Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008082.1 Hibiscus syriacus cultivar Beakdansim tig00110584_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: 6025995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 28
Found at i:431887 original size:14 final size:14
Alignment explanation
Indices: 431870--431897 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
431860 TCACATAATC
431870 GGATTTAGGGTTTA
1 GGATTTAGGGTTTA
431884 GGATTTAGGGTTTA
1 GGATTTAGGGTTTA
431898 AGGTTCATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (14 bp):
GGATTTAGGGTTTA
Found at i:432081 original size:25 final size:25
Alignment explanation
Indices: 432055--432103 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
432045 TAGTTATTTA
432055 AAATA-TTATCATTAGA-AATATATT
1 AAATATTTATCATTAGATAA-ATATT
*
432079 AAATATTTTTCATTAGATAAATATT
1 AAATATTTATCATTAGATAAATATT
432104 TTTTTTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 15 0.68
26 2 0.09
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (25 bp):
AAATATTTATCATTAGATAAATATT
Found at i:432904 original size:36 final size:36
Alignment explanation
Indices: 432789--433264 Score: 367
Period size: 36 Copynumber: 12.7 Consensus size: 36
432779 ATATATATAC
* * *
432789 ATATATATGTTATATAG-TTTAAAAACATTTTTAAAAAAA
1 ATATATATATTATATAGTTTTTAAAACA-TTTT---GAAA
* *
432828 CATATATATAATATATAGTTTTAAAAACATGTTTGAAAA
1 -ATATATATATTATATAGTTTTTAAAACAT-TTTG-AAA
432867 ATATATATATTATATAGTTTTTAAAACATTTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAA
* * ** *
432903 ATAAATATAATATATAACTTTTAAAAC--GTTGAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAA
432937 ATATATATATATATATTTA-TATATTATACAGTTTTTAAAACATTTTGAAA
1 ATATATATAT-TATA--TAGT-T-TT-TA-A--------AACATTTTGAAA
* * *
432987 ATAAATATAATATATAGTTTTTAAAATATTTTTG-AA
1 ATATATATATTATATAGTTTTTAAAACA-TTTTGAAA
* *
433023 A-ATATATATTATATAGTTTCTAAAACATTTTAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAA
* * * * *
433058 ATAAATATAATATATAATTTTTAAAATATTTTTAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAA
*
433094 A-ATATATATTATATAGTTTTTAAAACATTTTAAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAA
* * * *
433129 ATAAATATATTATATAATTTTTAAAATATTTTTAAA
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAA
*
433165 AGTATATATATTATATAGTTTTTAAAATATTTT-AGAA
1 A-TATATATATTATATAGTTTTTAAAACATTTTGA-AA
* * * * *
433202 ATAAATATAATATATAGTTTTTAAAATATTTTTAAG
1 ATATATATATTATATAGTTTTTAAAACATTTTGAAA
433238 A-ATATATATTATATAGGTTTTTGAAAA
1 ATATATATATTATATA-GTTTTT-AAAA
433265 TATTATTATT
Statistics
Matches: 362, Mismatches: 44, Indels: 63
0.77 0.09 0.13
Matches are distributed among these distances:
34 18 0.05
35 71 0.20
36 130 0.36
37 49 0.14
38 29 0.08
39 5 0.01
40 17 0.05
41 13 0.04
44 1 0.00
45 2 0.01
46 2 0.01
47 3 0.01
48 4 0.01
49 4 0.01
50 14 0.04
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (36 bp):
ATATATATATTATATAGTTTTTAAAACATTTTGAAA
Found at i:433024 original size:12 final size:11
Alignment explanation
Indices: 433004--433242 Score: 74
Period size: 11 Copynumber: 20.1 Consensus size: 11
432994 TAATATATAG
433004 TTTTTAAAATA
1 TTTTTAAAATA
433015 TTTTTGAAAATA
1 TTTTT-AAAATA
* *
433027 TATATT-ATATA
1 T-TTTTAAAATA
* *
433038 GTTTCTAAAACA
1 -TTTTTAAAATA
*
433050 TTTTAAAAATA
1 TTTTTAAAATA
** *
433061 AATATAATATATAA
1 TTTTTAA-A-AT-A
433075 TTTTTAAAATA
1 TTTTTAAAATA
433086 TTTTTAAAAATA
1 TTTTT-AAAATA
* *
433098 TATATT-ATATA
1 T-TTTTAAAATA
*
433109 GTTTTTAAAACA
1 -TTTTTAAAATA
*
433121 TTTTAAAAATAAA
1 TTTTTAAAAT--A
* *
433134 TATATT-ATATAA
1 T-TTTTAAAAT-A
433146 TTTTTAAAATA
1 TTTTTAAAATA
433157 TTTTTAAAAGTA
1 TTTTTAAAA-TA
*
433169 TATATATT-ATATA
1 T-T-T-TTAAAATA
433182 GTTTTTAAAATA
1 -TTTTTAAAATA
433194 -TTTTAGAAATA
1 TTTTTA-AAATA
** *
433205 AATATAATATATA
1 TTTTTAA-A-ATA
433218 GTTTTTAAAATA
1 -TTTTTAAAATA
433230 TTTTTAAGAATA
1 TTTTTAA-AATA
433242 T
1 T
433243 ATATTATATA
Statistics
Matches: 166, Mismatches: 35, Indels: 53
0.65 0.14 0.21
Matches are distributed among these distances:
10 5 0.03
11 71 0.43
12 51 0.31
13 22 0.13
14 15 0.09
15 2 0.01
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (11 bp):
TTTTTAAAATA
Found at i:433187 original size:73 final size:71
Alignment explanation
Indices: 432954--433264 Score: 496
Period size: 71 Copynumber: 4.3 Consensus size: 71
432944 TATATATATT
* * *
432954 TATATATTATACAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAATATTTT
1 TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAATATTTT
*
433019 TGAAAA
66 TAAAAA
*
433025 TATATATTATATAGTTTCTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAATATTTT
1 TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAATATTTT
433090 TAAAAA
66 TAAAAA
*
433096 TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATATTATATAATTTTTAAAATATTTT
1 TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAATATTTT
433161 TAAAAGTA
66 TAAAA--A
* * *
433169 TATATATTATATAGTTTTTAAAATATTTTAGAAATAAATATAATATATAGTTTTTAAAATATTTT
1 TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAATATTTT
*
433234 TAAGAA
66 TAAAAA
433240 TATATATTATATAGGTTTTTGAAAA
1 TATATATTATATA-GTTTTT-AAAA
433265 TATTATTATT
Statistics
Matches: 224, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
71 148 0.66
72 6 0.03
73 70 0.31
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (71 bp):
TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAATATTTT
TAAAAA
Found at i:433273 original size:3 final size:3
Alignment explanation
Indices: 433265--433292 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
433255 TTTTTGAAAA
433265 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
433293 TATTTCCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:433285 original size:144 final size:142
Alignment explanation
Indices: 432954--433264 Score: 496
Period size: 144 Copynumber: 2.2 Consensus size: 142
432944 TATATATATT
* * * *
432954 TATATATTATACAGTTTTTAAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAATATTTT
1 TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATATTATATAATTTTTAAAATATTTT
*
433019 TGAAAATATATATTATATAGTTTCTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAA
66 TAAAAATATATATTATATAGTTTCTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAA
433084 TATTTTTAAAAA
131 TATTTTTAAAAA
433096 TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATATTATATAATTTTTAAAATATTTT
1 TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATATTATATAATTTTTAAAATATTTT
* * * *
433161 TAAAAGTATATATATTATATAGTTTTTAAAATATTTTAGAAATAAATATAATATATAGTTTTTAA
66 TAAAA--ATATATATTATATAGTTTCTAAAACATTTTAAAAATAAATATAATATATAATTTTTAA
*
433226 AATATTTTTAAGAA
129 AATATTTTTAAAAA
433240 TATATATTATATAGGTTTTTGAAAA
1 TATATATTATATA-GTTTTT-AAAA
433265 TATTATTATT
Statistics
Matches: 155, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
142 65 0.42
144 80 0.52
145 6 0.04
146 4 0.03
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (142 bp):
TATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATATTATATAATTTTTAAAATATTTT
TAAAAATATATATTATATAGTTTCTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAAA
TATTTTTAAAAA
Found at i:433322 original size:14 final size:14
Alignment explanation
Indices: 433299--433341 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
433289 TATTTATTTC
433299 CTTTTATTTTATTAA
1 CTTTT-TTTTATTAA
433314 CTTTTTTTTATCTAA
1 CTTTTTTTTAT-TAA
* *
433329 CATTTGTTTATTA
1 CTTTTTTTTATTA
433342 TTATATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (14 bp):
CTTTTTTTTATTAA
Found at i:438841 original size:250 final size:244
Alignment explanation
Indices: 438393--439753 Score: 1236
Period size: 250 Copynumber: 5.5 Consensus size: 244
438383 TTTTTTTAAG
* * * * * *
438393 ACATCATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGA
1 ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATC--T-ACCAAAAGACCTTCGAGTTCGA
* * *
438458 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
63 CTACACTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAA
* * * * * *
438523 GACCCCCGAGTTCGATTACACTCAGCTCCGAGGGCATATCATTTGTAGTATAACTCAAGGCTAGA
128 GACCCTCGAGTTCGACTACACTCAGCTCC-AAGGCACATCATTTGCAGCATAACTCAAGGCTAGA
* * * * * *
438588 AGGGTTATCCGTCAACTAGAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGC
192 AGGGCTATCCGTC-ACCA-AAGACCCTCGAGTTCGACTACACTCAGCTCGAAGGC
* * * * * *
438643 ACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAAGACCCTCGAGTTCGATTA
1 ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTACCAAAAGACCTTCGAGTTCGACTA
* * * * * * *
438708 CACTCAACTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAA
66 CACTCAGC-TCGAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---CCAA
* * * * * * * *
438773 AGACCTTTGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGTAGCATAAATTAA-GTTGAG
127 AGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCT-AG
* * *
438837 AAGGGCTAT-C-T-GCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
191 AAGGGCTATCCGTCACCAAAGACCCTCGAGTTCGACTACACTCAGC-TCGAAGGC
* * *
438889 ACATCATTTGCAGCATAGCTTAAATCAAGAAGGGTTATCTGCCAACCAAAA-ACCTTTGAGTTCG
1 ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCT----ACCAAAAGACCTTCGAGTTCG
* * * *
438953 ACTACACTCAGCTTCGAGGGCACACCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCA
62 ACTACACTCAGC-TCGAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---
* * * * *
439018 ACCAAAAACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGC-CTAAG
123 -CCAAAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTC-AAG
* * * * * * *
439082 TCGAGAAGGGCTAT-C-T-ACCAAAGACCCCCGAGTTCGATTACATTCAGTTTCGAGGGC
186 GCTAGAAGGGCTATCCGTCACCAAAGACCCTCGAGTTCGACTACACTCAG-CTCGAAGGC
*
439139 ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTACCAACCAAAGACCTTTGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTACC-A--AAAGACCTTCGAGTTCGA
* * *
439204 CTACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
63 CTACACTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC-AA
* * * * * *
439269 AGACCCTCGAGTTCGATTACACTCAACTTCAAGGGCATATCATTTACAACATAACTCAAGGCTAG
127 AGACCCTCGAGTTCGACTACACTCAGCTCCAA-GGCACATCATTTGCAGCATAACTCAAGGCTAG
* * * * * *
439334 AAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
191 AAGGGCTATCCGTCACCAAAGACCCTCGAGTTCGACTACACTCAGCTCGAAGGC
* * * * * *
439388 ATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTACCAACAAAAGGCCTTTGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTA-C--CAAAAGACCTTCGAGTTCGA
* * * * *
439453 CTACGCTCAGCTC-AACGGTACATCATTTGCAACATAGCTTAAGTCGAGAAAGGCTATCTGCCAA
63 CTACACTCAGCTCGAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA
* * * * * * *
439517 AGACCCCCGAGTTCGA-TCACACTCAGCTTCGAGGGCATATCATTTACAGTATAGCTCAAGGCTA
127 AGACCCTCGAGTTCGACT-ACACTCAGC-TCCAAGGCACATCATTTGCAGCATAACTCAAGGCTA
* * ** * * * * *
439581 AAAGGGTTATATGTCACCAAAGACCTTCGAGTTCAACTACGCTAAGCTCTAAGGC
190 GAAGGGCTATCCGTCACCAAAGACCCTCGAGTTCGACTACACTCAGCTCGAAGGC
* * * * *
439636 ATATCATTTGCAGCACAACTTAAGTCTAA-AAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCG
1 ACATCATTTGCAGCATAACTTAAGTC-AAGAAGGGTTATCT---ACCAAAAGACCTTCGAGTTCG
* * *
439700 ACTACACTCAGCTC-AACGGCACATCATTTGTAGCATAGCTTAAGTTGAGGAAGG
62 ACTACACTCAGCTCGAA-GGCACATCATTTGCAGCATAACTTAAGTCGA-GAAGG
439754 TTATATGCTA
Statistics
Matches: 944, Mismatches: 132, Indels: 71
0.82 0.12 0.06
Matches are distributed among these distances:
245 26 0.03
246 74 0.08
247 62 0.07
248 246 0.26
249 238 0.25
250 267 0.28
251 30 0.03
252 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (244 bp):
ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTACCAAAAGACCTTCGAGTTCGACTA
CACTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
CCTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGG
CTATCCGTCACCAAAGACCCTCGAGTTCGACTACACTCAGCTCGAAGGC
Found at i:438938 original size:165 final size:163
Alignment explanation
Indices: 438393--439797 Score: 1237
Period size: 165 Copynumber: 8.5 Consensus size: 163
438383 TTTTTTTAAG
* * * * * ** *
438393 ACATCATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGA
1 ACATCATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTGCAACC-AAAGACCTTCGAGTTCGA
*
438458 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
65 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAA
* *
438523 GACCCCCGAGTTCGATTACACTCAGCTCCGAGGGC
130 GACCCTCGAGTTCGACTACACTCAGCT-CGAGGGC
* * * * * * * * *
438558 ATATCATTTGTAGTATAACTCAAGGCTAGAAGGGTTATCCGTCAACTAGAAGACCTTTGAGTTCG
1 ACATCATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTG-CAACCA-AAGACCTTCGAGTTCG
* * * *
438623 ACTACGCTCAGCTCTAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAA
64 ACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC-A
* *
438688 AAGACCCTCGAGTTCGATTACACTCAACTTCGAGGGC
128 AAGACCCTCGAGTTCGACTACACTCAGC-TCGAGGGC
* * * * * * *
438725 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCAAC
1 ACATCATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGAC
* * *
438790 TACGCTCAGCTCCAAGGCACATCATTTGTAGCATAAATTAAGTTGAGAAGGGCTATCTGCCAAAG
66 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAG
*
438855 ACCCTCGAGTTCGATTACACTCAGCTTCGAGGGC
131 ACCCTCGAGTTCGACTACACTCAGC-TCGAGGGC
* * * *
438889 ACATCATTTGCAGCATAGCTTAAATCAAGAAGGGTTATCTGCCAACCAAAAACCTTTGAGTTCGA
1 ACATCATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGA
* * * * * *
438954 CTACACTCAGCTTCGAGGGCACACCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAA
65 CTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG----
* * * * * *
439019 CCAAAAACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
125 CCAAAGACCCTCGAGTTCGACTACACTCAGCTCGAGGGC
* * * ** *
439058 ACATCATTTGCAGCATAGCCTAAGTCGAGAAGGGCTATCT---ACCAAAGACCCCCGAGTTCGAT
1 ACATCATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGAC
** * * * * * *
439120 TACATTCAGTTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTACCAAC
66 TACGCTCAG-CTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCT----GC
* * * * *
439185 CAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGC
126 CAAAGACCCTCGAGTTCGACTACACTCAGCTCGAGGGC
* * * * *
439223 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC--CAAAAGACCCTCGAGTTCGAT
1 ACATCATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGAC
* * * * * * * * * *
439286 TACACTCAACTTCAAGGGCATATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACC
66 TACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG---CC
* * * * *
439351 AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGC
127 AAAGACCCTCGAGTTCGACTACACTCAGCTCGAGGGC
* * * * * * * *
439388 ATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTACCAACAAAAGGCCTTTGAGTTCGA
1 ACATCATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCT-GCAACCAAAGACCTTCGAGTTCGA
* * * *
439453 CTACGCTCAGCT-CAACGGTACATCATTTGCAACATAGCTTAAGTCGAGAAAGGCTATCTGCCAA
65 CTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA
*
439517 AGACCCCCGAGTTCGA-TCACACTCAGCTTCGAGGGC
129 AGACCCTCGAGTTCGACT-ACACTCAGC-TCGAGGGC
* * * * * * * *
439553 ATATCATTTACAGTATAGCTCAAGGCTAAAAGGGTTATATGTC-ACCAAAGACCTTCGAGTTCAA
1 ACATCATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGA
* * * * * * * *
439617 CTACGCTAAGCTCTAAGGCATATCATTTGCAGCACAACTTAAGTCTAAAAGGGTTGTCTGCCAAC
65 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTG-C--C
* * * *
439682 AAAAGACCTTTGAGTTCGACTACACTCAGCTCAACGGC
127 -AAAGACCCTCGAGTTCGACTACACTCAGCTCGAGGGC
* * ** * *
439720 ACATCATTTGTAGCATAGCTTAAGT-TGAGGAA-GGTTATATGCTAACTGAAGACCTCCGGGTTC
1 ACATCATTTGCAGCATAGCTTAAGTCT-A-GAAGGGTTATCTGC-AACCAAAGACCTTCGAGTTC
* *
439783 GATTACGTTCAGCTC
63 GACTACGCTCAGCTC
439798 AGAGGCAAAC
Statistics
Matches: 1037, Mismatches: 166, Indels: 71
0.81 0.13 0.06
Matches are distributed among these distances:
163 1 0.00
164 159 0.15
165 398 0.38
166 187 0.18
167 144 0.14
168 79 0.08
169 43 0.04
170 26 0.03
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (163 bp):
ACATCATTTGCAGCATAGCTTAAGTCTAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGAC
TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAG
ACCCTCGAGTTCGACTACACTCAGCTCGAGGGC
Found at i:439004 original size:331 final size:329
Alignment explanation
Indices: 438393--439728 Score: 1386
Period size: 331 Copynumber: 4.0 Consensus size: 329
438383 TTTTTTTAAG
* * *
438393 ACATCATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGA
1 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACC-AAAGACCTTCGAGTTCGA
*
438458 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAA
65 CTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAA
* * * * * *
438523 GACCCCCGAGTTCGATTACACTCAGCTCCGAGGGCATATCATTTGTAGTATAACTCAAGGCTAGA
130 GACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTCAAGGCAAGA
* * * * *
438588 AGGGTTATCCGTCAACTAGAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTA
195 AGGGTTATCTG-CCACCA-AAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACATCATTTA
* * * * * * *
438653 CAGCATAGCTTAAGTCGAGAAGGGCTATCT-ACCAAAAGACCCTCGAGTTCGATTACACTCAACT
258 CAGCATAACTTAAGTCGAGAAGGGTTATCTCACCAAAAGACCTTTGAGTTCGACTACGCTCAGC-
* *
438717 TCGAGGGC
322 TCCAAGGC
* *
438725 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCAAC
1 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGAC
* * *
438790 TACGCTCAGCTCCAAGGCACATCATTTGTAGCATAAATTAAGTTGAGAAGGGCTATCTGCCAAAG
66 TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAG
* * **
438855 ACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTTAAATCAAGAA
131 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTCAAGGCAAGAA
* * * * * *
438920 GGGTTATCTGCCAACCAAAAACCTTTGAGTTCGACTACACTCAGCTTCGAGGGCACACCATTTGC
196 GGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTACACTCAGC-TCTAAGGCACATCATTTAC
*
438985 AGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAA-ACCTTTGAGTTCGACTACGCTCAG
259 AGCATAACTTAAGTCGAGAAGGGTTATCT--C-ACCAAAAGACCTTTGAGTTCGACTACGCTCAG
439049 CTCCAAGGC
321 CTCCAAGGC
* * * * * **
439058 ACATCATTTGCAGCATAGC-CTAAGTCGAGAAGGGCTATC--T-ACCAAAGACCCCCGAGTTCGA
1 ACATCATTTACAGCATAACTC-AAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGA
* ** * * * * * *
439119 TTACATTCAGTTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTACCAA
65 CTACGCTCAG-CTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCT----G
*** * * * * * *
439184 CCAAAGACCTTTGAGTTCGACTACGCTCAGC-TCTAAGGCACATCATTTGCAGCATAGCTTAAGT
125 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTCAAGG
* * * * * *
439248 CGAGAAGGGCTATCTGCCA--AAAGACCCTCGAGTTCGATTACACTCAACT-TCAAGGGCATATC
190 CAAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCT-AA-GGCACATC
* * * *
439310 ATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTTGAGTTCGACTACG
253 ATTTACAGCATAACTTAAGTCGAGAAGGGTTATC--TCACCAAAAGACCTTTGAGTTCGACTACG
439374 CTCAGCTCCAAGGC
316 CTCAGCTCCAAGGC
* * * * * * ** * * *
439388 ATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTACCAACAAAAGGCCTTTGAGTTCGA
1 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCT-GTAACCAAAGACCTTCGAGTTCGA
* * * *
439453 CTACGCTCAGCT-CAACGGTACATCATTTGCAACATAGCTTAAGTCGAGAAAGGCTATCTGCCAA
65 CTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAA
* * * *
439517 AGACCCCCGAGTTCGATCACACTCAGCTTCGAGGGCATATCATTTACAGTATAGCTCAAGGCTAA
129 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTCAAGGC-AA
* * * * * * *
439582 -AAGGGTTATATGTCACCAAAGACCTTCGAGTTCAACTACGCTAAGCTCTAAGGCATATCATTTG
193 GAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACATCATTTA
* * * * * *
439646 CAGCACAACTTAAGTCTAAAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACACTCAG
258 CAGCATAACTTAAGTCGAGAAGGGTTATCT--CACCAAAAGACCTTTGAGTTCGACTACGCTCAG
439711 CT-CAACGGC
321 CTCCAA-GGC
439720 ACATCATTT
1 ACATCATTT
439729 GTAGCATAGC
Statistics
Matches: 830, Mismatches: 142, Indels: 64
0.80 0.14 0.06
Matches are distributed among these distances:
329 29 0.03
330 159 0.19
331 328 0.40
332 112 0.13
333 79 0.10
334 89 0.11
335 34 0.04
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (329 bp):
ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTCGAGTTCGAC
TACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAG
ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTCAAGGCAAGAA
GGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACACTCAGCTCTAAGGCACATCATTTACAG
CATAACTTAAGTCGAGAAGGGTTATCTCACCAAAAGACCTTTGAGTTCGACTACGCTCAGCTCCA
AGGC
Found at i:439245 original size:84 final size:83
Alignment explanation
Indices: 438393--439757 Score: 1188
Period size: 84 Copynumber: 16.5 Consensus size: 83
438383 TTTTTTTAAG
* * * * * ** *
438393 ACATCATTTACAGCATAACTCAAGGCTATAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTTGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGA
* *
438458 CTACGCTCAGCTCCAAGGC
65 CTACACTCAGCTCGAAGGC
* * ** *
438477 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGAT
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGAC
*
438539 TACACTCAGCTCCGAGGGC
66 TACACTCAGCT-CGAAGGC
* * * * * * * * * *
438558 ATATCATTTGTAGTATAACTCAAGGCTAGAAGGGTTATCCGTCAACTAGAAGACCTTTGAGTTCG
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-CCACCA-AAGACCTTCGAGTTCG
* *
438623 ACTACGCTCAGCTCTAAGGC
64 ACTACACTCAGCTCGAAGGC
* * * * * *
438643 ACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTACCA--AAAGACCCTCGAGTTCGAT
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGAC
* *
438706 TACACTCAACTTCGAGGGC
66 TACACTCAGC-TCGAAGGC
* * * * ** * *
438725 ACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTAACCAAAGACCTTTGAGTTCAAC
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGAC
* *
438790 TACGCTCAGCTCCAAGGC
66 TACACTCAGCTCGAAGGC
* * * * * *
438808 ACATCATTTGTAGCATAAATTAAGTTGAGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGAT
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGAC
*
438870 TACACTCAGCTTCGAGGGC
66 TACACTCAGC-TCGAAGGC
* * * * *
438889 ACATCATTTGCAGCATAGCTTAAATCAAGAAGGGTTATCTGCCAACCAAAAACCTTTGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGA
*
438954 CTACACTCAGCTTCGAGGGC
65 CTACACTCAGC-TCGAAGGC
* * * *
438974 ACACCATTTGCAGCATAACTTAAATCGAGAAGGGTTATCTGCCAACCAAAAACCTTTGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGA
* *
439039 CTACGCTCAGCTCCAAGGC
65 CTACACTCAGCTCGAAGGC
* * * ** *
439058 ACATCATTTGCAGCATAGCCTAAGTCGAGAAGGGCTATCT---ACCAAAGACCCCCGAGTTCGAT
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGAC
* * *
439120 TACATTCAGTTTCGAGGGC
66 TACACTCAG-CTCGAAGGC
* * *
439139 ACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTACCAACCAAAGACCTTTGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGA
* *
439204 CTACGCTCAGCTCTAAGGC
65 CTACACTCAGCTCGAAGGC
* * * *
439223 ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCA--AAAGACCCTCGAGTTCGAT
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGAC
*
439286 TACACTCAACTTC-AAGGGC
66 TACACTCAGC-TCGAA-GGC
* * * * * * * *
439305 ATATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTTGAGTTCGAC
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGAC
* *
439370 TACGCTCAGCTCCAAGGC
66 TACACTCAGCTCGAAGGC
* * * * * * * *
439388 ATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTACCAACAAAAGGCCTTTGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGA
* *
439453 CTACGCTCAGCTC-AACGGT
65 CTACACTCAGCTCGAA-GGC
* * * * **
439472 ACATCATTTGCAACATAGCTTAAGTCGAGAAAGGCTATCTG---CCAAAGACCCCCGAGTTCGA-
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGAC
*
439533 TCACACTCAGCTTCGAGGGC
66 T-ACACTCAGC-TCGAAGGC
* * * * * * * * * * *
439553 ATATCATTTACAGTATAGCTCAAGGCTAAAAGGGTTATATGTCACCAAAGACCTTCGAGTTCAAC
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGAC
* * *
439618 TACGCTAAGCTCTAAGGC
66 TACACTCAGCTCGAAGGC
* * * * * * *
439636 ATATCATTTGCAGCACAACTTAAGTCTAAAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGA
1 ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGA
439701 CTACACTCAGCTC-AACGGC
65 CTACACTCAGCTCGAA-GGC
* * *
439720 ACATCATTTGTAGCATAGCTTAAGTTGAGGAA-GGTTAT
1 ACATCATTTGCAGCATAACTTAAGTCGA-GAAGGGTTAT
439758 ATGCTAACTG
Statistics
Matches: 1028, Mismatches: 217, Indels: 72
0.78 0.16 0.05
Matches are distributed among these distances:
79 1 0.00
80 98 0.10
81 204 0.20
82 84 0.08
83 124 0.12
84 320 0.31
85 173 0.17
86 24 0.02
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
ACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGAC
TACACTCAGCTCGAAGGC
Found at i:440433 original size:42 final size:41
Alignment explanation
Indices: 440387--440732 Score: 165
Period size: 36 Copynumber: 9.2 Consensus size: 41
440377 ATATATATAC
440387 ATATATATGTTATATAG-TTTAAAAACATTTTTAAAAAAACAT
1 ATATATAT-TTATATAGTTTTAAAAACATTTTTAAAAAAA-AT
* * * *
440429 ATATATATAATATATAGTTTTGAAAACATGTTT--GAAAAAT
1 ATATATAT-TTATATAGTTTTAAAAACATTTTTAAAAAAAAT
* * * *
440469 ATATATA-TTATATAGTTTTTAAAATATTTTGAAAATAAAT
1 ATATATATTTATATAGTTTTAAAAACATTTTTAAAAAAAAT
* * * *
440509 ATA-ATA--TATA-ACTTTT-AAAAC---GTTGAAAAATAT
1 ATATATATTTATATAGTTTTAAAAACATTTTTAAAAAAAAT
* * * *
440542 ATATATA-TTATACAGTTTTTAAAACA-TTTTGAAAATAA-
1 ATATATATTTATATAGTTTTAAAAACATTTTTAAAAAAAAT
* *
440580 ATATA-A--TATATAGTTTTTAAAACATTTTT----GAAA-
1 ATATATATTTATATAGTTTTAAAAACATTTTTAAAAAAAAT
440613 ATATATA-TTATATAGTTTCT-AAAACA-TTTTAAAAATAAAT
1 ATATATATTTATATAGTTT-TAAAAACATTTTTAAAAA-AAAT
* *
440653 ATA-ATA--TATA-A-TTTTTAAAATATTTTT----AAAA-
1 ATATATATTTATATAGTTTTAAAAACATTTTTAAAAAAAAT
* *
440684 ATATATA-TTATATAGTTTTTAAAATA-TTTTAAAAATAAAT
1 ATATATATTTATATAGTTTTAAAAACATTTTTAAAAA-AAAT
440724 ATAATATAT
1 AT-ATATAT
440733 AGTTTTTAAA
Statistics
Matches: 243, Mismatches: 28, Indels: 66
0.72 0.08 0.20
Matches are distributed among these distances:
31 3 0.01
32 6 0.02
33 22 0.09
34 13 0.05
35 32 0.13
36 35 0.14
37 20 0.08
38 33 0.14
39 20 0.08
40 22 0.09
41 9 0.04
42 15 0.06
43 13 0.05
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (41 bp):
ATATATATTTATATAGTTTTAAAAACATTTTTAAAAAAAAT
Found at i:440504 original size:36 final size:36
Alignment explanation
Indices: 440429--440848 Score: 408
Period size: 36 Copynumber: 11.9 Consensus size: 36
440419 AAAAAAACAT
* *
440429 ATATATATAATATATAGTTTTGAAAACATGTTTGAAAA
1 ATATATATAATATATAGTTTTTAAAATAT-TTTG-AAA
*
440467 ATATATATATTATATAGTTTTTAAAATATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
* ** **
440503 ATAAATATAATATATAACTTTT-AAA-ACGTTGAAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTG-AAA
* *
440538 ATATATATATATTATACAGTTTTTAAAACATTTTGAAA
1 ATATATATA-A-TATATAGTTTTTAAAATATTTTGAAA
* *
440576 ATAAATATAATATATAGTTTTTAAAACATTTTTGAAA
1 ATATATATAATATATAGTTTTTAAAATA-TTTTGAAA
* * *
440613 ATATATAT--TATATAGTTTCTAAAACATTTTAAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
* * *
440647 ATAAATATAATATATAATTTTTAAAATATTTTTAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
* *
440683 A-ATATATATTATATAGTTTTTAAAATATTTTAAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
*
440718 ATAAATATAATATATAGTTTTT-AAA-A----G---
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
*
440745 -TATATATATTATATAGTTTTTAAAATATTTT-AGAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGA-AA
* *
440780 ATAAATATAATATATAGTTTTTAAAATATTTTTAAGA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAA-A
440817 ATATATAT--TATATAGGTTTTTGAAAATATTTT
1 ATATATATAATATATA-GTTTTT-AAAATATTTT
440849 TATTTTTATT
Statistics
Matches: 321, Mismatches: 37, Indels: 49
0.79 0.09 0.12
Matches are distributed among these distances:
26 19 0.06
27 3 0.01
28 1 0.00
34 19 0.06
35 71 0.22
36 116 0.36
37 48 0.15
38 40 0.12
39 4 0.01
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.45
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAATATTTTGAAA
Found at i:440541 original size:71 final size:70
Alignment explanation
Indices: 440433--440848 Score: 461
Period size: 71 Copynumber: 5.9 Consensus size: 70
440423 AAACATATAT
* *
440433 ATATAATATATAGTTTTGAAAACATGTTTGAAAAATATATATATTATATAGTTTTTAAAATATTT
1 ATATAATATATAATTTTTAAAAC-T-TTT-AAAAA-ATATATATTATATAGTTTTTAAAATATTT
*
440498 TGAAAATAA
62 TAAAAATAA
* ** * *
440507 ATATAATATATAACTTTTAAAACGTTGAAAAATATATATATATTATACAGTTTTTAAAACATTTT
1 ATATAATATATAATTTTTAAAAC-TTTTAAAA-A-ATATATATTATATAGTTTTTAAAATATTTT
*
440572 GAAAATAA
63 AAAAATAA
* ** * *
440580 ATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATTATATAGTTTCTAAAACATTTTAA
1 ATATAATATATAATTTTTAAAAC-TTTTAAAAAATATATATTATATAGTTTTTAAAATATTTTAA
440645 AAATAA
65 AAATAA
* *
440651 ATATAATATATAATTTTTAAAATATTTTTAAAAATATATATTATATAGTTTTTAAAATATTTTAA
1 ATATAATATATAATTTTTAAAA-CTTTTAAAAAATATATATTATATAGTTTTTAAAATATTTTAA
440716 AAATAA
65 AAATAA
* * *
440722 ATATAATATATAGTTTTTAAAA---GT-----ATATATATTATATAGTTTTTAAAATATTTTAGA
1 ATATAATATATAATTTTTAAAACTTTTAAAAAATATATATTATATAGTTTTTAAAATATTTTAAA
440779 AATAA
66 AATAA
* * * *
440784 ATATAATATATAGTTTTTAAAATATTTTTAAGAATATATATTATATAGGTTTTTGAAAATATTTT
1 ATATAATATATAATTTTTAAAA-CTTTTAAAAAATATATATTATATA-GTTTTT-AAAATATTTT
440849 TATTTTTATT
Statistics
Matches: 302, Mismatches: 27, Indels: 27
0.85 0.08 0.08
Matches are distributed among these distances:
62 59 0.20
66 1 0.00
67 1 0.00
71 135 0.45
72 11 0.04
73 74 0.25
74 21 0.07
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (70 bp):
ATATAATATATAATTTTTAAAACTTTTAAAAAATATATATTATATAGTTTTTAAAATATTTTAAA
AATAA
Found at i:440740 original size:26 final size:26
Alignment explanation
Indices: 440710--440769 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
440700 TTTTAAAATA
440710 TTTTAAAAATAAATATAATATATAGT
1 TTTTAAAAATAAATATAATATATAGT
* * *
440736 TTTTAAAAGTATATATATTATATAGT
1 TTTTAAAAATAAATATAATATATAGT
440762 TTTTAAAA
1 TTTTAAAA
440770 TATTTTAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (26 bp):
TTTTAAAAATAAATATAATATATAGT
Found at i:440767 original size:62 final size:60
Alignment explanation
Indices: 440675--440805 Score: 235
Period size: 62 Copynumber: 2.1 Consensus size: 60
440665 TTTTAAAATA
440675 TTTTTAAAAATATATATTATATAGTTTTTAAAATATTTTAAAAATAAATATAATATATAG
1 TTTTTAAAAATATATATTATATAGTTTTTAAAATATTTTAAAAATAAATATAATATATAG
*
440735 TTTTTAAAAGTATATATATTATATAGTTTTTAAAATATTTTAGAAATAAATATAATATATAG
1 TTTTTAAAA--ATATATATTATATAGTTTTTAAAATATTTTAAAAATAAATATAATATATAG
440797 TTTTTAAAA
1 TTTTTAAAA
440806 TATTTTTAAG
Statistics
Matches: 68, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
60 9 0.13
62 59 0.87
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (60 bp):
TTTTTAAAAATATATATTATATAGTTTTTAAAATATTTTAAAAATAAATATAATATATAG
Found at i:440819 original size:12 final size:11
Alignment explanation
Indices: 440663--440820 Score: 61
Period size: 11 Copynumber: 13.2 Consensus size: 11
440653 ATAATATATA
440663 ATTTTTAAAAT
1 ATTTTTAAAAT
440674 ATTTTTAAAAAT
1 ATTTTT-AAAAT
* *
440686 ATATATT-ATAT
1 AT-TTTTAAAAT
440697 AGTTTTTAAAAT
1 A-TTTTTAAAAT
*
440709 ATTTTAAAAAT
1 ATTTTTAAAAT
** *
440720 AAATATAATATAT
1 ATTTTTAA-A-AT
440733 AGTTTTTAAAAGT
1 A-TTTTTAAAA-T
*
440746 ATATATATT-ATAT
1 AT-T-T-TTAAAAT
440759 AGTTTTTAAAAT
1 A-TTTTTAAAAT
440771 A-TTTTAGAAAT
1 ATTTTTA-AAAT
** *
440782 AAATATAATATAT
1 ATTTTTAA-A-AT
440795 AGTTTTTAAAAT
1 A-TTTTTAAAAT
440807 ATTTTTAAGAAT
1 ATTTTTAA-AAT
440819 AT
1 AT
440821 ATATTATATA
Statistics
Matches: 109, Mismatches: 19, Indels: 37
0.66 0.12 0.22
Matches are distributed among these distances:
10 5 0.05
11 41 0.38
12 32 0.29
13 17 0.16
14 12 0.11
15 2 0.02
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.48
Consensus pattern (11 bp):
ATTTTTAAAAT
Found at i:440872 original size:23 final size:24
Alignment explanation
Indices: 440846--440899 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
440836 TTGAAAATAT
440846 TTTTATTTTTATT-A-TTTATTTCC
1 TTTTATTTTTATTAACTTTATTT-C
*
440869 TTTTA-TTTTATTAACTTTATTTT
1 TTTTATTTTTATTAACTTTATTTC
440892 TTTTATTT
1 TTTTATTT
440900 ATCTAACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.26
23 11 0.41
24 9 0.33
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTATTTTTATTAACTTTATTTC
Found at i:440873 original size:133 final size:133
Alignment explanation
Indices: 440463--440848 Score: 448
Period size: 133 Copynumber: 2.8 Consensus size: 133
440453 AACATGTTTG
* * * * *
440463 AAAAATATATATATTATATAGTTTTTAAAATATTTTGAAAATAAATATAATATATAACTTTTAAA
1 AAAAGTATATATATTATATAGTTTCTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAA
** *** * * * *
440528 ACGTTGAAAAATATATATATATTATACAGTTTTTAAAACATTTTGAAAATAAATATAATATATAG
66 ATATTTTTAAA-A-ATATATATTATATAGTTTTTAAAATATTTTAAAAATAAATATAATATATAC
*
440593 TTTTT
129 CTTTT
*
440598 AAAACATTTTTGAAAATATATATTATATAGTTTCTAAAACATTTTAAAAATAAATATAATATATA
1 -AAA-A-----G--TATATATATTATATAGTTTCTAAAACATTTTAAAAATAAATATAATATATA
440663 ATTTTTAAAATATTTTTAAAAATATATATTATATAGTTTTTAAAATATTTTAAAAATAAATATAA
57 ATTTTTAAAATATTTTTAAAAATATATATTATATAGTTTTTAAAATATTTTAAAAATAAATATAA
**
440728 TATATAGTTTTT
122 TATATACCTTTT
* * * *
440740 AAAAGTATATATATTATATAGTTTTTAAAATATTTTAGAAATAAATATAATATATAGTTTTTAAA
1 AAAAGTATATATATTATATAGTTTCTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAA
*
440805 ATATTTTTAAGAATATATATTATATAGGTTTTTGAAAATATTTT
66 ATATTTTTAAAAATATATATTATATA-GTTTTT-AAAATATTTT
440849 TATTTTTATT
Statistics
Matches: 220, Mismatches: 20, Indels: 21
0.84 0.08 0.08
Matches are distributed among these distances:
133 80 0.36
134 6 0.03
135 11 0.05
136 3 0.01
137 1 0.00
140 1 0.00
141 3 0.01
142 53 0.24
143 1 0.00
144 61 0.28
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (133 bp):
AAAAGTATATATATTATATAGTTTCTAAAACATTTTAAAAATAAATATAATATATAATTTTTAAA
ATATTTTTAAAAATATATATTATATAGTTTTTAAAATATTTTAAAAATAAATATAATATATACCT
TTT
Found at i:440906 original size:23 final size:24
Alignment explanation
Indices: 440843--440947 Score: 65
Period size: 26 Copynumber: 4.3 Consensus size: 24
440833 TTTTTGAAAA
* * *
440843 TATTTTTATTTTTATTA-TTTATT
1 TATTTTTATTTATCTAACTTTATT
**
440866 TCCTTTTATTTTAT-TAACTTTATT
1 TATTTTTA-TTTATCTAACTTTATT
*
440890 T-TTTTTATTTATCTAACATTTGTT
1 TATTTTTATTTATCTAAC-TTTATT
*
440914 TATTATTATATTT-TCTAACATTTTTT
1 TATT-TT-TATTTATCTAAC-TTTATT
440940 TACTTTTT
1 TA-TTTTT
440948 TAGAAGAACT
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
22 5 0.07
23 17 0.25
24 17 0.25
25 3 0.04
26 18 0.27
27 7 0.10
ACGTcount: A:0.22, C:0.08, G:0.01, T:0.70
Consensus pattern (24 bp):
TATTTTTATTTATCTAACTTTATT
Found at i:441531 original size:16 final size:18
Alignment explanation
Indices: 441510--441543 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
441500 ATTCCAACCA
441510 CTTTGGAC-AA-GAATAT
1 CTTTGGACTAATGAATAT
441526 CTTTGGACTAATGAATAT
1 CTTTGGACTAATGAATAT
441544 TTTTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 2 0.12
18 6 0.38
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (18 bp):
CTTTGGACTAATGAATAT
Found at i:447532 original size:21 final size:21
Alignment explanation
Indices: 447506--447550 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
447496 GTTCTTTTTA
447506 AACTGCTTCAGGATTGATCTG
1 AACTGCTTCAGGATTGATCTG
447527 AACTGCTTCAGGATTGATCTG
1 AACTGCTTCAGGATTGATCTG
447548 AAC
1 AAC
447551 ATCATTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (21 bp):
AACTGCTTCAGGATTGATCTG
Found at i:451923 original size:2 final size:2
Alignment explanation
Indices: 451916--451952 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
451906 CGCCAACAAC
451916 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
451953 GAAATTGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:460538 original size:27 final size:23
Alignment explanation
Indices: 460476--460539 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 23
460466 GTTTCGCACC
*
460476 TCTGAATGATTCAGCAAAACAGT
1 TCTGAATGATTCAGCAAAACAAT
*
460499 GCTGAATGATTCAGCACAGAAGCACAT
1 TCTGAATGATTCAGCA-A-AA-CA-AT
460526 TCTGAATGATTCAG
1 TCTGAATGATTCAG
460540 AGTCATTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.44
24 1 0.03
25 2 0.06
26 2 0.06
27 14 0.41
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (23 bp):
TCTGAATGATTCAGCAAAACAAT
Found at i:465302 original size:27 final size:27
Alignment explanation
Indices: 465267--465334 Score: 109
Period size: 28 Copynumber: 2.5 Consensus size: 27
465257 CTTTATTTTG
*
465267 TTCGGGTCGGGTTTTTTTAGTGTGATA
1 TTCGGGTCGGGTTTTTTAAGTGTGATA
465294 TTCGGGTCGGGGTTTTTTAAGTGTGATA
1 TTCGGGTC-GGGTTTTTTAAGTGTGATA
*
465322 TTCAGGTCGGGTT
1 TTCGGGTCGGGTT
465335 CGGGTTTAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 13 0.34
28 25 0.66
ACGTcount: A:0.12, C:0.09, G:0.35, T:0.44
Consensus pattern (27 bp):
TTCGGGTCGGGTTTTTTAAGTGTGATA
Found at i:466319 original size:26 final size:26
Alignment explanation
Indices: 466290--466340 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
466280 GTAAGGGACT
*
466290 TTGTAAAATATTTGAATCAAGGTACC
1 TTGTAAAAGATTTGAATCAAGGTACC
* *
466316 TTGTAGAAGATTTGAATCGAGGTAC
1 TTGTAAAAGATTTGAATCAAGGTAC
466341 AAATAGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (26 bp):
TTGTAAAAGATTTGAATCAAGGTACC
Found at i:475038 original size:71 final size:71
Alignment explanation
Indices: 474933--475132 Score: 267
Period size: 71 Copynumber: 2.8 Consensus size: 71
474923 TATCTCGAGT
* * *
474933 GAGACGATAATTTTAAAGGGGAAATATTTCAAGTGATATGAAATTTTGCTTCGAGAGAAACTGTC
1 GAGACGAAAATTTTCAAGGGAAAATATTTCAAGTGATATGAAATTTTGCTTCGAGAGAAACTGTC
474998 TTGAGC
66 TTGAGC
* * * *
475004 GAGACGAAAAATTTCAAGGGAAAACATCTCAAGTGATATGAAATTTTGCTTCAAGAGAAACTGTC
1 GAGACGAAAATTTTCAAGGGAAAATATTTCAAGTGATATGAAATTTTGCTTCGAGAGAAACTGTC
*
475069 TTGAGT
66 TTGAGC
* * * * *
475075 GAGACGAGAATTTTCAAGGGAAAGTATTTCAAGTGAGATTAAATCTTG-TCTCGAGAGA
1 GAGACGAAAATTTTCAAGGGAAAATATTTCAAGTGATATGAAATTTTGCT-TCGAGAGA
475133 GACAATTATT
Statistics
Matches: 111, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
70 1 0.01
71 110 0.99
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.28
Consensus pattern (71 bp):
GAGACGAAAATTTTCAAGGGAAAATATTTCAAGTGATATGAAATTTTGCTTCGAGAGAAACTGTC
TTGAGC
Found at i:475076 original size:37 final size:37
Alignment explanation
Indices: 474964--475076 Score: 99
Period size: 37 Copynumber: 3.1 Consensus size: 37
474954 AAATATTTCA
*
474964 AGTGATATGAAATTTTGCTTCGAGAGAAACTGTCTTG
1 AGTGATATGAAATTTTGCTTCAAGAGAAACTGTCTTG
* * * ** * * **
475001 AGCGAGACGAAA-AAT--TTCAAGGGAAAAC-ATCTCA
1 AGTGATATGAAATTTTGCTTCAAGAG-AAACTGTCTTG
475035 AGTGATATGAAATTTTGCTTCAAGAGAAACTGTCTTG
1 AGTGATATGAAATTTTGCTTCAAGAGAAACTGTCTTG
475072 AGTGA
1 AGTGA
475077 GACGAGAATT
Statistics
Matches: 52, Mismatches: 19, Indels: 10
0.64 0.23 0.12
Matches are distributed among these distances:
34 18 0.35
35 5 0.10
36 5 0.10
37 24 0.46
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (37 bp):
AGTGATATGAAATTTTGCTTCAAGAGAAACTGTCTTG
Found at i:477238 original size:21 final size:21
Alignment explanation
Indices: 477213--477260 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
477203 GAGAACTGGC
*
477213 AAAACCGGGGTAAACCGGCTG
1 AAAACCGGAGTAAACCGGCTG
*
477234 AAAACCGGAGTGAACCGGCTG
1 AAAACCGGAGTAAACCGGCTG
477255 AAAACC
1 AAAACC
477261 AGTGTGAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.25, G:0.29, T:0.08
Consensus pattern (21 bp):
AAAACCGGAGTAAACCGGCTG
Found at i:477267 original size:21 final size:21
Alignment explanation
Indices: 477225--477271 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
477215 AACCGGGGTA
*
477225 AACCGGCTGAAAACCGGAGTG
1 AACCGGCTGAAAACCAGAGTG
*
477246 AACCGGCTGAAAACCAGTGTG
1 AACCGGCTGAAAACCAGAGTG
477267 AACCG
1 AACCG
477272 CCGGTTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.30, T:0.11
Consensus pattern (21 bp):
AACCGGCTGAAAACCAGAGTG
Found at i:478396 original size:36 final size:36
Alignment explanation
Indices: 478349--478524 Score: 219
Period size: 36 Copynumber: 4.9 Consensus size: 36
478339 AAGATGAACA
* **
478349 ATTGAGTCGAAAGTGCCGATGCTTTATTTCGTTCAC
1 ATTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
478385 ATTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
1 ATTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
* * *
478421 TTTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC
1 ATTGAATCGAAAGTGCCGATGCTTCCTTTCGTTC-AC
* * *
478458 -TTGAATCGAAAATGTCGATGCTTCCTTCCGTTCAC
1 ATTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
* ***
478493 TTTGAATCGAAAGTGTTTATGCTTCCTTTCGT
1 ATTGAATCGAAAGTGCCGATGCTTCCTTTCGT
478525 ACTTCTGATT
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
35 1 0.01
36 123 0.98
37 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (36 bp):
ATTGAATCGAAAGTGCCGATGCTTCCTTTCGTTCAC
Found at i:478477 original size:72 final size:72
Alignment explanation
Indices: 478350--478530 Score: 247
Period size: 72 Copynumber: 2.5 Consensus size: 72
478340 AGATGAACAA
* * ** * * *
478350 TTGAGTCGAAAGTGCCGATGCTTTATTTCGTTC-ACATTGAATCGAAAGTGCCGATGCTTCCTTT
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTC-TTGAATCGAAAATGCCGATGCTTCCTTC
478414 CGTTCACT
65 CGTTCACT
*
478422 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTCTTGAATCGAAAATGTCGATGCTTCCTTCC
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTCTTGAATCGAAAATGCCGATGCTTCCTTCC
478487 GTTCACT
66 GTTCACT
** *
478494 TTGAATCGAAAGTGTTTATGCTTCCTTTCGTACTTCT
1 TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTCT
478531 GATTCACCTT
Statistics
Matches: 97, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
72 96 0.99
73 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (72 bp):
TTGAATCGAAAGTGTCGATGCTTCCTTTCGTTCTTCTTGAATCGAAAATGCCGATGCTTCCTTCC
GTTCACT
Found at i:487053 original size:10 final size:10
Alignment explanation
Indices: 487038--487063 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
487028 CAAAGAAGGG
487038 CAAGAACCTC
1 CAAGAACCTC
487048 CAAGAACCTC
1 CAAGAACCTC
487058 CAAGAA
1 CAAGAA
487064 AAGAGGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.46, C:0.35, G:0.12, T:0.08
Consensus pattern (10 bp):
CAAGAACCTC
Found at i:491211 original size:19 final size:19
Alignment explanation
Indices: 491148--491213 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
491138 TGATAGTGAG
*
491148 TTATTATAA-AATATATTT
1 TTATTATAATTATATATTT
*
491166 TTATTGTAATTATATATTT
1 TTATTATAATTATATATTT
* *
491185 TTATTTATATTTTTATATTT
1 TTA-TTATAATTATATATTT
491205 TTATTATAA
1 TTATTATAA
491214 AAATATAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.20
19 16 0.40
20 16 0.40
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTATTATAATTATATATTT
Found at i:496226 original size:2 final size:2
Alignment explanation
Indices: 496210--496244 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
496200 TGCCGTGTCG
*
496210 AT AT -T AT AA 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
496245 TTGGTTACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:497259 original size:17 final size:17
Alignment explanation
Indices: 497237--497269 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
497227 AGATATCACA
497237 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
497254 ATATTATATTTTATAT
1 ATATTATATTTTATAT
497270 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:501023 original size:18 final size:19
Alignment explanation
Indices: 501000--501037 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
500990 GTTTTAATTG
501000 AATTTG-TAGGGTTTCTTT
1 AATTTGTTAGGGTTTCTTT
501018 AATTTGTTTAGGGTTTCTTT
1 AATTTG-TTAGGGTTTCTTT
501038 TTTAGGTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.16, C:0.05, G:0.21, T:0.58
Consensus pattern (19 bp):
AATTTGTTAGGGTTTCTTT
Found at i:509368 original size:21 final size:21
Alignment explanation
Indices: 509344--509388 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
509334 GGAGTACGGA
509344 GGACGGCGGACGGCAAGCGAC
1 GGACGGCGGACGGCAAGCGAC
* *
509365 GGACGGTGGATGGCAAGCGAC
1 GGACGGCGGACGGCAAGCGAC
509386 GGA
1 GGA
509389 TGACGATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.24, C:0.22, G:0.49, T:0.04
Consensus pattern (21 bp):
GGACGGCGGACGGCAAGCGAC
Found at i:509527 original size:2 final size:2
Alignment explanation
Indices: 509522--509547 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
509512 GCCTTTTTAA
509522 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
509548 GAAACCATAA
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:536511 original size:24 final size:25
Alignment explanation
Indices: 536453--536511 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
536443 ATTATTTAAA
*
536453 TTTTAAATTATAAAAGAATAGATAT
1 TTTTATATTATAAAAGAATAGATAT
* *
536478 CTTTATATTAT-AAA-AATAAGTTAT
1 TTTTATATTATAAAAGAAT-AGATAT
536502 TTTTATATTA
1 TTTTATATTA
536512 AATTTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 3 0.10
24 17 0.59
25 9 0.31
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (25 bp):
TTTTATATTATAAAAGAATAGATAT
Found at i:536856 original size:59 final size:59
Alignment explanation
Indices: 536733--536871 Score: 156
Period size: 59 Copynumber: 2.3 Consensus size: 59
536723 GAAATATTCA
* * * * *
536733 AAAAGTTTGGGGACCAATTTAGGATGAAGATCATAGCTTGGGGATGAAAATGAAATGTTT
1 AAAAGTTT-GGGACTAATTTAGAATAAAGATCATAGCTTAGGGATGAAAATGAAATGCTT
* *
536793 AAAAGTTTGTGGACTAATTTAGAATAATAG-TCATAG-TTATGGATGAAATTGAAATGCTT
1 AAAAGTTTG-GGACTAATTTAGAATAA-AGATCATAGCTTAGGGATGAAAATGAAATGCTT
*
536852 AAAAGCTTAGGGACTAATTT
1 AAAAG-TTTGGGACTAATTT
536872 TAAATAAGGG
Statistics
Matches: 68, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
59 35 0.51
60 31 0.46
61 2 0.03
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (59 bp):
AAAAGTTTGGGACTAATTTAGAATAAAGATCATAGCTTAGGGATGAAAATGAAATGCTT
Found at i:537105 original size:16 final size:16
Alignment explanation
Indices: 537060--537107 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
537050 TTTCGATTCA
* *
537060 GGTTATTTTCAG-TTC
1 GGTTACTTTCAGTTTG
* *
537075 GGTTGCTTTCGGTTTG
1 GGTTACTTTCAGTTTG
537091 GGTTACTTTCAGTTTG
1 GGTTACTTTCAGTTTG
537107 G
1 G
537108 CTAAAATTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.08, C:0.12, G:0.29, T:0.50
Consensus pattern (16 bp):
GGTTACTTTCAGTTTG
Found at i:537908 original size:16 final size:16
Alignment explanation
Indices: 537887--537917 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
537877 TGAATTAATA
537887 TTATAATTGATATATG
1 TTATAATTGATATATG
*
537903 TTATAATTTATATAT
1 TTATAATTGATATAT
537918 TTTTATTATT
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:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TTATAATTGATATATG
Found at i:538095 original size:3 final size:3
Alignment explanation
Indices: 538087--538111 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
538077 AGAAAGATTT
538087 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
538112 CTGCTATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:538697 original size:3 final size:3
Alignment explanation
Indices: 538689--538716 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
538679 AAATAGACTA
538689 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
538717 TATAGAAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:539880 original size:17 final size:18
Alignment explanation
Indices: 539848--539890 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
539838 GATTTTGAAC
539848 TTTTTAAAATGATAATAAT
1 TTTTTAAAAT-ATAATAAT
*
539867 TTTTTAAAAT-TAATTAT
1 TTTTTAAAATATAATAAT
539884 TTGTTTA
1 TT-TTTA
539891 TTGTACCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TTTTTAAAATATAATAAT
Found at i:540134 original size:25 final size:27
Alignment explanation
Indices: 540100--540161 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 27
540090 CTTCAACTTA
540100 GTCTTCATTT-C-TTGGATATCTAGGC
1 GTCTTCATTTGCTTTGGATATCTAGGC
540125 GTCTTCATTTGCTATGTTGGATATCTAGGC
1 GTCTTCATTTGC--T-TTGGATATCTAGGC
540155 GTCTTCA
1 GTCTTCA
540162 ATGCAAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 10 0.31
26 1 0.03
30 21 0.66
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (27 bp):
GTCTTCATTTGCTTTGGATATCTAGGC
Found at i:541558 original size:160 final size:165
Alignment explanation
Indices: 541294--541622 Score: 614
Period size: 160 Copynumber: 2.0 Consensus size: 165
541284 TGTTTGCAAT
541294 ATGTGAGCGTTACCTTGGGAAGGTAACACACACAGATTTAACAAAAGGGTCACGACTGAGATTAT
1 ATGTGAGCGTTACCTTGGGAAGGTAACACACACAGATTTAACAAAAGGGTCACGACTGAGATTAT
541359 CCTGGTTGGCAAATGAGTTTAAGCTCGATCCTCATTGT-A-AGCAAGACA-T-TATATGCAACTT
66 CCTGGTTGGCAAATGAGTTTAAGCTCGATCCTCATTGTAAGAGCAAGACATTATATATGCAACTT
541420 GAGCATATATATT-CGGTTGATCGACGGAATCTTG
131 GAGCATATATATTACGGTTGATCGACGGAATCTTG
541454 ATGTGAGCGTTACCTTGGGAAGGTAACACACACAGATTTAACAAAAGGGTCACGACTGAGATTAT
1 ATGTGAGCGTTACCTTGGGAAGGTAACACACACAGATTTAACAAAAGGGTCACGACTGAGATTAT
541519 CCTGGTTGGCAAATGAGTTTAAGCTCGATCCTCATTGTAATGAGCAAGACATTATATATGCAACT
66 CCTGGTTGGCAAATGAGTTTAAGCTCGATCCTCATTGTAA-GAGCAAGACATTATATATGCAACT
541584 TGAGCATATATATTACGGTTGATCGACGGAATCTTG
130 TGAGCATATATATTACGGTTGATCGACGGAATCTTG
541620 ATG
1 ATG
541623 CTGGATAAAT
Statistics
Matches: 163, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
160 103 0.63
161 1 0.01
163 9 0.06
164 1 0.01
165 25 0.15
166 24 0.15
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (165 bp):
ATGTGAGCGTTACCTTGGGAAGGTAACACACACAGATTTAACAAAAGGGTCACGACTGAGATTAT
CCTGGTTGGCAAATGAGTTTAAGCTCGATCCTCATTGTAAGAGCAAGACATTATATATGCAACTT
GAGCATATATATTACGGTTGATCGACGGAATCTTG
Found at i:542140 original size:16 final size:16
Alignment explanation
Indices: 542092--542146 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
542082 ATTAGTGAAT
542092 TTATTT-TTTATTATTG
1 TTATTTATTTATT-TTG
* *
542108 TTATATTA-TAATATTG
1 TTAT-TTATTTATTTTG
542124 TTATTTATTTATTTTG
1 TTATTTATTTATTTTG
542140 TTGATTT
1 TT-ATTT
542147 TTATAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 3 0.10
16 19 0.61
17 9 0.29
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (16 bp):
TTATTTATTTATTTTG
Found at i:542574 original size:24 final size:24
Alignment explanation
Indices: 542547--542594 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
542537 TTTTTACTAC
542547 TAAATAATTATTAGTAATAATTAT
1 TAAATAATTATTAGTAATAATTAT
* * * *
542571 TAAATCATTGTTTGTAATTATTAT
1 TAAATAATTATTAGTAATAATTAT
542595 AATTTCATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (24 bp):
TAAATAATTATTAGTAATAATTAT
Found at i:554395 original size:32 final size:32
Alignment explanation
Indices: 554349--554458 Score: 143
Period size: 32 Copynumber: 3.5 Consensus size: 32
554339 TAGTTATAGT
* *
554349 TTACTTATGTCCTTCGGGACATATGAAAAGGA
1 TTACCTATGTCCTTCGGGACATATGGAAAGGA
*
554381 TTACCTATGTCCTTCGGGACATATGGATAGGA
1 TTACCTATGTCCTTCGGGACATATGGAAAGGA
* * *
554413 TTACCTATGTCTTTCGCGACATATGGACA-G-
1 TTACCTATGTCCTTCGGGACATATGGAAAGGA
*
554443 TTACCTATGTTCTTCG
1 TTACCTATGTCCTTCG
554459 AAACTTATAG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
30 14 0.20
31 1 0.01
32 55 0.79
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.35
Consensus pattern (32 bp):
TTACCTATGTCCTTCGGGACATATGGAAAGGA
Found at i:554472 original size:62 final size:64
Alignment explanation
Indices: 554349--554473 Score: 146
Period size: 62 Copynumber: 2.0 Consensus size: 64
554339 TAGTTATAGT
* * ** *
554349 TTACTTATGTCCTTCGGGACATATGAAAAGGATTACCTATGTCCTTCGGGACATATGGATAGGA
1 TTACCTATGTCCTTCGCGACATATGAAAAGGATTACCTATGTCCTTCGAAACATATAGATAGGA
* * * * *
554413 TTACCTATGTCTTTCGCGACATATGGACA-G-TTACCTATGTTCTTCGAAACTTATAGATAGG
1 TTACCTATGTCCTTCGCGACATATGAAAAGGATTACCTATGTCCTTCGAAACATATAGATAGG
554474 TCTTTCGGGG
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 26 0.51
63 1 0.02
64 24 0.47
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
TTACCTATGTCCTTCGCGACATATGAAAAGGATTACCTATGTCCTTCGAAACATATAGATAGGA
Found at i:557399 original size:159 final size:159
Alignment explanation
Indices: 557110--557427 Score: 636
Period size: 159 Copynumber: 2.0 Consensus size: 159
557100 AACCGTGATC
557110 TTTTCCCTTAAGATCTGATGACACTATTTTTGCTGTGTGAAGTGTTACATTTACAATGATCATAA
1 TTTTCCCTTAAGATCTGATGACACTATTTTTGCTGTGTGAAGTGTTACATTTACAATGATCATAA
557175 GAGTCTGAAGTGCCTTATCACTCAGAAGGAGATTAATTTGAGACAACATCGGTGGTTGGAACTGC
66 GAGTCTGAAGTGCCTTATCACTCAGAAGGAGATTAATTTGAGACAACATCGGTGGTTGGAACTGC
557240 TTAAGGATTATGATTGTAAAATCAAGTAT
131 TTAAGGATTATGATTGTAAAATCAAGTAT
557269 TTTTCCCTTAAGATCTGATGACACTATTTTTGCTGTGTGAAGTGTTACATTTACAATGATCATAA
1 TTTTCCCTTAAGATCTGATGACACTATTTTTGCTGTGTGAAGTGTTACATTTACAATGATCATAA
557334 GAGTCTGAAGTGCCTTATCACTCAGAAGGAGATTAATTTGAGACAACATCGGTGGTTGGAACTGC
66 GAGTCTGAAGTGCCTTATCACTCAGAAGGAGATTAATTTGAGACAACATCGGTGGTTGGAACTGC
557399 TTAAGGATTATGATTGTAAAATCAAGTAT
131 TTAAGGATTATGATTGTAAAATCAAGTAT
557428 CACCTCGACA
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 159 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.35
Consensus pattern (159 bp):
TTTTCCCTTAAGATCTGATGACACTATTTTTGCTGTGTGAAGTGTTACATTTACAATGATCATAA
GAGTCTGAAGTGCCTTATCACTCAGAAGGAGATTAATTTGAGACAACATCGGTGGTTGGAACTGC
TTAAGGATTATGATTGTAAAATCAAGTAT
Found at i:566017 original size:15 final size:15
Alignment explanation
Indices: 565997--566032 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
565987 TTCCGGAAAA
*
565997 TGAATTACTATAATT
1 TGAATTACTAGAATT
*
566012 TGAATTACTGGAATT
1 TGAATTACTAGAATT
566027 TGAATT
1 TGAATT
566033 CTGAAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (15 bp):
TGAATTACTAGAATT
Found at i:566297 original size:49 final size:50
Alignment explanation
Indices: 566200--566298 Score: 114
Period size: 49 Copynumber: 2.0 Consensus size: 50
566190 TACAAATATT
*
566200 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATTATTTTA
1 AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
* * * *
566250 AAATATTA-AAATAAT-TTATTTATTATTAAATA-TTATTTTTATAATTTTA
1 AAATATAATAAATAATATTATTTATCA-TAAA-ACTTAATATTATAATTTTA
566299 TTAATAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
48 9 0.21
49 25 0.60
50 8 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (50 bp):
AAATATAATAAATAATATTATTTATCATAAAACTTAATATTATAATTTTA
Found at i:566407 original size:22 final size:21
Alignment explanation
Indices: 566382--566449 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
566372 AGTGTTATAT
566382 TATATTTTAAAATATTAATTA
1 TATATTTTAAAATATTAATTA
* *
566403 GTATATTTTAAATATCTTTATTA
1 -TATATTTTAAA-ATATTAATTA
* * * *
566426 AATATTTTTAAATATAAATAA
1 TATATTTTAAAATATTAATTA
566447 TAT
1 TAT
566450 TCATTATTAA
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
21 8 0.22
22 20 0.56
23 8 0.22
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
TATATTTTAAAATATTAATTA
Found at i:566477 original size:21 final size:22
Alignment explanation
Indices: 566428--566484 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
566418 CTTTATTAAA
*
566428 TATTT-TTAAATATAAATAATAT
1 TATTTATTAAATAT-AATAAAAT
566450 TCA-TTATTAAATAT-ATAAAAT
1 T-ATTTATTAAATATAATAAAAT
*
566471 TATTTATTATATAT
1 TATTTATTAAATAT
566485 TATTAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 1 0.03
21 17 0.57
22 3 0.10
23 9 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TATTTATTAAATATAATAAAAT
Found at i:566489 original size:17 final size:17
Alignment explanation
Indices: 566440--566568 Score: 59
Period size: 17 Copynumber: 7.4 Consensus size: 17
566430 TTTTTAAATA
566440 TAAATA-ATATTCATTAT
1 TAAATATATATT-ATTAT
**
566457 TAAATATATAAAATTAT
1 TAAATATATATTATTAT
* * *
566474 TTATTATATATTATTAAA
1 TAAATATATATTATT-AT
*
566492 TAAAAATATAATATATTAT
1 TAAATATAT-AT-TATTAT
*
566511 TATATATA-ATTGATTAT
1 TAAATATATATT-ATTAT
** ** *
566528 TTTATA-ATATTAAAAA
1 TAAATATATATTATTAT
566544 TACAATATTATATTATTA-
1 TA-AATA-TATATTATTAT
566562 TAAATAT
1 TAAATAT
566569 TAATAAAAAA
Statistics
Matches: 82, Mismatches: 21, Indels: 19
0.67 0.17 0.16
Matches are distributed among these distances:
16 6 0.07
17 44 0.54
18 12 0.15
19 16 0.20
20 4 0.05
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (17 bp):
TAAATATATATTATTAT
Found at i:566527 original size:54 final size:52
Alignment explanation
Indices: 566419--566563 Score: 126
Period size: 54 Copynumber: 2.8 Consensus size: 52
566409 TTTAAATATC
* * *
566419 TTTATTAAATATTTTTAAAT-ATAA-ATAATATTCATTATTAAATATATAAAATTA
1 TTTATTATATATTATTAAATAAAAATATAATA-T-ATTATT--ATATATAAAATTA
566473 TTTATTATATATTATTAAATAAAAATATAATATATTATTATATAT--AATTGA
1 TTTATTATATATTATTAAATAAAAATATAATATATTATTATATATAAAATT-A
* *
566524 -TTATTTTATAATATTAAA-AATACAATAT--TATATTATTATA
1 TTTATTATATATTATTAAATAA-A-AATATAATATATTATTATA
566564 AATATTAATA
Statistics
Matches: 81, Mismatches: 5, Indels: 15
0.80 0.05 0.15
Matches are distributed among these distances:
49 14 0.17
50 21 0.26
51 6 0.07
52 6 0.07
54 24 0.30
55 4 0.05
56 6 0.07
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
TTTATTATATATTATTAAATAAAAATATAATATATTATTATATATAAAATTA
Found at i:568945 original size:127 final size:128
Alignment explanation
Indices: 568781--569036 Score: 487
Period size: 127 Copynumber: 2.0 Consensus size: 128
568771 CAATTCTAAT
*
568781 TTTAATTTTAGTTACATTCGGGGCTAAAATGAACTTTTTGTTAACCTGTGAACCTATAACCTAAA
1 TTTAATTTCAGTTACATTCGGGGCTAAAATGAACTTTTTGTTAACCTGTGAACCTATAACCTAAA
568846 TATTTGGAACCTCAGTGGCTTAAAGTGGAAATTCCCTTTT-TTTTAATTAGGGAGTGGTCCCA
66 TATTTGGAACCTCAGTGGCTTAAAGTGGAAATTCCCTTTTCTTTTAATTAGGGAGTGGTCCCA
568908 TTTAATTTCAGTTACATTCGGGGCTAAAATGAACTTTTTGTTAACCTGTGAACCTATAACCTAAA
1 TTTAATTTCAGTTACATTCGGGGCTAAAATGAACTTTTTGTTAACCTGTGAACCTATAACCTAAA
*
568973 TATTTGGAACCTCAGTGGCTTTAAGTGGAAATTCCCTTTTCTTTTAATTAGGGAGTGGTCCCA
66 TATTTGGAACCTCAGTGGCTTAAAGTGGAAATTCCCTTTTCTTTTAATTAGGGAGTGGTCCCA
569036 T
1 T
569037 AAAGTTGGGA
Statistics
Matches: 126, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
127 103 0.82
128 23 0.18
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (128 bp):
TTTAATTTCAGTTACATTCGGGGCTAAAATGAACTTTTTGTTAACCTGTGAACCTATAACCTAAA
TATTTGGAACCTCAGTGGCTTAAAGTGGAAATTCCCTTTTCTTTTAATTAGGGAGTGGTCCCA
Found at i:571026 original size:13 final size:13
Alignment explanation
Indices: 571008--571040 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
570998 ATTTCATTTT
571008 GAAAATAAAAACA
1 GAAAATAAAAACA
*
571021 GAAAATAAAAATA
1 GAAAATAAAAACA
571034 GAAAATA
1 GAAAATA
571041 TTTTTTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.03, G:0.09, T:0.12
Consensus pattern (13 bp):
GAAAATAAAAACA
Found at i:571823 original size:15 final size:15
Alignment explanation
Indices: 571803--571836 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
571793 TTTCACCTTG
571803 ACACGAATTTTAGAA
1 ACACGAATTTTAGAA
571818 ACACGAATTTTAGAA
1 ACACGAATTTTAGAA
571833 ACAC
1 ACAC
571837 AAGGAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24
Consensus pattern (15 bp):
ACACGAATTTTAGAA
Found at i:578249 original size:28 final size:28
Alignment explanation
Indices: 578212--578306 Score: 136
Period size: 28 Copynumber: 3.4 Consensus size: 28
578202 AGTAAACAAA
* *
578212 AAACAGAGAGAATAAAACAAGTACACAG
1 AAACAAAGAGAAGAAAACAAGTACACAG
*
578240 AAACAAAGAGAAGAAAGCAAGTACACAG
1 AAACAAAGAGAAGAAAACAAGTACACAG
* *
578268 AAACAGAGAGAAGAAAACAAGTACACAT
1 AAACAAAGAGAAGAAAACAAGTACACAG
*
578296 AGACAAAGAGA
1 AAACAAAGAGA
578307 GAGAGCAACC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 59 1.00
ACGTcount: A:0.61, C:0.14, G:0.20, T:0.05
Consensus pattern (28 bp):
AAACAAAGAGAAGAAAACAAGTACACAG
Found at i:578285 original size:56 final size:56
Alignment explanation
Indices: 578197--578314 Score: 166
Period size: 56 Copynumber: 2.1 Consensus size: 56
578187 TTGTTCCTGC
*
578197 AAGCAAGTAAACAAAAAACAGAGAGAATAAAACAAGTACACAGAAACAAAGAGAAGA
1 AAGCAAGTAAACAAAAAACAGAGAGAAGAAAACAAGTACACAGAAACAAAGAG-AGA
* * * *
578254 AAGCAAGTACAC-AGAAACAGAGAGAAGAAAACAAGTACACATAGACAAAGAGAGA
1 AAGCAAGTAAACAAAAAACAGAGAGAAGAAAACAAGTACACAGAAACAAAGAGAGA
*
578309 GAGCAA
1 AAGCAA
578315 CCAGAAACAC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 8 0.15
56 36 0.65
57 11 0.20
ACGTcount: A:0.61, C:0.14, G:0.20, T:0.05
Consensus pattern (56 bp):
AAGCAAGTAAACAAAAAACAGAGAGAAGAAAACAAGTACACAGAAACAAAGAGAGA
Found at i:578334 original size:19 final size:19
Alignment explanation
Indices: 578310--578372 Score: 117
Period size: 19 Copynumber: 3.3 Consensus size: 19
578300 AAAGAGAGAG
578310 AGCAACCAGAAACACAACA
1 AGCAACCAGAAACACAACA
578329 AGCAACCAGAAACACAACA
1 AGCAACCAGAAACACAACA
*
578348 AGCAACCAGAAACACAATA
1 AGCAACCAGAAACACAACA
578367 AGCAAC
1 AGCAAC
578373 GAAAGAAAGA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.57, C:0.30, G:0.11, T:0.02
Consensus pattern (19 bp):
AGCAACCAGAAACACAACA
Found at i:582509 original size:30 final size:30
Alignment explanation
Indices: 582435--582519 Score: 95
Period size: 28 Copynumber: 2.9 Consensus size: 30
582425 TTGTTCCTGC
* * *
582435 AAGCAAGTACACAAACAAACATAGAGAAGA
1 AAGCAAGTACACAGAGAAACAGAGAGAAGA
* *
582465 AAGTAAGT--ACAGAGAAACAGAGAGAATA
1 AAGCAAGTACACAGAGAAACAGAGAGAAGA
582493 AAGCAAGTACACAGAGACAA-AGAGAGA
1 AAGCAAGTACACAGAGA-AACAGAGAGA
582520 GTAACCAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
28 23 0.50
30 21 0.46
31 2 0.04
ACGTcount: A:0.58, C:0.13, G:0.22, T:0.07
Consensus pattern (30 bp):
AAGCAAGTACACAGAGAAACAGAGAGAAGA
Found at i:583221 original size:29 final size:28
Alignment explanation
Indices: 583188--583242 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
583178 AAATTATATT
583188 ATTAGTACA-TATAGTTTATAATATTTTGA
1 ATTAG-ACACTATAGTTT-TAATATTTTGA
* *
583217 ATTAGAGACTATAGTTTTATTATTTT
1 ATTAGACACTATAGTTTTAATATTTT
583243 ACAATTTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 10 0.43
29 13 0.57
ACGTcount: A:0.35, C:0.04, G:0.11, T:0.51
Consensus pattern (28 bp):
ATTAGACACTATAGTTTTAATATTTTGA
Found at i:584389 original size:43 final size:42
Alignment explanation
Indices: 584342--584471 Score: 154
Period size: 43 Copynumber: 3.0 Consensus size: 42
584332 GAGTATATAC
*
584342 TTAGCGGTGTTTGTGAGAAAAAATGTCACTATAAACATAGTTA
1 TTAGCGGTGTTTGTGAG-AAAAATGCCACTATAAACATAGTTA
*
584385 TTAGCGGTGTTTGTGAGGAAAAACGCCACTATAAACATAAG-TA
1 TTAGCGGTGTTTGTGA-GAAAAATGCCACTATAAACAT-AGTTA
* * * * * *
584428 TTAGTGGCGTTTATGAGAAAAATACCACTATATACATAATTA
1 TTAGCGGTGTTTGTGAGAAAAATGCCACTATAAACATAGTTA
584470 TT
1 TT
584472 TGCGACGTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
41 1 0.01
42 22 0.29
43 49 0.65
44 3 0.04
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.32
Consensus pattern (42 bp):
TTAGCGGTGTTTGTGAGAAAAATGCCACTATAAACATAGTTA
Found at i:586976 original size:18 final size:18
Alignment explanation
Indices: 586953--587045 Score: 105
Period size: 18 Copynumber: 4.9 Consensus size: 18
586943 ACTGAATATT
586953 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
586971 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
586990 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
* *
587009 TGTCTCGAAGGACCACTGTT
1 TGTCCCGAAGGACCAC--TA
*
587029 TGTCCCGAAAGACCACT
1 TGTCCCGAAGGACCACT
587046 GATAATCCCT
Statistics
Matches: 63, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
18 31 0.49
19 2 0.03
20 30 0.48
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:587000 original size:20 final size:20
Alignment explanation
Indices: 586952--587048 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
586942 CACTGAATAT
586952 TTGTCCCGAAGGACCACT-A
1 TTGTCCCGAAGGACCACTGA
586971 -TGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTGA
* *
586990 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAGGACCACTGA
* *
587009 -TGTCTCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTGA
*
587028 TTGTCCCGAAAGACCACTGA
1 TTGTCCCGAAGGACCACTGA
587048 T
1 T
587049 AATCCCTCGA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
18 31 0.48
19 2 0.03
20 32 0.49
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (20 bp):
TTGTCCCGAAGGACCACTGA
Found at i:587000 original size:38 final size:38
Alignment explanation
Indices: 586952--587045 Score: 143
Period size: 38 Copynumber: 2.5 Consensus size: 38
586942 CACTGAATAT
586952 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
1 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
* * * *
586990 TTGTTCCGAAGAACCACTATGTCTCGAAGGACCACTGT
1 TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
*
587028 TTGTCCCGAAAGACCACT
1 TTGTCCCGAAGGACCACT
587046 GATAATCCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (38 bp):
TTGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGA
Found at i:591435 original size:11 final size:11
Alignment explanation
Indices: 591419--591462 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 11
591409 AGGCAACCAT
591419 TTTATTATTTA
1 TTTATTATTTA
591430 TTTA-T-TTTA
1 TTTATTATTTA
591439 TTT-TTATTT-
1 TTTATTATTTA
591448 TTTGATTATTTA
1 TTT-ATTATTTA
591460 TTT
1 TTT
591463 TTCTTTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
9 11 0.39
10 4 0.14
11 10 0.36
12 3 0.11
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.77
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:591444 original size:22 final size:21
Alignment explanation
Indices: 591418--591464 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
591408 GAGGCAACCA
591418 TTTTATTATTT-ATTTATTTTAT
1 TTTTATTATTTGA-TTA-TTTAT
*
591440 TTTTATTTTTTGATTATTTAT
1 TTTTATTATTTGATTATTTAT
591461 TTTT
1 TTTT
591465 CTTTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 13 0.57
23 1 0.04
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTATTATTTGATTATTTAT
Found at i:591457 original size:26 final size:27
Alignment explanation
Indices: 591427--591477 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
591417 ATTTTATTAT
591427 TTATTTATTTTAT-TTT-TATTTTTTGA
1 TTATTTATTTT-TCTTTATATTTTTTGA
591453 TTATTTATTTTTCTTTATATTTTTT
1 TTATTTATTTTTCTTTATATTTTTT
591478 AGTTACACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 1 0.04
26 14 0.61
27 8 0.35
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (27 bp):
TTATTTATTTTTCTTTATATTTTTTGA
Found at i:591464 original size:27 final size:26
Alignment explanation
Indices: 591427--591477 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
591417 ATTTTATTAT
*
591427 TTATTTATTTTATTTTTATTTTTTGA
1 TTATTTATTTTATTTATATTTTTTGA
*
591453 TTATTTATTTTTCTTTATATTTTTT
1 TTATTTA-TTTTATTTATATTTTTT
591478 AGTTACACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (26 bp):
TTATTTATTTTATTTATATTTTTTGA
Found at i:593002 original size:13 final size:13
Alignment explanation
Indices: 592986--593020 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
592976 TCATCTCTAC
*
592986 TTTTCTTTCTTTA
1 TTTTCTTTCATTA
*
592999 TTTTTTTTCATTA
1 TTTTCTTTCATTA
593012 TTTTCTTTC
1 TTTTCTTTC
593021 CACAAAGCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCTTTCATTA
Found at i:596372 original size:19 final size:18
Alignment explanation
Indices: 596348--596395 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
596338 TTAGTTATGT
596348 TTTTATATAATATTGTTTA
1 TTTTATATAATATT-TTTA
**
596367 TTTTATATGTTA-TTTTA
1 TTTTATATAATATTTTTA
596384 TTTTAT-TAATAT
1 TTTTATATAATAT
596396 GTTGCCTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 3 0.12
17 10 0.42
18 1 0.04
19 10 0.42
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
TTTTATATAATATTTTTA
Found at i:604289 original size:24 final size:24
Alignment explanation
Indices: 604262--604322 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
604252 TCAGATCATA
* *
604262 TATCAGAACAGAATCCATGTCAGG
1 TATCAGAACAAAATCCAGGTCAGG
* *
604286 TATCAAAACAAAATTCAGGTCAGG
1 TATCAGAACAAAATCCAGGTCAGG
*
604310 TATTAGAACAAAA
1 TATCAGAACAAAA
604323 ATCAGGTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.21
Consensus pattern (24 bp):
TATCAGAACAAAATCCAGGTCAGG
Found at i:604327 original size:24 final size:24
Alignment explanation
Indices: 604280--604329 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
604270 CAGAATCCAT
*
604280 GTCAGGTATCAAAACAAAATTCAG
1 GTCAGGTATCAAAACAAAAATCAG
* *
604304 GTCAGGTATTAGAACAAAAATCAG
1 GTCAGGTATCAAAACAAAAATCAG
604328 GT
1 GT
604330 AAAATATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.22
Consensus pattern (24 bp):
GTCAGGTATCAAAACAAAAATCAG
Found at i:604337 original size:24 final size:24
Alignment explanation
Indices: 604292--604337 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
604282 CAGGTATCAA
* * **
604292 AACAAAATTCAGGTCAGGTATTAG
1 AACAAAAATCAGGTAAAATATTAG
604316 AACAAAAATCAGGTAAAATATT
1 AACAAAAATCAGGTAAAATATT
604338 CATATGATTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.15, T:0.24
Consensus pattern (24 bp):
AACAAAAATCAGGTAAAATATTAG
Found at i:611905 original size:157 final size:157
Alignment explanation
Indices: 611619--611932 Score: 628
Period size: 157 Copynumber: 2.0 Consensus size: 157
611609 ATGTGGGGTT
611619 TTTTGCCATCTTGCTTACTCTGATTATTTTGGTTGTGAACTTGCAGGTGATGGTTCCCCGATGTA
1 TTTTGCCATCTTGCTTACTCTGATTATTTTGGTTGTGAACTTGCAGGTGATGGTTCCCCGATGTA
611684 GGTTGCCTTGGACACAAGTTCCAAGATTCTCTGCACATACCTTGGGTTTCTTCGGTTCTTGATTC
66 GGTTGCCTTGGACACAAGTTCCAAGATTCTCTGCACATACCTTGGGTTTCTTCGGTTCTTGATTC
611749 CAGCGCAGACATTCTTTTCTCCTGTGC
131 CAGCGCAGACATTCTTTTCTCCTGTGC
611776 TTTTGCCATCTTGCTTACTCTGATTATTTTGGTTGTGAACTTGCAGGTGATGGTTCCCCGATGTA
1 TTTTGCCATCTTGCTTACTCTGATTATTTTGGTTGTGAACTTGCAGGTGATGGTTCCCCGATGTA
611841 GGTTGCCTTGGACACAAGTTCCAAGATTCTCTGCACATACCTTGGGTTTCTTCGGTTCTTGATTC
66 GGTTGCCTTGGACACAAGTTCCAAGATTCTCTGCACATACCTTGGGTTTCTTCGGTTCTTGATTC
611906 CAGCGCAGACATTCTTTTCTCCTGTGC
131 CAGCGCAGACATTCTTTTCTCCTGTGC
611933 ATCTTTCTGT
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 157 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.39
Consensus pattern (157 bp):
TTTTGCCATCTTGCTTACTCTGATTATTTTGGTTGTGAACTTGCAGGTGATGGTTCCCCGATGTA
GGTTGCCTTGGACACAAGTTCCAAGATTCTCTGCACATACCTTGGGTTTCTTCGGTTCTTGATTC
CAGCGCAGACATTCTTTTCTCCTGTGC
Found at i:618288 original size:30 final size:31
Alignment explanation
Indices: 618253--618327 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
618243 CATTTTACAT
*
618253 AAATAGCACCTTTTTTTTAAA-TAATAACCA
1 AAATAGCACCTTTTTTTCAAATTAATAACCA
* * *
618283 TAATAGCACC-CTTTTTCAAATTAATTACCA
1 AAATAGCACCTTTTTTTCAAATTAATAACCA
*
618313 AAATAGCATCTTTTT
1 AAATAGCACCTTTTT
618328 GAATTAATTC
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
29 8 0.22
30 25 0.69
31 3 0.08
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (31 bp):
AAATAGCACCTTTTTTTCAAATTAATAACCA
Found at i:618332 original size:28 final size:28
Alignment explanation
Indices: 618265--618364 Score: 92
Period size: 28 Copynumber: 3.5 Consensus size: 28
618255 ATAGCACCTT
* * * * *
618265 TTTTTTAAATAATAACCATAATAGCACCC
1 TTTTTGAATTAATTACCAAAATAGCA-TC
*
618294 TTTTTCAAATTAATTACCAAAATAGCATC
1 TTTTT-GAATTAATTACCAAAATAGCATC
* *
618323 TTTTTGAATTAATTCCCAAAATAACATC
1 TTTTTGAATTAATTACCAAAATAGCATC
* *
618351 ATTTCGAATTAATT
1 TTTTTGAATTAATT
618365 CCCAGAATGT
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
28 32 0.53
29 11 0.18
30 17 0.28
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.39
Consensus pattern (28 bp):
TTTTTGAATTAATTACCAAAATAGCATC
Found at i:618365 original size:28 final size:28
Alignment explanation
Indices: 618296--618368 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
618286 TAGCACCCTT
* * * *
618296 TTTCAAATTAATTACCAAAATAGCATCT
1 TTTCGAATTAATTCCCAAAATAACATCA
*
618324 TTTTGAATTAATTCCCAAAATAACATCA
1 TTTCGAATTAATTCCCAAAATAACATCA
618352 TTTCGAATTAATTCCCA
1 TTTCGAATTAATTCCCA
618369 GAATGTCACC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (28 bp):
TTTCGAATTAATTCCCAAAATAACATCA
Found at i:624667 original size:111 final size:114
Alignment explanation
Indices: 624464--624748 Score: 400
Period size: 111 Copynumber: 2.5 Consensus size: 114
624454 TTCCCGAAAC
**
624464 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACGA-AGCTGAGGAGCCTGCAGTAAT
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCAC-ACAGCAAAGGAGCCTGCAGTAAT
* * * *
624528 AACGTCTCCATCCAGTCGCTTTCATCACTACAATGTGTAGGTTCCTCAG-
65 AACGTCCCCATCCAGTCACTTCCATCACTACAATGTGTAGGTTCCCCAGA
* *
624577 A-AC-CCCACCTGCACACCAGTAAAGACTTACCCTAAGCACACAGCAAAGGAGTCTGCAGTAATA
1 ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCAGTAATA
*
624640 ACTTCCCCATCCAGTCAC-TCCACTCACTACAATGTGTAGGTTCCCCAGAA
66 ACGTCCCCATCCAGTCACTTCCA-TCACTACAATGTGTAGGTTCCCCAG-A
*
624690 CCATACACCCACCTGCACACCAGTAAGGACTTACCCTGAGCACACAGCAAAGGAGCCTG
1 --ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTG
624749 AAATACTTTC
Statistics
Matches: 152, Mismatches: 12, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
110 4 0.03
111 93 0.61
112 2 0.01
113 1 0.01
115 1 0.01
116 2 0.01
117 49 0.32
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.19
Consensus pattern (114 bp):
ATACACCCACCTGCACACCAGTAAGGACTTACCCTAAGCACACAGCAAAGGAGCCTGCAGTAATA
ACGTCCCCATCCAGTCACTTCCATCACTACAATGTGTAGGTTCCCCAGA
Found at i:625710 original size:29 final size:29
Alignment explanation
Indices: 625670--625765 Score: 104
Period size: 29 Copynumber: 3.3 Consensus size: 29
625660 CATTTTACAT
* *
625670 AAATAACACCCTTTTTTAAATAATAACCA
1 AAATAGCACCCTTTTTCAAATAATAACCA
*
625699 TAATAGCACCCTTTTTCAAATTAA-ATACCA
1 AAATAGCACCCTTTTTCAAA-TAATA-ACCA
* * * *
625729 AAATAGCACTCTTTTTGAATTAATTACCA
1 AAATAGCACCCTTTTTCAAATAATAACCA
625758 AAATAGCA
1 AAATAGCA
625766 TCATTTCTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
29 33 0.59
30 23 0.41
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (29 bp):
AAATAGCACCCTTTTTCAAATAATAACCA
Found at i:625903 original size:5 final size:5
Alignment explanation
Indices: 625893--625918 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
625883 ACCGGTCAAC
625893 GGTCG GGTCG GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTCG GGTCG GGTCG G
625919 ACCGGTTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.62, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:626992 original size:3 final size:3
Alignment explanation
Indices: 626959--627048 Score: 76
Period size: 3 Copynumber: 30.0 Consensus size: 3
626949 CGTTTTACTT
* * * * *
626959 TTA TTT TTA TAA TTA TTA TAA TTA -TA TTTA TTA TAA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
* * *
627004 TTA TTA TTA -TA TTT TTA TTA TTA TTA TTAA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
627049 CAAAATAGGC
Statistics
Matches: 67, Mismatches: 16, Indels: 8
0.74 0.18 0.09
Matches are distributed among these distances:
2 4 0.06
3 59 0.88
4 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:629281 original size:24 final size:24
Alignment explanation
Indices: 629235--629281 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
629225 TATATATACT
*
629235 TATTATTTTCATAATATTTATATA
1 TATTATTTTCATAATATTAATATA
** *
629259 TATTATTTTTTTATTATTAATAT
1 TATTATTTTCATAATATTAATAT
629282 CTTTACTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTATTTTCATAATATTAATATA
Found at i:630899 original size:12 final size:12
Alignment explanation
Indices: 630882--630907 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
630872 ACATTCATAT
630882 ATTTACATTTGC
1 ATTTACATTTGC
630894 ATTTACATTTGC
1 ATTTACATTTGC
630906 AT
1 AT
630908 CTTTTATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:634059 original size:11 final size:11
Alignment explanation
Indices: 634030--634078 Score: 82
Period size: 11 Copynumber: 4.5 Consensus size: 11
634020 CTCATTCATC
634030 AGAAAAAAA-A
1 AGAAAAAAAGA
634040 AGAAGAAAAAGA
1 AGAA-AAAAAGA
634052 AGAAAAAAAGA
1 AGAAAAAAAGA
634063 AGAAAAAAAGA
1 AGAAAAAAAGA
634074 AGAAA
1 AGAAA
634079 TTGAATCAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
10 4 0.11
11 28 0.76
12 5 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:639784 original size:112 final size:116
Alignment explanation
Indices: 639548--639935 Score: 423
Period size: 112 Copynumber: 3.3 Consensus size: 116
639538 CAACTTTTCC
* * * * * * *
639548 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTACAT-GACTCTATCACAGAAGGAGAT
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCGAC-ATATCACAGACGTAGAT
* *
639612 AA-ATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAATAATGA
64 AACATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAA-GAGGA
* ** * *
639665 AGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCGA-AT-TCA-TTAC-TCGAT-G
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGACATATCACAGACGTAGATAA
** * *
639725 CATCAACATTTCCAGAGAAAGTTCATAATGCGAAGAACTTATCTGAAGAGGA
66 CATCAACATTTCCAGA-AGTGTTCATAATGAGAAGAACTCATCTGAAGAGGA
* * *
639777 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGACGCTATCACAGACGGAGATA
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGAC-ATATCACAGAC---G-TA
*
639842 GATCAACATCAACATTTTCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-
61 GAT-AACATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAG-AGGA
639899 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
1 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
639936 AATTTAATTC
Statistics
Matches: 224, Mismatches: 32, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
112 63 0.28
113 27 0.12
114 4 0.02
115 4 0.02
116 3 0.01
117 38 0.17
121 4 0.02
122 63 0.28
123 18 0.08
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.28
Consensus pattern (116 bp):
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCGACATATCACAGACGTAGATAA
CATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGA
Found at i:640305 original size:3 final size:3
Alignment explanation
Indices: 640270--640377 Score: 60
Period size: 3 Copynumber: 36.0 Consensus size: 3
640260 CTGTTTTCAT
* * * *
640270 TTA TTT TTA TAA TTA TT- TATA TTA TAA TAA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
640314 TAA TAA TAA TAA TTA TTA TTA TTA TTA TATA TT- TTT TTA TTA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TT-A
* * *
640360 TAA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
640378 CAAAATAGGC
Statistics
Matches: 86, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
2 5 0.06
3 75 0.87
4 6 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:644270 original size:3 final size:3
Alignment explanation
Indices: 644264--644310 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
644254 TGTTAGAAGA
644264 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
644311 ATATTTTAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:644546 original size:19 final size:18
Alignment explanation
Indices: 644500--644546 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
644490 ATAAAAGGAT
644500 AAATCAAAAGGAAATCAAA
1 AAAT-AAAAGGAAATCAAA
*
644519 AATAGAAAAGGAAAATCAAA
1 AA-ATAAAAGG-AAATCAAA
644539 AAATAAAA
1 AAATAAAA
644547 ACAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.72, C:0.06, G:0.11, T:0.11
Consensus pattern (18 bp):
AAATAAAAGGAAATCAAA
Found at i:644547 original size:20 final size:18
Alignment explanation
Indices: 644500--644547 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
644490 ATAAAAGGAT
*
644500 AAATCAAAAGGAAATCAA
1 AAATAAAAAGGAAATCAA
644518 AAATAGAAAAGGAAAATCAAA
1 AAATA-AAAAGG-AAATC-AA
644539 AAATAAAAA
1 AAATAAAAA
644548 CAATAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 4 0.15
19 6 0.23
20 9 0.35
21 7 0.27
ACGTcount: A:0.73, C:0.06, G:0.10, T:0.10
Consensus pattern (18 bp):
AAATAAAAAGGAAATCAA
Found at i:645679 original size:18 final size:18
Alignment explanation
Indices: 645630--645692 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
645620 GGACCTGATC
*
645630 AAATAGATAAAAAATAAA
1 AAATAAATAAAAAATAAA
* *
645648 TATATATTAATAAACAATAAA
1 -A-A-ATAAATAAAAAATAAA
*
645669 CAATAAATAAAAAATAAA
1 AAATAAATAAAAAATAAA
645687 AAATAA
1 AAATAA
645693 TTTTTGAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
18 19 0.54
19 2 0.06
20 1 0.03
21 13 0.37
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (18 bp):
AAATAAATAAAAAATAAA
Found at i:645900 original size:36 final size:35
Alignment explanation
Indices: 645810--646107 Score: 248
Period size: 36 Copynumber: 8.1 Consensus size: 35
645800 CATTTTCAAA
* *
645810 AAAATGTTTTCAAAAAATTATATATATATATATTTTTA
1 AAAATGTTTT--AAAAACTATATATATATATA-TTTTC
* *
645848 AAATATTTTTTAAAAACTATATAGTATATATGTTTTC
1 AAA-ATGTTTTAAAAACTATATA-TATATATATTTTC
645885 AAAATGCTTTT-AAAACTATATA-ATATATATGTCTTC
1 AAAATG-TTTTAAAAACTATATATATATATAT-T-TTC
*
645921 AAAAATGTTTTTTTAGAAAACTATATATTATATATATTTTA
1 -AAAATG---TTTTA-AAAACTATATA-TATATATATTTTC
* *
645962 AAAATGTTTTCAAAACTATATA-ATATATGTTTTC
1 AAAATGTTTTAAAAACTATATATATATATATTTTC
645996 AAACATGTTTTCAAAAACTATATAT-TATATATTTTC
1 AAA-ATGTTTT-AAAAACTATATATATATATATTTTC
* * * *
646032 AAATTATTTAAAAAAAACCATATAT-TATATAATTTTC
1 AAAATGTTT--TAAAAACTATATATATATAT-ATTTTC
* * *
646069 AAAATGATTT-CAAACTATATAATATATACATTTTC
1 AAAATGTTTTAAAAACTATAT-ATATATATATTTTC
646104 AAAA
1 AAAA
646108 CTATATATAT
Statistics
Matches: 216, Mismatches: 24, Indels: 43
0.76 0.08 0.15
Matches are distributed among these distances:
34 28 0.13
35 24 0.11
36 72 0.33
37 44 0.20
38 10 0.05
39 10 0.05
40 6 0.03
41 13 0.06
42 1 0.00
43 8 0.04
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (35 bp):
AAAATGTTTTAAAAACTATATATATATATATTTTC
Found at i:645954 original size:77 final size:72
Alignment explanation
Indices: 645810--646034 Score: 242
Period size: 77 Copynumber: 3.0 Consensus size: 72
645800 CATTTTCAAA
* * ** * *
645810 AAAATGTTTTCAAAAAATTATATATATATATAT-TTTTAAAATATTTTTTAAAAACTATATAGTA
1 AAAATGTTTTC--AAAACTATATA-ATATATGTCTTCAAAAATGTTTTTTAAAAACTATATATTA
645874 TATATGTTTTC
63 TATAT-TTTTC
645885 AAAATGCTTTT-AAAACTATATAATATATATGTCTTCAAAAATGTTTTTTTAGAAAACTATATAT
1 AAAATG-TTTTCAAAACTATAT-A-ATATATGTCTTCAAAAATG-TTTTTTA-AAAACTATATAT
*
645949 TATATATATTTTA
61 TATATAT-TTTTC
* * *
645962 AAAATGTTTTCAAAACTATATAATATATGTTTTCAAACATG-TTTTCAAAAACTATATATTATAT
1 AAAATGTTTTCAAAACTATATAATATATGTCTTCAAAAATGTTTTTTAAAAACTATATATTATAT
646026 A-TTTTC
66 ATTTTTC
646032 AAA
1 AAA
646035 TTATTTAAAA
Statistics
Matches: 132, Mismatches: 12, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
70 7 0.05
72 18 0.14
73 14 0.11
74 9 0.07
75 30 0.23
76 16 0.12
77 38 0.29
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (72 bp):
AAAATGTTTTCAAAACTATATAATATATGTCTTCAAAAATGTTTTTTAAAAACTATATATTATAT
ATTTTTC
Found at i:646117 original size:24 final size:25
Alignment explanation
Indices: 646075--646131 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
646065 TTTCAAAATG
646075 ATTTC-AAACTATATAATATATACAT
1 ATTTCAAAACTATATAATAT-TACAT
*
646100 -TTTCAAAACTATAT-ATATTATAT
1 ATTTCAAAACTATATAATATTACAT
646123 ATTTCAAAA
1 ATTTCAAAA
646132 TCATTTGCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.14
24 16 0.55
25 9 0.31
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTCAAAACTATATAATATTACAT
Found at i:646155 original size:2 final size:2
Alignment explanation
Indices: 646144--646178 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
646134 ATTTGCAAAC
646144 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
646179 AATGAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:647194 original size:2 final size:2
Alignment explanation
Indices: 647187--647223 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
647177 TAAACTAATG
647187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
647224 TTTACATAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:648511 original size:8 final size:8
Alignment explanation
Indices: 648500--648526 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
648490 GTCAAAAGAA
648500 TAAAATTT
1 TAAAATTT
648508 TAAAATTT
1 TAAAATTT
648516 TAAAATTT
1 TAAAATTT
648524 TAA
1 TAA
648527 GATAAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TAAAATTT
Found at i:651340 original size:19 final size:20
Alignment explanation
Indices: 651291--651342 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
651281 TTAATGTACT
*
651291 ATGTTGGAAATTAATGTTAGA
1 ATGTT-GAAATTGATGTTAGA
*
651312 GTGTTGAAATTGATGTTAGA
1 ATGTTGAAATTGATGTTAGA
651332 ATG-TGAAATTG
1 ATGTTGAAATTG
651343 GGTCATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 8 0.29
20 16 0.57
21 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (20 bp):
ATGTTGAAATTGATGTTAGA
Found at i:651447 original size:29 final size:31
Alignment explanation
Indices: 651392--651455 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
651382 ACTTAGGTCT
*
651392 CTAAACTTTTCTAAATTCTATATTTTGATCA
1 CTAAACTTTTCAAAATTCTATATTTTGATCA
*
651423 CTAAAC-TTTCAAAATT-TATATTTTGGTCA
1 CTAAACTTTTCAAAATTCTATATTTTGATCA
651452 CTAA
1 CTAA
651456 CCAAAAGACT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 16 0.52
30 9 0.29
31 6 0.19
ACGTcount: A:0.34, C:0.16, G:0.05, T:0.45
Consensus pattern (31 bp):
CTAAACTTTTCAAAATTCTATATTTTGATCA
Found at i:656584 original size:2 final size:2
Alignment explanation
Indices: 656577--656620 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
656567 TGATTAAAAG
656577 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
656618 TA T
1 TA T
656621 TATTGTGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:657690 original size:18 final size:17
Alignment explanation
Indices: 657667--657715 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
657657 CCAATAATCT
*
657667 ATTTATATGTAAATAATA
1 ATTTATATATAAATAA-A
*
657685 ATTTATA-AAAAATAAA
1 ATTTATATATAAATAAA
*
657701 ATTTATATTTAAATA
1 ATTTATATATAAATA
657716 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 8 0.31
17 11 0.42
18 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
ATTTATATATAAATAAA
Found at i:659244 original size:28 final size:28
Alignment explanation
Indices: 659200--659264 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
659190 TACTCAAACT
659200 TTTAGTTTTTTTCAAAATCATACCTAATG
1 TTTAG-TTTTTTCAAAATCATACCTAATG
659229 TTTAGTTTTTTCAAAATCATACCTAATG
1 TTTAGTTTTTTCAAAATCATACCTAATG
659257 TTTAGTTT
1 TTTAGTTT
659265 CTGTTTCGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 31 0.86
29 5 0.14
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (28 bp):
TTTAGTTTTTTCAAAATCATACCTAATG
Found at i:659614 original size:5 final size:5
Alignment explanation
Indices: 659604--659632 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
659594 TTAAGCATGA
659604 ATATT ATATT ATATT ATATT ATA-T ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT
659633 TGTTTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:665880 original size:75 final size:75
Alignment explanation
Indices: 665757--665976 Score: 377
Period size: 75 Copynumber: 2.9 Consensus size: 75
665747 CCATGTGAGA
* *
665757 CGTCACCCTCCATATGAGACTTTACACATAGCATCAAGAAAATAGCATAGAAAAGATTTTGCTTT
1 CGTCACCCTTCATATGAGACTTTACACATAGCATCAAGAAAATAGCATAGAAAAGATTTTACTTT
665822 TCCATATAGT
66 TCCATATAGT
* *
665832 CGTCACCCTTCATATGAGACTTTACACATGGCATCAAGAAAATAGCATAGAAAAGATTATACTTT
1 CGTCACCCTTCATATGAGACTTTACACATAGCATCAAGAAAATAGCATAGAAAAGATTTTACTTT
665897 TCCATATAGT
66 TCCATATAGT
* * *
665907 TGTCACCCTTCGTATGAGACTTTACACATAGCATCAAGAAAATAGCATAGAAAAGATTTTTCTTT
1 CGTCACCCTTCATATGAGACTTTACACATAGCATCAAGAAAATAGCATAGAAAAGATTTTACTTT
665972 TCCAT
66 TCCAT
665977 GTAGCGCTCT
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 136 1.00
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (75 bp):
CGTCACCCTTCATATGAGACTTTACACATAGCATCAAGAAAATAGCATAGAAAAGATTTTACTTT
TCCATATAGT
Found at i:670412 original size:30 final size:30
Alignment explanation
Indices: 670378--670435 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
670368 AGAATTCACT
*
670378 TGCAGCC-TCCGTGAACTTGGACTTTCAATC
1 TGCAGCCGT-CGTGAACTTGAACTTTCAATC
670408 TGCAGCCGTCGTGAACTTGAACTTTCAA
1 TGCAGCCGTCGTGAACTTGAACTTTCAA
670436 CAATCTCCCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (30 bp):
TGCAGCCGTCGTGAACTTGAACTTTCAATC
Found at i:672635 original size:30 final size:30
Alignment explanation
Indices: 672601--672658 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
672591 AGAATTCACT
672601 TGCAGCCACCGTGAACTTGGACTTTCAATC
1 TGCAGCCACCGTGAACTTGGACTTTCAATC
*
672631 TGCAGCCATCGTGAACTTGGACTTTCAA
1 TGCAGCCACCGTGAACTTGGACTTTCAA
672659 CAAATATAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (30 bp):
TGCAGCCACCGTGAACTTGGACTTTCAATC
Found at i:673035 original size:74 final size:76
Alignment explanation
Indices: 672903--673059 Score: 273
Period size: 74 Copynumber: 2.1 Consensus size: 76
672893 TCATGAATCC
*
672903 TCCATGTGAGACGTCACCCTCCATATGAGACTTTACACATATCATCAAGAAAATAACATAGAAAA
1 TCCATGTGAGACGTCACCCTCCATATGAGACTTTACACATAGCATCAAGAAAATAACATAGAAAA
672968 -ATTTTGCTTT
66 GATTTTGCTTT
* *
672978 TCCATGT-AGTCGTCACCCTCCGTATGAGACTTTACACATAGCATCAAGAAAATAACATAGAAAA
1 TCCATGTGAGACGTCACCCTCCATATGAGACTTTACACATAGCATCAAGAAAATAACATAGAAAA
673042 GATTTTGCTTT
66 GATTTTGCTTT
673053 TCCATGT
1 TCCATGT
673060 TGCGCTCTTA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
74 54 0.69
75 24 0.31
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (76 bp):
TCCATGTGAGACGTCACCCTCCATATGAGACTTTACACATAGCATCAAGAAAATAACATAGAAAA
GATTTTGCTTT
Found at i:677803 original size:65 final size:65
Alignment explanation
Indices: 677734--677939 Score: 339
Period size: 65 Copynumber: 3.2 Consensus size: 65
677724 GCAATAGTCG
* *
677734 AAGTTCGCGTTGCAATTTATTCCAAATTCGTTTCGATAGTCCAAGTTCGCGTTGCGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCC
677799 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCC
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCC
* * *
677864 AAGTT--CGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCATTGCGA--TAGTCG
1 AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCC
677925 AAGTTCGCGTTGCGA
1 AAGTTCGCGTTGCGA
677940 ATCTGGAAAC
Statistics
Matches: 134, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
61 9 0.07
63 57 0.43
65 68 0.51
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (65 bp):
AAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCC
Found at i:677832 original size:107 final size:104
Alignment explanation
Indices: 677695--677919 Score: 308
Period size: 107 Copynumber: 2.1 Consensus size: 104
677685 GATTTACATA
* *
677695 TTCGCATTGCGATTTATTCCAAGTTCGTTGCAATAGTCGAAGTTCGCGTTGCAATTTATTCCAAA
1 TTCGCATTGCGATTTATTCCAAATTCGTTGCAATAGTCCAAGTTCGCGTTGCAATTTATTCCAAA
* * *
677760 TTCGTTTCGA-TAGTCCAAGTTCGCGTTGCGATTTATTCCAAG
66 TTCGTTGCGATTAGTCCAAATT--CGTTGCGA--TAGTCCAAG
* * * *
677802 TTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAG
1 TTCGCATTGCGATTTATTCCAAATTCGTTGCAATAGTCCAAGTTCGCGTTGCAATTTATTCCAAA
*
677867 TTCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAG
66 TTCGTTGCGA-TTAGTCCAAATTCGTTGCGATAGTCCAAG
677907 TTCGCATTGCGAT
1 TTCGCATTGCGAT
677920 AGTCGAAGTT
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
105 20 0.19
107 76 0.72
109 9 0.09
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.37
Consensus pattern (104 bp):
TTCGCATTGCGATTTATTCCAAATTCGTTGCAATAGTCCAAGTTCGCGTTGCAATTTATTCCAAA
TTCGTTGCGATTAGTCCAAATTCGTTGCGATAGTCCAAG
Found at i:677916 original size:21 final size:21
Alignment explanation
Indices: 677695--677939 Score: 186
Period size: 21 Copynumber: 11.5 Consensus size: 21
677685 GATTTACATA
677695 TTCGCATTGCGATTTATTCCAAG
1 TTCGC-TTGCGA-TTATTCCAAG
* * *
677718 TTCG-TTGC-AATAGTCGAAG
1 TTCGCTTGCGATTATTCCAAG
* *
677737 TTCGCGTTGCAATTTATTCCAAA
1 TTCGC-TTGCGA-TTATTCCAAG
* *
677760 TTCG-TTTCGA-TAGTCCAAG
1 TTCGCTTGCGATTATTCCAAG
677779 TTCGCGTTGCGATTTATTCCAAG
1 TTCGC-TTGCGA-TTATTCCAAG
*
677802 TTCGCGTTGCGATTTATTCCAAA
1 TTCGC-TTGCGA-TTATTCCAAG
*
677825 TTCG-TTGCGA-TAGTCCAAG
1 TTCGCTTGCGATTATTCCAAG
677844 TTCGCGTTGCGATTTATTCCAAG
1 TTCGC-TTGCGA-TTATTCCAAG
*
677867 TTCG-TTGCGATTTATTCCAAA
1 TTCGCTTGCGA-TTATTCCAAG
*
677888 TTCG-TTGCGA-TAGTCCAAG
1 TTCGCTTGCGATTATTCCAAG
* *
677907 TTCGCATTGCGA-TAGTCGAAG
1 TTCGC-TTGCGATTATTCCAAG
677928 TTCGCGTTGCGA
1 TTCGC-TTGCGA
677940 ATCTGGAAAC
Statistics
Matches: 186, Mismatches: 22, Indels: 30
0.78 0.09 0.13
Matches are distributed among these distances:
19 44 0.24
20 1 0.01
21 80 0.43
22 1 0.01
23 60 0.32
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (21 bp):
TTCGCTTGCGATTATTCCAAG
Found at i:678438 original size:29 final size:30
Alignment explanation
Indices: 678406--678472 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
678396 AAAACAATTT
678406 GACCACCGAACT-TTCAATTGAATCAATCA
1 GACCACCGAACTATTCAATTGAATCAATCA
* * **
678435 GACCACCCAACTATTTAATTGGTTCAATCA
1 GACCACCGAACTATTCAATTGAATCAATCA
*
678465 AACCACCG
1 GACCACCG
678473 TCCGCTAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
29 11 0.35
30 20 0.65
ACGTcount: A:0.36, C:0.30, G:0.10, T:0.24
Consensus pattern (30 bp):
GACCACCGAACTATTCAATTGAATCAATCA
Found at i:687891 original size:14 final size:14
Alignment explanation
Indices: 687857--687885 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
687847 TAATGTAAGG
687857 GTCTAAATGTACTT
1 GTCTAAATGTACTT
687871 GTCTAAATGTACTT
1 GTCTAAATGTACTT
687885 G
1 G
687886 ATTAAAAAAT
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:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (14 bp):
GTCTAAATGTACTT
Found at i:687986 original size:14 final size:15
Alignment explanation
Indices: 687967--687995 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
687957 TTTGTTCGAC
687967 AAAAAT-AAATAATA
1 AAAAATAAAATAATA
687981 AAAAATAAAATAATA
1 AAAAATAAAATAATA
687996 TTAATGTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAAATAAAATAATA
Done.