Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008432.1 Hibiscus syriacus cultivar Beakdansim tig00111230_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: 128903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5149 original size:13 final size:13
Alignment explanation
Indices: 5131--5158 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5121 ACTATTGTTT
5131 AAAGATAACTCTC
1 AAAGATAACTCTC
5144 AAAGATAACTCTC
1 AAAGATAACTCTC
5157 AA
1 AA
5159 TTTTAACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (13 bp):
AAAGATAACTCTC
Found at i:8632 original size:17 final size:18
Alignment explanation
Indices: 8600--8635 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
8590 TGATATATGC
*
8600 AAAATAAAAACAAAAGAG
1 AAAACAAAAACAAAAGAG
8618 AAAACAAAAAC-AAAGAG
1 AAAACAAAAACAAAAGAG
8635 A
1 A
8636 TGATTTTGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.78, C:0.08, G:0.11, T:0.03
Consensus pattern (18 bp):
AAAACAAAAACAAAAGAG
Found at i:18758 original size:69 final size:69
Alignment explanation
Indices: 18647--18786 Score: 280
Period size: 69 Copynumber: 2.0 Consensus size: 69
18637 AAATTGTACT
18647 CTCTTATAATAAACACAATATTCTACATCCCTTAGGAATGTCAAAATATCTACAGTATAGCAATA
1 CTCTTATAATAAACACAATATTCTACATCCCTTAGGAATGTCAAAATATCTACAGTATAGCAATA
18712 AAAC
66 AAAC
18716 CTCTTATAATAAACACAATATTCTACATCCCTTAGGAATGTCAAAATATCTACAGTATAGCAATA
1 CTCTTATAATAAACACAATATTCTACATCCCTTAGGAATGTCAAAATATCTACAGTATAGCAATA
18781 AAAC
66 AAAC
18785 CT
1 CT
18787 TTGTATTCAA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (69 bp):
CTCTTATAATAAACACAATATTCTACATCCCTTAGGAATGTCAAAATATCTACAGTATAGCAATA
AAAC
Found at i:21810 original size:15 final size:17
Alignment explanation
Indices: 21786--21819 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
21776 TATAAATACT
21786 AAAATAGTTT-TTATAA
1 AAAATAGTTTATTATAA
21802 AAAAT-GTTTATTATAA
1 AAAATAGTTTATTATAA
21818 AA
1 AA
21820 TGTAATGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
AAAATAGTTTATTATAA
Found at i:24470 original size:19 final size:19
Alignment explanation
Indices: 24446--24486 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
24436 TTGTTGTTGA
* *
24446 AACTTATTCTTTAGATAAC
1 AACTTATTCTTCACATAAC
24465 AACTTATTCTTCACATAAC
1 AACTTATTCTTCACATAAC
24484 AAC
1 AAC
24487 CAACTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (19 bp):
AACTTATTCTTCACATAAC
Found at i:27233 original size:33 final size:33
Alignment explanation
Indices: 27191--27310 Score: 129
Period size: 33 Copynumber: 3.6 Consensus size: 33
27181 TAAAATAGAG
*
27191 AAATCAACCAATAGCTCATCAAAAAATCTCGACC
1 AAATCAACCAACA-CTCATCAAAAAATCTCGACC
* *
27225 AAAT-AACCAACCACTCATCGAAAAATCTAGACC
1 AAATCAACCAA-CACTCATCAAAAAATCTCGACC
*
27258 -AATCAACCAACAACTCATCCAAAAATCTCGACC
1 AAATCAACCAAC-ACTCATCAAAAAATCTCGACC
* *
27291 -AACCAACAAACAACTCATCA
1 AAATCAACCAAC-ACTCATCA
27311 GTAAGTTAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
32 4 0.05
33 66 0.88
34 5 0.07
ACGTcount: A:0.48, C:0.33, G:0.04, T:0.15
Consensus pattern (33 bp):
AAATCAACCAACACTCATCAAAAAATCTCGACC
Found at i:27871 original size:113 final size:117
Alignment explanation
Indices: 27591--27893 Score: 294
Period size: 118 Copynumber: 2.6 Consensus size: 117
27581 ATTGTCAGGC
* * * * * * *
27591 ATAAGGTGAAAGATTGAATATGTGAATAATGTCTTTCTTCCAACGCATGACTCCAACCTATTTAG
1 ATAAGGTGAAAGATAGGATATGTGAAGAATGTCTTTCTTCCAATGCATGACTCCAACCCATTCAA
* *
27656 CTCGTTCAAATAGAATTGAGATAACGCAAACAATAAATGTGTTTATGTTAGGA
66 CTCGTTCAAATAGAATTGAGATAAC-CAAACAATAAATGTGTTTATATAAGGA
* * * * ** *
27709 ATACGAT-AGAAGATCA-GATATGTAAAGAATGTTTTTCTTCTGATGCATGACTCTAACCCATTC
1 ATAAGGTGA-AAGAT-AGGATATGTGAAGAATGTCTTTCTTCCAATGCATGACTCCAACCCATTC
* * * * *
27772 AACTCGTTCGAATAGAATTGAGATGA-C-AA-AA-AATTGTGTTTTTATAAGGT
64 AACTCGTTCAAATAGAATTGAGATAACCAAACAATAAATGTGTTTATATAAGGA
* * * * *
27822 ATAAGGTGAAAGATAGGCTATGTGAAGAATGTCTTTCTTCCAATACATGACTACAACTCGTTCAA
1 ATAAGGTGAAAGATAGGATATGTGAAGAATGTCTTTCTTCCAATGCATGACTCCAACCCATTCAA
*
27887 TTCGTTC
66 CTCGTTC
27894 TGATATAATT
Statistics
Matches: 147, Mismatches: 34, Indels: 13
0.76 0.18 0.07
Matches are distributed among these distances:
112 1 0.01
113 69 0.47
114 3 0.02
115 2 0.01
116 1 0.01
117 1 0.01
118 70 0.48
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (117 bp):
ATAAGGTGAAAGATAGGATATGTGAAGAATGTCTTTCTTCCAATGCATGACTCCAACCCATTCAA
CTCGTTCAAATAGAATTGAGATAACCAAACAATAAATGTGTTTATATAAGGA
Found at i:34368 original size:99 final size:99
Alignment explanation
Indices: 34186--34520 Score: 349
Period size: 99 Copynumber: 3.4 Consensus size: 99
34176 ATGTTACCGA
* *
34186 TTGCACCTTGGTGTTATGTTAACTGGTTAAGTTATAGGAAGAAA-GCTCGTATATTATG-AAAAA
1 TTGCACCTTGGTGTTATGTTAACTGGTTAAGTTATAAGATGAAACG-T-GTATATTATGAAAAAA
* * *
34249 GTAATACAAACTTGGTTTCCTAGATAATATTATAGG
64 GTAAAACAAACATGGTTTCCTAGATAACATTATAGG
* * ** * *
34285 TTGCACCTTGGTGTTATTTTAAATGGTTGCGTTATAAGTTGAAATCGTGTATATTATGAAAAAAT
1 TTGCACCTTGGTGTTATGTTAACTGGTTAAGTTATAAGATGAAA-CGTGTATATTATGAAAAAAG
*
34350 TAAAACAAACATGG-TTCCTAGATAACATTATATG
65 TAAAACAAACATGGTTTCCTAGATAACATTATAGG
* * **
34384 TTGCACCTTGTTTTTATGTTAACTGGTTAAGTTATAACCTGAAACTGTGTATATTATG-AAAAAG
1 TTGCACCTTGGTGTTATGTTAACTGGTTAAGTTATAAGATGAAAC-GTGTATATTATGAAAAAAG
* * * *
34448 T-AAACTAAACCTGATTT-CTTGTATAACATTATAAG
65 TAAAAC-AAACATGGTTTCCTAG-ATAACATTATAGG
** * * *
34483 TTGTGCCTTGTTGTTATGTTAATTGGATAAGTTATAAG
1 TTGCACCTTGGTGTTATGTTAACTGGTTAAGTTATAAG
34521 CTTAAACCTT
Statistics
Matches: 198, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
97 4 0.02
98 16 0.08
99 159 0.80
100 18 0.09
101 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (99 bp):
TTGCACCTTGGTGTTATGTTAACTGGTTAAGTTATAAGATGAAACGTGTATATTATGAAAAAAGT
AAAACAAACATGGTTTCCTAGATAACATTATAGG
Found at i:34541 original size:198 final size:197
Alignment explanation
Indices: 34186--34555 Score: 435
Period size: 198 Copynumber: 1.9 Consensus size: 197
34176 ATGTTACCGA
**
34186 TTGCACCTTGGTGTTATGTTAACTGGTTAAGTTATAGGAAGAAAGCTCGTATATTATGAAAAAGT
1 TTGCACCTTGGTGTTATGTTAACTGGTTAAGTTATAACAAGAAAGCTCGTATATTATGAAAAAGT
* * * * * * **
34251 AATACAAACTTGGTTTCCTAGATAATATTATAGGTTGCACCTTGGTGTTATTTTAAATGGTTGCG
66 AATACAAACCTGATTTCCTAGATAACATTATAAGTTGCACCTTGGTGTTATGTTAAATGGATAAG
* *
34316 TTATAAGTTGAAATCGTGTATATTATGAAAAAATTAAAACAAACATGGTTCCTAGATAACATTAT
131 TTATAAGTTGAAACCGTGTACATTATG-AAAAATTAAAACAAACATGGTTCCTAGATAACATTAT
34381 ATG
195 ATG
* * ** *
34384 TTGCACCTTGTTTTTATGTTAACTGGTTAAGTTATAACCTGAAA-CTGTGTATATTATGAAAAAG
1 TTGCACCTTGGTGTTATGTTAACTGGTTAAGTTATAACAAGAAAGCT-CGTATATTATGAAAAAG
* ** * *
34448 TAA-ACTAAACCTGATTT-CTTGTATAACATTATAAGTTGTGCCTTGTTGTTATGTTAATTGGAT
65 TAATAC-AAACCTGATTTCCTAG-ATAACATTATAAGTTGCACCTTGGTGTTATGTTAAATGGAT
* *
34511 AAGTTATAAGCTT-AAACCTTAG-ACATTATGAAAAATTAATACAAA
128 AAGTTATAAG-TTGAAACCGT-GTACATTATGAAAAATTAAAACAAA
34556 TTGGTTAAGT
Statistics
Matches: 143, Mismatches: 24, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
197 21 0.15
198 119 0.83
199 3 0.02
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.38
Consensus pattern (197 bp):
TTGCACCTTGGTGTTATGTTAACTGGTTAAGTTATAACAAGAAAGCTCGTATATTATGAAAAAGT
AATACAAACCTGATTTCCTAGATAACATTATAAGTTGCACCTTGGTGTTATGTTAAATGGATAAG
TTATAAGTTGAAACCGTGTACATTATGAAAAATTAAAACAAACATGGTTCCTAGATAACATTATA
TG
Found at i:38920 original size:240 final size:239
Alignment explanation
Indices: 38493--38942 Score: 579
Period size: 240 Copynumber: 1.9 Consensus size: 239
38483 ATTTTAGATG
* ** *
38493 CAACCCATTTTATTGTTAAAAATAGTAAGATTCCATATTGCAACATATTTTCTTGGTGAACCTTG
1 CAACCCATTTTATTGATAAAAATAGTAAGATTCCATATTGCAACATATTTTCTCAGTGAACCATG
* * * *
38558 ACATTCTTTGGTGCAATCTATTTTATTAAAAAAATATTAACATTAAAGATCACAACTTATTTATT
66 AAATTATTAGGTGCAACCTATTTTATTAAAAAAATATTAACATTAAAGATCACAACTTATTTATT
* * *
38623 AGTGAATCATGATATTATTGGACGCAACTGTATTTAATATATATATTCATAACA-TTTTCAACTT
131 AATAAATCATGACATTATTGGACGCAACTGTATTTAATATATATATTCATAACATTTTTC-ACTT
38687 TTAACTTATTTTCTTAATGTGAGAATATCTAAGGTTCCATATGCA
195 TTAACTTATTTTCTTAATGTGAGAATATCTAAGGTTCCATATGCA
* * *
38732 CAACTCATTTTATT-ATAAAAAGTATTAAGATTCCATATTGCAACATGTTTTCTCAGTGAACCAT
1 CAACCCATTTTATTGATAAAAA-TAGTAAGATTCCATATTGCAACATATTTTCTCAGTGAACCAT
* *
38796 GAAATTATTAGGTGTAACCTATTTTCTTAATAAAAATATTAACATTACAA-ATCACAA-TATATT
65 GAAATTATTAGGTGCAACCTATTTTATTAA-AAAAATATTAACATTA-AAGATCACAACT-TATT
* * ** * *
38859 TCTTAATAAATCATGACATTATTCGG-TGCAA-TCGTATTTTTTGTATATATTCGTAACATTTTT
127 TATTAATAAATCATGACATTATT-GGACGCAACT-GTATTTAATATATATATTCATAACATTTTT
**
38922 CGTTTTTAACTTATTTTCTTA
190 CACTTTTAACTTATTTTCTTA
38943 TCGTGGGTAA
Statistics
Matches: 180, Mismatches: 24, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
238 6 0.03
239 76 0.42
240 89 0.49
241 9 0.05
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.42
Consensus pattern (239 bp):
CAACCCATTTTATTGATAAAAATAGTAAGATTCCATATTGCAACATATTTTCTCAGTGAACCATG
AAATTATTAGGTGCAACCTATTTTATTAAAAAAATATTAACATTAAAGATCACAACTTATTTATT
AATAAATCATGACATTATTGGACGCAACTGTATTTAATATATATATTCATAACATTTTTCACTTT
TAACTTATTTTCTTAATGTGAGAATATCTAAGGTTCCATATGCA
Found at i:39790 original size:38 final size:37
Alignment explanation
Indices: 39716--39791 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
39706 GTTGGAAAAT
*
39716 ATTTATATATTTTCTTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTTAAAAAATTAAAATCATAAA
* *
39753 ATTTATATAATTTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTTAAAAAATT-AAAATCATAAA
39791 A
1 A
39792 AAGTTTAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
37 8 0.24
38 22 0.65
39 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTTAAAAAATTAAAATCATAAA
Found at i:44104 original size:21 final size:21
Alignment explanation
Indices: 44078--44119 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
44068 CACTTAAAAA
44078 ACTAAGCACATACCCAACCAT
1 ACTAAGCACATACCCAACCAT
*
44099 ACTAAGCACGTACCCAACCAT
1 ACTAAGCACATACCCAACCAT
44120 TGAGCCAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.38, G:0.07, T:0.14
Consensus pattern (21 bp):
ACTAAGCACATACCCAACCAT
Found at i:44242 original size:23 final size:23
Alignment explanation
Indices: 44211--44271 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 23
44201 ATTCAAATTT
44211 TTTTATATATTAACTT-TAAAAATA
1 TTTT-TATATTAACTTAT-AAAATA
*
44235 TTTTTATATTAACTTATTAAATA
1 TTTTTATATTAACTTATAAAATA
44258 TATTTTATTATTAA
1 T-TTTTA-TATTAA
44272 TCTAATTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 17 0.52
24 10 0.30
25 6 0.18
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTTTATATTAACTTATAAAATA
Found at i:44254 original size:25 final size:25
Alignment explanation
Indices: 44211--44283 Score: 80
Period size: 25 Copynumber: 2.9 Consensus size: 25
44201 ATTCAAATTT
44211 TTTTATATATTAAC-T-TTAAAAATA
1 TTTT-TATATTAACTTATTAAAAATA
*
44235 TTTTTATATTAACTTATTAAATATA
1 TTTTTATATTAACTTATTAAAAATA
*
44260 -TTTTATTATTAATCTAATTAAAAA
1 TTTTTA-TATTAA-CTTATTAAAAA
44284 AATATCTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
23 9 0.21
24 10 0.24
25 14 0.33
26 9 0.21
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (25 bp):
TTTTTATATTAACTTATTAAAAATA
Found at i:44485 original size:26 final size:27
Alignment explanation
Indices: 44437--44519 Score: 91
Period size: 26 Copynumber: 3.1 Consensus size: 27
44427 AAAGTTTGGA
44437 TAAAAATAACATATATATTTAAAATAAAT
1 TAAAAATAA-A-ATATATTTAAAATAAAT
* *
44466 TAAAAATTAAATA-ATTTAAATTAAAT
1 TAAAAATAAAATATATTTAAAATAAAT
* *
44492 TCATAATAAAATATATTT--AATAAAT
1 TAAAAATAAAATATATTTAAAATAAAT
44517 TAA
1 TAA
44520 TATAAAAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 8 0.17
26 22 0.48
27 7 0.15
28 1 0.02
29 8 0.17
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
TAAAAATAAAATATATTTAAAATAAAT
Found at i:45059 original size:31 final size:31
Alignment explanation
Indices: 45022--45081 Score: 104
Period size: 31 Copynumber: 1.9 Consensus size: 31
45012 GAGCACACCA
45022 TAATTAAATAGAAA-TAAAAATGACTATATCT
1 TAATTAAATA-AAAGTAAAAATGACTATATCT
45053 TAATTAAATAAAAGTAAAAATGACTATAT
1 TAATTAAATAAAAGTAAAAATGACTATAT
45082 ATTATGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.32
Consensus pattern (31 bp):
TAATTAAATAAAAGTAAAAATGACTATATCT
Found at i:46732 original size:16 final size:15
Alignment explanation
Indices: 46711--46752 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
46701 TTTATATTCA
46711 ATTATAATTTGATC-TT
1 ATTAT-ATTT-ATCATT
46727 ATTATATTTATCATT
1 ATTATATTTATCATT
46742 ATTATTATTTA
1 ATTA-TATTTA
46753 GTTTAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 10 0.42
16 11 0.46
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (15 bp):
ATTATATTTATCATT
Found at i:59595 original size:103 final size:103
Alignment explanation
Indices: 59413--59732 Score: 505
Period size: 103 Copynumber: 3.1 Consensus size: 103
59403 GTCGAGGGTC
* * *
59413 TATGTGGTCCTTCGGGACATGTATGCATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
59478 TTGATCCTTTGCATATTTATATGATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
* * * *
59516 TACGTGGTCTTTCAGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
59581 TTGATCCTTGGCATATGTATATTATTCTTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
*
59619 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
59684 TTGATCCCTAGTATATGTATATGATTATTAAGGAATGA
66 TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
59722 TATGTGGTCCT
1 TATGTGGTCCT
59733 AATGGACAAT
Statistics
Matches: 197, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 197 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:59776 original size:23 final size:23
Alignment explanation
Indices: 59750--59812 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
59740 AATATTATAT
59750 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
59773 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
59796 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
59813 ATATGAGTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:64183 original size:15 final size:15
Alignment explanation
Indices: 64159--64212 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
64149 TAGTGCATCG
64159 ATGCACCGATAGGGA
1 ATGCACCGATAGGGA
* *
64174 ATGCATCGATA-CG-
1 ATGCACCGATAGGGA
64187 ATGCACCGATAGGGA
1 ATGCACCGATAGGGA
*
64202 ATGCATCGATA
1 ATGCACCGATA
64213 CACTGTGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 10 0.31
14 2 0.06
15 20 0.62
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (15 bp):
ATGCACCGATAGGGA
Found at i:64194 original size:28 final size:28
Alignment explanation
Indices: 64157--64213 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
64147 GGTAGTGCAT
64157 CGATGCACCGATAGGGAATGCATCGATA
1 CGATGCACCGATAGGGAATGCATCGATA
64185 CGATGCACCGATAGGGAATGCATCGATA
1 CGATGCACCGATAGGGAATGCATCGATA
64213 C
1 C
64214 ACTGTGCAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.18
Consensus pattern (28 bp):
CGATGCACCGATAGGGAATGCATCGATA
Found at i:65291 original size:103 final size:103
Alignment explanation
Indices: 64963--65283 Score: 588
Period size: 103 Copynumber: 3.1 Consensus size: 103
64953 GTCGAGGGTC
* *
64963 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATATGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
65028 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
65066 TATATGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
65131 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65169 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
65234 TTGATCCATAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65272 TATGTGGTCCTT
1 TATGTGGTCCTT
65284 ATGGACATTA
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTAGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:65367 original size:23 final size:23
Alignment explanation
Indices: 65290--65367 Score: 77
Period size: 23 Copynumber: 3.3 Consensus size: 23
65280 CCTTATGGAC
*
65290 ATTATTATATGGCACTAT-GGTGCA
1 ATTA-TATGTGGCACT-TCGGTGCA
* * * *
65314 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
*
65337 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTTCGGTGCA
65360 ATTATATG
1 ATTATATG
65368 AGCTGTGGTG
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTTCGGTGCA
Found at i:69412 original size:42 final size:42
Alignment explanation
Indices: 69325--69485 Score: 173
Period size: 42 Copynumber: 3.8 Consensus size: 42
69315 AAGATTTGGA
* * * * ** *
69325 TCTATTACAGCGTTTTAATACCAAACGCCACTAATATTCACC
1 TCTATTGCGGCGTTTTAGTAACAAACGCCACTAAGGTACACC
* *
69367 TCTATTGCGGCGTTTTTA-TAACAAATGCCACTAAGGTACAGC
1 TCTATTGCGGCG-TTTTAGTAACAAACGCCACTAAGGTACACC
* * * *
69409 TCTATAGCGGTGTTTTAGTGACAAACACCACTAAGGTTAC-CC
1 TCTATTGCGGCGTTTTAGTAACAAACGCCACTAAGG-TACACC
69451 TCTATTGCGGCGTTTTAGTAACAAACGCCACTAAG
1 TCTATTGCGGCGTTTTAGTAACAAACGCCACTAAG
69486 TTGCCTTTAT
Statistics
Matches: 98, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
41 5 0.05
42 85 0.87
43 8 0.08
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (42 bp):
TCTATTGCGGCGTTTTAGTAACAAACGCCACTAAGGTACACC
Found at i:69413 original size:84 final size:84
Alignment explanation
Indices: 69332--69485 Score: 197
Period size: 84 Copynumber: 1.8 Consensus size: 84
69322 GGATCTATTA
* * *
69332 CAGCGTTTTAAT-ACCAAACGCCACTAATATT-CACCTCTATTGCGGCGTTTTTA-TAACAAATG
1 CAGCGTTTTAATGA-CAAACACCACTAAGATTAC-CCTCTATTGCGGCG-TTTTAGTAACAAACG
69394 CCACTAAGGTACAGCTCTATAG
63 CCACTAAGGTACAGCTCTATAG
* * * *
69416 CGGTGTTTTAGTGACAAACACCACTAAGGTTACCCTCTATTGCGGCGTTTTAGTAACAAACGCCA
1 CAGCGTTTTAATGACAAACACCACTAAGATTACCCTCTATTGCGGCGTTTTAGTAACAAACGCCA
69481 CTAAG
66 CTAAG
69486 TTGCCTTTAT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
83 5 0.08
84 53 0.88
85 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.29
Consensus pattern (84 bp):
CAGCGTTTTAATGACAAACACCACTAAGATTACCCTCTATTGCGGCGTTTTAGTAACAAACGCCA
CTAAGGTACAGCTCTATAG
Found at i:69483 original size:126 final size:126
Alignment explanation
Indices: 69258--69484 Score: 285
Period size: 126 Copynumber: 1.8 Consensus size: 126
69248 CGCCGTTGTA
* * * **
69258 ATAACAAATGCCACTAATGTGCACCTCTACTGCGGTGTTTCAACAATAAACACCACTAAGATTTG
1 ATAACAAATGCCACTAAGGTACACCTCTACTGCGGTGTTTCAACAACAAACACCACTAAGATTAC
* *
69323 GATCTATTACAGCGTTTTAATACCAAACGCCACTAATATTCACCTCTATTGCGGCGTTTTT
66 CATCTATTACAGCGTTTTAATAACAAACGCCACTAATATTCACCTCTATTGCGGCGTTTTT
* * *** *
69384 ATAACAAATGCCACTAAGGTACAGCTCTA-TAGCGGTGTTTTAGTGACAAACACCACTAAGGTTA
1 ATAACAAATGCCACTAAGGTACACCTCTACT-GCGGTGTTTCAACAACAAACACCACTAAGATTA
* * * *
69448 CCCTCTATTGCGGCGTTTTAGTAACAAACGCCACTAA
65 CCATCTATTACAGCGTTTTAATAACAAACGCCACTAA
69485 GTTGCCTTTA
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
125 1 0.01
126 82 0.99
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (126 bp):
ATAACAAATGCCACTAAGGTACACCTCTACTGCGGTGTTTCAACAACAAACACCACTAAGATTAC
CATCTATTACAGCGTTTTAATAACAAACGCCACTAATATTCACCTCTATTGCGGCGTTTTT
Found at i:71239 original size:28 final size:28
Alignment explanation
Indices: 71199--71267 Score: 120
Period size: 28 Copynumber: 2.5 Consensus size: 28
71189 ACATGAGAAA
**
71199 AAAATAAAAGAAAGAAATCAAATTTTTT
1 AAAATAAAAGAAAGAAATCAAAAATTTT
71227 AAAATAAAAGAAAGAAATCAAAAATTTT
1 AAAATAAAAGAAAGAAATCAAAAATTTT
71255 AAAATAAAAGAAA
1 AAAATAAAAGAAA
71268 ATTAAAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (28 bp):
AAAATAAAAGAAAGAAATCAAAAATTTT
Found at i:71285 original size:19 final size:19
Alignment explanation
Indices: 71227--71288 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
71217 CAAATTTTTT
*
71227 AAAATAAAAGAAAGAAATCA-
1 AAAATTAAA-AAAGAAAT-AG
** *
71247 AAAATTTTAAAATAAA-AG
1 AAAATTAAAAAAGAAATAG
71265 AAAATTAAAAAAGAAATAG
1 AAAATTAAAAAAGAAATAG
71284 AAAAT
1 AAAAT
71289 ACTATTTTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
17 1 0.03
18 13 0.39
19 13 0.39
20 6 0.18
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.18
Consensus pattern (19 bp):
AAAATTAAAAAAGAAATAG
Found at i:71651 original size:14 final size:14
Alignment explanation
Indices: 71632--71662 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
71622 TTACTCTAAC
71632 TAAAACTCTTTTAA
1 TAAAACTCTTTTAA
71646 TAAAACTCTTTTAA
1 TAAAACTCTTTTAA
71660 TAA
1 TAA
71663 CTAAAAATAG
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:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAAACTCTTTTAA
Found at i:71794 original size:83 final size:83
Alignment explanation
Indices: 71647--71951 Score: 401
Period size: 83 Copynumber: 3.7 Consensus size: 83
71637 CTCTTTTAAT
* * * * *
71647 AAAACTCTTTTAATAACT-AA---AAATAGATAATAACATCTTTTAAATTTAAAATATTAAATCT
1 AAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAAATTTATAATATTAAACCT
* *
71708 GAGAGTTTTAATCTAACC
66 GAGAGTTTTACTCCAACC
* *
71726 AAAACTCTTTTAATATCTAAATTTAAACAGATTATAATATCTTTTAAATTTATAATACTAAACCT
1 AAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAAATTTATAATATTAAACCT
71791 GAGAGTTTTACTCCAACC
66 GAGAGTTTTACTCCAACC
* * *
71809 AAAACTCTTTTAATATCTAAATTTAAACATG-TTATAATATCTTTTACATTTATAATATAAAACC
1 AAAACTCTTTTAATATCTAAATTTAAACA-GATAATAATATCTTTTAAATTTATAATATTAAACC
*
71873 TCA-AGTTTTACTCCAACC
65 TGAGAGTTTTACTCCAACC
* *
71891 TAAACTCTTTTAATATCTAAATTTAAATAGATAATAATAT-TGTTTAAATTTA-AATATTAAA
1 AAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCT-TTTAAATTTATAATATTAAA
71952 TATATATATT
Statistics
Matches: 201, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
79 17 0.08
80 2 0.01
81 10 0.05
82 59 0.29
83 112 0.56
84 1 0.00
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.40
Consensus pattern (83 bp):
AAAACTCTTTTAATATCTAAATTTAAACAGATAATAATATCTTTTAAATTTATAATATTAAACCT
GAGAGTTTTACTCCAACC
Found at i:79826 original size:21 final size:21
Alignment explanation
Indices: 79802--79850 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
79792 AATGTTGCTT
79802 CTCTCTCTGCTTCTATCGATA
1 CTCTCTCTGCTTCTATCGATA
* * *
79823 CTCTCTCTGCTTCTCTCGTTG
1 CTCTCTCTGCTTCTATCGATA
79844 CTCTCTC
1 CTCTCTC
79851 CACTTCTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.06, C:0.39, G:0.10, T:0.45
Consensus pattern (21 bp):
CTCTCTCTGCTTCTATCGATA
Found at i:79856 original size:21 final size:21
Alignment explanation
Indices: 79823--79887 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
79813 TCTATCGATA
** *
79823 CTCTCTCTGCTTCTCTCGTTG
1 CTCTCTCCACTTCTCTCTTTG
79844 CTCTCTCCACTTCTCTCTTTG
1 CTCTCTCCACTTCTCTCTTTG
*
79865 CTTTCTCCACTTCTCTCTTTG
1 CTCTCTCCACTTCTCTCTTTG
79886 CT
1 CT
79888 TATCTCACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.03, C:0.40, G:0.08, T:0.49
Consensus pattern (21 bp):
CTCTCTCCACTTCTCTCTTTG
Found at i:79888 original size:21 final size:21
Alignment explanation
Indices: 79832--79898 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
79822 ACTCTCTCTG
* *
79832 CTTCTCTCGTTGCTCTCTCCA
1 CTTCTCTCTTTGCTTTCTCCA
79853 CTTCTCTCTTTGCTTTCTCCA
1 CTTCTCTCTTTGCTTTCTCCA
79874 CTTCTCTCTTTGCTTATCT-CA
1 CTTCTCTCTTTGCTT-TCTCCA
79895 CTTC
1 CTTC
79899 AGCTTCACTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
21 40 0.93
22 3 0.07
ACGTcount: A:0.06, C:0.39, G:0.06, T:0.49
Consensus pattern (21 bp):
CTTCTCTCTTTGCTTTCTCCA
Found at i:81863 original size:262 final size:255
Alignment explanation
Indices: 81476--82089 Score: 818
Period size: 262 Copynumber: 2.4 Consensus size: 255
81466 CCATCCGAGA
*
81476 CCGACCTGACCAAAATAAAGTTTCACCCGA--C--CCGAATATATGAATTAG-AA---ACCCGAC
1 CCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCGAATATATGAATTAGAAACCGACCCGAC
* ** *
81533 CCGAAATAATAATAAAAAAAAATTTATTCAATAAAAACAGTGACTTAATTAGAAAAAAATATATA
66 CCGAAATAATAA-AAAAATATTTTTATTCAATAAAAACAATGACTTAATTAGAAAAAAATATATA
*
81598 TAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGAAAAATTATATATTTTTTGGGTCGGG
130 TAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGAAAAATTATATA-TATTT---TCGGG
* *
81663 TCGGGTATTTTTCACCCTAAAC-CTAAACCCGACCCAACCCAAATATCACACTTAAAAAAAACTG
191 TCGGGTATTTTTCACCCTAAACTC-AAACCCGACCCAACCCAAATATAACACTT-AAAAAAACCG
81727 AC
254 AC
81729 CCGACCCGACCAAAAT-AAGTTTCACCCGACCCGACTCGAATATATGAATTAGAAATCCGACCCG
1 CCGACCCGACCAAAATAAAGTTTCACCCGACCCGAC-CGAATATATGAATTAGAAA-CCGACCCG
*
81793 ACCCGAAATAATAAAAAAATTATTTTTGTTCAATAAAAACAATGACTTAATT-GAAAAAAATTAT
64 ACCCGAAATAATAAAAAAA-TATTTTTATTCAATAAAAACAATGACTTAATTAGAAAAAAA-TAT
* *
81857 ATATAGAGGGGTATTATTGTAATTATTCCTAAATATTTAAGGTAAAATTATATATATTTTCGGGT
127 ATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGAAAAATTATATATATTTTCGGGT
* * * *
81922 CGGGTATTTTTCACCCTAAACTCGAACTCGACCCGACCCGAATATAACACTTAAAAAAACCGAC
192 CGGGTATTTTTCACCCTAAACTCAAACCCGACCCAACCCAAATATAACACTTAAAAAAACCGAC
* * *
81986 TCGACCCTACCAAAATAAAGTTTCACCCGACCCGACCCGACCCGAATGTATGAATTAGAAACCCG
1 CCGACCCGACCAAAATAAAGTTT----C-ACCCGACCCGA-CCGAATATATGAATTAGAAA-CCG
*
82051 ACACGACCCGAAATAATAAAAAAATATTTTTATTCAATA
59 ACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATA
82090 TATGAATAAG
Statistics
Matches: 320, Mismatches: 21, Indels: 31
0.86 0.06 0.08
Matches are distributed among these distances:
252 13 0.04
253 15 0.05
254 1 0.00
256 1 0.00
257 41 0.13
258 59 0.18
259 1 0.00
261 17 0.05
262 116 0.36
263 55 0.17
264 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.26
Consensus pattern (255 bp):
CCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCGAATATATGAATTAGAAACCGACCCGAC
CCGAAATAATAAAAAAATATTTTTATTCAATAAAAACAATGACTTAATTAGAAAAAAATATATAT
AGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGAAAAATTATATATATTTTCGGGTCGGG
TATTTTTCACCCTAAACTCAAACCCGACCCAACCCAAATATAACACTTAAAAAAACCGAC
Found at i:84923 original size:15 final size:15
Alignment explanation
Indices: 84890--84927 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
84880 AAAATTTAAT
84890 ATTTAAA-TAAAATA
1 ATTTAAATTAAAATA
* *
84904 TTTTAAATTAAATTA
1 ATTTAAATTAAAATA
84919 ATTTAAATT
1 ATTTAAATT
84928 TTAAAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTAAATTAAAATA
Found at i:85484 original size:2 final size:2
Alignment explanation
Indices: 85479--85503 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
85469 TTAATCATTA
85479 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
85504 ATGATATAAT
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:87666 original size:182 final size:182
Alignment explanation
Indices: 87359--87982 Score: 1020
Period size: 182 Copynumber: 3.4 Consensus size: 182
87349 TTACTATCGG
* *
87359 TTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTCTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
87424 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGA
* *
87489 TATTTATAATAAAATATCGACACTTTCAACATATTCGGTAGCTCTTTACCGA
131 TACTTATAATAAAATATCGACACTTTCAACATATCCGGTAGCTCTTTACCGA
* *
87541 TTTTGTCATTTCGAGATCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
*
87606 TTTATAAAGTATCGATACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGA
* *
87671 TACTTATAATAAAATATCGATACTTTCAACATATCCGGTAGTTCTTTACCGA
131 TACTTATAATAAAATATCGACACTTTCAACATATCCGGTAGCTCTTTACCGA
* *
87723 TTTTGTCATTTCGAGACCGATTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATATATT
1 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
* * *
87788 TTTGTAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGA
* * *
87853 TACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTG-
131 TACTTATAATAAAATATCGACACTTTCAACATATCCGGTAGCTCTTTACC-GA
** * * *
87905 TTTTGTCATTTATAGACCGGTTTTGTC--ATTTTTACCTGTTTTATTGTTATAGATCGATACATT
1 TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
87968 TTTATAAAGTATCGA
66 TTTATAAAGTATCGA
87983 TACTATCAAC
Statistics
Matches: 413, Mismatches: 28, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
180 47 0.11
182 365 0.88
183 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAAATATCGACACTTTCAACATATCCGGTAGCTCTTTACCGA
Found at i:88115 original size:113 final size:111
Alignment explanation
Indices: 87861--88183 Score: 522
Period size: 113 Copynumber: 2.9 Consensus size: 111
87851 GATACTTATA
87861 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
87926 TTTGTCA-TTTTTACCTGTTTTATTGTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
87971 ATAAAGTATCGATACTATCAACATATCCGGTAGCGTTTTACCTATTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGG-
* *
88036 TTTTATCATTTTTTTACCTGTTATATTATTATGGATCGATACATTTTT
65 TTTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * *
88084 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
88149 TTTGTCATTTTTTACCTGTTATATTGTTATGGATC
66 TTTGTCATTTTTTACCTGTTATATTGTTATGGATC
88184 TGTAGACGCA
Statistics
Matches: 194, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
110 61 0.31
111 34 0.18
112 7 0.04
113 92 0.47
ACGTcount: A:0.25, C:0.16, G:0.14, T:0.45
Consensus pattern (111 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:88263 original size:3 final size:3
Alignment explanation
Indices: 88255--88280 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
88245 AATTTATTTG
88255 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
88281 TTTTTTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:89632 original size:21 final size:21
Alignment explanation
Indices: 89595--89639 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
89585 CATTCAATAA
*
89595 TTATTTATTCCATTTTTA-TT
1 TTATTTATTCCACTTTTACTT
*
89615 TTATTTATTTCCCCTTTTACTT
1 TTATTTA-TTCCACTTTTACTT
89637 TTA
1 TTA
89640 CTATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTTATTCCACTTTTACTT
Found at i:96989 original size:2 final size:2
Alignment explanation
Indices: 96984--97008 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
96974 TGTATTTATG
96984 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
97009 TCATTTTACC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:97176 original size:20 final size:19
Alignment explanation
Indices: 97129--97179 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
97119 CTTTTTACTA
97129 TTATTATTAT-TTATTTAT
1 TTATTATTATATTATTTAT
*
97147 TTATGCTATTATATTATTATTT
1 TTAT--TATTATATTATT-TAT
97169 TTATTATTATA
1 TTATTATTATA
97180 CGTATATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.14
20 13 0.46
21 5 0.18
22 6 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTATTATATTATTTAT
Found at i:106527 original size:105 final size:104
Alignment explanation
Indices: 106344--107008 Score: 1079
Period size: 105 Copynumber: 6.4 Consensus size: 104
106334 AGGTTTTACC
106344 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
106409 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATT
* *
106449 TAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
106514 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAA-TT
*
106554 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
106619 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTC-AATT
*
106659 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
106724 ACGAAGGGACCGCTGGTTTTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAA-TT
*
106764 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
106829 ACGAAGGGACCGCTGCTTGTCAAC-AACGACTTCCCAATCT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAT-T
*
106869 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
106934 ACGAAGGGACCGCTGCTTGTCAACAAA-A-TT-TC-ATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
** * *
106969 CAGATTCAATTTCAACTTCACAACGAAGGACATCGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
107009 GAAACAACAC
Statistics
Matches: 533, Mismatches: 21, Indels: 17
0.93 0.04 0.03
Matches are distributed among these distances:
100 37 0.07
101 2 0.00
102 1 0.00
103 2 0.00
104 9 0.02
105 478 0.90
106 4 0.01
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (104 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:107334 original size:3 final size:3
Alignment explanation
Indices: 107326--107357 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
107316 AATTTATTTG
107326 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
107358 TTTTTTCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:108709 original size:21 final size:21
Alignment explanation
Indices: 108672--108715 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
108662 CATTCAATAA
*
108672 TTATTTATTCCATTTTTA-TT
1 TTATTTATTCCACTTTTACTT
*
108692 TTATTTATTTCCCCTTTTACTT
1 TTATTTA-TTCCACTTTTACTT
108714 TT
1 TT
108716 TACTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTATTCCACTTTTACTT
Found at i:109688 original size:112 final size:112
Alignment explanation
Indices: 109486--109740 Score: 404
Period size: 112 Copynumber: 2.3 Consensus size: 112
109476 GGTGGCGACA
* * *
109486 GGATCGATACATTTTTATAAAGTATCGACACTTTCAATATATCTGGTAGCGCTTTACCTGTTTTG
1 GGATAGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTG
*
109551 TCATTTATAGACCGATTTTGTCATTTTTTTACCTGTTATATTGTTAT
66 TCATTTATAGACCGATTTTATCATTTTTTTACCTGTTATATTGTTAT
* * *
109598 GGATAGATACATTTTTATAAAGTATAGACACTTTCAATATATCCGATAGTGCTTTACTTGTTTTG
1 GGATAGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTG
* *
109663 TCATTTATAGACCGGTTTTATCATTTTTTTACTTGTTATATTGTTAT
66 TCATTTATAGACCGATTTTATCATTTTTTTACCTGTTATATTGTTAT
*
109710 GGATCA-ATATATTTTTATAAAGTATCGACAC
1 GGAT-AGATACATTTTTATAAAGTATCGACAC
109741 AAACCGACAA
Statistics
Matches: 131, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
112 130 0.99
113 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (112 bp):
GGATAGATACATTTTTATAAAGTATCGACACTTTCAATATATCCGATAGCGCTTTACCTGTTTTG
TCATTTATAGACCGATTTTATCATTTTTTTACCTGTTATATTGTTAT
Found at i:110241 original size:25 final size:25
Alignment explanation
Indices: 110213--110294 Score: 92
Period size: 25 Copynumber: 3.1 Consensus size: 25
110203 TTTTTTAAGT
110213 TTATAATTTTGAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
* *
110238 TTATAAGTTTGGGAATATTTTTTATTTAA
1 TTATAA-TTT-TGAA-A-TTTTAATTTAA
* *
110267 ATATAATTTTAAAATTTTAATTTAA
1 TTATAATTTTGAAATTTTAATTTAA
110292 TTA
1 TTA
110295 ATTTTATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
25 18 0.39
26 4 0.09
27 5 0.11
28 4 0.09
29 15 0.33
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (25 bp):
TTATAATTTTGAAATTTTAATTTAA
Found at i:111269 original size:16 final size:15
Alignment explanation
Indices: 111248--111289 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
111238 TTTATATTCA
111248 ATTATAATTTGATC-TT
1 ATTAT-ATTT-ATCATT
111264 ATTATATTTATCATT
1 ATTATATTTATCATT
111279 ATTATTATTTA
1 ATTA-TATTTA
111290 GTTTAACAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.12
15 10 0.42
16 11 0.46
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (15 bp):
ATTATATTTATCATT
Found at i:112464 original size:41 final size:41
Alignment explanation
Indices: 112416--112497 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
112406 TGTAATTCAC
112416 GATGCAATCATTTGAATCAGTCAATTTGCAAGAGACCGTCA
1 GATGCAATCATTTGAATCAGTCAATTTGCAAGAGACCGTCA
112457 GATGCAATCATTTGAATCAGTCAATTTGCAAGAGACCGTCA
1 GATGCAATCATTTGAATCAGTCAATTTGCAAGAGACCGTCA
112498 ATGTGCGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (41 bp):
GATGCAATCATTTGAATCAGTCAATTTGCAAGAGACCGTCA
Found at i:115159 original size:74 final size:73
Alignment explanation
Indices: 115016--115159 Score: 180
Period size: 74 Copynumber: 2.0 Consensus size: 73
115006 TACAAACGAC
* * *
115016 CAACAGGTTCGCCATATAGCGACTTTTTTGGCACAAACACCGCAATAGATTTGATATTTATAGGC
1 CAACAGGTTCGCCATATAGCGACTTTTTAGGCACAAACACCGCAACAGATTTGATATTTAGAGGC
115081 GTTTCCCG
66 GTTTCCCG
* * * * ** *
115089 CAACATGTTCGCTATTTAGCGACATTTTTAGTCACAAATGCCGCAACAGATTTGATATTTAGCGG
1 CAACAGGTTCGCCATATAGCGAC-TTTTTAGGCACAAACACCGCAACAGATTTGATATTTAGAGG
*
115154 TGTTTC
65 CGTTTC
115160 GGGCACAAAC
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
73 20 0.34
74 39 0.66
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.33
Consensus pattern (73 bp):
CAACAGGTTCGCCATATAGCGACTTTTTAGGCACAAACACCGCAACAGATTTGATATTTAGAGGC
GTTTCCCG
Found at i:115582 original size:12 final size:11
Alignment explanation
Indices: 115567--115629 Score: 62
Period size: 12 Copynumber: 5.8 Consensus size: 11
115557 TACTTCTCTA
115567 TGCTTCTCTCGC
1 TGCTTCTCTC-C
*
115579 TGC-TCTAT-C
1 TGCTTCTCTCC
115588 TGCTTCTCTCCC
1 TGCTTCTCT-CC
115600 TGCTTCTCTCGC
1 TGCTTCTCTC-C
115612 TGC-TCTC-CC
1 TGCTTCTCTCC
115621 TGCTTCTCT
1 TGCTTCTCT
115630 TGCTTCAGCT
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
9 8 0.19
10 9 0.21
11 9 0.21
12 17 0.40
ACGTcount: A:0.02, C:0.43, G:0.13, T:0.43
Consensus pattern (11 bp):
TGCTTCTCTCC
Found at i:115606 original size:33 final size:33
Alignment explanation
Indices: 115567--115629 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
115557 TACTTCTCTA
*
115567 TGCTTCTCTCGCTGCTCTATCTGCTTCTCTCCC
1 TGCTTCTCTCGCTGCTCTACCTGCTTCTCTCCC
*
115600 TGCTTCTCTCGCTGCTCTCCCTGCTTCTCT
1 TGCTTCTCTCGCTGCTCTACCTGCTTCTCT
115630 TGCTTCAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.02, C:0.43, G:0.13, T:0.43
Consensus pattern (33 bp):
TGCTTCTCTCGCTGCTCTACCTGCTTCTCTCCC
Done.