Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold397
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: 433447
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
File 3 of 4
Found at i:266766 original size:2 final size:2
Alignment explanation
Indices: 266761--266793 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
266751 AAGTGTGTAC
266761 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
266794 GTACATGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:268565 original size:51 final size:51
Alignment explanation
Indices: 268491--268587 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
268481 TCTCCTGGTC
*
268491 AAGTACTTGATTTGCTATCTAAAAGGA-AATATTTTCAATTAGTACACGGTT
1 AAGTACTTGATTTGCTATCTAAAA-AATAATATTTTCAATTAGTACACGGTT
* * *
268542 AAGTACTT-AGTTTGTTATTTAAAAAATAATATTTTTAATTAGTACA
1 AAGTACTTGA-TTTGCTATCTAAAAAATAATATTTTCAATTAGTACA
268588 TGAATCTAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
50 2 0.05
51 38 0.95
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.41
Consensus pattern (51 bp):
AAGTACTTGATTTGCTATCTAAAAAATAATATTTTCAATTAGTACACGGTT
Found at i:277213 original size:83 final size:84
Alignment explanation
Indices: 277098--277265 Score: 284
Period size: 83 Copynumber: 2.0 Consensus size: 84
277088 GCTTCTTTCA
*
277098 TATGTTCCCTATATGGGGGGCAGCAATTCTTCTGTCTCTAAAACGAAATTGCTAGCCAATTCAGC
1 TATGTTCCCAATAT-GGGGGCAGCAATTCTTCTGTCTCTAAAACGAAATTGCTAGCCAATTCAGC
*
277163 AAAACAATATGCAAATTGCT
65 AAAACAATACGCAAATTGCT
* *
277183 TATGTTCCCAATAT-GGGGCAGCAATTCTTCTGTTTTTAAAACGAAATTGCTAGCCAATTCAGCA
1 TATGTTCCCAATATGGGGGCAGCAATTCTTCTGTCTCTAAAACGAAATTGCTAGCCAATTCAGCA
277247 AAACAATACGCAAATTGCT
66 AAACAATACGCAAATTGCT
277266 AGCCATGGAA
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
83 66 0.84
85 13 0.16
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (84 bp):
TATGTTCCCAATATGGGGGCAGCAATTCTTCTGTCTCTAAAACGAAATTGCTAGCCAATTCAGCA
AAACAATACGCAAATTGCT
Found at i:278231 original size:16 final size:16
Alignment explanation
Indices: 278203--278252 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
278193 ATATTTTCTA
278203 TCTTTCAACTTTTTTTC
1 TCTTTCAA-TTTTTTTC
278220 TCTTTCAATTTTTTATC
1 TCTTTCAATTTTTT-TC
*
278237 T-TTTTAATTTTCTTTC
1 TCTTTCAATTTT-TTTC
278253 CGCCCTATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (16 bp):
TCTTTCAATTTTTTTC
Found at i:278233 original size:15 final size:16
Alignment explanation
Indices: 278196--278239 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
278186 AAAAAATATA
*
278196 TTTTCTATCTTTCAAC
1 TTTTTTATCTTTCAAC
*
278212 TTTTTTTCTCTTTCAA-
1 -TTTTTTATCTTTCAAC
278228 TTTTTTATCTTT
1 TTTTTTATCTTT
278240 TTAATTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 11 0.46
17 13 0.54
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTATCTTTCAAC
Found at i:278507 original size:28 final size:28
Alignment explanation
Indices: 278470--278539 Score: 140
Period size: 28 Copynumber: 2.5 Consensus size: 28
278460 ACAACAAGAC
278470 CAACAAGTTTGCAAACAACCATTGTTGG
1 CAACAAGTTTGCAAACAACCATTGTTGG
278498 CAACAAGTTTGCAAACAACCATTGTTGG
1 CAACAAGTTTGCAAACAACCATTGTTGG
278526 CAACAAGTTTGCAA
1 CAACAAGTTTGCAA
278540 CAATTTATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.24
Consensus pattern (28 bp):
CAACAAGTTTGCAAACAACCATTGTTGG
Found at i:283159 original size:160 final size:157
Alignment explanation
Indices: 282852--283307 Score: 512
Period size: 160 Copynumber: 2.9 Consensus size: 157
282842 CGAAAGTATT
* *
282852 AATTCAATTTAATTTTATTTATTTTTGAAAATATCATTTCGTACCCTAATGGAAG-CTCGAAAGA
1 AATTCAATTTAATTTTATTTATTTTTGAAAATAT-ATTTCATACCCTAATGGAAGAC-CGAAAGG
* *
282916 ATAAGAAATGTTTTTGAAA-CTTTTATATCCCTACGGA-GCCCATAGGAATATAAAAGATTAGAA
64 ATACGAAACGTTTTTGAAATCTTTTATA-CCCTACGGATGCCCATAGGAATATAAAAGATTAGAA
* *
282979 AAAATAAATATTAGAATTTAT-CTCAAGAATGCC
128 AAAAT--A-ATTAAAATTTATCCTCAA-AATACC
* * *
283012 AATTCAATTTAATTTTATATATTTTTGAAAATACTATTTCATACCTTAATGGAAGACCAAAAGGA
1 AATTCAATTTAATTTTATTTATTTTTGAAAATA-TATTTCATACCCTAATGGAAGACCGAAAGGA
* *
283077 TACGAAAGGTTTTTGAAATCTTTTATACCCTTACGGATGTCCAT-GAGAATATAAAAGATTAGAT
65 TACGAAACGTTTTTGAAATCTTTTATACCC-TACGGATGCCCATAG-GAATATAAAAGATTAGA-
* **
283141 AAAAATAATTAAAATTTATCCTGAAAATATT
127 AAAAATAATTAAAATTTATCCTCAAAATACC
* * ** *
283172 AATTCACTTTGATTTTATTTGCTTTCGAAAATAATATTTCATACCCTAATGGAA-ACCCGAAAGG
1 AATTCAATTTAATTTTATTTATTTTTGAAAAT-ATATTTCATACCCTAATGGAAGA-CCGAAAGG
* * * ** *
283236 ATACAAAACGTTTTTTAAATCTCTTATACCCCTACAAATACCCATAGGAATATAAAAGATTA-AA
64 ATACGAAACGTTTTTGAAATCTTTTATA-CCCTACGGATGCCCATAGGAATATAAAAGATTAGAA
283300 AAAATAAT
128 AAAATAAT
283308 AAACATGGAA
Statistics
Matches: 255, Mismatches: 29, Indels: 26
0.82 0.09 0.08
Matches are distributed among these distances:
158 9 0.04
159 2 0.01
160 189 0.74
161 27 0.11
162 22 0.09
163 6 0.02
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (157 bp):
AATTCAATTTAATTTTATTTATTTTTGAAAATATATTTCATACCCTAATGGAAGACCGAAAGGAT
ACGAAACGTTTTTGAAATCTTTTATACCCTACGGATGCCCATAGGAATATAAAAGATTAGAAAAA
ATAATTAAAATTTATCCTCAAAATACC
Found at i:284094 original size:14 final size:13
Alignment explanation
Indices: 284069--284106 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
284059 TTCTACCTAT
284069 TTTCTCTTTTTTC
1 TTTCTCTTTTTTC
284082 TTTCTCTTTTTT-
1 TTTCTCTTTTTTC
* *
284094 TCTCTCATTTTTC
1 TTTCTCTTTTTTC
284107 AGCTGACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTCTTTTTTC
Found at i:285047 original size:168 final size:164
Alignment explanation
Indices: 284742--285047 Score: 395
Period size: 168 Copynumber: 1.8 Consensus size: 164
284732 GATTTTTTAA
* *
284742 GAAAAGGAAAATTTCAAGGAAAAAATTCGAAATTTATGAAAATGAATTGGTCTTTTAAAACTGAG
1 GAAAAAGAAAATTTCAAGGAAAAAATTCGAAATTTATGAAAATGAATTGATCTTTTAAAACTGAG
* ** * *
284807 TTAATATGAGTTAAAAGATGATATTTGATGAATTTCAAAAATTAAAAACCGAGAAAAATCTCCCT
66 TTAATATAAAATAAAAGATAATATTTGATGAATTTCAAAAATTAAAAACCAAGAAAAA-CTCCCT
284872 TGAAAAAAATTACGAAGTAGAAAATATCGTATTTC
130 TGAAAAAAATTACGAAGTAGAAAATATCGTATTTC
*
284907 GAAAAAGAGAAATTTCAAGGAAAAAATTC-AAATATGTATGAAAAATGAA-TGATTTTTTAAGAA
1 GAAAAAGA-AAATTTCAAGGAAAAAATTCGAAAT-T-TATG-AAAATGAATTGATCTTTTAA-AA
* * *
284970 CTGATTTAATATAAAATAAATA-ATAATATTTGATGAATTTTAAAAATTAAAAAACTAAGAAAAA
61 CTGAGTTAATATAAAATAAA-AGATAATATTTGATGAATTTCAAAAATT-AAAAACCAAGAAAAA
*
285034 -TCCTTTCGAAAAAA
124 CTCCCTT-GAAAAAA
285048 TTTTTCGGAG
Statistics
Matches: 121, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
165 11 0.09
166 21 0.17
167 18 0.15
168 57 0.47
169 14 0.12
ACGTcount: A:0.51, C:0.07, G:0.13, T:0.29
Consensus pattern (164 bp):
GAAAAAGAAAATTTCAAGGAAAAAATTCGAAATTTATGAAAATGAATTGATCTTTTAAAACTGAG
TTAATATAAAATAAAAGATAATATTTGATGAATTTCAAAAATTAAAAACCAAGAAAAACTCCCTT
GAAAAAAATTACGAAGTAGAAAATATCGTATTTC
Found at i:286931 original size:82 final size:82
Alignment explanation
Indices: 286794--286965 Score: 344
Period size: 82 Copynumber: 2.1 Consensus size: 82
286784 TATCTTTTCA
286794 AAAAGGTTGTTTATGGTTTGAAACAAGCTCCAAAAACTTGGTACAACAGAATTGATAAACACTTT
1 AAAAGGTTGTTTATGGTTTGAAACAAGCTCCAAAAACTTGGTACAACAGAATTGATAAACACTTT
286859 TGAACTTGGGATTTGCT
66 TGAACTTGGGATTTGCT
286876 AAAAGGTTGTTTATGGTTTGAAACAAGCTCCAAAAACTTGGTACAACAGAATTGATAAACACTTT
1 AAAAGGTTGTTTATGGTTTGAAACAAGCTCCAAAAACTTGGTACAACAGAATTGATAAACACTTT
286941 TGAACTTGGGATTTGCT
66 TGAACTTGGGATTTGCT
286958 AAAAGGTT
1 AAAAGGTT
286966 ACTTGAATCA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 90 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (82 bp):
AAAAGGTTGTTTATGGTTTGAAACAAGCTCCAAAAACTTGGTACAACAGAATTGATAAACACTTT
TGAACTTGGGATTTGCT
Found at i:290144 original size:13 final size:13
Alignment explanation
Indices: 290126--290167 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
290116 CAAATGCTGC
290126 TTTTTTTGTCAAT
1 TTTTTTTGTCAAT
*
290139 TTTTTTTTTCAAT
1 TTTTTTTGTCAAT
**
290152 TTTTCATGTCAAT
1 TTTTTTTGTCAAT
290165 TTT
1 TTT
290168 AATTTTTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (13 bp):
TTTTTTTGTCAAT
Found at i:291321 original size:16 final size:18
Alignment explanation
Indices: 291285--291323 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
291275 CCAAAAAAAC
291285 ATAAA-TACTAATTAGTT
1 ATAAATTACTAATTAGTT
291302 ATAAATTACTAA-TA-TT
1 ATAAATTACTAATTAGTT
291318 ATAAAT
1 ATAAAT
291324 AATTATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.38
17 7 0.33
18 6 0.29
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (18 bp):
ATAAATTACTAATTAGTT
Found at i:291868 original size:20 final size:20
Alignment explanation
Indices: 291827--291869 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
291817 GATTGGATTA
* *
291827 AAAATAATATTTTTTTAATT
1 AAAATAATATATTTATAATT
*
291847 AAAATAATATATTTATATTT
1 AAAATAATATATTTATAATT
291867 AAA
1 AAA
291870 TTTAATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
AAAATAATATATTTATAATT
Found at i:291885 original size:21 final size:22
Alignment explanation
Indices: 291861--291909 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
291851 TAATATATTT
291861 ATATTTAAAT-TTAAT-TATAAA
1 ATATTTAAATATTAATCTA-AAA
*
291882 ATATATAAATATTAATCTAAAA
1 ATATTTAAATATTAATCTAAAA
291904 ATATTT
1 ATATTT
291910 TTTAATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 13 0.54
23 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTTAAATATTAATCTAAAA
Found at i:292049 original size:10 final size:10
Alignment explanation
Indices: 292034--292058 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
292024 TATATAAATA
292034 AAAATTTAAT
1 AAAATTTAAT
292044 AAAATTTAAT
1 AAAATTTAAT
292054 AAAAT
1 AAAAT
292059 CAAGTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATTTAAT
Found at i:294275 original size:21 final size:23
Alignment explanation
Indices: 294237--294284 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 23
294227 TTGGTTGTTA
294237 TTTAATAAGTTTAAAATTTTTAT
1 TTTAATAAGTTTAAAATTTTTAT
*
294260 TTTAAT-A-TTTATAATTTTTAT
1 TTTAATAAGTTTAAAATTTTTAT
294281 TTTA
1 TTTA
294285 TTTTTAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 17 0.71
22 1 0.04
23 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTAATAAGTTTAAAATTTTTAT
Found at i:295585 original size:2 final size:2
Alignment explanation
Indices: 295578--295612 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
295568 ATGTAAATTG
295578 AT AT AT AT AT 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 AT AT AT AT AT A
295613 ATGGTACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:296712 original size:26 final size:27
Alignment explanation
Indices: 296682--296736 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
296672 AAAATATATA
296682 ATTAATTTA-TTTAAAATTTTTATTTT
1 ATTAATTTATTTTAAAATTTTTATTTT
**
296708 ATTAATTTATTTTAATTTTTTTATTTT
1 ATTAATTTATTTTAAAATTTTTATTTT
296735 AT
1 AT
296737 ATTTATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (27 bp):
ATTAATTTATTTTAAAATTTTTATTTT
Found at i:296715 original size:22 final size:22
Alignment explanation
Indices: 296667--296716 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
296657 CTTATAAATC
296667 AATTTAAAATATATAATTAATT
1 AATTTAAAATATATAATTAATT
* * * * *
296689 TATTTAAAATTTTTATTTTATT
1 AATTTAAAATATATAATTAATT
296711 AATTTA
1 AATTTA
296717 TTTTAATTTT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATTTAAAATATATAATTAATT
Found at i:296725 original size:19 final size:19
Alignment explanation
Indices: 296697--296784 Score: 56
Period size: 19 Copynumber: 4.6 Consensus size: 19
296687 TTTATTTAAA
*
296697 ATTTTTATTTTATTAATTT
1 ATTTTAATTTTATTAATTT
* *
296716 ATTTTAATTTTTTTATTTT
1 ATTTTAATTTTATTAATTT
* *
296735 ATATTT-ATCATTATTTA-TT
1 AT-TTTAAT-TTTATTAATTT
* *
296754 ATATTAATTATTTTTAATTT
1 ATTTTAATT-TTATTAATTT
296774 -TTTATAATTTT
1 ATTT-TAATTTT
296785 TATTTATTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
18 2 0.04
19 35 0.69
20 14 0.27
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTAATTTTATTAATTT
Found at i:296732 original size:14 final size:14
Alignment explanation
Indices: 296698--296740 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
296688 TTATTTAAAA
296698 TTTTTATTTT-ATT
1 TTTTTATTTTAATT
**
296711 AATTTATTTTAATT
1 TTTTTATTTTAATT
296725 TTTTTATTTTATATT
1 TTTTTATTTTA-ATT
296740 T
1 T
296741 ATCATTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 8 0.33
14 12 0.50
15 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTATTTTAATT
Found at i:296765 original size:26 final size:26
Alignment explanation
Indices: 296682--296793 Score: 92
Period size: 26 Copynumber: 4.5 Consensus size: 26
296672 AAAATATATA
* *
296682 ATTAATTTATTTAAAATTTTTATTTT
1 ATTAATTTATTTATAATTTTTATTAT
296708 ATTAATTTATTT-TAATTTTT-TTAT
1 ATTAATTTATTTATAATTTTTATTAT
* *
296732 -TT--TATATTTATCATTATTTATTAT
1 ATTAATTTATTTATAATT-TTTATTAT
* *
296756 ATTAA-TTATTTTTAATTTTTTATAAT
1 ATTAATTTATTTATAA-TTTTTATTAT
* *
296782 TTTTATTTATTT
1 ATTAATTTATTT
296794 TTATATAATA
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
21 6 0.09
22 4 0.06
23 5 0.07
24 7 0.10
25 9 0.13
26 29 0.43
27 8 0.12
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (26 bp):
ATTAATTTATTTATAATTTTTATTAT
Found at i:296795 original size:21 final size:20
Alignment explanation
Indices: 296752--296808 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
296742 TCATTATTTA
296752 TTATATTAATTATTTTTAATT
1 TTATA-TAATTATTTTTAATT
* * *
296773 TTTTATAATTTTTATTTATTT
1 TTATATAATTATT-TTTAATT
296794 TTATATAATATATTT
1 TTATATAAT-TATTT
296809 ATAAAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 7 0.24
21 19 0.66
22 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATATAATTATTTTTAATT
Found at i:296796 original size:19 final size:19
Alignment explanation
Indices: 296712--296798 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 19
296702 TATTTTATTA
* *
296712 ATTTATTTTAAT-TTTTTT
1 ATTTATTTTTATAATTTTT
* *
296730 ATTTTATATTTATCATTATTT
1 A-TTTATTTTTATAATT-TTT
* * *
296751 A-TTATATTAATTATTTTT
1 ATTTATTTTTATAATTTTT
*
296769 A-AT-TTTTTATAATTTTT
1 ATTTATTTTTATAATTTTT
296786 ATTTATTTTTATA
1 ATTTATTTTTATA
296799 TAATATATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
17 12 0.22
18 7 0.13
19 29 0.54
20 2 0.04
21 4 0.07
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTATTTTTATAATTTTT
Found at i:296797 original size:10 final size:10
Alignment explanation
Indices: 296697--296797 Score: 57
Period size: 10 Copynumber: 9.8 Consensus size: 10
296687 TTTATTTAAA
296697 ATTTTTATTTT
1 ATTTTTA-TTT
296708 ATTAATTTATTTT
1 ATT--TTTA-TTT
*
296721 AATTTT-TTT
1 ATTTTTATTT
296730 ATTTTATATTT
1 ATTTT-TATTT
**
296741 ATCATTATTT
1 ATTTTTATTT
*
296751 ATTATATTAATT
1 ATT-T-TTATTT
*
296763 ATTTTTA-AT
1 ATTTTTATTT
*
296772 -TTTTTA-TA
1 ATTTTTATTT
296780 ATTTTTATTT
1 ATTTTTATTT
296790 ATTTTTAT
1 ATTTTTAT
296798 ATAATATATT
Statistics
Matches: 71, Mismatches: 11, Indels: 17
0.72 0.11 0.17
Matches are distributed among these distances:
8 6 0.08
9 14 0.20
10 20 0.28
11 13 0.18
12 8 0.11
13 10 0.14
ACGTcount: A:0.28, C:0.01, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTTTATTT
Found at i:296806 original size:49 final size:48
Alignment explanation
Indices: 296707--296807 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 48
296697 ATTTTTATTT
* *
296707 TATTAATTTATTTTAATTTTTTTATTTTATATTTATCATTATTTATTA
1 TATTAATTTATTTTAATTTTTTTATTTTATATTTATCATTATATAATA
**
296755 TATTAA-TTATTTTTAATTTTTTATAATTTT-TATTTATTTTTATATAATA
1 TATTAATTTA-TTTTAATTTTTT-T-ATTTTATATTTATCATTATATAATA
296804 TATT
1 TATT
296808 TATAAAAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
47 3 0.07
48 18 0.39
49 20 0.43
50 5 0.11
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (48 bp):
TATTAATTTATTTTAATTTTTTTATTTTATATTTATCATTATATAATA
Found at i:297143 original size:7 final size:7
Alignment explanation
Indices: 297131--297156 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
297121 AAATTAATAA
297131 AATTTTT
1 AATTTTT
297138 AATTTTT
1 AATTTTT
297145 AATTTTT
1 AATTTTT
297152 AATTT
1 AATTT
297157 AATTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:299269 original size:16 final size:16
Alignment explanation
Indices: 299244--299290 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
299234 CTGAAATTCG
299244 ATTA-TTTAAATTTGA
1 ATTATTTTAAATTTGA
*
299259 ATTATTTTAAATTTAA
1 ATTATTTTAAATTTGA
* *
299275 ATTTTTTTAAAATTGA
1 ATTATTTTAAATTTGA
299291 GGCTATTCAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 4 0.15
16 23 0.85
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
ATTATTTTAAATTTGA
Found at i:299524 original size:21 final size:21
Alignment explanation
Indices: 299498--299541 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 21
299488 AAAATCTATA
299498 TTTATATATAAAATTAATTTG
1 TTTATATATAAAATTAATTTG
299519 --T-T-TATAAAATTAATTTG
1 TTTATATATAAAATTAATTTG
299536 TTTATA
1 TTTATA
299542 AAATTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 8
0.70 0.00 0.30
Matches are distributed among these distances:
17 15 0.79
18 1 0.05
19 2 0.11
20 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTATATATAAAATTAATTTG
Found at i:299543 original size:34 final size:37
Alignment explanation
Indices: 299477--299551 Score: 102
Period size: 34 Copynumber: 2.1 Consensus size: 37
299467 TTTTTAATAT
299477 ATTTATTTATTAAAATCTATATTTATATATAAAATTA
1 ATTTATTTATTAAAATCTATATTTATATATAAAATTA
* * *
299514 ATTTGTTTA-TAAAAT-TA-ATTTGTTTATAAAATTA
1 ATTTATTTATTAAAATCTATATTTATATATAAAATTA
299548 ATTT
1 ATTT
299552 TTAAATAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 19 0.54
35 2 0.06
36 6 0.17
37 8 0.23
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (37 bp):
ATTTATTTATTAAAATCTATATTTATATATAAAATTA
Found at i:299559 original size:17 final size:17
Alignment explanation
Indices: 299504--299551 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
299494 TATATTTATA
299504 TATAAAATTAATTTGTT
1 TATAAAATTAATTTGTT
299521 TATAAAATTAATTTGTT
1 TATAAAATTAATTTGTT
299538 TATAAAATTAATTT
1 TATAAAATTAATTT
299552 TTAAATAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TATAAAATTAATTTGTT
Found at i:303547 original size:30 final size:28
Alignment explanation
Indices: 303485--303571 Score: 90
Period size: 28 Copynumber: 3.1 Consensus size: 28
303475 TTACGATTAT
303485 ATATTTTATTATTATAATTATATTTAAA
1 ATATTTTATTATTATAATTATATTTAAA
* *
303513 ATATTTTTTTATTATATGTTAATAATTT-AA
1 ATATTTTATTATTATA-ATT-AT-ATTTAAA
*
303543 ATA-TTTATAATT-TAAGTTATATTTAAA
1 ATATTTTATTATTATAA-TTATATTTAAA
303570 AT
1 AT
303572 TACCAAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
26 4 0.08
27 6 0.12
28 19 0.39
29 9 0.18
30 7 0.14
31 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
ATATTTTATTATTATAATTATATTTAAA
Found at i:303948 original size:157 final size:159
Alignment explanation
Indices: 303773--304087 Score: 508
Period size: 158 Copynumber: 2.0 Consensus size: 159
303763 CTAACCAATT
*
303773 TTTTATTCCTAATTTTTTATTCTTGGCGATTTTTAAAATTTTT-ATAATATAATTAAATTATATA
1 TTTTATTCCTAATTTTTTATTCTTAGCGATTTTTAAAATTTTTGATAATATAATTAAATTATATA
* * *
303837 ATTTATTAATTTTAATTAAATCAGTCTATTTAATTTTTTTTATTTATGCATACAAGTTCAATTTA
66 ATTTATTAATTTTAATTAAATCAGTCCATTTAATTTTTTTTATTTATACATACAAATTCAATTTA
303902 -TTTTTTTAAAAGCATAAAGGGAAAAAAA
131 TTTTTTTTAAAAGCATAAAGGGAAAAAAA
* * *
303930 TTTTATTCTTAATTTTTTATTCTTATCGATTTTTAAAATTTTTGATAATATAATTAAATTATTTA
1 TTTTATTCCTAATTTTTTATTCTTAGCGATTTTTAAAATTTTTGATAATATAATTAAATTATATA
* *
303995 ATTTATTAATTTTGATTAAATCAGTCCATTTAATTTTTTTTATTTATACATACAAATTCGATTTA
66 ATTTATTAATTTTAATTAAATCAGTCCATTTAATTTTTTTTATTTATACATACAAATTCAATTTA
* *
304060 TTTTTTTTTAAGAGCGTAAAGGGAAAAA
131 -TTTTTTTTAAAAGCATAAAGGGAAAAA
304088 CAGTTCCTTT
Statistics
Matches: 144, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
157 40 0.28
158 80 0.56
160 24 0.17
ACGTcount: A:0.36, C:0.06, G:0.07, T:0.51
Consensus pattern (159 bp):
TTTTATTCCTAATTTTTTATTCTTAGCGATTTTTAAAATTTTTGATAATATAATTAAATTATATA
ATTTATTAATTTTAATTAAATCAGTCCATTTAATTTTTTTTATTTATACATACAAATTCAATTTA
TTTTTTTTAAAAGCATAAAGGGAAAAAAA
Found at i:304325 original size:2 final size:2
Alignment explanation
Indices: 304318--304353 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
304308 GATTAATCTC
*
304318 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
304354 AAGGATTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:304648 original size:24 final size:23
Alignment explanation
Indices: 304565--304651 Score: 61
Period size: 24 Copynumber: 3.6 Consensus size: 23
304555 GTAATTATAA
304565 AATAAATTATAAAAATTATTAAA--T
1 AATAAATT-TAAAAA--ATTAAATTT
*
304589 AAAAAATTTTAAATTAAATTAAATTT
1 AATAAA-TTTAAA--AAATTAAATTT
* * *
304615 ATTTATTTTAAAAAATTAATATTT
1 AATAAATTTAAAAAATTAA-ATTT
304639 AATAAATTTAAAA
1 AATAAATTTAAAA
304652 TATTCTATCA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
23 7 0.14
24 29 0.59
25 8 0.16
26 5 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAAATTTAAAAAATTAAATTT
Found at i:305740 original size:2 final size:2
Alignment explanation
Indices: 305733--305758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
305723 TATCTATCTT
305733 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
305759 CACACACAAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:315621 original size:47 final size:47
Alignment explanation
Indices: 315541--315649 Score: 175
Period size: 47 Copynumber: 2.3 Consensus size: 47
315531 TATTCGTTAG
*
315541 AAGG-TTTATAGCTTTCTTCATGTGAAAGCTGTTAAGGTATTGGATA
1 AAGGATTTGTAGCTTTCTTCATGTGAAAGCTGTTAAGGTATTGGATA
* * *
315587 AAGGATTTGTAGCTTTCTTCGTGTGAAAGTTGTTAAGGTATTTGATA
1 AAGGATTTGTAGCTTTCTTCATGTGAAAGCTGTTAAGGTATTGGATA
315634 AAGGATTTGTAGCTTT
1 AAGGATTTGTAGCTTT
315650 TTCCGTGCAA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
46 4 0.07
47 54 0.93
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (47 bp):
AAGGATTTGTAGCTTTCTTCATGTGAAAGCTGTTAAGGTATTGGATA
Found at i:325664 original size:28 final size:29
Alignment explanation
Indices: 325615--325671 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
325605 TTTAGGATTC
* *
325615 GGTTCTAAAAAAATTATGAAAATGCCCTT
1 GGTTCTAAAAAAATCATAAAAATGCCCTT
325644 GGTTCT-AAAAAATCATAAAAATGCCCTT
1 GGTTCTAAAAAAATCATAAAAATGCCCTT
325672 AGAGGATACC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 20 0.77
29 6 0.23
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (29 bp):
GGTTCTAAAAAAATCATAAAAATGCCCTT
Found at i:325961 original size:15 final size:17
Alignment explanation
Indices: 325936--325969 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
325926 GATAATAATT
325936 TTTTAATTTTT-AAAAA
1 TTTTAATTTTTGAAAAA
325952 TTTT-ATTTTTGAAAAA
1 TTTTAATTTTTGAAAAA
325968 TT
1 TT
325970 CATTTCGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTAATTTTTGAAAAA
Found at i:327282 original size:23 final size:21
Alignment explanation
Indices: 327255--327310 Score: 55
Period size: 20 Copynumber: 2.7 Consensus size: 21
327245 TATTCTTCTT
327255 TTCTATGCTGTTTTTTCTTTTC
1 TTCTATGCTGTTTTTT-TTTTC
*
327277 TCTCTAT-TTCG-TTTTTTTTTC
1 T-TCTATGCT-GTTTTTTTTTTC
327298 TTCT-TGCTGTTTT
1 TTCTATGCTGTTTT
327311 GATTTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
19 2 0.07
20 7 0.25
21 6 0.21
22 7 0.25
23 6 0.21
ACGTcount: A:0.04, C:0.18, G:0.09, T:0.70
Consensus pattern (21 bp):
TTCTATGCTGTTTTTTTTTTC
Found at i:327522 original size:59 final size:58
Alignment explanation
Indices: 327446--327560 Score: 176
Period size: 59 Copynumber: 2.0 Consensus size: 58
327436 TGTTGTTACA
*
327446 ATTTCTTCTCTTATTCATTTCAGCAACTTAATTATTTTATTAATTCATTTGTTGCTGTC
1 ATTTCTTCTCTTATTCATTTCAACAACTTAATTATTTT-TTAATTCATTTGTTGCTGTC
* * **
327505 ATTTCTTCTCTTATTCATTTCAACAGCTTAATTGTTTTTTGTTTCATTTGTTGCTG
1 ATTTCTTCTCTTATTCATTTCAACAACTTAATTATTTTTTAATTCATTTGTTGCTG
327561 CTGTTTCTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 16 0.31
59 35 0.69
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.56
Consensus pattern (58 bp):
ATTTCTTCTCTTATTCATTTCAACAACTTAATTATTTTTTAATTCATTTGTTGCTGTC
Found at i:330081 original size:27 final size:27
Alignment explanation
Indices: 330043--330104 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
330033 ATTGGTATCA
330043 AAGCTTTTGGTTTGAAAGAAAAATGCT
1 AAGCTTTTGGTTTGAAAGAAAAATGCT
* *
330070 AAGCTTTTGGTTTGAGAGAGAAATGCT
1 AAGCTTTTGGTTTGAAAGAAAAATGCT
330097 AAGCTTTT
1 AAGCTTTT
330105 AGTTCAAGGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.35
Consensus pattern (27 bp):
AAGCTTTTGGTTTGAAAGAAAAATGCT
Found at i:330120 original size:27 final size:27
Alignment explanation
Indices: 330063--330123 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
330053 TTTGAAAGAA
* **
330063 AAATGCTAAGCTTTTGGTTTGAGAGAG
1 AAATGCTAAGCTTTTAGTTCAAGAGAG
* *
330090 AAATGCTAAGCTTTTAGTTCAAGGGAT
1 AAATGCTAAGCTTTTAGTTCAAGAGAG
330117 AAATGCT
1 AAATGCT
330124 TCACTATAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.33
Consensus pattern (27 bp):
AAATGCTAAGCTTTTAGTTCAAGAGAG
Found at i:331358 original size:15 final size:14
Alignment explanation
Indices: 331333--331374 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
331323 AGTTTAAACA
*
331333 TATTAATTTTTTTGT
1 TATTAATTATTTT-T
331348 TATT--TTATTTTT
1 TATTAATTATTTTT
331360 TATTAATTATTTTT
1 TATTAATTATTTTT
331374 T
1 T
331375 CTCGATCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 5 0.21
13 6 0.25
14 9 0.38
15 4 0.17
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (14 bp):
TATTAATTATTTTT
Found at i:331433 original size:15 final size:15
Alignment explanation
Indices: 331396--331433 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
331386 CACTATTTTC
331396 AATAT-TAAATTCAA
1 AATATCTAAATTCAA
331410 AATTATCTAAATTCAA
1 AA-TATCTAAATTCAA
331426 AATATCTA
1 AATATCTA
331434 TATCGAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 9 0.41
16 11 0.50
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (15 bp):
AATATCTAAATTCAA
Found at i:332530 original size:17 final size:17
Alignment explanation
Indices: 332477--332530 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
332467 TTGGTTTCCC
* *
332477 TTTTTCTTTTTAACTTT
1 TTTTTATTTTTTACTTT
*
332494 TTTTTCATATTTTA-TTT
1 TTTTT-ATTTTTTACTTT
332511 TTTTTATTTTTTACTCTT
1 TTTTTATTTTTTACT-TT
332529 TT
1 TT
332531 AGGGTTATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.23
17 14 0.47
18 9 0.30
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATTTTTTACTTT
Found at i:338011 original size:75 final size:75
Alignment explanation
Indices: 337872--338015 Score: 200
Period size: 75 Copynumber: 1.9 Consensus size: 75
337862 TGGTAGATTT
* * * ** * *
337872 GGTAGATTTGATGCCATCTTTCAGTCACTAACTTCATAAGTAAGGTCCACAAGTGTTAGGAGAAA
1 GGTAGATTTGATGCCAGCTTTCAATCACTAACTTCATAACTAAGGTCCACAAGAATAAGAAGAAA
337937 TGACTAAGAG
66 TGACTAAGAG
*
337947 GGTAGATTTGATGCCAGCTTTCAATCACTAACTTCATGGACT-AGGTCCACAAGAATAAGAAGAA
1 GGTAGATTTGATGCCAGCTTTCAATCACTAACTTCAT-AACTAAGGTCCACAAGAATAAGAAGAA
338011 ATGAC
65 ATGAC
338016 AATCGGAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 58 0.97
76 2 0.03
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (75 bp):
GGTAGATTTGATGCCAGCTTTCAATCACTAACTTCATAACTAAGGTCCACAAGAATAAGAAGAAA
TGACTAAGAG
Found at i:338094 original size:14 final size:14
Alignment explanation
Indices: 338075--338108 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
338065 TTTTGCTGCG
338075 AGAAGAAA-AAAGAA
1 AGAAGAAACAAA-AA
338089 AGAAGAAACAAAAA
1 AGAAGAAACAAAAA
338103 AGAAGA
1 AGAAGA
338109 TAATTTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.84
15 3 0.16
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (14 bp):
AGAAGAAACAAAAA
Found at i:342634 original size:4 final size:4
Alignment explanation
Indices: 342576--342627 Score: 59
Period size: 4 Copynumber: 11.8 Consensus size: 4
342566 AATAAAAGTA
342576 AAAG AAAG AAAG AAAATG AACAG AAAG TTAAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG -AAA-G AA-AG AAAG --AAAG AAAG AAAG AAAG AAAG
342625 AAA
1 AAA
342628 AAGAAAGGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
4 29 0.67
5 8 0.19
6 6 0.14
ACGTcount: A:0.71, C:0.02, G:0.21, T:0.06
Consensus pattern (4 bp):
AAAG
Found at i:343526 original size:17 final size:17
Alignment explanation
Indices: 343504--343538 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
343494 TTAAAGTGGG
343504 AAAAAAAGAA-AAAGAA
1 AAAAAAAGAATAAAGAA
343520 AAAAAAAGAATAAAGAA
1 AAAAAAAGAATAAAGAA
343537 AA
1 AA
343539 TTTAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAAAAGAATAAAGAA
Found at i:349543 original size:15 final size:15
Alignment explanation
Indices: 349523--349551 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
349513 AACCAATAGA
349523 TAGCCTTGAATTATG
1 TAGCCTTGAATTATG
349538 TAGCCTTGAATTAT
1 TAGCCTTGAATTAT
349552 AATGTTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (15 bp):
TAGCCTTGAATTATG
Found at i:352440 original size:15 final size:15
Alignment explanation
Indices: 352409--352447 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
352399 AGTATATACT
352409 TAAATTGCATAAAATG
1 TAAATTG-ATAAAATG
*
352425 TAAATTGATGAAATG
1 TAAATTGATAAAATG
352440 TAAATTGA
1 TAAATTGA
352448 AATTAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (15 bp):
TAAATTGATAAAATG
Found at i:352793 original size:14 final size:14
Alignment explanation
Indices: 352774--352800 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
352764 ATTTGGATGA
352774 CTTGTCTCAAGCAT
1 CTTGTCTCAAGCAT
352788 CTTGTCTCAAGCA
1 CTTGTCTCAAGCA
352801 ACCTGGCAAA
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:0.22, C:0.30, G:0.15, T:0.33
Consensus pattern (14 bp):
CTTGTCTCAAGCAT
Found at i:354869 original size:73 final size:71
Alignment explanation
Indices: 354685--355329 Score: 358
Period size: 73 Copynumber: 8.7 Consensus size: 71
354675 CAAGCTGATA
* * * * * *
354685 AGTTAATATTATTAGATTCTTATTTAGATTTATTGGAATTAGAATTGATTATTATTTGTACAATT
1 AGTTAATATTATTAGTTTC-CATTTAGACTAATTTGAATTA-AATTGATCATTATTTGTACAATT
354750 CAATTCAATATAT
64 -AA-T---TATAT
* ** * *
354763 ACTTAATGCTATTAGATTCACATTTATACTAATTTGAATTAAAATTGATCATTATTTGTACAATT
1 AGTTAATATTATTAGTTTC-CATTTAGACTAATTTGAATT-AAATTGATCATTATTTGTACAATT
* *
354828 GAGTATAT
64 AATTATAT
* * * *
354836 AGTTAATATTATTAAGTTTCCAATTAGACTAA-TTG----AAATTGATTATTACTTGTACAAGTA
1 AGTTAATATTATT-AGTTTCCATTTAGACTAATTTGAATTAAATTGATCATTATTTGTACAATTA
* *
354896 ACTGTAT
65 ATTATAT
* * * * * * *
354903 AGTTAATATTATTAGATTCTTATTTAGATTTATTAGAATTGGAATTAATCATTATTTGTACAATT
1 AGTTAATATTATTAGTTTC-CATTTAGACTAATTTGAATT-AAATTGATCATTATTTGTACAATT
354968 CAATTCAATATAT
64 -AA-T---TATAT
* ** * * * *
354981 ACTTAATGCTATTAGATTTACATTTACACTAATTTGAATTAAAATTTATCATTATTTATACAATT
1 AGTTAATATTATTAG-TTTCCATTTAGACTAATTTGAATT-AAATTGATCATTATTTGTACAATT
*
355046 GATTATAT
64 AATTATAT
* * * *
355054 AGTTAATATTATTAAGTTTCCAATTAGACTAA-TTG----AAATTGATCATTACTTATACAAGTA
1 AGTTAATATTATT-AGTTTCCATTTAGACTAATTTGAATTAAATTGATCATTATTTGTACAATTA
355114 ATTATAT
65 ATTATAT
* * * * * *
355121 AGTTAATATTATTAGATTCTTATTTAGATTTATTAGAATTGGAATTGATCATTATTTGTACAATT
1 AGTTAATATTATTAGTTTC-CATTTAGACTAATTTGAATT-AAATTGATCATTATTTGTACAATT
355186 CAATTCAATTCAAT
64 -AATT--A-T--AT
* * * * * *
355200 A-TATACTTAATGCTATTTGATTTACATTTATACTAATTTGAAGTAAAATTGATCATTACTTGTA
1 AGT-TA-AT-AT--TATTAG-TTTCCATTTAGACTAATTTGAA-TTAAATTGATCATTATTTGTA
* *
355264 CAAGTAATTGTAT
59 CAATTAATTATAT
* * * * * *
355277 AGTTAATATTATTAGATTCTTATTTAGATTTATTGGAATTTGAATTGATCATT
1 AGTTAATATTATTAGTTTC-CATTTAGACTAATTTGAA-TTAAATTGATCATT
355330 GTTTCTAAAA
Statistics
Matches: 431, Mismatches: 98, Indels: 81
0.71 0.16 0.13
Matches are distributed among these distances:
66 10 0.02
67 96 0.22
68 4 0.01
72 8 0.02
73 122 0.28
74 13 0.03
75 2 0.00
76 3 0.01
77 8 0.02
78 107 0.25
79 9 0.02
80 1 0.00
81 2 0.00
82 4 0.01
83 39 0.09
84 3 0.01
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (71 bp):
AGTTAATATTATTAGTTTCCATTTAGACTAATTTGAATTAAATTGATCATTATTTGTACAATTAA
TTATAT
Found at i:354889 original size:67 final size:67
Alignment explanation
Indices: 354799--355134 Score: 253
Period size: 67 Copynumber: 4.8 Consensus size: 67
354789 TACTAATTTG
* * *
354799 AATTAAAATTGATCATTATTTGTACAATTGAGTATATAGTTAATATTATTAAGTTTCCAATTAGA
1 AATTGAAATTGATCATTATTTGTACAATTAATTATATAGTTAATATTATTAAGTTTCCAATTAGA
354864 CT
66 CT
* * * * * * * *
354866 AATTGAAATTGATTATTACTTGTACAAGTAACTGTATAGTTAATATTATT-AGATTCTTATTTAG
1 AATTGAAATTGATCATTATTTGTACAATTAATTATATAGTTAATATTATTAAGTTTC-CAATTAG
*
354930 ATTTATT
65 ----ACT
* * * ** *
354937 AGAATTGGAATTAATCATTATTTGTACAATTCAATTCAATATATACTTAATGCTATT-AGATTTA
1 --AATTGAAATTGATCATTATTTGTACAATT-AA-T---TATATAGTTAATATTATTAAG-TTTC
* *
355001 CATTTACACT
58 CAATTAGACT
* * *
355011 AATTTGAATTAAAATTTATCATTATTTATACAATTGATTATATAGTTAATATTATTAAGTTTCCA
1 AA-TTG-----AAATTGATCATTATTTGTACAATTAATTATATAGTTAATATTATTAAGTTTCCA
355076 ATTAGACT
60 ATTAGACT
* * *
355084 AATTGAAATTGATCATTACTTATACAAGTAATTATATAGTTAATATTATTA
1 AATTGAAATTGATCATTATTTGTACAATTAATTATATAGTTAATATTATTA
355135 GATTCTTATT
Statistics
Matches: 209, Mismatches: 40, Indels: 40
0.72 0.14 0.14
Matches are distributed among these distances:
66 5 0.02
67 90 0.43
71 2 0.01
72 5 0.02
73 55 0.26
74 6 0.03
76 1 0.00
77 1 0.00
78 42 0.20
79 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.45
Consensus pattern (67 bp):
AATTGAAATTGATCATTATTTGTACAATTAATTATATAGTTAATATTATTAAGTTTCCAATTAGA
CT
Found at i:355063 original size:218 final size:218
Alignment explanation
Indices: 354685--355290 Score: 996
Period size: 218 Copynumber: 2.8 Consensus size: 218
354675 CAAGCTGATA
* * *
354685 AGTTAATATTATTAGATTCTTATTTAGATTTATTGGAATTAGAATTGATTATTATTTGTACAATT
1 AGTTAATATTATTAGATTCTTATTTAGATTTATTAGAATTGGAATTGATCATTATTTGTACAATT
*
354750 CAATTCAATATATACTTAATGCTATTAGATTCACATTTATACTAATTTGAATTAAAATTGATCAT
66 CAATTCAATATATACTTAATGCTATTAGATTTACATTTATACTAATTTGAATTAAAATTGATCAT
* *
354815 TATTTGTACAATTGAGTATATAGTTAATATTATTAAGTTTCCAATTAGACTAATTGAAATTGATT
131 TATTTGTACAATTGATTATATAGTTAATATTATTAAGTTTCCAATTAGACTAATTGAAATTGATC
* *
354880 ATTACTTGTACAAGTAACTGTAT
196 ATTACTTATACAAGTAACTATAT
*
354903 AGTTAATATTATTAGATTCTTATTTAGATTTATTAGAATTGGAATTAATCATTATTTGTACAATT
1 AGTTAATATTATTAGATTCTTATTTAGATTTATTAGAATTGGAATTGATCATTATTTGTACAATT
* *
354968 CAATTCAATATATACTTAATGCTATTAGATTTACATTTACACTAATTTGAATTAAAATTTATCAT
66 CAATTCAATATATACTTAATGCTATTAGATTTACATTTATACTAATTTGAATTAAAATTGATCAT
*
355033 TATTTATACAATTGATTATATAGTTAATATTATTAAGTTTCCAATTAGACTAATTGAAATTGATC
131 TATTTGTACAATTGATTATATAGTTAATATTATTAAGTTTCCAATTAGACTAATTGAAATTGATC
*
355098 ATTACTTATACAAGTAATTATAT
196 ATTACTTATACAAGTAACTATAT
355121 AGTTAATATTATTAGATTCTTATTTAGATTTATTAGAATTGGAATTGATCATTATTTGTACAATT
1 AGTTAATATTATTAGATTCTTATTTAGATTTATTAGAATTGGAATTGATCATTATTTGT---A--
* *
355186 CAATTCAATTCAATATATACTTAATGCTATTTGATTTACATTTATACTAATTTGAAGTAAAATTG
61 CAATTCAATTCAATATATACTTAATGCTATTAGATTTACATTTATACTAATTTGAATTAAAATTG
* * * *
355251 ATCATTACTTGTACAAGTAATTGTATAGTTAATATTATTA
126 ATCATTATTTGTACAATTGATTATATAGTTAATATTATTA
355291 GATTCTTATT
Statistics
Matches: 360, Mismatches: 23, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
218 263 0.73
221 1 0.00
223 96 0.27
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.45
Consensus pattern (218 bp):
AGTTAATATTATTAGATTCTTATTTAGATTTATTAGAATTGGAATTGATCATTATTTGTACAATT
CAATTCAATATATACTTAATGCTATTAGATTTACATTTATACTAATTTGAATTAAAATTGATCAT
TATTTGTACAATTGATTATATAGTTAATATTATTAAGTTTCCAATTAGACTAATTGAAATTGATC
ATTACTTATACAAGTAACTATAT
Found at i:355161 original size:67 final size:67
Alignment explanation
Indices: 354685--355161 Score: 244
Period size: 67 Copynumber: 6.6 Consensus size: 67
354675 CAAGCTGATA
* *
354685 AGTTAATATTATTAGATTCTTATTTAGATTTATTGGAATTAGAATTGATTATTATTTGTACAATT
1 AGTTAATATTATTAGATTCTCATTTAGA--T-TT---ATTAGAATTGATCATTATTTGTACAATT
354750 CAATTCAATATAT
60 -AA-T---TATAT
* ** * * *
354763 ACTTAATGCTATTAGATTCACATTTATACTAATTTGAATTAAAATTGATCATTATTTGTACAATT
1 AGTTAATATTATTAGATTCTCA-TT-TA--GATTT--ATTAGAATTGATCATTATTTGTACAATT
* *
354828 GAGTATAT
60 AATTATAT
* * * * * * * *
354836 AGTTAATATTATTAAGTTTC-CAATTAGACTAATT-GAAATTGATTATTACTTGTACAAGTAACT
1 AGTTAATATTATT-AGATTCTCATTTAGATTTATTAG-AATTGATCATTATTTGTACAATTAATT
*
354899 GTAT
64 ATAT
*
354903 AGTTAATATTATTAGATTCTTATTTAGATTTATTAGAATTGGAATTAATCATTATTTGTACAATT
1 AGTTAATATTATTAGATTCTCATTTAGATTTATTAGAATT-G-----ATCATTATTTGTACAATT
354968 CAATTCAATATAT
60 -AA-T---TATAT
* ** * * * *
354981 ACTTAATGCTATTAGATT-TACATTTACACTAATTTGAATTAAAATTTATCATTATTTATACAAT
1 AGTTAATATTATTAGATTCT-CATTT--A--GATTT--ATTAGAATTGATCATTATTTGTACAAT
*
355045 TGATTATAT
59 TAATTATAT
* * * * * * *
355054 AGTTAATATTATTAAGTTTC-CAATTAGACTAATT-GAAATTGATCATTACTTATACAAGTAATT
1 AGTTAATATTATT-AGATTCTCATTTAGATTTATTAG-AATTGATCATTATTTGTACAATTAATT
355117 ATAT
64 ATAT
*
355121 AGTTAATATTATTAGATTCTTATTTAGATTTATTAGAATTG
1 AGTTAATATTATTAGATTCTCATTTAGATTTATTAGAATTG
355162 GAATTGATCA
Statistics
Matches: 306, Mismatches: 62, Indels: 73
0.69 0.14 0.17
Matches are distributed among these distances:
66 10 0.03
67 113 0.37
68 3 0.01
69 4 0.01
71 3 0.01
72 1 0.00
73 51 0.17
74 11 0.04
76 1 0.00
77 3 0.01
78 85 0.28
79 4 0.01
80 4 0.01
82 5 0.02
84 8 0.03
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.46
Consensus pattern (67 bp):
AGTTAATATTATTAGATTCTCATTTAGATTTATTAGAATTGATCATTATTTGTACAATTAATTAT
AT
Found at i:355413 original size:41 final size:37
Alignment explanation
Indices: 355366--355446 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 37
355356 GGTTTTCCAT
* *
355366 TAAAATTATAATTTCTAAAATTTATATTTATAAATAATGAA
1 TAAAATTATAA--TATAAAA-TTAT-TTTATAAATAATAAA
*
355407 TAAAATTATAATATAAAATTATTTTATAAATGATAAA
1 TAAAATTATAATATAAAATTATTTTATAAATAATAAA
355444 TAA
1 TAA
355447 TATATTGTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 16 0.43
38 4 0.11
39 6 0.16
41 11 0.30
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (37 bp):
TAAAATTATAATATAAAATTATTTTATAAATAATAAA
Found at i:357093 original size:20 final size:20
Alignment explanation
Indices: 357065--357139 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
357055 TTTTACCTAG
357065 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
* **
357085 ATATATCGATACA-TTCATA
1 ATGTATCGATACATTTTTTA
* * *
357104 CATGTATCGATATATTCTTCA
1 -ATGTATCGATACATTTTTTA
357125 ATGTATCGATACATT
1 ATGTATCGATACATT
357140 ATGCCTTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 4 0.09
20 37 0.86
21 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:358067 original size:22 final size:22
Alignment explanation
Indices: 358041--358095 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
358031 AGCCTTTGAC
358041 CATGCATTTTTTTATTACGTTT
1 CATGCATTTTTTTATTACGTTT
358063 CATGCATTTTTTTATTACGTTT
1 CATGCATTTTTTTATTACGTTT
358085 CATGCATTTTT
1 CATGCATTTTT
358096 AATATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.58
Consensus pattern (22 bp):
CATGCATTTTTTTATTACGTTT
Found at i:358521 original size:20 final size:19
Alignment explanation
Indices: 358494--358567 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
358484 TTTACCTTGG
*
358494 TGTATCGATACATTTTTCAA
1 TGTATCGATACATTTAT-AA
* *
358514 TATATCGATACATGTATGAA
1 TGTATCGATACATTTAT-AA
*
358534 TGTATCGATATATTCTATAA
1 TGTATCGATACATT-TATAA
358554 TGTATCGATACATT
1 TGTATCGATACATT
358568 ATGTCTTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 42 0.93
21 3 0.07
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTATAA
Found at i:358560 original size:40 final size:39
Alignment explanation
Indices: 358494--358570 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
358484 TTTACCTTGG
*
358494 TGTATCGATACATTTTTCAATATATCGATACATGTATGAA
1 TGTATCGATACATTTATCAATATATCGATACAT-TATGAA
* *
358534 TGTATCGATATATTCTAT-AATGTATCGATACATTATG
1 TGTATCGATACATT-TATCAATATATCGATACATTATG
358571 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 4 0.12
40 27 0.82
41 2 0.06
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (39 bp):
TGTATCGATACATTTATCAATATATCGATACATTATGAA
Found at i:359516 original size:23 final size:23
Alignment explanation
Indices: 359480--359535 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
359470 AGCCTTTGAC
359480 CATGCA-TTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
359502 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
359525 CATGCATTTTT
1 CATGCATTTTT
359536 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 6 0.18
23 27 0.82
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:359542 original size:20 final size:21
Alignment explanation
Indices: 359480--359542 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 21
359470 AGCCTTTGAC
**
359480 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
359502 CATGCATTTTTTTTATTATGTTT
1 CATGCA--TTTTTTAACATGTTT
359525 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
359543 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.26
22 6 0.16
23 22 0.58
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.59
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:367790 original size:24 final size:24
Alignment explanation
Indices: 367745--367789 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
367735 CTTCAAAATG
*
367745 ACAAAAAAAGTCAAAAGCAAAAGC
1 ACAAAAAAAGTCAAAAGAAAAAGC
*
367769 ACAAAAAAA-TGAAAAGAAAAA
1 ACAAAAAAAGTCAAAAGAAAAA
367790 AAGTGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.73, C:0.11, G:0.11, T:0.04
Consensus pattern (24 bp):
ACAAAAAAAGTCAAAAGAAAAAGC
Found at i:369189 original size:27 final size:27
Alignment explanation
Indices: 369147--369507 Score: 418
Period size: 27 Copynumber: 13.1 Consensus size: 27
369137 TGGCATTTCT
*
369147 TTTTAAAGTCCACAACTCCGTGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
* *
369175 TTTTAAGTCCACAACTCTGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* *
369202 TTTTAAAGTCCACAACTCCATGGCATCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
369230 TTTTAAGTCCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
369257 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
369285 TTTTAAAGTCCACAACTCCGTGGCA-CC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
369312 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTT-AAGTCCACAACTCCGTGGCACCC
*
369340 TTTTAAGTCCACAACTCCGTGGCACCT
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
369367 TTTTAAGTCTACAACTCTGTAGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * *
369394 TTTTAAGTTCACAAGTCAGTGGCACTCC
1 TTTTAAGTCCACAACTCCGTGGCAC-CC
** * *
369422 TTCAAAGTCCACAAGTCAGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
* * * *
369449 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTT-TAAGTCCACAACTCCGTGGCAC-CC
** * *
369478 TTCAAAGTCCACAAGTCAGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACCC
369505 TTT
1 TTT
369508 CAAAGCCCAC
Statistics
Matches: 302, Mismatches: 25, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
27 150 0.50
28 148 0.49
29 4 0.01
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.27
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCGTGGCACCC
Found at i:369216 original size:55 final size:55
Alignment explanation
Indices: 369122--369507 Score: 456
Period size: 55 Copynumber: 7.0 Consensus size: 55
369112 GACCTCTTCA
* * * *
369122 AAGTCCACGATTCAGTGGCATTTCTTTTTAAAGTCCACAACTCCGTGGCATCCTTTT
1 AAGTCCACAACTCAGTGGCA--TCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
* * *
369179 AAGTCCACAACTCTGTGGCATCCTTTTAAAGTCCACAACTCCATGGCATCCTTTT
1 AAGTCCACAACTCAGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
* *
369234 AAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCAGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
*
369289 AAAGTCCACAACTCCGTGGCA-CCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
1 -AAGTCCACAACTCAGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
* * * * *
369344 AAGTCCACAACTCCGTGGCA-CCTTTTTAAGTCTACAACTCTGTAGCACCCTTTT
1 AAGTCCACAACTCAGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
* * * * * *
369398 AAGTTCACAAGTCAGTGGCACTCC-TTCAAAGTCCACAAGTCAGTGGCACCCTTTCA
1 AAGTCCACAACTCAGTGGCA-TCCTTTTAAAGTCCACAACTCCGTGGCACCCTTT-T
* * * * *
369454 AAGCCCACAAGTCAGTGGCACTCC-TTCAAAGTCCACAAGTCAGTGGCACCCTTT
1 AAGTCCACAACTCAGTGGCA-TCCTTTTAAAGTCCACAACTCCGTGGCACCCTTT
369508 CAAAGCCCAC
Statistics
Matches: 300, Mismatches: 25, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
54 67 0.22
55 143 0.48
56 73 0.24
57 17 0.06
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (55 bp):
AAGTCCACAACTCAGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTT
Found at i:369219 original size:28 final size:28
Alignment explanation
Indices: 369147--369517 Score: 443
Period size: 28 Copynumber: 13.5 Consensus size: 28
369137 TGGCATTTCT
*
369147 TTTTAAAGTCCACAACTCCGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
369175 TTTT-AAGTCCACAACTCTGTGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
369202 TTTTAAAGTCCACAACTCCATGGCATCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
*
369230 TTTT-AAGTCCACAACTCTGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
369257 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
369285 TTTTAAAGTCCACAACTCCGTGGCA-CC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
369312 TTTTAAAGTCCACAACTCCGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
369340 TTTT-AAGTCCACAACTCCGTGGCA-CC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* * * *
369366 TTTTTAAGTCTACAACTCTGTAGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* * *
369394 TTTT-AAGTTCACAAGTCAGTGGCACTCC
1 TTTTAAAGTCCACAACTCCGTGGCAC-CC
* * *
369422 -TTCAAAGTCCACAAGTCAGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* * * *
369449 TTTCAAAGCCCACAAGTCAGTGGCACTCC
1 TTTTAAAGTCCACAACTCCGTGGCAC-CC
* * *
369478 -TTCAAAGTCCACAAGTCAGTGGCACCC
1 TTTTAAAGTCCACAACTCCGTGGCACCC
* *
369505 TTTCAAAGCCCAC
1 TTTTAAAGTCCAC
369518 GCAAGTTAGT
Statistics
Matches: 313, Mismatches: 20, Indels: 20
0.89 0.06 0.06
Matches are distributed among these distances:
26 6 0.02
27 136 0.43
28 169 0.54
29 2 0.01
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.27
Consensus pattern (28 bp):
TTTTAAAGTCCACAACTCCGTGGCACCC
Found at i:369547 original size:32 final size:32
Alignment explanation
Indices: 369505--370288 Score: 745
Period size: 32 Copynumber: 25.4 Consensus size: 32
369495 AGTGGCACCC
* * *
369505 TTTCAAAGCCCACGCAAGTTAGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* *
369537 CTTCAAAGCCCACACAAGTTGGTGGCAACTTA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* *
369569 CTTCAAAGCCCACACAAGTTGGTGGCAACTTA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* *
369601 CTTCAAAGCCCACACAAGTTGGTGGCAACTTA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* *
369633 CTTCAAAGCCCACACAAGTTGATGGCAACTCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* *
369665 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
369697 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* *
369729 TTTGAAAGCCCACACAAGTTGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* *
369761 TTTCAAAGCCCACACAAGTTGGTGGTAACTTA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* * *
369793 TTTCAAAGCCTAGACAAGTTGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* * *
369825 TTTTAAAGCCTACACAAGTTGGTGGCAAGTCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
369857 TTTCAAAGCCCACACAAGTTGGTGGCAAC-CTA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTC-A
*
369889 TTTCAAAGCCCACACAAGTTGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* * ** *
369921 TTTGAAAGCCCATACAAGTCAGTGGGAACTCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* *
369953 TTTCAAAGCCCACACAAGGTGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
*
369985 TTTCAAAGCCCACACAAGTCGGTGGC-A-T-A
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
** * *
370014 TTTTCAAAG-CC-CACAAGTCAGTGG-TA-TCC
1 -TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* *
370043 TTTCAAAG-CC-CATAAGTCT-GTGGC-A-TCC
1 TTTCAAAGCCCACACAAGT-TGGTGGCAACTCA
* *
370071 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* * * *
370103 TTTCAAAG--CTCACAAGTCGGTGGC--TTCT
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
**
370131 TTTCAAAG-CC-CACAAGTCAGTGGC-AC-CA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* ** *
370159 TTTTAAAG-CC-CACAAGTCAGTGGC-AC-CC
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* ** * *
370187 TTTCCAAG-CC-CACAAGTCAGTGG-TA-TCC
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
* *
370215 TTTCAAAG-CC-CATAAGTCT-GTGGC-A-TCT
1 TTTCAAAGCCCACACAAGT-TGGTGGCAACTCA
* * *
370243 TTTCAAAGCCCACATAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
*
370275 TTTCAAAGCTCACA
1 TTTCAAAGCCCACA
370289 AGTCAGTGGC
Statistics
Matches: 655, Mismatches: 74, Indels: 46
0.85 0.10 0.06
Matches are distributed among these distances:
28 149 0.23
29 8 0.01
30 46 0.07
31 4 0.01
32 447 0.68
33 1 0.00
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (32 bp):
TTTCAAAGCCCACACAAGTTGGTGGCAACTCA
Found at i:370029 original size:28 final size:28
Alignment explanation
Indices: 369985--370615 Score: 634
Period size: 28 Copynumber: 22.5 Consensus size: 28
369975 TGGCAACCCA
* *
369985 TTTCAAAGCCCACACAAGTCGGTGGCATAT
1 TTTCAAAG-CC-CACAAGTCAGTGGCATCT
* *
370015 TTTCAAAGCCCACAAGTCAGTGGTATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * *
370043 TTTCAAAGCCCATAAGTCTGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * *
370071 TTTCAAAGCCCACACAAGTCGGTGGCAACCCA
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCT
* * *
370103 TTTCAAAGCTCACAAGTCGGTGGCTTCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
*
370131 TTTCAAAGCCCACAAGTCAGTGGCACCAT
1 TTTCAAAGCCCACAAGTCAGTGGCATC-T
* *
370160 TTT-AAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * *
370187 TTTCCAAGCCCACAAGTCAGTGGTATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* *
370215 TTTCAAAGCCCATAAGTCTGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * *
370243 TTTCAAAGCCCACATAAGTCGGTGGCAACCCA
1 TTTCAAAGCCCAC--AAGTCAGTGGC-A-TCT
* *
370275 TTTCAAAGCTCACAAGTCAGTGGCTTCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * *
370303 TTTCAAAGCCCACAAGTCAGTGGTACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
*
370331 TTTCAAAGCCCACAAGTCAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* *
370358 TTTCCAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* *
370386 TTTCCAAG--C-C----CA-TGGCAACT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
** * *
370406 TTTCAAAGCCCATGAGTCAGTAGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
*
370434 TTTCAAAGCCCACAAGTCGGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
*
370462 TTTCAAAGCCCACAAGTCAGTGGCACCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * *
370490 TTTCAAAACCCACAAGTCAATGGTATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* *
370518 TTTCCAAGCCCACAAGTCAGTGGCAACT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* * *
370546 TTTCAAAGCCCACGAGTCAGTGACATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
*
370574 TTTCAAAGCCCACAAGTTAGTGGCATCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCT
* *
370602 CTTGAAAGCCCACA
1 TTTCAAAGCCCACA
370616 GAAGTTAGTA
Statistics
Matches: 504, Mismatches: 78, Indels: 40
0.81 0.13 0.06
Matches are distributed among these distances:
20 13 0.03
21 2 0.00
22 1 0.00
25 1 0.00
26 1 0.00
27 31 0.06
28 368 0.73
29 8 0.02
30 54 0.11
31 3 0.01
32 22 0.04
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCT
Found at i:370401 original size:20 final size:20
Alignment explanation
Indices: 370378--370419 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
370368 CACAAGTCAG
* *
370378 TGGCATCCTTTCCAAGCCCA
1 TGGCAACCTTTCAAAGCCCA
*
370398 TGGCAACTTTTCAAAGCCCA
1 TGGCAACCTTTCAAAGCCCA
370418 TG
1 TG
370420 AGTCAGTAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.33, G:0.17, T:0.26
Consensus pattern (20 bp):
TGGCAACCTTTCAAAGCCCA
Found at i:370756 original size:45 final size:45
Alignment explanation
Indices: 370706--370915 Score: 174
Period size: 45 Copynumber: 4.6 Consensus size: 45
370696 AAATCCGATA
* * * *
370706 TCGCTGGCATTAAATCAGCATATTGGCACCTTTATTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCACCTTTATTAGCTCAATG
* * *
370751 TCGCTGGCCTTGAATCAGCACATTTTCTA-TTTTCCCTTAGCTCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTC-ACCTTT--ATTAGCTCAATG
* * *
370798 TTGCTGGCCTTGAATCAGCACATTGTC-CACTTTACTAGCCCAATG
1 TCGCTGGCCTTGAATCAGCACATTGTCAC-CTTTATTAGCTCAATG
* * * *
370843 TCGCTGGCCTTG-ATCAGCACATTAGTCCACTTTTCCCTTAGCCCAACG
1 TCGCTGGCCTTGAATCAGCACATT-GT-CACCTTT--ATTAGCTCAATG
* **
370891 TCGCTGGCATTGAATTGGCACATTG
1 TCGCTGGCCTTGAATCAGCACATTG
370916 GCACTCCTCT
Statistics
Matches: 133, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
44 11 0.08
45 47 0.35
46 5 0.04
47 40 0.30
48 21 0.16
49 9 0.07
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (45 bp):
TCGCTGGCCTTGAATCAGCACATTGTCACCTTTATTAGCTCAATG
Found at i:370804 original size:47 final size:47
Alignment explanation
Indices: 370740--370915 Score: 214
Period size: 47 Copynumber: 3.8 Consensus size: 47
370730 GGCACCTTTA
* * *
370740 TTAGCTCAATGTCGCTGGCCTTGAATCAGCACATTTTCTATTTTCCC
1 TTAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
* * * *
370787 TTAGCTCAATGTTGCTGGCCTTGAATCAGCACATTGTCCACTTT-AC
1 TTAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
370833 -TAGCCCAATGTCGCTGGCCTTG-ATCAGCACATTAGTCCACTTTTCCC
1 TTAGCCCAATGTCGCTGGCCTTGAATCAGCACATT-GTCCA-TTTTCCC
* * **
370880 TTAGCCCAACGTCGCTGGCATTGAATTGGCACATTG
1 TTAGCCCAATGTCGCTGGCCTTGAATCAGCACATTG
370916 GCACTCCTCT
Statistics
Matches: 111, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
44 11 0.10
45 25 0.23
46 4 0.04
47 41 0.37
48 21 0.19
49 9 0.08
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.33
Consensus pattern (47 bp):
TTAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGTCCATTTTCCC
Found at i:370912 original size:93 final size:92
Alignment explanation
Indices: 370706--370915 Score: 262
Period size: 92 Copynumber: 2.3 Consensus size: 92
370696 AAATCCGATA
* * * * *
370706 TCGCTGGCATTAAATCAGCATATTG-GCACCTTTATTAGCTCAATGTCGCTGGCCTTGAATCAGC
1 TCGCTGGCATTGAATCAGCACATTGTCCA-CTTTACTAGCCCAATGTCGCTGGCCTTGAATCAGC
* * * *
370770 ACATTTTCTATTTTCCCTTAGCTCAATG
65 ACATTGTCCATTTTCCCTTAGCCCAACG
* *
370798 TTGCTGGCCTTGAATCAGCACATTGTCCACTTTACTAGCCCAATGTCGCTGGCCTTG-ATCAGCA
1 TCGCTGGCATTGAATCAGCACATTGTCCACTTTACTAGCCCAATGTCGCTGGCCTTGAATCAGCA
370862 CATTAGTCCACTTTTCCCTTAGCCCAACG
66 CATT-GTCCA-TTTTCCCTTAGCCCAACG
**
370891 TCGCTGGCATTGAATTGGCACATTG
1 TCGCTGGCATTGAATCAGCACATTG
370916 GCACTCCTCT
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
91 11 0.11
92 50 0.50
93 39 0.39
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (92 bp):
TCGCTGGCATTGAATCAGCACATTGTCCACTTTACTAGCCCAATGTCGCTGGCCTTGAATCAGCA
CATTGTCCATTTTCCCTTAGCCCAACG
Found at i:371321 original size:20 final size:20
Alignment explanation
Indices: 371293--371367 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
371283 TTTTGCCTAG
371293 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTTTTTA
* **
371313 ATATATCGATACA-TTCATA
1 ATGTATCGATACATTTTTTA
* * *
371332 CATGTATCGATATATTCTTCA
1 -ATGTATCGATACATTTTTTA
371353 ATGTATCGATACATT
1 ATGTATCGATACATT
371368 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 4 0.09
20 37 0.86
21 2 0.05
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTTTTTA
Found at i:377794 original size:21 final size:21
Alignment explanation
Indices: 377768--377810 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
377758 ACTTGCAGAA
*
377768 TCAACAATCCATTCCTTCTCT
1 TCAACAACCCATTCCTTCTCT
377789 TCAACAACCCATTCCTTCTCT
1 TCAACAACCCATTCCTTCTCT
377810 T
1 T
377811 TTAGAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.40, G:0.00, T:0.37
Consensus pattern (21 bp):
TCAACAACCCATTCCTTCTCT
Found at i:378563 original size:21 final size:21
Alignment explanation
Indices: 378515--378563 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
378505 TTTTCCCTAC
378515 TCATTTTTTACCTTTAAATTAA
1 TCATTTTTTA-CTTTAAATTAA
* *
378537 TAATTTTTTA-TTTAAATTTAT
1 TCATTTTTTACTTTAAA-TTAA
378558 TCATTT
1 TCATTT
378564 ATTTTATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.26
21 8 0.35
22 9 0.39
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.61
Consensus pattern (21 bp):
TCATTTTTTACTTTAAATTAA
Found at i:379603 original size:11 final size:12
Alignment explanation
Indices: 379589--379651 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 12
379579 TCATATCGAA
379589 TTTATATTAT-T
1 TTTATATTATAT
379600 TTTATATTATATCAT
1 TTTATA-T-TAT-AT
379615 ATTTATTATTATAT
1 -TTTA-TATTATAT
*
379629 TTTA-ATTATTT
1 TTTATATTATAT
379640 TTTATATTATAT
1 TTTATATTATAT
379652 ATATTGTGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
11 16 0.37
12 7 0.16
13 7 0.16
14 2 0.05
15 4 0.09
16 5 0.12
17 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATATTATAT
Found at i:380071 original size:28 final size:28
Alignment explanation
Indices: 380037--380124 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 28
380027 TTTTTTATAA
380037 ATTAATTAA-ATTTAATAAATAATAATAT
1 ATTAATTAATATTTAATAAA-AATAATAT
*
380065 ATTAATTATTATTTTTAATAAAAATAATAT
1 ATTAATTA--ATATTTAATAAAAATAATAT
*
380095 -TTAATTAACT-TTTAA-AAAAA-ATTAT
1 ATTAATTAA-TATTTAATAAAAATAATAT
380120 ATTAA
1 ATTAA
380125 CAATTAAAAT
Statistics
Matches: 53, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
25 4 0.08
26 9 0.17
27 6 0.11
28 9 0.17
29 7 0.13
30 9 0.17
31 9 0.17
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTAATATTTAATAAAAATAATAT
Found at i:380107 original size:27 final size:26
Alignment explanation
Indices: 380038--380122 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 26
380028 TTTTTATAAA
*
380038 TTAATTAAATTTAATAAATAATAATAT
1 TTAATTAATTTTAATAAA-AATAATAT
380065 ATTAATTATTATTTTTAATAAAAATAATAT
1 -TTAATTA--A-TTTTAATAAAAATAATAT
* *
380095 TTAATTAACTTTTAAAAAAAATTATAT
1 TTAATTAA-TTTTAATAAAAATAATAT
380122 T
1 T
380123 AACAATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
27 18 0.36
28 7 0.14
29 7 0.14
30 9 0.18
31 9 0.18
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAATTAATTTTAATAAAAATAATAT
Found at i:380174 original size:13 final size:14
Alignment explanation
Indices: 380147--380173 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
380137 TAATTATTTT
380147 TTTAAATAAAAAAA
1 TTTAAATAAAAAAA
380161 TTTAAATAAAAAA
1 TTTAAATAAAAAA
380174 TAAAAATGGT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TTTAAATAAAAAAA
Found at i:380360 original size:130 final size:126
Alignment explanation
Indices: 380081--380433 Score: 461
Period size: 130 Copynumber: 2.7 Consensus size: 126
380071 TATTATTTTT
* *
380081 AATAAAAATAATATTTAATTAACTTTTAAAAAAAATTATATTAACAATTAAAATATTAATTA-T-
1 AATAAAAATAATATTTAATTAA-GTTT--AAAAAATTACATTAACAATTAAAATATTAATTATTA
* *
380144 T-TTTTTAAATAAAAAAATTTAAATAAAAAATAAAAATGGTTTATTATTATTATTTTTTAATAA
63 TATTTTTAAATAAAAAAATTAAAATAAAAAATAAAAATGGTTTATTATTATTATATTTTAATAA
380207 AATTAAAAATAATATTTAATTAAGTTTAAAACAATTACATTAACAGATTAAAATATTAATTATTA
1 AA-TAAAAATAATATTTAATTAAGTTTAAAA-AATTACATTAACA-ATTAAAATATTAATTATTA
380272 TATTTTTACAAAAATAATAAAAAATATAAAAT-AAAAATAAAAA-GGTTT-TTATTA-TA-ATTT
63 TATTTTT----AAAT-A-AAAAAAT-TAAAATAAAAAATAAAAATGGTTTATTATTATTATATTT
380332 TAATAA
121 TAATAA
380338 AATAAAAATAATATTTAATTAAGTTTAAAAAATTTACATTAACAATTAAAATATTAATTATTATA
1 AATAAAAATAATATTTAATTAAGTTTAAAAAA-TTACATTAACAATTAAAATATTAATTATTATA
*
380403 TTTTTTAAAATAAAAAAATTAAATTAAAAAA
65 -TTTTT-AAATAAAAAAATTAAAATAAAAAA
380434 GTTTTTATTA
Statistics
Matches: 206, Mismatches: 5, Indels: 33
0.84 0.02 0.14
Matches are distributed among these distances:
124 9 0.04
125 24 0.12
126 22 0.11
127 26 0.13
128 1 0.00
129 28 0.14
130 44 0.21
131 11 0.05
132 2 0.01
133 10 0.05
134 6 0.03
135 18 0.09
136 5 0.02
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (126 bp):
AATAAAAATAATATTTAATTAAGTTTAAAAAATTACATTAACAATTAAAATATTAATTATTATAT
TTTTAAATAAAAAAATTAAAATAAAAAATAAAAATGGTTTATTATTATTATATTTTAATAA
Found at i:380739 original size:39 final size:38
Alignment explanation
Indices: 380687--380802 Score: 117
Period size: 39 Copynumber: 3.0 Consensus size: 38
380677 TTTAACGTTA
* *
380687 ATTAAAATCTAAAAGATATGACTAATGTATAAAATTTTT
1 ATTAGAATTTAAAAGATATGACTAAT-TATAAAATTTTT
* * * *
380726 ATTAGATTTTAAAAGATATTAATAATTAT-AGATTATTT
1 ATTAGAATTTAAAAGATATGACTAATTATAAAATT-TTT
* * *
380764 ATTAGAATTTAAAAAATGTGACCAATATATAAAATTTTT
1 ATTAGAATTTAAAAGATATGACTAAT-TATAAAATTTTT
380803 GATTGTAGTA
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
37 4 0.07
38 26 0.43
39 27 0.44
40 4 0.07
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.41
Consensus pattern (38 bp):
ATTAGAATTTAAAAGATATGACTAATTATAAAATTTTT
Found at i:380948 original size:121 final size:117
Alignment explanation
Indices: 380813--381122 Score: 366
Period size: 121 Copynumber: 2.6 Consensus size: 117
380803 GATTGTAGTA
380813 TAAACTTAATTAAATATTATTTTTTATTTTATTAAAAATTATAATAATATTTTTATTTTAAATTT
1 TAAACTTAATTAAATATTATTTTTTATTTTATTAAAAATTATAATAATATTTTTATTTTAAATTT
* *
380878 TTTTATATTTATAAAAACATAATAATTCATATTTTAATTTGTTAATGT-AATTTTTT
66 TTTT-TATTT-T-AAAA-A-AATAATTAATATTTTAATTTGTTAATGTAAAATTTTT
* *
380934 TAAACTTAATTAAATATTATTTTTAATTTTATTAAATAATAATAATAATAAAACCTTTTTATTTT
1 TAAACTTAATTAAATATTATTTTTTATTTTATTAAA-AAT--T-ATAATAATA--TTTTTATTTT
380999 -AA--TTTTTTATTTTAAAAAAATAATTAATATTTTAATTTGTTAATGTAAAATTTTT
60 AAATTTTTTTTATTTTAAAAAAATAATTAATATTTTAATTTGTTAATGTAAAATTTTT
* *
381054 TAAATTTAATTAAATATTATTTTTTA--TTA--AAAAATAATAATTAATATATTATTATTTATCA
1 TAAACTTAATTAAATATTATTTTTTATTTTATTAAAAATTATAA-TAATAT-TT-TTATTT-T-A
381115 AATTTTTT
61 AATTTTTT
381123 AAATTTAATT
Statistics
Matches: 166, Mismatches: 8, Indels: 33
0.80 0.04 0.16
Matches are distributed among these distances:
111 1 0.01
112 6 0.04
113 10 0.06
114 1 0.01
115 3 0.02
116 5 0.03
118 7 0.04
119 27 0.16
120 32 0.19
121 39 0.23
122 4 0.02
123 5 0.03
124 6 0.04
125 8 0.05
126 2 0.01
127 10 0.06
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (117 bp):
TAAACTTAATTAAATATTATTTTTTATTTTATTAAAAATTATAATAATATTTTTATTTTAAATTT
TTTTTATTTTAAAAAAATAATTAATATTTTAATTTGTTAATGTAAAATTTTT
Found at i:381007 original size:13 final size:13
Alignment explanation
Indices: 380989--381013 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
380979 TAATAAAACC
380989 TTTTTATTTTAAT
1 TTTTTATTTTAAT
381002 TTTTTATTTTAA
1 TTTTTATTTTAA
381014 AAAAATAATT
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:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTATTTTAAT
Found at i:381093 original size:72 final size:68
Alignment explanation
Indices: 381000--381134 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 68
380990 TTTTATTTTA
* *
381000 ATTTTTTATTTTAAAAAAATAATTAATATTTTAATT-TGTTAATGTAAAATTTTTTAAATTTAAT
1 ATTTTTTATTTAAAAAAAATAATTAATATATT-ATTAT-TT-A--TAAAATTTTTTAAATTTAAT
381064 TAAATATT
61 TAAATATT
*
381072 ATTTTTTA-TTAAAAAATAATAATTAATATATTATTATTTATCAAATTTTTTAAATTTAATTAA
1 ATTTTTTATTTAAAAAA-AATAATTAATATATTATTATTTATAAAATTTTTTAAATTTAATTAA
381135 TTTATAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
68 22 0.38
70 1 0.02
71 12 0.21
72 23 0.40
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (68 bp):
ATTTTTTATTTAAAAAAAATAATTAATATATTATTATTTATAAAATTTTTTAAATTTAATTAAAT
ATT
Found at i:381099 original size:119 final size:122
Alignment explanation
Indices: 380813--381099 Score: 351
Period size: 119 Copynumber: 2.4 Consensus size: 122
380803 GATTGTAGTA
* * * *
380813 TAAACTTAATTAAATATTATTTTTTATT-TTATTAAAAATT-ATAATAATATTTTTATTTTAAAT
1 TAAACTTAATTAAATATTATTTTTTATTATAAATAATAATTAATAATAAAATTTTTATTTTAAA-
* *
380876 TTTTTTATATTTATAAAAACATAATAATTCATATTTTAATTTGTTAATGTAATTTTTT
65 TTTTTTATATTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTTT
*
380934 TAAACTTAATTAAATATTATTTTTAATTTTATTAAATAATAA-TAATAATAAAACCTTTTTATTT
1 TAAACTTAATTAAATATTATTTTT--TATTA-TAAATAATAATTAATAATAAAA--TTTTTATTT
380998 T-AA-TTTTT-TATTT-T-AAAA-A-AATAATTAATATTTTAATTTGTTAATGTAAAATTTTT
61 TAAATTTTTTATATTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGT-AAATTTTT
* *
381054 TAAATTTAATTAAATATTATTTTTTATTAAAAAATAATAATTAATA
1 TAAACTTAATTAAATATTATTTTTTATT-ATAAATAATAATTAATA
381100 TATTATTATT
Statistics
Matches: 146, Mismatches: 10, Indels: 22
0.82 0.06 0.12
Matches are distributed among these distances:
118 12 0.08
119 33 0.23
120 31 0.21
121 28 0.19
122 1 0.01
123 8 0.05
124 6 0.04
125 15 0.10
126 2 0.01
127 10 0.07
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (122 bp):
TAAACTTAATTAAATATTATTTTTTATTATAAATAATAATTAATAATAAAATTTTTATTTTAAAT
TTTTTATATTTATAAAAACATAATAATTAATATTTTAATTTGTTAATGTAAATTTTT
Found at i:388479 original size:13 final size:13
Alignment explanation
Indices: 388457--388514 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
388447 GGCAGTAGCT
*
388457 TTGTAGCGATACA
1 TTGTATCGATACA
388470 TTGTATCGATACAACA
1 TTGTATCGAT---ACA
388486 CTTATGTATCGATACA
1 --T-TGTATCGATACA
388502 TTGTATCGATACA
1 TTGTATCGATACA
388515 ACACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:388495 original size:19 final size:19
Alignment explanation
Indices: 388471--388533 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
388461 AGCGATACAT
388471 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
388490 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
388503 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
388522 TGTATCGATACA
1 TGTATCGATACA
388534 GTTACTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
16 6 0.16
18 1 0.03
19 21 0.55
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:388504 original size:32 final size:32
Alignment explanation
Indices: 388458--388533 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
388448 GCAGTAGCTT
*
388458 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
388490 TGTATCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
388522 TGTATCGATACA
1 TGTATCGATACA
388534 GTTACTATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:390739 original size:18 final size:18
Alignment explanation
Indices: 390704--390756 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
390694 CATCAAGTTT
*
390704 ATTAAA-AAAAATACAATA
1 ATTAAATAAAAA-ATAATA
390722 ATTAAATAAAAAATAATA
1 ATTAAATAAAAAATAATA
*
390740 ATAATAATTAAAAAATA
1 AT--TAAATAAAAAATA
390757 GATTCGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 13 0.43
19 5 0.17
20 12 0.40
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
ATTAAATAAAAAATAATA
Found at i:390742 original size:21 final size:20
Alignment explanation
Indices: 390709--390756 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
390699 AGTTTATTAA
390709 AAAAAAT-ACAATAATTAAAT
1 AAAAAATAACAATAA-TAAAT
* *
390729 AAAAAATAATAATAATAATT
1 AAAAAATAACAATAATAAAT
390749 AAAAAATA
1 AAAAAATA
390757 GATTCGTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAAATAACAATAATAAAT
Found at i:390872 original size:12 final size:12
Alignment explanation
Indices: 390872--390906 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
390862 CATGCTTTCA
390872 TTTCATGCATGC
1 TTTCATGCATGC
*
390884 TTTCATGGATGC
1 TTTCATGCATGC
*
390896 TTTCATACATG
1 TTTCATGCATG
390907 AATATGGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (12 bp):
TTTCATGCATGC
Found at i:390875 original size:17 final size:17
Alignment explanation
Indices: 390853--390889 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
390843 AATTAAGTGG
390853 CATTTCATGCATGCTTT
1 CATTTCATGCATGCTTT
390870 CATTTCATGCATGCTTT
1 CATTTCATGCATGCTTT
390887 CAT
1 CAT
390890 GGATGCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.19, C:0.24, G:0.11, T:0.46
Consensus pattern (17 bp):
CATTTCATGCATGCTTT
Found at i:391666 original size:10 final size:10
Alignment explanation
Indices: 391651--391687 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
391641 CAAGAGAAAG
391651 AAGAAAAAAA
1 AAGAAAAAAA
*
391661 AAGAAAAGAA
1 AAGAAAAAAA
*
391671 AAGAAACAAA
1 AAGAAAAAAA
391681 AAGAAAA
1 AAGAAAA
391688 TACTTGGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:392168 original size:27 final size:27
Alignment explanation
Indices: 392138--392195 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
392128 TTTAGATATC
392138 TAATGAGGAGTTTGCATGAGATTTTAG
1 TAATGAGGAGTTTGCATGAGATTTTAG
*
392165 TAATGAGGAGTTTGCATGAGATTTTCG
1 TAATGAGGAGTTTGCATGAGATTTTAG
392192 TAAT
1 TAAT
392196 AAGGTCTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.05, G:0.28, T:0.38
Consensus pattern (27 bp):
TAATGAGGAGTTTGCATGAGATTTTAG
Found at i:393089 original size:12 final size:12
Alignment explanation
Indices: 393085--393129 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
393075 ATAATAAATA
*
393085 AAATAAAGTAAT
1 AAATAAAATAAT
393097 AAATAAAATAAT
1 AAATAAAATAAT
*
393109 AAATAACAACAAT
1 AAATAA-AATAAT
393122 -AATAAAAT
1 AAATAAAAT
393130 TCCCAAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 2 0.07
12 22 0.76
13 5 0.17
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (12 bp):
AAATAAAATAAT
Found at i:394992 original size:15 final size:15
Alignment explanation
Indices: 394972--395005 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
394962 CTTTTTCGAT
394972 ATAAATCTGCGATGG
1 ATAAATCTGCGATGG
394987 ATAAATCTGCGATGG
1 ATAAATCTGCGATGG
395002 ATAA
1 ATAA
395006 GAAAAGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.26
Consensus pattern (15 bp):
ATAAATCTGCGATGG
Found at i:402570 original size:13 final size:13
Alignment explanation
Indices: 402552--402576 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
402542 ACAACAATTA
402552 TGTATCGATACAT
1 TGTATCGATACAT
402565 TGTATCGATACA
1 TGTATCGATACA
402577 AATTGTTGAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:409794 original size:82 final size:82
Alignment explanation
Indices: 409652--409812 Score: 268
Period size: 82 Copynumber: 2.0 Consensus size: 82
409642 CTGGATACTT
*
409652 CTCCAAAATGGAACATGAAATCAAGCCATCTTTGAAAGGCATAGATAACAAACTACCAAATCTTC
1 CTCCAAAATGGAACATGAAATCAAGCCATCTTTAAAAGGCATAGATAACAAACTACCAAATCTTC
*
409717 GTAAGTATCCATCCTTC
66 ATAAGTATCCATCCTTC
* * *
409734 CTCCTAAATGGAACATGAAATCAAGCCATCTTTAAAAGGCTTAGATAACAGACTACCAAATCTTC
1 CTCCAAAATGGAACATGAAATCAAGCCATCTTTAAAAGGCATAGATAACAAACTACCAAATCTTC
*
409799 ATAAGTATCTATCC
66 ATAAGTATCCATCC
409813 CCTACTGACC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 73 1.00
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.25
Consensus pattern (82 bp):
CTCCAAAATGGAACATGAAATCAAGCCATCTTTAAAAGGCATAGATAACAAACTACCAAATCTTC
ATAAGTATCCATCCTTC
Found at i:410276 original size:44 final size:44
Alignment explanation
Indices: 410170--410869 Score: 361
Period size: 44 Copynumber: 16.0 Consensus size: 44
410160 GATTAGTCCC
** *
410170 TGGTCAAACTTTTCTCATTTCAATCTGACGTATGGTTACCA-CT
1 TGGTCAAACTTTTCTCATTTCTGTTTGACGTATGGTTACCACCT
* * ** *
410213 CTGATCGAATCCCTT-TCATTTCTGTTTGATGTATGGTTACCACCT
1 -TGGTC-AAACTTTTCTCATTTCTGTTTGACGTATGGTTACCACCT
* * * * *
410258 TGGTCAAACTTTTCTCATTTCAGTCTAATGTATGGTTACCACCC
1 TGGTCAAACTTTTCTCATTTCTGTTTGACGTATGGTTACCACCT
* * *
410302 TGGTCAGA-TTCTTCTTA-TTCTGATTTGACGTATGGTTACCACCC
1 TGGTCAAACTT-TTCTCATTTCTG-TTTGACGTATGGTTACCACCT
* *** * * ** *
410346 TAGTCAAA-TCCCCTTCATTTCT-ATTAAAATATGGTTACCACTT
1 TGGTCAAACTTTTC-TCATTTCTGTTTGACGTATGGTTACCACCT
* * * * * *
410389 TGGTTAAACTTTTTTTTCGTTTCGGTCTAACGTATGGTTACCACC-
1 TGGTCAAAC--TTTTCTCATTTCTGTTTGACGTATGGTTACCACCT
* *
410434 TGGTCAAA-TTCTTCTCA-TTCTAATTTAACGTATGGTTACCACCT
1 TGGTCAAACTT-TTCTCATTTCT-GTTTGACGTATGGTTACCACCT
* * * * * *
410478 TAGTCAAACTTTTCTTATTTC-GATCTGATGAATGATTACCACCT
1 TGGTCAAACTTTTCTCATTTCTG-TTTGACGTATGGTTACCACCT
* *
410522 TGGTCAGA-TTTGTCTCATTT-TGATTTGATGTATGGTTACCACCT
1 TGGTCAAACTTT-TCTCATTTCTG-TTTGACGTATGGTTACCACCT
* * * * *
410566 TGGTCAAATCTCTTTC-C-TTTATTTTTGACATATGGTTACCTCCC
1 TGGTCAAA-CT-TTTCTCATTTCTGTTTGACGTATGGTTACCACCT
* * * *
410610 TAGTCATACTTTTCTCATTT-TGGTCTGATGTATGGTTACCACCT
1 TGGTCAAACTTTTCTCATTTCT-GTTTGACGTATGGTTACCACCT
* * *
410654 TGGTCAGA-TTCATCTCATTT-TGATTTGACGTATGGTTACCACCC
1 TGGTCAAACTT-TTCTCATTTCTG-TTTGACGTATGGTTACCACCT
* **
410698 TAGTCAAATCGCCTTCT--TTTCTGTTTGACG--TGGTTACCACCT
1 TGGTCAAA-C-TTTTCTCATTTCTGTTTGACGTATGGTTACCACCT
* * * ** * *
410740 TGGTCAAATTTTTTTTATTTCAATCTGACGTATGGTTACCACTT
1 TGGTCAAACTTTTCTCATTTCTGTTTGACGTATGGTTACCACCT
* * * * ***
410784 TAGTCAGA-TTCTTTTCA-TTCTGATTTGACGTACGGTT-TTGCCT
1 TGGTCAAACTT-TTCTCATTTCTG-TTTGACGTATGGTTACCACCT
* * * *
410827 TGGTCAAA-TCTTTCTCCTTCCTGTTTGATGTATGTTTACCACC
1 TGGTCAAACT-TTTCTCATTTCTGTTTGACGTATGGTTACCACC
410870 CTATCAAACC
Statistics
Matches: 491, Mismatches: 124, Indels: 82
0.70 0.18 0.12
Matches are distributed among these distances:
40 3 0.01
42 37 0.08
43 95 0.19
44 299 0.61
45 33 0.07
46 22 0.04
47 2 0.00
ACGTcount: A:0.21, C:0.22, G:0.15, T:0.43
Consensus pattern (44 bp):
TGGTCAAACTTTTCTCATTTCTGTTTGACGTATGGTTACCACCT
Found at i:410972 original size:42 final size:41
Alignment explanation
Indices: 410913--411548 Score: 464
Period size: 42 Copynumber: 15.1 Consensus size: 41
410903 TTAACTGATT
* * * *
410913 GACTTCATTACCCTTAGTCTACCTATCGGCTTTGATCCTAGA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGA-CCTAGA
* * * *
410955 GACTTCTTTATCTTTAGTCTGCATGTCGGTTTTGACCTTGAA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCTAG-A
* * * * *
410997 GACTTCTTTGCCTTTAGTCTGCTTGTTGGTTTTGACCTTGAA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCTAG-A
* * *
411039 GACTT-TCTTACCTTTAGGT-TACCCGTCGACTTGACCCTTTGACACTGGA
1 GACTTCT-TTACCTTTA-GTCTGCCTGTCG----G---CTTTGAC-CTAGA
* *
411088 GACTTCTTTACCTTTAGTCTGCCTGTCGACTTTGACCTTGGA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACC-TAGA
* * *
411130 GACTT-TCTTACCTTTATTCTGCCTGTCGGCTTTGACTTTAAA
1 GACTTCT-TTACCTTTAGTCTGCCTGTCGGCTTTGAC-CTAGA
* * *
411172 GACTTTTTTACCTTTAGTTTGCCTGTCAGCTTTGACCATAGA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACC-TAGA
* * * *
411214 GACTTCTTTACTTTTAGTCTGCCTATCGGCATTGACCTGGA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCTAGA
* * * * *
411255 GACTTCCTTATC-TTAGTTTGCTTGTCGACTTTGACCCTAGA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGA-CCTAGA
* * ** ** *
411296 GACTTC-TTACC-TTAATTTGTTTGTCGATTTTGACCTTGGA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACC-TAGA
* *
411336 GACTT-TCTTACC-TTAGTCTGCTTGTCAGCTTTGACACTAGA
1 GACTTCT-TTACCTTTAGTCTGCCTGTCGGCTTTGAC-CTAGA
* * * *
411377 GACTTCTTTACCTTTAGTCTGCTTATCGGCTTCGACACTTGA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGAC-CTAGA
* *
411419 GACTTCCTTACC-TTAGTCTGCCTAT-GGCTTTGACCCTAGA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGA-CCTAGA
* * * * * * *
411459 AACTTCCTTACCCTTAATCTACCTATCGGTTTTGACCCTAGA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGA-CCTAGA
* *
411501 GGCTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCTTGGA
1 GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACC-TAGA
411543 GACTTC
1 GACTTC
411549 CTTATTTTTG
Statistics
Matches: 483, Mismatches: 82, Indels: 58
0.78 0.13 0.09
Matches are distributed among these distances:
39 2 0.00
40 70 0.14
41 91 0.19
42 282 0.58
43 3 0.01
46 1 0.00
48 2 0.00
49 28 0.06
50 4 0.01
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (41 bp):
GACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCTAGA
Found at i:411144 original size:133 final size:126
Alignment explanation
Indices: 410941--411539 Score: 404
Period size: 133 Copynumber: 4.8 Consensus size: 126
410931 CTACCTATCG
* * * *
410941 GCTTTGATCC-TAGAGACTTCTTTATCTTTAGTCTGCATGTCGGTTTTGACCTTGAAGAC-TTCT
1 GCTTTGA-CCATAGAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTC-
* * * *
411004 TTGCCTTTAGTCTGCTTGTTGGTTTTGACCTTGAAGACTTTCTTACCTTTAGGTTACCCGTCGA
64 TTACCTTTAGTCTGCTTGTCGGCTTTGACCTTAAAGACTTTCTTACCTTTAGGTTACCCGTC-A
* *
411068 CTTGACCCTTTGA-CACTGGAGACTTCTTTACCTTTAGTCTGCCTGTCGACTTTGACCTTGGAGA
1 ---G---CTTTGACCA-TAGAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGA
* * * * * * *
411132 CTTTCTTACCTTTATTCTGCCTGTCGGCTTTGACTTTAAAGACTTTTTTACCTTTAGTTTGCCTG
59 CTTTCTTACCTTTAGTCTGCTTGTCGGCTTTGACCTTAAAGACTTTCTTACCTTTAGGTTACCCG
411197 TCA
124 TCA
* * * *
411200 GCTTTGACCATAGAGACTTCTTTACTTTTAGTCTGCCTATCGGCATTGACC-TGGAGACTTCCTT
1 GCTTTGACCATAGAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
* * * * * ** ****
411264 ATC-TTAGTTTGCTTGTCGACTTTGACCCTAGAGAC-TTCTTACC-TTAATTTGTTTGTC-
66 ACCTTTAGTCTGCTTGTCGGCTTTGACCTTAAAGACTTTCTTACCTTTAGGTTACCCGTCA
* * * * * *
411321 GATTTTGACCTTGGAGACTT-TCTTACC-TTAGTCTGCTTGTCAGCTTTGACAC-TAGAGAC-TT
1 G-CTTTGACCATAGAGACTTCT-TTACCTTTAGTCTGCCTGTCGGCTTTGAC-CTTGGAGACTTT
* * * * * **
411382 CTTTACCTTTAGTCTGCTTATCGGCTTCGACACTT-GAGACTTCCTTACC-TTA-GTCTGCCTAT
63 C-TTACCTTTAGTCTGCTTGTCGGCTTTGAC-CTTAAAGACTTTCTTACCTTTAGGT-TACCCGT
*
411444 -G
125 CA
* * * * * * * * * * *
411445 GCTTTGACCCTAGAAACTTCCTTACCCTTAATCTACCTATCGGTTTTGACCCTAGAGGC-TTCTT
1 GCTTTGACCATAGAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTC-T
*
411509 TACCTTTAGTCTGCCTGTCGGCTTTGACCTT
65 TACCTTTAGTCTGCTTGTCGGCTTTGACCTT
411540 GGAGACTTCC
Statistics
Matches: 379, Mismatches: 71, Indels: 45
0.77 0.14 0.09
Matches are distributed among these distances:
121 23 0.06
122 41 0.11
123 55 0.15
124 95 0.25
125 14 0.04
126 42 0.11
127 2 0.01
129 1 0.00
130 1 0.00
131 1 0.00
132 1 0.00
133 100 0.26
134 3 0.01
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.41
Consensus pattern (126 bp):
GCTTTGACCATAGAGACTTCTTTACCTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTTCTT
ACCTTTAGTCTGCTTGTCGGCTTTGACCTTAAAGACTTTCTTACCTTTAGGTTACCCGTCA
Found at i:411380 original size:163 final size:165
Alignment explanation
Indices: 411077--411548 Score: 526
Period size: 163 Copynumber: 2.9 Consensus size: 165
411067 ACTTGACCCT
* * *
411077 TTGACACTGGAGACTTCTTTACCTTTAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTACC
1 TTGACACTGGAGACTTCCTTACC-TTAGTCTGCCTGTCGACTTTGACCCTAGAGAC-TTCTTACC
* * * * *
411142 TTTATTCTGCCTGTCGGCTTTGACTTTAAAGACTTTTTTACCTTTAGTTTGCCTGTCAGCTTTGA
64 TTAATTCTGCCTGTCGACTTTGACCTTAAAGACTTTCTTACCTTTAGTCTGCCTGTCAGCTTTGA
*
411207 CCATAGAGACTTCTTTACTTTTAGTCTGCCTATCGGC
129 CCATAGAGACTTCTTTACCTTTAGTCTGCCTATCGGC
* * *
411244 ATTGAC-CTGGAGACTTCCTTATCTTAGTTTGCTTGTCGACTTTGACCCTAGAGACTTCTTACCT
1 -TTGACACTGGAGACTTCCTTACCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTCTTACCT
** * ** *
411308 TAATT-TGTTTGTCGATTTTGACCTTGGAGACTTTCTTACC-TTAGTCTGCTTGTCAGCTTTGA-
65 TAATTCTGCCTGTCGACTTTGACCTTAAAGACTTTCTTACCTTTAGTCTGCCTGTCAGCTTTGAC
*
411370 CACTAGAGACTTCTTTACCTTTAGTCTGCTTATCGGC
130 CA-TAGAGACTTCTTTACCTTTAGTCTGCCTATCGGC
* * * *
411407 TTCGACACTTGAGACTTCCTTACCTTAGTCTGCCTAT-GGCTTTGACCCTAGAAACTTCCTTACC
1 TT-GACACTGGAGACTTCCTTACCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTT-CTTA-C
* * ** * * * *
411471 CTTAA-TCTACCTATCGGTTTTGACCCTAGAGGC-TTCTTTACCTTTAGTCTGCCTGTCGGCTTT
63 CTTAATTCTGCCTGTCGACTTTGACCTTAAAGACTTTC-TTACCTTTAGTCTGCCTGTCAGCTTT
* *
411534 GACCTTGGAGACTTC
127 GACCATAGAGACTTC
411549 CTTATTTTTG
Statistics
Matches: 257, Mismatches: 38, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
162 4 0.02
163 73 0.28
164 60 0.23
165 42 0.16
166 57 0.22
167 16 0.06
168 5 0.02
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (165 bp):
TTGACACTGGAGACTTCCTTACCTTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTCTTACCTT
AATTCTGCCTGTCGACTTTGACCTTAAAGACTTTCTTACCTTTAGTCTGCCTGTCAGCTTTGACC
ATAGAGACTTCTTTACCTTTAGTCTGCCTATCGGC
Found at i:411537 original size:247 final size:248
Alignment explanation
Indices: 411076--411548 Score: 532
Period size: 247 Copynumber: 1.9 Consensus size: 248
411066 GACTTGACCC
*
411076 TTTGACACTGGAGACTTCTTTACCTTTAGTCTGCCTGTCGACTTTGACCTTGGAGACTTTCTTAC
1 TTTGACACTGGAGACTTCTTTACCTTTAGTCTGCCTGTCGACTTTGACCTTAGAGACTTTCTTAC
* * * * ** * *
411141 CTTTATTCTGCCTGTCGGCTTTGACTTTAAAGACTTTTTTACCTTTAGTTTGCCTGTCAGCTTTG
66 CTTTAGTCTGCCTATCGGCTTCGACCTTAAAGACTTCCTTACCTTTAGTCTGCCTATCAGCTTTG
* * ** * * * *
411206 ACCATAGAGACTTCTTTACTTTTAGTCTGCCTATCGGCATTGACCTGGAGACTTCCTTATCTTAG
131 ACCATAGAAACTTCCTTACCCTTAATCTACCTATCGGCATTGACCTAGAGACTTCCTTACCTTAG
* *
411271 TTTGCTTGTCGACTTTGACCCTAGAGACTTCTTACCTTAATTTGTTTGTCGAT
196 TCTGCCTGTCGACTTTGACCCTAGAGACTTCTTACCTTAATTTGTTTGTCGAT
*
411324 TTTGAC-CTTGGAGACTT-TCTTACC-TTAGTCTGCTTGTC-AGCTTTGACAC-TAGAGAC-TTC
1 TTTGACAC-TGGAGACTTCT-TTACCTTTAGTCTGCCTGTCGA-CTTTGAC-CTTAGAGACTTTC
* * *
411383 TTTACCTTTAGTCTGCTTATCGGCTTCGACACTT-GAGACTTCCTTACC-TTAGTCTGCCTAT-G
62 -TTACCTTTAGTCTGCCTATCGGCTTCGAC-CTTAAAGACTTCCTTACCTTTAGTCTGCCTATCA
* ** * *
411445 GCTTTGACCCTAGAAACTTCCTTACCCTTAATCTACCTATCGGTTTTGACCCTAGAGGCTTCTTT
125 GCTTTGACCATAGAAACTTCCTTACCCTTAATCTACCTATCGGCATTGA-CCTAGAGACTTCCTT
* * *
411510 ACCTTTAGTCTGCCTGTCGGCTTTGACCTTGGAGACTTC
189 ACC-TTAGTCTGCCTGTCGACTTTGACCCTAGAGACTTC
411549 CTTATTTTTG
Statistics
Matches: 186, Mismatches: 31, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
245 40 0.22
246 29 0.16
247 94 0.51
248 23 0.12
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (248 bp):
TTTGACACTGGAGACTTCTTTACCTTTAGTCTGCCTGTCGACTTTGACCTTAGAGACTTTCTTAC
CTTTAGTCTGCCTATCGGCTTCGACCTTAAAGACTTCCTTACCTTTAGTCTGCCTATCAGCTTTG
ACCATAGAAACTTCCTTACCCTTAATCTACCTATCGGCATTGACCTAGAGACTTCCTTACCTTAG
TCTGCCTGTCGACTTTGACCCTAGAGACTTCTTACCTTAATTTGTTTGTCGAT
Found at i:412814 original size:10 final size:10
Alignment explanation
Indices: 412802--412840 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
412792 CAAGAGGAAG
412802 AAAAA-AAAA
1 AAAAAGAAAA
*
412811 GAAAAGAAAA
1 AAAAAGAAAA
*
412821 AAAAAGAAAG
1 AAAAAGAAAA
412831 AAAAAGAAAA
1 AAAAAGAAAA
412841 TACTTGGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
9 4 0.16
10 21 0.84
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:412822 original size:14 final size:14
Alignment explanation
Indices: 412799--412840 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
412789 TGACAAGAGG
412799 AAGAAAAAAAAAGAA
1 AAGAAAAAAAAAG-A
412814 AAGAAAAAAAAAGA
1 AAGAAAAAAAAAGA
412828 AAGAAAAAGAAAA
1 AAGAAAAA-AAAA
412841 TACTTGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAAGA
Found at i:416701 original size:20 final size:19
Alignment explanation
Indices: 416667--416704 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
416657 TAACAAGTTA
*
416667 ATTTTATATATAAATATAG
1 ATTTTATAAATAAATATAG
416686 ATTTTAATAAATAAATATA
1 ATTTT-ATAAATAAATATA
416705 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
ATTTTATAAATAAATATAG
Found at i:416708 original size:16 final size:18
Alignment explanation
Indices: 416689--416728 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
416679 AATATAGATT
416689 TTAATAAATAA-ATAT-A
1 TTAATAAATAACATATGA
416705 TTAA-AAATAACATATGA
1 TTAATAAATAACATATGA
416722 -TAATAAA
1 TTAATAAA
416729 AATTTACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (18 bp):
TTAATAAATAACATATGA
Found at i:416933 original size:15 final size:15
Alignment explanation
Indices: 416887--416939 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
416877 AAGCTCAAAT
*
416887 CTAAAAAAATTTAAT
1 CTAAAAAAATTTAAA
* *
416902 TTAAAAAAATCTAAAA
1 CTAAAAAAAT-TTAAA
*
416918 CTAAAATAATTTAAA
1 CTAAAAAAATTTAAA
416933 CATAAAA
1 C-TAAAA
416940 TGATTCAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 14 0.47
16 16 0.53
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (15 bp):
CTAAAAAAATTTAAA
Found at i:417568 original size:24 final size:24
Alignment explanation
Indices: 417479--417569 Score: 69
Period size: 24 Copynumber: 3.8 Consensus size: 24
417469 TAATATTTGT
*
417479 TTTTAAATATATTTTTTAAATATTA
1 TTTT-AATATAGTTTTTAAATATTA
* * *
417504 TTATATTACTA-TTTATAAATATTA
1 TTTTAATA-TAGTTTTTAAATATTA
* * * *
417528 TATTAAAAAAGTATTTAAATATTA
1 TTTTAATATAGTTTTTAAATATTA
417552 TTTTTAATATA-TTTTTAA
1 -TTTTAATATAGTTTTTAA
417570 GTGTAATTTG
Statistics
Matches: 49, Mismatches: 14, Indels: 7
0.70 0.20 0.10
Matches are distributed among these distances:
23 1 0.02
24 36 0.73
25 12 0.24
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (24 bp):
TTTTAATATAGTTTTTAAATATTA
Found at i:418631 original size:15 final size:15
Alignment explanation
Indices: 418598--418637 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
418588 AATGCTTAAT
*
418598 AATATTCAAAATAAA
1 AATATTGAAAATAAA
* *
418613 AATATTGAAAATTAC
1 AATATTGAAAATAAA
418628 AATATTGAAA
1 AATATTGAAA
418638 TAATTTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (15 bp):
AATATTGAAAATAAA
Found at i:419815 original size:29 final size:29
Alignment explanation
Indices: 419785--419849 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 29
419775 ATAATTTGAT
* *
419785 TTACTTTTTAAAGTTT-ATGTAATATATA
1 TTACTTTTTAAAGTTTAATATAAAATATA
419813 TT--TTTTTAAAGTTTAATATAAAATATA
1 TTACTTTTTAAAGTTTAATATAAAATATA
419840 CTTACTTTTT
1 -TTACTTTTT
419850 TTAAATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 12 0.39
27 10 0.32
28 4 0.13
30 5 0.16
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (29 bp):
TTACTTTTTAAAGTTTAATATAAAATATA
Found at i:420425 original size:23 final size:24
Alignment explanation
Indices: 420392--420439 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
420382 CTAAAATTTT
* *
420392 AAATAATAATA-ATTAATTAATTA
1 AAATAAAAATATATTAATAAATTA
*
420415 AAATAAAAATATTTTAATAAATTA
1 AAATAAAAATATATTAATAAATTA
420439 A
1 A
420440 TTTCAAAGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATAAAAATATATTAATAAATTA
Found at i:421261 original size:430 final size:429
Alignment explanation
Indices: 420789--421651 Score: 1602
Period size: 430 Copynumber: 2.0 Consensus size: 429
420779 TAAATACCTT
420789 TAAAAAAAAGAATTTTGGGTGGGTGGTTTTCTAAAACAAAAGGGTAATTTTTTGAAGGAAGTACT
1 TAAAAAAAAGAATTTTGGGTGGGTGGTTTTCTAAAACAAAAGGGTAATTTTTTGAAGGAAGTACT
* *
420854 TAATTTTTTAACTAAATTTGGATGGCTCTTTTAAAATTTTTATTAATGACTTTAAAAATTATTTT
66 TAATTTTTTAACTAAATTTGGATGGCCCTTTTAAAATTTTTATTAATGACTTTAAAAATGATTTT
*
420919 ATTGAATTATTAAAATATTTTGATAATTTATAATCAAAATTATTTTTACAGTATATCTACTTTAT
131 ATTGAATTATTAAAATATTTTGATAATTTATAATCAAAATTATTTTTACAGTATAACTACTTTAT
*
420984 ATATAACATGTTTTTTTGCAATAATATTTATCTTTATGTAAAAACAATAAAAAAATTGAAAAAAA
196 ATATAACATGTTTTTTTGCAATAATATTTATCTTTATGTAAAAACAAT-AAAAAATTAAAAAAAA
* *
421049 ATTAAAAAAATATGAG-TTTTTTTAATACTTTGACTTGTATCAATCAAGTCACGTAGATACATGA
260 ATTAAAAAAATATGAGTTTTTTTTAATACTTTGACTTGCATCAACCAAGTCACGTAGATACATGA
421113 ATATTTTTATTATTTTTTTAAAATTTTTGACTAAAATATGAAGGAATGGTGAAAATTTTTAAAAA
325 ATATTTTTATTATTTTTTT-AAATTTTTGACTAAAATATGAAGGAATGGTGAAAATTTTTAAAAA
*
421178 GTTCTGGATAATAAATATATTTTTTAAAAATCATGAATAAA
389 GTTATGGATAATAAATATATTTTTTAAAAATCATGAATAAA
*
421219 TAAAAAAAGGAATTTTGGGTGGGTGGTTTTCTAAAACAAAAGGGTAATTTTTTGAAGGAAGTACT
1 TAAAAAAAAGAATTTTGGGTGGGTGGTTTTCTAAAACAAAAGGGTAATTTTTTGAAGGAAGTACT
421284 TAATTTTTTAACTAAATTTGGATGGCCCTTTTAAAATTTTTATTAATGACTTTAAAAATGATTTT
66 TAATTTTTTAACTAAATTTGGATGGCCCTTTTAAAATTTTTATTAATGACTTTAAAAATGATTTT
421349 ATTGAATTATTAAAATATTTTGATAATTTATAATCAAAATTATTTTTACAGTATAACTACTTTAT
131 ATTGAATTATTAAAATATTTTGATAATTTATAATCAAAATTATTTTTACAGTATAACTACTTTAT
421414 ATATAACATGTTTTTTTGCAATAATATTTATCTTTATGTAAAAACAATAAAAAATTAAAAAAAAA
196 ATATAACATGTTTTTTTGCAATAATATTTATCTTTATGTAAAAACAATAAAAAATTAAAAAAAAA
*
421479 TTAAAAAAATATGAGTTTTTTTTAATACTTTGACTTGCATCAACCAAGTCACGTGGATACATGAA
261 TTAAAAAAATATGAGTTTTTTTTAATACTTTGACTTGCATCAACCAAGTCACGTAGATACATGAA
*
421544 TATTTTTATTATTTTTTTAAATTTTTGACTAAAATATGAAGGAATGGTGAAAATTTTTGAAAAGT
326 TATTTTTATTATTTTTTTAAATTTTTGACTAAAATATGAAGGAATGGTGAAAATTTTTAAAAAGT
*
421609 TATGGATAATAAATATATTTTTTTAAAATCATGAATAAA
391 TATGGATAATAAATATATTTTTTAAAAATCATGAATAAA
421648 TAAA
1 TAAA
421652 TATAATTTTA
Statistics
Matches: 421, Mismatches: 11, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
429 118 0.28
430 303 0.72
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (429 bp):
TAAAAAAAAGAATTTTGGGTGGGTGGTTTTCTAAAACAAAAGGGTAATTTTTTGAAGGAAGTACT
TAATTTTTTAACTAAATTTGGATGGCCCTTTTAAAATTTTTATTAATGACTTTAAAAATGATTTT
ATTGAATTATTAAAATATTTTGATAATTTATAATCAAAATTATTTTTACAGTATAACTACTTTAT
ATATAACATGTTTTTTTGCAATAATATTTATCTTTATGTAAAAACAATAAAAAATTAAAAAAAAA
TTAAAAAAATATGAGTTTTTTTTAATACTTTGACTTGCATCAACCAAGTCACGTAGATACATGAA
TATTTTTATTATTTTTTTAAATTTTTGACTAAAATATGAAGGAATGGTGAAAATTTTTAAAAAGT
TATGGATAATAAATATATTTTTTAAAAATCATGAATAAA
Found at i:421476 original size:11 final size:11
Alignment explanation
Indices: 421462--421487 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
421452 TAAAAACAAT
421462 AAAAAATTAAA
1 AAAAAATTAAA
421473 AAAAAATTAAA
1 AAAAAATTAAA
421484 AAAA
1 AAAA
421488 TATGAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAATTAAA
Found at i:421677 original size:30 final size:30
Alignment explanation
Indices: 421616--421677 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
421606 AGTTATGGAT
* ** *
421616 AATAAATATATTTTTTTAAAATCATGAATA
1 AATAAATATAATTTTAAAAAATCATCAATA
421646 AATAAATATAATTTTAAAAAATCA-CATATA
1 AATAAATATAATTTTAAAAAATCATCA-ATA
421676 AA
1 AA
421678 AATGAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (30 bp):
AATAAATATAATTTTAAAAAATCATCAATA
Found at i:422257 original size:21 final size:21
Alignment explanation
Indices: 422231--422273 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
422221 GCATCGATGC
422231 TTGGACAAATAACATAATCTA
1 TTGGACAAATAACATAATCTA
422252 TTGGACAAATAACATAATCTA
1 TTGGACAAATAACATAATCTA
422273 T
1 T
422274 GAACACCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (21 bp):
TTGGACAAATAACATAATCTA
Found at i:423853 original size:2 final size:2
Alignment explanation
Indices: 423846--423883 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
423836 GAATAATTAG
**
423846 AC AC AC AC TG AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
423884 TTCACTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.47, G:0.03, T:0.03
Consensus pattern (2 bp):
AC
Found at i:425131 original size:17 final size:18
Alignment explanation
Indices: 425099--425132 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
425089 ATAATTTTAT
*
425099 ATTAATATTTATATAATA
1 ATTAATATTTAAATAATA
425117 ATTAA-ATTTAAATAAT
1 ATTAATATTTAAATAAT
425133 TTTTTTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTAATATTTAAATAATA
Done.