Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008621.1 Hibiscus syriacus cultivar Beakdansim tig00111584_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1991651
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:922423 original size:20 final size:20
Alignment explanation
Indices: 922398--922459 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
922388 TATTATGCTT
922398 AAAAAAAAGAAGAAAAAGAG
1 AAAAAAAAGAAGAAAAAGAG
922418 AAAAAAAAGAA-AAAAAGAG
1 AAAAAAAAGAAGAAAAAGAG
922437 AAAAGAAAA-AAGAAAAAGA-
1 AAAA-AAAAGAAGAAAAAGAG
922456 AAAA
1 AAAA
922460 GGGGGGTCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
19 18 0.45
20 22 0.55
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAGAAAAAGAG
Found at i:922452 original size:28 final size:28
Alignment explanation
Indices: 922399--922459 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
922389 ATTATGCTTA
*
922399 AAAAAAAGAAGAAAAAGAGAAAAAAAAG
1 AAAAAAAGAAGAAAAAGAAAAAAAAAAG
922427 AAAAAAAG-AG-AAAAGAAAAAAGAAAAAG
1 AAAAAAAGAAGAAAAAG-AAAAA-AAAAAG
922455 AAAAA
1 AAAAA
922460 GGGGGGTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 5 0.17
27 6 0.20
28 19 0.63
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (28 bp):
AAAAAAAGAAGAAAAAGAAAAAAAAAAG
Found at i:923743 original size:83 final size:83
Alignment explanation
Indices: 923601--923823 Score: 401
Period size: 83 Copynumber: 2.7 Consensus size: 83
923591 GAACAAATGC
* * *
923601 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTAACTGATCTGGTTTGTTAAAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
923666 TATTGAATTTGGAAGAGG
66 TATTGAATTTGGAAGAGG
923684 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
923749 TATTGAATTTGGAAGAGG
66 TATTGAATTTGGAAGAGG
* *
923767 AATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGTA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
923824 TGAAACCACA
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 135 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.39
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAGT
TATTGAATTTGGAAGAGG
Found at i:924483 original size:52 final size:52
Alignment explanation
Indices: 924405--924509 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
924395 TATCGATATC
*
924405 TGTGAAATCATCTTGAAATATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
924457 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
924509 T
1 T
924510 CAACATGTTC
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.34
Consensus pattern (52 bp):
TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
Found at i:925001 original size:113 final size:113
Alignment explanation
Indices: 924803--925590 Score: 1130
Period size: 113 Copynumber: 7.0 Consensus size: 113
924793 GCAAAGATTT
* ** *
924803 AAATCCATCA-TTCAATGGATCAACAGTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTT-GATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAA
924867 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
924916 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAA
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
*
924981 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTTTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
925029 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAA
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
925094 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
925142 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATTTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
925207 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * * *** *
925255 AAATTCTTCATTTGACGGATTAGCTTTTCCAGAAAGAGTTCATAATGAGAAGAATTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
925320 AAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAA-CTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * * ****
925367 GAATTCATCACTTAATAGATCAACTTTTACAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
925432 AAGGAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGATT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *****
925480 GAATCCATCACTTGATGGATCAGCTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
* ** *
925545 AAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTGC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
925591 AGGACTCTAT
Statistics
Matches: 620, Mismatches: 53, Indels: 4
0.92 0.08 0.01
Matches are distributed among these distances:
112 97 0.16
113 521 0.84
114 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.29
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATCAACTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:925664 original size:33 final size:35
Alignment explanation
Indices: 925627--925692 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 35
925617 TCATAATCAG
* *
925627 CATTTCCAGAAG-G-AGTTCATAATGAGAAGAACT
1 CATTTCAAGAAGAGAAGTTCACAATGAGAAGAACT
*
925660 CATTTGAAGAAGAAGAAGTTCACAATGAGAAGA
1 CATTTCAAGAAG-AGAAGTTCACAATGAGAAGA
925693 GTTTGTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 10 0.37
35 1 0.04
36 16 0.59
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (35 bp):
CATTTCAAGAAGAGAAGTTCACAATGAGAAGAACT
Found at i:925720 original size:120 final size:123
Alignment explanation
Indices: 925498--925734 Score: 331
Period size: 120 Copynumber: 1.9 Consensus size: 123
925488 CACTTGATGG
* *
925498 ATCAGCTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCAT
1 ATCAGCATTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCT-AAGAAAGAAGAAGAAGTTCAC
*
925563 AATGAGAAGAGCTTGTTCGACCTTTTGCAGGACTCTATCACAGAAAGAGATATATCATA
65 AATGAGAAGAGCTTGTTCGACCTTTTGCAGAACTCTATCACAGAAAGAGATATATCATA
* *
925622 ATCAGCATTTCCAGAAG-GAGTTCATAATGAGAAGAACTCAT-T-TG-AAGAAGAAGAAGTTCAC
1 ATCAGCATTTCCA-AAGAAAGTTCATAATGAGAAGAACTCATCTAAGAAAGAAGAAGAAGTTCAC
* * * *
925683 AATGAGAAGAGTTTGTTC-AGCCTTTTGCATAATTCTATCACAGAAGGAGATA
65 AATGAGAAGAGCTTGTTCGA-CCTTTTGCAGAACTCTATCACAGAAAGAGATA
925735 GATTAGCATC
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
119 1 0.01
120 61 0.60
121 1 0.01
123 1 0.01
124 35 0.34
125 3 0.03
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (123 bp):
ATCAGCATTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTAAGAAAGAAGAAGAAGTTCACA
ATGAGAAGAGCTTGTTCGACCTTTTGCAGAACTCTATCACAGAAAGAGATATATCATA
Found at i:925941 original size:3 final size:3
Alignment explanation
Indices: 925935--925995 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
925925 TTTCCCGGTT
*
925935 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTTA TTA TATA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA TTA TTA TTA
*
925981 TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA
925996 CAACCAGGCC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:927170 original size:29 final size:32
Alignment explanation
Indices: 927105--927171 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 32
927095 TTAGTCCGTT
927105 AATTTTAATTAATATTTTAATCTGAATAGTATG
1 AATTTTAATT-ATATTTTAATCTGAATAGTATG
*
927138 --TTTTAATT-TATTTTAATCT-AATA-TCTG
1 AATTTTAATTATATTTTAATCTGAATAGTATG
927165 AATTTTA
1 AATTTTA
927172 TATAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
27 3 0.10
28 4 0.13
29 16 0.52
31 8 0.26
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.54
Consensus pattern (32 bp):
AATTTTAATTATATTTTAATCTGAATAGTATG
Found at i:929683 original size:2 final size:2
Alignment explanation
Indices: 929676--929705 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
929666 TTATTAGGTT
*
929676 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
929706 AAATTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:934237 original size:56 final size:54
Alignment explanation
Indices: 934177--934797 Score: 292
Period size: 55 Copynumber: 11.4 Consensus size: 54
934167 TCTTTTCGGG
*
934177 GAGTATAGAATTCAATAAATCTTCAGA-AAAATGGGT-TCGCTCCCTATTTCTTCAGA
1 GAGTATAGAATTCAAT-AATCTTCA-ACAAAAT-GGTCT-GCCCCCTATTTCTTCAGA
* * * * *
934233 GAGTATAAGACTTGAATCATCTTCAACAAACTTGTCTGCCCCCTATTTCTTCAGA
1 GAGTAT-AGAATTCAATAATCTTCAACAAAATGGTCTGCCCCCTATTTCTTCAGA
* * * * *
934288 GAGTATA-AGACTCGAACAATCTTCAAC-GATTGCGTCTGCCCCCTATTTCTTTAGA
1 GAGTATAGA-ATTC-AATAATCTTCAACAAAATG-GTCTGCCCCCTATTTCTTCAGA
* * *
934343 GAGTATA-AGA-CCAACAATCTTCATC--AATCGCGTCTGCCCCCTATTTCTTCAGA
1 GAGTATAGA-ATTCAATAATCTTCAACAAAAT-G-GTCTGCCCCCTATTTCTTCAGA
* * * * *
934396 GAGTATAAAATCCGAACAATCTTCAAC-GATTGCGTCTGCCCCCTATTTCTTCAGA
1 GAGTATAGAATTC-AATAATCTTCAACAAAATG-GTCTGCCCCCTATTTCTTCAGA
* * * * *
934451 GAGTATA-AGA-CCCACAATCTTCATC--AATCGCGTCTGCCCCCTATTTCTTCAGT
1 GAGTATAGA-ATTCAATAATCTTCAACAAAAT-G-GTCTGCCCCCTATTTCTTCAGA
* * * *
934504 GAGTATA-AGACTCGAACAATCTTCAAC-GATTGTGTCTGCCCCCTATTTCTTCAGA
1 GAGTATAGA-ATTC-AATAATCTTCAACAAAATG-GTCTGCCCCCTATTTCTTCAGA
* * * * *
934559 GAGTATA-AGA-CCCACAATCTTCATC--AATCGCGTTTGCCCCCTATTTCTTCAGA
1 GAGTATAGA-ATTCAATAATCTTCAACAAAAT-G-GTCTGCCCCCTATTTCTTCAGA
* * * * *
934612 GAGTATA-AGACTCGAACAATCTTCCAC-GATTGTGTCTGCCCCCTATTTCTTCAGA
1 GAGTATAGA-ATTC-AATAATCTTCAACAAAATG-GTCTGCCCCCTATTTCTTCAGA
* * * * *
934667 GAGTATA-AGA-CCCACAATCTTCATC--AATCGCGTTTGCCCCCTATTTCTTCAGA
1 GAGTATAGA-ATTCAATAATCTTCAACAAAAT-G-GTCTGCCCCCTATTTCTTCAGA
* * * * *
934720 GAGTATA-AGACTCGAACAATCTTCCAC-AAATGGGT-TCGCTCCCTATTTC-TCTAGG
1 GAGTATAGA-ATTC-AATAATCTTCAACAAAAT-GGTCT-GCCCCCTATTTCTTC-AGA
* *
934775 GAGTATAGAACTCAAAAATCTTC
1 GAGTATAGAATTCAATAATCTTC
934798 TTCTTACGGG
Statistics
Matches: 479, Mismatches: 59, Indels: 56
0.81 0.10 0.09
Matches are distributed among these distances:
52 8 0.02
53 173 0.36
54 28 0.06
55 233 0.49
56 29 0.06
57 8 0.02
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (54 bp):
GAGTATAGAATTCAATAATCTTCAACAAAATGGTCTGCCCCCTATTTCTTCAGA
Found at i:934781 original size:55 final size:54
Alignment explanation
Indices: 934218--934748 Score: 633
Period size: 55 Copynumber: 9.8 Consensus size: 54
934208 TGGGTTCGCT
* * *
934218 CCCTATTTCTTCAGAGAGTATAAGACTTGAATC-ATCTTCAACAAACT-TGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAA-CAATCTTCCAC-AA-TGCGTCTGCC
* *
934273 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCAC-AATGCGTCTGCC
*
934328 CCCTATTTCTTTAGAGAGTATAAGAC-C-AACAATCTT-CATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCA-CAAT-GCGTCTGCC
* * *
934381 CCCTATTTCTTCAGAGAGTATAA-AATCCGAACAATCTTCAACGATTGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACT-CGAACAATCTTCCAC-AATGCGTCTGCC
*
934436 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTT-CATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCA-CAAT-GCGTCTGCC
* * * *
934489 CCCTATTTCTTCAGTGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCAC-AATGCGTCTGCC
* *
934544 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTT-CATCAATCGCGTTTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCA-CAAT-GCGTCTGCC
* *
934597 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCACGATTGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCAC-AATGCGTCTGCC
* *
934652 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTT-CATCAATCGCGTTTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCA-CAAT-GCGTCTGCC
934705 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCACAA
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCACAA
934749 ATGGGTTCGC
Statistics
Matches: 414, Mismatches: 35, Indels: 54
0.82 0.07 0.11
Matches are distributed among these distances:
52 14 0.03
53 168 0.41
54 10 0.02
55 209 0.50
56 13 0.03
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (54 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCCACAATGCGTCTGCC
Found at i:934781 original size:108 final size:108
Alignment explanation
Indices: 934218--934743 Score: 867
Period size: 108 Copynumber: 4.9 Consensus size: 108
934208 TGGGTTCGCT
** * * **
934218 CCCTATTTCTTCAGAGAGTATAAGACTTGA-ATCATCTTCAACAAACTTGTCTGCCCCCTATTTC
1 CCCTATTTCTTCAGAGAGTATAAGAC-CCACA--ATCTTCATCAATCGCGTCTGCCCCCTATTTC
934282 TTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
63 TTCAGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
* *
934328 CCCTATTTCTTTAGAGAGTATAAGACCAACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
*
934393 AGAGAGTATAA-AATCCGAACAATCTTCAACGATTGCGTCTGCC
66 AGAGAGTATAAGACT-CGAACAATCTTCAACGATTGCGTCTGCC
934436 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
* *
934501 AGTGAGTATAAGACTCGAACAATCTTCAACGATTGTGTCTGCC
66 AGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
*
934544 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTTTGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
* *
934609 AGAGAGTATAAGACTCGAACAATCTTCCACGATTGTGTCTGCC
66 AGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
*
934652 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTTTGCCCCCTATTTCTTC
1 CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
934717 AGAGAGTATAAGACTCGAACAATCTTC
66 AGAGAGTATAAGACTCGAACAATCTTC
934744 CACAAATGGG
Statistics
Matches: 397, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
107 2 0.01
108 366 0.92
109 3 0.01
110 26 0.07
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.30
Consensus pattern (108 bp):
CCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCTGCCCCCTATTTCTTC
AGAGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCC
Found at i:934879 original size:105 final size:105
Alignment explanation
Indices: 934751--935049 Score: 324
Period size: 105 Copynumber: 2.9 Consensus size: 105
934741 TTCCACAAAT
* *
934751 GGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCACTCC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTC-AAAATCTTCTTC-TACGGGTTCGCTCC
* *
934816 TTCTCTCTTTAAGGAGTATAGAACTCGAACATC-TCTTC-AC
64 TTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCTTCTAC
* * * *
934856 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-GAA-CATCTTCAACTGGGTTCGCTCCC
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAAATCTTCTTCTAC-GGGTTCGCT-CC
* * *
934919 TT-TTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTAC
64 TTCTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCTTC-TAC
* * * ** * **
934961 GGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTC--AAACGGGTTCGCTCCT
1 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTC-AAAATCTTCTTCTACGGGTTCGCTCCT
935024 TCTTTCTTTAAGGAGTATAGAACTCG
65 TCTTTCTTTAAGGAGTATAGAACTCG
935050 CATATTTTCA
Statistics
Matches: 161, Mismatches: 24, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
101 2 0.01
102 39 0.24
103 11 0.07
104 4 0.02
105 98 0.61
106 3 0.02
107 1 0.01
108 3 0.02
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (105 bp):
GGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCAAAATCTTCTTCTACGGGTTCGCTCCTT
CTTTCTTTAAGGAGTATAGAACTCGAAAATCTTCTTCTAC
Found at i:934884 original size:51 final size:52
Alignment explanation
Indices: 934751--935049 Score: 311
Period size: 51 Copynumber: 5.7 Consensus size: 52
934741 TTCCACAAAT
* * * * *
934751 GGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCAAAAATCTTCTTCTTAC
1 GGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAACATC-TCTTC-TAC
* * *
934805 GGGTTCACTCCTTCTCTCTTTAAGGAGTATAGAACTCGAACATCTCTTC-AC
1 GGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTCTAC
* * * *
934856 GGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTCGAACA--TCTTCAAC
1 GGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTCTAC
* * * * *
934906 TGGGTTCGCTCCCTTTTTCTTCAGGGAGTATAGAACTCAAAAATCTTCTTCTTAC
1 -GGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAACATC-TCTTC-TAC
* * * *
934961 GGGTTCGCTCCTTCTCTCTTTAAAGAGTATAGAACTCGAACA--TCTTCAAAC
1 GGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTC-TAC
*
935012 GGGTTCGCTCCTTCTTTCTTTAAGGAGTATAGAACTCG
1 GGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCG
935050 CATATTTTCA
Statistics
Matches: 206, Mismatches: 33, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
49 5 0.02
50 2 0.01
51 117 0.57
53 5 0.02
54 75 0.36
55 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (52 bp):
GGGTTCGCTCCCTCTTTCTTTAAGGAGTATAGAACTCGAACATCTCTTCTAC
Found at i:934939 original size:156 final size:155
Alignment explanation
Indices: 934750--935049 Score: 487
Period size: 156 Copynumber: 1.9 Consensus size: 155
934740 CTTCCACAAA
934750 TGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCACTC
1 TGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCACTC
* *
934815 CTTCTCTCTTTAAGGAGTATAGAACTCGAACATCTCTTC-ACGGGTTCGCTCCCTCTTTCTCTAG
66 CTTCTCTCTTTAAAGAGTATAGAACTCGAACA--TCTTCAACGGGTTCGCTCCCTCTTTCTCTAA
*
934879 GGAGTATGGAACTCGAACATCTTCAAC
129 GGAGTATAGAACTCGAACATCTTCAAC
* *
934906 TGGGTTCGCTCCCTTTTTCT-TCAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCGCT
1 TGGGTTCGCTCCCTATTTCTCT-AGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCACT
* *
934970 CCTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCAAACGGGTTCGCTCCTTCTTTCTTTAA
65 CCTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTC-AACGGGTTCGCTCCCTCTTTCTCTAA
935035 GGAGTATAGAACTCG
129 GGAGTATAGAACTCG
935050 CATATTTTCA
Statistics
Matches: 134, Mismatches: 7, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
154 5 0.04
155 1 0.01
156 128 0.96
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (155 bp):
TGGGTTCGCTCCCTATTTCTCTAGGGAGTATAGAACTCAAAAATCTTCTTCTTACGGGTTCACTC
CTTCTCTCTTTAAAGAGTATAGAACTCGAACATCTTCAACGGGTTCGCTCCCTCTTTCTCTAAGG
AGTATAGAACTCGAACATCTTCAAC
Found at i:935386 original size:36 final size:36
Alignment explanation
Indices: 935328--935557 Score: 282
Period size: 36 Copynumber: 6.4 Consensus size: 36
935318 ACTCTTCTGA
* * * **
935328 GAAGGCTTAAAATGGATCTGCTTCACTATTTTTTGGT
1 GAAGGCTTAAGATGG-TTTGCTTCACTATTCTCCGGT
* * *
935365 GAAGACTTAAGATGGTTTGCTTCACTACTCTCTGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
935401 GAAGACTTATGATTGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* * *
935437 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
*
935473 GAAGGCTTCAGATGGTTTGCTTCACTATTCTCCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
* *
935509 GAAGGCTTAGGATGGTTTGCTTCACT-TCTCTTCGGT
1 GAAGGCTTAAGATGGTTTGCTTCACTAT-TCTCCGGT
935545 GAAGGCTTAAGAT
1 GAAGGCTTAAGAT
935558 TGACTTGCTC
Statistics
Matches: 172, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
35 1 0.01
36 158 0.92
37 13 0.08
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (36 bp):
GAAGGCTTAAGATGGTTTGCTTCACTATTCTCCGGT
Found at i:935496 original size:108 final size:108
Alignment explanation
Indices: 935328--935566 Score: 318
Period size: 108 Copynumber: 2.2 Consensus size: 108
935318 ACTCTTCTGA
* * * **
935328 GAAGGCTTAAAATGGATCTGCTTCACTATTTTTTGGTGAAGACTTAAGATGGTTTGCTTCACTAC
1 GAAGGCTTAAGATTGAT-TGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTAC
* * *
935393 TCTCTGGTGAAGACTTATGATTGTTTGCTTCACTAT-TCTCCGGT
65 TCTCCGGTGAAGACTTAGGATGGTTTGCTTCACT-TCTCTCCGGT
* * * *
935437 GAAGGCTTCAGATTGATTGCTTCACTATTCTCCGGTGAAGGCTTCAGATGGTTTGCTTCACTATT
1 GAAGGCTTAAGATTGATTGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTACT
* *
935502 CTCCGGTGAAGGCTTAGGATGGTTTGCTTCACTTCTCTTCGGT
66 CTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGGT
935545 GAAGGCTTAAGATTGACTTGCT
1 GAAGGCTTAAGATTGA-TTGCT
935567 CCAATCTCAT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
107 1 0.01
108 93 0.82
109 19 0.17
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (108 bp):
GAAGGCTTAAGATTGATTGCTTCACTATTCTCCGGTGAAGACTTAAGATGGTTTGCTTCACTACT
CTCCGGTGAAGACTTAGGATGGTTTGCTTCACTTCTCTCCGGT
Found at i:936968 original size:125 final size:125
Alignment explanation
Indices: 936762--936997 Score: 328
Period size: 125 Copynumber: 1.9 Consensus size: 125
936752 ATTTTATTCT
* * * * * *
936762 GGTACGGGCCTTCAAAATGCCTCAATATCTCAAATTATAAGGCTCATTCTCAATGCCTTCTTGGT
1 GGTACGAGCCTTCAAAATACCCCAACACCTCAAATTATAAGGCTCATTCTCAATGCCTTCTTCGT
** * *
936827 CTGAATCTTGTAATTTCATCATGATGTGGGTTCAGTCGCGCCCCAACATTATCTTATAAA
66 CTGAATCTTGTAATTTCAAAATGATGGGGGTTCAGTCACGCCCCAACATTATCTTATAAA
* * *
936887 GGTACGAGTCTTCAAAATACCCCAACACCTCAAATTGTAAGGCTTATTCTCAATGCCTTCTTCGT
1 GGTACGAGCCTTCAAAATACCCCAACACCTCAAATTATAAGGCTCATTCTCAATGCCTTCTTCGT
* * *
936952 CTGGATCTTGTCATTTCAAAATGATGGGGGTTCAGTCATGCCCCAA
66 CTGAATCTTGTAATTTCAAAATGATGGGGGTTCAGTCACGCCCCAA
936998 TGTGGGTATT
Statistics
Matches: 95, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
125 95 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (125 bp):
GGTACGAGCCTTCAAAATACCCCAACACCTCAAATTATAAGGCTCATTCTCAATGCCTTCTTCGT
CTGAATCTTGTAATTTCAAAATGATGGGGGTTCAGTCACGCCCCAACATTATCTTATAAA
Found at i:945827 original size:18 final size:19
Alignment explanation
Indices: 945791--945832 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
945781 AATAATTTTC
945791 AAAAAAAATCAAATACTTT
1 AAAAAAAATCAAATACTTT
* *
945810 AAAAATAATCATAT-CTTT
1 AAAAAAAATCAAATACTTT
945828 AAAAA
1 AAAAA
945833 CATAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAAAATCAAATACTTT
Found at i:947847 original size:34 final size:30
Alignment explanation
Indices: 947809--947877 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
947799 TTGATATAAC
947809 AATTTAAGGCAAAATGGTTTTTGGAATTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGAATT-AATTG
*
947843 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGAATTAATTG
947872 AATTTA
1 AATTTA
947878 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGAATTAATTG
Found at i:947888 original size:29 final size:30
Alignment explanation
Indices: 947818--947877 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
947808 CAATTTAAGG
947818 CAAAATGGTTTTTGGAATTGAATTGAATTTA
1 CAAAAT-GTTTTTGGAATTGAATTGAATTTA
*
947849 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGAATTGAATTGAATTTA
947878 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGAATTGAATTGAATTTA
Found at i:947975 original size:13 final size:13
Alignment explanation
Indices: 947957--948004 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
947947 AGGGTGTCAA
*
947957 AGTGCATCCCTGC
1 AGTGCATCCATGC
947970 AGTGCATCCATGC
1 AGTGCATCCATGC
947983 A-T-C-T-C-TGC
1 AGTGCATCCATGC
947991 AGTGCATCCATGC
1 AGTGCATCCATGC
948004 A
1 A
948005 CCTGCACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
8 4 0.14
9 2 0.07
10 2 0.07
11 2 0.07
12 2 0.07
13 17 0.59
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.25
Consensus pattern (13 bp):
AGTGCATCCATGC
Found at i:947985 original size:21 final size:20
Alignment explanation
Indices: 947959--948122 Score: 119
Period size: 20 Copynumber: 8.3 Consensus size: 20
947949 GGTGTCAAAG
*
947959 TGCATCCCTGCAGTGCATCCA
1 TGCAT-CCTGCAATGCATCCA
*
947980 TGCATCTCTGCAGTGCATCCA
1 TGCATC-CTGCAATGCATCCA
*
948001 TGCA-CCTGCACTAATGCATCGA
1 TGCATCCTG--C-AATGCATCCA
*
948023 TGCATCATGCAATGCATCCA
1 TGCATCCTGCAATGCATCCA
*
948043 TGCA--CT-CAA-GCATCGAA
1 TGCATCCTGCAATGCATC-CA
* * *
948060 TGCA--CT-TAGTGCATCGA
1 TGCATCCTGCAATGCATCCA
* *
948077 TGCATCCTGCCATGCATCGA
1 TGCATCCTGCAATGCATCCA
*
948097 TGCATCCTGCCATGCATCCA
1 TGCATCCTGCAATGCATCCA
948117 TGCATC
1 TGCATC
948123 AAGGCTGCAA
Statistics
Matches: 120, Mismatches: 13, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
16 5 0.04
17 16 0.13
18 6 0.05
19 5 0.04
20 48 0.40
21 25 0.21
22 12 0.10
23 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (20 bp):
TGCATCCTGCAATGCATCCA
Found at i:948093 original size:12 final size:12
Alignment explanation
Indices: 948076--948115 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
948066 TAGTGCATCG
948076 ATGCATCCTGCC
1 ATGCATCCTGCC
948088 ATGCAT-C-G--
1 ATGCATCCTGCC
948096 ATGCATCCTGCC
1 ATGCATCCTGCC
948108 ATGCATCC
1 ATGCATCC
948116 ATGCATCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
8 6 0.25
9 1 0.04
10 2 0.08
11 1 0.04
12 14 0.58
ACGTcount: A:0.20, C:0.38, G:0.17, T:0.25
Consensus pattern (12 bp):
ATGCATCCTGCC
Found at i:950704 original size:65 final size:63
Alignment explanation
Indices: 950582--950789 Score: 224
Period size: 65 Copynumber: 3.2 Consensus size: 63
950572 TTTCAAAGTG
* * ** *
950582 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACACCGAATGCATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTC--GGGATATTTTGAAACATCGAATGCATT
*
950645 TT
62 TA
*
950647 ATGCATCGATGCACACACCATGCATCGATGCACTGGGGAT-TTTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCGGGATATTT-TG-AAACATCGAATGCATTT
950711 A
63 A
* * * *
950712 ATGCATCGATGCATCAACCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCGGGATATTTTGAAACATCGAATGCATTTA
950776 ATGCATCGATGCAC
1 ATGCATCGATGCAC
950790 TAAGGGTCCA
Statistics
Matches: 124, Mismatches: 12, Indels: 16
0.82 0.08 0.11
Matches are distributed among these distances:
62 1 0.01
63 7 0.06
64 47 0.38
65 64 0.52
66 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCGGGATATTTTGAAACATCGAATGCATTTA
Found at i:951747 original size:21 final size:20
Alignment explanation
Indices: 951723--951761 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
951713 TGAAAAACCA
*
951723 CAAATAGAGAAAGCAAACATT
1 CAAACAGAGAAA-CAAACATT
*
951744 CAAACAGAGATACAAACA
1 CAAACAGAGAAACAAACA
951762 GTAGCAGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.59, C:0.18, G:0.13, T:0.10
Consensus pattern (20 bp):
CAAACAGAGAAACAAACATT
Found at i:955141 original size:14 final size:14
Alignment explanation
Indices: 955122--955160 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
955112 TAATGAGGAG
955122 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
955136 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
955150 GAATCTCTGCA
1 TAATCCCTGCA
955161 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:964349 original size:18 final size:18
Alignment explanation
Indices: 964326--964388 Score: 51
Period size: 20 Copynumber: 3.6 Consensus size: 18
964316 TAAATATTGA
964326 ATATTAATATTATTAATT
1 ATATTAATATTATTAATT
* *
964344 ATATT-ATAATATT--TA
1 ATATTAATATTATTAATT
*
964359 ATATTAAAATTATATAAATT
1 ATATTAATATTAT-T-AATT
*
964379 ATGTTAATAT
1 ATATTAATAT
964389 GTTATAATAA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
15 6 0.18
16 5 0.15
17 8 0.24
18 5 0.15
20 9 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
ATATTAATATTATTAATT
Found at i:964387 original size:33 final size:33
Alignment explanation
Indices: 964318--964388 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
964308 ATAAATGCTA
* *
964318 AATATTGAATATTAATATTATTAATTATATTAT
1 AATATTGAATATTAAAATTATTAATTATAGTAT
*
964351 AATATTTAATATTAAAATTATATAAATTAT-GT-T
1 AATATTGAATATTAAAATTAT-T-AATTATAGTAT
964384 AATAT
1 AATAT
964389 GTTATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 25 0.76
34 2 0.06
35 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (33 bp):
AATATTGAATATTAAAATTATTAATTATAGTAT
Found at i:964436 original size:19 final size:19
Alignment explanation
Indices: 964412--964450 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
964402 TAAGGTAAAA
964412 ATACTAGT-ATTAATTAATT
1 ATACTAGTAATTAA-TAATT
964431 ATACTAGTAATTAATAATT
1 ATACTAGTAATTAATAATT
964450 A
1 A
964451 ATATATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (19 bp):
ATACTAGTAATTAATAATT
Found at i:965684 original size:21 final size:20
Alignment explanation
Indices: 965617--965684 Score: 52
Period size: 21 Copynumber: 3.4 Consensus size: 20
965607 GATTGATTGT
* *
965617 AATCGGGCCTGTGTGCCTTGT
1 AATCGGG-CTGTGTTCCTTGA
**
965638 AATC-GGCTGTCCT-CTTGTA
1 AATCGGGCTGTGTTCCTTG-A
965657 AAT-GGGCATGTGTTCCTTGA
1 AATCGGGC-TGTGTTCCTTGA
965677 AATCGGGC
1 AATCGGGC
965685 CTTCGGGCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
18 4 0.11
19 10 0.28
20 10 0.28
21 12 0.33
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.32
Consensus pattern (20 bp):
AATCGGGCTGTGTTCCTTGA
Found at i:965831 original size:19 final size:19
Alignment explanation
Indices: 965807--965878 Score: 119
Period size: 19 Copynumber: 3.8 Consensus size: 19
965797 AAGATCATTC
*
965807 AGGAATTAATGCAATGAA-T
1 AGGAATTAATGCAA-CAATT
965826 AGGAATTAATGCAACAATT
1 AGGAATTAATGCAACAATT
965845 AGGAATTAATGCAACAATT
1 AGGAATTAATGCAACAATT
965864 AGGAATTAATGCAAC
1 AGGAATTAATGCAAC
965879 GAATAAGGGG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
18 2 0.04
19 49 0.96
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (19 bp):
AGGAATTAATGCAACAATT
Found at i:971741 original size:34 final size:36
Alignment explanation
Indices: 971670--971749 Score: 110
Period size: 34 Copynumber: 2.3 Consensus size: 36
971660 GGGGTTGGTC
* * *
971670 ATGTAATTGAAGTATTTTTGGAATTTTAGGTTTAGA
1 ATGTAATTGAAGCATTTTTAGAATTTGAGGTTTAGA
*
971706 ATGTAATTGAAGCA-TTTTAG-ATTTGGGGTTTAGA
1 ATGTAATTGAAGCATTTTTAGAATTTGAGGTTTAGA
971740 ATGTAATTGA
1 ATGTAATTGA
971750 TGATTGTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 22 0.55
35 5 0.12
36 13 0.32
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.44
Consensus pattern (36 bp):
ATGTAATTGAAGCATTTTTAGAATTTGAGGTTTAGA
Found at i:973241 original size:13 final size:13
Alignment explanation
Indices: 973197--973241 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
973187 GAAACAAATA
973197 TTTGAGATTTATCT
1 TTTG-GATTTATCT
973211 TTT-GA-TTAT-T
1 TTTGGATTTATCT
973221 TTTAGGATTTATCT
1 TTT-GGATTTATCT
973235 TTTGGAT
1 TTTGGAT
973242 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.15
11 4 0.15
12 4 0.15
13 8 0.30
14 7 0.26
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.60
Consensus pattern (13 bp):
TTTGGATTTATCT
Found at i:973251 original size:14 final size:14
Alignment explanation
Indices: 973240--973266 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
973230 TATCTTTTGG
973240 ATATTTTATTTTAA
1 ATATTTTATTTTAA
973254 ATATTTTATTTTA
1 ATATTTTATTTTA
973267 TCTTTAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATATTTTATTTTAA
Found at i:973281 original size:20 final size:19
Alignment explanation
Indices: 973241--973282 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
973231 ATCTTTTGGA
*
973241 TATTTTATTTTAAATATTT
1 TATTTTATTTTAAATAGTT
973260 TATTTTATCTTTAAGA-AGTT
1 TATTTTAT-TTTAA-ATAGTT
973280 TAT
1 TAT
973283 CTCTTATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 11 0.55
21 1 0.05
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (19 bp):
TATTTTATTTTAAATAGTT
Found at i:973429 original size:14 final size:12
Alignment explanation
Indices: 973388--973421 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
973378 TCTTTTTCCA
973388 TCTTTG-TTTTT
1 TCTTTGATTTTT
*
973399 ACTTTGATTTTT
1 TCTTTGATTTTT
973411 TCTTTGATTTT
1 TCTTTGATTTT
973422 CTTTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (12 bp):
TCTTTGATTTTT
Found at i:974054 original size:21 final size:21
Alignment explanation
Indices: 974028--974067 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
974018 TTTTTCCTTG
974028 ATTTATTTTCTTTAAATTTTT
1 ATTTATTTTCTTTAAATTTTT
974049 ATTTATTTTCTTTAAATTT
1 ATTTATTTTCTTTAAATTT
974068 CACAACCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (21 bp):
ATTTATTTTCTTTAAATTTTT
Found at i:979790 original size:22 final size:23
Alignment explanation
Indices: 979755--979800 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
979745 TTATTTTTCA
979755 TTTTAATTCCTTAACT-TTAATAT
1 TTTTAATTCCTTAA-TATTAATAT
*
979778 TTTTAATT-TTTAATATTAATAT
1 TTTTAATTCCTTAATATTAATAT
979800 T
1 T
979801 AGTTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 12 0.57
23 8 0.38
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTAATTCCTTAATATTAATAT
Found at i:982078 original size:25 final size:25
Alignment explanation
Indices: 982045--982097 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
982035 TACACTAAAC
982045 AAATCATACTCTAGTAAATCTCATA
1 AAATCATACTCTAGTAAATCTCATA
* *
982070 AAATTATACTGTAGTAAATCTCATA
1 AAATCATACTCTAGTAAATCTCATA
982095 AAA
1 AAA
982098 GAGTTATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (25 bp):
AAATCATACTCTAGTAAATCTCATA
Found at i:982199 original size:32 final size:31
Alignment explanation
Indices: 982161--982237 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
982151 TGGGGCTGTG
* *
982161 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCACA
** **
982193 GGGCCTACCCGAGAATGATCTCAGGGCCACA
1 GGGCCTACCTAAGAAACATCTCAGGGCCACA
*
982224 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
982238 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:983175 original size:29 final size:28
Alignment explanation
Indices: 983127--983286 Score: 178
Period size: 29 Copynumber: 5.5 Consensus size: 28
983117 ATTCGAAAAT
* *
983127 TCCCAAAATATTACCTTTTTTCAAAATAA
1 TCCCAAAATGTCACC-TTTTTCAAAATAA
* *
983156 TGCCAAGAATGTCACCTTTTGCAAAATAA
1 TCCCAA-AATGTCACCTTTTTCAAAATAA
* **
983185 TTCCCATAATGTCATTTTTTTCAAAATAA
1 -TCCCAAAATGTCACCTTTTTCAAAATAA
983214 TTCCCAAAATGTCA-CTTTTTCAAAATAA
1 -TCCCAAAATGTCACCTTTTTCAAAATAA
*
983242 TTCCCAACATGTCACCTTTTTCAAAATAA
1 -TCCCAAAATGTCACCTTTTTCAAAATAA
*
983271 TTCCCAAAATATCACC
1 -TCCCAAAATGTCACC
983287 GAGTCGGGTT
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
28 26 0.23
29 77 0.68
30 11 0.10
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (28 bp):
TCCCAAAATGTCACCTTTTTCAAAATAA
Found at i:983240 original size:57 final size:57
Alignment explanation
Indices: 983141--983285 Score: 204
Period size: 57 Copynumber: 2.5 Consensus size: 57
983131 AAAATATTAC
*
983141 CTTTTTTCAAAATAA-TGCCAAGAATGTCACCTTTTGCAAAATAATTCCCATA-ATGTCA
1 CTTTTTTCAAAATAATTCCCAA-AATGTCA-CTTTTGCAAAATAATTCCCA-ACATGTCA
* *
983199 TTTTTTTCAAAATAATTCCCAAAATGTCACTTTTTCAAAATAATTCCCAACATGTCA
1 CTTTTTTCAAAATAATTCCCAAAATGTCACTTTTGCAAAATAATTCCCAACATGTCA
* *
983256 CCTTTTTCAAAATAATTCCCAAAATATCAC
1 CTTTTTTCAAAATAATTCCCAAAATGTCAC
983286 CGAGTCGGGT
Statistics
Matches: 79, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
56 1 0.01
57 52 0.66
58 21 0.27
59 5 0.06
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.36
Consensus pattern (57 bp):
CTTTTTTCAAAATAATTCCCAAAATGTCACTTTTGCAAAATAATTCCCAACATGTCA
Found at i:983359 original size:19 final size:19
Alignment explanation
Indices: 983337--983373 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
983327 ACTGGTCAGA
*
983337 CCGGTTTGGACCGATCAAG
1 CCGGTTTAGACCGATCAAG
*
983356 CCGGTTTAGACCGGTCAA
1 CCGGTTTAGACCGATCAA
983374 CTATTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.27, G:0.30, T:0.22
Consensus pattern (19 bp):
CCGGTTTAGACCGATCAAG
Found at i:999074 original size:29 final size:29
Alignment explanation
Indices: 999040--999098 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
999030 CCTAAATTAA
999040 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
*
999069 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
999098 T
1 T
999099 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:1003755 original size:29 final size:29
Alignment explanation
Indices: 1003721--1003779 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1003711 CCTAAATTAA
1003721 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1003750 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1003779 T
1 T
1003780 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1006077 original size:20 final size:20
Alignment explanation
Indices: 1006052--1006091 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1006042 TTATTATGTT
*
1006052 CGTTCGCTTGTGTTCGTTTA
1 CGTTCGCTTATGTTCGTTTA
*
1006072 CGTTCGTTTATGTTCGTTTA
1 CGTTCGCTTATGTTCGTTTA
1006092 TCATTTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.17, G:0.23, T:0.53
Consensus pattern (20 bp):
CGTTCGCTTATGTTCGTTTA
Found at i:1006092 original size:10 final size:10
Alignment explanation
Indices: 1006025--1006092 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 10
1006015 GTGTTTGTGT
1006025 TGTTCGTTTA
1 TGTTCGTTTA
*
1006035 TGTTCATTTA
1 TGTTCGTTTA
1006045 T-TAT-G-TT-
1 TGT-TCGTTTA
* * *
1006052 CGTTCGCTTG
1 TGTTCGTTTA
1006062 TGTTCGTTTA
1 TGTTCGTTTA
*
1006072 CGTTCGTTTA
1 TGTTCGTTTA
1006082 TGTTCGTTTA
1 TGTTCGTTTA
1006092 T
1 T
1006093 CATTTAAATG
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
7 1 0.02
8 4 0.09
9 3 0.07
10 37 0.82
ACGTcount: A:0.10, C:0.13, G:0.19, T:0.57
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1008525 original size:10 final size:10
Alignment explanation
Indices: 1008510--1008537 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1008500 ATGTTCAAAC
1008510 GAAAAAAAGA
1 GAAAAAAAGA
1008520 GAAAAAAAGA
1 GAAAAAAAGA
1008530 GAAAAAAA
1 GAAAAAAA
1008538 TAGCATGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
GAAAAAAAGA
Found at i:1009205 original size:21 final size:20
Alignment explanation
Indices: 1009173--1009228 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
1009163 ATTTCAATCT
* *
1009173 ATATAAATTTTTTTTAATTAA
1 ATATATATTTTTTTGAA-TAA
1009194 AT-TACTATTTTTATTGAATAA
1 ATATA-TATTTTT-TTGAATAA
1009215 ATATATATTTTTTT
1 ATATATATTTTTTT
1009229 ATTATTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 4 0.13
21 20 0.67
22 6 0.20
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
ATATATATTTTTTTGAATAA
Found at i:1010869 original size:35 final size:34
Alignment explanation
Indices: 1010794--1010869 Score: 98
Period size: 34 Copynumber: 2.2 Consensus size: 34
1010784 AACACAATCA
* *
1010794 TCAATTATATTCTAAACCCAAAATCCAAAATGCT
1 TCAATTACATTCTAAACCCAAAATCCAAAATACT
* * *
1010828 TAAATTACATTCTAAACCTAAAATTCTAAAATACT
1 TCAATTACATTCTAAACCCAAAA-TCCAAAATACT
1010863 TCAATTA
1 TCAATTA
1010870 TATATCCAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
34 20 0.57
35 15 0.43
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (34 bp):
TCAATTACATTCTAAACCCAAAATCCAAAATACT
Found at i:1012654 original size:41 final size:41
Alignment explanation
Indices: 1012597--1012678 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
1012587 TAGACTGTCC
1012597 ATCCGTATGGGGATGAAATGCAGTGTTAAATTTCAGTCGAG
1 ATCCGTATGGGGATGAAATGCAGTGTTAAATTTCAGTCGAG
1012638 ATCCGTATGGGGATGAAATGCAGTGTTAAATTTCAGTCGAG
1 ATCCGTATGGGGATGAAATGCAGTGTTAAATTTCAGTCGAG
1012679 TCCCTAATGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (41 bp):
ATCCGTATGGGGATGAAATGCAGTGTTAAATTTCAGTCGAG
Found at i:1017232 original size:21 final size:21
Alignment explanation
Indices: 1017214--1017268 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
1017204 TTTGTCCCGT
*
1017214 AGGACCTCATGTATGTCCCAA
1 AGGACCTCATATATGTCCCAA
* *
1017235 AGGACCTCGTATATATCCCAA
1 AGGACCTCATATATGTCCCAA
1017256 AGGACCTCATATA
1 AGGACCTCATATA
1017269 ACCCTTGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (21 bp):
AGGACCTCATATATGTCCCAA
Found at i:1019100 original size:21 final size:22
Alignment explanation
Indices: 1019068--1019108 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1019058 TTTTTCATTG
1019068 ATTTATTTTTCTTTAAATTTTC
1 ATTTATTTTTCTTTAAATTTTC
*
1019090 ATTTA-TTTTCTTTTAATTT
1 ATTTATTTTTCTTTAAATTT
1019109 CACAACCCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (22 bp):
ATTTATTTTTCTTTAAATTTTC
Found at i:1025786 original size:14 final size:14
Alignment explanation
Indices: 1025767--1025795 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1025757 GTAGGAGAGA
1025767 GTGACTGGTTATTT
1 GTGACTGGTTATTT
1025781 GTGACTGGTTATTT
1 GTGACTGGTTATTT
1025795 G
1 G
1025796 GGAGAGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.31, T:0.48
Consensus pattern (14 bp):
GTGACTGGTTATTT
Found at i:1028458 original size:3 final size:3
Alignment explanation
Indices: 1028450--1028636 Score: 259
Period size: 3 Copynumber: 61.7 Consensus size: 3
1028440 TTTATCCATT
*
1028450 TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** *
1028498 GTA TTA TTA TTA TTA TTA GCA TT- TTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1028545 TTA TTA TCA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA GTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
1028591 TTA TTA TTA TTA ATA TTA TATA TTA TTA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TT
1028637 TAATAAATAA
Statistics
Matches: 162, Mismatches: 18, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
2 2 0.01
3 152 0.94
4 8 0.05
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1041313 original size:8 final size:9
Alignment explanation
Indices: 1041265--1041322 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
1041255 CTTGAAGAGG
1041265 AAAAAA-AA
1 AAAAAAGAA
1041273 AAAAAA-AA
1 AAAAAAGAA
*
1041281 AAAAAAGGA
1 AAAAAAGAA
*
1041290 AAGAAAGAA
1 AAAAAAGAA
1041299 AGAAAAAGAA
1 A-AAAAAGAA
*
1041309 GAAAAAGAA
1 AAAAAAGAA
1041318 AAAAA
1 AAAAA
1041323 GGGGGTCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
8 14 0.33
9 21 0.50
10 7 0.17
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:1042343 original size:52 final size:52
Alignment explanation
Indices: 1042265--1042976 Score: 1268
Period size: 52 Copynumber: 13.7 Consensus size: 52
1042255 TATGTGCTCA
*
1042265 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1042317 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1042368 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
1042420 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1042472 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1042523 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1042575 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1042627 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1042679 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1042731 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1042783 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
1042835 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
1042887 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT-GTTTGATCATAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
*
1042939 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1042977 CGAAGAAGTG
Statistics
Matches: 637, Mismatches: 20, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
51 102 0.16
52 535 0.84
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:1044241 original size:114 final size:113
Alignment explanation
Indices: 1043535--1044329 Score: 1158
Period size: 113 Copynumber: 6.9 Consensus size: 113
1043525 CAAAGATTCA
* * *
1043535 AATTCATCATTTGATGGATCATCATTACCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1043600 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * *
1043648 AATTCATCACTTGATGGATCAACATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCATCATCT
1 AATTCATCATTTGATGGATCATCTTTTCCAGAG-AA-AGTTCATAATGAGAAGAA--C-TCATCT
* *
1043713 GAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTG
61 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* *
1043766 AATTCATCACTTGATGGATCATTCTTTTCCAGAAGAAGAGTTCATAATAAGAAGAACTCATCTGA
1 AATTCATCATTTGATGGATCA-TCTTTTCCAG-AGAA-AGTTCATAATGAGAAGAACTCATCTGA
* * *
1043831 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAAACTTTTGCCTG
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* *
1043882 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
1043947 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* *
1043995 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* * * *
1044060 AGGAAGAAGAAGTTCATAAGGAGAAGAATTTGTTCAACCTTTTACCTG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * *
1044108 AATCCATCATTTGGTGGATCATCTTTTCCAGAGAAAATTCATGAATAAGAAGAACTCATCTGAAG
1 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAG
* * *
1044173 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTTA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * ** * *
1044222 AATTCATCATTTGATGGATCAACATGGCCAAAGAAAGTTCATGAATAAGAAGAACTCATCTGAAG
1 AATTCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCAT-AATGAGAAGAACTCATCTGAAG
*
1044287 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
1044330 GTTTGATATC
Statistics
Matches: 632, Mismatches: 42, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
113 256 0.41
114 167 0.26
115 27 0.04
116 72 0.11
117 2 0.00
118 78 0.12
119 28 0.04
120 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
AATTCATCATTTGATGGATCATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:1044634 original size:3 final size:3
Alignment explanation
Indices: 1044626--1044810 Score: 246
Period size: 3 Copynumber: 60.7 Consensus size: 3
1044616 TTTATCCATT
*
1044626 TTA TTA TTA TTA TTTA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* ** *
1044672 GTA TTA TTA TTA TTA TTA GCA TT- TTA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1044719 TTA TTA TCA TTA TTA ATA TTA TTA TTA TTA TTA TTA TTA GTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
1044765 TTA TTA TTA TTA ATA TTA TATA TTA TTA TTA TATA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA TT
1044811 TAATAAATAA
Statistics
Matches: 159, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
2 2 0.01
3 146 0.92
4 11 0.07
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1055198 original size:16 final size:18
Alignment explanation
Indices: 1055163--1055204 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
1055153 GAAAAAGAGG
1055163 AAGAAAAAGAGAGCACAA
1 AAGAAAAAGAGAGCACAA
1055181 AAGAAAAAGAGA-CA-AA
1 AAGAAAAAGAGAGCACAA
1055197 AAGAAAAA
1 AAGAAAAA
1055205 AAGCAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 2 0.08
18 12 0.50
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGAGAGCACAA
Found at i:1056240 original size:30 final size:30
Alignment explanation
Indices: 1056079--1056267 Score: 158
Period size: 30 Copynumber: 6.4 Consensus size: 30
1056069 AGTTTATGGT
* * *
1056079 TTTTTTTTATTTT-GGCCTATTAAATTACTA
1 TTTTTGTTATTTTAGTCCT-TTAAATTTCTA
*
1056109 TTTTTGTTATTTTAGTCAC-TTAAGTTTCTA
1 TTTTTGTTATTTTAGTC-CTTTAAATTTCTA
** *
1056139 TTTTTACTATTTTAGGCCTTTAAATTTCTA
1 TTTTTGTTATTTTAGTCCTTTAAATTTCTA
* * *
1056169 -TTTT-TTAATTTAGTCCCTT-AA-GTCTA
1 TTTTTGTTATTTTAGTCCTTTAAATTTCTA
* *
1056195 TTTTTTGTTAATTTAGTCCTTTAAATTTTTA
1 -TTTTTGTTATTTTAGTCCTTTAAATTTCTA
* *
1056226 TTCTTGTTATTTTAGTCCCTTAAATCTT-TA
1 TTTTTGTTATTTTAGTCCTTTAAAT-TTCTA
*
1056256 TTTTTGGTATTT
1 TTTTTGTTATTT
1056268 AATTTTATCT
Statistics
Matches: 129, Mismatches: 21, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
26 4 0.03
27 2 0.02
28 15 0.12
29 19 0.15
30 81 0.63
31 7 0.05
32 1 0.01
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (30 bp):
TTTTTGTTATTTTAGTCCTTTAAATTTCTA
Found at i:1058084 original size:29 final size:31
Alignment explanation
Indices: 1058047--1058104 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1058037 TGACTAATCA
* *
1058047 TTTCAACTAAC-TT-TTTTCTTTTTGTCTTG
1 TTTCAACTAACATTGATTTCCTTTTGTCTTG
*
1058076 TTTCTACTAACATTGATTTCCTTTTGTCT
1 TTTCAACTAACATTGATTTCCTTTTGTCT
1058105 GCTTTTGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.42
30 2 0.08
31 12 0.50
ACGTcount: A:0.16, C:0.19, G:0.07, T:0.59
Consensus pattern (31 bp):
TTTCAACTAACATTGATTTCCTTTTGTCTTG
Found at i:1059845 original size:7 final size:6
Alignment explanation
Indices: 1059835--1059956 Score: 69
Period size: 6 Copynumber: 20.3 Consensus size: 6
1059825 AATTAAAGCG
* * * *
1059835 AAGAGAA AAGAAA AACAAA GAG-AA AAGAAGCA AAGAAA AA-AAA GAG-CA
1 AAGA-AA AAGAAA AAGAAA AAGAAA AAGAA--A AAGAAA AAGAAA AAGAAA
*
1059883 AAGAAA AA-AAA AAGAAA AA-AAA AAGAAA AA-AACCA AA-ACAA AGGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAA--A AAGA-AA AAGAAA
* *
1059930 AAGCAA AAGAAA AAGCAAA GAGAAA AA
1 AAGAAA AAGAAA AAG-AAA AAGAAA AA
1059957 AGAAGACAAG
Statistics
Matches: 89, Mismatches: 14, Indels: 25
0.70 0.11 0.20
Matches are distributed among these distances:
5 23 0.26
6 45 0.51
7 14 0.16
8 7 0.08
ACGTcount: A:0.77, C:0.07, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:1059855 original size:17 final size:16
Alignment explanation
Indices: 1059835--1059912 Score: 56
Period size: 16 Copynumber: 4.9 Consensus size: 16
1059825 AATTAAAGCG
1059835 AAGAGAAAAGAAAAACA
1 AAGA-AAAAGAAAAACA
*
1059852 AAGAGAAAAG--AAGCA
1 AAGA-AAAAGAAAAACA
*
1059867 AAGAAAAA-AAAGAGCA
1 AAGAAAAAGAAA-AACA
*
1059883 AAGAAAAA-AAAAAGAA
1 AAGAAAAAGAAAAA-CA
*
1059899 AAAAAAAAGAAAAA
1 AAGAAAAAGAAAAA
1059913 AACCAAAACA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.08
15 10 0.19
16 23 0.44
17 15 0.29
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAAACA
Found at i:1059862 original size:24 final size:24
Alignment explanation
Indices: 1059835--1059960 Score: 102
Period size: 25 Copynumber: 5.3 Consensus size: 24
1059825 AATTAAAGCG
1059835 AAGAGAAAAGAAAAACAAAGAGAA
1 AAGAGAAAAGAAAAACAAAGAGAA
* *
1059859 AAGAAGCAAAGAAAAA-AAAGAGCA
1 AAG-AGAAAAGAAAAACAAAGAGAA
* * *
1059883 AAGA-AAAA-AAAAAGAAAAAAAA
1 AAGAGAAAAGAAAAACAAAGAGAA
*
1059905 AAGA-AAAAAACCAAAACAAAG-GAA
1 AAGAGAAAAGA--AAAACAAAGAGAA
1059929 AA-AGCAAAAGAAAAAGCAAAGAGAA
1 AAGAG-AAAAGAAAAA-CAAAGAGAA
*
1059954 AAAAGAA
1 AAGAGAA
1059961 GACAAGAAGT
Statistics
Matches: 82, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.06
22 16 0.20
23 7 0.09
24 22 0.27
25 30 0.37
26 2 0.02
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (24 bp):
AAGAGAAAAGAAAAACAAAGAGAA
Found at i:1059882 original size:16 final size:16
Alignment explanation
Indices: 1059857--1059906 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
1059847 AAACAAAGAG
1059857 AAAAGAAGCAAAGAAAA
1 AAAAG-AGCAAAGAAAA
1059874 AAAAGAGCAAAGAAAA
1 AAAAGAGCAAAGAAAA
*
1059890 AAAAAAG-AAA-AAAA
1 AAAAGAGCAAAGAAAA
1059904 AAA
1 AAA
1059907 GAAAAAAACC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 7 0.22
15 3 0.09
16 17 0.53
17 5 0.16
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAGAGCAAAGAAAA
Found at i:1059898 original size:11 final size:11
Alignment explanation
Indices: 1059882--1059914 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
1059872 AAAAAAGAGC
1059882 AAAGAAAAAAA
1 AAAGAAAAAAA
1059893 AAAGAAAAAAA
1 AAAGAAAAAAA
1059904 AAAGAAAAAAA
1 AAAGAAAAAAA
1059915 CCAAAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAA
Found at i:1059949 original size:17 final size:16
Alignment explanation
Indices: 1059838--1059912 Score: 66
Period size: 15 Copynumber: 4.8 Consensus size: 16
1059828 TAAAGCGAAG
1059838 AGAAAAGAAAAA-CAA
1 AGAAAAGAAAAAGCAA
* *
1059853 AGAGAA-AAGAAGCAA
1 AGAAAAGAAAAAGCAA
1059868 AGAAAA-AAAAGAGCAA
1 AGAAAAGAAAA-AGCAA
* *
1059884 AGAAAAAAAAAAGAAAA
1 AGAAAAGAAAAAG-CAA
*
1059901 AAAAAAGAAAAA
1 AGAAAAGAAAAA
1059913 AACCAAAACA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
14 4 0.08
15 16 0.33
16 13 0.27
17 16 0.33
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (16 bp):
AGAAAAGAAAAAGCAA
Found at i:1059962 original size:12 final size:11
Alignment explanation
Indices: 1059835--1059913 Score: 54
Period size: 11 Copynumber: 6.8 Consensus size: 11
1059825 AATTAAAGCG
*
1059835 AAGAGAAAAGA
1 AAGAAAAAAGA
1059846 AA-AACAAAGAGAA
1 AAGAA-AAA-AG-A
*
1059859 AAGAAGCAAAGA
1 AAGAA-AAAAGA
1059871 AA-AAAAAGAGCA
1 AAGAAAAA-AG-A
*
1059883 AAGAAAAAAAA
1 AAGAAAAAAGA
*
1059894 AAGAAAAAAAA
1 AAGAAAAAAGA
1059905 AAGAAAAAA
1 AAGAAAAAA
1059914 ACCAAAACAA
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
10 3 0.05
11 30 0.54
12 9 0.16
13 10 0.18
14 4 0.07
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAGA
Found at i:1061305 original size:38 final size:38
Alignment explanation
Indices: 1061257--1061335 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
1061247 AAAACCAGAT
* * *
1061257 TTTATCTCGCTTGAGATGGTTTCACTCGAAATAGAAGA
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
**
1061295 TTTATCTCGCTTGAGATAGTTTTGCTCGAAACAAAAGA
1 TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
1061333 TTT
1 TTT
1061336 TAAGAAACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (38 bp):
TTTATCTCGCTTGAGATAGTTTCACTCGAAACAAAAGA
Found at i:1061428 original size:42 final size:41
Alignment explanation
Indices: 1061368--1061493 Score: 144
Period size: 42 Copynumber: 3.0 Consensus size: 41
1061358 AAGGGTTTCT
* * *
1061368 TGATGAGTAAGTCATTCGGGCCATCAATAAGTCTTTTGAGCG
1 TGATG-GTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
*
1061410 TGATGCGTAAGTCCTTCGGGCCATCTATAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
* * * * * *
1061452 AGATGATAAGTCCTTCGAGCCATCCATAAGACCTTCGAGCA
1 TGATGGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
1061493 T
1 T
1061494 AATGTTTTCA
Statistics
Matches: 72, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 31 0.43
42 41 0.57
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (41 bp):
TGATGGTAAGTCCTTCGGGCCATCAATAAGTCTTTCGAGCA
Found at i:1061442 original size:20 final size:20
Alignment explanation
Indices: 1061417--1061491 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
1061407 GCGTGATGCG
*
1061417 TAAGTCCTTCGGGCCATCTA
1 TAAGTCCTTCGAGCCATCTA
* * **
1061437 TAAGTCTTTCGAGCAAGATGA
1 TAAGTCCTTCGAGCCATCT-A
*
1061458 TAAGTCCTTCGAGCCATCCA
1 TAAGTCCTTCGAGCCATCTA
*
1061478 TAAGACCTTCGAGC
1 TAAGTCCTTCGAGC
1061492 ATAATGTTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (20 bp):
TAAGTCCTTCGAGCCATCTA
Found at i:1061957 original size:67 final size:67
Alignment explanation
Indices: 1061846--1062202 Score: 411
Period size: 67 Copynumber: 5.4 Consensus size: 67
1061836 CAAATTTTAT
* * * *
1061846 CTTGAGACAGTTTCTCTTGAAACA-AAAGTCTTTAAATCTATTTCCCTTGAAACAAAATTTAGTC
1 CTTGAGACAGTTTCTCTTGAAACACAAA-TCTTTAAGTATGTTTCCCTTGAAACAAAATTTTGTC
1061910 TCC
65 TCC
* * *
1061913 CTTGAGACAGTTTCTCTTGAAACACAAGTATTTAAGTATGTTTCCCTTGGAACAAAATTTTGTCT
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTAAGTATGTTTCCCTTGAAACAAAATTTTGTCT
1061978 CC
66 CC
* * * *
1061980 CTTGAGACAGTTCCTCTTGAAACACAAATCTTTGAG-ATCGTTTCCCTTGAAAC-GAATTTTATC
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTAAGTAT-GTTTCCCTTGAAACAAAATTTTGTC
1062043 TCC
65 TCC
* * * * * *
1062046 GTTGAGACGGTTTCCCTTGGAACACCAATCTTTGAA-TATATTTCCCTTGAAACAAAATTTTGTC
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTT-AAGTATGTTTCCCTTGAAACAAAATTTTGTC
*
1062110 TCT
65 TCC
* * * *
1062113 CTTGAGACAGTTTCTCTTGAAATACAAATCTTTGAG-ATCGTTTCCCTTAAAAC-AAATTTTGCC
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTAAGTAT-GTTTCCCTTGAAACAAAATTTTGTC
*
1062176 TCT
65 TCC
* *
1062179 CTTAAGACAGTTTCCCTTGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
1062203 AATTTTGTTT
Statistics
Matches: 245, Mismatches: 38, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
66 89 0.36
67 154 0.63
68 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (67 bp):
CTTGAGACAGTTTCTCTTGAAACACAAATCTTTAAGTATGTTTCCCTTGAAACAAAATTTTGTCT
CC
Found at i:1062100 original size:133 final size:134
Alignment explanation
Indices: 1061846--1062202 Score: 474
Period size: 133 Copynumber: 2.7 Consensus size: 134
1061836 CAAATTTTAT
* * *
1061846 CTTGAGACAGTTTCTCTTGAAACA-AAAGTCTTT-AAATCTATTTCCCTTGAAACAAAATTTAGT
1 CTTGAGACAGTTTCTCTTGAAACACAAA-TCTTTGAGATC-GTTTCCCTTGAAACAAATTTTAGT
* * *
1061909 CTCCCTTGAGACAGTTTCTCTTGAAACACAAGTATTTAAGTATGTTTCCCTTGGAACAAAATTTT
64 CTCCCTTGAGACAGTTTCCCTTGAAACACAAGTATTTAAGTATATTTCCCTTGAAACAAAATTTT
1061974 GTCTCC
129 GTCTCC
* *
1061980 CTTGAGACAGTTCCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACGAATTTTA-TCT
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTAGTCT
* * * *
1062044 CCGTTGAGACGGTTTCCCTTGGAACACCAA-TCTTTGAA-TATATTTCCCTTGAAACAAAATTTT
66 CCCTTGAGACAGTTTCCCTTGAAACA-CAAGTATTT-AAGTATATTTCCCTTGAAACAAAATTTT
*
1062107 GTCTCT
129 GTCTCC
* * *
1062113 CTTGAGACAGTTTCTCTTGAAATACAAATCTTTGAGATCGTTTCCCTTAAAACAAATTTT-GCCT
1 CTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTAGTCT
* *
1062177 CTCTTAAGACAGTTTCCCTTGAAACA
66 CCCTTGAGACAGTTTCCCTTGAAACA
1062203 AATTTTGTTT
Statistics
Matches: 195, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
133 136 0.70
134 52 0.27
135 7 0.04
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.36
Consensus pattern (134 bp):
CTTGAGACAGTTTCTCTTGAAACACAAATCTTTGAGATCGTTTCCCTTGAAACAAATTTTAGTCT
CCCTTGAGACAGTTTCCCTTGAAACACAAGTATTTAAGTATATTTCCCTTGAAACAAAATTTTGT
CTCC
Found at i:1062168 original size:28 final size:29
Alignment explanation
Indices: 1062114--1062173 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
1062104 TTTGTCTCTC
*
1062114 TTGAGACAGTTTCTCTTGAAATACAAATCT
1 TTGAGACAGTTTCCCTTGAAATACAAAT-T
1062144 TTGAGATC-GTTTCCCTT-AAA-ACAAATT
1 TTGAGA-CAGTTTCCCTTGAAATACAAATT
1062171 TTG
1 TTG
1062174 CCTCTCTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 4 0.14
28 6 0.21
29 3 0.11
30 14 0.50
31 1 0.04
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (29 bp):
TTGAGACAGTTTCCCTTGAAATACAAATT
Found at i:1062202 original size:36 final size:36
Alignment explanation
Indices: 1062086--1062346 Score: 234
Period size: 36 Copynumber: 7.4 Consensus size: 36
1062076 TTTGAATATA
*
1062086 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTAAAAC-AAATTTTGTCTCTCTTGAGACAG
*
1062123 TTTCTCTTGAAATACAAA-------TCT-TTGAGATC-G
1 TTTCCCTT-AAA-ACAAATTTTGTCTCTCTTGAGA-CAG
* *
1062153 TTTCCCTTAAAACAAATTTTGCCTCTCTTAAGACAG
1 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * *
1062189 TTTCCCTTGAAACAAATTTTGTTTCCCTTGAGACAG
1 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
1062225 TTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGACGG
1 TTTCCCTTAAAACAAA-TTTTGTCTCTCTTGAGACAG
** * *
1062262 TTTCTTTTAAAAAAAATTTTGTCTGTCTTGAGACAG
1 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * *
1062298 TTTCCCTTAAAACAAGTTTTGTCTCTCTTGATACGG
1 TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
1062334 TTTCTCTTGAAAC
1 TTTCCCTTAAAAC
1062347 CATCATACCC
Statistics
Matches: 184, Mismatches: 27, Indels: 27
0.77 0.11 0.11
Matches are distributed among these distances:
28 5 0.03
29 3 0.02
30 14 0.08
31 4 0.02
35 4 0.02
36 109 0.59
37 38 0.21
38 5 0.03
39 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCCCTTAAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:1063113 original size:16 final size:18
Alignment explanation
Indices: 1063076--1063119 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 18
1063066 AAAAATGAGG
1063076 AAGAAAAAGAGAACACAA
1 AAGAAAAAGAGAACACAA
*
1063094 AAGAATAAGAG-ACA-AA
1 AAGAAAAAGAGAACACAA
1063110 AAGAAAAAGA
1 AAGAAAAAGA
1063120 AAGCAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.46
17 3 0.12
18 10 0.42
ACGTcount: A:0.73, C:0.07, G:0.18, T:0.02
Consensus pattern (18 bp):
AAGAAAAAGAGAACACAA
Found at i:1063946 original size:59 final size:60
Alignment explanation
Indices: 1063877--1064008 Score: 185
Period size: 59 Copynumber: 2.2 Consensus size: 60
1063867 GTAATTACTA
* * *
1063877 TTTACTCCCTTAAGTTTCTATTTTTACTATTTTGGCCCTTTAAA-TTATATTTTTGTTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTACTATTTTAGCCCTTTAAATTTATATTCTTGTTAT
* * * * *
1063936 TTTAGTCCCTTAAGTTTTTGTTTTTTCTATTTTAGTCCTTTAAATTTCTATTCTTGTTAT
1 TTTAGTCCCTTAAGTTTCTATTTTTACTATTTTAGCCCTTTAAATTTATATTCTTGTTAT
1063996 TTTAGTCCCTTAA
1 TTTAGTCCCTTAA
1064009 ATGTTTATTT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 38 0.59
60 26 0.41
ACGTcount: A:0.19, C:0.15, G:0.08, T:0.58
Consensus pattern (60 bp):
TTTAGTCCCTTAAGTTTCTATTTTTACTATTTTAGCCCTTTAAATTTATATTCTTGTTAT
Found at i:1063960 original size:30 final size:30
Alignment explanation
Indices: 1063877--1064027 Score: 137
Period size: 30 Copynumber: 5.1 Consensus size: 30
1063867 GTAATTACTA
* * * **
1063877 TTTACTCCCTTAAGTTTCTATTTTTACTAT
1 TTTAGTCCCTTAAATTTTTATTTTTGTTAT
* *
1063907 TTT-GGCCCTTTAAA-TTATATTTTTGTTAT
1 TTTAGTCCC-TTAAATTTTTATTTTTGTTAT
* *
1063936 TTTAGTCCCTTAAGTTTTTGTTTTT-TCTAT
1 TTTAGTCCCTTAAATTTTTATTTTTGT-TAT
* * *
1063966 TTTAGTCCTTTAAATTTCTATTCTTGTTAT
1 TTTAGTCCCTTAAATTTTTATTTTTGTTAT
* *
1063996 TTTAGTCCCTTAAATGTTTATTTTTGGTAT
1 TTTAGTCCCTTAAATTTTTATTTTTGTTAT
1064026 TT
1 TT
1064028 AATTTTATCT
Statistics
Matches: 96, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
29 23 0.24
30 72 0.75
31 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.60
Consensus pattern (30 bp):
TTTAGTCCCTTAAATTTTTATTTTTGTTAT
Found at i:1064027 original size:60 final size:58
Alignment explanation
Indices: 1063877--1064020 Score: 180
Period size: 60 Copynumber: 2.4 Consensus size: 58
1063867 GTAATTACTA
* * *
1063877 TTTACTCCCTTAAGTTTCTATTTTTACTATTTTGGCCCTTTAAATTATATTTTTGTTAT
1 TTTAGTCCCTTAAGTTT-TATTTTTACTATTTTAGCCCTTTAAATTATATTCTTGTTAT
* * * *
1063936 TTTAGTCCCTTAAGTTTTTGTTTTTTCTATTTTAGTCCTTTAAATTTCTATTCTTGTTAT
1 TTTAGTCCCTTAAG-TTTTATTTTTACTATTTTAGCCCTTTAAA-TTATATTCTTGTTAT
*
1063996 TTTAGTCCCTTAAATGTTTATTTTT
1 TTTAGTCCCTTAAGT-TTTATTTTT
1064021 GGTATTTAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
59 36 0.49
60 37 0.51
ACGTcount: A:0.19, C:0.14, G:0.08, T:0.60
Consensus pattern (58 bp):
TTTAGTCCCTTAAGTTTTATTTTTACTATTTTAGCCCTTTAAATTATATTCTTGTTAT
Found at i:1066495 original size:38 final size:39
Alignment explanation
Indices: 1066428--1066796 Score: 175
Period size: 37 Copynumber: 9.7 Consensus size: 39
1066418 ATAGTTTACG
1066428 AATGATTTTTGAAATATATATAATATATATAGTTTTGAA
1 AATGATTTTTGAAATATATATAATATATATAGTTTTGAA
*
1066467 AATGATTTTTGAAA-ATGGATAT-AT-TATATTGTTTTG-A
1 AATGATTTTTGAAATAT--ATATAATATATATAGTTTTGAA
* ** * *
1066504 AATCATTTTAAAAATTTATATAATAT-T-TGGGTTTT-AA
1 AATGATTTTTGAAATATATATAATATATAT-AGTTTTGAA
* * *
1066541 AA-AATATTTTGAAA-AT-TAT-ATAATATATGGTTTTTTAA
1 AATGAT-TTTTGAAATATATATAAT-ATATATAG-TTTTGAA
** *
1066579 AA--A-AATTGAAA-ATATAT-A-ATATATAGTTTTTAA
1 AATGATTTTTGAAATATATATAATATATATAGTTTTGAA
* * *
1066612 AA-CA-TGTTGAAAATATATATAAATAATATATAGTTTTTAA
1 AATGATTTTTG-AAATATATAT-AAT-ATATATAGTTTTGAA
* * *
1066652 AA-CATTTTTAATATATATATATATATATATATATAGTTTTTAA
1 AATGATTTTT--GA-A-ATATATATA-ATATATATAGTTTTGAA
* *
1066695 AA-CA-TTTTGAAA-ATATATATATAATATATAGTTTTTAA
1 AATGATTTTTGAAATATATATA-AT-ATATATAGTTTTGAA
*
1066733 AA-CA-TTTTGAAATATATAT-ATAATATATAGTTTT-AA
1 AATGATTTTTGAAATATATATAAT-ATATATAGTTTTGAA
*
1066769 AA-CA-TTTTGAAAATATATATAATATATA
1 AATGATTTTTG-AAATATATATAATATATA
1066797 GTTTTTTAAA
Statistics
Matches: 281, Mismatches: 18, Indels: 64
0.77 0.05 0.18
Matches are distributed among these distances:
33 9 0.03
34 13 0.05
35 16 0.06
36 32 0.11
37 75 0.27
38 50 0.18
39 23 0.08
40 24 0.09
41 3 0.01
42 5 0.02
43 21 0.07
44 10 0.04
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (39 bp):
AATGATTTTTGAAATATATATAATATATATAGTTTTGAA
Found at i:1066538 original size:37 final size:36
Alignment explanation
Indices: 1066503--1066795 Score: 134
Period size: 40 Copynumber: 7.8 Consensus size: 36
1066493 TATTGTTTTG
*
1066503 AAATCATTTTAAAAATTTATATAATATTTGGGTTTTAAA
1 AAAT-ATTTTAAAAA-TTATATAATATATGGGTTTT-AA
* *
1066542 AAATATTTTGAAAATTATATAATATATGGTTTTTTAA
1 AAATATTTTAAAAATTATATAATATATGG-GTTTTAA
* * * *
1066579 AAA-A-ATTGAAAA-TATATAATATATAGTTTTTAA
1 AAATATTTTAAAAATTATATAATATATGGGTTTTAA
* * * *
1066612 AACAT-GTTGAAAATATATATAAATAATATATAGTTTTTAA
1 AA-ATATTTTAAAA-AT-TAT--ATAATATATGGGTTTTAA
** *
1066652 AACAT-TTTTAATATATATATATATATATATATATAGTTTTTA
1 AA-ATATTTTAA-A-A-AT-TATATA-ATATAT-GGGTTTTAA
* * *
1066694 AAACATTTTGAAAATATATATATAATATATAGTTTTTAA
1 AAATATTTT-AAAA-AT-TATATAATATATGGGTTTTAA
* * *
1066733 AACAT-TTTGAAATATATATATAATATAT-AGTTTT-A
1 AA-ATATTTTAAAAAT-TATATAATATATGGGTTTTAA
* *
1066768 AAACATTTTGAAAATATATATAATATAT
1 AAATATTTTAAAAAT-TATATAATATAT
1066796 AGTTTTTTAA
Statistics
Matches: 209, Mismatches: 28, Indels: 38
0.76 0.10 0.14
Matches are distributed among these distances:
33 9 0.04
34 15 0.07
35 34 0.16
36 6 0.03
37 34 0.16
38 19 0.09
39 14 0.07
40 37 0.18
41 19 0.09
42 20 0.10
43 2 0.01
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (36 bp):
AAATATTTTAAAAATTATATAATATATGGGTTTTAA
Found at i:1066600 original size:34 final size:33
Alignment explanation
Indices: 1066520--1066630 Score: 123
Period size: 34 Copynumber: 3.2 Consensus size: 33
1066510 TTTAAAAATT
* *
1066520 TATATAATATTTGGGTTTTAAAAAATATTTTGAAAA
1 TATATAATATATGGTTTTTAAAAAA-A--TTGAAAA
1066556 TTATATAATATATGGTTTTTTAAAAAAATTGAAAA
1 -TATATAATATATGG-TTTTTAAAAAAATTGAAAA
* **
1066591 TATATAATATATAGTTTTTAAAACATGTTGAAAA
1 TATATAATATATGGTTTTTAAAA-AAATTGAAAA
1066625 TATATA
1 TATATA
1066631 TAAATAATAT
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
33 9 0.13
34 27 0.40
35 7 0.10
37 14 0.21
38 10 0.15
ACGTcount: A:0.47, C:0.01, G:0.09, T:0.43
Consensus pattern (33 bp):
TATATAATATATGGTTTTTAAAAAAATTGAAAA
Found at i:1066669 original size:2 final size:2
Alignment explanation
Indices: 1066662--1066686 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1066652 AACATTTTTA
1066662 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1066687 GTTTTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1066711 original size:35 final size:37
Alignment explanation
Indices: 1066434--1066816 Score: 365
Period size: 36 Copynumber: 10.2 Consensus size: 37
1066424 TACGAATGAT
* *
1066434 TTTTGAAATATATATA-ATATATATAGTTTTGAAAATGA
1 TTTTGAAATATATATATA-ATATATAGTTTTTAAAA-CA
** * * * *
1066472 TTTTTGAAA-ATGGATATATTATATTGTTTTGAAATCA
1 -TTTTGAAATATATATATAATATATAGTTTTTAAAACA
* * * * * *
1066509 TTTT-AAAAATTTATATAATATTTGGGTTTTAAAAAATA
1 TTTTGAAATATATATATAATATAT-AGTTTT-TAAAACA
*
1066547 TTTTGAAA-AT-TATATAATATATGGTTTTTTAAAA-A
1 TTTTGAAATATATATATAATATATAG-TTTTTAAAACA
**
1066582 AATTG-AA-A-ATATATAATATATAGTTTTTAAAACA
1 TTTTGAAATATATATATAATATATAGTTTTTAAAACA
*
1066616 TGTTGAAAATATATATAAATAATATATAGTTTTTAAAACA
1 TTTTG-AAATATATAT--ATAATATATAGTTTTTAAAACA
*
1066656 TTTTTAATATATATATATATATATATATATAGTTTTTAAAACA
1 -TTTT--GA-A-ATATATATATA-ATATATAGTTTTTAAAACA
1066699 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
1 TTTTG-AAATATATATATAATATATAGTTTTTAAAACA
1066737 TTTTGAAATATATATATAATATATAG-TTTTAAAACA
1 TTTTGAAATATATATATAATATATAGTTTTTAAAACA
*
1066773 TTTTGAAA-ATATATATAATATATAGTTTTTTAAACA
1 TTTTGAAATATATATATAATATATAGTTTTTAAAACA
1066809 TTTTGAAA
1 TTTTGAAA
1066817 ATTTAATTTT
Statistics
Matches: 297, Mismatches: 25, Indels: 47
0.80 0.07 0.13
Matches are distributed among these distances:
33 9 0.03
34 20 0.07
35 24 0.08
36 58 0.20
37 43 0.14
38 57 0.19
39 23 0.08
40 23 0.08
41 4 0.01
42 8 0.03
43 20 0.07
44 8 0.03
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (37 bp):
TTTTGAAATATATATATAATATATAGTTTTTAAAACA
Found at i:1066848 original size:72 final size:74
Alignment explanation
Indices: 1066434--1066816 Score: 360
Period size: 74 Copynumber: 5.1 Consensus size: 74
1066424 TACGAATGAT
* **
1066434 TTTTGAAATATATATA-ATATATATAGTTTTGAAAATGATTTTTGAAAATGGATATAT--TATAT
1 TTTTGAAATATATATATA-ATATATAGTTTT-AAAA-CA-TTTTGAAAATATATATATAATATAT
* * *
1066496 TGTTTTGAAATCA
62 AGTTTTTAAAACA
* * * * * *
1066509 TTTT-AAAAATTTATATAATATTTGGGTTTTAAAAAATATTTTG-AAA-AT-TATATAATATATG
1 TTTTGAAATATATATATAATATAT-AGTTTT--AAAACATTTTGAAAATATATATATAATATATA
1066570 GTTTTTTAAAA-A
63 G-TTTTTAAAACA
** *
1066582 AATTG-AA-A-ATATATAATATATAGTTTTTAAAACATGTTGAAAATATATATAAATAATATATA
1 TTTTGAAATATATATATAATATATAG-TTTTAAAACATTTTGAAAATATATAT--ATAATATATA
1066644 GTTTTTAAAACA
63 GTTTTTAAAACA
*
1066656 TTTTTAATATATATATATATATATATATATAGTTTTTAAAACATTTTGAAAATATATATATAATA
1 -TTTT--GA-A-ATATATATATA-ATATATAG-TTTTAAAACATTTTGAAAATATATATATAATA
1066721 TATAGTTTTTAAAACA
59 TATAGTTTTTAAAACA
1066737 TTTTGAAATATATATATAATATATAGTTTTAAAACATTTTG-AAA-ATATATATAATATATAGTT
1 TTTTGAAATATATATATAATATATAGTTTTAAAACATTTTGAAAATATATATATAATATATAGTT
*
1066800 TTTTAAACA
66 TTTAAAACA
1066809 TTTTGAAA
1 TTTTGAAA
1066817 ATTTAATTTT
Statistics
Matches: 260, Mismatches: 25, Indels: 49
0.78 0.07 0.15
Matches are distributed among these distances:
69 9 0.03
70 4 0.02
71 22 0.08
72 39 0.15
73 26 0.10
74 52 0.20
75 21 0.08
76 15 0.06
77 1 0.00
78 1 0.00
79 1 0.00
80 5 0.02
81 23 0.09
82 7 0.03
83 34 0.13
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (74 bp):
TTTTGAAATATATATATAATATATAGTTTTAAAACATTTTGAAAATATATATATAATATATAGTT
TTTAAAACA
Found at i:1067938 original size:15 final size:16
Alignment explanation
Indices: 1067918--1067947 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1067908 TTAGTATGTC
1067918 TTTTATT-TTATTTTT
1 TTTTATTATTATTTTT
1067933 TTTTATTATTATTTT
1 TTTTATTATTATTTT
1067948 ATCTATTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTATTATTATTTTT
Found at i:1068767 original size:64 final size:64
Alignment explanation
Indices: 1068699--1068863 Score: 160
Period size: 64 Copynumber: 2.6 Consensus size: 64
1068689 ATAAATATGC
* * *
1068699 TTCGATGTTTTGAA-AAAGCCTAG-GTGCATCGATGCATGGCT-TGTGCATCGGTGCATAAAATC
1 TTCGATGTTTT-AATAAA-CATAGAGTGCATCGATGCATGG-TATGTGCATCGGTACACAAAATC
1068761 AA
63 AA
* * * * *
1068763 TTCGATATTTTAATATATATGGAGTGCATCGATGCATGGTATGTGCATCGGTACACAAAATCCA
1 TTCGATGTTTTAATAAACATAGAGTGCATCGATGCATGGTATGTGCATCGGTACACAAAATCAA
* *
1068827 TTCGATG-TTCAATTAAAACA-AGGGTGCATCGATGCAT
1 TTCGATGTTTTAA-T-AAACATAGAGTGCATCGATGCAT
1068864 TGATTCATGC
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
63 9 0.11
64 70 0.85
65 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (64 bp):
TTCGATGTTTTAATAAACATAGAGTGCATCGATGCATGGTATGTGCATCGGTACACAAAATCAA
Found at i:1069229 original size:16 final size:17
Alignment explanation
Indices: 1069208--1069244 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1069198 CTCCCCCTTA
1069208 CTTTAAC-ACTTC-CCCC
1 CTTTAACGA-TTCTCCCC
1069224 CTTTAACGATTCTCCCC
1 CTTTAACGATTCTCCCC
1069241 CTTT
1 CTTT
1069245 TTGTTAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.16, C:0.43, G:0.03, T:0.38
Consensus pattern (17 bp):
CTTTAACGATTCTCCCC
Found at i:1069927 original size:21 final size:21
Alignment explanation
Indices: 1069891--1069937 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1069881 CCGGAAGAGG
** * *
1069891 AGGAGGAGCATGAGAAGCGGT
1 AGGAGGAGCACAAGAAGAGCT
1069912 AGGAGGAGCACAAGAAGAGCT
1 AGGAGGAGCACAAGAAGAGCT
1069933 AGGAG
1 AGGAG
1069938 CAGCTCGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.45, T:0.06
Consensus pattern (21 bp):
AGGAGGAGCACAAGAAGAGCT
Found at i:1070505 original size:19 final size:18
Alignment explanation
Indices: 1070469--1070505 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
1070459 TCAGAGAAAA
*
1070469 TTTTGAAAAAATGTTTGT
1 TTTTGAAAAAATGATTGT
1070487 TTTTGAAAAAATTGATTGT
1 TTTTGAAAAAA-TGATTGT
1070506 AAAATATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (18 bp):
TTTTGAAAAAATGATTGT
Found at i:1070923 original size:21 final size:21
Alignment explanation
Indices: 1070899--1070962 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 21
1070889 TCGGTGCATC
1070899 TTCATGATGTATCGATGCACA
1 TTCATGATGTATCGATGCACA
* * *
1070920 TTCAAAGGGATGCATCGATGCACT
1 TTC--A-TGATGTATCGATGCACA
1070944 TTCAT-AGTGTATCGATGCA
1 TTCATGA-TGTATCGATGCA
1070963 TTATGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 1 0.03
23 1 0.03
24 17 0.50
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (21 bp):
TTCATGATGTATCGATGCACA
Found at i:1070948 original size:45 final size:44
Alignment explanation
Indices: 1070869--1070962 Score: 122
Period size: 45 Copynumber: 2.1 Consensus size: 44
1070859 TTGTGCATCA
*
1070869 ATGCACATTCAAGGAGTGCATCGGTGCATCTTCAT-GATGTATCG
1 ATGCACATTCAAGGAGTGCATCGATGCATCTTCATAG-TGTATCG
1070913 ATGCACATTCAAAGG-GATGCATCGATGCA-CTTTCATAGTGTATCG
1 ATGCACATTC-AAGGAG-TGCATCGATGCATC-TTCATAGTGTATCG
1070958 ATGCA
1 ATGCA
1070963 TTATGCACAA
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
44 12 0.27
45 32 0.71
46 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (44 bp):
ATGCACATTCAAGGAGTGCATCGATGCATCTTCATAGTGTATCG
Found at i:1077269 original size:3 final size:3
Alignment explanation
Indices: 1077261--1077302 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
1077251 ATTTATTTCT
1077261 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA -TA TATA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TT
1077303 TTTTATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.17
3 26 0.74
4 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1077325 original size:29 final size:29
Alignment explanation
Indices: 1077213--1077328 Score: 74
Period size: 34 Copynumber: 3.7 Consensus size: 29
1077203 ATATTTTCCC
* *
1077213 TTTGATTTATTGAATATTTTTATCCTTTTTCT
1 TTTGATTTATTTAATA-TTTTAT--TTTTTAT
**
1077245 CCTTTGATTTATTTCTTTATTATTATTATTATTAT
1 --TTTGATTTATTT-AATATT-TTATT-TT-TTAT
*
1077280 TATT-ATTT-TATATATATTTTATTTTTTAT
1 T-TTGATTTATTTA-ATATTTTATTTTTTAT
1077309 TTTGATTTATTTAATATTTT
1 TTTGATTTATTTAATATTTT
1077329 TTCTTTGATT
Statistics
Matches: 66, Mismatches: 8, Indels: 21
0.69 0.08 0.22
Matches are distributed among these distances:
28 2 0.03
29 16 0.24
30 5 0.08
31 5 0.08
32 6 0.09
33 6 0.09
34 17 0.26
35 9 0.14
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.68
Consensus pattern (29 bp):
TTTGATTTATTTAATATTTTATTTTTTAT
Found at i:1077328 original size:23 final size:23
Alignment explanation
Indices: 1077277--1077352 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
1077267 TTATTATTAT
* *
1077277 TATTATTATTTT-ATATATATTTTA
1 TATTTTTATTTTGAT-T-TATTTAA
1077301 T-TTTTTATTTTGATTTATTTAA
1 TATTTTTATTTTGATTTATTTAA
1077323 TATTTTT-TCTTTGATTTATTTAA
1 TATTTTTAT-TTTGATTTATTTAA
1077346 TATTTTT
1 TATTTTT
1077353 CGAATTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.17
23 36 0.77
24 3 0.06
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (23 bp):
TATTTTTATTTTGATTTATTTAA
Found at i:1077352 original size:24 final size:24
Alignment explanation
Indices: 1077299--1077352 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 24
1077289 ATATATATTT
1077299 TATTTTTTATTTTGATTTATTTAA
1 TATTTTTTATTTTGATTTATTTAA
*
1077323 TATTTTTT-CTTTGATTTATTTAA
1 TATTTTTTATTTTGATTTATTTAA
1077346 TATTTTT
1 TATTTTT
1077353 CGAATTTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 21 0.72
24 8 0.28
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.72
Consensus pattern (24 bp):
TATTTTTTATTTTGATTTATTTAA
Found at i:1078939 original size:17 final size:17
Alignment explanation
Indices: 1078919--1078951 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1078909 TTACCTTACA
1078919 TATTTGTATAT-CTTATT
1 TATTT-TATATACTTATT
1078936 TATTTTATATACTTAT
1 TATTTTATATACTTAT
1078952 GTTGCATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTTTATATACTTATT
Found at i:1080050 original size:14 final size:15
Alignment explanation
Indices: 1080020--1080051 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1080010 TTCTCGATCC
1080020 TTAAGATTAATTTTT
1 TTAAGATTAATTTTT
*
1080035 TTAATATTAATTTTT
1 TTAAGATTAATTTTT
1080050 TT
1 TT
1080052 GTTGCCTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TTAAGATTAATTTTT
Found at i:1080271 original size:24 final size:25
Alignment explanation
Indices: 1080221--1080271 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
1080211 TTCGAGAAGT
*
1080221 GAAATTGAATAATAATTGAATAGACA
1 GAAATTGAATAATAA-TAAATAGACA
*
1080247 GAAATTGAATGATAA-AAATAGACA
1 GAAATTGAATAATAATAAATAGACA
1080271 G
1 G
1080272 GCGGAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 9 0.39
26 14 0.61
ACGTcount: A:0.55, C:0.04, G:0.18, T:0.24
Consensus pattern (25 bp):
GAAATTGAATAATAATAAATAGACA
Found at i:1080978 original size:8 final size:8
Alignment explanation
Indices: 1080965--1081009 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
1080955 AACAAGTCCC
1080965 TTTTGTTT
1 TTTTGTTT
1080973 TTTTGTCTT
1 TTTTGT-TT
1080982 TTTT-TGTT
1 TTTTGT-TT
1080990 TTTTGTTT
1 TTTTGTTT
*
1080998 TTTCGTTT
1 TTTTGTTT
1081006 TTTT
1 TTTT
1081010 TTGGGTGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 25 0.78
9 7 0.22
ACGTcount: A:0.00, C:0.04, G:0.11, T:0.84
Consensus pattern (8 bp):
TTTTGTTT
Found at i:1080997 original size:25 final size:25
Alignment explanation
Indices: 1080965--1081012 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1080955 AACAAGTCCC
*
1080965 TTTTGTTTTTTTGTCTTTTTTTGTT
1 TTTTGTTTTTTCGTCTTTTTTTGTT
*
1080990 TTTTGTTTTTTCGTTTTTTTTTG
1 TTTTGTTTTTTCGTCTTTTTTTG
1081013 GGTGACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.83
Consensus pattern (25 bp):
TTTTGTTTTTTCGTCTTTTTTTGTT
Found at i:1081008 original size:17 final size:16
Alignment explanation
Indices: 1080965--1081012 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1080955 AACAAGTCCC
*
1080965 TTTTGTTTTTTTGTCT
1 TTTTTTTTTTTTGTCT
*
1080981 TTTTTTGTTTTTTGTTT
1 TTTTTT-TTTTTTGTCT
1080998 TTTCGTTTTTTTTTG
1 TTT--TTTTTTTTTG
1081013 GGTGACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 7 0.26
19 3 0.11
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTTTTGTCT
Found at i:1087328 original size:3 final size:3
Alignment explanation
Indices: 1087322--1087356 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1087312 TATTATTATT
1087322 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1087357 ATTAACTTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:1088298 original size:13 final size:14
Alignment explanation
Indices: 1088275--1088306 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
1088265 ATTTAAATGA
1088275 AAAAAAGGAAAAAG
1 AAAAAAGGAAAAAG
1088289 AAAAAA-GAAAAAG
1 AAAAAAGGAAAAAG
1088302 AAAAA
1 AAAAA
1088307 TGTTGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAAGGAAAAAG
Found at i:1088841 original size:30 final size:30
Alignment explanation
Indices: 1088789--1088851 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
1088779 GTATTTACTA
1088789 TTTAGCCCTTTAAA-TTAATTTTTTTGCTAT
1 TTTAGCCCTTTAAATTTAATTTTTTTGC-AT
* * **
1088819 TTTAGTCCTTTAAGTTTTTTTTTTTTGCAT
1 TTTAGCCCTTTAAATTTAATTTTTTTGCAT
1088849 TTT
1 TTT
1088852 GGTCTTTGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.17, C:0.11, G:0.08, T:0.63
Consensus pattern (30 bp):
TTTAGCCCTTTAAATTTAATTTTTTTGCAT
Found at i:1093111 original size:13 final size:13
Alignment explanation
Indices: 1093095--1093143 Score: 64
Period size: 14 Copynumber: 3.6 Consensus size: 13
1093085 AGCAAAAATC
1093095 AAGAAAAAAAGAA
1 AAGAAAAAAAGAA
1093108 AAGAAAAAAAGAAA
1 AAGAAAAAAAG-AA
1093122 AAGAAAAACAA-AGA
1 AAGAAAAA-AAGA-A
1093136 AAGAAAAA
1 AAGAAAAA
1093144 GACAATAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 12 0.36
14 19 0.58
15 2 0.06
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:1093129 original size:20 final size:20
Alignment explanation
Indices: 1093100--1093145 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
1093090 AAATCAAGAA
*
1093100 AAAAAG-AAAAGAAAAAAAG
1 AAAAAGAAAAACAAAAAAAG
*
1093119 AAAAAGAAAAACAAAGAAAG
1 AAAAAGAAAAACAAAAAAAG
1093139 AAAAAGA
1 AAAAAGA
1093146 CAATAAGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAACAAAAAAAG
Found at i:1093148 original size:16 final size:16
Alignment explanation
Indices: 1093098--1093137 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 16
1093088 AAAAATCAAG
1093098 AAAA-AAAG-AAAAG-
1 AAAACAAAGAAAAAGA
1093111 AAAA-AAAGAAAAAGA
1 AAAACAAAGAAAAAGA
1093126 AAAACAAAGAAA
1 AAAACAAAGAAA
1093138 GAAAAAGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 4 0.17
16 7 0.29
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (16 bp):
AAAACAAAGAAAAAGA
Found at i:1095754 original size:81 final size:81
Alignment explanation
Indices: 1095661--1096144 Score: 815
Period size: 81 Copynumber: 6.0 Consensus size: 81
1095651 TCATTCATCA
* * * *
1095661 CAAAGGTATTTAACCTTTCATCTAACTTGCATGATTGACACATTTCTGTCAAATGCACAGTTAGA
1 CAAAGGAATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGG
1095726 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * * *
1095742 CAAAGGTATTTAACATTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGAACAGCTAGG
1 CAAAGGAATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGG
1095807 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* *
1095823 CAAAGGAATTTAACCTTTCATCTAACTGGCATGATTGGCACATTTCAGTCAAATGCACAGCTAGG
1 CAAAGGAATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGG
1095888 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* *
1095904 TAAAGGAATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGG
1 CAAAGGAATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGG
1095969 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * *
1095985 CAAAGGTATTTAACCTTTCATCTAATTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGG
1 CAAAGGAATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGG
*
1096050 CATTTAATATTTTACT
66 CATTTAATCTTTTACT
*
1096066 CAAAGGAATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTTTCAAATGCACAGCTAGG
1 CAAAGGAATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGG
1096131 CATTTAATCTTTTA
66 CATTTAATCTTTTA
1096145 TTTTAAAACT
Statistics
Matches: 376, Mismatches: 27, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 376 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (81 bp):
CAAAGGAATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGG
CATTTAATCTTTTACT
Found at i:1097822 original size:131 final size:129
Alignment explanation
Indices: 1097587--1098009 Score: 512
Period size: 131 Copynumber: 3.2 Consensus size: 129
1097577 GAGTATTACA
*
1097587 ACGTAGGAACTGTGTTATCAT-CCTAAAGATGGCATATCGTCCTCATCGCGTAGAAACCATGTCA
1 ACGTAGGAAC-GTGTTATCATCCCTAAAGATGGCATATCGTCCTCATCGCGTAGGAACCATGTCA
* **
1097651 TCCCTCGACCAGACCTCCTCATCACGTAGGAGTCGTGTCACCCTTAGATAACCAGTTATCCTCAT
65 TCCCCCGACCAGACCTCCTCATC-CGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCAT
*
1097716 G
129 C
* * ** * *
1097717 ATGTAGGAACAGTGTTATCATCACTAAAGATGGCATGCCGTCCTCATCGCATAGGAACCGTGTCA
1 ACGTAGGAAC-GTGTTATCATCCCTAAAGATGGCATATCGTCCTCATCGCGTAGGAACCATGTCA
* * * * * *
1097782 TCCCCCGATCAGATCTCCTCTTCGCGTAGGAGACGTGTCACCCTTAGATAATCAGCCGTCCTCAT
65 TCCCCCGACCAGACCTCCTCATC-CGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCAT
1097847 C
129 C
* * * * * *
1097848 ACATATGAACCGTGTTATCATCCCTAAAAGATGGCCTATCATCCTCATCACGTAGGAACCTTGTC
1 ACGTAGGAA-CGTGTTATCATCCCT-AAAGATGGCATATCGTCCTCATCGCGTAGGAACCATGTC
* *
1097913 AT-CTCCTACCAGACCTCCATCAT--GTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCA
64 ATCCCCCGACCAGACCTCC-TCATCCGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCA
1097975 TC
128 TC
*
1097977 ACGTAGGATTCGTGTTATCATCCCTAAAGATGG
1 ACGTAGGA-ACGTGTTATCATCCCTAAAGATGG
1098010 TCACTGTTTG
Statistics
Matches: 247, Mismatches: 41, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
128 8 0.03
129 59 0.24
130 19 0.08
131 123 0.50
132 38 0.15
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (129 bp):
ACGTAGGAACGTGTTATCATCCCTAAAGATGGCATATCGTCCTCATCGCGTAGGAACCATGTCAT
CCCCCGACCAGACCTCCTCATCCGTAGGAGTCGTGTCACCCTTAGATAACCAGTCGTCCTCATC
Found at i:1100812 original size:16 final size:16
Alignment explanation
Indices: 1100788--1100818 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1100778 TATTCCTACC
1100788 TTATCATTATTATTTA
1 TTATCATTATTATTTA
*
1100804 TTATTATTATTATTT
1 TTATCATTATTATTT
1100819 CGTAAAATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATCATTATTATTTA
Found at i:1104823 original size:12 final size:12
Alignment explanation
Indices: 1104798--1104864 Score: 57
Period size: 12 Copynumber: 5.4 Consensus size: 12
1104788 CATGTAGTAT
1104798 TATAAT-ATATA
1 TATAATAATATA
1104809 TATAAAGTAATATA
1 TAT-AA-TAATATA
1104823 TATAATAATATA
1 TATAATAATATA
*
1104835 CGTAAAATAA-ATA
1 --TATAATAATATA
*
1104848 CATAATAATATA
1 TATAATAATATA
*
1104860 CATAA
1 TATAA
1104865 ATAAATGTGT
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
11 9 0.19
12 17 0.36
13 6 0.13
14 15 0.32
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.34
Consensus pattern (12 bp):
TATAATAATATA
Found at i:1104878 original size:24 final size:25
Alignment explanation
Indices: 1104799--1104870 Score: 85
Period size: 25 Copynumber: 2.9 Consensus size: 25
1104789 ATGTAGTATT
* * *
1104799 ATAAT-ATATATATAAAGTAATATAT
1 ATAATAATATACATAAAATAA-ATAC
*
1104824 ATAATAATATACGTAAAATAAATAC
1 ATAATAATATACATAAAATAAATAC
1104849 ATAATAATATACAT-AAATAAAT
1 ATAATAATATACATAAAATAAAT
1104871 GTGTAATACA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 8 0.20
25 21 0.51
26 12 0.29
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (25 bp):
ATAATAATATACATAAAATAAATAC
Found at i:1106839 original size:105 final size:105
Alignment explanation
Indices: 1106703--1107662 Score: 1661
Period size: 105 Copynumber: 9.2 Consensus size: 105
1106693 TTTGTCGGAT
* ** * *
1106703 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTCGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
* *
1106768 GGAACAGGCTCTTCTCATTACGAACCTTCTCTTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
* *
1106808 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
* *
1106873 GGAACAGGCTCTTCTCATTACGAACCCTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
1106913 GAGTTCTTCTCATTATGAACTCTTCAGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
1106978 GGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
1107018 GAGTTCTTCTCATTATGAACTCTTCTGGAAATATTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1107083 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
1107123 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCATTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
*
1107188 GGAACAGGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
1107228 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1107293 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
1107333 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
* * *
1107398 GGAACAAGTTTTTCTCATTACAAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
1107438 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1107503 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
*
1107543 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCA----C-TCTGTGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
1107603 GGAACAAG----T-TCATTACGAACCTTCTCCTTTAGGAC
66 GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
1107638 GAGTTCTTCTCATTATGAACTCTTC
1 GAGTTCTTCTCATTATGAACTCTTC
1107663 ATAAATATTG
Statistics
Matches: 829, Mismatches: 26, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
95 51 0.06
96 1 0.00
100 26 0.03
101 1 0.00
105 750 0.90
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGGGTCACCTCCTTCTGTGGTGGATTTGAAA
GGAACAAGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
Found at i:1108604 original size:55 final size:54
Alignment explanation
Indices: 1108457--1109147 Score: 784
Period size: 54 Copynumber: 12.7 Consensus size: 54
1108447 AAAGTTTTAA
* ** * * * * *
1108457 AAAAAATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGACAA-TTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTT-AAAAGCTCATTTG
** * * * * * * *
1108511 AAAACATCAAGAAACCCCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* *
1108565 AGAAAAATCAAGAAACTT-TCGAAAATCAGACTTAGTTTCTTTAAAA-CACATTTG
1 A-AAACATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* * *
1108619 AAAAGCGTCAAGAAACTTCTAAAAATCCAGACTTAGTTTCTTTAAAAACTCA-TTG
1 AAAA-CATCAAGAAACTTCTGAAAAT-CAGACTTAGTTTCTTTAAAAGCTCATTTG
* * *
1108674 AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAA-CT-ATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAAGCTCATTTG
* * *
1108727 AAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCACTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* * *
1108781 AAAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAA-CTTATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTC-TTTAAAAGCTCATTTG
* * * *
1108836 AAATCATCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTTAAAACCTCACTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* *
1108890 AAAATCGTCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTTAAAAGCTCATTTG
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
*** * *
1108945 AAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTG
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
*** * * *
1108999 AAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTA
1 AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
*
1109053 AAAATCATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTA
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
*
1109108 AAAATCATCAAGAAACTTCTGAAGATCAGACTTAGTTTCT
1 AAAA-CATCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
1109148 AAAAAAATAC
Statistics
Matches: 564, Mismatches: 57, Indels: 31
0.87 0.09 0.05
Matches are distributed among these distances:
52 7 0.01
53 67 0.12
54 244 0.43
55 237 0.42
56 9 0.02
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (54 bp):
AAAACATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
Found at i:1108606 original size:109 final size:109
Alignment explanation
Indices: 1108457--1109147 Score: 783
Period size: 109 Copynumber: 6.4 Consensus size: 109
1108447 AAAGTTTTAA
** * * * * *
1108457 AAAAAATCAAGAAACCCCTGAAAACCAGGCTTAATTTCTTTGACAA-TTCATTTGAAAACATCAA
1 AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTGAAAACATCAA
** * * * * * * *
1108521 GAAACCCCTAAAAATTAGGCTTAATTTCTTTGAACGTTCATTTG
66 GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* *
1108565 AGAAAAATCAAGAAACTT-TCGAAAATCAGACTTAGTTTCTTT-AAAA-CACATTTGAAAAGCGT
1 A-AAAAATCAAGAAACTTCT-GAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTGAAAA-CAT
* *
1108627 CAAGAAACTTCTAAAAATCCAGACTTAGTTTCTTTAAAAACTCA-TTG
63 CAAGAAACTTCTGAAAAT-CAGACTTAGTTTCTTTAAAAGCTCATTTG
** * * *
1108674 AAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCGTTGAAAA-CT-ATTTGAAATCATCAA
1 AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTGAAAACATCAA
* *
1108737 GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAACTCACTTG
66 GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
* * * * *
1108781 AAAATCATCATGAAACTTCTGAAAATCAGACTTAGTTTCATTGAAAA-CTTATTTGAAATCATCA
1 AAAA-AATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTGAAAACATCA
* * *
1108845 AGAAACTTCTGAAAATAAGACTTAGTTTCTTTAAAACCTCACTTG
65 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
** * ***
1108890 AAAATCGTCAAGAAACTTCTGAAAATAAGACTTAGTTTCTTT-AAAAGCTCATTTGAAATTGTCA
1 AAAA-AATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTGAAAACATCA
* *
1108954 AGAAACTTCTGAAAATCAGACTTAATTTCTTTGAAAGCTCATTTG
65 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
*** * *
1108999 AAATTGTCAAGAAACTTCTGAAAATCAGACTTAATTTCTTTG-AAAGCTCATTTAAAAATCATCA
1 AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTGAAAA-CATCA
1109063 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTT-
65 AGAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
*
1109107 AAAAATCATCAAGAAACTTCTGAAGATCAGACTTAGTTTCT
1 AAAAA--ATCAAGAAACTTCTGAAAATCAGACTTAGTTTCT
1109148 AAAAAAATAC
Statistics
Matches: 512, Mismatches: 57, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
106 25 0.05
107 25 0.05
108 155 0.30
109 258 0.50
110 49 0.10
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (109 bp):
AAAAAATCAAGAAACTTCTGAAAATCAGACTTAGTTTCTTTGAAAAGCTCATTTGAAAACATCAA
GAAACTTCTGAAAATCAGACTTAGTTTCTTTAAAAGCTCATTTG
Found at i:1111147 original size:18 final size:18
Alignment explanation
Indices: 1111105--1111154 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
1111095 GTTGGATCTG
1111105 TCTATTTCTTTT-TTTTAA
1 TCTATTT-TTTTCTTTTAA
**
1111123 TCT-TTTTTTTCTTTTCC
1 TCTATTTTTTTCTTTTAA
*
1111140 TCTATTTTTCTCTTT
1 TCTATTTTTTTCTTT
1111155 CTTTTTTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 4 0.15
17 10 0.37
18 13 0.48
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (18 bp):
TCTATTTTTTTCTTTTAA
Done.