Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 162 of 322
Found at i:53210225 original size:4 final size:4
Alignment explanation
Indices: 53210191--53210215 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
53210181 ACATGTATGC
53210191 AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG A
53210216 CAAATGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:53210236 original size:22 final size:22
Alignment explanation
Indices: 53210195--53210249 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
53210185 GTATGCAATG
* *
53210195 AATGAATGAATGAATGAATGACA
1 AATGAATG-TTGAATAAATGACA
**
53210218 AATGAATGTTGAATAAATGGTA
1 AATGAATGTTGAATAAATGACA
53210240 AATGAATGTT
1 AATGAATGTT
53210250 AATCGTGAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (22 bp):
AATGAATGTTGAATAAATGACA
Found at i:53212533 original size:865 final size:865
Alignment explanation
Indices: 53210864--53213527 Score: 4115
Period size: 865 Copynumber: 3.0 Consensus size: 865
53210854 ATTCTGCTGA
53210864 TGATTTGCCCAGCCCACTATTCTTTATTGGGCCTCTTAACTTCTTATTTTCCAGATGAAGATCTC
1 TGATTTGCCCAGCCCACTATTCTTTATTGGGCCTCTTAACTTCTTATTTTCCAGATGAAGATCTC
53210929 TCAAGTTATTTCTTACAACTTCAGCCTCTTTTTGCACTTTCTCGGTTCTGGATCTTTCAATCTGA
66 TCAAGTTATTTCTTACAACTTCAGCCTCTTTTTGCACTTTCTCGGTTCTGGATCTTTCAATCTGA
53210994 ACGTCGATCTTCAATTGGTAGTTTTCCTTTTGAAGAGCACTAAGGTCCCAAGATATCTTCGCCTT
131 ACGTCGATCTTCAATTGGTAGTTTTCCTTTTGAAGAGCACTAAGGTCCCAAGATATCTTCGCCTT
53211059 TTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTCAGACGACATTTCCTCCGAGAAAGGATTCT
196 TTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTCAGACGACATTTCCTCCGAGAAAGGATTCT
53211124 GAACGGTGTAGTTCGTTGACGAGATTTGCTGACTATTCACCCGTTGCTTCCTCCTGATGTCATAA
261 GAACGGTGTAGTTCGTTGACGAGATTTGCTGACTATTCACCCGTTGCTTCCTCCTGATGTCATAA
53211189 TCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCCATCAGATAAAATTTCTTCCAAGACTTTGC
326 TCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCCATCAGATAAAATTTCTTCCAAGACTTTGC
53211254 AATGTCTCGGACCCTCTTCATATACCCTACACCTGCAAAAGCGAACTCGGACTGTGCTAATCCTC
391 AATGTCTCGGACCCTCTTCATATACCCTACACCTGCAAAAGCGAACTCGGACTGTGCTAATCCTC
53211319 CAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACCTTTAGACTAATAGCGGGACGTATCCAACT
456 CAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACCTTTAGACTAATAGCGGGACGTATCCAACT
53211384 CCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGATTTCCAACCTTGTATAACAGAACCGAAAG
521 CCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGATTTCCAACCTTGTATAACAGAACCGAAAG
53211449 GCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGCTCGAAGGTTCTGAAAAACTGAAACCCAAT
586 GCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGCTCGAAGGTTCTGAAAAACTGAAACCCAAT
53211514 GTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAAGATAGGCTTCCAATGGGCAAAAGTTTTTG
651 GTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAAGATAGGCTTCCAATGGGCAAAAGTTTTTG
53211579 AAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGAAATGGCTCAAAATCCAGACATTTAGTAAC
716 AAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGAAATGGCTCAAAATCCAGACATTTAGTAAC
53211644 TGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTCCTACAACTGTTTAAGGATCTAAAGGTCTC
781 TGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTCCTACAACTGTTTAAGGATCTAAAGGTCTC
53211709 GGCCAAGATAGTCGGGACAG
846 GGCCAAGATAGTCGGGACAG
53211729 TGATTTGCCCAGCCCACTATTCTTTATTGGGCCTCTTAACTTCTTATTTTCCAGATGAAGATCTC
1 TGATTTGCCCAGCCCACTATTCTTTATTGGGCCTCTTAACTTCTTATTTTCCAGATGAAGATCTC
53211794 TCAAGTTATTTCTTACAACTTCAGCCTCTTTTTGCACTTTCTCGGTTCTGGATCTTTCAATCTGA
66 TCAAGTTATTTCTTACAACTTCAGCCTCTTTTTGCACTTTCTCGGTTCTGGATCTTTCAATCTGA
53211859 ACGTCGATCTTCAATTGGTAGTTTTCCTTTTGAAGAGCACTAAGGTCCCAAGATATCTTCGCCTT
131 ACGTCGATCTTCAATTGGTAGTTTTCCTTTTGAAGAGCACTAAGGTCCCAAGATATCTTCGCCTT
53211924 TTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTCAGACGACATTTCCTCCGAGAAAGGATTCT
196 TTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTCAGACGACATTTCCTCCGAGAAAGGATTCT
53211989 GAACGGTGTAGTTCGTTGACGAGATTTGCTGACTATTCACCCGTTGCTTCCTCCTGATGTCATAA
261 GAACGGTGTAGTTCGTTGACGAGATTTGCTGACTATTCACCCGTTGCTTCCTCCTGATGTCATAA
53212054 TCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCCATCAGATAAAATTTCTTCCAAGACTTTGC
326 TCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCCATCAGATAAAATTTCTTCCAAGACTTTGC
53212119 AATGTCTCGGACCCTCTTCATATACCCTACACCTGCAAAAGCGAACTCGGACTGTGCTAATCCTC
391 AATGTCTCGGACCCTCTTCATATACCCTACACCTGCAAAAGCGAACTCGGACTGTGCTAATCCTC
53212184 CAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACCTTTAGACTAATAGCGGGACGTATCCAACT
456 CAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACCTTTAGACTAATAGCGGGACGTATCCAACT
53212249 CCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGATTTCCAACCTTGTATAACAGAACCGAAAG
521 CCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGATTTCCAACCTTGTATAACAGAACCGAAAG
53212314 GCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGCTCGAAGGTTCTGAAAAACTGAAACCCAAT
586 GCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGCTCGAAGGTTCTGAAAAACTGAAACCCAAT
53212379 GTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAAGATAGGCTTCCAATGGGCAAAAGTTTTTG
651 GTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAAGATAGGCTTCCAATGGGCAAAAGTTTTTG
53212444 AAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGAAATGGCTCAAAATCCAGACATTTAGTAAC
716 AAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGAAATGGCTCAAAATCCAGACATTTAGTAAC
53212509 TGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTCCTACAACTGTTTAAGGATCTAAAGGTCTC
781 TGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTCCTACAACTGTTTAAGGATCTAAAGGTCTC
53212574 GGCCAAGATAGTCGGGACAG
846 GGCCAAGATAGTCGGGACAG
* * *** ** * * * *
53212594 -G-GTTGACTCCTTG--TTTTAATT-TTTCAAAGAAGTCCACCACTGCAACTTC-TATGTGTCCA
1 TGATTTG-C-CC-AGCCCACT-ATTCTTT-ATTG--G---GCCTCT-TAACTTCTTAT-TTTCC-
* * *
53212653 AGGACTTTCGGGAAGATGATCAAACCGTAAATGGCCAAAGCGAATAGATTTACCCCTTTCAACAT
53 A-GA---T---G-A-A-GAT-----C-T--CT---C-AA--G--T-TATTT----CTTACAAC-T
** ** ** * * *** * * ** * *
53212718 GTCAGGATGGTTCAGAACCAATTCTC-GTAGGGAAGACCATGGAATAC-AAATGGTTTC-ATTCT
86 -TCAGCCTCTTTTTGCA-C-TTTCTCGGTTCTG--GATCTTTCAAT-CTGAA-CG--TCGA-TCT
** ** * * * * ** * *
53212780 TCTTCTTTATCTATTTTTCGGCCTATG-CGTCAGTCATGTCTGTCAATCTCCACTAAGGTCCCAA
141 TC--AATT-GGTAGTTTTC--CTTTTGAAG--AG-CA---C--T-AAGGTCC-C-AAGAT---AT
** ** *
53212844 GATATCTTCGCCTTTTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTCAGACGACATTTCCTC
187 CTTCGCCT-----TTTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTCAGACGACATTTCCTC
53212909 CGAGAAAGGATTCTGAACGGTGTAGTTCGTTGACGAGATTTGCTGACTATTCACCCGTTGCTTCC
247 CGAGAAAGGATTCTGAACGGTGTAGTTCGTTGACGAGATTTGCTGACTATTCACCCGTTGCTTCC
53212974 TCCTGATGTCATAATCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCCATCAGATAAAATTTC
312 TCCTGATGTCATAATCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCCATCAGATAAAATTTC
53213039 TTCCAAGACTTTGCAATGTCTCGGACCCTCTTCATATACCCTACACCTGCAAAAGCGAACTCGGA
377 TTCCAAGACTTTGCAATGTCTCGGACCCTCTTCATATACCCTACACCTGCAAAAGCGAACTCGGA
53213104 CTGTGCTAATCCTCCAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACCTTTAGACTAATAGCG
442 CTGTGCTAATCCTCCAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACCTTTAGACTAATAGCG
53213169 GGACGTATCCAACTCCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGATTTCCAACCTTGTAT
507 GGACGTATCCAACTCCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGATTTCCAACCTTGTAT
53213234 AACAGAACCGAAAGGCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGCTCGAAGGTTCTGAAA
572 AACAGAACCGAAAGGCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGCTCGAAGGTTCTGAAA
53213299 AACTGAAACCCAATGTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAAGATAGGCTTCCAATG
637 AACTGAAACCCAATGTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAAGATAGGCTTCCAATG
53213364 GGCAAAAGTTTTTGAAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGAAATGGCTCAAAATCC
702 GGCAAAAGTTTTTGAAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGAAATGGCTCAAAATCC
53213429 AGACATTTAGTAACTGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTCCTACAACTGTTTAAG
767 AGACATTTAGTAACTGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTCCTACAACTGTTTAAG
53213494 GATCTAAAGGTCTCGGCCAAGATAGTCGGGACAG
832 GATCTAAAGGTCTCGGCCAAGATAGTCGGGACAG
53213528 GGTTGACTCC
Statistics
Matches: 1672, Mismatches: 48, Indels: 89
0.92 0.03 0.05
Matches are distributed among these distances:
863 3 0.00
864 6 0.00
865 872 0.52
866 1 0.00
867 1 0.00
870 7 0.00
871 10 0.01
872 1 0.00
873 2 0.00
876 1 0.00
879 1 0.00
880 1 0.00
881 1 0.00
882 3 0.00
887 1 0.00
888 1 0.00
890 1 0.00
893 1 0.00
894 2 0.00
896 1 0.00
898 1 0.00
899 4 0.00
903 7 0.00
904 1 0.00
905 9 0.01
906 4 0.00
907 5 0.00
908 9 0.01
909 2 0.00
910 1 0.00
911 7 0.00
913 2 0.00
914 7 0.00
915 1 0.00
916 4 0.00
917 2 0.00
918 2 0.00
921 1 0.00
923 1 0.00
924 5 0.00
925 1 0.00
926 4 0.00
929 4 0.00
934 671 0.40
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (865 bp):
TGATTTGCCCAGCCCACTATTCTTTATTGGGCCTCTTAACTTCTTATTTTCCAGATGAAGATCTC
TCAAGTTATTTCTTACAACTTCAGCCTCTTTTTGCACTTTCTCGGTTCTGGATCTTTCAATCTGA
ACGTCGATCTTCAATTGGTAGTTTTCCTTTTGAAGAGCACTAAGGTCCCAAGATATCTTCGCCTT
TTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTCAGACGACATTTCCTCCGAGAAAGGATTCT
GAACGGTGTAGTTCGTTGACGAGATTTGCTGACTATTCACCCGTTGCTTCCTCCTGATGTCATAA
TCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCCATCAGATAAAATTTCTTCCAAGACTTTGC
AATGTCTCGGACCCTCTTCATATACCCTACACCTGCAAAAGCGAACTCGGACTGTGCTAATCCTC
CAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACCTTTAGACTAATAGCGGGACGTATCCAACT
CCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGATTTCCAACCTTGTATAACAGAACCGAAAG
GCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGCTCGAAGGTTCTGAAAAACTGAAACCCAAT
GTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAAGATAGGCTTCCAATGGGCAAAAGTTTTTG
AAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGAAATGGCTCAAAATCCAGACATTTAGTAAC
TGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTCCTACAACTGTTTAAGGATCTAAAGGTCTC
GGCCAAGATAGTCGGGACAG
Found at i:53213703 original size:934 final size:933
Alignment explanation
Indices: 53211896--53213768 Score: 3737
Period size: 934 Copynumber: 2.0 Consensus size: 933
53211886 TTTTGAAGAG
53211896 CACTAAGGTCCCAAGATATCTTCGCCTTTTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTCA
1 CACTAAGGTCCCAAGATATCTTCGCCTTTTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTCA
53211961 GACGACATTTCCTCCGAGAAAGGATTCTGAACGGTGTAGTTCGTTGACGAGATTTGCTGACTATT
66 GACGACATTTCCTCCGAGAAAGGATTCTGAACGGTGTAGTTCGTTGACGAGATTTGCTGACTATT
53212026 CACCCGTTGCTTCCTCCTGATGTCATAATCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCCA
131 CACCCGTTGCTTCCTCCTGATGTCATAATCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCCA
53212091 TCAGATAAAATTTCTTCCAAGACTTTGCAATGTCTCGGACCCTCTTCATATACCCTACACCTGCA
196 TCAGATAAAATTTCTTCCAAGACTTTGCAATGTCTCGGACCCTCTTCATATACCCTACACCTGCA
53212156 AAAGCGAACTCGGACTGTGCTAATCCTCCAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACCT
261 AAAGCGAACTCGGACTGTGCTAATCCTCCAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACCT
53212221 TTAGACTAATAGCGGGACGTATCCAACTCCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGAT
326 TTAGACTAATAGCGGGACGTATCCAACTCCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGAT
53212286 TTCCAACCTTGTATAACAGAACCGAAAGGCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGCT
391 TTCCAACCTTGTATAACAGAACCGAAAGGCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGCT
53212351 CGAAGGTTCTGAAAAACTGAAACCCAATGTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAAG
456 CGAAGGTTCTGAAAAACTGAAACCCAATGTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAAG
53212416 ATAGGCTTCCAATGGGCAAAAGTTTTTGAAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGAA
521 ATAGGCTTCCAATGGGCAAAAGTTTTTGAAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGAA
53212481 ATGGCTCAAAATCCAGACATTTAGTAACTGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTCC
586 ATGGCTCAAAATCCAGACATTTAGTAACTGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTCC
53212546 TACAACTGTTTAAGGATCTAAAGGTCTCGGCCAAGATAGTCGGGACAGGGTTGACTCCTTGTTTT
651 TACAACTGTTTAAGGATCTAAAGGTCTCGGCCAAGATAGTCGGGACAGGGTTGACTCCTTGTTTT
53212611 AATTTTTCAAAGAAGTCCACCACTGCAACTTCTATGTGTCCAAGGACTTTCGGGAAGATGATCAA
716 AATTTTTCAAAGAAGTCCACCACTGCAACTTCTATGTGTCCAAGGACTTTCGGGAAGATGATCAA
53212676 ACCGTAAATGGCCAAAGCGAATAGATTTACCCCTTTCAACATGTCAGGATGGTTCAGAACCAATT
781 ACCGTAAATGGCCAAAGCGAATAGATTTACCCCTTTCAACATGTCAGGATGGTTCAGAACCAATT
53212741 CTCGTAGGGAAGACCATGGAATACAAATGGTTTCATTCTTCTTCTTTATCTATTTTTCGGCCTAT
846 CTCGTAGGGAAGACCATGGAATACAAATGGTTTCATTCTTCTTCTTTATCTATTTTTCGGCCTAT
53212806 GCGTCAGTCATGTCTGTCAATCT
911 GCGTCAGTCATGTCTGTCAATCT
53212829 CCACTAAGGTCCCAAGATATCTTCGCCTTTTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTC
1 -CACTAAGGTCCCAAGATATCTTCGCCTTTTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTC
53212894 AGACGACATTTCCTCCGAGAAAGGATTCTGAACGGTGTAGTTCGTTGACGAGATTTGCTGACTAT
65 AGACGACATTTCCTCCGAGAAAGGATTCTGAACGGTGTAGTTCGTTGACGAGATTTGCTGACTAT
53212959 TCACCCGTTGCTTCCTCCTGATGTCATAATCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCC
130 TCACCCGTTGCTTCCTCCTGATGTCATAATCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCC
53213024 ATCAGATAAAATTTCTTCCAAGACTTTGCAATGTCTCGGACCCTCTTCATATACCCTACACCTGC
195 ATCAGATAAAATTTCTTCCAAGACTTTGCAATGTCTCGGACCCTCTTCATATACCCTACACCTGC
53213089 AAAAGCGAACTCGGACTGTGCTAATCCTCCAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACC
260 AAAAGCGAACTCGGACTGTGCTAATCCTCCAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACC
53213154 TTTAGACTAATAGCGGGACGTATCCAACTCCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGA
325 TTTAGACTAATAGCGGGACGTATCCAACTCCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGA
53213219 TTTCCAACCTTGTATAACAGAACCGAAAGGCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGC
390 TTTCCAACCTTGTATAACAGAACCGAAAGGCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGC
53213284 TCGAAGGTTCTGAAAAACTGAAACCCAATGTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAA
455 TCGAAGGTTCTGAAAAACTGAAACCCAATGTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAA
53213349 GATAGGCTTCCAATGGGCAAAAGTTTTTGAAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGA
520 GATAGGCTTCCAATGGGCAAAAGTTTTTGAAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGA
53213414 AATGGCTCAAAATCCAGACATTTAGTAACTGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTC
585 AATGGCTCAAAATCCAGACATTTAGTAACTGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTC
53213479 CTACAACTGTTTAAGGATCTAAAGGTCTCGGCCAAGATAGTCGGGACAGGGTTGACTCCTTGTTT
650 CTACAACTGTTTAAGGATCTAAAGGTCTCGGCCAAGATAGTCGGGACAGGGTTGACTCCTTGTTT
53213544 TAATTTTTCAAAGAAGTCCACCACTGCAACTTCTATGTGTCCAAGGACTTTCGGGAAGATGATCA
715 TAATTTTTCAAAGAAGTCCACCACTGCAACTTCTATGTGTCCAAGGACTTTCGGGAAGATGATCA
53213609 AACCGTAAATGGCCAAAGCGAATAGATTTACCCCTTTCAACATGTCAGGATGGTTCAGAACCAAT
780 AACCGTAAATGGCCAAAGCGAATAGATTTACCCCTTTCAACATGTCAGGATGGTTCAGAACCAAT
53213674 TCTCGTAGGGAAGACCATGGAATACAAATGGTTTCATTCTTCTTCTTTATCTATTTTTCGGCCTA
845 TCTCGTAGGGAAGACCATGGAATACAAATGGTTTCATTCTTCTTCTTTATCTATTTTTCGGCCTA
53213739 TGCGTCAGTCATGTCTGTCAATCT
910 TGCGTCAGTCATGTCTGTCAATCT
53213763 CACTAA
1 CACTAA
53213769 CTTTTTCTTG
Statistics
Matches: 939, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
933 6 0.01
934 933 0.99
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (933 bp):
CACTAAGGTCCCAAGATATCTTCGCCTTTTCTCGTTCAAATTCTTGTCTTGCCATTTCTAGCTCA
GACGACATTTCCTCCGAGAAAGGATTCTGAACGGTGTAGTTCGTTGACGAGATTTGCTGACTATT
CACCCGTTGCTTCCTCCTGATGTCATAATCTTAGGTGAGGGTATCAGCATATAGAGCCAATTCCA
TCAGATAAAATTTCTTCCAAGACTTTGCAATGTCTCGGACCCTCTTCATATACCCTACACCTGCA
AAAGCGAACTCGGACTGTGCTAATCCTCCAGTGGCAGGTATGAATTGTCCCGAAGAAAACTACCT
TTAGACTAATAGCGGGACGTATCCAACTCCTCCCCATAACCTGAGTAGTGGTACCTAATCTTGAT
TTCCAACCTTGTATAACAGAACCGAAAGGCGGATCCACGGTGCTCTCCAGGTTACATCTTCAGCT
CGAAGGTTCTGAAAAACTGAAACCCAATGTTCTTCAGTGACATCCTTTGGCCATTCCCTCTCAAG
ATAGGCTTCCAATGGGCAAAAGTTTTTGAAAACATGTAGTACGGTGTGCGCTCTACTTTCCAGAA
ATGGCTCAAAATCCAGACATTTAGTAACTGCGCGCATCTGATAAAGTGTCATTTCCCCGTTTTCC
TACAACTGTTTAAGGATCTAAAGGTCTCGGCCAAGATAGTCGGGACAGGGTTGACTCCTTGTTTT
AATTTTTCAAAGAAGTCCACCACTGCAACTTCTATGTGTCCAAGGACTTTCGGGAAGATGATCAA
ACCGTAAATGGCCAAAGCGAATAGATTTACCCCTTTCAACATGTCAGGATGGTTCAGAACCAATT
CTCGTAGGGAAGACCATGGAATACAAATGGTTTCATTCTTCTTCTTTATCTATTTTTCGGCCTAT
GCGTCAGTCATGTCTGTCAATCT
Found at i:53217297 original size:22 final size:20
Alignment explanation
Indices: 53217242--53217298 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
53217232 AACAATAGTA
53217242 ATAAAGATAAAAAT-ATATAC
1 ATAAA-ATAAAAATAATATAC
** *
53217262 ATAAAATAGTAATAATATAT
1 ATAAAATAAAAATAATATAC
53217282 ATAACTAATAAAAATAA
1 ATAA--AATAAAAATAA
53217299 AAATAAGGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 6 0.21
20 14 0.48
22 9 0.31
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (20 bp):
ATAAAATAAAAATAATATAC
Found at i:53217481 original size:24 final size:22
Alignment explanation
Indices: 53217436--53217501 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
53217426 TAGATAATGG
* *
53217436 TATTAGAA-ATATGCAT-ACAA
1 TATTAAAATATATACATAACAA
53217456 TATTACAAAATATATATC-TAACAA
1 TATT--AAAATATATA-CATAACAA
53217480 TATTAAAATATATACATAACAA
1 TATTAAAATATATACATAACAA
53217502 CAAAAGTATG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 4 0.11
21 1 0.03
22 19 0.50
23 5 0.13
24 9 0.24
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (22 bp):
TATTAAAATATATACATAACAA
Found at i:53217490 original size:22 final size:23
Alignment explanation
Indices: 53217444--53217501 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
53217434 GGTATTAGAA
*
53217444 ATATGCAT-ACAATATTACAAAAT
1 ATATACATAACAATATTA-AAAAT
53217467 ATATATC-TAACAATATT-AAAAT
1 ATATA-CATAACAATATTAAAAAT
53217489 ATATACATAACAA
1 ATATACATAACAA
53217502 CAAAAGTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 1 0.03
22 16 0.52
23 5 0.16
24 9 0.29
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (23 bp):
ATATACATAACAATATTAAAAAT
Found at i:53218231 original size:5 final size:5
Alignment explanation
Indices: 53218223--53218262 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
53218213 CAAATCAGAA
*
53218223 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
53218263 GGAGAGAGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:53219399 original size:20 final size:20
Alignment explanation
Indices: 53219369--53219442 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
53219359 AGTGACACAC
*
53219369 GCCCCTGTGGCCTGGGACAT
1 GCCCGTGTGGCCTGGGACAT
*
53219389 GCCTGTGTGGCCTGGGACAT
1 GCCCGTGTGGCCTGGGACAT
*
53219409 GCCCGTGTGGCCTGGAACAT
1 GCCCGTGTGGCCTGGGACAT
53219429 GCCCGTGTGGCCTG
1 GCCCGTGTGGCCTG
53219443 CCCATGGGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.09, C:0.31, G:0.38, T:0.22
Consensus pattern (20 bp):
GCCCGTGTGGCCTGGGACAT
Found at i:53220312 original size:53 final size:53
Alignment explanation
Indices: 53220255--53220390 Score: 231
Period size: 53 Copynumber: 2.6 Consensus size: 53
53220245 ATATCTCAGA
53220255 TATGGTCTTATACGGAATCACATTATCACATTGTACCGATGCCATAGCCCAGC
1 TATGGTCTTATACGGAATCACATTATCACATTGTACCGATGCCATAGCCCAGC
*
53220308 TATGGTCTTATACGGGATCACATTATCACATTGTACCGATGCCATAGCCCAGC
1 TATGGTCTTATACGGAATCACATTATCACATTGTACCGATGCCATAGCCCAGC
*
53220361 TATGGTCTTATACAGAAGT-ACA-TATCACAT
1 TATGGTCTTATACGGAA-TCACATTATCACAT
53220391 CTTTTCCGTC
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
52 8 0.10
53 70 0.89
54 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (53 bp):
TATGGTCTTATACGGAATCACATTATCACATTGTACCGATGCCATAGCCCAGC
Found at i:53226153 original size:30 final size:30
Alignment explanation
Indices: 53226096--53226176 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 30
53226086 ACCTATTACC
* *
53226096 AAGTTTTCATTTAAGTAGTGAATTATTC-AA
1 AAGTTTT-ATTTAAGTATTGAACTATTCGAA
53226126 AAGTTTTATTTAAGTCATTGAACTATTCGAA
1 AAGTTTTATTTAAGT-ATTGAACTATTCGAA
***
53226157 TTTTTTTATTTAAGTTATTG
1 AAGTTTTATTTAAG-TATTG
53226177 GGCTGTTATG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 8 0.19
30 17 0.40
31 17 0.40
32 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.49
Consensus pattern (30 bp):
AAGTTTTATTTAAGTATTGAACTATTCGAA
Found at i:53226892 original size:31 final size:31
Alignment explanation
Indices: 53226854--53226929 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
53226844 AATCTTTTGC
** *
53226854 AAAAAAGTTTAATTTGACCATCAACCTTTAA
1 AAAAAAGTCGAATTTAACCATCAACCTTTAA
* *
53226885 AAAAAAGTCGAATTTAACCATCAATCTTTCA
1 AAAAAAGTCGAATTTAACCATCAACCTTTAA
* *
53226916 AAAAGAGTCAAATT
1 AAAAAAGTCGAATT
53226930 GTTGTTTTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.08, T:0.29
Consensus pattern (31 bp):
AAAAAAGTCGAATTTAACCATCAACCTTTAA
Found at i:53228220 original size:3 final size:3
Alignment explanation
Indices: 53228212--53228390 Score: 86
Period size: 3 Copynumber: 59.3 Consensus size: 3
53228202 TAGTACAATG
* * * * * *
53228212 ATA ATA ATA AGA TTA ATA ATA A-A ATA ATA AAA ATA ACA AT- ATG TTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
53228258 CTA ATA ATA ATAA ATAA ATAA ATA ATG GTA ATA A-A TATA TATA A-A
1 ATA ATA ATA AT-A AT-A AT-A ATA ATA ATA ATA ATA -ATA -ATA ATA
* * *
53228303 ATA ATA GTA ACA GTA ATA A-A ATA A-A TATA AT- ATA ATA A-A TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -ATA
* * *
53228346 ATA ATA AGTA ATA ATA TATA ATA ATA ATA ACA ATA TTA AAA ATA A
1 ATA ATA A-TA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53228391 CACTCTCCCC
Statistics
Matches: 134, Mismatches: 28, Indels: 28
0.71 0.15 0.15
Matches are distributed among these distances:
2 13 0.10
3 97 0.72
4 24 0.18
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:53228252 original size:20 final size:20
Alignment explanation
Indices: 53228214--53228252 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53228204 GTACAATGAT
* * *
53228214 AATAATAAGATTAATAATAA
1 AATAATAAAAATAACAATAA
53228234 AATAATAAAAATAACAATA
1 AATAATAAAAATAACAATA
53228253 TGTTACTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
AATAATAAAAATAACAATAA
Found at i:53228302 original size:31 final size:30
Alignment explanation
Indices: 53228267--53228365 Score: 76
Period size: 32 Copynumber: 3.0 Consensus size: 30
53228257 ACTAATAATA
53228267 ATAAATAAATAAATAATGGTAATAAATATAT
1 ATAAATAAATAAATAAT-GTAATAAATATAT
**
53228298 ATAAAATAATAGTAACAGTAATAAAATAAATATA-
1 AT-AAATAA-A-TAA-A-TAATGTAATAAATATAT
53228332 ATATAATAAATATAATAATAAGTAAT-AATATAT
1 ATA-AATAAATA-AATAAT--GTAATAAATATAT
53228365 A
1 A
53228366 ATAATAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 18
0.71 0.05 0.24
Matches are distributed among these distances:
31 6 0.11
32 15 0.28
33 8 0.15
34 10 0.19
35 11 0.20
36 4 0.07
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (30 bp):
ATAAATAAATAAATAATGTAATAAATATAT
Found at i:53228352 original size:20 final size:20
Alignment explanation
Indices: 53228261--53228374 Score: 85
Period size: 20 Copynumber: 5.6 Consensus size: 20
53228251 TATGTTACTA
53228261 ATAATAATAA-ATAAATAAAT
1 ATAATAATAATAT-AATAAAT
**
53228281 AATGGTAATAAATATATATAAA-
1 -ATAATAAT-AATATA-ATAAAT
* *
53228303 ATAATAGTAACAGTAATAAA-
1 ATAATAATAATA-TAATAAAT
53228323 ATAA-ATATAATATAATAAAT
1 ATAATA-ATAATATAATAAAT
*
53228343 ATAATAATAA-GTAATAATAT
1 ATAATAATAATATAATAA-AT
53228363 ATAATAATAATA
1 ATAATAATAATA
53228375 ACAATATTAA
Statistics
Matches: 74, Mismatches: 10, Indels: 18
0.73 0.10 0.18
Matches are distributed among these distances:
19 14 0.19
20 36 0.49
21 14 0.19
22 3 0.04
23 7 0.09
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.32
Consensus pattern (20 bp):
ATAATAATAATATAATAAAT
Found at i:53229167 original size:23 final size:25
Alignment explanation
Indices: 53229115--53229168 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
53229105 AAATTAATAT
*
53229115 TTTAATTCATATTTTTGTTAAAAGA
1 TTTAATTCAAATTTTTGTTAAAAGA
* *
53229140 -ATAATTTAAATTTTT-TTAAAA-A
1 TTTAATTCAAATTTTTGTTAAAAGA
53229162 TTTAATT
1 TTTAATT
53229169 ATCATATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 11 0.46
24 12 0.50
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (25 bp):
TTTAATTCAAATTTTTGTTAAAAGA
Found at i:53230073 original size:25 final size:24
Alignment explanation
Indices: 53230040--53230088 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
53230030 TATTAAGTTG
53230040 CTTTTA-TTTTAAAAAATAAATTAT
1 CTTTTATTTTTAAAAAAT-AATTAT
*
53230064 CTTTTAATTTTTATAAAATAATTAT
1 CTTTT-ATTTTTAAAAAATAATTAT
53230089 ACAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 5 0.23
25 7 0.32
26 10 0.45
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
CTTTTATTTTTAAAAAATAATTAT
Found at i:53230196 original size:17 final size:15
Alignment explanation
Indices: 53230163--53230191 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
53230153 TAATATTAAT
53230163 TTTATCAAACAATAA
1 TTTATCAAACAATAA
53230178 TTTATCAAACAATA
1 TTTATCAAACAATA
53230192 TAATTACATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (15 bp):
TTTATCAAACAATAA
Found at i:53230317 original size:18 final size:18
Alignment explanation
Indices: 53230294--53230329 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53230284 CTTAATTTTT
53230294 AAATTTATCAAACAACAG
1 AAATTTATCAAACAACAG
53230312 AAATTTATCAAACAACAG
1 AAATTTATCAAACAACAG
53230330 CTTAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.22
Consensus pattern (18 bp):
AAATTTATCAAACAACAG
Found at i:53233279 original size:3 final size:3
Alignment explanation
Indices: 53233273--53233302 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
53233263 CCAACAAAAA
53233273 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
53233303 CACCTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:53236738 original size:27 final size:25
Alignment explanation
Indices: 53236689--53236738 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
53236679 TTAATCATAA
*
53236689 ATTTTTAATAAAAATAATTAATTTT
1 ATTTTTAATAAAAATAATAAATTTT
*
53236714 ATTTTTAATATAACATATATAAATT
1 ATTTTTAATA-AAAATA-ATAAATT
53236739 AATTTACCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 5 0.24
27 6 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
ATTTTTAATAAAAATAATAAATTTT
Found at i:53236743 original size:26 final size:25
Alignment explanation
Indices: 53236688--53236743 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
53236678 ATTAATCATA
*
53236688 AATTTTTAATAAAAATAATTAATTT
1 AATTTTTAATAAAAATAATTAAATT
* *
53236713 TATTTTTAATATAACAT-ATATAAATT
1 AATTTTTAATA-AAAATAAT-TAAATT
53236739 AATTT
1 AATTT
53236744 ACCTATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
AATTTTTAATAAAAATAATTAAATT
Found at i:53237432 original size:30 final size:30
Alignment explanation
Indices: 53237376--53237432 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
53237366 TACACCAAAT
* *
53237376 CAAAAATCTTGTATCAAAGTACATATTGGA
1 CAAAAATCATGTATAAAAGTACATATTGGA
*
53237406 CAAAAATTCATGTATAAAATTA-ATATT
1 CAAAAA-TCATGTATAAAAGTACATATT
53237433 TATCACTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 11 0.48
31 12 0.52
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (30 bp):
CAAAAATCATGTATAAAAGTACATATTGGA
Found at i:53238194 original size:27 final size:28
Alignment explanation
Indices: 53238141--53238194 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 28
53238131 CACTCGTTCA
53238141 TATTTAATATATATTCTCTAATCCAATC
1 TATTTAATATATATTCTCTAATCCAATC
*
53238169 TATTTAATATAT-TTCTCTAATTCAAT
1 TATTTAATATATATTCTCTAATCCAAT
53238195 TTAGTTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (28 bp):
TATTTAATATATATTCTCTAATCCAATC
Found at i:53244855 original size:12 final size:12
Alignment explanation
Indices: 53244838--53244872 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
53244828 GCCATTCATG
53244838 TACATATATACA
1 TACATATATACA
*
53244850 TACATAAATACA
1 TACATATATACA
*
53244862 TACATGTATAC
1 TACATATATAC
53244873 TCCTAGTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.03, T:0.31
Consensus pattern (12 bp):
TACATATATACA
Found at i:53255952 original size:31 final size:31
Alignment explanation
Indices: 53255914--53255978 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
53255904 TTATTAAATA
* *
53255914 ATTT-AAAATTTTTCATTTAAGTCATTGAACT
1 ATTTAAAAAATTTT-ATTCAAGTCATTGAACT
53255945 ATTTAAAAAATTTTATTCAAGTCATTGAACT
1 ATTTAAAAAATTTTATTCAAGTCATTGAACT
53255976 ATT
1 ATT
53255979 AAACCTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 23 0.74
32 8 0.26
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.46
Consensus pattern (31 bp):
ATTTAAAAAATTTTATTCAAGTCATTGAACT
Found at i:53257772 original size:22 final size:22
Alignment explanation
Indices: 53257747--53257817 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 22
53257737 CCGAATTATA
53257747 TATTAATATATATTTTTTATTT
1 TATTAATATATATTTTTTATTT
*
53257769 TATT--TTTA-ATTATTTTAATTT
1 TATTAATATATATT-TTTT-ATTT
*
53257790 T-TTAATATAACTATTTTTTATTA
1 TATTAATAT-A-TATTTTTTATTT
53257813 TATTA
1 TATTA
53257818 TTAATTTGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
19 3 0.08
20 9 0.24
21 5 0.13
22 6 0.16
23 5 0.13
24 7 0.18
25 3 0.08
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (22 bp):
TATTAATATATATTTTTTATTT
Found at i:53257868 original size:21 final size:21
Alignment explanation
Indices: 53257842--53257900 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
53257832 GTTTTAAGAA
53257842 TTGTTTTAATATTATTTTTAT
1 TTGTTTTAATATTATTTTTAT
*
53257863 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATA-TTATTTTTAT
*
53257885 GT-TTTTAA-ATATATTT
1 TTGTTTTAATAT-TATTT
53257901 GATTTATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
19 1 0.03
20 5 0.15
21 17 0.52
22 10 0.30
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (21 bp):
TTGTTTTAATATTATTTTTAT
Found at i:53257875 original size:12 final size:12
Alignment explanation
Indices: 53257830--53257881 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
53257820 AATTTGTGTA
* *
53257830 TTGTTTTAAGAA
1 TTGTTTTAATAT
53257842 TTGTTTTAATA-
1 TTGTTTTAATAT
*
53257853 TTATTTT--TAT
1 TTGTTTTAATAT
53257863 TTGTTTTAATAT
1 TTGTTTTAATAT
53257875 TTGTTTT
1 TTGTTTT
53257882 TATGTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
9 2 0.06
10 6 0.18
11 6 0.18
12 20 0.59
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:53257915 original size:26 final size:24
Alignment explanation
Indices: 53257871--53257920 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
53257861 ATTTGTTTTA
*
53257871 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
53257895 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
53257921 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:53259347 original size:17 final size:17
Alignment explanation
Indices: 53259327--53259374 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
53259317 TCCTTTTTCT
53259327 TTCTTTCTTTCTTTCCC
1 TTCTTTCTTTCTTTCCC
* * * *
53259344 TTCTATGTTTCGTCCCC
1 TTCTTTCTTTCTTTCCC
53259361 TTCTTTCTTTCTTT
1 TTCTTTCTTTCTTT
53259375 TCTATTCTTT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.02, C:0.31, G:0.04, T:0.62
Consensus pattern (17 bp):
TTCTTTCTTTCTTTCCC
Found at i:53259453 original size:15 final size:14
Alignment explanation
Indices: 53259433--53259465 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
53259423 TATTATACGA
53259433 ATATAATATAATATT
1 ATATAATAT-ATATT
53259448 ATATAATATATATT
1 ATATAATATATATT
53259462 -TATA
1 ATATA
53259466 CTTAAATACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 5 0.28
15 9 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATAATATATATT
Found at i:53260621 original size:60 final size:60
Alignment explanation
Indices: 53260547--53260668 Score: 235
Period size: 60 Copynumber: 2.0 Consensus size: 60
53260537 GAGTCAACGA
*
53260547 GTCAGTGGAATGACTTAAAACTTTCATTTTTCTTTTTCATTTTTTCCTTTCCCCTTTTAT
1 GTCAGGGGAATGACTTAAAACTTTCATTTTTCTTTTTCATTTTTTCCTTTCCCCTTTTAT
53260607 GTCAGGGGAATGACTTAAAACTTTCATTTTTCTTTTTCATTTTTTCCTTTCCCCTTTTAT
1 GTCAGGGGAATGACTTAAAACTTTCATTTTTCTTTTTCATTTTTTCCTTTCCCCTTTTAT
53260667 GT
1 GT
53260669 TCTTTCGAAT
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:0.18, C:0.20, G:0.10, T:0.52
Consensus pattern (60 bp):
GTCAGGGGAATGACTTAAAACTTTCATTTTTCTTTTTCATTTTTTCCTTTCCCCTTTTAT
Found at i:53261428 original size:31 final size:29
Alignment explanation
Indices: 53261393--53261464 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
53261383 ATCCCAAAAC
*
53261393 TATACATGAAATATGGTTTGATGTATAATGG
1 TATACATGAAATATGATTT--TGTATAATGG
* * **
53261424 TATACATGAATTTTGATTTTGTATAATTT
1 TATACATGAAATATGATTTTGTATAATGG
53261453 TATACATGAAAT
1 TATACATGAAAT
53261465 TTTGATTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.44
Consensus pattern (29 bp):
TATACATGAAATATGATTTTGTATAATGG
Found at i:53261456 original size:29 final size:30
Alignment explanation
Indices: 53261414--53261472 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
53261404 TATGGTTTGA
53261414 TGTATAATGGTATACATG-AATTTTGATTT
1 TGTATAATGGTATACATGAAATTTTGATTT
**
53261443 TGTATAATTTTATACATGAAATTTTGATTT
1 TGTATAATGGTATACATGAAATTTTGATTT
53261473 GATCAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 16 0.59
30 11 0.41
ACGTcount: A:0.32, C:0.03, G:0.14, T:0.51
Consensus pattern (30 bp):
TGTATAATGGTATACATGAAATTTTGATTT
Found at i:53268858 original size:46 final size:46
Alignment explanation
Indices: 53268786--53268951 Score: 235
Period size: 46 Copynumber: 3.6 Consensus size: 46
53268776 TCTAATATGG
* *
53268786 AATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGA
1 AATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGA
* **
53268832 AATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGGTATGA
1 AATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGA
*
53268878 AATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAA
1 AATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATG-A
* * *
53268924 AACGAGTAAAACCATAGTTGAAAGATAC
1 AATGAGTAAGACCATGGTTGAAAGATAC
53268952 TATGACATCA
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.01
46 106 0.99
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (46 bp):
AATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGACATGA
Found at i:53270169 original size:13 final size:13
Alignment explanation
Indices: 53270151--53270175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53270141 TGTCTGTCAT
53270151 ATTGTGTCTATTG
1 ATTGTGTCTATTG
53270164 ATTGTGTCTATT
1 ATTGTGTCTATT
53270176 CCTAGGATCC
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:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (13 bp):
ATTGTGTCTATTG
Found at i:53270291 original size:21 final size:21
Alignment explanation
Indices: 53270267--53270310 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
53270257 TTTGCCGCCC
53270267 AAATGCTCTTCCAGGTAAGGG
1 AAATGCTCTTCCAGGTAAGGG
53270288 AAATGCTCTTCCAGGTAAGGG
1 AAATGCTCTTCCAGGTAAGGG
53270309 AA
1 AA
53270311 GGTAATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.23
Consensus pattern (21 bp):
AAATGCTCTTCCAGGTAAGGG
Found at i:53272966 original size:3 final size:3
Alignment explanation
Indices: 53272958--53273324 Score: 145
Period size: 3 Copynumber: 123.7 Consensus size: 3
53272948 AAACATACAC
* **
53272958 TAA TAA TAA TAA TAA TAA TAA TAA T-A TGAA TTA -AA TGG TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * * * * * *
53273001 GAA TAA TAG TAA CAA TAA -AT TAA -AA AAA TGA TAA TAG TAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** * *
53273046 TAA AAA TAA TAA CGA TAA TAA TAA TAG TAAA TAG TAA TAA TAA TACA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TA-A
** * *
53273093 TTAA TAA TAA TAA T-A TGT TAA TAA CAA TAA -AT TAA TGAA TTAA TAA
1 -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA -TAA TAA
* * * * * * * *
53273139 CAA -AA CAG TAA GTAAA TAA -ACA CAA AAA TAA GATA TAA TTA TAA TAG
1 TAA TAA TAA TAA -T-AA TAA TA-A TAA TAA TAA TA-A TAA TAA TAA TAA
* *
53273186 TAA TAT TAA CAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * **
53273232 TAT TAA TAA -AA -AA TAA TAA TAA -AA GGAA TAA AAA CAA TGT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
* * * ** *
53273275 TAA CAA GAA TAT TAA TAA TGG TAA TAA TAA CAA TAA T-A TAAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
53273320 TAA TA
1 TAA TA
53273325 TATACATGAG
Statistics
Matches: 266, Mismatches: 71, Indels: 54
0.68 0.18 0.14
Matches are distributed among these distances:
2 28 0.11
3 214 0.80
4 19 0.07
5 5 0.02
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:53275356 original size:77 final size:76
Alignment explanation
Indices: 53275194--53275474 Score: 370
Period size: 75 Copynumber: 3.7 Consensus size: 76
53275184 AGAGACTAAA
* * * * *
53275194 AGGCTCGACTCACTTCTTGCAATATGAGTCGATTTTTTTGAAAAAACATAAATTGAAAATATCTC
1 AGGCTCAACTCACCTCTTGCAATATGAGTTGA-TTTTTTG-AAAAACAGAAATTGAAAATACCTC
* * * *
53275259 AGTGCGTGATTTG
64 AGCGTGTGACTCG
*
53275272 AGGCTCAACTCACCTCTCT-CAATATGAGTTGATTTTTTTGAAAAACAGGAATT-AAAGATACCT
1 AGGCTCAACTCACCTCT-TGCAATATGAGTTGA-TTTTTTGAAAAACAGAAATTGAAA-ATACCT
53275335 CAGCGTGTGACTCG
63 CAGCGTGTGACTCG
* * *
53275349 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAAATACTTCGG
1 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
*
53275413 CGTGTGACCCG
66 CGTGTGACTCG
53275424 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGAAAAACAGAAAT
1 AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGAAAAACAGAAAT
53275475 AAAAGTATCA
Statistics
Matches: 182, Mismatches: 16, Indels: 12
0.87 0.08 0.06
Matches are distributed among these distances:
75 66 0.36
76 24 0.13
77 56 0.31
78 35 0.19
79 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Consensus pattern (76 bp):
AGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTTGAAAAACAGAAATTGAAAATACCTCAG
CGTGTGACTCG
Found at i:53278091 original size:40 final size:40
Alignment explanation
Indices: 53277894--53278128 Score: 248
Period size: 39 Copynumber: 6.0 Consensus size: 40
53277884 ACTTGAAACC
* *
53277894 AATTACCAGCACA-AGCCTGCGGGAATTTAAACCCGG-TAT
1 AATT-CCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* * * *
53277933 AATACCAGCTCGA-AGCCTGCGGGACTTT-TGCCCGGACAT
1 AATTCCAGCAC-ATAGCCTGCGGGACTTTAAGCCCGGATAT
* * * * *
53277972 ATTTCCAGCACGTAGCCTGC-GGACCTTAAGTCCGGTTAT
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* * *
53278011 AATTCCAGCACATAGCCTGC-GGACCTTAAGTCCGGGTAT
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* *
53278050 AATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGATAT
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* *
53278090 AATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGATA
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATA
53278129 CACATCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
38 17 0.10
39 97 0.58
40 54 0.32
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
Found at i:53289998 original size:8 final size:8
Alignment explanation
Indices: 53289985--53290010 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
53289975 TGAGGCGATT
53289985 ATTTGAAA
1 ATTTGAAA
53289993 ATTTGAAA
1 ATTTGAAA
53290001 ATTTGAAA
1 ATTTGAAA
53290009 AT
1 AT
53290011 GAAATTTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (8 bp):
ATTTGAAA
Found at i:53290854 original size:3 final size:3
Alignment explanation
Indices: 53290840--53291234 Score: 107
Period size: 3 Copynumber: 131.3 Consensus size: 3
53290830 AAACATACAC
* * * * **
53290840 TAA TAT TAA TAA TAA TAA TAA TAG TAA TAA TATG TAT TAAA TGG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA
* * * * * * *
53290887 -AA GAA TAA TAG TAA CAA TAA -AT TAA -AA AAA TGA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * ** *
53290932 AAA TAA AAA TAA TAG CGA TAA TAA TAA TAA TAA TAA TAAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
** * *
53290978 TAA TAA TACA TTAA TAA TAA TAA T-A TGT TAA TAA CAA TAA -AT TAA
1 TAA TAA TA-A -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
53291023 TGAA TTAA TAA CAA -AA CAG TAA GTAAA TAA -ACA CAA AAA TAA GATA
1 T-AA -TAA TAA TAA TAA TAA TAA -T-AA TAA TA-A TAA TAA TAA TA-A
* * * * *
53291069 TAA TTA TAA TAG TAA TAT TAA CAA -AA TAA TAA TAA TAA T-A TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * ** *
53291115 TAA -AA -AA TAA TAA TAA -AA GGAA TAA AAA CAA TGT TAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
* * ** * *
53291158 GAA TAT TAA TAA TGG TAA CAA TAA CAA TAA T-A TAAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TA-A
* * * *
53291204 TACA TGA GAA AAA AAA T-A TAA TAA TAA TAA T
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA T
53291235 GATAGAAGTA
Statistics
Matches: 279, Mismatches: 86, Indels: 54
0.67 0.21 0.13
Matches are distributed among these distances:
2 25 0.09
3 222 0.80
4 27 0.10
5 5 0.02
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:53290997 original size:17 final size:16
Alignment explanation
Indices: 53290949--53291017 Score: 77
Period size: 17 Copynumber: 4.2 Consensus size: 16
53290939 AATAATAGCG
53290949 ATAATAA-TAATAATA
1 ATAATAATTAATAATA
* *
53290964 ATAATAAATAGTAATA
1 ATAATAATTAATAATA
53290980 ATAATACATTAATAATA
1 ATAATA-ATTAATAATA
* *
53290997 ATAATATGTTAATAACA
1 ATAATA-ATTAATAATA
53291014 ATAA
1 ATAA
53291018 ATTAATGAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
15 7 0.15
16 13 0.28
17 26 0.57
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
ATAATAATTAATAATA
Found at i:53291022 original size:14 final size:14
Alignment explanation
Indices: 53290949--53291033 Score: 75
Period size: 16 Copynumber: 5.7 Consensus size: 14
53290939 AATAATAGCG
53290949 ATAATAAT-AA-TA
1 ATAATAATAAATTA
53290961 ATAATAATAAATAGTA
1 ATAATAATAAAT--TA
*
53290977 ATAATAATACATTA
1 ATAATAATAAATTA
53290991 ATAATAATAATATGTTA
1 ATAATAATAA-A--TTA
*
53291008 ATAACAATAAATTA
1 ATAATAATAAATTA
53291022 ATGAATTAATAA
1 AT-AA-TAATAA
53291034 CAAAACAGTA
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
12 8 0.13
13 2 0.03
14 16 0.27
15 3 0.05
16 19 0.32
17 12 0.20
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (14 bp):
ATAATAATAAATTA
Found at i:53291098 original size:14 final size:13
Alignment explanation
Indices: 53291081--53291132 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
53291071 ATTATAATAG
*
53291081 TAATATTAACAAAA
1 TAATAATAA-AAAA
*
53291095 TAATAATAATAATA
1 TAATAATAA-AAAA
*
53291109 TATTAATAAAAAA
1 TAATAATAAAAAA
53291122 TAATAATAAAA
1 TAATAATAAAA
53291133 GGAATAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 13 0.41
14 19 0.59
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
TAATAATAAAAAA
Found at i:53298045 original size:11 final size:11
Alignment explanation
Indices: 53298011--53298100 Score: 50
Period size: 10 Copynumber: 8.5 Consensus size: 11
53298001 TAAATGCACA
53298011 TTTTTATTAATT
1 TTTTTA-TAATT
*
53298023 TTTTT-TATTT
1 TTTTTATAATT
53298033 TTTTTATAA--
1 TTTTTATAATT
53298042 TTTTTA-AA-T
1 TTTTTATAATT
* *
53298051 TATTT-TGATT
1 TTTTTATAATT
*
53298061 TTTTTATATTTT
1 TTTTTATA-ATT
53298073 ATTTTTATAA-T
1 -TTTTTATAATT
* *
53298084 ATTTTAGAATT
1 TTTTTATAATT
53298095 TTTTTA
1 TTTTTA
53298101 ATAACTACAA
Statistics
Matches: 59, Mismatches: 11, Indels: 17
0.68 0.13 0.20
Matches are distributed among these distances:
8 2 0.03
9 11 0.19
10 21 0.36
11 10 0.17
12 7 0.12
13 8 0.14
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:53298070 original size:16 final size:16
Alignment explanation
Indices: 53298051--53298100 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 16
53298041 ATTTTTAAAT
53298051 TATTTTGATTTTTTTA
1 TATTTTGATTTTTTTA
*
53298067 TATTTT-ATTTTTATAA
1 TATTTTGATTTTT-TTA
53298083 TATTTTAGAATTTTTTTA
1 TATTTT-G-ATTTTTTTA
53298101 ATAACTACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 6 0.21
16 14 0.50
18 2 0.07
19 6 0.21
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (16 bp):
TATTTTGATTTTTTTA
Found at i:53298561 original size:35 final size:35
Alignment explanation
Indices: 53298503--53298597 Score: 95
Period size: 35 Copynumber: 2.7 Consensus size: 35
53298493 ATAAATTTAG
* **
53298503 TATAAATACAATTTAATTTATATTTT-ATTATTTGAT
1 TATAAATATAATTTAA-AAATATTTTGA-TATTTGAT
* *
53298539 T-TAAATATAATTTGTAAAATATTTTGATATTTTAT
1 TATAAATATAATTT-AAAAATATTTTGATATTTGAT
*
53298574 TATGAATATAATTTAAAAATATTT
1 TATAAATATAATTTAAAAATATTT
53298598 AAATTTTATT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
35 35 0.71
36 14 0.29
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (35 bp):
TATAAATATAATTTAAAAATATTTTGATATTTGAT
Found at i:53298818 original size:21 final size:21
Alignment explanation
Indices: 53298794--53298866 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
53298784 CATTATTTCT
53298794 AATCTCACCGCTATAGTATCC
1 AATCTCACCGCTATAGTATCC
**
53298815 AATCTCATTGCTATAGTATCC
1 AATCTCACCGCTATAGTATCC
* * *
53298836 AATCTCATCGCTACAGTAAT-T
1 AATCTCACCGCTATAGT-ATCC
53298857 AATCTCACCG
1 AATCTCACCG
53298867 TTACAGCTGT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
21 43 0.96
22 2 0.04
ACGTcount: A:0.30, C:0.29, G:0.10, T:0.32
Consensus pattern (21 bp):
AATCTCACCGCTATAGTATCC
Found at i:53300407 original size:55 final size:55
Alignment explanation
Indices: 53300321--53300431 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
53300311 AAGAAACAAC
53300321 TAGCTTAATATAAAGAATTTAAATAACATTTTTTTTATAATTTATGTAATTTATT
1 TAGCTTAATATAAAGAATTTAAATAACATTTTTTTTATAATTTATGTAATTTATT
* *
53300376 TAGCTTAATATTAAGAATTTAAATAATATTTTTTTTATAATTTATGTAATTTATT
1 TAGCTTAATATAAAGAATTTAAATAACATTTTTTTTATAATTTATGTAATTTATT
53300431 T
1 T
53300432 GGTGCTTGGC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (55 bp):
TAGCTTAATATAAAGAATTTAAATAACATTTTTTTTATAATTTATGTAATTTATT
Found at i:53301776 original size:23 final size:23
Alignment explanation
Indices: 53301750--53301795 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
53301740 TCATTGCCAC
53301750 AAAATTTTAAAAAATATATTTTT
1 AAAATTTTAAAAAATATATTTTT
**
53301773 AAAATTTTAAATTATATATTTTT
1 AAAATTTTAAAAAATATATTTTT
53301796 TATTTACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AAAATTTTAAAAAATATATTTTT
Found at i:53303041 original size:17 final size:16
Alignment explanation
Indices: 53303009--53303077 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 16
53302999 TTAAATGCAC
*
53303009 ATTTTTATTTATTTTTT
1 ATTTTT-TTTAATTTTT
53303026 ATTTTTTTATAATTTTT
1 ATTTTTTT-TAATTTTT
**
53303043 AAAATTTTTTAATTTTT
1 -ATTTTTTTTAATTTTT
*
53303060 -TCTATTTTTAATTTTT
1 AT-TTTTTTTAATTTTT
53303076 AT
1 AT
53303078 GATATTTTAG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
16 14 0.33
17 22 0.52
18 6 0.14
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.74
Consensus pattern (16 bp):
ATTTTTTTTAATTTTT
Found at i:53303123 original size:9 final size:9
Alignment explanation
Indices: 53303029--53303123 Score: 56
Period size: 9 Copynumber: 10.6 Consensus size: 9
53303019 ATTTTTTATT
53303029 TTTTTATAA
1 TTTTTATAA
*
53303038 TTTTTAAAA
1 TTTTTATAA
53303047 TTTTT-TAA
1 TTTTTATAA
*
53303055 TTTTT-T-C
1 TTTTTATAA
53303062 TATTTT-TAA
1 T-TTTTATAA
*
53303071 TTTTTATGA
1 TTTTTATAA
*
53303080 TATTTTAGAA
1 T-TTTTATAA
53303090 TTTTT-TAA
1 TTTTTATAA
* *
53303098 TAATTATAAACA
1 T--TTTTATA-A
53303110 TTTTTATAA
1 TTTTTATAA
53303119 TTTTT
1 TTTTT
53303124 TTTTAGTTTT
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
7 1 0.02
8 20 0.30
9 27 0.41
10 15 0.23
11 1 0.02
12 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:53303617 original size:18 final size:18
Alignment explanation
Indices: 53303594--53303629 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
53303584 GGTTCTTAGT
53303594 GATGTCCATAGTAATAAC
1 GATGTCCATAGTAATAAC
53303612 GATGTCCATAGTAATAAC
1 GATGTCCATAGTAATAAC
53303630 CACTTGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (18 bp):
GATGTCCATAGTAATAAC
Found at i:53308909 original size:16 final size:16
Alignment explanation
Indices: 53308888--53308919 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53308878 AGTACTTGGC
53308888 CCTTCTGATGATGTAA
1 CCTTCTGATGATGTAA
53308904 CCTTCTGATGATGTAA
1 CCTTCTGATGATGTAA
53308920 AAGCCGTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
CCTTCTGATGATGTAA
Found at i:53317757 original size:17 final size:17
Alignment explanation
Indices: 53317735--53317769 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
53317725 AAGAAAGTGG
*
53317735 AGTGTAAAATCTAAAGC
1 AGTGTAAAATATAAAGC
53317752 AGTGTAAAATATAAAGC
1 AGTGTAAAATATAAAGC
53317769 A
1 A
53317770 CATAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (17 bp):
AGTGTAAAATATAAAGC
Found at i:53319050 original size:17 final size:17
Alignment explanation
Indices: 53319028--53319063 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
53319018 CCAGTAGAAA
53319028 ATACACCTTCAATAGTG
1 ATACACCTTCAATAGTG
53319045 ATACACCTTCAATAGTG
1 ATACACCTTCAATAGTG
53319062 AT
1 AT
53319064 CATTACCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (17 bp):
ATACACCTTCAATAGTG
Found at i:53328931 original size:23 final size:23
Alignment explanation
Indices: 53328901--53328948 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
53328891 AATAGTTTTA
53328901 ATTGTTTATTTGAGTGGTTGTTC
1 ATTGTTTATTTGAGTGGTTGTTC
53328924 ATTGTTTATTTGAGTGGTTGTTC
1 ATTGTTTATTTGAGTGGTTGTTC
53328947 AT
1 AT
53328949 CTACTTAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.15, C:0.04, G:0.25, T:0.56
Consensus pattern (23 bp):
ATTGTTTATTTGAGTGGTTGTTC
Found at i:53331902 original size:38 final size:38
Alignment explanation
Indices: 53331851--53331943 Score: 186
Period size: 38 Copynumber: 2.4 Consensus size: 38
53331841 TCCATCCAAT
53331851 TTGTTAATATTTATTCAAGGTAAGGCTGCACTGGCAAA
1 TTGTTAATATTTATTCAAGGTAAGGCTGCACTGGCAAA
53331889 TTGTTAATATTTATTCAAGGTAAGGCTGCACTGGCAAA
1 TTGTTAATATTTATTCAAGGTAAGGCTGCACTGGCAAA
53331927 TTGTTAATATTTATTCA
1 TTGTTAATATTTATTCA
53331944 TATTTTTGTC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (38 bp):
TTGTTAATATTTATTCAAGGTAAGGCTGCACTGGCAAA
Found at i:53351386 original size:19 final size:19
Alignment explanation
Indices: 53351346--53351390 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
53351336 AAATTTTAAG
*
53351346 TAATATAATGAATAGTAAA
1 TAATATAATGAATAATAAA
*
53351365 TAATATAAT-AGATAATATA
1 TAATATAATGA-ATAATAAA
53351384 TAATATA
1 TAATATA
53351391 CATAACTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (19 bp):
TAATATAATGAATAATAAA
Found at i:53356209 original size:18 final size:18
Alignment explanation
Indices: 53356183--53356221 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
53356173 AACAGATACA
*
53356183 GATGTAGATACAAATATT
1 GATGCAGATACAAATATT
**
53356201 GATGCAGATACTGATATT
1 GATGCAGATACAAATATT
53356219 GAT
1 GAT
53356222 ACGAATATAG
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:0.38, C:0.08, G:0.21, T:0.33
Consensus pattern (18 bp):
GATGCAGATACAAATATT
Found at i:53359811 original size:61 final size:61
Alignment explanation
Indices: 53359716--53359834 Score: 186
Period size: 61 Copynumber: 2.0 Consensus size: 61
53359706 AGAATTAATT
* * *
53359716 ATATTAATATTAAATTAATAAAATATTATATAGATAAATATTT-AATTTAATTTAATATCTC
1 ATATTAATACTAAATTAATAAAATACTATATAGATAAAT-TTTAAATTAAATTTAATATCTC
*
53359777 ATATTAATACTAAATTAATAAAATACTATCTAGATAAATTTTAAATTAAATTTAATAT
1 ATATTAATACTAAATTAATAAAATACTATATAGATAAATTTTAAATTAAATTTAATAT
53359835 TAAATTCATT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 3 0.06
61 50 0.94
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (61 bp):
ATATTAATACTAAATTAATAAAATACTATATAGATAAATTTTAAATTAAATTTAATATCTC
Found at i:53361797 original size:31 final size:31
Alignment explanation
Indices: 53361743--53361802 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
53361733 CTTTATTTGA
** *
53361743 TCAATTTTAGTCCCTCTACTTTTCGAATTGG
1 TCAATTTTAGTCCCAATACTTTTCAAATTGG
*
53361774 TCAATTTTAGTCCCAATAGTTTTCAAATT
1 TCAATTTTAGTCCCAATACTTTTCAAATT
53361803 TTGAAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (31 bp):
TCAATTTTAGTCCCAATACTTTTCAAATTGG
Found at i:53362783 original size:20 final size:20
Alignment explanation
Indices: 53362736--53362783 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
53362726 GCCACATCAA
53362736 TATTCTTATCCTAAATTTCAG
1 TATT-TTATCCTAAATTTCAG
* * *
53362757 GAGTTTATCCTTAATTTCAG
1 TATTTTATCCTAAATTTCAG
53362777 TATTTTA
1 TATTTTA
53362784 ATTTGGATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (20 bp):
TATTTTATCCTAAATTTCAG
Found at i:53369307 original size:19 final size:21
Alignment explanation
Indices: 53369285--53369328 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
53369275 TTTTTCTCAC
53369285 TTTATCTA-TTTT-TTTAAAT
1 TTTATCTACTTTTATTTAAAT
*
53369304 TTTATCTACTTTTATTTAATT
1 TTTATCTACTTTTATTTAAAT
53369325 TTTA
1 TTTA
53369329 GAATTACCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
20 4 0.18
21 10 0.45
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTATCTACTTTTATTTAAAT
Found at i:53379433 original size:4 final size:4
Alignment explanation
Indices: 53379424--53379479 Score: 112
Period size: 4 Copynumber: 14.0 Consensus size: 4
53379414 CATTTTAAGC
53379424 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53379472 CATA CATA
1 CATA CATA
53379480 TGCATGCGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:53384887 original size:48 final size:48
Alignment explanation
Indices: 53384831--53384924 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
53384821 AGGGAATTCT
* * *
53384831 GTTGAATCCTTTATTGTTGCG-AATT-GAGCTAACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTG-GAAATTAG-GCTAACTTAGGCATTTTTACG
*
53384879 GTTGAATCCATTATTGGTGGAAATTAGGCTGACTTAGGCATTTTTA
1 GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTA
53384925 AGCCAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 1 0.03
48 38 0.95
49 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTACG
Found at i:53386809 original size:48 final size:48
Alignment explanation
Indices: 53386753--53386846 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
53386743 AGGGAATTCT
* * *
53386753 GTTGAATCCTTTATTGTTGCG-AATT-GAGCTAACTTAGGCGTTTTTACG
1 GTTGAATCCATTATTGGTG-GAAATTAG-GCTAACTTAGGCATTTTTACG
*
53386801 GTTGAATCCATTATTGGTGGAAATTAGGCTGACTTAGGCATTTTTA
1 GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTA
53386847 AGCCAAGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
47 1 0.03
48 38 0.95
49 1 0.03
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (48 bp):
GTTGAATCCATTATTGGTGGAAATTAGGCTAACTTAGGCATTTTTACG
Found at i:53388392 original size:24 final size:25
Alignment explanation
Indices: 53388358--53388406 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
53388348 ATTTAATTAA
53388358 TAAATTTATATA-A-AAATTATTTT
1 TAAATTTATATACATAAATTATTTT
53388381 TAAATGTTATATACATAAATTATTTT
1 TAAAT-TTATATACATAAATTATTTT
53388407 AATTTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.22
24 7 0.30
25 1 0.04
26 10 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (25 bp):
TAAATTTATATACATAAATTATTTT
Found at i:53389902 original size:31 final size:31
Alignment explanation
Indices: 53389857--53389917 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
53389847 CTATAAAATG
53389857 TTAACATATAACTTTAGGAAAATGATTTATC
1 TTAACATATAACTTTAGGAAAATGATTTATC
* *
53389888 TTAACCTATCACTTTAGGAAAATGATTTAT
1 TTAACATATAACTTTAGGAAAATGATTTAT
53389918 GTTTTTGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.39
Consensus pattern (31 bp):
TTAACATATAACTTTAGGAAAATGATTTATC
Found at i:53392578 original size:47 final size:47
Alignment explanation
Indices: 53392508--53392638 Score: 160
Period size: 47 Copynumber: 2.8 Consensus size: 47
53392498 CACAATCGAT
* * *
53392508 AAGTACCTCTACCATGGCCCGTAGCCAAATCAAGGTAACT-TATC-CTG
1 AAGTACCTATACTATGGCCCGTAGCCAAATCAAGGTAACTCT-TCTC-A
* *
53392555 GAGTACCTATACTATGGCTCGTAGCCAAATCAAGGTAACTCTTCTCA
1 AAGTACCTATACTATGGCCCGTAGCCAAATCAAGGTAACTCTTCTCA
*
53392602 AAATACCTATA-TCATGGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACT-ATGGCCCGTAGCCAAATCAAGGTA
53392639 TTATTTGCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
46 1 0.01
47 70 0.96
48 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (47 bp):
AAGTACCTATACTATGGCCCGTAGCCAAATCAAGGTAACTCTTCTCA
Found at i:53400353 original size:11 final size:10
Alignment explanation
Indices: 53400319--53400361 Score: 56
Period size: 11 Copynumber: 4.5 Consensus size: 10
53400309 CAAAGCAACG
53400319 ATCA-CAAAA
1 ATCATCAAAA
53400328 A-CAT-AAAA
1 ATCATCAAAA
53400336 ATCATCAAAA
1 ATCATCAAAA
53400346 ATCGATCAAAA
1 ATC-ATCAAAA
53400357 ATCAT
1 ATCAT
53400362 ACCTTAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.23
9 4 0.13
10 9 0.30
11 10 0.33
ACGTcount: A:0.60, C:0.19, G:0.02, T:0.19
Consensus pattern (10 bp):
ATCATCAAAA
Found at i:53403231 original size:17 final size:16
Alignment explanation
Indices: 53403205--53403238 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
53403195 CAAAGTAGTT
53403205 TAAAATTATAGAAATA
1 TAAAATTATAGAAATA
*
53403221 TAAATATTATATAAATA
1 TAAA-ATTATAGAAATA
53403238 T
1 T
53403239 TTAAAGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
TAAAATTATAGAAATA
Found at i:53411867 original size:29 final size:29
Alignment explanation
Indices: 53411825--53411881 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
53411815 AAGCCATCAC
*
53411825 ATACAGTTCATACATGA-ATTTTGATTTT
1 ATACAGTTCATACATGAGATTTTCATTTT
*
53411853 ATACATGTTTATACATGAGATTTTCATTT
1 ATACA-GTTCATACATGAGATTTTCATTT
53411882 AGTTCATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 11 0.44
30 9 0.36
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (29 bp):
ATACAGTTCATACATGAGATTTTCATTTT
Found at i:53412142 original size:12 final size:12
Alignment explanation
Indices: 53412100--53412142 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
53412090 TATGAAGTGA
53412100 AAATGTATATATT
1 AAATG-ATATATT
*
53412113 AAATTATATATT
1 AAATGATATATT
* *
53412125 AGATGATATTTT
1 AAATGATATATT
53412137 AAATGA
1 AAATGA
53412143 GAATATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 21 0.84
13 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (12 bp):
AAATGATATATT
Found at i:53417975 original size:247 final size:246
Alignment explanation
Indices: 53417532--53418035 Score: 911
Period size: 247 Copynumber: 2.0 Consensus size: 246
53417522 AGATGATGGT
*
53417532 TTGAAAGTGATAACGACGAGTACTTGGAAGATTATGGATCATTATCTGACGATACAAAAATGGAA
1 TTGAAATTGATAACGACGAGTACTTGGAAGATTATGGATCATTATCTGACGATACAAAAATGGAA
* *
53417597 GTTGAACTTTCACCCGACTATCAGAATGATTGTATCCACAGTTGTGTGGATTCAATTGCCTAGTT
66 GTCGAACTTTCACCAGACTATCAGAATGATTGTATCCACAGTTGTGTGGATTCAATTGCCTAGTT
53417662 TACCTTTGGAATATTTCAATGAAGTACTTGTTAAAGTGGGGAAGATTGTTGGAAAACCCATTAAA
131 TACCTTTGGAATATTTCAATGAAGTACTTGTTAAAGTGGGGAAGATTGTTGGAAAACCCATTAAA
* *
53417727 TTATATTCTAATACGACTTATACTATTAGGGGGAAATTTGCAAGAGTTTGTG
196 TTAGATTCTAATACGACTTATACTACTA-GGGGAAATTTGCAAGAGTTTGTG
*
53417779 TTGAAATTGATAACGACGGGTACTTGGAAGATTATGGATCATTATCTGACGATACAAAAATGGAA
1 TTGAAATTGATAACGACGAGTACTTGGAAGATTATGGATCATTATCTGACGATACAAAAATGGAA
*
53417844 GTCGAACTTTCACCTAG-CTATCAGAATGATTGTATCCACAGTTGTGTGGATTCAATTGCCTGGT
66 GTCGAACTTTCACC-AGACTATCAGAATGATTGTATCCACAGTTGTGTGGATTCAATTGCCTAGT
53417908 TTACCTTTGGAATATTTCAATGAAGTACTTGTTAAAGTGGGGAAGATTGTTGGAAAACCCATTAA
130 TTACCTTTGGAATATTTCAATGAAGTACTTGTTAAAGTGGGGAAGATTGTTGGAAAACCCATTAA
*
53417973 ATTAGATTCTAATATGACTTATACTACTAGGGGAAATTTGCAAGAGTTTGTG
195 ATTAGATTCTAATACGACTTATACTACTAGGGGAAATTTGCAAGAGTTTGTG
53418025 TTGAAATTGAT
1 TTGAAATTGAT
53418036 TTGTGTAAGC
Statistics
Matches: 248, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
246 34 0.14
247 213 0.86
248 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.33
Consensus pattern (246 bp):
TTGAAATTGATAACGACGAGTACTTGGAAGATTATGGATCATTATCTGACGATACAAAAATGGAA
GTCGAACTTTCACCAGACTATCAGAATGATTGTATCCACAGTTGTGTGGATTCAATTGCCTAGTT
TACCTTTGGAATATTTCAATGAAGTACTTGTTAAAGTGGGGAAGATTGTTGGAAAACCCATTAAA
TTAGATTCTAATACGACTTATACTACTAGGGGAAATTTGCAAGAGTTTGTG
Found at i:53418486 original size:14 final size:14
Alignment explanation
Indices: 53418467--53418494 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53418457 GGGAAGCCAA
53418467 CGTGTGATAGATAT
1 CGTGTGATAGATAT
53418481 CGTGTGATAGATAT
1 CGTGTGATAGATAT
53418495 GGGAGATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
CGTGTGATAGATAT
Found at i:53434262 original size:24 final size:24
Alignment explanation
Indices: 53434233--53434282 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
53434223 CCCATGAAAG
*
53434233 CAGTGCTATCAATTTCTAGGACAT
1 CAGTGCCATCAATTTCTAGGACAT
53434257 CAGTGCCATCAATTTCTAGGACAT
1 CAGTGCCATCAATTTCTAGGACAT
53434281 CA
1 CA
53434283 ACCTCTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (24 bp):
CAGTGCCATCAATTTCTAGGACAT
Found at i:53437006 original size:14 final size:14
Alignment explanation
Indices: 53436987--53437013 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53436977 TTGGTAACCG
53436987 GTAAAAGCTTTTCC
1 GTAAAAGCTTTTCC
53437001 GTAAAAGCTTTTC
1 GTAAAAGCTTTTC
53437014 AGGCTTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.37
Consensus pattern (14 bp):
GTAAAAGCTTTTCC
Found at i:53437190 original size:18 final size:19
Alignment explanation
Indices: 53437159--53437196 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
53437149 ACTCTTCTTC
*
53437159 TCCCCTTTCTCCTTCCCCT
1 TCCCATTTCTCCTTCCCCT
53437178 TCCCATTTC-CCTTCCCCT
1 TCCCATTTCTCCTTCCCCT
53437196 T
1 T
53437197 GGGTTGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.03, C:0.55, G:0.00, T:0.42
Consensus pattern (19 bp):
TCCCATTTCTCCTTCCCCT
Found at i:53441498 original size:46 final size:46
Alignment explanation
Indices: 53441431--53441745 Score: 407
Period size: 46 Copynumber: 6.8 Consensus size: 46
53441421 GCTTTCTAAA
* * * *
53441431 ATGAAATGTGTAGGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * *
53441477 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* *
53441523 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTAAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * *
53441569 ATGAAATGAATAAGACCATAGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
** * *
53441615 ATGAAATGAACAAGGCCATGGTTGAAAGATACCATAGCAACGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
** * *
53441661 ATGAAATGAACAAGACCATGGTTGAAAGATATCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
* * *
53441707 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 ATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
53441746 TCATGTCAAA
Statistics
Matches: 243, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.00
46 242 1.00
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAC
Found at i:53443037 original size:19 final size:20
Alignment explanation
Indices: 53443013--53443058 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
53443003 CATCCAAACA
53443013 CCAGAAAAGTAAACCA-TTT
1 CCAGAAAAGTAAACCATTTT
**
53443032 CCAGAAAAGTAAGTCATTTT
1 CCAGAAAAGTAAACCATTTT
53443052 CCAGAAA
1 CCAGAAA
53443059 TTATTTTCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.46, C:0.20, G:0.13, T:0.22
Consensus pattern (20 bp):
CCAGAAAAGTAAACCATTTT
Found at i:53448764 original size:16 final size:16
Alignment explanation
Indices: 53448740--53448770 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53448730 CTCTTTAATC
*
53448740 TTTAGTAAAATCAAAT
1 TTTACTAAAATCAAAT
53448756 TTTACTAAAATCAAA
1 TTTACTAAAATCAAA
53448771 GTGTGAATAA
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:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (16 bp):
TTTACTAAAATCAAAT
Found at i:53450350 original size:23 final size:21
Alignment explanation
Indices: 53450305--53450351 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
53450295 GAGAAGAAGA
**
53450305 AAAGAATATAAAAAAAAGTTT
1 AAAGAATATAAAAAAAAAATT
53450326 AAAGAATATCAAAGAAAAAAATT
1 AAAGAATAT-AAA-AAAAAAATT
53450349 AAA
1 AAA
53450352 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 3 0.14
23 10 0.45
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (21 bp):
AAAGAATATAAAAAAAAAATT
Found at i:53461447 original size:19 final size:19
Alignment explanation
Indices: 53461418--53461455 Score: 60
Period size: 18 Copynumber: 2.0 Consensus size: 19
53461408 TTTTGAAATT
53461418 AAAAATATATAAAATTTTAA
1 AAAAATATAT-AAATTTTAA
53461438 AAAAAT-TATAAATTTTAA
1 AAAAATATATAAATTTTAA
53461456 TTAAGTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 3 0.17
20 6 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATATATAAATTTTAA
Found at i:53467440 original size:16 final size:17
Alignment explanation
Indices: 53467409--53467442 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
53467399 GGCATGTATC
53467409 TTTTTTAAAATATTTAT
1 TTTTTTAAAATATTTAT
*
53467426 TTTTTTAATAT-TTTAT
1 TTTTTTAAAATATTTAT
53467442 T
1 T
53467443 ATGTCTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAAAATATTTAT
Found at i:53467673 original size:21 final size:22
Alignment explanation
Indices: 53467643--53467699 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
53467633 ATACTAGTTA
* *
53467643 TAAAAATTATATA-ATTTTAAT
1 TAAAACTTATATATATTTCAAT
53467664 TAAAACTTATA-ATATTTCAAT
1 TAAAACTTATATATATTTCAAT
*
53467685 T-ATACTTATATATAT
1 TAAAACTTATATATAT
53467700 ATATATATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 9 0.29
21 22 0.71
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
TAAAACTTATATATATTTCAAT
Found at i:53469132 original size:23 final size:24
Alignment explanation
Indices: 53469102--53469156 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
53469092 GATTTTTTCC
53469102 CCAACGGTAAAA-ATTCAAACACT
1 CCAACGGTAAAATATTCAAACACT
* *
53469125 CCAACGGTAAAATATTGAAACAGT
1 CCAACGGTAAAATATTCAAACACT
53469149 CCAACGGT
1 CCAACGGT
53469157 GACTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (24 bp):
CCAACGGTAAAATATTCAAACACT
Found at i:53469483 original size:16 final size:15
Alignment explanation
Indices: 53469453--53469497 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 15
53469443 TAATTAAGTT
*
53469453 ATTTTTTAAGTTTTAA
1 ATTTTTTAA-ATTTAA
53469469 AGTTTTTTAAATTTAA
1 A-TTTTTTAAATTTAA
53469485 ATTATTTTAAATT
1 ATT-TTTTAAATT
53469498 ATTCTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 2 0.08
16 16 0.62
17 8 0.31
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (15 bp):
ATTTTTTAAATTTAA
Found at i:53469492 original size:17 final size:17
Alignment explanation
Indices: 53469436--53469497 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 17
53469426 TTAAATTTTG
*
53469436 TTATTTTT-AA-TTAAG
1 TTATTTTTAAATTTAAA
*
53469451 TTATTTTTTAAGTTTTAAA
1 TTA-TTTTTAA-ATTTAAA
*
53469470 GT-TTTTTAAATTTAAA
1 TTATTTTTAAATTTAAA
53469486 TTA-TTTTAAATT
1 TTATTTTTAAATT
53469498 ATTCTATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
15 3 0.08
16 21 0.57
17 8 0.22
19 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (17 bp):
TTATTTTTAAATTTAAA
Found at i:53471619 original size:25 final size:25
Alignment explanation
Indices: 53471531--53471619 Score: 135
Period size: 25 Copynumber: 3.6 Consensus size: 25
53471521 TTACATGTCT
53471531 GCTCATACGAGCT-ATGAATCGGTAA
1 GCTCATACGAGCTGA-GAATCGGTAA
*
53471556 GCTCATACGAGCTGTGAATCGGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
* *
53471581 GCTTATACGAGCTGAGAATTGGTAA
1 GCTCATACGAGCTGAGAATCGGTAA
53471606 GCTCATACGAGCTG
1 GCTCATACGAGCTG
53471620 TCGTGTGTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (25 bp):
GCTCATACGAGCTGAGAATCGGTAA
Found at i:53478610 original size:15 final size:16
Alignment explanation
Indices: 53478570--53478611 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
53478560 ATAATTAACT
53478570 AATTTTTAAAAACTAA
1 AATTTTTAAAAACTAA
* *
53478586 AAATTATAAAAA-TAA
1 AATTTTTAAAAACTAA
53478601 AATTTTTAAAA
1 AATTTTTAAAA
53478612 TGTAAATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AATTTTTAAAAACTAA
Found at i:53479086 original size:17 final size:18
Alignment explanation
Indices: 53479058--53479092 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
53479048 TTAGCTATGG
53479058 TATATAAATTTTGATTTT
1 TATATAAATTTTGATTTT
*
53479076 TATAT-AATTTTTATTTT
1 TATATAAATTTTGATTTT
53479093 CGTTTGTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TATATAAATTTTGATTTT
Found at i:53479916 original size:7 final size:7
Alignment explanation
Indices: 53479904--53479944 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
53479894 TTTTCGGTCC
53479904 TCAATTT
1 TCAATTT
53479911 TCAATTT
1 TCAATTT
53479918 TCAATTT
1 TCAATTT
*
53479925 TCAATTC
1 TCAATTT
53479932 TCAATTT
1 TCAATTT
53479939 TCAATT
1 TCAATT
53479945 ATTATTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (7 bp):
TCAATTT
Found at i:53485271 original size:24 final size:24
Alignment explanation
Indices: 53485239--53485290 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
53485229 TTTCAATAAT
53485239 TTTACATAGCTTCCGTGCATCTAG
1 TTTACATAGCTTCCGTGCATCTAG
*
53485263 TTTACATAGCTTCCGTGCATTTAG
1 TTTACATAGCTTCCGTGCATCTAG
53485287 TTTA
1 TTTA
53485291 AGTGTGTGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.42
Consensus pattern (24 bp):
TTTACATAGCTTCCGTGCATCTAG
Found at i:53487184 original size:19 final size:20
Alignment explanation
Indices: 53487143--53487187 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
53487133 ACCAAACTTT
53487143 ATTTTAATATTTGTTTATAC
1 ATTTTAATATTTGTTTATAC
* *
53487163 ATTTTAATTTTTG-TTATGC
1 ATTTTAATATTTGTTTATAC
53487182 ATTTTA
1 ATTTTA
53487188 TTACCTCTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.62
Consensus pattern (20 bp):
ATTTTAATATTTGTTTATAC
Found at i:53488443 original size:21 final size:22
Alignment explanation
Indices: 53488403--53488443 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
53488393 TTAAATATAA
53488403 TTATATTAGTAATGTTTTTATT
1 TTATATTAGTAATGTTTTTATT
* *
53488425 TTATTTTAG-AATTTTTTTA
1 TTATATTAGTAATGTTTTTA
53488444 AAATTTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (22 bp):
TTATATTAGTAATGTTTTTATT
Found at i:53489482 original size:11 final size:11
Alignment explanation
Indices: 53489468--53489517 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
53489458 TTTCAATATT
53489468 CTCTCAAATTC
1 CTCTCAAATTC
53489479 CTCTCAAA-T-
1 CTCTCAAATTC
*
53489488 CTCTCAAATTT
1 CTCTCAAATTC
*
53489499 CTCTTAAATTC
1 CTCTCAAATTC
53489510 CTCTCAAA
1 CTCTCAAA
53489518 ACTCTCGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
9 8 0.24
10 2 0.06
11 24 0.71
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (11 bp):
CTCTCAAATTC
Found at i:53489492 original size:20 final size:21
Alignment explanation
Indices: 53489460--53489517 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
53489450 CTTCAATCTT
53489460 TCAATATTCTCTCAAATTCCTC
1 TCAA-ATTCTCTCAAATTCCTC
*
53489482 TCAAA-TCTCTCAAATTTCTC
1 TCAAATTCTCTCAAATTCCTC
*
53489502 TTAAATTCCTCTCAAA
1 TCAAATT-CTCTCAAA
53489518 ACTCTCGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 18 0.56
21 2 0.06
22 12 0.38
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (21 bp):
TCAAATTCTCTCAAATTCCTC
Found at i:53491345 original size:18 final size:18
Alignment explanation
Indices: 53491322--53491358 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
53491312 TGCCAGGTAC
*
53491322 GTATCCTAGCCCTTTTAT
1 GTATCCTAGCCCTTATAT
53491340 GTATCCTAGCCCTTATAT
1 GTATCCTAGCCCTTATAT
53491358 G
1 G
53491359 CTTCATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.41
Consensus pattern (18 bp):
GTATCCTAGCCCTTATAT
Found at i:53491955 original size:117 final size:117
Alignment explanation
Indices: 53491749--53492134 Score: 763
Period size: 117 Copynumber: 3.3 Consensus size: 117
53491739 TATTTGTACA
*
53491749 AACATTTTGAATCTTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
53491814 TGCAATTTACTTTTATATTTTTTAATAAAATGTAAATTATTTTAAATAAGGC
66 TGCAATTTACTTTTATATTTTTTAATAAAATGTAAATTATTTTAAATAAGGC
53491866 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
53491931 TGCAATTTACTTTTATATTTTTTAATAAAATGTAAATTATTTTAAATAAGGC
66 TGCAATTTACTTTTATATTTTTTAATAAAATGTAAATTATTTTAAATAAGGC
53491983 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
53492048 TGCAATTTACTTTTATATTTTTTAATAAAATGTAAATTATTTTAAATAAGGC
66 TGCAATTTACTTTTATATTTTTTAATAAAATGTAAATTATTTTAAATAAGGC
53492100 AACATTTTGAATATTTTTATATTATTTCATGTAAT
1 AACATTTTGAATATTTTTATATTATTTCATGTAAT
53492135 AAAATATAAA
Statistics
Matches: 268, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
117 268 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.48
Consensus pattern (117 bp):
AACATTTTGAATATTTTTATATTATTTCATGTAATTAGATAAAAGGTTGTTTTAAATAAAGTAAT
TGCAATTTACTTTTATATTTTTTAATAAAATGTAAATTATTTTAAATAAGGC
Found at i:53492145 original size:61 final size:61
Alignment explanation
Indices: 53491836--53492145 Score: 255
Period size: 61 Copynumber: 5.2 Consensus size: 61
53491826 TTATATTTTT
*
53491836 TAATAAAATGTAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATG
1 TAATAAAATATAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATG
* * * * *
53491897 TAATTAGATA-AAAGGTTGTTTTAAATAAAG-TA-A--TTGCAAT-TTACTTT-TA-TATTT--T
1 TAATAAAATATAAA--TTATTTTAAATAAGGCAACATTTTG-AATATT--TTTATATTATTTCAT
*
53491952 T
61 G
*
53491953 TAATAAAATGTAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATG
1 TAATAAAATATAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATG
* * * * *
53492014 TAATTAGATA-AAAGGTTGTTTTAAATAAAG-TA-A--TTGCAAT-TTACTTT-TA-TATTT--T
1 TAATAAAATATAAA--TTATTTTAAATAAGGCAACATTTTG-AATATT--TTTATATTATTTCAT
*
53492069 T
61 G
*
53492070 TAATAAAATGTAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATG
1 TAATAAAATATAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATG
53492131 TAATAAAATATAAAT
1 TAATAAAATATAAAT
53492146 AATACAACAT
Statistics
Matches: 190, Mismatches: 29, Indels: 60
0.68 0.10 0.22
Matches are distributed among these distances:
55 26 0.14
56 18 0.09
57 14 0.07
58 30 0.16
59 30 0.16
60 14 0.07
61 32 0.17
62 26 0.14
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (61 bp):
TAATAAAATATAAATTATTTTAAATAAGGCAACATTTTGAATATTTTTATATTATTTCATG
Found at i:53495384 original size:126 final size:125
Alignment explanation
Indices: 53495154--53495687 Score: 856
Period size: 126 Copynumber: 4.3 Consensus size: 125
53495144 GCCCAAGTTA
* *
53495154 TTTCAGAAACCACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
**
53495219 TGCATCCTGCTTGAAGCGTTTTTGACACTATTTATGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTT-ACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * * *
53495280 TTTCAGAGACTACTGTAGCAAAAGAGCATCCATGTGGGAGCTTCTTCCAGTAATTTTGCTGAAAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
53495345 TGCATCCTGCTTGAAGCGTTTTTACCACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCGTTTTTA-CACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* *
53495406 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGAAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
* **
53495471 TGCATCCCGCTTGAAGCGTTTTTTACACTATTTGCATAGACACGTCTTCTCAAAATTATTT
66 TGCATCCTGCTTGAAGCG-TTTTTACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
* * ** *
53495532 TTTTAGATACTACTGTAGCAAAAGAGCGTTTACGTGGGAGCTTCTTTCAGTACTTTTGCTGACAA
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
*
53495597 TGCATCCTGCTTGAAGCGTTTTT-GACTATTTGCGCAGACACGTCTTCTCAAAATT-TTT
66 TGCATCCTGCTTGAAGCGTTTTTACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
53495655 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCAC
1 TTTCAGAGACTACTGTAGCAAAAGAGCGTCCAC
53495688 CTAGAAACTT
Statistics
Matches: 376, Mismatches: 30, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
123 32 0.09
124 29 0.08
125 6 0.02
126 303 0.81
127 6 0.02
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (125 bp):
TTTCAGAGACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTCAGTACTTTTGCTGAAAA
TGCATCCTGCTTGAAGCGTTTTTACACTATTTGCGCAGACACGTCTTCTCAAAATTATTT
Found at i:53495989 original size:15 final size:16
Alignment explanation
Indices: 53495969--53496013 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
53495959 AACTTTTTTC
53495969 TTTAAAACCCTAAAAT
1 TTTAAAACCCTAAAAT
*
53495985 TTAAAAACCC-AAAAT
1 TTTAAAACCCTAAAAT
53496000 TCTTAAAACCCTAA
1 T-TTAAAACCCTAA
53496014 CCCTAATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.24
16 17 0.68
17 2 0.08
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (16 bp):
TTTAAAACCCTAAAAT
Found at i:53497578 original size:22 final size:21
Alignment explanation
Indices: 53497548--53497594 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
53497538 TACAAATTAA
53497548 ATCTCCAAGATTACAAGATCAT
1 ATCTCCAAGATTAC-AGATCAT
* * *
53497570 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
53497591 ATCT
1 ATCT
53497595 AAGATTGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:53497588 original size:16 final size:16
Alignment explanation
Indices: 53497567--53497617 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 16
53497557 ATTACAAGAT
53497567 CATATCTTCAAGATTG
1 CATATCTTCAAGATTG
53497583 CATATCATATCTAAGATTG
1 CATATC-T-TC-AAGATTG
*
53497602 CATATCCTTAAAGATT
1 CATAT-CTTCAAGATT
53497618 ATATTTCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 3 0.10
19 13 0.43
20 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (16 bp):
CATATCTTCAAGATTG
Found at i:53497600 original size:19 final size:21
Alignment explanation
Indices: 53497565--53497607 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
53497555 AGATTACAAG
53497565 ATCATATCTTCAAGATTGCAT
1 ATCATATCTTCAAGATTGCAT
53497586 ATCATATC-T-AAGATTGCAT
1 ATCATATCTTCAAGATTGCAT
53497605 ATC
1 ATC
53497608 CTTAAAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
20 1 0.05
21 8 0.36
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (21 bp):
ATCATATCTTCAAGATTGCAT
Found at i:53498298 original size:87 final size:89
Alignment explanation
Indices: 53498189--53498378 Score: 242
Period size: 87 Copynumber: 2.2 Consensus size: 89
53498179 GCACAGGAAT
* * * *
53498189 GTCAGATCTGCTAGGTCTTCGATCTATTCCCTGTAAACATAGGGATGCCAAATCATTTTGGATCT
1 GTCAGATCTGCTATGTCTTCGATCTACTCCCTGTAAACATAAGGATGCCAAATCATTTTAGATCT
*
53498254 ACTTC-A-GCGTAAACA-CCTGAAG
66 ACTTCAATGCGAAAACATCC-GAAG
* * * *
53498276 GTCAGATCTGCTATGTCTTCGATTTGCTCCTTGTAAACATAAGGATGCTAAATCATTTTAGATCT
1 GTCAGATCTGCTATGTCTTCGATCTACTCCCTGTAAACATAAGGATGCCAAATCATTTTAGATCT
* * *
53498341 GCTTCAATGTGAAAATATCCGAAG
66 ACTTCAATGCGAAAACATCCGAAG
53498365 GTCAGATCTGCTAT
1 GTCAGATCTGCTAT
53498379 ACTTTAACCT
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
87 61 0.69
88 1 0.01
89 24 0.27
90 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (89 bp):
GTCAGATCTGCTATGTCTTCGATCTACTCCCTGTAAACATAAGGATGCCAAATCATTTTAGATCT
ACTTCAATGCGAAAACATCCGAAG
Found at i:53498520 original size:128 final size:128
Alignment explanation
Indices: 53498319--53498689 Score: 665
Period size: 128 Copynumber: 2.9 Consensus size: 128
53498309 TAAACATAAG
* * *
53498319 GATGCTAAATCATTTTAGATCTGCTTCAATGTGAAA-A-TATCCGAAGGTCAGATCTGCTATACT
1 GATGCCAAATCATCTTAGATCTGCTTCAGTGT-AAACACT-T--GAAGGTCAGATCTGCTATACT
53498382 TTAACCTATTATCCTACTGCTTAGGGGGTTAAGGCGCATCTTCGATCTGCTCTCCATCGAACACA
62 TTAACCTATTATCCTACTGCTTAGGGGGTTAAGGCGCATCTTCGATCTGCTCTCCATCGAACACA
53498447 GA
127 GA
53498449 GATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACTTGAAGGTCAGATCTGCTATACTTTAA
1 GATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACTTGAAGGTCAGATCTGCTATACTTTAA
53498514 CCTATTATCCTACTGCTTAGGGGGTTAAGGCGCATCTTCGATCTGCTCTCCATCGAACACAGA
66 CCTATTATCCTACTGCTTAGGGGGTTAAGGCGCATCTTCGATCTGCTCTCCATCGAACACAGA
53498577 GATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACTTGAAGGTCAGATCTGCTATACTTTAA
1 GATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACTTGAAGGTCAGATCTGCTATACTTTAA
53498642 CCTATTATCCTACTGCTTAGGGGGTTAAGGCGCATCTTCGATCTGCTC
66 CCTATTATCCTACTGCTTAGGGGGTTAAGGCGCATCTTCGATCTGCTC
53498690 CACTACTGCT
Statistics
Matches: 236, Mismatches: 3, Indels: 6
0.96 0.01 0.02
Matches are distributed among these distances:
128 201 0.85
129 3 0.01
130 31 0.13
131 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (128 bp):
GATGCCAAATCATCTTAGATCTGCTTCAGTGTAAACACTTGAAGGTCAGATCTGCTATACTTTAA
CCTATTATCCTACTGCTTAGGGGGTTAAGGCGCATCTTCGATCTGCTCTCCATCGAACACAGA
Found at i:53498740 original size:84 final size:84
Alignment explanation
Indices: 53498637--53499842 Score: 1550
Period size: 84 Copynumber: 14.4 Consensus size: 84
53498627 TCTGCTATAC
* * *
53498637 TTTAACCTATTATCCTACTGCTTAGGGGGTTAAGGCGCA-TCTTCGATCTGCTCCACTACTGCTT
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG-AGTCTTCGATCTGCTCCACTACTGCTT
*
53498701 AGGGAGATAAGATCTGTAAA
65 AGGGAGATAAGATCTGCAAA
* * *
53498721 TTTAACCTGTTACTCTACTGCTTAGGGGATTAAGGAGAGTCGTCGTCGATCTGCTCCGCTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTC-T--TCGATCTGCTCCACTACTGC
*
53498786 TTAGGGAGATAAGATCTGTAAA
63 TTAGGGAGATAAGATCTGCAAA
* * *
53498808 TTTAACCTGTTACTCTACTGCTTAGGGGATTAAGGAGAGTCGTCGTCGATCTGCTCCGCTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTC-T--TCGATCTGCTCCACTACTGC
53498873 TTAGGGAGATAAGATCTGC---
63 TTAGGGAGATAAGATCTGCAAA
* * * * *
53498892 --GAACCTGTTACCCTACTGCTTAAGGGATTAAGGCGGGTATTCGATCTGGTCCACTACTGCTTA
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
*
53498955 AGGAGATAAGATCTGCAAA
66 GGGAGATAAGATCTGCAAA
* *
53498974 TTTAACCTGTTACTCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTCGATCTGCTCCGCTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTC-T--TCGATCTGCTCCACTACTGC
53499039 TTAGGGAGATAAGATCTGC---
63 TTAGGGAGATAAGATCTGCAAA
* * **
53499058 --GAACCTGTTACCTTACTGCTTAGAAGATTAAGGC-AGGTCTTCGATCTGCTCCACTACTGCTT
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGA-GTCTTCGATCTGCTCCACTACTGCTT
*
53499120 AGGGAGATAAGATCTGTAAA
65 AGGGAGATAAGATCTGCAAA
* * * *
53499140 TTTAACTTGTTACCCTACTACTTAGGGGATTAAGGTGAGTCGTCGTCGATCTGCTCCGCTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTC-T--TCGATCTGCTCCACTACTGC
53499205 TTAGGGAGATAAGATCTGC---
63 TTAGGGAGATAAGATCTGCAAA
* * **
53499224 --GAACCTGTTACCTTACTGCTTAGAAGATTAAGGC-AGGTCTTCGATCTGCTCCACTACTGCTT
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGA-GTCTTCGATCTGCTCCACTACTGCTT
*
53499286 AGGGAGATAAGATCTGTAAA
65 AGGGAGATAAGATCTGCAAA
* * *
53499306 TTTAACTTGTTACCCTACTGCTTAGGGGATTAAGGTGAGTCGTCGTCGATCTGCTCCGCTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTC-T--TCGATCTGCTCCACTACTGC
*
53499371 TTAGGGAGATAAGATTTGC---
63 TTAGGGAGATAAGATCTGCAAA
* * * * *
53499390 --GAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTTGATCTGCTTCGCTACTGT
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTC-T--TCGATCTGCTCCACTACTGC
* *
53499453 TTAGGGAGATAAGATATGC-GA
63 TTAGGGAGATAAGATCTGCAAA
* * *
53499474 ---AA-CTGTTACCATACTGCTTAGGGGATTAATGCGAGTCTTCGATCTACTCCACTACTGCTTA
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
53499535 GGGAGATAAGATCTGCAAA
66 GGGAGATAAGATCTGCAAA
*
53499554 TTTAACCTGTTACCCTACCGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
*
53499619 GGGAGGTAAGATCTGCAAA
66 GGGAGATAAGATCTGCAAA
*
53499638 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGAGAGTCTTCGATCTGCTCCACTACTGCTTA
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
*
53499703 GGGAGATAAAATCTGCAAA
66 GGGAGATAAGATCTGCAAA
* *
53499722 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGTGAGTCTTCGATCCGCTCCACTACTGCTTA
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
53499787 GGGAGATAAGATCTGCAAA
66 GGGAGATAAGATCTGCAAA
53499806 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG
53499843 CTGAATTTTG
Statistics
Matches: 996, Mismatches: 87, Indels: 78
0.86 0.07 0.07
Matches are distributed among these distances:
79 143 0.14
80 1 0.00
81 6 0.01
82 203 0.20
83 5 0.01
84 399 0.40
85 6 0.01
87 233 0.23
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (84 bp):
TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCTTCGATCTGCTCCACTACTGCTTA
GGGAGATAAGATCTGCAAA
Found at i:53498834 original size:43 final size:43
Alignment explanation
Indices: 53498692--53498834 Score: 141
Period size: 43 Copynumber: 3.3 Consensus size: 43
53498682 ATCTGCTCCA
53498692 CTACTGCTTAGGGAGATAAGATCTGTAAATTTAACCTGTTACT
1 CTACTGCTTAGGGAGATAAGATCTGTAAATTTAACCTGTTACT
** ** * * * *
53498735 CTACTGCTTAGGG-GATTAAGGAGAGTC-GT--CGTCGATCTGCTCCG
1 CTACTGCTTAGGGAGA-T-A--AGA-TCTGTAAATTTAACCTGTTACT
53498779 CTACTGCTTAGGGAGATAAGATCTGTAAATTTAACCTGTTACT
1 CTACTGCTTAGGGAGATAAGATCTGTAAATTTAACCTGTTACT
53498822 CTACTGCTTAGGG
1 CTACTGCTTAGGG
53498835 GATTAAGGAG
Statistics
Matches: 75, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
40 2 0.03
41 5 0.07
42 2 0.03
43 35 0.47
44 22 0.29
45 2 0.03
46 5 0.07
47 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (43 bp):
CTACTGCTTAGGGAGATAAGATCTGTAAATTTAACCTGTTACT
Found at i:53498977 original size:166 final size:166
Alignment explanation
Indices: 53498637--53499842 Score: 1607
Period size: 166 Copynumber: 7.2 Consensus size: 166
53498627 TCTGCTATAC
* * * *
53498637 TTTAACCTATTATCCTACTGCTTAGGGGGTTAAGGCGCA-TC-T--TCGATCTGCTCCACTACTG
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG-AGTCGTCGTCGATCTGCTCCGCTACTG
** * *
53498698 CTTAGGGAGATAAGATCTGTAAATTTAACCTGTTACTCTACTGCTTAGGGGATTAAGGAGAGTCG
65 CTTAGGGAGATAAGATCTG-----CGAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG-G--G
* * *
53498763 TCGTCGATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTGTAAA
122 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAA
* *
53498808 TTTAACCTGTTACTCTACTGCTTAGGGGATTAAGGAGAGTCGTCGTCGATCTGCTCCGCTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTCGATCTGCTCCGCTACTGC
* *
53498873 TTAGGGAGATAAGATCTGCGAACCTGTTACCCTACTGCTTAAGGGATTAAGGCGGGTATTCGATC
66 TTAGGGAGATAAGATCTGCGAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGGGTCTTCGATC
* *
53498938 TGGTCCACTACTGCTTAAGGAGATAAGATCTGCAAA
131 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAA
*
53498974 TTTAACCTGTTACTCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTCGATCTGCTCCGCTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTCGATCTGCTCCGCTACTGC
* ** *
53499039 TTAGGGAGATAAGATCTGCGAACCTGTTACCTTACTGCTTAGAAGATTAAGGCAGGTCTTCGATC
66 TTAGGGAGATAAGATCTGCGAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGGGTCTTCGATC
*
53499104 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAA
131 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAA
* * *
53499140 TTTAACTTGTTACCCTACTACTTAGGGGATTAAGGTGAGTCGTCGTCGATCTGCTCCGCTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTCGATCTGCTCCGCTACTGC
* ** *
53499205 TTAGGGAGATAAGATCTGCGAACCTGTTACCTTACTGCTTAGAAGATTAAGGCAGGTCTTCGATC
66 TTAGGGAGATAAGATCTGCGAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGGGTCTTCGATC
*
53499270 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAAA
131 TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAA
* *
53499306 TTTAACTTGTTACCCTACTGCTTAGGGGATTAAGGTGAGTCGTCGTCGATCTGCTCCGCTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTCGATCTGCTCCGCTACTGC
*
53499371 TTAGGGAGATAAGATTTGCGAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTT-
66 TTAGGGAGATAAGATCTGCGAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG-G--GTC-TTC
* * * * *
53499435 GATCTGCTTCGCTACTGTTTAGGGAGATAAGATATGC-GA
127 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAA
* * * *
53499474 ---AA-CTGTTACCATACTGCTTAGGGGATTAATGCGAGTC-T--TCGATCTACTCCACTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTCGATCTGCTCCGCTACTGC
* * *
53499532 TTAGGGAGATAAGATCTGCAAATTTAACCTGTTACCCTACCGCTTAGGGGATTAAGGCGAGTCTT
66 TTAGGGAGATAAGATCTGC-----GAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGGGTCTT
*
53499597 CGATCTGCTCCACTACTGCTTAGGGAGGTAAGATCTGCAAA
126 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAA
* *
53499638 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGAGAGTC-T--TCGATCTGCTCCACTACTGC
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTCGATCTGCTCCGCTACTGC
* * * *
53499700 TTAGGGAGATAAAATCTGCAAATTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGTGAGTCTT
66 TTAGGGAGATAAGATCTGC-----GAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGGGTCTT
*
53499765 CGATCCGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAA
126 CGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAA
53499806 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG
1 TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCG
53499843 CTGAATTTTG
Statistics
Matches: 947, Mismatches: 69, Indels: 41
0.90 0.07 0.04
Matches are distributed among these distances:
161 36 0.04
162 2 0.00
163 36 0.04
164 32 0.03
165 2 0.00
166 504 0.53
167 3 0.00
168 191 0.20
169 66 0.07
170 3 0.00
171 34 0.04
172 1 0.00
174 37 0.04
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (166 bp):
TTTAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGAGTCGTCGTCGATCTGCTCCGCTACTGC
TTAGGGAGATAAGATCTGCGAACCTGTTACCCTACTGCTTAGGGGATTAAGGCGGGTCTTCGATC
TGCTCCACTACTGCTTAGGGAGATAAGATCTGCAAA
Found at i:53499659 original size:43 final size:43
Alignment explanation
Indices: 53499525--53499832 Score: 206
Period size: 43 Copynumber: 7.3 Consensus size: 43
53499515 ATCTACTCCA
53499525 CTACTGCTTAGGGAGATAAGATCTGCAAATTTAACCTGTTACC
1 CTACTGCTTAGGGAGATAAGATCTGCAAATTTAACCTGTTACC
* * * * * *
53499568 CTACCGCTTAGGG-GATTAAG----GCGAGTCTTCGATCTGCT-CC
1 CTACTGCTTAGGGAGA-TAAGATCTGCAAAT-TT-AACCTGTTACC
*
53499608 ACTACTGCTTAGGGAGGTAAGATCTGCAAATTTAACCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGCAAATTTAACCTGTTACC
* * * *
53499652 CTACTGCTTAGGG-GATTAAG----G-AGAGTCTTCGATCTGCT-CC
1 CTACTGCTTAGGGAGA-TAAGATCTGCA-AAT-TT-AACCTGTTACC
*
53499692 ACTACTGCTTAGGGAGATAAAATCTGCAAATTTAACCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGCAAATTTAACCTGTTACC
* * * *
53499736 CTACTGCTTAGGG-GATTAAG--GTG--AGTCTTCGATCC-GCT-CC
1 CTACTGCTTAGGGAGA-TAAGATCTGCAAAT-TT--AACCTGTTACC
53499776 ACTACTGCTTAGGGAGATAAGATCTGCAAATTTAACCTGTTACC
1 -CTACTGCTTAGGGAGATAAGATCTGCAAATTTAACCTGTTACC
53499820 CTACTGCTTAGGG
1 CTACTGCTTAGGG
53499833 GATTAAGGCG
Statistics
Matches: 199, Mismatches: 32, Indels: 68
0.67 0.11 0.23
Matches are distributed among these distances:
38 1 0.01
39 9 0.05
40 12 0.06
41 63 0.32
42 16 0.08
43 76 0.38
44 12 0.06
45 9 0.05
46 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (43 bp):
CTACTGCTTAGGGAGATAAGATCTGCAAATTTAACCTGTTACC
Found at i:53500836 original size:10 final size:9
Alignment explanation
Indices: 53500788--53500850 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
53500778 GGCCTCTCCA
53500788 TTTTTTTTC
1 TTTTTTTTC
53500797 TTTTTTCTT-
1 TTTTTT-TTC
* *
53500806 TTTATTTTA
1 TTTTTTTTC
* *
53500815 TTTTATTCC
1 TTTTTTTTC
53500824 TTTTCTTTTC
1 TTTT-TTTTC
*
53500834 TTTTTTTCC
1 TTTTTTTTC
53500843 TTTTTTTT
1 TTTTTTTT
53500851 TGAAATAGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
8 2 0.05
9 31 0.74
10 9 0.21
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:53500851 original size:19 final size:19
Alignment explanation
Indices: 53500788--53500851 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
53500778 GGCCTCTCCA
53500788 TTTTTTTTC-TTTTTT-CT
1 TTTTTTTTCTTTTTTTCCT
* *
53500805 TTTTATTTTATTTTATTCCT
1 TTTT-TTTTCTTTTTTTCCT
*
53500825 TTTCTTTTCTTTTTTTCCT
1 TTTTTTTTCTTTTTTTCCT
53500844 TTTTTTTT
1 TTTTTTTT
53500852 GAAATAGAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
17 4 0.11
18 4 0.11
19 25 0.66
20 5 0.13
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTTTTCTTTTTTTCCT
Found at i:53506459 original size:22 final size:21
Alignment explanation
Indices: 53506434--53506480 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
53506424 TACAAATTAA
53506434 ATCTCCAAGATTACAGGATCAT
1 ATCTCCAAGATTACA-GATCAT
* * *
53506456 ATCTTCAAGATTGCATATCAT
1 ATCTCCAAGATTACAGATCAT
53506477 ATCT
1 ATCT
53506481 AAGATTGTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (21 bp):
ATCTCCAAGATTACAGATCAT
Found at i:53506486 original size:19 final size:19
Alignment explanation
Indices: 53506451--53506509 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 19
53506441 AGATTACAGG
53506451 ATCATATCTTCAAGATTGCAT
1 ATCATATC-T-AAGATTGCAT
53506472 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
53506489 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
53506508 AT
1 AT
53506510 TCTTAAAGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 17 0.47
19 10 0.28
20 1 0.03
21 8 0.22
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:53507613 original size:18 final size:20
Alignment explanation
Indices: 53507590--53507628 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
53507580 GATATGATAC
53507590 TAAAAT-TAT-TAAAAAAAT
1 TAAAATATATATAAAAAAAT
53507608 TAAAATATATATAAAAAAAT
1 TAAAATATATATAAAAAAAT
53507628 T
1 T
53507629 CGGGAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 10 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATATATATAAAAAAAT
Done.