Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000051.1 Hibiscus syriacus cultivar Beakdansim tig00000078_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: 190034
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Found at i:2025 original size:11 final size:12
Alignment explanation
Indices: 2004--2032 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1994 CACTCAACTT
2004 AAAACAGACTAA
1 AAAACAGACTAA
2016 AAAACA-ACTAA
1 AAAACAGACTAA
2027 AAAACA
1 AAAACA
2033 TCATTACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.72, C:0.17, G:0.03, T:0.07
Consensus pattern (12 bp):
AAAACAGACTAA
Found at i:16655 original size:111 final size:109
Alignment explanation
Indices: 16498--16764 Score: 342
Period size: 111 Copynumber: 2.4 Consensus size: 109
16488 TAATGTAAGT
* * * *
16498 GGTTAAAAATAACAA-TCACAACTGTTAACGTTACTCCTACTTATAAGGTAACCGATACAAAACA
1 GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACA
* * * *
16562 AAACAA-GACTCAACTGTAAACATTACTCATATTTTAATAAGGTAACC
66 AAACAATG-CGCAACCGTAAACATTACTCAT-GTTT-AT-AGGTAACA
* *
16609 GGTTAAAAATGA-AAGGCGCAACCGTTAACGTTACTCCTACTCATAAGGTAACCGATAAAAAACA
1 GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACA
* * *
16673 AAACAATGCGCAACCGTAAACGTTACTCCTGTTTGTAGGTAACA
66 AAACAATGCGCAACCGTAAACATTACTCATGTTTATAGGTAACA
* *
16717 TGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCTTACTTATAAG
1 GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAG
16765 TTGTGCAATC
Statistics
Matches: 136, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
108 17 0.12
109 34 0.25
110 5 0.04
111 79 0.58
112 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (109 bp):
GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACA
AAACAATGCGCAACCGTAAACATTACTCATGTTTATAGGTAACA
Found at i:16662 original size:53 final size:54
Alignment explanation
Indices: 16498--16764 Score: 225
Period size: 56 Copynumber: 4.9 Consensus size: 54
16488 TAATGTAAGT
* * *
16498 GGTTAAAAATAACAA-TCACAACTGTTAACGTTACTCCTACTTATAAGGTAACC
1 GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACC
* * * * * * * * * *
16551 GATACAAAACAAAACAAGACTCAACTGTAAACATTACTCATATTTTAATAAGGTAACC
1 GGT-TAAAA-ATAACAAGGCGCAACCGTTAACGTTACTCCTA-CTT-ATAAGGTAACC
* *
16609 GGTTAAAAATGA-AAGGCGCAACCGTTAACGTTACTCCTACTCATAAGGTAACC
1 GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACC
* * * * * ** * *
16662 GATAAAAAACAAAACAATGCGCAACCGTAAACGTTACTCCTGTTTGT-AGGTAACA
1 GGT-TAAAA-ATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACC
* *
16717 TGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCTTACTTATAAG
1 GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAG
16765 TTGTGCAATC
Statistics
Matches: 163, Mismatches: 42, Indels: 17
0.73 0.19 0.08
Matches are distributed among these distances:
53 45 0.28
54 15 0.09
55 37 0.23
56 47 0.29
57 6 0.04
58 13 0.08
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (54 bp):
GGTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACC
Found at i:17038 original size:54 final size:54
Alignment explanation
Indices: 16873--17038 Score: 139
Period size: 56 Copynumber: 3.1 Consensus size: 54
16863 CGTAAATGTC
* * * * *
16873 ACTCCTACTTATAAGGTAACCAGTTAAAAATAACAA-GT--AGCCTATAATATT
1 ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAATATT
* * * * *
16924 ACTCTTAC--TTATGAGCTAACTGGTAAAAAACAA-AACCTGGTGCAACC-ATAAATGTT
1 ACTCATACTTTTATG-G-TAACCGGTTAAAAATAACAA---GGTGCAACCTAT-AATATT
16980 ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAATATT
1 ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAATATT
17034 ACTCA
1 ACTCA
17039 AGAATGTTAA
Statistics
Matches: 88, Mismatches: 14, Indels: 23
0.70 0.11 0.18
Matches are distributed among these distances:
49 3 0.03
50 3 0.03
51 20 0.23
54 21 0.24
55 4 0.05
56 29 0.33
57 3 0.03
58 5 0.06
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (54 bp):
ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAATATT
Found at i:17913 original size:18 final size:18
Alignment explanation
Indices: 17879--17914 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17869 CGATCCGTTT
*
17879 ACCCGACCCATTGACCCG
1 ACCCGACCCATTAACCCG
*
17897 ACCCGACCCGTTAACCCG
1 ACCCGACCCATTAACCCG
17915 TTGACCGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.50, G:0.17, T:0.11
Consensus pattern (18 bp):
ACCCGACCCATTAACCCG
Found at i:17929 original size:16 final size:15
Alignment explanation
Indices: 17904--17943 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
17894 CCGACCCGAC
*
17904 CCGTTAACCCGTTGA
1 CCGTTGACCCGTTGA
17919 CCGTTTGACCCGTTGA
1 CCG-TTGACCCGTTGA
17935 CCGTTGACC
1 CCGTTGACC
17944 GGAGTTGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.15, C:0.35, G:0.23, T:0.28
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:22681 original size:18 final size:18
Alignment explanation
Indices: 22658--22729 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
22648 ACCGGTCACA
*
22658 ACCCGACCCGATCCGTTG
1 ACCCGACCCGACCCGTTG
*
22676 ACCCGACCCGACCCGTTT
1 ACCCGACCCGACCCGTTG
22694 ACCCGACCC-A----TTG
1 ACCCGACCCGACCCGTTG
*
22707 ACCCGACCCGACCCGTTA
1 ACCCGACCCGACCCGTTG
22725 ACCCG
1 ACCCG
22730 TTGACCGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
13 11 0.24
14 1 0.02
17 1 0.02
18 32 0.71
ACGTcount: A:0.19, C:0.49, G:0.18, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:22708 original size:31 final size:31
Alignment explanation
Indices: 22663--22729 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
22653 TCACAACCCG
* * *
22663 ACCCGATCCGTTGACCCGACCCGACCCGTTT
1 ACCCGACCCATTGACCCGACCCGACCCGTTA
22694 ACCCGACCCATTGACCCGACCCGACCCGTTA
1 ACCCGACCCATTGACCCGACCCGACCCGTTA
22725 ACCCG
1 ACCCG
22730 TTGACCGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.19, C:0.48, G:0.18, T:0.15
Consensus pattern (31 bp):
ACCCGACCCATTGACCCGACCCGACCCGTTA
Found at i:22728 original size:8 final size:8
Alignment explanation
Indices: 22716--22757 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
22706 GACCCGACCC
22716 GACCCGTT
1 GACCCGTT
*
22724 AACCCGTT
1 GACCCGTT
22732 GA-CCGTT
1 GACCCGTT
22739 GACCCGTT
1 GACCCGTT
22747 GA-CCGTT
1 GACCCGTT
22754 GACC
1 GACC
22758 GGAGTTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 14 0.47
8 16 0.53
ACGTcount: A:0.17, C:0.36, G:0.24, T:0.24
Consensus pattern (8 bp):
GACCCGTT
Found at i:22729 original size:13 final size:13
Alignment explanation
Indices: 22680--22716 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
22670 CCGTTGACCC
22680 GACCCGACCCGTT
1 GACCCGACCCGTT
* *
22693 TACCCGACCCATT
1 GACCCGACCCGTT
22706 GACCCGACCCG
1 GACCCGACCCG
22717 ACCCGTTAAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:22739 original size:7 final size:7
Alignment explanation
Indices: 22727--22758 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
22717 ACCCGTTAAC
22727 CCGTTGA
1 CCGTTGA
22734 CCGTTGA
1 CCGTTGA
22741 CCCGTTGA
1 -CCGTTGA
22749 CCGTTGA
1 CCGTTGA
22756 CCG
1 CCG
22759 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:22743 original size:15 final size:15
Alignment explanation
Indices: 22719--22757 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
22709 CCGACCCGAC
*
22719 CCGTTAACCCGTTGA
1 CCGTTGACCCGTTGA
22734 CCGTTGACCCGTTGA
1 CCGTTGACCCGTTGA
22749 CCGTTGACC
1 CCGTTGACC
22758 GGAGTTGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.15, C:0.36, G:0.23, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCGTTGA
Found at i:26389 original size:2 final size:2
Alignment explanation
Indices: 26382--26416 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
26372 ATTAATGACA
26382 AT 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 AT A
26417 GGTAACTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29854 original size:27 final size:26
Alignment explanation
Indices: 29810--29867 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
29800 ATATCAAAAG
*
29810 TAAAAATCTAATCAAATTCATAAAAT-A
1 TAAAAATCTAAACAAATT--TAAAATAA
* *
29837 TAAAAATTTAAACGAATTTAAAATAA
1 TAAAAATCTAAACAAATTTAAAATAA
29863 TAAAA
1 TAAAA
29868 TTAAGTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.22
26 6 0.22
27 15 0.56
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (26 bp):
TAAAAATCTAAACAAATTTAAAATAA
Found at i:30122 original size:25 final size:24
Alignment explanation
Indices: 30075--30122 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
30065 TCTATGAGTA
30075 TTCAAATAATAAATAAATGATATT
1 TTCAAATAATAAATAAATGATATT
*
30099 TTCAAATTAA-AATATAAATTATAT
1 TTCAAA-TAATAA-ATAAATGATAT
30123 ATTTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TTCAAATAATAAATAAATGATATT
Found at i:30634 original size:14 final size:14
Alignment explanation
Indices: 30615--30691 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
30605 TTCAACCAAA
30615 GGCTCATATGTAAC
1 GGCTCATATGTAAC
* *
30629 GGCTCATA-GGAGC
1 GGCTCATATGTAAC
***
30642 CTATCATATGTAAC
1 GGCTCATATGTAAC
* *
30656 GGCTCATA-GGAGC
1 GGCTCATATGTAAC
***
30669 CTATCATATGTAAC
1 GGCTCATATGTAAC
30683 GGCTCATAT
1 GGCTCATAT
30692 TCAACCAATG
Statistics
Matches: 41, Mismatches: 20, Indels: 4
0.63 0.31 0.06
Matches are distributed among these distances:
13 16 0.39
14 25 0.61
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (14 bp):
GGCTCATATGTAAC
Found at i:30656 original size:27 final size:27
Alignment explanation
Indices: 30618--30690 Score: 146
Period size: 27 Copynumber: 2.7 Consensus size: 27
30608 AACCAAAGGC
30618 TCATATGTAACGGCTCATAGGAGCCTA
1 TCATATGTAACGGCTCATAGGAGCCTA
30645 TCATATGTAACGGCTCATAGGAGCCTA
1 TCATATGTAACGGCTCATAGGAGCCTA
30672 TCATATGTAACGGCTCATA
1 TCATATGTAACGGCTCATA
30691 TTCAACCAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (27 bp):
TCATATGTAACGGCTCATAGGAGCCTA
Found at i:31443 original size:2 final size:2
Alignment explanation
Indices: 31436--31462 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31426 CGTGATTCAT
31436 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
31463 AATCCATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31813 original size:11 final size:11
Alignment explanation
Indices: 31797--31869 Score: 53
Period size: 10 Copynumber: 6.9 Consensus size: 11
31787 AAGATGCTTG
*
31797 TTAATTTATTC
1 TTAATTTATTA
*
31808 TTAATTTA-AA
1 TTAATTTATTA
* *
31818 TTTATTTATTC
1 TTAATTTATTA
* *
31829 GTAATTTA-AA
1 TTAATTTATTA
* *
31839 TTAATATATTT
1 TTAATTTATTA
31850 TTAATTTA-TA
1 TTAATTTATTA
31860 TTAATTTATT
1 TTAATTTATT
31870 GTTGGTATTG
Statistics
Matches: 44, Mismatches: 15, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
10 22 0.50
11 22 0.50
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (11 bp):
TTAATTTATTA
Found at i:31824 original size:21 final size:21
Alignment explanation
Indices: 31797--31869 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
31787 AAGATGCTTG
31797 TTAATTTATTCTTAATTTAAA
1 TTAATTTATTCTTAATTTAAA
* *
31818 TTTATTTATTCGTAATTTAAA
1 TTAATTTATTCTTAATTTAAA
* * *
31839 TTAATATATTTTTAATTTATA
1 TTAATTTATTCTTAATTTAAA
31860 TTAATTTATT
1 TTAATTTATT
31870 GTTGGTATTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
TTAATTTATTCTTAATTTAAA
Found at i:32034 original size:21 final size:21
Alignment explanation
Indices: 32008--32066 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
31998 TTCAAAAAAA
*
32008 GAATTATATTAATCTATTCTT
1 GAATTATATTAATTTATTCTT
*
32029 GAATTAAATTAATTTATTCTT
1 GAATTATATTAATTTATTCTT
*
32050 -AGTTATATTAATTTATT
1 GAATTATATTAATTTATT
32067 GTTGGTATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (21 bp):
GAATTATATTAATTTATTCTT
Found at i:32179 original size:198 final size:198
Alignment explanation
Indices: 31834--32199 Score: 626
Period size: 197 Copynumber: 1.8 Consensus size: 198
31824 TATTCGTAAT
* * *
31834 TTAAATTAATATATTTTTAATTTATATTAATTTATTGTTGGTATTGTAATGTCATTGTTTCGGTG
1 TTAAATTAATATATTCTTAAGTTATATTAATTTATTGTTGGTATTGTAATGTCATCGTTTCGGTG
* *
31899 CACTTTTTTCCCTCCGATTAGGTGTAGGGAGGTTTTTTAACAGGCCCGATTCGATGTTTTGTTTT
66 CACTTTTTTCCCTCCAATTAGGTGTAGGGAGGTTTTGTAACAGGCCCGATTCGATGTTTTGTTTT
31964 GTATGCTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAAGAATTATATTAATCTATTCTT
131 GTATGCTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAAGAATTATATTAATCTATTCTT
32029 GAA
196 GAA
*
32032 TTAAATTAATTTATTCTT-AGTTATATTAATTTATTGTTGGTATTGTAATGTCATCGTTTCGGTG
1 TTAAATTAATATATTCTTAAGTTATATTAATTTATTGTTGGTATTGTAATGTCATCGTTTCGGTG
* * *
32096 CACTTTTTTTCCTCCAATTAGGTGTAGGGAGGTTTTGTAACGTGGCCCGATTTGATGTTTTGTTT
66 CACTTTTTTCCCTCCAATTAGGTGTAGGGAGGTTTTGTAAC-AGGCCCGATTCGATGTTTTGTTT
*
32161 TGTATGGTTTTTCTCTATCTATACAAAACACCCCTTTCA
130 TGTATGCTTTTTCTCTATCTATACAAAACACCCCTTTCA
32200 TTTTTTCTTA
Statistics
Matches: 157, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
197 82 0.52
198 75 0.48
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (198 bp):
TTAAATTAATATATTCTTAAGTTATATTAATTTATTGTTGGTATTGTAATGTCATCGTTTCGGTG
CACTTTTTTCCCTCCAATTAGGTGTAGGGAGGTTTTGTAACAGGCCCGATTCGATGTTTTGTTTT
GTATGCTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAAGAATTATATTAATCTATTCTT
GAA
Found at i:32234 original size:21 final size:21
Alignment explanation
Indices: 32208--32257 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
32198 CATTTTTTCT
*
32208 TAATTTATATTAAGTTATTCA
1 TAATTTATATTAACTTATTCA
* *
32229 TAATTTATGTTAACTTATTCT
1 TAATTTATATTAACTTATTCA
32250 TAATTTAT
1 TAATTTAT
32258 TCTTAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (21 bp):
TAATTTATATTAACTTATTCA
Found at i:32252 original size:11 final size:11
Alignment explanation
Indices: 32199--32268 Score: 72
Period size: 11 Copynumber: 6.5 Consensus size: 11
32189 CACCCCTTTC
*
32199 ATTTTTTCTTA
1 ATTTATTCTTA
*
32210 ATTTA-TATTA
1 ATTTATTCTTA
* *
32220 AGTTATTCATA
1 ATTTATTCTTA
*
32231 ATTTA-TGTTA
1 ATTTATTCTTA
*
32241 ACTTATTCTTA
1 ATTTATTCTTA
32252 ATTTATTCTTA
1 ATTTATTCTTA
32263 ATTTAT
1 ATTTAT
32269 ATTAATATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
10 15 0.33
11 31 0.67
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (11 bp):
ATTTATTCTTA
Found at i:34051 original size:21 final size:21
Alignment explanation
Indices: 34018--34068 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
34008 AAAAGCATTG
34018 TTAATTT-TTCTTGAATTATA
1 TTAATTTATTCTTGAATTATA
34038 TTAATTTATTCTTGAATTATA
1 TTAATTTATTCTTGAATTATA
*
34059 TAAATTTATT
1 TTAATTTATT
34069 TAAAATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 7 0.24
21 22 0.76
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (21 bp):
TTAATTTATTCTTGAATTATA
Found at i:39916 original size:92 final size:91
Alignment explanation
Indices: 39754--39936 Score: 330
Period size: 92 Copynumber: 2.0 Consensus size: 91
39744 GTTAAAAAGG
* *
39754 ATCACGATGTGCAATATATCTGATAATGACCTTGCTCTGTCACTTCATCACGGATATTCATGCAT
1 ATCACGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
39819 TAGTTTATTCATCATTTTTTTCTCAGA
66 TAGTTTATTCATC-TTTTTTTCTCAGA
*
39846 ATCATGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
1 ATCACGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
39911 TAGTTTATTCATCTTTTTTTCTCAGA
66 TAGTTTATTCATCTTTTTTTCTCAGA
39937 TTACATGTCA
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
91 13 0.15
92 75 0.85
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (91 bp):
ATCACGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
TAGTTTATTCATCTTTTTTTCTCAGA
Found at i:40191 original size:27 final size:27
Alignment explanation
Indices: 40153--40231 Score: 158
Period size: 27 Copynumber: 2.9 Consensus size: 27
40143 ATTCTCCAAA
40153 TTGTAATTAGTAATTCTTAGCTTATCT
1 TTGTAATTAGTAATTCTTAGCTTATCT
40180 TTGTAATTAGTAATTCTTAGCTTATCT
1 TTGTAATTAGTAATTCTTAGCTTATCT
40207 TTGTAATTAGTAATTCTTAGCTTAT
1 TTGTAATTAGTAATTCTTAGCTTAT
40232 TTGTAACTTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.52
Consensus pattern (27 bp):
TTGTAATTAGTAATTCTTAGCTTATCT
Found at i:41834 original size:28 final size:28
Alignment explanation
Indices: 41802--41859 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
41792 TATACCAAAG
*
41802 TTAATCTATTTAGTGTGGTGCTCACTGT
1 TTAATCTATTTAATGTGGTGCTCACTGT
*
41830 TTAATCTATTTAATGTGGTGCTCATTGT
1 TTAATCTATTTAATGTGGTGCTCACTGT
41858 TT
1 TT
41860 CATACATCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (28 bp):
TTAATCTATTTAATGTGGTGCTCACTGT
Found at i:47128 original size:18 final size:18
Alignment explanation
Indices: 47105--47141 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
47095 CTGTTTTTAA
47105 TTCCGAAAGATTAGAAAC
1 TTCCGAAAGATTAGAAAC
47123 TTCCGAAAGATTAGAAAC
1 TTCCGAAAGATTAGAAAC
47141 T
1 T
47142 AATTACCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (18 bp):
TTCCGAAAGATTAGAAAC
Found at i:49316 original size:11 final size:12
Alignment explanation
Indices: 49295--49324 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
49285 CACTTAACAT
49295 AAAACATACTAA
1 AAAACATACTAA
49307 AAAACA-ACTAA
1 AAAACATACTAA
49318 AAAACAT
1 AAAACAT
49325 CATTACACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.70, C:0.17, G:0.00, T:0.13
Consensus pattern (12 bp):
AAAACATACTAA
Found at i:52857 original size:21 final size:23
Alignment explanation
Indices: 52806--52857 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
52796 CGATTTCCTG
52806 TGGGGGGAATCGGTTCCCCTTCA
1 TGGGGGGAATCGGTTCCCCTTCA
**
52829 AAGGGGGAATCGGTT-CCC-TCA
1 TGGGGGGAATCGGTTCCCCTTCA
52850 TGGGGGGA
1 TGGGGGGA
52858 TCGATTCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 3 0.12
23 13 0.52
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
TGGGGGGAATCGGTTCCCCTTCA
Found at i:60968 original size:110 final size:109
Alignment explanation
Indices: 60827--61091 Score: 358
Period size: 110 Copynumber: 2.4 Consensus size: 109
60817 AATGTAAGTG
* * * *
60827 GTTAAAAATAACAA-TCACAACTGTTAACGTTACTCCTACTTATAAGGTAACCGATACAAAACAA
1 GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACAA
*
60891 AACAA-GACTCAACCGTAAACATTACTCATATTTAATAAGGTAACCA-
66 AACAATG-CGCAACCGTAAACATTACTCATATTT-AT-AGGTAA-CAT
*
60937 GTTAAAAATGA-AAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACAA
1 GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACAA
* * * *
61001 AACAATGCGCAACCGTAAACGTTACTCCTGTTTGTAGGTAACAT
66 AACAATGCGCAACCGTAAACATTACTCATATTTATAGGTAACAT
* *
61045 GTTAAAAATAACAAGGCGTAACCGTTAACGTTACTCTTACTTATAAG
1 GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAG
61092 TTGTGCAATC
Statistics
Matches: 138, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
107 2 0.01
108 16 0.12
109 36 0.26
110 83 0.60
111 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (109 bp):
GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACAA
AACAATGCGCAACCGTAAACATTACTCATATTTATAGGTAACAT
Found at i:60997 original size:53 final size:55
Alignment explanation
Indices: 60844--61091 Score: 229
Period size: 56 Copynumber: 4.5 Consensus size: 55
60834 ATAACAATCA
* * *
60844 CAACTGTTAACGTTACTCCTACTTATAAGGTAACCGATACAAAACAAAACAAGACT
1 CAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATA-AAAACAAAACAAGGCG
* * * * * **
60900 CAACCGTAAACATTACTCATATTTAATAAGGTAACC-AGTTAAAA-ATGA-AAGGCG
1 CAACCGTTAACGTTACTCCTACTT-ATAAGGTAACCGA-TAAAAACAAAACAAGGCG
*
60954 CAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACAAAACAATGCG
1 CAACCGTTAACGTTACTCCTACTTATAAGGTAACCGAT-AAAAACAAAACAAGGCG
* ** * * * *
61010 CAACCGTAAACGTTACTCCTGTTTGT-AGGTAACATG-TTAAAA-ATAACAAGGCG
1 CAACCGTTAACGTTACTCCTACTTATAAGGTAAC-CGATAAAAACAAAACAAGGCG
* *
61063 TAACCGTTAACGTTACTCTTACTTATAAG
1 CAACCGTTAACGTTACTCCTACTTATAAG
61092 TTGTGCAATC
Statistics
Matches: 152, Mismatches: 32, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
53 41 0.27
54 35 0.23
55 12 0.08
56 52 0.34
57 12 0.08
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (55 bp):
CAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAACAAAACAAGGCG
Found at i:61372 original size:54 final size:54
Alignment explanation
Indices: 61204--61372 Score: 139
Period size: 54 Copynumber: 3.1 Consensus size: 54
61194 CGTAAATGTC
* * * * ** * *
61204 ACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGAAGTAGCCTATAATATT
1 ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAATATT
* * * * *
61258 ACTCTTAC--TTATGAGCTAACTGGTAAAAAACAA-AACCTGGTGCAACC-ATAAATGTT
1 ACTCATACTTTTATG-G-TAACCGGTTAAAAATAACAA---GGTGCAACCTAT-AATATT
61314 ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAATATT
1 ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAATATT
61368 ACTCA
1 ACTCA
61373 AGAATGTTAA
Statistics
Matches: 88, Mismatches: 17, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
52 3 0.03
53 3 0.03
54 39 0.44
55 4 0.05
56 31 0.35
57 3 0.03
58 5 0.06
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.28
Consensus pattern (54 bp):
ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAATATT
Found at i:62749 original size:2 final size:2
Alignment explanation
Indices: 62742--62794 Score: 72
Period size: 2 Copynumber: 27.0 Consensus size: 2
62732 GTCATTTTTC
**
62742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT CC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
62783 AT AA AT AT AT AT
1 AT AT AT AT AT AT
62795 TCATCTTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:65383 original size:25 final size:24
Alignment explanation
Indices: 65336--65383 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
65326 TCTATGAGTA
65336 TTCAAATAATAAATAAATGATATT
1 TTCAAATAATAAATAAATGATATT
*
65360 TTCAAATTAA-AATATAAATTATAT
1 TTCAAA-TAATAA-ATAAATGATAT
65384 ATTTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TTCAAATAATAAATAAATGATATT
Found at i:65915 original size:27 final size:27
Alignment explanation
Indices: 65877--65976 Score: 200
Period size: 27 Copynumber: 3.7 Consensus size: 27
65867 AACCAAAGGC
65877 TCATATGTAACGGCTCATAGGAGCCTA
1 TCATATGTAACGGCTCATAGGAGCCTA
65904 TCATATGTAACGGCTCATAGGAGCCTA
1 TCATATGTAACGGCTCATAGGAGCCTA
65931 TCATATGTAACGGCTCATAGGAGCCTA
1 TCATATGTAACGGCTCATAGGAGCCTA
65958 TCATATGTAACGGCTCATA
1 TCATATGTAACGGCTCATA
65977 TTCAACCAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 73 1.00
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (27 bp):
TCATATGTAACGGCTCATAGGAGCCTA
Found at i:66726 original size:2 final size:2
Alignment explanation
Indices: 66719--66747 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
66709 CGTGATTCAT
66719 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
66748 AATCCATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:67095 original size:11 final size:11
Alignment explanation
Indices: 67079--67151 Score: 53
Period size: 10 Copynumber: 6.9 Consensus size: 11
67069 AAGATGCTTG
*
67079 TTAATTTATTC
1 TTAATTTATTA
*
67090 TTAATTTA-AA
1 TTAATTTATTA
* *
67100 TTTATTTATTC
1 TTAATTTATTA
* *
67111 GTAATTTA-AA
1 TTAATTTATTA
* *
67121 TTAATATATTT
1 TTAATTTATTA
67132 TTAATTTA-TA
1 TTAATTTATTA
67142 TTAATTTATT
1 TTAATTTATT
67152 GTTGGTATTG
Statistics
Matches: 44, Mismatches: 15, Indels: 6
0.68 0.23 0.09
Matches are distributed among these distances:
10 22 0.50
11 22 0.50
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (11 bp):
TTAATTTATTA
Found at i:67106 original size:21 final size:21
Alignment explanation
Indices: 67079--67151 Score: 101
Period size: 21 Copynumber: 3.5 Consensus size: 21
67069 AAGATGCTTG
67079 TTAATTTATTCTTAATTTAAA
1 TTAATTTATTCTTAATTTAAA
* *
67100 TTTATTTATTCGTAATTTAAA
1 TTAATTTATTCTTAATTTAAA
* * *
67121 TTAATATATTTTTAATTTATA
1 TTAATTTATTCTTAATTTAAA
67142 TTAATTTATT
1 TTAATTTATT
67152 GTTGGTATTG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
TTAATTTATTCTTAATTTAAA
Found at i:67315 original size:21 final size:21
Alignment explanation
Indices: 67289--67347 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
67279 TTTCAAAAAA
*
67289 GAATTATATTAATCTATTCTT
1 GAATTATATTAATTTATTCTT
*
67310 GAATTAAATTAATTTATTCTT
1 GAATTATATTAATTTATTCTT
*
67331 -AGTTATATTAATTTATT
1 GAATTATATTAATTTATT
67348 GTTGGTATTG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (21 bp):
GAATTATATTAATTTATTCTT
Found at i:67459 original size:197 final size:197
Alignment explanation
Indices: 67116--67480 Score: 624
Period size: 196 Copynumber: 1.9 Consensus size: 197
67106 TATTCGTAAT
* * *
67116 TTAAATTAATATATTTTTAATTTATATTAATTTATTGTTGGTATTGTAATGTCATTGTTTCGGTG
1 TTAAATTAATATATTCTTAAGTTATATTAATTTATTGTTGGTATTGTAATGTCATCGTTTCGGTG
* *
67181 CACTTTTTTCCCTCCGATTAGGTGTAGGGAGGTTTTTTAACAGGCCCGATTCGATGTTTTGTTTT
66 CACTTTTTTCCCTCCAATTAGGTGTAGGGAGGTTTTGTAACAGGCCCGATTCGATGTTTTGTTTT
67246 GTATGCTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAGAATTATATTAATCTATTCTTG
131 GTATGCTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAGAATTATATTAATCTATTCTTG
67311 AA
196 AA
*
67313 TTAAATTAATTTATTCTT-AGTTATATTAATTTATTGTTGGTATTGTAATGTCATCGTTTCGGTG
1 TTAAATTAATATATTCTTAAGTTATATTAATTTATTGTTGGTATTGTAATGTCATCGTTTCGGTG
* * *
67377 CACTTTTTTTCCTCCAATTAGGTGTAGGGAGGTTTTGTAACGTGGCCCGATTTGATGTTTTGTTT
66 CACTTTTTTCCCTCCAATTAGGTGTAGGGAGGTTTTGTAAC-AGGCCCGATTCGATGTTTTGTTT
*
67442 TGTATGGTTTTTCTCTATCTATACAAAACACCCCTTTCA
130 TGTATGCTTTTTCTCTATCTATACAAAACACCCCTTTCA
67481 TTTTTTCTTA
Statistics
Matches: 157, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
196 82 0.52
197 75 0.48
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (197 bp):
TTAAATTAATATATTCTTAAGTTATATTAATTTATTGTTGGTATTGTAATGTCATCGTTTCGGTG
CACTTTTTTCCCTCCAATTAGGTGTAGGGAGGTTTTGTAACAGGCCCGATTCGATGTTTTGTTTT
GTATGCTTTTTCTCTATCTATACAAAACACCCCTTTCAAAAAAGAATTATATTAATCTATTCTTG
AA
Found at i:67515 original size:21 final size:21
Alignment explanation
Indices: 67489--67538 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
67479 CATTTTTTCT
*
67489 TAATTTATATTAAGTTATTCA
1 TAATTTATATTAACTTATTCA
* *
67510 TAATTTATGTTAACTTATTCT
1 TAATTTATATTAACTTATTCA
67531 TAATTTAT
1 TAATTTAT
67539 TCTTAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.06, G:0.04, T:0.56
Consensus pattern (21 bp):
TAATTTATATTAACTTATTCA
Found at i:67533 original size:11 final size:11
Alignment explanation
Indices: 67480--67549 Score: 72
Period size: 11 Copynumber: 6.5 Consensus size: 11
67470 CACCCCTTTC
*
67480 ATTTTTTCTTA
1 ATTTATTCTTA
*
67491 ATTTA-TATTA
1 ATTTATTCTTA
* *
67501 AGTTATTCATA
1 ATTTATTCTTA
*
67512 ATTTA-TGTTA
1 ATTTATTCTTA
*
67522 ACTTATTCTTA
1 ATTTATTCTTA
67533 ATTTATTCTTA
1 ATTTATTCTTA
67544 ATTTAT
1 ATTTAT
67550 ATTAATATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
10 15 0.33
11 31 0.67
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (11 bp):
ATTTATTCTTA
Found at i:69332 original size:21 final size:21
Alignment explanation
Indices: 69299--69349 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
69289 AAAAGCATTG
69299 TTAATTT-TTCTTGAATTATA
1 TTAATTTATTCTTGAATTATA
*
69319 TTAATTTATTCTTGAATTTTA
1 TTAATTTATTCTTGAATTATA
*
69340 TAAATTTATT
1 TTAATTTATT
69350 TAAAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (21 bp):
TTAATTTATTCTTGAATTATA
Found at i:75211 original size:92 final size:91
Alignment explanation
Indices: 75049--75231 Score: 330
Period size: 92 Copynumber: 2.0 Consensus size: 91
75039 GTTAAAAAGG
* *
75049 ATCACGATGTGCAATATATCTGATAATGACCTTGCTCTGTCACTTCATCACGGATATTCATGCAT
1 ATCACGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
75114 TAGTTTATTCATCATTTTTTTCTCAGA
66 TAGTTTATTCATC-TTTTTTTCTCAGA
*
75141 ATCATGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
1 ATCACGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
75206 TAGTTTATTCATCTTTTTTTCTCAGA
66 TAGTTTATTCATCTTTTTTTCTCAGA
75232 TTACATGTCA
Statistics
Matches: 88, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
91 13 0.15
92 75 0.85
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (91 bp):
ATCACGATGTGCAATATATCTGATAATGACCTTGCTCAGTCACTTCATCACAGATATTCATGCAT
TAGTTTATTCATCTTTTTTTCTCAGA
Found at i:75486 original size:27 final size:27
Alignment explanation
Indices: 75448--75526 Score: 158
Period size: 27 Copynumber: 2.9 Consensus size: 27
75438 ATTCTCCAAA
75448 TTGTAATTAGTAATTCTTAGCTTATCT
1 TTGTAATTAGTAATTCTTAGCTTATCT
75475 TTGTAATTAGTAATTCTTAGCTTATCT
1 TTGTAATTAGTAATTCTTAGCTTATCT
75502 TTGTAATTAGTAATTCTTAGCTTAT
1 TTGTAATTAGTAATTCTTAGCTTAT
75527 TTGTAACTGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.27, C:0.10, G:0.11, T:0.52
Consensus pattern (27 bp):
TTGTAATTAGTAATTCTTAGCTTATCT
Found at i:77129 original size:28 final size:28
Alignment explanation
Indices: 77097--77154 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
77087 TATACCAAAG
*
77097 TTAATCTATTTAGTGTGGTGCTCACTGT
1 TTAATCTATTTAATGTGGTGCTCACTGT
*
77125 TTAATCTATTTAATGTGGTGCTCATTGT
1 TTAATCTATTTAATGTGGTGCTCACTGT
77153 TT
1 TT
77155 CATACATCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (28 bp):
TTAATCTATTTAATGTGGTGCTCACTGT
Found at i:92164 original size:110 final size:109
Alignment explanation
Indices: 91778--92167 Score: 328
Period size: 110 Copynumber: 3.6 Consensus size: 109
91768 ATACTGATCG
*
91778 ACCATTAACGTTACTCCTATTTGT-AGGTAACAGGTTAAAAATAACAAGGCGCAACCGT-TAACG
1 ACCATAAACGTTACTCCTATTT-TAAGGTAACAGGTTAAAAATAACAAGGCGCAACC-TATAACG
* * *
91841 TTACTCTTACTTATAAGGTAACAGGTAAAAAAACAAAA-CATTGTGCA
64 TTACTCTTACTTATAAGCTAACTGGT-AAAAAACAAAACCA-GGTGCA
* * * * * * * * *
91888 ATCGTAAACATTACTCCTATCTGTAAGGTAACATGTTAAAATTAAAAAGGCACAACCTATTACGT
1 ACCATAAACGTTACTCCTAT-TTTAAGGTAACAGGTTAAAAATAACAAGGCGCAACCTATAACGT
* * * ***
91953 TACTC---CTTATAAGTTAA-TCGATAAAAAACAAAACAAGACACA
65 TACTCTTACTTATAAGCTAACT-GGTAAAAAACAAAACCAGGTGCA
* * * * * ** * * **
91995 ATCGTAAATGTCACTCCTACTTATAAGGTAACCA-GTTAAAAATAACAAGAAGTAGCCTATAATA
1 ACCATAAACGTTACTCCTA-TTTTAAGGTAA-CAGGTTAAAAATAACAAGGCGCAACCTATAACG
92059 TTACTCTTACTTATAAGCTAACTGGTAAAAAACAAAACCAGGTGCA
64 TTACTCTTACTTATAAGCTAACTGGTAAAAAACAAAACCAGGTGCA
* * * * *
92105 ACCATAAATGTTACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCTATAAC
1 ACCATAAACGTTACTCCTA-TTTTAAGGTAACAGGTTAAAAATAACAAGGCGCAACCTATAAC
92168 ATTGCTCAAG
Statistics
Matches: 218, Mismatches: 50, Indels: 24
0.75 0.17 0.08
Matches are distributed among these distances:
107 64 0.29
108 17 0.08
109 1 0.00
110 96 0.44
111 40 0.18
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (109 bp):
ACCATAAACGTTACTCCTATTTTAAGGTAACAGGTTAAAAATAACAAGGCGCAACCTATAACGTT
ACTCTTACTTATAAGCTAACTGGTAAAAAACAAAACCAGGTGCA
Found at i:94381 original size:16 final size:16
Alignment explanation
Indices: 94360--94391 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
94350 AAGTGGAGTT
94360 GGGGGAATTCTAAGAA
1 GGGGGAATTCTAAGAA
94376 GGGGGAATTCTAAGAA
1 GGGGGAATTCTAAGAA
94392 TGGAGAATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.38, T:0.19
Consensus pattern (16 bp):
GGGGGAATTCTAAGAA
Found at i:94399 original size:16 final size:16
Alignment explanation
Indices: 94364--94399 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
94354 GGAGTTGGGG
*
94364 GAATTCTAAGAAGGGG
1 GAATTCTAAGAAGGGA
*
94380 GAATTCTAAGAATGGA
1 GAATTCTAAGAAGGGA
94396 GAAT
1 GAAT
94400 GGCTCGGTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.31, T:0.22
Consensus pattern (16 bp):
GAATTCTAAGAAGGGA
Found at i:101763 original size:2 final size:2
Alignment explanation
Indices: 101756--101803 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
101746 GTGGACTTCA
101756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
101798 AT AT AT
1 AT AT AT
101804 TGTTATTGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102303 original size:109 final size:110
Alignment explanation
Indices: 102026--102371 Score: 423
Period size: 110 Copynumber: 3.2 Consensus size: 110
102016 AATGTAAGTG
* * * *
102026 GTTAAAAATAACAA-TCACAACTGTTAACGTTACTCCTACTTATAAGGTAACCGATACAAAACAA
1 GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACAA
* * **
102090 AACAA-GACT-CAACCGTAAACATTACTCATATTTAATAAGGTAACCG
66 AACAATG--TGCAACCGTAAACATTACTCCTATTT-GTAAGGTAACAT
* * *
102136 GTCAAAAATGA-AAGGCGCAACCGTTAACGTTACTCCTACTCATAAGGTAACCGATAAAAAACAA
1 GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACAA
* *
102200 AACAATGTGCAACCGTAAACGTTACTCCTGTTTGT-AGGTAACAT
66 AACAATGTGCAACCGTAAACATTACTCCTATTTGTAAGGTAACAT
* * * *
102244 GTTAAAAATAACAAGGCGTAACCGTTAACGTTACTCTTACTTATAAGGTAACAGGTAAAAAAACA
1 GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGAT-AAAAAACA
* * *
102309 AAACATTGTGCAATCGTAAACATTACTCCTATCTGTAAGGTAACAT
65 AAACAATGTGCAACCGTAAACATTACTCCTATTTGTAAGGTAACAT
* *
102355 GTTAAAATTAAAAAGGC
1 GTTAAAAATAACAAGGC
102372 ACAAGTTAAT
Statistics
Matches: 203, Mismatches: 27, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
108 16 0.08
109 43 0.21
110 119 0.59
111 25 0.12
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (110 bp):
GTTAAAAATAACAAGGCGCAACCGTTAACGTTACTCCTACTTATAAGGTAACCGATAAAAAACAA
AACAATGTGCAACCGTAAACATTACTCCTATTTGTAAGGTAACAT
Found at i:102586 original size:54 final size:53
Alignment explanation
Indices: 102409--102586 Score: 121
Period size: 54 Copynumber: 3.2 Consensus size: 53
102399 AGACACAATC
* * * * ** * *
102409 ATAAATGTCACTCCTACTTATAAGGTAACCAGTTAAAAATAACAAGAAGTAGCCT
1 ATAAAT-T-ACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCT
* * * *
102464 ATAATATTACTCTTAC--TTATGAGCTAACTGGTAAAAAACAA-AACTTGGTGCAACC-
1 ATAA-ATTACTCATACTTTTATG-G-TAACCGGTTAAAAATAACAA---GGTGCAACCT
102519 ATAAATGTTACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCT
1 ATAAA--TTACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCT
102574 ATAACATTACTCA
1 ATAA-ATTACTCA
102587 ATAATGTTAA
Statistics
Matches: 95, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
52 3 0.03
53 3 0.03
54 37 0.39
55 13 0.14
56 31 0.33
57 3 0.03
58 5 0.05
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (53 bp):
ATAAATTACTCATACTTTTATGGTAACCGGTTAAAAATAACAAGGTGCAACCT
Found at i:105577 original size:10 final size:9
Alignment explanation
Indices: 105523--105602 Score: 70
Period size: 10 Copynumber: 8.3 Consensus size: 9
105513 CTGCTGGAAA
*
105523 ACCGGTTTA
1 ACCGGTTTG
*
105532 ACCAGTTTTG
1 ACC-GGTTTG
105542 AACCGGTTTG
1 -ACCGGTTTG
*
105552 ACCGGTTCG
1 ACCGGTTTG
105561 AACCGGTTTG
1 -ACCGGTTTG
105571 ACTCGGTTTG
1 AC-CGGTTTG
*
105581 ACCGGTCTG
1 ACCGGTTTG
*
105590 AACCGGGTTG
1 -ACCGGTTTG
105600 ACC
1 ACC
105603 CGACCCGACT
Statistics
Matches: 58, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
9 22 0.38
10 33 0.57
11 3 0.05
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:105584 original size:19 final size:19
Alignment explanation
Indices: 105522--105600 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
105512 GCTGCTGGAA
* *
105522 AACCGGTTTAACCAGTTTTG
1 AACCGGTTTGACC-GGTTTG
*
105542 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTTG
105561 AACCGGTTTGACTCGGTTTG
1 AACCGGTTTGAC-CGGTTTG
* *
105581 -ACCGGTCTGAACCGGGTTG
1 AACCGGTTTG-ACCGGTTTG
105600 A
1 A
105601 CCCGACCCGA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
19 30 0.60
20 20 0.40
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTG
Found at i:105618 original size:17 final size:17
Alignment explanation
Indices: 105596--105636 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
105586 TCTGAACCGG
*
105596 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
105613 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
105630 GTTGACC
1 GTTGACC
105637 GTGACCGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:105638 original size:7 final size:7
Alignment explanation
Indices: 105626--105668 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
105616 GACCCGACCC
105626 GACCGTT
1 GACCGTT
105633 GACCG-T
1 GACCGTT
105639 GACCGTT
1 GACCGTT
105646 GACCG-T
1 GACCGTT
105652 GACCGTT
1 GACCGTT
105659 GACCGTT
1 GACCGTT
105666 GAC
1 GAC
105669 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:105644 original size:13 final size:13
Alignment explanation
Indices: 105626--105664 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
105616 GACCCGACCC
105626 GACCGTTGACCGT
1 GACCGTTGACCGT
105639 GACCGTTGACCGT
1 GACCGTTGACCGT
105652 GACCGTTGACCGT
1 GACCGTTGACCGT
105665 TGACTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:105651 original size:20 final size:20
Alignment explanation
Indices: 105626--105668 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
105616 GACCCGACCC
105626 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
105646 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCG-TGACCGTT
105666 GAC
1 GAC
105669 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:106605 original size:63 final size:63
Alignment explanation
Indices: 106537--106660 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
106527 CTAATGTGAC
* * *
106537 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
106599 T
63 T
* *
106600 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
106661 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:106620 original size:32 final size:32
Alignment explanation
Indices: 106537--106660 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
106527 CTAATGTGAC
* * *
106537 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
106567 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
106600 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
106631 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
106661 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:108834 original size:27 final size:26
Alignment explanation
Indices: 108790--108847 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
108780 ATATCAAAAG
*
108790 TAAAAATCTAATCAAATTCATAAAAT-A
1 TAAAAATCTAAACAAATT--TAAAATAA
* *
108817 TAAAAATTTAAACGAATTTAAAATAA
1 TAAAAATCTAAACAAATTTAAAATAA
108843 TAAAA
1 TAAAA
108848 TTAAGTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.22
26 6 0.22
27 15 0.56
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (26 bp):
TAAAAATCTAAACAAATTTAAAATAA
Found at i:109103 original size:25 final size:24
Alignment explanation
Indices: 109056--109103 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
109046 TCTATGAGTA
109056 TTCAAATAATAAATAAATGATATT
1 TTCAAATAATAAATAAATGATATT
*
109080 TTCAAATTAA-AATATAAATTATAT
1 TTCAAA-TAATAA-ATAAATGATAT
109104 ATTTTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TTCAAATAATAAATAAATGATATT
Found at i:109879 original size:27 final size:27
Alignment explanation
Indices: 109841--109913 Score: 137
Period size: 27 Copynumber: 2.7 Consensus size: 27
109831 CATATGTAGC
109841 GAGCCTATCATATGTAACGGCTCATAG
1 GAGCCTATCATATGTAACGGCTCATAG
*
109868 GAGCCTATCATATGTAACGGGTCATAG
1 GAGCCTATCATATGTAACGGCTCATAG
109895 GAGCCTATCATATGTAACG
1 GAGCCTATCATATGTAACG
109914 AGCCTATCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (27 bp):
GAGCCTATCATATGTAACGGCTCATAG
Found at i:109918 original size:18 final size:18
Alignment explanation
Indices: 109895--109931 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
109885 CGGGTCATAG
109895 GAGCCTATCATATGTAAC
1 GAGCCTATCATATGTAAC
109913 GAGCCTATCATATGTAAC
1 GAGCCTATCATATGTAAC
109931 G
1 G
109932 GCTCATATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (18 bp):
GAGCCTATCATATGTAAC
Found at i:109920 original size:72 final size:72
Alignment explanation
Indices: 109803--109938 Score: 254
Period size: 72 Copynumber: 1.9 Consensus size: 72
109793 AACCAACGGC
*
109803 TCATATGTAACGGCTCATAGGAGCCTATCATATGTAGCGAGCCTATCATATGTAACGGCTCATAG
1 TCATATGTAACGGCTCATAGGAGCCTATCATATGTAACGAGCCTATCATATGTAACGGCTCATAG
109868 GAGCCTA
66 GAGCCTA
*
109875 TCATATGTAACGGGTCATAGGAGCCTATCATATGTAACGAGCCTATCATATGTAACGGCTCATA
1 TCATATGTAACGGCTCATAGGAGCCTATCATATGTAACGAGCCTATCATATGTAACGGCTCATA
109939 TTCAACCAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (72 bp):
TCATATGTAACGGCTCATAGGAGCCTATCATATGTAACGAGCCTATCATATGTAACGGCTCATAG
GAGCCTA
Found at i:110691 original size:2 final size:2
Alignment explanation
Indices: 110684--110710 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
110674 CGTGATTCAT
110684 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
110711 AATCCATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:111072 original size:21 final size:21
Alignment explanation
Indices: 111046--111137 Score: 123
Period size: 21 Copynumber: 4.4 Consensus size: 21
111036 AGATGCTTGA
111046 TAATTTATTCTTAATTTAAAT
1 TAATTTATTCTTAATTTAAAT
* *
111067 TTATTTATTCGTAATTTAAAT
1 TAATTTATTCTTAATTTAAAT
* * *
111088 TAATATATTTTTAATTTATAT
1 TAATTTATTCTTAATTTAAAT
*
111109 TAATTTATTCTTAA-TTATAT
1 TAATTTATTCTTAATTTAAAT
111129 TAATTTATT
1 TAATTTATT
111138 GTTGGTATTG
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
20 15 0.24
21 47 0.76
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (21 bp):
TAATTTATTCTTAATTTAAAT
Found at i:111302 original size:21 final size:21
Alignment explanation
Indices: 111276--111355 Score: 126
Period size: 21 Copynumber: 3.9 Consensus size: 21
111266 TTCAAAAAAA
*
111276 GAATTATATTAATTTATTCTT
1 GAATTAAATTAATTTATTCTT
111297 GAATTAAATTAATTTATTCTT
1 GAATTAAATTAATTTATTCTT
*
111318 GATTTAAATTAATTTATTC-T
1 GAATTAAATTAATTTATTCTT
*
111338 GAATTATATTAATTTATT
1 GAATTAAATTAATTTATT
111356 GTTGGTATTG
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
20 17 0.31
21 38 0.69
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (21 bp):
GAATTAAATTAATTTATTCTT
Found at i:111522 original size:21 final size:21
Alignment explanation
Indices: 111498--111637 Score: 192
Period size: 21 Copynumber: 6.7 Consensus size: 21
111488 TCAAAACAAA
111498 TTATATTAATTTATTCTTAAT
1 TTATATTAATTTATTCTTAAT
* *
111519 TTATGTTAATTTAATCTTAA-
1 TTATATTAATTTATTCTTAAT
* *
111539 TTATATTAGTTTATTCTTAAA
1 TTATATTAATTTATTCTTAAT
*
111560 TTAAATTAATTTATTCTTAAT
1 TTATATTAATTTATTCTTAAT
* *
111581 TTAAATTAATTTATTCATAAT
1 TTATATTAATTTATTCTTAAT
*
111602 TTATATTAACTTATTCTTAAT
1 TTATATTAATTTATTCTTAAT
*
111623 TTATATTAATATATT
1 TTATATTAATTTATT
111638 AATATAGTTT
Statistics
Matches: 104, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
20 17 0.16
21 87 0.84
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.57
Consensus pattern (21 bp):
TTATATTAATTTATTCTTAAT
Found at i:111554 original size:218 final size:217
Alignment explanation
Indices: 111069--111574 Score: 766
Period size: 218 Copynumber: 2.3 Consensus size: 217
111059 ATTTAAATTT
* * * *
111069 ATTTATTCGTAATTTAAATTAATATATTTTTAATTTATATTAATTTATTCTTAATTATATTAATT
1 ATTTATTCTTAATTTAAATTAATTTATTCTTAA-TTATATTAATTTATTCTAAATTATATTAATT
* *
111134 TATTGTTGGTATTGTAATGTCATTGTTTCGGTGCACTTTTTTCCCTCCGATTAGGTGTAGGGAGG
65 TATTGTTGGTATTGTAATGTCATCGTTTCGGTGCACTTTTTTCCCTCCAATTAGGTGTAGGGAGG
*
111199 TTTTTTAACAGGCCCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCC
130 GTTTTTAACAGGCCCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCC
111264 CTTTCAAAAAAAGAATTATATTA
195 CTTTCAAAAAAAGAATTATATTA
* * *
111287 ATTTATTCTTGAA-TTAAATTAATTTATTCTTGATTTAAATTAATTTATTCTGAATTATATTAAT
1 ATTTATTCTT-AATTTAAATTAATTTATTCTT-AATTATATTAATTTATTCTAAATTATATTAAT
111351 TTATTGTTGGTATTGTAATGTCATCGTTTCGGTGCACTTTTTTTTCCCTCCAATTAGGTGTAGGG
64 TTATTGTTGGTATTGTAATGTCATCGTTTCGGTGCAC--TTTTTTCCCTCCAATTAGGTGTAGGG
*
111416 AGGGTTTTTAATGAGGCCCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAAC
127 AGGGTTTTTAA-CAGGCCCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAAC
* *
111481 ACTCCTTTC-AAAACA-AATTATATTA
191 ACCCCTTTCAAAAAAAGAATTATATTA
** * * *
111506 ATTTATTCTTAATTTATGTTAATTTAATCTTAATTATATTAGTTTATTCTTAAATTAAATTAATT
1 ATTTATTCTTAATTTAAATTAATTTATTCTTAATTATATTAATTTATTC-TAAATTATATTAATT
111571 TATT
65 TATT
111575 CTTAATTTAA
Statistics
Matches: 261, Mismatches: 20, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
218 106 0.41
219 55 0.21
220 40 0.15
221 60 0.23
ACGTcount: A:0.28, C:0.11, G:0.12, T:0.49
Consensus pattern (217 bp):
ATTTATTCTTAATTTAAATTAATTTATTCTTAATTATATTAATTTATTCTAAATTATATTAATTT
ATTGTTGGTATTGTAATGTCATCGTTTCGGTGCACTTTTTTCCCTCCAATTAGGTGTAGGGAGGG
TTTTTAACAGGCCCGATTCGATGTTTTGTTTTGTATGGTTTTTCTCTATCTATACAAAACACCCC
TTTCAAAAAAAGAATTATATTA
Found at i:111592 original size:62 final size:63
Alignment explanation
Indices: 111495--111637 Score: 198
Period size: 62 Copynumber: 2.3 Consensus size: 63
111485 CTTTCAAAAC
** * **
111495 AAATTATATTAATTTATTCTTAATTTATGTTAATTTAATCTTAA-TTATATTAGTTTATTCTT
1 AAATTATATTAATTTATTCTTAATTTAAATTAATTTAATCATAATTTATATTAACTTATTCTT
* *
111557 AAATTAAATTAATTTATTCTTAATTTAAATTAATTTATTCATAATTTATATTAACTTATTCTT
1 AAATTATATTAATTTATTCTTAATTTAAATTAATTTAATCATAATTTATATTAACTTATTCTT
* *
111620 AATTTATATTAATATATT
1 AAATTATATTAATTTATT
111638 AATATAGTTT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
62 39 0.56
63 31 0.44
ACGTcount: A:0.38, C:0.05, G:0.01, T:0.56
Consensus pattern (63 bp):
AAATTATATTAATTTATTCTTAATTTAAATTAATTTAATCATAATTTATATTAACTTATTCTT
Found at i:113368 original size:18 final size:19
Alignment explanation
Indices: 113347--113402 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
113337 AATTAAAAAG
*
113347 GAATTGTTAATTT-TTCTT
1 GAATTATTAATTTATTCTT
113365 GAATTATATTAATTTATTCTT
1 GAA-T-TATTAATTTATTCTT
113386 GAATTAAATTAATTTAT
1 GAATT--ATTAATTTAT
113403 ATTCATTGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.09
19 2 0.06
20 9 0.28
21 18 0.56
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.55
Consensus pattern (19 bp):
GAATTATTAATTTATTCTT
Found at i:113386 original size:21 final size:21
Alignment explanation
Indices: 113353--113402 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
113343 AAAGGAATTG
*
113353 TTAATTT-TTCTTGAATTATA
1 TTAATTTATTCTTGAATTAAA
113373 TTAATTTATTCTTGAATTAAA
1 TTAATTTATTCTTGAATTAAA
113394 TTAATTTAT
1 TTAATTTAT
113403 ATTCATTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (21 bp):
TTAATTTATTCTTGAATTAAA
Found at i:135096 original size:4 final size:4
Alignment explanation
Indices: 135087--135111 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
135077 TTGACATCCA
135087 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
135112 GAGTAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:150350 original size:23 final size:24
Alignment explanation
Indices: 150321--150368 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
150311 TGTTCAAAAG
150321 AAGACTTCA-TTCCCTGATAATGA
1 AAGACTTCATTTCCCTGATAATGA
150344 AAGACTTCATTTCCCTGATAATGA
1 AAGACTTCATTTCCCTGATAATGA
150368 A
1 A
150369 CGTTTAACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.31
Consensus pattern (24 bp):
AAGACTTCATTTCCCTGATAATGA
Found at i:153526 original size:40 final size:42
Alignment explanation
Indices: 153473--153569 Score: 130
Period size: 40 Copynumber: 2.4 Consensus size: 42
153463 TTCGGTTTGC
153473 AAAAAACCGGTTTTTAAAAAAAAACCGGATTTTT-T-CGGAT
1 AAAAAACCGGTTTTTAAAAAAAAACCGGATTTTTATCCGGAT
* * * *
153513 AAAAAATCAGTTTTT--TAAAAAACCGGTTTTTTATCCGGAT
1 AAAAAACCGGTTTTTAAAAAAAAACCGGATTTTTATCCGGAT
153553 AAAAAACCGGTTTTTAA
1 AAAAAACCGGTTTTTAA
153570 TCCGGTAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
38 15 0.32
39 1 0.02
40 31 0.66
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (42 bp):
AAAAAACCGGTTTTTAAAAAAAAACCGGATTTTTATCCGGAT
Found at i:153533 original size:16 final size:16
Alignment explanation
Indices: 153512--153545 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
153502 TTTTTTCGGA
*
153512 TAAAAAATCAGTTTTT
1 TAAAAAACCAGTTTTT
*
153528 TAAAAAACCGGTTTTT
1 TAAAAAACCAGTTTTT
153544 TA
1 TA
153546 TCCGGATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (16 bp):
TAAAAAACCAGTTTTT
Found at i:153566 original size:23 final size:23
Alignment explanation
Indices: 153528--153587 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 23
153518 ATCAGTTTTT
*
153528 TAAAAAACCGGTTTTTTATCCGG
1 TAAAAAACCGGTTTTTAATCCGG
153551 ATAAAAAACCGGTTTTTAATCCGG
1 -TAAAAAACCGGTTTTTAATCCGG
153575 TAAAAAAACCGGT
1 T-AAAAAACCGGT
153588 CGTTCAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (23 bp):
TAAAAAACCGGTTTTTAATCCGG
Found at i:157918 original size:2 final size:2
Alignment explanation
Indices: 157911--157940 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
157901 CTGCTCATTG
157911 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
157941 GATCTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:162763 original size:21 final size:21
Alignment explanation
Indices: 162737--162787 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
162727 ATTTTGGTAG
* *
162737 GTGTTCGTGTTCGATCATTTA
1 GTGTTCATGTTCGATCATATA
*
162758 GTGTTCATGTTTGATCATATA
1 GTGTTCATGTTCGATCATATA
*
162779 ATGTTCATG
1 GTGTTCATG
162788 AACATGTTCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.47
Consensus pattern (21 bp):
GTGTTCATGTTCGATCATATA
Found at i:182932 original size:11 final size:11
Alignment explanation
Indices: 182916--182940 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
182906 CACCGGGAAT
182916 TTTATTTATTA
1 TTTATTTATTA
182927 TTTATTTATTA
1 TTTATTTATTA
182938 TTT
1 TTT
182941 TTTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:183548 original size:12 final size:12
Alignment explanation
Indices: 183531--183603 Score: 65
Period size: 12 Copynumber: 5.7 Consensus size: 12
183521 TTTAAAAATT
183531 ATATTATTATTA
1 ATATTATTATTA
*
183543 ATATTATTTTTA
1 ATATTATTATTA
*
183555 ATAAAATAATTATTA
1 AT---ATTATTATTA
*
183570 ATATTATTTTTA
1 ATATTATTATTA
*
183582 ATAAATAATTATTA
1 AT--ATTATTATTA
183596 ATATTATT
1 ATATTATT
183604 GATTTATGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
12 28 0.58
14 10 0.21
15 10 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATATTATTATTA
Found at i:183567 original size:30 final size:30
Alignment explanation
Indices: 183520--183618 Score: 100
Period size: 27 Copynumber: 3.4 Consensus size: 30
183510 ATTATTAAAG
*
183520 TTTTAA-AAATTATATTATTATTAATATTAT
1 TTTTAATAAAATA-ATTATTATTAATATTAT
183550 TTTTAATAAAAT-A--ATTATTAATATTAT
1 TTTTAATAAAATAATTATTATTAATATTAT
* *
183577 TTTTAAT-AAATAATTATTAATATTATTGAT
1 TTTTAATAAAATAATTATTATTAATATT-AT
* *
183607 TTATGATAAAAT
1 TTTTAATAAAAT
183619 GATGATCTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
26 4 0.07
27 22 0.38
29 11 0.19
30 13 0.22
31 8 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
TTTTAATAAAATAATTATTATTAATATTAT
Found at i:183587 original size:26 final size:27
Alignment explanation
Indices: 183536--183603 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
183526 AAATTATATT
183536 ATTATTAATATTATTTTTAATAAAATA
1 ATTATTAATATTATTTTTAATAAAATA
183563 ATTATTAATATTATTTTTAAT-AAATA
1 ATTATTAATATTATTTTTAATAAAATA
183589 ATTATTAATATTATT
1 ATTATTAATATTATT
183604 GATTTATGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
26 20 0.49
27 21 0.51
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTATTAATATTATTTTTAATAAAATA
Found at i:183814 original size:26 final size:26
Alignment explanation
Indices: 183785--183846 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
183775 TATTAAAAAA
* *
183785 TAATTTATTATGAATGTCGTGTTTAT
1 TAATTTAATAAGAATGTCGTGTTTAT
183811 TAATTTAATAAGAATGTCGTGTTTAT
1 TAATTTAATAAGAATGTCGTGTTTAT
183837 TAATTTAATA
1 TAATTTAATA
183847 TCTCACTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (26 bp):
TAATTTAATAAGAATGTCGTGTTTAT
Found at i:184872 original size:16 final size:16
Alignment explanation
Indices: 184851--184918 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 16
184841 ATCTAAACTG
184851 AAAATAACTCAAATAA
1 AAAATAACTCAAATAA
** **
184867 AAAATAACTTGAATCG
1 AAAATAACTCAAATAA
* * *
184883 AAAGTAACCCAAATTA
1 AAAATAACTCAAATAA
* *
184899 AAAATAACTCGAACAA
1 AAAATAACTCAAATAA
184915 AAAA
1 AAAA
184919 CGGCCTAGAA
Statistics
Matches: 37, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.62, C:0.15, G:0.06, T:0.18
Consensus pattern (16 bp):
AAAATAACTCAAATAA
Found at i:186471 original size:15 final size:14
Alignment explanation
Indices: 186437--186473 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
186427 GTTAAAAAAT
186437 AAAAAAT-TAATTA
1 AAAAAATATAATTA
*
186450 AAAAAATATTATTA
1 AAAAAATATAATTA
186464 AAAAAA-ATAA
1 AAAAAATATAA
186474 AAAGTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAAAATATAATTA
Found at i:186485 original size:18 final size:17
Alignment explanation
Indices: 186430--186494 Score: 53
Period size: 18 Copynumber: 3.7 Consensus size: 17
186420 ATGTCATGTT
186430 AAAAAATAAAAAATTAATTA
1 AAAAAAT-AAAAATT-A-TA
**
186450 AAAAAAT-ATTATTA-A
1 AAAAAATAAAAATTATA
186465 AAAAAATAAAAAGTTATA
1 AAAAAATAAAAA-TTATA
*
186483 AAAACATAAAAA
1 AAAAAATAAAAA
186495 ACTGGTTTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
15 8 0.22
16 2 0.05
17 4 0.11
18 16 0.43
20 7 0.19
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (17 bp):
AAAAAATAAAAATTATA
Done.