Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008361.1 Hibiscus syriacus cultivar Beakdansim tig00111100_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: 1124086
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:558131 original size:14 final size:14
Alignment explanation
Indices: 558094--558135 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
558084 TTGGAGGATT
*
558094 AAGATAAAATGAAAA
1 AAGAGAAAAT-AAAA
*
558109 AAAAG-AAATAAAA
1 AAGAGAAAATAAAA
558122 AAGAGAAAATAAAA
1 AAGAGAAAATAAAA
558136 TGGATGCCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 8 0.35
14 12 0.52
15 3 0.13
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (14 bp):
AAGAGAAAATAAAA
Found at i:559773 original size:29 final size:29
Alignment explanation
Indices: 559731--559805 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
559721 AACCCAACCA
**
559731 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
559760 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
559789 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
559806 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:559811 original size:29 final size:29
Alignment explanation
Indices: 559732--559819 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
559722 ACCCAACCAT
* * ****
559732 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
559761 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
559790 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
559819 A
1 A
559820 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:560071 original size:29 final size:29
Alignment explanation
Indices: 560036--560122 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
560026 GTTGGCTGGT
*
560036 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
560065 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
560094 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
560123 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:561999 original size:46 final size:47
Alignment explanation
Indices: 561912--562001 Score: 123
Period size: 46 Copynumber: 1.9 Consensus size: 47
561902 TTAAGCTCGA
*
561912 CTCAAATTCAAAAAAAAATGTTAAAACTAGACTCGAACTCGAAAAAG
1 CTCAAACTCAAAAAAAAATGTTAAAACTAGACTCGAACTCGAAAAAG
*
561959 CTCAAACTC-AAAAAAAAT-TTAAAAACTCGACT-GAAGCTCGAAA
1 CTCAAACTCAAAAAAAAATGTT-AAAACTAGACTCGAA-CTCGAAA
562002 CTCAAACTCG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 5 0.13
46 26 0.67
47 8 0.21
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (47 bp):
CTCAAACTCAAAAAAAAATGTTAAAACTAGACTCGAACTCGAAAAAG
Found at i:563934 original size:11 final size:11
Alignment explanation
Indices: 563918--563980 Score: 69
Period size: 11 Copynumber: 5.9 Consensus size: 11
563908 GTATTATAGA
563918 ATTTTTAATAT
1 ATTTTTAATAT
563929 ATTTTTAA-A-
1 ATTTTTAATAT
563938 ATTTTATAAT-T
1 ATTTT-TAATAT
***
563949 ATCAATAATAT
1 ATTTTTAATAT
563960 ATTTTTAATAT
1 ATTTTTAATAT
563971 ATTTTTAATA
1 ATTTTTAATA
563981 ATGTAATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 29 0.69
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:565597 original size:23 final size:22
Alignment explanation
Indices: 565558--565612 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 22
565548 AGCACCATTA
* **
565558 AATTATAAAGTACTAAACGTTT
1 AATTATAAATTACTAAAAATTT
*
565580 AATTATAAATTAGTTAAAAATTT
1 AATTATAAATTA-CTAAAAATTT
*
565603 AAATATAAAT
1 AATTATAAAT
565613 ATAATTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 11 0.41
23 16 0.59
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (22 bp):
AATTATAAATTACTAAAAATTT
Found at i:568914 original size:16 final size:16
Alignment explanation
Indices: 568893--568931 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
568883 CATTTAATAA
*
568893 ATAAACGAACACGAAC
1 ATAAACGAACACAAAC
568909 ATAAACGAACACAAAC
1 ATAAACGAACACAAAC
568925 ATAAACG
1 ATAAACG
568932 TTGAAGTCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.59, C:0.23, G:0.10, T:0.08
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:572519 original size:23 final size:23
Alignment explanation
Indices: 572476--572525 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
572466 AAGGCAAAGG
*
572476 AAAACATGTCATAAAGACATATA
1 AAAACATGTCATAAAGACATAAA
572499 AAAACAT-TCTATAAA-ATCATAAA
1 AAAACATGTC-ATAAAGA-CATAAA
572522 AAAA
1 AAAA
572526 ACCCGGTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 3 0.12
23 21 0.88
ACGTcount: A:0.62, C:0.12, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAACATGTCATAAAGACATAAA
Found at i:572567 original size:2 final size:2
Alignment explanation
Indices: 572560--572593 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
572550 TAGAAATTAA
572560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
572594 AGAAAATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:573125 original size:28 final size:27
Alignment explanation
Indices: 573083--573137 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 27
573073 TTTTAAACCG
*
573083 AAAAGTTAAACAAATATTATTATATAA
1 AAAAGTTAAAAAAATATTATTATATAA
573110 AAAAGTATAAAAAAATATTATTATATAA
1 AAAAGT-TAAAAAAATATTATTATATAA
573138 TATAATGGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (27 bp):
AAAAGTTAAAAAAATATTATTATATAA
Found at i:574410 original size:20 final size:20
Alignment explanation
Indices: 574365--574410 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
574355 ATTTATTGAT
574365 TTTTTATATTATAATTAATA
1 TTTTTATATTATAATTAATA
*
574385 TATTTATATCTAT-A-TAATTA
1 TTTTTATAT-TATAATTAA-TA
574405 TTTTTA
1 TTTTTA
574411 ATCACATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.14
20 16 0.73
21 3 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTATATTATAATTAATA
Found at i:576881 original size:30 final size:30
Alignment explanation
Indices: 576827--576902 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
576817 AAATTGAAGA
*
576827 TTTATATAAAATTTAAAATGAAAAT-ATAT
1 TTTATATAAAATTTAAAATGAAAATGACAT
* *
576856 TCTTATCTAAAATTT-AAAGGTAAAATGACAT
1 T-TTATATAAAATTTAAAATG-AAAATGACAT
576887 TTTATATAAAATTTAA
1 TTTATATAAAATTTAA
576903 TATCAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 5 0.13
30 29 0.74
31 5 0.13
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTATATAAAATTTAAAATGAAAATGACAT
Found at i:581640 original size:2 final size:2
Alignment explanation
Indices: 581628--581677 Score: 64
Period size: 2 Copynumber: 24.0 Consensus size: 2
581618 GGACGAGATC
* *
581628 TA TA TA GA TA TA TGA GA TCA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
581672 TA TA TA
1 TA TA TA
581678 GGGAGATGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 39 0.93
3 3 0.07
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:587477 original size:36 final size:36
Alignment explanation
Indices: 587430--587622 Score: 332
Period size: 36 Copynumber: 5.4 Consensus size: 36
587420 TCAACAAACT
*
587430 CATCATCCTGATCATCAAATTCATCCAATACAAGCA
1 CATCATCCTGATCATCAAATTCATCCGATACAAGCA
* *
587466 CATCATCCTGATCATCAAATTCTTCCGATACAAGCG
1 CATCATCCTGATCATCAAATTCATCCGATACAAGCA
587502 CATCATCCTGATCATCAAATTCATCCGATACAAGCA
1 CATCATCCTGATCATCAAATTCATCCGATACAAGCA
*
587538 CATCATCCTGATTATCAAATTCATCCGATACAAGCA
1 CATCATCCTGATCATCAAATTCATCCGATACAAGCA
* *
587574 CATCATCCTGATCATAAAATTCATCCGATACAAGCT
1 CATCATCCTGATCATCAAATTCATCCGATACAAGCA
587610 CATCATCCTGATC
1 CATCATCCTGATC
587623 GAAGACTTCA
Statistics
Matches: 148, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 148 1.00
ACGTcount: A:0.35, C:0.30, G:0.08, T:0.27
Consensus pattern (36 bp):
CATCATCCTGATCATCAAATTCATCCGATACAAGCA
Found at i:587615 original size:18 final size:18
Alignment explanation
Indices: 587522--587617 Score: 58
Period size: 18 Copynumber: 5.3 Consensus size: 18
587512 ATCATCAAAT
*
587522 TCATCCGATACAAGCACA
1 TCATCCGATACAAGCTCA
*
587540 TCATCCTGATTATCAA-AT--
1 TCATCC-GA-TA-CAAGCTCA
*
587558 TCATCCGATACAAGCACA
1 TCATCCGATACAAGCTCA
* **
587576 TCATCCTGATCATAAAAT--
1 TCATCC-GAT-ACAAGCTCA
587594 TCATCCGATACAAGCTCA
1 TCATCCGATACAAGCTCA
587612 TCATCC
1 TCATCC
587618 TGATCGAAGA
Statistics
Matches: 57, Mismatches: 11, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
15 3 0.05
16 6 0.11
17 5 0.09
18 30 0.53
19 5 0.09
20 5 0.09
21 3 0.05
ACGTcount: A:0.35, C:0.30, G:0.08, T:0.26
Consensus pattern (18 bp):
TCATCCGATACAAGCTCA
Found at i:596913 original size:17 final size:18
Alignment explanation
Indices: 596882--596915 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
596872 TTTAAAAATA
596882 ATTAAAATATAATATGAT
1 ATTAAAATATAATATGAT
596900 ATTAAAAT-TAATATGA
1 ATTAAAATATAATATGA
596916 AAATTATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
ATTAAAATATAATATGAT
Found at i:596987 original size:3 final size:3
Alignment explanation
Indices: 596981--597005 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
596971 GTATAACATG
596981 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
597006 TTGTCTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:602537 original size:35 final size:35
Alignment explanation
Indices: 602491--602560 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
602481 TTTGGGGTTG
602491 TTTAAAATTGTATGAATTCATATAGGAAAACATTC
1 TTTAAAATTGTATGAATTCATATAGGAAAACATTC
602526 TTTAAAATTGTATGAATTCATATAGGAAAACATTC
1 TTTAAAATTGTATGAATTCATATAGGAAAACATTC
602561 ACGTATGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.37
Consensus pattern (35 bp):
TTTAAAATTGTATGAATTCATATAGGAAAACATTC
Found at i:604171 original size:16 final size:16
Alignment explanation
Indices: 604150--604183 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
604140 TTACTATTCA
*
604150 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
604166 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
604182 CG
1 CG
604184 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:604953 original size:15 final size:16
Alignment explanation
Indices: 604933--604964 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
604923 TGGCAGATCC
604933 AAATCCAG-ACGGGAA
1 AAATCCAGAACGGGAA
604948 AAATCCAGAACGGGAA
1 AAATCCAGAACGGGAA
604964 A
1 A
604965 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAATCCAGAACGGGAA
Found at i:608861 original size:13 final size:13
Alignment explanation
Indices: 608843--608868 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
608833 CCAAAGAGAA
608843 ATCAATGGTCTTG
1 ATCAATGGTCTTG
608856 ATCAATGGTCTTG
1 ATCAATGGTCTTG
608869 CAACTTTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (13 bp):
ATCAATGGTCTTG
Found at i:617727 original size:17 final size:18
Alignment explanation
Indices: 617700--617741 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
617690 AATTTAACTA
* *
617700 ATAATATAAAGAATAAAT
1 ATAATAAAAAGAACAAAT
*
617718 -TAATAAAAAGTACAAAT
1 ATAATAAAAAGAACAAAT
617735 ATAATAA
1 ATAATAA
617742 CTAGATTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (18 bp):
ATAATAAAAAGAACAAAT
Found at i:618579 original size:16 final size:16
Alignment explanation
Indices: 618558--618590 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
618548 TTTTTTCTGT
618558 CATTGGTTCCTTAGAA
1 CATTGGTTCCTTAGAA
618574 CATTGGTTCCTTAGAA
1 CATTGGTTCCTTAGAA
618590 C
1 C
618591 TATAAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.36
Consensus pattern (16 bp):
CATTGGTTCCTTAGAA
Found at i:626895 original size:29 final size:29
Alignment explanation
Indices: 626861--626919 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
626851 CCTAAATTAA
*
626861 TTTGATGTCATTGTTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
626890 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
626919 T
1 T
626920 AGGTGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:635130 original size:60 final size:60
Alignment explanation
Indices: 635064--635241 Score: 178
Period size: 60 Copynumber: 3.0 Consensus size: 60
635054 GCATCATATG
* * **
635064 TCCCTAAACTATAACCCTCATTTTAAATTGGTCA-TTAAACTTTTGAATGTTCTAATTTCA
1 TCCCTAAACTATAACCCTCATTCTAAATTAGT-ATTTAAACTTTTGAAAATTCTAATTTCA
* * * *
635124 TCCCTAAACTATGACTCTCATTCTAAATTAGTATTTAAACTTTTTAAAATTTTAATTTCA
1 TCCCTAAACTATAACCCTCATTCTAAATTAGTATTTAAACTTTTGAAAATTCTAATTTCA
* * * * * * * * * *
635184 TCCCTAAAATATTACACTCTTTCCAAATTAGTACTCAAACTTTTTAATATTCCAATTT
1 TCCCTAAACTATAACCCTCATTCTAAATTAGTATTTAAACTTTTGAAAATTCTAATTT
635242 TATACCCAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 1 0.01
60 98 0.99
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.43
Consensus pattern (60 bp):
TCCCTAAACTATAACCCTCATTCTAAATTAGTATTTAAACTTTTGAAAATTCTAATTTCA
Found at i:635462 original size:57 final size:57
Alignment explanation
Indices: 635374--635533 Score: 153
Period size: 60 Copynumber: 2.7 Consensus size: 57
635364 GTTTATACAT
* * * * * * *
635374 ATAGTTTGGGATAAAATTGGATTGCTGAAAAAGTTTGGGGACCCATTTAGAATG-GTC
1 ATAGTTTGGGATGAAATTGAAAT-CTTAAAAAGTTTGAGGACCAATCTAGAATGTGTC
*
635431 ATAGTTTAGGGATGAAATTGAAATCTTAAAAAGTTTGAGGACTAATCTAGAATGTTAGTC
1 ATAGTTT-GGGATGAAATTGAAATCTTAAAAAGTTTGAGGACCAATCTAGAATG-T-GTC
* * *
635491 ATAATTTTGGGATGAAATTGAAA-CATTTAAAAGTTTAAGGACC
1 AT-AGTTTGGGATGAAATTGAAATC-TTAAAAAGTTTGAGGACC
635534 TATTTAAACT
Statistics
Matches: 85, Mismatches: 12, Indels: 9
0.80 0.11 0.08
Matches are distributed among these distances:
57 32 0.38
58 13 0.15
59 1 0.01
60 35 0.41
61 4 0.05
ACGTcount: A:0.37, C:0.07, G:0.23, T:0.33
Consensus pattern (57 bp):
ATAGTTTGGGATGAAATTGAAATCTTAAAAAGTTTGAGGACCAATCTAGAATGTGTC
Found at i:639072 original size:16 final size:16
Alignment explanation
Indices: 639051--639084 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
639041 TTACTATTCA
*
639051 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
639067 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
639083 CG
1 CG
639085 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:651789 original size:15 final size:15
Alignment explanation
Indices: 651769--651802 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
651759 CAAACATTTA
651769 TAAATTATATTTTTT
1 TAAATTATATTTTTT
651784 TAAATTATATTTTTT
1 TAAATTATATTTTTT
651799 TAAA
1 TAAA
651803 GATAGTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TAAATTATATTTTTT
Found at i:651811 original size:15 final size:15
Alignment explanation
Indices: 651769--651811 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
651759 CAAACATTTA
*
651769 TAAATTATATTTTTT
1 TAAATGATATTTTTT
*
651784 TAAATTATATTTTTT
1 TAAATGATATTTTTT
*
651799 TAAA-GATAGTTTT
1 TAAATGATATTTTT
651812 ACGATCGACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 7 0.27
15 19 0.73
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (15 bp):
TAAATGATATTTTTT
Found at i:652351 original size:26 final size:25
Alignment explanation
Indices: 652303--652356 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
652293 TCACACTTCC
*
652303 TAAAATTTTATAAATTCTGCTCTACT
1 TAAAATTTTATAAATCCTGCTCT-CT
652329 TAAAATTTTATAAATCC-GTCTCTCT
1 TAAAATTTTATAAATCCTG-CTCTCT
652354 TAA
1 TAA
652357 CATAAAATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.44
Consensus pattern (25 bp):
TAAAATTTTATAAATCCTGCTCTCT
Found at i:653726 original size:19 final size:19
Alignment explanation
Indices: 653702--653743 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
653692 TAAGTTAAAG
653702 ACACTTGAAGAAGGTTGCA
1 ACACTTGAAGAAGGTTGCA
653721 ACACTTGAAGAAGGTTGCA
1 ACACTTGAAGAAGGTTGCA
653740 ACAC
1 ACAC
653744 CTATCCAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (19 bp):
ACACTTGAAGAAGGTTGCA
Found at i:659902 original size:18 final size:18
Alignment explanation
Indices: 659879--659916 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
659869 CCCTTGAGAT
659879 TGTACC-ACACAGACAGCC
1 TGTACCTACACAG-CAGCC
*
659897 TGTACCTACGCAGCAGCC
1 TGTACCTACACAGCAGCC
659915 TG
1 TG
659917 CTCATCCGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.26, C:0.37, G:0.21, T:0.16
Consensus pattern (18 bp):
TGTACCTACACAGCAGCC
Found at i:670134 original size:42 final size:42
Alignment explanation
Indices: 670088--670171 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
670078 TGTGAGTGTC
670088 AAGTAATTAGTGGAGACTGCTTAAGGGGAATAACTATGATAA
1 AAGTAATTAGTGGAGACTGCTTAAGGGGAATAACTATGATAA
670130 AAGTAATTAGTGGAGACTGCTTAAGGGGAATAACTATGATAA
1 AAGTAATTAGTGGAGACTGCTTAAGGGGAATAACTATGATAA
670172 TATTATATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.40, C:0.07, G:0.26, T:0.26
Consensus pattern (42 bp):
AAGTAATTAGTGGAGACTGCTTAAGGGGAATAACTATGATAA
Found at i:679954 original size:131 final size:131
Alignment explanation
Indices: 679720--679971 Score: 477
Period size: 131 Copynumber: 1.9 Consensus size: 131
679710 AGGTAATATC
*
679720 TGTTCAATGATAACTCTCAACCTTTTAACATTGAACGCTCCTATCTGACATTCCTAATGCTCGAA
1 TGTTCAAAGATAACTCTCAACCTTTTAACATTGAACGCTCCTATCTGACATTCCTAATGCTCGAA
*
679785 CCCGGGACCTCAAGGAATAACAACAATTACTTTACCACCGAGGTCACTAATTTTAACATTCCTAT
66 CCCGGGACCTCAAAGAATAACAACAATTACTTTACCACCGAGGTCACTAATTTTAACATTCCTAT
679850 A
131 A
*
679851 TGTTCAAAGATAACTCTTAACCTTTTAACATTGAACGCTCCTATCTGACATTCCTAATGCTCGAA
1 TGTTCAAAGATAACTCTCAACCTTTTAACATTGAACGCTCCTATCTGACATTCCTAATGCTCGAA
679916 CCCGGGACCTCAAAGAATAACAACAATTACTTTACCACCGAGGTCACTAATTTTAA
66 CCCGGGACCTCAAAGAATAACAACAATTACTTTACCACCGAGGTCACTAATTTTAA
679972 ATATTTTCAT
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
131 118 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (131 bp):
TGTTCAAAGATAACTCTCAACCTTTTAACATTGAACGCTCCTATCTGACATTCCTAATGCTCGAA
CCCGGGACCTCAAAGAATAACAACAATTACTTTACCACCGAGGTCACTAATTTTAACATTCCTAT
A
Found at i:682529 original size:14 final size:14
Alignment explanation
Indices: 682510--682539 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
682500 ATTAATTAAT
*
682510 TAATTATATATAAA
1 TAATTATAAATAAA
682524 TAATTATAAATAAA
1 TAATTATAAATAAA
682538 TA
1 TA
682540 GATAAATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTATAAATAAA
Found at i:682754 original size:20 final size:20
Alignment explanation
Indices: 682731--682798 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
682721 GTATTAAAAT
682731 TTTTAATATTTGAGTATATA
1 TTTTAATATTTGAGTATATA
* * * *
682751 TTTTAATA-TAGCATTAAAAA
1 TTTTAATATTTG-AGTATATA
* *
682771 TCTTGATATTTGAGTATATA
1 TTTTAATATTTGAGTATATA
682791 TTTTAATA
1 TTTTAATA
682799 AAATATTAAT
Statistics
Matches: 34, Mismatches: 12, Indels: 4
0.68 0.24 0.08
Matches are distributed among these distances:
19 2 0.06
20 30 0.88
21 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (20 bp):
TTTTAATATTTGAGTATATA
Found at i:682807 original size:40 final size:40
Alignment explanation
Indices: 682693--682807 Score: 140
Period size: 40 Copynumber: 2.9 Consensus size: 40
682683 ATGATATACA
* * * * * *
682693 TTGATATTTGAGAACAGATTTTGATATAGTATTAAAATTT
1 TTGATATTTGAGTATATATTTTAATATAGTATTAAAAATC
* *
682733 TTAATATTTGAGTATATATTTTAATATAGCATTAAAAATC
1 TTGATATTTGAGTATATATTTTAATATAGTATTAAAAATC
* *
682773 TTGATATTTGAGTATATATTTTAATAAAATATTAA
1 TTGATATTTGAGTATATATTTTAATATAGTATTAA
682808 TTTTGAACCA
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (40 bp):
TTGATATTTGAGTATATATTTTAATATAGTATTAAAAATC
Found at i:683792 original size:27 final size:27
Alignment explanation
Indices: 683753--683815 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 27
683743 TAGAAAAGCT
*
683753 TCTCTTAATTTATTATGAGAAAAAATAA
1 TCTC-TAACTTATTATGAGAAAAAATAA
683781 TCTCTAAC---TTATGAGAAAAAATAA
1 TCTCTAACTTATTATGAGAAAAAATAA
*
683805 TCTTTAACTTA
1 TCTCTAACTTA
683816 GAAAAACACT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
24 23 0.77
27 3 0.10
28 4 0.13
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.38
Consensus pattern (27 bp):
TCTCTAACTTATTATGAGAAAAAATAA
Found at i:683821 original size:21 final size:24
Alignment explanation
Indices: 683765--683815 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
683755 TCTTAATTTA
683765 TTATGAGAAAAAATAATCTCTAAC
1 TTATGAGAAAAAATAATCTCTAAC
*
683789 TTATGAGAAAAAATAATCTTTAAC
1 TTATGAGAAAAAATAATCTCTAAC
683813 TTA
1 TTA
683816 GAAAAACACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (24 bp):
TTATGAGAAAAAATAATCTCTAAC
Found at i:686264 original size:60 final size:60
Alignment explanation
Indices: 686190--686317 Score: 152
Period size: 61 Copynumber: 2.1 Consensus size: 60
686180 AATATATCAC
* * *
686190 TTTCATCCATAAACTAT-AACTATCATTCTAAATTAGT-CCTAAAACTTTAGAATATTTTAA
1 TTTCAT-CATAAACTATGAACT-TCATTCTAAATTAGTCCCCAAAACTTTAGAACATTTCAA
* * * *
686250 TTTCATCATCAAACTATGACCTTCATTCTAAATTGGTCCCCAAAATTTTTGAACATTTCAA
1 TTTCATCAT-AAACTATGAACTTCATTCTAAATTAGTCCCCAAAACTTTAGAACATTTCAA
686311 TTTCATC
1 TTTCATC
686318 TCAGATTATA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
59 3 0.05
60 27 0.47
61 28 0.48
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (60 bp):
TTTCATCATAAACTATGAACTTCATTCTAAATTAGTCCCCAAAACTTTAGAACATTTCAA
Found at i:696643 original size:19 final size:20
Alignment explanation
Indices: 696610--696648 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
696600 ACACATTTGA
696610 ATATAATTTATAATTTTTTT
1 ATATAATTTATAATTTTTTT
*
696630 ATATATTTTA-AATTTTTTT
1 ATATAATTTATAATTTTTTT
696649 CAAGGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATATAATTTATAATTTTTTT
Found at i:696910 original size:74 final size:73
Alignment explanation
Indices: 696742--697134 Score: 382
Period size: 74 Copynumber: 5.4 Consensus size: 73
696732 TATTTATTAT
* * * * *
696742 ATTAAAAATATATAAAAATGTTGTAAATAATAGTTAATAAATAAAAACTAAGAATTATTTCTTTC
1 ATTAAAAATATATAAAAATATTATAAATTATAGTTAATAAATAAAAATTAAGAATT-TTTCTTCC
*
696807 TTTAACAAAA
65 ATTAAC-AAA
696817 ATTAAAAATATATAAAAATATTATAAATTATAGTTAATAAAT-AAAATTAAGAATTGTTTCTTCC
1 ATTAAAAATATATAAAAATATTATAAATTATAGTTAATAAATAAAAATTAAGAATT-TTTCTTCC
*
696881 ATTAATGAAA
65 ATTAA-CAAA
* * * * ** *
696891 ACTAAAAATGTATAAAAATA-TATAAATTATAGTTAGTAAATAAAAAATAATTATTCTTTATTCC
1 ATTAAAAATATATAAAAATATTATAAATTATAGTTAATAAATAAAAATTAAGAATT-TTTCTTCC
696955 ATTAA-AAA
65 ATTAACAAA
* * * * *
696963 TTTAAAAA-ATATATAAATATTATAAAATATAGTTAATAAATACAAATT----A--TTTCTTCTA
1 ATTAAAAATATATAAAAATATTATAAATTATAGTTAATAAATAAAAATTAAGAATTTTTCTTCCA
697021 TTAACAAA
66 TTAACAAA
* * * *
697029 ATTTTAAAATATATAAAAAAAGTTGTAAATTA-ATTTTAATAAATAAAAATTAAGAA-TTTT-TT
1 A-TTAAAAATATATAAAAATA-TTATAAATTATA-GTTAATAAATAAAAATTAAGAATTTTTCTT
697091 CTCATTAACAAAA
63 C-CATTAAC-AAA
*
697104 ATAAAAAATATATAAAAA-ATTATAAATTATA
1 ATTAAAAATATATAAAAATATTATAAATTATA
697135 TTTATATAGG
Statistics
Matches: 264, Mismatches: 38, Indels: 34
0.79 0.11 0.10
Matches are distributed among these distances:
65 11 0.04
66 3 0.01
67 6 0.02
68 11 0.04
69 23 0.09
71 9 0.03
72 42 0.16
73 26 0.10
74 90 0.34
75 43 0.16
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (73 bp):
ATTAAAAATATATAAAAATATTATAAATTATAGTTAATAAATAAAAATTAAGAATTTTTCTTCCA
TTAACAAA
Found at i:696994 original size:145 final size:150
Alignment explanation
Indices: 696744--697134 Score: 386
Period size: 141 Copynumber: 2.7 Consensus size: 150
696734 TTTATTATAT
* * * * * *
696744 TAAAAATATATAAAAATGTTGTAAATAATAGTTAATAAATAAAAACTAAGAATTATTTCTTTCTT
1 TAAAAATATATAAAAATGATATAAATAATAGTTAATAAATAAAAAATAAGAATTATTTATTCCAT
*
696809 TAACAAAAATTAAAAATATATAAAAATATTATAAATTATAGTTAATAAATA-AAATTAAGAATTG
66 TAACAAAAATTAAAAATATATAAAAATATTATAAAATATAGTTAATAAATACAAATTAAGAATTG
696873 TTTCTTCCATTAATGAAAAC
131 TTTCTTCCATTAATGAAAAC
* * * ** *
696893 TAAAAATGTATAAAAAT-ATATAAATTATAGTTAGTAAATAAAAAATAATTATTCTTTATTCCAT
1 TAAAAATATATAAAAATGATATAAATAATAGTTAATAAATAAAAAATAAGAATTATTTATTCCAT
* *
696957 T-A-AAAATTTAAAAA-ATATATAAATATTATAAAATATAGTTAATAAATACAAATT----A---
66 TAACAAAAATTAAAAATATATAAAAATATTATAAAATATAGTTAATAAATACAAATTAAGAATTG
* * *
697012 TTTCTTCTATTAA-CAAAATT
131 TTTCTTCCATTAATGAAAA-C
* * * * * *
697032 TTAAAATATATAAAAAAAGTTGTAAATTAAT-TTTAATAAATAAAAATTAAGAA-T-TTT-TTCT
1 TAAAAATATAT-AAAAATGATATAAA-TAATAGTTAATAAATAAAAAATAAGAATTATTTATTC-
* *
697093 CATTAACAAAAATAAAAAATATATAAAAA-ATTATAAATTATA
63 CATTAACAAAAATTAAAAATATATAAAAATATTATAAAATATA
697135 TTTATATAGG
Statistics
Matches: 200, Mismatches: 33, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
138 7 0.04
139 28 0.14
140 7 0.04
141 44 0.22
142 12 0.06
145 32 0.16
146 16 0.08
147 1 0.00
148 37 0.19
149 16 0.08
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (150 bp):
TAAAAATATATAAAAATGATATAAATAATAGTTAATAAATAAAAAATAAGAATTATTTATTCCAT
TAACAAAAATTAAAAATATATAAAAATATTATAAAATATAGTTAATAAATACAAATTAAGAATTG
TTTCTTCCATTAATGAAAAC
Found at i:700097 original size:14 final size:14
Alignment explanation
Indices: 700073--700110 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
700063 TTTGAGAGTA
700073 AATATATATATTATT
1 AATA-ATATATTATT
700088 AATAATATATTATT
1 AATAATATATTATT
700102 AATAATATA
1 AATAATATA
700111 AATTTTTGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATATATTATT
Found at i:700233 original size:2 final size:2
Alignment explanation
Indices: 700226--700251 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
700216 TTCATCGTAA
700226 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
700252 CTCTGTGCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:701506 original size:23 final size:23
Alignment explanation
Indices: 701463--701508 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
701453 AATAAAGATT
*
701463 TATGATTTTATTTACTTTTATAA
1 TATGATTTTATCTACTTTTATAA
*
701486 TATGTTTTTATCTA-TTCTTATAA
1 TATGATTTTATCTACTT-TTATAA
701509 CACGTCTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.28, C:0.07, G:0.04, T:0.61
Consensus pattern (23 bp):
TATGATTTTATCTACTTTTATAA
Found at i:710200 original size:16 final size:17
Alignment explanation
Indices: 710175--710208 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
710165 ATAAAATAAT
*
710175 ATTTTTAAAAAC-AAAA
1 ATTTTGAAAAACTAAAA
710191 ATTTTGAAAAACTAAAA
1 ATTTTGAAAAACTAAAA
710208 A
1 A
710209 AAACTAAAAA
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:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
ATTTTGAAAAACTAAAA
Found at i:718426 original size:18 final size:18
Alignment explanation
Indices: 718405--718449 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
718395 TACTAATAAA
718405 AAAATATTTAAAAATTTT
1 AAAATATTTAAAAATTTT
*
718423 AAAATATAT-AAAATTTT
1 AAAATATTTAAAAATTTT
*
718440 ATAAT-TTTAA
1 AAAATATTTAA
718450 GAGGAGACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 2 0.09
17 13 0.57
18 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AAAATATTTAAAAATTTT
Found at i:719033 original size:21 final size:21
Alignment explanation
Indices: 718996--719035 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
718986 TTAAAATAAT
*
718996 TTTATAAATTTTAATTAAATA
1 TTTATAAATTTAAATTAAATA
719017 TTTAT-AATTTAATATTAAA
1 TTTATAAATTTAA-ATTAAA
719036 GTTTAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTTATAAATTTAAATTAAATA
Found at i:723796 original size:28 final size:28
Alignment explanation
Indices: 723764--723822 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
723754 GCATCGCCGT
* * *
723764 TATTTCGAGCACTGACTCTATGACATAA
1 TATTTCAAGCACTAACTCGATGACATAA
*
723792 TATTTCAAGCACTAACTCGATGATATAA
1 TATTTCAAGCACTAACTCGATGACATAA
723820 TAT
1 TAT
723823 AAACATATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (28 bp):
TATTTCAAGCACTAACTCGATGACATAA
Found at i:727960 original size:16 final size:16
Alignment explanation
Indices: 727941--727974 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
727931 ATTGCCTTTC
727941 CCTGGCTCTGCCTCCT
1 CCTGGCTCTGCCTCCT
727957 CCTGGCTCTGCCTCCT
1 CCTGGCTCTGCCTCCT
727973 CC
1 CC
727975 ATTTTCTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.53, G:0.18, T:0.29
Consensus pattern (16 bp):
CCTGGCTCTGCCTCCT
Found at i:728647 original size:18 final size:17
Alignment explanation
Indices: 728600--728663 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
728590 ACCCGATCCG
*
728600 AAATAATATTTATAAAA
1 AAATAATATTTATTAAA
*
728617 TAAATATTAATTTATTAAA
1 -AAATAAT-ATTTATTAAA
728636 AAATAGATATTTATTTGAAA
1 AAATA-ATATTTA-TT-AAA
728656 AAATAATA
1 AAATAATA
728664 AATAAAGAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
18 16 0.41
19 15 0.38
20 8 0.21
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAATAATATTTATTAAA
Found at i:732245 original size:17 final size:17
Alignment explanation
Indices: 732223--732260 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
732213 GAAATTGCCT
732223 TTTTAATTATTTTAA-AA
1 TTTTAATT-TTTTAATAA
732240 TTTTAATTTTTTAATAA
1 TTTTAATTTTTTAATAA
732257 TTTT
1 TTTT
732261 TTTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTAATTTTTTAATAA
Found at i:732602 original size:21 final size:20
Alignment explanation
Indices: 732576--732616 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
732566 TTTTAAGTAA
*
732576 TAAAATATAGAAATATATAAT
1 TAAAATAAAGAAATAT-TAAT
*
732597 TAAAATAAAGCAATATTAAT
1 TAAAATAAAGAAATATTAAT
732617 ATTAATGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (20 bp):
TAAAATAAAGAAATATTAAT
Found at i:745562 original size:26 final size:28
Alignment explanation
Indices: 745514--745580 Score: 86
Period size: 26 Copynumber: 2.4 Consensus size: 28
745504 ATTTTAAAAC
745514 TAAAATATGTAAA-TAATATAATTAAATTA
1 TAAAA-AT-TAAATTAATATAATTAAATTA
*
745543 TAAAAA-TAAATTAATA-AATTGAATTA
1 TAAAAATTAAATTAATATAATTAAATTA
745569 TAAAAATTAAAT
1 TAAAAATTAAAT
745581 ATATAACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 19 0.54
27 10 0.29
28 1 0.03
29 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (28 bp):
TAAAAATTAAATTAATATAATTAAATTA
Found at i:745575 original size:14 final size:14
Alignment explanation
Indices: 745533--745586 Score: 67
Period size: 13 Copynumber: 3.9 Consensus size: 14
745523 TAAATAATAT
745533 AATTAAATTATAAA
1 AATTAAATTATAAA
*
745547 AA-TAAATTA-ATA
1 AATTAAATTATAAA
*
745559 AATTGAATTATAAA
1 AATTAAATTATAAA
745573 AATTAAATATATAA
1 AATTAAAT-TATAA
745587 CTTAGGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 4 0.12
13 13 0.39
14 11 0.33
15 5 0.15
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AATTAAATTATAAA
Found at i:747390 original size:14 final size:15
Alignment explanation
Indices: 747295--747428 Score: 94
Period size: 14 Copynumber: 8.5 Consensus size: 15
747285 TAATAAGGTT
747295 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
747310 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
747325 A-TTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
747339 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
747358 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
747376 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
* * *
747390 ATTTATTAGTATGAATTG
1 ATTTATT--T-TAAAATA
747408 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
747422 ATTTATT
1 ATTTATT
747429 AGTATTGATT
Statistics
Matches: 96, Mismatches: 11, Indels: 25
0.73 0.08 0.19
Matches are distributed among these distances:
14 34 0.35
15 29 0.30
16 6 0.06
17 3 0.03
18 11 0.11
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:747413 original size:18 final size:18
Alignment explanation
Indices: 747390--747446 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
747380 ATTTTAAATA
747390 ATTTATTAGTATGAATTG
1 ATTTATTAGTATGAATTG
* *
747408 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGAATTG
747422 ATTTATTAGTATTG-ATTG
1 ATTTATTAGTA-TGAATTG
747440 ATTTATT
1 ATTTATT
747447 TTAAAATATG
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
14 10 0.33
15 1 0.03
16 2 0.07
18 17 0.57
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (18 bp):
ATTTATTAGTATGAATTG
Found at i:747415 original size:32 final size:32
Alignment explanation
Indices: 747376--747767 Score: 160
Period size: 32 Copynumber: 12.4 Consensus size: 32
747366 TTTTAAAATA
747376 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
747408 ATTTATTTTAAATAATTTATTAGTATTG-ATTG
1 ATTTATTTTAAATAATTTATTAGTA-TGAATTG
** **
747440 ATTTATTTTAAA-ATATGGATT-G-ATTTATT-
1 ATTTATTTTAAATA-ATTTATTAGTATGAATTG
* * * * *
747469 ATTGTAGTTGTGTGGATTGATTTATT--T-T-AAATA
1 ATT-TA-TT-T-T-AAATAATTTATTAGTATGAATTG
* * * *
747502 ATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATT--T-TA-AATAATTTA--TT--AGTATGAATTG
747542 ATTTATTTTAAATAATTTATTAGTATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
747574 ATTTA-TTT---TAA---A--A-TATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
*
747596 ATTTATTTTAAAA----TA-T-G---G-ATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
747618 ATTTATTTTAAATAATTTATTAGTAT-AGATTG
1 ATTTATTTTAAATAATTTATTAGTATGA-ATTG
* * *
747650 ATTTATTTAAAATATGGATTGATTATTTTAAAATATGGATTG
1 ATTTATTTTAAATA---A-T--TTA--TT--AGTATGAATTG
*
747692 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
* *
747724 ATTTATTTTAAATAATTTATTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTG
747756 ATTTATTTTAAA
1 ATTTATTTTAAA
747768 ATATAGATTG
Statistics
Matches: 283, Mismatches: 27, Indels: 100
0.69 0.07 0.24
Matches are distributed among these distances:
22 30 0.11
23 5 0.02
25 2 0.01
26 2 0.01
27 1 0.00
28 4 0.01
29 4 0.01
30 6 0.02
31 9 0.03
32 147 0.52
33 7 0.02
34 12 0.04
35 1 0.00
36 11 0.04
37 2 0.01
38 6 0.02
39 2 0.01
40 11 0.04
42 21 0.07
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTG
Found at i:747503 original size:80 final size:83
Alignment explanation
Indices: 747376--748197 Score: 909
Period size: 80 Copynumber: 10.2 Consensus size: 83
747366 TTTTAAAATA
* *
747376 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATTTATTAGTATTGATTGA
1 ATTTA-TTT-AAT-ATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
747441 TTTATTTTAAAATATGGATTG
63 TTTATTTTAAAATATGGATTG
* * *
747462 ATTTA-TT-AT-TGTAGTT-GTGTGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATT
1 ATTTATTTAATATTTA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
747523 TATTTTAAAATATGGATTG
65 TATTTTAAAATATGGATTG
*
747542 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT-AA-AA--TA-T-G-A---ATTGA
1 ATTTA-TTT-AAT-ATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
747597 TTTATTTTAAAATATGGATTG
63 TTTATTTTAAAATATGGATTG
*
747618 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTA--TT---TAA---A--A-TATGGATTGA
1 ATTTA-TTT-AAT-ATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
747672 -TTATTTTAAAATATGGATTG
63 TTTATTTTAAAATATGGATTG
*
747692 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGA
1 ATTTA-TTT-AAT-ATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
*
747757 TTTATTTTAAAATATAGATTG
63 TTTATTTTAAAATATGGATTG
* *
747778 ATTTA-TT-AT-TGTAGTT-GTATGGATTGA-TTATTTTAAATAA-TTATTAATATGGATTGATT
1 ATTTATTTAATATTTA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
747837 TATTTTAAAATATGGATTG
65 TATTTTAAAATATGGATTG
747856 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G-A---A-TGA
1 ATTTA-TTT-AAT-ATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
747910 TTTATTTTAAAATATGGATTG
63 TTTATTTTAAAATATGGATTG
* * *
747931 ATTTATTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAGTTTATTTGTATGGATTGAT
1 ATTTATTT-AAT-ATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
747996 TTATTTTAAAATATGGATTG
64 TTATTTTAAAATATGGATTG
* *
748016 ATTTA-TT-AT-TGTAGTT-GTATGAATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
1 ATTTATTTAATATTTA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
748077 TATTTTAAAATATGGATTG
65 TATTTTAAAATATGGATTG
* *
748096 ATTTA-TT-AT-TGTAGTT-GTATCGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
1 ATTTATTTAATATTTA-TTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATT
748157 TATTTTAAAATATGGATTG
65 TATTTTAAAATATGGATTG
748176 ATTTATTTTAAATAATTTATTA
1 ATTTA-TTT-AAT-ATTTATTA
748198 TTGTAGTTAT
Statistics
Matches: 654, Mismatches: 28, Indels: 108
0.83 0.04 0.14
Matches are distributed among these distances:
72 2 0.00
73 2 0.00
74 92 0.14
75 36 0.06
76 65 0.10
78 42 0.06
79 19 0.03
80 233 0.36
81 9 0.01
82 17 0.03
83 4 0.01
84 29 0.04
85 52 0.08
86 52 0.08
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (83 bp):
ATTTATTTAATATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTT
ATTTTAAAATATGGATTG
Found at i:747590 original size:22 final size:22
Alignment explanation
Indices: 747565--747703 Score: 145
Period size: 22 Copynumber: 6.0 Consensus size: 22
747555 AATTTATTAG
*
747565 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
747587 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
747609 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
747633 TTTATTAGTATAGATTGATTTATTTAAAA
1 --TA-T-GGATTGATTTA-TT--TTAAAA
747662 TATGGATTGA-TTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
747683 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
747704 TAATTTATTA
Statistics
Matches: 100, Mismatches: 7, Indels: 20
0.79 0.06 0.16
Matches are distributed among these distances:
21 16 0.16
22 49 0.49
23 4 0.04
24 4 0.04
25 5 0.05
26 3 0.03
27 3 0.03
28 8 0.08
29 4 0.04
30 2 0.02
31 2 0.02
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:747671 original size:21 final size:21
Alignment explanation
Indices: 747645--747705 Score: 97
Period size: 21 Copynumber: 2.9 Consensus size: 21
747635 TATTAGTATA
747645 GATTGATTTATTTAAAATATG
1 GATTGATTTATTTAAAATATG
747666 GATTGA-TTATTTTAAAATATG
1 GATTGATTTA-TTTAAAATATG
*
747687 GATTGATTTATTTTAAATA
1 GATTGATTTATTTAAAATA
747706 ATTTATTAGT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
20 3 0.08
21 31 0.84
22 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (21 bp):
GATTGATTTATTTAAAATATG
Found at i:747759 original size:18 final size:18
Alignment explanation
Indices: 747706--747763 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
747696 ATTTTAAATA
*
747706 ATTTATTAGTATGGATTG
1 ATTTATTTGTATGGATTG
* *
747724 ATTTATTT-TA---AATA
1 ATTTATTTGTATGGATTG
747738 ATTTATTTGTATGGATTG
1 ATTTATTTGTATGGATTG
747756 ATTTATTT
1 ATTTATTT
747764 TAAAATATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 10 0.32
15 2 0.06
17 2 0.06
18 17 0.55
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (18 bp):
ATTTATTTGTATGGATTG
Found at i:747848 original size:22 final size:22
Alignment explanation
Indices: 747823--747938 Score: 99
Period size: 22 Copynumber: 4.9 Consensus size: 22
747813 AATAATTATT
747823 AATATGGATTGATTTATTTTAA
1 AATATGGATTGATTTATTTTAA
747845 AATATGGATTGATTTATTTTAAA
1 AATATGGATTGATTTATTTT-AA
* * *
747868 TAATTTATTAGTATGGATTGATTTATTTTAA
1 -AA--TA-T-GGATTGATTTA-TT---TTAA
*
747899 AATAT-GAATGATTTATTTTAA
1 AATATGGATTGATTTATTTTAA
747920 AATATGGATTGATTTATTT
1 AATATGGATTGATTTATTT
747939 AAATAATTTA
Statistics
Matches: 75, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
21 9 0.12
22 32 0.43
23 2 0.03
24 4 0.05
25 6 0.08
26 2 0.03
27 2 0.03
28 10 0.13
29 2 0.03
30 2 0.03
31 2 0.03
32 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (22 bp):
AATATGGATTGATTTATTTTAA
Found at i:747864 original size:132 final size:128
Alignment explanation
Indices: 747399--747973 Score: 457
Period size: 128 Copynumber: 4.4 Consensus size: 128
747389 AATTTATTAG
* * *
747399 TATGAATTGATTTATTTTAAATAATTTATTAGTATTGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTA-TTTAAATAATTTATTAATATAGATTGATTTATTTTAAAATATGGATTGAT
* *
747464 TTA--TT--AT--TGTAGTT-GTGTGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGAT
65 TTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTT-AA-AA--TA-T-G---A-A-TGAT
747522 TTATTTTAAAA
118 TTATTTTAAAA
* *
747533 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-GAATTGATTTATTTTAAAATATGAATTGA
1 TATGGATTGATTTA-TTTAAATAATTTATTAATATAG-ATTGATTTATTTTAAAATATGGATTGA
* * ** * * ** *
747597 TTTATTTTAAAATATGGATTGATTTA-TTTTAAATAATTTA--TTAGTATA-GATTGATTTA-TT
64 TTTATTTT-AAATA---ATTTA-TTAGTATGGATTGATTTATTTTAAAATATGAATGATTTATTT
747657 TAAAA
124 TAAAA
** * * * * ** * * *
747662 TATGGATTGA-TTATTTTAAA-ATATGGATTGATTTA-TTTTAAATAATTTATTAGTATGGATTG
1 TATGGATTGATTTA-TTTAAATA-ATTTATTAATATAGATTGATTTATTTTA-AAATATGGATTG
* *
747724 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTG
63 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-GAATGATTTA-T-TT-
***
747789 TAGTTG
124 TA-AAA
*
747795 TATGGATTGA-TTATTTTAAATAA-TTATTAATATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTA-TTTAAATAATTTATTAATATAGATTGATTTATTTTAAAATATGGATTGAT
747858 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATGATTTATTTTAAAA
65 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATGATTTATTTTAAAA
*
747922 TATGGATTGATTTATTTAAATAATTTATTAGTATAGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTAAATAATTTATTAATATAGATTGATTTATTTTAAA
747974 TAGTTTATTT
Statistics
Matches: 355, Mismatches: 57, Indels: 64
0.75 0.12 0.13
Matches are distributed among these distances:
123 2 0.01
124 13 0.04
126 6 0.02
127 34 0.10
128 76 0.21
129 19 0.05
130 8 0.02
131 11 0.03
132 66 0.19
133 31 0.09
134 65 0.18
135 1 0.00
136 2 0.01
138 2 0.01
139 2 0.01
140 1 0.00
141 1 0.00
142 2 0.01
144 13 0.04
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.52
Consensus pattern (128 bp):
TATGGATTGATTTATTTAAATAATTTATTAATATAGATTGATTTATTTTAAAATATGGATTGATT
TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATGATTTATTTTAAAA
Found at i:747885 original size:32 final size:32
Alignment explanation
Indices: 747847--748005 Score: 138
Period size: 32 Copynumber: 4.7 Consensus size: 32
747837 TATTTTAAAA
747847 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
* * *
747879 TATGGATTGATTTATTTTAAAATATGAATGATTTAT
1 TATGGATTGATTTATTTT-AAATA--ATTTA-TTAG
* ** *
747915 TTTAAAATATGGATTGATTTATTTAAATAATTTATTAG
1 TAT-GGAT-T-GATT--TAT-TTTAAATAATTTATTAG
* * *
747953 TATAGATTGATTTATTTTAAATAGTTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
747985 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
748006 ATATGGATTG
Statistics
Matches: 101, Mismatches: 16, Indels: 20
0.74 0.12 0.15
Matches are distributed among these distances:
32 53 0.52
33 7 0.07
35 7 0.07
36 6 0.06
37 5 0.05
38 6 0.06
39 7 0.07
41 7 0.07
42 3 0.03
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:747941 original size:21 final size:22
Alignment explanation
Indices: 747879--747938 Score: 104
Period size: 21 Copynumber: 2.8 Consensus size: 22
747869 AATTTATTAG
747879 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
747901 TAT-GAATGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
747922 TATGGATTGATTTATTT
1 TATGGATTGATTTATTT
747939 AAATAATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 20 0.57
22 15 0.43
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:747998 original size:18 final size:17
Alignment explanation
Indices: 747944--748001 Score: 50
Period size: 18 Copynumber: 3.5 Consensus size: 17
747934 TATTTAAATA
*
747944 ATTTATTAGTATAGATTG
1 ATTTATTTGTAT-GATTG
* *
747962 ATTTATTT-TA-AATAG
1 ATTTATTTGTATGATTG
747977 -TTTATTTGTATGGATTG
1 ATTTATTTGTAT-GATTG
747994 ATTTATTT
1 ATTTATTT
748002 TAAAATATGG
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
14 7 0.23
15 5 0.16
17 5 0.16
18 14 0.45
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (17 bp):
ATTTATTTGTATGATTG
Found at i:748077 original size:18 final size:18
Alignment explanation
Indices: 748056--748103 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
748046 ATTTTAAATA
*
748056 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
748074 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
748096 ATTTATTA
1 ATTTATTA
748104 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:748170 original size:22 final size:22
Alignment explanation
Indices: 748145--748187 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
748135 AATTTATTAG
748145 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
748167 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
748188 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:748247 original size:31 final size:31
Alignment explanation
Indices: 748212--748270 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
748202 AGTTATATGG
* *
748212 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
748243 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
748271 CTTTTTAAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:748327 original size:20 final size:16
Alignment explanation
Indices: 748289--748330 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
748279 GTTTAAAAAA
748289 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
748305 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
*
748321 T-AGTTCATTT
1 TCAGTTTATTT
748331 TAGCAGTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (16 bp):
TCAGTTTATTTATATT
Found at i:748807 original size:26 final size:26
Alignment explanation
Indices: 748755--748831 Score: 100
Period size: 26 Copynumber: 2.8 Consensus size: 26
748745 TAATAAGGTT
748755 ATTTATTTTAAAATAATTTATTTTAAAATA
1 ATTTATTTTAAAATAA-TTA---TAAAATA
748785 ATTTATTTTAAAATAATTATAAAATA
1 ATTTATTTTAAAATAATTATAAAATA
*
748811 ATTTACTTTAAAATAAATTAT
1 ATTTATTTTAAAAT-AATTAT
748832 TATAAAATAT
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
26 20 0.44
27 6 0.13
29 3 0.07
30 16 0.36
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTATTTTAAAATAATTATAAAATA
Found at i:748813 original size:41 final size:41
Alignment explanation
Indices: 748763--748879 Score: 138
Period size: 41 Copynumber: 3.0 Consensus size: 41
748753 TTATTTATTT
748763 TAAAATAATTTATTTTAAAATAATTTATTTTAAAATAATTA
1 TAAAATAATTTATTTTAAAATAATTTATTTTAAAATAATTA
* * * *
748804 TAAAATAATTTACTTTAAAATAAATTATTATAAAAT-ATGGA
1 TAAAATAATTTATTTTAAAATAATTTATTTTAAAATAAT-TA
*
748845 T----TGATTTATTTTAAAATAATTTATTTT-AAATAATT
1 TAAAATAATTTATTTTAAAATAATTTATTTTAAAATAATT
748880 TATTAGTATG
Statistics
Matches: 65, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
36 4 0.06
37 24 0.37
40 2 0.03
41 35 0.54
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.48
Consensus pattern (41 bp):
TAAAATAATTTATTTTAAAATAATTTATTTTAAAATAATTA
Found at i:748877 original size:14 final size:15
Alignment explanation
Indices: 748755--748883 Score: 133
Period size: 15 Copynumber: 8.5 Consensus size: 15
748745 TAATAAGGTT
748755 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
748770 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
748785 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
748800 A-TTA---TAAAATA
1 ATTTATTTTAAAATA
*
748811 ATTTACTTTAAAATA
1 ATTTATTTTAAAATA
* *
748826 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
748845 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
748863 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
748877 ATTTATT
1 ATTTATT
748884 AGTATGAATT
Statistics
Matches: 98, Mismatches: 5, Indels: 23
0.78 0.04 0.18
Matches are distributed among these distances:
11 8 0.08
12 3 0.03
14 15 0.15
15 52 0.53
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:748969 original size:31 final size:32
Alignment explanation
Indices: 748934--749017 Score: 143
Period size: 32 Copynumber: 2.7 Consensus size: 32
748924 TATTTTAAAA
748934 TATGGATTGATTTATTTTAAATAA-TTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
748965 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
748997 TATAGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
749018 ATATGGATTG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
31 24 0.48
32 26 0.52
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.54
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:749009 original size:18 final size:18
Alignment explanation
Indices: 748958--749013 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
748948 TTTTAAATAA
* *
748958 TTATTAGTATGGATTGAT
1 TTATTTGTATAGATTGAT
*
748976 TTATTT-TA-A-A-TAAT
1 TTATTTGTATAGATTGAT
748990 TTATTTGTATAGATTGAT
1 TTATTTGTATAGATTGAT
749008 TTATTT
1 TTATTT
749014 TAAAATATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
14 9 0.30
15 3 0.10
16 1 0.03
17 3 0.10
18 14 0.47
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (18 bp):
TTATTTGTATAGATTGAT
Found at i:749089 original size:30 final size:32
Alignment explanation
Indices: 749051--749126 Score: 120
Period size: 31 Copynumber: 2.4 Consensus size: 32
749041 GTTGTATAGA
749051 TGATTTATTTTAAATAA-TTATTAATATGGAT
1 TGATTTATTTTAAATAATTTATTAATATGGAT
* *
749082 TGA-TTATTTTAAATAATTTGTTAGTATGGAT
1 TGATTTATTTTAAATAATTTATTAATATGGAT
749113 TGATTTATTTTAAA
1 TGATTTATTTTAAA
749127 ATATGAATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
30 13 0.32
31 18 0.44
32 10 0.24
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.53
Consensus pattern (32 bp):
TGATTTATTTTAAATAATTTATTAATATGGAT
Found at i:749126 original size:32 final size:32
Alignment explanation
Indices: 749051--749234 Score: 169
Period size: 32 Copynumber: 6.4 Consensus size: 32
749041 GTTGTATAGA
*
749051 TGATTTATTTTAAATAA-TTATTAATATGGAT
1 TGATTTATTTTAAATAATTTATTAGTATGGAT
*
749082 TGA-TTATTTTAAATAATTTGTTAGTATGGAT
1 TGATTTATTTTAAATAATTTATTAGTATGGAT
749113 TGATTTATTTT-AA-AA--TA-T-G-A---AT
1 TGATTTATTTTAAATAATTTATTAGTATGGAT
*
749135 TGATTTATTTTAAAA----------TATGGAT
1 TGATTTATTTTAAATAATTTATTAGTATGGAT
*
749157 TGATTTATTTTAAATAATTTATTAGTATAGAT
1 TGATTTATTTTAAATAATTTATTAGTATGGAT
*
749189 TGATTTATTTTAAATAATTTATTTGTATGGAT
1 TGATTTATTTTAAATAATTTATTAGTATGGAT
749221 TGATTTATTTTAAA
1 TGATTTATTTTAAA
749235 ATATGGATTG
Statistics
Matches: 128, Mismatches: 7, Indels: 35
0.75 0.04 0.21
Matches are distributed among these distances:
19 1 0.01
22 29 0.23
23 2 0.02
25 1 0.01
26 1 0.01
27 1 0.01
28 1 0.01
30 15 0.12
31 20 0.16
32 57 0.45
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (32 bp):
TGATTTATTTTAAATAATTTATTAGTATGGAT
Found at i:749131 original size:22 final size:22
Alignment explanation
Indices: 749106--749170 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
749096 AATTTGTTAG
749106 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
749128 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
749150 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
749171 TAATTTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:749178 original size:14 final size:14
Alignment explanation
Indices: 749159--749212 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
749149 ATATGGATTG
749159 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
749173 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
749191 ATTTATTTTAAATA
1 ATTTATTTTAAATA
749205 ATTTATTT
1 ATTTATTT
749213 GTATGGATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:749243 original size:217 final size:221
Alignment explanation
Indices: 748863--749419 Score: 759
Period size: 217 Copynumber: 2.4 Consensus size: 221
748853 TTTTAAAATA
*
748863 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTAAATAATTATTAGTATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTAAATAATTATTAGAATTGATTTATT
*
748928 TTAAAATATGGATTGATTTATTTTAAATAATTATTAGTATGGATTGATTTATTTTAAATAATTTA
66 TTAAAATATGGATTGATTTATTTTAAATAATTATTAGTATAGATTGATTTATTTTAAATAATTTA
748993 TTTGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGA-TGATTT
131 TTTGTATAGATTGATTTATTTTAAAATATGGATTGA-TTATTATTGTAGTTGTATAGATTGATTT
749057 ATTTTAAATAA-TTATTAATATGGATTG
195 A-TTTAAATAATTTATTAATATGGATTG
* * *
749084 A-TTATTTTAAATAATTTGTTAGTATGGATTGATTTATTTTAA-AA-TA-T-GAATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTAAATAATTATTAGAATTGATTTATT
749144 TTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTT
66 TTAAAATATGGATTGATTTATTTTAAATAA-TTATTAGTATAGATTGATTTATTTTAAATAATTT
* *
749209 ATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTATTATTGTAGTTGTATGGATTGATTT
130 ATTTGTATAGATTGATTTATTTTAAAATATGGATTGATTATTATTGTAGTTGTATAGATTGATTT
* *
749274 ATTTAAATAATTTATTAGTATGTATTG
195 ATTTAAATAATTTATTAATATGGATTG
749301 ATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATT
1 ATTTATTTT--AA-AT--A---ATTTATTA--GTA--TG-A---ATTGATTTA-TTTAAATAA-T
749366 TATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATT
48 TATTAG-A---ATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATT
749420 TATATTGTAG
Statistics
Matches: 294, Mismatches: 12, Indels: 38
0.85 0.03 0.11
Matches are distributed among these distances:
216 71 0.24
217 92 0.31
218 9 0.03
219 2 0.01
220 40 0.14
221 3 0.01
223 1 0.00
226 7 0.02
228 3 0.01
230 2 0.01
234 9 0.03
235 5 0.02
236 2 0.01
238 2 0.01
239 1 0.00
240 1 0.00
241 1 0.00
243 2 0.01
244 41 0.14
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (221 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTAAATAATTATTAGAATTGATTTATT
TTAAAATATGGATTGATTTATTTTAAATAATTATTAGTATAGATTGATTTATTTTAAATAATTTA
TTTGTATAGATTGATTTATTTTAAAATATGGATTGATTATTATTGTAGTTGTATAGATTGATTTA
TTTAAATAATTTATTAATATGGATTG
Found at i:749308 original size:22 final size:22
Alignment explanation
Indices: 749283--749355 Score: 53
Period size: 22 Copynumber: 3.3 Consensus size: 22
749273 TATTTAAATA
749283 ATTTATTAGTATGTATTGATTT
1 ATTTATTAGTATGTATTGATTT
* * *
749305 ATTT-TAAAATATGGATTGATTT
1 ATTTAT-TAGTATGTATTGATTT
* *
749327 A-TTATT-GTAGTTGTATGGATTG
1 ATTTATTAGTA--TGTATTGATTT
749349 ATTTATT
1 ATTTATT
749356 TTAAATAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 28 0.74
23 5 0.13
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (22 bp):
ATTTATTAGTATGTATTGATTT
Found at i:749397 original size:22 final size:22
Alignment explanation
Indices: 749372--749414 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
749362 AATTTATTAG
749372 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
749394 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
749415 TAATTTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:749475 original size:31 final size:31
Alignment explanation
Indices: 749438--749496 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
749428 AGTTGTATGG
* *
749438 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
749469 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
749497 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:749556 original size:16 final size:16
Alignment explanation
Indices: 749514--749544 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
749504 GTTTAAAAAA
749514 TCAGTTTATTTATATT
1 TCAGTTTATTTATATT
749530 TCAGTTTATTTATAT
1 TCAGTTTATTTATAT
749545 CTTAGTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (16 bp):
TCAGTTTATTTATATT
Found at i:749957 original size:20 final size:20
Alignment explanation
Indices: 749929--750042 Score: 81
Period size: 21 Copynumber: 5.6 Consensus size: 20
749919 AGAAAGTTTG
*
749929 GGATCGATCCCTTCA-CAAAA
1 GGATTGATCCC-TCACCAAAA
**
749949 GGATTGATCCCTCAAGAAAAA
1 GGATTGATCCCTC-ACCAAAA
* **
749970 TGATTGATCCCTCGATGAAAA
1 GGATTGATCCCTC-ACCAAAA
*
749991 GGATCGATTCCCTC-CCATAAA
1 GGATTGA-TCCCTCACCA-AAA
* *
750012 GAATTTATCCCTCACCAAAA
1 GGATTGATCCCTCACCAAAA
750032 GGATTGA-CCCT
1 GGATTGATCCCT
750043 TCCCTTAAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
19 6 0.08
20 26 0.35
21 36 0.49
22 6 0.08
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (20 bp):
GGATTGATCCCTCACCAAAA
Found at i:750614 original size:32 final size:32
Alignment explanation
Indices: 750573--750640 Score: 109
Period size: 32 Copynumber: 2.1 Consensus size: 32
750563 TTGAGAGGGT
*
750573 GTGTATTCAAGATTTTGGGTATAAACCTCGAA
1 GTGTATTCAAGATTTTGAGTATAAACCTCGAA
* *
750605 GTGTATTCAAGTTTTTGAGTATAAACCTTGAA
1 GTGTATTCAAGATTTTGAGTATAAACCTCGAA
750637 GTGT
1 GTGT
750641 TGCAAGGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.38
Consensus pattern (32 bp):
GTGTATTCAAGATTTTGAGTATAAACCTCGAA
Found at i:772485 original size:32 final size:30
Alignment explanation
Indices: 772427--772520 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 30
772417 CGTATTTAAA
* *
772427 TATTAAATTTATTATAGATTATAAAATTAT
1 TATTAAATTTATTAAATATTATAAAATTAT
*
772457 TATTAAATTTTATTGAAATATTATAAAATAAT
1 TATTAAA-TTTATT-AAATATTATAAAATTAT
* * *
772489 TACTAAATTTATTTAAT-TTTTAAAATTAT
1 TATTAAATTTATTAAATATTATAAAATTAT
772518 TAT
1 TAT
772521 CATTTAACCA
Statistics
Matches: 54, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
29 12 0.22
30 10 0.19
31 12 0.22
32 20 0.37
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (30 bp):
TATTAAATTTATTAAATATTATAAAATTAT
Found at i:778680 original size:15 final size:14
Alignment explanation
Indices: 778651--778704 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 14
778641 AGTTCATCTA
*
778651 TTTTAA-TAGATTT
1 TTTTAATTATATTT
778664 TTTTATATTATATTT
1 TTTTA-ATTATATTT
778679 TTTTAATTAACTATTT
1 TTTTAATT-A-TATTT
778695 TTTTAATTAT
1 TTTTAATTAT
778705 TCTTACATTG
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
13 5 0.14
14 5 0.14
15 13 0.36
16 13 0.36
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (14 bp):
TTTTAATTATATTT
Found at i:778693 original size:16 final size:15
Alignment explanation
Indices: 778660--778703 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
778650 ATTTTAATAG
778660 ATTTTTTTATATT-AT
1 ATTTTTTTA-ATTAAT
778675 ATTTTTTTAATTAACT
1 ATTTTTTTAATTAA-T
778691 ATTTTTTTAATTA
1 ATTTTTTTAATTA
778704 TTCTTACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.11
15 10 0.37
16 14 0.52
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTTTAATTAAT
Found at i:787724 original size:2 final size:2
Alignment explanation
Indices: 787719--787758 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
787709 GAGCGGAGAG
787719 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
787759 TGTTAATGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:793531 original size:60 final size:60
Alignment explanation
Indices: 793400--793531 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 60
793390 AAAAGACGAG
* ** * *
793400 TTTTGTAACTTTTAAGAGTTGGAGAACTCAACAAAGCAACGTCCTATAGTCGAATGACTA
1 TTTTGTAACTTTTAAGAGTAGGAGAACTCAACAAAGCAACACCCTATAGTCGAAGGACCA
* *
793460 TTTTGTAACTTTTAATAGTCAGGAG-ACTCAACAAAGCATCACCCTATAGTC-ACAGGACCA
1 TTTTGTAACTTTTAAGAGT-AGGAGAACTCAACAAAGCAACACCCTATAGTCGA-AGGACCA
793520 TTTGTGT-ACTTT
1 TTT-TGTAACTTT
793532 ACCCAAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
59 1 0.02
60 54 0.87
61 7 0.11
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (60 bp):
TTTTGTAACTTTTAAGAGTAGGAGAACTCAACAAAGCAACACCCTATAGTCGAAGGACCA
Found at i:802728 original size:14 final size:13
Alignment explanation
Indices: 802706--802735 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
802696 AATGCAAATA
802706 AATTTATAATTAT
1 AATTTATAATTAT
802719 AATTTAATAATTAT
1 AATTT-ATAATTAT
802733 AAT
1 AAT
802736 AAATAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTATAATTAT
Found at i:805850 original size:23 final size:23
Alignment explanation
Indices: 805820--805865 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
805810 GCAGTGTTAA
805820 CTCGTAAACAATTTCTTTCAATC
1 CTCGTAAACAATTTCTTTCAATC
805843 CTCGTAAACAATTTCTTTCAATC
1 CTCGTAAACAATTTCTTTCAATC
805866 AAGGTTGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.39
Consensus pattern (23 bp):
CTCGTAAACAATTTCTTTCAATC
Found at i:812455 original size:22 final size:22
Alignment explanation
Indices: 812424--812466 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
812414 AAGTTATAAA
*
812424 TATAATACATCAT-AGTAATTAT
1 TATAACACATCATCA-TAATTAT
812446 TATAACACATCATCATAATTA
1 TATAACACATCATCATAATTA
812467 GTTGCATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (22 bp):
TATAACACATCATCATAATTAT
Found at i:814765 original size:2 final size:2
Alignment explanation
Indices: 814740--814791 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
814730 TGGGACAATG
* * * *
814740 GA GA GA GG GA GG GC GA GA GC GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
814782 GA GA GA -A GA G
1 GA GA GA GA GA G
814792 TGAAGAAGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.42, C:0.04, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:817298 original size:20 final size:21
Alignment explanation
Indices: 817273--817365 Score: 91
Period size: 21 Copynumber: 4.5 Consensus size: 21
817263 TTTTCCCAAT
*
817273 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
817293 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
* *
817314 CCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
817334 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
817355 TCGCAATGCGA
1 TCGCAATGCGA
817366 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.46
21 30 0.54
ACGTcount: A:0.40, C:0.19, G:0.25, T:0.16
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:817379 original size:20 final size:20
Alignment explanation
Indices: 817354--817445 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
817344 AATTGGGAAA
*
817354 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
817374 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
817395 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
817415 TTCGCAACGTGATACTGACT
1 ATCGCAACGCGATACTGACT
*
817435 TTCGCAACGCG
1 ATCGCAACGCG
817446 TTAATACATA
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 43 0.75
21 14 0.25
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:817380 original size:41 final size:41
Alignment explanation
Indices: 817274--817365 Score: 175
Period size: 41 Copynumber: 2.2 Consensus size: 41
817264 TTTCCCAATT
817274 CGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAAC
1 CGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAAC
*
817315 CGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAAT
1 CGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAAC
817356 CGCAATGCGA
1 CGCAATGCGA
817366 TACTGACTAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.15
Consensus pattern (41 bp):
CGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAAC
Found at i:817664 original size:22 final size:22
Alignment explanation
Indices: 817636--817679 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
817626 CACTCTCTCA
817636 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
817658 CCCATCTCCGGCGAAATTCGTC
1 CCCATCTCCGACGAAATCCGTC
817680 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:817952 original size:20 final size:20
Alignment explanation
Indices: 817923--817966 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
817913 GCGATTTTAG
817923 TTTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
817943 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
817963 TTTC
1 TTTC
817967 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:819307 original size:18 final size:18
Alignment explanation
Indices: 819286--819330 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
819276 TCCACTTCGG
*
819286 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
819304 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
819322 GAGCCATCA
1 GAGCCATCA
819331 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:819866 original size:19 final size:20
Alignment explanation
Indices: 819812--819878 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
819802 TAGTTTACTT
* *
819812 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
819832 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
819852 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
819871 TCGCAACG
1 TCGCAACG
819879 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:819886 original size:14 final size:14
Alignment explanation
Indices: 819867--819925 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
819857 ATGCGAAATG
819867 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
819881 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
819900 AAAATCGCAACGAC
1 AAAATCGCAACGAC
819914 AAAATCGCAACG
1 AAAATCGCAACG
819926 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:819905 original size:19 final size:19
Alignment explanation
Indices: 819851--819909 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
819841 GGAAATGGCT
819851 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
819870 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
819884 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
819903 ATCGCAA
1 ATCGCAA
819910 CGACAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:819941 original size:33 final size:33
Alignment explanation
Indices: 819851--819930 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
819841 GGAAATGGCT
819851 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
819884 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
819917 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
819931 CACAAATCGC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:819959 original size:19 final size:19
Alignment explanation
Indices: 819937--820058 Score: 101
Period size: 19 Copynumber: 6.6 Consensus size: 19
819927 GAAACACAAA
*
819937 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
819956 TCGCGTTGCGA-TTT--TG
1 TCGCGTTGCGATTTTCATT
819972 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* ***
819989 TCGCATTGCGATAGCCATT
1 TCGCGTTGCGATTTTCATT
**
820008 TCCGCGTTGCGATAGTCATT
1 T-CGCGTTGCGATTTTCATT
*
820028 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
820048 TCGTGTTGCGA
1 TCGCGTTGCGA
820059 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 3 0.04
19 36 0.43
20 29 0.35
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:820019 original size:20 final size:19
Alignment explanation
Indices: 819985--820039 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
819975 TTGCGATTTT
*
819985 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
820004 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
820024 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
820040 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:822057 original size:14 final size:16
Alignment explanation
Indices: 822038--822115 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 16
822028 CGAAATGGCT
822038 ATCGCAA-CG-AGAAA
1 ATCGCAAGCGAAGAAA
822052 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG-AA-GAAA
*
822071 ATCGCAATGCGAAATAAAA
1 ATCGCAA-GCG-AA-GAAA
822090 ATCGCAA-CG-AGAAA
1 ATCGCAAGCGAAGAAA
822104 ATCGCAATGCGA
1 ATCGCAA-GCGA
822116 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
14 17 0.31
15 1 0.02
16 4 0.07
17 2 0.04
18 1 0.02
19 29 0.54
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (16 bp):
ATCGCAAGCGAAGAAA
Found at i:822070 original size:19 final size:19
Alignment explanation
Indices: 822048--822115 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
822038 ATCGCAACGA
822048 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
822067 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
822086 AAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
822100 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
822116 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
19 29 0.66
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:822191 original size:20 final size:20
Alignment explanation
Indices: 822135--822191 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
822125 CGCATTGCGG
* *
822135 TTTTCTCGTTGCGATAACCA
1 TTTTCGCGTTGCGATAGCCA
822155 TTTTCGCGTTGCGATAGCCA
1 TTTTCGCGTTGCGATAGCCA
822175 TTTTCGCGTTGCGATAG
1 TTTTCGCGTTGCGATAG
822192 TCAAATGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (20 bp):
TTTTCGCGTTGCGATAGCCA
Found at i:823498 original size:12 final size:12
Alignment explanation
Indices: 823481--823505 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
823471 ATATAATCCT
823481 GAAGAAGAAAAA
1 GAAGAAGAAAAA
823493 GAAGAAGAAAAA
1 GAAGAAGAAAAA
823505 G
1 G
823506 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:824874 original size:19 final size:20
Alignment explanation
Indices: 824852--824894 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
824842 AAATCGCAAC
824852 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
824871 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
824891 GCGA
1 GCGA
824895 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:824879 original size:14 final size:14
Alignment explanation
Indices: 824880--824913 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
824870 TGCGATTTTC
824880 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
824894 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
824908 ATTTTC
1 ATTTTC
824914 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:825054 original size:14 final size:14
Alignment explanation
Indices: 825035--825071 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
825025 CATCAATTAA
825035 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
825049 ACAAATCACCTTTT
1 ACAAATCAACTTTT
*
825063 ATAAATCAA
1 ACAAATCAA
825072 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:826493 original size:21 final size:21
Alignment explanation
Indices: 826427--826493 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
826417 GTGAATCGGG
*
826427 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
826447 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
826469 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
826490 CTCT
1 CTCT
826494 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:826512 original size:42 final size:41
Alignment explanation
Indices: 826427--826549 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
826417 GTGAATCGGG
* * * *
826427 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAATGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
*
826469 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAATGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
826511 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAATGGTGGGAGGGGACTCTCGA-GGATGATAGG
826550 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (41 bp):
CTCTTGAATGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:828631 original size:33 final size:33
Alignment explanation
Indices: 828574--828672 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
828564 ACGAGATAAT
* *
828574 GAGAATCGCAATGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
828608 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
828641 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
828673 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 45 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Done.