Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 18 of 125
Found at i:5669274 original size:26 final size:26
Alignment explanation
Indices: 5669245--5669304 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
5669235 GCATCATGTG
5669245 AGCTCAATCTGTAAGCTCATTATGCA
1 AGCTCAATCTGTAAGCTCATTATGCA
* *
5669271 AGCTCAATTTGTGAGCTCATTATGCA
1 AGCTCAATCTGTAAGCTCATTATGCA
5669297 AGCTCAAT
1 AGCTCAAT
5669305 ATGGATCCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (26 bp):
AGCTCAATCTGTAAGCTCATTATGCA
Found at i:5671691 original size:93 final size:93
Alignment explanation
Indices: 5671532--5671716 Score: 343
Period size: 93 Copynumber: 2.0 Consensus size: 93
5671522 CAATAGTGGA
* *
5671532 TCTCCAATTTTACCATATACCATTGTTATTTGTGGGTTTTAGTAAAATAAGTCAATTTTTATTCG
1 TCTCCAATTTTACCATATACCATTGTTATTTGTGGATTTTAGTAAAATAAATCAATTTTTATTCG
5671597 GATTATTTTGATTCTTAGTTCGTTTGTG
66 GATTATTTTGATTCTTAGTTCGTTTGTG
*
5671625 TCTCCAATTTTACCATATACCATTGTTATTTGTGGATTTTAGTAAAATAAATTAATTTTTATTCG
1 TCTCCAATTTTACCATATACCATTGTTATTTGTGGATTTTAGTAAAATAAATCAATTTTTATTCG
5671690 GATTATTTTGATTCTTAGTTCGTTTGT
66 GATTATTTTGATTCTTAGTTCGTTTGT
5671717 CCTTAGTATA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.50
Consensus pattern (93 bp):
TCTCCAATTTTACCATATACCATTGTTATTTGTGGATTTTAGTAAAATAAATCAATTTTTATTCG
GATTATTTTGATTCTTAGTTCGTTTGTG
Found at i:5674297 original size:19 final size:19
Alignment explanation
Indices: 5674255--5674297 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
5674245 ATAAAACCAT
*
5674255 CATTATCTTCAAAATGTTA
1 CATTATCTTCAAAATATTA
* * *
5674274 TATTATCTTTAGAATATTA
1 CATTATCTTCAAAATATTA
5674293 CATTA
1 CATTA
5674298 CCACCATAGT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (19 bp):
CATTATCTTCAAAATATTA
Found at i:5683038 original size:27 final size:27
Alignment explanation
Indices: 5682983--5683038 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
5682973 GTTTTGCTGT
* *
5682983 CAATCATCCGTTTCTAGATTGTTAAAA
1 CAATCATCCGCTTCTAGATTGTCAAAA
*
5683010 CAATCATCCGCTTCTAGATTGTCAGAA
1 CAATCATCCGCTTCTAGATTGTCAAAA
5683037 CA
1 CA
5683039 TCCTATCGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (27 bp):
CAATCATCCGCTTCTAGATTGTCAAAA
Found at i:5688104 original size:3 final size:3
Alignment explanation
Indices: 5688096--5688132 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5688086 CCCCAAGTAA
5688096 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
5688133 GGAGGAGGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5690358 original size:64 final size:64
Alignment explanation
Indices: 5690190--5690379 Score: 280
Period size: 64 Copynumber: 3.0 Consensus size: 64
5690180 CTATTGTATT
* * *
5690190 AGGCGACACTAATATGTATTTTTTGAAAAATACTCGAAAAAATATGGGTATATCGATG-AAAAA
1 AGGCGACACTGATATGTATTTTTTGAAAAATACTCGAGAAAATATGGGTATACCGATGAAAAAA
* * *
5690253 AGTG-G-CACCGATATGTATTTTTTG-AAAATACTCAAGAAAATACGGGTATACCGATGAAAAAA
1 AG-GCGACACTGATATGTATTTTTTGAAAAATACTCGAGAAAATATGGGTATACCGATGAAAAAA
*
5690315 AGGCGACACTGGTATGTATTTTTTGAAAAATACTCGAGAAAATATGGGTATACCGATGAAAAAA
1 AGGCGACACTGATATGTATTTTTTGAAAAATACTCGAGAAAATATGGGTATACCGATGAAAAAA
5690379 A
1 A
5690380 ATATTTTTTA
Statistics
Matches: 112, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
61 29 0.26
62 25 0.22
63 20 0.18
64 38 0.34
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.27
Consensus pattern (64 bp):
AGGCGACACTGATATGTATTTTTTGAAAAATACTCGAGAAAATATGGGTATACCGATGAAAAAA
Found at i:5692318 original size:22 final size:24
Alignment explanation
Indices: 5692272--5692320 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
5692262 AAATTATGGA
*
5692272 TTATTATATTAAATATAGTCTTTT
1 TTATTATATTAAATATACTCTTTT
*
5692296 TTATTATA-TGAA-ATACTCTTTT
1 TTATTATATTAAATATACTCTTTT
5692318 TTA
1 TTA
5692321 AAAATAACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 12 0.52
23 3 0.13
24 8 0.35
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TTATTATATTAAATATACTCTTTT
Found at i:5696881 original size:19 final size:18
Alignment explanation
Indices: 5696857--5696903 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
5696847 TTGTTTATGT
*
5696857 TTTTAATTATTAAATTATC
1 TTTTAATT-TTAAATTAAC
5696876 TTTTAACCTTTTAAATTAAC
1 TTTTAA--TTTTAAATTAAC
5696896 -TTTAATTT
1 TTTTAATTT
5696904 CATAAAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
19 11 0.44
20 9 0.36
21 2 0.08
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTAATTTTAAATTAAC
Found at i:5713304 original size:6 final size:6
Alignment explanation
Indices: 5713243--5713292 Score: 91
Period size: 6 Copynumber: 8.2 Consensus size: 6
5713233 AGTTTTCTCC
5713243 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AGAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG
5713292 A
1 A
5713293 CCTGAAAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
6 37 0.86
7 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:5715490 original size:25 final size:25
Alignment explanation
Indices: 5715450--5715497 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5715440 TGAACAATTT
5715450 CAAACATCCTACTGTCTACTAGTAA
1 CAAACATCCTACTGTCTACTAGTAA
* * *
5715475 CAAACATCTTAGTGTCTATTAGT
1 CAAACATCCTACTGTCTACTAGT
5715498 TTTTTTCCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (25 bp):
CAAACATCCTACTGTCTACTAGTAA
Found at i:5717748 original size:14 final size:14
Alignment explanation
Indices: 5717726--5717758 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5717716 TCATATGGTA
5717726 AGAGAATCTAGTAG
1 AGAGAATCTAGTAG
*
5717740 AGAGGATCTAGTAG
1 AGAGAATCTAGTAG
5717754 A-AGAA
1 AGAGAA
5717759 GGATAGTCCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.45, C:0.06, G:0.30, T:0.18
Consensus pattern (14 bp):
AGAGAATCTAGTAG
Found at i:5720238 original size:21 final size:22
Alignment explanation
Indices: 5720202--5720252 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
5720192 TATTTTTGTC
5720202 TTTTTCTTCTTTTTTTCCCTCAA
1 TTTTT-TTCTTTTTTTCCCTCAA
**
5720225 TTTTTTTCTTTTTTT-TTTCAA
1 TTTTTTTCTTTTTTTCCCTCAA
5720246 TTTTTTT
1 TTTTTTT
5720253 TTCAATTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 11 0.42
22 10 0.38
23 5 0.19
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTTTCTTTTTTTCCCTCAA
Found at i:5720239 original size:33 final size:32
Alignment explanation
Indices: 5720202--5720265 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 32
5720192 TATTTTTGTC
5720202 TTTTTCTTC-TTTTTTTCCCTCAATTTTTTTCTT
1 TTTTTCTTCATTTTTTT--CTCAATTTTTTTCTT
* *
5720235 TTTTTTTTCAATTTTTTTTTCAATTTTTTTC
1 TTTTTCTTC-ATTTTTTTCTCAATTTTTTTC
5720266 AATTTTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 20 0.74
35 7 0.26
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (32 bp):
TTTTTCTTCATTTTTTTCTCAATTTTTTTCTT
Found at i:5720240 original size:10 final size:10
Alignment explanation
Indices: 5720225--5720290 Score: 51
Period size: 10 Copynumber: 6.3 Consensus size: 10
5720215 TTTCCCTCAA
5720225 TTTTTTTCTTT
1 TTTTTTTC-TT
5720236 TTTTTTTCAATT
1 TTTTTTTC--TT
**
5720248 TTTTTTTCAA
1 TTTTTTTCTT
**
5720258 TTTTTTTCAA
1 TTTTTTTCTT
**
5720268 TTTTTTGATT
1 TTTTTTTCTT
5720278 TTTTTTTCTT
1 TTTTTTTCTT
5720288 TTT
1 TTT
5720291 CTAAATAATA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
10 27 0.60
11 8 0.18
12 10 0.22
ACGTcount: A:0.11, C:0.08, G:0.02, T:0.80
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:5720240 original size:12 final size:11
Alignment explanation
Indices: 5720225--5720290 Score: 59
Period size: 11 Copynumber: 6.3 Consensus size: 11
5720215 TTTCCCTCAA
*
5720225 TTTTTTTCTTT
1 TTTTTTTCATT
5720236 TTTTTTTCAATT
1 TTTTTTTC-ATT
*
5720248 TTTTTTTCA-A
1 TTTTTTTCATT
5720258 TTTTTTTCA--
1 TTTTTTTCATT
* *
5720267 ATTTTTTGATT
1 TTTTTTTCATT
5720278 TTTTTTTC-TT
1 TTTTTTTCATT
5720288 TTT
1 TTT
5720291 CTAAATAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
9 7 0.15
10 14 0.30
11 15 0.33
12 10 0.22
ACGTcount: A:0.11, C:0.08, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTTTCATT
Found at i:5720249 original size:9 final size:10
Alignment explanation
Indices: 5720221--5720273 Score: 61
Period size: 10 Copynumber: 5.0 Consensus size: 10
5720211 TTTTTTTCCC
5720221 TCAATTTTTT
1 TCAATTTTTT
**
5720231 TCTTTTTTTTT
1 TC-AATTTTTT
5720242 TCAATTTTTTTT
1 TCAA--TTTTTT
5720254 TCAATTTTTT
1 TCAATTTTTT
5720264 TCAATTTTTT
1 TCAATTTTTT
5720274 GATTTTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 18 0.50
11 8 0.22
12 10 0.28
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.75
Consensus pattern (10 bp):
TCAATTTTTT
Found at i:5720253 original size:22 final size:22
Alignment explanation
Indices: 5720202--5720273 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
5720192 TATTTTTGTC
* **
5720202 TTTTTCTTCTTTTTTTCCCTCAA
1 TTTTTTTTCTTTTTTT-TTTCAA
5720225 -TTTTTTTCTTTTTTTTTTCAA
1 TTTTTTTTCTTTTTTTTTTCAA
**
5720246 TTTTTTTT-TCAATTTTTTTCAA
1 TTTTTTTTCT-TTTTTTTTTCAA
5720268 TTTTTT
1 TTTTTT
5720274 GATTTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
21 5 0.12
22 37 0.88
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTTTTCTTTTTTTTTTCAA
Found at i:5721238 original size:6 final size:6
Alignment explanation
Indices: 5721219--5721256 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
5721209 AATAGTGCAT
5721219 AATTAA AA-TAA AATTAA AATTAA AA-TAA AATTGAA AAT
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATT-AA AAT
5721257 AAATATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
5 10 0.34
6 14 0.48
7 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (6 bp):
AATTAA
Found at i:5721239 original size:17 final size:18
Alignment explanation
Indices: 5721219--5721265 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
5721209 AATAGTGCAT
5721219 AATTAAAATAAAATT-AA
1 AATTAAAATAAAATTGAA
5721236 AATTAAAATAAAATTGAA
1 AATTAAAATAAAATTGAA
5721254 AA-TAAATATAAA
1 AATTAAA-ATAAA
5721266 TATAAATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
AATTAAAATAAAATTGAA
Found at i:5723469 original size:12 final size:13
Alignment explanation
Indices: 5723441--5723469 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5723431 AAAATAAAAT
5723441 AAAATTAAATATA
1 AAAATTAAATATA
5723454 AAAATTAAAT-TA
1 AAAATTAAATATA
5723466 AAAA
1 AAAA
5723470 CAAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAATATA
Found at i:5723474 original size:18 final size:18
Alignment explanation
Indices: 5723436--5723475 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5723426 CCTATAAAAT
* *
5723436 AAAATAAAATTAAATATA
1 AAAATAAAATTAAAAACA
*
5723454 AAAATTAAATTAAAAACA
1 AAAATAAAATTAAAAACA
5723472 AAAA
1 AAAA
5723476 AATATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATAAAATTAAAAACA
Found at i:5724584 original size:25 final size:23
Alignment explanation
Indices: 5724556--5724601 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
5724546 GTTGGATCTA
5724556 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
5724581 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
5724602 CCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:5733892 original size:14 final size:14
Alignment explanation
Indices: 5733856--5733893 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
5733846 TTTATTACTT
5733856 AAAAGTCCATTTAC
1 AAAAGTCCATTTAC
*
5733870 AAGAGTCCATTTAC
1 AAAAGTCCATTTAC
*
5733884 AAAAATCCAT
1 AAAAGTCCAT
5733894 ACAAGCCCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (14 bp):
AAAAGTCCATTTAC
Found at i:5734670 original size:3 final size:3
Alignment explanation
Indices: 5734652--5734715 Score: 58
Period size: 3 Copynumber: 20.7 Consensus size: 3
5734642 GTAGTCTTAT
* *
5734652 TAA TAA TTAA TAAA TAA TAA TAG TAA TAA T-A TAA TAA TTAG TAA TAA
1 TAA TAA -TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
* *
5734699 TAT TAA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TA
5734716 CAAAGAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 39 0.80
4 8 0.16
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5734689 original size:27 final size:28
Alignment explanation
Indices: 5734654--5734709 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
5734644 AGTCTTATTA
5734654 ATAATTAATAAATAATAATAGTAATAAT
1 ATAATTAATAAATAATAATAGTAATAAT
* * *
5734682 ATAA-TAATTAGTAATAATATTAATAAT
1 ATAATTAATAAATAATAATAGTAATAAT
5734709 A
1 A
5734710 AAAATACAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.38
Consensus pattern (28 bp):
ATAATTAATAAATAATAATAGTAATAAT
Found at i:5734696 original size:24 final size:24
Alignment explanation
Indices: 5734652--5734715 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
5734642 GTAGTCTTAT
*
5734652 TAATAAT-TAATAAATAATAATAG
1 TAATAATATAATAAATAATAATAA
* *
5734675 TAATAATATAATAATTAGTAATAA
1 TAATAATATAATAAATAATAATAA
*
5734699 TATTAATAATAA-AAATA
1 TAATAAT-ATAATAAATA
5734716 CAAAGAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
23 7 0.21
24 23 0.68
25 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (24 bp):
TAATAATATAATAAATAATAATAA
Found at i:5735795 original size:30 final size:30
Alignment explanation
Indices: 5735761--5736079 Score: 207
Period size: 29 Copynumber: 10.8 Consensus size: 30
5735751 CCCTAAACTA
5735761 TCCAAAAATTTCATTTTTACCCTCAAAATT
1 TCCAAAAATTTCATTTTTACCCTCAAAATT
* * *
5735791 TCC-AAAA-TTCTATTTTTGA-CCACGAATTT
1 TCCAAAAATTTC-ATTTTT-ACCCTCAAAATT
* *
5735820 TCCAAAAATTACATTTTTACCC-CTAAACTT
1 TCCAAAAATTTCATTTTTACCCTC-AAAATT
* * ** *
5735850 TCC-AAAATTCCATTTTTAACCTTGAATTT
1 TCCAAAAATTTCATTTTTACCCTCAAAATT
* *
5735879 TCC-AAAATTTCATTTTTACCCTCGAACTT
1 TCCAAAAATTTCATTTTTACCCTCAAAATT
* * * * *
5735908 TTC-AAAATTCCAATTTTGA-CCTTAAAGTT
1 TCCAAAAATTTC-ATTTTTACCCTCAAAATT
*
5735937 TCCAAAAATTGCATTTTTACCCTC-AAATAT
1 TCCAAAAATTTCATTTTTACCCTCAAAAT-T
* *
5735967 T-CAAAAATTCCATTTTTGA-CCTTAAAATT
1 TCCAAAAATTTCATTTTT-ACCCTCAAAATT
* * ** *
5735996 TCCACAAATTACCA-TTTTACCC-CCGAATG
1 TCCAAAAATT-TCATTTTTACCCTCAAAATT
*
5736025 TCTAAAAATTTCATTTTTGACCC-CAAAATT
1 TCCAAAAATTTCATTTTT-ACCCTCAAAATT
* *
5736055 CCCAAAAATTTCCATTTTTGCCCTC
1 TCCAAAAATTT-CATTTTTACCCTC
5736080 GAGTGTCCAA
Statistics
Matches: 227, Mismatches: 42, Indels: 39
0.74 0.14 0.13
Matches are distributed among these distances:
28 5 0.02
29 130 0.57
30 79 0.35
31 13 0.06
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (30 bp):
TCCAAAAATTTCATTTTTACCCTCAAAATT
Found at i:5735835 original size:59 final size:59
Alignment explanation
Indices: 5735761--5736005 Score: 298
Period size: 59 Copynumber: 4.2 Consensus size: 59
5735751 CCCTAAACTA
* **
5735761 TCCAAAAATTTCATTTTTACCCTCAAAATTTCCAAAATTCTATTTTTGACCACGAATTT
1 TCCAAAAATTTCATTTTTACCCTCAAAATTTCCAAAATTCCATTTTTGACCTTGAATTT
* * *
5735820 TCCAAAAATTACATTTTTACCC-CTAAACTTTCCAAAATTCCATTTTTAACCTTGAATTT
1 TCCAAAAATTTCATTTTTACCCTC-AAAATTTCCAAAATTCCATTTTTGACCTTGAATTT
* * * * * *
5735879 TCC-AAAATTTCATTTTTACCCTCGAACTTTTCAAAATTCCAATTTTGACCTTAAAGTT
1 TCCAAAAATTTCATTTTTACCCTCAAAATTTCCAAAATTCCATTTTTGACCTTGAATTT
* * * *
5735937 TCCAAAAATTGCATTTTTACCCTC-AAATATTCAAAAATTCCATTTTTGACCTTAAAATT
1 TCCAAAAATTTCATTTTTACCCTCAAAAT-TTCCAAAATTCCATTTTTGACCTTGAATTT
*
5735996 TCCACAAATT
1 TCCAAAAATT
5736006 ACCATTTTAC
Statistics
Matches: 162, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
58 53 0.33
59 109 0.67
ACGTcount: A:0.34, C:0.22, G:0.03, T:0.40
Consensus pattern (59 bp):
TCCAAAAATTTCATTTTTACCCTCAAAATTTCCAAAATTCCATTTTTGACCTTGAATTT
Found at i:5735917 original size:117 final size:117
Alignment explanation
Indices: 5735765--5736079 Score: 323
Period size: 117 Copynumber: 2.7 Consensus size: 117
5735755 AAACTATCCA
* * * * *
5735765 AAAATTTCATTTTTACCCTCAAAATTTCCAAAATTCTATTTTTGACCACGAATTTTCCAAAAATT
1 AAAATTTCATTTTTACCCTCGAAATTTCCAAAATTCCAATTTTGACCACAAAGTTTCCAAAAATT
* * *
5735830 ACATTTTTACCC-CTAAACT-TTCCAAAATTCCATTTTTAACCTTGAATTTTCC
66 ACATTTTTACCCTC-AAA-TATTCAAAAATTCCATTTTTAACCTTAAAATTTCC
* * **
5735882 AAAATTTCATTTTTACCCTCGAACTTTTCAAAATTCCAATTTTGACCTTAAAGTTTCCAAAAATT
1 AAAATTTCATTTTTACCCTCGAAATTTCCAAAATTCCAATTTTGACCACAAAGTTTCCAAAAATT
* *
5735947 GCATTTTTACCCTCAAATATTCAAAAATTCCATTTTTGACCTTAAAATTTCC
66 ACATTTTTACCCTCAAATATTCAAAAATTCCATTTTTAACCTTAAAATTTCC
* * * * * * * * *
5735999 ACAAATTACCA-TTTTACCCCCG-AATGTCTAAAAATTTCATTTTTGACCCCAAAATTCCCAAAA
1 A-AAATT-TCATTTTTACCCTCGAAATTTC-CAAAATTCCAATTTTGACCACAAAGTTTCCAAAA
* *
5736062 ATTTCCATTTTTGCCCTC
63 A-TTACATTTTTACCCTC
5736080 GAGTGTCCAA
Statistics
Matches: 164, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
116 1 0.01
117 103 0.63
118 44 0.27
119 16 0.10
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (117 bp):
AAAATTTCATTTTTACCCTCGAAATTTCCAAAATTCCAATTTTGACCACAAAGTTTCCAAAAATT
ACATTTTTACCCTCAAATATTCAAAAATTCCATTTTTAACCTTAAAATTTCC
Found at i:5736014 original size:59 final size:58
Alignment explanation
Indices: 5735761--5736079 Score: 295
Period size: 59 Copynumber: 5.4 Consensus size: 58
5735751 CCCTAAACTA
* * * *** *
5735761 TCCAAAAATTTCATTTTTACCCTCAAAATTTCCAAAATTCTATTTTTGACCACGAATTT
1 TCCAAAAATTCCATTTTTACCCTC-AAATTTCAAAAATTCCATTTTTGACCTTAAAATT
* * * * *
5735820 TCCAAAAATTACATTTTTACCC-CTAAACTTTCCAAAATTCCATTTTTAACCTTGAATTT
1 TCCAAAAATTCCATTTTTACCCTC-AAA-TTTCAAAAATTCCATTTTTGACCTTAAAATT
* * * *
5735879 TCC-AAAATTTCATTTTTACCCTCGAACTTTTC-AAAATTCCAATTTTGACCTTAAAGTT
1 TCCAAAAATTCCATTTTTACCCTC-AA-ATTTCAAAAATTCCATTTTTGACCTTAAAATT
*
5735937 TCCAAAAATTGCATTTTTACCCTCAAATATTCAAAAATTCCATTTTTGACCTTAAAATT
1 TCCAAAAATTCCATTTTTACCCTCAAAT-TTCAAAAATTCCATTTTTGACCTTAAAATT
* * * * * **
5735996 TCCACAAATTACCA-TTTTACCCCCGAATGTCTAAAAATTTCATTTTTGACCCCAAAATT
1 TCCAAAAATT-CCATTTTTACCCTCAAATTTC-AAAAATTCCATTTTTGACCTTAAAATT
* *
5736055 CCCAAAAATTTCCATTTTTGCCCTC
1 TCCAAAAA-TTCCATTTTTACCCTC
5736080 GAGTGTCCAA
Statistics
Matches: 221, Mismatches: 29, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.00
58 53 0.24
59 155 0.70
60 12 0.05
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (58 bp):
TCCAAAAATTCCATTTTTACCCTCAAATTTCAAAAATTCCATTTTTGACCTTAAAATT
Found at i:5736099 original size:59 final size:59
Alignment explanation
Indices: 5735968--5736158 Score: 169
Period size: 59 Copynumber: 3.3 Consensus size: 59
5735958 CTCAAATATT
* ** * * * * *
5735968 CAAAAATTCCATTTTTGACCTTAAAATTTCCACAAATTACCA-TTTTACCCCCGAATGTC
1 CAAAAATTACATTTTTGACCCCAAAA-TTCCAAAAATTTCCATTTTTGCCCACGAGTGTC
* * *
5736027 TAAAAATTTCATTTTTGACCCCAAAATTCCCAAAAATTTCCATTTTTGCCCTCGAGTGTC
1 CAAAAATTACATTTTTGACCCCAAAATT-CCAAAAATTTCCATTTTTGCCCACGAGTGTC
* * *
5736087 CAAAAA-TACATTTTTG--CCCACGAGTGTCCAAAAA--TACATTTTTGCCCACGAGTGTC
1 CAAAAATTACATTTTTGACCCCA-AAAT-TCCAAAAATTTCCATTTTTGCCCACGAGTGTC
5736143 CAAAAATTACTATTTT
1 CAAAAATTAC-ATTTT
5736159 GCCTCGAGGT
Statistics
Matches: 111, Mismatches: 15, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
56 26 0.23
57 7 0.06
58 16 0.14
59 43 0.39
60 19 0.17
ACGTcount: A:0.33, C:0.25, G:0.08, T:0.34
Consensus pattern (59 bp):
CAAAAATTACATTTTTGACCCCAAAATTCCAAAAATTTCCATTTTTGCCCACGAGTGTC
Found at i:5736170 original size:29 final size:28
Alignment explanation
Indices: 5736067--5736158 Score: 157
Period size: 28 Copynumber: 3.2 Consensus size: 28
5736057 CAAAAATTTC
*
5736067 CATTTTTGCCCTCGAGTGTCCAAAAATA
1 CATTTTTGCCCACGAGTGTCCAAAAATA
5736095 CATTTTTGCCCACGAGTGTCCAAAAATA
1 CATTTTTGCCCACGAGTGTCCAAAAATA
5736123 CATTTTTGCCCACGAGTGTCCAAAAATTA
1 CATTTTTGCCCACGAGTGTCCAAAAA-TA
5736152 CTATTTT
1 C-ATTTT
5736159 GCCTCGAGGT
Statistics
Matches: 61, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
28 53 0.87
29 3 0.05
30 5 0.08
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (28 bp):
CATTTTTGCCCACGAGTGTCCAAAAATA
Found at i:5737798 original size:23 final size:23
Alignment explanation
Indices: 5737779--5737823 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5737769 TTTATTTTAT
5737779 TTTAAATTCAATTTAAATTTAAA
1 TTTAAATTCAATTTAAATTTAAA
* *
5737802 TTTGAATTTAATTTAAATTTAA
1 TTTAAATTCAATTTAAATTTAA
5737824 TATTATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTAAATTCAATTTAAATTTAAA
Found at i:5737816 original size:5 final size:6
Alignment explanation
Indices: 5737779--5737823 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
5737769 TTTATTTTAT
* *
5737779 TTTAAA -TTCAA TTTAAA TTTAAA TTTGAA TTT-AA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
5737824 TATTATTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 9 0.26
6 25 0.74
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:5737821 original size:11 final size:11
Alignment explanation
Indices: 5737753--5737824 Score: 72
Period size: 11 Copynumber: 6.5 Consensus size: 11
5737743 TACTTTGAAA
*
5737753 TTAAATTAAAT
1 TTAATTTAAAT
* * *
5737764 TTATTTTTATT
1 TTAATTTAAAT
*
5737775 TTATTTTAAAT
1 TTAATTTAAAT
*
5737786 TCAATTTAAAT
1 TTAATTTAAAT
*
5737797 TTAAATTTGAAT
1 TT-AATTTAAAT
5737809 TTAATTTAAAT
1 TTAATTTAAAT
5737820 TTAAT
1 TTAAT
5737825 ATTATTATAA
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
11 39 0.80
12 10 0.20
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (11 bp):
TTAATTTAAAT
Found at i:5737821 original size:17 final size:16
Alignment explanation
Indices: 5737750--5737841 Score: 78
Period size: 17 Copynumber: 5.6 Consensus size: 16
5737740 TTTTACTTTG
* *
5737750 AAATTAAATTAAATTT
1 AAATTTAATTTAATTT
** * *
5737766 ATTTTTATTTTATTTT
1 AAATTTAATTTAATTT
*
5737782 AAATTCAATTTAAATTT
1 AAATTTAATTT-AATTT
5737799 AAATTTGAATTTAATTT
1 AAATTT-AATTTAATTT
5737816 AAATTTAATATT-ATTAT
1 AAATTTAAT-TTAATT-T
5737833 AAATTTAAT
1 AAATTTAAT
5737842 AAAAAGTCCA
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
16 23 0.38
17 32 0.53
18 5 0.08
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (16 bp):
AAATTTAATTTAATTT
Found at i:5738648 original size:18 final size:18
Alignment explanation
Indices: 5738625--5738672 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
5738615 GTTTCTTTAA
5738625 TAATATTAATAACCT-TTT
1 TAATATTAATAA-CTATTT
5738643 TAATATTAATAACTATTT
1 TAATATTAATAACTATTT
5738661 T-ATCATTAATAA
1 TAAT-ATTAATAA
5738673 TAAATACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATATTAATAACTATTT
Found at i:5738703 original size:18 final size:18
Alignment explanation
Indices: 5738646--5738708 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
5738636 ACCTTTTTAA
*
5738646 TATTAATAACT-ATTTTAT
1 TATTAATAA-TAATATTAT
* * *
5738664 CATTAATAATAA-ATACAG
1 TATTAATAATAATAT-TAT
5738682 TATTAATAATAATATTAT
1 TATTAATAATAATATTAT
5738700 TATT-ATAAT
1 TATTAATAAT
5738709 TTTTTAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
17 7 0.20
18 26 0.74
19 2 0.06
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (18 bp):
TATTAATAATAATATTAT
Found at i:5739829 original size:29 final size:29
Alignment explanation
Indices: 5739774--5740188 Score: 238
Period size: 29 Copynumber: 14.1 Consensus size: 29
5739764 CCTTGGAGGT
* **
5739774 CCCTAAATTATCCAAAAATTGTA-TTTTGC
1 CCCTAAACT-TCCAAAAATTACATTTTTGC
* *
5739803 CCCTAAACTTTCAAAAATTCCATTTTTGAC
1 CCCTAAACTTCCAAAAATTACATTTTTG-C
* * * *
5739833 CCCAAAACTTCCTAAAATTATATTTTTAC
1 CCCTAAACTTCCAAAAATTACATTTTTGC
*
5739862 CCCTAAAACTTCCAAAAATTCCATTTTTGC
1 CCCT-AAACTTCCAAAAATTACATTTTTGC
** * *
5739892 CCCCGAACTTCCAAAAATTCCATTTTTGA
1 CCCTAAACTTCCAAAAATTACATTTTTGC
* *
5739921 CCCTAAAACTTCCTAAAATTACATTTTTAC
1 CCCT-AAACTTCCAAAAATTACATTTTTGC
* * **
5739951 CCTCAAAATTTAAAAAAATTACATTTTT-C
1 CC-CTAAACTTCCAAAAATTACATTTTTGC
* *
5739980 ACCCCAAACTTCCAAAACTTACATTTTTGC
1 -CCCTAAACTTCCAAAAATTACATTTTTGC
** *
5740010 CCCCCAACTTCCAAAAATTCCATTTTTGAC
1 CCCTAAACTTCCAAAAATTACATTTTTG-C
* * ** *
5740040 CTCGAAACTT-CTTAAATTACCA-TTTTAC
1 CCCTAAACTTCCAAAAATTA-CATTTTTGC
* *
5740068 CCTCGAAA-GTCCAAAAATT-CTATTTTTGCC
1 CC-CTAAACTTCCAAAAATTAC-ATTTTTG-C
* * *
5740098 CCCGAGA-GTCC-AAAATTACCA-TTTTGC
1 CCCTAAACTTCCAAAAATTA-CATTTTTGC
* ** * *
5740125 CCTTAGAAGATCCAAAAATTTCATTTTTGAT
1 CCCTA-AACTTCCAAAAATTACATTTTTG-C
* **
5740156 CCCGATTCTTCCAAAAATTACCA-TTTTGC
1 CCCTAAACTTCCAAAAATTA-CATTTTTGC
5740185 CCCT
1 CCCT
5740189 CGAGAGTCCA
Statistics
Matches: 299, Mismatches: 65, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
27 5 0.02
28 26 0.09
29 131 0.44
30 131 0.44
31 6 0.02
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTACATTTTTGC
Found at i:5739850 original size:30 final size:30
Alignment explanation
Indices: 5739784--5740182 Score: 261
Period size: 30 Copynumber: 13.6 Consensus size: 30
5739774 CCCTAAATTA
** *
5739784 TCCAAAAATTGTA-TTTTG-CCCCTAAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACT
*
5739812 TTCAAAAATTCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACT
* **
5739842 TCCTAAAATTATATTTTT-ACCCCTAAAACT
1 TCCAAAAATTCCATTTTTGACCCC-AAAACT
**
5739872 TCCAAAAATTCCATTTTTG-CCCCCGAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACT
*
5739901 TCCAAAAATTCCATTTTTGACCCTAAAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACT
* * *
5739931 TCCTAAAATTACATTTTT-ACCCTCAAAATT
1 TCCAAAAATTCCATTTTTGACCC-CAAAACT
** * *
5739961 TAAAAAAATTACATTTTTCACCCC-AAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACT
* * **
5739990 TCCAAAACTTACATTTTTG-CCCCCCAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACT
* *
5740019 TCCAAAAATTCCATTTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTTGACCCCAAAACT
** * *
5740049 T-CTTAAATTACCA-TTTT-ACCCTCGAAA-G
1 TCCAAAAATT-CCATTTTTGACCC-CAAAACT
* * * * *
5740077 TCCAAAAATTCTATTTTTGCCCCCGAGA-G
1 TCCAAAAATTCCATTTTTGACCCCAAAACT
* * **
5740106 TCC-AAAATTACCA-TTTTG-CCCTTAGAAGA
1 TCCAAAAATT-CCATTTTTGACCC-CAAAACT
* * * **
5740135 TCCAAAAATTTCATTTTTGATCCCGATTCT
1 TCCAAAAATTCCATTTTTGACCCCAAAACT
5740165 TCCAAAAATTACCATTTT
1 TCCAAAAATT-CCATTTT
5740183 GCCCCTCGAG
Statistics
Matches: 291, Mismatches: 59, Indels: 39
0.75 0.15 0.10
Matches are distributed among these distances:
27 3 0.01
28 32 0.11
29 117 0.40
30 127 0.44
31 12 0.04
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.35
Consensus pattern (30 bp):
TCCAAAAATTCCATTTTTGACCCCAAAACT
Found at i:5739929 original size:89 final size:89
Alignment explanation
Indices: 5739784--5740050 Score: 310
Period size: 89 Copynumber: 3.0 Consensus size: 89
5739774 CCCTAAATTA
** * *
5739784 TCCAAAAATTGTA-TTTTGCCCCTAAACTTTCAAAAATTCCATTTTTGACCCCAAAACTTCCTAA
1 TCCAAAAATTACATTTTTGCCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCTAA
*
5739848 AATTATATTTTTACCC-CTAAAACT
66 AATTACATTTTTACCCTC-AAAACT
* * *
5739872 TCCAAAAATTCCATTTTTGCCCCCGAACTTCCAAAAATTCCATTTTTGACCCTAAAACTTCCTAA
1 TCCAAAAATTACATTTTTGCCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCTAA
*
5739937 AATTACATTTTTACCCTCAAAATT
66 AATTACATTTTTACCCTCAAAACT
** * * ** *
5739961 TAAAAAAATTACATTTTT-CACCCCAAACTTCCAAAACTTACATTTTTG-CCCCCCAACTTCCAA
1 TCCAAAAATTACATTTTTGC-CCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCTA
* *
5740024 AAATTCCATTTTTGA-CCTCGAAACT
65 AAATTACATTTTT-ACCCTCAAAACT
5740049 TC
1 TC
5740051 TTAAATTACC
Statistics
Matches: 153, Mismatches: 22, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
88 44 0.29
89 108 0.71
90 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (89 bp):
TCCAAAAATTACATTTTTGCCCCCAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCTAA
AATTACATTTTTACCCTCAAAACT
Found at i:5740064 original size:59 final size:57
Alignment explanation
Indices: 5739784--5740095 Score: 227
Period size: 59 Copynumber: 5.3 Consensus size: 57
5739774 CCCTAAATTA
** * * * * *
5739784 TCCAAAAATTGTA-TTTTGCCCCTAAACTTTCAAAAATTCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTGACCCAAAAC-TTCTAAAATTACATTTTTG-CCCCCAAACT
* ** * * *
5739842 TCCTAAAATTATATTTTT-ACCCCTAAAACTTCCAAAAATTCCATTTTTGCCCCCGAACT
1 TCCAAAAATTCCATTTTTGA-CCC-AAAACTT-CTAAAATTACATTTTTGCCCCCAAACT
* * *
5739901 TCCAAAAATTCCATTTTTGACCCTAAAACTTCCTAAAATTACATTTTTACCCTCAAAATT
1 TCCAAAAATTCCATTTTTGACCC-AAAACTT-CTAAAATTACATTTTTGCCC-CCAAACT
** * * * * *
5739961 TAAAAAAATTACATTTTTCACCCCAAACTTCCAAAACTTACATTTTTGCCCCCCAACT
1 TCCAAAAATTCCATTTTTGACCCAAAACTTCTAAAA-TTACATTTTTGCCCCCAAACT
* * * * *
5740019 TCCAAAAATTCCATTTTTGACCTCGAAACTTCTTAAATTACCA-TTTTACCCTCGAAA-G
1 TCCAAAAATTCCATTTTTGACC-CAAAACTTCTAAAATTA-CATTTTTGCCC-CCAAACT
*
5740077 TCCAAAAATTCTATTTTTG
1 TCCAAAAATTCCATTTTTG
5740096 CCCCCGAGAG
Statistics
Matches: 207, Mismatches: 37, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
58 66 0.32
59 96 0.46
60 45 0.22
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (57 bp):
TCCAAAAATTCCATTTTTGACCCAAAACTTCTAAAATTACATTTTTGCCCCCAAACT
Found at i:5740209 original size:29 final size:30
Alignment explanation
Indices: 5740053--5740211 Score: 127
Period size: 29 Copynumber: 5.4 Consensus size: 30
5740043 GAAACTTCTT
* *
5740053 AAATTACCATTTT-ACCCTCGAAAGTCCAA
1 AAATTACCATTTTGCCCCTCGAGAGTCCAA
*
5740082 AAATT-CTATTTTTGCCCC-CGAGAGTCC-A
1 AAATTACCA-TTTTGCCCCTCGAGAGTCCAA
* *
5740110 AAATTACCATTTTGCCCTTAGA-AGATCCAA
1 AAATTACCATTTTGCCCCTCGAGAG-TCCAA
* ** ***
5740140 AAATT-TCATTTTTGATCC-CGATTCTTCCAA
1 AAATTACCA-TTTTGCCCCTCGA-GAGTCCAA
5740170 AAATTACCATTTTGCCCCTCGAGAGTCC-A
1 AAATTACCATTTTGCCCCTCGAGAGTCCAA
5740199 AAATTACCATTTT
1 AAATTACCATTTT
5740212 TTGGGTATCC
Statistics
Matches: 100, Mismatches: 19, Indels: 22
0.71 0.13 0.16
Matches are distributed among these distances:
28 18 0.18
29 42 0.42
30 35 0.35
31 5 0.05
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.33
Consensus pattern (30 bp):
AAATTACCATTTTGCCCCTCGAGAGTCCAA
Found at i:5742027 original size:34 final size:33
Alignment explanation
Indices: 5741970--5742047 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 33
5741960 GGCCCAAACC
* *
5741970 ATTTTGAAATTAAATTTATTTTAATTTTGAAT-TT
1 ATTTT-AAATTAAATTTAATTTAAATTT-AATATT
*
5742004 ATTTTAAATTCAATTTTAATTTAAATTTAATATT
1 ATTTTAAATT-AAATTTAATTTAAATTTAATATT
*
5742038 ATTATAAATT
1 ATTTTAAATT
5742048 TTAAAAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
33 8 0.21
34 30 0.79
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (33 bp):
ATTTTAAATTAAATTTAATTTAAATTTAATATT
Found at i:5742048 original size:17 final size:16
Alignment explanation
Indices: 5741970--5742048 Score: 77
Period size: 17 Copynumber: 4.7 Consensus size: 16
5741960 GGCCCAAACC
*
5741970 ATTTTGAAATTAAATTT
1 ATTTT-AAATTTAATTT
*
5741987 ATTTTAATTTTGAATTT
1 ATTTTAAATTT-AATTT
*
5742004 ATTTTAAATTCAATTTT
1 ATTTTAAATTTAA-TTT
*
5742021 AATTTAAATTTAATATT
1 ATTTTAAATTTAAT-TT
*
5742038 ATTATAAATTT
1 ATTTTAAATTT
5742049 TAAAAAAAGA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
16 7 0.14
17 44 0.86
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (16 bp):
ATTTTAAATTTAATTT
Found at i:5743068 original size:434 final size:433
Alignment explanation
Indices: 5742228--5743094 Score: 1680
Period size: 434 Copynumber: 2.0 Consensus size: 433
5742218 AACCAGTCAA
5742228 ACCTTGAAGTCAGAATCTGATCTTCCCACGTGATTTTGCCCACCAGCTCCATCTGCCACCAGCTT
1 ACCTTGAAGTCAGAATCTGATCTTCCCACGTGATTTTGCCCACCAGCTCCATCTGCCACCAGCTT
*
5742293 CACCATGTCCTACCATCGCCGATGCCAGAGAAAAAACCTACAACAAGCAATAGAGACATTCATTT
66 CACCATGTCCTACCATCGCCGATGCCAGAGAAAAAACCTACAACAAGCAACAGAGACATTCATTT
5742358 AATGGCAAACAACAAAGTATCATCATTGTAAATCTGGCTATAAAACCAGACTTAATTTCTGTAAT
131 AATGGCAAACAACAAAGTATCATCATTGTAAATCTGGCTATAAAACCAGACTTAATTTCTGTAAT
5742423 GAAGGGGGGTTACAATTTTTTTTTCTTTTACAAATATCAATACCAAAAGTAGTATACTGAGAACC
196 GAAGGGGGGTTACAATTTTTTTTTCTTTTACAAATATCAATACCAAAAGTAGTATACTGAGAACC
5742488 AAAACAAAAGGGTAGACAAGAATCATCAGCAATCAAAAGGCAGATTATTAGCATCTTGAAGGTAC
261 AAAACAAAAGGGTAGACAAGAATCATCAGCAATCAAAAGGCAGATTATTAGCATCTTGAAGGTAC
5742553 ATCCAATAAATACATTTACTGACTGTTCATTGTTCTAAGGTTTTGTTTAAAATTATGCATGGATG
326 ATCCAATAAATACATTTACTGACTGTTCATTGTTCTAAGGTTTTGTTTAAAATTATGCATGGATG
5742618 TACATTCATTGATTATCACTTATTAATTGCTCATTCAAAGAAG
391 TACATTCATTGATTATCACTTATTAATTGCTCATTCAAAGAAG
5742661 ACCTTGAAGTCAGAATCTGATCTTCCCACGTGATTTTGCCCACCAGCTCCATCTGCCACCAGCTT
1 ACCTTGAAGTCAGAATCTGATCTTCCCACGTGATTTTGCCCACCAGCTCCATCTGCCACCAGCTT
* *
5742726 CACCATGTCCTGCCATCGCCGATGCCAGAGAAAAAACCTGCAACAAGCAACAGAGACATTCATTT
66 CACCATGTCCTACCATCGCCGATGCCAGAGAAAAAACCTACAACAAGCAACAGAGACATTCATTT
*
5742791 AATGGCAAACAACAAAGTATCATCATTGTAAATCTGGCTATAAAACTAGACTTAATTTCTGTAAT
131 AATGGCAAACAACAAAGTATCATCATTGTAAATCTGGCTATAAAACCAGACTTAATTTCTGTAAT
5742856 GAAGGGGGGGTTACAATTTTTTTTTCTTTTACAAATATCAATACCAAAAGTAGTATACTGAGAAC
196 GAA-GGGGGGTTACAATTTTTTTTTCTTTTACAAATATCAATACCAAAAGTAGTATACTGAGAAC
5742921 CAAAACAAAAGGGTAGACAAGAATCATCAGCAATCAAAAGGCAGATTATTAGCATCTTGAAGGTA
260 CAAAACAAAAGGGTAGACAAGAATCATCAGCAATCAAAAGGCAGATTATTAGCATCTTGAAGGTA
*
5742986 CATTCAATAAATACATTTACTGACTGTTCATTGTTCTAAGGTTTTGTTTAAAATTATGCATGGAT
325 CATCCAATAAATACATTTACTGACTGTTCATTGTTCTAAGGTTTTGTTTAAAATTATGCATGGAT
5743051 GTACATTCATTGATTATCACTTATTAATTGCTCATTCAAAGAAG
390 GTACATTCATTGATTATCACTTATTAATTGCTCATTCAAAGAAG
5743095 CTTTGAAACT
Statistics
Matches: 428, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
433 194 0.45
434 234 0.55
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (433 bp):
ACCTTGAAGTCAGAATCTGATCTTCCCACGTGATTTTGCCCACCAGCTCCATCTGCCACCAGCTT
CACCATGTCCTACCATCGCCGATGCCAGAGAAAAAACCTACAACAAGCAACAGAGACATTCATTT
AATGGCAAACAACAAAGTATCATCATTGTAAATCTGGCTATAAAACCAGACTTAATTTCTGTAAT
GAAGGGGGGTTACAATTTTTTTTTCTTTTACAAATATCAATACCAAAAGTAGTATACTGAGAACC
AAAACAAAAGGGTAGACAAGAATCATCAGCAATCAAAAGGCAGATTATTAGCATCTTGAAGGTAC
ATCCAATAAATACATTTACTGACTGTTCATTGTTCTAAGGTTTTGTTTAAAATTATGCATGGATG
TACATTCATTGATTATCACTTATTAATTGCTCATTCAAAGAAG
Found at i:5743664 original size:9 final size:9
Alignment explanation
Indices: 5743634--5743658 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5743624 AGTTTAAAAG
5743634 AAAGAAGAA
1 AAAGAAGAA
5743643 AAAGAAGAA
1 AAAGAAGAA
5743652 AAAGAAG
1 AAAGAAG
5743659 GGAAAGGAGT
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:0.24, T:0.00
Consensus pattern (9 bp):
AAAGAAGAA
Found at i:5744424 original size:30 final size:30
Alignment explanation
Indices: 5744390--5744658 Score: 90
Period size: 29 Copynumber: 9.1 Consensus size: 30
5744380 GAAATCATAT
5744390 TTTTAATCC-CGATTTCACCAAAAATTACCA
1 TTTTAA-CCGCGATTTCACCAAAAATTACCA
* * *
5744420 TTTTACCCTCAAACTTT--CC-AAAATT-CCA
1 TTTTAACCGC-GA-TTTCACCAAAAATTACCA
*
5744448 TTTTAACCGCGATTTCACGAAAAATTACCA
1 TTTTAACCGCGATTTCACCAAAAATTACCA
* *
5744478 TTTT-ACCCCTAAACTTT--CC-AAAATT-CCA
1 TTTTAACCGC--GA-TTTCACCAAAAATTACCA
* * *
5744506 TTTTTGACCCCGATTTCACCAAAAAATTACCG
1 -TTTTAACCGCGATTTCACC-AAAAATTACCA
* * *
5744538 TTTTACCCCCGAACTTT--CC--AAATT-TCA
1 TTTTAACCGCG-A-TTTCACCAAAAATTACCA
* **
5744565 TTTTTGACCTTGATTTCACCAAAAATTACCA
1 -TTTTAACCGCGATTTCACCAAAAATTACCA
* *
5744596 TTTTACCCTCGAACTTT--CC-AAAATT-CCA
1 TTTTAACCGCG-A-TTTCACCAAAAATTACCA
* ** *
5744624 TTTTCGACCTTGATTTCACCGAAAATTACCA
1 TTTT-AACCGCGATTTCACCAAAAATTACCA
5744655 TTTT
1 TTTT
5744659 GCCCCCGCGA
Statistics
Matches: 181, Mismatches: 26, Indels: 63
0.67 0.10 0.23
Matches are distributed among these distances:
26 6 0.03
27 9 0.05
28 38 0.21
29 42 0.23
30 42 0.23
31 29 0.16
32 12 0.07
33 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.05, T:0.36
Consensus pattern (30 bp):
TTTTAACCGCGATTTCACCAAAAATTACCA
Found at i:5744477 original size:58 final size:59
Alignment explanation
Indices: 5744348--5744665 Score: 392
Period size: 59 Copynumber: 5.4 Consensus size: 59
5744338 CCTGGGCTGT
* * * * *
5744348 CCAAAAATTACCATTTTACCCCCGAGCTTTTCGAAA-TCATATTTTTAATCC-CGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTC-CATTTTTGA-CCTCGATTTCA
* * * *
5744407 CCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCA-TTTTAACCGCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCA
* ** *
5744465 CGAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCA
* * *
5744524 CCAAAAAATTACCGTTTTACCCCCGAACTTTCC-AAATTTCATTTTTGACCTTGATTTCA
1 CC-AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCA
* * *
5744583 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTCGACCTTGATTTCA
1 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCA
* *
5744642 CCGAAAATTACCATTTTGCCCCCG
1 CCAAAAATTACCATTTTACCCCCG
5744666 CGAGTCAAAA
Statistics
Matches: 229, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
57 2 0.01
58 80 0.35
59 118 0.52
60 29 0.13
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCA
Found at i:5744510 original size:29 final size:29
Alignment explanation
Indices: 5744410--5744509 Score: 95
Period size: 29 Copynumber: 3.5 Consensus size: 29
5744400 GATTTCACCA
5744410 AAAATTACCATTTTA-CCCTCAAACTTTCC
1 AAAATTACCATTTTACCCCT-AAACTTTCC
* *
5744439 AAAATT-CCATTTTAACCGC--GA-TTTCAC
1 AAAATTACCATTTT-ACCCCTAAACTTTC-C
5744466 GAAAAATTACCATTTTACCCCTAAACTTTCC
1 --AAAATTACCATTTTACCCCTAAACTTTCC
5744497 AAAATT-CCATTTT
1 AAAATTACCATTTT
5744510 TGACCCCGAT
Statistics
Matches: 58, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
26 4 0.07
27 2 0.03
28 14 0.24
29 23 0.40
30 9 0.16
31 2 0.03
32 4 0.07
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCTAAACTTTCC
Found at i:5746772 original size:17 final size:18
Alignment explanation
Indices: 5746742--5746775 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5746732 GCTTTAGAGA
*
5746742 ATATGCCAAGATCTTCAC
1 ATATGCCAAAATCTTCAC
5746760 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
5746776 GGTGCATCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:5748223 original size:16 final size:16
Alignment explanation
Indices: 5748198--5748228 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5748188 AAAGAACATT
*
5748198 TTAATTTTTTTAATTA
1 TTAATATTTTTAATTA
5748214 TTAATATTTTTAATT
1 TTAATATTTTTAATT
5748229 TCTGAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTAATATTTTTAATTA
Found at i:5748768 original size:22 final size:22
Alignment explanation
Indices: 5748743--5748785 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5748733 TCTCCCTATT
5748743 TTGCTACAATTTCATTATTATG
1 TTGCTACAATTTCATTATTATG
* **
5748765 TTGCTACTATTTTGTTATTAT
1 TTGCTACAATTTCATTATTAT
5748786 TATTTGGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.56
Consensus pattern (22 bp):
TTGCTACAATTTCATTATTATG
Found at i:5749750 original size:32 final size:32
Alignment explanation
Indices: 5749709--5749772 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
5749699 GAGAGTGTTC
5749709 TATCATATGAACCATACGAAAACCACACCCAA
1 TATCATATGAACCATACGAAAACCACACCCAA
*
5749741 TATCATATGAACCATACGAAAATCACACCCAA
1 TATCATATGAACCATACGAAAACCACACCCAA
5749773 CATGATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.47, C:0.30, G:0.06, T:0.17
Consensus pattern (32 bp):
TATCATATGAACCATACGAAAACCACACCCAA
Found at i:5750611 original size:30 final size:28
Alignment explanation
Indices: 5750509--5750729 Score: 79
Period size: 30 Copynumber: 7.5 Consensus size: 28
5750499 CTTTCGGGGC
*
5750509 TAAAAATGTAATTTTTGGTGAAA-CTAGGG-
1 TAAAAATG-GATTTTTGG-GAAATC-AGGGT
* * *
5750538 TCAAAATGGAATTTT-GGAAAGTTCAGGGC
1 TAAAAATGGATTTTTGGGAAA--TCAGGGT
*
5750567 TAAAACA-GTAATTTTTGGTGAAATCAGGGT
1 TAAAA-ATG-GATTTTTGG-GAAATCAGGGT
*
5750597 TAAAAATAGGA-TTTT-GGAAAGTTC-GGTGG
1 TAAAAAT-GGATTTTTGGGAAA--TCAGG-GT
5750626 T-AAAATGGTAATTTTTGGTGAAATC-GAGGT
1 TAAAAATGG--ATTTTTGG-GAAATCAG-GGT
* *
5750656 TAAAAATGGGA-TTTT-GGAAAGTTTAGGGG
1 TAAAAAT-GGATTTTTGGGAAA--TCAGGGT
5750685 T-AAAATGGTAATTTTTGGGGAAATCAGGGT
1 TAAAAATGG--ATTTTT-GGGAAATCAGGGT
5750715 TAAAAATGAGATTTT
1 TAAAAATG-GATTTT
5750730 GGAGGTAAAA
Statistics
Matches: 147, Mismatches: 14, Indels: 61
0.66 0.06 0.27
Matches are distributed among these distances:
26 4 0.03
27 13 0.09
28 23 0.16
29 32 0.22
30 44 0.30
31 15 0.10
32 16 0.11
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (28 bp):
TAAAAATGGATTTTTGGGAAATCAGGGT
Found at i:5750630 original size:59 final size:57
Alignment explanation
Indices: 5750511--5750866 Score: 394
Period size: 59 Copynumber: 6.2 Consensus size: 57
5750501 TTCGGGGCTA
* *
5750511 AAAAT-GTAATTTTTGGTGAAA-CTAGGG-TCAAAATGGAATTTTGGAAAGTTCAGGGCT
1 AAAATGGTAATTTTTGGTGAAATC-AGGGTTAAAAATGG-ATTTTGGAAAGTT-AGGGGT
** *
5750568 AAAACAGTAATTTTTGGTGAAATCAGGGTTAAAAATAGGATTTTGGAAAGTTCGGTGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAAT-GGATTTTGGAAAGTTAGG-GGT
5750627 AAAATGGTAATTTTTGGTGAAATC-GAGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAG-GGTTAAAAAT-GGATTTTGGAAAG-TTAGGGGT
*
5750686 AAAATGGTAATTTTTGGGGAAATCAGGGTTAAAAATGAGATTTT-G---G--A--GGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATG-GATTTTGGAAAGTTAGGGGT
* *
5750736 AAAATGGTAATTTTTTGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGG-ATTTTGGAAAG-TTAGGGGT
* ** * *
5750795 AAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGGGGCTTTAGAAAGTTAATGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAAT-GGATTTTGGAAAGTT-AGGGGT
5750854 AAAATGGTAATTT
1 AAAATGGTAATTT
5750867 ATGAACAATT
Statistics
Matches: 259, Mismatches: 19, Indels: 40
0.81 0.06 0.13
Matches are distributed among these distances:
49 1 0.00
50 42 0.16
51 1 0.00
52 1 0.00
54 1 0.00
55 1 0.00
57 5 0.02
58 27 0.10
59 171 0.66
60 9 0.03
ACGTcount: A:0.36, C:0.03, G:0.28, T:0.33
Consensus pattern (57 bp):
AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGATTTTGGAAAGTTAGGGGT
Found at i:5750639 original size:29 final size:28
Alignment explanation
Indices: 5750535--5750699 Score: 76
Period size: 29 Copynumber: 5.6 Consensus size: 28
5750525 GGTGAAACTA
5750535 GGGTCAAAATGG-AATTTTGGAAAGTTCAG
1 GGGT-AAAATGGTAATTTTGGAAAGTTC-G
* **
5750564 GGCTAAAACAGTAATTTTTGGTGAAA--TCAG
1 GGGTAAAATGGTAA-TTTT-G-GAAAGTTC-G
*
5750594 GGTTAAAAATAGG--ATTTTGGAAAGTTCG
1 GGGT-AAAAT-GGTAATTTTGGAAAGTTCG
5750622 GTGGTAAAATGGTAATTTTTGGTGAAA--TCG
1 G-GGTAAAATGGTAA-TTTT-G-GAAAGTTCG
* * *
5750652 AGGTTAAAAATGG-GATTTTGGAAAGTTTAG
1 -GGGT-AAAATGGTAATTTTGGAAAG-TTCG
5750682 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
5750700 TGGGGAAATC
Statistics
Matches: 104, Mismatches: 12, Indels: 40
0.67 0.08 0.26
Matches are distributed among these distances:
27 10 0.10
28 21 0.20
29 26 0.25
30 24 0.23
31 14 0.13
32 9 0.09
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTGGAAAGTTCG
Found at i:5750758 original size:50 final size:50
Alignment explanation
Indices: 5750683--5750832 Score: 158
Period size: 50 Copynumber: 2.8 Consensus size: 50
5750673 AAAGTTTAGG
5750683 GGTAAAATGGTAATTTTTGGGGAAATCAGGGTTAAAAAT-GAGATTTTGGA
1 GGTAAAATGGTAATTTTTGGGGAAATCAGGGTTAAAAATGGA-ATTTTGGA
* * *
5750733 GGTAAAATGGTAATTTTTTGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTA
1 GGTAAAATGGTAATTTTTGGGGAAATCAGGGTTAAAAATGGAATTTT-G---G---A
**
5750790 GGGGTAAAATGGTAATTTTTGGTAAAATCAGGGTTAAAAATGG
1 --GGTAAAATGGTAATTTTTGGGGAAATCAGGGTTAAAAATGG
5750833 GGCTTTAGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
50 41 0.49
51 3 0.04
54 1 0.01
57 1 0.01
59 38 0.45
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (50 bp):
GGTAAAATGGTAATTTTTGGGGAAATCAGGGTTAAAAATGGAATTTTGGA
Found at i:5750818 original size:109 final size:109
Alignment explanation
Indices: 5750624--5750831 Score: 371
Period size: 109 Copynumber: 1.9 Consensus size: 109
5750614 AAAGTTCGGT
*
5750624 GGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAA
1 GGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAA
*
5750689 ATGGTAATTTTTGGGGAAATCAGGGTTAAAAATGAGATTTTGGA
66 ATGGTAATTTTTGGGAAAATCAGGGTTAAAAATGAGATTTTGGA
* *
5750733 GGTAAAATGGTAATTTTTTGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAA
1 GGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAA
*
5750798 ATGGTAATTTTTGGTAAAATCAGGGTTAAAAATG
66 ATGGTAATTTTTGGGAAAATCAGGGTTAAAAATG
5750832 GGGCTTTAGA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 94 1.00
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.34
Consensus pattern (109 bp):
GGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAA
ATGGTAATTTTTGGGAAAATCAGGGTTAAAAATGAGATTTTGGA
Found at i:5750828 original size:30 final size:30
Alignment explanation
Indices: 5750735--5750828 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
5750725 ATTTTGGAGG
* * *
5750735 TAAAATGGTAATTTTTTGTGAAATCGGGGT
1 TAAAATGGTAATTTTTGGTAAAATCAGGGT
* * *
5750765 TAAAAATGG-AA-TTTTGG-AAAGTTTAGGGG
1 T-AAAATGGTAATTTTTGGTAAA-ATCAGGGT
5750794 TAAAATGGTAATTTTTGGTAAAATCAGGGT
1 TAAAATGGTAATTTTTGGTAAAATCAGGGT
5750824 TAAAA
1 TAAAA
5750829 ATGGGGCTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
28 9 0.18
29 12 0.24
30 19 0.38
31 10 0.20
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (30 bp):
TAAAATGGTAATTTTTGGTAAAATCAGGGT
Found at i:5751207 original size:32 final size:33
Alignment explanation
Indices: 5751146--5751209 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
5751136 TTATCGGGCC
*
5751146 AAATTAAAAATAATTAAAAGTATGAAAAGGACT
1 AAATTAAAAATAATTAAAAGAATGAAAAGGACT
*
5751179 AAATT-AAAATAATTAAAA-AATGTGAAAGGAC
1 AAATTAAAAATAATTAAAAGAATG-AAAAGGAC
5751210 CAAACGGCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 3 0.11
32 20 0.71
33 5 0.18
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.23
Consensus pattern (33 bp):
AAATTAAAAATAATTAAAAGAATGAAAAGGACT
Found at i:5753221 original size:18 final size:18
Alignment explanation
Indices: 5753195--5753232 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5753185 AATCAATTTT
*
5753195 TTAATTGAATT-AGATCGA
1 TTAACTGAATTGA-ATCGA
5753213 TTAACTGAATTGAATCGA
1 TTAACTGAATTGAATCGA
5753231 TT
1 TT
5753233 CGATCGCGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (18 bp):
TTAACTGAATTGAATCGA
Found at i:5753806 original size:13 final size:13
Alignment explanation
Indices: 5753784--5753818 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
5753774 TGTTCAGGAG
*
5753784 TTGATAAATGCGA
1 TTGATTAATGCGA
5753797 TTGATTAATGCGA
1 TTGATTAATGCGA
5753810 TTGATTAAT
1 TTGATTAAT
5753819 ATTGAATTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGATTAATGCGA
Found at i:5765568 original size:17 final size:17
Alignment explanation
Indices: 5765538--5765589 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
5765528 TTTTAAAATA
* *
5765538 TATATATTTATAATTTT
1 TATATTTTTTTAATTTT
5765555 TATATTTTTTTAATAATTT
1 TATATTTTTTTAAT--TTT
5765574 T-TATTTTTTTGAATTT
1 TATATTTTTTT-AATTT
5765590 AAAAAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 14 0.47
18 9 0.30
19 7 0.23
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TATATTTTTTTAATTTT
Found at i:5765580 original size:18 final size:20
Alignment explanation
Indices: 5765547--5765583 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5765537 ATATATATTT
5765547 ATAATTTTTATATTTTTTTA
1 ATAATTTTTATATTTTTTTA
5765567 ATAATTTTTAT-TTTTTT
1 ATAATTTTTATATTTTTT
5765584 GAATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
ATAATTTTTATATTTTTTTA
Found at i:5768774 original size:29 final size:31
Alignment explanation
Indices: 5768740--5768800 Score: 90
Period size: 29 Copynumber: 2.0 Consensus size: 31
5768730 ACGAAAGTAC
5768740 TCAAATAAAAAT-AAAATTTTTTAA-AATGA
1 TCAAATAAAAATCAAAATTTTTTAATAATGA
* *
5768769 TCAAATAAAGATCAAACTTTTTTAATAATGA
1 TCAAATAAAAATCAAAATTTTTTAATAATGA
5768800 T
1 T
5768801 TTTTTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (31 bp):
TCAAATAAAAATCAAAATTTTTTAATAATGA
Found at i:5772215 original size:23 final size:22
Alignment explanation
Indices: 5772179--5772361 Score: 157
Period size: 23 Copynumber: 8.5 Consensus size: 22
5772169 AGTGTTAGGC
*
5772179 AACAGAAAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAA-TGCTA
*
5772202 AACAGAGAGTACACAAA-G-T-
1 AACAGAGAGCACACAAATGCTA
*
5772221 -ACTGA-A-CACACAAAGTGCTA
1 AACAGAGAGCACACAAA-TGCTA
* * **
5772241 ATCAGAGAGCACGAGACGTGCTA
1 AACAGAGAGCAC-ACAAATGCTA
* *
5772264 AACAGAGAGCACACATA-GCTG
1 AACAGAGAGCACACAAATGCTA
*
5772285 AACAGATAGCACACACAATGCTA
1 AACAGAGAGCACACA-AATGCTA
*
5772308 AACAGAGAGCACACACA-GCTA
1 AACAGAGAGCACACAAATGCTA
*
5772329 AACAGATAGCACACACAATGCTA
1 AACAGAGAGCACACA-AATGCTA
5772352 AACAGAGAGC
1 AACAGAGAGC
5772362 GCGCTAGCGT
Statistics
Matches: 126, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
16 7 0.06
17 1 0.01
18 5 0.04
19 1 0.01
20 1 0.01
21 39 0.31
22 6 0.05
23 64 0.51
24 2 0.02
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.10
Consensus pattern (22 bp):
AACAGAGAGCACACAAATGCTA
Found at i:5772307 original size:44 final size:44
Alignment explanation
Indices: 5772259--5772361 Score: 188
Period size: 44 Copynumber: 2.3 Consensus size: 44
5772249 GCACGAGACG
* *
5772259 TGCTAAACAGAGAGCACACATAGCTGAACAGATAGCACACACAA
1 TGCTAAACAGAGAGCACACACAGCTAAACAGATAGCACACACAA
5772303 TGCTAAACAGAGAGCACACACAGCTAAACAGATAGCACACACAA
1 TGCTAAACAGAGAGCACACACAGCTAAACAGATAGCACACACAA
5772347 TGCTAAACAGAGAGC
1 TGCTAAACAGAGAGC
5772362 GCGCTAGCGT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.46, C:0.25, G:0.18, T:0.11
Consensus pattern (44 bp):
TGCTAAACAGAGAGCACACACAGCTAAACAGATAGCACACACAA
Found at i:5775937 original size:25 final size:23
Alignment explanation
Indices: 5775896--5775942 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
5775886 TCAATTAGGG
5775896 AATTATTGTTTAGATTTAATTTA
1 AATTATTGTTTAGATTTAATTTA
* *
5775919 AATTATCTTTTTAGAATTTCATTT
1 AATTAT-TGTTTAG-ATTTAATTT
5775943 GGATCCAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.32, C:0.04, G:0.06, T:0.57
Consensus pattern (23 bp):
AATTATTGTTTAGATTTAATTTA
Found at i:5781963 original size:23 final size:25
Alignment explanation
Indices: 5781937--5781982 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5781927 CCAATTAGGG
5781937 AATTAT-TGTTTAG-ATTTAATTCA
1 AATTATCTGTTTAGAATTTAATTCA
*
5781960 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
5781983 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCA
Found at i:5788826 original size:26 final size:27
Alignment explanation
Indices: 5788797--5788856 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
5788787 AAACATAGAA
*
5788797 TTTAAAAATATGAAAAATA-AAA-ATTC
1 TTTAAAAATA-AAAAAATAGAAAGATTC
*
5788823 TTTAAAAATAAAAAAATAGAAAGATTT
1 TTTAAAAATAAAAAAATAGAAAGATTC
5788850 TTTAAAA
1 TTTAAAA
5788857 TAATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 7 0.23
26 13 0.43
27 10 0.33
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (27 bp):
TTTAAAAATAAAAAAATAGAAAGATTC
Found at i:5788829 original size:25 final size:28
Alignment explanation
Indices: 5788801--5788858 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 28
5788791 ATAGAATTTA
*
5788801 AAAATAT-GAAAAATA-AAA-ATTCTTT
1 AAAATATAAAAAAATAGAAAGATTCTTT
*
5788826 AAAA-ATAAAAAAATAGAAAGATTTTTT
1 AAAATATAAAAAAATAGAAAGATTCTTT
5788853 AAAATA
1 AAAATA
5788859 ATTTTAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 2 0.07
25 11 0.41
26 3 0.11
27 10 0.37
28 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (28 bp):
AAAATATAAAAAAATAGAAAGATTCTTT
Found at i:5789411 original size:19 final size:20
Alignment explanation
Indices: 5789359--5789411 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
5789349 TTTATTTTTT
* *
5789359 TAAAAATATATTTTAAAAATT
1 TAAAAAT-TAATTTAAAAATA
* *
5789380 TAAAATTTTATTT-AAAATA
1 TAAAAATTAATTTAAAAATA
5789399 TAAAAATTAATTT
1 TAAAAATTAATTT
5789412 TTAAAATTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 16 0.62
20 4 0.15
21 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAAATTAATTTAAAAATA
Found at i:5789836 original size:21 final size:21
Alignment explanation
Indices: 5789810--5789853 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
5789800 AAATAATAAA
5789810 ATATTAAAAACATATAGTTTT
1 ATATTAAAAACATATAGTTTT
* **
5789831 ATATTAATATTATATAGTTTT
1 ATATTAAAAACATATAGTTTT
5789852 AT
1 AT
5789854 TAGAACTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (21 bp):
ATATTAAAAACATATAGTTTT
Found at i:5793610 original size:21 final size:21
Alignment explanation
Indices: 5793570--5793619 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
5793560 GAGTTTTTAG
*
5793570 TATCGGTAGAAGCATGACTTA
1 TATCGGTAGAAGCATCACTTA
* *
5793591 TTTCGGTAGAAGTCA-CACTTG
1 TATCGGTAGAAG-CATCACTTA
5793612 TATCGGTA
1 TATCGGTA
5793620 TAAATCTGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (21 bp):
TATCGGTAGAAGCATCACTTA
Found at i:5795706 original size:49 final size:49
Alignment explanation
Indices: 5795610--5795716 Score: 124
Period size: 49 Copynumber: 2.2 Consensus size: 49
5795600 GTGGCATGAA
* * ** * *
5795610 ACTTGAACTCATGACTGCTTAACCATTGCCAATTAGGGGCCCGAGTTAT
1 ACTTGAACCCATGACTGCATAACCACCGCCAACTAGGAGCCCGAGTTAT
** *
5795659 ACTTGAACCCATGACTGCATAACCACCGTTAACTAGGAGCCCTAGTTAT
1 ACTTGAACCCATGACTGCATAACCACCGCCAACTAGGAGCCCGAGTTAT
*
5795708 ACATGAACC
1 ACTTGAACC
5795717 TGTGATCGTA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (49 bp):
ACTTGAACCCATGACTGCATAACCACCGCCAACTAGGAGCCCGAGTTAT
Found at i:5807212 original size:43 final size:44
Alignment explanation
Indices: 5807125--5807213 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
5807115 ATCTATACTC
*
5807125 AATACTCATAATCATATTCTACACTGTAACATACATAGGCATTT
1 AATACTCATAATCATATTCTACACTGTAACATACAAAGGCATTT
5807169 AATACTCATAATCATATTCTACACT-TAACATACAAAGGCATTT
1 AATACTCATAATCATATTCTACACTGTAACATACAAAGGCATTT
5807212 AA
1 AA
5807214 CGTTAAATTA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 19 0.43
44 25 0.57
ACGTcount: A:0.42, C:0.20, G:0.06, T:0.33
Consensus pattern (44 bp):
AATACTCATAATCATATTCTACACTGTAACATACAAAGGCATTT
Found at i:5809054 original size:111 final size:111
Alignment explanation
Indices: 5808841--5809103 Score: 321
Period size: 111 Copynumber: 2.4 Consensus size: 111
5808831 GTTCCCCTAT
* * ** * * * * *
5808841 TGCAAGCCTTATAGCGAGAAGTCAATAAGGGGAGCTCACGATCCCAACTTGGACTAGATAAGGTC
1 TGCAAGCCTTACAACGAGAAGTCAGCAAGGGGAGCTCGCGATACCAACTCGAACCAGATAAGGTC
* * *
5808906 TGGGTCGCCTACCTATAACCCGACTAGAGCCTGCTAGATGGATGCG
66 CGGGTCGCCTACCAATAACCCGACTAGAGCCTACTAGATGGATGCG
* * *
5808952 TGCAAGTCTTACAACGAGAAGTTAGCAAGGGGAGCTCGCGATATCAACTCGAACCAGATAAGGTC
1 TGCAAGCCTTACAACGAGAAGTCAGCAAGGGGAGCTCGCGATACCAACTCGAACCAGATAAGGTC
* * * * *
5809017 CGGGTTGTCTACCAATGACCTGATTAGA-CACTACTAGATGGATGCG
66 CGGGTCGCCTACCAATAACCCGACTAGAGC-CTACTAGATGGATGCG
*
5809063 TGCAAGCCTTACAGCGAGAAGTCAGCAAGGGGAGCTCGCGA
1 TGCAAGCCTTACAACGAGAAGTCAGCAAGGGGAGCTCGCGA
5809104 CCTTAGCTCG
Statistics
Matches: 128, Mismatches: 23, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
110 1 0.01
111 127 0.99
ACGTcount: A:0.29, C:0.23, G:0.28, T:0.20
Consensus pattern (111 bp):
TGCAAGCCTTACAACGAGAAGTCAGCAAGGGGAGCTCGCGATACCAACTCGAACCAGATAAGGTC
CGGGTCGCCTACCAATAACCCGACTAGAGCCTACTAGATGGATGCG
Found at i:5825549 original size:30 final size:30
Alignment explanation
Indices: 5825513--5825570 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
5825503 TACATAAAAT
**
5825513 AAAAATCAAAAGACAGAATTTATCAAAAGA
1 AAAAATCAAAAGACAGAATCCATCAAAAGA
5825543 AAAAATCAAAAGACAGAATCCATCAAAA
1 AAAAATCAAAAGACAGAATCCATCAAAA
5825571 ACTAAGCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.64, C:0.14, G:0.09, T:0.14
Consensus pattern (30 bp):
AAAAATCAAAAGACAGAATCCATCAAAAGA
Found at i:5825570 original size:17 final size:16
Alignment explanation
Indices: 5825516--5825561 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 16
5825506 ATAAAATAAA
5825516 AATCAAAAGACAGAATT
1 AATCAAAAGACAGAA-T
*
5825533 TATCAAAAGA-A-AA-
1 AATCAAAAGACAGAAT
5825546 AATCAAAAGACAGAAT
1 AATCAAAAGACAGAAT
5825562 CCATCAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
13 9 0.38
14 1 0.04
15 4 0.17
16 1 0.04
17 9 0.38
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.15
Consensus pattern (16 bp):
AATCAAAAGACAGAAT
Found at i:5826512 original size:15 final size:15
Alignment explanation
Indices: 5826488--5826541 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
5826478 TTCCATTAAG
5826488 TTTTTATATTATTTA
1 TTTTTATATTATTTA
*
5826503 TTTTTTTATTATTTA
1 TTTTTATATTATTTA
* *
5826518 -TTATATAATATTTA
1 TTTTTATATTATTTA
**
5826532 AATTTATATT
1 TTTTTATATT
5826542 TTCATTTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTATATTATTTA
Found at i:5826553 original size:18 final size:19
Alignment explanation
Indices: 5826526--5826569 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
5826516 TATTATATAA
* * *
5826526 TATTTAAATTTATATTTTC
1 TATTTTAATTAATATATTC
5826545 -ATTTTAATTAATATATTC
1 TATTTTAATTAATATATTC
5826563 TATTTTA
1 TATTTTA
5826570 TTTTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTAATTAATATATTC
Found at i:5826818 original size:18 final size:19
Alignment explanation
Indices: 5826794--5826845 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
5826784 AATAAAAAAG
5826794 AATATATTAGTTAAAATAAA
1 AATATA-TAGTTAAAATAAA
* *
5826814 AATATATA-TTTAAATTAA
1 AATATATAGTTAAAATAAA
* *
5826832 ATTATATATTTAAA
1 AATATATAGTTAAA
5826846 TATTATATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 15 0.56
19 6 0.22
20 6 0.22
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AATATATAGTTAAAATAAA
Found at i:5826833 original size:23 final size:23
Alignment explanation
Indices: 5826758--5826833 Score: 59
Period size: 23 Copynumber: 3.3 Consensus size: 23
5826748 AAAAAAGAGT
**
5826758 TTAAATAAAAATACGT-TTTAAAA
1 TTAAATAAAAATAAATATTT-AAA
*
5826781 TTAAATAAAAA-AGAATATATT-AG
1 TTAAATAAAAATA-AATAT-TTAAA
*
5826804 TTAAAATAAAAATATATATTTAAA
1 TT-AAATAAAAATAAATATTTAAA
5826828 TTAAAT
1 TTAAAT
5826834 TATATATTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
22 1 0.02
23 21 0.50
24 17 0.40
25 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (23 bp):
TTAAATAAAAATAAATATTTAAA
Found at i:5827707 original size:14 final size:14
Alignment explanation
Indices: 5827638--5827707 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
5827628 ACCTTGAATC
*
5827638 TTAAACTTTAAGGT
1 TTAAAATTTAAGGT
* *
5827652 TTATAATTTAGGGT
1 TTAAAATTTAAGGT
* *
5827666 TTGAAGTTT-AGGT
1 TTAAAATTTAAGGT
* * *
5827679 TTGAGA-TTGAGGT
1 TTAAAATTTAAGGT
5827692 TTAAAATTTAAGGT
1 TTAAAATTTAAGGT
5827706 TT
1 TT
5827708 GAGGCTTAGG
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
12 2 0.05
13 15 0.36
14 25 0.60
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.46
Consensus pattern (14 bp):
TTAAAATTTAAGGT
Found at i:5827733 original size:40 final size:40
Alignment explanation
Indices: 5827648--5827725 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
5827638 TTAAACTTTA
* * *
5827648 AGGTTTATAATTTAGGGTTTGAAGTTTAGGTTTGAGATTG
1 AGGTTTAAAATTTAAGGTTTGAAGCTTAGGTTTGAGATTG
*
5827688 AGGTTTAAAATTTAAGGTTTGAGGCTTAGGTTT-AGATT
1 AGGTTTAAAATTTAAGGTTTGAAGCTTAGGTTTGAGATT
5827726 TGGGGTTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 5 0.15
40 29 0.85
ACGTcount: A:0.27, C:0.01, G:0.28, T:0.44
Consensus pattern (40 bp):
AGGTTTAAAATTTAAGGTTTGAAGCTTAGGTTTGAGATTG
Found at i:5829409 original size:30 final size:30
Alignment explanation
Indices: 5829373--5829434 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
5829363 CATCAATGGC
5829373 GGTAGAGGGTAGAGTTTTGGAGATTTGGGT
1 GGTAGAGGGTAGAGTTTTGGAGATTTGGGT
5829403 GGTAGAGGGTAGAGTTTTGGAGATTTGGGT
1 GGTAGAGGGTAGAGTTTTGGAGATTTGGGT
5829433 GG
1 GG
5829435 CAAAAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.19, C:0.00, G:0.48, T:0.32
Consensus pattern (30 bp):
GGTAGAGGGTAGAGTTTTGGAGATTTGGGT
Found at i:5832559 original size:2 final size:2
Alignment explanation
Indices: 5832552--5832597 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5832542 CTTATAGCCT
5832552 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5832594 TC TC
1 TC TC
5832598 CATCTCCTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5842716 original size:16 final size:16
Alignment explanation
Indices: 5842689--5842732 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
5842679 TCAAATGTAG
*
5842689 ATTCTCAAACAATAATT
1 ATTCT-AAACAATAACT
*
5842706 TTTCTAAACAATAACT
1 ATTCTAAACAATAACT
5842722 ATTCTAAACAA
1 ATTCTAAACAA
5842733 GAGTTGTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (16 bp):
ATTCTAAACAATAACT
Found at i:5852708 original size:32 final size:34
Alignment explanation
Indices: 5852650--5852723 Score: 116
Period size: 32 Copynumber: 2.2 Consensus size: 34
5852640 CATAAATTAA
*
5852650 ACCCAAATATTTTTAATTTTTTACCTTTTATCTT
1 ACCCAAATATTTTTAATTTTTTACCTTTTACCTT
5852684 ACCCAAATATTTTT-A-TTTTTACCTTTTACCTT
1 ACCCAAATATTTTTAATTTTTTACCTTTTACCTT
*
5852716 ACTCAAAT
1 ACCCAAAT
5852724 GTTGTTTACT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 23 0.61
33 1 0.03
34 14 0.37
ACGTcount: A:0.28, C:0.20, G:0.00, T:0.51
Consensus pattern (34 bp):
ACCCAAATATTTTTAATTTTTTACCTTTTACCTT
Found at i:5854466 original size:25 final size:27
Alignment explanation
Indices: 5854438--5854488 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
5854428 CAAAAAATAA
5854438 TAAATTT-TTAATAA-ATTTTT-TAATG
1 TAAATTTATTAA-AATATTTTTATAATG
5854463 TAAATTTATTAAAATATTTTTATAAT
1 TAAATTTATTAAAATATTTTTATAAT
5854489 TATTATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.39
26 10 0.43
27 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TAAATTTATTAAAATATTTTTATAATG
Found at i:5858646 original size:24 final size:24
Alignment explanation
Indices: 5858617--5858673 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
5858607 TTTAGCCAAC
*
5858617 ACGAGCCCAAAATGGTTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
* *
5858641 ATGAGCCCATAATGATTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
5858665 ACGAGCCCA
1 ACGAGCCCA
5858674 GACAGAGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (24 bp):
ACGAGCCCAAAATGATTAGCTCTT
Found at i:5861348 original size:40 final size:40
Alignment explanation
Indices: 5861238--5861425 Score: 186
Period size: 40 Copynumber: 4.7 Consensus size: 40
5861228 TGTGCGTTTA
* * *
5861238 TCCTGTTAGCACTACGGTGCTGCC-GATAATACTTTCATAC
1 TCCTTTTAGCACTACGGTGCT-CCTGATAGTACTTTCGTAC
* *
5861278 T-CTTGTTAGCA-TACGGTGCTCTTGATAGTACTTTCGTAA
1 TCCTT-TTAGCACTACGGTGCTCCTGATAGTACTTTCGTAC
* *
5861317 TCCTTTTAGCACTACAGTGCTCCTTATAGTACTTTCGTAC
1 TCCTTTTAGCACTACGGTGCTCCTGATAGTACTTTCGTAC
* * * * *
5861357 T-CTTGTTAGCATTACGATTCTCATGATAGTACTTTTGTAC
1 TCCTT-TTAGCACTACGGTGCTCCTGATAGTACTTTCGTAC
* * *
5861397 TCCTGTTAGCATTATGGTGCTCCTGATAG
1 TCCTTTTAGCACTACGGTGCTCCTGATAG
5861426 CATATTCATG
Statistics
Matches: 121, Mismatches: 21, Indels: 12
0.79 0.14 0.08
Matches are distributed among these distances:
38 1 0.01
39 34 0.28
40 84 0.69
41 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (40 bp):
TCCTTTTAGCACTACGGTGCTCCTGATAGTACTTTCGTAC
Found at i:5861368 original size:79 final size:80
Alignment explanation
Indices: 5861237--5861425 Score: 247
Period size: 80 Copynumber: 2.4 Consensus size: 80
5861227 ATGTGCGTTT
* * *
5861237 ATCCTGTTAGCACTACGGTGCTGCC-GATAATACTTTCATACTCTTGTTAGCA-TACGGTGCTCT
1 ATCCTGTTAGCACTACGGTGCT-CCTGATAGTACTTTCATACTCTTGTTAGCATTACGATGCTCA
5861300 TGATAGTACTTTCGTA
65 TGATAGTACTTTCGTA
* * * * *
5861316 ATCCTTTTAGCACTACAGTGCTCCTTATAGTACTTTCGTACTCTTGTTAGCATTACGATTCTCAT
1 ATCCTGTTAGCACTACGGTGCTCCTGATAGTACTTTCATACTCTTGTTAGCATTACGATGCTCAT
*
5861381 GATAGTACTTTTGTA
66 GATAGTACTTTCGTA
* * *
5861396 CTCCTGTTAGCATTATGGTGCTCCTGATAG
1 ATCCTGTTAGCACTACGGTGCTCCTGATAG
5861426 CATATTCATG
Statistics
Matches: 93, Mismatches: 15, Indels: 3
0.84 0.14 0.03
Matches are distributed among these distances:
78 2 0.02
79 44 0.47
80 47 0.51
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.39
Consensus pattern (80 bp):
ATCCTGTTAGCACTACGGTGCTCCTGATAGTACTTTCATACTCTTGTTAGCATTACGATGCTCAT
GATAGTACTTTCGTA
Found at i:5863585 original size:24 final size:23
Alignment explanation
Indices: 5863549--5863623 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
5863539 CTAGACAAAA
5863549 TTAGCTCTCACGAGCCCAAGATGG
1 TTAGCTCT-ACGAGCCCAAGATGG
*
5863573 TTAGCTTCTACGAGCCCAGGATGG
1 TTAGC-TCTACGAGCCCAAGATGG
* *
5863597 TTAGCTCTTAAGAGCCCAAAATGG
1 TTAGCTC-TACGAGCCCAAGATGG
5863621 TTA
1 TTA
5863624 ACCAGTATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.04
24 40 0.89
25 3 0.07
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.25
Consensus pattern (23 bp):
TTAGCTCTACGAGCCCAAGATGG
Found at i:5871151 original size:62 final size:59
Alignment explanation
Indices: 5871085--5871201 Score: 137
Period size: 62 Copynumber: 1.9 Consensus size: 59
5871075 ATTAACTATC
* * * * *
5871085 TTAATATTAAATTAAAT-TGAATGTTTATGTTATAGATAAATATTTTATTATTTTAATAAGAT
1 TTAATAGTAAATTAAATCT-AATATTTAT-TT-T-GATAAATATTATACTAATTTAATAAGAT
*
5871147 TTAATAGTAAATTTAATCTAATATTTATTTTGATAAATATTATACTAATTTAATA
1 TTAATAGTAAATTAAATCTAATATTTATTTTGATAAATATTATACTAATTTAATA
5871202 TTAAAATAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
59 21 0.44
60 1 0.02
61 2 0.04
62 23 0.48
63 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.50
Consensus pattern (59 bp):
TTAATAGTAAATTAAATCTAATATTTATTTTGATAAATATTATACTAATTTAATAAGAT
Found at i:5877365 original size:25 final size:23
Alignment explanation
Indices: 5877337--5877387 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
5877327 CAATGTGCGA
*
5877337 CAATGAGAGAAGGAAAAATGGACAG
1 CAATG-GAGAAGAAAAAATGG-CAG
*
5877362 CAATGGAGAATAAAAAATGGCAG
1 CAATGGAGAAGAAAAAATGGCAG
5877385 CAA
1 CAA
5877388 CTTATGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 6 0.25
24 13 0.54
25 5 0.21
ACGTcount: A:0.53, C:0.10, G:0.27, T:0.10
Consensus pattern (23 bp):
CAATGGAGAAGAAAAAATGGCAG
Found at i:5885539 original size:81 final size:81
Alignment explanation
Indices: 5885410--5886445 Score: 1471
Period size: 81 Copynumber: 12.8 Consensus size: 81
5885400 GGAGCTAGTA
* * * * *
5885410 GAGGACTAGAGTTATGAAGAGGATTTGATCCTCTCAGAGTTTCTCTCTTCACGATGACATTAAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
* * * *
5885475 CTAGTAGGTGCTTACG
66 CCACTAGGTGCCTGCG
** * * *
5885491 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCAAGGAGTTTCTCTCTTCACAATGATATTTAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
*
5885556 CTACTAGGTGCCTGCG
66 CCACTAGGTGCCTGCG
* * *
5885572 GAGGATTAGAATTATGAAGAGGATTTGGTCCTTCCGGAGTTTCTCTCTTCGCAATGACATTAAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
* * *
5885637 CCATTAGGAGCTTGCG
66 CCACTAGGTGCCTGCG
** ** *
5885653 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCTAGAGTTTCTCTCTTCACGATGATGTTTAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
5885718 CCACTAGGTGCCTGCG
66 CCACTAGGTGCCTGCG
* * *
5885734 GATGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCCCTCTTCACAATGACATTAAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
* *
5885799 CCACTAGGTGCTTGTG
66 CCACTAGGTGCCTGCG
*
5885815 GAGGATTAGAATTATGAAGAGGATTTGATCCTCCCGGAGTTTCT-TACTTCACGATGACATTAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCT-CTTCACGATGACATTAAA
*
5885879 AGCACTAGGTGCCTGCG
65 ACCACTAGGTGCCTGCG
* * *
5885896 GAGGATTAGAATTGTGAAGAGGATTTGGCCCTCCCGGAGTTTCTCGCTTCACGATGACATTAAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
* *
5885961 CTACTAGGTGCTTGCG
66 CCACTAGGTGCCTGCG
* *
5885977 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCTCCCGGAGTTTCTCGCTTCACGATAACATTA
1 GAGGATTAGAATTATGAAGAGGATTTGG---TCCTCCCGGAGTTTCTCTCTTCACGATGACATTA
**
5886042 AAACCACTAGGTGCCTGTA
63 AAACCACTAGGTGCCTGCG
* * * *
5886061 GAGGATTAGAATTGTGAAGAGGATTTGGCCCTCCTGGAGTTTCTCGCTTCACGATGACATTAAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
* *
5886126 CTACTAGGTGCTTGCG
66 CCACTAGGTGCCTGCG
*
5886142 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCGCTTCACGATGACATTAAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
5886207 CCACTAGGTGCCTGCG
66 CCACTAGGTGCCTGCG
* * *
5886223 GAGGATTAGAATTATGAAGAGGATTTGGCCCTCCTGGAGTTTCTCGCTTCACGATGACATTAAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
5886288 CCACTAGGTGCCTGCG
66 CCACTAGGTGCCTGCG
* * *
5886304 GAGGATTAGAATTGTGAAGAGGATTTGGCCCTCCCGGAGTTTCTCGCTTCACGATGACATTAAAA
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
*
5886369 CCACTAGGTGCCTGTG
66 CCACTAGGTGCCTGCG
* *** **
5886385 GAGGATTAGAATTATGAAGATGATTTGGTCCTCCTAAAGTTTCTCTCCCCACGATGACATT
1 GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATT
5886446 TTTAATGGCA
Statistics
Matches: 859, Mismatches: 91, Indels: 10
0.89 0.09 0.01
Matches are distributed among these distances:
80 1 0.00
81 784 0.91
84 74 0.09
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.30
Consensus pattern (81 bp):
GAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTCTCTTCACGATGACATTAAAA
CCACTAGGTGCCTGCG
Found at i:5887606 original size:20 final size:20
Alignment explanation
Indices: 5887581--5887650 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 20
5887571 ACTATATTGT
5887581 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTAC
5887601 TGTTTTGGTTGATTTTTTTTAC
1 TGTTTTGG-TG-TTTTTTTTAC
* * *
5887623 TGTTTTTGAGTTGTTTTTTAT
1 TGTTTTGGTGTT-TTTTTTAC
5887644 TGTTTTG
1 TGTTTTG
5887651 ATTGCTATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 10 0.23
21 16 0.37
22 17 0.40
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (20 bp):
TGTTTTGGTGTTTTTTTTAC
Found at i:5887619 original size:22 final size:21
Alignment explanation
Indices: 5887581--5887641 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 21
5887571 ACTATATTGT
5887581 TGTTTTGG-TGTTTTTTTTAC
1 TGTTTTGGTTGTTTTTTTTAC
5887601 TGTTTTGGTTGATTTTTTTTAC
1 TGTTTTGGTTG-TTTTTTTTAC
5887623 TGTTTTTGAGTTGTTTTTT
1 TG-TTTTG-GTTGTTTTTT
5887642 ATTGTTTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.22
21 2 0.05
22 12 0.32
23 11 0.30
24 4 0.11
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (21 bp):
TGTTTTGGTTGTTTTTTTTAC
Found at i:5887651 original size:20 final size:19
Alignment explanation
Indices: 5887581--5887650 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 19
5887571 ACTATATTGT
*
5887581 TGTTTTGGTGTTTTTTTTAC
1 TGTTTTGGT-TGTTTTTTAC
5887601 TGTTTTGGTTGATTTTTTTTAC
1 TGTTTTGGTTG---TTTTTTAC
*
5887623 TGTTTTTGAGTTGTTTTTTAT
1 TG-TTTTG-GTTGTTTTTTAC
5887644 TGTTTTG
1 TGTTTTG
5887651 ATTGCTATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
19 1 0.02
20 14 0.33
21 9 0.21
22 10 0.23
23 5 0.12
24 4 0.09
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (19 bp):
TGTTTTGGTTGTTTTTTAC
Found at i:5887662 original size:21 final size:21
Alignment explanation
Indices: 5887593--5887649 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
5887583 TTTTGGTGTT
5887593 TTTTTTACTG-TTTTG-GTTG
1 TTTTTTACTGTTTTTGAGTTG
5887612 ATTTTTTTTACTGTTTTTGAGTTG
1 ---TTTTTTACTGTTTTTGAGTTG
*
5887636 TTTTTTATTGTTTT
1 TTTTTTACTGTTTT
5887650 GATTGCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 13 0.41
22 10 0.31
23 5 0.16
24 4 0.12
ACGTcount: A:0.09, C:0.04, G:0.16, T:0.72
Consensus pattern (21 bp):
TTTTTTACTGTTTTTGAGTTG
Found at i:5887684 original size:12 final size:12
Alignment explanation
Indices: 5887666--5887714 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
5887656 TATTTTTGTA
*
5887666 TTATTTTT-CTG
1 TTATTTTTATTG
*
5887677 TTATTTTTGTTG
1 TTATTTTTATTG
*
5887689 TTGTTTTTATTG
1 TTATTTTTATTG
*
5887701 TTATTTTTGTTG
1 TTATTTTTATTG
5887713 TT
1 TT
5887715 TTTAATGTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.08, C:0.02, G:0.14, T:0.76
Consensus pattern (12 bp):
TTATTTTTATTG
Found at i:5887696 original size:24 final size:24
Alignment explanation
Indices: 5887643--5887714 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
5887633 TTGTTTTTTA
* * *
5887643 TTGTTTTGATTGCTATTTTTG-TA
1 TTGTTTTTATTGTTATTTTTGTTG
* *
5887666 TTATTTTT-CTGTTATTTTTGTTG
1 TTGTTTTTATTGTTATTTTTGTTG
5887689 TTGTTTTTATTGTTATTTTTGTTG
1 TTGTTTTTATTGTTATTTTTGTTG
5887713 TT
1 TT
5887715 TTTAATGTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 10 0.25
23 14 0.35
24 16 0.40
ACGTcount: A:0.10, C:0.03, G:0.15, T:0.72
Consensus pattern (24 bp):
TTGTTTTTATTGTTATTTTTGTTG
Found at i:5887712 original size:21 final size:21
Alignment explanation
Indices: 5887637--5887728 Score: 71
Period size: 21 Copynumber: 4.2 Consensus size: 21
5887627 TTTGAGTTGT
* * *
5887637 TTTTTATTGTTTTGATTGCTA
1 TTTTTGTTGTTTTTATTGTTA
5887658 TTTTTGTAT-TATTTT-TCTGTTA
1 TTTTTGT-TGT-TTTTAT-TGTTA
5887680 TTTTTGTTGTTGTTTTTATTGTTA
1 --TTT-TTGTTGTTTTTATTGTTA
* *
5887704 TTTTTGTTGTTTTTAATGTTG
1 TTTTTGTTGTTTTTATTGTTA
5887725 TTTT
1 TTTT
5887729 ACTGTTATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
21 28 0.48
22 11 0.19
24 13 0.22
25 6 0.10
ACGTcount: A:0.11, C:0.02, G:0.14, T:0.73
Consensus pattern (21 bp):
TTTTTGTTGTTTTTATTGTTA
Found at i:5887740 original size:12 final size:12
Alignment explanation
Indices: 5887666--5887740 Score: 52
Period size: 12 Copynumber: 6.7 Consensus size: 12
5887656 TATTTTTGTA
5887666 TTATTTTT-CTG
1 TTATTTTTACTG
**
5887677 TTATTTTTGTTG
1 TTATTTTTACTG
* *
5887689 TTGTTTTTATTG
1 TTATTTTTACTG
5887701 TTA-TTTT--TG
1 TTATTTTTACTG
* *
5887710 TTGTTTTTAATG
1 TTATTTTTACTG
*
5887722 TT-GTTTTACTG
1 TTATTTTTACTG
5887733 TTATTTTT
1 TTATTTTT
5887741 GCTGCTGTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
9 4 0.08
10 4 0.08
11 21 0.41
12 22 0.43
ACGTcount: A:0.11, C:0.03, G:0.13, T:0.73
Consensus pattern (12 bp):
TTATTTTTACTG
Found at i:5887779 original size:56 final size:56
Alignment explanation
Indices: 5887666--5887784 Score: 159
Period size: 56 Copynumber: 2.1 Consensus size: 56
5887656 TATTTTTGTA
* * * *
5887666 TTATTTTTCTGTTATTTTTGTTGTTGTTTTTATTGTTATTTTTGTTGTTTTTAATG
1 TTATTTTACTGTTATTTTTGCTGCTGTTTTTATTATTATTTTTGTTGTTTTTAATG
* * *
5887722 TTGTTTTACTGTTATTTTTGCTGCTGTTTTTGTTATTAATTTTTGTTG-TTTTGATG
1 TTATTTTACTGTTATTTTTGCTGCTGTTTTTATTATT-ATTTTTGTTGTTTTTAATG
5887778 TTATTTT
1 TTATTTT
5887785 TTATGCGTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
56 44 0.81
57 10 0.19
ACGTcount: A:0.11, C:0.03, G:0.15, T:0.71
Consensus pattern (56 bp):
TTATTTTACTGTTATTTTTGCTGCTGTTTTTATTATTATTTTTGTTGTTTTTAATG
Found at i:5887785 original size:21 final size:21
Alignment explanation
Indices: 5887720--5887786 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
5887710 TTGTTTTTAA
5887720 TGTTGTTTT-ACTGTTATTTTT
1 TGTTGTTTTGA-TGTTATTTTT
* * * *
5887741 GCTGCTGTTTTTGTTATTAATTTT
1 --TGTTG-TTTTGATGTTATTTTT
5887765 TGTTGTTTTGATGTTATTTTT
1 TGTTGTTTTGATGTTATTTTT
5887786 T
1 T
5887787 ATGCGTTTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
21 14 0.41
22 4 0.12
23 4 0.12
24 12 0.35
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.69
Consensus pattern (21 bp):
TGTTGTTTTGATGTTATTTTT
Found at i:5890616 original size:6 final size:6
Alignment explanation
Indices: 5890605--5890630 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5890595 GTGGATGACA
5890605 GGGGTG GGGGTG GGGGTG GGGGTG GG
1 GGGGTG GGGGTG GGGGTG GGGGTG GG
5890631 AGAAATGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.85, T:0.15
Consensus pattern (6 bp):
GGGGTG
Found at i:5891539 original size:40 final size:40
Alignment explanation
Indices: 5891493--5891581 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
5891483 TAACGGACAT
*
5891493 ACTGACGTGGCCGTTAATTGACTAACGATCAATATTAACC
1 ACTGACGTGGCCGTTAATTGACTAACGATCAACATTAACC
5891533 ACTGACGTGGCCGTTAATTGACTAACGATCAACATTAACC
1 ACTGACGTGGCCGTTAATTGACTAACGATCAACATTAACC
5891573 ACTGACGTG
1 ACTGACGTG
5891582 ACTGTCCAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (40 bp):
ACTGACGTGGCCGTTAATTGACTAACGATCAACATTAACC
Found at i:5891686 original size:3 final size:3
Alignment explanation
Indices: 5891655--5891724 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
5891645 TGATTTTAAA
* * * * *
5891655 ATC ACC ATC ACC ATC ACC ATC ACC ATC ATC ATC ATC ATC CTC ATTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A-TC
*
5891701 CTC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC
5891725 GTTCCTCATC
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
3 52 0.96
4 2 0.04
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.29
Consensus pattern (3 bp):
ATC
Found at i:5891718 original size:28 final size:28
Alignment explanation
Indices: 5891678--5891734 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
5891668 TCACCATCAC
*
5891678 CATCATCATCATCATCCTCATTCCTCAT
1 CATCATCATCATCATCATCATTCCTCAT
*
5891706 CATCATCATCATCATCATCGTTCCTCAT
1 CATCATCATCATCATCATCATTCCTCAT
5891734 C
1 C
5891735 CTTTTTTGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.39, G:0.02, T:0.35
Consensus pattern (28 bp):
CATCATCATCATCATCATCATTCCTCAT
Found at i:5915061 original size:20 final size:22
Alignment explanation
Indices: 5915024--5915063 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5915014 ATAATATATC
5915024 AAACACTTAAAAACAATAAAAG
1 AAACACTTAAAAACAATAAAAG
5915046 AAACA-TTAAAAA-AATAAA
1 AAACACTTAAAAACAATAAA
5915064 CAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (22 bp):
AAACACTTAAAAACAATAAAAG
Found at i:5915374 original size:22 final size:21
Alignment explanation
Indices: 5915298--5915373 Score: 102
Period size: 19 Copynumber: 3.7 Consensus size: 21
5915288 AATAACAGTG
*
5915298 AAACATCACCAAAACAGT--A
1 AAACAGCACCAAAACAGTAAA
5915317 AAACAGCACCAAAACAGTAAAA
1 AAACAGCACCAAAACAGT-AAA
* *
5915339 AAATAACACCAAAACAGTAAA
1 AAACAGCACCAAAACAGTAAA
5915360 AAACAGCACCAAAA
1 AAACAGCACCAAAA
5915374 AATAATATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.35
21 15 0.31
22 17 0.35
ACGTcount: A:0.63, C:0.24, G:0.07, T:0.07
Consensus pattern (21 bp):
AAACAGCACCAAAACAGTAAA
Found at i:5917117 original size:46 final size:46
Alignment explanation
Indices: 5917046--5917140 Score: 154
Period size: 46 Copynumber: 2.1 Consensus size: 46
5917036 TTATAAATGA
* * *
5917046 AATAAAAACCTAATATAATAGAGAAAATAAGTAAAACTAAAACTTT
1 AATAAAAACCTAATATAATAAAGAAAATAAATAAAACTAAAACTCT
*
5917092 AATAAAAACCTGATATAATAAAGAAAATAAATAAAACTAAAACTCT
1 AATAAAAACCTAATATAATAAAGAAAATAAATAAAACTAAAACTCT
5917138 AAT
1 AAT
5917141 TGTTGTTGTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.23
Consensus pattern (46 bp):
AATAAAAACCTAATATAATAAAGAAAATAAATAAAACTAAAACTCT
Found at i:5920164 original size:18 final size:18
Alignment explanation
Indices: 5920119--5920187 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
5920109 TGGTCACATC
* *
5920119 TTGGTTGAGCTCGCATGT
1 TTGGATGAGCTCGCAAGT
5920137 TTGG-TGAGCTCGCAAGT
1 TTGGATGAGCTCGCAAGT
5920154 TTGGATGAGCTCGC-AGCT
1 TTGGATGAGCTCGCAAG-T
*
5920172 TTCGATGAGCTCGCAA
1 TTGGATGAGCTCGCAA
5920188 TTGTGTTTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
17 18 0.39
18 27 0.59
19 1 0.02
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.30
Consensus pattern (18 bp):
TTGGATGAGCTCGCAAGT
Found at i:5926703 original size:27 final size:27
Alignment explanation
Indices: 5926665--5926717 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
5926655 AAGTAAGGAC
*
5926665 TAGTGCCGCCTA-CCTCATAGGCACCAT
1 TAGTGCCGCCTAGCC-CATAGACACCAT
*
5926692 TAGTGCGGCCTAGCCCATAGACACCA
1 TAGTGCCGCCTAGCCCATAGACACCA
5926718 CCCGAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.25, C:0.36, G:0.21, T:0.19
Consensus pattern (27 bp):
TAGTGCCGCCTAGCCCATAGACACCAT
Found at i:5931867 original size:21 final size:21
Alignment explanation
Indices: 5931840--5931903 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
5931830 ATTATTTTGA
*
5931840 TGTTGTT-TTTTTTATTGTTT
1 TGTTGTTATTTTTTACTGTTT
* *
5931860 TGGTTGTTGTTTTTTGCTGTTT
1 T-GTTGTTATTTTTTACTGTTT
* *
5931882 TGATGTTATTTTTTACTATTT
1 TGTTGTTATTTTTTACTGTTT
5931903 T
1 T
5931904 AGTTTTTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 23 0.64
22 12 0.33
ACGTcount: A:0.08, C:0.03, G:0.17, T:0.72
Consensus pattern (21 bp):
TGTTGTTATTTTTTACTGTTT
Found at i:5931880 original size:22 final size:21
Alignment explanation
Indices: 5931841--5931911 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
5931831 TTATTTTGAT
*
5931841 GTTGTTTTTTTTATTGTTTTG
1 GTTGTTTTTTTTACTGTTTTG
*
5931862 GTTGTTGTTTTTTGCTGTTTT-
1 GTTGTT-TTTTTTACTGTTTTG
* * *
5931883 GATGTTATTTTTTACTATTTTA
1 GTTGTT-TTTTTTACTGTTTTG
5931905 GTT-TTTT
1 GTTGTTTT
5931912 ATTATTTTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
20 2 0.05
21 25 0.61
22 14 0.34
ACGTcount: A:0.08, C:0.03, G:0.17, T:0.72
Consensus pattern (21 bp):
GTTGTTTTTTTTACTGTTTTG
Found at i:5931946 original size:22 final size:22
Alignment explanation
Indices: 5931916--5931957 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5931906 TTTTTTATTA
5931916 TTTTGTTGTTGTTTTAGTTGCT
1 TTTTGTTGTTGTTTTAGTTGCT
* * *
5931938 TTTTTTTGTTTTTTTTGTTG
1 TTTTGTTGTTGTTTTAGTTG
5931958 TTGTTTTGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.02, C:0.02, G:0.19, T:0.76
Consensus pattern (22 bp):
TTTTGTTGTTGTTTTAGTTGCT
Done.