Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001523.1 Hibiscus syriacus cultivar Beakdansim tig00002982_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: 1321709
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:702911 original size:47 final size:47
Alignment explanation
Indices: 702753--703072 Score: 457
Period size: 47 Copynumber: 6.7 Consensus size: 47
702743 TAAAATCTTA
* * **
702753 TTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGG--T
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
* * *
702798 TTTGAAAACATCAAGCATTGAATGGCTTACAGATGACCCGAAGG-TT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
* *
702844 TTTGAAAACATCAAGCACTGAAGGGCTTACAGATGGCCCGAAGGTTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
702891 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG----TTT
*
702942 TTTGAAAACATCATGCACTGAAGAGCTTACAGATGACCCGAAGGTTGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T-TT
*
702991 TTTGAAAACATCATGCACTGAAGGGCTTACATATGACCCGAAGGTTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
*
703038 TTTGAAAACATCATGCACTAAAGGGCTTACAGATG
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
703073 TGGGAAATAG
Statistics
Matches: 251, Mismatches: 17, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
45 37 0.15
46 42 0.17
47 79 0.31
48 3 0.01
49 44 0.18
51 46 0.18
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (47 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTT
Found at i:703062 original size:147 final size:138
Alignment explanation
Indices: 702753--703072 Score: 453
Period size: 147 Copynumber: 2.3 Consensus size: 138
702743 TAAAATCTTA
* * ** *
702753 TTTGAAAACATCATGCACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAAGCATTG
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACTG
*
702818 AATGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGGCCC
66 AATGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCC
702883 GAAGGTTT
131 GAAGGTTT
*
702891 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTTTTTTGAAAACATCAT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG------TTTTGAAAACATCAA
*
702956 GCACTGAA-GAGCTTACAGATGACCCGAAGGTTGTTTTTGAAAACATCATGCACTGAAGGGCTTA
60 GCACTGAATG-GCTTACAGATGACCCGAA-G--GTTTTTGAAAACATCAAGCACTGAAGGGCTTA
*
703020 CATATGACCCGAAGGTTT
121 CAGATGACCCGAAGGTTT
*
703038 TTTGAAAACATCATGCACTAAAGGGCTTACAGATG
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
703073 TGGGAAATAG
Statistics
Matches: 162, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
138 40 0.25
143 1 0.01
144 39 0.24
145 1 0.01
147 81 0.50
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (138 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAGCACTG
AATGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAGCACTGAAGGGCTTACAGATGACCC
GAAGGTTT
Found at i:705088 original size:75 final size:75
Alignment explanation
Indices: 704965--705294 Score: 446
Period size: 75 Copynumber: 4.4 Consensus size: 75
704955 ACATGATGAT
* ** * * * * *
704965 ATGGGCCTTCAGCATGCCCCAGTAATTGCTGATACAAACATTCAAAATGCGTCAACATTCCT-AT
1 ATGGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATACATCAATATTCCTGA-
705029 TTCTGATTGAA
65 TTCTGATTGAA
* * * * * * **
705040 ATGGGCTTTCAGCATACCCCGACATTTACTGATACAAAGGTTTAAAATGCATCAATATTTTTGAT
1 ATGGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATACATCAATATTCCTGAT
705105 TCTGATTGAA
66 TCTGATTGAA
* **
705115 ATGGGCTTTCAGCATGCTCCAACATTTGCTGATATGAACGTTCAAAATACATCAATATTCCTGAT
1 ATGGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATACATCAATATTCCTGAT
705180 TCTGATTGAA
66 TCTGATTGAA
**
705190 ATGGGCTTTCAGCATGCCCCAACATTTGCTGATATGAACGTTCAAAATACATCAATATTCCTGAT
1 ATGGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATACATCAATATTCCTGAT
705255 TCTGATTGAA
66 TCTGATTGAA
*
705265 ATGGGCTTTCAGCATGCCCCGACATTTGCT
1 ATGGGCTTTCAGCATGCCCCAACATTTGCT
705295 TCTTGTTGAT
Statistics
Matches: 227, Mismatches: 27, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
75 226 1.00
76 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (75 bp):
ATGGGCTTTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATACATCAATATTCCTGAT
TCTGATTGAA
Found at i:710824 original size:34 final size:34
Alignment explanation
Indices: 710782--710900 Score: 229
Period size: 34 Copynumber: 3.5 Consensus size: 34
710772 GCAAAGATGC
710782 AAATGCAAAAATGAAAATGTAAATACAAACATAA
1 AAATGCAAAAATGAAAATGTAAATACAAACATAA
710816 AAATGCAAAAATGAAAATGTAAATACAAACATAA
1 AAATGCAAAAATGAAAATGTAAATACAAACATAA
*
710850 AAATGCAAAAATAAAAATGTAAATACAAACATAA
1 AAATGCAAAAATGAAAATGTAAATACAAACATAA
710884 AAATGCAAAAATGAAAA
1 AAATGCAAAAATGAAAA
710901 ATACAAATGC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 83 1.00
ACGTcount: A:0.66, C:0.08, G:0.08, T:0.17
Consensus pattern (34 bp):
AAATGCAAAAATGAAAATGTAAATACAAACATAA
Found at i:710878 original size:20 final size:20
Alignment explanation
Indices: 710782--710888 Score: 76
Period size: 20 Copynumber: 6.0 Consensus size: 20
710772 GCAAAGATGC
* *
710782 AAATGCAAAAATGAAAATGT
1 AAATACAAAAATAAAAATGT
*
710802 AAATACAAACATAAAAATG-
1 AAATACAAAAATAAAAATGT
*
710821 -----CAAAAATGAAAATGT
1 AAATACAAAAATAAAAATGT
*
710836 AAATACAAACATAAAAATG-
1 AAATACAAAAATAAAAATGT
710855 -----CAAAAATAAAAATGT
1 AAATACAAAAATAAAAATGT
*
710870 AAATACAAACATAAAAATG
1 AAATACAAAAATAAAAATG
710889 CAAAAATGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 24
0.67 0.09 0.24
Matches are distributed among these distances:
14 25 0.38
20 41 0.62
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.18
Consensus pattern (20 bp):
AAATACAAAAATAAAAATGT
Found at i:711011 original size:21 final size:21
Alignment explanation
Indices: 710987--711043 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
710977 AAAAGTACAA
*
710987 ATGCGAAATGAAAATGCAAAG
1 ATGCAAAATGAAAATGCAAAG
*
711008 ATGCAAAATAAAAATGCAAAG
1 ATGCAAAATGAAAATGCAAAG
*
711029 ATGCAAAATGCAAAT
1 ATGCAAAATGAAAAT
711044 AAATGTATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.56, C:0.11, G:0.18, T:0.16
Consensus pattern (21 bp):
ATGCAAAATGAAAATGCAAAG
Found at i:711041 original size:7 final size:7
Alignment explanation
Indices: 710985--711042 Score: 66
Period size: 7 Copynumber: 8.3 Consensus size: 7
710975 ATAAAAGTAC
*
710985 AAATGCG
1 AAATGCA
710992 AAATG-A
1 AAATGCA
710998 AAATGCA
1 AAATGCA
711005 AAGATGCA
1 AA-ATGCA
*
711013 AAAT-AA
1 AAATGCA
711019 AAATGCA
1 AAATGCA
711026 AAGATGCA
1 AA-ATGCA
711034 AAATGCA
1 AAATGCA
711041 AA
1 AA
711043 TAAATGTATG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
6 10 0.23
7 20 0.45
8 14 0.32
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.14
Consensus pattern (7 bp):
AAATGCA
Found at i:714930 original size:21 final size:20
Alignment explanation
Indices: 714906--714947 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
714896 TAAAGATAAT
714906 TAATAAAGAAATAT-ATAAAAA
1 TAAT-AAGAAA-ATCATAAAAA
*
714927 TAATATGAAAATCATAAAAA
1 TAATAAGAAAATCATAAAAA
714947 T
1 T
714948 TTTGAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 2 0.11
20 13 0.68
21 4 0.21
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (20 bp):
TAATAAGAAAATCATAAAAA
Found at i:716715 original size:3 final size:3
Alignment explanation
Indices: 716709--716784 Score: 89
Period size: 3 Copynumber: 25.0 Consensus size: 3
716699 TTTTATTTTA
* *
716709 AAT AAT AAT AAT AAT ATT TAT AAT AAT AAT AAT AAT AATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
* ** *
716755 AAT AAT AAT AGT AAT TTT AAA AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
716785 TTAAGTAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:719655 original size:20 final size:21
Alignment explanation
Indices: 719627--719666 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
719617 ACCTATTCAA
719627 TCAAAAAAATCA-TTATATAC
1 TCAAAAAAATCATTTATATAC
* *
719647 TCAACAAAATTATTTATATA
1 TCAAAAAAATCATTTATATA
719667 TGAATTCAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
TCAAAAAAATCATTTATATAC
Found at i:726083 original size:2 final size:2
Alignment explanation
Indices: 726076--726112 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
726066 ATTTTATAAC
726076 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
726113 TTCTTCATTT
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:726733 original size:30 final size:31
Alignment explanation
Indices: 726668--726730 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
726658 TTCTAGTGAG
726668 TTTAACGAGCAACGAGTCGAGCAATATATTT
1 TTTAACGAGCAACGAGTCGAGCAATATATTT
726699 TTTAACGAGC-ACGAGTCGAGCAATA-ATTT
1 TTTAACGAGCAACGAGTCGAGCAATATATTT
726728 TTT
1 TTT
726731 TAAAGAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 7 0.22
30 15 0.47
31 10 0.31
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (31 bp):
TTTAACGAGCAACGAGTCGAGCAATATATTT
Found at i:726746 original size:31 final size:30
Alignment explanation
Indices: 726678--726739 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
726668 TTTAACGAGC
* *
726678 AACGAGTCGAGCAATATATTTTTTAACGAG
1 AACGAGTCGAGCAATATATTTTTTAAAGAA
*
726708 CACGAGTCGAGCAATA-ATTTTTTTAAAGAA
1 AACGAGTCGAGCAATATA-TTTTTTAAAGAA
726738 AA
1 AA
726740 ATGAGTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (30 bp):
AACGAGTCGAGCAATATATTTTTTAAAGAA
Found at i:729399 original size:109 final size:108
Alignment explanation
Indices: 729208--729425 Score: 418
Period size: 109 Copynumber: 2.0 Consensus size: 108
729198 GGGTAAGTCT
729208 TTATGGGCCTGAGGGCACACCCCTCAGGTGGGCACCTACGCTTCAACTAGGATTAGACCTTATGA
1 TTATGGGCCTGAGGGCACACCCCTCAGGTGGGCACCTACGCTTCAACTAGGATTAGACCTTATGA
729273 ACCCAAGGTGCTCCCTTAGGTTGTCACCTACGCCCTTTGGGTCC
66 ACCCAAGGTGCTCCCTTAGGTTGTCACCTACGCCCTTT-GGTCC
*
729317 TTATGGGCCTGAGGGCACACCCCTCAGGTGGGCACCTACGCTTCAGCTAGGATTAGACCTTATGA
1 TTATGGGCCTGAGGGCACACCCCTCAGGTGGGCACCTACGCTTCAACTAGGATTAGACCTTATGA
729382 ACCCAAGGTGCTCCCTTAGGTTGTCACCTACGCCCTTTGGTCC
66 ACCCAAGGTGCTCCCTTAGGTTGTCACCTACGCCCTTTGGTCC
729425 T
1 T
729426 AAGGTAAGTC
Statistics
Matches: 108, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
108 6 0.06
109 102 0.94
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (108 bp):
TTATGGGCCTGAGGGCACACCCCTCAGGTGGGCACCTACGCTTCAACTAGGATTAGACCTTATGA
ACCCAAGGTGCTCCCTTAGGTTGTCACCTACGCCCTTTGGTCC
Found at i:730253 original size:21 final size:20
Alignment explanation
Indices: 730227--730286 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 20
730217 GGCATGTGAA
*
730227 ATCTATGTCCCGAAGGACGT
1 ATCTATGTCCCGAAGGACCT
730247 CATCTATGTCCCGAAGGACCT
1 -ATCTATGTCCCGAAGGACCT
730268 ATCATATGTCCCGAAGGAC
1 ATC-TATGTCCCGAAGGAC
730287 ATATGTAACC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
20 3 0.08
21 34 0.92
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCTATGTCCCGAAGGACCT
Found at i:737173 original size:21 final size:21
Alignment explanation
Indices: 737146--737227 Score: 132
Period size: 21 Copynumber: 4.0 Consensus size: 21
737136 TGGCATGCGA
*
737146 TATC-TATGTCCCGAAGGACG
1 TATCATATGTCCCGAAGGACC
737166 TCATC-TATGTCCCGAAGGACC
1 T-ATCATATGTCCCGAAGGACC
737187 TATCATATGTCCCGAAGGACC
1 TATCATATGTCCCGAAGGACC
737208 TATCATATGTCCCGAAGGAC
1 TATCATATGTCCCGAAGGAC
737228 ATATGTAACC
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
20 4 0.07
21 55 0.93
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (21 bp):
TATCATATGTCCCGAAGGACC
Found at i:737349 original size:22 final size:22
Alignment explanation
Indices: 737324--737374 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
737314 TTCATGTATT
737324 TATATCAT-TTCTCTTATAATCA
1 TATATCATCTTCTCTTAT-ATCA
* *
737346 TATAT-ATCTTCTCTTCTGTCA
1 TATATCATCTTCTCTTATATCA
737367 TATATCAT
1 TATATCAT
737375 ATGTACGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.27, C:0.20, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATCATCTTCTCTTATATCA
Found at i:737855 original size:17 final size:17
Alignment explanation
Indices: 737830--737864 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
737820 CCAAGGAATG
737830 GTACCGATACTTCCCTA
1 GTACCGATACTTCCCTA
*
737847 GTACTGATACTTCCCTA
1 GTACCGATACTTCCCTA
737864 G
1 G
737865 CTATAGTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (17 bp):
GTACCGATACTTCCCTA
Found at i:739419 original size:21 final size:21
Alignment explanation
Indices: 739375--739421 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
739365 AAGAAAACTA
* * **
739375 TAAAATTAATTGTAAATAGTC
1 TAAAATTAACTATAAATAAAC
739396 TAAAATTAACTATAAATAAAC
1 TAAAATTAACTATAAATAAAC
739417 TAAAA
1 TAAAA
739422 ATATACCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (21 bp):
TAAAATTAACTATAAATAAAC
Found at i:744904 original size:22 final size:22
Alignment explanation
Indices: 744879--744938 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
744869 ATTTAATTCA
744879 TTTTTATTTTTATTTTATC-TCC
1 TTTTTATTTTTATTTTATCAT-C
* *
744901 TTTTCATTTTTATCTTATCATC
1 TTTTTATTTTTATTTTATCATC
744923 -TTTTA-TTTTATTTTAT
1 TTTTTATTTTTATTTTAT
744939 TTTAATCACT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 10 0.30
21 4 0.12
22 18 0.55
23 1 0.03
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTATTTTTATTTTATCATC
Found at i:745140 original size:32 final size:32
Alignment explanation
Indices: 745097--745171 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
745087 ATCAGGAAAT
* *
745097 ATATGACATATAGTTATATAATATAAATATAC
1 ATATGATATATAGTTACATAATATAAATATAC
* * *
745129 ATATGATATATAGTTACGTAATATATATATAT
1 ATATGATATATAGTTACATAATATAAATATAC
745161 ATAT-ATATATA
1 ATATGATATATA
745172 TATATATTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
31 7 0.18
32 31 0.82
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (32 bp):
ATATGATATATAGTTACATAATATAAATATAC
Found at i:745276 original size:2 final size:2
Alignment explanation
Indices: 745111--745265 Score: 128
Period size: 2 Copynumber: 78.5 Consensus size: 2
745101 GACATATAGT
* * **
745111 TA TA TA -A TA TA AA TA TA CA TA TGA TA TA TA GT- TA CG TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA -TA TA TA TA TA TA
* **
745152 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TCA T- TA AA TA GG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
*
745193 CTA CT- TA -A CT- TT 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
745233 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 T
745266 CCCAAATATA
Statistics
Matches: 125, Mismatches: 15, Indels: 26
0.75 0.09 0.16
Matches are distributed among these distances:
1 8 0.06
2 109 0.87
3 8 0.06
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:747873 original size:19 final size:20
Alignment explanation
Indices: 747846--747886 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
747836 AAAAAAATAG
* *
747846 AGGGCATTTGAATAAATAAA
1 AGGGCATTTGAACAAAAAAA
747866 AGGG-ATTTGAACAAAAAAA
1 AGGGCATTTGAACAAAAAAA
747885 AG
1 AG
747887 ATGGAACCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.54, C:0.05, G:0.22, T:0.20
Consensus pattern (20 bp):
AGGGCATTTGAACAAAAAAA
Found at i:749085 original size:2 final size:2
Alignment explanation
Indices: 749071--749110 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
749061 TAAATATACA
749071 AT AT AT -T ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
749111 TTTATGACCC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:749820 original size:11 final size:12
Alignment explanation
Indices: 749794--749834 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
749784 CATATTTTGT
749794 TTTTTAAATGAT-
1 TTTTTAAAT-ATG
749806 TTTTTAAAT-TG
1 TTTTTAAATATG
*
749817 TTTTAAAATATG
1 TTTTTAAATATG
749829 TTTTTA
1 TTTTTA
749835 GGTACTCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 1 0.04
11 8 0.32
12 16 0.64
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (12 bp):
TTTTTAAATATG
Found at i:755943 original size:137 final size:137
Alignment explanation
Indices: 755687--755964 Score: 310
Period size: 137 Copynumber: 2.0 Consensus size: 137
755677 CAAGGTTATC
* * **
755687 TCCAAATACAGCTAGACATTCTCAACACGAAGGAACAATTTCATCCACTGACCAGATCTCCTCAA
1 TCCAAATACAGCTAGACATCCTCAACACGAAAGAACAATTTCATCCACCCACCAGATCTCCTCAA
* * ** * * * *
755752 TGCAAATGAGTAATGTCATCCTCTGACAATCAGATTTCCTCAACACGAAGGAACCGTGTTGTCTC
66 TACAAAGGAACAATGTCATCCTCTGACAATCAGACTTCCTCAACACGAAAGAACCATGTTATCTC
755817 CAAATTA
131 CAAATTA
* *
755824 TCCAAATAC-GTCTAGACATCCTCAACACGAAAGAATAATGTT-ATCCACCCACTAGATCTCCTC
1 TCCAAATACAG-CTAGACATCCTCAACACGAAAGAACAAT-TTCATCCACCCACCAGATCTCCTC
** * * **
755887 AATATGAAGGAACAGTGTTATCCTCAT-ACAATCAGACTTCCTCAATGCGAAAGAACCATGTTAT
64 AATACAAAGGAACAATGTCATCCTC-TGACAATCAGACTTCCTCAACACGAAAGAACCATGTTAT
**
755951 CTTTAAATTA
128 CTCCAAATTA
755961 TCCA
1 TCCA
755965 TATTGACTCG
Statistics
Matches: 116, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
136 1 0.01
137 112 0.97
138 3 0.03
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (137 bp):
TCCAAATACAGCTAGACATCCTCAACACGAAAGAACAATTTCATCCACCCACCAGATCTCCTCAA
TACAAAGGAACAATGTCATCCTCTGACAATCAGACTTCCTCAACACGAAAGAACCATGTTATCTC
CAAATTA
Found at i:756618 original size:3 final size:3
Alignment explanation
Indices: 756612--756670 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
756602 GTTTTTTTTT
* * * *
756612 TTA TTA TTA TTA TTA TCA TTA TTG TTA TTA TTA TTA TTA CTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
756660 TTT TTA TTA TT
1 TTA TTA TTA TT
756671 TTCAGGTTAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:759111 original size:20 final size:21
Alignment explanation
Indices: 759086--759125 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
759076 GATTAATTTG
759086 AAAATC-TCAATTTTTTTAAT
1 AAAATCATCAATTTTTTTAAT
* *
759106 AAAATCATTATTTTTTTTAA
1 AAAATCATCAATTTTTTTAA
759126 AGGAAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (21 bp):
AAAATCATCAATTTTTTTAAT
Found at i:760284 original size:5 final size:5
Alignment explanation
Indices: 760274--760479 Score: 412
Period size: 5 Copynumber: 41.2 Consensus size: 5
760264 TTTGCATTTG
760274 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
760324 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
760374 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
760424 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
760474 TATAT T
1 TATAT T
760480 TAATAGTTTT
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 201 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:783078 original size:64 final size:64
Alignment explanation
Indices: 783010--783167 Score: 160
Period size: 64 Copynumber: 2.5 Consensus size: 64
783000 TTGAAGGTGT
*** *
783010 ATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAATCTAA-AAACATCGAATGCAATTAGTG
1 ATCGATGCACAGGTAGTGCATCGATGCATC-CCAGTAAT-AAACAAACATCGAATGCAATTAGTG
783073 C
64 C
* * * * *
783074 ATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAAACAAACATCGAATGTATTTTGTGC
1 ATCGATGCA-CAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATGCAATTAGTGC
* * *
783138 ACCGATGCACAAGTAGTGCATCGATTCATC
1 ATCGATGCACAGGTAGTGCATCGATGCATC
783168 GGTAGGGAAT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
63 5 0.07
64 66 0.87
65 5 0.07
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCACAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATGCAATTAGTGC
Found at i:784178 original size:103 final size:103
Alignment explanation
Indices: 783953--784170 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
783943 GTCGAGGGTC
* * *
783953 TATGTGGTCCTTCGGGACATGTATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
* *
784018 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
784056 TATGTGGTCATTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
*
784121 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
784159 TATGTGGTCCTT
1 TATGTGGTCCTT
784171 ATGGACATTA
Statistics
Matches: 107, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:784236 original size:23 final size:23
Alignment explanation
Indices: 784177--784238 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
784167 CCTTATGGAC
* *
784177 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGATGCA
* * * *
784201 ATTCTACGCGGCACTCCGATGCA
1 ATTATATGTGGCACTACGATGCA
784224 ATTATATGTGGCACT
1 ATTATATGTGGCACT
784239 TCAGTTTAAT
Statistics
Matches: 29, Mismatches: 9, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 26 0.90
24 3 0.10
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACGATGCA
Found at i:786630 original size:2 final size:2
Alignment explanation
Indices: 786623--786667 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
786613 GATACAATTG
786623 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
786665 TA T
1 TA T
786668 TCAGATCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:790038 original size:103 final size:103
Alignment explanation
Indices: 789813--790030 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
789803 GTCGAGGGTC
* *
789813 TATGTGGTCCTTCGGGAAATATATGTATTCTTTGGAACATGTGTGAAGTTTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
789878 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
789916 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
789981 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATTA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
790019 TATGTGGTCCTT
1 TATGTGGTCCTT
790031 ATGGACATTA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 109 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:790095 original size:23 final size:23
Alignment explanation
Indices: 790069--790113 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
790059 AATTCTACGC
790069 GGCAC-TCTGGTGCAATTATATGT
1 GGCACTTC-GGTGCAATTATATGT
790092 GGCACTTCGGTGCAATTATATG
1 GGCACTTCGGTGCAATTATATG
790114 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 19 0.90
24 2 0.10
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTATATGT
Found at i:792313 original size:21 final size:21
Alignment explanation
Indices: 792289--792328 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
792279 TAGTTTACCC
792289 AAAATAAAAT-AAAAGGAAATG
1 AAAA-AAAATCAAAAGGAAATG
*
792310 AAAAAAAGTCAAAAGGAAA
1 AAAAAAAATCAAAAGGAAA
792329 GGGAAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (21 bp):
AAAAAAAATCAAAAGGAAATG
Found at i:795187 original size:24 final size:24
Alignment explanation
Indices: 795144--795215 Score: 108
Period size: 24 Copynumber: 2.9 Consensus size: 24
795134 TCAAAAAAAA
*
795144 AAAATTTAGAAGTTCGATTGAAGCCT
1 AAAATTT-G-AGTTCAATTGAAGCCT
795170 AAAATTTGAGTTCAATTGAAGCCT
1 AAAATTTGAGTTCAATTGAAGCCT
*
795194 AAAATTTGAGCTCAATTGAAGC
1 AAAATTTGAGTTCAATTGAAGC
795216 GAAAAAATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
24 36 0.82
25 1 0.02
26 7 0.16
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (24 bp):
AAAATTTGAGTTCAATTGAAGCCT
Found at i:798986 original size:2 final size:2
Alignment explanation
Indices: 798979--799006 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
798969 CACTTTAGAA
798979 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
799007 TATTTTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:804566 original size:2 final size:2
Alignment explanation
Indices: 804559--804593 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
804549 GCGTGACTAC
804559 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 T
804594 GTAGAGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:805006 original size:2 final size:2
Alignment explanation
Indices: 804999--805062 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
804989 GAGTTATTCA
804999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
805041 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
805063 GTTTTACAAT
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):
AT
Found at i:808202 original size:42 final size:40
Alignment explanation
Indices: 808143--808288 Score: 125
Period size: 42 Copynumber: 3.5 Consensus size: 40
808133 AATTCTGTGT
808143 TATTTAGCGGCGTTTGTAACAAAAAAGCCGCAATATGT-CACA
1 TATTTAGCGGCGTTTGTAACAAAAAAGCCGC--TATGTAC-CA
* *
808185 TATTTAGCGGCGTTTGTATCAGAAAATGCCGCTATGTACCA
1 TATTTAGCGGCGTTTGTAACA-AAAAAGCCGCTATGTACCA
* * *
808226 -ACTTTTAGCGGCGTTTGTATACTAAAAACGTCGCTATATACCA
1 TA--TTTAGCGGCGTTTGTA-AC-AAAAAAGCCGCTATGTACCA
* *
808269 GGAATATAGCGGCGTTTGTA
1 --TATTTAGCGGCGTTTGTA
808289 TCCTAAAAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 16
0.79 0.06 0.14
Matches are distributed among these distances:
40 1 0.01
41 7 0.08
42 37 0.42
43 26 0.30
44 16 0.18
46 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (40 bp):
TATTTAGCGGCGTTTGTAACAAAAAAGCCGCTATGTACCA
Found at i:808287 original size:44 final size:44
Alignment explanation
Indices: 808189--808417 Score: 232
Period size: 44 Copynumber: 5.2 Consensus size: 44
808179 GTCACATATT
* * * * *
808189 TAGCGGCGTTTGTAT-C-AGAAAATGCCGCTATGTACCA-ACTTT
1 TAGCGGCGTTTGTATCCTA-AAAACGCCGCTATATACCAGTCCTA
* * ***
808231 TAGCGGCGTTTGTATACTAAAAACGTCGCTATATACCAGGAATA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGTCCTA
* *
808275 TAGCGGCGTTTGTATCCTAAAAATGCCACTATATACCAGTCCTA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGTCCTA
* *
808319 TCGCGGCGTTTGTATCCTAAAAATGCCGCTATATACCAGTCCTA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGTCCTA
* * * *
808363 TCGCGGCATTTTTATCCTAAAAACGCCGCTAAATACCA-TACCTA
1 TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGT-CCTA
* *
808407 TTGTGGCGTTT
1 TAGCGGCGTTT
808418 TCATAAAAAA
Statistics
Matches: 160, Mismatches: 23, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
42 15 0.09
43 18 0.11
44 127 0.79
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (44 bp):
TAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACCAGTCCTA
Found at i:808339 original size:88 final size:87
Alignment explanation
Indices: 808147--808417 Score: 246
Period size: 88 Copynumber: 3.1 Consensus size: 87
808137 CTGTGTTATT
* * ** * *
808147 TAGCGGCGTTTGTA-AC-AAAAAAGCCGCAATATGTCA-CATATTTAGCGGCGTTTGTAT-C-AG
1 TAGCGGCGTTTGTATACTAAAAACGCCGCTATATACCAGGA-ATATAGCGGCGTTTGTATCCTA-
* * * *
808207 AAAATGCCGCTATGTACCAACTTT
64 AAAATGCCGCTATATACCATCCTA
*
808231 TAGCGGCGTTTGTATACTAAAAACGTCGCTATATACCAGGAATATAGCGGCGTTTGTATCCTAAA
1 TAGCGGCGTTTGTATACTAAAAACGCCGCTATATACCAGGAATATAGCGGCGTTTGTATCCTAAA
*
808296 AATGCCACTATATACCAGTCCTA
66 AATGCCGCTATATACCA-TCCTA
* * * *** * * *
808319 TCGCGGCGTTTGTATCCTAAAAATGCCGCTATATACCAGTCCTATCGCGGCATTTTTATCCTAAA
1 TAGCGGCGTTTGTATACTAAAAACGCCGCTATATACCAGGAATATAGCGGCGTTTGTATCCTAAA
* *
808384 AACGCCGCTAAATACCATACCTA
66 AATGCCGCTATATACCAT-CCTA
* *
808407 TTGTGGCGTTT
1 TAGCGGCGTTT
808418 TCATAAAAAA
Statistics
Matches: 153, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
84 14 0.09
85 2 0.01
86 32 0.21
87 20 0.13
88 85 0.56
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (87 bp):
TAGCGGCGTTTGTATACTAAAAACGCCGCTATATACCAGGAATATAGCGGCGTTTGTATCCTAAA
AATGCCGCTATATACCATCCTA
Found at i:811639 original size:20 final size:20
Alignment explanation
Indices: 811614--811683 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
811604 GCTAGAGTTG
811614 ATTTTGAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATGAA
*
811634 ATTTTGAAAATCAAAATGAT
1 ATTTTGAAAATCAAAATGAA
811654 ATTTTGAAAATCAAAATGAA
1 ATTTTGAAAATCAAAATGAA
811674 ATTTTGAAAA
1 ATTTTGAAAA
811684 ATGATTTAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.53, C:0.04, G:0.10, T:0.33
Consensus pattern (20 bp):
ATTTTGAAAATCAAAATGAA
Found at i:812132 original size:23 final size:22
Alignment explanation
Indices: 812094--812166 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
812084 TTTAGTGCAG
812094 GGGGAATCGATACCCCCTTGAA
1 GGGGAATCGATACCCCCTTGAA
812116 GGGGAATCGATACCCCCTTGAA
1 GGGGAATCGATACCCCCTTGAA
* *
812138 GGGGAACCGATTCCCCCTTTGAA
1 GGGGAATCGATACCCCC-TTGAA
*
812161 TGGGAA
1 GGGGAA
812167 CCGTTTCCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 37 0.79
23 10 0.21
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (22 bp):
GGGGAATCGATACCCCCTTGAA
Found at i:812174 original size:23 final size:22
Alignment explanation
Indices: 812094--812175 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
812084 TTTAGTGCAG
* *
812094 GGGGAATCGATACCCCCTTGAA
1 GGGGAACCGATTCCCCCTTGAA
* *
812116 GGGGAATCGATACCCCCTTGAA
1 GGGGAACCGATTCCCCCTTGAA
812138 GGGGAACCGATTCCCCCTTTGAA
1 GGGGAACCGATTCCCCC-TTGAA
* *
812161 TGGGAACCGTTTCCC
1 GGGGAACCGATTCCC
812176 TCATTGAGGG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
22 37 0.67
23 18 0.33
ACGTcount: A:0.23, C:0.29, G:0.27, T:0.21
Consensus pattern (22 bp):
GGGGAACCGATTCCCCCTTGAA
Found at i:813041 original size:34 final size:32
Alignment explanation
Indices: 812998--813069 Score: 99
Period size: 34 Copynumber: 2.2 Consensus size: 32
812988 CATTTTGAAA
*
812998 AGGGTAAAGGTTCTAGCTTAGCCCGTGTAAAAGCT
1 AGGG-AAAGGTTCTAGCTTAGCCCG-G-AAAAACT
*
813033 AGGGAAAGGTTCTAGTTTAGCCCGGAAAAACT
1 AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
813065 AGGGA
1 AGGGA
813070 GTTTGTAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
32 11 0.31
33 1 0.03
34 19 0.54
35 4 0.11
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (32 bp):
AGGGAAAGGTTCTAGCTTAGCCCGGAAAAACT
Found at i:817440 original size:15 final size:15
Alignment explanation
Indices: 817420--817456 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
817410 AATTTAAACC
817420 TGCTTATCTGTGGAT
1 TGCTTATCTGTGGAT
817435 TGCTTATCTGTGGAT
1 TGCTTATCTGTGGAT
817450 TGCTTAT
1 TGCTTAT
817457 TTTTGGTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.49
Consensus pattern (15 bp):
TGCTTATCTGTGGAT
Found at i:818230 original size:2 final size:2
Alignment explanation
Indices: 818225--818294 Score: 90
Period size: 2 Copynumber: 35.5 Consensus size: 2
818215 AGTAAAAATA
* *
818225 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AA AT AA AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
818265 AGT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
818295 AATTAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
1 2 0.03
2 55 0.93
3 2 0.03
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:818313 original size:49 final size:48
Alignment explanation
Indices: 818194--818344 Score: 179
Period size: 49 Copynumber: 3.1 Consensus size: 48
818184 ATAAAACAAG
*
818194 TATATAAA-ATAAT-AATAAAAAAGTAAAAATA-ATATATATATATATA
1 TATATAAATATAATAAATAAATAA-TAAAAATATATATATATATATATA
* *
818240 TATATATATATAATAAATAAATAATAGTAAATATATATATATATATATA
1 TATATAAATATAATAAATAAATAATA-AAAATATATATATATATATATA
818289 TATATAAAT-TAATAAAACTGATAATAA-AAAAATA-ATATATATATATATA
1 TATATAAATATAAT-AAA-T-A-AATAATAAAAATATATATATATATATATA
818338 TATATAA
1 TATATAA
818345 TCTAAAAAAA
Statistics
Matches: 92, Mismatches: 5, Indels: 13
0.84 0.05 0.12
Matches are distributed among these distances:
46 7 0.08
47 7 0.08
48 17 0.18
49 48 0.52
50 6 0.07
51 2 0.02
52 5 0.05
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.36
Consensus pattern (48 bp):
TATATAAATATAATAAATAAATAATAAAAATATATATATATATATATA
Found at i:819461 original size:39 final size:36
Alignment explanation
Indices: 819418--819508 Score: 119
Period size: 39 Copynumber: 2.4 Consensus size: 36
819408 CGAGGGTTTG
*
819418 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGTGC
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTT-T-T-C
* * *
819457 GTGTTTCAAGAGAAACAATTTCGAGGGTTTTTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTC
819493 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
819509 TGCCTCAAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
36 16 0.33
37 1 0.02
38 1 0.02
39 30 0.62
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (36 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTTC
Found at i:819534 original size:36 final size:36
Alignment explanation
Indices: 819494--819727 Score: 218
Period size: 36 Copynumber: 6.6 Consensus size: 36
819484 TTTTTTTTTG
* *
819494 TGTTTCAAGAGAAACTGCCTCAAGAGGGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
819530 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
819567 AG-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
819603 TGTTTCAAG-GAAA-AGATATTC-A-A-AG----ATTT
1 TGTTTCAAGAGAAACTG-T-CTCAAGAGAGACAAAATT
*
819632 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
819668 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATT
* *
819705 TGTTTCAAGGGAAATTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAA
819728 AACTCGTTTT
Statistics
Matches: 166, Mismatches: 17, Indels: 29
0.78 0.08 0.14
Matches are distributed among these distances:
29 14 0.08
30 6 0.04
31 2 0.01
32 2 0.01
33 2 0.01
34 1 0.01
35 6 0.04
36 76 0.46
37 57 0.34
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:819728 original size:102 final size:102
Alignment explanation
Indices: 819528--819714 Score: 272
Period size: 102 Copynumber: 1.8 Consensus size: 102
819518 AGGGACAAAA
*
819528 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
819593 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
66 AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
** * **
819630 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TCAAGGGAAACTGTCTCAAGA
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCT-AAAAGAAACTGTCTCAAGA
819693 GAGAC-AAGATTTTGTTTCAAGG
65 GAGACGAA-A-TTTGTTTCAAGG
819715 GAAATTGTCT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
100 3 0.04
101 27 0.36
102 46 0.61
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
AGACGAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
Found at i:819843 original size:37 final size:37
Alignment explanation
Indices: 819792--819980 Score: 141
Period size: 37 Copynumber: 5.4 Consensus size: 37
819782 TTAAGGTTTA
*
819792 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
**
819829 TGTTTCAAGGGAAACTATCTCAAGACAGACAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
** * * * *
819865 AATTTCAAAGGAAA-TGTTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACT-ATCTCAAGGGAGACAAAATTT
*
819893 ATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
* * * *
819931 TGTTTCAAGGGAAACTACCCCAAGCGAGATAAAA-TT
1 TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
*
819967 TATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
819981 TGTTTTCAAT
Statistics
Matches: 117, Mismatches: 22, Indels: 27
0.70 0.13 0.16
Matches are distributed among these distances:
28 2 0.02
29 15 0.13
30 1 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 33 0.28
37 60 0.51
38 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGGGAGACAAAATTT
Found at i:819878 original size:102 final size:102
Alignment explanation
Indices: 819765--820004 Score: 401
Period size: 102 Copynumber: 2.4 Consensus size: 102
819755 ATATTTTGTG
* *
819765 TTTCAAGGGAAATGTTTTTAAGGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* *
819830 GTTTCAAGGGAAACTATCTCAAGAC-AGACAAAATTAA
66 GTTTCAAGGGAAACTACCCCAAG-CGAGACAAAATTAA
*
819867 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* *
819932 GTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTA
66 GTTTCAAGGGAAACTACCCCAAGCGAGACAAAATTAA
819969 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
1 TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
820005 GGAGACAAAA
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
101 1 0.01
102 128 0.99
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (102 bp):
TTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTACCCCAAGCGAGACAAAATTAA
Found at i:820004 original size:87 final size:87
Alignment explanation
Indices: 819913--820178 Score: 469
Period size: 87 Copynumber: 3.1 Consensus size: 87
819903 AGAAACTATC
* * * *
819913 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
819978 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
* * *
820000 TCAAGGGAGACAAAATATCGTTTCAAGGGAAACTATCTCAATCGAGATAAAATGCATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
820065 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
820087 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
820152 AAATGTTTTCAATGTTTATGTT
66 AAATGTTTTCAATGTTTATGTT
820174 TCAAG
1 TCAAG
820179 AGAAACTGTC
Statistics
Matches: 169, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 169 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.32
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTT
Found at i:820252 original size:174 final size:170
Alignment explanation
Indices: 819913--820233 Score: 402
Period size: 174 Copynumber: 1.9 Consensus size: 170
819903 AGAAACTATC
*
819913 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
* **
819978 AAATGTTTTCAATGTTTATGTTTCAAGGGAGACAAAATATCGTTTCAAGGGAAACTATCTCAATC
66 AAATGTTTTCAATGTTTATGTTTCAA-GGAG--AAAATATCGTCTCAAGGGAAAAAATCTCAATC
* * * *
820043 GAGATAAAATGCATTTCAAGGGAAATGTTTTCAATGTTTATGTT
128 AAAAGAAAATG-ATCTCAAGGGAAATGTTTTCAATGTTTATGTT
* * *
820087 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
* * *
820152 AAATGTTTTCAATGTTTATGTTTCAA-GAG-AAA-CT-GTCTCAAGGGAGACAAAAT-TTAGTTC
66 AAATGTTTTCAATGTTTATGTTTCAAGGAGAAAATATCGTCTCAAGGGA-A-AAAATCTCA-AT-
820212 CAAAAGAAAATG-TCTCAAGGGA
127 CAAAAGAAAATGATCTCAAGGGA
820234 GACGAAATTA
Statistics
Matches: 129, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
167 10 0.08
168 13 0.10
169 7 0.05
170 9 0.07
172 3 0.02
174 87 0.67
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (170 bp):
TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
AAATGTTTTCAATGTTTATGTTTCAAGGAGAAAATATCGTCTCAAGGGAAAAAATCTCAATCAAA
AGAAAATGATCTCAAGGGAAATGTTTTCAATGTTTATGTT
Found at i:820553 original size:63 final size:63
Alignment explanation
Indices: 820454--820590 Score: 166
Period size: 63 Copynumber: 2.2 Consensus size: 63
820444 ATCCTCCGTC
* * * * *
820454 GTGAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGACAGCCAGCCGCCCCTTCGCT
1 GTGAAGTTGAAATTGGCTCTGAAACTAAGAAATTGTTTGTTGACAACCAACCACCCCTTCGCT
* ** * * *
820517 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTTTTGACAACCAACCATCCCTTCGTT
1 GTGAAGTTGAAATTGGCTCTGAAACTAAGAAATTGTTTGTTGACAACCAACCACCCCTTCGCT
*
820580 GTGGAGTTGAA
1 GTGAAGTTGAA
820591 CTTGTGTTGT
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGAAGTTGAAATTGGCTCTGAAACTAAGAAATTGTTTGTTGACAACCAACCACCCCTTCGCT
Found at i:821303 original size:32 final size:32
Alignment explanation
Indices: 821202--821291 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
821192 ATTCCCAAAG
* **
821202 ATGCCCCAATATTCAATGTTGAATCTAAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTAAAAAA
*
821234 ATGCCCCAACATTTGATGTTAAATCTAAAAAA
1 ATGCCCCAACATTTGATGTTGAATCTAAAAAA
821266 ATGCCCCAACATTTGATGTTGAATCT
1 ATGCCCCAACATTTGATGTTGAATCT
821292 TCAAAGATGC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (32 bp):
ATGCCCCAACATTTGATGTTGAATCTAAAAAA
Found at i:822381 original size:11 final size:13
Alignment explanation
Indices: 822367--822426 Score: 74
Period size: 13 Copynumber: 4.8 Consensus size: 13
822357 TTTTCTTCAA
822367 TTTTC-CTTTGTTT
1 TTTTCTCTTTG-TT
822380 TTTTCTCTTT-TT
1 TTTTCTCTTTGTT
822392 ATTTTCTCTTTGTT
1 -TTTTCTCTTTGTT
822406 TTTTCTC-TT-TT
1 TTTTCTCTTTGTT
822417 TTTTCTCTTT
1 TTTTCTCTTT
822427 TTGTTCTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.21
12 6 0.14
13 22 0.51
14 6 0.14
ACGTcount: A:0.02, C:0.17, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTCTCTTTGTT
Found at i:822431 original size:26 final size:26
Alignment explanation
Indices: 822366--822426 Score: 92
Period size: 26 Copynumber: 2.4 Consensus size: 26
822356 TTTTTCTTCA
822366 ATTTTC-CTTTGTTTTTTTCTCTTTTT
1 ATTTTCTCTTTG-TTTTTTCTCTTTTT
822392 ATTTTCTCTTTGTTTTTTCTC-TTTT
1 ATTTTCTCTTTGTTTTTTCTCTTTTT
822417 -TTTTCTCTTT
1 ATTTTCTCTTT
822427 TTGTTCTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 10 0.29
25 4 0.12
26 15 0.44
27 5 0.15
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.77
Consensus pattern (26 bp):
ATTTTCTCTTTGTTTTTTCTCTTTTT
Found at i:822433 original size:11 final size:12
Alignment explanation
Indices: 822377--822428 Score: 79
Period size: 13 Copynumber: 4.2 Consensus size: 12
822367 TTTTCCTTTG
822377 TTTTTTTCTCTT
1 TTTTTTTCTCTT
822389 TTTATTTTCTCTT
1 TTT-TTTTCTCTT
822402 TGTTTTTTCTC-T
1 T-TTTTTTCTCTT
822414 TTTTTTTCTCTT
1 TTTTTTTCTCTT
822426 TTT
1 TTT
822429 GTTCTAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.24
12 9 0.24
13 17 0.46
14 2 0.05
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTTTTCTCTT
Found at i:825611 original size:10 final size:10
Alignment explanation
Indices: 825598--825646 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
825588 ATAAATATAA
825598 AAAAATAAAG
1 AAAAATAAAG
825608 AAAAATAAAG
1 AAAAATAAAG
* *
825618 AAAAAGAAGG
1 AAAAATAAAG
*
825628 AAAACATATA-
1 AAAA-ATAAAG
825638 AAAAATAAA
1 AAAAATAAA
825647 ACAAGTAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
9 4 0.12
10 26 0.81
11 2 0.06
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (10 bp):
AAAAATAAAG
Found at i:825611 original size:23 final size:24
Alignment explanation
Indices: 825556--825622 Score: 68
Period size: 23 Copynumber: 2.9 Consensus size: 24
825546 AAAAGATAAG
* *
825556 ATAAAG-AAAGTAAAGATAAAATA
1 ATAAAGAAAAATAAAGATAAAAAA
* * *
825579 GT-AAGTAAAATAAATATAAAAAA
1 ATAAAGAAAAATAAAGATAAAAAA
825602 ATAAAGAAAAATAAAGA-AAAA
1 ATAAAGAAAAATAAAGATAAAA
825623 GAAGGAAAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
22 3 0.09
23 20 0.57
24 12 0.34
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.16
Consensus pattern (24 bp):
ATAAAGAAAAATAAAGATAAAAAA
Found at i:825823 original size:74 final size:75
Alignment explanation
Indices: 825665--825808 Score: 165
Period size: 74 Copynumber: 2.0 Consensus size: 75
825655 ATAAAATAAT
* * *
825665 AAAA-ATAAAATAAAAATAATATATATATATATAATAAATAAAAAATAGTATATATATATAAATT
1 AAAATATAAAATAAAAATAATATATATATATATAATAAATAAAAAATAGAAAATATATATAAAGT
825729 AATAAAAATG
66 AATAAAAATG
* * *
825739 ATAATA-AAAAT-AATATACATATATATATATATAATCTAA-AAAAAATA-AAAATATATACTAA
1 AAAATATAAAATAAAAATA-ATATATATATATATAAT-AAATAAAAAATAGAAAATATATA-TAA
825800 AGTAA-AAAA
63 AGTAATAAAA
825809 GAAAATGCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
73 17 0.28
74 40 0.67
75 3 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (75 bp):
AAAATATAAAATAAAAATAATATATATATATATAATAAATAAAAAATAGAAAATATATATAAAGT
AATAAAAATG
Found at i:826523 original size:15 final size:15
Alignment explanation
Indices: 826503--826543 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
826493 GTTATGCAAG
826503 TCTTCATTCTCCTGA
1 TCTTCATTCTCCTGA
826518 TCTTCATTCTCCTGA
1 TCTTCATTCTCCTGA
826533 TCTTCATTCTC
1 TCTTCATTCTC
826544 GTTCCTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.12, C:0.34, G:0.05, T:0.49
Consensus pattern (15 bp):
TCTTCATTCTCCTGA
Found at i:826988 original size:45 final size:45
Alignment explanation
Indices: 826939--827032 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
826929 TGTAACATGT
826939 TTAATATTTTTATTGCATTATTTTAAAACTAGGTATTATCTTGAG
1 TTAATATTTTTATTGCATTATTTTAAAACTAGGTATTATCTTGAG
826984 TTAATATTTTTATTGCATTATTTTAAAACTAGGTATTATCTTGAG
1 TTAATATTTTTATTGCATTATTTTAAAACTAGGTATTATCTTGAG
827029 TTAA
1 TTAA
827033 GTAGGCTTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.32, C:0.06, G:0.11, T:0.51
Consensus pattern (45 bp):
TTAATATTTTTATTGCATTATTTTAAAACTAGGTATTATCTTGAG
Found at i:829267 original size:22 final size:22
Alignment explanation
Indices: 829242--829287 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
829232 ATGCTCAAAG
* *
829242 GTGGATAGATGTGGTAATACAA
1 GTGGATAGATATGGCAATACAA
*
829264 GTGGATAGATATGGCAATATAA
1 GTGGATAGATATGGCAATACAA
829286 GT
1 GT
829288 ACATCCACCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.30, T:0.28
Consensus pattern (22 bp):
GTGGATAGATATGGCAATACAA
Found at i:832687 original size:20 final size:20
Alignment explanation
Indices: 832638--832693 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 20
832628 CACCAGAAGG
*
832638 GGGTATCGATACCATAGTAT
1 GGGTATCGATACCATAGTAA
*
832658 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
832680 GGGTATCGATACCA
1 GGGTATCGATACCA
832694 GGAAACATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.44
22 18 0.56
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:832712 original size:95 final size:96
Alignment explanation
Indices: 832562--832762 Score: 273
Period size: 95 Copynumber: 2.1 Consensus size: 96
832552 ATACCGACGA
* * *
832562 GGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGCAACATCGAATCTAATTTTTGTATCG
1 GGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACATCAAATCTAATTTTGGTATCG
832627 ACACCAGAAGGGGGTATC-GATACCATAGTAT
66 ACACCAGAAGGGGGTATCAG-TACCATAGTAT
* *
832658 GGTAGTATCGATACCATGGTAA-GGGTATCGATACCAGGAAACATCAAA-CTTAATTTTGGTATC
1 GGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACATCAAATC-TAATTTTGGTATC
* * *
832721 GATACTAGAAGGGGGTATCAGTAGCATAGTAT
65 GACACCAGAAGGGGGTATCAGTACCATAGTAT
* *
832753 AGAAGTATCG
1 GGTAGTATCG
832763 GTACTAGGGT
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
94 1 0.01
95 70 0.75
96 22 0.24
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.26
Consensus pattern (96 bp):
GGTAGTATCGATACCATGATAAGGGGTATCGATACCAAGAAACATCAAATCTAATTTTGGTATCG
ACACCAGAAGGGGGTATCAGTACCATAGTAT
Found at i:833198 original size:55 final size:55
Alignment explanation
Indices: 833111--833412 Score: 401
Period size: 55 Copynumber: 5.3 Consensus size: 55
833101 CTATGTGTAC
* * * *
833111 TACAGGCACATT-GTGTTCATATTCACGAAATTCATAATGAGTTAATGAATCATCG
1 TACAGGCAC-TTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCG
833166 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCGTATAGCCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAAT---C--AT---CG
* * *
833229 TATAGGCACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCG
*
833284 TACAGGCACTTCATGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCG
*
833339 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGGTGAATCATCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCG
* *
833394 AACATGCACTAT-GTGTGCA
1 TACAGGCACT-TCGTGTGCA
833413 GCCCACAGAA
Statistics
Matches: 222, Mismatches: 15, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
54 2 0.01
55 164 0.74
56 1 0.00
58 2 0.01
60 3 0.01
63 50 0.23
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (55 bp):
TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCATCG
Found at i:839276 original size:19 final size:20
Alignment explanation
Indices: 839252--839302 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
839242 CGGCCAAGAG
* *
839252 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
839271 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
839291 CATGTATTTTCA
1 CATGTATTTTCA
839303 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:842138 original size:19 final size:20
Alignment explanation
Indices: 842099--842139 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
842089 ATCAGATTGT
*
842099 CCAGGGGGTACAGGTTCCCC
1 CCAGGGGGTACAGATTCCCC
842119 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
842139 C
1 C
842140 TGCAGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.37, G:0.32, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:842223 original size:20 final size:20
Alignment explanation
Indices: 842172--842234 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 20
842162 AACAGAATGT
842172 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATT-CCCC
* * *
842193 CGCAAGAGGTACCGATTCCCC
1 C-CAGGGGGTACAGATTCCCC
842214 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
842234 C
1 C
842235 TGCAGGTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
20 17 0.49
21 6 0.17
22 12 0.34
ACGTcount: A:0.21, C:0.38, G:0.27, T:0.14
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:842268 original size:95 final size:95
Alignment explanation
Indices: 842113--842286 Score: 330
Period size: 95 Copynumber: 1.8 Consensus size: 95
842103 GGGGTACAGG
842113 TTCCCCCCAGGGGGTACAGATTCCCCCTGCAGGTTTTTGACTCTGAGAAAACAGAATGTCCAGGG
1 TTCCCCCCAGGGGGTACAGATTCCCCCTGCAGGTTTTTGACTCTGAGAAAACAGAATGTCCAGGG
842178 GGTACAGATTCCCCCCGCAAGAGGTACCGA
66 GGTACAGATTCCCCCCGCAAGAGGTACCGA
*
842208 TTCCCCCCAGGGGGTACAGATTCCCCCTGCAGGTTTTTGACTCTGAGAAAATAGAATGTCCAGGG
1 TTCCCCCCAGGGGGTACAGATTCCCCCTGCAGGTTTTTGACTCTGAGAAAACAGAATGTCCAGGG
*
842273 GGTACTGATTCCCC
66 GGTACAGATTCCCC
842287 TCTGTCTAAC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
95 77 1.00
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (95 bp):
TTCCCCCCAGGGGGTACAGATTCCCCCTGCAGGTTTTTGACTCTGAGAAAACAGAATGTCCAGGG
GGTACAGATTCCCCCCGCAAGAGGTACCGA
Found at i:846169 original size:95 final size:96
Alignment explanation
Indices: 846000--846198 Score: 249
Period size: 95 Copynumber: 2.1 Consensus size: 96
845990 TACCGATGAG
* * * * *
846000 GTAGTATCGATACCATGATAAGGGGTACCGATACTAAGCAACATTGAATCTAATTTTGGTATCAA
1 GTAGTATCAATACCATGATAAGGGGTACCAATACCAAGAAACATCGAATCTAATTTTGGTATCAA
846065 TACCAGAAGGGGGTATCGGTACCATAGTATA
66 TACCAGAAGGGGGTATCGGTACCATAGTATA
* * * *
846096 GTAGTATCAATACCATGATAA-GGGTATCAATTCCAGGAAACATCGAA-CTTAATTTTGGTATCG
1 GTAGTATCAATACCATGATAAGGGGTACCAATACCAAGAAACATCGAATC-TAATTTTGGTATCA
* ** *
846159 GTACTGGAAGGGGGTATCGGTAGCATAGTATA
65 ATACCAGAAGGGGGTATCGGTACCATAGTATA
*
846191 GAAGTATC
1 GTAGTATC
846199 GGTACCAGGG
Statistics
Matches: 88, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
94 1 0.01
95 67 0.76
96 20 0.23
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (96 bp):
GTAGTATCAATACCATGATAAGGGGTACCAATACCAAGAAACATCGAATCTAATTTTGGTATCAA
TACCAGAAGGGGGTATCGGTACCATAGTATA
Found at i:846638 original size:55 final size:55
Alignment explanation
Indices: 846550--846840 Score: 381
Period size: 55 Copynumber: 5.3 Consensus size: 55
846540 TGTGTACTAT
* * *
846550 AGGCACTTCATGTGCATATTCAC-ATAATTCATCATTAGTTGATGAATCACCATAC
1 AGGCACTTCGTGTGCATATTCACGA-AATTCATCATGAGTTGATGAATCACCGTAC
* * * *
846605 ATGG-ACTTCGTGTGCATATTCATGGAATTCATCATGAGTTAATGAATCACCATAC
1 A-GGCACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTAC
* * * *
846660 AAGCACTTTGTGTGCATATTCACGAAATTCATCTTGAGTTGATGAATCACCGTGC
1 AGGCACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTAC
* * *
846715 CGGCACTTCGTTTGTATATTCACGAAATTCATCATGAGTTGATGAATCACCGTAC
1 AGGCACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTAC
* *
846770 AGGCACTTCGTGTGCATATTCACGGAATTCATCATAAGTTGATGAATCACCGTAC
1 AGGCACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTAC
*
846825 AGGAACTAT-GTGTGCA
1 AGGCACT-TCGTGTGCA
846841 GCCCACAGAA
Statistics
Matches: 206, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
54 1 0.00
55 202 0.98
56 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (55 bp):
AGGCACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTAC
Found at i:846861 original size:17 final size:17
Alignment explanation
Indices: 846839--846874 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
846829 ACTATGTGTG
846839 CAGCCCAC-AGAATTCAT
1 CAGCCCACGA-AATTCAT
846856 CAGCCCACGAAATTCAT
1 CAGCCCACGAAATTCAT
846873 CA
1 CA
846875 TAAGTTGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.36, C:0.36, G:0.11, T:0.17
Consensus pattern (17 bp):
CAGCCCACGAAATTCAT
Found at i:852931 original size:20 final size:20
Alignment explanation
Indices: 852882--852935 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 20
852872 TGCGAGAAGG
*
852882 GGGTATCGATACCATAGTAT
1 GGGTATCGATACCATAGTAA
* *
852902 GGTAGTATCGATTCCATGGTAA
1 GG--GTATCGATACCATAGTAA
852924 GGGTATCGATAC
1 GGGTATCGATAC
852936 ATGGAAACAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 11 0.39
22 17 0.61
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:853004 original size:95 final size:95
Alignment explanation
Indices: 852829--853006 Score: 245
Period size: 95 Copynumber: 1.9 Consensus size: 95
852819 CCATCATAAG
* *
852829 GGGTATCGATACCAAGCAACATTGAATCTAATTTTGGTATCGATGCGAGAAGGGGGTATCGATAC
1 GGGTATCGATACCAAGAAACATTGAATCTAATTTTGGTATCGATACGAGAAGGGGGTATCGATAC
* *
852894 CATAGTATGGTAGTATCGATTCCATGGTAA
66 CATAGTATAGAAGTATCGATTCCATGGTAA
* *
852924 GGGTATCGATA-CATGGAAACATTGAA-CTTAATTTTGGTATCGATACTG-GAAGGGGGTATCGG
1 GGGTATCGATACCA-AGAAACATTGAATC-TAATTTTGGTATCGATAC-GAGAAGGGGGTATCGA
*
852986 TACCATAGTGTAGAAGTATCG
63 TACCATAGTATAGAAGTATCG
853007 GTACCAGGGT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
94 3 0.04
95 69 0.95
96 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.28, T:0.29
Consensus pattern (95 bp):
GGGTATCGATACCAAGAAACATTGAATCTAATTTTGGTATCGATACGAGAAGGGGGTATCGATAC
CATAGTATAGAAGTATCGATTCCATGGTAA
Found at i:853023 original size:20 final size:21
Alignment explanation
Indices: 852979--853026 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
852969 CTGGAAGGGG
*
852979 GTATCGGTACCATAGTGTAGAA
1 GTATCGGTACCA-AGGGTAGAA
*
853001 GTATCGGTACC-AGGGTAGTA
1 GTATCGGTACCAAGGGTAGAA
853021 GTATCG
1 GTATCG
853027 ATATTATGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (21 bp):
GTATCGGTACCAAGGGTAGAA
Found at i:853025 original size:95 final size:95
Alignment explanation
Indices: 852846--853029 Score: 239
Period size: 95 Copynumber: 1.9 Consensus size: 95
852836 GATACCAAGC
* * *
852846 AACATTGAATCTAATTTTGGTATCGATGCGAGAAGGGGGTATCGATACCATAGTATGGTAGTATC
1 AACATTGAATCTAATTTTGGTATCGATACGAGAAGGGGGTATCGATACCATAGTATAGAAGTATC
* * *
852911 GATTCCATGGTAAGGGTATCGATACATGGA
66 GATACCAGGGTAAGAGTATCGATACATGGA
* *
852941 AACATTGAA-CTTAATTTTGGTATCGATACTG-GAAGGGGGTATCGGTACCATAGTGTAGAAGTA
1 AACATTGAATC-TAATTTTGGTATCGATAC-GAGAAGGGGGTATCGATACCATAGTATAGAAGTA
*
853004 TCGGTACCAGGGT-AGTAGTATCGATA
64 TCGATACCAGGGTAAG-AGTATCGATA
853030 TTATGTAGAC
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
94 3 0.04
95 73 0.95
96 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.29
Consensus pattern (95 bp):
AACATTGAATCTAATTTTGGTATCGATACGAGAAGGGGGTATCGATACCATAGTATAGAAGTATC
GATACCAGGGTAAGAGTATCGATACATGGA
Found at i:853430 original size:55 final size:55
Alignment explanation
Indices: 853341--853719 Score: 557
Period size: 55 Copynumber: 6.9 Consensus size: 55
853331 CTATGTGTAC
*
853341 TACAGGCACTTCTTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* *
853396 TACATGCACTTCGTGTGCATATTCACGGAATTCATAATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* *
853451 TACAGGCACTTCGTTTTCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* *
853506 TACAGGCACTTCATGTGCATATTCACGGATTTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
*
853561 TACAGGCACTTCGTGTGTATATTCACGGAATTCATCATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* * * * *
853616 TACATGCAGTTCATGTGCATATTCACGAAATTCATAATGAGTTGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
* ** * *
853671 TACAGGCGCTAT-GTGTG-A-AGCCCACGAAATTCATCATAAGTTGATGAAT
1 TACAGGCACT-TCGTGTGCATA-TTCACGGAATTCATCATGAGTTGATGAAT
853720 TCCCATATAG
Statistics
Matches: 294, Mismatches: 28, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
53 1 0.00
54 26 0.09
55 266 0.90
56 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (55 bp):
TACAGGCACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACCG
Found at i:855088 original size:29 final size:31
Alignment explanation
Indices: 855037--855098 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
855027 AAAATTTAAA
* *
855037 TAGTGACCAAAATGGAAA-TTTTG-AAAGTT
1 TAGTGACCAAAATAGAAACTTTGGAAAAGTT
* *
855066 TAGTGACCAAAGTATAAACTTTGGAAAAGTT
1 TAGTGACCAAAATAGAAACTTTGGAAAAGTT
855097 TA
1 TA
855099 AGGACTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 15 0.56
30 4 0.15
31 8 0.30
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (31 bp):
TAGTGACCAAAATAGAAACTTTGGAAAAGTT
Found at i:856864 original size:24 final size:24
Alignment explanation
Indices: 856837--856884 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
856827 GCATGACATG
856837 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
856861 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
856885 CTGGAAGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCAT
Found at i:871487 original size:3 final size:3
Alignment explanation
Indices: 871479--871507 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
871469 ATTTTTACCA
871479 ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
871508 TTTTTCAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:873010 original size:35 final size:35
Alignment explanation
Indices: 872931--873011 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
872921 ATGTTTTTTG
* * **
872931 AAACTGCCTTATTAAGATTTTAATTTTTTTTTTCA
1 AAACTACCTCATTAAGATTTTAATTTTTTTTGACA
*
872966 AAACTACCTCATTAAGATTTTAATTTTTTTTGAGA
1 AAACTACCTCATTAAGATTTTAATTTTTTTTGACA
873001 AAA-TAACCTCA
1 AAACT-ACCTCA
873012 GTGACAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 1 0.03
35 39 0.98
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.46
Consensus pattern (35 bp):
AAACTACCTCATTAAGATTTTAATTTTTTTTGACA
Found at i:873168 original size:21 final size:21
Alignment explanation
Indices: 873142--873194 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
873132 GTTTCCAGAT
873142 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
*
873163 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
873184 TCGCAATGCGA
1 TCGCAACGCGA
873195 TTTTCCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.32, G:0.21, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:873247 original size:42 final size:40
Alignment explanation
Indices: 873190--873277 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 40
873180 ACTATCGCAA
873190 TGCGA-TTTTCCAAATT-CGTTGAGATAGTCCAAGTTCGCGT
1 TGCGATTTTTCCAAATTCCGTTGAGATAGTCCAAGTT--CGT
*
873230 TGCGATTTATTCCAAATTCGCGTTGTGATAGTCCAAGTTCGT
1 TGCGATTT-TTCCAAATTC-CGTTGAGATAGTCCAAGTTCGT
873272 TGCGAT
1 TGCGAT
873278 AGTCAAAGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
40 5 0.12
41 2 0.05
42 18 0.42
44 18 0.42
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (40 bp):
TGCGATTTTTCCAAATTCCGTTGAGATAGTCCAAGTTCGT
Found at i:873297 original size:63 final size:61
Alignment explanation
Indices: 873198--873340 Score: 196
Period size: 63 Copynumber: 2.3 Consensus size: 61
873188 AATGCGATTT
* * * *
873198 TCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGTGATAG
1 TCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTGCGATAG
*
873261 TCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
*
873322 TCGAAGTTCGCGTTGCGAT
1 TCCAAGTT--CGTTGCGAT
873341 TTATTCCAAG
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
61 17 0.24
63 55 0.76
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (61 bp):
TCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAG
Found at i:873307 original size:42 final size:42
Alignment explanation
Indices: 873261--873392 Score: 246
Period size: 42 Copynumber: 3.1 Consensus size: 42
873251 GTTGTGATAG
*
873261 TCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
873303 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
873345 TCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
873387 TCCAAG
1 TCCAAG
873393 CATAGCTATA
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (42 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:873329 original size:105 final size:102
Alignment explanation
Indices: 873190--873382 Score: 289
Period size: 105 Copynumber: 1.9 Consensus size: 102
873180 ACTATCGCAA
873190 TGCGATTTTCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTG
1 TGCGATTTTCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CGTTG
873255 TGATAGTCCAAGTT-CGTTGCGATAGTCAAAGTTCGCGT
64 TGATAGTCCAAGTTCCGTTGCGATAGTCAAAGTTCGCGT
* * * *
873293 TGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTG
1 TGCGA-TT-TTCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTG
*
873358 TGATAGTCGAAGTTCGCGTTGCGAT
64 TGATAGTCCAAGTTC-CGTTGCGAT
873383 TTATTCCAAG
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
103 23 0.28
104 2 0.02
105 56 0.69
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (102 bp):
TGCGATTTTCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGTG
ATAGTCCAAGTTCCGTTGCGATAGTCAAAGTTCGCGT
Found at i:873357 original size:63 final size:61
Alignment explanation
Indices: 873198--873357 Score: 180
Period size: 63 Copynumber: 2.5 Consensus size: 61
873188 AATGCGATTT
* * *
873198 TCCAAATTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGTGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTC-CGTTGCGATTTATTCCAAATTC-CGTTGCGATAG
* *
873261 TCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAGTT-CGTTGCGATAG
1 TCCAAGTTCGTTGCGATAGTCCAAGTTC-CGTTGCGATTTATTCCAAATTCCGTTGCGATAG
* *
873322 TCGAAGTTCGCGTTGCGATTTATTCCAAGTT-CGTTG
1 TCCAAGTT--CGTTGCGA--TAGTCCAAGTTCCGTTG
873358 TGATAGTCGA
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
61 17 0.20
63 59 0.69
65 9 0.11
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (61 bp):
TCCAAGTTCGTTGCGATAGTCCAAGTTCCGTTGCGATTTATTCCAAATTCCGTTGCGATAG
Found at i:877569 original size:198 final size:198
Alignment explanation
Indices: 877231--877625 Score: 727
Period size: 198 Copynumber: 2.0 Consensus size: 198
877221 ATTAAAAAAG
*
877231 TTGTAATCAAAATTACATTCTTTTAATGTTTACTTATTGTATTCGGGATAATTAAAATCATATGT
1 TTGTAATCAAAATTACATTCTTTTAATGTTTACTTACTGTATTCGGGATAATTAAAATCATATGT
877296 ATATCAAATATACATATATTAACTCCAGATATATTTTAGTAACATAAAACAAATTTTGCATATTT
66 ATATCAAATATACATATATTAACTCCAGATATATTTTAGTAACATAAAACAAATTTTGCATATTT
* *
877361 TCTCATTTCAATCATATGGTGTGACCCTGTAGGTTCTTGTAACGTTAGTAGTAATTATTAGAACA
131 GCTCATTTCAATCATAGGGTGTGACCCTGTAGGTTCTTGTAACGTTAGTAGTAATTATTAGAACA
877426 ATT
196 ATT
877429 TTGTAATCAAAATTACATTCTTTTAATGTTTACTTACTGTATTCGGGATAATTAAAATCATATGT
1 TTGTAATCAAAATTACATTCTTTTAATGTTTACTTACTGTATTCGGGATAATTAAAATCATATGT
* *
877494 ATATCAAATATACATATATTAACTCCAGATATATTTTAGTAACATACAACAAATTTTGCATCTTT
66 ATATCAAATATACATATATTAACTCCAGATATATTTTAGTAACATAAAACAAATTTTGCATATTT
* *
877559 GCTCATTTCAATCCTAGGGTGTGACCCTGTAGGTTCTTGTAATGTTAGTAGTAATTATTAGAACA
131 GCTCATTTCAATCATAGGGTGTGACCCTGTAGGTTCTTGTAACGTTAGTAGTAATTATTAGAACA
877624 AT
196 AT
877626 CTAATATTAC
Statistics
Matches: 190, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
198 190 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (198 bp):
TTGTAATCAAAATTACATTCTTTTAATGTTTACTTACTGTATTCGGGATAATTAAAATCATATGT
ATATCAAATATACATATATTAACTCCAGATATATTTTAGTAACATAAAACAAATTTTGCATATTT
GCTCATTTCAATCATAGGGTGTGACCCTGTAGGTTCTTGTAACGTTAGTAGTAATTATTAGAACA
ATT
Found at i:884279 original size:17 final size:17
Alignment explanation
Indices: 884257--884304 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
884247 CTGTTGACCA
884257 TTGACCATTGATCGCCG
1 TTGACCATTGATCGCCG
* *
884274 TTGACCATTGACCACCG
1 TTGACCATTGATCGCCG
*
884291 TTGACCATTTATCG
1 TTGACCATTGATCG
884305 TTGACCGCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (17 bp):
TTGACCATTGATCGCCG
Found at i:891157 original size:15 final size:15
Alignment explanation
Indices: 891136--891179 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
891126 GGACCGGTTA
891136 AGATCGAGCCGAACT
1 AGATCGAGCCGAACT
* *
891151 GGATCGAACCGAACT
1 AGATCGAGCCGAACT
891166 AGA-CTGAGCCGAAC
1 AGATC-GAGCCGAAC
891180 CGTTAACTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 1 0.04
15 23 0.96
ACGTcount: A:0.34, C:0.27, G:0.27, T:0.11
Consensus pattern (15 bp):
AGATCGAGCCGAACT
Found at i:895639 original size:24 final size:24
Alignment explanation
Indices: 895611--895658 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
895601 AGCTGGAGGA
895611 GCTTAAGGCTAGATAAACTTAGCT
1 GCTTAAGGCTAGATAAACTTAGCT
895635 GCTTAAGGCTAGATAAACTTAGCT
1 GCTTAAGGCTAGATAAACTTAGCT
895659 AGTTGGACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (24 bp):
GCTTAAGGCTAGATAAACTTAGCT
Found at i:901513 original size:17 final size:17
Alignment explanation
Indices: 901491--901527 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
901481 AATGTCATGT
901491 AACCCAATTTGTTTACC
1 AACCCAATTTGTTTACC
901508 AACCCAATTTGTTTACC
1 AACCCAATTTGTTTACC
901525 AAC
1 AAC
901528 AAACATGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.05, T:0.32
Consensus pattern (17 bp):
AACCCAATTTGTTTACC
Found at i:901774 original size:2 final size:2
Alignment explanation
Indices: 901769--901800 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
901759 TGCGCGCGCG
901769 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
901801 AGCTACAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:903235 original size:2 final size:2
Alignment explanation
Indices: 903230--903284 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
903220 CTTCACACAC
903230 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
903272 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
903285 CACTTGCATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:911779 original size:16 final size:16
Alignment explanation
Indices: 911758--911788 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
911748 GAACATATGA
*
911758 CTAGTTTTAATTAGTT
1 CTAGTTTGAATTAGTT
911774 CTAGTTTGAATTAGT
1 CTAGTTTGAATTAGT
911789 GATCGAGCAT
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:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (16 bp):
CTAGTTTGAATTAGTT
Found at i:913602 original size:13 final size:13
Alignment explanation
Indices: 913584--913608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
913574 CCCAATTTAC
913584 ATATTGTTTATGA
1 ATATTGTTTATGA
913597 ATATTGTTTATG
1 ATATTGTTTATG
913609 GACTAATGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
ATATTGTTTATGA
Found at i:915820 original size:24 final size:24
Alignment explanation
Indices: 915783--915860 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
915773 TCGGGCTTTG
*
915783 TATATAATAATAATAATATTATTAT
1 TATATCAT-ATAATAATATTATTAT
915808 TATATCATATAATAATATTATTAT
1 TATATCATATAATAATATTATTAT
915832 TATATCATATAATAATATTATTAT
1 TATATCATATAATAATATTATTAT
915856 ATATA
1 -TATA
915861 ATAGATACGT
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
24 40 0.78
25 11 0.22
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATCATATAATAATATTATTAT
Found at i:915828 original size:18 final size:18
Alignment explanation
Indices: 915783--915863 Score: 60
Period size: 16 Copynumber: 4.5 Consensus size: 18
915773 TCGGGCTTTG
* *
915783 TATATAATAATAATAATA
1 TATATAATAATATTATTA
* * *
915801 T-TATTATTATATCA-TA
1 TATATAATAATATTATTA
*
915817 TA-ATAATATTATTATTATA
1 TATATAATAATATTA-T-TA
915836 TCATATAATAATATTATTA
1 T-ATATAATAATATTATTA
915855 TATATAATA
1 TATATAATA
915864 GATACGTCAC
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
16 11 0.23
17 9 0.19
18 9 0.19
19 6 0.12
20 2 0.04
21 11 0.23
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATAATAATATTATTA
Found at i:922309 original size:3 final size:3
Alignment explanation
Indices: 922303--922344 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
922293 ATTTATTTAT
922303 TTA TTA TTA TTA TTA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
922345 AAAAATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:922309 original size:15 final size:14
Alignment explanation
Indices: 922295--922340 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 14
922285 TTTTTTTTAT
922295 TTATTTATTTATTA
1 TTATTTATTTATTA
922309 TTA-TTA-TTATTA
1 TTATTTATTTATTA
*
922321 TTATATATATTATTA
1 TTATTTAT-TTATTA
922336 TTATT
1 TTATT
922341 ATTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 9 0.33
13 5 0.19
14 3 0.11
15 10 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTATTTATTA
Found at i:923662 original size:16 final size:15
Alignment explanation
Indices: 923614--923659 Score: 67
Period size: 16 Copynumber: 3.1 Consensus size: 15
923604 TTATTTGCAA
923614 TATTA-TTTTATTAT
1 TATTATTTTTATTAT
*
923628 TATTGTTTTTAATTAT
1 TATTATTTTT-ATTAT
923644 TATTATTTTTATTAT
1 TATTATTTTTATTAT
923659 T
1 T
923660 TATATAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.14
15 10 0.36
16 14 0.50
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (15 bp):
TATTATTTTTATTAT
Found at i:923662 original size:19 final size:20
Alignment explanation
Indices: 923614--923662 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
923604 TTATTTGCAA
923614 TATTATTTTATTATTATTGTT
1 TATTA-TTTATTATTATTGTT
*
923635 T-TTAATTATTATTATT-TT
1 TATTATTTATTATTATTGTT
923653 TATTATTTAT
1 TATTATTTAT
923663 ATAAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 3 0.12
19 18 0.72
20 3 0.12
21 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (20 bp):
TATTATTTATTATTATTGTT
Found at i:923672 original size:2 final size:2
Alignment explanation
Indices: 923660--923695 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
923650 TTTTATTATT
*
923660 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
923696 TTGTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:925991 original size:8 final size:7
Alignment explanation
Indices: 925967--926008 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
925957 TTTTCATACA
925967 TGCA-TT
1 TGCATTT
925973 TGCATTT
1 TGCATTT
925980 TGCATCTT
1 TGCAT-TT
925988 TGCATTT
1 TGCATTT
* *
925995 TTCATTG
1 TGCATTT
926002 TGCATTT
1 TGCATTT
926009 ATACTCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:925991 original size:15 final size:14
Alignment explanation
Indices: 925967--926008 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
925957 TTTTCATACA
925967 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
925980 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
925995 TTCATTGTGCATTT
1 TGCATTTTGCATTT
926009 ATACTCTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:929079 original size:2 final size:2
Alignment explanation
Indices: 929072--929107 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
929062 TTATCCTTTA
929072 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
929108 CCTTTGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:929424 original size:26 final size:26
Alignment explanation
Indices: 929394--929471 Score: 106
Period size: 26 Copynumber: 3.0 Consensus size: 26
929384 TAGTATACTC
929394 ATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
929420 ATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
** *
929446 A-AGAGGAAA-AAAGAAAAAAAGAAAA
1 ATCCAGCAAAGAAAG-AAAAAAGAAAA
929471 A
1 A
929472 AAAGGAAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
24 4 0.08
25 17 0.35
26 27 0.56
ACGTcount: A:0.73, C:0.08, G:0.17, T:0.03
Consensus pattern (26 bp):
ATCCAGCAAAGAAAGAAAAAAGAAAA
Found at i:929448 original size:18 final size:17
Alignment explanation
Indices: 929427--929507 Score: 83
Period size: 17 Copynumber: 4.6 Consensus size: 17
929417 AAAATCCAGC
929427 AAAGAAAGAAAAAAGAAA
1 AAAGAAA-AAAAAAGAAA
**
929445 AAAGAGGAAAAAAGAAAA
1 AAAGAAAAAAAAAG-AAA
*
929463 AAAGAAAAAAAAGGAAA
1 AAAGAAAAAAAAAGAAA
*
929480 GAAGAAAAAAAACA-AAA
1 AAAGAAAAAAAA-AGAAA
*
929497 AAATAAAAAAA
1 AAAGAAAAAAA
929508 TCGAATCAGG
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
17 33 0.63
18 19 0.37
ACGTcount: A:0.83, C:0.01, G:0.15, T:0.01
Consensus pattern (17 bp):
AAAGAAAAAAAAAGAAA
Found at i:929456 original size:17 final size:15
Alignment explanation
Indices: 929431--929507 Score: 70
Period size: 14 Copynumber: 5.2 Consensus size: 15
929421 TCCAGCAAAG
929431 AAAGAAAAAAGAAAA
1 AAAGAAAAAAGAAAA
929446 AAGAGGAAAAAAGAAAA
1 AA-A-GAAAAAAGAAAA
**
929463 AAAGAAAAAA-AAGG
1 AAAGAAAAAAGAAAA
*
929477 AAAGAAGAAA-AAAA
1 AAAGAAAAAAGAAAA
* *
929491 ACA-AAAAAATAAAA
1 AAAGAAAAAAGAAAA
929505 AAA
1 AAA
929508 TCGAATCAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
13 5 0.10
14 21 0.41
15 9 0.18
16 2 0.04
17 14 0.27
ACGTcount: A:0.83, C:0.01, G:0.14, T:0.01
Consensus pattern (15 bp):
AAAGAAAAAAGAAAA
Found at i:929463 original size:8 final size:8
Alignment explanation
Indices: 929431--929507 Score: 75
Period size: 8 Copynumber: 9.4 Consensus size: 8
929421 TCCAGCAAAG
929431 AAAG-AAA
1 AAAGAAAA
929438 AAAGAAAA
1 AAAGAAAA
*
929446 AAGAGGAAA
1 AA-AGAAAA
929455 AAAGAAAA
1 AAAGAAAA
929463 AAAGAAAAA
1 AAAG-AAAA
*
929472 AAAGGAAA
1 AAAGAAAA
*
929480 GAAGAAAAA
1 AAAG-AAAA
*
929489 AAACAAAA
1 AAAGAAAA
*
929497 AAATAAAA
1 AAAGAAAA
929505 AAA
1 AAA
929508 TCGAATCAGG
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
7 4 0.07
8 34 0.59
9 20 0.34
ACGTcount: A:0.83, C:0.01, G:0.14, T:0.01
Consensus pattern (8 bp):
AAAGAAAA
Found at i:929463 original size:25 final size:24
Alignment explanation
Indices: 929435--929499 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 24
929425 GCAAAGAAAG
929435 AAAAAAGAAAAAAGAGGAAAAAAGA
1 AAAAAAGAAAAAA-AGGAAAAAAGA
*
929460 AAAAAAGAAAAAAAAGGAAAGAAGAA
1 AAAAAAG-AAAAAAAGGAAAAAAG-A
*
929486 AAAAAACAAAAAAA
1 AAAAAAGAAAAAAA
929500 TAAAAAAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
25 23 0.64
26 13 0.36
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAAGAAAAAAAGGAAAAAAGA
Found at i:932060 original size:114 final size:114
Alignment explanation
Indices: 931722--932060 Score: 536
Period size: 113 Copynumber: 3.0 Consensus size: 114
931712 AAGTGCCATG
** *
931722 TGCTCATAGTAGAAATAAAAAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
*
931787 TGGTTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
*
931836 TGCTCATAGTAGAAATAAGGAG-CCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATC
1 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
931900 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTAAAAAATGAATT
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
* * *
931949 TGCTCATAGTAGAAATAAGGAGACCCAATAGCCTCTTCTGGAAATGTTCTTTGAGTTATCTGATA
1 TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * * * *
932014 TGGTTCGGTAGGAACCACAGAACCAATCATTAGAATTGAAAGATGAA
66 TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAA
932061 CTGCATGATC
Statistics
Matches: 206, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
113 108 0.52
114 98 0.48
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (114 bp):
TGCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATT
Found at i:934613 original size:22 final size:22
Alignment explanation
Indices: 934582--934636 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
934572 ATCTACACTC
934582 TTCAAAGATGATAGATTCTCGTT
1 TTCAAAGATGATAGATTCTC-TT
934605 TT-AAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
934626 TTCAAAGATGA
1 TTCAAAGATGA
934637 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.13
22 25 0.81
23 2 0.06
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:935722 original size:342 final size:339
Alignment explanation
Indices: 935043--935808 Score: 1110
Period size: 342 Copynumber: 2.3 Consensus size: 339
935033 GATTCAAATC
935043 CATCACTTGATGGATCAGCTTTTCTAGAAAAAGTTCATAAT--G-AGAACTCATCTGAAGAAGGA
1 CATCACTTGATGGATCAGCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
935105 AGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
*** ** *
935170 GGTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
131 ACATCCCCAGAAAAAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
* * * *
935235 AGAATAATTTGTTCAACCTTTTGCTCAAATCTATCATTTGATGGATCAGCTTTTCCAGAAAAAGT
196 AGAAGAACTTGTTCAACCTTTTGCTCAAATCTATCATTTGATGGATCAGCATTGCCAGAAAAAGT
* *
935300 TCATAATGAGAAGAACTCATCTGAATAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
261 TCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
* *
935365 CTTTTGTTTGAATT
326 CTTTTGCTCGAATT
*
935379 CATCACTTGATGGATCAGCTTTTCCAGAAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCACTTGATGGATCAGCTTTTCTAG-AAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * ** *
935444 AAGAAGAAGTTCATAATGAAAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATC
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATC
* *
935509 AACATCCCCAGTGAAAGAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
130 AACATCCCCA--GAAAAAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAATTCATA
** **
935574 ATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAAT-TCATCATTTGATGGATCAGCATTGCCAGGG
193 ATGAGAAGAACTTGTTCAACCTTTT-GCTCAAATCT-ATCATTTGATGGATCAGCATTGCCAGAA
** *
935637 CGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTGT
256 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGT
*
935702 TCAACTTTTTGCTCGAATT
321 TCAACCTTTTGCTCGAATT
* * * * * * *
935721 CATCACTCGATAGATCAACTTTTTTAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGA
1 CATCACTTGATGGATCAGCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
935786 AGAAGAAGTTCATAATGAGAAGA
66 AGAAGAAGTTCATAATGAGAAGA
935809 GCTTGTTTGA
Statistics
Matches: 382, Mismatches: 40, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
336 26 0.07
337 14 0.04
339 1 0.00
340 83 0.22
341 63 0.16
342 195 0.51
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (339 bp):
CATCACTTGATGGATCAGCTTTTCTAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCATTTGATGGATCA
ACATCCCCAGAAAAAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAATTCATAATG
AGAAGAACTTGTTCAACCTTTTGCTCAAATCTATCATTTGATGGATCAGCATTGCCAGAAAAAGT
TCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAC
CTTTTGCTCGAATT
Done.