Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr3
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: 26558743
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1281270 characters in sequence are not A, C, G, or T
File 3 of 79
Found at i:913944 original size:134 final size:136
Alignment explanation
Indices: 913699--913968 Score: 370
Period size: 134 Copynumber: 2.0 Consensus size: 136
913689 ATACATGCAT
*
913699 ACATACATACATACATCTCCATTGTTTCCTTCCCAATCAAAACCTGAAATTCAACACAAACCAAT
1 ACATACATACATACATCTCCATTGCTTCCTTCCCAATCAAAACCTGAAATTCAACACAAACCAAT
* * * ** * *
913764 CTTTTGCACCCATATTTTTTTTTCCTTCCCCTGATTCATCACATAACCGTAGCATTGAATCAT-G
66 CCTTTACACCCATA-TTTTTTTCCCTTCCCCTGATTCATCACATAACAATAGAACTGAATCATGG
913828 AACTTTC
130 AACTTTC
* *
913835 ACATACATACATACATTTCCATTGCTTCC-T-CCAATCAAAACCTGAAATTCAACACCACAACCG
1 ACATACATACATACATCTCCATTGCTTCCTTCCCAATCAAAACCTGAAATTCAACA-CA-AACCA
*
913898 ATCCTTTACACCCATA-TTTTTTCCCTTCCCCT-AGTTCATCATATAACAATAGAACTGAATCAT
64 ATCCTTTACACCCATATTTTTTTCCCTTCCCCTGA-TTCATCACATAACAATAGAACTGAATCAT
913961 GGAACTTT
128 GGAACTTT
913969 GAACTTTCCC
Statistics
Matches: 119, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
133 1 0.01
134 63 0.53
135 10 0.08
136 45 0.38
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (136 bp):
ACATACATACATACATCTCCATTGCTTCCTTCCCAATCAAAACCTGAAATTCAACACAAACCAAT
CCTTTACACCCATATTTTTTTCCCTTCCCCTGATTCATCACATAACAATAGAACTGAATCATGGA
ACTTTC
Found at i:924746 original size:69 final size:69
Alignment explanation
Indices: 924635--924796 Score: 234
Period size: 69 Copynumber: 2.3 Consensus size: 69
924625 GTACATCAGG
* * * * * *
924635 TGAAAGATCCTATCTTTAGTAAAGTTAAGCTCTTTCATCAAATGACTCAACCATCTAATAACAAT
1 TGAAAGGTCCTCTCTTTAGTAAAGTCAAGCTCTGTCATCAAATGACTCAACCATCTAATAAAAAC
924700 TGGA
66 TGGA
*
924704 TGAAAGGTCCTCTCTTTAATAAAGTCAAGCTCTGTCATCAAATGACTCAACCATCTAATAAAAAC
1 TGAAAGGTCCTCTCTTTAGTAAAGTCAAGCTCTGTCATCAAATGACTCAACCATCTAATAAAAAC
*
924769 TGGG
66 TGGA
*
924773 TGAAAAGGTCCTCTATTTAGTAAA
1 TG-AAAGGTCCTCTCTTTAGTAAA
924797 TTATTCAACT
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
69 63 0.77
70 19 0.23
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (69 bp):
TGAAAGGTCCTCTCTTTAGTAAAGTCAAGCTCTGTCATCAAATGACTCAACCATCTAATAAAAAC
TGGA
Found at i:925238 original size:6 final size:6
Alignment explanation
Indices: 925194--925234 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
925184 TCAGCCTCAT
* * *
925194 CTTCTC CTTCAC CTTCAC CTTCAC CTTCAA CTTCAG CTTCA
1 CTTCAC CTTCAC CTTCAC CTTCAC CTTCAC CTTCAC CTTCA
925235 GCTTTCGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.17, C:0.44, G:0.02, T:0.37
Consensus pattern (6 bp):
CTTCAC
Found at i:926345 original size:230 final size:231
Alignment explanation
Indices: 925932--926394 Score: 910
Period size: 230 Copynumber: 2.0 Consensus size: 231
925922 ATATTATAGG
925932 TCCCTCTATTTTTTGTAATTTTAAAATTTAGTCTTTATATTTTTATTTTTAAAAATTTAATTTAT
1 TCCCTCTA-TTTTTGTAATTTTAAAATTTAGTCTTTATATTTTTATTTTTAAAAATTTAATTTAT
925997 TTACCTTTCATATTTTAAAATTTAATTCTAACTATTAAATTTATTTTGTTAAATTCAAATTAATT
65 TTACCTTTCATATTTTAAAATTTAATTCTAACTATTAAATTTATTTTGTTAAATTCAAATTAATT
926062 ATAATATTTTTTTAATTATAATTGTCTAATTGTAAACACAATAGCATTAGTCTTAGAGTTATAAG
130 ATAATATTTTTTTAATTATAATTGTCTAATTGTAAACACAATAGCATTAGTCTTAGAGTTATAAG
926127 CAACTCATAGCATATTTTGGTAAGATTGCATAATGGA
195 CAACTCATAGCATATTTTGGTAAGATTGCATAATGGA
926164 TCCCTCTA-TTTTGTAATTTTAAAATTTAGTCTTTATATTTTTATTTTTAAAAATTTAATTTATT
1 TCCCTCTATTTTTGTAATTTTAAAATTTAGTCTTTATATTTTTATTTTTAAAAATTTAATTTATT
926228 TACCTTTCATATTTTAAAATTTAATTCTAACTATTAAATTTATTTTGTTAAATTCAAATTAATTA
66 TACCTTTCATATTTTAAAATTTAATTCTAACTATTAAATTTATTTTGTTAAATTCAAATTAATTA
926293 TAATATTTTTTTAATTATAATTGTCTAATTGTAAACACAATAGCATTAGTCTTAGAGTTATAAGC
131 TAATATTTTTTTAATTATAATTGTCTAATTGTAAACACAATAGCATTAGTCTTAGAGTTATAAGC
926358 AACTCATAGCATATTTTGGTAAGATTGCATAATGGA
196 AACTCATAGCATATTTTGGTAAGATTGCATAATGGA
926394 T
1 T
926395 TTTAGAAAAA
Statistics
Matches: 231, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
230 223 0.97
232 8 0.03
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (231 bp):
TCCCTCTATTTTTGTAATTTTAAAATTTAGTCTTTATATTTTTATTTTTAAAAATTTAATTTATT
TACCTTTCATATTTTAAAATTTAATTCTAACTATTAAATTTATTTTGTTAAATTCAAATTAATTA
TAATATTTTTTTAATTATAATTGTCTAATTGTAAACACAATAGCATTAGTCTTAGAGTTATAAGC
AACTCATAGCATATTTTGGTAAGATTGCATAATGGA
Found at i:927714 original size:21 final size:21
Alignment explanation
Indices: 927684--927734 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
927674 ACATATTATA
*
927684 AAAATTAAATAAATAATATTTC
1 AAAA-TAAATAAAAAATATTTC
* *
927706 ATAATAAATAAAAAATATTTT
1 AAAATAAATAAAAAATATTTC
927727 AAAATAAA
1 AAAATAAA
927735 AGATTTTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATAAATAAAAAATATTTC
Found at i:931054 original size:27 final size:27
Alignment explanation
Indices: 931005--931056 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
930995 AGTTTTATAT
* *
931005 ATAAAAATAATATTGATTATAATTTAA
1 ATAAAAATAAAATTAATTATAATTTAA
931032 ATAAAAATAAAATTTAATT-TAATTT
1 ATAAAAATAAAA-TTAATTATAATTT
931057 TGGATAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (27 bp):
ATAAAAATAAAATTAATTATAATTTAA
Found at i:931794 original size:24 final size:24
Alignment explanation
Indices: 931767--931842 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
931757 CCATCAATGG
931767 CACCAACCCCATCAATGAGCTCAT
1 CACCAACCCCATCAATGAGCTCAT
* * * *
931791 CACC-TCCTTCACCAATG-GCTCCT
1 CACCAACC-CCATCAATGAGCTCAT
* *
931814 ACACCAACCCCATCAATGAGTTCAG
1 -CACCAACCCCATCAATGAGCTCAT
931839 CACC
1 CACC
931843 GCCACCAATG
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
23 7 0.18
24 26 0.68
25 5 0.13
ACGTcount: A:0.29, C:0.43, G:0.09, T:0.18
Consensus pattern (24 bp):
CACCAACCCCATCAATGAGCTCAT
Found at i:939177 original size:17 final size:18
Alignment explanation
Indices: 939155--939212 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
939145 ATTTAATTAC
939155 ATAAAA-TATAAAATATT
1 ATAAAACTATAAAATATT
*
939172 ATAAAATTATAAAATTATT
1 ATAAAACTATAAAA-TATT
* *
939191 AAAAAACTAATAAAATTTT
1 ATAAAACT-ATAAAATATT
939210 ATA
1 ATA
939213 CAACACAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 15 0.44
20 6 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAAACTATAAAATATT
Found at i:939296 original size:84 final size:85
Alignment explanation
Indices: 939198--939367 Score: 333
Period size: 84 Copynumber: 2.0 Consensus size: 85
939188 ATTAAAAAAC
939198 TAATAAAATTTTATACAACACAAATTACATAAAATTGATAAATTTTATGATATTTTATTTAAAAG
1 TAATAAAATTTTATACAACACAAATTACATAAAATTGATAAATTTTATGATATTTTATTTAAAAG
939263 GAAGCTGAAACTATTGAGAT
66 GAAGCTGAAACTATTGAGAT
939283 TAATAAAA-TTTATACAACACAAATTACATAAAATTGATAAATTTTATGATATTTTATTTAAAAG
1 TAATAAAATTTTATACAACACAAATTACATAAAATTGATAAATTTTATGATATTTTATTTAAAAG
939347 GAAGCTGAAACTATTGAGAT
66 GAAGCTGAAACTATTGAGAT
939367 T
1 T
939368 TCCTTAAAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 77 0.91
85 8 0.09
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.36
Consensus pattern (85 bp):
TAATAAAATTTTATACAACACAAATTACATAAAATTGATAAATTTTATGATATTTTATTTAAAAG
GAAGCTGAAACTATTGAGAT
Found at i:942977 original size:19 final size:20
Alignment explanation
Indices: 942941--942988 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
942931 AACTACATAA
* *
942941 AATAAAAATATTATAAAA-T
1 AATAAAATTATTAAAAAACT
*
942960 TATAAAATTATTAAAAAACT
1 AATAAAATTATTAAAAAACT
942980 AATAAAATT
1 AATAAAATT
942989 TTATACAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAAATTATTAAAAAACT
Found at i:953544 original size:50 final size:50
Alignment explanation
Indices: 953497--954445 Score: 429
Period size: 50 Copynumber: 19.0 Consensus size: 50
953487 GTAAGATCCA
* * * *
953497 CCGTTGTGGCTTCAATCTTTTCAATTACGCTGTCGGGGAAATCAGATCCG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
** * * * *** * * * * **
953547 CCGTTGTGACTTCAATCTGCTCCACTACACCACCAGGGAAGTAAAATAGG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
* * ** *
953597 CCGCTGT-ATCTTCAATCTTTTTAATTGTGCTGTCGGGGAAA-CTAGATCCG
1 CCGTTGTGA-CTTCAATCTTTTCAATTGCACTGTCGGGGAAATC-AGATCTG
* * * * * * * *
953647 CCGTTGTGACTTCAATCTTCTCTACTGCACCGCCAGGGAAGTAAGATCTG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
* * * * *
953697 CCGTTGTGGCTTCAATCTTTTTAATTACGCTGTCGGGGAAACCAGATCTG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
* * * ** * * * * * * * *
953747 CTGTTGTGACTTTAACCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
* * ** *
953797 CCATTGTGACTTCAATCTTTTTAATTGCGTTGTCGGGGAAACCAGATCTG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
* ** * * * * * * *
953847 CCGTTGAGACTTCAATCTGCTCCACTGCACCG-CTAGGGAAGTAAGATCCG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTC-GGGGAAATCAGATCTG
* * ** * * * *
953897 TCGTTGTGGCTTTGATCTTTTTAATTACGCTGTCGGGGAAACCAGATCTG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
** * * * * * * *
953947 CCGTTGTGACTTCAATCTGCTCCACTGCACCG-CTAGGGAAGTAAGATCCG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTC-GGGGAAATCAGATCTG
* * * * *
953997 CCATTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATCTG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
* * ** * * * * ** *
954047 CTGTCGT-AGCTTCAATCTGCTCCACTACACCGTCAAGGAAAGTAAGATCTG
1 CCGTTGTGA-CTTCAATCTTTTCAATTGCACTGTCGGGGAAA-TCAGATCTG
* * * * * *
954098 CCGTTGTGGCTTTAATCTTTTTAATTACGCTGTCGGGGAAACCAGATCTG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
** * * * * * * * *
954148 CCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
* * * * * *
954198 TCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTTGGGGAAACCAGATCTG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
* * * * * * * * *
954248 TCGTTGAGACTTCAAACTGCTCCAA-TGCACCG-CTAGGGAAGTAAGATCTG
1 CCGTTGTGACTTCAATCT-TTTCAATTGCACTGTC-GGGGAAATCAGATCTG
* * * * * *
954298 GCGTTGTGGCTTCGATCTTTTTAATTGCGCTGTCGGGGAAACCAGATCTG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
** * * * * * * * *
954348 CCGTTGTGACTTCAATCTGCTCCACTACACCG-CTAGGGAAGTAAGATCCG
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTC-GGGGAAATCAGATCTG
* * * *
954398 CCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACCAGATC
1 CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATC
954446 CGATGTCGTA
Statistics
Matches: 604, Mismatches: 278, Indels: 34
0.66 0.30 0.04
Matches are distributed among these distances:
49 7 0.01
50 555 0.92
51 42 0.07
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (50 bp):
CCGTTGTGACTTCAATCTTTTCAATTGCACTGTCGGGGAAATCAGATCTG
Found at i:953610 original size:100 final size:100
Alignment explanation
Indices: 953440--954518 Score: 1433
Period size: 100 Copynumber: 10.8 Consensus size: 100
953430 CGAGGAAATA
* * * ** * * * * *
953440 AGATCCGCCGTCGTAACTTCAATCTATTCAACTGCACCGCTAAGGAGGTAAGATCCACCGTTGTG
1 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTG
* * *
953505 GCTTCAATCTTTTCAATTACGCTGTCGGGGAAATC
66 GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
* * * * ** * *
953540 AGATCCGCCGTTGTGACTTCAATCTGCTCCACTACACCACCAGGGAAGTAAAATAGGCCGCTGTA
1 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTG
* * *
953605 TCTTCAATCTTTTTAATTGTGCTGTCGGGGAAACT
66 GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
* * * *
953640 AGATCCGCCGTTGTGACTTCAATCTTCTCTACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTG
1 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTG
*
953705 GCTTCAATCTTTTTAATTACGCTGTCGGGGAAACC
66 GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
* * * *
953740 AGATCTGCTGTTGTGACTTTAACCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCATTGTG
1 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTG
* *
953805 ACTTCAATCTTTTTAATTGCGTTGTCGGGGAAACC
66 GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
* * *
953840 AGATCTGCCGTTGAGACTTCAATCTGCTCCACTGCACCGCTAGGGAAGTAAGATCCGTCGTTGTG
1 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTG
** *
953905 GCTTTGATCTTTTTAATTACGCTGTCGGGGAAACC
66 GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
* *
953940 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCTAGGGAAGTAAGATCCGCCATTGTG
1 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTG
**
954005 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAACC
66 GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
* * * * * *
954040 AGATCTGCTGTCGT-AGCTTCAATCTGCTCCACTACACCGTCAAGGAAAGTAAGATCTGCCGTTG
1 AGATCTGCCGTTGTGA-CTTCAATCTGCTCCACTGCACCG-CCAGGGAAGTAAGATCCGCCGTTG
* *
954104 TGGCTTTAATCTTTTTAATTACGCTGTCGGGGAAACC
64 TGGCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
*
954141 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGTCGTTGTG
1 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTG
*
954206 GCTTCAATCTTTTTAATTGCGCTGTTGGGGAAACC
66 GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
* * * * * * *
954241 AGATCTGTCGTTGAGACTTCAAACTGCTCCAATGCACCGCTAGGGAAGTAAGATCTGGCGTTGTG
1 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTG
*
954306 GCTTCGATCTTTTTAATTGCGCTGTCGGGGAAACC
66 GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
* *
954341 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTACACCGCTAGGGAAGTAAGATCCGCCGTTGTG
1 AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTG
**
954406 GCTTCAATCTTTTTAATTGCAATGTCGGGGAAACC
66 GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
* ** * * * * * *
954441 AGATCCGATGTCGT-AGCTTCAATCTGCTCCACTACACCGCCAAGGAAATAAGATCTGTCGTTGT
1 AGATCTGCCGTTGTGA-CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGT
954505 GGCTTCAATCTTTT
65 GGCTTCAATCTTTT
954519 CCTCTGTAAT
Statistics
Matches: 860, Mismatches: 115, Indels: 8
0.87 0.12 0.01
Matches are distributed among these distances:
99 2 0.00
100 770 0.90
101 87 0.10
102 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (100 bp):
AGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCGCCGTTGTG
GCTTCAATCTTTTTAATTGCGCTGTCGGGGAAACC
Found at i:954510 original size:50 final size:50
Alignment explanation
Indices: 953433--954515 Score: 396
Period size: 50 Copynumber: 21.6 Consensus size: 50
953423 ACAATGTCGA
* * ** ** * *
953433 GGAAATAAGATCCGCCGTCGTAACTTCAATCTATTCAACTGCACCG-CTAA
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTC-AG
** ** ** * * * * * *
953483 GGAGGTAAGATCCACCGTTGTGGCTTCAATCTTTTCAATTACGCTGTCGG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
* * * * **
953533 GGAAATCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACACCACCAG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
* * ** * ** ** ** * ** * *
953583 GGAAGTAAAATAGGCCGCTGTATCTTCAATCTTTTTAATTGTGCTGTCGG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
* * * * *
953633 GGAAACT-AGATCCGCCGTTGTGACTTCAATCTTCTCTACTGCACCGCCAG
1 GGAAA-TAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
* ** ** * * * * *
953683 GGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAATTACGCTGTCGG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
** * * * * *
953733 GGAAACCAGATCTGCTGTTGTGACTTTAACCTGCTCCACTGCACCGCCAG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
* * * * ** ** * *** *
953783 GGAAGTAAGATCCGCCATTGTGACTTCAATCTTTTTAATTGCGTTGTCGG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
** * *
953833 GGAAACCAGATCTGCCGTTGAGACTTCAATCTGCTCCACTGCACCG-CTAG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTC-AG
* * * ** ** ** * * * * *
953883 GGAAGTAAGATCCGTCGTTGTGGCTTTGATCTTTTTAATTACGCTGTCGG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
** *
953933 GGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCG-CTAG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTC-AG
* * * ** ** * ** *
953983 GGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTTAATTGCAATGTCGG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
** * * * * *
954033 GGAAACCAGATCTGCTGTCGTAGCTTCAATCTGCTCCACTACACCGTCAA
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
* ** ** * * * * *
954083 GGAAAGTAAGATCTGCCGTTGTGGCTTTAATCTTTTTAATTACGCTGTCGG
1 GGAAA-TAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
** * *
954134 GGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCACTGCACCGCCAG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
* * * ** ** * * * **
954184 GGAAGTAAGATCCGTCGTTGTGGCTTCAATCTTTTTAATTGCGCTGTTGG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
** * * * * *
954234 GGAAACCAGATCTGTCGTTGAGACTTCAAACTGCTCCAATGCACCG-CTAG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTC-AG
* * * ** ** * * * *
954284 GGAAGTAAGATCTGGCGTTGTGGCTTCGATCTTTTTAATTGCGCTGTCGG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
** * *
954334 GGAAACCAGATCTGCCGTTGTGACTTCAATCTGCTCCACTACACCG-CTAG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTC-AG
* * ** ** * ** *
954384 GGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGG
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
** * ** * * * * *
954434 GGAAACCAGATCCGATGTCGTAGCTTCAATCTGCTCCACTACACCGCCAA
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
*
954484 GGAAATAAGATCTGTCGTTGTGGCTTCAATCT
1 GGAAATAAGATCTGCCGTTGTGGCTTCAATCT
954516 TTTCCTCTGT
Statistics
Matches: 698, Mismatches: 323, Indels: 24
0.67 0.31 0.02
Matches are distributed among these distances:
49 4 0.01
50 653 0.94
51 41 0.06
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (50 bp):
GGAAATAAGATCTGCCGTTGTGGCTTCAATCTGCTCCACTGCACCGTCAG
Found at i:954830 original size:88 final size:88
Alignment explanation
Indices: 954717--955291 Score: 704
Period size: 88 Copynumber: 6.5 Consensus size: 88
954707 AAGACTGATG
* * * * * * *
954717 TCTTCGATTTGCTTCGCTGCCAGTACAGGAAGGCAAGATCTGCCATTTTTTACCTACTCAACTGC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTAC
*
954782 TGCCCAGGGAGACAAGGCTGGTA
66 TACCCAGGGAGACAAGGCTGGTA
954805 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTAC
954870 TACCCAGGGAGACAAGGCTGGTA
66 TACCCAGGGAGACAAGGCTGGTA
*
954893 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCTACTCCACTA-
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTAC
** *
954957 TTGCGAGGGAGACAAGGCTGGTA
66 TACCCAGGGAGACAAGGCTGGTA
* * ** * * *
954980 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTAC
* * * *
955045 AAACCCAGGGAGGCAAGGTTGGTG
66 -TACCCAGGGAGACAAGGCTGGTA
* * * * * ** * *
955069 TCTTTGATATGCTTCAT-TGTCAGTACAAGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTA
1 TCTTCGATCTGCTTC-TCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTA
* * ** *
955133 CAAACCCAGGGAGGCAAGATTGGTG
65 C-TACCCAGGGAGACAAGGCTGGTA
* * * * * *
955158 TCTTTGATCTGCTTCGCTGTCAGTACAGGAAGGTAAAATCTGTTATTTTCAACCTACTCCACTAC
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTAC
* *
955223 TGCCCAAGGAGACAAGGCTGGTA
66 TACCCAGGGAGACAAGGCTGGTA
955246 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTAT
1 TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTAT
955292 CTTCAGTCTG
Statistics
Matches: 430, Mismatches: 53, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
87 78 0.18
88 200 0.47
89 151 0.35
90 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (88 bp):
TCTTCGATCTGCTTCTCTGTCAGTACAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTAC
TACCCAGGGAGACAAGGCTGGTA
Found at i:955060 original size:45 final size:45
Alignment explanation
Indices: 955005--955152 Score: 115
Period size: 45 Copynumber: 3.3 Consensus size: 45
954995 TCTGTCAGTA
955005 CAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAAACC
1 CAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAAACC
* * * * * * * * ** *
955050 CAGGGAGGCAAGGT-TGGTGTCTT-TGATATGCTTCATTGTCAGTA--
1 CAGGAAGGCAAGATCTGCTATATTCAG-TCTGCTCCGCTG-CA-AACC
* *
955094 CAAGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTACAAACC
1 CAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAAACC
*
955139 CAGGGAGGCAAGAT
1 CAGGAAGGCAAGAT
955153 TGGTGTCTTT
Statistics
Matches: 70, Mismatches: 26, Indels: 14
0.64 0.24 0.13
Matches are distributed among these distances:
43 2 0.03
44 27 0.39
45 39 0.56
46 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (45 bp):
CAGGAAGGCAAGATCTGCTATATTCAGTCTGCTCCGCTGCAAACC
Found at i:956576 original size:15 final size:15
Alignment explanation
Indices: 956564--956596 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
956554 CCACTTTTAC
956564 TTTTTCCATTTTTCA
1 TTTTTCCATTTTTCA
956579 TTTTT-CA-TTTTCA
1 TTTTTCCATTTTTCA
956592 TTTTT
1 TTTTT
956597 TTCACATCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.61
14 2 0.11
15 5 0.28
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTCCATTTTTCA
Found at i:956577 original size:8 final size:7
Alignment explanation
Indices: 956564--956596 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
956554 CCACTTTTAC
956564 TTTTTCCA
1 TTTTT-CA
956572 TTTTTCA
1 TTTTTCA
956579 TTTTTCA
1 TTTTTCA
956586 -TTTTCA
1 TTTTTCA
956592 TTTTT
1 TTTTT
956597 TTCACATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 13 0.54
8 5 0.21
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:961860 original size:18 final size:18
Alignment explanation
Indices: 961839--961885 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
961829 ATATTTGGAT
961839 TATAAAATATATA-AAAA
1 TATAAAATATATATAAAA
961856 CTATAAAA-ATATTATAAAA
1 -TATAAAATATA-TATAAAA
961875 TAT-AAATATAT
1 TATAAAATATAT
961886 GTACGTGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.27
18 15 0.58
19 4 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
TATAAAATATATATAAAA
Found at i:973398 original size:394 final size:394
Alignment explanation
Indices: 972670--973447 Score: 1538
Period size: 394 Copynumber: 2.0 Consensus size: 394
972660 CCTCTCCAGG
*
972670 TTTTTTTTCGATCTTTTATTTTACTTTAAGATTCAATCATAAAATGAAGTAACGAATTACCTTAT
1 TTTTTTTTCGATCTATTATTTTACTTTAAGATTCAATCATAAAATGAAGTAACGAATTACCTTAT
972735 AATGATCCTTCTGACATGTCTTGTTGCAGGTCCCAAGATTACTGATCCAGCTTTGCTGAGGAAGC
66 AATGATCCTTCTGACATGTCTTGTTGCAGGTCCCAAGATTACTGATCCAGCTTTGCTGAGGAAGC
972800 AAGCAAAGGAACTCGTAAACAACTGGCCTGAAGAGTTAATTAGATTGATTGATCTCAGCCCAGAT
131 AAGCAAAGGAACTCGTAAACAACTGGCCTGAAGAGTTAATTAGATTGATTGATCTCAGCCCAGAT
972865 GAGACAATCAGTAAAACCCCGCTTGTTGATCGTTGGTTATGGCCGGGTTTAAGCCCTCCTGCTTC
196 GAGACAATCAGTAAAACCCCGCTTGTTGATCGTTGGTTATGGCCGGGTTTAAGCCCTCCTGCTTC
972930 AACCGGCAAAGTAGTGCTGGTTGGGGATGCTTGGCATCCGATGACTCCCAATCTCGGGCAAGGTG
261 AACCGGCAAAGTAGTGCTGGTTGGGGATGCTTGGCATCCGATGACTCCCAATCTCGGGCAAGGTG
972995 CTTGTTGTGCTTTAGAGGATTCTGTCATACTGACCAGGAAATTAGCTGATGCAATTAAACTCCAG
326 CTTGTTGTGCTTTAGAGGATTCTGTCATACTGACCAGGAAATTAGCTGATGCAATTAAACTCCAG
973060 GTTT
391 GTTT
973064 TTTTTTTTCGATCTATTATTTTACTTTAAGATTCAATCATAAAATGAAGTAACGAATTACCTTAT
1 TTTTTTTTCGATCTATTATTTTACTTTAAGATTCAATCATAAAATGAAGTAACGAATTACCTTAT
973129 AATGATCCTTCTGACATGTCTTGTTGCAGGTCCCAAGATTACTGATCCAGCTTTGCTGAGGAAGC
66 AATGATCCTTCTGACATGTCTTGTTGCAGGTCCCAAGATTACTGATCCAGCTTTGCTGAGGAAGC
973194 AAGCAAAGGAACTCGTAAACAACTGGCCTGAAGAGTTAATTAGATTGATTGATCTCAGCCCAGAT
131 AAGCAAAGGAACTCGTAAACAACTGGCCTGAAGAGTTAATTAGATTGATTGATCTCAGCCCAGAT
*
973259 GAGACGATCAGTAAAACCCCGCTTGTTGATCGTTGGTTATGGCCGGGTTTAAGCCCTCCTGCTTC
196 GAGACAATCAGTAAAACCCCGCTTGTTGATCGTTGGTTATGGCCGGGTTTAAGCCCTCCTGCTTC
973324 AACCGGCAAAGTAGTGCTGGTTGGGGATGCTTGGCATCCGATGACTCCCAATCTCGGGCAAGGTG
261 AACCGGCAAAGTAGTGCTGGTTGGGGATGCTTGGCATCCGATGACTCCCAATCTCGGGCAAGGTG
973389 CTTGTTGTGCTTTAGAGGATTCTGTCATACTGACCAGGAAATTAGCTGATGCAATTAAA
326 CTTGTTGTGCTTTAGAGGATTCTGTCATACTGACCAGGAAATTAGCTGATGCAATTAAA
973448 TCCGGACCAA
Statistics
Matches: 382, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
394 382 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (394 bp):
TTTTTTTTCGATCTATTATTTTACTTTAAGATTCAATCATAAAATGAAGTAACGAATTACCTTAT
AATGATCCTTCTGACATGTCTTGTTGCAGGTCCCAAGATTACTGATCCAGCTTTGCTGAGGAAGC
AAGCAAAGGAACTCGTAAACAACTGGCCTGAAGAGTTAATTAGATTGATTGATCTCAGCCCAGAT
GAGACAATCAGTAAAACCCCGCTTGTTGATCGTTGGTTATGGCCGGGTTTAAGCCCTCCTGCTTC
AACCGGCAAAGTAGTGCTGGTTGGGGATGCTTGGCATCCGATGACTCCCAATCTCGGGCAAGGTG
CTTGTTGTGCTTTAGAGGATTCTGTCATACTGACCAGGAAATTAGCTGATGCAATTAAACTCCAG
GTTT
Found at i:974754 original size:22 final size:22
Alignment explanation
Indices: 974724--974765 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
974714 ACAGCAAAAC
*
974724 AGGCTTTTAGCGGCCTTTTTTT
1 AGGCCTTTAGCGGCCTTTTTTT
*
974746 AGGCCTTTAGCGGCGTTTTT
1 AGGCCTTTAGCGGCCTTTTT
974766 ATGCGCCGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.10, C:0.19, G:0.26, T:0.45
Consensus pattern (22 bp):
AGGCCTTTAGCGGCCTTTTTTT
Found at i:974922 original size:43 final size:43
Alignment explanation
Indices: 974852--975045 Score: 289
Period size: 43 Copynumber: 4.5 Consensus size: 43
974842 AAAAAGCGCT
* * * *
974852 GCTAAAGAACATTACATTTAGCAGCGCTTCTATCACAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCC
* *
974895 GCTAAAGAACATGACCTCTAGCGGCGCTTTTATCTCAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCC
* * *
974938 GTTAAAGAACATGACCTCTAGCGGCGCTTTTATCACAAATGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCC
*
974981 GTTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCC
1 GCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCC
*
975024 GCTAAATAACATGACCTTTAGC
1 GCTAAAGAACATGACCTTTAGC
975046 CTCATTTATG
Statistics
Matches: 138, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 138 1.00
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (43 bp):
GCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACGCC
Found at i:983708 original size:9 final size:9
Alignment explanation
Indices: 983694--983970 Score: 129
Period size: 9 Copynumber: 30.0 Consensus size: 9
983684 TAAGTATAAT
983694 TAAGTTATG
1 TAAGTTATG
983703 TAAGTTATGG
1 TAAGTTAT-G
* * *
983713 TATGATATA
1 TAAGTTATG
983722 TAAGTTAT-
1 TAAGTTATG
983730 TAAGTTATG
1 TAAGTTATG
*
983739 TAAGTTATA
1 TAAGTTATG
*
983748 TGAGTTATG
1 TAAGTTATG
983757 TAAGTTATG
1 TAAGTTATG
* * *
983766 ATATGATATA
1 -TAAGTTATG
*
983776 T-A--TATA
1 TAAGTTATG
983782 TAAGTTAT-
1 TAAGTTATG
983790 TAAGTTATG
1 TAAGTTATG
*
983799 TATGTTATG
1 TAAGTTATG
983808 TAAGTTATG
1 TAAGTTATG
* *
983817 ATATGATATATATA
1 -TA--A-GT-TATG
983831 TAAGTTAT-
1 TAAGTTATG
*
983839 TAAGTTAAG
1 TAAGTTATG
*
983848 ATCCCAAGTCT-TT
1 -T---AAGT-TATG
* * *
983861 TATAATTCTT
1 TA-AGTTATG
983871 TAAAGTTATG
1 T-AAGTTATG
*
983881 TAAATTATG
1 TAAGTTATG
983890 TAAGTTATG
1 TAAGTTATG
*
983899 TAAGTTTTG
1 TAAGTTATG
* * *
983908 ATATGATATA
1 -TAAGTTATG
*
983918 T-ATTTATG
1 TAAGTTATG
983926 TAAGTTATG
1 TAAGTTATG
*
983935 TAAATTATG
1 TAAGTTATG
*
983944 CAAGTTATG
1 TAAGTTATG
*
983953 TAACTTATG
1 TAAGTTATG
983962 TAAGTTATG
1 TAAGTTATG
983971 ATATATATTT
Statistics
Matches: 202, Mismatches: 43, Indels: 46
0.69 0.15 0.16
Matches are distributed among these distances:
6 5 0.02
7 1 0.00
8 27 0.13
9 122 0.60
10 32 0.16
11 2 0.01
12 2 0.01
13 7 0.03
14 4 0.02
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:983815 original size:51 final size:51
Alignment explanation
Indices: 983696--983845 Score: 209
Period size: 51 Copynumber: 2.9 Consensus size: 51
983686 AGTATAATTA
*
983696 AGTTATGTAAGTTATGGTATGATATATA-AGTTATTAAGTTATGTAAGTTATATG
1 AGTTATGTAAGTTATGATATGATATATATA--TA-TAAGTTAT-TAAGTTATATG
*
983750 AGTTATGTAAGTTATGATATGATATATATATATAAGTTATTAAGTTATGT-
1 AGTTATGTAAGTTATGATATGATATATATATATAAGTTATTAAGTTATATG
983800 ATGTTATGTAAGTTATGATATG--ATATATATATAAGTTATTAAGTTA
1 A-GTTATGTAAGTTATGATATGATATATATATATAAGTTATTAAGTTA
983846 AGATCCCAAG
Statistics
Matches: 92, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
49 24 0.26
50 1 0.01
51 29 0.32
52 8 0.09
53 2 0.02
54 27 0.29
55 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.45
Consensus pattern (51 bp):
AGTTATGTAAGTTATGATATGATATATATATATAAGTTATTAAGTTATATG
Found at i:983934 original size:54 final size:56
Alignment explanation
Indices: 983873--983988 Score: 166
Period size: 54 Copynumber: 2.1 Consensus size: 56
983863 TAATTCTTTA
* *
983873 AAGTTATGTAAATTATGTAAGTTATGTAAGTT-T-T-GATATGATATATATTTATGT
1 AAGTTATGTAAATTATGCAAGTTATGTAACTTATGTAGATATGATATATATTT-TGT
*
983927 AAGTTATGTAAATTATGCAAGTTATGTAACTTATGTAAGTTATGATATATATTTTGT
1 AAGTTATGTAAATTATGCAAGTTATGTAACTTATGT-AGATATGATATATATTTTGT
983984 AAGTT
1 AAGTT
983989 TTAAAAACAT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
54 30 0.55
55 1 0.02
56 1 0.02
57 8 0.15
58 15 0.27
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (56 bp):
AAGTTATGTAAATTATGCAAGTTATGTAACTTATGTAGATATGATATATATTTTGT
Found at i:984183 original size:27 final size:27
Alignment explanation
Indices: 984153--984235 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 27
984143 AATCAAATAT
*
984153 TAAGTTTTGATATGATATATATTTATG
1 TAAGTTATGATATGATATATATTTATG
* * * *
984180 TAAGTTATGTAAATTATGTA-AGTTATG
1 TAAGTTATG-ATATGATATATATTTATG
* *
984207 TAAGTTGTGATATGATTTATATTTATG
1 TAAGTTATGATATGATATATATTTATG
984234 TA
1 TA
984236 TTATGTAAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
26 7 0.16
27 30 0.68
28 7 0.16
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (27 bp):
TAAGTTATGATATGATATATATTTATG
Found at i:984187 original size:9 final size:9
Alignment explanation
Indices: 984175--984258 Score: 77
Period size: 9 Copynumber: 9.6 Consensus size: 9
984165 TGATATATAT
984175 TTATGTAAG
1 TTATGTAAG
*
984184 TTATGTAAA
1 TTATGTAAG
984193 TTATGTAAG
1 TTATGTAAG
984202 TTATGTAAG
1 TTATGTAAG
*
984211 TTGTG-ATA-
1 TTATGTA-AG
* * *
984219 TGATTTATAT
1 TTATGTA-AG
984229 TTATGT-A-
1 TTATGTAAG
984236 TTATGTAAG
1 TTATGTAAG
984245 TTATGTAAG
1 TTATGTAAG
984254 TTATG
1 TTATG
984259 ATCCAAGTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
7 6 0.10
8 5 0.08
9 47 0.76
10 4 0.06
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:984218 original size:54 final size:52
Alignment explanation
Indices: 984153--984258 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 52
984143 AATCAAATAT
*
984153 TAAGTTTTGATATGATATATATTTATGTAAGTTATGTAAATTATGTAAGTTATG
1 TAAGTTGTGATATGATATATATTTATGT-A-TTATGTAAATTATGTAAGTTATG
* *
984207 TAAGTTGTGATATGATTTATATTTATGTATTATGTAAGTTATGTAAGTTATG
1 TAAGTTGTGATATGATATATATTTATGTATTATGTAAATTATGTAAGTTATG
984259 ATCCAAGTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 22 0.45
53 1 0.02
54 26 0.53
ACGTcount: A:0.33, C:0.00, G:0.18, T:0.49
Consensus pattern (52 bp):
TAAGTTGTGATATGATATATATTTATGTATTATGTAAATTATGTAAGTTATG
Found at i:985956 original size:25 final size:23
Alignment explanation
Indices: 985903--985975 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
985893 AATTTATATC
* * *
985903 AATTTTAAATAATTAATTTTTGA
1 AATTTTATATAATTAAATTTTAA
*
985926 AATTTTATGTAATATAAATTTTAA
1 AATTTTATATAAT-TAAATTTTAA
985950 AATTTTTATATAATT---TTTTAA
1 AA-TTTTATATAATTAAATTTTAA
985971 AATTT
1 AATTT
985976 AAACTTTAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
20 3 0.07
21 8 0.19
23 11 0.26
24 11 0.26
25 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (23 bp):
AATTTTATATAATTAAATTTTAA
Found at i:985962 original size:20 final size:21
Alignment explanation
Indices: 985937--985975 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
985927 ATTTTATGTA
985937 ATATAA-ATTTTAAAATTTTT
1 ATATAATATTTTAAAATTTTT
*
985957 ATATAATTTTTTAAAATTT
1 ATATAATATTTTAAAATTT
985976 AAACTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATAATATTTTAAAATTTTT
Found at i:986133 original size:7 final size:7
Alignment explanation
Indices: 986121--986189 Score: 54
Period size: 7 Copynumber: 9.7 Consensus size: 7
986111 ACATGAACTA
986121 TAAACCC
1 TAAACCC
986128 TAAACCCC
1 TAAA-CCC
986136 T-AACCC
1 TAAACCC
*
986142 TTAACCCC
1 -TAAACCC
986150 T-AACACC
1 TAAAC-CC
*
986157 TAAACCT
1 TAAACCC
986164 TAAACCC
1 TAAACCC
986171 T-AACCC
1 TAAACCC
*
986177 TTAAACCA
1 -TAAACCC
986185 TAAAC
1 TAAAC
986190 TATAAATCAT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
6 10 0.20
7 25 0.50
8 15 0.30
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:986140 original size:14 final size:14
Alignment explanation
Indices: 986123--986162 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
986113 ATGAACTATA
986123 AACCCTAAACCCCT
1 AACCCTAAACCCCT
*
986137 AACCCTTAACCCCT
1 AACCCTAAACCCCT
986151 AACACCTAAACC
1 AAC-CCTAAACC
986163 TTAAACCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.38, C:0.47, G:0.00, T:0.15
Consensus pattern (14 bp):
AACCCTAAACCCCT
Found at i:986147 original size:21 final size:22
Alignment explanation
Indices: 986121--986189 Score: 72
Period size: 21 Copynumber: 3.2 Consensus size: 22
986111 ACATGAACTA
* *
986121 TAAACCCTAAACCCCTAACCCT
1 TAAACCCTAAACACCTAAACCT
*
986143 TAACCCCT-AACACCTAAACCT
1 TAAACCCTAAACACCTAAACCT
*
986164 TAAACCCT-AAC-CCTTAAACCA
1 TAAACCCTAAACACC-TAAACCT
986185 TAAAC
1 TAAAC
986190 TATAAATCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 2 0.05
21 32 0.78
22 7 0.17
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.19
Consensus pattern (22 bp):
TAAACCCTAAACACCTAAACCT
Found at i:986607 original size:41 final size:39
Alignment explanation
Indices: 986557--986671 Score: 122
Period size: 41 Copynumber: 2.9 Consensus size: 39
986547 TTTGCGGCAT
*
986557 TTTTCAAAAAGCGCTGCTAATGCTCGATCTATAGCAACG
1 TTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAACG
* * * * **
986596 CTTTCTGAAAAAACGCCACTAAAGCTCGATCTATAGCGGCG
1 -TTT-TCAAAAAGCGCCGCTAATGCTCGATCTATAGCAACG
* * *
986637 TTTTCAAGAAGCGCCGCTATTGCTTGATCTATAGC
1 TTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGC
986672 GGCGATTTTT
Statistics
Matches: 60, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
39 25 0.42
40 6 0.10
41 29 0.48
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (39 bp):
TTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCAACG
Found at i:986848 original size:40 final size:39
Alignment explanation
Indices: 986749--986850 Score: 123
Period size: 39 Copynumber: 2.6 Consensus size: 39
986739 TTTGCGACGC
* * *
986749 TTTTCAAAAAGCACCGCCAATGGTCGACCTATAGCGGCG
1 TTTTCAAAAAGCACCGCTAATGCTCGACCTATAGCAGCG
* * *
986788 TGTTCAAAAAGCACCACTAATGCTCGATCTATAGCAGCG
1 TTTTCAAAAAGCACCGCTAATGCTCGACCTATAGCAGCG
* *
986827 TTTTTCAAAATGCGCCGCTAATGC
1 -TTTTCAAAAAGCACCGCTAATGC
986851 CACTAAAGCT
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
39 33 0.63
40 19 0.37
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (39 bp):
TTTTCAAAAAGCACCGCTAATGCTCGACCTATAGCAGCG
Found at i:993388 original size:5 final size:5
Alignment explanation
Indices: 993377--993416 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
993367 TGAGCGTTCG
* *
993377 ATCGA GTCGA GTCGA ATCGA ATCGA ATCGA ATCGA ATCGA
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA
993417 GTGAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (5 bp):
ATCGA
Found at i:993805 original size:27 final size:26
Alignment explanation
Indices: 993767--993834 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
993757 TTATATATTT
*
993767 TTTTAAAATTTTTTAAAAAATATAAA
1 TTTTAAATTTTTTTAAAAAATATAAA
* * * * *
993793 TTTTAGAATTTTTATAAATATTTTGAA
1 TTTTA-AATTTTTTTAAAAAATATAAA
993820 TTTTAAAATTTTTTT
1 TTTT-AAATTTTTTT
993835 GTATTTTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 5 0.15
27 27 0.82
28 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (26 bp):
TTTTAAATTTTTTTAAAAAATATAAA
Found at i:993822 original size:19 final size:18
Alignment explanation
Indices: 993787--993831 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
993777 TTTTAAAAAA
993787 TATAAATTTTAGAATTTT
1 TATAAATTTTAGAATTTT
*
993805 TATAAATATTTTGAA-TTT
1 TATAAAT-TTTAGAATTTT
993823 TA-AAATTTT
1 TATAAATTTT
993832 TTTGTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 3 0.12
17 4 0.16
18 12 0.48
19 6 0.24
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (18 bp):
TATAAATTTTAGAATTTT
Found at i:993961 original size:17 final size:16
Alignment explanation
Indices: 993941--993984 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 16
993931 CTAACTATTC
993941 TATAAATTTTGAATTTT
1 TATAAATTTTGAA-TTT
993958 TATAAATATTTTGAATTT
1 TAT-AA-ATTTTGAATTT
993976 TA-AAATTTT
1 TATAAATTTT
993985 TTTGTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.20
16 2 0.08
17 3 0.12
18 7 0.28
19 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
TATAAATTTTGAATTT
Found at i:993974 original size:153 final size:154
Alignment explanation
Indices: 993787--994093 Score: 607
Period size: 153 Copynumber: 2.0 Consensus size: 154
993777 TTTTAAAAAA
993787 TATAAATTTTAGAATTTTTATAAATATTTTGAATTTTAAAATTTTTTTGTATTTTTTGAAGATTA
1 TATAAATTTTAGAATTTTTATAAATATTTTGAATTTTAAAATTTTTTTGTATTTTTTGAAGATTA
993852 TTTTGTATTATTTTATAATTTTATTAAGAGACTAATTTGCTCAATTTCAAACTTGACAGGAACTA
66 TTTTGTATTATTTTATAATTTTATTAAGAGACTAATTTGCTCAATTTCAAACTTGACAGGAACTA
993917 ACTAATCTATTATTCTAACTATTC
131 ACTAATCTATTATTCTAACTATTC
993941 TATAAATTTT-GAATTTTTATAAATATTTTGAATTTTAAAATTTTTTTGTATTTTTTGAAGATTA
1 TATAAATTTTAGAATTTTTATAAATATTTTGAATTTTAAAATTTTTTTGTATTTTTTGAAGATTA
994005 TTTTGTATTATTTTATAATTTTATTAAGAGACTAATTTGCTCAATTTCAAACTTGACAGGAACTA
66 TTTTGTATTATTTTATAATTTTATTAAGAGACTAATTTGCTCAATTTCAAACTTGACAGGAACTA
994070 ACTAATCTATTATTCTAACTATTC
131 ACTAATCTATTATTCTAACTATTC
994094 GAGTTATTTG
Statistics
Matches: 153, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
153 143 0.93
154 10 0.07
ACGTcount: A:0.34, C:0.08, G:0.08, T:0.50
Consensus pattern (154 bp):
TATAAATTTTAGAATTTTTATAAATATTTTGAATTTTAAAATTTTTTTGTATTTTTTGAAGATTA
TTTTGTATTATTTTATAATTTTATTAAGAGACTAATTTGCTCAATTTCAAACTTGACAGGAACTA
ACTAATCTATTATTCTAACTATTC
Found at i:993988 original size:18 final size:18
Alignment explanation
Indices: 993946--993985 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
993936 TATTCTATAA
993946 ATTTTGAATTTTTATAAAT
1 ATTTTGAA-TTTTATAAAT
993965 ATTTTGAATTTTA-AAAT
1 ATTTTGAATTTTATAAAT
993982 -TTTT
1 ATTTT
993986 TTGTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.19
17 4 0.19
18 5 0.24
19 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
ATTTTGAATTTTATAAAT
Found at i:1024267 original size:39 final size:39
Alignment explanation
Indices: 1024213--1024291 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1024203 TGAAAACTTT
1024213 ATCCTCACCTAATCCTTTGTTCATTGGCCATACAGTAAA
1 ATCCTCACCTAATCCTTTGTTCATTGGCCATACAGTAAA
1024252 ATCCTCACCTAATCCTTTGTTCATTGGCCATACAGTAAA
1 ATCCTCACCTAATCCTTTGTTCATTGGCCATACAGTAAA
1024291 A
1 A
1024292 GCCATTGGGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.28, G:0.10, T:0.33
Consensus pattern (39 bp):
ATCCTCACCTAATCCTTTGTTCATTGGCCATACAGTAAA
Found at i:1028277 original size:10 final size:10
Alignment explanation
Indices: 1028262--1028288 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1028252 ATATAAAGCG
1028262 TATAAAAATA
1 TATAAAAATA
1028272 TATAAAAATA
1 TATAAAAATA
1028282 TATAAAA
1 TATAAAA
1028289 TTACTTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TATAAAAATA
Found at i:1035686 original size:16 final size:15
Alignment explanation
Indices: 1035660--1035698 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1035650 TTTTGGATAA
*
1035660 TTTAGAATTTTTAGAG
1 TTTA-AATTTTTAAAG
1035676 TTTTAAATTTTTAAAG
1 -TTTAAATTTTTAAAG
1035692 TTTAAAT
1 TTTAAAT
1035699 CATTTTGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 10 0.48
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.54
Consensus pattern (15 bp):
TTTAAATTTTTAAAG
Found at i:1046293 original size:6 final size:6
Alignment explanation
Indices: 1046282--1046312 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1046272 TGAATACTCC
*
1046282 CTTCAT CTTCAT CTTCAT CTTCTT CTTCAT C
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT C
1046313 CTTTTCCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.35, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTCAT
Found at i:1051586 original size:25 final size:25
Alignment explanation
Indices: 1051548--1051595 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
1051538 GAAATTAGAA
1051548 AAATAAAAGAACTAAATTATAAAAG
1 AAATAAAAGAACTAAATTATAAAAG
* * *
1051573 AAATATAAGGACTAAATTCTAAA
1 AAATAAAAGAACTAAATTATAAA
1051596 TTATTGAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.62, C:0.06, G:0.08, T:0.23
Consensus pattern (25 bp):
AAATAAAAGAACTAAATTATAAAAG
Found at i:1057811 original size:16 final size:18
Alignment explanation
Indices: 1057780--1057816 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
1057770 CACGATAGCT
*
1057780 TTTATCTTTATCTTCATC
1 TTTATCTTTATCTTCACC
1057798 TTTAT-TTT-TCTTCACC
1 TTTATCTTTATCTTCACC
1057814 TTT
1 TTT
1057817 TTCCCCATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTATCTTTATCTTCACC
Found at i:1063522 original size:12 final size:12
Alignment explanation
Indices: 1063505--1063532 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1063495 TTCTCTGGCA
1063505 TCACTGGTGCCT
1 TCACTGGTGCCT
1063517 TCACTGGTGCCT
1 TCACTGGTGCCT
1063529 TCAC
1 TCAC
1063533 CCGAATGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.11, C:0.36, G:0.21, T:0.32
Consensus pattern (12 bp):
TCACTGGTGCCT
Found at i:1064183 original size:361 final size:364
Alignment explanation
Indices: 1063518--1064399 Score: 1564
Period size: 361 Copynumber: 2.4 Consensus size: 364
1063508 CTGGTGCCTT
* * * * ** * *
1063518 CACTGGTGCCTTCACCCGAATGACCACATATCTCATTGTCTAGAAAACATAATCAATATTTAC--
1 CACTGGTGCCTTCACCCAAATCATCATATATCTTGTCGTCTAGAAAACATAATTAATATTTACAA
* * * *
1063581 --AAGATTATTATAGTGTGACAGTTTAAGAATGCT-GACACCAAATTATAACTGTAGATTAACAT
66 GTAAGATTGTTATA--CTGACAGTTTAAGAATG-TAAACATCAAATTATAACTGTAGATTAACAT
*
1063643 AATAGAATATCAACTTGCAGCCATTACCTGACAGATCACAGAGTCCAAAATAACCAAAGTTTTCC
128 AATAGAATATCAACTTGCAGCCATTACCTGACAGACCACAGAGTCCAAAATAACCAAAGTTTTCC
1063708 ATATCAGAAGAACACAGCAGTGACGGAAGAACCTATATGCAAAAGAGAATCAGATCTGATCCAAA
193 ATATCAGAAGAACACAGCAGTGACGGAAGAACCTATATGCAAAAGAGAATCAGATCTGATCCAAA
1063773 ACTAAGCAAATTGAATTTAAAAAATATATACACGCCAAAACCTACAGGATCAACAGTAAAGGTGT
258 ACTAAGCAAATTGAATTTAAAAAATATATACACGCCAAAACCTACAGGATCAACAGTAAAGGTGT
1063838 TCTCTTGTGACAGTTCCATATTGTGTGGATTTGCTATAGCAC
323 TCTCTTGTGACAGTTCCATATTGTGTGGATTTGCTATAGCAC
1063880 CACTGGTGCCTTCACCCAAATCATCATATATCTTGTCGTCTAGAAAACATAATTAATATTTACAA
1 CACTGGTGCCTTCACCCAAATCATCATATATCTTGTCGTCTAGAAAACATAATTAATATTTACAA
1063945 GTAAGATTGTTATACTGACAGTTTAAGAATGTAAACATCAAATTATAACTGTAGATTAACATAAT
66 GTAAGATTGTTATACTGACAGTTTAAGAATGTAAACATCAAATTATAACTGTAGATTAACATAAT
1064010 AGAATATCAACTTGCAGCCATTACCTGACAGACCACAGAGTCCAAAATAACCAAAG-TTTCCATA
131 AGAATATCAACTTGCAGCCATTACCTGACAGACCACAGAGTCCAAAATAACCAAAGTTTTCCATA
1064074 TCAG-A-AACACAGCAGTGACGGAAGAACCTATATGCAAAAGAGAATCAGATCTGATCCAAAACT
196 TCAGAAGAACACAGCAGTGACGGAAGAACCTATATGCAAAAGAGAATCAGATCTGATCCAAAACT
1064137 AAGCAAATTGAATTTAAAAAATATATACACGCCAAAACCTACAGGATCAACAGTAAAGGTGTTCT
261 AAGCAAATTGAATTTAAAAAATATATACACGCCAAAACCTACAGGATCAACAGTAAAGGTGTTCT
1064202 CTTGTGACAGTTCCATATTGTGTGGATTTGCTATAGCAC
326 CTTGTGACAGTTCCATATTGTGTGGATTTGCTATAGCAC
1064241 CACTGGTGCCTTCACCCAAATCATCATATATCTTGTCGTCTAGAAAACATAATTAATATTTACAA
1 CACTGGTGCCTTCACCCAAATCATCATATATCTTGTCGTCTAGAAAACATAATTAATATTTACAA
1064306 GTAAGATTGTTATACTGACAGTTTAAGAATGTAAACATCAAATTATAACTGTAGATTAACATAAT
66 GTAAGATTGTTATACTGACAGTTTAAGAATGTAAACATCAAATTATAACTGTAGATTAACATAAT
1064371 AGAATATCAACTTGCAGCCATTACCTGAC
131 AGAATATCAACTTGCAGCCATTACCTGAC
1064400 CGATTACAGA
Statistics
Matches: 502, Mismatches: 13, Indels: 11
0.95 0.02 0.02
Matches are distributed among these distances:
361 321 0.64
362 56 0.11
363 13 0.03
364 101 0.20
366 11 0.02
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (364 bp):
CACTGGTGCCTTCACCCAAATCATCATATATCTTGTCGTCTAGAAAACATAATTAATATTTACAA
GTAAGATTGTTATACTGACAGTTTAAGAATGTAAACATCAAATTATAACTGTAGATTAACATAAT
AGAATATCAACTTGCAGCCATTACCTGACAGACCACAGAGTCCAAAATAACCAAAGTTTTCCATA
TCAGAAGAACACAGCAGTGACGGAAGAACCTATATGCAAAAGAGAATCAGATCTGATCCAAAACT
AAGCAAATTGAATTTAAAAAATATATACACGCCAAAACCTACAGGATCAACAGTAAAGGTGTTCT
CTTGTGACAGTTCCATATTGTGTGGATTTGCTATAGCAC
Found at i:1075480 original size:17 final size:16
Alignment explanation
Indices: 1075458--1075515 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 16
1075448 ATTAGATTAA
1075458 ATTATATTTTATGTAT
1 ATTATATTTTATGTAT
**
1075474 CATTATATTGAAT-TAT
1 -ATTATATTTTATGTAT
*
1075490 TTATATATTTTATGTATT
1 AT-TATATTTTATGTA-T
1075508 ATTATATT
1 ATTATATT
1075516 AAATTATTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.03
16 11 0.34
17 18 0.56
18 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (16 bp):
ATTATATTTTATGTAT
Found at i:1075497 original size:33 final size:33
Alignment explanation
Indices: 1075460--1075530 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1075450 TAGATTAAAT
*
1075460 TATATTTTATGTATCATTATATTGAATTATTTA
1 TATATTTTATGTATCATTATATTAAATTATTTA
*
1075493 TATATTTTATGTATTATTATATTAAATTATTTA
1 TATATTTTATGTATCATTATATTAAATTATTTA
*
1075526 AATAT
1 TATAT
1075531 CATATAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (33 bp):
TATATTTTATGTATCATTATATTAAATTATTTA
Found at i:1079030 original size:21 final size:22
Alignment explanation
Indices: 1078954--1079031 Score: 61
Period size: 22 Copynumber: 3.6 Consensus size: 22
1078944 ATATTTAAAT
* * *
1078954 AATAACAATAAAATAATAATAA
1 AATAACAGTAAAACAATAAGAA
*
1078976 CATAGA-AGTAAAACAATAAGAA
1 AATA-ACAGTAAAACAATAAGAA
* *
1078998 AATAACATTAAAACAGT-AGAA
1 AATAACAGTAAAACAATAAGAA
**
1079019 AATATGAGTAAAA
1 AATAACAGTAAAA
1079032 AAACTTTACT
Statistics
Matches: 44, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
21 15 0.34
22 28 0.64
23 1 0.02
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.19
Consensus pattern (22 bp):
AATAACAGTAAAACAATAAGAA
Found at i:1086445 original size:31 final size:31
Alignment explanation
Indices: 1086410--1086474 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
1086400 TCATTATAGA
1086410 GACCAAAACT-GAAAAAGTTG-CAAAATTCAGG
1 GACC-AAACTAGAAAAAGTTGTC-AAATTCAGG
* *
1086441 GACCAAATTAGAAAAAGTTGTCAAATTTAGG
1 GACCAAACTAGAAAAAGTTGTCAAATTCAGG
1086472 GAC
1 GAC
1086475 TTAGATATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 4 0.13
31 25 0.83
32 1 0.03
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (31 bp):
GACCAAACTAGAAAAAGTTGTCAAATTCAGG
Found at i:1086726 original size:15 final size:15
Alignment explanation
Indices: 1086706--1086741 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1086696 TCGAAACCCA
* *
1086706 ATCATCTTCTTCATC
1 ATCATCGTCGTCATC
1086721 ATCATCGTCGTCATC
1 ATCATCGTCGTCATC
1086736 ATCATC
1 ATCATC
1086742 CCCTTTAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.33, G:0.06, T:0.39
Consensus pattern (15 bp):
ATCATCGTCGTCATC
Found at i:1097541 original size:9 final size:9
Alignment explanation
Indices: 1097527--1097577 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
1097517 AAAATAATTT
1097527 AAAAATTAA
1 AAAAATTAA
1097536 AAAAATT-A
1 AAAAATTAA
1097544 AAAAATATAA
1 AAAAAT-TAA
* * *
1097554 AATATTTAT
1 AAAAATTAA
*
1097563 AAAAATTCA
1 AAAAATTAA
1097572 AAAAAT
1 AAAAAT
1097578 AAACATAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
8 7 0.21
9 21 0.64
10 5 0.15
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (9 bp):
AAAAATTAA
Found at i:1099153 original size:30 final size:30
Alignment explanation
Indices: 1099117--1099179 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1099107 ACTTAACAAG
*
1099117 CAAATGTCTCTAAAATAATAATAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
*
1099147 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
1099177 CAA
1 CAA
1099180 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:1105024 original size:17 final size:17
Alignment explanation
Indices: 1105002--1105035 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1104992 TATATTTTAT
1105002 ATTTTTAATCAAATATA
1 ATTTTTAATCAAATATA
1105019 ATTTTTAATCAAATATA
1 ATTTTTAATCAAATATA
1105036 TATTAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTTTAATCAAATATA
Found at i:1111530 original size:22 final size:21
Alignment explanation
Indices: 1111505--1111547 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1111495 AGAAAAAAAA
*
1111505 ATTTAATTTTCCTATTATTATT
1 ATTTAATTTTACTATT-TTATT
*
1111527 ATTTATTTTTACTATTTTATT
1 ATTTAATTTTACTATTTTATT
1111548 TTATTTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTAATTTTACTATTTTATT
Found at i:1111984 original size:3 final size:3
Alignment explanation
Indices: 1111978--1112018 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1111968 CAAAAAAAAA
1111978 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1112019 AATACTCCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1122116 original size:22 final size:23
Alignment explanation
Indices: 1122088--1122130 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1122078 TGAGCAAGTG
1122088 GGCGACGGTGA-CGT-GCGGCGAT
1 GGCGAC-GTGACCGTGGCGGCGAT
1122110 GGCGACGTGACCGTGGCGGCG
1 GGCGACGTGACCGTGGCGGCG
1122131 TCAGAAGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.12, C:0.26, G:0.51, T:0.12
Consensus pattern (23 bp):
GGCGACGTGACCGTGGCGGCGAT
Found at i:1123469 original size:76 final size:76
Alignment explanation
Indices: 1123343--1123581 Score: 379
Period size: 76 Copynumber: 3.1 Consensus size: 76
1123333 TCTCACTTAG
* * * * *
1123343 ACCATTGAGATTCAAACACTAAATCATCAAATAAACACATACTGTCTGTATCTTCAGTTCATAAA
1 ACCATTGAGATCCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
*
1123408 TATCCCAATAA
66 CATCCCAATAA
*
1123419 ACCATTGAGATCCAAACACAAAACCATCACACAAACGCATACTGTCTGTATCTTCAGTTCATAAA
1 ACCATTGAGATCCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
1123484 CATCCCAATAA
66 CATCCCAATAA
* * *
1123495 ACCATTCAGATCCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTTAGTTCATCAA
1 ACCATTGAGATCCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
1123560 CATCCTCAATAA
66 CATCC-CAATAA
1123572 ACCATTGAGA
1 ACCATTGAGA
1123582 ATGTATTTCA
Statistics
Matches: 150, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
76 135 0.90
77 15 0.10
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (76 bp):
ACCATTGAGATCCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
CATCCCAATAA
Found at i:1124817 original size:17 final size:16
Alignment explanation
Indices: 1124797--1124848 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
1124787 TATTATATTA
1124797 AATTAAAAATTAAAAAT
1 AATT-AAAATTAAAAAT
*
1124814 AATTAAAATTAAAGAT
1 AATTAAAATTAAAAAT
* *
1124830 AATTTAACATTTAAAAT
1 AA-TTAAAATTAAAAAT
1124847 AA
1 AA
1124849 AAAAATGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 13 0.43
17 17 0.57
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (16 bp):
AATTAAAATTAAAAAT
Found at i:1130995 original size:17 final size:17
Alignment explanation
Indices: 1130973--1131027 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
1130963 TCACCTCGTA
1130973 AAACGGTTGTTTTTAAT
1 AAACGGTTGTTTTTAAT
1130990 AAACGGTTTAGATTTATTAA-
1 AAACGG-TT-G-TTT-TTAAT
*
1131010 AAATGGTTGTTTTTAAT
1 AAACGGTTGTTTTTAAT
1131027 A
1 A
1131028 TTTCAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 4 0.12
17 10 0.31
18 3 0.09
19 3 0.09
20 8 0.25
21 4 0.12
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (17 bp):
AAACGGTTGTTTTTAAT
Found at i:1134924 original size:23 final size:23
Alignment explanation
Indices: 1134880--1134924 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1134870 ACACTTTACC
**
1134880 TTTTTTTTATCCACCATGTGCAA
1 TTTTTTTTATCCACCAAATGCAA
* *
1134903 TTTTTTTTCTCCTCCAAATGCA
1 TTTTTTTTATCCACCAAATGCA
1134925 GGAATGCTGG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.07, T:0.49
Consensus pattern (23 bp):
TTTTTTTTATCCACCAAATGCAA
Found at i:1137709 original size:89 final size:89
Alignment explanation
Indices: 1137544--1137711 Score: 284
Period size: 89 Copynumber: 1.9 Consensus size: 89
1137534 TGATCTTGAC
* *
1137544 AACTCGGGAAGTTGGACGGATGATTTGTTCCGAAGTAATGTTTGCAAGCTACTATTTAATGAATT
1 AACTCGGGAAGTTGGACGGATGATTTGTTCCCAAGTAATGTCTGCAAGCTACTATTTAATGAATT
1137609 TATTTTCTCTTTGAATATTTTCAG
66 TATTTTCTCTTTGAATATTTTCAG
* *
1137633 AACTTGGGAAGTTGGAGGGATGATTTGTTCCCAAGTAATGTCTGCAAGCTACTATTTAATGAATT
1 AACTCGGGAAGTTGGACGGATGATTTGTTCCCAAGTAATGTCTGCAAGCTACTATTTAATGAATT
1137698 TAATTTT-TCTTTGA
66 T-ATTTTCTCTTTGA
1137712 GCTATATTGA
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
89 69 0.93
90 5 0.07
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (89 bp):
AACTCGGGAAGTTGGACGGATGATTTGTTCCCAAGTAATGTCTGCAAGCTACTATTTAATGAATT
TATTTTCTCTTTGAATATTTTCAG
Found at i:1144842 original size:73 final size:73
Alignment explanation
Indices: 1144759--1144925 Score: 246
Period size: 73 Copynumber: 2.3 Consensus size: 73
1144749 CCCGACTCGC
* *
1144759 TTTTCTAAAAACGCCGCTAAATCCCCGAAAAACTTAGAAAACGGCGTCGTTGGGCTTAGG-TTTT
1 TTTTC-AAAAACGCCGCTAAATCCCCG-AAAACTTAGAAAACGACGTAGTTGGGCTTAGGTTTTT
*
1144823 TTGCTGCGCT
64 TTGCGGCGCT
* *
1144833 TTTTCAAAAACGCCGCTAAATCCCCGAAAGCTTAGAAAACGATGTAGTTGGGCTTAGGTTTTTTT
1 TTTTCAAAAACGCCGCTAAATCCCCGAAAACTTAGAAAACGACGTAGTTGGGCTTAGGTTTTTTT
1144898 GCGGCGCT
66 GCGGCGCT
* *
1144906 TTTTCGAAAATGCCGCTAAA
1 TTTTCAAAAACGCCGCTAAA
1144926 GCCCTGAGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 3
0.89 0.07 0.03
Matches are distributed among these distances:
72 28 0.33
73 52 0.61
74 5 0.06
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (73 bp):
TTTTCAAAAACGCCGCTAAATCCCCGAAAACTTAGAAAACGACGTAGTTGGGCTTAGGTTTTTTT
GCGGCGCT
Found at i:1145122 original size:12 final size:12
Alignment explanation
Indices: 1145105--1145130 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1145095 TTTTTTATCT
1145105 AAACGCCGCTAA
1 AAACGCCGCTAA
1145117 AAACGCCGCTAA
1 AAACGCCGCTAA
1145129 AA
1 AA
1145131 GCCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:1145452 original size:76 final size:76
Alignment explanation
Indices: 1145318--1145632 Score: 508
Period size: 76 Copynumber: 4.1 Consensus size: 76
1145308 TCTCACTTCG
* *
1145318 ACCATTGAGATTCAAACACAAAATCATCACATAAACACATACTGTCTG-AGT-TTGCAGTTCATA
1 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTA-TCTT-CAGTTCATA
1145381 AACATCCCAATAA
64 AACATCCCAATAA
* *
1145394 ACCATTGAGATTCAAACACAAAACCATCACACAAACGCATATTGTCTGTATCTTCAGTTCATAAA
1 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
1145459 CATCCCAATAA
66 CATCCCAATAA
*
1145470 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTTAGTTCATAAA
1 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
*
1145535 CATTCCAATAA
66 CATCCCAATAA
* *
1145546 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTTTGTATCTTCAGTTCATCAA
1 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
*
1145611 CATCCTCGATAA
66 CATCC-CAATAA
1145623 ACCATTGAGA
1 ACCATTGAGA
1145633 ATGTATTTCA
Statistics
Matches: 223, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
76 205 0.92
77 18 0.08
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.25
Consensus pattern (76 bp):
ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
CATCCCAATAA
Found at i:1153533 original size:76 final size:76
Alignment explanation
Indices: 1153405--1153719 Score: 531
Period size: 76 Copynumber: 4.1 Consensus size: 76
1153395 TCTCAGTTAG
* *
1153405 ACCATTGAGATTCAAACACAAAACCATCACATAAACACATAGTGTCTGTATCTTCAGTTCATAAA
1 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
1153470 CATCCCAATAA
66 CATCCCAATAA
** *
1153481 ACCATTGAGATTCAAACACAAAACCATCACACAAATGCATACTGTCTCTATCTTCAGTTCATAAA
1 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
*
1153546 CATCCTAATAA
66 CATCCCAATAA
* *
1153557 ACCATTGAGATCCAAACACAAAACCATCACACAAACACAGACTGTCTGTATCTTCAGTTCATAAA
1 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
1153622 CATCCCAATAA
66 CATCCCAATAA
* *
1153633 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTTTGTATCTTCAGTTCATCAA
1 ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
1153698 CATCCTCAATAA
66 CATCC-CAATAA
1153710 ACCATTGAGA
1 ACCATTGAGA
1153720 AAGTATTTCA
Statistics
Matches: 222, Mismatches: 16, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
76 206 0.93
77 16 0.07
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (76 bp):
ACCATTGAGATTCAAACACAAAACCATCACACAAACACATACTGTCTGTATCTTCAGTTCATAAA
CATCCCAATAA
Found at i:1153831 original size:42 final size:42
Alignment explanation
Indices: 1153772--1153909 Score: 168
Period size: 42 Copynumber: 3.3 Consensus size: 42
1153762 TGCAATCCCG
* * ***
1153772 CTAGCTTCAGTAGGTTTTCTTCTAACTCAGCTTTGTCCTTCT
1 CTAGCTTCAGTTGGTTTTCTTTTAACTCAGCTTCACCCTTCT
1153814 CTAGCTTCAGTTGGTTTTCTTTTAACTCAGCTTCACCCTTCT
1 CTAGCTTCAGTTGGTTTTCTTTTAACTCAGCTTCACCCTTCT
* * * * *
1153856 CCACCTTCAGTTTGTTTTCTTTTAAATCAGCTTCTCCCTTCT
1 CTAGCTTCAGTTGGTTTTCTTTTAACTCAGCTTCACCCTTCT
* *
1153898 CCACCTTCAGTT
1 CTAGCTTCAGTT
1153910 CGCCTTCCCT
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 86 1.00
ACGTcount: A:0.14, C:0.30, G:0.11, T:0.45
Consensus pattern (42 bp):
CTAGCTTCAGTTGGTTTTCTTTTAACTCAGCTTCACCCTTCT
Found at i:1158800 original size:35 final size:34
Alignment explanation
Indices: 1158758--1158844 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 34
1158748 CTAACTCAGT
* *
1158758 ACAGTATCAAATATGCAGTGGGGCCTTAGCCCATC
1 ACAGTATC-AATATGCAGTAGGACCTTAGCCCATC
* *
1158793 ACAGTATCAGTATGC-GTTAGGATCTTAGCCCATC
1 ACAGTATCAATATGCAG-TAGGACCTTAGCCCATC
* *
1158827 ATAGTATCAATATACAGT
1 ACAGTATCAATATGCAGT
1158845 CATGCAGTGT
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
33 1 0.02
34 33 0.77
35 9 0.21
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.28
Consensus pattern (34 bp):
ACAGTATCAATATGCAGTAGGACCTTAGCCCATC
Found at i:1164032 original size:38 final size:39
Alignment explanation
Indices: 1163983--1164056 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
1163973 TCCCTACTCA
* * *
1163983 AATATTTTAGGAGATATTTACCTGTTACTTATAATTCAG
1 AATATTTTAGGAAATATTCACCTGTAACTTATAATTCAG
1164022 AATA-TTTAGGAAATATTCACCTGTAACTTATAATT
1 AATATTTTAGGAAATATTCACCTGTAACTTATAATT
1164057 GGTGGAGTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 28 0.88
39 4 0.12
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (39 bp):
AATATTTTAGGAAATATTCACCTGTAACTTATAATTCAG
Found at i:1165460 original size:12 final size:11
Alignment explanation
Indices: 1165436--1165477 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
1165426 ATTAAAATCA
*
1165436 TTAAAAATGTG
1 TTAAAAATTTG
1165447 TTAAAAATTATG
1 TTAAAAATT-TG
1165459 TTAAAATATTT-
1 TTAAAA-ATTTG
1165470 TTAAAAAT
1 TTAAAAAT
1165478 AAAAATTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 2 0.07
11 14 0.50
12 9 0.32
13 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (11 bp):
TTAAAAATTTG
Found at i:1165826 original size:20 final size:20
Alignment explanation
Indices: 1165803--1165843 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1165793 TACTTATTTT
*
1165803 TGCCTCCCCTTAGTTATTAC
1 TGCCTCCCCTTAGCTATTAC
1165823 TGCCTCCCCTTAGCTATTAC
1 TGCCTCCCCTTAGCTATTAC
1165843 T
1 T
1165844 AACTTTCACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.37, G:0.10, T:0.39
Consensus pattern (20 bp):
TGCCTCCCCTTAGCTATTAC
Found at i:1166417 original size:27 final size:28
Alignment explanation
Indices: 1166387--1166444 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1166377 AGAATGTAAG
* *
1166387 TTTTGGTTTTAA-T-AAATCTAGGTTTGA
1 TTTT-GTTTTAACTGAAATCAAGCTTTGA
1166414 TTTTGTTTTAACTGAAATCAAGCTTTGA
1 TTTTGTTTTAACTGAAATCAAGCTTTGA
1166442 TTT
1 TTT
1166445 CTAAAGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 7 0.26
27 5 0.19
28 15 0.56
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.52
Consensus pattern (28 bp):
TTTTGTTTTAACTGAAATCAAGCTTTGA
Found at i:1166668 original size:32 final size:33
Alignment explanation
Indices: 1166619--1166704 Score: 83
Period size: 33 Copynumber: 2.7 Consensus size: 33
1166609 ATTTATTTAA
* * *
1166619 TATTTTAACATA-A-TTTTTAATAATTTATATT
1 TATTTTAACATATATTTTTTAAAAATTTAGAAT
1166650 TATTTTAA-ATATATTTTTTTAAAAATTTAGAAT
1 TATTTTAACATATA-TTTTTTAAAAATTTAGAAT
*
1166683 TATTGTTAAGA-AT-TTTTTTAAA
1 TATT-TTAACATATATTTTTTAAA
1166705 GTAAAATGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
30 3 0.06
31 9 0.19
32 9 0.19
33 19 0.40
34 6 0.13
35 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (33 bp):
TATTTTAACATATATTTTTTAAAAATTTAGAAT
Found at i:1166669 original size:14 final size:15
Alignment explanation
Indices: 1166644--1166672 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1166634 TTTAATAATT
1166644 TATATTTATTTTAAA
1 TATATTTATTTTAAA
1166659 TATATTT-TTTTAAA
1 TATATTTATTTTAAA
1166673 AATTTAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTTATTTTAAA
Found at i:1168548 original size:36 final size:36
Alignment explanation
Indices: 1168508--1168580 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
1168498 TTAATAGGGA
* * *
1168508 TCTTACGCTTTGAAC-AATGTGTAAAAAGCAAGTTGC
1 TCTTACGCTGTG-ACGAACGTGCAAAAAGCAAGTTGC
*
1168544 TCTTACGCTGTGACGACCGTGCAAAAAGCAAGTTGC
1 TCTTACGCTGTGACGAACGTGCAAAAAGCAAGTTGC
1168580 T
1 T
1168581 TGAGACCGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 2 0.06
36 30 0.94
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (36 bp):
TCTTACGCTGTGACGAACGTGCAAAAAGCAAGTTGC
Found at i:1172592 original size:42 final size:42
Alignment explanation
Indices: 1172505--1172592 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
1172495 AAGGCAAGCG
* *
1172505 GAAGGTGGAGAAGGGCGAAGCTGATTTAAAAGAAAACAGACT
1 GAAGGTGGAGAAGGGCGAAGCTGAGTTAAAAGAAAACAGAAT
* *
1172547 GAAGGTGGTGAAGGGCGAAGCTGGGTTAAAAGAAAA-ACGAAT
1 GAAGGTGGAGAAGGGCGAAGCTGAGTTAAAAGAAAACA-GAAT
1172589 GAAG
1 GAAG
1172593 CTGAGGTAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 40 0.98
ACGTcount: A:0.42, C:0.08, G:0.36, T:0.14
Consensus pattern (42 bp):
GAAGGTGGAGAAGGGCGAAGCTGAGTTAAAAGAAAACAGAAT
Found at i:1177890 original size:16 final size:17
Alignment explanation
Indices: 1177853--1177892 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1177843 ATATACTTTG
1177853 ATTTTAAATTCGATTGT
1 ATTTTAAATTCGATTGT
*
1177870 ATTTTAAATTGGATT-T
1 ATTTTAAATTCGATTGT
1177886 ATTTTAA
1 ATTTTAA
1177893 TTATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.55
Consensus pattern (17 bp):
ATTTTAAATTCGATTGT
Found at i:1178527 original size:28 final size:28
Alignment explanation
Indices: 1178474--1178527 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
1178464 TTATTATGAA
* *
1178474 ATTAATTAATTTAATTTTTGCTAAAATT
1 ATTAATCAATTTAATTTTTGCCAAAATT
*
1178502 ATTAATCAACTTTTATTTTT-CCAAAA
1 ATTAATCAA-TTTAATTTTTGCCAAAA
1178528 AAAATTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 13 0.59
29 9 0.41
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (28 bp):
ATTAATCAATTTAATTTTTGCCAAAATT
Found at i:1183448 original size:57 final size:57
Alignment explanation
Indices: 1183356--1183471 Score: 223
Period size: 57 Copynumber: 2.0 Consensus size: 57
1183346 AAAGGAGAGA
*
1183356 AGATAGCAAGGCAGTTCATTTGGGGTGGTTCTGCTGGGCATCCAAAAGTAGATTGGG
1 AGATAGCAAGGCAGTTCATTTGGGGTGGTTATGCTGGGCATCCAAAAGTAGATTGGG
1183413 AGATAGCAAGGCAGTTCATTTGGGGTGGTTATGCTGGGCATCCAAAAGTAGATTGGG
1 AGATAGCAAGGCAGTTCATTTGGGGTGGTTATGCTGGGCATCCAAAAGTAGATTGGG
1183470 AG
1 AG
1183472 TCCATTTGTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.26, C:0.13, G:0.35, T:0.26
Consensus pattern (57 bp):
AGATAGCAAGGCAGTTCATTTGGGGTGGTTATGCTGGGCATCCAAAAGTAGATTGGG
Found at i:1189266 original size:21 final size:22
Alignment explanation
Indices: 1189229--1189272 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1189219 CAATTGTTGA
* *
1189229 ACTCAGATTGTTCTACCTGAAC
1 ACTCAGATTGATCTACCCGAAC
1189251 ACTCAGATT-ATCTACCCGAAC
1 ACTCAGATTGATCTACCCGAAC
1189272 A
1 A
1189273 TTAGTTAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.32, C:0.30, G:0.11, T:0.27
Consensus pattern (22 bp):
ACTCAGATTGATCTACCCGAAC
Found at i:1190214 original size:42 final size:42
Alignment explanation
Indices: 1190168--1190304 Score: 211
Period size: 42 Copynumber: 3.3 Consensus size: 42
1190158 TAGAAAAGAC
** *
1190168 AAACTGAAGCTGGAGAAGGATGAAGCTGACTTAAAAGAGAAG
1 AAACTGAAGCTGGATCAGGACGAAGCTGACTTAAAAGAGAAG
1190210 AAACTGAAGCTGGATCAGGACGAAGCTGACTTAAAAGAGAAG
1 AAACTGAAGCTGGATCAGGACGAAGCTGACTTAAAAGAGAAG
* * *
1190252 AAACTGAAGCTGGATCAGGACGAAGCTGAGTTAAAAGAAAAC
1 AAACTGAAGCTGGATCAGGACGAAGCTGACTTAAAAGAGAAG
*
1190294 CAACTGAAGCT
1 AAACTGAAGCT
1190305 AGCCAGGTTG
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.44, C:0.14, G:0.28, T:0.15
Consensus pattern (42 bp):
AAACTGAAGCTGGATCAGGACGAAGCTGACTTAAAAGAGAAG
Found at i:1190488 original size:74 final size:75
Alignment explanation
Indices: 1190357--1190551 Score: 302
Period size: 74 Copynumber: 2.6 Consensus size: 75
1190347 TTTGAAATAC
* * *
1190357 AATCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACTGCCAGTATGCATTTGTGTGATGG
1 AATCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAATATGCATTTGTGTGATGG
1190422 -TTGTGTTTG
66 TTTGTGTTTG
* * **
1190431 AATGTCAATGGTTTATTGGGATGTTTATGAACTGAAGATGCAGACAATATGTGTTTGTGTGATGG
1 AATCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAATATGCATTTGTGTGATGG
1190496 TTTTGTGTTTG
66 -TTTGTGTTTG
*
1190507 AATCCCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGAC
1 AATCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGAC
1190552 TGTATTTGTG
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
74 58 0.53
76 51 0.47
ACGTcount: A:0.26, C:0.09, G:0.27, T:0.39
Consensus pattern (75 bp):
AATCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACAGACAATATGCATTTGTGTGATGG
TTTGTGTTTG
Found at i:1191418 original size:170 final size:171
Alignment explanation
Indices: 1191127--1191468 Score: 535
Period size: 170 Copynumber: 2.0 Consensus size: 171
1191117 CCTATGCATC
* * * *
1191127 GGGTTGAGTTTGGGTTAGAATTAAGCATGATGTTAACACATATTTTGGTTGTCAAGATCGACTAG
1 GGGTTGAGTTTCGGTTAGAATTAAGCATGATGTTAACACATATTTTGGTTGTCAAGA-CAACCAA
* * *
1191192 ACCTAGTCTGAAATATGTATCTAAAATTTGTTTAAGCCCATCCATACTTGTAAATAGTTAACCCA
65 ACCCAGTCTGAAATATGTACCTAAAATTTGTTTAAGCCCATCCATACTTATAAATAGTTAACCCA
*
1191257 AATCCATTTTAAATCCACCCATATTATTATTTTTAAAAATTA
130 AATCCATTTTAAATCCACCCATATAATTATTTTTAAAAATTA
* * *
1191299 GGGTTGAGTTTCGGTTAGATTTAAGTATGTTGTTAACACAT-TTTCTGGTTGTCAAGA-AACCAA
1 GGGTTGAGTTTCGGTTAGAATTAAGCATGATGTTAACACATATTT-TGGTTGTCAAGACAACCAA
1191362 ACCCAGTCTGAAATATGTACCTAAAATTTGTTTAAGCCCATCCATACTTATAAATAGTTAACCCA
65 ACCCAGTCTGAAATATGTACCTAAAATTTGTTTAAGCCCATCCATACTTATAAATAGTTAACCCA
* *
1191427 AATTCATTTTAAATCCACCCATATAATTATTTTTTAAAATTA
130 AATCCATTTTAAATCCACCCATATAATTATTTTTAAAAATTA
1191469 TTTATATTAT
Statistics
Matches: 156, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
170 104 0.67
171 3 0.02
172 49 0.31
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (171 bp):
GGGTTGAGTTTCGGTTAGAATTAAGCATGATGTTAACACATATTTTGGTTGTCAAGACAACCAAA
CCCAGTCTGAAATATGTACCTAAAATTTGTTTAAGCCCATCCATACTTATAAATAGTTAACCCAA
ATCCATTTTAAATCCACCCATATAATTATTTTTAAAAATTA
Found at i:1191483 original size:21 final size:22
Alignment explanation
Indices: 1191452--1191493 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1191442 CACCCATATA
*
1191452 ATTATTTTTTAAAATTATTTAT
1 ATTATTTTTTAAAACTATTTAT
*
1191474 ATTA-TTTTTAATACTATTTA
1 ATTATTTTTTAAAACTATTTA
1191494 ATAATTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTATTTTTTAAAACTATTTAT
Found at i:1192902 original size:55 final size:55
Alignment explanation
Indices: 1192826--1192965 Score: 210
Period size: 55 Copynumber: 2.5 Consensus size: 55
1192816 ACAAATGATC
* * *
1192826 TAAACATATAAACAATCGATTCAAAAGAAGTAGTATTCCAACATAACAATCAATT
1 TAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACACAACAACCAATT
* * *
1192881 TGAACATATAAACAATGGATTCAAAAGCAA-CAGTATTCCAACACAACAACCGATT
1 TAAACATATAAACAATCGATTCAAAAG-AAGCAGTATTCCAACACAACAACCAATT
1192936 TAAACATATAAACAATCGATTCAAAAGAAG
1 TAAACATATAAACAATCGATTCAAAAGAAG
1192966 AAAAAGTAGT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
54 2 0.03
55 71 0.95
56 2 0.03
ACGTcount: A:0.51, C:0.18, G:0.09, T:0.22
Consensus pattern (55 bp):
TAAACATATAAACAATCGATTCAAAAGAAGCAGTATTCCAACACAACAACCAATT
Found at i:1193994 original size:21 final size:20
Alignment explanation
Indices: 1193946--1194020 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 20
1193936 TAGGAGTTTG
* **
1193946 AATCAATTCAAACAATAATG
1 AATCAATTCAAACAACAAAC
*
1193966 AATTAATTCAAAACAACAAAC
1 AATCAATTC-AAACAACAAAC
* * *
1193987 AATCAATTGAAATAAGCAAAG
1 AATCAATTCAAACAA-CAAAC
*
1194008 AATCGATTCAAAC
1 AATCAATTCAAAC
1194021 TCCAACATAA
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 13 0.31
21 29 0.69
ACGTcount: A:0.56, C:0.16, G:0.07, T:0.21
Consensus pattern (20 bp):
AATCAATTCAAACAACAAAC
Found at i:1194232 original size:55 final size:55
Alignment explanation
Indices: 1194163--1194393 Score: 275
Period size: 55 Copynumber: 4.2 Consensus size: 55
1194153 ATGTGTTATG
* *
1194163 TAACAATCGATTTAAACATATA-AGCAATCGATTCAAAAGAAGTAATATTCCAACA
1 TAACAATCGATTTAAACATATACA-CAATCGATTCAAAAGAAGCAGTATTCCAACA
* * * *
1194218 TAATAATCGATTTAATCATATACACAATCAATTAAAAAGAAGCAGTATTCCAACA
1 TAACAATCGATTTAAACATATACACAATCGATTCAAAAGAAGCAGTATTCCAACA
* * * * *
1194273 TAACAATCAATTTAATCATATACACAATCGATTCAAAAGAAGTAGTGTTCCAACT
1 TAACAATCGATTTAAACATATACACAATCGATTCAAAAGAAGCAGTATTCCAACA
* * * * * *
1194328 TGACAATCGATTTAAACATATAAAGAATTGACTCAAAAGAAGCACTATTCCAACA
1 TAACAATCGATTTAAACATATACACAATCGATTCAAAAGAAGCAGTATTCCAACA
* *
1194383 TGATAATCGAT
1 TAACAATCGAT
1194394 CCAAAAGAAG
Statistics
Matches: 150, Mismatches: 25, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
55 149 0.99
56 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (55 bp):
TAACAATCGATTTAAACATATACACAATCGATTCAAAAGAAGCAGTATTCCAACA
Found at i:1199373 original size:47 final size:47
Alignment explanation
Indices: 1199313--1199409 Score: 117
Period size: 47 Copynumber: 2.1 Consensus size: 47
1199303 CTTTATTTGA
* * *
1199313 TTTGATTTGATTTTGAA-TGTATCATATATGTTGAAATGTTGCATTAG
1 TTTGATTTGATTTTGAATTG-AACATATATATCGAAATGTTGCATTAG
* *
1199360 TTTGATCTT-ATTTTTACTTGAACATATATATCGAAATGTTGCATTAG
1 TTTGAT-TTGATTTTGAATTGAACATATATATCGAAATGTTGCATTAG
1199407 TTT
1 TTT
1199410 CTTATTTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
47 39 0.91
48 4 0.09
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.49
Consensus pattern (47 bp):
TTTGATTTGATTTTGAATTGAACATATATATCGAAATGTTGCATTAG
Found at i:1210615 original size:19 final size:19
Alignment explanation
Indices: 1210555--1210615 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
1210545 CAAATCCAAA
* *
1210555 TTGGATGAGAGTTTTTAAA
1 TTGGATGAGGGTTTTTAAG
* * ** *
1210574 TTTGAAGAGGAACTTTTATG
1 TTGGATGAGG-GTTTTTAAG
1210594 TTGGATGAGGGTTTTTAAG
1 TTGGATGAGGGTTTTTAAG
1210613 TTG
1 TTG
1210616 ATTCATCCAT
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.26, C:0.02, G:0.30, T:0.43
Consensus pattern (19 bp):
TTGGATGAGGGTTTTTAAG
Found at i:1211092 original size:112 final size:113
Alignment explanation
Indices: 1210958--1211182 Score: 443
Period size: 112 Copynumber: 2.0 Consensus size: 113
1210948 AAATATTAAC
1210958 TATGAATAAGAAAGATGGTAAAGTAGAATATAACAAATTCACCCAAAAATATTGTAGTAACACGT
1 TATGAATAAGAAAGATGGTAAAGTAGAATATAACAAATTCACCCAAAAATATTGTAGTAACACGT
1211023 GTTCTGTTAGGTGTTTTATGTTAAATTATAGGATATAGAGAAAATATA
66 GTTCTGTTAGGTGTTTTATGTTAAATTATAGGATATAGAGAAAATATA
1211071 TATGAATAAG-AAGATGGTAAAGTAGAATATAACAAATTCACCCAAAAATATTGTAGTAACACGT
1 TATGAATAAGAAAGATGGTAAAGTAGAATATAACAAATTCACCCAAAAATATTGTAGTAACACGT
1211135 GTTCTGTTAGGTGTTTTATGTTAAATTATAGGATATAGAGAAAATATA
66 GTTCTGTTAGGTGTTTTATGTTAAATTATAGGATATAGAGAAAATATA
1211183 AGGCAAGGCA
Statistics
Matches: 112, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
112 102 0.91
113 10 0.09
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (113 bp):
TATGAATAAGAAAGATGGTAAAGTAGAATATAACAAATTCACCCAAAAATATTGTAGTAACACGT
GTTCTGTTAGGTGTTTTATGTTAAATTATAGGATATAGAGAAAATATA
Found at i:1222214 original size:89 final size:90
Alignment explanation
Indices: 1222052--1222230 Score: 351
Period size: 89 Copynumber: 2.0 Consensus size: 90
1222042 AGAGTTTCAA
1222052 ACAGTTGAAAGCTATGATAACAGAAGTTCCAAAATTGAATTTGGAATAGTATTGAAGAACATTAT
1 ACAGTTGAAAGCTATGATAACAGAAGTTCCAAAATTGAATTTGGAATAGTATTGAAGAACATTAT
1222117 TCTTGGTAATTCACTTAACTTGTGC
66 TCTTGGTAATTCACTTAACTTGTGC
1222142 ACAGTTGAAA-CTATGATAACAGAAGTTCCAAAATTGAATTTGGAATAGTATTGAAGAACATTAT
1 ACAGTTGAAAGCTATGATAACAGAAGTTCCAAAATTGAATTTGGAATAGTATTGAAGAACATTAT
1222206 TCTTGGTAATTCACTTAACTTGTGC
66 TCTTGGTAATTCACTTAACTTGTGC
1222231 TTTTAATCAG
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 79 0.89
90 10 0.11
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (90 bp):
ACAGTTGAAAGCTATGATAACAGAAGTTCCAAAATTGAATTTGGAATAGTATTGAAGAACATTAT
TCTTGGTAATTCACTTAACTTGTGC
Found at i:1223154 original size:29 final size:29
Alignment explanation
Indices: 1223106--1223161 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1223096 ATTAATTATT
1223106 TTAATCTTATTACTACTATCATCATATCA
1 TTAATCTTATTACTACTATCATCATATCA
* * * *
1223135 TTAATGTTATTATTATTATCATTATAT
1 TTAATCTTATTACTACTATCATCATAT
1223162 TTCCACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (29 bp):
TTAATCTTATTACTACTATCATCATATCA
Found at i:1223318 original size:22 final size:24
Alignment explanation
Indices: 1223290--1223348 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
1223280 TACGTATACA
*
1223290 TATATATATATATTAA-ACT-TATT
1 TATATATATATATGAATACTCT-TT
*
1223313 TA-ATATATACATGAATACTCTTT
1 TATATATATATATGAATACTCTTT
1223336 TATATATATATAT
1 TATATATATATAT
1223349 AGGTATATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 11 0.37
23 9 0.30
24 10 0.33
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (24 bp):
TATATATATATATGAATACTCTTT
Found at i:1229168 original size:40 final size:39
Alignment explanation
Indices: 1229123--1229198 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
1229113 GTTTGGAACA
*
1229123 AAAGCGCCACAAAAAATAGAGCATTAGCGGCGATTTAGCC
1 AAAGCGCCACAAAAAATAGAGCATCAGCGGCG-TTTAGCC
* * **
1229163 AAAGCGCCGCTAAAGGTAGAGCATCAGCGGCGTTTA
1 AAAGCGCCACAAAAAATAGAGCATCAGCGGCGTTTA
1229199 TACGGAAGCG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 4 0.13
40 27 0.87
ACGTcount: A:0.36, C:0.22, G:0.26, T:0.16
Consensus pattern (39 bp):
AAAGCGCCACAAAAAATAGAGCATCAGCGGCGTTTAGCC
Found at i:1229371 original size:41 final size:41
Alignment explanation
Indices: 1229300--1229578 Score: 360
Period size: 42 Copynumber: 6.7 Consensus size: 41
1229290 TTTAAACATT
*
1229300 TAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGGGTCTA
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
* *
1229341 TAGCAGCGTCTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
* *
1229382 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCCGAGTCTT
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCT-CGGGTCTA
* * * * *
1229424 TAGCGGCGCTTTCGTCTAAGTGCCGCTAATGCTCCGAGTCTT
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCT-CGGGTCTA
*
1229466 TAGCGGCGTTTTCGTCTAAGCGCCGCTAATGCTCTGGGTCTA
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTC-GGGTCTA
* * * * *
1229508 TAGCGGCGTTTTCGCCTATGCGCCGCTAATGCTCGGGTTTT
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
* * *
1229549 TAGCGGCGTTTTTATATATGCGCCGCTAAT
1 TAGCGGCGTTTTTGTCTAAGCGCCGCTAAT
1229579 TCCGTTTGTA
Statistics
Matches: 214, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
41 101 0.47
42 113 0.53
ACGTcount: A:0.15, C:0.26, G:0.27, T:0.32
Consensus pattern (41 bp):
TAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCGGGTCTA
Found at i:1229428 original size:25 final size:25
Alignment explanation
Indices: 1229400--1229470 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 25
1229390 TTTTTGTCTA
1229400 AGCGCCGCTAATGCTCCGAGTCTTT
1 AGCGCCGCTAATGCTCCGAGTCTTT
* *
1229425 AGCGGCGCT--T--T-C--GTC-TA
1 AGCGCCGCTAATGCTCCGAGTCTTT
*
1229442 AGTGCCGCTAATGCTCCGAGTCTTT
1 AGCGCCGCTAATGCTCCGAGTCTTT
1229467 AGCG
1 AGCG
1229471 GCGTTTTCGT
Statistics
Matches: 32, Mismatches: 6, Indels: 16
0.59 0.11 0.30
Matches are distributed among these distances:
17 8 0.25
18 3 0.09
19 1 0.03
20 1 0.03
21 2 0.06
22 1 0.03
23 1 0.03
24 3 0.09
25 12 0.38
ACGTcount: A:0.15, C:0.30, G:0.27, T:0.28
Consensus pattern (25 bp):
AGCGCCGCTAATGCTCCGAGTCTTT
Found at i:1235830 original size:20 final size:20
Alignment explanation
Indices: 1235805--1235843 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1235795 CTTATCTTTA
1235805 GTGGTAAGTTTAATGGTTTG
1 GTGGTAAGTTTAATGGTTTG
1235825 GTGGTAAGTTTAATGGTTT
1 GTGGTAAGTTTAATGGTTT
1235844 ATTGGGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (20 bp):
GTGGTAAGTTTAATGGTTTG
Found at i:1239640 original size:18 final size:19
Alignment explanation
Indices: 1239617--1239654 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
1239607 TTTATATTTA
1239617 GAAAA-TAAATAATTTTTT
1 GAAAATTAAATAATTTTTT
1239635 GAAAATTTAAATAATTTTTT
1 GAAAA-TTAAATAATTTTTT
1239655 TAGAATTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
20 13 0.72
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (19 bp):
GAAAATTAAATAATTTTTT
Found at i:1248154 original size:16 final size:16
Alignment explanation
Indices: 1248128--1248168 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
1248118 ATTATACTTA
1248128 GTAATTAAAAGATACAG
1 GTAA-TAAAAGATACAG
*
1248145 TTAATAAAAGATACAG
1 GTAATAAAAGATACAG
1248161 GTAATAAA
1 GTAATAAA
1248169 TAAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.24
Consensus pattern (16 bp):
GTAATAAAAGATACAG
Found at i:1249235 original size:47 final size:47
Alignment explanation
Indices: 1249166--1249259 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 47
1249156 TGCTTCGATT
*
1249166 CCCCTTCCAAAAGATAATTTAGGGCTTGATTAATGCATATGGAGGTG
1 CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTG
* * * *
1249213 CCCCTTCTAAAATATAATTTAGGATTTGATTAATGCATGTGGAGGTG
1 CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTG
1249260 GTCTAGCGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (47 bp):
CCCCTTCCAAAAGATAATTTAGGACTTGATTAATGCATATGGAGGTG
Found at i:1249933 original size:22 final size:22
Alignment explanation
Indices: 1249899--1249940 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1249889 CGACGCTGTT
1249899 ATATAATACATAACTTACATTA
1 ATATAATACATAACTTACATTA
* *
1249921 ATATTATATATAACTTACAT
1 ATATAATACATAACTTACAT
1249941 AACTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATAATACATAACTTACATTA
Found at i:1249942 original size:31 final size:31
Alignment explanation
Indices: 1249898--1250026 Score: 118
Period size: 31 Copynumber: 3.9 Consensus size: 31
1249888 GCGACGCTGT
1249898 TATATAA--TACATAACTTACATTAATATTA
1 TATATAACTTACATAACTTACATTAATATTA
*
1249927 TATATAACTTACATAACTTAATTAATTAATATTA
1 TATATAACTTACATAACTT-A--CATTAATATTA
1249961 TACATAACTTACAACTTACATAACTTACATTAATATTA
1 T--AT-A--T--AACTTACATAACTTACATTAATATTA
* * *
1249999 CACATAAATTACATAACTTACATTAATA
1 TATATAACTTACATAACTTACATTAATA
1250027 CGACATAACT
Statistics
Matches: 83, Mismatches: 5, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
29 7 0.08
31 32 0.39
32 1 0.01
33 1 0.01
34 11 0.13
35 1 0.01
36 3 0.04
37 1 0.01
38 10 0.12
39 1 0.01
40 1 0.01
41 14 0.17
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (31 bp):
TATATAACTTACATAACTTACATTAATATTA
Found at i:1249944 original size:9 final size:9
Alignment explanation
Indices: 1249930--1250021 Score: 61
Period size: 9 Copynumber: 10.2 Consensus size: 9
1249920 AATATTATAT
1249930 ATAACTTAC
1 ATAACTTAC
1249939 ATAACTTA-
1 ATAACTTAC
1249947 ATTAA-TTA-
1 A-TAACTTAC
*
1249955 AT-ATTATAC
1 ATAACT-TAC
1249964 ATAACTTAC
1 ATAACTTAC
1249973 --AACTTAC
1 ATAACTTAC
1249980 ATAACTTAC
1 ATAACTTAC
*
1249989 ATTAATATTACAC
1 A-TAA-CTT--AC
*
1250002 ATAAATTAC
1 ATAACTTAC
1250011 ATAACTTAC
1 ATAACTTAC
1250020 AT
1 AT
1250022 TAATACGACA
Statistics
Matches: 69, Mismatches: 3, Indels: 22
0.73 0.03 0.23
Matches are distributed among these distances:
6 1 0.01
7 9 0.13
8 7 0.10
9 36 0.52
10 5 0.07
11 5 0.07
12 3 0.04
13 3 0.04
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (9 bp):
ATAACTTAC
Found at i:1250004 original size:38 final size:41
Alignment explanation
Indices: 1249932--1250021 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 41
1249922 TATTATATAT
* *
1249932 AACTTACATAACTTAATTAATTAATATTATACATAACTTAC-
1 AACTTACATAACTTAA-TAATTAATATTACACATAAATTACA
*
1249973 AACTTACATAACTT-A-CATTAATATTACACATAAATTACA
1 AACTTACATAACTTAATAATTAATATTACACATAAATTACA
1250012 TAACTTACAT
1 -AACTTACAT
1250022 TAATACGACA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
38 20 0.45
40 10 0.23
41 14 0.32
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (41 bp):
AACTTACATAACTTAATAATTAATATTACACATAAATTACA
Found at i:1255539 original size:21 final size:21
Alignment explanation
Indices: 1255489--1255533 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1255479 CTACAACTTA
* *
1255489 AAGCAGATGCGGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
1255510 AAGCAGAGGCAGCAGCGAGAG
1 AAGCAGAGGCAGCAGCGAGAG
1255531 AAG
1 AAG
1255534 TTGAGGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.42, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCAGCAGCGAGAG
Found at i:1255576 original size:87 final size:87
Alignment explanation
Indices: 1255423--1255615 Score: 275
Period size: 87 Copynumber: 2.2 Consensus size: 87
1255413 GGTCAGACTA
* * *
1255423 AAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAGCTACAACTT
1 AAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAAAAAAGACATGAAGAACTCCAGCTACAACTT
1255488 AAAGCAGATGCGGCAGCGAGAG
66 AAAGCAGATGCGGCAGCGAGAG
* * * *
1255510 AAGCAGAGGCAGCAGCGAGAGAAGTTGAGGTTCAACGAAAG-CATGAAGAACTCCAGC-AGCAGC
1 AAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAA-AAAAGACATGAAGAACTCCAGCTA-CAAC
1255573 TTAAAGCAGATGCGGCAGCGAGAG
64 TTAAAGCAGATGCGGCAGCGAGAG
1255597 AAGCAGAGGCTAA-AGCGAG
1 AAGCAGAGGC-AACAGCGAG
1255616 TAAAGTAGAG
Statistics
Matches: 95, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
86 1 0.01
87 89 0.94
88 5 0.05
ACGTcount: A:0.39, C:0.19, G:0.32, T:0.11
Consensus pattern (87 bp):
AAGCAGAGGCAACAGCGAGAGAAGCTGAGGTTCAAAAAAGACATGAAGAACTCCAGCTACAACTT
AAAGCAGATGCGGCAGCGAGAG
Found at i:1255613 original size:21 final size:21
Alignment explanation
Indices: 1255589--1255628 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1255579 CAGATGCGGC
1255589 AGCGAG-AGAAGCAGAGGCTAA
1 AGCGAGTA-AAGCAGAGGCTAA
*
1255610 AGCGAGTAAAGTAGAGGCT
1 AGCGAGTAAAGCAGAGGCT
1255629 GCGGCGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.40, C:0.12, G:0.38, T:0.10
Consensus pattern (21 bp):
AGCGAGTAAAGCAGAGGCTAA
Found at i:1256044 original size:43 final size:43
Alignment explanation
Indices: 1255991--1256168 Score: 143
Period size: 43 Copynumber: 4.1 Consensus size: 43
1255981 CAGCCTATTA
* * *
1255991 TGGCGTTTTTTTGCATAAGCGCCGCGAAAGATCCCCGTCTGTAG
1 TGGCG-TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAG
* * * *
1256035 TGGCGTTTTTAG-ACTAAGCGCCGCAAAAGAACCCTATCTATCG
1 TGGCGTTTTTTGCA-TAAGCGCCGCGAAAGAACCCCATCTATAG
* ** *
1256078 TGGCGTTTCTTGCATAAGCGCCG-GAAAAGAACCTTATCTATCG
1 TGGCGTTTTTTGCATAAGCGCCGCG-AAAGAACCCCATCTATAG
*
1256121 TGGCGTTTCCTATTG---AAGCGCCG-GAGAAGAACCCTATCTATAG
1 TGGCGTTT--T-TTGCATAAGCGCCGCGA-AAGAACCCCATCTATAG
1256164 TGGCG
1 TGGCG
1256169 AGTAGAGTAC
Statistics
Matches: 113, Mismatches: 14, Indels: 15
0.80 0.10 0.11
Matches are distributed among these distances:
42 2 0.02
43 102 0.90
44 6 0.05
46 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (43 bp):
TGGCGTTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAG
Found at i:1257024 original size:43 final size:43
Alignment explanation
Indices: 1256953--1257598 Score: 755
Period size: 43 Copynumber: 15.1 Consensus size: 43
1256943 CAAAATTAGC
* *
1256953 GGCGTTTTTTGCATAAGCGCCACTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * *
1256996 GGCATTTTTTTCCTAAGCGCCGCGAAAGACAATGGTCTATAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * *
1257039 GGCATTTTTCGCCTAAGCGCCGCGAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
1257082 GGCGTTTTTCGCCTAAGCGCCACTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * * **
1257125 GGCATTTTTTG-GTCAGCGCCACTAAAGACCACAGTCTATAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * *
1257167 GGCGTTTTTTTCCTAAGCGCCGCGAAAAACCATGGTCTATATT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* *
1257210 GGCGTTTTTCGCCTAAGCGCCGCGAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
*
1257253 GGCGTTTTTCGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* ** *
1257296 GGCGTTTGTTGGTTAAGCGCCGCTAAAGACCATGGTCTGTAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * ** *
1257339 GGCATTTGTTGGTTAAGCGCCGCTAAAGACCATGGTCTGTAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * ** *
1257382 GGCATTTGTTGGTTAAGCGCCGCTAAAGACCATGGTCTGTAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* ** *
1257425 GGCGTTTGTTGGTTAAGCACCGCTAAAGACCATGGTCTATAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * * *
1257468 GGCATTTTTTG-GTAAGCGTCGCTAAAGACCACGGTTTATAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * *
1257510 GGCGTTTTTT--TTAAGCGCCGCTAAAGATCACGGTCTATAGT
1 GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
* * * *
1257551 GGTGTTTTTAT--TTAAGCGCCGCTAAAGAACATGGTCTATAGC
1 GGCGTTTTT-TGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
1257593 GGCGTT
1 GGCGTT
1257599 GTAAAAAAAA
Statistics
Matches: 542, Mismatches: 59, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
41 35 0.06
42 105 0.19
43 402 0.74
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (43 bp):
GGCGTTTTTTGCCTAAGCGCCGCTAAAGACCATGGTCTATAGT
Found at i:1257874 original size:42 final size:42
Alignment explanation
Indices: 1257811--1257953 Score: 169
Period size: 42 Copynumber: 3.4 Consensus size: 42
1257801 AGCTAATATT
* *
1257811 AGAAAAGACAGACTGAAGCTGGAGAAGGATGGAGCTGACTTAAA
1 AGAAAAGA-A-ACTGAAGCTGGAGAAGGACGAAGCTGACTTAAA
* **
1257855 AGAGAAGAAACTGAAGCTGGATCAGGACGAAGCTGACTTAAA
1 AGAAAAGAAACTGAAGCTGGAGAAGGACGAAGCTGACTTAAA
** **
1257897 AGAAAAGAAACTGAAGCTGGATCAGGACGAAGCTGGGTTAAA
1 AGAAAAGAAACTGAAGCTGGAGAAGGACGAAGCTGACTTAAA
**
1257939 AGAAAACCAACTGAA
1 AGAAAAGAAACTGAA
1257954 TCTAGCCAGT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 81 0.91
43 1 0.01
44 7 0.08
ACGTcount: A:0.45, C:0.13, G:0.29, T:0.13
Consensus pattern (42 bp):
AGAAAAGAAACTGAAGCTGGAGAAGGACGAAGCTGACTTAAA
Found at i:1258199 original size:76 final size:76
Alignment explanation
Indices: 1258009--1258275 Score: 457
Period size: 76 Copynumber: 3.5 Consensus size: 76
1257999 TTTGAAATAC
* * * **
1258009 AATCTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACTGCCAGTATGCATTTGTGTGATGG
1 AATCCCAATGGTTTATTGGGATGTTTATGAACTGAAGATACTGACAATATGTGTTTGTGTGATGG
1258074 --TTGTGTTTG
66 TTTTGTGTTTG
**
1258083 AATGTCAATGGTTTATTGGGATGTTTATGAACTGAAGATACTGACAATATGTGTTTGTGTGATGG
1 AATCCCAATGGTTTATTGGGATGTTTATGAACTGAAGATACTGACAATATGTGTTTGTGTGATGG
1258148 TTTTGTGTTTG
66 TTTTGTGTTTG
1258159 AATCCCAATGGTTTATTGGGATGTTTATGAACTGAAGATACTGACAATATGTGTTTGTGTGATGG
1 AATCCCAATGGTTTATTGGGATGTTTATGAACTGAAGATACTGACAATATGTGTTTGTGTGATGG
1258224 TTTTGTGTTTG
66 TTTTGTGTTTG
1258235 AATCCCAATGGTTTATTGGGATGTTTATGAACTGAAGATAC
1 AATCCCAATGGTTTATTGGGATGTTTATGAACTGAAGATAC
1258276 AGACTGTGTT
Statistics
Matches: 184, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
74 60 0.33
76 124 0.67
ACGTcount: A:0.25, C:0.08, G:0.26, T:0.41
Consensus pattern (76 bp):
AATCCCAATGGTTTATTGGGATGTTTATGAACTGAAGATACTGACAATATGTGTTTGTGTGATGG
TTTTGTGTTTG
Found at i:1259043 original size:21 final size:22
Alignment explanation
Indices: 1259012--1259053 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1259002 CACCCATATA
*
1259012 ATTATTTTTTAAAATTATTTAT
1 ATTATTTTTTAAAACTATTTAT
*
1259034 ATTA-TTTTTAATACTATTTA
1 ATTATTTTTTAAAACTATTTA
1259054 ATAANNNNNN
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTATTTTTTAAAACTATTTAT
Found at i:1259320 original size:30 final size:31
Alignment explanation
Indices: 1259270--1259330 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
1259260 TAATGTTTTT
1259270 TTTAATTTTTACGATATTATATATTACTATAAA
1 TTTAATTTTTA-GATATTATATATTAC-ATAAA
1259303 TTTAATTTTT-G-TATTATATATTACATAA
1 TTTAATTTTTAGATATTATATATTACATAA
1259331 TATATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 4 0.14
30 13 0.46
31 1 0.04
33 10 0.36
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (31 bp):
TTTAATTTTTAGATATTATATATTACATAAA
Found at i:1260143 original size:29 final size:29
Alignment explanation
Indices: 1260111--1260250 Score: 83
Period size: 29 Copynumber: 5.3 Consensus size: 29
1260101 CCTTCCAAAA
1260111 TTCTCTCAAATCCATATTTAATTTCAATT
1 TTCTCTCAAATCCATATTTAATTTCAATT
** * **
1260140 TTCTCT----T--A-ATTTCCTTCCAAAA
1 TTCTCTCAAATCCATATTTAATTTCAATT
1260162 TTCTCTCAAATCCATATTTAATTTCAATT
1 TTCTCTCAAATCCATATTTAATTTCAATT
** * **
1260191 TTCTCT----T--A-ATTTCCTTCCAAAA
1 TTCTCTCAAATCCATATTTAATTTCAATT
1260213 TTCTCTCAAATCCATATTTAATTTCAATT
1 TTCTCTCAAATCCATATTTAATTTCAATT
*
1260242 TGCTCTCAA
1 TTCTCTCAA
1260251 TTTCCTTTTT
Statistics
Matches: 76, Mismatches: 21, Indels: 28
0.61 0.17 0.22
Matches are distributed among these distances:
22 30 0.39
23 2 0.03
25 2 0.03
26 2 0.03
28 2 0.03
29 38 0.50
ACGTcount: A:0.29, C:0.24, G:0.01, T:0.46
Consensus pattern (29 bp):
TTCTCTCAAATCCATATTTAATTTCAATT
Found at i:1260172 original size:51 final size:51
Alignment explanation
Indices: 1260086--1260257 Score: 308
Period size: 51 Copynumber: 3.4 Consensus size: 51
1260076 GCTCTCTCGT
*
1260086 ATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCA
1 ATTTTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCA
*
1260137 ATTTTCTCTTAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCA
1 ATTTTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCA
*
1260188 ATTTTCTCTTAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCA
1 ATTTTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCA
*
1260239 ATTTGCTCTCAATTTCCTT
1 ATTTTCTCTCAATTTCCTT
1260258 TTTAAAAATA
Statistics
Matches: 117, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
51 117 1.00
ACGTcount: A:0.28, C:0.25, G:0.01, T:0.47
Consensus pattern (51 bp):
ATTTTCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATTTCA
Found at i:1262091 original size:18 final size:18
Alignment explanation
Indices: 1262070--1262104 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1262060 CGTTTCCTAG
1262070 CCCTTATATGTATCCTTA
1 CCCTTATATGTATCCTTA
1262088 CCCTTATATGTATCCTT
1 CCCTTATATGTATCCTT
1262105 TTCCGAGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.20, C:0.29, G:0.06, T:0.46
Consensus pattern (18 bp):
CCCTTATATGTATCCTTA
Found at i:1262701 original size:23 final size:23
Alignment explanation
Indices: 1262667--1263244 Score: 611
Period size: 23 Copynumber: 26.3 Consensus size: 23
1262657 AACCTAATTA
1262667 AATT-AATTAAAAACCCTAACCT
1 AATTAAATTAAAAACCCTAACCT
*
1262689 AATTAAATTAAAAACACTAA-C-
1 AATTAAATTAAAAACCCTAACCT
1262710 AATTAAATTAAAAACCCTAACCT
1 AATTAAATTAAAAACCCTAACCT
*
1262733 AATTAAATTCAAAACCCTAACC-
1 AATTAAATTAAAAACCCTAACCT
* *
1262755 -CTTAACTTAAAAACCCTAACCT
1 AATTAAATTAAAAACCCTAACCT
* *
1262777 AATTAAATTAAGAACCCTAACTT
1 AATTAAATTAAAAACCCTAACCT
1262800 AATTAAATTAAAAACCCTAACC-
1 AATTAAATTAAAAACCCTAACCT
** * *
1262822 CGTT-ACTTAAAAACTCTAACC-
1 AATTAAATTAAAAACCCTAACCT
* **
1262843 -CTTAGCTTAAAAACCCTAACC-
1 AATTAAATTAAAAACCCTAACCT
* **
1262864 -CTTAACGT-AAAACCCTAACCT
1 AATTAAATTAAAAACCCTAACCT
*
1262885 AATTAAATTAAGAACCCTAACCT
1 AATTAAATTAAAAACCCTAACCT
1262908 AATTAAATTAAAAACCCTAA-C-
1 AATTAAATTAAAAACCCTAACCT
1262929 AATTAAATTAAAAACCCTAACCT
1 AATTAAATTAAAAACCCTAACCT
*
1262952 AATTAAATTAAAAACTCTAACCT
1 AATTAAATTAAAAACCCTAACCT
*
1262975 AATTAAATTAAAAATCCTAA-CT
1 AATTAAATTAAAAACCCTAACCT
* **
1262997 -CTTAGCTTAAAAACCCTAA-C-
1 AATTAAATTAAAAACCCTAACCT
1263017 AATTAAATTAAAAACCCTAACCT
1 AATTAAATTAAAAACCCTAACCT
*
1263040 AATTAAATTTAAAACCCTAACC-
1 AATTAAATTAAAAACCCTAACCT
* * *
1263062 -CTTAACTTAAAAACTCTAACCT
1 AATTAAATTAAAAACCCTAACCT
*
1263084 AATTAAATTAAAAACCTTAA-C-
1 AATTAAATTAAAAACCCTAACCT
1263105 AATTAAATTAAAAACCCTAACC-
1 AATTAAATTAAAAACCCTAACCT
* *
1263127 -CTTAACTTAAAAACCCTAACCT
1 AATTAAATTAAAAACCCTAACCT
1263149 AATTAAATTAAAAACCCTAAACC-
1 AATTAAATTAAAAACCCT-AACCT
* *
1263172 -CTTAACTTAAAAACCCTAACC-
1 AATTAAATTAAAAACCCTAACCT
* * *
1263193 -CTTAACTTAAAAACCCTAAACT
1 AATTAAATTAAAAACCCTAACCT
*
1263215 AAGTT-AATTAAAAACCCTAAACT
1 AA-TTAAATTAAAAACCCTAACCT
1263238 AAGTTAA
1 AA-TTAA
1263245 TAATTTTACT
Statistics
Matches: 477, Mismatches: 55, Indels: 46
0.83 0.10 0.08
Matches are distributed among these distances:
20 14 0.03
21 204 0.43
22 35 0.07
23 217 0.45
24 7 0.01
ACGTcount: A:0.49, C:0.23, G:0.01, T:0.26
Consensus pattern (23 bp):
AATTAAATTAAAAACCCTAACCT
Found at i:1262725 original size:44 final size:44
Alignment explanation
Indices: 1262667--1263234 Score: 622
Period size: 44 Copynumber: 13.0 Consensus size: 44
1262657 AACCTAATTA
*
1262667 AATT-AATTAAAAACCCTAACCTAATTAAATTAAAAACACTAAC
1 AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
*
1262710 AATTAAATTAAAAACCCTAACCTAATTAAATTCAAAACCCTAAC
1 AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
** * *
1262754 CCTTAACTTAAAAACCCTAACCTAATTAAATTAAGAACCCTAAC
1 AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
** * *
1262798 TTAATTAAATTAAAAACCCTAACC-CGTT-ACTTAAAAACTCTAAC
1 --AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
** ** * **
1262842 CCTTAGCTTAAAAACCCTAACC--CTTAACGT-AAAACCCTAACC
1 AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA-C
*
1262884 TAATTAAATTAAGAACCCTAACCTAATTAAATTAAAAACCCTAAC
1 -AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
*
1262929 AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACTCTAACC
1 AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA-C
* * **
1262974 TAATTAAATTAAAAATCCTAA-CT-CTTAGCTTAAAAACCCTAAC
1 -AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
*
1263017 AATTAAATTAAAAACCCTAACCTAATTAAATTTAAAACCCTAAC
1 AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
** * * *
1263061 CCTTAACTTAAAAACTCTAACCTAATTAAATTAAAAACCTTAAC
1 AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
* *
1263105 AATTAAATTAAAAACCCTAACC--CTTAACTTAAAAACCCTAACC
1 AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAA-C
* *
1263148 TAATTAAATTAAAAACCCTAAACC--CTTAACTTAAAAACCCTAAC
1 -AATTAAATTAAAAACCCT-AACCTAATTAAATTAAAAACCCTAAC
** * *
1263192 CCTTAACTTAAAAACCCTAAACTAAGTT-AATTAAAAACCCTAA
1 AATTAAATTAAAAACCCTAACCTAA-TTAAATTAAAAACCCTAA
1263235 ACTAAGTTAA
Statistics
Matches: 445, Mismatches: 61, Indels: 37
0.82 0.11 0.07
Matches are distributed among these distances:
41 11 0.02
42 60 0.13
43 40 0.09
44 250 0.56
45 36 0.08
46 48 0.11
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.26
Consensus pattern (44 bp):
AATTAAATTAAAAACCCTAACCTAATTAAATTAAAAACCCTAAC
Done.