Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold117
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: 3231771
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 68836 characters in sequence are not A, C, G, or T
File 17 of 18
Found at i:2832696 original size:27 final size:27
Alignment explanation
Indices: 2832661--2832731 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
2832651 AAACAACAAG
*
2832661 CCATAATTTTTGACGAATAAAAAGGAA
1 CCATAATTTTTGACAAATAAAAAGGAA
* * *
2832688 CCATCATTTTTGACAAATATAAAGTAA
1 CCATAATTTTTGACAAATAAAAAGGAA
*
2832715 CCACT-ATTGTTGACAAA
1 CCA-TAATTTTTGACAAA
2832732 CATAAAGGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
27 37 0.97
28 1 0.03
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (27 bp):
CCATAATTTTTGACAAATAAAAAGGAA
Found at i:2839211 original size:25 final size:26
Alignment explanation
Indices: 2839170--2839218 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
2839160 TATATTTTTA
* *
2839170 AAATATTATATTTAATATTTATATGT
1 AAATATTATATTAAATATTAATATGT
2839196 AAATA-TATATTAAATATTAATAT
1 AAATATTATATTAAATATTAATAT
2839219 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
AAATATTATATTAAATATTAATATGT
Found at i:2840309 original size:21 final size:21
Alignment explanation
Indices: 2840284--2840323 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2840274 TTCCAGGAAT
*
2840284 TATCCTTGGAAAGGTAAGAAG
1 TATCCTTAGAAAGGTAAGAAG
2840305 TATCCTTAGAAAGGTAAGA
1 TATCCTTAGAAAGGTAAGA
2840324 CTTAAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (21 bp):
TATCCTTAGAAAGGTAAGAAG
Found at i:2845078 original size:68 final size:68
Alignment explanation
Indices: 2844966--2845100 Score: 243
Period size: 68 Copynumber: 2.0 Consensus size: 68
2844956 GAAGTTGGGG
* * *
2844966 CTGATTTGATGGTTTTGAAGGATATGTGGTTGCAATTGGTGCTTTGGAGGAGTTTTTATTCAACC
1 CTGATTTGATGCTTTTGAAGGAAATGTGGTTGCAATTGGAGCTTTGGAGGAGTTTTTATTCAACC
2845031 AAA
66 AAA
2845034 CTGATTTGATGCTTTTGAAGGAAATGTGGTTGCAATTGGAGCTTTGGAGGAGTTTTTATTCAACC
1 CTGATTTGATGCTTTTGAAGGAAATGTGGTTGCAATTGGAGCTTTGGAGGAGTTTTTATTCAACC
2845099 AA
66 AA
2845101 GTTTGTTGAT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (68 bp):
CTGATTTGATGCTTTTGAAGGAAATGTGGTTGCAATTGGAGCTTTGGAGGAGTTTTTATTCAACC
AAA
Found at i:2846009 original size:2 final size:2
Alignment explanation
Indices: 2846002--2846028 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2845992 GCTTGAGATT
2846002 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
2846029 TCATGTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2848610 original size:20 final size:21
Alignment explanation
Indices: 2848572--2848610 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2848562 TATTTGTATT
*
2848572 TAATTTTTATATGTCATTATA
1 TAATTTTTATATGTAATTATA
*
2848593 TAATTTTTATCTG-AATTA
1 TAATTTTTATATGTAATTA
2848611 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
TAATTTTTATATGTAATTATA
Found at i:2849255 original size:54 final size:54
Alignment explanation
Indices: 2849151--2849255 Score: 131
Period size: 54 Copynumber: 1.9 Consensus size: 54
2849141 AATCACAGCT
* * * * * *
2849151 CCGTGAATGACTTTTCAAATCATAAGGCATTTCAACATAAAGTGAGTCAATACC
1 CCGTGAATGACTTTTCAAATCATAAGACACTTCAACACAAAATCAATCAATACC
*
2849205 CCGTGAGTGACTTTTCAAATCAT-AGAACACTTCAACACAAAATCAATCAAT
1 CCGTGAATGACTTTTCAAATCATAAG-ACACTTCAACACAAAATCAATCAAT
2849256 GTCTCGTGGG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 2 0.05
54 41 0.95
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (54 bp):
CCGTGAATGACTTTTCAAATCATAAGACACTTCAACACAAAATCAATCAATACC
Found at i:2850332 original size:14 final size:11
Alignment explanation
Indices: 2850261--2850314 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
2850251 TTTTTAAACT
2850261 TAATTATAAATA
1 TAATTA-AAATA
* *
2850273 TGA-TATAATA
1 TAATTAAAATA
*
2850283 TAATATAAAAAA
1 TAAT-TAAAATA
2850295 TAATTAAAATA
1 TAATTAAAATA
2850306 TAATTAAAA
1 TAATTAAAA
2850315 ATATGATATT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
10 6 0.18
11 17 0.50
12 11 0.32
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
TAATTAAAATA
Found at i:2859144 original size:21 final size:22
Alignment explanation
Indices: 2859115--2859160 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2859105 TGTTCAGATA
** *
2859115 AGTAGTACTCCGCAGCAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2859137 AGTA-TACTCCAAAACAGGTGG
1 AGTAGTACTCCAAAACAGGTGG
2859158 AGT
1 AGT
2859161 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAGGTGG
Found at i:2861107 original size:24 final size:26
Alignment explanation
Indices: 2861041--2861107 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 26
2861031 AAAAGCCACC
2861041 CTTTG-TGTTTGTCAAAAATAGTGGTT
1 CTTTGTTGTTTGTCAAAAATAGTGG-T
* * *
2861067 CTTTTTTATTTGTCAAAAATTGTGG-
1 CTTTGTTGTTTGTCAAAAATAGTGGT
2861092 C-TTGTTGTTTGTCAAA
1 CTTTGTTGTTTGTCAAA
2861108 TTCGGTGGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 13 0.37
25 1 0.03
26 4 0.11
27 17 0.49
ACGTcount: A:0.22, C:0.09, G:0.19, T:0.49
Consensus pattern (26 bp):
CTTTGTTGTTTGTCAAAAATAGTGGT
Found at i:2863259 original size:68 final size:68
Alignment explanation
Indices: 2863148--2863282 Score: 252
Period size: 68 Copynumber: 2.0 Consensus size: 68
2863138 GAAGTTGGGG
*
2863148 CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGGTGCTTTGGAGGAGGTTTTATTCAACC
1 CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGATGCTTTGGAGGAGGTTTTATTCAACC
2863213 AAA
66 AAA
*
2863216 CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGATGCTTTGGAGGAGTTTTTATTCAACC
1 CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGATGCTTTGGAGGAGGTTTTATTCAACC
2863281 AA
66 AA
2863283 GTTTGTTGAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.25, C:0.07, G:0.30, T:0.38
Consensus pattern (68 bp):
CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGATGCTTTGGAGGAGGTTTTATTCAACC
AAA
Found at i:2864831 original size:19 final size:20
Alignment explanation
Indices: 2864795--2864832 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2864785 AAATATATTT
*
2864795 AAAAATAAAAGATTTATATA
1 AAAAATAAAAGATATATATA
*
2864815 AAAAAT-AAAGGTATATAT
1 AAAAATAAAAGATATATAT
2864833 GATAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAAATAAAAGATATATATA
Found at i:2867125 original size:20 final size:21
Alignment explanation
Indices: 2867087--2867125 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2867077 TATTTGTATT
*
2867087 TAATTTTTATATGTCATTATA
1 TAATTTTTATATGTAATTATA
*
2867108 TAATTTTTATCTG-AATTA
1 TAATTTTTATATGTAATTA
2867126 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
TAATTTTTATATGTAATTATA
Found at i:2867509 original size:22 final size:22
Alignment explanation
Indices: 2867474--2867518 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2867464 TAAATAATAT
* * *
2867474 TTTTTATTATTTTTTTATTTTA
1 TTTTTAATAATTTTATATTTTA
2867496 TTTTTAATAATTTTATATTTTA
1 TTTTTAATAATTTTATATTTTA
2867518 T
1 T
2867519 AATATATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTAATAATTTTATATTTTA
Found at i:2867510 original size:15 final size:15
Alignment explanation
Indices: 2867475--2867521 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2867465 AAATAATATT
* *
2867475 TTTTATTATTTTTTTA
1 TTTTA-TATTTTATAA
2867491 TTTTAT-TTTTAATAA
1 TTTTATATTTT-ATAA
2867506 TTTTATATTTTATAA
1 TTTTATATTTTATAA
2867521 T
1 T
2867522 ATATAATGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTATATTTTATAA
Found at i:2867790 original size:54 final size:54
Alignment explanation
Indices: 2867646--2867808 Score: 145
Period size: 54 Copynumber: 3.0 Consensus size: 54
2867636 GGTGATATTC
* * * * * *
2867646 CAAACCCTAGAACACTTCCAACCCAAAGTTAATCACA-GCCCCGTGGATAACTTTC
1 CAAACCATAGAACACTT-CAACACAAAGTCAATCA-ATGCCCCGTGGGTGACTTTT
* * * *
2867701 CAAACCGTA-AGGCATTTCAACACAAAGTGC-GTCAATGCCCCGTGGGTGACTTTT
1 CAAACCATAGA-ACACTTCAACACAAAGT-CAATCAATGCCCCGTGGGTGACTTTT
* * *
2867755 CAAACCATAGAACACTTCAACACAAAATCAATCAATGTCTCGTGGGTGA-TTTT
1 CAAACCATAGAACACTTCAACACAAAGTCAATCAATGCCCCGTGGGTGACTTTT
2867808 C
1 C
2867809 CATGCAAACA
Statistics
Matches: 87, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
53 7 0.08
54 67 0.77
55 13 0.15
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (54 bp):
CAAACCATAGAACACTTCAACACAAAGTCAATCAATGCCCCGTGGGTGACTTTT
Found at i:2868158 original size:19 final size:19
Alignment explanation
Indices: 2868123--2868163 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2868113 TGCTTTTTTT
*
2868123 TTTATTTTTTTATTTTTAA
1 TTTATTTTTTTAATTTTAA
2868142 TTTA-TTTTTTACATTTTAA
1 TTTATTTTTTTA-ATTTTAA
2868161 TTT
1 TTT
2868164 CTCGCTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTATTTTTTTAATTTTAA
Found at i:2881994 original size:19 final size:19
Alignment explanation
Indices: 2881970--2882025 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
2881960 GCTGCCCACC
2881970 CCCCCCCCCCCCCA-TACCA
1 CCCCCCCCCCCCCACT-CCA
*
2881989 CCCCCCCCCCACCACTCCA
1 CCCCCCCCCCCCCACTCCA
2882008 CCCACCCCCCCCCC-CTCC
1 CCC-CCCCCCCCCCACTCC
2882026 CCGCCCCCGC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 23 0.70
20 10 0.30
ACGTcount: A:0.12, C:0.82, G:0.00, T:0.05
Consensus pattern (19 bp):
CCCCCCCCCCCCCACTCCA
Found at i:2891190 original size:15 final size:17
Alignment explanation
Indices: 2891172--2891203 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2891162 TCTTTTTTTT
2891172 CTTTTCT-TTTT-CCTC
1 CTTTTCTCTTTTGCCTC
2891187 CTTTTCTCTTTTGCCTC
1 CTTTTCTCTTTTGCCTC
2891204 TCTACCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 4 0.27
17 4 0.27
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.62
Consensus pattern (17 bp):
CTTTTCTCTTTTGCCTC
Found at i:2891832 original size:21 final size:21
Alignment explanation
Indices: 2891806--2891845 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2891796 TTGCTTTTTT
**
2891806 TTTTTTTTTATTTTAATTTAA
1 TTTTTTTACATTTTAATTTAA
2891827 TTTTTTTACATTTTAATTT
1 TTTTTTTACATTTTAATTT
2891846 CTGCGCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTTTACATTTTAATTTAA
Found at i:2895588 original size:18 final size:19
Alignment explanation
Indices: 2895550--2895589 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
2895540 GGTATTTGCA
*
2895550 AAGAAAGATGGATCTCTAC
1 AAGAAAGATGGATCGCTAC
*
2895569 AAGAAAGAT-GTTCGCTAC
1 AAGAAAGATGGATCGCTAC
2895587 AAG
1 AAG
2895590 GCAAGATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (19 bp):
AAGAAAGATGGATCGCTAC
Found at i:2902104 original size:15 final size:17
Alignment explanation
Indices: 2902079--2902111 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2902069 TAGCTTTATG
2902079 AGAAGGCAAATAC-ACC
1 AGAAGGCAAATACGACC
2902095 AGAA-GCAAATACGACC
1 AGAAGGCAAATACGACC
2902111 A
1 A
2902112 TTGTGTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.24, G:0.18, T:0.06
Consensus pattern (17 bp):
AGAAGGCAAATACGACC
Found at i:2975496 original size:67 final size:68
Alignment explanation
Indices: 2975386--2975519 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 68
2975376 GAAGTTGGGG
*
2975386 CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGGTGCTTTGGAGGAG-TTTTATTCAACC
1 CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGATGCTTTGGAGGAGTTTTTATTCAACC
2975450 AAA
66 AAA
2975453 CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGATGCTTTGGAGGAGTTTTTATTCAACC
1 CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGATGCTTTGGAGGAGTTTTTATTCAACC
2975518 AA
66 AA
2975520 GTTTGTTGAT
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
67 51 0.78
68 14 0.22
ACGTcount: A:0.25, C:0.07, G:0.29, T:0.38
Consensus pattern (68 bp):
CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGATGCTTTGGAGGAGTTTTTATTCAACC
AAA
Found at i:2977072 original size:19 final size:20
Alignment explanation
Indices: 2977036--2977073 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2977026 AAATATATTT
*
2977036 AAAAATAAAAGATTTATATA
1 AAAAATAAAAGATATATATA
*
2977056 AAAAAT-AAAGGTATATAT
1 AAAAATAAAAGATATATAT
2977074 GATAATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (20 bp):
AAAAATAAAAGATATATATA
Found at i:2977663 original size:13 final size:13
Alignment explanation
Indices: 2977647--2977671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2977637 TAACAGTGTA
2977647 AATAAAAATAATG
1 AATAAAAATAATG
2977660 AATAAAAATAAT
1 AATAAAAATAAT
2977672 AGTAGTAAAT
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:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (13 bp):
AATAAAAATAATG
Found at i:2979306 original size:22 final size:22
Alignment explanation
Indices: 2979272--2979323 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
2979262 ATTTATATAA
*
2979272 AATATGTTCACCTAACACACCT
1 AATATATTCACCTAACACACCT
* *
2979294 AATATATTTACCTAACACACTT
1 AATATATTCACCTAACACACCT
2979316 AATATATT
1 AATATATT
2979324 ACTCACCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.02, T:0.35
Consensus pattern (22 bp):
AATATATTCACCTAACACACCT
Found at i:2984066 original size:10 final size:11
Alignment explanation
Indices: 2984031--2984064 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
2984021 ATGATATAAT
2984031 ATAATATAAAAA
1 ATAAT-TAAAAA
2984043 ATAATTAAAAA
1 ATAATTAAAAA
2984054 ATAATTAAAAA
1 ATAATTAAAAA
2984065 TATGATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 17 0.77
12 5 0.23
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
ATAATTAAAAA
Found at i:2986747 original size:30 final size:30
Alignment explanation
Indices: 2986711--2986771 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
2986701 TGTTCCTCAA
2986711 GAAAAGTACAGAGGAAAAAATTAAACATAC
1 GAAAAGTACAGAGGAAAAAATTAAACATAC
*
2986741 GAAAAGTACAGAGGAAAAAATTAAGCATAC
1 GAAAAGTACAGAGGAAAAAATTAAACATAC
2986771 G
1 G
2986772 CCATGATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.10, G:0.20, T:0.13
Consensus pattern (30 bp):
GAAAAGTACAGAGGAAAAAATTAAACATAC
Found at i:2993552 original size:14 final size:14
Alignment explanation
Indices: 2993529--2993558 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2993519 AATAATTAAA
*
2993529 AAAATTAAAATTAT
1 AAAATAAAAATTAT
2993543 AAAATAAAAATTAT
1 AAAATAAAAATTAT
2993557 AA
1 AA
2993559 CGTATTAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATAAAAATTAT
Found at i:2994767 original size:38 final size:38
Alignment explanation
Indices: 2994694--2994767 Score: 87
Period size: 38 Copynumber: 1.9 Consensus size: 38
2994684 TAAATTAAAC
** *
2994694 AATAAATAATGACAACAAAAAAAGATATTATCACAATA
1 AATAAATAATGACAACAAAAAAAGATAAAACCACAATA
* *
2994732 AATAAATAATGACAATAAGAAAAA-CTAAAACCACAA
1 AATAAATAATGACAACAA-AAAAAGATAAAACCACAA
2994768 ATTAACAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 25 0.83
39 5 0.17
ACGTcount: A:0.65, C:0.12, G:0.05, T:0.18
Consensus pattern (38 bp):
AATAAATAATGACAACAAAAAAAGATAAAACCACAATA
Found at i:2996660 original size:53 final size:53
Alignment explanation
Indices: 2996586--2996709 Score: 144
Period size: 53 Copynumber: 2.3 Consensus size: 53
2996576 TAGCCACAGT
* * * * * *
2996586 CCCCGTGGATGACTTTCCAAACCATA-AGACATTTCAACACGAAGTGAGTCAATG
1 CCCCGTGG-TGACTTTTCAAACCATAGA-ACACTTCAACACAAAATCAATCAATG
2996640 CCCCGTGGTGACTTTTCAAACCATAGAACACTTCAACACAAAATCAATCAATG
1 CCCCGTGGTGACTTTTCAAACCATAGAACACTTCAACACAAAATCAATCAATG
*
2996693 TCCCGTGGGTGA-TTTTC
1 CCCCGT-GGTGACTTTTC
2996710 CATGCAAACA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
53 47 0.77
54 14 0.23
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (53 bp):
CCCCGTGGTGACTTTTCAAACCATAGAACACTTCAACACAAAATCAATCAATG
Found at i:2997785 original size:14 final size:11
Alignment explanation
Indices: 2997732--2997767 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2997722 AATATGATAT
2997732 AATATAATATAA
1 AATATAAT-TAA
*
2997744 AAAATAATTAA
1 AATATAATTAA
2997755 AATATAATTAA
1 AATATAATTAA
2997766 AA
1 AA
2997768 ATATGATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATATAATTAA
Found at i:3008196 original size:24 final size:26
Alignment explanation
Indices: 3008130--3008196 Score: 77
Period size: 27 Copynumber: 2.7 Consensus size: 26
3008120 AAAAACCACC
3008130 CTTTG-TGTTTGTCAAAAATGGTGGTT
1 CTTTGTTGTTTGTCAAAAATGGTGG-T
* * *
3008156 CTTTTTTATTTGTCAAAAATTGTGG-
1 CTTTGTTGTTTGTCAAAAATGGTGGT
3008181 C-TTGTTGTTTGTCAAA
1 CTTTGTTGTTTGTCAAA
3008197 TTTGGTGGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 13 0.37
25 1 0.03
26 4 0.11
27 17 0.49
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.49
Consensus pattern (26 bp):
CTTTGTTGTTTGTCAAAAATGGTGGT
Found at i:3010298 original size:69 final size:68
Alignment explanation
Indices: 3010185--3010320 Score: 245
Period size: 69 Copynumber: 2.0 Consensus size: 68
3010175 GAAGTTGGGG
* *
3010185 CTGATTTGATGGTTTTGAAGGAAATGTGGTTGGAATTGGTGCTTTGGAGGAGTTTTTAATTCAAC
1 CTGATTTGATGCTTTTGAAGGAAATGTGGTTGGAATTGGGGCTTTGGAGGAGTTTTT-ATTCAAC
3010250 CAAA
65 CAAA
3010254 CTGATTTGATGCTTTTGAAGGAAATGTGGTTGGAATTGGGGCTTTGGAGGAGTTTTTATTCAACC
1 CTGATTTGATGCTTTTGAAGGAAATGTGGTTGGAATTGGGGCTTTGGAGGAGTTTTTATTCAACC
3010319 AA
66 AA
3010321 GTTTGTTGAT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
68 10 0.15
69 55 0.85
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.38
Consensus pattern (68 bp):
CTGATTTGATGCTTTTGAAGGAAATGTGGTTGGAATTGGGGCTTTGGAGGAGTTTTTATTCAACC
AAA
Found at i:3011175 original size:2 final size:2
Alignment explanation
Indices: 3011168--3011202 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3011158 GCTTGAGTTT
3011168 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3011203 TCATGTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:3011597 original size:6 final size:6
Alignment explanation
Indices: 3011586--3011610 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3011576 AATTAAACTC
3011586 ATATTA ATATTA ATATTA ATATTA A
1 ATATTA ATATTA ATATTA ATATTA A
3011611 CGAAATTCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:3014441 original size:54 final size:54
Alignment explanation
Indices: 3014383--3014500 Score: 137
Period size: 54 Copynumber: 2.2 Consensus size: 54
3014373 GCCCCGTAGA
* * * * * * *
3014383 TGACTTTCCAAACCGTAAAACATTTCAATACGAAGTGAGTCAATGTCCCATGGG
1 TGACTTTCCAAACCATAAAACACTTCAACACAAAATCAATCAATGTCCCATGGG
* * *
3014437 TGACTTTTCAAACCATAGAACACTTCAACACAAAATCAATCAATGTCCCGTGGG
1 TGACTTTCCAAACCATAAAACACTTCAACACAAAATCAATCAATGTCCCATGGG
*
3014491 TGATTTTCCA
1 TGACTTTCCA
3014501 TACAAACAAC
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (54 bp):
TGACTTTCCAAACCATAAAACACTTCAACACAAAATCAATCAATGTCCCATGGG
Found at i:3014978 original size:23 final size:22
Alignment explanation
Indices: 3014952--3015013 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
3014942 GATACATATC
*
3014952 AATAAAAAATTATATTTTAATTT
1 AATAAAAAA-TATATTTTAAATT
3014975 AATAATAATAA-ATATTTTAAATT
1 AATAA-AA-AATATATTTTAAATT
3014998 -ATAAAAAATAT-TTTTA
1 AATAAAAAATATATTTTA
3015014 TTAAAATTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
20 7 0.20
21 4 0.11
22 4 0.11
23 16 0.46
24 2 0.06
25 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATAAAAAATATATTTTAAATT
Found at i:3015236 original size:13 final size:14
Alignment explanation
Indices: 3015220--3015256 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3015210 TTATTAAAAT
*
3015220 AATATTATT-TTAA
1 AATATTATTATCAA
3015233 AATA-TATTATCAA
1 AATATTATTATCAA
3015246 AATATTATTAT
1 AATATTATTAT
3015257 TTTTGTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 4 0.19
13 11 0.52
14 6 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (14 bp):
AATATTATTATCAA
Found at i:3015581 original size:19 final size:19
Alignment explanation
Indices: 3015541--3015586 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
3015531 ATAAATATTT
*
3015541 TAAATAATAAATAATATCA
1 TAAATAATAAATAATATAA
*
3015560 TAATTAATAAATTAA-ATAA
1 TAAATAATAAA-TAATATAA
3015579 TAAATAAT
1 TAAATAAT
3015587 GACAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATAATAAATAATATAA
Found at i:3015810 original size:55 final size:55
Alignment explanation
Indices: 3015702--3015815 Score: 142
Period size: 55 Copynumber: 2.1 Consensus size: 55
3015692 TAGGTAATTA
*
3015702 TCCAAACCCTAAAACACTTCCAACACAAAGTCAGTCACAGCCCCACGGTTGATTT
1 TCCAAACCCTAAAACACTTCCAACACAAAGTCAGTCACAGCCCCACGGCTGATTT
* * * **
3015757 TCCAAACCCATAAAATACTT-CTACACAAAGTCAGTCA-ATGCTCCGTGGCTGATTT
1 TCCAAACCC-TAAAACACTTCCAACACAAAGTCAGTCACA-GCCCCACGGCTGATTT
3015812 TCCA
1 TCCA
3015816 CACAAACAAC
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
54 1 0.02
55 41 0.80
56 9 0.18
ACGTcount: A:0.33, C:0.32, G:0.11, T:0.24
Consensus pattern (55 bp):
TCCAAACCCTAAAACACTTCCAACACAAAGTCAGTCACAGCCCCACGGCTGATTT
Found at i:3016981 original size:15 final size:15
Alignment explanation
Indices: 3016961--3016989 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3016951 CCATCTTGAT
3016961 TTAATAATAAATCAA
1 TTAATAATAAATCAA
3016976 TTAATAATAAATCA
1 TTAATAATAAATCA
3016990 TAAGATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAATAATAAATCAA
Found at i:3022604 original size:16 final size:16
Alignment explanation
Indices: 3022585--3022642 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
3022575 TAATTACTCG
*
3022585 TAAATTTAATGAATTT
1 TAAATATAATGAATTT
* * *
3022601 TAAATAAAATTACTTT
1 TAAATATAATGAATTT
* * *
3022617 TAAATTTGATGAATAT
1 TAAATATAATGAATTT
3022633 TAAATATAAT
1 TAAATATAAT
3022643 TACTCGTAAA
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (16 bp):
TAAATATAATGAATTT
Found at i:3022621 original size:32 final size:31
Alignment explanation
Indices: 3022554--3022655 Score: 134
Period size: 32 Copynumber: 3.3 Consensus size: 31
3022544 GATATTGATT
*
3022554 GTAAATTTAATGAA-TTAGATATAATTACTC
1 GTAAATTTAATGAATTTAAATATAATTACTC
* *
3022584 GTAAATTTAATGAATTTTAAATAAAATTACTT
1 GTAAATTTAATGAA-TTTAAATATAATTACTC
* *
3022616 TTAAATTTGATGAATATTAAATATAATTACTC
1 GTAAATTTAATGAAT-TTAAATATAATTACTC
3022648 GTAAATTT
1 GTAAATTT
3022656 TGTTATTTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
30 14 0.23
31 1 0.02
32 46 0.75
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (31 bp):
GTAAATTTAATGAATTTAAATATAATTACTC
Found at i:3026157 original size:14 final size:14
Alignment explanation
Indices: 3026134--3026163 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3026124 TTTTTAATAT
*
3026134 ATATTTAAATATAA
1 ATATTAAAATATAA
3026148 ATATTAAAATATAA
1 ATATTAAAATATAA
3026162 AT
1 AT
3026164 TTTTTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATTAAAATATAA
Found at i:3026165 original size:26 final size:26
Alignment explanation
Indices: 3026129--3026182 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
3026119 ATTTATTTTT
*
3026129 AATATATATTTAAATATAAATAT-TAA
1 AATATAAATTT-AATATAAATATATAA
**
3026155 AATATAAATTTTTTATAAATATATAA
1 AATATAAATTTAATATAAATATATAA
3026181 AA
1 AA
3026183 AATTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
AATATAAATTTAATATAAATATATAA
Found at i:3028221 original size:21 final size:21
Alignment explanation
Indices: 3028181--3028244 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 21
3028171 TCGATATATT
*
3028181 TAAAA-AATTAAAATTTTAATA
1 TAAAATAATTAAAA-TATAATA
3028202 TAAAATAATTAAAATATAATA
1 TAAAATAATTAAAATATAATA
3028223 TAAAAATAATATAAATATATAA
1 T-AAAATAAT-TAAA-ATATAA
3028245 ATATTTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
21 12 0.32
22 16 0.42
23 4 0.11
24 6 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAATAATTAAAATATAATA
Found at i:3028230 original size:13 final size:12
Alignment explanation
Indices: 3028197--3028244 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
3028187 ATTAAAATTT
3028197 TAATAT-AAA-A
1 TAATATAAAATA
3028207 TAAT-TAAAATA
1 TAATATAAAATA
3028218 TAATATAAAA-A
1 TAATATAAAATA
3028229 TAATATAAATATA
1 TAATATAAA-ATA
3028242 TAA
1 TAA
3028245 ATATTTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
9 1 0.03
10 7 0.21
11 15 0.45
12 6 0.18
13 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAATATAAAATA
Found at i:3028266 original size:25 final size:25
Alignment explanation
Indices: 3028234--3028300 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
3028224 AAAAATAATA
3028234 TAAA-TATATAAATATTTTAAAATT
1 TAAATTATATAAATATTTTAAAATT
* *
3028258 TAAATTATATAAATTATTTTTATATT
1 TAAATTATATAAA-TATTTTAAAATT
*
3028284 AAAATTTATATAAATAT
1 TAAA-TTATATAAATAT
3028301 AAAATATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 4 0.11
25 8 0.22
26 16 0.43
27 9 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAATTATATAAATATTTTAAAATT
Found at i:3028274 original size:9 final size:8
Alignment explanation
Indices: 3028198--3028271 Score: 50
Period size: 8 Copynumber: 9.4 Consensus size: 8
3028188 TTAAAATTTT
3028198 AATATA-A
1 AATATATA
3028205 AATA-ATTA
1 AATATA-TA
3028213 AA-ATAT-
1 AATATATA
*
3028219 AATATAAA
1 AATATATA
3028227 AATAATATA
1 AAT-ATATA
3028236 AATATATA
1 AATATATA
*
3028244 AATATTTTA
1 AATA-TATA
*
3028253 AA-ATTTA
1 AATATATA
3028260 AATTATATA
1 AA-TATATA
3028269 AAT
1 AAT
3028272 TATTTTTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
6 3 0.06
7 15 0.28
8 18 0.33
9 18 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
AATATATA
Found at i:3028278 original size:27 final size:25
Alignment explanation
Indices: 3028234--3028298 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 25
3028224 AAAAATAATA
3028234 TAAA-TATATAAA-TATTTTAAAATT
1 TAAATTATATAAATTATTTT-AAATT
*
3028258 TAAATTATATAAATTATTTTTATATT
1 TAAATTATATAAATTA-TTTTAAATT
*
3028284 AAAATTTATATAAAT
1 TAAA-TTATATAAAT
3028299 ATAAAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 4 0.11
25 8 0.23
26 9 0.26
27 14 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAATTATATAAATTATTTTAAATT
Found at i:3028321 original size:15 final size:15
Alignment explanation
Indices: 3028185--3028322 Score: 54
Period size: 17 Copynumber: 8.9 Consensus size: 15
3028175 TATATTTAAA
3028185 AAAT-TAAAAT-TTT
1 AAATATAAAATATTT
*
3028198 -AATATAAAATAATT
1 AAATATAAAATATTT
* **
3028212 AAA-ATATAATATAA
1 AAATATAAAATATTT
*
3028226 AAATAATATAAATATAT
1 AAAT-ATA-AAATATTT
*
3028243 AAATATTTTAAA-ATTT
1 AAATA--TAAAATATTT
3028259 AAATTATATAAATTATTT
1 AAA-TATA-AAA-TATTT
** *
3028277 TTATATTAAAATTTATAT
1 AAATA-TAAAA--TATTT
3028295 AAATATAAAATATTT
1 AAATATAAAATATTT
3028310 AAA-ATAAGAATAT
1 AAATATAA-AATAT
3028323 AATTTTATAA
Statistics
Matches: 94, Mismatches: 16, Indels: 28
0.68 0.12 0.20
Matches are distributed among these distances:
12 3 0.03
13 6 0.06
14 16 0.17
15 15 0.16
16 13 0.14
17 25 0.27
18 16 0.17
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (15 bp):
AAATATAAAATATTT
Found at i:3030221 original size:70 final size:70
Alignment explanation
Indices: 3030129--3030265 Score: 256
Period size: 70 Copynumber: 2.0 Consensus size: 70
3030119 AATCTGCATT
* *
3030129 TTTTTTTTTATAAAAAATTCTTTAACTTTTTTTGATATATTTAAGATGATTTTAGCATAGAACTT
1 TTTTTTTTAATAAAAAATTCTTTAACTTATTTTGATATATTTAAGATGATTTTAGCATAGAACTT
3030194 TTGTA
66 TTGTA
3030199 TTTTTTTTAATAAAAAATTCTTTAACTTATTTTGATATATTTAAGATGATTTTAGCATAGAACTT
1 TTTTTTTTAATAAAAAATTCTTTAACTTATTTTGATATATTTAAGATGATTTTAGCATAGAACTT
3030264 TT
66 TT
3030266 ACAGATTTGG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.53
Consensus pattern (70 bp):
TTTTTTTTAATAAAAAATTCTTTAACTTATTTTGATATATTTAAGATGATTTTAGCATAGAACTT
TTGTA
Found at i:3032164 original size:2 final size:2
Alignment explanation
Indices: 3032157--3032190 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3032147 CCTGTAACGA
3032157 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3032191 TTTTATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3035290 original size:1 final size:1
Alignment explanation
Indices: 3035284--3035313 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3035274 TCAAGATCTG
3035284 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3035314 CTTAATGTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3040592 original size:2 final size:2
Alignment explanation
Indices: 3040585--3040610 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3040575 TCTTGTTTGA
3040585 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
3040611 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3040896 original size:19 final size:19
Alignment explanation
Indices: 3040872--3040931 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 19
3040862 TATATAAATA
3040872 TTAATATAAAATAATTATT
1 TTAATATAAAATAATTATT
**
3040891 TT-A-ATAATTTAATATATT
1 TTAATATAAAATAAT-TATT
*
3040909 TTAAATAATAAAATAAGTATT
1 TT-AAT-ATAAAATAATTATT
3040930 TT
1 TT
3040932 TAATTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
17 8 0.26
18 7 0.23
19 2 0.06
20 1 0.03
21 6 0.19
22 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAATATAAAATAATTATT
Found at i:3040910 original size:18 final size:18
Alignment explanation
Indices: 3040883--3040917 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3040873 TAATATAAAA
3040883 TAATTATTTT-AATAATT
1 TAATTATTTTAAATAATT
3040900 TAATATATTTTAAATAAT
1 TAAT-TATTTTAAATAAT
3040918 AAAATAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 6 0.38
19 6 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TAATTATTTTAAATAATT
Found at i:3041854 original size:20 final size:21
Alignment explanation
Indices: 3041829--3041876 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
3041819 CTATTTATAA
3041829 ATATTAAAATATTTAT-TTTT
1 ATATTAAAATATTTATATTTT
*
3041849 ATATT--ATTATTTATATTTT
1 ATATTAAAATATTTATATTTT
3041868 ATAATTAAA
1 AT-ATTAAA
3041877 TTTAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
20 8 0.35
22 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTAAAATATTTATATTTT
Found at i:3041879 original size:19 final size:19
Alignment explanation
Indices: 3041839--3041890 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
3041829 ATATTAAAAT
*
3041839 ATTTAT-TTTTATATTATT
1 ATTTATATTTTATATTATA
3041857 ATTTATATTTTATAATTA-A
1 ATTTATATTTTAT-ATTATA
3041876 ATTTAAATATTTTAT
1 ATTT--ATATTTTAT
3041891 TGATTAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.21
19 10 0.34
20 4 0.14
21 9 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTATATTTTATATTATA
Found at i:3042479 original size:12 final size:11
Alignment explanation
Indices: 3042458--3042484 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3042448 CATTTTCATT
3042458 AAAAAGAAAAA
1 AAAAAGAAAAA
3042469 AAAAAGAAAAA
1 AAAAAGAAAAA
3042480 AAAAA
1 AAAAA
3042485 CGTTATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:3044569 original size:22 final size:22
Alignment explanation
Indices: 3044541--3044582 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
3044531 TGACTCATCC
3044541 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
3044563 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
3044583 AATTAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:3054377 original size:16 final size:17
Alignment explanation
Indices: 3054356--3054393 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3054346 CTCTAACATA
*
3054356 TAAAATATTTTATTA-T
1 TAAAATATTTTAATATT
*
3054372 TAAAATTTTTTAATATT
1 TAAAATATTTTAATATT
3054389 TAAAA
1 TAAAA
3054394 ATTAGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAAATATTTTAATATT
Found at i:3058752 original size:39 final size:39
Alignment explanation
Indices: 3058675--3058753 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
3058665 CTTCAGCATT
* * *
3058675 CAACTCACTTGCAGAAATACTTGAATCTGCAAATAACTC
1 CAACTCACTTCCAAAAATACTTGAATCTGCAAAGAACTC
* *
3058714 CAACTCACTTCCAAAAATACTTGAATCTGCGAGGAACTC
1 CAACTCACTTCCAAAAATACTTGAATCTGCAAAGAACTC
3058753 C
1 C
3058754 TGAACAATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (39 bp):
CAACTCACTTCCAAAAATACTTGAATCTGCAAAGAACTC
Found at i:3067798 original size:9 final size:9
Alignment explanation
Indices: 3067786--3067810 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3067776 TTTAATATAT
3067786 TTAAAAAAA
1 TTAAAAAAA
3067795 TTAAAAAAA
1 TTAAAAAAA
3067804 TTAAAAA
1 TTAAAAA
3067811 TTATAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:3067821 original size:17 final size:16
Alignment explanation
Indices: 3067790--3067824 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
3067780 ATATATTTAA
3067790 AAAAATTAAAAAAATT
1 AAAAATTAAAAAAATT
*
3067806 AAAAATTATAATAAATT
1 AAAAATTA-AAAAAATT
3067823 AA
1 AA
3067825 TATTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATTAAAAAAATT
Found at i:3068333 original size:16 final size:16
Alignment explanation
Indices: 3068312--3068347 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
3068302 ATCAGTTGGA
3068312 TCAATTTTAGATTAAT
1 TCAATTTTAGATTAAT
3068328 TCAATTTTAGATTAAT
1 TCAATTTTAGATTAAT
3068344 TCAA
1 TCAA
3068348 ATATTACCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (16 bp):
TCAATTTTAGATTAAT
Found at i:3068650 original size:2 final size:2
Alignment explanation
Indices: 3068643--3068679 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3068633 TTAACTAAGA
3068643 AT AT AT AT 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 AT AT AT AT A
3068680 GAATAATCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3069475 original size:21 final size:22
Alignment explanation
Indices: 3069451--3069491 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3069441 TATTTTTATT
* *
3069451 TAAAT-TTAATTATAAAATATA
1 TAAATATTAATAAAAAAATATA
3069472 TAAATATTAATAAAAAAATA
1 TAAATATTAATAAAAAAATA
3069492 ATTTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATATTAATAAAAAAATATA
Found at i:3070171 original size:14 final size:15
Alignment explanation
Indices: 3070154--3070183 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3070144 TAATTAAATT
3070154 AAAT-TTACATTTTA
1 AAATATTACATTTTA
3070168 AAATATTACATTTTA
1 AAATATTACATTTTA
3070183 A
1 A
3070184 GAGGATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATATTACATTTTA
Found at i:3076827 original size:31 final size:30
Alignment explanation
Indices: 3076791--3076949 Score: 111
Period size: 31 Copynumber: 4.9 Consensus size: 30
3076781 TTTTAAACCA
*
3076791 TGCCACCGATTAAGAATAGTAGTTTTTATCG
1 TGCCACCGA-TAAGAATAGTAGTTTTTACCG
* *
3076822 TGCCACCGGATAAGAATAATGGTTTTTACCG
1 TGCCACC-GATAAGAATAGTAGTTTTTACCG
* * * * *
3076853 TGTCATCGGATAAGAATAGTGATTTTTTGCCT
1 TGCCA-CCGATAAGAATAGT-AGTTTTTACCG
*
3076885 TGCCACCGACTAAGAATAGTGATTTTTGTTCCGACCCG
1 TGCCACCGA-TAAGAATAGT-A-GTTT-TT---A-CCG
* *
3076923 TGTCACCGGTAAGAATAGTAGTTTTTA
1 TGCCACCGATAAGAATAGTAGTTTTTA
3076950 TTCTGAACCG
Statistics
Matches: 101, Mismatches: 17, Indels: 20
0.73 0.12 0.14
Matches are distributed among these distances:
31 44 0.44
32 26 0.26
33 4 0.04
34 4 0.04
35 3 0.03
36 1 0.01
37 10 0.10
38 9 0.09
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (30 bp):
TGCCACCGATAAGAATAGTAGTTTTTACCG
Found at i:3076985 original size:38 final size:38
Alignment explanation
Indices: 3076885--3076995 Score: 129
Period size: 37 Copynumber: 3.0 Consensus size: 38
3076875 TTTTTTGCCT
* * *
3076885 TGCCACCGACTAAGAATAGT-GATTTTTGTTCCGACCCG
1 TGCCACCGAATAAGAATAGTAG-TTTTTGTTCTGAACCG
* * *
3076923 TGTCACCG-GTAAGAATAGTAGTTTTTATTCTGAACCG
1 TGCCACCGAATAAGAATAGTAGTTTTTGTTCTGAACCG
*
3076960 TGCCACCGAATTAGAATAGTAGTTTTTGTTCT-AACC
1 TGCCACCGAATAAGAATAGTAGTTTTTGTTCTGAACC
3076996 TATGCCGCAG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
37 34 0.55
38 28 0.45
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (38 bp):
TGCCACCGAATAAGAATAGTAGTTTTTGTTCTGAACCG
Found at i:3081026 original size:16 final size:17
Alignment explanation
Indices: 3081002--3081035 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3080992 CAAAGTTGGC
*
3081002 TAAATAAAT-CTGAAAA
1 TAAAAAAATCCTGAAAA
3081018 TAAAAAAATCCTGAAAA
1 TAAAAAAATCCTGAAAA
3081035 T
1 T
3081036 TTTAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.62, C:0.09, G:0.06, T:0.24
Consensus pattern (17 bp):
TAAAAAAATCCTGAAAA
Found at i:3081570 original size:15 final size:15
Alignment explanation
Indices: 3081551--3081585 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3081541 AAATTATGAC
3081551 ATAATAAATATATTTT
1 ATAATAAAT-TATTTT
3081567 -TAATAAATTATTTT
1 ATAATAAATTATTTT
3081581 ATAAT
1 ATAAT
3081586 CGTAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAATAAATTATTTT
Found at i:3082479 original size:31 final size:31
Alignment explanation
Indices: 3082433--3082574 Score: 122
Period size: 31 Copynumber: 4.6 Consensus size: 31
3082423 TACCACCAGT
* * * **
3082433 TAAGAATAGTAGTTTTTGCCGTGCCATCGGT
1 TAAGAATAATGGTTTTTGCCGTGCCACCGAA
* * *
3082464 TAAGGATAATGGTTTTTACCATGCCACCGAA
1 TAAGAATAATGGTTTTTGCCGTGCCACCGAA
* * * *
3082495 TAAGAAAAATAGTTTTTGTCGTGCCACCGGA
1 TAAGAATAATGGTTTTTGCCGTGCCACCGAA
* * * * *
3082526 TAGGAATAGTGGCTTTTACCGTGCCATCGAA
1 TAAGAATAATGGTTTTTGCCGTGCCACCGAA
*
3082557 TAAGAATAGTGGTTTTTG
1 TAAGAATAATGGTTTTTG
3082575 TTCCAACCCA
Statistics
Matches: 84, Mismatches: 27, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 84 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (31 bp):
TAAGAATAATGGTTTTTGCCGTGCCACCGAA
Found at i:3082572 original size:62 final size:62
Alignment explanation
Indices: 3082433--3082575 Score: 180
Period size: 62 Copynumber: 2.3 Consensus size: 62
3082423 TACCACCAGT
* * * *
3082433 TAAGAATAGTAGTTTTTGCCGTGCCATCGGTTAAGGATAATGGTTTTTACCATGCCACCGAA
1 TAAGAATAGTAGTTTTTGTCGTGCCACCGGATAAGGATAATGGCTTTTACCATGCCACCGAA
* * * * *
3082495 TAAGAAAAATAGTTTTTGTCGTGCCACCGGAT-AGGAATAGTGGCTTTTACCGTGCCATCGAA
1 TAAGAATAGTAGTTTTTGTCGTGCCACCGGATAAGG-ATAATGGCTTTTACCATGCCACCGAA
*
3082557 TAAGAATAGTGGTTTTTGT
1 TAAGAATAGTAGTTTTTGT
3082576 TCCAACCCAT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
61 3 0.04
62 65 0.96
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (62 bp):
TAAGAATAGTAGTTTTTGTCGTGCCACCGGATAAGGATAATGGCTTTTACCATGCCACCGAA
Found at i:3082629 original size:37 final size:37
Alignment explanation
Indices: 3082543--3082657 Score: 135
Period size: 37 Copynumber: 3.1 Consensus size: 37
3082533 AGTGGCTTTT
* *
3082543 ACCGTGCCATCGAATAAGAATAGTGGTTTTTGTTCCA
1 ACCGTGCCATCGAATAAGAATAGTAGTTTTTGTTCTA
* *
3082580 ACCCATGTCATCG-ATAAGAATAGTAGTTTTTGTTCTGA
1 A-CCGTGCCATCGAATAAGAATAGTAGTTTTTGTTCT-A
* *
3082618 ACCGTGCCATCGAATTAGAATAGTTA-TTTTTATTCTA
1 ACCGTGCCATCGAATAAGAATAG-TAGTTTTTGTTCTA
3082655 ACC
1 ACC
3082658 TATGTCACAG
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
37 35 0.53
38 29 0.44
39 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (37 bp):
ACCGTGCCATCGAATAAGAATAGTAGTTTTTGTTCTA
Found at i:3083197 original size:42 final size:41
Alignment explanation
Indices: 3083126--3083209 Score: 109
Period size: 41 Copynumber: 2.0 Consensus size: 41
3083116 GAAAATAACG
3083126 ATTTTATAAATTGAAAAGTTAAAAACTTTATA-AGTTATAA
1 ATTTTATAAATTGAAAAGTTAAAAACTTTATATAGTTATAA
* *
3083166 ATTTTAATATAATT-AAAATTTAAAATACTTTATATATTTATAA
1 ATTTT-ATA-AATTGAAAAGTTAAAA-ACTTTATATAGTTATAA
3083209 A
1 A
3083210 ATTCATCTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
40 5 0.13
41 13 0.34
42 12 0.32
43 8 0.21
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (41 bp):
ATTTTATAAATTGAAAAGTTAAAAACTTTATATAGTTATAA
Found at i:3084155 original size:16 final size:17
Alignment explanation
Indices: 3084134--3084171 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
3084124 CTCTAACATA
*
3084134 TAAAATATTTTATTA-T
1 TAAAATATTTTAATATT
3084150 TAAAATATTTTAATATT
1 TAAAATATTTTAATATT
3084167 TAAAA
1 TAAAA
3084172 ATTAAATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAAATATTTTAATATT
Found at i:3085360 original size:17 final size:17
Alignment explanation
Indices: 3085317--3085360 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3085307 AGAATAGAAA
3085317 CTAATTAATACCTAATTT
1 CTAATT-ATACCTAATTT
** *
3085335 CTAGCTATACCTTATTT
1 CTAATTATACCTAATTT
3085352 CTAATTATA
1 CTAATTATA
3085361 AGTTACGGAT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.34, C:0.18, G:0.02, T:0.45
Consensus pattern (17 bp):
CTAATTATACCTAATTT
Found at i:3086143 original size:27 final size:27
Alignment explanation
Indices: 3086113--3086191 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
3086103 TAAAAATTAG
* *
3086113 CCACCAAATTTGACAAACAAAAAGGAA
1 CCACCAATTTTGACAAACACAAAGGAA
* * * *
3086140 CCACCATTTTTTACAAATACAAAGTAA
1 CCACCAATTTTGACAAACACAAAGGAA
3086167 CCA-CAATTTTTGACAAACACAAAGG
1 CCACCAA-TTTTGACAAACACAAAGG
3086192 GTGGCTTTTG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
26 2 0.05
27 39 0.95
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.20
Consensus pattern (27 bp):
CCACCAATTTTGACAAACACAAAGGAA
Found at i:3104531 original size:16 final size:19
Alignment explanation
Indices: 3104496--3104542 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
3104486 TAATTTAATT
3104496 TAATATATTTAAAAATATTA
1 TAATATA-TTAAAAATATTA
3104516 -AA-ATATTAAAAA-ATTA
1 TAATATATTAAAAATATTA
3104532 TAATATATTAA
1 TAATATATTAA
3104543 TATTTATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.16
17 9 0.36
18 10 0.40
19 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATATATTAAAAATATTA
Found at i:3104572 original size:14 final size:15
Alignment explanation
Indices: 3104534--3104573 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
3104524 AAAAATTATA
3104534 ATATATTAA-TATTT
1 ATATATTAATTATTT
3104548 ATATATT--TTATTT
1 ATATATTAATTATTT
3104561 ATAT-TTAATTATT
1 ATATATTAATTATT
3104574 AATTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.09
13 9 0.39
14 12 0.52
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATATTAATTATTT
Found at i:3104816 original size:20 final size:18
Alignment explanation
Indices: 3104768--3104817 Score: 50
Period size: 20 Copynumber: 2.8 Consensus size: 18
3104758 GATTGAATTA
3104768 AAATAATTT-T-AATATT
1 AAATAATTTATAAATATT
* *
3104784 AAATAAATAATAAATATAAT
1 AAATAATTTATAAATAT--T
3104804 AAATAATTTATAAA
1 AAATAATTTATAAA
3104818 AATATATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.27
17 1 0.04
18 5 0.19
20 13 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAATAATTTATAAATATT
Found at i:3104912 original size:14 final size:15
Alignment explanation
Indices: 3104893--3104921 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3104883 TATCACTTAT
3104893 AAAAAT-ATTTTTTA
1 AAAAATAATTTTTTA
3104907 AAAAATAATTTTTTA
1 AAAAATAATTTTTTA
3104922 TTTTTGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAATAATTTTTTA
Found at i:3105600 original size:2 final size:2
Alignment explanation
Indices: 3105593--3105626 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3105583 CACTACATAC
3105593 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
3105627 GCATGCACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3106132 original size:58 final size:57
Alignment explanation
Indices: 3106036--3106145 Score: 134
Period size: 58 Copynumber: 1.9 Consensus size: 57
3106026 ATTTATATTT
* * *
3106036 AATAATTTAAAAATATTTTTACTTAAATTTAATTATAAAATATATATATTAATACAAA
1 AATAATTTAAAAATATTTTTACTTAAATTTAATAAT-AAATATAGATAATAATACAAA
* *
3106094 AATAATTTCAAAATTTTTTTA-TT-AATTATGAATAATAAATATAGATAATAAT
1 AATAATTTAAAAATATTTTTACTTAAATT-T-AATAATAAATATAGATAATAAT
3106146 TTTTCTCACA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 4 0.09
57 17 0.38
58 24 0.53
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (57 bp):
AATAATTTAAAAATATTTTTACTTAAATTTAATAATAAATATAGATAATAATACAAA
Found at i:3115175 original size:21 final size:21
Alignment explanation
Indices: 3115134--3115175 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3115124 ATTTCTGATT
*
3115134 ATAAAATTTATTAATAAAAAA
1 ATAAAATTTATCAATAAAAAA
*
3115155 ATAAAATTTATCCAATTAAAA
1 ATAAAATTTAT-CAATAAAAA
3115176 TATTTTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAAATTTATCAATAAAAAA
Found at i:3116616 original size:2 final size:2
Alignment explanation
Indices: 3116609--3116642 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3116599 AGGTGGAAAT
* *
3116609 GA GA GA GA GA TA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3116643 TGCATACATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.03
Consensus pattern (2 bp):
GA
Found at i:3117312 original size:27 final size:27
Alignment explanation
Indices: 3117282--3117337 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
3117272 CAAGTTGCAT
3117282 AAAAATATTTTGTATGATTTAAGTGAA
1 AAAAATATTTTGTATGATTTAAGTGAA
*
3117309 AAAAATATTTTGTATGATTTGAGTGAA
1 AAAAATATTTTGTATGATTTAAGTGAA
3117336 AA
1 AA
3117338 TAATTATTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (27 bp):
AAAAATATTTTGTATGATTTAAGTGAA
Found at i:3118743 original size:30 final size:32
Alignment explanation
Indices: 3118707--3118774 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
3118697 TAAAAAATAA
*
3118707 TTTTAA-TTAAGTTATATTAAAAAT-A-ATTAT
1 TTTTAATTTAA-TAATATTAAAAATAATATTAT
*
3118737 TTTTAATTTAATAATATTAAAGATAATATTAT
1 TTTTAATTTAATAATATTAAAAATAATATTAT
3118769 TTTTAA
1 TTTTAA
3118775 AATTTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 17 0.52
31 5 0.15
32 11 0.33
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (32 bp):
TTTTAATTTAATAATATTAAAAATAATATTAT
Found at i:3118852 original size:22 final size:21
Alignment explanation
Indices: 3118825--3118870 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3118815 ATGATATTTT
3118825 ATTTTTAAAATTTTTAAAAATA
1 ATTTTT-AAATTTTTAAAAATA
* * *
3118847 ATTTTTTATTTTTTTAAAATA
1 ATTTTTAAATTTTTAAAAATA
3118868 ATT
1 ATT
3118871 ATTGATCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTTAAATTTTTAAAAATA
Found at i:3119790 original size:27 final size:26
Alignment explanation
Indices: 3119750--3119823 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 26
3119740 ATTAAATTTT
*
3119750 ATATAAATATAATATAAATTATATATTAA
1 ATATAAA-A-AATATAAATCATATA-TAA
3119779 AT-TAAACAAATATAAATCATATATAA
1 ATATAAA-AAATATAAATCATATATAA
3119805 ATATAAAAATATATAAATC
1 ATATAAAAA-ATATAAATC
3119824 TAAATTAACT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
26 7 0.17
27 27 0.66
28 5 0.12
29 2 0.05
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (26 bp):
ATATAAAAAATATAAATCATATATAA
Found at i:3120278 original size:20 final size:20
Alignment explanation
Indices: 3120240--3120277 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3120230 GTATATATAT
*
3120240 ATATTTATAATTATATTTTA
1 ATATTTATAATAATATTTTA
3120260 ATATTTATAATAA-ATTTT
1 ATATTTATAATAATATTTT
3120278 TTGATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATTTATAATAATATTTTA
Found at i:3122119 original size:20 final size:20
Alignment explanation
Indices: 3122085--3122122 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3122075 AATAATATTC
3122085 AAAATAAAATATTTAAAATT
1 AAAATAAAATATTTAAAATT
3122105 AAAATTAAAAT-TTTAAAA
1 AAAA-TAAAATATTTAAAA
3122123 GACTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAATAAAATATTTAAAATT
Found at i:3122733 original size:20 final size:20
Alignment explanation
Indices: 3122710--3122747 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3122700 TAAAAAAATC
* *
3122710 ATATTTTTGTTTAATTTTTA
1 ATATTTTTATTAAATTTTTA
3122730 ATATTTTTATTAAATTTT
1 ATATTTTTATTAAATTTT
3122748 AAAATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
ATATTTTTATTAAATTTTTA
Found at i:3122789 original size:29 final size:30
Alignment explanation
Indices: 3122742--3122807 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
3122732 ATTTTTATTA
**
3122742 AATTTTAAAATATTAATAATTTAAATATAT
1 AATTTTAAAATATTAATAAAATAAATATAT
* *
3122772 -ATTTTAATAT-TTATATAAAATAAATATTT
1 AATTTTAAAATATTA-ATAAAATAAATATAT
3122801 AATTTTA
1 AATTTTA
3122808 TGAACACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 3 0.10
29 21 0.70
30 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
AATTTTAAAATATTAATAAAATAAATATAT
Found at i:3123558 original size:30 final size:31
Alignment explanation
Indices: 3123514--3123576 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
3123504 GTTAAAAAAG
3123514 TATTTTAATTTTTATA-TTATTAAATT-TAA
1 TATTTTAATTTTTATATTTATTAAATTATAA
* *
3123543 TATTTTATTTTTTTATATTTTTTAAATTATAA
1 TATTTTA-ATTTTTATATTTATTAAATTATAA
3123575 TA
1 TA
3123577 AATATTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.24
30 8 0.28
31 9 0.31
32 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TATTTTAATTTTTATATTTATTAAATTATAA
Found at i:3123749 original size:18 final size:18
Alignment explanation
Indices: 3123728--3123783 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 18
3123718 TATGTTATTA
3123728 TTTTATTATATTTAATTT
1 TTTTATTATATTTAATTT
*
3123746 TTTTAATAT-TATTAATTATT
1 TTTTATTATAT-TTAA-T-TT
3123766 TTTTATT-TATTATAATTT
1 TTTTATTATATT-TAATTT
3123784 AAAAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
17 1 0.03
18 14 0.45
19 4 0.13
20 12 0.39
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATTATATTTAATTT
Found at i:3123803 original size:14 final size:14
Alignment explanation
Indices: 3123786--3123835 Score: 66
Period size: 14 Copynumber: 3.5 Consensus size: 14
3123776 TATAATTTAA
3123786 AAAATATAAATATT
1 AAAATATAAATATT
3123800 AAAATATTAAAT-TT
1 AAAATA-TAAATATT
*
3123814 AATAATATAAAAATT
1 AA-AATATAAATATT
3123829 AAAATAT
1 AAAATAT
3123836 TTTTTATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 19 0.59
15 13 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATATAAATATT
Found at i:3123806 original size:8 final size:8
Alignment explanation
Indices: 3123793--3123836 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
3123783 TAAAAAATAT
3123793 AAATATTA
1 AAATATTA
3123801 AAATATT-
1 AAATATTA
3123808 AAAT-TTA
1 AAATATTA
3123815 ATAATA-TA
1 A-AATATTA
3123823 AAA-ATTA
1 AAATATTA
3123830 AAATATT
1 AAATATT
3123837 TTTTATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
6 3 0.10
7 12 0.39
8 16 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AAATATTA
Found at i:3123823 original size:29 final size:31
Alignment explanation
Indices: 3123773--3123836 Score: 96
Period size: 29 Copynumber: 2.1 Consensus size: 31
3123763 ATTTTTTATT
*
3123773 TATTATAATTTAAAAAATATAAATATTAAAA
1 TATTATAATTTAAAAAATATAAAAATTAAAA
*
3123804 TATTA-AATTT-AATAATATAAAAATTAAAA
1 TATTATAATTTAAAAAATATAAAAATTAAAA
3123833 TATT
1 TATT
3123837 TTTTATTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 21 0.68
30 5 0.16
31 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (31 bp):
TATTATAATTTAAAAAATATAAAAATTAAAA
Found at i:3123847 original size:29 final size:28
Alignment explanation
Indices: 3123778--3123854 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 28
3123768 TTATTTATTA
* *
3123778 TAATTTAAAAAATATAAATATTAAAATAT
1 TAATTT-AATAATATAAAAATTAAAATAT
3123807 TAAATTTAATAATATAAAAATTAAAATAT
1 T-AATTTAATAATATAAAAATTAAAATAT
*
3123836 T-TTTTATTATAATATAAAA
1 TAATTTA--ATAATATAAAA
3123855 TTTTGTAATA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.10
29 33 0.79
30 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TAATTTAATAATATAAAAATTAAAATAT
Found at i:3124099 original size:2 final size:2
Alignment explanation
Indices: 3124092--3124126 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3124082 TTTGTTGTAT
*
3124092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3124127 TAATTGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3124622 original size:25 final size:27
Alignment explanation
Indices: 3124576--3124627 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
3124566 TTTTTTTTAA
* *
3124576 TTTATTTTTTATTTTACACTTTGCTTT
1 TTTATTTTTTACTTAACACTTTGCTTT
*
3124603 TTTATTTTTT-CTTAAC-CTTTTCTTT
1 TTTATTTTTTACTTAACACTTTGCTTT
3124628 AAGCAAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 8 0.36
26 4 0.18
27 10 0.45
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTATTTTTTACTTAACACTTTGCTTT
Found at i:3127170 original size:16 final size:16
Alignment explanation
Indices: 3127149--3127184 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3127139 TTTTGTTCAA
* *
3127149 TAAATTTAATTTATAT
1 TAAATTAAATTTAAAT
3127165 TAAATTAAATTTAAAT
1 TAAATTAAATTTAAAT
3127181 TAAA
1 TAAA
3127185 AATTTTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATTAAATTTAAAT
Found at i:3127272 original size:28 final size:27
Alignment explanation
Indices: 3127221--3127274 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
3127211 TTGACTCAAA
3127221 TTATTTTTTAAATAATAAAAATTAATT
1 TTATTTTTTAAATAATAAAAATTAATT
* *
3127248 TTATTTTATTTAATAATAAATATTAAT
1 TTATTTT-TTAAATAATAAAAATTAAT
3127275 ATAAATATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTATTTTTTAAATAATAAAAATTAATT
Found at i:3127280 original size:12 final size:12
Alignment explanation
Indices: 3127257--3127316 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
3127247 TTTATTTTAT
3127257 TTAATAATAAATA
1 TTAAT-ATAAATA
3127270 TTAATATAAATA
1 TTAATATAAATA
*
3127282 -TAACTTTTAAATA
1 TTAA--TATAAATA
* *
3127295 TTATTTTAAATA
1 TTAATATAAATA
*
3127307 GTAATATAAA
1 TTAATATAAA
3127317 CTTTTGGATC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 3 0.08
12 22 0.56
13 12 0.31
14 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (12 bp):
TTAATATAAATA
Found at i:3127593 original size:24 final size:24
Alignment explanation
Indices: 3127566--3127613 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3127556 ATTTTATTAT
3127566 TTTTAAATAATAAT-AAAAATTTAA
1 TTTTAAATAA-AATAAAAAATTTAA
3127590 TTTTAAATAAAATAAAAAATTTAA
1 TTTTAAATAAAATAAAAAATTTAA
3127614 ACTATCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
TTTTAAATAAAATAAAAAATTTAA
Found at i:3129186 original size:22 final size:22
Alignment explanation
Indices: 3129125--3129187 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
3129115 TTAATCATAA
* *
3129125 TTTCTGTACTTTTCTCATATGGAT
1 TTTCTGTAC-TTTCT-TTAAGGAT
**
3129149 TTTCT-TTTTTTGCTTTAAGGAT
1 TTTCTGTACTTT-CTTTAAGGAT
3129171 TTTCTGTACTTTCTTTA
1 TTTCTGTACTTTCTTTA
3129188 TATTATTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
22 19 0.61
23 7 0.23
24 5 0.16
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.60
Consensus pattern (22 bp):
TTTCTGTACTTTCTTTAAGGAT
Found at i:3129842 original size:17 final size:15
Alignment explanation
Indices: 3129801--3129835 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
3129791 TTAAATATCA
3129801 AATATAAATATATATTT
1 AATATAAATAT-T-TTT
3129818 AATATAAATATTTTT
1 AATATAAATATTTTT
3129833 AAT
1 AAT
3129836 TTATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 1 0.06
17 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATATAAATATTTTT
Found at i:3138101 original size:5 final size:5
Alignment explanation
Indices: 3138091--3138124 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
3138081 AGTTAATTTT
*
3138091 AATTA AATTA AATTA AATTA AATTA ATTTA AATT
1 AATTA AATTA AATTA AATTA AATTA AATTA AATT
3138125 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (5 bp):
AATTA
Found at i:3138133 original size:15 final size:16
Alignment explanation
Indices: 3138115--3138155 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
3138105 AAATTAAATT
3138115 AATTTAAATTTT-TAA
1 AATTTAAATTTTATAA
* *
3138130 AATTTATATTTTATTA
1 AATTTAAATTTTATAA
3138146 AA-TTAAATTT
1 AATTTAAATTT
3138156 ATTTTAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTAAATTTTATAA
Found at i:3138166 original size:10 final size:10
Alignment explanation
Indices: 3138151--3138197 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
3138141 TATTAAATTA
3138151 AATTTATTTT
1 AATTTATTTT
3138161 AATTTATTTT
1 AATTTATTTT
3138171 AATTT-TTAAATT
1 AATTTATT---TT
*
3138183 AAATTATTTT
1 AATTTATTTT
3138193 AATTT
1 AATTT
3138198 TAAATTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
9 2 0.06
10 21 0.68
12 6 0.19
13 2 0.06
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
AATTTATTTT
Found at i:3138184 original size:22 final size:21
Alignment explanation
Indices: 3138159--3138209 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
3138149 TAAATTTATT
3138159 TTAATTTATTTTAATTTTTAAA
1 TTAATTTATTTTAA-TTTTAAA
*
3138181 TTAAATTATTTTAATTTTAAA
1 TTAATTTATTTTAATTTTAAA
*
3138202 TTATTTTA
1 TTAATTTA
3138210 AAATCAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTAATTTATTTTAATTTTAAA
Found at i:3138200 original size:21 final size:22
Alignment explanation
Indices: 3138159--3138204 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3138149 TAAATTTATT
*
3138159 TTAATTTATTTTAATTTTTAAA
1 TTAAATTATTTTAATTTTTAAA
3138181 TTAAATTATTTTAA-TTTTAAA
1 TTAAATTATTTTAATTTTTAAA
3138202 TTA
1 TTA
3138205 TTTTAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTAAATTATTTTAATTTTTAAA
Found at i:3138218 original size:16 final size:16
Alignment explanation
Indices: 3138124--3138220 Score: 65
Period size: 16 Copynumber: 6.0 Consensus size: 16
3138114 TAATTTAAAT
*
3138124 TTTTAAAATT-TA-TA
1 TTTTAAAATTAAATTA
3138138 TTTTATTAAATTAAATTTA
1 TTTTA--AAATTAAA-TTA
* **
3138157 TTTT-AATTTATTTTAA
1 TTTTAAAATTAAATT-A
*
3138173 TTTTTAAATTAAATTA
1 TTTTAAAATTAAATTA
**
3138189 TTTTAATTTTAAATTA
1 TTTTAAAATTAAATTA
*
3138205 TTTTAAAATCAAATTA
1 TTTTAAAATTAAATTA
3138221 ATTAATTTTT
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
14 5 0.08
15 2 0.03
16 42 0.67
17 8 0.13
19 6 0.10
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTAAAATTAAATTA
Found at i:3139274 original size:2 final size:2
Alignment explanation
Indices: 3139267--3139292 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3139257 ATCTATTTTC
3139267 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
3139293 GTTAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3140842 original size:11 final size:10
Alignment explanation
Indices: 3140817--3140856 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
3140807 AAAATTGATT
*
3140817 TAAATTAATA
1 TAAAATAATA
3140827 TAAAATAATA
1 TAAAATAATA
3140837 T-AAA-AATA
1 TAAAATAATA
3140845 -AAAATAATA
1 TAAAATAATA
3140854 TAA
1 TAA
3140857 TACTAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
8 7 0.27
9 7 0.27
10 12 0.46
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAAATAATA
Found at i:3140850 original size:17 final size:18
Alignment explanation
Indices: 3140823--3140856 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3140813 GATTTAAATT
3140823 AATATAAAATAATATAAA
1 AATATAAAATAATATAAA
3140841 AATA-AAAATAATATAA
1 AATATAAAATAATATAA
3140857 TACTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AATATAAAATAATATAAA
Done.