Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006516.1 Hibiscus syriacus cultivar Beakdansim tig00015871_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: 73446
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:3721 original size:44 final size:44
Alignment explanation
Indices: 3607--3713 Score: 171
Period size: 44 Copynumber: 2.4 Consensus size: 44
3597 GTTGATCCAC
* *
3607 CTCATTTTGTGATAGAATCAAACAAAATGTTGATATTGATCTAT
1 CTCATTCTGTGATAGAATCAAACAAAATGTTGATACTGATCTAT
*
3651 CTTC-TTCTGTGATAGAATCAAACAAAATGTTGATGCTGATCTAT
1 C-TCATTCTGTGATAGAATCAAACAAAATGTTGATACTGATCTAT
3695 CTCATTCTGTGATAGAATC
1 CTCATTCTGTGATAGAATC
3714 GAGCAAAAGA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
43 2 0.03
44 54 0.93
45 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (44 bp):
CTCATTCTGTGATAGAATCAAACAAAATGTTGATACTGATCTAT
Found at i:4283 original size:104 final size:105
Alignment explanation
Indices: 4072--4282 Score: 304
Period size: 105 Copynumber: 2.0 Consensus size: 105
4062 TGAGATAAAA
* * * *
4072 TTTTGTTTCGAGTAAACAATTTTAAATTTTTGTGTTTCAAGGGAAAATATGCTCAAGCGAGACGA
1 TTTTGTTTCGAGGAAACAATTTCAAATATTTGTGTTCCAAGGGAAAATATGCTCAAGCGAGACGA
*
4137 AATTGATTTTAAGAAAGAGAATTTCAAGTGAGATGAATTT
66 AATTGATTTTAAGAAAGACAATTTCAAGTGAGATGAATTT
* * *
4177 TTTTGTTTTGAGCGAAACAATTTCAAA-ATTTGTGTTCCAAGGGAAACTGT-CTCAAGCGAGACG
1 TTTTGTTTCGAG-GAAACAATTTCAAATATTTGTGTTCCAAGGGAAAATATGCTCAAGCGAGACG
*
4240 AAATTGATTTTAA-AAA-ACAATTTCAAGTGAGTTGAATTT
65 AAATTGATTTTAAGAAAGACAATTTCAAGTGAGATGAATTT
4279 TTTT
1 TTTT
4283 TCGAGCGAGA
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
102 25 0.26
103 3 0.03
104 26 0.27
105 30 0.31
106 12 0.12
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.36
Consensus pattern (105 bp):
TTTTGTTTCGAGGAAACAATTTCAAATATTTGTGTTCCAAGGGAAAATATGCTCAAGCGAGACGA
AATTGATTTTAAGAAAGACAATTTCAAGTGAGATGAATTT
Found at i:4337 original size:159 final size:159
Alignment explanation
Indices: 4127--4447 Score: 409
Period size: 159 Copynumber: 2.0 Consensus size: 159
4117 AATATGCTCA
* * * * * * **
4127 AGCGAGACGAAATTGATTTTAAGAAAGAGAATTTCAAGTGAGATGAATTTTTTTGTTTTGAGCGA
1 AGCGAGACAAAATTCATTTTAAGAAAAAGAATCTCAAATGAGAT-AA-ATTTTTGTTTCAAGCGA
*
4192 AACAATTTC-AAAATTTGTGTTCCAAGGG-AAACTGTCTCAAGCGAGACGAAATTGATTTT-A-A
64 AACAATTTCAAAAATTTGT-TT-CAAGGGAAAACTGCCTCAAGCGAGACGAAATTGATTTTAAGA
* * *
4253 AAAACAATTTCAAGTGAGTTGAATTTTTTTTCG
127 AAAACAATTTCAAGTGAGATAAATTTTGTTTCG
**
4286 AGCGAGACAAAATTCATTTTAAGAAAAATCATCTCAAATG-GAATAAATTTTTGTTTCAAGCGAA
1 AGCGAGACAAAATTCATTTTAAGAAAAAGAATCTCAAATGAG-ATAAATTTTTGTTTCAAGCGAA
* *
4350 ACAATTTCAAAAAATTTGTTTTAAGGGAAAATTGCCTCAAGCGAGACGAAATTGATTTTAAGAAA
65 ACAATTTC-AAAAATTTGTTTCAAGGGAAAACTGCCTCAAGCGAGACGAAATTGATTTTAAGAAA
4415 AACAATTTCAAGTGAGATAAATTTTGTTTCG
129 AACAATTTCAAGTGAGATAAATTTTGTTTCG
4446 AG
1 AG
4448 TGAAAATTTC
Statistics
Matches: 140, Mismatches: 16, Indels: 11
0.84 0.10 0.07
Matches are distributed among these distances:
157 28 0.20
158 34 0.24
159 45 0.32
160 33 0.24
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (159 bp):
AGCGAGACAAAATTCATTTTAAGAAAAAGAATCTCAAATGAGATAAATTTTTGTTTCAAGCGAAA
CAATTTCAAAAATTTGTTTCAAGGGAAAACTGCCTCAAGCGAGACGAAATTGATTTTAAGAAAAA
CAATTTCAAGTGAGATAAATTTTGTTTCG
Found at i:4641 original size:100 final size:100
Alignment explanation
Indices: 4289--4619 Score: 382
Period size: 100 Copynumber: 3.3 Consensus size: 100
4279 TTTTTCGAGC
* * *
4289 GAGACAAAATTCATTTTAAGAAAAATCATCTCAAATGGAATAAATTTTTGTTTCAAGCGAAACAA
1 GAGACAAAATTGATTTTAAGAAAAA-CATCTCAAATGGAATAAATTTTTGTTTCGAGTGAAACAA
* * *
4354 TTTCAAAAAATTTGTTTTAAGGGAAAATTGCCTCAAGC
65 TTTCAAAAAA--TGTTTCAAGGGAAAACTGCCTCAAGT
* * *
4392 GAGACGAAATTGATTTTAAGAAAAACAATTTCAAGT-GAGATAAA-TTTTGTTTCGAGTG-AA-A
1 GAGACAAAATTGATTTTAAGAAAAAC-ATCTCAAATGGA-ATAAATTTTTGTTTCGAGTGAAACA
*** * *
4453 ATTTCAAATTTTTGTGTTTCAAGGGAAACCTGTCTCAAGT
64 ATTTCAAA---AAATGTTTCAAGGGAAAACTGCCTCAAGT
* *
4493 GAGACAAAATTAATTTTAAGAAAATCATCTCAAATGGAATAAATTTTTGTTTCGAGTGAAACAAT
1 GAGACAAAATTGATTTTAAGAAAAACATCTCAAATGGAATAAATTTTTGTTTCGAGTGAAACAAT
*** *
4558 TTCAAAAAAAAATTCAAAGGAAAACTGCCTCAAGT
66 TTCAAAAAATGTTTCAAGGGAAAACTGCCTCAAGT
4593 GAGACAAAATTGATTTTAAGAAAAACA
1 GAGACAAAATTGATTTTAAGAAAAACA
4620 ATTTCAAGTG
Statistics
Matches: 189, Mismatches: 30, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
100 66 0.35
101 62 0.33
102 17 0.09
103 44 0.23
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (100 bp):
GAGACAAAATTGATTTTAAGAAAAACATCTCAAATGGAATAAATTTTTGTTTCGAGTGAAACAAT
TTCAAAAAATGTTTCAAGGGAAAACTGCCTCAAGT
Found at i:6027 original size:14 final size:14
Alignment explanation
Indices: 6008--6037 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5998 CTTTGTTAAG
*
6008 CTCAAATTCAGCTC
1 CTCAAATTCAACTC
6022 CTCAAATTCAACTC
1 CTCAAATTCAACTC
6036 CT
1 CT
6038 AAGTTGTTAT
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:0.30, C:0.37, G:0.03, T:0.30
Consensus pattern (14 bp):
CTCAAATTCAACTC
Found at i:9289 original size:20 final size:20
Alignment explanation
Indices: 9266--9311 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
9256 AAAGTTAAAG
9266 AAAATATAAG-AAATGAAATA
1 AAAAT-TAAGTAAATGAAATA
9286 AAAACTTAAGTAAATGAAATA
1 AAAA-TTAAGTAAATGAAATA
*
9307 GAAAT
1 AAAAT
9312 GAATTAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.22
Consensus pattern (20 bp):
AAAATTAAGTAAATGAAATA
Found at i:9738 original size:175 final size:175
Alignment explanation
Indices: 9447--9787 Score: 664
Period size: 175 Copynumber: 1.9 Consensus size: 175
9437 CTTGTCGATG
*
9447 AAGAAACAATGCTAAGTAGCAAAGCCCCGCTCTTTATAAACTTGCTTGAGGGATGGTAGAAGTGT
1 AAGAAACAATGCTAAGTAGAAAAGCCCCGCTCTTTATAAACTTGCTTGAGGGATGGTAGAAGTGT
9512 CTTAAACCCAATAGATATTGAATCTATGAATTATAAGAATCAAAGTGAATAGAATGAAGCCACAA
66 CTTAAACCCAATAGATATTGAATCTATGAATTATAAGAATCAAAGTGAATAGAATGAAGCCACAA
9577 GTATAGAAATACACTTGCTCAATCGATATAGTTCTTGCTCAATCT
131 GTATAGAAATACACTTGCTCAATCGATATAGTTCTTGCTCAATCT
9622 AAGAAACAATGCTAAGTAGAAAAGCCCCGCTCTTTATAAACTTGCTTGAGGGATGGTAGAAGTGT
1 AAGAAACAATGCTAAGTAGAAAAGCCCCGCTCTTTATAAACTTGCTTGAGGGATGGTAGAAGTGT
9687 CTTAAACCCAATAGATATTGAATCTATGAATTATAAGAATCAAAGTGAATAGAATGAAGCCACAA
66 CTTAAACCCAATAGATATTGAATCTATGAATTATAAGAATCAAAGTGAATAGAATGAAGCCACAA
*
9752 GTATAGAAATGCACTTGCTCAATCGATATAGTTCTT
131 GTATAGAAATACACTTGCTCAATCGATATAGTTCTT
9788 AAAGAACTTG
Statistics
Matches: 164, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
175 164 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (175 bp):
AAGAAACAATGCTAAGTAGAAAAGCCCCGCTCTTTATAAACTTGCTTGAGGGATGGTAGAAGTGT
CTTAAACCCAATAGATATTGAATCTATGAATTATAAGAATCAAAGTGAATAGAATGAAGCCACAA
GTATAGAAATACACTTGCTCAATCGATATAGTTCTTGCTCAATCT
Found at i:14408 original size:15 final size:15
Alignment explanation
Indices: 14390--14421 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
14380 CCCCCTTACT
14390 TTAACACTACTCCTC
1 TTAACACTACTCCTC
14405 TTAACACTACTCCTC
1 TTAACACTACTCCTC
14420 TT
1 TT
14422 TAAAACGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAACACTACTCCTC
Found at i:16735 original size:21 final size:21
Alignment explanation
Indices: 16709--16748 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16699 CAGAACCCCA
*
16709 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
16730 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
16749 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:16783 original size:20 final size:21
Alignment explanation
Indices: 16731--16791 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
16721 TTCCCCTGTG
16731 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
16754 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
16774 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
16792 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:18593 original size:15 final size:15
Alignment explanation
Indices: 18573--18608 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
18563 ATTATTAGCT
*
18573 TTATAATATATGTTA
1 TTATAATATATATTA
18588 TTATAATATATATTA
1 TTATAATATATATTA
*
18603 TGATAA
1 TTATAA
18609 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:22865 original size:15 final size:15
Alignment explanation
Indices: 22845--22880 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
22835 ATTATTAGCT
*
22845 TTATAATATATGTTA
1 TTATAATATATATTA
22860 TTATAATATATATTA
1 TTATAATATATATTA
*
22875 TGATAA
1 TTATAA
22881 GAATATTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (15 bp):
TTATAATATATATTA
Found at i:29510 original size:158 final size:160
Alignment explanation
Indices: 29189--29510 Score: 612
Period size: 160 Copynumber: 2.0 Consensus size: 160
29179 ATCATAGTAA
29189 ATAAAACCATGTATATATATATAAATTAAAATTTTATGTTAAATTATATTTAAATTATTAATCAT
1 ATAAAACCATGTATATATATATAAATTAAAATTTTATGTTAAATTATATTTAAATTATTAATCAT
29254 TTATACATTATAATAACGATATAAACTTATTCATATTTTATATAATCTAATTTTTAATCTAATAA
66 TTATACATTATAATAACGATATAAACTTATTCATATTTTATATAATCTAATTTTTAATCTAATAA
29319 AATTAATAATCAATAAATAAATCATTTAAT
131 AATTAATAATCAATAAATAAATCATTTAAT
29349 ATAAAACCATGTATATATATATAAATTAAAATTTTATGTTAAATTATATTTAAATTATTAATCAT
1 ATAAAACCATGTATATATATATAAATTAAAATTTTATGTTAAATTATATTTAAATTATTAATCAT
* *
29414 TTATACATTATAATAACGATATAAACTTATTGATA-TTT-TATAATTTAATTTTTAATCTAATAA
66 TTATACATTATAATAACGATATAAACTTATTCATATTTTATATAATCTAATTTTTAATCTAATAA
29477 AATTAATAATCAATAAATAAATCATTTAAT
131 AATTAATAATCAATAAATAAATCATTTAAT
29507 ATAA
1 ATAA
29511 TTAATTTAAT
Statistics
Matches: 160, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
158 58 0.36
159 3 0.02
160 99 0.62
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (160 bp):
ATAAAACCATGTATATATATATAAATTAAAATTTTATGTTAAATTATATTTAAATTATTAATCAT
TTATACATTATAATAACGATATAAACTTATTCATATTTTATATAATCTAATTTTTAATCTAATAA
AATTAATAATCAATAAATAAATCATTTAAT
Found at i:29584 original size:18 final size:18
Alignment explanation
Indices: 29561--29798 Score: 80
Period size: 18 Copynumber: 13.7 Consensus size: 18
29551 ATTATTAATT
*
29561 TATACTATATAGTCTATA
1 TATACTATATAATCTATA
29579 TATACTA-ATGAA-CTATA
1 TATACTATAT-AATCTATA
*
29596 TA-A-TATATAATTTATA
1 TATACTATATAATCTATA
* *
29612 TATACCATATAATTTATA
1 TATACTATATAATCTATA
29630 TATACTA-ATGAAT-TATA
1 TATACTATAT-AATCTATA
* * *
29647 TTGTTTATTAATATAAT-TATT
1 ---TATACT-ATATAATCTATA
* *
29668 TAAACTATATAAACTATA
1 TATACTATATAATCTATA
* *
29686 TAT--TTTATAGT-T-TA
1 TATACTATATAATCTATA
*
29700 T-TA--ATATAAACTATA
1 TATACTATATAATCTATA
*
29715 TATA-TATAT-ATATATA
1 TATACTATATAATCTATA
29731 TATA-TATATAATCATATA
1 TATACTATATAATC-TATA
* *
29749 GTTTA-TATATAGTTCATATA
1 -TATACTATATA-ATC-TATA
* * *
29769 TACACTACATAATTTATA
1 TATACTATATAATCTATA
* *
29787 TACAATATATAA
1 TATACTATATAA
29799 AACTGTAAAT
Statistics
Matches: 167, Mismatches: 31, Indels: 44
0.69 0.13 0.18
Matches are distributed among these distances:
13 5 0.03
14 4 0.02
15 8 0.05
16 30 0.18
17 28 0.17
18 55 0.33
19 12 0.07
20 16 0.10
21 7 0.04
22 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (18 bp):
TATACTATATAATCTATA
Found at i:29735 original size:29 final size:28
Alignment explanation
Indices: 29673--29759 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 28
29663 TTATTTAAAC
* *
29673 TATATAAACTATATATTTTATAGTTTAT
1 TATATAAACTATATATTATATAGTATAT
29701 TAATATAAACTATATA-TATATA-TATA-
1 T-ATATAAACTATATATTATATAGTATAT
* * *
29727 TATATATA-TATATAATCATATAGTTTA-
1 TATATAAACTATAT-ATTATATAGTATAT
29754 TATATA
1 TATATA
29760 GTTCATATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
24 5 0.10
25 7 0.14
26 6 0.12
27 12 0.24
28 6 0.12
29 14 0.28
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (28 bp):
TATATAAACTATATATTATATAGTATAT
Found at i:29770 original size:2 final size:2
Alignment explanation
Indices: 29711--29759 Score: 64
Period size: 2 Copynumber: 24.0 Consensus size: 2
29701 TAATATAAAC
*
29711 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TCA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA -TA TA
29754 TA TA TA
1 TA TA TA
29760 GTTCATATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
1 1 0.02
2 38 0.90
3 3 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:34634 original size:223 final size:215
Alignment explanation
Indices: 34205--34671 Score: 719
Period size: 223 Copynumber: 2.1 Consensus size: 215
34195 TAAAAGTATT
*
34205 TTTTTTATTATTTCGGGTCGGGTC--G-GG-TTTCTAATTCATTATTCGAGTCGGGTCGGGTGAA
1 TTTTTTATTATTTCGGGTCGGGTCGGGTGGATTTCTAATTCATTATTCGAGTCGGGTCGGATGAA
34266 ACTTTATTTTGGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCAGGTTTA
66 ACTTTATTTTGGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCAGGTTTA
* * *
34331 GGGTGAAAAAACCCGGACTGACCCGAAAATATATATAATTCAGGTCGGGTCGAATTAAGTCACTG
131 GGGTGAAAAAAACCGGACGGACCCGAAAATATATATAATTCAGGTCGGGTCGAATTAAGTCAATG
34396 TTTTTATTAAATAAAAATAA
196 TTTTTATTAAATAAAAATAA
*
34416 TTTTTTATTATTTCGGGTCGGGTCGGGTTGGATTTCTAATTCATATATTCGGGTCGGGTCGGATG
1 TTTTTTATTATTTCGGGTCGGGTCGGG-TGGATTTCTAATTCAT-TATTCGAGTCGGGTCGGATG
*
34481 AAACTTTATTTTGTTCGGGTCAGG-TCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTT
64 AAACTTTATTTTGGTCGGGTC-GGATCGGGTTTTTTTAAGTGTGATA-T----TCGGGTCGGGTT
* * *
34545 CGGGTTTAGGGTGAAAAAAACCGGACCGGGCCCGAAAATATATATAATTCGGGTCGGGTCGAATT
123 CAGGTTTAGGGTGAAAAAAACCGGA-CGGACCCGAAAATATATATAATTCAGGTCGGGTCGAATT
34610 AAGTCAATGTTTTTATTAAATAAAAATAA
187 AAGTCAATGTTTTTATTAAATAAAAATAA
*
34639 TTTTTTATTATTTCGGGTTGGGTCGGGTCGGAT
1 TTTTTTATTATTTCGGGTCGGGTCGGGT-GGAT
34672 AAAACTTTAT
Statistics
Matches: 232, Mismatches: 10, Indels: 16
0.90 0.04 0.06
Matches are distributed among these distances:
211 24 0.10
213 1 0.00
215 2 0.01
216 12 0.05
217 60 0.26
218 3 0.01
222 36 0.16
223 94 0.41
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (215 bp):
TTTTTTATTATTTCGGGTCGGGTCGGGTGGATTTCTAATTCATTATTCGAGTCGGGTCGGATGAA
ACTTTATTTTGGTCGGGTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCAGGTTTA
GGGTGAAAAAAACCGGACGGACCCGAAAATATATATAATTCAGGTCGGGTCGAATTAAGTCAATG
TTTTTATTAAATAAAAATAA
Found at i:34750 original size:38 final size:38
Alignment explanation
Indices: 34692--34779 Score: 128
Period size: 38 Copynumber: 2.3 Consensus size: 38
34682 TTTGTTCGGT
*
34692 TCGGATCGGG-TTTTTTAAGTGTGATATTC-GAGTC-GAG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAG-GTCAG-G
34729 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCAGG
1 TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCAGG
34767 TCGGGTCGGGTTT
1 TCGGGTCGGGTTT
34780 AGGGTAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
37 9 0.19
38 36 0.77
39 2 0.04
ACGTcount: A:0.15, C:0.11, G:0.35, T:0.39
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATATTCAGGTCAGG
Found at i:38130 original size:2 final size:2
Alignment explanation
Indices: 38123--38162 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
38113 TATTTATACA
38123 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
38163 GTTCATTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39109 original size:107 final size:105
Alignment explanation
Indices: 38922--39220 Score: 378
Period size: 107 Copynumber: 2.9 Consensus size: 105
38912 TATTGCTCCA
* * *
38922 AGTCCAATATCCTTCGTCGTGAAGTTGAAATTGGTTCTGGAACTGGAAAATTGTTTGTTGACAGT
1 AGTCCAATATCCTTCGT-GTGAAGTTGAAATTGGATATGAAACTGGAAAATTGTTTGTTGACAGT
38987 CAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTATATTTG
65 CAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTATA-TTG
* * **
39029 GGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATATGAAATTGGGGAATTGTTTGTTGACAGT
1 AGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGATATGAAACTGGAAAATTGTTTGTTGACAGT
* *
39094 CAGCCGCCCTTTCGCCGTGAAGTTGAGCTTGTGCTGTATTG
65 CAGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTATATTG
* ** *
39135 AGTCCAATATCCTTCGTTGTGAAGTTGAAATT-GA-CT----CT-GAAAGCTGTTTGTTGACAAT
1 AGTCCAATATCCTTCG-TGTGAAGTTGAAATTGGATATGAAACTGGAAAATTGTTTGTTGACAGT
* *
39193 CAGCTGCCCCTTCGTCGTGAAGTTGAGC
65 CAGCCGCCCCTTCGCCGTGAAGTTGAGC
39221 CTCAAATAAC
Statistics
Matches: 170, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
99 40 0.24
100 1 0.01
104 1 0.01
105 2 0.01
106 33 0.19
107 92 0.54
108 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTGTGAAGTTGAAATTGGATATGAAACTGGAAAATTGTTTGTTGACAGTC
AGCCGCCCCTTCGCCGTGAAGTTGAGCTTGTGCTATATTG
Found at i:40416 original size:10 final size:11
Alignment explanation
Indices: 40399--40428 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
40389 AAACGATTTT
40399 CTTTTTTTTCC
1 CTTTTTTTTCC
*
40410 CTTTTTTTTCT
1 CTTTTTTTTCC
40421 CTTTTTTT
1 CTTTTTTT
40429 AACTTAGGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
CTTTTTTTTCC
Found at i:40474 original size:71 final size:71
Alignment explanation
Indices: 40332--40475 Score: 155
Period size: 71 Copynumber: 2.0 Consensus size: 71
40322 TTCTTTCTCC
* * * * * * **
40332 TTTTTCTCTTTTCCTTTTCTTTTTTTCATTTAGGGCGCCCTTTCGGGTTCTCACCCTAAACGATT
1 TTTTTCCCTTTTCCTTTTCTTTTTTTAACTTAGGACACCCTCTCGGGTTCTCACCCTAAACGAAG
*
40397 TTCTTT
66 TACTTT
* * * *
40403 TTTTTCCCTTTT-TTTTCTCTTTTTTTAACTTAGGACACCCTCTCGGGTTTTCATCCTAAGCGAA
1 TTTTTCCCTTTTCCTTT-TCTTTTTTTAACTTAGGACACCCTCTCGGGTTCTCACCCTAAACGAA
40467 GTACTTT
65 GTACTTT
40474 TT
1 TT
40476 GACTGCATCC
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
70 3 0.05
71 56 0.95
ACGTcount: A:0.12, C:0.24, G:0.11, T:0.52
Consensus pattern (71 bp):
TTTTTCCCTTTTCCTTTTCTTTTTTTAACTTAGGACACCCTCTCGGGTTCTCACCCTAAACGAAG
TACTTT
Found at i:41306 original size:16 final size:16
Alignment explanation
Indices: 41285--41320 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
41275 CGGATGAATT
41285 TGCCCGATGACGTCTA
1 TGCCCGATGACGTCTA
41301 TGCCCGATGACGTCTA
1 TGCCCGATGACGTCTA
41317 TGCC
1 TGCC
41321 AAATACAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (16 bp):
TGCCCGATGACGTCTA
Found at i:50835 original size:19 final size:18
Alignment explanation
Indices: 50808--50864 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
50798 GAAAAATATG
50808 AAAACATAAAACAAAAGC
1 AAAACATAAAACAAAAGC
*
50826 AAATACATAAAA-AAAAGG
1 AAA-ACATAAAACAAAAGC
* *
50844 AAAAAACAAAACAAAAG-
1 AAAACATAAAACAAAAGC
50861 AAAA
1 AAAA
50865 AGAAAATATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 10 0.29
18 16 0.47
19 8 0.24
ACGTcount: A:0.77, C:0.11, G:0.07, T:0.05
Consensus pattern (18 bp):
AAAACATAAAACAAAAGC
Found at i:50866 original size:24 final size:24
Alignment explanation
Indices: 50820--50870 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
50810 AACATAAAAC
*
50820 AAAAGCAAATACATAAAAAAAAGGA
1 AAAAACAAATACATAAAAAAAA-GA
50845 AAAAACAAA-ACA-AAAGAAAAAGA
1 AAAAACAAATACATAAA-AAAAAGA
50868 AAA
1 AAA
50871 TATGAAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.33
24 8 0.33
25 8 0.33
ACGTcount: A:0.78, C:0.08, G:0.10, T:0.04
Consensus pattern (24 bp):
AAAAACAAATACATAAAAAAAAGA
Found at i:51225 original size:16 final size:16
Alignment explanation
Indices: 51204--51239 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
51194 TAATAACTTT
51204 AAAAAACATTAAAATA
1 AAAAAACATTAAAATA
* *
51220 AAAAAATATTAGAATA
1 AAAAAACATTAAAATA
51236 AAAA
1 AAAA
51240 TAATTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (16 bp):
AAAAAACATTAAAATA
Found at i:59520 original size:37 final size:36
Alignment explanation
Indices: 59395--59523 Score: 104
Period size: 37 Copynumber: 3.5 Consensus size: 36
59385 ACAAAAAACC
* *
59395 TGAGAT-TTTTTCTTTGAAAC-AAATTTCATCTCACT
1 TGAGATATTTTTC-TTGAAACAAAATTTTATCTCATT
* * * *
59430 CGAGAT-TTTCTCTAGAAACAAATTTTTTTATCTCACTT
1 TGAGATATTTTTCTTGAAACAAA--ATTTTATCTCA-TT
* *
59468 GTG-GTTGTTTTTCTTGAAACAAAATTTTATCTCATT
1 -TGAGATATTTTTCTTGAAACAAAATTTTATCTCATT
59504 TGAGATATTTTATCTTGAAA
1 TGAGATATTTT-TCTTGAAA
59524 TCATTTCATT
Statistics
Matches: 73, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
34 6 0.08
35 14 0.19
36 8 0.11
37 27 0.37
38 3 0.04
39 15 0.21
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.47
Consensus pattern (36 bp):
TGAGATATTTTTCTTGAAACAAAATTTTATCTCATT
Found at i:60385 original size:118 final size:118
Alignment explanation
Indices: 59913--60452 Score: 616
Period size: 119 Copynumber: 4.6 Consensus size: 118
59903 AGGTTTTCAA
* * * *
59913 ATAATGGAGAAGAACTCACCCGGTGAGAGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACAT
1 ATAAT-GAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC-C
* * * * ** *
59978 TTTTCTCAAATCCATCATAGAAGGAGGTAGACCAACATTTCCAATGGAATGATTC
64 TTTTCTCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATAGAGGGGTTC
* * ** * * *
60033 ATAATGAGAAGAACTCGTCTGAAAAGGAACAAGAAGTTCATAATGAGAGGAACTTGTTCAACCTT
1 ATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-T
* * ** *
60098 TTTCTCAAATCCATCACAGAATGAGGTGGATTAACATTTGAAATAGAGGGGTCC
65 TTTCTCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATAGAGGGGTTC
* * * * *
60152 ATAATGATAAGAACTCATCCAATGATGGAGAATAAGTTCATAATGAGAAGAACTTGTGC-ACCTT
1 ATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
* * * *
60216 TTCTTAAATCCGTCACAGAAGGAGGTGGATAAACATTTGCAATAGAGGGGTTC
66 TTCTCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATAGAGGGGTTC
* * * *
60269 ACAATGAGAATAACTCATCCGATGAGGGAGAAGAAATTTATAATGAGAAGAACTTGTTCAACCTT
1 ATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
* *
60334 TTCTCAAATCCATCATAGAAGGAGGTGGATCAACATTTCCAAT-GAATGGGTTC
66 TTCTCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATAG-AGGGGTTC
* * * * ** * *
60387 ATATTAAGAAGAACGCATCCAAAAAGGAAGAAGAATTTCATAATGAGAAGAACTTGTTCAACCTT
1 ATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
60452 T
66 T
60453 CGCTCAAGTT
Statistics
Matches: 350, Mismatches: 67, Indels: 8
0.82 0.16 0.02
Matches are distributed among these distances:
117 100 0.29
118 108 0.31
119 137 0.39
120 5 0.01
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (118 bp):
ATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
TTCTCAAATCCATCACAGAAGGAGGTGGATCAACATTTCCAATAGAGGGGTTC
Found at i:61608 original size:21 final size:22
Alignment explanation
Indices: 61566--61608 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
61556 CACAAGTGAT
* *
61566 GGCGATCGATGCGGTGGTCGAC
1 GGCGACCGATGCGGTGGCCGAC
61588 GGCGACCGATGC-GTGGCCGAC
1 GGCGACCGATGCGGTGGCCGAC
61609 AATGGAGCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.14, C:0.28, G:0.44, T:0.14
Consensus pattern (22 bp):
GGCGACCGATGCGGTGGCCGAC
Found at i:65494 original size:21 final size:21
Alignment explanation
Indices: 65454--65502 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
65444 GTGGTCCTTT
* * *
65454 GGGACATCTATGTGGTCATTC
1 GGGACATATATATGGGCATTC
65475 GGGACATATATATGGGCATTC
1 GGGACATATATATGGGCATTC
65496 GGGACAT
1 GGGACAT
65503 TTCTACGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (21 bp):
GGGACATATATATGGGCATTC
Found at i:65521 original size:22 final size:22
Alignment explanation
Indices: 65491--65545 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
65481 TATATATGGG
*
65491 CATTCGGGACATTTCTACGCAT
1 CATTTGGGACATTTCTACGCAT
65513 CATTTGGGACATTTCTACGCAT
1 CATTTGGGACATTTCTACGCAT
65535 CATTTGGGACA
1 CATTTGGGACA
65546 AATTCTATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (22 bp):
CATTTGGGACATTTCTACGCAT
Done.