Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003118.1 Hibiscus syriacus cultivar Beakdansim tig00006530_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: 86799
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:3118 original size:35 final size:36
Alignment explanation
Indices: 3048--3120 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
3038 TCACTAATTT
*
3048 AGGTTTCATAAGAAATTTGGGTATTTTTCTTATTAA
1 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
*
3084 AGGTTTCATGAGAAATTTGAGTA-TTTTCTTATTAA
1 AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
3119 AG
1 AG
3121 CTTAATTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 14 0.40
36 21 0.60
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (36 bp):
AGGTTTCATAAGAAATTTGAGTATTTTTCTTATTAA
Found at i:7553 original size:14 final size:14
Alignment explanation
Indices: 7534--7563 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7524 TTTAGATTTT
*
7534 TTAAAATTACATTA
1 TTAAAAATACATTA
7548 TTAAAAATACATTA
1 TTAAAAATACATTA
7562 TT
1 TT
7564 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:7655 original size:7 final size:7
Alignment explanation
Indices: 7643--7830 Score: 143
Period size: 7 Copynumber: 26.9 Consensus size: 7
7633 TTATGTAATA
7643 GGTTTAT
1 GGTTTAT
*
7650 GGTTTAG
1 GGTTTAT
*
7657 GGTTTAG
1 GGTTTAT
7664 GGTTTA-
1 GGTTTAT
*
7670 GGATTTAG
1 GG-TTTAT
7678 GGTTTAT
1 GGTTTAT
7685 GGTTTAT
1 GGTTTAT
*
7692 GATTTAT
1 GGTTTAT
* *
7699 AAG-TTAG
1 -GGTTTAT
*
7706 GGTTTGT
1 GGTTTAT
7713 GGTTTAT
1 GGTTTAT
* *
7720 GATTCAT
1 GGTTTAT
* *
7727 AAG-TTAG
1 -GGTTTAT
7734 GGTTTAT
1 GGTTTAT
7741 GGTTTAT
1 GGTTTAT
*
7748 GGTTT-G
1 GGTTTAT
*
7754 GGATTCAT
1 GG-TTTAT
7762 GGTTTAT
1 GGTTTAT
7769 GGTTTAT
1 GGTTTAT
7776 GGTTTAT
1 GGTTTAT
*
7783 GATTTAT
1 GGTTTAT
7790 GGTTTAT
1 GGTTTAT
*
7797 GGTTT-G
1 GGTTTAT
*
7803 GGATTCAT
1 GG-TTTAT
7811 GGTTTAT
1 GGTTTAT
*
7818 GATTTAT
1 GGTTTAT
7825 GGTTTA
1 GGTTTA
7831 ATTTATACAC
Statistics
Matches: 141, Mismatches: 30, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
6 8 0.06
7 127 0.90
8 6 0.04
ACGTcount: A:0.19, C:0.02, G:0.30, T:0.50
Consensus pattern (7 bp):
GGTTTAT
Found at i:9475 original size:16 final size:16
Alignment explanation
Indices: 9454--9484 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9444 AGTAAAATAA
*
9454 AACAATCAGGATGTTT
1 AACAATCAGCATGTTT
9470 AACAATCAGCATGTT
1 AACAATCAGCATGTT
9485 ACTGTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (16 bp):
AACAATCAGCATGTTT
Found at i:9886 original size:17 final size:17
Alignment explanation
Indices: 9864--9896 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
9854 TTCGAGTTCG
9864 AGTTCGAGCTTGAATCA
1 AGTTCGAGCTTGAATCA
9881 AGTTCGAGCTTGAATC
1 AGTTCGAGCTTGAATC
9897 GGGCTCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (17 bp):
AGTTCGAGCTTGAATCA
Found at i:9927 original size:35 final size:35
Alignment explanation
Indices: 9881--9991 Score: 168
Period size: 35 Copynumber: 3.1 Consensus size: 35
9871 GCTTGAATCA
* *
9881 AGTTCGAGCTTGAATCGGGCTCAAATTTGAGTTTG
1 AGTTCGAGCTTGAATCGAGCTCAAATTCGAGTTTG
9916 AGTTCGAGCTTGAATCGAGCTCAAATTCGAGTTTG
1 AGTTCGAGCTTGAATCGAGCTCAAATTCGAGTTTG
* *
9951 AGTTCGAGCTTGAATCGAGCTCGAGTCTCGAGTTTCG
1 AGTTCGAGCTTGAATCGAGCTCAAAT-TCGAGTTT-G
9988 AGTT
1 AGTT
9992 TCAATCGAGC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
35 57 0.81
36 8 0.11
37 5 0.07
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (35 bp):
AGTTCGAGCTTGAATCGAGCTCAAATTCGAGTTTG
Found at i:9935 original size:11 final size:11
Alignment explanation
Indices: 9919--9971 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
9909 GAGTTTGAGT
9919 TCGAGCTTGAA
1 TCGAGCTTGAA
**
9930 TCGAGCTCAAA
1 TCGAGCTTGAA
* *
9941 TTCGAGTTTGAGT
1 -TCGAGCTTGA-A
9954 TCGAGCTTGAA
1 TCGAGCTTGAA
9965 TCGAGCT
1 TCGAGCT
9972 CGAGTCTCGA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
11 16 0.50
12 16 0.50
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:9976 original size:23 final size:23
Alignment explanation
Indices: 9855--9982 Score: 63
Period size: 23 Copynumber: 5.7 Consensus size: 23
9845 AGGTTCAAAT
*
9855 TCGAGTTCGAGTTCGAGCTTGAA
1 TCGAGCTCGAGTTCGAGCTTGAA
9878 TC-A-----AGTTCGAGCTTGAA
1 TCGAGCTCGAGTTCGAGCTTGAA
* * * * * *
9895 TCGGGCTCAAATTTGAGTTTGAGT
1 TCGAGCTCGAGTTCGAGCTTGA-A
* * **
9919 TCGAGCTTGA-ATCGAGCTCAAA
1 TCGAGCTCGAGTTCGAGCTTGAA
* *
9941 TTCGAGTTTGAGTTCGAGCTTGAA
1 -TCGAGCTCGAGTTCGAGCTTGAA
9965 TCGAGCTCGAGTCTCGAG
1 TCGAGCTCGAGT-TCGAG
9983 TTTCGAGTTT
Statistics
Matches: 75, Mismatches: 20, Indels: 19
0.66 0.18 0.17
Matches are distributed among these distances:
17 16 0.21
22 1 0.01
23 37 0.49
24 21 0.28
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (23 bp):
TCGAGCTCGAGTTCGAGCTTGAA
Found at i:15914 original size:29 final size:30
Alignment explanation
Indices: 15881--15947 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
15871 CTCTTAAAAA
* * *
15881 AAATTTGAGGACTAAATTG-AATTTTTATT
1 AAATTTGAGGACCAAAGTGAAATTTTGATT
* *
15910 TAATTCGAGGACCAAAGTGAAATTTTGATT
1 AAATTTGAGGACCAAAGTGAAATTTTGATT
15940 AAATTTGA
1 AAATTTGA
15948 ATCCAAATTC
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (30 bp):
AAATTTGAGGACCAAAGTGAAATTTTGATT
Found at i:18063 original size:21 final size:21
Alignment explanation
Indices: 18037--18076 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
18027 AGATTATACA
18037 GGGGGTA-CAGATTCCCCCTTG
1 GGGGGTATC-GATTCCCCCTTG
18058 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
18077 AAAGAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.12, C:0.30, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCCTTG
Found at i:18672 original size:16 final size:16
Alignment explanation
Indices: 18651--18682 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18641 ATATATAACA
18651 TGTGAATATACTTGAG
1 TGTGAATATACTTGAG
18667 TGTGAATATACTTGAG
1 TGTGAATATACTTGAG
18683 AAATACATGT
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:0.31, C:0.06, G:0.25, T:0.38
Consensus pattern (16 bp):
TGTGAATATACTTGAG
Found at i:26264 original size:18 final size:17
Alignment explanation
Indices: 26237--26275 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
26227 TCATATTTAT
26237 TTATAT-AAAATATAATA
1 TTATATAAAAATA-AATA
26254 TTATATGAAAAATAAATA
1 TTATAT-AAAAATAAATA
26272 TTAT
1 TTAT
26276 TTTTAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 8 0.40
19 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TTATATAAAAATAAATA
Found at i:52585 original size:42 final size:42
Alignment explanation
Indices: 52521--52640 Score: 213
Period size: 42 Copynumber: 2.9 Consensus size: 42
52511 TTTCCCCGAA
* *
52521 TTCCAGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
*
52563 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
52605 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
52641 TGTAATTCAT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACATT
Found at i:52852 original size:18 final size:17
Alignment explanation
Indices: 52829--52869 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
52819 TAATTATTAA
*
52829 AATATTTAAAATATATTT
1 AATATTTAAAATA-ATAT
*
52847 AATATTTATAATAATAT
1 AATATTTAAAATAATAT
52864 AATATT
1 AATATT
52870 ATATTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AATATTTAAAATAATAT
Found at i:52864 original size:21 final size:20
Alignment explanation
Indices: 52833--52887 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
52823 TATTAAAATA
52833 TTTAA-AATATAT-TTAATAT
1 TTTAATAATATATATT-ATAT
52852 TTATAATAATATAATATTATAT
1 TT-TAATAATAT-ATATTATAT
*
52874 TTTAATATTATATA
1 TTTAATAATATATA
52888 AATAATCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 13 0.42
22 8 0.26
23 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAATAATATATATTATAT
Found at i:52884 original size:29 final size:29
Alignment explanation
Indices: 52839--52948 Score: 95
Period size: 29 Copynumber: 3.7 Consensus size: 29
52829 AATATTTAAA
52839 ATATATTTAATATTTATAATAATATAATATT
1 ATAT-TTTAATA-TTATAATAATATAATATT
52870 ATATTTTAATATTAT-ATAA-ATAATCAATT
1 ATATTTTAATATTATAATAATATAAT--ATT
* *
52899 ATATTATAATA-TATAGATATTAT-AT-TT
1 ATATTTTAATATTATA-ATAATATAATATT
*
52926 TTATTTTAATAATATATAATAAT
1 ATATTTTAAT-AT-TATAATAAT
52949 TTTTTATATA
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
27 15 0.23
28 8 0.12
29 21 0.32
30 16 0.24
31 6 0.09
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (29 bp):
ATATTTTAATATTATAATAATATAATATT
Found at i:52891 original size:50 final size:51
Alignment explanation
Indices: 52829--52943 Score: 127
Period size: 50 Copynumber: 2.3 Consensus size: 51
52819 TAATTATTAA
*
52829 AATATT-TA-AAATATATTTAA-TAT-TTATAATAATATA-ATATTATATTTT
1 AATATTATATAAATATA-TCAATTATATTATAAT-ATATAGATATTATATTTT
52877 AATATTATATAAATA-ATCAATTATATTATAATATATAGATATTATATTTT
1 AATATTATATAAATATATCAATTATATTATAATATATAGATATTATATTTT
* *
52927 TATTTTA-ATAATATATA
1 AATATTATATAA-ATATA
52944 ATAATTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 11
0.80 0.04 0.15
Matches are distributed among these distances:
48 9 0.16
49 15 0.26
50 32 0.56
51 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (51 bp):
AATATTATATAAATATATCAATTATATTATAATATATAGATATTATATTTT
Found at i:52953 original size:21 final size:21
Alignment explanation
Indices: 52929--52969 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52919 TATATTTTTA
*
52929 TTTTAATA-ATATATAATAAT
1 TTTTTATATATATATAATAAT
*
52949 TTTTTATATATATTTAATAAT
1 TTTTTATATATATATAATAAT
52970 GAATAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTTATATATATATAATAAT
Found at i:52956 original size:50 final size:49
Alignment explanation
Indices: 52851--52967 Score: 130
Period size: 50 Copynumber: 2.3 Consensus size: 49
52841 ATATTTAATA
52851 TTTATAATAATATAATATTATATTTTAATATTATATAAATAATCAATTAT
1 TTTATAAT-ATATAATATTATATTTTAATATTATATAAATAATCAATTAT
* * * *
52901 ATTATAATATATAGATATTATATTTTTATTTTAATAATATATAAT-AATT-T
1 TTTATAATATATA-ATATTATATTTTAATATT-AT-ATAAATAATCAATTAT
*
52951 TTTATATATATTTAATA
1 TTTATA-ATATATAATA
52968 ATGAATAATA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
49 5 0.09
50 32 0.56
51 12 0.21
52 8 0.14
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (49 bp):
TTTATAATATATAATATTATATTTTAATATTATATAAATAATCAATTAT
Found at i:53245 original size:20 final size:20
Alignment explanation
Indices: 53167--53236 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
53157 TTTCCAGATG
53167 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
53187 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
53207 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
53227 TTTTCCAGAA
1 TTTTCCAGAA
53237 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:53245 original size:40 final size:40
Alignment explanation
Indices: 53167--53245 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
53157 TTTCCAGATG
* **
53167 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
53207 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
53246 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:53255 original size:15 final size:15
Alignment explanation
Indices: 53219--53300 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
53209 TTACAGAAAT
**
53219 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
53234 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
** *
53248 GTAATTCATTTTTCA
1 GTAATTCAAATTCCA
53263 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
53278 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
53293 GTAATTCA
1 GTAATTCA
53301 TTTTCTGGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:53269 original size:30 final size:30
Alignment explanation
Indices: 53219--53300 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
53209 TTACAGAAAT
53219 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
53248 GTAATTCATTTTTCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
53278 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
53301 TTTTCTGGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 15 0.31
30 33 0.69
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:53293 original size:45 final size:44
Alignment explanation
Indices: 53219--53304 Score: 145
Period size: 45 Copynumber: 1.9 Consensus size: 44
53209 TTACAGAAAT
**
53219 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTTCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTTCA
53263 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTT
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTT
53305 CTGGAAAACC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTTCA
Found at i:53609 original size:42 final size:42
Alignment explanation
Indices: 53546--53662 Score: 216
Period size: 42 Copynumber: 2.8 Consensus size: 42
53536 TTTCCCCGAA
*
53546 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
*
53588 TTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
53630 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCG
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCG
53663 AAATGTAATT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.46
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTT
Found at i:53875 original size:22 final size:23
Alignment explanation
Indices: 53837--53916 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 23
53827 CATTTTCATC
*
53837 AAAATATTAATTATTAAAATTT-T
1 AAAATA-TATTTATTAAAATTTAT
*
53860 AAAATATATTTATTAATATTTAT
1 AAAATATATTTATTAAAATTTAT
* *
53883 AATATAATATTATATTTTAATATTATAT
1 AAAAT-ATATT-TA--TTAAAATT-TAT
53911 AAAATA
1 AAAATA
53917 ATCAATTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
22 13 0.28
23 11 0.23
24 5 0.11
25 2 0.04
27 9 0.19
28 7 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATATTTATTAAAATTTAT
Found at i:53886 original size:21 final size:20
Alignment explanation
Indices: 53846--53905 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
53836 CAAAATATTA
* *
53846 ATTATTAAAATTTTAAAATAT
1 ATTATTAATA-TTTATAATAT
53867 ATTTATTAATATTTATAATAT
1 A-TTATTAATATTTATAATAT
*
53888 AATATT-ATATTT-TAATAT
1 ATTATTAATATTTATAATAT
53906 TATATAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 6 0.17
19 6 0.17
20 4 0.11
21 11 0.31
22 8 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTATTAATATTTATAATAT
Found at i:53903 original size:13 final size:13
Alignment explanation
Indices: 53872--53910 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
53862 AATATATTTA
*
53872 TTAATATTTATAAT
1 TTAATA-TTATATT
*
53886 ATAATATTATATT
1 TTAATATTATATT
53899 TTAATATTATAT
1 TTAATATTATAT
53911 AAAATAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 17 0.77
14 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATATTATATT
Found at i:53905 original size:18 final size:20
Alignment explanation
Indices: 53870--53910 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
53860 AAAATATATT
53870 TATTAATATTTATAATATAA
1 TATTAATATTTATAATATAA
*
53890 TATT-ATATTT-TAATATTA
1 TATTAATATTTATAATATAA
53908 TAT
1 TAT
53911 AAAATAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
19 6 0.30
20 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTAATATTTATAATATAA
Found at i:53927 original size:30 final size:28
Alignment explanation
Indices: 53872--53971 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
53862 AATATATTTA
*
53872 TTAATATT-TATAATATAATATTATATT
1 TTAATATTATATAAAATAATATTATATT
53899 TTAATATTATATAAAATAATCAATTATATT
1 TTAATATTATATAAAATAAT--ATTATATT
* * *
53929 ATAATA--ATATAAGATATTATATTTTTATT
1 TTAATATTATATAA-A-ATAATA-TTATATT
*
53958 TTAATAATATATAA
1 TTAATATTATATAA
53972 TAATTTTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
27 8 0.13
28 17 0.28
29 12 0.20
30 17 0.28
31 6 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
TTAATATTATATAAAATAATATTATATT
Found at i:54267 original size:20 final size:20
Alignment explanation
Indices: 54189--54258 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
54179 TTTCCAGATG
54189 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
54209 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
* *
54229 TTTTACAGAAATATAATTCA
1 TTTTCCAGAAATGTAATTCA
54249 TTTTCCAGAA
1 TTTTCCAGAA
54259 TTTAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:54275 original size:29 final size:30
Alignment explanation
Indices: 54242--54312 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
54232 TACAGAAATA
*
54242 TAATTCATTTTCCAG-AATTTAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAG
*
54271 TAATTCATTTTTCAGTAATTCAAATTCCAG
1 TAATTCATTTTCCAGTAATTCAAATTCCAG
54301 TAATTCATTTTC
1 TAATTCATTTTC
54313 TGGAAAACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 14 0.37
30 24 0.63
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (30 bp):
TAATTCATTTTCCAGTAATTCAAATTCCAG
Found at i:54286 original size:15 final size:15
Alignment explanation
Indices: 54242--54312 Score: 81
Period size: 15 Copynumber: 4.8 Consensus size: 15
54232 TACAGAAATA
54242 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
* **
54257 -AATTTAAATTCCAG
1 TAATTCATTTTCCAG
*
54271 TAATTCATTTTTCAG
1 TAATTCATTTTCCAG
**
54286 TAATTCAAATTCCAG
1 TAATTCATTTTCCAG
54301 TAATTCATTTTC
1 TAATTCATTTTC
54313 TGGAAAACCA
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
14 11 0.26
15 32 0.74
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (15 bp):
TAATTCATTTTCCAG
Found at i:54325 original size:29 final size:30
Alignment explanation
Indices: 54262--54325 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 30
54252 TCCAGAATTT
* **
54262 AAATTCCAGTAATTCATTTTTCAGTAATTC
1 AAATTCCAGTAATTCATTTTTCAGGAAAAC
*
54292 AAATTCCAGTAATTCA-TTTTCTGGAAAAC
1 AAATTCCAGTAATTCATTTTTCAGGAAAAC
*
54321 CAATT
1 AAATT
54326 ACAGCTAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (30 bp):
AAATTCCAGTAATTCATTTTTCAGGAAAAC
Found at i:59568 original size:25 final size:26
Alignment explanation
Indices: 59501--59560 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
59491 GAATCCAACC
* * * *
59501 CGACTCGAACACAATCTTTTAAAAAT
1 CGACCCGAACACCACCTTTAAAAAAT
59527 CGACCCGAACACCACCTTTAAAAAAT
1 CGACCCGAACACCACCTTTAAAAAAT
59553 CGACCCGA
1 CGACCCGA
59561 CTCGACCTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.32, G:0.10, T:0.18
Consensus pattern (26 bp):
CGACCCGAACACCACCTTTAAAAAAT
Found at i:60878 original size:16 final size:16
Alignment explanation
Indices: 60845--60879 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
60835 CGCTCTATTA
60845 TTAGTTTTAATTTGTT
1 TTAGTTTTAATTTGTT
60861 TTAGTATTTAATTT-TT
1 TTAGT-TTTAATTTGTT
60877 TTA
1 TTA
60880 AATTATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (16 bp):
TTAGTTTTAATTTGTT
Found at i:63301 original size:18 final size:18
Alignment explanation
Indices: 63267--63312 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
63257 CAATATTCGA
63267 ATAATTT-AATCGAATAT
1 ATAATTTAAATCGAATAT
*
63284 ATAATTTAAATTGAATAT
1 ATAATTTAAATCGAATAT
*
63302 AAAATCTTAAA
1 ATAAT-TTAAA
63313 ATTCAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 7 0.28
18 13 0.52
19 5 0.20
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (18 bp):
ATAATTTAAATCGAATAT
Found at i:69242 original size:20 final size:21
Alignment explanation
Indices: 69217--69262 Score: 85
Period size: 20 Copynumber: 2.2 Consensus size: 21
69207 ATACATGAGA
69217 TAAAACATAATTATTTAAG-T
1 TAAAACATAATTATTTAAGAT
69237 TAAAACATAATTATTTAAGAT
1 TAAAACATAATTATTTAAGAT
69258 TAAAA
1 TAAAA
69263 ACCCATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (21 bp):
TAAAACATAATTATTTAAGAT
Found at i:69847 original size:88 final size:88
Alignment explanation
Indices: 69670--69847 Score: 191
Period size: 88 Copynumber: 2.0 Consensus size: 88
69660 TTTCAATACT
* *
69670 TTCAAATTTCATTTTTGAAAGTTCTAAATCCTTCTTCAATATTTCATTTTGATTTTCAAAATCCA
1 TTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCATTTTGATTTTCAAAATCCA
* ****
69735 TTTAGTTTCTAGAAGTTTTTTAA
66 TTTAGTTTCTAAAAGTAAGATAA
* * * * * *
69758 TTCAGATTTCGTTTTTGAAAGCTCTAACTCCTT-TCTCAACATTTCATTTTGATTTTCCAATTCT
1 TTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACATTTCATTTTGATTTTCAAAATCC
69822 ATTTTAGATTTC-AAAAG-AAGATAA
65 A-TTTAG-TTTCTAAAAGTAAGATAA
69846 TT
1 TT
69848 TTTAGCTATA
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
87 1 0.01
88 60 0.81
89 9 0.12
90 4 0.05
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (88 bp):
TTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCATTTTGATTTTCAAAATCCA
TTTAGTTTCTAAAAGTAAGATAA
Found at i:71480 original size:18 final size:18
Alignment explanation
Indices: 71450--71495 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
71440 TTATATTCGA
71450 ATAATTT-AATCGAATAT
1 ATAATTTAAATCGAATAT
71467 ATAATTTAAATCGAATAT
1 ATAATTTAAATCGAATAT
*
71485 AAAATCTTAAA
1 ATAAT-TTAAA
71496 ATTCAATAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 7 0.27
18 14 0.54
19 5 0.19
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (18 bp):
ATAATTTAAATCGAATAT
Found at i:73264 original size:2 final size:2
Alignment explanation
Indices: 73257--73291 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
73247 AGGCTAAAAG
73257 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
73292 ATTTTAAATA
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:79665 original size:21 final size:21
Alignment explanation
Indices: 79641--79688 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
79631 TAATATTAGT
79641 ATTTTTAATACATAT-ATTTAA
1 ATTTTTAATA-ATATAATTTAA
* *
79662 ATTTTTAGTAATCTAATTTAA
1 ATTTTTAATAATATAATTTAA
79683 ATTTTT
1 ATTTTT
79689 TGTATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 3 0.12
21 21 0.88
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTTAATAATATAATTTAA
Done.