Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168381.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_6, 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: 26551601
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 64000 characters in sequence are not A, C, G, or T
File 21 of 130
Found at i:5569248 original size:45 final size:45
Alignment explanation
Indices: 5569199--5569298 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 45
5569189 TATTTAACTT
* * *
5569199 TAGATTAGCTGGTA-CACAAGCTCAAATTAGTTGGCATTTTAAGCC
1 TAGATTAGCTGATAGC-CAAGCTCAAATTAGTTGACACTTTAAGCC
* * *
5569244 TAGATAAGTTGATAGCCAAGCTCAGATTAGTTGACACTTTAAGCC
1 TAGATTAGCTGATAGCCAAGCTCAAATTAGTTGACACTTTAAGCC
5569289 TAGATTAGCT
1 TAGATTAGCT
5569299 AGCATTTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 45 0.98
46 1 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (45 bp):
TAGATTAGCTGATAGCCAAGCTCAAATTAGTTGACACTTTAAGCC
Found at i:5569293 original size:23 final size:23
Alignment explanation
Indices: 5569224--5569318 Score: 63
Period size: 23 Copynumber: 4.2 Consensus size: 23
5569214 ACAAGCTCAA
* *
5569224 ATTAGTTGGCATTTTAAGCCTAG
1 ATTAGTTGACACTTTAAGCCTAG
* * *
5569247 ATAAGTTGATAGC--CAAG-CTCAG
1 ATTAGTTGACA-CTTTAAGCCT-AG
5569269 ATTAGTTGACACTTTAAGCCTAG
1 ATTAGTTGACACTTTAAGCCTAG
* * *
5569292 ATTAGCT-AGCATTTTAAGCCCAG
1 ATTAGTTGA-CACTTTAAGCCTAG
5569315 ATTA
1 ATTA
5569319 AGTGGCACCC
Statistics
Matches: 55, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
21 3 0.05
22 15 0.27
23 35 0.64
24 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (23 bp):
ATTAGTTGACACTTTAAGCCTAG
Found at i:5569393 original size:23 final size:23
Alignment explanation
Indices: 5569359--5569422 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
5569349 TCAGATAAGA
5569359 TTAAGCCCAGATTATA-TGGCATT
1 TTAAGCCCAGATTA-ACTGGCATT
*
5569382 TTAAGCCTAGATTAACTGGCATT
1 TTAAGCCCAGATTAACTGGCATT
*
5569405 TTAATCCCAGATTAACTG
1 TTAAGCCCAGATTAACTG
5569423 ACACCCAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (23 bp):
TTAAGCCCAGATTAACTGGCATT
Found at i:5569449 original size:100 final size:100
Alignment explanation
Indices: 5569281--5569467 Score: 259
Period size: 100 Copynumber: 1.9 Consensus size: 100
5569271 TAGTTGACAC
* * *
5569281 TTTAAGCCTAGATTAGCTAGCATTTTAAGCCCAGATTAAGTGGCACCCAAATCCAATTTAACTAG
1 TTTAAGCCTAGATTAACTAGCATTTTAAGCCCAGATTAACTGACACCCAAATCCAATTTAACTAG
* *
5569346 CACTCAGATAAGATTAAGCCCAGATTATATGGCAT
66 CACTCAGAAAAGATTAACCCCAGATTATATGGCAT
* * * * *
5569381 TTTAAGCCTAGATTAACTGGCATTTTAATCCCAGATTAACTGACACCCAAA-CCTAGTTTAGCTT
1 TTTAAGCCTAGATTAACTAGCATTTTAAGCCCAGATTAACTGACACCCAAATCC-AATTTAACTA
*
5569445 GCACTTAGAAAAGATTAACCCCA
65 GCACTCAGAAAAGATTAACCCCA
5569468 AATCAATTGG
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
99 2 0.03
100 73 0.97
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.28
Consensus pattern (100 bp):
TTTAAGCCTAGATTAACTAGCATTTTAAGCCCAGATTAACTGACACCCAAATCCAATTTAACTAG
CACTCAGAAAAGATTAACCCCAGATTATATGGCAT
Found at i:5569721 original size:56 final size:56
Alignment explanation
Indices: 5569597--5569710 Score: 144
Period size: 56 Copynumber: 2.1 Consensus size: 56
5569587 CCTACGCCAA
* * *
5569597 GTTAACTAGCA--TATATGAGATCTAAGCCTAGATTAACTGATACTTTAAGCTCAG
1 GTTAACTAGCACCTAGATGAGATCTAAGCCTAGATTAACTGACACTTTAAGCCCAG
* * *
5569651 TTTAACTAGCACCTAGATGAGATTTAAGCCTAGATTAGCT-AGCACTTTAAGCCCAG
1 GTTAACTAGCACCTAGATGAGATCTAAGCCTAGATTAACTGA-CACTTTAAGCCCAG
5569707 GTTA
1 GTTA
5569711 GTTAGTACCT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 10 0.20
55 1 0.02
56 39 0.78
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (56 bp):
GTTAACTAGCACCTAGATGAGATCTAAGCCTAGATTAACTGACACTTTAAGCCCAG
Found at i:5570060 original size:43 final size:44
Alignment explanation
Indices: 5569971--5570060 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 44
5569961 AAGCAAAATG
* * *
5569971 TTTTAAAATTTTTAAAGTTTTAATACCTCTGTTTAGAGGAACTT
1 TTTTAAAATTTTTAAAGTTTCAATACCTCTATTTAGAAGAACTT
* * *
5570015 TTTTAAATTTTTTAAAGTTTCAA-AGTCTCTATTTA-AAGAAGTT
1 TTTTAAAATTTTTAAAGTTTCAATA-CCTCTATTTAGAAGAACTT
5570058 TTT
1 TTT
5570061 CCATTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
43 10 0.26
44 29 0.74
ACGTcount: A:0.32, C:0.08, G:0.10, T:0.50
Consensus pattern (44 bp):
TTTTAAAATTTTTAAAGTTTCAATACCTCTATTTAGAAGAACTT
Found at i:5570328 original size:8 final size:8
Alignment explanation
Indices: 5570315--5570365 Score: 57
Period size: 8 Copynumber: 5.9 Consensus size: 8
5570305 TTTTTCTTTA
5570315 AAAAAAAT
1 AAAAAAAT
5570323 AAAAAAAT
1 AAAAAAAT
*
5570331 CAAAAAAT
1 AAAAAAAT
5570339 AAAGAAAATCTT
1 AAA-AAAA---T
5570351 AAAAAAAT
1 AAAAAAAT
5570359 AAAAAAA
1 AAAAAAA
5570366 ACTTTTACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 25 0.68
9 4 0.11
11 4 0.11
12 4 0.11
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.14
Consensus pattern (8 bp):
AAAAAAAT
Found at i:5570377 original size:21 final size:20
Alignment explanation
Indices: 5570315--5570366 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
5570305 TTTTTCTTTA
5570315 AAAAAAAT-AAAAAAATC--
1 AAAAAAATAAAAAAAATCTT
*
5570332 -AAAAAATAAAGAAAATCTT
1 AAAAAAATAAAAAAAATCTT
5570351 AAAAAAATAAAAAAAA
1 AAAAAAATAAAAAAAA
5570367 CTTTTACAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 7 0.24
17 8 0.28
20 14 0.48
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (20 bp):
AAAAAAATAAAAAAAATCTT
Found at i:5570652 original size:22 final size:22
Alignment explanation
Indices: 5570624--5570666 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5570614 ATAAAATCTA
* *
5570624 GTCTAATTTTATTTGGGTTAAG
1 GTCTAATTTAATTGGGGTTAAG
5570646 GTCTAATTTAATTGGGGTTAA
1 GTCTAATTTAATTGGGGTTAA
5570667 TGCAGTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.47
Consensus pattern (22 bp):
GTCTAATTTAATTGGGGTTAAG
Found at i:5573954 original size:18 final size:18
Alignment explanation
Indices: 5573928--5573978 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
5573918 TACAAATTAT
*
5573928 TAAAATATAAATATGATA
1 TAAATTATAAATATGATA
*
5573946 TAAATTATAAAATAT-ATT
1 TAAATTAT-AAATATGATA
5573964 TAAATT-TAAATATGA
1 TAAATTATAAATATGA
5573979 ATATGATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 6 0.21
17 2 0.07
18 15 0.52
19 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (18 bp):
TAAATTATAAATATGATA
Found at i:5574103 original size:29 final size:29
Alignment explanation
Indices: 5574066--5574158 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 29
5574056 ACGAATAAAT
* * *
5574066 ATGAATAATACAAATATGCATGAATAGAC
1 ATGACTAATAAAAATATACATGAATAGAC
* ***
5574095 ATTACTAATATGGATATACATGAATAGAC
1 ATGACTAATAAAAATATACATGAATAGAC
* *
5574124 ATGACTAATAAAAATATATAT-AA-AAAC
1 ATGACTAATAAAAATATACATGAATAGAC
5574151 ATGACTAA
1 ATGACTAA
5574159 AATAATAAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
27 11 0.21
28 2 0.04
29 39 0.75
ACGTcount: A:0.53, C:0.10, G:0.11, T:0.27
Consensus pattern (29 bp):
ATGACTAATAAAAATATACATGAATAGAC
Found at i:5574826 original size:57 final size:57
Alignment explanation
Indices: 5574715--5574825 Score: 160
Period size: 56 Copynumber: 2.0 Consensus size: 57
5574705 AGAATAAACA
* *
5574715 CAAAACATATTTTTTAAAACAAATATATGATTTTTTTGTATTATTTTTATATCATAT
1 CAAAACATATTTTTAAAAACAAATATATGAATTTTTTGTATTATTTTTATATCATAT
*
5574772 CAAAACAT-TTTTTAAAAATAAATATAT-AATTTTTT-TATTA-TTTT-TATCATAT
1 CAAAACATATTTTTAAAAACAAATATATGAATTTTTTGTATTATTTTTATATCATAT
5574824 CA
1 CA
5574826 TTGATGGACA
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
52 10 0.20
53 4 0.08
54 5 0.10
55 7 0.14
56 17 0.33
57 8 0.16
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.50
Consensus pattern (57 bp):
CAAAACATATTTTTAAAAACAAATATATGAATTTTTTGTATTATTTTTATATCATAT
Found at i:5592838 original size:42 final size:40
Alignment explanation
Indices: 5592783--5592862 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 40
5592773 AAGAATCATA
**
5592783 ATTTTGAAATTTAAGGATTTGCAATCGAATTCAAAGATTCGC
1 ATTTTGAAATTTAAAAATTTGCAA--GAATTCAAAGATTCGC
* *
5592825 ATTTTGAAGTTTAAAAATTTGCAAGATTTCAAAGATTC
1 ATTTTGAAATTTAAAAATTTGCAAGAATTCAAAGATTC
5592863 ACAAGAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 13 0.38
42 21 0.62
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (40 bp):
ATTTTGAAATTTAAAAATTTGCAAGAATTCAAAGATTCGC
Found at i:5592877 original size:18 final size:18
Alignment explanation
Indices: 5592856--5592898 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
5592846 CAAGATTTCA
* *
5592856 AAGATTCACAAGAATTTG
1 AAGATTCAAAAAAATTTG
5592874 AAGATTCAAAAAAATTTG
1 AAGATTCAAAAAAATTTG
*
5592892 AATATTC
1 AAGATTC
5592899 GTAAGAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (18 bp):
AAGATTCAAAAAAATTTG
Found at i:5593043 original size:33 final size:33
Alignment explanation
Indices: 5593006--5593115 Score: 100
Period size: 33 Copynumber: 3.3 Consensus size: 33
5592996 CAAGGATTTC
* *
5593006 AAATTCGTAAGGATTTAGAA-TAGCAAGAATTGA
1 AAATTCGCAAGGATTCA-AATTAGCAAGAATTGA
* *
5593039 AAATTCGCAAAGATTCAAATTTGCAAGAATTGA
1 AAATTCGCAAGGATTCAAATTAGCAAGAATTGA
* * *
5593072 ACATTTGCAAGGATTCAGATTTA-CAAGAATT-A
1 AAATTCGCAAGGATTCA-AATTAGCAAGAATTGA
*
5593104 AAGATTCACAAG
1 AA-ATTCGCAAG
5593116 ATTTTTAGAT
Statistics
Matches: 62, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
32 4 0.06
33 55 0.89
34 3 0.05
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (33 bp):
AAATTCGCAAGGATTCAAATTAGCAAGAATTGA
Found at i:5593079 original size:17 final size:16
Alignment explanation
Indices: 5593028--5593102 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
5593018 ATTTAGAATA
*
5593028 GCAAGAATTGAAAATTC
1 GCAAGAATTG-AAATTT
*
5593045 GCAA-AGATTCAAATTT
1 GCAAGA-ATTGAAATTT
5593061 GCAAGAATTGAACATTT
1 GCAAGAATTGAA-ATTT
* * *
5593078 GCAAGGATTCAGATTT
1 GCAAGAATTGAAATTT
*
5593094 ACAAGAATT
1 GCAAGAATT
5593103 AAAGATTCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
16 26 0.55
17 21 0.45
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (16 bp):
GCAAGAATTGAAATTT
Found at i:5593150 original size:17 final size:17
Alignment explanation
Indices: 5593130--5593188 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
5593120 TTAGATTCGT
*
5593130 AAGAATTTCAGTTTTAC
1 AAGAATTTCAGTTTTAA
* * *
5593147 AAGAATTTCACTTTCAT
1 AAGAATTTCAGTTTTAA
*
5593164 AAGAATTTTTAGTTTTAA
1 AAGAA-TTTCAGTTTTAA
5593182 AAGAATT
1 AAGAATT
5593189 CAGATTCCTA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 21 0.62
18 13 0.38
ACGTcount: A:0.39, C:0.08, G:0.10, T:0.42
Consensus pattern (17 bp):
AAGAATTTCAGTTTTAA
Found at i:5593201 original size:34 final size:35
Alignment explanation
Indices: 5593113--5593209 Score: 99
Period size: 34 Copynumber: 2.8 Consensus size: 35
5593103 AAAGATTCAC
* * * * *
5593113 AAGATTTTTAGATTCGTAAGAA-TTTCAGTTTTAC
1 AAGAATTTCAGATTCATAAGAATTTTTAGTTTTAA
**
5593147 AAGAATTTCACTTTCATAAGAATTTTTAGTTTTAA
1 AAGAATTTCAGATTCATAAGAATTTTTAGTTTTAA
* *
5593182 AAGAA-TTCAGATTCCTAAGATTTTTTAG
1 AAGAATTTCAGATTCATAAGAATTTTTAG
5593210 CTCGTAAAAG
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
34 36 0.71
35 15 0.29
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.43
Consensus pattern (35 bp):
AAGAATTTCAGATTCATAAGAATTTTTAGTTTTAA
Found at i:5601550 original size:26 final size:27
Alignment explanation
Indices: 5601494--5601555 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
5601484 TTTTAAATTT
***
5601494 CAAAAAATAAAAAATAAAAAATATTTT
1 CAAAAAATAAAAAATAAAAAATATAAG
* *
5601521 CAAAAAATAAAAATTAAAAATTA-AAG
1 CAAAAAATAAAAAATAAAAAATATAAG
5601547 CAAAAAATA
1 CAAAAAATA
5601556 TTTTCATTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.21
Consensus pattern (27 bp):
CAAAAAATAAAAAATAAAAAATATAAG
Found at i:5621873 original size:26 final size:26
Alignment explanation
Indices: 5621777--5621966 Score: 97
Period size: 26 Copynumber: 6.9 Consensus size: 26
5621767 TTACTTATAA
* *
5621777 ATAATATTATATTAATAAATAATATATT
1 ATAATAATATA-TAATTAATAA-ATATT
* *
5621805 ATATTAATAAATAACATAATAATAAATATT
1 ATAATAATATAT-A-AT--TAATAAATATT
5621835 AT--TAAT-T-TAATTAATAAATATT
1 ATAATAATATATAATTAATAAATATT
* *
5621857 ATAATAATATATTATTAATAAATAACAT
1 ATAATAATATATAATTAATAAAT-A-TT
*
5621885 ACTATTAATATAATAAATTAATAAATATT
1 A-TAATAATAT-AT-AATTAATAAATATT
5621914 ATTAATAA-ATA-ATATT-ATAATATATT
1 A-TAATAATATATA-ATTAATAA-ATATT
* *
5621940 AATAAGTAATATAAAGAATAATAAATA
1 -ATAA-TAATATATA-ATTAATAAATA
5621967 GTTTTATTTT
Statistics
Matches: 128, Mismatches: 14, Indels: 39
0.71 0.08 0.22
Matches are distributed among these distances:
22 13 0.10
24 6 0.05
25 7 0.05
26 23 0.18
27 7 0.05
28 20 0.16
29 23 0.18
30 14 0.11
31 15 0.12
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (26 bp):
ATAATAATATATAATTAATAAATATT
Found at i:5621939 original size:83 final size:82
Alignment explanation
Indices: 5621771--5621966 Score: 204
Period size: 83 Copynumber: 2.3 Consensus size: 82
5621761 ATAATTTTAC
*
5621771 TTATAAATAATAT-TATATTAATAAATAATATATTATATTAATAAATAACATAATAATAAATATT
1 TTAT-AATAATATATATATTAATAAATAACATA-TATATTAATAAATAACAT-ATAATAAATATT
*
5621835 ATTAATTTAATTAATAAATA
63 ATTAATATAATTAATAAATA
*
5621855 TTATAATAATATAT-TATTAATAAATAACATA-CTATTAATATAATAA-AT-TAATAAATATTAT
1 TTATAATAATATATATATTAATAAATAACATATATATTAATA-AATAACATATAATAAATATTAT
*
5621916 TAATAAATAATATTATAATATA
65 TAAT--ATAAT-TAATAA-ATA
* * *
5621938 TTAATAAGTAATATAAAGAATAATAAATA
1 TT-ATAA-TAATATATATATTAATAAATA
5621967 GTTTTATTTT
Statistics
Matches: 96, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
79 17 0.18
81 14 0.15
82 10 0.10
83 29 0.30
84 9 0.09
85 7 0.07
86 10 0.10
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (82 bp):
TTATAATAATATATATATTAATAAATAACATATATATTAATAAATAACATATAATAAATATTATT
AATATAATTAATAAATA
Found at i:5621943 original size:16 final size:16
Alignment explanation
Indices: 5621760--5621935 Score: 97
Period size: 18 Copynumber: 11.0 Consensus size: 16
5621750 TATTTTTTAG
*
5621760 AATAATTTTACTT-ATA
1 AATAATATTA-TTAATA
5621776 AATAATATTATATTAATA
1 AATAATA-T-TATTAATA
5621794 AATAATATATTATATTAATA
1 AAT-A-ATA-T-TATTAATA
* *
5621814 AATAACA-TAATAATA
1 AATAATATTATTAATA
* *
5621829 AATATTATTAATTTAATT
1 AATAATATT-A-TTAATA
5621847 AATAAATATTA-TAAT-
1 AAT-AATATTATTAATA
5621862 AAT-ATATTATTAATA
1 AATAATATTATTAATA
*
5621877 AATAACATACTATTAAT-
1 AAT-A-ATATTATTAATA
*
5621894 -ATAATA-AATTAAT-
1 AATAATATTATTAATA
5621907 -A-AATATTATTAATA
1 AATAATATTATTAATA
5621921 AATAATATTA-TAATA
1 AATAATATTATTAATA
5621936 TATTAATAAG
Statistics
Matches: 131, Mismatches: 11, Indels: 37
0.73 0.06 0.21
Matches are distributed among these distances:
12 4 0.03
13 19 0.15
14 7 0.05
15 25 0.19
16 20 0.15
17 4 0.03
18 28 0.21
19 7 0.05
20 17 0.13
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAATATTATTAATA
Found at i:5622004 original size:19 final size:18
Alignment explanation
Indices: 5621980--5622027 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
5621970 TTATTTTAAG
*
5621980 TATTTTTATATTAACATAA
1 TATTTTAATATTAA-ATAA
*
5621999 TATTTTAATAATAAATAA
1 TATTTTAATATTAAATAA
5622017 T-TTTTAATATT
1 TATTTTAATATT
5622028 TTAATAGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 9 0.35
18 5 0.19
19 12 0.46
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TATTTTAATATTAAATAA
Found at i:5622023 original size:17 final size:18
Alignment explanation
Indices: 5621981--5622025 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
5621971 TATTTTAAGT
*
5621981 ATTTTT-ATATTAACATA
1 ATTTTTAATAATAACATA
5621998 ATATTTTAATAATAA-ATA
1 AT-TTTTAATAATAACATA
5622016 ATTTTTAATA
1 ATTTTTAATA
5622026 TTTTAATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 9 0.36
19 6 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTTAATAATAACATA
Found at i:5623105 original size:29 final size:30
Alignment explanation
Indices: 5623073--5623132 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
5623063 TAAGTCCCTG
* *
5623073 TACTTTTA-TTGTATTCAAATAAGCCCTTA
1 TACTTTGATTTGTATCCAAATAAGCCCTTA
5623102 TACTTTGATTTGTATCCAAATAAGCCCTTA
1 TACTTTGATTTGTATCCAAATAAGCCCTTA
5623132 T
1 T
5623133 TTCAAATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 7 0.25
30 21 0.75
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.43
Consensus pattern (30 bp):
TACTTTGATTTGTATCCAAATAAGCCCTTA
Found at i:5623223 original size:30 final size:30
Alignment explanation
Indices: 5623155--5623232 Score: 113
Period size: 31 Copynumber: 2.6 Consensus size: 30
5623145 AATGATTTAT
5623155 GTTAAGGGCTTATTTAGGTACAAATTAAAAG
1 GTTAAGGGCTTATTT-GGTACAAATTAAAAG
*
5623186 TTTAAGGGCTTATTTGGATACAAATT-AAAG
1 GTTAAGGGCTTATTTGG-TACAAATTAAAAG
*
5623216 GTTAAGGGTTTATTTGG
1 GTTAAGGGCTTATTTGG
5623233 GTGCAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 21 0.49
31 22 0.51
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.37
Consensus pattern (30 bp):
GTTAAGGGCTTATTTGGTACAAATTAAAAG
Found at i:5623245 original size:30 final size:30
Alignment explanation
Indices: 5623155--5623245 Score: 119
Period size: 30 Copynumber: 3.0 Consensus size: 30
5623145 AATGATTTAT
*
5623155 GTTAAGGGCTTATTTAGGTACAAATTAAAAG
1 GTTAAGGGCTTATTTGGGTACAAATT-AAAG
* *
5623186 TTTAAGGGCTTATTTGGATACAAATTAAAG
1 GTTAAGGGCTTATTTGGGTACAAATTAAAG
* * *
5623216 GTTAAGGGTTTATTTGGGTGCAAAATAAAG
1 GTTAAGGGCTTATTTGGGTACAAATTAAAG
5623246 ACTAAGGATT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
30 29 0.56
31 23 0.44
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.34
Consensus pattern (30 bp):
GTTAAGGGCTTATTTGGGTACAAATTAAAG
Found at i:5623252 original size:30 final size:30
Alignment explanation
Indices: 5623157--5623261 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 30
5623147 TGATTTATGT
* * **
5623157 TAAGGGCTTATTTAGG-TACAAATTAAAAGTT
1 TAAGGGTTTATTT-GGATACAAAAT-AAAGAC
* * **
5623188 TAAGGGCTTATTTGGATACAAATTAAAGGT
1 TAAGGGTTTATTTGGATACAAAATAAAGAC
* *
5623218 TAAGGGTTTATTTGGGTGCAAAATAAAGAC
1 TAAGGGTTTATTTGGATACAAAATAAAGAC
*
5623248 TAAGGATTTATTTG
1 TAAGGGTTTATTTG
5623262 AATGCAATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
30 44 0.68
31 21 0.32
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.35
Consensus pattern (30 bp):
TAAGGGTTTATTTGGATACAAAATAAAGAC
Found at i:5631621 original size:16 final size:17
Alignment explanation
Indices: 5631602--5631641 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
5631592 TAATATTATC
5631602 TTTGCATAATA-ATTTA
1 TTTGCATAATATATTTA
5631618 TTTGTC-TAATATATTTA
1 TTTG-CATAATATATTTA
5631635 TTTGCAT
1 TTTGCAT
5631642 GATTGGTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (17 bp):
TTTGCATAATATATTTA
Found at i:5631695 original size:20 final size:21
Alignment explanation
Indices: 5631654--5631699 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
5631644 TTGGTATATT
* *
5631654 TATTTGTGTGATTTATTAATA
1 TATTTGCGTGATTTACTAATA
5631675 TATTTGCGTGA-TTACTAATA
1 TATTTGCGTGATTTACTAATA
5631695 TATTT
1 TATTT
5631700 ATTTGTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.54
Consensus pattern (21 bp):
TATTTGCGTGATTTACTAATA
Found at i:5631704 original size:24 final size:23
Alignment explanation
Indices: 5631624--5631785 Score: 120
Period size: 24 Copynumber: 7.1 Consensus size: 23
5631614 TTTATTTGTC
5631624 TAATATATTTATTTGCATGA-T-
1 TAATATATTTATTTGCATGATTA
** **
5631645 TGGTATATTTATTTGTGTGATT-
1 TAATATATTTATTTGCATGATTA
* * *
5631667 TATTA-ATATATTTGCGTGATTA
1 TAATATATTTATTTGCATGATTA
* *
5631689 CTAATATATTTATTTGTATAATTA
1 -TAATATATTTATTTGCATGATTA
*
5631713 TATTCA-ATTTGA-TTGCATGATTA
1 TAAT-ATATTT-ATTTGCATGATTA
* * *
5631736 TTAATATATTTAATTACTTGATTA
1 -TAATATATTTATTTGCATGATTA
5631760 TTAATATATTTATTTGCATGATTA
1 -TAATATATTTATTTGCATGATTA
5631784 TA
1 TA
5631786 TATTTAATTG
Statistics
Matches: 110, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
21 30 0.27
22 4 0.04
23 24 0.22
24 52 0.47
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.53
Consensus pattern (23 bp):
TAATATATTTATTTGCATGATTA
Found at i:5631743 original size:47 final size:45
Alignment explanation
Indices: 5631648--5631747 Score: 121
Period size: 47 Copynumber: 2.2 Consensus size: 45
5631638 GCATGATTGG
* * *
5631648 TATATTTATTTGTGTGATTTATTAATATATTTGCGTGATTACTAA
1 TATATTTATTTGTATAATTTATTAATATATTTGCATGATTACTAA
* *
5631693 TATATTTATTTGTATAATTATATTCAATTTGA-TTGCATGATTATTAA
1 TATATTTATTTGTATAATT-TATT-AATAT-ATTTGCATGATTACTAA
5631740 TATATTTA
1 TATATTTA
5631748 ATTACTTGAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
45 17 0.36
46 4 0.09
47 25 0.53
48 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (45 bp):
TATATTTATTTGTATAATTTATTAATATATTTGCATGATTACTAA
Found at i:5631788 original size:20 final size:21
Alignment explanation
Indices: 5631624--5631791 Score: 74
Period size: 21 Copynumber: 7.5 Consensus size: 21
5631614 TTTATTTGTC
5631624 TAATATATTTATTTGCATGAT
1 TAATATATTTATTTGCATGAT
** **
5631645 TGGTATATTTATTTGTGTGAT
1 TAATATATTTATTTGCATGAT
* * *
5631666 TTAT-TAATATATTTGCGTGATT
1 TAATAT-ATTTATTTGCATGA-T
* *
5631688 ACTAATATATTTATTTGTATAAT
1 --TAATATATTTATTTGCATGAT
5631711 T-ATATTCAATTTGA-TTGCATGATTAT
1 TAATA-T--ATTT-ATTTGCATG---AT
** *
5631737 TAATATATTTAATTACTTGATTAT
1 TAATATATTT-ATT--TGCATGAT
5631761 TAATATATTTATTTGCATGAT
1 TAATATATTTATTTGCATGAT
5631782 T-ATATATTTA
1 TAATATATTTA
5631792 ATTGTATGTT
Statistics
Matches: 109, Mismatches: 22, Indels: 33
0.66 0.13 0.20
Matches are distributed among these distances:
20 13 0.12
21 39 0.36
22 1 0.01
23 13 0.12
24 31 0.28
25 2 0.02
26 4 0.04
27 6 0.06
ACGTcount: A:0.32, C:0.04, G:0.10, T:0.54
Consensus pattern (21 bp):
TAATATATTTATTTGCATGAT
Found at i:5631809 original size:32 final size:32
Alignment explanation
Indices: 5631768--5631923 Score: 107
Period size: 32 Copynumber: 5.5 Consensus size: 32
5631758 TATTAATATA
5631768 TTTATTTGCATGATTATATATTTAATTGTATG
1 TTTATTTGCATGATTATATATTTAATTGTATG
* *
5631800 TTTACTTGCATGATT-T-TATGT-A---T-TG
1 TTTATTTGCATGATTATATATTTAATTGTATG
* * *
5631825 -TTAGTTGCATGATTATATATTTAATTGCATA
1 TTTATTTGCATGATTATATATTTAATTGTATG
*
5631856 TTTATTTTCATG-TT-TATA--T-A---TA--
1 TTTATTTGCATGATTATATATTTAATTGTATG
**
5631878 TTTATTTGCATGATTATATATTTAATTACAT-
1 TTTATTTGCATGATTATATATTTAATTGTATG
5631909 TTTATTTGCATGATT
1 TTTATTTGCATGATT
5631924 TACATTGTTA
Statistics
Matches: 96, Mismatches: 11, Indels: 35
0.68 0.08 0.25
Matches are distributed among these distances:
22 11 0.11
23 2 0.02
24 18 0.19
25 3 0.03
26 6 0.06
27 3 0.03
28 1 0.01
29 1 0.01
30 9 0.09
31 19 0.20
32 23 0.24
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (32 bp):
TTTATTTGCATGATTATATATTTAATTGTATG
Found at i:5631833 original size:56 final size:53
Alignment explanation
Indices: 5631773--5631946 Score: 210
Period size: 54 Copynumber: 3.2 Consensus size: 53
5631763 ATATATTTAT
* * *
5631773 TTGCATGATTATATATTTAATTGTATGTTTACTTGCATGATTTTATGTATTGTTAG
1 TTGCATGATTATATATTTAATTGCAT-TTTATTTGCATGA-TTTAT-TATTGTTAA
* *
5631829 TTGCATGATTATATATTTAATTGCATATTTATTTTCATG-TTTATATATAT-TTAT
1 TTGCATGATTATATATTTAATTGCAT-TTTATTTGCATGATTTAT-TAT-TGTTAA
* *
5631883 TTGCATGATTATATATTTAATTACATTTTATTTGCATGATTTA-CATTGTTAA
1 TTGCATGATTATATATTTAATTGCATTTTATTTGCATGATTTATTATTGTTAA
5631935 TTGCATGATTAT
1 TTGCATGATTAT
5631947 TAATTTATTT
Statistics
Matches: 105, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
51 1 0.01
52 17 0.16
53 11 0.10
54 40 0.38
55 1 0.01
56 35 0.33
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.54
Consensus pattern (53 bp):
TTGCATGATTATATATTTAATTGCATTTTATTTGCATGATTTATTATTGTTAA
Found at i:5631854 original size:20 final size:20
Alignment explanation
Indices: 5631829--5631904 Score: 74
Period size: 20 Copynumber: 4.1 Consensus size: 20
5631819 GTATTGTTAG
5631829 TTGCATGATTATATATTTAA
1 TTGCATGATTATATATTTAA
*
5631849 TTGCAT-ATT-TAT-TTTCA
1 TTGCATGATTATATATTTAA
* * *
5631866 -TG-TTTA-TATATATTTAT
1 TTGCATGATTATATATTTAA
5631883 TTGCATGATTATATATTTAA
1 TTGCATGATTATATATTTAA
5631903 TT
1 TT
5631905 ACATTTTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
15 2 0.05
16 6 0.14
17 7 0.16
18 5 0.12
19 5 0.12
20 18 0.42
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (20 bp):
TTGCATGATTATATATTTAA
Found at i:5631880 original size:22 final size:22
Alignment explanation
Indices: 5631853--5631898 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
5631843 ATTTAATTGC
* *
5631853 ATATTTATTTTCATGTTTATAT
1 ATATTTATTTGCATGATTATAT
5631875 ATATTTATTTGCATGATTATAT
1 ATATTTATTTGCATGATTATAT
5631897 AT
1 AT
5631899 TTAATTACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (22 bp):
ATATTTATTTGCATGATTATAT
Found at i:5631928 original size:20 final size:21
Alignment explanation
Indices: 5631903--5631944 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5631893 ATATATTTAA
*
5631903 TTACATT-TTATTTGCATGAT
1 TTACATTGTTAATTGCATGAT
5631923 TTACATTGTTAATTGCATGAT
1 TTACATTGTTAATTGCATGAT
5631944 T
1 T
5631945 ATTAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.52
Consensus pattern (21 bp):
TTACATTGTTAATTGCATGAT
Found at i:5632031 original size:56 final size:53
Alignment explanation
Indices: 5631740--5632064 Score: 235
Period size: 56 Copynumber: 6.0 Consensus size: 53
5631730 TGATTATTAA
* * * *
5631740 TATATTTAATTACTTGATTATTAATATATTTATTTGCATGATTATATATTTAAT
1 TATATTTTATTGCATGATTATT-ATATATTTATTTGCATGATTATATATTTATT
* * *
5631794 TGTATGTTTACTTGCATGATT-TTATGTATTGTTAGTTGCATGATTATATATTTAATT
1 TATAT-TTTA-TTGCATGATTATTATATA-T-TTATTTGCATGATTATATATTT-ATT
* * * *
5631851 GCATA-TTTATTTTCATGTTTA-TATATATTTATTTGCATGATTATATATTTAAT
1 -TATATTTTA-TTGCATGATTATTATATATTTATTTGCATGATTATATATTTATT
* * *
5631904 TACATTTTATTTGCATGA-T-TTACAT-TGTTAATTGCATGATTAT-TAATTTATT
1 TATATTTTA-TTGCATGATTATTATATAT-TTATTTGCATGATTATAT-ATTTATT
* ** *
5631956 TATATGTGTGATTATATGATTATTAGTATATTTATTTGCAT-AGTTATTTATTTATT
1 TATAT-T-TTATTGCATGATTATTA-TATATTTATTTGCATGA-TTATATATTTATT
5632012 TATTATTATTATTGCATGA-T-TT-TATATTTA-TTGCATGATTA-ATATTATATT
1 TA-TATT-TTATTGCATGATTATTATATATTTATTTGCATGATTATATATT-TATT
5632063 TA
1 TA
5632065 AATGATATTT
Statistics
Matches: 216, Mismatches: 33, Indels: 47
0.73 0.11 0.16
Matches are distributed among these distances:
50 4 0.02
51 17 0.08
52 41 0.19
53 20 0.09
54 34 0.16
55 12 0.06
56 79 0.37
57 7 0.03
58 2 0.01
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.56
Consensus pattern (53 bp):
TATATTTTATTGCATGATTATTATATATTTATTTGCATGATTATATATTTATT
Found at i:5632062 original size:19 final size:20
Alignment explanation
Indices: 5632009--5632062 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
5631999 TTATTTATTT
*
5632009 ATTTATTATTATTATTGCATG
1 ATTTAATATTA-TATTGCATG
*
5632030 ATTTTATATT-TATTGCATG
1 ATTTAATATTATATTGCATG
5632049 A-TTAATATTATATT
1 ATTTAATATTATATT
5632063 TAAATGATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 7 0.24
19 14 0.48
21 8 0.28
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.57
Consensus pattern (20 bp):
ATTTAATATTATATTGCATG
Found at i:5632324 original size:38 final size:36
Alignment explanation
Indices: 5632271--5632343 Score: 101
Period size: 38 Copynumber: 2.0 Consensus size: 36
5632261 TAATATACTT
*
5632271 GCATGACATTCTTACATGAATATTTTAGTATGATTTAG
1 GCATGACATTATTACATG-ATA-TTTAGTATGATTTAG
* *
5632309 GCATGATATTATTACATGATATTTGGTATGATTTA
1 GCATGACATTATTACATGATATTTAGTATGATTTA
5632344 TAGTATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 13 0.41
37 3 0.09
38 16 0.50
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (36 bp):
GCATGACATTATTACATGATATTTAGTATGATTTAG
Found at i:5634118 original size:14 final size:14
Alignment explanation
Indices: 5634099--5634125 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5634089 AGAAGATTTC
5634099 AAAAGAAATGATAA
1 AAAAGAAATGATAA
5634113 AAAAGAAATGATA
1 AAAAGAAATGATA
5634126 TGAAGGAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
AAAAGAAATGATAA
Found at i:5651114 original size:3 final size:3
Alignment explanation
Indices: 5651106--5651137 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5651096 CCCCACTTTC
5651106 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5651138 AACCAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:5653808 original size:22 final size:20
Alignment explanation
Indices: 5653783--5653827 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
5653773 TCATATATTT
*
5653783 TAATGTTAAATATCATGAAAAA
1 TAATGTTAAA-AT-ATAAAAAA
*
5653805 TAATTTTAAAATATAAAAAA
1 TAATGTTAAAATATAAAAAA
5653825 TAA
1 TAA
5653828 AAGTGTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 10 0.48
21 2 0.10
22 9 0.43
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
TAATGTTAAAATATAAAAAA
Found at i:5654912 original size:2 final size:2
Alignment explanation
Indices: 5654905--5654945 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5654895 CAGTGAAGTT
5654905 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5654946 GTATGTACAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5655328 original size:20 final size:19
Alignment explanation
Indices: 5655303--5655343 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
5655293 TAACAATAAT
5655303 AATTAAAAATCAATAAAAAA
1 AATTAAAAATCAA-AAAAAA
* *
5655323 AATTAAATATTAAAAAAAA
1 AATTAAAAATCAAAAAAAA
5655342 AA
1 AA
5655344 GATCAGAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
AATTAAAAATCAAAAAAAA
Found at i:5656362 original size:27 final size:29
Alignment explanation
Indices: 5656317--5656373 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
5656307 CTAAATGTTG
*
5656317 AAAAATTAAAATGTTAAAAATATT-TTTT
1 AAAAATTAAAATGTAAAAAATATTCTTTT
*
5656345 AAAAATTAAAAT-TAAAAAATTTTCTTTT
1 AAAAATTAAAATGTAAAAAATATTCTTTT
5656373 A
1 A
5656374 CAAACAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 9 0.35
28 17 0.65
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAAATTAAAATGTAAAAAATATTCTTTT
Found at i:5656711 original size:16 final size:16
Alignment explanation
Indices: 5656681--5656732 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 16
5656671 ATAATAATAA
*
5656681 TAAAATTTTTAAAACCT
1 TAAAA-TTTTGAAACCT
*
5656698 TAAAATTTTGAAACCC
1 TAAAATTTTGAAACCT
*
5656714 T-AAATCTTGAAA-CT
1 TAAAATTTTGAAACCT
5656728 TAAAA
1 TAAAA
5656733 AATTGAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 13 0.43
16 10 0.33
17 5 0.17
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (16 bp):
TAAAATTTTGAAACCT
Found at i:5657689 original size:17 final size:17
Alignment explanation
Indices: 5657667--5657699 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5657657 GAAATTTAAT
*
5657667 AATAATTTTTTTAAAAA
1 AATAATTTTATTAAAAA
5657684 AATAATTTTATTAAAA
1 AATAATTTTATTAAAA
5657700 TTCTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAATTTTATTAAAAA
Found at i:5658553 original size:14 final size:14
Alignment explanation
Indices: 5658483--5658555 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
5658473 GGTTTTTAAG
5658483 ATTTTGAGGTTTTA
1 ATTTTGAGGTTTTA
* *
5658497 AGTTTT-AAGTTTTGG
1 A-TTTTGAGGTTTT-A
* *
5658512 AGTTTCAGGGTTTTA
1 ATTTTGA-GGTTTTA
*
5658527 A-TTTAAGGATTTTA
1 ATTTTGAGG-TTTTA
5658541 ATTTTGAGGTTTTA
1 ATTTTGAGGTTTTA
5658555 A
1 A
5658556 GGTTTGAATG
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
13 2 0.04
14 26 0.57
15 13 0.28
16 5 0.11
ACGTcount: A:0.25, C:0.01, G:0.22, T:0.52
Consensus pattern (14 bp):
ATTTTGAGGTTTTA
Found at i:5659137 original size:13 final size:13
Alignment explanation
Indices: 5659119--5659143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5659109 ATAAAATCAT
5659119 TTATTTTTAATTA
1 TTATTTTTAATTA
5659132 TTATTTTTAATT
1 TTATTTTTAATT
5659144 TCCAAAAATA
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (13 bp):
TTATTTTTAATTA
Found at i:5659191 original size:20 final size:20
Alignment explanation
Indices: 5659166--5659203 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5659156 TACTTCAATG
* *
5659166 AAAATTATTTTTATTATTGT
1 AAAATTACTATTATTATTGT
5659186 AAAATTACTATTATTATT
1 AAAATTACTATTATTATT
5659204 TGTTGAGAAT
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:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (20 bp):
AAAATTACTATTATTATTGT
Found at i:5660525 original size:52 final size:52
Alignment explanation
Indices: 5660439--5660595 Score: 194
Period size: 52 Copynumber: 3.0 Consensus size: 52
5660429 TATAACCATA
* * *
5660439 CAAACTTGCCCATTAAGAAT-CTTTCTCCTCTTAGAATTCTT-TTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCATT-TCCTCTTAGAATTCTTCTT-CTGCAAGT
* *
5660491 CAAACTTGCCTATTAAGAATCCATTTCCTTTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCATTTCCTCTTAGAATTCTTCTTCTGCAAGT
* * *
5660543 CAAACTTACCTATTAAGAATCTTATTT-CTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC-CATTTCCTCTTAGAATTCTTCTTCTGCAAGT
5660595 C
1 C
5660596 TTTTAATCCA
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
52 85 0.90
53 9 0.10
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCATTTCCTCTTAGAATTCTTCTTCTGCAAGT
Found at i:5660636 original size:11 final size:11
Alignment explanation
Indices: 5660620--5660650 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
5660610 TCAATATCTG
5660620 ACAAATCTCAA
1 ACAAATCTCAA
5660631 ACAAATCTCAA
1 ACAAATCTCAA
5660642 ACAAATCTC
1 ACAAATCTC
5660651 TTATGAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:5660968 original size:24 final size:24
Alignment explanation
Indices: 5660907--5661017 Score: 78
Period size: 24 Copynumber: 4.5 Consensus size: 24
5660897 TCATATCTTA
* * * *
5660907 AACCTTTAACTCTTCCTATATCTCA
1 AACCTTCAACTCTTTC-ACATCTCG
* * *
5660932 AACTTTCAGCTCTTTCACGTCTCG
1 AACCTTCAACTCTTTCACATCTCG
* * *
5660956 AACCTTCGACTCTTCCACATCTTG
1 AACCTTCAACTCTTTCACATCTCG
* * *
5660980 AATCTTTAACTCTTCTCACATTTCG
1 AACCTTCAACTCTT-TCACATCTCG
*
5661005 AACCTTCAGCTCT
1 AACCTTCAACTCT
5661018 GATACCATTT
Statistics
Matches: 63, Mismatches: 22, Indels: 2
0.72 0.25 0.02
Matches are distributed among these distances:
24 34 0.54
25 29 0.46
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.38
Consensus pattern (24 bp):
AACCTTCAACTCTTTCACATCTCG
Found at i:5661597 original size:52 final size:52
Alignment explanation
Indices: 5661511--5661667 Score: 176
Period size: 52 Copynumber: 3.0 Consensus size: 52
5661501 TATAACCATA
* * * *
5661511 CAAACTGACCCATTAAAAATC-CCTCTTCTCTTAGAATTCTTTTTTTGTAAGT
1 CAAACTTACCTATTAAAAATCTTCTC-TCTCTTAGAATTCTTTTTTTGCAAGT
* * * *
5661563 CAAACTTACCTATTAAAAATCTAT-TTTTTTTTAGAATT-TTTTCCTTGCAAGT
1 CAAACTTACCTATTAAAAATCT-TCTCTCTCTTAGAATTCTTTT-TTTGCAAGT
* *
5661615 CAAACTTACCTATTAAGAATCTTCTCTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAAAAATCTTCTCTCTCTTAGAATTCTTTTTTTGCAAGT
5661667 C
1 C
5661668 TTTTTATCCA
Statistics
Matches: 86, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
51 5 0.06
52 77 0.90
53 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (52 bp):
CAAACTTACCTATTAAAAATCTTCTCTCTCTTAGAATTCTTTTTTTGCAAGT
Found at i:5664162 original size:35 final size:35
Alignment explanation
Indices: 5664088--5664162 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
5664078 GATTGAGCCG
* * * *
5664088 TAAGTTAGAGAATAAAGATGACTGAAACTGAATCG
1 TAAGTTAGAGAATAAAAATAACTGAAACTAAATCA
*
5664123 TAAGTTAGAGAATAAAAATAACT-ATGACTAAATCA
1 TAAGTTAGAGAATAAAAATAACTGA-AACTAAATCA
5664158 TAAGT
1 TAAGT
5664163 CAAGAAATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (35 bp):
TAAGTTAGAGAATAAAAATAACTGAAACTAAATCA
Found at i:5664754 original size:22 final size:23
Alignment explanation
Indices: 5664708--5664751 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
5664698 TATCAAAGGT
*
5664708 TTTGACAATTTTAAAATTTTAAC
1 TTTGACAATTTAAAAATTTTAAC
5664731 TTTGA-AATTTAAAACATTTTA
1 TTTGACAATTTAAAA-ATTTTA
5664752 CTTATAAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.48
Consensus pattern (23 bp):
TTTGACAATTTAAAAATTTTAAC
Found at i:5665209 original size:50 final size:50
Alignment explanation
Indices: 5665152--5665275 Score: 137
Period size: 48 Copynumber: 2.5 Consensus size: 50
5665142 GGAACTTGGT
* * *
5665152 TATCACCACCAAGTGAATATGCAAATGATAATCAAATATGAATACTCAAA
1 TATCACCACCAAGTGAAAATGCAAATGATAATCAAACATAAATACTCAAA
* ** * *
5665202 TATCACCACTAA--GAAAACT-TTAATGATATTCAAACATAAATACTCATA
1 TATCACCACCAAGTGAAAA-TGCAAATGATAATCAAACATAAATACTCAAA
*
5665250 TATCACCACCAAGTAAAAATGCAAAT
1 TATCACCACCAAGTGAAAATGCAAAT
5665276 TAATTTAGAT
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
48 38 0.66
49 2 0.03
50 18 0.31
ACGTcount: A:0.48, C:0.19, G:0.07, T:0.25
Consensus pattern (50 bp):
TATCACCACCAAGTGAAAATGCAAATGATAATCAAACATAAATACTCAAA
Found at i:5665562 original size:56 final size:55
Alignment explanation
Indices: 5665417--5665563 Score: 132
Period size: 56 Copynumber: 2.6 Consensus size: 55
5665407 CTTAAAATGT
* * * *
5665417 TAGCTAAACTGAGCTTAAATTCGAGTGCTAGCTAATATAGGCTTAAAACTATGTGC
1 TAGCTAAATTGGGCTTAAA-TCGAGTGCAAGCTAATATAGGCTTAAAACTAAGTGC
* * * * * * **
5665473 TAGCTAAATTGGGTTTAAATCTATGAGCAAGCTAATCTGGGTTTAACTCTAAGTGC
1 TAGCTAAATTGGGCTTAAATCGA-GTGCAAGCTAATATAGGCTTAAAACTAAGTGC
* * *
5665529 TAGCTAAGTTGTGCTTAAATCCGAGTGCCAGCTAA
1 TAGCTAAATTGGGCTTAAAT-CGAGTGCAAGCTAA
5665564 ATTAGGTTAA
Statistics
Matches: 71, Mismatches: 18, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
55 3 0.04
56 66 0.93
57 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.31
Consensus pattern (55 bp):
TAGCTAAATTGGGCTTAAATCGAGTGCAAGCTAATATAGGCTTAAAACTAAGTGC
Found at i:5665613 original size:29 final size:27
Alignment explanation
Indices: 5665543--5665620 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
5665533 TAAGTTGTGC
* * *
5665543 TTAAATCCGAGTGCCAGCTAAATTAGG
1 TTAAATCTGGGTGTCAGCTAAATTAGG
*
5665570 TTAAATCTGGGTGTCAGCTAAGTTAGG
1 TTAAATCTGGGTGTCAGCTAAATTAGG
*
5665597 CTTAAAATTTGGGTGTCAGCTAAA
1 -TT-AAATCTGGGTGTCAGCTAAA
5665621 CTGAGCTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 23 0.53
28 2 0.05
29 18 0.42
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (27 bp):
TTAAATCTGGGTGTCAGCTAAATTAGG
Found at i:5665628 original size:29 final size:29
Alignment explanation
Indices: 5665572--5665634 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
5665562 AAATTAGGTT
* *
5665572 AAATCTGGGTGTCAGCTAAGTTAGGCTTA
1 AAATCTGGGTGTCAGCTAACTGAGGCTTA
*
5665601 AAATTTGGGTGTCAGCTAAACTGA-GCTTA
1 AAATCTGGGTGTCAGCT-AACTGAGGCTTA
5665630 AAATC
1 AAATC
5665635 GTATGCCAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 25 0.86
30 4 0.14
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (29 bp):
AAATCTGGGTGTCAGCTAACTGAGGCTTA
Found at i:5665669 original size:28 final size:28
Alignment explanation
Indices: 5665440--5665688 Score: 134
Period size: 28 Copynumber: 8.9 Consensus size: 28
5665430 CTTAAATTCG
* *
5665440 AGTGCTAGCT-AATATAGGCTTAAAACTA
1 AGTGCCAGCTAAAT-TAGGCTTAAATCTA
* * * *
5665468 TGTGCTAGCTAAATTGGGTTTAAATCTA
1 AGTGCCAGCTAAATTAGGCTTAAATCTA
* * * * * *
5665496 TGAGCAAGCT-AATCTGGGTTTAACTCTA
1 AGTGCCAGCTAAAT-TAGGCTTAAATCTA
* * **
5665524 AGTGCTAGCTAAGTT-GTGCTTAAATCCG
1 AGTGCCAGCTAAATTAG-GCTTAAATCTA
*
5665552 AGTGCCAGCTAAATTAGG-TTAAATCTG
1 AGTGCCAGCTAAATTAGGCTTAAATCTA
* * * * *
5665579 GGTGTCAGCTAAGTTAGGCTTAAAATTTG
1 AGTGCCAGCTAAATTAGGCTT-AAATCTA
* * *
5665608 GGTGTCAGCTAAACT-GAGCTTAAAATCGT-
1 AGTGCCAGCTAAATTAG-GCTT-AAATC-TA
*
5665637 A-TGCCAACTAAATTAGGCTTAAATCTA
1 AGTGCCAGCTAAATTAGGCTTAAATCTA
* *
5665664 AGTGCCAGTTAAACTAGGCTTAAAT
1 AGTGCCAGCTAAATTAGGCTTAAAT
5665689 GTGTTTTGCA
Statistics
Matches: 177, Mismatches: 32, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.01
27 33 0.19
28 107 0.60
29 35 0.20
30 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.31
Consensus pattern (28 bp):
AGTGCCAGCTAAATTAGGCTTAAATCTA
Found at i:5666677 original size:12 final size:12
Alignment explanation
Indices: 5666658--5666688 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5666648 TTGAAATAAG
5666658 TTTT-TTTATTT
1 TTTTATTTATTT
5666669 TTTTATTTATTT
1 TTTTATTTATTT
5666681 TTTTATTT
1 TTTTATTT
5666689 CTCAACAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTATTTATTT
Found at i:5667919 original size:17 final size:17
Alignment explanation
Indices: 5667887--5667918 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5667877 AATCATCAAT
5667887 TTTAATTTTTTCTTTTG
1 TTTAATTTTTTCTTTTG
5667904 TTTAA-TTTTTCTTTT
1 TTTAATTTTTTCTTTT
5667919 TTTTTCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.06, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTAATTTTTTCTTTTG
Found at i:5670380 original size:38 final size:39
Alignment explanation
Indices: 5670337--5670437 Score: 109
Period size: 38 Copynumber: 2.7 Consensus size: 39
5670327 TTATCTATTG
* * *
5670337 AGATGTGCATGAAG-TAGAATACATATACTGCCTAATTA
1 AGATGTACATGAAGATAAAATACATATACTACCTAATTA
* * *
5670375 AGATGTTCAAG-AGATAAAATACATGTACTACCTAATTA
1 AGATGTACATGAAGATAAAATACATATACTACCTAATTA
* *
5670413 AGATGTACATG-AGATGAAATGCATA
1 AGATGTACATGAAGATAAAATACATA
5670438 AATTATTATC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 2 0.04
38 50 0.96
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.28
Consensus pattern (39 bp):
AGATGTACATGAAGATAAAATACATATACTACCTAATTA
Found at i:5670739 original size:3 final size:3
Alignment explanation
Indices: 5670731--5670765 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
5670721 AATTTTTGTG
5670731 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5670766 GAACTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5672958 original size:22 final size:22
Alignment explanation
Indices: 5672913--5673004 Score: 82
Period size: 22 Copynumber: 4.1 Consensus size: 22
5672903 TTTTTAAGAT
* *
5672913 TTTGAAGTTTTAGGTTTCATGG
1 TTTGAAGTTTTAGGTTTTAGGG
5672935 TTTGAAGTTTTAGGATTTTA-GG
1 TTTGAAGTTTTAGG-TTTTAGGG
* *
5672957 TTTTAGGGTTTT-GGATTTTAGGG
1 TTTGA-AGTTTTAGG-TTTTAGGG
*
5672980 TTTTAA-TTTTGAGGTTTTAGGG
1 TTTGAAGTTTT-AGGTTTTAGGG
5673002 TTT
1 TTT
5673005 AAATGATGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
21 4 0.07
22 39 0.64
23 18 0.30
ACGTcount: A:0.17, C:0.01, G:0.28, T:0.53
Consensus pattern (22 bp):
TTTGAAGTTTTAGGTTTTAGGG
Found at i:5672959 original size:15 final size:15
Alignment explanation
Indices: 5672919--5673005 Score: 72
Period size: 15 Copynumber: 5.9 Consensus size: 15
5672909 AGATTTTGAA
* *
5672919 GTTTTAGGTTTCATG
1 GTTTTAGGTTTTAGG
* *
5672934 GTTTGAAGTTTTAGG
1 GTTTTAGGTTTTAGG
*
5672949 ATTTTAGGTTTTAGG
1 GTTTTAGGTTTTAGG
5672964 GTTTT-GGATTTTAGG
1 GTTTTAGG-TTTTAGG
*
5672979 GTTTTA-ATTTT-GAG
1 GTTTTAGGTTTTAG-G
*
5672993 GTTTTAGGGTTTA
1 GTTTTAGGTTTTA
5673006 AATGATGTTT
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
13 1 0.02
14 13 0.23
15 42 0.75
ACGTcount: A:0.17, C:0.01, G:0.29, T:0.53
Consensus pattern (15 bp):
GTTTTAGGTTTTAGG
Found at i:5673003 original size:8 final size:8
Alignment explanation
Indices: 5672941--5673004 Score: 57
Period size: 8 Copynumber: 8.5 Consensus size: 8
5672931 ATGGTTTGAA
5672941 GTTTTAGG
1 GTTTTAGG
*
5672949 ATTTTA-G
1 GTTTTAGG
5672956 GTTTTAGG
1 GTTTTAGG
5672964 GTTTT-GG
1 GTTTTAGG
*
5672971 ATTTTAGG
1 GTTTTAGG
5672979 GTTTTA--
1 GTTTTAGG
*
5672985 ATTTT-GAG
1 GTTTTAG-G
5672993 GTTTTAGG
1 GTTTTAGG
5673001 GTTT
1 GTTT
5673005 AAATGATGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
6 4 0.09
7 12 0.27
8 27 0.61
9 1 0.02
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.55
Consensus pattern (8 bp):
GTTTTAGG
Found at i:5673606 original size:20 final size:20
Alignment explanation
Indices: 5673581--5673618 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5673571 CACTTCAATA
*
5673581 AAAATTATTTTTATTATTGT
1 AAAATTATTATTATTATTGT
5673601 AAAATTATTATTATTATT
1 AAAATTATTATTATTATT
5673619 ATTATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
AAAATTATTATTATTATTGT
Found at i:5673610 original size:3 final size:3
Alignment explanation
Indices: 5673604--5673630 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5673594 TTATTGTAAA
5673604 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
5673631 TGTTAAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:5676664 original size:2 final size:2
Alignment explanation
Indices: 5676657--5676692 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5676647 GCTAACATTC
5676657 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
5676693 CAACAAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5677107 original size:12 final size:12
Alignment explanation
Indices: 5677076--5677114 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5677066 TTTGTTAATT
5677076 TTTTA-AAAATAA
1 TTTTATAAAA-AA
*
5677088 TTTAATAAAAAA
1 TTTTATAAAAAA
5677100 TTTTATAAAAAA
1 TTTTATAAAAAA
5677112 TTT
1 TTT
5677115 AAAATGATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTTATAAAAAA
Found at i:5677370 original size:22 final size:23
Alignment explanation
Indices: 5677347--5677390 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
5677337 ATTTAATTAT
5677347 TTTTA-ATAAAAAATT-TTTGAA
1 TTTTACATAAAAAATTATTTGAA
*
5677368 TTTTACTTAAAAAATTATTTGAA
1 TTTTACATAAAAAATTATTTGAA
5677391 ACTTTCCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 9 0.45
23 6 0.30
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (23 bp):
TTTTACATAAAAAATTATTTGAA
Found at i:5681694 original size:23 final size:23
Alignment explanation
Indices: 5681644--5681693 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
5681634 TTTTATTCGC
5681644 TTTTTATCAAGGTTTTTAGTTCA
1 TTTTTATCAAGGTTTTTAGTTCA
*
5681667 TTTTTATTCAATGTTTTTA-TT-A
1 TTTTTA-TCAAGGTTTTTAGTTCA
5681689 TTTTT
1 TTTTT
5681694 TGTTTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 6 0.24
23 8 0.32
24 11 0.44
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.66
Consensus pattern (23 bp):
TTTTTATCAAGGTTTTTAGTTCA
Found at i:5692005 original size:13 final size:13
Alignment explanation
Indices: 5691987--5692011 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5691977 ACGGTTGTTG
5691987 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
5692000 TTTTTCTTTTTT
1 TTTTTCTTTTTT
5692012 TAATGGAATA
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:5692098 original size:3 final size:3
Alignment explanation
Indices: 5692090--5692119 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5692080 TCGTTATATT
5692090 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5692120 TTTTTATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5692191 original size:58 final size:58
Alignment explanation
Indices: 5692123--5692244 Score: 235
Period size: 58 Copynumber: 2.1 Consensus size: 58
5692113 AATAATATTT
*
5692123 TTATGATCTTATTTATTATAATAAAAATATTCTTAATAAAAATATTTGACAATTGTAC
1 TTATTATCTTATTTATTATAATAAAAATATTCTTAATAAAAATATTTGACAATTGTAC
5692181 TTATTATCTTATTTATTATAATAAAAATATTCTTAATAAAAATATTTGACAATTGTAC
1 TTATTATCTTATTTATTATAATAAAAATATTCTTAATAAAAATATTTGACAATTGTAC
5692239 TTATTA
1 TTATTA
5692245 ATACATGTAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.47
Consensus pattern (58 bp):
TTATTATCTTATTTATTATAATAAAAATATTCTTAATAAAAATATTTGACAATTGTAC
Found at i:5693083 original size:19 final size:18
Alignment explanation
Indices: 5693046--5693084 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
5693036 TTATTTATTT
*
5693046 TTAAATAACAATTATATA
1 TTAAATAACAATTACATA
*
5693064 TTAAATATATAATTACATA
1 TTAAATA-ACAATTACATA
5693083 TT
1 TT
5693085 TTTGTAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (18 bp):
TTAAATAACAATTACATA
Found at i:5693938 original size:20 final size:21
Alignment explanation
Indices: 5693902--5693953 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5693892 CTTGAAATTA
5693902 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
5693924 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
5693945 AT-AAATATT
1 ATAAAATATT
5693954 TAAAATTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:5693944 original size:21 final size:22
Alignment explanation
Indices: 5693902--5693953 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
5693892 CTTGAAATTA
5693902 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
5693924 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
5693945 AT-AAATATT
1 ATAAAATATT
5693954 TAAAATTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:5696880 original size:16 final size:17
Alignment explanation
Indices: 5696849--5696897 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
5696839 TAAAATTTTT
*
5696849 TTTTAAATTATA--TAA
1 TTTTATATTATATTTAA
5696864 TTTTATA-TATATTTAA
1 TTTTATATTATATTTAA
5696880 TTTTATATTTATATTTAA
1 TTTTATA-TTATATTTAA
5696898 AATAATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 4 0.14
15 6 0.21
16 10 0.34
18 9 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTATATTATATTTAA
Found at i:5698680 original size:20 final size:21
Alignment explanation
Indices: 5698646--5698684 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
5698636 AATTGTCATA
*
5698646 TAAAAATTTATAAAATTTTTT
1 TAAAAATTTAAAAAATTTTTT
5698667 TAAAAA-TTAAAAAATTTT
1 TAAAAATTTAAAAAATTTT
5698685 GATGCATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAAATTTAAAAAATTTTTT
Found at i:5698819 original size:15 final size:16
Alignment explanation
Indices: 5698801--5698830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5698791 AATTTTCTTA
5698801 TTAAA-TTTTATTAAT
1 TTAAATTTTTATTAAT
5698816 TTAAATTTTTATTAA
1 TTAAATTTTTATTAA
5698831 ATTATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAATTTTTATTAAT
Found at i:5699622 original size:2 final size:2
Alignment explanation
Indices: 5699615--5699644 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5699605 TGAGCTTAAG
*
5699615 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5699645 GCATATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5709116 original size:183 final size:182
Alignment explanation
Indices: 5708809--5709176 Score: 603
Period size: 183 Copynumber: 2.0 Consensus size: 182
5708799 TGACTCTATC
* *
5708809 TTAATGCACAATAAAAACAAGCAAGTCTTTCACTAGATATTATAATTTATTATTTCCCAGAAAGG
1 TTAATGCACAATAAAAACAAGCAAATCTCTCACTAGATATTATAATTTATTATTTCCCAGAAAGG
*
5708874 TCTAACAATTGCTCCACCTTAATAACAGCATATCCATTATTTAGACATCTAGGAGCAGAAATTCA
66 TCTAACAATTGCTCCACCTTAATAACAGCATATCCATTATTTAGACATCTAGAAGCAGAAATTCA
* *
5708939 AATAACTCAAGTCTGAGCAACACAGAGATAAAGACATCTAGGGGCGTATCTG
131 AATAACTCAAGTCTGAGCAACACAAAGATAAAGACATCTAGGGGCATATCTG
* ** *
5708991 TTAATGCATAATAATGAGAAGCAAATCTCTCACTAGATATTATAATTTATTATTT-CCAGGAAAG
1 TTAATGCACAATAAAAACAAGCAAATCTCTCACTAGATATTATAATTTATTATTTCCCA-GAAAG
**
5709055 GTCTAACAAATTGCTCCACCTTAATAACAGCATATCTGTTATTTAGACATCTAGAAGCAGAAATT
65 GTCTAAC-AATTGCTCCACCTTAATAACAGCATATCCATTATTTAGACATCTAGAAGCAGAAATT
*
5709120 CAAATAACTTAAGTCTGAGCAACACAAAGATAAAGACATCTAGGGGCATATCTG
129 CAAATAACTCAAGTCTGAGCAACACAAAGATAAAGACATCTAGGGGCATATCTG
5709174 TTA
1 TTA
5709177 TTTAGAAGAA
Statistics
Matches: 172, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
181 3 0.02
182 61 0.35
183 108 0.63
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (182 bp):
TTAATGCACAATAAAAACAAGCAAATCTCTCACTAGATATTATAATTTATTATTTCCCAGAAAGG
TCTAACAATTGCTCCACCTTAATAACAGCATATCCATTATTTAGACATCTAGAAGCAGAAATTCA
AATAACTCAAGTCTGAGCAACACAAAGATAAAGACATCTAGGGGCATATCTG
Found at i:5709758 original size:13 final size:13
Alignment explanation
Indices: 5709740--5709764 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5709730 TTTATACCAT
5709740 TGTTATAGGCATC
1 TGTTATAGGCATC
5709753 TGTTATAGGCAT
1 TGTTATAGGCAT
5709765 GCAATTTAGT
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:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (13 bp):
TGTTATAGGCATC
Found at i:5714901 original size:6 final size:6
Alignment explanation
Indices: 5714890--5714921 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5714880 GGTAAAATTA
5714890 TATAAT TATAAT TATAAT TATAAT TATAAT TA
1 TATAAT TATAAT TATAAT TATAAT TATAAT TA
5714922 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TATAAT
Found at i:5715163 original size:6 final size:6
Alignment explanation
Indices: 5715152--5715183 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5715142 AATAAAGTTA
5715152 ATTCTC ATTCTC ATTCTC ATTCTC ATTCTC AT
1 ATTCTC ATTCTC ATTCTC ATTCTC ATTCTC AT
5715184 AATTAACTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTCTC
Found at i:5718468 original size:21 final size:21
Alignment explanation
Indices: 5718442--5718535 Score: 73
Period size: 21 Copynumber: 4.5 Consensus size: 21
5718432 TATAACTTTG
*
5718442 ATTTTGATAATTTTTTATAAA
1 ATTTTGATAATTTTTTATATA
* * ** *
5718463 ATTTTGGTAATATTCAATACA
1 ATTTTGATAATTTTTTATATA
* *
5718484 ATCTTAATAATTTTTTATATTA
1 ATTTTGATAATTTTTTATA-TA
* *
5718506 A-TTTGATAATTTATGATATA
1 ATTTTGATAATTTTTTATATA
*
5718526 ATTTGGATAA
1 ATTTTGATAA
5718536 CCATTAATAA
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
20 3 0.06
21 49 0.91
22 2 0.04
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.51
Consensus pattern (21 bp):
ATTTTGATAATTTTTTATATA
Found at i:5718468 original size:27 final size:27
Alignment explanation
Indices: 5718417--5718468 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5718407 ATTAGTAAAA
*
5718417 TTTGATAACTTTTTATATAACTTTGAT
1 TTTGATAACTTTTTATAAAACTTTGAT
* *
5718444 TTTGATAATTTTTTATAAAATTTTG
1 TTTGATAACTTTTTATAAAACTTTG
5718469 GTAATATTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.58
Consensus pattern (27 bp):
TTTGATAACTTTTTATAAAACTTTGAT
Found at i:5718912 original size:22 final size:22
Alignment explanation
Indices: 5718873--5718928 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
5718863 AAAATATTTT
*
5718873 ATCAATAATTGATAATTAAGTA
1 ATCAATAATTTATAATTAAGTA
* * * *
5718895 ATCATTAATTTATTATTATGTT
1 ATCAATAATTTATAATTAAGTA
*
5718917 ATCAGTAATTTA
1 ATCAATAATTTA
5718929 CTACTAAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.46
Consensus pattern (22 bp):
ATCAATAATTTATAATTAAGTA
Found at i:5718974 original size:22 final size:22
Alignment explanation
Indices: 5718924--5719001 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
5718914 GTTATCAGTA
**
5718924 ATTTACTACTAAGCTAGCAAAT-
1 ATTTACTACTAAAATAGC-AATG
* * *
5718946 ATATACTGCTAAAATATCAATG
1 ATTTACTACTAAAATAGCAATG
* *
5718968 ATTTACTACTAAATTAGCATTG
1 ATTTACTACTAAAATAGCAATG
5718990 ATTTACTACTAA
1 ATTTACTACTAA
5719002 TTTATGAAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
21 3 0.07
22 42 0.93
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (22 bp):
ATTTACTACTAAAATAGCAATG
Found at i:5719015 original size:22 final size:22
Alignment explanation
Indices: 5718990--5719047 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
5718980 ATTAGCATTG
5718990 ATTTACTACTAATTTATGAAAA
1 ATTTACTACTAATTTATGAAAA
** **
5719012 ATTTACTACTAGGTTATGAATG
1 ATTTACTACTAATTTATGAAAA
5719034 ATTTACTACTAATT
1 ATTTACTACTAATT
5719048 ATTGATGATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (22 bp):
ATTTACTACTAATTTATGAAAA
Found at i:5722689 original size:2 final size:2
Alignment explanation
Indices: 5722682--5722719 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
5722672 TTCACATTTT
*
5722682 TA TA TA TA AA TGA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA T
5722720 TTGACTCATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5750611 original size:2 final size:2
Alignment explanation
Indices: 5750606--5750634 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5750596 TGTGTGTGTC
5750606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5750635 CCAAAATTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5752705 original size:27 final size:27
Alignment explanation
Indices: 5752666--5752717 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
5752656 TGGATCGAAC
5752666 GGTTTAGGACTGGCTCTGATACCACAT
1 GGTTTAGGACTGGCTCTGATACCACAT
5752693 GGTTTAAGG-CTGGCTCTGATACCAC
1 GGTTT-AGGACTGGCTCTGATACCAC
5752718 TTGTCACGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (27 bp):
GGTTTAGGACTGGCTCTGATACCACAT
Found at i:5754471 original size:24 final size:24
Alignment explanation
Indices: 5754413--5754471 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
5754403 TAAAATTGAT
* *
5754413 TCAAATCAAATAAAAAATTCAATC
1 TCAAATCAATTAAAAAATTCAAAC
* * *
5754437 -CAAACTAAATTAAATATTTCAAAC
1 TCAAA-TCAATTAAAAAATTCAAAC
5754461 TCAAATCAATT
1 TCAAATCAATT
5754472 TTTAAATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
23 4 0.15
24 19 0.70
25 4 0.15
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (24 bp):
TCAAATCAATTAAAAAATTCAAAC
Found at i:5756027 original size:11 final size:11
Alignment explanation
Indices: 5756011--5756035 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5756001 CCCATCTTCT
5756011 TTAAACTTAGA
1 TTAAACTTAGA
5756022 TTAAACTTAGA
1 TTAAACTTAGA
5756033 TTA
1 TTA
5756036 CTTTGATAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
TTAAACTTAGA
Found at i:5758686 original size:12 final size:14
Alignment explanation
Indices: 5758652--5758681 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5758642 ATAAAATAAA
5758652 ATAATATTATTTAAT
1 ATAATATTATTT-AT
5758667 ATAATATTATTTAT
1 ATAATATTATTTAT
5758681 A
1 A
5758682 ATATTTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 3 0.20
15 12 0.80
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAATATTATTTAT
Found at i:5762777 original size:14 final size:15
Alignment explanation
Indices: 5762758--5762791 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5762748 ATCATCAAAC
5762758 ATTTATTTT-TAAAA
1 ATTTATTTTATAAAA
5762772 ATTTATTTTATAAAA
1 ATTTATTTTATAAAA
*
5762787 TTTTA
1 ATTTA
5762792 AATCGTATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTATTTTATAAAA
Found at i:5763849 original size:18 final size:18
Alignment explanation
Indices: 5763826--5763861 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
5763816 TTTTTTTTGG
*
5763826 GGGGGGGGGGGGGGGGGA
1 GGGGGGAGGGGGGGGGGA
*
5763844 GGGGGGAGGGGTGGGGGA
1 GGGGGGAGGGGGGGGGGA
5763862 CCGAATCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.89, T:0.03
Consensus pattern (18 bp):
GGGGGGAGGGGGGGGGGA
Found at i:5770113 original size:16 final size:15
Alignment explanation
Indices: 5770081--5770123 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
5770071 ATTGGAGATG
*
5770081 TTTCTTTTTTGTGTT
1 TTTCTTTTTTTTGTT
5770096 TTATCTTTTTTTT-TT
1 TT-TCTTTTTTTTGTT
*
5770111 TTTTTTTTTTTTG
1 TTTCTTTTTTTTG
5770124 AAAATTGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 9 0.38
15 6 0.25
16 9 0.38
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (15 bp):
TTTCTTTTTTTTGTT
Found at i:5790699 original size:17 final size:18
Alignment explanation
Indices: 5790664--5790725 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 18
5790654 CATTATCAAG
* *
5790664 ATATAAATATTTAATAAA
1 ATATTAATATGTAATAAA
5790682 ATATTAATATGT-ATAAA
1 ATATTAATATGTAATAAA
* * *
5790699 AAATAAAT-TTTAATAAA
1 ATATTAATATGTAATAAA
5790716 ATATTAATAT
1 ATATTAATAT
5790726 ATGTAAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
16 2 0.06
17 22 0.63
18 11 0.31
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATATTAATATGTAATAAA
Found at i:5790713 original size:34 final size:34
Alignment explanation
Indices: 5790666--5790740 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
5790656 TTATCAAGAT
*
5790666 ATAAATATTTAATAAAATATTAATATGTATAAAAA
1 ATAAAT-TTTAATAAAATATTAATATATATAAAAA
*
5790701 ATAAATTTTAATAAAATATTAATATATGTAAAAA
1 ATAAATTTTAATAAAATATTAATATATATAAAAA
5790735 A-AAATT
1 ATAAATT
5790741 CAATCATTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 5 0.13
34 27 0.71
35 6 0.16
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (34 bp):
ATAAATTTTAATAAAATATTAATATATATAAAAA
Found at i:5790838 original size:19 final size:18
Alignment explanation
Indices: 5790808--5790850 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
5790798 TAAATTTTTT
*
5790808 AAATTATAAAAATTCAAA
1 AAATTTTAAAAATTCAAA
5790826 AATATTTTAAAAATTCAAA
1 AA-ATTTTAAAAATTCAAA
5790845 AAATTT
1 AAATTT
5790851 GAAGAACACC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
AAATTTTAAAAATTCAAA
Found at i:5791931 original size:10 final size:10
Alignment explanation
Indices: 5791919--5792014 Score: 70
Period size: 10 Copynumber: 9.8 Consensus size: 10
5791909 TGAAATTTTT
*
5791919 AATTTTTTAT
1 AATTTTTTAA
*
5791929 AATTTTTAAA
1 AATTTTTTAA
** *
5791939 AAACTTTTAG
1 AATTTTTTAA
*
5791949 AATTTTTT-T
1 AATTTTTTAA
5791958 AA-TTTTTAA
1 AATTTTTTAA
* *
5791967 AAATTTTTAC
1 AATTTTTTAA
* *
5791977 AGTTTCTTAA
1 AATTTTTTAA
5791987 AATTTTTTAA
1 AATTTTTTAA
* *
5791997 AAATTTTTAG
1 AATTTTTTAA
5792007 AATTTTTT
1 AATTTTTT
5792015 TATATTTAAA
Statistics
Matches: 64, Mismatches: 20, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
8 5 0.08
9 4 0.06
10 55 0.86
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.57
Consensus pattern (10 bp):
AATTTTTTAA
Found at i:5791971 original size:19 final size:18
Alignment explanation
Indices: 5791943--5792031 Score: 63
Period size: 20 Copynumber: 4.7 Consensus size: 18
5791933 TTTAAAAAAC
*
5791943 TTTTAGAATTTTTTTAAT
1 TTTTAAAATTTTTTTAAT
*
5791961 TTTTAAAA-ATTTTTACAGT
1 TTTTAAAATTTTTTTA-A-T
*
5791980 TTCTTAAAATTTTTTAAAAAT
1 TT-TTAAAATTTTTT--TAAT
*
5792001 TTTTAGAATTTTTTTATAT
1 TTTTAAAATTTTTTTA-AT
**
5792020 TTAAAAAATTTT
1 TTTTAAAATTTT
5792032 AATACAGATG
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
17 6 0.11
18 9 0.16
19 14 0.25
20 17 0.31
21 7 0.13
22 1 0.02
23 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTAAAATTTTTTTAAT
Found at i:5791999 original size:58 final size:55
Alignment explanation
Indices: 5791911--5792034 Score: 167
Period size: 58 Copynumber: 2.2 Consensus size: 55
5791901 TTTTTTTTTG
* * *
5791911 AAATTTTTAATTTTTTATAATTTTTAAAAAACTTTTAGAATTTTTTTAATTTTTAA
1 AAATTTTTAATTTCTTAAAATTTTTAAAAAACTTTTAGAATTTTTTT-ATATTTAA
* *
5791967 AAATTTTTACAGTTTCTTAAAATTTTTTAAAAATTTTTAGAATTTTTTTATATTTAA
1 AAATTTTTA-A-TTTCTTAAAATTTTTAAAAAACTTTTAGAATTTTTTTATATTTAA
*
5792024 AAAATTTTAAT
1 AAATTTTTAAT
5792035 ACAGATGTAG
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
55 1 0.02
56 10 0.17
57 16 0.27
58 33 0.55
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (55 bp):
AAATTTTTAATTTCTTAAAATTTTTAAAAAACTTTTAGAATTTTTTTATATTTAA
Found at i:5793012 original size:130 final size:130
Alignment explanation
Indices: 5792779--5793032 Score: 490
Period size: 130 Copynumber: 2.0 Consensus size: 130
5792769 AATTACATTA
*
5792779 ACCAACTAGAATCCAGGGCGTCTGAGGTCAGTTTCTTCTCTGATTCTGCTTTTTTAAAACCTTTT
1 ACCAACTAGAATCCAGGGCGTCTGAGATCAGTTTCTTCTCTGATTCTGCTTTTTTAAAACCTTTT
5792844 AATTTTGTTAGATTAGTTGAAATGATTTTATTGCATATATTTTGAAACTGAGGCAGTTTTGGTAT
66 AATTTTGTTAGATTAGTTGAAATGATTTTATTGCATATATTTTGAAACTGAGGCAGTTTTGGTAT
5792909 ACCAACTAGAATCCAGGGCGTCTGAGATCAGTTTCTTCTCTGATTCTGCTTTTTTAAAACCTTTT
1 ACCAACTAGAATCCAGGGCGTCTGAGATCAGTTTCTTCTCTGATTCTGCTTTTTTAAAACCTTTT
*
5792974 AATTTTGTTAGATTAGTTGAAATGGTTTTATTGCATATATTTTGAAACTGAGGCAGTTT
66 AATTTTGTTAGATTAGTTGAAATGATTTTATTGCATATATTTTGAAACTGAGGCAGTTT
5793033 CATATATAAA
Statistics
Matches: 122, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
130 122 1.00
ACGTcount: A:0.26, C:0.14, G:0.18, T:0.42
Consensus pattern (130 bp):
ACCAACTAGAATCCAGGGCGTCTGAGATCAGTTTCTTCTCTGATTCTGCTTTTTTAAAACCTTTT
AATTTTGTTAGATTAGTTGAAATGATTTTATTGCATATATTTTGAAACTGAGGCAGTTTTGGTAT
Found at i:5793054 original size:2 final size:2
Alignment explanation
Indices: 5793034--5793078 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
5793024 AGGCAGTTTC
* *
5793034 AT AT AT AA AT AA AT A- 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
5793075 AT AT
1 AT AT
5793079 TAAGATTGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5798113 original size:2 final size:2
Alignment explanation
Indices: 5798106--5798136 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5798096 GTAAAATGTC
5798106 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 A
5798137 CACACAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5801131 original size:29 final size:28
Alignment explanation
Indices: 5801098--5801180 Score: 103
Period size: 29 Copynumber: 2.9 Consensus size: 28
5801088 GATTTTTAGT
5801098 AATTTAGTTCCTATAGTATTATTTAAAGA
1 AATTTAGTTCCTATAGTATTATTTAAA-A
* *
5801127 AATTTAGTTCTTATAATATTACTTTTAAAA
1 AATTTAGTTCCTATAGTATTA--TTTAAAA
* *
5801157 ATTTTAGTCCCTATAGTATTATTT
1 AATTTAGTTCCTATAGTATTATTT
5801181 TTTAAGTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
28 3 0.07
29 19 0.41
30 18 0.39
31 6 0.13
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.49
Consensus pattern (28 bp):
AATTTAGTTCCTATAGTATTATTTAAAA
Found at i:5801181 original size:29 final size:30
Alignment explanation
Indices: 5801098--5801209 Score: 113
Period size: 30 Copynumber: 3.8 Consensus size: 30
5801088 GATTTTTAGT
5801098 AATTTAGTTCCTATAGTATTA-TTTAAAGA
1 AATTTAGTTCCTATAGTATTATTTTAAAGA
* *
5801127 AATTTAGTTCTTATAATATTACTTTTAAA-A
1 AATTTAGTTCCTATAGTATTA-TTTTAAAGA
* * * *
5801157 ATTTTAGTCCCTATAGTATTATTTTTTAAGT
1 AATTTAGTTCCTATAGTATTA-TTTTAAAGA
* *
5801188 AATTTAGTCCCTAT-GCATTATT
1 AATTTAGTTCCTATAGTATTATT
5801210 AAGGATTAAA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 21 0.30
30 29 0.42
31 19 0.28
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (30 bp):
AATTTAGTTCCTATAGTATTATTTTAAAGA
Found at i:5802958 original size:17 final size:18
Alignment explanation
Indices: 5802933--5802974 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5802923 TTAAGATATT
* *
5802933 AAATAATATTTTTTAATA
1 AAATAATATATTTAAATA
5802951 AAAT-ATATATTTAAAT-
1 AAATAATATATTTAAATA
5802967 AAATAATA
1 AAATAATA
5802975 AAATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 4 0.19
17 13 0.62
18 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATAATATATTTAAATA
Found at i:5803223 original size:10 final size:10
Alignment explanation
Indices: 5803208--5803263 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
5803198 AAATAAAATT
*
5803208 AAAAAAACAC
1 AAAAAAAAAC
*
5803218 AAAAAAGTAAAT
1 AAAAAA--AAAC
5803230 AAAAAAATAA-
1 AAAAAAA-AAC
5803240 AAAAAAAAAC
1 AAAAAAAAAC
*
5803250 AAAACAAAAC
1 AAAAAAAAAC
5803260 AAAA
1 AAAA
5803264 GAACGGAGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 2 0.05
12 8 0.21
ACGTcount: A:0.84, C:0.09, G:0.02, T:0.05
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:5803229 original size:23 final size:22
Alignment explanation
Indices: 5803195--5803263 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
5803185 AAATTTAATT
5803195 AAAAAATAAAATTAAAAAAACACA
1 AAAAAATAAAA-TAAAAAAACA-A
* *
5803219 AAAAAGT-AAATAAAAAAATAA
1 AAAAAATAAAATAAAAAAACAA
5803240 AAAAAA-AAACA-AAACAAAACAA
1 AAAAAATAAA-ATAAA-AAAACAA
5803262 AA
1 AA
5803264 GAACGGAGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
21 11 0.29
22 18 0.47
23 3 0.08
24 6 0.16
ACGTcount: A:0.83, C:0.07, G:0.01, T:0.09
Consensus pattern (22 bp):
AAAAAATAAAATAAAAAAACAA
Found at i:5804066 original size:10 final size:10
Alignment explanation
Indices: 5804053--5804086 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
5804043 AATGATAGAG
5804053 AAAAAAGAAA
1 AAAAAAGAAA
*
5804063 AAAAAAGTAA
1 AAAAAAGAAA
5804073 AAAAAA-AAA
1 AAAAAAGAAA
5804082 AAAAA
1 AAAAA
5804087 CATTTGGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.32
10 15 0.68
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:5804074 original size:11 final size:10
Alignment explanation
Indices: 5804053--5804086 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
5804043 AATGATAGAG
5804053 AAAAAAGAAA
1 AAAAAAGAAA
5804063 AAAAAAGTAAA
1 AAAAAAG-AAA
5804074 AAAAAA-AAA
1 AAAAAAGAAA
5804083 AAAA
1 AAAA
5804087 CATTTGGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 7 0.30
10 7 0.30
11 9 0.39
ACGTcount: A:0.91, C:0.00, G:0.06, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAA
Done.