12
Alignment explanation
Indices: 95843049--95843083 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
95843039 GTGACGATTT
95843049 TAAAAAAAAA-A
1 TAAAAAAAAATA
95843060 TAAAAAAAAATA
1 TAAAAAAAAATA
95843072 TGAAAAAAAAAT
1 T-AAAAAAAAAT
95843084 CAAATTAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 10 0.45
12 2 0.09
13 10 0.45
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (12 bp):
TAAAAAAAAATA
Found at i:95848320 original size:102 final size:105
Alignment explanation
Indices: 95848142--95848379 Score: 275
Period size: 107 Copynumber: 2.3 Consensus size: 105
95848132 TATGATTTGG
** ** * * *
95848142 ATTAAAGTGCATGATTATTGTTTGGTTATTGTACATGACAGAAATGGATTTTTTTGTATTAAATT
1 ATTAAAGTGTTTGATTATTGTTT-GCCA-TGTACATGACAAAAATAGATTTGTTTGTATTAAATT
* *
95848207 ATTT-TTGT-T-TTGGTTATTGTCTACCATTGCCTCGGTTGT
64 ATTTGTTGTGTATTGGTTATTATCTACCATTGCCTAGGTTGT
* *
95848246 ATTAAAGTGTTTGGTTATTGTTTGCCATGTATATGACAAAAATAGATTTGTTTGTATTAAATTAT
1 ATTAAAGTGTTTGATTATTGTTTGCCATGTACATGACAAAAATAGATTTGTTTGTATTAAATTAT
* ***
95848311 TTGGTTTTTGTATTGGTTATTATCTGTTATTGCCTAGGTTGT
66 TT-G-TTGTGTATTGGTTATTATCTACCATTGCCTAGGTTGT
*
95848353 ATTAAAGTGTTTGATTATTTTTTGCCA
1 ATTAAAGTGTTTGATTATTGTTTGCCA
95848380 CTACCTTTAT
Statistics
Matches: 112, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
102 36 0.32
103 2 0.02
104 20 0.18
105 3 0.03
106 1 0.01
107 50 0.45
ACGTcount: A:0.24, C:0.07, G:0.19, T:0.50
Consensus pattern (105 bp):
ATTAAAGTGTTTGATTATTGTTTGCCATGTACATGACAAAAATAGATTTGTTTGTATTAAATTAT
TTGTTGTGTATTGGTTATTATCTACCATTGCCTAGGTTGT
Found at i:95852988 original size:21 final size:20
Alignment explanation
Indices: 95852972--95853048 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 20
95852962 GTTCAGCACG
*
95852972 AAGCTACCCCAACTCAGTAA
1 AAGCTACCCCAACTCAGCAA
* * *
95852992 TAACCTACTCTAACTCAGCAAA
1 -AAGCTACCCCAACTCAGC-AA
* *
95853014 AAGCTGCCCCAACTCATCAA
1 AAGCTACCCCAACTCAGCAA
*
95853034 CAAACTACCCCAACT
1 -AAGCTACCCCAACT
95853049 TACCAATAAG
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.05
21 39 0.91
22 2 0.05
ACGTcount: A:0.39, C:0.38, G:0.06, T:0.17
Consensus pattern (20 bp):
AAGCTACCCCAACTCAGCAA
Found at i:95859963 original size:21 final size:21
Alignment explanation
Indices: 95859937--95859982 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
95859927 ATTAGAGAAA
95859937 AAGTGGTAAATGGCACCATAC
1 AAGTGGTAAATGGCACCATAC
**
95859958 AAGTGGTCGATGGCACCATAC
1 AAGTGGTAAATGGCACCATAC
95859979 AAGT
1 AAGT
95859983 TAACTTTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (21 bp):
AAGTGGTAAATGGCACCATAC
Found at i:95861243 original size:14 final size:14
Alignment explanation
Indices: 95861224--95861253 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
95861214 ATAAGTACAG
*
95861224 TAGAGGGTTATTTA
1 TAGAGGCTTATTTA
95861238 TAGAGGCTTATTTA
1 TAGAGGCTTATTTA
95861252 TA
1 TA
95861254 CTGAGCATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.43
Consensus pattern (14 bp):
TAGAGGCTTATTTA
Found at i:95869196 original size:45 final size:45
Alignment explanation
Indices: 95869091--95869224 Score: 146
Period size: 45 Copynumber: 3.0 Consensus size: 45
95869081 TCCAATCACT
* * * * *
95869091 CCAA-ATTTACAGATAAGCTGCTAAGTAGGTTGTGGAT-AAACCA
1 CCAATATTCACAGACAAGCTGCCATGTAGGTTGTGGATGAAGCCA
* ** *
95869134 CTAATATTTGCAGACAAGTTGCCATGTAGGTTGTGGATGAAGCCA
1 CCAATATTCACAGACAAGCTGCCATGTAGGTTGTGGATGAAGCCA
* * *
95869179 CCAATATTCATAGACAAGCTGTCATATAGGTTGTGGATGAAGCCA
1 CCAATATTCACAGACAAGCTGCCATGTAGGTTGTGGATGAAGCCA
95869224 C
1 C
95869225 TAATTCTTCC
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
43 3 0.04
44 28 0.37
45 44 0.59
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (45 bp):
CCAATATTCACAGACAAGCTGCCATGTAGGTTGTGGATGAAGCCA
Found at i:95870102 original size:13 final size:13
Alignment explanation
Indices: 95870084--95870120 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
95870074 AGATAATTAG
95870084 CAAATCATACATA
1 CAAATCATACATA
95870097 CAAATCATACATA
1 CAAATCATACATA
*
95870110 TAAACTCATAC
1 CAAA-TCATAC
95870121 CAAACTATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (13 bp):
CAAATCATACATA
Found at i:95871504 original size:19 final size:18
Alignment explanation
Indices: 95871471--95871518 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
95871461 ATTTTCCCTT
* *
95871471 TTTCTTTTTCTTTTCTTC-
1 TTTCTTTCTCTTTTC-ACG
95871489 TTTCTTTCTCTCTTTCACG
1 TTTCTTTCTCT-TTTCACG
95871508 TTTCTTTCTCT
1 TTTCTTTCTCT
95871519 GTAATTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTCTTTCTCTTTTCACG
Found at i:95874965 original size:27 final size:27
Alignment explanation
Indices: 95874935--95875020 Score: 104
Period size: 27 Copynumber: 3.2 Consensus size: 27
95874925 AAAACATCAC
*
95874935 GAAAAGGAAGCTTTTGTGGCTATCTAT
1 GAAAAGGAAGCCTTTGTGGCTATCTAT
*
95874962 GAAAAGGAAGCCTTTATGGTCATAT-T-T
1 GAAAAGGAAGCCTTTGTGG-C-TATCTAT
* *
95874989 GAAAAGGAAGCCTTCGTGGCGATCTAT
1 GAAAAGGAAGCCTTTGTGGCTATCTAT
95875016 GAAAA
1 GAAAA
95875021 CAATGCCCTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 41 0.82
28 2 0.04
29 3 0.06
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.28
Consensus pattern (27 bp):
GAAAAGGAAGCCTTTGTGGCTATCTAT
Found at i:95877524 original size:21 final size:21
Alignment explanation
Indices: 95877500--95877591 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
95877490 CAAGTGGTTG
* *
95877500 CCCCAATTCAGCAAGAAGCTA
1 CCCCAACTCAGCAAAAAGCTA
*
95877521 CCCCAACTCAGCAACAAGCTA
1 CCCCAACTCAGCAAAAAGCTA
*
95877542 CTCCAACTCAGCAAAAAGCTA
1 CCCCAACTCAGCAAAAAGCTA
*
95877563 CCCCAACTCATCAACAAA-CTA
1 CCCCAACTCAGCAA-AAAGCTA
*
95877584 CCTCAACT
1 CCCCAACT
95877592 TACCAACAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
21 60 0.95
22 3 0.05
ACGTcount: A:0.39, C:0.39, G:0.08, T:0.14
Consensus pattern (21 bp):
CCCCAACTCAGCAAAAAGCTA
Found at i:95877591 original size:42 final size:42
Alignment explanation
Indices: 95877502--95877584 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
95877492 AGTGGTTGCC
* * *
95877502 CCAATTCAGCAAGAAGCTACCCCAACTCAGCAACAAGCTACT
1 CCAACTCAGCAAAAAGCTACCCCAACTCAGCAACAAACTACT
*
95877544 CCAACTCAGCAAAAAGCTACCCCAACTCATCAACAAACTAC
1 CCAACTCAGCAAAAAGCTACCCCAACTCAGCAACAAACTAC
95877585 CTCAACTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.41, C:0.37, G:0.08, T:0.13
Consensus pattern (42 bp):
CCAACTCAGCAAAAAGCTACCCCAACTCAGCAACAAACTACT
Found at i:95881567 original size:24 final size:25
Alignment explanation
Indices: 95881540--95881594 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
95881530 CATTAATGAT
*
95881540 TTTAAATTA-TTTTTTA-TCATTTAC
1 TTTAAATTACTTTTCTAGT-ATTTAC
* *
95881564 TTTAAGTTACTTTTCTAGTATTTAT
1 TTTAAATTACTTTTCTAGTATTTAC
95881589 TTTAAA
1 TTTAAA
95881595 CTCTTTACAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 8 0.32
25 16 0.64
26 1 0.04
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTAAATTACTTTTCTAGTATTTAC
Found at i:95885359 original size:19 final size:20
Alignment explanation
Indices: 95885332--95885374 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
95885322 TCTTTTTGCA
* *
95885332 TTCATTCATTTGCATTACAT
1 TTCATTCATATGCATTAAAT
95885352 TTCA-TCATATGCATTAAAT
1 TTCATTCATATGCATTAAAT
95885371 TTCA
1 TTCA
95885375 CGAAAAGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATTCATATGCATTAAAT
Found at i:95893899 original size:45 final size:45
Alignment explanation
Indices: 95893726--95893931 Score: 131
Period size: 45 Copynumber: 4.6 Consensus size: 45
95893716 TCTACCATGG
* *
95893726 CAAATCTTATCTCTCTGAAATTGCAGTAGAGCAGATTAAAGCCATTAG
1 CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAG--A-TAA
* * ** * * *
95893774 C--A--TTATCTC-CTGAAGATGCAGTGGAGTGGTTTGAAA-TTAC
1 CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATT-AAAGATAA
* * * * ** *
95893814 CAAGTCTTATTTCCCTGAAGTTGCAGTGGAATAGACTAAAGATAA
1 CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGATAA
*
95893859 CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCT-A
1 CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGATAA
* **
95893903 TAAATCCCATAC-CTCTGAAGTTGCAGTAG
1 CAAATCTTAT-CTCTCTGAAGTTGCAGTAG
95893932 GTCGGATCAA
Statistics
Matches: 122, Mismatches: 28, Indels: 20
0.72 0.16 0.12
Matches are distributed among these distances:
40 3 0.02
43 17 0.14
44 44 0.36
45 56 0.46
46 1 0.01
48 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (45 bp):
CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGATAA
Found at i:95894062 original size:227 final size:223
Alignment explanation
Indices: 95893627--95894054 Score: 551
Period size: 227 Copynumber: 1.9 Consensus size: 223
95893617 GAGCATATCG
* * *
95893627 AAGATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAGGCTAAATCCTATACATCT
1 AAGATAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTAAATCCCATACATCT
*
95893692 GAAGATGCAGTGGGTCGGATCAAATCTACCATGGCAAATCTTATCTCTCTGAAATTGCAGTAGAG
66 GAAGATGCAGTAGGTCGGATCAAATCTACCATGGCAAATCTTATCTCTCTGAAATTGCAGTAGAG
* * * * ** *
95893757 CAGATTAAAGCCATTAGCATTATCTCCTGAAGATGCAGTGGAGTGGTTTGAAATTACCAAGTCTT
131 CAGATTAAAGCCA-TAACATCATCTCCTAAAGATGCAATGGACAGGTTTGAAATTACCAAATCTT
*
95893822 ATTTCCCTGAAGTTGCAGTGGAATAGACTA
195 A-TGCCCTGAAGTTGCAGTGGAATAGACTA
*
95893852 AAGATAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAATCCCATACCT
1 AAGATAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGC--TAAATCCCATACAT
* * * *
95893917 CTGAAGTTGCAGTAGGTCGGATCAAGT-TACCATGGCAAATCTTATCTC-CTTGAAGTTGCAGTG
64 CTGAAGATGCAGTAGGTCGGATCAAATCTACCATGGCAAATCTTATCTCTC-TGAAATTGCAGTA
* * * *
95893980 GAGTAGATTGAAGTCGCA-AACCTCATCTCCCTAAAGATGCAATGGAACAGG-TTGAAATTATCA
128 GAGCAGATTAAAG-C-CATAACATCATCT-CCTAAAGATGCAATGG-ACAGGTTTGAAATTACCA
95894043 AATCTTA-GCCCT
189 AATCTTATGCCCT
95894055 TTGAAGTTCT
Statistics
Matches: 175, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
225 52 0.30
226 50 0.29
227 68 0.39
228 5 0.03
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (223 bp):
AAGATAACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTAAATCCCATACATCT
GAAGATGCAGTAGGTCGGATCAAATCTACCATGGCAAATCTTATCTCTCTGAAATTGCAGTAGAG
CAGATTAAAGCCATAACATCATCTCCTAAAGATGCAATGGACAGGTTTGAAATTACCAAATCTTA
TGCCCTGAAGTTGCAGTGGAATAGACTA
Found at i:95895615 original size:22 final size:22
Alignment explanation
Indices: 95895590--95895634 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
95895580 CTATTATATG
95895590 TATTATCCATTTTAAATTGTTT
1 TATTATCCATTTTAAATTGTTT
** *
95895612 TATTATGTATTTTAAATTTTTT
1 TATTATCCATTTTAAATTGTTT
95895634 T
1 T
95895635 TTGTATGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (22 bp):
TATTATCCATTTTAAATTGTTT
Found at i:95895642 original size:23 final size:22
Alignment explanation
Indices: 95895598--95895640 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
95895588 TGTATTATCC
95895598 ATTTTAAATTGTTTTATTATGT
1 ATTTTAAATTGTTTTATTATGT
95895620 ATTTTAAATT-TTTT-TT-TGT
1 ATTTTAAATTGTTTTATTATGT
95895639 AT
1 AT
95895641 GTTATTACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 2 0.10
21 4 0.19
22 10 0.48
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (22 bp):
ATTTTAAATTGTTTTATTATGT
Found at i:95906076 original size:20 final size:20
Alignment explanation
Indices: 95906053--95906090 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
95906043 CTGCCTACCA
95906053 TTTTTTTCTTCTTTTTGCCC
1 TTTTTTTCTTCTTTTTGCCC
* *
95906073 TTTTTTTTTTTTTTTTGC
1 TTTTTTTCTTCTTTTTGC
95906091 ATGTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTTTCTTCTTTTTGCCC
Found at i:95908085 original size:27 final size:27
Alignment explanation
Indices: 95908055--95908106 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
95908045 TTTTAAGTCT
95908055 ATATATGTTATTTTAATTT-TTTTAAAA
1 ATATAT-TTATTTTAATTTATTTTAAAA
*
95908082 ATATATTTATTTTATTTTATTTTAA
1 ATATATTTATTTTAATTTATTTTAA
95908107 TATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (27 bp):
ATATATTTATTTTAATTTATTTTAAAA
Found at i:95908562 original size:21 final size:22
Alignment explanation
Indices: 95908515--95908563 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
95908505 CCTTGAATCT
*
95908515 TTAAACAATGAACCTCAAACTC
1 TTAAACAATGAACCTCAAACCC
*
95908537 ATAAACAAT-AACC-CTAAACCC
1 TTAAACAATGAACCTC-AAACCC
95908558 TTAAAC
1 TTAAAC
95908564 GTGAACTCTG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 8 0.35
ACGTcount: A:0.49, C:0.29, G:0.02, T:0.20
Consensus pattern (22 bp):
TTAAACAATGAACCTCAAACCC
Found at i:95908617 original size:21 final size:21
Alignment explanation
Indices: 95908550--95908617 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
95908540 AACAATAACC
* *
95908550 CTAAACCCTTAAAC-GTGAACT
1 CTAAA-CCTTAAACTTTAAACT
* *
95908571 CTGAACCTTAAA-TCTCAAACAT
1 CTAAACCTTAAACT-TTAAAC-T
95908593 -TAAACCTTAAACTTTAAACT
1 CTAAACCTTAAACTTTAAACT
95908613 CTAAA
1 CTAAA
95908618 TCCAAACCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
20 8 0.22
21 26 0.72
22 2 0.06
ACGTcount: A:0.43, C:0.25, G:0.04, T:0.28
Consensus pattern (21 bp):
CTAAACCTTAAACTTTAAACT
Found at i:95913587 original size:29 final size:29
Alignment explanation
Indices: 95913554--95913618 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
95913544 TGCTCTATTT
95913554 TTAAATTT-TTTTTGTGT-ACATTATTGATA
1 TTAAATTTCTTTTT-T-TCACATTATTGATA
* *
95913583 TTAAATTTCTTTTTTTCACATTATTTATT
1 TTAAATTTCTTTTTTTCACATTATTGATA
95913612 TTAAATT
1 TTAAATT
95913619 CATTTCTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.03
29 26 0.81
30 5 0.16
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.62
Consensus pattern (29 bp):
TTAAATTTCTTTTTTTCACATTATTGATA
Found at i:95914700 original size:15 final size:15
Alignment explanation
Indices: 95914682--95914728 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
95914672 TTATTATTAC
95914682 TAAATTAAAATTTTA
1 TAAATTAAAATTTTA
**
95914697 TAAATTATAAATGACT-
1 TAAATTA-AAAT-TTTA
95914713 TAAATTAAAATTTTA
1 TAAATTAAAATTTTA
95914728 T
1 T
95914729 CATTTTAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
14 1 0.04
15 12 0.48
16 11 0.44
17 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (15 bp):
TAAATTAAAATTTTA
Found at i:95915254 original size:22 final size:22
Alignment explanation
Indices: 95915202--95915245 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
95915192 TTTTTTGAAT
* *
95915202 TTTGACTTTTGTTTCAATTGGTG
1 TTTG-CTTTTGTTCCAATTGATG
95915225 TTTGCTTTTGTTCCAATTGAT
1 TTTGCTTTTGTTCCAATTGAT
95915246 TTGTTCTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.14, C:0.11, G:0.18, T:0.57
Consensus pattern (22 bp):
TTTGCTTTTGTTCCAATTGATG
Found at i:95916471 original size:22 final size:22
Alignment explanation
Indices: 95916446--95916503 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
95916436 CATGAAGCAA
95916446 CCCCATACCCCCACTACAACAG
1 CCCCATACCCCCACTACAACAG
95916468 CCCCATACCCCCACTACAACAG
1 CCCCATACCCCCACTACAACAG
* *
95916490 TCCCATACCTCCAC
1 CCCCATACCCCCAC
95916504 AGTCCTCGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.29, C:0.55, G:0.03, T:0.12
Consensus pattern (22 bp):
CCCCATACCCCCACTACAACAG
Found at i:95918300 original size:27 final size:28
Alignment explanation
Indices: 95918259--95918320 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
95918249 CTATCTTATG
* *
95918259 TATATACTTCTAACACTA-TA-TATATA
1 TATATATTTCCAACACTACTACTATATA
*
95918285 TAGTATATTTCCAACACTACTACTATTTA
1 TA-TATATTTCCAACACTACTACTATATA
95918314 TATATAT
1 TATATAT
95918321 ATATACATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
26 2 0.07
27 14 0.47
28 7 0.23
29 7 0.23
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.44
Consensus pattern (28 bp):
TATATATTTCCAACACTACTACTATATA
Found at i:95919954 original size:19 final size:19
Alignment explanation
Indices: 95919930--95919966 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
95919920 AATTTACTCT
95919930 CTGATCAAACATACAAAAA
1 CTGATCAAACATACAAAAA
95919949 CTGATCAAACATACAAAA
1 CTGATCAAACATACAAAA
95919967 TGAACTTGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.22, G:0.05, T:0.16
Consensus pattern (19 bp):
CTGATCAAACATACAAAAA
Found at i:95922418 original size:22 final size:22
Alignment explanation
Indices: 95922393--95922436 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
95922383 TAGTCATATA
95922393 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
95922415 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
95922437 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:95922490 original size:15 final size:16
Alignment explanation
Indices: 95922460--95922501 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
95922450 AATTTTATTT
95922460 TAATAATAAGTTTTAAA
1 TAATAATAA-TTTTAAA
95922477 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
95922492 TAA-AATAATT
1 TAATAATAATT
95922502 CACATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:95922673 original size:24 final size:24
Alignment explanation
Indices: 95922647--95922691 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
95922637 GTAATTTAGT
*
95922647 TTTTGTACTTTTA-TTTTCAAAAA
1 TTTTGTACCTTTACTTTTCAAAAA
*
95922670 TTTTGTCCCTTTACTTTTCAAA
1 TTTTGTACCTTTACTTTTCAAA
95922692 TTTGAAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTTGTACCTTTACTTTTCAAAAA
Found at i:95923062 original size:14 final size:13
Alignment explanation
Indices: 95923043--95923081 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 13
95923033 CCAGGAAAGT
95923043 AAATCATTTTCCAG
1 AAATCATTTTCC-G
95923057 AAATCATTTTCCG
1 AAATCATTTTCCG
95923070 AAAGTCATTTTC
1 AAA-TCATTTTC
95923082 AGTGAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (13 bp):
AAATCATTTTCCG
Found at i:95924060 original size:15 final size:15
Alignment explanation
Indices: 95924040--95924070 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
95924030 TAAAAATATG
*
95924040 TATAAACCTAACAAA
1 TATAAACCCAACAAA
95924055 TATAAACCCAACAAA
1 TATAAACCCAACAAA
95924070 T
1 T
95924071 TTAATTGTAT
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:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (15 bp):
TATAAACCCAACAAA
Found at i:95925221 original size:21 final size:21
Alignment explanation
Indices: 95925197--95925240 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
95925187 GCATCGATAC
* *
95925197 TTTTTGTCAAGTATCAATAAA
1 TTTTAGTCAAGCATCAATAAA
* *
95925218 TTTTAGTTAAGCATCGATAAA
1 TTTTAGTCAAGCATCAATAAA
95925239 TT
1 TT
95925241 CATAGTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (21 bp):
TTTTAGTCAAGCATCAATAAA
Found at i:95934861 original size:2 final size:2
Alignment explanation
Indices: 95934856--95934931 Score: 57
Period size: 2 Copynumber: 38.5 Consensus size: 2
95934846 GCATTCCCCC
* * *
95934856 CT CT CT CT CT CT CT CT CT GC- CT CT CC CT CC CT CC CT CT CT CT
1 CT CT CT CT CT CT CT CT CT -CT CT CT CT CT CT CT CT CT CT CT CT
* * * * *
95934898 CC CT CG CC CT CT CC CT CT CC CT CT CT CT C- CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
95934932 AATTTAACAC
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
1 2 0.04
2 53 0.95
3 1 0.02
ACGTcount: A:0.00, C:0.61, G:0.03, T:0.37
Consensus pattern (2 bp):
CT
Found at i:95934879 original size:14 final size:14
Alignment explanation
Indices: 95934862--95934927 Score: 73
Period size: 14 Copynumber: 4.7 Consensus size: 14
95934852 CCCCCTCTCT
* *
95934862 CTCTCTCTCTCTGC
1 CTCTCTCTCCCTCC
*
95934876 CTCTCCCTCCCTCC
1 CTCTCTCTCCCTCC
95934890 CTCTCTCTCCCTCGC
1 CTCTCTCTCCCTC-C
95934905 C-CTCTC-CCTCTCC
1 CTCTCTCTCC-CTCC
95934918 CTCTCTCTCC
1 CTCTCTCTCC
95934928 TCTCAATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
13 4 0.09
14 36 0.82
15 4 0.09
ACGTcount: A:0.00, C:0.62, G:0.03, T:0.35
Consensus pattern (14 bp):
CTCTCTCTCCCTCC
Found at i:95934902 original size:24 final size:22
Alignment explanation
Indices: 95934860--95934931 Score: 74
Period size: 24 Copynumber: 3.2 Consensus size: 22
95934850 TCCCCCCTCT
* *
95934860 CTCTCTCTCTCTCTGCCTCTCC
1 CTCTCCCTCTCTCTCCCTCTCC
*
95934882 CTCCCTCCCTCTCTCTCCCTCGCC
1 CT--CTCCCTCTCTCTCCCTCTCC
* *
95934906 CTCTCCCTCTCCCTCTCTCT-C
1 CTCTCCCTCTCTCTCCCTCTCC
95934927 CTCTC
1 CTCTC
95934932 AATTTAACAC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
21 6 0.14
22 17 0.40
24 19 0.45
ACGTcount: A:0.00, C:0.61, G:0.03, T:0.36
Consensus pattern (22 bp):
CTCTCCCTCTCTCTCCCTCTCC
Found at i:95946283 original size:33 final size:33
Alignment explanation
Indices: 95946241--95946337 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
95946231 TCTTCTTGAC
*
95946241 ATTCCAGCTCCTGTCCAGCAACCAAACACTTCA
1 ATTCCAGCTCCTGTCCAGCAACCAAACACTCCA
*
95946274 ATTCCAGCTCCTGTCCAGCAACCAAACACTCCT
1 ATTCCAGCTCCTGTCCAGCAACCAAACACTCCA
*
95946307 ATTCCAGCTCCTGTCCAGCAATCAAACACTC
1 ATTCCAGCTCCTGTCCAGCAACCAAACACTC
95946338 TCACTCAGAC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.29, C:0.40, G:0.09, T:0.22
Consensus pattern (33 bp):
ATTCCAGCTCCTGTCCAGCAACCAAACACTCCA
Found at i:95951148 original size:20 final size:20
Alignment explanation
Indices: 95951123--95951162 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
95951113 ACAGCATTGA
*
95951123 ATAGCTAATCTTTAGGGATT
1 ATAGCTAATCTTTAGAGATT
* *
95951143 ATAGCTGATTTTTAGAGATT
1 ATAGCTAATCTTTAGAGATT
95951163 CTAATTAGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (20 bp):
ATAGCTAATCTTTAGAGATT
Found at i:95953078 original size:13 final size:13
Alignment explanation
Indices: 95953062--95953112 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 13
95953052 TAAGTTTAAA
95953062 AATTAAAATTTTT
1 AATTAAAATTTTT
*
95953075 AATTAAAAATTTT
1 AATTAAAATTTTT
95953088 AATTAGTTAAATTTTTT
1 AATTA---AAA-TTTTT
95953105 AATTAAAA
1 AATTAAAA
95953113 ATCTATTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 17 0.53
14 3 0.09
16 3 0.09
17 9 0.28
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
AATTAAAATTTTT
Found at i:95963547 original size:16 final size:16
Alignment explanation
Indices: 95963526--95963578 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
95963516 AGAGTGGAAA
95963526 GAAAATTAGAAGGATG
1 GAAAATTAGAAGGATG
* *
95963542 GAAAATT-GAAGGGGTA
1 GAAAATTAGAA-GGATG
*
95963558 GAAAACTAGAAGGATG
1 GAAAATTAGAAGGATG
95963574 GAAAA
1 GAAAA
95963579 CATAATTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 3 0.10
16 24 0.80
17 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.32, T:0.15
Consensus pattern (16 bp):
GAAAATTAGAAGGATG
Found at i:95968148 original size:4 final size:4
Alignment explanation
Indices: 95968139--95968209 Score: 133
Period size: 4 Copynumber: 17.5 Consensus size: 4
95968129 AATTTCATAT
95968139 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG
95968187 ATAG ATAG ATAG ATAG ATCAG AT
1 ATAG ATAG ATAG ATAG AT-AG AT
95968210 TCAAATATAG
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
4 62 0.94
5 4 0.06
ACGTcount: A:0.49, C:0.01, G:0.24, T:0.25
Consensus pattern (4 bp):
ATAG
Found at i:95968866 original size:27 final size:27
Alignment explanation
Indices: 95968836--95968899 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
95968826 AATGTGCAAT
*
95968836 ATGTGAAATTATAGGGTTG-TCGTCGTG
1 ATGTGAAATTACAGGGTTGAT-GTCGTG
*
95968863 ATGTGAAATTGCAGGGTTGATGTCGTG
1 ATGTGAAATTACAGGGTTGATGTCGTG
*
95968890 ACGTGAAATT
1 ATGTGAAATT
95968900 TCGCGTAGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.33, T:0.34
Consensus pattern (27 bp):
ATGTGAAATTACAGGGTTGATGTCGTG
Found at i:95970405 original size:25 final size:25
Alignment explanation
Indices: 95970343--95970396 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
95970333 AGCTTGCAAT
95970343 AGCATCCCATTATTTAGTGCTTATG
1 AGCATCCCATTATTTAGTGCTTATG
95970368 AGCATCCCATTATTTAGCT-CTTATG
1 AGCATCCCATTATTTAG-TGCTTATG
95970393 AGCA
1 AGCA
95970397 ATCCGTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (25 bp):
AGCATCCCATTATTTAGTGCTTATG
Done.