Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 13
Found at i:864349 original size:42 final size:42
Alignment explanation
Indices: 864286--864405 Score: 195
Period size: 42 Copynumber: 2.8 Consensus size: 42
864276 TGGTGTTTGA
* *
864286 GTGCATGGATGCACTGTATGGTGCATCGATGCACTAGTGCAG
1 GTGCATGAATGCACTGCATGGTGCATCGATGCACTAGTGCAG
864328 GTGCATGAATGCACTGCATGGTGCATCGATGCACTAGTGCAG
1 GTGCATGAATGCACTGCATGGTGCATCGATGCACTAGTGCAG
* *
864370 GTGCATGAATGCACTGCAGGGATGCATGGATGCACT
1 GTGCATGAATGCACTGCATGG-TGCATCGATGCACT
864406 TTGACACCCT
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
42 60 0.82
43 13 0.18
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (42 bp):
GTGCATGAATGCACTGCATGGTGCATCGATGCACTAGTGCAG
Found at i:864506 original size:29 final size:30
Alignment explanation
Indices: 864474--864542 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
864464 TACACCTTTT
*
864474 AAAAC-TTTGAATAAATTGAATT-AAGTCCA
1 AAAACATTT-AATAAATTCAATTCAAGTCCA
**
864503 AAAACATTTTTTAAATTCAATTCAAGTCCA
1 AAAACATTTAATAAATTCAATTCAAGTCCA
864533 AAAACCATTT
1 AAAA-CATTT
864543 TGCCTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.44
30 14 0.41
31 5 0.15
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.33
Consensus pattern (30 bp):
AAAACATTTAATAAATTCAATTCAAGTCCA
Found at i:864532 original size:30 final size:30
Alignment explanation
Indices: 864485--864543 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
864475 AAACTTTGAA
*
864485 TAAATTGAATTAAGTCCAAAAA-CATTTTT
1 TAAATTCAATTAAGTCCAAAAACCATTTTT
864514 TAAATTCAATTCAAGTCCAAAAACCATTTT
1 TAAATTCAATT-AAGTCCAAAAACCATTTT
864544 GCCTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTT
Found at i:868164 original size:17 final size:17
Alignment explanation
Indices: 868142--868178 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
868132 GATCAACAGT
*
868142 GGTAAACGCCGGTCAAC
1 GGTAAACGCAGGTCAAC
868159 GGTAAACGCAGGTCAAC
1 GGTAAACGCAGGTCAAC
868176 GGT
1 GGT
868179 CAACAATCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.24, G:0.32, T:0.14
Consensus pattern (17 bp):
GGTAAACGCAGGTCAAC
Found at i:876002 original size:2 final size:2
Alignment explanation
Indices: 875995--876040 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
875985 ACAATCTGTT
875995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
876037 TA TA
1 TA TA
876041 AACTTCCAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:876998 original size:2 final size:2
Alignment explanation
Indices: 876991--877016 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
876981 GACTATTCTA
876991 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
877017 TATTTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:879017 original size:14 final size:15
Alignment explanation
Indices: 878980--879018 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
878970 AATGATATTT
878980 AAAATAT-TTATTTTA
1 AAAATATATT-TTTTA
878995 AAAATATATTTTTTA
1 AAAATATATTTTTTA
879010 AATAATATA
1 AA-AATATA
879019 ATAATAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AAAATATATTTTTTA
Found at i:883760 original size:41 final size:41
Alignment explanation
Indices: 883731--883810 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
883721 TATTGTGGCG
* * *
883731 TTTGTTTATAAAATGTCAAAAAATGATACTATATAGCGACA
1 TTTGTTTAGAAAACGTCAAAAAATGATACTCTATAGCGACA
*
883772 TTTGTTTAGAAAACGTCAGAAAATGATACTCTATAGCGA
1 TTTGTTTAGAAAACGTCAAAAAATGATACTCTATAGCGA
883811 TGTTTTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.41, C:0.11, G:0.15, T:0.33
Consensus pattern (41 bp):
TTTGTTTAGAAAACGTCAAAAAATGATACTCTATAGCGACA
Found at i:885823 original size:13 final size:14
Alignment explanation
Indices: 885799--885831 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
885789 TTATTCTTAA
885799 TATTTATATATTTT
1 TATTTATATATTTT
885813 TATTTAT-TATTTT
1 TATTTATATATTTT
*
885826 TGTTTA
1 TATTTA
885832 ATAAGATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (14 bp):
TATTTATATATTTT
Found at i:893413 original size:44 final size:44
Alignment explanation
Indices: 893363--893464 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
893353 TGGTGCACAG
* * * *
893363 TGCATCGATACACTATTAAAG-TGTACCGATGCATTCCTTGAATA
1 TGCATCGATACACTA-TAAAGATGCACCGATACATGCCTTAAATA
* * *
893407 TGCATCGATGCACTATGAAGATGCACCGATACATGCCTTAAATG
1 TGCATCGATACACTATAAAGATGCACCGATACATGCCTTAAATA
893451 TGCATCGATACACT
1 TGCATCGATACACT
893465 TGTCGGATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
43 4 0.08
44 45 0.92
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACTATAAAGATGCACCGATACATGCCTTAAATA
Found at i:893937 original size:13 final size:13
Alignment explanation
Indices: 893914--893956 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
893904 AAAACTCCAT
893914 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAC
893928 ATTGTTTTCAAAC
1 ATTGTTTTCAAAC
*
893941 ATAGTTTTCAAA-
1 ATTGTTTTCAAAC
893953 ATTG
1 ATTG
893957 CCCATTAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 3 0.11
13 20 0.74
14 4 0.15
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:896098 original size:55 final size:55
Alignment explanation
Indices: 896013--896136 Score: 185
Period size: 55 Copynumber: 2.3 Consensus size: 55
896003 TTATAGAGGG
* * * * * *
896013 ATGTACTGATACAATATTTTATGTATCGATGCACACCCTAATTCGAATGCGTTTT
1 ATGTACCGATGCACTATTTGATGTATCGATGCACACCCTAAATCGAATGCATTTT
*
896068 GTGTACCGATGCACTATTTGATGTATCGATGCACACCCTAAATCGAATGCATTTT
1 ATGTACCGATGCACTATTTGATGTATCGATGCACACCCTAAATCGAATGCATTTT
896123 ATGTACCGATGCAC
1 ATGTACCGATGCAC
896137 AGACCATGCA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (55 bp):
ATGTACCGATGCACTATTTGATGTATCGATGCACACCCTAAATCGAATGCATTTT
Found at i:899966 original size:29 final size:30
Alignment explanation
Indices: 899931--899999 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
899921 TAATAATAAT
* *
899931 TTATTATGATTTATTTTTTTGAA-ATA-TTA
1 TTATTATGATTT-TTTTTTCGAAGAAATTTA
899960 TTATTATGA-TTTTTTTTCGAAGAAATTTA
1 TTATTATGATTTTTTTTTCGAAGAAATTTA
899989 TTATTATGATT
1 TTATTATGATT
900000 ATAGGTGCAC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
27 9 0.26
28 4 0.11
29 21 0.60
30 1 0.03
ACGTcount: A:0.30, C:0.01, G:0.09, T:0.59
Consensus pattern (30 bp):
TTATTATGATTTTTTTTTCGAAGAAATTTA
Found at i:911635 original size:25 final size:25
Alignment explanation
Indices: 911582--911632 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
911572 ATAATTTTAA
* * *
911582 TAAATTAAAATAAATTATATATTTT
1 TAAATGAAAATAAAATAAATATTTT
911607 TAAATGAAAATGAAAATAAATATTTT
1 TAAATGAAAAT-AAAATAAATATTTT
911633 AAAAATAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (25 bp):
TAAATGAAAATAAAATAAATATTTT
Found at i:911717 original size:15 final size:16
Alignment explanation
Indices: 911692--911721 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
911682 TTTTAAGTTA
911692 ATATATATATATAATT
1 ATATATATATATAATT
911708 ATAT-TATATATAAT
1 ATATATATATATAAT
911722 CCAGGTCACG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATATATATATAATT
Found at i:912109 original size:20 final size:18
Alignment explanation
Indices: 912070--912105 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
912060 TGAGAATTAC
912070 AAATAAAAATATAATATA
1 AAATAAAAATATAATATA
912088 AAATAAAAATAT-ATATA
1 AAATAAAAATATAATATA
912105 A
1 A
912106 TAAATCGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATAAAAATATAATATA
Found at i:915612 original size:15 final size:15
Alignment explanation
Indices: 915556--915625 Score: 59
Period size: 15 Copynumber: 4.7 Consensus size: 15
915546 TACACATGTA
* *
915556 GATAACGATGATGAT
1 GATAATGATGATGGT
*
915571 GATAATGATGATTGT
1 GATAATGATGATGGT
* * *
915586 AATGATGGTGATGGT
1 GATAATGATGATGGT
* *
915601 GATAATGTTGATGCT
1 GATAATGATGATGGT
*
915616 GATGATGATG
1 GATAATGATG
915626 CTAATGAAGA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.34
Consensus pattern (15 bp):
GATAATGATGATGGT
Found at i:916267 original size:3 final size:3
Alignment explanation
Indices: 916259--916284 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
916249 ATGGAAATGG
916259 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
916285 TATGAAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:917888 original size:16 final size:16
Alignment explanation
Indices: 917867--917909 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
917857 TCTAAAAAGA
917867 CATCCTCTTCTGGTGG
1 CATCCTCTTCTGGTGG
*
917883 CATCCTCTTTTGGTGG
1 CATCCTCTTCTGGTGG
917899 CATCCTCTTCT
1 CATCCTCTTCT
917910 TATCACTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.33, G:0.19, T:0.42
Consensus pattern (16 bp):
CATCCTCTTCTGGTGG
Found at i:921366 original size:23 final size:23
Alignment explanation
Indices: 921335--921407 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
921325 AAAACTACCA
* * *
921335 AAAGACAGAGATAAATGTGTTAC
1 AAAGGCAGAGATAAACGTGTCAC
921358 AAAGGCAGAGATAAACGTGTCAC
1 AAAGGCAGAGATAAACGTGTCAC
* *
921381 AAAGGTAGAGATAAAGGTGTCAC
1 AAAGGCAGAGATAAACGTGTCAC
921404 AAAG
1 AAAG
921408 ATAGAATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.47, C:0.11, G:0.26, T:0.16
Consensus pattern (23 bp):
AAAGGCAGAGATAAACGTGTCAC
Found at i:926197 original size:31 final size:31
Alignment explanation
Indices: 926149--926256 Score: 144
Period size: 31 Copynumber: 3.5 Consensus size: 31
926139 AAAAAAAACA
*
926149 TAAGTTATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATATGGTCACTTTCGTTTTTATTTAAT
* *
926180 TAAGATATGATCACTTTCATTTTTATTTAAT
1 TAAGATATGGTCACTTTCGTTTTTATTTAAT
* * *
926211 TAAGATATGGTTACTTTCGTTTCTATTTAAC
1 TAAGATATGGTCACTTTCGTTTTTATTTAAT
* *
926242 TAATATGTGGTCACT
1 TAAGATATGGTCACT
926257 CGAGTTAACC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 66 1.00
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.50
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCGTTTTTATTTAAT
Found at i:926462 original size:25 final size:26
Alignment explanation
Indices: 926396--926468 Score: 76
Period size: 25 Copynumber: 2.8 Consensus size: 26
926386 TGAAAATAAA
*
926396 AATAAAATATTTTTAAATTAAGCTATT
1 AATAAAATATTTTT-AATTAAGCTAAT
* * *
926423 AATAAAATATATTTAA-TACGTTAAT
1 AATAAAATATTTTTAATTAAGCTAAT
*
926448 ATTAAAATATTTTTAAGTTAA
1 AATAAAATATTTTTAA-TTAA
926469 TATATATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 20 0.54
26 2 0.05
27 15 0.41
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (26 bp):
AATAAAATATTTTTAATTAAGCTAAT
Found at i:926493 original size:15 final size:16
Alignment explanation
Indices: 926469--926499 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
926459 TTTAAGTTAA
926469 TATATATATATATAAT
1 TATATATATATATAAT
926485 TATAT-TATATATAAT
1 TATATATATATATAAT
926500 CCGGGTCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATATATATATAAT
Found at i:926610 original size:2 final size:2
Alignment explanation
Indices: 926599--926627 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
926589 TTTAAAAGTC
926599 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
926628 ATCTACACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:926864 original size:38 final size:38
Alignment explanation
Indices: 926768--926870 Score: 117
Period size: 39 Copynumber: 2.7 Consensus size: 38
926758 GAACGATAAT
926768 GTGAAATAATTTAAGAAATTAGAATTTAGAATTTTATG
1 GTGAAATAATTTAAGAAATTAGAATTTAGAATTTTATG
*
926806 GTGTCAAAT--TTTAAGAAATTAGGATTTTAGAATTTTA-G
1 GTG--AAATAATTTAAGAAATTA-GAATTTAGAATTTTATG
*
926844 AGTGAAATAATTTGAG-AATTA-AATTTA
1 -GTGAAATAATTTAAGAAATTAGAATTTA
926871 TTTTAATTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
36 5 0.09
37 4 0.07
38 21 0.38
39 22 0.39
40 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.17, T:0.40
Consensus pattern (38 bp):
GTGAAATAATTTAAGAAATTAGAATTTAGAATTTTATG
Found at i:926929 original size:31 final size:31
Alignment explanation
Indices: 926894--926962 Score: 113
Period size: 31 Copynumber: 2.2 Consensus size: 31
926884 AAAATATATA
926894 ACTAAATTGAGAGAATATTTAAATAGA-AGGG
1 ACTAAATTGAGAGAATATTTAAATA-ATAGGG
926925 ACTAAATTGAGAGAATATTTAAATAATAGGG
1 ACTAAATTGAGAGAATATTTAAATAATAGGG
*
926956 ACCAAAT
1 ACTAAAT
926963 GTATGATTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (31 bp):
ACTAAATTGAGAGAATATTTAAATAATAGGG
Found at i:927066 original size:31 final size:33
Alignment explanation
Indices: 927024--927087 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 33
927014 TGACCACATC
*
927024 TTAATTGAATAAAAACAAAAGTGA-C-TATATT
1 TTAATTAAATAAAAACAAAAGTGATCATATATT
*
927055 TTAATTAAATAAAAACGAAAGTGATCATATATT
1 TTAATTAAATAAAAACAAAAGTGATCATATATT
927088 ATGTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 22 0.76
32 1 0.03
33 6 0.21
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (33 bp):
TTAATTAAATAAAAACAAAAGTGATCATATATT
Found at i:942262 original size:49 final size:49
Alignment explanation
Indices: 942202--942296 Score: 129
Period size: 49 Copynumber: 1.9 Consensus size: 49
942192 GGTGACCGTT
*
942202 TTGTAACTTTTAATAGTCGAGGGAA-TCAATAAAACAACATCCTATACTG
1 TTGTAACTTTTAATAGTCGA-GAAATTCAATAAAACAACATCCTATACTG
* * * *
942251 TTGTAAGTTTTAATAGTTGAGAAATTCAATAAAACACCATTCTATA
1 TTGTAACTTTTAATAGTCGAGAAATTCAATAAAACAACATCCTATA
942297 GTCGAGGACC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 3 0.08
49 37 0.93
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (49 bp):
TTGTAACTTTTAATAGTCGAGAAATTCAATAAAACAACATCCTATACTG
Found at i:942405 original size:15 final size:15
Alignment explanation
Indices: 942385--942415 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
942375 GTGATCCAAT
*
942385 TATAAATATCAATTA
1 TATAAATATAAATTA
942400 TATAAATATAAATTA
1 TATAAATATAAATTA
942415 T
1 T
942416 TTTTATGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
TATAAATATAAATTA
Found at i:942640 original size:31 final size:34
Alignment explanation
Indices: 942578--942651 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 34
942568 AGGATTAAGG
*
942578 CGATGACAAAGGGTGGTTGATAACTAACGAGGGTC
1 CGATGATAAAGGGTGGTT-ATAACTAACGAGGGTC
942613 CGATGATAAAGGGTGGTT-T-A-TAACGAGGGTC
1 CGATGATAAAGGGTGGTTATAACTAACGAGGGTC
942644 CGATGATA
1 CGATGATA
942652 GGTAGATAGG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
31 19 0.50
32 1 0.03
33 1 0.03
35 17 0.45
ACGTcount: A:0.31, C:0.12, G:0.34, T:0.23
Consensus pattern (34 bp):
CGATGATAAAGGGTGGTTATAACTAACGAGGGTC
Found at i:962792 original size:20 final size:20
Alignment explanation
Indices: 962767--962804 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
962757 TTTTCATTTA
962767 TCTTTCATTATTAA-TTTTTC
1 TCTTTCATT-TTAACTTTTTC
962787 TCTTTCATTTTAACTTTT
1 TCTTTCATTTTAACTTTT
962805 ACATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.66
Consensus pattern (20 bp):
TCTTTCATTTTAACTTTTTC
Found at i:968779 original size:17 final size:16
Alignment explanation
Indices: 968748--968781 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
968738 CATGTGAGGA
968748 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
968764 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
968781 T
1 T
968782 ACTATTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:980648 original size:22 final size:22
Alignment explanation
Indices: 980616--980662 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
980606 AGATTTATTA
* *
980616 ATATTTTTAATAAT-ATAACATT
1 ATATTTCTAAT-ATCATAACAAT
980638 ATATTTCTAATATCATAACAAT
1 ATATTTCTAATATCATAACAAT
980660 ATA
1 ATA
980663 CTCAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTTCTAATATCATAACAAT
Found at i:982260 original size:16 final size:16
Alignment explanation
Indices: 982238--982281 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
982228 AATAAATAAT
982238 CGAACATAAACGAACA
1 CGAACATAAACGAACA
* *
982254 TGAACATAAATGAACA
1 CGAACATAAACGAACA
982270 CGAACATAAACG
1 CGAACATAAACG
982282 TTGGAGACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.55, C:0.20, G:0.14, T:0.11
Consensus pattern (16 bp):
CGAACATAAACGAACA
Found at i:983394 original size:14 final size:14
Alignment explanation
Indices: 983377--983418 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
983367 AATAAACATA
983377 AACGAACATAACCG
1 AACGAACATAACCG
983391 AACGAACAT-A---
1 AACGAACATAACCG
983401 AACGAACATAACCG
1 AACGAACATAACCG
983415 AACG
1 AACG
983419 TTCACGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
13 1 0.04
14 13 0.54
ACGTcount: A:0.52, C:0.26, G:0.14, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:983398 original size:24 final size:24
Alignment explanation
Indices: 983371--983418 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
983361 TAAATGAATA
983371 AACATAAACGAACATAACCGAACG
1 AACATAAACGAACATAACCGAACG
983395 AACATAAACGAACATAACCGAACG
1 AACATAAACGAACATAACCGAACG
983419 TTCACGAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (24 bp):
AACATAAACGAACATAACCGAACG
Found at i:985542 original size:15 final size:15
Alignment explanation
Indices: 985522--985564 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
985512 CAGGTACCCG
985522 GATTTTCGGGTACTC
1 GATTTTCGGGTACTC
985537 GATTTTCGGGTACTC
1 GATTTTCGGGTACTC
985552 GATTTTCGGGTAC
1 GATTTTCGGGTAC
985565 CCGGAACTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.14, C:0.19, G:0.28, T:0.40
Consensus pattern (15 bp):
GATTTTCGGGTACTC
Found at i:985587 original size:32 final size:30
Alignment explanation
Indices: 985522--985589 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 30
985512 CAGGTACCCG
* * *
985522 GATTTTCGGGTACTCGATTTTCGGGTACTC
1 GATTTTCGGGTACCCGACTTTCGGGTACAC
985552 GATTTTCGGGTACCCGGAACTTTCGGGT-CGAC
1 GATTTTCGGGTACCC-G-ACTTTCGGGTAC-AC
985584 GATTTT
1 GATTTT
985590 TCGGCATGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 14 0.44
31 2 0.06
32 16 0.50
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.37
Consensus pattern (30 bp):
GATTTTCGGGTACCCGACTTTCGGGTACAC
Found at i:985634 original size:15 final size:15
Alignment explanation
Indices: 985605--985670 Score: 62
Period size: 15 Copynumber: 4.3 Consensus size: 15
985595 ATGTGTCCCG
*
985605 ACCCGGTTA-CGGGT
1 ACCCGGTAATCGGGT
985619 ACCCGGTAATCGGGT
1 ACCCGGTAATCGGGT
* **
985634 ATCCGGATTTTGCGGGT
1 ACCCGG-TAAT-CGGGT
*
985651 ACCTGGTAATCGGGT
1 ACCCGGTAATCGGGT
985666 ACCCG
1 ACCCG
985671 ATACCCGATT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
14 8 0.20
15 19 0.47
16 4 0.10
17 9 0.22
ACGTcount: A:0.17, C:0.26, G:0.33, T:0.24
Consensus pattern (15 bp):
ACCCGGTAATCGGGT
Found at i:988438 original size:3 final size:3
Alignment explanation
Indices: 988432--988556 Score: 146
Period size: 3 Copynumber: 42.0 Consensus size: 3
988422 TTTATTTAAA
** * * *
988432 ATT ATT ATT ATT AAA ATT ATT ATT ATT AGT ATT ATT ATT AGT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
988480 ATT ATT ATT ATT A-T AAT AAT AAT ATT ATT ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
988526 ATT ATT ATT AAT ATT ATAT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
988557 TAATAAATAA
Statistics
Matches: 106, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
2 4 0.04
3 99 0.93
4 3 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:995037 original size:2 final size:2
Alignment explanation
Indices: 995030--995083 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
995020 TTATCCTTTA
995030 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
995072 AT AT AT AT AT AT
1 AT AT AT AT AT AT
995084 CCTTTGTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:998974 original size:54 final size:54
Alignment explanation
Indices: 998892--999003 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
998882 CAATGATTGA
* ***
998892 GAACATCTGAGCATAAGCCACAAAAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
** *
998946 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCACTGTTAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
999000 GAAC
1 GAAC
999004 CTGCTATTCG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 51 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAGCCACAAAAAAGGATGAATGCACTGTCAAATGTTTTAC
Found at i:1000199 original size:76 final size:76
Alignment explanation
Indices: 1000073--1001015 Score: 1701
Period size: 76 Copynumber: 12.4 Consensus size: 76
1000063 CTATTTCTCA
* *
1000073 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCGTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1000138 AACCTTCGGGT
66 AACCTTCGGGT
1000149 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1000214 AACCTTCGGGT
66 AACCTTCGGGT
*
1000225 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGAATGTTTTCA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTG-ATGTTTTCA
*
1000290 AATCCTTCGGGT
65 AAACCTTCGGGT
1000302 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1000367 ATCCTTCGGGT
66 AACCTTCGGGT
1000378 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1000443 ATCCTTCGGGT
66 AACCTTCGGGT
1000454 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1000519 AGCCTTCGGGT
66 AACCTTCGGGT
*
1000530 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1000595 AACCTTCGGGT
66 AACCTTCGGGT
*
1000606 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1000671 AAACCTTCGGGT
65 AAACCTTCGGGT
* * *
1000683 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAACCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1000748 AGCCTTCGGGT
66 AACCTTCGGGT
1000759 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
1000824 AAACCTT-GGGG
65 AAACCTTCGGGT
*
1000835 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATG-TTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1000899 AGCCTTCGGGT
66 AACCTTCGGGT
1000910 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1000975 AACCTTCGGGT
66 AACCTTCGGGT
1000986 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1001016 TCAACGTTTC
Statistics
Matches: 839, Mismatches: 23, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
74 7 0.01
75 64 0.08
76 615 0.73
77 153 0.18
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTCGGGT
Found at i:1000474 original size:229 final size:228
Alignment explanation
Indices: 1000073--1001015 Score: 1694
Period size: 229 Copynumber: 4.1 Consensus size: 228
1000063 CTATTTCTCA
* *
1000073 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCGTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1000138 AACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1000203 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
*
1000268 GAGAGCTTTTTGAATGTTTTCAAATCCTTCGGGT
196 GAGAGCTTTTTG-ATGTTTTCAAAGCCTTCGGGT
1000302 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1000367 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
*
1000432 GATGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
*
1000497 GGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
196 GAGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
*
1000530 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1000595 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* *
1000660 GATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAACCTT
131 GATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
1000725 C-AGGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
195 CGA-GAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
1000759 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
1000824 AAACCTT-GGGGCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 AAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
1000888 TGATG-TTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
130 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
* *
1000952 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
195 CGAGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
1000986 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1001016 TCAACGTTTC
Statistics
Matches: 688, Mismatches: 22, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
227 113 0.16
228 160 0.23
229 407 0.59
230 8 0.01
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (228 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
GAGAGCTTTTTGATGTTTTCAAAGCCTTCGGGT
Found at i:1000680 original size:305 final size:304
Alignment explanation
Indices: 1000073--1001015 Score: 1701
Period size: 305 Copynumber: 3.1 Consensus size: 304
1000063 CTATTTCTCA
* *
1000073 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCGTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1000138 AACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
1000203 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
* *
1000268 GAGAGCTTTTTGAATGTTTTCAAATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
196 GGGAGCTTTTTG-ATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
*
1000333 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAATCCTTCGGGT
260 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
1000378 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1000443 ATCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* *
1000508 GATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
131 GATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
*
1000573 GGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTCC
196 GGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
1000638 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAAACCTTCGGGT
261 AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-AAAACCTTCGGGT
* * *
1000683 CATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAACCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1000748 AGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
66 AACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* *
1000813 GATGTTTTCAAAAACCTT-GGGGCATCTGTAAGTCCTCCAGTGCATGATGTTTCCAAAAAGCCTT
131 GATGTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTT
*
1000877 CGGGAGCTTTTTGATG-TTTCAAAGCCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
195 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTC
1000941 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
260 CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
1000986 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
1001016 TCAACGTTTC
Statistics
Matches: 616, Mismatches: 20, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
303 42 0.07
304 160 0.26
305 407 0.66
306 7 0.01
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.35
Consensus pattern (304 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTCC
AAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGT
Found at i:1001153 original size:3 final size:3
Alignment explanation
Indices: 1001147--1001274 Score: 148
Period size: 3 Copynumber: 42.0 Consensus size: 3
1001137 TTCATTTAAA
** * *
1001147 ATT ATT ATT ATT AAA ATT ATT ATT ATT AGT ATT ATT ATT ATT ATT AGT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * * *
1001195 ATT AGT ATT ATT ATT ATT ATA ATA ATA ATA ATT ATT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
*
1001241 ATT ATT ATT ATT AAT ATT ATAT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT
1001275 TAATAAATAA
Statistics
Matches: 109, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
3 103 0.94
4 6 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1005005 original size:10 final size:10
Alignment explanation
Indices: 1004992--1005051 Score: 75
Period size: 10 Copynumber: 5.6 Consensus size: 10
1004982 ACGTTCGTAA
*
1004992 ATGTTCGGTT
1 ATGTTCGTTT
1005002 ATGTTCGTTT
1 ATGTTCGTTT
1005012 ATGTTCGTTCGGTT
1 ATGTTCG-T---TT
1005026 ATGTTCGTTT
1 ATGTTCGTTT
1005036 ATGTTCGTTT
1 ATGTTCGTTT
1005046 ATGTTC
1 ATGTTC
1005052 ATTCATTTAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 34 0.76
11 1 0.02
13 1 0.02
14 9 0.20
ACGTcount: A:0.10, C:0.12, G:0.23, T:0.55
Consensus pattern (10 bp):
ATGTTCGTTT
Found at i:1005021 original size:24 final size:24
Alignment explanation
Indices: 1004994--1005044 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1004984 GTTCGTAAAT
1004994 GTTCGGTTATGTTCGTTTATGTTC
1 GTTCGGTTATGTTCGTTTATGTTC
1005018 GTTCGGTTATGTTCGTTTATGTTC
1 GTTCGGTTATGTTCGTTTATGTTC
1005042 GTT
1 GTT
1005045 TATGTTCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.08, C:0.12, G:0.25, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCGTTTATGTTC
Found at i:1005021 original size:34 final size:34
Alignment explanation
Indices: 1004970--1005051 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
1004960 CATATGTCTC
*
1004970 GTTCGTTCAT-TTACGTTC-GTAAATGTTCGGTTAT
1 GTTCGTTTATGTT-CGTTCGGT-AATGTTCGGTTAT
* *
1005004 GTTCGTTTATGTTCGTTCGGTTATGTTCGTTTAT
1 GTTCGTTTATGTTCGTTCGGTAATGTTCGGTTAT
1005038 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1005052 ATTCATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
34 39 0.91
35 4 0.09
ACGTcount: A:0.12, C:0.13, G:0.22, T:0.52
Consensus pattern (34 bp):
GTTCGTTTATGTTCGTTCGGTAATGTTCGGTTAT
Found at i:1005027 original size:14 final size:14
Alignment explanation
Indices: 1004994--1005034 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
1004984 GTTCGTAAAT
1004994 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
1005008 G-T---TTATGTTC
1 GTTCGGTTATGTTC
1005018 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
1005032 GTT
1 GTT
1005035 TATGTTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
13 1 0.04
14 12 0.52
ACGTcount: A:0.07, C:0.12, G:0.27, T:0.54
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:1005062 original size:34 final size:34
Alignment explanation
Indices: 1004992--1005064 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
1004982 ACGTTCGTAA
* *
1004992 ATGTTCGGTTATGTTCGTTTATGTTCGTTCGGTT
1 ATGTTCGGTTATGTTCGTTTATGTTCATTCAGTT
* *
1005026 ATGTTCGTTTATGTTCGTTTATGTTCATTCATTT
1 ATGTTCGGTTATGTTCGTTTATGTTCATTCAGTT
1005060 ATGTT
1 ATGTT
1005065 TAACCCAATC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (34 bp):
ATGTTCGGTTATGTTCGTTTATGTTCATTCAGTT
Found at i:1005993 original size:16 final size:16
Alignment explanation
Indices: 1005972--1006038 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
1005962 GTCTCCAATG
1005972 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
1005988 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
1006004 TTTATTTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
1006020 CTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
1006034 TTTAT
1 TTTAT
1006039 TAAATGAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 4 0.09
15 2 0.04
16 39 0.87
ACGTcount: A:0.10, C:0.12, G:0.18, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:1007537 original size:18 final size:19
Alignment explanation
Indices: 1007495--1007534 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1007485 TTTGGTTCAC
1007495 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAG-G
*
1007515 GGAATGTAAGATTATCAGG
1 GGAATGTAAGATTACCAGG
1007534 G
1 G
1007535 AATAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.35, C:0.07, G:0.33, T:0.25
Consensus pattern (19 bp):
GGAATGTAAGATTACCAGG
Found at i:1007762 original size:37 final size:37
Alignment explanation
Indices: 1007689--1007763 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
1007679 GTTGGAAAAT
* *
1007689 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
1007726 ATTTATATAATTTT-TTTAACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAA-AAAATTGAAAATCATAAA
1007763 A
1 A
1007764 GGTTTAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 19 0.56
38 15 0.44
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:1012963 original size:18 final size:19
Alignment explanation
Indices: 1012942--1012977 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1012932 CAAAGGCTTA
1012942 TTAAAAAATAAAA-ATTCT
1 TTAAAAAATAAAACATTCT
*
1012960 TTAAAATATAAAACATTC
1 TTAAAAAATAAAACATTC
1012978 AAATATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TTAAAAAATAAAACATTCT
Found at i:1013049 original size:6 final size:6
Alignment explanation
Indices: 1013007--1013039 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1012997 TATAAACTAT
1013007 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAA
1013040 TATAAATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:1013835 original size:24 final size:24
Alignment explanation
Indices: 1013782--1013835 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 24
1013772 ATATCACAAT
* * *
1013782 AAAT-AAAATTTTAAATTTTAAAT
1 AAATAAAAATTTAAAATGTTAAAA
* *
1013805 TACTAAAAATTTAAAATGTTAAAA
1 AAATAAAAATTTAAAATGTTAAAA
1013829 AAATAAA
1 AAATAAA
1013836 TTATACATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATAAAAATTTAAAATGTTAAAA
Found at i:1015466 original size:20 final size:20
Alignment explanation
Indices: 1015441--1015480 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1015431 TCGCTCAATG
1015441 ATGGTGGCTAGTTATAATTT
1 ATGGTGGCTAGTTATAATTT
1015461 ATGGTGGCTAGTTATAATTT
1 ATGGTGGCTAGTTATAATTT
1015481 GGGTGCTGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.25, T:0.45
Consensus pattern (20 bp):
ATGGTGGCTAGTTATAATTT
Found at i:1015800 original size:2 final size:2
Alignment explanation
Indices: 1015793--1015826 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1015783 TTTATACTCG
1015793 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1015827 CTCAAAGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1019410 original size:36 final size:36
Alignment explanation
Indices: 1019363--1019517 Score: 283
Period size: 36 Copynumber: 4.3 Consensus size: 36
1019353 CAAAAGTTTG
*
1019363 TTCCGATTCAAGTCGAACGGAGGGAAGCATCTGCAC
1 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
1019399 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
1019435 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
*
1019471 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
*
1019507 TTCCGTTTCAA
1 TTCCGATTCAA
1019518 TGATGTTGTT
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 116 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.19
Consensus pattern (36 bp):
TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
Found at i:1019662 original size:36 final size:36
Alignment explanation
Indices: 1019615--1019855 Score: 446
Period size: 36 Copynumber: 6.7 Consensus size: 36
1019605 CAAAAGTTTG
* *
1019615 TTCCGATTCAAGTCGAACGGAGGGAAGCATCTGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
*
1019651 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
*
1019687 TTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1019723 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1019759 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1019795 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1 TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
1019831 TTCCGATTCAAGTCGAACGGAAGGA
1 TTCCGATTCAAGTCGAACGGAAGGA
1019856 TGTGTCTTAC
Statistics
Matches: 203, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 203 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.17
Consensus pattern (36 bp):
TTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCAC
Found at i:1019704 original size:252 final size:252
Alignment explanation
Indices: 1019259--1019769 Score: 1013
Period size: 252 Copynumber: 2.0 Consensus size: 252
1019249 CGGATCAAAT
1019259 GTTTCAATGATGTTGTTGGTGTTTGGTTTGTTTCACATTTTTGTTATAGAATAGGTTTTTCTTTT
1 GTTTCAATGATGTTGTTGGTGTTTGGTTTGTTTCACATTTTTGTTATAGAATAGGTTTTTCTTTT
1019324 AGAATTTTTTGTTGAATGTTCATTCACATCAAAAGTTTGTTCCGATTCAAGTCGAACGGAGGGAA
66 AGAATTTTTTGTTGAATGTTCATTCACATCAAAAGTTTGTTCCGATTCAAGTCGAACGGAGGGAA
1019389 GCATCTGCACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACG
131 GCATCTGCACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACG
1019454 GAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCC
196 GAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCC
1019511 GTTTCAATGATGTTGTTGGTGTTTGGTTTGTTTCACATTTTTGTTATAGAATAGGTTTTTCTTTT
1 GTTTCAATGATGTTGTTGGTGTTTGGTTTGTTTCACATTTTTGTTATAGAATAGGTTTTTCTTTT
1019576 AGAATTTTTTGTTGAATGTTCATTCACATCAAAAGTTTGTTCCGATTCAAGTCGAACGGAGGGAA
66 AGAATTTTTTGTTGAATGTTCATTCACATCAAAAGTTTGTTCCGATTCAAGTCGAACGGAGGGAA
1019641 GCATCTGCACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACG
131 GCATCTGCACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACG
1019706 GAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCC
196 GAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCC
*
1019763 GATTCAA
1 GTTTCAA
1019770 GTCGAACGGA
Statistics
Matches: 258, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
252 258 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (252 bp):
GTTTCAATGATGTTGTTGGTGTTTGGTTTGTTTCACATTTTTGTTATAGAATAGGTTTTTCTTTT
AGAATTTTTTGTTGAATGTTCATTCACATCAAAAGTTTGTTCCGATTCAAGTCGAACGGAGGGAA
GCATCTGCACTTCCGATTCAAGTCGAACGGAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACG
GAGGGAAGCATCGGCACTTCCGATTCAAGTCGAACGGAAGGAAGCATCGGCACTTCC
Found at i:1029578 original size:21 final size:21
Alignment explanation
Indices: 1029554--1029603 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1029544 TGATATGATT
1029554 GACAAAATTTCAAAAATATTG
1 GACAAAATTTCAAAAATATTG
*
1029575 GACAAAATTTTAAAAATATTG
1 GACAAAATTTCAAAAATATTG
*
1029596 GTCAAAAT
1 GACAAAAT
1029604 GAAAAAGGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (21 bp):
GACAAAATTTCAAAAATATTG
Found at i:1029800 original size:74 final size:77
Alignment explanation
Indices: 1029676--1029826 Score: 263
Period size: 74 Copynumber: 2.0 Consensus size: 77
1029666 TTAAATTTTC
*
1029676 AACTAATTTATTATTATATACGTTGAGTCATTTAGAATTTAAATTTTTATAAATTAGATTAATGG
1 AACTAATTTATTATTATATACGTTGAGTCATTTAGAATTTAAATTTTTATAAATTAGATTAATGA
1029741 TGTTCGTCGTTA
66 TGTTCGTCGTTA
*
1029753 AACTAATTTATTA-T-TATA-GTTGAGTCATTTAGAATTTAATTTTTTATAAATTAGATTAATGA
1 AACTAATTTATTATTATATACGTTGAGTCATTTAGAATTTAAATTTTTATAAATTAGATTAATGA
1029815 TGTTCGTCGTTA
66 TGTTCGTCGTTA
1029827 GTGGTACTCA
Statistics
Matches: 72, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
74 54 0.75
75 4 0.06
76 1 0.01
77 13 0.18
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.48
Consensus pattern (77 bp):
AACTAATTTATTATTATATACGTTGAGTCATTTAGAATTTAAATTTTTATAAATTAGATTAATGA
TGTTCGTCGTTA
Found at i:1034535 original size:2 final size:2
Alignment explanation
Indices: 1034528--1034582 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1034518 GATTATTAGA
1034528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1034570 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1034583 CAAATTAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1042103 original size:25 final size:25
Alignment explanation
Indices: 1042071--1042127 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
1042061 AATTAATTGA
*
1042071 TGGGTTGAAATCCTTGAATCTTTAT
1 TGGGTTGAAATCATTGAATCTTTAT
1042096 TGGGTTGAAATCATTGAATCTTTAT
1 TGGGTTGAAATCATTGAATCTTTAT
1042121 TGGGTTG
1 TGGGTTG
1042128 TGATCTTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.23, C:0.09, G:0.25, T:0.44
Consensus pattern (25 bp):
TGGGTTGAAATCATTGAATCTTTAT
Found at i:1045527 original size:23 final size:24
Alignment explanation
Indices: 1045483--1045529 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1045473 AAAATTAATC
*
1045483 AAATAATATATATTAATAAAAATA
1 AAATAATATATACTAATAAAAATA
*
1045507 AAATAATA-ATACTAATTAAAATA
1 AAATAATATATACTAATAAAAATA
1045530 TTAAACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATAATATATACTAATAAAAATA
Found at i:1045564 original size:11 final size:11
Alignment explanation
Indices: 1045496--1045582 Score: 56
Period size: 11 Copynumber: 7.8 Consensus size: 11
1045486 TAATATATAT
*
1045496 TAATAAAAATA
1 TAATTAAAATA
*
1045507 -AAATAATAATA
1 TAATTAA-AATA
1045518 CTAATT-AAA-A
1 -TAATTAAAATA
1045528 T-ATTAAACATA
1 TAATTAAA-ATA
1045539 TAAAATTAAAATA
1 T--AATTAAAATA
* *
1045552 TATTTAAACTA
1 TAATTAAAATA
1045563 TAATTAAAATA
1 TAATTAAAATA
*
1045574 AAATTAAAA
1 TAATTAAAA
1045583 CTAAATATAA
Statistics
Matches: 59, Mismatches: 8, Indels: 18
0.69 0.09 0.21
Matches are distributed among these distances:
8 3 0.05
9 3 0.05
10 6 0.10
11 33 0.56
12 1 0.02
13 7 0.12
14 6 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (11 bp):
TAATTAAAATA
Found at i:1045580 original size:22 final size:22
Alignment explanation
Indices: 1045496--1045594 Score: 64
Period size: 22 Copynumber: 4.4 Consensus size: 22
1045486 TAATATATAT
* *
1045496 TAATAAAAATAAAA-TAATAATA
1 TAATTAAAATAAAATTAA-ACTA
1045518 CTAATTAAAAT---ATTAAACATA
1 -TAATTAAAATAAAATTAAAC-TA
* *
1045539 TAAAATTAAAATATATTTAAACTA
1 T--AATTAAAATAAAATTAAACTA
1045563 TAATTAAAATAAAATTAAAACTA
1 TAATTAAAATAAAATT-AAACTA
1045586 -AATATAAAA
1 TAAT-TAAAA
1045595 AGTAATAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
20 3 0.05
21 5 0.08
22 25 0.40
23 20 0.32
24 3 0.05
25 6 0.10
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (22 bp):
TAATTAAAATAAAATTAAACTA
Found at i:1046488 original size:22 final size:20
Alignment explanation
Indices: 1046446--1046510 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 20
1046436 TCGTTGGTAG
1046446 TTTTTCTTTTCTTTC-GTTTT
1 TTTTTCTTTTCTTTCTG-TTT
1046466 TTTTTCTTCTCTCTTTCTGTTT
1 TTTTTCTT-T-TCTTTCTGTTT
1046488 TTTTTCTTTTTTCTTT-TGTTT
1 TTTTTC--TTTTCTTTCTGTTT
1046509 TT
1 TT
1046511 CTCTGCTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
20 8 0.20
21 8 0.20
22 20 0.50
23 2 0.05
24 2 0.05
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTTTCTTTTCTTTCTGTTT
Found at i:1046513 original size:37 final size:38
Alignment explanation
Indices: 1046447--1046525 Score: 92
Period size: 37 Copynumber: 2.1 Consensus size: 38
1046437 CGTTGGTAGT
*
1046447 TTTTCTTTTCTTTCGTTTTTTTTTCTTCTCT-CTTTCTG
1 TTTTCTTTTCTTTC-TTTTTTTTTCTTCTCTGCTCTCTG
*
1046485 TTTT-TTTTCTTT-TTTCTTTTGTTTTTCTCTGCTCTCTG
1 TTTTCTTTTCTTTCTTT-TTTT-TTCTTCTCTGCTCTCTG
1046523 TTT
1 TTT
1046526 CTGTATCTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
35 3 0.08
36 4 0.11
37 16 0.44
38 13 0.36
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.75
Consensus pattern (38 bp):
TTTTCTTTTCTTTCTTTTTTTTTCTTCTCTGCTCTCTG
Found at i:1046941 original size:11 final size:11
Alignment explanation
Indices: 1046925--1046977 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
1046915 TTTGGGCTTG
* *
1046925 TAATAATTATT
1 TAATAATAATA
1046936 TAATAATAATA
1 TAATAATAATA
1046947 TAATAATAATAA
1 TAATAATAAT-A
*
1046959 TATTTAATAATAA
1 TA-ATAATAAT-A
1046972 TAATAA
1 TAATAA
1046978 ATTTAAATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 19 0.53
12 6 0.17
13 11 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAATAATAATA
Found at i:1046942 original size:3 final size:3
Alignment explanation
Indices: 1046936--1046977 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
1046926 AATAATTATT
*
1046936 TAA TAA TAA T-A TAA TAA TAA TAA TATT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
1046978 ATTTAAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:1046944 original size:14 final size:13
Alignment explanation
Indices: 1046925--1046973 Score: 71
Period size: 14 Copynumber: 3.6 Consensus size: 13
1046915 TTTGGGCTTG
1046925 TAATAATTATTTAA
1 TAATAA-TATTTAA
*
1046939 TAATAATATAATAA
1 TAATAATAT-TTAA
1046953 TAATAATATTTAA
1 TAATAATATTTAA
1046966 TAATAATA
1 TAATAATA
1046974 ATAAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
13 14 0.44
14 18 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:1046968 original size:16 final size:14
Alignment explanation
Indices: 1046936--1046976 Score: 64
Period size: 16 Copynumber: 2.8 Consensus size: 14
1046926 AATAATTATT
1046936 TAATAATAATATAA
1 TAATAATAATATAA
1046950 TAATAATAATATTTAA
1 TAATAATAATA--TAA
1046966 TAATAATAATA
1 TAATAATAATA
1046977 AATTTAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 11 0.44
16 14 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:1046968 original size:19 final size:18
Alignment explanation
Indices: 1046946--1046983 Score: 67
Period size: 19 Copynumber: 2.1 Consensus size: 18
1046936 TAATAATAAT
1046946 ATAATAATAATAATATTTA
1 ATAATAATAATAA-ATTTA
1046965 ATAATAATAATAAATTTA
1 ATAATAATAATAAATTTA
1046983 A
1 A
1046984 ATGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATAATAATAATAAATTTA
Found at i:1047259 original size:76 final size:76
Alignment explanation
Indices: 1047104--1047975 Score: 1512
Period size: 76 Copynumber: 11.5 Consensus size: 76
1047094 GATGGAAATG
* * *
1047104 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGG-TTTTGAAAACATCAAAAAGC
1047169 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* * *
1047181 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1047246 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
1047257 TTTGGAAACATCATGCACTGAAGGACTTACAGATAACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
*
1047322 CCCAAAGGCTT
66 CCCGAAGGCTT
* * *
1047333 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1047398 CCCGAAGGCTT
66 CCCGAAGGCTT
1047409 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
*
1047474 CCCGATGGCTT
66 CCCGAAGGCTT
1047485 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
*
1047549 CCCAAAGGCTT
66 CCCGAAGGCTT
* *
1047560 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1047625 CCCGAAGGCTT
66 CCCGAAGGCTT
*
1047636 TTTGGAAACATCATGCACTGAAGGACTTATAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1047701 CCCGAAGGCTT
66 CCCGAAGGCTT
1047712 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
*
1047777 TCCGAAGGCTT
66 CCCGAAGGCTT
* *
1047788 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
*
1047853 TCCGAAGGCTT
66 CCCGAAGGCTT
1047864 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1047929 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
1047940 TTTGGAAACATCATGCACTGTAGGACTTACATATGA
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA
1047976 GGGAAATAGT
Statistics
Matches: 763, Mismatches: 31, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
75 72 0.09
76 650 0.85
77 41 0.05
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:1049125 original size:54 final size:54
Alignment explanation
Indices: 1049043--1049198 Score: 249
Period size: 54 Copynumber: 2.9 Consensus size: 54
1049033 AGAATAGCAG
* ***
1049043 GTTCGTAAAACATTTGATAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* *
1049097 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
1049151 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
1049199 CAAGATTTCT
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 93 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:1051389 original size:114 final size:114
Alignment explanation
Indices: 1051189--1051411 Score: 356
Period size: 114 Copynumber: 2.0 Consensus size: 114
1051179 GATCATGCAG
* * * * *
1051189 TTCATCTTTCAATTTCAATGATTGGTTATGGGATTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGGGATTCATACCAAACCAAATCAGATAACTCAAAGA
* *
1051254 ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
* *
1051303 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTATGGGATTCATACCAAACCAAATCAGATAACTCAAAGA
*
1051368 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGA
66 ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGA
1051412 TCACATGGCA
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTATGGGATTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTATGAGCAAA
Found at i:1053594 original size:10 final size:10
Alignment explanation
Indices: 1053579--1053630 Score: 86
Period size: 10 Copynumber: 5.0 Consensus size: 10
1053569 CTTGATTCAA
1053579 TTTTTTTCTT
1 TTTTTTTCTT
1053589 TTTTTTTCTT
1 TTTTTTTCTT
1053599 TTTTTTCCTCTT
1 TTTTTT--TCTT
1053611 TTTTTTTCTT
1 TTTTTTTCTT
1053621 TTTTTTTCTT
1 TTTTTTTCTT
1053631 CTTTCTTTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
10 30 0.75
12 10 0.25
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:1053610 original size:22 final size:22
Alignment explanation
Indices: 1053585--1053626 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1053575 TCAATTTTTT
1053585 TCTTTTTTTTTCTTTTTTTTCC
1 TCTTTTTTTTTCTTTTTTTTCC
1053607 TCTTTTTTTTTCTTTTTTTT
1 TCTTTTTTTTTCTTTTTTTT
1053627 TCTTCTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (22 bp):
TCTTTTTTTTTCTTTTTTTTCC
Found at i:1059203 original size:23 final size:24
Alignment explanation
Indices: 1059159--1059205 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
1059149 AAAATTAATC
*
1059159 AAATAATATATATTAATAAAAATA
1 AAATAATATATACTAATAAAAATA
*
1059183 AAATAATA-ATACTAATTAAAATA
1 AAATAATATATACTAATAAAAATA
1059206 TTAAACATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (24 bp):
AAATAATATATACTAATAAAAATA
Found at i:1059237 original size:17 final size:17
Alignment explanation
Indices: 1059181--1059263 Score: 66
Period size: 17 Copynumber: 4.9 Consensus size: 17
1059171 TTAATAAAAA
1059181 TAAAA-TAATAATACTAAT
1 TAAAATTAA-AATA-TAAT
* *
1059199 TAAAATATTAAACAT-A-
1 TAAAAT-TAAAATATAAT
*
1059215 TAAAATTAAAATATATT
1 TAAAATTAAAATATAAT
*
1059232 TAAAATTAAAATAAAAT
1 TAAAATTAAAATATAAT
*
1059249 TAAAACT-AAATATAA
1 TAAAATTAAAATATAA
1059264 AAAGTAATAA
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
15 6 0.12
16 13 0.25
17 22 0.42
18 6 0.12
19 3 0.06
20 2 0.04
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATTAAAATATAAT
Found at i:1060145 original size:18 final size:18
Alignment explanation
Indices: 1060124--1060183 Score: 50
Period size: 21 Copynumber: 3.1 Consensus size: 18
1060114 AGTTTTTCTT
1060124 TTCTTTCGTTTTTTTTTCTTC
1 TTCTTTCG--TTTTTTT-TTC
1060145 TCTCTTTCTGTTTTTTTTTC
1 T-TCTTTC-GTTTTTTTTTC
*
1060165 TTTTTTC-TTTTGTTTTTC
1 TTCTTTCGTTTT-TTTTTC
1060183 T
1 T
1060184 CTGCTCTCTG
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 4 0.11
18 7 0.20
19 5 0.14
20 4 0.11
21 8 0.23
22 6 0.17
23 1 0.03
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (18 bp):
TTCTTTCGTTTTTTTTTC
Found at i:1060145 original size:23 final size:23
Alignment explanation
Indices: 1060119--1060181 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
1060109 TTGGTAGTTT
1060119 TTCTTTTCTTTCGTTTTTTTTTC
1 TTCTTTTCTTTCGTTTTTTTTTC
*
1060142 TTC-TCTCTTTCTGTTTTTTTTTC
1 TTCTTTTCTTTC-GTTTTTTTTTC
*
1060165 TT-TTTTCTTTTGTTTTT
1 TTCTTTTCTTTCGTTTTT
1060182 CTCTGCTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
22 13 0.37
23 22 0.63
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (23 bp):
TTCTTTTCTTTCGTTTTTTTTTC
Found at i:1060194 original size:39 final size:38
Alignment explanation
Indices: 1060115--1060196 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 38
1060105 ATCGTTGGTA
*
1060115 GTTTTTCTTTTCTTTCGTTTTTTTTTCTTCTCTCTTTCT
1 GTTTTTCTTTTCTTTC-TTTTTTTTTCTTCTCTCTCTCT
*
1060154 GTTTTT-TTTTCTTT-TTTCTTTTGTTTTTCTCTGCTCTCT
1 GTTTTTCTTTTCTTTCTTT-TTTT-TTCTTCTCT-CTCTCT
1060193 GTTT
1 GTTT
1060197 CTGTATCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
36 3 0.08
37 4 0.11
38 16 0.42
39 15 0.39
ACGTcount: A:0.00, C:0.18, G:0.07, T:0.74
Consensus pattern (38 bp):
GTTTTTCTTTTCTTTCTTTTTTTTTCTTCTCTCTCTCT
Found at i:1060612 original size:11 final size:11
Alignment explanation
Indices: 1060596--1060672 Score: 70
Period size: 11 Copynumber: 7.0 Consensus size: 11
1060586 TTTGGGCTTG
* *
1060596 TAATAATTATT
1 TAATAATAATA
1060607 TAATAATAATA
1 TAATAATAATA
1060618 TAATAATAATAA
1 TAATAATAAT-A
*
1060630 TATTTAATAATAA
1 TA-ATAATAAT-A
1060643 TAATAATAATA
1 TAATAATAATA
*
1060654 -AA-AAT-ATT
1 TAATAATAATA
1060662 TAATAATAATA
1 TAATAATAATA
1060673 ATAAATTTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
8 2 0.04
9 5 0.09
10 5 0.09
11 22 0.40
12 10 0.18
13 11 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATAATAATA
Found at i:1060613 original size:3 final size:3
Alignment explanation
Indices: 1060607--1060676 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
1060597 AATAATTATT
*
1060607 TAA TAA TAA T-A TAA TAA TAA TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
* *
1060652 TAA AAA TATT TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA
1060677 ATTTAAATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.03
3 52 0.90
4 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1060620 original size:19 final size:19
Alignment explanation
Indices: 1060598--1060672 Score: 66
Period size: 19 Copynumber: 4.1 Consensus size: 19
1060588 TGGGCTTGTA
*
1060598 ATAATTATTTAATAATAAT
1 ATAATTATATAATAATAAT
1060617 ATAA-TA-ATAATAAT-AT
1 ATAATTATATAATAATAAT
* *
1060633 TTAATAATAATAATAATAAT
1 ATAATTAT-ATAATAATAAT
* * *
1060653 AAAAATATTTAATAATAAT
1 ATAATTATATAATAATAAT
1060672 A
1 A
1060673 ATAAATTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
16 5 0.11
17 8 0.18
18 2 0.05
19 23 0.52
20 6 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAATTATATAATAATAAT
Found at i:1060648 original size:28 final size:28
Alignment explanation
Indices: 1060596--1060676 Score: 137
Period size: 28 Copynumber: 2.9 Consensus size: 28
1060586 TTTGGGCTTG
1060596 TAATAATTATTTAATAATAAT-ATAATAA
1 TAATAA-TATTTAATAATAATAATAATAA
1060624 TAATAATATTTAATAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAATAA
*
1060652 TAAAAATATTTAATAATAATAATAA
1 TAATAATATTTAATAATAATAATAA
1060677 ATTTAAATGA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 14 0.27
28 37 0.73
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
TAATAATATTTAATAATAATAATAATAA
Found at i:1060673 original size:22 final size:21
Alignment explanation
Indices: 1060607--1060677 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 21
1060597 AATAATTATT
*
1060607 TAATAATAAT-ATAATAATAA
1 TAATAAAAATAATAATAATAA
**
1060627 TAATATTTAATAATAATAATAA
1 TAATA-AAAATAATAATAATAA
*
1060649 TAATAAAAATATTTAATAATAA
1 TAATAAAAATA-ATAATAATAA
1060671 TAATAAA
1 TAATAAA
1060678 TTTAAATGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.11
21 8 0.18
22 31 0.70
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATAAAAATAATAATAATAA
Found at i:1063646 original size:16 final size:16
Alignment explanation
Indices: 1063627--1063657 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1063617 CCAGCACCAA
1063627 AATTAACCTGAACCGT
1 AATTAACCTGAACCGT
1063643 AATTAACCTGAACCG
1 AATTAACCTGAACCG
1063658 AAAGTAAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (16 bp):
AATTAACCTGAACCGT
Found at i:1066408 original size:35 final size:35
Alignment explanation
Indices: 1066357--1066431 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
1066347 CGTCACGAAC
*
1066357 AGTAAGGCCCTAAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTAAGCACAAAGCCGAGGAGCCTCCA
*
1066392 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTAAGCACAAAGCCGAGGAGCCTCCA
1066427 AGTAA
1 AGTAA
1066432 TCTTCCTCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.35, C:0.28, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTAAGCACAAAGCCGAGGAGCCTCCA
Found at i:1066541 original size:24 final size:23
Alignment explanation
Indices: 1066513--1066599 Score: 93
Period size: 24 Copynumber: 3.7 Consensus size: 23
1066503 ATTCAAGTCA
* *
1066513 AGTATCATATCAGAATCCATATC
1 AGTATCAGATCAGAATCCATGTC
*
1066536 ATGTATCAGATTAGAATCCATGTC
1 A-GTATCAGATCAGAATCCATGTC
* *
1066560 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCATGTC
* *
1066583 AGGTATCATAACAGAAT
1 A-GTATCAGATCAGAAT
1066600 TCAAATTTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
23 21 0.40
24 32 0.60
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCATGTC
Found at i:1066599 original size:47 final size:48
Alignment explanation
Indices: 1066509--1066599 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 48
1066499 CATAATTCAA
* * * **
1066509 GTCAAGTATCATATCAGAATCCATATCATGTATCAGATTAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAATCCAT
* *
1066557 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAAT
1066600 TCAAATTTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 31 0.86
48 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAATCCAT
Found at i:1068950 original size:7 final size:7
Alignment explanation
Indices: 1068938--1068969 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1068928 TGGTCAACTC
1068938 CGGTCAA
1 CGGTCAA
1068945 CGGTCAA
1 CGGTCAA
1068952 CGGGTCAA
1 C-GGTCAA
1068960 CGGTCAA
1 CGGTCAA
1068967 CGG
1 CGG
1068970 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:1068959 original size:8 final size:8
Alignment explanation
Indices: 1068939--1068985 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
1068929 GGTCAACTCC
1068939 GGTCAAC-
1 GGTCAACG
1068946 GGTCAACG
1 GGTCAACG
1068954 GGTCAAC-
1 GGTCAACG
1068961 GGTCAACG
1 GGTCAACG
1068969 GGT---CG
1 GGTCAACG
1068974 GGTCAACG
1 GGTCAACG
1068982 GGTC
1 GGTC
1068986 GGGTCGGGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:1068959 original size:15 final size:15
Alignment explanation
Indices: 1068939--1068985 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
1068929 GGTCAACTCC
1068939 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
1068954 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
1068969 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
1068982 GGTC
1 GGTC
1068986 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:1068977 original size:5 final size:5
Alignment explanation
Indices: 1068967--1069030 Score: 51
Period size: 5 Copynumber: 12.0 Consensus size: 5
1068957 CAACGGTCAA
*
1068967 CGGGT CGGGT CAACGGGT CGGGT CGGGT C-AG- CGGGT CGGGT CGGGT
1 CGGGT CGGGT C---GGGT CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT
1069013 CAACGGGT CGGGT CGGGT
1 ---CGGGT CGGGT CGGGT
1069031 TGTGACCGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
3 1 0.02
4 2 0.04
5 36 0.73
8 10 0.20
ACGTcount: A:0.08, C:0.22, G:0.53, T:0.17
Consensus pattern (5 bp):
CGGGT
Found at i:1068979 original size:13 final size:13
Alignment explanation
Indices: 1068946--1069026 Score: 66
Period size: 13 Copynumber: 6.3 Consensus size: 13
1068936 TCCGGTCAAC
*
1068946 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1068961 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1068974 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1068987 GGT---CGGGTCAGCG
1 GGTCAACGGGT---CG
1069000 GGT---CGGGTCG
1 GGTCAACGGGTCG
1069010 GGTCAACGGGTCG
1 GGTCAACGGGTCG
1069023 GGTC
1 GGTC
1069027 GGGTTGTGAC
Statistics
Matches: 59, Mismatches: 1, Indels: 14
0.80 0.01 0.19
Matches are distributed among these distances:
10 10 0.17
13 37 0.63
15 12 0.20
ACGTcount: A:0.14, C:0.23, G:0.47, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1068990 original size:18 final size:18
Alignment explanation
Indices: 1068967--1069030 Score: 119
Period size: 18 Copynumber: 3.6 Consensus size: 18
1068957 CAACGGTCAA
1068967 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1068985 CGGGTCGGGTCAGCGGGT
1 CGGGTCGGGTCAACGGGT
1069003 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
1069021 CGGGTCGGGT
1 CGGGTCGGGT
1069031 TGTGACCGGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.08, C:0.22, G:0.53, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1074359 original size:21 final size:21
Alignment explanation
Indices: 1074333--1074374 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1074323 AAAACAACTC
1074333 ACAATCATAATTAATTTTCGG
1 ACAATCATAATTAATTTTCGG
1074354 ACAATCATAATTAATTTTCGG
1 ACAATCATAATTAATTTTCGG
1074375 CCGCTCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (21 bp):
ACAATCATAATTAATTTTCGG
Found at i:1078449 original size:14 final size:15
Alignment explanation
Indices: 1078430--1078458 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1078420 TATATGATTT
1078430 TTATT-ATTTTTAAA
1 TTATTAATTTTTAAA
1078444 TTATTAATTTTTAAA
1 TTATTAATTTTTAAA
1078459 AAATACAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTAATTTTTAAA
Found at i:1079160 original size:19 final size:19
Alignment explanation
Indices: 1079136--1079201 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
1079126 CCGGTTTTGG
1079136 TAATTAAAATGTAAATACA
1 TAATTAAAATGTAAATACA
* *
1079155 TAATTAATAAAT-AAAATTA-T
1 TAATT-A-AAATGTAAA-TACA
*
1079175 TAAAATAAAATGTAAATACA
1 T-AATTAAAATGTAAATACA
1079195 TAATTAA
1 TAATTAA
1079202 TAAATAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
19 16 0.46
20 10 0.29
21 9 0.26
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
TAATTAAAATGTAAATACA
Found at i:1079178 original size:13 final size:13
Alignment explanation
Indices: 1079156--1079214 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
1079146 GTAAATACAT
1079156 AATTAATAAATAA
1 AATTAATAAATAA
*
1079169 AATTATTAAAATAA
1 AATTAAT-AAATAA
*
1079183 AA-T-GTAAATACA
1 AATTAATAAATA-A
1079195 TAATTAATAAATAA
1 -AATTAATAAATAA
1079209 AATTAA
1 AATTAA
1079215 ATTTTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
11 5 0.13
12 2 0.05
13 15 0.39
14 10 0.26
15 6 0.16
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (13 bp):
AATTAATAAATAA
Found at i:1080928 original size:38 final size:38
Alignment explanation
Indices: 1080877--1080953 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
1080867 ATCTAATTAC
*
1080877 AGCAACTCCATGAGCAGTGATCAACGGCAACCGCAACT
1 AGCAACTCCATGAGCAATGATCAACGGCAACCGCAACT
* * *
1080915 AGCAAC-CACATGAGCAATGATCAGCTGCAACCTCAACT
1 AGCAACTC-CATGAGCAATGATCAACGGCAACCGCAACT
1080953 A
1 A
1080954 CTTTACTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 1 0.03
38 33 0.97
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.14
Consensus pattern (38 bp):
AGCAACTCCATGAGCAATGATCAACGGCAACCGCAACT
Found at i:1082696 original size:42 final size:42
Alignment explanation
Indices: 1082637--1082716 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
1082627 CTTACTTCAA
* *
1082637 CTTCAGCACTATCACTTATGGCCATGTCATCAGCATGTTGAG
1 CTTCAGCACCATCACTTATAGCCATGTCATCAGCATGTTGAG
* *
1082679 CTTCAGCACCATCACTTATAGCCATGTTATCAGTATGT
1 CTTCAGCACCATCACTTATAGCCATGTCATCAGCATGT
1082717 CGTTCTGAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (42 bp):
CTTCAGCACCATCACTTATAGCCATGTCATCAGCATGTTGAG
Found at i:1090577 original size:10 final size:10
Alignment explanation
Indices: 1090562--1090588 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1090552 TCTTCCTACT
1090562 TTCTTTCCCA
1 TTCTTTCCCA
1090572 TTCTTTCCCA
1 TTCTTTCCCA
1090582 TTCTTTC
1 TTCTTTC
1090589 TCAATCTCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.56
Consensus pattern (10 bp):
TTCTTTCCCA
Found at i:1091594 original size:22 final size:22
Alignment explanation
Indices: 1091555--1091596 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1091545 TAACCAATTT
* * *
1091555 GGTTGGGTTGAGGGAGAAGAGG
1 GGTTGGGTTAAAGAAGAAGAGG
1091577 GGTTGGGTTAAAGAAGAAGA
1 GGTTGGGTTAAAGAAGAAGA
1091597 AGAGATGATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.50, T:0.19
Consensus pattern (22 bp):
GGTTGGGTTAAAGAAGAAGAGG
Found at i:1101127 original size:7 final size:7
Alignment explanation
Indices: 1101117--1101144 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1101107 CTAGTAAGTT
1101117 GTAGCCA
1 GTAGCCA
1101124 GTAGCCA
1 GTAGCCA
1101131 GTAGCCA
1 GTAGCCA
1101138 GTAGCCA
1 GTAGCCA
1101145 AGCGGGAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.29, T:0.14
Consensus pattern (7 bp):
GTAGCCA
Found at i:1105247 original size:19 final size:19
Alignment explanation
Indices: 1105221--1105261 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1105211 ATTCGCACAA
1105221 AAACATTTATTT-CGAGAC
1 AAACATTTATTTACGAGAC
*
1105239 AAACTATTTATTTATGAGAC
1 AAAC-ATTTATTTACGAGAC
1105259 AAA
1 AAA
1105262 ATATATAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 8 0.40
20 8 0.40
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (19 bp):
AAACATTTATTTACGAGAC
Found at i:1107157 original size:36 final size:36
Alignment explanation
Indices: 1107110--1107184 Score: 132
Period size: 36 Copynumber: 2.1 Consensus size: 36
1107100 AAAACCCCGT
*
1107110 GATGGGTTAGTCCTGGGCGTTCAGTTGTTGACTTCC
1 GATGGGTTAGTCCTGGGCGTTCAGTTGTTGAATTCC
*
1107146 GATGGGTTAGTCCTGGGTGTTCAGTTGTTGAATTCC
1 GATGGGTTAGTCCTGGGCGTTCAGTTGTTGAATTCC
1107182 GAT
1 GAT
1107185 CTCCACGCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.13, C:0.16, G:0.33, T:0.37
Consensus pattern (36 bp):
GATGGGTTAGTCCTGGGCGTTCAGTTGTTGAATTCC
Found at i:1107378 original size:16 final size:17
Alignment explanation
Indices: 1107357--1107392 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1107347 ATAAATAAAT
*
1107357 AAAATAAAATAT-TTAA
1 AAAATAAAAAATGTTAA
1107373 AAAATAAAAAATGTTAA
1 AAAATAAAAAATGTTAA
1107390 AAA
1 AAA
1107393 TATATATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
AAAATAAAAAATGTTAA
Found at i:1107381 original size:5 final size:5
Alignment explanation
Indices: 1107334--1107367 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1107324 GACCTGGACC
1107334 AAAAT AAAAT AAAAT -AAAT -AAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A
1107368 TTTAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.29
5 20 0.71
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:1107450 original size:14 final size:12
Alignment explanation
Indices: 1107425--1107474 Score: 66
Period size: 12 Copynumber: 4.0 Consensus size: 12
1107415 TATATTATAT
1107425 ATATTTTCAAAA
1 ATATTTTCAAAA
1107437 ATATTTCTCAAAAA
1 ATATTT-TC-AAAA
1107451 TATATTTTCAAAA
1 -ATATTTTCAAAA
1107464 ATATTTT-AAAA
1 ATATTTTCAAAA
1107475 CTATATATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.11
12 13 0.37
13 6 0.17
14 6 0.17
15 6 0.17
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:1107480 original size:27 final size:26
Alignment explanation
Indices: 1107421--1107539 Score: 97
Period size: 27 Copynumber: 4.6 Consensus size: 26
1107411 ATAATATATT
1107421 ATATATATTTTCAAAAATATTTCTCAAA
1 ATATATATTTTCAAAAATATTT-T-AAA
1107449 A-ATATATTTTCAAAAATATTTTAAA
1 ATATATATTTTCAAAAATATTTTAAA
* * *
1107474 ACTATATATTAT-ATATATATTTT-AA
1 A-TATATATTTTCAAAAATATTTTAAA
* *
1107499 A-A-ATGTTTTCAAAACTATATTTT-AT
1 ATATATATTTTCAAAA--ATATTTTAAA
*
1107524 ATATATTTTTTCAAAA
1 ATATATATTTTCAAAA
1107540 GAATTCAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
22 5 0.07
23 3 0.04
25 16 0.21
26 11 0.15
27 39 0.52
28 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.47
Consensus pattern (26 bp):
ATATATATTTTCAAAAATATTTTAAA
Found at i:1107539 original size:76 final size:76
Alignment explanation
Indices: 1107450--1107728 Score: 374
Period size: 76 Copynumber: 3.7 Consensus size: 76
1107440 TTTCTCAAAA
1107450 ATATATTTTCAAAAATATTTT-AAAACTATATATTATATATATATTTTAAAAATGTTTTCAAAAC
1 ATATATTTTC-AAAATATTTTCAAAACTATATATTATATATATATTTTAAAAATGTTTTCAAAAC
*
1107514 TATATTTTATAT
65 TATATATTATAT
* * * * *
1107526 ATATTTTTTCAAAAGA-ATTCAAAA--ACTATATTATATATATATATTCAAAATGTTTTCAAAAT
1 ATATATTTTCAAAATATTTTCAAAACTA-TATATTATATATATATTTTAAAAATGTTTTCAAAA-
1107588 CTATATA-T-TAT
64 CTATATATTATAT
* *
1107599 ATATATTTTCAAAATATTTTCAGAAACTATATATTATATATATATTTTCAAAATATTTTCAAAAA
1 ATATATTTTCAAAATATTTTCA-AAACTATATATTATATATATATTTTAAAAATGTTTTC-AAAA
1107664 CTATATATTATAT
64 CTATATATTATAT
*
1107677 ATATATTTTCAAAATATTTTCAAAAACTATATATTATATATAT-TTTCAAAAA
1 ATATATTTTCAAAATATTTTC-AAAACTATATATTATATATATATTTTAAAAA
1107729 ACCGATTTTT
Statistics
Matches: 179, Mismatches: 13, Indels: 21
0.84 0.06 0.10
Matches are distributed among these distances:
73 18 0.10
74 40 0.22
75 18 0.10
76 45 0.25
77 13 0.07
78 44 0.25
79 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (76 bp):
ATATATTTTCAAAATATTTTCAAAACTATATATTATATATATATTTTAAAAATGTTTTCAAAACT
ATATATTATAT
Found at i:1107592 original size:26 final size:26
Alignment explanation
Indices: 1107563--1107613 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1107553 ATATTATATA
*
1107563 TATATATTCA-AAATGTTTTCAAAATC
1 TATATATT-ATAAATATTTTCAAAATC
*
1107589 TATATATTATATATATTTTCAAAAT
1 TATATATTATAAATATTTTCAAAAT
1107614 ATTTTCAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (26 bp):
TATATATTATAAATATTTTCAAAATC
Found at i:1107615 original size:11 final size:11
Alignment explanation
Indices: 1107601--1107701 Score: 62
Period size: 11 Copynumber: 8.1 Consensus size: 11
1107591 TATATTATAT
1107601 ATATTTTCAAA
1 ATATTTTCAAA
1107612 ATATTTTCAGAA
1 ATATTTTCA-AA
1107624 ACTATATATT-ATATA
1 A-TAT-T-TTCA-A-A
1107639 TATATTTTCAAA
1 -ATATTTTCAAA
1107651 ATATTTTCAAAA
1 ATATTTTC-AAA
1107663 ACTATATATT-ATATA
1 A-TAT-T-TTCA-A-A
1107678 TATATTTTCAAA
1 -ATATTTTCAAA
1107690 ATATTTTCAAA
1 ATATTTTCAAA
1107701 A
1 A
1107702 ACTATATATT
Statistics
Matches: 74, Mismatches: 1, Indels: 30
0.70 0.01 0.29
Matches are distributed among these distances:
11 29 0.39
12 9 0.12
13 13 0.18
14 9 0.12
15 12 0.16
16 2 0.03
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.46
Consensus pattern (11 bp):
ATATTTTCAAA
Found at i:1107632 original size:39 final size:37
Alignment explanation
Indices: 1107450--1107727 Score: 352
Period size: 39 Copynumber: 7.4 Consensus size: 37
1107440 TTTCTCAAAA
1107450 ATATATTTTCAAAAATATTTT-AAAACTATATATTATAT
1 ATATATTTTC-AAAATATTTTCAAAACTATATATT-TAT
* *
1107488 ATATATTTTAAAAATGTTTTCAAAACTATAT-TTTAT
1 ATATATTTTCAAAATATTTTCAAAACTATATATTTAT
* * *
1107524 ATATATTTTTTCAAAAGA-ATTCAAAAACTATAT-TATAT
1 ATATA--TTTTCAAAATATTTTC-AAAACTATATATTTAT
* *
1107562 ATATATATTCAAAATGTTTTCAAAATCTATATA-TTAT
1 ATATATTTTCAAAATATTTTCAAAA-CTATATATTTAT
1107599 ATATATTTTCAAAATATTTTCAGAAACTATATATTATAT
1 ATATATTTTCAAAATATTTTCA-AAACTATATATT-TAT
1107638 ATATATTTTCAAAATATTTTCAAAAACTATATATTATAT
1 ATATATTTTCAAAATATTTTC-AAAACTATATATT-TAT
1107677 ATATATTTTCAAAATATTTTCAAAAACTATATA-TTAT
1 ATATATTTTCAAAATATTTTC-AAAACTATATATTTAT
1107714 ATATATTTTCAAAA
1 ATATATTTTCAAAA
1107728 AACCGATTTT
Statistics
Matches: 215, Mismatches: 14, Indels: 23
0.85 0.06 0.09
Matches are distributed among these distances:
36 20 0.09
37 70 0.33
38 51 0.24
39 73 0.34
40 1 0.00
ACGTcount: A:0.45, C:0.07, G:0.01, T:0.46
Consensus pattern (37 bp):
ATATATTTTCAAAATATTTTCAAAACTATATATTTAT
Done.