Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001308.1 Hibiscus syriacus cultivar Beakdansim tig00002550_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: 81385
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5903 original size:17 final size:16
Alignment explanation
Indices: 5881--5914 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
5871 TAAAAATAAT
5881 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
5898 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
5914 A
1 A
5915 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:15799 original size:54 final size:54
Alignment explanation
Indices: 15717--16330 Score: 897
Period size: 54 Copynumber: 11.4 Consensus size: 54
15707 TACGGTAATT
* * *
15717 TTGCACACATAGTACATGTACGGTTGTTCATCAACATATGATGAATTCCATGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
** * *
15771 TTGCACTTATAGTGCATGTACGGTTGTTCATCAACATATGATGAATTCCGTGGG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* * *
15825 TTACACACATAGTGTCTGTACGGTTGTTCATCAACATATGATGAATTCTGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* *
15879 TTGCACACATAGTGCCTGTATGGTAGTTCATCAACATATGATGAATTCCGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
**
15933 TTGCACACATAGTATCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* * *
15987 TTGCACACATAGAGCCTGTACGGTTGTTCATCAAAATATGATGAATTACGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* * *
16041 TTGCACACATAGAGCCTGTACGGTTGTTCATCAAAATATGATGAATTACGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
*
16095 TTGCACACATAGTGCCTGTACGATTGTTCATCAACATATGATGAATTCCGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* * * **
16149 TTGCATACATAGTGCCTGTACTGTTGTTCATCAATATATGATGAATTATGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* * * * **
16203 TTGAACACATAGTGCATCTACGGTTGTTCATCAACATATGGTGAATTATGTGAG
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
* *
16257 TTGCACACATAGTGCATGTACGGTTGTTCATCAACATATGATGAATTTCGTG-G
1 TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
*
16310 TTTGCACACATAGTGCTTGTA
1 -TTGCACACATAGTGCCTGTA
16331 GTACACCTAC
Statistics
Matches: 510, Mismatches: 49, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
53 1 0.00
54 509 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.33
Consensus pattern (54 bp):
TTGCACACATAGTGCCTGTACGGTTGTTCATCAACATATGATGAATTCCGTGAG
Found at i:15888 original size:27 final size:27
Alignment explanation
Indices: 15858--15997 Score: 75
Period size: 27 Copynumber: 5.2 Consensus size: 27
15848 TTGTTCATCA
15858 ACATATGATGAATTCTGTGAGTTGCAC
1 ACATATGATGAATTCTGTGAGTTGCAC
** *
15885 ACATA-G-TGCCTGTATG-GTAGTT-CATC
1 ACATATGATGAAT-TCTGTG-AGTTGCA-C
*
15911 AACATATGATGAATTCCGTGAGTTGCAC
1 -ACATATGATGAATTCTGTGAGTTGCAC
15939 ACATA-G-T--A-TCTGT-ACGGTTGTTCATC
1 ACATATGATGAATTCTGTGA--GTTG--CA-C
*
15965 AACATATGATGAATTCCGTGAGTTGCAC
1 -ACATATGATGAATTCTGTGAGTTGCAC
15993 ACATA
1 ACATA
15998 GAGCCTGTAC
Statistics
Matches: 84, Mismatches: 9, Indels: 40
0.63 0.07 0.30
Matches are distributed among these distances:
21 1 0.01
22 4 0.05
23 5 0.06
25 9 0.11
26 11 0.13
27 25 0.30
28 10 0.12
29 9 0.11
31 5 0.06
32 4 0.05
33 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (27 bp):
ACATATGATGAATTCTGTGAGTTGCAC
Found at i:16062 original size:26 final size:26
Alignment explanation
Indices: 15981--16062 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 26
15971 TGATGAATTC
15981 CGTGAGTTGCACACATAGAGCCTGTA
1 CGTGAGTTGCACACATAGAGCCTGTA
* * **
16007 CG-GTTGTT-CATCAAAATATGATGAAT-TA
1 CGTG-AGTTGCA-C-ACATA-GA-GCCTGTA
16035 CGTGAGTTGCACACATAGAGCCTGTA
1 CGTGAGTTGCACACATAGAGCCTGTA
16061 CG
1 CG
16063 GTTGTTCATC
Statistics
Matches: 40, Mismatches: 8, Indels: 16
0.62 0.12 0.25
Matches are distributed among these distances:
25 5 0.12
26 12 0.30
27 8 0.20
28 10 0.25
29 5 0.12
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (26 bp):
CGTGAGTTGCACACATAGAGCCTGTA
Found at i:16293 original size:27 final size:26
Alignment explanation
Indices: 16209--16294 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 26
16199 TGAGTTGAAC
16209 ACATAGTGCATCTACGGTTGTTCATCA
1 ACATAGTGCAT-TACGGTTGTTCATCA
* * *
16236 ACATATGGTGAATTA-TGTGAGTTGCA-C-
1 ACATA--GTGCATTACGGT-TGTT-CATCA
16263 ACATAGTGCATGTACGGTTGTTCATCA
1 ACATAGTGCAT-TACGGTTGTTCATCA
16290 ACATA
1 ACATA
16295 TGATGAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 16
0.67 0.09 0.24
Matches are distributed among these distances:
25 7 0.16
26 6 0.13
27 19 0.42
28 6 0.13
29 7 0.16
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (26 bp):
ACATAGTGCATTACGGTTGTTCATCA
Found at i:18664 original size:74 final size:75
Alignment explanation
Indices: 18520--18776 Score: 354
Period size: 75 Copynumber: 3.4 Consensus size: 75
18510 CTTAACCGTT
* * * * *
18520 TAAAATAAAATAGGCGCTACCTATTATGTTAAACTACCTATCGGTTTGTTTGAAGGTTGCTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAAGGTTACTAATA
*
18585 ATGTAAATGG
66 ATGTAAACGG
* * * * *
18595 TAAAATAAAATAGGTGCTATCTATTACGTTAAAATATCTA-CTGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAAGGTTACTAATA
18659 ATGTAAACGG
66 ATGTAAACGG
* * *
18669 TAAAATAAAATACGCGCTACCTATTGCGTTAAACTACCTACCAATTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAAGGTTACTAATA
*
18734 ATATAAACGG
66 ATGTAAACGG
* *
18744 TAAAATAAAATAAGCGCTACCTATTATGTTAAA
1 TAAAATAAAATAGGCGCTACCTATTACGTTAAA
18777 TAGGCGCTAC
Statistics
Matches: 160, Mismatches: 21, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
74 64 0.40
75 96 0.60
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (75 bp):
TAAAATAAAATAGGCGCTACCTATTACGTTAAACTACCTACCAGTTTGTTTAAAGGTTACTAATA
ATGTAAACGG
Found at i:18783 original size:23 final size:23
Alignment explanation
Indices: 18751--18796 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
18741 CGGTAAAATA
18751 AAATAAGCGCTACCTATTATGTT
1 AAATAAGCGCTACCTATTATGTT
*
18774 AAATAGGCGCTACCTATTATGTT
1 AAATAAGCGCTACCTATTATGTT
18797 GAACTAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (23 bp):
AAATAAGCGCTACCTATTATGTT
Found at i:19097 original size:155 final size:153
Alignment explanation
Indices: 18830--19125 Score: 459
Period size: 155 Copynumber: 1.9 Consensus size: 153
18820 ATGTTAATAA
*
18830 TAATGTAAACGATAAAATATATACAACTTAACCGTTTGAAATATTTTTTTAAAATTTGAAAATAT
1 TAATGTAAACGATAAAATATATACAACTTAACCGTTTGAAATATTTTTTTAAAATTCGAAAATAT
* * * *
18895 GGATACTTACTTTAAAAGAATGGATACTTTAAAGGTTAATAATAATGTATCCATACTTACTCTAA
66 GGATACTTACTCTAAAAGAATAGATACTCTAAAGATTAATAATAATGTATCCATACTTACTCTAA
18960 AAGTATGGATAATGTTTCGACAG
131 AAGTATGGATAATGTTTCGACAG
* *
18983 TAATGTAAAC-AGTAGAATATATACAACTTAACCGTTTGAAATATTTTTTTTTAAAATTCGAAAG
1 TAATGTAAACGA-TAAAATATATACAACTTAACCGTTTGAAATA--TTTTTTTAAAATTCGAAAA
** *
19047 TATGGATACTTACTCTAAAATTATAGATACTCTAAAGATTAATAATAATGTATCCATAGTTACTC
63 TATGGATACTTACTCTAAAAGAATAGATACTCTAAAGATTAATAATAATGTATCCATACTTACTC
*
19112 TAAAAGTATTGATA
128 TAAAAGTATGGATA
19126 TTTGCTAAAG
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
152 1 0.01
153 40 0.31
155 88 0.68
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (153 bp):
TAATGTAAACGATAAAATATATACAACTTAACCGTTTGAAATATTTTTTTAAAATTCGAAAATAT
GGATACTTACTCTAAAAGAATAGATACTCTAAAGATTAATAATAATGTATCCATACTTACTCTAA
AAGTATGGATAATGTTTCGACAG
Found at i:19443 original size:108 final size:108
Alignment explanation
Indices: 19312--19593 Score: 327
Period size: 108 Copynumber: 2.6 Consensus size: 108
19302 TGTTAATATT
* ** * * *
19312 TATTTATAACAAAATAAAAAATTAACCTATTTTGTTGTTGTGGGATTTCGAAGG-CCCAATCAGC
1 TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTGAGATTTCGAAGGTCCC-ATCAGC
*
19376 TTAAACTTTGGTAACATTTTAGGCGCT-ACATAATATGTTGATAA
65 TTAAACTTTGATAACATTTTAGGCG-TGACATAATATGTTGATAA
* * * * *
19420 TATTAATAACAAAATAAGTAATTAACTTATTTCGTTATCGTTATATTTCTAAGGTCCCATCAGCT
1 TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTGAGATTTCGAAGGTCCCATCAGCT
* * *
19485 TAAACTTTGATAATATTTTGGGCGTGACCTAATATGTTGATAA
66 TAAACTTTGATAACATTTTAGGCGTGACATAATATGTTGATAA
* * * * * *
19528 TATTGATAACAAATTAAGTAATCAACCTATTTTGTTATCGTCGA-ATTTCTAAGGTCTCATTAGC
1 TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGT-GAGATTTCGAAGGTCCCATCAGC
19592 TT
65 TT
19594 TAAAAAGACG
Statistics
Matches: 148, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
107 1 0.01
108 143 0.97
109 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (108 bp):
TATTAATAACAAAATAAGTAATTAACCTATTTTGTTATCGTGAGATTTCGAAGGTCCCATCAGCT
TAAACTTTGATAACATTTTAGGCGTGACATAATATGTTGATAA
Found at i:19746 original size:226 final size:226
Alignment explanation
Indices: 19436--19898 Score: 610
Period size: 226 Copynumber: 2.0 Consensus size: 226
19426 TAACAAAATA
* * * * * *
19436 AGTAATTAACTTATTTCGTTATCGTTATATTTCTAAGGTCCCATCAGCTTAAACTTTGATAATAT
1 AGTAATTAACCTATTTCGTTATCGTCAGATTTCTAAGGACCCATCAACTTAAACTTTGATAACAT
* * *
19501 TTTGGGCGTGACCTAATATGTTGATAATATTGATAACAAATTAAGTAATCAACCTATTTTGTTAT
66 TTTAGGCGTGACATAATATGTTGATAATATTGATAACAAATCAAGTAATCAACCTATTTTGTTAT
* * *
19566 CGTCGA-ATTTCTAAGG-TCTCATTAGCTTTAAAAAGACGTTACCTACTACATTAAATAAACGCT
131 CGTC-ATATTTCTAAGGCTC-CATCAACTTTAAAAAGACGATACCTACTACATTAAATAAACGCT
*
19629 ACT-TGTTATGTTATTATGGTTTATAATGTTTCC
194 A-TATGTTATGTTATTATGGTTGATAATGTTTCC
* * * ** *
19662 AGTAATTAGCCTATTTTGTTATCGTCGGATTTCTAAGGACCTGTCAACTTAAACTTTGGTAACAT
1 AGTAATTAACCTATTTCGTTATCGTCAGATTTCTAAGGACCCATCAACTTAAACTTTGATAACAT
*
19727 TTTAGGCGCT-ACATAATATGTTGATAATATTGATAACAAATCAAGTAATTAACCTATTTTGTTA
66 TTTAGGCG-TGACATAATATGTTGATAATATTGATAACAAATCAAGTAATCAACCTATTTTGTTA
* * * * * * *
19791 TCGTCATATTTTTAAGGCTCCATCAACTTTAAAATGGCGATACCTATTACGTTACATAAGCGCTA
130 TCGTCATATTTCTAAGGCTCCATCAACTTTAAAAAGACGATACCTACTACATTAAATAAACGCTA
*
19856 TATGTTATGTTATTATGGTTGATAATGTTTCT
195 TATGTTATGTTATTATGGTTGATAATGTTTCC
19888 AGTAATTAACC
1 AGTAATTAACC
19899 GGTTATGTTA
Statistics
Matches: 204, Mismatches: 29, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
225 2 0.01
226 199 0.98
227 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (226 bp):
AGTAATTAACCTATTTCGTTATCGTCAGATTTCTAAGGACCCATCAACTTAAACTTTGATAACAT
TTTAGGCGTGACATAATATGTTGATAATATTGATAACAAATCAAGTAATCAACCTATTTTGTTAT
CGTCATATTTCTAAGGCTCCATCAACTTTAAAAAGACGATACCTACTACATTAAATAAACGCTAT
ATGTTATGTTATTATGGTTGATAATGTTTCC
Found at i:25645 original size:4 final size:4
Alignment explanation
Indices: 25636--25704 Score: 79
Period size: 4 Copynumber: 16.8 Consensus size: 4
25626 CCGTTATATT
*
25636 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTGT- TTT- TTTGT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA TTT-A
25684 TTTA TTTA TTTTA TTTTA TTT
1 TTTA TTTA -TTTA -TTTA TTT
25705 CAATTAAGCA
Statistics
Matches: 60, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
3 4 0.07
4 43 0.72
5 13 0.22
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:30272 original size:14 final size:15
Alignment explanation
Indices: 30247--30285 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
30237 AATGTCTTTT
* *
30247 AAAATAATTTTAAGA
1 AAAAAAATTTAAAGA
30262 AAAAAAATTTAAAGA
1 AAAAAAATTTAAAGA
*
30277 CAAAAAATT
1 AAAAAAATT
30286 AGTCTGCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (15 bp):
AAAAAAATTTAAAGA
Found at i:35457 original size:9 final size:10
Alignment explanation
Indices: 35437--35498 Score: 76
Period size: 11 Copynumber: 6.3 Consensus size: 10
35427 TATAAATAAG
35437 AAAAAA-AG-
1 AAAAAACAGA
*
35445 AAAAAACATA
1 AAAAAACAGA
35455 AAAAAACAGAA
1 AAAAAACAG-A
35466 AAAAAACAGAA
1 AAAAAACAG-A
35477 AAAAAACAGA
1 AAAAAACAGA
35487 AAAAAA-AGA
1 AAAAAACAGA
35496 AAA
1 AAA
35499 CGAAGAAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
8 6 0.12
9 7 0.14
10 15 0.31
11 21 0.43
ACGTcount: A:0.84, C:0.06, G:0.08, T:0.02
Consensus pattern (10 bp):
AAAAAACAGA
Found at i:35468 original size:11 final size:11
Alignment explanation
Indices: 35445--35493 Score: 82
Period size: 11 Copynumber: 4.5 Consensus size: 11
35435 AGAAAAAAAG
*
35445 AAAAAACA-TA
1 AAAAAACAGAA
35455 AAAAAACAGAA
1 AAAAAACAGAA
35466 AAAAAACAGAA
1 AAAAAACAGAA
35477 AAAAAACAGAA
1 AAAAAACAGAA
35488 AAAAAA
1 AAAAAA
35494 GAAAACGAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
10 8 0.22
11 29 0.78
ACGTcount: A:0.84, C:0.08, G:0.06, T:0.02
Consensus pattern (11 bp):
AAAAAACAGAA
Found at i:35510 original size:16 final size:16
Alignment explanation
Indices: 35473--35530 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
35463 GAAAAAAAAC
*
35473 AGAAAAAAAACAGAA-A
1 AGAAAGAAAAC-GAAGA
*
35489 AAAAAGAAAACGAAGA
1 AGAAAGAAAACGAAGA
*
35505 AGAAAGAAAACGGAGA
1 AGAAAGAAAACGAAGA
35521 AGAAAGAAAA
1 AGAAAGAAAA
35531 ATATAGAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
15 3 0.08
16 34 0.92
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (16 bp):
AGAAAGAAAACGAAGA
Found at i:35568 original size:11 final size:10
Alignment explanation
Indices: 35437--35560 Score: 74
Period size: 10 Copynumber: 11.9 Consensus size: 10
35427 TATAAATAAG
35437 AAAAAAAG-A
1 AAAAAAAGAA
* *
35446 AAAAACATAA
1 AAAAAAAGAA
*
35456 AAAAACAGAA
1 AAAAAAAGAA
35466 AAAAAACAGAA
1 AAAAAA-AGAA
35477 AAAAAACAG-A
1 AAAAAA-AGAA
35487 AAAAAAAGAA
1 AAAAAAAGAA
*
35497 AACGAAGAAGAA
1 AA--AAAAAGAA
* * *
35509 AGAAAACGGA
1 AAAAAAAGAA
* *
35519 GAAGAAAGAA
1 AAAAAAAGAA
35529 AAATATAGAA-AA
1 AAA-A-A-AAGAA
35541 AAAAAAAGAA
1 AAAAAAAGAA
35551 AAGAAAAAGA
1 AA-AAAAAGA
35561 GGAAAAAATG
Statistics
Matches: 89, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
9 10 0.11
10 42 0.47
11 21 0.24
12 14 0.16
13 2 0.02
ACGTcount: A:0.78, C:0.05, G:0.15, T:0.02
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:41318 original size:45 final size:45
Alignment explanation
Indices: 41165--41508 Score: 525
Period size: 45 Copynumber: 7.6 Consensus size: 45
41155 GTAAGCATGC
* * *
41165 AAATAAGCTTATGAGCTTAT-GACAT-AATGGCAATTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGA-ATAAATGGTAAGTATATTAGTA
* *
41209 AAATAAGCTTACGAGCTAATGGAATAAATGCTAAGTATATTAGTAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGT-A
*
41255 AAATAAGATTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
*
41300 AAATAAGCTTACAAGCTTATGGAATAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
41345 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATT-GATA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAG-TA
*
41390 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
* *
41435 AAATAAGCTTGCGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
*
41480 AAATAAGCTTACAAGCTTATAGG-ATAAAT
1 AAATAAGCTTACGAGCTTAT-GGAATAAAT
41509 TATAAGAAAT
Statistics
Matches: 280, Mismatches: 14, Indels: 11
0.92 0.05 0.04
Matches are distributed among these distances:
44 21 0.08
45 214 0.76
46 45 0.16
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTAGTA
Found at i:41440 original size:24 final size:24
Alignment explanation
Indices: 41412--41485 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
41402 GAGCTTATGG
41412 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
* * **
41436 AATAAGCTTGCGAGCT-TA-TGG---
1 AATAA-ATGGTAAG-TATATTGGTAA
41457 AATAAATGGTAAGTATATTGGTAA
1 AATAAATGGTAAGTATATTGGTAA
41481 AATAA
1 AATAA
41486 GCTTACAAGC
Statistics
Matches: 35, Mismatches: 8, Indels: 14
0.61 0.14 0.25
Matches are distributed among these distances:
19 1 0.03
20 6 0.17
21 8 0.23
24 13 0.37
25 6 0.17
26 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.22, T:0.31
Consensus pattern (24 bp):
AATAAATGGTAAGTATATTGGTAA
Found at i:42046 original size:12 final size:12
Alignment explanation
Indices: 42029--42070 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
42019 CACACTATCC
42029 ACTGTTCATGGT
1 ACTGTTCATGGT
*
42041 ACTGTTTAT--T
1 ACTGTTCATGGT
42051 ACTGTTCATGGT
1 ACTGTTCATGGT
*
42063 ACTATTCA
1 ACTGTTCA
42071 AAAAAAATCT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (12 bp):
ACTGTTCATGGT
Found at i:42829 original size:22 final size:22
Alignment explanation
Indices: 42804--42847 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
42794 TTAAACCACT
42804 ATAAACAAGTTTGTCCGTACTG
1 ATAAACAAGTTTGTCCGTACTG
42826 ATAAACAAGTTTGTCCGTACTG
1 ATAAACAAGTTTGTCCGTACTG
42848 TAATGGAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (22 bp):
ATAAACAAGTTTGTCCGTACTG
Found at i:45345 original size:37 final size:36
Alignment explanation
Indices: 45286--45399 Score: 178
Period size: 35 Copynumber: 3.2 Consensus size: 36
45276 ATCCCATTAT
* *
45286 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
45322 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
45358 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
45393 CATTTTT
1 CATTTTT
45400 TTAAAGTTGG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
35 35 0.49
36 17 0.24
37 20 0.28
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.32
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:45361 original size:21 final size:21
Alignment explanation
Indices: 45337--45397 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
45327 TTCAAAGAAA
45337 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
*
45358 CATTT-TCAAA----G-AAA-
1 CATTTACCAAACTTTGAAAAC
45372 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAC
45393 CATTT
1 CATTT
45398 TTTTAAAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAC
Found at i:49941 original size:37 final size:36
Alignment explanation
Indices: 49899--50007 Score: 148
Period size: 35 Copynumber: 3.0 Consensus size: 36
49889 ATTTTTTAAC
*
49899 AAACATCTACCAAACTTTGAAAAACTATTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAAC-ATTTTTCAAAG
* *
49936 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAT
1 AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
* *
49971 AAATATTTACCAAACTTTGAAAATCATTTTTTCAAAG
1 AAACATTTACCAAACTTTGAAAAACA-TTTTTCAAAG
50008 TTGGTTACCA
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
35 32 0.50
36 1 0.02
37 31 0.48
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (36 bp):
AAACATTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:49999 original size:21 final size:21
Alignment explanation
Indices: 49939--49999 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
49929 TTCAAAGAAA
*
49939 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAACTTTGAAAAT
*
49960 CATTT-TCAAA---T--AAAT
1 CATTTACCAAACTTTGAAAAT
49975 -ATTTACCAAACTTTGAAAAT
1 CATTTACCAAACTTTGAAAAT
49995 CATTT
1 CATTT
50000 TTTCAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 14
0.64 0.06 0.30
Matches are distributed among these distances:
14 4 0.13
15 7 0.23
17 1 0.03
18 1 0.03
20 8 0.27
21 9 0.30
ACGTcount: A:0.43, C:0.18, G:0.03, T:0.36
Consensus pattern (21 bp):
CATTTACCAAACTTTGAAAAT
Found at i:50693 original size:60 final size:60
Alignment explanation
Indices: 50627--50761 Score: 141
Period size: 60 Copynumber: 2.2 Consensus size: 60
50617 AGTTTTGAAT
* * **
50627 ATTCTAATTTAATCTCC-AATCTA-TGTCTCTCATTT-TAAATTAGTCTTTAAACTTTTAAAC
1 ATTCTAATTTAATC-CCTAAACTATTG-CCCT-ATTTCTAAATTAGTCCCTAAACTTTTAAAC
* * *
50687 ATTCTAATTTCATCCCTAAACTATTGCCCTATTTCTAAATTAGTCCCTAAACTTTTGAAT
1 ATTCTAATTTAATCCCTAAACTATTGCCCTATTTCTAAATTAGTCCCTAAACTTTTAAAC
* *
50747 ATTCCAATTTTATCC
1 ATTCTAATTTAATCC
50762 TCAATTCATC
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
59 6 0.10
60 55 0.87
61 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.04, T:0.44
Consensus pattern (60 bp):
ATTCTAATTTAATCCCTAAACTATTGCCCTATTTCTAAATTAGTCCCTAAACTTTTAAAC
Found at i:50978 original size:60 final size:62
Alignment explanation
Indices: 50925--51042 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 62
50915 AAAGTTTGGG
* *
50925 GAAAAATTTAGAATGA-ACGTTATAGTTTAGGGATGAAATT-GAA-ATGTTCAAAAGTTTACA
1 GAAAAATTTAGAATGATA-GTCATAATTTAGGGATGAAATTAGAATATGTTCAAAAGTTTACA
**
50985 GACGAATTTAGAATGATAGTCATAATTTAGGGATGAAATTAGAATAT-TT-AAAAGTTTA
1 GAAAAATTTAGAATGATAGTCATAATTTAGGGATGAAATTAGAATATGTTCAAAAGTTTA
51043 AGATTAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
60 43 0.84
61 6 0.12
62 2 0.04
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.33
Consensus pattern (62 bp):
GAAAAATTTAGAATGATAGTCATAATTTAGGGATGAAATTAGAATATGTTCAAAAGTTTACA
Found at i:66713 original size:29 final size:30
Alignment explanation
Indices: 66680--66750 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
66670 ATTCTCTTAA
*
66680 TTAGTGACCAAAACATAAATTT-TGAAAGT
1 TTAGTGACCAAAACATAAATTTAAGAAAGT
* * ** *
66709 TTAGTGGCTAAATTATAAATTTAAGAAATT
1 TTAGTGACCAAAACATAAATTTAAGAAAGT
*
66739 TTAGGGACCAAA
1 TTAGTGACCAAA
66751 GTGGTAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.32
Consensus pattern (30 bp):
TTAGTGACCAAAACATAAATTTAAGAAAGT
Found at i:69916 original size:22 final size:20
Alignment explanation
Indices: 69865--69918 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
69855 GAATTAAACT
*
69865 AGTATCGATACTCTAGTATG
1 AGTATCGATACTATAGTATG
*
69885 AGTATTGATACTATGATGT-TG
1 AGTATCGATACTAT-A-GTATG
69906 AGGTATCGATACT
1 A-GTATCGATACT
69919 TGACTGAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (20 bp):
AGTATCGATACTATAGTATG
Found at i:71384 original size:5 final size:5
Alignment explanation
Indices: 71351--71428 Score: 68
Period size: 5 Copynumber: 15.0 Consensus size: 5
71341 ACGTCAATAC
* * * **
71351 TAAAA TTAAA TAAAA CAGAATA AAAAA TAAAA T-AAA TAAAA TAAAA TATTA
1 TAAAA TAAAA TAAAA TA-AA-A TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
71402 TAAATA TAAAA TAAAA TAAAAA TAAAA
1 TAAA-A TAAAA TAAAA T-AAAA TAAAA
71429 ATATTATTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
4 4 0.07
5 39 0.66
6 14 0.24
7 2 0.03
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:71390 original size:16 final size:17
Alignment explanation
Indices: 71358--71428 Score: 64
Period size: 16 Copynumber: 4.5 Consensus size: 17
71348 TACTAAAATT
*
71358 AAATAAAACAGAATA-AA
1 AAATAAAATA-AATATAA
71375 AAATAAAAT-AA-AT-A
1 AAATAAAATAAATATAA
*
71389 AAATAAAAT-ATTATAA
1 AAATAAAATAAATATAA
*
71405 ATATAAAATAAA-ATAA
1 AAATAAAATAAATATAA
71421 AAATAAAA
1 AAATAAAA
71429 ATATTATTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
14 12 0.27
15 4 0.09
16 20 0.44
17 9 0.20
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.21
Consensus pattern (17 bp):
AAATAAAATAAATATAA
Found at i:71393 original size:31 final size:31
Alignment explanation
Indices: 71351--71428 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
71341 ACGTCAATAC
*
71351 TAAAATTAAATAAAACAGAATAAAAAATAAAA
1 TAAAATAAAATAAAACAGAAT-AAAAATAAAA
* ** *
71383 T-AAATAAAATAAAATATTATAAATATAAAA
1 TAAAATAAAATAAAACAGAATAAAAATAAAA
71413 TAAAATAAAAATAAAA
1 TAAAAT-AAAATAAAA
71429 ATATTATTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
30 10 0.26
31 19 0.49
32 10 0.26
ACGTcount: A:0.74, C:0.01, G:0.01, T:0.23
Consensus pattern (31 bp):
TAAAATAAAATAAAACAGAATAAAAATAAAA
Found at i:71445 original size:31 final size:34
Alignment explanation
Indices: 71369--71435 Score: 100
Period size: 35 Copynumber: 2.0 Consensus size: 34
71359 AATAAAACAG
*
71369 AATAAAAAATAAAATAAATAAAATAAAATATTATA
1 AATATAAAATAAAATAAA-AAAATAAAATATTATA
*
71404 AATATAAAATAAAATAAAAATA-AAAATATTAT
1 AATATAAAATAAAATAAAAAAATAAAATATTAT
71436 TTAATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 10 0.33
34 3 0.10
35 17 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (34 bp):
AATATAAAATAAAATAAAAAAATAAAATATTATA
Found at i:72903 original size:21 final size:21
Alignment explanation
Indices: 72879--72918 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
72869 TTTTTACTAA
* *
72879 TTTGGTTGGATTTGGTGACTG
1 TTTGGCTGGATTTGATGACTG
72900 TTTGGCTGGATTTGATGAC
1 TTTGGCTGGATTTGATGAC
72919 GACGGCAGCT
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:0.12, C:0.07, G:0.35, T:0.45
Consensus pattern (21 bp):
TTTGGCTGGATTTGATGACTG
Found at i:73266 original size:3 final size:3
Alignment explanation
Indices: 73251--73376 Score: 135
Period size: 3 Copynumber: 39.7 Consensus size: 3
73241 TTATTTATAC
* * *
73251 TAA TAA TAG TAA TAA TAA TAA TAA TTAA TAA TAA TAA TAA TTAC TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA -TAA TAA
* *
73298 TAA TAA TAA TAA TAA TTAG TAA TAA TAA TTAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
*
73345 TAA GTAA TAT TAA TTAA TAA TAA TAA TTAA TA
1 TAA -TAA TAA TAA -TAA TAA TAA TAA -TAA TA
73377 TGTACAATTA
Statistics
Matches: 105, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
3 86 0.82
4 19 0.18
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:73281 original size:13 final size:13
Alignment explanation
Indices: 73251--73376 Score: 128
Period size: 13 Copynumber: 10.4 Consensus size: 13
73241 TTATTTATAC
*
73251 TAATAATAGTAA-
1 TAATAATAATAAT
73263 TAATAATAATAAT
1 TAATAATAATAAT
73276 TAATAATAATAA-
1 TAATAATAATAAT
* *
73288 TAATTACTATTAA-
1 TAA-TAATAATAAT
73301 TAATAATAATAAT
1 TAATAATAATAAT
*
73314 TAGTAATAATAAT
1 TAATAATAATAAT
73327 TAATAAT--T-A-
1 TAATAATAATAAT
*
73336 TAATAATAATAAG
1 TAATAATAATAAT
73349 TAAT-AT--TAAT
1 TAATAATAATAAT
73359 TAATAATAATAAT
1 TAATAATAATAAT
73372 TAATA
1 TAATA
73377 TGTACAATTA
Statistics
Matches: 96, Mismatches: 8, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
9 7 0.07
10 8 0.08
11 4 0.04
12 24 0.25
13 53 0.55
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:73281 original size:16 final size:16
Alignment explanation
Indices: 73251--73371 Score: 140
Period size: 16 Copynumber: 7.4 Consensus size: 16
73241 TTATTTATAC
*
73251 TAATAAT-AGTAATAA
1 TAATAATAATTAATAA
73266 TAATAATAATTAATAA
1 TAATAATAATTAATAA
73282 TAATAATAATTACTATTAA
1 TAATAATAATTA--A-TAA
*
73301 TAATAATAA-TAATTAG
1 TAATAATAATTAA-TAA
73317 TAATAATAATTAATAA
1 TAATAATAATTAATAA
*
73333 TTATAATAA-TAATAA
1 TAATAATAATTAATAA
*
73348 GTAATATTAATTAATAA
1 -TAATAATAATTAATAA
73365 TAATAAT
1 TAATAAT
73372 TAATATGTAC
Statistics
Matches: 92, Mismatches: 7, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
15 13 0.14
16 55 0.60
17 9 0.10
18 3 0.03
19 12 0.13
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (16 bp):
TAATAATAATTAATAA
Found at i:73388 original size:26 final size:23
Alignment explanation
Indices: 73251--73377 Score: 122
Period size: 22 Copynumber: 5.7 Consensus size: 23
73241 TTATTTATAC
*
73251 TAATAAT-AGTAATAATAA-TAA
1 TAATAATAAGTAATATTAATTAA
* *
73272 TAATTAATAA-TAATAATAATTAC
1 TAA-TAATAAGTAATATTAATTAA
* * *
73295 TATTAATAA-TAATAATAATTAG
1 TAATAATAAGTAATATTAATTAA
*
73317 TAATAATAATTAATAATT-A-TAA
1 TAATAATAAGTAAT-ATTAATTAA
73339 TAATAATAAGTAATATTAATTAA
1 TAATAATAAGTAATATTAATTAA
*
73362 TAATAATAATTAATAT
1 TAATAATAAGTAATAT
73378 GTACAATTAA
Statistics
Matches: 91, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.07
22 55 0.60
23 28 0.31
24 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.39
Consensus pattern (23 bp):
TAATAATAAGTAATATTAATTAA
Found at i:75115 original size:10 final size:10
Alignment explanation
Indices: 75082--75116 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
75072 TATTTTATTA
* *
75082 TTTTATTCTA
1 TTTTTTTCTT
75092 TTTTTTTCTT
1 TTTTTTTCTT
75102 TTTTTTTCTT
1 TTTTTTTCTT
75112 TTTTT
1 TTTTT
75117 AGGTTTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTCTT
Done.