Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001926.1 Hibiscus syriacus cultivar Beakdansim tig00003897_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: 70650
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4315 original size:21 final size:20
Alignment explanation
Indices: 4282--4342 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 20
4272 ATATGTAATA
4282 AAAAAAGAGAAAAAG-AAAG
1 AAAAAAGAGAAAAAGAAAAG
4301 AAAAAAGCAGAAAAAGAAAAG
1 AAAAAAG-AGAAAAAGAAAAG
*
4322 AAAAGGAATAGAAAAAGAAAA
1 AAAA--AAGAGAAAAAGAAAA
4343 AATCTAGAGA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 7 0.19
20 8 0.22
21 8 0.22
22 12 0.32
23 2 0.05
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAAAAGAGAAAAAGAAAAG
Found at i:4334 original size:11 final size:11
Alignment explanation
Indices: 4289--4342 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
4279 ATAAAAAAAG
4289 AGAAAAAG-AA
1 AGAAAAAGAAA
**
4299 AGAAAAA-AGC
1 AGAAAAAGAAA
4309 AGAAAAAGAAA
1 AGAAAAAGAAA
* *
4320 AGAAAAGGAAT
1 AGAAAAAGAAA
4331 AGAAAAAGAAA
1 AGAAAAAGAAA
4342 A
1 A
4343 AATCTAGAGA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
10 14 0.41
11 20 0.59
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (11 bp):
AGAAAAAGAAA
Found at i:7193 original size:20 final size:20
Alignment explanation
Indices: 7165--7203 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7155 TATATTGGAT
*
7165 TATTGTCTATTGTTTATGGC
1 TATTGTCTATGGTTTATGGC
*
7185 TATTTTCTATGGTTTATGG
1 TATTGTCTATGGTTTATGG
7204 TTTATTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.08, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTTTATGGC
Found at i:10934 original size:38 final size:38
Alignment explanation
Indices: 10892--10972 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 38
10882 ATGTCTTTGG
* * *
10892 GGGGTAGAGGAGAGACGCATGGAGTTCAATGCATCTTC
1 GGGGTAGAGGAGAGACACATGGACTGCAATGCATCTTC
* * *
10930 GGGGTAGGGGAGAGACACATGGACTGCAATGTATCTTT
1 GGGGTAGAGGAGAGACACATGGACTGCAATGCATCTTC
10968 GGGGT
1 GGGGT
10973 GTACTGTAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.25, C:0.14, G:0.40, T:0.22
Consensus pattern (38 bp):
GGGGTAGAGGAGAGACACATGGACTGCAATGCATCTTC
Found at i:17032 original size:20 final size:20
Alignment explanation
Indices: 17009--17050 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
16999 CCCATATGCA
* *
17009 ATATAAATATTTTATATATG
1 ATATAAATATATAATATATG
*
17029 ATATAGATATATAATATATG
1 ATATAAATATATAATATATG
17049 AT
1 AT
17051 TAAGAGGTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATATAAATATATAATATATG
Found at i:17688 original size:3 final size:3
Alignment explanation
Indices: 17682--17747 Score: 78
Period size: 3 Copynumber: 21.0 Consensus size: 3
17672 TTTTTTCATT
** *
17682 TTA TTA TTA TTA TTA AAA TTA TCA TTA TTA TTA TTA TGTA TTA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA T-TA
17729 TATA TTA TTA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA
17748 AAAAAATATA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 45 0.82
4 10 0.18
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:17756 original size:27 final size:28
Alignment explanation
Indices: 17677--17757 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 28
17667 CAATTTTTTT
*
17677 TCATT-TTATTATTATTATTAAAAT-TA
1 TCATTATTATTATTATTAATAAAATATA
* *
17703 TCATTATTATTATTATGT-ATTATATATA
1 TCATTATTATTATTAT-TAATAAAATATA
*
17731 T-ATTATTATTATTATTAAAAAAATATA
1 TCATTATTATTATTATTAATAAAATATA
17758 AAATAATTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
26 6 0.13
27 35 0.78
28 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (28 bp):
TCATTATTATTATTATTAATAAAATATA
Found at i:19226 original size:16 final size:15
Alignment explanation
Indices: 19203--19235 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
19193 AAAAATCCTA
19203 TTTATA-AAATTAAT
1 TTTATATAAATTAAT
*
19217 TTTATATAAATTACT
1 TTTATATAAATTAAT
19232 TTTA
1 TTTA
19236 AGAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATAAATTAAT
Found at i:25384 original size:26 final size:26
Alignment explanation
Indices: 25354--25432 Score: 149
Period size: 26 Copynumber: 3.0 Consensus size: 26
25344 TCTTATACTC
25354 ATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
25380 ATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
*
25406 ATCCAGTAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAA
25432 A
1 A
25433 AAGAAAAAAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.70, C:0.10, G:0.15, T:0.05
Consensus pattern (26 bp):
ATCCAGCAAAGAAAGAAAAAAGAAAA
Found at i:25442 original size:26 final size:26
Alignment explanation
Indices: 25361--25459 Score: 92
Period size: 26 Copynumber: 3.8 Consensus size: 26
25351 CTCATCCAGC
** **
25361 AAAGAAAGAAAAAAGAAAAATCCAGC
1 AAAGAAAGAAAAAAGAAAAAAACAAA
** **
25387 AAAGAAAGAAAAAAGAAAAATCCAGT
1 AAAGAAAGAAAAAAGAAAAAAACAAA
*
25413 AAAGAAAGAAAAAAGAAAAAAAGAAA
1 AAAGAAAGAAAAAAGAAAAAAACAAA
* *
25439 AAAG-ATGAAAAAGGAAAAAAA
1 AAAGAAAGAAAAAAGAAAAAAA
25460 GGGAAAAAGA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
25 15 0.23
26 50 0.77
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (26 bp):
AAAGAAAGAAAAAAGAAAAAAACAAA
Found at i:25448 original size:25 final size:26
Alignment explanation
Indices: 25420--25469 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
25410 AGTAAAGAAA
25420 GAAAAAAGAAAAAAA-GAAAAAAGAT
1 GAAAAAAGAAAAAAAGGAAAAAAGAT
* *
25445 GAAAAAGGAAAAAAAGGGAAAAAGA
1 GAAAAAAGAAAAAAAGGAAAAAAGA
25470 AAAATGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (26 bp):
GAAAAAAGAAAAAAAGGAAAAAAGAT
Found at i:25458 original size:9 final size:8
Alignment explanation
Indices: 25417--25473 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
25407 TCCAGTAAAG
25417 AAAG-AAA
1 AAAGAAAA
25424 AAAGAAAA
1 AAAGAAAA
25432 AAAG-AAA
1 AAAGAAAA
25439 AAAGATGAAA
1 AAAGA--AAA
*
25449 AAGGAAAA
1 AAAGAAAA
**
25457 AAAGGGAA
1 AAAGAAAA
25465 AAAGAAAA
1 AAAGAAAA
25473 A
1 A
25474 TGGGAGAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
7 11 0.28
8 22 0.55
10 7 0.17
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAGAAAA
Found at i:25458 original size:52 final size:51
Alignment explanation
Indices: 25354--25457 Score: 133
Period size: 52 Copynumber: 2.0 Consensus size: 51
25344 TCTTATACTC
*
25354 ATCCAGCAAAGAAAGAAAAAAGAAAAATCCAGCAAAGAAAGAAAAAAGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAAA-CAAGCAAAGAAAGAAAAAAGAAAA
*
25406 ATCCAGTAAAGAAAGAAAAAAGAAAAA-AAG-AAA-AAAGATGAAAAAGGAAAA
1 ATCCAGCAAAGAAAGAAAAAAGAAAAACAAGCAAAGAAAGA--AAAAA-GAAAA
25457 A
1 A
25458 AAGGGAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
48 5 0.11
49 3 0.06
50 7 0.15
51 6 0.13
52 26 0.55
ACGTcount: A:0.71, C:0.08, G:0.16, T:0.05
Consensus pattern (51 bp):
ATCCAGCAAAGAAAGAAAAAAGAAAAACAAGCAAAGAAAGAAAAAAGAAAA
Found at i:29450 original size:23 final size:23
Alignment explanation
Indices: 29424--29474 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
29414 CATATAAATA
*
29424 CACCGAAGTGCATCATAGAATTG
1 CACCGAAGTGCAGCATAGAATTG
* * *
29447 CACCGTAGTGCCGCGTAGAATTG
1 CACCGAAGTGCAGCATAGAATTG
29470 CACCG
1 CACCG
29475 TAGTTCCATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.20
Consensus pattern (23 bp):
CACCGAAGTGCAGCATAGAATTG
Found at i:29616 original size:18 final size:18
Alignment explanation
Indices: 29593--29628 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29583 GAATACATAT
29593 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
29611 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
29629 TATCATTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:29644 original size:121 final size:121
Alignment explanation
Indices: 29489--29973 Score: 853
Period size: 121 Copynumber: 4.0 Consensus size: 121
29479 TCCATATAAT
** *
29489 AATGTCCATAAGGACCACATATTATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
*
29554 ATCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
* * * *
29610 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
29675 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
*
29731 AATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
*
29796 GTCTCACCAGACTTCACACATATTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
* *
29852 AATGTCCCGAAAGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGT
1 AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
*
29917 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATATCCCGAAGGACCAC
66 GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
29973 A
1 A
29974 TAGACCCTCG
Statistics
Matches: 345, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 345 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.25
Consensus pattern (121 bp):
AATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGC
GTCTCACCAGACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:29737 original size:18 final size:18
Alignment explanation
Indices: 29714--29749 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29704 GAATACATAT
29714 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
*
29732 ATGTCCTGAAGGACCACA
1 ATGTCCCGAAGGACCACA
29750 TATCATTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:29858 original size:18 final size:18
Alignment explanation
Indices: 29835--29870 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29825 GAATACATAT
*
29835 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAAGACCACA
29853 ATGTCCCGAAAGACCACA
1 ATGTCCCGAAAGACCACA
29871 TATCATTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.33, G:0.19, T:0.11
Consensus pattern (18 bp):
ATGTCCCGAAAGACCACA
Found at i:33266 original size:22 final size:22
Alignment explanation
Indices: 33237--33291 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
33227 ATCTACACTC
*
33237 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTATCTT
*
33259 TTTAAAGATGATAGATTATCTT
1 TTCAAAGATGATAGATTATCTT
33281 TTCAAAGATGA
1 TTCAAAGATGA
33292 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTATCTT
Found at i:34258 original size:37 final size:36
Alignment explanation
Indices: 34175--34517 Score: 281
Period size: 37 Copynumber: 9.4 Consensus size: 36
34165 CACAGAACTT
** ** * *
34175 TCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTG
1 TCTCACTTGAGACAGTTTCACTTGAAACAAAATTTA
* * *
34211 TCTCGCTTGAGACAGTTTCACTCGAAACAGAACTTTA
1 TCTCACTTGAGACAGTTTCACTTGAAACA-AAATTTA
** ** * *
34248 TCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTG
1 TCTCACTTGAGACAGTTTCACTTGAAACAAAATTTA
* * *
34284 TCTCGCTTGAGACAGTTTCACTCGAAACAGAACTTTA
1 TCTCACTTGAGACAGTTTCACTTGAAACA-AAATTTA
** ** * *
34321 TCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTG
1 TCTCACTTGAGACAGTTTCACTTGAAACAAAATTTA
* * *
34357 TCTCGCTTGAGACAGTTTCACTCGAAACAGAACTTTA
1 TCTCACTTGAGACAGTTTCACTTGAAACA-AAATTTA
** ** * *
34394 TCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTT
1 TCTCACTTGAGACAGTTTCACTTGAAACAAAATTTA
*
34430 TCTCGCTTGAGACAGTTTCACTTGAAACAAAAATTTA
1 TCTCACTTGAGACAGTTTCACTTGAAAC-AAAATTTA
* ** * * *
34467 TCTCACTTGAGACTGTTTTTCATAAAACAAAGATTTG
1 TCTCACTTGAGACAGTTTCACTTGAAACAAA-ATTTA
34504 TCTCACTTGAGACA
1 TCTCACTTGAGACA
34518 ATTATTTCGA
Statistics
Matches: 233, Mismatches: 69, Indels: 9
0.75 0.22 0.03
Matches are distributed among these distances:
36 106 0.45
37 127 0.55
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (36 bp):
TCTCACTTGAGACAGTTTCACTTGAAACAAAATTTA
Found at i:34283 original size:73 final size:73
Alignment explanation
Indices: 34166--34517 Score: 618
Period size: 73 Copynumber: 4.8 Consensus size: 73
34156 GGATGTTTTC
34166 ACAGAAC-TT-TCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
1 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
34229 CACTCGAA
66 CACTCGAA
34237 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
1 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
34302 CACTCGAA
66 CACTCGAA
34310 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
1 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
34375 CACTCGAA
66 CACTCGAA
*
34383 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTTTCTCGCTTGAGACAGTTT
1 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
*
34448 CACTTGAA
66 CACTCGAA
* * * * *
34456 ACAAAAATTTATCTCACTTGAGACTGTTTTTCATAAAACAAAGATTTGTCTCACTTGAGACA
1 ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-ATTTGTCTCGCTTGAGACA
34518 ATTATTTCGA
Statistics
Matches: 270, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
71 7 0.03
72 2 0.01
73 244 0.90
74 17 0.06
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.37
Consensus pattern (73 bp):
ACAGAACTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCGCTTGAGACAGTTT
CACTCGAA
Found at i:34853 original size:3 final size:3
Alignment explanation
Indices: 34845--34889 Score: 63
Period size: 3 Copynumber: 14.0 Consensus size: 3
34835 TTTTTTCATT
34845 TTA TTA TTA TTA TGTA TTA TATA TATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA T-TA T-TA TTA TTA TTA TTA TTA TTA
34890 AAAAATAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 30 0.75
4 10 0.25
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:36351 original size:16 final size:15
Alignment explanation
Indices: 36328--36360 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
36318 AAAAATCCTA
36328 TTTATA-AAATTAAT
1 TTTATATAAATTAAT
*
36342 TTTATATAAATTACT
1 TTTATATAAATTAAT
36357 TTTA
1 TTTA
36361 AGAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATAAATTAAT
Found at i:40451 original size:2 final size:2
Alignment explanation
Indices: 40440--40487 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
40430 TAGTATGAAT
40440 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40481 TA TA TA T
1 TA TA TA T
40488 TTGACATTGA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51531 original size:20 final size:20
Alignment explanation
Indices: 51502--51539 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51492 TCATCCCAAA
*
51502 TCATCTAATATCGATACTAT
1 TCATCCAATATCGATACTAT
*
51522 TCATCCAATATCGTTACT
1 TCATCCAATATCGATACT
51540 TGAACCTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (20 bp):
TCATCCAATATCGATACTAT
Found at i:61185 original size:47 final size:47
Alignment explanation
Indices: 61067--61168 Score: 159
Period size: 47 Copynumber: 2.2 Consensus size: 47
61057 AATTTAGTCG
* **
61067 ACTAGAGCCAGTTTTGGGTACCTCTAGCAATTCTTGAATGTGTAACA
1 ACTAGAGCCAGTTTTGGGCACCTCTAGCAATTCTTGAATGCATAACA
* *
61114 ACTAGAGCCAGTTTTGGGCACCTCTAGCAATTCTTTATTGCATAACA
1 ACTAGAGCCAGTTTTGGGCACCTCTAGCAATTCTTGAATGCATAACA
61161 ACTAGAGC
1 ACTAGAGC
61169 TGATTTCTGG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (47 bp):
ACTAGAGCCAGTTTTGGGCACCTCTAGCAATTCTTGAATGCATAACA
Found at i:62080 original size:8 final size:8
Alignment explanation
Indices: 62069--62106 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
62059 TAAAAATGAG
62069 AAAAATAA
1 AAAAATAA
62077 AAAAATAA
1 AAAAATAA
*
62085 ATAAATAA
1 AAAAATAA
*
62093 AACAA-AA
1 AAAAATAA
62100 AAAAATA
1 AAAAATA
62107 TCAAATGAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAATAA
Found at i:67306 original size:3 final size:3
Alignment explanation
Indices: 67298--67330 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
67288 ATGCATAAAT
67298 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
67331 TATTCAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:68217 original size:17 final size:17
Alignment explanation
Indices: 68197--68266 Score: 104
Period size: 17 Copynumber: 4.1 Consensus size: 17
68187 TTTAACAAAG
*
68197 TAGTTCATTGATTAAAC
1 TAGTTCATTCATTAAAC
68214 TAGTTCATTCATTAAAC
1 TAGTTCATTCATTAAAC
* *
68231 TATTTCATTCATCAAAC
1 TAGTTCATTCATTAAAC
*
68248 TAGTTCATTTATTAAAC
1 TAGTTCATTCATTAAAC
68265 TA
1 TA
68267 ACTCTTAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 47 1.00
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.43
Consensus pattern (17 bp):
TAGTTCATTCATTAAAC
Found at i:68221 original size:34 final size:34
Alignment explanation
Indices: 68183--68258 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
68173 AGCTATGCAC
* * *
68183 TTCATTTAACAAAGTAGTTCATTGATTAAACTAG
1 TTCATTTAACAAACTAGTTCATTCATCAAACTAG
* ** *
68217 TTCATTCATTAAACTATTTCATTCATCAAACTAG
1 TTCATTTAACAAACTAGTTCATTCATCAAACTAG
68251 TTCATTTA
1 TTCATTTA
68259 TTAAACTAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.42
Consensus pattern (34 bp):
TTCATTTAACAAACTAGTTCATTCATCAAACTAG
Done.