Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000969.1 Hibiscus syriacus cultivar Beakdansim tig00001934_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: 53174
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4976 original size:246 final size:248
Alignment explanation
Indices: 4533--4981 Score: 643
Period size: 246 Copynumber: 1.8 Consensus size: 248
4523 TTATCATTTA
* *
4533 ATTTAATATTCTAGAAAATGAAATTTTTGGAAAGTAAGAAGTTTCTTACCCAGTAAAATATTTAT
1 ATTTAATATTCTAGAAAATCAAATTTTTGGAAAG-AAGAAGTCTCTTACCCAGTAAAATATTTAT
* * * *
4598 CACAAATTTGTAAATCCTTCGGGTTATCTATCAGTCTTTCAAGCATGAAGTTAAAACCTTCAGGT
65 CACAAATTTGTAAATCCTTCGGGTAATCTATAAGTCCTTCAAGAATGAAGTTAAAACCTTCAGGT
* * * *
4663 CATCTATTAGTCTTTCAAGCCAGATGATAAGTCCTTAGGGCCATCAGTCAAACCTTTGGGTAGGA
130 CATCTATTAGTCTTTCAAGCAAGATGATAACTCCTTAGGGCCATCAGCCAAACCTTTGGGCAGGA
4728 TGTTTACATATGATTTTCGCATGAAAATGAGATAACGATTTTCAAAGTTTTCTC
195 TGTTTACATATGATTTTCGCATGAAAATGAGATAACGATTTTCAAAGTTTTCTC
* *
4782 ATTTAATGTTCTAGAAAATCAAATTTTT-GAAA-AA-AAGTCTCTTACCCAGTAAAATATTTCTC
1 ATTTAATATTCTAGAAAATCAAATTTTTGGAAAGAAGAAGTCTCTTACCCAGTAAAATATTTATC
* * * * ** *
4844 ACGAATTTGTAAATCCTTCGGGTAATCTGTAAGTCCTTCGAGAATGATGTTTAAATTCTTCGGGT
66 ACAAATTTGTAAATCCTTCGGGTAATCTATAAGTCCTTCAAGAATGAAG-TTAAAACCTTCAGGT
* * * * *
4909 CATCTGTTAGTCTTTCGAGCAAGATTATAACTCCTTAGGGCCATCCGCCAGACCTTTGGGCAGGA
130 CATCTATTAGTCTTTCAAGCAAGATGATAACTCCTTAGGGCCATCAGCCAAACCTTTGGGCAGGA
4974 TGTTTACA
195 TGTTTACA
4982 CTCTTTAATT
Statistics
Matches: 175, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
245 67 0.38
246 78 0.45
248 4 0.02
249 26 0.15
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (248 bp):
ATTTAATATTCTAGAAAATCAAATTTTTGGAAAGAAGAAGTCTCTTACCCAGTAAAATATTTATC
ACAAATTTGTAAATCCTTCGGGTAATCTATAAGTCCTTCAAGAATGAAGTTAAAACCTTCAGGTC
ATCTATTAGTCTTTCAAGCAAGATGATAACTCCTTAGGGCCATCAGCCAAACCTTTGGGCAGGAT
GTTTACATATGATTTTCGCATGAAAATGAGATAACGATTTTCAAAGTTTTCTC
Found at i:5152 original size:3 final size:3
Alignment explanation
Indices: 5144--5235 Score: 73
Period size: 3 Copynumber: 30.0 Consensus size: 3
5134 TTGTATGTTT
*
5144 TTA TTA TTAA TTA -TA TTA TTA TTA TTA TATA TAA TTA TATA TTA -TA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA T-TA TTA TTA T-TA TTA TTA
* * * *
5190 CTA CTA TTA TTA TATA TGA -TA TTA TGA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
5236 AATAATATTA
Statistics
Matches: 74, Mismatches: 7, Indels: 16
0.76 0.07 0.16
Matches are distributed among these distances:
2 5 0.07
3 55 0.74
4 14 0.19
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:5188 original size:31 final size:34
Alignment explanation
Indices: 5145--5235 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 34
5135 TGTATGTTTT
*
5145 TATTATTA-ATTATATTATTATTATTATATAT-A
1 TATTATGATATTATATTATTATTATTATATATGA
* *
5177 -ATTAT-ATATTATACTACTATTATTATATATGA
1 TATTATGATATTATATTATTATTATTATATATGA
5209 TATTATGATA-TATTATTATTATTATTA
1 TATTATGATATTA-TATTATTATTATTA
5236 AATAATATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
30 1 0.02
31 26 0.52
32 1 0.02
33 7 0.14
34 15 0.30
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (34 bp):
TATTATGATATTATATTATTATTATTATATATGA
Found at i:5211 original size:28 final size:29
Alignment explanation
Indices: 5144--5230 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 29
5134 TTGTATGTTT
*
5144 TTATTAT-TAATTATATTAT--TAT--TA
1 TTATTATATAATGATATTATGATATACTA
* *
5168 TTA-TATATAATTATA-TATTATACTACTA
1 TTATTATATAATGATATTATGATA-TACTA
*
5196 TTATTATAT-ATGATATTATGATATATTA
1 TTATTATATAATGATATTATGATATACTA
5224 TTATTAT
1 TTATTAT
5231 TATTAAATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
23 6 0.12
24 11 0.21
25 2 0.04
26 1 0.02
28 21 0.40
29 11 0.21
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (29 bp):
TTATTATATAATGATATTATGATATACTA
Found at i:7273 original size:2 final size:2
Alignment explanation
Indices: 7266--7540 Score: 96
Period size: 2 Copynumber: 144.5 Consensus size: 2
7256 ATCATACGTA
* * *
7266 AT AT AT AT AT GT AT AT GT GAT AT -T AT AT AT AT -T CT 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
* *
7307 A- AT AT A- AT AT A- AT A- AT AT -T TT AT AT -T GT AT ACT AT ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T
* * *
7345 AA AT ACT AT AGT AT AT AT AA AT ACT AT GT A- AT AT AT AT AT AT
1 AT AT A-T AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * *
7387 AT AT AT AT -T AC AT AGT AT TT AT AT AT -T AT AT AT -T TT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
7427 AT ACT AT AT ACT AT AA AT GCT AT AT A- AT AT A- AC GT AT AC A-
1 AT A-T AT AT A-T AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
*
7467 AT AT A- AT AT -T AT A- AT AT AC AT -T AT ACT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
7504 AT AT -T AA AT AT A- AT AT AT AT -T AT AA AC AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7541 ATTCTAAATA
Statistics
Matches: 204, Mismatches: 33, Indels: 72
0.66 0.11 0.23
Matches are distributed among these distances:
1 25 0.12
2 159 0.78
3 20 0.10
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:7303 original size:9 final size:9
Alignment explanation
Indices: 7285--7540 Score: 95
Period size: 9 Copynumber: 28.3 Consensus size: 9
7275 TGTATATGTG
7285 ATATTATAT
1 ATATTATAT
*
7294 ATATTCTAT
1 ATATTATAT
*
7303 ATATAATAT
1 ATATTATAT
*
7312 AATATAATA-
1 -ATATTATAT
7321 ATATT-T-T
1 ATATTATAT
*
7328 ATATTGTAT
1 ATATTATAT
*
7337 ACTA-TACTAA
1 A-TATTA-TAT
*
7347 ATACTATAGT
1 ATATTATA-T
*
7357 ATA-TATAA
1 ATATTATAT
* *
7365 ATACTATGT
1 ATATTATAT
7374 A-A-TATAT
1 ATATTATAT
7381 ATATATATAT
1 ATAT-TATAT
*
7391 ATATTACAT
1 ATATTATAT
7400 AGTATT-TAT
1 A-TATTATAT
7409 ATATTATAT
1 ATATTATAT
*
7418 ATTTTATAT
1 ATATTATAT
*
7427 ATACTATAT
1 ATATTATAT
* *
7436 ACTATAAATGCT
1 A-TAT-TAT-AT
*
7448 ATATAATAT
1 ATATTATAT
* *
7457 A-ACGTATACA
1 ATA-TTATA-T
*
7467 ATATAATAT
1 ATATTATAT
*
7476 -TATAATAT
1 ATATTATAT
*
7484 ACATTATACT
1 ATATTATA-T
*
7494 ATATAATAT
1 ATATTATAT
7503 AATATTA-A-
1 -ATATTATAT
*
7511 ATATAATAT
1 ATATTATAT
*
7520 ATATTATAA
1 ATATTATAT
*
7529 ACATTATAT
1 ATATTATAT
7538 ATA
1 ATA
7541 ATTCTAAATA
Statistics
Matches: 185, Mismatches: 37, Indels: 50
0.68 0.14 0.18
Matches are distributed among these distances:
7 16 0.09
8 24 0.13
9 85 0.46
10 52 0.28
11 6 0.03
12 2 0.01
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (9 bp):
ATATTATAT
Found at i:10331 original size:15 final size:16
Alignment explanation
Indices: 10302--10332 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10292 ATAGGAGAAG
10302 GAGTAAGGTTAGATAA
1 GAGTAAGGTTAGATAA
10318 GAGTAAGG-TAGATAA
1 GAGTAAGGTTAGATAA
10333 AATTGGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.32, T:0.23
Consensus pattern (16 bp):
GAGTAAGGTTAGATAA
Found at i:10457 original size:31 final size:32
Alignment explanation
Indices: 10422--10496 Score: 80
Period size: 36 Copynumber: 2.2 Consensus size: 32
10412 TTTTGTTCAA
10422 CTTCAAA-AAGGTTTTCTTCATTTGAATTTTC
1 CTTCAAACAAGGTTTTCTTCATTTGAATTTTC
* *
10453 CTTCAAACGTTCAAGTTTTTCTTCATTTGAATTTTT
1 CTTCAAA----CAAGGTTTTCTTCATTTGAATTTTC
*
10489 CTCCAAAC
1 CTTCAAAC
10497 GTTCTCTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
31 7 0.19
32 1 0.03
36 28 0.78
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.47
Consensus pattern (32 bp):
CTTCAAACAAGGTTTTCTTCATTTGAATTTTC
Found at i:10489 original size:16 final size:16
Alignment explanation
Indices: 10433--10490 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
10423 TTCAAAAAGG
10433 TTTTCTTCATTTGAAT
1 TTTTCTTCATTTGAAT
* * *
10449 TTTCCTTCAAACGTTCAAGT
1 TTTTCTTC--A-TTTGAA-T
10469 TTTTCTTCATTTGAAT
1 TTTTCTTCATTTGAAT
10485 TTTTCT
1 TTTTCT
10491 CCAAACGTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 14 0.44
17 4 0.12
18 2 0.06
19 4 0.12
20 8 0.25
ACGTcount: A:0.19, C:0.17, G:0.07, T:0.57
Consensus pattern (16 bp):
TTTTCTTCATTTGAAT
Found at i:15531 original size:19 final size:19
Alignment explanation
Indices: 15503--15547 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
15493 CGAGTCCCAT
*
15503 GGAGGACATTTCATAATTC
1 GGAGGTCATTTCATAATTC
15522 GGAGGTCATTTCATAATTC
1 GGAGGTCATTTCATAATTC
*
15541 GGTGGTC
1 GGAGGTC
15548 TTCTACGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (19 bp):
GGAGGTCATTTCATAATTC
Found at i:24403 original size:12 final size:12
Alignment explanation
Indices: 24386--24420 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
24376 TATTTATTAT
24386 ATATTT-ATAAAA
1 ATATTTAAT-AAA
24398 ATATTTAATAAA
1 ATATTTAATAAA
24410 ATATTTAATAA
1 ATATTTAATAA
24421 TATAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 20 0.91
13 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATATTTAATAAA
Found at i:24488 original size:19 final size:18
Alignment explanation
Indices: 24460--24508 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
24450 AATATATTTA
24460 AAAACAATAAAATAAATG
1 AAAACAATAAAATAAATG
*
24478 AAAACATATAAAATAACTG
1 AAAACA-ATAAAATAAATG
24497 AAAA-AATAAAAT
1 AAAACAATAAAAT
24509 TAAAAATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.18
Consensus pattern (18 bp):
AAAACAATAAAATAAATG
Found at i:24748 original size:29 final size:30
Alignment explanation
Indices: 24703--24761 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
24693 TATTTTAATA
24703 TGAAGGACTAAAATAAATAAAATTA-AAATT
1 TGAAGGACTAAAATAAA-AAAATTATAAATT
* *
24733 TGAA-GACTAAATTAAAAATATTATAAATT
1 TGAAGGACTAAAATAAAAAAATTATAAATT
24762 CAATTTAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 6 0.23
29 16 0.62
30 4 0.15
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (30 bp):
TGAAGGACTAAAATAAAAAAATTATAAATT
Found at i:25334 original size:25 final size:23
Alignment explanation
Indices: 25300--25350 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 23
25290 GTTTGTATTT
*
25300 TCTCTGTTTTTTTTTTCTATGTCTC
1 TCTCTATTTTTTTTTTC--TGTCTC
25325 TCTCTATTTTTTTTTTCTGTCTC
1 TCTCTATTTTTTTTTTCTGTCTC
25348 TCT
1 TCT
25351 GTCTCGTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 9 0.36
25 16 0.64
ACGTcount: A:0.04, C:0.22, G:0.06, T:0.69
Consensus pattern (23 bp):
TCTCTATTTTTTTTTTCTGTCTC
Found at i:25828 original size:11 final size:11
Alignment explanation
Indices: 25805--25836 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
25795 TGTAATTTAT
25805 TATTTATATATA
1 TATTTA-ATATA
25817 TATTTAATATA
1 TATTTAATATA
25828 TATTTAATA
1 TATTTAATA
25837 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:25840 original size:3 final size:3
Alignment explanation
Indices: 25832--25905 Score: 139
Period size: 3 Copynumber: 24.7 Consensus size: 3
25822 AATATATATT
*
25832 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25880 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
25906 TGGATAAAAA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:26355 original size:113 final size:113
Alignment explanation
Indices: 26219--26775 Score: 956
Period size: 113 Copynumber: 4.9 Consensus size: 113
26209 TGATAGTATC
* *
26219 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
26283 TCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTC
66 TCATTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTT
* *
26331 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
26396 TCATTTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTT
66 TCA-TTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTT
26445 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*** * *
26510 TCATTATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTT
26558 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
26623 TCATTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTT
66 TCATTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTT
26671 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* * *
26736 TCATTATGAAC-TTATCTGGCAATGAATGATCCATCAAGTG
66 TCATTATGAACTTTCTCTGGCAA-AAATAATCCATCAAGTG
26776 GATTTGAAAT
Statistics
Matches: 423, Mismatches: 19, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
112 14 0.03
113 300 0.71
114 109 0.26
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (113 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTT
Found at i:26610 original size:227 final size:225
Alignment explanation
Indices: 26219--26772 Score: 966
Period size: 227 Copynumber: 2.4 Consensus size: 225
26209 TGATAGTATC
* *
26219 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
** * * *
26283 TCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACA
66 TCATTATGAA-CTTCTCTGGCAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACA
26348 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTTATGAACTTTCT
130 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA-TTATGAACTTTCT
26413 CTGGCAAAAATAATCCATCAAGTGATGAATTT
194 CTGGCAAAAATAATCCATCAAGTGATGAATTT
26445 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
26510 TCATTATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACA
66 TCATTATGAAC-TTCTCTGGCAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACA
*
26575 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
130 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
26640 TGGCAAAAATAATCCATCAAGTGATGAATTT
195 TGGCAAAAATAATCCATCAAGTGATGAATTT
26671 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
26736 TCATTATGAACTTATCTGGCAATGAATGATCCATCAA
66 TCATTATGAACTTCTCTGGCAATG-ATGATCCATCAA
26773 GTGGATTTGA
Statistics
Matches: 313, Mismatches: 12, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
225 12 0.04
226 137 0.44
227 164 0.52
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (225 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACTTCTCTGGCAATGATGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAA
ATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
GGCAAAAATAATCCATCAAGTGATGAATTT
Found at i:27837 original size:84 final size:84
Alignment explanation
Indices: 27515--27837 Score: 555
Period size: 84 Copynumber: 3.9 Consensus size: 84
27505 CCTACTGAAT
*
27515 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCTAAATTCA
27579 ATGATT-GTTCTGTCCAAC
66 ATGATTGGTTCTGTCCAAC
*
27597 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCTAAATTCA
* *
27662 ATGATTGATTATGTCCAAC
66 ATGATTGGTTCTGTCCAAC
27681 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTT-TCAAATTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCT-AAATTC
*
27745 AATGATTGGTTCTG-CCAAAT
65 AATGATTGGTTCTGTCC-AAC
27765 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCTAAATTCA
27830 ATGATTGG
66 ATGATTGG
27838 ACTAAGATAT
Statistics
Matches: 228, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
82 42 0.18
83 28 0.12
84 157 0.69
85 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (84 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCTAAATTCA
ATGATTGGTTCTGTCCAAC
Found at i:29018 original size:11 final size:11
Alignment explanation
Indices: 28955--29024 Score: 70
Period size: 11 Copynumber: 6.2 Consensus size: 11
28945 ACCTTGACCC
*
28955 CTTTTCTTTTT
1 CTTTTTTTTTT
* *
28966 CTTCTCTTTTT
1 CTTTTTTTTTT
*
28977 -TTTTTATTTT
1 CTTTTTTTTTT
28987 CTATTTTTTTCTCT
1 CT-TTTTTTT-T-T
29001 CTTTTTTTTTT
1 CTTTTTTTTTT
29012 CTTTTTTTTTT
1 CTTTTTTTTTT
29023 CT
1 CT
29025 CTTCAAGCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
10 7 0.14
11 25 0.50
12 7 0.14
13 8 0.16
14 3 0.06
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:40420 original size:13 final size:13
Alignment explanation
Indices: 40396--40430 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
40386 TATTTATTAT
40396 ATATTT-ATAAAA
1 ATATTTAATAAAA
40408 ATATTTAAT-AAA
1 ATATTTAATAAAA
40420 ATATTTAATAA
1 ATATTTAATAA
40431 TATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTAATAAAA
Found at i:40498 original size:19 final size:18
Alignment explanation
Indices: 40470--40518 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
40460 AATATATTTA
40470 AAAACAATAAAATAAATG
1 AAAACAATAAAATAAATG
*
40488 AAAACATATAAAATAACTG
1 AAAACA-ATAAAATAAATG
40507 AAAA-AATAAAAT
1 AAAACAATAAAAT
40519 TAAAAATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.71, C:0.06, G:0.04, T:0.18
Consensus pattern (18 bp):
AAAACAATAAAATAAATG
Found at i:40761 original size:29 final size:30
Alignment explanation
Indices: 40716--40774 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
40706 TATTTTAATA
40716 TGAAGGACTAAAATAAATAAAATTA-AAATT
1 TGAAGGACTAAAATAAA-AAAATTATAAATT
* *
40746 TGAA-GACTAAATTAAAAATATTATAAATT
1 TGAAGGACTAAAATAAAAAAATTATAAATT
40775 CAATTTAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 6 0.23
29 16 0.62
30 4 0.15
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.31
Consensus pattern (30 bp):
TGAAGGACTAAAATAAAAAAATTATAAATT
Found at i:41345 original size:25 final size:23
Alignment explanation
Indices: 41311--41361 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 23
41301 GTTTGTATTT
*
41311 TCTCTGTTTTTTTTTTCTATGTCTC
1 TCTCTATTTTTTTTTTC--TGTCTC
41336 TCTCTATTTTTTTTTTCTGTCTC
1 TCTCTATTTTTTTTTTCTGTCTC
41359 TCT
1 TCT
41362 GTCTCGTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 9 0.36
25 16 0.64
ACGTcount: A:0.04, C:0.22, G:0.06, T:0.69
Consensus pattern (23 bp):
TCTCTATTTTTTTTTTCTGTCTC
Found at i:41840 original size:11 final size:11
Alignment explanation
Indices: 41817--41848 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
41807 TGTAATTTAT
41817 TATTTATATATA
1 TATTTA-ATATA
41829 TATTTAATATA
1 TATTTAATATA
41840 TATTTAATA
1 TATTTAATA
41849 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:41852 original size:3 final size:3
Alignment explanation
Indices: 41844--41917 Score: 130
Period size: 3 Copynumber: 24.7 Consensus size: 3
41834 AATATATATT
* *
41844 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAC
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
41892 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
41918 TGGATAAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:43874 original size:373 final size:370
Alignment explanation
Indices: 43243--43916 Score: 844
Period size: 373 Copynumber: 1.8 Consensus size: 370
43233 CCAATTTTGA
* * * * * *
43243 AAAACAAATTCAACTTCTTGTCCATGATGGCTAGTTTACTCCTTTCATTCTCATGTCAATTTATA
1 AAAACAAATTCAACTTCTTGTCCAAGATGGCTAATTTACACCTCTCATCCTCATATCAATTTATA
* * *
43308 AATTAAAATAAAATATATAAAATACCCCTCAATAGGTTGAGTAAATTCAGTCACCTTATAGAATA
66 AATTAAAATAAAATATATAAAATA-CCCTCAATAGGCTGAGTAAATTCAGTCAACTAATAGAATA
* * *
43373 TGGTTGACCAAATTTTCATTACATGAATTAAATGATCTTATGTTCATTGTTGGATTAATTTATGC
130 TGGTTGACAAAATTTTCAATACATGAATTAAAAGATCTTATGTTCATTGTTGGATTAATTTATGC
** * * * * *
43438 ATGCATTGTCTTCGTTATAATGGATTTATCTTGAGCTCCTAACATCAGATTGAGACGTTTCAAGA
195 ATGCATTGTCAACGTTATAATGGATTTATATTGAGCTCCCAACATCAAATTAAGACATTTCAAGA
* *
43503 TGCATCA-AAAAGT-TAAGTGACAATCAATCTTACTGAAAGAGACATATTGACCAGGAAATGCTC
260 TACAT-AGAAAA-TCTAAGAGACAATCAATCTTA-TGAAAGAGACATATTGACCAGGAAATGCTC
43566 AAATCCTATTCAAAAAGTCGTAATAAACCTGTTGATGTTCTAGCCTTGT
322 AAATCCTATTCAAAAAGTCGTAATAAACCTGTTGATGTTCTAGCCTTGT
* *
43615 AAAACAACTTCAACTTCTTGTCCAAGATGGCTAATTTACACCTCTCATCCTCGTATCAACTTT-T
1 AAAACAAATTCAACTTCTTGTCCAAGATGGCTAATTTACACCTCTCATCCTCATATCAA-TTTAT
* * * * *
43679 AAATTAAGATAAAA-ACTATAAAATA-CCTCACATTGAGCTGATTAAATT-TGATTAACTAATAG
65 AAATTAAAATAAAATA-TATAAAATACCCTCA-ATAG-GCTGAGTAAATTCAG-TCAACTAATAG
*
43741 AATA-GGATTGAACAAAATTTTCAATACATGAATTAAAAGAT-TTCATGTTCTTTGTTGGATTAA
126 AATATGG-TTG-ACAAAATTTTCAATACATGAATTAAAAGATCTT-ATGTTCATTGTTGGATTAA
** * **
43804 TTTATGCATGTGTTGTCAACGTTATGATGGATTTATATTGAGCTCCCGCCATCAAATTCAAG-CA
188 TTTATGCATGCATTGTCAACGTTATAATGGATTTATATTGAGCTCCCAACATCAAATT-AAGACA
* *
43868 TTTCAAGATACATAGGAAATCTAAGAGACAATCGATCTTATGAAAGAGA
252 TTTCAAGATACATAGAAAATCTAAGAGACAATCAATCTTATGAAAGAGA
43917 TAAAACAAAT
Statistics
Matches: 255, Mismatches: 36, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
370 5 0.02
371 7 0.03
372 112 0.44
373 129 0.51
374 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (370 bp):
AAAACAAATTCAACTTCTTGTCCAAGATGGCTAATTTACACCTCTCATCCTCATATCAATTTATA
AATTAAAATAAAATATATAAAATACCCTCAATAGGCTGAGTAAATTCAGTCAACTAATAGAATAT
GGTTGACAAAATTTTCAATACATGAATTAAAAGATCTTATGTTCATTGTTGGATTAATTTATGCA
TGCATTGTCAACGTTATAATGGATTTATATTGAGCTCCCAACATCAAATTAAGACATTTCAAGAT
ACATAGAAAATCTAAGAGACAATCAATCTTATGAAAGAGACATATTGACCAGGAAATGCTCAAAT
CCTATTCAAAAAGTCGTAATAAACCTGTTGATGTTCTAGCCTTGT
Found at i:47207 original size:14 final size:14
Alignment explanation
Indices: 47180--47241 Score: 79
Period size: 14 Copynumber: 4.4 Consensus size: 14
47170 AAGTTAACGG
*
47180 GTTGACTCATATGA
1 GTTGACTCAGATGA
*
47194 GTTGATTCAGATGA
1 GTTGACTCAGATGA
* *
47208 GTTGACTCGGAAGA
1 GTTGACTCAGATGA
*
47222 GTTGAATCAGATGA
1 GTTGACTCAGATGA
47236 GTTGAC
1 GTTGAC
47242 AAAGTCAGGG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (14 bp):
GTTGACTCAGATGA
Found at i:53097 original size:18 final size:18
Alignment explanation
Indices: 53074--53115 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
53064 AGGATCGGGG
53074 TTAGGATTTGAAGGAGGA
1 TTAGGATTTGAAGGAGGA
53092 TTAGGATTTGAAGGAGGA
1 TTAGGATTTGAAGGAGGA
53110 TTAGGA
1 TTAGGA
53116 GACATTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.29
Consensus pattern (18 bp):
TTAGGATTTGAAGGAGGA
Done.