Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold146
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: 254200
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 25 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:142409 original size:21 final size:20
Alignment explanation
Indices: 142365--142409 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
142355 AACAAATCAT
* **
142365 TCTTCAAATTCTTTAATTTT
1 TCTTCAAATTCTTCAATTAC
142385 TCTTCAAATTTCTTCAATTAC
1 TCTTCAAA-TTCTTCAATTAC
142406 TCTT
1 TCTT
142410 TAAAATCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (20 bp):
TCTTCAAATTCTTCAATTAC
Found at i:142739 original size:14 final size:14
Alignment explanation
Indices: 142720--142748 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
142710 TTGTACTTAA
142720 CCTTTATTTCTTTG
1 CCTTTATTTCTTTG
142734 CCTTTATTTCTTTG
1 CCTTTATTTCTTTG
142748 C
1 C
142749 TTTTGTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.24, G:0.07, T:0.62
Consensus pattern (14 bp):
CCTTTATTTCTTTG
Found at i:143653 original size:20 final size:20
Alignment explanation
Indices: 143628--143665 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
143618 GTATCAATAC
143628 ATTGTATCGATACATGAAGA
1 ATTGTATCGATACATGAAGA
143648 ATTGTATCGATACATGAA
1 ATTGTATCGATACATGAA
143666 ACTGGTAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
ATTGTATCGATACATGAAGA
Found at i:143717 original size:20 final size:20
Alignment explanation
Indices: 143690--143744 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
143680 CCCTATCACT
*
143690 ATTTGTATCGATACATGGGA
1 ATTTGTATCGATACATAGGA
*
143710 CA-TTGTATCGATACATAGTA
1 -ATTTGTATCGATACATAGGA
143730 ATTTGTATCGATACA
1 ATTTGTATCGATACA
143745 CTGTGCCTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
ATTTGTATCGATACATAGGA
Found at i:145327 original size:16 final size:18
Alignment explanation
Indices: 145289--145330 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
145279 TACTTGTTTG
145289 ATTTTCTATCTCTTAATTA
1 ATTTT-TATCTCTTAATTA
*
145308 ATTTTTATCT-TT-ATTT
1 ATTTTTATCTCTTAATTA
145324 ATTTTTA
1 ATTTTTA
145331 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 10 0.45
17 2 0.09
18 5 0.23
19 5 0.23
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTATCTCTTAATTA
Found at i:146012 original size:29 final size:29
Alignment explanation
Indices: 145962--146108 Score: 188
Period size: 29 Copynumber: 5.1 Consensus size: 29
145952 ACTTCATTTT
145962 GTCAGTGGCACCCTTTTCCAAAGCCCACAA
1 GTCAGTGGCA-CCTTTTCCAAAGCCCACAA
*
145992 GTCAGTGGCATCTTTTCCAAAGCCCACAA
1 GTCAGTGGCACCTTTTCCAAAGCCCACAA
*
146021 GTCAGTGGCACCTTTTCCAAAGCCCATAA
1 GTCAGTGGCACCTTTTCCAAAGCCCACAA
* * * * *
146050 GTCAATGGTATCTCTTCAAAAGCCCACAA
1 GTCAGTGGCACCTTTTCCAAAGCCCACAA
* * *
146079 GTCAGTGGCAAC-TTTCAAAAGCACACAA
1 GTCAGTGGCACCTTTTCCAAAGCCCACAA
146107 GT
1 GT
146109 TGGTGCAACC
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
28 16 0.16
29 77 0.75
30 10 0.10
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (29 bp):
GTCAGTGGCACCTTTTCCAAAGCCCACAA
Found at i:146128 original size:29 final size:27
Alignment explanation
Indices: 146064--146144 Score: 90
Period size: 28 Copynumber: 2.8 Consensus size: 27
146054 ATGGTATCTC
* **
146064 TTCAAAAGCCCACAAGTCAGTGGCAACT
1 TTCAAAAGCACACAAGTTGGT-GCAACT
146092 TTCAAAAGCACACAAGTTGGTGCAACCCT
1 TTCAAAAGCACACAAGTTGGTGCAA--CT
146121 TTCAAAAGTCCACACAAGTTGGTG
1 TTCAAAAG--CACACAAGTTGGTG
146145 GCATCTTCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
27 4 0.09
28 18 0.39
29 10 0.22
31 14 0.30
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (27 bp):
TTCAAAAGCACACAAGTTGGTGCAACT
Found at i:146268 original size:49 final size:49
Alignment explanation
Indices: 146151--146378 Score: 237
Period size: 43 Copynumber: 4.8 Consensus size: 49
146141 GGTGGCATCT
*
146151 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA----C-
1 TCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* *
146196 -CTTTAAGTCCAATATAGCTGGCCTTGAGTCAGCATATTGGCACCTTCA
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
* * * *
146244 TCTTTAAATCCAATGTAGCTGGCCTTGAATTAGCACACTGGCA----C-
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
*
146288 -CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCA
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-CA
* * *
146339 TCTTTAAGTTCAATGTTGCTGGCCTTGAATCAGCACATTG
1 TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
146379 ACATCCTTTT
Statistics
Matches: 150, Mismatches: 18, Indels: 23
0.79 0.09 0.12
Matches are distributed among these distances:
43 73 0.49
44 3 0.02
45 1 0.01
47 1 0.01
49 36 0.24
50 1 0.01
52 35 0.23
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (49 bp):
TCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCA
Found at i:146320 original size:92 final size:94
Alignment explanation
Indices: 146151--146375 Score: 346
Period size: 92 Copynumber: 2.4 Consensus size: 94
146141 GGTGGCATCT
* * *
146151 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGCTG
1 TCTT-TAAGTCCAATGTAGCTGGCCTTGAATCAGCACACTGGCACCTTTAAGTCCAATATAGCTG
*
146216 GCCTTGAGTCAGCATATTGGCACC-TT-CA
65 GCCTTGAATCAGCATATTGGCACCTTTCCA
* *
146244 TCTTTAAATCCAATGTAGCTGGCCTTGAATTAGCACACTGGCACCTTTAAGTCCAATATAGCTGG
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACACTGGCACCTTTAAGTCCAATATAGCTGG
146309 CCTTGAATCAGCATATTGGCACCTTTTCCA
66 CCTTGAATCAGCATATTGGCACC-TTTCCA
* *
146339 TCTTTAAGTTCAATGTTGCTGGCCTTGAATCAGCACA
1 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACA
146376 TTGACATCCT
Statistics
Matches: 119, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
92 78 0.66
93 4 0.03
94 2 0.02
95 35 0.29
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (94 bp):
TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACACTGGCACCTTTAAGTCCAATATAGCTGG
CCTTGAATCAGCATATTGGCACCTTTCCA
Found at i:146366 original size:52 final size:55
Alignment explanation
Indices: 146288--146425 Score: 160
Period size: 52 Copynumber: 2.6 Consensus size: 55
146278 ACACTGGCAC
* *
146288 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * *
146340 CTTTAAGTTCAATGTTGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* *
146395 CTTTGAA-CCCAATATCA-CTGGCCGTGAATCA
1 CTTT-AAGTCCAATAT-AGCTGGCCTTGAATCA
146426 ACGTATTGGT
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
52 37 0.52
53 2 0.03
54 5 0.07
55 25 0.35
56 2 0.03
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:147092 original size:13 final size:13
Alignment explanation
Indices: 147074--147130 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
147064 CATAAAGTGT
147074 TGTATCGATACAA
1 TGTATCGATACAA
147087 TGTATCGATACATAA
1 TGTATCGATAC--AA
147102 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
147119 TGTATCGATACA
1 TGTATCGATACA
147131 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:147109 original size:32 final size:32
Alignment explanation
Indices: 147054--147154 Score: 184
Period size: 32 Copynumber: 3.1 Consensus size: 32
147044 TTCAACAATT
147054 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
147087 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
147119 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
147151 TGTA
1 TGTA
147155 AGCTACAACC
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
32 54 0.81
33 13 0.19
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:147111 original size:19 final size:18
Alignment explanation
Indices: 147052--147149 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
147042 ATTTCAACAA
147052 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
147071 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
147087 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
147103 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
147119 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
147135 TTTTGTATCGATACA
1 -TTTGTATCGATACA
147150 ATGTAAGCTA
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
19 24 0.36
20 12 0.18
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:147175 original size:65 final size:65
Alignment explanation
Indices: 147054--147182 Score: 154
Period size: 65 Copynumber: 2.0 Consensus size: 65
147044 TTCAACAATT
* * ****
147054 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACACAAAAAATGTATCGATACAA
* *
147119 TGTATCGATACAT-AAGTTTTGTATCGATACAATGTA-AGCTACAACCAAAAAATGTATCGATAC
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATAC-A-CAAAAAATGTATCGATAC
147182 A
64 A
147183 TTACTCAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
63 4 0.07
64 23 0.43
65 27 0.50
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (65 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAATGTATAGATACACAAAAAATGTATCGATACAA
Found at i:147268 original size:52 final size:52
Alignment explanation
Indices: 147225--147405 Score: 335
Period size: 52 Copynumber: 3.5 Consensus size: 52
147215 CACTGATCTT
*
147225 TGTATCAATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
147277 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
147329 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
147381 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
147406 TCATATTTCG
Statistics
Matches: 125, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 125 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:151537 original size:30 final size:30
Alignment explanation
Indices: 151502--151566 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
151492 AAATAATGTA
* * *
151502 AGTGATTTAATTTATTAATAGTAAAAATTT
1 AGTGATATAATTTAATAAAAGTAAAAATTT
*
151532 AGTGATATAATTTAATAAAATTAAAAATTT
1 AGTGATATAATTTAATAAAAGTAAAAATTT
151562 -GTGAT
1 AGTGAT
151567 CTATATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (30 bp):
AGTGATATAATTTAATAAAAGTAAAAATTT
Found at i:152227 original size:3 final size:3
Alignment explanation
Indices: 152219--152251 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
152209 GTAAAAATAA
*
152219 ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
152252 TGATTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:152388 original size:2 final size:2
Alignment explanation
Indices: 152381--152411 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
152371 GCATTATTAC
*
152381 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
152412 AAAGGTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:152594 original size:27 final size:24
Alignment explanation
Indices: 152531--152594 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 24
152521 TATTTTTTAC
152531 ATATATATTTAAATATTAAATTTTT
1 ATAT-TATTTAAATATTAAATTTTT
**
152556 ATATTAAATAAATAATTAAATATTTT
1 ATATTATTTAAAT-ATTAAAT-TTTT
152582 -TAATTTATTTAAA
1 AT-A-TTATTTAAA
152595 ATTTAACATA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
24 7 0.23
25 12 0.39
26 5 0.16
27 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
ATATTATTTAAATATTAAATTTTT
Found at i:156565 original size:22 final size:22
Alignment explanation
Indices: 156530--156581 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
156520 ATTGATTAAA
*
156530 AAAAATTATTTAAAT-TTAATTAT
1 AAAAA-TATATAAATATTAA-TAT
156553 AAAAATATATAAATATTAATAT
1 AAAAATATATAAATATTAATAT
156575 AAAAATA
1 AAAAATA
156582 AATTTTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAAATATATAAATATTAATAT
Found at i:158317 original size:2 final size:2
Alignment explanation
Indices: 158304--158351 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
158294 AAAGTATCTC
*
158304 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
158346 AT AT AT
1 AT AT AT
158352 CCGATTCAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:158947 original size:22 final size:23
Alignment explanation
Indices: 158922--158964 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
158912 CATTATTGGC
* *
158922 TAAAAAT-AATTTTTAGAATTAT
1 TAAAAATGAAATTTTACAATTAT
158944 TAAAAATGAAATTTTACAATT
1 TAAAAATGAAATTTTACAATT
158965 GCTGAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (23 bp):
TAAAAATGAAATTTTACAATTAT
Found at i:162606 original size:52 final size:52
Alignment explanation
Indices: 162521--162649 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
162511 CGAAATATGA
*
162521 AAATTTGCCTGAATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
162573 AAATTTGCCCGCATGTATCGATACAGTTT-ATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTTCATAGTGTATCGATACATCTGGGC
162625 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
162650 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
52 70 0.96
53 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:162676 original size:13 final size:13
Alignment explanation
Indices: 162658--162682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
162648 CAAAGATCAG
162658 TGTATCGATACAA
1 TGTATCGATACAA
162671 TGTATCGATACA
1 TGTATCGATACA
162683 TTTGAGTAAT
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:162770 original size:32 final size:32
Alignment explanation
Indices: 162729--162790 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
162719 CTTCGTAGCG
162729 ATACATTGTATCGATACAAAACTTATGTATCA
1 ATACATTGTATCGATACAAAACTTATGTATCA
*
162761 ATACATTGTATCGATACAACACTTATGTAT
1 ATACATTGTATCGATACAAAACTTATGTAT
162791 TGATATAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (32 bp):
ATACATTGTATCGATACAAAACTTATGTATCA
Found at i:163605 original size:49 final size:48
Alignment explanation
Indices: 163535--163806 Score: 290
Period size: 49 Copynumber: 5.7 Consensus size: 48
163525 CGAAGAATGA
* **
163535 CAATGTGCTGATTCTTGGCCAGCGACATTGATCTTAAAGATGACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGA-CTTAAAGATGACGGTGC
* * * * * *
163584 CAATATGTTGATTCAAAGCCAGCGATATCAGACTTAAAGATGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACAT-TGACTTAAAGATGACGGTGC
* * * *
163633 TAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GACTTAAAGATGACGGTGC
*
163682 CAATA--CTGATTCAAGGCCAGCGATATTGGACTT--A-A--A-GGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GACTTAAAGATGACGGTGC
*
163723 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GACTTAAAGATGACGGTGC
*
163772 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 CAATATGCTGATTCAAGGCCAGCGACATT-GACTT
163807 GGAAGAAGAT
Statistics
Matches: 185, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
41 9 0.05
42 1 0.01
43 27 0.15
44 1 0.01
45 2 0.01
46 1 0.01
47 25 0.14
48 1 0.01
49 116 0.63
50 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGACTTAAAGATGACGGTGC
Found at i:163882 original size:29 final size:29
Alignment explanation
Indices: 163850--164045 Score: 157
Period size: 28 Copynumber: 6.8 Consensus size: 29
163840 AATAGGGTTG
* *
163850 CACTAACTTGTGTGCTTTTGAAAAGATAC
1 CACTAACTTGTGGGCTTTTGAAAAGATGC
* *
163879 CACTAACTTGTGGGCTTTTG-AAGGTTGC
1 CACTAACTTGTGGGCTTTTGAAAAGATGC
* * * *
163907 CACTGACTTATGGGCTTTGGAAAAGGGTGC
1 CACTAACTTGTGGGCTTTTGAAAA-GATGC
* * *
163937 CACTGACTTGTGGGCTTTTG-AAGGTTGC
1 CACTAACTTGTGGGCTTTTGAAAAGATGC
* * * * * *
163965 CACTGATTTGTAGGC-TTTGGAAGGTTGC
1 CACTAACTTGTGGGCTTTTGAAAAGATGC
* * *
163993 CACTGACTTGTGGGCTTTGGAAAGGATGC
1 CACTAACTTGTGGGCTTTTGAAAAGATGC
*
164022 CA-TGAACTTGTGGGCTTTGGAAAA
1 CACT-AACTTGTGGGCTTTTGAAAA
164046 TGTGAGGAAT
Statistics
Matches: 140, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
27 4 0.03
28 61 0.44
29 53 0.38
30 22 0.16
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (29 bp):
CACTAACTTGTGGGCTTTTGAAAAGATGC
Found at i:163920 original size:28 final size:28
Alignment explanation
Indices: 163878--164043 Score: 217
Period size: 28 Copynumber: 5.8 Consensus size: 28
163868 TGAAAAGATA
* *
163878 CCACTAACTTGTGGGCTTTTGAAGGTTG
1 CCACTGACTTGTGGGCTTTGGAAGGTTG
* *
163906 CCACTGACTTATGGGCTTTGGAAAAGGGTG
1 CCACTGACTTGTGGGCTTTGG--AAGGTTG
*
163936 CCACTGACTTGTGGGCTTTTGAAGGTTG
1 CCACTGACTTGTGGGCTTTGGAAGGTTG
* *
163964 CCACTGATTTGTAGGCTTTGGAAGGTTG
1 CCACTGACTTGTGGGCTTTGGAAGGTTG
*
163992 CCACTGACTTGTGGGCTTTGGAAAGGATG
1 CCACTGACTTGTGGGCTTTGG-AAGGTTG
164021 CCA-TGAACTTGTGGGCTTTGGAA
1 CCACTG-ACTTGTGGGCTTTGGAA
164044 AATGTGAGGA
Statistics
Matches: 121, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
28 72 0.60
29 24 0.20
30 25 0.21
ACGTcount: A:0.19, C:0.17, G:0.32, T:0.32
Consensus pattern (28 bp):
CCACTGACTTGTGGGCTTTGGAAGGTTG
Found at i:163940 original size:58 final size:58
Alignment explanation
Indices: 163829--164045 Score: 246
Period size: 58 Copynumber: 3.8 Consensus size: 58
163819 CACCAACTTG
* * * * * *
163829 TGTGGGCTTTTAATAGGGTTG-CACTAACTTGTGTGCTTTTGAAAA-GATACCACTAACT
1 TGTGGGCTTTTGA-A-GGTTGCCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTGACT
* *
163887 TGTGGGCTTTTGAAGGTTGCCACTGACTTATGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTGACT
* * *
163945 TGTGGGCTTTTGAAGGTTGCCACTGATTTGTAGGCTTTGG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTGACT
* *
164001 TGTGGGCTTTGGAAAGGATGCCA-TGAACTTGTGGGCTTTGGAAAA
1 TGTGGGCTTTTG-AAGGTTGCCACTG-ACTTGTGGGCTTTGGAAAA
164046 TGTGAGGAAT
Statistics
Matches: 137, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
56 33 0.24
57 43 0.31
58 59 0.43
59 2 0.01
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.33
Consensus pattern (58 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTGGAAAAGGATGCCACTGACT
Found at i:163988 original size:86 final size:86
Alignment explanation
Indices: 163850--164045 Score: 252
Period size: 86 Copynumber: 2.3 Consensus size: 86
163840 AATAGGGTTG
* * * *
163850 CACTAACTTGTGTGCTTTTGAAAAGATACCACTAACTTGTGGGCTTTTGAAGGTTGCCACTGACT
1 CACTGACTTGTGGGCTTTTGAAAAGATACCACTAACTTGTAGGCTTTGGAAGGTTGCCACTGACT
*
163915 TATGGGCTTTGGAAAAGGGTGC
66 TATGGGCTTTGG-AAAGGATGC
* * * * *
163937 CACTGACTTGTGGGCTTTTG-AAGGTTGCCACTGATTTGTAGGCTTTGGAAGGTTGCCACTGACT
1 CACTGACTTGTGGGCTTTTGAAAAGATACCACTAACTTGTAGGCTTTGGAAGGTTGCCACTGACT
*
164001 TGTGGGCTTTGGAAAGGATGC
66 TATGGGCTTTGGAAAGGATGC
*
164022 CA-TGAACTTGTGGGCTTTGGAAAA
1 CACTG-ACTTGTGGGCTTTTGAAAA
164046 TGTGAGGAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
84 2 0.02
85 24 0.26
86 50 0.53
87 18 0.19
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (86 bp):
CACTGACTTGTGGGCTTTTGAAAAGATACCACTAACTTGTAGGCTTTGGAAGGTTGCCACTGACT
TATGGGCTTTGGAAAGGATGC
Found at i:165496 original size:1 final size:1
Alignment explanation
Indices: 165492--165579 Score: 59
Period size: 1 Copynumber: 88.0 Consensus size: 1
165482 TTTGTTGTTG
* * * * * * * **
165492 TTTTTATTTTTTTTCTTTGTTTTTTTGTTTTTTGTTTTTTGTTTTTTTTTGTTTTTTTCATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * **
165557 TTTTGTTTATTTGGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTT
165580 GTAGAGGACG
Statistics
Matches: 64, Mismatches: 23, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.03, C:0.02, G:0.09, T:0.85
Consensus pattern (1 bp):
T
Found at i:165511 original size:19 final size:17
Alignment explanation
Indices: 165480--165581 Score: 96
Period size: 19 Copynumber: 5.6 Consensus size: 17
165470 ATCCGGACCC
* *
165480 TTTTTGTTGTTGTTTTTA
1 TTTTTTTTGTT-TTTTTT
*
165498 TTTTTTTTCTTTGTTTTT
1 TTTTTTTTGTTT-TTTTT
*
165516 TTGTTTTTTGTTTTTTGT
1 TT-TTTTTTGTTTTTTTT
165534 TTTTTTTTGTTTTTTTCAT
1 TTTTTTTTGTTTTTTT--T
*
165553 TTTTTTTTGTTTATTTGGT
1 TTTTTTTTGTTT-TTT-TT
165572 TTTTTTTTGT
1 TTTTTTTTGT
165582 AGAGGACGCC
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
17 14 0.20
18 21 0.30
19 33 0.46
20 3 0.04
ACGTcount: A:0.03, C:0.02, G:0.12, T:0.83
Consensus pattern (17 bp):
TTTTTTTTGTTTTTTTT
Found at i:165517 original size:33 final size:32
Alignment explanation
Indices: 165480--165549 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 32
165470 ATCCGGACCC
*
165480 TTTTTG-TTGTTGTTTTTATTTTTTTTCTTTGTT
1 TTTTTGTTTGTTGTTTTT-TGTTTTTT-TTTGTT
*
165513 TTTTTGTTTTTTGTTTTTTGTTTTTTTTTGTT
1 TTTTTGTTTGTTGTTTTTTGTTTTTTTTTGTT
165545 TTTTT
1 TTTTT
165550 CATTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
32 11 0.32
33 13 0.38
34 10 0.29
ACGTcount: A:0.01, C:0.01, G:0.11, T:0.86
Consensus pattern (32 bp):
TTTTTGTTTGTTGTTTTTTGTTTTTTTTTGTT
Found at i:165540 original size:44 final size:45
Alignment explanation
Indices: 165481--165581 Score: 127
Period size: 44 Copynumber: 2.2 Consensus size: 45
165471 TCCGGACCCT
*
165481 TTTTGTTGTTGTTTTTAT-TTTTTTTCTTTGTTTTTTTGTTT-TTT-G
1 TTTT-TTGTTGTTTTT-TGTTTTTTTCATT-TTTTTTTGTTTATTTGG
*
165526 TTTTTTGTTTTTTTTTGTTTTTTTCATTTTTTTTTGTTTATTTGG
1 TTTTTTGTTGTTTTTTGTTTTTTTCATTTTTTTTTGTTTATTTGG
*
165571 TTTTTTTTTGT
1 TTTTTTGTTGT
165582 AGAGGACGCC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
43 12 0.24
44 23 0.47
45 14 0.29
ACGTcount: A:0.03, C:0.02, G:0.12, T:0.83
Consensus pattern (45 bp):
TTTTTTGTTGTTTTTTGTTTTTTTCATTTTTTTTTGTTTATTTGG
Found at i:179554 original size:52 final size:52
Alignment explanation
Indices: 179408--179536 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
179398 CGAAATATGA
* *
179408 AAATTTGCCTGCATATATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATAAATCTAGGC
* * *
179460 AAATTTGCCCGCATGTATCGATACATTTTATAGTGTATCGATAAATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATAAATCTAGGC
179512 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
179537 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATAAATCTAGGC
Found at i:179563 original size:13 final size:13
Alignment explanation
Indices: 179545--179569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
179535 CAAAGATCAG
179545 TGTATCGATACAA
1 TGTATCGATACAA
179558 TGTATCGATACA
1 TGTATCGATACA
179570 TTTGAGTAAT
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:179655 original size:32 final size:32
Alignment explanation
Indices: 179614--179684 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
179604 AGCTTCGTAG
179614 CGATACATTGTATCGACACAAAACTTATGTAT
1 CGATACATTGTATCGACACAAAACTTATGTAT
* *
179646 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGACACAAAACTTATGTAT
*
179678 TGATACA
1 CGATACA
179685 AATCGTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGACACAAAACTTATGTAT
Found at i:179659 original size:13 final size:13
Alignment explanation
Indices: 179641--179665 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
179631 ACAAAACTTA
179641 TGTATCGATACAT
1 TGTATCGATACAT
179654 TGTATCGATACA
1 TGTATCGATACA
179666 ACACTTATGT
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:180971 original size:28 final size:28
Alignment explanation
Indices: 180920--180989 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
180910 ATATCTTTTC
*
180920 TTTTCTTTTTTTTTAAACCTAAAT-TCTTA
1 TTTTC-TTTTTTTTAAACCGAAATCT-TTA
* * *
180949 TTTTCTTTATTTTAAATCGAAATCTTTC
1 TTTTCTTTTTTTTAAACCGAAATCTTTA
180977 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
180990 TCCTTTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
28 29 0.83
29 6 0.17
ACGTcount: A:0.20, C:0.13, G:0.01, T:0.66
Consensus pattern (28 bp):
TTTTCTTTTTTTTAAACCGAAATCTTTA
Found at i:181416 original size:21 final size:21
Alignment explanation
Indices: 181391--181437 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
181381 GAATGCAATG
*
181391 ATGCATTGGTTGGATGAAAGA
1 ATGCATTGGTTGGATGAAAAA
** *
181412 ATGCATTTTTTGGATTAAAAA
1 ATGCATTGGTTGGATGAAAAA
181433 ATGCA
1 ATGCA
181438 ACTTTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.34
Consensus pattern (21 bp):
ATGCATTGGTTGGATGAAAAA
Found at i:181443 original size:21 final size:21
Alignment explanation
Indices: 181400--181443 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
181390 GATGCATTGG
* **
181400 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAAAATGCAACTT
*
181421 TTGGATTAAAAAATGCAACTT
1 TTGGATGAAAAAATGCAACTT
181442 TT
1 TT
181444 AATAACCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (21 bp):
TTGGATGAAAAAATGCAACTT
Found at i:185880 original size:2 final size:2
Alignment explanation
Indices: 185873--185910 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
185863 TTTTTAATGC
185873 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
185911 ATTTATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:192482 original size:20 final size:20
Alignment explanation
Indices: 192457--192512 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
192447 TTTTGCCTGC
*
192457 ATGTATCGATACATTTCATA
1 ATGTATTGATACATTTCATA
192477 ATGTATTGATACATTTCATA
1 ATGTATTGATACATTTCATA
192497 ATGTATTGATACATTT
1 ATGTATTGATACATTT
192513 TGGTAAAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (20 bp):
ATGTATTGATACATTTCATA
Found at i:193248 original size:15 final size:13
Alignment explanation
Indices: 193223--193256 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
193213 TTAATAACAA
193223 AAAATTAT-TTTT
1 AAAATTATATTTT
193235 AATAATTATATTTT
1 AA-AATTATATTTT
193249 AAAATTAT
1 AAAATTAT
193257 CCCTAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 12 0.60
14 6 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AAAATTATATTTT
Found at i:195585 original size:47 final size:47
Alignment explanation
Indices: 195516--195609 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
195506 CATATATATA
*
195516 TATATATATGAATGCAATGATTGGTGTCATTAGTTAAAGAATGCTTG
1 TATATATATGAATGCAATGATTGGTGTCATTACTTAAAGAATGCTTG
195563 TATATATATGAATGCAATGATTGGTGTCATTACTTAAAGAATGCTTG
1 TATATATATGAATGCAATGATTGGTGTCATTACTTAAAGAATGCTTG
195610 CATAATTCAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.38
Consensus pattern (47 bp):
TATATATATGAATGCAATGATTGGTGTCATTACTTAAAGAATGCTTG
Found at i:195891 original size:2 final size:2
Alignment explanation
Indices: 195884--195941 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
195874 CCATATTCTA
* *
195884 AT AT AT AT AT AT AT AT AA AT AT AT AT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
195926 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
195942 TAGAGTATGG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:196524 original size:21 final size:21
Alignment explanation
Indices: 196498--196539 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
196488 CCGAGGCAAA
196498 GAGTTCCATACAATCTAAAAC
1 GAGTTCCATACAATCTAAAAC
196519 GAGTTCCATACAATCTAAAAC
1 GAGTTCCATACAATCTAAAAC
196540 ACCCGACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (21 bp):
GAGTTCCATACAATCTAAAAC
Found at i:198897 original size:21 final size:21
Alignment explanation
Indices: 198864--198904 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
198854 TTAAGTAAAA
198864 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
198885 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
198905 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:198969 original size:20 final size:19
Alignment explanation
Indices: 198944--199014 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 19
198934 ACCCTGAAAA
198944 GTATCGATACACATTTAAAT
1 GTATCGATACACA-TTAAAT
* **
198964 GTATCGATACAAATTGCAT
1 GTATCGATACACATTAAAT
**
198983 AGTATCGATACACACAAATAT
1 -GTATCGATACACATTAA-AT
199004 GTATCGATACA
1 GTATCGATACA
199015 GGACATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 4 0.10
20 35 0.85
21 2 0.05
ACGTcount: A:0.41, C:0.17, G:0.13, T:0.30
Consensus pattern (19 bp):
GTATCGATACACATTAAAT
Found at i:199062 original size:53 final size:53
Alignment explanation
Indices: 198984--199120 Score: 220
Period size: 53 Copynumber: 2.6 Consensus size: 53
198974 AAATTGCATA
*
198984 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAACTT
* * *
199038 GTATCGATACATACAATATGTATCGATACAGGTCATTGGCAGTAGCGAAACTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAACTT
*
199091 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
199121 TTGGAAGTAG
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 64 0.83
54 13 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAACTT
Found at i:199180 original size:22 final size:21
Alignment explanation
Indices: 199152--199206 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 21
199142 TTTCACTATT
199152 CATCACTATTCAGGTATCGATA
1 CATCACT-TTCAGGTATCGATA
**
199174 CATCACTTTCTTGTATCGATA
1 CATCACTTTCAGGTATCGATA
199195 CATCACTGTTCA
1 CATCACT-TTCA
199207 TACTGTTCTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 19 0.66
22 10 0.34
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.36
Consensus pattern (21 bp):
CATCACTTTCAGGTATCGATA
Found at i:199864 original size:34 final size:35
Alignment explanation
Indices: 199801--199867 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
199791 CTAAGTGATT
199801 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
199837 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
199868 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:203487 original size:21 final size:22
Alignment explanation
Indices: 203463--203503 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
203453 GACATGCTGT
203463 AAATGCATGAAACAT-AGCTCA
1 AAATGCATGAAACATGAGCTCA
*
203484 AAATGCATGAATCATGAGCT
1 AAATGCATGAAACATGAGCT
203504 GTTAACATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (22 bp):
AAATGCATGAAACATGAGCTCA
Found at i:204427 original size:13 final size:13
Alignment explanation
Indices: 204409--204434 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
204399 AGGGTAGCTT
204409 TTGTATCGATACA
1 TTGTATCGATACA
204422 TTGTATCGATACA
1 TTGTATCGATACA
204435 ACACTTATGT
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:205043 original size:5 final size:5
Alignment explanation
Indices: 205030--205059 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
205020 AAGATTTTGG
*
205030 AAAAC AAAAT AAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
205060 TAAATATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.80, C:0.17, G:0.00, T:0.03
Consensus pattern (5 bp):
AAAAC
Found at i:205045 original size:10 final size:10
Alignment explanation
Indices: 205030--205063 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
205020 AAGATTTTGG
205030 AAAACAAAAT
1 AAAACAAAAT
*
205040 AAAACAAAAC
1 AAAACAAAAT
205050 AAAACAAAACT
1 AAAACAAAA-T
205061 AAA
1 AAA
205064 TATATACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.86
11 3 0.14
ACGTcount: A:0.79, C:0.15, G:0.00, T:0.06
Consensus pattern (10 bp):
AAAACAAAAT
Found at i:205273 original size:65 final size:65
Alignment explanation
Indices: 205142--205508 Score: 328
Period size: 65 Copynumber: 5.6 Consensus size: 65
205132 AACCATAATA
* * * *
205142 AACTAAGGGTGGCTAGGACAAAACCTAAGTCTAAAAAGGGTTAAC-AAGGGTGAAACCATAATAG
1 AACTAAGGGTGACTAGGACAAAACCTAAGT-TGAAAAGGGTTGACTAA-GGTCAAACCATAATAG
205206 TC
64 TC
* ** * * * *
205208 AACTAAGGGTGATTAGGACGGAACTTAAGTTGAAAAGGGTTAACTAAGGTCAAGCTATAATAGTC
1 AACTAAGGGTGACTAGGACAAAACCTAAGTTGAAAAGGGTTGACTAAGGTCAAACCATAATAGTC
* * * *
205273 AACTAA-GGTAACTAGGACAAAACCTAAGTTTAAGAAGGGGTTGACTAAGGTGAAACCATGATAG
1 AACTAAGGGTGACTAGGACAAAACCTAAGTTGAA-AA-GGGTTGACTAAGGTCAAACCATAATAG
205337 TC
64 TC
** * * * * **
205339 AACTAAGAATGACTAAGACAGAACCTAAGTTGAAAAGGGTTGA-TCAGGGCAAAACCATGGTAGT
1 AACTAAGGGTGACTAGGACAAAACCTAAGTTGAAAAGGGTTGACTAAGGTC-AAACCATAATAGT
205403 C
65 C
** * * * * * *
205404 AACTAAGGGCAACTAGGACGAAACTTAAGTCTAAAAATAGGTTGA-TTAGGGCGAAACCATAATA
1 AACTAAGGGTGACTAGGACAAAACCTAAGT-TGAAAA-GGGTTGACTAAGGTC-AAACCATAATA
205468 GTC
63 GTC
* * *
205471 AACTAAAGGTGACTAGGACGAAACCTAAGTCGAAAAGG
1 AACTAAGGGTGACTAGGACAAAACCTAAGTTGAAAAGG
205509 AGTATCTGAA
Statistics
Matches: 243, Mismatches: 51, Indels: 15
0.79 0.17 0.05
Matches are distributed among these distances:
64 25 0.10
65 79 0.33
66 68 0.28
67 71 0.29
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (65 bp):
AACTAAGGGTGACTAGGACAAAACCTAAGTTGAAAAGGGTTGACTAAGGTCAAACCATAATAGTC
Found at i:205476 original size:132 final size:129
Alignment explanation
Indices: 205154--205508 Score: 399
Period size: 131 Copynumber: 2.7 Consensus size: 129
205144 CTAAGGGTGG
* * *
205154 CTAGGACAAAACCTAAGTCTAAAAAGGGTTAACAAGGGTGAAACCATAATAGTCAACTAAGGGTG
1 CTAGGACAAAACCTAAGTCTAAAAAGGGTTGACTAGGGTGAAACCATAATAGTCAACTAAGAGTG
* * * * * *
205219 ATTAGGACGGAACTTAAGTTGAAAAGGGTTAACTAAGGTCAAGCTATAATAGTCAACTAAGGTAA
66 ACTAGGAC-GAACCTAAGTTGAAAAGGGTTAACTAAGGGCAAACCATAATAGTCAACTAAGGCAA
* * * * *
205284 CTAGGACAAAACCTAAGTTTAAGAAGGGGTTGACTAAGGTGAAACCATGATAGTCAACTAAGAAT
1 CTAGGACAAAACCTAAGTCTAA-AAAGGGTTGACTAGGGTGAAACCATAATAGTCAACTAAGAGT
* * * **
205349 GACTAAGACAGAACCTAAGTTGAAAAGGGTTGA-TCAGGGCAAAACCATGGTAGTCAACTAAGGG
65 GACTAGGAC-GAACCTAAGTTGAAAAGGGTTAACTAAGGGC-AAACCATAATAGTCAACTAA-GG
205413 CAA
127 CAA
* * * * *
205416 CTAGGACGAAACTTAAGTCTAAAAATAGGTTGATTAGGGCGAAACCATAATAGTCAACTAA-AGG
1 CTAGGACAAAACCTAAGTCTAAAAA-GGGTTGACTAGGGTGAAACCATAATAGTCAACTAAGA-G
*
205480 TGACTAGGACGAAACCTAAGTCGAAAAGG
64 TGACTAGGACG-AACCTAAGTTGAAAAGG
205509 AGTATCTGAA
Statistics
Matches: 187, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
130 26 0.14
131 83 0.44
132 78 0.42
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (129 bp):
CTAGGACAAAACCTAAGTCTAAAAAGGGTTGACTAGGGTGAAACCATAATAGTCAACTAAGAGTG
ACTAGGACGAACCTAAGTTGAAAAGGGTTAACTAAGGGCAAACCATAATAGTCAACTAAGGCAA
Found at i:207110 original size:20 final size:20
Alignment explanation
Indices: 207085--207122 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
207075 CGTTGGCTCA
*
207085 ATGTATCGATACATTTCACC
1 ATGTATCGATACAATTCACC
207105 ATGTATCGATACAATTCA
1 ATGTATCGATACAATTCA
207123 ATCATGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:209800 original size:19 final size:20
Alignment explanation
Indices: 209776--209828 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
209766 ATATAGTCGA
209776 AATGTATCGATACAATTT-T
1 AATGTATCGATACAATTTCT
* *
209795 AATGTATTGATGCAAATTTCT
1 AATGTATCGATAC-AATTTCT
*
209816 -TTGTATCGATACA
1 AATGTATCGATACA
209829 TCTGGAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 12 0.44
20 14 0.52
21 1 0.04
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (20 bp):
AATGTATCGATACAATTTCT
Found at i:209992 original size:15 final size:15
Alignment explanation
Indices: 209972--210002 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
209962 ATTCAATAAC
*
209972 ATTCATAAACACTTA
1 ATTCATAAACAATTA
209987 ATTCATAAACAATTA
1 ATTCATAAACAATTA
210002 A
1 A
210003 CCACGCAACA
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:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTCATAAACAATTA
Found at i:210684 original size:21 final size:21
Alignment explanation
Indices: 210651--210691 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
210641 CTAAGTAAAA
210651 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
210672 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
210692 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:210757 original size:21 final size:20
Alignment explanation
Indices: 210728--210784 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
210718 AAAACCCTGA
**
210728 AAAGTATCGATACACATTTT
1 AAAGTATCGATACACATTGC
*
210748 AAATGTATCGATACAGATTGC
1 AAA-GTATCGATACACATTGC
*
210769 ATAGTATCGATACACA
1 AAAGTATCGATACACA
210785 CAAATATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (20 bp):
AAAGTATCGATACACATTGC
Found at i:210855 original size:53 final size:53
Alignment explanation
Indices: 210772--210909 Score: 231
Period size: 53 Copynumber: 2.6 Consensus size: 53
210762 AGATTGCATA
*
210772 GTATCGATACACACAAATATGTATCGATACAAGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAAGACACTGGCAGTAGCCAAATTT
* *
210826 GTATCGATACACACAATATGTATCGATACAGGTCACTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAAGACACTGGCAGTAGCCAAATTT
*
210879 GTATCGATACACAAAATATGTATCGATACAA
1 GTATCGATACACACAATATGTATCGATACAA
210910 TGGTAGTAGC
Statistics
Matches: 79, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
53 65 0.82
54 14 0.18
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAAGACACTGGCAGTAGCCAAATTT
Found at i:210951 original size:10 final size:10
Alignment explanation
Indices: 210932--210962 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
210922 AATCTCATTT
210932 TCACTGTTCA
1 TCACTGTTCA
*
210942 TCACTATTCA
1 TCACTGTTCA
210952 TCACTGTTCA
1 TCACTGTTCA
210962 T
1 T
210963 GTATCGATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:210989 original size:20 final size:22
Alignment explanation
Indices: 210950--211004 Score: 87
Period size: 20 Copynumber: 2.6 Consensus size: 22
210940 CATCACTATT
*
210950 CATCACTGTTCATGTATCGATG
1 CATCACTGTTCATGTATCGATA
210972 CATCACT-TTCAT-TATCGATA
1 CATCACTGTTCATGTATCGATA
210992 CATCACTGTTCAT
1 CATCACTGTTCAT
211005 ACTGTTCACG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 14 0.45
21 10 0.32
22 7 0.23
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:211079 original size:13 final size:13
Alignment explanation
Indices: 211061--211087 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
211051 TCACTATTCA
211061 TGTATCGATACAG
1 TGTATCGATACAG
211074 TGTATCGATACAG
1 TGTATCGATACAG
211087 T
1 T
211088 ATAAATAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:216125 original size:19 final size:19
Alignment explanation
Indices: 216101--216159 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
216091 AACAGTAAGC
216101 GTATCGATACATAAGTGTT
1 GTATCGATACATAAGTGTT
216120 GTATCGATAC--AA----T
1 GTATCGATACATAAGTGTT
216133 GTATCGATACATAAGTGTT
1 GTATCGATACATAAGTGTT
216152 GTATCGAT
1 GTATCGAT
216160 GCAATGTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.32
15 2 0.06
17 2 0.06
19 19 0.56
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (19 bp):
GTATCGATACATAAGTGTT
Found at i:216137 original size:13 final size:13
Alignment explanation
Indices: 216119--216143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
216109 ACATAAGTGT
216119 TGTATCGATACAA
1 TGTATCGATACAA
216132 TGTATCGATACA
1 TGTATCGATACA
216144 TAAGTGTTGT
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:216142 original size:32 final size:32
Alignment explanation
Indices: 216101--216175 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
216091 AACAGTAAGC
216101 GTATCGATACATAAGTGTTGTATCGATACAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
*
216133 GTATCGATACATAAGTGTTGTATCGATGCAAT
1 GTATCGATACATAAGTGTTGTATCGATACAAT
*
216165 GTATCGCTACA
1 GTATCGATACA
216176 AAGCTACTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (32 bp):
GTATCGATACATAAGTGTTGTATCGATACAAT
Found at i:223403 original size:52 final size:52
Alignment explanation
Indices: 223255--223383 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
223245 CGAAATATGA
* *
223255 AAATTTACCTGCATATATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
223307 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
223359 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
223384 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:223410 original size:13 final size:13
Alignment explanation
Indices: 223392--223416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223382 CAAAGATCAG
223392 TGTATCGATACAA
1 TGTATCGATACAA
223405 TGTATCGATACA
1 TGTATCGATACA
223417 GTTGAGTAAT
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:223496 original size:13 final size:13
Alignment explanation
Indices: 223478--223502 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
223468 ACAAAACTTA
223478 TGTATCGATACAT
1 TGTATCGATACAT
223491 TGTATCGATACA
1 TGTATCGATACA
223503 ACACTTATGT
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:223498 original size:32 final size:32
Alignment explanation
Indices: 223457--223521 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
223447 AGTAGCTTAA
223457 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
223489 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
223521 A
1 A
223522 ACACTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAC
Found at i:223532 original size:20 final size:19
Alignment explanation
Indices: 223459--223542 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
223449 TAGCTTAAAT
*
223459 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
223478 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
223491 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
223510 TGTATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
223530 TGTATCGATACAA
1 TGTATCGATACAA
223543 ATCGTTGAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 13
0.80 0.01 0.18
Matches are distributed among these distances:
13 9 0.16
14 1 0.02
16 5 0.09
18 1 0.02
19 25 0.44
20 16 0.28
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:224493 original size:55 final size:52
Alignment explanation
Indices: 224393--224913 Score: 278
Period size: 49 Copynumber: 10.9 Consensus size: 52
224383 GAAAAGTGAT
* * * * * * **
224393 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAAATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAAATG-G-A
* * *
224447 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAAATGGA
* *
224500 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAAATGGA
*
224543 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAA-AATGGA
* * * *
224593 AAA-GTGCCAATATGCTGATTCAAGGCTAGCAATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAAATGGA
* * *
224635 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAAATGGA
* * * * *
224685 -AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT--AAAT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAAATGGA
* * * *
224731 ----GTGCCAATGTACTGATTCAAGGCCAGCTAAATT-AGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGA-ACTTAAAAATGGA
* * *
224777 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAAATGGA
* * * * *
224819 AAAGGTACCAATGTGCTGATTTAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAAATGGA
* * *
224869 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAA
224914 GGTGCCAATG
Statistics
Matches: 381, Mismatches: 52, Indels: 73
0.75 0.10 0.14
Matches are distributed among these distances:
42 3 0.01
43 140 0.37
44 3 0.01
45 3 0.01
46 1 0.00
47 3 0.01
48 2 0.01
49 144 0.38
50 3 0.01
51 1 0.00
52 32 0.08
53 6 0.02
54 5 0.01
55 35 0.09
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAAATGGA
Found at i:224535 original size:22 final size:22
Alignment explanation
Indices: 224510--224575 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 22
224500 AAAGGTGCCA
224510 ATATGCTGATTCAAGGCCAGCT
1 ATATGCTGATTCAAGGCCAGCT
*
224532 ATAT--TGGACTTAAAGGTGCCA---
1 ATATGCT-GA-TTCAA-G-GCCAGCT
224553 ATATGCTGATTCAAGGCCAGCT
1 ATATGCTGATTCAAGGCCAGCT
224575 A
1 A
224576 CATTGGACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 18
0.62 0.04 0.34
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 10 0.30
22 11 0.33
23 2 0.06
24 4 0.12
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (22 bp):
ATATGCTGATTCAAGGCCAGCT
Found at i:224561 original size:43 final size:43
Alignment explanation
Indices: 224500--224958 Score: 531
Period size: 43 Copynumber: 10.1 Consensus size: 43
224490 TAAAGATGGA
224500 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
224543 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
224586 AAAGAAAAAAGTGCCAATATGCTGATTCAAGGCTAGCAATATTGGACTT
1 AAAG------GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
224635 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
224678 AAAGATGAAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTT
1 -AA-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * * *
224727 AAATGTGCCAATGTACTGATTCAAGGCCAGCTAAATTAGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
224770 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * * *
224819 AAAGGTACCAATGTGCTGATTTAAGGCCAGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
224862 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
224911 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
224954 AAAGG
1 AAAGG
224959 AAGATGCCAC
Statistics
Matches: 355, Mismatches: 37, Indels: 48
0.81 0.08 0.11
Matches are distributed among these distances:
43 195 0.55
44 3 0.01
45 3 0.01
46 1 0.00
47 3 0.01
48 3 0.01
49 147 0.41
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:224568 original size:21 final size:21
Alignment explanation
Indices: 224501--224568 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
224491 AAAGATGGAA
224501 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* ** *
224522 AA-G-GCCAGCTATATTGGACTTA
1 AAGGTGCCA-ATATGCT-GA-TTC
224544 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
224565 AAGG
1 AAGG
224569 CCAGCTACAT
Statistics
Matches: 34, Mismatches: 8, Indels: 10
0.65 0.15 0.19
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 10 0.29
22 6 0.18
23 5 0.15
24 4 0.12
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:224634 original size:92 final size:92
Alignment explanation
Indices: 224447--224957 Score: 788
Period size: 92 Copynumber: 5.5 Consensus size: 92
224437 AAAATGAGAA
* *
224447 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AAAAGGTGCCAAT
*
224512 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
224543 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAAGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
* *
224608 TGATTCAAGGCTAGCAATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
** *
224635 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
*
224700 TGATTCAAGGCCAACGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * * * **
224727 AAATGTGCCAATGTACTGATTCAAGGCCAGCTAAATTAGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
224792 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
* * **
224819 AAAGGTACCAATGTGCTGATTTAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
224884 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
224911 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
224958 GAAGATGCCA
Statistics
Matches: 386, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
92 341 0.88
95 40 0.10
96 5 0.01
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAAAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:225000 original size:33 final size:32
Alignment explanation
Indices: 224963--225116 Score: 218
Period size: 33 Copynumber: 4.7 Consensus size: 32
224953 TAAAGGAAGA
* *
224963 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AGAAGGT
**
224996 TGCCACCGACTTGTGTGGGCTTTAGAGGGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGT
** *
225028 TGCCACTAACTTGTGTGAGCTTTAGAGAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAGAAGGT
225060 ATGCCACCGACTTGTGTGGGCTTTAGAGAAGGTT
1 -TGCCACCGACTTGTGTGGGCTTTAGAGAAGG-T
225094 TGCCACCGACTTGTGTGGGCTTT
1 TGCCACCGACTTGTGTGGGCTTT
225117 TGAAAAGGAG
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
32 32 0.30
33 74 0.69
34 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTAGAGAAGGT
Found at i:225067 original size:65 final size:66
Alignment explanation
Indices: 224963--225124 Score: 231
Period size: 65 Copynumber: 2.5 Consensus size: 66
224953 TAAAGGAAGA
* *
224963 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAG-GGGG
1 TGCCACCAACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGG
225027 T
66 T
* *
225028 TGCCACTAACTTGTGTGAGCTTTAG-AGAAGGTATGCCACCGACTTGTGTGGGCTTTAGAGAAGG
1 TGCCACCAACTTGTGTGGGCTTTAGAAGAAGGT-TGCCACCGACTTGTGTGGGCTTTAGAGAAGG
*
225092 TT
65 GT
* *
225094 TGCCACCGACTTGTGTGGGCTTTTGAA-AAGG
1 TGCCACCAACTTGTGTGGGCTTTAGAAGAAGG
225125 AGAAAGATGC
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 7 0.08
65 49 0.58
66 28 0.33
67 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.30
Consensus pattern (66 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGG
T
Found at i:225172 original size:27 final size:27
Alignment explanation
Indices: 225132--225185 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
225122 AGGAGAAAGA
*
225132 TGCCACGGAGTTGTAGACTTAAAAGGG
1 TGCCACGGAATTGTAGACTTAAAAGGG
* *
225159 TGCCATGGAATTGTGGACTTAAAAGGG
1 TGCCACGGAATTGTAGACTTAAAAGGG
225186 AAAAAGAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.13, G:0.33, T:0.24
Consensus pattern (27 bp):
TGCCACGGAATTGTAGACTTAAAAGGG
Found at i:225356 original size:69 final size:66
Alignment explanation
Indices: 225152--225786 Score: 559
Period size: 69 Copynumber: 9.4 Consensus size: 66
225142 TTGTAGACTT
* * * * * * * *
225152 AAAAGGGTGCCATGGAATTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACAGAGTTGCGGGCTTTG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAAAG-GTGCCACGGAGTTGTGGACTTAG
225216 AAAGGG
63 AAA--G
* * *
225222 AAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCACGAAGTCGTAGACTTA-A
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGA
225283 AAGG
64 AA-G
* * * * *
225287 AACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGAAAAGAATGCCACGGAGTTGTGGACTTAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAAAG-GTGCCACGGAGTTGTGGACTTAG
*
225352 AAGG
63 AAAG
* *
225356 AAAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTTGA
1 AAAAAG-GTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGA
225421 AAGG
64 AA-G
* * * * * * * * *
225425 AACAAGGTGCCACGGGGTCGTGGACTTAAAAAG-AAAAGGTGCCACAGAGTGGTGGGCTTTGAAA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAG-AA
225489 AG
65 AG
* *
225491 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAG-AAAAAGGTGCCACGGAGTTGTGGAC-TTAG
225556 AAAG
63 AAAG
* * * * *
225560 AAAAAGGTGCCACAGAATTGTGGGCTTTAAAAAGAAAAAGGGTACCACGGAGTTGTGGGCTTTGA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAA-GGTGCCACGGAGTTGTGGACTTAG-
225625 AAAG
63 AAAG
* * * * * * * *
225629 AAGAAGGTGCCACGAAGTTGTGGGCTTTAAAGGAACAAGGTGCCATGGGGTCGTGGACTTAAAAA
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAA
225694 G
66 G
* * *
225695 -AAAAGGTGCCACGGAGTGGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTG-A
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAA
225758 AG
65 AG
* * * *
225760 AAAAA-ATGCCACTGAGTCGTGGACTTT
1 AAAAAGGTGCCACGGAGTTGTGGGCTTT
225787 GAGACAAAAT
Statistics
Matches: 465, Mismatches: 78, Indels: 49
0.79 0.13 0.08
Matches are distributed among these distances:
63 4 0.01
64 20 0.04
65 53 0.11
66 86 0.18
67 45 0.10
68 61 0.13
69 141 0.30
70 28 0.06
71 21 0.05
72 2 0.00
73 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (66 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAA
G
Found at i:225694 original size:237 final size:238
Alignment explanation
Indices: 225223--225786 Score: 770
Period size: 237 Copynumber: 2.4 Consensus size: 238
225213 TTGAAAGGGA
* * * * *
225223 AAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAG---AAGGTGCCACGAAGTCGTAGAC-TTAAA
1 AAAAG-GTGCCACGGAGTGGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAA
* * * * * * *
225284 AGGAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGAAAAGAATGCCACGGAGTTGTGGACT
65 AGAAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGAGAAAAAGAATGCCACAGAATTGTGGACT
* * * * *
225349 TAGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGG
130 TAAAAAGAAAAAGAGTACCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGAAGTTGTGG
225414 ACTTTGAAAGGAACAAGGTGCCACGGGGTCGTGGACTTAAAAAG
195 ACTTTGAAAGGAACAAGGTGCCACGGGGTCGTGGACTTAAAAAG
*
225458 AAAAGGTGCCACAGAGTGGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAAGGTGCCACGGAGTGGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAA
* * *
225523 AGAAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAG-GTGCCACAGAATTGTGGGCT
65 AGAAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGAGAAAAAGAATGCCACAGAATTGTGGAC-
* * *
225586 TTAAAAAGAAAAAGGGTACCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGAAGTTGTG
129 TTAAAAAGAAAAAGAGTACCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGAAGTTGTG
* *
225651 GGCTTT-AAAGGAACAAGGTGCCATGGGGTCGTGGACTTAAAAAG
194 GACTTTGAAAGGAACAAGGTGCCACGGGGTCGTGGACTTAAAAAG
*
225695 AAAAGGTGCCACGGAGTGGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-GAA
1 AAAAGGTGCCACGGAGTGGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
* *
225759 GAAAAAA--TGCCACTGAGTCGTGGACTTT
66 GAAAAAAGGTGCCACGGAGTTGTGGACTTT
225787 GAGACAAAAT
Statistics
Matches: 292, Mismatches: 31, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
233 18 0.06
234 26 0.09
235 14 0.05
237 130 0.45
238 70 0.24
239 34 0.12
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (238 bp):
AAAAGGTGCCACGGAGTGGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
GAAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAGAGAAAAAGAATGCCACAGAATTGTGGACTT
AAAAAGAAAAAGAGTACCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGAAGTTGTGGA
CTTTGAAAGGAACAAGGTGCCACGGGGTCGTGGACTTAAAAAG
Found at i:225755 original size:34 final size:34
Alignment explanation
Indices: 225185--225788 Score: 599
Period size: 34 Copynumber: 17.9 Consensus size: 34
225175 ACTTAAAAGG
* * *
225185 GAAAAAGAGTGCCACAGAGTTGCGGGCTTTGAAAGG
1 GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAA-A
225221 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA
1 GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAA
* * * *
225256 G---AAGGTGCCACGAAGTCGTAGAC-TT-AAAA
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
* * *
225285 GGAACAAGGTGCCACGGGGTTGTGGACTTT-AAAA
1 -GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
* * * * *
225319 GGGGAAAAGAATGCCACGGAGTTGTGGACTTAG-AAG
1 --GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAA
* *
225355 GAAAAAGAGTGCCATGGAGTTGTGGGCTTTAAAAA
1 GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAA
* *
225390 GAAAAAGGTGCCACGGAGTTGTGGACTTTGAAAG
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
* * * * *
225424 GAACAAGGTGCCACGGGGTCGTGGAC-TTAAAAA
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
* *
225457 G-AAAAGGTGCCACAGAGTGGTGGGCTTTGAAAA
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
*
225490 GAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
*
225524 GAAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAA
1 G-AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
* * *
225559 GAAAAAGGTGCCACAGAATTGTGGGCTTTAAAAA
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
*
225593 GAAAAAGGGTACCACGGAGTTGTGGGCTTTGAAAA
1 GAAAAA-GGTGCCACGGAGTTGTGGGCTTTGAAAA
* * *
225628 GAAGAAGGTGCCACGAAGTTGTGGGCTTT-AAAG
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
* * * * * *
225661 GAACAAGGTGCCATGGGGTCGTGGAC-TTAAAAA
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
*
225694 G-AAAAGGTGCCACGGAGTGGTGGGCTTTGAAAA
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
225727 GAAAAAGGTGCCACGGAGTTGTGGGCTTTG--AA
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
* * * *
225759 GAAAAA-ATGCCACTGAGTCGTGGACTTTGA
1 GAAAAAGGTGCCACGGAGTTGTGGGCTTTGA
225789 GACAAAATGC
Statistics
Matches: 481, Mismatches: 70, Indels: 38
0.82 0.12 0.06
Matches are distributed among these distances:
29 4 0.01
30 3 0.01
31 34 0.07
32 51 0.11
33 65 0.14
34 192 0.40
35 79 0.16
36 53 0.11
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
GAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
Found at i:225949 original size:63 final size:62
Alignment explanation
Indices: 225678--226004 Score: 394
Period size: 63 Copynumber: 5.2 Consensus size: 62
225668 GTGCCATGGG
** * * *
225678 GTCGTGGACTTAAAAAGAAAAGG-TGCCACGGAGTGGTGGGCTTTGAAAAGA-AAAAGGTGCCAC
1 GTCGTGGACTT-TGAAGAAAAGGATGCCACTGAGTCGTGGACTTTG---AGACAAAA--TGCCAC
*
225741 GGA
60 TGA
* * *
225744 GTTGTGGGCTTTGAAGAAAA-AATGCCACTGAGTCGTGGACTTTGAGACAAAATGCCACTGA
1 GTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAAAATGCCACTGA
* * *
225805 GTCGTGAACTTTAAAGAAAAGGATGCCACTGAGTCATGGACTTTGAGACAAAATGCCACTGA
1 GTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAAAATGCCACTGA
* *
225867 GTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTCGAG-CAGAGATTGCCACTGA
1 GTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACA-A-AATGCCACTGA
*
225930 GTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGA-AGAGATTGCCACTGA
1 GTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACA-A-AATGCCACTGA
225993 GTCGTGGACTTT
1 GTCGTGGACTTT
226005 AAAAAGGTAT
Statistics
Matches: 234, Mismatches: 21, Indels: 15
0.87 0.08 0.06
Matches are distributed among these distances:
61 26 0.11
62 86 0.37
63 87 0.37
65 26 0.11
66 9 0.04
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.23
Consensus pattern (62 bp):
GTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAAAATGCCACTGA
Found at i:226986 original size:27 final size:27
Alignment explanation
Indices: 226956--227009 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
226946 TCCCTTCTTC
226956 TTCTTTTTTT-TTGTT-TCTTCTTTTTTT
1 TTCTTTTTTTGTT-TTGT-TTCTTTTTTT
226983 TTCTTTTTTTGTTTTGTTTCTTTTTTT
1 TTCTTTTTTTGTTTTGTTTCTTTTTTT
227010 GGAAAAGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 22 0.88
28 3 0.12
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (27 bp):
TTCTTTTTTTGTTTTGTTTCTTTTTTT
Found at i:226997 original size:17 final size:17
Alignment explanation
Indices: 226953--227010 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
226943 TTTTCCCTTC
226953 TTCTTCTTTTT-TTTTGT
1 TTCTT-TTTTTGTTTTGT
*
226970 TTC--TTCTT-TTTT-T
1 TTCTTTTTTTGTTTTGT
226983 TTCTTTTTTTGTTTTGT
1 TTCTTTTTTTGTTTTGT
227000 TTCTTTTTTTG
1 TTCTTTTTTTG
227011 GAAAAGAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 4 0.11
14 8 0.23
15 4 0.11
16 4 0.11
17 15 0.43
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (17 bp):
TTCTTTTTTTGTTTTGT
Found at i:226998 original size:30 final size:29
Alignment explanation
Indices: 226953--227009 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
226943 TTTTCCCTTC
226953 TTCTTCTTTTTTTTTGTTTCTTCTTTTTTT
1 TTCTTCTTTTTTTTTGTTTCTT-TTTTTTT
226983 TTCTT-TTTTTGTTTTGTTTCTTTTTTT
1 TTCTTCTTTTT-TTTTGTTTCTTTTTTT
227010 GGAAAAGAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (29 bp):
TTCTTCTTTTTTTTTGTTTCTTTTTTTTT
Found at i:234281 original size:13 final size:13
Alignment explanation
Indices: 234263--234287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
234253 CAAAGATCAG
234263 TGTATCGATACAA
1 TGTATCGATACAA
234276 TGTATCGATACA
1 TGTATCGATACA
234288 GTTGAGTAAT
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:234354 original size:19 final size:18
Alignment explanation
Indices: 234330--234427 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
234320 TAGCTTAAAT
234330 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
234349 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
234362 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
234381 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
234394 TGTATTGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
234414 TGTATCGATACAAA
1 TGTATCGATACAAA
234428 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.38
20 12 0.19
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:234367 original size:13 final size:13
Alignment explanation
Indices: 234349--234405 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
234339 ACAAAACTTA
234349 TGTATCGATACAT
1 TGTATCGATACAT
234362 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
234380 ATGTATCGATACAT
1 -TGTATCGATACAT
*
234394 TGTATTGATACA
1 TGTATCGATACA
234406 ACACTTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:234369 original size:32 final size:32
Alignment explanation
Indices: 234328--234425 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
234318 AGTAGCTTAA
*
234328 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
234360 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
234392 ATTGTATTGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
234425 A
1 A
234426 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 48 0.76
33 15 0.24
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:235119 original size:18 final size:16
Alignment explanation
Indices: 235096--235138 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 16
235086 AACACAACTT
235096 TTTACAACACAAATTGAA
1 TTTACAA-AC-AATTGAA
235114 TTTACAAAC--TTGAA
1 TTTACAAACAATTGAA
235128 TTTACAAACAA
1 TTTACAAACAA
235139 GGTGGAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 14 0.61
17 2 0.09
18 7 0.30
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (16 bp):
TTTACAAACAATTGAA
Found at i:235128 original size:14 final size:14
Alignment explanation
Indices: 235104--235136 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
235094 TTTTTACAAC
235104 ACAAA-TTGAATTT
1 ACAAACTTGAATTT
235117 ACAAACTTGAATTT
1 ACAAACTTGAATTT
235131 ACAAAC
1 ACAAAC
235137 AAGGTGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.48, C:0.15, G:0.06, T:0.30
Consensus pattern (14 bp):
ACAAACTTGAATTT
Found at i:235471 original size:20 final size:20
Alignment explanation
Indices: 235446--235483 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
235436 GTTGGGCTCA
*
235446 ATGTATCGATACATTTCACC
1 ATGTATCGATACAATTCACC
*
235466 ATGTATTGATACAATTCA
1 ATGTATCGATACAATTCA
235484 ATCATGAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCACC
Found at i:235563 original size:20 final size:20
Alignment explanation
Indices: 235540--235605 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
235530 ACATTTTATG
235540 ATGTATCGATACAAAGCAAT
1 ATGTATCGATACAAAGCAAT
*
235560 ATGTATCGAT---ATG----
1 ATGTATCGATACAAAGCAAT
*
235573 ATGTATCGATACCAAGCAAT
1 ATGTATCGATACAAAGCAAT
235593 ATGTATCGATACA
1 ATGTATCGATACA
235606 TCTGGGTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 14
0.68 0.06 0.26
Matches are distributed among these distances:
13 10 0.28
16 2 0.06
17 2 0.06
20 22 0.61
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAAT
Found at i:235578 original size:33 final size:33
Alignment explanation
Indices: 235536--235603 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
235526 CGGTACATTT
235536 TATGATGTATCGATACAAAGCAATATGTATCGA
1 TATGATGTATCGATACAAAGCAATATGTATCGA
*
235569 TATGATGTATCGATACCAAGCAATATGTATCGA
1 TATGATGTATCGATACAAAGCAATATGTATCGA
235602 TA
1 TA
235604 CATCTGGGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (33 bp):
TATGATGTATCGATACAAAGCAATATGTATCGA
Found at i:236399 original size:75 final size:75
Alignment explanation
Indices: 236305--236469 Score: 276
Period size: 75 Copynumber: 2.2 Consensus size: 75
236295 GAAAAGATGG
* *
236305 GGTTGGAGTATCCCCATGGATGACAAAAATTTTTACTAAGGAAAAGTTTTAAACCTTAACAATTT
1 GGTTGGAGTATCCCTATGGATGACAAAAATTTTGACTAAGGAAAAGTTTTAAACCTTAACAATTT
*
236370 TGAAAAGCGA
66 TGAAAAACGA
* *
236380 GGTTGGAGTGTCCCTATGGATGACAAAAATTTTGACTAAGGAAAGGTTTTAAACCTTAACAATTT
1 GGTTGGAGTATCCCTATGGATGACAAAAATTTTGACTAAGGAAAAGTTTTAAACCTTAACAATTT
236445 TGAAAAACGA
66 TGAAAAACGA
*
236455 GGTTGAAGTATCCCT
1 GGTTGGAGTATCCCT
236470 TTAGAAAGTC
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 83 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (75 bp):
GGTTGGAGTATCCCTATGGATGACAAAAATTTTGACTAAGGAAAAGTTTTAAACCTTAACAATTT
TGAAAAACGA
Found at i:239739 original size:161 final size:154
Alignment explanation
Indices: 239418--239960 Score: 516
Period size: 155 Copynumber: 3.5 Consensus size: 154
239408 CTAAGTTCAA
* * * * * ** *
239418 GAAAAATTATGAAAATGCCCTTAGAAGATACCTTCGACGTAGAAGTACCCGATATCCCTAAAGGA
1 GAAAAATTATAAAAATGCCCTTAGAGGATATCTTCGACGTAAAAGTACCTGCCACCCCTAAAGGA
* * * * * * * * * *
239483 CTTAAAAAAGACTATAAAAGGGATGAACCTATCCTAAATACCCACCTTTGGTATAAAAGCGGACC
66 CTT-AAAAGGACAATAGATGGGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGAACC
* * * *
239548 TGGTTATAACCTAGGACTCGGTTCT
130 TGGTGACAACTTAGGACTCGATTCT
*
239573 GAAAAATTATGAAAATAT-CCC-TAGAGGATATCTTCGACGTGAAAGTATCCTAGTACCTAGCAC
1 GAAAAATTAT-AAAA-ATGCCCTTAGAGGATATCTTCGACGTAAAAGTA-CCT-G--CC-A-C-C
* * * *
239636 CCTAAAGGACCTAAAAGGACAATAGATGGGGTGAATCTATCCTAAATATCTACCTTCGACATAAA
57 CCTAAAGGACTTAAAAGGACAATAGATGGGATGAACCTATCCTAAATATCTACCTTCGGCATAAA
* *
239701 AGTGAACCCGGTGACAACTTAGGACTCGATTTT
122 AGTGAACCTGGTGACAACTTAGGACTCGATTCT
* * * * *
239734 GAAAAATTATCAAAATGCCCTTAGGGGGTATCTTTGACGTAAAAGTACCTGGCACCCCTAAAGGA
1 GAAAAATTATAAAAATGCCCTTAGAGGATATCTTCGACGTAAAAGTACCTGCCACCCCTAAAGGA
* * * * **
239799 CTTAAAGAGGATAATAGATGAGATGGACCTATCCCAAATATCTATTTTCGGCATAAAAGTGAACC
66 CTTAAA-AGGACAATAGATGGGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGAACC
* *
239864 TAGTGACAACTTAGGACTCGATTCC
130 TGGTGACAACTTAGGACTCGATTCT
* * * * * **
239889 AAAAAATTATAAAAATGCCCTTAGGGGTTA-CTTTTGACGTAAAAGTACCCGATACCCCTAAAGG
1 GAAAAATTATAAAAATGCCCTTAGAGGATATC-TTCGACGTAAAAGTACCTGCCACCCCTAAAGG
239953 ACTTAAAA
65 ACTTAAAA
239961 AGACTAGAAA
Statistics
Matches: 320, Mismatches: 55, Indels: 27
0.80 0.14 0.07
Matches are distributed among these distances:
154 17 0.05
155 166 0.52
156 9 0.03
157 4 0.01
159 3 0.01
160 10 0.03
161 99 0.31
162 12 0.04
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (154 bp):
GAAAAATTATAAAAATGCCCTTAGAGGATATCTTCGACGTAAAAGTACCTGCCACCCCTAAAGGA
CTTAAAAGGACAATAGATGGGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGAACCT
GGTGACAACTTAGGACTCGATTCT
Found at i:241583 original size:11 final size:11
Alignment explanation
Indices: 241563--241600 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
241553 TTTGCTTGGA
241563 TTTT-TCTTTT
1 TTTTCTCTTTT
241573 TTTTCTCTTTT
1 TTTTCTCTTTT
241584 TTTTCTTCTTCTT
1 TTTTC-TCTT-TT
241597 TTTT
1 TTTT
241601 TCTCACTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 11 0.44
12 4 0.16
13 6 0.24
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTCTTTT
Found at i:241603 original size:14 final size:14
Alignment explanation
Indices: 241569--241601 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
241559 TGGATTTTTC
241569 TTTTTT-TTCTCTT
1 TTTTTTCTTCTCTT
241582 TTTTTTCTTCTTCTT
1 TTTTTTCTTC-TCTT
241597 TTTTT
1 TTTTT
241602 CTCACTTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 3 0.17
15 9 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTCTTCTCTT
Found at i:242790 original size:167 final size:165
Alignment explanation
Indices: 242251--243030 Score: 837
Period size: 165 Copynumber: 4.7 Consensus size: 165
242241 ATTTCAACAA
* * * *
242251 AAAAAAATTC-AAAACTGATAAAAATGAATTAATTTATT-AAAA-TAGAATTCATATG-AATCAA
1 AAAAAAA-TCAAAAACTCATGAAAATGAATGAATTT-TTGAAAACTA-AATTAATATGAAAT-AA
* * * * * *
242312 ATGATGATGTTTGATGAATTCTAAAAATAGAAAACCGAGAAAAATCCCCTCGAAAAAATGTACGG
62 ATGATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAAT-TACAG
* * * ** *
242377 AGTAGAAAATATCGTAGTTAGGAAAAAGTGGAGTTTCAAG
126 AGTAGAAAATACCATATTTAGGAAAAAAAGGAATTTCAAG
* * * * ** * *
242417 GAAAAAACCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTGAATTACTATGACGTATATAA
1 AAAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATGA
* * * *
242482 TAATGTTTGATGAATTTTAAAAATTGAAAA-CAGAGAAAAATCCCCTCAAAAAAATTTCGGAGTA
66 TAATATTTGATGAATTTTAAAAATTGAAAACCA-AGAAAAATCCCCTCGAAAAAATTACAGAGTA
* * * * * *
242546 AAAAACACCATATTTCGGGAAAAGAGGAATTTCGAG
130 GAAAATACCATATTTAGGAAAAAAAGGAATTTCAAG
* * *
242582 AAAAAAATAAAAAACTCATGAAAATGAATAAAATTTTGAAAACTAAATTAATATGAAATAAATGA
1 AAAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATGA
* ** *
242647 TAATATTTTATGAATTTTAAAAATTGAAAACCAAGAAAAATCCTTTCAAAAAAATTACAGAGTAG
66 TAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTACAGAGTAG
* **
242712 AAAATACCGTATTTAAAAAAAAAAGAGAATTTCAAG
131 AAAATACCATATTTAGGAAAAAAAG-GAATTTCAAG
* *
242748 TAAAAAAATGAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAAATTAATATAAAATAAATG
1 -AAAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATG
*
242813 ATAATATTTGATGAATTTTAAAAATTGAAAACCGAGAAAAATCCCCTCGAAAAAATTA-AGAAGT
65 ATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTACAG-AGT
* *
242877 -G-AAATACTATATTT-CGAAAAAAAGAGAATTTCAAG
129 AGAAAATACCATATTTAGGAAAAAAAG-GAATTTCAAG
* * * * *
242912 GAAAAAATCAAAAACTCAAGAAAATAAATGAATTTTT-CAAACTAAATTAGTAT-ACAATAAATG
1 AAAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAAATTAATATGA-AATAAATG
* * ** **
242975 ATAATATTTTATAAATTTTAAAAATT-AAAATGAAGAAAAATCATCTCGAAAAAATT
65 ATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATT
243031 TACGGAGAAA
Statistics
Matches: 524, Mismatches: 80, Indels: 25
0.83 0.13 0.04
Matches are distributed among these distances:
161 26 0.05
162 46 0.09
163 33 0.06
164 19 0.04
165 176 0.34
166 106 0.20
167 118 0.23
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.27
Consensus pattern (165 bp):
AAAAAAATCAAAAACTCATGAAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAATGA
TAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCCCCTCGAAAAAATTACAGAGTAG
AAAATACCATATTTAGGAAAAAAAGGAATTTCAAG
Found at i:244750 original size:20 final size:19
Alignment explanation
Indices: 244685--244758 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
244675 AAAACCCATA
* * *
244685 ATGTATTGATACAATGAGTG
1 ATGTATTGATAC-ATTACTT
244705 ATGTATTGATACATTACTAGT
1 ATGTATTGATACATTACT--T
244726 ATGTATTGATACATTCACTT
1 ATGTATTGATACATT-ACTT
*
244746 ATGTATCGATACA
1 ATGTATTGATACA
244759 ATTTTTTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.09
20 25 0.53
21 15 0.32
22 3 0.06
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (19 bp):
ATGTATTGATACATTACTT
Found at i:245172 original size:22 final size:22
Alignment explanation
Indices: 245125--245174 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
245115 CCACTTGAAG
* *
245125 TTGAAGGCATCTTTAAAAAATG
1 TTGAAGGCATCATTAAAAAATA
* *
245147 TTGAAGGCATCATTAGAAATTA
1 TTGAAGGCATCATTAAAAAATA
245169 TTGAAG
1 TTGAAG
245175 ATAAAATACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (22 bp):
TTGAAGGCATCATTAAAAAATA
Found at i:246100 original size:15 final size:15
Alignment explanation
Indices: 246075--246116 Score: 66
Period size: 16 Copynumber: 2.7 Consensus size: 15
246065 TTTGTTTAAT
246075 TTTTTATTTTTTTCA
1 TTTTTATTTTTTTCA
*
246090 TTTTTCATTTTTTTGA
1 TTTTT-ATTTTTTTCA
246106 TTTTTATTTTT
1 TTTTTATTTTT
246117 GAAATTGCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.81
Consensus pattern (15 bp):
TTTTTATTTTTTTCA
Done.