Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004681.1 Hibiscus syriacus cultivar Beakdansim tig00010495_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: 74300
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2280 original size:26 final size:26
Alignment explanation
Indices: 2234--2284 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2224 GAATCGGGTG
*
2234 AAACCTTAATTTCGTCAGATCGAATA
1 AAACCTTAATTTCATCAGATCGAATA
* *
2260 AAACCTTAATTTTATCGGATCGAAT
1 AAACCTTAATTTCATCAGATCGAAT
2285 CACAGATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (26 bp):
AAACCTTAATTTCATCAGATCGAATA
Found at i:12624 original size:31 final size:32
Alignment explanation
Indices: 12583--12643 Score: 97
Period size: 31 Copynumber: 1.9 Consensus size: 32
12573 TGGGGTAAAT
12583 TATGTGTTTAGTACCTAAAATATCAATTTTGA
1 TATGTGTTTAGTACCTAAAATATCAATTTTGA
* *
12615 TATGT-TTTAGTACCTAAACTTTCAATTTT
1 TATGTGTTTAGTACCTAAAATATCAATTTT
12644 TTCATAACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (32 bp):
TATGTGTTTAGTACCTAAAATATCAATTTTGA
Found at i:13981 original size:60 final size:61
Alignment explanation
Indices: 13887--14007 Score: 181
Period size: 60 Copynumber: 2.0 Consensus size: 61
13877 AAGTTTTATG
13887 TTGTCTTATTCTGTATTAAAAAAAACTATAAATATCGACTGTTAATGAATTAATATTTTTA
1 TTGTCTTATTCTGTATTAAAAAAAACTATAAATATCGACTGTTAATGAATTAATATTTTTA
* * ** * *
13948 TTGTGTTATTCTTTATTTTAAAAAA-TATAAATATTGGCTGTTAATGAATTAATATTTTTA
1 TTGTCTTATTCTGTATTAAAAAAAACTATAAATATCGACTGTTAATGAATTAATATTTTTA
14008 AACGAATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
60 33 0.61
61 21 0.39
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.48
Consensus pattern (61 bp):
TTGTCTTATTCTGTATTAAAAAAAACTATAAATATCGACTGTTAATGAATTAATATTTTTA
Found at i:14023 original size:60 final size:61
Alignment explanation
Indices: 13892--14024 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 61
13882 TTATGTTGTC
* ** ** **
13892 TTATTCTGTATTAAAAAAAACTATAAATATCGACTGTTAATGAATTAATATTTTTATTGTG
1 TTATTCTTTATTTTAAAAAACTATAAATATCGACTGTTAATGAATTAATATTTTTAACGAA
* *
13953 TTATTCTTTATTTTAAAAAA-TATAAATATTGGCTGTTAATGAATTAATATTTTTAAACGAA
1 TTATTCTTTATTTTAAAAAACTATAAATATCGACTGTTAATGAATTAATATTTTT-AACGAA
14014 TTATT-TTTATT
1 TTATTCTTTATT
14025 AAAAACAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
60 38 0.61
61 24 0.39
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.48
Consensus pattern (61 bp):
TTATTCTTTATTTTAAAAAACTATAAATATCGACTGTTAATGAATTAATATTTTTAACGAA
Found at i:14781 original size:24 final size:24
Alignment explanation
Indices: 14754--14814 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
14744 CTTGTACGAT
*
14754 ACGCCTTTAGGTGATTCATTGTTC
1 ACGCCCTTAGGTGATTCATTGTTC
14778 ACGCCCTTAGGTGATTCATTGTTC
1 ACGCCCTTAGGTGATTCATTGTTC
14802 ACGCCCTTAGGTG
1 ACGCCCTTAGGTG
14815 TAGCTAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (24 bp):
ACGCCCTTAGGTGATTCATTGTTC
Found at i:19522 original size:12 final size:12
Alignment explanation
Indices: 19507--19541 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
19497 TGAGGATGAC
19507 GATGATGACGAT
1 GATGATGACGAT
*
19519 GATGATGACGGT
1 GATGATGACGAT
*
19531 GGTGATGACGA
1 GATGATGACGA
19542 CGACGACGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.09, G:0.40, T:0.23
Consensus pattern (12 bp):
GATGATGACGAT
Found at i:24951 original size:2 final size:2
Alignment explanation
Indices: 24944--24982 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24934 ATTAAATGCT
24944 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
24983 GTAATTAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33151 original size:19 final size:19
Alignment explanation
Indices: 33124--33190 Score: 100
Period size: 19 Copynumber: 3.5 Consensus size: 19
33114 TCTACAGTTG
33124 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTTCAAAT
* *
33143 TCATTGCGATTTTCCAAAT
1 TCGTTGCGATTTTTCAAAT
33162 TCGTTGCGA-TTTTCTAAAT
1 TCGTTGCGATTTTTC-AAAT
33181 TCGTTGCGAT
1 TCGTTGCGAT
33191 AGTCTACAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
18 4 0.10
19 38 0.90
ACGTcount: A:0.21, C:0.18, G:0.16, T:0.45
Consensus pattern (19 bp):
TCGTTGCGATTTTTCAAAT
Found at i:33224 original size:21 final size:22
Alignment explanation
Indices: 33181--33233 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
33171 TTTTCTAAAT
*
33181 TCGTTGCGATAGTCTACAGTTG
1 TCGTTGCGATACTCTACAGTTG
*
33203 TCGTTGCGATACT-TATAGTTG
1 TCGTTGCGATACTCTACAGTTG
*
33224 TCATTGCGAT
1 TCGTTGCGAT
33234 TTTCCAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 16 0.57
22 12 0.43
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.40
Consensus pattern (22 bp):
TCGTTGCGATACTCTACAGTTG
Found at i:34681 original size:50 final size:50
Alignment explanation
Indices: 34622--34724 Score: 206
Period size: 50 Copynumber: 2.1 Consensus size: 50
34612 ACAAGAAGAG
34622 AAAGATACACAGAAATCAACGATAGCAAGCAACGGGAAAGAAATAAGGGC
1 AAAGATACACAGAAATCAACGATAGCAAGCAACGGGAAAGAAATAAGGGC
34672 AAAGATACACAGAAATCAACGATAGCAAGCAACGGGAAAGAAATAAGGGC
1 AAAGATACACAGAAATCAACGATAGCAAGCAACGGGAAAGAAATAAGGGC
34722 AAA
1 AAA
34725 TAGGTTAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.53, C:0.16, G:0.23, T:0.08
Consensus pattern (50 bp):
AAAGATACACAGAAATCAACGATAGCAAGCAACGGGAAAGAAATAAGGGC
Found at i:49466 original size:22 final size:22
Alignment explanation
Indices: 49441--49489 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
49431 TTGTTTCATT
49441 TTAATACAC-CAATGTTAAAAAC
1 TTAATAC-CTCAATGTTAAAAAC
*
49463 TTAATGCCTCAATGTTAAAAAC
1 TTAATACCTCAATGTTAAAAAC
49485 TTAAT
1 TTAAT
49490 GCGTTTAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (22 bp):
TTAATACCTCAATGTTAAAAAC
Found at i:49490 original size:22 final size:22
Alignment explanation
Indices: 49450--49491 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
49440 TTTAATACAC
49450 CAATGTTAAAAACTTAATGCCT
1 CAATGTTAAAAACTTAATGCCT
49472 CAATGTTAAAAACTTAATGC
1 CAATGTTAAAAACTTAATGC
49492 GTTTAGTACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (22 bp):
CAATGTTAAAAACTTAATGCCT
Found at i:50089 original size:2 final size:2
Alignment explanation
Indices: 50082--50121 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
50072 CTGTCTATGA
50082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50122 TAAAAACAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52278 original size:20 final size:20
Alignment explanation
Indices: 52250--52321 Score: 108
Period size: 20 Copynumber: 3.6 Consensus size: 20
52240 ATCCTATTCC
*
52250 CTGGTAATCTTATATTCCCA
1 CTGGTAATCTTACATTCCCA
*
52270 CTGGCAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
52290 CTGATAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
*
52310 CTAGTAATCTTA
1 CTGGTAATCTTA
52322 TATTTCGTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:54552 original size:112 final size:112
Alignment explanation
Indices: 54364--55087 Score: 1106
Period size: 112 Copynumber: 6.5 Consensus size: 112
54354 ATATGTACAA
* * *
54364 AAAGTATCAATACTTTTAACATATACGGTAGCTCTTTACCGGTTTTGTCATAATGAAACAGGTTT
1 AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
* * * * *
54429 TATCATGTTTTTACTTGTTATATCGTTATGTATCGATACATTTTTAT
66 TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
* * * * *
54476 AAAGTATAGATACTTTTAATATATCCGATAGCTCTTTACCGGTTTTGTCATTATAAAACTGGTTT
1 AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
* *
54541 TGTCATATTTTTACCTATTATATTGTTATGTATTAATACATTTTTAT
66 TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
* * *
54588 AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGATTTTGTCATAACGAAACTGATTT
1 AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
*
54653 TGTCATATTTTTACCTGTTATATTGTTATGTATTAATACATTTTTAT
66 TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
* * *
54700 AAAATATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTTTCATAATGAAACTGATTT
1 AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
*
54765 TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAA
66 TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
* ** * *
54812 AAAGTATCGATACTTTTAACATATTCGACATCTCTTTACCAGTTTTGTCATAATGAAACTGGTTT
1 AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
* * *
54877 TATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTGT
66 TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
54924 AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
1 AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
* * * *
54989 TGTTATATTTTTAACTGTTATATTGTTATGTATCGATACATTTTTAA
66 TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
* **
55036 AAAGTATCGATACTTTTAACATATCCGGTATCTCTTTACTAGTTTTGTCATA
1 AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTGTCATA
55088 TTTTTACCTG
Statistics
Matches: 557, Mismatches: 55, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
112 557 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.46
Consensus pattern (112 bp):
AAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTT
TGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAT
Found at i:54768 original size:224 final size:223
Alignment explanation
Indices: 54362--55256 Score: 1243
Period size: 224 Copynumber: 4.1 Consensus size: 223
54352 ATATATGTAC
* * * * *
54362 AAAAAGTATCAATACTTTTAACATATACGGTAGCTCTTTACCGGTTTTGTCATAATGAAACAGGT
1 AAAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACC-ATTTTGTCATAACGAAACTGGT
* * * *
54427 TTTATCATGTTTTTACTTGTTATATCGTTATGTATCGATACATTTTTATAAAGTATAGATACTTT
65 TTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTT
* * * *
54492 TAATATATCCGATAGCTCTTTACCGGTTTTGTCATTATAAAACTGGTTTTGTCATATTTTTACCT
130 TAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCT
* *
54557 ATTATATTGTTATGTATTAATACATTTTT
195 GTTATATTGTTATGTATCAATACATTTTT
* *
54586 ATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGATTTTGTCATAACGAAACTGAT
1 AAAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACC-ATTTTGTCATAACGAAACTGGT
* ** *
54651 TTTGTCATATTTTTACCTGTTATATTGTTATGTATTAATACATTTTTATAAAATATCGATACTTT
65 TTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTT
* *
54716 TAACATATCCGGTAGCTCTTTACCGGTTTTTTCATAATGAAACTGATTTTGTCATATTTTTACCT
130 TAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCT
54781 GTTATATTGTTATGTATCAATACATTTTT
195 GTTATATTGTTATGTATCAATACATTTTT
* ** * *
54810 AAAAAGTATCGATACTTTTAACATATTCGACATCTCTTTACCAGTTTTGTCATAATGAAACTGGT
1 AAAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCA-TTTTGTCATAACGAAACTGGT
*
54875 TTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTGTAAAGTATCGATACTTT
65 TTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTT
* *
54940 TAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTTATATTTTTAACT
130 TAACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCT
*
55005 GTTATATTGTTATGTATCGATACATTTTT
195 GTTATATTGTTATGTATCAATACATTTTT
*
55034 AAAAAGTATCGATACTTTTAACATATCCGGTA--TC--T--C----T-T--T------ACTAGTT
1 AAAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCATTTTGTCATAACGAAACTGGTT
* * * * *
55080 TTGTCATATTTTTACCTGTTATATTGTTATGTATTGATACATTTTTATGAAGTGTCGATATTTTT
66 TTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTTT
55145 AACATATCCGGTAGCTCTTTACCGGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCT
131 AACATATCCGGTAGCTCTTTACCGG-TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCT
** *
55210 GTTATATTGTTATGTATTGATACACTTTT
195 GTTATATTGTTATGTATCAATACATTTTT
*
55239 ATAAAGTATCGATACTTT
1 AAAAAGTATCGATACTTT
55257 ATAGGCACTA
Statistics
Matches: 614, Mismatches: 55, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
204 90 0.15
205 81 0.13
210 1 0.00
212 1 0.00
213 1 0.00
218 1 0.00
220 1 0.00
222 2 0.00
223 1 0.00
224 435 0.71
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (223 bp):
AAAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCATTTTGTCATAACGAAACTGGTT
TTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTTT
AACATATCCGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTG
TTATATTGTTATGTATCAATACATTTTT
Found at i:54999 original size:336 final size:334
Alignment explanation
Indices: 54362--55256 Score: 1279
Period size: 336 Copynumber: 2.7 Consensus size: 334
54352 ATATATGTAC
* * *
54362 AAAAAGTATCAATACTTTTAACATATACGGTAGCTCTTTACCGGTTTTGTCATAATGAAACAGGT
1 AAAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTTTCATAATGAAAC--GT
* * * * *
54427 TTTATCATGTTTTTACTTGTTATATCGTTATGTATCGATACATTTTTATAAAGTATAGATACTTT
64 TTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTT
* * *
54492 TAATATATCCGATAGCTCTTTACCGGTTTTGTCATTATAAAACTGGTTTTGTCATATTTTTACCT
129 TAACATATCCGATAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCT
* *
54557 ATTATATTGTTATGTATTAATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTC
194 GTTATATTGTTATGTATTGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTC
* *
54622 TTTACCGATTTTGTCATAACGAAACTGATTTTGTCATATTTTTACCTGTTATATTGTTATGTATT
259 TTTACCGATTTTGTCATAACGAAACTGATTTTGTCATATTTTTAACTGTTATATTGTTATGTATC
54687 AATACATTTTT
324 AATACATTTTT
54698 ATAAAA-TATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTTTCATAATGAAACTGA
1 A-AAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTTTCATAATGAAAC-G-
* *
54762 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCAATACATTTTTAAAAAGTATCGATACTT
63 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTT
* * * * *
54827 TTAACATATTCGACATCTCTTTACCAGTTTTGTCATAATGAAACTGGTTTTATCATATTTTTACC
128 TTAACATATCCGATAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACC
* *
54892 TGTTATATTGTTATGTATCGATACATTTTTGTAAAGTATCGATACTTTTAACATATCCGGTAGCT
193 TGTTATATTGTTATGTATTGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCT
* * * *
54957 CTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTTATATTTTTAACTGTTATATTGTTATGTAT
258 CTTTACCGATTTTGTCATAACGAAACTGATTTTGTCATATTTTTAACTGTTATATTGTTATGTAT
*
55022 CGATACATTTTT
323 CAATACATTTTT
*
55034 AAAAAGTATCGATACTTTTAACATATCCGGTA--TC--T--C------TT--TACT---A-GTTT
1 AAAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTTTCATAATGAAACGTTT
* * * *
55081 TGTCATATTTTTACCTGTTATATTGTTATGTATTGATACATTTTTATGAAGTGTCGATATTTTTA
66 TGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTTTA
*
55146 ACATATCCGGTAGCTCTTTACCGGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTG
131 ACATATCCGATAGCTCTTTACCGG-TTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTG
*
55211 TTATATTGTTATGTATTGATACACTTTTATAAAGTATCGATACTTT
195 TTATATTGTTATGTATTGATACATTTTTATAAAGTATCGATACTTT
55257 ATAGGCACTA
Statistics
Matches: 509, Mismatches: 46, Indels: 27
0.87 0.08 0.05
Matches are distributed among these distances:
316 81 0.16
317 83 0.16
319 1 0.00
322 3 0.01
324 2 0.00
330 1 0.00
332 1 0.00
334 2 0.00
335 5 0.01
336 326 0.64
337 4 0.01
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (334 bp):
AAAAAGTATCGATACTTTTAACATATCCGGTAGCTCTTTACCGGTTTTTTCATAATGAAACGTTT
TGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACTTTTA
ACATATCCGATAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTACCTGT
TATATTGTTATGTATTGATACATTTTTATAAAGTATCGATACTTTTAACATATCCGGTAGCTCTT
TACCGATTTTGTCATAACGAAACTGATTTTGTCATATTTTTAACTGTTATATTGTTATGTATCAA
TACATTTTT
Found at i:55089 original size:92 final size:92
Alignment explanation
Indices: 54985--55180 Score: 293
Period size: 92 Copynumber: 2.1 Consensus size: 92
54975 AATGAAACTG
*
54985 GTTTTGTTATATTTTTAACTGTTATATTGTTATGTATCGATACATTTTTAAAAAGTATCGATACT
1 GTTTTGTCATATTTTTAACTGTTATATTGTTATGTATCGATACATTTTTAAAAAGTATCGATACT
* *
55050 TTTAACATATCCGGTATCTCTTTACTA
66 TTTAACATATCCGGTAGCTCTTTACCA
* * ** * *
55077 GTTTTGTCATATTTTTACCTGTTATATTGTTATGTATTGATACATTTTTATGAAGTGTCGATATT
1 GTTTTGTCATATTTTTAACTGTTATATTGTTATGTATCGATACATTTTTAAAAAGTATCGATACT
*
55142 TTTAACATATCCGGTAGCTCTTTACCG
66 TTTAACATATCCGGTAGCTCTTTACCA
55169 GTTTTTGTCATA
1 G-TTTTGTCATA
55181 ATGAAACTGG
Statistics
Matches: 93, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
92 83 0.89
93 10 0.11
ACGTcount: A:0.25, C:0.12, G:0.13, T:0.49
Consensus pattern (92 bp):
GTTTTGTCATATTTTTAACTGTTATATTGTTATGTATCGATACATTTTTAAAAAGTATCGATACT
TTTAACATATCCGGTAGCTCTTTACCA
Found at i:55096 original size:204 final size:205
Alignment explanation
Indices: 54873--55256 Score: 662
Period size: 204 Copynumber: 1.9 Consensus size: 205
54863 AATGAAACTG
*
54873 GTTTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTGTAAAGTATCGATACT
1 GTTTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACT
*
54938 TTTAACATATCCGGTAGCTCTTTACCGG-TTTTGTCATAATGAAACTGGTTTTGTTATATTTTTA
66 TTTAACATATCCGGTAGCTCTTTACCGGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTA
*
55002 ACTGTTATATTGTTATGTATCGATACATTTTTAAAAAGTATCGATACTTTTAACATATCCGGTAT
131 ACTGTTATATTGTTATGTATCGATACACTTTTAAAAAGTATCGATACTTTTAACATATCCGGTAT
55067 CTCTTTACTA
196 CTCTTTACTA
* * * * *
55077 GTTTTGTCATATTTTTACCTGTTATATTGTTATGTATTGATACATTTTTATGAAGTGTCGATATT
1 GTTTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACT
55142 TTTAACATATCCGGTAGCTCTTTACCGGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTA
66 TTTAACATATCCGGTAGCTCTTTACCGGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTA
* * *
55207 CCTGTTATATTGTTATGTATTGATACACTTTTATAAAGTATCGATACTTT
131 ACTGTTATATTGTTATGTATCGATACACTTTTAAAAAGTATCGATACTTT
55257 ATAGGCACTA
Statistics
Matches: 168, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
204 87 0.52
205 81 0.48
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (205 bp):
GTTTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTATAAAGTATCGATACT
TTTAACATATCCGGTAGCTCTTTACCGGTTTTTGTCATAATGAAACTGGTTTTGTCATATTTTTA
ACTGTTATATTGTTATGTATCGATACACTTTTAAAAAGTATCGATACTTTTAACATATCCGGTAT
CTCTTTACTA
Found at i:55577 original size:72 final size:73
Alignment explanation
Indices: 55344--55594 Score: 306
Period size: 74 Copynumber: 3.4 Consensus size: 73
55334 ATCCGGTAGG
* * * * *
55344 TATTTTAATGTAATAGGTTGCGCATATTTTATTTTACCGTTTACATTATTAGTAATCTTTAAACA
1 TATTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTATTAGCAA-CCTTAAAAA
* *
55409 AACTGATAGG
64 AACCGATAGA
* * * * * *
55419 TATTTTAATATAATATGTAACACTTATTTTTTTTACCGTTTACAATATTAGCAACCTTAAAAAAA
1 TATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTT-AAAAAA
*
55484 ACCGATTGA
65 ACCGATAGA
* * *
55493 TAATTTAATGTAATAGGTAGCGCCTA-TTTTTTTACCATTTACATTATTAGCAACCTTCAAAAAA
1 TATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAA
55557 CCGATAGA
66 CCGATAGA
*
55565 TATTCTAATGTAATAGGTAGCGCCTATTTT
1 TATTTTAATGTAATAGGTAGCGCCTATTTT
55595 ATATTTTCGA
Statistics
Matches: 149, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
72 37 0.25
73 35 0.23
74 53 0.36
75 24 0.16
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.41
Consensus pattern (73 bp):
TATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAA
CCGATAGA
Found at i:55950 original size:11 final size:11
Alignment explanation
Indices: 55934--55972 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
55924 CATTTACTCT
55934 TAAAAAAATAA
1 TAAAAAAATAA
55945 TAAAAAAAATAA
1 T-AAAAAAATAA
55957 TAAAAAAATAA
1 TAAAAAAATAA
55968 TAAAA
1 TAAAA
55973 GGTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
TAAAAAAATAA
Found at i:55952 original size:12 final size:12
Alignment explanation
Indices: 55935--55972 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
55925 ATTTACTCTT
55935 AAAAAAATAATA
1 AAAAAAATAATA
55947 AAAAAAATAAT-
1 AAAAAAATAATA
55958 AAAAAAATAATA
1 AAAAAAATAATA
55970 AAA
1 AAA
55973 GGTTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAATAATA
Found at i:61982 original size:19 final size:19
Alignment explanation
Indices: 61958--61996 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
61948 TTTAAATCGT
61958 ATAATGATCATACATGAAA
1 ATAATGATCATACATGAAA
61977 ATAATGATCATACATGAAA
1 ATAATGATCATACATGAAA
61996 A
1 A
61997 AAAGTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (19 bp):
ATAATGATCATACATGAAA
Found at i:73940 original size:16 final size:14
Alignment explanation
Indices: 73912--73959 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 14
73902 AAATCGAAAC
73912 CGGTTTTTTCGGTT
1 CGGTTTTTTCGGTT
73926 CGGTTTTTTAACGGTT
1 CGGTTTTTT--CGGTT
73942 CAGG-TTTTTC-GTT
1 C-GGTTTTTTCGGTT
73955 CGGTT
1 CGGTT
73960 CGTTTATCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.07
13 5 0.17
14 10 0.33
16 11 0.37
17 2 0.07
ACGTcount: A:0.06, C:0.15, G:0.27, T:0.52
Consensus pattern (14 bp):
CGGTTTTTTCGGTT
Done.