Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001718.1 Hibiscus syriacus cultivar Beakdansim tig00003478_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: 116267
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4584 original size:15 final size:15
Alignment explanation
Indices: 4543--4576 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4533 ATTAAATATA
*
4543 ATTAATAATTATGTC
1 ATTAAAAATTATGTC
*
4558 ATTAAAAATTATGTT
1 ATTAAAAATTATGTC
4573 ATTA
1 ATTA
4577 TCAATTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (15 bp):
ATTAAAAATTATGTC
Found at i:5124 original size:59 final size:59
Alignment explanation
Indices: 5006--5138 Score: 160
Period size: 59 Copynumber: 2.2 Consensus size: 59
4996 CAAAAGTTTG
* * *
5006 GGATGAAATTGGAATATTCAAAATTTTGGAGACCAATATAGAATAAGGGTCATAATTTAA
1 GGATG-AATTGAAATATTCAAAAGTTTGGAGACCAATATAGAATAAGAGTCATAATTTAA
* * * * *
5066 GGATGAATTTGAAATATTGAAAAGTTTGGA-ATCTATTTAGAATAAGAGTCATAGTTTAA
1 GGATGAA-TTGAAATATTCAAAAGTTTGGAGACCAATATAGAATAAGAGTCATAATTTAA
*
5125 AGATGAATTGAAAT
1 GGATGAATTGAAAT
5139 GATTTAAACA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 7 0.11
59 32 0.51
60 24 0.38
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (59 bp):
GGATGAATTGAAATATTCAAAAGTTTGGAGACCAATATAGAATAAGAGTCATAATTTAA
Found at i:5818 original size:30 final size:30
Alignment explanation
Indices: 5759--5820 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
5749 CTAGAAGAAT
* *
5759 CGGCTGAAAATCGGAAAAATTGGGGTGAAC
1 CGGCTGAAAACCGGAAAAATCGGGGTGAAC
* **
5789 CGGCTGAAAACCGGCAAAATCGGTTTGAAC
1 CGGCTGAAAACCGGAAAAATCGGGGTGAAC
5819 CG
1 CG
5821 CCGGTTCACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.31, T:0.16
Consensus pattern (30 bp):
CGGCTGAAAACCGGAAAAATCGGGGTGAAC
Found at i:6072 original size:24 final size:24
Alignment explanation
Indices: 6042--6092 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
6032 TAGAAGTTCG
6042 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
6066 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
6090 ATT
1 ATT
6093 AAAGTGAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:13794 original size:22 final size:22
Alignment explanation
Indices: 13768--13817 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
13758 TAGTCCAATA
*
13768 TTGGTGGCTTGGAGTAGTCACG
1 TTGGTGGCTTGGAGTAGCCACG
**
13790 TTGGTGTTTTGGAGTAGCCACG
1 TTGGTGGCTTGGAGTAGCCACG
13812 TTGGTG
1 TTGGTG
13818 TTAAAGCTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.40, T:0.36
Consensus pattern (22 bp):
TTGGTGGCTTGGAGTAGCCACG
Found at i:13818 original size:22 final size:22
Alignment explanation
Indices: 13776--13819 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
13766 TATTGGTGGC
*
13776 TTGGAGTAGTCACGTTGGTGTT
1 TTGGAGTAGCCACGTTGGTGTT
13798 TTGGAGTAGCCACGTTGGTGTT
1 TTGGAGTAGCCACGTTGGTGTT
13820 AAAGCTTCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.14, C:0.11, G:0.36, T:0.39
Consensus pattern (22 bp):
TTGGAGTAGCCACGTTGGTGTT
Found at i:17159 original size:9 final size:9
Alignment explanation
Indices: 17120--17152 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
17110 ATATTATTCT
17120 TTAATTAAA
1 TTAATTAAA
*
17129 TT-ATAAAA
1 TTAATTAAA
17137 TTAATTAAA
1 TTAATTAAA
17146 TTAATTA
1 TTAATTA
17153 GAATAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAATTAAA
Found at i:17712 original size:24 final size:25
Alignment explanation
Indices: 17685--17738 Score: 58
Period size: 27 Copynumber: 2.1 Consensus size: 25
17675 TTAAAATATT
*
17685 TAAA-TATAA-AAGATAATAATAAAA
1 TAAATTATAATAA-ATAATAAAAAAA
17709 TAAAATTATAATTAAATAATAAAAAAA
1 T-AAATTATAA-TAAATAATAAAAAAA
17736 TAA
1 TAA
17739 TTCCATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
24 1 0.04
25 3 0.12
26 7 0.28
27 12 0.48
28 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAATTATAATAAATAATAAAAAAA
Found at i:17738 original size:19 final size:19
Alignment explanation
Indices: 17677--17740 Score: 55
Period size: 19 Copynumber: 3.5 Consensus size: 19
17667 TACTAGATTT
*
17677 AAAATATTTAAAT-ATAAA
1 AAAATAATTAAATAATAAA
17695 AGATAATAA-T-AA-AATAAA
1 A-A-AATAATTAAATAATAAA
**
17713 ATTATAATTAAATAATAAA
1 AAAATAATTAAATAATAAA
17732 AAAATAATT
1 AAAATAATT
17741 CCATTATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 11
0.69 0.10 0.22
Matches are distributed among these distances:
16 4 0.11
17 1 0.03
18 11 0.31
19 15 0.43
20 4 0.11
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATAATTAAATAATAAA
Found at i:17749 original size:27 final size:24
Alignment explanation
Indices: 17699--17768 Score: 68
Period size: 29 Copynumber: 2.7 Consensus size: 24
17689 TATAAAAGAT
*
17699 AATAATAAAATAAAATTATAATTA
1 AATAATAAAAAAAAATTATAATTA
*
17723 AATAATAAAAAAATAATTCCATTATTAAA
1 AATAATAAAAAAA-AATT--ATAATT--A
*
17752 AATAATAATAAAAAATT
1 AATAATAAAAAAAAATT
17769 GAAAAAGAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
24 12 0.32
25 4 0.11
27 5 0.13
28 4 0.11
29 13 0.34
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (24 bp):
AATAATAAAAAAAAATTATAATTA
Found at i:18173 original size:9 final size:9
Alignment explanation
Indices: 18159--18191 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
18149 TATCGTATGC
18159 TAATTAATT
1 TAATTAATT
18168 TAATTAATT
1 TAATTAATT
*
18177 TTA-TAATT
1 TAATTAATT
18185 TAATTAA
1 TAATTAA
18192 AGAATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATTAATT
Found at i:18970 original size:62 final size:61
Alignment explanation
Indices: 18864--19231 Score: 459
Period size: 62 Copynumber: 5.9 Consensus size: 61
18854 ACTTTGCTGG
* * * *
18864 GGAGTCAGGAATAATAAATGTTGACTTCTATTCACGAGGAAGTCAATGATTGACTCTACTGA
1 GGAGTCAGAAATAATAAAGGTTGACTTCTCTTCACGAGGAAGTCAA-AATTGACTCTACTGA
* * * *
18926 GGAGTCAAAAATAACAAATGTTGACTTCTCTTCGCGAAGG-AGTCAAATATTGACTCTACTGA
1 GGAGTCAGAAATAATAAAGGTTGACTTCTCTTCACG-AGGAAGTCAAA-ATTGACTCTACTGA
** * *
18988 GGAGTCAGAAATAATAAATATTGACTTCTCTTCACGAGGGAGTCAGAAATTGACTCTACTAA
1 GGAGTCAGAAATAATAAAGGTTGACTTCTCTTCACGAGGAAGTCA-AAATTGACTCTACTGA
* ** **
19050 GGAGTCAGAAATAATAAAGGTTGACTTCTCTTCAAGAGGAAGTCAAAAATAAACTCTACCAA
1 GGAGTCAGAAATAATAAAGGTTGACTTCTCTTCACGAGGAAGTC-AAAATTGACTCTACTGA
* **
19112 GGAGTCAGAAATAATAAAGGTTGACTTCTCTTCAAGAGGAAGTCAGAAATAAACTCTACTGA
1 GGAGTCAGAAATAATAAAGGTTGACTTCTCTTCACGAGGAAGTCA-AAATTGACTCTACTGA
* * *
19174 GAAGTCAGAAATAATAAAGGTTGACTTCTCTTCAAGAGAAAGTCAGAAATTGACTCTA
1 GGAGTCAGAAATAATAAAGGTTGACTTCTCTTCACGAGGAAGTCA-AAATTGACTCTA
19232 GGAAACAAGA
Statistics
Matches: 276, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
61 4 0.01
62 266 0.96
63 6 0.02
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (61 bp):
GGAGTCAGAAATAATAAAGGTTGACTTCTCTTCACGAGGAAGTCAAAATTGACTCTACTGA
Found at i:23662 original size:24 final size:25
Alignment explanation
Indices: 23618--23678 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
23608 AATTTATTAT
* *
23618 TATTTTAGTTATTCTGTAATTAA-A
1 TATTTTAGATATTATGTAATTAACA
23642 TATTTTACGATATTATG-AATTAACA
1 TATTTTA-GATATTATGTAATTAACA
* *
23667 TTTTTTAAATAT
1 TATTTTAGATAT
23679 ATATATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
24 17 0.55
25 14 0.45
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (25 bp):
TATTTTAGATATTATGTAATTAACA
Found at i:27041 original size:48 final size:47
Alignment explanation
Indices: 26965--27066 Score: 186
Period size: 48 Copynumber: 2.1 Consensus size: 47
26955 TTTATCGTAT
26965 CGATCTTCACACATAAGATCTTTAGAGAACTAGATATAAAAGAAGTCA
1 CGATCTTCACACATAAGATCTTTAGAGAACTAGATAT-AAAGAAGTCA
*
27013 CGATCTTCACACATAAGATCTTTGGAGAACTAGATATAAAGAAGTCA
1 CGATCTTCACACATAAGATCTTTAGAGAACTAGATATAAAGAAGTCA
27060 CGATCTT
1 CGATCTT
27067 TTGACATGAC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 17 0.32
48 36 0.68
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (47 bp):
CGATCTTCACACATAAGATCTTTAGAGAACTAGATATAAAGAAGTCA
Found at i:28077 original size:32 final size:32
Alignment explanation
Indices: 28041--28111 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
28031 GCTGATGTAT
* *
28041 CACATACCACATCATTATCTTAGGTAATGTGA
1 CACATACCACATCATCATATTAGGTAATGTGA
* *
28073 CACATATCACGTCATCATATTAGGTAATGTGA
1 CACATACCACATCATCATATTAGGTAATGTGA
*
28105 CATATAC
1 CACATAC
28112 TATGTCATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.31
Consensus pattern (32 bp):
CACATACCACATCATCATATTAGGTAATGTGA
Found at i:36290 original size:21 final size:21
Alignment explanation
Indices: 36264--36305 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
36254 GTTATGCAGT
*
36264 TCGAGGGATCGTAATGGCGAC
1 TCGAGGGATCATAATGGCGAC
36285 TCGAGGGATCATAATGGCGAC
1 TCGAGGGATCATAATGGCGAC
36306 GAGAATGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (21 bp):
TCGAGGGATCATAATGGCGAC
Found at i:37705 original size:155 final size:157
Alignment explanation
Indices: 37530--37841 Score: 583
Period size: 155 Copynumber: 2.0 Consensus size: 157
37520 ATTCAGTGCG
*
37530 TCTTCTTCTGGTTATGGATTTAAGCTCGATTTCCATAGTCTTCTTGTTTAACAAGCCATTAAATC
1 TCTTCTTCTGGTTATGGATTTAAACTCGATTTCCATAGTCTTCTTGTTTAACAAGCCATTAAATC
37595 ATTTGAACTCGATCTCTCTTTTCATCCAG-TT-TGTGTGTATATATAAGCAAATCATTCAAGTGA
66 ATTTGAACTCGATCTCTCTTTTCATCCAGTTTGTGTGTGTATATATAAGCAAATCATTCAAGTGA
37658 AGTTGAAATCATAAACAATTATGAGTA
131 AGTTGAAATCATAAACAATTATGAGTA
*
37685 TCTTCTTCTGGTTATGGATTTAAACTCGATTTCCATAGTCTTCTTGTTTAACAATCCATTAAATC
1 TCTTCTTCTGGTTATGGATTTAAACTCGATTTCCATAGTCTTCTTGTTTAACAAGCCATTAAATC
*
37750 ATTTGAACTCGATCTCTCTTTTTATCCAGTTTGTGTGTGTATATATAAGCAAATCATTCAAGTGA
66 ATTTGAACTCGATCTCTCTTTTCATCCAGTTTGTGTGTGTATATATAAGCAAATCATTCAAGTGA
37815 AGTTGAAATCATAAACAATTATGAGTA
131 AGTTGAAATCATAAACAATTATGAGTA
37842 AGTCATTCAT
Statistics
Matches: 152, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
155 91 0.60
156 2 0.01
157 59 0.39
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (157 bp):
TCTTCTTCTGGTTATGGATTTAAACTCGATTTCCATAGTCTTCTTGTTTAACAAGCCATTAAATC
ATTTGAACTCGATCTCTCTTTTCATCCAGTTTGTGTGTGTATATATAAGCAAATCATTCAAGTGA
AGTTGAAATCATAAACAATTATGAGTA
Found at i:45588 original size:3 final size:3
Alignment explanation
Indices: 45580--45731 Score: 223
Period size: 3 Copynumber: 50.7 Consensus size: 3
45570 TTTTTATCCA
* * *
45580 TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TTT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
45628 TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
45676 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45724 TAT TAT TA
1 TAT TAT TA
45732 AATATATTAA
Statistics
Matches: 131, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 131 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:46218 original size:12 final size:12
Alignment explanation
Indices: 46201--46230 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
46191 AAAAAAAGGG
46201 GACAGAAAGAGA
1 GACAGAAAGAGA
46213 GACAGAAAGAGA
1 GACAGAAAGAGA
46225 GACAGA
1 GACAGA
46231 GACAGAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.33, T:0.00
Consensus pattern (12 bp):
GACAGAAAGAGA
Found at i:46262 original size:15 final size:16
Alignment explanation
Indices: 46242--46271 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46232 ACAGAACCGG
46242 AGAGAAAA-AAAAAAC
1 AGAGAAAAGAAAAAAC
46257 AGAGAAAAGAAAAAA
1 AGAGAAAAGAAAAAA
46272 ACAAACTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AGAGAAAAGAAAAAAC
Found at i:59764 original size:52 final size:52
Alignment explanation
Indices: 59686--59878 Score: 368
Period size: 52 Copynumber: 3.7 Consensus size: 52
59676 GAATATGCCA
*
59686 ATAGCATCGTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
59738 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
59790 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
59842 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGAT
59879 TGGACAGAAT
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 138 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:60720 original size:113 final size:113
Alignment explanation
Indices: 60520--61063 Score: 824
Period size: 113 Copynumber: 4.8 Consensus size: 113
60510 GACTCAAATC
* * * ** * *
60520 CATCATCTGGTGGATCATCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCGTCATCTAAAGAA
1 CATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAA
**
60585 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATT
63 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
* * * *
60636 CATCACTTGATGGATTA-TTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCAGCTTTT-CCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
60700 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATC
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
*
60749 CATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGA
1 CATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
60814 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAA-T
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
60861 CTATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 C-ATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
60926 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
* * *
60975 CATCATTTGATGGATCAACATTGCCAG-GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTTGATGGATCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
61039 AAGAAAAAGTTCATAATGAGAAGAA
65 AAGAAGAAGTTCATAATGAGAAGAA
61064 CTCATCAAGA
Statistics
Matches: 397, Mismatches: 26, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
112 2 0.01
113 349 0.88
114 7 0.02
115 4 0.01
116 35 0.09
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
CATCATTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATT
Found at i:61320 original size:3 final size:3
Alignment explanation
Indices: 61312--61447 Score: 193
Period size: 3 Copynumber: 45.7 Consensus size: 3
61302 TTTTTATCCA
* * * *
61312 TAT TAT TAT TAT TTT TAT TAT TAT TTT TAT TAT TTT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
61360 TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
61408 T-T TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
61448 AATATATTAA
Statistics
Matches: 116, Mismatches: 16, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
2 2 0.02
3 114 0.98
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:61936 original size:12 final size:12
Alignment explanation
Indices: 61919--61948 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
61909 AAAAAAAGGG
61919 GACAGAAAGAGA
1 GACAGAAAGAGA
61931 GACAGAAAGAGA
1 GACAGAAAGAGA
61943 GACAGA
1 GACAGA
61949 GACAGAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.57, C:0.10, G:0.33, T:0.00
Consensus pattern (12 bp):
GACAGAAAGAGA
Found at i:61980 original size:15 final size:16
Alignment explanation
Indices: 61960--61989 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
61950 ACAGAACCGG
61960 AGAGAAAA-AAAAAAC
1 AGAGAAAAGAAAAAAC
61975 AGAGAAAAGAAAAAA
1 AGAGAAAAGAAAAAA
61990 ACAAACTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AGAGAAAAGAAAAAAC
Found at i:62918 original size:24 final size:22
Alignment explanation
Indices: 62870--62918 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
62860 GTTTTAATAG
* *
62870 TATTTTTATTTTTATGAATAAA
1 TATTTTTATTTTCATAAATAAA
*
62892 TATTTTTATATATTCATAAATATA
1 TATTTTTAT-T-TTCATAAATAAA
62916 TAT
1 TAT
62919 ATAATAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 9 0.41
23 1 0.05
24 12 0.55
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTTTATTTTCATAAATAAA
Found at i:66612 original size:36 final size:35
Alignment explanation
Indices: 66547--66614 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
66537 TAAGATTTTA
* * *
66547 TTTAAAAAAAATATTATTAATATTTATGTATTGAT
1 TTTAAAAAAAATATCAGTAAGATTTATGTATTGAT
66582 TTTAAAAAAAATA-CAGTAAGATTTTCATGTATT
1 TTTAAAAAAAATATCAGTAAGA-TTT-ATGTATT
66615 TAAGGTTCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 5 0.18
35 16 0.57
36 7 0.25
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (35 bp):
TTTAAAAAAAATATCAGTAAGATTTATGTATTGAT
Found at i:68324 original size:24 final size:24
Alignment explanation
Indices: 68296--68344 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
68286 TAAAGAACCG
*
68296 AAATAAA-CTTAAATATACCATTAA
1 AAATAAAGCTTAAACAT-CCATTAA
*
68320 AAATAAAGTTTAAACATCCATTAA
1 AAATAAAGCTTAAACATCCATTAA
68344 A
1 A
68345 CCAACCACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (24 bp):
AAATAAAGCTTAAACATCCATTAA
Found at i:73412 original size:64 final size:64
Alignment explanation
Indices: 73344--73521 Score: 214
Period size: 64 Copynumber: 2.8 Consensus size: 64
73334 GAACACTTGA
* ** *
73344 TGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-G
1 TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAG
*** * **
73408 TGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAG
* * *
73473 TGCATCGATGCATGTAGTGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTT
73522 CAATTAATTC
Statistics
Matches: 96, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
64 50 0.52
65 46 0.48
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAG
Found at i:73495 original size:65 final size:65
Alignment explanation
Indices: 73359--73521 Score: 222
Period size: 65 Copynumber: 2.5 Consensus size: 65
73349 CGGTGCACCA
*
73359 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGG
** * **
73423 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATG
*
73487 T
65 G
* *
73488 AGTGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
73522 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.31
Consensus pattern (65 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGG
Found at i:73753 original size:20 final size:21
Alignment explanation
Indices: 73730--73769 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
73720 GAATCAAATA
73730 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
73750 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
73770 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:75110 original size:44 final size:42
Alignment explanation
Indices: 74996--75113 Score: 128
Period size: 44 Copynumber: 2.7 Consensus size: 42
74986 AAAACCCGAC
* * *
74996 GGATGCATCGGTGCATGGTCTTATGCATCGATGCATATTCAAG
1 GGATGCATCGGTGCATTGT-TAATGCATCGATACATATTCAAG
* * *
75039 GCATGCATCGGTGCATCATGGTGATGCATCGATACATATTCAAAG
1 GGATGCATCGGTGCAT--TGTTAATGCATCGATACATATTC-AAG
*
75084 GGATGCATCGATGCATTGTTAAATGCATCG
1 GGATGCATCGGTGCATTGTT-AATGCATCG
75114 GTGCATGAAG
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
43 18 0.29
44 26 0.42
45 18 0.29
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (42 bp):
GGATGCATCGGTGCATTGTTAATGCATCGATACATATTCAAG
Found at i:80957 original size:64 final size:64
Alignment explanation
Indices: 80889--81066 Score: 205
Period size: 64 Copynumber: 2.8 Consensus size: 64
80879 GAACACTTGA
* ** *
80889 TGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-G
1 TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAG
*** * **
80953 TGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAG
* * * *
81018 TGGATCGATGCATGTAGTGTGCATCGGTGCATGGAATGCATTCGATGTT
1 TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTT
81067 CAATTAATTC
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
64 50 0.53
65 45 0.47
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAG
Found at i:81040 original size:65 final size:65
Alignment explanation
Indices: 80904--81066 Score: 213
Period size: 65 Copynumber: 2.5 Consensus size: 65
80894 CGGTGCACCA
*
80904 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTGGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGG
** * ** *
80968 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGGATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAG-GTGCATCGATGCATG
*
81032 T
65 G
* *
81033 AGTGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
81067 CAATTAATTC
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.31
Consensus pattern (65 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGGTGCATCGATGCATGG
Found at i:81306 original size:20 final size:21
Alignment explanation
Indices: 81283--81322 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
81273 GAATCGAATA
81283 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
81303 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
81323 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:82627 original size:24 final size:24
Alignment explanation
Indices: 82582--82631 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
82572 ATAAAGAACC
*
82582 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
82606 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
82630 AA
1 AA
82632 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:87768 original size:2 final size:2
Alignment explanation
Indices: 87761--87793 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
87751 TAATTCGGTG
87761 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
87794 TAAAATCGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:94390 original size:237 final size:237
Alignment explanation
Indices: 93973--94400 Score: 718
Period size: 237 Copynumber: 1.8 Consensus size: 237
93963 TTTCGAATTG
* *
93973 GAGCATGTGACATTTGTTGCTGACATAGGGATGGATCCATCAATTATTTAAGCTGATAGCTTTAT
1 GAGCATGTGACATTTGTTGCTGACATAGAGATGGATCCATCAATTATTTAAGCTGATAGCTTTAG
94038 ATTATCTTCTTAAGTGCTTACAAAATCATTCTAGAACTTACGTCATTAGATTGTAGTTATGCTTC
66 ATTATCTTCTTAAGTGCTTACAAAATCATTCTAGAACTTACGTCATTAGATTGTAGTTATGCTTC
* *
94103 TATTATTCCATTTGATAATCTAATTGAGCTTCATTATATCGTCGCTGCTTGAAGCTTTGAATTGT
131 TATTATTCCATTCGACAATCTAATTGAGCTTCATTATATCGTCGCTGCTTGAAGCTTTGAATTGT
94168 TTGACTGTGATTTATTTGGAGTATTCTTAGAATTGGAGCACT
196 TTGACTGTGATTTATTTGGAGTATTCTTAGAATTGGAGCACT
* * *
94210 GAGCATGTGGCATTTGTTGCTGATATAGAGATGGATCCGTCAATTATTTAAGCTGATAGCTTTAG
1 GAGCATGTGACATTTGTTGCTGACATAGAGATGGATCCATCAATTATTTAAGCTGATAGCTTTAG
*
94275 ATTATCTTCTTTAAGTGCTTACAAAATTATTCTAGAACTTATC-TCATTAGATTGTA-TTATGCT
66 ATTATCTTC-TTAAGTGCTTACAAAATCATTCTAGAACTTA-CGTCATTAGATTGTAGTTATGCT
* *
94338 TCTATTATTCCATTCGACAATCTAATTGAGCTTCATTATATCATTC-CTGCTTGAAGTTTTGAA
129 TCTATTATTCCATTCGACAATCTAATTGAGCTTCATTATATC-GTCGCTGCTTGAAGCTTTGAA
94401 CTGGTTATCA
Statistics
Matches: 178, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
237 132 0.74
238 45 0.25
239 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (237 bp):
GAGCATGTGACATTTGTTGCTGACATAGAGATGGATCCATCAATTATTTAAGCTGATAGCTTTAG
ATTATCTTCTTAAGTGCTTACAAAATCATTCTAGAACTTACGTCATTAGATTGTAGTTATGCTTC
TATTATTCCATTCGACAATCTAATTGAGCTTCATTATATCGTCGCTGCTTGAAGCTTTGAATTGT
TTGACTGTGATTTATTTGGAGTATTCTTAGAATTGGAGCACT
Found at i:106769 original size:20 final size:20
Alignment explanation
Indices: 106733--106771 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
106723 TCGGACTGAA
**
106733 CTGAGTCAACTTGAACCGAC
1 CTGAGTCAACTCAAACCGAC
106753 CTGAGTCAACTCAAACCGA
1 CTGAGTCAACTCAAACCGA
106772 TTTGATCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.18
Consensus pattern (20 bp):
CTGAGTCAACTCAAACCGAC
Found at i:109666 original size:32 final size:32
Alignment explanation
Indices: 109630--109695 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
109620 ATGCGATTTT
*
109630 ATTATTTTGAGTGACATGATAAATATCATGTC
1 ATTATTTTGAGTGACATGATAAATATCACGTC
* *
109662 ATTATTTTGGGTGACATGATACATATCACGTC
1 ATTATTTTGAGTGACATGATAAATATCACGTC
109694 AT
1 AT
109696 CAATTAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (32 bp):
ATTATTTTGAGTGACATGATAAATATCACGTC
Found at i:111865 original size:27 final size:27
Alignment explanation
Indices: 111835--111896 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
111825 TCAGGACTAT
*
111835 TGATGTTACATTTTTTATCTTCAAAGA
1 TGATGTGACATTTTTTATCTTCAAAGA
111862 TGATGTGACATTTTTTATCTTCAAAGA
1 TGATGTGACATTTTTTATCTTCAAAGA
111889 TGATGTGA
1 TGATGTGA
111897 TATTATCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (27 bp):
TGATGTGACATTTTTTATCTTCAAAGA
Done.