Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2178
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: 184922
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:16662 original size:20 final size:19
Alignment explanation
Indices: 16608--16663 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
16598 AAAACCCTTA
*
16608 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
16628 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
16648 AATGTATCGATACATA
1 AAAGTATCGATACATA
16664 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:16756 original size:32 final size:33
Alignment explanation
Indices: 16715--16776 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
16705 TAGCCAAACT
**
16715 TGTATCGATACACAAAGTA-TGTATCGATATAA
1 TGTATCGATACACAAAAAATTGTATCGATATAA
16747 TGTATCGATACACAAAAAATTGTATCGATA
1 TGTATCGATACACAAAAAATTGTATCGATA
16777 CATTGGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.31
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATATAA
Found at i:20841 original size:15 final size:15
Alignment explanation
Indices: 20821--20851 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20811 TAAAAATGTC
*
20821 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
20836 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
20851 C
1 C
20852 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:23067 original size:79 final size:79
Alignment explanation
Indices: 22961--23162 Score: 226
Period size: 79 Copynumber: 2.6 Consensus size: 79
22951 AATAACGGGG
* * * * * * *
22961 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAG
*
23025 AAAAAAAAATCAGGA
65 AAAAAAAAACCAGGA
* * *
23040 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
* * * * *
23105 GAATAAAGCCGGGG
66 AAAAAAAACCAGGA
* *
23119 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
23163 GAAATAACAA
Statistics
Matches: 103, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 1 0.01
79 102 0.99
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (79 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAAACCAGGA
Found at i:23170 original size:28 final size:28
Alignment explanation
Indices: 23114--23185 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
23104 GGAATAAAGC
** *
23114 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
23142 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
**
23170 CAAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
23186 TCGACTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:23238 original size:52 final size:52
Alignment explanation
Indices: 23174--23561 Score: 192
Period size: 52 Copynumber: 7.4 Consensus size: 52
23164 AAATAACAAG
* * * * *
23174 GTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTTGGAAATAAAATC-GGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGT-GTTTTGGAAATAAAACCAGGA
* * * * * *
23226 GTTGGAGTATCCTCGATTAAG-GGAAAATTGGTGTTTCGAAAATAAAACC-GGG
1 GTTGGAGTATCCCCGATT--GTGAAAAATTAGTGTTTTGGAAATAAAACCAGGA
* *
23278 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCAGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTAGTGTTTTGGAAATAAAACCAGGA
* * * * * **
23331 -TTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCAGG-
1 GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCAGGA
* * ** * * * * *
23381 GTTGGAGTATCCCC--TCG-GAAATAA--CG-GGGTTGGAGTATCCCCGATGATCAACGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AATTAGTGTTTTGGA-AAT-----A-AAACCA-GGA
* *
23436 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATC-GGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATTAGTG--TTTTGGAAATAAAACCAGGA
** * * *
23490 GTTGGAGTATCCCCGATCAT-AGAAAATTAGTGTCTTGAAAATAAAATC-GGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTAGTGTTTTGGAAATAAAACCAGGA
*
23541 GTTGGAATATCCCCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
23562 GAGAATTGAG
Statistics
Matches: 254, Mismatches: 55, Indels: 54
0.70 0.15 0.15
Matches are distributed among these distances:
46 5 0.02
47 2 0.01
48 4 0.02
49 3 0.01
50 1 0.00
51 70 0.28
52 89 0.35
53 23 0.09
54 24 0.09
55 14 0.06
56 1 0.00
57 3 0.01
58 5 0.02
59 1 0.00
60 1 0.00
61 1 0.00
62 2 0.01
63 5 0.02
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.29
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAACCAGGA
Found at i:23386 original size:51 final size:52
Alignment explanation
Indices: 23265--23394 Score: 154
Period size: 51 Copynumber: 2.5 Consensus size: 52
23255 GGTGTTTCGA
* * * * *
23265 AAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG
1 AAATAAAACCAGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
* * * *
23317 CAATAAAACCAGGATTGGAATATCCCCGATTAT-GAAAAATCAATATTTTGG
1 AAATAAAACCAGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
**
23368 AAATAAAGTCAGGGTTGGAGTATCCCC
1 AAATAAAACCAGGGTTGGAGTATCCCC
23395 TCGGAAATAA
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
51 36 0.56
52 28 0.44
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (52 bp):
AAATAAAACCAGGGTTGGAGTATCCCCGATTATGGAAAAATCAATATTTTAG
Found at i:23408 original size:263 final size:263
Alignment explanation
Indices: 23068--23563 Score: 750
Period size: 263 Copynumber: 1.9 Consensus size: 263
23058 AATAACGGGG
* * * *
23068 TTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCCCCT
1 TTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCAGGGTTGGAGTATCCCCT
* *
23133 CGGAAGTAACGGGGTTGGAGTATCCCCGATGAAAT-AACAAGGTTGGAGTATCCTCGACTGTGAA
66 CGGAAATAACGGGGTTGGAGTATCCCCGATG--ATCAACAAGGTTGGAGTATCCCCGACTGTGAA
* * *
23197 -AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTA-AGGGAAAATTGGTG
129 GAAATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATCATA--GAAAATTAGTG
* *
23259 T-TTCGAAAATAAAACCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
192 TCTT-GAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAA
23323 AACCAGGA
256 AACCAGGA
* *
23331 TTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCAGGGTTGGAGTATCCCCT
1 TTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCAGGGTTGGAGTATCCCCT
** *
23396 CGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACGGGGTTGGAGTATCCCCGATTGTGAAGA
66 CGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGTGAAGA
*
23461 AATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATCATAGAAAATTAGTGTCTT
131 AATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATCATAGAAAATTAGTGTCTT
*
23526 GAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
196 GAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGA
23564 GAATTGAGAA
Statistics
Matches: 210, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
261 2 0.01
262 25 0.12
263 143 0.68
264 39 0.19
265 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (263 bp):
TTGGAATATCCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCAGGGTTGGAGTATCCCCT
CGGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGTGAAGA
AATTGGTGATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATCATAGAAAATTAGTGTCTT
GAAAATAAAACCGGAGTTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAACCA
GGA
Found at i:23414 original size:28 final size:28
Alignment explanation
Indices: 23379--23449 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
23369 AATAAAGTCA
23379 GGGTTGGAGTATCCCCTCGGA-AAT-AACG
1 GGGTTGGAGTATCCCC-C-GATAATCAACG
*
23407 GGGTTGGAGTAT-CCCCGATGATCAACG
1 GGGTTGGAGTATCCCCCGATAATCAACG
23434 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
23450 GATTGTGAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 2 0.05
26 3 0.08
27 19 0.49
28 15 0.38
ACGTcount: A:0.21, C:0.23, G:0.34, T:0.23
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCCGATAATCAACG
Found at i:25939 original size:13 final size:13
Alignment explanation
Indices: 25921--25946 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25911 ACAAAGATCC
25921 ATGTATCGATACA
1 ATGTATCGATACA
25934 ATGTATCGATACA
1 ATGTATCGATACA
25947 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:25942 original size:33 final size:33
Alignment explanation
Indices: 25900--25966 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
25890 AAAATTTCCA
***
25900 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
25933 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
25966 A
1 A
25967 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:26010 original size:19 final size:18
Alignment explanation
Indices: 25986--26085 Score: 103
Period size: 19 Copynumber: 5.9 Consensus size: 18
25976 CAGTAGCTAA
25986 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
26005 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
26020 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
26037 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
26052 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
26069 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
26086 TCGTTGAATT
Statistics
Matches: 69, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.32
14 2 0.03
16 4 0.06
18 5 0.07
19 36 0.52
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:26026 original size:13 final size:13
Alignment explanation
Indices: 26008--26064 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
25998 ACAATACTTA
26008 TGTATCGATACAT
1 TGTATCGATACAT
26021 TGTATCGATACAAAACTT
1 TGTATCGATAC---A--T
26039 ATGTATCGATACAT
1 -TGTATCGATACAT
26053 TGTATCGATACA
1 TGTATCGATACA
26065 AAACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:26030 original size:32 final size:32
Alignment explanation
Indices: 25989--26083 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
25979 TAGCTAATTA
*
25989 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
26021 TGTATCGATACAAAACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
26053 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
26084 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:27281 original size:13 final size:13
Alignment explanation
Indices: 27263--27300 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
27253 CATTTTTCTT
27263 TGTATCGATACAA
1 TGTATCGATACAA
*
27276 TGTATCGATACAC
1 TGTATCGATACAA
27289 TGTATCGATACA
1 TGTATCGATACA
27301 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:27461 original size:20 final size:20
Alignment explanation
Indices: 27418--27463 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
27408 AAATCTTTTG
27418 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
27439 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
27459 CAAAA
1 CAAAA
27464 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:29870 original size:13 final size:13
Alignment explanation
Indices: 29852--29877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29842 TACACAAAGT
29852 ATGTATCGATACA
1 ATGTATCGATACA
29865 ATGTATCGATACA
1 ATGTATCGATACA
29878 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:29875 original size:32 final size:33
Alignment explanation
Indices: 29834--29897 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
29824 TAGCCAAACT
**
29834 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
29866 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
29898 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:31466 original size:13 final size:13
Alignment explanation
Indices: 31425--31473 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
31415 CGTGACAAGC
31425 CAATGTATCGATA
1 CAATGTATCGATA
*
31438 CAAT-T-T-GGT-
1 CAATGTATCGATA
31447 C-ATGTATCGATA
1 CAATGTATCGATA
31459 CAATGTATCGATA
1 CAATGTATCGATA
31472 CA
1 CA
31474 TCTTGTATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 3 0.10
11 3 0.10
12 2 0.07
13 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:31468 original size:34 final size:32
Alignment explanation
Indices: 31425--31493 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
31415 CGTGACAAGC
31425 CAATGTATCGATACAAT-TTGGTCATGTATCGATA
1 CAATGTATCGATAC-ATCTT-GT-ATGTATCGATA
31459 CAATGTATCGATACATCTTGTATGTATCGATA
1 CAATGTATCGATACATCTTGTATGTATCGATA
31491 CAA
1 CAA
31494 ACAGTTAAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 14 0.41
33 4 0.12
34 16 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATCTTGTATGTATCGATA
Found at i:31580 original size:13 final size:13
Alignment explanation
Indices: 31562--31586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31552 TACAGTGGTC
31562 ATGTATCGATACA
1 ATGTATCGATACA
31575 ATGTATCGATAC
1 ATGTATCGATAC
31587 TATGCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:34076 original size:13 final size:13
Alignment explanation
Indices: 34058--34095 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
34048 ATAAACCCTT
*
34058 TGTATCGATACAC
1 TGTATCGATACAA
34071 TGTATCGATACAA
1 TGTATCGATACAA
34084 TGTATCGATACA
1 TGTATCGATACA
34096 GAGAATGCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:40237 original size:13 final size:13
Alignment explanation
Indices: 40219--40243 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40209 ACACATAGTA
40219 TGTATCGATACAT
1 TGTATCGATACAT
40232 TGTATCGATACA
1 TGTATCGATACA
40244 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:40240 original size:32 final size:33
Alignment explanation
Indices: 40199--40266 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
40189 GTAGCTAAAC
** *
40199 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCAATACA
40231 TTGTATCGATACACCATAAAATGTATCAATACA
1 TTGTATCGATACACCATAAAATGTATCAATACA
40264 TTG
1 TTG
40267 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCAATACA
Found at i:46388 original size:13 final size:13
Alignment explanation
Indices: 46370--46408 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
46360 ACATCATTCT
46370 TTGTATCGATACA
1 TTGTATCGATACA
*
46383 TTGTATCGATATA
1 TTGTATCGATACA
*
46396 CTGTATCGATACA
1 TTGTATCGATACA
46409 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:46872 original size:20 final size:21
Alignment explanation
Indices: 46847--46889 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
46837 GCAGCACCTA
*
46847 CCAGGTCGCGACC-GGCAGTC
1 CCAGGTCGCAACCGGGCAGTC
46867 CCAGGTCGCAACCGGGCAGTC
1 CCAGGTCGCAACCGGGCAGTC
46888 CC
1 CC
46890 CACACTAGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.16, C:0.42, G:0.33, T:0.09
Consensus pattern (21 bp):
CCAGGTCGCAACCGGGCAGTC
Found at i:48919 original size:13 final size:13
Alignment explanation
Indices: 48901--48925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48891 ACACATAGTA
48901 TGTATCGATACAT
1 TGTATCGATACAT
48914 TGTATCGATACA
1 TGTATCGATACA
48926 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:48922 original size:32 final size:33
Alignment explanation
Indices: 48881--48948 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
48871 GTAGCTAAAC
**
48881 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
*
48913 TTGTATCGATACACCATAAAATGTATCGATATA
1 TTGTATCGATACACCATAAAATGTATCGATACA
48946 TTG
1 TTG
48949 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:49927 original size:13 final size:13
Alignment explanation
Indices: 49886--49935 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
49876 CGTTACAAGC
49886 CAATGTATCGATA
1 CAATGTATCGATA
*
49899 CAAT-T-T-GGT-
1 CAATGTATCGATA
49908 C-ATGTATCGATA
1 CAATGTATCGATA
49920 CAATGTATCGATA
1 CAATGTATCGATA
49933 CAA
1 CAA
49936 ACAGTTAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
8 2 0.07
9 2 0.07
10 3 0.10
11 3 0.10
12 2 0.07
13 18 0.60
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:51510 original size:106 final size:107
Alignment explanation
Indices: 51326--51554 Score: 257
Period size: 106 Copynumber: 2.1 Consensus size: 107
51316 AGGTCTTATT
* ** * * * *
51326 AGCTTGTGTAGGCTTTGAGATGGGTAAGTGTCTTGCCTTTTGAGGGCTAGAGGCAGGTTAGATAA
1 AGCTTGTGTAGGCTTTAAGATGGGTAAGCATCTTGCCTTTTGAAGACTAGAGGCAGGTAAGAAAA
** * *
51391 AGTGTCCTACTCTTTGAAGACTGA-GATAGGTAGGTGCCACC
66 AGCATCCTACTCTTTGAAGACTGAGGATAGGAAAGTGCCACC
*
51432 AGCTTGTGT-GGCCTTTAAGATGGGTAAGCATCTTG-CTCTTTGAAGACTAGAGGTAGGTAAGAA
1 AGCTTGTGTAGG-CTTTAAGATGGGTAAGCATCTTGCCT-TTTGAAGACTAGAGGCAGGTAAGAA
* * * * *
51495 AAAGCATTCTGCTCTTTGAGGATTGAGGGTAGGAAAGTGCCACC
64 AAAGCATCCTACTCTTTGAAGACTGAGGATAGGAAAGTGCCACC
*
51539 AACTTGTGTAGGCTTT
1 AGCTTGTGTAGGCTTT
51555 GTGTAAGGGT
Statistics
Matches: 101, Mismatches: 18, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
105 4 0.04
106 69 0.68
107 26 0.26
108 2 0.02
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (107 bp):
AGCTTGTGTAGGCTTTAAGATGGGTAAGCATCTTGCCTTTTGAAGACTAGAGGCAGGTAAGAAAA
AGCATCCTACTCTTTGAAGACTGAGGATAGGAAAGTGCCACC
Found at i:51698 original size:106 final size:105
Alignment explanation
Indices: 51581--51872 Score: 304
Period size: 106 Copynumber: 2.8 Consensus size: 105
51571 AACATCTTTT
* * ** *
51581 TCTTTGAGGACTAAAGT-GGATAGGT-CTCACTAGCTTGTGTGGGCTTTGGGATGGGTAAGTGTT
1 TCTTTGAGGACT-AAGTAGG-TAGGTGC-CACCAGCTTGTGTGGGCTTTGAGATGGGTAAGCATC
* * * * *
51644 TTGCTTTTTGAGGGCTAGAAGTAGGTAAGATAAAA-TGTCATAC
63 TTGCTCTTTGAAGACTAGAAGTACGTAAGA-AAAAGCGTCATAC
*
51687 TCTTTGAGGACTGAGATAGGTAGGTGCCACCAGCTTGTGTGGGCTTTGAGATGGGTAAGCATCTT
1 TCTTTGAGGACTAAG-TAGGTAGGTGCCACCAGCTTGTGTGGGCTTTGAGATGGGTAAGCATCTT
* * *
51752 GCTCTTTGAAGACTAGAGGTACGTAAGAAAAAGCGTCCTGC
65 GCTCTTTGAAGACTAGAAGTACGTAAGAAAAAGCGTCATAC
* * * * * *
51793 TCTTTGAGGACTGAGGTAGGTAGGTGCCACCAACTTGTGTGGGCTTTGATATGAGTGAGCATCCT
1 TCTTTGAGGACT-AAGTAGGTAGGTGCCACCAGCTTGTGTGGGCTTTGAGATGGGTAAGCATCTT
*
51858 ACTCTTT-AAGGACTA
65 GCTCTTTGAA-GACTA
51873 AGGAAGATAA
Statistics
Matches: 158, Mismatches: 22, Indels: 12
0.82 0.11 0.06
Matches are distributed among these distances:
105 8 0.05
106 146 0.92
107 4 0.03
ACGTcount: A:0.24, C:0.15, G:0.30, T:0.31
Consensus pattern (105 bp):
TCTTTGAGGACTAAGTAGGTAGGTGCCACCAGCTTGTGTGGGCTTTGAGATGGGTAAGCATCTTG
CTCTTTGAAGACTAGAAGTACGTAAGAAAAAGCGTCATAC
Found at i:51708 original size:286 final size:287
Alignment explanation
Indices: 51206--51840 Score: 1022
Period size: 286 Copynumber: 2.2 Consensus size: 287
51196 AGGTAGGTGT
* * **
51206 AAAAAGTATCCTGCTCTTTGAGGATTGAGGGTAGGAAGGTGCCATCAACTTGTGTAGTTTTTGTG
1 AAAAAGCATCCTGCTCTTTGAGGATTGAGGGTAGGAAGGTGCCACCAACTTGTGTAGGCTTTGTG
* *
51271 TAAGGGTAAAAAAAAGCATCATTTTCTTTGAGGACTAAAGTGGATAGGTCTTATTAGCTTGTGTA
66 TAAGGGTAAAAAAAAGCATCATTTTCTTTGAGGACTAAAGTGGATAGGTCTCACTAGCTTGTGTA
* * * *
51336 GGCTTTGAGATGGGTAAGTGTCTTGCCTTTTGAGGGCTAGAGGCAGGTTAGATAAAGTGTCCTAC
131 GGCTTTGAGATGGGTAAGTGTCTTGCCTTTTGAGGGCTAGAAGCAGGTAAGATAAAATGTCATAC
51401 TCTTTGAAGACTGAGATAGGTAGGTGCCACCAGCTTGTGTGGCCTTTAAGATGGGTAAGCATCTT
196 TCTTTGAAGACTGAGATAGGTAGGTGCCACCAGCTTGTGTGGCCTTTAAGATGGGTAAGCATCTT
*
51466 GCTCTTTGAAGACTAGAGGTAGGTAAG
261 GCTCTTTGAAGACTAGAGGTACGTAAG
* *
51493 AAAAAGCATTCTGCTCTTTGAGGATTGAGGGTAGGAAAGTGCCACCAACTTGTGTAGGCTTTGTG
1 AAAAAGCATCCTGCTCTTTGAGGATTGAGGGTAGGAAGGTGCCACCAACTTGTGTAGGCTTTGTG
* *
51558 TAAGGGTAAAAAAAA-CATCTTTTTCTTTGAGGACTAAAGTGGATAGGTCTCACTAGCTTGTGTG
66 TAAGGGTAAAAAAAAGCATCATTTTCTTTGAGGACTAAAGTGGATAGGTCTCACTAGCTTGTGTA
* * * *
51622 GGCTTTGGGATGGGTAAGTGTTTTGCTTTTTGAGGGCTAGAAGTAGGTAAGATAAAATGTCATAC
131 GGCTTTGAGATGGGTAAGTGTCTTGCCTTTTGAGGGCTAGAAGCAGGTAAGATAAAATGTCATAC
* * *
51687 TCTTTGAGGACTGAGATAGGTAGGTGCCACCAGCTTGTGTGGGCTTTGAGATGGGTAAGCATCTT
196 TCTTTGAAGACTGAGATAGGTAGGTGCCACCAGCTTGTGTGGCCTTTAAGATGGGTAAGCATCTT
51752 GCTCTTTGAAGACTAGAGGTACGTAAG
261 GCTCTTTGAAGACTAGAGGTACGTAAG
* * * *
51779 AAAAAGCGTCCTGCTCTTTGAGGACTGA-GGTAGGTAGGTGCCACCAACTTGTGTGGGCTTTG
1 AAAAAGCATCCTGCTCTTTGAGGATTGAGGGTAGGAAGGTGCCACCAACTTGTGTAGGCTTTG
51841 ATATGAGTGA
Statistics
Matches: 320, Mismatches: 28, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
285 31 0.10
286 215 0.67
287 74 0.23
ACGTcount: A:0.26, C:0.14, G:0.30, T:0.31
Consensus pattern (287 bp):
AAAAAGCATCCTGCTCTTTGAGGATTGAGGGTAGGAAGGTGCCACCAACTTGTGTAGGCTTTGTG
TAAGGGTAAAAAAAAGCATCATTTTCTTTGAGGACTAAAGTGGATAGGTCTCACTAGCTTGTGTA
GGCTTTGAGATGGGTAAGTGTCTTGCCTTTTGAGGGCTAGAAGCAGGTAAGATAAAATGTCATAC
TCTTTGAAGACTGAGATAGGTAGGTGCCACCAGCTTGTGTGGCCTTTAAGATGGGTAAGCATCTT
GCTCTTTGAAGACTAGAGGTACGTAAG
Found at i:52012 original size:115 final size:113
Alignment explanation
Indices: 51875--52110 Score: 260
Period size: 115 Copynumber: 2.1 Consensus size: 113
51865 AAGGACTAAG
* *
51875 GAAGATAAGTGATGCCACCAACTTGTAT-AGGCTTTGAAGAAGAAAAAGGTATCCTACTTTTTGA
1 GAAGATAAGTGATGCCACCAACTTGTATGA-GCTTTGAAGAA-AAAAAGGCATCCTACTCTTTGA
* * * * * *
51939 GGACTAGAGTAGATAAGTGAAGAAAATGCGTCCTGCTT-TTTGAGGACTGGA
64 GAACTAAAGTAAATAAGT-AAAAAAAGGCATCCTG-TTCTTTGAGGACTGGA
* * * * * * * *
51990 GAAGATAAGTTATGCCATCAACTTGTGTGAGTTTTTAAGAATAAAAGGCATCTTGCTCTTTGAGA
1 GAAGATAAGTGATGCCACCAACTTGTATGAGCTTTGAAGAAAAAAAGGCATCCTACTCTTTGAGA
* *
52055 ACTAAAGTAAATAAGTAAAAAAAGGCATCTTGTTCTTTGAGGATTGGA
66 ACTAAAGTAAATAAGTAAAAAAAGGCATCCTGTTCTTTGAGGACTGGA
52103 GAAGATAA
1 GAAGATAA
52111 TTTGATACCT
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
112 2 0.02
113 32 0.32
114 32 0.32
115 34 0.34
116 1 0.01
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (113 bp):
GAAGATAAGTGATGCCACCAACTTGTATGAGCTTTGAAGAAAAAAAGGCATCCTACTCTTTGAGA
ACTAAAGTAAATAAGTAAAAAAAGGCATCCTGTTCTTTGAGGACTGGA
Found at i:62886 original size:3 final size:3
Alignment explanation
Indices: 62878--62989 Score: 134
Period size: 3 Copynumber: 37.3 Consensus size: 3
62868 TATGCAATGT
* * *
62878 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TCA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * ** * *
62926 TCA TAA TCA TCG TTA TTA TCA TTA TTA TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62974 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
62990 ATAGATGGTT
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:64645 original size:622 final size:599
Alignment explanation
Indices: 63464--64683 Score: 1615
Period size: 622 Copynumber: 2.0 Consensus size: 599
63454 TTTAATTTTA
* * * *
63464 ATTAATTTATCTAAAAGTTAATAATTAATTGAGAAAAATAAAGAACAAGGAATAAAGTAAGAGTA
1 ATTAATTTATCTAAAAGTTAATAATTAATTAAGAAAAATAAAGAAAAAGAAAGAAAGTAAGAGTA
* * *
63529 TTCTTAAATAGAGAATGATAAAGACCCATGTATTACACAAGTCGTGTTGATAAAGTCCCATGCTA
66 TTCTTAAACAGAGAATGATAAAGACCAATGTATTACACAAGTCGTGTTGAGAAAGTCCCATGCTA
*
63594 TATGCTTGTAAAACCTTGTCATAAATCTAAAGTGGGTTACAATGGAACAAAAAATGCTTGAAACA
131 TATACTTGTAAAACCTTGTCATAAATCTAAAGTGGGTTACAATGGAACAAAAAATGCTTGAAACA
* * * * * *
63659 GAAAGCGTTTGTTATTTCTTTCTTTTTGCAGATGATAAATGTATGCATAATAAAATTGAAATAGG
196 GAAAGCATCTGCTATTTCTTTCTTTATACAGATGATAAATGTATGCATAATAAAATTGAAATAGA
*
63724 AACTTTTTTACCACTGCAATTCACCATGCTTTTTTTTCAATTGCCACAACTTTGCAAAAACTTCC
261 AACTTTTTTACCACTGCAATTCACCATGCTTTTTTTTCAATTGCCACAACTCTGCAAAAACTTCC
* * ** **
63789 CCTATAGCAATTTTCAATATTCACAATCGAAAAAAATATAATTTTTTTGCCCCTCTCTCTTTAAT
326 ACTAGAGCAATTTTCAATATTCACAATCGAAAAAAATATAATCATTTAACCCCTCTCTCTTTAAT
*
63854 TTACATTTCTATTAATTGTTTCTTTGGTTATTTTTTAAATTAATTCTCCTGTTAGGTTCTAATTT
391 TTACATTTCTATTAATTGTTTCTTTAGTTATTTTTTAAATTAATTCTCCTGTTAGGTTCTAATTT
* * * * *
63919 TTATTTTGTAGTTCTGTAAGTTTTTTATTATTTTACATGTATTTTTTAATTTTTAACCAAAGATA
456 TTATTTGGTAATTCTGCAAGTTTTTAATTATTTTACACGTATTTTTTAATTTTTAACCAAAGATA
* * *
63984 AAGGTGAATTAATTATTTAATTAGAATTTTTAGTGATTTATTAAATAATTTTGCCTTAGTGATTT
521 AAGGTGAATTAATTATTTAATTAGAATTTTTAGTGATTTATCAAATAATTTTACCTAAGTGATTT
64049 ATTCAAAAGGCATG
586 ATTCAAAAGGCATG
* * *
64063 ATTAATTTATCTAGAAGTTAATAATTAATTAAGAAAGAA-CAAGTAAAAAGAAAGAAAGTAAGAT
1 ATTAATTTATCTAAAAGTTAATAATTAATTAAGAAA-AATAAAG-AAAAAGAAAGAAAGTAAGAG
* * *
64127 TATTGTTAAACAGGGAATGAT-AAGACCTAAGTGTTAGTTACACAAGTCGTGTTGAGAAAGTCTC
64 TATTCTTAAACAGAGAATGATAAAGACC-AA-TG-TA-TTACACAAGTCGTGTTGAGAAAGTCCC
* *
64191 ATTCTATATACTTTTAAAACCTTAAAGTCATAAATCTAAAGTGGGTTACAATGGAACAAAAAATG
125 ATGCTATATACTTGTAAAACCTT---GTCATAAATCTAAAGTGGGTTACAATGGAACAAAAAATG
* * * *
64256 CTTGAAATA-AAACGCATCTGCTATTTCTTTCTTTATATAGATGATAAATGTATGCGTAATATAA
187 CTTGAAACAGAAA-GCATCTGCTATTTCTTTCTTTATACAGATGATAAATGTATGCATAATAAAA
64320 TTGAAATA-AAAGCTTTTTTACCACTGCAATTCACCATGCTTGCCTACAACATTTTTTCAATTGC
251 TTGAAATAGAAA-CTTTTTTACCACTGCAATTCACCATGC-T---T------TTTTTTCAATTGC
* * * * *
64384 CCCAAAGTCTGTAGAGACTTCTCACTAGAGCAATTTTCAATATTCACAATCGAAAAAAAAAAATA
305 CAC-AACTCTGCAAAAACTTC-CACTAGAGCAATTTTCAATATTCACAATCG----AAAAAAATA
** * * *
64449 TAATCATTTAACCTTTCTCTCTTTAATTTACTTTTTTGTTAATTGTTTCTTTAGTTATTTTTTAA
364 TAATCATTTAACCCCTCTCTCTTTAATTTACATTTCTATTAATTGTTTCTTTAGTTATTTTTTAA
** *
64514 ATTAATTCTTTTGTTAGGTT-TCAATTTTT-TTTGGTAATTTTGCAAGTTTTTAATTATTTTACA
429 ATTAATTCTCCTGTTAGGTTCT-AATTTTTATTTGGTAATTCTGCAAGTTTTTAATTATTTTACA
*
64577 CGTACTTTTTTAATTTTTAACCAAAGATAAAGGTGAGTTAATTATTTAATTAGAATTTTTAGTGA
493 CGTA-TTTTTTAATTTTTAACCAAAGATAAAGGTGAATTAATTATTTAATTAGAATTTTTAGTGA
* *
64642 TTTATCAAGTAATTTTACCTAAGTGATTTATTCAAATGGCAT
557 TTTATCAAATAATTTTACCTAAGTGATTTATTCAAAAGGCAT
64684 TCCCATGTTA
Statistics
Matches: 534, Mismatches: 58, Indels: 35
0.85 0.09 0.06
Matches are distributed among these distances:
599 43 0.08
600 37 0.07
601 2 0.00
602 2 0.00
603 45 0.08
605 5 0.01
606 125 0.23
607 1 0.00
610 1 0.00
616 15 0.03
617 12 0.02
618 28 0.05
621 33 0.06
622 185 0.35
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (599 bp):
ATTAATTTATCTAAAAGTTAATAATTAATTAAGAAAAATAAAGAAAAAGAAAGAAAGTAAGAGTA
TTCTTAAACAGAGAATGATAAAGACCAATGTATTACACAAGTCGTGTTGAGAAAGTCCCATGCTA
TATACTTGTAAAACCTTGTCATAAATCTAAAGTGGGTTACAATGGAACAAAAAATGCTTGAAACA
GAAAGCATCTGCTATTTCTTTCTTTATACAGATGATAAATGTATGCATAATAAAATTGAAATAGA
AACTTTTTTACCACTGCAATTCACCATGCTTTTTTTTCAATTGCCACAACTCTGCAAAAACTTCC
ACTAGAGCAATTTTCAATATTCACAATCGAAAAAAATATAATCATTTAACCCCTCTCTCTTTAAT
TTACATTTCTATTAATTGTTTCTTTAGTTATTTTTTAAATTAATTCTCCTGTTAGGTTCTAATTT
TTATTTGGTAATTCTGCAAGTTTTTAATTATTTTACACGTATTTTTTAATTTTTAACCAAAGATA
AAGGTGAATTAATTATTTAATTAGAATTTTTAGTGATTTATCAAATAATTTTACCTAAGTGATTT
ATTCAAAAGGCATG
Found at i:65227 original size:23 final size:23
Alignment explanation
Indices: 65197--65245 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
65187 TACAAGGAAT
65197 TTACACCATATGACTAAAAGAAG
1 TTACACCATATGACTAAAAGAAG
* * *
65220 TTACACCATATGGCTCATAGAAG
1 TTACACCATATGACTAAAAGAAG
65243 TTA
1 TTA
65246 ACTACCCGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (23 bp):
TTACACCATATGACTAAAAGAAG
Found at i:65974 original size:13 final size:13
Alignment explanation
Indices: 65956--65980 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
65946 CATTATGCTT
65956 TGTATCGATACAA
1 TGTATCGATACAA
65969 TGTATCGATACA
1 TGTATCGATACA
65981 TGTTCATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:65977 original size:33 final size:32
Alignment explanation
Indices: 65935--65999 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
65925 ACACACTCAG
*
65935 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATACA
65968 ATGTATCGATACATGTTCATTGTATCGATACA
1 ATGTATCGATACATGTTCATTGTATCGATACA
66000 TGGACAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACATGTTCATTGTATCGATACA
Found at i:66011 original size:20 final size:20
Alignment explanation
Indices: 65965--66021 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
65955 TTGTATCGAT
*
65965 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
*
65984 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
*
66003 ACAATTGTATCGGTACATG
1 ACAATTGTATCGATACATG
66022 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 1 0.03
19 16 0.50
20 15 0.47
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:66087 original size:13 final size:13
Alignment explanation
Indices: 66066--66095 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
66056 CGATACATGG
*
66066 TACATTGTATCGA
1 TACAATGTATCGA
66079 TACAATGTATCGA
1 TACAATGTATCGA
66092 TACA
1 TACA
66096 TGATGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:66095 original size:33 final size:33
Alignment explanation
Indices: 66053--66115 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
66043 CCACTGTTTA
* *
66053 TATCGATACATGGT-ACATTGTATCGATACAATG
1 TATCGATACATGATGA-ATTATATCGATACAATG
66086 TATCGATACATGATGAATTATATCGATACA
1 TATCGATACATGATGAATTATATCGATACA
66116 TTGCTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (33 bp):
TATCGATACATGATGAATTATATCGATACAATG
Found at i:67357 original size:13 final size:13
Alignment explanation
Indices: 67339--67364 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67329 TACAGCAAGT
67339 ATGTATCGATACA
1 ATGTATCGATACA
67352 ATGTATCGATACA
1 ATGTATCGATACA
67365 TAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:69613 original size:21 final size:21
Alignment explanation
Indices: 69580--69624 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
69570 TTGCAAGTTG
*
69580 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
69602 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
69622 AAA
1 AAA
69625 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:71448 original size:15 final size:15
Alignment explanation
Indices: 71428--71458 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
71418 TAAAAATGTC
*
71428 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
71443 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
71458 C
1 C
71459 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:73555 original size:13 final size:13
Alignment explanation
Indices: 73537--73562 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
73527 ACATTTTTCC
73537 TTGTATCGATACA
1 TTGTATCGATACA
73550 TTGTATCGATACA
1 TTGTATCGATACA
73563 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:76139 original size:13 final size:13
Alignment explanation
Indices: 76121--76146 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
76111 TACAGCAAGT
76121 ATGTATCGATACA
1 ATGTATCGATACA
76134 ATGTATCGATACA
1 ATGTATCGATACA
76147 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:82341 original size:21 final size:22
Alignment explanation
Indices: 82317--82366 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
82307 ATCAAATCTT
* *
82317 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
82338 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
82360 --TCAAAAT
1 CTTCAAAAT
82367 TATGAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:84260 original size:423 final size:423
Alignment explanation
Indices: 83474--84294 Score: 1615
Period size: 423 Copynumber: 1.9 Consensus size: 423
83464 GCCGGGATTC
*
83474 TCATTTCTTGACCACGCATCATCGGTTACAAAACCATGGCCAAGATTGGCTATGAAGTAAGAAAC
1 TCATTTCTTGACCACGCATCATCGGTTACAAAACCATGGCCAAGATTGGCTATGAAATAAGAAAC
*
83539 TGATCATTGGTACCTCGACAGCGTGATGATCCTGCTCCCCAAGTGGATGAGCAAGAGGAACCACA
66 CGATCATTGGTACCTCGACAGCGTGATGATCCTGCTCCCCAAGTGGATGAGCAAGAGGAACCACA
83604 ACAAATGGAAGAAGATGCTCCTCCTTCTCCTCCACCCGAAGCCTCTTCATCAACGTCGTCCATCC
131 ACAAATGGAAGAAGATGCTCCTCCTTCTCCTCCACCCGAAGCCTCTTCATCAACGTCGTCCATCC
83669 GAGAGTTGATCACTTCACTTTAACAACACATGAGTGAGCAATTCACTTCTCTCTCGCAGCGTATG
196 GAGAGTTGATCACTTCACTTTAACAACACATGAGTGAGCAATTCACTTCTCTCTCGCAGCGTATG
83734 GATAAGCACTTTGGTGCACTTAACCGACAGATCCACCTAATGGATGCTCGACTTTCCAAACTTGA
261 GATAAGCACTTTGGTGCACTTAACCGACAGATCCACCTAATGGATGCTCGACTTTCCAAACTTGA
83799 GCATCAATCCTCCCCCTACTCCGACTAACTCTAGTGACGATGAGTCTTAGATTTAGTCTTCGTAT
326 GCATCAATCCTCCCCCTACTCCGACTAACTCTAGTGACGATGAGTCTTAGATTTAGTCTTCGTAT
83864 TAGGACTAAGACCATGCAAACTTGAGCAGCAAT
391 TAGGACTAAGACCATGCAAACTTGAGCAGCAAT
83897 TCATTTCTTGACCACGCATCATCGGTTACAAAACCATGGCCAAGATTGGCTATGAAATAAGAAAC
1 TCATTTCTTGACCACGCATCATCGGTTACAAAACCATGGCCAAGATTGGCTATGAAATAAGAAAC
83962 CGATCATTGGTACCTCGACAGCGTGATGATCCTGCTCCCCAAGTGGATGAGCAAGAGGAACCACA
66 CGATCATTGGTACCTCGACAGCGTGATGATCCTGCTCCCCAAGTGGATGAGCAAGAGGAACCACA
84027 ACAAATGGAAGAAGATGCTCCTCCTTCTCCTCCACCCGAAGCCTCTTCATCAACGTCGTCCATCC
131 ACAAATGGAAGAAGATGCTCCTCCTTCTCCTCCACCCGAAGCCTCTTCATCAACGTCGTCCATCC
84092 GAGAGTTGATCACTTCACTTTAACAACACATGAGTGAGCAATTCACTTCTCTCTCGCAGCGTATG
196 GAGAGTTGATCACTTCACTTTAACAACACATGAGTGAGCAATTCACTTCTCTCTCGCAGCGTATG
84157 GATAAGCACTTTGGTGCACTTAACCGACAGATCCACCTAATGGATGCTCGACTTTCCAAACTTGA
261 GATAAGCACTTTGGTGCACTTAACCGACAGATCCACCTAATGGATGCTCGACTTTCCAAACTTGA
*
84222 GCATCAATCCTCCCCCTACTCCGACTAACTCTAGTGACGATGAGTCTTAGATTTAGTCTTTGTAT
326 GCATCAATCCTCCCCCTACTCCGACTAACTCTAGTGACGATGAGTCTTAGATTTAGTCTTCGTAT
84287 TAGGACTA
391 TAGGACTA
84295 GTCGTACTTG
Statistics
Matches: 395, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
423 395 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (423 bp):
TCATTTCTTGACCACGCATCATCGGTTACAAAACCATGGCCAAGATTGGCTATGAAATAAGAAAC
CGATCATTGGTACCTCGACAGCGTGATGATCCTGCTCCCCAAGTGGATGAGCAAGAGGAACCACA
ACAAATGGAAGAAGATGCTCCTCCTTCTCCTCCACCCGAAGCCTCTTCATCAACGTCGTCCATCC
GAGAGTTGATCACTTCACTTTAACAACACATGAGTGAGCAATTCACTTCTCTCTCGCAGCGTATG
GATAAGCACTTTGGTGCACTTAACCGACAGATCCACCTAATGGATGCTCGACTTTCCAAACTTGA
GCATCAATCCTCCCCCTACTCCGACTAACTCTAGTGACGATGAGTCTTAGATTTAGTCTTCGTAT
TAGGACTAAGACCATGCAAACTTGAGCAGCAAT
Found at i:84524 original size:22 final size:21
Alignment explanation
Indices: 84494--84549 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
84484 TTATCAAAAT
84494 AAATTTTTATCAAGGGGGAGA
1 AAATTTTTATCAAGGGGGAGA
*
84515 AAATCTTTTATCAAGGGTGAGA
1 AAAT-TTTTATCAAGGGGGAGA
* *
84537 AATTTTTTTTCAA
1 AAATTTTTATCAA
84550 AAGGGAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 12 0.39
22 19 0.61
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (21 bp):
AAATTTTTATCAAGGGGGAGA
Found at i:85156 original size:13 final size:13
Alignment explanation
Indices: 85138--85162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85128 CATTATGCTT
85138 TGTATCGATACAA
1 TGTATCGATACAA
85151 TGTATCGATACA
1 TGTATCGATACA
85163 TGGACAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:85176 original size:20 final size:19
Alignment explanation
Indices: 85147--85184 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
85137 TTGTATCGAT
85147 ACAATGTATCGATACATGG
1 ACAATGTATCGATACATGG
85166 ACAATTGTATCGATACATG
1 ACAA-TGTATCGATACATG
85185 AAACTGGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (19 bp):
ACAATGTATCGATACATGG
Found at i:85232 original size:13 final size:13
Alignment explanation
Indices: 85214--85238 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
85204 TACCACTGTT
85214 TGTATCGATACAA
1 TGTATCGATACAA
85227 TGTATCGATACA
1 TGTATCGATACA
85239 TGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:89475 original size:13 final size:13
Alignment explanation
Indices: 89457--89484 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
89447 ATACATTATT
89457 CATTGTATCGATA
1 CATTGTATCGATA
89470 CATTGTATCGATA
1 CATTGTATCGATA
89483 CA
1 CA
89485 ATATTCATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:89534 original size:20 final size:19
Alignment explanation
Indices: 89508--89602 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 19
89498 GTTTACCCAG
89508 ATGTATCGATACATTTTGCA
1 ATGTATCGATACATTTT-CA
* * *
89528 TTGTATCGATATATTGCTCA
1 ATGTATCGATACATT-TTCA
* ***
89548 TTGTATCGATACATCACCCA
1 ATGTATCGATACAT-TTTCA
89568 GATGTATCGATACATTTTACA
1 -ATGTATCGATACATTTT-CA
89589 ATGTATCGATACAT
1 ATGTATCGATACAT
89603 ACAAGCATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
20 45 0.74
21 16 0.26
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:90396 original size:129 final size:129
Alignment explanation
Indices: 90246--90566 Score: 489
Period size: 129 Copynumber: 2.5 Consensus size: 129
90236 ATTTTTTATC
* *
90246 TCGGGGATACTCCAACCCCGATTTTATTTCCAAAACATCATTTTTTCATAATCGGGGATACTTTA
1 TCGGGGATACT-CAACTCCGATTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTTTA
* *
90311 ATCCCATTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAA
65 ATCCCATTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAA
*
90376 TCGGGGATACTCAACTCCGATTTTATTTCCAAAACATCAAATTTTCATAATCGGGGATACTTTAA
1 TCGGGGATACTCAACTCCGATTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTTTAA
** * * *
90441 TCCTGTTATTTTCGAGGGGATACTCCAACCTCGGTTTTATTTCTAAAACACCAATTTTCCACAA
66 TCCCATTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAA
* * * * *
90505 TCGGGGATACTTCAACTCCGATTTTATTTTCAAAACACCAATCTTCCACAATCGGGGATACT
1 TCGGGGATAC-TCAACTCCGATTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACT
90567 CCAACTCTGA
Statistics
Matches: 174, Mismatches: 16, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
129 118 0.68
130 56 0.32
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.34
Consensus pattern (129 bp):
TCGGGGATACTCAACTCCGATTTTATTTCCAAAACATCAATTTTTCATAATCGGGGATACTTTAA
TCCCATTATTTTCGAAGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTTTCCACAA
Found at i:90400 original size:50 final size:51
Alignment explanation
Indices: 90328--90436 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 51
90318 TATTTTCGAA
* * *
90328 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCG
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAATTTTCACAATCG
* * *
90379 GGGATACT-CAACTCCGATTTTATTTCCAAAACATCAAATTTTCATAATCG
1 GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAATTTTCACAATCG
90429 GGGATACT
1 GGGATACT
90437 TTAATCCTGT
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
50 44 0.85
51 8 0.15
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACCCCGATTTTATTTCCAAAACACCAAATTTTCACAATCG
Found at i:90616 original size:50 final size:51
Alignment explanation
Indices: 90456--90621 Score: 246
Period size: 51 Copynumber: 3.3 Consensus size: 51
90446 TTATTTTCGA
* *
90456 GGGGATACTCCAAC-CTCGGTTTTATTTCTAAAACACCAATTTTCCACAATC
1 GGGGATACTCCAACTCT-GATTTTATTTCCAAAACACCAATTTTCCACAATC
* * * *
90507 GGGGATACTTCAACTCCGATTTTATTTTCAAAACACCAATCTTCCACAATC
1 GGGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTTCCACAATC
*
90558 GGGGATACTCCAACTCTGATTTTATTTCCAAAA-ACCAATTTTTCACAATC
1 GGGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTTCCACAATC
90608 GGGGATACTCCAAC
1 GGGGATACTCCAAC
90622 CTTGTTGTTT
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
50 29 0.28
51 73 0.71
52 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:90660 original size:28 final size:27
Alignment explanation
Indices: 90605--90681 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 27
90595 ATTTTTCACA
* * *
90605 ATCGGGGATACTCCAACCTTGTTGTTTT
1 ATCGGGGATACTCCAACCCTATT-ATTT
90633 ATCGGGGATACTCCAACCCTATTATTT
1 ATCGGGGATACTCCAACCCTATTATTT
90660 -TCGAGGCGATACTCCAACCCTA
1 ATCG-GG-GATACTCCAACCCTA
90682 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
27 5 0.11
28 36 0.82
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.31
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCTATTATTT
Found at i:90730 original size:51 final size:51
Alignment explanation
Indices: 90668--90781 Score: 129
Period size: 51 Copynumber: 2.2 Consensus size: 51
90658 TTTCGAGGCG
* * * **
90668 ATACTCCAACCCTAGCTTTATTCCTAAAATATTGATTTCTCACAATCGGGC
1 ATACTCCAACCCCAGCCTTATTCCTAAAACATCAATTTCTCACAATCGGGC
* * * * *
90719 ATACTCCAACCCCGGCCTTATTTCTAAAGCATCAATTTTTCACAATCGGGG
1 ATACTCCAACCCCAGCCTTATTCCTAAAACATCAATTTCTCACAATCGGGC
*
90770 ATGCTCCAACCC
1 ATACTCCAACCC
90782 ATTTATTTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (51 bp):
ATACTCCAACCCCAGCCTTATTCCTAAAACATCAATTTCTCACAATCGGGC
Found at i:90915 original size:79 final size:78
Alignment explanation
Indices: 90719--90935 Score: 229
Period size: 79 Copynumber: 2.7 Consensus size: 78
90709 ACAATCGGGC
*** * * * * * *
90719 ATACTCCAACCCCGGCCTTATTTCTAAAGCATCAATTTTTCACAATCGGGGATGCTCCAACCCAT
1 ATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCATAATC-GGGATACTCCAACCCAT
*
90784 TTATTTTTGAGGGG
65 TTATTTTCGAGGGG
* * * ** *
90798 ATACTCTAACCCCGATTTTATTTTCAAAATACTGATTTTCTATAATCAGGGATACTCCAACCC-T
1 ATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCATAATC-GGGATACTCCAACCCAT
90862 ATTATTTTCGAGGGG
65 -TTATTTTCGAGGGG
**
90877 ATACTCCAACCCCGATTTTATTTCCCGAACACCAATTTTCCATAATCGAGGATACTCCA
1 ATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCATAATCG-GGATACTCCA
90936 GCCTCATTGT
Statistics
Matches: 111, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
78 2 0.02
79 109 0.98
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (78 bp):
ATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCATAATCGGGATACTCCAACCCATT
TATTTTCGAGGGG
Found at i:93239 original size:13 final size:13
Alignment explanation
Indices: 93221--93245 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93211 CATTTTATGG
93221 TGTATCGATACAA
1 TGTATCGATACAA
93234 TGTATCGATACA
1 TGTATCGATACA
93246 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:93261 original size:32 final size:33
Alignment explanation
Indices: 93198--93265 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
93188 CATTACAAGC
**
93198 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
93231 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
93263 CAA
1 CAA
93266 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:93361 original size:20 final size:20
Alignment explanation
Indices: 93319--93368 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
93309 TCTTTTTCAA
*
93319 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
93339 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
93359 GTATCGATAC
1 GTATCGATAC
93369 TTTTTAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:95613 original size:20 final size:21
Alignment explanation
Indices: 95584--95624 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
95574 TGTTTTTGAA
95584 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
95603 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
95625 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:95774 original size:13 final size:13
Alignment explanation
Indices: 95756--95793 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
95746 ATAATCCCCC
95756 TGTATCGATACAG
1 TGTATCGATACAG
95769 TGTATCGATACAG
1 TGTATCGATACAG
95782 TGTATCGATACA
1 TGTATCGATACA
95794 AAGAATGCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:100316 original size:3 final size:3
Alignment explanation
Indices: 100308--100341 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
100298 TCTGAGTCAC
* *
100308 CAT CAT CAT CAT CAT CTT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
100342 CTTGATGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.38
Consensus pattern (3 bp):
CAT
Found at i:100322 original size:9 final size:9
Alignment explanation
Indices: 100308--100341 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
100298 TCTGAGTCAC
*
100308 CATCATCAT
1 CATCATCTT
100317 CATCATCTT
1 CATCATCTT
100326 CATCATCTT
1 CATCATCTT
100335 CATCATC
1 CATCATC
100342 CTTGATGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.38
Consensus pattern (9 bp):
CATCATCTT
Found at i:101966 original size:13 final size:13
Alignment explanation
Indices: 101948--101972 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
101938 CATTTTATGG
101948 TGTATCGATACAA
1 TGTATCGATACAA
101961 TGTATCGATACA
1 TGTATCGATACA
101973 TACTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:101988 original size:32 final size:33
Alignment explanation
Indices: 101925--101992 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
101915 CGTTACAAGC
**
101925 CAATGTATCGATACATTTTATGGTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
*
101958 CAATGTATCGATACATACTGT-GTGTATCGATA
1 CAATGTATCGATACATACTATGGTGTATCGATA
101990 CAA
1 CAA
101993 GTTTGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (33 bp):
CAATGTATCGATACATACTATGGTGTATCGATA
Found at i:102088 original size:20 final size:20
Alignment explanation
Indices: 102046--102095 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
102036 TCTTTTTCAA
*
102046 GTATCGATACAATGCAACAT
1 GTATCGATACAATGAAACAT
* **
102066 GTATCGATACAATTAAATGT
1 GTATCGATACAATGAAACAT
102086 GTATCGATAC
1 GTATCGATAC
102096 TTTTCAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACAATGAAACAT
Found at i:102925 original size:4 final size:4
Alignment explanation
Indices: 102916--102942 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
102906 TTTTGAGGTG
102916 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
102943 GTTTGTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:112965 original size:31 final size:31
Alignment explanation
Indices: 112886--113048 Score: 123
Period size: 32 Copynumber: 5.0 Consensus size: 31
112876 AATTCTTCAT
*
112886 ATCTCTTCTCAAAGTCCACGACTCAGTGGCA
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGCA
* * * *
112917 CT-TTTTTCTCCAAAGTCCACAACTTAGTGGCA
1 ATCTCTTT-T-CAAAGTCCACGACTCAGTGGCA
112949 ATCTCTTTTCAAAGTCCACGACTCAGTGGC-
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGCA
* * * *
112979 ATCTTTTTCCTGCAAAGCCCACAACTCCGTGGCA
1 ATCTCTTT--T-CAAAGTCCACGACTCAGTGGCA
* *
113013 CTCTTTTTCCTTCTTAAAGTCCACGACTCAGTGGCA
1 ATC-TCTT--TTC--AAAGTCCACGACTCAGTGGCA
113049 TTTTGTACCA
Statistics
Matches: 103, Mismatches: 17, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
30 10 0.10
31 21 0.20
32 23 0.22
33 22 0.21
34 3 0.03
35 5 0.05
36 18 0.17
37 1 0.01
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (31 bp):
ATCTCTTTTCAAAGTCCACGACTCAGTGGCA
Found at i:112986 original size:63 final size:64
Alignment explanation
Indices: 112886--113135 Score: 244
Period size: 64 Copynumber: 3.9 Consensus size: 64
112876 AATTCTTCAT
* * * *
112886 ATCTCTTCTCAAAGTCCACGACTCAGTGGCA-CTTTTTTCTCCAAAGTCCACAACTTAGTGGCA
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGCATCTTTTTCCTCCAAAGCCCACAACTCAGTGGCA
* *
112949 ATCTCTTTTCAAAGTCCACGACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCCGTGGCA
1 ATCTCTTTTCAAAGTCCACGACTCAGTGGCATCTTTTTCCTCCAAAGCCCACAACTCAGTGGCA
* * * * * *
113013 CTCTTTTTCCTTCTTAAAGTCCACGACTCAGTGGCAT-TTTGT--ACCAAAGCTCACGACTCAGT
1 ATC-TCTT--TTC--AAAGTCCACGACTCAGTGGCATCTTTTTCCTCCAAAGCCCACAACTCAGT
113075 GGC-
61 GGCA
* * *
113078 AT-TTTTTCTCCAAAGTCCACAACTCTA-TGGCATCTTTTTCCTGCAAAGCCCACAACTC
1 ATCTCTTT-T-CAAAGTCCACGACTC-AGTGGCATCTTTTTCCTCCAAAGCCCACAACTC
113136 CATGGCACTC
Statistics
Matches: 154, Mismatches: 21, Indels: 23
0.78 0.11 0.12
Matches are distributed among these distances:
61 20 0.13
62 6 0.04
63 35 0.23
64 42 0.27
65 4 0.03
66 18 0.12
67 3 0.02
68 4 0.03
69 22 0.14
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (64 bp):
ATCTCTTTTCAAAGTCCACGACTCAGTGGCATCTTTTTCCTCCAAAGCCCACAACTCAGTGGCA
Found at i:113023 original size:34 final size:34
Alignment explanation
Indices: 112894--113306 Score: 256
Period size: 34 Copynumber: 12.9 Consensus size: 34
112884 ATATCTCTTC
* *
112894 TCAAAGTCCACGACTCAGTGGCACT-TTTTT-CT
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
* ** * *
112926 CCAAAGTCCACAACTTAGTGGCAATC-TCTT--T
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
* *
112957 TCAAAGTCCACGACTCAGTGGCA-TCTTTTTCCT
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
* *
112990 GCAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
* * * *
113024 TCTTAAAGTCCACGACTCAGTGGCA-T-TTTGTAC-
1 TC--AAAGTCCACAACTCCGTGGCACTCTTTTTCCT
* *
113057 -CAAAG-CTCACGACTCAGTGGCA-T-TTTTT-CT
1 TCAAAGTC-CACAACTCCGTGGCACTCTTTTTCCT
* **
113087 CCAAAGTCCACAACTCTATGGCA-TCTTTTTCCT
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
* * * *
113120 GCAAAGCCCACAACTCCATGGCACTCTATTTCCT
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
** * *
113154 TTTAAGTCCACAACTCTGTGGCAC-C--CTT--T
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
* *
113183 T--AAGCCCACAACTCCGTGGCAGTCTTTTTCCT
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
*
113215 TCTAAGTCCACAACTCCGTGGCA--C-----CCT
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
** *
113242 TTGAAGCCCACAACTCCGTGGCACTCTTTTTCCT
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
** *
113276 TCAAAGTCCATGACTCCATGGCAC-CTTTTTC
1 TCAAAGTCCACAACTCCGTGGCACTCTTTTTC
113307 TTCTCTAAAG
Statistics
Matches: 305, Mismatches: 48, Indels: 55
0.75 0.12 0.13
Matches are distributed among these distances:
27 41 0.13
28 1 0.00
29 5 0.02
30 28 0.09
31 44 0.14
32 34 0.11
33 50 0.16
34 83 0.27
35 1 0.00
36 18 0.06
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (34 bp):
TCAAAGTCCACAACTCCGTGGCACTCTTTTTCCT
Found at i:113125 original size:130 final size:132
Alignment explanation
Indices: 112890--113177 Score: 385
Period size: 130 Copynumber: 2.2 Consensus size: 132
112880 CTTCATATCT
* * * *
112890 CTTCTCAAAGTCCACGACTCAGTGGCACTTTTTTCTCCAAAGTCCACAACTTAGTGGCAATCTCT
1 CTTCTTAAAGTCCACGACTCAGTGGCACTTTTGTCACCAAAGTCCACAACTCAGTGGCAATCTCT
* * *
112955 TTTCAAAGTCCACGACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCCGTGGCACTCTTTT
66 TTTCAAAGTCCACAACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCCATGGCACTCTATT
113020 TC
131 TC
* *
113022 CTTCTTAAAGTCCACGACTCAGTGGCA-TTTTGT-ACCAAAG-CTCACGACTCAGTGGC-AT-TT
1 CTTCTTAAAGTCCACGACTCAGTGGCACTTTTGTCACCAAAGTC-CACAACTCAGTGGCAATCTC
113082 TTTCTCCAAAGTCCACAACTCTA-TGGCATCTTTTTCCTGCAAAGCCCACAACTCCATGGCACTC
65 TTT-T-CAAAGTCCACAACTC-AGTGGCATCTTTTTCCTGCAAAGCCCACAACTCCATGGCACTC
113146 TATTTC
127 TATTTC
* *
113152 CTT-TT-AAGTCCACAACTCTGTGGCAC
1 CTTCTTAAAGTCCACGACTCAGTGGCAC
113178 CCTTTTAAGC
Statistics
Matches: 140, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
128 22 0.16
129 6 0.04
130 80 0.57
131 6 0.04
132 26 0.19
ACGTcount: A:0.24, C:0.31, G:0.14, T:0.31
Consensus pattern (132 bp):
CTTCTTAAAGTCCACGACTCAGTGGCACTTTTGTCACCAAAGTCCACAACTCAGTGGCAATCTCT
TTTCAAAGTCCACAACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCCATGGCACTCTATT
TC
Found at i:113142 original size:64 final size:64
Alignment explanation
Indices: 112891--113306 Score: 271
Period size: 61 Copynumber: 6.5 Consensus size: 64
112881 TTCATATCTC
* * * * *
112891 TTCTCAAAGTCCACGACTCAGTGGCA-CTTTTTTCTCCAAAGTCCACAACTTAGTGGCAATCTCT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCAGTGGC-ATCTTT
*
112955 TT-TCAAAGTCCACGACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCCGTGGCACTCTTT
1 TTCTCAAAGTCCACGACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCAGTGGCA-TCTTT
* * * *
113019 TTCCTTCTTAAAGTCCACGACTCAGTGGCAT-TTTGTAC--CAAAGCTCACGACTCAGTGGCAT-
1 TT-C-TC--AAAGTCCACGACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCAGTGGCATC
113080 TTT
62 TTT
*
113083 TTCTCCAAAGTCCACAACTCTA-TGGCATCTTTTTCCTGCAAAGCCCACAACTCCA-TGGCACTC
1 TTCT-CAAAGTCCACGACTC-AGTGGCATCTTTTTCCTGCAAAGCCCACAACT-CAGTGGCA-TC
113146 TATT
62 T-TT
* ** * * ** *
113150 TCCTTTTAAGTCCACAACTCTGTGGCA-CCCTTT--T---AAGCCCACAACTCCGTGGCAGTCTT
1 TTC-TCAAAGTCCACGACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCAGTGGCA-TCTT
113209 T
64 T
* * * ** *
113210 TTCCTTCTAAGTCCACAACTCCGTGGCA-C-CCTT--TG--AAGCCCACAACTCCGTGGCACTCT
1 TT-C-TCAAAGTCCACGACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCAGTGGCA-TCT
113269 TT
63 TT
* *
113271 TTCCTTCAAAGTCCATGACTCCA-TGGCACCTTTTTC
1 TT-C-TCAAAGTCCACGACT-CAGTGGCATCTTTTTC
113307 TTCTCTAAAG
Statistics
Matches: 292, Mismatches: 35, Indels: 50
0.77 0.09 0.13
Matches are distributed among these distances:
60 8 0.03
61 110 0.38
62 9 0.03
63 28 0.10
64 57 0.20
65 4 0.01
66 24 0.08
67 24 0.08
68 6 0.02
69 22 0.08
ACGTcount: A:0.22, C:0.32, G:0.14, T:0.31
Consensus pattern (64 bp):
TTCTCAAAGTCCACGACTCAGTGGCATCTTTTTCCTGCAAAGCCCACAACTCAGTGGCATCTTT
Found at i:113182 original size:27 final size:27
Alignment explanation
Indices: 113151--113271 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 27
113141 CACTCTATTT
* *
113151 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
113178 CCTTTTAAGCCCACAACTCCGTGGCAGTC
1 CCTTTTAAGCCCACAACTCCGTGGCA--C
* *
113207 TTTTTCCTTCTAAGTCCACAACTCCGTGGCAC
1 -----CCTTTTAAGCCCACAACTCCGTGGCAC
*
113239 CCTTTGAAGCCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
113266 TCTTTT
1 CCTTTT
113272 TCCTTCAAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
27 52 0.67
29 1 0.01
32 1 0.01
34 24 0.31
ACGTcount: A:0.20, C:0.36, G:0.15, T:0.30
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAC
Found at i:113221 original size:61 final size:63
Alignment explanation
Indices: 112992--113285 Score: 280
Period size: 61 Copynumber: 4.7 Consensus size: 63
112982 TTTTTCCTGC
* * **
112992 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTTAAAGTCCACGACTCAGTGGCA-TTTTGTA
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTC-T-AAGTCCACAACTCTGTGGCACCCTT-T-
*
113056 CC
62 CT
* * * * * * **
113058 AAAGCTCACGACTCAGTGGCA-T-TTTTT-CTCCAAAGTCCACAACTCTATGGCATCTTTTTCCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCA-CCCTTT-CT
* * *
113120 GCAAAGCCCACAACTCCATGGCACTCTATTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTT-T
1 --AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTCT
* *
113184 -AAGCCCACAACTCCGTGGCAGTCTTTTTCCTTCTAAGTCCACAACTCCGTGGCACCC-TT-T
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTCT
* *
113244 GAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGTCCA
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCA
113286 TGACTCCATG
Statistics
Matches: 192, Mismatches: 28, Indels: 21
0.80 0.12 0.09
Matches are distributed among these distances:
60 3 0.02
61 108 0.56
62 2 0.01
63 7 0.04
64 23 0.12
65 2 0.01
66 26 0.14
67 21 0.11
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.30
Consensus pattern (63 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCTGTGGCACCCTTTCT
Found at i:113430 original size:49 final size:49
Alignment explanation
Indices: 113373--114305 Score: 1000
Period size: 49 Copynumber: 19.0 Consensus size: 49
113363 GTGGCATCAC
* *
113373 CTTTAAGTCCAAAATAGCTAGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * *
113422 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGTACATTGGCA-C----T
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
*
113466 -TTTAAGTCCAATATAGCCGGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * *
113514 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCA-C-----
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
*
113557 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * * * * *
113606 CTTTAAGTCCAATGTAGCTGGCCTTCAATTAGCACATTGACACC-CT-T
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* *
113653 C--TAAGTCCAATATAGTTGGCCTTGAATCTGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* * *
113700 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* *
113749 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-AT
* * *
113801 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* *
113850 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-AT
* * *
113902 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* *
113951 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-AT
* * *
114003 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
* *
114052 CTTTAAGTCCAATATCGCTGGCCTTGAATCATCATATTGGCACCTTTGTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-AT
* *
114104 CTTTAAGTCCAATGTCA-CTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATAT-AGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
*** * * * *
114153 CTTTAAGTCTGGTATCGCTGGCCTTGGATCAGCATATTGACGCCTTCGTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT--T-AT
** * * * * * **
114205 CTTTAAAACCTAATGTTGTTGGCCTTGAATCAGCACAATGGCATTTTTCTCAT
1 CTTTAAGTCC-AATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTT-T-AT
* * * * * *
114258 CTTCATGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CCTTT
114306 TTCTCATCTT
Statistics
Matches: 747, Mismatches: 102, Indels: 68
0.81 0.11 0.07
Matches are distributed among these distances:
43 76 0.10
44 3 0.00
45 34 0.05
46 1 0.00
47 4 0.01
48 4 0.01
49 362 0.48
50 8 0.01
51 9 0.01
52 212 0.28
53 32 0.04
54 2 0.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
Found at i:113581 original size:22 final size:22
Alignment explanation
Indices: 113514--113581 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
113504 GCACCTTTAT
*
113514 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
* * * *
113536 CTTGAA-T-CAACACA-TTGGCAC
1 CTTTAAGTCCAATATAGCTGG--C
113557 CTTTAAGTCCAATATAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
113579 CTT
1 CTT
113582 GAATCAGCAT
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 10 0.31
23 5 0.16
24 3 0.09
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATATAGCTGGC
Found at i:113837 original size:101 final size:101
Alignment explanation
Indices: 113373--114319 Score: 1214
Period size: 101 Copynumber: 9.6 Consensus size: 101
113363 GTGGCATCAC
* * *
113373 CTTTAAGTCCAAAATAGCTAGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
*
113435 GTAGCTGGCCTTGAATCAGTACATTGGCA----C-T
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
113466 -TTTAAGTCCAATATAGCCGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
*
113527 GTAGCTGGCCTTGAATCAACACATTGGCA----C--
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* *
113557 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATC-TT-T-ATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
* * *
113619 GTAGCTGGCCTTCAATTAGCACATTGACACC--C-T
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
* * * *
113652 -TCTAAGTCCAATATAGTTGGCCTTGAATCTGCATATTGGCACC-TT-T-ATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
113713 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
113749 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
113814 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
113850 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
* *
113915 GTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
113951 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
* *
114016 GTCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
66 GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*
114052 CTTTAAGTCCAATATCGCTGGCCTTGAATCATCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
*
114117 GTCA-CTGGCCTTGAATCAGCATATTGGCACCTTCAT
66 GT-AGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
*** * * * * **
114153 CTTTAAGTCTGGTATCGCTGGCCTTGGATCAGCATATTGACGCCTTCGTCATCTTTAAAACCTAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCC-AA
* * * **
114218 TGTTGTTGGCCTTGAATCAGCACAATGGCATTTTTCTCAT
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA--CCT-TCAT
* * * * * *
114258 CTTCATGTCCAATGTCGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCATCTTTAAG
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CC--TTTGTCATCTTTAAG
114320 CCTAATATCG
Statistics
Matches: 778, Mismatches: 56, Indels: 25
0.91 0.07 0.03
Matches are distributed among these distances:
92 170 0.22
94 86 0.11
96 1 0.00
97 1 0.00
98 38 0.05
99 2 0.00
100 1 0.00
101 400 0.51
102 27 0.03
104 1 0.00
105 37 0.05
106 2 0.00
108 12 0.02
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.34
Consensus pattern (101 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGGCACCTTCAT
Found at i:114473 original size:53 final size:52
Alignment explanation
Indices: 114376--114487 Score: 120
Period size: 53 Copynumber: 2.1 Consensus size: 52
114366 TTTCTCACCT
* * *
114376 TCATCTTTAAATCCAATATTGTTGGCCTTGAATTCGCATATTGGC-GTCTTC
1 TCATCTTTAAATCCAATATCGTTGGCCTTGAAATCGCACATTGGCAGTCTTC
* * * *
114427 GTCATCTTTGAAGTCCAATGTCGTTGGCCTT-AAATCAGCACGTTGGCATTCTTC
1 -TCATCTTT-AAATCCAATATCGTTGGCCTTGAAATC-GCACATTGGCAGTCTTC
114481 TCATCTT
1 TCATCTT
114488 CAAGTCTAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
52 12 0.24
53 33 0.66
54 5 0.10
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.39
Consensus pattern (52 bp):
TCATCTTTAAATCCAATATCGTTGGCCTTGAAATCGCACATTGGCAGTCTTC
Found at i:115318 original size:13 final size:13
Alignment explanation
Indices: 115300--115324 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
115290 ATTACTCAAC
115300 TGTATCGATACAT
1 TGTATCGATACAT
115313 TGTATCGATACA
1 TGTATCGATACA
115325 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:115375 original size:52 final size:52
Alignment explanation
Indices: 115333--115458 Score: 234
Period size: 52 Copynumber: 2.4 Consensus size: 52
115323 CACTAATCTT
115333 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* *
115385 TGTATTGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
115437 TGTATCGATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
115459 ATTTCATATT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:121185 original size:5 final size:6
Alignment explanation
Indices: 121171--121195 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
121161 TAATTTTAAG
121171 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
121196 CATAGCTTAT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:126181 original size:78 final size:78
Alignment explanation
Indices: 126069--126343 Score: 275
Period size: 79 Copynumber: 3.5 Consensus size: 78
126059 AATATAAAAA
* * * **
126069 AAACTAACCCTAAT-GACTCTGTTTCGATGAAAGGTATGAAACTAAATTAAAAAGGCTCAGTTTT
1 AAACTAAACCTAATAGACTCAGTTTCGATGGAAGGTACAAAACTAAATTAAAAAGGCTCAGTTTT
* *
126133 GATAGAAGATACG
66 AATAGAAGGTACG
* * *
126146 AAACTAAACCTAATAGACTCAGTTTCAATGGAAGGTACAAAACTAAACTTAAAAAGGCTTAATTT
1 AAACTAAACCTAATAGACTCAGTTTCGATGGAAGGTACAAAACTAAA-TTAAAAAGGCTCAGTTT
*
126211 TAATAGAAGGTATG
65 TAATAGAAGGTACG
* * * ** ** * * * *
126225 ATACTAAACATAATGGACTTGGTTTCGATGGAAAATACAAAACTAATTTTAAAAAAGTTCAGTGT
1 AAACTAAACCTAATAGACTCAGTTTCGATGGAAGGTACAAAACTAA-ATTAAAAAGGCTCAGTTT
126290 TAATAGAAGGTACG
65 TAATAGAAGGTACG
* * * * *
126304 AAA-TTAACCTAATAGACTCAATTTTGATGAAAAGTACAAA
1 AAACTAAACCTAATAGACTCAGTTTCGATGGAAGGTACAAA
126344 TTTACCCTAG
Statistics
Matches: 159, Mismatches: 36, Indels: 5
0.80 0.18 0.03
Matches are distributed among these distances:
77 13 0.08
78 55 0.35
79 91 0.57
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (78 bp):
AAACTAAACCTAATAGACTCAGTTTCGATGGAAGGTACAAAACTAAATTAAAAAGGCTCAGTTTT
AATAGAAGGTACG
Found at i:126231 original size:40 final size:40
Alignment explanation
Indices: 126099--126233 Score: 139
Period size: 39 Copynumber: 3.4 Consensus size: 40
126089 GTTTCGATGA
* *
126099 AAGGTATGAAACTAAA-TTAAAAAGGCTCAGTTTTGATAG
1 AAGGTACGAAACTAAACTTAAAAAGGCTCAGTTTTAATAG
* * * * * *
126138 AAGATACGAAACTAAACCT-AATAGACTCAGTTTCAATGG
1 AAGGTACGAAACTAAACTTAAAAAGGCTCAGTTTTAATAG
* * *
126177 AAGGTACAAAACTAAACTTAAAAAGGCTTAATTTTAATAG
1 AAGGTACGAAACTAAACTTAAAAAGGCTCAGTTTTAATAG
* *
126217 AAGGTATGATACTAAAC
1 AAGGTACGAAACTAAAC
126234 ATAATGGACT
Statistics
Matches: 74, Mismatches: 20, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
39 45 0.61
40 29 0.39
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (40 bp):
AAGGTACGAAACTAAACTTAAAAAGGCTCAGTTTTAATAG
Found at i:145872 original size:17 final size:16
Alignment explanation
Indices: 145824--145891 Score: 63
Period size: 15 Copynumber: 4.4 Consensus size: 16
145814 TCCTTTTTCT
145824 AAAAAACAAACAA-A-A
1 AAAAAACAAA-AAGAGA
*
145839 AAAAAACAAAAACA-A
1 AAAAAACAAAAAGAGA
**
145854 AATTAA-AAAAAGAGA
1 AAAAAACAAAAAGAGA
145869 AAAAAAGCAAAAAGAGA
1 AAAAAA-CAAAAAGAGA
145886 AAAAAA
1 AAAAAA
145892 AAGAACCTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
14 8 0.18
15 21 0.48
17 15 0.34
ACGTcount: A:0.82, C:0.07, G:0.07, T:0.03
Consensus pattern (16 bp):
AAAAAACAAAAAGAGA
Found at i:145874 original size:19 final size:17
Alignment explanation
Indices: 145835--145893 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
145825 AAAAACAAAC
* *
145835 AAAAAAAAAACAAAAACA
1 AAAAAAAAAAGAGAAA-A
145853 AAATTAAAAAAAGAGAAAA
1 AAA--AAAAAAAGAGAAAA
**
145872 AAAGCAAAAAGAGAAAA
1 AAAAAAAAAAGAGAAAA
145889 AAAAA
1 AAAAA
145894 GAACCTGTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
17 15 0.45
18 3 0.09
19 4 0.12
20 11 0.33
ACGTcount: A:0.83, C:0.05, G:0.08, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAGAGAAAA
Found at i:145894 original size:19 final size:19
Alignment explanation
Indices: 145838--145894 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
145828 AACAAACAAA
* **
145838 AAAAAAACAAAAACAAAATT
1 AAAAAAAGAAAAA-AAAAGC
*
145858 AAAAAAAGAGAAAAAAAGC
1 AAAAAAAGAAAAAAAAAGC
*
145877 AAAAAGAGAAAAAAAAAG
1 AAAAAAAGAAAAAAAAAG
145895 AACCTGTCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 20 0.65
20 11 0.35
ACGTcount: A:0.81, C:0.05, G:0.11, T:0.04
Consensus pattern (19 bp):
AAAAAAAGAAAAAAAAAGC
Found at i:146956 original size:61 final size:60
Alignment explanation
Indices: 146858--147425 Score: 510
Period size: 61 Copynumber: 9.0 Consensus size: 60
146848 ACCTTTTATC
*** *
146858 CTTTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACATAAGTTGGTGGCA
1 CTTTCAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
146918 CTTTCCAGTCCTTAAAGAGTAAGACACCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCA
1 CTTT-CAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
146979 CTTTCTAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACAAAAGTTGGTGGCA
1 CTTTC-AGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * *
147040 CCTTTCAGTCCTCAAAGAGCAAGACTTTTTTTCCTTTTAAAGCCCATACGAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
147101 CCTTCCAG-CCTGCAAAGAGCGGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGACA
1 -CTTTCAGTCCT-CAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * * * *
147162 CATTTCAGTCCTAAAAAAGTAGGAC-GCCTTTCCTTTTAAAGCCCACACAAGATGGTGGCA
1 C-TTTCAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * **
147222 CCTTTCAGTCTTCAAAGAGTAGGACATTTTTTCCTTCCAAAGCCCACACAAGTTGGTGGCA
1 -CTTTCAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
** * * **
147283 CCATCTAGTCCCCAAAGAGCATGACACTTCTTTTTTTTTTTAAAAAAAGTAAAGCCCACACAAGT
1 CTTTC-AGTCCTCAAAGAGCAGGACA--TC--TTTTCCTTT--------TAAAGCCCACACAAGT
147348 TGGTGGCA
53 TGGTGGCA
* * *
147356 CCTTCTAGTCCTCAAAGAGCAGGATGCCTCTCTCCATTTCCATCTTAAAGCCCACACAAGTTGGT
1 CTTTC-AGTCCTCAAAGAGCAGGA---C-ATCT---TTTCC-TTTTAAAGCCCACACAAGTTGGT
147421 GGCA
57 GGCA
147425 C
1 C
147426 CTATCTACTT
Statistics
Matches: 416, Mismatches: 63, Indels: 49
0.79 0.12 0.09
Matches are distributed among these distances:
60 63 0.15
61 260 0.62
62 8 0.02
63 1 0.00
65 6 0.01
69 25 0.06
73 45 0.11
75 2 0.00
76 4 0.01
77 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (60 bp):
CTTTCAGTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:147096 original size:183 final size:182
Alignment explanation
Indices: 146857--147384 Score: 585
Period size: 183 Copynumber: 2.8 Consensus size: 182
146847 AACCTTTTAT
** * *
146857 CCTTTCAGTCCTCAAAGAGCAGGA-TGCCTTTTCCTTTTAAAGCCCACATAAGTTGGTGGCACTT
1 CCTTTCAGTCCTCAAAGAGCAGGACT-TTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCT
* *
146921 TCCAGTCCTTAAAGAGTAAGACACCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTA
65 TCCAGTCCTCAAAGAGCAAGACACCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTA
* * *
146986 GTCCTCAAAGAGCAGGACATCTTTTCCTTTTAAAGCCCACAAAAGTTGGTGGCA
130 GTCCTCAAAGAGCAGGAC-GCCTTTCCTTTTAAAGCCCACAAAAGATGGTGGCA
* * *
147040 CCTTTCAGTCCTCAAAGAGCAAGACTTTTTTTCCTTTTAAAGCCCATACGAGTTGGTGGCACCTT
1 CCTTTCAGTCCTCAAAGAGCAGGACTTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
** ** * *
147105 CCAG-CCTGCAAAGAGCGGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGACACATTTC-
66 CCAGTCCT-CAAAGAGCAAGACACCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCT
* * * *
147168 AGTCCTAAAAAAGTAGGACGCCTTTCCTTTTAAAGCCCACACAAGATGGTGGCA
129 AGTCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACAAAAGATGGTGGCA
* * * ** *
147222 CCTTTCAGTCTTCAAAGAGTAGGACATTTTTTCCTTCCAAAGCCCACACAAGTTGGTGGCACCAT
1 CCTTTCAGTCCTCAAAGAGCAGGACTTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
* * * *
147287 CTAGTCCCCAAAGAGCATGACACTTCTTTTTTTTTTTAAAAAAAGTAAAGCCCACACAAGTTGGT
66 CCAGTCCTCAAAGAGCAAGACAC--C--TTTTCTTTT--------TAAAGCCCACACAAGTTGGT
* *
147352 GGCACCTTCTAGTCCTCAAAGAGCAGGATGCCT
119 GGCACTTTCTAGTCCTCAAAGAGCAGGACGCCT
147385 CTCTCCATTT
Statistics
Matches: 283, Mismatches: 45, Indels: 23
0.81 0.13 0.07
Matches are distributed among these distances:
182 104 0.37
183 120 0.42
184 6 0.02
186 7 0.02
193 3 0.01
194 43 0.15
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (182 bp):
CCTTTCAGTCCTCAAAGAGCAGGACTTTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTT
CCAGTCCTCAAAGAGCAAGACACCTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAG
TCCTCAAAGAGCAGGACGCCTTTCCTTTTAAAGCCCACAAAAGATGGTGGCA
Found at i:149336 original size:159 final size:160
Alignment explanation
Indices: 149045--149711 Score: 687
Period size: 159 Copynumber: 4.2 Consensus size: 160
149035 AAATGCATAT
* * * * *
149045 TCCAACCCCGTTATTTTTGAGGGGATACTCCAACTCTGGTTTTATTTCCAACACA-CTGATTGTT
1 TCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATC-GATTTTT
* * * * ** *
149109 TCATAATCGAGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTTGATTTTATTTCC
65 TAATAATCGAGGATACTCTAACCCCATTATTTTCGAGAGGATACTCCAACCCCGAGTTTATTTCC
* *
149174 AAAACATTGATTTTTTTCATAATCAGGGATAT
130 AAAACATTGA-TTTTTTCACAATCAGGGATAC
*
149206 TCCAACCCTGTTA-TTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTTT
1 TCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTTT
** ** * *
149270 AAT-ATCCG-GGATACTCTAACCCTGTTATTTTTTAGAAGATACTCCAACCCCGAGTTTATTTTC
66 AATAAT-CGAGGATACTCTAACCCCATTATTTTCGAGAGGATACTCCAACCCCGAGTTTATTTCC
** * *
149333 AAAACGCTAATTTTTTTCACAATCTGGGATAC
130 AAAACATTGA-TTTTTTCACAATCAGGGATAC
* * * * *
149365 TCCAA-CCCGTT-CTTCCTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAT-TAATTTT
1 TCCAACCCCGTTATTTTC-GAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTT
** ** * *
149427 CCACCATCGAGGATACTCTAACCCTATTATTTTCGAGAGGATACTCCAA-CCCTAGTTTATTTCC
65 TAATAATCGAGGATACTCTAACCCCATTATTTTCGAGAGGATACTCCAACCCCGAGTTTATTTCC
* *
149491 AAAACATCGA-TTTTTCACTATCAGGGATAC
130 AAAACATTGATTTTTTCACAATCAGGGATAC
** * * * *
149521 TCCAACCCTATTATTTTCGAGAGGATACTCGAACCCCAGTTTTATTTCCAAAACATCTA-TTTTT
1 TCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTTT
* * * * * *
149585 CATAATCGGGGATACTAC-AACCCCATTATTTTTGAG-GGATGCTCTAACCCCG-GTTTATTTCT
66 AATAATCGAGGATACT-CTAACCCCATTATTTTCGAGAGGATACTCCAACCCCGAGTTTATTTCC
* * * * *
149647 AAAACA-TCAATTTTCCACCATCGGGGATAC
130 AAAACATTGATTTTTTCACAATCAGGGATAC
149677 TCCAACCCCGTTATTTTCGAGGGGATACTCCAACC
1 TCCAACCCCGTTATTTTCGAGGGGATACTCCAACC
149712 TCATTTTTAT
Statistics
Matches: 424, Mismatches: 70, Indels: 29
0.81 0.13 0.06
Matches are distributed among these distances:
155 1 0.00
156 95 0.22
157 74 0.17
158 41 0.10
159 152 0.36
160 48 0.11
161 13 0.03
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (160 bp):
TCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTTT
AATAATCGAGGATACTCTAACCCCATTATTTTCGAGAGGATACTCCAACCCCGAGTTTATTTCCA
AAACATTGATTTTTTCACAATCAGGGATAC
Found at i:149487 original size:78 final size:79
Alignment explanation
Indices: 149045--149743 Score: 598
Period size: 78 Copynumber: 8.8 Consensus size: 79
149035 AAATGCATAT
* * * ** * * *
149045 TCCAACCCCGTTATTTTTGAGGGGATACTCCAACTCTGGTTTTATTTCCAACACACTGATTGTTT
1 TCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATTAATT-TTT
*
149110 CATAATCGAGGATAC
65 CACAATCGAGGATAC
* ** *
149125 TCCAACCCCGTTATTTTCGAGGGGATACTCCAA-CCTTGATTTTATTTCCAAAACATTGATTTTT
1 TCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCAG-TTTTATTTCCAAAACATT-A-ATTT
* *
149189 TTCATAATC-AGGGATAT
63 TTCACAATCGA-GGATAC
* ** *
149206 TCCAACCCTGTTA-TTTCGAGGGGATACTCCAACCCCGGTTTTATTTCCAAAACATCGATTTTTT
1 TCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATTAATTTTTC
149270 A-ATATCCG-GGATAC
66 ACA-AT-CGAGGATAC
* ** ** * **
149284 TCTAACCCTGTTATTTTTTAGAAGATACTCCAACCCCGAG-TTTATTTTCAAAACGCTAATTTTT
1 TCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCC-AGTTTTATTTCCAAAACATTAA--TTT
149348 TTCACAATCTG-GGATAC
63 TTCACAATC-GAGGATAC
* * * * *
149365 TCCAACCC-GTT-CTTCCTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACATTAATTTTC
1 TCCAACCCTGTTATTTTC-GAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATTAATTTTT
*
149428 CACCATCGAGGATAC
65 CACAATCGAGGATAC
* * * * **
149443 TCTAACCCTATTATTTTCGAGAGGATACTCCAACCCTAG-TTTATTTCCAAAACATCGATTTTTC
1 TCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATTAATTTTTC
*
149507 ACTATC-AGGGATAC
66 ACAATCGA-GGATAC
* * *
149521 TCCAACCCTATTATTTTCGAGAGGATACTCGAACCCCAGTTTTATTTCCAAAACATCT-ATTTTT
1 TCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACAT-TAATTTTT
* *
149585 CATAATCGGGGATAC
65 CACAATCGAGGATAC
* ** * * * * * * *
149600 TACAACCCCATTATTTTTGA-GGGATGCTCTAACCCC-GGTTTATTTCTAAAACATCAATTTTCC
1 TCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATTAATTTTTC
* *
149663 ACCATCGGGGATAC
66 ACAATCGAGGATAC
* * * * * *
149677 TCCAACCCCGTTATTTTCGAGGGGATACTCCAACCTCATTTTTATCTCCAGAATATTAAATTTTT
1 TCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATT-AATTTTT
149742 CA
65 CA
149744 TCGAGGGATG
Statistics
Matches: 505, Mismatches: 87, Indels: 54
0.78 0.13 0.08
Matches are distributed among these distances:
77 54 0.11
78 142 0.28
79 122 0.24
80 132 0.26
81 52 0.10
82 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (79 bp):
TCCAACCCTGTTATTTTCGAGGGGATACTCCAACCCCAGTTTTATTTCCAAAACATTAATTTTTC
ACAATCGAGGATAC
Found at i:152100 original size:13 final size:13
Alignment explanation
Indices: 152082--152107 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
152072 AAATAGTGCT
152082 AATGTATCGATAC
1 AATGTATCGATAC
152095 AATGTATCGATAC
1 AATGTATCGATAC
152108 TAAGAACTCA
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:156590 original size:3 final size:3
Alignment explanation
Indices: 156582--156626 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
156572 AGTCAACTTT
* *
156582 ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC ATC TTC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
156627 TTTGATGGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.29, C:0.33, G:0.00, T:0.38
Consensus pattern (3 bp):
ATC
Found at i:158328 original size:20 final size:20
Alignment explanation
Indices: 158264--158334 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
158254 TGCCAGTTTC
*
158264 ATGTATCGATA-CAATTCAAT
1 ATGTATCGATACCAA-GCAAT
* *
158284 GTGTATCGATACCAAG-AAC
1 ATGTATCGATACCAAGCAAT
* *
158303 ATGTATCAATACTAAGCAAT
1 ATGTATCGATACCAAGCAAT
158323 ATGTATCGATAC
1 ATGTATCGATAC
158335 ATCTAGGTGT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 15 0.37
20 23 0.56
21 3 0.07
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACCAAGCAAT
Found at i:158456 original size:20 final size:21
Alignment explanation
Indices: 158431--158470 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
158421 GATACTTTGG
158431 ATTATTTTT-TACTTGAAAAC
1 ATTATTTTTATACTTGAAAAC
*
158451 ATTATTTTTATGCTTGAAAA
1 ATTATTTTTATACTTGAAAA
158471 ATATTTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (21 bp):
ATTATTTTTATACTTGAAAAC
Found at i:158460 original size:19 final size:18
Alignment explanation
Indices: 158431--158482 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 18
158421 GATACTTTGG
158431 ATTATTTTTTACTTGAAAA
1 ATTA-TTTTTACTTGAAAA
158450 CATTATTTTTATGCTTGAAAA
1 -ATTATTTTTA--CTTGAAAA
*
158471 A-TATTTATACTT
1 ATTATTTTTACTT
158483 AACTCTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.10
19 13 0.45
20 5 0.17
21 8 0.28
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.52
Consensus pattern (18 bp):
ATTATTTTTACTTGAAAA
Found at i:166080 original size:20 final size:20
Alignment explanation
Indices: 166055--166107 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
166045 GTTGGGCTCA
166055 ATGTATCGATACAATTCACC
1 ATGTATCGATACAATTCACC
* * *
166075 ATGTATTGATGCAATTCATC
1 ATGTATCGATACAATTCACC
166095 AT-TATCGATACAA
1 ATGTATCGATACAA
166108 AGTGAGTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:166963 original size:13 final size:13
Alignment explanation
Indices: 166945--166970 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
166935 CAATTTTTTG
166945 TGTATCGATACAT
1 TGTATCGATACAT
166958 TGTATCGATACAT
1 TGTATCGATACAT
166971 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:167629 original size:30 final size:30
Alignment explanation
Indices: 167593--167652 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
167583 AAAATAAATT
167593 TAACAAATTTGTACATTCTCCCCCTTAATG
1 TAACAAATTTGTACATTCTCCCCCTTAATG
167623 TAACAAATTTGTACATTCTCCCCCTTAATG
1 TAACAAATTTGTACATTCTCCCCCTTAATG
167653 AAATAATTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (30 bp):
TAACAAATTTGTACATTCTCCCCCTTAATG
Found at i:167679 original size:38 final size:38
Alignment explanation
Indices: 167636--167721 Score: 172
Period size: 38 Copynumber: 2.3 Consensus size: 38
167626 CAAATTTGTA
167636 CATTCTCCCCCTTAATGAAATAATTGTAGCAATTTACG
1 CATTCTCCCCCTTAATGAAATAATTGTAGCAATTTACG
167674 CATTCTCCCCCTTAATGAAATAATTGTAGCAATTTACG
1 CATTCTCCCCCTTAATGAAATAATTGTAGCAATTTACG
167712 CATTCTCCCC
1 CATTCTCCCC
167722 TTTATCTCCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.29, C:0.28, G:0.09, T:0.34
Consensus pattern (38 bp):
CATTCTCCCCCTTAATGAAATAATTGTAGCAATTTACG
Found at i:167767 original size:21 final size:21
Alignment explanation
Indices: 167726--167769 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
167716 CTCCCCTTTA
* *
167726 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
167747 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
167768 TC
1 TC
167770 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:169592 original size:13 final size:13
Alignment explanation
Indices: 169574--169612 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
169564 ATAATCACCC
169574 TGTATCGATACAA
1 TGTATCGATACAA
169587 TGTATCGATACAA
1 TGTATCGATACAA
169600 TGTATCGATACAA
1 TGTATCGATACAA
169613 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:171711 original size:15 final size:15
Alignment explanation
Indices: 171691--171721 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
171681 ATTTCGTTTG
*
171691 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
171706 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
171721 G
1 G
171722 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:173554 original size:21 final size:21
Alignment explanation
Indices: 173525--173569 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
173515 AAGTTTTCAT
*
173525 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
173545 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
173567 TTT
1 TTT
173570 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:175521 original size:29 final size:30
Alignment explanation
Indices: 175498--175583 Score: 84
Period size: 36 Copynumber: 2.6 Consensus size: 30
175488 ATCTTTGAAG
*
175498 GCTAAGATAGAAACCTCTCATCTTTTCACGA
1 GCTAAGATAG-AACCTCTCATCTTTTCAAGA
175529 GCTAAGATAGAACCTCTCTCTCTATCTTTTTCAA-A
1 GCTAAGATAGAA---C-CTCTC-ATC-TTTTCAAGA
175564 GACTAAGATAGAACCTCTCA
1 G-CTAAGATAGAACCTCTCA
175584 ATCACTTAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 14
0.76 0.02 0.23
Matches are distributed among these distances:
30 2 0.04
31 11 0.23
32 5 0.11
33 2 0.04
34 5 0.11
35 5 0.11
36 17 0.36
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (30 bp):
GCTAAGATAGAACCTCTCATCTTTTCAAGA
Found at i:176038 original size:20 final size:20
Alignment explanation
Indices: 176013--176065 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
176003 GTTGGGCTCA
*
176013 ATGTATCGTTACAATTCACC
1 ATGTATCGATACAATTCACC
* * *
176033 ATGTATTGATGCAATTCATC
1 ATGTATCGATACAATTCACC
176053 AT-TATCGATACAA
1 ATGTATCGATACAA
176066 AGTGAGTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:176920 original size:13 final size:13
Alignment explanation
Indices: 176902--176927 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
176892 CAATTTTTTG
176902 TGTATCGATACAT
1 TGTATCGATACAT
176915 TGTATCGATACAT
1 TGTATCGATACAT
176928 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:177458 original size:20 final size:21
Alignment explanation
Indices: 177433--177473 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
177423 ATACTTTGAA
177433 TTATTTT-TACTTGAAAAACG
1 TTATTTTATACTTGAAAAACG
*
177453 TTATTTTGATGCTTGAAAAAC
1 TTATTTT-ATACTTGAAAAAC
177474 ATCTATACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (21 bp):
TTATTTTATACTTGAAAAACG
Found at i:179856 original size:13 final size:13
Alignment explanation
Indices: 179838--179868 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
179828 ATATTTCTTC
179838 ATGTATCGATACA
1 ATGTATCGATACA
179851 ATGTATCGATACA
1 ATGTATCGATACA
*
179864 TTGTA
1 ATGTA
179869 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:179957 original size:19 final size:19
Alignment explanation
Indices: 179913--179968 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
179903 CTACCAGTTG
***
179913 CATGTATCGATACAATTTTC
1 CATGTATCGATACAA-TGAA
179933 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
179952 CATGTATCGATACAATG
1 CATGTATCGATACAATG
179969 TATCGATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:179971 original size:13 final size:14
Alignment explanation
Indices: 179953--179994 Score: 59
Period size: 13 Copynumber: 2.9 Consensus size: 14
179943 TACAATGAAC
179953 ATGTATCGATACA-
1 ATGTATCGATACAG
179966 ATGTATCGATACAAAG
1 ATGTATCGATAC--AG
179982 ATGTATCGATACA
1 ATGTATCGATACA
179995 TCTGGGTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 12 0.46
14 1 0.04
15 1 0.04
16 12 0.46
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (14 bp):
ATGTATCGATACAG
Found at i:179975 original size:32 final size:29
Alignment explanation
Indices: 179934--179994 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
179924 ACAATTTTCC
179934 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATAC-A--AACATGTATCGATACA
*
179966 ATGTATCGATACAAAGATGTATCGATACA
1 ATGTATCGATACAAACATGTATCGATACA
179995 TCTGGGTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 15 0.54
31 1 0.04
32 12 0.43
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (29 bp):
ATGTATCGATACAAACATGTATCGATACA
Found at i:180506 original size:13 final size:13
Alignment explanation
Indices: 180488--180513 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
180478 CATTAGAAAG
180488 TTCAAATATCAAA
1 TTCAAATATCAAA
180501 TTCAAATATCAAA
1 TTCAAATATCAAA
180514 GTTTTCGTTT
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:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TTCAAATATCAAA
Found at i:180593 original size:40 final size:40
Alignment explanation
Indices: 180542--180623 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
180532 AAAAATTTTA
*
180542 TTTCTCCCCCTTAAACGATTATCTACCCCTTTATAAAAAT
1 TTTCTCCCCCTTAAACGATAATCTACCCCTTTATAAAAAT
* *
180582 TTTCTCTCCCTTAAACGATAATCTCCCCCTTTATAAAAAT
1 TTTCTCCCCCTTAAACGATAATCTACCCCTTTATAAAAAT
180622 TT
1 TT
180624 ATTTTCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.29, C:0.29, G:0.02, T:0.39
Consensus pattern (40 bp):
TTTCTCCCCCTTAAACGATAATCTACCCCTTTATAAAAAT
Found at i:180611 original size:19 final size:19
Alignment explanation
Indices: 180544--180612 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
180534 AAATTTTATT
180544 TCTCCCCCTTAAACGATTA
1 TCTCCCCCTTAAACGATTA
* ** *
180563 TCTACCCCTTTATAAAAATTT
1 TCT-CCCCCTTA-AACGATTA
* *
180584 TCTCTCCCTTAAACGATAA
1 TCTCCCCCTTAAACGATTA
180603 TCTCCCCCTT
1 TCTCCCCCTT
180613 TATAAAAATT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
19 16 0.43
20 13 0.35
21 8 0.22
ACGTcount: A:0.26, C:0.35, G:0.03, T:0.36
Consensus pattern (19 bp):
TCTCCCCCTTAAACGATTA
Found at i:182328 original size:20 final size:19
Alignment explanation
Indices: 182287--182326 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 19
182277 TTTTGTTGAT
182287 GATTTTGATGAAAAATGAAA
1 GATTTTGATGAAAAAT-AAA
182307 GATTTTGAAGTGAAAAATAA
1 GATTTTG-A-TGAAAAATAA
182327 GAAATTTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (19 bp):
GATTTTGATGAAAAATAAA
Done.