Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008954.1 Hibiscus syriacus cultivar Beakdansim tig00112282_pilon, whole genome shotgun sequence
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: 488355
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:249147 original size:21 final size:21
Alignment explanation
Indices: 249121--249162 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
249111 AGACGAACTA
*
249121 TGACTTTGCAATAATTCTCCT
1 TGACTTTGCAATAATGCTCCT
**
249142 TGACTTTTTAATAATGCTCCT
1 TGACTTTGCAATAATGCTCCT
249163 CGACACTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (21 bp):
TGACTTTGCAATAATGCTCCT
Found at i:253798 original size:21 final size:21
Alignment explanation
Indices: 253774--253818 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
253764 AAATGTTAAT
253774 TATTAGTAAGATA-AAAAAATA
1 TATTAGTAA-ATATAAAAAATA
* *
253795 TATTATTGAATATAAAAAATA
1 TATTAGTAAATATAAAAAATA
253816 TAT
1 TAT
253819 CGTTTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (21 bp):
TATTAGTAAATATAAAAAATA
Found at i:254922 original size:28 final size:28
Alignment explanation
Indices: 254850--254922 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
254840 TCGTCCGGGT
* *
254850 TTATTTTTATTATTATTATTATTATCTTA
1 TTATTTTTTTTAAT-TTATTATTATCTTA
* *
254879 TCT-TATTTATTT-ATTTATTATTATGTTA
1 T-TAT-TTTTTTTAATTTATTATTATCTTA
254907 TTATTTTTTTTAATTT
1 TTATTTTTTTTAATTT
254923 TTTTTTAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
27 7 0.20
28 19 0.54
29 3 0.09
30 6 0.17
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (28 bp):
TTATTTTTTTTAATTTATTATTATCTTA
Found at i:254924 original size:11 final size:11
Alignment explanation
Indices: 254910--254937 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
254900 TATGTTATTA
254910 TTTTTTTTAAT
1 TTTTTTTTAAT
254921 TTTTTTTTAAT
1 TTTTTTTTAAT
254932 TTTTTT
1 TTTTTT
254938 ATTATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTTAAT
Found at i:254972 original size:17 final size:17
Alignment explanation
Indices: 254927--254961 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
254917 TAATTTTTTT
254927 TTAAT-TTTTT-TATTA
1 TTAATATTTTTATATTA
254942 TTAATATTTTTATATTA
1 TTAATATTTTTATATTA
254959 TTA
1 TTA
254962 TTTTGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 5 0.28
17 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTAATATTTTTATATTA
Found at i:256262 original size:2 final size:2
Alignment explanation
Indices: 256257--256290 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
256247 TTAAATATGA
256257 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
256291 CCTTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:256480 original size:151 final size:150
Alignment explanation
Indices: 256309--256591 Score: 433
Period size: 151 Copynumber: 1.9 Consensus size: 150
256299 TTAACCCTTT
* * * * *
256309 CTATTTATTATCTTCTATATTTAATAGTTATTTTTGGTAAATATATTCATATTTTGCTTCAACTT
1 CTATTTATTATCTTCCATATTTAATAGTTATGTTAGGTAAACATATTCATATCTTGCTTCAACTT
* * *
256374 ACCCTTACTATTTTACCTT-AATAATTAGCATATATTTATAATGCTTCCATATATCATACGGTAA
66 ACCCTTACTATTTTA-CTTCAATAATTAGCATATATGTATAATGCTTCCATATACCATACGGCAA
256438 TTTATATATATATAGCCCTGG
130 TTTATATATATATAGCCCTGG
* * *
256459 CTATTTATTTGTCTTCCATATTTAATAGTTATGTTAGGTAAGCATATTCATATCTTGCTTTAACT
1 CTATTTA-TTATCTTCCATATTTAATAGTTATGTTAGGTAAACATATTCATATCTTGCTTCAACT
*
256524 TACCCTTACTATTTTACTTCAGTAATTAGCATATATGTATAATGCTTCCATATACCATACGGCAA
65 TACCCTTACTATTTTACTTCAATAATTAGCATATATGTATAATGCTTCCATATACCATACGGCAA
256589 TTT
130 TTT
256592 TATGCTTAGT
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
150 10 0.08
151 109 0.92
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (150 bp):
CTATTTATTATCTTCCATATTTAATAGTTATGTTAGGTAAACATATTCATATCTTGCTTCAACTT
ACCCTTACTATTTTACTTCAATAATTAGCATATATGTATAATGCTTCCATATACCATACGGCAAT
TTATATATATATAGCCCTGG
Found at i:256923 original size:4 final size:4
Alignment explanation
Indices: 256903--256968 Score: 60
Period size: 4 Copynumber: 15.5 Consensus size: 4
256893 TTCCTTTTTG
* * **
256903 TTTA TATTA TATA TTTA TTTA TTTA TTTA TCTTCG TTTA GCTA TTTTA
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTTA T-TT-A TTTA TTTA -TTTA
256951 TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TT
256969 CCCGTTTAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
4 39 0.78
5 10 0.20
6 1 0.02
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:258066 original size:2 final size:2
Alignment explanation
Indices: 258059--258116 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
258049 TATTATAGAA
258059 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
258101 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
258117 CAATGTTTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:258957 original size:19 final size:19
Alignment explanation
Indices: 258933--258975 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
258923 AGTGAACCGG
*
258933 CGGTTCAAACTGGTTTTGC
1 CGGTTCAAACTGGTTTTCC
**
258952 CGGTTCACCCTGGTTTTCC
1 CGGTTCAAACTGGTTTTCC
258971 CGGTT
1 CGGTT
258976 TTCAGCCGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.09, C:0.28, G:0.26, T:0.37
Consensus pattern (19 bp):
CGGTTCAAACTGGTTTTCC
Found at i:261101 original size:27 final size:28
Alignment explanation
Indices: 261071--261124 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
261061 TTAAAATAAA
261071 CTTGTTACTCAACTCG-TGCTCGTTAAG
1 CTTGTTACTCAACTCGTTGCTCGTTAAG
* **
261098 CTTGTTGCTCGTCTCGTTGCTCGTTAA
1 CTTGTTACTCAACTCGTTGCTCGTTAA
261125 TCGAATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.13, C:0.26, G:0.20, T:0.41
Consensus pattern (28 bp):
CTTGTTACTCAACTCGTTGCTCGTTAAG
Found at i:267797 original size:44 final size:45
Alignment explanation
Indices: 267749--267855 Score: 130
Period size: 44 Copynumber: 2.4 Consensus size: 45
267739 GGCGTTTATA
* * * * *
267749 TAAAAAACGTCGTTGTATACCA-ACCTTTAGCGGCGTTTGTATTC
1 TAAAAAACGCCGCTATATACAAGACCTTTAGCGGCGTTTGTATCC
*
267793 T-AAAAACGCCGCTATATACAAGATCTTTAGCGGCGTTTGTATCC
1 TAAAAAACGCCGCTATATACAAGACCTTTAGCGGCGTTTGTATCC
*
267837 T-AAAAACACCGCTATATAC
1 TAAAAAACGCCGCTATATAC
267856 CGGACCTGAT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 16 0.29
44 39 0.71
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (45 bp):
TAAAAAACGCCGCTATATACAAGACCTTTAGCGGCGTTTGTATCC
Found at i:267811 original size:43 final size:44
Alignment explanation
Indices: 267764--267862 Score: 146
Period size: 44 Copynumber: 2.3 Consensus size: 44
267754 AACGTCGTTG
* *
267764 TATACCA-ACCTTTAGCGGCGTTTGTATTCTAAAAACGCCGCTA
1 TATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAACACCGCTA
* *
267807 TATACAAGATCTTTAGCGGCGTTTGTATCCTAAAAACACCGCTA
1 TATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAACACCGCTA
*
267851 TATACCGGACCT
1 TATACCAGACCT
267863 GATAAAAACA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 6 0.12
44 42 0.88
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (44 bp):
TATACCAGACCTTTAGCGGCGTTTGTATCCTAAAAACACCGCTA
Found at i:274400 original size:14 final size:14
Alignment explanation
Indices: 274383--274413 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
274373 ATAATAAATA
274383 ATTATAAATATATT
1 ATTATAAATATATT
274397 ATTATAAATATATT
1 ATTATAAATATATT
274411 ATT
1 ATT
274414 TTAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTATAAATATATT
Found at i:274430 original size:57 final size:56
Alignment explanation
Indices: 274330--274436 Score: 146
Period size: 57 Copynumber: 1.9 Consensus size: 56
274320 TTATTAAAAA
*
274330 TATAAAAATTATTATAAAATGTATTATTTTAATAGTTTAAAATA-TAATAAATAAT
1 TATAAAAATTATTATAAAATATATTATTTTAATAGTTTAAAATATTAATAAATAAT
* *
274385 TATAAATATATTATTAT-AAATATATTATTTTAATTATTTTCAAATATTAATA
1 TATAAA-A-ATTATTATAAAATATATTATTTTAA-TAGTTTAAAATATTAATA
274437 TATTTGGATC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
55 6 0.13
56 16 0.36
57 18 0.40
58 5 0.11
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (56 bp):
TATAAAAATTATTATAAAATATATTATTTTAATAGTTTAAAATATTAATAAATAAT
Found at i:274840 original size:12 final size:12
Alignment explanation
Indices: 274825--274879 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
274815 GTTATTTAAA
274825 CGGGTATTGGGC
1 CGGGTATTGGGC
*
274837 CGGGTATTGGGT
1 CGGGTATTGGGC
274849 CGGGTATTGGGC
1 CGGGTATTGGGC
* * *
274861 CGAGAATCGGGC
1 CGGGTATTGGGC
274873 CGGGTAT
1 CGGGTAT
274880 ATATATATAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.13, C:0.16, G:0.47, T:0.24
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:275011 original size:13 final size:12
Alignment explanation
Indices: 274980--275016 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
274970 TTTTAATATT
*
274980 TATCGGGTCGGG
1 TATCGGGGCGGG
274992 TATCGGGGCGGG
1 TATCGGGGCGGG
275004 TAATCGGGGCGGG
1 T-ATCGGGGCGGG
275017 GATTACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.11, C:0.16, G:0.54, T:0.19
Consensus pattern (12 bp):
TATCGGGGCGGG
Found at i:276553 original size:31 final size:31
Alignment explanation
Indices: 276506--276582 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
276496 GTTAACTTTC
* * **
276506 AGTGGCCATATCTTAATTAAAATGAAATGAA
1 AGTGACCAAATCTTAATTAAAACAAAATGAA
*
276537 AGTGACCAAATCTTAATTAAAACAAAATGTA
1 AGTGACCAAATCTTAATTAAAACAAAATGAA
*
276568 AGTGATCAAATCTTA
1 AGTGACCAAATCTTA
276583 TGTTTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.29
Consensus pattern (31 bp):
AGTGACCAAATCTTAATTAAAACAAAATGAA
Found at i:284059 original size:13 final size:13
Alignment explanation
Indices: 284038--284069 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
284028 TTGGTCTTAG
*
284038 TCACTATCTACAA
1 TCACCATCTACAA
284051 TCACCATCTACAA
1 TCACCATCTACAA
284064 TCACCA
1 TCACCA
284070 AATCTCTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (13 bp):
TCACCATCTACAA
Found at i:286901 original size:17 final size:17
Alignment explanation
Indices: 286881--286917 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
286871 GTTTCTCACA
286881 TCTCCTCGCATCTCTCC
1 TCTCCTCGCATCTCTCC
286898 TCTCCTCGCATCTCTCC
1 TCTCCTCGCATCTCTCC
286915 TCT
1 TCT
286918 TAACTTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.51, G:0.05, T:0.38
Consensus pattern (17 bp):
TCTCCTCGCATCTCTCC
Found at i:292366 original size:37 final size:36
Alignment explanation
Indices: 292294--292367 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 36
292284 GTTGGAAAAT
* *
292294 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
*
292330 ATTTATATAATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTA-AAAATTAAAAATCATAAA
292367 A
1 A
292368 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 8 0.24
37 15 0.45
38 10 0.30
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTAAAAATCATAAA
Found at i:293378 original size:17 final size:18
Alignment explanation
Indices: 293335--293375 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
293325 AAATTATATT
293335 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
293352 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
293370 ATTAAA
1 AGTAAA
293376 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:293682 original size:51 final size:51
Alignment explanation
Indices: 293619--293748 Score: 135
Period size: 51 Copynumber: 2.5 Consensus size: 51
293609 CCCTTACGTG
* **
293619 GCATATAGCGCGGATCAGGAGGCGCGCTATA-CACACGTGTAAC-CCATGTCA
1 GCATATAACGCGGATCAGGAGGCGCGCTATACCACACGTG--ACGCCAAATCA
* *
293670 GCATATAACGCGG-TACAGG-GAACGCGCTATACCTCACGTGACGCCAAATCA
1 GCATATAACGCGGAT-CAGGAG-GCGCGCTATACCACACGTGACGCCAAATCA
293721 GCATATAACGCGGGA-CAGGAGGCGCGCT
1 GCATATAACGC-GGATCAGGAGGCGCGCT
293749 TTACTGTTAC
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
50 4 0.06
51 52 0.79
52 10 0.15
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.15
Consensus pattern (51 bp):
GCATATAACGCGGATCAGGAGGCGCGCTATACCACACGTGACGCCAAATCA
Found at i:300076 original size:181 final size:181
Alignment explanation
Indices: 299585--300245 Score: 912
Period size: 182 Copynumber: 3.6 Consensus size: 181
299575 TCGATACAAA
* * * *
299585 TAAAAAATGTATCAATCCATAGCAATATAACAAGTAAAAATATGACAAAACCGGTCTCAAAATGA
1 TAAAAAATGTATCGATCAATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGA
* * * *
299650 CCAAACCGGTAAAACGCTACCAGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACT
66 CAAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
* * *
299715 TTTGGAATTTAAAAGACAAGCAGTCATAGCGCCTATAAAGTGTCGATACTT
131 TTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCAATAATT
* * *
299766 TAAAAAAATGTATCGA-CACTTAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCAAAAT
1 T-AAAAAATGTATCGATCA-ATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAAT
* * ** * * * *
299830 GACAAAAACGGTAAAGAGCTACTGGATATGTTAAAAGTGTCGATACTTTATTATAAGTGTCGACA
64 GACAAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
*
299895 CTTTTGAAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCAATAATT
129 CTTTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCAATAATT
* * * *
299948 TAAAAAATGTATCGATCAATAACGATATAACATGTAAAAATATGACAAAACCGATCTCGAAATGA
1 TAAAAAATGTATCGATCAATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGA
*
300013 CAAAACCGGTAAAGCGCTACC-GAATATATTGAAAGTGTCGATACTTTAATATAAATATCGACAC
66 CAAAACCGGTAAAGCGCTACCAG-ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACAC
* * ** * *
300077 TTTGGGAATTTAAAAGAGAAGCAGTAATATTGTCTATAAAGTGTCAATATTT
130 TTTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCAATAATT
* * * * *
300129 TATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACGAAATCGGTATCGAAATG
1 TA-AAAAATGTATCGATCAATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATG
*
300194 ACAAAATCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATA
65 ACAAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATA
300246 AGTACGCGTA
Statistics
Matches: 425, Mismatches: 49, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
180 1 0.00
181 157 0.37
182 266 0.63
183 1 0.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (181 bp):
TAAAAAATGTATCGATCAATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCAAAATGA
CAAAACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACT
TTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCAATAATT
Found at i:302252 original size:22 final size:23
Alignment explanation
Indices: 302201--302256 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
302191 ACGTTTTTGT
* *
302201 TTTTTTTATATAAAATGATAGTA
1 TTTTATTATATAAAATGATAGAA
*
302224 TAGTTATTATATAAAATGATA-AA
1 T-TTTATTATATAAAATGATAGAA
302247 TTTTATTATA
1 TTTTATTATA
302257 AATGTAGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 17 0.61
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (23 bp):
TTTTATTATATAAAATGATAGAA
Found at i:304529 original size:19 final size:19
Alignment explanation
Indices: 304505--304553 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
304495 AATGTAGGGT
304505 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
304524 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
304543 TAATTTTGTAT
1 TAATTTTGTAT
304554 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:305346 original size:201 final size:199
Alignment explanation
Indices: 304994--306351 Score: 2042
Period size: 200 Copynumber: 6.8 Consensus size: 199
304984 GAGAATAGGT
* *
304994 ACGCATGAAGTGTCGATACATTTATAAAAAGTATTGATCCAAAAAACATCGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCC-AAAAACATCGAAACCCATAATTAT
*
305059 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATTAGAGAATAGGTCT
65 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCT
305124 ACATAATGTATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAAG
130 ACATAATGTATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAA-
305189 GGGTGC
194 GGGTGC
*
305195 ACGCATAAAGTGTCGATACATTTATAAAAAGTATTGATCACAAAAACATCGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATC-CAAAAACATCGAAACCCATAATTAT
305260 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCT
65 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCT
* * *
305325 ACATAATGTATCGACACTTGTGAAACTTGAGTCGATACTTTTTGTCCAGAATGAATGCCCAAAAG
130 ACATAATGTATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAA-
305390 GGGTGC
194 GGGTGC
* *
305396 ACGCATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAAATATCGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCC-AAAAACATCGAAACCCATAATTAT
*
305461 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATATCGGTTTTATGAGAGAATAGGTCT
65 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCT
* *
305526 ACATAATGTATCGACACTTGTGGAACTTGTGTCGATACTT-TTTTTCAGAATGAATGCCCAAAAG
130 ACATAATGTATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAA-
305590 GGGTGC
194 GGGTGC
* *
305596 ACTCATAAAGTGTCGATACATTTATAAAAAGTATTGATCCAAACAACATCGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAA-AACATCGAAACCCATAATTAT
* **
305661 AATGTAATAGGTAA-TTTTCAATGTAATCGGTATAAATATACCTATTTTATGAGAG-A-A----T
65 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCT
* * *
305719 --AT-GTGTA-C-ATACTTGTGGAACTTGTGTCGATACTTGTTGTCCATAATGAATGCCCAAAAG
130 ACATAATGTATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAAG
*
305779 AGTGC
195 GGTGC
*
305784 ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAATATCGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCC-AAAAACATCGAAACCCATAATTAT
* * * *
305849 AATGTAATAGGTAATTTTTTAACGTAACTGGTATAAATATACCAGTTTTATGAGAGAATAGGTCT
65 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCT
* * *
305914 ACATAGTGTATCGACACTTGTGGAACTTGTATCGATACTCGTTGTCCAGAATGAATGCCCAAAAG
130 ACATAATGTATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAAG
*
305979 GTTGC
195 GGTGC
* * *
305984 ACGCATAAAGTGTTGATACATTTATAAAAAGTATCGATCCCAAAAACATTGAAACCCATATTTAT
1 ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGAT-CCAAAAACATCGAAACCCATAATTAT
* * * * * * * * *
306049 AATGTAATAGGTAAATTTACAATGTAACCGATAGAAATTTACCAGTTTT-TGAAAAAAAAAGGTC
65 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATG-AGAGAATAGGTC
* *
306113 TACATAATGTATTGACACTTGTGGAACTTGTGTCAATACTTGTTGTCCAGAATGAATGCCCAAAA
129 TACATAATGTATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAA
306178 GGGTGC
194 GGGTGC
306184 ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGAT-CCAAAAACATCGAAACCCATAATTAT
* * * * * * *
306249 AATGTAGTAGGTAAATTTACAATGTAATCGGTAGAAATTTACCGGTTTTATGAGAAAATAGGTCT
65 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCT
* *
306314 ACATAATGTATCGACACTTGTTGAACCTGTGTCGATAC
130 ACATAATGTATCGACACTTGTGGAACTTGTGTCGATAC
306352 CTTTTCAAAT
Statistics
Matches: 1061, Mismatches: 76, Indels: 41
0.90 0.06 0.03
Matches are distributed among these distances:
188 103 0.10
189 59 0.06
190 5 0.00
191 3 0.00
193 1 0.00
195 1 0.00
197 3 0.00
198 6 0.01
199 43 0.04
200 476 0.45
201 360 0.34
202 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (199 bp):
ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAACATCGAAACCCATAATTATA
ATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTA
CATAATGTATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAAGG
GTGC
Found at i:306166 original size:589 final size:588
Alignment explanation
Indices: 304994--306318 Score: 1985
Period size: 589 Copynumber: 2.2 Consensus size: 588
304984 GAGAATAGGT
*
304994 ACGCATGAAGTGTCGATACATTTATAAAAAGTATTGATCCAAAAAACATCGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATAAAAAGTATTGATCC-AAAAACATCGAAACCCATAATTAT
* *
305059 AATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATTAGAGAATAGGTCT
65 AATGTAATAGGTAA-TTTTCAATGTAATCGGTATAAATATACCGGTTTTATGAGAG-A-A----T
* *
305124 ACATAATGTATCGACACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAAG
123 --AT-GTGTA-C-ATACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAAG
* *
305189 GGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATTGATCACAAAAACATCGAAACCCAT
183 GAGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCACAAAAACATCGAAACCCAT
* *
305254 AATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAAT
248 AATTATAATGTAATAGGTAATTTTTCAACGTAACCGGTATAAATATACCAGTTTTATGAGAGAAT
**
305319 AGGTCTACATAATGTATCGACACTTGTGAAACTTGAGTCGATACTTTTTGTCCAGAATGAATGCC
313 AGGTCTACATAATGTATCGACACTTGTGAAACTTGAGTCGATACTCGTTGTCCAGAATGAATGCC
* *
305384 CAAAAGGGGTGCACGCATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAAATATCGAA
378 CAAAAGGGGTGCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAA
* * * * * *
305449 ACCCATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATATCGGTTTTATGA
443 ACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCGATAGAAATATACCAGTTTTATGA
* * * * * *
305514 GAGAATAGGTCTACATAATGTATCGACACTTGTGGAACTTGTGTCGATACTTTTTTTCAGAATGA
508 AAAAAAAGGTCTACATAATGTATCGACACTTGTGGAACTTGTGTCAATACTTTTGTCCAGAATGA
305579 ATGCCCAAAAGGGGTGC
573 ATGCCCAAAA-GGGTGC
*
305596 ACTCATAAAGTGTCGATACATTTATAAAAAGTATTGATCCAAACAACATCGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATAAAAAGTATTGATCCAAA-AACATCGAAACCCATAATTAT
**
305661 AATGTAATAGGTAATTTTCAATGTAATCGGTATAAATATACCTATTTTATGAGAGAATATGTGTA
65 AATGTAATAGGTAATTTTCAATGTAATCGGTATAAATATACCGGTTTTATGAGAGAATATGTGTA
*
305726 CATACTTGTGGAACTTGTGTCGATACTTGTTGTCCATAATGAATGCCCAAAA-GAGTGCACGCAT
130 CATACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAAGGAGTGCACGCAT
*
305790 AAAGTGTCGATACATTTATAAAAAGTATCGATC-CAAAAAATATCGAAACCCATAATTATAATGT
195 AAAGTGTCGATACATTTATAAAAAGTATCGATCAC-AAAAACATCGAAACCCATAATTATAATGT
* *
305854 AATAGGTAATTTTTTAACGTAACTGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACATA
259 AATAGGTAATTTTTCAACGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACATA
* * *
305919 GTGTATCGACACTTGTGGAACTTGTA-TCGATACTCGTTGTCCAGAATGAATGCCCAAAA-GGTT
324 ATGTATCGACACTTGTGAAACTTG-AGTCGATACTCGTTGTCCAGAATGAATGCCCAAAAGGGGT
* * * *
305982 GCACGCATAAAGTGTTGATACATTTATAAAAAGTATCGATCCCAAAAACATTGAAACCCATATTT
388 GCACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCCATAATT
*
306047 ATAATGTAATAGGTAAATTTACAATGTAACCGATAGAAATTTACCAGTTTT-TGAAAAAAAAAGG
453 ATAATGTAATAGGTAAATTTACAATGTAACCGATAGAAATATACCAGTTTTATG-AAAAAAAAGG
*
306111 TCTACATAATGTATTGACACTTGTGGAACTTGTGTCAATACTTGTTGTCCAGAATGAATGCCCAA
517 TCTACATAATGTATCGACACTTGTGGAACTTGTGTCAATACTT-TTGTCCAGAATGAATGCCCAA
306176 AAGGGTGC
581 AAGGGTGC
*
306184 ACGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTAT
1 ACGCATAAAGTGTCGATACATTTATAAAAAGTATTGAT-CCAAAAACATCGAAACCCATAATTAT
* * * * * * *
306249 AATGTAGTAGGTAAATTTACAATGTAATCGGTAGAAATTTACCGGTTTTATGAGAAAATAGGTCT
65 AATGTAATAGGT-AATTTTCAATGTAATCGGTATAAATATACCGGTTTTATGAGAGAATATGTGT
306314 ACATA
129 ACATA
306319 ATGTATCGAC
Statistics
Matches: 664, Mismatches: 52, Indels: 27
0.89 0.07 0.04
Matches are distributed among these distances:
587 2 0.00
588 229 0.34
589 260 0.39
590 50 0.08
591 1 0.00
592 4 0.01
593 2 0.00
595 1 0.00
599 1 0.00
600 1 0.00
601 40 0.06
602 73 0.11
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.31
Consensus pattern (588 bp):
ACGCATAAAGTGTCGATACATTTATAAAAAGTATTGATCCAAAAACATCGAAACCCATAATTATA
ATGTAATAGGTAATTTTCAATGTAATCGGTATAAATATACCGGTTTTATGAGAGAATATGTGTAC
ATACTTGTGGAACTTGTGTCGATACTTGTTGTCCAGAATGAATGCCCAAAAGGAGTGCACGCATA
AAGTGTCGATACATTTATAAAAAGTATCGATCACAAAAACATCGAAACCCATAATTATAATGTAA
TAGGTAATTTTTCAACGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACATAAT
GTATCGACACTTGTGAAACTTGAGTCGATACTCGTTGTCCAGAATGAATGCCCAAAAGGGGTGCA
CGCATAAAGTGTCGATACATTTATAAAAAGTATCGATCCAAAAAACATCGAAACCCATAATTATA
ATGTAATAGGTAAATTTACAATGTAACCGATAGAAATATACCAGTTTTATGAAAAAAAAGGTCTA
CATAATGTATCGACACTTGTGGAACTTGTGTCAATACTTTTGTCCAGAATGAATGCCCAAAAGGG
TGC
Found at i:308976 original size:11 final size:11
Alignment explanation
Indices: 308960--308984 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
308950 TGTGGGTTTG
308960 ATTATTTGAAC
1 ATTATTTGAAC
308971 ATTATTTGAAC
1 ATTATTTGAAC
308982 ATT
1 ATT
308985 GTTATGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTATTTGAAC
Found at i:311110 original size:198 final size:198
Alignment explanation
Indices: 310584--311771 Score: 1738
Period size: 198 Copynumber: 6.0 Consensus size: 198
310574 TCAGTAATCT
* * *
310584 CCAGAATGAATGACCAATGAGGTGCACAAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
1 CCAGAATGAATGCCCAACGAGGTGCAC-TATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
* * * *
310649 CAAAAATATCGAATACGATAATTATATTGTAATAGGTCAATTTCCAATGTAACCGGTAGAAA-AG
65 CAAAAACATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAGTAGAAATA-
* * * *
310713 TATCGATTAATTAGAAAATAGGTCTACCTAATGTATCGACACTTTTTAAAGTTATGTCGATAATT
129 TACCGATTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAAGTTGTGTCGATACTT
310778 TTTTA
194 TTTTA
* * * *
310783 CCATAATGAATGCCCAACGAGGTGCACGAATAAAGTGTCGATACACTTATAAAAAAGTATCGATA
1 CCAGAATGAATGCCCAACGAGGTGCAC-TATAAAGTGTCGATACATTTAT-AAAAAGTATCGATC
* * *
310848 ACAAAAATATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAATAGAAATA
64 CCAAAAACATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAGTAGAAATA
* * * *
310913 TACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACAATTTTTAAACTTGTGTCAATACTT
129 TACCGATTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAAGTTGTGTCGATACTT
*
310978 TTTGA
194 TTTTA
* *
310983 CCAGAATGAATGACCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAACGTATCGATCCC
1 CCAGAATGAATGCCCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
* *
311048 AAAAACATCGAATACGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAATAGAAATATA
66 AAAAACATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAGTAGAAATATA
311113 CCGATTAATTAG-AAATAGGTCTACATAA--TATCGACACTTTTTAAAGTTGTGTCGATACTTTT
131 CCGATTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTT
311175 TTA
196 TTA
* * *
311178 CCAGAATAAATGCCCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAACAGTATCGATTCC
1 CCAGAATGAATGCCCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
* * * * *
311243 AAAAACATTGAATAAGATAACTATAATGCAAAAGGTCAATTTCCAATGTAACCGGTAGAAATATA
66 AAAAACATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAGTAGAAATATA
* * *
311308 CCGGTTAATTAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAAGTTGCGTCGATACTTTT
131 CCGATTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTT
311373 TTA
196 TTA
* *
311376 CCATAATGAATGCCCAACAAGGTGCACTATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
1 CCAGAATGAATGCCCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
* * * *
311441 AAAAATATAGAATAAGATAATTATAATGTAATATGTCAATTTCCAATGTAACCGGTAGAAATATA
66 AAAAACATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAGTAGAAATATA
* * * * *
311506 CTGATTAATTAGATAATATGTCTATATAATGTATCAACACTTTTTAAAGTTGTGTCGATACTTTT
131 CCGATTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTT
311571 TTA
196 TTA
* * * *
311574 GCATAATGAATGCCCAACGAGGTGCACTATAAACTGTCGATACATTTATAAAATGTATCGATCCC
1 CCAGAATGAATGCCCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
* * * * *
311639 AAAAACATCAAATACGATAATTATAATGTAATATG-AAACTTTACAATGTAACCAGTAGAAATAT
66 AAAAACATCGAATAAGATAATTATAATGTAATAGGTCAA-TTTCCAATGTAACCAGTAGAAATAT
* * * *
311703 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATTGACACCTTTTAAATTTGTGTCGATACTTT
130 ACCGATTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAAGTTGTGTCGATACTTT
311768 TTTA
195 TTTA
311772 AATTACGTGT
Statistics
Matches: 897, Mismatches: 86, Indels: 13
0.90 0.09 0.01
Matches are distributed among these distances:
195 162 0.18
196 16 0.02
197 18 0.02
198 478 0.53
199 65 0.07
200 157 0.18
201 1 0.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (198 bp):
CCAGAATGAATGCCCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
AAAAACATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAGTAGAAATATA
CCGATTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTT
TTA
Found at i:311355 original size:393 final size:393
Alignment explanation
Indices: 310584--311769 Score: 1784
Period size: 393 Copynumber: 3.0 Consensus size: 393
310574 TCAGTAATCT
* *
310584 CCAGAATGAATGACCAATGAGGTGCACAAATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
1 CCAGAATGAATGACCAACGAGGTGCAC-TATAAAGTGTCGATACATTTATAAAAAGTATCGATCC
*
310649 CAAAAATATCGAATACGATAATTATATTGTAATAGGTCAATTTCCAATGTAACCGGTAGAAA-AG
65 CAAAAATATCGAATACGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATA-
* * * *
310713 TATCGATTAATTAGAAAATAGGTCTACCTAATGTATCGACACTTTTTAAAGTTATGTCGATAATT
129 TACCGATTAATTAG-AAATAGGTCTACATAA-GTATCGACACTTTTTAAAGTTGTGTCGATACTT
* *
310778 TTTTACCATAATGAATGCCCAACGAGGTGCACGAATAAAGTGTCGATACACTTATAAAAAAGTAT
192 TTTTACCATAATGAATGCCCAACGAGGTGCAC-TATAAAGTGTCGATACA-TT-TATAAAAGTAT
* * *
310843 CGATAACAAAAATATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAATAG
254 CGATACCAAAAACATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAGTAG
* *
310908 AAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACAATTTTTAAACTTGTGTCAA
319 AAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAACTTGTGTCGA
310973 TACTTTTTGA
384 TACTTTTTGA
*
310983 CCAGAATGAATGACCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAACGTATCGATCCC
1 CCAGAATGAATGACCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
* **
311048 AAAAACATCGAATACGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAATAGAAATATA
66 AAAAATATCGAATACGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATATA
311113 CCGATTAATTAGAAATAGGTCTACATAA-TATCGACACTTTTTAAAGTTGTGTCGATACTTTTTT
131 CCGATTAATTAGAAATAGGTCTACATAAGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTTT
* * *
311177 ACCAGAATAAATGCCCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAACAGTATCGATTC
196 ACCATAATGAATGCCCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAA-AGTATCGATAC
* * * * *
311242 CAAAAACATTGAATAAGATAACTATAATGCAAAAGGTCAATTTCCAATGTAACCGGTAGAAATAT
260 CAAAAACATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAGTAGAAATAT
* * *
311307 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCAACACTTTTTAAAGTTGCGTCGATACTTT
325 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAACTTGTGTCGATACTTT
*
311372 TTTA
390 TTGA
* * *
311376 CCATAATGAATGCCCAACAAGGTGCACTATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
1 CCAGAATGAATGACCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
* * *
311441 AAAAATATAGAATAAGATAATTATAATGTAATATGTCAATTTCCAATGTAACCGGTAGAAATATA
66 AAAAATATCGAATACGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATATA
* * * *
311506 CTGATTAATTAGATAATATGTCTATATAATGTATCAACACTTTTTAAAGTTGTGTCGATACTTTT
131 CCGATTAATTAGA-AATAGGTCTACATAA-GTATCGACACTTTTTAAAGTTGTGTCGATACTTTT
* *
311571 TTAGCATAATGAATGCCCAACGAGGTGCACTATAAACTGTCGATACATTTATAAAATGTATCGAT
194 TTACCATAATGAATGCCCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAA-GTATCGAT
* * * * * *
311636 CCCAAAAACATCAAATACGATAATTATAATGTAATATG-AAACTTTACAATGTAACCAGTAGAAA
258 ACCAAAAACATCGAATAAGATAATTATAATGTAATAGGTCAA-TTTCCAATGTAACCAGTAGAAA
* * *
311700 TATACCGGTTAATTAGAAAATAGGTCTACATAATGTATTGACACCTTTTAAATTTGTGTCGATAC
322 TATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAACTTGTGTCGATAC
311765 TTTTT
387 TTTTT
311770 TAAATTACGT
Statistics
Matches: 716, Mismatches: 64, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
392 5 0.01
393 264 0.37
394 29 0.04
395 63 0.09
396 207 0.29
397 15 0.02
398 106 0.15
399 27 0.04
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (393 bp):
CCAGAATGAATGACCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAAAGTATCGATCCC
AAAAATATCGAATACGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCGGTAGAAATATA
CCGATTAATTAGAAATAGGTCTACATAAGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTTT
ACCATAATGAATGCCCAACGAGGTGCACTATAAAGTGTCGATACATTTATAAAAGTATCGATACC
AAAAACATCGAATAAGATAATTATAATGTAATAGGTCAATTTCCAATGTAACCAGTAGAAATATA
CCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAACTTGTGTCGATACTTTT
TGA
Found at i:313421 original size:19 final size:19
Alignment explanation
Indices: 313397--313444 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
313387 ATGTAGGGGA
*
313397 AATTTTGTATACGA-TTCAT
1 AATTTTGTATACAATTTC-T
*
313416 AATTTTGTATATAATTTCT
1 AATTTTGTATACAATTTCT
313435 AATTTTGTAT
1 AATTTTGTAT
313445 GTGAATGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 23 0.88
20 3 0.12
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.54
Consensus pattern (19 bp):
AATTTTGTATACAATTTCT
Found at i:316300 original size:200 final size:199
Alignment explanation
Indices: 315925--316368 Score: 592
Period size: 200 Copynumber: 2.2 Consensus size: 199
315915 ACCTAAATAT
* *
315925 GTGTCGATACATTT-TCTAAAAGTATCTA-CTCCAAAAACATCAAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATC-CCAAAAACATCGAAACCAATAATTATAATGTAA
* * * * * *
315988 TAGGTAAATAAACAATGTAACCGGTATAAATATACTGGTTAATTAGAAAACATGTCAACGTAATG
64 TAGGTAAATAAACAATGTAACCAGTATAAATATACCGGTTAATGAGAAAACAGGTCAACATAAAG
*
316053 TATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCCAAACGAGGTGCAC
129 TATCGACACTTGTGAAATTTGTGTCGATACTTATTGTCCAGAATGAATG-CCAAACGAGGTGCAC
316118 GCATAAA
193 GCATAAA
* * *
316125 GTGTCGATACGTTTATTAAAAGTATCGATCCCAATAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
** * * * * *
316190 GGTAAATTTACATTGTAGCCAGTATAAATATACCGGTTTTATGAGAAAATAGGTCAGCATAAAGT
66 GGTAAATAAACAATGTAACCAGTATAAATATACCGG-TTAATGAGAAAACAGGTCAACATAAAGT
* *
316255 ATCGACACTTGCT-AAATTTGTGTCGATACATT-TT-TCCATAATGAATGCCAAACGGGGTGCAC
130 ATCGACACTTG-TGAAATTTGTGTCGATAC-TTATTGTCCAGAATGAATGCCAAACGAGGTGCAC
316317 GCATAAA
193 GCATAAA
* *
316324 GTGTCGATACATATATTAAAAGTATCGATCCTAAAAACATCGAAA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAA
316369 ATATTACATG
Statistics
Matches: 214, Mismatches: 25, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
199 62 0.29
200 98 0.46
201 51 0.24
202 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (199 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAATA
GGTAAATAAACAATGTAACCAGTATAAATATACCGGTTAATGAGAAAACAGGTCAACATAAAGTA
TCGACACTTGTGAAATTTGTGTCGATACTTATTGTCCAGAATGAATGCCAAACGAGGTGCACGCA
TAAA
Found at i:316703 original size:64 final size:64
Alignment explanation
Indices: 316635--316754 Score: 231
Period size: 64 Copynumber: 1.9 Consensus size: 64
316625 TACCTATTAC
*
316635 ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATGCCTATTTT
1 ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTT
316699 ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATG
1 ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATG
316755 ATATAACATA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.43
Consensus pattern (64 bp):
ATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGCCTATTTT
Found at i:331915 original size:38 final size:37
Alignment explanation
Indices: 331841--331916 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
331831 GTTAAAAAAT
* *
331841 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
* *
331878 ATTTATATAATTTTTTTTACAAAATTAAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATT-AAAAATCATAAA
331916 A
1 A
331917 AATATTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.24
38 21 0.64
39 4 0.12
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTAAAAATCATAAA
Found at i:339355 original size:22 final size:21
Alignment explanation
Indices: 339327--339367 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
339317 AATCCTTTTA
339327 TTATTTTATTATTACTTTCTTT
1 TTATTTTATTATTA-TTTCTTT
*
339349 TTATTTTTTTATTATTTCT
1 TTATTTTATTATTATTTCT
339368 GTTATTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATTTTATTATTATTTCTTT
Found at i:339380 original size:25 final size:25
Alignment explanation
Indices: 339324--339381 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
339314 TTTAATCCTT
* * *
339324 TTATTATTTTATTATTACTTTCTTT
1 TTATTTTTTTATTATTACTTTATTG
*
339349 TTATTTTTTTATTATTTCTGTTATTG
1 TTATTTTTTTATTATTACT-TTATTG
339375 TT-TTTTT
1 TTATTTTT
339382 ACATTAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (25 bp):
TTATTTTTTTATTATTACTTTATTG
Found at i:339438 original size:2 final size:2
Alignment explanation
Indices: 339431--339456 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
339421 TTAATATTTG
339431 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
339457 GTATGTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:339573 original size:17 final size:18
Alignment explanation
Indices: 339553--339591 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
339543 ATATGTGTAG
339553 TATTATTAT-TTT-CTTTA
1 TATTATT-TGTTTCCTTTA
339570 TATTATTTGTTTCCTTTA
1 TATTATTTGTTTCCTTTA
339588 TATT
1 TATT
339592 TATCTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 10 0.50
18 9 0.45
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (18 bp):
TATTATTTGTTTCCTTTA
Found at i:339626 original size:15 final size:15
Alignment explanation
Indices: 339601--339640 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
339591 TTATCTTTAT
*
339601 TTTACTTTATTTCTA
1 TTTATTTTATTTCTA
* *
339616 TTTCTTTTATTTCTC
1 TTTATTTTATTTCTA
339631 TTTATTTTAT
1 TTTATTTTAT
339641 GTATTTTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTTATTTCTA
Found at i:339667 original size:34 final size:34
Alignment explanation
Indices: 339588--339674 Score: 97
Period size: 34 Copynumber: 2.5 Consensus size: 34
339578 GTTTCCTTTA
* * *
339588 TATTTATCTTTATTTTACTTTATTTCTATTTCTTT
1 TATTTATCTTTATTTTA-TGTATTTCTATTACTTG
*
339623 TATTTCTCTTTATTTTATGTATTT-TAGTTACTTGG
1 TATTTATCTTTATTTTATGTATTTCTA-TTACTT-G
339658 T-TTTATCTTTATTTTAT
1 TATTTATCTTTATTTTAT
339675 CTCATGTGTA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
33 2 0.04
34 26 0.58
35 17 0.38
ACGTcount: A:0.17, C:0.09, G:0.05, T:0.69
Consensus pattern (34 bp):
TATTTATCTTTATTTTATGTATTTCTATTACTTG
Found at i:346348 original size:65 final size:66
Alignment explanation
Indices: 346228--346351 Score: 205
Period size: 65 Copynumber: 1.9 Consensus size: 66
346218 CTCTAGATTG
* **
346228 GATTTCAACTTCAGGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATAAA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAAGGGGCCATAAA
346293 T
66 T
*
346294 GATTTCAACTTCACGACGAAGGATAT-CAATTCAAAACTCAACTTCACAATGAAGGGGC
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAAGGGGC
346352 TTCCCAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
65 29 0.54
66 25 0.46
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.22
Consensus pattern (66 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAAGGGGCCATAAA
T
Found at i:346568 original size:32 final size:35
Alignment explanation
Indices: 346483--346575 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 35
346473 ACAATACTTG
*
346483 GATTTCAACTTCATGACGAAGGATATCCAATTCAA
1 GATTTCAACTTCATGACGAAGGATATCCAATCCAA
* ** * *
346518 GA-CTCAACTTCACAACGAAGGA-GT-C-ATCCAC
1 GATTTCAACTTCATGACGAAGGATATCCAATCCAA
346549 GATTTCAACTTCATGACGAAGGATATC
1 GATTTCAACTTCATGACGAAGGATATC
346576 GTGCCATCAA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
31 6 0.13
32 18 0.40
33 2 0.04
34 17 0.38
35 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (35 bp):
GATTTCAACTTCATGACGAAGGATATCCAATCCAA
Found at i:346627 original size:120 final size:120
Alignment explanation
Indices: 346479--346771 Score: 462
Period size: 120 Copynumber: 2.4 Consensus size: 120
346469 ACAAACAATA
*
346479 CTTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGACTCAACTTCACAACGAA-GGAGTC
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGACTCAACTTCACAACGAATGG-GTC
* * * *
346543 ATCCACGATTTCAACTTCATGACGAAGGATATCGTGCCATCAACATTCATTTTTAT
65 ATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAGCAACATTCATCTTTAG
*
346599 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGACTTAACTTCACAACGAATGGGTCA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGACTCAACTTCACAACGAATGGGTCA
* * *
346664 TCCACGGTTTCAACTTTACGACGAAGGATATCGTGCTAGCAACATTCATCTTTAG
66 TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAGCAACATTCATCTTTAG
* * *
346719 ATTGAATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACA
1 CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGACTCAACTTCACA
346772 GAGAAAGAGC
Statistics
Matches: 159, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
120 157 0.99
121 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (120 bp):
CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGACTCAACTTCACAACGAATGGGTCA
TCCACGATTTCAACTTCACGACGAAGGATATCGTGCCAGCAACATTCATCTTTAG
Found at i:347997 original size:13 final size:14
Alignment explanation
Indices: 347964--348002 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
347954 ATATATATAT
347964 TATTTC-TT-TTTA
1 TATTTCTTTATTTA
347976 -ATTTCTTTATTTA
1 TATTTCTTTATTTA
347989 TATTT-TTTATTTA
1 TATTTCTTTATTTA
348002 T
1 T
348003 TTCTTCTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.21
12 2 0.08
13 13 0.54
14 4 0.17
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (14 bp):
TATTTCTTTATTTA
Found at i:348168 original size:15 final size:15
Alignment explanation
Indices: 348124--348171 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
348114 TATTGATATG
* *
348124 TATATATTATTTCTT
1 TATATATTTTTTATT
*
348139 TTTA-ATTTCTTTATT
1 TATATATTT-TTTATT
348154 TATATATTTTTTATT
1 TATATATTTTTTATT
348169 TAT
1 TAT
348172 TTCTTCTTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
14 3 0.11
15 20 0.74
16 4 0.15
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (15 bp):
TATATATTTTTTATT
Found at i:348237 original size:17 final size:18
Alignment explanation
Indices: 348217--348255 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
348207 ATATGTGTAG
348217 TATTATTAT-TTTCC-TTA
1 TATTATT-TGTTTCCTTTA
348234 TATTATTTGTTTCCTTTA
1 TATTATTTGTTTCCTTTA
348252 TATT
1 TATT
348256 TATCTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 1 0.05
17 12 0.60
18 7 0.35
ACGTcount: A:0.21, C:0.10, G:0.03, T:0.67
Consensus pattern (18 bp):
TATTATTTGTTTCCTTTA
Found at i:348272 original size:10 final size:10
Alignment explanation
Indices: 348247--348288 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
348237 TATTTGTTTC
348247 CTTTATATTTA
1 CTTTAT-TTTA
348258 TCTTTATTTTA
1 -CTTTATTTTA
348269 CTTTATTTCTA
1 CTTTATTT-TA
348280 -TTTATTTTA
1 CTTTATTTTA
348289 TTTCTCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 2 0.07
10 15 0.52
11 6 0.21
12 6 0.21
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (10 bp):
CTTTATTTTA
Found at i:348288 original size:15 final size:15
Alignment explanation
Indices: 348265--348304 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
348255 TTATCTTTAT
*
348265 TTTACTTTATTTCTA
1 TTTATTTTATTTCTA
*
348280 TTTATTTTATTTCTC
1 TTTATTTTATTTCTA
348295 TTTATTTTAT
1 TTTATTTTAT
348305 GTATTTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTTATTTCTA
Found at i:351984 original size:17 final size:17
Alignment explanation
Indices: 351937--352038 Score: 73
Period size: 17 Copynumber: 5.9 Consensus size: 17
351927 TTAATTTATG
* *
351937 TCTGATTACTGTAAAACA
1 TCTGATAACTGT-AAATA
*
351955 TATGATATA-TGTAAATA
1 TCTGATA-ACTGTAAATA
351972 TCTGATAACTGT-AATCA
1 TCTGATAACTGTAAAT-A
* *
351989 TCTGATATCTGTAAATG
1 TCTGATAACTGTAAATA
* *
352006 TCTGGTAACTGAAAATGA
1 TCTGATAACTGTAAAT-A
* *
352024 TATGATAATTGTAAA
1 TCTGATAACTGTAAA
352039 CATTTAGAAT
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.06
17 38 0.58
18 22 0.34
19 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (17 bp):
TCTGATAACTGTAAATA
Found at i:352002 original size:34 final size:35
Alignment explanation
Indices: 351937--352038 Score: 102
Period size: 34 Copynumber: 2.9 Consensus size: 35
351927 TTAATTTATG
*
351937 TCTGATTACTGTAAAACATATGATATATGTAAATA
1 TCTGATAACTGTAAAACATATGATATATGTAAATA
* * * *
351972 TCTGATAACTGT-AATCATCTGATATCTGTAAATG
1 TCTGATAACTGTAAAACATATGATATATGTAAATA
* *
352006 TCTGGTAACTG-AAAATGATATGATA-ATTGTAAA
1 TCTGATAACTGTAAAA-CATATGATATA-TGTAAA
352039 CATTTAGAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
34 30 0.56
35 24 0.44
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (35 bp):
TCTGATAACTGTAAAACATATGATATATGTAAATA
Found at i:359108 original size:2 final size:2
Alignment explanation
Indices: 359103--359137 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
359093 ACACACACAC
359103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
359138 ACCCCATTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:359378 original size:24 final size:24
Alignment explanation
Indices: 359351--359488 Score: 165
Period size: 24 Copynumber: 5.8 Consensus size: 24
359341 CATAATTCAT
* * * *
359351 GTCAAGTATCATATCAAAATCTAG
1 GTCAAGTATCAGATCAGAATCCAA
*
359375 GTCAAATATC--ATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
359397 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
359421 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
359445 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
* *
359469 GTAAAGTATCAGATTAGAAT
1 GTCAAGTATCAGATCAGAAT
359489 TCAAATCGAA
Statistics
Matches: 102, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.18
23 2 0.02
24 80 0.78
25 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:359504 original size:48 final size:48
Alignment explanation
Indices: 359385--359506 Score: 131
Period size: 48 Copynumber: 2.5 Consensus size: 48
359375 GTCAAATATC
* * *
359385 ATCAGAATCCAAGTCA-AGTATCAGATCAGAATCCAAGTCAAGTATCAG
1 ATCAGAATCCAAATCAGA-AATCAGATCAGAATCCAAGTAAAGTATCAG
** * *
359433 ATCAGAATCCATGTCAGATATCAGATCAGAATCCATGTAAAGTATCAG
1 ATCAGAATCCAAATCAGAAATCAGATCAGAATCCAAGTAAAGTATCAG
* *
359481 ATTAGAATTCAAATC-GAAAATCAGAT
1 ATCAGAATCCAAATCAG-AAATCAGAT
359507 AAAATATTCA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
47 1 0.02
48 62 0.97
49 1 0.02
ACGTcount: A:0.43, C:0.18, G:0.16, T:0.24
Consensus pattern (48 bp):
ATCAGAATCCAAATCAGAAATCAGATCAGAATCCAAGTAAAGTATCAG
Found at i:362449 original size:20 final size:20
Alignment explanation
Indices: 362420--362467 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
362410 ACTGAAATTA
*
362420 ACGACGAATGGCGACGATTC
1 ACGACAAATGGCGACGATTC
362440 ACGACAAATGGCGACGATTC
1 ACGACAAATGGCGACGATTC
362460 ACGACAAA
1 ACGACAAA
362468 AGGTTTGAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.25, T:0.12
Consensus pattern (20 bp):
ACGACAAATGGCGACGATTC
Found at i:367178 original size:22 final size:23
Alignment explanation
Indices: 367148--367197 Score: 84
Period size: 22 Copynumber: 2.2 Consensus size: 23
367138 CAGATTTGAC
367148 TTATGAAGAAGAACCAATAC-AA
1 TTATGAAGAAGAACCAATACAAA
*
367170 TTATTAAGAAGAACCAATACAAA
1 TTATGAAGAAGAACCAATACAAA
367193 TTATG
1 TTATG
367198 GCTCGAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (23 bp):
TTATGAAGAAGAACCAATACAAA
Found at i:367643 original size:22 final size:22
Alignment explanation
Indices: 367618--367668 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
367608 GAATCGATAT
*
367618 TGTTCATGGTATTGTTCATAAC
1 TGTTCATGGTACTGTTCATAAC
* *
367640 TGTTCACGGTACTGTTCATCAC
1 TGTTCATGGTACTGTTCATAAC
*
367662 TATTCAT
1 TGTTCAT
367669 AAAAAATCTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.43
Consensus pattern (22 bp):
TGTTCATGGTACTGTTCATAAC
Found at i:371964 original size:20 final size:20
Alignment explanation
Indices: 371935--371972 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
371925 CCCCTTCAAA
*
371935 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
371955 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
371973 TGCACCAAAA
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:0.13, C:0.26, G:0.34, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:375459 original size:22 final size:21
Alignment explanation
Indices: 375418--375457 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
375408 GAGTTTATTT
375418 TCATTTTTCAATTTTAAAACA
1 TCATTTTTCAATTTTAAAACA
375439 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
375458 ACTATTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:378378 original size:31 final size:31
Alignment explanation
Indices: 378321--378392 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 31
378311 AATTAAAATT
* *
378321 AAAAATTCAAAGTTAGAGTGATTAAATTATAA
1 AAAAATTAAAAGTTAGAGTAATTAAATT-TAA
* *
378353 ATAATTTAAAAGTTA-AGTAATTAAATTTAA
1 AAAAATTAAAAGTTAGAGTAATTAAATTTAA
378383 AAAAATTAAA
1 AAAAATTAAA
378393 CTTTAGTGAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 11 0.32
31 11 0.32
32 12 0.35
ACGTcount: A:0.57, C:0.01, G:0.08, T:0.33
Consensus pattern (31 bp):
AAAAATTAAAAGTTAGAGTAATTAAATTTAA
Found at i:378552 original size:20 final size:20
Alignment explanation
Indices: 378515--378567 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
378505 AAAACAATAA
378515 ATAAA-TAAATAAATATTA-GT
1 ATAAATTAAA-AAA-ATTATGT
*
378535 TTAAATTTAAAAAAATTATGT
1 ATAAA-TTAAAAAAATTATGT
378556 ATAAATTAAAAA
1 ATAAATTAAAAA
378568 GATAAATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
20 15 0.54
21 9 0.32
22 4 0.14
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
ATAAATTAAAAAAATTATGT
Found at i:379772 original size:13 final size:13
Alignment explanation
Indices: 379754--379781 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
379744 TTCCTTTTGC
379754 GAGGAGTATCTTG
1 GAGGAGTATCTTG
379767 GAGGAGTATCTTG
1 GAGGAGTATCTTG
379780 GA
1 GA
379782 AGTATCTCGC
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:0.25, C:0.07, G:0.39, T:0.29
Consensus pattern (13 bp):
GAGGAGTATCTTG
Found at i:381168 original size:44 final size:43
Alignment explanation
Indices: 381102--381307 Score: 247
Period size: 44 Copynumber: 4.7 Consensus size: 43
381092 GATAGATTTG
*
381102 TTTTTATTT-TTTTGTTTCTTAATGTTTTTATTTAATTATAGAC
1 TTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTAT-GAC
381145 TTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATGAAC
1 TTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATG-AC
* *
381189 GTTTTATTTGTTTTATTTCTTAATGTTTTTATTTAATTATGGA-
1 TTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTAT-GAC
* * *
381232 -TTTTATTTATTTATTTTTCTTAATGTTTTTATTATTTAATTACGAA
1 TTTTTATTTATTT-TATTTCTTAATG--TTT-TTATTTAATTATGAC
* * *
381278 TTTTTATTTATTTTGTTTATTAATATTTTT
1 TTTTTATTTATTTTATTTCTTAATGTTTTT
381308 GTTATTTAAT
Statistics
Matches: 145, Mismatches: 9, Indels: 18
0.84 0.05 0.10
Matches are distributed among these distances:
42 11 0.08
43 23 0.16
44 73 0.50
45 6 0.04
46 20 0.14
47 12 0.08
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.67
Consensus pattern (43 bp):
TTTTTATTTATTTTATTTCTTAATGTTTTTATTTAATTATGAC
Found at i:384962 original size:20 final size:20
Alignment explanation
Indices: 384933--384987 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
384923 TATGTGATCC
384933 TTTGGAACATATATACGGT-T
1 TTTGGAACATATAT-CGGTAT
* *
384953 TTTGGGACATATACTTGGTAT
1 TTTGGAACATATA-TCGGTAT
384974 TTTGGAACATATAT
1 TTTGGAACATATAT
384988 GTGGTCATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (20 bp):
TTTGGAACATATATCGGTAT
Found at i:385025 original size:23 final size:23
Alignment explanation
Indices: 384985--385072 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 23
384975 TTGGAACATA
**
384985 TATGTGGTCATTATGGACAATTC
1 TATGTGGTCATTCGGGACAATTC
*
385008 TATGTGGTCATTCGGGAC-A-TA
1 TATGTGGTCATTCGGGACAATTC
* *
385029 TATGTGGTCATCCGGGAAAATTC
1 TATGTGGTCATTCGGGACAATTC
* * *
385052 TACGAGGTCCTTCGGGACAAT
1 TATGTGGTCATTCGGGACAAT
385073 GTTATATGGC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
21 17 0.33
22 2 0.04
23 33 0.63
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (23 bp):
TATGTGGTCATTCGGGACAATTC
Found at i:385037 original size:21 final size:21
Alignment explanation
Indices: 384912--385045 Score: 85
Period size: 21 Copynumber: 6.3 Consensus size: 21
384902 TACACAGTCC
* *
384912 TTCGGGACATATATGTGATCC
1 TTCGGGACATATATGTGGTCA
* * ** *
384933 TTTGGAACATATATACGGT-T
1 TTCGGGACATATATGTGGTCA
*
384953 TTTGGGACATATACT-TGGT-A
1 TTCGGGACATATA-TGTGGTCA
* *
384973 TTTTGGAACATATATGTGGTCA
1 -TTCGGGACATATATGTGGTCA
** *
384995 TTATGGACAATTCTATGTGGTCA
1 TTCGGGAC-A-TATATGTGGTCA
385018 TTCGGGACATATATGTGGTCA
1 TTCGGGACATATATGTGGTCA
*
385039 TCCGGGA
1 TTCGGGA
385046 AAATTCTACG
Statistics
Matches: 89, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
20 16 0.18
21 53 0.60
22 3 0.03
23 17 0.19
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (21 bp):
TTCGGGACATATATGTGGTCA
Found at i:385051 original size:44 final size:44
Alignment explanation
Indices: 384980--385070 Score: 119
Period size: 44 Copynumber: 2.1 Consensus size: 44
384970 GTATTTTGGA
* * * * *
384980 ACATATATGTGGTCATTATGGACAATTCTATGTGGTCATTCGGG
1 ACATATATGTGGTCATCAGGGAAAATTCTACGAGGTCATTCGGG
* *
385024 ACATATATGTGGTCATCCGGGAAAATTCTACGAGGTCCTTCGGG
1 ACATATATGTGGTCATCAGGGAAAATTCTACGAGGTCATTCGGG
385068 ACA
1 ACA
385071 ATGTTATATG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (44 bp):
ACATATATGTGGTCATCAGGGAAAATTCTACGAGGTCATTCGGG
Found at i:388002 original size:22 final size:23
Alignment explanation
Indices: 387968--388018 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
387958 TATATGGCAC
* *
387968 TCGGTGCATTTCTATGCGACACT
1 TCGGTGCAATTCTACGCGACACT
* *
387991 TCGGTG-AATTCTACGTGGCACT
1 TCGGTGCAATTCTACGCGACACT
388013 TCGGTG
1 TCGGTG
388019 TATTTTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (23 bp):
TCGGTGCAATTCTACGCGACACT
Found at i:389368 original size:21 final size:21
Alignment explanation
Indices: 389344--389438 Score: 84
Period size: 21 Copynumber: 4.5 Consensus size: 21
389334 TTATACATAT
*
389344 TCAAATGACCAAATATATGTC
1 TCAAAGGACCAAATATATGTC
*
389365 TCAAAGGACCAAATATGTGTC
1 TCAAAGGACCAAATATATGTC
* * *
389386 TCAAAGAACCATATAAATGT-
1 TCAAAGGACCAAATATATGTC
** * *
389406 TCCAAAGGATTATATATACGTC
1 T-CAAAGGACCAAATATATGTC
*
389428 TCGAAGGACCA
1 TCAAAGGACCA
389439 CGTATACCCT
Statistics
Matches: 58, Mismatches: 14, Indels: 4
0.76 0.18 0.05
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (21 bp):
TCAAAGGACCAAATATATGTC
Found at i:392273 original size:21 final size:21
Alignment explanation
Indices: 392249--392381 Score: 90
Period size: 21 Copynumber: 6.3 Consensus size: 21
392239 TATCCCGGAG
* *
392249 GACCATATATATGTCCCGAAT
1 GACCACATATATGTCCCGAAA
* ** *
392270 GACCACATAGAATTGTCCATAAG
1 GACCACATA-TA-TGTCCCGAAA
* **
392293 GACCACATATATGTTCTAAAA
1 GACCACATATATGTCCCGAAA
*
392314 GACCAAATATATGTCCCGAAA
1 GACCACATATATGTCCCGAAA
** *
392335 GACCGTATATATGTTCC-AAA
1 GACCACATATATGTCCCGAAA
* *
392355 GGATCACATATATGT-CCGAAT
1 -GACCACATATATGTCCCGAAA
392376 GACCAC
1 GACCAC
392382 GTAGAACCCT
Statistics
Matches: 86, Mismatches: 22, Indels: 9
0.74 0.19 0.08
Matches are distributed among these distances:
20 10 0.12
21 58 0.67
22 2 0.02
23 16 0.19
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (21 bp):
GACCACATATATGTCCCGAAA
Found at i:392346 original size:42 final size:41
Alignment explanation
Indices: 392299--392379 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 41
392289 TAAGGACCAC
*
392299 ATATATGTTCTAAAAGACCAAATATATGTCCCGAAAGACCGT
1 ATATATGTTCCAAAAGACCAAATATATGT-CCGAAAGACCGT
* * * *
392341 ATATATGTTCCAAAGGATCACATATATGTCCGAATGACC
1 ATATATGTTCCAAAAGACCAAATATATGTCCGAAAGACC
392380 ACGTAGAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 9 0.26
42 25 0.74
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (41 bp):
ATATATGTTCCAAAAGACCAAATATATGTCCGAAAGACCGT
Found at i:396012 original size:16 final size:17
Alignment explanation
Indices: 395986--396020 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
395976 GTTACAATTC
*
395986 AAACAATTAAATAACAA
1 AAACAATTAAAAAACAA
396003 AAAC-ATTAAAAAACAA
1 AAACAATTAAAAAACAA
396019 AA
1 AA
396021 TAAATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.74, C:0.11, G:0.00, T:0.14
Consensus pattern (17 bp):
AAACAATTAAAAAACAA
Found at i:396071 original size:24 final size:23
Alignment explanation
Indices: 395982--396075 Score: 68
Period size: 24 Copynumber: 3.9 Consensus size: 23
395972 AAAAGTTACA
* *
395982 ATTCAAACAATTAAATAACAAAAAC
1 ATTCAAAAAAATAAAT-A-AAAAAC
*
396007 ATT-AAAAAACA-AAATAAATAAAA
1 ATTCAAAAAA-ATAAATAAA-AAAC
*
396030 ATTCATAATTAAAT-AATAAAAAAC
1 ATTCA-AA-AAAATAAATAAAAAAC
396054 ATTCAGAAAAAATAAATAAAAA
1 ATTCA-AAAAAATAAATAAAAA
396076 GTCCATAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
22 2 0.04
23 11 0.20
24 28 0.51
25 12 0.22
26 2 0.04
ACGTcount: A:0.69, C:0.09, G:0.01, T:0.21
Consensus pattern (23 bp):
ATTCAAAAAAATAAATAAAAAAC
Found at i:396118 original size:24 final size:24
Alignment explanation
Indices: 396085--396161 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
396075 AGTCCATAAT
396085 TAAATAAAAACATTAAGAAATAAAA
1 TAAAT-AAAACATTAAGAAATAAAA
** *
396110 TAAATAAAATGTT-AG---T-AAT
1 TAAATAAAACATTAAGAAATAAAA
396129 TAAATAAAACATTAAGAAATAAAA
1 TAAATAAAACATTAAGAAATAAAA
396153 TAAATAAAA
1 TAAATAAAA
396162 GTCTATAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
19 13 0.32
20 3 0.07
23 3 0.07
24 17 0.41
25 5 0.12
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (24 bp):
TAAATAAAACATTAAGAAATAAAA
Found at i:396151 original size:19 final size:21
Alignment explanation
Indices: 396086--396195 Score: 82
Period size: 21 Copynumber: 5.1 Consensus size: 21
396076 GTCCATAATT
396086 AAATAAAAACATTAAGAAATA
1 AAATAAAAACATTAAGAAATA
* * * *
396107 AAATAAATAAAATGTTAGTAATT
1 AAATAAA-AACAT-TAAGAAATA
396130 AAAT-AAAACATTAAGAAATA
1 AAATAAAAACATTAAGAAATA
* * *
396150 AAATAAATAAAAGTCT-A-TAATT
1 AAATAAA-AACA-T-TAAGAAATA
*
396172 AAATAAAAACATTAAGAAAAA
1 AAATAAAAACATTAAGAAATA
396193 AAA
1 AAA
396196 AATAAAAATA
Statistics
Matches: 66, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
19 1 0.02
20 12 0.18
21 21 0.32
22 19 0.29
23 12 0.18
24 1 0.02
ACGTcount: A:0.67, C:0.04, G:0.05, T:0.24
Consensus pattern (21 bp):
AAATAAAAACATTAAGAAATA
Found at i:396152 original size:43 final size:42
Alignment explanation
Indices: 396001--396202 Score: 234
Period size: 43 Copynumber: 4.7 Consensus size: 42
395991 ATTAAATAAC
* *
396001 AAAAACATTAAAAAACAAAATAAATAAAAAT-TCATAATTAAATAAT
1 AAAAACATTAAGAAA-AAAATAAATAAAAGTCT-ATAATT--A-AAT
* *
396047 AAAAAACATTCAG-AAAAAATAAATAAAAAGTCCATAATTAAAT
1 -AAAAACATTAAGAAAAAAATAAAT-AAAAGTCTATAATTAAAT
396090 AAAAACATTAAGAAATAAAATAAATAAAATGT-TAGTAATTAAAT
1 AAAAACATTAAGAAA-AAAATAAATAAAA-GTCTA-TAATTAAAT
396134 -AAAACATTAAGAAATAAAATAAATAAAAGTCTATAATTAAAT
1 AAAAACATTAAGAAA-AAAATAAATAAAAGTCTATAATTAAAT
396176 AAAAACATTAAGAAAAAAA-AAATAAAA
1 AAAAACATTAAGAAAAAAATAAATAAAA
396203 ATAAATCTAT
Statistics
Matches: 141, Mismatches: 6, Indels: 22
0.83 0.04 0.13
Matches are distributed among these distances:
41 8 0.06
42 26 0.18
43 54 0.38
44 21 0.15
45 9 0.06
46 13 0.09
47 10 0.07
ACGTcount: A:0.68, C:0.05, G:0.04, T:0.23
Consensus pattern (42 bp):
AAAAACATTAAGAAAAAAATAAATAAAAGTCTATAATTAAAT
Found at i:399232 original size:32 final size:30
Alignment explanation
Indices: 399150--399232 Score: 85
Period size: 32 Copynumber: 2.7 Consensus size: 30
399140 GTCACTAAAG
* ** *
399150 TTTAATTTTTTTAAATTTAATTACTTAATT
1 TTTAATTTTTTTATATTTAAACACTTAACT
* *
399180 TTTAAATTATTTATACTTTAAACACTCTAACT
1 TTTAATTTTTTTATA-TTTAAACACT-TAACT
399212 TTTAATTTTTTTATTATTTAA
1 TTTAATTTTTTTA-TATTTAA
399233 TTATATATCA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
30 12 0.29
31 8 0.19
32 20 0.48
33 2 0.05
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTAATTTTTTTATATTTAAACACTTAACT
Found at i:406070 original size:16 final size:16
Alignment explanation
Indices: 406046--406093 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
406036 AATTTGACCT
* *
406046 GAATAAAAAACAATCC
1 GAATCAAAAACAACCC
**
406062 GAATCAAAATTAACCC
1 GAATCAAAAACAACCC
*
406078 GAATCAAAAGCAACCC
1 GAATCAAAAACAACCC
406094 TAATTGAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.54, C:0.25, G:0.08, T:0.12
Consensus pattern (16 bp):
GAATCAAAAACAACCC
Found at i:414151 original size:16 final size:16
Alignment explanation
Indices: 414130--414160 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
414120 TTACCCGACC
414130 TGTTTTCAACCTGACA
1 TGTTTTCAACCTGACA
*
414146 TGTTTTTAACCTGAC
1 TGTTTTCAACCTGAC
414161 CTGTAAATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.13, T:0.42
Consensus pattern (16 bp):
TGTTTTCAACCTGACA
Found at i:414373 original size:22 final size:24
Alignment explanation
Indices: 414348--414391 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
414338 CCTATTATAT
414348 AAAATTATTT-AATA-AAATTAAC
1 AAAATTATTTAAATATAAATTAAC
414370 AAAATTATTTAAATATAAATTA
1 AAAATTATTTAAATATAAATTA
414392 GATAAAACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (24 bp):
AAAATTATTTAAATATAAATTAAC
Found at i:414443 original size:14 final size:14
Alignment explanation
Indices: 414421--414467 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
414411 TGCAAAGGAA
*
414421 AATTAATATAGTTT
1 AATTTATATAGTTT
414435 AATTTATATA----
1 AATTTATATAGTTT
414445 AA-TTATATAGTTT
1 AATTTATATAGTTT
414458 AATTTATATA
1 AATTTATATA
414468 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:414454 original size:23 final size:24
Alignment explanation
Indices: 414420--414469 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
414410 ATGCAAAGGA
414420 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
414444 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
414467 AAA
1 AAA
414470 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:414973 original size:12 final size:12
Alignment explanation
Indices: 414941--414993 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 12
414931 AATTTTTCTA
414941 TTCCCTCTAAAT
1 TTCCCTCTAAAT
414953 TT-CC-C--AAT
1 TTCCCTCTAAAT
414961 TTCCCTCTAAAT
1 TTCCCTCTAAAT
414973 TT-CC-C--AAT
1 TTCCCTCTAAAT
414981 TTCCCTCTAAAT
1 TTCCCTCTAAAT
414993 T
1 T
414994 CCCAATTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 16
0.67 0.00 0.33
Matches are distributed among these distances:
8 10 0.30
9 4 0.12
10 4 0.12
11 4 0.12
12 11 0.33
ACGTcount: A:0.25, C:0.34, G:0.00, T:0.42
Consensus pattern (12 bp):
TTCCCTCTAAAT
Found at i:414997 original size:19 final size:20
Alignment explanation
Indices: 414941--415005 Score: 123
Period size: 20 Copynumber: 3.3 Consensus size: 20
414931 AATTTTTCTA
414941 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
414961 TTCCCTCTAAATTTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
414981 TTCCCTCTAAA-TTCCCAAT
1 TTCCCTCTAAATTTCCCAAT
415000 TTCCCT
1 TTCCCT
415006 ATATTCTCAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 14 0.31
20 31 0.69
ACGTcount: A:0.23, C:0.37, G:0.00, T:0.40
Consensus pattern (20 bp):
TTCCCTCTAAATTTCCCAAT
Found at i:415045 original size:27 final size:27
Alignment explanation
Indices: 414992--415044 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
414982 TCCCTCTAAA
*
414992 TTCCCAATTTCCCTATATTCTCAAAAT
1 TTCCCAATTTCCCTAAATTCTCAAAAT
* *
415019 TTCCTAATTTCCTCTAAATTCCCAAA
1 TTCCCAATTTCC-CTAAATTCTCAAA
415045 TAAAATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (27 bp):
TTCCCAATTTCCCTAAATTCTCAAAAT
Found at i:415703 original size:17 final size:18
Alignment explanation
Indices: 415681--415723 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
415671 TTAGGAAATT
*
415681 TTGAGAA-CATAGGGAAA
1 TTGAGAATCAGAGGGAAA
*
415698 TTGAGAATTTAGAGGGAAA
1 TTGAGAA-TCAGAGGGAAA
415717 TTGAGAA
1 TTGAGAA
415724 ATTTAGAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
19 15 0.68
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.23
Consensus pattern (18 bp):
TTGAGAATCAGAGGGAAA
Found at i:415713 original size:19 final size:20
Alignment explanation
Indices: 415691--415731 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
415681 TTGAGAACAT
415691 AGGGAAATTGAG-AATTTAG
1 AGGGAAATTGAGAAATTTAG
415710 AGGGAAATTGAGAAATTTAG
1 AGGGAAATTGAGAAATTTAG
415730 AG
1 AG
415732 AAAATAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (20 bp):
AGGGAAATTGAGAAATTTAG
Found at i:415736 original size:19 final size:20
Alignment explanation
Indices: 415695--415746 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
415685 GAACATAGGG
*
415695 AAATTGAG-AATTTAGAGGG
1 AAATTGAGAAATTTAGAGGA
415714 AAATTGAGAAATTTAGA-GA
1 AAATTGAGAAATTTAGAGGA
* *
415733 AAATAGAAAAATTT
1 AAATTGAGAAATTT
415747 GGGAAGTTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (20 bp):
AAATTGAGAAATTTAGAGGA
Found at i:415745 original size:46 final size:46
Alignment explanation
Indices: 415656--415745 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
415646 TTTTATTTGG
* * **
415656 GAATTTAGAGGGAAATTAGGAAATTTTGAGAACATAGGGAAATTGA
1 GAATTTAGAGGGAAATTAGGAAATTTAGAGAAAATAGAAAAATTGA
415702 GAATTTAGAGGGAAATT-GAGAAATTTAGAGAAAATAGAAAAATT
1 GAATTTAGAGGGAAATTAG-GAAATTTAGAGAAAATAGAAAAATT
415746 TGGGAAGTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 1 0.03
46 38 0.97
ACGTcount: A:0.48, C:0.01, G:0.26, T:0.26
Consensus pattern (46 bp):
GAATTTAGAGGGAAATTAGGAAATTTAGAGAAAATAGAAAAATTGA
Found at i:415997 original size:21 final size:19
Alignment explanation
Indices: 415965--416076 Score: 66
Period size: 21 Copynumber: 5.4 Consensus size: 19
415955 TATAGTTTAT
415965 ATAAACCTTAAACTCTAAATC
1 ATAAACC-TAAAC-CTAAATC
415986 ATAAATCCTAAACACTAAA-C
1 ATAAA-CCTAAAC-CTAAATC
* * *
416006 TTTAAATCATAAATACTAAATC
1 -ATAAA-CCTAAA-CCTAAATC
*
416028 CTAAACCCTAAACCATAAAT-
1 ATAAA-CCTAAACC-TAAATC
416048 ACTAAACCTTAAACCATAAATC
1 A-TAAACC-TAAACC-TAAATC
416070 ATAAACC
1 ATAAACC
416077 CTAATATATG
Statistics
Matches: 74, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
20 4 0.05
21 66 0.89
22 4 0.05
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (19 bp):
ATAAACCTAAACCTAAATC
Found at i:415998 original size:28 final size:27
Alignment explanation
Indices: 415966--416074 Score: 130
Period size: 28 Copynumber: 3.9 Consensus size: 27
415956 ATAGTTTATA
*
415966 TAAACCTTAAACTCTAAATCATAAATCC
1 TAAACC-TAAACTCTAAATCATAAATAC
*
415994 TAAACACTAAACTTTAAATCATAAATAC
1 TAAAC-CTAAACTCTAAATCATAAATAC
* *
416022 TAAATCCTAAACCCTAAACCATAAATAC
1 TAAA-CCTAAACTCTAAATCATAAATAC
416050 TAAACCTTAAAC-CATAAATCATAAA
1 TAAACC-TAAACTC-TAAATCATAAA
416075 CCCTAATATA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
27 3 0.04
28 66 0.93
29 2 0.03
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (27 bp):
TAAACCTAAACTCTAAATCATAAATAC
Found at i:416037 original size:7 final size:7
Alignment explanation
Indices: 415966--416080 Score: 50
Period size: 7 Copynumber: 16.4 Consensus size: 7
415956 ATAGTTTATA
*
415966 TAAACCT
1 TAAACCC
*
415973 TAAACTC
1 TAAACCC
* *
415980 TAAATCA
1 TAAACCC
*
415987 TAAATCC
1 TAAACCC
*
415994 TAAACAC
1 TAAACCC
**
416001 TAAACTT
1 TAAACCC
* *
416008 TAAATCA
1 TAAACCC
**
416015 TAAATAC
1 TAAACCC
*
416022 TAAATCC
1 TAAACCC
416029 TAAACCC
1 TAAACCC
*
416036 TAAACCA
1 TAAACCC
**
416043 TAAATAC
1 TAAACCC
*
416050 TAAACCT
1 TAAACCC
*
416057 TAAACCA
1 TAAACCC
* *
416064 TAAATCA
1 TAAACCC
416071 TAAACCC
1 TAAACCC
416078 TAA
1 TAA
416081 TATATGTATA
Statistics
Matches: 80, Mismatches: 28, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 80 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAACCC
Found at i:416093 original size:18 final size:20
Alignment explanation
Indices: 416070--416147 Score: 76
Period size: 18 Copynumber: 4.2 Consensus size: 20
416060 ACCATAAATC
* *
416070 ATAAACCCTA-ATA-TATGT
1 ATAAACCATATATAGTATAT
416088 ATAAACCATATATAGTATAT
1 ATAAACCATATATAGTATAT
*
416108 ATAAACTATATATA-TATAT
1 ATAAACCATATATAGTATAT
* *
416127 ATATA-TATATATA-TATAT
1 ATAAACCATATATAGTATAT
416145 ATA
1 ATA
416148 TATATATATA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
18 25 0.46
19 12 0.22
20 17 0.31
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.40
Consensus pattern (20 bp):
ATAAACCATATATAGTATAT
Found at i:416166 original size:2 final size:2
Alignment explanation
Indices: 416095--416157 Score: 99
Period size: 2 Copynumber: 30.5 Consensus size: 2
416085 TGTATAAACC
*
416095 AT AT AT AGT AT AT AT AA ACT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
416139 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
416158 AACTATATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 54 0.95
3 3 0.05
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:416280 original size:2 final size:2
Alignment explanation
Indices: 416273--416411 Score: 142
Period size: 2 Copynumber: 69.0 Consensus size: 2
416263 TAATGCATAC
* * *
416273 AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AC AT AT AA ACT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * *
416313 AT AT AGT TT AT AT AGT TT AT AC AT AT AT AGT TT AT AT AT AT AT
1 AT AT A-T AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT
416356 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
416398 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
416412 TAATATAAAT
Statistics
Matches: 115, Mismatches: 13, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
1 4 0.03
2 105 0.91
3 6 0.05
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:416417 original size:6 final size:6
Alignment explanation
Indices: 416348--416422 Score: 51
Period size: 6 Copynumber: 12.5 Consensus size: 6
416338 TATAGTTTAT
* * * * * * * *
416348 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
* * *
416396 ATATAT ATATAT ATATTA ATATAA ATA
1 ATATAA ATATAA ATATAA ATATAA ATA
416423 ATATTTTATA
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 66 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATAA
Found at i:416468 original size:15 final size:15
Alignment explanation
Indices: 416448--416479 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
416438 TATACTTTTT
416448 TAAAGTTTATACATA
1 TAAAGTTTATACATA
*
416463 TAAAGTTTATATATA
1 TAAAGTTTATACATA
416478 TA
1 TA
416480 GTTCACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (15 bp):
TAAAGTTTATACATA
Found at i:416542 original size:18 final size:18
Alignment explanation
Indices: 416498--416652 Score: 111
Period size: 18 Copynumber: 8.2 Consensus size: 18
416488 AAACATAATT
*
416498 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
416516 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
416534 TATAAATATAGTTTATAA
1 TATATATATAGTTTATAA
*
416552 TTTTATATACATAGTTTATATA
1 ---TATATATATAGTTTATA-A
* * **
416574 TGTAGTTCACATA-AATATAA
1 TATA--T-ATATAGTTTATAA
416594 TTTATATATATAGTTTATAA
1 --TATATATATAGTTTATAA
416614 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
416632 TATAAATATAGTTTAT-A
1 TATATATATAGTTTATAA
416649 TATA
1 TATA
416653 ATTTTATATT
Statistics
Matches: 111, Mismatches: 12, Indels: 29
0.73 0.08 0.19
Matches are distributed among these distances:
17 7 0.06
18 59 0.53
19 9 0.08
20 7 0.06
21 20 0.18
22 9 0.08
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.48
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:416594 original size:98 final size:98
Alignment explanation
Indices: 416466--416648 Score: 330
Period size: 98 Copynumber: 1.9 Consensus size: 98
416456 ATACATATAA
416466 AGTTTATATATATAGTTCACAAAAACATAATTTATATATATAGCTTATAATAATTATATAGTTTA
1 AGTTTATATATATAGTTCACAAAAACATAATTTATATATATAGCTTATAATAATTATATAGTTTA
416531 TAATATAAATATAGTTTATAATTTTATATACAT
66 TAATATAAATATAGTTTATAATTTTATATACAT
* * * *
416564 AGTTTATATATGTAGTTCACATAAATATAATTTATATATATAGTTTATAATAATTATATAGTTTA
1 AGTTTATATATATAGTTCACAAAAACATAATTTATATATATAGCTTATAATAATTATATAGTTTA
416629 TAATATAAATATAGTTTATA
66 TAATATAAATATAGTTTATA
416649 TATAATTTTA
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 81 1.00
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (98 bp):
AGTTTATATATATAGTTCACAAAAACATAATTTATATATATAGCTTATAATAATTATATAGTTTA
TAATATAAATATAGTTTATAATTTTATATACAT
Found at i:416647 original size:36 final size:38
Alignment explanation
Indices: 416596--416673 Score: 108
Period size: 36 Copynumber: 2.1 Consensus size: 38
416586 AAATATAATT
*
416596 TATATATATAGTTTATA-ATAATTATATAGTT-TATA-A
1 TATAAATATAGTTTATATATAATTATATA-TTATATATA
*
416632 TATAAATATAGTTTATATATAATTTTATATTATATATA
1 TATAAATATAGTTTATATATAATTATATATTATATATA
416670 TATA
1 TATA
416674 TTATATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 18 0.49
37 14 0.38
38 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (38 bp):
TATAAATATAGTTTATATATAATTATATATTATATATA
Found at i:416659 original size:30 final size:30
Alignment explanation
Indices: 416625--416681 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
416615 AATTATATAG
416625 TTTATAATATAAATATAGT-TTATATATAAT
1 TTTATAATATAAATATA-TATTATATATAAT
* *
416655 TTTATATTATATATATATATTATATAT
1 TTTATAATATAAATATATATTATATAT
416682 TTTTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTATAATATAAATATATATTATATATAAT
Found at i:416681 original size:13 final size:13
Alignment explanation
Indices: 416588--416681 Score: 56
Period size: 13 Copynumber: 7.2 Consensus size: 13
416578 GTTCACATAA
416588 ATATA-ATT-TAT
1 ATATATATTATAT
416599 ATATATAGTT-TAT
1 ATATATA-TTATAT
416612 A-ATA-ATTATAT
1 ATATATATTATAT
* * *
416623 AGTTTATAATATAA
1 A-TATATATTATAT
416637 ATATAGT-TTATAT
1 ATATA-TATTATAT
416650 ATAATTTTATATTATAT
1 AT-A---TATATTATAT
416667 ATATATATTATAT
1 ATATATATTATAT
416680 AT
1 AT
416682 TTTTTAAATT
Statistics
Matches: 65, Mismatches: 6, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
10 2 0.03
11 10 0.15
12 4 0.06
13 29 0.45
14 8 0.12
16 2 0.03
17 10 0.15
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (13 bp):
ATATATATTATAT
Found at i:417030 original size:12 final size:12
Alignment explanation
Indices: 417013--417039 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
417003 TTTCTTCAAT
417013 TTTGTCATTAAA
1 TTTGTCATTAAA
417025 TTTGTCATTAAA
1 TTTGTCATTAAA
417037 TTT
1 TTT
417040 ATATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (12 bp):
TTTGTCATTAAA
Found at i:417477 original size:64 final size:64
Alignment explanation
Indices: 417349--417488 Score: 194
Period size: 64 Copynumber: 2.2 Consensus size: 64
417339 GAACTGAAAA
* *
417349 TGACCCGATCTGAACCTGATCTGGATCTGGTGTCAAATCAACCTGAAAATAACCTGAACTGATT
1 TGACCCGACCTGAACCTGATCTGGATCTGGTGTCAAATCAACCTGAAAATAACCTGAACCGATT
* **
417413 TGACCTGACCTGAACCTGATCTGGATCTGGTGTCAAATCAACCTG-AGTTAACCT-ATACACGAT
1 TGACCCGACCTGAACCTGATCTGGATCTGGTGTCAAATCAACCTGAAAATAACCTGA-AC-CGAT
417476 T
64 T
*
417477 TTACCCGACCTG
1 TGACCCGACCTG
417489 CCAAGATCCG
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
62 1 0.01
63 9 0.13
64 57 0.85
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (64 bp):
TGACCCGACCTGAACCTGATCTGGATCTGGTGTCAAATCAACCTGAAAATAACCTGAACCGATT
Found at i:419532 original size:7 final size:7
Alignment explanation
Indices: 419520--419559 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
419510 GTTAGATTAT
419520 ACCCTAA
1 ACCCTAA
419527 ACCCTAA
1 ACCCTAA
* *
419534 ATCATAA
1 ACCCTAA
*
419541 TCCCTAA
1 ACCCTAA
419548 ACCCTAA
1 ACCCTAA
419555 ACCCT
1 ACCCT
419560 TAATCTAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (7 bp):
ACCCTAA
Found at i:419593 original size:110 final size:110
Alignment explanation
Indices: 419471--419690 Score: 316
Period size: 110 Copynumber: 2.0 Consensus size: 110
419461 CATTATATAT
* *
419471 TACTAAAAGAAAAATAAAAACTCATTTAATTAAGCACATGTTAGATTATACCCTAAACC-CTAAA
1 TACTAAAAGAAAAATAAAAACCCATTTAATTAAGCACATGTTAGATTAAACCCTAAACCTC-AAA
* * * * * *
419535 TCATAATCCCTAAACCCTAAACCCTTAATCTAATTATATGATAGGG
65 CCACAAACCCCAAACCATAAACCCTTAATCCAATTATATGATAGGG
* *
419581 TACTAAAAGAAAAATAAAATCCCATTTAATTAAGCACATGTTATATTAAACCCTAAACCTCAAAC
1 TACTAAAAGAAAAATAAAAACCCATTTAATTAAGCACATGTTAGATTAAACCCTAAACCTCAAAC
* *
419646 CCCAAACCCCAAACCATAAACCCTTAATCCGATTATATGATAGGG
66 CACAAACCCCAAACCATAAACCCTTAATCCAATTATATGATAGGG
419691 GTTAAGTTAT
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
110 96 0.99
111 1 0.01
ACGTcount: A:0.45, C:0.22, G:0.07, T:0.26
Consensus pattern (110 bp):
TACTAAAAGAAAAATAAAAACCCATTTAATTAAGCACATGTTAGATTAAACCCTAAACCTCAAAC
CACAAACCCCAAACCATAAACCCTTAATCCAATTATATGATAGGG
Found at i:419647 original size:14 final size:14
Alignment explanation
Indices: 419628--419668 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
419618 ATGTTATATT
*
419628 AAACCCTAAACCTC
1 AAACCCTAAACCCC
*
419642 AAACCCCAAACCCC
1 AAACCCTAAACCCC
*
419656 AAACCATAAACCC
1 AAACCCTAAACCC
419669 TTAATCCGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.07
Consensus pattern (14 bp):
AAACCCTAAACCCC
Found at i:419654 original size:21 final size:21
Alignment explanation
Indices: 419628--419668 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
419618 ATGTTATATT
*
419628 AAACCCTAAACC-TCAAACCCC
1 AAACCCCAAACCAT-AAACCCC
419649 AAACCCCAAACCATAAACCC
1 AAACCCCAAACCATAAACCC
419669 TTAATCCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.07
Consensus pattern (21 bp):
AAACCCCAAACCATAAACCCC
Found at i:421145 original size:23 final size:23
Alignment explanation
Indices: 421087--421145 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
421077 TAGTACCTTG
**
421087 AGCTTGAATCGAATTCAAAATCA
1 AGCTTGAATCGAGCTCAAAATCA
*
421110 AGCTTGAATCGAGCTCAAAATTA
1 AGCTTGAATCGAGCTCAAAATCA
*
421133 AGCTTCAATCGAG
1 AGCTTGAATCGAG
421146 TTCGAGTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (23 bp):
AGCTTGAATCGAGCTCAAAATCA
Found at i:421163 original size:24 final size:24
Alignment explanation
Indices: 421133--421261 Score: 173
Period size: 24 Copynumber: 5.7 Consensus size: 24
421123 CTCAAAATTA
*
421133 AGCTTCAATCGAGTTCGAGTCTCG
1 AGCTTCAATCGAGCTCGAGTCTCG
421157 AGCTTC-A---A--TC-AGTCTCG
1 AGCTTCAATCGAGCTCGAGTCTCG
421174 AGCTTCAATCGAGCTCGAGTCTCG
1 AGCTTCAATCGAGCTCGAGTCTCG
421198 AGCTTCAATCGAGCTCGAGTCTCG
1 AGCTTCAATCGAGCTCGAGTCTCG
*
421222 AGCTTCAATCAAGCTCGAGTCTCG
1 AGCTTCAATCGAGCTCGAGTCTCG
* *
421246 AGTTTCAATTGAGCTC
1 AGCTTCAATCGAGCTC
421262 TTGAGTTTTT
Statistics
Matches: 94, Mismatches: 4, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
17 13 0.14
18 3 0.03
20 1 0.01
21 1 0.01
23 3 0.03
24 73 0.78
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.28
Consensus pattern (24 bp):
AGCTTCAATCGAGCTCGAGTCTCG
Found at i:421216 original size:17 final size:18
Alignment explanation
Indices: 421147--421192 Score: 78
Period size: 17 Copynumber: 2.7 Consensus size: 18
421137 TCAATCGAGT
421147 TCGAGTCTCGAGCTTCAA
1 TCGAGTCTCGAGCTTCAA
421165 TC-AGTCTCGAGCTTCAA
1 TCGAGTCTCGAGCTTCAA
421182 TCGAG-CTCGAG
1 TCGAGTCTCGAG
421193 TCTCGAGCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.22, C:0.28, G:0.24, T:0.26
Consensus pattern (18 bp):
TCGAGTCTCGAGCTTCAA
Found at i:422456 original size:16 final size:16
Alignment explanation
Indices: 422430--422468 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
422420 ATCATTCATT
*
422430 TTTTA-TTTTTTATTA
1 TTTTATTTTTTTTTTA
422445 -TTTATTTTTTTTTTA
1 TTTTATTTTTTTTTTA
422460 TTTTATTTT
1 TTTTATTTT
422469 AAGATATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 8 0.38
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTATTTTTTTTTTA
Found at i:424119 original size:8 final size:8
Alignment explanation
Indices: 424105--424191 Score: 63
Period size: 8 Copynumber: 10.6 Consensus size: 8
424095 ATAAATTTAG
424105 TAAAAAAA
1 TAAAAAAA
*
424113 GAAAAAAA
1 TAAAAAAA
424121 -AATAAAAA
1 TAA-AAAAA
*
424129 TGGAAAAAA
1 T-AAAAAAA
424138 TAAAATAAA
1 TAAAA-AAA
424147 TAAAAAAA
1 TAAAAAAA
424155 TAAAATAAA
1 TAAAA-AAA
* *
424164 -AAAATAG
1 TAAAAAAA
424171 TAAATAAAA
1 TAAA-AAAA
*
424180 -AACAAAA
1 TAAAAAAA
424187 TAAAA
1 TAAAA
424192 TGAAAAGAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 16
0.71 0.10 0.18
Matches are distributed among these distances:
7 7 0.11
8 35 0.56
9 19 0.31
10 1 0.02
ACGTcount: A:0.80, C:0.01, G:0.05, T:0.14
Consensus pattern (8 bp):
TAAAAAAA
Found at i:424152 original size:17 final size:16
Alignment explanation
Indices: 424114--424207 Score: 93
Period size: 15 Copynumber: 5.8 Consensus size: 16
424104 GTAAAAAAAG
424114 AAAAAAAAATAAAA-A
1 AAAAAAAAATAAAATA
***
424129 TGGAAAAAATAAAATA
1 AAAAAAAAATAAAATA
424145 AATAAAAAAATAAAATA
1 AA-AAAAAAATAAAATA
* *
424162 AAAAAATAGT-AAATA
1 AAAAAAAAATAAAATA
424177 AAAAACAAAATAAAATGA
1 AAAAA-AAAATAAAAT-A
424195 AAAGAAAAAATAA
1 AAA-AAAAAATAA
424208 GTAATAACTA
Statistics
Matches: 63, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
15 21 0.33
16 10 0.16
17 19 0.30
18 11 0.17
19 2 0.03
ACGTcount: A:0.80, C:0.01, G:0.05, T:0.14
Consensus pattern (16 bp):
AAAAAAAAATAAAATA
Found at i:424156 original size:12 final size:13
Alignment explanation
Indices: 424142--424191 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
424132 AAAAAATAAA
424142 ATAAATAAAAAA-
1 ATAAATAAAAAAC
*
424154 ATAAAATAAAAAAAT
1 AT-AAAT-AAAAAAC
424169 AGTAAATAAAAAAC
1 A-TAAATAAAAAAC
424183 A-AAATAAAA
1 ATAAATAAAA
424192 TGAAAAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 10 0.30
13 4 0.12
14 13 0.39
15 5 0.15
16 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (13 bp):
ATAAATAAAAAAC
Found at i:424157 original size:32 final size:29
Alignment explanation
Indices: 424114--424207 Score: 109
Period size: 32 Copynumber: 3.0 Consensus size: 29
424104 GTAAAAAAAG
424114 AAAAAAAAATAAAAATGGAAAAAATAAAATA
1 AAAAAAAAAT-AAAAT-GAAAAAATAAAATA
*
424145 AATAAAAAAATAAAATAAAAAAATAGTAAATA
1 AA-AAAAAAATAAAATGAAAAAATA--AAATA
424177 AAAAACAAAATAAAATGAAAAGAA-AAAATA
1 AAAAA-AAAATAAAATGAAAA-AATAAAATA
424207 A
1 A
424208 GTAATAACTA
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
30 14 0.25
31 10 0.18
32 30 0.54
33 2 0.04
ACGTcount: A:0.80, C:0.01, G:0.05, T:0.14
Consensus pattern (29 bp):
AAAAAAAAATAAAATGAAAAAATAAAATA
Found at i:424162 original size:13 final size:13
Alignment explanation
Indices: 424139--424191 Score: 65
Period size: 13 Copynumber: 4.1 Consensus size: 13
424129 TGGAAAAAAT
424139 AAAAT-AAATAAA
1 AAAATAAAATAAA
424151 AAAATAAAATAAA
1 AAAATAAAATAAA
424164 AAAATAGTAAAT-AA
1 AAAATA--AAATAAA
*
424178 AAAACAAAATAAA
1 AAAATAAAATAAA
424191 A
1 A
424192 TGAAAAGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
12 9 0.25
13 16 0.44
14 7 0.19
15 4 0.11
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:424166 original size:45 final size:45
Alignment explanation
Indices: 424106--424207 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 45
424096 TAAATTTAGT
* *
424106 AAAAAAAGAA-AAAAAAATA-AAAATGGAAAAAATAAAAT-AAAT-A
1 AAAAAAAAAATAAAAAAATAGAAAAT--AAAAAACAAAATAAAATGA
*
424149 AAAAAATAAAATAAAAAAATAGTAAATAAAAAACAAAATAAAATGA
1 AAAAAA-AAAATAAAAAAATAGAAAATAAAAAACAAAATAAAATGA
*
424195 AAAGAAAAAATAA
1 AAAAAAAAAATAA
424208 GTAATAACTA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
43 6 0.12
44 14 0.28
45 20 0.40
46 10 0.20
ACGTcount: A:0.80, C:0.01, G:0.06, T:0.13
Consensus pattern (45 bp):
AAAAAAAAAATAAAAAAATAGAAAATAAAAAACAAAATAAAATGA
Found at i:424991 original size:28 final size:27
Alignment explanation
Indices: 424927--424996 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 27
424917 CTTCCTTGTA
*
424927 GTTGTGTGGCTT-TTGG-TCGTTGTTTT
1 GTTGTGTGG-TTGTTGGTTCGATGTTTT
*
424953 -TT-TGTGTTTGTTGGTTCGATGTTCTT
1 GTTGTGTGGTTGTTGGTTCGATGTT-TT
424979 GTTGTGTGGTTG-TGGTTC
1 GTTGTGTGGTTGTTGGTTC
424997 CCGTTTTCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
23 2 0.06
24 8 0.22
25 9 0.25
26 2 0.06
27 8 0.22
28 7 0.19
ACGTcount: A:0.01, C:0.07, G:0.34, T:0.57
Consensus pattern (27 bp):
GTTGTGTGGTTGTTGGTTCGATGTTTT
Found at i:425477 original size:6 final size:6
Alignment explanation
Indices: 425466--425490 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
425456 AAATATTGAT
425466 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
425491 TATATATATA
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
Done.