Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002242.1 Hibiscus syriacus cultivar Beakdansim tig00004560_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: 87940
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:150 original size:21 final size:21
Alignment explanation
Indices: 124--182 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
114 TCGAGGGTTC
*
124 TACGAGGTCTTTCGGGACATA
1 TACGAGGTCCTTCGGGACATA
**
145 TACGAGGTCCTTCTAGACATA
1 TACGAGGTCCTTCGGGACATA
*
166 TATGAGGTCCTTCGGGA
1 TACGAGGTCCTTCGGGA
183 TAATTTTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (21 bp):
TACGAGGTCCTTCGGGACATA
Found at i:4433 original size:16 final size:16
Alignment explanation
Indices: 4412--4443 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4402 GACGATGGAT
4412 TTTATGATGGGGTTAC
1 TTTATGATGGGGTTAC
4428 TTTATGATGGGGTTAC
1 TTTATGATGGGGTTAC
4444 CCTTAGCTCC
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:0.19, C:0.06, G:0.31, T:0.44
Consensus pattern (16 bp):
TTTATGATGGGGTTAC
Found at i:6739 original size:18 final size:18
Alignment explanation
Indices: 6712--6757 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
6702 GCATGGCTAG
6712 TGCA-TCGATGCATCAAA
1 TGCATTCGATGCATCAAA
6729 TGCATTCGATGCATCAAA
1 TGCATTCGATGCATCAAA
6747 TGCATTCGATG
1 TGCATTCGATG
6758 TTTTCATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (18 bp):
TGCATTCGATGCATCAAA
Found at i:6782 original size:83 final size:82
Alignment explanation
Indices: 6654--6822 Score: 236
Period size: 83 Copynumber: 2.0 Consensus size: 82
6644 AGAGTGCATA
* * *
6654 GATGCATCAAGTGCATTCGATGTTTCAAAATAGCTAGAGTGCATCGATGCATGGCT-AGTGCATC
1 GATGCATCAAATGCATTCGATGTTTCAAAATACCTACAGTGCATCGATGCATGG-TAAGTGCATC
6718 GATGCATCAAATGCATTC
65 GATGCATCAAATGCATTC
*
6736 GATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCT-CAGTGCATCGGTGCATGGTAAGTGCA
1 GATGCATCAAATGCATTCGATG-TTTCA-AAATA-CCTACAGTGCATCGATGCATGGTAAGTGCA
*
6799 TCGATGCATGAAATGCATTC
63 TCGATGCATCAAATGCATTC
6819 GATG
1 GATG
6823 TTTAATTTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
82 22 0.28
83 51 0.65
84 5 0.06
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (82 bp):
GATGCATCAAATGCATTCGATGTTTCAAAATACCTACAGTGCATCGATGCATGGTAAGTGCATCG
ATGCATCAAATGCATTC
Found at i:6845 original size:64 final size:65
Alignment explanation
Indices: 6729--6854 Score: 150
Period size: 65 Copynumber: 1.9 Consensus size: 65
6719 ATGCATCAAA
* **
6729 TGCATTCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAA
1 TGCATTCGATGCATCAAATGCATTCGATGTTTTAATAAAAT-CTCAGTGCATCAATGCATGGTAA
6794 G
65 G
* **
6795 TGCA-TCGATGCATGAAATGCATTCGATG-TTTAATTTAAT-TCATGGTGCATCAATGCATGG
1 TGCATTCGATGCATCAAATGCATTCGATGTTTTAATAAAATCTCA--GTGCATCAATGCATGG
6855 ATTGGTTCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
62 3 0.06
64 22 0.42
65 23 0.44
66 4 0.08
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (65 bp):
TGCATTCGATGCATCAAATGCATTCGATGTTTTAATAAAATCTCAGTGCATCAATGCATGGTAAG
Found at i:6886 original size:20 final size:20
Alignment explanation
Indices: 6837--6892 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
6827 ATTTAATTCA
*
6837 TGGTGCATCAATGCATGGAT
1 TGGTGCATCGATGCATGGAT
* *
6857 TGGTTCATCGATGTATGGAT
1 TGGTGCATCGATGCATGGAT
*
6877 TGGTGCATCGTTGCAT
1 TGGTGCATCGATGCAT
6893 CACTCTGAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.14, G:0.30, T:0.36
Consensus pattern (20 bp):
TGGTGCATCGATGCATGGAT
Found at i:15454 original size:19 final size:19
Alignment explanation
Indices: 15430--15481 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
15420 AATAGCCAGA
15430 GTGCATCGATGCATGGTTG
1 GTGCATCGATGCATGGTTG
15449 GTGCATCGATGCATGGTTG
1 GTGCATCGATGCATGGTTG
15468 GTGCATCGATGCAT
1 GTGCATCGATGCAT
15482 CAAATGCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.35, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGTTG
Found at i:17056 original size:21 final size:21
Alignment explanation
Indices: 17030--17109 Score: 142
Period size: 21 Copynumber: 3.8 Consensus size: 21
17020 TCGAGGGTTC
17030 TACGAGGTCCTTCGGGACATA
1 TACGAGGTCCTTCGGGACATA
17051 TACGAGGTCCTTCGGGACATA
1 TACGAGGTCCTTCGGGACATA
17072 TACGAGGTCCTTCGGGACATA
1 TACGAGGTCCTTCGGGACATA
* *
17093 TATGAGGTCTTTCGGGA
1 TACGAGGTCCTTCGGGA
17110 TAATTTTATA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (21 bp):
TACGAGGTCCTTCGGGACATA
Found at i:18393 original size:49 final size:48
Alignment explanation
Indices: 18340--18433 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 48
18330 GATGCCTTAA
18340 TTCTATTTATTTTTCAGCTATGCTTATTTTTTTAATAACATACAATTAG
1 TTCTATTTATTTTTCAGCTATGCTTA-TTTTTTAATAACATACAATTAG
* * * * *
18389 TTCTATTTGTTTTTTAGTTATGTTTATTTTTTAATAATATACAAT
1 TTCTATTTATTTTTCAGCTATGCTTATTTTTTAATAACATACAAT
18434 AAAAATGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
48 18 0.45
49 22 0.55
ACGTcount: A:0.28, C:0.09, G:0.06, T:0.57
Consensus pattern (48 bp):
TTCTATTTATTTTTCAGCTATGCTTATTTTTTAATAACATACAATTAG
Found at i:19165 original size:20 final size:20
Alignment explanation
Indices: 19142--19198 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
19132 TTCCATATTT
19142 TTTCATACTCTTCCATAAGG-
1 TTTCATACTCTTCCA-AAGGA
*
19162 TTTCATACATC-TCCAGAGGA
1 TTTCATAC-TCTTCCAAAGGA
*
19182 TTTCACACTCTTCCAAA
1 TTTCATACTCTTCCAAA
19199 AGCTTCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 5 0.16
20 24 0.77
21 2 0.06
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.35
Consensus pattern (20 bp):
TTTCATACTCTTCCAAAGGA
Found at i:19256 original size:20 final size:19
Alignment explanation
Indices: 19233--19289 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
19223 TCTAGAGTTC
19233 TCTAGAATGTTCTAGAAA-A
1 TCTAGAAT-TTCTAGAAACA
* *
19252 TTCTACACTTCTCTAGAAACA
1 -TCTAGAATT-TCTAGAAACA
19273 TCTAGAATTTTCTAGAA
1 TCTAGAA-TTTCTAGAA
19290 CCTCTCCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.03
20 26 0.87
21 3 0.10
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (19 bp):
TCTAGAATTTCTAGAAACA
Found at i:21551 original size:21 final size:20
Alignment explanation
Indices: 21511--21551 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
21501 TTCGAACTCT
21511 TTCTTCAATAGTTATATTCA
1 TTCTTCAATAGTTATATTCA
21531 TTCTCTCATATAGTT-TATTCA
1 TTCT-TCA-ATAGTTATATTCA
21552 ATTATGGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 9 0.47
22 6 0.32
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (20 bp):
TTCTTCAATAGTTATATTCA
Found at i:24716 original size:30 final size:31
Alignment explanation
Indices: 24670--24729 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
24660 GGAAATGGTC
* *
24670 CCTAATGTTATAGATCCGTTTGAT-TTAGTA
1 CCTAATATTATAGATCCGTTCGATGTTAGTA
*
24700 CCTAATATTATCGATCCGTTCGATGTTAGT
1 CCTAATATTATAGATCCGTTCGATGTTAGT
24730 CCCTCAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (31 bp):
CCTAATATTATAGATCCGTTCGATGTTAGTA
Found at i:26362 original size:13 final size:13
Alignment explanation
Indices: 26341--26380 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
26331 AACAACTATC
*
26341 CCTAGTTTTCTCT
1 CCTAATTTTCTCT
*
26354 CCTAATTTTATCT
1 CCTAATTTTCTCT
*
26367 TCTAATTTTCTCT
1 CCTAATTTTCTCT
26380 C
1 C
26381 ATTGATAAGT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.15, C:0.28, G:0.03, T:0.55
Consensus pattern (13 bp):
CCTAATTTTCTCT
Found at i:27282 original size:3 final size:3
Alignment explanation
Indices: 27276--27303 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27266 AATTATTATC
27276 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
27304 AATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:27311 original size:3 final size:3
Alignment explanation
Indices: 27305--27331 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
27295 TAATAATAAA
27305 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
27332 TTGCATCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:28196 original size:17 final size:17
Alignment explanation
Indices: 28176--28214 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
28166 ATATTTAAAG
28176 AAAACCCTAATTTAGAC
1 AAAACCCTAATTTAGAC
*
28193 AAAACTCTAATTTAGAC
1 AAAACCCTAATTTAGAC
28210 AAAAC
1 AAAAC
28215 AAACCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.05, T:0.23
Consensus pattern (17 bp):
AAAACCCTAATTTAGAC
Found at i:44497 original size:25 final size:24
Alignment explanation
Indices: 44413--44497 Score: 59
Period size: 25 Copynumber: 3.4 Consensus size: 24
44403 TTTTTTTTTC
* *
44413 AAAATTATTAAATATAAAAGTAATTT
1 AAAATAATTAAAT-TAAAA-TTATTT
*
44439 AAAATAAAT-AA-TAAAATAATATTTT
1 AAAATAATTAAATTAAAAT--TA-TTT
*
44464 ATAAT-ATTAAATTTAAAATTATTT
1 AAAATAATTAAA-TTAAAATTATTT
44488 AAAATAATTA
1 AAAATAATTA
44498 TTATCATTTG
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
22 1 0.02
23 5 0.11
24 10 0.22
25 17 0.37
26 7 0.15
27 6 0.13
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (24 bp):
AAAATAATTAAATTAAAATTATTT
Found at i:45393 original size:18 final size:19
Alignment explanation
Indices: 45360--45396 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
45350 TGACAAACAA
45360 TTAAATTAAATTTTATATT
1 TTAAATTAAATTTTATATT
*
45379 TTAAATT-ATTTTTATATT
1 TTAAATTAAATTTTATATT
45397 AAATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAAATTAAATTTTATATT
Found at i:48052 original size:27 final size:28
Alignment explanation
Indices: 47981--48065 Score: 145
Period size: 28 Copynumber: 3.1 Consensus size: 28
47971 AATTCCATAG
*
47981 AAGCAGAGGCAACTGAAATACATAATAT
1 AAGCATAGGCAACTGAAATACATAATAT
48009 AAGCATAGGCAACTGAAATACATAATAT
1 AAGCATAGGCAACTGAAATACATAATAT
*
48037 AAGC-TAGGCAAATGAAATACATAATAT
1 AAGCATAGGCAACTGAAATACATAATAT
48064 AA
1 AA
48066 TCATGGATTC
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
27 24 0.44
28 31 0.56
ACGTcount: A:0.52, C:0.13, G:0.15, T:0.20
Consensus pattern (28 bp):
AAGCATAGGCAACTGAAATACATAATAT
Found at i:49475 original size:41 final size:41
Alignment explanation
Indices: 49430--49510 Score: 126
Period size: 41 Copynumber: 2.0 Consensus size: 41
49420 ATTTATTTAT
* *
49430 GTTTTTATATATTTTTACTTAATTCGTATCATAATTAAATA
1 GTTTTTATATATTATTACTTAATTCGAATCATAATTAAATA
* *
49471 GTTTTTATATATTATTACTTAATTTGAATCGTAATTAAAT
1 GTTTTTATATATTATTACTTAATTCGAATCATAATTAAAT
49511 TTAAGGTGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (41 bp):
GTTTTTATATATTATTACTTAATTCGAATCATAATTAAATA
Found at i:49808 original size:43 final size:43
Alignment explanation
Indices: 49649--49815 Score: 219
Period size: 43 Copynumber: 3.9 Consensus size: 43
49639 CGGGTTTAAA
* * **
49649 AAAAATGCTGCTAAATAACAAACTTGTTGTGGCGTTTGTGCCT
1 AAAAACGCTGCTAAATAACAAACATGTTGCAGCGTTTGTGCCT
* *
49692 AAAAACACTGCTAAATAACAAACATGTTG-TGCAGTTTGTGCCT
1 AAAAACGCTGCTAAATAACAAACATGTTGCAGC-GTTTGTGCCT
* * *
49735 AAAAACGCAGCTAGATAAAAAACATGTTGCAGCGTTTGTGCCT
1 AAAAACGCTGCTAAATAACAAACATGTTGCAGCGTTTGTGCCT
* *
49778 AAAAACGCTGCTAAATAACAAACCTATTGCAGCGTTTG
1 AAAAACGCTGCTAAATAACAAACATGTTGCAGCGTTTG
49816 AAAATACAAA
Statistics
Matches: 108, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 2 0.02
43 104 0.96
44 2 0.02
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (43 bp):
AAAAACGCTGCTAAATAACAAACATGTTGCAGCGTTTGTGCCT
Found at i:53879 original size:60 final size:60
Alignment explanation
Indices: 53793--53911 Score: 229
Period size: 60 Copynumber: 2.0 Consensus size: 60
53783 TTCCAATTGT
53793 TGAGGCATACAACACCTTCACCATGTGTGCACATTCTTCCTCCGTATTTTGTGATTGTTA
1 TGAGGCATACAACACCTTCACCATGTGTGCACATTCTTCCTCCGTATTTTGTGATTGTTA
*
53853 TGAGGCATACAACACCTTCACCATGTGTGCACATTCTTCCTCCGTCTTTTGTGATTGTT
1 TGAGGCATACAACACCTTCACCATGTGTGCACATTCTTCCTCCGTATTTTGTGATTGTT
53912 CTTTGGAGAG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (60 bp):
TGAGGCATACAACACCTTCACCATGTGTGCACATTCTTCCTCCGTATTTTGTGATTGTTA
Found at i:54804 original size:21 final size:22
Alignment explanation
Indices: 54778--54820 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
54768 ATAATCTCTT
* *
54778 GCATGTC-TGAACCTGCAACAA
1 GCATGTCATCAACATGCAACAA
54799 GCATGTCATCAACATGCAACAA
1 GCATGTCATCAACATGCAACAA
54821 TAAAATAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.37, C:0.28, G:0.16, T:0.19
Consensus pattern (22 bp):
GCATGTCATCAACATGCAACAA
Found at i:59192 original size:30 final size:29
Alignment explanation
Indices: 59158--59232 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 29
59148 TCTGGACGAT
* * *
59158 TTTCCCGATATATCACCGGTGAACAGTATA
1 TTTCCCGATATAACACAGGTCAA-AGTATA
* *
59188 TTTCCCGATCTAACACAGGTCAAATTATA
1 TTTCCCGATATAACACAGGTCAAAGTATA
*
59217 TTTCCCGATCTAACAC
1 TTTCCCGATATAACAC
59233 CCTTAGCAGT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 21 0.52
30 19 0.47
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.31
Consensus pattern (29 bp):
TTTCCCGATATAACACAGGTCAAAGTATA
Found at i:59535 original size:12 final size:10
Alignment explanation
Indices: 59494--59534 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
59484 TTTATCACAC
59494 CAAATTCTCT
1 CAAATTCTCT
59504 CAAATTCTCT
1 CAAATTCTCT
59514 -AAATTTCTCT
1 CAAA-TTCTCT
*
59524 CAAATACTCT
1 CAAATTCTCT
59534 C
1 C
59535 TTTTAAGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:59797 original size:110 final size:111
Alignment explanation
Indices: 59657--59877 Score: 390
Period size: 110 Copynumber: 2.0 Consensus size: 111
59647 TGGAAATCAT
*
59657 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* **
59722 TATTTAGTT-ATTTGTTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
*
59767 ATATCTCGACACTTTGCTGATATGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
59832 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
59878 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 34 0.32
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:61394 original size:15 final size:15
Alignment explanation
Indices: 61374--61403 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
61364 GCAGGACCTT
61374 CCCAGCAGCCACCGC
1 CCCAGCAGCCACCGC
61389 CCCAGCAGCCACCGC
1 CCCAGCAGCCACCGC
61404 AACTATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (15 bp):
CCCAGCAGCCACCGC
Found at i:61427 original size:18 final size:18
Alignment explanation
Indices: 61400--61439 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
61390 CCAGCAGCCA
*
61400 CCGCAACTATATATTATG
1 CCGCAACTATATATGATG
*
61418 CCGCAGCTATATATGATG
1 CCGCAACTATATATGATG
61436 CCGC
1 CCGC
61440 CATCGCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
CCGCAACTATATATGATG
Found at i:64909 original size:51 final size:51
Alignment explanation
Indices: 64833--64953 Score: 233
Period size: 51 Copynumber: 2.4 Consensus size: 51
64823 TACAAAACGC
*
64833 GTACCTGCCCCGCGCTATATAAAATTATGTCAGGAGTAAAGGTATGTCGCG
1 GTACCTGCCCCGCGCTATATAAAATTATGTCAAGAGTAAAGGTATGTCGCG
64884 GTACCTGCCCCGCGCTATATAAAATTATGTCAAGAGTAAAGGTATGTCGCG
1 GTACCTGCCCCGCGCTATATAAAATTATGTCAAGAGTAAAGGTATGTCGCG
64935 GTACCTGCCCCGCGCTATA
1 GTACCTGCCCCGCGCTATA
64954 CCCCTACGTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (51 bp):
GTACCTGCCCCGCGCTATATAAAATTATGTCAAGAGTAAAGGTATGTCGCG
Found at i:65071 original size:51 final size:50
Alignment explanation
Indices: 64965--65088 Score: 124
Period size: 51 Copynumber: 2.4 Consensus size: 50
64955 CCCTACGTGG
* * *
64965 CGTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTATATGCCAGATCAC
1 CGTATAGCGCG-TGCAGGGGCCGCGCTATACCCACGTAGACGCCAAATCAC
* * **
65016 CGTATAGCGCAGTGCAGGTGCCGCGCTATACCCCACGT-GGCGCCAAATCGT
1 CGTATAGCGC-GTGCAGGGGCCGCGCTATA-CCCACGTAGACGCCAAATCAC
*
65067 CGTATAACGCGGTGCAAGGGGC
1 CGTATAGCGC-GTGC-AGGGGC
65089 GCACTTTACT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
51 47 0.78
52 13 0.22
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.17
Consensus pattern (50 bp):
CGTATAGCGCGTGCAGGGGCCGCGCTATACCCACGTAGACGCCAAATCAC
Found at i:68268 original size:12 final size:12
Alignment explanation
Indices: 68251--68275 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
68241 GTAAACGAGG
68251 AGAGATATTATA
1 AGAGATATTATA
68263 AGAGATATTATA
1 AGAGATATTATA
68275 A
1 A
68276 TTTAAAGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
AGAGATATTATA
Found at i:68318 original size:40 final size:40
Alignment explanation
Indices: 68263--68339 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
68253 AGATATTATA
* * *
68263 AGAGATATTATAATTTAAAGTTGAAAAATAATAATTTAGG
1 AGAGATAGTATAATTTAAAGTTAAAAAACAATAATTTAGG
68303 AGAGATAGTATAATTTAAAGTTAAAAAACAATAATTT
1 AGAGATAGTATAATTTAAAGTTAAAAAACAATAATTT
68340 TAGAACGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.52, C:0.01, G:0.13, T:0.34
Consensus pattern (40 bp):
AGAGATAGTATAATTTAAAGTTAAAAAACAATAATTTAGG
Found at i:68678 original size:13 final size:13
Alignment explanation
Indices: 68656--68685 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
68646 AATCATCAAT
*
68656 TTCAGTTAAAAGA
1 TTCAGGTAAAAGA
68669 TTCAGGTAAAAGA
1 TTCAGGTAAAAGA
68682 TTCA
1 TTCA
68686 AAACTAGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (13 bp):
TTCAGGTAAAAGA
Found at i:73103 original size:20 final size:21
Alignment explanation
Indices: 73066--73105 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
73056 AAATTAAGTT
73066 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
73087 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
73106 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:73391 original size:65 final size:63
Alignment explanation
Indices: 73275--73481 Score: 220
Period size: 65 Copynumber: 3.2 Consensus size: 63
73265 ATTTGAGGTG
* * * * *
73275 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATTC
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
73339 C
63 C
* *
73340 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * * **
73405 ATGCATCAATGCA-CAAGCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATC-A-CCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
73469 ATGCATCGATGCA
1 ATGCACCGATGCA
73482 CACTTGGTGC
Statistics
Matches: 122, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
63 1 0.01
64 36 0.30
65 83 0.68
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:81594 original size:20 final size:21
Alignment explanation
Indices: 81557--81596 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
81547 AAATTAAGTT
81557 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
81578 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
81597 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:81882 original size:65 final size:63
Alignment explanation
Indices: 81766--81964 Score: 189
Period size: 65 Copynumber: 3.2 Consensus size: 63
81756 ATTTGAGGTG
* * * * *
81766 ATGCACCGATGCATCAACCATGCATCGATGCATTAGTGAAT-TAATTGAAACATCGAATGCATTC
1 ATGCACCGATGCATC-ACCATGCATCGATGCACT-CTGAATAT-TTTCAAACATCGAATGCATTT
81830 C
63 C
* *
81831 ATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTG
1 ATGCACCGATGCA-TCACCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTTC
* * **
81896 ATGCA-C-A---A--GCCATGCATCGATGCACTCAGGCTATTTTCAAACATCGAATGCATTTC
1 ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
*
81952 ATGCATCGATGCA
1 ATGCACCGATGCA
81965 CACTTGGTGC
Statistics
Matches: 114, Mismatches: 12, Indels: 20
0.78 0.08 0.14
Matches are distributed among these distances:
56 22 0.19
57 27 0.24
58 1 0.01
60 1 0.01
61 1 0.01
63 1 0.01
64 8 0.07
65 51 0.45
66 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.28
Consensus pattern (63 bp):
ATGCACCGATGCATCACCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTTC
Found at i:81945 original size:56 final size:57
Alignment explanation
Indices: 81848--81956 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
81838 GATGCATTCT
* *
81848 CCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTTGATGCACAAG
1 CCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCACAAG
**
81905 CCATGCATCGATGCACTCAGGCTATTTTC-AAACATCGAATGCATTTCATGCA
1 CCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCA
81957 TCGATGCACA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
56 22 0.46
57 26 0.54
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (57 bp):
CCATGCATCGATGCACTCAGAATATTTTCAAAACATCGAATGCATTTCATGCACAAG
Found at i:85521 original size:183 final size:181
Alignment explanation
Indices: 85095--85571 Score: 760
Period size: 183 Copynumber: 2.6 Consensus size: 181
85085 GATCCAAATT
* * * *
85095 AAAAATGTATCGATCCATATCAATATAACAAGTAAAAATATGACAAAACCGGTCA-CGAAAAGAT
1 AAAAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCGGT-ATCGAAATGAT
* * *
85159 AATACCGGTAAAGCGCTACCAGATATATTGAAAGTGTCGATAC-TTAATATAAGTATCGACATTT
65 AAAACCAGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
*
85223 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAGTGTCGATACTTTAT
130 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAGTGTCGATACTTTAA
* * *
85275 AAAAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCGGTATCGAAATGATA
*
85340 AAACCTGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
66 AAACCAGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
* *
85405 GTGAATTTAAAAGAGAAGTAGTTTTAGCGCCTATAAAGTGTCGATACTTTAAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCATAT-AAGTGTCGATACTTT-AA
* *
85458 AAAAATGTATCGATCCACAACGATATAACATGTAAAAATATGACAAAACCAGTATCGAAATGATA
1 AAAAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCGGTATCGAAATGATA
*
85523 AAACCAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
66 AAACCAGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATA
85572 AGTACGTGTA
Statistics
Matches: 274, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
179 1 0.00
180 96 0.35
181 53 0.19
182 15 0.05
183 109 0.40
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCACAACGATATAACAAGTAAAAATATGACAAAACCGGTATCGAAATGATA
AAACCAGTAAAGCGCTACCAGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
GTGAATTTAAAAGAGAAGCAGTTTTAGCGCATATAAGTGTCGATACTTTAA
Found at i:86926 original size:198 final size:192
Alignment explanation
Indices: 86621--87192 Score: 541
Period size: 197 Copynumber: 2.9 Consensus size: 192
86611 TCTACAACAT
* ** * *
86621 GTATCGACACTTTTTAATATTGTGTCGATACTTTTTGTCCAGAATGGATGCCAAA-AAGGGTGAA
1 GTATCGACACTTTTTAAT-TTGTGTCGATAC-TTTTGTCCATAATTAATGCCAAACGA-GGTG-C
* * * *
86685 CGCACAAAGTGTTGATACATTT-TAAAAACGTGTCGAT-CCAAAAACATCGAAATCCATAATTAT
62 CGCATAAAATGTCGATACATTTAT-AAAA-GTATCGATCCCAAAAACATCGAAA-CCA-AATTAT
* *
86748 AATATAATAGGTAAA-TTACAATGTAACCGGTATAAATATATCGGGTTTATGAAAAAATAGGT-G
123 AATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA-C-GGTTTATGAAAAAATAGATCG
*
86811 AGCATAAA
186 A-AATAAA
*
86819 GTATCGACACTTGTTAAATTTGTGTCGATACATTTTGTCCATAATTAATGCCAAACGAGGTGCCG
1 GTATCGACACTT-TTTAATTTGTGTCGATAC-TTTTGTCCATAATTAATGCCAAACGAGGTGCCG
* * * *
86884 CATAGATTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACGAAAATTACAATG
64 CATAAAATGTCGATACATTTA-TAAAAGTATCGATCCCAAAAACATCGAAAC-CAAATTATAATG
* * * *
86949 TGATAGGTAAATTTTACAATGTACCCGGTATAAATATACGGTTTATGAGAAAATAGATCTAAATA
127 TAATAGGTAAA-TTTACAATGTAACCGGTATAAATATACGGTTTATGAAAAAATAGATCGAAATA
*
87014 AT
191 AA
* * * *
87016 GTAGCTACACCTTTTTAGTTTGTGTCGATACTTTT-TCCAGAATGAAATATGAATGCCCAACGAG
1 GTATCGACA-CTTTTTAATTTGTGTCGATACTTTTGTCC---AT--AAT-T-AATGCCAAACGAG
* * ** *
87080 GTGCAAGCATAAAATGTCGATACATTTA-AAATTGTATCGATCTAAAAAACATCGAAACC-AATA
58 GTGC-CGCATAAAATGTCGATACATTTATAAA-AGTATCGATCCCAAAAACATCGAAACCAAATT
* *
87143 ATAATGTAATAGATAAATTTACAATGTTACC-GTATAAATATACCGGTTTA
121 ATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATA-CGGTTTA
87193 CTTCGAAAAT
Statistics
Matches: 314, Mismatches: 40, Indels: 39
0.80 0.10 0.10
Matches are distributed among these distances:
195 3 0.01
196 4 0.01
197 88 0.28
198 86 0.27
199 50 0.16
200 20 0.06
201 4 0.01
202 39 0.12
203 20 0.06
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (192 bp):
GTATCGACACTTTTTAATTTGTGTCGATACTTTTGTCCATAATTAATGCCAAACGAGGTGCCGCA
TAAAATGTCGATACATTTATAAAAGTATCGATCCCAAAAACATCGAAACCAAATTATAATGTAAT
AGGTAAATTTACAATGTAACCGGTATAAATATACGGTTTATGAAAAAATAGATCGAAATAAA
Found at i:87345 original size:25 final size:23
Alignment explanation
Indices: 87284--87333 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
87274 CGGTTAAATG
*
87284 CCTATTTTATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
*
87307 CCTATTACATTATATAAGCGCTA
1 CCTATTATATTATATAAGCGCTA
87330 CCTA
1 CCTA
87334 ATATGTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (23 bp):
CCTATTATATTATATAAGCGCTA
Done.