Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 45 of 208
Found at i:12409291 original size:910 final size:902
Alignment explanation
Indices: 12407413--12409096 Score: 2503
Period size: 910 Copynumber: 1.9 Consensus size: 902
12407403 TTTGCAGCGG
* * ** * * * * *
12407413 CTAATAATCACTAAAACATTTCTTTCATCGTTTAGAAATCATATAAGAAC-AATTCATGCATCAA
1 CTAATAATTACCAAAACATTTCGATCAACATTTAGAAATCACATAA-AACAAATT-ATGGATAAA
12407477 ACCTTATTACCAAAATAGTGTCCCATACCACAGTTCATAATATAAAATTTAAAGTCCCAAAACCA
64 ACCTTATTACCAAAATAGTGTCCCATACCACAGTTCATAATATAAAATTTAAAGTCCCAAAACCA
*
12407542 TTTAAACAAACCCAATTTAAAGTTCATAGTAAAAGTCCAAAAGAAGTTAAAAAAGCCTATAAAAA
129 TTTAAACAAACCCAATTTAAAGTCCATAGTAAAAGTCCAAAAGAAGTTAAAAAAGCCTATAAAAA
* * *
12407607 TACCAAACCATTTCCAAAATCCATAACCACGAAAACATATTATACCGAGAGCCTCTCCGAAGATC
194 CACCAAACCATTTCCAAAATCCATAACCACGAAAACATATTATACCGAGAGCCTATCCAAAGATC
* *
12407672 CAAATCTGAGCCGTAAGTATGAGGATTACCTGAAACACACGAAAATCATGGGTGAGCTTTAAAAG
259 CAAATCTGAGCCGTAAGTATAAGGATCACCTGAAACACACGAAAATCATGGGTGAGCTTTAAAAG
*
12407737 ACTCAGTGTGAGATCAATACAAACAGTTATTTTAACACATAACATAACACATCAAAATATCACAA
324 ACTCAGTGTGAGATCAATACAAACAATTATTTTAACACATAACATAACACATCAAAATATCACAA
* * *
12407802 AGCATTTTTCATAGAATTCACATATTATCACATTTATTGAATCAAAACATGACATGCTTATGAAC
389 AGCATCTTTCACAGAATTCACATATTATCACATTTATTGAATCAAAACATGACATGCTTACGAAC
*
12407867 AATGCACAATTACAGGATTTCCTACCCATCTCCGCTACACACTAATATCGAGTTCCACAAAACTC
454 AATGCACAATTACAGGATTTCCTACCCATCTCCGCTACACACCAATATCGAGTTCCACAAAACTC
** * * * *
12407932 ATCCATCCAATAACACACCAGTTTGTGGATAATCCATAACACAGATACCGATGAACGGTCACATA
519 ATCCATCCAATAACACACCAACTTATGGACAAGCCACAACACAGATACCGATGAACGGTCACATA
* * * *
12407997 GCACATCGTGGACAAGTCACCATATAATTGCCAATAACGACCACATAATTGAAGTTAAACTGCCA
584 GCACATCATGGACAAGCCACCACATAATTGCCAATAACAACCACATAATTGAAGTTAAACTGCCA
*
12408062 CATAGCTTCCTCCTTTCACAAACCCGCGCCATGCATGTGATATGACCATTTTAACACATATTTAT
649 CATAGCTTCCTCCTTTCACAAACCCACGCCATGCATGTGATATGACCATTTTAACACATATTTAT
12408127 CACTTATCACATTTTTCACATTTTCATGCTCATAACTCATGTATCTCAATTTTCACATATCCATA
714 CACTTATCACATTTTTCACATTTTCATGCTCATAACTCATGTATCTCAATTTTCACATATCCATA
* * * * ** *
12408192 CATCATAACTCATGCATGTATCTCGATTTTTTAAAAGATCTTGTACTTTTCATTATATAGTTATG
779 CATCATAACTCAT-CATGTATCTCGA-TTATCAAAAGATCTTGCACTTTGCATTATATACATACG
** * * ** * * *
12408257 TGTTCCTTTATATTTAAAAATGATTTGAAATGTAACTTAGTTTTTAAAACACTTATTTGGAGCAA
842 TAATCC-TTATAGTTAAAAATGATTTGAAATATAAC-TA--TTACAAAACACGTATTTAGAGAAA
* ** * *
12408322 CTAATAATTACTAAAACATTTCTTTCATCATTTAGAAATCACATAAAACAATTTATGGATAAAAC
1 CTAATAATTACCAAAACATTTCGATCAACATTTAGAAATCACATAAAACAAATTATGGATAAAAC
*
12408387 CTTATTATATCAAAATAGTGTCCCATACCACAGTTCATAATATAAAATTTAAAGTCCCAAAACCA
66 CTTA-T-TACCAAAATAGTGTCCCATACCACAGTTCATAATATAAAATTTAAAGTCCCAAAACCA
* *
12408452 TTTAAACAAACCCAATTTAAAGTCCATAGTAAAATTCCAAAAGAAGTTCAAAAAGTCC-ATAAAA
129 TTTAAACAAACCCAATTTAAAGTCCATAGTAAAAGTCCAAAAGAAGTTAAAAAAG-CCTATAAAA
* * *
12408516 ACACTAAACCATTTCCAAAATCCATAACCACGAAAAGATATTATACTGAGAGCCTATCCAAAGAT
193 ACACCAAACCATTTCCAAAATCCATAACCACGAAAACATATTATACCGAGAGCCTATCCAAAGAT
* * * * *
12408581 CGAAATAC-GAGCCTTAAGTATAAGGATCACTTGAGACACATGAAAATCATGGGTGAGCTTTAAA
258 CCAAAT-CTGAGCCGTAAGTATAAGGATCACCTGAAACACACGAAAATCATGGGTGAGCTTTAAA
* * *
12408645 AGACTCAGTGTGAGATCAGTACAGACAATTATTTTAACATATAACATAACACATCAAAATATCAC
322 AGACTCAGTGTGAGATCAATACAAACAATTATTTTAACACATAACATAACACATCAAAATATCAC
* * *
12408710 AAAGCATCTTTCACAGAATTCACATATTATCGCATTTATTGCATCAAAACATGGCATGCTTACGA
387 AAAGCATCTTTCACAGAATTCACATATTATCACATTTATTGAATCAAAACATGACATGCTTACGA
*
12408775 ACAATGCACAATTACAGGATTTCCTACCCATCTCCGCTACACACCAATATCGAGTTCCCCAAAAC
452 ACAATGCACAATTACAGGATTTCCTACCCATCTCCGCTACACACCAATATCGAGTTCCACAAAAC
* * * * *
12408840 TCGTCCATCCAATAACACACCAACTTATGTACAAGCCACCACATAGATACCGATGATCGGTCACA
517 TCATCCATCCAATAACACACCAACTTATGGACAAGCCACAACACAGATACCGATGAACGGTCACA
*
12408905 TAGCACATCATGGACAAGCCACCACATAATTGCCGATAACAACCACATAATTGAAGTTAAACTGC
582 TAGCACATCATGGACAAGCCACCACATAATTGCCAATAACAACCACATAATTGAAGTTAAACTGC
* *
12408970 CACATAGCTTCCTCCTTTCACAAACCCAC-CACATGCATGTGATATGGCCATTTTAATACATATT
647 CACATAGCTTCCTCCTTTCACAAACCCACGC-CATGCATGTGATATGACCATTTTAACACATATT
* *
12409034 TATCACTTATCACATTTTTCGCATTTTCATGCTCATAACTCATGTATCTTAATTTTCACATAT
711 TATCACTTATCACATTTTTCACATTTTCATGCTCATAACTCATGTATCTCAATTTTCACATAT
12409097 GCATGTATCA
Statistics
Matches: 713, Mismatches: 56, Indels: 11
0.91 0.07 0.01
Matches are distributed among these distances:
908 16 0.02
909 48 0.07
910 646 0.91
911 3 0.00
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.28
Consensus pattern (902 bp):
CTAATAATTACCAAAACATTTCGATCAACATTTAGAAATCACATAAAACAAATTATGGATAAAAC
CTTATTACCAAAATAGTGTCCCATACCACAGTTCATAATATAAAATTTAAAGTCCCAAAACCATT
TAAACAAACCCAATTTAAAGTCCATAGTAAAAGTCCAAAAGAAGTTAAAAAAGCCTATAAAAACA
CCAAACCATTTCCAAAATCCATAACCACGAAAACATATTATACCGAGAGCCTATCCAAAGATCCA
AATCTGAGCCGTAAGTATAAGGATCACCTGAAACACACGAAAATCATGGGTGAGCTTTAAAAGAC
TCAGTGTGAGATCAATACAAACAATTATTTTAACACATAACATAACACATCAAAATATCACAAAG
CATCTTTCACAGAATTCACATATTATCACATTTATTGAATCAAAACATGACATGCTTACGAACAA
TGCACAATTACAGGATTTCCTACCCATCTCCGCTACACACCAATATCGAGTTCCACAAAACTCAT
CCATCCAATAACACACCAACTTATGGACAAGCCACAACACAGATACCGATGAACGGTCACATAGC
ACATCATGGACAAGCCACCACATAATTGCCAATAACAACCACATAATTGAAGTTAAACTGCCACA
TAGCTTCCTCCTTTCACAAACCCACGCCATGCATGTGATATGACCATTTTAACACATATTTATCA
CTTATCACATTTTTCACATTTTCATGCTCATAACTCATGTATCTCAATTTTCACATATCCATACA
TCATAACTCATCATGTATCTCGATTATCAAAAGATCTTGCACTTTGCATTATATACATACGTAAT
CCTTATAGTTAAAAATGATTTGAAATATAACTATTACAAAACACGTATTTAGAGAAA
Found at i:12413404 original size:24 final size:25
Alignment explanation
Indices: 12413363--12413409 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
12413353 TGCACATCAA
*
12413363 TCGAATCATCTCGAGACACACATAT
1 TCGAATCATATCGAGACACACATAT
* *
12413388 TCGAAT-ATATCGCGACAGACAT
1 TCGAATCATATCGAGACACACAT
12413410 TCATAGTATG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (25 bp):
TCGAATCATATCGAGACACACATAT
Found at i:12414172 original size:191 final size:189
Alignment explanation
Indices: 12413661--12414231 Score: 1115
Period size: 191 Copynumber: 3.0 Consensus size: 189
12413651 TATCGTGACC
12413661 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCGTCCAGTGACCTTTGT
1 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCGTCCAGTGACCTTTGT
12413726 GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
66 GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTA-TT
12413791 TTTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
130 TTTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
12413851 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCGTCCAGTGACCTTTGT
1 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCGTCCAGTGACCTTTGT
12413916 GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
66 GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
12413981 TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCCAAATACGTA
131 TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTAT-CAAATA-GTA
12414042 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCGTCCAGTGACCTTTGT
1 AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCGTCCAGTGACCTTTGT
12414107 GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
66 GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
12414172 TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
131 TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
12414231 A
1 A
12414232 TTAAGTCATG
Statistics
Matches: 379, Mismatches: 0, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
189 57 0.15
190 139 0.37
191 183 0.48
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (189 bp):
AAACTCTCCCTAATAACATACTATTACGAAAGCTACTCAATCAGTGCTCGTCCAGTGACCTTTGT
GTTACTCTTATATGATACCTTAATCTCTTTGGGATAATATTCGTTCTCCTAATATGATCCTATTT
TTTTATCATGGTAATCATTACATCTTTCTTCATAAAAAGTCATTTACTATCAAATAGTA
Found at i:12416598 original size:43 final size:43
Alignment explanation
Indices: 12416504--12416601 Score: 117
Period size: 43 Copynumber: 2.3 Consensus size: 43
12416494 ACTGGCACTC
* * *
12416504 ATAATGCATCATCGGATAAACCGAAGCAATCATACTGGCACAC
1 ATAATGCATCATCGGATAAACCGAAACAATCATACTGACACAA
* * * *
12416547 ATAGTGCATCATCGGATAAATCGAAACAAAT-ATATTGACATAA
1 ATAATGCATCATCGGATAAACCGAAAC-AATCATACTGACACAA
12416590 ATAATGCATCAT
1 ATAATGCATCAT
12416602 TGGCCAAACC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 43 0.93
44 3 0.07
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.23
Consensus pattern (43 bp):
ATAATGCATCATCGGATAAACCGAAACAATCATACTGACACAA
Found at i:12418485 original size:19 final size:20
Alignment explanation
Indices: 12418461--12418499 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12418451 AATTCATTGT
*
12418461 ATAATTTAA-AAATAAAATA
1 ATAATTGAAGAAATAAAATA
*
12418480 ATAATTGAAGTAATAAAATA
1 ATAATTGAAGAAATAAAATA
12418500 TATTTATTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (20 bp):
ATAATTGAAGAAATAAAATA
Found at i:12421680 original size:14 final size:14
Alignment explanation
Indices: 12421642--12421680 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
12421632 AATAGATGTC
12421642 GATAATGGCAATTG
1 GATAATGGCAATTG
*
12421656 GACAATGGCAATTG
1 GATAATGGCAATTG
*
12421670 GATAATCGCAA
1 GATAATGGCAA
12421681 AAATAAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (14 bp):
GATAATGGCAATTG
Found at i:12422862 original size:156 final size:156
Alignment explanation
Indices: 12422563--12422867 Score: 486
Period size: 156 Copynumber: 2.0 Consensus size: 156
12422553 TACCTTGTAA
* * *
12422563 GTATATGAAAATCCACTGAATTATTTTTCAATGTTCTTTATTGGGATTCACCATGTATCCACTAA
1 GTATATGAAAATCCACTAAATTATTTTTCAATATTCTTTATCGGGATTCACCATGTATCCACTAA
* *
12422628 CCACACTAACTGCATATGACAAATCTAGACGTAAGCAAACCATAGTGTACATGAGAGATCCCACT
66 CCACACTAACTGCATATGACAAATCTAGACGTAAGCAAACCATAGTATACACGAGAGATCCCACT
*
12422693 GCTCTAAATTATGGAACACATGACAT
131 GCACTAAATTATGGAACACATGACAT
* * *
12422719 GTATCTGAAAATCCACTAAATTGTTTTTCAATATTCTTTATCGGGATTCACCATGTATCTACTAA
1 GTATATGAAAATCCACTAAATTATTTTTCAATATTCTTTATCGGGATTCACCATGTATCCACTAA
* * *
12422784 CCACACTAACTGCATATGACAAATCTGGATGTAAGCAAACCATAGTATACACGAGAGATCCCATT
66 CCACACTAACTGCATATGACAAATCTAGACGTAAGCAAACCATAGTATACACGAGAGATCCCACT
12422849 GCACTAGAA-TATGGAACAC
131 GCACTA-AATTATGGAACAC
12422868 GTAATATGTA
Statistics
Matches: 136, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
156 134 0.99
157 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (156 bp):
GTATATGAAAATCCACTAAATTATTTTTCAATATTCTTTATCGGGATTCACCATGTATCCACTAA
CCACACTAACTGCATATGACAAATCTAGACGTAAGCAAACCATAGTATACACGAGAGATCCCACT
GCACTAAATTATGGAACACATGACAT
Found at i:12428567 original size:7 final size:6
Alignment explanation
Indices: 12428502--12428566 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
12428492 CAACACATAG
***
12428502 AATAAA AATAAA AAT--- AATAAA AATTTT AAT-AA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
*
12428546 AATAAA ATATAAA ACTAAA AA
1 AATAAA A-ATAAA AATAAA AA
12428567 CCTAATCTAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
3 3 0.06
5 3 0.06
6 35 0.74
7 6 0.13
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (6 bp):
AATAAA
Found at i:12430704 original size:3 final size:3
Alignment explanation
Indices: 12430696--12430720 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12430686 CAAGCTCAAG
12430696 CTC CTC CTC CTC CTC CTC CTC CTC C
1 CTC CTC CTC CTC CTC CTC CTC CTC C
12430721 ACCGGTTCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CTC
Found at i:12437819 original size:50 final size:50
Alignment explanation
Indices: 12437728--12437915 Score: 151
Period size: 50 Copynumber: 3.6 Consensus size: 50
12437718 TCTTGTACTA
* * * **
12437728 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATAGGTG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTG
* * * * ** * *
12437778 CCCATGCCCTGTCCCAGGCATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTG
* * * *
12437828 CCAAAGCCATGTCCTAGACATAGTCTTACATGAGACCTCTCATAATCTCAATGATG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GGTG
* *
12437884 CCAATGTCATGTCCCAGACATGGTCTTACATG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATG
12437916 TGATCTCTTT
Statistics
Matches: 105, Mismatches: 27, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
50 73 0.70
53 1 0.01
56 31 0.30
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
CCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTG
Found at i:12442232 original size:16 final size:16
Alignment explanation
Indices: 12442208--12442238 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12442198 TCACCAAAGT
*
12442208 GAAGGGATGATGGTTG
1 GAAGAGATGATGGTTG
12442224 GAAGAGATGATGGTT
1 GAAGAGATGATGGTT
12442239 TTAGGGATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.45, T:0.26
Consensus pattern (16 bp):
GAAGAGATGATGGTTG
Found at i:12442608 original size:14 final size:14
Alignment explanation
Indices: 12442589--12442619 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
12442579 ATGTTCACCA
12442589 CCACTTAAAGCTTG
1 CCACTTAAAGCTTG
12442603 CCACTTAAAGCTTG
1 CCACTTAAAGCTTG
12442617 CCA
1 CCA
12442620 AAGTGCCCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (14 bp):
CCACTTAAAGCTTG
Found at i:12445726 original size:25 final size:24
Alignment explanation
Indices: 12445697--12445753 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
12445687 TCAACCCCCG
* **
12445697 TCTTCGTCTCCACCCCTCATTTTCA
1 TCTTCATCTCCA-CCCTCACCTTCA
*
12445722 TCTTCATCTCGACCCTCACCTTCA
1 TCTTCATCTCCACCCTCACCTTCA
12445746 TCTTCATC
1 TCTTCATC
12445754 CCTTCCCCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.14, C:0.44, G:0.04, T:0.39
Consensus pattern (24 bp):
TCTTCATCTCCACCCTCACCTTCA
Found at i:12446518 original size:20 final size:18
Alignment explanation
Indices: 12446471--12446577 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 18
12446461 CATGATAAAC
12446471 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
12446488 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
**
12446508 ATTAAATTAATAAAATAAT
1 ATTAAATTAAT-ATTTAAT
*
12446527 ATTAAGA-TAAGTATTAAAT
1 ATTAA-ATTAA-TATTTAAT
* * *
12446546 -TTAATTTAATAATAAACT
1 ATTAAATTAATATTTAA-T
*
12446564 ATTAAAATAATATT
1 ATTAAATTAATATT
12446578 ATTTTTGGAT
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
17 14 0.20
18 9 0.13
19 28 0.41
20 18 0.26
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:12446567 original size:37 final size:37
Alignment explanation
Indices: 12446484--12446578 Score: 104
Period size: 37 Copynumber: 2.5 Consensus size: 37
12446474 AAATTAAATT
*
12446484 TAATATTAAGATAATCACTTTAATATTAAATTAATAAAA
1 TAATATTAAGATAAT-A-TTAAATATTAAATTAATAAAA
*
12446523 TAATATTAAGATAAGTATTAAAT-TTAATTTAATAATAA
1 TAATATTAAGATAA-TATTAAATATTAAATTAATAA-AA
* *
12446561 -ACTATTAAAATAATATTA
1 TAATATTAAGATAATATTA
12446579 TTTTTGGATT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
36 5 0.10
37 22 0.44
38 7 0.14
39 15 0.30
40 1 0.02
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (37 bp):
TAATATTAAGATAATATTAAATATTAAATTAATAAAA
Found at i:12451245 original size:49 final size:49
Alignment explanation
Indices: 12451181--12451274 Score: 152
Period size: 49 Copynumber: 1.9 Consensus size: 49
12451171 TGCTATGCAA
* * *
12451181 TGCTAAACTTGGTCTTCCACTGTCTACACTCTTATCATTATTTATAGAT
1 TGCTAAAATTAGTCTTCCACTGTCTACACTCTTATCACTATTTATAGAT
*
12451230 TGCTAAAATTAGTCTTCCACTGTCTACATTCTTATCACTATTTAT
1 TGCTAAAATTAGTCTTCCACTGTCTACACTCTTATCACTATTTAT
12451275 CCCTTCTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.26, C:0.22, G:0.09, T:0.44
Consensus pattern (49 bp):
TGCTAAAATTAGTCTTCCACTGTCTACACTCTTATCACTATTTATAGAT
Found at i:12456291 original size:19 final size:20
Alignment explanation
Indices: 12456256--12456295 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
12456246 AGCATTCCAT
*
12456256 AACTCAGGATAACATAAAAA
1 AACTCAGGATAAAATAAAAA
12456276 AACTCA-GATAAAATAAAAA
1 AACTCAGGATAAAATAAAAA
12456295 A
1 A
12456296 TCATACTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.15
Consensus pattern (20 bp):
AACTCAGGATAAAATAAAAA
Found at i:12470046 original size:39 final size:41
Alignment explanation
Indices: 12469910--12470034 Score: 125
Period size: 40 Copynumber: 3.1 Consensus size: 41
12469900 CGTTGAATAA
* * *
12469910 AAAACGCCGCTAAAAATCAAGCATTAG-TG-GCGCTTTTCA-
1 AAAACGCCGCTAAAAAT-GAGCATTAGCAGCGCGCTTTTTAG
* * *
12469949 AAAATCGCCGCTAAAGATCCAGCATTAGCAGCGCGCTTTTTGG
1 AAAA-CGCCGCTAAAAAT-GAGCATTAGCAGCGCGCTTTTTAG
*
12469992 AAAACGCCGCTAAAAATGAGCATTAGC-G-GCGTTTTTTAG
1 AAAACGCCGCTAAAAATGAGCATTAGCAGCGCGCTTTTTAG
12470031 AAAA
1 AAAA
12470035 GTGCCGCAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
39 17 0.23
40 22 0.30
41 10 0.14
42 20 0.27
43 4 0.05
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (41 bp):
AAAACGCCGCTAAAAATGAGCATTAGCAGCGCGCTTTTTAG
Found at i:12470238 original size:41 final size:42
Alignment explanation
Indices: 12470086--12470359 Score: 385
Period size: 41 Copynumber: 6.6 Consensus size: 42
12470076 CTTTCGAGAA
* *
12470086 TTTAGCGGTG-TTTTTGGAAAAGCGCCGCTAATGCTCAGACC
1 TTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCAGACC
* * *
12470127 CTTAGCGGCGTTTTTTGGAGAAGCGCCGCTAATGCTCAGACC
1 TTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCAGACC
* *
12470169 TTTAGCGGCGTTTTTTGGAGAAGCGCCGCTAATGCTCAGACC
1 TTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCAGACC
* *
12470211 TTTAGCGGC-ATTTTTGAAAAAGTGCCGCTAATGCTCAGACC
1 TTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCAGACC
* * * *
12470252 TTTAGCGGTG-TTTTTAAAAAAGCGCCGCTAATGCTTAGAGC
1 TTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCAGACC
* *
12470293 TTTAGCGGCTTTTTTTG-AAAAGCGTCGCTAATGCTCAGACC
1 TTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCAGACC
12470334 TTTAGCGGCGTTTTTTGAAAAAGCGC
1 TTTAGCGGCGTTTTTTGAAAAAGCGC
12470360 TGCAAAAACA
Statistics
Matches: 208, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
41 116 0.56
42 92 0.44
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.30
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCAGACC
Found at i:12470791 original size:14 final size:15
Alignment explanation
Indices: 12470763--12470795 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
12470753 AAGGTTTATA
12470763 GATTATGGAATTAGG
1 GATTATGGAATTAGG
12470778 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
12470792 GATT
1 GATT
12470796 CTAGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:12473540 original size:18 final size:18
Alignment explanation
Indices: 12473517--12473575 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
12473507 AACAGAACTT
12473517 ATGTAATTCTAATATAGA
1 ATGTAATTCTAATATAGA
* * ***
12473535 ATGTAA-AC-AATTTTCTT
1 ATGTAATTCTAA-TATAGA
12473552 ATGTAATTCTAATATAGA
1 ATGTAATTCTAATATAGA
12473570 ATGTAA
1 ATGTAA
12473576 CTTGTTTTAA
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
16 2 0.07
17 9 0.32
18 15 0.54
19 2 0.07
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (18 bp):
ATGTAATTCTAATATAGA
Found at i:12473838 original size:43 final size:43
Alignment explanation
Indices: 12473777--12474166 Score: 629
Period size: 43 Copynumber: 9.1 Consensus size: 43
12473767 AATTCATGTT
*
12473777 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTATTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
12473820 TTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
12473863 TTTAGCGGCGTTTGTGGGAAATGCGCTGCTAAAGTTCTTGGTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
12473906 TTTAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
12473949 TTTAGCGGCGTTTGTGGGAAATGCGCCGCTAAAGTTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
12473992 TTTAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
12474035 TTTAGCGGCGTTTGTGGGAAAAGCGCTGCTAAAGGTCCTGGTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
12474078 TTTAGCGGCGTTTGTGGGATAAGCGCCGCTAAAGGTC-TGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
12474120 TTTAGCGGCGCTTGTGGGAAAAGCGCCGCTAAAGGTATTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
12474163 TTTA
1 TTTA
12474167 AAAAACGCCG
Statistics
Matches: 318, Mismatches: 28, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
42 38 0.12
43 280 0.88
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:12474707 original size:12 final size:12
Alignment explanation
Indices: 12474690--12474714 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12474680 TTAGGACTTG
12474690 AATGATGTTGAT
1 AATGATGTTGAT
12474702 AATGATGTTGAT
1 AATGATGTTGAT
12474714 A
1 A
12474715 TTGTGAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AATGATGTTGAT
Found at i:12475351 original size:5 final size:5
Alignment explanation
Indices: 12475341--12475365 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12475331 TATTTTTAGC
12475341 TTATT TTATT TTATT TTATT TTATT
1 TTATT TTATT TTATT TTATT TTATT
12475366 ATCCTTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:12476871 original size:17 final size:16
Alignment explanation
Indices: 12476844--12476875 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12476834 TGATAGATCT
12476844 TCGATGAGCTTCCAAA
1 TCGATGAGCTTCCAAA
12476860 TCGATCGAGCTTCCAA
1 TCGAT-GAGCTTCCAA
12476876 TTATCTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (16 bp):
TCGATGAGCTTCCAAA
Found at i:12479476 original size:18 final size:20
Alignment explanation
Indices: 12479447--12479484 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
12479437 TTTTTAGTTT
12479447 TGTTTTTAGTAATT-TTTTA
1 TGTTTTTAGTAATTGTTTTA
12479466 TGTTTTT-GTAATTGTTTTA
1 TGTTTTTAGTAATTGTTTTA
12479485 GCTTAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.18, C:0.00, G:0.13, T:0.68
Consensus pattern (20 bp):
TGTTTTTAGTAATTGTTTTA
Found at i:12481295 original size:21 final size:21
Alignment explanation
Indices: 12481269--12481314 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
12481259 AACACGGGCT
* * *
12481269 TGTGGAGTGGCCATACGAGCA
1 TGTGGAATAGCCATACGACCA
12481290 TGTGGAATAGCCATACGACCA
1 TGTGGAATAGCCATACGACCA
12481311 TGTG
1 TGTG
12481315 TTTTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.22
Consensus pattern (21 bp):
TGTGGAATAGCCATACGACCA
Found at i:12481546 original size:20 final size:19
Alignment explanation
Indices: 12481501--12481547 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
12481491 GTGACCCCTG
*
12481501 TTTTCAAAATTTTCAAGTT
1 TTTTCAAAATTATCAAGTT
* *
12481520 TTTTCAAAATTATCTATTT
1 TTTTCAAAATTATCAAGTT
12481539 TGTTTCAAA
1 T-TTTCAAA
12481548 TTGATCCCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.32, C:0.11, G:0.04, T:0.53
Consensus pattern (19 bp):
TTTTCAAAATTATCAAGTT
Found at i:12485446 original size:34 final size:33
Alignment explanation
Indices: 12485408--12485506 Score: 79
Period size: 34 Copynumber: 3.2 Consensus size: 33
12485398 TGTTGAAATG
12485408 GACTATGCATGATATATGGCTAAATTAATAATTT
1 GACTATG-ATGATATATGGCTAAATTAATAATTT
* * * *
12485442 GAC--T-A-G-TA-ATGG-TACATT-TTGAAATG
1 GACTATGATGATATATGGCTAAATTAAT-AATTT
12485468 GACTATGTATGATATATGGCTAAATTAATAATTT
1 GACTATG-ATGATATATGGCTAAATTAATAATTT
12485502 GACTA
1 GACTA
12485507 GTAATGGTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 20
0.63 0.11 0.27
Matches are distributed among these distances:
25 1 0.02
26 11 0.23
27 4 0.09
28 3 0.06
29 1 0.02
30 2 0.04
31 1 0.02
32 3 0.06
33 4 0.09
34 16 0.34
35 1 0.02
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (33 bp):
GACTATGATGATATATGGCTAAATTAATAATTT
Found at i:12485467 original size:60 final size:60
Alignment explanation
Indices: 12485400--12485521 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
12485390 TATAAATATG
12485400 TTGAAATGGACTATGCATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
1 TTGAAATGGACTATGCATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
*
12485460 TTGAAATGGACTATGTATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
1 TTGAAATGGACTATGCATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
12485520 TT
1 TT
12485522 CGCTGTTAAG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (60 bp):
TTGAAATGGACTATGCATGATATATGGCTAAATTAATAATTTGACTAGTAATGGTACATT
Found at i:12492298 original size:20 final size:20
Alignment explanation
Indices: 12492268--12492305 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12492258 TAAGAATGAC
12492268 ATTTGAATTTGATTATTTGTT
1 ATTTGAATTTGA-TATTTGTT
12492289 ATTT-AATTTGATATTTG
1 ATTTGAATTTGATATTTG
12492306 AATGGTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (20 bp):
ATTTGAATTTGATATTTGTT
Found at i:12493656 original size:39 final size:38
Alignment explanation
Indices: 12493605--12493680 Score: 107
Period size: 39 Copynumber: 2.0 Consensus size: 38
12493595 AGGGGTATTG
* *
12493605 TTATTTATATATATAATATATATATGCATGCATGGGTC
1 TTATATATATATATAATATATATATACATGCATGGGTC
* *
12493643 TTATATATAATATATAATATATATTTACGTGCATGGGT
1 TTATATAT-ATATATAATATATATATACATGCATGGGT
12493681 GGTATATGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 7 0.21
39 26 0.79
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.45
Consensus pattern (38 bp):
TTATATATATATATAATATATATATACATGCATGGGTC
Found at i:12493687 original size:39 final size:39
Alignment explanation
Indices: 12493613--12493697 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
12493603 TGTTATTTAT
* *
12493613 ATATATAATATATATATGCATGCATGGGTCTTATATATA
1 ATATATAATATATATATACATGCATGGGTCGTATATATA
* * * *
12493652 ATATATAATATATATTTACGTGCATGGGTGGTATATGTA
1 ATATATAATATATATATACATGCATGGGTCGTATATATA
*
12493691 AAATATA
1 ATATATA
12493698 TTTGTGTGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.40
Consensus pattern (39 bp):
ATATATAATATATATATACATGCATGGGTCGTATATATA
Found at i:12497200 original size:22 final size:22
Alignment explanation
Indices: 12497146--12497188 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
12497136 TTTATTGTTC
12497146 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
12497168 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
12497189 TAGCCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:12500463 original size:30 final size:32
Alignment explanation
Indices: 12500429--12500507 Score: 99
Period size: 30 Copynumber: 2.5 Consensus size: 32
12500419 GTTTTGTTAT
*
12500429 TTATATATAATATATA-TGCA-TGCATGGGTG
1 TTATATATAATATATATTGAAGTGCATGGGTG
* *
12500459 TTATATATAGTATATATTTAAGTGCATGGGTG
1 TTATATATAATATATATTGAAGTGCATGGGTG
12500491 TTATATGTATAATATAT
1 TTATA--TATAATATAT
12500508 TTGCGTGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 15 0.37
31 2 0.05
32 15 0.37
34 9 0.22
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (32 bp):
TTATATATAATATATATTGAAGTGCATGGGTG
Found at i:12500474 original size:32 final size:30
Alignment explanation
Indices: 12500429--12500508 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 30
12500419 GTTTTGTTAT
*
12500429 TTATATATAATATATATGCA-TGCATGGGTG
1 TTATATATAATATAT-TGAAGTGCATGGGTG
*
12500459 TTATATATAGTATATATTTAAGTGCATGGGTG
1 TTATATATA--ATATATTGAAGTGCATGGGTG
12500491 TTATATGTATAATATATT
1 TTATA--TATAATATATT
12500509 TGCGTGGGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 9 0.21
31 2 0.05
32 28 0.65
34 4 0.09
ACGTcount: A:0.34, C:0.04, G:0.17, T:0.45
Consensus pattern (30 bp):
TTATATATAATATATTGAAGTGCATGGGTG
Found at i:12500509 original size:32 final size:32
Alignment explanation
Indices: 12500449--12500509 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
12500439 TATATATGCA
12500449 TGCATGGGTGTTATATATAGTATATATTTAAG
1 TGCATGGGTGTTATATATAGTATATATTTAAG
*
12500481 TGCATGGGTGTTATATGTA-TAATATATTT
1 TGCATGGGTGTTATATATAGT-ATATATTT
12500510 GCGTGGGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (32 bp):
TGCATGGGTGTTATATATAGTATATATTTAAG
Found at i:12503287 original size:25 final size:24
Alignment explanation
Indices: 12503243--12503291 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
12503233 TTTCATCTTA
* *
12503243 TTTTTGTTATTATTATTTTTCTTTC
1 TTTTTGTAATTATTACTTTT-TTTC
*
12503268 TTTTTGTAATTATTCCTTTTTTTC
1 TTTTTGTAATTATTACTTTTTTTC
12503292 CGGGAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.73
Consensus pattern (24 bp):
TTTTTGTAATTATTACTTTTTTTC
Found at i:12510197 original size:21 final size:21
Alignment explanation
Indices: 12510171--12510225 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
12510161 AGAATCTCGT
*
12510171 TGTTTTGCTATTGTTTTTCCA
1 TGTTTTGCTACTGTTTTTCCA
*
12510192 TGTTTTGTTACTGTTTTTCCA
1 TGTTTTGCTACTGTTTTTCCA
*
12510213 CT-TTTTTCTACTG
1 -TGTTTTGCTACTG
12510226 CTATGCTAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.09, C:0.16, G:0.13, T:0.62
Consensus pattern (21 bp):
TGTTTTGCTACTGTTTTTCCA
Found at i:12510866 original size:31 final size:30
Alignment explanation
Indices: 12510824--12510923 Score: 87
Period size: 31 Copynumber: 3.2 Consensus size: 30
12510814 GATGAGTCAG
*
12510824 TTTACACTTTGGTCACTCTTGTATTAGTAAA
1 TTTACAATTTGGTCA-TCTTGTATTAGTAAA
**
12510855 TTTACAATTTGGTCAAT-TAAATATTAGTAAA
1 TTTACAATTTGGTC-ATCT-TGTATTAGTAAA
* * *
12510886 ATTATAATTTGGTCA-CTTGACTATTAGCAAA
1 TTTACAATTTGGTCATCTTG--TATTAGTAAA
12510917 TTTACAA
1 TTTACAA
12510924 GTCATTCTGA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
30 3 0.06
31 50 0.93
32 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (30 bp):
TTTACAATTTGGTCATCTTGTATTAGTAAA
Found at i:12511438 original size:25 final size:26
Alignment explanation
Indices: 12511388--12511439 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
12511378 ATAAATGAGG
* *
12511388 TTTAACCCTACTTTAAAAAAATAAAT
1 TTTAACCATAATTTAAAAAAATAAAT
12511414 TTTAACCATAATTTAAAAAAA-AAAT
1 TTTAACCATAATTTAAAAAAATAAAT
12511439 T
1 T
12511440 CTTTTTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.35
Consensus pattern (26 bp):
TTTAACCATAATTTAAAAAAATAAAT
Found at i:12515730 original size:243 final size:243
Alignment explanation
Indices: 12515404--12515872 Score: 807
Period size: 243 Copynumber: 1.9 Consensus size: 243
12515394 TGAAGTCGTG
* * * *
12515404 ACACTAAGCATGTTATGTCATGACACCGATCCTCAAAGTCACAACTACAAACCCTTGAGGTCGTA
1 ACACTAAGCATGTTATGTCACGACACCGATCCTCAAAGTCACAACTACAAACCCTCGAGGTAGCA
12515469 AATCCAAGAAAATTTTTGAAATGAAGAAACCTAATGGCTATTATCATCGAGGTTACAACACCAAC
66 AATCCAAGAAAATTTTTGAAATGAAGAAACCTAATGGCTATTATCATCGAGGTTACAACACCAAC
* *
12515534 AAGGTTGTGTCGCGACACCAAGTGCCCCTAAGTCAA-ACTCGTGCCCACTTTCA-AGAGTGTCAC
131 AAGGTTGTGTCGCGACACCAAGTGCCCCCAAGTCAAGA-TCGTGCCCACTTTCACA-AATGTCAC
*
12515597 GACACTAAAGCTTGGGTGTTGCGACTTTGAAGTCAGCCGTTGAAGTCACA
194 GACACTAAAGCTTGGGTGTTGCGACTTTAAAGTCAGCCGTTGAAGTCACA
12515647 ACACTAAGCATGTTATGTCACGACACCGATCCTCAAAGTCACAACTACAAACCCTCGAGGTAGCA
1 ACACTAAGCATGTTATGTCACGACACCGATCCTCAAAGTCACAACTACAAACCCTCGAGGTAGCA
* *
12515712 AATCCAAGAAAATTTTTGAAATGAAGAAACCTAATGGCTATTATCATTGAGGTTACAACACCAGC
66 AATCCAAGAAAATTTTTGAAATGAAGAAACCTAATGGCTATTATCATCGAGGTTACAACACCAAC
*
12515777 AAGGTTGTGTCGCGACACCAAGTGCCCCCAAGTCAAGATCGTGCGCACTTTCACAAATGTCACGA
131 AAGGTTGTGTCGCGACACCAAGTGCCCCCAAGTCAAGATCGTGCCCACTTTCACAAATGTCACGA
*
12515842 CACTAAAGCTTGGGTGTTGTGACTTTAAAGT
196 CACTAAAGCTTGGGTGTTGCGACTTTAAAGT
12515873 TTGGCAGGTG
Statistics
Matches: 213, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
243 211 0.99
244 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (243 bp):
ACACTAAGCATGTTATGTCACGACACCGATCCTCAAAGTCACAACTACAAACCCTCGAGGTAGCA
AATCCAAGAAAATTTTTGAAATGAAGAAACCTAATGGCTATTATCATCGAGGTTACAACACCAAC
AAGGTTGTGTCGCGACACCAAGTGCCCCCAAGTCAAGATCGTGCCCACTTTCACAAATGTCACGA
CACTAAAGCTTGGGTGTTGCGACTTTAAAGTCAGCCGTTGAAGTCACA
Found at i:12517212 original size:3 final size:3
Alignment explanation
Indices: 12517206--12517256 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
12517196 TATTATGTGC
12517206 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12517254 ATT
1 ATT
12517257 TNNNNNNNNN
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12519871 original size:17 final size:17
Alignment explanation
Indices: 12519844--12519889 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 17
12519834 AAAGTTTAGG
12519844 GGGGAAATAAAAAGTTTT
1 GGGGAAAT-AAAAGTTTT
12519862 GGGG-AATAAAAG-TTT
1 GGGGAAATAAAAGTTTT
12519877 GAGGGAAAGTAAA
1 G-GGGAAA-TAAA
12519890 TAGAGGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.16
16 8 0.32
17 5 0.20
18 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.22
Consensus pattern (17 bp):
GGGGAAATAAAAGTTTT
Found at i:12520258 original size:9 final size:9
Alignment explanation
Indices: 12520244--12520280 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12520234 TATAGTTTGA
12520244 TATTCGAAT
1 TATTCGAAT
12520253 TATTCGAAT
1 TATTCGAAT
*
12520262 TATTCGAGT
1 TATTCGAAT
12520271 TATTCGAAT
1 TATTCGAAT
12520280 T
1 T
12520281 CGAAATCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:12528912 original size:37 final size:34
Alignment explanation
Indices: 12528855--12528924 Score: 88
Period size: 37 Copynumber: 2.0 Consensus size: 34
12528845 TTACTTTCAT
12528855 ATTAAATTAATAAAATACTATTAAGATAAGTATTAA
1 ATTAAATTAATAAAATACTATTAA-ATAA-TATTAA
*
12528891 ATTAAATTTAATATTAA-ACTATTAAATAATATTA
1 ATTAAA-TTAATA-AAATACTATTAAATAATATTA
12528925 TTTTTGTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
35 5 0.16
36 10 0.32
37 14 0.45
38 2 0.06
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (34 bp):
ATTAAATTAATAAAATACTATTAAATAATATTAA
Found at i:12529198 original size:10 final size:10
Alignment explanation
Indices: 12529183--12529214 Score: 50
Period size: 9 Copynumber: 3.4 Consensus size: 10
12529173 GCAATATCAT
12529183 ATTAATTTTA
1 ATTAATTTTA
12529193 ATTAATTTT-
1 ATTAATTTTA
12529202 ATTAA-TTTA
1 ATTAATTTTA
12529211 ATTA
1 ATTA
12529215 TACTTGATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 3 0.14
9 9 0.43
10 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
ATTAATTTTA
Found at i:12530124 original size:24 final size:24
Alignment explanation
Indices: 12530092--12530144 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
12530082 AATGTATCAT
* *
12530092 TCTACCAATGAATACATTTATGTC
1 TCTACCAATGAATACATCTATATC
12530116 TCTACCAATGAATACATCTATATC
1 TCTACCAATGAATACATCTATATC
12530140 TCTAC
1 TCTAC
12530145 TCGTGGATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.36
Consensus pattern (24 bp):
TCTACCAATGAATACATCTATATC
Found at i:12530449 original size:4 final size:4
Alignment explanation
Indices: 12530440--12530465 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12530430 GTGAAATTAA
12530440 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
12530466 CGTTCAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:12534040 original size:11 final size:13
Alignment explanation
Indices: 12534016--12534047 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
12534006 TAGTTTATTA
12534016 ATATTTTAATATG
1 ATATTTTAATATG
12534029 AT-TTTTAA-ATG
1 ATATTTTAATATG
12534040 ATATTTTA
1 ATATTTTA
12534048 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:12537993 original size:25 final size:25
Alignment explanation
Indices: 12537910--12538169 Score: 302
Period size: 25 Copynumber: 10.6 Consensus size: 25
12537900 TTATTATGCA
12537910 CTAATGAA-CAGAGAGCACTGAA-GTG
1 CTAAT-AATCAGAGAGCACT-AACGTG
* * *
12537935 CT-AT-A-CAGATAGCACAAATGTG
1 CTAATAATCAGAGAGCACTAACGTG
*
12537957 CT-A-AA-CAGAGAGCACTGACGTG
1 CTAATAATCAGAGAGCACTAACGTG
*
12537979 CCAATAATCAGAGAGCACTAACGTG
1 CTAATAATCAGAGAGCACTAACGTG
*
12538004 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAATCAGAGAGCACTAACGTG
*
12538029 CTAATAATCAGAGAGCACCAACGTG
1 CTAATAATCAGAGAGCACTAACGTG
* *
12538054 CTAATAATCAGAGAGCACTGATGTG
1 CTAATAATCAGAGAGCACTAACGTG
* * *
12538079 CTAATAATTAGAAAGCACTAATGTG
1 CTAATAATCAGAGAGCACTAACGTG
*
12538104 CTAATAATCAGAGAGCACTGACGTG
1 CTAATAATCAGAGAGCACTAACGTG
* * *
12538129 CTAATAATCGGAGAGCACTGATGTG
1 CTAATAATCAGAGAGCACTAACGTG
12538154 CTAATAATCAGAGAGC
1 CTAATAATCAGAGAGC
12538170 GCGCTAAAGT
Statistics
Matches: 207, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
21 2 0.01
22 31 0.15
23 1 0.00
24 4 0.02
25 169 0.82
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.20
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTAACGTG
Found at i:12539157 original size:5 final size:5
Alignment explanation
Indices: 12539147--12539205 Score: 118
Period size: 5 Copynumber: 11.8 Consensus size: 5
12539137 TTGTTTCTTT
12539147 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
12539197 TATAA TATA
1 TATAA TATA
12539206 TACTTAACTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 54 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TATAA
Found at i:12540038 original size:16 final size:17
Alignment explanation
Indices: 12539997--12540043 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
12539987 TAGAATTATT
12539997 AAATACTAAAT-TAAAAA
1 AAATA-TAAATATAAAAA
*
12540014 TAATATAAATATAAAAA
1 AAATATAAATATAAAAA
*
12540031 AAAT-TAAAAATAA
1 AAATATAAATATAA
12540044 TATGAGTGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATATAAATATAAAAA
Found at i:12540581 original size:19 final size:19
Alignment explanation
Indices: 12540523--12540583 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
12540513 AAGTTATAAA
12540523 AAAATTTTAAAAAAATTCT
1 AAAATTTTAAAAAAATTCT
*
12540542 -AAATATATAAAAAAATT-T
1 AAAAT-TTTAAAAAAATTCT
**
12540560 AAAATTTTAAAAATGTTCT
1 AAAATTTTAAAAAAATTCT
12540579 AAAAT
1 AAAAT
12540584 AATATTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 14 0.40
19 21 0.60
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATTTTAAAAAAATTCT
Found at i:12541541 original size:3 final size:3
Alignment explanation
Indices: 12541533--12541564 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
12541523 ATTTTAAATA
12541533 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12541565 AAGCAAAGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12562397 original size:137 final size:136
Alignment explanation
Indices: 12562084--12562500 Score: 690
Period size: 138 Copynumber: 3.0 Consensus size: 136
12562074 TAGAAAAAAG
* *
12562084 AATTATATTCTTTCCAAAATAATATTAATTTCCATGTATTGTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTT-TATATTTTGACCGAAATTAATTAA
*
12562149 TATAACGGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
65 TATAACTGTTTATATTAATAAATTCGATAAAATATATACAATT-ATATTTTGTATGAATCAAATT
12562214 CATATATT
129 CATATATT
* *
12562222 AATTATATTCTTTCCAAAAGAATATTAATTTACATGTCTATTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCT-TTATATTTTGACCGAAATTAATTAA
* * *
12562287 TATAACTGTTTATATTAATAAATTTGATAAAATATATAAAATTATATTTTGTATGAATCAAATTT
65 TATAACTGTTTATATTAATAAATTCGATAAAATATATACAATTATATTTTGTATGAATCAAATTC
12562352 ATATATT
130 ATATATT
* *
12562359 AATTATATTCTTTCCAAAAGAATATTAATTTCCGTGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTC-TTTATATTTTGACCGAAATTAATTAA
*
12562424 TATAACTGTTTATATTAATAAATTCGATAAAATATATACAATTAGTATTTTGTATGAATCAAATA
65 TATAACTGTTTATATTAATAAATTCGATAAAATATATACAATTA-TATTTTGTATGAATCAAATT
12562489 CATATATT
129 CATATATT
12562497 AATT
1 AATT
12562501 TTATCTATGT
Statistics
Matches: 260, Mismatches: 16, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
137 129 0.50
138 130 0.50
139 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (136 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTATATTTTGACCGAAATTAATTAAT
ATAACTGTTTATATTAATAAATTCGATAAAATATATACAATTATATTTTGTATGAATCAAATTCA
TATATT
Found at i:12565091 original size:3 final size:3
Alignment explanation
Indices: 12565083--12565131 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
12565073 ATGAATTAAA
* *
12565083 TAT TAT TAT TA- TAT TA- TAT TAT TAT AAT GTAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
12565127 TAT TA
1 TAT TA
12565132 ACTAATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.85
4 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:12565102 original size:13 final size:13
Alignment explanation
Indices: 12565086--12565131 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
12565076 AATTAAATAT
12565086 TATTATTATATTA
1 TATTATTATATTA
* *
12565099 TATTATTATAATG
1 TATTATTATATTA
*
12565112 TATTATTAT-TAA
1 TATTATTATATTA
12565124 TATTATTA
1 TATTATTA
12565132 ACTAATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 8 0.29
13 20 0.71
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (13 bp):
TATTATTATATTA
Found at i:12565103 original size:16 final size:16
Alignment explanation
Indices: 12565082--12565129 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
12565072 TATGAATTAA
12565082 ATATTATTATTATATT
1 ATATTATTATTATATT
12565098 ATATTATTA-TA-A-T
1 ATATTATTATTATATT
*
12565111 GTATTATTATTAATATT
1 ATATTATTATT-ATATT
12565128 AT
1 AT
12565130 TAACTAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
13 9 0.35
14 2 0.08
15 3 0.12
16 10 0.38
17 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATATTATTATTATATT
Found at i:12565604 original size:17 final size:18
Alignment explanation
Indices: 12565582--12565615 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12565572 TAAATGAGTT
12565582 AATTA-GGATTAAATTGG
1 AATTAGGGATTAAATTGG
*
12565599 AATTAGGGTTTAAATTG
1 AATTAGGGATTAAATTG
12565616 AAAAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.38
Consensus pattern (18 bp):
AATTAGGGATTAAATTGG
Found at i:12568874 original size:7 final size:7
Alignment explanation
Indices: 12568862--12568896 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
12568852 TGAGGACCAA
12568862 TTGAAGC
1 TTGAAGC
12568869 TTGAAGC
1 TTGAAGC
12568876 TTGAAGC
1 TTGAAGC
*
12568883 TTGAAGG
1 TTGAAGC
12568890 TTGAAGC
1 TTGAAGC
12568897 GATAAACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (7 bp):
TTGAAGC
Found at i:12579195 original size:2 final size:2
Alignment explanation
Indices: 12579188--12579212 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12579178 ATTGTAGAAT
12579188 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
12579213 TAAAATGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12580978 original size:22 final size:22
Alignment explanation
Indices: 12580940--12580981 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12580930 GGAAGAATAA
*
12580940 AAAAATAGTAATAAAGAAATCG
1 AAAAATAGTAAAAAAGAAATCG
12580962 AAAAA-AGTAAAAGAAGAAAT
1 AAAAATAGTAAAA-AAGAAAT
12580982 TTGAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.69, C:0.02, G:0.14, T:0.14
Consensus pattern (22 bp):
AAAAATAGTAAAAAAGAAATCG
Found at i:12595013 original size:45 final size:44
Alignment explanation
Indices: 12594950--12595176 Score: 201
Period size: 45 Copynumber: 5.1 Consensus size: 44
12594940 GGGACAGACT
*
12594950 GAAGATAG-AGATCTTGTCTTCCTGTATTGGCAGAAAAGTAGATC
1 GAAGATAGCAG-TATTGTCTTCCTGTATTGGCAGAAAAGTAGATC
* * *
12594994 GAAGATGGCAAGTATTGTCTTTCTGTATTGGCAGTGAAA-TAGATC
1 GAAGATAGC-AGTATTGTCTTCCTGTATTGGCAG-AAAAGTAGATC
* * *
12595039 GAAGATAGTAGATCTTGTCTTCCTGTATTGGCA-ACGAAGTAGATC
1 GAAGATAGCAG-TATTGTCTTCCTGTATTGGCAGA-AAAGTAGATC
* * *
12595084 GAAGATAGCAG-ACCTTGTATTCCTGTATTGGCAGCAAAGTACATC
1 GAAGATAGCAGTA--TTGTCTTCCTGTATTGGCAGAAAAGTAGATC
* * * * ** *
12595129 GAAGATAGCAGATCTTATCTTTCTGTACTGGCAGTGAAGAAGATC
1 GAAGATAGCAG-TATTGTCTTCCTGTATTGGCAGAAAAGTAGATC
12595174 GAA
1 GAA
12595177 AACACCAGTC
Statistics
Matches: 147, Mismatches: 25, Indels: 21
0.76 0.13 0.11
Matches are distributed among these distances:
44 11 0.07
45 131 0.89
46 5 0.03
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (44 bp):
GAAGATAGCAGTATTGTCTTCCTGTATTGGCAGAAAAGTAGATC
Found at i:12595070 original size:90 final size:88
Alignment explanation
Indices: 12594950--12595176 Score: 271
Period size: 90 Copynumber: 2.5 Consensus size: 88
12594940 GGGACAGACT
* * *
12594950 GAAGATAGAGATCTTGTCTTCCTGTATTGGCAGAAAAGTAGATCGAAGATGGCAAGTA-TTGTCT
1 GAAGATAGAGATCTTGTCTTCCTGTATTGGCAGAGAAGTAGATCGAAGATAGC-AG-ACTTGTAT
* * *
12595014 TTCTGTATTGGCAGTGAAA-TAGATC
64 TCCTGTATTGGCAG-CAAAGTACATC
12595039 GAAGATAGTAGATCTTGTCTTCCTGTATTGGCA-ACGAAGTAGATCGAAGATAGCAGACCTTGTA
1 GAAGATAG-AGATCTTGTCTTCCTGTATTGGCAGA-GAAGTAGATCGAAGATAGCAGA-CTTGTA
12595103 TTCCTGTATTGGCAGCAAAGTACATC
63 TTCCTGTATTGGCAGCAAAGTACATC
* * * * *
12595129 GAAGATAGCAGATCTTATCTTTCTGTACTGGCAGTGAAGAAGATCGAA
1 GAAGATAG-AGATCTTGTCTTCCTGTATTGGCAGAGAAGTAGATCGAA
12595177 AACACCAGTC
Statistics
Matches: 120, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
88 1 0.01
89 14 0.12
90 105 0.88
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (88 bp):
GAAGATAGAGATCTTGTCTTCCTGTATTGGCAGAGAAGTAGATCGAAGATAGCAGACTTGTATTC
CTGTATTGGCAGCAAAGTACATC
Found at i:12595859 original size:21 final size:21
Alignment explanation
Indices: 12595833--12595894 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
12595823 CAGCGCCGCA
12595833 TCACCACGCGTCCCCTCCACG
1 TCACCACGCGTCCCCTCCACG
*
12595854 TCACCACGCG---CC-GCA--
1 TCACCACGCGTCCCCTCCACG
*
12595869 TCACCAAGCGTCCCCTCCACG
1 TCACCACGCGTCCCCTCCACG
12595890 TCACC
1 TCACC
12595895 GTGCCTCCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
15 9 0.28
17 2 0.06
18 4 0.12
19 2 0.06
21 15 0.47
ACGTcount: A:0.18, C:0.55, G:0.15, T:0.13
Consensus pattern (21 bp):
TCACCACGCGTCCCCTCCACG
Found at i:12595872 original size:36 final size:36
Alignment explanation
Indices: 12595825--12595894 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
12595815 ACAACCTTCA
*
12595825 GCGCCGCATCACCACGCGTCCCCTCCACGTCACCAC
1 GCGCCGCATCACCAAGCGTCCCCTCCACGTCACCAC
12595861 GCGCCGCATCACCAAGCGTCCCCTCCACGTCACC
1 GCGCCGCATCACCAAGCGTCCCCTCCACGTCACC
12595895 GTGCCTCCGC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.17, C:0.54, G:0.17, T:0.11
Consensus pattern (36 bp):
GCGCCGCATCACCAAGCGTCCCCTCCACGTCACCAC
Found at i:12595989 original size:15 final size:16
Alignment explanation
Indices: 12595969--12596001 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12595959 ACAGATTGTA
12595969 TTATTTTA-TTTTATT
1 TTATTTTATTTTTATT
12595984 TTATTTTATTTTTATT
1 TTATTTTATTTTTATT
12596000 TT
1 TT
12596002 GAATAGGCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (16 bp):
TTATTTTATTTTTATT
Found at i:12595998 original size:6 final size:5
Alignment explanation
Indices: 12595969--12596001 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
12595959 ACAGATTGTA
12595969 TTATT TTATT TTATT TTATT TTATTT TTATT TT
1 TTATT TTATT TTATT TTATT TTA-TT TTATT TT
12596002 GAATAGGCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:12596144 original size:9 final size:10
Alignment explanation
Indices: 12596125--12596153 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
12596115 TTATAGTTTC
12596125 CTTTTTCTTT
1 CTTTTTCTTT
12596135 CTTTTT-TTT
1 CTTTTTCTTT
12596144 CTTTTTCTTT
1 CTTTTTCTTT
12596154 TTGATTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
CTTTTTCTTT
Found at i:12599187 original size:25 final size:25
Alignment explanation
Indices: 12599122--12599190 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
12599112 TTTAGCTCTT
* *
12599122 ATGAGCTTCCCGA-TACTCAGCTCGC
1 ATGAGCTTCCC-ATTATTCAGCTCAC
*
12599147 ATGAGCTTCCCCTTATTCAGCTCAC
1 ATGAGCTTCCCATTATTCAGCTCAC
12599172 ATGAGCTTCCCATTATTCA
1 ATGAGCTTCCCATTATTCA
12599191 ACTCGGAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.22, C:0.33, G:0.14, T:0.30
Consensus pattern (25 bp):
ATGAGCTTCCCATTATTCAGCTCAC
Found at i:12599202 original size:25 final size:25
Alignment explanation
Indices: 12599149--12599204 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
12599139 CAGCTCGCAT
* * *
12599149 GAGCTTCCCCTTATTCAGCTCACAT
1 GAGCTTCCCATTATTCAACTCACAG
**
12599174 GAGCTTCCCATTATTCAACTCGGAG
1 GAGCTTCCCATTATTCAACTCACAG
12599199 GAGCTT
1 GAGCTT
12599205 ACCGTTTACA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.30, G:0.18, T:0.30
Consensus pattern (25 bp):
GAGCTTCCCATTATTCAACTCACAG
Found at i:12602617 original size:41 final size:41
Alignment explanation
Indices: 12602555--12602645 Score: 128
Period size: 41 Copynumber: 2.2 Consensus size: 41
12602545 TCGAATTTAT
* * * *
12602555 TGCCAGTGAAATAATTCAGACTTTAGGTCTAGCAGGCTTGA
1 TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGCTTAA
* *
12602596 TGCTGGTGAAATTATTCAGACTATACGTCTAGCAGGCTTAA
1 TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGCTTAA
12602637 TGCCGGTGA
1 TGCCGGTGA
12602646 TACGTTTCGA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (41 bp):
TGCCGGTGAAATAATTCAGACTATACGTCTAGCAGGCTTAA
Found at i:12602660 original size:41 final size:41
Alignment explanation
Indices: 12602555--12602674 Score: 120
Period size: 41 Copynumber: 2.9 Consensus size: 41
12602545 TCGAATTTAT
* * * *
12602555 TGCCAGTGAAA-TAATTCAGACTTTAGGTCTAGCAGGCTTGA
1 TGCCGGTGAAAGT-ATTCAGACTATAAGTCTAGCAGGCTTAA
* * *
12602596 TGCTGGTGAAATTATTCAGACTATACGTCTAGCAGGCTTAA
1 TGCCGGTGAAAGTATTCAGACTATAAGTCTAGCAGGCTTAA
*
12602637 TGCCGGTGATACGT-TTC-GAACTATAAGTCTAGCAGGCT
1 TGCCGGTGA-AAGTATTCAG-ACTATAAGTCTAGCAGGCT
12602675 AAAAACTGGT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
40 1 0.01
41 63 0.94
42 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (41 bp):
TGCCGGTGAAAGTATTCAGACTATAAGTCTAGCAGGCTTAA
Found at i:12612623 original size:20 final size:20
Alignment explanation
Indices: 12612504--12612628 Score: 67
Period size: 20 Copynumber: 6.2 Consensus size: 20
12612494 TTGTACGGGA
** *
12612504 TTGCACTTCAATGCCTCTGT
1 TTGCACTTCGGTGCTTCTGT
**
12612524 TTGCACTTTTGTGCTTCT-T
1 TTGCACTTCGGTGCTTCTGT
** * * *
12612543 TCACACATCGATGTTTCTGT
1 TTGCACTTCGGTGCTTCTGT
* * *
12612563 TTGCACTTTGGTGCCTCTGA
1 TTGCACTTCGGTGCTTCTGT
* *
12612583 TCGCACATT-TGTGCCTT-TGT
1 TTGCAC-TTCGGTG-CTTCTGT
12612603 TTGCACTTCGGTGCTTCTGT
1 TTGCACTTCGGTGCTTCTGT
12612623 TATGCA
1 T-TGCA
12612629 TCTATGGTGC
Statistics
Matches: 74, Mismatches: 25, Indels: 11
0.67 0.23 0.10
Matches are distributed among these distances:
19 17 0.23
20 49 0.66
21 8 0.11
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
TTGCACTTCGGTGCTTCTGT
Found at i:12619228 original size:57 final size:58
Alignment explanation
Indices: 12619152--12619330 Score: 257
Period size: 51 Copynumber: 3.2 Consensus size: 58
12619142 CTTACACGAA
* *
12619152 ATCACTTATCATTTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTT
1 ATCACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
12619209 ATCACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCT---AC--
1 ATCACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
* *
12619262 --CACTTATCACTTGTCACTTGTCATTGATCAGATAAGTGCAGCTAAAGCTACCACTT
1 ATCACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
*
12619318 ATCACTTGTCACT
1 ATCACTTATCACT
12619331 GATCAGAAGT
Statistics
Matches: 109, Mismatches: 5, Indels: 15
0.84 0.04 0.12
Matches are distributed among these distances:
51 47 0.43
54 2 0.02
55 2 0.02
57 43 0.39
58 15 0.14
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (58 bp):
ATCACTTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:12621059 original size:16 final size:16
Alignment explanation
Indices: 12621038--12621070 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12621028 TTCGCTGTAT
12621038 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
12621054 TGGAATAGAGTCGTAA
1 TGGAATAGAGGCGTAA
12621070 T
1 T
12621071 AGCAAATCAA
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:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:12621114 original size:45 final size:44
Alignment explanation
Indices: 12621050--12621139 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
12621040 GAATAGAGGC
*
12621050 GTAATGGAATAGAGTCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
12621095 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
12621139 G
1 G
12621140 GAATAGAGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 18 0.44
45 22 0.54
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:12621320 original size:16 final size:16
Alignment explanation
Indices: 12621283--12621324 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12621273 TTAATCATAT
*
12621283 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
12621299 TT-AAATATATTATAA
1 TTAAAATATATTATAA
12621314 TTAAAATATAT
1 TTAAAATATAT
12621325 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:12621331 original size:14 final size:15
Alignment explanation
Indices: 12621292--12621333 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12621282 TTTAAACATA
*
12621292 ATTATTATTAAATAT
1 ATTATAATTAAATAT
12621307 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
12621321 A-TATAATTTAATA
1 ATTATAATTAAATA
12621334 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:12625864 original size:21 final size:21
Alignment explanation
Indices: 12625838--12625877 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12625828 ATGTGTTTTT
12625838 ATTTATT-TATATATTTTTTAA
1 ATTTATTAT-TATATTTTTTAA
12625859 ATTTATTATTATATTTTTT
1 ATTTATTATTATATTTTTT
12625878 TGAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTATTATTATATTTTTTAA
Found at i:12625884 original size:24 final size:25
Alignment explanation
Indices: 12625835--12625919 Score: 70
Period size: 25 Copynumber: 3.3 Consensus size: 25
12625825 TTTATGTGTT
12625835 TTTATTTATTTATATATTTTTTAAA
1 TTTATTTATTTATATATTTTTTAAA
12625860 TTTA-TTA-TTATAT-TTTTTTGAAAATA
1 TTTATTTATTTATATATTTTTT---AA-A
* *
12625886 TTTATGTATTTTTATATATTTTTTGAA
1 TTTAT-T-TATTTATATATTTTTTAAA
12625913 TTT-TTTA
1 TTTATTTA
12625920 GAATTAGGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 19
0.69 0.04 0.27
Matches are distributed among these distances:
22 6 0.12
23 6 0.12
24 4 0.08
25 7 0.15
26 6 0.12
27 4 0.08
28 2 0.04
29 1 0.02
30 6 0.12
31 6 0.12
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (25 bp):
TTTATTTATTTATATATTTTTTAAA
Found at i:12625887 original size:22 final size:23
Alignment explanation
Indices: 12625844--12625887 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
12625834 TTTTATTTAT
*
12625844 TTATATATTTTTTAAATTTATTA
1 TTATATATTTTTTAAATATATTA
12625867 TTATAT-TTTTTTGAAA-ATATT
1 TTATATATTTTTT-AAATATATT
12625888 TATGTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTATATATTTTTTAAATATATTA
Found at i:12625890 original size:23 final size:21
Alignment explanation
Indices: 12625837--12625898 Score: 54
Period size: 22 Copynumber: 2.8 Consensus size: 21
12625827 TATGTGTTTT
12625837 TATTTATTTATATATTTTTTAAA
1 TATTTA-TTATAT-TTTTTTAAA
*
12625860 TTTATTATTATATTTTTTTGAAAA
1 TAT-TTATTATATTTTTTT--AAA
*
12625884 TATTTA-TGTATTTTT
1 TATTTATTATATTTTT
12625899 ATATATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 14 0.42
23 11 0.33
24 8 0.24
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (21 bp):
TATTTATTATATTTTTTTAAA
Found at i:12627034 original size:22 final size:23
Alignment explanation
Indices: 12626985--12627037 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
12626975 CCGGCCCGGT
12626985 TTTTTAATAAACACAAAAAAAATA
1 TTTTTAA-AAACACAAAAAAAATA
*
12627009 -TTTTAAAAATA-AAAAAAAATA
1 TTTTTAAAAACACAAAAAAAATA
12627030 TTTTTAAA
1 TTTTTAAA
12627038 GTATTTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 10 0.37
22 11 0.41
23 6 0.22
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (23 bp):
TTTTTAAAAACACAAAAAAAATA
Found at i:12627459 original size:2 final size:2
Alignment explanation
Indices: 12627452--12627498 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
12627442 CACCTGAAGT
12627452 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12627494 TA TA T
1 TA TA T
12627499 TAGATTTTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12628351 original size:17 final size:16
Alignment explanation
Indices: 12628330--12628363 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12628320 TAAAATAATG
*
12628330 TAAAAATTAAAAATTT
1 TAAAAAATAAAAATTT
*
12628346 TAAAAAATAATAATTT
1 TAAAAAATAAAAATTT
12628362 TA
1 TA
12628364 CAAAGTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAAAATAAAAATTT
Found at i:12632968 original size:50 final size:50
Alignment explanation
Indices: 12632908--12633151 Score: 335
Period size: 50 Copynumber: 4.9 Consensus size: 50
12632898 CATTTGGGTA
* *
12632908 GAGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGTACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
*
12632958 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
* * * *
12633008 GAGAGGTCCCATGTAAGACCATGTCTGGGATATGGTGTTAGCAACGAGAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
** * * * *
12633058 GAGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATAT
1 GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
** *
12633108 GAGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 GAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
12633152 TGTTATGATC
Statistics
Matches: 170, Mismatches: 23, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
50 137 0.81
51 33 0.19
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (50 bp):
GAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
Found at i:12639107 original size:9 final size:8
Alignment explanation
Indices: 12639095--12639156 Score: 65
Period size: 9 Copynumber: 7.4 Consensus size: 8
12639085 ATTAAAAATA
12639095 TTTTATACT
1 TTTTATA-T
12639104 TTTTATACT
1 TTTTATA-T
12639113 TTTTATA-
1 TTTTATAT
12639120 TTTTATAAT
1 TTTTAT-AT
12639129 TTTTATAAT
1 TTTTAT-AT
12639138 TTTTA-ATT
1 TTTTATA-T
12639146 TTTTATAT
1 TTTTATAT
12639154 TTT
1 TTT
12639157 AAAAAATTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.14
8 11 0.22
9 31 0.63
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTATAT
Found at i:12639120 original size:25 final size:25
Alignment explanation
Indices: 12639091--12639156 Score: 89
Period size: 25 Copynumber: 2.6 Consensus size: 25
12639081 AAATATTAAA
*
12639091 AATATTTTATACTTTTTATACTTTTT
1 AATATTTTATA-TTTTTATAATTTTT
12639117 -ATATTTTATAATTTTTATAATTTTT
1 AATATTTTAT-ATTTTTATAATTTTT
*
12639142 AATTTTTTATATTTT
1 AATATTTTATATTTT
12639157 AAAAAATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
25 27 0.75
26 9 0.25
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (25 bp):
AATATTTTATATTTTTATAATTTTT
Found at i:12639125 original size:16 final size:16
Alignment explanation
Indices: 12639104--12639157 Score: 74
Period size: 16 Copynumber: 3.3 Consensus size: 16
12639094 ATTTTATACT
*
12639104 TTTTATACTTTTTATA
1 TTTTATAATTTTTATA
12639120 TTTTATAATTTTTATAA
1 TTTTATAATTTTTAT-A
12639137 TTTT-TAATTTTTTATA
1 TTTTATAA-TTTTTATA
12639153 TTTTA
1 TTTTA
12639158 AAAAATTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
16 22 0.65
17 12 0.35
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTATAATTTTTATA
Found at i:12640178 original size:21 final size:19
Alignment explanation
Indices: 12640136--12640173 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12640126 AATAGAATCG
*
12640136 TATCATATCTAAGATTACA
1 TATCATATATAAGATTACA
12640155 TATCATATATAAGATTACA
1 TATCATATATAAGATTACA
12640174 CATATTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (19 bp):
TATCATATATAAGATTACA
Found at i:12643567 original size:13 final size:13
Alignment explanation
Indices: 12643549--12643573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12643539 TAGATTAGAT
12643549 TTGATTATGTAAA
1 TTGATTATGTAAA
12643562 TTGATTATGTAA
1 TTGATTATGTAA
12643574 TCTTGTAAAT
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:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTGATTATGTAAA
Found at i:12646813 original size:2 final size:2
Alignment explanation
Indices: 12646806--12646831 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12646796 ATTATAAGCG
12646806 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
12646832 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:12650795 original size:2 final size:2
Alignment explanation
Indices: 12650788--12650817 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12650778 GAAAGCAAGC
*
12650788 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12650818 CTTGGAAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12654650 original size:18 final size:18
Alignment explanation
Indices: 12654627--12654662 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12654617 AAGCAGAAAA
*
12654627 AAAATGTTAATGCACATG
1 AAAATGCTAATGCACATG
12654645 AAAATGCTAATGCACATG
1 AAAATGCTAATGCACATG
12654663 CAACCTAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (18 bp):
AAAATGCTAATGCACATG
Found at i:12655168 original size:111 final size:109
Alignment explanation
Indices: 12655021--12655240 Score: 386
Period size: 111 Copynumber: 2.0 Consensus size: 109
12655011 CATCATAAAT
12655021 ATTGAACTTAGTTACCTCACCATCATGCCTTCATGCATGTCAATTTTAGTTTAGATGTTTTTTTG
1 ATTGAACTTAGTTACCTCACCATCATGCCTTCATGCATGTCAATTTTAGTTTAGAT-TTTTTTT-
**
12655086 AAAAGGTCTTCCTAATAAAATTTGTGTTGAATGATGAGTAAAATCA
64 AAAAGGTCTTCCTAATAAAATTTGTGCCGAATGATGAGTAAAATCA
*
12655132 ATTGAACTTAGTTACCTCACCTTCATGCCTTCATGCATGTCAATTTTAGTTTAGATTTTTTTTAA
1 ATTGAACTTAGTTACCTCACCATCATGCCTTCATGCATGTCAATTTTAGTTTAGATTTTTTTTAA
*
12655197 AAGGTCTTCTTAATAAAATTTGTGCCGAATGATGAGTAAAATCA
66 AAGGTCTTCCTAATAAAATTTGTGCCGAATGATGAGTAAAATCA
12655241 TTTTTCATAT
Statistics
Matches: 105, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
109 43 0.41
110 7 0.07
111 55 0.52
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (109 bp):
ATTGAACTTAGTTACCTCACCATCATGCCTTCATGCATGTCAATTTTAGTTTAGATTTTTTTTAA
AAGGTCTTCCTAATAAAATTTGTGCCGAATGATGAGTAAAATCA
Found at i:12669866 original size:4 final size:4
Alignment explanation
Indices: 12669848--12669888 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
12669838 CCGTGCATTC
12669848 TCTT TCTT T-TCT TCTT TCTCT T-TT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCT-T TCTT TCT-T TCTT TCTT TCTT TCTT TCTT T
12669889 TCTTAGTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.09
4 27 0.82
5 3 0.09
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:12675075 original size:22 final size:21
Alignment explanation
Indices: 12675050--12675092 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
12675040 AAAAATTTAA
12675050 AAATA-TAAAAAGAATGAAAAAT
1 AAATATTAAAAA-AAT-AAAAAT
12675072 AAATATTAAAAAAATAAAAAT
1 AAATATTAAAAAAATAAAAAT
12675093 GATAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 8 0.40
23 6 0.30
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (21 bp):
AAATATTAAAAAAATAAAAAT
Found at i:12675235 original size:25 final size:26
Alignment explanation
Indices: 12675206--12675254 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
12675196 TTCATTTTGG
12675206 ATATAATT-TTAAAATTATAAAAAAT
1 ATATAATTATTAAAATTATAAAAAAT
* *
12675231 ATATATTTATTAAAATTGTAAAAA
1 ATATAATTATTAAAATTATAAAAA
12675255 TATTATGACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (26 bp):
ATATAATTATTAAAATTATAAAAAAT
Found at i:12676474 original size:2 final size:2
Alignment explanation
Indices: 12676469--12676505 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
12676459 AGTATGTGTC
12676469 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12676506 TGTTTGAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12676579 original size:17 final size:17
Alignment explanation
Indices: 12676528--12676593 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 17
12676518 TATTCTCATT
12676528 TTTTTATAATTTT-ATAA
1 TTTTTATAATTTTAAT-A
*
12676545 TTTTTTACATATTTTTAAATA
1 -TTTTT--ATAATTTT-AATA
*
12676566 TTTTT-TAATTTTAATT
1 TTTTTATAATTTTAATA
12676582 TTTTTATAATTT
1 TTTTTATAATTT
12676594 AAAAATTATG
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
16 8 0.20
17 12 0.30
18 5 0.12
20 12 0.30
21 1 0.03
22 2 0.05
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTATAATTTTAATA
Found at i:12676724 original size:22 final size:21
Alignment explanation
Indices: 12676693--12676738 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
12676683 AATTTTTAAA
12676693 TATTTTTATTCTTT-TAAATTT
1 TATTTTTATT-TTTATAAATTT
*
12676714 TATTTCTTATTTTTATAAGTTT
1 TATTT-TTATTTTTATAAATTT
12676736 TAT
1 TAT
12676739 AATATGTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (21 bp):
TATTTTTATTTTTATAAATTT
Found at i:12682865 original size:45 final size:45
Alignment explanation
Indices: 12682816--12682905 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
12682806 AATGCACAGG
12682816 GATGAGCTATTACTTTACCAACTTTGTCTAAAAGAAAATTTTATT
1 GATGAGCTATTACTTTACCAACTTTGTCTAAAAGAAAATTTTATT
12682861 GATGAGCTATTACTTTACCAACTTTGTCTAAAAGAAAATTTTATT
1 GATGAGCTATTACTTTACCAACTTTGTCTAAAAGAAAATTTTATT
12682906 CTTTAGTAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (45 bp):
GATGAGCTATTACTTTACCAACTTTGTCTAAAAGAAAATTTTATT
Found at i:12686814 original size:13 final size:13
Alignment explanation
Indices: 12686774--12686807 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
12686764 TTTAAGTAGG
12686774 GTCACACGGTCGT
1 GTCACACGGTCGT
12686787 GTCACACGGTCGT
1 GTCACACGGTCGT
12686800 GTCACACG
1 GTCACACG
12686808 CCCGTGTGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (13 bp):
GTCACACGGTCGT
Found at i:12687776 original size:36 final size:36
Alignment explanation
Indices: 12687727--12687918 Score: 228
Period size: 36 Copynumber: 5.3 Consensus size: 36
12687717 ATTCCAACCA
* *
12687727 AAACACACTAGATGCTCATAAGAGCTAATCCATCCG
1 AAACACACCAGATGCTCATAAGAGCTAGTCCATCCG
* *
12687763 AAACACACCAGATGCTCATAAGAGCTAATCCATCCA
1 AAACACACCAGATGCTCATAAGAGCTAGTCCATCCG
* * *
12687799 AAACACACCAGATGCTCATATGAGCCAGTCTATCCG
1 AAACACACCAGATGCTCATAAGAGCTAGTCCATCCG
* *
12687835 ATAACACACCA-ATGCTCATATGAGCCAGTCCATCCG
1 A-AACACACCAGATGCTCATAAGAGCTAGTCCATCCG
*
12687871 ATAACACACCA-ATGGCTC-TAAAGAGCTAGTCCAACCG
1 A-AACACACCAGAT-GCTCAT-AAGAGCTAGTCCATCCG
12687908 AAAACACACCA
1 -AAACACACCA
12687919 AAACAAATAG
Statistics
Matches: 141, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
36 104 0.74
37 36 0.26
38 1 0.01
ACGTcount: A:0.39, C:0.31, G:0.14, T:0.17
Consensus pattern (36 bp):
AAACACACCAGATGCTCATAAGAGCTAGTCCATCCG
Found at i:12696968 original size:26 final size:26
Alignment explanation
Indices: 12696939--12697002 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 26
12696929 TAAATTAAAA
*
12696939 TTTTCAAAATCAC-TTTTAATAAGTAC
1 TTTTCAAAAGCACTTTTTAA-AAGTAC
* *
12696965 TTTTCCATAGCACTTTTTAAAAGTAC
1 TTTTCAAAAGCACTTTTTAAAAGTAC
* *
12696991 TTCTCAACAGCA
1 TTTTCAAAAGCA
12697003 ATTCTAAACT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 25 0.81
27 6 0.19
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (26 bp):
TTTTCAAAAGCACTTTTTAAAAGTAC
Found at i:12704420 original size:12 final size:12
Alignment explanation
Indices: 12704403--12704446 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
12704393 TAAACTTTAA
12704403 ATTAGGAATTTT
1 ATTAGGAATTTT
* *
12704415 ATTAGGACTTTAA
1 ATTAGGAATTT-T
*
12704428 ATTAGGAATTCT
1 ATTAGGAATTTT
12704440 ATTAGGA
1 ATTAGGA
12704447 CTTTCCCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (12 bp):
ATTAGGAATTTT
Found at i:12704424 original size:25 final size:25
Alignment explanation
Indices: 12704396--12704450 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
12704386 TTCCTTATAA
*
12704396 ACTTTAAATTAGGAATTTTATTAGG
1 ACTTTAAATTAGGAATTCTATTAGG
12704421 ACTTTAAATTAGGAATTCTATTAGG
1 ACTTTAAATTAGGAATTCTATTAGG
12704446 ACTTT
1 ACTTT
12704451 CCCTTTGTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.44
Consensus pattern (25 bp):
ACTTTAAATTAGGAATTCTATTAGG
Found at i:12704433 original size:13 final size:13
Alignment explanation
Indices: 12704396--12704434 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
12704386 TTCCTTATAA
12704396 ACTTTAAATTAGG
1 ACTTTAAATTAGG
* *
12704409 AATTT-TATTAGG
1 ACTTTAAATTAGG
12704421 ACTTTAAATTAGG
1 ACTTTAAATTAGG
12704434 A
1 A
12704435 ATTCTATTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.41
Consensus pattern (13 bp):
ACTTTAAATTAGG
Found at i:12712298 original size:18 final size:18
Alignment explanation
Indices: 12712266--12712300 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12712256 TGTACCGGAC
**
12712266 TGCTAAGTGGTTAGTTTA
1 TGCTAAGTGCATAGTTTA
12712284 TGCTAAGTGCATAGTTT
1 TGCTAAGTGCATAGTTT
12712301 TAAAAATTGG
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:0.23, C:0.09, G:0.26, T:0.43
Consensus pattern (18 bp):
TGCTAAGTGCATAGTTTA
Found at i:12712954 original size:20 final size:20
Alignment explanation
Indices: 12712920--12712961 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
12712910 AACTATTTAA
** *
12712920 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
12712940 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
12712960 AT
1 AT
12712962 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:12719936 original size:36 final size:38
Alignment explanation
Indices: 12719891--12719977 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 38
12719881 GGAGTTGTAA
* * *
12719891 GTGACTATTCATCTATATCAC-TAAATGC-TAGGAGTT
1 GTGACTATTCATCTACATAACTTAAATACATAGGAGTT
*
12719927 GTGACTATTCATTTACATAACTTAAATACTATAGGAGTT
1 GTGACTATTCATCTACATAACTTAAATAC-ATAGGAGTT
12719966 GTGACTATTCAT
1 GTGACTATTCAT
12719978 GCATGTGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 18 0.41
37 6 0.14
39 20 0.45
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (38 bp):
GTGACTATTCATCTACATAACTTAAATACATAGGAGTT
Found at i:12724442 original size:36 final size:38
Alignment explanation
Indices: 12724397--12724483 Score: 115
Period size: 39 Copynumber: 2.3 Consensus size: 38
12724387 GGAGTTGTAA
* * *
12724397 GTGACTATTCATCTATATCAC-TAAATGC-TAGGAGTT
1 GTGACTATTCATCTACATAACTTAAATACATAGGAGTT
*
12724433 GTGACTATTCATTTACATAACTTAAATACTATAGGAGTT
1 GTGACTATTCATCTACATAACTTAAATAC-ATAGGAGTT
12724472 GTGACTATTCAT
1 GTGACTATTCAT
12724484 GCATGTGTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 18 0.41
37 6 0.14
39 20 0.45
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (38 bp):
GTGACTATTCATCTACATAACTTAAATACATAGGAGTT
Found at i:12724529 original size:32 final size:32
Alignment explanation
Indices: 12724492--12724568 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
12724482 ATGCATGTGT
* *
12724492 GTAACTTTTCATCTTCAAGTCTCTTT-GCATTA
1 GTAACTTTTCATATTCAAGTCT-TTTCACATTA
* * *
12724524 TTAACTCTTCATATTCAAGTCTTTTCACATTC
1 GTAACTTTTCATATTCAAGTCTTTTCACATTA
12724556 GTAACTTTTCATA
1 GTAACTTTTCATA
12724569 ATTTATTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
31 3 0.08
32 34 0.92
ACGTcount: A:0.25, C:0.22, G:0.06, T:0.47
Consensus pattern (32 bp):
GTAACTTTTCATATTCAAGTCTTTTCACATTA
Found at i:12725991 original size:14 final size:14
Alignment explanation
Indices: 12725945--12725992 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
12725935 GTATATAAAA
12725945 TTTATCATTTAATT
1 TTTATCATTTAATT
* * *
12725959 TTTATGAATATAATA
1 TTTAT-CATTTAATT
12725974 TTTATCATTTAATT
1 TTTATCATTTAATT
12725988 TTTAT
1 TTTAT
12725993 ATATATATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.60
Consensus pattern (14 bp):
TTTATCATTTAATT
Found at i:12725997 original size:2 final size:2
Alignment explanation
Indices: 12725990--12726047 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
12725980 ATTTAATTTT
12725990 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12726032 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
12726048 AGTGATAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12725998 original size:29 final size:30
Alignment explanation
Indices: 12725936--12726004 Score: 106
Period size: 29 Copynumber: 2.3 Consensus size: 30
12725926 AACAATGGGG
*
12725936 TATATAAAATTTATCATTTAATTTTTATGA
1 TATATAATATTTATCATTTAATTTTTATGA
12725966 -ATATAATATTTATCATTTAATTTTTAT-A
1 TATATAATATTTATCATTTAATTTTTATGA
12725994 TATATATATAT
1 TATATA-ATAT
12726005 ATATATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 1 0.03
29 31 0.86
30 4 0.11
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (30 bp):
TATATAATATTTATCATTTAATTTTTATGA
Found at i:12726361 original size:26 final size:26
Alignment explanation
Indices: 12726332--12726389 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
12726322 GAGCTTATTG
* *
12726332 TCTTAATTAGTTTATTTAGTTTAAAA
1 TCTTAATCAGTTTATTCAGTTTAAAA
12726358 TCTTAATCAGTTTATTCAGTTTAAAA
1 TCTTAATCAGTTTATTCAGTTTAAAA
*
12726384 TGTTAA
1 TCTTAA
12726390 AACCAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.50
Consensus pattern (26 bp):
TCTTAATCAGTTTATTCAGTTTAAAA
Found at i:12738209 original size:7 final size:7
Alignment explanation
Indices: 12738197--12738250 Score: 99
Period size: 7 Copynumber: 7.7 Consensus size: 7
12738187 TAAGATGAAA
12738197 AGAAAAG
1 AGAAAAG
12738204 AGAAAAG
1 AGAAAAG
12738211 AGAAAAG
1 AGAAAAG
12738218 AGAAAAG
1 AGAAAAG
12738225 AGAAAAG
1 AGAAAAG
*
12738232 GGAAAAG
1 AGAAAAG
12738239 AGAAAAG
1 AGAAAAG
12738246 AGAAA
1 AGAAA
12738251 GAGCAATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (7 bp):
AGAAAAG
Done.