Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007040.1 Hibiscus syriacus cultivar Beakdansim tig00018249_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: 68956
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:6564 original size:23 final size:23
Alignment explanation
Indices: 6526--6586 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
6516 AATTAACCAC
6526 TACCTATT--ATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
6547 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
6570 TACCTATTACATCATAT
1 TACCTATTACATTATAT
6587 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.24
23 26 0.76
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:7037 original size:39 final size:39
Alignment explanation
Indices: 6983--7108 Score: 234
Period size: 39 Copynumber: 3.2 Consensus size: 39
6973 TCAAGTTGTA
6983 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
7022 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
* *
7061 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
7100 GATTTTGAT
1 GATTTTGAT
7109 GAGCATCGGA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.17, C:0.13, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
Found at i:7391 original size:18 final size:18
Alignment explanation
Indices: 7368--7404 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
7358 CGAAATATAT
7368 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
7386 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
7404 A
1 A
7405 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:7677 original size:25 final size:25
Alignment explanation
Indices: 7649--7699 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
7639 TTAATCCAAA
*
7649 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
7674 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
7699 T
1 T
7700 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:8027 original size:23 final size:23
Alignment explanation
Indices: 7974--8036 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
7964 CAATATACCA
7974 CTACCTATTACATTA-ATAAACG
1 CTACCTATTACATTATATAAACG
* * **
7996 ATACATATTACATTATATAAGGG
1 CTACCTATTACATTATATAAACG
*
8019 CTACCTATTACATCATAT
1 CTACCTATTACATTATAT
8037 GTTTACCTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
22 13 0.39
23 20 0.61
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
CTACCTATTACATTATATAAACG
Found at i:8430 original size:23 final size:23
Alignment explanation
Indices: 8400--8462 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
8390 AATATACCAC
8400 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
8423 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
8446 TACCTATTACATCATAT
1 TACCTATTACATTATAT
8463 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:10327 original size:33 final size:33
Alignment explanation
Indices: 10290--10355 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
10280 CATCTTAATA
*
10290 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
10323 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
10356 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:10429 original size:21 final size:21
Alignment explanation
Indices: 10389--10453 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
10379 CCCCTTATTC
* *
10389 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
10410 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
10431 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
10452 CT
1 CT
10454 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.40
Consensus pattern (21 bp):
CTCTCGAGTTTCTCTTCGACT
Found at i:12702 original size:16 final size:17
Alignment explanation
Indices: 12681--12721 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
12671 ATATATCCGG
12681 TATCAT-TTACCGGTTT
1 TATCATGTTACCGGTTT
12697 TATCATTTGTTACCGGTTT
1 TATCA--TGTTACCGGTTT
12716 TATCAT
1 TATCAT
12722 ATTTTTACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 1 0.05
19 15 0.68
ACGTcount: A:0.20, C:0.17, G:0.12, T:0.51
Consensus pattern (17 bp):
TATCATGTTACCGGTTT
Found at i:12739 original size:20 final size:19
Alignment explanation
Indices: 12686--12730 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
12676 TCCGGTATCA
12686 TTTACCGGTTTTATCATTT
1 TTTACCGGTTTTATCATTT
*
12705 GTTACCGGTTTTATCATATT
1 TTTACCGGTTTTATCAT-TT
12725 TTTACC
1 TTTACC
12731 TGTTATATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:13355 original size:225 final size:225
Alignment explanation
Indices: 12960--13404 Score: 743
Period size: 225 Copynumber: 2.0 Consensus size: 225
12950 TTAAAACTGC
12960 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
13025 TTAATTTAATAATTTAATTTACACAAAATTATATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAATATATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
13090 TTAGAATTTAAATTTAACAATATTAACCAAA-TATAAT-AATATGTTTTCAACAGTGAAATAAGT
131 TTAGAATTTAAATTTAACAATATTAACCAAAGAATAATAAATATATTTTC-ACAGTGAAATAAGT
*
13153 ATGGACACTTTTATAAAAATGATATATACTT
195 ATGGACACTTTTATAAAAAGGATATATACTT
* *
13184 TTTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCTCCTACAAT
1 TTTT-AAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAAT
*
13249 ATTAATTTAATAATTTCATTTACACAAAAA-ATTATTTGATTGTTTTGATATTTTATAAAATATT
65 ATTAATTTAATAATTTAATTTACACAAAAATA-TATTTGATTGTTTTGATATTTTATAAAATATT
* *
13313 ATTTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATA
129 ATTTAGAATTTAAATTTAACAATATTAACCAAAG--AATAATAAATATATTTTCACAGTGAAATA
13378 AGTATGGACACTTTTATAAAAAGGATA
192 AGTATGGACACTTTTATAAAAAGGATA
13405 GATAATTTAC
Statistics
Matches: 206, Mismatches: 9, Indels: 8
0.92 0.04 0.04
Matches are distributed among these distances:
224 5 0.02
225 149 0.72
228 42 0.20
229 10 0.05
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (225 bp):
TTTTAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAATATATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGAATAATAAATATATTTTCACAGTGAAATAAGTA
TGGACACTTTTATAAAAAGGATATATACTT
Found at i:16363 original size:23 final size:24
Alignment explanation
Indices: 16311--16363 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
16301 TCTAGATCAG
*
16311 ATTTGCTTTGTAAATGGGCCTCCA
1 ATTTGTTTTGTAAATGGGCCTCCA
* **
16335 ACTTGTTTTGTATTTGGGCC-CCA
1 ATTTGTTTTGTAAATGGGCCTCCA
16358 ATTTGT
1 ATTTGT
16364 ATTATTTAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (24 bp):
ATTTGTTTTGTAAATGGGCCTCCA
Found at i:16383 original size:3 final size:3
Alignment explanation
Indices: 16377--16419 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
16367 ATTTAGGCTT
* *
16377 ATA ATA AT- TTA ATA ATA ATA ATA ATA ATA AT- ATA ATT ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16420 TAACTAGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 3 0.09
3 31 0.91
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:16419 original size:11 final size:11
Alignment explanation
Indices: 16377--16422 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
16367 ATTTAGGCTT
*
16377 ATAATAATTTA
1 ATAATAATATA
16388 ATAATAATAATA
1 ATAATAAT-ATA
16400 ATAATAATATA
1 ATAATAATATA
*
16411 ATTATAATATA
1 ATAATAATATA
16422 A
1 A
16423 CTAGGAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATAATAATATA
Found at i:18164 original size:27 final size:28
Alignment explanation
Indices: 18134--18189 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
18124 TTAAAAAATA
18134 TATATAATATATA-ATTTTGAAAACATT
1 TATATAATATATAGATTTTGAAAACATT
* * *
18161 TATATATTATATAGTTTTTTAAAACATT
1 TATATAATATATAGATTTTGAAAACATT
18189 T
1 T
18190 TGAAAACGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (28 bp):
TATATAATATATAGATTTTGAAAACATT
Found at i:18209 original size:37 final size:37
Alignment explanation
Indices: 18147--18362 Score: 221
Period size: 37 Copynumber: 5.8 Consensus size: 37
18137 ATAATATATA
*
18147 ATTTTGAAAACATTTATATATTATATAGTTTTTTAAAAC
1 ATTTTGAAAAC--TTATATAATATATAGTTTTTTAAAAC
* * *
18186 ATTTTGAAAACGTATATAGTATATAGTTTTTTAAAAT
1 ATTTTGAAAACTTATATAATATATAGTTTTTTAAAAC
* * *
18223 ATTTATGAAAAATTATATATTATATAG-TTTTAAAAAC
1 ATTT-TGAAAACTTATATAATATATAGTTTTTTAAAAC
* * *
18260 ATATTTGAAAAATTATATAATATATAG-TTTTAAAAAT
1 AT-TTTGAAAACTTATATAATATATAGTTTTTTAAAAC
18297 ATTTTTTTGGAAAACTTATAT-A-ATAT--TTTTTTAAAAC
1 A---TTTT-GAAAACTTATATAATATATAGTTTTTTAAAAC
18334 ATTTTGAAAAC-TATATAATATATAGTTTT
1 ATTTTGAAAACTTATATAATATATAGTTTT
18363 AAAAACTTTT
Statistics
Matches: 153, Mismatches: 13, Indels: 25
0.80 0.07 0.13
Matches are distributed among these distances:
32 5 0.03
33 7 0.05
34 8 0.05
36 4 0.03
37 77 0.50
38 25 0.16
39 15 0.10
40 12 0.08
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (37 bp):
ATTTTGAAAACTTATATAATATATAGTTTTTTAAAAC
Found at i:18228 original size:65 final size:65
Alignment explanation
Indices: 18093--18215 Score: 167
Period size: 64 Copynumber: 1.9 Consensus size: 65
18083 ATTTTCGAAA
* *
18093 ATTTATATATTATACAGTTTTTTGAAAATATTTAAAAAATATATATAATATATAATTTTGAAAAC
1 ATTTATATATTATACAGTTTTTTGAAAACATTTAAAAAACATATATAATATATAATTTTGAAAAC
* ** * * *
18158 ATTTATATATTATATAGTTTTTT-AAAACATTTTGAAAACGTATATAGTATATAGTTTT
1 ATTTATATATTATACAGTTTTTTGAAAACATTTAAAAAACATATATAATATATAATTTT
18216 TTAAAATATT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
64 28 0.56
65 22 0.44
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (65 bp):
ATTTATATATTATACAGTTTTTTGAAAACATTTAAAAAACATATATAATATATAATTTTGAAAAC
Found at i:18239 original size:75 final size:73
Alignment explanation
Indices: 18147--18367 Score: 258
Period size: 75 Copynumber: 3.0 Consensus size: 73
18137 ATAATATATA
*
18147 ATTTTGAAAACATTTATATATTATATAGTTTTTTAAAACATTTTGAAAACGTATATAGTATATAG
1 ATTTTGAAAA-A-TTATATATTATATAGTTTTTTAAAACATTTTGAAAAC-TATATAATATATAG
*
18212 TTTTTTAAAAT
63 TTTTTAAAAAT
* *
18223 ATTTATGAAAAATTATATATTATATAG-TTTTAAAAACATATTTGAAAAATTATATAATATATAG
1 ATTT-TGAAAAATTATATATTATATAGTTTTTTAAAACAT-TTTG-AAAACTATATAATATATAG
18287 -TTTTAAAAAT
63 TTTTTAAAAAT
*
18297 ATTTTTTTGGAAAACTTATATA--ATAT--TTTTTTAAAACATTTTGAAAACTATATAATATATA
1 A---TTTT-GAAAAATTATATATTATATAGTTTTTTAAAACATTTTGAAAACTATATAATATATA
18358 G-TTTTAAAAA
62 GTTTTTAAAAA
18368 CTTTTTAAAT
Statistics
Matches: 130, Mismatches: 7, Indels: 20
0.83 0.04 0.13
Matches are distributed among these distances:
72 27 0.21
73 4 0.03
74 32 0.25
75 36 0.28
76 10 0.08
77 21 0.16
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (73 bp):
ATTTTGAAAAATTATATATTATATAGTTTTTTAAAACATTTTGAAAACTATATAATATATAGTTT
TTAAAAAT
Found at i:18382 original size:30 final size:32
Alignment explanation
Indices: 18346--18426 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 32
18336 TTTGAAAACT
* *
18346 ATATAATATATAGTTTTAAAAA-CTTTTT-AA
1 ATATAATATATAGTTTAAAAAATATTTTTGAA
18376 ATATAATATATAGTTTAAAAAATATTTTTGAA
1 ATATAATATATAGTTTAAAAAATATTTTTGAA
18408 ATATATATTATATAGTTTA
1 ATATA-A-TATATAGTTTA
18427 TATCATGTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 21 0.47
31 5 0.11
32 7 0.16
33 1 0.02
34 11 0.24
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (32 bp):
ATATAATATATAGTTTAAAAAATATTTTTGAA
Found at i:18386 original size:37 final size:35
Alignment explanation
Indices: 18161--18425 Score: 129
Period size: 37 Copynumber: 7.5 Consensus size: 35
18151 TGAAAACATT
* * * **
18161 TATATATTATATAGTTTTTTAAAACATTTTGAAAACG
1 TATATAATATATAG-TTTTAAAAAC-TTTTTAAAAAA
* * *
18198 TATATAGTATATAGTTTTTTAAAATA-TTTATGAAAAAT
1 TATATAATATATAG--TTTTAAAA-ACTTT-TTAAAAAA
* * *
18236 TATATATTATATAGTTTTAAAAACATATTTGAAAAAT
1 TATATAATATATAGTTTTAAAAAC-T-TTTTAAAAAA
* **
18273 TATATAATATATAGTTTTAAAAATATTTTTTTGGAAAACT
1 TATATAATATATAGTTTT-AAAA-A-CTTTTT--AAAAAA
* * * *
18313 TATATAATAT-T--TTTTTAAAACATTTTGAAAAC
1 TATATAATATATAGTTTTAAAAACTTTTTAAAAAA
18345 TATATAATATATAGTTTTAAAAACTTTTT----AA
1 TATATAATATATAGTTTTAAAAACTTTTTAAAAAA
* **
18376 -ATATAATATATAG-TTTAAAAAATATTTT-TGAAA
1 TATATAATATATAGTTTTAAAAACT-TTTTAAAAAA
*
18409 TATATATTATATAGTTT
1 TATATAATATATAGTTT
18426 ATATCATGTT
Statistics
Matches: 188, Mismatches: 20, Indels: 42
0.75 0.08 0.17
Matches are distributed among these distances:
29 9 0.05
30 17 0.09
31 1 0.01
32 13 0.07
33 3 0.02
34 16 0.09
35 17 0.09
36 11 0.06
37 46 0.24
38 36 0.19
39 4 0.02
40 15 0.08
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (35 bp):
TATATAATATATAGTTTTAAAAACTTTTTAAAAAA
Found at i:19723 original size:19 final size:20
Alignment explanation
Indices: 19675--19722 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
19665 CTTTTTTTTA
19675 TATTTCTTTAAAAACATCTTT
1 TATTT-TTTAAAAACATCTTT
19696 TATTTTTTAAAAACATCTTT
1 TATTTTTTAAAAACATCTTT
19716 TATTTTT
1 TATTTTT
19723 ACTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTTTTAAAAACATCTTT
Found at i:19851 original size:4 final size:4
Alignment explanation
Indices: 19834--19907 Score: 50
Period size: 4 Copynumber: 19.2 Consensus size: 4
19824 TTCCCTTTCA
* * *
19834 ATTT ATTTT CTTT ATTT ATTT GTTT ATTT ATTT ATTGT TTTT A-TT A-TT
1 ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT
* *
19882 ATTT -TCT -TTT ATTT -TTG ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT A
19908 AATGGTTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
3 12 0.22
4 37 0.67
5 6 0.11
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:23627 original size:20 final size:20
Alignment explanation
Indices: 23581--23619 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
23571 TGTAAATATT
23581 AAATTTTAAAAATATATTCA
1 AAATTTTAAAAATATATTCA
23601 AAATTTTAAAAA-ATATTCA
1 AAATTTTAAAAATATATTCA
23620 TTAATTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATTTTAAAAATATATTCA
Found at i:24313 original size:8 final size:8
Alignment explanation
Indices: 24291--24329 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
24281 TTTAAATTTA
24291 ATTATATAT
1 ATTATA-AT
24300 ATTTATAAT
1 A-TTATAAT
24309 ATTATAAT
1 ATTATAAT
*
24317 ATTATGAT
1 ATTATAAT
24325 ATTAT
1 ATTAT
24330 TTTATTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 19 0.68
9 4 0.14
10 5 0.18
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (8 bp):
ATTATAAT
Found at i:26079 original size:50 final size:51
Alignment explanation
Indices: 25982--26111 Score: 173
Period size: 50 Copynumber: 2.6 Consensus size: 51
25972 CACCCTTAGC
*
25982 AGGAAAGCGC-CCCCCTGAACCGCGCTATATGCTGATTTGGCGTCACGTGG
1 AGGAAAGCGCGCCCCCTGAACCGCGCTATATGCTGATCTGGCGTCACGTGG
26032 AGGAAAGCGCGCCCCCTGAACCGCGCTATATGCTGA-CTGG-GTACACGTGG
1 AGGAAAGCGCGCCCCCTGAACCGCGCTATATGCTGATCTGGCGT-CACGTGG
26082 -GGTATAA-CGCGCCCCCTGATA-CGCGCTATA
1 AGG-A-AAGCGCGCCCCCTGA-ACCGCGCTATA
26112 CATCACGTAG
Statistics
Matches: 74, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
49 4 0.05
50 42 0.57
51 28 0.38
ACGTcount: A:0.22, C:0.31, G:0.29, T:0.18
Consensus pattern (51 bp):
AGGAAAGCGCGCCCCCTGAACCGCGCTATATGCTGATCTGGCGTCACGTGG
Found at i:28548 original size:12 final size:10
Alignment explanation
Indices: 28534--28574 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
28524 TATCTTAAAA
*
28534 GAGAGTATTT
1 GAGAGAATTT
28544 GAGAGAAATTT
1 GAGAG-AATTT
28555 -AGAGAATTT
1 GAGAGAATTT
28564 GAGAGAATTT
1 GAGAGAATTT
28574 G
1 G
28575 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:28749 original size:50 final size:50
Alignment explanation
Indices: 28695--28792 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 50
28685 AGATATCCAG
* * *
28695 GTATAGCGCAGATCA-GGCGGCACGCTATATCCACGTGGCGCCAGATCACC
1 GTATAGCGCAGAGCAGGGC-GCACGCTATATCCACGTGGAGCCAAATCACC
* * * *
28745 GTATATCGCGGGGCAGGGCGCGCGCTATATCCACGTGGAGCCAAATCA
1 GTATAGCGCAGAGCAGGGCGCACGCTATATCCACGTGGAGCCAAATCA
28793 GCATATAGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 37 0.93
51 3 0.08
ACGTcount: A:0.23, C:0.30, G:0.31, T:0.16
Consensus pattern (50 bp):
GTATAGCGCAGAGCAGGGCGCACGCTATATCCACGTGGAGCCAAATCACC
Found at i:28812 original size:50 final size:50
Alignment explanation
Indices: 28717--28820 Score: 127
Period size: 50 Copynumber: 2.1 Consensus size: 50
28707 TCAGGCGGCA
* * * **
28717 CGCTATATCCACGTGGCGCCAGATCACCGTATATCGCGGGGCAGGGCGCG
1 CGCTATATCCACGTGGAGCCAAATCACCATATAGAGCGGGGCAGGGCGCG
* ** *
28767 CGCTATATCCACGTGGAGCCAAATCAGCATATAGAGCGGTTCAGGGGGCG
1 CGCTATATCCACGTGGAGCCAAATCACCATATAGAGCGGGGCAGGGCGCG
28817 CGCT
1 CGCT
28821 TTCCTACTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.21, C:0.29, G:0.33, T:0.17
Consensus pattern (50 bp):
CGCTATATCCACGTGGAGCCAAATCACCATATAGAGCGGGGCAGGGCGCG
Found at i:34077 original size:18 final size:16
Alignment explanation
Indices: 34056--34089 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
34046 TATGATAAAA
34056 TTAATTTTTAATATTTAT
1 TTAA-TTTTAA-ATTTAT
34074 TTAATTTTAAATTTAT
1 TTAATTTTAAATTTAT
34090 AATATATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 6 0.38
18 4 0.25
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATTTTAAATTTAT
Found at i:34259 original size:23 final size:27
Alignment explanation
Indices: 34224--34275 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 27
34214 AGTAATTAGG
*
34224 TTTATAATGAAA-AATATTTTA-TATT
1 TTTATAATAAAATAATATTTTAGTATT
34249 TTTA-AATAAAATAATATTTTAGTATT
1 TTTATAATAAAATAATATTTTAGTATT
34275 T
1 T
34276 AATTAAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 6 0.25
25 13 0.54
26 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (27 bp):
TTTATAATAAAATAATATTTTAGTATT
Found at i:34288 original size:24 final size:23
Alignment explanation
Indices: 34224--34289 Score: 62
Period size: 24 Copynumber: 2.7 Consensus size: 23
34214 AGTAATTAGG
*
34224 TTTATAATGAAAAATATTTTATATT
1 TTTA-AATAAAAAATATTTTATA-T
34249 TTTAAATAAAATAATATTTTAGTA-
1 TTTAAATAAAA-AATATTTTA-TAT
*
34273 TTTAATTAAACAAATAT
1 TTTAAATAAA-AAATAT
34290 ATAAAATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
24 20 0.56
25 14 0.39
26 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (23 bp):
TTTAAATAAAAAATATTTTATAT
Found at i:34657 original size:16 final size:16
Alignment explanation
Indices: 34632--34692 Score: 95
Period size: 16 Copynumber: 3.8 Consensus size: 16
34622 TAATAAATAA
34632 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
34648 ACGAATATAAACAAAC
1 ACGAACATAAACGAAC
*
34664 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
34680 ACGAACATAAACG
1 ACGAACATAAACG
34693 TACATAAACG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.57, C:0.21, G:0.11, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:34892 original size:16 final size:16
Alignment explanation
Indices: 34861--34892 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
34851 ATTGAAACTC
*
34861 GACTCGAACTCGAAAA
1 GACTCGAACTCAAAAA
34877 GACTCGAACTCAAAAA
1 GACTCGAACTCAAAAA
34893 AAAATTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
GACTCGAACTCAAAAA
Found at i:34945 original size:11 final size:11
Alignment explanation
Indices: 34927--34967 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
34917 TCGAGACTCG
34927 AGCTCGATTCA
1 AGCTCGATTCA
* *
34938 ATCTCGATTCTG
1 AGCTCGATTC-A
34950 AGCTCGATTCA
1 AGCTCGATTCA
34961 AGCTCGA
1 AGCTCGA
34968 CATTGCCCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:34956 original size:23 final size:24
Alignment explanation
Indices: 34902--34967 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
34892 AAAAATTTAA
*
34902 GAGCTCGATTAAAACTCGAGACTC
1 GAGCTCGATTCAAACTCGAGACTC
* **
34926 GAGCTCGATTCAATCTCGATTCT-
1 GAGCTCGATTCAAACTCGAGACTC
*
34949 GAGCTCGATTCAAGCTCGA
1 GAGCTCGATTCAAACTCGA
34968 CATTGCCCCA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 18 0.49
24 19 0.51
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (24 bp):
GAGCTCGATTCAAACTCGAGACTC
Found at i:35854 original size:24 final size:24
Alignment explanation
Indices: 35827--35888 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
35817 ATAAATGAAT
*
35827 GAACATAAACGAGCATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
* *
35851 GAACATAAATGAACATAATCGAAC
1 GAACATAAACGAACATAACCGAAC
*
35875 GAACATAACCGAAC
1 GAACATAAACGAAC
35889 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.52, C:0.23, G:0.15, T:0.11
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:35878 original size:14 final size:14
Alignment explanation
Indices: 35834--35889 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
35824 AATGAACATA
*
35834 AACGAGCATAACCG
1 AACGAACATAACCG
35848 AACGAACAT-A---
1 AACGAACATAACCG
* *
35858 AATGAACATAATCG
1 AACGAACATAACCG
35872 AACGAACATAACCG
1 AACGAACATAACCG
35886 AACG
1 AACG
35890 TTCACGAACG
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
13 1 0.03
14 24 0.71
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:44151 original size:20 final size:20
Alignment explanation
Indices: 44126--44171 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
44116 TTTCAAGTAG
44126 ATTAATTCTATATCTAATAA
1 ATTAATTCTATATCTAATAA
* *
44146 ATTAATTCTGTATCTAATAG
1 ATTAATTCTATATCTAATAA
44166 ATTAAT
1 ATTAAT
44172 CCAAAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (20 bp):
ATTAATTCTATATCTAATAA
Found at i:49650 original size:16 final size:17
Alignment explanation
Indices: 49622--49654 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
49612 ATCGCCGAAA
49622 AAATTTCACTATTCACG
1 AAATTTCACTATTCACG
49639 AAATTT-ACTATTCACG
1 AAATTTCACTATTCACG
49655 TGAACAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (17 bp):
AAATTTCACTATTCACG
Found at i:56798 original size:31 final size:31
Alignment explanation
Indices: 56750--56830 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
56740 ATATTTAATG
*
56750 TTTACTTTTT-TTTCATTTTCATACTTGGTT
1 TTTACTTTTTGTTTCATTTTCATACTTGATT
56780 TTTACTTTTTGTTTCATTTTCATACTTGATT
1 TTTACTTTTTGTTTCATTTTCATACTTGATT
*
56811 TTTACTTTTTGTTTTATTTT
1 TTTACTTTTTGTTTCATTTT
56831 AGTACCTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 10 0.21
31 38 0.79
ACGTcount: A:0.14, C:0.11, G:0.06, T:0.69
Consensus pattern (31 bp):
TTTACTTTTTGTTTCATTTTCATACTTGATT
Done.