Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008888.1 Hibiscus syriacus cultivar Beakdansim tig00112153_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: 1025554
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:688520 original size:165 final size:165
Alignment explanation
Indices: 688248--688577 Score: 660
Period size: 165 Copynumber: 2.0 Consensus size: 165
688238 CCCTCACCAC
688248 GCCATTGTTATATCCCTCTCCCCAAATCTTTTATTTTTCTTGGAGAGTTAATAATAATGGCGGTT
1 GCCATTGTTATATCCCTCTCCCCAAATCTTTTATTTTTCTTGGAGAGTTAATAATAATGGCGGTT
688313 GGTCGAGAAGTAGCAATATCACTTGATGGTGTGAGGGACAAGAACGTGATGATGTTAAAGGAACT
66 GGTCGAGAAGTAGCAATATCACTTGATGGTGTGAGGGACAAGAACGTGATGATGTTAAAGGAACT
688378 CAACATTGCTATCTTCCCCGTTCGTTACAACGAAA
131 CAACATTGCTATCTTCCCCGTTCGTTACAACGAAA
688413 GCCATTGTTATATCCCTCTCCCCAAATCTTTTATTTTTCTTGGAGAGTTAATAATAATGGCGGTT
1 GCCATTGTTATATCCCTCTCCCCAAATCTTTTATTTTTCTTGGAGAGTTAATAATAATGGCGGTT
688478 GGTCGAGAAGTAGCAATATCACTTGATGGTGTGAGGGACAAGAACGTGATGATGTTAAAGGAACT
66 GGTCGAGAAGTAGCAATATCACTTGATGGTGTGAGGGACAAGAACGTGATGATGTTAAAGGAACT
688543 CAACATTGCTATCTTCCCCGTTCGTTACAACGAAA
131 CAACATTGCTATCTTCCCCGTTCGTTACAACGAAA
688578 ATTACTACGC
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
165 165 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (165 bp):
GCCATTGTTATATCCCTCTCCCCAAATCTTTTATTTTTCTTGGAGAGTTAATAATAATGGCGGTT
GGTCGAGAAGTAGCAATATCACTTGATGGTGTGAGGGACAAGAACGTGATGATGTTAAAGGAACT
CAACATTGCTATCTTCCCCGTTCGTTACAACGAAA
Found at i:691507 original size:2 final size:2
Alignment explanation
Indices: 691500--691537 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
691490 TCAATCGACA
691500 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
691538 CGACATACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:691633 original size:26 final size:26
Alignment explanation
Indices: 691604--691668 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
691594 AATGACGAGC
*
691604 AATGTAAGTCGTAAATGTGCGTCATA
1 AATGTAAGTCATAAATGTGCGTCATA
** *
691630 AATGTGCGTCATAAATGTGTGTCATA
1 AATGTAAGTCATAAATGTGCGTCATA
* *
691656 AATGCACGTCATA
1 AATGTAAGTCATA
691669 GATTTATGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.31
Consensus pattern (26 bp):
AATGTAAGTCATAAATGTGCGTCATA
Found at i:691668 original size:13 final size:13
Alignment explanation
Indices: 691615--691659 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
691605 ATGTAAGTCG
691615 TAAATGTGCGTCA
1 TAAATGTGCGTCA
691628 TAAATGTGCGTCA
1 TAAATGTGCGTCA
*
691641 TAAATGTGTGTCA
1 TAAATGTGCGTCA
691654 TAAATG
1 TAAATG
691660 CACGTCATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (13 bp):
TAAATGTGCGTCA
Found at i:692646 original size:13 final size:13
Alignment explanation
Indices: 692622--692660 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
692612 CGTCCGAGTG
*
692622 ACGTTTATTATAT
1 ACGTTTAATATAT
*
692635 ATGTTTAATATAT
1 ACGTTTAATATAT
692648 ACGTTT-ATATAT
1 ACGTTTAATATAT
692660 A
1 A
692661 ATAATAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 7 0.30
13 16 0.70
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (13 bp):
ACGTTTAATATAT
Found at i:694771 original size:54 final size:54
Alignment explanation
Indices: 694688--695241 Score: 801
Period size: 54 Copynumber: 10.3 Consensus size: 54
694678 TACCAAATCA
* * *
694688 GCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACAATCGTATCG
1 GCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCG
* *
694742 ACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGATCGTATCG
1 GCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCG
* * * * * *
694796 ACACTAAGTGTGTAAGCGACGGAATTCATAATAAGTTTATGAACAACCGTATCG
1 GCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCG
*
694850 GCACTAAGTGTGCAA--CACATGAAATCCATAATAAGTTTATGAACGACCGTATCG
1 GCACTAAGTGTGCAACCCACA-G-AATTCATAATAAGTTTATGAACGACCGTATCG
* *
694904 GCACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCGTATTG
1 GCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCG
*
694958 GCACTAAGTGTGCAACCCAC-GAATATCATAATAAGTTAATGAACGACCGTATCG
1 GCACTAAGTGTGCAACCCACAGAAT-TCATAATAAGTTTATGAACGACCGTATCG
* * *
695012 GTACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATTAACGACCGTATCG
1 GCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCG
*
695066 GCACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGAGCGTATCG
1 GCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCGTATCG
*
695120 GCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGATCGTATCG
1 GCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCG
* * ** *
695174 GCACTAAGTGTGCAACCCACGGAATTCATAATGAGAGTATGAATGACCGTATCG
1 GCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCG
* *
695228 GTACTACGTGTGCA
1 GCACTAAGTGTGCA
695242 CCCCCAACGA
Statistics
Matches: 457, Mismatches: 35, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
52 2 0.00
53 6 0.01
54 440 0.96
55 6 0.01
56 3 0.01
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (54 bp):
GCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCG
Found at i:698232 original size:22 final size:22
Alignment explanation
Indices: 698197--698238 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
698187 TTTAAATTTA
** *
698197 TATAGAAATTTATCGTTATTAT
1 TATAGAAAAGTATCGATATTAT
698219 TATAGAAAAGTATCGATATT
1 TATAGAAAAGTATCGATATT
698239 TTCGACTTCC
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:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (22 bp):
TATAGAAAAGTATCGATATTAT
Found at i:700580 original size:2 final size:2
Alignment explanation
Indices: 700573--700613 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
700563 AAACCGTTCT
700573 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
700614 TTTTATTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:701896 original size:14 final size:14
Alignment explanation
Indices: 701877--701915 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
701867 TAATGGGAAT
701877 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
701891 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
701905 GAATCTCTGCA
1 TAATCCCTGCA
701916 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:712388 original size:17 final size:16
Alignment explanation
Indices: 712366--712399 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
712356 CTCGAATGTG
712366 TGTGCCTGATATGAGTA
1 TGTGCCTGATATG-GTA
*
712383 TGTGCCTTATATGGTA
1 TGTGCCTGATATGGTA
712399 T
1 T
712400 ATTAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.41
Consensus pattern (16 bp):
TGTGCCTGATATGGTA
Found at i:715205 original size:14 final size:15
Alignment explanation
Indices: 715186--715233 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
715176 ATACACTAAA
715186 TAAATTTTATA-ACT
1 TAAATTTTATACACT
*
715200 TAAATTTTA-ATACT
1 TAAATTTTATACACT
*
715214 T-AATTTTGTACACT
1 TAAATTTTATACACT
715228 TAAATT
1 TAAATT
715234 GTGGCTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 7 0.24
14 18 0.62
15 4 0.14
ACGTcount: A:0.40, C:0.08, G:0.02, T:0.50
Consensus pattern (15 bp):
TAAATTTTATACACT
Found at i:716190 original size:7 final size:6
Alignment explanation
Indices: 716158--716189 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
716148 TTATATTAAA
716158 TATTTAT TATTTT TATTTT TATTTT TATTTT T
1 TATTT-T TATTTT TATTTT TATTTT TATTTT T
716190 TTGTTAGCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:718974 original size:2 final size:2
Alignment explanation
Indices: 718967--719011 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
718957 GTTTAACTTT
* *
718967 TA TA TA TA TA TA TA TA AA TA AA 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
719009 TA T
1 TA T
719012 TCATATTGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:719227 original size:2 final size:2
Alignment explanation
Indices: 719220--719272 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
719210 CTATGTTGTT
* *
719220 TA TA TA TA T- TA TA TCA TA T- TA TT TA TA TA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA
719261 TA TA TA TA TA TA
1 TA TA TA TA TA TA
719273 AATTAATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:719353 original size:18 final size:19
Alignment explanation
Indices: 719317--719354 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
719307 TAACGTCTAT
*
719317 TTTATTTTATTTGACTTTA
1 TTTATTTTATTTCACTTTA
*
719336 TTTA-TTTATTTCATTTTA
1 TTTATTTTATTTCACTTTA
719354 T
1 T
719355 AAGATGATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (19 bp):
TTTATTTTATTTCACTTTA
Found at i:730806 original size:24 final size:23
Alignment explanation
Indices: 730794--730867 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
730784 AGGAACAAAT
*
730794 AAAAAGATGAAAACAAGAAAAAGA
1 AAAAAAATGAAAA-AAGAAAAAGA
*
730818 AAAAAAATGAAAAATGAAAAAATGAA
1 AAAAAAATGAAAAAAG-AAAAA-G-A
*
730844 ATGAAAAAATGAAAAGAGAAAAAG
1 A--AAAAAATGAAAAAAGAAAAAG
730868 GAGGGTTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.05
24 17 0.41
25 1 0.02
26 3 0.07
27 5 0.12
28 13 0.32
ACGTcount: A:0.74, C:0.01, G:0.16, T:0.08
Consensus pattern (23 bp):
AAAAAAATGAAAAAAGAAAAAGA
Found at i:730822 original size:16 final size:17
Alignment explanation
Indices: 730810--730858 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 17
730800 ATGAAAACAA
730810 GAAAAA-GAAAAAAAAT
1 GAAAAATGAAAAAAAAT
730826 GAAAAATGAAAAAATGAAAT
1 GAAAAATG-AAAAA--AAAT
730846 GAAAAAATGAAAA
1 G-AAAAATGAAAA
730859 GAGAAAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.21
17 1 0.04
18 5 0.18
20 9 0.32
21 7 0.25
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (17 bp):
GAAAAATGAAAAAAAAT
Found at i:730830 original size:8 final size:8
Alignment explanation
Indices: 730779--730858 Score: 57
Period size: 8 Copynumber: 10.5 Consensus size: 8
730769 CTTGAAGAAA
*
730779 AAAAAAGG
1 AAAAAATG
*
730787 AACAAAT-
1 AAAAAATG
730794 AAAAAGATG
1 AAAAA-ATG
730803 AAAACAA-G
1 AAAA-AATG
*
730811 AAAAAGA-A
1 AAAAA-ATG
730819 AAAAAATG
1 AAAAAATG
730827 -AAAAATG
1 AAAAAATG
730834 AAAAAATG
1 AAAAAATG
730842 ---AAATG
1 AAAAAATG
730847 AAAAAATG
1 AAAAAATG
730855 AAAA
1 AAAA
730859 GAGAAAAAGG
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
5 5 0.09
7 13 0.22
8 34 0.59
9 5 0.09
10 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.14, T:0.09
Consensus pattern (8 bp):
AAAAAATG
Found at i:730865 original size:13 final size:13
Alignment explanation
Indices: 730819--730866 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
730809 AGAAAAAGAA
730819 AAAAAATGAAAAATG
1 AAAAAATG-AAAA-G
*
730834 AAAAAATGAAATG
1 AAAAAATGAAAAG
730847 AAAAAATGAAAAG
1 AAAAAATGAAAAG
730860 AGAAAAA
1 A-AAAAA
730867 GGAGGGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
13 14 0.47
14 8 0.27
15 8 0.27
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (13 bp):
AAAAAATGAAAAG
Found at i:731980 original size:91 final size:90
Alignment explanation
Indices: 731864--732031 Score: 284
Period size: 92 Copynumber: 1.9 Consensus size: 90
731854 TGAGGGATTG
731864 ACATTTTCAGGAGAGTTCATAATGAGAAGAACTCATCCAAC-GAGGAAGAAGAAGTTCATAATGA
1 ACATTTTCAGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGA
731928 GAAGAACTTGTTCAACTTCGCATCA
66 GAAGAACTTGTTCAACTTCGCATCA
* *
731953 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTTC-A-GGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAAT
*
732018 GAGAAGAGCTTGTT
64 GAGAAGAACTTGTT
732032 TGACCTATCA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
89 8 0.11
90 1 0.01
91 31 0.42
92 33 0.45
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (90 bp):
ACATTTTCAGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACTTCGCATCA
Found at i:732291 original size:105 final size:105
Alignment explanation
Indices: 732089--732369 Score: 339
Period size: 105 Copynumber: 2.6 Consensus size: 105
732079 TGAGGGATCG
*
732089 ACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATGAGAA
1 ACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCATCATAAGGGAGAAAGTTCATAATGAGAA
* * * *
732154 GAACTTGTTCCTTTCAAATTCACCACAGAAGGAGGTGAACCA
64 AAACATGTTCCTTTCAAATCCACCACAAAAGGAGGTGAACCA
*
732196 ACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCATAAGGGAGAAAGTTCATAATGAGAAAA
1 ACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAGGGAGAAAGTTCATAATGAGAAAA
* * ** ***
732261 ACATGTTCC-TTCTAAGTCCACCGCAAAAGGATTTGGTTCA
66 ACATGTTCCTTTC-AAATCCACCACAAAAGGAGGTGAACCA
* *
732301 AGATTTCCAGTTGAGAGTTCATAATGAGAAGAACTCATCCAATAAGGGAGAAGGAGTTCATAATG
1 ACATTTCCAG--AAGAGTTCATAATGAGAAGAACTCAT-C-ATAAGGGAGAA--AGTTCATAATG
732366 AGAA
60 AGAA
732370 GAATTTGTTC
Statistics
Matches: 151, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
104 3 0.02
105 88 0.58
106 1 0.01
107 32 0.21
108 1 0.01
109 11 0.07
111 15 0.10
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.24
Consensus pattern (105 bp):
ACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAGGGAGAAAGTTCATAATGAGAAAA
ACATGTTCCTTTCAAATCCACCACAAAAGGAGGTGAACCA
Found at i:734536 original size:2 final size:2
Alignment explanation
Indices: 734529--734567 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
734519 GTGTTTAACT
734529 TA 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 TA T
734568 TCATATTGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:737709 original size:21 final size:21
Alignment explanation
Indices: 737685--737732 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
737675 ATTGGTACTA
*
737685 GTAATAATAGTACTGATAATG
1 GTAATAATAGTACCGATAATG
* *
737706 GTAATAATAGTACCGGTACTG
1 GTAATAATAGTACCGATAATG
737727 GTAATA
1 GTAATA
737733 GTAATATCGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (21 bp):
GTAATAATAGTACCGATAATG
Found at i:737774 original size:21 final size:22
Alignment explanation
Indices: 737728--737768 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
737718 CCGGTACTGG
*
737728 TAATAGTAATATC-GATGCTAA
1 TAATAGTAATATCAGATACTAA
737749 TAATAGTAATATCAG-TACTA
1 TAATAGTAATATCAGATACTA
737769 GAAATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (22 bp):
TAATAGTAATATCAGATACTAA
Found at i:739328 original size:21 final size:20
Alignment explanation
Indices: 739222--739350 Score: 73
Period size: 21 Copynumber: 6.3 Consensus size: 20
739212 GAACAGTATT
*
739222 GATACTAGTATTA-TAATATC
1 GATACT-GTAATAGTAATATC
* **
739242 GATACTGGAATAAAAATAAT-
1 GATACTGTAATAGTAAT-ATC
* * * *
739262 GGTACTGTAGTAGTAGTATA
1 GATACTGTAATAGTAATATC
* * *
739282 GATATTGGTAATAGTAGTACC
1 GATACT-GTAATAGTAATATC
*
739303 AATACTAGTAATAGTAATATC
1 GATACT-GTAATAGTAATATC
* *
739324 GATACTGATAATTGCAATATC
1 GATACTG-TAATAGTAATATC
739345 GATACT
1 GATACT
739351 CGAAAAAATA
Statistics
Matches: 82, Mismatches: 22, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
19 6 0.07
20 25 0.30
21 51 0.62
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.33
Consensus pattern (20 bp):
GATACTGTAATAGTAATATC
Found at i:742306 original size:16 final size:16
Alignment explanation
Indices: 742285--742316 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
742275 ATTTCTACTT
742285 TTAAAAAATTTAAATA
1 TTAAAAAATTTAAATA
742301 TTAAAAAATTTAAATA
1 TTAAAAAATTTAAATA
742317 AACTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAAAATTTAAATA
Found at i:751472 original size:41 final size:41
Alignment explanation
Indices: 751427--751699 Score: 166
Period size: 41 Copynumber: 6.7 Consensus size: 41
751417 CATTTAAACA
*
751427 ACAAACGCCGCAACAGAGTAGTACTTTAGCGGCGTTTTTAT
1 ACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTAT
** * * * *
751468 ACAAACGCCATAATAG-GT--TCATTTATAGTGGTGTTTCTCA-
1 ACAAACGCCGCAATAGAGTAGT-ACTT-TAGCGGCGTTT-TTAT
* * * * * *
751508 AAAAATGCCGTGAA-AAAGTAGTACTTTAGTGGCTTTTTTAT
1 ACAAACGCCG-CAATAGAGTAGTACTTTAGCGGCGTTTTTAT
** * * * * *
751549 ACAAACGCTACAATAGGGT--TCATCTATAGTGGCATTTTGCA-
1 ACAAACGCCGCAATAGAGTAGT-A-CTTTAGCGGCGTTTT-TAT
* * *
751590 ACAAACGCAGCAAAAGAGTAGTACTTTAGCGGCGTTTTTCT
1 ACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTAT
* * * *
751631 ATAAACGCTGCAACAGAATAGTACTTTAGCGGCGTTTTTAT
1 ACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTAT
* *
751672 ACAAATGCCGCAATAGAATAGTACTTTA
1 ACAAACGCCGCAATAGAGTAGTACTTTA
751700 ACGCCGCAAT
Statistics
Matches: 173, Mismatches: 44, Indels: 30
0.70 0.18 0.12
Matches are distributed among these distances:
38 1 0.01
39 4 0.02
40 24 0.14
41 137 0.79
42 5 0.03
43 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (41 bp):
ACAAACGCCGCAATAGAGTAGTACTTTAGCGGCGTTTTTAT
Found at i:751617 original size:82 final size:82
Alignment explanation
Indices: 751364--751639 Score: 279
Period size: 82 Copynumber: 3.3 Consensus size: 82
751354 CAAAATGGTA
* * ** * * * *
751364 ACTTTAGCGGTGTTTGTATACAAAAACGACGTAATTGGGTTCATCGATAGTGGCATTTAAACAAC
1 ACTTTAGCGGCGTTTTTATACAAACGCTAC--AATAGGGTTCATCTATAGTGGCATTT-ATCAAC
*
751429 AAACGCCGCAACAGAGTAGT
63 AAACGCCGCAAAAGAGTAGT
* * * ** * *
751449 ACTTTAGCGGCGTTTTTATACAAACGCCATAATA-GGTTCATTTATAGTGGTGTTTCTCAAAAAA
1 ACTTTAGCGGCGTTTTTATACAAACGCTACAATAGGGTTCATCTATAGTGGCATTTATCAACAAA
* *
751513 TGCCGTGAAAA-AGTAGT
66 CGCCG-CAAAAGAGTAGT
* *
751530 ACTTTAGTGGCTTTTTTATACAAACGCTACAATAGGGTTCATCTATAGTGGCATTT-TGCAACAA
1 ACTTTAGCGGCGTTTTTATACAAACGCTACAATAGGGTTCATCTATAGTGGCATTTAT-CAACAA
*
751594 ACGCAGCAAAAGAGTAGT
65 ACGCCGCAAAAGAGTAGT
* *
751612 ACTTTAGCGGCGTTTTTCTATAAACGCT
1 ACTTTAGCGGCGTTTTTATACAAACGCT
751640 GCAACAGAAT
Statistics
Matches: 155, Mismatches: 32, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
81 51 0.33
82 77 0.50
83 3 0.02
85 24 0.15
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (82 bp):
ACTTTAGCGGCGTTTTTATACAAACGCTACAATAGGGTTCATCTATAGTGGCATTTATCAACAAA
CGCCGCAAAAGAGTAGT
Found at i:755165 original size:43 final size:43
Alignment explanation
Indices: 755077--755492 Score: 498
Period size: 43 Copynumber: 9.8 Consensus size: 43
755067 AAACTTGCCT
**
755077 ATAGCATTAGCGGCGTTTGTGGC-AAAAACGCCACTAAAAAAA
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCCACTAAAACCA
* * * * *
755119 ATAGCATTAGCAGCATTTATAGCAAAAAAGGCCACTAAAACCA
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCCACTAAAACCA
* ** *
755162 ATAGCATTAGCGGCATTTGT-GCAAAAAATACCCCTAAAACCA
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCCACTAAAACCA
* *
755204 ATAGCATTAGCGGCATTTGTGGCAAAAAACGCCACTAAAATCA
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCCACTAAAACCA
* * *
755247 ATAGCATTAGCGGCGTTTATGGAAAAAAATGCCACTAAAACCA
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCCACTAAAACCA
* *
755290 ATAGCATTAGCGGCGTTTGTGGTAAAAAACGCCACTAAAATCA
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCCACTAAAACCA
* *
755333 ATAGCATTAGCGGCGTTTGTGGTAAAAAATGCCACTAAAACCA
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCCACTAAAACCA
** * *
755376 ATAGCATTAGC-GCGTTTGTGGTGAAAAACCCCACTAAAACTA
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCCACTAAAACCA
* * ***
755418 ATAGCAATAGCGGCGTTTGTGGTAAAAAA-GCCACTAAAGGTA
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCCACTAAAACCA
* * * * *
755460 AGAGAATTAGCGGCGTTTTTGGCCACAAACGCC
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCC
755493 GCTATATAAC
Statistics
Matches: 327, Mismatches: 43, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
42 127 0.39
43 200 0.61
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (43 bp):
ATAGCATTAGCGGCGTTTGTGGCAAAAAACGCCACTAAAACCA
Found at i:755476 original size:85 final size:86
Alignment explanation
Indices: 755077--755492 Score: 518
Period size: 85 Copynumber: 4.9 Consensus size: 86
755067 AAACTTGCCT
* ** * * * *
755077 ATAGCATTAGCGGCGTTTGTGGC-AAAAACGCCACTAAAAAAAATAGCATTAGCAGCATTTATAG
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAATGCCACTAAAACCAATAGCATTAGCGGCGTTTGTGG
* *
755141 CAAAAAAGGCCACTAAAACCA
66 CAAAAAACGCCACTAAAATCA
* * * *
755162 ATAGCATTAGCGGCATTTGT-GCAAAAAATACCCCTAAAACCAATAGCATTAGCGGCATTTGTGG
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAATGCCACTAAAACCAATAGCATTAGCGGCGTTTGTGG
755226 CAAAAAACGCCACTAAAATCA
66 CAAAAAACGCCACTAAAATCA
* *
755247 ATAGCATTAGCGGCGTTTATGGAAAAAAATGCCACTAAAACCAATAGCATTAGCGGCGTTTGTGG
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAATGCCACTAAAACCAATAGCATTAGCGGCGTTTGTGG
*
755312 TAAAAAACGCCACTAAAATCA
66 CAAAAAACGCCACTAAAATCA
*
755333 ATAGCATTAGCGGCGTTTGTGGTAAAAAATGCCACTAAAACCAATAGCATTAGC-GCGTTTGTGG
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAATGCCACTAAAACCAATAGCATTAGCGGCGTTTGTGG
** *
755397 TGAAAAACCCCACTAAAA-CTA
66 CAAAAAACGCCACTAAAATC-A
* * *** * * *
755418 ATAGCAATAGCGGCGTTTGTGGTAAAAAA-GCCACTAAAGGTAAGAGAATTAGCGGCGTTTTTGG
1 ATAGCATTAGCGGCGTTTGTGGCAAAAAATGCCACTAAAACCAATAGCATTAGCGGCGTTTGTGG
* *
755482 CCACAAACGCC
66 CAAAAAACGCC
755493 GCTATATAAC
Statistics
Matches: 294, Mismatches: 33, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
84 22 0.07
85 160 0.54
86 112 0.38
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (86 bp):
ATAGCATTAGCGGCGTTTGTGGCAAAAAATGCCACTAAAACCAATAGCATTAGCGGCGTTTGTGG
CAAAAAACGCCACTAAAATCA
Found at i:762871 original size:21 final size:21
Alignment explanation
Indices: 762833--762872 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
762823 AACGTCTAAT
* *
762833 ATTAATATTTTCGGTAGAAAA
1 ATTAATATTTTAGATAGAAAA
762854 ATTAATATTTTAGATAGAA
1 ATTAATATTTTAGATAGAA
762873 CTCTACCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (21 bp):
ATTAATATTTTAGATAGAAAA
Found at i:770695 original size:14 final size:14
Alignment explanation
Indices: 770676--770712 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
770666 CTATGACCCT
*
770676 CTCTCTCTCTCCCA
1 CTCTCTCTCTCACA
*
770690 CTCTCTCTCTGACA
1 CTCTCTCTCTCACA
770704 CTCTCTCTC
1 CTCTCTCTC
770713 ATGCTTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.51, G:0.03, T:0.38
Consensus pattern (14 bp):
CTCTCTCTCTCACA
Found at i:770982 original size:14 final size:14
Alignment explanation
Indices: 770963--770989 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
770953 AGTGAGATGC
770963 ATTTGATATCTATT
1 ATTTGATATCTATT
770977 ATTTGATATCTAT
1 ATTTGATATCTAT
770990 AAAATTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (14 bp):
ATTTGATATCTATT
Found at i:777485 original size:11 final size:11
Alignment explanation
Indices: 777469--777496 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
777459 GTAAATTAGA
777469 AAAGAGAGAAT
1 AAAGAGAGAAT
777480 AAAGAGAGAAT
1 AAAGAGAGAAT
777491 AAAGAG
1 AAAGAG
777497 TGAAAGTGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (11 bp):
AAAGAGAGAAT
Found at i:778316 original size:3 final size:3
Alignment explanation
Indices: 778308--778350 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
778298 ATTTATCATT
*
778308 TTA TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
778351 CATTTTTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:778337 original size:22 final size:22
Alignment explanation
Indices: 778307--778350 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
778297 AATTTATCAT
*
778307 TTTATTATTATTATTATTATTA
1 TTTACTATTATTATTATTATTA
778329 TTTACTATTATTATTATTATTA
1 TTTACTATTATTATTATTATTA
778351 CATTTTTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTACTATTATTATTATTATTA
Found at i:780134 original size:19 final size:19
Alignment explanation
Indices: 780110--780237 Score: 130
Period size: 19 Copynumber: 6.4 Consensus size: 19
780100 TTATTTTGGA
780110 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
780129 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
780151 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
780173 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
* *
780192 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
* *
780211 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
780230 ATTTTTCA
1 -TTTTTCA
780238 AAATCGCGTT
Statistics
Matches: 96, Mismatches: 6, Indels: 13
0.83 0.05 0.11
Matches are distributed among these distances:
19 63 0.66
20 5 0.05
21 4 0.04
22 12 0.12
23 6 0.06
25 6 0.06
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.34
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:780207 original size:38 final size:38
Alignment explanation
Indices: 780111--780234 Score: 158
Period size: 38 Copynumber: 3.1 Consensus size: 38
780101 TATTTTGGAT
* * *
780111 TTTTCACTATCGCAACACTTTTTCACTATCGCAACAACA
1 TTTTAACTATCGCAACACATTTTAACTATCGCAAC-ACA
*
780150 CGTTTTTCAAACTCTCGCAACACATTTTAACTATCGCAACACA
1 ---TTTT--AACTATCGCAACACATTTTAACTATCGCAACACA
780193 TTTTAACTATCGCAACACATTTTAACTATCGCAACACA
1 TTTTAACTATCGCAACACATTTTAACTATCGCAACACA
780231 TTTT
1 TTTT
780235 TCAAAATCGC
Statistics
Matches: 75, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
38 37 0.49
40 4 0.05
42 4 0.05
43 3 0.04
44 27 0.36
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (38 bp):
TTTTAACTATCGCAACACATTTTAACTATCGCAACACA
Found at i:782410 original size:32 final size:31
Alignment explanation
Indices: 782344--782403 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
782334 TAAATTTCAG
**
782344 AAAAGAAAAATAATAAATATAAAAAAATGTT
1 AAAAGAAAAATAATAAATATAAAAAAATAAT
782375 AAAAGATAAAATAA-AAA-ATAAAAAAATAA
1 AAAAGA-AAAATAATAAATATAAAAAAATAA
782404 AATAAAATAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 10 0.38
31 9 0.35
32 7 0.27
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (31 bp):
AAAAGAAAAATAATAAATATAAAAAAATAAT
Found at i:785779 original size:19 final size:19
Alignment explanation
Indices: 785735--785805 Score: 65
Period size: 21 Copynumber: 3.6 Consensus size: 19
785725 ATCAAATCAA
*
785735 AGCAAAGAAGAAAAA-AAAG
1 AGCAAA-AAAAAAAACAAAG
* *
785754 CACCAAAAAAAAAAACAAAT
1 -AGCAAAAAAAAAAACAAAG
785774 AGCAAAGAAAAAAAAACAAAG
1 AGC-AA-AAAAAAAAACAAAG
785795 AG-AAAAAAAAA
1 AGCAAAAAAAAA
785806 GAAAAGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 7 0.16
19 11 0.26
20 10 0.23
21 15 0.35
ACGTcount: A:0.77, C:0.10, G:0.11, T:0.01
Consensus pattern (19 bp):
AGCAAAAAAAAAAACAAAG
Found at i:785795 original size:14 final size:15
Alignment explanation
Indices: 785776--785804 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
785766 AAACAAATAG
785776 CAAAGA-AAAAAAAA
1 CAAAGAGAAAAAAAA
785790 CAAAGAGAAAAAAAA
1 CAAAGAGAAAAAAAA
785805 AGAAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (15 bp):
CAAAGAGAAAAAAAA
Found at i:785810 original size:21 final size:21
Alignment explanation
Indices: 785758--785810 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
785748 AAAAAGCACC
*
785758 AAAAAAAAAAACAAATAGCAA
1 AAAAAAAAAAACAAAGAGCAA
*
785779 AGAAAAAAAAACAAAGAG-AA
1 AAAAAAAAAAACAAAGAGCAA
785799 AAAAAAAGAAAA
1 AAAAAAA-AAAA
785811 GAAAAGATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.83, C:0.06, G:0.09, T:0.02
Consensus pattern (21 bp):
AAAAAAAAAAACAAAGAGCAA
Found at i:785811 original size:17 final size:16
Alignment explanation
Indices: 785779--785812 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
785769 CAAATAGCAA
*
785779 AGAAAAAAAAACAAAG
1 AGAAAAAAAAAAAAAG
785795 AGAAAAAAAAAGAAAAG
1 AGAAAAAAAAA-AAAAG
785812 A
1 A
785813 AAAGATGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AGAAAAAAAAAAAAAG
Found at i:786763 original size:25 final size:24
Alignment explanation
Indices: 786712--786773 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
786702 GCAATAATTG
786712 TTTTT-AAAATTTTTTATTAAACA
1 TTTTTCAAAATTTTTTATTAAACA
*
786735 TTTTTCAAAATTATTTTAATTAATC-
1 TTTTTCAAAATT-TTTT-ATTAAACA
*
786760 TTTTCCAAAATTTT
1 TTTTTCAAAATTTT
786774 GAAAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
23 5 0.15
24 8 0.24
25 15 0.44
26 6 0.18
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTTCAAAATTTTTTATTAAACA
Found at i:788638 original size:97 final size:98
Alignment explanation
Indices: 788452--788763 Score: 362
Period size: 101 Copynumber: 3.1 Consensus size: 98
788442 ATTTTTCTTA
788452 AAACAAAATTTACCTCACTTGAGATTGTTCTTCCCAAAACAACA-TTTGT-TCACTTGAGACATT
1 AAACAAAATTTACCTCACTTGAGATTGTT-TT--CAAAACAA-ATTTTGTCTCACTTGAGACA--
** *
788515 TTTTTCTTTGAAATACAAATTCTGAAATTGTTTCACTTG
60 TTTTTCTTCAAAACACAAATTCTGAAATTGTTTCACTTG
* *
788554 AAA-TAAATTTACCTCACTTGAGATTATTTTCAAAACAAATTTTGTCTCACTTGAGACATTTTTC
1 AAACAAAATTTACCTCACTTGAGATTGTTTTCAAAACAAATTTTGTCTCACTTGAGACATTTTTC
788618 TTCAAAACACAAATTCTGAAATTGTTTCACTTG
66 TTCAAAACACAAATTCTGAAATTGTTTCACTTG
* * *** * **
788651 AAACAAAAGTGATAACATTTGAGATTGTTTTCTTAAAAACAAATTTTGTCTTGCTTGAGACAATT
1 AAACAAAATTTACCTCACTTGAGATTGTTTTC---AAAACAAATTTTGTCTCACTTGAGAC-ATT
*
788716 TTTCCTCAAAACACAAAATT-TGGAAATTGTTTCACTTG
62 TTTCTTCAAAACAC-AAATTCT-GAAATTGTTTCACTTG
788754 AAACAAAATT
1 AAACAAAATT
788764 GATAAACCTT
Statistics
Matches: 184, Mismatches: 17, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
97 40 0.22
98 33 0.18
99 12 0.07
100 2 0.01
101 47 0.26
102 20 0.11
103 30 0.16
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (98 bp):
AAACAAAATTTACCTCACTTGAGATTGTTTTCAAAACAAATTTTGTCTCACTTGAGACATTTTTC
TTCAAAACACAAATTCTGAAATTGTTTCACTTG
Found at i:788757 original size:103 final size:103
Alignment explanation
Indices: 788529--788819 Score: 352
Period size: 103 Copynumber: 2.9 Consensus size: 103
788519 TCTTTGAAAT
* * ** *
788529 ACAAATTCTGAAATTGTTTCACTTGAAA-TAAA-T-TTACCTCACTTGAGATTATTT-TC--AAA
1 ACAAATTCTGAAATTGTTTCACTTGAAACAAAAGTGATA-AACATTTGAGATTATTTCTCTTAAA
* *
788588 ACAAATTTTGTCTCACTTGAGAC-ATTTTTCTTCAAAAC
65 ACAAATTTTGTCTCGCTTGAGACAATTTTTCCTCAAAAC
*
788626 ACAAATTCTGAAATTGTTTCACTTGAAACAAAAGTGAT-AACATTTGAGATTGTTT-TCTTAAAA
1 ACAAATTCTGAAATTGTTTCACTTGAAACAAAAGTGATAAACATTTGAGATTATTTCTCTT-AAA
*
788689 ACAAATTTTGTCTTGCTTGAGACAATTTTTCCTCAAAAC
65 ACAAATTTTGTCTCGCTTGAGACAATTTTTCCTCAAAAC
* * *
788728 ACAAAATT-TGGAAATTGTTTCACTTGAAACAAAATTGATAAACCTTTGAGATTATTTCTCTTGA
1 AC-AAATTCT-GAAATTGTTTCACTTGAAACAAAAGTGATAAACATTTGAGATTATTTCTCTTAA
*
788792 AACAAA-TTTGTCTCGCTTGTGACAATTT
64 AACAAATTTTGTCTCGCTTGAGACAATTT
788820 CTCTTGGAAC
Statistics
Matches: 168, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
97 28 0.17
98 18 0.11
99 1 0.01
100 1 0.01
101 24 0.14
102 17 0.10
103 53 0.32
104 22 0.13
105 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (103 bp):
ACAAATTCTGAAATTGTTTCACTTGAAACAAAAGTGATAAACATTTGAGATTATTTCTCTTAAAA
CAAATTTTGTCTCGCTTGAGACAATTTTTCCTCAAAAC
Found at i:788904 original size:66 final size:65
Alignment explanation
Indices: 788765--789057 Score: 424
Period size: 66 Copynumber: 4.5 Consensus size: 65
788755 AACAAAATTG
* *
788765 ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGTGACAATTTCTCTTGGAAC
1 ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGAGACAATTTCTCTTGAAAC
* * * * * *
788830 ATAAACCTTTGAGATTGTTTCCCTTGAAACAACTTTTGTATCACTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTATTTCTCTTGAAACAA-ATTTGTCTCGCTTGAGACAATTTCTCTTGAAA
*
788895 T
65 C
*
788896 ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGAAACAATTTCTCTTGAAAC
1 ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGAGACAATTTCTCTTGAAAC
* * * * *
788961 ATAAACCTTTGAGATTTTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTTCTTGAAA
1 ATAAACCTTTGAGATTATTTCTCTTGAAACAAA-TTTGTCTCGCTTGAGACAATTTCTCTTGAAA
789026 C
65 C
*
789027 ATAAACCTTTGAGATTGTTTCTCTTGAAACA
1 ATAAACCTTTGAGATTATTTCTCTTGAAACA
789058 GTTTCTCTTG
Statistics
Matches: 201, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
65 88 0.44
66 113 0.56
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (65 bp):
ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGAGACAATTTCTCTTGAAAC
Found at i:788920 original size:131 final size:131
Alignment explanation
Indices: 788765--789400 Score: 733
Period size: 131 Copynumber: 5.0 Consensus size: 131
788755 AACAAAATTG
** *
788765 ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGTGACAATTTCTCTTGGAAC
1 ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGAAACAATTTCTCTTGAAAC
*
788830 ATAAACCTTTGAGATTGTTTCCCTTGAAACAACTTTTGTATCACTTGAGACAGTTTCTCTTGAAA
66 ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTATCACTTGAGACAGTTTCTCTTGAAA
*
788895 T
131 C
788896 ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGAAACAATTTCTCTTGAAAC
1 ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGAAACAATTTCTCTTGAAAC
* * * *
788961 ATAAACCTTTGAGATTTTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTTCTTGAAA
66 ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTATCACTTGAGACAGTTTCTCTTGAAA
789026 C
131 C
* *
789027 ATAAACCTTTGAGATTGTTTCTCTTGAAAC--AGTT-TCT--CTTGAAAC-A-------T-AAAC
1 ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGAAACAATTTCTCTTGAAAC
* * * * *
789078 -T-----TTTGAGATTGTTTCTCTTGAAAAAAAATTTGTCTCATTTGAGACAGTTTCTCTTGAAA
66 ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTATCACTTGAGACAGTTTCTCTTGAAA
789137 C
131 C
* * *** * * *
789138 ATAAACCTTTGAGATTGTTTCCCTTGAAA-TTTTGTTGTCTTGCTTGAGACAGTTTCTCTTGAAA
1 ATAAACCTTTGAGATTATTTCTCTTGAAACAAAT-TTGTCTCGCTTGAAACAATTTCTCTTGAAA
* * * * *
789202 CATAAACCTTTGAGATTGCTTCCCTTGAAACAATTTTTGTCTCGA-TTGAGACAATTTCTCTTTA
65 CATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTATC-ACTTGAGACAGTTTCTCTTGA
*
789266 AAT
129 AAC
* * * * *
789269 ATAAACCTTTGAGATTGTTTCTATTGAAACAAATTTTGTCTCCCATGAGACAATTTCTCTTGAAA
1 ATAAACCTTTGAGATTATTTCTCTTGAAACAAA-TTTGTCTCGCTTGAAACAATTTCTCTTGAAA
* * * *
789334 TATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAGTTT-TCTTGAA
65 CATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTATCACTTGAGACAGTTTCTCTTGAA
789398 AC
130 AC
789400 A
1 A
789401 AATTTTATCT
Statistics
Matches: 432, Mismatches: 48, Indels: 50
0.82 0.09 0.09
Matches are distributed among these distances:
111 80 0.19
113 2 0.00
114 3 0.01
116 8 0.02
117 4 0.01
118 1 0.00
124 1 0.00
125 5 0.01
126 9 0.02
128 3 0.01
129 3 0.01
131 235 0.54
132 77 0.18
133 1 0.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.40
Consensus pattern (131 bp):
ATAAACCTTTGAGATTATTTCTCTTGAAACAAATTTGTCTCGCTTGAAACAATTTCTCTTGAAAC
ATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTATCACTTGAGACAGTTTCTCTTGAAA
C
Found at i:788958 original size:15 final size:15
Alignment explanation
Indices: 788912--788961 Score: 55
Period size: 15 Copynumber: 3.0 Consensus size: 15
788902 CTTTGAGATT
788912 ATTTCTCTTGAAACAA
1 ATTTCTCTTGAAAC-A
788928 ATTTGTCTCGCTTGAAACA
1 A-TT-TCT--CTTGAAACA
788947 ATTTCTCTTGAAACA
1 ATTTCTCTTGAAACA
788962 TAAACCTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 9 0.30
16 1 0.03
17 5 0.17
18 5 0.17
19 2 0.07
20 8 0.27
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (15 bp):
ATTTCTCTTGAAACA
Found at i:789051 original size:45 final size:45
Alignment explanation
Indices: 788996--789100 Score: 174
Period size: 45 Copynumber: 2.3 Consensus size: 45
788986 GAAACAAATT
* * *
788996 TTGTCTCTCTTGAGACAGTTTTTCTTGAAACATAAACCTTTGAGA
1 TTGTTTCTCTTGAAACAGTTTCTCTTGAAACATAAACCTTTGAGA
*
789041 TTGTTTCTCTTGAAACAGTTTCTCTTGAAACATAAACTTTTGAGA
1 TTGTTTCTCTTGAAACAGTTTCTCTTGAAACATAAACCTTTGAGA
789086 TTGTTTCTCTTGAAA
1 TTGTTTCTCTTGAAA
789101 AAAAATTTGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (45 bp):
TTGTTTCTCTTGAAACAGTTTCTCTTGAAACATAAACCTTTGAGA
Found at i:789053 original size:15 final size:15
Alignment explanation
Indices: 789043--789072 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
789033 CTTTGAGATT
789043 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
789058 GTTTCTCTTGAAACA
1 GTTTCTCTTGAAACA
789073 TAAACTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (15 bp):
GTTTCTCTTGAAACA
Found at i:789057 original size:30 final size:30
Alignment explanation
Indices: 788817--788926 Score: 78
Period size: 30 Copynumber: 3.5 Consensus size: 30
788807 CTTGTGACAA
*
788817 TTTCTCTTGGAACATAAACCTTTGAGATTG
1 TTTCTCTTGAAACATAAACCTTTGAGATTG
* * * **
788847 TTTCCCTTGAAACAACTTTTGTATCAC-TTGAGACAG
1 TTTCTCTTGAAAC-A----T-AAAC-CTTTGAGATTG
* *
788883 TTTCTCTTGAAATATAAACCTTTGAGATTA
1 TTTCTCTTGAAACATAAACCTTTGAGATTG
788913 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
788927 AATTTGTCTC
Statistics
Matches: 58, Mismatches: 14, Indels: 16
0.66 0.16 0.18
Matches are distributed among these distances:
29 1 0.02
30 32 0.55
31 2 0.03
35 2 0.03
36 20 0.34
37 1 0.02
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (30 bp):
TTTCTCTTGAAACATAAACCTTTGAGATTG
Found at i:789086 original size:242 final size:242
Alignment explanation
Indices: 788817--789299 Score: 707
Period size: 242 Copynumber: 2.0 Consensus size: 242
788807 CTTGTGACAA
* * **
788817 TTTCTCTTGGAACATAAACCTTTGAGATTGTTTCCCTTGAAACAACTTTTGTATCACTTGAGACA
1 TTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAAAAAAATTTGTATCACTTGAGACA
* *
788882 GTTTCTCTTGAAATATAAACCTTTGAGATTATTTCTCTTGAAACAAAT-TTGTCTCGCTTGAAAC
66 GTTTCTCTTGAAACATAAACCTTTGAGATTATTTCCCTTGAAA-AAATGTTGTCTCGCTTGAAAC
** **
788946 AATTTCTCTTGAAACATAAACCTTTGAGATTTTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGA
130 AATTTCTCTTGAAACATAAACCTTTGAGATTGCTTCCCTTGAAACAAATTTTGTCTCGATTGAGA
* * *
789011 CAGTTTTTCTTGAAACATAAACCTTTGAGATTGTTTCTCTTGAAACAG
195 CAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTATTGAAACAG
* * * *
789059 TTTCTCTTGAAACATAAACTTTTGAGATTGTTTCTCTTGAAAAAAAATTTGTCTCATTTGAGACA
1 TTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAAAAAAATTTGTATCACTTGAGACA
* *** * *
789124 GTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAATTTTGTTGTCTTGCTTGAGACA
66 GTTTCTCTTGAAACATAAACCTTTGAGATTATTTCCCTTGAAAAAATGTTGTCTCGCTTGAAACA
* *
789189 GTTTCTCTTGAAACATAAACCTTTGAGATTGCTTCCCTTGAAACAATTTTTGTCTCGATTGAGAC
131 ATTTCTCTTGAAACATAAACCTTTGAGATTGCTTCCCTTGAAACAAATTTTGTCTCGATTGAGAC
* *
789254 AATTTCTCTTTAAATATAAACCTTTGAGATTGTTTCTATTGAAACA
196 AATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTATTGAAACA
789300 AATTTTGTCT
Statistics
Matches: 213, Mismatches: 27, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
241 1 0.00
242 212 1.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.41
Consensus pattern (242 bp):
TTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAAAAAAATTTGTATCACTTGAGACA
GTTTCTCTTGAAACATAAACCTTTGAGATTATTTCCCTTGAAAAAATGTTGTCTCGCTTGAAACA
ATTTCTCTTGAAACATAAACCTTTGAGATTGCTTCCCTTGAAACAAATTTTGTCTCGATTGAGAC
AATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCTATTGAAACAG
Found at i:789094 original size:30 final size:30
Alignment explanation
Indices: 789058--789166 Score: 103
Period size: 30 Copynumber: 3.4 Consensus size: 30
789048 TCTTGAAACA
789058 GTTTCTCTTGAAACATAAACTTTTGAGATT
1 GTTTCTCTTGAAACATAAACTTTTGAGATT
* **
789088 GTTTCTCTTGAAA-AAAAATTTGTCTCATTTGAGACA
1 GTTTCTCTTGAAACATAAA-----CT--TTTGAGATT
*
789124 GTTTCTCTTGAAACATAAACCTTTGAGATT
1 GTTTCTCTTGAAACATAAACTTTTGAGATT
*
789154 GTTTCCCTTGAAA
1 GTTTCTCTTGAAA
789167 TTTTGTTGTC
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
29 4 0.06
30 32 0.51
32 1 0.02
34 2 0.03
36 20 0.32
37 4 0.06
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (30 bp):
GTTTCTCTTGAAACATAAACTTTTGAGATT
Found at i:789095 original size:176 final size:176
Alignment explanation
Indices: 788873--789233 Score: 539
Period size: 176 Copynumber: 2.1 Consensus size: 176
788863 TTTTGTATCA
* * *
788873 CTTGAGACAGTTTCTCTTGAAATATAAACCTTTGAGATTATTTCTCTTG-AAACAAATTTGTCTC
1 CTTGAAACAGTTTCTCTTGAAACATAAACCTTTGAGATTATTTCTCTTGAAAAAAAATTTGTCTC
* *
788937 GCTTGAAACAATTTCTCTTGAAACATAAACCTTTGAGATTTTTTCCCTTGAAACAAATT-TTGTC
66 ACTTGAAACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTG-AA-AAATTGTTGTC
* * *
789001 TCT-CTTGAGACAGTTTTTCTTGAAACATAAACCTTTGAGATTGTTTCT
129 T-TGCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGCTTCC
* *
789049 CTTGAAACAGTTTCTCTTGAAACATAAACTTTTGAGATTGTTTCTCTTGAAAAAAAATTTGTCTC
1 CTTGAAACAGTTTCTCTTGAAACATAAACCTTTGAGATTATTTCTCTTGAAAAAAAATTTGTCTC
* * * **
789114 ATTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAATTTTGTTGTCTT
66 ACTTGAAACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAAAATTGTTGTCTT
789179 GCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGCTTCC
131 GCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGCTTCC
789225 CTTGAAACA
1 CTTGAAACA
789234 ATTTTTGTCT
Statistics
Matches: 167, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
175 4 0.02
176 104 0.62
177 59 0.35
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (176 bp):
CTTGAAACAGTTTCTCTTGAAACATAAACCTTTGAGATTATTTCTCTTGAAAAAAAATTTGTCTC
ACTTGAAACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAAAATTGTTGTCTT
GCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGCTTCC
Found at i:789133 original size:111 final size:111
Alignment explanation
Indices: 788938--789166 Score: 370
Period size: 111 Copynumber: 2.1 Consensus size: 111
788928 ATTTGTCTCG
* * *
788938 CTTGAAACAATTTCTCTTGAAACATAAACCTTTGAGATTTTTTCCCTTGAAACAAATTTTGTCTC
1 CTTGAAACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAAAAAAATTTGTCTC
* *
789003 TCTTGAGACAGTTTTTCTTGAAACATAAACCTTTGAGATTGTTTCT
66 TCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCC
* * *
789049 CTTGAAACAGTTTCTCTTGAAACATAAACTTTTGAGATTGTTTCTCTTGAAAAAAAATTTGTCTC
1 CTTGAAACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAAAAAAATTTGTCTC
789114 AT-TTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCC
66 -TCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCC
789160 CTTGAAA
1 CTTGAAA
789167 TTTTGTTGTC
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
111 108 0.99
112 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (111 bp):
CTTGAAACAATTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAAAAAAATTTGTCTC
TCTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCC
Found at i:789164 original size:66 final size:66
Alignment explanation
Indices: 789049--789400 Score: 451
Period size: 66 Copynumber: 5.4 Consensus size: 66
789039 GATTGTTTCT
* * * * *
789049 CTTGAAACAGTTTCTCTTGAAACATAAACTTTTGAGATTGTTTCTCTTGAAAAAAAATTTGTCTC
1 CTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTC
789114 A
66 A
* **
789115 TTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTG-AA-ATTTTGTTGTCT
1 CTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAACAAATT-TTGTCT
**
789178 TG
65 CA
* *
789180 CTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGCTTCCCTTGAAACAATTTTTGTCTC
1 CTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTC
789245 GA
66 -A
* * * **
789247 -TTGAGACAATTTCTCTTTAAATATAAACCTTTGAGATTGTTTCTATTGAAACAAATTTTGTCTC
1 CTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTC
*
789311 C
66 A
* * * *
789312 CATGAGACAATTTCTCTTGAAATATAAACCTTTGAGATTATTTCCCTTGAAACAAATTTTGTCTC
1 CTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTC
*
789377 G
66 A
789378 CTTGAGACAGTTT-TCTTGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
789401 AATTTTATCT
Statistics
Matches: 250, Mismatches: 31, Indels: 11
0.86 0.11 0.04
Matches are distributed among these distances:
64 2 0.01
65 64 0.26
66 180 0.72
67 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (66 bp):
CTTGAGACAGTTTCTCTTGAAACATAAACCTTTGAGATTGTTTCCCTTGAAACAAATTTTGTCTC
A
Found at i:789438 original size:36 final size:36
Alignment explanation
Indices: 789352--789465 Score: 142
Period size: 36 Copynumber: 3.2 Consensus size: 36
789342 TTTGAGATTA
* *
789352 TTTCCCTTGAAACAAATTTTGTCTCGCTTGAGACAG
1 TTTCTCTTGAAACAAATTTTATCTCGCTTGAGACAG
*
789388 TTT-TCTTGAAACAAATTTTATCTTG-TGTGAGACAG
1 TTTCTCTTGAAACAAATTTTATCTCGCT-TGAGACAG
* * *
789423 TTTCTCTTGAAACAAATTTAATCTCACTTGAGACTG
1 TTTCTCTTGAAACAAATTTTATCTCGCTTGAGACAG
789459 TTGTCTC
1 TT-TCTC
789466 CAAATTATCC
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 30 0.45
36 31 0.46
37 5 0.07
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTTATCTCGCTTGAGACAG
Found at i:789714 original size:139 final size:139
Alignment explanation
Indices: 789462--789731 Score: 387
Period size: 139 Copynumber: 1.9 Consensus size: 139
789452 GAGACTGTTG
* * * * * *
789462 TCTCCAAATTATCCCTAAAGACGGCTAGACATCCTCATCACGTAGGAAGAATGTGGTCCACTGAC
1 TCTCCAAATTATCCCTAAAGACAGCTAGACATCCTCATCACGTAAGAACAACGTCGTCCACCGAC
* * ** *
789527 CAGATCTCCTCAATGCGTAGGAGCAGCGTCATCCTCAGATAACCAGACTTCCTCATCACGTAGGA
66 CAGATCTCCTCAACGCGAAGGAAAAGCGTCACCCTCAGATAACCAGACTTCCTCATCACGTAGGA
789592 ATCACGTTA
131 ATCACGTTA
* *
789601 TCTCCAAATTATCCCTAAAGATAGCTAGACGTCCTCATCACGTAAGAACAACGTCGTCCACCGAC
1 TCTCCAAATTATCCCTAAAGACAGCTAGACATCCTCATCACGTAAGAACAACGTCGTCCACCGAC
* * **
789666 CAGTTCTCCTCAACGCGAAGGAAAAGTGTCACCCTCAGATAATTAGACTTCCTCATCACGTAGGA
66 CAGATCTCCTCAACGCGAAGGAAAAGCGTCACCCTCAGATAACCAGACTTCCTCATCACGTAGGA
789731 A
131 A
789732 CCGTGTTGTC
Statistics
Matches: 114, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
139 114 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (139 bp):
TCTCCAAATTATCCCTAAAGACAGCTAGACATCCTCATCACGTAAGAACAACGTCGTCCACCGAC
CAGATCTCCTCAACGCGAAGGAAAAGCGTCACCCTCAGATAACCAGACTTCCTCATCACGTAGGA
ATCACGTTA
Found at i:789752 original size:139 final size:139
Alignment explanation
Indices: 789457--789759 Score: 385
Period size: 139 Copynumber: 2.2 Consensus size: 139
789447 CACTTGAGAC
** * * * *
789457 TGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACATCCTCATCACGTAGGAAGAATGTGGTCCA
1 TGTTGTCTCCAAATTATCCCTAAAGATAGCTAGACATCCTCATCACGTAAGAACAACGTCGTCCA
* * * ** *
789522 CTGACCAGATCTCCTCAATGCGTAGGAGCAGCGTCATCCTCAGATAACCAGACTTCCTCATCACG
66 CCGACCAGATCTCCTCAACGCGAAGGAAAAGCGTCACCCTCAGATAACCAGACTTCCTCATCACG
*
789587 TAGGAATCA
131 TAGGAACCA
* * *
789596 CGTTATCTCCAAATTATCCCTAAAGATAGCTAGACGTCCTCATCACGTAAGAACAACGTCGTCCA
1 TGTTGTCTCCAAATTATCCCTAAAGATAGCTAGACATCCTCATCACGTAAGAACAACGTCGTCCA
* * **
789661 CCGACCAGTTCTCCTCAACGCGAAGGAAAAGTGTCACCCTCAGATAATTAGACTTCCTCATCACG
66 CCGACCAGATCTCCTCAACGCGAAGGAAAAGCGTCACCCTCAGATAACCAGACTTCCTCATCACG
*
789726 TAGGAACCG
131 TAGGAACCA
* *
789735 TGTTGTCACCAATTTAT--CTAAAGAT
1 TGTTGTCTCCAAATTATCCCTAAAGAT
789760 TGACATGATT
Statistics
Matches: 139, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
137 8 0.06
139 131 0.94
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (139 bp):
TGTTGTCTCCAAATTATCCCTAAAGATAGCTAGACATCCTCATCACGTAAGAACAACGTCGTCCA
CCGACCAGATCTCCTCAACGCGAAGGAAAAGCGTCACCCTCAGATAACCAGACTTCCTCATCACG
TAGGAACCA
Found at i:790011 original size:3 final size:3
Alignment explanation
Indices: 789994--790050 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
789984 AGGTTCTAAT
* * * *
789994 TTA TCA TTA -TA TTA TTA TTA TTA TTA CTA TCA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
790041 ATA TTA TTA T
1 TTA TTA TTA T
790051 ATTTTTGTAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:799603 original size:22 final size:24
Alignment explanation
Indices: 799567--799610 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
799557 ATGGAAGCTA
799567 AAAAACACCACCAACA-TTGAAAT
1 AAAAACACCACCAACACTTGAAAT
*
799590 AAAATCACCA-CAACACTTGAA
1 AAAAACACCACCAACACTTGAA
799611 CACAATACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.55, C:0.27, G:0.05, T:0.14
Consensus pattern (24 bp):
AAAAACACCACCAACACTTGAAAT
Found at i:806031 original size:20 final size:20
Alignment explanation
Indices: 806002--806040 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
805992 ATTTCACCAC
*
806002 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
806022 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
806041 TATGAGCTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:816266 original size:136 final size:136
Alignment explanation
Indices: 816018--816301 Score: 523
Period size: 136 Copynumber: 2.1 Consensus size: 136
816008 TCCGTCCTAG
*
816018 ATGTCGCGACAATCATATTTTGCTCTGTAGTCTCATCATGTCATGGCAATTTCCTTTTGCTTATC
1 ATGTCGCGACAATCACATTTTGCTCTGTAGTCTCATCATGTCATGGCAATTTCCTTTTGCTTATC
*
816083 TTTGCTCCCAAATCCTGCACATCATTAAACAAGACATATTCCCCATAACGCAACACTGATTACAA
66 TTTGCTCCCAAATCCTGCACATCATTAAACAAAACATATTCCCCATAACGCAACACTGATTACAA
816148 AATAAA
131 AATAAA
*
816154 ATGTCGCGACAATCGCATTTTGCTCTGTAGTCTCATCATGTCATGGCAATTTCCTTTTGCTTATC
1 ATGTCGCGACAATCACATTTTGCTCTGTAGTCTCATCATGTCATGGCAATTTCCTTTTGCTTATC
*
816219 TTTGCTCCCAAATCCTGCACATCATTAAACAAAACATATTCCTCATAACGCAACACTGATTACAA
66 TTTGCTCCCAAATCCTGCACATCATTAAACAAAACATATTCCCCATAACGCAACACTGATTACAA
816284 AATAAA
131 AATAAA
*
816290 ATGTCACGACAA
1 ATGTCGCGACAA
816302 ACAAAATTTC
Statistics
Matches: 143, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 143 1.00
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (136 bp):
ATGTCGCGACAATCACATTTTGCTCTGTAGTCTCATCATGTCATGGCAATTTCCTTTTGCTTATC
TTTGCTCCCAAATCCTGCACATCATTAAACAAAACATATTCCCCATAACGCAACACTGATTACAA
AATAAA
Found at i:827762 original size:16 final size:17
Alignment explanation
Indices: 827741--827776 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
827731 AGTTTGGAAT
827741 TTTAATTAAAGT-TTGA
1 TTTAATTAAAGTATTGA
*
827757 TTTAATTAATGTATTGA
1 TTTAATTAAAGTATTGA
827774 TTT
1 TTT
827777 TTATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (17 bp):
TTTAATTAAAGTATTGA
Found at i:831689 original size:21 final size:21
Alignment explanation
Indices: 831663--831702 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
831653 CCGAAATTAT
831663 TGTAGC-AGTGTATCGATACAC
1 TGTAGCAAG-GTATCGATACAC
831684 TGTAGCAAGGTATCGATAC
1 TGTAGCAAGGTATCGATAC
831703 CCCTATAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (21 bp):
TGTAGCAAGGTATCGATACAC
Found at i:833249 original size:16 final size:16
Alignment explanation
Indices: 833228--833265 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
833218 GTACTGCTCG
833228 ACATGTTATCAACCTA
1 ACATGTTATCAACCTA
* *
833244 ACATGTTATGAACCTG
1 ACATGTTATCAACCTA
833260 ACATGT
1 ACATGT
833266 AATTGAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (16 bp):
ACATGTTATCAACCTA
Found at i:833438 original size:15 final size:15
Alignment explanation
Indices: 833418--833451 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
833408 CTATATTGCA
833418 TTAGAATATTTAATT
1 TTAGAATATTTAATT
* *
833433 TTAGAATCTTTTATT
1 TTAGAATATTTAATT
833448 TTAG
1 TTAG
833452 TCATTTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.56
Consensus pattern (15 bp):
TTAGAATATTTAATT
Found at i:833488 original size:2 final size:2
Alignment explanation
Indices: 833481--833511 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
833471 ATGTACACAA
833481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
833512 CAAAAGGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:834688 original size:2 final size:2
Alignment explanation
Indices: 834674--834743 Score: 97
Period size: 2 Copynumber: 35.0 Consensus size: 2
834664 TATTTAAGCC
* *
834674 AT AT AT A- AGT AT AT AT AC AT AT AT AT AT AT AT AT GT 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 AT
*
834716 AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
834744 TTGTGTACAT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
1 1 0.02
2 58 0.97
3 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:834879 original size:19 final size:18
Alignment explanation
Indices: 834848--834883 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
834838 TTTTTGTAAT
*
834848 ATAAATTGGCTTATATTA
1 ATAAAATGGCTTATATTA
834866 ATAAAATGGACTTATATT
1 ATAAAATGG-CTTATATT
834884 TATTTCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.06, G:0.11, T:0.42
Consensus pattern (18 bp):
ATAAAATGGCTTATATTA
Found at i:835010 original size:2 final size:2
Alignment explanation
Indices: 835005--835131 Score: 179
Period size: 2 Copynumber: 63.5 Consensus size: 2
834995 TGCGCGCGCG
*
835005 TA TA TA TA TA TA TA CA CTA -A TA TA TA TA TA TA TCA TA TA CTA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA TA -TA
*
835047 -A TA TA TA TA TA TA T- TC 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
*
835087 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA 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
835129 TA T
1 TA T
835132 CGTACATAAG
Statistics
Matches: 114, Mismatches: 5, Indels: 12
0.87 0.04 0.09
Matches are distributed among these distances:
1 3 0.03
2 106 0.93
3 5 0.04
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:835340 original size:2 final size:2
Alignment explanation
Indices: 835333--835363 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
835323 ATTTATTTCA
835333 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
835364 AGTGTAACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:838782 original size:26 final size:26
Alignment explanation
Indices: 838708--838776 Score: 138
Period size: 26 Copynumber: 2.7 Consensus size: 26
838698 AAGGGCTATA
838708 TTGAGTGAAAAAATGGAGGTCCATAT
1 TTGAGTGAAAAAATGGAGGTCCATAT
838734 TTGAGTGAAAAAATGGAGGTCCATAT
1 TTGAGTGAAAAAATGGAGGTCCATAT
838760 TTGAGTGAAAAAATGGA
1 TTGAGTGAAAAAATGGA
838777 TTTCCAATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 43 1.00
ACGTcount: A:0.41, C:0.06, G:0.28, T:0.26
Consensus pattern (26 bp):
TTGAGTGAAAAAATGGAGGTCCATAT
Found at i:843962 original size:131 final size:131
Alignment explanation
Indices: 843728--843989 Score: 470
Period size: 131 Copynumber: 2.0 Consensus size: 131
843718 TAACCAAGTA
* * *
843728 TACCTAGAAACACTCGTAAGAACATGTTACATCAAGAGTAACCATATTAAGTGTAATACACCAAA
1 TACCTAGAAACACTCGTAAGAACAGGTTACATAAAGAGTAACCATATTAAGCGTAATACACCAAA
*
843793 ATATCTTTGAACGAGGACGAATACGAATATTCATGATCAAGATCGTTCAGGAGACATTCGATAAG
66 ATATCTTTGAACGAGGACGAATACGAATAGTCATGATCAAGATCGTTCAGGAGACATTCGATAAG
843858 C
131 C
* *
843859 TACCTGGAAACACTCGTAAGAACAGGTTACGTAAAGAGTAACCATATTAAGCGTAATACACCAAA
1 TACCTAGAAACACTCGTAAGAACAGGTTACATAAAGAGTAACCATATTAAGCGTAATACACCAAA
843924 ATATCTTTGAACGAGGACGAATACGAATAGTCATGATCAAGATCGTTCAGGAGACATTCGATAAG
66 ATATCTTTGAACGAGGACGAATACGAATAGTCATGATCAAGATCGTTCAGGAGACATTCGATAAG
843989 C
131 C
843990 GGTACGATAA
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 125 1.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (131 bp):
TACCTAGAAACACTCGTAAGAACAGGTTACATAAAGAGTAACCATATTAAGCGTAATACACCAAA
ATATCTTTGAACGAGGACGAATACGAATAGTCATGATCAAGATCGTTCAGGAGACATTCGATAAG
C
Found at i:844907 original size:31 final size:31
Alignment explanation
Indices: 844860--844945 Score: 127
Period size: 31 Copynumber: 2.8 Consensus size: 31
844850 GATACTAGTT
* *
844860 AGTTATGTATTCAGATAATGCACAATATGTC
1 AGTTATGCATTTAGATAATGCACAATATGTC
844891 AGTTATGCATTTAGATAATGCACAATATGTC
1 AGTTATGCATTTAGATAATGCACAATATGTC
* * *
844922 AGTTATGCATGTATATAGTGCACA
1 AGTTATGCATTTAGATAATGCACA
844946 TGATTACCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (31 bp):
AGTTATGCATTTAGATAATGCACAATATGTC
Found at i:852578 original size:31 final size:31
Alignment explanation
Indices: 852540--852627 Score: 124
Period size: 31 Copynumber: 2.9 Consensus size: 31
852530 CCAAATACTA
*
852540 GTCAGTTATGCATTCAAATAATGCACAATAT
1 GTCAGTTATGTATTCAAATAATGCACAATAT
* * *
852571 GTCAGTTATGTATTCAGATAATGCATAGTAT
1 GTCAGTTATGTATTCAAATAATGCACAATAT
*
852602 GTCAGTTATGTATAC-AATAATGCACA
1 GTCAGTTATGTATTCAAATAATGCACA
852628 GGATTACTAG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 9 0.18
31 41 0.82
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (31 bp):
GTCAGTTATGTATTCAAATAATGCACAATAT
Found at i:854747 original size:17 final size:17
Alignment explanation
Indices: 854725--854760 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
854715 ACCAAACGAC
854725 TTCGATTGTAAAATGAA
1 TTCGATTGTAAAATGAA
854742 TTCGATTGTAAAATGAA
1 TTCGATTGTAAAATGAA
854759 TT
1 TT
854761 GTTGTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (17 bp):
TTCGATTGTAAAATGAA
Found at i:855403 original size:18 final size:20
Alignment explanation
Indices: 855380--855430 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 20
855370 CACCATCACC
855380 ACTTCCATATCCTGA-CCA-
1 ACTTCCATATCCTGATCCAG
* *
855398 ACTTCCGTACCCTGATCCAG
1 ACTTCCATATCCTGATCCAG
855418 AC--CCATATCCTGA
1 ACTTCCATATCCTGA
855431 ACCTCCATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 22 0.81
19 3 0.11
20 2 0.07
ACGTcount: A:0.25, C:0.39, G:0.10, T:0.25
Consensus pattern (20 bp):
ACTTCCATATCCTGATCCAG
Found at i:855477 original size:21 final size:21
Alignment explanation
Indices: 855452--855493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
855442 ATCCGCCGCT
855452 GCCGCCACCTCC-CCTACCTCC
1 GCCGCCACCTCCACC-ACCTCC
*
855473 GCCGCCGCCTCCACCACCTCC
1 GCCGCCACCTCCACCACCTCC
855494 TATCCCACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.10, C:0.67, G:0.12, T:0.12
Consensus pattern (21 bp):
GCCGCCACCTCCACCACCTCC
Found at i:855579 original size:6 final size:6
Alignment explanation
Indices: 855568--855630 Score: 81
Period size: 6 Copynumber: 10.5 Consensus size: 6
855558 CCATAGCCTT
* * *
855568 CACCTC CACCTC CACCTC CACCTC CACCTC CTCCTC CACCAC CACCAC
1 CACCTC CACCTC CACCTC CACCTC CACCTC CACCTC CACCTC CACCTC
* *
855616 TACCTC CTCCTC CAC
1 CACCTC CACCTC CAC
855631 TTCGTCCTGA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 49 1.00
ACGTcount: A:0.17, C:0.65, G:0.00, T:0.17
Consensus pattern (6 bp):
CACCTC
Found at i:855603 original size:24 final size:24
Alignment explanation
Indices: 855568--855630 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
855558 CCATAGCCTT
* * *
855568 CACCTCCACCTCCACCTCCACCTC
1 CACCTCCTCCTCCACCACCACCAC
855592 CACCTCCTCCTCCACCACCACCAC
1 CACCTCCTCCTCCACCACCACCAC
*
855616 TACCTCCTCCTCCAC
1 CACCTCCTCCTCCAC
855631 TTCGTCCTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.17, C:0.65, G:0.00, T:0.17
Consensus pattern (24 bp):
CACCTCCTCCTCCACCACCACCAC
Found at i:859717 original size:22 final size:22
Alignment explanation
Indices: 859692--859736 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
859682 ACATGAAGTC
* *
859692 TTTGAGCTGAAATGAGTAAATT
1 TTTGAGCTAAAATGAGAAAATT
*
859714 TTTGAGTTAAAATGAGAAAATT
1 TTTGAGCTAAAATGAGAAAATT
859736 T
1 T
859737 GGGCTTGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (22 bp):
TTTGAGCTAAAATGAGAAAATT
Found at i:866666 original size:22 final size:22
Alignment explanation
Indices: 866632--866676 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
866622 ACATGAAGTG
* *
866632 TTTGAGCTGAAATAAGTAAATA
1 TTTGAGCTAAAATAAGAAAATA
*
866654 TTTGAGTTAAAATAAGAAAATA
1 TTTGAGCTAAAATAAGAAAATA
866676 T
1 T
866677 GGGCTTGGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.16, T:0.33
Consensus pattern (22 bp):
TTTGAGCTAAAATAAGAAAATA
Found at i:874417 original size:31 final size:30
Alignment explanation
Indices: 874286--874451 Score: 142
Period size: 29 Copynumber: 5.6 Consensus size: 30
874276 AACATTTGAA
*
874286 AATTCCCAAAATGTCA-CTTTTTTAAAAAT
1 AATTCCCAAAATGTCACCTTTTTTCAAAAT
* * ***
874315 AATTCCCAGAGTGTCACC-TTTTAGGAAAT
1 AATTCCCAAAATGTCACCTTTTTTCAAAAT
* * *
874344 AATTCCCAATATGTTACC-TTTTCCAAAAT
1 AATTCCCAAAATGTCACCTTTTTTCAAAAT
* *
874373 ATTTCCCATAATGTCACCTTTTTTTCAAAAT
1 AATTCCCAAAATGTCACC-TTTTTTCAAAAT
* * *
874404 AATACCCAAAATGTCACC-TTTATCGAAAT
1 AATTCCCAAAATGTCACCTTTTTTCAAAAT
* * *
874433 ATTTCCCAGAATATCACCT
1 AATTCCCAAAATGTCACCT
874452 AATAACAATT
Statistics
Matches: 107, Mismatches: 26, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
29 81 0.76
30 1 0.01
31 25 0.23
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.36
Consensus pattern (30 bp):
AATTCCCAAAATGTCACCTTTTTTCAAAAT
Found at i:884365 original size:16 final size:16
Alignment explanation
Indices: 884344--884378 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
884334 ATTATTTTAC
884344 CATTACATTGTAAGAG
1 CATTACATTGTAAGAG
884360 CATTACATTGTAAGAG
1 CATTACATTGTAAGAG
884376 CAT
1 CAT
884379 CGAGAGATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (16 bp):
CATTACATTGTAAGAG
Found at i:885481 original size:81 final size:76
Alignment explanation
Indices: 885350--885494 Score: 175
Period size: 81 Copynumber: 1.8 Consensus size: 76
885340 AAATAAAATA
* *
885350 TTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATCTGAATTACAATC-TTTAATGT
1 TTATTTAATTAATTCAATTAAATATACATAAAAGACTTATAATCTAAATTACAATCTTTTAATGT
885414 TTATTTAAAAC
66 TTATTTAAAAC
* * * *
885425 TTATTTAATTATTTCGAATTATATATATACCCAATAAAAGAGTTGTAATCTAAATTACATTCTTT
1 TTATTTAATTAATTC-AATTA-A-ATATA--C-ATAAAAGACTTATAATCTAAATTACAATCTTT
885490 TAATG
60 TAATG
885495 CTTACTTACT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
75 14 0.25
76 5 0.09
77 1 0.02
78 5 0.09
80 1 0.02
81 24 0.42
82 7 0.12
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.44
Consensus pattern (76 bp):
TTATTTAATTAATTCAATTAAATATACATAAAAGACTTATAATCTAAATTACAATCTTTTAATGT
TTATTTAAAAC
Found at i:899130 original size:20 final size:20
Alignment explanation
Indices: 899087--899131 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
899077 ATTAATAATT
*
899087 TTAATTAATTATAAAAAATA
1 TTAAATAATTATAAAAAATA
* *
899107 -TAAATAATTATTAAAAGTA
1 TTAAATAATTATAAAAAATA
899126 TTAAAT
1 TTAAAT
899132 TTATCCTTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TTAAATAATTATAAAAAATA
Found at i:902110 original size:20 final size:20
Alignment explanation
Indices: 902056--902111 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
902046 TTCAGTCAAG
*
902056 TATTAATAATT-TTAATTAAT
1 TATTAA-AATTATTAAATAAT
* *
902076 TATAAAAAATA-TAAATAAT
1 TATTAAAATTATTAAATAAT
902095 TATTAAAATTATTAAAT
1 TATTAAAATTATTAAAT
902112 TTATCCTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTAAAATTATTAAATAAT
Found at i:906731 original size:32 final size:31
Alignment explanation
Indices: 906695--906775 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
906685 GATAGTCATG
*
906695 TGCATTATTTGAATACAACACTG-ACTCTGTTA
1 TGCATTATTTGAATACAACA-TGAAAT-TGTTA
* * *
906727 TGCATTATCTAAATGCAACATGAAATTGTTA
1 TGCATTATTTGAATACAACATGAAATTGTTA
* *
906758 AGCATTATTTGAACACAA
1 TGCATTATTTGAATACAA
906776 GATTAACTAG
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
31 20 0.51
32 19 0.49
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (31 bp):
TGCATTATTTGAATACAACATGAAATTGTTA
Found at i:926791 original size:105 final size:105
Alignment explanation
Indices: 926609--926818 Score: 411
Period size: 105 Copynumber: 2.0 Consensus size: 105
926599 TCGAAATACT
926609 TTGTAAAATTATTTTGAAATTGTTTTAAGATTAAAACTTAATTTTACACTTGAGTAAGGATTAAA
1 TTGTAAAATTATTTTGAAATTGTTTTAAGATTAAAACTTAATTTTACACTTGAGTAAGGATTAAA
926674 AATGACTTTTGAAAGATTTAGAGTAATGTTTTGATATTCG
66 AATGACTTTTGAAAGATTTAGAGTAATGTTTTGATATTCG
*
926714 TTGTAAAATTATTTTGAAATTGTTTTAAGATTAAAACTTAATTTTATACTTGAGTAAGGATTAAA
1 TTGTAAAATTATTTTGAAATTGTTTTAAGATTAAAACTTAATTTTACACTTGAGTAAGGATTAAA
926779 AATGACTTTTGAAAGATTTAGAGTAATGTTTTGATATTCG
66 AATGACTTTTGAAAGATTTAGAGTAATGTTTTGATATTCG
926819 AATAATTATA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 104 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.43
Consensus pattern (105 bp):
TTGTAAAATTATTTTGAAATTGTTTTAAGATTAAAACTTAATTTTACACTTGAGTAAGGATTAAA
AATGACTTTTGAAAGATTTAGAGTAATGTTTTGATATTCG
Found at i:929357 original size:20 final size:20
Alignment explanation
Indices: 929285--929364 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
929275 CAGAACCCCA
* *
929285 GGGGGTATCGATTCCCCTAT
1 GGGGGAATCGATTCCCTTAT
* * *
929305 GGAGGAATCGGTTCCCATTCAAA
1 GGGGGAATCGATTCCC-TT--AT
*
929328 GGGGGAATCGGTTCCCTTAT
1 GGGGGAATCGATTCCCTTAT
*
929348 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
929365 CTGTACCAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
20 29 0.60
21 1 0.02
22 2 0.04
23 16 0.33
ACGTcount: A:0.19, C:0.23, G:0.31, T:0.28
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTTAT
Found at i:933130 original size:22 final size:21
Alignment explanation
Indices: 933088--933127 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
933078 GAGTTTATTT
*
933088 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
933109 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
933128 ACAACTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:935325 original size:11 final size:11
Alignment explanation
Indices: 935309--935338 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
935299 ATATTCGTTG
935309 TAAAATTATTT
1 TAAAATTATTT
935320 TAAAATTATTT
1 TAAAATTATTT
*
935331 TAAGATTA
1 TAAAATTA
935339 AAACTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (11 bp):
TAAAATTATTT
Found at i:935389 original size:105 final size:105
Alignment explanation
Indices: 935203--935410 Score: 371
Period size: 105 Copynumber: 2.0 Consensus size: 105
935193 GAAATACTTC
* * *
935203 GTAAAATTATTTTGAAATTGTTTTAAGATTAAAACTTAATTTTACACTTGAGTAAGGATTAAAAA
1 GTAAAATTATTTTAAAATTATTTTAAGATTAAAACTTAATTTTACACTTGAATAAGGATTAAAAA
*
935268 TGACTTTTGAATGATTTAAAGTAATGTTTTGATATTCGTT
66 TGACTTTTGAAAGATTTAAAGTAATGTTTTGATATTCGTT
935308 GTAAAATTATTTTAAAATTATTTTAAGATTAAAACTTAATTTTACACTTGAATAAGGATTAAAAA
1 GTAAAATTATTTTAAAATTATTTTAAGATTAAAACTTAATTTTACACTTGAATAAGGATTAAAAA
*
935373 TGACTTTTGAAAGATTTAGAGTAATGTTTTGATATTCG
66 TGACTTTTGAAAGATTTAAAGTAATGTTTTGATATTCG
935411 AATAATTATA
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.39, C:0.05, G:0.13, T:0.43
Consensus pattern (105 bp):
GTAAAATTATTTTAAAATTATTTTAAGATTAAAACTTAATTTTACACTTGAATAAGGATTAAAAA
TGACTTTTGAAAGATTTAAAGTAATGTTTTGATATTCGTT
Found at i:938588 original size:23 final size:23
Alignment explanation
Indices: 938558--938604 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
938548 AAATGGAGAA
938558 AGTTCAAAATTCAACTTTGTTAG
1 AGTTCAAAATTCAACTTTGTTAG
938581 AGTTCAAAATTCAACTTTGTTAG
1 AGTTCAAAATTCAACTTTGTTAG
938604 A
1 A
938605 AAAAGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (23 bp):
AGTTCAAAATTCAACTTTGTTAG
Found at i:942265 original size:44 final size:43
Alignment explanation
Indices: 942168--942267 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 43
942158 TTTATGTGCA
* * *
942168 ATGCATCGATACACTAGAAAGTGTAATGATGCATCCTTTGAAT
1 ATGCATCGATACACTAGAAAGTGCAACGATGAATCCTTTGAAT
* *
942211 ATGCATCGATACACTATGAAGGTGCACCGATGAATTCC-TTGAAT
1 ATGCATCGATACACTA-GAAAGTGCAACGATGAA-TCCTTTGAAT
*
942255 GTGCATCGATACA
1 ATGCATCGATACA
942268 TTGTACAGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
43 16 0.33
44 30 0.61
45 3 0.06
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (43 bp):
ATGCATCGATACACTAGAAAGTGCAACGATGAATCCTTTGAAT
Found at i:946651 original size:17 final size:19
Alignment explanation
Indices: 946626--946663 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
946616 AAATTGTCTC
946626 ATTTATATTCT-TAAT-GA
1 ATTTATATTCTCTAATAGA
*
946643 ATTTTTATTCTCTAATAGA
1 ATTTATATTCTCTAATAGA
946662 AT
1 AT
946664 GCTTCCACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
18 4 0.22
19 4 0.22
ACGTcount: A:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTTATATTCTCTAATAGA
Found at i:950637 original size:32 final size:32
Alignment explanation
Indices: 950587--950713 Score: 105
Period size: 32 Copynumber: 4.0 Consensus size: 32
950577 CCTAAGGTGA
* * *
950587 CCTTGGGCAGGCTTTAAGGCCCCAAGGCATTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATTT
* * *
950619 CCTTGGGTAAGCTCTAAGGTCTCAAGGTACTTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTA-TTT
* * * *
950652 -CTTGAGTAGGCTCTTAGGCCCTAAGGTA-CT
1 CCTTGGGTAGGCTCTAAGGCCCCAAGGTATTT
* * *
950682 CCTTTGGGTAGGATCTCAGGCCCCAAGATATT
1 CC-TTGGGTAGGCTCTAAGGCCCCAAGGTATT
950714 CTATTAGGTT
Statistics
Matches: 72, Mismatches: 19, Indels: 7
0.73 0.19 0.07
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 67 0.93
33 3 0.04
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.29
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAGGTATTT
Found at i:953719 original size:27 final size:27
Alignment explanation
Indices: 953685--953747 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
953675 TGAATGAAAG
** *
953685 AAAATGACTGAAATACCCTTGAACTGT
1 AAAATGACAAAAATACCCCTGAACTGT
* *
953712 AATATGACCAAAAATACCCCTGAAGTGT
1 AAAATGA-CAAAAATACCCCTGAACTGT
953740 AAAATGAC
1 AAAATGAC
953748 CTAAAATATC
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.22
Consensus pattern (27 bp):
AAAATGACAAAAATACCCCTGAACTGT
Found at i:953732 original size:29 final size:28
Alignment explanation
Indices: 953695--953760 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
953685 AAAATGACTG
* *
953695 AAATACCCTTGAACTGTAATATGACCAA
1 AAATACCCCTGAACTGTAAAATGACCAA
* *
953723 AAATACCCCTGAAGTGTAAAATGACCTA
1 AAATACCCCTGAACTGTAAAATGACCAA
953751 AAATATCCCC
1 AAATA-CCCC
953761 AAGCCTTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 29 0.88
29 4 0.12
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.23
Consensus pattern (28 bp):
AAATACCCCTGAACTGTAAAATGACCAA
Found at i:954885 original size:32 final size:33
Alignment explanation
Indices: 954844--954964 Score: 99
Period size: 32 Copynumber: 3.8 Consensus size: 33
954834 CCTAAGGTGA
** *
954844 CCTTGGGTAGGCTTTGAGGCCCCAATGCA-TTT
1 CCTTGGGTAGGCTTCAAGGCCCCAAGGCACTTT
*
954876 CCTTGGGTAGGC-TCAAGGCCCCAAGGTACTTT
1 CCTTGGGTAGGCTTCAAGGCCCCAAGGCACTTT
* * * * * *
954908 -CTTGGGTAGGCTCCTAGGCCCTATGGTACTCT
1 CCTTGGGTAGGCTTCAAGGCCCCAAGGCACTTT
*
954940 -CTTGGGTAGGATCTC-AGGCCCCAAG
1 CCTTGGGTAGGCT-TCAAGGCCCCAAG
954965 ATATTCCTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
31 23 0.32
32 49 0.67
33 1 0.01
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (33 bp):
CCTTGGGTAGGCTTCAAGGCCCCAAGGCACTTT
Found at i:955984 original size:21 final size:20
Alignment explanation
Indices: 955960--955998 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
955950 CACCTTTTTT
*
955960 TCACTCTCTCCTTCATTCTCA
1 TCACTCTCTACTTC-TTCTCA
*
955981 TCACTTTCTACTTCTTCT
1 TCACTCTCTACTTCTTCT
955999 TCAGCTTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.13, C:0.38, G:0.00, T:0.49
Consensus pattern (20 bp):
TCACTCTCTACTTCTTCTCA
Found at i:968512 original size:17 final size:17
Alignment explanation
Indices: 968490--968522 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
968480 ATTTACATGA
968490 CACCACAAAAGAATACC
1 CACCACAAAAGAATACC
968507 CACCACAAAAGAATAC
1 CACCACAAAAGAATAC
968523 ATGCACTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.55, C:0.33, G:0.06, T:0.06
Consensus pattern (17 bp):
CACCACAAAAGAATACC
Found at i:971978 original size:19 final size:20
Alignment explanation
Indices: 971948--971986 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
971938 TTTTTGAAAA
971948 TTAATCCCCCTTACTATATT
1 TTAATCCCCCTTACTATATT
971968 TTAAT-CCCCTTACTATATT
1 TTAATCCCCCTTACTATATT
971987 CTCCCCCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (20 bp):
TTAATCCCCCTTACTATATT
Found at i:976816 original size:18 final size:18
Alignment explanation
Indices: 976790--976825 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
976780 GGGTTCTAGG
976790 TGCTAAAAAATTATGGCT
1 TGCTAAAAAATTATGGCT
*
976808 TGCTGAAAAATTATGGCT
1 TGCTAAAAAATTATGGCT
976826 AATATCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.33
Consensus pattern (18 bp):
TGCTAAAAAATTATGGCT
Found at i:981396 original size:20 final size:20
Alignment explanation
Indices: 981371--981408 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
981361 TTTTATACCA
981371 GTTCATCCAATATCGATAAT
1 GTTCATCCAATATCGATAAT
981391 GTTCATCCAATATCGATA
1 GTTCATCCAATATCGATA
981409 CTCAACCCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
GTTCATCCAATATCGATAAT
Found at i:984681 original size:23 final size:23
Alignment explanation
Indices: 984615--984694 Score: 81
Period size: 26 Copynumber: 3.3 Consensus size: 23
984605 TTTTTAAATT
*
984615 AATTTCTTAGTTTATTTCAATTTTC
1 AATTT-TTA-TTTATTTTAATTTTC
*
984640 AATTTTTATTCTTTATTTTTA-TTTC
1 AATTTTTA---TTTATTTTAATTTTC
984665 AAGTTTTTATTTATTTTAATTTTC
1 AA-TTTTTATTTATTTTAATTTTC
984689 AATTTT
1 AATTTT
984695 CAATTTTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
23 13 0.28
24 9 0.19
25 11 0.23
26 14 0.30
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (23 bp):
AATTTTTATTTATTTTAATTTTC
Found at i:985835 original size:27 final size:28
Alignment explanation
Indices: 985774--985839 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
985764 CACGAATCCG
985774 ACCCGACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
*
985802 ACTCGACCCGAATATCACACTT-AAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
985829 ACCCGACCCGA
1 ACCCGACCCGA
985840 CCCGAACAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 15 0.42
28 21 0.58
ACGTcount: A:0.42, C:0.35, G:0.09, T:0.14
Consensus pattern (28 bp):
ACCCGACCCGAATATCACACTTAAAAAA
Found at i:988349 original size:22 final size:22
Alignment explanation
Indices: 988323--988371 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
988313 ATCGGGGAGT
988323 ATTTATGTTCCCTCTCTAATGC
1 ATTTATGTTCCCTCTCTAATGC
988345 ATTTATGTTCCCTCTCTAATGC
1 ATTTATGTTCCCTCTCTAATGC
988367 ATTTA
1 ATTTA
988372 ATTTTCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.47
Consensus pattern (22 bp):
ATTTATGTTCCCTCTCTAATGC
Found at i:1000381 original size:3 final size:3
Alignment explanation
Indices: 1000364--1000442 Score: 135
Period size: 3 Copynumber: 26.7 Consensus size: 3
1000354 CTACCAAAAA
1000364 TAT TAAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1000409 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1000443 ATCAAACTTA
Statistics
Matches: 73, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.05
3 66 0.90
4 3 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1002013 original size:59 final size:60
Alignment explanation
Indices: 1001947--1002062 Score: 146
Period size: 59 Copynumber: 1.9 Consensus size: 60
1001937 GTGGTTTAAT
* * *
1001947 CCTTTAAATGT-CTATTTTTACTATTTTAGTCCCTTAAGTTTTTGTT-TTTCTATTTTGGA
1 CCTTTAAAT-TCCTATTTGTACTATTTTAGTCCCTTAAGTTTCTATTGTTTCTATTTTGGA
* ***
1002006 CCTTTAAATTCCTATTTGTATTATTTTAGTTGTTTAAGTTTCTATTGTTTCTATTTT
1 CCTTTAAATTCCTATTTGTACTATTTTAGTCCCTTAAGTTTCTATTGTTTCTATTTT
1002063 AGTCCTTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
58 1 0.02
59 37 0.77
60 10 0.21
ACGTcount: A:0.19, C:0.12, G:0.09, T:0.59
Consensus pattern (60 bp):
CCTTTAAATTCCTATTTGTACTATTTTAGTCCCTTAAGTTTCTATTGTTTCTATTTTGGA
Found at i:1002098 original size:86 final size:86
Alignment explanation
Indices: 1001941--1002162 Score: 200
Period size: 86 Copynumber: 2.5 Consensus size: 86
1001931 TTATTTGTGG
* * * ** * *
1001941 TTTAATCCTTTAAATGTCTATTTT-TACTATTTTAGTCCCTTAAGTTTTTGTTTTTCTATTTTGG
1 TTTAATCCCTTAAGTTTCTATTTTAT-CTATTTTAGT-CCTTAA-AATAT-TTTTTCTATTTTAG
* *
1002005 ACCTTTAAAT-T-CCTATTTGTATTAT
62 ACATTTAAATGTACCTATTT-T-CTAT
* *** *
1002030 TTTAGTTGTTTAAGTTTCTATTGTT-TCTATTTTAGTCCTTAAAATATTTTTTCTATTTTAGTCA
1 TTTAATCCCTTAAGTTTCTATT-TTATCTATTTTAGTCCTTAAAATATTTTTTCTATTTTAGACA
**
1002094 TTTAAATGTATGTATTTTCTAT
65 TTTAAATGTACCTATTTTCTAT
*
1002116 TTTAATCCCTTAAGTTTCTATTTTATCTATTTTAGTCCTTTAAATAT
1 TTTAATCCCTTAAGTTTCTATTTTATCTATTTTAGTCCTTAAAATAT
1002163 CTATATTCAC
Statistics
Matches: 110, Mismatches: 19, Indels: 11
0.79 0.14 0.08
Matches are distributed among these distances:
85 2 0.02
86 63 0.57
87 4 0.04
88 11 0.10
89 27 0.25
90 3 0.03
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.58
Consensus pattern (86 bp):
TTTAATCCCTTAAGTTTCTATTTTATCTATTTTAGTCCTTAAAATATTTTTTCTATTTTAGACAT
TTAAATGTACCTATTTTCTAT
Found at i:1002145 original size:30 final size:29
Alignment explanation
Indices: 1001957--1002272 Score: 223
Period size: 30 Copynumber: 10.7 Consensus size: 29
1001947 CCTTTAAATG
1001957 TCTATTTTTACTATTTTAGTCCCTTAAGTT
1 TCTATTTTT-CTATTTTAGTCCCTTAAGTT
* * * * * *
1001987 TTTGTTTTTCTATTTTGGACCTTTAAATT
1 TCTATTTTTCTATTTTAGTCCCTTAAGTT
* ***
1002016 CCTATTTGTAT-TATTTTAGTTGTTTAAGTT
1 TCTATTT-T-TCTATTTTAGTCCCTTAAGTT
**
1002046 TCTATTGTTTCTATTTTAGT-CCTTAA-AA
1 TCTATT-TTTCTATTTTAGTCCCTTAAGTT
* ** *
1002074 TAT-TTTTTCTATTTTAGTCATTTAAATGTA
1 TCTATTTTTCTATTTTAGTCCCTT-AA-GTT
* *
1002104 TGTA-TTTTCTATTTTAATCCCTTAAGTT
1 TCTATTTTTCTATTTTAGTCCCTTAAGTT
* * *
1002132 TCTATTTTATCTATTTTAGTCCTTTAAATA
1 TCTATTTT-TCTATTTTAGTCCCTTAAGTT
**
1002162 TCTATATTCACTATTTTAGTCCCTTAAGTT
1 TCTAT-TTTTCTATTTTAGTCCCTTAAGTT
* * * *
1002192 TTTGTTTTTGTTATTTTAGTCCATTCAA-TT
1 TCTATTTTT-CTATTTTAGTCCCTT-AAGTT
1002222 TCTATTTTGT-TATTTTAGTCCCTTAAGTT
1 TCTATTTT-TCTATTTTAGTCCCTTAAGTT
*
1002251 TCTATTTTTACTATTTTGGTCC
1 TCTATTTTT-CTATTTTAGTCC
1002273 TCAAATTTTT
Statistics
Matches: 220, Mismatches: 48, Indels: 36
0.72 0.16 0.12
Matches are distributed among these distances:
26 13 0.06
27 4 0.02
28 12 0.05
29 55 0.25
30 129 0.59
31 7 0.03
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.58
Consensus pattern (29 bp):
TCTATTTTTCTATTTTAGTCCCTTAAGTT
Found at i:1005761 original size:11 final size:11
Alignment explanation
Indices: 1005745--1005796 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
1005735 ATCAAAGAAG
1005745 AGAAAAAACAA
1 AGAAAAAACAA
1005756 AG--AAAACAA
1 AGAAAAAACAA
*
1005765 AGTAAAATACAAA
1 AG-AAAAAAC-AA
1005778 AGAAAAAACAA
1 AGAAAAAACAA
1005789 AGAGAAAA
1 AGA-AAAA
1005797 GAAGACAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 9 0.26
11 7 0.21
12 14 0.41
13 4 0.12
ACGTcount: A:0.77, C:0.08, G:0.12, T:0.04
Consensus pattern (11 bp):
AGAAAAAACAA
Found at i:1007036 original size:37 final size:38
Alignment explanation
Indices: 1006964--1007036 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
1006954 ATTGATGTTG
* * *
1006964 TTTCTCTCGAAACAAAATGTTGTCTCGCTTGAGACAGT
1 TTTCTCTCAAAACAAAATGTTGTCTCACTTAAGACAGT
1007002 TTTCTCTCAAAAC-AAAT-TTCGTCTCACTTAAGACA
1 TTTCTCTCAAAACAAAATGTT-GTCTCACTTAAGACA
1007037 TAACCCATCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 2 0.06
37 17 0.55
38 12 0.39
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (38 bp):
TTTCTCTCAAAACAAAATGTTGTCTCACTTAAGACAGT
Found at i:1007199 original size:67 final size:63
Alignment explanation
Indices: 1007043--1007202 Score: 212
Period size: 67 Copynumber: 2.4 Consensus size: 63
1007033 GACATAACCC
* *
1007043 ATCTTTGAGTCTGTTTCTTTGAAAACAAATTTTTTCTCTTGAGACAATTTGTTTTGAGAAAAAA
1 ATCTTTGAGTATGTTTCTTTG-AAACAAATTTTTTCTCTTGAGACAATTTCTTTTGAGAAAAAA
* *
1007107 ATCTTTGAGTATGTTTCTCTGGAAACAAAGTTTTGTCTCTCTTGAGATAATTTCTTTTGAGAAAA
1 ATCTTTGAGTATGTTTCT-TTGAAACAAA-TTTT-T-TCTCTTGAGACAATTTCTTTTGAGAAAA
*
1007172 CA
62 AA
*
1007174 ATCTTTGAATATGTTTCCTTTGAAACAAA
1 ATCTTTGAGTATGTTT-CTTTGAAACAAA
1007203 ACACCCATCT
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 24 0.29
65 6 0.07
66 1 0.01
67 51 0.61
68 2 0.02
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (63 bp):
ATCTTTGAGTATGTTTCTTTGAAACAAATTTTTTCTCTTGAGACAATTTCTTTTGAGAAAAAA
Found at i:1007627 original size:135 final size:130
Alignment explanation
Indices: 1007324--1007685 Score: 424
Period size: 135 Copynumber: 2.7 Consensus size: 130
1007314 TTTTATGTCA
* * * *
1007324 TCTTCATCACGTAGGAATCGTGTCATCCCCCGACCAGACCTCCTCATCATGTAGGAGTCGTGGCA
1 TCTTCATCACGTAGGAATCGTGTCAT-CCCCGACCAGATCTCCTCATCACGTAGGAGCCATGGCA
* * *
1007389 CCCCTAGATAACCTGTCGTCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCATATC
65 CCCCTAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCAGAAC
1007454 G
130 G
* * **
1007455 TCCTCATCACGTAGGAATCGTGTCATCCCCTGACCAGATCTCATCATCACGTAGGAGCCATGTTA
1 TCTTCATCACGTAGGAATCGTGTCATCCCC-GACCAGATCTCCTCATCACGTAGGAGCCATGGCA
*
1007520 CCCCCTAGATAACCAGTCGTCCTCATCGCGTAGGAA-CAGTGTTATCACCCTTCCTAAAGATGGC
65 -CCCCTAGATAACCAGTCGTCCTCATCACGTAGGAACCA-TGTTATCA---TTCCTAAAGATGG-
1007584 CAGAAC-
124 CAGAACG
* * * *
1007590 TCTTCATCACGTATGAGTCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAAG-CGTGTC
1 TCTTCATCACGTAGGAATCGTGTCATCC-CCGACCAGATCTCCTCATCACGTAGG-AGCCATGGC
* * * * *
1007654 ACCCTTAGACAACCAGACCTCTTCATCACGTA
64 ACCCCTAGATAACCAGTCGTCCTCATCACGTA
1007686 TGAGCAATGT
Statistics
Matches: 198, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
130 4 0.02
131 54 0.27
132 41 0.21
134 25 0.13
135 66 0.33
136 8 0.04
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (130 bp):
TCTTCATCACGTAGGAATCGTGTCATCCCCGACCAGATCTCCTCATCACGTAGGAGCCATGGCAC
CCCTAGATAACCAGTCGTCCTCATCACGTAGGAACCATGTTATCATTCCTAAAGATGGCAGAACG
Found at i:1009336 original size:30 final size:30
Alignment explanation
Indices: 1009301--1009630 Score: 180
Period size: 30 Copynumber: 11.1 Consensus size: 30
1009291 CCTTTAAATG
1009301 TCTATTTTTACTATTTTAGTCCCTTAAGTT
1 TCTATTTTTACTATTTTAGTCCCTTAAGTT
** * * *
1009331 TCTATTTTTTTTATTTTGGACCTTTAA--T
1 TCTATTTTTACTATTTTAGTCCCTTAAGTT
* * *
1009359 TC-ATGTTTGTATTATTTTAGTCCTTTACGTT
1 TCTAT-TTT-TACTATTTTAGTCCCTTAAGTT
* * * * *
1009390 TTTGTTGTTGCTATTTTAGT-CCTCTAAATT
1 TCTATTTTTACTATTTTAGTCCCT-TAAGTT
* * * *
1009420 TTTGTTTTTTCTATTTTAGTCCTTTAAATGTAT
1 TCTATTTTTACTATTTTAGTCCCTT-AA-GT-T
* *
1009453 GC-A-TTTT-CTATTTTAGTCCCTTAAGTA
1 TCTATTTTTACTATTTTAGTCCCTTAAGTT
* * *
1009480 TCTA-TTTTATCTATTTTAGTCCTTTAAATG
1 TCTATTTTTA-CTATTTTAGTCCCTTAAGTT
* * * * *
1009510 TATGTATTCATTATTTTAGTCCCTTATA-TT
1 TCTATTTTTACTATTTTAGTCCCTTA-AGTT
* * *
1009540 TCAATTTTT-GTTTTTTAGTCCCTTAAGTT
1 TCTATTTTTACTATTTTAGTCCCTTAAGTT
*
1009569 TCTA-TTTTGCTATTTTAGTCCCTTAAGTT
1 TCTATTTTTACTATTTTAGTCCCTTAAGTT
* * * *
1009598 TTTATTTTTTTCTATTTTTGT-CCTCAAGTT
1 TCTA-TTTTTACTATTTTAGTCCCTTAAGTT
1009628 TCT
1 TCT
1009631 GTTAATCCTA
Statistics
Matches: 229, Mismatches: 52, Indels: 38
0.72 0.16 0.12
Matches are distributed among these distances:
27 3 0.01
28 18 0.08
29 59 0.26
30 117 0.51
31 29 0.13
32 2 0.01
33 1 0.00
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.58
Consensus pattern (30 bp):
TCTATTTTTACTATTTTAGTCCCTTAAGTT
Found at i:1009560 original size:149 final size:148
Alignment explanation
Indices: 1009285--1009594 Score: 326
Period size: 149 Copynumber: 2.1 Consensus size: 148
1009275 TTATTTTTTG
* * * * * *
1009285 TTTAATCCTTTAAATGTCTATTTTTACTATTTTAGTCCCTTAAGTTTCTATTTTTTTTATTTTGG
1 TTTAGTCCTTTAAATGTATATTTTTACTATTTTAGTCCCTTAAGTATCTATTTTATCTATTTTAG
* * * ***
1009350 ACCTTTAATTCATGTTTGTATTATTTTAGTCCTTTACGTTTTTGTTGTTGCTATTTTAGT-CCTC
66 ACCTTTAATTCATGTTTGCATTATTTTAGTCCCTTACATTTCAATTGTTGCTATTTTAGTCCCT-
* * *
1009414 TAAATTTTTGTTTTTTCTAT
130 TAAATTTCT-ATTTTGCTAT
1009434 TTTAGTCCTTTAAATGTATGCA-TTTT-CTATTTTAGTCCCTTAAGTATCTATTTTATCTATTTT
1 TTTAGTCCTTTAAATGTAT--ATTTTTACTATTTTAGTCCCTTAAGTATCTATTTTATCTATTTT
* * * *
1009497 AGTCCTTTAAATGT-ATGTATT-CATTATTTTAGTCCCTTATATTTCAATTTTTG-TTTTTTAGT
64 AGACCTTT-AAT-TCATGT-TTGCATTATTTTAGTCCCTTACATTTCAATTGTTGCTATTTTAGT
*
1009559 CCCTTAAGTTTCTATTTTGCTAT
126 CCCTTAAATTTCTATTTTGCTAT
*
1009582 TTTAGTCCCTTAA
1 TTTAGTCCTTTAA
1009595 GTTTTTATTT
Statistics
Matches: 134, Mismatches: 21, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
148 20 0.15
149 72 0.54
150 38 0.28
151 4 0.03
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (148 bp):
TTTAGTCCTTTAAATGTATATTTTTACTATTTTAGTCCCTTAAGTATCTATTTTATCTATTTTAG
ACCTTTAATTCATGTTTGCATTATTTTAGTCCCTTACATTTCAATTGTTGCTATTTTAGTCCCTT
AAATTTCTATTTTGCTAT
Done.