Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 101 of 433
Found at i:30893788 original size:21 final size:21
Alignment explanation
Indices: 30893727--30893782 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 21
30893717 TATATTAGCT
* *
30893727 AATAATATTATA--AAAATAA
1 AATAAAATTATATTAAATTAA
30893746 AATAAAATTATATTAAATTAA
1 AATAAAATTATATTAAATTAA
*
30893767 AATACAA-TA-ATTAAAT
1 AATAAAATTATATTAAAT
30893783 CCTAAATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 18 0.56
20 2 0.06
21 12 0.38
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AATAAAATTATATTAAATTAA
Found at i:30894210 original size:24 final size:24
Alignment explanation
Indices: 30894183--30894229 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
30894173 TTTTATAATT
*
30894183 ATTTTTTAA-TAATATTAATTTTAA
1 ATTTTATAATTAAT-TTAATTTTAA
*
30894207 ATTTTATAATTAATTTTATTTTA
1 ATTTTATAATTAATTTAATTTTA
30894230 TAAAAATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTATAATTAATTTAATTTTAA
Found at i:30894229 original size:17 final size:18
Alignment explanation
Indices: 30894196--30894232 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
30894186 TTTTAATAAT
30894196 ATTAATTTTAAATTTTATA
1 ATTAATTTT-AATTTTATA
30894215 ATTAATTTT-ATTTTATA
1 ATTAATTTTAATTTTATA
30894232 A
1 A
30894233 AAATCAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
19 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTAATTTTAATTTTATA
Found at i:30894685 original size:18 final size:18
Alignment explanation
Indices: 30894662--30894703 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
30894652 GTAGTATTTA
* *
30894662 AAAAAAATACTGTTAGGG
1 AAAAAAAGACTGTAAGGG
*
30894680 AAAAAAAGATTGTAAGGG
1 AAAAAAAGACTGTAAGGG
30894698 AAAAAA
1 AAAAAA
30894704 TTTTAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.02, G:0.21, T:0.17
Consensus pattern (18 bp):
AAAAAAAGACTGTAAGGG
Found at i:30895170 original size:21 final size:20
Alignment explanation
Indices: 30895139--30895189 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
30895129 TTGTTGATAT
* *
30895139 ATATTTTTTAATAGGAGTTA
1 ATATTTTTTAATAGAAGCTA
30895159 ATATTGTTTTAATAGAAGCTA
1 ATATT-TTTTAATAGAAGCTA
30895180 ATATTTTTTA
1 ATATTTTTTA
30895190 TTTTTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (20 bp):
ATATTTTTTAATAGAAGCTA
Found at i:30895756 original size:13 final size:13
Alignment explanation
Indices: 30895713--30895761 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
30895703 TTACAAATAA
30895713 AAATA-TAATATTT
1 AAATATTAA-ATTT
* *
30895726 AAACATTACATCTT
1 AAATATTAAAT-TT
30895740 AAATATTAAATTT
1 AAATATTAAATTT
30895753 AAATATTAA
1 AAATATTAA
30895762 CAATAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
13 17 0.57
14 13 0.43
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATATTAAATTT
Found at i:30897802 original size:17 final size:17
Alignment explanation
Indices: 30897760--30897819 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
30897750 CGCCTTTCCT
*
30897760 ATTTTTTTTACAC-ACAA
1 ATTTTTTTTACTCAAC-A
30897777 ATTTATTTTTACTCAACA
1 ATTT-TTTTTACTCAACA
* *
30897795 ATTTTTTTAACTCATCA
1 ATTTTTTTTACTCAACA
30897812 ATTTTTTT
1 ATTTTTTT
30897820 AAAAAAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 23 0.61
18 13 0.34
19 2 0.05
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTTTTTACTCAACA
Found at i:30899927 original size:16 final size:16
Alignment explanation
Indices: 30899906--30899939 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30899896 TACTTTGAAA
30899906 ATAATTTCAAATATAT
1 ATAATTTCAAATATAT
* *
30899922 ATAATTTTAAATTTAT
1 ATAATTTCAAATATAT
30899938 AT
1 AT
30899940 TCTCCAACAT
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:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAATTTCAAATATAT
Found at i:30900060 original size:19 final size:19
Alignment explanation
Indices: 30900036--30900073 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
30900026 ACTCAAATTT
* *
30900036 AATTTAATTTAATTTAAAA
1 AATTTAAATTAAATTAAAA
30900055 AATTTAAATTAAATTAAAA
1 AATTTAAATTAAATTAAAA
30900074 TAATAAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTTAAATTAAATTAAAA
Found at i:30900397 original size:20 final size:21
Alignment explanation
Indices: 30900372--30900411 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
30900362 TTTAAACTCC
30900372 ACAAATGATAT-TAAAAATAA
1 ACAAATGATATATAAAAATAA
*
30900392 ACAAATGTTATATAAAAATA
1 ACAAATGATATATAAAAATA
30900412 TTTTATCCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (21 bp):
ACAAATGATATATAAAAATAA
Found at i:30900543 original size:31 final size:29
Alignment explanation
Indices: 30900500--30900581 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 29
30900490 AAAATTTAAA
30900500 TTAATAAA-AATAAAATTATATTTTAATCTT
1 TTAA-AAATAATAAAATTATATTTT-ATCTT
30900530 TCTAAAAATAATAAAAATT-TAATTTTATCTT
1 T-TAAAAATAAT-AAAATTAT-ATTTTATCTT
* *
30900561 TTAAAAATTATAAAAATATAT
1 TTAAAAATAATAAAATTATAT
30900582 AATTTAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
29 7 0.16
30 14 0.31
31 13 0.29
32 11 0.24
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (29 bp):
TTAAAAATAATAAAATTATATTTTATCTT
Found at i:30900555 original size:32 final size:30
Alignment explanation
Indices: 30900511--30900586 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 30
30900501 TAATAAAAAT
30900511 AAAA-TTATATTTTAATCTTTCTAAAAATAATA
1 AAAATTTA-ATTTT-ATCTTT-TAAAAATAATA
*
30900543 AAAATTTAATTTTATCTTTTAAAAATTATA
1 AAAATTTAATTTTATCTTTTAAAAATAATA
30900573 AAAATATATAATTT
1 AAAAT-T-TAATTT
30900587 AATTTAAACA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
30 15 0.38
31 7 0.17
32 15 0.38
33 3 0.08
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (30 bp):
AAAATTTAATTTTATCTTTTAAAAATAATA
Found at i:30902973 original size:22 final size:23
Alignment explanation
Indices: 30902939--30902983 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
30902929 TTAAAAAAAA
*
30902939 CATAAATGCATTT-AAACCTCAT
1 CATAAATGAATTTCAAACCTCAT
* *
30902961 CATAAATTAATTTCAAACTTCAT
1 CATAAATGAATTTCAAACCTCAT
30902984 TTAAACTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.42, C:0.20, G:0.02, T:0.36
Consensus pattern (23 bp):
CATAAATGAATTTCAAACCTCAT
Found at i:30903919 original size:35 final size:35
Alignment explanation
Indices: 30903860--30903926 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
30903850 AATCCCTTCA
* * *
30903860 AAACACACCAAGGGGGACCAAAGTGCCAAGCCGCC
1 AAACACACCAAAGAGCACCAAAGTGCCAAGCCGCC
* *
30903895 AAACACACCAAAGAGCACCTAAGTGCTAAGCC
1 AAACACACCAAAGAGCACCAAAGTGCCAAGCC
30903927 CAAAGGCGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.40, C:0.33, G:0.21, T:0.06
Consensus pattern (35 bp):
AAACACACCAAAGAGCACCAAAGTGCCAAGCCGCC
Found at i:30908732 original size:79 final size:81
Alignment explanation
Indices: 30908583--30908800 Score: 225
Period size: 79 Copynumber: 2.7 Consensus size: 81
30908573 GAATCACGTA
*** * **
30908583 CCTTCGGAAT-TTAA-CCGGATATAACGACTCGCTCAAATGCCTTCGGGACAAAGCCCGG-TTAT
1 CCTTCGG-ATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTAT
*
30908645 AGTAACTCGCACGAATG
65 AGTAACTCGCACGAACG
* * *
30908662 CCTTTGGGA-CTTAACCCGGGTTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATT-T
1 CC-TTCGGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTAT
*
30908724 ATTAACTCGCACGAACG
65 AGTAACTCGCACGAACG
** * *
30908741 CCTTCGGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGATCTTAACCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
30908801 CATCATTCAA
Statistics
Matches: 114, Mismatches: 18, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
78 5 0.04
79 57 0.50
80 52 0.46
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CCTTCGGATCTTAACCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTATA
GTAACTCGCACGAACG
Found at i:30908800 original size:40 final size:39
Alignment explanation
Indices: 30908609--30908800 Score: 181
Period size: 40 Copynumber: 4.8 Consensus size: 39
30908599 GGATATAACG
* ** *
30908609 ACTCGCTCAAATGCCTTCGGGACAAAGCCCGGTTATAGTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * * * *
30908649 ACTCGCACGAATGCCTTTGGGACTTAACCCGGGTTTAGTA
1 ACTCGCAC-AAAGCCTTCGGGACTTAGCCCGGATATAGTA
* *
30908689 ACTCGCACAAATGCCTTCGGG-CTTAGCCCGGATTTATTA
1 ACTCGCACAAA-GCCTTCGGGACTTAGCCCGGATATAGTA
* * *
30908728 ACTCGCACGAACGCCTTC-GGATCTTAGTCCGGATATAGTC
1 ACTCGCAC-AAAGCCTTCGGGA-CTTAGCCCGGATATAGTA
*
30908768 ACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 AC-TCGCACAAAGCCTTCGGGACTTAGCCCGGA
30908801 CATCATTCAA
Statistics
Matches: 124, Mismatches: 21, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 81 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
ACTCGCACAAAGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:30911332 original size:3 final size:3
Alignment explanation
Indices: 30911324--30911355 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
30911314 ACACTAAGCT
30911324 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
30911356 AAAACATCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:30917726 original size:40 final size:40
Alignment explanation
Indices: 30917630--30917813 Score: 194
Period size: 40 Copynumber: 4.5 Consensus size: 40
30917620 TATTCGGATG
* * * *
30917630 ATATCCAGGTTAAGTACCGAAGGCATTTATGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGC---TAGCTGCT
* *
30917673 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGCTG-CT
*
30917713 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAG-TGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGCTG-CT
* * * *
30917753 ATATCCGGGCTAAGACCCGAAGGCAGTTGTGCGAGCTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGCTGCT
*
30917793 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
30917814 ATACTTGGGT
Statistics
Matches: 124, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
39 15 0.12
40 80 0.65
41 2 0.02
43 27 0.22
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGCTGCT
Found at i:30917774 original size:80 final size:80
Alignment explanation
Indices: 30917630--30917813 Score: 221
Period size: 80 Copynumber: 2.3 Consensus size: 80
30917620 TATTCGGATG
* * * *
30917630 ATATCCAGGTTAAGTACCGAAGGCATTTATGCGAGTAGTTGCTATACCCGGGCTAAGTCCCGAAG
1 ATATCC-GGCTAAGTCCCGAAGGCATTCATGC--GTAGTTGCTATACCCGGGCTAAGACCCGAAG
* *
30917695 GCATTTGTGCTAG-TGACT
63 GCAGTTGTGCGAGCTG-CT
*
30917713 ATATCCGGGCTAAGTCCCGAAGGCATTCATGC-TAG-TGACTATATCCGGGCTAAGACCCGAAGG
1 ATATCC-GGCTAAGTCCCGAAGGCATTCATGCGTAGTTG-CTATACCCGGGCTAAGACCCGAAGG
30917776 CAGTTGTGCGAGCTGCT
64 CAGTTGTGCGAGCTGCT
*
30917793 ATATCCGGCTAAATCCCGAAG
1 ATATCCGGCTAAGTCCCGAAG
30917814 ATACTTGGGT
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
79 16 0.18
80 44 0.49
81 2 0.02
83 28 0.31
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
ATATCCGGCTAAGTCCCGAAGGCATTCATGCGTAGTTGCTATACCCGGGCTAAGACCCGAAGGCA
GTTGTGCGAGCTGCT
Found at i:30925733 original size:40 final size:40
Alignment explanation
Indices: 30925678--30925818 Score: 196
Period size: 40 Copynumber: 3.5 Consensus size: 40
30925668 TATTCGGATG
30925678 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* **
30925718 ATATCCGGGCTAAGTCCCGAAGGTATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * *
30925758 ATATCCTGGCTAAGACCCGAAGGCATTTGTGCGAGCTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
30925798 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
30925819 ATACTTGGGT
Statistics
Matches: 89, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 13 0.15
40 74 0.83
41 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:30937581 original size:17 final size:18
Alignment explanation
Indices: 30937539--30937587 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
30937529 AGTTGAAAAG
30937539 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
30937558 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
30937575 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
30937588 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:30938476 original size:40 final size:40
Alignment explanation
Indices: 30938410--30938576 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
30938400 AAATTGAATG
* * *
30938410 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
30938449 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
30938489 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
30938529 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
30938569 ATATCCGG
1 ATATCCGG
30938577 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:30945578 original size:17 final size:18
Alignment explanation
Indices: 30945536--30945584 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
30945526 AGTTGAAAAG
30945536 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
30945555 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
30945572 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
30945585 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:30946472 original size:40 final size:40
Alignment explanation
Indices: 30946406--30946572 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
30946396 AAATTGAATG
* * *
30946406 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
30946445 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
30946485 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
30946525 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
30946565 ATATCCGG
1 ATATCCGG
30946573 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:30957014 original size:30 final size:30
Alignment explanation
Indices: 30956978--30957037 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
30956968 TCCCCGAGCC
*
30956978 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
30957008 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
30957038 CATATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:30959031 original size:40 final size:40
Alignment explanation
Indices: 30958971--30959050 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
30958961 GGCATTGTAT
* * *
30958971 GGGCTTAAATGTCGTACACCTTTGTATTGGACTGAACTTA
1 GGGCGTAAATGTCGTACACCTTTGTACTGCACTGAACTTA
30959011 GGGCGTAAATGTCGTACACCTTTGTACTGCACTGAACTTA
1 GGGCGTAAATGTCGTACACCTTTGTACTGCACTGAACTTA
30959051 AGGAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (40 bp):
GGGCGTAAATGTCGTACACCTTTGTACTGCACTGAACTTA
Found at i:30965005 original size:12 final size:12
Alignment explanation
Indices: 30964988--30965012 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30964978 AGTTGCAAAA
30964988 GTTGATTCAGAT
1 GTTGATTCAGAT
30965000 GTTGATTCAGAT
1 GTTGATTCAGAT
30965012 G
1 G
30965013 ATTTTGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (12 bp):
GTTGATTCAGAT
Found at i:30967466 original size:29 final size:29
Alignment explanation
Indices: 30967373--30967467 Score: 97
Period size: 29 Copynumber: 3.3 Consensus size: 29
30967363 GTGAGCATGA
*
30967373 ATAT-AATATGATTTGGGCCTA-ATGGGCC
1 ATATGAATATGAATTGGGCC-AGATGGGCC
* *
30967401 ATATGAAGATGAATTGGGCGTAG-TGGGCC
1 ATATGAATATGAATTGGGC-CAGATGGGCC
* *
30967430 ATAAGAATATGAACTGGGCCAGATGGGCC
1 ATATGAATATGAATTGGGCCAGATGGGCC
*
30967459 ATTTGAATA
1 ATATGAATA
30967468 AGATTGGACC
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
28 6 0.11
29 48 0.89
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (29 bp):
ATATGAATATGAATTGGGCCAGATGGGCC
Found at i:30973613 original size:15 final size:15
Alignment explanation
Indices: 30973593--30973627 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
30973583 CTTTTTTGGG
30973593 TCATTTGGATTGATA
1 TCATTTGGATTGATA
30973608 TCATTTGGATTGATA
1 TCATTTGGATTGATA
30973623 TCATT
1 TCATT
30973628 CTATATGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.49
Consensus pattern (15 bp):
TCATTTGGATTGATA
Found at i:30975429 original size:51 final size:49
Alignment explanation
Indices: 30975249--30975437 Score: 180
Period size: 50 Copynumber: 3.8 Consensus size: 49
30975239 GAGCCAAAGC
* * * * * *
30975249 TATCTGGTACGCATAGTAGCCTTCACATAGTACTACACATGCGACCAAT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
* * * *
30975298 TATCCGGTACACGTAGTAGCCTACACTTAGTACTACACACATGACCTAAC
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACC-AAT
* * * * * *
30975348 CATCTGATACACGTAGTAGCTTGCACTTAGTACTACACACGTGATCACAGT
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAAT
* * *
30975399 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACA
30975438 TGCGACCTCA
Statistics
Matches: 113, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
49 38 0.34
50 40 0.35
51 34 0.30
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (49 bp):
TATCCGGTACACATAGTAGCCTGCACTTAGTACTACACACGTGACCAAT
Found at i:30996867 original size:39 final size:40
Alignment explanation
Indices: 30996813--30996967 Score: 206
Period size: 39 Copynumber: 3.9 Consensus size: 40
30996803 TGTGTATGAA
* *
30996813 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGTCCCGAAGGCAAT
30996852 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGTCCCGAAGGCAAT
* * *
30996891 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAGTCCCGAAGGCAAT
* ** * *
30996931 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGGC
1 TGTGCGAGTTATGATATCCGGGCTAAGTCCCGAAGGC
30996968 GTTTGAACGA
Statistics
Matches: 103, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 62 0.60
40 41 0.40
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (40 bp):
TGTGCGAGTTATGATATCCGGGCTAAGTCCCGAAGGCAAT
Found at i:30996952 original size:79 final size:79
Alignment explanation
Indices: 30996813--30996967 Score: 222
Period size: 79 Copynumber: 2.0 Consensus size: 79
30996803 TGTGTATGAA
** *
30996813 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAA
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAA
30996878 G-CCCGAAGGCAAT
66 GTCCCGAAGGCAAT
* * * *
30996891 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAACCGGGCTA
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTACCATAACCGGGCTA
*
30996956 TGTCCCGAAGGC
65 AGTCCCGAAGGC
30996968 GTTTGAACGA
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
78 25 0.37
79 33 0.49
80 9 0.13
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.25
Consensus pattern (79 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAA
GTCCCGAAGGCAAT
Found at i:30996994 original size:79 final size:78
Alignment explanation
Indices: 30996823--30997005 Score: 199
Period size: 79 Copynumber: 2.3 Consensus size: 78
30996813 TGTGCGAATT
* ** *
30996823 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGC
1 GTGATATCCGGGTTAAGCCCGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAGCCCGAAGGC
** *
30996888 AATTGTGCGAGTT
66 AATTGAACGAGTA
* * *
30996901 GTGATATCCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAACCGGGCTATGTCCCGAAG
1 GTGATATCCGGGTTAAG-CCCGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAG-CCCGAAG
**
30996966 GCGTTTGAACGAGTA
64 GCAATTGAACGAGTA
*
30996981 GCT-ATATCC-GGTTAAACTCCGAAGG
1 G-TGATATCCGGGTTAAGC-CCGAAGG
30997006 TATGTGATTT
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
78 17 0.19
79 46 0.52
80 24 0.27
81 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (78 bp):
GTGATATCCGGGTTAAGCCCGAAGGCAATTGTGCGAGTTACCATAACCGGGCTAAGCCCGAAGGC
AATTGAACGAGTA
Found at i:31002989 original size:58 final size:59
Alignment explanation
Indices: 31002871--31003032 Score: 195
Period size: 58 Copynumber: 2.8 Consensus size: 59
31002861 GTGACGAGAT
* *
31002871 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTGGAAAAATA
1 TGGCACTGAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAAATA
***
31002929 TGGCACTGAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTGAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAAATA
* ** * **
31002987 TGGCACTGTGTGTGCGGGCT-TAAATCGCATGGCACTAAGTGTGCGA
1 TGGCACTGAGTGTGCATGCTGGAAAT-ATATGGCACTAAGTGTGCGA
31003033 AATCGAGTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
57 4 0.04
58 86 0.95
59 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (59 bp):
TGGCACTGAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAAATA
Found at i:31002993 original size:29 final size:29
Alignment explanation
Indices: 31002871--31002972 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
31002861 GTGACGAGAT
31002871 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
31002900 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
31002929 TGGCACTGAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
31002958 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
31002973 GAGCTCGAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:31007519 original size:28 final size:28
Alignment explanation
Indices: 31007466--31007519 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
31007456 CCAAGTTGAT
* *
31007466 AAATGACTGTTATGCCGCTATGAGATAA
1 AAATGACTATTATGCCGCTATAAGATAA
*
31007494 AAATGATTATTATGCC-CTTATAAGAT
1 AAATGACTATTATGCCGC-TATAAGAT
31007520 GTATGACTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 1 0.05
28 21 0.95
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (28 bp):
AAATGACTATTATGCCGCTATAAGATAA
Found at i:31007851 original size:34 final size:33
Alignment explanation
Indices: 31007796--31007862 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
31007786 CTGTTACCAA
*
31007796 AATGGGCTAAGGCCCACACTGACACTGATACTGT
1 AATGGGCTAAGGCCCACACTGAAACTGA-ACTGT
*
31007830 AATGGGCTAAGGCCTTA-ACTGAAACTGAACTGT
1 AATGGGCTAAGGCC-CACACTGAAACTGAACTGT
31007863 TAGTGATCTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 5 0.17
34 24 0.80
35 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (33 bp):
AATGGGCTAAGGCCCACACTGAAACTGAACTGT
Found at i:31014326 original size:26 final size:24
Alignment explanation
Indices: 31014288--31014339 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
31014278 CTCTGCTTAA
* *
31014288 GCCGAATATCTTTTCTTTCTCTTGTT
1 GCCGAATA-CCTTTCTTTC-CTTCTT
*
31014314 GCCGAATCCCTTTCTTTCCTTCTT
1 GCCGAATACCTTTCTTTCCTTCTT
31014338 GC
1 GC
31014340 TTGTTGAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 7 0.30
25 9 0.39
26 7 0.30
ACGTcount: A:0.10, C:0.31, G:0.12, T:0.48
Consensus pattern (24 bp):
GCCGAATACCTTTCTTTCCTTCTT
Found at i:31023119 original size:5 final size:5
Alignment explanation
Indices: 31023109--31023134 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31023099 TTTTTCTTGC
31023109 AATTT AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT A
31023135 TTATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
AATTT
Found at i:31027114 original size:35 final size:35
Alignment explanation
Indices: 31027075--31027147 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
31027065 GCACATTCTT
31027075 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
31027110 TATTCTCGTCAGATCAATCTCACATAAATAATATA
1 TATTCTCGTCAGATCAATCTCACATAAATAATATA
31027145 TAT
1 TAT
31027148 ATCACATACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.36
Consensus pattern (35 bp):
TATTCTCGTCAGATCAATCTCACATAAATAATATA
Found at i:31027785 original size:20 final size:22
Alignment explanation
Indices: 31027750--31027795 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
31027740 TAGAAAGAAT
*
31027750 AAAATAATGAAAAAAA-AGAGG
1 AAAATAATGAAAAAAACAAAGG
*
31027771 AAAAT-ATGAAGAAAACAAAGG
1 AAAATAATGAAAAAAACAAAGG
31027792 AAAA
1 AAAA
31027796 AAAAGTGTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.72, C:0.02, G:0.17, T:0.09
Consensus pattern (22 bp):
AAAATAATGAAAAAAACAAAGG
Found at i:31028034 original size:7 final size:7
Alignment explanation
Indices: 31028022--31028046 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31028012 GTTGTCTTCT
31028022 TGTTTGA
1 TGTTTGA
31028029 TGTTTGA
1 TGTTTGA
31028036 TGTTTGA
1 TGTTTGA
31028043 TGTT
1 TGTT
31028047 GTGGTGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (7 bp):
TGTTTGA
Found at i:31028982 original size:27 final size:28
Alignment explanation
Indices: 31028886--31028985 Score: 112
Period size: 27 Copynumber: 3.5 Consensus size: 28
31028876 TCATGAGATT
* * *
31028886 GCACTAAGTGTGCGGGTTTTAAATTTGTACA
1 GCACTAAGTGTGCGAG-TTT-AA-TTATATA
31028917 GCACTAAGTGTGCGAGTTTAATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
* * *
31028945 GCACTAGGTGTGCGAG-TTGATTTTATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
31028972 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
31028986 GACTCACTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
27 22 0.35
28 20 0.32
29 2 0.03
30 3 0.05
31 15 0.24
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATATA
Found at i:31030058 original size:17 final size:18
Alignment explanation
Indices: 31030016--31030064 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
31030006 AGTTGAAAAG
31030016 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
31030035 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
31030052 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
31030065 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:31030952 original size:40 final size:40
Alignment explanation
Indices: 31030886--31031036 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
31030876 AAATTGAATG
* * *
31030886 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
31030925 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
31030965 ACATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
31031005 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
31031037 ACTTGATTAT
Statistics
Matches: 91, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
39 16 0.18
40 73 0.80
41 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:31031050 original size:40 final size:40
Alignment explanation
Indices: 31030922--31031052 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
31030912 TATGCTGGAA
* * * *
31030922 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
** * *
31030962 GCTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTT-
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
*
31031002 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACTTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
31031042 ATTATATCCGG
1 ATTATATCCGG
31031053 TTATATTCCG
Statistics
Matches: 74, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 3 0.04
40 70 0.95
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
Found at i:31040704 original size:72 final size:71
Alignment explanation
Indices: 31040588--31040752 Score: 321
Period size: 72 Copynumber: 2.3 Consensus size: 71
31040578 CGATTTGTCT
31040588 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
31040653 CTTTCA
66 CTTTCA
31040659 CGTAGCTCTCTCTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTA
1 CGTAGCTCTCT-TGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTA
31040724 TCTTTCA
65 TCTTTCA
31040731 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
31040753 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
71 22 0.24
72 71 0.76
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:31057133 original size:40 final size:40
Alignment explanation
Indices: 31057089--31057268 Score: 274
Period size: 40 Copynumber: 4.5 Consensus size: 40
31057079 ACTAGATTGT
* * *
31057089 CTTCGGGACA-TAGCCCGG-TTATAGTAATTCGCGCAAATGC
1 CTTCGGGA-ATTAACCCGGATT-TAGTAACTCGCACAAATGC
* * *
31057129 CTTCGGGACTTAACCCGGATTTGGTAACTCGCACAATTGC
1 CTTCGGGAATTAACCCGGATTTAGTAACTCGCACAAATGC
31057169 CTTCGGGAATTAACCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGAATTAACCCGGATTTAGTAACTCGCACAAATGC
31057209 CTTCGGGAATTAACCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGAATTAACCCGGATTTAGTAACTCGCACAAATGC
31057249 CTTCGGGAATTAACCCGGAT
1 CTTCGGGAATTAACCCGGAT
31057269 ATCATTCGAA
Statistics
Matches: 129, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
40 127 0.98
41 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CTTCGGGAATTAACCCGGATTTAGTAACTCGCACAAATGC
Found at i:31059792 original size:9 final size:9
Alignment explanation
Indices: 31059778--31059809 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
31059768 TCTGCTATCA
31059778 AGAAATAAG
1 AGAAATAAG
31059787 AGAAATAAG
1 AGAAATAAG
31059796 AGAAATAAG
1 AGAAATAAG
31059805 AGAAA
1 AGAAA
31059810 ATGATGCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (9 bp):
AGAAATAAG
Found at i:31070458 original size:37 final size:37
Alignment explanation
Indices: 31070399--31070544 Score: 256
Period size: 37 Copynumber: 3.9 Consensus size: 37
31070389 AGCTCAGACG
* *
31070399 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
31070436 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
31070473 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
31070510 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
31070545 ATATATTTCC
Statistics
Matches: 106, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 106 1.00
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:31070647 original size:48 final size:48
Alignment explanation
Indices: 31070589--31070974 Score: 664
Period size: 48 Copynumber: 8.0 Consensus size: 48
31070579 TGTTACAACA
31070589 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
31070637 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
31070685 TTCATATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* ** *
31070733 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCGTACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
31070781 TTCACATTGGCCCTTTGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
**
31070829 TTCACATTAGCCGCTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
31070877 TTCATATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
31070925 TTCATATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
31070973 TT
1 TT
31070975 ATTTATCTTG
Statistics
Matches: 318, Mismatches: 20, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 318 1.00
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:31079152 original size:29 final size:29
Alignment explanation
Indices: 31079120--31079197 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
31079110 ATACCCTCCG
** *
31079120 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
* *
31079149 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
31079178 AGCACGCACACTTAGTGCCG
1 AGCTCGCACACTTAGTGCCG
31079198 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCGTATATTTCC
Found at i:31087003 original size:29 final size:29
Alignment explanation
Indices: 31086971--31087048 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
31086961 ATACCCTCCG
** *
31086971 AGCTCGCACACCCAGTGCCGTATTTTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
* *
31087000 AGCTTGCACACTTAGTGCCATATATTTCC
1 AGCTCGCACACTTAGTGCCGTATATTTCC
*
31087029 AGCACGCACACTTAGTGCCG
1 AGCTCGCACACTTAGTGCCG
31087049 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (29 bp):
AGCTCGCACACTTAGTGCCGTATATTTCC
Found at i:31090226 original size:52 final size:52
Alignment explanation
Indices: 31090063--31090229 Score: 187
Period size: 52 Copynumber: 3.2 Consensus size: 52
31090053 TCTTACACGG
* *
31090063 ATCACATAACATACCGATGCCATATCCCAGATATGGTCTTATAC-GAAATCACATT
1 ATCACAT--CATACCGATGCCATAGCCCAGCTATGGTCTTATACAGAAAT-ACA-T
* * *
31090118 ATCACATCACACCGATGCCATAGCCCAGCTATAGTCTTATACAGGAACT-CGA-
1 ATCACATCATACCGATGCCATAGCCCAGCTATGGTCTTATACA-GAAATAC-AT
** *
31090170 ATCACATTGTACCGATGCCATAGCCTAGCTATGGTCTTATACAGAAATACAT
1 ATCACATCATACCGATGCCATAGCCCAGCTATGGTCTTATACAGAAATACAT
31090222 ATCACATC
1 ATCACATC
31090230 TTTTCCGTCA
Statistics
Matches: 95, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
51 5 0.05
52 46 0.48
53 32 0.34
54 1 0.01
55 11 0.12
ACGTcount: A:0.34, C:0.27, G:0.13, T:0.26
Consensus pattern (52 bp):
ATCACATCATACCGATGCCATAGCCCAGCTATGGTCTTATACAGAAATACAT
Found at i:31097484 original size:46 final size:51
Alignment explanation
Indices: 31097420--31097546 Score: 122
Period size: 53 Copynumber: 2.5 Consensus size: 51
31097410 ACACGCAGAA
** * *
31097420 GCCATAGCCCTGCCATGGTCTTACAC-GGATCAC-AT-A-A-CATACCGAT
1 GCCATAGCCCAACTATGGTCTTACACAGAATCACTATCAGATCATACCGAT
* *
31097466 GCCATATCCCAGA-TATGGTCTTATACAGAATCACATTATCAGATCATACCGAT
1 GCCATAGCCCA-ACTATGGTCTTACACAGAATCAC--TATCAGATCATACCGAT
*
31097519 GCCATAGCCCAACTATGGTCTTATACAG
1 GCCATAGCCCAACTATGGTCTTACACAG
31097547 GAACTCGAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 11
0.78 0.08 0.13
Matches are distributed among these distances:
46 20 0.31
47 6 0.09
50 2 0.03
51 1 0.02
52 2 0.03
53 34 0.52
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (51 bp):
GCCATAGCCCAACTATGGTCTTACACAGAATCACTATCAGATCATACCGAT
Found at i:31097611 original size:52 final size:52
Alignment explanation
Indices: 31097448--31097614 Score: 160
Period size: 52 Copynumber: 3.2 Consensus size: 52
31097438 TCTTACACGG
* * *
31097448 ATCACATAACATACCGATGCCATATCCCAGATATGGTCTTATAC-AGAATCACATT
1 ATCACAT--CATACCGATGCCATAGCCCAGCTATGGTCTTATACGAAAAT-ACA-T
* * * *
31097503 ATCAGATCATACCGATGCCATAGCCCAACTATGGTCTTATACAGGAACT-CGA-
1 ATCACATCATACCGATGCCATAGCCCAGCTATGGTCTTATAC-GAAAATAC-AT
** * *
31097555 ATCACATTGTACTGATGCCATAGCCTAGCTATGGTCTTATACGAAAATACAT
1 ATCACATCATACCGATGCCATAGCCCAGCTATGGTCTTATACGAAAATACAT
31097607 ATCACATC
1 ATCACATC
31097615 TTTTCCGTCA
Statistics
Matches: 91, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
51 5 0.05
52 44 0.48
53 33 0.36
54 1 0.01
55 8 0.09
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (52 bp):
ATCACATCATACCGATGCCATAGCCCAGCTATGGTCTTATACGAAAATACAT
Found at i:31115322 original size:31 final size:31
Alignment explanation
Indices: 31115256--31115322 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
31115246 ATTAAATAGT
* * * *
31115256 TAAATAATTTAATATAATAATAGATGATATT
1 TAAATAATTTAATATAATAATACATAAAATA
31115287 TAAATAATTTAATATAATGAA-ACATAAAATA
1 TAAATAATTTAATATAAT-AATACATAAAATA
31115318 TAAAT
1 TAAAT
31115323 TAATCTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (31 bp):
TAAATAATTTAATATAATAATACATAAAATA
Found at i:31119185 original size:17 final size:19
Alignment explanation
Indices: 31119165--31119210 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 19
31119155 ATGGGATATG
31119165 ATATGATA-AT-ATATGAA
1 ATATGATACATGATATGAA
31119182 ATATGGTACTACATGATATGAA
1 ATAT-G-A-TACATGATATGAA
31119204 ATATGAT
1 ATATGAT
31119211 TTTATAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
17 4 0.17
18 1 0.04
19 2 0.08
20 3 0.12
21 3 0.12
22 11 0.46
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (19 bp):
ATATGATACATGATATGAA
Found at i:31126638 original size:16 final size:17
Alignment explanation
Indices: 31126611--31126643 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31126601 GGTCCCTTGA
*
31126611 ATTTATGGTTAACATGG
1 ATTTATGGTTAAAATGG
31126628 ATTTA-GGTTAAAATGG
1 ATTTATGGTTAAAATGG
31126644 TTAGATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.24, T:0.39
Consensus pattern (17 bp):
ATTTATGGTTAAAATGG
Found at i:31129905 original size:26 final size:26
Alignment explanation
Indices: 31129866--31129973 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
31129856 TGGTACAAAT
31129866 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
31129892 TGGTAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
31129918 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
31129944 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
31129970 TGAT
1 TGAT
31129974 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:31136931 original size:26 final size:26
Alignment explanation
Indices: 31136902--31137009 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
31136892 TGGTACAAAT
31136902 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
31136928 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
31136954 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
31136980 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
31137006 TGAT
1 TGAT
31137010 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:31143777 original size:40 final size:41
Alignment explanation
Indices: 31143732--31143898 Score: 155
Period size: 40 Copynumber: 4.2 Consensus size: 41
31143722 CGGAATATAA
*
31143732 CCGGATATAATCAAGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
31143772 CCGGATAGAAT-AACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * * * * *
31143812 CCGGATGT-AGCCACTAGCACAATTGCCTTCGAGTCTTAAC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
31143852 CCGGATATAAT-TTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
31143891 CCGGATAT
1 CCGGATAT
31143899 CATTCAATTT
Statistics
Matches: 103, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
39 17 0.17
40 85 0.83
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.26
Consensus pattern (41 bp):
CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:31144747 original size:17 final size:19
Alignment explanation
Indices: 31144724--31144769 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
31144714 AAGAAGCATG
31144724 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
31144742 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
31144760 AATCATGCTC
1 AATCATGCTC
31144770 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:31152150 original size:77 final size:77
Alignment explanation
Indices: 31152023--31152175 Score: 288
Period size: 77 Copynumber: 2.0 Consensus size: 77
31152013 AATGGCTCAA
*
31152023 CAACCTCCAGCCCCTCCCATACCCCTACCTGTCCTCGTTATTCCTCAGGGTTTAGAACAAGTACG
1 CAACCTCCAGCCCCTCCCATACCCCTACCTGTCCTCGTTATTCCTCAGGGTTTAGAACAAGTACA
*
31152088 TGTAAGTAAGCG
66 TGCAAGTAAGCG
31152100 CAACCTCCAGCCCCTCCCATACCCCTACCTGTCCTCGTTATTCCTCAGGGTTTAGAACAAGTACA
1 CAACCTCCAGCCCCTCCCATACCCCTACCTGTCCTCGTTATTCCTCAGGGTTTAGAACAAGTACA
31152165 TGCAAGTAAGC
66 TGCAAGTAAGC
31152176 CTTCAGTTGA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (77 bp):
CAACCTCCAGCCCCTCCCATACCCCTACCTGTCCTCGTTATTCCTCAGGGTTTAGAACAAGTACA
TGCAAGTAAGCG
Found at i:31156373 original size:5 final size:5
Alignment explanation
Indices: 31156363--31156388 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31156353 TGAGCATTCG
31156363 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
31156389 AATTTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:31157430 original size:9 final size:9
Alignment explanation
Indices: 31157412--31157448 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
31157402 TATAGTTTGA
31157412 TATTCGAAT
1 TATTCGAAT
*
31157421 TATTCAAAT
1 TATTCGAAT
*
31157430 TATTCGAGT
1 TATTCGAAT
31157439 TATTCGAAT
1 TATTCGAAT
31157448 T
1 T
31157449 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31174644 original size:38 final size:38
Alignment explanation
Indices: 31174602--31174676 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
31174592 CACACAGACG
*
31174602 TGTGGATTCTAGGCCAAGCCGTGTGATCCACATGGGCT
1 TGTGGATTCTAGGCCAAGCCGTGTGATCCACACGGGCT
31174640 TGTGGATTCTAGGCCAAGCCGTGTGATCCACACGGGC
1 TGTGGATTCTAGGCCAAGCCGTGTGATCCACACGGGC
31174677 AAGGCCAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.19, C:0.25, G:0.32, T:0.24
Consensus pattern (38 bp):
TGTGGATTCTAGGCCAAGCCGTGTGATCCACACGGGCT
Found at i:31174689 original size:38 final size:38
Alignment explanation
Indices: 31174609--31174689 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 38
31174599 ACGTGTGGAT
* ** * *
31174609 TCTAGGCCAAGCCGTGTGATCCACATGGGCTTGTGGAT
1 TCTAGGCCAAGCCGTGTGATCCACACGGGCAAGTGCAA
31174647 TCTAGGCCAAGCCGTGTGATCCACACGGGCAAG-GCCAA
1 TCTAGGCCAAGCCGTGTGATCCACACGGGCAAGTG-CAA
31174685 TCTAG
1 TCTAG
31174690 ACGTGTGGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.03
38 36 0.97
ACGTcount: A:0.22, C:0.27, G:0.30, T:0.21
Consensus pattern (38 bp):
TCTAGGCCAAGCCGTGTGATCCACACGGGCAAGTGCAA
Found at i:31181096 original size:47 final size:46
Alignment explanation
Indices: 31180854--31181114 Score: 149
Period size: 47 Copynumber: 5.6 Consensus size: 46
31180844 CATTTGTGTG
* * * * *
31180854 TGAGCTAGAGTAAGA-CATGTTTGGGACATGCATCGGC--CAGATTA
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTTGAGA-TA
*
31180898 TGAGAGCCAGTGTAAGACCGTGTCTGGGACATGGCATCGACATTGAGATGA
1 T--GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGAC-TTGAGAT-A
* * * * * * * **
31180949 -AAGCTAGTGTAAGA-TATATCTGGGACATGCACCGGCCTCGAGACG
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGCATC-GACTTGAGATA
* ** * * ** *
31180994 TAAGCCAGTGTAA-AAAATGTCTTGGACATGCATCGGCTACA-AAA
1 TGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTTGAGATA
* *
31181038 TGATAGTCAGTGTAAGACCCTGTCTGGGACATTGCATCGACTTGAGATA
1 TG--AGCCAGTGTAAGACCATGTCTGGGACA-TGCATCGACTTGAGATA
*
31181087 TGAGCCAGTGTAAGACCATGTTTGGGAC
1 TGAGCCAGTGTAAGACCATGTCTGGGAC
31181115 GTAGCATCTA
Statistics
Matches: 162, Mismatches: 39, Indels: 29
0.70 0.17 0.13
Matches are distributed among these distances:
44 3 0.02
45 5 0.03
46 57 0.35
47 59 0.36
48 29 0.18
49 4 0.02
50 1 0.01
51 4 0.02
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (46 bp):
TGAGCCAGTGTAAGACCATGTCTGGGACATGCATCGACTTGAGATA
Found at i:31189405 original size:1 final size:1
Alignment explanation
Indices: 31189399--31189428 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
31189389 CTTCTTCCTC
31189399 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
31189429 GCAAATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:31191551 original size:18 final size:18
Alignment explanation
Indices: 31191528--31191631 Score: 63
Period size: 18 Copynumber: 5.8 Consensus size: 18
31191518 AAATTATCAC
31191528 TATTTTTATATATTATTA
1 TATTTTTATATATTATTA
*
31191546 TATTTTTCACATA-TATTA
1 TATTTTT-ATATATTATTA
*
31191564 TATATTTAT-TAATTATATA
1 TATTTTTATAT-ATTAT-TA
* * * *
31191583 TATATTTACATGTTATTT
1 TATTTTTATATATTATTA
* *
31191601 TA-TATTATAT-CTATTA
1 TATTTTTATATATTATTA
*
31191617 TAATTCTTATATATT
1 T-ATTTTTATATATT
31191632 TATATTACAT
Statistics
Matches: 65, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
16 6 0.09
17 8 0.12
18 31 0.48
19 19 0.29
20 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.60
Consensus pattern (18 bp):
TATTTTTATATATTATTA
Found at i:31191608 original size:44 final size:44
Alignment explanation
Indices: 31191556--31191674 Score: 123
Period size: 48 Copynumber: 2.6 Consensus size: 44
31191546 TATTTTTCAC
31191556 ATATATTATATATTTATTAATTATATATATAT-TTACATGTTATT
1 ATATATTATATATTTATT-ATTATATATATATATTACATGTTATT
* * * *
31191600 TTATATTATATCTATTATAATTCTTATATATTTATATTACATTTTATT
1 ATATATTATA--TATT-T-ATTATTATATATATATATTACATGTTATT
* * *
31191648 ATATAATATTTATTTATTTTTATATAT
1 ATATATTATATATTTATTATTATATAT
31191675 GTTATGTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
44 20 0.32
45 1 0.02
46 8 0.13
47 12 0.19
48 21 0.34
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (44 bp):
ATATATTATATATTTATTATTATATATATATATTACATGTTATT
Found at i:31197206 original size:32 final size:32
Alignment explanation
Indices: 31197165--31197226 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
31197155 AAATATTAGG
*
31197165 AAAACTTTATTTTTATTAATTTAGCCATTTAA
1 AAAACTTTATTTCTATTAATTTAGCCATTTAA
31197197 AAAACTTTATTTCTATTAATTTAGCCATTT
1 AAAACTTTATTTCTATTAATTTAGCCATTT
31197227 TAATTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.03, T:0.50
Consensus pattern (32 bp):
AAAACTTTATTTCTATTAATTTAGCCATTTAA
Found at i:31201525 original size:53 final size:54
Alignment explanation
Indices: 31201457--31201660 Score: 207
Period size: 53 Copynumber: 3.8 Consensus size: 54
31201447 TTTTCTTTTT
* * * *
31201457 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCTTTGCCTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTGCCTTATA
* * * *
31201510 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCTTTACCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTGCCTTATA
* * * * * *
31201564 GTAAC-CAATCAATACCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTT-TA
1 G-AACTC-ACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTGCCTTATA
* * * *
31201618 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATC
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATC
31201661 CTTATCTTAT
Statistics
Matches: 124, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
53 81 0.65
54 5 0.04
55 38 0.31
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.35
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCTTTGCCTTATA
Found at i:31201697 original size:47 final size:47
Alignment explanation
Indices: 31201642--31201763 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
31201632 CATGCCTTGG
* * *
31201642 CATGGTCTTACATGATATCCTTATCTTATCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
*
31201689 CATGGTCTTACATGGCATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
31201736 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
31201764 GTGCCAATGC
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 70 1.00
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:31202537 original size:30 final size:29
Alignment explanation
Indices: 31202501--31202557 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
31202491 TCCCTAACTC
* *
31202501 AAACTTTTTCAAAATTATAATTTTGCCCTT
1 AAAC-TTTACAAAATTACAATTTTGCCCTT
*
31202531 AAACTTTACAGAATTACAATTTTGCCC
1 AAACTTTACAAAATTACAATTTTGCCC
31202558 CTAGGCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.40
Consensus pattern (29 bp):
AAACTTTACAAAATTACAATTTTGCCCTT
Found at i:31206301 original size:40 final size:40
Alignment explanation
Indices: 31206104--31206307 Score: 245
Period size: 40 Copynumber: 5.1 Consensus size: 40
31206094 CGGAGTTTAA
** *
31206104 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31206144 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31206184 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
31206224 CCGGATTTA-TAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
31206263 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGT
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
31206303 CCGGA
1 CCGGA
31206308 CATCATTCGA
Statistics
Matches: 147, Mismatches: 12, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
38 3 0.02
39 33 0.22
40 100 0.68
41 11 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:31206307 original size:79 final size:81
Alignment explanation
Indices: 31206123--31206307 Score: 245
Period size: 79 Copynumber: 2.3 Consensus size: 81
31206113 GCTACTCGTT
*
31206123 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
31206187 GATTTAGTAACTCGCA
66 GATATAGTAACTAGCA
* **
31206203 CAAATGCCTTCGGGACTTAACCCGGATT-TA-TAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
*
31206265 GGATATAGTCACTTAGCA
65 GGATATAGTAAC-TAGCA
*
31206283 CAAA-GCCTTCGGGACTTAGTCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31206308 CATCATTCGA
Statistics
Matches: 93, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
78 3 0.03
79 55 0.59
80 33 0.35
81 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
GATATAGTAACTAGCA
Found at i:31209338 original size:42 final size:41
Alignment explanation
Indices: 31209157--31209344 Score: 161
Period size: 40 Copynumber: 4.6 Consensus size: 41
31209147 CCGCACCAAG
* * * * * *
31209157 GCCTACGGGACTTA-CCCGGATATCA-CGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATCAGCTACTAGCACAATT
* * * * *
31209196 GCCTTCGGGTCTTAGCCCGGATTTAAACAACTTGCACGAA-T
1 GCCTTCGGGTCTTAGCCCGGATATCAGCTACTAGCAC-AATT
31209237 GCCTTCGGGTCTTAGCCCGGATAT-AGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATCAGCTACTAGCACAATT
* * * *
31209277 GCCTTCGGGTCTTAACCCGGATATCA-CGATTTCAGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATCAGCTA-CT-AGCACAATT
* *
31209319 GTCTTCGGGGCTTAGCCCGGATATCA
1 GCCTTCGGGTCTTAGCCCGGATATCA
31209345 TTCAATTTCT
Statistics
Matches: 125, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 14 0.11
40 44 0.35
41 34 0.27
42 33 0.26
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (41 bp):
GCCTTCGGGTCTTAGCCCGGATATCAGCTACTAGCACAATT
Found at i:31210187 original size:17 final size:19
Alignment explanation
Indices: 31210164--31210209 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
31210154 AAGAAGCATG
31210164 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
31210182 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
31210200 AATCATGCTC
1 AATCATGCTC
31210210 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:31217305 original size:80 final size:80
Alignment explanation
Indices: 31217221--31217369 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
31217211 TATGGTAACC
* * * *
31217221 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
31217285 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
31217301 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
31217366 CCGG
66 CCGG
31217370 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:31217311 original size:40 final size:38
Alignment explanation
Indices: 31217262--31217369 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
31217252 ATCACGATTT
*
31217262 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
31217302 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
31217342 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
31217370 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:31219117 original size:18 final size:18
Alignment explanation
Indices: 31219086--31219126 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
31219076 GGGCTGTCAC
*
31219086 ATTCTGATTCTGATTCTA
1 ATTCTCATTCTGATTCTA
*
31219104 ATTCTCATTTTGATTCTA
1 ATTCTCATTCTGATTCTA
*
31219122 GTTCT
1 ATTCT
31219127 GATAATGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.54
Consensus pattern (18 bp):
ATTCTCATTCTGATTCTA
Found at i:31221771 original size:28 final size:27
Alignment explanation
Indices: 31221711--31221776 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 27
31221701 AGATAGCTAA
31221711 AAAAAGAAAG-GAAAAAAGAGGAAAAG
1 AAAAAGAAAGTGAAAAAAGAGGAAAAG
*
31221737 AATAAAGAAAGTGAAAAAA-ATGAGAGAAG
1 AA-AAAGAAAGTGAAAAAAGA-G-GAAAAG
31221766 AAAAAGAAAGT
1 AAAAAGAAAGT
31221777 AAAGATGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
26 2 0.06
27 9 0.26
28 17 0.49
29 7 0.20
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.06
Consensus pattern (27 bp):
AAAAAGAAAGTGAAAAAAGAGGAAAAG
Found at i:31225857 original size:40 final size:41
Alignment explanation
Indices: 31225813--31226037 Score: 270
Period size: 40 Copynumber: 5.7 Consensus size: 41
31225803 GCTACTCGTT
* * *
31225813 CAAATACCTTCGGGA-CATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATT-TAGTAACTCGCA
*
31225853 CAAATGCCTTCGGGA-CTTATCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
* *
31225893 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTAGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
*
31225933 CAAATGCCTTC-GGATCTTAGCCTGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
* * * *
31225973 CAATTGCCTTC-GGATCTTAGTCCAGATTT-GTAACTTAGCA
1 CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAAC-TCGCA
31226013 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTCGGGATCTTAGCCCGGA
31226038 CATCATTCGA
Statistics
Matches: 163, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
39 23 0.14
40 138 0.85
41 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.28
Consensus pattern (41 bp):
CAAATGCCTTCGGGATCTTAGCCCGGATTTAGTAACTCGCA
Found at i:31225934 original size:80 final size:80
Alignment explanation
Indices: 31225841--31226037 Score: 301
Period size: 80 Copynumber: 2.5 Consensus size: 80
31225831 AGCCCGGTTA
* * *
31225841 TAGTAGCTCGCACAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTCGCACAAATGCCTTCGG
1 TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGG
*
31225906 ATCTTAGTCCGGATT
66 ATCTTAGTCCAGATT
* *
31225921 TAGTAACTAGCACAAATGCCTTC-GGATCTTAGCCTGGATTTAGTAACTCGCACAATTGCCTTCG
1 TAGTAACTAGCACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCG
31225985 GATCTTAGTCCAGATT
65 GATCTTAGTCCAGATT
31226001 T-GTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TAGTAAC-TAGCACAAATGCCTTCGGGACTTAGCCCGGA
31226038 CATCATTCGA
Statistics
Matches: 107, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
79 24 0.22
80 83 0.78
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (80 bp):
TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGG
ATCTTAGTCCAGATT
Found at i:31233940 original size:38 final size:38
Alignment explanation
Indices: 31233876--31234050 Score: 234
Period size: 38 Copynumber: 4.6 Consensus size: 38
31233866 TACTCGTTCA
*
31233876 AATGCCTTCGGGACTTA-TCCCG-TTTAGTAACTCGCAC
1 AATGCCTTC-GGACTTAGTCCGGATTTAGTAACTCGCAC
31233913 AATGCCTTCGGACTTAGTCCGGATTTAGTAACTCGCAC
1 AATGCCTTCGGACTTAGTCCGGATTTAGTAACTCGCAC
31233951 AAATGCCTTCGGATCTTAG-CCGGATTTAGTAACTCGCAC
1 -AATGCCTTCGGA-CTTAGTCCGGATTTAGTAACTCGCAC
*
31233990 AATGCCTTCGGATCTTAGTCCGGA-TTAGT-ACTTAGCAC
1 AATGCCTTCGGA-CTTAGTCCGGATTTAGTAAC-TCGCAC
* *
31234028 AAAGCCTTCGGACTTAGCCCGGA
1 AATGCCTTCGGACTTAGTCCGGA
31234051 CATCATTCGA
Statistics
Matches: 128, Mismatches: 4, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
36 7 0.05
37 25 0.20
38 54 0.42
39 37 0.29
40 5 0.04
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (38 bp):
AATGCCTTCGGACTTAGTCCGGATTTAGTAACTCGCAC
Found at i:31234000 original size:77 final size:75
Alignment explanation
Indices: 31233874--31234048 Score: 257
Period size: 77 Copynumber: 2.3 Consensus size: 75
31233864 GCTACTCGTT
*
31233874 CAAATGCCTTCGGGACTTATCCCGTTTAGTAACTCGCACAATGCCTTCGGA-CTTAGTCCGGATT
1 CAAATGCCTTC-GGACTTAGCCCGTTTAGTAACTCGCACAATGCCTTCGGATCTTAGTCCGGA-T
*
31233938 TAGTAAC-TCGCA
64 TAGT-ACTTAGCA
*
31233950 CAAATGCCTTCGGATCTTAGCCGGATTTAGTAACTCGCACAATGCCTTCGGATCTTAGTCCGGAT
1 CAAATGCCTTCGGA-CTTAGCCCG-TTTAGTAACTCGCACAATGCCTTCGGATCTTAGTCCGGAT
31234015 TAGTACTTAGCA
64 TAGTACTTAGCA
31234027 CAAA-GCCTTCGGACTTAGCCCG
1 CAAATGCCTTCGGACTTAGCCCG
31234049 GACATCATTC
Statistics
Matches: 91, Mismatches: 4, Indels: 9
0.88 0.04 0.09
Matches are distributed among these distances:
75 11 0.12
76 29 0.32
77 40 0.44
78 11 0.12
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.28
Consensus pattern (75 bp):
CAAATGCCTTCGGACTTAGCCCGTTTAGTAACTCGCACAATGCCTTCGGATCTTAGTCCGGATTA
GTACTTAGCA
Found at i:31239825 original size:47 final size:47
Alignment explanation
Indices: 31239754--31240053 Score: 456
Period size: 47 Copynumber: 6.3 Consensus size: 47
31239744 CCCTTCGGGA
* * * * * *
31239754 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
31239801 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
31239848 CTTATCACATATATACACTTTCACATTCATCACATCGACCATTAGTC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31239895 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31239942 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
31239991 CTTATCACATATATATACACTTTCACATTCATCAACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATC-ACATCGGCCATTAGGC
31240041 CTTATCACATATA
1 CTTATCACATATA
31240054 CTATCATGTA
Statistics
Matches: 238, Mismatches: 12, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
47 137 0.58
48 5 0.02
49 72 0.30
50 24 0.10
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:31239832 original size:25 final size:25
Alignment explanation
Indices: 31239804--31239882 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
31239794 ACTCGGCCCT
31239804 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
31239829 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
31239851 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
31239876 ATCACAT
1 ATCACAT
31239883 CGACCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:31247789 original size:28 final size:29
Alignment explanation
Indices: 31247722--31247793 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 29
31247712 ATAGTGAATC
*
31247722 CGCACACTTAGTGCTATATACATTCAGCT
1 CGCACACTTAGTGCTATATACATTCAACT
31247751 CGCACACTTAGTGCTATATA-A-TCAAACT
1 CGCACACTTAGTGCTATATACATTC-AACT
31247779 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
31247794 GTACAATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 2 0.05
28 19 0.46
29 20 0.49
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATACATTCAACT
Found at i:31247815 original size:30 final size:28
Alignment explanation
Indices: 31247721--31247821 Score: 89
Period size: 28 Copynumber: 3.5 Consensus size: 28
31247711 TATAGTGAAT
* *
31247721 CCGCACACTTAGTGCTATATACATTC-AGC
1 CCGCACACTTAGTGC--TATACAATCAAAC
* *
31247750 TCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* * *
31247778 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATACAA--TCAAAC
31247808 CCGCACACTT-GTGC
1 CCGCACACTTAGTGC
31247822 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.11
28 22 0.36
29 18 0.30
30 14 0.23
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATCAAAC
Found at i:31253870 original size:2 final size:2
Alignment explanation
Indices: 31253863--31253979 Score: 234
Period size: 2 Copynumber: 58.5 Consensus size: 2
31253853 AGTGACAGCA
31253863 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
31253905 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
31253947 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31253980 ATATATATAT
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 115 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:31253984 original size:2 final size:2
Alignment explanation
Indices: 31253979--31254007 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31253969 TCTCTCTCTC
31253979 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31254008 TGGCAAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31255203 original size:32 final size:32
Alignment explanation
Indices: 31255167--31255231 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
31255157 ATTAATGTAA
31255167 TTTGTGTTAAGTTATTATTATTACTATTCCTT
1 TTTGTGTTAAGTTATTATTATTACTATTCCTT
*
31255199 TTTGTGTTAAGTTATTATTATTACTATTGCTT
1 TTTGTGTTAAGTTATTATTATTACTATTCCTT
31255231 T
1 T
31255232 CTATGCCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.60
Consensus pattern (32 bp):
TTTGTGTTAAGTTATTATTATTACTATTCCTT
Found at i:31268534 original size:21 final size:21
Alignment explanation
Indices: 31268510--31268549 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31268500 GCCTAATATG
*
31268510 TGAATTGGATTGAATTGAGTA
1 TGAATTGGATTAAATTGAGTA
*
31268531 TGAATTGTATTAAATTGAG
1 TGAATTGGATTAAATTGAG
31268550 CTAAATTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (21 bp):
TGAATTGGATTAAATTGAGTA
Found at i:31269040 original size:25 final size:26
Alignment explanation
Indices: 31268995--31269067 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
31268985 GCAGCTCTTA
* *
31268995 TGAGCGTCCTGA-TATATGGCTCCTTG
1 TGAGCTTCCTGATTA-AAGGCTCCTTG
*
31269021 -GAGCTT-CTCGATTAAAGGCTCTTTG
1 TGAGCTTCCT-GATTAAAGGCTCCTTG
*
31269046 TGAGCTTCCTGATTAATGGCTC
1 TGAGCTTCCTGATTAAAGGCTC
31269068 TCCGAAGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 2 0.05
25 16 0.41
26 19 0.49
27 2 0.05
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.36
Consensus pattern (26 bp):
TGAGCTTCCTGATTAAAGGCTCCTTG
Found at i:31269175 original size:49 final size:50
Alignment explanation
Indices: 31269112--31269238 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 50
31269102 CCGATATAAG
* *
31269112 GCTATACA-GAGCTTCTTGATTAATGGCTCTTCA-GAGCTACCCGTTAT-TG
1 GCTA-ACATGAGCTTCCTGATTAATGGCTCTT-ATGAGCTACCCGTTATATA
** * *
31269161 GCTCGCATGAGCTTCCTGAAT-ATGGCTCTTATGAGCTTCCCGTTATATA
1 GCTAACATGAGCTTCCTGATTAATGGCTCTTATGAGCTACCCGTTATATA
31269210 GCTAACATGAGCTTCCT-ATTAAATGGCTC
1 GCTAACATGAGCTTCCTGATT-AATGGCTC
31269239 GAGAGAGAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
47 1 0.02
48 26 0.41
49 30 0.47
50 7 0.11
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.34
Consensus pattern (50 bp):
GCTAACATGAGCTTCCTGATTAATGGCTCTTATGAGCTACCCGTTATATA
Found at i:31274995 original size:47 final size:47
Alignment explanation
Indices: 31274751--31275110 Score: 205
Period size: 47 Copynumber: 7.7 Consensus size: 47
31274741 TGATTTGTGT
* *
31274751 GCCAGAGTAAGACATGTCTGGGACATGCATCGGCCTCAACAGAGATA
1 GCCAGTGTAAGACATGTCTGGGACAGGCATCGGCCTCAACAGAGATA
* * ** *
31274798 GACAGTGTAAGACGTGTCTGGGACACACATCGG-CT-AAGC-GTTG-T-
1 GCCAGTGTAAGACATGTCTGGGACAGGCATCGGCCTCAA-CAG-AGATA
* * * * * *
31274842 GCTAGTGTAAGACATGTTTGGGACATGCATCAGCACACATA-A-ATGAGA
1 GCCAGTGTAAGACATGTCTGGGACAGGCATCGGC-CTCA-ACAGA-GATA
* *
31274890 GCCAGTGTAAGACCATGTTTGAGACATGGCATCGG---C-ACAGAGATGA
1 GCCAGTGTAAGA-CATGTCTGGGACA-GGCATCGGCCTCAACAGAGAT-A
*
31274936 GTGCCAGAGTAAGACATGTCTGGGACAGGCATCGGCCTCAACAGAGATA
1 --GCCAGTGTAAGACATGTCTGGGACAGGCATCGGCCTCAACAGAGATA
* * * * *
31274985 GCCAGTGTAAGACGTGTCTGGGACACGCATC-GACT-AAGAGTTG-TA
1 GCCAGTGTAAGACATGTCTGGGACAGGCATCGGCCTCAACAG-AGATA
** * * * *
31275030 -ATAGTGTAAGACATGTCTGGGACATGCATCAGCACGCATATATGAG--A
1 GCCAGTGTAAGACATGTCTGGGACAGGCATCGGC-CTCA-ACA-GAGATA
*
31275077 GCCAGTGTAAGACCATGTCTGGCACATGGCATCG
1 GCCAGTGTAAGA-CATGTCTGGGACA-GGCATCG
31275111 ACAATATATC
Statistics
Matches: 240, Mismatches: 43, Indels: 57
0.71 0.13 0.17
Matches are distributed among these distances:
44 53 0.22
45 14 0.06
46 22 0.09
47 70 0.29
48 35 0.15
49 27 0.11
50 19 0.08
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.21
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTCTGGGACAGGCATCGGCCTCAACAGAGATA
Found at i:31275050 original size:91 final size:91
Alignment explanation
Indices: 31274757--31275059 Score: 335
Period size: 91 Copynumber: 3.3 Consensus size: 91
31274747 GTGTGCCAGA
*
31274757 GTAAGACATGTCTGGGACATGCATCGGCCTCAACAGAGATAGACAGTGTAAGACGTGTCTGGGAC
1 GTAAGACATGTCTGGGACATGCATCGGCCTCAACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
* * **
31274822 ACACATCGGCTAAGCGTTGTGCTAGT
66 ACGCATCGGCTAAGAGTTGTAATAGT
* * * * * *
31274848 GTAAGACATGTTTGGGACATGCATCAGCACACATA-A-ATGAGAGCCAGTGTAAGACCATGTTTG
1 GTAAGACATGTCTGGGACATGCATCGGC-CTCA-ACAGA-GATAGCCAGTGTAAGA-CGTGTCTG
* * * * *
31274911 AGACATGGCATCGGC-ACAGAGATG-AGTGCCAGA
62 GGACA-CGCATCGGCTA-AGAGTTGTAAT---AGT
*
31274944 GTAAGACATGTCTGGGACAGGCATCGGCCTCAACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
1 GTAAGACATGTCTGGGACATGCATCGGCCTCAACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
*
31275009 ACGCATCGACTAAGAGTTGTAATAGT
66 ACGCATCGGCTAAGAGTTGTAATAGT
31275035 GTAAGACATGTCTGGGACATGCATC
1 GTAAGACATGTCTGGGACATGCATC
31275060 AGCACGCATA
Statistics
Matches: 170, Mismatches: 29, Indels: 26
0.76 0.13 0.12
Matches are distributed among these distances:
91 53 0.31
92 18 0.11
93 26 0.15
94 26 0.15
95 19 0.11
96 28 0.16
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (91 bp):
GTAAGACATGTCTGGGACATGCATCGGCCTCAACAGAGATAGCCAGTGTAAGACGTGTCTGGGAC
ACGCATCGGCTAAGAGTTGTAATAGT
Found at i:31275064 original size:187 final size:187
Alignment explanation
Indices: 31274749--31275110 Score: 609
Period size: 187 Copynumber: 1.9 Consensus size: 187
31274739 GGTGATTTGT
*
31274749 GTGCCAGAGTAAGACATGTCTGGGACATGCATCGGCCTCAACAGAGATAGACAGTGTAAGACGTG
1 GTGCCAGAGTAAGACATGTCTGGGACAGGCATCGGCCTCAACAGAGATAGACAGTGTAAGACGTG
* * ** *
31274814 TCTGGGACACACATCGGCTAAGCGTTGTGCTAGTGTAAGACATGTTTGGGACATGCATCAGCACA
66 TCTGGGACACACATCGACTAAGAGTTGTAATAGTGTAAGACATGTCTGGGACATGCATCAGCACA
*
31274879 CATAAATGAGAGCCAGTGTAAGACCATGTTTGAG-ACATGGCATCGGCACAGAGATGA
131 CATAAATGAGAGCCAGTGTAAGACCATGTCTG-GCACATGGCATCGGCACAGAGATGA
*
31274936 GTGCCAGAGTAAGACATGTCTGGGACAGGCATCGGCCTCAACAGAGATAGCCAGTGTAAGACGTG
1 GTGCCAGAGTAAGACATGTCTGGGACAGGCATCGGCCTCAACAGAGATAGACAGTGTAAGACGTG
* *
31275001 TCTGGGACACGCATCGACTAAGAGTTGTAATAGTGTAAGACATGTCTGGGACATGCATCAGCACG
66 TCTGGGACACACATCGACTAAGAGTTGTAATAGTGTAAGACATGTCTGGGACATGCATCAGCACA
*
31275066 CATATATGAGAGCCAGTGTAAGACCATGTCTGGCACATGGCATCG
131 CATAAATGAGAGCCAGTGTAAGACCATGTCTGGCACATGGCATCG
31275111 ACAATATATC
Statistics
Matches: 163, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
186 1 0.01
187 162 0.99
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (187 bp):
GTGCCAGAGTAAGACATGTCTGGGACAGGCATCGGCCTCAACAGAGATAGACAGTGTAAGACGTG
TCTGGGACACACATCGACTAAGAGTTGTAATAGTGTAAGACATGTCTGGGACATGCATCAGCACA
CATAAATGAGAGCCAGTGTAAGACCATGTCTGGCACATGGCATCGGCACAGAGATGA
Found at i:31282487 original size:40 final size:40
Alignment explanation
Indices: 31282429--31282616 Score: 270
Period size: 40 Copynumber: 4.7 Consensus size: 40
31282419 ATAACCACAA
* * * *
31282429 GCACAATTGCCTTTGGGTCTTAACCCGGGTATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
31282469 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
*
31282509 GCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
* *
31282549 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT-AGCAACTC
* *
31282589 GCATAAATGCCTTCGGGGCTTAGCCCGG
1 GCACAAATGCCTTCGGGTCTTAGCCCGG
31282617 GTATCATTCA
Statistics
Matches: 135, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 133 0.99
41 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTC
Found at i:31282514 original size:80 final size:79
Alignment explanation
Indices: 31282409--31282620 Score: 318
Period size: 80 Copynumber: 2.7 Consensus size: 79
31282399 TCTTCGGAAT
* * *
31282409 TTAG-CCGGATATAACCACAAGCACAATTGCCTTTGGGTCTTAACCCGGGTATAGCAACTCGCAC
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
31282473 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* *
31282488 TTAGCCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCAC
1 TTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCAC
31282553 AAATGCCTTCGGGTC
65 AAATGCCTTCGGGTC
* * *
31282568 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGGCTTAGCCCGGGTAT
1 TTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTAT
31282621 CATTCAAATG
Statistics
Matches: 120, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
79 5 0.04
80 114 0.95
81 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
TTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACA
AATGCCTTCGGGTC
Found at i:31284819 original size:12 final size:12
Alignment explanation
Indices: 31284802--31284826 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31284792 ATGTAAGTGA
31284802 TCTTGATGATTT
1 TCTTGATGATTT
31284814 TCTTGATGATTT
1 TCTTGATGATTT
31284826 T
1 T
31284827 TACATTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.16, T:0.60
Consensus pattern (12 bp):
TCTTGATGATTT
Found at i:31285733 original size:48 final size:48
Alignment explanation
Indices: 31285540--31285755 Score: 143
Period size: 47 Copynumber: 4.6 Consensus size: 48
31285530 GGTGATTTGT
* * *
31285540 GTGCCAGAGTAAGA-CATGTCTGGGACATGCATCAGC-CTCA-ACA-GA
1 GTGCCAGTGTAAGACCATGTCTGAGACATGCATCAGCAC-CAGAAATGA
** * *
31285585 GATAGCCAGTGTAAGA-TGTGTCTTG-GACATGCATCGGCTA--AG-AAT-T
1 G-T-GCCAGTGTAAGACCATGTC-TGAGACATGCATCAGC-ACCAGAAATGA
* * *
31285631 GTGCTAGTGTAAG-CCATGTCTGGGACATGCATCAGCACGCATAAATGA
1 GTGCCAGTGTAAGACCATGTCTGAGACATGCATCAGCAC-CAGAAATGA
* * *
31285679 GAGCCAGTGTAAGACCATGTCTGAGACATGACATCGGCA-CAGAGATGA
1 GTGCCAGTGTAAGACCATGTCTGAGACATG-CATCAGCACCAGAAATGA
* *
31285727 GTGCCAGAGTAAGA-CATGTCTAAGACATG
1 GTGCCAGTGTAAGACCATGTCTGAGACATG
31285756 TTTGGGACTT
Statistics
Matches: 134, Mismatches: 21, Indels: 30
0.72 0.11 0.16
Matches are distributed among these distances:
43 3 0.02
44 26 0.19
45 2 0.01
46 5 0.04
47 44 0.33
48 32 0.24
49 15 0.11
50 7 0.05
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (48 bp):
GTGCCAGTGTAAGACCATGTCTGAGACATGCATCAGCACCAGAAATGA
Found at i:31285887 original size:198 final size:198
Alignment explanation
Indices: 31285549--31285915 Score: 581
Period size: 198 Copynumber: 1.9 Consensus size: 198
31285539 TGTGCCAGAG
* *
31285549 TAAGACATGTCTGGGACATGCATCAGCCTCAACAGAGATAGCCAGTGTAAGATGTGTCTTGGACA
1 TAAGACATGTCTGGGACATGCATCAGCCTCAACAGAGATAGCCAGTGTAAAATGTGTCTGGGACA
* * * *
31285614 TGCATCGGCTAAGAATTGTGCTAGTGTAAGCCATGTCTGGGACATGCATCAGCACGCATAAATGA
66 CGCATAGGCTAAGAATTGTCCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCATAAATGA
31285679 GAGCCAGTGTAAGACCATGTCTGAGACATGACATCGGCACAGAGATGAGTGCCAGAGTAAGACAT
131 GAGCCAGTGTAAGACCATGTCTGAGACATGACATCGGCACAGAGATGAGTGCCAGAGTAAGACAT
31285744 GTC
196 GTC
* * * *
31285747 TAAGACATGTTTGGGACTTTCATCGGCCTCAACAGAGATAGCCAGTGTAAAATGTGTCTGGGACA
1 TAAGACATGTCTGGGACATGCATCAGCCTCAACAGAGATAGCCAGTGTAAAATGTGTCTGGGACA
* * * *
31285812 CGCATAGGCTAAGAGTTGTCCTTGTGTAAGACATGTTTGGGACATGCATCAGCACGCATATATGA
66 CGCATAGGCTAAGAATTGTCCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCATAAATGA
* * *
31285877 GAGCCAGTGTAAGACCATGTCTGGGATATGGCATCGGCA
131 GAGCCAGTGTAAGACCATGTCTGAGACATGACATCGGCA
31285916 ATATATACCA
Statistics
Matches: 152, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
198 152 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (198 bp):
TAAGACATGTCTGGGACATGCATCAGCCTCAACAGAGATAGCCAGTGTAAAATGTGTCTGGGACA
CGCATAGGCTAAGAATTGTCCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGCATAAATGA
GAGCCAGTGTAAGACCATGTCTGAGACATGACATCGGCACAGAGATGAGTGCCAGAGTAAGACAT
GTC
Found at i:31287302 original size:16 final size:16
Alignment explanation
Indices: 31287283--31287353 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
31287273 GTTTGGTTTA
*
31287283 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
*
31287299 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
31287315 CTATAATGGAGTAGAG
1 CTGTAATGGAATAGAG
* *
31287331 TTGTACTGGAATAGAG
1 CTGTAATGGAATAGAG
31287347 CTGTAAT
1 CTGTAAT
31287354 CAGTAATTCA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.30
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:31287530 original size:25 final size:26
Alignment explanation
Indices: 31287501--31287550 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
31287491 TAGATAAATA
*
31287501 ATTATTGTT-ATTAAATTTTAATAAG
1 ATTATTGTTAAATAAATTTTAATAAG
*
31287526 ATTATTGTTAAATATATTTTAATAA
1 ATTATTGTTAAATAAATTTTAATAA
31287551 AAATAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (26 bp):
ATTATTGTTAAATAAATTTTAATAAG
Found at i:31287578 original size:59 final size:57
Alignment explanation
Indices: 31287526--31287649 Score: 149
Period size: 59 Copynumber: 2.1 Consensus size: 57
31287516 TTTTAATAAG
* * *
31287526 ATTATTGTTAAATATATTTTAATAAAAATAAAAAAATAATTTAATCATATTTTAACATA
1 ATTATTATTAAATACAATTTAAT-AAAAT-AAAAAATAATTTAATCATATTTTAACATA
* * * * *
31287585 ATTATTATTAAATACAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATA
1 ATTATTATTAAATACAATTTAATAAAATAAAAAATAATTTAATCATATT-TTAACATA
31287643 ATTATTA
1 ATTATTA
31287650 ATAATATTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
57 17 0.30
58 19 0.34
59 20 0.36
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (57 bp):
ATTATTATTAAATACAATTTAATAAAATAAAAAATAATTTAATCATATTTTAACATA
Found at i:31287627 original size:12 final size:11
Alignment explanation
Indices: 31287600--31287674 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 11
31287590 TATTAAATAC
31287600 AATTTAATAA-
1 AATTTAATAAT
31287610 AA--TAATATAT
1 AATTTAATA-AT
*
31287620 AATTTAATAAC
1 AATTTAATAAT
*
31287631 ATTCTTAAT-AT
1 AAT-TTAATAAT
31287642 AATTATTAATAAT
1 AA-T-TTAATAAT
31287655 -ATTTAATAAT
1 AATTTAATAAT
31287665 AATTTTAATA
1 AA-TTTAATA
31287675 TAAAATTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
8 5 0.10
9 1 0.02
10 12 0.24
11 7 0.14
12 24 0.47
13 2 0.04
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:31287666 original size:13 final size:12
Alignment explanation
Indices: 31287612--31287674 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
31287602 TTTAATAAAA
31287612 TAATATATAA-TT
1 TAATA-ATAATTT
*
31287624 TAATAA-CATTCT
1 TAATAATAATT-T
31287636 TAAT-ATAATTAT
1 TAATAATAATT-T
31287648 TAATAAT-A-TT
1 TAATAATAATTT
31287658 TAATAATAATTT
1 TAATAATAATTT
31287670 TAATA
1 TAATA
31287675 TAAAATTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
10 9 0.21
11 5 0.12
12 26 0.62
13 2 0.05
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATAATAATTT
Found at i:31293898 original size:40 final size:39
Alignment explanation
Indices: 31293807--31293957 Score: 126
Period size: 40 Copynumber: 3.8 Consensus size: 39
31293797 ATAACCACGT
* * *
31293807 GCACAAATGCCTTTGGGTCTTAGCCCGGATAGAATGTCTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
*
31293847 GCACGAATGCCTTCGGGTCTTAGCCCGGAT-GTA-GCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATAGAATG--ACTA
* * ** *
31293887 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
* * *
31293927 GCATAATTGTCTTCGGGGCTTAGCCCGGATA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATA
31293958 TCATTCAATT
Statistics
Matches: 91, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
38 1 0.01
39 4 0.04
40 85 0.93
41 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.27
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTA
Found at i:31293941 original size:80 final size:80
Alignment explanation
Indices: 31293807--31293956 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
31293797 ATAACCACGT
* * *
31293807 GCACAAATGCCTTTGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC
31293872 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * * * *
31293887 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGGCTTAG
31293950 CCCGGAT
64 CCCGGAT
31293957 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 3 0.05
80 57 0.95
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:31302007 original size:16 final size:17
Alignment explanation
Indices: 31301981--31302013 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
31301971 ACTAAATTTT
31301981 CCTTTTCTTTTTCTTTC
1 CCTTTTCTTTTTCTTTC
31301998 CCTTTT-TTTTTCTTTC
1 CCTTTTCTTTTTCTTTC
31302014 TTTCCCTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
CCTTTTCTTTTTCTTTC
Found at i:31302139 original size:21 final size:21
Alignment explanation
Indices: 31302076--31302141 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
31302066 TCTTTTATTT
* * *
31302076 ATTATAACTATTATATTATATC
1 ATTATAATTATTATATTTTA-A
*
31302098 ATTATTATTATTATATTTTAA
1 ATTATAATTATTATATTTTAA
31302119 ATTATAATTATTAT-TTCTTAA
1 ATTATAATTATTATATT-TTAA
31302140 AT
1 AT
31302142 ATTAAGTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
20 2 0.05
21 19 0.50
22 17 0.45
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTATAATTATTATATTTTAA
Found at i:31303885 original size:53 final size:54
Alignment explanation
Indices: 31303808--31304005 Score: 188
Period size: 53 Copynumber: 3.7 Consensus size: 54
31303798 TTTTTAAACC
* *
31303808 TACCATTG-CATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAACT
1 TACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACT
* * * * * * * **
31303860 CACCATTGTCATGCCTTGGCATGGTCTTACATGGGATCGTTGCCTTATCGTAGTT
1 TACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG-AACT
* * * * * *
31303915 TATCAATGCCATGTCTTGACATGGT-TTACATGATTTCCTTGCCTTGTAAAACT
1 TACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACT
*
31303968 TACCAATGCCATGCCTTGGCATGGTCTTA-ATTGGTATC
1 TACCAATGCCATGCCTTGACATGGTCTTACA-TGGTATC
31304006 ATTAAACTCT
Statistics
Matches: 114, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
52 7 0.06
53 60 0.53
54 26 0.23
55 21 0.18
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (54 bp):
TACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAGAACT
Found at i:31304134 original size:20 final size:20
Alignment explanation
Indices: 31304109--31304149 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
31304099 ATCATCAAGG
31304109 AATAAATTTACAAAATAAAT
1 AATAAATTTACAAAATAAAT
31304129 AATAAATTTACAAAATAAAT
1 AATAAATTTACAAAATAAAT
31304149 A
1 A
31304150 TATAGATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (20 bp):
AATAAATTTACAAAATAAAT
Found at i:31323592 original size:40 final size:40
Alignment explanation
Indices: 31323548--31323727 Score: 161
Period size: 40 Copynumber: 4.5 Consensus size: 40
31323538 GCTCGATTGT
* * *
31323548 CTTCGGGACATAGCCCGG-TTATAGTGATTCGCACAATTGC
1 CTTCGGGACATAGCCCGGATT-TAGTAACTCGCACAAATGC
*
31323588 CTTCGGGA-ATTAGCCCGGATTTAGTAACTCGCATAAATGC
1 CTTCGGGACA-TAGCCCGGATTTAGTAACTCGCACAAATGC
* * * * * * *
31323628 CTTGGGGACTTAACCCGGTTTTGGTAACTCGCACCAATGG
1 CTTCGGGACATAGCCCGGATTTAGTAACTCGCACAAATGC
* * *
31323668 CTTCGGGA-ATTA-CCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACA-TAGCCCGGATTTAGTAAC-TCGCACAAATGC
*
31323708 CTTCGGGACTTAGCCCGGAT
1 CTTCGGGACATAGCCCGGAT
31323728 ATCATTCGAA
Statistics
Matches: 111, Mismatches: 22, Indels: 13
0.76 0.15 0.09
Matches are distributed among these distances:
39 13 0.12
40 89 0.80
41 9 0.08
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (40 bp):
CTTCGGGACATAGCCCGGATTTAGTAACTCGCACAAATGC
Found at i:31323647 original size:80 final size:80
Alignment explanation
Indices: 31323548--31323725 Score: 216
Period size: 80 Copynumber: 2.2 Consensus size: 80
31323538 GCTCGATTGT
* * *
31323548 CTTCGGGACATAGCCCGGTTATAGTGATTCGCA-CAATTGCCTTCGGGAATTAGCCCGGATTTAG
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACCAA-TGCCTTCGGGAATTA-CCCGGATTTAG
* * *
31323612 TAAC-TCGCATAAATGC
64 TAACTTAGCACAAAAGC
* * * * * *
31323628 CTTGGGGACTTAACCCGGTTTTGGTAACTCGCACCAATGGCTTCGGGAATTACCCGGATTTAGTC
1 CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACCAATGCCTTCGGGAATTACCCGGATTTAGTA
31323693 ACTTAGCACAAAAGC
66 ACTTAGCACAAAAGC
31323708 CTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGG
31323726 ATATCATTCG
Statistics
Matches: 82, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
79 14 0.17
80 65 0.79
81 3 0.04
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGTTATAGTAACTCGCACCAATGCCTTCGGGAATTACCCGGATTTAGTA
ACTTAGCACAAAAGC
Found at i:31325797 original size:29 final size:28
Alignment explanation
Indices: 31325765--31325867 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
31325755 GTGACGAGAT
* *
31325765 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
31325794 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
31325823 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
31325852 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
31325868 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Done.