Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004027.1 Hibiscus syriacus cultivar Beakdansim tig00008797_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: 85447
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:242 original size:74 final size:72
Alignment explanation
Indices: 150--340 Score: 223
Period size: 74 Copynumber: 2.7 Consensus size: 72
140 GTTCAAATGT
*
150 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCCAACATTTGCTAAT-AC-AGACTTC
1 TATTCCGATTTCTGATTGAAATGGGCTTTCAGCATG-CCCCAACATTTG-T--TGACGAGA-TTC
*
213 -AAATGTACCAA
61 AAAATGCACCAA
*
224 TATTCCGATTTCTGATTGAAATGGGCTTTCAGCATG-CCCAACATTTGTTGACGTGATTCAAAAT
1 TATTCCGATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGTTGACGAGATTCAAAAT
*
288 GCATCAA
66 GCACCAA
* * *
295 TATTCCTGA--TCTAATTGAAATGAGCTTTCAGTATGCCCCAACATTT
1 TATTCC-GATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTT
341 TCTTTTTGTT
Statistics
Matches: 105, Mismatches: 7, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
69 1 0.01
70 28 0.27
71 28 0.27
72 13 0.12
74 35 0.33
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.34
Consensus pattern (72 bp):
TATTCCGATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAACATTTGTTGACGAGATTCAAAAT
GCACCAA
Found at i:6068 original size:20 final size:20
Alignment explanation
Indices: 6039--6078 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
6029 TGCAAAGATA
* *
6039 TAAATGCAAAAATGAAAATG
1 TAAATACAAAAATAAAAATG
*
6059 TAAATACAAACATAAAAATG
1 TAAATACAAAAATAAAAATG
6079 CAAAGATGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.20
Consensus pattern (20 bp):
TAAATACAAAAATAAAAATG
Found at i:6078 original size:34 final size:35
Alignment explanation
Indices: 6031--6103 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
6021 TATAATTATG
* * *
6031 CAAAGATATAAATGCAAAAATG-AAAATGTAAATA
1 CAAACATAAAAATGCAAAAATGCAAAATGCAAATA
*
6065 CAAACATAAAAATGCAAAGATGCAAAATGCAAATA
1 CAAACATAAAAATGCAAAAATGCAAAATGCAAATA
6100 CAAA
1 CAAA
6104 TGTAAATATG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 19 0.56
35 15 0.44
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (35 bp):
CAAACATAAAAATGCAAAAATGCAAAATGCAAATA
Found at i:6209 original size:7 final size:7
Alignment explanation
Indices: 6174--6214 Score: 59
Period size: 6 Copynumber: 6.0 Consensus size: 7
6164 ATAAAAGTAC
6174 AAATGCA
1 AAATGCA
6181 AAATG-A
1 AAATGCA
6187 AAATGCA
1 AAATGCA
6194 AAGATGCA
1 AA-ATGCA
6202 AAATGC-
1 AAATGCA
6208 AAATGCA
1 AAATGCA
6215 TGTATGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 12 0.39
7 12 0.39
8 7 0.23
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:10359 original size:3 final size:3
Alignment explanation
Indices: 10351--10417 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
10341 TATTTATTTA
* *
10351 AAT AAT AAT AAT AAT AAT AAT ATAT GAT ATAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT
**
10398 TTT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
10418 AATGAAATGA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
3 49 0.91
4 5 0.09
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:11719 original size:22 final size:22
Alignment explanation
Indices: 11675--11729 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
11665 CGATGTTCCC
11675 TGGTATCGATA-CCCTCCACAA
1 TGGTATCGATACCCCTCCACAA
*
11696 TGGTATCGATACCCCTTCC-TAA
1 TGGTATCGATACCCC-TCCACAA
11718 TGGTATCGATAC
1 TGGTATCGATAC
11730 TGTTCATACA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 11 0.35
22 17 0.55
23 3 0.10
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.29
Consensus pattern (22 bp):
TGGTATCGATACCCCTCCACAA
Found at i:13186 original size:19 final size:19
Alignment explanation
Indices: 13162--13204 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
13152 TGACTTTGAC
13162 TTGACCGTTGACCTGCCCA
1 TTGACCGTTGACCTGCCCA
*
13181 TTGACCGTTGACCTGCCCG
1 TTGACCGTTGACCTGCCCA
13200 TTGAC
1 TTGAC
13205 TTTGACCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.14, C:0.35, G:0.23, T:0.28
Consensus pattern (19 bp):
TTGACCGTTGACCTGCCCA
Found at i:15133 original size:36 final size:36
Alignment explanation
Indices: 15093--15163 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
15083 ATTCTGGAGT
* *
15093 ATGTAGGTTCAGCT-CTGATCAAGCTGGTAATTCCTC
1 ATGTAGGTTCAG-TACCGATCAAGCTAGTAATTCCTC
* *
15129 ATGTAGGTTTAGTACCGATCAAGCTAGTAGTTCCT
1 ATGTAGGTTCAGTACCGATCAAGCTAGTAATTCCT
15164 TATATACCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.03
36 29 0.97
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.34
Consensus pattern (36 bp):
ATGTAGGTTCAGTACCGATCAAGCTAGTAATTCCTC
Found at i:21112 original size:31 final size:31
Alignment explanation
Indices: 21071--21130 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
21061 AAGAGTTTAT
*
21071 GAGTTCCTAGTGAGAAGGACATATTGAATGG
1 GAGTTCCTAGTGAGAAAGACATATTGAATGG
*
21102 GAGTTTCTAGTGAGAAAGACATATTGAAT
1 GAGTTCCTAGTGAGAAAGACATATTGAAT
21131 TCACCAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.28, T:0.28
Consensus pattern (31 bp):
GAGTTCCTAGTGAGAAAGACATATTGAATGG
Found at i:23455 original size:38 final size:38
Alignment explanation
Indices: 23394--23529 Score: 157
Period size: 38 Copynumber: 3.5 Consensus size: 38
23384 ATTAAACCTT
*
23394 TTCAACAATTACACACCTCTTCAATTTTTATCTTTTTTAA
1 TTCAACAATTA-A-ACCTCTTCAATTTTTATCTTTTTAAA
* * *
23434 TTCAAAAATTAAACCTCTTCAACTTTTATCTTTCTAAA
1 TTCAACAATTAAACCTCTTCAATTTTTATCTTTTTAAA
* * * *
23472 TTCAACAATTAAGCCTCTTCAACTTTTATAAC-TGTTCAA
1 TTCAACAATTAAACCTCTTCAA-TTTT-TATCTTTTTAAA
23511 TTCAACAATTAAACCTCTT
1 TTCAACAATTAAACCTCTT
23530 TAAATTAAAT
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
38 43 0.52
39 26 0.32
40 13 0.16
ACGTcount: A:0.34, C:0.23, G:0.01, T:0.42
Consensus pattern (38 bp):
TTCAACAATTAAACCTCTTCAATTTTTATCTTTTTAAA
Found at i:24888 original size:14 final size:15
Alignment explanation
Indices: 24869--24908 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
24859 ATTCAATTCG
24869 TTGAGTCAAC-CCAA
1 TTGAGTCAACTCCAA
*
24883 TTGAGTCAACTCGAA
1 TTGAGTCAACTCCAA
*
24898 TAGAGTCAACT
1 TTGAGTCAACT
24909 ATTGACTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (15 bp):
TTGAGTCAACTCCAA
Found at i:25533 original size:3 final size:3
Alignment explanation
Indices: 25525--25587 Score: 101
Period size: 3 Copynumber: 21.0 Consensus size: 3
25515 CCATTTACTT
*
25525 TTA TTA TTA TTA ATA TTA TTA TTA -TA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
25570 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
25588 AAAAAATATT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:26550 original size:29 final size:30
Alignment explanation
Indices: 26505--26579 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
26495 TTACAACATG
*
26505 TTTTTATATATATTATAATTCAGTCTATTAA
1 TTTTTATATATATTATAATTCAGTC-ACTAA
*
26536 TTTTTAT-T-TATTATAATTTAGTCACTAA
1 TTTTTATATATATTATAATTCAGTCACTAA
26564 TTTAGTTATATATATT
1 TTT--TTATATATATT
26580 TTAGGTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 7 0.18
29 14 0.37
30 5 0.13
31 8 0.21
32 4 0.11
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.57
Consensus pattern (30 bp):
TTTTTATATATATTATAATTCAGTCACTAA
Found at i:26860 original size:16 final size:17
Alignment explanation
Indices: 26817--26889 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 17
26807 TAATACTTTC
26817 ATTTATTTTTACAAGTTTT
1 ATTTATTTTT-CAA-TTTT
26836 A-TTACTTTTT-AATTTT
1 ATTTA-TTTTTCAATTTT
*
26852 ATTTATTTTAGTCATTGTTT
1 ATTTATTTT--TCAAT-TTT
26872 ATTTATATTTT-AATTTT
1 ATTTAT-TTTTCAATTTT
26889 A
1 A
26890 CATGTTTATA
Statistics
Matches: 45, Mismatches: 2, Indels: 16
0.71 0.03 0.25
Matches are distributed among these distances:
16 9 0.20
17 9 0.20
18 6 0.13
19 9 0.20
20 9 0.20
21 3 0.07
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (17 bp):
ATTTATTTTTCAATTTT
Found at i:27330 original size:2 final size:2
Alignment explanation
Indices: 27293--27320 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
27283 TATAAAAATA
27293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27321 GTTAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27869 original size:25 final size:24
Alignment explanation
Indices: 27840--27922 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 24
27830 TTATATATAC
27840 TTATTATTTTCA-TAATATTTTATA
1 TTATTATTTTCATTAATATTTT-TA
27864 TATATTATTTT-ATTAATATTTTTA
1 T-TATTATTTTCATTAATATTTTTA
* *
27888 TT-TTATTTTCAATTATTAAATTTTA
1 TTATTATTTTC-ATTAAT-ATTTTTA
27913 TTATTTATTT
1 TTA-TTATTT
27923 GTTTGCCAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
22 7 0.14
23 1 0.02
24 10 0.20
25 26 0.52
27 6 0.12
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATTATTTTCATTAATATTTTTA
Found at i:27871 original size:28 final size:28
Alignment explanation
Indices: 27819--27888 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
27809 AATTCTTTCC
27819 TTTCAAAATTTTTATATATACTTATTAT
1 TTTCAAAATTTTTATATATACTTATTAT
*
27847 TTTCATAATATTTTATATATA-TTATT-T
1 TTTCAAAAT-TTTTATATATACTTATTAT
*
27874 TATT-AATATTTTTAT
1 T-TTCAAAATTTTTAT
27889 TTTATTTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
26 6 0.16
27 5 0.14
28 15 0.41
29 11 0.30
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTCAAAATTTTTATATATACTTATTAT
Found at i:34997 original size:9 final size:9
Alignment explanation
Indices: 34980--35015 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
34970 AATCATTTTT
34980 TTTACATTC
1 TTTACATTC
*
34989 TTTATATTC
1 TTTACATTC
*
34998 TTTACATTT
1 TTTACATTC
35007 TTTACATTC
1 TTTACATTC
35016 ATTATTTCTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTACATTC
Found at i:38524 original size:8 final size:7
Alignment explanation
Indices: 38497--38522 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38487 AATGATGAAA
38497 AAAAATG
1 AAAAATG
38504 AAAAATG
1 AAAAATG
38511 AAAAATG
1 AAAAATG
38518 AAAAA
1 AAAAA
38523 ATATATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:38891 original size:21 final size:23
Alignment explanation
Indices: 38867--38925 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
38857 TTTATTATTT
*
38867 ATTCCAA-GTATTC-TTTTTTAA
1 ATTCCAATGTATTCATTTTTGAA
*
38888 ATT-CAATTTATTCATTTTTGAA
1 ATTCCAATGTATTCATTTTTGAA
*
38910 ATT-CAATTTATTCATT
1 ATTCCAATGTATTCATT
38926 CATATAAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
20 3 0.09
21 8 0.24
22 23 0.68
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54
Consensus pattern (23 bp):
ATTCCAATGTATTCATTTTTGAA
Found at i:38911 original size:22 final size:22
Alignment explanation
Indices: 38875--38925 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
38865 TTATTCCAAG
*
38875 TATTC-TTTTTTAAATTCAATT
1 TATTCATTTTTGAAATTCAATT
38896 TATTCATTTTTGAAATTCAATT
1 TATTCATTTTTGAAATTCAATT
38918 TATTCATT
1 TATTCATT
38926 CATATAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (22 bp):
TATTCATTTTTGAAATTCAATT
Found at i:39206 original size:20 final size:20
Alignment explanation
Indices: 39177--39222 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
39167 AATGTTTTAC
39177 GAACCAGTAATTATGGTGTT
1 GAACCAGTAATTATGGTGTT
*
39197 GAACCGGTAATTATGGTGTT
1 GAACCAGTAATTATGGTGTT
*
39217 AAACCA
1 GAACCA
39223 ATGTTGTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (20 bp):
GAACCAGTAATTATGGTGTT
Found at i:39605 original size:20 final size:22
Alignment explanation
Indices: 39560--39622 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
39550 ACATCTACAT
39560 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
39582 TCTTCAAATATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* * *
39604 TTTTCAAAGAAGAAAGATT
1 TCTTCAAAGATGATAGATT
39623 TATTATATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:40005 original size:118 final size:118
Alignment explanation
Indices: 39813--40492 Score: 780
Period size: 118 Copynumber: 5.7 Consensus size: 118
39803 CACTCAATGG
*
39813 ATCAACATTTCCT-GAAGAGTTCATAATGAGAAGAACTCATCTGAACAAGGAAGAAGAAGTTCAT
1 ATCAACATTT-CTGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * **
39877 AATGAAAAGAACCTGTTCAACCTTTTGCTCTAATTCATCACTCGATGGATCAGT
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTCGATGGATCAAC
39931 ATCAACATTTCTGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAGTTCAT
1 ATCAACATTTCTGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCAT
*
39995 AATGAGAAGAACTTGTTCAACCTTTTGCCCAAATTCATCACTCGATGGATCAAC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTCGATGGATCAAC
* * * * *
40049 ATCAACATTTCCGGAAGAGTTCATAATGAGAAGAGCTCATATGAAGAATGAAGAAGAAATTCATA
1 ATCAACATTTCTGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
* * * ***
40114 ATGAGAATAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGCATTTGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTCGATGGATCAAC
* * * *
40167 ATCAACTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAATAAGAAGTTCA
1 ATCAACATTT-CTG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* *
40231 TAATGAGAAGAACTTGTTCAACCTTTTTCTCAAATTCATCACTAGATGGATCAAC
64 TAATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTCGATGGATCAAC
* ** * * * *
40286 ATCAACTTTTC-CAAAGAAAGTTCATAATGAGAATAACTTATCTAAAG-AGGAAGAAGAAGATCA
1 ATCAACATTTCTGGAAG--AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
* * * * ** ** *** *
40349 TAATGAGAAGAGCTTGTTCAATCTTTTACATGACTCTATCAGAGAAGGAGATAGATCAAC
64 TAATGAGAAGAACTTGTTCAACCTTTTGC-TCA-AAT-TC--ATCACTCGATGGATCAAC
** *
40409 ATCAACATTT-TCAAAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGG-AGAAGAAGTTCAT
1 ATCAACATTTCT-GGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
40472 AATAAGAAGAACTTGTTCAAC
65 AATGAGAAGAACTTGTTCAAC
40493 TTTAATTTAA
Statistics
Matches: 484, Mismatches: 62, Indels: 28
0.84 0.11 0.05
Matches are distributed among these distances:
116 2 0.00
117 4 0.01
118 258 0.53
119 130 0.27
120 4 0.01
121 2 0.00
122 55 0.11
123 25 0.05
124 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (118 bp):
ATCAACATTTCTGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCAAATTCATCACTCGATGGATCAAC
Found at i:40281 original size:237 final size:235
Alignment explanation
Indices: 39813--40492 Score: 811
Period size: 237 Copynumber: 2.9 Consensus size: 235
39803 CACTCAATGG
* *
39813 ATCAACATTTCCTGAAGAGTTCATAATGAGAAGAACTCATCTGAACAAGGAAGAAGAAGTTCATA
1 ATCAACATTTCC-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
* * * * * *
39878 ATGAAAAGAACCTGTTCAACCTTTTGCTCTAATTCATCACTCGATGGATCAGTATCAACATTTCT
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGCATCAGCATCAACATTTCA
*
39943 GGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAGAAAGTTCATAATGAGAAGAACT
130 GGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAGAAAGTTCATAATGAGAAGAACT
*
40008 TGTTCAACCTTTTGCCCAAATTCATCACTCGATGGATCAAC
195 TGTTCAACCTTTTGCCCAAATTCATCACTAGATGGATCAAC
* * *
40049 ATCAACATTTCCGGAAGAGTTCATAATGAGAAGAGCTCATATGAAGAATGAAGAAGAAATTCATA
1 ATCAACATTTCC-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATA
* ** *
40114 ATGAGAATAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGCATTTGCATCAACTTTTCC
65 ATGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGCATCAGCATCAACATTT-C
*
40179 AGAGAA-AGTTCATAATGAGAAGAACTTATCTGAAGAAGGAATAAG-AAGTTCATAATGAGAAGA
129 AG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA-AAGAAAGTTCATAATGAGAAGA
* *
40242 ACTTGTTCAACCTTTTTCTCAAATTCATCACTAGATGGATCAAC
192 ACTTGTTCAACCTTTTGCCCAAATTCATCACTAGATGGATCAAC
* * * * *
40286 ATCAACTTTTCCAAAGAAAGTTCATAATGAGAATAACTTATCTAAAG-AGGAAGAAGAAGA-TCA
1 ATCAACATTTCCGAAG--AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-ATTCA
* * * * *** *
40349 TAATGAGAAGAGCTTGTTCAATCTTTTACAT-G-ACTCTATCAGAGAAGGAGATAG-ATCAACAT
63 TAATGAGAAGAACTTGTTCAACCTTTTGC-TCGAATTC-ATC-----ACTCGAT-GCATCAGCAT
* * *
40411 CAACATTTTCA-AAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAGAAG-AAGTTCATAA
120 CAACA-TTTCAGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAGAAAGTTCATAA
*
40474 TAAGAAGAACTTGTTCAAC
184 TGAGAAGAACTTGTTCAAC
40493 TTTAATTTAA
Statistics
Matches: 382, Mismatches: 46, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
236 119 0.31
237 148 0.39
238 31 0.08
240 33 0.09
241 32 0.08
242 15 0.04
243 4 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (235 bp):
ATCAACATTTCCGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCTCGAATTCATCACTCGATGCATCAGCATCAACATTTCAG
GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAGAAAGTTCATAATGAGAAGAACTT
GTTCAACCTTTTGCCCAAATTCATCACTAGATGGATCAAC
Found at i:40908 original size:3 final size:3
Alignment explanation
Indices: 40900--40981 Score: 132
Period size: 3 Copynumber: 28.0 Consensus size: 3
40890 CCATTTTCTT
* *
40900 TTA TTA TTA ATA ATA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40947 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40982 CTAATAAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
2 4 0.05
3 71 0.95
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:40940 original size:32 final size:32
Alignment explanation
Indices: 40900--40981 Score: 146
Period size: 32 Copynumber: 2.6 Consensus size: 32
40890 CCATTTTCTT
* *
40900 TTATTATTAATAATATTATTATATTATTATTA
1 TTATTATTATTATTATTATTATATTATTATTA
40932 TTATTATTATTATTATTATTATATTATTATTA
1 TTATTATTATTATTATTATTATATTATTATTA
40964 TTATTATTATTATTATTA
1 TTATTATTATTATTATTA
40982 CTAATAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
TTATTATTATTATTATTATTATATTATTATTA
Found at i:42719 original size:2 final size:2
Alignment explanation
Indices: 42712--42742 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
42702 ATAAAAATAA
42712 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42743 TTTCTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:50280 original size:8 final size:8
Alignment explanation
Indices: 50269--50315 Score: 62
Period size: 8 Copynumber: 6.1 Consensus size: 8
50259 TGAGTTCTTT
50269 CTTTCTAG
1 CTTTCTAG
50277 CTTTCTAG
1 CTTTCTAG
*
50285 CTTGC-AG
1 CTTTCTAG
50292 CTTTCTAG
1 CTTTCTAG
*
50300 CTTGC-AG
1 CTTTCTAG
50307 CTTTCTAG
1 CTTTCTAG
50315 C
1 C
50316 CTTGTCGGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 12 0.36
8 21 0.64
ACGTcount: A:0.13, C:0.28, G:0.17, T:0.43
Consensus pattern (8 bp):
CTTTCTAG
Found at i:50295 original size:15 final size:15
Alignment explanation
Indices: 50275--50315 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
50265 CTTTCTTTCT
50275 AGCTTTCTAGCTTGC
1 AGCTTTCTAGCTTGC
50290 AGCTTTCTAGCTTGC
1 AGCTTTCTAGCTTGC
50305 AGCTTTCTAGC
1 AGCTTTCTAGC
50316 CTTGTCGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.39
Consensus pattern (15 bp):
AGCTTTCTAGCTTGC
Found at i:67278 original size:14 final size:15
Alignment explanation
Indices: 67259--67295 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
67249 TAAATTACTA
67259 TAAAAAATCCTTA-T
1 TAAAAAATCCTTATT
67273 TAAAAAATCCTTATT
1 TAAAAAATCCTTATT
67288 TAAAAAAT
1 TAAAAAAT
67296 TTCTGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAAAATCCTTATT
Found at i:74784 original size:202 final size:201
Alignment explanation
Indices: 74418--74924 Score: 615
Period size: 202 Copynumber: 2.5 Consensus size: 201
74408 GGTTTGAAAT
* * * *
74418 CATTTTCAACTG-GAATTTAACCCCGCTTACTATGTCTCGTATGTGTCGATATTAACCTCAACTG
1 CATTTTCAA-TGCGATTTTTACCCCGCTTACAATGTCTCGTATGTGTCGATATTAGCCTCAACTG
* * *
74482 AAAGATAAGTTCCAATACAACACCTCTAATCTTATAAATTATGAAAACATTTCGATTAACTTCCC
65 AAAGATAAGTTCCAATACTACATCTCTAATCTTATAAATTATGAAAACATTTCAATTAACTTCCC
* * * * ** *
74547 CTAAATACCCTTCAAACATGTCTATCAAACCATTTTTAGTTTCTTTTTCAAGCACAAAACCAAAC
130 CAAAATACCCCTCAAACATGCCTAACAAACCA-TTTTAACTTCTTCTTCAAGCACAAAACCAAAC
74612 TTTGGAAC
194 TTTGGAAC
* **
74620 CATTTTCAATGCGATTTTTACGCCGCTTACAATGTCTCGTATG-CACTGATATTAGCCTCAACTG
1 CATTTTCAATGCGATTTTTACCCCGCTTACAATGTCTCGTATGTGTC-GATATTAGCCTCAACTG
* * * *
74684 AAAGATAAGTTCAAATTCTACGTCTCTAATCTTATAAATTATGAAAA-ATTCTCAATTAACTTCT
65 AAAGATAAGTTCCAATACTACATCTCTAATCTTATAAATTATGAAAACATT-TCAATTAACTTCC
* * * * ** *
74748 CGAAAATACCCCTCGAACATGCCTAACAAGCCATTTTAACTTGTTCTTCATTCACAAAACCAAGC
129 CCAAAATACCCCTCAAACATGCCTAACAAACCATTTTAACTTCTTCTTCAAGCACAAAACCAAAC
*
74813 TTTGGAAT
194 TTTGGAAC
* * * * * * *
74821 AATTTTCAACGCGATTTTTGCCCCACCTACAATGTCTCATATGTGTCGATATTAGCATCAACTGA
1 CATTTTCAATGCGATTTTTACCCCGCTTACAATGTCTCGTATGTGTCGATATTAGCCTCAACTGA
* *
74886 AAGATAAATTCCAATACTATATCTCTAATCTTATAAATT
66 AAGATAAGTTCCAATACTACATCTCTAATCTTATAAATT
74925 GCAAAAAAAA
Statistics
Matches: 257, Mismatches: 44, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
201 125 0.49
202 132 0.51
ACGTcount: A:0.34, C:0.23, G:0.10, T:0.34
Consensus pattern (201 bp):
CATTTTCAATGCGATTTTTACCCCGCTTACAATGTCTCGTATGTGTCGATATTAGCCTCAACTGA
AAGATAAGTTCCAATACTACATCTCTAATCTTATAAATTATGAAAACATTTCAATTAACTTCCCC
AAAATACCCCTCAAACATGCCTAACAAACCATTTTAACTTCTTCTTCAAGCACAAAACCAAACTT
TGGAAC
Found at i:74890 original size:201 final size:202
Alignment explanation
Indices: 74449--74924 Score: 598
Period size: 201 Copynumber: 2.4 Consensus size: 202
74439 CCCGCTTACT
* * *
74449 ATGTCTCGTATGTGTCGATATTAACCTCAACTGAAAGATAAGTTCCAATACAACACCTCTAATCT
1 ATGTCTCGTATGTGTCGATATTAGCCTCAACTGAAAGATAAGTTCCAATACTACATCTCTAATCT
* * * * *
74514 TATAAATTATGAAAACATTTCGATTAACTTCCCCTAAATACCCTTCAAACATGTCTATCAAACCA
66 TATAAATTATGAAAACATTTCAATTAACTTCCCCAAAATACCCCTCAAACATGCCTAACAAACCA
** * * * *
74579 TTTTTAGTTTCTTTTTCAAGCACAAAACCAAACTTTGGAACCATTTTCAATGCGATTTTTACGCC
131 TTTTTAACTTCTTCTTCAAGCACAAAACCAAACTTTGGAACAATTTTCAACGCGATTTTTACCCC
* *
74644 GCTTACA
196 ACCTACA
** * * *
74651 ATGTCTCGTATG-CACTGATATTAGCCTCAACTGAAAGATAAGTTCAAATTCTACGTCTCTAATC
1 ATGTCTCGTATGTGTC-GATATTAGCCTCAACTGAAAGATAAGTTCCAATACTACATCTCTAATC
* * * *
74715 TTATAAATTATGAAAA-ATTCTCAATTAACTTCTCGAAAATACCCCTCGAACATGCCTAACAAGC
65 TTATAAATTATGAAAACATT-TCAATTAACTTCCCCAAAATACCCCTCAAACATGCCTAACAAAC
* ** * * *
74779 CA-TTTTAACTTGTTCTTCATTCACAAAACCAAGCTTTGGAATAATTTTCAACGCGATTTTTGCC
129 CATTTTTAACTTCTTCTTCAAGCACAAAACCAAACTTTGGAACAATTTTCAACGCGATTTTTACC
74843 CCACCTACA
194 CCACCTACA
* * * *
74852 ATGTCTCATATGTGTCGATATTAGCATCAACTGAAAGATAAATTCCAATACTATATCTCTAATCT
1 ATGTCTCGTATGTGTCGATATTAGCCTCAACTGAAAGATAAGTTCCAATACTACATCTCTAATCT
74917 TATAAATT
66 TATAAATT
74925 GCAAAAAAAA
Statistics
Matches: 231, Mismatches: 40, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
201 123 0.53
202 108 0.47
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (202 bp):
ATGTCTCGTATGTGTCGATATTAGCCTCAACTGAAAGATAAGTTCCAATACTACATCTCTAATCT
TATAAATTATGAAAACATTTCAATTAACTTCCCCAAAATACCCCTCAAACATGCCTAACAAACCA
TTTTTAACTTCTTCTTCAAGCACAAAACCAAACTTTGGAACAATTTTCAACGCGATTTTTACCCC
ACCTACA
Found at i:84491 original size:14 final size:14
Alignment explanation
Indices: 84472--84499 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
84462 AATAAATGTT
84472 AAAGAAGAAAAAAA
1 AAAGAAGAAAAAAA
84486 AAAGAAGAAAAAAA
1 AAAGAAGAAAAAAA
84500 TAATAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAAAAAA
Found at i:84635 original size:29 final size:31
Alignment explanation
Indices: 84584--84643 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
84574 AAAAACAAAT
*
84584 AAAAAATACTAATAATACTAATAAT-AAAGG
1 AAAAAATAATAATAATACTAATAATGAAAGG
84614 AAAAAA-AATAATATATAC-AATAATGAAAGG
1 AAAAAATAATAATA-ATACTAATAATGAAAGG
84644 GACTGAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.65, C:0.05, G:0.08, T:0.22
Consensus pattern (31 bp):
AAAAAATAATAATAATACTAATAATGAAAGG
Done.