Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 151 of 198
Found at i:47811448 original size:26 final size:27
Alignment explanation
Indices: 47811417--47811472 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 27
47811407 TGAAAAATGA
* *
47811417 AATTTTTT-ATTTTTTATTTTTTTAA-
1 AATTTTTTAAATTTATATTTTTTTAAG
47811442 AATTTTTTAAATTTATATTTTTTTAAG
1 AATTTTTTAAATTTATATTTTTTTAAG
47811469 AATT
1 AATT
47811473 AAGACTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 8 0.30
26 15 0.56
27 4 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (27 bp):
AATTTTTTAAATTTATATTTTTTTAAG
Found at i:47815466 original size:6 final size:6
Alignment explanation
Indices: 47815455--47815486 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
47815445 TTTGCTCAAA
47815455 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT AT
47815487 TTTTATTTTT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATAAAT
Found at i:47823575 original size:65 final size:65
Alignment explanation
Indices: 47823471--47823596 Score: 252
Period size: 65 Copynumber: 1.9 Consensus size: 65
47823461 TGAGATTACG
47823471 CTTTAACAAAGTTGACCTAAGGCTCTAAGAAGCTAAAGAAAGAACTCGACTCCAAAGGAAGAACT
1 CTTTAACAAAGTTGACCTAAGGCTCTAAGAAGCTAAAGAAAGAACTCGACTCCAAAGGAAGAACT
47823536 CTTTAACAAAGTTGACCTAAGGCTCTAAGAAGCTAAAGAAAGAACTCGACTCCAAAGGAAG
1 CTTTAACAAAGTTGACCTAAGGCTCTAAGAAGCTAAAGAAAGAACTCGACTCCAAAGGAAG
47823597 TAAGTTGCGC
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (65 bp):
CTTTAACAAAGTTGACCTAAGGCTCTAAGAAGCTAAAGAAAGAACTCGACTCCAAAGGAAGAACT
Found at i:47823893 original size:9 final size:9
Alignment explanation
Indices: 47823879--47823934 Score: 51
Period size: 9 Copynumber: 6.0 Consensus size: 9
47823869 ATTTAACCCA
47823879 TAATTTTTT
1 TAATTTTTT
47823888 TAATTTTTT
1 TAATTTTTT
47823897 T-ATCTTTTT
1 TAAT-TTTTT
* *
47823906 CGAATTTTCT
1 -TAATTTTTT
*
47823916 TGATTTTTGT
1 TAATTTTT-T
47823926 TAATTTTTT
1 TAATTTTTT
47823935 GTGGGAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
8 2 0.05
9 21 0.57
10 12 0.32
11 2 0.05
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (9 bp):
TAATTTTTT
Found at i:47825029 original size:49 final size:49
Alignment explanation
Indices: 47824972--47825070 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
47824962 GATTCAAAGT
47824972 ATGTTTCAAATTTAAAAGACAAATATTCAAACGCTATGCAGACATATCA
1 ATGTTTCAAATTTAAAAGACAAATATTCAAACGCTATGCAGACATATCA
*
47825021 ATGTTTCAAATTTAAAAGACAGATATTCAAACGCTATGCAGACATATCA
1 ATGTTTCAAATTTAAAAGACAAATATTCAAACGCTATGCAGACATATCA
47825070 A
1 A
47825071 CCCAAAAATG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.28
Consensus pattern (49 bp):
ATGTTTCAAATTTAAAAGACAAATATTCAAACGCTATGCAGACATATCA
Found at i:47826031 original size:13 final size:13
Alignment explanation
Indices: 47826013--47826050 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
47826003 AGTTCTTTAT
*
47826013 TGCTTTTAAGAAG
1 TGCTTTTGAGAAG
47826026 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
47826039 TGCTTTTGAGAA
1 TGCTTTTGAGAA
47826051 ATTTGGGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:47826653 original size:12 final size:12
Alignment explanation
Indices: 47826636--47826665 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
47826626 GTCATTAACC
47826636 CTAGATTATATT
1 CTAGATTATATT
47826648 CTAGATTATATT
1 CTAGATTATATT
47826660 CTAGAT
1 CTAGAT
47826666 CCAAATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (12 bp):
CTAGATTATATT
Found at i:47834332 original size:21 final size:18
Alignment explanation
Indices: 47834307--47834352 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
47834297 ATATGATTTT
47834307 TTATTAAAATCTTAGTATTAA
1 TTATTAAAA--TTA-TATTAA
*
47834328 TTATTTAAATTATATTAA
1 TTATTAAAATTATATTAA
47834346 TTATTAA
1 TTATTAA
47834353 GTAATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 12 0.52
19 3 0.13
21 8 0.35
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATTAAAATTATATTAA
Found at i:47834383 original size:14 final size:14
Alignment explanation
Indices: 47834364--47834393 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
47834354 TAATTAAAAC
47834364 AATAAAGTAAATAA
1 AATAAAGTAAATAA
47834378 AATAAAGTAAATAA
1 AATAAAGTAAATAA
47834392 AA
1 AA
47834394 GAAACTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (14 bp):
AATAAAGTAAATAA
Found at i:47834420 original size:9 final size:9
Alignment explanation
Indices: 47834390--47834438 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
47834380 TAAAGTAAAT
47834390 AAAAGAAAC
1 AAAAGAAAC
* *
47834399 TAAAGAAAT
1 AAAAGAAAC
*
47834408 AAAAGAAAG
1 AAAAGAAAC
**
47834417 AAAAGAAGT
1 AAAAGAAAC
47834426 AAAAGAAAC
1 AAAAGAAAC
47834435 AAAA
1 AAAA
47834439 AGAACAGCAG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.76, C:0.04, G:0.14, T:0.06
Consensus pattern (9 bp):
AAAAGAAAC
Found at i:47834438 original size:18 final size:18
Alignment explanation
Indices: 47834381--47834438 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
47834371 TAAATAAAAT
*
47834381 AAAGTAAATAAAAGAAACT
1 AAAG-AAATAAAAGAAACA
*
47834400 AAAGAAATAAAAGAAAGA
1 AAAGAAATAAAAGAAACA
*
47834418 AAAGAAGTAAAAGAAACA
1 AAAGAAATAAAAGAAACA
47834436 AAA
1 AAA
47834439 AGAACAGCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
18 31 0.89
19 4 0.11
ACGTcount: A:0.74, C:0.03, G:0.14, T:0.09
Consensus pattern (18 bp):
AAAGAAATAAAAGAAACA
Found at i:47835213 original size:18 final size:18
Alignment explanation
Indices: 47835190--47835227 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
47835180 GTATATTGAT
47835190 TTGAAT-GTGAAATTGAAA
1 TTGAATAGTGAAATT-AAA
*
47835208 TTGAATAGTGATATTAAA
1 TTGAATAGTGAAATTAAA
47835226 TT
1 TT
47835228 TGGTATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (18 bp):
TTGAATAGTGAAATTAAA
Found at i:47835378 original size:23 final size:23
Alignment explanation
Indices: 47835347--47835457 Score: 97
Period size: 23 Copynumber: 5.0 Consensus size: 23
47835337 GGTTTTGTCG
* *
47835347 ATCAAGCACTTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* *
47835370 ATCAGGCACTTTATGTGCCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* **
47835393 TTCAGGCACCTCGTGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
**
47835416 -T-AGGCACCTCGTGTGTCGT-T
1 ATCAGGCACCTTATGTGTCGTAT
*
47835436 -TCAGGCA-CTTATGTATCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
47835457 A
1 A
47835458 CTGATAAGGT
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
20 11 0.15
21 24 0.32
22 1 0.01
23 39 0.52
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.36
Consensus pattern (23 bp):
ATCAGGCACCTTATGTGTCGTAT
Found at i:47835422 original size:21 final size:22
Alignment explanation
Indices: 47835360--47835443 Score: 100
Period size: 23 Copynumber: 3.8 Consensus size: 22
47835350 AAGCACTTTA
* **
47835360 TGTGTCGTATATCAGGCACTTTA
1 TGTGTCGTAT-TCAGGCACCTCG
*
47835383 TGTGCCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
47835406 TGTGTCGTATT-AGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
47835427 TGTGTCGT-TTCAGGCAC
1 TGTGTCGTATTCAGGCAC
47835444 TTATGTATCG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
20 2 0.04
21 24 0.44
22 2 0.04
23 25 0.46
24 1 0.02
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:47859177 original size:15 final size:17
Alignment explanation
Indices: 47859159--47859192 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
47859149 TATAGGTGAA
47859159 CCCC-TATAAGCGAACC
1 CCCCATATAAGCGAACC
*
47859175 CCCCATATATGCGAACC
1 CCCCATATAAGCGAACC
47859192 C
1 C
47859193 ATATGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.29, C:0.44, G:0.12, T:0.15
Consensus pattern (17 bp):
CCCCATATAAGCGAACC
Found at i:47859330 original size:45 final size:45
Alignment explanation
Indices: 47859281--47859385 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 45
47859271 TATCTATTGA
*
47859281 AATATGCAAACCCTATATGTTATTTACGCAAACCCTACATGTGGT
1 AATATGCAAACCCTATATGTCATTTACGCAAACCCTACATGTGGT
*** * * * * * *
47859326 AATATATGAGCCTTATATGTCGTTTATGCGAACCCTATATGTGGT
1 AATATGCAAACCCTATATGTCATTTACGCAAACCCTACATGTGGT
47859371 AATATGCAAACCCTA
1 AATATGCAAACCCTA
47859386 ATTGTTTATA
Statistics
Matches: 45, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (45 bp):
AATATGCAAACCCTATATGTCATTTACGCAAACCCTACATGTGGT
Found at i:47859364 original size:22 final size:23
Alignment explanation
Indices: 47859339--47859385 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
47859329 ATATGAGCCT
* *
47859339 TATATGTCGT-TTATGCGAACCC
1 TATATGTCGTAATATGCAAACCC
*
47859361 TATATGTGGTAATATGCAAACCC
1 TATATGTCGTAATATGCAAACCC
47859384 TA
1 TA
47859386 ATTGTTTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (23 bp):
TATATGTCGTAATATGCAAACCC
Found at i:47859382 original size:23 final size:23
Alignment explanation
Indices: 47859281--47859385 Score: 81
Period size: 22 Copynumber: 4.7 Consensus size: 23
47859271 TATCTATTGA
47859281 AATATGCAAACCCTATATGT--T
1 AATATGCAAACCCTATATGTGGT
* * *
47859302 ATTTACGCAAACCCTACATGTGGT
1 A-ATATGCAAACCCTATATGTGGT
*** * * *
47859326 AATATATGAGCCTTATATGTCGT
1 AATATGCAAACCCTATATGTGGT
* *
47859349 -TTATGCGAACCCTATATGTGGT
1 AATATGCAAACCCTATATGTGGT
47859371 AATATGCAAACCCTA
1 AATATGCAAACCCTA
47859386 ATTGTTTATA
Statistics
Matches: 60, Mismatches: 20, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
21 1 0.02
22 32 0.53
23 25 0.42
24 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (23 bp):
AATATGCAAACCCTATATGTGGT
Found at i:47859434 original size:16 final size:16
Alignment explanation
Indices: 47859413--47859452 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
47859403 ACTCTATATG
47859413 TGCAAACCCTAATGTA
1 TGCAAACCCTAATGTA
* *
47859429 TGCAAACACTTATGTA
1 TGCAAACCCTAATGTA
47859445 TGCAAACC
1 TGCAAACC
47859453 TTAGGAATGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (16 bp):
TGCAAACCCTAATGTA
Found at i:47859462 original size:15 final size:16
Alignment explanation
Indices: 47859428--47859468 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
47859418 ACCCTAATGT
* *
47859428 ATGCAAACACTTATGT
1 ATGCAAACACTTAGGA
47859444 ATGCAAAC-CTTAGGA
1 ATGCAAACACTTAGGA
47859459 ATGCAAACAC
1 ATGCAAACAC
47859469 CTATGAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (16 bp):
ATGCAAACACTTAGGA
Found at i:47866775 original size:23 final size:23
Alignment explanation
Indices: 47866748--47866836 Score: 97
Period size: 23 Copynumber: 3.9 Consensus size: 23
47866738 GAACGAACAG
47866748 TGAACAATGAAGATTCTCTACGA
1 TGAACAATGAAGATTCTCTACGA
** * * *
47866771 TGAACTGTGAAAATTTTCTACAA
1 TGAACAATGAAGATTCTCTACGA
*
47866794 TGAACAATGAAGTTTCTCTACGA
1 TGAACAATGAAGATTCTCTACGA
* * *
47866817 TTAACATTGAAGGTTCTCTA
1 TGAACAATGAAGATTCTCTA
47866837 AAAAATACAA
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (23 bp):
TGAACAATGAAGATTCTCTACGA
Found at i:47867124 original size:22 final size:22
Alignment explanation
Indices: 47867082--47867124 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
47867072 ATTTTCTAGA
* *
47867082 TTTTAAAATTTTAAGTGTTTAC
1 TTTTAAAAATTTAAATGTTTAC
47867104 TTTTAAAAAATTTAAAT-TTTA
1 TTTT-AAAAATTTAAATGTTTA
47867125 AACAAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (22 bp):
TTTTAAAAATTTAAATGTTTAC
Found at i:47867151 original size:15 final size:15
Alignment explanation
Indices: 47867133--47867181 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
47867123 TAAACAAATC
47867133 AATTAAGTTTTCAAA
1 AATTAAGTTTTCAAA
* *
47867148 AATTTATTTTTCAAA
1 AATTAAGTTTTCAAA
*
47867163 ATTTAAGTTTTCAAA
1 AATTAAGTTTTCAAA
47867178 AATT
1 AATT
47867182 TTTGCTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (15 bp):
AATTAAGTTTTCAAA
Found at i:47867211 original size:17 final size:16
Alignment explanation
Indices: 47867141--47867215 Score: 66
Period size: 15 Copynumber: 4.8 Consensus size: 16
47867131 TCAATTAAGT
**
47867141 TTTCAAAAA-TTTATT
1 TTTCAAAAATTTTAGC
* *
47867156 TTTC-AAAATTTAAGT
1 TTTCAAAAATTTTAGC
*
47867171 TTTCAAAAATTTTTGC
1 TTTCAAAAATTTTAGC
47867187 TTT-AAAAAGTTTCTAGC
1 TTTCAAAAA-TTT-TAGC
47867204 TTTCAAAAATTT
1 TTTCAAAAATTT
47867216 AAGTTTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
14 4 0.08
15 17 0.35
16 14 0.29
17 9 0.18
18 5 0.10
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.48
Consensus pattern (16 bp):
TTTCAAAAATTTTAGC
Found at i:47870916 original size:17 final size:16
Alignment explanation
Indices: 47870848--47870918 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
47870838 AAAACAAATC
*
47870848 AAATTTGAGCTTTCAA
1 AAATTTTAGCTTTCAA
* **
47870864 AAATTTAAAATTTCAA
1 AAATTTTAGCTTTCAA
*
47870880 AAATTTTAGCTTTAAA
1 AAATTTTAGCTTTCAA
47870896 AAATTTCTAGCTTTCAA
1 AAATTT-TAGCTTTCAA
47870913 AAATTT
1 AAATTT
47870919 AAGTTTTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
16 31 0.67
17 15 0.33
ACGTcount: A:0.44, C:0.10, G:0.06, T:0.41
Consensus pattern (16 bp):
AAATTTTAGCTTTCAA
Found at i:47880611 original size:18 final size:18
Alignment explanation
Indices: 47880588--47880624 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
47880578 TTCAGAAAGT
47880588 ACTAACTACAGTATTTCC
1 ACTAACTACAGTATTTCC
47880606 ACTAACTACAGTATTTCC
1 ACTAACTACAGTATTTCC
47880624 A
1 A
47880625 GAGTATTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.27, G:0.05, T:0.32
Consensus pattern (18 bp):
ACTAACTACAGTATTTCC
Found at i:47881368 original size:6 final size:6
Alignment explanation
Indices: 47881357--47881391 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
47881347 ATGTCCATTT
47881357 CAGATA CAGATA CAGATA CAGATA CAGATAA CAGA
1 CAGATA CAGATA CAGATA CAGATA CAGAT-A CAGA
47881392 ATCATATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.14
Consensus pattern (6 bp):
CAGATA
Found at i:47881862 original size:18 final size:18
Alignment explanation
Indices: 47881835--47881880 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
47881825 TTCAAAATTT
* *
47881835 TGGGCTTACATGCCCGTG
1 TGGGCCTACACGCCCGTG
47881853 TGGGCCTACACGCCCGTG
1 TGGGCCTACACGCCCGTG
*
47881871 -CGGCCTACAC
1 TGGGCCTACAC
47881881 ACCCAGATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.13, C:0.37, G:0.30, T:0.20
Consensus pattern (18 bp):
TGGGCCTACACGCCCGTG
Found at i:47883668 original size:16 final size:16
Alignment explanation
Indices: 47883644--47883677 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
47883634 TTGACTGAAC
47883644 AATTAGAAAAAAGATA
1 AATTAGAAAAAAGATA
* *
47883660 AATTCGAAAAAGGATA
1 AATTAGAAAAAAGATA
47883676 AA
1 AA
47883678 ACAAATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.15, T:0.18
Consensus pattern (16 bp):
AATTAGAAAAAAGATA
Found at i:47887415 original size:29 final size:29
Alignment explanation
Indices: 47887352--47887425 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
47887342 GGCATTGAAA
* * *
47887352 TCCCTTAATTTTCTCCCCTATAGTTTTCG
1 TCCCTTGATTTCCTCCCCTATAGTGTTCG
47887381 TCCCTTGATTTCCTCCCCTATAGGTGTT-G
1 TCCCTTGATTTCCTCCCCTATA-GTGTTCG
* *
47887410 TTCCTTTGATTCCCTC
1 -TCCCTTGATTTCCTC
47887426 AAGGTTGTTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 21 0.55
30 17 0.45
ACGTcount: A:0.11, C:0.32, G:0.11, T:0.46
Consensus pattern (29 bp):
TCCCTTGATTTCCTCCCCTATAGTGTTCG
Found at i:47887810 original size:6 final size:6
Alignment explanation
Indices: 47887799--47887842 Score: 88
Period size: 6 Copynumber: 7.3 Consensus size: 6
47887789 TAAAGTATTT
47887799 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TA
47887843 TATATTTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:47888491 original size:19 final size:19
Alignment explanation
Indices: 47888443--47888482 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
47888433 GTACATTATC
47888443 TATTATATA-T-TACATAA
1 TATTATATATTATACATAA
*
47888460 TATTATATATTATACATAT
1 TATTATATATTATACATAA
47888479 TATT
1 TATT
47888483 GTTTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 1 0.05
19 10 0.50
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTATATATTATACATAA
Found at i:47888574 original size:15 final size:15
Alignment explanation
Indices: 47888554--47888585 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
47888544 TTAGCATTCC
*
47888554 TACTATATTATATCA
1 TACTATATCATATCA
47888569 TACTATATCATATCA
1 TACTATATCATATCA
47888584 TA
1 TA
47888586 TATTGATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (15 bp):
TACTATATCATATCA
Found at i:47889780 original size:11 final size:11
Alignment explanation
Indices: 47889761--47889796 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
47889751 GACGGTTTAG
47889761 TTTTCGCTCGT
1 TTTTCGCTCGT
*
47889772 TTTTTGCTCGT
1 TTTTCGCTCGT
47889783 TTTTCGCTC-T
1 TTTTCGCTCGT
47889793 TTTT
1 TTTT
47889797 GCTTCCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.00, C:0.22, G:0.14, T:0.64
Consensus pattern (11 bp):
TTTTCGCTCGT
Found at i:47892637 original size:13 final size:13
Alignment explanation
Indices: 47892619--47892645 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
47892609 TCTTAAGCCA
47892619 CTACAATGTTATT
1 CTACAATGTTATT
47892632 CTACAATGTTATT
1 CTACAATGTTATT
47892645 C
1 C
47892646 GTAATGTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (13 bp):
CTACAATGTTATT
Found at i:47893556 original size:36 final size:35
Alignment explanation
Indices: 47893501--47893571 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 35
47893491 CCATTGATTA
47893501 CATTAATATCATCATCATCAAATCACAACTTCATT
1 CATTAATATCATCATCATCAAATCACAACTTCATT
*
47893536 CATTACAT-TCATACATCATCAAATCGCAACTTCATT
1 CATTA-ATATCAT-CATCATCAAATCACAACTTCATT
47893572 GCTGCCACCC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.38, C:0.27, G:0.01, T:0.34
Consensus pattern (35 bp):
CATTAATATCATCATCATCAAATCACAACTTCATT
Found at i:47901095 original size:30 final size:30
Alignment explanation
Indices: 47901061--47901136 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
47901051 CATAAGTTAG
*
47901061 CTTGTGTGAGAAACTTTGATAAAATGACAA
1 CTTGTGTGAGCAACTTTGATAAAATGACAA
* ** * * *
47901091 CTTGTATGAGCAACCCTGATATAATGTCAG
1 CTTGTGTGAGCAACTTTGATAAAATGACAA
47901121 CTTGTGTGAGCAACTT
1 CTTGTGTGAGCAACTT
47901137 ATTCACCCAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (30 bp):
CTTGTGTGAGCAACTTTGATAAAATGACAA
Found at i:47904360 original size:11 final size:11
Alignment explanation
Indices: 47904344--47904378 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
47904334 ATAAAAGCTG
*
47904344 AATTATAATTA
1 AATTATAAGTA
47904355 AATTATAAGTA
1 AATTATAAGTA
*
47904366 AATTATATGTA
1 AATTATAAGTA
47904377 AA
1 AA
47904379 GGGACTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (11 bp):
AATTATAAGTA
Found at i:47905755 original size:17 final size:17
Alignment explanation
Indices: 47905733--47905766 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
47905723 TTTGAAATGG
*
47905733 AAAATGTTATTGAAATA
1 AAAATGCTATTGAAATA
47905750 AAAATGCTATTGAAATA
1 AAAATGCTATTGAAATA
47905767 GAAAGTGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (17 bp):
AAAATGCTATTGAAATA
Found at i:47906697 original size:21 final size:21
Alignment explanation
Indices: 47906673--47906714 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
47906663 ATTTTATCAC
47906673 TTTTGAAATAAGGTATCGATA
1 TTTTGAAATAAGGTATCGATA
* **
47906694 TTTTGACATTTGGTATCGATA
1 TTTTGAAATAAGGTATCGATA
47906715 CCTGACCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (21 bp):
TTTTGAAATAAGGTATCGATA
Found at i:47915238 original size:32 final size:32
Alignment explanation
Indices: 47915197--47915260 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
47915187 AGCCTTGGCC
47915197 TCTCTTGGGTATGATCCTCAGAGTATTCACTT
1 TCTCTTGGGTATGATCCTCAGAGTATTCACTT
*
47915229 TCTCTTGGGTATGATCCTCAGGGTATTCACTT
1 TCTCTTGGGTATGATCCTCAGAGTATTCACTT
47915261 ACTTCGTTGT
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:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (32 bp):
TCTCTTGGGTATGATCCTCAGAGTATTCACTT
Found at i:47921727 original size:21 final size:21
Alignment explanation
Indices: 47921701--47921749 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
47921691 TACTCCAGGC
* *
47921701 CTCGAGATAGGAACCCCTTTT
1 CTCGAGAAAGGAACCCCTTGT
*
47921722 CTCGAGAAATGAACCCCTTGT
1 CTCGAGAAAGGAACCCCTTGT
47921743 CTCGAGA
1 CTCGAGA
47921750 CATTCAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (21 bp):
CTCGAGAAAGGAACCCCTTGT
Found at i:47921850 original size:22 final size:22
Alignment explanation
Indices: 47921805--47921857 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
47921795 TCGAGAGTCA
*
47921805 GTCTCGAGACTTGAGAATTCAT
1 GTCTCGAGACATGAGAATTCAT
*
47921827 GTCTCGAGACATG-GATTTCAAT
1 GTCTCGAGACATGAGAATTC-AT
*
47921849 GTCTTGAGA
1 GTCTCGAGA
47921858 TGTGTCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (22 bp):
GTCTCGAGACATGAGAATTCAT
Found at i:47922505 original size:222 final size:222
Alignment explanation
Indices: 47922118--47922565 Score: 815
Period size: 222 Copynumber: 2.0 Consensus size: 222
47922108 GAAATATTCT
* *
47922118 GAGTTGTTTCGAAAACATAATGTGATGTTACACATTTAGAGCCAATGACTAACTCATGTGTGGGG
1 GAGTTGTTTCGAAAACATAATGTGATGTTACACATTTAGAGCCAATGACTAAATCAGGTGTGGGG
47922183 CGTCACAAATAGGATGTGTTGGGATAGGTTCATCATATACTAACGGATAAGCAATCCATTGATAG
66 CGTCACAAATAGGATGTGTTGGGATAGGTTCATCATATACTAACGGATAAGCAATCCATTGATAG
* *
47922248 AAACCTACTTATACTTACAGAATTGGATTGTCAATAAAAGTAAGCATTGGTATATGATGAACTAT
131 AAACCTACTTATACTTACAGAATTGGATCGTCAATAAAAGTAAGCAATGGTATATGATGAACTAT
47922313 TTGTAGTAAGAAATCCTAAATAGAATG
196 TTGTAGTAAGAAATCCTAAATAGAATG
47922340 GAGTTGTTTCGAAAACATAATGTGATGTTACACATTTAGAGCCAATGACTAAATCAGGTGTGGGG
1 GAGTTGTTTCGAAAACATAATGTGATGTTACACATTTAGAGCCAATGACTAAATCAGGTGTGGGG
* * *
47922405 CGTCACAAATAGGATGTGTTGGGATAGGTTCATCATATACTAATGGATAAGTAATCCGTTGATAG
66 CGTCACAAATAGGATGTGTTGGGATAGGTTCATCATATACTAACGGATAAGCAATCCATTGATAG
47922470 AAACCTACTTATACTTACAGAATTGGATCGTCAATAAAAGTAAGCAATGGTATATGATGAACTAT
131 AAACCTACTTATACTTACAGAATTGGATCGTCAATAAAAGTAAGCAATGGTATATGATGAACTAT
* *
47922535 TTTTAGTGAGAAATCCTAAATAGAATG
196 TTGTAGTAAGAAATCCTAAATAGAATG
47922562 GAGT
1 GAGT
47922566 AAAAAATTTC
Statistics
Matches: 217, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
222 217 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.30
Consensus pattern (222 bp):
GAGTTGTTTCGAAAACATAATGTGATGTTACACATTTAGAGCCAATGACTAAATCAGGTGTGGGG
CGTCACAAATAGGATGTGTTGGGATAGGTTCATCATATACTAACGGATAAGCAATCCATTGATAG
AAACCTACTTATACTTACAGAATTGGATCGTCAATAAAAGTAAGCAATGGTATATGATGAACTAT
TTGTAGTAAGAAATCCTAAATAGAATG
Found at i:47922864 original size:29 final size:29
Alignment explanation
Indices: 47922832--47922974 Score: 144
Period size: 29 Copynumber: 5.0 Consensus size: 29
47922822 TGGAAAATCT
* * *
47922832 AAAGTACAATCTAAAGTGGTGGGCAGTCC
1 AAAGTACAAGCCAAAGTGGTGGACAGTCC
** * * * * *
47922861 AAAGTGTAAGTCAAAGTGATAGCCATTCC
1 AAAGTACAAGCCAAAGTGGTGGACAGTCC
*
47922890 AAAGTGCAAGCCAAAGTGGTGGACAGTCC
1 AAAGTACAAGCCAAAGTGGTGGACAGTCC
* * *
47922919 AAAGTACAAGCCAAAGTGGCGAACAATCC
1 AAAGTACAAGCCAAAGTGGTGGACAGTCC
*
47922948 -AAGTACAAGCCAAAGTGGTAGACAGTC
1 AAAGTACAAGCCAAAGTGGTGGACAGTC
47922975 TAACTACGAA
Statistics
Matches: 91, Mismatches: 23, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
28 23 0.25
29 68 0.75
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (29 bp):
AAAGTACAAGCCAAAGTGGTGGACAGTCC
Found at i:47927699 original size:25 final size:25
Alignment explanation
Indices: 47927669--47927723 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
47927659 TATTTGCGCA
47927669 ATTTTTATTATTATCGTTATTATATT
1 ATTTTTATT-TTATCGTTATTATATT
* * *
47927695 ATTTTTATTTTCTTGTTATTTTATT
1 ATTTTTATTTTATCGTTATTATATT
47927720 ATTT
1 ATTT
47927724 CTTTATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (25 bp):
ATTTTTATTTTATCGTTATTATATT
Found at i:47931078 original size:7 final size:7
Alignment explanation
Indices: 47931052--47931102 Score: 75
Period size: 7 Copynumber: 7.3 Consensus size: 7
47931042 CTTATTCATC
47931052 ATCACAT
1 ATCACAT
* * *
47931059 CTCATAA
1 ATCACAT
47931066 ATCACAT
1 ATCACAT
47931073 ATCACAT
1 ATCACAT
47931080 ATCACAT
1 ATCACAT
47931087 ATCACAT
1 ATCACAT
47931094 ATCACAT
1 ATCACAT
47931101 AT
1 AT
47931103 TGATGGTACA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.29
Consensus pattern (7 bp):
ATCACAT
Found at i:47932654 original size:29 final size:29
Alignment explanation
Indices: 47932620--47932718 Score: 128
Period size: 29 Copynumber: 3.4 Consensus size: 29
47932610 ACGAACTATT
*
47932620 TGGCAGACAGTCCAAAATACAAGCCAAAG
1 TGGCAGACAGTCCAAAGTACAAGCCAAAG
* * **
47932649 TGGCAGGCAGTTCAAAGTGTAAGCCAAAG
1 TGGCAGACAGTCCAAAGTACAAGCCAAAG
*
47932678 TGGCAGACAATCCAAAGTACAAGCCAAAG
1 TGGCAGACAGTCCAAAGTACAAGCCAAAG
47932707 TGGC-GAACAGTC
1 TGGCAG-ACAGTC
47932719 TAACTACGAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
28 1 0.02
29 57 0.98
ACGTcount: A:0.39, C:0.22, G:0.25, T:0.13
Consensus pattern (29 bp):
TGGCAGACAGTCCAAAGTACAAGCCAAAG
Found at i:47940998 original size:31 final size:32
Alignment explanation
Indices: 47940962--47941026 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
47940952 CTTAGATAAT
47940962 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
47940993 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
47941025 TT
1 TT
47941027 GTAATTTGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 9 0.27
32 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGGATTCAATTACTC
Found at i:47941613 original size:23 final size:23
Alignment explanation
Indices: 47941587--47941646 Score: 113
Period size: 22 Copynumber: 2.7 Consensus size: 23
47941577 AAAAAAAAGT
47941587 AAAAAGCGCAAAAAAGAAGAAGC
1 AAAAAGCGCAAAAAAGAAGAAGC
47941610 AAAAAGCGC-AAAAAGAAGAAGC
1 AAAAAGCGCAAAAAAGAAGAAGC
47941632 AAAAAGCGCAAAAAA
1 AAAAAGCGCAAAAAA
47941647 AAAGTTGCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 22 0.61
23 14 0.39
ACGTcount: A:0.67, C:0.13, G:0.20, T:0.00
Consensus pattern (23 bp):
AAAAAGCGCAAAAAAGAAGAAGC
Found at i:47947218 original size:31 final size:32
Alignment explanation
Indices: 47947182--47947246 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
47947172 CTTAGATAAT
*
47947182 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGAATTCAATTACTC
47947213 TTTAAAGAGTTTTTATTAGAATTCAATTACTC
1 TTTAAAGAGTTTTTATTAGAATTCAATTACTC
47947245 TT
1 TT
47947247 GTAATTTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 9 0.28
32 23 0.72
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.48
Consensus pattern (32 bp):
TTTAAAGAGTTTTTATTAGAATTCAATTACTC
Found at i:47948635 original size:24 final size:24
Alignment explanation
Indices: 47948607--47948654 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
47948597 TGACTTTGAA
47948607 AATAATTTAATTGAGTCGATTTAT
1 AATAATTTAATTGAGTCGATTTAT
*
47948631 AATAATTTAATTGAGTTGATTTAT
1 AATAATTTAATTGAGTCGATTTAT
47948655 TCGATGTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (24 bp):
AATAATTTAATTGAGTCGATTTAT
Found at i:47953946 original size:24 final size:24
Alignment explanation
Indices: 47953919--47953974 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
47953909 TAAATATGGA
**
47953919 AATAAATAACAAAGATTTTATGCT
1 AATAAATAACAAAGATACTATGCT
** *
47953943 AATAAATGTCAAATATACTATGCT
1 AATAAATAACAAAGATACTATGCT
47953967 AATAAATA
1 AATAAATA
47953975 CTAAATCTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.32
Consensus pattern (24 bp):
AATAAATAACAAAGATACTATGCT
Found at i:47962838 original size:13 final size:13
Alignment explanation
Indices: 47962820--47962845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
47962810 AAAAAAGTTT
47962820 TTTTATTTTTTTA
1 TTTTATTTTTTTA
47962833 TTTTATTTTTTTA
1 TTTTATTTTTTTA
47962846 GTCTTTAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:47962856 original size:21 final size:21
Alignment explanation
Indices: 47962817--47962858 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
47962807 ATAAAAAAAG
* * *
47962817 TTTTTTTATTTTTTTATTTTA
1 TTTTTTTAGTCTTTAATTTTA
47962838 TTTTTTTAGTCTTTAATTTTA
1 TTTTTTTAGTCTTTAATTTTA
47962859 CATTATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTTTAGTCTTTAATTTTA
Found at i:47976686 original size:18 final size:19
Alignment explanation
Indices: 47976665--47976710 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
47976655 TTTACTTTTT
47976665 TATTTTTTA-TTTT-ATAA
1 TATTTTTTAGTTTTCATAA
47976682 -ATATTTTTAGTTTTCATAA
1 TAT-TTTTTAGTTTTCATAA
47976701 TACTTTTTTA
1 TA-TTTTTTA
47976711 AGCCAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.08
17 6 0.25
18 4 0.17
19 4 0.17
20 7 0.29
21 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TATTTTTTAGTTTTCATAA
Found at i:47979839 original size:55 final size:55
Alignment explanation
Indices: 47979777--47979909 Score: 169
Period size: 55 Copynumber: 2.4 Consensus size: 55
47979767 TAAGTTGTTT
* * * *
47979777 TATGTTTAAATCGATTGTCATGTTGGAATACTACTTCTTTTAAATCA-ATTATTTA
1 TATGTTTAAATCGATTGTTATGTTGGAATACTACTACATTTAAAT-AGACTATTTA
* * * *
47979832 TATGTTTAAATCTATTGTTATGTTGGAATACTGCTACATTTGAATAGACTGTTTA
1 TATGTTTAAATCGATTGTTATGTTGGAATACTACTACATTTAAATAGACTATTTA
*
47979887 TATGTTTAAATTGATTGTTATGT
1 TATGTTTAAATCGATTGTTATGT
47979910 AGCATGTCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
54 1 0.01
55 66 0.99
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.48
Consensus pattern (55 bp):
TATGTTTAAATCGATTGTTATGTTGGAATACTACTACATTTAAATAGACTATTTA
Found at i:47984502 original size:161 final size:161
Alignment explanation
Indices: 47984318--47984632 Score: 612
Period size: 161 Copynumber: 2.0 Consensus size: 161
47984308 CTTGAATTTC
*
47984318 TTTCTCTTAGTTACGGTTTTCATAGAAAATTTGGGGAAGATGATGAAATAAAATTATTTTATTCA
1 TTTCTCTTAGCTACGGTTTTCATAGAAAATTTGGGGAAGATGATGAAATAAAATTATTTTATTCA
47984383 ATTAATTAACTTATCATCTTTTAATTTTTCAACTTTCCAATTTCATCATTTTCTTTTCTTGAATT
66 ATTAATTAACTTATCATCTTTTAATTTTTCAACTTTCCAATTTCATCATTTTCTTTTCTTGAATT
47984448 TCCATGAATGAGTCATTATAATTAGCTAGGG
131 TCCATGAATGAGTCATTATAATTAGCTAGGG
*
47984479 TTTCTCTTAGCTAGGGTTTTCATAGAAAATTTGGGGAAGATGATGAAATAAAATTATTTTATTCA
1 TTTCTCTTAGCTACGGTTTTCATAGAAAATTTGGGGAAGATGATGAAATAAAATTATTTTATTCA
47984544 ATTAATTAACTTATCATCTTTTAATTTTTCAACTTTCCAATTTCATCATTTTCTTTTCTTGAATT
66 ATTAATTAACTTATCATCTTTTAATTTTTCAACTTTCCAATTTCATCATTTTCTTTTCTTGAATT
47984609 TCCATGAATGAGTCATTATAATTA
131 TCCATGAATGAGTCATTATAATTA
47984633 TCTACTAACT
Statistics
Matches: 152, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 152 1.00
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (161 bp):
TTTCTCTTAGCTACGGTTTTCATAGAAAATTTGGGGAAGATGATGAAATAAAATTATTTTATTCA
ATTAATTAACTTATCATCTTTTAATTTTTCAACTTTCCAATTTCATCATTTTCTTTTCTTGAATT
TCCATGAATGAGTCATTATAATTAGCTAGGG
Found at i:47989571 original size:15 final size:15
Alignment explanation
Indices: 47989551--47989586 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
47989541 AACAACATGA
*
47989551 AATAATAGGAATAAT
1 AATAATAGCAATAAT
47989566 AATAATAGCAATAAT
1 AATAATAGCAATAAT
47989581 AATAAT
1 AATAAT
47989587 GATAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (15 bp):
AATAATAGCAATAAT
Found at i:47993359 original size:24 final size:25
Alignment explanation
Indices: 47993331--47993398 Score: 79
Period size: 24 Copynumber: 2.8 Consensus size: 25
47993321 CTTTCTAATA
47993331 TTGGCTCTCTTGAGCTTCCC-AT-T
1 TTGGCTCTCTTGAGCTTCCCGATAT
47993354 TATGGCTCT-TATGAGCTTCCCGATAT
1 T-TGGCTCTCT-TGAGCTTCCCGATAT
* *
47993380 TTGGCTCGCATGAGCTTCC
1 TTGGCTCTCTTGAGCTTCC
47993399 AGTTACATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
23 2 0.05
24 17 0.45
25 17 0.45
26 2 0.05
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (25 bp):
TTGGCTCTCTTGAGCTTCCCGATAT
Found at i:47993392 original size:25 final size:23
Alignment explanation
Indices: 47993331--47993398 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 23
47993321 CTTTCTAATA
*
47993331 TTGGCTCTCTTGAGCTTCCCATT
1 TTGGCTCTCATGAGCTTCCCATT
*
47993354 TATGGCTCTTATGAGCTTCCCGATAT
1 T-TGGCTCTCATGAGCTTCCC-AT-T
*
47993380 TTGGCTCGCATGAGCTTCC
1 TTGGCTCTCATGAGCTTCC
47993399 AGTTACATGG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 17 0.45
25 18 0.47
26 2 0.05
ACGTcount: A:0.13, C:0.28, G:0.21, T:0.38
Consensus pattern (23 bp):
TTGGCTCTCATGAGCTTCCCATT
Found at i:47993409 original size:25 final size:25
Alignment explanation
Indices: 47993381--47993437 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
47993371 TCCCGATATT
* *
47993381 TGGCTCGCATGAGCTTCCAGTTACA
1 TGGCTCGCATGAACTTCCAGTTAAA
* *
47993406 TGGCTCACATGAACTTCCTGTTAAA
1 TGGCTCGCATGAACTTCCAGTTAAA
47993431 TGGCTCG
1 TGGCTCG
47993438 TAAGAGCTAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.30
Consensus pattern (25 bp):
TGGCTCGCATGAACTTCCAGTTAAA
Found at i:47995168 original size:38 final size:39
Alignment explanation
Indices: 47995065--47995204 Score: 210
Period size: 39 Copynumber: 3.6 Consensus size: 39
47995055 CATGTTTTTT
* *
47995065 TGAGTATTGTGATATATGCTTGAATATTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
47995104 TGGGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
47995143 TGAGTATTGT-ATATATGTTTCAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* *
47995181 TGTGTAATGTGATATATGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
47995205 AGTGAATATA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 34 0.38
39 56 0.62
ACGTcount: A:0.30, C:0.03, G:0.21, T:0.46
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:48000383 original size:55 final size:55
Alignment explanation
Indices: 48000317--48000453 Score: 168
Period size: 55 Copynumber: 2.5 Consensus size: 55
48000307 ATTTCCCAAA
* * * * *
48000317 AATATTGCTTCTTTTGGATTGATTTTTTTTATATTTAAATCGACTT-TCGTGTTGG
1 AATATTGCTTCTTTTGAATCGATTGTTTATATATTTAAATCGA-TTATCATGTTGG
*
48000372 AATATTGCTTCTTTTGAATCGATTGTTTATATCTTTAAATCGATTATCATGTTGG
1 AATATTGCTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTATCATGTTGG
* * * *
48000427 AATACTACTTATTTTGAATCAATTGTT
1 AATATTGCTTCTTTTGAATCGATTGTT
48000454 ATGGATGAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
54 2 0.03
55 69 0.97
ACGTcount: A:0.25, C:0.10, G:0.14, T:0.51
Consensus pattern (55 bp):
AATATTGCTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTATCATGTTGG
Found at i:48000534 original size:61 final size:60
Alignment explanation
Indices: 48000439--48000595 Score: 208
Period size: 61 Copynumber: 2.6 Consensus size: 60
48000429 TACTACTTAT
* * * *
48000439 TTTGAATCAATTGTTATGGAT-GAATACTACTTCTTCTTCTTTTGAATTGATTGTTTATATG
1 TTTGAATCGATTGTTATGG-TGGAATA-TTCTTCTTCTTCTTTTGAATCGACTGTTTATATG
*
48000500 TTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTCTTTTGAATCGACTGTTTGTATG
1 TTTGAATCGATTGTTATGGTGGAATATT-CTTCTTCTTCTTTTGAATCGACTGTTTATATG
* *
48000561 TTTAAATCGATTGTTATGTTGGAATACTTCTTCTT
1 TTTGAATCGATTGTTATGGTGGAATA-TTCTTCTT
48000596 TTGAATCGAT
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
60 2 0.02
61 82 0.95
62 2 0.02
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (60 bp):
TTTGAATCGATTGTTATGGTGGAATATTCTTCTTCTTCTTTTGAATCGACTGTTTATATG
Found at i:48000608 original size:34 final size:36
Alignment explanation
Indices: 48000565--48000649 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 36
48000555 TGTATGTTTA
48000565 AATCGATTGTTA-TGTTGGAATA-CTTCTTC-TTTTG
1 AATCGATTGTTATTG-TGGAATATCTTCTTCTTTTTG
48000599 AATCGATTGTTATTGTGGAATATTGCTTCTTCTTATTTTG
1 AATCGATTGTTATTGTGGAATA-T-CTTCTTC-T-TTTTG
48000639 AATCGATTGTT
1 AATCGATTGTT
48000650 TATATATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
34 19 0.43
35 2 0.05
37 7 0.16
40 16 0.36
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.51
Consensus pattern (36 bp):
AATCGATTGTTATTGTGGAATATCTTCTTCTTTTTG
Found at i:48000617 original size:95 final size:95
Alignment explanation
Indices: 48000500--48000704 Score: 338
Period size: 95 Copynumber: 2.2 Consensus size: 95
48000490 TGTTTATATG
* * *
48000500 TTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTCTTTTGAATCGACTGTTTGTATGTTTA
1 TTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTATTTTGAATCGACTGTTTATATATTTA
48000565 AATCGATTGTTATGTTGGAATACTTCTTCT
66 AATCGATTGTTATGTTGGAATACTTCTTCT
* *
48000595 TTTGAATCGATTGTTATTGTGGAATATTGCTTCTTCTTATTTTGAATCGATTGTTTATATATTTA
1 TTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTATTTTGAATCGACTGTTTATATATTTA
* *
48000660 AATCGATTGTTATGTTGGATTATTTCTTCT
66 AATCGATTGTTATGTTGGAATACTTCTTCT
*
48000690 ATTGAATCGATTGTT
1 TTTGAATCGATTGTT
48000705 TATATGTTTA
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
95 102 1.00
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (95 bp):
TTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTATTTTGAATCGACTGTTTATATATTTA
AATCGATTGTTATGTTGGAATACTTCTTCT
Found at i:48000695 original size:55 final size:55
Alignment explanation
Indices: 48000636--48000759 Score: 176
Period size: 55 Copynumber: 2.3 Consensus size: 55
48000626 TCTTCTTATT
* * * * *
48000636 TTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGATTATTTCTTCTA
1 TTGAATCGATTGTTTATATATTTAAATCGATTATTATGTTAGAATACTGCTTCTA
* *
48000691 TTGAATCGATTGTTTATATGTTTAAATCGATTATTATGTTAGAATACTGCTTCTT
1 TTGAATCGATTGTTTATATATTTAAATCGATTATTATGTTAGAATACTGCTTCTA
*
48000746 TTGAATCAATTGTT
1 TTGAATCGATTGTT
48000760 ATGGTGGAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.51
Consensus pattern (55 bp):
TTGAATCGATTGTTTATATATTTAAATCGATTATTATGTTAGAATACTGCTTCTA
Found at i:48000746 original size:150 final size:150
Alignment explanation
Indices: 48000324--48000880 Score: 722
Period size: 156 Copynumber: 3.7 Consensus size: 150
48000314 AAAAATATTG
* * * * ** *
48000324 CTTCTTTTGGATTGATTTTTTTTATATTTAAATCGACTT-TCGTGTTGGAATATTGCTTCTTTTG
1 CTTCTTTTGAATCGATTGTTTATATATTTAAATCGA-TTGTTATGTTGGAATATTTCTTCTTTTG
* * *
48000388 AATCGATTGTTTATATCTTTAAATCGATTATCATGTTGGAATACTACTTATTTTGAATCAATTGT
65 AATCGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATACTACTTCTTTTGAATCAATTGT
* *
48000453 TATGGAT-GAATACTACTTCTT
130 TATGG-TGGAATATTGCTTCTT
* * * *
48000474 CTTCTTTTGAATTGATTGTTTATATGTTTGAATCGATTGTTATGGTGGAATATTGCTTCTTCTTC
1 CTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGAATA-----T-TTCTTC
* * * * *
48000539 TTTTGAATCGACTGTTTGTATGTTTAAATCGATTGTTATGTTGGAATACTTCTTCTTTTGAATCG
60 TTTTGAATCGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATACTACTTCTTTTGAATCA
*
48000604 ATTGTTATTGTGGAATATTGCTTCTT
125 ATTGTTATGGTGGAATATTGCTTCTT
* * *
48000630 CTTATTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGATTATTTCTTCTATTGA
1 CTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGAATATTTCTTCTTTTGA
* *
48000695 ATCGATTGTTTATATGTTTAAATCGATTATTATGTTAGAATACTGCTTCTTTTGAATCAATTGTT
66 ATCGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATACTACTTCTTTTGAATCAATTGTT
*
48000760 ATGGTGGAATATTGCTTTTTT
131 ATGGTGGAATATTGC-TTCTT
* *
48000781 TTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGAATATTACTTCTTTTGA
1 CTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGAATATTTCTTCTTTTGA
* * *
48000846 ATTGATTGTTTATATGTTCAAATCGATTGTTATGT
66 ATCGATTGTTTATATGTTTAAATCGATTATTATGT
48000881 AGCACGTCTA
Statistics
Matches: 355, Mismatches: 43, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
149 2 0.01
150 125 0.35
151 97 0.27
155 2 0.01
156 129 0.36
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.51
Consensus pattern (150 bp):
CTTCTTTTGAATCGATTGTTTATATATTTAAATCGATTGTTATGTTGGAATATTTCTTCTTTTGA
ATCGATTGTTTATATGTTTAAATCGATTATTATGTTGGAATACTACTTCTTTTGAATCAATTGTT
ATGGTGGAATATTGCTTCTT
Found at i:48003021 original size:39 final size:39
Alignment explanation
Indices: 48002978--48003113 Score: 152
Period size: 39 Copynumber: 3.5 Consensus size: 39
48002968 CATTTTCACT
*
48002978 TTTAAGCATATATCACATTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* *
48003017 TTTAAGCATATATCAGAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACACATATAATCACATAACA
* * *
48003056 TTCAAGCATATAT-ATCAACA-ATCATGTAATCACATAACA
1 TTTAAGCATATATCA-CAATACA-CATATAATCACATAACA
* * *
48003095 TTCAAGAATAT-TCTCAATA
1 TTTAAGCATATATCACAATA
48003114 TTCAAAAACA
Statistics
Matches: 83, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
38 6 0.07
39 77 0.93
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACACATATAATCACATAACA
Found at i:48005745 original size:16 final size:16
Alignment explanation
Indices: 48005724--48005756 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
48005714 AAGTTAAAAC
*
48005724 TTAATCGACAACTTTA
1 TTAATCCACAACTTTA
48005740 TTAATCCACAACTTTA
1 TTAATCCACAACTTTA
48005756 T
1 T
48005757 ATTTCAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (16 bp):
TTAATCCACAACTTTA
Found at i:48005919 original size:20 final size:20
Alignment explanation
Indices: 48005887--48005929 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
48005877 AGATAAAATC
48005887 ATTTTCAACCATCCTCTTTT
1 ATTTTCAACCATCCTCTTTT
48005907 ATTTTGCAA-CATCCTCTTTT
1 ATTTT-CAACCATCCTCTTTT
48005927 ATT
1 ATT
48005930 GTACAAACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.21, C:0.26, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTTCAACCATCCTCTTTT
Found at i:48010682 original size:3 final size:3
Alignment explanation
Indices: 48010674--48010703 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
48010664 TATTAGTTAA
*
48010674 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
48010704 CACGATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:48014464 original size:19 final size:19
Alignment explanation
Indices: 48014442--48014481 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
48014432 GAAGGGTGGC
*
48014442 AATATCAAATCTGGGTGAA
1 AATATCAAATCCGGGTGAA
*
48014461 AATATCATATCCGGGTGAA
1 AATATCAAATCCGGGTGAA
48014480 AA
1 AA
48014482 GAGGTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (19 bp):
AATATCAAATCCGGGTGAA
Found at i:48038676 original size:25 final size:24
Alignment explanation
Indices: 48038527--48038673 Score: 68
Period size: 25 Copynumber: 5.9 Consensus size: 24
48038517 CTTATGACCG
*
48038527 TCCTGATATATGGCTCTTCGTGAGCT
1 TCCTGATA-ATGGCTCTTCG-GAACT
* * **
48038553 TCCTGATTAAAGGCTTTTTATGAACT
1 TCCTGA-TAATGGC-TCTTCGGAACT
* *
48038579 TCCTGAGTAATGGATCTCCGGAACT
1 TCCTGA-TAATGGCTCTTCGGAACT
*
48038604 TCCCGAT-ATGGCTCGCTT--GAACT
1 TCCTGATAATGGCT--CTTCGGAACT
* * * *
48038627 TCCCGATATATGACT-ATCTGGAGCT
1 TCCTGATA-ATGGCTCTTC-GGAACT
48038652 TCCTGATTAATGGCTCTTCGGA
1 TCCTGA-TAATGGCTCTTCGGA
48038674 GCTACCCGTT
Statistics
Matches: 89, Mismatches: 21, Indels: 23
0.67 0.16 0.17
Matches are distributed among these distances:
22 1 0.01
23 17 0.19
24 1 0.01
25 36 0.40
26 29 0.33
27 5 0.06
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (24 bp):
TCCTGATAATGGCTCTTCGGAACT
Found at i:48038724 original size:73 final size:73
Alignment explanation
Indices: 48038570--48038729 Score: 171
Period size: 73 Copynumber: 2.2 Consensus size: 73
48038560 TAAAGGCTTT
* * * *
48038570 TTATGAACTTCCTGAGTAATGGATCTCCGGAACTTCCCGATATGGCTCGCTTGAACTTCCCGATA
1 TTATGAGCTTCCTGAGTAATGGATCTCCGGAACTACCCGATATGGCTCGCATGAACTTCCCGAAA
48038635 TATGACTA
66 TATGACTA
* * * * * * *
48038643 TCT-GGAGCTTCCTGATTAATGGCTCTTCGGAGCTACCCGTTATTGGCTCGCATGAACTT-CCTA
1 T-TATGAGCTTCCTGAGTAATGGATCTCCGGAACTACCCGATA-TGGCTCGCATGAACTTCCCGA
* *
48038706 AATATGGCTC
64 AATATGACTA
48038716 TTATGAGCTTCCTG
1 TTATGAGCTTCCTG
48038730 TTATACAGCC
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
72 1 0.01
73 53 0.76
74 16 0.23
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.33
Consensus pattern (73 bp):
TTATGAGCTTCCTGAGTAATGGATCTCCGGAACTACCCGATATGGCTCGCATGAACTTCCCGAAA
TATGACTA
Found at i:48042169 original size:16 final size:16
Alignment explanation
Indices: 48042136--48042169 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48042126 TATTGTACAC
**
48042136 ATATATATGTATTTGA
1 ATATATATGTATGCGA
48042152 ATATATATGTATGCGA
1 ATATATATGTATGCGA
48042168 AT
1 AT
48042170 TTTCATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
ATATATATGTATGCGA
Found at i:48046511 original size:7 final size:7
Alignment explanation
Indices: 48046499--48046538 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
48046489 AAAAGTGATG
48046499 TGAAAAA
1 TGAAAAA
48046506 TGAAAAGA
1 TGAAAA-A
48046514 TG-AAAA
1 TGAAAAA
48046520 TGAAAAA
1 TGAAAAA
48046527 TGAAAAA
1 TGAAAAA
48046534 -GAAAA
1 TGAAAA
48046539 TGGAGAGGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 8 0.26
7 20 0.65
8 3 0.10
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.12
Consensus pattern (7 bp):
TGAAAAA
Found at i:48046519 original size:14 final size:13
Alignment explanation
Indices: 48046502--48046538 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
48046492 AGTGATGTGA
48046502 AAAATGAAAAGATG
1 AAAATGAAAA-ATG
48046516 AAAATGAAAAATG
1 AAAATGAAAAATG
*
48046529 AAAAAGAAAA
1 AAAATGAAAA
48046539 TGGAGAGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.73, C:0.00, G:0.16, T:0.11
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:48046523 original size:21 final size:19
Alignment explanation
Indices: 48046499--48046540 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 19
48046489 AAAAGTGATG
48046499 TGAAAAATGAAAAGATGAAAA
1 TGAAAAATGAAAA-A-GAAAA
48046520 TGAAAAATGAAAAAGAAAA
1 TGAAAAATGAAAAAGAAAA
48046539 TG
1 TG
48046541 GAGAGGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 1 0.05
21 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (19 bp):
TGAAAAATGAAAAAGAAAA
Found at i:48048720 original size:88 final size:88
Alignment explanation
Indices: 48048619--48048789 Score: 197
Period size: 88 Copynumber: 1.9 Consensus size: 88
48048609 TGAAGCCAAT
* * * *
48048619 AATTCTACTTCCCTG-GG-CAGCAGTGGAATAGATTGAAGATTTCAG-A-TCTTGTCTCCATAAG
1 AATTCTACCTCCCTGTGGTCA-CAGTGGAATACATTGAAG--CT-AGTATTCTTATCTCCATAAG
48048680 CAGTAGTGGAGCAGATCAAAGATGGTG
62 CAGTAGTGGAGCAGATCAAAGATGGTG
* * * *
48048707 AATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTATTCTTATCTCCCTAAGCAGT
1 AATTCTACCTCCCTGTGGTCACAGTGGAATACATTGAAGCTAGTATTCTTATCTCCATAAGCAGT
*
48048772 AGTGGAGCAGATCGAAGA
66 AGTGGAGCAGATCAAAGA
48048790 CCCAGTCTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
86 2 0.03
87 2 0.03
88 47 0.67
89 18 0.26
90 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (88 bp):
AATTCTACCTCCCTGTGGTCACAGTGGAATACATTGAAGCTAGTATTCTTATCTCCATAAGCAGT
AGTGGAGCAGATCAAAGATGGTG
Found at i:48048789 original size:132 final size:131
Alignment explanation
Indices: 48047895--48048755 Score: 1190
Period size: 132 Copynumber: 6.5 Consensus size: 131
48047885 CATAGACAGC
* * *
48047895 GGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGG-GAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* * *
48047960 ATTCTACTTCCCTGGTCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTCTCCCCAAGCAGTA
65 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
48048025 GT
130 GT
* *
48048027 GGAGCAGATCAAAGATGGTGAATTTTACCTCACTGTGGTTA-AGTGGAGAACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGG-GAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* * * * * ** **
48048091 ATTCTACTTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATATTGCCTTCCTGCATAAAC
65 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCT-AAGCAGT
48048156 AGT
129 AGT
* * * *
48048159 GGAGCAAATCAAAGATGGCGAATTTTACCTCCATGTGGTTACAGAGGAGTACATTGAAGCCAGAA
1 GGAGCAGATCAAAGATGG-GAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* * *
48048224 ATTATACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGCAGTA
65 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
48048289 GT
130 GT
* * * *
48048291 GGAACATATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGCCAGTA
1 GGAGCAGATCAAAGATGGGA-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* * *
48048356 ATTCTACTTCCCTAGGCAGCAATGGAATAGATTGAAGATTTTAGATCTTGTCTCCCTAAGCAGTA
65 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
48048421 GT
130 GT
* * * *
48048423 GGAACAGATCAAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAGGACAGTA
1 GGAGCAGATCAAAGATGGGA-ATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
* * * * * *
48048488 ATTCTA-TCTCCCTGGGCAACAGTGGAATAAATTGAAGATTACAGATTTTATCTCCCTAAACAGT
65 ATTCTACT-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGT
48048552 AGT
129 AGT
* * *
48048555 GGAGCAAATCAAAGATGGCAGATTTTACCTCTCC-GTGGTTACAGTGGAGTACATTGAAGCCAAT
1 GGAGCAGATCAAAGATGGGA-ATTTTACCTC-CCTGTGGTTACAGTGGAGTACATTGAAGCCAGT
*
48048619 AATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCATAAGCAGT
64 AATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGT
48048684 AGT
129 AGT
*
48048687 GGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGT-
1 GGAGCAGATCAAAGATGG-GAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
48048751 ATTCT
65 ATTCT
48048756 TATCTCCCTA
Statistics
Matches: 647, Mismatches: 74, Indels: 17
0.88 0.10 0.02
Matches are distributed among these distances:
131 81 0.13
132 492 0.76
133 74 0.11
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (131 bp):
GGAGCAGATCAAAGATGGGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAA
TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAG
T
Found at i:48050270 original size:3 final size:3
Alignment explanation
Indices: 48050255--48050284 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
48050245 TACTATGACT
*
48050255 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48050285 CTGTACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:48050350 original size:23 final size:25
Alignment explanation
Indices: 48050324--48050371 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
48050314 TATACATACA
48050324 TACTTTT-TAATATTT-TATATTTT
1 TACTTTTCTAATATTTATATATTTT
48050347 TACTTTTCTAATATTTATATATTTT
1 TACTTTTCTAATATTTATATATTTT
48050372 ATATTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.30
24 8 0.35
25 8 0.35
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (25 bp):
TACTTTTCTAATATTTATATATTTT
Found at i:48050384 original size:24 final size:23
Alignment explanation
Indices: 48050328--48050384 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 23
48050318 CATACATACT
48050328 TTTTA-ATATTTTATATTTTTAC
1 TTTTATATATTTTATATTTTTAC
*
48050350 TTTTCTAATATTTATATATTTTATA-
1 TTTTAT-ATATTT-TATATTTT-TAC
48050375 TTTTATATAT
1 TTTTATATAT
48050385 ATGCATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 4 0.14
24 10 0.34
25 13 0.45
26 2 0.07
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATATATTTTATATTTTTAC
Found at i:48050547 original size:16 final size:16
Alignment explanation
Indices: 48050526--48050559 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
48050516 TATTGTACAC
*
48050526 ATATATATGTATTTGA
1 ATATATATGTATGTGA
48050542 ATATATATGTATGTGA
1 ATATATATGTATGTGA
48050558 AT
1 AT
48050560 TTTCATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (16 bp):
ATATATATGTATGTGA
Found at i:48053751 original size:7 final size:7
Alignment explanation
Indices: 48053739--48053778 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
48053729 AAAAGTGATG
48053739 TGAAAAA
1 TGAAAAA
48053746 TGAAAAGA
1 TGAAAA-A
48053754 T-AAAAA
1 TGAAAAA
48053760 TGAAAAA
1 TGAAAAA
48053767 TGAAAAA
1 TGAAAAA
48053774 -GAAAA
1 TGAAAA
48053779 TGGAGAGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 7 0.23
7 22 0.71
8 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
TGAAAAA
Found at i:48055150 original size:45 final size:44
Alignment explanation
Indices: 48055015--48055150 Score: 130
Period size: 45 Copynumber: 3.1 Consensus size: 44
48055005 GATCAGTGAT
* *
48055015 GATAACAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAA
1 GATAACAGATCTTGCCTTCCT-CATAGACAGTGGAGCAGATCGAA
* * * * * ** * *
48055060 GACACCA-ACCTCGCCTCCCTCGGAGACAGTGGAGCAGGTTGAA
1 GATAACAGATCTTGCCTTCCTCATAGACAGTGGAGCAGATCGAA
* *
48055103 GATAACAGATCTTGCCTTCCTCCATAGACAGCGGAGCAGATCAAA
1 GATAACAGATCTTGCCTTCCT-CATAGACAGTGGAGCAGATCGAA
48055148 GAT
1 GAT
48055151 GGTAAATTTT
Statistics
Matches: 67, Mismatches: 22, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
43 22 0.33
44 20 0.30
45 25 0.37
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (44 bp):
GATAACAGATCTTGCCTTCCTCATAGACAGTGGAGCAGATCGAA
Found at i:48055297 original size:132 final size:132
Alignment explanation
Indices: 48055135--48055381 Score: 397
Period size: 132 Copynumber: 1.9 Consensus size: 132
48055125 CATAGACAGC
* *
48055135 GGAGCAGATCAAAGATGGTAAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGGTAAATTTTACCTCACTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
* *
48055200 ATTCTACTTCCCT-GGTTAGCAGTGGAATAGATTAAAGATTTAAGATCTTGTCTCCCCAAGCAGT
66 ATTCTACTTCCCTAGG-CAGCAGCGGAATAGATTAAAGATTTAAGATCTTGTCTCCCCAAGCAGT
48055264 AGT
130 AGT
* *
48055267 GGAGCAGATCAAAGATGGTGAATTTTACCTCACTGTGGTTACAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGGTAAATTTTACCTCACTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
* * *
48055332 GTTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTTG
66 ATTCTACTTCCCTAGGCAGCAGCGGAATAGATTAAAGATTTAAGATCTTG
48055382 CCTTTCTGTA
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
132 103 0.98
133 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (132 bp):
GGAGCAGATCAAAGATGGTAAATTTTACCTCACTGAGGTTACAGTGGAGTACATTGAAGCCAGTA
ATTCTACTTCCCTAGGCAGCAGCGGAATAGATTAAAGATTTAAGATCTTGTCTCCCCAAGCAGTA
GT
Found at i:48055453 original size:227 final size:227
Alignment explanation
Indices: 48055187--48055608 Score: 641
Period size: 227 Copynumber: 1.9 Consensus size: 227
48055177 AGTGGAGTAC
** * * *
48055187 ATTGAAGCCAGTAATTCTACTTCCCTGGTTAGCAGTGGAATAGATTAAAGATTTAAGATCTTGTC
1 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAACAGTGGAATAGATTAAAGATTGAAGATCTTATC
* * * *
48055252 TCCCCAAGCAGTAGTGGAGCAGATCAAAGATGG-TGAATTTTACCTCACTGTGGTTACAGTGGAG
66 TCCCCAAACAGTAGTGGAGCAAATCAAAGATGGCAG-ATTTTACCTCACCGTGGTTACAGTGGAG
* * *
48055316 TACATTGAAGCCAGTAGTTCTACTTCCCTAGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTT
130 TACATTGAAGCCAATAATTCTACTTCCCTAGGCAACAGCGGAATAGATTGAAGATTTCAGATCTT
48055381 GCCTTTCTGTATAGACAGTGGAGCAAATCAAAG
195 GCCTTTCTGTATAGACAGTGGAGCAAATCAAAG
* * *
48055414 ATTGATGCCAGTAATTCTA-TCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATCTTAT
1 ATTGAAGCCAGTAATTCTACT-TCCCTGGGCAACAGTGGAATAGATTAAAGATTGAAGATCTTAT
* *
48055478 CTCCCTAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCTCCGTGGTTACAGTGGAG
65 CTCCCCAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCACCGTGGTTACAGTGGAG
* *
48055543 TACATTGAAGCCAATAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTT
130 TACATTGAAGCCAATAATTCTACTTCCCTAGGCAACAGCGGAATAGATTGAAGATTTCAGATCTT
48055608 G
195 G
48055609 TCTCCCTAAG
Statistics
Matches: 174, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
226 1 0.01
227 172 0.99
228 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (227 bp):
ATTGAAGCCAGTAATTCTACTTCCCTGGGCAACAGTGGAATAGATTAAAGATTGAAGATCTTATC
TCCCCAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCACCGTGGTTACAGTGGAGT
ACATTGAAGCCAATAATTCTACTTCCCTAGGCAACAGCGGAATAGATTGAAGATTTCAGATCTTG
CCTTTCTGTATAGACAGTGGAGCAAATCAAAG
Found at i:48055578 original size:132 final size:132
Alignment explanation
Indices: 48055414--48055703 Score: 435
Period size: 132 Copynumber: 2.2 Consensus size: 132
48055404 CAAATCAAAG
* *
48055414 ATTGATGCCAGTAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATCTTATC
1 ATTGAAGCCAATAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATCTTATC
48055479 TCCCTAAACAGTAGTGGAGCAAATCAAAGATGGCAG-ATTTTACCTCTCC-GTGGTTACAGTGGA
66 TCCCTAAACAGTAGTGGAGCAAATCAAAGATGG-AGAATTTTACCTC-CCTGTGGTTACAGTGGA
48055542 GTAC
129 GTAC
* *
48055546 ATTGAAGCCAATAATTCTA-CTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGT
1 ATTGAAGCCAATAATTCTATC-TCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATCTTAT
* * *
48055610 CTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAG
65 CTCCCTAAACAGTAGTGGAGCAAATCAAAGATGGAGAATTTTACCTCCCTGTGGTTACAGTGGAG
48055675 TAC
130 TAC
* *
48055678 ATTGAAGCTAGT-ATTCTTATCTCCCT
1 ATTGAAGCCAATAATTC-TATCTCCCT
48055704 AAGCAGTAGT
Statistics
Matches: 144, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
131 8 0.06
132 135 0.94
133 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (132 bp):
ATTGAAGCCAATAATTCTATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATCTTATC
TCCCTAAACAGTAGTGGAGCAAATCAAAGATGGAGAATTTTACCTCCCTGTGGTTACAGTGGAGT
AC
Found at i:48055659 original size:88 final size:88
Alignment explanation
Indices: 48055558--48055728 Score: 204
Period size: 88 Copynumber: 1.9 Consensus size: 88
48055548 TGAAGCCAAT
* * * *
48055558 AATTCTACTTCCCTG-GGCAACAGTGGAATAGATTGAAGATTTCAG-A-TCTTGTCTCCCTAAGC
1 AATTCTACCTCCCTGTGGCAACAGTGGAATACATTGAAG--CT-AGTATTCTTATCTCCCTAAGC
48055620 AGTAGTGGAGCAGATCAAAGATGGTG
63 AGTAGTGGAGCAGATCAAAGATGGTG
* ** *
48055646 AATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTATTCTTATCTCCCTAAGCAGT
1 AATTCTACCTCCCTGTGGCAACAGTGGAATACATTGAAGCTAGTATTCTTATCTCCCTAAGCAGT
* *
48055711 AGTGGAGTAGATCGAAGA
66 AGTGGAGCAGATCAAAGA
48055729 CCCCAGTCTT
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
86 2 0.03
87 2 0.03
88 47 0.67
89 19 0.27
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (88 bp):
AATTCTACCTCCCTGTGGCAACAGTGGAATACATTGAAGCTAGTATTCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCAAAGATGGTG
Found at i:48055759 original size:132 final size:132
Alignment explanation
Indices: 48055414--48055765 Score: 356
Period size: 132 Copynumber: 2.7 Consensus size: 132
48055404 CAAATCAAAG
* * ** * ***
48055414 ATTGATGCCAGTAATTCTA-TCTCCCTGGGCAACAGTGGAATAGATTGAAGATTGCAGATCTTAT
1 ATTGAAGCCAATAATTCTACT-TCCCTAAGCAACAGTGGAATAGATCGAAGACCCCAGATCTTAT
* *
48055478 CTCCCTAAACAGTAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCTCCGTGGTTACAGTGGAG
65 CTCCCTAAGCAGCAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCTCCGTGGTTACAGTGGAG
48055543 TAC
130 TAC
** * *** *
48055546 ATTGAAGCCAATAATTCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTGTC
1 ATTGAAGCCAATAATTCTACTTCCCTAAGCAACAGTGGAATAGATCGAAGACCCCAGATCTTATC
* * *
48055611 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG-TGAATTTTACCTC-CCTGTGGTTACAGTGGA
66 TCCCTAAGCAGCAGTGGAGCAAATCAAAGATGGCAG-ATTTTACCTCTCC-GTGGTTACAGTGGA
48055674 GTAC
129 GTAC
* * ** *
48055678 ATTGAAGCTAGT-ATTCTTA-TCTCCCTAAGCAGTAGTGGAGTAGATCGAAGACCCCAG-TCTTA
1 ATTGAAGCCAATAATTC-TACT-TCCCTAAGCAACAGTGGAATAGATCGAAGACCCCAGATCTTA
* **
48055740 TCTTCCTGAAGTTGCAGTGGAGCAAA
64 TCTCCCT-AAGCAGCAGTGGAGCAAA
48055766 CAGAAGTATA
Statistics
Matches: 190, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
131 18 0.09
132 171 0.90
133 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (132 bp):
ATTGAAGCCAATAATTCTACTTCCCTAAGCAACAGTGGAATAGATCGAAGACCCCAGATCTTATC
TCCCTAAGCAGCAGTGGAGCAAATCAAAGATGGCAGATTTTACCTCTCCGTGGTTACAGTGGAGT
AC
Found at i:48057212 original size:3 final size:3
Alignment explanation
Indices: 48057197--48057247 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
48057187 TACTATTGCT
*
48057197 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48057245 TTA
1 TTA
48057248 CTGTACATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:48057523 original size:16 final size:16
Alignment explanation
Indices: 48057490--48057523 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48057480 TATTGTACAC
**
48057490 ATATATATGTATTTGA
1 ATATATATGTATGCGA
48057506 ATATATATGTATGCGA
1 ATATATATGTATGCGA
48057522 AT
1 AT
48057524 TTTCATGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (16 bp):
ATATATATGTATGCGA
Found at i:48062327 original size:71 final size:71
Alignment explanation
Indices: 48062211--48062345 Score: 216
Period size: 71 Copynumber: 1.9 Consensus size: 71
48062201 GGGCTTCCAA
* * *
48062211 TTCACGGTGGTTATATAGTCACGGGTTGAAGTATAACTAGGGCTCTCAATTGACTATGGTTATGT
1 TTCACGATGGTTATATAGTCACGGGTTGAACTATAACTAGGGCTCTCAATTGACAATGGTTATGT
48062276 GGTTAG
66 GGTTAG
* * *
48062282 TTCACGATGGTTATATGGTCACGGGTTGAACTATAACTAGGGCTCTTAGTTGACAATGGTTATG
1 TTCACGATGGTTATATAGTCACGGGTTGAACTATAACTAGGGCTCTCAATTGACAATGGTTATG
48062346 CGATCACGGG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.35
Consensus pattern (71 bp):
TTCACGATGGTTATATAGTCACGGGTTGAACTATAACTAGGGCTCTCAATTGACAATGGTTATGT
GGTTAG
Found at i:48064729 original size:74 final size:74
Alignment explanation
Indices: 48064603--48064752 Score: 210
Period size: 74 Copynumber: 2.0 Consensus size: 74
48064593 CCAGCTGTAA
* * **
48064603 AGATAAGGTTCGCGGGAGTGAGCTCTCCGAAATGGAAATGTGTGCACATGAATATGAATTGACGG
1 AGATAAGGTTCGCAGGAGTGAGCTCTCCGAAATGAAAATGTGCACACATGAATATGAATTGACGG
*
48064668 ACCCGGAAT
66 ACCCAGAAT
* * * * *
48064677 AGATGAGGTTTGCAGGAGTGTGCTTTCTGAAATGAAAATGTGCACACATGAATATGAATTGACGG
1 AGATAAGGTTCGCAGGAGTGAGCTCTCCGAAATGAAAATGTGCACACATGAATATGAATTGACGG
48064742 ACCCAGAAT
66 ACCCAGAAT
48064751 AG
1 AG
48064753 TACGCTAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (74 bp):
AGATAAGGTTCGCAGGAGTGAGCTCTCCGAAATGAAAATGTGCACACATGAATATGAATTGACGG
ACCCAGAAT
Found at i:48080629 original size:21 final size:22
Alignment explanation
Indices: 48080604--48080654 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
48080594 TAACACATAA
48080604 AGTGCCTGAA-ACGACACACAT
1 AGTGCCTGAATACGACACACAT
* *
48080625 GGTGCCT-AATACGACACATAT
1 AGTGCCTGAATACGACACACAT
48080646 AGTGCCTGA
1 AGTGCCTGA
48080655 TCGGCAAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 22 0.88
22 1 0.04
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (22 bp):
AGTGCCTGAATACGACACACAT
Found at i:48081140 original size:17 final size:18
Alignment explanation
Indices: 48081108--48081141 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
48081098 AATTTCTTTT
48081108 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
48081126 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
48081142 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:48081625 original size:3 final size:3
Alignment explanation
Indices: 48081610--48081655 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
48081600 ATATATTAGT
* *
48081610 TAA TAA TAT TAA TAA TAA TACA TTA TAA TAA T-A TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
48081654 TA
1 TA
48081656 TTTAATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
2 4 0.11
3 30 0.83
4 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:48081656 original size:13 final size:13
Alignment explanation
Indices: 48081610--48081656 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
48081600 ATATATTAGT
*
48081610 TAATAATATTA-A
1 TAATAATATAATA
* *
48081622 TAATAATACATTA
1 TAATAATATAATA
48081635 TAATAATATAATA
1 TAATAATATAATA
48081648 TAATAATAT
1 TAATAATAT
48081657 TTAATTTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 8 0.28
13 21 0.72
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:48083718 original size:22 final size:24
Alignment explanation
Indices: 48083690--48083749 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
48083680 TTAAGGAAAC
48083690 GAACTGT-GTTGCA-TAATACTGT
1 GAACTGTAGTTGCAGTAATACTGT
* *
48083712 GAACTGTATTTGTAGTAATACTGT
1 GAACTGTAGTTGCAGTAATACTGT
* *
48083736 GAATTGTATTTGCA
1 GAACTGTAGTTGCA
48083750 AAAATGTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 7 0.22
23 4 0.12
24 21 0.66
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (24 bp):
GAACTGTAGTTGCAGTAATACTGT
Found at i:48083935 original size:24 final size:24
Alignment explanation
Indices: 48083854--48083944 Score: 76
Period size: 24 Copynumber: 3.8 Consensus size: 24
48083844 GAATATCGCA
* ***
48083854 AACTGTATTTGCAGAAATGTTGCG
1 AACTGTATTTACAGAAATGTAATG
* * * *
48083878 AACTGTATTTGCA-AAATTTTATTTT
1 AACTGTATTTACAGAAA-TGTA-ATG
48083903 AACTGTATTTACAGAAATGTAATG
1 AACTGTATTTACAGAAATGTAATG
*
48083927 AACTGTATTTACACAAAT
1 AACTGTATTTACAGAAAT
48083945 TCCGTGAATT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
23 3 0.06
24 33 0.61
25 15 0.28
26 3 0.06
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.38
Consensus pattern (24 bp):
AACTGTATTTACAGAAATGTAATG
Found at i:48084104 original size:47 final size:47
Alignment explanation
Indices: 48083979--48084133 Score: 156
Period size: 46 Copynumber: 3.3 Consensus size: 47
48083969 CTGTGAATTG
* * *
48083979 TATTTGCATAAATG-TCGCAAATTGTATCGTAGAACATTACGAACTA
1 TATTTGCATAAATGCTCGCGAATTGTATCGTAGAATATTGCGAACTA
* * * * * *
48084025 TATTTACA-AAA-ACATCGTGAACTGTTTTGTAGAATTATTGCGAACTA
1 TATTTGCATAAATGC-TCGCGAATTGTATCGTAGAA-TATTGCGAACTA
* *
48084072 TATTTGCATAAATGCT-GCGAATTGTATCGTAGAATATTGCGAATTG
1 TATTTGCATAAATGCTCGCGAATTGTATCGTAGAATATTGCGAACTA
*
48084118 TTTTTGCATAAATGCT
1 TATTTGCATAAATGCT
48084134 GCAAACTGTA
Statistics
Matches: 86, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
45 3 0.03
46 47 0.55
47 31 0.36
48 4 0.05
49 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (47 bp):
TATTTGCATAAATGCTCGCGAATTGTATCGTAGAATATTGCGAACTA
Found at i:48084124 original size:46 final size:47
Alignment explanation
Indices: 48083960--48084144 Score: 148
Period size: 46 Copynumber: 4.0 Consensus size: 47
48083950 GAATTGTTCT
* * * * *
48083960 GTAGAATTACTGTGAATTGTATTTGCATAAATG-TCGCAAATTGTATC
1 GTAGAATTATTGCGAACTATATTTGCATAAATGCT-GCAAACTGTATC
* * * * * *
48084007 GTAGAA-CATTACGAACTATATTTACAAAAACAT-CGTG--AACTGTTTT
1 GTAGAATTATTGCGAACTATATTTGC-ATAA-ATGC-TGCAAACTGTATC
* *
48084053 GTAGAATTATTGCGAACTATATTTGCATAAATGCTGCGAATTGTATC
1 GTAGAATTATTGCGAACTATATTTGCATAAATGCTGCAAACTGTATC
* * *
48084100 GTAGAA-TATTGCGAATTGTTTTTGCATAAATGCTGCAAACTGTAT
1 GTAGAATTATTGCGAACTATATTTGCATAAATGCTGCAAACTGTAT
48084145 TTACAGAAAT
Statistics
Matches: 107, Mismatches: 23, Indels: 17
0.73 0.16 0.12
Matches are distributed among these distances:
45 4 0.04
46 62 0.58
47 37 0.35
48 3 0.03
49 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (47 bp):
GTAGAATTATTGCGAACTATATTTGCATAAATGCTGCAAACTGTATC
Found at i:48084580 original size:54 final size:54
Alignment explanation
Indices: 48084369--48084783 Score: 316
Period size: 54 Copynumber: 7.9 Consensus size: 54
48084359 ACAAACCGTA
* * * * *
48084369 AGATTCGTAAAATCTCAAAAGT---AGGTCGTGATTGTATATCAACGGACAAGG
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
* * *
48084420 AGATTCGTAAAAT-TTAGAAAGTAGAAGGACATGATCT-TAAATCAGCGAACCATG
1 AGATTCGTAAAATCTCA-AAAGTAGAAGGTCATGAT-TGTAAATCAGCGGACCATG
* * * *
48084474 AGATTCGTGAAATCTC----G-A-AAGGTCATGATTGTAAATTAGCAGACCGTG
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
* * * ** *
48084522 AGATTCGTAAAATCTCAAAAGTTGAAGGTCGTGATCGTAAATCAATGGACCATA
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
* * * ** ** *
48084576 AGATTCCTAAAATCTCAAAAGTAGAAGGTCATGATCGTAAACCAGCAAACGGTT
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
* ** *
48084630 AGATTCGTAAAATCTCGAAAGTAGAAGG-CAATGATTGTAAATCAGTAGACTATG
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTC-ATGATTGTAAATCAGCGGACCATG
** * ** * * * *
48084684 ACCTTTGTAAAATCTCGAAAA-TAGAAGGTTGTGATTGTAAATCAGTGAACCGTA
1 AGATTCGTAAAATCTC-AAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
* * * *
48084738 AGATTCATAAAATTTCTAATGTAGAAGGTCATGATTGTAAATCAGC
1 AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGC
48084784 ATGACAACCC
Statistics
Matches: 281, Mismatches: 66, Indels: 31
0.74 0.17 0.08
Matches are distributed among these distances:
47 1 0.00
48 38 0.14
49 1 0.00
50 3 0.01
51 18 0.06
52 1 0.00
53 3 0.01
54 211 0.75
55 5 0.02
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.27
Consensus pattern (54 bp):
AGATTCGTAAAATCTCAAAAGTAGAAGGTCATGATTGTAAATCAGCGGACCATG
Found at i:48089164 original size:31 final size:31
Alignment explanation
Indices: 48089129--48089202 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
48089119 TCAAATAACT
48089129 AAGTACTAATTTGAACCACAGAA-CCAAATTC
1 AAGTACTAATTTGAACCA-AGAAGCCAAATTC
* * * *
48089160 AAGTACCAATTTGAATCAAGAAGCTAAGTTC
1 AAGTACTAATTTGAACCAAGAAGCCAAATTC
48089191 AAGTATCTAATT
1 AAGTA-CTAATT
48089203 GGACCAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 4 0.11
31 27 0.75
32 5 0.14
ACGTcount: A:0.43, C:0.18, G:0.12, T:0.27
Consensus pattern (31 bp):
AAGTACTAATTTGAACCAAGAAGCCAAATTC
Found at i:48090526 original size:22 final size:21
Alignment explanation
Indices: 48090492--48090532 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
48090482 TTTCCCCCCC
*
48090492 AATTGATAGAAAATGAAAAAAA
1 AATTGAAAGAAAA-GAAAAAAA
*
48090514 AATTGAAATAAAAGAAAAA
1 AATTGAAAGAAAAGAAAAA
48090533 CAGAAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (21 bp):
AATTGAAAGAAAAGAAAAAAA
Found at i:48090841 original size:13 final size:13
Alignment explanation
Indices: 48090823--48090854 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
48090813 CTTTCTAGCC
48090823 TTCTACTTTTCCA
1 TTCTACTTTTCCA
48090836 TTCTACTTTTCCA
1 TTCTACTTTTCCA
*
48090849 CTCTAC
1 TTCTAC
48090855 CAAACACACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.34, G:0.00, T:0.50
Consensus pattern (13 bp):
TTCTACTTTTCCA
Found at i:48097718 original size:18 final size:19
Alignment explanation
Indices: 48097678--48097721 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
48097668 GATTAAGTTA
48097678 AAAATGTTTTAATTATGATT
1 AAAAT-TTTTAATTATGATT
*
48097698 AAAATTTTTAATTATTA-T
1 AAAATTTTTAATTATGATT
48097716 AAAATT
1 AAAATT
48097722 AAAAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 11 0.48
20 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
AAAATTTTTAATTATGATT
Found at i:48098611 original size:18 final size:19
Alignment explanation
Indices: 48098585--48098628 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
48098575 TATTCTTTAG
48098585 AATTTTTTT-AAAAATATA
1 AATTTTTTTAAAAAATATA
48098603 TAATTTTTTTAAAAAATATA
1 -AATTTTTTTAAAAAATATA
48098623 AATTTT
1 AATTTT
48098629 GGAATTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTTTTTAAAAAATATA
Found at i:48098666 original size:18 final size:18
Alignment explanation
Indices: 48098643--48098687 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
48098633 TTTTTCTAAA
48098643 TATTTTGAATTTAAAAAT
1 TATTTTGAATTTAAAAAT
* *
48098661 TATTTTAAAATTTGAAAAT
1 TATTTT-GAATTTAAAAAT
48098680 TATTTTGA
1 TATTTTGA
48098688 TTCTTTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (18 bp):
TATTTTGAATTTAAAAAT
Found at i:48100525 original size:30 final size:31
Alignment explanation
Indices: 48100489--48100557 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
48100479 TGATTTCAAT
48100489 TCAGTCACTCAACT-TT-CAAAAAA-TGACAAA
1 TCAGTCACT-AA-TGTTACAAAAAAGTGACAAA
*
48100519 TCAGTCACTAATGTTATAAAAAAGTGACAAA
1 TCAGTCACTAATGTTACAAAAAAGTGACAAA
48100550 TCAGTCAC
1 TCAGTCAC
48100558 CCACAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 1 0.03
29 4 0.11
30 15 0.43
31 15 0.43
ACGTcount: A:0.45, C:0.20, G:0.10, T:0.25
Consensus pattern (31 bp):
TCAGTCACTAATGTTACAAAAAAGTGACAAA
Found at i:48102327 original size:21 final size:21
Alignment explanation
Indices: 48102301--48102427 Score: 105
Period size: 21 Copynumber: 6.0 Consensus size: 21
48102291 TTTGGGTGGA
**
48102301 TCAGCTTTCATAAGCTTCTGT
1 TCAGCTTTCACGAGCTTCTGT
48102322 TCAGCTTTCACGAGCTTCTGT
1 TCAGCTTTCACGAGCTTCTGT
*
48102343 TCAGCTCTCACGAGCTTCTGT
1 TCAGCTTTCACGAGCTTCTGT
* * *
48102364 TTAGCTCTT-ACGAGTTTTTGT
1 TCAGCT-TTCACGAGCTTCTGT
* * * **
48102385 TTAGCTTTTATGATTTTCTGT
1 TCAGCTTTCACGAGCTTCTGT
* *
48102406 TCAG-TTCTTATGAGCTTCTGT
1 TCAGCTT-TCACGAGCTTCTGT
48102427 T
1 T
48102428 GGAGTGTTCG
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
20 4 0.04
21 85 0.94
22 1 0.01
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.46
Consensus pattern (21 bp):
TCAGCTTTCACGAGCTTCTGT
Found at i:48109502 original size:50 final size:50
Alignment explanation
Indices: 48109391--48109687 Score: 310
Period size: 50 Copynumber: 5.8 Consensus size: 50
48109381 ATTTGGGTAA
* *
48109391 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
* *
48109447 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
48109497 AGAGGTCCCATGTGAGGCCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
48109547 AGAGGTCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * *
48109597 AGAACTCCCATGTAAGACCATATCTAGGATATGGCATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** *
48109646 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
48109688 TGTTATTATC
Statistics
Matches: 210, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 127 0.60
53 3 0.01
55 1 0.00
56 39 0.19
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:48112519 original size:2 final size:2
Alignment explanation
Indices: 48112501--48112535 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
48112491 AGTTATATGT
*
48112501 TA TA T- TA TA TT 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
48112536 GTGAACTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:48119967 original size:25 final size:24
Alignment explanation
Indices: 48119916--48119966 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
48119906 TTGAATATTA
* *
48119916 TTTAATATTTTTTATTTATGTAAT
1 TTTAATAATTTTTATTTATATAAT
48119940 TTTAATTAATTTTTATTT-TATAAT
1 TTTAA-TAATTTTTATTTATATAAT
48119964 TTT
1 TTT
48119967 TTATAGCAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTAATAATTTTTATTTATATAAT
Found at i:48121319 original size:42 final size:42
Alignment explanation
Indices: 48121260--48121356 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
48121250 GCCCGTGTGG
* *
48121260 TCAGGCCGTGTGGCTCACACGGTCAAGAGACACACCTGTGTC
1 TCAGGCCGTGTGGCTCACACGGTCAAGAGACACACCCGTATC
48121302 TCAGGCCGTGTGGCTCACACGGTCAAGAGACACACCCGTATC
1 TCAGGCCGTGTGGCTCACACGGTCAAGAGACACACCCGTATC
48121344 TCAGGCCGTGTGG
1 TCAGGCCGTGTGG
48121357 GCTTTCGAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.21, C:0.31, G:0.30, T:0.19
Consensus pattern (42 bp):
TCAGGCCGTGTGGCTCACACGGTCAAGAGACACACCCGTATC
Found at i:48122539 original size:33 final size:34
Alignment explanation
Indices: 48122484--48122559 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 34
48122474 TGGCCCTACC
* * * *
48122484 ATGGTCTTA-CATTCGTAGTGCCATAACCCAATT
1 ATGGTCTTATCATTAGTAATGCCACAACCCAACT
* *
48122517 ATGGTCTTATCATTAG-AATGCCACAGCCCAGCT
1 ATGGTCTTATCATTAGTAATGCCACAACCCAACT
48122550 ATGGTCTTAT
1 ATGGTCTTAT
48122560 GTGCAAATGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 31 0.86
34 5 0.14
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (34 bp):
ATGGTCTTATCATTAGTAATGCCACAACCCAACT
Found at i:48123100 original size:19 final size:20
Alignment explanation
Indices: 48123071--48123111 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
48123061 CATAATTTCC
48123071 ATGTATCAACATATCAAGAT
1 ATGTATCAACATATCAAGAT
48123091 ATGTAT-AACATATCAAGAT
1 ATGTATCAACATATCAAGAT
48123110 AT
1 AT
48123112 TAATATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (20 bp):
ATGTATCAACATATCAAGAT
Done.