Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 51
Found at i:2826236 original size:18 final size:18
Alignment explanation
Indices: 2826190--2826241 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
2826180 GTTCAAATTT
*
2826190 AGATTTCAATTCC-TGAC
1 AGATTTCAATTCCTTCAC
*
2826207 AAATTTCAATTCCTTCAC
1 AGATTTCAATTCCTTCAC
*
2826225 AGATTCCAATTCCTTCA
1 AGATTTCAATTCCTTCA
2826242 TAAACATTCC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.37
Consensus pattern (18 bp):
AGATTTCAATTCCTTCAC
Found at i:2827870 original size:20 final size:20
Alignment explanation
Indices: 2827845--2827894 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2827835 TTTGAGTTAA
2827845 TTAAAATATGTTTAAAG-TGT
1 TTAAAATATGTTTAAAGCT-T
* *
2827865 TTAAAATGTGTTTTAAGCTT
1 TTAAAATATGTTTAAAGCTT
2827885 TTAAAATATG
1 TTAAAATATG
2827895 AAAAACACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (20 bp):
TTAAAATATGTTTAAAGCTT
Found at i:2828107 original size:21 final size:21
Alignment explanation
Indices: 2828052--2828105 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
2828042 TTTAAGTAAG
* *
2828052 AGTTTCGAAACTTTGA-TAAA
1 AGTTTAGAAACTTTCATTAAA
*
2828072 AGTTTTGAAACTTTCATTAAA
1 AGTTTAGAAACTTTCATTAAA
2828093 A-TTTAGAAACTTT
1 AGTTTAGAAACTTT
2828106 TCCCATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 25 0.83
21 5 0.17
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (21 bp):
AGTTTAGAAACTTTCATTAAA
Found at i:2829267 original size:17 final size:18
Alignment explanation
Indices: 2829247--2829288 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2829237 ATGCATGCAT
* *
2829247 TTCATTTAA-GCATGTAG
1 TTCATTTAACACATATAG
2829264 TTCA-TTAACACATATAG
1 TTCATTTAACACATATAG
2829281 TTCATTTA
1 TTCATTTA
2829289 GTTATGCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 4 0.19
17 14 0.67
18 3 0.14
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (18 bp):
TTCATTTAACACATATAG
Found at i:2829318 original size:17 final size:17
Alignment explanation
Indices: 2829278--2829320 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
2829268 TTAACACATA
*
2829278 TAGTTCATTTAGTTATG
1 TAGTTCATTTAGTTAAG
* * *
2829295 CACTTCATTTTGTTAAG
1 TAGTTCATTTAGTTAAG
2829312 TAGTTCATT
1 TAGTTCATT
2829321 GATGAATATG
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (17 bp):
TAGTTCATTTAGTTAAG
Found at i:2830696 original size:20 final size:22
Alignment explanation
Indices: 2830654--2830694 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2830644 CAACAACCAT
* *
2830654 CACTCTTTCATCACCTTCAAAC
1 CACTCTTTCATAACCTACAAAC
2830676 CACT-TTTCATAACCTACAA
1 CACTCTTTCATAACCTACAA
2830695 CCTTTCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.32, C:0.37, G:0.00, T:0.32
Consensus pattern (22 bp):
CACTCTTTCATAACCTACAAAC
Found at i:2831394 original size:20 final size:20
Alignment explanation
Indices: 2831352--2831395 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2831342 ATATTTTTTT
* *
2831352 GGTATCGATACCCTATAGTA
1 GGTATCAATACCCTATAGAA
2831372 GGTATCAATACCCATATA-AA
1 GGTATCAATACCC-TATAGAA
2831392 GGTA
1 GGTA
2831396 CAAATTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (20 bp):
GGTATCAATACCCTATAGAA
Found at i:2831888 original size:42 final size:42
Alignment explanation
Indices: 2831732--2832168 Score: 328
Period size: 43 Copynumber: 10.2 Consensus size: 42
2831722 TGAGAACAAA
* * * *
2831732 AAACGCCGCAATAGGTCAATATCTATTA-CGGCGTTTTTTGAAC
1 AAACGCCGCAAAAGGTC-AGACCTA-TAGCGGCGTTTTTAGAAC
* ** * *
2831775 AAACGTCC-CAAAAGGTCGATATTTATAGCGGCGTTTTTGGAAT
1 AAACG-CCGCAAAAGGTC-AGACCTATAGCGGCGTTTTTAGAAC
* * * * *
2831818 AAACGCCGCAAAAAGTTATG-CTATATAGCGGCGTTTCTAGAAA
1 AAACGCCGCAAAAGGTCA-GAC-CTATAGCGGCGTTTTTAGAAC
* * *
2831861 AAACGCCGTAAAAGGTCAGATCTATAGCGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAGA-AC
* * * *
2831904 AAATGCCGCAAAAGATAAGACCTATA-CTGGCGTTTTTAGTAC
1 AAACGCCGCAAAAGGTCAGACCTATAGC-GGCGTTTTTAGAAC
* * * * *
2831946 AAACACCGTAAAAGGTCAGACCTATAGTGGTGTTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAGA-AC
* *
2831989 AAACGCCGCAAAAGATAAGACCTATA-CTGGCGTTTTTAGAAC
1 AAACGCCGCAAAAGGTCAGACCTATAGC-GGCGTTTTTAGAAC
* * * * *
2832031 AAATGCCGTAAAAGGTCAGACCTATAGTGGCATTTTTGGACAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAGA-AC
** * * *
2832074 AAACATCGCAAAATGTCATACCTATAACGGCGTTTTT-GAACAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAG-A-AC
** * *
2832117 AAACGCCGCAAAAAATCAGACCTATAGCGGCATTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAGA-AC
2832160 AAACGCCGC
1 AAACGCCGC
2832169 TAATTACCTT
Statistics
Matches: 311, Mismatches: 68, Indels: 30
0.76 0.17 0.07
Matches are distributed among these distances:
42 90 0.29
43 218 0.70
44 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTCAGACCTATAGCGGCGTTTTTAGAAC
Found at i:2831938 original size:85 final size:84
Alignment explanation
Indices: 2831758--2832168 Score: 400
Period size: 85 Copynumber: 4.8 Consensus size: 84
2831748 CAATATCTAT
* * * * ** *
2831758 TACGGCGTTTTTTGAACAAACGTCC-CAAAAGGTCGATATTTATAGCGGCGTTTTTGGA-ATAAA
1 TACGGCGTTTTTAGAAAAAACG-CCGTAAAAGGTC-AGACCTATAGCGGCGTTTTTGGACACAAA
* * *
2831821 CGCCGCAAAAAGTTATG-CTATA
64 CGCCGC-AAAAGATAAGAC-CTA
* * * *
2831843 TAGCGGCGTTTCTAGAAAAAACGCCGTAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAAT
1 TA-CGGCGTTTTTAGAAAAAACGCCGTAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAAC
2831908 GCCGCAAAAGATAAGACCTA
65 GCCGCAAAAGATAAGACCTA
* * * * *
2831928 TACTGGCGTTTTTAGTACAAACACCGTAAAAGGTCAGACCTATAGTGGTGTTTTTGGACACAAAC
1 TAC-GGCGTTTTTAGAAAAAACGCCGTAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAAC
2831993 GCCGCAAAAGATAAGACCTA
65 GCCGCAAAAGATAAGACCTA
* * * *
2832013 TACTGGCGTTTTTAGAACAAATGCCGTAAAAGGTCAGACCTATAGTGGCATTTTTGGACACAAAC
1 TAC-GGCGTTTTTAGAAAAAACGCCGTAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAAC
** * *
2832078 ATCGCAAAATG-TCATACCTA
65 GCCGCAAAA-GATAAGACCTA
* ** * *
2832098 TAACGGCGTTTTT-GAACACAAACGCCGCAAAAAATCAGACCTATAGCGGCATTTTTGGATACAA
1 T-ACGGCGTTTTTAGAA-A-AAACGCCGTAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAA
2832162 ACGCCGC
63 ACGCCGC
2832169 TAATTACCTT
Statistics
Matches: 279, Mismatches: 38, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
84 4 0.01
85 193 0.69
86 82 0.29
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (84 bp):
TACGGCGTTTTTAGAAAAAACGCCGTAAAAGGTCAGACCTATAGCGGCGTTTTTGGACACAAACG
CCGCAAAAGATAAGACCTA
Found at i:2831996 original size:128 final size:129
Alignment explanation
Indices: 2831861--2832168 Score: 379
Period size: 128 Copynumber: 2.4 Consensus size: 129
2831851 TTTCTAGAAA
* * *
2831861 AAACGCCGTAAAAGGTCAGATCTATAGCGGCGTTTTTGGATACAAATGCCGCAAAAGATAAGACC
1 AAACGCCGCAAAAGATCAGACCTATAGCGGCGTTTTTGGATACAAATGCCGCAAAAGATAAGACC
* * * ** * *
2831926 TATACTGGCGTTTTTAG-TACAAACACCGTAAAAGGTCAGACCTATAGTGGTGTTTTTGGACAC
66 TATACTGGCATTTTTAGACACAAACACCGCAAAAGGTCAGACCTATAACGGCGTTTTTGAACAC
* * * * *
2831989 AAACGCCGCAAAAGATAAGACCTATA-CTGGCGTTTTTAGA-ACAAATGCCGTAAAAGGTCAGAC
1 AAACGCCGCAAAAGATCAGACCTATAGC-GGCGTTTTTGGATACAAATGCCGCAAAAGATAAGAC
* * * * *
2832052 CTATAGTGGCATTTTTGGACACAAACATCGCAAAATGTCATACCTATAACGGCGTTTTTGAACAC
65 CTATACTGGCATTTTTAGACACAAACACCGCAAAAGGTCAGACCTATAACGGCGTTTTTGAACAC
* * *
2832117 AAACGCCGCAAAAAATCAGACCTATAGCGGCATTTTTGGATACAAACGCCGC
1 AAACGCCGCAAAAGATCAGACCTATAGCGGCGTTTTTGGATACAAATGCCGC
2832169 TAATTACCTT
Statistics
Matches: 150, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
127 36 0.24
128 104 0.69
129 10 0.07
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (129 bp):
AAACGCCGCAAAAGATCAGACCTATAGCGGCGTTTTTGGATACAAATGCCGCAAAAGATAAGACC
TATACTGGCATTTTTAGACACAAACACCGCAAAAGGTCAGACCTATAACGGCGTTTTTGAACAC
Found at i:2834025 original size:23 final size:23
Alignment explanation
Indices: 2833995--2834053 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
2833985 ATGCTATAGT
2833995 GTTTGAAAGGTTGTGCATGACAA
1 GTTTGAAAGGTTGTGCATGACAA
* *
2834018 GTTTGAAAGGATATGCATGACAA
1 GTTTGAAAGGTTGTGCATGACAA
2834041 GTTTGAAA-GTTGT
1 GTTTGAAAGGTTGT
2834054 TAATGCCCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 3 0.09
23 29 0.91
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.32
Consensus pattern (23 bp):
GTTTGAAAGGTTGTGCATGACAA
Found at i:2835601 original size:41 final size:41
Alignment explanation
Indices: 2835527--2835885 Score: 344
Period size: 41 Copynumber: 8.6 Consensus size: 41
2835517 TTGTAAACTT
* * * * * *
2835527 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATA
1 GCGGCGTTTGTATA-A-AAATGCCACTAAAGTACGAGTCTTTA
* * *
2835570 ACGGCGTTTGAATAAAAATGCCACTAAAGTACGCGTCTTTA
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTA
* *
2835611 GCGGAGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTA
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTA
* * * * *
2835652 GCGGCGTTTTTATAAAAACGCCACTAAATTATGAGTCTTTC
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTA
* * * * *
2835693 GCGGCGTTTGTAAACACAAACGCCACTATAGTAC-ATGTGTATA
1 GCGGCGTTTGTATA-A-AAATGCCACTAAAGTACGA-GTCTTTA
* * * *
2835736 ACGGCGTTTGTATAAAAATGCCACTAAAGTACAATTCTATA
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTA
* *
2835777 GCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTT
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTA
** * * * *
2835818 GCGAAGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTT
1 GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTA
2835859 GCGGCGTTTGT-TGAAAAAATGCCACTA
1 GCGGCGTTTGTAT--AAAAATGCCACTA
2835886 TAGATGAACC
Statistics
Matches: 262, Mismatches: 48, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
40 1 0.00
41 203 0.77
42 17 0.06
43 41 0.16
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (41 bp):
GCGGCGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTA
Found at i:2835690 original size:82 final size:82
Alignment explanation
Indices: 2835571--2835929 Score: 339
Period size: 82 Copynumber: 4.4 Consensus size: 82
2835561 AAGTGTATAA
* * * *
2835571 CGGCGTTTGAATAAAAATGCCACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAAAAATGCCACT
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACT
2835636 AAAGTATGAGTCTTTAG
66 AAAGTATGAGTCTTTAG
* * * * * *
2835653 CGGCGTTTTTATAAAAACGCCACTAAATTATGAGTCTTTCGCGGCGTTTGTAAACACAAACGCCA
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATA-A-AAATGCCA
* * * * *
2835718 CTATAGTA-CATGTGTATAA
64 CTAAAGTATGA-GTCTTTAG
* * * *
2835737 CGGCGTTTGTATAAAAATGCCACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACT
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACT
* * *
2835802 AAATTACGAGTCTTTTG
66 AAAGTATGAGTCTTTAG
** * * *
2835819 CGAAGTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAAAATGCCA
1 CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTAT--AAAAATGCCA
* **
2835883 CTATAG-ATGAACCTATT-G
64 CTAAAGTATGAGTCT-TTAG
* **
2835901 CGGCGTTTTTATAAAAACGCTGCTAAAGT
1 CGGCGTTTGTATAAAAACGCCACTAAAGT
2835930 TACCATTTTG
Statistics
Matches: 221, Mismatches: 49, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
81 1 0.00
82 136 0.62
83 20 0.09
84 64 0.29
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (82 bp):
CGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAATGCCACT
AAAGTATGAGTCTTTAG
Found at i:2835750 original size:125 final size:123
Alignment explanation
Indices: 2835575--2835920 Score: 366
Period size: 125 Copynumber: 2.8 Consensus size: 123
2835565 GTATAACGGC
* * * *
2835575 GTTTG-AATAAAAATGCCACTAAAGTAC-GCGTCTTTAGCGGAGTTTGTATAAAAATGCCACTAA
1 GTTTGTAA-AAAAACGCCACTAAAGTACTAC-TCTTTAACGGCGTTTGTATAAAAATGCCACTAA
* * **
2835638 AGTATGAGTCTTTAGCGGCGTTTTTATAAAAACGCCACTAAATTATGAGTCTTTCGCGGC
64 AGTATGAATCTTTAGCGGCGTTTTTATAAAAACGCCACTAAATTACGAGTCTTTCGCGAA
* *
2835698 GTTTGTAAACACAAACGCCACTATAGTAC-A-TGTGTATAACGGCGTTTGTATAAAAATGCCACT
1 GTTTGTAAA-A-AAACGCCACTAAAGTACTACTCT-T-TAACGGCGTTTGTATAAAAATGCCACT
* * * * *
2835761 AAAGTA-CAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTTGCGAA
62 AAAGTATGAA-TCTTTAGCGGCGTTTTTATAAAAACGCCACTAAATTACGAGTCTTTCGCGAA
* ** *
2835823 GTTTGTATAAAAACGCCACTAAAGTACTACTCTTTTGCGGCGTTTGT-TGAAAAAATGCCACTAT
1 GTTTGTAAAAAAACGCCACTAAAGTACTACTCTTTAACGGCGTTTGTAT--AAAAATGCCACTAA
*
2835887 AG-ATGAACCTATT-GCGGCGTTTTTATAAAAACGC
64 AGTATGAATCT-TTAGCGGCGTTTTTATAAAAACGC
2835921 TGCTAAAGTT
Statistics
Matches: 185, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
122 1 0.01
123 57 0.31
124 26 0.14
125 101 0.55
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.31
Consensus pattern (123 bp):
GTTTGTAAAAAAACGCCACTAAAGTACTACTCTTTAACGGCGTTTGTATAAAAATGCCACTAAAG
TATGAATCTTTAGCGGCGTTTTTATAAAAACGCCACTAAATTACGAGTCTTTCGCGAA
Found at i:2835801 original size:166 final size:166
Alignment explanation
Indices: 2835527--2835869 Score: 526
Period size: 166 Copynumber: 2.1 Consensus size: 166
2835517 TTGTAAACTT
2835527 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCC
** * * **
2835592 ACTAAAGTACGCGTCTTTAGCGGAGTTTGTATAAAAATGCCACTAAAGTATGAGTCTTTAGCGGC
66 ACTAAAGTACAAGTCTATAGCGGAGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGAA
* * *
2835657 GTTTTTATAAAAACGCCACTAAATTA-TGAGTCTTTC
131 GTTTGTATAAAAACGCCACTAAAGTACT-ACTCTTTC
* *
2835693 GCGGCGTTTGTAAACACAAACGCCACTATAGTACATGTGTATAACGGCGTTTGTATAAAAATGCC
1 GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCC
* * * *
2835758 ACTAAAGTACAATTCTATAGCGGCGTTTGTATAAAAATGCCACTAAATTACGAGTCTTTTGCGAA
66 ACTAAAGTACAAGTCTATAGCGGAGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGAA
*
2835823 GTTTGTATAAAAACGCCACTAAAGTACTACTCTTTT
131 GTTTGTATAAAAACGCCACTAAAGTACTACTCTTTC
2835859 GCGGCGTTTGT
1 GCGGCGTTTGT
2835870 TGAAAAAATG
Statistics
Matches: 160, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
166 159 0.99
167 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (166 bp):
GCGGCGTTTGTAAACACAAACGCCACTATAGTACAAGTGTATAACGGCGTTTGAATAAAAATGCC
ACTAAAGTACAAGTCTATAGCGGAGTTTGTATAAAAATGCCACTAAAGTACGAGTCTTTAGCGAA
GTTTGTATAAAAACGCCACTAAAGTACTACTCTTTC
Found at i:2844012 original size:64 final size:63
Alignment explanation
Indices: 2843964--2844086 Score: 162
Period size: 64 Copynumber: 1.9 Consensus size: 63
2843954 TGCACTAAGA
*
2843964 GTGCATCGATGCATAAAATGCTTTCGATG-TTTCA-AAATAGC-CTGAGTGCATCGATGCATGGC
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATGCA--GC
2844026 TG
62 TG
* *
2844028 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACTCTGAGTGCATCAATGCA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTCTGAGTGCATCGATGCA
2844087 TGAAATGCAT
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
64 28 0.53
65 22 0.42
66 3 0.06
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACTCTGAGTGCATCGATGCAGCTG
Found at i:2847428 original size:24 final size:24
Alignment explanation
Indices: 2847401--2847491 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
2847391 CATAATTCAA
*
2847401 GTCAAGTATCATA-CTAGAATCCAG
1 GTCAAGTATCAGATC-AGAATCCAG
* *
2847425 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
2847449 ATCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
2847472 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
2847492 TCAAATTTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 20 0.36
24 34 0.62
25 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:2850389 original size:525 final size:525
Alignment explanation
Indices: 2849399--2850451 Score: 1962
Period size: 525 Copynumber: 2.0 Consensus size: 525
2849389 TCTACCACAT
2849399 TCATATCGAGTGTAGAAACTAATTAACTACACAAATGAGACCAACATTGTCTTAATCATGCATTT
1 TCATATCGAGTGTAGAAACTAATTAACTACACAAATGAGACCAACATTGTCTTAATCATGCATTT
* **
2849464 ACCAATATTCAGATGTTCCAAAAAGCATAAAGAGGTAGTAAAGTATTACCTTGATTTCTGTGCAA
66 ACCAATATTCACATGTTCCAAAAAGCATAAAGAGGTAGTAAAGTATTACCTCAATTTCTGTGCAA
*
2849529 TACTGATCGACCATAAAAATTCCATTCGAATGCCTTTGATCTTCAATTCAACTTCAAATAATTCC
131 TACTGATCGACCATAAAAATTCCATTCGAACGCCTTTGATCTTCAATTCAACTTCAAATAATTCC
2849594 TCAGATACATATCAACATAAATTATATCAGAAACGGAGCTTAATTGCGATAAACGGATCGAATCA
196 TCAGATACATATCAACATAAATTATATCAGAAACGGAGCTTAATTGCGATAAACGGATCGAATCA
*
2849659 GGTGATAAATCAGTGAAAAATAGCTTACCGGGTTCGAATGTGGAGAAACGGACTTCGGATTCGGA
261 GGTGATAAATCAGTGAAAAATAGCTTACCGGGTTCGAATGTGGAGAAACGGACTTCGGATTCAGA
2849724 TTCAGGACGTCGAAAGCATAAAATATGACTTTTCGGAAATTTGGAATTTTTGGTCAAAACCAAAG
326 TTCAGGACGTCGAAAGCATAAAATATGACTTTTCGGAAATTTGGAATTTTTGGTCAAAACCAAAG
* *
2849789 TCAACGGGTTTGACCAGCAATTTCGAGGCCTTTGGGTTCGAATTTTGAAAAACGGACAGCGGAAT
391 TCAACGGGTTTGACCAGCAATTTCGAGGCCTTCGGGTTCGAATTTCGAAAAACGGACAGCGGAAT
*
2849854 CGGATTTGGAACGTCGAAAAATGTCAGGATAGGTATACTCGGTCGAAGTCAAAGGTCGTTTAATG
456 CGGATTTGGAACATCGAAAAATGTCAGGATAGGTATACTCGGTCGAAGTCAAAGGTCGTTTAATG
2849919 CCCGG
521 CCCGG
2849924 TCATATCGAGTGTAGAAACTAATTAACTACACAAATGAGACCAACATTGTCTTAATCATGCATTT
1 TCATATCGAGTGTAGAAACTAATTAACTACACAAATGAGACCAACATTGTCTTAATCATGCATTT
2849989 ACCAATATTCACATGTTCCAAAAAGCATAAAGAGGTAGTAAAGTATTACCTCAATTTCTGTGCAA
66 ACCAATATTCACATGTTCCAAAAAGCATAAAGAGGTAGTAAAGTATTACCTCAATTTCTGTGCAA
*
2850054 TACTGATCGACCATAAAAATTCCATTCGAACGCCTTTGATCTTTAATTCAACTTCAAATAATTCC
131 TACTGATCGACCATAAAAATTCCATTCGAACGCCTTTGATCTTCAATTCAACTTCAAATAATTCC
* *
2850119 TCAGATACATATCAACATAAATTATATCATAAACGGAGCTTAATTGCGATAAACGGATCGAATCG
196 TCAGATACATATCAACATAAATTATATCAGAAACGGAGCTTAATTGCGATAAACGGATCGAATCA
*
2850184 GGTGATAAATCAGTGAAAAATAGCTTACCGGGTTCGAATGTGGAGAAACGGACTTTGGATTCAGA
261 GGTGATAAATCAGTGAAAAATAGCTTACCGGGTTCGAATGTGGAGAAACGGACTTCGGATTCAGA
2850249 TTCAGGACGTCGAAAGCATAAAATATGACTTTTCGGAAATTTGGAATTTTTGGTCAAAACCAAAG
326 TTCAGGACGTCGAAAGCATAAAATATGACTTTTCGGAAATTTGGAATTTTTGGTCAAAACCAAAG
* *
2850314 TTAATGGGTTTGACCAGCAATTTCGAGGCCTTCGGGTTCGAATTTCGAAAAACGGACAGCGGAAT
391 TCAACGGGTTTGACCAGCAATTTCGAGGCCTTCGGGTTCGAATTTCGAAAAACGGACAGCGGAAT
* *
2850379 CGGATTTGGAACATCGAAAAATGTCAGGATAGGTATACTCGGTCGAATTCAAAGGTTGTTTAATG
456 CGGATTTGGAACATCGAAAAATGTCAGGATAGGTATACTCGGTCGAAGTCAAAGGTCGTTTAATG
2850444 CCCGG
521 CCCGG
2850449 TCA
1 TCA
2850452 AAGTTTTGGT
Statistics
Matches: 512, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
525 512 1.00
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (525 bp):
TCATATCGAGTGTAGAAACTAATTAACTACACAAATGAGACCAACATTGTCTTAATCATGCATTT
ACCAATATTCACATGTTCCAAAAAGCATAAAGAGGTAGTAAAGTATTACCTCAATTTCTGTGCAA
TACTGATCGACCATAAAAATTCCATTCGAACGCCTTTGATCTTCAATTCAACTTCAAATAATTCC
TCAGATACATATCAACATAAATTATATCAGAAACGGAGCTTAATTGCGATAAACGGATCGAATCA
GGTGATAAATCAGTGAAAAATAGCTTACCGGGTTCGAATGTGGAGAAACGGACTTCGGATTCAGA
TTCAGGACGTCGAAAGCATAAAATATGACTTTTCGGAAATTTGGAATTTTTGGTCAAAACCAAAG
TCAACGGGTTTGACCAGCAATTTCGAGGCCTTCGGGTTCGAATTTCGAAAAACGGACAGCGGAAT
CGGATTTGGAACATCGAAAAATGTCAGGATAGGTATACTCGGTCGAAGTCAAAGGTCGTTTAATG
CCCGG
Found at i:2850503 original size:13 final size:13
Alignment explanation
Indices: 2850485--2850516 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
2850475 CGCCGGTCAA
2850485 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2850498 CGGGTCAACGGGT
1 CGGGTCAACGGGT
2850511 CGGGTC
1 CGGGTC
2850517 GGGCCAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:2851540 original size:23 final size:22
Alignment explanation
Indices: 2851510--2851590 Score: 74
Period size: 23 Copynumber: 3.6 Consensus size: 22
2851500 GCATGGCAGT
2851510 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
2851532 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
2851554 GTGTATCGATGCATATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
*
2851577 GATACATCGATGCA
1 G-TGCATCGATGCA
2851591 TTGTTAAGTG
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
21 14 0.31
22 2 0.04
23 19 0.42
24 10 0.22
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:2857276 original size:64 final size:65
Alignment explanation
Indices: 2857208--2857341 Score: 157
Period size: 64 Copynumber: 2.1 Consensus size: 65
2857198 TGCACTAAGA
* *
2857208 GTGCAAAGATGCATAAAATGCATTTGATGTTTCAAAATA-GCC-TGAGTGCATCGATGCATGG-T
1 GTGCAAAGATGCATAAAATGCATTCGATG-TTCAAAATATGCCATG-GTGCATCGATGCAAGGAT
2857270 TG
64 TG
** * ** *
2857272 GTGCATCGATGCATCAAATGCATTCGATGTTCAATTTATTCCATGGTGCATCGATGCAAGGATTG
1 GTGCAAAGATGCATAAAATGCATTCGATGTTCAAAATATGCCATGGTGCATCGATGCAAGGATTG
2857337 GTGCA
1 GTGCA
2857342 TCGGTGCATC
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
63 7 0.12
64 42 0.71
65 10 0.17
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (65 bp):
GTGCAAAGATGCATAAAATGCATTCGATGTTCAAAATATGCCATGGTGCATCGATGCAAGGATTG
Found at i:2857850 original size:12 final size:11
Alignment explanation
Indices: 2857805--2857843 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
2857795 GGTAAGTTTA
2857805 ATTTAAATTTTT
1 ATTT-AATTTTT
2857817 ATTTAATTTTT
1 ATTTAATTTTT
*
2857828 AGTGTAATTTTT
1 A-TTTAATTTTT
2857840 ATTT
1 ATTT
2857844 TTATTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:2860597 original size:17 final size:17
Alignment explanation
Indices: 2860576--2860627 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
2860566 AAATGTAAAA
2860576 ATATTAACAATATTTTT
1 ATATTAACAATATTTTT
* * ***
2860593 TTATTAAAAATATAAAT
1 ATATTAACAATATTTTT
2860610 ATATTAACAATATTTTT
1 ATATTAACAATATTTTT
2860627 A
1 A
2860628 ACATTTTTAC
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATTAACAATATTTTT
Found at i:2860601 original size:34 final size:34
Alignment explanation
Indices: 2860562--2860626 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
2860552 TATTAAAGTT
*
2860562 TTAAAAATGTAAAAATATTAACAATATTTTTTTA
1 TTAAAAATATAAAAATATTAACAATATTTTTTTA
*
2860596 TTAAAAATATAAATATATTAACAATATTTTT
1 TTAAAAATATAAAAATATTAACAATATTTTT
2860627 AACATTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (34 bp):
TTAAAAATATAAAAATATTAACAATATTTTTTTA
Found at i:2861794 original size:39 final size:39
Alignment explanation
Indices: 2861740--2861826 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
2861730 CCACCCTAGA
2861740 CTGAAGACAACAGGTAAGCTTGGAGTCTTCCTATTTTGC
1 CTGAAGACAACAGGTAAGCTTGGAGTCTTCCTATTTTGC
* * * *
2861779 CTGAAGACGACAGGTAAGTTTGGAGTCTTTCTATTTTTC
1 CTGAAGACAACAGGTAAGCTTGGAGTCTTCCTATTTTGC
*
2861818 CTAAAGACA
1 CTGAAGACA
2861827 CCATGCACTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (39 bp):
CTGAAGACAACAGGTAAGCTTGGAGTCTTCCTATTTTGC
Found at i:2868315 original size:32 final size:32
Alignment explanation
Indices: 2868279--2868346 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
2868269 CAGGTCAATA
*
2868279 TTGGGTCGGGTCAATACCGGATCGGTTGATTT
1 TTGGGTCGGGTCAATACCAGATCGGTTGATTT
* **
2868311 TTGGGTCGGGTTAATATTAGATCGGTTGATTT
1 TTGGGTCGGGTCAATACCAGATCGGTTGATTT
2868343 TTGG
1 TTGG
2868347 TTTAGGTCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.16, C:0.10, G:0.34, T:0.40
Consensus pattern (32 bp):
TTGGGTCGGGTCAATACCAGATCGGTTGATTT
Found at i:2869085 original size:16 final size:16
Alignment explanation
Indices: 2869061--2869114 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
2869051 GTTAAAATTT
2869061 GGTTCGGGTTGCTTTC
1 GGTTCGGGTTGCTTTC
* **
2869077 GGTTTGGGTTAATTTC
1 GGTTCGGGTTGCTTTC
* *
2869093 GGTTCGGATTGCTTTT
1 GGTTCGGGTTGCTTTC
2869109 GGTTCG
1 GGTTCG
2869115 AGTTAATTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.06, C:0.13, G:0.35, T:0.46
Consensus pattern (16 bp):
GGTTCGGGTTGCTTTC
Found at i:2869098 original size:32 final size:32
Alignment explanation
Indices: 2869056--2869125 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
2869046 TTCTGGTTAA
* * *
2869056 AATTT-GGTTCGGGTTGCTTTCGGTTTGGGTT
1 AATTTCGGTTCGGATTGCTTTCGGTTCGAGTT
*
2869087 AATTTCGGTTCGGATTGCTTTTGGTTCGAGTT
1 AATTTCGGTTCGGATTGCTTTCGGTTCGAGTT
2869119 AATTTCG
1 AATTTCG
2869126 ATTTCGGTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 5 0.15
32 29 0.85
ACGTcount: A:0.11, C:0.11, G:0.30, T:0.47
Consensus pattern (32 bp):
AATTTCGGTTCGGATTGCTTTCGGTTCGAGTT
Found at i:2870875 original size:10 final size:10
Alignment explanation
Indices: 2870860--2870930 Score: 54
Period size: 10 Copynumber: 6.7 Consensus size: 10
2870850 CATTTAATAA
2870860 ATAAACGAAC
1 ATAAACGAAC
2870870 ATAAACGAACAC
1 ATAAACG-A-AC
2870882 ATAAACGAAC
1 ATAAACGAAC
** *
2870892 ACGAAC-ATAA
1 ATAAACGA-AC
2870902 ATAAAGACGAAC
1 AT-AA-ACGAAC
*
2870914 ATAAATGAAC
1 ATAAACGAAC
2870924 ATAAACG
1 ATAAACG
2870931 TTGGAGACCC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
9 1 0.02
10 26 0.55
11 5 0.11
12 14 0.30
13 1 0.02
ACGTcount: A:0.59, C:0.18, G:0.11, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:2870885 original size:12 final size:12
Alignment explanation
Indices: 2870860--2870893 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2870850 CATTTAATAA
2870860 ATAAACG-A-AC
1 ATAAACGAACAC
2870870 ATAAACGAACAC
1 ATAAACGAACAC
2870882 ATAAACGAACAC
1 ATAAACGAACAC
2870894 GAACATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 7 0.32
11 1 0.05
12 14 0.64
ACGTcount: A:0.59, C:0.24, G:0.09, T:0.09
Consensus pattern (12 bp):
ATAAACGAACAC
Found at i:2870901 original size:16 final size:16
Alignment explanation
Indices: 2870864--2870924 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 16
2870854 TAATAAATAA
2870864 ACGAACATAAACG-A-
1 ACGAACATAAACGAAC
2870878 AC--ACATAAACGAAC
1 ACGAACATAAACGAAC
** *
2870892 ACGAACATAAATAAAG
1 ACGAACATAAACGAAC
*
2870908 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
2870924 A
1 A
2870925 TAAACGTTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 9 0.24
13 1 0.03
14 4 0.11
16 24 0.63
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:2870927 original size:22 final size:21
Alignment explanation
Indices: 2870862--2870928 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
2870852 TTTAATAAAT
* *
2870862 AAACGAACATAAACGAACACA
1 AAACGAACATAAATGAACATA
*
2870883 TAAACGAACACGAACAT-AA-ATA
1 -AAACGAACA-TAA-ATGAACATA
2870905 AAGACGAACATAAATGAACATA
1 AA-ACGAACATAAATGAACATA
2870927 AA
1 AA
2870929 CGTTGGAGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
20 2 0.06
21 6 0.17
22 23 0.64
23 4 0.11
24 1 0.03
ACGTcount: A:0.61, C:0.18, G:0.10, T:0.10
Consensus pattern (21 bp):
AAACGAACATAAATGAACATA
Found at i:2871966 original size:14 final size:14
Alignment explanation
Indices: 2871949--2872013 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
2871939 GATTGGGTTA
* *
2871949 AACATAAATGAATG
1 AACATAAACGAACG
2871963 AACATAAACGAACG
1 AACATAAACGAACG
*
2871977 AACAT--A--AACT
1 AACATAAACGAACG
*
2871987 AACATAACCGAACG
1 AACATAAACGAACG
2872001 AACATAAACGAAC
1 AACATAAACGAAC
2872014 ATAACCGAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
10 8 0.20
12 1 0.02
14 32 0.78
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.12
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:2871998 original size:24 final size:24
Alignment explanation
Indices: 2871962--2872023 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
2871952 ATAAATGAAT
*
2871962 GAACATAAACGAACGAACATAAAC
1 GAACATAACCGAACGAACATAAAC
*
2871986 TAACATAACCGAACGAACATAAAC
1 GAACATAACCGAACGAACATAAAC
2872010 GAACATAACCGAAC
1 GAACATAACCGAAC
2872024 CTTCACGAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.55, C:0.24, G:0.11, T:0.10
Consensus pattern (24 bp):
GAACATAACCGAACGAACATAAAC
Found at i:2877256 original size:13 final size:13
Alignment explanation
Indices: 2877235--2877299 Score: 69
Period size: 13 Copynumber: 5.0 Consensus size: 13
2877225 AATGACGCTC
*
2877235 AATGCGCGTCATA
1 AATGAGCGTCATA
2877248 AATGAGCGTCATA
1 AATGAGCGTCATA
*
2877261 AAT-ATGTGTCATA
1 AATGA-GCGTCATA
* *
2877274 AATGCGTGTCATA
1 AATGAGCGTCATA
*
2877287 AATGTGCGTCATA
1 AATGAGCGTCATA
2877300 GATTTATGAC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
12 1 0.02
13 44 0.98
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (13 bp):
AATGAGCGTCATA
Found at i:2877272 original size:26 final size:26
Alignment explanation
Indices: 2877240--2877299 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
2877230 CGCTCAATGC
2877240 GCGTCATAAATGAGCGTCATAAATAT
1 GCGTCATAAATGAGCGTCATAAATAT
* * * *
2877266 GTGTCATAAATGCGTGTCATAAATGT
1 GCGTCATAAATGAGCGTCATAAATAT
2877292 GCGTCATA
1 GCGTCATA
2877300 GATTTATGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (26 bp):
GCGTCATAAATGAGCGTCATAAATAT
Found at i:2880931 original size:45 final size:45
Alignment explanation
Indices: 2880781--2881296 Score: 759
Period size: 45 Copynumber: 11.4 Consensus size: 45
2880771 TATATATAGT
* **
2880781 ATCCATTCATG-CTTATAATGCA-CAATATGCATTTCATTTTATGGC
1 ATCCTTTCATGCCTT-TAATGCACCGTTATGCATTTCA-TTTATGGC
* * * *
2880826 ATACTTTCATGCATTTAATGTACCGTTATGTATTTCATTTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCA-TTTATGGC
* * *
2880872 ATCATTTCACGCCTTTAATGCATCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
*
2880917 ATCCTTTCATGCCTTTAATG-ACCTTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
*
2880961 ATTCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
*
2881006 ATGCCTTTAATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
1 AT-CCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
* *
2881052 ATTCTTTCATGTCTTTAATGCACCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
*
2881097 ATCATTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
*
2881142 ATCCTTTCATGCCTTTAATGCACTGTTATGCATTTCATTTATGGC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
* * *
2881187 ATACTTTCACGCCTTTAATGCACCGTTATGCATTTCATTTATGAC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
* * *
2881232 ATCCTCTCATGCCTTTAATGCACCGTTATACATTTCATTTATGAC
1 ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
*
2881277 ATACTTTCATGCCTTTAATG
1 ATCCTTTCATGCCTTTAATG
2881297 TAAAGTTAGA
Statistics
Matches: 427, Mismatches: 40, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
44 41 0.10
45 291 0.68
46 95 0.22
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (45 bp):
ATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGC
Found at i:2884759 original size:2 final size:2
Alignment explanation
Indices: 2884752--2884800 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2884742 CCATAAAAGC
2884752 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
2884794 TA TA TA T
1 TA TA TA T
2884801 CTTTCTGACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2886504 original size:33 final size:33
Alignment explanation
Indices: 2886462--2886527 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
2886452 TCATACTTGT
2886462 ATATGCTTCACATAATCTCAATATTACAAAAAC
1 ATATGCTTCACATAATCTCAATATTACAAAAAC
2886495 ATATGCTTCACATAATCTCAATATTACAAAAAC
1 ATATGCTTCACATAATCTCAATATTACAAAAAC
2886528 TCTTAAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.30
Consensus pattern (33 bp):
ATATGCTTCACATAATCTCAATATTACAAAAAC
Found at i:2887700 original size:13 final size:13
Alignment explanation
Indices: 2887682--2887720 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
2887672 CTCTGCCGCG
2887682 CCCCAAAACAGCA
1 CCCCAAAACAGCA
2887695 CCCCAAAACAGCA
1 CCCCAAAACAGCA
2887708 --CCAAAACAGCA
1 CCCCAAAACAGCA
2887719 CC
1 CC
2887721 GCCACCGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.46
13 13 0.54
ACGTcount: A:0.46, C:0.46, G:0.08, T:0.00
Consensus pattern (13 bp):
CCCCAAAACAGCA
Found at i:2887713 original size:11 final size:11
Alignment explanation
Indices: 2887684--2887720 Score: 56
Period size: 11 Copynumber: 3.2 Consensus size: 11
2887674 CTGCCGCGCC
2887684 CCAAAACAGCA
1 CCAAAACAGCA
2887695 CCCCAAAACAGCA
1 --CCAAAACAGCA
2887708 CCAAAACAGCA
1 CCAAAACAGCA
2887719 CC
1 CC
2887721 GCCACCGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.54
13 11 0.46
ACGTcount: A:0.49, C:0.43, G:0.08, T:0.00
Consensus pattern (11 bp):
CCAAAACAGCA
Found at i:2893892 original size:2 final size:2
Alignment explanation
Indices: 2893880--2893921 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2893870 AATTTGTTAC
*
2893880 AT AT GT 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
2893922 TGATTAATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2894332 original size:17 final size:17
Alignment explanation
Indices: 2894294--2894333 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2894284 AATAGTGAAA
*
2894294 CCTAAAAAACCCTAATC
1 CCTAAAAAACCCTAAAC
* *
2894311 TCTAATAAACCCTAAAC
1 CCTAAAAAACCCTAAAC
2894328 CCTAAA
1 CCTAAA
2894334 CTCTAAATGA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.20
Consensus pattern (17 bp):
CCTAAAAAACCCTAAAC
Found at i:2895666 original size:22 final size:22
Alignment explanation
Indices: 2895638--2895692 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
2895628 GTGAACCCAG
2895638 AACCTGAACCTAGGTAGAGCCT
1 AACCTGAACCTAGGTAGAGCCT
*
2895660 AACCTGAACTTAGGTAGAGCCT
1 AACCTGAACCTAGGTAGAGCCT
*
2895682 AACCCGAACCT
1 AACCTGAACCT
2895693 TATGAGTCCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (22 bp):
AACCTGAACCTAGGTAGAGCCT
Found at i:2901535 original size:45 final size:45
Alignment explanation
Indices: 2901484--2901646 Score: 168
Period size: 45 Copynumber: 3.6 Consensus size: 45
2901474 AGAAGAGTCG
* *
2901484 ATCTTTTAGTGTTGTCCTACTTGACTCTCTTGTGAAGAGAAATAA
1 ATCTTTTAGTGTTGTCATTCTTGACTCTCTTGTGAAGAGAAATAA
* * * * **
2901529 ACCTTTTAGTGGTGTTATTCTTGACTTTCTCATG-GAA-AGAAGAATCG
1 ATCTTTTAGTGTTGTCATTCTTGAC--TCTCTTGTGAAGAG-A-AATAA
*
2901576 ATCTTTTAGTGTTGTCATTCTTGACTCTCTTGTGAAGAGAAGTAA
1 ATCTTTTAGTGTTGTCATTCTTGACTCTCTTGTGAAGAGAAATAA
* * *
2901621 ATCTTTCAATGTTGTTATTCTTGACT
1 ATCTTTTAGTGTTGTCATTCTTGACT
2901647 TTCTCAAAAG
Statistics
Matches: 94, Mismatches: 18, Indels: 12
0.76 0.15 0.10
Matches are distributed among these distances:
45 53 0.56
46 8 0.09
47 33 0.35
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.42
Consensus pattern (45 bp):
ATCTTTTAGTGTTGTCATTCTTGACTCTCTTGTGAAGAGAAATAA
Found at i:2901599 original size:92 final size:91
Alignment explanation
Indices: 2901443--2901652 Score: 298
Period size: 92 Copynumber: 2.3 Consensus size: 91
2901433 GGAGTCAATC
* * *
2901443 TTTAGTGTTGTT-TTCGTTGACTTTCTC-GCATAGAAGAGTCGATCTTTTAGTGTTGTCCTACTT
1 TTTAGTGTTGTTATTC-TTGACTTTCTCAGCAAAGAAGAATCGATCTTTTAGTGTTGTCATACTT
2901506 GACTCTCTTGTGAAGAGAAATAAACCT
65 GACTCTCTTGTGAAGAGAAATAAACCT
* * *
2901533 TTTAGTGGTGTTATTCTTGACTTTCTCATGGAAAGAAGAATCGATCTTTTAGTGTTGTCATTCTT
1 TTTAGTGTTGTTATTCTTGACTTTCTCA-GCAAAGAAGAATCGATCTTTTAGTGTTGTCATACTT
* *
2901598 GACTCTCTTGTGAAGAGAAGTAAATCT
65 GACTCTCTTGTGAAGAGAAATAAACCT
* *
2901625 TTCAATGTTGTTATTCTTGACTTTCTCA
1 TTTAGTGTTGTTATTCTTGACTTTCTCA
2901653 AAAGGGGAAG
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
90 22 0.21
91 3 0.03
92 81 0.76
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (91 bp):
TTTAGTGTTGTTATTCTTGACTTTCTCAGCAAAGAAGAATCGATCTTTTAGTGTTGTCATACTTG
ACTCTCTTGTGAAGAGAAATAAACCT
Found at i:2901796 original size:51 final size:50
Alignment explanation
Indices: 2901680--2901799 Score: 127
Period size: 51 Copynumber: 2.4 Consensus size: 50
2901670 TTTGGTGATG
* * *
2901680 TCATTCTTAACTTGATTTTCTCGCAGAGAGTAGTCAACTTTTCAGTAGTA
1 TCATTCTTAACTTGACTTGCTCGCAGAGAGAAGTCAACTTTTCAGTAGTA
** * *
2901730 TCATTTTCCTT--CTTGACTTGCTCGTGGAGAGAAGTTAACTTTTTAGTAGTA
1 TCA--TT-CTTAACTTGACTTGCTCGCAGAGAGAAGTCAACTTTTCAGTAGTA
2901781 TCATATCTTAACTTGACTT
1 TCAT-TCTTAACTTGACTT
2901800 TCTAGTGTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
49 4 0.07
50 4 0.07
51 44 0.77
52 2 0.04
53 3 0.05
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.42
Consensus pattern (50 bp):
TCATTCTTAACTTGACTTGCTCGCAGAGAGAAGTCAACTTTTCAGTAGTA
Found at i:2904063 original size:23 final size:23
Alignment explanation
Indices: 2904029--2904074 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
2904019 ACATATTATA
2904029 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
2904052 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
2904075 CGCTCCTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.26, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:2907734 original size:154 final size:161
Alignment explanation
Indices: 2907552--2907866 Score: 581
Period size: 161 Copynumber: 2.0 Consensus size: 161
2907542 TTATTTTATT
2907552 TCGATTGAAGTAAGAATTAATTACCTCA-GTTATGAGGGA-TTATTTCTT-TCAATATGAAATAA
1 TCGATTGAAGTAAGAATTAATTACCTCAGGTTATGAGGGATTTATTTCTTCTCAATATGAAATAA
2907614 TTTAATATTA-TATATTTCAT-GT-AAATTCATA-TTTTGTTGTTTTATGGGATAAAAAATCAAA
66 TTTAATATTATTATATTTCATGGTAAAATTCATATTTTTGTTGTTTTATGGGATAAAAAATCAAA
2907675 TTAAATTCGAATTTGTAAATTTCATTGCAAA
131 TTAAATTCGAATTTGTAAATTTCATTGCAAA
2907706 TCGATTGAAGTAAGAATTAATTACCTCAGGTTATGAGGGATTTATTTCTTCTCAATATGAAATAA
1 TCGATTGAAGTAAGAATTAATTACCTCAGGTTATGAGGGATTTATTTCTTCTCAATATGAAATAA
2907771 TTTAATATTATTATATTTCATGGTAAAATTCATATTTTTGTTGTTTTATGGGATAAAAAATCAAA
66 TTTAATATTATTATATTTCATGGTAAAATTCATATTTTTGTTGTTTTATGGGATAAAAAATCAAA
2907836 TTAAATTCGAATTTGTAAATTTCATTGCAAA
131 TTAAATTCGAATTTGTAAATTTCATTGCAAA
2907867 GACATTAATT
Statistics
Matches: 154, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
154 28 0.18
155 11 0.07
156 9 0.06
157 24 0.16
158 10 0.06
159 2 0.01
160 9 0.06
161 61 0.40
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (161 bp):
TCGATTGAAGTAAGAATTAATTACCTCAGGTTATGAGGGATTTATTTCTTCTCAATATGAAATAA
TTTAATATTATTATATTTCATGGTAAAATTCATATTTTTGTTGTTTTATGGGATAAAAAATCAAA
TTAAATTCGAATTTGTAAATTTCATTGCAAA
Found at i:2915069 original size:37 final size:36
Alignment explanation
Indices: 2914942--2915507 Score: 333
Period size: 37 Copynumber: 15.1 Consensus size: 36
2914932 TGAGATTGGG
* * *
2914942 GCAAGTCAACCTTAAGCCTTCACCGAAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCACAG-AGAGTAGTGAA
*
2914979 GCAAATCAATCTTAAGCCTTCACCAAAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCA-CAGAGAGTAGTGAA
*
2915016 GTAAATCAATCTTAAGCCTTCACAGAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCACAGAGAGTAGTGAA
* * * * * ***
2915052 GCAAAGCCATCAGTAAGCCTTCTGAGCATGATGATTAAATCCT
1 GCAAATCAATC-TTAAGCCTTC--A-CA-GA-GAGT-AGTGAA
* *** * *
2915095 TCGGGTC-ATTTGTCAAG-CTTC-C-GAGA-AAGATGAA
1 GCAAATCAATCT-T-AAGCCTTCACAGAGAGTAG-TGAA
*
2915129 --AAGTACTCCGAGCCATCTTAAGCCTTCACCAAAGAGTAGTGAA
1 GCAA--A-T-C-A---ATCTTAAGCCTTCA-CAGAGAGTAGTGAA
** * *
2915172 GCAAATCCCTCTTAACCCTTCACTGAAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCACAG-AGAGTAGTGAA
* * *
2915209 GCAAATCCATCTTAAGCCTTCACCGAAGAGTAATGAA
1 GCAAATCAATCTTAAGCCTTCACAG-AGAGTAGTGAA
*
2915246 GCAAATC-ATCTTAAGCCTTCACCAAAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCA-CAGAGAGTAGTGAA
* * * *
2915282 GAAAATTC-ATTTTAAGCCTTCACCGAAGAGTAGAGAA
1 GCAAA-TCAATCTTAAGCCTTCACAG-AGAGTAGTGAA
* * *
2915319 ACAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCACAG-AGAGTAGTGAA
* *
2915356 GCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCA-CAGAGAGTAGTGAA
* * *
2915393 G-AAAGTCCATTTTAAGCCTTCACCGAAGAGTAGTGAA
1 GCAAA-TCAATCTTAAGCCTTCACAG-AGAGTAGTGAA
* * *
2915430 GAAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAA
1 GCAAATCAATCTTAAGCCTTCACAG-AGAGTAGTGAA
** * ** *
2915467 AAAAATCCATCTTAAGCCTTCATGGAAGAGTAGTAAA
1 GCAAATCAATCTTAAGCCTTCACAG-AGAGTAGTGAA
2915504 GCAA
1 GCAA
2915508 GCCATCACTA
Statistics
Matches: 426, Mismatches: 67, Indels: 72
0.75 0.12 0.13
Matches are distributed among these distances:
33 1 0.00
34 1 0.00
35 3 0.01
36 60 0.14
37 307 0.72
38 6 0.01
39 4 0.01
40 7 0.02
41 6 0.01
42 12 0.03
43 15 0.04
44 2 0.00
45 2 0.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (36 bp):
GCAAATCAATCTTAAGCCTTCACAGAGAGTAGTGAA
Found at i:2915073 original size:74 final size:74
Alignment explanation
Indices: 2914952--2915507 Score: 536
Period size: 74 Copynumber: 7.4 Consensus size: 74
2914942 GCAAGTCAAC
*
2914952 CTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCAAAGAGTAGTGAAG
1 CTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAG
* *
2915017 TAAATCAAT
66 CAAATCCAT
* * * * * *
2915026 CTTAAGCCTTCACAG-AGAGTAGTGAAGCAAAGCCATCAGTAAGCCTTCTGAGC-ATGA-TGATT
1 CTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATC-TTAAGCCTTC--ACCAAAGAGT-AGT
* * **
2915088 AAATC-CTTCGGGTCAT
62 GAAGCAAATC----CAT
* * * ** ** *
2915104 TTGTCAAG-CTTC-CGAGAAAGATGAAAAGT-ACTCCGAGCCATCTTAAGCCTTCACCAAAGAGT
1 CT-T-AAGCCTTCAC-CG-AAGA-G--TAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGT
*
2915166 AGTGAAGCAAATCCCT
59 AGTGAAGCAAATCCAT
* * * *
2915182 CTTAACCCTTCACTGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCGAAGAGTAATGAAG
1 CTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAG
2915247 CAAAT-CAT
66 CAAATCCAT
* * * * * * *
2915255 CTTAAGCCTTCACCAAAGAGTAGTGAAGAAAATTCATTTTAAGCCTTCACCGAAGAGTAGAGAAA
1 CTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAG
2915320 CAAATCCAT
66 CAAATCCAT
2915329 CTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAG
1 CTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAG
2915394 -AAAGTCCAT
66 CAAA-TCCAT
* * * *
2915403 TTTAAGCCTTCACCGAAGAGTAGTGAAGAAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAA
1 CTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAG
*
2915468 AAAATCCAT
66 CAAATCCAT
** *
2915477 CTTAAGCCTTCATGGAAGAGTAGTAAAGCAA
1 CTTAAGCCTTCACCGAAGAGTAGTGAAGCAA
2915508 GCCATCACTA
Statistics
Matches: 392, Mismatches: 65, Indels: 50
0.77 0.13 0.10
Matches are distributed among these distances:
73 89 0.23
74 222 0.57
75 11 0.03
76 8 0.02
77 6 0.02
78 8 0.02
79 7 0.02
80 5 0.01
81 11 0.03
82 13 0.03
83 9 0.02
84 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.23
Consensus pattern (74 bp):
CTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCTTAAGCCTTCACCAAAGAGTAGTGAAG
CAAATCCAT
Found at i:2915500 original size:111 final size:110
Alignment explanation
Indices: 2915141--2915488 Score: 556
Period size: 111 Copynumber: 3.1 Consensus size: 110
2915131 GTACTCCGAG
* * * *
2915141 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATCCCTCTTAACCCTTCACTGAAGAGTAGT
1 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAG-AAATCCATTTTAAGCCTTCACCGAAGAGTAGT
* *
2915206 GAAGCAAATCCATCTTAAGCCTTCACCGAAGAGTAATGAAGCAAAT
65 GAAGAAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* *
2915252 -CATCTTAAGCCTTCACCAAAGAGTAGTGAAGAAAATTCATTTTAAGCCTTCACCGAAGAGTAGA
1 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAG-AAATCCATTTTAAGCCTTCACCGAAGAGTAGT
2915316 GAA-ACAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
65 GAAGA-AAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
2915362 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGAAAGTCCATTTTAAGCCTTCACCGAAGAGTAGT
1 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGAAA-TCCATTTTAAGCCTTCACCGAAGAGTAGT
**
2915427 GAAGAAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAAAAAAT
65 GAAGAAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
2915473 CCATCTTAAGCCTTCA
1 CCATCTTAAGCCTTCA
2915489 TGGAAGAGTA
Statistics
Matches: 220, Mismatches: 13, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
110 103 0.47
111 116 0.53
112 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (110 bp):
CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGAAATCCATTTTAAGCCTTCACCGAAGAGTAGTG
AAGAAAATCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
Found at i:2915782 original size:3 final size:3
Alignment explanation
Indices: 2915769--2915805 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
2915759 GGGATATAAA
*
2915769 TAT TA- TAT TAT TAT TAT TAT TAT TA- TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2915806 AATTTACATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:2926282 original size:82 final size:82
Alignment explanation
Indices: 2926168--2927143 Score: 1195
Period size: 82 Copynumber: 11.9 Consensus size: 82
2926158 AGAAAAGCGA
* * * * * * *
2926168 AGCAGACCCGTCTTCCAATATTGATTTGTCTACCTAAAAAAGAGGCACAGATAAAGTTTAATTTC
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
**
2926233 CCCTGAATGAATGGCAG
66 CCCTGAATGAATGGTGG
* * * * *
2926250 AGCATACACGTATTCCAACATTGATTTGTCTACCCGAAAAAGAAGCACATATCAAGTCTGATTTC
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
*
2926315 CCCTAAATGAATGGTGG
66 CCCTGAATGAATGGTGG
* * * * * * * *
2926332 AGCAGACACGTCATCGAACATTAATTTGTCTACCCAAAAAATAGACACATATCAAATATGATTTC
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
*
2926397 CCTTGAATGAATGGTGG
66 CCCTGAATGAATGGTGG
* *
2926414 AGTAGACACGTCTTCCAACATTGATTTGTCTA-CCAGAAAAAGAGGCACAGATCAAGTCTGATTT
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCA-AAAAAGAGGCACAAATCAAGTCTGATTT
* * *
2926478 CCCCTGAATGATTTGTAG
65 CCCCTGAATGAATGGTGG
* * *
2926496 AGCAGTCACGTCTTCCAACATTGATTTGTGTACCCGAAAAAGAGGCACAAATCAAGTCTGATTTC
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
* *
2926561 TCCTGAATCAATGGTGG
66 CCCTGAATGAATGGTGG
* * * *
2926578 AGCAGACATGTCTTCCAACATTGATTTGTCTACACAAAAATA-AGGCACAAATGAAGTATGATTT
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAA-AGAGGCACAAATCAAGTCTGATTT
* **
2926642 CCCCTGAATGAGTAATGG
65 CCCCTGAATGAATGGTGG
* * * *
2926660 ACCAGACACGTCTTCCAACATTGATTTGTCTACCTAAAAAAGAGGCACATATTAAGTCTGATTTC
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
***
2926725 CCCTGAATGAATGAAAG
66 CCCTGAATGAATGGTGG
* * * * *
2926742 ACCAGACACGTCTTCCAACATTGATTTGTCTACCCGAAAAA-AGGCATAAATAAAGTGTGATTTC
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
*
2926806 CCCTAAATGAATGGTGG
66 CCCTGAATGAATGGTGG
* * * *
2926823 AGCAGACACGTCTTTCAACATTGATTTGTCTGCCCGAAAAAGAGGCACAAATCAAGTTTGATTTC
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
* * ***
2926888 CTCTAAATGAATGACAG
66 CCCTGAATGAATGGTGG
* * *
2926905 AGCAGACACGTCTTCCAACATTGATTTGTCTACCTAAAAAAGAGGCACATATCAAGTCTGATTTT
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
* * * *
2926970 TCCTGAATAAATAGTGT
66 CCCTGAATGAATGGTGG
* * * * *
2926987 AACAGACACGTCTTCCAACATTGATTTATCTACCCGAAAAAGAGGCACAAATCAAGTCTTATCT-
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
*
2927051 CCCTGAATGAATAGTGG
66 CCCTGAATGAATGGTGG
* * *
2927068 AGCAGACACGTCTTCCAAAATTGATTTGTCTACCCGAAAAAGAGTCACAAATCAAGTCTGATTTC
1 AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
2927133 CCCTGAATGAA
66 CCCTGAATGAA
2927144 AGAATAGTAT
Statistics
Matches: 763, Mismatches: 125, Indels: 12
0.85 0.14 0.01
Matches are distributed among these distances:
81 146 0.19
82 614 0.80
83 3 0.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (82 bp):
AGCAGACACGTCTTCCAACATTGATTTGTCTACCCAAAAAAGAGGCACAAATCAAGTCTGATTTC
CCCTGAATGAATGGTGG
Found at i:2927520 original size:34 final size:33
Alignment explanation
Indices: 2927448--2927521 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 33
2927438 CTATATATTA
* *
2927448 TATATAATCATAATTATATACATATTATATATACG
1 TATA-AATCATAATTAAATACATA-TATATACACG
*
2927483 TATAAATCAATAATTAAATAACATA-ATATACATG
1 TATAAATC-ATAATTAAAT-ACATATATATACACG
2927517 TATAA
1 TATAA
2927522 CGTTAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 16 0.47
35 13 0.38
36 5 0.15
ACGTcount: A:0.51, C:0.08, G:0.03, T:0.38
Consensus pattern (33 bp):
TATAAATCATAATTAAATACATATATATACACG
Found at i:2931077 original size:31 final size:31
Alignment explanation
Indices: 2931017--2931077 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2931007 AACTTGGGTA
* * *
2931017 ACCACATCTTAATTAAATAAAACCGAAAGTT
1 ACCACATCATAATTAAATAAAAACAAAAGTT
2931048 ACCACATCATAATTAAATAAAAACAAAAGT
1 ACCACATCATAATTAAATAAAAACAAAAGT
2931078 GACTATATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.18, G:0.05, T:0.23
Consensus pattern (31 bp):
ACCACATCATAATTAAATAAAAACAAAAGTT
Found at i:2935882 original size:5 final size:5
Alignment explanation
Indices: 2935872--2937173 Score: 2514
Period size: 5 Copynumber: 261.8 Consensus size: 5
2935862 AAATAAAAGT
*
2935872 ATAAC AAAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2935922 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2935972 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936022 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936072 ATAAC ATAAC AT-A- ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936120 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC A-AAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936169 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936219 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC --AAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936267 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC --AAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936315 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936365 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936415 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936465 ATAACAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 AT-A-AC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936517 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936567 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936617 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936667 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936717 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936767 ATAAC ATAAC ATAAC ATAAC ATAAC A-AAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936816 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936866 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936916 ATAAC ATAAC AT-AC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2936965 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2937015 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2937065 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2937115 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
2937165 ATAAC ATAA
1 ATAAC ATAA
2937174 TATACGTATT
Statistics
Matches: 1284, Mismatches: 2, Indels: 22
0.98 0.00 0.02
Matches are distributed among these distances:
3 8 0.01
4 14 0.01
5 1256 0.98
6 2 0.00
7 4 0.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAC
Found at i:2937264 original size:2 final size:2
Alignment explanation
Indices: 2937253--2937401 Score: 88
Period size: 2 Copynumber: 78.5 Consensus size: 2
2937243 ATTTTTAAAA
2937253 AT AT AT -T AT AT A- AT AT -T AT AT AT AT AT A- AT ACT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
2937292 AT TT AT AT AT AT AT AT AT ACT AT AT A- AC AT TT A- AT AA AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
2937333 AT A- AC AT AA AT ACT AT AT -T AT AT AT A- AA AC AT AA AT ACC AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
2937374 AT AT AT A- AT AT AT A- AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2937402 AAATATACCA
Statistics
Matches: 115, Mismatches: 16, Indels: 32
0.71 0.10 0.20
Matches are distributed among these distances:
1 12 0.10
2 96 0.83
3 7 0.06
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:2937270 original size:10 final size:9
Alignment explanation
Indices: 2937259--2937430 Score: 90
Period size: 9 Copynumber: 19.0 Consensus size: 9
2937249 AAAAATATAT
2937259 TATATAATA
1 TATATAATA
2937268 T-TAT-ATA
1 TATATAATA
2937275 TATATAATA
1 TATATAATA
2937284 CTATAT-ATA
1 -TATATAATA
*
2937293 TTTAT-ATA
1 TATATAATA
2937301 TATATATATA
1 TATATA-ATA
*
2937311 CTATATAACA
1 -TATATAATA
*
2937321 TTTAATAA-A
1 TAT-ATAATA
*
2937330 TATATAACA
1 TATATAATA
* *
2937339 TAAATACTA
1 TATATAATA
2937348 TAT-T-ATA
1 TATATAATA
* *
2937355 TATAAAACA
1 TATATAATA
*
2937364 TAAATACCATA
1 TATATA--ATA
2937375 TATATAATA
1 TATATAATA
2937384 TATAATATATAA
1 TAT-ATA-AT-A
*
2937396 TATATAAAA
1 TATATAATA
**
2937405 TATACCATA
1 TATATAATA
*
2937414 -ATATAAAA
1 TATATAATA
2937422 TATATAATA
1 TATATAATA
2937431 AAACACTAAT
Statistics
Matches: 123, Mismatches: 24, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
7 9 0.07
8 27 0.22
9 47 0.38
10 18 0.15
11 18 0.15
12 4 0.03
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (9 bp):
TATATAATA
Found at i:2937280 original size:16 final size:15
Alignment explanation
Indices: 2937253--2937427 Score: 110
Period size: 14 Copynumber: 11.5 Consensus size: 15
2937243 ATTTTTAAAA
2937253 ATATAT-TATATAAT
1 ATATATATATATAAT
2937267 ATTATATATATATAAT
1 A-TATATATATATAAT
*
2937283 ACTATATATAT-TTAT
1 A-TATATATATATAAT
*
2937298 ATATATATATATACT
1 ATATATATATATAAT
* *
2937313 ATATA-ACATTTAAT
1 ATATATATATATAAT
* *
2937327 AAATATATAACATAAAT
1 ATATATAT-ATAT-AAT
2937344 ACTATATTATATATAA-
1 A-TATA-TATATATAAT
* * **
2937360 A-ACATAAATACCAT
1 ATATATATATATAAT
2937374 ATATATAATATATAAT
1 ATATAT-ATATATAAT
*
2937390 ATATA-ATATATAAA
1 ATATATATATATAAT
* *
2937404 ATATACCATAATATAAA
1 ATATA-TAT-ATATAAT
2937421 ATATATA
1 ATATATA
2937428 ATAAAACACT
Statistics
Matches: 124, Mismatches: 23, Indels: 26
0.72 0.13 0.15
Matches are distributed among these distances:
13 6 0.05
14 36 0.29
15 20 0.16
16 35 0.28
17 18 0.15
18 6 0.05
19 3 0.02
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (15 bp):
ATATATATATATAAT
Found at i:2937333 original size:43 final size:41
Alignment explanation
Indices: 2937253--2937427 Score: 118
Period size: 43 Copynumber: 4.3 Consensus size: 41
2937243 ATTTTTAAAA
* * *
2937253 ATATATTATATA-ATAT-TATATAT-ATAT-AATACTATAT
1 ATATAATATATATATATATATATATAACATAAATACAATAT
* *
2937290 ATATTTATATATATATATATACTATATAACATTTAATA-AATAT
1 ATA-TAATATATATATATATA-TATATAACA-TAAATACAATAT
* * *
2937333 ATA-ACATAAATACTATATTATATATAAAACATAAATACCATAT
1 ATATA-ATATATA-TATA-TATATATATAACATAAATACAATAT
* *
2937376 ATATAATATATA-ATATATAATATATAA-A-ATATACCATA-
1 ATATAATATATATATATAT-ATATATAACATAAATACAATAT
*
2937414 ATATAAAATATATA
1 ATATAATATATATA
2937428 ATAAAACACT
Statistics
Matches: 111, Mismatches: 13, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
37 3 0.03
38 18 0.16
39 14 0.13
40 6 0.05
41 15 0.14
42 13 0.12
43 33 0.30
44 9 0.08
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.41
Consensus pattern (41 bp):
ATATAATATATATATATATATATATAACATAAATACAATAT
Found at i:2937357 original size:25 final size:27
Alignment explanation
Indices: 2937328--2937401 Score: 91
Period size: 25 Copynumber: 2.8 Consensus size: 27
2937318 ACATTTAATA
2937328 AATATATAACATAAATACTATAT-TAT
1 AATATATAACATAAATACTATATATAT
* *
2937354 -ATATAAAACATAAATACCATATATAT
1 AATATATAACATAAATACTATATATAT
*
2937380 AATATATAATATATAATA-TATA
1 AATATATAACATA-AATACTATA
2937402 AAATATACCA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 20 0.50
26 3 0.08
27 13 0.32
28 4 0.10
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (27 bp):
AATATATAACATAAATACTATATATAT
Found at i:2937384 original size:7 final size:7
Alignment explanation
Indices: 2937374--2937430 Score: 66
Period size: 7 Copynumber: 8.4 Consensus size: 7
2937364 TAAATACCAT
2937374 ATATATA
1 ATATATA
2937381 ATATATA
1 ATATATA
2937388 ATATATA
1 ATATATA
2937395 ATATATA
1 ATATATA
2937402 A-A-AT-
1 ATATATA
*
2937406 ATACCATA
1 ATA-TATA
*
2937414 ATATAAA
1 ATATATA
2937421 ATATATA
1 ATATATA
2937428 ATA
1 ATA
2937431 AAACACTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 1 0.02
7 35 0.81
8 3 0.07
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (7 bp):
ATATATA
Found at i:2938667 original size:156 final size:155
Alignment explanation
Indices: 2938347--2938677 Score: 352
Period size: 156 Copynumber: 2.1 Consensus size: 155
2938337 ATAATTTCTC
* * *
2938347 CATTGTGAGTTAAGTCGATCTTGGGATTTTTCCAGCTCAATATCATTCTTCGTGAAGTTGAAATT
1 CATTGCGAGTTAAGTCGATCTTGGGATTTTTCAAGCTCAATATCATTCTTCGTAAAGTTGAAATT
* ** * *
2938412 AACTATAAAATATTTTAACCTTCTGTAGGTCAAATTGATTGAGATACAACTCCTTGTCGTTGATT
66 AACTATAAAATATTTCAACCTTCTGTAGGTCAAATTGATTGAGATACAACTCCTCATCGTCGAGT
*
2938477 TAAACTATGTCATAGACAACTCCTC
131 TAAACTATGTCATAGACAACTCCTA
*
2938502 CATTACGAGTTAAGTC-ATTCTTTGGTG-TTTTTCAAGCTCAATATCATTCGTT-GTAAAGTTGA
1 CATTGCGAGTTAAGTCGA-TC-TTGG-GATTTTTCAAGCTCAATATCATTC-TTCGTAAAGTTGA
** * * ** * *
2938564 AATTGGCT-TAAAGAT-TTATCGACCTTCTGTAGGTCAACTTGATTGAGATGTAGCTTCTCATCG
62 AATTAACTATAAA-ATATT-TCAACCTTCTGTAGGTCAAATTGATTGAGATACAACTCCTCATCG
* *
2938627 TCGAGTTAAGCTATGTTGCA-A-ACGACTCCTA
125 TCGAGTTAAACTATG-T-CATAGACAACTCCTA
*
2938658 CATTGCGAGTTAAGTTGATC
1 CATTGCGAGTTAAGTCGATC
2938678 CCGAGTTTAC
Statistics
Matches: 145, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
154 1 0.01
155 22 0.15
156 114 0.79
157 6 0.04
158 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (155 bp):
CATTGCGAGTTAAGTCGATCTTGGGATTTTTCAAGCTCAATATCATTCTTCGTAAAGTTGAAATT
AACTATAAAATATTTCAACCTTCTGTAGGTCAAATTGATTGAGATACAACTCCTCATCGTCGAGT
TAAACTATGTCATAGACAACTCCTA
Found at i:2958147 original size:32 final size:33
Alignment explanation
Indices: 2958119--2958180 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
2958109 TTGGGGCTTG
*
2958119 AGAGCCTATCC-AAGAAAGATTCTCGGGGCTAC
1 AGAGCCTACCCAAAGAAAGATTCTCGGGGCTAC
**
2958151 AGAGTTTACCCAAAGAAAGATTCTCGGGGC
1 AGAGCCTACCCAAAGAAAGATTCTCGGGGC
2958181 CGTATAGCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 8 0.31
33 18 0.69
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (33 bp):
AGAGCCTACCCAAAGAAAGATTCTCGGGGCTAC
Found at i:2958359 original size:68 final size:67
Alignment explanation
Indices: 2958232--2958413 Score: 168
Period size: 68 Copynumber: 2.7 Consensus size: 67
2958222 TACTAGTCTG
* * * * * * * * *
2958232 TGCTAAACCTATATAAGTAATTACCAACAATGACTGAACCTACCAGAGA-AAAGGAATTACCAAT
1 TGCTAAACCTATACAAGGAATTACCAGCAACGACTAAACATGCTAGATATAAA-GAATTACCAAT
2958296 AGA
65 AGA
* * *
2958299 TGCTGAACCTATACAAAGGAATTACCAGCAACGATTAAACATGCTAGATATAAAGAATTACCAGT
1 TGCTAAACCTATAC-AAGGAATTACCAGCAACGACTAAACATGCTAGATATAAAGAATTACCAAT
* *
2958364 CGG
65 AGA
* * * * *
2958367 TTCTAAACCTATACAAGTAATTACCAGCAGCGACTGAACCTGCTAGA
1 TGCTAAACCTATACAAGGAATTACCAGCAACGACTAAACATGCTAGA
2958414 GTCTTCATGT
Statistics
Matches: 92, Mismatches: 21, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
67 40 0.43
68 49 0.53
69 3 0.03
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (67 bp):
TGCTAAACCTATACAAGGAATTACCAGCAACGACTAAACATGCTAGATATAAAGAATTACCAATA
GA
Found at i:2958506 original size:19 final size:19
Alignment explanation
Indices: 2958482--2958520 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2958472 TATATCAGAA
* *
2958482 ATCAGAGCAGAGATAAAAG
1 ATCAGAGAAGAAATAAAAG
2958501 ATCAGAGAAGAAATAAAAG
1 ATCAGAGAAGAAATAAAAG
2958520 A
1 A
2958521 AAACATCCGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.59, C:0.08, G:0.23, T:0.10
Consensus pattern (19 bp):
ATCAGAGAAGAAATAAAAG
Found at i:2959149 original size:2 final size:2
Alignment explanation
Indices: 2959142--2959170 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2959132 AGATGGTACA
2959142 AT AT 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 AT AT A
2959171 CCATTGGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2959421 original size:27 final size:28
Alignment explanation
Indices: 2959371--2959430 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
2959361 GGCTTAGAGA
* *
2959371 TATTTTGGATTATTTTACTCTTTATGGG
1 TATTTTGGATTATTTTACGCTTTAAGGG
* *
2959399 TATTTTGG-TTATTTTGCGGTTTAAGGG
1 TATTTTGGATTATTTTACGCTTTAAGGG
2959426 TATTT
1 TATTT
2959431 CAATAATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.17, C:0.05, G:0.22, T:0.57
Consensus pattern (28 bp):
TATTTTGGATTATTTTACGCTTTAAGGG
Found at i:2960273 original size:13 final size:13
Alignment explanation
Indices: 2960255--2960279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2960245 TTAACTTTTT
2960255 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
2960268 GGTCAAAGTCAA
1 GGTCAAAGTCAA
2960280 TAGGTTGACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.16
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:2961611 original size:132 final size:143
Alignment explanation
Indices: 2961356--2961639 Score: 437
Period size: 132 Copynumber: 2.0 Consensus size: 143
2961346 CTCCGTCAAT
2961356 TTTATTTTCTTTATTTTCTTATTCCTTTTGTGGTAACCTCCATAACCAAGCTTCAAGGGGATAAC
1 TTTATTTTCTTTATTTTCTTATTCCTTTTGTGGTAACCTCCATAACCAAGCTTCAAGGGG-----
2961421 AAGGTAGGCCTTTGAGAGAAGATAGCTTGCTAAGACGGTTCATGGTGGTTCGAGGAAGATCATGT
61 -AGGTAGGCCTTTGAGAGAAGATAGCTTGCTAAGACGGTTCATGGTGGTTCGAGGAAGATCATGT
2961486 CAGCTCGAGAGTTTGGGAG
125 CAGCTCGAGAGTTTGGGAG
2961505 TTTATTTTCTTTATTTTCTTATT-CTTTTGTGGTAACCTCCATAACCAA-CTTCAA-GGG-GGTA
1 TTTATTTTCTTTATTTTCTTATTCCTTTTGTGGTAACCTCCATAACCAAGCTTCAAGGGGAGGTA
2961566 -G-C-TTG-GAGAAG-T-G-TTGCTAAGACGGTTCATGGTGGTTCGAGGAAGATCATGTCAGCTC
66 GGCCTTTGAGAGAAGATAGCTTGCTAAGACGGTTCATGGTGGTTCGAGGAAGATCATGTCAGCTC
2961624 GAGAGTTTGGGAG
131 GAGAGTTTGGGAG
2961637 TTT
1 TTT
2961640 TGCTTTTCCC
Statistics
Matches: 135, Mismatches: 0, Indels: 17
0.89 0.00 0.11
Matches are distributed among these distances:
132 61 0.45
133 1 0.01
134 1 0.01
135 6 0.04
136 3 0.02
137 1 0.01
138 1 0.01
139 4 0.03
146 3 0.02
147 6 0.04
148 25 0.19
149 23 0.17
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (143 bp):
TTTATTTTCTTTATTTTCTTATTCCTTTTGTGGTAACCTCCATAACCAAGCTTCAAGGGGAGGTA
GGCCTTTGAGAGAAGATAGCTTGCTAAGACGGTTCATGGTGGTTCGAGGAAGATCATGTCAGCTC
GAGAGTTTGGGAG
Found at i:2964136 original size:25 final size:23
Alignment explanation
Indices: 2964095--2964145 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 23
2964085 TCACTTATTT
*
2964095 CCATTATATGTTCAAATCTTTCCAC
1 CCATTATATGTTAAAAT-TTTCC-C
2964120 CCATTATTAT-TTAAAATTTTCCC
1 CCATTA-TATGTTAAAATTTTCCC
2964143 CCA
1 CCA
2964146 CATTGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 5 0.21
25 12 0.50
26 3 0.12
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.41
Consensus pattern (23 bp):
CCATTATATGTTAAAATTTTCCC
Found at i:2981480 original size:9 final size:9
Alignment explanation
Indices: 2981468--2981507 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
2981458 ACCAGTTCAA
*
2981468 ACCGGTTTG
1 ACCGGTCTG
2981477 ACCGGTCTG
1 ACCGGTCTG
*
2981486 AACCGGTTTG
1 -ACCGGTCTG
2981496 ACCGGTCTG
1 ACCGGTCTG
2981505 ACC
1 ACC
2981508 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:2981491 original size:19 final size:19
Alignment explanation
Indices: 2981467--2981505 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
2981457 AACCAGTTCA
2981467 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
2981486 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
2981505 A
1 A
2981506 CCCGACCCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.26
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:2981528 original size:22 final size:22
Alignment explanation
Indices: 2981503--2981544 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2981493 TTGACCGGTC
2981503 TGACCCGACCCGACCCGACCAT
1 TGACCCGACCCGACCCGACCAT
*
2981525 TGACTCGACCCGACCCGACC
1 TGACCCGACCCGACCCGACC
2981545 GGACCGTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.50, G:0.19, T:0.10
Consensus pattern (22 bp):
TGACCCGACCCGACCCGACCAT
Found at i:2981535 original size:27 final size:27
Alignment explanation
Indices: 2981504--2981555 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2981494 TGACCGGTCT
2981504 GACCCGACCCGACCCGACCATTGACTC
1 GACCCGACCCGACCCGACCATTGACTC
* *
2981531 GACCCGACCCGACCGGACCGTTGAC
1 GACCCGACCCGACCCGACCATTGAC
2981556 CGTTGACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.46, G:0.23, T:0.10
Consensus pattern (27 bp):
GACCCGACCCGACCCGACCATTGACTC
Found at i:2988601 original size:19 final size:20
Alignment explanation
Indices: 2988561--2988607 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2988551 GGCTGCTGGA
2988561 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTAACCGGTTTTC
*
2988581 AACCGGTTTTACCGG-TTTC
1 AACCGGTTTAACCGGTTTTC
*
2988600 AACTGGTT
1 AACCGGTT
2988608 CGAATTGGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36
Consensus pattern (20 bp):
AACCGGTTTAACCGGTTTTC
Found at i:2988682 original size:27 final size:27
Alignment explanation
Indices: 2988646--2988721 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
2988636 TTGATCGGTC
2988646 TGACCCGACCCGACCGTTGACCCAACA
1 TGACCCGACCCGACCGTTGACCCAACA
* * *
2988673 TGACCTGACCCGACCGTTGACCCGACC
1 TGACCCGACCCGACCGTTGACCCAACA
* *
2988700 CGACCCGACCCGACCATTGACC
1 TGACCCGACCCGACCGTTGACC
2988722 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.22, C:0.46, G:0.20, T:0.12
Consensus pattern (27 bp):
TGACCCGACCCGACCGTTGACCCAACA
Found at i:2993195 original size:19 final size:20
Alignment explanation
Indices: 2993152--2993199 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2993142 TACTATGCTG
* *
2993152 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
2993172 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
2993191 GAAATTGAT
1 GAAATTGAT
2993200 CCATTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:2994467 original size:22 final size:21
Alignment explanation
Indices: 2994430--2994472 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2994420 TTATATATAC
*
2994430 GATGTTTATCATGAATACATAT
1 GATGTTTATCAAGAATA-ATAT
*
2994452 GATGTTTATTAAGAATAATAT
1 GATGTTTATCAAGAATAATAT
2994473 TTTGGGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (21 bp):
GATGTTTATCAAGAATAATAT
Found at i:2995695 original size:30 final size:31
Alignment explanation
Indices: 2995660--2995718 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
2995650 AGAGAAATTT
*
2995660 GGGGACC-ATTATG-TAATTTTTGAAAAGTTG
1 GGGGACCAATT-TGTTAATTTTGGAAAAGTTG
2995690 GGGGACCAATTTGTTAATTTTGGAAAAGT
1 GGGGACCAATTTGTTAATTTTGGAAAAGT
2995719 AGTGAATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.31, C:0.07, G:0.27, T:0.36
Consensus pattern (31 bp):
GGGGACCAATTTGTTAATTTTGGAAAAGTTG
Found at i:2997247 original size:17 final size:18
Alignment explanation
Indices: 2997215--2997248 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2997205 GCTTTTATTA
*
2997215 TTATTATATTAAAATAAT
1 TTATTATATAAAAATAAT
2997233 TTATT-TATAAAAATAA
1 TTATTATATAAAAATAA
2997249 AATATTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATTATATAAAAATAAT
Found at i:3005413 original size:26 final size:26
Alignment explanation
Indices: 3005378--3005465 Score: 131
Period size: 26 Copynumber: 3.3 Consensus size: 26
3005368 ACCAGGAACT
*
3005378 GCCTCAGCTCGCTACCTCCTCTCGGAC
1 GCCT-AGCTCGCTAGCTCCTCTCGGAC
* *
3005405 GCCTAGCTCACTAGCTTCTCTCGGAC
1 GCCTAGCTCGCTAGCTCCTCTCGGAC
*
3005431 GCCTAGCTCGCTAGCTCCTCTTGGAC
1 GCCTAGCTCGCTAGCTCCTCTCGGAC
3005457 GCCTAGCTC
1 GCCTAGCTC
3005466 ACCACTCCAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
26 51 0.93
27 4 0.07
ACGTcount: A:0.12, C:0.42, G:0.20, T:0.25
Consensus pattern (26 bp):
GCCTAGCTCGCTAGCTCCTCTCGGAC
Found at i:3008092 original size:114 final size:115
Alignment explanation
Indices: 3007892--3008122 Score: 455
Period size: 114 Copynumber: 2.0 Consensus size: 115
3007882 TATAACTCCA
3007892 TAAAAGGCTATATTTTGTGCCTTTTTACTTAGGTTATTGGTTGTTTAAAAGCCCATTTCATGGCA
1 TAAAAGGCTATATTTTGTGCCTTTTTACTTAGGTTATTGGTTGTTTAAAAGCCCATTTCATGGCA
3007957 TATAGTTGCATTTAGACCTATATAGATGCATATGGTGGCATTTG-TTTGC
66 TATAGTTGCATTTAGACCTATATAGATGCATATGGTGGCATTTGTTTTGC
3008006 TAAAAGGCTATATTTTGTGCCTTTTTACTTAGGTTATTGGTTGTTTAAAAGCCCATTTCATGGCA
1 TAAAAGGCTATATTTTGTGCCTTTTTACTTAGGTTATTGGTTGTTTAAAAGCCCATTTCATGGCA
3008071 TATAGTTGCATTTAGACCTATATAGATGCATATGGTGGCATTTGTTTTGC
66 TATAGTTGCATTTAGACCTATATAGATGCATATGGTGGCATTTGTTTTGC
3008121 TA
1 TA
3008123 TAACATTTTA
Statistics
Matches: 116, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
114 109 0.94
115 7 0.06
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (115 bp):
TAAAAGGCTATATTTTGTGCCTTTTTACTTAGGTTATTGGTTGTTTAAAAGCCCATTTCATGGCA
TATAGTTGCATTTAGACCTATATAGATGCATATGGTGGCATTTGTTTTGC
Found at i:3019183 original size:21 final size:21
Alignment explanation
Indices: 3019140--3019183 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3019130 GTTTCATTGC
* *
3019140 AGGAATTCATGGCCTCGATAA
1 AGGAATTCATGGCCTCAACAA
* *
3019161 AGGATTTCATGGCTTCAACAA
1 AGGAATTCATGGCCTCAACAA
3019182 AG
1 AG
3019184 ACACTGATGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (21 bp):
AGGAATTCATGGCCTCAACAA
Found at i:3024535 original size:552 final size:551
Alignment explanation
Indices: 3023487--3024588 Score: 1934
Period size: 552 Copynumber: 2.0 Consensus size: 551
3023477 GAATGCATAG
** *
3023487 GAGCACCAGTCATGCGTGACAAACCGACATCAACAGTACATGATGCCCAAGAGTTTTCCTTACTT
1 GAGCACCAGTCATGCACGACAAACCGACATCAACAGCACATGATGCCCAAGAGTTTTCCTTACTT
* * *
3023552 ACCTTAACACAATTCGTTGCCTAGGCAACGAAAATCTTAATTTTGTACGTAAATAAATTAAGTTA
66 ACATTAACACAATTCGTTACCTAGGCAACGAAAATCTTAATTTTGTACATAAATAAATTAAGTTA
3023617 TTTTATGCACTAGTTATATGTTTTACTTTATTTATGCTTTTTTATTTATTGCAGGCACGCATGGT
131 TTTTATGCACTAGTTATATGTTTTACTTTATTTATGCTTTTTTATTTATTGCAGGCACGCATGGT
*
3023682 ACATGTGGCAGCATGGGGTGAGAACTTACACATGAAAAGAAGAGATACCCTAGAGCAAAAGAGGT
196 ACATGTGGCAGCATGGGGTGAGAACTTACACATGAAAAGAAGAGAAACCCTAGAGCAAAAGAGGT
*
3023747 TTTGGCGGCAATTGTAAAGAGGGAAACTATCTTTTCCCCACTTGACGTTTAATCAAATATTGAGA
261 TTTGGCGGCAATTGTAAAGAGGGAAACTATCTTTTCCCCACTTGACGTCTAATCAAATATTGAGA
*
3023812 ATTCAATGTCATATCTTTTCCCCTCTCATTTTGAGCAAATTGCCCTGAAGAAACCACCTATTAAC
326 ATTCAATGTCATATCTTTTCCCCTCTCATTTTGAGCAAATTGCCCTGAAGAAACCACCCATTAAC
* *
3023877 TTTCCAGAAAAACCAACTTCAACTCCATCTTCATCATTATGCATTATTTTCTCTCATTCAAAAAC
391 TTTCCAGAAAAACCAACTTCAACTCCATCTTCATCATCATGCATTATTTTCTCTCATTCAAAAAA
* * * *
3023942 AATTCCCTTCAAAAACTTCCCCCATCGTCGTCGCGAAACACATTGTACCAACGAGTATCATGGCT
456 AATTCCCTTCAAAAACCTCCCCCATCGCCGTCACAAAACACATTGTACCAACGAGTATCATGGCT
3024007 AGATCGAAGAAAAACCCATCCCCAACACCAT
521 AGATCGAAGAAAAACCCATCCCCAACACCAT
* *
3024038 GAGCACCAGTCATGCACGACAAATCGACATCAACAGCACATGATGCCCAATAGTTTTCCTTACTT
1 GAGCACCAGTCATGCACGACAAACCGACATCAACAGCACATGATGCCCAAGAGTTTTCCTTACTT
* *
3024103 ACATTAACATAATTTGTTACCTAGGCAACGAAAATCTTAATTTTGTACATAAATAAATTAAGTTA
66 ACATTAACACAATTCGTTACCTAGGCAACGAAAATCTTAATTTTGTACATAAATAAATTAAGTTA
* * * * *
3024168 TTTTATGCACTAGTTATCTGTTTTATTTTATTTCTGTTCTTTTTATTTATTGCAGGCATGCATGG
131 TTTTATGCACTAGTTATATGTTTTACTTTATTTATGCT-TTTTTATTTATTGCAGGCACGCATGG
*
3024233 TACATGTGGCAGCATGGGGTGAGAACTTACACATGAAAGGAAGAGAAACCCTAGAGCAAAAGAGG
195 TACATGTGGCAGCATGGGGTGAGAACTTACACATGAAAAGAAGAGAAACCCTAGAGCAAAAGAGG
*
3024298 TTTTGGCGGCAATTGTAAAGAGGGAAACTATCTTTTCCCCACTTTACGTCTAATCAAATATTGAG
260 TTTTGGCGGCAATTGTAAAGAGGGAAACTATCTTTTCCCCACTTGACGTCTAATCAAATATTGAG
*
3024363 AATTCAATGTCATATCTTTTCCCCTCTCATTTTGAGCAAATTGCCCTGAAGAAACCACCCATTCA
325 AATTCAATGTCATATCTTTTCCCCTCTCATTTTGAGCAAATTGCCCTGAAGAAACCACCCATTAA
*
3024428 CTTTCCAGAAAACCCAACTTCAACTCCATCTTCATCATCATGCATTATTTTCTCTCATTCAAAAA
390 CTTTCCAGAAAAACCAACTTCAACTCCATCTTCATCATCATGCATTATTTTCTCTCATTCAAAAA
*
3024493 AAATTCCCTTCAAAAACCTCCCTCATCGCCGTCACAAAACACATTGTACCAACGAGTATCATGGC
455 AAATTCCCTTCAAAAACCTCCCCCATCGCCGTCACAAAACACATTGTACCAACGAGTATCATGGC
3024558 TAGATCGAAGAAAAACCCATCCCCAACACCA
520 TAGATCGAAGAAAAACCCATCCCCAACACCA
3024589 GGCTTTGAGC
Statistics
Matches: 521, Mismatches: 29, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
551 154 0.30
552 367 0.70
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (551 bp):
GAGCACCAGTCATGCACGACAAACCGACATCAACAGCACATGATGCCCAAGAGTTTTCCTTACTT
ACATTAACACAATTCGTTACCTAGGCAACGAAAATCTTAATTTTGTACATAAATAAATTAAGTTA
TTTTATGCACTAGTTATATGTTTTACTTTATTTATGCTTTTTTATTTATTGCAGGCACGCATGGT
ACATGTGGCAGCATGGGGTGAGAACTTACACATGAAAAGAAGAGAAACCCTAGAGCAAAAGAGGT
TTTGGCGGCAATTGTAAAGAGGGAAACTATCTTTTCCCCACTTGACGTCTAATCAAATATTGAGA
ATTCAATGTCATATCTTTTCCCCTCTCATTTTGAGCAAATTGCCCTGAAGAAACCACCCATTAAC
TTTCCAGAAAAACCAACTTCAACTCCATCTTCATCATCATGCATTATTTTCTCTCATTCAAAAAA
AATTCCCTTCAAAAACCTCCCCCATCGCCGTCACAAAACACATTGTACCAACGAGTATCATGGCT
AGATCGAAGAAAAACCCATCCCCAACACCAT
Found at i:3032842 original size:28 final size:26
Alignment explanation
Indices: 3032810--3032873 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 26
3032800 ATATTTCTTT
*
3032810 CTTTTCTTTCATATCATTGTTCTTAAA
1 CTTTTCTTTCATATCATT-TCCTTAAA
* * *
3032837 CCTTTTCCTTCTTTTCATTTCCTTAAA
1 -CTTTTCTTTCATATCATTTCCTTAAA
3032864 CTATTTCTTT
1 CT-TTTCTTT
3032874 GTCTTTCCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 2 0.07
27 13 0.43
28 15 0.50
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.58
Consensus pattern (26 bp):
CTTTTCTTTCATATCATTTCCTTAAA
Found at i:3035565 original size:24 final size:24
Alignment explanation
Indices: 3035538--3035590 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
3035528 TCATAAAATG
3035538 GAGGCTAAAATCATGAAGATATAT
1 GAGGCTAAAATCATGAAGATATAT
*
3035562 GAGGCTTAAATCATGAAGATATAT
1 GAGGCTAAAATCATGAAGATATAT
3035586 GAGGC
1 GAGGC
3035591 AAGCACCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.25, T:0.25
Consensus pattern (24 bp):
GAGGCTAAAATCATGAAGATATAT
Found at i:3036785 original size:28 final size:27
Alignment explanation
Indices: 3036743--3036797 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
3036733 ATATTCCTTT
* *
3036743 CTTTTCTTTCATTTCATTGTTCTTAAAC
1 CTTTTCATTCATTTCATT-TCCTTAAAC
*
3036771 CTTTTCATTCTTTTCATTTCCTTAAAC
1 CTTTTCATTCATTTCATTTCCTTAAAC
3036798 AATTTCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.18, C:0.24, G:0.02, T:0.56
Consensus pattern (27 bp):
CTTTTCATTCATTTCATTTCCTTAAAC
Found at i:3036803 original size:27 final size:28
Alignment explanation
Indices: 3036745--3036803 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
3036735 ATTCCTTTCT
* * **
3036745 TTTCTTTCATTTCATTGTTCTTAAACCT
1 TTTCATTCATTTCATTGTCCTTAAACAA
*
3036773 TTTCATTCTTTTCATT-TCCTTAAACAA
1 TTTCATTCATTTCATTGTCCTTAAACAA
3036800 TTTC
1 TTTC
3036804 TTTTATCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTCATTCATTTCATTGTCCTTAAACAA
Found at i:3039841 original size:5 final size:5
Alignment explanation
Indices: 3039825--3039957 Score: 71
Period size: 5 Copynumber: 26.0 Consensus size: 5
3039815 AAATCAATAC
* *
3039825 ATAAT ATTAT ATAAT ATAAT ATAAT ATAAT AATATT AATAAT AT-AT A-AATT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT -ATAAT ATAAT ATAA-T
* * *
3039876 ATATT AT-AT ATAAT ATGTACT ATATAT GTAAT AT-AT A-AAT ATATAT
1 ATAAT ATAAT ATAAT A--TAAT ATA-AT ATAAT ATAAT ATAAT ATA-AT
* * *
3039922 GTCAT ACTACAT ATAAT ATAGT ATAAT AT-AT ATAAT
1 ATAAT A-TA-AT ATAAT ATAAT ATAAT ATAAT ATAAT
3039958 TTATTATTTT
Statistics
Matches: 98, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
4 17 0.17
5 55 0.56
6 19 0.19
7 7 0.07
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (5 bp):
ATAAT
Found at i:3039885 original size:2 final size:2
Alignment explanation
Indices: 3039828--3039955 Score: 61
Period size: 2 Copynumber: 69.5 Consensus size: 2
3039818 TCAATACATA
3039828 AT AT -T AT AT A- AT AT A- AT AT A- AT AT A- AT A- AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3039862 AT A- AT AT AT AA AT -T AT AT -T AT AT AT A- AT AT GT ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * *
3039901 AT GT A- AT AT AT AA AT AT AT AT GT CAT ACT AC AT AT A- AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT A-T
3039944 AT A- AT AT AT AT A
1 AT AT AT AT AT AT A
3039956 ATTTATTATT
Statistics
Matches: 95, Mismatches: 12, Indels: 38
0.66 0.08 0.26
Matches are distributed among these distances:
1 15 0.16
2 73 0.77
3 7 0.07
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3039904 original size:11 final size:11
Alignment explanation
Indices: 3039841--3039954 Score: 52
Period size: 11 Copynumber: 10.9 Consensus size: 11
3039831 TTATATAATA
*
3039841 TAATATA-ATA
1 TAATATATATG
3039851 TAATA-ATAT-
1 TAATATATATG
*
3039860 TAATA-ATATA
1 TAATATATATG
3039870 TAA-ATTATAT-
1 TAATA-TATATG
3039880 TATATATAATATG
1 TA-ATAT-ATATG
*
3039893 TACTATATATG
1 TAATATATATG
3039904 TAATATATA--
1 TAATATATATG
3039913 -AATATATATG
1 TAATATATATG
* * *
3039923 TCATACTACATA
1 TAATA-TATATG
3039935 TAATATAGTA--
1 TAATATA-TATG
3039945 TAATATATAT
1 TAATATATAT
3039955 AATTTATTAT
Statistics
Matches: 83, Mismatches: 7, Indels: 28
0.70 0.06 0.24
Matches are distributed among these distances:
8 8 0.10
9 13 0.16
10 19 0.23
11 24 0.29
12 17 0.20
13 2 0.02
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (11 bp):
TAATATATATG
Found at i:3040094 original size:20 final size:17
Alignment explanation
Indices: 3040069--3040122 Score: 54
Period size: 20 Copynumber: 2.9 Consensus size: 17
3040059 ATACCATATT
3040069 ATATATAAAACATGAATACC
1 ATATATAAAA-AT--ATACC
*
3040089 ATATATATAAATATACC
1 ATATATAAAAATATACC
3040106 ATAATATAAAATATATA
1 AT-ATATAAAA-ATATA
3040123 ATAAAATACT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 7 0.23
18 7 0.23
19 7 0.23
20 9 0.30
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.31
Consensus pattern (17 bp):
ATATATAAAAATATACC
Found at i:3040106 original size:17 final size:17
Alignment explanation
Indices: 3040084--3040120 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
3040074 TAAAACATGA
3040084 ATACCAT-ATATATAAAT
1 ATACCATAATATA-AAAT
3040101 ATACCATAATATAAAAT
1 ATACCATAATATAAAAT
3040118 ATA
1 ATA
3040121 TAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (17 bp):
ATACCATAATATAAAAT
Found at i:3045863 original size:64 final size:63
Alignment explanation
Indices: 3045777--3045986 Score: 183
Period size: 65 Copynumber: 3.3 Consensus size: 63
3045767 TGTACTAAGA
* * * *
3045777 GTGCAACGATTCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
* ** *
3045841 GTGCATCGATGCATCAAATGCATTCAATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
3045905 T
63 G
* * * ** *
3045906 GTGCATCGATGCATGAAATGAATTCGAT-ATTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG--
3045969 TG
62 TG
*
3045971 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
3045987 CTCTGTAAAA
Statistics
Matches: 116, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 44 0.38
65 63 0.54
66 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:3049450 original size:159 final size:159
Alignment explanation
Indices: 3049161--3049480 Score: 640
Period size: 159 Copynumber: 2.0 Consensus size: 159
3049151 GGATGGGATA
3049161 TTTAGTGAGACAAATAGCATTAGTATTGTCACACTTGATAGGAATGGTACCTACTTCAATTCCAT
1 TTTAGTGAGACAAATAGCATTAGTATTGTCACACTTGATAGGAATGGTACCTACTTCAATTCCAT
3049226 AATCAAAAAGTTGTTGTTTCATCCATAAAACTTGTGCACAACAACTACCAGCTAAAATGTATTCA
66 AATCAAAAAGTTGTTGTTTCATCCATAAAACTTGTGCACAACAACTACCAGCTAAAATGTATTCA
3049291 GCTTCTGTGGTAGATAATGCAACACAATT
131 GCTTCTGTGGTAGATAATGCAACACAATT
3049320 TTTAGTGAGACAAATAGCATTAGTATTGTCACACTTGATAGGAATGGTACCTACTTCAATTCCAT
1 TTTAGTGAGACAAATAGCATTAGTATTGTCACACTTGATAGGAATGGTACCTACTTCAATTCCAT
3049385 AATCAAAAAGTTGTTGTTTCATCCATAAAACTTGTGCACAACAACTACCAGCTAAAATGTATTCA
66 AATCAAAAAGTTGTTGTTTCATCCATAAAACTTGTGCACAACAACTACCAGCTAAAATGTATTCA
3049450 GCTTCTGTGGTAGATAATGCAACACAATT
131 GCTTCTGTGGTAGATAATGCAACACAATT
3049479 TT
1 TT
3049481 GTTTCTTTGA
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 161 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (159 bp):
TTTAGTGAGACAAATAGCATTAGTATTGTCACACTTGATAGGAATGGTACCTACTTCAATTCCAT
AATCAAAAAGTTGTTGTTTCATCCATAAAACTTGTGCACAACAACTACCAGCTAAAATGTATTCA
GCTTCTGTGGTAGATAATGCAACACAATT
Found at i:3054170 original size:17 final size:17
Alignment explanation
Indices: 3054145--3054231 Score: 138
Period size: 17 Copynumber: 5.1 Consensus size: 17
3054135 GAGATAACCT
3054145 TACAACTCCCTCAAGAA
1 TACAACTCCCTCAAGAA
*
3054162 TATAACTCCCTCAAGAA
1 TACAACTCCCTCAAGAA
*
3054179 TACAACTCCCTTAAGAA
1 TACAACTCCCTCAAGAA
*
3054196 TACAACTCTCTCAAGAA
1 TACAACTCCCTCAAGAA
*
3054213 TACAACTACCTCAAGAA
1 TACAACTCCCTCAAGAA
3054230 TA
1 TA
3054232 TACCCCAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 63 1.00
ACGTcount: A:0.43, C:0.30, G:0.06, T:0.22
Consensus pattern (17 bp):
TACAACTCCCTCAAGAA
Found at i:3054749 original size:18 final size:17
Alignment explanation
Indices: 3054695--3054743 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
3054685 TTGGATCCTT
* *
3054695 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
3054713 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
3054731 AGTGCATTCGATG
1 AGTGCA-TCGATG
3054744 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:3054863 original size:65 final size:64
Alignment explanation
Indices: 3054689--3054875 Score: 209
Period size: 65 Copynumber: 2.9 Consensus size: 64
3054679 TGACCGTTGG
* * *
3054689 ATCCTTAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAA
1 ATCCTAAGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAA
3054752 T
64 T
* * * * *
3054753 AGCCAAAGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTTATAAA
1 ATCCTAAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAA
3054818 -
64 T
* * *
3054818 ATCCTCAGTGCATCGGTGCATGGTATGTGCATCTATGCATGAAATGCATTCGATGTTT
1 ATCCTAAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTTT
3054876 AATTTAATTC
Statistics
Matches: 103, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 45 0.44
65 53 0.51
66 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (64 bp):
ATCCTAAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAT
Found at i:3054866 original size:129 final size:130
Alignment explanation
Indices: 3054689--3054924 Score: 300
Period size: 129 Copynumber: 1.8 Consensus size: 130
3054679 TGACCGTTGG
* *
3054689 ATCCTTAGTGCATCGGTGCACTAAGAGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-
1 ATCCTCAGTGCATCGGTGCACTAAGAGTGCATCGATGCATCAAATGCATTCGATGTTT-AAAATA
3054753 AGCCAAAGTGCATCGATGCATGG-CTGGTGCATCGATGCATCAAATGCATTCGATGTTTTTATAA
65 AGCCAAAGTGCATCGATGCATGGACTGGTGCATCGATGCATCAAATGCATTCGATGTTTTTATAA
3054817 A
130 A
* * * **
3054818 ATCCTCAGTGCATCGGTGCA-T-GGTATGTGCATCTATGCATGAAATGCATTCGATGTTTAATTT
1 ATCCTCAGTGCATCGGTGCACTAAG-A-GTGCATCGATGCATCAAATGCATTCGATGTTTAAAAT
** ** * *
3054881 AATTCATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
64 AAGCCAAAGTGCATCGATGCATGGACTGGTGCATCGATGCATCA
3054925 CTCTGAAAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
127 1 0.01
128 5 0.06
129 67 0.74
130 17 0.19
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (130 bp):
ATCCTCAGTGCATCGGTGCACTAAGAGTGCATCGATGCATCAAATGCATTCGATGTTTAAAATAA
GCCAAAGTGCATCGATGCATGGACTGGTGCATCGATGCATCAAATGCATTCGATGTTTTTATAAA
Found at i:3054913 original size:65 final size:65
Alignment explanation
Indices: 3054715--3054924 Score: 209
Period size: 65 Copynumber: 3.2 Consensus size: 65
3054705 TGCACTAAGA
* * * * *
3054715 GTGCATCGATGCATCAAGTGCATTCGATG-TTTCA-AAATAGCCA-AAGTGCATCGATGCATGGC
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTTATAAA-A-TCATCAGTGCATCGATGCATGGT
3054777 TG
64 TG
* *
3054779 GTGCATCGATGCATCAAATGCATTCGATGTTTTTATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTTATAAAATCATCAGTGCATCGATGCATGGT-T
3054844 -
65 G
* * * *
3054844 GTGCATCTATGCATGAAATGCATTCGATGTTTAATT-T-AATTCAT-GGTGCATCGATGCATGGA
1 GTGCATCGATGCATCAAATGCATTCGATGTTT--TTATAAAATCATCAGTGCATCGATGCATGG-
3054906 TTG
63 TTG
*
3054909 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
3054925 CTCTGAAAAA
Statistics
Matches: 122, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
64 45 0.37
65 70 0.57
66 5 0.04
67 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTTATAAAATCATCAGTGCATCGATGCATGGTTG
Found at i:3060085 original size:16 final size:16
Alignment explanation
Indices: 3060059--3060101 Score: 70
Period size: 15 Copynumber: 2.7 Consensus size: 16
3060049 TTTTTAGTAG
3060059 TTATCTTAAAAAATTAT
1 TTAT-TTAAAAAATTAT
3060076 TTATTT-AAAAATTAT
1 TTATTTAAAAAATTAT
3060091 TTATTTAAAAA
1 TTATTTAAAAA
3060102 TAATTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 15 0.60
16 6 0.24
17 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TTATTTAAAAAATTAT
Found at i:3060087 original size:15 final size:15
Alignment explanation
Indices: 3060067--3060112 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
3060057 AGTTATCTTA
3060067 AAAAATTATTTATTT
1 AAAAATTATTTATTT
3060082 AAAAATTATTTATTT
1 AAAAATTATTTATTT
* *
3060097 AAAAATAATTAATTT
1 AAAAATTATTTATTT
3060112 A
1 A
3060113 CTAATAGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAATTATTTATTT
Found at i:3060169 original size:45 final size:43
Alignment explanation
Indices: 3060104--3060203 Score: 128
Period size: 45 Copynumber: 2.3 Consensus size: 43
3060094 TTTAAAAATA
* * *
3060104 ATTAATTTACTAATAGATAATAAAAATATAATAAATGACTAATCT
1 ATTATTTTACTAATAAATAATAAAAA-ATAATAAATGAATAAT-T
* * *
3060149 ATTATTTTTCTAATAAATAATAAAAAATACTAAATTAATAATT
1 ATTATTTTACTAATAAATAATAAAAAATAATAAATGAATAATT
3060192 ATTATTTTACTA
1 ATTATTTTACTA
3060204 CACCCTAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 12 0.25
44 13 0.27
45 23 0.48
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (43 bp):
ATTATTTTACTAATAAATAATAAAAAATAATAAATGAATAATT
Found at i:3063382 original size:12 final size:12
Alignment explanation
Indices: 3063365--3063394 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3063355 ACCATTGTTG
3063365 ACAATATTTAAA
1 ACAATATTTAAA
3063377 ACAATATTTAAA
1 ACAATATTTAAA
*
3063389 AAAATA
1 ACAATA
3063395 AAAGTTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (12 bp):
ACAATATTTAAA
Found at i:3066317 original size:14 final size:14
Alignment explanation
Indices: 3066300--3066334 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3066290 ATTTGTTTTA
* *
3066300 AATTATTAATTATT
1 AATTAATAATTATC
3066314 AATTAATAATTATC
1 AATTAATAATTATC
3066328 AATTAAT
1 AATTAAT
3066335 GATTGTTCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTAATAATTATC
Found at i:3074779 original size:19 final size:19
Alignment explanation
Indices: 3074755--3074793 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3074745 AACTAGTACA
*
3074755 TAGTGATGATGATCAATCC
1 TAGTGATGATGAGCAATCC
3074774 TAGTGATGATGAGCAATCC
1 TAGTGATGATGAGCAATCC
3074793 T
1 T
3074794 TCTTTTAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (19 bp):
TAGTGATGATGAGCAATCC
Found at i:3076534 original size:24 final size:24
Alignment explanation
Indices: 3076489--3076535 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
3076479 TATTTATTAT
* **
3076489 TCATGAACGTGTTCGTTTACATGC
1 TCATGAACGTGTTCATGAACATGC
3076513 TCATGAACGTGTTCATGAACATG
1 TCATGAACGTGTTCATGAACATG
3076536 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (24 bp):
TCATGAACGTGTTCATGAACATGC
Found at i:3078667 original size:25 final size:25
Alignment explanation
Indices: 3078633--3078710 Score: 156
Period size: 25 Copynumber: 3.1 Consensus size: 25
3078623 CTTGATTCAT
3078633 ATCGGCTTGTCATCGATCTTCTAGA
1 ATCGGCTTGTCATCGATCTTCTAGA
3078658 ATCGGCTTGTCATCGATCTTCTAGA
1 ATCGGCTTGTCATCGATCTTCTAGA
3078683 ATCGGCTTGTCATCGATCTTCTAGA
1 ATCGGCTTGTCATCGATCTTCTAGA
3078708 ATC
1 ATC
3078711 TCAGCCATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (25 bp):
ATCGGCTTGTCATCGATCTTCTAGA
Found at i:3081354 original size:22 final size:22
Alignment explanation
Indices: 3081329--3081370 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3081319 TTTTCAGCCG
3081329 TTTGTAACTCATGTAATTACAC
1 TTTGTAACTCATGTAATTACAC
* *
3081351 TTTGTAACTCTTGTGATTAC
1 TTTGTAACTCATGTAATTAC
3081371 TCTGGCACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (22 bp):
TTTGTAACTCATGTAATTACAC
Found at i:3084061 original size:40 final size:40
Alignment explanation
Indices: 3084006--3084167 Score: 279
Period size: 40 Copynumber: 4.0 Consensus size: 40
3083996 TGCAGGTTTA
3084006 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
3084046 TAATACACTTCGGTGTATATGATGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* * *
3084086 TAATAAACTTCGGTGTATATGGTGGGCACAACCTTATGTC
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
3084126 TAATACACTTCGGTGTATATGGTGGGCAAGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
3084166 TA
1 TA
3084168 GCACTACGGT
Statistics
Matches: 113, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 113 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:3085076 original size:31 final size:31
Alignment explanation
Indices: 3085038--3085107 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
3085028 TGGGGCATAT
3085038 GGGCCTACAAAAGAAAGATCTCAGGGCCGCA
1 GGGCCTACAAAAGAAAGATCTCAGGGCCGCA
** * * *
3085069 GGGCCTACCCAAGAATGATCTCGGGGCTGCA
1 GGGCCTACAAAAGAAAGATCTCAGGGCCGCA
*
3085100 GAGCCTAC
1 GGGCCTAC
3085108 CCAAGAGTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.29, C:0.29, G:0.30, T:0.13
Consensus pattern (31 bp):
GGGCCTACAAAAGAAAGATCTCAGGGCCGCA
Found at i:3085108 original size:31 final size:31
Alignment explanation
Indices: 3085048--3085113 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
3085038 GGGCCTACAA
*
3085048 AAGAAAGATCTCAGGGCCGCAGGGCCTACCC
1 AAGAAAGATCTCAGGGCCGCAGAGCCTACCC
* * *
3085079 AAGAATGATCTCGGGGCTGCAGAGCCTACCC
1 AAGAAAGATCTCAGGGCCGCAGAGCCTACCC
3085110 AAGA
1 AAGA
3085114 GTCACATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.29, G:0.29, T:0.12
Consensus pattern (31 bp):
AAGAAAGATCTCAGGGCCGCAGAGCCTACCC
Found at i:3087770 original size:13 final size:13
Alignment explanation
Indices: 3087752--3087776 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3087742 TGACTTTTTG
3087752 GTCAAAGTCAACA
1 GTCAAAGTCAACA
3087765 GTCAAAGTCAAC
1 GTCAAAGTCAAC
3087777 GCCTGCCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.24, G:0.16, T:0.16
Consensus pattern (13 bp):
GTCAAAGTCAACA
Found at i:3087807 original size:17 final size:17
Alignment explanation
Indices: 3087787--3087828 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
3087777 GCCTGCCAAA
3087787 GGTCAATGAAGGTCAAC
1 GGTCAATGAAGGTCAAC
*
3087804 GGTCAGTGAAGGTCAAC
1 GGTCAATGAAGGTCAAC
3087821 GGTCAATG
1 GGTCAATG
3087829 GCTCAGTCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.31, C:0.17, G:0.33, T:0.19
Consensus pattern (17 bp):
GGTCAATGAAGGTCAAC
Found at i:3089948 original size:31 final size:30
Alignment explanation
Indices: 3089913--3090025 Score: 106
Period size: 31 Copynumber: 3.7 Consensus size: 30
3089903 TGGGGTATAT
3089913 GGGCCTACCCAAGAATGATCTTAGTGCCGTA
1 GGGCCTACCCAAGAATGATCTTAG-GCCGTA
* *
3089944 GGGCCTACCCAAGGATGATCTCAGGGCC--A
1 GGGCCTACCCAAGAATGATCTTA-GGCCGTA
** *
3089973 CGGGACCTACCCAAGAAACATAC-TAGGGCGTA
1 -GGG-CCTACCCAAGAATGAT-CTTAGGCCGTA
*
3090005 GGGCTTACCCAAGAATGATCT
1 GGGCCTACCCAAGAATGATCT
3090026 CGGGGCCGCA
Statistics
Matches: 65, Mismatches: 10, Indels: 15
0.72 0.11 0.17
Matches are distributed among these distances:
29 2 0.03
30 19 0.29
31 41 0.63
32 3 0.05
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (30 bp):
GGGCCTACCCAAGAATGATCTTAGGCCGTA
Found at i:3092680 original size:13 final size:13
Alignment explanation
Indices: 3092642--3092681 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
3092632 TTGACTTTTT
*
3092642 GGTCAAAGTCAAA
1 GGTCAAAGTCAAC
3092655 GGTCAAAGTCAAC
1 GGTCAAAGTCAAC
*
3092668 GGTTAAAGTCAAC
1 GGTCAAAGTCAAC
3092681 G
1 G
3092682 CCAGTTATCG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (13 bp):
GGTCAAAGTCAAC
Found at i:3094257 original size:20 final size:20
Alignment explanation
Indices: 3094217--3094258 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3094207 GACTGTCACG
* * *
3094217 AAACTTACATTATAATTTAC
1 AAACTTACATGACAATCTAC
3094237 AAACTTACATGACAATCTAC
1 AAACTTACATGACAATCTAC
3094257 AA
1 AA
3094259 TATTGATGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (20 bp):
AAACTTACATGACAATCTAC
Found at i:3094390 original size:7 final size:7
Alignment explanation
Indices: 3094375--3094404 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
3094365 AAAATTATTT
*
3094375 AAATTTA
1 AAATATA
3094382 AAATATA
1 AAATATA
3094389 AAATATA
1 AAATATA
3094396 AAATATA
1 AAATATA
3094403 AA
1 AA
3094405 TAATTATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
AAATATA
Done.