Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017164.1 Corchorus olitorius cultivar O-4 contig17197, 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: 169517
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:545 original size:20 final size:20
Alignment explanation
Indices: 505--562 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
495 ACCAATATTC
* *
505 AATTATACTTTTTTTTAAAGG
1 AATTATAC-TTGTTTTGAAGG
526 AATTATACTTGTTTTGAAGG
1 AATTATACTTGTTTTGAAGG
546 AATTATACTTGTTTTGA
1 AATTATACTTGTTTTGA
563 TATATGATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
20 27 0.77
21 8 0.23
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (20 bp):
AATTATACTTGTTTTGAAGG
Found at i:27683 original size:18 final size:17
Alignment explanation
Indices: 27643--27675 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27633 AGAGGAATTT
27643 AAAAA-AAAAAGAAAGA
1 AAAAAGAAAAAGAAAGA
27659 AAGAAAGAAAAAGAAAG
1 AA-AAAGAAAAAGAAAG
27676 GACAAAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 3 0.20
18 10 0.67
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAAGAAAGA
Found at i:38669 original size:21 final size:20
Alignment explanation
Indices: 38641--38788 Score: 152
Period size: 21 Copynumber: 7.0 Consensus size: 20
38631 GAGATGATGA
38641 AGGGTTTGAAGAGTGACCAGC
1 AGGGTTTGAAGA-TGACCAGC
* * *
38662 AAGTTTTGATGATCGACCAGC
1 AGGGTTTGAAGAT-GACCAGC
38683 AGGGTTTGAAGACTGACCAGC
1 AGGGTTTGAAGA-TGACCAGC
* * *
38704 AAGTTTTGATGATCGACCAGC
1 AGGGTTTGAAGAT-GACCAGC
38725 AGGGTTTGAAGACTGACCAGC
1 AGGGTTTGAAGA-TGACCAGC
* * *
38746 AGGTTTTGATGATCGAGCAGC
1 AGGGTTTGAAGAT-GACCAGC
38767 AGGGTTTGAAGACTGACCAGC
1 AGGGTTTGAAGA-TGACCAGC
38788 A
1 A
38789 CGTGAGTTAC
Statistics
Matches: 103, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
20 3 0.03
21 97 0.94
22 3 0.03
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (20 bp):
AGGGTTTGAAGATGACCAGC
Found at i:38700 original size:42 final size:42
Alignment explanation
Indices: 38641--38788 Score: 269
Period size: 42 Copynumber: 3.5 Consensus size: 42
38631 GAGATGATGA
*
38641 AGGGTTTGAAGAGTGACCAGCAAGTTTTGATGATCGACCAGC
1 AGGGTTTGAAGACTGACCAGCAAGTTTTGATGATCGACCAGC
38683 AGGGTTTGAAGACTGACCAGCAAGTTTTGATGATCGACCAGC
1 AGGGTTTGAAGACTGACCAGCAAGTTTTGATGATCGACCAGC
* *
38725 AGGGTTTGAAGACTGACCAGCAGGTTTTGATGATCGAGCAGC
1 AGGGTTTGAAGACTGACCAGCAAGTTTTGATGATCGACCAGC
38767 AGGGTTTGAAGACTGACCAGCA
1 AGGGTTTGAAGACTGACCAGCA
38789 CGTGAGTTAC
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 103 1.00
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (42 bp):
AGGGTTTGAAGACTGACCAGCAAGTTTTGATGATCGACCAGC
Found at i:67164 original size:100 final size:100
Alignment explanation
Indices: 67044--67243 Score: 373
Period size: 100 Copynumber: 2.0 Consensus size: 100
67034 ATCCCCACCC
67044 AAGCAATCCACTTGAAGAAGTCTCGAACTCGAGTCTCCACTCCCCACCTAAGTTAGATCTAAGTA
1 AAGCAATCCACTTGAAGAAGTCTCGAACTCGAGTCTCCACTCCCCACCTAAGTTAGATCTAAGTA
**
67109 AATATTCACTCAAGAGTCTTTACTCCACATTCTAA
66 AATATTCACTCAAGAGTCTCCACTCCACATTCTAA
*
67144 AAGCAATCCACTTGAAGAAGTCTCGAACTCGAGTCTCCACTCTCCACCTAAGTTAGATCTAAGTA
1 AAGCAATCCACTTGAAGAAGTCTCGAACTCGAGTCTCCACTCCCCACCTAAGTTAGATCTAAGTA
67209 AATATTCACTCAAGAGTCTCCACTCCACATTCTAA
66 AATATTCACTCAAGAGTCTCCACTCCACATTCTAA
67244 TTCGAGTCTC
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.27
Consensus pattern (100 bp):
AAGCAATCCACTTGAAGAAGTCTCGAACTCGAGTCTCCACTCCCCACCTAAGTTAGATCTAAGTA
AATATTCACTCAAGAGTCTCCACTCCACATTCTAA
Found at i:68442 original size:3 final size:3
Alignment explanation
Indices: 68434--68460 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
68424 CTCTGACCCC
68434 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
68461 CAAGAGTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:73016 original size:4 final size:4
Alignment explanation
Indices: 72997--73044 Score: 55
Period size: 4 Copynumber: 12.2 Consensus size: 4
72987 ACTTCCTATG
* *
72997 TAAA GTAAA AAAA TAAA TAAA TAAA TAAA -AAA TAAA -AAA TAAA AAAA
1 TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
73044 T
1 T
73045 TAGGGAGATA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
3 6 0.16
4 27 0.73
5 4 0.11
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (4 bp):
TAAA
Found at i:73031 original size:7 final size:7
Alignment explanation
Indices: 73011--73042 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
73001 GTAAAAAAAT
73011 AAATAAA
1 AAATAAA
73018 TAAATAAA
1 -AAATAAA
73026 AAATAAA
1 AAATAAA
73033 AAATAAA
1 AAATAAA
73040 AAA
1 AAA
73043 ATTAGGGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:78714 original size:2 final size:2
Alignment explanation
Indices: 78677--78706 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
78667 TGAGTTCGAA
78677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78707 TCATATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81237 original size:19 final size:19
Alignment explanation
Indices: 81226--81262 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
81216 AATTTTTAAG
81226 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
*
81245 TAAAAATTTAATAT-TAAA
1 TAAAAATATAATATATAAA
81263 ACAGTTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:83236 original size:51 final size:51
Alignment explanation
Indices: 83165--83267 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 51
83155 TATTTCTGAA
* **
83165 AGAGAAACACGAATACAGTGTTTTTATGTCCGGAGACAAGAT-TGAAACAAG
1 AGAGAAACACGAAAACAGTGTTTGGATGTCCGGAGACAAGATCT-AAACAAG
* * * *
83216 AGAGAAACACTAAAAGAGTGTTTGGGTGTCCTGAGACAAGATCTAAACAAG
1 AGAGAAACACGAAAACAGTGTTTGGATGTCCGGAGACAAGATCTAAACAAG
83267 A
1 A
83268 AAAATATGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 43 0.98
52 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (51 bp):
AGAGAAACACGAAAACAGTGTTTGGATGTCCGGAGACAAGATCTAAACAAG
Found at i:91933 original size:32 final size:33
Alignment explanation
Indices: 91874--91947 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 33
91864 TAAATTGTTG
91874 TGAATTTTAAGTTCACCTATGTAGTATTTTAAA
1 TGAATTTTAAGTTCACCTATGTAGTATTTTAAA
*
91907 TGAACTTTAAGTTCACC-ATGTAGTATTTTAAA
1 TGAATTTTAAGTTCACCTATGTAGTATTTTAAA
91939 TGAATTTTA
1 TGAATTTTA
91948 GTTTGAAATG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 23 0.59
33 16 0.41
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (33 bp):
TGAATTTTAAGTTCACCTATGTAGTATTTTAAA
Found at i:98357 original size:251 final size:251
Alignment explanation
Indices: 97904--98358 Score: 732
Period size: 251 Copynumber: 1.8 Consensus size: 251
97894 TGATCTTATG
* * * * *
97904 TAGAATTAGTGGTTAACATGAAAGCACTAATTATTTTGTCTCAGCATATCCCCGTGGCAGCAAAA
1 TAGAATAAGCGGTTAACATGAAAGCACAAATTATTTTGTCTCAACATATCCCCATGGCAGCAAAA
*
97969 GGAGAATGCGTGGAAGGTATTGGTCAGACATGGTACTTCCAATGGGGTTAGGTTGAGGGAAGGTT
66 GGAGAATGCGTGGAAGGTAATGGTCAGACATGGTACTTCCAATGGGGTTAGGTTGAGGGAAGGTT
* *
98034 CAAGGTGAGTGCGCCGCGTAACCTCATTTGAAGTACGGCAACGTAAGAAGTAACCTTATTTCTGA
131 CAAGGTGAGTGCGCCGCATAACCCCATTTGAAGTACGGCAACGTAAGAAGTAACCTTATTTCTGA
98099 ATTTACTCCTTTCATTTAGTTTTCAAATGTGCTTTATATAATTTATGTTTAACATT
196 ATTTACTCCTTTCATTTAGTTTTCAAATGTGCTTTATATAATTTATGTTTAACATT
* * *
98155 TAGAATAAGCGGTTAACATGAAAGCACAAATTCTTTTGTCTCAACGTATCGCCATGGCAGCAAAA
1 TAGAATAAGCGGTTAACATGAAAGCACAAATTATTTTGTCTCAACATATCCCCATGGCAGCAAAA
* * * * *
98220 GGATAATGTGTGGAAGGTAATGGTCGGACATGGTACTTCGAATGGGGTTATGTTGAGGGAAGGTT
66 GGAGAATGCGTGGAAGGTAATGGTCAGACATGGTACTTCCAATGGGGTTAGGTTGAGGGAAGGTT
* *
98285 CAAGGTGAGTGCGCCGCATAACCCCATTTGAAGTACGGCTGA-GTATGAAGTAACCTTATTTCTG
131 CAAGGTGAGTGCGCCGCATAACCCCATTTGAAGTACGGC-AACGTAAGAAGTAACCTTATTTCTG
98349 AATTTACTCC
195 AATTTACTCC
98359 CGTTCAGTTT
Statistics
Matches: 185, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
251 184 0.99
252 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (251 bp):
TAGAATAAGCGGTTAACATGAAAGCACAAATTATTTTGTCTCAACATATCCCCATGGCAGCAAAA
GGAGAATGCGTGGAAGGTAATGGTCAGACATGGTACTTCCAATGGGGTTAGGTTGAGGGAAGGTT
CAAGGTGAGTGCGCCGCATAACCCCATTTGAAGTACGGCAACGTAAGAAGTAACCTTATTTCTGA
ATTTACTCCTTTCATTTAGTTTTCAAATGTGCTTTATATAATTTATGTTTAACATT
Found at i:99600 original size:31 final size:31
Alignment explanation
Indices: 99537--99600 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
99527 ACCCAAAGTT
* * *
99537 ATATTGGGCCTACTTTTTTTTTTGCAATAAA
1 ATATTGGGCCTACTTTGTATTTTGCAAGAAA
*
99568 ATATTGGGCCTAGTTTGTATTTT-CAACGAAA
1 ATATTGGGCCTACTTTGTATTTTGCAA-GAAA
99599 AT
1 AT
99601 GTTTTTCGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (31 bp):
ATATTGGGCCTACTTTGTATTTTGCAAGAAA
Found at i:101831 original size:301 final size:302
Alignment explanation
Indices: 101263--101855 Score: 677
Period size: 301 Copynumber: 2.0 Consensus size: 302
101253 CGTTCCGGGT
* * **
101263 TCTCGGCTCAGTTTTGCATGATTTTCGGCGCCAAAGTTCCTTGAAATATCAATATTCATCTAAGT
1 TCTCGACTCAGTTTTGCATGATTTTCGGCGCCAAAGCTCCTTGAAATATCAATATTCATCTAACC
* * *
101328 AAATCTCAACATTATTGGATTCAAGGATTTGTTTTAATGAGCATCTAAATCTTGTTTCGATTTAA
66 AAATCTCAACATCATTGGATTCAAGGATTTGATTTAACGAGCATCTAAATCTTGTTTCGATTTAA
* * * *
101393 TTAGAAATTAATTCAGAAAAACAAGAAAAATGATATTAGAAGCGCGAAAGTCCCTTCGATATTTT
131 TCAGAAATTAATTCAGAAAAACAAGAAAAACGATATTAGAAGCGCGAAAGTCACTTCAATATTTT
** *
101458 TGGCGTTGAAATATATATTTTTTATGGGTATTTTTGCCATAAATTGAGGAAAAATCTTTCGAATC
196 TGGCGTTGAAATATATATTTTTTATAAGTATTTGTGCCATAAATTGAGGAAAAATCTTTCGAATC
101523 AATTTTTGCAAAA-TATAGCCGAAATCGTGTATGTTCTAGGG
261 AATTTTTGCAAAATTATAGCCGAAATCGTGTATGTTCTAGGG
* * **
101564 TCTCGACTCAGTTTTGCATGATTTTTGGCGCC-AAGACTCGTTGAAATATGTATATTCATCTAAC
1 TCTCGACTCAGTTTTGCATGATTTTCGGCGCCAAAG-CTCCTTGAAATATCAATATTCATCTAAC
* * * * * *
101628 CAAATCTTAGCCA-CATTGGATTTAAGTATATT-ATTTGACGAGCATCTGAAT-TATGTTTCGAT
65 CAAATCTCA-ACATCATTGGATTCAAGGAT-TTGATTTAACGAGCATCTAAATCT-TGTTTCGAT
* * * *
101690 TTAATCATAAATTAATTCAGAAAAA-ATAGGAAAAGCGATATTAGAAGCGTGAAAAG-CACTTTA
127 TTAATCAGAAATTAATTCAGAAAAACA-A-GAAAAACGATATTAGAAGCGCG-AAAGTCACTTCA
* * * *
101753 ATCTTTTTGGTGTTGAATTATATATTTTTTATAAGTA-TTGTGCTCA-AGATGTGAGGAAAAAAT
189 ATATTTTTGGCGTTGAAATATATATTTTTTATAAGTATTTGTGC-CATAAAT-TGAGG-AAAAAT
* * * * * *
101816 -TTTCGGAT-TATTTTTGTAAAATTTTAGCCGACATTGTGTA
251 CTTTCGAATCAATTTTTGCAAAATTATAGCCGAAATCGTGTA
101856 CTAACCATCA
Statistics
Matches: 243, Mismatches: 38, Indels: 21
0.80 0.13 0.07
Matches are distributed among these distances:
300 5 0.02
301 140 0.58
302 88 0.36
303 10 0.04
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (302 bp):
TCTCGACTCAGTTTTGCATGATTTTCGGCGCCAAAGCTCCTTGAAATATCAATATTCATCTAACC
AAATCTCAACATCATTGGATTCAAGGATTTGATTTAACGAGCATCTAAATCTTGTTTCGATTTAA
TCAGAAATTAATTCAGAAAAACAAGAAAAACGATATTAGAAGCGCGAAAGTCACTTCAATATTTT
TGGCGTTGAAATATATATTTTTTATAAGTATTTGTGCCATAAATTGAGGAAAAATCTTTCGAATC
AATTTTTGCAAAATTATAGCCGAAATCGTGTATGTTCTAGGG
Found at i:103664 original size:666 final size:659
Alignment explanation
Indices: 101567--105359 Score: 3871
Period size: 666 Copynumber: 5.7 Consensus size: 659
101557 TCTAGGGTCT
* ** * *
101567 CGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCGTTGAAATATGTATA-TTCATCTAACCAA
1 CGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATAACTATATTTTATCTAACAAA
* * * * * * * **
101631 ATCTTAGCCACATTGG--ATTTAAGTATATT-ATTTGACGAGCATCTGAATTATGTTTCGATTT-
66 ATCTCAGACACA--GGATATTTAAGGAT-TTGTTTTTACGAGAATCAGAATTCGGTTTCGATTTA
* * * * * * * *
101692 AATCATAAATTAATTCAGAAAAAATAGGAAAAGCGATATTAGAAGC-GTGAAAAGCACTTTAATC
128 AAT-AAAAATTAATTCGGAAAAAA-AGAAAAAACAATATTAGAA-CTGTGAAAAGCCCTTAAATA
* * * *
101756 TTTTTGGTGTTGAATTATATATTTTTTAT-AAGTATTGTGCTCAAGATGTGAGGAAAAAATTTTC
190 TTTTTGGCGTTGAATTATATATTTTTTATGAA-TATTGTGGTAAAAAT-TGA-GAAAAAATTTTC
* ** * * * * * *
101820 -GG--ATTATTTTTGTAAAATTTTAGCCGACATTGTGTACTAACCATCACGGTTTATGGCTAAAA
252 AGGTCAAT-TTTTTGGGAACTTTTAACCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAA
* * * * * * * *
101882 ACGCGTTCTGGGGCCGCAGA-TAAGTTTTGCATGATTTTTGGCGCCCAGACACATTGAAATAACT
316 ACGCGTTC-GGGGCCCCCGACTCAGTTTTGCATGATTTTCGGCGCCAAGACTCCTTGAAATATCT
* ** * * * ** * * * *
101946 ATATTTTATCTAAAAAAATGTTAGAC--AACCGATATTTAAGGATTTG-TTTTTACGAGAATCAA
380 ATA-TTCATCTAAGTAAATCTCA-ACTTTATTG-GATTCAAGGATTTGTTTTTTA-GAGCATCAG
*
102008 AAT-TTGGATTCGATTTAATTAGAAATTAATTCAGAAACAAAAAGAAAAACAATATTAGAAGTCT
441 AATCTT-GTTTCGATTTAATTAGAAATTAATTCAGAAA-AAAAAGAAAAACAATATTAGAAG-CT
* * ***
102072 GAAAAG-CCCTTAAATATTTTTGGCGTTGAATTATATATATATATTTTGATTAGTATTGTGGTAA
503 G-AAAGTCCCTTCAATATTTTTGGCGTTGAA-T-TATATAT-T-TTTT-ATGAGTATTGT-GCCC
* * * * *
102136 AAAAT-TGAGAAAAAAATTTTCGGGTCAATTTTTTTGGAAACTTTTAACCGAAATCGTGTACTAA
561 AAAATGTGAGGAAAAAATTTTCGGGTC-A-GTTTTTGTAAAATTTTAGCCGAAATCGTGTACTAA
* * *
102200 CCATCACTGTTTTTGTCTAAAAATGCGTTCGGGGGCCC
624 CCATCACT-TTTATGGCTAAAAACGCGTT-GGGGGCCC
* * * * * * * * * *
102238 CAACTCAGTTTCGAATAATTTTCGGCGCCAAGACTCCTTGAAATATCTATA-TTCATTTAA-TAA
1 CGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATAACTATATTTTATCTAACAAA
** * **
102301 ATCTCA-ACTTTATTGG--ATTTAAGGATTTGTTGTTACGA-ACATCAGAA-TCTTTTTCGATTT
66 ATCTCAGAC---ACAGGATATTTAAGGATTTGTTTTTACGAGA-ATCAGAATTCGGTTTCGATTT
* * * * *
102361 AATTATAAATTAATTC--------AG-AAAAACGATATTAGTAGC-GTG-AAAGTCCCTTCAATA
127 AAATAAAAATTAATTCGGAAAAAAAGAAAAAACAATATTAG-AACTGTGAAAAG-CCCTTAAATA
* * ** * **
102415 TTTTTGGCCTTGAAATATATA-TTTTTATGGGTATTTTGGCCCAAAATGTGAGGAAAAAAATTTT
190 TTTTTGGCGTTGAATTATATATTTTTTATGAATATTGTGG-TAAAAAT-TGA-G-AAAAAATTTT
* ** * * *
102479 CAGGTC-AGTTTTTGTAAAATTTTAACCGAAATCGTGTATTAACCATCACAGTTTATGGCTAAAA
251 CAGGTCAATTTTTTGGGAACTTTTAACCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAA
* * * * * * *
102543 ACACGTTCTGGGG-CCCTGGCTCAGTTTTGCATGATTTTTGTCG-CACAGACTCATTGAAATAAC
316 ACGCGTTC-GGGGCCCCCGACTCAGTTTTGCATGATTTTCGGCGCCA-AGACTCCTTGAAATATC
* * * * * * * *
102606 AATATTTTATCT-AGAAAAATCTCAAATACTCAAT--ATTTAAGGATTTG-TTTTTACGAGAATC
379 TATA-TTCATCTAAG-TAAATCTCAACT--TTATTGGATTCAAGGATTTGTTTTTTA-GAGCATC
* * * * *
102667 AGTAT-TTGGATTCAATTTAATTAGAAATTAATTCGGAAACAAAAAGAAAAATAATATTAGAAGT
439 AGAATCTT-GTTTCGATTTAATTAGAAATTAATTCAGAAA-AAAAAGAAAAACAATATTAGAAG-
* * * * ***
102731 CTGAAAAG-CCCTTAAATATTTTTGGCATTGAATTGTATATTTTTTTTATTAGTATTGTGATAAA
501 CTG-AAAGTCCCTTCAATATTTTTGGCGTTGAA-T-TATATATTTTTTATGAGTATTGTGCCCAA
** * * ** * *
102795 AAAATGAGAAAAAAAATTTTCGGGTCAATTTTTTTGGGAACTTTTAACCGAAATCGTGTACTAAC
563 AATGTGAG-GAAAAAATTTTCGGGTC-A-GTTTTTGTAAAATTTTAGCCGAAATCGTGTACTAAC
* * * * *
102860 TATTACTGTTTTTGTCTAAAAACGCGTTCGGGGGCCG
625 CATCACT-TTTATGGCTAAAAACGCGTT-GGGGGCCC
* * * *
102897 CGACTCAGTTTCGCATGATTTTCGGCGCCAAGACTCCTTGAAATATCTATATTTTATCTAACAAA
1 CGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATAACTATATTTTATCTAACAAA
*
102962 ATCTCAGACACATGATATTTAAGGATTTGTTTTTACGAGAATCAGAATTCGGTTTCGATTTAAAT
66 ATCTCAGACACAGGATATTTAAGGATTTGTTTTTACGAGAATCAGAATTCGGTTTCGATTTAAAT
*
103027 AAAAATTAATTCGGAATTAAAAAGAAAAAAACAATA-TATGAACTGTGAGAAGCCCTTAAATATT
131 AAAAATTAATTCGGAA--AAAAAG-AAAAAACAATATTA-GAACTGTGAAAAGCCCTTAAATATT
* * * *
103091 TTTGGGGTTGAATTATATATTTTTTATGAATATTGTGGTAAAAAGTTGATAAAAACTTTTCGGGT
192 TTTGGCGTTGAATTATATATTTTTTATGAATATTGTGGTAAAAA-TTGAGAAAAAATTTTCAGGT
*
103156 CAATTTTTTGGGAACTTTTAACCGAAATCGTGTATTAATCATCACGGTTTTTTGGCTAAAAACGC
256 CAATTTTTTGGGAACTTTTAACCGAAATCGTGTATTAACCATCACGG-TTTTTGGCTAAAAACGC
* * *
103221 GTTCGGGGCCCCCGACTCAGTTTTGCATGATTTTCGGCACGAACACTCCTTGAAATATCTATATT
320 GTTCGGGGCCCCCGACTCAGTTTTGCATGATTTTCGGCGCCAAGACTCCTTGAAATATCTATATT
* * *
103286 CATCTAAGTAAATCTCAACTTTATTGGATTCAAAGATTTGTTTTTTAGAGCATCAGAATGTAGTT
385 CATCTAAGTAAATCTCAACTTTATTGGATTCAAGGATTTGTTTTTTAGAGCATCAGAATCTTGTT
* *
103351 TCGATTTAATTAGAAATTAATTCAGAAAAACAAGAAAAACGATATTAGAAGCGTGAAAGTCCCTT
450 TCGATTTAATTAGAAATTAATTCAGAAAAAAAAGAAAAACAATATTAGAAGC-TGAAAGTCCCTT
*
103416 CAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGCCCAAAATGTGAGGAAAAACT
514 CAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGCCCAAAATGTGAGGAAAAAAT
*
103481 TTTCGGGTCAGTTTTTGTAAAATTTTAGCCTAAATCGTGTACTAACCATCACATTTTATGGCTAA
579 TTTCGGGTCAGTTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-TTTTATGGCTAA
* * *
103546 AAACTC-TTGTTGGGCAC
643 AAACGCGTTG-GGGGCCC
* *
103563 TGACTCAGTTTTGCATGATTTTTGGCG-CATAGACTCATTGAAATAAATATATTTTATCTAACAA
1 CGACTCAGTTTTGCATGATTTTTGGCGCCA-AGACTCATTGAAATAACTATATTTTATCTAACAA
* * * * *
103627 AATCTCAGACACAGGATATTTAAGAATTTGATTTTACGAGAATCCGAATTCGGTTTCGAATTAAT
65 AATCTCAGACACAGGATATTTAAGGATTTGTTTTTACGAGAATCAGAATTCGGTTTCGATTTAAA
*** * *
103692 TTCTAATTAATTCGAAAACAAAAGGAAAAAACAATATTAGAACTGTGAAAAGTCCTTAAATATTT
130 TAAAAATTAATTCGGAAA-AAAA-GAAAAAACAATATTAGAACTGTGAAAAGCCCTTAAATATTT
* *
103757 TTGACGTTCAATTATATATTTTTTTATGAATATTGTGGTAAAATATTGAGAAAAAATCTTTC-GG
193 TTGGCGTTGAATTATATA-TTTTTTATGAATATTGTGGTAAAA-ATTGAGAAAAAAT-TTTCAGG
* * * * *
103821 TTCATTTTTTTTTGGGGAACTTTTAACCAAAAT--TGT-GT-ACCATCACAGTTTTTGGATAAAA
255 -TCA--ATTTTTT-GGGAACTTTTAACCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAA
* * *
103882 ACGCGTTCGGGGCGCCCGATTCAATTTTGCATGATTTTCGGCGCCAAGACTCCTTGAAATATCTA
316 ACGCGTTCGGGGCCCCCGACTCAGTTTTGCATGATTTTCGGCGCCAAGACTCCTTGAAATATCTA
* * *
103947 TATTCATCTAAGCAAATCTCAACTTTATTGAATTCAAGGATTTGTTTTTTAGAGCATTAGAATCT
381 TATTCATCTAAGTAAATCTCAACTTTATTGGATTCAAGGATTTGTTTTTTAGAGCATCAGAATCT
* * *
104012 TGTTTGGATTTAATTAGAAATTAATTCAG-----AAA-AAAAACTATATTAGAAGTGTGAAAGTC
446 TGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAAAGAAAAACAATATTAGAAG-CTGAAAGTC
* * *
104071 CCATCAATATTTTTGGCGTTGAATTGTATATTTTTTATGATTATTGTGCCCAAAATGTGAGGAAA
510 CCTTCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGCCCAAAATGTGAGGAAA
* * * *
104136 AAATTTTCGGGTTAGTATTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTATAG
575 AAATTTTCGGGTCAGTTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-TTTTATGG
*
104201 CTAAAAACGCGTTCTGGGGCCC
639 CTAAAAACGCGTT-GGGGGCCC
* *
104223 CGGCTCAGTTTTGCATGATTTTTGGCGCCCAGACTCATTGAAATAACTATATTTTATCTAACAAA
1 CGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATAACTATATTTTATCTAACAAA
* * *
104288 ATCTCAGACACACGATATTTAAGGATTTGTTTTTACGAGAATCAGTATTCGGTTTCGATTCAAAT
66 ATCTCAGACACAGGATATTTAAGGATTTGTTTTTACGAGAATCAGAATTCGGTTTCGATTTAAAT
* *
104353 AAAAATTAATTCGGAAACAAAAAGAAAAAACAATA-TATGAATTGTGAGAAGCCCTTAAATACTT
131 AAAAATTAATTCGG-AA-AAAAAGAAAAAACAATATTA-GAACTGTGAAAAGCCCTTAAATA-TT
* * * * *
104417 TTAGG-GTTGAATTATATA-TTTTTATGAATATTGTGGTAAAAAAATTTATAAAAATTTTTCAAG
192 TTTGGCGTTGAATTATATATTTTTTATGAATATTGTGGT--AAAAATTGAGAAAAAATTTTCAGG
* * *
104480 CCAATTTTTTGGGAACTTTTAACCGAAATCGTGTGTTAACCATCACGATTTTTTGGCTAAAAACG
255 TCAATTTTTTGGGAACTTTTAACCGAAATCGTGTATTAACCATCACG-GTTTTTGGCTAAAAACG
* * *
104545 CGTTTGGGGCCCCCCGACTCAGTTTTGCATGATTTTCGGCGCGAACACTCCTTGAAATATCTATA
319 CGTTCGGGG-CCCCCGACTCAGTTTTGCATGATTTTCGGCGCCAAGACTCCTTGAAATATCTATA
* ** *
104610 TTTATCTAAGTAAATCTCAAAATTATTGGATTCAAGGATTT-TTTTTTAGAGCATCAGAATGTTG
383 TTCATCTAAGTAAATCTCAACTTTATTGGATTCAAGGATTTGTTTTTTAGAGCATCAGAATCTTG
* * *
104674 TTTCGATTTAATTAGAAATTAATTCAGAAAAACAAGAAGAACGATATTAGAAGCATGAAAGTCCC
448 TTTCGATTTAATTAGAAATTAATTCAGAAAAAAAAGAAAAACAATATTAGAAGC-TGAAAGTCCC
* * * *
104739 TTCAATATTTTTGGTGTTGAATTATGTCTTTTTTATGAGTATTGTGCCCAAAATGTGTGGAAAAA
512 TTCAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGCCCAAAATGTGAGGAAAAA
* * * * * * *
104804 TTTTTTGGGTAAGTTTTTTTTTAAATTTTAGTCGAAATCGTGTACTAACCATCACGGTTTATGGC
577 ATTTTCGGGTCAG-TTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-TTTTATGGC
**
104869 TAAAAACGCGTTCTGGGCCC
640 TAAAAACGCGTTGGGGGCCC
* * * *
104889 CGGCTCAGTTTTGCCTGATTTTTGGTGCCCAGACTCATTGAAATAACTATATTTTATCTAACAAA
1 CGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATAACTATATTTTATCTAACAAA
** * *
104954 ATCTCAGACACACAATATTTAAGGATTTGTTTTTACGAGAATCATAATTCGGTTTCGATTTAATT
66 ATCTCAGACACAGGATATTTAAGGATTTGTTTTTACGAGAATCAGAATTCGGTTTCGATTTAAAT
* *
105019 AGAAATTAATTCGGAAACAAGACGAAAAAAAACAATATTAGAACTGTGAAAAGCCCTTAAATATT
131 AAAAATTAATTCGGAAA-AA-A--AGAAAAAACAATATTAGAACTGTGAAAAGCCCTTAAATATT
*
105084 TTTGGTGTTGAATTATATATTTTTCTATGAATATTGTGGTAAAAAATTGAGAAAAAATATTTCAG
192 TTTGGCGTTGAATTATATATTTTT-TATGAATATTGTGGT-AAAAATTGAGAAAAAAT-TTTCAG
* * * * *
105149 GTCAATTTTTTGGGAACATTTAATCGAAATCGTGTACTAACCATCACTGTTTTTGGATAAAAACG
254 GTCAATTTTTTGGGAACTTTTAACCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACG
* * * *
105214 CGTTCGGGGCTCCCTACTCAGTTTTGCATGATTTTCGGTGCCAAGTA-TCCTTGAAATATCAATA
319 CGTTCGGGGCCCCCGACTCAGTTTTGCATGATTTTCGGCGCCAAG-ACTCCTTGAAATATCTATA
* * * *
105278 TTCATCTAAGTAAATCTCAACTTTATTGGATTGAAGTATTTATTTTTTAGACCATCAGAATCTTG
383 TTCATCTAAGTAAATCTCAACTTTATTGGATTCAAGGATTTGTTTTTTAGAGCATCAGAATCTTG
*
105343 TTTGGATTTAATTAGAA
448 TTTCGATTTAATTAGAA
105360 TTTTTTTTTT
Statistics
Matches: 2686, Mismatches: 329, Indels: 216
0.83 0.10 0.07
Matches are distributed among these distances:
655 18 0.01
656 6 0.00
657 9 0.00
658 58 0.02
659 369 0.14
660 281 0.10
661 379 0.14
662 29 0.01
664 3 0.00
665 221 0.08
666 416 0.15
667 121 0.05
668 134 0.05
669 129 0.05
670 142 0.05
671 61 0.02
672 61 0.02
673 112 0.04
674 117 0.04
675 20 0.01
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (659 bp):
CGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAAATAACTATATTTTATCTAACAAA
ATCTCAGACACAGGATATTTAAGGATTTGTTTTTACGAGAATCAGAATTCGGTTTCGATTTAAAT
AAAAATTAATTCGGAAAAAAAGAAAAAACAATATTAGAACTGTGAAAAGCCCTTAAATATTTTTG
GCGTTGAATTATATATTTTTTATGAATATTGTGGTAAAAATTGAGAAAAAATTTTCAGGTCAATT
TTTTGGGAACTTTTAACCGAAATCGTGTATTAACCATCACGGTTTTTGGCTAAAAACGCGTTCGG
GGCCCCCGACTCAGTTTTGCATGATTTTCGGCGCCAAGACTCCTTGAAATATCTATATTCATCTA
AGTAAATCTCAACTTTATTGGATTCAAGGATTTGTTTTTTAGAGCATCAGAATCTTGTTTCGATT
TAATTAGAAATTAATTCAGAAAAAAAAGAAAAACAATATTAGAAGCTGAAAGTCCCTTCAATATT
TTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGCCCAAAATGTGAGGAAAAAATTTTCGGG
TCAGTTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACCATCACTTTTATGGCTAAAAACGCGT
TGGGGGCCC
Found at i:107964 original size:333 final size:331
Alignment explanation
Indices: 107160--107989 Score: 848
Period size: 333 Copynumber: 2.5 Consensus size: 331
107150 AAAAGAGACA
* * *
107160 TTAATTAGAAATTAATTCAGAAAAACAAGAAAGAGGATATTAGAAGCGTGAAAGTCCTT--TCAA
1 TTAATTAGAAATTAATTCAAAAAAACAAGAAAAACGATATTAGAAGCGTGAAAGTCCTTCCTCAA
* *
107223 TTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTG-CCCAAAATGTGAGGAAAAA-CTT
66 TTTTTTTGGCGTTGAA-TATATATTTTTTATGAGTATTTTGTCACAAAAT-TGAGGAAAAATC-T
* * *
107286 TTCGGGTCAGTTTTTT-TAAATTTTAGCCGAAATCGTGTACTAACAATCACGATTTATGGATAAA
128 TT--GCTCAATTTTTTGCAAATTTTAGCCGAAATCGTGTACTAACAATCACGATTTATGGATAAA
* ** *
107350 AACGCGTTTTGGGGCCCCGACTCAGTTTTACATGATTTTTGGCGCCCAGACTCATTGAAATAGCT
191 AACGCGTTTCGAAGCCCCGACTCAGTTTTACATGATTTTTGGCGCCAAGACTCATTGAAATAGCT
* * * * *
107415 AAATTTTATCTAACAAAATCCCAGACACACTGGATTTAATGATTTGTTTTTACGAGAATCAAAAT
256 AAATTTCATCTAACAAAATCCCAAACACACTGGATTCAAGGATTTGTTTTTACGAGAATCAAAAC
*
107480 CTGGTTTCGAT
321 CTGATTTCGAT
* * * * *
107491 TCAATTAGAAATTAATTCAGAAACAATAAGAAAAAACGATATTAGAAGTGTGAAAAG-CC--CTT
1 TTAATTAGAAATTAATTCA-AAAAAACAAG-AAAAACGATATTAGAAGCGTG-AAAGTCCTTCCT
* * * * *
107553 AAATTTTTTTGGCGTTGAATTATATATTTTTTATGAATATTGTGGT-AAAAAATTGAGAAAAAAA
63 CAATTTTTTTGGCGTTGAA-TATATATTTTTTATGAGTATT-TTGTCACAAAATTGAG-GAAAAA
* * * * * * *
107617 TCTTT-CCCAATTTTTTGGAAACTTTTAACCGAAATCGTGTACTAATAATCACGGTTTTTGGCTA
125 TCTTTGCTCAATTTTTTGCAAA-TTTTAGCCGAAATCGTGTACTAACAATCACGATTTATGGATA
* * * * *
107681 AAAACGCGTTTCGAAG-CCCGACTCAGTTTTACATGATTTTTTGCGCTAAGACTCCTTGAAGTAT
189 AAAACGCGTTTCGAAGCCCCGACTCAGTTTTACATGATTTTTGGCGCCAAGACTCATTGAAATAG
* * * *
107745 CTATA-TTCATCTAAGC-AAAT-CTAAACATTA-TCGGATTCAAGGATTTGTTTTTACGAGCATC
254 CTAAATTTCATCTAA-CAAAATCCCAAACA-CACT-GGATTCAAGGATTTGTTTTTACGAGAATC
* * * *
107806 AGAACCTTATTTTGGT
316 AAAACCTGATTTCGAT
*
107822 TTAATTAGAAATTAATTCAAAAAAACAAGAAAAACGATATTAGAAGCGCGAAAGTTCCTTCCCTC
1 TTAATTAGAAATTAATTCAAAAAAACAAGAAAAACGATATTAGAAGCGTGAAAG-TCCTT-CCTC
* * * * * *
107887 AATATTTTTGGCAG-TCAA-ATATATATTTTATGGGTATTTTGTCTCAAAATTTAGGAAAAATCA
64 AATTTTTTTGGC-GTTGAATATATATTTTTTATGAGTATTTTGTCACAAAATTGAGGAAAAATC-
* *
107950 TTTGCATTAATTTTTTGCAAAATTTAGCCGAAATCGTGTA
127 TTTGC-TCAATTTTTTGCAAATTTTAGCCGAAATCGTGTA
107990 TGTTCCAGGG
Statistics
Matches: 407, Mismatches: 68, Indels: 47
0.78 0.13 0.09
Matches are distributed among these distances:
328 4 0.01
329 19 0.05
330 26 0.06
331 121 0.30
332 75 0.18
333 142 0.35
334 19 0.05
335 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (331 bp):
TTAATTAGAAATTAATTCAAAAAAACAAGAAAAACGATATTAGAAGCGTGAAAGTCCTTCCTCAA
TTTTTTTGGCGTTGAATATATATTTTTTATGAGTATTTTGTCACAAAATTGAGGAAAAATCTTTG
CTCAATTTTTTGCAAATTTTAGCCGAAATCGTGTACTAACAATCACGATTTATGGATAAAAACGC
GTTTCGAAGCCCCGACTCAGTTTTACATGATTTTTGGCGCCAAGACTCATTGAAATAGCTAAATT
TCATCTAACAAAATCCCAAACACACTGGATTCAAGGATTTGTTTTTACGAGAATCAAAACCTGAT
TTCGAT
Found at i:108052 original size:2 final size:2
Alignment explanation
Indices: 108045--108069 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
108035 ACTCCTTGAA
108045 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
108070 ATAAAATACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:109087 original size:123 final size:123
Alignment explanation
Indices: 108841--109090 Score: 432
Period size: 122 Copynumber: 2.0 Consensus size: 123
108831 CTTTCGGGAC
108841 TATTTTTGGGAAACTTTTAACCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAACGCAT
1 TATTTTTGGGAAACTTTTAACCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAACGCAT
108906 TTCGGGGCGCCGACTCATTTTGCATAATTTATGGCGCTAAGACTCCTTGAAGTATCTA
66 TTCGGGGCGCCGACTCATTTTGCATAATTTATGGCGCTAAGACTCCTTGAAGTATCTA
*
108964 TATTTTT-GGAAACTTTTAACCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAACGCGT
1 TATTTTTGGGAAACTTTTAACCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAACGCAT
* * *
109028 TTTGGGGC-CTCGGCTCAGTTTTGCATAATTTTTGGCGCTAAGACTCCTTGAAGTATCTA
66 TTCGGGGCGC-CGACTCA-TTTTGCATAATTTATGGCGCTAAGACTCCTTGAAGTATCTA
109087 TATT
1 TATT
109091 CATCTAAGCA
Statistics
Matches: 121, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
121 1 0.01
122 69 0.57
123 51 0.42
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.36
Consensus pattern (123 bp):
TATTTTTGGGAAACTTTTAACCGAAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAACGCAT
TTCGGGGCGCCGACTCATTTTGCATAATTTATGGCGCTAAGACTCCTTGAAGTATCTA
Found at i:120201 original size:22 final size:21
Alignment explanation
Indices: 120160--120209 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
120150 TTTTTTTTGC
*
120160 ACAAAGAAAGAAAAAAAAAGA
1 ACAAAGAAAAAAAAAAAAAGA
*
120181 ACAAGGAAAAAAAGAAAAAAGA
1 ACAAAGAAAAAAA-AAAAAAGA
120203 ACAAAGA
1 ACAAAGA
120210 CCTCAAGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (21 bp):
ACAAAGAAAAAAAAAAAAAGA
Found at i:123177 original size:12 final size:12
Alignment explanation
Indices: 123160--123192 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
123150 AGGTAAAGCG
123160 GAGAGATTCAAA
1 GAGAGATTCAAA
123172 GAGAGATTCAAA
1 GAGAGATTCAAA
*
123184 GACAGATTC
1 GAGAGATTC
123193 TAACTAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.18
Consensus pattern (12 bp):
GAGAGATTCAAA
Found at i:124905 original size:11 final size:11
Alignment explanation
Indices: 124889--124913 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
124879 CAAAGTACAA
124889 GCAACATCAGT
1 GCAACATCAGT
124900 GCAACATCAGT
1 GCAACATCAGT
124911 GCA
1 GCA
124914 GTTAGAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.16
Consensus pattern (11 bp):
GCAACATCAGT
Found at i:129193 original size:13 final size:13
Alignment explanation
Indices: 129175--129201 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
129165 AGAGATTGAT
129175 GGACAATAAAAGA
1 GGACAATAAAAGA
129188 GGACAATAAAAGA
1 GGACAATAAAAGA
129201 G
1 G
129202 AGAATGTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.26, T:0.07
Consensus pattern (13 bp):
GGACAATAAAAGA
Found at i:130386 original size:2 final size:2
Alignment explanation
Indices: 130379--130409 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
130369 GTTTTTATTA
130379 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 A
130410 ACTAATAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:131919 original size:45 final size:45
Alignment explanation
Indices: 131868--131959 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
131858 ACTCCGTCTT
131868 TAACTTTTCTCACATCATCTCCTTTTACTTTCCGCTTCGTCAAAA
1 TAACTTTTCTCACATCATCTCCTTTTACTTTCCGCTTCGTCAAAA
*
131913 TAACTTTTCTCATATCATCTCCTTTTACTTTCCGCTTCGTCAAAA
1 TAACTTTTCTCACATCATCTCCTTTTACTTTCCGCTTCGTCAAAA
131958 TA
1 TA
131960 TCTGCTAGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.23, C:0.29, G:0.04, T:0.43
Consensus pattern (45 bp):
TAACTTTTCTCACATCATCTCCTTTTACTTTCCGCTTCGTCAAAA
Found at i:134251 original size:20 final size:20
Alignment explanation
Indices: 134226--134301 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
134216 TCTATGAGCC
134226 AACAAACCCCTTCCCAAACA
1 AACAAACCCCTTCCCAAACA
* * *
134246 AACAAACCCAGTGAAATCTCATTACA
1 AACAAACCC-CT----TCCCA-AACA
134272 ATACAAACCCCTTCCCAAACA
1 A-ACAAACCCCTTCCCAAACA
134293 AACAAACCC
1 AACAAACCC
134302 AGTGAAATCT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
20 17 0.40
21 5 0.12
22 4 0.09
25 4 0.09
26 5 0.12
27 8 0.19
ACGTcount: A:0.46, C:0.38, G:0.03, T:0.13
Consensus pattern (20 bp):
AACAAACCCCTTCCCAAACA
Found at i:134282 original size:47 final size:47
Alignment explanation
Indices: 134227--134325 Score: 189
Period size: 47 Copynumber: 2.1 Consensus size: 47
134217 CTATGAGCCA
134227 ACAAACCCCTTCCCAAACAAACAAACCCAGTGAAATCTCATTACAAT
1 ACAAACCCCTTCCCAAACAAACAAACCCAGTGAAATCTCATTACAAT
134274 ACAAACCCCTTCCCAAACAAACAAACCCAGTGAAATCTCATTACAAT
1 ACAAACCCCTTCCCAAACAAACAAACCCAGTGAAATCTCATTACAAT
*
134321 TCAAA
1 ACAAA
134326 TAAATCTTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.45, C:0.33, G:0.04, T:0.17
Consensus pattern (47 bp):
ACAAACCCCTTCCCAAACAAACAAACCCAGTGAAATCTCATTACAAT
Found at i:134319 original size:26 final size:26
Alignment explanation
Indices: 134243--134319 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
134233 CCCTTCCCAA
134243 ACAAACAAACCCAGTGAAATCTCATT
1 ACAAACAAACCCAGTGAAATCTCATT
* * *
134269 ACAATACAAACCC-CT----TCCCA-A
1 ACAA-ACAAACCCAGTGAAATCTCATT
134290 ACAAACAAACCCAGTGAAATCTCATT
1 ACAAACAAACCCAGTGAAATCTCATT
134316 ACAA
1 ACAA
134320 TTCAAATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 14
0.66 0.10 0.24
Matches are distributed among these distances:
20 8 0.21
21 5 0.13
22 4 0.11
25 4 0.11
26 9 0.24
27 8 0.21
ACGTcount: A:0.47, C:0.31, G:0.05, T:0.17
Consensus pattern (26 bp):
ACAAACAAACCCAGTGAAATCTCATT
Found at i:135429 original size:46 final size:46
Alignment explanation
Indices: 135362--135453 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
135352 ATCTGTAATA
135362 CTCCAACATGAACAAGTATGAAACTACTTAAATGGATAATGGTTGT
1 CTCCAACATGAACAAGTATGAAACTACTTAAATGGATAATGGTTGT
135408 CTCCAACATGAACAAGTATGAAACTACTTAAATGGATAATGGTTGT
1 CTCCAACATGAACAAGTATGAAACTACTTAAATGGATAATGGTTGT
135454 TTACTTGTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.28
Consensus pattern (46 bp):
CTCCAACATGAACAAGTATGAAACTACTTAAATGGATAATGGTTGT
Found at i:142497 original size:19 final size:20
Alignment explanation
Indices: 142473--142512 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
142463 CGTGTATCTG
142473 TAATTGTTTCACTACT-ATT
1 TAATTGTTTCACTACTGATT
*
142492 TAATTGTTTCATTACTGATT
1 TAATTGTTTCACTACTGATT
142512 T
1 T
142513 GGGTTCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.25, C:0.12, G:0.07, T:0.55
Consensus pattern (20 bp):
TAATTGTTTCACTACTGATT
Found at i:145456 original size:17 final size:17
Alignment explanation
Indices: 145436--145489 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
145426 GAATGTGAAA
145436 GCACATAGAATGAACAT
1 GCACATAGAATGAACAT
* *
145453 GCACACA-ATAAGAA-A-
1 GCACATAGA-ATGAACAT
*
145468 GCACATAGAATGAGCAT
1 GCACATAGAATGAACAT
145485 GCACA
1 GCACA
145490 ATTTGGTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
15 9 0.32
16 4 0.14
17 15 0.54
ACGTcount: A:0.48, C:0.20, G:0.19, T:0.13
Consensus pattern (17 bp):
GCACATAGAATGAACAT
Found at i:161246 original size:26 final size:26
Alignment explanation
Indices: 161217--161269 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
161207 TGTACCAACC
*
161217 CGTAAATATAACTGAAATTAGAAACT
1 CGTAAATATAACTGAAATTAAAAACT
*
161243 CGTAAATGTAACTGAAATTAAAAACT
1 CGTAAATATAACTGAAATTAAAAACT
161269 C
1 C
161270 AAACATGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.49, C:0.13, G:0.11, T:0.26
Consensus pattern (26 bp):
CGTAAATATAACTGAAATTAAAAACT
Found at i:161284 original size:26 final size:26
Alignment explanation
Indices: 161226--161285 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
161216 CCGTAAATAT
* * *
161226 AACTGAAATTAGAAACTCGTAAATGT
1 AACTGAAATTAAAAACTCGAAAATGC
161252 AACTGAAATTAAAAACTC-AAACATGC
1 AACTGAAATTAAAAACTCGAAA-ATGC
*
161278 AATTGAAA
1 AACTGAAA
161286 AAATTGGAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.52, C:0.13, G:0.12, T:0.23
Consensus pattern (26 bp):
AACTGAAATTAAAAACTCGAAAATGC
Found at i:168499 original size:26 final size:26
Alignment explanation
Indices: 168463--168515 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
168453 GGTAATTTAT
168463 GCTATACTTACATATCATGCACTGAC
1 GCTATACTTACATATCATGCACTGAC
168489 GCTATACTTACATATCATGCACTGAC
1 GCTATACTTACATATCATGCACTGAC
168515 G
1 G
168516 ATCGATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.30
Consensus pattern (26 bp):
GCTATACTTACATATCATGCACTGAC
Done.