Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001952.1 Hibiscus syriacus cultivar Beakdansim tig00003948_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: 53889
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:171 original size:17 final size:17
Alignment explanation
Indices: 149--183 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
139 TATATTCACA
* *
149 TGAATAGTGAATTTTTG
1 TGAATAGTAAAATTTTG
166 TGAATAGTAAAATTTTG
1 TGAATAGTAAAATTTTG
183 T
1 T
184 CGTGATACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (17 bp):
TGAATAGTAAAATTTTG
Found at i:4197 original size:21 final size:21
Alignment explanation
Indices: 4173--4233 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
4163 CCAACTTTGA
4173 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
4194 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
4208 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
4229 AAATG
1 AAATG
4234 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:4254 original size:36 final size:35
Alignment explanation
Indices: 4167--4281 Score: 187
Period size: 35 Copynumber: 3.3 Consensus size: 35
4157 TGGTAACCAA
4167 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
4202 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
4237 CTTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
4273 -GTTGAAAAT
1 CTTTGAAAAT
4282 AGGAATGGGT
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
34 5 0.07
35 43 0.57
36 28 0.37
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (35 bp):
CTTTGAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:5261 original size:20 final size:19
Alignment explanation
Indices: 5205--5270 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 19
5195 AATGATACCA
5205 ATACCCCCATA-GGTATCG
1 ATACCCCCATATGGTATCG
5223 ATACCCCCATGCAATGGTATCG
1 ATACCCCCAT---ATGGTATCG
5245 ATACCCCTCATATGGTATCG
1 ATACCCC-CATATGGTATCG
5265 ATACCC
1 ATACCC
5271 TAAGGCATAT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
18 10 0.23
20 15 0.35
21 1 0.02
22 14 0.33
23 3 0.07
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.24
Consensus pattern (19 bp):
ATACCCCCATATGGTATCG
Found at i:11057 original size:23 final size:23
Alignment explanation
Indices: 11001--11108 Score: 75
Period size: 23 Copynumber: 4.8 Consensus size: 23
10991 ATTTTTGTGC
**
11001 ATAGAGTATCGATA-CCCCTGAGA
1 ATAG-GTATCGATACCCCCTTTGA
*
11024 CTA-GTATCGATACCCCCTTTGA
1 ATAGGTATCGATACCCCCTTTGA
*
11046 ATAGGTATCGATA---CCTCTGCA
1 ATAGGTATCGATACCCCCTTTG-A
* **
11067 ATAGGTATTGATATCATCC-TTGA
1 ATAGGTATCGATA-CCCCCTTTGA
*
11090 ATGGGTATCGATACCCCCT
1 ATAGGTATCGATACCCCCT
11109 GATGATACTG
Statistics
Matches: 66, Mismatches: 11, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
20 5 0.08
21 22 0.33
22 12 0.18
23 23 0.35
24 2 0.03
25 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (23 bp):
ATAGGTATCGATACCCCCTTTGA
Found at i:12696 original size:27 final size:27
Alignment explanation
Indices: 12661--12719 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
12651 GGAAACTCCA
12661 GGAGCTAGTTCTTCACGAGCTCCACCT
1 GGAGCTAGTTCTTCACGAGCTCCACCT
*
12688 GGAGTTAGTTCTTCACGAGCTCCACCT
1 GGAGCTAGTTCTTCACGAGCTCCACCT
12715 GGAGC
1 GGAGC
12720 GGACGACGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (27 bp):
GGAGCTAGTTCTTCACGAGCTCCACCT
Found at i:26150 original size:16 final size:16
Alignment explanation
Indices: 26129--26159 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26119 TTTCTTGTTT
*
26129 AATCATTTTATATTTA
1 AATCATTTTAAATTTA
26145 AATCATTTTAAATTT
1 AATCATTTTAAATTT
26160 TGATTATATT
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:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
AATCATTTTAAATTTA
Found at i:28100 original size:60 final size:60
Alignment explanation
Indices: 28022--28178 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
28012 GAATTTAGGG
* * * *
28022 ATGAAATTATAATATTCAAAAGTTTGGA-GACTAATTTAGAAAGAGAGACATAGTTTACGA
1 ATGAAATTAGAATATTCAAAAGTTT-AATGACTAATTTACAAAGAAAGACATAGTTTACGA
* * * * *
28082 ATGAAATTAGAATGTTCAAAAGTTTAATGACTAATTTACAATGAAAGTCATAGTTT-GGG
1 ATGAAATTAGAATATTCAAAAGTTTAATGACTAATTTACAAAGAAAGACATAGTTTACGA
* * *
28141 ATCG-AATTAGGATATTCAAAAGTTTAAGGACCAATTTA
1 AT-GAAATTAGAATATTCAAAAGTTTAATGACTAATTTA
28179 AAAATAATGG
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 34 0.41
60 48 0.59
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.32
Consensus pattern (60 bp):
ATGAAATTAGAATATTCAAAAGTTTAATGACTAATTTACAAAGAAAGACATAGTTTACGA
Found at i:28854 original size:59 final size:60
Alignment explanation
Indices: 28791--28943 Score: 159
Period size: 59 Copynumber: 2.5 Consensus size: 60
28781 AATTGGACTT
*
28791 TAAACTTTTGAATATTCTAATTTCATCCCCAAACTATGACCCCA-TTCTAAATTA-ATCAA
1 TAAACTTTTGAATATTCTAATTTAATCCCCAAACTATGACCCCATTTCTAAATTAGATC-A
* *** ** * *
28850 TAAACTTTTGAACATTCTAATTTAATCTGTAAACTATGATTCCATTTCTAAATTAGTTCC
1 TAAACTTTTGAATATTCTAATTTAATCCCCAAACTATGACCCCATTTCTAAATTAGATCA
* *
28910 CAAACTTTTTGAATATT-TCAATTTTATCCCCAAA
1 TAAAC-TTTTGAATATTCT-AATTTAATCCCCAAA
28944 TTCATCCAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
59 37 0.49
60 15 0.20
61 23 0.31
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (60 bp):
TAAACTTTTGAATATTCTAATTTAATCCCCAAACTATGACCCCATTTCTAAATTAGATCA
Found at i:29134 original size:61 final size:60
Alignment explanation
Indices: 29056--29176 Score: 140
Period size: 61 Copynumber: 2.0 Consensus size: 60
29046 GTGATAGTAT
* * * *
29056 ATATCTATAGTTTGGGATGA-AGTTGGAATGTTCAAAAAGTTT-AGGGACTAATTTTGAATAA
1 ATATCTATAATTTGGGATGATA-TTGAAATATTCAAAAA-TTTGA-GGACTAATTTAGAATAA
*
29117 ATATC-ATAATTTGGGGATGATATTGAAATATTCAAAAATTTGAGTACTAATTTAGAATAA
1 ATATCTATAATTT-GGGATGATATTGAAATATTCAAAAATTTGAGGACTAATTTAGAATAA
29177 TAATTATAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
60 24 0.46
61 27 0.52
62 1 0.02
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (60 bp):
ATATCTATAATTTGGGATGATATTGAAATATTCAAAAATTTGAGGACTAATTTAGAATAA
Found at i:29853 original size:7 final size:7
Alignment explanation
Indices: 29734--29854 Score: 70
Period size: 7 Copynumber: 17.4 Consensus size: 7
29724 CTCTAAACTA
*
29734 TAAACCA
1 TAAACCC
29741 TAAACCC
1 TAAACCC
*
29748 TACACCC
1 TAAACCC
29755 -AAA-CC
1 TAAACCC
29760 TAAA-CC
1 TAAACCC
*
29766 TAAAACC
1 TAAACCC
29773 TAAAACCC
1 T-AAACCC
**
29781 TAAACTA
1 TAAACCC
*
29788 TAAAACCA
1 T-AAACCC
* *
29796 TAAATCA
1 TAAACCC
29803 TAAATCCC
1 TAAA-CCC
*
29811 -AAACCT
1 TAAACCC
**
29817 TAAACTA
1 TAAACCC
*
29824 TAAACTC
1 TAAACCC
29831 TAAACCC
1 TAAACCC
*
29838 TAAAACC
1 TAAACCC
29845 TAAACCC
1 TAAACCC
29852 TAA
1 TAA
29855 GAAATAAACC
Statistics
Matches: 91, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
5 2 0.02
6 13 0.14
7 63 0.69
8 13 0.14
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:29854 original size:21 final size:20
Alignment explanation
Indices: 29699--29854 Score: 86
Period size: 21 Copynumber: 7.5 Consensus size: 20
29689 ATATTACACT
*
29699 CTAAACCCTAAACTTAAAAC
1 CTAAACCCTAAACCTAAAAC
* * *
29719 TTAATCTCTAAA-CTATAAAC
1 CTAAACCCTAAACCTA-AAAC
* *
29739 CATAAACCCTACACC-CAAAC
1 C-TAAACCCTAAACCTAAAAC
29759 CTAAA-CCTAAAACCTAAAACC
1 CTAAACCCT-AAACCTAAAA-C
** *
29780 CTAAACTATAAAACCATAAATC
1 CTAAACCCT-AAACC-TAAAAC
* *
29802 ATAAATCCC-AAACCTTAAAC
1 CTAAA-CCCTAAACCTAAAAC
* *
29822 TATAAACTCTAAACCCTAAAAC
1 -CTAAACCCTAAA-CCTAAAAC
29844 CTAAACCCTAA
1 CTAAACCCTAA
29855 GAAATAAACC
Statistics
Matches: 101, Mismatches: 23, Indels: 23
0.69 0.16 0.16
Matches are distributed among these distances:
18 3 0.03
19 10 0.10
20 27 0.27
21 36 0.36
22 20 0.20
23 5 0.05
ACGTcount: A:0.49, C:0.30, G:0.00, T:0.21
Consensus pattern (20 bp):
CTAAACCCTAAACCTAAAAC
Found at i:31573 original size:16 final size:16
Alignment explanation
Indices: 31552--31585 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
31542 AGTTCTTCAA
*
31552 TTTTTTTAAGTTTGAG
1 TTTTTTTAAGTTCGAG
*
31568 TTTTTTTGAGTTCGAG
1 TTTTTTTAAGTTCGAG
31584 TT
1 TT
31586 AAATTCTAAT
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:0.15, C:0.03, G:0.21, T:0.62
Consensus pattern (16 bp):
TTTTTTTAAGTTCGAG
Found at i:39297 original size:60 final size:60
Alignment explanation
Indices: 39166--39302 Score: 168
Period size: 60 Copynumber: 2.3 Consensus size: 60
39156 TTTCACTATA
* * * * * * *
39166 CAACCTCAAACTAAGACTCTCATTCTAAATTAGTCCTTACACTTTTGAGCATTCTAATTT
1 CAACCTCAAACTATGACTCTCATCCTAAATTAGTCCCTAAACTTTTGAACATTCTAAATC
* *
39226 CAACC-CTAAACTATGACTTTCATCCTAAATTAGTCCCTAAAGTTTTGAACATTCTAAATC
1 CAACCTC-AAACTATGACTCTCATCCTAAATTAGTCCCTAAACTTTTGAACATTCTAAATC
*
39286 CATCCTCAAACTATGAC
1 CAACCTCAAACTATGAC
39303 CCTAATTCTA
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.02
60 63 0.97
61 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.07, T:0.34
Consensus pattern (60 bp):
CAACCTCAAACTATGACTCTCATCCTAAATTAGTCCCTAAACTTTTGAACATTCTAAATC
Found at i:39470 original size:29 final size:30
Alignment explanation
Indices: 39433--39537 Score: 108
Period size: 29 Copynumber: 3.5 Consensus size: 30
39423 CATAGTTTGG
* *
39433 GGATGAATTTGGAAT-TTTCAAAAGTTTAA
1 GGATCAATTTAGAATGTTTCAAAAGTTTAA
* *
39462 GGATCAATTTAGAATGATGGTC-AAAGTTTAG
1 GGATCAATTTAGAATG-T-TTCAAAAGTTTAA
* *
39493 GGATTAAGTTAGAATGTTT-AAAAGTTTAA
1 GGATCAATTTAGAATGTTTCAAAAGTTTAA
*
39522 GGACCAATTTAGAATG
1 GGATCAATTTAGAATG
39538 AGGGTCATAG
Statistics
Matches: 61, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
29 35 0.57
30 1 0.02
31 23 0.38
32 2 0.03
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (30 bp):
GGATCAATTTAGAATGTTTCAAAAGTTTAA
Found at i:39491 original size:31 final size:31
Alignment explanation
Indices: 39453--39556 Score: 122
Period size: 31 Copynumber: 3.4 Consensus size: 31
39443 GGAATTTTCA
39453 AAAGTTTAAGGATCAATTTAGAATGATGGTC
1 AAAGTTTAAGGATCAATTTAGAATGATGGTC
* * * * *
39484 AAAGTTTAGGGATTAAGTTAGAATG-T-TTA
1 AAAGTTTAAGGATCAATTTAGAATGATGGTC
* *
39513 AAAGTTTAAGGACCAATTTAGAATGAGGGTC
1 AAAGTTTAAGGATCAATTTAGAATGATGGTC
*
39544 ATAGTTTAAGGAT
1 AAAGTTTAAGGAT
39557 GTATAGTCCA
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
29 22 0.39
30 1 0.02
31 34 0.60
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (31 bp):
AAAGTTTAAGGATCAATTTAGAATGATGGTC
Found at i:39516 original size:60 final size:60
Alignment explanation
Indices: 39410--39557 Score: 201
Period size: 60 Copynumber: 2.5 Consensus size: 60
39400 TGAGGGATAT
* * * *
39410 TTTAGAAT-AGGGTCATAGTTTGGGGATGAATTTGGAATTTTCAAAAGTTTAAGGATCAA
1 TTTAGAATGAGGGTCATAGTTTAGGGATGAAGTTAGAATTTTCAAAAGTTTAAGGACCAA
* * *
39469 TTTAGAATGATGGTCAAAGTTTAGGGATTAAGTTAGAATGTTT-AAAAGTTTAAGGACCAA
1 TTTAGAATGAGGGTCATAGTTTAGGGATGAAGTTAGAAT-TTTCAAAAGTTTAAGGACCAA
*
39529 TTTAGAATGAGGGTCATAGTTTAAGGATG
1 TTTAGAATGAGGGTCATAGTTTAGGGATG
39558 TATAGTCCAA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
59 8 0.11
60 65 0.86
61 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (60 bp):
TTTAGAATGAGGGTCATAGTTTAGGGATGAAGTTAGAATTTTCAAAAGTTTAAGGACCAA
Found at i:40118 original size:3 final size:3
Alignment explanation
Indices: 40110--40143 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
40100 CACCGCACCA
* *
40110 ATC ATC ATC ATC ATC ATC ATT ATC ATC ACC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
40144 CCGTTGTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.35, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:43410 original size:32 final size:32
Alignment explanation
Indices: 43374--43494 Score: 138
Period size: 32 Copynumber: 3.8 Consensus size: 32
43364 AGAACAATGA
43374 GGGCA-TTTTTGAAGATTCAACATCAAATATTG
1 GGGCATTTTTTG-AGATTCAACATCAAATATTG
* * *
43406 GGGCATTTTTTTTAGATTTAACATCAAATGTTG
1 GGGCA-TTTTTTGAGATTCAACATCAAATATTG
* *
43439 GGGAATTTTTTGAGATTCAACATCGAATATTG
1 GGGCATTTTTTGAGATTCAACATCAAATATTG
* *
43471 GGGCA-TCTTTGGGAATTCAACATC
1 GGGCATTTTTTGAG-ATTCAACATC
43495 CTGATGCAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
31 6 0.08
32 42 0.56
33 22 0.29
34 5 0.07
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (32 bp):
GGGCATTTTTTGAGATTCAACATCAAATATTG
Found at i:44492 original size:36 final size:37
Alignment explanation
Indices: 44452--44523 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 37
44442 AAATATAAAC
*
44452 ATTGAAAATA-TTTCCCTTGAAATG-AATTTTATCTCG
1 ATTG-AAATAGTTTCCCTTGAAACGAAATTTTATCTCG
* *
44488 ATTGAGATAGTTTCCCTTGAAACGAAATTTTGTCTC
1 ATTGAAATAGTTTCCCTTGAAACGAAATTTTATCTC
44524 CCTTGAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
35 4 0.13
36 17 0.55
37 10 0.32
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATTGAAATAGTTTCCCTTGAAACGAAATTTTATCTCG
Found at i:44508 original size:87 final size:87
Alignment explanation
Indices: 44352--44616 Score: 433
Period size: 87 Copynumber: 3.1 Consensus size: 87
44342 GACAGTTTCT
* * *
44352 CTTGAAACGT-AACATTGAAAACATTTCCCTTGGAATGAATTTTATCTCGATTGAGAAAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
44416 CTTGAAACGAAATTTTGTCTCC
66 CTTGAAACGAAATTTTGTCTCC
* *
44438 CTTGAAATATAAACATTGAAAATATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
44503 CTTGAAACGAAATTTTGTCTCC
66 CTTGAAACGAAATTTTGTCTCC
* * * *
44525 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
*
44590 CTTGAAACAAAATTTTGTCTCC
66 CTTGAAACGAAATTTTGTCTCC
44612 CTTGA
1 CTTGA
44617 GACAGTTTCT
Statistics
Matches: 166, Mismatches: 12, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
86 8 0.05
87 158 0.95
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (87 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTTATCTCGATTGAGATAGTTTCC
CTTGAAACGAAATTTTGTCTCC
Found at i:44624 original size:37 final size:37
Alignment explanation
Indices: 44549--44635 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
44539 ATTGAAAACA
* * * **
44549 TTTCCCTTGAAA-TAAATTTTATCTCGCTTGGGGTAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
*
44585 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
*
44622 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
44636 TAAACATTGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
36 12 0.28
37 31 0.72
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTATCTCCCTTGAGACAG
Found at i:44639 original size:102 final size:102
Alignment explanation
Indices: 44525--44760 Score: 339
Period size: 102 Copynumber: 2.3 Consensus size: 102
44515 TTTTGTCTCC
* *
44525 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
*
44590 CTTG-AAACAAAATTTTGTCTCCCTTGAGACAGTTTCT
66 CTCGAAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCT
* * * *
44627 CTTGAAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTTGTCTCTCTTGAGATAGTTTCC
1 CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
*** *
44692 CTCGAAAACTTTTTTTGTCTCCCTTGAGATAGTTTCT
66 CTCGAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
* *
44729 CTTGAAACATAAACCTTGAAAACGTTTCCCTT
1 CTTGAAACATAAACATTGAAAACATTTCCCTT
44761 AAAAAACAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
102 115 0.97
103 4 0.03
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (102 bp):
CTTGAAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCC
CTCGAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
Found at i:44852 original size:37 final size:37
Alignment explanation
Indices: 44802--44901 Score: 175
Period size: 36 Copynumber: 2.7 Consensus size: 37
44792 AAAATGAGTT
44802 TTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCGC
1 TTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCGC
* *
44839 TTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCGC
44875 TTGAGACAGTTTCCCTTGAAACAAAAT
1 TTGAGACAGTTTCCCTTGAAACAAAAT
44902 CTTTAAATAT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
36 34 0.57
37 26 0.43
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (37 bp):
TTGAGACAGTTTCCCTTGAAACAAAATATTGTCTCGC
Found at i:44921 original size:29 final size:29
Alignment explanation
Indices: 44888--44957 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
44878 AGACAGTTTC
44888 CCTTGAAACAAAATCTTTAAATATCTTTT
1 CCTTGAAACAAAATCTTTAAATATCTTTT
44917 CCTTGAAACAAAATCTTTAAATATCTTTT
1 CCTTGAAACAAAATCTTTAAATATCTTTT
44946 CCTTGAAACAAA
1 CCTTGAAACAAA
44958 TTTCGTCTCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.19, G:0.04, T:0.37
Consensus pattern (29 bp):
CCTTGAAACAAAATCTTTAAATATCTTTT
Found at i:45009 original size:37 final size:36
Alignment explanation
Indices: 44948--45064 Score: 146
Period size: 36 Copynumber: 3.2 Consensus size: 36
44938 TATCTTTTCC
* *
44948 TTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTT
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
* *
44984 TT-AGAACTAAGTTTTGTCTCTCTTGAGACAATTTCTT
1 TTGA-AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTT
* * *
45021 TTGAAACAAATTTTATCCCTCTTGAGACAGTTTCTC
1 TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
45057 TTGAAACA
1 TTGAAACA
45065 CAAAAAAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 1 0.01
36 37 0.54
37 30 0.43
38 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTT
Found at i:45095 original size:37 final size:37
Alignment explanation
Indices: 45050--45139 Score: 135
Period size: 37 Copynumber: 2.4 Consensus size: 37
45040 TCTTGAGACA
45050 GTTTCTCTTGAAACACAAAAAAAAAACCCTCGAAATT
1 GTTTCTCTTGAAACACAAAAAAAAAACCCTCGAAATT
* * * * *
45087 TTTTCTCTTGAAACACACACAAAAAACCTTTGAAATT
1 GTTTCTCTTGAAACACAAAAAAAAAACCCTCGAAATT
45124 GTTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
45140 CAAACCCTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (37 bp):
GTTTCTCTTGAAACACAAAAAAAAAACCCTCGAAATT
Found at i:46549 original size:22 final size:23
Alignment explanation
Indices: 46524--46569 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
46514 TTTATTTCTG
* *
46524 TTTTCTTA-TTTAGTAC-TATTA
1 TTTTTTTATTTTAATACTTATTA
46545 TTTTTTTATTTTAATACTTATTA
1 TTTTTTTATTTTAATACTTATTA
46568 TT
1 TT
46570 ACTATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 7 0.33
23 7 0.33
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTTTATTTTAATACTTATTA
Found at i:51976 original size:8 final size:7
Alignment explanation
Indices: 51962--52126 Score: 56
Period size: 8 Copynumber: 22.6 Consensus size: 7
51952 TGACAATTAA
51962 TATACTT
1 TATACTT
51969 TAATACTT
1 T-ATACTT
51977 TATA-TT
1 TATACTT
51983 TATAC-T
1 TATACTT
51989 TATA-TT
1 TATACTT
*
51995 ATATAGTT
1 -TATACTT
52003 TAATACTT
1 T-ATACTT
* *
52011 TATAATA
1 TATACTT
52018 TATAC-T
1 TATACTT
52024 TAGTACTT
1 TA-TACTT
*
52032 ATGTACTT
1 -TATACTT
52040 ATATACTTATT
1 -TATAC---TT
*
52051 TATA-GT
1 TATACTT
*
52057 TATATTT
1 TATACTT
52064 ATATACTT
1 -TATACTT
52072 TAATAC-T
1 T-ATACTT
**
52079 TATATCCA
1 TATA-CTT
* *
52087 AACACTT
1 TATACTT
52094 TATTACTT
1 TA-TACTT
*
52102 T-TATTT
1 TATACTT
52108 ATATACTT
1 -TATACTT
52116 TATACTT
1 TATACTT
52123 TATA
1 TATA
52127 ATTTTTATAT
Statistics
Matches: 119, Mismatches: 19, Indels: 40
0.67 0.11 0.22
Matches are distributed among these distances:
6 26 0.22
7 39 0.33
8 47 0.39
9 1 0.01
10 4 0.03
11 2 0.02
ACGTcount: A:0.35, C:0.10, G:0.02, T:0.53
Consensus pattern (7 bp):
TATACTT
Found at i:52081 original size:22 final size:22
Alignment explanation
Indices: 52056--52122 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 22
52046 TTATTTATAG
*
52056 TTATATTTATATACTTTAATAC
1 TTATATCTATATACTTTAATAC
* * * *
52078 TTATATCCAAACACTTTATTAC
1 TTATATCTATATACTTTAATAC
* *
52100 TTTTATTTATATACTTT-ATAC
1 TTATATCTATATACTTTAATAC
52121 TT
1 TT
52123 TATAATTTTT
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
21 5 0.15
22 29 0.85
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATATCTATATACTTTAATAC
Found at i:52713 original size:17 final size:18
Alignment explanation
Indices: 52670--52706 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
52660 CATTATACTT
52670 TATA-TATATACTATATA
1 TATACTATATACTATATA
*
52687 TATACT-TATACTTTATA
1 TATACTATATACTATATA
52704 TAT
1 TAT
52707 GTATATAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (18 bp):
TATACTATATACTATATA
Found at i:53637 original size:503 final size:515
Alignment explanation
Indices: 52153--53644 Score: 2172
Period size: 527 Copynumber: 2.9 Consensus size: 515
52143 ATATACACAC
* *
52153 ATATACT-TATAT-TTTATAGTTTTATATGTATATAAAGTACCAAATTGAACAAACATGAAATTG
1 ATATACTATATATACTTATACTTTTATATGTATATAAAGTACCAAATTGAACAAACATGAAATTG
* * *
52216 GAAATAAAAAATTGAATAAATTAAACAATACGCATTGATGA-GGATGAAATTGAATTATTTATAA
66 GAAATAAAAAATTGAATAAATTAAGCAACACGCATTGATGAGGGATGAAATTGAATTAATTATAA
*
52280 AATGTGAAGCTGATATTAATATAAAAATGGACTAAATTGCATACA-TTAAAAGTTGGTGAACATA
131 AATGTGAAGCTGATATTAATATAAAAATGGACTAAATTGCATACATTTAAAAGTTGATGAACATA
* *
52344 ATTTGAAAAGAAATTTATTATGTGATTTACATTTTATAGGGTTTGTTTTAAGTAAATT----AA-
196 ATTTGAAAATAAATTTATTATGTGATTTACATTTTATA--G--AGTTTTAAGTAAATTACAAAAT
* * *
52404 A-AAATAAGTATGAGTCAATTTCAGATAC-GA-ATAATTTGAAGGACTAAATTGAACAAATATGA
257 ATAAATAAGTGTGGGTCAATTTCAGATACAAATATAATTTGAAGGACTAAATT-AACAAATATGA
*
52466 AATTACAAATTCAAATTTAAATACAATAAACAACATAAAAGGATCAAATCAAAAAAATTGTAAAT
321 AATTACAAATTAAAATTTAAATACAATAAACAACATAAAAGGATCAAATCAAAAAAATTGTAAAT
52531 GTGAGGAAAATTGTAAAATGGACTGAATTGCATTAATTTCAAAAGTTGGGGAAAATTAAAACAAT
386 GTGAGGAAAATTGTAAAATGGACTGAATTGCATTAATTTCAAAAGTTGGGGAAAATTAAAACAAT
52596 TAT-ATATATATATATAATATGTATAATGAATGTCATGATAATATGATGCATTTATATAAATGTA
451 TATAATATATATATAT-ATATGTATAATGAATGTCATGATAATATGATGC---------AATG--
52660 CATTATACTTTATAT
504 -ATTATA--TTATAT
52675 ATATACTATATATATACTTATACTTTATATATGTATATAAAGTACCAAATTGAACAAACATGAAA
1 ATATAC--TATATATACTTATACTTT-TATATGTATATAAAGTACCAAATTGAACAAACATGAAA
* *
52740 CTGGAAATAAAAATTTGAATAAATTAAGCAACACGCATTGATGAGGGATGAAATTGAATTAATTA
63 TTGGAAATAAAAAATTGAATAAATTAAGCAACACGCATTGATGAGGGATGAAATTGAATTAATTA
*
52805 TAAAATGTGAAGCTGATAATAATATAAAAAT-GACTAAATTGCATACATTTAAAAGTTGATGAAC
128 TAAAATGTGAAGCTGATATTAATATAAAAATGGACTAAATTGCATACATTTAAAAGTTGATGAAC
*
52869 ATAATTTGAAAATAAATTTATTATGTGATTTACATTTTATAGGGTTTTAAGTAAATTACAAAATA
193 ATAATTTGAAAATAAATTTATTATGTGATTTACATTTTATAGAGTTTTAAGTAAATTACAAAATA
*
52934 T-AATAAGTGTGGGTC-ATTTCATATACAAATATAATTTGAAGGACTAAATTAA-AAA-ATGAAA
258 TAAATAAGTGTGGGTCAATTTCAGATACAAATATAATTTGAAGGACTAAATTAACAAATATGAAA
* *
52995 TTACAAATTTAAATTTAAATACAATAAACAACATAAAAGGGTCAAATCAAAAAAATTGTAAAATG
323 TTACAAATTAAAATTTAAATACAATAAACAACATAAAAGGATCAAATCAAAAAAATTGT-AAATG
53060 TGAGGAAAAATTGTAAAATGGACTGAATTGCATTAATTTCAAAAGTTGGGGAAAATTAAAACAAT
387 TGAGG-AAAATTGTAAAATGGACTGAATTGCATTAATTTCAAAAGTTGGGGAAAATTAAAACAAT
*
53125 TATAATATATATATATATATGTATAATGAATGTTTATGATAATATGATGC-ATG-TT-TA-TATA
451 TATAATATATATATATATATGTATAATGAATG-TCATGATAATATGATGCAATGATTATATTATA
53186 -
515 T
* *
53186 ATGTAC-AT-TATACTTATAC-TTTATATGTATAT-AAGTATC-AATTGAAC-AA-ATGAAATTG
1 ATATACTATATATACTTATACTTTTATATGTATATAAAGTACCAAATTGAACAAACATGAAATTG
** *
53244 GAAATAAAAAATTGAATAAATTAAGCAACAAACATTGACGAGGGATGAAATTGAATTAATTATAA
66 GAAATAAAAAATTGAATAAATTAAGCAACACGCATTGATGAGGGATGAAATTGAATTAATTATAA
* *
53309 AATGTGAAGCTGATATTAATATAAAAATGGATTAAATTGAATACATTTAAAAAGTTGATGAACAT
131 AATGTGAAGCTGATATTAATATAAAAATGGACTAAATTGCATACATTT-AAAAGTTGATGAACAT
53374 AATTTGAAAATAAATTTATTATGTGATTTACATTTTATAGAGTTTTAAGTAAATTACAAAAATAT
195 AATTTGAAAATAAATTTATTATGTGATTTACATTTTATAGAGTTTTAAGTAAATTAC-AAAATAT
*
53439 AAATAAGTGTGGGTCAATTTCAGATACAAATATAATTTGAAGTACTAAATTAAACAAATATGAAA
259 AAATAAGTGTGGGTCAATTTCAGATACAAATATAATTTGAAGGACTAAATT-AACAAATATGAAA
* *
53504 TTACAAATTAAAATTTAAATA-AATAAACAATATAAAAGGATC-AATC-AAAAATTTGTAAATGT
323 TTACAAATTAAAATTTAAATACAATAAACAACATAAAAGGATCAAATCAAAAAAATTGTAAATGT
** *
53566 GAGGAAACATTGT-AAATGTTCTGAATTGCATTAATTTCAAAAGTTGGGGAAAATTATAAC-ATT
388 GAGGAAA-ATTGTAAAATGGACTGAATTGCATTAATTTCAAAAGTTGGGGAAAATTAAAACAATT
53629 ATAATATATATATATA
452 ATAATATATATATATA
53645 AGTACCAAAT
Statistics
Matches: 904, Mismatches: 38, Indels: 75
0.89 0.04 0.07
Matches are distributed among these distances:
501 96 0.11
502 19 0.02
503 99 0.11
504 60 0.07
505 40 0.04
506 44 0.05
507 17 0.02
508 24 0.03
509 26 0.03
511 5 0.01
512 4 0.00
515 2 0.00
516 2 0.00
520 3 0.00
522 6 0.01
524 15 0.02
525 5 0.01
526 9 0.01
527 157 0.17
528 129 0.14
529 94 0.10
530 48 0.05
ACGTcount: A:0.47, C:0.06, G:0.13, T:0.34
Consensus pattern (515 bp):
ATATACTATATATACTTATACTTTTATATGTATATAAAGTACCAAATTGAACAAACATGAAATTG
GAAATAAAAAATTGAATAAATTAAGCAACACGCATTGATGAGGGATGAAATTGAATTAATTATAA
AATGTGAAGCTGATATTAATATAAAAATGGACTAAATTGCATACATTTAAAAGTTGATGAACATA
ATTTGAAAATAAATTTATTATGTGATTTACATTTTATAGAGTTTTAAGTAAATTACAAAATATAA
ATAAGTGTGGGTCAATTTCAGATACAAATATAATTTGAAGGACTAAATTAACAAATATGAAATTA
CAAATTAAAATTTAAATACAATAAACAACATAAAAGGATCAAATCAAAAAAATTGTAAATGTGAG
GAAAATTGTAAAATGGACTGAATTGCATTAATTTCAAAAGTTGGGGAAAATTAAAACAATTATAA
TATATATATATATATGTATAATGAATGTCATGATAATATGATGCAATGATTATATTATAT
Done.