Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003301.1 Hibiscus syriacus cultivar Beakdansim tig00006947_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: 59668
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:759 original size:20 final size:18
Alignment explanation
Indices: 724--771 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
714 ATAAAATCCT
*
724 AGTGCA-TCGGTGCATGGTA
1 AGTGCATTCGATGCAT-G-A
743 AGTGCATTCGATGCATGA
1 AGTGCATTCGATGCATGA
*
761 AATGCATTCGA
1 AGTGCATTCGA
772 GTTCATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 7 0.27
20 8 0.31
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (18 bp):
AGTGCATTCGATGCATGA
Found at i:801 original size:63 final size:64
Alignment explanation
Indices: 616--803 Score: 172
Period size: 64 Copynumber: 3.0 Consensus size: 64
606 GTGCACTAAG
* * * * *
616 AGTGCATCGATGCATCAATGCATTCGATGTT-TCA-AAATAGCCAGAGTGCATCGATGCATGGCT
1 AGTGCATTGATGCATCAAAGCATTCGATGTTATTATAAA-A-TCATAGTGCATCGATGCATGGCT
*
679 G
64 A
* * * *
680 GGTGCATTGATGCATCAAAGCATTCGATGTTTTTATAAAATCCTAGTGCATCGGTGCATGG-TA
1 AGTGCATTGATGCATCAAAGCATTCGATGTTATTATAAAATCATAGTGCATCGATGCATGGCTA
* * *
743 AGTGCATTCGATGCATGAAATGCATTCGA-GTTCATT-T-AATTCATGGTGCATCGATGCATGG
1 AGTGCATT-GATGCATCAAA-GCATTCGATGTT-ATTATAAAATCATAGTGCATCGATGCATGG
804 ATTGGTTTCG
Statistics
Matches: 103, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
63 28 0.27
64 59 0.57
65 13 0.13
66 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
AGTGCATTGATGCATCAAAGCATTCGATGTTATTATAAAATCATAGTGCATCGATGCATGGCTA
Found at i:1196 original size:32 final size:32
Alignment explanation
Indices: 1155--1403 Score: 357
Period size: 32 Copynumber: 7.8 Consensus size: 32
1145 GAAGGACCTA
1155 TCCATATGTTCCGAAGAACATAGGTAATCATG
1 TCCATATGTTCCGAAGAACATAGGTAATCATG
*
1187 TCCATATGTTCCGGAGAAACATAGGTAATCATG
1 TCCATATGTTCCGAAG-AACATAGGTAATCATG
* *
1220 TCCATATGTT-CGAATAACATAGGTAATCCTG
1 TCCATATGTTCCGAAGAACATAGGTAATCATG
*
1251 TCCATATGTTCCGGAGAACATAGGTAATCATG
1 TCCATATGTTCCGAAGAACATAGGTAATCATG
*
1283 TCCCATATGTTCCGAAGAACATAGGTAATAATG
1 T-CCATATGTTCCGAAGAACATAGGTAATCATG
1316 TCCATATGTTCCGAAGAACATAGGTAATCATG
1 TCCATATGTTCCGAAGAACATAGGTAATCATG
*
1348 TCCATATGTTCCGAAGAAC--AGGTAATC-TA
1 TCCATATGTTCCGAAGAACATAGGTAATCATG
*
1377 TCCACATG-TCTCGAA-AGACATAGGTAA
1 TCCATATGTTC-CGAAGA-ACATAGGTAA
1404 CTCGACTCTT
Statistics
Matches: 198, Mismatches: 12, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
28 3 0.02
29 14 0.07
30 8 0.04
31 31 0.16
32 86 0.43
33 56 0.28
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (32 bp):
TCCATATGTTCCGAAGAACATAGGTAATCATG
Found at i:5691 original size:21 final size:22
Alignment explanation
Indices: 5647--5699 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
5637 TTGTAACAAG
*
5647 GGGATCGATCCTTTTTGGTGAA
1 GGGATCGATCCTTTTTGGTAAA
*
5669 GGGATAGATCCTTTTT-GTAAA
1 GGGATCGATCCTTTTTGGTAAA
5690 GGGATCGATC
1 GGGATCGATC
5700 TCAAACTCAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (22 bp):
GGGATCGATCCTTTTTGGTAAA
Found at i:10382 original size:25 final size:25
Alignment explanation
Indices: 10354--10414 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
10344 AAATCTAGGG
10354 GGTGTGAAATTGCAAATTTTCATGT
1 GGTGTGAAATTGCAAATTTTCATGT
10379 GGTGTGAAATTGCAAATTTTCATGT
1 GGTGTGAAATTGCAAATTTTCATGT
*
10404 GGTGCGAAATT
1 GGTGTGAAATT
10415 AGATCATCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (25 bp):
GGTGTGAAATTGCAAATTTTCATGT
Found at i:15735 original size:68 final size:68
Alignment explanation
Indices: 15621--15757 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
15611 GGCGATTTTC
* *
15621 ACACATTATACATTAAATGATTTAGATCCAAAAATAATTTTTAAACACCTATATATATATATATA
1 ACACATGATACATTAAATGATTTAGATCCAAAAATAATTTTCAAACACCTATATATATATATATA
15686 TAT
66 TAT
15689 ACACATGATACATTAAATGATTTAGATCCAAAAATAATTTTCAAACACCTATATATATATATATA
1 ACACATGATACATTAAATGATTTAGATCCAAAAATAATTTTCAAACACCTATATATATATATATA
15754 TAT
66 TAT
15757 A
1 A
15758 TATATTTAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.36
Consensus pattern (68 bp):
ACACATGATACATTAAATGATTTAGATCCAAAAATAATTTTCAAACACCTATATATATATATATA
TAT
Found at i:15745 original size:2 final size:2
Alignment explanation
Indices: 15738--15762 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15728 TTCAAACACC
15738 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
15763 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16641 original size:2 final size:2
Alignment explanation
Indices: 16628--16664 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
16618 TTTTAAGAAA
16628 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16665 AATAAATAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17001 original size:2 final size:2
Alignment explanation
Indices: 16994--17041 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
16984 TATCATTTAT
16994 TA TA TA 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
17036 TA TA TA
1 TA TA TA
17042 CATGATTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18497 original size:3 final size:3
Alignment explanation
Indices: 18489--18568 Score: 101
Period size: 3 Copynumber: 27.0 Consensus size: 3
18479 TATTTTTTAT
* *
18489 TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA -AA TAA TAA TAG TAA TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
* *
18537 TAA -AA TAT TAA TAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
18569 ACAAATGGAT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 4 0.06
3 59 0.89
4 3 0.05
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:19052 original size:121 final size:119
Alignment explanation
Indices: 18905--19466 Score: 577
Period size: 121 Copynumber: 4.7 Consensus size: 119
18895 GAATTAAGGC
* *
18905 AAGGTTGAACAAGTTCTTATTATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* *
18969 TGAACACTTCTGGAAATGTGGATGTTGATTTATATCCTTCTGTGATAGAGTCATGC-A
66 TGAACACTTCTGGAAATGTTGATGTTGA-TTACAT-C-TCTGTGAT-GAGTCATGCAA
* *
19026 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTTATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * * ** *
19090 TGAAC-TTTCTATGAAAAAGTTGATGCTGA-TCCATCGAT-TGATGAATTCGA-GCAA
66 TGAACACTTC--TGGAAATGTTGATGTTGATTACATCTCTGTGATG-AGTC-ATGCAA
19144 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
19209 TGAACACTTCTGGAAATGTTGATATTGATGTATC-TCTTTCTGTGATAAAGTTATGCAA
66 TGAACACTTCTGGAAATGTTGATGTTGAT-TA-CATC--TCTGTGAT-GAGTCATGCAA
* *
19267 AAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
** * * * *
19331 TGAACTTTCTCTAGAAA-----A-GTTGATT-CATCT-AGTGATGAAT-TTGAACAA
66 TGAACACT-TCTGGAAATGTTGATGTTGATTACATCTCTGTGATGAGTCATG--CAA
*
19379 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
19444 CGAACTTCTT-TGGGAATGTTGAT
66 TGAAC-ACTTCTGGAAATGTTGAT
19467 CCATTGAGTA
Statistics
Matches: 369, Mismatches: 44, Indels: 59
0.78 0.09 0.12
Matches are distributed among these distances:
110 2 0.01
111 2 0.01
112 51 0.14
113 28 0.08
114 3 0.01
115 2 0.01
116 2 0.01
117 15 0.04
118 58 0.16
119 28 0.08
120 12 0.03
121 62 0.17
122 48 0.13
123 56 0.15
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (119 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACACTTCTGGAAATGTTGATGTTGATTACATCTCTGTGATGAGTCATGCAA
Found at i:19464 original size:235 final size:237
Alignment explanation
Indices: 18905--19466 Score: 848
Period size: 235 Copynumber: 2.4 Consensus size: 237
18895 GAATTAAGGC
* *
18905 AAGGTTGAACAAGTTCTTATTATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * *
18969 TGAACACTTCTGGAAATGTGGATGTTGATTTATATCCTTCTGTGATAGAGTCATGCAAAGGTTGA
66 TGAACACTTCTGGAAATGTTGATATTGATGTATATCCTTCTGTGATAAAGTCATGCAAAGGTTGA
* *
19034 ACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTTATTATGAACTTTC
131 ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTC
* *
19099 TATGAAAAAGTTGATGCTGATCCATCGATTGATGAATTCGAGCAA
196 TATGAAAAAGTTGA--CT-ATCCATCGAGTGATGAATTCGAACAA
19144 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
19209 TGAACACTTCTGGAAATGTTGATATTGATGTATCTCTTTCTGTGATAAAGTTATGCAAAAGGTTG
66 TGAACACTTCTGGAAATGTTGATATTGATGTATATCCTTCTGTGATAAAGTCATGC-AAAGGTTG
19274 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTT
130 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTT
* * *
19339 CTCT-AGAAAAGTTGA-T-T-CATCTAGTGATGAATTTGAACAA
195 CTATGA-AAAAGTTGACTATCCATCGAGTGATGAATTCGAACAA
*
19379 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTTTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * *
19444 CGAACTTCTT-TGGGAATGTTGAT
66 TGAAC-ACTTCTGGAAATGTTGAT
19467 CCATTGAGTA
Statistics
Matches: 299, Mismatches: 20, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
235 99 0.33
236 4 0.01
238 1 0.00
239 34 0.11
240 78 0.26
241 83 0.28
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (237 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACACTTCTGGAAATGTTGATATTGATGTATATCCTTCTGTGATAAAGTCATGCAAAGGTTGA
ACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTC
TATGAAAAAGTTGACTATCCATCGAGTGATGAATTCGAACAA
Found at i:23906 original size:35 final size:35
Alignment explanation
Indices: 23836--23906 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
23826 ACATATTTCC
** * *
23836 GAAATGATATAGTAAATTTATGAAATAAATATAAA
1 GAAATGATATAGTAAAAATATAAAAAAAATATAAA
* *
23871 GAAATGATATAGTAAAAATGTAAAAAAAATGTAAA
1 GAAATGATATAGTAAAAATATAAAAAAAATATAAA
23906 G
1 G
23907 TATAAAGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (35 bp):
GAAATGATATAGTAAAAATATAAAAAAAATATAAA
Found at i:29573 original size:3 final size:3
Alignment explanation
Indices: 29560--29596 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
29550 TACATGATTA
29560 AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29597 TAAATATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29998 original size:21 final size:21
Alignment explanation
Indices: 29969--30015 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
29959 ATTCTGACTA
29969 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
29990 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
30011 TCGCA
1 TCGCA
30016 ATTGAATACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.19, C:0.26, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:30042 original size:20 final size:20
Alignment explanation
Indices: 30019--30122 Score: 163
Period size: 20 Copynumber: 5.2 Consensus size: 20
30009 ATTCGCAATT
*
30019 GAATACGTAAATTGCAATGC
1 GAATACGTAAATCGCAATGC
*
30039 GAATACGTAAATTGCAATGC
1 GAATACGTAAATCGCAATGC
*
30059 GATTACGTAAATCGCAATGC
1 GAATACGTAAATCGCAATGC
*
30079 GAATACGTAAATCGCAATAC
1 GAATACGTAAATCGCAATGC
*
30099 AAATACGTAAATCGCAATGC
1 GAATACGTAAATCGCAATGC
30119 GAAT
1 GAAT
30123 CTGACTATCG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 77 1.00
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.23
Consensus pattern (20 bp):
GAATACGTAAATCGCAATGC
Found at i:30343 original size:22 final size:22
Alignment explanation
Indices: 30318--30383 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
30308 GGAGACATTC
30318 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
30340 GTCCCCATCTCCCACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
30362 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
30384 TTCACAGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.24, C:0.41, G:0.14, T:0.21
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:30807 original size:20 final size:20
Alignment explanation
Indices: 30719--30809 Score: 96
Period size: 20 Copynumber: 4.6 Consensus size: 20
30709 GCGATTTTGT
30719 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
30738 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
*
30758 CGTTGCGATAGTT-ATTTTCG
1 CGTTGCGAT-TTTCATTTTCG
*
30778 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
30798 TGTTGCGATTTT
1 CGTTGCGATTTT
30810 AAGTTTCAGA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
19 14 0.23
20 45 0.75
21 1 0.02
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:30816 original size:20 final size:20
Alignment explanation
Indices: 30773--30816 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
30763 CGATAGTTAT
* *
30773 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
30793 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
30813 TTTC
1 TTTC
30817 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:32709 original size:20 final size:20
Alignment explanation
Indices: 32684--32820 Score: 86
Period size: 20 Copynumber: 7.5 Consensus size: 20
32674 AGAATAGTTT
32684 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
32704 ACTATCGCAACGTGAAAATG
1 ACTATCGCAATGCGAAAATG
*
32724 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
32740 A--ATTGCAATGCG-AAATG
1 ACTATCGCAATGCGAAAATG
**
32757 AAAATCGCAA--C-AACAA--
1 ACTATCGCAATGCGAA-AATG
*
32773 A--ATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
32791 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
32811 ACTATCGCAA
1 ACTATCGCAA
32821 CGAAAGAATC
Statistics
Matches: 93, Mismatches: 10, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
14 13 0.14
16 10 0.11
17 8 0.09
18 4 0.04
19 6 0.06
20 52 0.56
ACGTcount: A:0.42, C:0.21, G:0.19, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:32786 original size:33 final size:33
Alignment explanation
Indices: 32707--32787 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 33
32697 GAAAATGACT
* ** * * *
32707 ATCGCAACGTGAAAATGACTATCGCAACGAGAGA
1 ATCGCAACGCG-AAATGAAAATCGCAACAACAAA
* *
32741 ATTGCAATGCGAAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACAACAAA
32774 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
32788 ATGACTATCG
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
33 29 0.78
34 8 0.22
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACAACAAA
Found at i:32801 original size:53 final size:53
Alignment explanation
Indices: 32744--32858 Score: 126
Period size: 53 Copynumber: 2.2 Consensus size: 53
32734 CGAGAGAATT
**
32744 GCAATGCGAA-ATGAAAATCGCAAC-AACAAAATCGCAACGCGAAAATGACTATC
1 GCAATGCGAATATGAAAATCGCAACGAA-AAAATCGCAACGCG-AAATGAAAATC
* ** * *
32797 GCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATGCGAAATGAAAATC
1 GCAATGCGAATATGAAAATCGCAACGAAAAAATCGCAACGCGAAATGAAAATC
*
32850 GCATTGCGA
1 GCAATGCGA
32859 TAGTCAAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
53 27 0.52
54 23 0.44
55 2 0.04
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.17
Consensus pattern (53 bp):
GCAATGCGAATATGAAAATCGCAACGAAAAAATCGCAACGCGAAATGAAAATC
Found at i:32835 original size:87 final size:87
Alignment explanation
Indices: 32687--32852 Score: 269
Period size: 87 Copynumber: 1.9 Consensus size: 87
32677 ATAGTTTACT
* * * *
32687 ATCGCAATGCGAAAATGACTATCGCAACGTGAAAATGACTATCGCAACGAGAGAATTGCAATGCG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
32752 AAATGAAAATCGCAACAACAAA
66 AAATGAAAATCGCAACAACAAA
* **
32774 ATCGCAACGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCGCAATGCG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
32839 AAATGAAAATCGCA
66 AAATGAAAATCGCA
32853 TTGCGATAGT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (87 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG
AAATGAAAATCGCAACAACAAA
Found at i:32934 original size:20 final size:20
Alignment explanation
Indices: 32848--32931 Score: 123
Period size: 20 Copynumber: 4.2 Consensus size: 20
32838 GAAATGAAAA
**
32848 TCGCATTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTT
*
32868 TCGCATTGCGATAGTCTTTT
1 TCGCATTGCGATAGTCATTT
32888 TCGCATTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
* *
32908 TCGCGTTGTGATAGTCATTT
1 TCGCATTGCGATAGTCATTT
32928 TCGC
1 TCGC
32932 GTTACGATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATAGTCATTT
Found at i:33448 original size:18 final size:18
Alignment explanation
Indices: 33425--33460 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
33415 CTCACCTGTC
33425 ATCGTTCAAGAGGCCCCT
1 ATCGTTCAAGAGGCCCCT
*
33443 ATCGTTCAAGAGTCCCCT
1 ATCGTTCAAGAGGCCCCT
33461 CCCACCGTTC
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:0.22, C:0.33, G:0.19, T:0.25
Consensus pattern (18 bp):
ATCGTTCAAGAGGCCCCT
Found at i:33490 original size:21 final size:20
Alignment explanation
Indices: 33423--33503 Score: 76
Period size: 21 Copynumber: 4.0 Consensus size: 20
33413 GACTCACCTG
33423 TCATCGTTCAAGAGGCCC-C
1 TCATCGTTCAAGAGGCCCTC
*
33442 T-ATCGTTCAAGAGTCCCCTC
1 TCATCGTTCAAGAG-GCCCTC
* * *
33462 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
33483 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGG-CCCTC
33504 CCAACATTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
18 12 0.25
19 4 0.08
20 3 0.06
21 27 0.56
22 2 0.04
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:34906 original size:14 final size:14
Alignment explanation
Indices: 34887--34922 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
34877 ATTGTTTAAT
34887 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
34901 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
34915 TGATTTGT
1 TGATTTGT
34923 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:35061 original size:14 final size:14
Alignment explanation
Indices: 35042--35095 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
35032 GGAAATGACT
35042 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
35056 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
35075 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
35089 ATCGCAA
1 ATCGCAA
35096 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:35065 original size:34 final size:34
Alignment explanation
Indices: 35022--35117 Score: 158
Period size: 33 Copynumber: 2.9 Consensus size: 34
35012 AAAACAGACT
**
35022 ATCGCAATGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
35056 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
35089 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGGAAATGAAAATCGCAACG
35118 CGAAACTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 31 0.53
34 27 0.47
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.14
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:35113 original size:20 final size:19
Alignment explanation
Indices: 35055--35122 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
35045 GCAACGAGAG
35055 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35074 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
35088 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
35108 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
35123 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:35157 original size:20 final size:19
Alignment explanation
Indices: 35128--35194 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
35118 CGAAACTAAA
*
35128 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
35148 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
35164 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
35181 TTCGCATTGCGATT
1 TTCGCATTGCGATT
35195 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 3 0.08
18 4 0.10
19 8 0.21
20 11 0.28
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:35175 original size:34 final size:34
Alignment explanation
Indices: 35132--35227 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
35122 ACTAAATTCG
35132 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
35166 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
** * *
35199 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
35228 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.42
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:35224 original size:20 final size:20
Alignment explanation
Indices: 35199--35267 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 20
35189 GCGATTCTCT
35199 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
35219 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
35239 TGTTACGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
35259 CATTGCGAT
1 CGTTGCGAT
35268 TTCCGCGTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:38639 original size:20 final size:20
Alignment explanation
Indices: 38577--38630 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
38567 AAATTCAGTA
38577 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
38597 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCTCG
38617 TTGCGATAGTCAGA
1 TTGCGATAGTCAGA
38631 TTCGTGTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCTCG
Found at i:38650 original size:20 final size:20
Alignment explanation
Indices: 38627--38743 Score: 96
Period size: 20 Copynumber: 5.8 Consensus size: 20
38617 TTGCGATAGT
* *
38627 CAGATTCGTGTTGTGATTTA
1 CAGATTCGCGTTGCGATTTA
38647 CAGATTCGCGTTGCGATTTA
1 CAGATTCGCGTTGCGATTTA
*
38667 C-GTATTCGCATTGCGATTTA
1 CAG-ATTCGCGTTGCGATTTA
* * *
38687 C-GTATTCGCATTGTGATTTTC
1 CAG-ATTCGCGTTGCGA-TTTA
* *
38708 CAAATTCGCATTGCGATTTA
1 CAGATTCGCGTTGCGATTTA
*
38728 C-GTATTCGCATTGCGA
1 CAG-ATTCGCGTTGCGA
38744 ATTAGGAAAA
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
19 1 0.01
20 67 0.80
21 16 0.19
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
CAGATTCGCGTTGCGATTTA
Found at i:38674 original size:40 final size:40
Alignment explanation
Indices: 38641--38743 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 40
38631 TTCGTGTTGT
*
38641 GATTTACAG-ATTCGCGTTGCGATTTACGTATTCGCATTGC
1 GATTTAC-GTATTCGCATTGCGATTTACGTATTCGCATTGC
* * **
38681 GATTTACGTATTCGCATTGTGATTTTCCAAATTCGCATTGC
1 GATTTACGTATTCGCATTGCGA-TTTACGTATTCGCATTGC
38722 GATTTACGTATTCGCATTGCGA
1 GATTTACGTATTCGCATTGCGA
38744 ATTAGGAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
39 1 0.02
40 18 0.33
41 36 0.65
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (40 bp):
GATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGC
Found at i:38758 original size:41 final size:41
Alignment explanation
Indices: 38672--38758 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
38662 ATTTACGTAT
* * * *
38672 TCGCATTGCGATTTACGTATTCGCATTGTGATTTTCCAAAT
1 TCGCATTGCGATTTACGTATTCGCATTGCGAATTACCAAAA
**
38713 TCGCATTGCGATTTACGTATTCGCATTGCGAATTAGGAAAA
1 TCGCATTGCGATTTACGTATTCGCATTGCGAATTACCAAAA
38754 TCGCA
1 TCGCA
38759 ACGCGAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (41 bp):
TCGCATTGCGATTTACGTATTCGCATTGCGAATTACCAAAA
Found at i:38764 original size:21 final size:21
Alignment explanation
Indices: 38740--38785 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
38730 TATTCGCATT
*
38740 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCACAAC
* *
38761 GCGAATTTGGAAAATCACAAT
1 GCGAATTAGGAAAATCACAAC
38782 GCGA
1 GCGA
38786 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCACAAC
Found at i:40169 original size:3 final size:3
Alignment explanation
Indices: 40163--40248 Score: 77
Period size: 3 Copynumber: 29.0 Consensus size: 3
40153 AGTATTTTTT
* * * * * *
40163 TAA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TTA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
40210 TAA TAG TAA TAAA TAA -AA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
40249 AAAAAACAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
2 4 0.05
3 67 0.91
4 3 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:43583 original size:14 final size:14
Alignment explanation
Indices: 43550--43579 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
43540 TATTTTTTGA
43550 TTATATTTATATAT
1 TTATATTTATATAT
43564 TTATATTTAT-TAT
1 TTATATTTATATAT
43577 TTA
1 TTA
43580 ATATGTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATATTTATATAT
Done.