Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008225.1 Hibiscus syriacus cultivar Beakdansim tig00110858_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: 1890193
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:262076 original size:23 final size:23
Alignment explanation
Indices: 262046--262102 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
262036 TAAAGATCTC
*
262046 AGAACCAATTTTAGAAGGGTTCA
1 AGAACCAATTCTAGAAGGGTTCA
262069 AGAACCAATTCTAGAAGGGTTCA
1 AGAACCAATTCTAGAAGGGTTCA
*
262092 AGAACAAATTC
1 AGAACCAATTC
262103 AGATCAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (23 bp):
AGAACCAATTCTAGAAGGGTTCA
Found at i:262595 original size:85 final size:84
Alignment explanation
Indices: 262335--262895 Score: 748
Period size: 85 Copynumber: 6.8 Consensus size: 84
262325 TTTTTAAACA
* * * * *
262335 ATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGATTA
262400 CACTCAGCTTCGAGGGCAC
66 CACTCAGCTTCGAGGGCAC
* * **
262419 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGATTA
262481 CACTCAGCTTCGAGGGCAC
66 CACTCAGCTTCGAGGGCAC
262500 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGATT
262565 ACACTCAGCTTCGAGGGCAC
65 ACACTCAGCTTCGAGGGCAC
262585 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGATT
*
262650 ACACTCAGCTTCGAGGGCAT
65 ACACTCAGCTTCGAGGGCAC
* ** *
262670 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG---CCAAAGACCCCCGAGTTCGACTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGATTA
* * *
262732 CGCTCAGC-TCCAGGGCAT
66 CACTCAGCTTCGAGGGCAC
* * * * * *
262750 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGATT
* * *
262815 ACGCTCAGC-TCAACGGCAC
65 ACACTCAGCTTCGAGGGCAC
* * * *
262834 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CTAAAGACCTTCTAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGATTA
262896 TATTCAACTT
Statistics
Matches: 430, Mismatches: 39, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
80 63 0.15
81 104 0.24
84 101 0.23
85 162 0.38
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (84 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGATTA
CACTCAGCTTCGAGGGCAC
Found at i:262608 original size:166 final size:166
Alignment explanation
Indices: 262335--262895 Score: 735
Period size: 166 Copynumber: 3.4 Consensus size: 166
262325 TTTTTAAACA
* * * * *
262335 ATCATTTGCAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGATTA
* *
262400 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-CCAAAG
66 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCCAAAG
**
262464 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
131 ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
262500 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGATT
262565 ACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC
65 ACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTG-C--CC
*
262630 AAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCAT
127 AAAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* ** *
262670 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG---CCAAAGACCCCCGAGTTCGACTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGATTA
* * * * * *
262732 CGCTCAGC-TCCAGGGCATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAA
66 CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC--C-A
* * * * *
262796 AAGACCTTTGAGTTCGACTACGCTCAGC-TCAACGGCAC
128 AAGACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * *
262834 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---CTAAAGACCTTCTAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGATTA
262896 TATTCAACTT
Statistics
Matches: 356, Mismatches: 32, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
162 1 0.00
164 65 0.18
165 106 0.30
166 107 0.30
170 77 0.22
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.25
Consensus pattern (166 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGATTA
CACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCCAAAG
ACCTTCGAGTTCGATTACACTCAGCTTCGAGGGCAC
Found at i:263580 original size:72 final size:68
Alignment explanation
Indices: 263499--263698 Score: 220
Period size: 74 Copynumber: 2.8 Consensus size: 68
263489 TCCATATTTT
* *
263499 TTTATATATTATATAATTTTGAAAACATTTTGAAAATATATGATATATAGTTTTTAAAACATTTT
1 TTTATATATTATATAGTTTT-AAAAC-TTTTGAAAATATAT-ATATATAATTTTTAAAACATTTT
263564 AAAAACA
63 AAAAA-A
* *
263571 TTTATATATTATATAGTTTTAAAACTTTTTTGAAAAGAAATATAATATATAATTTTCAAAACATT
1 TTTATATATTATATAGTTTTAAAAC--TTTTG-AAA-ATATAT-ATATATAATTTTTAAAACATT
**
263636 TTTGAAAA
61 TTAAAAAA
* *
263644 TATATATATTATATAGTTTTTAAAACGTTTGAAAATTAATATATATATAATTTTT
1 TTTATATATTATATAG-TTTTAAAACTTTTGAAAA-T-ATATATATATAATTTTT
263699 TTGAAAAACA
Statistics
Matches: 110, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
70 1 0.01
71 20 0.18
72 32 0.29
73 19 0.17
74 38 0.35
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.47
Consensus pattern (68 bp):
TTTATATATTATATAGTTTTAAAACTTTTGAAAATATATATATATAATTTTTAAAACATTTTAAA
AAA
Found at i:263639 original size:37 final size:36
Alignment explanation
Indices: 263501--263750 Score: 185
Period size: 37 Copynumber: 6.9 Consensus size: 36
263491 CATATTTTTT
* *
263501 TATATATTATATAATTTTGAAAACATTTTG-AAA-A
1 TATATAATATATAATTTTTAAAACATTTTGAAAATA
* * * *
263535 TATATGATATATAGTTTTTAAAACATTTTAAAAACA
1 TATATAATATATAATTTTTAAAACATTTTGAAAATA
* * * *
263571 TTTAT-ATATTATATAGTTTTAAAACTTTTTTGAAAAGA
1 TATATAATA-TATA-ATTTTTAAAAC-ATTTTGAAAATA
* *
263609 AATATAATATATAATTTTCAAAACATTTTTGAAAATA
1 TATATAATATATAATTTTTAAAACA-TTTTGAAAATA
* * *
263646 TATATATTATATAGTTTTTAAAAC-GTTTGAAAAT-
1 TATATAATATATAATTTTTAAAACATTTTGAAAATA
**
263680 TA-ATATATATATAATTTTTTTGAAAAACA-TTTGAAAGCA
1 TATATA-ATATATAA--TTTTT--AAAACATTTTGAAAATA
* *
263719 TATATAATATGTAA-TTTT-AAACATTTTTAAAA
1 TATATAATATATAATTTTTAAAACATTTTGAAAA
263751 ATTATATGGT
Statistics
Matches: 171, Mismatches: 29, Indels: 32
0.74 0.12 0.14
Matches are distributed among these distances:
33 8 0.05
34 39 0.23
35 15 0.09
36 18 0.11
37 48 0.28
38 28 0.16
39 12 0.07
40 3 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
TATATAATATATAATTTTTAAAACATTTTGAAAATA
Found at i:263776 original size:32 final size:33
Alignment explanation
Indices: 263737--263860 Score: 99
Period size: 32 Copynumber: 3.7 Consensus size: 33
263727 ATGTAATTTT
263737 AAACATTTTTAAAAAT-TATATGGTTTTTAAAA
1 AAACATTTTTAAAAATATATATGGTTTTTAAAA
* *
263769 AAACATTTTTGAAAAT-TATATAGTTTTTTAAAA
1 AAACATTTTTAAAAATATATAT-GGTTTTTAAAA
***** *
263802 TGTTTTTTTTAAATTATATATATATAGTTTTTAAAA
1 AAACATTTTTAAA--A-ATATATATGGTTTTTAAAA
* *
263838 GAAACAGTTTTAAAAATGTATAT
1 -AAACATTTTTAAAAATATATAT
263861 ATATAGTTTT
Statistics
Matches: 69, Mismatches: 17, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
32 20 0.29
33 17 0.25
34 7 0.10
35 2 0.03
36 11 0.16
37 12 0.17
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (33 bp):
AAACATTTTTAAAAATATATATGGTTTTTAAAA
Found at i:263884 original size:3 final size:3
Alignment explanation
Indices: 263876--263941 Score: 68
Period size: 3 Copynumber: 22.7 Consensus size: 3
263866 GTTTTTATAT
*
263876 TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTTA TTA TTA TT- TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
263920 TTA TCA CTTA TT- TTA TT- TTA TT
1 TTA TTA -TTA TTA TTA TTA TTA TT
263942 TTTTCCCGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
2 8 0.15
3 41 0.76
4 5 0.09
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:263945 original size:12 final size:13
Alignment explanation
Indices: 263873--263945 Score: 62
Period size: 13 Copynumber: 5.6 Consensus size: 13
263863 ATAGTTTTTA
*
263873 TATTTATTATTAT
1 TATTTTTTATTAT
263886 TATTATTATTATTAT
1 TATT-TT-TTATTAT
* *
263901 CATTATTTATTAT
1 TATTTTTTATTAT
*
263914 TATTTTTTATCACT
1 TATTTTTTATTA-T
263928 TA--TTTTATT-T
1 TATTTTTTATTAT
263938 TATTTTTT
1 TATTTTTT
263946 CCCGTTTCAG
Statistics
Matches: 48, Mismatches: 7, Indels: 11
0.73 0.11 0.17
Matches are distributed among these distances:
10 3 0.06
12 10 0.21
13 20 0.42
14 5 0.10
15 10 0.21
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTTTTTATTAT
Found at i:264146 original size:16 final size:15
Alignment explanation
Indices: 264125--264154 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
264115 CCGGCCGAAA
264125 ATCCCGGGACTGACCC
1 ATCCCGGGA-TGACCC
264141 ATCCCGGGATGACC
1 ATCCCGGGATGACC
264155 GGCCTCAACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (15 bp):
ATCCCGGGATGACCC
Found at i:273020 original size:23 final size:19
Alignment explanation
Indices: 272990--273044 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 19
272980 TTGTGCATAA
272990 GGTATCGATACCTCCCTTGAATT
1 GGTATCGATACC-CCC-TG-A-T
273013 GGTATCGATACCCCCTGAT
1 GGTATCGATACCCCCTGAT
*
273032 GGTACCGATACCC
1 GGTATCGATACCC
273045 TCTTCGGGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.42
20 1 0.03
21 2 0.06
22 3 0.10
23 12 0.39
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (19 bp):
GGTATCGATACCCCCTGAT
Found at i:275541 original size:19 final size:20
Alignment explanation
Indices: 275513--275564 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
275503 ATGCTCGAAA
* *
275513 GGTACTGATACCCCCCATA-
1 GGTACCGATACCCCCCAGAT
* *
275532 GGTATCGATACCCCTCAGAT
1 GGTACCGATACCCCCCAGAT
275552 GGTACCGATACCC
1 GGTACCGATACCC
275565 TAAGGCATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (20 bp):
GGTACCGATACCCCCCAGAT
Found at i:278595 original size:21 final size:21
Alignment explanation
Indices: 278569--278613 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
278559 GATTTCTGGG
* *
278569 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
278590 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
278611 CAA
1 CAA
278614 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:279575 original size:31 final size:31
Alignment explanation
Indices: 279537--279661 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
279527 AGGGTCGAGG
279537 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
279568 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
279599 GTTTACCTATGTCCTTCGGGACATATGTACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
279630 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
279661 G
1 G
279662 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:283043 original size:132 final size:132
Alignment explanation
Indices: 282884--283147 Score: 492
Period size: 132 Copynumber: 2.0 Consensus size: 132
282874 ACTAAACAAT
*
282884 GCCATTAATGTCCAGTGTTTCATTTCAGACTGATTTTGCTTCTTGATTATAGAAAGTGGATTCAT
1 GCCATTAATGTCCAGTGTTTCATTTCAGACTGAATTTGCTTCTTGATTATAGAAAGTGGATTCAT
* *
282949 TGGTTGTTACACATAGCAACCAAGTTAACACAAGCTGCAAAATTTTATTAAAGCTAAGATCTAAA
66 TGGTTGTTACACATACCAACCAAGTTAACACAAGCTGCAAAATTTTATTAAAACTAAGATCTAAA
283014 AC
131 AC
283016 GCCATTAATGTCCAGTGTTTCATTTCAGACTGAATTTGCTTCTTGATTATAGAAAGTGGATTCAT
1 GCCATTAATGTCCAGTGTTTCATTTCAGACTGAATTTGCTTCTTGATTATAGAAAGTGGATTCAT
*
283081 TGGTTGTTACACATACCATCCAAGTTAACACAAGCTGCAAAATTTTATTAAAACTAAGATCTAAA
66 TGGTTGTTACACATACCAACCAAGTTAACACAAGCTGCAAAATTTTATTAAAACTAAGATCTAAA
283146 AC
131 AC
283148 TTTTAGTTTT
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 128 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (132 bp):
GCCATTAATGTCCAGTGTTTCATTTCAGACTGAATTTGCTTCTTGATTATAGAAAGTGGATTCAT
TGGTTGTTACACATACCAACCAAGTTAACACAAGCTGCAAAATTTTATTAAAACTAAGATCTAAA
AC
Found at i:284239 original size:2 final size:2
Alignment explanation
Indices: 284234--284297 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
284224 TTTTTTTTAT
284234 TA TA TA TA TA TA 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 TA TA TA
284276 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
284298 GCCGTCTCCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:284615 original size:16 final size:16
Alignment explanation
Indices: 284591--284621 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
284581 ACCGACTATA
284591 ATATAATGAATTATTT
1 ATATAATGAATTATTT
*
284607 ATATTATGAATTATT
1 ATATAATGAATTATT
284622 AGATTTTGTG
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:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATAATGAATTATTT
Found at i:284639 original size:22 final size:22
Alignment explanation
Indices: 284614--284655 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
284604 TTTATATTAT
* *
284614 GAATTATTAGATTTTGTGTTTC
1 GAATTATTAAATTTTATGTTTC
*
284636 GAATTTTTAAATTTTATGTT
1 GAATTATTAAATTTTATGTT
284656 CGGATATTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.57
Consensus pattern (22 bp):
GAATTATTAAATTTTATGTTTC
Found at i:286044 original size:29 final size:29
Alignment explanation
Indices: 286012--286082 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
286002 TTTCATTTAA
*
286012 GTACTTAAAGTATTTTTCGGTCAAAATAG
1 GTACTTAAAGTATTTTTCGATCAAAATAG
* * *
286041 GTACCTAAAGTATTTTTTGATCAAAGTAG
1 GTACTTAAAGTATTTTTCGATCAAAATAG
286070 GTA-TATAAAGTAT
1 GTACT-TAAAGTAT
286083 CAATTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (29 bp):
GTACTTAAAGTATTTTTCGATCAAAATAG
Found at i:290320 original size:22 final size:21
Alignment explanation
Indices: 290295--290340 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
290285 TCATAATTAT
290295 TAAAAAAAATTAAATAAAAATA
1 TAAAAAAAATTAAATAAAAA-A
* *
290317 TAAAAAATATTTAATAAAAAA
1 TAAAAAAAATTAAATAAAAAA
290338 TAA
1 TAA
290341 TTTTTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAAAAAATTAAATAAAAAA
Found at i:292127 original size:24 final size:23
Alignment explanation
Indices: 292082--292131 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
292072 TATTGAATGC
*
292082 TAAAAAAAGAAAAAAATGAATAA
1 TAAAAAAAGAAAAAAATAAATAA
* *
292105 TAAAACAAATAAATAAATAAATAA
1 TAAAA-AAAGAAAAAAATAAATAA
292129 TAA
1 TAA
292132 TGTATTATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (23 bp):
TAAAAAAAGAAAAAAATAAATAA
Found at i:292906 original size:3 final size:3
Alignment explanation
Indices: 292898--292957 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
292888 ATATATAAAT
* * * *
292898 TAA TAA TAA TAA TAC TAA AAA TAA TAA TAA GTAA TTA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
* *
292944 TAG TAA TAA CAA TA
1 TAA TAA TAA TAA TA
292958 TAAAAAAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:292907 original size:21 final size:21
Alignment explanation
Indices: 292881--292963 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 21
292871 GGGCCTAAAA
* *
292881 AATAATTATA-TATAAATTAAT
1 AATAATAATACTA-AAAATAAT
292902 AATAATAATACTAAAAATAAT
1 AATAATAATACTAAAAATAAT
* *
292923 AATAAGTAATTATTATAATAATAGT
1 AATAA-TAA-TACTA-AA-AATAAT
*
292948 AATAACAATA-TAAAAA
1 AATAATAATACTAAAAA
292964 AAATTTAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
20 2 0.04
21 23 0.44
22 7 0.13
23 6 0.12
24 4 0.08
25 10 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
AATAATAATACTAAAAATAAT
Found at i:304744 original size:23 final size:23
Alignment explanation
Indices: 304718--304778 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
304708 CTCATATAAA
*
304718 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
304741 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
304764 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
304779 TATAAAAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:304965 original size:103 final size:103
Alignment explanation
Indices: 304794--305114 Score: 590
Period size: 103 Copynumber: 3.1 Consensus size: 103
304784 AAATGTCCAT
* *
304794 AAGGACCACATATCATTCCTTAAGAATCATATACATAT-ACTAGAGATCAAGTATGTGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGTGTCTCACC
304858 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
65 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
304897 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
304962 GACTTCACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
305000 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
305065 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
305103 AATGACCACATA
1 AAGGACCACATA
305115 GACCCTCGAC
Statistics
Matches: 212, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
103 209 0.99
104 3 0.01
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:306314 original size:21 final size:21
Alignment explanation
Indices: 306290--306334 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
306280 TTTTGTTCGT
* *
306290 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
306311 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
306332 TTG
1 TTG
306335 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:316205 original size:21 final size:20
Alignment explanation
Indices: 316119--316276 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
316109 AAATGACCAA
**
316119 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
316138 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
316158 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
316178 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
316199 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
316220 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
316240 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
316261 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
316277 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:316269 original size:20 final size:20
Alignment explanation
Indices: 316244--316436 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
316234 GATTTTCCAG
* ** *
316244 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
316264 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
316284 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
316304 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
316324 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
316344 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
316364 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
316384 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
316405 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
316425 AATCGCAACGCG
1 AATCGCAACGCG
316437 ATTTTTAAAG
Statistics
Matches: 151, Mismatches: 17, Indels: 10
0.85 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 131 0.87
21 19 0.13
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:316853 original size:33 final size:33
Alignment explanation
Indices: 316814--316884 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
316804 TTCACTTAGA
316814 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
316847 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
316880 TTTCA
1 TTTCA
316885 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:316990 original size:21 final size:20
Alignment explanation
Indices: 316964--317070 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
316954 TGCAGAAGAG
316964 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
316985 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
317005 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
317027 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
317041 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
317060 TCGCAACGAGA
1 TCGCAACGAGA
317071 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:317044 original size:14 final size:14
Alignment explanation
Indices: 317025--317081 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
317015 GAAAAATGAA
317025 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
317039 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
317058 AATCGCAACGAGAG
1 AATCGCAACGAGAG
317072 AATCGCAACG
1 AATCGCAACG
317082 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:317056 original size:33 final size:33
Alignment explanation
Indices: 317018--317097 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
317008 GCAACGAGAA
317018 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
317051 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
317084 AAACCAAAATCGCA
1 AAATGAAAATCGCA
317098 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:317115 original size:19 final size:19
Alignment explanation
Indices: 317093--317220 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
317083 GAAACCAAAA
*
317093 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
317112 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
317126 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
317145 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
317159 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
317179 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
317199 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
317219 TC
1 TC
317221 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:317134 original size:14 final size:14
Alignment explanation
Indices: 317115--317171 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
317105 TTTCATTTCG
317115 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
317129 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
317148 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
317162 CGTTGCGATT
1 CGTTGCGATT
317172 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:317140 original size:33 final size:33
Alignment explanation
Indices: 317098--317220 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
317088 CAAAATCGCA
317098 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
317131 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
317164 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
317205 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
317221 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:317182 original size:21 final size:21
Alignment explanation
Indices: 317156--317220 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
317146 CGCGTTGCGA
317156 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
317177 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
317197 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
317218 TTC
1 TTC
317221 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:319060 original size:93 final size:93
Alignment explanation
Indices: 318901--319216 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
318891 TAGATTGCTT
* *
318901 AGTAAATTTATTTGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
318966 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
318994 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
319059 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
319087 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
319152 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
319180 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
319217 AATACCCTGA
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 221 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:319351 original size:14 final size:14
Alignment explanation
Indices: 319332--319388 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
319322 CGAAACTTAA
319332 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
319346 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
319365 AATCGCAACGACAG
1 AATCGCAACGAGAG
319379 AATCGCAACG
1 AATCGCAACG
319389 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:319370 original size:19 final size:18
Alignment explanation
Indices: 319346--319437 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
319336 GCAACGAGAG
319346 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
319365 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
319379 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
319398 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
319412 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
319431 AATCGCA
1 AATCGCA
319438 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:319372 original size:33 final size:33
Alignment explanation
Indices: 319314--319437 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
319304 TAGTTTACTT
* * *
319314 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
319348 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
319381 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
319414 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
319438 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:319414 original size:14 final size:14
Alignment explanation
Indices: 319363--319421 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
319353 ACGCGAAATG
319363 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
319377 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
319396 AAAATCGCAACGAC
1 AAAATCGCAACGAC
319410 AAAATCGCAACG
1 AAAATCGCAACG
319422 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:319455 original size:19 final size:19
Alignment explanation
Indices: 319433--319605 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
319423 GAAACCAAAA
*
319433 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
319452 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
319466 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
319485 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
319501 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
319518 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
319537 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
319556 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
319575 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
319595 TCGTGTTGCGA
1 TCGCGTTGCGA
319606 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 17 0.13
16 8 0.06
17 8 0.06
19 81 0.64
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:319474 original size:14 final size:14
Alignment explanation
Indices: 319455--319511 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
319445 TTTCATTTCG
319455 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
319469 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
319486 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
319502 CGTTGCGATT
1 CGTTGCGATT
319512 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:319563 original size:38 final size:38
Alignment explanation
Indices: 319433--319605 Score: 168
Period size: 33 Copynumber: 4.8 Consensus size: 38
319423 GAAACCAAAA
*
319433 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
319468 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
319501 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
319537 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
319575 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
319606 AAGTAAACTA
Statistics
Matches: 115, Mismatches: 15, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 52 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:321547 original size:14 final size:14
Alignment explanation
Indices: 321528--321563 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
321518 ATTGTTTAAT
321528 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
321542 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
321556 TGATTTGT
1 TGATTTGT
321564 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:321678 original size:19 final size:19
Alignment explanation
Indices: 321654--321741 Score: 123
Period size: 19 Copynumber: 4.8 Consensus size: 19
321644 GCATTATGTT
321654 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
321673 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAATGC
*
321690 G--A-GAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC
321706 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAATGC
321725 GGAAATGAAAATCGCAA
1 -GAAATGAAAATCGCAA
321742 CGAGAGAATC
Statistics
Matches: 61, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 29 0.48
20 16 0.26
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAATGC
Found at i:321745 original size:53 final size:52
Alignment explanation
Indices: 321654--321760 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 52
321644 GCATTATGTT
321654 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
321706 GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC
1 GAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGC
321759 GA
1 GA
321761 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 19 0.35
53 35 0.65
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (52 bp):
GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
Found at i:321815 original size:33 final size:33
Alignment explanation
Indices: 321756--321934 Score: 166
Period size: 33 Copynumber: 5.2 Consensus size: 33
321746 AGAATCGCAA
*
321756 TGCGATTTTCATTTCCGCATTACGATTCTCTCGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
321790 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
321828 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
321861 TGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
321895 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
321928 TACGATT
1 TGCGATT
321935 GTAATTTCCG
Statistics
Matches: 117, Mismatches: 16, Indels: 25
0.74 0.10 0.16
Matches are distributed among these distances:
31 4 0.03
32 6 0.05
33 45 0.38
34 31 0.26
35 5 0.04
36 4 0.03
37 2 0.02
38 8 0.07
39 3 0.03
40 9 0.08
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:321843 original size:52 final size:53
Alignment explanation
Indices: 321750--321920 Score: 308
Period size: 53 Copynumber: 3.2 Consensus size: 53
321740 AACGAGAGAA
* *
321750 TCGCAATGCGATTTTCATTTCCGCATTACGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
321803 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
321855 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
321908 TCGCATTGCGATT
1 TCGCATTGCGATT
321921 CTCTCGTTAC
Statistics
Matches: 114, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
52 51 0.45
53 63 0.55
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:321942 original size:33 final size:33
Alignment explanation
Indices: 321871--321942 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
321861 TGCGATTTTC
** * *
321871 ATTTCCGCATTGCGATTCTCTCGTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTCTCGTTACGATTGTA
321905 ATTTCGCATTGCGATTCTCTCGTTACGATTGTA
1 ATTTCGCATTGCGATTCTCTCGTTACGATTGTA
321938 ATTTC
1 ATTTC
321943 CGTGTTGCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.88
34 4 0.12
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTACGATTGTA
Found at i:323618 original size:12 final size:12
Alignment explanation
Indices: 323601--323625 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
323591 TCTTCGGGGA
323601 CTTTTTCTTCTT
1 CTTTTTCTTCTT
323613 CTTTTTCTTCTT
1 CTTTTTCTTCTT
323625 C
1 C
323626 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:323833 original size:24 final size:24
Alignment explanation
Indices: 323799--323845 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
323789 TCTGAACATC
323799 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
323823 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
323846 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:324534 original size:20 final size:20
Alignment explanation
Indices: 324506--324694 Score: 200
Period size: 20 Copynumber: 9.4 Consensus size: 20
324496 AAATTTCAGT
* * *
324506 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
324526 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
324546 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
324566 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
324586 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
324606 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
324626 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
324646 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
324666 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
324686 GTTGCGATT
1 GTTGCGATT
324695 CTTTAAAATC
Statistics
Matches: 147, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 146 0.99
21 1 0.01
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:324747 original size:21 final size:20
Alignment explanation
Indices: 324662--324759 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
324652 ATTTATGTGT
* *
324662 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
324682 TCGCGTTGCGATTCTTTAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
324703 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
324724 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
324745 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
324760 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:324755 original size:42 final size:43
Alignment explanation
Indices: 324662--324760 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
324652 ATTTATGTGT
* *
324662 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTTAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
324703 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
324745 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
324761 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:325913 original size:8 final size:7
Alignment explanation
Indices: 325900--325950 Score: 57
Period size: 8 Copynumber: 6.6 Consensus size: 7
325890 AACGATTTTC
325900 TATAATCA
1 TATAAT-A
325908 TATAATA
1 TATAATA
325915 TATATATA
1 TATA-ATA
325923 TATATATA
1 TATA-ATA
325931 TATATATA
1 TATA-ATA
325939 TATATATA
1 TATA-ATA
325947 TATA
1 TATA
325951 TCTTCATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.12
8 37 0.88
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (7 bp):
TATAATA
Found at i:325919 original size:2 final size:2
Alignment explanation
Indices: 325907--325951 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
325897 TTCTATAATC
325907 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
325948 AT AT
1 AT AT
325952 CTTCATATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:327395 original size:14 final size:14
Alignment explanation
Indices: 327376--327409 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
327366 AATACCTCGT
*
327376 AAAATATTTTTATG
1 AAAATATTCTTATG
327390 AAAATATTCTTATG
1 AAAATATTCTTATG
327404 AAAATA
1 AAAATA
327410 AAATATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (14 bp):
AAAATATTCTTATG
Found at i:335280 original size:7 final size:7
Alignment explanation
Indices: 335270--335335 Score: 60
Period size: 7 Copynumber: 8.9 Consensus size: 7
335260 TATTAATTAT
335270 ATATATA
1 ATATATA
* *
335277 ATATTTT
1 ATATATA
*
335284 ATATATT
1 ATATATA
*
335291 TTATATTA
1 ATATA-TA
335299 ATTATATATA
1 A-TATA--TA
335309 ATATATA
1 ATATATA
335316 ATATATA
1 ATATATA
335323 ATATATA
1 ATATATA
335330 ATATAT
1 ATATAT
335336 TTTTAATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
7 37 0.76
8 1 0.02
9 8 0.16
10 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
ATATATA
Found at i:335303 original size:9 final size:7
Alignment explanation
Indices: 335302--335335 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
335292 TATATTAATT
335302 ATATATA
1 ATATATA
335309 ATATATA
1 ATATATA
335316 ATATATA
1 ATATATA
335323 ATATATA
1 ATATATA
335330 ATATAT
1 ATATAT
335336 TTTTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATA
Found at i:335321 original size:32 final size:34
Alignment explanation
Indices: 335233--335308 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
335223 CGCCTCGATA
* * *
335233 TATATATATAATATTTTTTTTATTTTTTATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
335267 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATTTTATATATTTTATATTAAT
335301 TATATATA
1 TATATATA
335309 ATATATAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (34 bp):
TATATATATAATATTTTATATATTTTATATTAAT
Found at i:335321 original size:34 final size:34
Alignment explanation
Indices: 335233--335322 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
335223 CGCCTCGATA
** * * *
335233 TATATATATAATATTTTTTTTATTTTTTATTAAT
1 TATATATATAATATAATATATATTTTATATTAAT
**
335267 TATATATATAATATTTTATATATTTTATATTAAT
1 TATATATATAATATAATATATATTTTATATTAAT
335301 TATATATA-ATATATAATATATA
1 TATATATATA-ATATAATATATA
335323 ATATATAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
33 1 0.02
34 49 0.98
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (34 bp):
TATATATATAATATAATATATATTTTATATTAAT
Found at i:340201 original size:2 final size:2
Alignment explanation
Indices: 340196--340220 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
340186 ACAGACATTC
340196 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
340221 GTGTAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:345712 original size:21 final size:21
Alignment explanation
Indices: 345670--345712 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
345660 TTTCTGGGTT
* * *
345670 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
345691 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
345712 A
1 A
345713 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:345772 original size:66 final size:67
Alignment explanation
Indices: 345692--345842 Score: 225
Period size: 66 Copynumber: 2.3 Consensus size: 67
345682 ACCCATTCAA
*
345692 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAA-GACTAGAGGGGAATCGATACCCCC
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATG-CTAGAGGGGAATCGATACCCCC
345756 -GG
65 AGG
* * *
345758 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
345823 GGG
66 -GG
*
345826 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
345843 ATGAGAGAAA
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
66 58 0.75
67 1 0.01
68 18 0.23
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.17
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:346600 original size:149 final size:149
Alignment explanation
Indices: 346330--346623 Score: 561
Period size: 149 Copynumber: 2.0 Consensus size: 149
346320 GTCTGCGCGG
*
346330 TTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACATACTTGATCC
1 TTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCC
*
346395 ATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCACT
66 ATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGAACT
346460 ACGGTGCAATTCTACACGA
131 ACGGTGCAATTCTACACGA
*
346479 TTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGGAAGACACATACTTGATCC
1 TTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCC
346544 ATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGAACT
66 ATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGAACT
346609 ACGGTGCAATTCTAC
131 ACGGTGCAATTCTAC
346624 GGGGCACTTC
Statistics
Matches: 142, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 142 1.00
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (149 bp):
TTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCC
ATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGAACT
ACGGTGCAATTCTACACGA
Found at i:352738 original size:21 final size:21
Alignment explanation
Indices: 352696--352738 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
352686 TTTCTGGGTT
* * *
352696 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
352717 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
352738 A
1 A
352739 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:352799 original size:67 final size:68
Alignment explanation
Indices: 352718--352870 Score: 236
Period size: 67 Copynumber: 2.2 Consensus size: 68
352708 ACCCATTCAA
*
352718 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAAGGCTAGAGGGGAATCGATACCCCC-
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAAGGCTAGAGGGGAATCGATACCCCCA
352782 GGG
66 GGG
* * * *
352785 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAAGGCTAGAGGGGAATCGATACCCCCA
352850 GGGG
66 -GGG
*
352854 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
352871 ATGAGAGAAA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
67 59 0.76
69 19 0.24
ACGTcount: A:0.27, C:0.28, G:0.28, T:0.16
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAAGGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:353619 original size:149 final size:149
Alignment explanation
Indices: 353349--353651 Score: 579
Period size: 149 Copynumber: 2.0 Consensus size: 149
353339 GGGTAGAGGG
* *
353349 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACCTGTGTGAAGTCTTGAAAGACACAT
1 TCTACACGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
353414 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
353479 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
*
353498 TCTACACGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGGAAGACACAT
1 TCTACACGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
353563 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
353628 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
353647 TCTAC
1 TCTAC
353652 GGGGCACTTC
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACACGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:353675 original size:23 final size:23
Alignment explanation
Indices: 353631--353675 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
353621 ATCATTATAT
*
353631 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
353654 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
353676 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:357839 original size:356 final size:356
Alignment explanation
Indices: 357185--357895 Score: 1287
Period size: 356 Copynumber: 2.0 Consensus size: 356
357175 TATAGACGTT
357185 TGTCAACTCTTCTGCTTAAGGAAGGCATCACACACCGTGTCACGTGTCCACACACGTCAGAACAG
1 TGTCAACTCTTCTGCTTAAGGAAGGCATCACACACCGTGTCACGTGTCCACACACGTCAGAACAG
*
357250 AACGGAGTGGTGGAACGCAAGCATCGTCACATTATCGAACTTGCACTTGTGCTTCTTGCACAAAC
66 AACGGAGTGGTGGAACGCAAGCATCATCACATTATCGAACTTGCACTTGTGCTTCTTGCACAAAC
357315 ATCTATGCCTATTCGTTTTTGGTCTTATGCAGTGGTTACTGCAATTCACCTAATTAACAGGTTAC
131 ATCTATGCCTATTCGTTTTTGGTCTTATGCAGTGGTTACTGCAATTCACCTAATTAACAGGTTAC
*
357380 CAACCAAAATATTGCAAGGAATGTCGCCATTTGAGAATTTATTTTGCAAGACACCCGAGTATGAG
196 CAACCAAAATATTGCAAGGAATGTCGCCATTTGAGAAGTTATTTTGCAAGACACCCGAGTATGAG
*
357445 GCATTAAAGGTGTTTGGCTGTCGATGCTTTCAACACTTGAGACCCTTCTTGAAGCATAAACTTCA
261 GCATTAAAGGTGTTTGGCTGTCGATGCTTTCAACACTTGAGACCATTCTTGAAGCATAAACTTCA
357510 GTTTCGATCACATCCATGCGTTTTTCTTGGC
326 GTTTCGATCACATCCATGCGTTTTTCTTGGC
* * * *
357541 TGTCAACTCTTCTTCTTAAGGAATGCATCACACACTGTGTCACGTGTCTACACACGTCAGAACAG
1 TGTCAACTCTTCTGCTTAAGGAAGGCATCACACACCGTGTCACGTGTCCACACACGTCAGAACAG
* * *
357606 AACGGAGTGGTGGAACGTAAGCATCATCACATTATCGAACTTGCACTTGTGCTTCTTGCATAAGC
66 AACGGAGTGGTGGAACGCAAGCATCATCACATTATCGAACTTGCACTTGTGCTTCTTGCACAAAC
* *
357671 ATCTATGCCTATTCGTTTTTGGTCTTATGTAGTGGTTACTGCAATTCACCTAATTAATAGGTTAC
131 ATCTATGCCTATTCGTTTTTGGTCTTATGCAGTGGTTACTGCAATTCACCTAATTAACAGGTTAC
357736 CAACCAAAATATTGCAAGGAATGTCGCCATTTGAGAAGTTATTTTGCAAGACACCCGAGTATGAG
196 CAACCAAAATATTGCAAGGAATGTCGCCATTTGAGAAGTTATTTTGCAAGACACCCGAGTATGAG
*
357801 GCATTAAAGGTGTTTGGCTGTCGATGCTTTCCACACTTGAGACCATTCTTGAAGCATAAACTTCA
261 GCATTAAAGGTGTTTGGCTGTCGATGCTTTCAACACTTGAGACCATTCTTGAAGCATAAACTTCA
* *
357866 GTTTTGATCACATTCATGCGTTTTTCTTGG
326 GTTTCGATCACATCCATGCGTTTTTCTTGG
357896 ATACAGCCCC
Statistics
Matches: 340, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
356 340 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (356 bp):
TGTCAACTCTTCTGCTTAAGGAAGGCATCACACACCGTGTCACGTGTCCACACACGTCAGAACAG
AACGGAGTGGTGGAACGCAAGCATCATCACATTATCGAACTTGCACTTGTGCTTCTTGCACAAAC
ATCTATGCCTATTCGTTTTTGGTCTTATGCAGTGGTTACTGCAATTCACCTAATTAACAGGTTAC
CAACCAAAATATTGCAAGGAATGTCGCCATTTGAGAAGTTATTTTGCAAGACACCCGAGTATGAG
GCATTAAAGGTGTTTGGCTGTCGATGCTTTCAACACTTGAGACCATTCTTGAAGCATAAACTTCA
GTTTCGATCACATCCATGCGTTTTTCTTGGC
Found at i:362820 original size:24 final size:23
Alignment explanation
Indices: 362757--362821 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
362747 TTCAACTAAG
*
362757 AAAACTCATAAACATAGTTAGAGT
1 AAAACT-AAAAACATAGTTAGAGT
*
362781 AAAAGTAAAAACATAGTTAGA-T
1 AAAACTAAAAACATAGTTAGAGT
*
362803 CACAAACTAAAAATATAGT
1 -A-AAACTAAAAACATAGT
362822 CAAAAACATA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.03
23 15 0.43
24 19 0.54
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (23 bp):
AAAACTAAAAACATAGTTAGAGT
Found at i:366106 original size:12 final size:12
Alignment explanation
Indices: 366091--366117 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
366081 TCGTACGATT
366091 TTTCGTTATAAA
1 TTTCGTTATAAA
366103 TTTCGTTATAAA
1 TTTCGTTATAAA
366115 TTT
1 TTT
366118 TTTATTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (12 bp):
TTTCGTTATAAA
Found at i:366413 original size:17 final size:18
Alignment explanation
Indices: 366391--366429 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
366381 TTTTTGCAGA
366391 TAAAAT-ATTAAATAAAG
1 TAAAATGATTAAATAAAG
* *
366408 TAAAATGCTTAAATAAAT
1 TAAAATGATTAAATAAAG
366426 TAAA
1 TAAA
366430 TACATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (18 bp):
TAAAATGATTAAATAAAG
Found at i:367113 original size:30 final size:31
Alignment explanation
Indices: 367073--367131 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
367063 AACTGTAAAA
*
367073 AAATAAATAC-AAATACTATCGGTGCTGATT
1 AAATAAATACAAAAAACTATCGGTGCTGATT
* *
367103 AAATATATACATAAAAACTATGGGTGCTG
1 AAATAAATACA-AAAAACTATCGGTGCTG
367132 TGCTGGTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 9 0.38
32 15 0.62
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (31 bp):
AAATAAATACAAAAAACTATCGGTGCTGATT
Found at i:372134 original size:14 final size:16
Alignment explanation
Indices: 372115--372149 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
372105 GTTTTTAAAG
372115 TTAATT-AA-AATATT
1 TTAATTAAATAATATT
372129 TTAATTAAATAATATT
1 TTAATTAAATAATATT
372145 TTAAT
1 TTAAT
372150 CCTTAATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 2 0.11
16 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATTAAATAATATT
Found at i:372902 original size:13 final size:14
Alignment explanation
Indices: 372884--372912 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
372874 GGATATTATT
372884 TTTTCTAAAA-ATA
1 TTTTCTAAAACATA
372897 TTTTCTAAAACATA
1 TTTTCTAAAACATA
372911 TT
1 TT
372913 CAATAGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTTCTAAAACATA
Found at i:373336 original size:15 final size:15
Alignment explanation
Indices: 373316--373364 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
373306 AAATCTTCAC
*
373316 AAATATATCTATTTT
1 AAATATATATATTTT
*
373331 AAATATATATTTTTT
1 AAATATATATATTTT
373346 AAAT-TA-ATATTATT
1 AAATATATATATT-TT
373360 AAATA
1 AAATA
373365 GTTTTTAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 4 0.14
14 8 0.28
15 17 0.59
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
AAATATATATATTTT
Found at i:394719 original size:23 final size:23
Alignment explanation
Indices: 394674--394739 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 23
394664 TAATTATTAA
* *
394674 AATATTTAAAAT-ATATATTTATT
1 AATATTTATAATAATATA-ATATT
394697 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* * *
394720 -ATTTTTTTAATATTATAATA
1 AATATTTATAATAATATAATA
394740 AAATAATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 17 0.46
23 15 0.41
24 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:394722 original size:26 final size:23
Alignment explanation
Indices: 394657--394714 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
394647 CATTTTCATC
*
394657 AAAATAT-TAATTATTAAAATATTT
1 AAAATATATATTTATT--AATATTT
394681 AAAATATATATTTATTAATATTT
1 AAAATATATATTTATTAATATTT
*
394704 ATAATAATATA
1 AAAAT-ATATA
394715 ATATTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 11 0.37
24 12 0.40
25 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAAATATATATTTATTAATATTT
Found at i:394824 original size:29 final size:29
Alignment explanation
Indices: 394784--394867 Score: 88
Period size: 26 Copynumber: 3.0 Consensus size: 29
394774 TATATTTTTA
394784 TTTT-TAT-TTTAATAAATATATAATATT
1 TTTTATATATTTAATAAATATATAATATT
*
394811 TTTTATATATTTAAT-AAT-GA-AATATT
1 TTTTATATATTTAATAAATATATAATATT
*
394837 ATTTATATATTTAATATTAATATAATAATAT
1 TTTTATATATTTAATA--AATAT-ATAATAT
394868 AATAATATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
26 20 0.43
27 5 0.11
28 6 0.13
29 9 0.20
31 1 0.02
32 5 0.11
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
TTTTATATATTTAATAAATATATAATATT
Found at i:394904 original size:23 final size:23
Alignment explanation
Indices: 394878--394922 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
394868 AATAATATTT
394878 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
394901 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
394923 ATATAACACG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:395064 original size:19 final size:22
Alignment explanation
Indices: 395021--395070 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 22
395011 TAAAATTATA
395021 AAAATAATATTTAATAATAAAT
1 AAAATAATATTTAATAATAAAT
*
395043 AAAATAAT-TTTAAT-AT-ATT
1 AAAATAATATTTAATAATAAAT
395062 AAAATAATA
1 AAAATAATA
395071 ATATTAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 10 0.38
20 2 0.08
21 6 0.23
22 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATAATATTTAATAATAAAT
Found at i:395071 original size:22 final size:20
Alignment explanation
Indices: 395014--395077 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 20
395004 TTTTTAATAA
395014 AATTATAAAAATAATATTTAAT
1 AATTA-AAAAATAAT-TTTAAT
*
395036 AATAAATAAAATAATTTTAAT
1 AATTAA-AAAATAATTTTAAT
*
395057 ATATTAAAATAATAATATTAA
1 A-ATTAAAA-AATAATTTTAA
395078 GTTTTATGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 10 0.28
22 26 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTAAAAAATAATTTTAAT
Found at i:395259 original size:15 final size:14
Alignment explanation
Indices: 395239--395272 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
395229 AAATGTAATT
*
395239 CATTTTACGGAAAA
1 CATTTTTCGGAAAA
395253 CATTTTTCGGAAAA
1 CATTTTTCGGAAAA
*
395267 CGTTTT
1 CATTTT
395273 CCAGAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (14 bp):
CATTTTTCGGAAAA
Found at i:395306 original size:20 final size:20
Alignment explanation
Indices: 395269--395307 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
395259 TCGGAAAACG
**
395269 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
395289 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
395308 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:395362 original size:14 final size:15
Alignment explanation
Indices: 395281--395370 Score: 103
Period size: 15 Copynumber: 6.1 Consensus size: 15
395271 TTCCAGAAAT
*
395281 GTAATTCATTTTCCA
1 GTAATTCAATTTCCA
*
395296 G-AATTCAAATTCCA
1 GTAATTCAATTTCCA
*
395310 GTAATTCATTTTTCCA
1 GTAATTCA-ATTTCCA
395326 GTAATTCAATTTCCA
1 GTAATTCAATTTCCA
*
395341 GTAATTCAA-TTCTA
1 GTAATTCAATTTCCA
* *
395355 GTAGTTCAAATTCCA
1 GTAATTCAATTTCCA
395370 G
1 G
395371 AAAACCAATT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
14 24 0.38
15 27 0.42
16 13 0.20
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (15 bp):
GTAATTCAATTTCCA
Found at i:395368 original size:29 final size:30
Alignment explanation
Indices: 395281--395370 Score: 112
Period size: 29 Copynumber: 3.0 Consensus size: 30
395271 TTCCAGAAAT
*
395281 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATATTCCAGTAATTCAAATTCCA
* *
395310 GTAATTCATTTTTCCAGTAATTCAATTTCCA
1 GTAATTCA-TATTCCAGTAATTCAAATTCCA
* *
395341 GTAATTCA-ATTCTAGTAGTTCAAATTCCA
1 GTAATTCATATTCCAGTAATTCAAATTCCA
395370 G
1 G
395371 AAAACCAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
29 26 0.48
30 8 0.15
31 20 0.37
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (30 bp):
GTAATTCATATTCCAGTAATTCAAATTCCA
Found at i:399503 original size:20 final size:20
Alignment explanation
Indices: 399480--399532 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
399470 AATCAGTATG
399480 AGTCAACCCAAACCGAAT-TA
1 AGTCAACCCAAACC-AATCTA
* *
399500 AGTCAACTCAGACCAATCTA
1 AGTCAACCCAAACCAATCTA
*
399520 AGTCAACCAAAAC
1 AGTCAACCCAAAC
399533 TGGTCTGACC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.45, C:0.30, G:0.09, T:0.15
Consensus pattern (20 bp):
AGTCAACCCAAACCAATCTA
Found at i:402287 original size:2 final size:2
Alignment explanation
Indices: 402280--402313 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
402270 TCTATTTTTA
402280 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
402314 GATTTTCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:403396 original size:36 final size:35
Alignment explanation
Indices: 403356--403484 Score: 102
Period size: 35 Copynumber: 3.6 Consensus size: 35
403346 GTTCAGTTCT
*
403356 GATCAAGCTGACAATTCCTTATATTGGTTCAATATC
1 GATC-AGCTGATAATTCCTTATATTGGTTCAATATC
* *
403392 GATCAGTTGGTAATTCC-T-TATTGCATGTTCAATTAT-
1 GATCAGCTGATAATTCCTTATATTG---GTTCAA-TATC
* * * ** *
403428 GATCAAACTGGTAATTCCTTATATAGGTTCAGCACC
1 GATC-AGCTGATAATTCCTTATATTGGTTCAATATC
403464 GATCAGCTGATAATTCCTTAT
1 GATCAGCTGATAATTCCTTAT
403485 GGACCTAAGG
Statistics
Matches: 74, Mismatches: 11, Indels: 17
0.73 0.11 0.17
Matches are distributed among these distances:
33 5 0.07
34 1 0.01
35 26 0.35
36 23 0.31
37 14 0.19
38 1 0.01
39 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (35 bp):
GATCAGCTGATAATTCCTTATATTGGTTCAATATC
Found at i:403447 original size:72 final size:72
Alignment explanation
Indices: 403341--403484 Score: 180
Period size: 72 Copynumber: 2.0 Consensus size: 72
403331 ATGAAGTCTC
* * * * * * * *
403341 TGCAGGTTCAGTTCTGATCAAGCTGACAATTCCTTATATTGGTTCAATATCGATCAGTTGGTAAT
1 TGCAGGTTCAATTATGATCAAACTGACAATTCCTTATATAGGTTCAACACCGATCAGCTGATAAT
403406 TCCTTAT
66 TCCTTAT
* ** *
403413 TGCATGTTCAATTATGATCAAACTGGTAATTCCTTATATAGGTTCAGCACCGATCAGCTGATAAT
1 TGCAGGTTCAATTATGATCAAACTGACAATTCCTTATATAGGTTCAACACCGATCAGCTGATAAT
403478 TCCTTAT
66 TCCTTAT
403485 GGACCTAAGG
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 60 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (72 bp):
TGCAGGTTCAATTATGATCAAACTGACAATTCCTTATATAGGTTCAACACCGATCAGCTGATAAT
TCCTTAT
Found at i:405292 original size:24 final size:21
Alignment explanation
Indices: 405222--405299 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 21
405212 ATTGAAAATT
*
405222 TTATAAATAACTA-AAAATATA
1 TTATAAATAA-TATATAATATA
*
405243 TTCATAAATAATATATAATAGAA
1 TT-ATAAATAATATATAATA-TA
405266 TTATAAATGAATATAATAATTATA
1 TTATAAAT-AATAT-ATAA-TATA
405290 TTATAAATAA
1 TTATAAATAA
405300 AATTAACATA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
21 4 0.08
22 19 0.40
23 10 0.21
24 13 0.27
25 2 0.04
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (21 bp):
TTATAAATAATATATAATATA
Found at i:405600 original size:32 final size:32
Alignment explanation
Indices: 405555--405620 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
405545 CACTCTGTTT
*
405555 ATTTAATATCTTATCCTATGATTATTATCACA
1 ATTTAATAACTTATCCTATGATTATTATCACA
*
405587 ATTTAATAACTTATTCTATGATTATTATCACA
1 ATTTAATAACTTATCCTATGATTATTATCACA
405619 AT
1 AT
405621 ATGATTATCG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.47
Consensus pattern (32 bp):
ATTTAATAACTTATCCTATGATTATTATCACA
Found at i:406206 original size:60 final size:61
Alignment explanation
Indices: 406140--406264 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 61
406130 GTGTTTAATG
* * ** *
406140 TCATCCCCAAACTATGACTATCATTATAAATTAGTCATTAAAC-TTTTGAACATTTCATTT
1 TCATCCCCAAACCATGACCATCATTATAAATTAGTCACCAAACTTTTTGAACATTTCAATT
* * * * *
406200 TCATCCCTAAACCATGACCCTCTTTATAACTTAGTCCCCAAACTTTTTGAACATTTCAATT
1 TCATCCCCAAACCATGACCATCATTATAAATTAGTCACCAAACTTTTTGAACATTTCAATT
406261 TCAT
1 TCAT
406265 GACAAATTCA
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
60 34 0.63
61 20 0.37
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (61 bp):
TCATCCCCAAACCATGACCATCATTATAAATTAGTCACCAAACTTTTTGAACATTTCAATT
Found at i:406582 original size:60 final size:60
Alignment explanation
Indices: 406395--406585 Score: 197
Period size: 60 Copynumber: 3.2 Consensus size: 60
406385 GTATATATGT
* * * ** *
406395 ATAGTTTG-GAATGAAATTGGAATGTTCAGAAAGTTTGGGGACTAATTTTGAATGAAGGTC
1 ATAGTTTGAGGATGAAATTAGAATGTTCA-AAAGTTTAGGGACTAATTTAAAATGATGGTC
* * * * * **
406455 ATAGTTTGGGGATGGAATGA-AATGTTCAAAAGTTTAAGGACTAATTTATAATGATAATC
1 ATAGTTTGAGGATGAAATTAGAATGTTCAAAAGTTTAGGGACTAATTTAAAATGATGGTC
* * * *
406514 ATAGTTTGAGGATGAAATTAGAATATTTAAAAGTTTAGGGACTAACTTAAAATGATGGGC
1 ATAGTTTGAGGATGAAATTAGAATGTTCAAAAGTTTAGGGACTAATTTAAAATGATGGTC
*
406574 ATACTTTGAGGA
1 ATAGTTTGAGGA
406586 CATATGATGC
Statistics
Matches: 106, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
59 41 0.39
60 58 0.55
61 7 0.07
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (60 bp):
ATAGTTTGAGGATGAAATTAGAATGTTCAAAAGTTTAGGGACTAATTTAAAATGATGGTC
Found at i:412406 original size:13 final size:13
Alignment explanation
Indices: 412388--412417 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
412378 TAAAATATAC
412388 AAATATAAAAAAT
1 AAATATAAAAAAT
*
412401 AAATATAAAAATT
1 AAATATAAAAAAT
412414 AAAT
1 AAAT
412418 TACTAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AAATATAAAAAAT
Found at i:412729 original size:20 final size:20
Alignment explanation
Indices: 412704--412752 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
412694 TGGCCACCAA
412704 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
412724 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
*
412744 CCCTCCACT
1 GCCTCCACT
412753 CACAGTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.45, G:0.12, T:0.33
Consensus pattern (20 bp):
GCCTCCACTAGTCCTTGTCT
Found at i:412965 original size:20 final size:19
Alignment explanation
Indices: 412931--412971 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
412921 TATTTTCTAT
412931 TTTTTATTACAATTTCTTTA
1 TTTTTATTACAATTT-TTTA
**
412951 TTTTTATTATTATTTTTTA
1 TTTTTATTACAATTTTTTA
412970 TT
1 TT
412972 GATTTTCTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTATTACAATTTTTTA
Found at i:413047 original size:25 final size:25
Alignment explanation
Indices: 412987--413039 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
412977 TCTGTTTTGA
*
412987 ATTTTTAATAG-TTTTTATTTATTT
1 ATTTTCAATAGTTTTTTATTTATTT
413011 ATTTTCAATAGTTTTTTA-TTA-TT
1 ATTTTCAATAGTTTTTTATTTATTT
413034 ATTTTC
1 ATTTTC
413040 GAAATAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 13 0.48
25 6 0.22
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (25 bp):
ATTTTCAATAGTTTTTTATTTATTT
Found at i:413793 original size:15 final size:14
Alignment explanation
Indices: 413781--413811 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
413771 CGAATTTTCC
*
413781 TTTATTCTTTTTTA
1 TTTACTCTTTTTTA
413795 TTTACTCTTTTTTA
1 TTTACTCTTTTTTA
413809 TTT
1 TTT
413812 CGATTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTACTCTTTTTTA
Found at i:414742 original size:16 final size:16
Alignment explanation
Indices: 414721--414760 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
414711 TTTTTTGTAT
*
414721 TTTTTTTCTTTCG-TTA
1 TTTTTTTATTT-GTTTA
414737 TTTTTTTATTTGTTTA
1 TTTTTTTATTTGTTTA
414753 TTTTTTTA
1 TTTTTTTA
414761 CTAACTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.80
Consensus pattern (16 bp):
TTTTTTTATTTGTTTA
Found at i:417353 original size:39 final size:39
Alignment explanation
Indices: 417299--417378 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
417289 CACCCGGAGT
* *
417299 ATTACCCGAGGACTCATCCGCTACTAAAGGGAAAGTTGC
1 ATTACCCGAGGACTCATCCGCTACCAAAGGGAAAGCTGC
*
417338 ATTACCCG-GTGACTCATCCTCTACCAAAGGGAAAGCTGC
1 ATTACCCGAG-GACTCATCCGCTACCAAAGGGAAAGCTGC
417377 AT
1 AT
417379 CTACTGTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (39 bp):
ATTACCCGAGGACTCATCCGCTACCAAAGGGAAAGCTGC
Found at i:425116 original size:80 final size:80
Alignment explanation
Indices: 425017--425291 Score: 185
Period size: 80 Copynumber: 3.3 Consensus size: 80
425007 ACAACATTGG
*
425017 ATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
1 ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
425082 TTTCATTCAGAGCCA
66 TTTCATTCAGAGCCA
* * ** *
425097 ATTTCAACTTCAC-GACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCAC-GACGAA
1 ATTTCAACTTCACAG-CGAAGGATA-T---C-C---A-ATTCA-AAGCTCAACTCCACAG-CGAA
* * *
425160 --GGATAT--C-GTGCTCA--CA-AACAACA
54 GGGGCT-TCCCAGT-TTCATTCAGAGC--CA
* *
425183 TTGGATTTCAACTTTACAGCGAAGGATATCCAATTTAAAGCTCAACTCCACAGCGAAGGGGCTTC
1 ----ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTC
425248 CCAGTTTCATTCAGAGCCA
62 CCAGTTTCATTCAGAGCCA
425267 ATTTCAACTTCAC-GACGAAGGATAT
1 ATTTCAACTTCACAG-CGAAGGATAT
425292 TGGACTCAAA
Statistics
Matches: 144, Mismatches: 20, Indels: 62
0.64 0.09 0.27
Matches are distributed among these distances:
79 2 0.01
80 57 0.40
81 6 0.04
82 4 0.03
83 4 0.03
84 7 0.05
85 6 0.04
86 7 0.05
87 4 0.03
88 4 0.03
89 7 0.05
90 35 0.24
91 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.24
Consensus pattern (80 bp):
ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
TTTCATTCAGAGCCA
Found at i:425524 original size:170 final size:170
Alignment explanation
Indices: 424920--425509 Score: 1117
Period size: 170 Copynumber: 3.5 Consensus size: 170
424910 GGTTCTAGCT
* *
424920 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
424985 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
66 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
425050 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
131 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
425090 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
*
425155 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTTA
66 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
425220 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
131 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
*
425260 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACATCCACGATTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
425325 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
66 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
*
425390 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAATTTCATTC
131 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
* *
425430 AGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGATTTTAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
425495 ACGAAGGATATCGTG
66 ACGAAGGATATCGTG
425510 TCCACCAGCA
Statistics
Matches: 411, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 411 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (170 bp):
AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
Found at i:426156 original size:20 final size:20
Alignment explanation
Indices: 426131--426179 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
426121 TGGCCACCAA
426131 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
426151 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
*
426171 CCCTCCACT
1 GCCTCCACT
426180 CACAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.45, G:0.12, T:0.33
Consensus pattern (20 bp):
GCCTCCACTAGTCCTTGTCT
Found at i:426474 original size:25 final size:25
Alignment explanation
Indices: 426414--426466 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
426404 TCTGTTTTGA
*
426414 ATTTTTAATAG-TTTTTATTTATTT
1 ATTTTCAATAGTTTTTTATTTATTT
426438 ATTTTCAATAGTTTTTTA-TTA-TT
1 ATTTTCAATAGTTTTTTATTTATTT
426461 ATTTTC
1 ATTTTC
426467 GAAATAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 13 0.48
25 6 0.22
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (25 bp):
ATTTTCAATAGTTTTTTATTTATTT
Found at i:427219 original size:15 final size:14
Alignment explanation
Indices: 427207--427237 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
427197 CGAATTTTCC
*
427207 TTTATTCTTTTTTA
1 TTTACTCTTTTTTA
427221 TTTACTCTTTTTTA
1 TTTACTCTTTTTTA
427235 TTT
1 TTT
427238 CGATTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTACTCTTTTTTA
Found at i:430777 original size:39 final size:39
Alignment explanation
Indices: 430723--430802 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
430713 CACCTGGAGT
* *
430723 ATTACCCGAGGACTCATCCGCTACTAAAGGGAAAGTTGC
1 ATTACCCGAGGACTCATCCGCTACCAAAGGGAAAGCTGC
*
430762 ATTACCCG-GTGACTCATCCTCTACCAAAGGGAAAGCTGC
1 ATTACCCGAG-GACTCATCCGCTACCAAAGGGAAAGCTGC
430801 AT
1 AT
430803 CTACTGTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (39 bp):
ATTACCCGAGGACTCATCCGCTACCAAAGGGAAAGCTGC
Found at i:439377 original size:20 final size:20
Alignment explanation
Indices: 439320--439377 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
439310 TGGTTCACGA
* *
439320 AATATAAGATTATCAGTAGG
1 AATAAAAGATTATCAGTGGG
439340 AATAAAAGATTATCAGTGGG
1 AATAAAAGATTATCAGTGGG
439360 AATAAAAGATTATCAGTG
1 AATAAAAGATTATCAGTG
439378 AATAGGATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.28
Consensus pattern (20 bp):
AATAAAAGATTATCAGTGGG
Found at i:439585 original size:37 final size:37
Alignment explanation
Indices: 439532--439618 Score: 151
Period size: 37 Copynumber: 2.4 Consensus size: 37
439522 GTTAAAAAAT
439532 ATTTATAT-ATTTTCTTTAAAAATAT-AAATTCATAAA
1 ATTTATATAATTTTCTTTAAAAAT-TCAAATTCATAAA
439568 ATTTATATAATTTTCTTTAAAAATTCAAATTCATAAA
1 ATTTATATAATTTTCTTTAAAAATTCAAATTCATAAA
439605 ATTTATATAATTTT
1 ATTTATATAATTTT
439619 TTACAAAATT
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
36 9 0.18
37 40 0.82
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTATATAATTTTCTTTAAAAATTCAAATTCATAAA
Found at i:441549 original size:18 final size:19
Alignment explanation
Indices: 441509--441549 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
441499 GAATAAATGA
441509 AAATAAATATACATATAAC
1 AAATAAATATACATATAAC
441528 -AATAAATAATA-ATA-AAC
1 AAATAAAT-ATACATATAAC
441545 AAATA
1 AAATA
441550 TACATGCGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.15
18 14 0.70
19 3 0.15
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAATATACATATAAC
Found at i:442912 original size:32 final size:32
Alignment explanation
Indices: 442871--442935 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
442861 AAGATTAAAA
*
442871 GACACAAATTTCGTCCATATCGAATATCCTCT
1 GACACAAATTTCGTCCATATCGAACATCCTCT
*
442903 GACACAAATTTCGTCCATATCGAACATCTTCT
1 GACACAAATTTCGTCCATATCGAACATCCTCT
442935 G
1 G
442936 TCATAGAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (32 bp):
GACACAAATTTCGTCCATATCGAACATCCTCT
Found at i:443435 original size:105 final size:105
Alignment explanation
Indices: 443288--444480 Score: 1917
Period size: 105 Copynumber: 11.4 Consensus size: 105
443278 TGTTCTGAGC
* * * *
443288 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATTGAGAAATATTTGTTGACAACCAAC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAACCAGC
443353 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
443393 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGGATTGAGAAATGGTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAACCAGC
* *
443458 GGTCCCTTCATCGTGAAGTTGAACTTACGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
443498 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAACCAGC
* *
443563 GGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGCCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * *
443603 CTAATATCCTTCGTTGTGAAGTTGAGATTGGCTCT-GAATTGGAGAAATGTCTGGTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATT-GAGAAATGTTTGTTGACAACCAG
*
443667 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
443708 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTTTGAAATTGAGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAACCAGC
*
443773 GGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
443813 CCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCT-GAATTGGCGAAATGTTCGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATT-GAGAAATGTTTGTTGACAACCAG
*
443877 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
443918 CCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCT-GAATTGGCGAAATGTTCGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATT-GAGAAATGTTTGTTGACAACCAG
*
443982 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
444023 CCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCT-GAATTGGAGAAATGTTTGGTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATT-GAGAAATGTTTGTTGACAACCAG
*
444087 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTCGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
444128 CCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAACGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAACCAGC
*
444193 GGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
444233 CCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTGAGAAACGTTTGTTGACAACCAGT
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAACCAGC
*
444298 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTCGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
444338 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAAAAACGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAACCAGC
*
444403 GGTCCCTTCGTCGTGAAGTTGAAGTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
444443 CCAATATCCTTCGTTGTGAAGTTGAAAATTGACTCTGG
1 CCAATATCCTTCGTTGTGAAGTTG-AAATTGGCTCTGG
444481 GTAAAACCTG
Statistics
Matches: 1019, Mismatches: 64, Indels: 9
0.93 0.06 0.01
Matches are distributed among these distances:
104 8 0.01
105 992 0.97
106 19 0.02
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:445320 original size:11 final size:11
Alignment explanation
Indices: 445299--445329 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
445289 GTTCTTCTCT
445299 TTTTGTTTTTTG
1 TTTT-TTTTTTG
445311 TTTTTTTTTTG
1 TTTTTTTTTTG
445322 TTTTTTTT
1 TTTTTTTT
445330 GTTTTTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:456018 original size:18 final size:19
Alignment explanation
Indices: 455978--456018 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
455968 GAATAAATGA
455978 AAATAAATATACATATAAC
1 AAATAAATATACATATAAC
455997 -AATAAATAATA-ATA-AAC
1 AAATAAAT-ATACATATAAC
456014 AAATA
1 AAATA
456019 TACATGCGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.15
18 14 0.70
19 3 0.15
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAATATACATATAAC
Found at i:458507 original size:18 final size:18
Alignment explanation
Indices: 458473--458507 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
458463 TATATAATAA
*
458473 TAATAATTTATTCAAAAG
1 TAATAATTTATTAAAAAG
458491 TAATAATTTATTAAAAA
1 TAATAATTTATTAAAAA
458508 TTAAGTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
TAATAATTTATTAAAAAG
Found at i:459098 original size:13 final size:13
Alignment explanation
Indices: 459080--459105 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
459070 CTTCATCAAG
459080 TTTTTATTCTTTT
1 TTTTTATTCTTTT
459093 TTTTTATTCTTTT
1 TTTTTATTCTTTT
459106 CATTTTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTCTTTT
Found at i:463046 original size:22 final size:22
Alignment explanation
Indices: 463021--463070 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
463011 GATGTACCGA
*
463021 ATCGCGATTTTGAAACGATCCG
1 ATCGCGATTTTGAAACAATCCG
463043 ATCGCGATTTTGAAACAATCCG
1 ATCGCGATTTTGAAACAATCCG
*
463065 AACGCG
1 ATCGCG
463071 TTCGTACCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
ATCGCGATTTTGAAACAATCCG
Found at i:473253 original size:32 final size:33
Alignment explanation
Indices: 473220--473318 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
473210 AGTTTATGAT
* * *
473220 AATTGAAATACTTAAATACTTTCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
* *
473253 AATTCAAATATTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
*
473286 AATTCAAATACTTAAAAAC-TTAAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
473318 A
1 A
473319 TTGAAACAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
32 12 0.21
33 46 0.79
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTTCAAGTTCGATA
Found at i:473353 original size:21 final size:21
Alignment explanation
Indices: 473306--473354 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
473296 CTTAAAAACT
473306 TAAAG-TT-CGATAATTGAAA
1 TAAAGTTTACGATAATTGAAA
*
473325 CAAAGTTTACGATAATTGAAA
1 TAAAGTTTACGATAATTGAAA
473346 TAAAGTTTA
1 TAAAGTTTA
473355 AAAATAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 2 0.08
21 20 0.77
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (21 bp):
TAAAGTTTACGATAATTGAAA
Done.