Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006163.1 Hibiscus syriacus cultivar Beakdansim tig00014639_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 117207
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:7404 original size:17 final size:18
Alignment explanation
Indices: 7377--7410 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
7367 AATGTGTGCC
7377 AAAAAAGGGTGGTGTGAT
1 AAAAAAGGGTGGTGTGAT
7395 AAAAAA-GGTGGTGTGA
1 AAAAAAGGGTGGTGTGA
7411 CTGTGGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.41, C:0.00, G:0.38, T:0.21
Consensus pattern (18 bp):
AAAAAAGGGTGGTGTGAT
Found at i:20554 original size:40 final size:40
Alignment explanation
Indices: 20510--20631 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
20500 ACCGTAGTGC
20510 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
20550 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
20590 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
20630 TA
1 TA
20632 TAAACCTGCA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:33704 original size:167 final size:172
Alignment explanation
Indices: 33409--33754 Score: 531
Period size: 167 Copynumber: 2.0 Consensus size: 172
33399 AAGTCATTGA
* *
33409 GAATTGGGTTCAAATGATCTCTTATTGCTCTTGGTCTTGCAACTTGAAGATTAATTATTGTATCG
1 GAATTGAGTTCAAATGATCTCTTATTGATCTTGGTCTTGCAACTTGAAGATTAA-TA-T-TATCG
* * *
33474 GGATGGTCGTGATCTCCCATGTTGTTGCCTTGTAATTGTAGTTGGTTTAAATGTTCTCTGGTTAT
63 GGATCGTCATGATCTCCCATGTTGTTGCCTTGTAATTGTAGTTGGCTTAAATGTTCTCTGGTTAT
* * * *
33539 TTGGTCACGTAGCCTCTTTCTGAATAATTGTTTAACTTTAGGGTC
128 TTGGTCACGTAGCCTATGTCTGAATAATTGTTCAACTTCAGGGTC
*
33584 GAATTGAGTTTAAATGATCTCTTATTGATCTTGGTCTTGCAACTTGAAGATT-A-A-T-T-GGGA
1 GAATTGAGTTCAAATGATCTCTTATTGATCTTGGTCTTGCAACTTGAAGATTAATATTATCGGGA
33644 TCGTCATGATCTCCCATGTTGTTGCCTTGTAATTGTAGTTGGCTTAAATGTTCTCTGGTTATTTG
66 TCGTCATGATCTCCCATGTTGTTGCCTTGTAATTGTAGTTGGCTTAAATGTTCTCTGGTTATTTG
*
33709 GTCACGTAGCCTATGTCTGAATGATTGTTCAACTTCAGGGTC
131 GTCACGTAGCCTATGTCTGAATAATTGTTCAACTTCAGGGTC
33751 GAAT
1 GAAT
33755 GGTTCTAATG
Statistics
Matches: 160, Mismatches: 11, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
167 107 0.67
168 1 0.01
169 1 0.01
172 1 0.01
174 1 0.01
175 49 0.31
ACGTcount: A:0.21, C:0.15, G:0.22, T:0.42
Consensus pattern (172 bp):
GAATTGAGTTCAAATGATCTCTTATTGATCTTGGTCTTGCAACTTGAAGATTAATATTATCGGGA
TCGTCATGATCTCCCATGTTGTTGCCTTGTAATTGTAGTTGGCTTAAATGTTCTCTGGTTATTTG
GTCACGTAGCCTATGTCTGAATAATTGTTCAACTTCAGGGTC
Found at i:36474 original size:130 final size:131
Alignment explanation
Indices: 36162--36657 Score: 631
Period size: 131 Copynumber: 3.8 Consensus size: 131
36152 ATTCAATGAA
* * * * *
36162 AGAAAATGATAATATCTAATTATTTCCGATCGAGAATAAATGACCTCTCATGCCTTAAACCA-AT
1 AGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAGA-
* * * ** *
36226 CATTTATTACTCCAATCAAAAT-AAAGAGATATCACTATTTCTTC-TTAAAATTCAATATCAAAT
65 CATTTATTACTCCAATCGAAATGAAA-AGATATCACTATTCCATCTTTAAAA-TCAATATTGATT
36289 CGAG
128 CGAG
* ** * * * *
36293 TGAAAACGATAATATCTAATGATTTATAATCGATAATAAATGACATCTCATACCTTACAGTAGAC
1 AGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAGAC
* *
36358 ATTTATTGCTCCAATCGAAATGAAAAGATATCAGTATTCCATCTTTAAAATCAATATTGATTCGA
66 ATTTATTACTCCAATCGAAATGAAAAGATATCACTATTCCATCTTTAAAATCAATATTGATTCGA
36423 G
131 G
**
36424 AG-AAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCATTC
1 AGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAGAC
* * * *
36488 ATTTATTGCTCCAATCGAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTGTTTCGA
66 ATTTATTACTCCAATCGAAATGAAAAGATATCACTATTCCATCTTTAAAATCAATATTGATTCGA
36553 G
131 G
* * * * *
36554 AGAAAACGATAATATCGAATTATTTCCAATCGAGAATAAATGACCTATCATGCCTTAAAGCAGTC
1 AGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAGAC
* * *
36619 ATTTATTACTCCAACCGAGATGAAAAGATATTACTATTC
66 ATTTATTACTCCAATCGAAATGAAAAGATATCACTATTC
36658 TCGATATCGA
Statistics
Matches: 318, Mismatches: 43, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
130 118 0.37
131 190 0.60
132 10 0.03
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (131 bp):
AGAAAACGATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCAGAC
ATTTATTACTCCAATCGAAATGAAAAGATATCACTATTCCATCTTTAAAATCAATATTGATTCGA
G
Found at i:36644 original size:261 final size:261
Alignment explanation
Indices: 36169--36649 Score: 692
Period size: 261 Copynumber: 1.8 Consensus size: 261
36159 GAAAGAAAAT
* * *
36169 GATAATATCTAATTATTTCCGATCGAGAATAAATGACCTCTCATGCCTTAAACCAATCATTTATT
1 GATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAACCAATCATTTATT
* * * *
36234 ACTCCAATCAAAATAAAGAGATATCACTATTTCTTCTTAAAATTCAATATCAAATCGAGTGAAAA
66 ACTCCAATCAAAATAAAGAGATATCACTATTCCATCTTAAAAATCAATATCAAATCGAGAGAAAA
* * * * * *
36299 CGATAATATCTAATGATTTATAATCGATAATAAATGACATCTCATACCTTACAGTAGACATTTAT
131 CGATAATATCGAATGATTTACAATCGAGAATAAATGACATATCATACCTTAAAGCAGACATTTAT
* *
36364 TGCTCCAATCGAAATGAAAAGATATCAGTATTCCATCTTTAAAATCAATATTGATTCGAGAGAAA
196 TACTCCAACCGAAATGAAAAGATATCAGTATTCCATCTTTAAAATCAATATTGATTCGAGAGAAA
36429 C
261 C
* *
36430 GATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAAGCATTCATTTATT
1 GATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAACCAATCATTTATT
* * * ****
36495 GCTCCAATCGAAATGAAGAGATATCACTATTCCATCTTAAAAATCAATATTGTTTCGAGAGAAAA
66 ACTCCAATCAAAATAAAGAGATATCACTATTCCATCTTAAAAATCAATATCAAATCGAGAGAAAA
* * * * *
36560 CGATAATATCGAATTATTTCCAATCGAGAATAAATGACCTATCATGCCTTAAAGCAGTCATTTAT
131 CGATAATATCGAATGATTTACAATCGAGAATAAATGACATATCATACCTTAAAGCAGACATTTAT
*
36625 TACTCCAACCGAGATGAAAAGATAT
196 TACTCCAACCGAAATGAAAAGATAT
36650 TACTATTCTC
Statistics
Matches: 190, Mismatches: 30, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
261 190 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.31
Consensus pattern (261 bp):
GATAATATCTAATGATTTCCAATCGAGAATAAATGACCTCTCATACCTTAAACCAATCATTTATT
ACTCCAATCAAAATAAAGAGATATCACTATTCCATCTTAAAAATCAATATCAAATCGAGAGAAAA
CGATAATATCGAATGATTTACAATCGAGAATAAATGACATATCATACCTTAAAGCAGACATTTAT
TACTCCAACCGAAATGAAAAGATATCAGTATTCCATCTTTAAAATCAATATTGATTCGAGAGAAA
C
Found at i:38839 original size:18 final size:18
Alignment explanation
Indices: 38818--38878 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
38808 AAATAAAAAA
38818 ATTAATAATAATAATAAT
1 ATTAATAATAATAATAAT
* *
38836 ATTATTATTAATAATAATT
1 ATTAATAATAATAATAA-T
* *
38855 ATAAATCA-AATAATAAT
1 ATTAATAATAATAATAAT
38872 ATTAATA
1 ATTAATA
38879 TTATCGGGAC
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
17 6 0.18
18 23 0.68
19 5 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTAATAATAATAATAAT
Found at i:39555 original size:41 final size:40
Alignment explanation
Indices: 39510--39618 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 40
39500 CCTGAAGGTT
* *
39510 TTATAGATGGCCCGAAGTACTTATCATCTTGCTCGAAAGGC
1 TTATAGATGGCCCGAAG-ACTTATCATCATGCTCGAAAGAC
* * *
39551 TTATAGATGACCCAAAGAGTTTAATCATCATGCTCGAAAGAC
1 TTATAGATGGCCCGAAGA-CTT-ATCATCATGCTCGAAAGAC
39593 TTACT-GATGGCCCGAAGGACTTATCA
1 TTA-TAGATGGCCCGAA-GACTTATCA
39619 AATTTGGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
40 1 0.02
41 21 0.38
42 31 0.55
43 3 0.05
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (40 bp):
TTATAGATGGCCCGAAGACTTATCATCATGCTCGAAAGAC
Found at i:39561 original size:225 final size:222
Alignment explanation
Indices: 39164--39615 Score: 536
Period size: 225 Copynumber: 2.0 Consensus size: 222
39154 TGGAAATAGT
* * **
39164 TTACTAGGTAAGAAACTTTGGAAATCATTTTCTTACTTTTCAAAAATTTCACTCTCTGAAGAAAC
1 TTACTAAGTAAGAAACTTTGGAAATCATTTTCTCACTTTTCAAAAATTT--CTCAATGAAGAAAC
* * ** * *
39229 TTTGAAAATATCTTTCTCATTTTTCAAATCATGTGAAAACATCCTGCCCGAAAGTCTTACGAATG
64 TTTGAAAATAGCCTTCTCATTTTTCAAATCACATGAAAACATCATGCCCGAAAGTCTTAAGAATG
* * *
39294 TCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTAAAGATGACCCGAAG-GATTTAGGCATCATG
129 GCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTAAAGATGACCCAAAGAG-TTTAAGCATCATG
* *
39358 ATCAAAAGACTTATTGATGGCCTAAAGGAC
193 ATCAAAAGACTTACTGATGGCCCAAAGGAC
39388 TTACTAAGTAAGAAACTTTGGAAATCATTTTCTCACTTTTCAGAAAAGATTT-T-AATG-AGAAA
1 TTACTAAGTAAGAAACTTTGGAAATCATTTTCTCACTTTTC--AAAA-ATTTCTCAATGAAGAAA
* * * * * *
39450 CTTTGGAAATCGCCTTCTCATTTTTCAAATTATCACATGAAAGCATCATGCCTGAAGGTTTTATA
63 CTTTGAAAATAGCCTTCTCATTTTTC-AA--ATCACATGAAAACATCATGCCCGAAAGTCTTA-A
* * *
39515 G-ATGGCCCGAAGTACTTATCATCTTGCTCGAAAGGCTTATAGATGACCCAAAGAGTTTAATCAT
124 GAATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTAAAGATGACCCAAAGAGTTTAAGCAT
* * *
39579 CATGCTCGAAAGACTTACTGATGGCCCGAAGGAC
189 CATGATCAAAAGACTTACTGATGGCCCAAAGGAC
39613 TTA
1 TTA
39616 TCAAATTTGG
Statistics
Matches: 193, Mismatches: 27, Indels: 15
0.82 0.11 0.06
Matches are distributed among these distances:
222 27 0.14
223 4 0.02
224 40 0.21
225 112 0.58
226 6 0.03
227 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (222 bp):
TTACTAAGTAAGAAACTTTGGAAATCATTTTCTCACTTTTCAAAAATTTCTCAATGAAGAAACTT
TGAAAATAGCCTTCTCATTTTTCAAATCACATGAAAACATCATGCCCGAAAGTCTTAAGAATGGC
CCGAAGGACTTATCATCTTGCTCGAAAGGCTTAAAGATGACCCAAAGAGTTTAAGCATCATGATC
AAAAGACTTACTGATGGCCCAAAGGAC
Found at i:40067 original size:239 final size:237
Alignment explanation
Indices: 39633--40081 Score: 605
Period size: 239 Copynumber: 1.9 Consensus size: 237
39623 TGGAAATATT
* * * **
39633 TTACTAGGTAAGAAACTTTGGAAATCACTTTCATACTTTTCAAAAATTTTATTTTCTGAAAATAC
1 TTACTAAGTAAGAAACTTTGGAAATCACTTTCATACTTTTAAAAAAATCAATTTTCTGAAAATAC
*
39698 TAAATGAGAAACTTTGAAAATCGTTTTCTCATTTTTCGAAAATCATGTGAAATCATGCTGCTCAA
66 TAAATGAGAAACTTTGAAAATCATTTTCTCATTTTTCGAAAATCATGTGAAA-CATGCTGCTCAA
** * ** * *
39763 AGGTCTTATAGATGGCCTGAAGGATTTATCATCTTGCTTGAAAGACTAAAAGATGACCCGAAGGA
130 AGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCAAAAGACTAAAAGATGAACAGAAGGA
39828 TTTAAGCATCATGCTCAAAAGACATAGTGATGGCTCGAGGGAC
195 TTTAAGCATCATGCTCAAAAGACATAGTGATGGCTCGAGGGAC
*** * *
39871 TTACTAAGTAAGAAACTTTGGAAATTGTTTTCTTAC-TTTAAAAAAATCAATTTTTTAGAAAATA
1 TTACTAAGTAAGAAACTTTGGAAATCACTTTCATACTTTTAAAAAAATCAATTTTCT-GAAAATA
* * * *
39935 TTTAAATGAGAAACTTTGAAAATCATTTTTTCATTTTTCGAACATCATTTGAAA-ATGTCATGCT
65 -CTAAATGAGAAACTTTGAAAATCATTTTCTCATTTTTCGAAAATCATGTGAAACATG-C-TGCT
* * * *
39999 CGAAGGTCTTATGGATGGCCCAAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGAACAGAA
127 CAAAGGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCAAAAGACTAAAAGATGAACAGAA
40064 GGATTTAAGCATCATGCT
192 GGATTTAAGCATCATGCT
40082 TGAAAGACTT
Statistics
Matches: 181, Mismatches: 26, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
237 18 0.10
238 39 0.22
239 124 0.69
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (237 bp):
TTACTAAGTAAGAAACTTTGGAAATCACTTTCATACTTTTAAAAAAATCAATTTTCTGAAAATAC
TAAATGAGAAACTTTGAAAATCATTTTCTCATTTTTCGAAAATCATGTGAAACATGCTGCTCAAA
GGTCTTATAGATGGCCCAAAGGACTTATCATCTTGCTCAAAAGACTAAAAGATGAACAGAAGGAT
TTAAGCATCATGCTCAAAAGACATAGTGATGGCTCGAGGGAC
Found at i:40249 original size:57 final size:57
Alignment explanation
Indices: 40113--40274 Score: 184
Period size: 58 Copynumber: 2.8 Consensus size: 57
40103 AAGGACATAC
* * * * *
40113 TCATCAAGAAACCCATAAAAATTAAGCTTAGTTTC-TTAAAAACTTTCATTTACAATTA
1 TCATCAAGAAACCCATAAAAATTAGGCTTAGCTTCTTTAAAAA--ATCATTGACAATAA
* *
40171 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTAAAAAATCATTGGA-AGTAA
1 TCATCAAGAAACCCATAAAAATTAGGCTTAGCTTCTTTAAAAAATCATT-GACAATAA
* * *
40228 TCATCAAGAAACCCATGAAAATTAGGCTTATCTTATTTTAAAAAATC
1 TCATCAAGAAACCCATAAAAATTAGGCTTAGCTT-CTTTAAAAAATC
40275 CATCATGTCA
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
57 39 0.43
58 44 0.49
59 7 0.08
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.31
Consensus pattern (57 bp):
TCATCAAGAAACCCATAAAAATTAGGCTTAGCTTCTTTAAAAAATCATTGACAATAA
Found at i:40489 original size:52 final size:52
Alignment explanation
Indices: 40433--40542 Score: 157
Period size: 52 Copynumber: 2.1 Consensus size: 52
40423 TCAAAACTTA
* * * * * *
40433 TTTGAAAATATCAAGAAACCCTTGAAAATTAGGCTTAGTTTCTAAAAATTCT
1 TTTGAAAACATCAAAAAACCCCTGAAAATCAGGCATAGTTTCTAAAAAATCT
*
40485 TTTGAAAACATCAAAAAACCCCTGACAATCAGGCATAGTTTCTAAAAAATCT
1 TTTGAAAACATCAAAAAACCCCTGAAAATCAGGCATAGTTTCTAAAAAATCT
40537 TTTGAA
1 TTTGAA
40543 TCACCAAGTC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.31
Consensus pattern (52 bp):
TTTGAAAACATCAAAAAACCCCTGAAAATCAGGCATAGTTTCTAAAAAATCT
Found at i:45386 original size:818 final size:819
Alignment explanation
Indices: 43811--46254 Score: 4829
Period size: 818 Copynumber: 3.0 Consensus size: 819
43801 TGGAGTAATC
43811 AGTTGGGCTTGAGCAACTTGGGATATAGTTTGTTGTATAAAAATGAAGGAAAACTGAGAAGAAGC
1 AGTTGGGCTTGAGCAACTTGGGATATAGTTTGTTGTATAAAAATGAAGGAAAACTGAGAAGAAGC
43876 TCTTTTGACTTCATTTTCTCTTTGCCACTATTATGATCATCTTGAAGACCTAGTGAATGATCATT
66 TCTTTTGACTTCATTTTCTCTTTGCCACTATTATGATCATCTTGAAGACCTAGTGAATGATCATT
43941 GAGATATTCATTTTGAAGGTTCAACTTTTGACCAACATCTTGTGGGAGACATTGGTTTTTAGATC
131 GAGATATTCATTTTGAAGGTTCAACTTTTGACCAACATCTTGTGGGAGACATTGGTTTTTAGATC
44006 TCCTCTTATCAATAAGTTCTGGTCTTTCAGGGAGCTTAGGTTTTCTATCTTCAAAGCATAACAAC
196 TCCTCTTATCAATAAGTTCTGGTCTTTCAGGGAGCTTAGGTTTTCTATCTTCAAAGCATAACAAC
44071 CCCTTCATGATGAGGTTTTGAACCTTTAATATCATAACCGCAAAACTTTTCGTAGAGTGGCTAAA
261 CCCTTCATGATGAGGTTTTGAACCTTTAATATCATAACCGCAAAACTTTTCGTAGAGTGGCTAAA
44136 ATCT-CAGAATGATATCTGTATGAATTTTTGACATCTTGCCAATCTAGACACAAATAAATATTAG
326 ATCTCCAGAATGATATCTGTATGAATTTTTGACATCTTGCCAATCTAGACACAAATAAATATTAG
44200 GTCTTGGAGGAACATGTTCTAGAAGGCCACTTTCGAAGATGAATGGTATCAAGTCTGAATATGAC
391 GTCTTGGAGGAACATGTTCTAGAAGGCCACTTTCGAAGATGAATGGTATCAAGTCTGAATATGAC
44265 CCTAGAATTGGAATGAGATATATCCTCCTCTTTTTCTTCTTATTCTTTTTAGCTTTCTTTACTAG
456 CCTAGAATTGGAATGAGATATATCCTCCTCTTTTTCTTCTTATTCTTTTTAGCTTTCTTTACTAG
44330 AATTTGAACTTCCTCTATGCCTTTCTTCTTTGAGTTAGACTTAACTTTCGTGTCAGAAGTTTCAA
521 AATTTGAACTTCCTCTATGCCTTTCTTCTTTGAGTTAGACTTAACTTTCGTGTCAGAAGTTTCAA
44395 CATCAATTTTCGCTTTTCCTAACATGATATGTGTCACATTTTCTGGAATCTTACCGATTGTTGGA
586 CATCAATTTTCGCTTTTCCTAACATGATATGTGTCACATTTTCTGGAATCTTACCGATTGTTGGA
44460 GTTGACTTGGATTAACATACTCCCCAATAGGTTCTTGATCATCTTTTATCCTCACATTGGCTGCA
651 GTTGACTTGGATTAACATACTCCCCAATAGGTTCTTGATCATCTTTTATCCTCACATTGGCTGCA
44525 CAACCAACATTTATATTTTCACTCAAAGTCTTCATCTTTCCTGGCATAATATAGTTCTCTAACGA
716 CAACCAACATTTATATTTTCACTCAAAGTCTTCATCTTTCCTGGCATAATATAGTTCTCTAACGA
44590 TTTCTCCCTATATATCACTGTAATTATCCCTATATCCCA
781 TTTCTCCCTATATATCACTGTAATTATCCCTATATCCCA
44629 AGTTGGGCTTGAGCAACTTGGGATATAGTTTGTTGTATAAAAATGAAGGAAAACTGAGAAGAAGC
1 AGTTGGGCTTGAGCAACTTGGGATATAGTTTGTTGTATAAAAATGAAGGAAAACTGAGAAGAAGC
44694 TCTTTTGACTTCATTTTCTCTTTGCCACTATTATGATCATCTTGAAGACCTAGTGAATGATCATT
66 TCTTTTGACTTCATTTTCTCTTTGCCACTATTATGATCATCTTGAAGACCTAGTGAATGATCATT
44759 GAGATATTCATTTTGAAGGTTCAACTTTTGACCAACATCTTGTGGGAGACATTGGTTTTTAGATC
131 GAGATATTCATTTTGAAGGTTCAACTTTTGACCAACATCTTGTGGGAGACATTGGTTTTTAGATC
44824 TCCTCTTATCAATAAGTTCTGGTCTTTC-GGGAGCTTAGGTTTTCTATCTTCAAAGCATAACAAC
196 TCCTCTTATCAATAAGTTCTGGTCTTTCAGGGAGCTTAGGTTTTCTATCTTCAAAGCATAACAAC
44888 CCCTTCATGATGAGGTTTTGAACCTTTAATATCATAACCGCAAAACTTTTCGTAGAGTGGCTAAA
261 CCCTTCATGATGAGGTTTTGAACCTTTAATATCATAACCGCAAAACTTTTCGTAGAGTGGCTAAA
44953 ATCTCCAGAATGATATCTGTATGAATTTTTGACATCTTGCCAATCTAGACACAAATAAATATTAG
326 ATCTCCAGAATGATATCTGTATGAATTTTTGACATCTTGCCAATCTAGACACAAATAAATATTAG
45018 GTCTTGGAGGAACATGTTCTAGAAGGCCACTTTCGAAGATGAATGGTATCAAGTCTGAATATGAC
391 GTCTTGGAGGAACATGTTCTAGAAGGCCACTTTCGAAGATGAATGGTATCAAGTCTGAATATGAC
45083 CCTAGAATTGGAATGAGATATATCCTCCTCTTTTTCTTCTTATTCTTTTTAGCTTTCTTTACTAG
456 CCTAGAATTGGAATGAGATATATCCTCCTCTTTTTCTTCTTATTCTTTTTAGCTTTCTTTACTAG
45148 AATTTGAACTTCCTCTATGCCTTTCTTCTTTGAGTTAGACTTAACTTTCGTGTCAGAAGTTTCAA
521 AATTTGAACTTCCTCTATGCCTTTCTTCTTTGAGTTAGACTTAACTTTCGTGTCAGAAGTTTCAA
45213 CATCAATTTTCGCTTTTCCTAACATGATATGTGTCACATTTTCTGGAATCTTACCGATTGTTGGA
586 CATCAATTTTCGCTTTTCCTAACATGATATGTGTCACATTTTCTGGAATCTTACCGATTGTTGGA
45278 GTTGACTTGGATTAACATACTCCCCAATAGGTTCTTGATCATCTTTTATCCTCACATTGGCTGCA
651 GTTGACTTGGATTAACATACTCCCCAATAGGTTCTTGATCATCTTTTATCCTCACATTGGCTGCA
45343 CAACCAACATTTATATTTTCACTCAAAGTCTTCATCTTTCCTGGCATAATATAGTTCTCTAACGA
716 CAACCAACATTTATATTTTCACTCAAAGTCTTCATCTTTCCTGGCATAATATAGTTCTCTAACGA
45408 TTTCTCCCTATATATCACTGTAATTATCCCTATATCCCA
781 TTTCTCCCTATATATCACTGTAATTATCCCTATATCCCA
45447 AGTTGGGCTTGAGCAACTTGGGATATAGTTTGTTGTATAAAAATGAAGGAAAACTGAGAAGAAGC
1 AGTTGGGCTTGAGCAACTTGGGATATAGTTTGTTGTATAAAAATGAAGGAAAACTGAGAAGAAGC
45512 TCTTTTGACTTCATTTTCTCTTTGCCACTATTATGATCATCTTGAAGACCTAGTGAATGATCATT
66 TCTTTTGACTTCATTTTCTCTTTGCCACTATTATGATCATCTTGAAGACCTAGTGAATGATCATT
45577 GAGATATTCATTTTGAAGGTTCAACTTTTGACCAACATCTTGTGGGAGACATTGGTTTTTAGATC
131 GAGATATTCATTTTGAAGGTTCAACTTTTGACCAACATCTTGTGGGAGACATTGGTTTTTAGATC
*
45642 TCCTCTTATCAATAAGTTCTGGTCTTTCGGGGAGCTTAGGTTTTCTATCTTCAAAGCATAACAAC
196 TCCTCTTATCAATAAGTTCTGGTCTTTCAGGGAGCTTAGGTTTTCTATCTTCAAAGCATAACAAC
45707 CCCTTCATGATGAGGTTTTGAACCTTTAATATCATAACCGCAAAACTTTTCGTAGAGTGGCTAAA
261 CCCTTCATGATGAGGTTTTGAACCTTTAATATCATAACCGCAAAACTTTTCGTAGAGTGGCTAAA
*
45772 ATCTCCAGAATGATATCTGTATGAATTTTTGACATCTTGCCAATCTATACACAAATAAATATTAG
326 ATCTCCAGAATGATATCTGTATGAATTTTTGACATCTTGCCAATCTAGACACAAATAAATATTAG
45837 GTCTTGGAGGAACATGTTCTAGAAGGCCACTTTCGAAGATGAATGGTATCAAGTCTGAATATGAC
391 GTCTTGGAGGAACATGTTCTAGAAGGCCACTTTCGAAGATGAATGGTATCAAGTCTGAATATGAC
45902 CCTAGAATTGGAATGAGATATATCCTCCTCTTTTTCTTCTTATTCTTTTTAGCTTTCTTTACTAG
456 CCTAGAATTGGAATGAGATATATCCTCCTCTTTTTCTTCTTATTCTTTTTAGCTTTCTTTACTAG
*
45967 AATTTGAACTTCCTCTATGCCTTTCTTCTTTGAGTCAGACTTAACTTTCGTGTCAGAAGTTTCAA
521 AATTTGAACTTCCTCTATGCCTTTCTTCTTTGAGTTAGACTTAACTTTCGTGTCAGAAGTTTCAA
46032 CATCAATTTTCGCTTTTCCTAACATGATATGTGTCACATTTTCTGGAATCTTACCGATTGTTGGA
586 CATCAATTTTCGCTTTTCCTAACATGATATGTGTCACATTTTCTGGAATCTTACCGATTGTTGGA
*
46097 GTTGACTTGGATTAACATACTCCCCAATAGGTTCTTGATCATCTTTTATCCTCATATTGGCTGCA
651 GTTGACTTGGATTAACATACTCCCCAATAGGTTCTTGATCATCTTTTATCCTCACATTGGCTGCA
*
46162 CAACCAACATTTATATTTTCACTCAAAGTCTTCATCTTTTCTGGCATAATATAGTTCTCTAACGA
716 CAACCAACATTTATATTTTCACTCAAAGTCTTCATCTTTCCTGGCATAATATAGTTCTCTAACGA
46227 TTTCTCCCTATATATCACTGTAATTATC
781 TTTCTCCCTATATATCACTGTAATTATC
46255 ATGCTCATCA
Statistics
Matches: 1620, Mismatches: 4, Indels: 3
1.00 0.00 0.00
Matches are distributed among these distances:
817 105 0.06
818 935 0.58
819 580 0.36
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (819 bp):
AGTTGGGCTTGAGCAACTTGGGATATAGTTTGTTGTATAAAAATGAAGGAAAACTGAGAAGAAGC
TCTTTTGACTTCATTTTCTCTTTGCCACTATTATGATCATCTTGAAGACCTAGTGAATGATCATT
GAGATATTCATTTTGAAGGTTCAACTTTTGACCAACATCTTGTGGGAGACATTGGTTTTTAGATC
TCCTCTTATCAATAAGTTCTGGTCTTTCAGGGAGCTTAGGTTTTCTATCTTCAAAGCATAACAAC
CCCTTCATGATGAGGTTTTGAACCTTTAATATCATAACCGCAAAACTTTTCGTAGAGTGGCTAAA
ATCTCCAGAATGATATCTGTATGAATTTTTGACATCTTGCCAATCTAGACACAAATAAATATTAG
GTCTTGGAGGAACATGTTCTAGAAGGCCACTTTCGAAGATGAATGGTATCAAGTCTGAATATGAC
CCTAGAATTGGAATGAGATATATCCTCCTCTTTTTCTTCTTATTCTTTTTAGCTTTCTTTACTAG
AATTTGAACTTCCTCTATGCCTTTCTTCTTTGAGTTAGACTTAACTTTCGTGTCAGAAGTTTCAA
CATCAATTTTCGCTTTTCCTAACATGATATGTGTCACATTTTCTGGAATCTTACCGATTGTTGGA
GTTGACTTGGATTAACATACTCCCCAATAGGTTCTTGATCATCTTTTATCCTCACATTGGCTGCA
CAACCAACATTTATATTTTCACTCAAAGTCTTCATCTTTCCTGGCATAATATAGTTCTCTAACGA
TTTCTCCCTATATATCACTGTAATTATCCCTATATCCCA
Found at i:46555 original size:13 final size:13
Alignment explanation
Indices: 46529--46565 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
46519 AGCATTATGA
*
46529 ATGC-AAATGTAG
1 ATGCAAAATGAAG
46541 ATGCAAAATGAAG
1 ATGCAAAATGAAG
46554 ATGCAAAATGAA
1 ATGCAAAATGAA
46566 AATGAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.17
13 19 0.83
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.19
Consensus pattern (13 bp):
ATGCAAAATGAAG
Found at i:56362 original size:18 final size:18
Alignment explanation
Indices: 56336--56370 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
56326 AGTTTCATGG
* *
56336 GTATTAGACTCGTTTTGA
1 GTATCAGACTCGCTTTGA
56354 GTATCAGACTCGCTTTG
1 GTATCAGACTCGCTTTG
56371 TGTAGCAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (18 bp):
GTATCAGACTCGCTTTGA
Found at i:56379 original size:18 final size:18
Alignment explanation
Indices: 56341--56379 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
56331 CATGGGTATT
* *
56341 AGACTCGTTTTGAGTATC
1 AGACTCGCTTTGAGTAGC
*
56359 AGACTCGCTTTGTGTAGC
1 AGACTCGCTTTGAGTAGC
56377 AGA
1 AGA
56380 GTTATATGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (18 bp):
AGACTCGCTTTGAGTAGC
Found at i:58017 original size:18 final size:18
Alignment explanation
Indices: 57991--58025 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
57981 AGTTTCATGG
*
57991 GTATTAGACTCGTTTTGA
1 GTATCAGACTCGTTTTGA
58009 GTATCAGACTCGTTTTG
1 GTATCAGACTCGTTTTG
58026 TGTAGCAGAG
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:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (18 bp):
GTATCAGACTCGTTTTGA
Found at i:58034 original size:18 final size:18
Alignment explanation
Indices: 57996--58034 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
57986 CATGGGTATT
*
57996 AGACTCGTTTTGAGTATC
1 AGACTCGTTTTGAGTAGC
*
58014 AGACTCGTTTTGTGTAGC
1 AGACTCGTTTTGAGTAGC
58032 AGA
1 AGA
58035 GTTATATGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (18 bp):
AGACTCGTTTTGAGTAGC
Found at i:61581 original size:53 final size:53
Alignment explanation
Indices: 61536--61793 Score: 390
Period size: 53 Copynumber: 4.9 Consensus size: 53
61526 TCTAAAAATA
* * * *
61536 GGTTCGCTCCCTATTGCTTCAGGGAGTAGAACTCGAATAATCTTCTGCTTACG
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACG
* * *
61589 AGTTCGCTCCCTCTTGCTTCAGGGGGTAGAGCTCGAACAATCTTCTACCTACG
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACG
* * * *
61642 GGTTCACTCCCTCTTGCTTCAGGGAGTAGAAATCGAACAATCTTTTGCCTACG
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACG
* *
61695 GGTTCGCTCCCTCTTGTTTCAGGGAGTAAAACTCGAACAATCTTCTACCTACG
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACG
*
61748 GGTTCGCTCCCTCTTACTTCAGGGAGTAGAACTCGAACAATCTTCT
1 GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCT
61794 GGTGTGATTC
Statistics
Matches: 182, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
53 182 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (53 bp):
GGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACG
Found at i:62347 original size:42 final size:42
Alignment explanation
Indices: 62301--62380 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
62291 AAATTACCCG
*
62301 AAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCA
1 AAGGACTTAATCATCATGCTCAAAAGACTTACTGATGGCCCA
* *
62343 AAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
1 AAGGACTTAATCATCATGCTCAAAAGACTTACTGATGG
62381 GTTTGCTTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (42 bp):
AAGGACTTAATCATCATGCTCAAAAGACTTACTGATGGCCCA
Found at i:62368 original size:122 final size:122
Alignment explanation
Indices: 62201--62759 Score: 751
Period size: 122 Copynumber: 4.5 Consensus size: 122
62191 ATCTTGCTTG
** * * * * *
62201 AAAGACTTACAAATGACCCGAAGGATTTCATTATCATGCTTGAAAGACTTACTGATGGATTTGCT
1 AAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGGTTTGCT
*
62266 TCACTAG-TCTTCGGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCA
66 TCACT-GCTCTTCTGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCA
*
62323 AAAGACTTACTGATGGCCCAAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGGTTTGCT
1 AAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGGTTTGCT
* * * *
62388 TCACTACTCTTCCGTGAAGGCTTACAAATTTCCCGAAGGATTTAATCATCATGCTCG
66 TCACTGCTCTTCTGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCA
* *
62445 AAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTTGAAAGACTTACTGATGGGTTTACT
1 AAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGGTTTGCT
* * *
62510 TCACTGCTCTTCTGTGAAGGCTTACAAATTTCCCGAATGATTTAATCATCATGCTCG
66 TCACTGCTCTTCTGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCA
62567 AAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCAAAAGACTTACTGATGGCACTTAC
1 AAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTC----GA---A---A--G-ACTTAC
* *
62632 TGATGGGTTTGCTTCACTGCTCTTTTGTGAAGGCTTACAAATTACCCTAAGGATTTAATCATCAT
53 TGATGGGTTTGCTTCACTGCTCTTCTGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCAT
62697 GCTCA
118 GCTCA
* * * * * *
62702 AAATACTTACTGATGGCCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
1 AAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGG
62760 CCCGAAGGGC
Statistics
Matches: 392, Mismatches: 31, Indels: 28
0.87 0.07 0.06
Matches are distributed among these distances:
122 276 0.70
123 1 0.00
125 1 0.00
126 2 0.01
128 1 0.00
129 1 0.00
131 2 0.01
132 1 0.00
134 1 0.00
135 106 0.27
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (122 bp):
AAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGGTTTGCT
TCACTGCTCTTCTGTGAAGGCTTACAAATTACCCGAAGGATTTAATCATCATGCTCA
Found at i:62467 original size:42 final size:42
Alignment explanation
Indices: 62419--62767 Score: 194
Period size: 42 Copynumber: 8.2 Consensus size: 42
62409 TTACAAATTT
62419 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * *
62461 CCCGAAGGACTTCATCATCATGCTTGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
*** * * * * * ** **
62503 ---G-TTTACTTCACTGC-TC-TTCT-GTGAAGGCTTACAAATTT
1 CCCGAAGGA-TTTAAT-CATCATGCTCG-AAAGACTTACTGATGG
*
62541 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * *
62583 CCCGAAGGACTTCATCATCATGCTCAAAAGACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * * * * * ** **
62625 CACTTACTGATGGGTTT--GCTTCACTGCTCTTTTGTGAAGGCTTACAAATTA
1 C-C---C-GAAGGATTTAATCATCA-TGCTC----G-AAAGACTTACTGATGG
* * *
62676 CCCTAAGGATTTAATCATCATGCTCAAAATACTTACTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * *
62718 CCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTGATGG
1 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
62760 CCCGAAGG
1 CCCGAAGG
62768 GCTTACTAAG
Statistics
Matches: 222, Mismatches: 62, Indels: 46
0.67 0.19 0.14
Matches are distributed among these distances:
37 1 0.00
38 14 0.06
39 5 0.02
40 2 0.01
41 7 0.03
42 147 0.66
43 2 0.01
45 4 0.02
46 12 0.05
47 12 0.05
48 4 0.02
50 1 0.00
51 11 0.05
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (42 bp):
CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:62631 original size:13 final size:13
Alignment explanation
Indices: 62613--62637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62603 TGCTCAAAAG
62613 ACTTACTGATGGC
1 ACTTACTGATGGC
62626 ACTTACTGATGG
1 ACTTACTGATGG
62638 GTTTGCTTCA
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:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:62737 original size:135 final size:135
Alignment explanation
Indices: 62491--62760 Score: 423
Period size: 135 Copynumber: 2.0 Consensus size: 135
62481 TGCTTGAAAG
* *
62491 ACTTACTGATGGGTTTACTTCACTGCTCTTCTGTGAAGGCTTACAAATTTCCCGAATGATTTAAT
1 ACTTACTGATGGGTTTACTTCACTGCTCTTCTGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
* * *
62556 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGCTCAAAAGACTTACTG
66 CATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTAAGCATCATGCTCAAAAGACTTACTG
62621 ATGGC
131 ATGGC
* * *
62626 ACTTACTGATGGGTTTGCTTCACTGCTCTTTTGTGAAGGCTTACAAATTACCCTAAGGATTTAAT
1 ACTTACTGATGGGTTTACTTCACTGCTCTTCTGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
* * * * *
62691 CATCATGCTCAAAATACTTACTGATGGCCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTG
66 CATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTAAGCATCATGCTCAAAAGACTTACTG
62756 ATGGC
131 ATGGC
62761 CCGAAGGGCT
Statistics
Matches: 122, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
135 122 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (135 bp):
ACTTACTGATGGGTTTACTTCACTGCTCTTCTGTGAAGGCTTACAAATTACCCGAAGGATTTAAT
CATCATGCTCAAAAGACTTACTGATGGCCCGAAGGACTTAAGCATCATGCTCAAAAGACTTACTG
ATGGC
Found at i:71264 original size:2 final size:2
Alignment explanation
Indices: 71257--71289 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
71247 TAACGTGGCA
71257 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 A
71290 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75582 original size:16 final size:16
Alignment explanation
Indices: 75561--75597 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
75551 CTCTTCAAAC
75561 TTTTT-CTTTCTTTTAT
1 TTTTTCCTTT-TTTTAT
75577 TTTTTCCTTTTTTTAT
1 TTTTTCCTTTTTTTAT
75593 TTTTT
1 TTTTT
75598 ATTTTGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.05, C:0.11, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTTCCTTTTTTTAT
Found at i:77081 original size:17 final size:17
Alignment explanation
Indices: 77059--77125 Score: 116
Period size: 17 Copynumber: 3.9 Consensus size: 17
77049 AATCAAGAGT
* *
77059 TAGTTTAATAAATGAAC
1 TAGTTTGATGAATGAAC
77076 TAGTTTGATGAATGAAC
1 TAGTTTGATGAATGAAC
77093 TAGTTTGATGAATGAAC
1 TAGTTTGATGAATGAAC
77110 TAGTTTGATGAATGAA
1 TAGTTTGATGAATGAA
77126 ATAACTTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (17 bp):
TAGTTTGATGAATGAAC
Found at i:77098 original size:34 final size:34
Alignment explanation
Indices: 77059--77176 Score: 121
Period size: 34 Copynumber: 3.4 Consensus size: 34
77049 AATCAAGAGT
*
77059 TAGTTTAATAAATGAACTAGTTTGATGAATGAAC
1 TAGTTTAATAAATGAACTAGTTTGATGAATGAAA
* *
77093 TAGTTTGATGAATGAACTAGTTTGATGAATGAAA
1 TAGTTTAATAAATGAACTAGTTTGATGAATGAAA
* * * * *
77127 TAACTTTATTCAATGAACTAG-ATGCATGAATGAAG
1 T-AGTTTAATAAATGAACTAGTTTG-ATGAATGAAA
* *
77162 TAGCTTACTAAATGA
1 TAGTTTAATAAATGA
77177 TATAAATATG
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
34 44 0.64
35 25 0.36
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.34
Consensus pattern (34 bp):
TAGTTTAATAAATGAACTAGTTTGATGAATGAAA
Found at i:84180 original size:28 final size:28
Alignment explanation
Indices: 84135--84198 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
84125 CGTCTTGAAT
**
84135 TACCCCTAACTTGCTTAAACCTTTTATG
1 TACCCCTAACTTAATTAAACCTTTTATG
84163 TACCCCTAACTTAATTAAACCTTTTATG
1 TACCCCTAACTTAATTAAACCTTTTATG
84191 TACCCCTA
1 TACCCCTA
84199 GGTTTTAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.28, C:0.30, G:0.05, T:0.38
Consensus pattern (28 bp):
TACCCCTAACTTAATTAAACCTTTTATG
Found at i:90623 original size:18 final size:18
Alignment explanation
Indices: 90595--90637 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
90585 TCTTCTTATT
*
90595 TTTACTTTAATTACTTTTA
1 TTTA-TTTAATCACTTTTA
*
90614 TTTATTTAATCGCTTTTA
1 TTTATTTAATCACTTTTA
90632 -TTATTT
1 TTTATTT
90638 CAATATCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 12 0.55
19 4 0.18
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCACTTTTA
Found at i:94905 original size:23 final size:25
Alignment explanation
Indices: 94870--94924 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
94860 TTGAATGAAA
94870 GAAAGAAG-AAAAAAATAGC-AGTTC
1 GAAAGAAGAAAAAAAATAGCTA-TTC
94894 GAAA-AAGAAAAAAAATAGCTATTC
1 GAAAGAAGAAAAAAAATAGCTATTC
94918 GAAAGAA
1 GAAAGAA
94925 AAATAGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.11
24 22 0.79
25 3 0.11
ACGTcount: A:0.62, C:0.07, G:0.18, T:0.13
Consensus pattern (25 bp):
GAAAGAAGAAAAAAAATAGCTATTC
Found at i:95841 original size:8 final size:8
Alignment explanation
Indices: 95828--95855 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
95818 CAATTATCTT
95828 TTTTATTA
1 TTTTATTA
95836 TTTTATTA
1 TTTTATTA
95844 TTTTATTA
1 TTTTATTA
95852 TTTT
1 TTTT
95856 CTTTGCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTATTA
Found at i:96656 original size:18 final size:19
Alignment explanation
Indices: 96603--96656 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
96593 TCTACTTATT
*
96603 TTTACTTTAATTA-CTTTTA
1 TTTA-TTTAATCATCTTTTA
96622 TTTATTTAATCAT-TTTTA
1 TTTATTTAATCATCTTTTA
96640 -TTATTTTAAT-ATCTTTT
1 TTTA-TTTAATCATCTTTT
96657 TACCAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.16
18 22 0.71
19 4 0.13
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTATTTAATCATCTTTTA
Found at i:99153 original size:30 final size:30
Alignment explanation
Indices: 99117--99184 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
99107 ACCCTTTTAT
*
99117 TTTAAGACTATTGAAAGCGACCTCTTAGGC
1 TTTAAGACTATTGAAAGCGACCTCTTAAGC
*
99147 TTTAAGACTATTGAAAGCGACCTCTTAATC
1 TTTAAGACTATTGAAAGCGACCTCTTAAGC
99177 TTTAAGAC
1 TTTAAGAC
99185 AATCACTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (30 bp):
TTTAAGACTATTGAAAGCGACCTCTTAAGC
Found at i:100654 original size:3 final size:3
Alignment explanation
Indices: 100648--100687 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
100638 GATGATGATG
*
100648 ATA ATA ATA ATA ATA ATA TTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
100688 CGGTCTCCAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:102869 original size:5 final size:5
Alignment explanation
Indices: 102849--102888 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
102839 AATATAATAA
102849 GAAAT G-AAT G-AAT GAAAT GAAAT GAAAAT GAAAT GAAAT G
1 GAAAT GAAAT GAAAT GAAAT GAAAT G-AAAT GAAAT GAAAT G
102889 TTAGAGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.24
5 20 0.61
6 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (5 bp):
GAAAT
Found at i:102879 original size:11 final size:11
Alignment explanation
Indices: 102855--102886 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
102845 ATAAGAAATG
102855 AATG-AATG-A
1 AATGAAATGAA
102864 AATGAAATGAA
1 AATGAAATGAA
102875 AATGAAATGAA
1 AATGAAATGAA
102886 A
1 A
102887 TGTTAGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 4 0.19
10 4 0.19
11 13 0.62
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (11 bp):
AATGAAATGAA
Found at i:102880 original size:16 final size:17
Alignment explanation
Indices: 102849--102888 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
102839 AATATAATAA
102849 GAAATGAATGAATGAAAT
1 GAAATGAA-GAATGAAAT
102867 GAAATGAA-AATGAAAT
1 GAAATGAAGAATGAAAT
102883 GAAATG
1 GAAATG
102889 TTAGAGATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 14 0.64
18 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (17 bp):
GAAATGAAGAATGAAAT
Found at i:106216 original size:60 final size:60
Alignment explanation
Indices: 106103--106228 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
106093 ATAGTTGAAT
* * *
106103 GACCATTTTGTAACTTTTAATAGTCGATGGACTCAACAAAGCATCATCATATAGTCGAGG
1 GACCATTTTGAAACTTTTAATAGTCGATGGACTCAAAAAAGAATCATCATATAGTCGAGG
* * * ** *
106163 GACCATTTTGAAACTTTTAATAGTCGATTGACTTAATAAAATAAT-ATTTTATAGTCGGGG
1 GACCATTTTGAAACTTTTAATAGTCGATGGACTCAA-AAAAGAATCATCATATAGTCGAGG
106223 GACCAT
1 GACCAT
106229 ATGTGTACTT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 51 0.91
61 5 0.09
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (60 bp):
GACCATTTTGAAACTTTTAATAGTCGATGGACTCAAAAAAGAATCATCATATAGTCGAGG
Found at i:107841 original size:24 final size:24
Alignment explanation
Indices: 107809--107872 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
107799 TCATTAACGC
*
107809 TAAACAAACACGTTCATAAACATA
1 TAAACAAACACGTTCACAAACATA
* *
107833 TAAATAAACACGTTCGCAAACATA
1 TAAACAAACACGTTCACAAACATA
* *
107857 -AAACGAACATGTTCAC
1 TAAACAAACACGTTCAC
107873 GACGTCACAC
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
23 12 0.36
24 21 0.64
ACGTcount: A:0.50, C:0.22, G:0.08, T:0.20
Consensus pattern (24 bp):
TAAACAAACACGTTCACAAACATA
Done.