Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002621.1 Hibiscus syriacus cultivar Beakdansim tig00005336_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: 58883
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:242 original size:39 final size:39
Alignment explanation
Indices: 189--268 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
179 AAGTTGTAGA
*
189 TTTGATTTCCTTTTGCTTGGCATCATATGAGATTTGGAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGAT
** *
228 TTTGATTTTTTTTTGCTTGGCACCATATGAGCTTTGGAT
1 TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGAT
267 TT
1 TT
269 GATGAGCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.51
Consensus pattern (39 bp):
TTTGATTTCCTTTTGCTTGGCACCATATGAGATTTGGAT
Found at i:548 original size:18 final size:18
Alignment explanation
Indices: 525--561 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
515 CGAAATATAT
525 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
543 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
561 A
1 A
562 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:978 original size:24 final size:24
Alignment explanation
Indices: 946--994 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
936 TTTTTCCAAA
*
946 TAATGTA-CCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTT-AAT
970 TAATGTACCCACAACAATGTTAAT
1 TAATGTACCCACAACAATGTTAAT
994 T
1 T
995 GATTTGTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.48
25 12 0.52
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (24 bp):
TAATGTACCCACAACAATGTTAAT
Found at i:1216 original size:23 final size:23
Alignment explanation
Indices: 1190--1251 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
1180 ATATAACCAC
1190 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
1213 TACCTA-TACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
1235 TACCTATTACATCATAT
1 TACCTATTACATTATAT
1252 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:1238 original size:22 final size:23
Alignment explanation
Indices: 1180--1251 Score: 83
Period size: 23 Copynumber: 3.2 Consensus size: 23
1170 ACACTTTACA
* *
1180 ATATAACCACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
*
1203 ATATAAACGATACCTA-TACATT
1 ATATAAACGCTACCTATTACATT
** *
1225 ATATAAGGGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
1248 ATAT
1 ATAT
1252 GTTTACCTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 19 0.46
23 22 0.54
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:4603 original size:183 final size:183
Alignment explanation
Indices: 4043--4920 Score: 1595
Period size: 182 Copynumber: 4.8 Consensus size: 183
4033 CTTAAATTAC
*
4043 CGACACTTTTTTAAATGGTATCGACCACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
1 CGACACTTTTTTAAATCGTATCGA-CACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
4108 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAA-CGGTATATTTATACCGGT
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
4172 TATATTACAAAATTATCTATTACA-TATAAATATGGGTTCCGATGTGTAAATGT
130 TATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
4225 CGATACTTTTTTAAATCGTATCGACAC-TTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
* *
4289 ATTATAAAGTGTCGAGATAGGTTGTAGACCTATTCGCGCAT-AAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
4353 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
4406 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
4471 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGATATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
4536 ATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
4589 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
4654 ATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
*
4718 ATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
131 ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
4771 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
4836 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * *
4901 ATATTGCAAATTTACCTATT
131 ATATTACAAAATTATCTATT
4921 TTTTATATAT
Statistics
Matches: 674, Mismatches: 17, Indels: 9
0.96 0.02 0.01
Matches are distributed among these distances:
179 3 0.00
180 118 0.18
181 58 0.09
182 278 0.41
183 217 0.32
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (183 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:4740 original size:365 final size:363
Alignment explanation
Indices: 4043--4920 Score: 1598
Period size: 365 Copynumber: 2.4 Consensus size: 363
4033 CTTAAATTAC
*
4043 CGACACTTTTTTAAATGGTATCGACCACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
1 CGACACTTTTTTAAATCGTATCGA-CACATTTTTCTTCCAATATGGACATAAAGTACCGACACAA
4108 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAA-CGGTATATTTATACCGGT
65 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGT
*
4172 TATATTACAAAATTATCTATTACATATAAATATGGGTTCCGATGTGTAAATGTCGATACTTTTTT
130 TATATTACAAAATTATCTATTACATATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
4237 AAATCGTATCGACACTTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTATAAAGTGTC
195 AAATCGTATCGACACTTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTATAAAGTGTC
4302 GAGATAGGTTGTAGACCTATTCGCGCATAAACCGGTATATTTATACCGGTTATATTACAAAATTA
260 GAGATAGGTTGTAGACCTATTCGCGCATAAACCGGTATATTTATACCGGTTATATTACAAAATTA
*
4367 TCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
325 TCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
*
4406 CGATACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
*
4471 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGATATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* *
4536 ATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
131 ATATTACAAAATTATCTATTACA-TATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTT
4601 AAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTA-AAAGTGT
195 AAATCGTATCGACAC-TTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTATAAAGTGT
*
4665 CGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTTATATTACAAAAT
259 CGAGATAGGTTGTAGACCTATTCGCGCAT-AAACCGGTATATTTATACCGGTTATATTACAAAAT
*
4730 TATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGT
323 TATCTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
4771 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
1 CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
4836 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
66 ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
* * *
4901 ATATTGCAAATTTACCTATT
131 ATATTACAAAATTATCTATT
4921 TTTTATATAT
Statistics
Matches: 496, Mismatches: 15, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
362 86 0.17
363 62 0.12
364 89 0.18
365 259 0.52
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (363 bp):
CGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAATATGGACATAAAGTACCGACACAAT
ATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCATAAAACCGGTATATTTATACCGGTT
ATATTACAAAATTATCTATTACATATAAATATGGGTTCCGATGTGTAAATGTCGACACTTTTTTA
AATCGTATCGACACTTTTTCTTCCAATATGGACATAAAGTACCGACACAATATTATAAAGTGTCG
AGATAGGTTGTAGACCTATTCGCGCATAAACCGGTATATTTATACCGGTTATATTACAAAATTAT
CTATTACATTATAAATATGGGTTCCGATGTGTAAATGT
Found at i:6346 original size:3 final size:3
Alignment explanation
Indices: 6338--6391 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
6328 ACTTGTTTGG
* * *
6338 ATC ATC ATC TTC ATC ATC ATC ATC ATC ATC GTC ATC ATC ATC GTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
6386 TTC ATC
1 ATC ATC
6392 GTCAGCTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:6355 original size:12 final size:12
Alignment explanation
Indices: 6338--6395 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
6328 ACTTGTTTGG
* *
6338 ATCATCATCTTC
1 ATCATCGTCATC
*
6350 ATCATCATCATC
1 ATCATCGTCATC
6362 ATCATCGTCATC
1 ATCATCGTCATC
6374 ATCATCGTCATC
1 ATCATCGTCATC
*
6386 TTCATCGTCA
1 ATCATCGTCA
6396 GCTTCATCTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 43 1.00
ACGTcount: A:0.26, C:0.33, G:0.05, T:0.36
Consensus pattern (12 bp):
ATCATCGTCATC
Found at i:6361 original size:18 final size:18
Alignment explanation
Indices: 6338--6406 Score: 75
Period size: 18 Copynumber: 3.8 Consensus size: 18
6328 ACTTGTTTGG
* *
6338 ATCATCATCTTCATCATC
1 ATCATCATCATCTTCATC
*
6356 ATCATCATCATCGTCATC
1 ATCATCATCATCTTCATC
*
6374 ATCATCGTCATCTTCATC
1 ATCATCATCATCTTCATC
* * *
6392 GTCAGCTTCATCTTC
1 ATCATCATCATCTTC
6407 TGCGCCGCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (18 bp):
ATCATCATCATCTTCATC
Found at i:6400 original size:12 final size:12
Alignment explanation
Indices: 6351--6403 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
6341 ATCATCTTCA
* *
6351 TCATCATCATCA
1 TCATCGTCATCT
*
6363 TCATCGTCATCA
1 TCATCGTCATCT
6375 TCATCGTCATCT
1 TCATCGTCATCT
*
6387 TCATCGTCAGCT
1 TCATCGTCATCT
6399 TCATC
1 TCATC
6404 TTCTGCGCCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.23, C:0.34, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:8935 original size:580 final size:580
Alignment explanation
Indices: 7855--9004 Score: 1911
Period size: 580 Copynumber: 2.0 Consensus size: 580
7845 TTTAAATTAG
*
7855 TATCGACACAAACTATATTAGTGTCGACACATTTTTTAGACATATTCTATCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTATCATAAAACCGGTATA
7920 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATA---------TC----ATTTTGGGAT
* **
7985 CGACACTTTTTATATATGGATCGGCACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
118 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAA
*
8050 AATATCGACACAAACTATATTAGCGTCGACACATTATTTAGACTATCTCTCATAAAATAAGTATA
183 AATATCGACACAAACTATATTAGCGTCGACACATTATTTAGACTATCTCTCATAAAACAAGTATA
8115 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
248 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* **
8180 CGACACTTTTTATATATGGATCGACACTTTTTGGGTGCACCCTGTTTTCCATTCATTCTGGAAAA
313 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAA
*
8245 CAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
378 AAAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
8310 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATATACTTTTGGGTTCGATGATTTTGG
443 TATAATTGTACCGGTTAGATTGAAAAATTACATATTACATATACTTTTGGGTTCGATGATTTTGG
*
8375 GATCGACACTTT-TTATATATGGATCGA-AACTTTATGGGTGCACCCTGTTTTCCATTCATTCTG
508 GATCGACACTTTGTTATATATGGATCGACAA-TTTATGGGTGCACCATGTTTTCCATTCATTCTG
8438 GAAAACAAA
572 GAAAACAAA
* *
8447 TATCGACACAAACTATA-TAGTGTCGACACATTATTTATACATATTCTCTCAT-AAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTATCATAAAACCGGTATA
8510 ATTGTACCGGTTAGATTG-AAAATTACATATTACATTATA-C-TTTTGGGATCGACACTTTTTAT
66 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATATCATTTTGGGATCGACACTTTTTAT
8572 ATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAAAACAATATCGACA
131 ATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGG--AAAA-AATATCGACA
* **
8637 CAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACC
193 CAAACTATATTAGCGTCGACACATTATTTAGAC-TA-TCTCTCATAAAACAAGTATAATTGTACC
8702 GGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTT
256 GGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-T
*
8767 TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCGTTCTGGAAAAAAAATAT
320 TTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAAAAAATAT
8832 CGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATT
385 CGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATT
8897 GTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGA
450 GTACCGGTTAGATTGAAAAATTACATATTACA-TATACTTTTGGGTTCGATGATTTTGGGATCGA
8961 CACTTTGTTATATATGGATCGACAATTTATGGGTGCACCATGTT
514 CACTTTGTTATATATGGATCGACAATTTATGGGTGCACCATGTT
9005 GGCCATATTG
Statistics
Matches: 533, Mismatches: 16, Indels: 29
0.92 0.03 0.05
Matches are distributed among these distances:
574 67 0.13
576 4 0.01
577 42 0.08
578 2 0.00
579 117 0.22
580 167 0.31
581 33 0.06
582 2 0.00
589 21 0.04
590 29 0.05
591 32 0.06
592 17 0.03
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (580 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTATCATAAAACCGGTATA
ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATATCATTTTGGGATCGACACTTTTTAT
ATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAAAATATCGACACAA
ACTATATTAGCGTCGACACATTATTTAGACTATCTCTCATAAAACAAGTATAATTGTACCGGTTA
GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
ATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCATTCTGGAAAAAAAATATCGACAC
AAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCG
GTTAGATTGAAAAATTACATATTACATATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTG
TTATATATGGATCGACAATTTATGGGTGCACCATGTTTTCCATTCATTCTGGAAAACAAA
Found at i:8974 original size:199 final size:200
Alignment explanation
Indices: 8550--9010 Score: 863
Period size: 199 Copynumber: 2.3 Consensus size: 200
8540 TACATTATAC
8550 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCAT
1 TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCAT
8615 TCTGGAAAAAACAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTC
66 TCTGGAAAAAACAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTC
8680 ATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTC
131 ATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTC
8745 GATGA
196 GATGA
*
8750 TTTTGGGATCGACACTTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCG
1 TTTTGGGATCGACAC-TTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCA
8815 TTCTGGAAAAAA-AATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCT
65 TTCTGGAAAAAACAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCT
8879 CATAAAACCGGTATAATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTT
130 CATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTT
8943 CGATGA
195 CGATGA
* *
8949 TTTTGGGATCGACACTTTGTTATATATGGATCGACAATTTATGGGTGCACCATGTTGGCCAT
1 TTTTGGGATCGACACTTT-TTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCAT
9011 ATTGTAAATT
Statistics
Matches: 256, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
198 3 0.01
199 105 0.41
200 88 0.34
201 60 0.23
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (200 bp):
TTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCCTGTTGGCCATTCAT
TCTGGAAAAAACAATATCGACACAAACTATATTAGTGTCGACACATTATTTAGACATATTCTCTC
ATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTC
GATGA
Found at i:9161 original size:19 final size:18
Alignment explanation
Indices: 9123--9169 Score: 69
Period size: 19 Copynumber: 2.6 Consensus size: 18
9113 TTATATTCAC
9123 ATACAAAA-TATAATCGT
1 ATACAAAATTATAATCGT
*
9140 ATACAAAATTATAAATCTT
1 ATACAAAATTAT-AATCGT
9159 ATACAAAATTA
1 ATACAAAATTA
9170 ACCCTACATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 8 0.30
18 3 0.11
19 16 0.59
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (18 bp):
ATACAAAATTATAATCGT
Found at i:10997 original size:33 final size:33
Alignment explanation
Indices: 10960--11025 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
10950 CATCTTAATA
* * *
10960 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACACCAACTTCATTCACCACT
* *
10993 TCACCCCTCAACACATCTACTTCATTCACCACT
1 TCACCCCTCAACACACCAACTTCATTCACCACT
11026 CCATCTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.47, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACACCAACTTCATTCACCACT
Found at i:11099 original size:21 final size:21
Alignment explanation
Indices: 11059--11123 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
11049 CCCCTTATGC
* *
11059 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTTTCTCTTCGACT
*
11080 CTCTCGAGTTTCTCTACGACT
1 CTCTCGAGTTTCTCTTCGACT
* *
11101 -TGATCAAGTTTCTCTTCGACT
1 CT-CTCGAGTTTCTCTTCGACT
11122 CT
1 CT
11124 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:13376 original size:17 final size:18
Alignment explanation
Indices: 13354--13396 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
13344 ATATATCCGG
13354 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
13371 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
13391 TATCAT
1 TATCAT
13397 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:13414 original size:20 final size:19
Alignment explanation
Indices: 13359--13405 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
13349 TCCGGTATCA
13359 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
13378 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
13399 TTTTACC
1 TTTTACC
13406 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:13553 original size:20 final size:20
Alignment explanation
Indices: 13527--13572 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
13517 CACTTTTAAA
13527 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
13546 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
13567 TTTACC
1 TTTACC
13573 TGTATATCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:14722 original size:2 final size:2
Alignment explanation
Indices: 14717--14771 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
14707 TTTCTGTTTG
14717 AT 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 AT
14759 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
14772 CTGGCTGTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27650 original size:157 final size:154
Alignment explanation
Indices: 27350--27659 Score: 586
Period size: 157 Copynumber: 2.0 Consensus size: 154
27340 GACAACCATG
27350 CTTCGGAGAAGATAAAAACCCTAACATGGAAATGAATGAAGCAGCGAAAATTTCAATGAAGAGTT
1 CTTCGGAGAAGATAAAAACCCTAACATGGAAATGAATGAAGCAGCGAAAATTTCAATGAAGAGTT
27415 TCCCTAAAAGTGTAGGGAGAAAAAAAAACAAGAAAATTGCCTCCTCAGCTTTGATTAAGGGTCAG
66 TCCCTAAAAGTGTAGGGAG--AAAAAAACAAGAAAATTGCCTCCTCAGCTTTGATTAAGGGTCAG
27480 TGGACAGATGAGGAGGACAGGTGATA
129 TGGACAGATGAGGAGGACAGGTGATA
27506 CTTCGGCAGAAGATAAAAACCCTAACATGGAAATGAATGAAGCAGCGAAAATTTCAATGAAGAGT
1 CTTCGG-AGAAGATAAAAACCCTAACATGGAAATGAATGAAGCAGCGAAAATTTCAATGAAGAGT
27571 TTCCCTAAAAGTGTAGGGAG-AAAAAACAAGAAAATTGCCTCCTCAGCTTTGATTAAGGGTCAGT
65 TTCCCTAAAAGTGTAGGGAGAAAAAAACAAGAAAATTGCCTCCTCAGCTTTGATTAAGGGTCAGT
27635 GGACAGATGAGGAGGACAGGTGATA
130 GGACAGATGAGGAGGACAGGTGATA
27660 TATAGAACAG
Statistics
Matches: 153, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
154 69 0.45
156 6 0.04
157 78 0.51
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (154 bp):
CTTCGGAGAAGATAAAAACCCTAACATGGAAATGAATGAAGCAGCGAAAATTTCAATGAAGAGTT
TCCCTAAAAGTGTAGGGAGAAAAAAACAAGAAAATTGCCTCCTCAGCTTTGATTAAGGGTCAGTG
GACAGATGAGGAGGACAGGTGATA
Found at i:33140 original size:34 final size:32
Alignment explanation
Indices: 33102--33164 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
33092 ACCATATGCA
33102 AAGTTGGCCACCAACCAAAGATGAATTTTTCAAT
1 AAGTTGGCCACCAACC-AAGATG-ATTTTTCAAT
* *
33136 AAGTTGGTCACCAAGCAAGATGATTTTTC
1 AAGTTGGCCACCAACCAAGATGATTTTTC
33165 CAACTTGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 7 0.26
33 6 0.22
34 14 0.52
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (32 bp):
AAGTTGGCCACCAACCAAGATGATTTTTCAAT
Found at i:35316 original size:7 final size:7
Alignment explanation
Indices: 35304--35332 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
35294 AGATCTTTTG
35304 CTTTGGA
1 CTTTGGA
35311 CTTTGGA
1 CTTTGGA
35318 CTTTGGA
1 CTTTGGA
35325 CTTTGGA
1 CTTTGGA
35332 C
1 C
35333 GTTATCTGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.17, G:0.28, T:0.41
Consensus pattern (7 bp):
CTTTGGA
Found at i:58259 original size:16 final size:17
Alignment explanation
Indices: 58238--58289 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
58228 TTTTTAATTT
58238 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
58254 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
58269 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
58286 AATT
1 AATT
58290 TATTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Done.