Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004543.1 Hibiscus syriacus cultivar Beakdansim tig00010075_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: 50407
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:928 original size:19 final size:20
Alignment explanation
Indices: 886--946 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
876 GAAACTAAAA
*
886 TCGCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCAGTT
906 TCGCGTTGCGATTTTCA-TT
1 TCGCGTTGCGATTTTCAGTT
*
925 TCGCGTTGCAATTTTCAGTT
1 TCGCGTTGCGATTTTCAGTT
945 TC
1 TC
947 AAATAGTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 18 0.46
20 21 0.54
ACGTcount: A:0.11, C:0.21, G:0.20, T:0.48
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCAGTT
Found at i:1267 original size:22 final size:22
Alignment explanation
Indices: 1239--1307 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
1229 ATAGAGGGGG
*
1239 GTCGCCGGATATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
* *
1261 GTCGCCGGAGATGAGGACGAAT
1 GTCGCCGGAGATGGGGACGGAT
1283 GTCGCCGGAGATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
1305 GTC
1 GTC
1308 ACCGTAGAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.20, C:0.19, G:0.45, T:0.16
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACGGAT
Found at i:1516 original size:20 final size:20
Alignment explanation
Indices: 1493--1539 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1483 TGGAAACTGA
* *
1493 GTTGCGATATTGGAGTTCGC
1 GTTGCGATATTCGAGATCGC
1513 GTTGCGA-ATTCGAGATCGC
1 GTTGCGATATTCGAGATCGC
*
1532 GTTTCGAT
1 GTTGCGAT
1540 TTTGTTGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.17, C:0.17, G:0.32, T:0.34
Consensus pattern (20 bp):
GTTGCGATATTCGAGATCGC
Found at i:1533 original size:19 final size:19
Alignment explanation
Indices: 1449--1534 Score: 68
Period size: 19 Copynumber: 4.4 Consensus size: 19
1439 CGCTTTTAAA
1449 ATCGCGTTGCGAATATAGA-
1 ATCGCGTTGCGAAT-TAGAG
*
1468 ATCGCGTTGCGAATTTG-G
1 ATCGCGTTGCGAATTAGAG
* * *
1486 AAACTGAGTTGCGATATTGGAG
1 -ATC-GCGTTGCGA-ATTAGAG
* *
1508 TTCGCGTTGCGAATTCGAG
1 ATCGCGTTGCGAATTAGAG
1527 ATCGCGTT
1 ATCGCGTT
1535 TCGATTTTGT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.04
19 29 0.55
20 16 0.30
21 5 0.09
22 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (19 bp):
ATCGCGTTGCGAATTAGAG
Found at i:14779 original size:82 final size:81
Alignment explanation
Indices: 14674--14896 Score: 322
Period size: 81 Copynumber: 2.7 Consensus size: 81
14664 TTGTTCTTCA
* * * * *
14674 TCTAACTTGTATTAGTGGCACCTTTCTACAAAAATGCACCGTTAGGCATTAGTCTTTTATCCTAA
1 TCTAACTTGCATTATTGGCACCTTTCTGC-CAAATGCACAGTTAGGCATTAGTCTTTTATCCTAA
14739 AGGCATTTAA-ACTTTCT
65 AGGCATTTAACA-TTTCT
* * * *
14756 TCTAACTTGCATTATTGGTACCTTTTTGCCAAATACACAGTTAGGCATTAGTCTTTTATTCTAAA
1 TCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTAGTCTTTTATCCTAAA
14821 GGCATTTAACATTTCT
66 GGCATTTAACATTTCT
*
14837 TCTAACTTGCATTATTGACACCTTTCTGCCAAATGCACAGTTAGGCATTTAGTCTTTTAT
1 TCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCA-TTAGTCTTTTAT
14897 TTTAGAACAG
Statistics
Matches: 126, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
81 89 0.71
82 37 0.29
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (81 bp):
TCTAACTTGCATTATTGGCACCTTTCTGCCAAATGCACAGTTAGGCATTAGTCTTTTATCCTAAA
GGCATTTAACATTTCT
Found at i:15088 original size:54 final size:54
Alignment explanation
Indices: 15008--15289 Score: 411
Period size: 54 Copynumber: 5.2 Consensus size: 54
14998 ATTAAGATGA
* * * * * * *
15008 ACACGTAGTGCCTATACGGTCGTTCATCAACACATGATGAATTCTGTGGGTTGC
1 ACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAGTTGC
* * *
15062 ACACATAGTGACAAAACAGTTGTTCATCAACATATGATGAATTCCGTGAGTTGC
1 ACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAGTTGC
* *
15116 ACACATAGTGCCGAAACGGTTGTTTATTAACATATGATGAATTCCGTGAGTTGC
1 ACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAGTTGC
* * *
15170 AAACATAGTGCCGAAACGGTTGTTCATCAACATATGATAAATTTCGTGAGTTGC
1 ACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAGTTGC
* *
15224 ACACATAATGCTGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAGTTGC
1 ACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAGTTGC
15278 ACACATAGTGCC
1 ACACATAGTGCC
15290 TGTAGTACAC
Statistics
Matches: 202, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 202 1.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (54 bp):
ACACATAGTGCCGAAACGGTTGTTCATCAACATATGATGAATTCCGTGAGTTGC
Found at i:15174 original size:27 final size:27
Alignment explanation
Indices: 15144--15284 Score: 69
Period size: 27 Copynumber: 5.2 Consensus size: 27
15134 GTTGTTTATT
15144 AACATATGATGAATTCCGTGAGTTGCA
1 AACATATGATGAATTCCGTGAGTTGCA
** * * *
15171 AACATAGTGCCGAA-ACGGT-TGTT-CA
1 AACATA-TGATGAATTCCGTGAGTTGCA
* *
15196 TCAACATATGATAAATTTCGTGAGTTGCA
1 --AACATATGATGAATTCCGTGAGTTGCA
* * * * *
15225 CACATAATGCTGAA-ACGGT-TGTT-CA
1 AACAT-ATGATGAATTCCGTGAGTTGCA
15250 TCAACATATGATGAATTCCGTGAGTTGCA
1 --AACATATGATGAATTCCGTGAGTTGCA
*
15279 CACATA
1 AACATA
15285 GTGCCTGTAG
Statistics
Matches: 77, Mismatches: 25, Indels: 24
0.61 0.20 0.19
Matches are distributed among these distances:
25 4 0.05
26 17 0.22
27 35 0.45
28 17 0.22
29 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (27 bp):
AACATATGATGAATTCCGTGAGTTGCA
Found at i:25215 original size:2 final size:2
Alignment explanation
Indices: 25210--25246 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
25200 GAGTTTATTA
25210 AT AT AT AT 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 A
25247 AAAGATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25604 original size:3 final size:3
Alignment explanation
Indices: 25596--25638 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
25586 TATATGACTA
25596 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
25639 GTTAAATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27892 original size:137 final size:138
Alignment explanation
Indices: 27731--28075 Score: 439
Period size: 137 Copynumber: 2.5 Consensus size: 138
27721 AAGGCAGAAT
** *
27731 AAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAAATGAGTTATTCTCATTGTGAACTTCTTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTGTGAACTTCTTC
* * * *
27796 TGGAAATGCTGATCCTCAAAAGAGGTG-TCGTTAATTCAACTTCATATG-TGATGAATTAAGGC-
66 TGGAAATGCTGATCCTCAAAAGAGATGCTCGTTAATTCAACTCCATA-GATGATAAATCAA-GCT
*
27858 AAGGTTGAAC
129 AAGGTCGAAC
* *
27868 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTATGAAC--CCTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTGTGAACTTCTTC
* * * ** * *
27931 TGAAAATGTTGATCCTCCAGGGAGATGCTTCTTTCATTCAACTCCATAGATGATAAATCAAGCTA
66 TGGAAATGCTGATCCTCAAAAGAGATGC-TCGTTAATTCAACTCCATAGATGATAAATCAAGCTA
27996 AGGTCGAAC
130 AGGTCGAAC
* * * *
28005 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATCGTAAACTTCTTG
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTGTGAACTTCTTC
28070 TGGAAA
66 TGGAAA
28076 CGTTGATGCT
Statistics
Matches: 178, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
135 24 0.13
136 3 0.02
137 144 0.81
139 7 0.04
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (138 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTGTGAACTTCTTC
TGGAAATGCTGATCCTCAAAAGAGATGCTCGTTAATTCAACTCCATAGATGATAAATCAAGCTAA
GGTCGAAC
Found at i:28308 original size:123 final size:123
Alignment explanation
Indices: 27980--28324 Score: 531
Period size: 119 Copynumber: 2.9 Consensus size: 123
27970 AACTCCATAG
* *
27980 ATGATA-AATCAAGC-TAAGGTCGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
1 ATGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
** * * * *
28043 TGAGTTCTTCTCATCGTAAACTTCTTGTGGAAACGTTGATGCTGATCTATCTCCTTCT
66 TGAGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCT
* * * *
28101 GTGATAGAATCGAGCAAAA-GCTGAACAAGTTC-T-T-ATTATGAACTTTTTCTTCCTCTTCAGA
1 ATGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
28162 TGAGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCT
66 TGAGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCT
*
28220 ATGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTCTTCAGA
1 ATGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
28285 TGAGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGAT
66 TGAGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGAT
28325 CCATCGAGTG
Statistics
Matches: 201, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
119 95 0.47
120 13 0.06
121 7 0.03
122 19 0.09
123 67 0.33
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (123 bp):
ATGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGA
TGAGTTCTTCTCATTATGAACTTCCTCTGGAAATGTTGATGCTGATCTATCTCCTTCT
Found at i:28403 original size:36 final size:36
Alignment explanation
Indices: 28363--28556 Score: 160
Period size: 36 Copynumber: 5.3 Consensus size: 36
28353 AATGAAACTG
* *
28363 TCTCAAGCGAGACTAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACTAATGTTGTTTTAAGAAAAACAA
* ** * **
28399 TCTCAAGTGAGA-TAAATTGTTGTTTTGAGTGACACTG
1 TCTCAAGTGAGACT-AA-TGTTGTTTTAAGAAAAACAA
* *
28436 TCTCAAGTGAGACAAATTTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACTAATGTTGTTTTAAGAAAAACAA
* ** **
28472 TCTCAAGTGAGA-TAAATTGTTGTTTCAAGTGAAACTG
1 TCTCAAGTGAGACT-AA-TGTTGTTTTAAGAAAAACAA
* **
28509 TCTCAAGCGAGACGCA-GTTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACTAATG-TTGTTTTAAGAAAAACAA
28545 TCTCAAGTGAGA
1 TCTCAAGTGAGA
28557 TAAATTGTTA
Statistics
Matches: 119, Mismatches: 32, Indels: 14
0.72 0.19 0.08
Matches are distributed among these distances:
35 2 0.02
36 64 0.54
37 53 0.45
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (36 bp):
TCTCAAGTGAGACTAATGTTGTTTTAAGAAAAACAA
Found at i:28424 original size:37 final size:37
Alignment explanation
Indices: 28381--28565 Score: 203
Period size: 37 Copynumber: 5.1 Consensus size: 37
28371 GAGACTAATC
28381 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
* ** * ** *
28418 TTGTTTTGAGTGACACTGTCTCAAGTGAGACAAATT-
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
28454 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
* ** ** * *** *
28491 TTGTTTCAAGTGAAACTGTCTCAAGCGAGACGCAGT-
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
28527 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
28564 TT
1 TT
28566 ATTTGAAAAT
Statistics
Matches: 112, Mismatches: 34, Indels: 4
0.75 0.23 0.03
Matches are distributed among these distances:
36 55 0.49
37 57 0.51
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (37 bp):
TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
Found at i:28458 original size:73 final size:73
Alignment explanation
Indices: 28346--28565 Score: 343
Period size: 73 Copynumber: 3.0 Consensus size: 73
28336 TGGAAATTTC
* *
28346 TGTTTCTAA-TGAAACTGTCTCAAGCGAGACTAATCTTGTTTTAAGAAAAACAATCTCAAGTGAG
1 TGTTTC-AAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAG
28410 ATAAATTGT
65 ATAAATTGT
** * *
28419 TGTTTTGAGTGACACTGTCTCAAGTGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCAAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
28484 TAAATTGT
66 TAAATTGT
** *
28492 TGTTTCAAGTGAAACTGTCTCAAGCGAGACGCAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCAAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
28557 TAAATTGT
66 TAAATTGT
28565 T
1 T
28566 ATTTGAAAAT
Statistics
Matches: 133, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
72 1 0.01
73 132 0.99
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (73 bp):
TGTTTCAAGTGAAACTGTCTCAAGCGAGACAAATTTTGTTTTAAGAAAAACAATCTCAAGTGAGA
TAAATTGT
Found at i:35626 original size:43 final size:44
Alignment explanation
Indices: 35564--35647 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
35554 TGCATCAAAT
* * *
35564 AAAACTTTTACATGTAGGGGACATCTTTCAGTCCTAACTTCAAC
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAAC
* *
35608 AAAAC-TTTACATATAGGGGATAACTTTCCCTCCTAACTTC
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTC
35648 TCTAAAGCCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 30 0.86
44 5 0.14
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (44 bp):
AAAACTTTTACATATAGGGGACAACTTTCACTCCTAACTTCAAC
Found at i:36146 original size:36 final size:36
Alignment explanation
Indices: 36099--36171 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
36089 ACTCTTACCA
* *
36099 TAGAATGCTTTTGGTATCAATCTAACAGGATCTTTG
1 TAGAATACTTTTGGTATCAATATAACAGGATCTTTG
*
36135 TAGAATACTTTTGGTATTAATATAACAGGATCTTTG
1 TAGAATACTTTTGGTATCAATATAACAGGATCTTTG
36171 T
1 T
36172 GTGCATAGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.41
Consensus pattern (36 bp):
TAGAATACTTTTGGTATCAATATAACAGGATCTTTG
Found at i:37034 original size:8 final size:8
Alignment explanation
Indices: 37018--37048 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
37008 TTTAATATCT
37018 AAAAATAA
1 AAAAATAA
*
37026 AATAATAA
1 AAAAATAA
37034 AAAAATAA
1 AAAAATAA
37042 AAAAATA
1 AAAAATA
37049 TAATAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:37919 original size:2 final size:2
Alignment explanation
Indices: 37912--37939 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
37902 ATAAATATCT
37912 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
37940 AATTAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40454 original size:17 final size:17
Alignment explanation
Indices: 40428--40461 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40418 CAACATGTTC
40428 ATGTTCATGTTAAGCAT
1 ATGTTCATGTTAAGCAT
* *
40445 ATGTTTATGTTTAGCAT
1 ATGTTCATGTTAAGCAT
40462 GCATACCTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (17 bp):
ATGTTCATGTTAAGCAT
Found at i:41544 original size:8 final size:7
Alignment explanation
Indices: 41531--41598 Score: 72
Period size: 6 Copynumber: 9.9 Consensus size: 7
41521 ATTTAAGTGC
41531 AAAAGAA
1 AAAAGAA
41538 GAAAAG-A
1 -AAAAGAA
*
41545 AAAAG-G
1 AAAAGAA
41551 AAAAGAA
1 AAAAGAA
41558 AAAAG-A
1 AAAAGAA
41564 AAAAGAA
1 AAAAGAA
41571 GAAAAGAA
1 -AAAAGAA
41579 AAAAG-A
1 AAAAGAA
41585 AAAAGAA
1 AAAAGAA
41592 GAAAAGA
1 -AAAAGA
41599 GGAAAAATAA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
6 22 0.42
7 13 0.25
8 18 0.34
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:41560 original size:13 final size:13
Alignment explanation
Indices: 41538--41598 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
41528 TGCAAAAGAA
41538 GAAAAG-AAAAAG
1 GAAAAGAAAAAAG
41550 GAAAAGAAAAAAG
1 GAAAAGAAAAAAG
*
41563 AAAAAGAAGAAAAG
1 GAAAAGAA-AAAAG
* *
41577 AAAAAAGAAAAAGAA
1 -GAAAAGAAAAA-AG
41592 GAAAAGA
1 GAAAAGA
41599 GGAAAAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
12 6 0.14
13 13 0.31
14 14 0.33
15 9 0.21
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
GAAAAGAAAAAAG
Found at i:41573 original size:33 final size:35
Alignment explanation
Indices: 41531--41598 Score: 113
Period size: 33 Copynumber: 2.0 Consensus size: 35
41521 ATTTAAGTGC
*
41531 AAAAGAAGAAAAG-AAAAAGGAAAAGAA-AAAAGA
1 AAAAGAAGAAAAGAAAAAAGAAAAAGAAGAAAAGA
41564 AAAAGAAGAAAAGAAAAAAGAAAAAGAAGAAAAGA
1 AAAAGAAGAAAAGAAAAAAGAAAAAGAAGAAAAGA
41599 GGAAAAATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 13 0.41
34 13 0.41
35 6 0.19
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (35 bp):
AAAAGAAGAAAAGAAAAAAGAAAAAGAAGAAAAGA
Found at i:41576 original size:21 final size:21
Alignment explanation
Indices: 41531--41598 Score: 113
Period size: 21 Copynumber: 3.3 Consensus size: 21
41521 ATTTAAGTGC
41531 AAAAGAAGAAAAGAAAAAG--G
1 AAAAGAA-AAAAGAAAAAGAAG
41551 AAAAGAAAAAAGAAAAAGAAG
1 AAAAGAAAAAAGAAAAAGAAG
41572 AAAAGAAAAAAGAAAAAGAAG
1 AAAAGAAAAAAGAAAAAGAAG
41593 AAAAGA
1 AAAAGA
41599 GGAAAAATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
19 11 0.24
20 7 0.15
21 28 0.61
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAGAAAAAGAAG
Found at i:41610 original size:28 final size:26
Alignment explanation
Indices: 41531--41611 Score: 76
Period size: 29 Copynumber: 3.0 Consensus size: 26
41521 ATTTAAGTGC
**
41531 AAAAGAAGAAAAGA-AAAAGGAAAAG
1 AAAAGAAGAAAAGAGAAAAAAAAAAG
41556 AAAA-AAGAAAAAGAAGAAAAGAAAAAAG
1 AAAAGAAG-AAAAG-AGAAAA-AAAAAAG
*
41584 AAAAAGAAGAAAAGAGGAAAAATAAAAG
1 -AAAAGAAGAAAAGA-GAAAAAAAAAAG
41612 CAAATCAAAG
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
24 3 0.07
25 9 0.20
26 1 0.02
27 4 0.09
28 12 0.26
29 14 0.30
30 3 0.07
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (26 bp):
AAAAGAAGAAAAGAGAAAAAAAAAAG
Done.