Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021185.1 Corchorus olitorius cultivar O-4 contig21218, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 215013
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1499 original size:27 final size:27
Alignment explanation
Indices: 1458--1555 Score: 142
Period size: 27 Copynumber: 3.6 Consensus size: 27
1448 AGTGAGCTTA
* *
1458 AAATGACCAAAATGCCCCTGAATGTGT
1 AAATGACAAAAATGCCCCTGAATGTGC
* * *
1485 AAATGACCAAGATGCCCTTGAATGTGC
1 AAATGACAAAAATGCCCCTGAATGTGC
*
1512 AAATGACAAAAATGCCCCTGGATGTGC
1 AAATGACAAAAATGCCCCTGAATGTGC
1539 AAATGACAAAAATGCCC
1 AAATGACAAAAATGCCC
1556 TATATATGAC
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACAAAAATGCCCCTGAATGTGC
Found at i:2805 original size:10 final size:10
Alignment explanation
Indices: 2790--2818 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2780 TTTGTACTTA
2790 TAACTTTGTG
1 TAACTTTGTG
2800 TAACTTTGTG
1 TAACTTTGTG
2810 TAACTTTGT
1 TAACTTTGT
2819 TCATGAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.17, T:0.52
Consensus pattern (10 bp):
TAACTTTGTG
Found at i:4937 original size:2 final size:2
Alignment explanation
Indices: 4930--4960 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4920 TAATATTTAG
4930 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4961 CATTTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20662 original size:10 final size:9
Alignment explanation
Indices: 20644--20701 Score: 50
Period size: 10 Copynumber: 6.4 Consensus size: 9
20634 TAAAAGTAAC
20644 TAAGAAAAA
1 TAAGAAAAA
20653 TAACGAAAAA
1 TAA-GAAAAA
*
20663 TTAA-AGAAA
1 -TAAGAAAAA
20672 -AAGAAAAA
1 TAAGAAAAA
20680 TAACGAAAAA
1 TAA-GAAAAA
*
20690 TAA-AAAGA
1 TAAGAAAAA
20698 TAAG
1 TAAG
20702 GGTAAGAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
7 2 0.05
8 11 0.28
9 9 0.22
10 15 0.38
11 3 0.08
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (9 bp):
TAAGAAAAA
Found at i:20687 original size:16 final size:17
Alignment explanation
Indices: 20657--20695 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
20647 GAAAAATAAC
20657 GAAAAATTAAAGAAAAA
1 GAAAAATTAAAGAAAAA
*
20674 GAAAAA-TAACGAAAAA
1 GAAAAATTAAAGAAAAA
*
20690 TAAAAA
1 GAAAAA
20696 GATAAGGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (17 bp):
GAAAAATTAAAGAAAAA
Found at i:22427 original size:76 final size:76
Alignment explanation
Indices: 22277--22420 Score: 175
Period size: 76 Copynumber: 1.9 Consensus size: 76
22267 ACTAGGATCC
* * * * *
22277 CGACTCCATCTGGGCGCCCACATGGTTGCCTTGAGGACCCATGTGGTTTGCTTGAGAACCCAGGT
1 CGACTCCAGCTGGGCGCCCACATGGTTGCCTTGAAGACCCATGTGGTTTACCTGAGAACCCAGAT
22342 GGGCAGTGTCA
66 GGGCAGTGTCA
* * **
22353 CGACTCCAGCTGGGTGCCCACATGGTTTGTC-TGAAGACCCATGT-GTTTCACCTGATCACCCAG
1 CGACTCCAGCTGGGCGCCCACATGG-TTGCCTTGAAGACCCATGTGGTTT-ACCTGAGAACCCAG
22416 ATGGG
64 ATGGG
22421 TTGTGTCTTA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
75 4 0.07
76 49 0.86
77 4 0.07
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.24
Consensus pattern (76 bp):
CGACTCCAGCTGGGCGCCCACATGGTTGCCTTGAAGACCCATGTGGTTTACCTGAGAACCCAGAT
GGGCAGTGTCA
Found at i:30243 original size:27 final size:27
Alignment explanation
Indices: 30205--30295 Score: 137
Period size: 27 Copynumber: 3.4 Consensus size: 27
30195 GTACTTGAAG
* **
30205 TGACCAAAATGCCCTTGGATGTGCAAA
1 TGACCAAAATGCCCCTGGACATGCAAA
30232 TGACCAAAATGCCCCTGGACATGCAAA
1 TGACCAAAATGCCCCTGGACATGCAAA
*
30259 TGACCAAAATGCCCCTGGACATGTAAA
1 TGACCAAAATGCCCCTGGACATGCAAA
*
30286 TGACAAAAAT
1 TGACCAAAAT
30296 AAGAATTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (27 bp):
TGACCAAAATGCCCCTGGACATGCAAA
Found at i:36196 original size:8 final size:8
Alignment explanation
Indices: 36185--36219 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
36175 CAAAAAAATG
*
36185 AAAATAAA
1 AAAACAAA
36193 AAAACAAA
1 AAAACAAA
36201 AAAACAAA
1 AAAACAAA
36209 AAAATCAAA
1 AAAA-CAAA
36218 AA
1 AA
36220 TCAAAAATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 19 0.76
9 6 0.24
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.06
Consensus pattern (8 bp):
AAAACAAA
Found at i:36980 original size:50 final size:50
Alignment explanation
Indices: 36832--36980 Score: 192
Period size: 50 Copynumber: 3.0 Consensus size: 50
36822 GTTTTATAAC
* * * ** *
36832 AAGATTTCTTTCCATTTATGAGTTCAAGATCAAAATTAACTTTTCAAAAT
1 AAGATTGCTTTCCAGTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGT
* *
36882 AAAATTGCTTTCC-GTTTGTGAGTTCAAGATTAAAATTCGCTTTTCAAAGT
1 AAGATTGCTTTCCAG-TTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGT
* *
36932 AAGATTGCATTCCAGTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAG
1 AAGATTGCTTTCCAGTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAG
36981 GGCATTTAAG
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
50 84 0.99
51 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (50 bp):
AAGATTGCTTTCCAGTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAGT
Found at i:37332 original size:27 final size:27
Alignment explanation
Indices: 37261--37334 Score: 68
Period size: 26 Copynumber: 2.8 Consensus size: 27
37251 TCAGCATGAA
*
37261 CAAGAAAGCAA-ATTC-AAGGACAAAT
1 CAAGAAAGCAAGATTCGAAGCACAAAT
*
37286 CAAGAAGAGC-AGAAAT-GAAGCAC-AAT
1 CAAGAA-AGCAAG-ATTCGAAGCACAAAT
37312 CAAGAAAGCAAGGATTCGAAGCA
1 CAAGAAAGCAA-GATTCGAAGCA
37335 ACAGTCCAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
25 10 0.26
26 15 0.38
27 14 0.36
ACGTcount: A:0.53, C:0.16, G:0.22, T:0.09
Consensus pattern (27 bp):
CAAGAAAGCAAGATTCGAAGCACAAAT
Found at i:37598 original size:50 final size:50
Alignment explanation
Indices: 37523--37706 Score: 278
Period size: 50 Copynumber: 3.7 Consensus size: 50
37513 GAATGCTTAA
37523 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGG
1 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGG
* * *
37573 GCTTTTCCATAAGCCAAACTCGTTTCCAGACGAGTCAATCATCAACATGG
1 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGG
**
37623 GCTTTTCCACAAGCCAAACTCGCGTCCATACGAGTCAATTATCAACATGG
1 GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGG
* * **
37673 GCTTCTCCATAAGCCACAGTTCGTTTCCATACGA
1 GCTTTTCCACAAGCCA-AACTCGTTTCCATACGA
37707 TACATTACCA
Statistics
Matches: 119, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 106 0.89
51 13 0.11
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (50 bp):
GCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATGG
Found at i:37772 original size:35 final size:35
Alignment explanation
Indices: 37722--37917 Score: 293
Period size: 35 Copynumber: 5.6 Consensus size: 35
37712 TACCATCTTC
* * ** *
37722 TCAGATCACTTGGTGTAGCATCTTCAAAGTTATAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGACAAAT
** *
37757 TCAGATGACTCGGTGTAGCATCTTCAAAGTTATAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGACAAAT
37792 TCAGATGACTCGGTGTAGCATCTTCAAAGACAAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGACAAAT
**
37827 TCAGATGACTCATTGTAGCATCTTCAAAGACAAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGACAAAT
37862 TCAGATGACTCGGTGTAGCATCTTCAAAGACAAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGACAAAT
*
37897 TCAGATGACTCGGTGCAGCAT
1 TCAGATGACTCGGTGTAGCAT
37918 GATCTAGCCA
Statistics
Matches: 151, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 151 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (35 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGACAAAT
Found at i:41933 original size:20 final size:20
Alignment explanation
Indices: 41908--41950 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
41898 CAACTCAGAC
41908 ATCTCAAGCCAAAAGACACA
1 ATCTCAAGCCAAAAGACACA
41928 ATCTCAAGCCAAAAGACACA
1 ATCTCAAGCCAAAAGACACA
41948 ATC
1 ATC
41951 ATGCTGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.30, G:0.09, T:0.12
Consensus pattern (20 bp):
ATCTCAAGCCAAAAGACACA
Found at i:43821 original size:11 final size:12
Alignment explanation
Indices: 43798--43825 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
43788 TTATTTCCCC
43798 AATTTTTGAAAA
1 AATTTTTGAAAA
43810 AATTTTTGAAAA
1 AATTTTTGAAAA
43822 AATT
1 AATT
43826 GATTTTTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
AATTTTTGAAAA
Found at i:46663 original size:35 final size:35
Alignment explanation
Indices: 46551--46666 Score: 164
Period size: 35 Copynumber: 3.3 Consensus size: 35
46541 GACCGATCAC
*
46551 AGCATCTTCAAA-AACAAATTCAGATGACTCGGTGT
1 AGCATCTTCAAAGAA-TAATTCAGATGACTCGGTGT
* *
46586 AGCATCTCCAAAG-TTGAATTCAGATGACTCGGTGT
1 AGCATCTTCAAAGAAT-AATTCAGATGACTCGGTGT
*
46621 AGCATCTTCAAAGAATAATTCAGATGACTCGGTGA
1 AGCATCTTCAAAGAATAATTCAGATGACTCGGTGT
46656 AGCATCTTCAA
1 AGCATCTTCAA
46667 TATGGGCTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
35 71 0.99
36 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (35 bp):
AGCATCTTCAAAGAATAATTCAGATGACTCGGTGT
Found at i:71264 original size:50 final size:50
Alignment explanation
Indices: 71189--71435 Score: 397
Period size: 50 Copynumber: 4.9 Consensus size: 50
71179 TGGCTCGACC
* * *
71189 ATGCTCATTATCTTGGCTTGTTGCAATGTGGAACTTCTTTGTGACTTGAT
1 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCTTTGTGACTTGAT
71239 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAACTTT-TTTGTGACTTGAT
1 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAA-TTTCTTTGTGACTTGAT
*
71289 ATGCTCATCAACTTGGCTTGCTGCAATGTGGAATTTCTTTGTGACTTGAT
1 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCTTTGTGACTTGAT
* * * *
71339 ATGCTCATCATCTTCGCTTGCTGCAAAGTGGAATTTCCTTGTGACTCGAT
1 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCTTTGTGACTTGAT
*
71389 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCCTTGTGACTT
1 ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCTTTGTGACTT
71436 ATCATGTTTG
Statistics
Matches: 183, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
49 3 0.02
50 178 0.97
51 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (50 bp):
ATGCTCATCATCTTGGCTTGCTGCAATGTGGAATTTCTTTGTGACTTGAT
Found at i:72814 original size:27 final size:27
Alignment explanation
Indices: 72766--72836 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
72756 ACTTGAAGTA
* *
72766 ACCAAAATGCCCCTAGATGTGCAAATG
1 ACCAAAATGCCCCTGGACGTGCAAATG
*
72793 ACCAAAATGCTCCTGGACGTGCAAATG
1 ACCAAAATGCCCCTGGACGTGCAAATG
72820 ACCAAAATGCCCCTGGA
1 ACCAAAATGCCCCTGGA
72837 AATGTAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (27 bp):
ACCAAAATGCCCCTGGACGTGCAAATG
Found at i:73927 original size:87 final size:85
Alignment explanation
Indices: 73766--73928 Score: 220
Period size: 87 Copynumber: 1.9 Consensus size: 85
73756 AAATATTAAC
* * * *
73766 AAAGTTGAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGGTTTAGGAGATTTT
1 AAAGTTGAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAAAATAT
* *
73831 TTAAGAAATAAATAAATTAT
66 TAAAAAAATAAATAAATTAT
* *
73851 AAAGTTGAATCATAATGAGAATATTTTTTTTAAATCTTGCCAAATTGTGGGAGATTT-GGAAAAT
1 AAAGTTGAATAATAATGAGAATA--TTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAAAAT
73915 ATTAAATAAAATAA
64 ATTAAA-AAAATAA
73929 TAATAAAAGG
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
85 22 0.33
86 9 0.13
87 36 0.54
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.36
Consensus pattern (85 bp):
AAAGTTGAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTAGGAAAATAT
TAAAAAAATAAATAAATTAT
Found at i:74679 original size:327 final size:328
Alignment explanation
Indices: 74252--74913 Score: 1121
Period size: 327 Copynumber: 2.0 Consensus size: 328
74242 TTGTCATTTT
* *
74252 GACAGGCGTTGTTGGGGTGCTAATACCTTCCCTACACGTAATCGAACCCCCGGACCCAAAATTTG
1 GACAGGCGTTGTAGGGGTGCTAATACCTTCCCTACACGTAATCGAACCCCCGAACCCAAAATTTG
* *
74317 GTAACAAAGACCAATGTTTGATCTTTATTAATGAACTTAATTTAACATCAAGGGCACATTAAAAT
66 GTAACAAAGACCAATGTTTGATCATTATTAATGAACTTAATTTAACATCAAGGACACATTAAAAT
* *
74382 GGTTAATCAAATTTAGGT-CGCCAATCACACCTAGAAAAAAGATTGGTGGCGACTCCTTTGCAAT
131 GGTTAATCAAATTTAGGTGC-CCAATCACACCTAGAAAAAAGAATGGTGGCGACTCCTTTCCAAT
* * *
74446 GCGTCTAGCGCTCAAGTCTCGCGA-TTGCACGTTACGATAGTTGCTCAGGCACACAAATTTCATG
195 GCGTCTAGCGCTCAAGTCTCACGATTTGCACGTTACAACAGTTGCTCAGGCACACAAATTTCATG
74510 GAAGGTGCTCTTTCCAATATGTCCGGACTTTCAATCCAAGGTGAGGAAGGAGATGCTGTGGCGGT
260 GAAGGTGCTCTTTCCAATATGTCCGGACTTTCAATCCAAGGTGAGGAAGGAGATGCTGTGGCGGT
74575 TGCC
325 TGCC
*
74579 GACATGCGTTGTAGGGGTGCTAATACCTTCCCTACACGTAATCGAACCCCCGAACCCAAAATTTG
1 GACAGGCGTTGTAGGGGTGCTAATACCTTCCCTACACGTAATCGAACCCCCGAACCCAAAATTTG
* *
74644 GTAACAAAGACCAATGTTTGATCATTATTAATGAACTTAATTTAACATTAAGGACAGATTAAAAT
66 GTAACAAAGACCAATGTTTGATCATTATTAATGAACTTAATTTAACATCAAGGACACATTAAAAT
*
74709 GGTTAATCAAATTTAGGTGCCCAATCACACCTAGATAAAAGAATGGTGGCGACTCCTTTCCAATG
131 GGTTAATCAAATTTAGGTGCCCAATCACACCTAGAAAAAAGAATGGTGGCGACTCCTTTCCAATG
* * *
74774 CGTCTAGCGCTCAAGTCTCACGATTTGCACGTTACAACAGTTTCTCAGGTACACAAATTTTATGG
196 CGTCTAGCGCTCAAGTCTCACGATTTGCACGTTACAACAGTTGCTCAGGCACACAAATTTCATGG
* * *
74839 AAGGTGCTCTTTCCAATATGTTCGGACTTTCAATCCAAGGTGAGGAAGGAGATGTTGTGTCGGTT
261 AAGGTGCTCTTTCCAATATGTCCGGACTTTCAATCCAAGGTGAGGAAGGAGATGCTGTGGCGGTT
74904 GCC
326 GCC
74907 GATCAGG
1 GA-CAGG
74914 ATTGGTTGGG
Statistics
Matches: 312, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
327 205 0.66
328 104 0.33
329 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (328 bp):
GACAGGCGTTGTAGGGGTGCTAATACCTTCCCTACACGTAATCGAACCCCCGAACCCAAAATTTG
GTAACAAAGACCAATGTTTGATCATTATTAATGAACTTAATTTAACATCAAGGACACATTAAAAT
GGTTAATCAAATTTAGGTGCCCAATCACACCTAGAAAAAAGAATGGTGGCGACTCCTTTCCAATG
CGTCTAGCGCTCAAGTCTCACGATTTGCACGTTACAACAGTTGCTCAGGCACACAAATTTCATGG
AAGGTGCTCTTTCCAATATGTCCGGACTTTCAATCCAAGGTGAGGAAGGAGATGCTGTGGCGGTT
GCC
Found at i:77461 original size:76 final size:76
Alignment explanation
Indices: 77324--77464 Score: 187
Period size: 76 Copynumber: 1.9 Consensus size: 76
77314 TGGCTGTCCC
* * *
77324 CGACTCTACCTGGGCGCCCACGTGGTTGCCTTGAATACCCATGTGATTTCCTTGAGGACCCAGGT
1 CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAAGACCCATGTGATTTCCTTGAGCACCCAGGT
77389 GGGCAATGTCA
66 GGGCAATGTCA
* * * *
77400 CGACTCTACCTGGGTGCCCACATGGTTTG-TTTGAGGACCCATGTGATGTTCC-TGATCACCCAG
1 CGACTCTACCTGGGCGCCCACATGG-TTGCCTTGAAGACCCATGTGAT-TTCCTTGAGCACCCAG
77463 GT
64 GT
77465 AAGCTGTGTC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
76 49 0.88
77 7 0.12
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (76 bp):
CGACTCTACCTGGGCGCCCACATGGTTGCCTTGAAGACCCATGTGATTTCCTTGAGCACCCAGGT
GGGCAATGTCA
Found at i:81532 original size:18 final size:18
Alignment explanation
Indices: 81509--81543 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
81499 CATAAACAAC
*
81509 TTCAAATACTCAACCTCT
1 TTCAAACACTCAACCTCT
81527 TTCAAACACTCAACCTC
1 TTCAAACACTCAACCTC
81544 ATTCTTCAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.37, G:0.00, T:0.29
Consensus pattern (18 bp):
TTCAAACACTCAACCTCT
Found at i:83627 original size:55 final size:55
Alignment explanation
Indices: 83567--83672 Score: 212
Period size: 55 Copynumber: 1.9 Consensus size: 55
83557 AAACAAGGTA
83567 ATGCTAATTTTAGGGTGTAAGCCCCTAAGTGGCAAAGTGGCCTTAGTCTTGAGTG
1 ATGCTAATTTTAGGGTGTAAGCCCCTAAGTGGCAAAGTGGCCTTAGTCTTGAGTG
83622 ATGCTAATTTTAGGGTGTAAGCCCCTAAGTGGCAAAGTGGCCTTAGTCTTG
1 ATGCTAATTTTAGGGTGTAAGCCCCTAAGTGGCAAAGTGGCCTTAGTCTTG
83673 TGTGGAGCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (55 bp):
ATGCTAATTTTAGGGTGTAAGCCCCTAAGTGGCAAAGTGGCCTTAGTCTTGAGTG
Found at i:91717 original size:20 final size:20
Alignment explanation
Indices: 91692--91731 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
91682 TCATGAAGAA
*
91692 AAGTATTGTATATGGTTTTC
1 AAGTATTGCATATGGTTTTC
91712 AAGTATTGCATATGGTTTTC
1 AAGTATTGCATATGGTTTTC
91732 TCTGTCTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (20 bp):
AAGTATTGCATATGGTTTTC
Found at i:92836 original size:35 final size:35
Alignment explanation
Indices: 92785--92851 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
92775 GGATATTGTT
*
92785 GTGTAGTGATTACATTTGATGGAATAGCATTCTAA
1 GTGTAGTGATGACATTTGATGGAATAGCATTCTAA
*
92820 GTGTAGTGATGGCATTTGATGGAATAGCATTC
1 GTGTAGTGATGACATTTGATGGAATAGCATTC
92852 CTTGTGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.27, T:0.36
Consensus pattern (35 bp):
GTGTAGTGATGACATTTGATGGAATAGCATTCTAA
Found at i:101016 original size:13 final size:13
Alignment explanation
Indices: 100994--101033 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
100984 TGGAGAATAT
100994 TATCAACAGAAGA
1 TATCAACAGAAGA
*
101007 TATCATCAGAAGA
1 TATCAACAGAAGA
* *
101020 TTTCAACTGAAGA
1 TATCAACAGAAGA
101033 T
1 T
101034 TATCTGGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (13 bp):
TATCAACAGAAGA
Found at i:101046 original size:11 final size:11
Alignment explanation
Indices: 101026--101056 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
101016 AAGATTTCAA
101026 CTGAAGATTAT
1 CTGAAGATTAT
*
101037 CTGGAGATTAT
1 CTGAAGATTAT
101048 CTGAAGATT
1 CTGAAGATT
101057 TAAGTAGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (11 bp):
CTGAAGATTAT
Found at i:101514 original size:15 final size:16
Alignment explanation
Indices: 101494--101523 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
101484 GATCTTCCAA
101494 TCTTAAGTT-TTTATT
1 TCTTAAGTTGTTTATT
101509 TCTTAAGTTGTTTAT
1 TCTTAAGTTGTTTAT
101524 ATTATTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (16 bp):
TCTTAAGTTGTTTATT
Found at i:101616 original size:41 final size:41
Alignment explanation
Indices: 101561--101671 Score: 109
Period size: 40 Copynumber: 2.7 Consensus size: 41
101551 ATATTATTTA
** * * *
101561 AAAATTACCATTGACACCAAAAGTTGTCTCTTTGGTAAATT
1 AAAATTACTTTTGACACCAAAAGTTGTCACTCTAGTAAATT
* *
101602 AAAATTACTTTTGACACTAGAAG-TGTCACTCTAGTAAATT
1 AAAATTACTTTTGACACCAAAAGTTGTCACTCTAGTAAATT
* * *
101642 ATAATTA-TTGTTAACACCAAAAATTGTCAC
1 AAAATTACTT-TTGACACCAAAAGTTGTCAC
101672 CTTGAATTAC
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
39 2 0.04
40 29 0.52
41 25 0.45
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (41 bp):
AAAATTACTTTTGACACCAAAAGTTGTCACTCTAGTAAATT
Found at i:103002 original size:27 final size:26
Alignment explanation
Indices: 102947--103007 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 26
102937 CGTGAAGGCT
102947 AAGGGAAGAAGAAGAAATAACAAAGG
1 AAGGGAAGAAGAAGAAATAACAAAGG
102973 AAGAGGAAGAAGAAGAAA-ACACATAA-G
1 AAG-GGAAGAAGAAGAAATA-ACA-AAGG
103000 AAGGGAAG
1 AAGGGAAG
103008 GCTGGGCTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 9 0.28
27 21 0.66
28 2 0.06
ACGTcount: A:0.61, C:0.05, G:0.31, T:0.03
Consensus pattern (26 bp):
AAGGGAAGAAGAAGAAATAACAAAGG
Found at i:107413 original size:21 final size:22
Alignment explanation
Indices: 107389--107431 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
107379 TTTTCCTCAT
107389 GCATTCATTCAT-CATGCCATG
1 GCATTCATTCATGCATGCCATG
* *
107410 GCATTCGTTCATGCATTCCATG
1 GCATTCATTCATGCATGCCATG
107432 AAGCCTTAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.35
Consensus pattern (22 bp):
GCATTCATTCATGCATGCCATG
Found at i:112468 original size:50 final size:51
Alignment explanation
Indices: 112390--112541 Score: 191
Period size: 50 Copynumber: 3.0 Consensus size: 51
112380 GTTTTATAAT
112390 AAGATTGCATTCCATTTGTGAGGT-CAAGATCAAAATTCGCTTTTCAAAATC
1 AAGATTGCATTCCATTTGTGA-GTCCAAGATCAAAATTCGCTTTTCAAAATC
* * * *
112441 AA-ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTTGCTTGTCAAAGTT
1 AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAATC
* * * *
112491 AAGATTGCACTCCATTTGTGAGACCAAGACCAAAAGCTCGCTTTTTCAAAA
1 AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAA-TTCGC-TTTTCAAAA
112542 GGCATTTTAG
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
49 2 0.02
50 43 0.50
51 31 0.36
52 3 0.03
53 7 0.08
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.32
Consensus pattern (51 bp):
AAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAAATC
Found at i:113399 original size:69 final size:69
Alignment explanation
Indices: 113173--113629 Score: 670
Period size: 69 Copynumber: 6.7 Consensus size: 69
113163 TCAATTAGCA
* * *
113173 ACATAAGCTTTTCCACAAGCCAAACTCGTTTCCATAAG-GATAAGTT-AAGCCTTGGTTCCATCC
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAG-TCAGTTGAAGCCTTGGTTCCATCC
113236 AAGCC
65 AAGCC
* * * *
113241 ACATAGGCTTTTCCACAAGCCAAACTCATTTCCATACGGGTAAGTT-AAACCTTGGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCA
*
113305 AACC
66 AGCC
*
113309 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCA
113374 AGCC
66 AGCC
* *
113378 ACATAGGTTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCCTCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCA
113443 AGCC
66 AGCC
* * *
113447 ACATAGGTTTTTCCACAAGCCAAACTCATTTCCATACGAGTCAGTTGAAGCCTTGGTTCTATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCA
113512 AGCC
66 AGCC
* * *
113516 ACGTAGGCTTGTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTAGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCA
113581 AGCC
66 AGCC
* * * * * *
113585 A-TTAGACTTTTCCATAAGTCAAACTCATTTCCATGCGAGTCAGTT
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTT
113630 TAAACATTTG
Statistics
Matches: 358, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
68 141 0.39
69 217 0.61
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.28
Consensus pattern (69 bp):
ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTGAAGCCTTGGTTCCATCCA
AGCC
Found at i:116258 original size:22 final size:22
Alignment explanation
Indices: 116215--116258 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
116205 ATCTCTTGGA
* *
116215 TTCTCCTTCATTCACACCCCCT
1 TTCTCATTCATTCACACACCCT
*
116237 TTCTCATTCATTCACAGACCCT
1 TTCTCATTCATTCACACACCCT
116259 CTCGAGACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.18, C:0.43, G:0.02, T:0.36
Consensus pattern (22 bp):
TTCTCATTCATTCACACACCCT
Found at i:120248 original size:11 final size:11
Alignment explanation
Indices: 120232--120264 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
120222 ATTTGCTTTA
120232 GTTGGGATTTT
1 GTTGGGATTTT
120243 GTTGGGATTTT
1 GTTGGGATTTT
120254 GTTGGGATTTT
1 GTTGGGATTTT
120265 ATTTTTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.09, C:0.00, G:0.36, T:0.55
Consensus pattern (11 bp):
GTTGGGATTTT
Found at i:124412 original size:19 final size:18
Alignment explanation
Indices: 124379--124414 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
124369 TTGAAATTAT
124379 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
124397 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
124415 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:126926 original size:22 final size:22
Alignment explanation
Indices: 126901--126976 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
126891 TTGCCTTCTT
* *
126901 GTCGACACTTGCTTCTTCTTAA
1 GTCGACAATTGCTTCCTCTTAA
*
126923 GTCGATAATTGCTTCCTCTTAA
1 GTCGACAATTGCTTCCTCTTAA
* **
126945 GTCGACTATTTTTTCCTCTTTAA
1 GTCGACAATTGCTTCCTC-TTAA
126968 GTCGACAAT
1 GTCGACAAT
126977 CCCTTTGTCG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.21, C:0.24, G:0.13, T:0.42
Consensus pattern (22 bp):
GTCGACAATTGCTTCCTCTTAA
Found at i:127536 original size:25 final size:24
Alignment explanation
Indices: 127502--127549 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
127492 CCTGCCATCA
*
127502 CGCAGCGGCAGCAGCAGGCTTGCTC
1 CGCAGAGGCAGCAGC-GGCTTGCTC
*
127527 CGCAGAGGCAGCAGCTGCTTGCT
1 CGCAGAGGCAGCAGCGGCTTGCT
127550 GCGGTGTAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.17, C:0.33, G:0.35, T:0.15
Consensus pattern (24 bp):
CGCAGAGGCAGCAGCGGCTTGCTC
Found at i:132768 original size:6 final size:6
Alignment explanation
Indices: 132757--132785 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
132747 CAAATTAAAT
132757 AGAAAA AG-AAA AGAAAA AGAAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
132786 TAATAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:134323 original size:19 final size:18
Alignment explanation
Indices: 134290--134325 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
134280 TTGAAATTAT
134290 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
134308 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
134326 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:137772 original size:21 final size:21
Alignment explanation
Indices: 137748--137787 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
137738 TTGTTTAAGA
* *
137748 GAGAAGTCGACTTGAGCAAGG
1 GAGAAATCGACTTAAGCAAGG
137769 GAGAAATCGACTTAAGCAA
1 GAGAAATCGACTTAAGCAA
137788 ATCGATTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.15, G:0.30, T:0.15
Consensus pattern (21 bp):
GAGAAATCGACTTAAGCAAGG
Found at i:141792 original size:11 final size:11
Alignment explanation
Indices: 141776--141802 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
141766 GATTCTATAG
141776 AAGATTTCTCA
1 AAGATTTCTCA
141787 AAGATTTCTCA
1 AAGATTTCTCA
141798 AAGAT
1 AAGAT
141803 CTCAACACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (11 bp):
AAGATTTCTCA
Found at i:143873 original size:36 final size:36
Alignment explanation
Indices: 143816--143930 Score: 171
Period size: 37 Copynumber: 3.2 Consensus size: 36
143806 TATTCATTTC
*
143816 TCTTTTTCTGACCTCTTTCTATTTTAGG-CCAAGTTTT
1 TCTTTTTC-GACCTCTCTCTATTTTAGGTCC-AGTTTT
143853 TCTTTTTCGACCTCTCTCTATTTTAGGTCCAGTTTTT
1 TCTTTTTCGACCTCTCTCTATTTTAGGTCCAG-TTTT
*
143890 TCTTTTTCGACCCCTCTCTATTTTAGGTCCAGTTTT
1 TCTTTTTCGACCTCTCTCTATTTTAGGTCCAGTTTT
143926 T-TTTT
1 TCTTTT
143931 ATTGCCTCCT
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
35 4 0.05
36 25 0.34
37 45 0.61
ACGTcount: A:0.11, C:0.23, G:0.10, T:0.55
Consensus pattern (36 bp):
TCTTTTTCGACCTCTCTCTATTTTAGGTCCAGTTTT
Found at i:143942 original size:36 final size:36
Alignment explanation
Indices: 143818--143942 Score: 143
Period size: 36 Copynumber: 3.5 Consensus size: 36
143808 TTCATTTCTC
* *
143818 TTTTTCTGACCT-CTTTCTATTTTAGG-CCAAGTTTT
1 TTTTTTTGACCTCCTCTCTATTTTAGGTCC-AGTTTT
*
143853 TCTTTTTCGACCT-CTCTCTATTTTAGGTCCAGTTTT
1 T-TTTTTTGACCTCCTCTCTATTTTAGGTCCAGTTTT
143889 TTCTTTTTCGACC-CCTCTCTATTTTAGGTCCAGTTTT
1 TT-TTTTT-GACCTCCTCTCTATTTTAGGTCCAGTTTT
143926 TTTTTATTG-CCTCCTCT
1 TTTTT-TTGACCTCCTCT
143943 TAGGCATAGT
Statistics
Matches: 79, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
35 4 0.05
36 42 0.53
37 33 0.42
ACGTcount: A:0.11, C:0.25, G:0.10, T:0.54
Consensus pattern (36 bp):
TTTTTTTGACCTCCTCTCTATTTTAGGTCCAGTTTT
Found at i:153923 original size:69 final size:69
Alignment explanation
Indices: 153848--154423 Score: 873
Period size: 69 Copynumber: 8.3 Consensus size: 69
153838 TTAATTAGCA
* * * * *
153848 ACATAGGCTTTTCCACAAGCCAAACTCATTTCCATAAGAGTCAATTCAACCCTTGGTTTCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
153913 AGCC
66 AGCC
* *
153917 AGATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGTCTTGGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
153982 AGCC
66 AGCC
*
153986 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTCGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
*
154051 AGCA
66 AGCC
* * * *
154055 ACTTAGGATTTTCCACAAGCCAAACTCGTTTCCATGCGAGTCAGTTCAAGCCTTGCTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
*
154120 AGCA
66 AGCC
*
154124 ACATAGGCTTTTCTACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
*
154189 AGCA
66 AGCC
154193 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
154258 AGCC
66 AGCC
* * **
154262 ACGTATGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCGGTCCA
1 ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
154327 AGCC
66 AGCC
* * * * *
154331 ACGTAGGCTTTTCCATCAAGCCAAACTCGTTTCCATACGAGCCAGTTTAAGCCTTGGTTCAACCC
1 ACATAGGCTTTTCCA-CAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCC
*
154396 AAGCA
65 AAGCC
** * *
154401 ACAGGGGCTTTCCCATAAGCCAA
1 ACATAGGCTTTTCCACAAGCCAA
154424 GTTCATTTCC
Statistics
Matches: 467, Mismatches: 39, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
69 408 0.87
70 59 0.13
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (69 bp):
ACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTCCATCCA
AGCC
Found at i:154538 original size:105 final size:105
Alignment explanation
Indices: 154353--154541 Score: 247
Period size: 105 Copynumber: 1.8 Consensus size: 105
154343 CCATCAAGCC
* * * *
154353 AAACTCGTTTCCATACGAGCCAGTTTAAGCCTTGGTTCAACCCAAGCAACAGGGGCTTTCCCATA
1 AAACTCGTTTCCATACGAGCCAGTTCAAGCCTTGGTTCAACCCAAGCAACAGAGGCTTTCCAACA
*
154418 AGCCAAGTTCATTTCCATATGAATTCAGTCTTCCAAGACT
66 AGCCAAGTCCATTTCCATATGAATTCAGTCTTCCAAGACT
* * * * *
154458 AAACTCGTTTCCATACGAGTCAGTTCAAGCCTTGGTTTC-ATCCAAGCCACATAGGCTTTTCAAC
1 AAACTCGTTTCCATACGAGCCAGTTCAAGCCTTGG-TTCAACCCAAGCAACAGAGGCTTTCCAAC
*
154522 AAGCCACA-TCCGTTTCCATA
65 AAGCCA-AGTCCATTTCCATA
154542 CGGTGCATTA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
105 67 0.94
106 4 0.06
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.28
Consensus pattern (105 bp):
AAACTCGTTTCCATACGAGCCAGTTCAAGCCTTGGTTCAACCCAAGCAACAGAGGCTTTCCAACA
AGCCAAGTCCATTTCCATATGAATTCAGTCTTCCAAGACT
Found at i:154985 original size:27 final size:27
Alignment explanation
Indices: 154953--155030 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
154943 GCATTAGGGT
* *
154953 CATCTAGGGGCATTTTAGTCATTTGCA
1 CATCTAAGGGCATTTTGGTCATTTGCA
*
154980 CGTCTAAGGGCATTTTGGTCATTTGCA
1 CATCTAAGGGCATTTTGGTCATTTGCA
*
155007 CAT-TCATGGGCATTTTGGTCATTT
1 CATCT-AAGGGCATTTTGGTCATTT
155031 TAAGTTCTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
26 1 0.02
27 44 0.98
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (27 bp):
CATCTAAGGGCATTTTGGTCATTTGCA
Found at i:159083 original size:16 final size:16
Alignment explanation
Indices: 159062--159094 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
159052 AAGAGGTAAT
*
159062 AAAAGGTTTTTTTCAA
1 AAAAGGTTTTTCTCAA
159078 AAAAGGTTTTTCTCAA
1 AAAAGGTTTTTCTCAA
159094 A
1 A
159095 TCATGTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (16 bp):
AAAAGGTTTTTCTCAA
Found at i:164846 original size:59 final size:59
Alignment explanation
Indices: 164780--165007 Score: 246
Period size: 59 Copynumber: 3.8 Consensus size: 59
164770 GAATTATAAT
* *
164780 AGAAACTCTCGACCAGAGACCTAGAACAGGAATTTAAAGTGAAACAAGATATTTAAAAC
1 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAGTGAAACAAGATATTTAAAAC
* * * ** *
164839 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAATGGAACAAGAAAGGATTTTGAAG
1 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAGTGAAACAAG--A-TATTTAAAAC
* * * * * *
164901 A-AAACTCCCGGCTA-ATGACCTCGATCAGGATTTTAAAGTGAAACAAGATATTTGAAAT
1 AGAAACTCTCGACCAGA-GACCTCGAACAGGATTTTAAAGTGAAACAAGATATTTAAAAC
* *
164959 AGAAACTATCGACCAGAGACCTCGAACAAGATTTTATAA-TGAAACAAGA
1 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTA-AAGTGAAACAAGA
165008 CTTTGAACTG
Statistics
Matches: 138, Mismatches: 24, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
58 7 0.05
59 81 0.59
60 4 0.03
61 39 0.28
62 7 0.05
ACGTcount: A:0.44, C:0.17, G:0.18, T:0.21
Consensus pattern (59 bp):
AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAGTGAAACAAGATATTTAAAAC
Found at i:165163 original size:140 final size:139
Alignment explanation
Indices: 164891--165147 Score: 406
Period size: 140 Copynumber: 1.8 Consensus size: 139
164881 AACAAGAAAG
*
164891 GATTTTGAAGAAAACTCCCGGCTAATGACCTCGATCAGGATTTTAAAGTGAAACAAGATATTTGA
1 GATTTTGAAGAAAACTCCCGGCGAATGACCTCGATCAGGATTTTAAAGTGAAACAAGATATTTGA
*
164956 AATAGAAACTATCGACCAGAGACCTCGAACAAGATTTTATAATGAAACAAGACTTTGAACTGAAA
66 AATAGAAACTATCGACCAGAGACCTCGAACAAGATTTTAAAATGAAACAAGACTTTGAACTGAAA
165021 ACATAACAA
131 ACATAACAA
* * * * *
165030 GATTTTGGAAGAAAACTCTCGGCGAGTGATCTTGATCAGGATTTTAATGTGAAACAAGATATTTG
1 GATTTT-GAAGAAAACTCCCGGCGAATGACCTCGATCAGGATTTTAAAGTGAAACAAGATATTTG
* * * *
165095 AAATAGAAACTCTTGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGA
65 AAATAGAAACTATCGACCAGAGACCTCGAACAAGATTTTAAAATGAAACAAGA
165148 TTTTTTAATT
Statistics
Matches: 106, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
139 6 0.06
140 100 0.94
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (139 bp):
GATTTTGAAGAAAACTCCCGGCGAATGACCTCGATCAGGATTTTAAAGTGAAACAAGATATTTGA
AATAGAAACTATCGACCAGAGACCTCGAACAAGATTTTAAAATGAAACAAGACTTTGAACTGAAA
ACATAACAA
Found at i:165189 original size:64 final size:64
Alignment explanation
Indices: 165099--165392 Score: 498
Period size: 64 Copynumber: 4.6 Consensus size: 64
165089 TATTTGAAAT
* * *
165099 AGAAACTCTTGACTAGAGACCTCGAACAGGATTTTAAAATGAAACAAGATTTTTTAATTAAAAC
1 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAATGAAACAAGATTTTTGAATTAAAAC
165163 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAATGAAACAAGATTTTTGAATTAAAAC
1 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAATGAAACAAGATTTTTGAATTAAAAC
* * * * *
165227 AGAAACTCTTGGCCAGAGACCTCGAATAGGATTTTCAAATGAAACAAGATTTTTGAATTAAAAT
1 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAATGAAACAAGATTTTTGAATTAAAAC
*
165291 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTCAAATGAAACAAGATTTTTGAATTAAAAC
1 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAATGAAACAAGATTTTTGAATTAAAAC
*
165355 AGAAACTCTCGACTAGAGACCTCGAACAGGATTTTAAA
1 AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAA
165393 GTTGTTTATA
Statistics
Matches: 216, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 216 1.00
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (64 bp):
AGAAACTCTCGACCAGAGACCTCGAACAGGATTTTAAAATGAAACAAGATTTTTGAATTAAAAC
Found at i:167033 original size:51 final size:51
Alignment explanation
Indices: 166931--167040 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 51
166921 GTTCATCAAA
* **
166931 TTTTC-CTTGTTCAGATCTTGTCTCAGGACAATCAAACACTTTTTTACTGT
1 TTTTCTCTTGTTCAGATCTTGTCTCAGGACAATCAAACACTTGTACACTGT
*
166981 TTTTCTCTTGTTTCA-ATCTTGTCTCCGGAC-ATACAAACAC-TGTACACGTGT
1 TTTTCTCTTG-TTCAGATCTTGTCTCAGGACAAT-CAAACACTTGTACAC-TGT
*
167032 TTCTCTCTT
1 TTTTCTCTT
167041 AGAAATAACA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
50 11 0.22
51 36 0.71
52 4 0.08
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.44
Consensus pattern (51 bp):
TTTTCTCTTGTTCAGATCTTGTCTCAGGACAATCAAACACTTGTACACTGT
Found at i:168128 original size:27 final size:27
Alignment explanation
Indices: 168090--168154 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
168080 ATTTACTTCT
*
168090 CATTTTGGTCATTTGCGCATCC-AGGGG
1 CATTTTGGTCATTTACGCATCCGA-GGG
168117 CATTTTGGTCATTTACGCATCCGAGGG
1 CATTTTGGTCATTTACGCATCCGAGGG
168144 CATTTTGGTCA
1 CATTTTGGTCA
168155 CTTCAAGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 35 0.97
28 1 0.03
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (27 bp):
CATTTTGGTCATTTACGCATCCGAGGG
Found at i:172332 original size:13 final size:14
Alignment explanation
Indices: 172316--172344 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
172306 AAGAGGTAAT
172316 AAAAATG-TTTTCA
1 AAAAATGTTTTTCA
172329 AAAAATGTTTTTCA
1 AAAAATGTTTTTCA
172343 AA
1 AA
172345 TCATGCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (14 bp):
AAAAATGTTTTTCA
Found at i:172509 original size:30 final size:31
Alignment explanation
Indices: 172445--172525 Score: 103
Period size: 30 Copynumber: 2.6 Consensus size: 31
172435 AGCTAATCCG
*
172445 AAAGAAGATTTTGGAAAATAAGGTAACTCCCA
1 AAAGAAGATTTTGGAAAATAAGATAAC-CCCA
172477 AAAGAAGATTTTGGAAAATAAAGAT-A-CCCA
1 AAAGAAGATTTTGGAAAAT-AAGATAACCCCA
* *
172507 AAAGAAGACTTTGGGAAAT
1 AAAGAAGATTTTGGAAAAT
172526 TAATAAAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
30 21 0.47
32 20 0.44
33 4 0.09
ACGTcount: A:0.49, C:0.10, G:0.20, T:0.21
Consensus pattern (31 bp):
AAAGAAGATTTTGGAAAATAAGATAACCCCA
Found at i:185170 original size:21 final size:21
Alignment explanation
Indices: 185131--185179 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
185121 TCAATGCTTT
**
185131 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
185153 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
185174 A-GAAGC
1 AGGAAGC
185180 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:190192 original size:29 final size:30
Alignment explanation
Indices: 190149--190205 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
190139 TCCCTCTGAA
*
190149 AAAAAAAAACAAAAGAGTGTTAGTAACCTC
1 AAAAAAAAACAAAAGAGAGTTAGTAACCTC
* *
190179 AAAAGAAAA-AAAAGGGAGTTAGTAACC
1 AAAAAAAAACAAAAGAGAGTTAGTAACC
190206 CCTAAATCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.58, C:0.11, G:0.18, T:0.14
Consensus pattern (30 bp):
AAAAAAAAACAAAAGAGAGTTAGTAACCTC
Found at i:193531 original size:2 final size:2
Alignment explanation
Indices: 193524--193559 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
193514 TGGTACTCAA
193524 AT AT AT AT AT -T CAT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
193560 TAAATTCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.94
3 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:194312 original size:50 final size:50
Alignment explanation
Indices: 194255--194524 Score: 416
Period size: 50 Copynumber: 5.4 Consensus size: 50
194245 CAGAAGGGTG
* *
194255 AATTGGAAGATAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTG
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTA
*
194305 AATTGGAAGACAGTTCAAATGATAAGCGGAAGACGGTCCTTTTAAGATTA
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTA
194355 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTA
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTA
* *
194405 AATTGGAAGACCGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAGGATTA
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTA
* * * * * *
194455 AATTGGAAGACAATTCAAAGGATAAGCGAAAGATGGTCCTTTTTATATTT
1 AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTA
*
194505 GATTGGAAGAC-GATTCAAAG
1 AATTGGAAGACAG-TTCAAAG
194525 AAGTTGAGTT
Statistics
Matches: 203, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
50 203 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (50 bp):
AATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTA
Found at i:194463 original size:27 final size:27
Alignment explanation
Indices: 194332--194465 Score: 86
Period size: 27 Copynumber: 5.3 Consensus size: 27
194322 AATGATAAGC
*
194332 GGAAGACGGTCCTTTTAAGATTAAATT
1 GGAAGACGGTCCTTTTAGGATTAAATT
* *** **
194359 GGAAGACAGT--TCAAAGGA-T-AAGC
1 GGAAGACGGTCCTTTTAGGATTAAATT
*
194382 GGAAGACGGTCCTTTTAAGATTAAATT
1 GGAAGACGGTCCTTTTAGGATTAAATT
* *** **
194409 GGAAGACCGT--TCAAAGGA-T-AAGC
1 GGAAGACGGTCCTTTTAGGATTAAATT
194432 GGAAGACGGTCCTTTTAGGATTAAATT
1 GGAAGACGGTCCTTTTAGGATTAAATT
194459 GGAAGAC
1 GGAAGAC
194466 AATTCAAAGG
Statistics
Matches: 72, Mismatches: 27, Indels: 16
0.63 0.23 0.14
Matches are distributed among these distances:
23 22 0.31
24 2 0.03
25 17 0.24
26 2 0.03
27 29 0.40
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.25
Consensus pattern (27 bp):
GGAAGACGGTCCTTTTAGGATTAAATT
Found at i:194566 original size:27 final size:26
Alignment explanation
Indices: 194510--194584 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
194500 TATTTGATTG
* *
194510 GAAGACGATTCAAAGAAGTTGAGTTG
1 GAAGACGATTCAAAGAAGTTGAATTA
***
194536 GAAGACGATTCCCCGAAGATTGAATTA
1 GAAGACGATTCAAAGAAG-TTGAATTA
* * *
194563 GAAGGCAATTCGAAGAAGTTGA
1 GAAGACGATTCAAAGAAGTTGA
194585 TCGGGAGACA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 19 0.50
27 19 0.50
ACGTcount: A:0.39, C:0.12, G:0.28, T:0.21
Consensus pattern (26 bp):
GAAGACGATTCAAAGAAGTTGAATTA
Found at i:194835 original size:27 final size:27
Alignment explanation
Indices: 194797--194861 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
194787 ATTTACTTCT
* *
194797 CATTTTGGTCATTTGCGCGTCCATGGG
1 CATTTTGGTCATTTGCGCATCCAGGGG
*
194824 CATTTTGGTCATTTGTGCATCCAGGGG
1 CATTTTGGTCATTTGCGCATCCAGGGG
194851 CATTTTGGTCA
1 CATTTTGGTCA
194862 CTTCAAGTAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.14, C:0.20, G:0.28, T:0.38
Consensus pattern (27 bp):
CATTTTGGTCATTTGCGCATCCAGGGG
Found at i:198310 original size:242 final size:241
Alignment explanation
Indices: 197881--198380 Score: 883
Period size: 242 Copynumber: 2.1 Consensus size: 241
197871 TGATATGTTT
*
197881 GCAATTTTGATTTGAAAATGCATGATTTTTGGGTATTTATGGTTCAAAGGTTGTATCTTTTGGTT
1 GCAATTTTGATTTGAAAATGCATGATTTTTGGGTATTTATGGTTCAAAGGTTGTATCTTTTGATT
* * * * *
197946 AATTAAGTGTGTAATGTCAAAGCCTGGATTTTTTATGTTTAAATTAACTTGAAATTGATCTTTAT
66 AATTAAGTGTGTAATATCAAAGCCTGGATCTTTTAGGTTTAAATCAACTTGAAATTGATCTCTAT
* *
198011 GTTAATCAAGCTTCATGATTCTTTGATTGAATTCCCTTTGTGTTAGAATGTGAGATCTATGTTTG
131 GTTAATCAAGCTTCATGATTCTTTGATTGAATTCCCTTTGTGTTAGAATGGGAGATCTATGATTG
*
198076 AAGATGCTTGTTTGCTTAATTTAAAAATGGGAATTTAATTAATGGA
196 AAGATGCTTGTTTGCTCAATTTAAAAATGGGAATTTAATTAATGGA
198122 GCAATTTTGATTTGAAAATGCATGATTTTTGGGTATTTATGGTTCAAAGGTTGTATCTTTTGATT
1 GCAATTTTGATTTGAAAATGCATGATTTTTGGGTATTTATGGTTCAAAGGTTGTATCTTTTGATT
* *
198187 AATTTAAGTGTGTAATATCAAAGCTTGGATCTTTTAGGTTTAAATCAACTTTAAATTGATCTCTA
66 AA-TTAAGTGTGTAATATCAAAGCCTGGATCTTTTAGGTTTAAATCAACTTGAAATTGATCTCTA
*
198252 TGTTAATCAAGCTTCATGATTCTTTGATTGAATTGCCTTTGTGTTAGAATGGGAGATCTATGATT
130 TGTTAATCAAGCTTCATGATTCTTTGATTGAATTCCCTTTGTGTTAGAATGGGAGATCTATGATT
198317 GAAGATGCTTGTTTGCTCAATTTAAAAATGGGAATTTAATTAATGGA
195 GAAGATGCTTGTTTGCTCAATTTAAAAATGGGAATTTAATTAATGGA
198364 GCAATTTTGATTTGAAA
1 GCAATTTTGATTTGAAA
198381 GTGGGAGCTT
Statistics
Matches: 246, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
241 66 0.27
242 180 0.73
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.43
Consensus pattern (241 bp):
GCAATTTTGATTTGAAAATGCATGATTTTTGGGTATTTATGGTTCAAAGGTTGTATCTTTTGATT
AATTAAGTGTGTAATATCAAAGCCTGGATCTTTTAGGTTTAAATCAACTTGAAATTGATCTCTAT
GTTAATCAAGCTTCATGATTCTTTGATTGAATTCCCTTTGTGTTAGAATGGGAGATCTATGATTG
AAGATGCTTGTTTGCTCAATTTAAAAATGGGAATTTAATTAATGGA
Found at i:199290 original size:13 final size:14
Alignment explanation
Indices: 199274--199302 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
199264 AAGAGGTAAT
199274 AAAAATG-TTTTCA
1 AAAAATGTTTTTCA
199287 AAAAATGTTTTTCA
1 AAAAATGTTTTTCA
199301 AA
1 AA
199303 TCATGCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (14 bp):
AAAAATGTTTTTCA
Found at i:199467 original size:30 final size:31
Alignment explanation
Indices: 199400--199483 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 31
199390 TTAAGCTAAT
* * *
199400 CCAAAAGAAGAATTTGAAAAATAAGGTAACTC
1 CCAAAAGAAGATTTTGGAAAATAAGATAAC-C
199432 CCAAAAGAAGATTTTGGAAAATAAAGAT-A-C
1 CCAAAAGAAGATTTTGGAAAAT-AAGATAACC
* *
199462 CCAAAAGAAGGTTTTGGGAAAT
1 CCAAAAGAAGATTTTGGAAAAT
199484 TAATAAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 21 0.46
32 21 0.46
33 4 0.09
ACGTcount: A:0.50, C:0.11, G:0.19, T:0.20
Consensus pattern (31 bp):
CCAAAAGAAGATTTTGGAAAATAAGATAACC
Found at i:203159 original size:22 final size:22
Alignment explanation
Indices: 203131--203172 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
203121 AGTTCTGAGG
203131 CTACCCGGCCCCGAGTACCCCC
1 CTACCCGGCCCCGAGTACCCCC
*
203153 CTACCCGGCCCCGGGTACCC
1 CTACCCGGCCCCGAGTACCC
203173 TCAGGAACGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.57, G:0.21, T:0.10
Consensus pattern (22 bp):
CTACCCGGCCCCGAGTACCCCC
Found at i:204116 original size:24 final size:25
Alignment explanation
Indices: 204082--204129 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
204072 ATTGGAGTAT
*
204082 TTATTTATCTTGTTTCTTAATTTTC
1 TTATTTATCTTGTTTATTAATTTTC
*
204107 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTTATTAATTTT
204130 ATGGTTACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.15, C:0.08, G:0.04, T:0.73
Consensus pattern (25 bp):
TTATTTATCTTGTTTATTAATTTTC
Found at i:206401 original size:18 final size:18
Alignment explanation
Indices: 206380--206420 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
206370 AAGTTTCTGA
206380 TTTTCT-GATTTTTTCACT
1 TTTTCTGGATTTTTT-ACT
*
206398 TTTT-TGGATTTTTTTCT
1 TTTTCTGGATTTTTTACT
206415 TTTTCT
1 TTTTCT
206421 ATCTCTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.07, C:0.12, G:0.07, T:0.73
Consensus pattern (18 bp):
TTTTCTGGATTTTTTACT
Found at i:207534 original size:76 final size:76
Alignment explanation
Indices: 207395--207538 Score: 175
Period size: 76 Copynumber: 1.9 Consensus size: 76
207385 GTGATGAGCT
* * *
207395 ATGACACAGCCCATCTGGGTGATCAGGCGAAACACATGGGTCTTCAGACAAACTATGTAGGCACC
1 ATGACACAGCCCACCTGGGTGATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTAGGCACC
207460 CAGCTGGAGTC
66 CAGCTGGAGTC
* ** * * *
207471 ATGACACTGCCCACCTGGGTTCTCAAGC-AAACCACATGGGTGTTCAAGGC-AACCATGTGGGCA
1 ATGACACAGCCCACCTGGGTGATCAAGCGAAA-CACATGGGTCTTC-AGACAAACCATGTAGGCA
207534 CCCAG
64 CCCAG
207539 GTGGGGTCGG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
75 3 0.05
76 51 0.89
77 3 0.05
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (76 bp):
ATGACACAGCCCACCTGGGTGATCAAGCGAAACACATGGGTCTTCAGACAAACCATGTAGGCACC
CAGCTGGAGTC
Found at i:209733 original size:21 final size:21
Alignment explanation
Indices: 209694--209742 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
209684 TCAATGCTTT
**
209694 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
209716 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
209737 A-GAAGC
1 AGGAAGC
209743 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:214753 original size:26 final size:26
Alignment explanation
Indices: 214719--214768 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
214709 TGTCCCTCTG
*
214719 AAAAAAAAAAGAGCGTTAGTAACCTC
1 AAAAAAAAAAGAGAGTTAGTAACCTC
* *
214745 AAAAGAAAAAGGGAGTTAGTAACC
1 AAAAAAAAAAGAGAGTTAGTAACC
214769 CCTAAATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.54, C:0.12, G:0.20, T:0.14
Consensus pattern (26 bp):
AAAAAAAAAAGAGAGTTAGTAACCTC
Done.