Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005109.1 Hibiscus syriacus cultivar Beakdansim tig00011482_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: 62108
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:1775 original size:19 final size:19
Alignment explanation
Indices: 1740--1776 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1730 ATGACCAACA
* *
1740 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCAATCTCT
1759 AAATCGCAACGCAATCTC
1 AAATCGCAACGCAATCTC
1777 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCAATCTCT
Found at i:1860 original size:20 final size:20
Alignment explanation
Indices: 1835--1884 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1825 CATTGCGATA
1835 ATCGCAACGCGATTATGACT
1 ATCGCAACGCGATTATGACT
*
1855 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTATGACT
1875 ATCGCAACGC
1 ATCGCAACGC
1885 TGAATTTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.28, C:0.30, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTATGACT
Found at i:1867 original size:34 final size:34
Alignment explanation
Indices: 1802--1867 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1792 GTTTCTAGAT
* **
1802 TCGCAACGCGATTTTGACTATCACATTGCGATAA
1 TCGCAACGCGATTATGACTATCACAACGCGATAA
*
1836 TCGCAACGCGATTATGACTATCGCAACGCGAT
1 TCGCAACGCGATTATGACTATCACAACGCGAT
1868 TCTGACTATC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (34 bp):
TCGCAACGCGATTATGACTATCACAACGCGATAA
Found at i:2860 original size:28 final size:28
Alignment explanation
Indices: 2820--2874 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
2810 CTCTGTTTAC
2820 ATTATGTCATCGAGACAATGCTTGAAAT
1 ATTATGTCATCGAGACAATGCTTGAAAT
* *
2848 ATTATGTTATCGAGCCAATGCTTGAAA
1 ATTATGTCATCGAGACAATGCTTGAAA
2875 GCAATTTCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.33
Consensus pattern (28 bp):
ATTATGTCATCGAGACAATGCTTGAAAT
Found at i:3973 original size:22 final size:23
Alignment explanation
Indices: 3943--3986 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3933 ATCCGAAGAA
3943 AAAACATATTACAAAAA-TAAAT
1 AAAACATATTACAAAAAGTAAAT
* *
3965 AAAATATATTATAAAAAGTAAA
1 AAAACATATTACAAAAAGTAAA
3987 GTCATTCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAACATATTACAAAAAGTAAAT
Found at i:18637 original size:3 final size:3
Alignment explanation
Indices: 18629--18654 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
18619 ATCATAATTA
18629 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
18655 ACATGATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:19890 original size:8 final size:8
Alignment explanation
Indices: 19877--19920 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
19867 TGTTATGAGT
19877 AAATTTTA
1 AAATTTTA
19885 AAATTTTA
1 AAATTTTA
* **
19893 AAAATAAA
1 AAATTTTA
19901 AAATTTTA
1 AAATTTTA
19909 AAATTTTA
1 AAATTTTA
19917 AAAT
1 AAAT
19921 AAACAAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
AAATTTTA
Found at i:19909 original size:24 final size:23
Alignment explanation
Indices: 19877--19923 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
19867 TGTTATGAGT
19877 AAATTTTAAAATTTTAAAAATAAA
1 AAATTTTAAAATTTT-AAAATAAA
19901 AAATTTTAAAATTTTAAAATAAA
1 AAATTTTAAAATTTTAAAATAAA
19924 CAAAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AAATTTTAAAATTTTAAAATAAA
Found at i:25784 original size:35 final size:35
Alignment explanation
Indices: 25739--25811 Score: 110
Period size: 35 Copynumber: 2.1 Consensus size: 35
25729 ATTTTAAAAT
*
25739 TTTAACTTTGCTATTACATAAATTTTATAATGATA
1 TTTAACTTTGCCATTACATAAATTTTATAATGATA
* * *
25774 TTTAATTTTGCCATTATATAAGTTTTATAATGATA
1 TTTAACTTTGCCATTACATAAATTTTATAATGATA
25809 TTT
1 TTT
25812 CAATGTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (35 bp):
TTTAACTTTGCCATTACATAAATTTTATAATGATA
Found at i:27094 original size:18 final size:16
Alignment explanation
Indices: 27071--27144 Score: 53
Period size: 16 Copynumber: 4.4 Consensus size: 16
27061 TTAAAAAATA
27071 AAATATAAGTAAATATT
1 AAATATAA-TAAATATT
* *
27088 -AATATATTCAATACATT
1 AAATATAAT-AA-ATATT
*
27105 AAATATAA-AAATAATA
1 AAATATAATAAAT-ATT
27121 AAATATAAGTAAATATT
1 AAATATAA-TAAATATT
27138 AAGATAT
1 AA-ATAT
27145 TCAATATACA
Statistics
Matches: 44, Mismatches: 6, Indels: 13
0.70 0.10 0.21
Matches are distributed among these distances:
15 2 0.05
16 20 0.45
17 8 0.18
18 14 0.32
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (16 bp):
AAATATAATAAATATT
Found at i:27130 original size:50 final size:52
Alignment explanation
Indices: 27063--27177 Score: 166
Period size: 50 Copynumber: 2.2 Consensus size: 52
27053 TATTTAGATT
* *
27063 AAAA-AATAAAATATAAGTAAATATTAATATATTC-A-ATACATTAA-ATATA
1 AAAATAATAAAATATAAGTAAATATTAAGATATTCAATATACA-AAATATATA
27112 AAAATAATAAAATATAAGTAAATATTAAGATATTCAATATACAAAATATATA
1 AAAATAATAAAATATAAGTAAATATTAAGATATTCAATATACAAAATATATA
27164 AAAATAAATAAAAT
1 AAAAT-AATAAAAT
27178 TATTTATGCC
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
49 4 0.07
50 29 0.49
51 3 0.05
52 15 0.25
53 8 0.14
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (52 bp):
AAAATAATAAAATATAAGTAAATATTAAGATATTCAATATACAAAATATATA
Found at i:27999 original size:13 final size:13
Alignment explanation
Indices: 27978--28008 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
27968 CCACACCGAT
*
27978 CGTCATCCTTTAC
1 CGTCGTCCTTTAC
27991 CGTCGTCCTTTAC
1 CGTCGTCCTTTAC
28004 CGTCG
1 CGTCG
28009 ACAAAGCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.10, C:0.39, G:0.16, T:0.35
Consensus pattern (13 bp):
CGTCGTCCTTTAC
Found at i:28881 original size:20 final size:20
Alignment explanation
Indices: 28856--29028 Score: 206
Period size: 20 Copynumber: 8.6 Consensus size: 20
28846 GATGTTCCAG
* ** *
28856 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
28876 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
*
28896 AATCTCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28916 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
28936 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
28956 AATCGCAACGCGTATTCGTA
1 AATCGCAACGCGTATCCGTA
* *
28976 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
28997 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
29017 AATCGCAACGCG
1 AATCGCAACGCG
29029 ATTTTTAAAG
Statistics
Matches: 132, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 112 0.85
21 19 0.14
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:29450 original size:33 final size:33
Alignment explanation
Indices: 29406--29478 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
29396 ATTTCACTTA
29406 GATTTT-ATTTCGCGTTACGATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
* *
29438 GATTTTCATTTCGCGTTGCTATTCTCTCGTTGC
1 GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
29471 GATTTTCA
1 GATTTTCA
29479 AGTTAGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.12, C:0.22, G:0.18, T:0.48
Consensus pattern (33 bp):
GATTTTCATTTCGCGTTACGATTCTCTCGTTGC
Found at i:29584 original size:21 final size:20
Alignment explanation
Indices: 29558--29664 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
29548 TGCAGAAGAG
29558 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
29579 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
29599 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
29621 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
29635 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
29654 TCGCAACGAGA
1 TCGCAACGAGA
29665 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:29638 original size:14 final size:14
Alignment explanation
Indices: 29619--29675 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
29609 GAAAAATGAA
29619 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
29633 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
29652 AATCGCAACGAGAG
1 AATCGCAACGAGAG
29666 AATCGCAACG
1 AATCGCAACG
29676 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:29650 original size:33 final size:33
Alignment explanation
Indices: 29612--29691 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
29602 GCAACGAGAA
29612 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
29645 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
29678 AAACCAAAATCGCA
1 AAATGAAAATCGCA
29692 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:29783 original size:20 final size:19
Alignment explanation
Indices: 29687--29786 Score: 119
Period size: 19 Copynumber: 5.1 Consensus size: 19
29677 GAAACCAAAA
*
29687 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29706 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
29725 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
29745 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
29765 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
29785 TC
1 TC
29787 AACCAAAAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
19 37 0.52
20 21 0.30
21 13 0.18
ACGTcount: A:0.12, C:0.24, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:31630 original size:93 final size:93
Alignment explanation
Indices: 31471--31786 Score: 596
Period size: 93 Copynumber: 3.4 Consensus size: 93
31461 TAGATTGCTT
*
31471 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31536 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
31564 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACCGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
31629 TTTGTCTTTGTTTTGTCATTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
31657 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
31722 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
31750 AGTAAATTTGTTCGGTTGCTGCCAATTATGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
31787 AATACCCTGA
Statistics
Matches: 217, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 217 1.00
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:31921 original size:14 final size:14
Alignment explanation
Indices: 31902--31958 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
31892 CGAAACTTAA
31902 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
31916 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
31935 AATCGCAACGACAG
1 AATCGCAACGAGAG
31949 AATCGCAACG
1 AATCGCAACG
31959 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:31940 original size:19 final size:18
Alignment explanation
Indices: 31916--32007 Score: 65
Period size: 19 Copynumber: 5.4 Consensus size: 18
31906 GCAACGAGAG
31916 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
31935 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
31949 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
*
31968 AATCGCAA--CG--ACAA
1 AATCGCAACGCGAAAGAA
*
31982 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
32001 AATCGCA
1 AATCGCA
32008 TTGCGATTTT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 7 0.12
17 6 0.10
18 1 0.02
19 26 0.43
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:31942 original size:33 final size:33
Alignment explanation
Indices: 31884--32007 Score: 185
Period size: 33 Copynumber: 3.7 Consensus size: 33
31874 TAGTTTACTT
* * *
31884 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGACAGAA
**
31918 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
*
31951 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGACAGAA
31984 TCGCAACGCGAAACCAAAATCGCA
1 TCGCAACGCGAAACCAAAATCGCA
32008 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 71 0.86
34 12 0.14
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAACCAAAATCGCAACGACAGAA
Found at i:31984 original size:14 final size:14
Alignment explanation
Indices: 31933--31991 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
31923 ACGCGAAATG
31933 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
31947 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
31966 AAAATCGCAACGAC
1 AAAATCGCAACGAC
31980 AAAATCGCAACG
1 AAAATCGCAACG
31992 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:32025 original size:19 final size:19
Alignment explanation
Indices: 32003--32175 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
31993 GAAACCAAAA
*
32003 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
32022 TCGCATTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
32036 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
32055 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
32071 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
32088 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
32107 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
32126 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
32145 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
32165 TCGTGTTGCGA
1 TCGCGTTGCGA
32176 AAGTAAACTA
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 16 0.13
16 8 0.06
17 8 0.06
19 82 0.65
20 12 0.10
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:32050 original size:33 final size:33
Alignment explanation
Indices: 32008--32100 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
31998 CAAAATCGCA
32008 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
32041 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
32074 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
32101 TTGGTTTCGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:32065 original size:52 final size:52
Alignment explanation
Indices: 32003--32141 Score: 140
Period size: 52 Copynumber: 2.7 Consensus size: 52
31993 GAAACCAAAA
* *
32003 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCGTTTCGCATTGCGATTCTCGCGTTGCGATTTTCATT
* * **
32055 TCGCATTGCGATTCTGTCGTTGCG-ATTTTC-ATT-TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATT-T-TCGTTTCGCA-TTGCGATTCTCGCGTTGCGATTTTCATT
* * * *
32107 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTC
1 TCGCATTGCGATTTTCGTTTCGCATTGCGATTCTC
32142 ATTTCGCGTT
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.62
53 5 0.07
54 9 0.13
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCGTTTCGCATTGCGATTCTCGCGTTGCGATTTTCATT
Found at i:32133 original size:38 final size:38
Alignment explanation
Indices: 32003--32175 Score: 159
Period size: 33 Copynumber: 4.8 Consensus size: 38
31993 GAAACCAAAA
* *
32003 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
32038 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
32071 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
32107 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
32145 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
32176 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 53 0.46
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.38
39 11 0.09
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:34119 original size:14 final size:14
Alignment explanation
Indices: 34100--34135 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
34090 ATTGTTTAAT
34100 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
34114 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
34128 TGATTTGT
1 TGATTTGT
34136 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:34258 original size:19 final size:19
Alignment explanation
Indices: 34242--34320 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 19
34232 AAAAATGACT
34242 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
34261 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
34280 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
34294 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
34314 ATCGCAA
1 ATCGCAA
34321 CGAGAGAATC
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 1 0.02
17 3 0.06
19 27 0.52
20 10 0.19
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:34314 original size:34 final size:34
Alignment explanation
Indices: 34260--34338 Score: 151
Period size: 34 Copynumber: 2.4 Consensus size: 34
34250 GCGAAATGAA
34260 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
34293 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
34327 AATCGCAATGCG
1 AATCGCAATGCG
34339 ATTTTCATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 11 0.24
34 34 0.76
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (34 bp):
AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:34455 original size:105 final size:109
Alignment explanation
Indices: 34335--34604 Score: 434
Period size: 105 Copynumber: 2.6 Consensus size: 109
34325 AGAATCGCAA
34335 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
34400 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
34440 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
34505 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-AT
*
34551 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
34605 GTAATTTCCG
Statistics
Matches: 157, Mismatches: 2, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
105 122 0.78
106 14 0.09
107 3 0.02
108 3 0.02
109 3 0.02
111 12 0.08
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (109 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
Found at i:34572 original size:72 final size:72
Alignment explanation
Indices: 34357--34590 Score: 297
Period size: 72 Copynumber: 3.3 Consensus size: 72
34347 TTCGCATTGC
*
34357 GATTTTCATTTCCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGATTTT
1 GATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTT
*
34416 CAT-TTCG
65 CATGTTGG
* * * * *
34423 CA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTC
1 GATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTT
*
34487 TC-TCGTTGC
64 TCAT-GTTGG
34496 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
34561 ATGTTGG
66 ATGTTGG
34568 GATTTTCATTTCGCATTGCGATT
1 GATTTTCATTTCGCATTGCGATT
34591 CTCTCGTTGC
Statistics
Matches: 142, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
65 3 0.02
66 12 0.08
67 1 0.01
68 3 0.02
69 4 0.03
71 16 0.11
72 93 0.65
73 7 0.05
74 3 0.02
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (72 bp):
GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
ATGTTGG
Found at i:34619 original size:53 final size:52
Alignment explanation
Indices: 34335--34604 Score: 415
Period size: 53 Copynumber: 5.1 Consensus size: 52
34325 AGAATCGCAA
34335 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
34388 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
34440 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
34493 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
34551 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
34598 TGCGATT
1 TGCGATT
34605 GTAATTTCCG
Statistics
Matches: 207, Mismatches: 3, Indels: 20
0.90 0.01 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 62 0.30
53 109 0.53
54 3 0.01
55 3 0.01
56 3 0.01
58 12 0.06
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:36905 original size:12 final size:12
Alignment explanation
Indices: 36888--36912 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36878 TCTTCGGGGA
36888 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36900 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36912 C
1 C
36913 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:37121 original size:24 final size:24
Alignment explanation
Indices: 37087--37133 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
37077 CTGAAACATC
37087 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
37111 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
37134 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:37854 original size:20 final size:20
Alignment explanation
Indices: 37826--38094 Score: 252
Period size: 20 Copynumber: 13.4 Consensus size: 20
37816 AAATTTCAGT
* * *
37826 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
37846 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* * **
37866 GTTGTGATTTACAGATTCTT
1 GTTGCGATTTACGGATTCGC
**
37886 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* **
37906 GTTGCGATTTACAGATTCTT
1 GTTGCGATTTACGGATTCGC
**
37926 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
37946 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
37966 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
37986 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
38006 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
38026 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
38046 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
38066 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
38086 GTTGCGATT
1 GTTGCGATT
38095 CTTGAAAATC
Statistics
Matches: 211, Mismatches: 36, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
20 210 1.00
21 1 0.00
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:38147 original size:21 final size:20
Alignment explanation
Indices: 38062--38159 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
38052 ATTTATGTGT
* *
38062 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCAAAA
*
38082 TCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGATT-TTCAAAA
** **
38103 TCGCAATGCGAATTTGT-ACTA
1 TCGCGTTGCG-ATTT-TCAAAA
*
38124 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAA-AA
38145 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
38160 GGAAACTGAT
Statistics
Matches: 62, Mismatches: 11, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
19 1 0.02
20 18 0.29
21 39 0.63
22 4 0.06
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAAAA
Found at i:38155 original size:42 final size:43
Alignment explanation
Indices: 38062--38160 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
38052 ATTTATGTGT
* *
38062 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
**
38103 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTTCAA-AA
*
38145 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
38161 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 12 0.26
42 32 0.68
43 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTCAAAA
Found at i:40344 original size:19 final size:20
Alignment explanation
Indices: 40298--40344 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
40288 ACTAAAAATA
40298 ATCTTATT-TTTTAAGTTTT
1 ATCTTATTGTTTTAAGTTTT
40317 AT-TTCATTGTTTT-AGTTTT
1 ATCTT-ATTGTTTTAAGTTTT
*
40336 CTCTTATTG
1 ATCTTATTG
40345 GTATGCTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
19 16 0.67
20 6 0.25
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66
Consensus pattern (20 bp):
ATCTTATTGTTTTAAGTTTT
Found at i:43465 original size:21 final size:20
Alignment explanation
Indices: 43422--43469 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
43412 ATAAAGACTT
*
43422 AAAC-ATAAAATAAATGCCC
1 AAACTATAAAATAAATGCAC
* *
43441 AAACATATAAAATAAGTGCAT
1 AAAC-TATAAAATAAATGCAC
43462 AAACTATA
1 AAACTATA
43470 GTGCATAACG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 4 0.17
21 16 0.67
ACGTcount: A:0.58, C:0.15, G:0.06, T:0.21
Consensus pattern (20 bp):
AAACTATAAAATAAATGCAC
Found at i:45273 original size:35 final size:35
Alignment explanation
Indices: 45229--45341 Score: 156
Period size: 35 Copynumber: 3.2 Consensus size: 35
45219 AAAACAATTC
*
45229 TCAATTTCATTCT-AACCCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACCC-CAAATTCCAAAATAAT
*
45264 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
* * * *
45299 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
45334 TCAATTTC
1 TCAATTTC
45342 TGTCTTTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 64 0.93
36 5 0.07
ACGTcount: A:0.42, C:0.24, G:0.01, T:0.34
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:46414 original size:35 final size:35
Alignment explanation
Indices: 46359--46470 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
46349 ATTTCTCCTT
* *
46359 AAATTGAAGTATTTTAGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* * *
46394 TAATTTAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
* * * * *
46429 AAATTGAATTACTTTGAAATTTGAGATTTATAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
46464 AAATTGA
1 AAATTGA
46471 GGAATGTTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.37, C:0.01, G:0.20, T:0.43
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
Found at i:49641 original size:28 final size:28
Alignment explanation
Indices: 49605--49668 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
49595 CGTCGGAGCT
49605 ACCACCTCAATCAGCATCAGCAAATACC
1 ACCACCTCAATCAGCATCAGCAAATACC
49633 ACCACCTCAATCAGCATCAGCAAATACC
1 ACCACCTCAATCAGCATCAGCAAATACC
49661 ACCACCTC
1 ACCACCTC
49669 CATACTAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.38, C:0.42, G:0.06, T:0.14
Consensus pattern (28 bp):
ACCACCTCAATCAGCATCAGCAAATACC
Found at i:54715 original size:2 final size:2
Alignment explanation
Indices: 54710--54742 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54700 AATATATTTT
54710 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54743 CACATCGAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57215 original size:69 final size:70
Alignment explanation
Indices: 57101--57256 Score: 228
Period size: 70 Copynumber: 2.2 Consensus size: 70
57091 TATCATAATC
* * *
57101 ATGTAATTAAGA-TATTTTTCTCAACAAGATATTTTTATTACATATAAAGTACAA-TCTTACCCG
1 ATGTAATTAAGATTATTTTTCTCAACAAGATATATTTATTACATATAAAGCACAAGCCTTACCCG
57164 ATTGT
66 ATTGT
* *
57169 ATGTAATTAAGATTTTTTTTCCTCAACAAGATA-ATTTATTAGATATAAAGCACAAGCCTTACCC
1 ATGTAATTAAGATTATTTTT-CTCAACAAGATATATTTATTACATATAAAGCACAAGCCTTACCC
57233 GATTGT
65 GATTGT
57239 ATGTTAATTAAGATTATT
1 ATG-TAATTAAGATTATT
57257 ATATGTAATG
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
68 12 0.15
69 25 0.32
70 28 0.36
71 13 0.17
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (70 bp):
ATGTAATTAAGATTATTTTTCTCAACAAGATATATTTATTACATATAAAGCACAAGCCTTACCCG
ATTGT
Found at i:58780 original size:12 final size:12
Alignment explanation
Indices: 58763--58789 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
58753 ATTGCAGTCT
58763 CTGACCATTTTA
1 CTGACCATTTTA
58775 CTGACCATTTTA
1 CTGACCATTTTA
58787 CTG
1 CTG
58790 CACGTCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.26, G:0.11, T:0.41
Consensus pattern (12 bp):
CTGACCATTTTA
Found at i:59866 original size:2 final size:2
Alignment explanation
Indices: 59861--59893 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59851 ACATACATAC
59861 AT 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 AT A
59894 AACAGATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.