Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004821.1 Hibiscus syriacus cultivar Beakdansim tig00010865_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: 427682
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:284223 original size:31 final size:31
Alignment explanation
Indices: 284182--284260 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
284172 TTTTGAAAAC
* *
284182 ATTAAAAATTTAAATATTATAATAAATTAAA
1 ATTAATAATTTAAATACTATAATAAATTAAA
284213 ATTAATAATTTAAATACTATAATAAATTAAA
1 ATTAATAATTTAAATACTATAATAAATTAAA
284244 ATTAATAATTTAAATAC
1 ATTAATAATTTAAATAC
284261 AGAACATGTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (31 bp):
ATTAATAATTTAAATACTATAATAAATTAAA
Found at i:291002 original size:31 final size:30
Alignment explanation
Indices: 290967--291045 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 30
290957 GGTATTAATT
290967 AAAGAATACTTTAGGTACCTATTTTGACCAA
1 AAAG-ATACTTTAGGTACCTATTTTGACCAA
* *
290998 AAAGATAACTTTAGGAACTTATTTTGACCAA
1 AAAGAT-ACTTTAGGTACCTATTTTGACCAA
* *
291029 AAATATACTTTAAGTAC
1 AAAGATACTTTAGGTAC
291046 TTGAATGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 11 0.26
31 31 0.74
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.33
Consensus pattern (30 bp):
AAAGATACTTTAGGTACCTATTTTGACCAA
Found at i:297900 original size:23 final size:23
Alignment explanation
Indices: 297874--297921 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
297864 TTTATTGACG
*
297874 AATTTATA-ATATTTTAAAATATA
1 AATTTATATA-ATTTTAAAAAATA
297897 AATTTATATAATTTTAAAAAATA
1 AATTTATATAATTTTAAAAAATA
297920 AA
1 AA
297922 AAATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTTATATAATTTTAAAAAATA
Found at i:297928 original size:24 final size:23
Alignment explanation
Indices: 297884--297930 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
297874 AATTTATAAT
* **
297884 ATTTTAAAATATAAATTTATATA
1 ATTTTAAAAAATAAAAATATATA
297907 ATTTTAAAAAATAAAAAATATATA
1 ATTTTAAAAAAT-AAAAATATATA
297931 TATAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTTAAAAAATAAAAATATATA
Found at i:302741 original size:14 final size:14
Alignment explanation
Indices: 302722--302751 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
302712 AACTCAATTA
*
302722 ATTTATGTTGGTTT
1 ATTTATGTTCGTTT
302736 ATTTATGTTCGTTT
1 ATTTATGTTCGTTT
302750 AT
1 AT
302752 CGTTTAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (14 bp):
ATTTATGTTCGTTT
Found at i:310851 original size:15 final size:14
Alignment explanation
Indices: 310822--310867 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
310812 TTGACAACCG
310822 AAAA-ATATT-ATA
1 AAAATATATTAATA
*
310834 AAAATATTTTCAATA
1 AAAATATATT-AATA
310849 AAAATATATTAA-A
1 AAAATATATTAATA
310862 AAAATA
1 AAAATA
310868 AATATTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 11 0.38
14 2 0.07
15 12 0.41
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATATATTAATA
Found at i:312241 original size:21 final size:21
Alignment explanation
Indices: 312215--312259 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
312205 ATATGATTAA
312215 TCATATGTCGAT-TTTTCCTTT
1 TCATATGTC-ATATTTTCCTTT
*
312236 TCATATGTCATATTTTTCTTT
1 TCATATGTCATATTTTCCTTT
312257 TCA
1 TCA
312260 GACGGAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.58
Consensus pattern (21 bp):
TCATATGTCATATTTTCCTTT
Found at i:319745 original size:32 final size:32
Alignment explanation
Indices: 319708--319770 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
319698 AAGCAAACCC
*
319708 TTTGAAATTTATTTGAATTAATCACTTATATA
1 TTTGAAATTTATTTGAATTAATCACTGATATA
*
319740 TTTGAAATTTGTTTGAATTAATCACTGATAT
1 TTTGAAATTTATTTGAATTAATCACTGATAT
319771 TTAATATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (32 bp):
TTTGAAATTTATTTGAATTAATCACTGATATA
Found at i:322188 original size:2 final size:2
Alignment explanation
Indices: 322181--322233 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
322171 CCATGCCCCA
322181 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
*
322223 AT -T TT AT AT AT
1 AT AT AT AT AT AT
322234 TTCTTTTGTA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:323786 original size:21 final size:21
Alignment explanation
Indices: 323762--323805 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
323752 GTTGTGTCTG
323762 TAAGATATATACGTTATCAAT
1 TAAGATATATACGTTATCAAT
323783 TAAGATATATACGTTATCAAT
1 TAAGATATATACGTTATCAAT
323804 TA
1 TA
323806 GTTAGGAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (21 bp):
TAAGATATATACGTTATCAAT
Found at i:325278 original size:14 final size:16
Alignment explanation
Indices: 325249--325280 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
325239 ATGTCATTAT
325249 TTTATTAGAGATTAAA
1 TTTATTAGAGATTAAA
325265 TTTATTA-A-ATTAAA
1 TTTATTAGAGATTAAA
325279 TT
1 TT
325281 CAAACTATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 1 0.06
16 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTATTAGAGATTAAA
Found at i:330336 original size:29 final size:29
Alignment explanation
Indices: 330293--330375 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
330283 CTCACCTAAC
330293 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
330323 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
330352 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
330376 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:335103 original size:29 final size:29
Alignment explanation
Indices: 335060--335142 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
335050 CTCACCTAAC
335060 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
335090 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
335119 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
335143 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:335205 original size:2 final size:2
Alignment explanation
Indices: 335198--335222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
335188 ATGATCCAAC
335198 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 A
335223 AGAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:336097 original size:24 final size:24
Alignment explanation
Indices: 336069--336115 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
336059 TAAATCCTTT
*
336069 TATCTTTCTATTTAAAGTTGTAAA
1 TATCTTTCTAATTAAAGTTGTAAA
336093 TATCTTTCTAATTAAAGTTGTAA
1 TATCTTTCTAATTAAAGTTGTAA
336116 TTCAATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.49
Consensus pattern (24 bp):
TATCTTTCTAATTAAAGTTGTAAA
Found at i:339128 original size:28 final size:28
Alignment explanation
Indices: 339096--339154 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
339086 ATTTTATGTG
* * * *
339096 AGGGGTATATTTGAATTTTTAAAATTCT
1 AGGGGTAAATTTAAACTTATAAAATTCT
*
339124 AGGGGTAAATTTAAACTTATAAAATTTT
1 AGGGGTAAATTTAAACTTATAAAATTCT
339152 AGG
1 AGG
339155 AAAGACGAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.03, G:0.19, T:0.41
Consensus pattern (28 bp):
AGGGGTAAATTTAAACTTATAAAATTCT
Found at i:340995 original size:27 final size:27
Alignment explanation
Indices: 340957--341009 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
340947 GAATACATAT
340957 AAAATCGCCTTTTGAAAGAAAATTTTG
1 AAAATCGCCTTTTGAAAGAAAATTTTG
* * *
340984 AAAATCTCCTTTTTAAAGATAATTTT
1 AAAATCGCCTTTTGAAAGAAAATTTT
341010 AAGATGGGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (27 bp):
AAAATCGCCTTTTGAAAGAAAATTTTG
Found at i:341670 original size:20 final size:20
Alignment explanation
Indices: 341643--341695 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
341633 AATGCTAATG
*
341643 CATG-ATAAAGATAAAAGTAT
1 CATGAATAAAAATAAAA-TAT
341663 -ATGAATAAAAATAAAATAT
1 CATGAATAAAAATAAAATAT
*
341682 CATTAATAAAAATA
1 CATGAATAAAAATA
341696 TTTACTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (20 bp):
CATGAATAAAAATAAAATAT
Found at i:344206 original size:19 final size:18
Alignment explanation
Indices: 344177--344213 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
344167 TGTTCCTTTT
344177 GACACTCATTAATCCAAA
1 GACACTCATTAATCCAAA
344195 GACACATCATTAATCCAAA
1 GACAC-TCATTAATCCAAA
344214 TAGATGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.46, C:0.27, G:0.05, T:0.22
Consensus pattern (18 bp):
GACACTCATTAATCCAAA
Found at i:345003 original size:7 final size:7
Alignment explanation
Indices: 344991--345068 Score: 77
Period size: 7 Copynumber: 11.3 Consensus size: 7
344981 GTGTATAACT
344991 TAAACCC
1 TAAACCC
*
344998 TAAACCA
1 TAAACCC
*
345005 TGAACCC
1 TAAACCC
*
345012 TTAACCC
1 TAAACCC
* *
345019 TTAACAC
1 TAAACCC
*
345026 TTAACCC
1 TAAACCC
345033 TAAACCC
1 TAAACCC
*
345040 TAAATCC
1 TAAACCC
345047 T-AACCC
1 TAAACCC
*
345053 TAAACCT
1 TAAACCC
345060 TAAACCC
1 TAAACCC
345067 TA
1 TA
345069 TCACATAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
6 5 0.08
7 54 0.92
ACGTcount: A:0.40, C:0.37, G:0.01, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:345052 original size:20 final size:19
Alignment explanation
Indices: 344991--345065 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 19
344981 GTGTATAACT
344991 TAAACCCTAAACCATGAACCC
1 TAAACCCTAAACC-T-AACCC
* *
345012 TTAACCCTTAACACTTAACCC
1 TAAACCC-TAA-ACCTAACCC
345033 TAAACCCTAAATCCTAACCC
1 TAAACCCTAAA-CCTAACCC
*
345053 TAAACCTTAAACC
1 TAAACCCTAAACC
345066 CTATCACATA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.07
20 20 0.43
21 17 0.37
22 4 0.09
23 2 0.04
ACGTcount: A:0.40, C:0.37, G:0.01, T:0.21
Consensus pattern (19 bp):
TAAACCCTAAACCTAACCC
Found at i:345568 original size:36 final size:36
Alignment explanation
Indices: 345503--345572 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
345493 GAGTGTATAC
* *
345503 CTTAACCCTAACTTTATTCTCAACTTAAAATCTTCT
1 CTTAACCCTAACTTTATCCTCAACCTAAAATCTTCT
*
345539 CTTAACCCTAATTTTAATCCT-AACCTAAAATCTT
1 CTTAACCCTAACTTT-ATCCTCAACCTAAAATCTT
345573 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 26 0.87
37 4 0.13
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (36 bp):
CTTAACCCTAACTTTATCCTCAACCTAAAATCTTCT
Found at i:346111 original size:29 final size:29
Alignment explanation
Indices: 346075--346131 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
346065 TTTAGGTTTC
*
346075 ATTTTGGTTCCTACATTAAAAACTTCATG
1 ATTTTGGTTCCCACATTAAAAACTTCATG
*
346104 ATTTTGGTTCCCGCATTAAAAACTTCAT
1 ATTTTGGTTCCCACATTAAAAACTTCAT
346132 ATTAATGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (29 bp):
ATTTTGGTTCCCACATTAAAAACTTCATG
Found at i:349397 original size:14 final size:14
Alignment explanation
Indices: 349378--349408 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
349368 ACCCATCTTG
349378 CATCCCATTGCTTC
1 CATCCCATTGCTTC
349392 CATCCCATTGCTTC
1 CATCCCATTGCTTC
349406 CAT
1 CAT
349409 TAGGCCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.42, G:0.06, T:0.35
Consensus pattern (14 bp):
CATCCCATTGCTTC
Found at i:373562 original size:24 final size:24
Alignment explanation
Indices: 373535--373585 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
373525 TTAAAAACCA
*
373535 TAAAATCAAGTGAAACAAAATAAT
1 TAAAATCAACTGAAACAAAATAAT
* * *
373559 TAAAATCAACTGCAACATAATATT
1 TAAAATCAACTGAAACAAAATAAT
373583 TAA
1 TAA
373586 GGTAAAACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.57, C:0.12, G:0.06, T:0.25
Consensus pattern (24 bp):
TAAAATCAACTGAAACAAAATAAT
Found at i:374709 original size:21 final size:21
Alignment explanation
Indices: 374671--374772 Score: 86
Period size: 21 Copynumber: 4.8 Consensus size: 21
374661 CATAATCAAA
*
374671 TTAAGGGTTTAGGGTTTAAGAT
1 TTAA-GGTTTAAGGTTTAAGAT
* * *
374693 TTAAGGCTTAAGGTTTATGGT
1 TTAAGGTTTAAGGTTTAAGAT
374714 TT-AGGTTTTAAGGTTT-AGTAT
1 TTAAGG-TTTAAGGTTTAAG-AT
374735 TTAAGGTTTATA-GTTTATAG-T
1 TTAAGGTTTA-AGGTTTA-AGAT
*
374756 TTAAGGTTTAGGGTTTA
1 TTAAGGTTTAAGGTTTA
374773 GGGTGTAATC
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
20 4 0.06
21 51 0.78
22 8 0.12
23 2 0.03
ACGTcount: A:0.25, C:0.01, G:0.26, T:0.47
Consensus pattern (21 bp):
TTAAGGTTTAAGGTTTAAGAT
Found at i:374776 original size:7 final size:7
Alignment explanation
Indices: 374671--374772 Score: 77
Period size: 7 Copynumber: 14.4 Consensus size: 7
374661 CATAATCAAA
374671 TTAAGGGT
1 TTAA-GGT
*
374679 TTAGGGT
1 TTAAGGT
*
374686 TTAAGAT
1 TTAAGGT
*
374693 TTAAGGC
1 TTAAGGT
374700 TTAAGGT
1 TTAAGGT
*
374707 TTATGGT
1 TTAAGGT
374714 TT-AGGTT
1 TTAAGG-T
374721 TTAAGGT
1 TTAAGGT
*
374728 TT-AGTAT
1 TTAAG-GT
374735 TTAAGGT
1 TTAAGGT
374742 TTATA-GT
1 TTA-AGGT
374749 TTATA-GT
1 TTA-AGGT
374756 TTAAGGT
1 TTAAGGT
*
374763 TTAGGGT
1 TTAAGGT
374770 TTA
1 TTA
374773 GGGTGTAATC
Statistics
Matches: 77, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
6 5 0.06
7 63 0.82
8 9 0.12
ACGTcount: A:0.25, C:0.01, G:0.26, T:0.47
Consensus pattern (7 bp):
TTAAGGT
Found at i:376559 original size:231 final size:231
Alignment explanation
Indices: 376156--376624 Score: 938
Period size: 231 Copynumber: 2.0 Consensus size: 231
376146 TTTAGAAAAT
376156 TAGTAATTATTAATTAGACTTTTTAATGGAATAATGTTTTAAATTAATTATTAAAAAATATAAAA
1 TAGTAATTATTAATTAGACTTTTTAATGGAATAATGTTTTAAATTAATTATTAAAAAATATAAAA
376221 AAGGTTAATGAACTGTTCGTGAATTTATCAAATCGAGTTGGATCTTGCTCGACTCAACTCGTAAA
66 AAGGTTAATGAACTGTTCGTGAATTTATCAAATCGAGTTGGATCTTGCTCGACTCAACTCGTAAA
376286 GGTCTTGAGTCAAGCGCAAGTTTGAGTTGAATCAACCTGAGTCAAGTGTTGACGTAGTTTTGACT
131 GGTCTTGAGTCAAGCGCAAGTTTGAGTTGAATCAACCTGAGTCAAGTGTTGACGTAGTTTTGACT
376351 GAGTCAAGTTCGAGCAGCTCACTCATTAAGCACCCC
196 GAGTCAAGTTCGAGCAGCTCACTCATTAAGCACCCC
376387 TAGTAATTATTAATTAGACTTTTTAATGGAATAATGTTTTAAATTAATTATTAAAAAATATAAAA
1 TAGTAATTATTAATTAGACTTTTTAATGGAATAATGTTTTAAATTAATTATTAAAAAATATAAAA
376452 AAGGTTAATGAACTGTTCGTGAATTTATCAAATCGAGTTGGATCTTGCTCGACTCAACTCGTAAA
66 AAGGTTAATGAACTGTTCGTGAATTTATCAAATCGAGTTGGATCTTGCTCGACTCAACTCGTAAA
376517 GGTCTTGAGTCAAGCGCAAGTTTGAGTTGAATCAACCTGAGTCAAGTGTTGACGTAGTTTTGACT
131 GGTCTTGAGTCAAGCGCAAGTTTGAGTTGAATCAACCTGAGTCAAGTGTTGACGTAGTTTTGACT
376582 GAGTCAAGTTCGAGCAGCTCACTCATTAAGCACCCC
196 GAGTCAAGTTCGAGCAGCTCACTCATTAAGCACCCC
376618 TAGTAAT
1 TAGTAAT
376625 AACGTTGATA
Statistics
Matches: 238, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
231 238 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (231 bp):
TAGTAATTATTAATTAGACTTTTTAATGGAATAATGTTTTAAATTAATTATTAAAAAATATAAAA
AAGGTTAATGAACTGTTCGTGAATTTATCAAATCGAGTTGGATCTTGCTCGACTCAACTCGTAAA
GGTCTTGAGTCAAGCGCAAGTTTGAGTTGAATCAACCTGAGTCAAGTGTTGACGTAGTTTTGACT
GAGTCAAGTTCGAGCAGCTCACTCATTAAGCACCCC
Found at i:377828 original size:2 final size:2
Alignment explanation
Indices: 377821--377846 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
377811 GTATTCAGAG
377821 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
377847 CTTGTAGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:382451 original size:22 final size:21
Alignment explanation
Indices: 382420--382478 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
382410 CATTATGGTG
* *
382420 TTGACATGACAGTTCACAGGTA
1 TTGATATGACAGTTCACA-ATA
*
382442 TTGATGTGAC-GTTCCACAATA
1 TTGATATGACAGTT-CACAATA
382463 TTGATATGACAGTTCA
1 TTGATATGACAGTTCA
382479 TATGTCATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 16 0.52
22 15 0.48
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (21 bp):
TTGATATGACAGTTCACAATA
Found at i:385013 original size:18 final size:18
Alignment explanation
Indices: 384975--385013 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
384965 GGAAGACAAG
*
384975 TGATTATCAAGGCATACT
1 TGATTATCAAGGCATAAT
*
384993 TGATTATCAAGGCCTAAT
1 TGATTATCAAGGCATAAT
385011 TGA
1 TGA
385014 GAAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (18 bp):
TGATTATCAAGGCATAAT
Found at i:388261 original size:37 final size:37
Alignment explanation
Indices: 388191--388264 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
388181 TCATTAAACT
* *
388191 TTTTATATTTTATATTTTTGTAAAAAAATTATATAAA
1 TTTTATAATTTAAATTTTTGTAAAAAAATTATATAAA
388228 TTTTATGAATTTAAATTTTT-TAAAGAAAA-TATATAAA
1 TTTTAT-AATTTAAATTTTTGTAAA-AAAATTATATAAA
388265 ATATTTTCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 18 0.55
38 15 0.45
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (37 bp):
TTTTATAATTTAAATTTTTGTAAAAAAATTATATAAA
Found at i:390648 original size:5 final size:5
Alignment explanation
Indices: 390638--390678 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
390628 AGTTAATGGG
*
390638 ATATT ATATT ATATT ATATC ATATT ATATT ATATT ATATT A
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT A
390679 AAATGATTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (5 bp):
ATATT
Found at i:391965 original size:5 final size:5
Alignment explanation
Indices: 391955--391989 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
391945 AAATATTTTT
391955 TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA
391990 AAATAACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:392421 original size:14 final size:14
Alignment explanation
Indices: 392402--392428 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
392392 TCATCCTCTC
392402 ATTTCCATTTTCTT
1 ATTTCCATTTTCTT
392416 ATTTCCATTTTCT
1 ATTTCCATTTTCT
392429 CTCTTGTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTTCCATTTTCTT
Found at i:392523 original size:22 final size:22
Alignment explanation
Indices: 392490--392552 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 22
392480 ACATGCAAGG
*
392490 TTCATCCTCTTTATTTTTTCTCTT
1 TTCA-CCTCTTTATTTTTTCT-TC
*
392514 TTC-CCTCTTTA-TTCTTCTTC
1 TTCACCTCTTTATTTTTTCTTC
392534 TTCATCCTCTTTATTTTTT
1 TTCA-CCTCTTTATTTTTT
392553 TGGTATTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 4 0.12
21 6 0.18
22 16 0.48
23 4 0.12
24 3 0.09
ACGTcount: A:0.08, C:0.27, G:0.00, T:0.65
Consensus pattern (22 bp):
TTCACCTCTTTATTTTTTCTTC
Found at i:393125 original size:21 final size:20
Alignment explanation
Indices: 393099--393138 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
393089 CAAAACATAA
*
393099 AAAAATAAAACTATACTTTTTT
1 AAAATTAAAA-TATA-TTTTTT
393121 AAAATTAAAATATATTTT
1 AAAATTAAAATATATTTT
393139 ATCATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 4 0.24
22 9 0.53
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTAAAATATATTTTTT
Found at i:394771 original size:19 final size:19
Alignment explanation
Indices: 394747--394796 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
394737 TGTTCTGCCC
394747 AGTTTCGAAACTTTCTAGG
1 AGTTTCGAAACTTTCTAGG
*
394766 AGTTTCGAAACTTTCTGGG
1 AGTTTCGAAACTTTCTAGG
*
394785 AGTTTTGAAACT
1 AGTTTCGAAACT
394797 ATGACCCAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (19 bp):
AGTTTCGAAACTTTCTAGG
Found at i:394827 original size:17 final size:17
Alignment explanation
Indices: 394805--394838 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
394795 CTATGACCCA
394805 GAGTATCGATACTCTTT
1 GAGTATCGATACTCTTT
394822 GAGTATCGATACTCTTT
1 GAGTATCGATACTCTTT
394839 CCCAGAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (17 bp):
GAGTATCGATACTCTTT
Found at i:395962 original size:29 final size:29
Alignment explanation
Indices: 395920--395981 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
395910 TAGTCAGGAC
* *
395920 AAAACCTTAAAATCAAGAGGGTAGCCAAG
1 AAAACCTTAAAATCAAGAGGGTAACCAAA
*
395949 AAAACCTTAAAATCGAGAGGGTAACCAAA
1 AAAACCTTAAAATCAAGAGGGTAACCAAA
395978 AAAA
1 AAAA
395982 TTAAAAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.53, C:0.16, G:0.18, T:0.13
Consensus pattern (29 bp):
AAAACCTTAAAATCAAGAGGGTAACCAAA
Found at i:397052 original size:21 final size:22
Alignment explanation
Indices: 397028--397074 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
397018 TCTTTACTTA
*
397028 AAACTC-TAAATTATAAACC-CT
1 AAACTCTTAAATCAT-AACCACT
397049 AAAC-CTTAAATCATAACCACT
1 AAACTCTTAAATCATAACCACT
397070 AAACT
1 AAACT
397075 ATAATCCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (22 bp):
AAACTCTTAAATCATAACCACT
Found at i:406460 original size:15 final size:16
Alignment explanation
Indices: 406440--406478 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
406430 GTTTACTTCA
*
406440 GAATGATT-AAGTGTT
1 GAATGATTCAAATGTT
406455 GAATGATTCAAATGTT
1 GAATGATTCAAATGTT
406471 GAATGATT
1 GAATGATT
406479 TAGAGGTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.36, C:0.03, G:0.23, T:0.38
Consensus pattern (16 bp):
GAATGATTCAAATGTT
Found at i:408003 original size:20 final size:21
Alignment explanation
Indices: 407971--408015 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
407961 ATACAAATGA
407971 TTAATGAGTGTCAAT-TTATGT
1 TTAATGAGTGTCAATATTAT-T
407992 TTAATG-GTGTCAATATTATT
1 TTAATGAGTGTCAATATTATT
408012 TTAA
1 TTAA
408016 AATGTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.31, C:0.04, G:0.16, T:0.49
Consensus pattern (21 bp):
TTAATGAGTGTCAATATTATT
Found at i:409312 original size:20 final size:20
Alignment explanation
Indices: 409287--409400 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
409277 AATTGGGAAA
*
409287 ATCGCAATGTGATACTGACT
1 ATCGCAATGCGATACTGACT
*
409307 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
409327 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
409348 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
409368 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
409388 TTCGCAACGCGAT
1 ATCGCAATGCGAT
409401 TTACATAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:409331 original size:61 final size:61
Alignment explanation
Indices: 409284--409400 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
409274 GCGAATTGGG
* * * * *
409284 AAAATCGCAATGTGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
409345 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
409401 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:410027 original size:19 final size:19
Alignment explanation
Indices: 410002--410164 Score: 165
Period size: 19 Copynumber: 8.7 Consensus size: 19
409992 AATCACATTA
*
410002 CGATTTTTATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
*
410021 TGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
*
410040 CGATTTTTATTTCGCGGTTG
1 CGATTTTCATTTCGC-GTTG
410060 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
* *
410079 CGATTGTC---T-G-GTCG
1 CGATTTTCATTTCGCGTTG
**
410093 CGATAGTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
**
410112 CGATAGTCATTTCAGCGTTG
1 CGATTTTCATTTC-GCGTTG
* *
410132 CGATTCTCATTATCTCGTTG
1 CGATTTTCATT-TCGCGTTG
410152 CGATTTTCATTTC
1 CGATTTTCATTTC
410165 AACCAAAAGA
Statistics
Matches: 123, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 59 0.48
20 48 0.39
21 2 0.02
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:410076 original size:39 final size:38
Alignment explanation
Indices: 410002--410164 Score: 156
Period size: 39 Copynumber: 4.3 Consensus size: 38
409992 AATCACATTA
*
410002 CGATTTTTATTTCGCGTTGTGATTTTCATTTCGCGTTG
1 CGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGTTG
410040 CGATTTTTATTTCGCGGTTGCGATTTTCATTTCGCGTTG
1 CGATTTTTATTTCGC-GTTGCGATTTTCATTTCGCGTTG
* * * **
410079 CGA---TTGTCT-G-GTCGCGATAGTCATTTCGCGTTG
1 CGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGTTG
** * * *
410112 CGATAGTCATTTCAGCGTTGCGATTCTCATTATCTCGTTG
1 CGATTTTTATTTC-GCGTTGCGATTTTCATT-TCGCGTTG
*
410152 CGATTTTCATTTC
1 CGATTTTTATTTC
410165 AACCAAAAGA
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
33 23 0.23
35 1 0.01
36 7 0.07
38 16 0.16
39 37 0.36
40 18 0.18
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (38 bp):
CGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGTTG
Found at i:411518 original size:20 final size:21
Alignment explanation
Indices: 411475--411519 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
411465 ATACAAATGA
411475 TTAATGAGTGTAAAATTATGT
1 TTAATGAGTGTAAAATTATGT
*
411496 TTAATG-GTGTCAATATTAT-T
1 TTAATGAGTGT-AAAATTATGT
411516 TTAA
1 TTAA
411520 AATGTATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.36, C:0.02, G:0.16, T:0.47
Consensus pattern (21 bp):
TTAATGAGTGTAAAATTATGT
Found at i:412815 original size:20 final size:20
Alignment explanation
Indices: 412790--412903 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
412780 AATTGGGAAA
*
412790 ATCGCAATGTGATACTGACT
1 ATCGCAATGCGATACTGACT
*
412810 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
412830 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
412851 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
412871 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
412891 TTCGCAACGCGAT
1 ATCGCAATGCGAT
412904 TTACATAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:412834 original size:61 final size:61
Alignment explanation
Indices: 412787--412903 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
412777 GCGAATTGGG
* * * * *
412787 AAAATCGCAATGTGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
412848 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
412904 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:413525 original size:19 final size:19
Alignment explanation
Indices: 413500--413662 Score: 165
Period size: 19 Copynumber: 8.7 Consensus size: 19
413490 AATCACATTA
*
413500 CGATTTTTATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
*
413519 TGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
*
413538 CGATTTTTATTTCGCGGTTG
1 CGATTTTCATTTCGC-GTTG
413558 CGATTTTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
* *
413577 CGATTGTC---T-G-GTCG
1 CGATTTTCATTTCGCGTTG
**
413591 CGATAGTCATTTCGCGTTG
1 CGATTTTCATTTCGCGTTG
**
413610 CGATAGTCATTTCAGCGTTG
1 CGATTTTCATTTC-GCGTTG
* *
413630 CGATTCTCATTATCTCGTTG
1 CGATTTTCATT-TCGCGTTG
413650 CGATTTTCATTTC
1 CGATTTTCATTTC
413663 AACCAAAAGA
Statistics
Matches: 123, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
14 10 0.08
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 59 0.48
20 48 0.39
21 2 0.02
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
CGATTTTCATTTCGCGTTG
Found at i:413574 original size:39 final size:38
Alignment explanation
Indices: 413500--413662 Score: 156
Period size: 39 Copynumber: 4.3 Consensus size: 38
413490 AATCACATTA
*
413500 CGATTTTTATTTCGCGTTGTGATTTTCATTTCGCGTTG
1 CGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGTTG
413538 CGATTTTTATTTCGCGGTTGCGATTTTCATTTCGCGTTG
1 CGATTTTTATTTCGC-GTTGCGATTTTCATTTCGCGTTG
* * * **
413577 CGA---TTGTCT-G-GTCGCGATAGTCATTTCGCGTTG
1 CGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGTTG
** * * *
413610 CGATAGTCATTTCAGCGTTGCGATTCTCATTATCTCGTTG
1 CGATTTTTATTTC-GCGTTGCGATTTTCATT-TCGCGTTG
*
413650 CGATTTTCATTTC
1 CGATTTTTATTTC
413663 AACCAAAAGA
Statistics
Matches: 102, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
33 23 0.23
35 1 0.01
36 7 0.07
38 16 0.16
39 37 0.36
40 18 0.18
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (38 bp):
CGATTTTTATTTCGCGTTGCGATTTTCATTTCGCGTTG
Found at i:415744 original size:43 final size:43
Alignment explanation
Indices: 415663--415747 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
415653 GCCCGACTCG
* * * *
415663 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGGTCAAGAGGCCC
* * *
415706 CCTATCATTCCTCGAGAGTCCCCTCCCACCGGTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGGTCAAGAGGCC
415748 ACTGTCATCG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.21, C:0.40, G:0.18, T:0.21
Consensus pattern (43 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGGTCAAGAGGCCC
Found at i:417144 original size:14 final size:14
Alignment explanation
Indices: 417125--417160 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
417115 ATTGTTTAAT
417125 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
417139 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
417153 TGATTTGT
1 TGATTTGT
417161 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:417327 original size:19 final size:19
Alignment explanation
Indices: 417305--417455 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
417295 CGAAATAAAA
417305 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
417324 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
417339 -CCTCGTTGCGAATTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
417357 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
417371 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
417390 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
417405 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
417423 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
417442 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
417456 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:417355 original size:33 final size:32
Alignment explanation
Indices: 417309--417435 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
417299 ATAAAATTCG
417309 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
417342 CGTTGCGAATTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
417375 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
417408 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
417436 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:417398 original size:66 final size:66
Alignment explanation
Indices: 417302--417434 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
417292 ACGCGAAATA
*
417302 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGAATTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGAATTTCATTTCGCATTGC
417367 G
66 G
* *
417368 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGAATTTCATTTCGCATTGC
417433 G
66 G
417434 A
1 A
417435 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGAATTTCATTTCGCATTGC
G
Found at i:418431 original size:21 final size:21
Alignment explanation
Indices: 418405--418447 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
418395 TTTCTGGGTT
* *
418405 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
418426 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
418447 A
1 A
418448 CGAAATGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:418537 original size:69 final size:68
Alignment explanation
Indices: 418427--418580 Score: 204
Period size: 69 Copynumber: 2.2 Consensus size: 68
418417 ACCCATTCAA
* * *
418427 GGGGAACCGATACCCCTTCAACGAAATGAATTTCCAGAATGCAAGAGGGGAATCGATACCCCA-A
1 GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCAGA
418491 GGGG
66 -GGG
* * *
418495 GGGGAACCGATACCCCCTCATCGTATAA-GAAATTCCAGAATGCTATAGGGGAACCGATACCCCA
1 GGGGAACCGATACCCCCTCAACG-A-AATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCA
418559 GAGGG
64 GAGGG
*
418564 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
418581 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
68 21 0.28
69 52 0.68
70 3 0.04
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.15
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAAATGAAATTCCAGAATGCAAGAGGGGAACCGATACCCCAGA
GGG
Found at i:418914 original size:29 final size:29
Alignment explanation
Indices: 418882--418953 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
418872 TTCCATATGA
** *
418882 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAACGTAT
*
418911 TACATGACATGAATTCATATTATACGTAT
1 TACATGACATGAATTCATATTAAACGTAT
418940 TACATGACATGAAT
1 TACATGACATGAAT
418954 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAACGTAT
Found at i:419010 original size:30 final size:29
Alignment explanation
Indices: 418967--419044 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 29
418957 CAGAAAAAGT
*
418967 TATATGCACTATGTGATAAAGGTATGTAAA
1 TATATGC-CTATGTGATAAAGGTATGGAAA
* *
418997 TGATATGCCTATGTGTTAAAGTTATGGAAA
1 T-ATATGCCTATGTGATAAAGGTATGGAAA
* *
419027 TACTATGTCTACGTGATA
1 TA-TATGCCTATGTGATA
419045 TGAACTACGG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 1 0.03
30 33 0.82
31 6 0.15
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.36
Consensus pattern (29 bp):
TATATGCCTATGTGATAAAGGTATGGAAA
Found at i:419319 original size:22 final size:22
Alignment explanation
Indices: 419245--419311 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
419235 TTATGGACAT
419245 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
419267 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
419289 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
419311 A
1 A
419312 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:425322 original size:20 final size:21
Alignment explanation
Indices: 425297--425338 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
425287 GATTTGGGTT
*
425297 AGGGGAATCG-TACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
425317 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
425338 A
1 A
425339 CAACAATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:425421 original size:67 final size:69
Alignment explanation
Indices: 425318--425471 Score: 190
Period size: 67 Copynumber: 2.2 Consensus size: 69
425308 ACCCATTCAA
* * *
425318 GGGGAACCGATACCCCTTCAACAACAATGAATTTCCAGAATGC-A-AGAGGGAATCGATACCCCA
1 GGGGAACCGATACCCCCTCAACAACAATGAAATTCCAGAATGCTATAG-GGGAACCGATACCCCA
425381 -AGGG
65 GAGGG
* * *
425385 GGGGAACCGATACCCCCTCATCGTATAA-GAAATTCCAGAATGCTTATAGGGGAACCGATACCCC
1 GGGGAACCGATACCCCCTCAAC-AACAATGAAATTCCAGAATGC-TATAGGGGAACCGATACCCC
425449 AGAGGG
64 AGAGGG
*
425455 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
425472 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
67 34 0.45
68 3 0.04
69 16 0.21
70 22 0.29
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (69 bp):
GGGGAACCGATACCCCCTCAACAACAATGAAATTCCAGAATGCTATAGGGGAACCGATACCCCAG
AGGG
Found at i:425806 original size:27 final size:29
Alignment explanation
Indices: 425776--425845 Score: 99
Period size: 27 Copynumber: 2.5 Consensus size: 29
425766 CATATTATGA
**
425776 TACATGACATGAATTTGTATTA-A-ATAT
1 TACATGACATGAATTCATATTATACATAT
*
425803 TACATGACATGAATTCATATTATACGTAT
1 TACATGACATGAATTCATATTATACATAT
425832 TACATGACATGAAT
1 TACATGACATGAAT
425846 ATGCAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 20 0.53
28 1 0.03
29 17 0.45
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (29 bp):
TACATGACATGAATTCATATTATACATAT
Found at i:426196 original size:21 final size:21
Alignment explanation
Indices: 426136--426199 Score: 119
Period size: 21 Copynumber: 3.0 Consensus size: 21
426126 TTATGGACAT
*
426136 AATTCTACGGGCACTTCGGGC
1 AATTCTACGGGCACTTCGTGC
426157 AATTCTACGGGCACTTCGTGC
1 AATTCTACGGGCACTTCGTGC
426178 AATTCTACGGGCACTTCGTGC
1 AATTCTACGGGCACTTCGTGC
426199 A
1 A
426200 TTTATACTGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.27
Consensus pattern (21 bp):
AATTCTACGGGCACTTCGTGC
Done.