Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006813.1 Hibiscus syriacus cultivar Beakdansim tig00017315_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: 61172
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:345 original size:6 final size:6
Alignment explanation
Indices: 336--360 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
326 ATTATAATTA
336 GTTTAC GTTTAC GTTTAC GTTTAC G
1 GTTTAC GTTTAC GTTTAC GTTTAC G
361 ATTATGCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (6 bp):
GTTTAC
Found at i:1635 original size:19 final size:21
Alignment explanation
Indices: 1592--1645 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
1582 ACAGGTAACG
*
1592 AATTTGACAAAATCGATTGGA
1 AATTTGACAAAACCGATTGGA
1613 AA-TTGACAAAACCGATT-GA
1 AATTTGACAAAACCGATTGGA
1632 AATTTGACAAAACC
1 AATTTGACAAAACC
1646 TATTTCAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 4 0.13
20 25 0.81
21 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (21 bp):
AATTTGACAAAACCGATTGGA
Found at i:2058 original size:198 final size:195
Alignment explanation
Indices: 1686--2060 Score: 463
Period size: 198 Copynumber: 1.9 Consensus size: 195
1676 TGCTGAAATT
* *
1686 GTTGAAATTTGTATCGATACATTTATAAATATATGTATCAAAGTATCAGTATTGTAGGAATTTAA
1 GTTGAAATTTGTATCGATACATTTATAAATATATGCACCAAAGTATCAGTATTGTAGGAATTTAA
* * *
1751 AAGAAATGAAAAAAAGGAAAATGTCTCTAAAGTATTAATACCTTACACATGTATCGATACATGAC
66 AAGAAATGAAAAAAAGG---ACGCCTATAAAGTATTAATACCTTACACATGTATCGATACATGAC
* * * * *
1816 AATATAACATGTTAAAGTTTGACAAAACCGGTTTAGTTTGACAAAACCAATAAAGAGATACCGGA
128 AATATAACATATTAAAGTTTGAAAAAACCAGTTTAATATGACAAAACCAATAAAGAGATACCGGA
1881 ATG
193 ATG
* * *
1884 GTTGACATTTGTATCGATAC-TTATATAAGTATATGCACCAAATTATCAGTACTT-TAGGAATTT
1 GTTGAAATTTGTATCGATACATT-TATAAATATATGCACCAAAGTATCAGTA-TTGTAGGAATTT
* * * *
1947 AAAAGAATTGCAATAATA-G-CGCCTATAAAGTATTGATACCTTAGACACATGTATCGATACATG
64 AAAAGAAATG-AAAAAAAGGACGCCTATAAAGTATTAATACCTT--ACACATGTATCGATACATG
2010 ACAATATAACATATTGAAA-TTTGATAAAAACCAGTTTCAATATGACAAAAC
126 ACAATATAACATATT-AAAGTTTGA-AAAAACCAGTTT-AATATGACAAAAC
2061 TGGTAAAGCG
Statistics
Matches: 152, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
194 19 0.12
196 38 0.25
197 15 0.10
198 73 0.48
199 7 0.05
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (195 bp):
GTTGAAATTTGTATCGATACATTTATAAATATATGCACCAAAGTATCAGTATTGTAGGAATTTAA
AAGAAATGAAAAAAAGGACGCCTATAAAGTATTAATACCTTACACATGTATCGATACATGACAAT
ATAACATATTAAAGTTTGAAAAAACCAGTTTAATATGACAAAACCAATAAAGAGATACCGGAATG
Found at i:2148 original size:195 final size:193
Alignment explanation
Indices: 1778--2148 Score: 453
Period size: 195 Copynumber: 1.9 Consensus size: 193
1768 AAAATGTCTC
* *
1778 TAAAGTATTAATACCTTACACATGTATCGATACATGACAATATAACATGTTAAAGTTTGACAAAA
1 TAAAGTATTAATACCTTACACATGTATCGATACATGACAATATAACATATTAAAGTTTGAAAAAA
* * * * *
1843 CCGGTTTAGTTTGACAAAACCAATAAAGAGATACCGGAATGGTTGACATTTGTATCGATACTTAT
66 CCAGTTTAATATGACAAAACCAATAAAGAGATACCGGAATGGTTGA-ATTGGTATCCATACTTAT
* * *
1908 ATAAGTATATGCACCAAATTATCAGTACTTTAGGAATTTAAAAGAATTGCAATAATAGCGCCTA
130 ATAAGTATATGCAACAAAGTATCAGTACTTTAGGAATTGAAAAGAATTGCAATAATAGCGCCTA
*
1972 TAAAGTATTGATACCTTAGACACATGTATCGATACATGACAATATAACATATTGAAA-TTTGATA
1 TAAAGTATTAATACCTT--ACACATGTATCGATACATGACAATATAACATATT-AAAGTTTGA-A
*** * * *
2036 AAAACCAGTTTCAATATGACAAAACTGGTAAAGCGCTACTGGATAT-GTTG-A-TGGTATCCATA
62 AAAACCAGTTT-AATATGACAAAACCAATAAAGAGATACCGGA-ATGGTTGAATTGGTATCCATA
* * * **
2098 CTTTTATAAGTATATGTAACATAGTATTTGTACTTTAGGAATTGAAAAGAA
125 CTTATATAAGTATATGCAACAAAGTATCAGTACTTTAGGAATTGAAAAGAA
2149 ATAAAAAATG
Statistics
Matches: 149, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
194 16 0.11
195 52 0.35
196 39 0.26
197 13 0.09
198 27 0.18
199 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (193 bp):
TAAAGTATTAATACCTTACACATGTATCGATACATGACAATATAACATATTAAAGTTTGAAAAAA
CCAGTTTAATATGACAAAACCAATAAAGAGATACCGGAATGGTTGAATTGGTATCCATACTTATA
TAAGTATATGCAACAAAGTATCAGTACTTTAGGAATTGAAAAGAATTGCAATAATAGCGCCTA
Found at i:2449 original size:14 final size:14
Alignment explanation
Indices: 2430--2466 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2420 TTTAAAAATA
2430 GGGGTTAGGTTTAT
1 GGGGTTAGGTTTAT
2444 GGGGTTAGGTTTAT
1 GGGGTTAGGTTTAT
*
2458 GGGTTTAGG
1 GGGGTTAGG
2467 GTTTTTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.46, T:0.41
Consensus pattern (14 bp):
GGGGTTAGGTTTAT
Found at i:8099 original size:19 final size:19
Alignment explanation
Indices: 8075--8124 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
8065 AATTATGTTG
8075 TTTTTAATTTCAAGTTGAA
1 TTTTTAATTTCAAGTTGAA
* *
8094 TTTTTAATTTGAATTTGAA
1 TTTTTAATTTCAAGTTGAA
*
8113 -TTTGAATTTCAA
1 TTTTTAATTTCAA
8125 TTTAAGCTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (19 bp):
TTTTTAATTTCAAGTTGAA
Found at i:8110 original size:6 final size:6
Alignment explanation
Indices: 8089--8127 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
8079 TAATTTCAAG
* *
8089 TTGAATT TTTAAT TTGAAT TTGAAT TTGAAT TTCAAT TT
1 TTGAA-T TTGAAT TTGAAT TTGAAT TTGAAT TTGAAT TT
8128 AAGCTCCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
6 25 0.86
7 4 0.14
ACGTcount: A:0.31, C:0.03, G:0.10, T:0.56
Consensus pattern (6 bp):
TTGAAT
Found at i:8114 original size:12 final size:12
Alignment explanation
Indices: 8080--8127 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
8070 TGTTGTTTTT
*
8080 AATTTCAAGTTG
1 AATTTCAATTTG
*
8092 AATTTTTAATTTG
1 AA-TTTCAATTTG
*
8105 AATTTGAATTTG
1 AATTTCAATTTG
8117 AATTTCAATTT
1 AATTTCAATTT
8128 AAGCTCCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
12 21 0.68
13 10 0.32
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.52
Consensus pattern (12 bp):
AATTTCAATTTG
Found at i:9715 original size:21 final size:21
Alignment explanation
Indices: 9686--9727 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9676 AGGCGTAAAC
9686 ATAACGTATCAATACTTATTAT
1 ATAACGTATCAATACTT-TTAT
*
9708 ATAA-GTATCGATACTTTTAT
1 ATAACGTATCAATACTTTTAT
9728 TCCAGTATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 11 0.58
22 4 0.21
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (21 bp):
ATAACGTATCAATACTTTTAT
Found at i:9785 original size:21 final size:19
Alignment explanation
Indices: 9761--9799 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
9751 TGCACGCACA
*
9761 AAGTATTGATACATGTATAAC
1 AAGTATCGATA-AT-TATAAC
9782 AAGTATCGATAATTATAA
1 AAGTATCGATAATTATAA
9800 TTTCGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (19 bp):
AAGTATCGATAATTATAAC
Found at i:10033 original size:199 final size:197
Alignment explanation
Indices: 9589--10251 Score: 820
Period size: 199 Copynumber: 3.3 Consensus size: 197
9579 ACAAAGTTTT
* * * * *
9589 GATACTTAGAATTTTGAAACGTATTACTTTAAAGTAAT-GCTTAAATTTACAATATAAACGGTTA
1 GATACATAGAATTTCGAAACG-ATTACTTTAAAGTAATAG-GTAAATTTACAATGTAAACGGTAA
* * *
9653 AAATCTACTGGTTTAATGATAATAGGCGTAAACATAACGTATCAATACTTATTATATAAGTATCG
64 AAATCTACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATAC-T-TTATATAAGTATCG
*
9718 ATACTTTTATTCCAGTATGCGTCTCAAACAATTTGCACGCACAAAGTATTGAT--ACATGTATAA
127 ATACTTTTATTCCAGTATGCATCTCAAACAATTTGCACGCACAAAGTATTGATACACATGTAT-A
9781 CAAGTATC
191 -AAGTATC
* * *
9789 GATA-ATTATAATTTCGAAACCTATTTCTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAA
1 GATACA-TAGAATTTCGAAA-CGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGT-A
9853 AAAAT-TACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATAC-TTATATAAGTATCGA
63 AAAATCTACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTATATAAGTATCGA
* * *
9916 TACTTTTATTCCAGTTTGCATCTCAAACAATTTACACGCAAAAAAAGTATTGATACACATGTATA
128 TACTTTTATTCCAGTATGCATCTCAAACAATTTGCACGC--ACAAAGTATTGATACACATGTATA
9981 AAGTATC
191 AAGTATC
* * * *
9988 GATACGCT-GAATTTCGAAACCGATTACTTTAAAGTTATAGGTAAATTTACAATGTAAACAGTGA
1 GATAC-ATAGAATTTCGAAA-CGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAA
* * * * * * * *
10052 AAGTCTACCGATTTAATGATAATAGACGTAAACATCAAGTATTGGTACGTTTTGTATAGGTATCG
64 AAATCTACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATAC--TTTATATAAGTATCG
* * * * *
10117 ATACTTTTAGTCCAATATGCTTCTC-AACAATTTGCAGGCACAAAGTATCGATACACATGTATAA
127 ATACTTTTATTCCAGTATGCATCTCAAACAATTTGCACGCACAAAGTATTGATACACATGTATAA
10181 AGTATC
192 AGTATC
* * *
10187 GATACATGGAATTTCGAAACGATTACTTTAAAGTTATAAGTAAATTTACAATGTAAACGGTAAAA
1 GATACATAGAATTTCGAAACGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAA
10252 CCAATTGAAC
Statistics
Matches: 406, Mismatches: 42, Indels: 32
0.85 0.09 0.07
Matches are distributed among these distances:
197 51 0.13
198 48 0.12
199 155 0.38
200 92 0.23
201 27 0.07
202 33 0.08
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (197 bp):
GATACATAGAATTTCGAAACGATTACTTTAAAGTAATAGGTAAATTTACAATGTAAACGGTAAAA
ATCTACCGGTTTAATGATAATAGGCGTAAACATAAAGTATCGATACTTTATATAAGTATCGATAC
TTTTATTCCAGTATGCATCTCAAACAATTTGCACGCACAAAGTATTGATACACATGTATAAAGTA
TC
Found at i:11124 original size:2 final size:2
Alignment explanation
Indices: 11112--11154 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
11102 ATTGTTATTG
11112 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11153 AT
1 AT
11155 TAAACAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15556 original size:21 final size:22
Alignment explanation
Indices: 15532--15575 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
15522 TCTTATGTGC
**
15532 TATGTAAAGTATATATGA-ATA
1 TATGTAAACAATATATGACATA
15553 TATGTAAACAATATATGACATA
1 TATGTAAACAATATATGACATA
15575 T
1 T
15576 GTATATGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.48, C:0.05, G:0.11, T:0.36
Consensus pattern (22 bp):
TATGTAAACAATATATGACATA
Found at i:15939 original size:23 final size:23
Alignment explanation
Indices: 15909--15975 Score: 100
Period size: 23 Copynumber: 2.9 Consensus size: 23
15899 GAGTTGAGGG
*
15909 TCTACGTGGTCCTTC-AGGATAAT
1 TCTACGTGGTCCTTCGA-GACAAT
15932 TCTACGTGGTCCTTCGAGACAAT
1 TCTACGTGGTCCTTCGAGACAAT
*
15955 TCTACGTGGTCCTTCGGGACA
1 TCTACGTGGTCCTTCGAGACA
15976 TATATGTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.24, T:0.31
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGAGACAAT
Found at i:16898 original size:11 final size:11
Alignment explanation
Indices: 16884--16915 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
16874 ATTTTACGAA
16884 AGTATTGTAGC
1 AGTATTGTAGC
16895 AGTATTGTAGC
1 AGTATTGTAGC
16906 AGTATTGTAG
1 AGTATTGTAG
16916 TAGGGTATCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (11 bp):
AGTATTGTAGC
Found at i:20926 original size:18 final size:18
Alignment explanation
Indices: 20905--20960 Score: 112
Period size: 18 Copynumber: 3.1 Consensus size: 18
20895 GATAAAGGAG
20905 TTAGAGAAGATTAAAGAT
1 TTAGAGAAGATTAAAGAT
20923 TTAGAGAAGATTAAAGAT
1 TTAGAGAAGATTAAAGAT
20941 TTAGAGAAGATTAAAGAT
1 TTAGAGAAGATTAAAGAT
20959 TT
1 TT
20961 GGAGTTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (18 bp):
TTAGAGAAGATTAAAGAT
Found at i:23103 original size:22 final size:22
Alignment explanation
Indices: 23066--23175 Score: 141
Period size: 22 Copynumber: 5.0 Consensus size: 22
23056 TACGGAAGTA
* *
23066 CTGTAGCA-GGGTATCGATTCC
1 CTGTAGCAGGGGAATCGGTTCC
* * *
23087 CTGTAACAAGGGAATCGGTTCT
1 CTGTAGCAGGGGAATCGGTTCC
*
23109 GTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
*
23131 GTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
*
23153 CTGTAGCAGGGGAATCAGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
23175 C
1 C
23176 CTCTTTGAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
21 7 0.09
22 71 0.91
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGGTTCC
Found at i:23505 original size:22 final size:22
Alignment explanation
Indices: 23461--23505 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
23451 ATAAAATAAG
* *
23461 TATTTAAATTTTATTAATTTTT
1 TATTTAAATTTTATAAATATTT
23483 TATTTAAATATTTA-AAATATTT
1 TATTTAAAT-TTTATAAATATTT
23505 T
1 T
23506 GATCAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTAAATTTTATAAATATTT
Found at i:28325 original size:30 final size:30
Alignment explanation
Indices: 28281--28359 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
28271 TTAAGGGATT
* *
28281 AAATAGCAAAAAACAGAAATTTAAAGTACCA
1 AAATAGC-ATAAACAGAAATTTAAAGGACCA
* **
28312 AAATAGCATAAACATAAATTTAAAGGATTA
1 AAATAGCATAAACAGAAATTTAAAGGACCA
* *
28342 AAATAGTATTAACAGAAA
1 AAATAGCATAAACAGAAA
28360 CTAGAAGGAT
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 33 0.82
31 7 0.17
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.22
Consensus pattern (30 bp):
AAATAGCATAAACAGAAATTTAAAGGACCA
Found at i:29741 original size:3 final size:3
Alignment explanation
Indices: 29735--29788 Score: 90
Period size: 3 Copynumber: 17.7 Consensus size: 3
29725 ATTATTATTT
*
29735 ATA ATAA ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
29781 ATA ATA AT
1 ATA ATA AT
29789 TATTATTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30122 original size:43 final size:47
Alignment explanation
Indices: 30023--30125 Score: 142
Period size: 47 Copynumber: 2.3 Consensus size: 47
30013 ATAACACAGT
* **
30023 TCCTACGTGATGAGGACGACTGGTTATCTAAAGGATGATGACACGGT
1 TCCTACGTGATGAGGACGACTGATTATCTAAAGGATGATGACACGAC
*
30070 TCCTACGTGATGAGGACGACTGATTATCT-GA-GA-G-TGACACGAC
1 TCCTACGTGATGAGGACGACTGATTATCTAAAGGATGATGACACGAC
30113 TCCTACGTGATGA
1 TCCTACGTGATGA
30126 AGAGATCTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
43 20 0.38
44 1 0.02
45 2 0.04
46 1 0.02
47 28 0.54
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (47 bp):
TCCTACGTGATGAGGACGACTGATTATCTAAAGGATGATGACACGAC
Found at i:30158 original size:40 final size:42
Alignment explanation
Indices: 30016--30165 Score: 128
Period size: 47 Copynumber: 3.5 Consensus size: 42
30006 AGGGATGATA
* * *
30016 ACACAGTTCCTACGTGATGAGGACGACTGGTTATCTAAAGGATGATG
1 ACACGGTTCCTACGTGATGAAGACGACT-G-TATCT-GA-GA-GATG
*
30063 ACACGGTTCCTACGTGATGAGGACGACTGATTATCTGAGAG-TG
1 ACACGGTTCCTACGTGATGAAGACGACTG--TATCTGAGAGATG
** * *
30106 ACACGACTCCTACGTGATGAAGA-GATCTG-GTC-GAGGGATG
1 ACACGGTTCCTACGTGATGAAGACGA-CTGTATCTGAGAGATG
30146 ACACGGTTCCTACGTGATGA
1 ACACGGTTCCTACGTGATGA
30166 GGATGACATG
Statistics
Matches: 91, Mismatches: 9, Indels: 13
0.81 0.08 0.12
Matches are distributed among these distances:
39 4 0.04
40 22 0.24
42 2 0.02
43 25 0.27
44 1 0.01
45 2 0.02
46 2 0.02
47 33 0.36
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (42 bp):
ACACGGTTCCTACGTGATGAAGACGACTGTATCTGAGAGATG
Found at i:30228 original size:131 final size:130
Alignment explanation
Indices: 30016--30267 Score: 328
Period size: 131 Copynumber: 1.9 Consensus size: 130
30006 AGGGATGATA
** * **
30016 ACACAGTTCCTACGTGATGAGGACGACTGGTTATCTAAAGGATGATGACACGGTTCCTACGTGAT
1 ACACAGTTCCTACGTGATGAGGACGACTGGCCATCTAAAGGATGATAACACAATTCCTACGTGAT
* *
30081 GAGGACGACTGATTATCTGAGAG-TGACACGACTCCTACGTGATGAAGAGATCTGGTCGAGGGAT
66 GAGGACGACTGATTATCTAAG-GTTGACACGACTCCTACATGATGAAGAGATCTGGTCGAGGGAT
30145 G
130 G
* * * *
30146 ACACGGTTCCTACGTGATGAGGATGACAT-GCCATCATTAGGGATGATAACACAATTCCTACGTG
1 ACACAGTTCCTACGTGATGAGGACGAC-TGGCCATC-TAAAGGATGATAACACAATTCCTACGTG
* * * *
30210 ATGAGGACGGCTGGTTATCTAAGGTTGACACGGCTCCTACATGATGAGGAGATCTGGT
64 ATGAGGACGACTGATTATCTAAGGTTGACACGACTCCTACATGATGAAGAGATCTGGT
30268 GGTGGATGAC
Statistics
Matches: 104, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
130 30 0.29
131 74 0.71
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (130 bp):
ACACAGTTCCTACGTGATGAGGACGACTGGCCATCTAAAGGATGATAACACAATTCCTACGTGAT
GAGGACGACTGATTATCTAAGGTTGACACGACTCCTACATGATGAAGAGATCTGGTCGAGGGATG
Found at i:30249 original size:43 final size:43
Alignment explanation
Indices: 30016--30267 Score: 167
Period size: 43 Copynumber: 5.7 Consensus size: 43
30006 AGGGATGATA
*
30016 ACACAGTTCCTACGTGATGAGGACGACTGGTTATCTAAAGGATGATG
1 ACACGGTTCCTACGTGATGAGGACGACTGGTTATCT-AAGG-T--TG
* *
30063 ACACGGTTCCTACGTGATGAGGACGACTGATTATCTGAGAG-TG
1 ACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAG-GTTG
** * * * *
30106 ACACGACTCCTACGTGATGAAGA-GATCTGG---TCGAGGGATG
1 ACACGGTTCCTACGTGATGAGGACGA-CTGGTTATCTAAGGTTG
* ** * *
30146 ACACGGTTCCTACGTGATGAGGATGACAT-GCCATCATTAGGGATGATA
1 ACACGGTTCCTACGTGATGAGGACGAC-TGGTTATC--TAAGG-T--TG
** *
30194 ACACAATTCCTACGTGATGAGGACGGCTGGTTATCTAAGGTTG
1 ACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTG
* *
30237 ACACGGCTCCTACATGATGAGGA-GATCTGGT
1 ACACGGTTCCTACGTGATGAGGACGA-CTGGT
30268 GGTGGATGAC
Statistics
Matches: 161, Mismatches: 29, Indels: 34
0.72 0.13 0.15
Matches are distributed among these distances:
39 1 0.01
40 27 0.17
41 3 0.02
42 3 0.02
43 52 0.32
45 5 0.03
46 6 0.04
47 36 0.22
48 28 0.17
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (43 bp):
ACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGTTG
Found at i:36941 original size:25 final size:25
Alignment explanation
Indices: 36913--36979 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
36903 TAACTTAAAA
*
36913 AAACCCTAAACCAGACCTGAACCCT
1 AAACCCTAAACCAGACCTAAACCCT
* ** * *
36938 AAACCTTAAACTTGATCTAAACCTT
1 AAACCCTAAACCAGACCTAAACCCT
*
36963 AAACCCTAAACCCGACC
1 AAACCCTAAACCAGACC
36980 CGACCGAATA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.36, G:0.06, T:0.18
Consensus pattern (25 bp):
AAACCCTAAACCAGACCTAAACCCT
Found at i:42260 original size:14 final size:14
Alignment explanation
Indices: 42241--42284 Score: 88
Period size: 14 Copynumber: 3.1 Consensus size: 14
42231 GTCGCCAATG
42241 CTTCCACCTGCCTT
1 CTTCCACCTGCCTT
42255 CTTCCACCTGCCTT
1 CTTCCACCTGCCTT
42269 CTTCCACCTGCCTT
1 CTTCCACCTGCCTT
42283 CT
1 CT
42285 AATTAAATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.07, C:0.50, G:0.07, T:0.36
Consensus pattern (14 bp):
CTTCCACCTGCCTT
Found at i:42921 original size:31 final size:29
Alignment explanation
Indices: 42858--42932 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 29
42848 TTCATTCAAG
*
42858 TACCTAAAGTATTTTTTTATCAAAATAAA
1 TACCTAAAGTATTTTTTAATCAAAATAAA
* * *
42887 TACCTAAAGTTATCTTTTTAATTAAACTAGA
1 TACCTAAAG-TAT-TTTTTAATCAAAATAAA
*
42918 TACCTAAAATATTTT
1 TACCTAAAGTATTTT
42933 ATGCCAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 12 0.31
30 6 0.15
31 21 0.54
ACGTcount: A:0.41, C:0.12, G:0.04, T:0.43
Consensus pattern (29 bp):
TACCTAAAGTATTTTTTAATCAAAATAAA
Found at i:43116 original size:31 final size:31
Alignment explanation
Indices: 43065--43140 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
43055 TTTGACCAAG
*
43065 AAATACTTTAAGTACCTATTTTGA-TAAAAA
1 AAATACTTTAAGTACCTATTTGGACTAAAAA
*
43095 AAATAACTTT-AGATACTTATTTGGACT-AAAA
1 AAAT-ACTTTAAG-TACCTATTTGGACTAAAAA
*
43126 AAATACTTCAAGTAC
1 AAATACTTTAAGTAC
43141 TTAAATGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 13 0.33
31 25 0.64
32 1 0.03
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.34
Consensus pattern (31 bp):
AAATACTTTAAGTACCTATTTGGACTAAAAA
Found at i:46934 original size:19 final size:19
Alignment explanation
Indices: 46899--46937 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
46889 CAATTAATGA
*
46899 TTTTTATCTAACTATAAAT
1 TTTTTATCTAACAATAAAT
46918 TTTTTATCTTAA-AATAAAT
1 TTTTTATC-TAACAATAAAT
46937 T
1 T
46938 CTTAAAGACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTTTATCTAACAATAAAT
Found at i:46964 original size:2 final size:2
Alignment explanation
Indices: 46957--46988 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
46947 TTAAATGCTT
46957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46989 CCTGTGTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50706 original size:18 final size:20
Alignment explanation
Indices: 50685--50730 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
50675 CAATTATGTC
50685 TTTATTTTATTTTA-TAT-T
1 TTTATTTTATTTTATTATCT
*
50703 TTTAATTT-TTTTATTATCT
1 TTTATTTTATTTTATTATCT
*
50722 TTTGTTTTA
1 TTTATTTTA
50731 ATTGTTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
17 5 0.23
18 10 0.45
19 7 0.32
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTATTTTATTTTATTATCT
Found at i:50769 original size:22 final size:22
Alignment explanation
Indices: 50689--50773 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 22
50679 TATGTCTTTA
* *
50689 TTTTATTTTATATTTTTAATTT
1 TTTTATTTTATAGTTTTAATTG
* *
50711 TTTTATTATCTTTTGTTTTAATTG
1 TTTTATT-T-TATAGTTTTAATTG
* *
50735 --TTAGTTGAT--TTTTAATTG
1 TTTTATTTTATAGTTTTAATTG
50753 TTTTATTTTATAGTTTTAATT
1 TTTTATTTTATAGTTTTAATT
50774 CTAAATTTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
18 9 0.19
20 8 0.17
21 1 0.02
22 19 0.40
23 1 0.02
24 10 0.21
ACGTcount: A:0.21, C:0.01, G:0.07, T:0.71
Consensus pattern (22 bp):
TTTTATTTTATAGTTTTAATTG
Found at i:53779 original size:32 final size:31
Alignment explanation
Indices: 53710--53785 Score: 125
Period size: 31 Copynumber: 2.4 Consensus size: 31
53700 ATCAAGTTCA
*
53710 TTAAGGGTAAATCAGTATAGATATTTTAATT
1 TTAAGGGTAAATTAGTATAGATATTTTAATT
*
53741 TCAAGGGTAAATTAGTATAGATATTTTTAATT
1 TTAAGGGTAAATTAGTATAGATA-TTTTAATT
53773 TTAAGGGTAAATT
1 TTAAGGGTAAATT
53786 GGTAATTTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 21 0.51
32 20 0.49
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (31 bp):
TTAAGGGTAAATTAGTATAGATATTTTAATT
Found at i:55591 original size:21 final size:21
Alignment explanation
Indices: 55564--55632 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
55554 ATATGATAGG
55564 TCCTTCGGGACATAGATGACA
1 TCCTTCGGGACATAGATGACA
*
55585 ACCTTCGGG--ATA-AT-A-A
1 TCCTTCGGGACATAGATGACA
*
55601 GTCCTTCGGGACACAGATGACA
1 -TCCTTCGGGACATAGATGACA
55623 TCCTTCGGGA
1 TCCTTCGGGA
55633 TGATAGGTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
16 1 0.03
17 9 0.23
18 2 0.05
19 5 0.13
20 2 0.05
21 19 0.49
22 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.23
Consensus pattern (21 bp):
TCCTTCGGGACATAGATGACA
Found at i:55611 original size:38 final size:39
Alignment explanation
Indices: 55546--55656 Score: 136
Period size: 38 Copynumber: 2.9 Consensus size: 39
55536 TTACATATGT
* *
55546 CCTTCGGGATATGATAGGTCCTTCGGGACATAGATGACAA
1 CCTTCGGGATA-GATAAGTCCTTCGGGACACAGATGACAA
*
55586 CCTTCGGGATA-ATAAGTCCTTCGGGACACAGATGACAT
1 CCTTCGGGATAGATAAGTCCTTCGGGACACAGATGACAA
* * * *
55624 CCTTCGGGAT-GATAGGTTCTTCGAGATACAGAT
1 CCTTCGGGATAGATAAGTCCTTCGGGACACAGAT
55657 TTCACATGCC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
38 52 0.83
40 11 0.17
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (39 bp):
CCTTCGGGATAGATAAGTCCTTCGGGACACAGATGACAA
Found at i:57630 original size:52 final size:54
Alignment explanation
Indices: 57573--57681 Score: 186
Period size: 53 Copynumber: 2.1 Consensus size: 54
57563 AATTACATTG
* *
57573 TTTTCATGT-AATAAGGTTAATCCTGAATACTC-TTCCCCCTGAGGATACCTCT
1 TTTTCATGTAAATAAGGTTAATCCTGAATACTCGTCCCCCCTAAGGATACCTCT
57625 TTTTCATGTAAATAAGGTTAATCCTGAATACTCGTCCCCCCTAAGGATACCTCT
1 TTTTCATGTAAATAAGGTTAATCCTGAATACTCGTCCCCCCTAAGGATACCTCT
57679 TTT
1 TTT
57682 ACAAAGACTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
52 9 0.17
53 23 0.43
54 21 0.40
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.37
Consensus pattern (54 bp):
TTTTCATGTAAATAAGGTTAATCCTGAATACTCGTCCCCCCTAAGGATACCTCT
Found at i:58028 original size:30 final size:28
Alignment explanation
Indices: 57994--58064 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 28
57984 AGAAGAAATG
57994 ATATAGAAAAGGAAAATAGAAAAAGGAAAA
1 ATATAGAAAAGGAAAA-AGAAAAAGG-AAA
58024 ATATAGAAAAGG--AAA-AAAAAGGAAA
1 ATATAGAAAAGGAAAAAGAAAAAGGAAA
58049 ATATAG-AAAGGAAAAA
1 ATATAGAAAAGGAAAAA
58065 AAGAAAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
24 5 0.13
25 9 0.23
26 10 0.26
27 1 0.03
28 2 0.05
30 12 0.31
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (28 bp):
ATATAGAAAAGGAAAAAGAAAAAGGAAA
Found at i:58035 original size:16 final size:16
Alignment explanation
Indices: 57994--58040 Score: 71
Period size: 15 Copynumber: 3.1 Consensus size: 16
57984 AGAAGAAATG
57994 ATATAGAAAAGG-AAA
1 ATATAGAAAAGGAAAA
*
58009 ATAGA-AAAAGGAAAA
1 ATATAGAAAAGGAAAA
58024 ATATAGAAAAGGAAAA
1 ATATAGAAAAGGAAAA
58040 A
1 A
58041 AAAGGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 6 0.21
15 11 0.39
16 11 0.39
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (16 bp):
ATATAGAAAAGGAAAA
Found at i:58048 original size:16 final size:16
Alignment explanation
Indices: 57998--58049 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
57988 GAAATGATAT
*
57998 AGAAAAGG-AAAATAG
1 AGAAAAGGAAAAATAA
*
58013 A-AAAAGGAAAAATAT
1 AGAAAAGGAAAAATAA
58028 AGAAAAGGAAAAA-AA
1 AGAAAAGGAAAAATAA
58043 AGGAAAA
1 A-GAAAA
58050 TATAGAAAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.19
15 10 0.31
16 16 0.50
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (16 bp):
AGAAAAGGAAAAATAA
Found at i:58058 original size:24 final size:26
Alignment explanation
Indices: 57994--58066 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 26
57984 AGAAGAAATG
57994 ATATAGAAAAGGAAAATAGAAAAAGGAAAA
1 ATATAGAAAAGG--AA-A-AAAAAGGAAAA
58024 ATATAGAAAAGGAAAAAAAAGG-AAA
1 ATATAGAAAAGGAAAAAAAAGGAAAA
58049 ATATAG-AAAGGAAAAAAA
1 ATATAGAAAAGGAAAAAAA
58067 GAAAAAAAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.28
25 9 0.21
26 7 0.16
27 1 0.02
28 2 0.05
30 12 0.28
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (26 bp):
ATATAGAAAAGGAAAAAAAAGGAAAA
Found at i:58072 original size:8 final size:8
Alignment explanation
Indices: 58059--58101 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
58049 ATATAGAAAG
58059 GAAAAAAA
1 GAAAAAAA
58067 GAAAAAAA
1 GAAAAAAA
58075 GCAGAAAAAA
1 G-A-AAAAAA
*
58085 GAATAAAA
1 GAAAAAAA
58093 GAAATAAAA
1 GAAA-AAAA
58102 ATGAGAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 17 0.57
9 6 0.20
10 7 0.23
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (8 bp):
GAAAAAAA
Found at i:58073 original size:24 final size:25
Alignment explanation
Indices: 58013--58138 Score: 87
Period size: 24 Copynumber: 4.8 Consensus size: 25
58003 AGGAAAATAG
*
58013 AAAAAGGAAAAATATAGAAAAGGAA
1 AAAAAGAAAAAATATAGAAAAGGAA
*
58038 AAAAA-AGGAAAATATAG-AAAGGAA
1 AAAAAGA-AAAAATATAGAAAAGGAA
* *
58062 AAAAAGAAAAAA-AGCAGAAAAAAGAA
1 AAAAAGAAAAAATA-TAG-AAAAGGAA
* *
58088 TAAAAGAAATAAAAATGAGAGAGAAGGAA
1 AAAAAGAAA-AAATAT-AGA-A-AAGGAA
* *
58117 AAAGAAGAAAGAATAAAGAAAA
1 AAA-AAGAAAAAATATAGAAAA
58139 AAATCCAACA
Statistics
Matches: 78, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
23 1 0.01
24 18 0.23
25 15 0.19
26 16 0.21
27 5 0.06
28 7 0.09
29 10 0.13
30 6 0.08
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (25 bp):
AAAAAGAAAAAATATAGAAAAGGAA
Found at i:58074 original size:25 final size:25
Alignment explanation
Indices: 57994--58074 Score: 83
Period size: 25 Copynumber: 3.0 Consensus size: 25
57984 AGAAGAAATG
57994 ATATAGAAAAGGAAAATAGAAAAAGGAAAA
1 ATATAGAAAAGG-AAA-A-AAAAA--AAAA
**
58024 ATATAGAAAAGGAAAAAAAAGGAAA
1 ATATAGAAAAGGAAAAAAAAAAAAA
58049 ATATAG-AAAGGAAAAAAAGAAAAAA
1 ATATAGAAAAGGAAAAAAA-AAAAAA
58074 A
1 A
58075 GCAGAAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
24 12 0.26
25 14 0.30
27 4 0.09
28 1 0.02
29 3 0.07
30 12 0.26
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.09
Consensus pattern (25 bp):
ATATAGAAAAGGAAAAAAAAAAAAA
Found at i:58075 original size:17 final size:17
Alignment explanation
Indices: 58055--58141 Score: 57
Period size: 18 Copynumber: 4.7 Consensus size: 17
58045 GAAAATATAG
58055 AAAGGAAAAAAAGAAAA
1 AAAGGAAAAAAAGAAAA
* *
58072 AAAGCAGAAAAAAGAATA
1 AAAGGA-AAAAAAGAAAA
* *
58090 AAAGAAATAAAAATGAGAGA
1 AAAGGAA-AAAAA-GA-AAA
*
58110 GAAGGAAAAAGAAGAAAGA
1 AAAGGAAAAA-AAGAAA-A
*
58129 ATAAAGAAAAAAA
1 A-AAGGAAAAAAA
58142 TCCAACACTT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
17 6 0.11
18 21 0.39
19 10 0.19
20 17 0.31
ACGTcount: A:0.75, C:0.01, G:0.20, T:0.05
Consensus pattern (17 bp):
AAAGGAAAAAAAGAAAA
Found at i:58083 original size:40 final size:40
Alignment explanation
Indices: 58000--58085 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
57990 AATGATATAG
* * * *
58000 AAAAGGAAAATAGAAAAAGGAAAAATATAGAAAAGGAAAA
1 AAAAGGAAAATAGAAAAAGGAAAAAAAGAAAAAAAGAAAA
* * *
58040 AAAAGGAAAATATAGAAAGGAAAAAAAGAAAAAAAGCAGAA
1 AAAAGGAAAATAGAAAAAGGAAAAAAAGAAAAAAAG-AAAA
58081 AAAAG
1 AAAAG
58086 AATAAAAGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 30 0.79
41 8 0.21
ACGTcount: A:0.73, C:0.01, G:0.20, T:0.06
Consensus pattern (40 bp):
AAAAGGAAAATAGAAAAAGGAAAAAAAGAAAAAAAGAAAA
Found at i:59809 original size:42 final size:42
Alignment explanation
Indices: 59715--59915 Score: 218
Period size: 41 Copynumber: 4.9 Consensus size: 42
59705 CAAGCTTGAT
* * * *
59715 GGACCAAC-TAATATTTA-GGGTTCCTTGATGATAATCTTGAG
1 GGACCAACGTGATATGTAGGGGTTCCTTGATGACAAT-TAGAG
*
59756 TGA-CAGACGTGATATGTAGGGGTTCCTTGATGACAATTAGAG
1 GGACCA-ACGTGATATGTAGGGGTTCCTTGATGACAATTAGAG
* * * *
59798 GGACTAACGTGATATGTA-GGGTTCCTTAATGATAGCTT-GAG
1 GGACCAACGTGATATGTAGGGGTTCCTTGATGACA-ATTAGAG
59839 GGACCAACGTGATATGTAGGGGGTT-CTTGATGACAATTAGAG
1 GGACCAACGTGATATGTA-GGGGTTCCTTGATGACAATTAGAG
* *
59881 GGACCAACGTGACATATAGGGG-TCCTTGATGACAA
1 GGACCAACGTGATATGTAGGGGTTCCTTGATGACAA
59916 CTATAAGATT
Statistics
Matches: 135, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
40 3 0.02
41 55 0.41
42 54 0.40
43 23 0.17
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (42 bp):
GGACCAACGTGATATGTAGGGGTTCCTTGATGACAATTAGAG
Found at i:59872 original size:83 final size:84
Alignment explanation
Indices: 59715--59912 Score: 269
Period size: 83 Copynumber: 2.4 Consensus size: 84
59705 CAAGCTTGAT
* * * *
59715 GGACCAAC-TAATATTTAGGGTTCCTTGATGATAATCTTGAGTGACAGACGTGATATGTAGGGGT
1 GGACCAACGTGATATATAGGGTTCCTTGATGATAAGCTTGAGGGACAGACGTGATATGTAGGGGT
59779 TCCTTGATGACAATTAGAG
66 TCCTTGATGACAATTAGAG
* * *
59798 GGACTAACGTGATATGTAGGGTTCCTTAATGAT-AGCTTGAGGGACCA-ACGTGATATGTAGGGG
1 GGACCAACGTGATATATAGGGTTCCTTGATGATAAGCTTGAGGGA-CAGACGTGATATGTA-GGG
59861 GTT-CTTGATGACAATTAGAG
64 GTTCCTTGATGACAATTAGAG
* *
59881 GGACCAACGTGACATATAGGGGTCCTTGATGA
1 GGACCAACGTGATATATAGGGTTCCTTGATGA
59913 CAACTATAAG
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
83 72 0.71
84 29 0.29
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (84 bp):
GGACCAACGTGATATATAGGGTTCCTTGATGATAAGCTTGAGGGACAGACGTGATATGTAGGGGT
TCCTTGATGACAATTAGAG
Found at i:59915 original size:41 final size:41
Alignment explanation
Indices: 59715--59915 Score: 210
Period size: 42 Copynumber: 4.9 Consensus size: 41
59705 CAAGCTTGAT
* * * * *
59715 GGACCAAC-TAATATTTAGGGTTCCTTGATGATAATCTTGAG
1 GGACCAACGTGATATGTAGGGGTCCTTGATGACAAT-TAGAG
*
59756 TGA-CAGACGTGATATGTAGGGGTTCCTTGATGACAATTAGAG
1 GGACCA-ACGTGATATGTAGGGG-TCCTTGATGACAATTAGAG
* * * * *
59798 GGACTAACGTGATATGTAGGGTTCCTTAATGATAGCTT-GAG
1 GGACCAACGTGATATGTAGGGGTCCTTGATGACA-ATTAGAG
*
59839 GGACCAACGTGATATGTAGGGGGTTCTTGATGACAATTAGAG
1 GGACCAACGTGATATGTA-GGGGTCCTTGATGACAATTAGAG
* *
59881 GGACCAACGTGACATATAGGGGTCCTTGATGACAA
1 GGACCAACGTGATATGTAGGGGTCCTTGATGACAA
59916 CTATAAGATT
Statistics
Matches: 132, Mismatches: 21, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
40 2 0.02
41 52 0.39
42 64 0.48
43 14 0.11
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (41 bp):
GGACCAACGTGATATGTAGGGGTCCTTGATGACAATTAGAG
Found at i:60265 original size:41 final size:42
Alignment explanation
Indices: 60207--60311 Score: 133
Period size: 41 Copynumber: 2.5 Consensus size: 42
60197 CAATGGTTTC
* * *
60207 TGATGAGTAAGTACTTCGGGCCATC-GTAAGTATGTCGAGCA
1 TGATGCGTAAGTCCTTCGGGCCATCTATAAGTATGTCGAGCA
* *
60248 TGATGCGTAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCA
1 TGATGCGTAAGTCCTTCGGGCCATCTATAAGTATGTCGAGCA
* *
60290 AGAT-CATAAGTCCTTCGGGCCA
1 TGATGCGTAAGTCCTTCGGGCCA
60312 GCCTAAGACC
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 40 0.71
42 16 0.29
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (42 bp):
TGATGCGTAAGTCCTTCGGGCCATCTATAAGTATGTCGAGCA
Found at i:60280 original size:20 final size:19
Alignment explanation
Indices: 60255--60311 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
60245 GCATGATGCG
60255 TAAGTCCTTCGGGCCATCTA
1 TAAGTCCTTCGGGCCATC-A
* * *
60275 TAAGTCTTTCGAGCAAGATCA
1 TAAGTCCTTCGGGC--CATCA
60296 TAAGTCCTTCGGGCCA
1 TAAGTCCTTCGGGCCA
60312 GCCTAAGACC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 1 0.03
20 12 0.41
21 13 0.45
22 3 0.10
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (19 bp):
TAAGTCCTTCGGGCCATCA
Found at i:61149 original size:127 final size:126
Alignment explanation
Indices: 60923--61168 Score: 311
Period size: 127 Copynumber: 1.9 Consensus size: 126
60913 AGAGATTGTT
* * * *
60923 CAACTGTTTGCTCGAATCTATCACAGAAGAGGTAGACCAGCACGATATCTCGTTCGATTCCATCA
1 CAACTGTTTGCTCGAATCTATCACAAAAGAGGTAGACCAACACAATATCTCGTTCAATTCCATCA
** *
60988 CGGTAGGAGGTGGATCGACTTTTATTTTCGCTCAAATTCATCAACAAAAGGAGTTTGATCAG
66 CGAAAGGAGGTGGATCGACTTTTATTTTCGCTCAAATCCATC-ACAAAAGGAGTTTGATCAG
* * *
61050 CAACT-TTTAGCTCGATTCTAT-ACAAAAGGAGGTAGATCAACACCAAT-TCTTGTTCAATTCCA
1 CAACTGTTT-GCTCGAATCTATCACAAAA-GAGGTAGACCAACA-CAATATCTCGTTCAATTCCA
* *
61112 TCAC-AAAGGAGGTGGATCGACATTTTATTTTCTCTCAAATCCATCGCAAAAGGAGTT
63 TCACGAAAGGAGGTGGATCGAC-TTTTATTTTCGCTCAAATCCATCACAAAAGGAGTT
61169 GGAT
Statistics
Matches: 103, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
126 34 0.33
127 66 0.64
128 3 0.03
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (126 bp):
CAACTGTTTGCTCGAATCTATCACAAAAGAGGTAGACCAACACAATATCTCGTTCAATTCCATCA
CGAAAGGAGGTGGATCGACTTTTATTTTCGCTCAAATCCATCACAAAAGGAGTTTGATCAG
Done.