Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_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: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 23
Found at i:5510723 original size:262 final size:263
Alignment explanation
Indices: 5510341--5511113 Score: 705
Period size: 264 Copynumber: 2.9 Consensus size: 263
5510331 AGGAGGTTGT
* * * ** * *
5510341 AATAT-GAATTTTAATATTTTTAATAATAAAATGGGTTACGTCTAAAA-GTTATCAGAGTTTAAG
1 AATATAGAATCTTACTATTTTTAATAATAAAATGGGTTGCACCTAAAATATTATCAAAG-TTAAG
* * * * *
5510404 TTGGA-AGAGCATTG-GATTTACCTACAATAAGAAAATAAGTTAAAAACG-GAAAATGTTATGAA
65 CT-GATAGAACCTTGAAATTTACC-ACAATAAGAAAATAAGTT-AAAA-GTTAAAATGTTATGAA
* * * *
5510466 TATATATAAGAAATACAGCTGCGCATAACAATGTCCTGGTTCACTAAG-A-AATAAGTTGAGATA
126 TATATATAAGAAATACAGCTGCACACAACAATGTCATAGTTCACTAAGAATAATAAGTTGAGATA
* * *
5510529 TGTAATGTTACTATTTTTATTAATAAAATAGTTTGCGCTC-AAGAATGTCAAGGTCCACTAAAAA
191 TGTAATGTTAATATTTTT-TTAATAAAATAGGTTGCGC-CGAAGAATGTCAAGGTCCAATAAAAA
*
5510593 ATCATGTTAC
254 AGCATGTTAC
* * *
5510603 AATCTAGAATCTTGACT-TTTTTAATAATAAAAT-GGTTGCGCCTAAAATGTTATCAAAG-TAAG
1 AATATAGAATCTT-ACTATTTTTAATAATAAAATGGGTTGCACCTAAAATATTATCAAAGTTAAG
* * * *
5510665 CTGATGGAGCCTTG-AATTTTCTCACGATAAGAAAAATAAGTTAAAAGTTAAGAATGTTATGAAT
65 CTGATAGAACCTTGAAATTTAC-CACAATAAG-AAAATAAGTTAAAAGTTAA-AATGTTATGAAT
* * * * * * * *
5510729 ATGTATAATAAATACGGTTGCACCCAATAATGTCATAGTTCACTAAGAAATAATAAGTTGTGATC
127 ATATATAAGAAATACAGCTGCACACAACAATGTCATAGTTCACTAAG-AATAATAAGTTGAGATA
* * ** *
5510794 TGTAATGTTAATATTTTTTTAATAAAATAGGTTGTGCCGAAGAATGTCATGGTTTAATAAGAAAG
191 TGTAATGTTAATATTTTTTTAATAAAATAGGTTGCGCCGAAGAATGTCAAGGTCCAATAAAAAAG
*
5510859 CATGTTGC
256 CATGTTAC
* * * * *
5510867 AATATGGAATCTTACTATTTTTAGTAATAAAATGGGTTGCACCTAATATATTATTAGAGTTTAAG
1 AATATAGAATCTTACTATTTTTAATAATAAAATGGGTTGCACCTAAAATATTATCAAAG-TTAAG
5510932 CTGATAGAACCTTGAAATTTACCACAATAAGAAAATAAGTTAAAAGCTTAAAATGTTATGAATAT
65 CTGATAGAACCTTGAAATTTACCACAATAAGAAAATAAGTTAAAAG-TTAAAATGTTATGAATAT
* * * ** * * * * *
5510997 ATACAAGAAATACGGTTGTGTC-CAAGAATGTTATGGTTCACTAAGAA-AGTAAGATGCA-ATAT
129 ATATAAGAAATACAGCTG-CACACAACAATGTCATAGTTCACTAAGAATAATAAGTTG-AGATAT
* * * * *
5511059 GTAATG-TAATATTAATATTTTTTATAAAATATGTTGCGCCAAAAAATGTAAAGGT
192 GTAATGTTAATA-T--T-TTTTTAATAAAATAGGTTGCGCCGAAGAATGTCAAGGT
5511114 TTTGAATAGA
Statistics
Matches: 421, Mismatches: 66, Indels: 43
0.79 0.12 0.08
Matches are distributed among these distances:
260 3 0.01
261 30 0.07
262 76 0.18
263 40 0.10
264 90 0.21
265 51 0.12
266 65 0.15
267 60 0.14
268 6 0.01
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.33
Consensus pattern (263 bp):
AATATAGAATCTTACTATTTTTAATAATAAAATGGGTTGCACCTAAAATATTATCAAAGTTAAGC
TGATAGAACCTTGAAATTTACCACAATAAGAAAATAAGTTAAAAGTTAAAATGTTATGAATATAT
ATAAGAAATACAGCTGCACACAACAATGTCATAGTTCACTAAGAATAATAAGTTGAGATATGTAA
TGTTAATATTTTTTTAATAAAATAGGTTGCGCCGAAGAATGTCAAGGTCCAATAAAAAAGCATGT
TAC
Found at i:5513051 original size:99 final size:98
Alignment explanation
Indices: 5512781--5513120 Score: 407
Period size: 99 Copynumber: 3.4 Consensus size: 98
5512771 TAACTTAACT
* * * * * * * *
5512781 GGTTTGTACTAATTTTTCATAATGTATAAGGTTTCAACCTATAACTTATCTAGTTAACATAACAA
1 GGTTTGTATTAATTTTTCATAATATACACGGTTTCAGCCTATAAC-TAACCAATTAACATAACAA
*
5512846 CAAGGAGCAACCTATAATGTTATCTAGGAAACCA
65 CAAGGCGCAACCTATAATGTTATCTAGGAAACCA
* *
5512880 GGTTTAGT-TT-GTTTTTCATAATATACACGG-TTCTAGCCTATAATTTAACCAATTAACATAAC
1 GGTTT-GTATTAATTTTTCATAATATACACGGTTTC-AGCCTATAA-CTAACCAATTAACATAAC
5512942 AACAAGGCGCAACCTATAATGTTATCTAGGAAACCA
63 AACAAGGCGCAACCTATAATGTTATCTAGGAAACCA
* * * * *
5512978 GGTTTGTTTTAATTTTTCATAATATACATGGTTTCAGCCTATAACGTGACCAATTAAAATAACAC
1 GGTTTGTATTAATTTTTCATAATATACACGGTTTCAGCCTATAAC-TAACCAATTAACATAACAA
* * *
5513043 CAATGCGCAACCTATAATGTTATCTGGGATACCA
65 CAAGGCGCAACCTATAATGTTATCTAGGAAACCA
* * * *
5513077 GGTTTGTATTACTTTTTAATAATATACACGATTTCAGCTTATAA
1 GGTTTGTATTAATTTTTCATAATATACACGGTTTCAGCCTATAA
5513121 ATTAATTAGT
Statistics
Matches: 208, Mismatches: 26, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
97 5 0.02
98 80 0.38
99 118 0.57
100 5 0.02
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (98 bp):
GGTTTGTATTAATTTTTCATAATATACACGGTTTCAGCCTATAACTAACCAATTAACATAACAAC
AAGGCGCAACCTATAATGTTATCTAGGAAACCA
Found at i:5518736 original size:53 final size:53
Alignment explanation
Indices: 5518659--5518766 Score: 207
Period size: 53 Copynumber: 2.0 Consensus size: 53
5518649 TTACTTTAAC
*
5518659 ACTTCTCCCATTTATCATTTAAAAAACACATTTAACACATTTATCATTTAAAA
1 ACTTCTCCCATTTATCATTAAAAAAACACATTTAACACATTTATCATTTAAAA
5518712 ACTTCTCCCATTTATCATTAAAAAAACACATTTAACACATTTATCATTTAAAA
1 ACTTCTCCCATTTATCATTAAAAAAACACATTTAACACATTTATCATTTAAAA
5518765 AC
1 AC
5518767 ACTTTTAACA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (53 bp):
ACTTCTCCCATTTATCATTAAAAAAACACATTTAACACATTTATCATTTAAAA
Found at i:5518773 original size:28 final size:28
Alignment explanation
Indices: 5518667--5518777 Score: 133
Period size: 29 Copynumber: 4.0 Consensus size: 28
5518657 ACACTTCTCC
5518667 CATTTATCATTTAAAAAACACATTTAACA
1 CATTTATCATTT-AAAAACACATTTAACA
*
5518696 CATTTATCATTT-AAAA-AC-TTCT--CC
1 CATTTATCATTTAAAAACACATT-TAACA
*
5518720 CATTTATCATTAAAAAAACACATTTAACA
1 CATTTATCATT-TAAAAACACATTTAACA
*
5518749 CATTTATCATTTAAAAACACTTTTAACA
1 CATTTATCATTTAAAAACACATTTAACA
5518777 C
1 C
5518778 TTCTCCCCCT
Statistics
Matches: 70, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
24 12 0.17
25 2 0.03
26 7 0.10
27 7 0.10
28 18 0.26
29 24 0.34
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (28 bp):
CATTTATCATTTAAAAACACATTTAACA
Found at i:5520867 original size:20 final size:20
Alignment explanation
Indices: 5520830--5520868 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5520820 AGATTGAGTG
* * *
5520830 GATTTTTATGTTGTTTGCAT
1 GATTTTAATGATGATTGCAT
5520850 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
5520869 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.05, G:0.21, T:0.51
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAT
Found at i:5527134 original size:37 final size:35
Alignment explanation
Indices: 5527093--5527204 Score: 88
Period size: 37 Copynumber: 3.1 Consensus size: 35
5527083 GGAAAATCTT
5527093 AAAATCCATTTAACTTAATTTGTTATATCGAAATATC
1 AAAAT-CATTTAACTTAATTTGTTATAT-GAAATATC
** * * *
5527130 AAAATGTTTTCAAC-AAATCTT-TTGTA--AAATCTC
1 AAAATCATTT-AACTTAAT-TTGTTATATGAAATATC
*
5527163 AAAATTCATTTAACTTAATTTGTTATATTGAAACATC
1 AAAA-TCATTTAACTTAATTTGTTATA-TGAAATATC
5527200 AAAAT
1 AAAAT
5527205 GTTTTCAATA
Statistics
Matches: 56, Mismatches: 11, Indels: 17
0.67 0.13 0.20
Matches are distributed among these distances:
33 15 0.27
34 11 0.20
36 11 0.20
37 19 0.34
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (35 bp):
AAAATCATTTAACTTAATTTGTTATATGAAATATC
Found at i:5527159 original size:70 final size:70
Alignment explanation
Indices: 5527074--5527212 Score: 224
Period size: 70 Copynumber: 2.0 Consensus size: 70
5527064 TATACTTAGA
* *
5527074 AAATCATTTGGAAAATCTTAAAATCCATTTAACTTAATTTGTTATATCGAAATATCAAAATGTTT
1 AAATCATTTGGAAAATCTCAAAATCCATTTAACTTAATTTGTTATATCGAAACATCAAAATGTTT
5527139 TCAAC
66 TCAAC
* * * *
5527144 AAATCTTTTGTAAAATCTCAAAATTCATTTAACTTAATTTGTTATATTGAAACATCAAAATGTTT
1 AAATCATTTGGAAAATCTCAAAATCCATTTAACTTAATTTGTTATATCGAAACATCAAAATGTTT
5527209 TCAA
66 TCAA
5527213 TAATCTCCCC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 63 1.00
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.40
Consensus pattern (70 bp):
AAATCATTTGGAAAATCTCAAAATCCATTTAACTTAATTTGTTATATCGAAACATCAAAATGTTT
TCAAC
Found at i:5527421 original size:13 final size:13
Alignment explanation
Indices: 5527403--5527427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5527393 AGCCATTAGT
5527403 TTCATAATCAATA
1 TTCATAATCAATA
5527416 TTCATAATCAAT
1 TTCATAATCAAT
5527428 GTGAAATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCATAATCAATA
Found at i:5535219 original size:33 final size:34
Alignment explanation
Indices: 5535182--5535252 Score: 108
Period size: 37 Copynumber: 2.0 Consensus size: 34
5535172 TATCTTTAGT
5535182 AGTAATGAG-TTAGGAACCCACATACTTCTAACG
1 AGTAATGAGTTTAGGAACCCACATACTTCTAACG
5535215 AGTAATGAGTTCTTTAGGAACCCACATACTTCTAACG
1 AGTAATGAG---TTTAGGAACCCACATACTTCTAACG
5535252 A
1 A
5535253 TTTTTCCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 9 0.26
37 25 0.74
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (34 bp):
AGTAATGAGTTTAGGAACCCACATACTTCTAACG
Found at i:5543973 original size:8 final size:9
Alignment explanation
Indices: 5543940--5543972 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
5543930 GATAAACCAT
5543940 TTTATTATA
1 TTTATTATA
5543949 TTATATTATA
1 TT-TATTATA
5543959 TTTATT-TA
1 TTTATTATA
5543967 TTTATT
1 TTTATT
5543973 TTTCTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.35
9 6 0.26
10 9 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTATTATA
Found at i:5544830 original size:22 final size:22
Alignment explanation
Indices: 5544804--5544846 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5544794 GGTTAATTGT
5544804 TTTTTATTTG-TTAATCTTGTCA
1 TTTTTATTTGATT-ATCTTGTCA
*
5544826 TTTTTGTTTGATTATCTTGTC
1 TTTTTATTTGATTATCTTGTC
5544847 TAACTCCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.09, G:0.12, T:0.65
Consensus pattern (22 bp):
TTTTTATTTGATTATCTTGTCA
Found at i:5545292 original size:20 final size:20
Alignment explanation
Indices: 5545247--5545283 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5545237 GGTTATTTTG
5545247 TTATTATTTTATTTAAAAAT
1 TTATTATTTTATTTAAAAAT
*
5545267 TAATTATTTTA-TTAAAA
1 TTATTATTTTATTTAAAA
5545284 CTCTTATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTATTATTTTATTTAAAAAT
Found at i:5547280 original size:15 final size:15
Alignment explanation
Indices: 5547252--5547295 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 15
5547242 TGAATATGAG
5547252 ATATGAGAATATGTTTT
1 ATATGA-AA-ATGTTTT
5547269 ATATGAAAATGTTTT
1 ATATGAAAATGTTTT
*
5547284 ATGTGAAAATGT
1 ATATGAAAATGT
5547296 GCTAAGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 18 0.69
16 2 0.08
17 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (15 bp):
ATATGAAAATGTTTT
Found at i:5547304 original size:15 final size:15
Alignment explanation
Indices: 5547272--5547323 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 15
5547262 ATGTTTTATA
* *
5547272 TGAAAATGTTTTATG
1 TGAAAATGTTCTAAG
*
5547287 TGAAAATGTGCTAAG
1 TGAAAATGTTCTAAG
*
5547302 TGAAAATGTTCTACG
1 TGAAAATGTTCTAAG
5547317 TGAAAAT
1 TGAAAAT
5547324 ACCCTATCTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (15 bp):
TGAAAATGTTCTAAG
Found at i:5547481 original size:24 final size:24
Alignment explanation
Indices: 5547454--5547499 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
5547444 GATTCGAGGG
5547454 TTCTAAGCGGTCCTTCGGGACAAA
1 TTCTAAGCGGTCCTTCGGGACAAA
*
5547478 TTCTACGCGGTCCTTCGGGACA
1 TTCTAAGCGGTCCTTCGGGACA
5547500 TATCTATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (24 bp):
TTCTAAGCGGTCCTTCGGGACAAA
Found at i:5547529 original size:24 final size:24
Alignment explanation
Indices: 5547502--5547555 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
5547492 TCGGGACATA
5547502 TCTATGTGGCACTTCAGTGCAAAT
1 TCTATGTGGCACTTCAGTGCAAAT
* *
5547526 TCTACGTGGCACTTCGGTGCAAAT
1 TCTATGTGGCACTTCAGTGCAAAT
*
5547550 TATATG
1 TCTATG
5547556 AGCAGTTGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (24 bp):
TCTATGTGGCACTTCAGTGCAAAT
Found at i:5557026 original size:40 final size:42
Alignment explanation
Indices: 5556881--5557026 Score: 137
Period size: 42 Copynumber: 3.5 Consensus size: 42
5556871 TTTTAAAATT
*
5556881 TTATTTTTTAA-TCTTTATAATT-AAA-TTCTAATTTTATTCAATA
1 TTATTTTTTAACT-TTTATAATTGAAATTTGTAATTTT-TT--ATA
** *
5556924 TTCCTTTTT-ATTTTTATAATTGAAATTTGTAATTTTTTATA
1 TTATTTTTTAACTTTTATAATTGAAATTTGTAATTTTTTATA
*
5556965 TTATTTTTTTACTTTTATAATTGAAATCTT-TAATTTTTTA-A
1 TTATTTTTTAACTTTTATAATTGAAAT-TTGTAATTTTTTATA
5557006 TT-TTATTTTAAC-TTTATAATT
1 TTATT-TTTTAACTTTTATAATT
5557027 AAGAACCTGA
Statistics
Matches: 90, Mismatches: 7, Indels: 15
0.80 0.06 0.13
Matches are distributed among these distances:
40 11 0.12
41 19 0.21
42 36 0.40
43 15 0.17
44 9 0.10
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.62
Consensus pattern (42 bp):
TTATTTTTTAACTTTTATAATTGAAATTTGTAATTTTTTATA
Found at i:5557201 original size:44 final size:42
Alignment explanation
Indices: 5557150--5557339 Score: 181
Period size: 44 Copynumber: 4.5 Consensus size: 42
5557140 ATTTCCACCG
*
5557150 TTTATCTTTACAATTGAGGCTCCTAAGTTTTTTCAATCTTAATT
1 TTTATCTTTATAATTGAGGC-CCTAAG-TTTTTCAATCTTAATT
* * *
5557194 TTTATCTTTATAATTGAGACCCCTAA-TTTTT-AATCCT-ACT
1 TTTATCTTTATAATTGAG-GCCCTAAGTTTTTCAATCTTAATT
* *
5557234 TTTAACATTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCAATT
1 TTTATC-TTTATAATTGAGGCCC-TAAG-TTTTTCAATCTTAATT
* * * *
5557279 TCTACCTTTATAGTTAAGGGCCCTAAGTTTTTCAATCTTAA-T
1 TTTATCTTTATAATTGA-GGCCCTAAGTTTTTCAATCTTAATT
**
5557321 TAAATCTTTATAATTGAGG
1 TTTATCTTTATAATTGAGG
5557340 TCCTTATCCC
Statistics
Matches: 119, Mismatches: 19, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
40 10 0.08
41 22 0.18
42 18 0.15
43 18 0.15
44 39 0.33
45 12 0.10
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.46
Consensus pattern (42 bp):
TTTATCTTTATAATTGAGGCCCTAAGTTTTTCAATCTTAATT
Found at i:5557303 original size:85 final size:86
Alignment explanation
Indices: 5557153--5557345 Score: 223
Period size: 85 Copynumber: 2.3 Consensus size: 86
5557143 TCCACCGTTT
* * * * *
5557153 ATCTTTACAATTGAGGCTCC-TAAGTTTTTTCAATCTTAATTTTTATCTTTATAATTGAGACCCC
1 ATCTTTATAATTGAGGC-CCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTAAGACCCC
* *
5557217 TAA-TTTTT-AATCCTACTTTTA
65 TAAGTTTTTCAATCCTA-ATTAA
* **
5557238 A-CATTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAGTTAAGGGCCC
1 ATC-TTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTAAGACCCC
*
5557302 TAAGTTTTTCAATCTTAATTAA
65 TAAGTTTTTCAATCCTAATTAA
*
5557324 ATCTTTATAATTGAGGTCCTTA
1 ATCTTTATAATTGAGGCCCTTA
5557346 TCCCTTTCTT
Statistics
Matches: 91, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
84 3 0.03
85 54 0.59
86 27 0.30
87 7 0.08
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (86 bp):
ATCTTTATAATTGAGGCCCTTAAGTTTTTTCAATCTCAATTTCTACCTTTATAATTAAGACCCCT
AAGTTTTTCAATCCTAATTAA
Found at i:5566892 original size:18 final size:19
Alignment explanation
Indices: 5566841--5566896 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
5566831 ATGTTTAATG
*
5566841 AAAAAGATACTAA-TGTTA
1 AAAAAGATACCAATTGTTA
*
5566859 ACAAAAGCATATCAATTGTT-
1 A-AAAAG-ATACCAATTGTTA
5566879 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
5566897 GGAAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
18 12 0.38
19 10 0.31
20 6 0.19
21 4 0.12
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:5574782 original size:96 final size:97
Alignment explanation
Indices: 5574675--5574888 Score: 267
Period size: 96 Copynumber: 2.2 Consensus size: 97
5574665 ATTTTCAATA
* **
5574675 CTTTTTTTACTTTTATAATTGATGCCCCTAATTTTTTAAATCTA-TTTTTTAA-CTTTATAATTA
1 CTTTTTCTACTTTTATAATTGATGCCCCTAATTTTTT-AATC-ACACTTTTAAGCTTTATAATTA
* * *
5574738 AGATCCTTAAG-TTTTTTCTATCTCACCTTCTAC
64 AGACCCTTAAGTTTTTTTCAATCTCACCTTCCAC
* *
5574771 CTTTTTCTACTTTTATAATTGATGCCTCTAATTTTTTAATCACACTTTTAAGCTTTATAATTGAG
1 CTTTTTCTACTTTTATAATTGATGCCCCTAATTTTTTAATCACACTTTTAAGCTTTATAATTAAG
* *
5574836 CCCCTTAAGTTTTTTTCAATCTCACTTTCCAC
66 ACCCTTAAGTTTTTTTCAATCTCACCTTCCAC
*
5574868 C-TTTTCTA-TCTTTACAATTGA
1 CTTTTTCTACT-TTTATAATTGA
5574889 GGCTCTTAAG
Statistics
Matches: 103, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
94 1 0.01
95 11 0.11
96 71 0.69
97 20 0.19
ACGTcount: A:0.24, C:0.20, G:0.05, T:0.51
Consensus pattern (97 bp):
CTTTTTCTACTTTTATAATTGATGCCCCTAATTTTTTAATCACACTTTTAAGCTTTATAATTAAG
ACCCTTAAGTTTTTTTCAATCTCACCTTCCAC
Found at i:5574897 original size:54 final size:52
Alignment explanation
Indices: 5574823--5574923 Score: 130
Period size: 54 Copynumber: 1.9 Consensus size: 52
5574813 CACTTTTAAG
* * *
5574823 CTTTATAATTGAGCCCCTTAAGTTTTTTTCAATCTCACTTTCCACCTTTTCTAT
1 CTTTACAATTGAGCCCCTTAAG-TATTTT-AATCTCAATTTCCACCTTTTCTAT
* * *
5574877 CTTTACAATTGAGGCTCTTAAGTATTTTAATCTCAATTTCTACCTTT
1 CTTTACAATTGAGCCCCTTAAGTATTTTAATCTCAATTTCCACCTTT
5574924 ATAATCGAGG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 17 0.41
53 5 0.12
54 19 0.46
ACGTcount: A:0.23, C:0.23, G:0.07, T:0.48
Consensus pattern (52 bp):
CTTTACAATTGAGCCCCTTAAGTATTTTAATCTCAATTTCCACCTTTTCTAT
Found at i:5574926 original size:97 final size:97
Alignment explanation
Indices: 5574675--5574946 Score: 238
Period size: 96 Copynumber: 2.8 Consensus size: 97
5574665 ATTTTCAATA
* * * * * ** *
5574675 CTTTTTTTACTTTTATAATTGATGCCCCTAATTTTTTAAATCTA-TTTTTTAA-CTTTATAATTA
1 CTTTTTCTACTTTTACAATTGAGGCCTCTAATATTTT-AATC-ACAATTTTAACCTTTATAATTG
** * *
5574738 AGATCCTTAAG-TTTTTTCTATCTCACCTTCTAC
64 AGCCCCTTAAGTTTTTTTCAATCTCACCTTCCAC
* * * * *
5574771 CTTTTTCTACTTTTATAATTGATGCCTCTAATTTTTTAATCACACTTTTAAGCTTTATAATTGAG
1 CTTTTTCTACTTTTACAATTGAGGCCTCTAATATTTTAATCACAATTTTAACCTTTATAATTGAG
*
5574836 CCCCTTAAGTTTTTTTCAATCTCACTTTCCAC
66 CCCCTTAAGTTTTTTTCAATCTCACCTTCCAC
*
5574868 C-TTTTCTA-TCTTTACAATTGAGG-CTCTTAAGTATTTTAATCTCAATTTCT-ACCTTTATAAT
1 CTTTTTCTACT-TTTACAATTGAGGCCTC-TAA-TATTTTAATCACAATTT-TAACCTTTATAAT
*
5574929 CGAGGCCCC-TAA-TTTTTT
62 TGA-GCCCCTTAAGTTTTTT
5574947 AATCCCAGTT
Statistics
Matches: 151, Mismatches: 17, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
94 1 0.01
95 14 0.09
96 81 0.54
97 49 0.32
98 6 0.04
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.50
Consensus pattern (97 bp):
CTTTTTCTACTTTTACAATTGAGGCCTCTAATATTTTAATCACAATTTTAACCTTTATAATTGAG
CCCCTTAAGTTTTTTTCAATCTCACCTTCCAC
Found at i:5575012 original size:44 final size:43
Alignment explanation
Indices: 5574870--5575083 Score: 175
Period size: 44 Copynumber: 4.9 Consensus size: 43
5574860 CTTTCCACCT
* * * *
5574870 TTTCTA-TCTTTACAATTGAGGCTCTTAAGTATTTTAATCTCAA
1 TTTCTACT-TTTATAATTGAGGCCCTTAAATTTTTTAATCTCAA
* * * * *
5574913 TTTCTACCTTTATAATCGAGGCCCCT-AATTTTTTAATCCCAGT
1 TTTCTACTTTTATAATTGAGGCCCTTAAATTTTTTAATCTCA-A
* * *
5574956 TTTTTAATTTTATAATTGAGGCCATTAAATTTTTTAAATCTCAA
1 TTTCTACTTTTATAATTGAGGCCCTTAAATTTTTT-AATCTCAA
* * * *
5575000 TTT-TAACATTTATAACTGCGACCCTTAAATTTTTTCAATCTCAA
1 TTTCT-ACTTTTATAATTGAGGCCCTTAAATTTTTT-AATCTCAA
* * *
5575044 TTTCTACTTTTATAATTAAGGGCCC-TAAGTTTTTCAATCT
1 TTTCTACTTTTATAATTGA-GGCCCTTAAATTTTTTAATCT
5575084 TAACTATATC
Statistics
Matches: 133, Mismatches: 31, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
42 12 0.09
43 46 0.35
44 64 0.48
45 11 0.08
ACGTcount: A:0.29, C:0.18, G:0.08, T:0.46
Consensus pattern (43 bp):
TTTCTACTTTTATAATTGAGGCCCTTAAATTTTTTAATCTCAA
Found at i:5578071 original size:19 final size:19
Alignment explanation
Indices: 5578044--5578087 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5578034 TCTTAATTAC
* *
5578044 GAAAATTAAAATTTAAATT
1 GAAATTTAAAAATTAAATT
5578063 GAAATTTAAAAATTAAATT
1 GAAATTTAAAAATTAAATT
*
5578082 CAAATT
1 GAAATT
5578088 ATTTACCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
GAAATTTAAAAATTAAATT
Found at i:5578171 original size:20 final size:20
Alignment explanation
Indices: 5578134--5578171 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5578124 TATATCAAAC
*
5578134 AAAATATTATATGGTAAAAT
1 AAAATATTATATGATAAAAT
5578154 AAAATATTGA-ATGATAAA
1 AAAATATT-ATATGATAAA
5578172 CAAAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAATATTATATGATAAAAT
Found at i:5578223 original size:3 final size:3
Alignment explanation
Indices: 5578215--5578244 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5578205 AACTTTTAAG
5578215 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5578245 TAAAAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5578296 original size:28 final size:27
Alignment explanation
Indices: 5578264--5578319 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
5578254 GTCACAAGAG
* *
5578264 AAATAAATAAAAATTAGGGAAAATATTA
1 AAATAAACAAAAATTA-AGAAAATATTA
*
5578292 AAATAAACAATAATTAAGAAAATATTA
1 AAATAAACAAAAATTAAGAAAATATTA
5578319 A
1 A
5578320 TGTCTAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (27 bp):
AAATAAACAAAAATTAAGAAAATATTA
Found at i:5579712 original size:83 final size:83
Alignment explanation
Indices: 5579573--5579776 Score: 266
Period size: 83 Copynumber: 2.5 Consensus size: 83
5579563 AACTTCTTGT
** * *
5579573 TGACAGATAGCCCTTCTCGCCTTGAGCTATACTATAAATTTGATATGTCCGTGAGCTGAATGTAA
1 TGACAGATAGCCCTTCTTACCTTGAGCTATGCTATAAATTTGACATGTCCGTGAGCTGAATGTAA
5579638 TCGAACTCAAAGATTTAC
66 TCGAACTCAAAGATTTAC
* * * * *
5579656 TGACAGATAGCTCTTCTTACCTTAAGCTATGCTGTAAATTTGCCATGTCCTTGAGCTGAATGTAA
1 TGACAGATAGCCCTTCTTACCTTGAGCTATGCTATAAATTTGACATGTCCGTGAGCTGAATGTAA
* * **
5579721 TCGAACTCGAAGGTTTTT
66 TCGAACTCAAAGATTTAC
* *
5579739 TG-CAGATAACCCTTCTTACCTTGAGCTATGCTACAAAT
1 TGACAGATAGCCCTTCTTACCTTGAGCTATGCTATAAAT
5579777 GATGTGCCTT
Statistics
Matches: 103, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
82 31 0.30
83 72 0.70
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (83 bp):
TGACAGATAGCCCTTCTTACCTTGAGCTATGCTATAAATTTGACATGTCCGTGAGCTGAATGTAA
TCGAACTCAAAGATTTAC
Found at i:5580177 original size:243 final size:242
Alignment explanation
Indices: 5579569--5580385 Score: 959
Period size: 243 Copynumber: 3.4 Consensus size: 242
5579559 TTGAAACTTC
* * ** ** * * *
5579569 TTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATACTATAAATTTGATATGTCC-GTGAGCTGAA
1 TTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGTTGCAAA--TGATGTG-CCTTTGAGCTGAG
* * * * * * * *
5579633 TGTAATCGAACTCAAAGAT-TTACTGACAGATAGCTCTTCTTACCTTAAGCTATGCTGTAAATTT
63 TGTAATCGAACTCGAAGGTCTT--TGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA--T
* * *
5579697 GCCATG-TCC-TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCAGATAACCCTTCTTACCT
124 G--ATGTTCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGATAACCCTTCTTGCCT
* * *
5579760 TGAGCTATGCTACAAATGATGTGCCTTTGAGTTAAGTGTAATCGAACTCGAAGGTCTT
187 TGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA-GT-TT
* * * * * *
5579818 TTGTTGGCAAATAACCCTTATTGCCTTTAGCTATGTTGCAAATGATGTGCCTTTGAGCTAAGTGT
1 TTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGT
**
5579883 AATCGAACTCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTTC
66 AATCGAACTCGAAGGTCTTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTTC
* *
5579948 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGGTAGCCCTTCTTGCCTTGAGCTATG
131 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGATAACCCTTCTTGCCTTGAGCTATG
5580013 CTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAACGTTT
196 CTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA-GTTT
* * *
5580061 TTGTTGATAGATAACCCTTCTAACCTTGAGCTATGTTGTAAATGATGTGCCTTTGAGCTGAGTGT
1 TTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGT
* ** *
5580126 AATCAAACTTAAAGGTCTTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGC
66 AATCGAACTCGAAGGTCTTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTTC
* * * *
5580191 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAAATAACCTTTCTCGCCTTGAGCTATG
131 CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGATAACCCTTCTTGCCTTGAGCTATG
* * * *
5580256 CTGCAAATGATGCT-ACTTTGAGCTGAATGGAATCGAACTCGAA-TAT
196 CTGCAAATGATG-TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGTTT
* * * * *
5580302 CT-TT-AGCAGATAACCCTTCTAGCCTTGAGTTAT-TATGCAAATCATGTGCATCTGAGCTGAGT
1 TTGTTGA-CAGATAACCCTTCTAGCCTTGAGCTATGT-TGCAAATGATGTGCCTTTGAGCTGAGT
5580364 GTAATCGAACTCGAAGGTCTTT
64 GTAATCGAACTCGAAGGTCTTT
5580386 ATCAAACTCG
Statistics
Matches: 494, Mismatches: 67, Indels: 23
0.85 0.11 0.04
Matches are distributed among these distances:
239 2 0.00
240 68 0.14
241 3 0.01
242 3 0.01
243 217 0.44
244 103 0.21
246 34 0.07
247 30 0.06
248 2 0.00
249 32 0.06
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.34
Consensus pattern (242 bp):
TTGTTGACAGATAACCCTTCTAGCCTTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTGAGTGT
AATCGAACTCGAAGGTCTTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTTC
CTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGATAACCCTTCTTGCCTTGAGCTATG
CTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGTTT
Found at i:5580249 original size:323 final size:322
Alignment explanation
Indices: 5579624--5580381 Score: 986
Period size: 323 Copynumber: 2.3 Consensus size: 322
5579614 GATATGTCCG
* * * * *
5579624 TGAGCTGAATGTAATCGAACTCAAAGAT-TTACTGACAGATAGCTCTTCTTACCTTAAGCTATGC
1 TGAGCTGAATGTAATCGAACTCGAAGATCTT-TTG-CAGATAGCCCTTCTTGCCTTGAGCTATGC
* *
5579688 TGTAAATTTGCCATGT-CC-TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCAGATAACCC
64 TGCAAA--TG--ATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTTGCAGATAACCC
* * * *
5579751 TTCTTACCTTGAGCTATGCTACAAATGATGTGCCTTTGAGTTAAGTGTAATCGAACTCGAAGGTC
125 TTCTAACCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTAAGTGTAATCAAACTCAAAGGTC
* *
5579816 TTTTGTTGGCAAATAACCCTTATTGCCTTTAGCTATGTTGCAAATGATGTGCCTTTGAGCTAAGT
190 --TTGTTGGCAAATAACCCTTATTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTAAGT
** * * *
5579881 GTAATCGAACTCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGT
253 GTAATCGAACTCGAAGGTCTTTGGCAAATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGC
*
5579946 TCCTT
318 TACTT
* * *
5579951 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTG
1 TGAGCTGAATGTAATCGAACTCGAAGATCTTTTGCAGATAGCCCTTCTTGCCTTGAGCTATGCTG
* *
5580016 CAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAACGTTTTTGTTGATAGATAACCCTTC
66 CAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA-GGTTTT-TTG-CAGATAACCCTTC
* ** * *
5580081 TAACCTTGAGCTATGTTGTAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTTAAAGGTC-T-
128 TAACCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTAAGTGTAATCAAACTCAAAGGTCTTG
* * *
5580144 TTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAAT
193 TTGGCAAATAACCCTTATTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAAT
*
5580209 CGAACTCGAAGGTCTTTGGCAAATAACCTTTCTCGCCTTGAGCTATGCTGCAAATGATGCTACTT
258 CGAACTCGAAGGTCTTTGGCAAATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGCTACTT
* * * * * * **
5580274 TGAGCTGAATGGAATCGAACTCGAATATCTTTAGCAGATAACCCTTCTAGCCTTGAGTTATTATG
1 TGAGCTGAATGTAATCGAACTCGAAGATCTTTTGCAGATAGCCCTTCTTGCCTTGAGCTATGCTG
* * *
5580339 CAAATCATGTGCATCTGAGCTGAGTGTAATCGAACTCGAAGGT
66 CAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
5580382 CTTTATCAAA
Statistics
Matches: 377, Mismatches: 48, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
322 6 0.02
323 211 0.56
324 28 0.07
325 5 0.01
326 33 0.09
327 92 0.24
328 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (322 bp):
TGAGCTGAATGTAATCGAACTCGAAGATCTTTTGCAGATAGCCCTTCTTGCCTTGAGCTATGCTG
CAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTTTTTTGCAGATAACCCTTCTAA
CCTTGAGCTATGCTACAAATGATGTGCCTTTGAGCTAAGTGTAATCAAACTCAAAGGTCTTGTTG
GCAAATAACCCTTATTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTAAGTGTAATCGA
ACTCGAAGGTCTTTGGCAAATAACCCTTCTCGCCTTGAGCTATGCTGCAAATGATGCTACTT
Found at i:5580386 original size:80 final size:80
Alignment explanation
Indices: 5579624--5580385 Score: 875
Period size: 80 Copynumber: 9.4 Consensus size: 80
5579614 GATATGTCCG
* * * * * * * *
5579624 TGAGCTGAATGTAATCGAACTCAAAGAT-TTACTGACAGATAGCTCTTCTTACCTTAAGCTATGC
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTT--TGGCAGATAACCCTTCTTGCCTTGAGCTATGC
*
5579688 TGTAAATTTGCCATGT-CC-T
64 TGCAAA--TG--ATGTGCCTT
* * * * *
5579707 TGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCAGATAACCCTTCTTACCTTGAGCTATGCTA
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
5579772 CAAATGATGTGCCTT
66 CAAATGATGTGCCTT
* * * * *
5579787 TGAGTTAAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTATTGCCTTTAGCTAT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGCCTTGAGCTAT
*
5579852 GTTGCAAATGATGTGCCTT
62 GCTGCAAATGATGTGCCTT
* * *
5579871 TGAGCTAAGTGTAATCGAACTCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
*
5579936 CAAATGATGTTCCTT
66 CAAATGATGTGCCTT
* * *
5579951 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
5580016 CAAATGATGTGCCTT
66 CAAATGATGTGCCTT
* * * **
5580031 TGAGCTGAGTGTAATCGAACTCGAACGTTTTTGTTGATAGATAACCCTTCTAACCTTGAGCTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCCTTGAGCTATG
* *
5580096 TTGTAAATGATGTGCCTT
63 CTGCAAATGATGTGCCTT
* ** * *
5580114 TGAGCTGAGTGTAATCAAACTTAAAGGTCTTTGGCAAATAGCCCTTCTTGCCTTGAGCTATGCTG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
5580179 CAAATGATGTGCCTT
66 CAAATGATGTGCCTT
* * *
5580194 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAAATAACCTTTCTCGCCTTGAGCTATGCTG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
*
5580259 CAAATGATGCT-ACTT
66 CAAATGATG-TGCCTT
* * ** * * * **
5580274 TGAGCTGAATGGAATCGAACTCGAATATCTTTAGCAGATAACCCTTCTAGCCTTGAGTTATTATG
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
* * *
5580339 CAAATCATGTGCATC
66 CAAATGATGTGCCTT
5580354 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTT
1 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTT
5580386 ATCAAACTCG
Statistics
Matches: 588, Mismatches: 79, Indels: 27
0.85 0.11 0.04
Matches are distributed among these distances:
78 4 0.01
79 3 0.01
80 379 0.64
81 3 0.01
82 32 0.05
83 94 0.16
84 73 0.12
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (80 bp):
TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGCTATGCTG
CAAATGATGTGCCTT
Found at i:5581716 original size:98 final size:98
Alignment explanation
Indices: 5581588--5581791 Score: 381
Period size: 98 Copynumber: 2.1 Consensus size: 98
5581578 GCCATTGTCT
*
5581588 GGCTAGCTGAATCATATCCATAAAGCTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAA
1 GGCTAGCTAAATCATATCCATAAAGCTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAA
5581653 CTTTATTGTATATATATTATAATCACCTTTACA
66 CTTTATTGTATATATATTATAATCACCTTTACA
*
5581686 GGCTAGCTAAATCATATCCATAAAGCTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAG
1 GGCTAGCTAAATCATATCCATAAAGCTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAA
*
5581751 CTTTATTTTATATATATTATAATCACCTTTACA
66 CTTTATTGTATATATATTATAATCACCTTTACA
5581784 GGCTAGCT
1 GGCTAGCT
5581792 GAAGGATTCA
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 103 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (98 bp):
GGCTAGCTAAATCATATCCATAAAGCTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAA
CTTTATTGTATATATATTATAATCACCTTTACA
Found at i:5586586 original size:2 final size:2
Alignment explanation
Indices: 5586579--5586635 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
5586569 TCAATCTACA
5586579 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
5586621 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
5586636 CGAAATACAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5587545 original size:64 final size:64
Alignment explanation
Indices: 5587477--5587698 Score: 238
Period size: 64 Copynumber: 3.5 Consensus size: 64
5587467 GTTTAAAGGT
* ** * *
5587477 GCATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAATACATCGAATGCAATTTG
1 GCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAGAAA-ACATCGAATGCAATTAG
5587540 C
64 C
* * *
5587541 GCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGAAACATCGAATGCAATTAGT
1 GCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGC
* * * * * *
5587605 GCATCGATGCATAAGGTA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTA-T
1 GCATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGC
*
5587668 GCACCGATGCATCA-GTAGTGCATCGATGCAT
1 GCATCGATGCAT-AGGTAGTGCATCGATGCAT
5587699 ACCTTCATTA
Statistics
Matches: 137, Mismatches: 17, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
62 3 0.02
63 26 0.19
64 99 0.72
65 9 0.07
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
GCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAAGAAAACATCGAATGCAATTAGC
Found at i:5588572 original size:103 final size:103
Alignment explanation
Indices: 5588448--5588670 Score: 446
Period size: 103 Copynumber: 2.2 Consensus size: 103
5588438 GTCGAGGGTC
5588448 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
5588513 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
5588551 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
5588616 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
5588654 TATGTGGTCCTTCGGGA
1 TATGTGGTCCTTCGGGA
5588671 CATTATTATA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 120 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAGTGA
Found at i:5588715 original size:23 final size:23
Alignment explanation
Indices: 5588682--5588744 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
5588672 ATTATTATAT
5588682 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
5588705 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
5588728 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
5588745 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:5589673 original size:13 final size:13
Alignment explanation
Indices: 5589655--5589687 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5589645 CAATAAACGC
5589655 CATAAATGAGTGT
1 CATAAATGAGTGT
*
5589668 CATAAATGTGTGT
1 CATAAATGAGTGT
5589681 CATAAAT
1 CATAAAT
5589688 ACGCGTCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (13 bp):
CATAAATGAGTGT
Found at i:5593208 original size:12 final size:13
Alignment explanation
Indices: 5593191--5593220 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5593181 GAATTTTCAA
5593191 GAAAATC-ATTTT
1 GAAAATCAATTTT
5593203 GAAAATCAATTTT
1 GAAAATCAATTTT
5593216 GAAAA
1 GAAAA
5593221 ATTTTACTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (13 bp):
GAAAATCAATTTT
Found at i:5595540 original size:23 final size:22
Alignment explanation
Indices: 5595506--5595585 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
5595496 TACAACAGAG
5595506 TGCATCGATGCACATTCAAGGCA
1 TGCATCGATGCACATTCAAGG-A
* *
5595529 TGCATCGGTGCAGC-TTCATGG-
1 TGCATCGATGCA-CATTCAAGGA
*
5595550 TGAATCGATGCACATTCAAGGAA
1 TGCATCGATGCACATTCAAGG-A
*
5595573 TGTATCGATGCAC
1 TGCATCGATGCAC
5595586 TAGGTAATGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.02
21 16 0.34
23 29 0.62
24 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:5599395 original size:21 final size:22
Alignment explanation
Indices: 5599369--5599411 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5599359 GAGATTATTT
5599369 TCATTTTTCA-ATTTT-GAAATA
1 TCATTTTT-ATATTTTAGAAATA
5599390 TCATTTTTATATTTTAGAAATA
1 TCATTTTTATATTTTAGAAATA
5599412 ATTTCTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 13 0.65
22 6 0.30
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.53
Consensus pattern (22 bp):
TCATTTTTATATTTTAGAAATA
Found at i:5599420 original size:21 final size:20
Alignment explanation
Indices: 5599370--5599421 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
5599360 AGATTATTTT
5599370 CATTTTTCA-ATTTTGAAATA
1 CATTTTT-ATATTTTGAAATA
5599390 TCATTTTTATATTTTAGAAATA
1 -CATTTTTATATTTT-GAAATA
5599412 -ATTTCTTATA
1 CATTT-TTATA
5599422 ATCAGAAGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 5 0.18
21 17 0.61
22 6 0.21
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (20 bp):
CATTTTTATATTTTGAAATA
Found at i:5601467 original size:63 final size:64
Alignment explanation
Indices: 5601312--5601468 Score: 185
Period size: 65 Copynumber: 2.4 Consensus size: 64
5601302 GTACACTAGG
* * *
5601312 GTGTGTATCGGTGCACAAATTTGCTTCGATGTTTCAAAATAGTCTAGAGTGCATCGATGCATGGT
1 GTGTGCATCGGTGCATAAATTT-ATTCGATGTTTCAAAATAGTCTAGAGTGCATCGATGCATGGT
* *** *
5601377 GTGTGCATCGGTACATAAAACCAATTCGATGTTTCATAAA-A-TTTAGAGTGCATCGATGCATGG
1 GTGTGCATCGGTGCAT-AAATTTATTCGATGTTTCA-AAATAGTCTAGAGTGCATCGATGCATGG
5601440 T
64 T
5601441 -TGTGCATCGGTGCATAAATTGTATTCGA
1 GTGTGCATCGGTGCATAAATT-TATTCGA
5601469 AATGGGTGTG
Statistics
Matches: 77, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
62 3 0.04
63 20 0.26
64 22 0.29
65 26 0.34
66 6 0.08
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.33
Consensus pattern (64 bp):
GTGTGCATCGGTGCATAAATTTATTCGATGTTTCAAAATAGTCTAGAGTGCATCGATGCATGGT
Found at i:5601484 original size:34 final size:34
Alignment explanation
Indices: 5601436--5601517 Score: 137
Period size: 34 Copynumber: 2.4 Consensus size: 34
5601426 GCATCGATGC
*
5601436 ATGGTTGTGCATCGGTGCATAAATTGTATTCGAA
1 ATGGGTGTGCATCGGTGCATAAATTGTATTCGAA
5601470 ATGGGTGTGCATCGGTGCATAAATTGTATTCGAA
1 ATGGGTGTGCATCGGTGCATAAATTGTATTCGAA
* *
5601504 ATAGGTGTGTATCG
1 ATGGGTGTGCATCG
5601518 ATGAAATGGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (34 bp):
ATGGGTGTGCATCGGTGCATAAATTGTATTCGAA
Found at i:5602077 original size:20 final size:20
Alignment explanation
Indices: 5602040--5602077 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
5602030 AAAATCAAAC
*
5602040 AAAATATTAGATGGTAAAAT
1 AAAATATTAGATGCTAAAAT
5602060 AAAATATT-GAATGCTAAA
1 AAAATATTAG-ATGCTAAA
5602078 CAAAAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.55, C:0.03, G:0.13, T:0.29
Consensus pattern (20 bp):
AAAATATTAGATGCTAAAAT
Found at i:5607906 original size:34 final size:34
Alignment explanation
Indices: 5607862--5607927 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
5607852 CTAAAAAAAT
* * *
5607862 AAGTCTATTCATCAAATGACATGACTTTATAATA
1 AAGTCCATTCACCAAATGACATGACTATATAATA
* *
5607896 AAGTCCATTCACCAAGTGACGTGACTATATAA
1 AAGTCCATTCACCAAATGACATGACTATATAA
5607928 ATAGCATCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (34 bp):
AAGTCCATTCACCAAATGACATGACTATATAATA
Done.