Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003010.1 Hibiscus syriacus cultivar Beakdansim tig00006235_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: 61296
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:5126 original size:34 final size:33
Alignment explanation
Indices: 5088--5163 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 33
5078 AACAAATGAG
5088 AAACTGATTCAGGATACAAAGCACACAAAGGGCA
1 AAACTGATTCAGGATACAAAGCACACAAAGGG-A
* **
5122 AAACTGATTTAGGATACAAAGCGTACAAAGGGA
1 AAACTGATTCAGGATACAAAGCACACAAAGGGA
5155 AAAGCTGAT
1 AAA-CTGAT
5164 CCCTAAGTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 4 0.11
34 34 0.89
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (33 bp):
AAACTGATTCAGGATACAAAGCACACAAAGGGA
Found at i:7365 original size:30 final size:29
Alignment explanation
Indices: 7329--7436 Score: 101
Period size: 30 Copynumber: 3.6 Consensus size: 29
7319 TACCCCTATA
*
7329 TTTGTTTCTTTGTTTTTGTTGTGATGGGCT
1 TTTGTTTCTTTG-TTTTGTTGTGATGGGTT
* *
7359 TTTGTTTCCTTTGCTTCTGCTGTGA-GGGTT
1 TTTGTTT-CTTTG-TTTTGTTGTGATGGGTT
* *
7389 TTTGTTTTCTTTGGTTTGTTGTGGTGGGTT
1 TTTG-TTTCTTTGTTTTGTTGTGATGGGTT
* *
7419 TCTTCTTTCTTTGATTTG
1 T-TTGTTTCTTTGTTTTG
7437 CTTTCATGGG
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
29 7 0.11
30 38 0.59
31 19 0.30
ACGTcount: A:0.03, C:0.10, G:0.26, T:0.61
Consensus pattern (29 bp):
TTTGTTTCTTTGTTTTGTTGTGATGGGTT
Found at i:15037 original size:83 final size:83
Alignment explanation
Indices: 14898--15064 Score: 289
Period size: 83 Copynumber: 2.0 Consensus size: 83
14888 TTGCATTTAG
* * *
14898 GAAGGCATCTAAATTCTAACGTTATTCTTGTCGTTCAGTATTATTCAAAATGCTCATTGGAATTG
1 GAAGGCATCTAAATTCTAACGTTATTCTTATCATTCAATATTATTCAAAATGCTCATTGGAATTG
*
14963 AATGAAGCAGATACATCT
66 AATAAAGCAGATACATCT
14981 GAAGGCATCTAAATTCTAACGTTATTCTTATCATTCAATATTATTCAAAATGCTCATTGGAATTG
1 GAAGGCATCTAAATTCTAACGTTATTCTTATCATTCAATATTATTCAAAATGCTCATTGGAATTG
*
15046 AATAAAGCAGATGCATCT
66 AATAAAGCAGATACATCT
15064 G
1 G
15065 TTTCTCAAAG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Consensus pattern (83 bp):
GAAGGCATCTAAATTCTAACGTTATTCTTATCATTCAATATTATTCAAAATGCTCATTGGAATTG
AATAAAGCAGATACATCT
Found at i:19560 original size:21 final size:21
Alignment explanation
Indices: 19510--19567 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
19500 TGAAGCACGC
*
19510 TCACTCGTTGAATCTTCTCAT
1 TCACTTGTTGAATCTTCTCAT
**
19531 TCAAATGTTGAATCTTCTC-T
1 TCACTTGTTGAATCTTCTCAT
*
19551 TACACTTGTTGATTCTT
1 T-CACTTGTTGAATCTT
19568 TAGCGAAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.21, C:0.22, G:0.10, T:0.47
Consensus pattern (21 bp):
TCACTTGTTGAATCTTCTCAT
Found at i:22271 original size:3 final size:3
Alignment explanation
Indices: 22265--22329 Score: 80
Period size: 3 Copynumber: 21.7 Consensus size: 3
22255 CTCCATTTTC
22265 TAT TAT TAT TAT T-T TAT ATAT TAT TAT TAT TAT TAT T-T TATT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TA-T TAT
* *
22310 TAT TAT TAA AAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
22330 CAAACAGGCC
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
2 4 0.07
3 44 0.81
4 6 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:22297 original size:24 final size:24
Alignment explanation
Indices: 22265--22317 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
22255 CTCCATTTTC
22265 TATTATTATTATTTTATATATTAT
1 TATTATTATTATTTTATATATTAT
*
22289 TATTATTATTATTTTATTTATTAT
1 TATTATTATTATTTTATATATTAT
22313 TATTA
1 TATTA
22318 AAATTATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
TATTATTATTATTTTATATATTAT
Found at i:23674 original size:3 final size:3
Alignment explanation
Indices: 23666--23697 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
23656 TGTTTACTTG
*
23666 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23698 TAACCATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:23916 original size:20 final size:20
Alignment explanation
Indices: 23891--23933 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
23881 TTATTTTATA
23891 AATTATATATTAATTGTTTT
1 AATTATATATTAATTGTTTT
* * *
23911 AATTATTTATTTATTTTTTT
1 AATTATATATTAATTGTTTT
23931 AAT
1 AAT
23934 ATCAAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTATATATTAATTGTTTT
Found at i:24569 original size:26 final size:27
Alignment explanation
Indices: 24517--24574 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
24507 TAATTCTTTC
*
24517 TTTTCAAAATTTTTATATATACCTATTA
1 TTTTCAAAATATTTATATATA-CTATTA
* *
24545 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
24571 TTTT
1 TTTT
24575 ATTAATGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.59
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:26201 original size:6 final size:6
Alignment explanation
Indices: 26192--26231 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
26182 ACATTCACAT
* * *
26192 ATTTAC ATTTGC ATTTAC ATTTGC ATTTAC ATTTGC ATTT
1 ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTTAC ATTT
26232 TTTTACGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (6 bp):
ATTTAC
Found at i:26209 original size:12 final size:12
Alignment explanation
Indices: 26192--26231 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
26182 ACATTCACAT
26192 ATTTACATTTGC
1 ATTTACATTTGC
26204 ATTTACATTTGC
1 ATTTACATTTGC
26216 ATTTACATTTGC
1 ATTTACATTTGC
26228 ATTT
1 ATTT
26232 TTTTACGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.25, C:0.15, G:0.07, T:0.53
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:26242 original size:28 final size:28
Alignment explanation
Indices: 26205--26261 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
26195 TACATTTGCA
26205 TTTACATTTGCATTTACATTTGCATTTT
1 TTTACATTTGCATTTACATTTGCATTTT
* ** *
26233 TTTACGTTTGTTTTTACATTTTCATTTT
1 TTTACATTTGCATTTACATTTGCATTTT
26261 T
1 T
26262 ACATAATTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.07, T:0.63
Consensus pattern (28 bp):
TTTACATTTGCATTTACATTTGCATTTT
Found at i:28220 original size:2 final size:2
Alignment explanation
Indices: 28213--28254 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
28203 TTATCCTTTA
28213 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
28255 CCTTTGTTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28572 original size:18 final size:16
Alignment explanation
Indices: 28549--28619 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 16
28539 CTCATCCAGC
28549 AAAGAAAGAAGAAGGAAA
1 AAAGAAAGAA-AAGG-AA
*
28567 AAAGAAA-AAAAAGAA
1 AAAGAAAGAAAAGGAA
28582 AAAG---GAAAAGGAA
1 AAAGAAAGAAAAGGAA
28595 AAAGAAAAGAAAAAGGAA
1 AAAG-AAAG-AAAAGGAA
28613 AAAGAAA
1 AAAGAAA
28620 AAAGAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
13 11 0.24
15 6 0.13
16 3 0.07
17 6 0.13
18 19 0.42
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAGAAAGAAAAGGAA
Found at i:28573 original size:7 final size:7
Alignment explanation
Indices: 28553--28651 Score: 71
Period size: 7 Copynumber: 14.4 Consensus size: 7
28543 TCCAGCAAAG
*
28553 AAAGAAG
1 AAAGAAA
*
28560 AAGGAAA
1 AAAGAAA
28567 AAAGAAA
1 AAAGAAA
*
28574 AAAAAGAA
1 AAAGA-AA
*
28582 AAAG-GA
1 AAAGAAA
*
28588 AAAGGAA
1 AAAGAAA
28595 AAAG--A
1 AAAGAAA
28600 AAAG-AA
1 AAAGAAA
*
28606 AAAGGAA
1 AAAGAAA
28613 AAAGAAA
1 AAAGAAA
28620 AAAGAAA
1 AAAGAAA
*
28627 AAAAACAA
1 AAAGA-AA
*
28635 AAACAAA
1 AAAGAAA
*
28642 AAGGAAA
1 AAAGAAA
28649 AAA
1 AAA
28652 CAAGGAAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
5 5 0.07
6 10 0.14
7 48 0.65
8 11 0.15
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:28583 original size:6 final size:6
Alignment explanation
Indices: 28574--28650 Score: 70
Period size: 6 Copynumber: 12.8 Consensus size: 6
28564 AAAAAAGAAA
*
28574 AAAAAG AAAAAGG AAAAGG AAAAAG -AAAAG AAAAAGG AAAAAG AAAAA-
1 AAAAAG AAAAA-G AAAAAG AAAAAG AAAAAG AAAAA-G AAAAAG AAAAAG
* * *
28622 AGAAA- AAAAAC AAAAAC AAAAAGG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAA-G AAAAA
28651 ACAAGGAAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
5 13 0.21
6 32 0.52
7 16 0.26
ACGTcount: A:0.81, C:0.03, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:31108 original size:114 final size:114
Alignment explanation
Indices: 30908--31355 Score: 815
Period size: 114 Copynumber: 3.9 Consensus size: 114
30898 CACGTTCTCG
*
30908 TAGTAGAAATAAGGAGACCCAATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
30973 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
31022 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
*
31087 GGTATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
* *
31136 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGTAAGTGTTCTTTGAGTTATCTAATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
*
31201 GGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTGCTCA
66 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
* *
31250 TAGTAGAAATAAGGAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
* *
31315 GGTATGAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAA
31356 CTGCATGATC
Statistics
Matches: 321, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 321 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
GGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTGCTCA
Found at i:32435 original size:109 final size:109
Alignment explanation
Indices: 32306--32544 Score: 433
Period size: 109 Copynumber: 2.2 Consensus size: 109
32296 CCAGAAATAG
*
32306 AATATTGGGGCATTTTGAAGGCTCACAACAATATGAATATTTGGGCATTCTTGGAGGCTCATCTC
1 AATATTGGGGCATTTTGAAGGCTCACAACAATATGAATATTTAGGCATTCTTGGAGGCTCATCTC
32371 AACAAGAAATAATGTTGAGCACACTTTTAACATCGGTATCAGCA
66 AACAAGAAATAATGTTGAGCACACTTTTAACATCGGTATCAGCA
32415 AATATTGGGGCATTTTGAAGGCTCACAACAATATGAATATTTAGGCATTCTTGGAGGCTCATCTC
1 AATATTGGGGCATTTTGAAGGCTCACAACAATATGAATATTTAGGCATTCTTGGAGGCTCATCTC
*
32480 AACAAGAAATAATGTTGAGCACACTTTTAACATCTGTATCAGCA
66 AACAAGAAATAATGTTGAGCACACTTTTAACATCGGTATCAGCA
* * *
32524 AATGTTAGGGCATTTTAAAGG
1 AATATTGGGGCATTTTGAAGG
32545 TTCTTTTAGA
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 125 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (109 bp):
AATATTGGGGCATTTTGAAGGCTCACAACAATATGAATATTTAGGCATTCTTGGAGGCTCATCTC
AACAAGAAATAATGTTGAGCACACTTTTAACATCGGTATCAGCA
Found at i:32976 original size:91 final size:91
Alignment explanation
Indices: 32821--33001 Score: 308
Period size: 91 Copynumber: 2.0 Consensus size: 91
32811 TATTTCCAAA
* * * *
32821 GAGACGGAAAGATATGAAGAATGGAAATGATAAAACAGTGACAGTCAATCTGACTACACATAATT
1 GAGACAGAAAGATATGAAGAATGAAAATGATAAAACAATAACAGTCAATCTGACTACACATAATT
32886 GCTTCGTTCATCAGGCAGTTGCATTT
66 GCTTCGTTCATCAGGCAGTTGCATTT
* *
32912 GAGACAGAAAGATATGAAGAATGAAAATGGTGAAACAATAACAGTCAATCTGACTACACATAATT
1 GAGACAGAAAGATATGAAGAATGAAAATGATAAAACAATAACAGTCAATCTGACTACACATAATT
32977 GCTTCGTTCATCAGGCAGTTGCATT
66 GCTTCGTTCATCAGGCAGTTGCATT
33002 AGGGTCCTGT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (91 bp):
GAGACAGAAAGATATGAAGAATGAAAATGATAAAACAATAACAGTCAATCTGACTACACATAATT
GCTTCGTTCATCAGGCAGTTGCATTT
Found at i:34289 original size:225 final size:228
Alignment explanation
Indices: 33932--34917 Score: 1334
Period size: 225 Copynumber: 4.3 Consensus size: 228
33922 AGTACCAGTT
33932 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
*
33997 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAATATTGCCAGGTAGAGTTCATAATGAGAA
66 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
34062 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC-TCAAA
131 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCAT-AAA
*
34126 TCCATCAC-TT-GAT-GGATCAGCTTTTCCAGAG
195 TCCATCACATTAGATAGCATCAGCTTTTCCAGAG
34157 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * *
34222 TCGACCTTTTATTTGAATTCATCATTTGATGCATCAACATTGCCAGGTAGAGTTCATAATAAGAA
66 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
* * ** *
34287 GAACTCGTCATCTGAAGAAGAAGAGATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAAT
131 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAAAT
* * * *
34352 TCAT--CATTCGAT-GGATCAACTTTTCC--AG
196 CCATCACATTAGATAGCATCAGCTTTTCCAGAG
* *
34380 AAAGTTCATAAT--G-AGAACTTATCTGAAG-AGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
* * * * *
34441 TCAACTTTTTGTTTGAATTCATCATTCGATGGATCAA-ATTTTCCA--AAAAGTTCATAATGAGA
66 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACA-TTGCCAGGTAGAGTTCATAATGAGA
*
34503 AAAACT--T-ATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCAT
130 AGAACTCGTCATCTG-A-A-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCAT
* *
34565 AATTCTATCACATAAGGAGATAGATCAGCATCAGCTTTTCCAGAG
192 AAATCCATCACAT-------TAGAT-AGCATCAGCTTTTCCAGAG
34610 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
34675 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
66 TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
*
34740 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAATT
131 GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAAAT
* **
34805 CTATCACAGAAGGAGAGAGATCAGCATCAGCTTTTCCAGAG
196 CCATCAC------A-TTAGAT-AGCATCAGCTTTTCCAGAG
* **
34846 AAAGTTCATAATGAGAAGAACTCATCTG-A-AA--AAGAAGAAGTTCACAATGAGAAGAGCTTGT
1 AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
34907 TCAACCTTTTG
66 TCAACCTTTTG
34918 CATAATTCTA
Statistics
Matches: 677, Mismatches: 47, Indels: 67
0.86 0.06 0.08
Matches are distributed among these distances:
214 5 0.01
215 2 0.00
216 1 0.00
217 64 0.09
218 1 0.00
219 72 0.11
220 14 0.02
221 1 0.00
223 15 0.02
224 2 0.00
225 203 0.30
226 5 0.01
228 12 0.02
230 14 0.02
232 39 0.06
233 14 0.02
234 74 0.11
235 2 0.00
236 128 0.19
237 1 0.00
238 2 0.00
239 5 0.01
242 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (228 bp):
AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGT
TCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAA
GAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAAAT
CCATCACATTAGATAGCATCAGCTTTTCCAGAG
Found at i:34653 original size:453 final size:453
Alignment explanation
Indices: 33903--35165 Score: 1479
Period size: 453 Copynumber: 2.7 Consensus size: 453
33893 GATTTAAATC
* ** *
33903 CATCATTCAATGGATCAACAGTACCAGTTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAACTTTTCCAG--AAAGTTCATAAT-AGAAGAACTCATCTGAAG-AGGA
*
33968 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATC-
62 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTAGATGGATCA
* * *
34032 AATATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTG-A-A-GAAGAAGAAATTCATA
127 AAT-TTTCCA--AAAAGTTCATAATGAGAAGAACT--T-ATCTGAAGAGGAAGAAGAAATTCATA
* *
34094 ATGAGAAGAATTTGTTCAACCTTTTGC-TCAAATCCATCAC-T------T-GAT--GGATCAGCT
186 ATGAGAAGAATTTGTTCAACCTTTTGCAT-AAATCTATCACATAAGGAATAGATCAGCATCAGCT
34148 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
250 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
34213 AGAATTTGTTCGACCTTTTATTTGAATTCATCATTTGATGCATCAACATTGCCAGGTAGAGTTCA
315 AGAATTTGTTCAACCTTTTATTTGAATTCATCATTTGATGCATCAACATTGCCAGGTAGAGTTCA
* *
34278 TAATAAGAAGAACTCGTCATCTGAAGAAGAAGAGATTCATAATGAGAAGAATTTGTTCAACTTTT
380 TAATAAGAAGAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTT
**
34343 TGTTTGAATT
445 TGCAT-AATT
*
34353 CATCATTCGATGGATCAACTTTTCCAGAAAGTTCATAAT-G-AGAACTTATCTGAAGAGGAAGAA
1 CATCATTCGATGGATCAACTTTTCCAGAAAGTTCATAATAGAAGAACTCATCTGAAGAGGAAGAA
* * *
34416 GAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGTTTGAATTCATCATTCGATGGATCAAATT
66 GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTAGATGGATCAAATT
*
34481 TTCCAAAAAGTTCATAATGAGAAAAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAA
131 TTCCAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAA
*
34546 TTTGTTCAACCTTTTGCATAATTCTATCACATAAGGAGATAGATCAGCATCAGCTTTTCCAGAGA
196 TTTGTTCAACCTTTTGCATAAATCTATCACATAAGGA-ATAGATCAGCATCAGCTTTTCCAGAGA
34611 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
260 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
* * *
34676 CAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGTAGAGTTCATAATGAGAAG
325 CAACCTTTTATTTGAATTCATCATTTGATGCATCAACATTGCCAGGTAGAGTTCATAATAAGAAG
34741 AACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAATT
390 AACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAATT
*** *
34805 CTATCACAGAAGGAGAGAGATCAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCA
1 C-AT--CA-TTCGA-TG-GAT---CA--A-CTTTTCC--AGAAAGTTCATAAT-AGAAGAACTCA
* ** **
34870 TCTGAA-A--AAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCAT-AATTCTATCA
51 TCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC-AT--
* * * * *
34931 CAGAAGGAGATAGATCAGCATCAAATTTTCCAAAGAAAGTTCATAATAAGAAGAACTCATTTGAA
113 C------A-TTAGAT--GGATCAAATTTTCC-AA-AAAGTTCATAATGAGAAGAACTTATCTGAA
* * * * * * * *
34996 GAAGAAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAG
167 G-AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAAATCTATCACATAAG
* * * * *
35061 GAAATAGGTCAACATCAACTTTTCCAGGGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGA
231 G-AATAGATCAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
35126 AGAAGAATTTTATAATAAGAAGAACTTGTTCAACCCTTTT
295 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAA-CCTTTT
35166 CCAAATTACA
Statistics
Matches: 704, Mismatches: 59, Indels: 69
0.85 0.07 0.08
Matches are distributed among these distances:
439 5 0.01
440 2 0.00
441 1 0.00
442 72 0.10
443 2 0.00
444 70 0.10
445 17 0.02
446 1 0.00
448 12 0.02
450 24 0.03
451 3 0.00
452 5 0.01
453 202 0.29
455 2 0.00
456 2 0.00
457 1 0.00
458 3 0.00
461 2 0.00
463 1 0.00
464 7 0.01
465 5 0.01
466 53 0.08
468 3 0.00
469 13 0.02
474 1 0.00
475 4 0.01
477 13 0.02
478 2 0.00
479 27 0.04
480 142 0.20
481 7 0.01
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (453 bp):
CATCATTCGATGGATCAACTTTTCCAGAAAGTTCATAATAGAAGAACTCATCTGAAGAGGAAGAA
GAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTAGATGGATCAAATT
TTCCAAAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAA
TTTGTTCAACCTTTTGCATAAATCTATCACATAAGGAATAGATCAGCATCAGCTTTTCCAGAGAA
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTATTTGAATTCATCATTTGATGCATCAACATTGCCAGGTAGAGTTCATAATAAGAAGA
ACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCATAATT
Found at i:34668 original size:124 final size:124
Alignment explanation
Indices: 34473--35190 Score: 831
Period size: 124 Copynumber: 5.9 Consensus size: 124
34463 CATTCGATGG
* * * *
34473 ATCAAATTTTCCA-A-AAAGTTCATAATGAGAAAAACTTATCTGAAG-AGGAAGAAGAAATTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
34535 AATGAGAAGAATTTGTTCAACCTTTTGCATAATTCTATCACATAAGGAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
*
34594 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* ** * * *
34659 AATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTC-AT--C------A-TTTGAT--GG
66 AATGAGAAGAACTTGTTCAACCTTTTGCAT-AATTCTATCACAGAAGGAGATAGATCAGC
* * *
34707 ATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAA-GAAG-A-AA-T
1 ATCAACTTTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGT
* *
34767 TCATAATGAGAAGAATTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGAGAGATCAGC
62 TCATAATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
* *
34830 ATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG-A-AA--AAGAAGAAGTTCAC
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
34891 AATGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
* * * * *
34950 ATCAAATTTTCCAAAGAAAGTTCATAATAAGAAGAACTCATTTGAAGAAGAAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * * * *
35015 AATGAGAAGAACTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTCAAC
66 AATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
* * * *
35074 ATCAACTTTTCCAGGGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAATTTTAT
1 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
35139 AATAAGAAGAACTTGTTCAACCCTTTTCCA-AATTAC-ATCACAGAATGAGATA
66 AATGAGAAGAACTTGTTCAA-CCTTTTGCATAATT-CTATCACAGAAGGAGATA
35191 TTATCATCCC
Statistics
Matches: 510, Mismatches: 57, Indels: 57
0.82 0.09 0.09
Matches are distributed among these distances:
111 5 0.01
112 36 0.07
113 33 0.06
114 2 0.00
115 9 0.02
116 13 0.03
117 3 0.01
118 3 0.01
119 3 0.01
120 107 0.21
121 16 0.03
122 4 0.01
123 60 0.12
124 203 0.40
125 13 0.03
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (124 bp):
ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTTTTGCATAATTCTATCACAGAAGGAGATAGATCAGC
Found at i:35396 original size:3 final size:3
Alignment explanation
Indices: 35388--35434 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
35378 CTCCATTTTC
* *
35388 TAT TAT TAT TAT TAT TAT T-T TATT TAT TAT TAT TAA AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT
35433 TA
1 TA
35435 CAAACAGGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:36736 original size:3 final size:3
Alignment explanation
Indices: 36728--36762 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
36718 TGTTTACTTG
*
36728 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
36763 TAACCATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:39733 original size:16 final size:18
Alignment explanation
Indices: 39712--39750 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
39702 TTGGTACATG
39712 TGTGTG-CAC-CTCTATA
1 TGTGTGCCACTCTCTATA
*
39728 TGTGTGCCTCTCTCTATA
1 TGTGTGCCACTCTCTATA
39746 TGTGT
1 TGTGT
39751 TTCCGCTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 2 0.10
18 12 0.60
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.44
Consensus pattern (18 bp):
TGTGTGCCACTCTCTATA
Found at i:41703 original size:235 final size:227
Alignment explanation
Indices: 41403--41829 Score: 577
Period size: 235 Copynumber: 1.8 Consensus size: 227
41393 AAGATAAACA
* * * * **
41403 CTCATAGATATTGTGCCTTACCTTGCTCATGCGAGTGCCTTTTCTCTTGCCTTGTGCCTTGAGCA
1 CTCATAGATATGGTGCCTTACATTGCTCATGCGAGTGCATTATCTCTTGCCTTGCACCTTGAGCA
* ** * * *
41468 ATATAACGGTTCTAGTGCCTAGAATTTGTCTTTCACCCTAAACAAGAATGTGCTAGAATAACCTC
66 ATATAAAGGTTCTAGCACCTAG-A-TTGTCGTGCACCCTAAACAACAATGTGCTAGAATAA--TC
* * *
41533 TATAATGCTTATGCTTTATGTTGCAGAAGGATCAAGGAAAAAAGGACCTAGTGTTCTGCCTTTGA
127 --T-ATG-TAATGCTTTATGTTGCAGAAGGATCAAGGAAAAAAGGACCAAGTGTTCAGCCTTTGA
41598 TAGGATCATAGGACTATACAGGGGGTAGTACTGTTATACG
188 TAGGATCATAGGACTATACAGGGGGTAGTACTGTTATACG
* * *
41638 CTCATAGATATGGTGCCTTACATTGCTCATGTGTGTGCATTATCT-TGTGCCTTGCATCTTGAGC
1 CTCATAGATATGGTGCCTTACATTGCTCATGCGAGTGCATTATCTCT-TGCCTTGCACCTTGAGC
*
41702 AATATAAAGGTTCTAGCACCTAGATTGTCGTGCACCCTAAACAACAATGTGCTAGAATAATCTCT
65 AATATAAAGGTTCTAGCACCTAGATTGTCGTGCACCCTAAACAACAATGTGCTAGAATAATCTAT
* *
41767 GTAATGCTTTATGTTGCTGAAGGATCATGGAAAAAAGGACCAAGTGTTCAGCCTTTGATAGGA
130 GTAATGCTTTATGTTGCAGAAGGATCAAGGAAAAAAGGACCAAGTGTTCAGCCTTTGATAGGA
41830 GTTTATGGAA
Statistics
Matches: 170, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
227 57 0.34
228 2 0.01
229 1 0.01
231 2 0.01
233 33 0.19
234 2 0.01
235 73 0.43
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (227 bp):
CTCATAGATATGGTGCCTTACATTGCTCATGCGAGTGCATTATCTCTTGCCTTGCACCTTGAGCA
ATATAAAGGTTCTAGCACCTAGATTGTCGTGCACCCTAAACAACAATGTGCTAGAATAATCTATG
TAATGCTTTATGTTGCAGAAGGATCAAGGAAAAAAGGACCAAGTGTTCAGCCTTTGATAGGATCA
TAGGACTATACAGGGGGTAGTACTGTTATACG
Found at i:54167 original size:47 final size:47
Alignment explanation
Indices: 54102--54206 Score: 174
Period size: 47 Copynumber: 2.2 Consensus size: 47
54092 ATTGATGGAT
*
54102 GGGATTTGCTTGCATGTCTCTGGTTAAAAGCACAACAGTTTTGATCA
1 GGGATTTGCTTGCATGTCTCTAGTTAAAAGCACAACAGTTTTGATCA
* **
54149 GGGATTTGCTTGCTTGTCTCTAGTTAAAAGCACAATGGTTTTGATCA
1 GGGATTTGCTTGCATGTCTCTAGTTAAAAGCACAACAGTTTTGATCA
54196 GGGATTTGCTT
1 GGGATTTGCTT
54207 TTGTTTATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 54 1.00
ACGTcount: A:0.23, C:0.15, G:0.25, T:0.37
Consensus pattern (47 bp):
GGGATTTGCTTGCATGTCTCTAGTTAAAAGCACAACAGTTTTGATCA
Found at i:55243 original size:32 final size:33
Alignment explanation
Indices: 55206--55269 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
55196 TCGTCTGTTC
55206 CTTTCC-TCCAAATCAGGACAATACAACCCCTT
1 CTTTCCTTCCAAATCAGGACAATACAACCCCTT
55238 CTTTCCTTCCAAATCAGGACAATACAACCCCT
1 CTTTCCTTCCAAATCAGGACAATACAACCCCT
55270 AAAGGATCGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.31, C:0.38, G:0.06, T:0.25
Consensus pattern (33 bp):
CTTTCCTTCCAAATCAGGACAATACAACCCCTT
Done.