Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006983.1 Hibiscus syriacus cultivar Beakdansim tig00017992_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: 72011
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:6871 original size:21 final size:21
Alignment explanation
Indices: 6847--6887 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
6837 GCTTTGGAAT
*
6847 TTTTCCTGGGTTGCAACCATC
1 TTTTCCTGGGATGCAACCATC
*
6868 TTTTCCTGGGATGTAACCAT
1 TTTTCCTGGGATGCAACCAT
6888 TGCTAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (21 bp):
TTTTCCTGGGATGCAACCATC
Found at i:9269 original size:24 final size:24
Alignment explanation
Indices: 9215--9269 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
9205 TCAGAGTAAG
** *
9215 TTTCAATCCCTTTTTTACAATCGA
1 TTTCAATCCCCCTTTTACAATAGA
* *
9239 -TTGAATCCCCCTTTTACAGTAGA
1 TTTCAATCCCCCTTTTACAATAGA
9262 TTTCAATC
1 TTTCAATC
9270 AGGTTTTATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.42
Consensus pattern (24 bp):
TTTCAATCCCCCTTTTACAATAGA
Found at i:10270 original size:20 final size:20
Alignment explanation
Indices: 10247--10304 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 20
10237 ACCCGAATGT
*
10247 CTTACAGATGGCCCGAAAGA
1 CTTACAAATGGCCCGAAAGA
** * *
10267 CTTATCATCTTGCTCGAAAGA
1 CTTA-CAAATGGCCCGAAAGA
*
10288 CTTACAAATGACCCGAA
1 CTTACAAATGGCCCGAA
10305 GAATTTAAGC
Statistics
Matches: 28, Mismatches: 9, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (20 bp):
CTTACAAATGGCCCGAAAGA
Found at i:10304 original size:41 final size:42
Alignment explanation
Indices: 10247--10334 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
10237 ACCCGAATGT
* * * *
10247 CTTACAGATGGCCCGAA-AGACTT-ATCATCTTGCTCGAAAGA
1 CTTACAAATGACCCGAAGA-ACTTAAGCATCATGCTCGAAAGA
*
10288 CTTACAAATGACCCGAAGAATTTAAGCATCATGCTCGAAAGA
1 CTTACAAATGACCCGAAGAACTTAAGCATCATGCTCGAAAGA
10330 CTTAC
1 CTTAC
10335 TGATTGCCTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
41 18 0.45
42 22 0.55
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (42 bp):
CTTACAAATGACCCGAAGAACTTAAGCATCATGCTCGAAAGA
Found at i:10486 original size:255 final size:258
Alignment explanation
Indices: 9777--10713 Score: 1282
Period size: 255 Copynumber: 3.7 Consensus size: 258
9767 AGTGAGATCG
* * ** * * * *
9777 ACAGATAACCCGAAGGATTTAATCATCACACTCGAAAGACTTACAGAATGACATGAATGACTTAC
1 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATTGACCTGAAGGACTTAC
* * * *
9842 AAATTTTGGAAATAATTTATTGGGTAAAAAACTTTGAAAATCGCTTTCTTACTTTTAAAAAATTT
66 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
**
9907 CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATTTCTTTCTCATTTTTCAAAGTTCATGTG
131 CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAA-TTCATGTG
* * *
9972 AAAACATCCTACCCGAAGGTCTTATGGATAGCTC-AAATGACTTATCATCTTGCTCG-AAGACTT
195 AAAACATCCTACCCGAATGTCTTATAGATAGCCCGAAA-GACTTATCATCTTGCTCGAAAGACTT
* * * *
10035 ATAGATGACCCGAAGGATTTAAGCATCATGATCGAAAGACTTACTGA-TGGCCCGAAGGACTTAC
1 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATTGACCTGAAGGACTTAC
* * ** *
10099 AAATTTTGGAAATAATTTAATGGGTAAGAAACATTGGAAATTACTTTTTTACTTTTCAAAAATTT
66 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
* * *
10164 CGTTTTCTGAAAACATTAAATGAGAAACTTTGG-AATCGCTTTCTCATTTTTGAAGTTCATGTGA
131 CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGA
* *
10228 AAACATCCTACCCGAATGTCTTACAGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACTT
196 AAACATCCTACCCGAATGTCTTATAGATAGCCCGAAAGACTTATCATCTTGCTCGAAAGACTT
* *
10291 ACAAATGACCCGAAGAATTTAAGCATCATGCTCGAAAGACTTACTGATTG-CCTGAAGGACTTAC
1 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATTGACCTGAAGGACTTAC
**
10355 AAATTTTGGAAATAATTTACT-GGTAA-AAACTTTGGAAATTTCTTTCTTACTTTTCAAAAATTT
66 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
* *
10418 CATTTTCTGAAAATACTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGA
131 CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGA
* * * * *
10483 AAACATCCTACCCGAAAT-TCTTATAGATTA-CCCGAAGGACTTATCATATTCCTTGAAAGACTG
196 AAACATCCTACCCG-AATGTCTTATAGA-TAGCCCGAAAGACTTATCATCTTGCTCGAAAGACTT
* * * * * *
10546 ACAGTTGACCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTGA-TGACCAGATGTACTTAA
1 ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATTGACCTGAAGGACTTAC
*
10610 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAACCGCTTTCTTACTTTTCAAAAATTT
66 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
* * * *
10675 TATTTTCTAAAAAGATTTAAATGAGGAACTTTGGAAATC
131 CATTTTCTGAAAACA-TTAAATGAGAAACTTTGGAAATC
10714 ATTTTCTTAA
Statistics
Matches: 603, Mismatches: 66, Indels: 20
0.88 0.10 0.03
Matches are distributed among these distances:
254 66 0.11
255 213 0.35
256 113 0.19
257 150 0.25
258 61 0.10
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (258 bp):
ACAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATTGACCTGAAGGACTTAC
AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTT
CATTTTCTGAAAACATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCATGTGA
AAACATCCTACCCGAATGTCTTATAGATAGCCCGAAAGACTTATCATCTTGCTCGAAAGACTT
Found at i:19944 original size:25 final size:24
Alignment explanation
Indices: 19916--19986 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
19906 ATTCTTGGGT
19916 TTTTTTCACAGTAGGTTTCAATCCC
1 TTTTTT-ACAGTAGGTTTCAATCCC
* * *
19941 TTTTTTTACAATCGG-TTAAATCCC
1 -TTTTTTACAGTAGGTTTCAATCCC
**
19965 CCTTTTACAGTAGGTTTCAATC
1 TTTTTTACAGTAGGTTTCAATC
19987 GGGTTTTATA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
23 10 0.28
24 14 0.39
25 6 0.17
26 6 0.17
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.44
Consensus pattern (24 bp):
TTTTTTACAGTAGGTTTCAATCCC
Found at i:20333 original size:3 final size:3
Alignment explanation
Indices: 20325--20372 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
20315 GAAACTTAAT
20325 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
20370 TAA
1 TAA
20373 CCCGGACAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:24708 original size:191 final size:192
Alignment explanation
Indices: 24381--24799 Score: 533
Period size: 191 Copynumber: 2.2 Consensus size: 192
24371 CTATTAGCGG
*
24381 TATAAATGACAGGTTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAGTTACGTCA
1 TATAAATGACA--TTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAGTTACATCA
24446 CTAAATTATAGAAAATTTTGTTATTAATAATTCACATCGTCACGAATAATACATTAAAATCAAGC
64 CTAAATTATAGAAAATTTTGTTATTAATAATTCACATCGTCACGAATAATACATTAAAATCAAGC
* *
24511 TATATGTGACGAAAGATATATTGTTACATTTTTAGTGACGTAATATAAAGTTACCTAATAGTAT
129 TATATGTGACGAAAGAGATATTGTTAAATTTTTAGTGACGTAATATAAAGTTACCTAATAGTAT
* * * **
24575 TATAAATGACACTTATGCATAACGTCATTTTATAACTT-ATATTCCATGACAGTTAGTTACATCA
1 TATAAATGACA-TTATGCATAACGTCACTTTATAA-TTGATACTCAATGACAACTAGTTACATCA
* * * * *
24639 CTAAATTATATAATA-TTT-TTATTAATAATTTATATCGTCATGAATAATACGA-TAAAATCAA-
64 CTAAATTATAGAAAATTTTGTTATTAATAATTCACATCGTCACGAATAATAC-ATTAAAATCAAG
* * * **
24700 CTTATATGTTACGAAATAGATATTGTTAAATTTTTAGTGACGTAATATAACGTTATGTAATAGTA
128 C-TATATGTGACGAAAGAGATATTGTTAAATTTTTAGTGACGTAATATAAAGTTACCTAATAGTA
24765 T
192 T
* * * * *
24766 TTTGAATGATGATTATGCATAACGCCACCTTATA
1 TATAAATGA-CATTATGCATAACGTCACTTTATA
24800 CAATTTTCTC
Statistics
Matches: 196, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
190 1 0.01
191 121 0.62
192 5 0.03
193 56 0.29
194 13 0.07
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.37
Consensus pattern (192 bp):
TATAAATGACATTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAGTTACATCACT
AAATTATAGAAAATTTTGTTATTAATAATTCACATCGTCACGAATAATACATTAAAATCAAGCTA
TATGTGACGAAAGAGATATTGTTAAATTTTTAGTGACGTAATATAAAGTTACCTAATAGTAT
Found at i:38394 original size:3 final size:3
Alignment explanation
Indices: 38386--38468 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
38376 AATATATATT
*
38386 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38434 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
38469 TGGGTAAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:38950 original size:113 final size:113
Alignment explanation
Indices: 38766--40108 Score: 2261
Period size: 113 Copynumber: 11.9 Consensus size: 113
38756 GAATTCAGAC
*
38766 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
38831 TATGAACCTTCTCTGGCAAA-AATAATCCATCAAGTGATGAATTC-AGAC
66 TATGAACTTTCTCTGG-AAATGATGATCCATCAAATGATGGATTCAAG-T
38879 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
38944 TATGAACCTTCTCTGGCAAA-AATAATCCATCAAGTGATGAATTC-AGAC
66 TATGAACTTTCTCTGG-AAATGATGATCCATCAAATGATGGATTCAAG-T
*
38992 AAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
39057 TATGAACCTTCTCTGGCAAA-AATAATCCATCAAGTGATGAATTC-AGAC
66 TATGAACTTTCTCTGG-AAATGATGATCCATCAAATGATGGATTCAAG-T
*
39105 AAAAGGTTGAATAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * *
39170 TATGAACCTTCTCTGGCAAA-AATAATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGG-AAATGATGATCCATCAAATGATGGATTCAAGT
*
39218 AAAAGGTTGAACAAATTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
**
39283 TATGAACTTTCTCTGGAAATGATGATTTATCAAATGATGGATTCAAGT
66 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
39331 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
39396 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
66 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
39444 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
39509 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
66 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
*
39557 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
39622 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
66 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
39670 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
39735 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
66 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
*
39783 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
39848 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
66 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
39896 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
39961 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
66 TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
40009 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
40074 TATGAACTTTCTCTGGAAATG-TCAATCCATCAAAT
66 TATGAACTTTCTCTGGAAATGAT-GATCCATCAAAT
40109 AATAATTTTG
Statistics
Matches: 1205, Mismatches: 22, Indels: 6
0.98 0.02 0.00
Matches are distributed among these distances:
112 4 0.00
113 1200 1.00
114 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGT
Found at i:41045 original size:83 final size:83
Alignment explanation
Indices: 40905--43413 Score: 4725
Period size: 83 Copynumber: 30.2 Consensus size: 83
40895 CTTATTTCTA
* *
40905 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
40970 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
40988 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATAAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
41053 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
41071 CTATGAGCACATTTATCTTCTAAATTCAATTATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
41136 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
41154 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
*
41219 GAACACTTACAGAAGATG
66 GAACACTTCCAGAAGATG
41237 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
41302 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
41320 CTATGAGCACATTCATCTTCTAAATTTAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
41385 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
41403 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
41468 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
41486 TTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCCGTCTAACCAAATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
*
41551 GAACACTTCCAGAAGAAG
66 GAACACTTCCAGAAGATG
41569 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
41634 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
41652 CTATGAGCACATTCATCTTCTAAATTTAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
41717 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
41735 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
41800 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
41818 TTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCCGTCTAACCAAATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
*
41883 GAACACTTCCAGAAGAAG
66 GAACACTTCCAGAAGATG
41901 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
41966 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
41984 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTT-TCGTCTAACCAGATCAGATAACTCAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCT-GTCTAACCAGATCAGATAACTCAA
42048 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
42067 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
42132 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
42150 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
42215 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
42233 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
*
42298 GAACACTTACAGAAGATG
66 GAACACTTCCAGAAGATG
* *
42316 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTTTTTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
42381 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
42399 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
42464 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
42482 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
42547 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
42565 TTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCCGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
*
42630 GAACACTTCCAGAAGAAG
66 GAACACTTCCAGAAGATG
*
42648 CTATGAGCACATTCATCTTCTAAATTCTATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
42713 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
42731 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTT-TCGTCTAACCAGATCAGATAACTCAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCT-GTCTAACCAGATCAGATAACTCAA
42795 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
*
42814 CTATGAGCACATTCATCTTCTAAATTCAATGATTAGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
42879 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
42897 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
*
42962 GAACACTTCTAGAAGATG
66 GAACACTTCCAGAAGATG
42980 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
**
43045 GAACACTTATAGAAGATG
66 GAACACTTCCAGAAGATG
43063 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
43128 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
43146 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
43211 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
43229 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
*
43294 GAACACTTACAGAAGATG
66 GAACACTTCCAGAAGATG
43312 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
*
43377 GAACACTTACAGAAGATG
66 GAACACTTCCAGAAGATG
43395 CTATGAGCACATTCATCTT
1 CTATGAGCACATTCATCTT
43414 TTAGTTAATG
Statistics
Matches: 2371, Mismatches: 51, Indels: 8
0.98 0.02 0.00
Matches are distributed among these distances:
82 2 0.00
83 2367 1.00
84 2 0.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:44556 original size:1 final size:1
Alignment explanation
Indices: 44550--44633 Score: 51
Period size: 1 Copynumber: 84.0 Consensus size: 1
44540 TAACCCTCCC
* * * * * * * * **
44550 TTTTTTTTTCTTTTCTTTCTTCTCTTTTTTTTTCTTTCTTTTTTTCTTTTTTTTCCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
44615 CTTTCTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTT
44634 CTTTCTTTTC
Statistics
Matches: 59, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (1 bp):
T
Found at i:44568 original size:9 final size:9
Alignment explanation
Indices: 44551--44645 Score: 90
Period size: 9 Copynumber: 10.8 Consensus size: 9
44541 AACCCTCCCT
*
44551 TTTTTTTTC
1 TTTTCTTTC
44560 TTTTCTTTC
1 TTTTCTTTC
* *
44569 TTCTCTTTTT
1 TTTTC-TTTC
44579 TTTTCTTTC
1 TTTTCTTTC
44588 TTTT-TTTC
1 TTTTCTTTC
*
44596 TTTTTTTTC
1 TTTTCTTTC
*
44605 -CTT-TTT-
1 TTTTCTTTC
44611 TTTTCTTTC
1 TTTTCTTTC
*
44620 TTTTTTTTTC
1 -TTTTCTTTC
44630 TTTTCTTTC
1 TTTTCTTTC
44639 TTTTCTT
1 TTTTCTT
44646 CAAGCATAAT
Statistics
Matches: 71, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
7 5 0.07
8 13 0.18
9 38 0.54
10 15 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:44576 original size:24 final size:24
Alignment explanation
Indices: 44549--44645 Score: 137
Period size: 24 Copynumber: 4.1 Consensus size: 24
44539 TTAACCCTCC
*
44549 CTTTTTTTTTCTTTTCTTTCTTCT
1 CTTTTTTTTTCTTTTCTTTCTTTT
44573 CTTTTTTTTTC-TTTCTTT-TTTT
1 CTTTTTTTTTCTTTTCTTTCTTTT
* *
44595 CTTTTTTTTCCTTTT-TTTTTCTTT
1 CTTTTTTTTTCTTTTCTTTCT-TTT
44619 CTTTTTTTTTCTTTTCTTTCTTTT
1 CTTTTTTTTTCTTTTCTTTCTTTT
44643 CTT
1 CTT
44646 CAAGCATAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
22 16 0.25
23 11 0.17
24 34 0.52
25 4 0.06
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (24 bp):
CTTTTTTTTTCTTTTCTTTCTTTT
Found at i:44577 original size:14 final size:13
Alignment explanation
Indices: 44556--44645 Score: 87
Period size: 14 Copynumber: 6.8 Consensus size: 13
44546 TCCCTTTTTT
44556 TTTCTTTTCTTTC
1 TTTCTTTTCTTTC
*
44569 TTCTCTTTTTTTTTC
1 TT-TC-TTTTCTTTC
44584 TTTCTTTT-TTTC
1 TTTCTTTTCTTTC
* *
44596 TTTTTTTTCCTT-
1 TTTCTTTTCTTTC
44608 TTT-TTTTCTTTC
1 TTTCTTTTCTTTC
*
44620 TTTTTTTTTCTTTTC
1 -TTTCTTTTC-TTTC
44635 TTTCTTTTCTT
1 TTTCTTTTCTT
44646 CAAGCATAAT
Statistics
Matches: 65, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
11 7 0.11
12 14 0.22
13 13 0.20
14 17 0.26
15 14 0.22
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTCTTTTCTTTC
Found at i:44614 original size:32 final size:36
Alignment explanation
Indices: 44552--44645 Score: 133
Period size: 32 Copynumber: 2.7 Consensus size: 36
44542 ACCCTCCCTT
44552 TTTTTTTCTTTTCTTTCTTCTCTTTTTTTTTCTTTC
1 TTTTTTTCTTTTCTTTCTTCTCTTTTTTTTTCTTTC
44588 TTTTTTTC-TTT-TTT-TTC-CTTTTTTTTTCTTTC
1 TTTTTTTCTTTTCTTTCTTCTCTTTTTTTTTCTTTC
*
44620 TTTTTTTTTCTTTTCTTTCTTTTCTT
1 --TTTTTTTCTTTTCTTTCTTCTCTT
44646 CAAGCATAAT
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
32 15 0.29
33 3 0.06
34 11 0.22
35 6 0.12
36 11 0.22
37 2 0.04
38 3 0.06
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (36 bp):
TTTTTTTCTTTTCTTTCTTCTCTTTTTTTTTCTTTC
Found at i:44642 original size:19 final size:19
Alignment explanation
Indices: 44549--44642 Score: 103
Period size: 19 Copynumber: 5.3 Consensus size: 19
44539 TTAACCCTCC
44549 CTTTTTTTTTCTTTTCTTT
1 CTTTTTTTTTCTTTTCTTT
*
44568 CTTCTCTTTTT-TTTTCTTT
1 CTT-TTTTTTTCTTTTCTTT
44587 C--TTTTTTTC-TTT-TTT
1 CTTTTTTTTTCTTTTCTTT
**
44602 -TTCCTTTTT-TTTTCTTT
1 CTTTTTTTTTCTTTTCTTT
44619 CTTTTTTTTTCTTTTCTTT
1 CTTTTTTTTTCTTTTCTTT
44638 CTTTT
1 CTTTT
44643 CTTCAAGCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 16
0.73 0.07 0.19
Matches are distributed among these distances:
15 3 0.05
16 17 0.28
17 3 0.05
18 7 0.11
19 25 0.41
20 6 0.10
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (19 bp):
CTTTTTTTTTCTTTTCTTT
Found at i:57412 original size:18 final size:17
Alignment explanation
Indices: 57386--57419 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
57376 TAATTGGGTC
57386 TGTAATTAATATTATATA
1 TGTAATTAATA-TATATA
*
57404 TGTATTTAATATATAT
1 TGTAATTAATATATAT
57420 TAATAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TGTAATTAATATATATA
Found at i:57428 original size:3 final size:3
Alignment explanation
Indices: 57410--57469 Score: 93
Period size: 3 Copynumber: 19.7 Consensus size: 3
57400 TATATGTATT
* *
57410 TAA TATA TAT TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57456 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
57470 TGGGTAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:64714 original size:13 final size:13
Alignment explanation
Indices: 64696--64721 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64686 AAAGTTCTAA
64696 CTCATGGTTTCAT
1 CTCATGGTTTCAT
64709 CTCATGGTTTCAT
1 CTCATGGTTTCAT
64722 GATTTCATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.15, T:0.46
Consensus pattern (13 bp):
CTCATGGTTTCAT
Found at i:64890 original size:26 final size:25
Alignment explanation
Indices: 64861--64952 Score: 107
Period size: 26 Copynumber: 3.6 Consensus size: 25
64851 TCACTTTGAA
64861 TTCATTTTCTTTTATTTTTATTTTTC
1 TTCATTTTCTTTT-TTTTTATTTTTC
*
64887 TTCATTTT-TTTTCTTTTTCTTTTTC
1 TTCATTTTCTTTT-TTTTTATTTTTC
* *
64912 TTCGTTTTCTTTTTCTTTTATTCTTTT
1 TTCATTTTCTTTTT-TTTTATT-TTTC
64939 TTC-TTTTCTTTTTT
1 TTCATTTTCTTTTTT
64953 CATTAGCAAC
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
25 24 0.41
26 28 0.48
27 6 0.10
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.79
Consensus pattern (25 bp):
TTCATTTTCTTTTTTTTTATTTTTC
Found at i:64903 original size:6 final size:6
Alignment explanation
Indices: 64865--64951 Score: 63
Period size: 6 Copynumber: 13.7 Consensus size: 6
64855 TTTGAATTCA
* *
64865 TTTTC- TTTTAT TTTTAT TTTTCT TCATTT-T TTTTCT TTTTCT TTTTCTT
1 TTTTCT TTTTCT TTTTCT TTTTCT T--TTTCT TTTTCT TTTTCT TTTTC-T
64914 CGTTTTCT TTTTCTT TTATTCT TTTT-T CTTTTCT TTTT
1 --TTTTCT TTTTC-T TT-TTCT TTTTCT -TTTTCT TTTT
64952 TCATTAGCAA
Statistics
Matches: 69, Mismatches: 2, Indels: 21
0.75 0.02 0.23
Matches are distributed among these distances:
5 8 0.12
6 39 0.57
7 10 0.14
8 7 0.10
9 5 0.07
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:64903 original size:25 final size:25
Alignment explanation
Indices: 64861--64930 Score: 86
Period size: 25 Copynumber: 2.7 Consensus size: 25
64851 TCACTTTGAA
*
64861 TTCATTTTCTTTTATTTTTATTTTTC
1 TTCATTTT-TTTTCTTTTTATTTTTC
*
64887 TTCATTTTTTTTCTTTTTCTTTTTC
1 TTCATTTTTTTTCTTTTTATTTTTC
*
64912 TTCGTTTTCTTTTTCTTTT
1 TTC-ATTT-TTTTTCTTTT
64931 ATTCTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
25 18 0.46
26 11 0.28
27 10 0.26
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.79
Consensus pattern (25 bp):
TTCATTTTTTTTCTTTTTATTTTTC
Found at i:64909 original size:15 final size:15
Alignment explanation
Indices: 64865--64952 Score: 62
Period size: 15 Copynumber: 6.1 Consensus size: 15
64855 TTTGAATTCA
64865 TTTTCTTTTAT-TTTT
1 TTTTCTTTT-TCTTTT
* *
64880 ATTT-TTCTTCATTTT
1 TTTTCTTTTTC-TTTT
64895 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCTTTT
* *
64910 TCTTCGTTTTCTTTT
1 TTTTCTTTTTCTTTT
* *
64925 TCTT-TTATTC--TT
1 TTTTCTTTTTCTTTT
64937 TTTTC-TTTTCTTTT
1 TTTTCTTTTTCTTTT
64951 TT
1 TT
64953 CATTAGCAAC
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
12 9 0.16
13 1 0.02
14 11 0.19
15 31 0.54
16 5 0.09
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.81
Consensus pattern (15 bp):
TTTTCTTTTTCTTTT
Found at i:64921 original size:21 final size:19
Alignment explanation
Indices: 64875--64951 Score: 77
Period size: 19 Copynumber: 3.9 Consensus size: 19
64865 TTTTCTTTTA
* *
64875 TTTTTATTTTTCTTCATT-T
1 TTTTTCTTTTTCTT-TTTCT
64894 TTTTTCTTTTTCTTTTTCT
1 TTTTTCTTTTTCTTTTTCT
64913 TCGTTTTCTTTTTCTTTTATTCT
1 T--TTTTCTTTTTC-TTT-TTCT
64936 TTTTTC-TTTTCTTTTT
1 TTTTTCTTTTTCTTTTT
64952 TCATTAGCAA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.08
19 18 0.35
20 5 0.10
21 16 0.31
22 3 0.06
23 5 0.10
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.81
Consensus pattern (19 bp):
TTTTTCTTTTTCTTTTTCT
Found at i:65645 original size:18 final size:19
Alignment explanation
Indices: 65619--65665 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
65609 CCCCTTATTA
*
65619 TTTTATTTTATTTT-GTTC
1 TTTTCTTTTATTTTCGTTC
* *
65637 TTTTCTTTTTTTTTCTTTC
1 TTTTCTTTTATTTTCGTTC
65656 TTTTCATTTT
1 TTTTC-TTTT
65666 TCCTTTCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 12 0.50
19 8 0.33
20 4 0.17
ACGTcount: A:0.06, C:0.11, G:0.02, T:0.81
Consensus pattern (19 bp):
TTTTCTTTTATTTTCGTTC
Found at i:65655 original size:14 final size:14
Alignment explanation
Indices: 65638--65709 Score: 51
Period size: 14 Copynumber: 5.0 Consensus size: 14
65628 ATTTTGTTCT
65638 TTTCTTTTTTTTTC
1 TTTCTTTTTTTTTC
65652 TTTCTTTTCATTTTTCC
1 TTTCTTTT--TTTTT-C
*
65669 TTTCTATTTTTCTT-
1 TTTCT-TTTTTTTTC
* *
65683 TTTC-TCTTTTCTC
1 TTTCTTTTTTTTTC
65696 TTT-TATTTTTTTTC
1 TTTCT-TTTTTTTTC
65710 AAGCAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
12 5 0.11
13 3 0.07
14 19 0.42
16 9 0.20
17 6 0.13
18 3 0.07
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTCTTTTTTTTTC
Found at i:65666 original size:26 final size:26
Alignment explanation
Indices: 65637--65709 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
65627 TATTTTGTTC
*
65637 TTTTCTTTT-TTTTTCTTTCTTTTCAT
1 TTTTCTTTTATTTTTCTTTCTTCTC-T
65663 TTTTCCTTTCTATTTTTCTTT-TTCTCT
1 TTTT-CTTT-TATTTTTCTTTCTTCTCT
65690 TTTCTCTTTTATTTTT-TTTC
1 TTT-TCTTTTATTTTTCTTTC
65710 AAGCAAAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
25 3 0.07
26 11 0.27
27 12 0.29
28 6 0.15
29 9 0.22
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (26 bp):
TTTTCTTTTATTTTTCTTTCTTCTCT
Done.