Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008654.1 Hibiscus syriacus cultivar Beakdansim tig00111648_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3533819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 18
Found at i:2232392 original size:13 final size:14
Alignment explanation
Indices: 2232363--2232390 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2232353 GAATGAGGTT
2232363 ATATGACCCTAAAA
1 ATATGACCCTAAAA
2232377 ATATGACCCTAAAA
1 ATATGACCCTAAAA
2232391 TACTTCCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (14 bp):
ATATGACCCTAAAA
Found at i:2235835 original size:21 final size:21
Alignment explanation
Indices: 2235811--2235863 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 21
2235801 GTCAGAATTA
*
2235811 TAAAATTTTAAAATTTTATTT
1 TAAAATTTTAAAAATTTATTT
* *
2235832 TAAAAAATTAAAAAATTTATTT
1 T-AAAATTTTAAAAATTTATTT
*
2235854 AAAAATTTTA
1 TAAAATTTTA
2235864 TATGCTTGAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATTTTAAAAATTTATTT
Found at i:2236270 original size:65 final size:65
Alignment explanation
Indices: 2236128--2236332 Score: 322
Period size: 65 Copynumber: 3.2 Consensus size: 65
2236118 ATTTCAAATG
* * *
2236128 AAGTTTGAGTTATAAAATAAGATTCGAATAACTTGAAA-TTTTAGTAATTAGTGGATTGGTTTTT
1 AAGTTTGAGTTATAAAATAAGACTCGAATAACTTAAAATTTTTAGTAATTAGTGGATTGGTTTTC
*
2236192 AAGTTTGAGTTATAAAATAAGACTCGAATAACTTTAAATTTTTAGTAATTAGTGGATTGGTTTTC
1 AAGTTTGAGTTATAAAATAAGACTCGAATAACTTAAAATTTTTAGTAATTAGTGGATTGGTTTTC
* * * * *
2236257 AAGCTTGAATTATAAAATAAGACTCGAATAACTCAAAATTTTTAGTAATTAGTGAATTGATTTTC
1 AAGTTTGAGTTATAAAATAAGACTCGAATAACTTAAAATTTTTAGTAATTAGTGGATTGGTTTTC
2236322 AAGTTTGAGTT
1 AAGTTTGAGTT
2236333 GAGTCTCTCA
Statistics
Matches: 129, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 36 0.28
65 93 0.72
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.40
Consensus pattern (65 bp):
AAGTTTGAGTTATAAAATAAGACTCGAATAACTTAAAATTTTTAGTAATTAGTGGATTGGTTTTC
Found at i:2245402 original size:19 final size:19
Alignment explanation
Indices: 2245367--2245406 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
2245357 ATATTAACAA
*
2245367 TAAATAACTTAATTGATATT
1 TAAATAACTTAAGTGAT-TT
2245387 TAAATAA-TTAAGTGATTT
1 TAAATAACTTAAGTGATTT
2245405 TA
1 TA
2245407 TTGACAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 8 0.42
20 7 0.37
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (19 bp):
TAAATAACTTAAGTGATTT
Found at i:2249783 original size:31 final size:31
Alignment explanation
Indices: 2249735--2249805 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
2249725 AAAATAAGTT
*
2249735 CCTAAAGTATATCACATTTTTCATCTAGGTA
1 CCTAAAGTATATCACATTTTTCATCTAGATA
*
2249766 CCTAGAGTATA-CGACATTTTTCATCTAGATA
1 CCTAAAGTATATC-ACATTTTTCATCTAGATA
2249797 CCTAAAGTA
1 CCTAAAGTA
2249806 ATTTTTAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.03
31 35 0.97
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (31 bp):
CCTAAAGTATATCACATTTTTCATCTAGATA
Found at i:2249993 original size:59 final size:61
Alignment explanation
Indices: 2249894--2250040 Score: 165
Period size: 59 Copynumber: 2.4 Consensus size: 61
2249884 CACTTTAGAT
* * ** *
2249894 AAAAGAATGATATACTTTAGGTACTTACCTTGA-TTGAAAAATACTT-TAGGTACCTAGA-CA
1 AAAAG-ATGATATACTTTATGTACCTACCTTGACTAAAAAAATA-TTGTAGATACCTAGATCA
* * * *
2249954 AAAAGGTGATATACTTTATGTACCTACTTTGACTAAAAAAATATTGTAGATGCCTAGATGA
1 AAAAGATGATATACTTTATGTACCTACCTTGACTAAAAAAATATTGTAGATACCTAGATCA
*
2250015 AAAATATGATATACTTTATGTACCTA
1 AAAAGATGATATACTTTATGTACCTA
2250041 TTTCTAGAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
59 25 0.34
60 23 0.32
61 25 0.34
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (61 bp):
AAAAGATGATATACTTTATGTACCTACCTTGACTAAAAAAATATTGTAGATACCTAGATCA
Found at i:2252449 original size:30 final size:30
Alignment explanation
Indices: 2252380--2252454 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 30
2252370 GGCAAGTACA
2252380 AAAATAAAACAAAAAGTAAATGTTAGGTATG
1 AAAATAAAACAAAAAG-AAATGTTAGGTATG
*** * *
2252411 ATTTTAAAACAAACAA-AAATTTTAGGTATT
1 AAAATAAAACAAA-AAGAAATGTTAGGTATG
*
2252441 AAAATAAAATAAAA
1 AAAATAAAACAAAA
2252455 TTAATAGTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
29 1 0.03
30 21 0.62
31 10 0.29
32 2 0.06
ACGTcount: A:0.60, C:0.04, G:0.09, T:0.27
Consensus pattern (30 bp):
AAAATAAAACAAAAAGAAATGTTAGGTATG
Found at i:2253038 original size:22 final size:22
Alignment explanation
Indices: 2253000--2253042 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
2252990 TTAATATCTC
2253000 ATTTAAAAGCTTGAAAATAAATA
1 ATTTAAAAGCTTGAAAA-AAATA
2253023 ATTTAAAAG-TTGAAAAAAAT
1 ATTTAAAAGCTTGAAAAAAAT
2253043 TAAAAAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.30
Consensus pattern (22 bp):
ATTTAAAAGCTTGAAAAAAATA
Found at i:2253821 original size:75 final size:75
Alignment explanation
Indices: 2253740--2253893 Score: 290
Period size: 75 Copynumber: 2.1 Consensus size: 75
2253730 GGGAGTCTCG
*
2253740 CCCCAATATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCATGGATGCTACGGTG
1 CCCCAATATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCATGGATGCTACAGTG
2253805 CTTGCAAATT
66 CTTGCAAATT
*
2253815 CCCCAATATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCGTGGATGCTACAGTG
1 CCCCAATATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCATGGATGCTACAGTG
2253880 CTTGCAAATT
66 CTTGCAAATT
2253890 CCCC
1 CCCC
2253894 GGTTCTAAAG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (75 bp):
CCCCAATATGTGATAATATGAATGATGATGAATCAATGGGTGGTGTTCCCATGGATGCTACAGTG
CTTGCAAATT
Found at i:2259094 original size:36 final size:34
Alignment explanation
Indices: 2258906--2259141 Score: 179
Period size: 37 Copynumber: 6.4 Consensus size: 34
2258896 ACATATAGCG
* *
2258906 TATATAATATATAGTGTTGAAAACAGTTTTTTTAAAAATA
1 TATATAATATATAGTTTTGAAAACA----TTTT-GAAA-A
* *
2258946 TATATAATATATAGTTTTGAGAAATATTTTGAATA
1 TATATAATATATAGTTTTGA-AAACATTTTGAAAA
2258981 TATATAATATATATAGTTTTGAAAACATTTTCGAAAA
1 TATAT-A-ATATATAGTTTTGAAAACATTTT-GAAAA
*
2259018 TATACATAATATATAGTTTT-AAAACGTTATTGAAAA
1 TAT--ATAATATATAGTTTTGAAAACATT-TTGAAAA
*
2259054 TATATAATATATA-TTTTAGAAAACATGTTGGAAAA
1 TATATAATATATAGTTTT-GAAAACAT-TTTGAAAA
* * **
2259089 CTATATAATATTTGGGTTTTGAAAATGTTTTTTGAAATA
1 -TATATAATATAT-AGTTTTGAAAA--CATTTTGAAA-A
2259128 TATATATATATATA
1 TATATA-ATATATA
2259142 TTATAGTATA
Statistics
Matches: 163, Mismatches: 16, Indels: 36
0.76 0.07 0.17
Matches are distributed among these distances:
33 4 0.02
34 10 0.06
35 18 0.11
36 38 0.23
37 44 0.27
38 17 0.10
39 9 0.06
40 19 0.12
41 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (34 bp):
TATATAATATATAGTTTTGAAAACATTTTGAAAA
Found at i:2259161 original size:6 final size:6
Alignment explanation
Indices: 2259152--2259179 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2259142 TTATAGTATA
2259152 TTTATT TTTATT TTTATT TTTATT TTTA
1 TTTATT TTTATT TTTATT TTTATT TTTA
2259180 GGTCCAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:2260504 original size:20 final size:21
Alignment explanation
Indices: 2260468--2260506 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2260458 GTATTTAACT
2260468 TTTTTTTTATTTATTTTATCC
1 TTTTTTTTATTTATTTTATCC
*
2260489 TTTTTTTTGTTT-TTTTAT
1 TTTTTTTTATTTATTTTAT
2260507 ATTTATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.10, C:0.05, G:0.03, T:0.82
Consensus pattern (21 bp):
TTTTTTTTATTTATTTTATCC
Found at i:2261615 original size:17 final size:17
Alignment explanation
Indices: 2261583--2261614 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2261573 ATTTTTTTCC
2261583 TTTTCCTTTTATTTTTG
1 TTTTCCTTTTATTTTTG
2261600 TTTT-CTTTTATTTTT
1 TTTTCCTTTTATTTTT
2261615 TATCATTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.06, C:0.09, G:0.03, T:0.81
Consensus pattern (17 bp):
TTTTCCTTTTATTTTTG
Found at i:2274379 original size:33 final size:33
Alignment explanation
Indices: 2274315--2274379 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
2274305 TTTTTTCAAA
* *
2274315 AATATATAATATATAGTTTTGAGAAATTTTTTG
1 AATATATAATATATAGTTTGGAGAAAATTTTTG
*
2274348 AATATATGATATATAGTTTGGA-AAACATTTTT
1 AATATATAATATATAGTTTGGAGAAA-ATTTTT
2274380 CAAAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (33 bp):
AATATATAATATATAGTTTGGAGAAAATTTTTG
Found at i:2274393 original size:33 final size:33
Alignment explanation
Indices: 2274306--2274393 Score: 79
Period size: 33 Copynumber: 2.6 Consensus size: 33
2274296 TTGAAAGCAT
* *
2274306 TTTTTCAAAAATATATAATATATAGTTTTGAGAAA
1 TTTTTCAAAAA-A-ATAATATATAGTTTGGAAAAA
** * * *
2274341 TTTTTTGAATATATGATATATAGTTTGGAAAACA
1 TTTTTCAAAAAAATAATATATAGTTTGGAAAA-A
2274375 TTTTTCAAAAAAAT-ATATA
1 TTTTTCAAAAAAATAATATA
2274394 ATATATATTT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
33 22 0.54
34 11 0.27
35 8 0.20
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.43
Consensus pattern (33 bp):
TTTTTCAAAAAAATAATATATAGTTTGGAAAAA
Found at i:2274416 original size:70 final size:71
Alignment explanation
Indices: 2274279--2274434 Score: 187
Period size: 70 Copynumber: 2.2 Consensus size: 71
2274269 TACATATAAC
* * *
2274279 ATATATAATACATAGTGTTGAAAGCATTTTTTCAAAAATATATAATATATAGTTTTGAGAAATTT
1 ATATATAATATATAGTGTTGAAAACATTTTTTCAAAAATATATAATATATAGTTTTGAGAAAGTT
2274344 TTTG-A
66 TTTGAA
* *
2274349 ATATATGATATATAGT-TTGGAAAACA-TTTTTCAAAAAAATATATAATATATA-TTTTTA-AAA
1 ATATATAATATATAGTGTT-GAAAACATTTTTTC--AAAAATATATAATATATAGTTTTGAGAAA
2274410 CGTTTTTGAAA
63 -GTTTTTG-AA
2274421 ATATATAATATATA
1 ATATATAATATATA
2274435 TTTTTAAAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
69 11 0.15
70 31 0.42
71 18 0.24
72 14 0.19
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (71 bp):
ATATATAATATATAGTGTTGAAAACATTTTTTCAAAAATATATAATATATAGTTTTGAGAAAGTT
TTTGAA
Found at i:2274427 original size:34 final size:34
Alignment explanation
Indices: 2274279--2274541 Score: 199
Period size: 34 Copynumber: 7.4 Consensus size: 34
2274269 TACATATAAC
* * * *
2274279 ATATATAATACATAGTGTTGAAAGCATTTTTTCAAAA
1 ATATATAATATATA-TTTTGAAAACA-TTTTT-GAAA
*
2274316 ATATATAATATATAGTTTTGAGAAA-TTTTTTG--A
1 ATATATAATATATA-TTTTGA-AAACATTTTTGAAA
* * *
2274349 ATATATGATATATAGTTTGGAAAACATTTTTCAAAAAA
1 ATATATAATATATA-TTTTGAAAACATTTTT---GAAA
* *
2274387 ATATATAATATATATTTTTAAAACGTTTTTGAAA
1 ATATATAATATATATTTTGAAAACATTTTTGAAA
* ***
2274421 ATATATAATATATATTTTTAAAATGGTTTTGAAA
1 ATATATAATATATATTTTGAAAACATTTTTGAAA
* * *
2274455 ATATATAATATATATTTTAAAAACATGTTGGAAA
1 ATATATAATATATATTTTGAAAACATTTTTGAAA
* * * *
2274489 ACTATATAATATTTGGGTTTTGAAAACATTTTTCAAT
1 A-TATATAATATAT--ATTTTGAAAACATTTTTGAAA
2274526 ATATATATATATATAT
1 ATATATA-ATATATAT
2274542 ATATATACTT
Statistics
Matches: 184, Mismatches: 31, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
32 3 0.02
33 25 0.14
34 64 0.35
35 12 0.07
36 11 0.06
37 53 0.29
38 16 0.09
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.43
Consensus pattern (34 bp):
ATATATAATATATATTTTGAAAACATTTTTGAAA
Found at i:2274531 original size:2 final size:2
Alignment explanation
Indices: 2274524--2274548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2274514 ACATTTTTCA
2274524 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2274549 CTTGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2275831 original size:17 final size:18
Alignment explanation
Indices: 2275797--2275831 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2275787 AAATTTAACA
*
2275797 TTTTTATTTT-TTATTTT
1 TTTTTATTTTAATATTTT
2275814 TTTTTATTTTAATATTTT
1 TTTTTATTTTAATATTTT
2275832 CTTAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTATTTTAATATTTT
Found at i:2275846 original size:37 final size:37
Alignment explanation
Indices: 2275805--2275881 Score: 120
Period size: 37 Copynumber: 2.1 Consensus size: 37
2275795 CATTTTTATT
**
2275805 TTTTATTT-TTTTTTATTTTAATATTTTCTTAATTTTA
1 TTTTATTTGTTTTTT-TTAAAATATTTTCTTAATTTTA
2275842 TTTTATTTGTTTTTTTTAAAATATTTTCTTAATTTTA
1 TTTTATTTGTTTTTTTTAAAATATTTTCTTAATTTTA
2275879 TTT
1 TTT
2275882 CTTTTCGTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 31 0.84
38 6 0.16
ACGTcount: A:0.22, C:0.03, G:0.01, T:0.74
Consensus pattern (37 bp):
TTTTATTTGTTTTTTTTAAAATATTTTCTTAATTTTA
Found at i:2275897 original size:32 final size:32
Alignment explanation
Indices: 2275805--2275898 Score: 107
Period size: 37 Copynumber: 2.8 Consensus size: 32
2275795 CATTTTTATT
2275805 TTTTATTTTTTTTTATTTTAATATTTTCTTAA
1 TTTTATTTTTTTTTATTTTAATATTTTCTTAA
*
2275837 TTTTATTTTATTTGTTTTTTTTAAAATATTTTCTTAA
1 TTTTA-TTT-TTT-TTTATTTT--AATATTTTCTTAA
* **
2275874 TTTTATTTCTTTTCGTTTTAATATT
1 TTTTATTTTTTTTTATTTTAATATT
2275899 GTGTATTTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
32 11 0.21
33 3 0.06
34 9 0.17
35 9 0.17
36 3 0.06
37 18 0.34
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.72
Consensus pattern (32 bp):
TTTTATTTTTTTTTATTTTAATATTTTCTTAA
Found at i:2285504 original size:89 final size:89
Alignment explanation
Indices: 2285393--2285665 Score: 270
Period size: 89 Copynumber: 3.1 Consensus size: 89
2285383 TACAAGAACC
* * *
2285393 AAAATAGCAAAAACATAAACTTAAAGGACCAAAATAGTACAAACATG-AATTTAAAGGACTAAAA
1 AAAATAGCAAAAACAGAAACTTAAAGGACTAAAATAGTA-AAACA-GAAACTTAAAGGACTAAAA
*
2285457 TAATAAAAACAAAAACTTAAAGGGCT
64 TAACAAAAACAAAAACTTAAAGGGCT
* *
2285483 AAAA-AG-AATAAACAGAAACTTAAAAGG-CTAAAACAGCAAAAACAGAAACTTAAAGGACT-AA
1 AAAATAGCAA-AAACAGAAACTT-AAAGGACTAAAATAG-TAAAACAGAAACTTAAAGGACTAAA
* * * **
2285544 ACAACAAAAACATAAACCTAAAGGATT
63 ATAACAAAAACAAAAACTTAAAGGGCT
* * * * *
2285571 AAAATAGCAAAAATAGATACTTAAAAGACTAAAATAGCTAAAACAGAAAGTTAAAAGACTAAAAT
1 AAAATAGCAAAAACAGAAACTTAAAGGACTAAAATAG-TAAAACAGAAACTTAAAGGACTAAAAT
* * *
2285636 AGCAAAAATAGAAACTT-AAGGGACT
65 AACAAAAACAAAAACTTAAAGGG-CT
2285661 AAAAT
1 AAAAT
2285666 GGTATTAACA
Statistics
Matches: 149, Mismatches: 25, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
88 34 0.23
89 81 0.54
90 34 0.23
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (89 bp):
AAAATAGCAAAAACAGAAACTTAAAGGACTAAAATAGTAAAACAGAAACTTAAAGGACTAAAATA
ACAAAAACAAAAACTTAAAGGGCT
Found at i:2285505 original size:29 final size:30
Alignment explanation
Indices: 2285393--2285665 Score: 279
Period size: 30 Copynumber: 9.2 Consensus size: 30
2285383 TACAAGAACC
* *
2285393 AAAATAGCAAAAACATAAACTTAAAGGACC
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
2285423 AAAATAGTACAAACATG-AATTTAAAGGACT
1 AAAATAGCAAAAACA-GAAACTTAAAGGACT
** * *
2285453 AAAATAATAAAAACAAAAACTTAAAGGGCT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
2285483 AAAA-AG-AATAAACAGAAACTTAAAAGG-CT
1 AAAATAGCAA-AAACAGAAACTT-AAAGGACT
*
2285512 AAAACAGCAAAAACAGAAACTTAAAGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
2285542 AAACA-A-CAAAAACATAAACCTAAAGGATT
1 AAA-ATAGCAAAAACAGAAACTTAAAGGACT
* * *
2285571 AAAATAGCAAAAATAGATACTTAAAAGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
2285601 AAAATAGCTAAAACAGAAAGTTAAAAGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* *
2285631 AAAATAGCAAAAATAGAAACTTAAGGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
2285661 AAAAT
1 AAAAT
2285666 GGTATTAACA
Statistics
Matches: 203, Mismatches: 30, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
28 3 0.01
29 47 0.23
30 150 0.74
31 3 0.01
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (30 bp):
AAAATAGCAAAAACAGAAACTTAAAGGACT
Found at i:2285693 original size:60 final size:60
Alignment explanation
Indices: 2285393--2285686 Score: 183
Period size: 59 Copynumber: 5.0 Consensus size: 60
2285383 TACAAGAACC
* * * * * * *
2285393 AAAATAGCAAAAACATAAACTTAAAGGACCAAAATAG-TACAAACATG-AATTTAAAGGACT
1 AAAATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTA-AAACA-GAAAATCAAAAGACT
** * * * * * * * *
2285453 AAAATAATAAAAACAAAAACTTAAAGGGCTAAAA-AG-AATAAACAGAAACTTAAAAGGCT
1 AAAATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTA-AAACAGAAAATCAAAAGACT
* * * * * * * *
2285512 AAAACAGCAAAAACAGAAACTTAAAGGACTAAACA-A-CAAAAACA-TAAACCTAAAGGATT
1 AAAATAGCAAAAATAGAAACTTAAAAGACTAAA-ATAGCTAAAACAGAAAATC-AAAAGACT
* * *
2285571 AAAATAGCAAAAATAGATACTTAAAAGACTAAAATAGCTAAAACAGAAAGTTAAAAGACT
1 AAAATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTAAAACAGAAAATCAAAAGACT
** * *
2285631 AAAATAGCAAAAATAGAAACTTAAGGGACTAAAAT-GGTATTAACA-AAAATCAAAAG
1 AAAATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTA-AAACAGAAAATCAAAAG
2285687 GGCTAAACAT
Statistics
Matches: 186, Mismatches: 40, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
58 4 0.02
59 98 0.53
60 82 0.44
61 2 0.01
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (60 bp):
AAAATAGCAAAAATAGAAACTTAAAAGACTAAAATAGCTAAAACAGAAAATCAAAAGACT
Found at i:2285982 original size:16 final size:16
Alignment explanation
Indices: 2285963--2286000 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
2285953 CTTAACTATA
2285963 AATAACATTAAAGTAC
1 AATAACATTAAAGTAC
*
2285979 AATAACATTAAATTAC
1 AATAACATTAAAGTAC
2285995 AATAAC
1 AATAAC
2286001 CTCATCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (16 bp):
AATAACATTAAAGTAC
Found at i:2286881 original size:3 final size:3
Alignment explanation
Indices: 2286873--2286926 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
2286863 AAACAAAATA
2286873 AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
2286919 AAT AAT AA
1 AAT AAT AA
2286927 ATAAAAAAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2287528 original size:133 final size:134
Alignment explanation
Indices: 2287102--2287593 Score: 423
Period size: 130 Copynumber: 3.7 Consensus size: 134
2287092 ATGAAGAGGT
* * * * * **
2287102 CTGGTTGTCTAAGAGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGTAGATGACACAACT
1 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAACT
* * * * * * * *
2287167 CATA---G-TGAAGA-GTTCTGGTCATCTTTAGAAAGGGTGATAACACAGTCCCTACACGATAAG
66 CATACGCGATGAAGACGTTAT-GCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCTATGAG
2287227 GACGA
130 GACGA
* * * * ***
2287232 CAGGTTATCTAGGGGTGATACGACTCCTACGTGATGATGAGGTTTGGTCGGGGGATGACACGGTT
1 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAACT
* * * ** * * *
2287297 CCTATGCGATGAGGACGGCATTCCATCTTTAAGAA---TGATAATACGGTTCCTACG-TGATGAG
66 CATACGCGATGAAGACGTTATGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCT-ATGAG
*
2287358 GACGG
130 GACGA
* * * * *
2287363 CTGGTTAT-TAGGGGCGAAACGGCTCCTACGTGATGAGGAGGTGTGGTCGGGGGATGGCACAACT
1 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAACT
* * ** *
2287427 CATACGCGATGAAGA-GTTATGGCCATCTTTAGGAAGGGCGATAACATGGTTCAAATGCTATGAG
66 CATACGCGATGAAGACGTTAT-GCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCTATGAG
*
2287491 GACAA
130 GACGA
* **
2287496 CTGGTTATCTA-GGGTGACACGACTCCTACGTGATGAAGAGGTCTGGTCGGGGGGATGACACAGT
1 CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTC-GGGGGATGACACAAC
* * * *
2287560 TCCTACGTGATGAGGACGATATGCCATCTTTAGG
65 TCATACGCGATGAAGACGTTATGCCATCTTTAGG
2287594 GATAATCGTT
Statistics
Matches: 281, Mismatches: 67, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
129 3 0.01
130 125 0.44
131 30 0.11
133 62 0.22
134 55 0.20
135 6 0.02
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (134 bp):
CTGGTTATCTAGGGGTGACACGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAACT
CATACGCGATGAAGACGTTATGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCTATGAGG
ACGA
Found at i:2287706 original size:34 final size:35
Alignment explanation
Indices: 2287667--2287734 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
2287657 ACAAAATTCA
*
2287667 TTTCAAGGGAAAC-GACTCAAAGATAGGTATTTTG
1 TTTCAAGGGAAACAAACTCAAAGATAGGTATTTTG
* *
2287701 TTTCAATGGAAACAAACTCAAAGATAGGTGTTTT
1 TTTCAAGGGAAACAAACTCAAAGATAGGTATTTT
2287735 CAAAAGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 12 0.40
35 18 0.60
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (35 bp):
TTTCAAGGGAAACAAACTCAAAGATAGGTATTTTG
Found at i:2287834 original size:65 final size:64
Alignment explanation
Indices: 2287697--2287874 Score: 230
Period size: 65 Copynumber: 2.7 Consensus size: 64
2287687 AGATAGGTAT
* * * * *
2287697 TTTGTTTCAATGGAAACAAACTCAAAGATAGGTGTTTTCAAAAGAAACTGTCTCGAGAGACAAAA
1 TTTGTTTCAAAGGAAACAAACTCAAAGAT--TTTTTTTCAAAAGAAACTGACTCAAGAGACAAAA
*
2287762 T
64 C
* *
2287763 TTTGTTTTAAAGGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGACTCAAGAGACAAAAC
1 TTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTT-TCAAAAGAAACTGACTCAAGAGACAAAAC
* *
2287828 TTTGTTTCCAATGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAAC
1 TTTGTTTCAAAGGAAACAAACTCAAAGATTTTT-TTTCAAAAGAAAC
2287875 AACTCAAAGA
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
64 4 0.04
65 65 0.66
66 29 0.30
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (64 bp):
TTTGTTTCAAAGGAAACAAACTCAAAGATTTTTTTTCAAAAGAAACTGACTCAAGAGACAAAAC
Found at i:2287888 original size:29 final size:29
Alignment explanation
Indices: 2287828--2287924 Score: 122
Period size: 31 Copynumber: 3.2 Consensus size: 29
2287818 GAGACAAAAC
* *
2287828 TTTGTTTCCAATGAAACAAACTCAAAGATT
1 TTTGTTTCAAAAGAAAC-AACTCAAAGATT
2287858 TTTGTTTCAAAAGAAACAACTCAAAGATTTT
1 TTTGTTTCAAAAGAAACAACTCAAAGA--TT
* *
2287889 TTTATTTCAAAAGAAACGACTCAAAGATT
1 TTTGTTTCAAAAGAAACAACTCAAAGATT
*
2287918 TTGGTTT
1 TTTGTTT
2287925 GTTTCCAGTG
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
29 17 0.29
30 15 0.25
31 27 0.46
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.36
Consensus pattern (29 bp):
TTTGTTTCAAAAGAAACAACTCAAAGATT
Found at i:2288044 original size:34 final size:36
Alignment explanation
Indices: 2287949--2288048 Score: 107
Period size: 34 Copynumber: 2.8 Consensus size: 36
2287939 AAATTCATAA
* * *
2287949 TTTG-GAAAATTGTCTTGAGTGAGACAACATTTTGT
1 TTTGAGAAAATTGTCTTAAGCGAGACAACAATTTGT
* *
2287984 TTTGAGAGAAATTATCTCAAGCGAGACAA-AATTTGT
1 TTTGAGA-AAATTGTCTTAAGCGAGACAACAATTTGT
* *
2288020 TTT-AGAAAAATGTCTTTAGCGAGACAACA
1 TTTGAGAAAATTGTCTTAAGCGAGACAACA
2288049 TCAAAGGATA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
34 17 0.32
35 8 0.15
36 11 0.21
37 17 0.32
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (36 bp):
TTTGAGAAAATTGTCTTAAGCGAGACAACAATTTGT
Found at i:2289671 original size:2 final size:2
Alignment explanation
Indices: 2289664--2289710 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2289654 GTATACATAC
2289664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2289706 AT AT A
1 AT AT A
2289711 GAGTAAATGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2290149 original size:21 final size:22
Alignment explanation
Indices: 2290099--2290151 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
2290089 AATTTCCAGA
* *
2290099 ATGCTACAGGGGTATCGATACCC
1 ATGCTACA-GTGTACCGATACCC
*
2290122 A-GTTACAGTGTACCGATA-CC
1 ATGCTACAGTGTACCGATACCC
2290142 ATGCTACAGT
1 ATGCTACAGT
2290152 AATTTTGGCC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.12
21 16 0.64
22 5 0.20
23 1 0.04
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (22 bp):
ATGCTACAGTGTACCGATACCC
Found at i:2296113 original size:30 final size:30
Alignment explanation
Indices: 2296082--2296354 Score: 221
Period size: 30 Copynumber: 9.2 Consensus size: 30
2296072 TATAATAACC
* * *
2296082 AAAATAGCAAAAACATAAACTCAAAGGACC
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * * *
2296112 AAAATAGTATAAACAGGAATTTAAAGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
** *
2296142 AAAATAATAAAAATAGAAACTTAAAGGGA-T
1 AAAATAGCAAAAACAGAAACTTAAA-GGACT
* * * *
2296172 AAAACAACATAAACAAAAACTTAAAAGG-CT
1 AAAATAGCAAAAACAGAAACTT-AAAGGACT
* * * *
2296202 AAAACAAC-AAAACAGAAACTTAAA-AAAT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * * *
2296230 TAAATAGCAAAAACAAAAACCTAAAGGATT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
2296260 AAAATAGCAAAAACATATACTTAAAAGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
2296290 AAAATAGCTAAAACAGAAAGTTAAAAGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
* * *
2296320 AAAATAGCAAAAAAATAAACTTAAGGGACT
1 AAAATAGCAAAAACAGAAACTTAAAGGACT
2296350 AAAAT
1 AAAAT
2296355 GATATTAACA
Statistics
Matches: 193, Mismatches: 44, Indels: 12
0.78 0.18 0.05
Matches are distributed among these distances:
28 9 0.05
29 25 0.13
30 153 0.79
31 6 0.03
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.16
Consensus pattern (30 bp):
AAAATAGCAAAAACAGAAACTTAAAGGACT
Found at i:2296233 original size:29 final size:30
Alignment explanation
Indices: 2296171--2296233 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
2296161 CTTAAAGGGA
**
2296171 TAAAACAACATAAACAAAAACTTAAAAGGC
1 TAAAACAACATAAACAAAAACTTAAAAAAC
* *
2296201 TAAAACAACA-AAACAGAAACTTAAAAAAT
1 TAAAACAACATAAACAAAAACTTAAAAAAC
2296230 TAAA
1 TAAA
2296234 TAGCAAAAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.66
30 10 0.34
ACGTcount: A:0.67, C:0.14, G:0.05, T:0.14
Consensus pattern (30 bp):
TAAAACAACATAAACAAAAACTTAAAAAAC
Found at i:2297346 original size:7 final size:7
Alignment explanation
Indices: 2297277--2297342 Score: 123
Period size: 7 Copynumber: 9.4 Consensus size: 7
2297267 TACTCCCTAT
2297277 TTCCCTC
1 TTCCCTC
2297284 TTCCCTC
1 TTCCCTC
2297291 TTCCCTC
1 TTCCCTC
2297298 TTCCCTC
1 TTCCCTC
2297305 TTCCCTC
1 TTCCCTC
2297312 TTCCCTC
1 TTCCCTC
2297319 TTCCCTC
1 TTCCCTC
2297326 TTCCCTC
1 TTCCCTC
*
2297333 TTCTCTC
1 TTCCCTC
2297340 TTC
1 TTC
2297343 TCTCATCTGG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 58 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (7 bp):
TTCCCTC
Found at i:2305202 original size:20 final size:20
Alignment explanation
Indices: 2305166--2305203 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2305156 CTTGAACATC
*
2305166 GACGAAACCAATATTTCGCA
1 GACGAAACAAATATTTCGCA
2305186 GACGAAATCAAAT-TTTCG
1 GACGAAA-CAAATATTTCG
2305204 GACCGTGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.24
Consensus pattern (20 bp):
GACGAAACAAATATTTCGCA
Found at i:2313851 original size:3 final size:3
Alignment explanation
Indices: 2313843--2313934 Score: 184
Period size: 3 Copynumber: 30.7 Consensus size: 3
2313833 GGCTTAATAC
2313843 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2313891 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2313935 ATTATGTTTC
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2316347 original size:18 final size:18
Alignment explanation
Indices: 2316319--2316363 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 18
2316309 CAAGAAAAGA
2316319 GGTATTGATTCCTTAGCTT
1 GGTA-TGATTCCTTAGCTT
2316338 GGTATGATTCCTTAGCTT
1 GGTATGATTCCTTAGCTT
2316356 GGTATGAT
1 GGTATGAT
2316364 ATATGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.18, C:0.13, G:0.24, T:0.44
Consensus pattern (18 bp):
GGTATGATTCCTTAGCTT
Found at i:2317169 original size:23 final size:23
Alignment explanation
Indices: 2317125--2317170 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2317115 ATTCTTAAAC
**
2317125 CATCTCAATAAATATGTCAATAT
1 CATCTCAATAAATATGGAAATAT
2317148 CATCTCTAAT-AATATGGAAATAT
1 CATCTC-AATAAATATGGAAATAT
2317171 ATAATAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 17 0.85
24 3 0.15
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (23 bp):
CATCTCAATAAATATGGAAATAT
Found at i:2321375 original size:13 final size:13
Alignment explanation
Indices: 2321357--2321421 Score: 85
Period size: 13 Copynumber: 5.0 Consensus size: 13
2321347 ATCATAAATC
*
2321357 TATGACGCGCATT
1 TATGACGCACATT
*
2321370 TATGACACACATT
1 TATGACGCACATT
2321383 TATGACGCACATT
1 TATGACGCACATT
* *
2321396 TATGAAGCACATG
1 TATGACGCACATT
*
2321409 TATGACGCTCATT
1 TATGACGCACATT
2321422 GCGCGTCATT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:2321586 original size:2 final size:2
Alignment explanation
Indices: 2321579--2321609 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2321569 TGTCGTAAAT
2321579 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2321610 TGTAGATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2337319 original size:109 final size:109
Alignment explanation
Indices: 2337109--2337317 Score: 296
Period size: 109 Copynumber: 1.9 Consensus size: 109
2337099 TCACGGGATG
* *
2337109 ACTCTACTTGACTAGCTCGAGGGTGGAAGGTATGCTCCCTTTCACCTAGAGTGTGGGATGGTAGG
1 ACTCTACTTGACTAGCTCGAGGGTGGAAGCTATGCTCACTTTCACCTAGAGTGTGGGATGGTAGG
* * * **
2337174 TGTGATGTGCTGACTCTCCTCGAAGTAGTGTAAAAAGAAATCAA
66 TGTGATGAGATGACTCCCCTAAAAGTAGTGTAAAAAGAAATCAA
* * * *
2337218 ACTCTGCTTGACTAGCTCGGGGGTGGAAGCTATGCTCATTTTCACTTAGAGTGTGGGATGGTA-G
1 ACTCTACTTGACTAGCTCGAGGGTGGAAGCTATGCTCACTTTCACCTAGAGTGTGGGATGGTAGG
2337282 TGTGATGAGATGACTCCCCTAAAAGTA-TGTTAAAAA
66 TGTGATGAGATGACTCCCCTAAAAGTAGTG-TAAAAA
2337318 AGTTAAAGTT
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
107 2 0.02
108 29 0.33
109 57 0.65
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (109 bp):
ACTCTACTTGACTAGCTCGAGGGTGGAAGCTATGCTCACTTTCACCTAGAGTGTGGGATGGTAGG
TGTGATGAGATGACTCCCCTAAAAGTAGTGTAAAAAGAAATCAA
Found at i:2342558 original size:108 final size:108
Alignment explanation
Indices: 2342351--2342547 Score: 297
Period size: 108 Copynumber: 1.8 Consensus size: 108
2342341 TCACGGGATG
* *
2342351 ACTCTACTTGACTAGCTCAGGGGTGGATGGTATGCTCCCTTTCACCTAGAGTGTGGGATGGTAGG
1 ACTCTACTTGACTAGCTCAGGGGTGGAAGCTATGCTCCCTTTCACCTAGAGTGTGGGATGGTAGG
* * **
2342416 TGTGATGGCTGACTCTCCTCGAAGCAGTGTAAAAAGATATCAA
66 TGTGATGGATGACTCCCCTAAAAGCAGTGTAAAAAGATATCAA
* *
2342459 ACTCTACTTGACTAGCTCGGGGGTGGAAGCTATGCTCCCTTTCACTTAGAGTGTGGGATGGTA-G
1 ACTCTACTTGACTAGCTCAGGGGTGGAAGCTATGCTCCCTTTCACCTAGAGTGTGGGATGGTAGG
*
2342523 TGTGATGAGATTACTCCCCTAAAAG
66 TGTGATG-GATGACTCCCCTAAAAG
2342548 TATGTTAAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 8 0.10
108 71 0.90
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.28
Consensus pattern (108 bp):
ACTCTACTTGACTAGCTCAGGGGTGGAAGCTATGCTCCCTTTCACCTAGAGTGTGGGATGGTAGG
TGTGATGGATGACTCCCCTAAAAGCAGTGTAAAAAGATATCAA
Found at i:2344683 original size:23 final size:23
Alignment explanation
Indices: 2344657--2344708 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
2344647 TATTGATCAT
*
2344657 GAAGCAATAAAGCACATAAAATG
1 GAAGCAATAAAACACATAAAATG
*
2344680 GAAGCAGTAAAACACATAAAATG
1 GAAGCAATAAAACACATAAAATG
2344703 GAAGCA
1 GAAGCA
2344709 TAAGTTGAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.56, C:0.13, G:0.19, T:0.12
Consensus pattern (23 bp):
GAAGCAATAAAACACATAAAATG
Found at i:2347065 original size:15 final size:15
Alignment explanation
Indices: 2347041--2347074 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2347031 CTTCATAACT
*
2347041 ACAA-ATGAATGGTG
1 ACAAGATGAATGGTC
2347055 ACAAGATGAATGGTC
1 ACAAGATGAATGGTC
2347070 ACAAG
1 ACAAG
2347075 CATTATTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.44, C:0.12, G:0.26, T:0.18
Consensus pattern (15 bp):
ACAAGATGAATGGTC
Found at i:2356034 original size:18 final size:18
Alignment explanation
Indices: 2356007--2356052 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
2355997 TCCCCTCCTA
* *
2356007 AAGAATAAGGGATCAACT
1 AAGAAGAAGGGATAAACT
2356025 AAGAAGAAGGGATAAACT
1 AAGAAGAAGGGATAAACT
2356043 AAGAAGAAGG
1 AAGAAGAAGG
2356053 TATTTGTAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.54, C:0.07, G:0.28, T:0.11
Consensus pattern (18 bp):
AAGAAGAAGGGATAAACT
Found at i:2357793 original size:18 final size:18
Alignment explanation
Indices: 2357767--2357801 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2357757 CTAGAAAGCA
2357767 AAAGAGGTACCGATACTC
1 AAAGAGGTACCGATACTC
*
2357785 AAAGGGGTACCGATACT
1 AAAGAGGTACCGATACT
2357802 ACTTTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.20, G:0.26, T:0.17
Consensus pattern (18 bp):
AAAGAGGTACCGATACTC
Found at i:2357927 original size:21 final size:22
Alignment explanation
Indices: 2357890--2357930 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
2357880 TTAAATATTA
2357890 TAAAGGAAGTACTGATACTCAT
1 TAAAGGAAGTACTGATACTCAT
2357912 TAAAGG-AGTA-TCGATACTC
1 TAAAGGAAGTACT-GATACTC
2357931 CCTGTCCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 11 0.61
22 6 0.33
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGAAGTACTGATACTCAT
Found at i:2359920 original size:37 final size:37
Alignment explanation
Indices: 2359850--2359920 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
2359840 ATTTAAACAT
* *
2359850 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAG
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAG
2359887 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
2359921 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAG
Found at i:2361177 original size:16 final size:16
Alignment explanation
Indices: 2361114--2361173 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
2361104 ATGTAATTTG
2361114 TAATATA-TATATATATA
1 TAATATATTATAT-TA-A
* * **
2361131 TAATAAATAATAAAAA
1 TAATATATTATATTAA
2361147 TAATATATTATATTAA
1 TAATATATTATATTAA
2361163 TAATA-ATTATA
1 TAATATATTATA
2361174 ATTATTATTA
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
15 6 0.18
16 18 0.53
17 7 0.21
18 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATATTATATTAA
Found at i:2361182 original size:22 final size:22
Alignment explanation
Indices: 2361138--2361191 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2361128 ATATAATAAA
2361138 TAATAAAAATAATATATTATAT
1 TAATAAAAATAATATATTATAT
* *
2361160 TAATAATAATTATA-ATTATTAT
1 TAATAAAAATAATATATTA-TAT
*
2361182 T-ATGAAAATA
1 TAATAAAAATA
2361192 TTAATGTCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TAATAAAAATAATATATTATAT
Found at i:2361655 original size:151 final size:152
Alignment explanation
Indices: 2361303--2361943 Score: 1146
Period size: 151 Copynumber: 4.2 Consensus size: 152
2361293 GATGAAAATA
* * *
2361303 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGA-CCTAAAGGCTTTTGAAAACATCAAAAAG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT-AAGGC-TTTGAAAACATCAAAAAG
2361367 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAA
64 CTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAA
2361432 ACATCAAAAAGCTCCCGAAGGCTT
129 ACATCAAAAAGCTCCCGAAGGCTT
*
2361456 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2361520 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
*
2361584 ATCAAAAAGCTCCCGAATGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
2361606 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
* *
2361671 CCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-TTTGGAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
2361735 ATCAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
2361757 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
* *
2361822 CCCAAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGAACCTAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
2361887 ATCAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
2361909 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
2361944 TGGGAAATAG
Statistics
Matches: 470, Mismatches: 15, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
150 73 0.16
151 293 0.62
152 65 0.14
153 37 0.08
154 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (152 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTT
Found at i:2361970 original size:76 final size:76
Alignment explanation
Indices: 2361303--2361943 Score: 1146
Period size: 76 Copynumber: 8.5 Consensus size: 76
2361293 GATGAAAATA
* * *
2361303 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGA-CCTAAAGGCTTTTGAAAACATCAAAAAG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCT-AAGGC-TTTGAAAACATCAAAAAG
2361367 CTCCCGAAGGCTT
64 CTCCCGAAGGCTT
2361380 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2361445 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2361456 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2361520 CCCGAAGGCTT
66 CCCGAAGGCTT
*
2361531 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGG-TTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2361595 CCCGAATGCTT
66 CCCGAAGGCTT
2361606 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2361671 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
2361682 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGG-TTTGGAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2361746 CCCGAAGGCTT
66 CCCGAAGGCTT
2361757 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
2361822 CCCAAAGGCTT
66 CCCGAAGGCTT
*
2361833 TTTGGAAACATCATGCACTGTAGGACTTACAGATGAACCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
2361898 CCCGAAGGCTT
66 CCCGAAGGCTT
2361909 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
2361944 TGGGAAATAG
Statistics
Matches: 547, Mismatches: 14, Indels: 7
0.96 0.02 0.01
Matches are distributed among these distances:
75 221 0.40
76 285 0.52
77 38 0.07
78 3 0.01
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:2362645 original size:22 final size:22
Alignment explanation
Indices: 2362617--2362671 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
2362607 CATAAAGCTT
2362617 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
2362639 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
2362661 TCATCTTTGAA
1 TCATCTTTGAA
2362672 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2363117 original size:54 final size:54
Alignment explanation
Indices: 2363035--2363144 Score: 166
Period size: 54 Copynumber: 2.0 Consensus size: 54
2363025 TCAGAATAGC
* * * *
2363035 ATGTTCGTAAAACATTTGACAGCGCATTCATCCTTTCATGTGGCTTCTGCTCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAG
* *
2363089 ATGTTCGTAAAACATTTGACAACACATTCATCATTTCTTGTGGTTTCTGCCCAG
1 ATGTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAG
2363143 AT
1 AT
2363145 TTCTGGTCAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (54 bp):
ATGTTCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTCTGCCCAG
Found at i:2371931 original size:19 final size:18
Alignment explanation
Indices: 2371891--2371945 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
2371881 TTAATATCTG
2371891 AATAAAATAA-AAAAATATT
1 AATAAAATAATAAAAA-A-T
2371910 AATAAAATAATATAAAAAT
1 AATAAAATAATA-AAAAAT
*
2371929 AAT-AAGTAATAAAAAAT
1 AATAAAATAATAAAAAAT
2371946 TGAAAGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 14 0.42
20 2 0.06
21 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
AATAAAATAATAAAAAAT
Found at i:2372821 original size:37 final size:37
Alignment explanation
Indices: 2372751--2372821 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
2372741 ATTTAAACAT
* *
2372751 ATAAAATTAAAATATAAATAAACAATGAGTAAAATAG
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAG
2372788 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATATAAATA-AAAAATG-AATAAAA
2372822 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAG
Found at i:2374027 original size:2 final size:2
Alignment explanation
Indices: 2374020--2374061 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2374010 GTAATTTGTA
2374020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2374062 TTTAATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2374072 original size:3 final size:3
Alignment explanation
Indices: 2374064--2374097 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
2374054 ATATATATTT
*
2374064 TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2374098 TTATGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2380655 original size:78 final size:78
Alignment explanation
Indices: 2380573--2380733 Score: 191
Period size: 78 Copynumber: 2.1 Consensus size: 78
2380563 TATGAACCAT
* * *
2380573 ATTTAAAAAAAATAAAATTATA-TTAAAATTTTATTTAACGAATCAA-AAGTTACAAACACAATT
1 ATTTAAAAAAAA-AAAATTAAATTTAAAATTTTATTTAACGAAACAATAA-TTACAAACACAACT
2380636 TAAATCACAAGACAA
64 TAAATCACAAGACAA
* *** ** * *
2380651 ATTTATAATTCAAATCTTAAATTTAAAATTTTATTTAACGAAACAATAATTATAAGCACAACTTA
1 ATTTAAAAAAAAAAAATTAAATTTAAAATTTTATTTAACGAAACAATAATTACAAACACAACTTA
2380716 AATCACAAGACAA
66 AATCACAAGACAA
2380729 ATTTA
1 ATTTA
2380734 TAATTCAAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
77 6 0.09
78 62 0.89
79 2 0.03
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.32
Consensus pattern (78 bp):
ATTTAAAAAAAAAAAATTAAATTTAAAATTTTATTTAACGAAACAATAATTACAAACACAACTTA
AATCACAAGACAA
Found at i:2380734 original size:78 final size:79
Alignment explanation
Indices: 2380595--2380754 Score: 261
Period size: 78 Copynumber: 2.0 Consensus size: 79
2380585 TAAAATTATA
* *
2380595 TTAAAATTTTATTTAACGAATCAAAAGTTACAAACACAATTTAAATCACAAGACAAATTTATAAT
1 TTAAAATTTTATTTAACGAAACAAAAGTTACAAACACAACTTAAATCACAAGACAAATTTATAAT
2380660 TCAAATCTT-AAAT
66 TCAAATCTTAAAAT
* *
2380673 TTAAAATTTTATTTAACGAAACAATAA-TTATAAGCACAACTTAAATCACAAGACAAATTTATAA
1 TTAAAATTTTATTTAACGAAACAA-AAGTTACAAACACAACTTAAATCACAAGACAAATTTATAA
2380737 TTCAAATCTTAAAAT
65 TTCAAATCTTAAAAT
2380752 TTA
1 TTA
2380755 TTTAAGATTT
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
78 67 0.88
79 9 0.12
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (79 bp):
TTAAAATTTTATTTAACGAAACAAAAGTTACAAACACAACTTAAATCACAAGACAAATTTATAAT
TCAAATCTTAAAAT
Found at i:2382913 original size:31 final size:31
Alignment explanation
Indices: 2382840--2382921 Score: 84
Period size: 31 Copynumber: 2.7 Consensus size: 31
2382830 TAGTGTTATA
*
2382840 ATAATATATT-TAATTATATTATAATAATAT
1 ATAATAAATTATAATTATATTATAATAATAT
* *
2382870 AT-ATAAGTTTATAATTTTAATT-TAATAATAT
1 ATAATAA-ATTATAATTAT-ATTATAATAATAT
2382901 ATAATAAATTAT-ATTAT-TTAT
1 ATAATAAATTATAATTATATTAT
2382922 TTTAGAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 11
0.72 0.09 0.19
Matches are distributed among these distances:
28 2 0.05
29 4 0.10
30 8 0.19
31 21 0.50
32 7 0.17
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (31 bp):
ATAATAAATTATAATTATATTATAATAATAT
Found at i:2382946 original size:49 final size:48
Alignment explanation
Indices: 2382892--2382984 Score: 134
Period size: 49 Copynumber: 1.9 Consensus size: 48
2382882 AATTTTAATT
* *
2382892 TAATAATA-TATAATAAATTATATTATTTATTTTAGAAATAATATTTCAA
1 TAATAATATTA-AATAAATTATATTA-ATATTTTAAAAATAATATTTCAA
*
2382941 TAATAATATTAAATAAATTATTTTAATATTTTAAAAATAATATT
1 TAATAATATTAAATAAATTATATTAATATTTTAAAAATAATATT
2382985 ATTTTTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
48 17 0.43
49 21 0.52
50 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (48 bp):
TAATAATATTAAATAAATTATATTAATATTTTAAAAATAATATTTCAA
Found at i:2383001 original size:21 final size:20
Alignment explanation
Indices: 2382969--2383009 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
2382959 TATTTTAATA
*
2382969 TTTTAAAAATAATATTATTT
1 TTTTAAAAATAATAGTATTT
2382989 TTTTAATAAATAATAGTATTT
1 TTTTAA-AAATAATAGTATTT
2383010 ATTATATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTAAAAATAATAGTATTT
Found at i:2383119 original size:12 final size:13
Alignment explanation
Indices: 2383096--2383120 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2383086 CAAATATCGT
2383096 AAAATTATTTTTA
1 AAAATTATTTTTA
2383109 AAAATTATTTTT
1 AAAATTATTTTT
2383121 CACAAAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AAAATTATTTTTA
Found at i:2384466 original size:11 final size:11
Alignment explanation
Indices: 2384450--2384475 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2384440 GAGACATTAC
2384450 CCGCCCCGCAT
1 CCGCCCCGCAT
2384461 CCGCCCCGCAT
1 CCGCCCCGCAT
2384472 CCGC
1 CCGC
2384476 TCGCCCCGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.65, G:0.19, T:0.08
Consensus pattern (11 bp):
CCGCCCCGCAT
Found at i:2384507 original size:31 final size:30
Alignment explanation
Indices: 2384461--2384527 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 30
2384451 CGCCCCGCAT
2384461 CCGCCCCGCATCCGCTCGCCCCGCATCCGC
1 CCGCCCCGCATCCGCTCGCCCCGCATCCGC
*
2384491 TCGCCCCGCATCCCGCTCGCCCCGCATCCGC
1 CCGCCCCGCAT-CCGCTCGCCCCGCATCCGC
2384522 CCGCCC
1 CCGCCC
2384528 AGCTAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 10 0.29
31 24 0.71
ACGTcount: A:0.06, C:0.64, G:0.19, T:0.10
Consensus pattern (30 bp):
CCGCCCCGCATCCGCTCGCCCCGCATCCGC
Found at i:2384508 original size:16 final size:15
Alignment explanation
Indices: 2384462--2384527 Score: 114
Period size: 15 Copynumber: 4.3 Consensus size: 15
2384452 GCCCCGCATC
2384462 CGCCCCGCATCCGCT
1 CGCCCCGCATCCGCT
2384477 CGCCCCGCATCCGCT
1 CGCCCCGCATCCGCT
2384492 CGCCCCGCATCCCGCT
1 CGCCCCGCAT-CCGCT
*
2384508 CGCCCCGCATCCGCC
1 CGCCCCGCATCCGCT
2384523 CGCCC
1 CGCCC
2384528 AGCTAAATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
15 34 0.69
16 15 0.31
ACGTcount: A:0.06, C:0.64, G:0.20, T:0.11
Consensus pattern (15 bp):
CGCCCCGCATCCGCT
Found at i:2385522 original size:37 final size:36
Alignment explanation
Indices: 2385443--2385547 Score: 142
Period size: 36 Copynumber: 2.9 Consensus size: 36
2385433 TTGATAATAA
*
2385443 CTCAAATTAGG-TTTTCCAATTAGTATTGGAAATATG
1 CTCAAATTAGGTTTTTCC-ACTAGTATTGGAAATATG
*
2385479 CT-AAATTAGGTTTTTTCCACTAGTATTGCAAATATG
1 CTCAAATTAGG-TTTTTCCACTAGTATTGGAAATATG
* *
2385515 CTCAAATTAGGTTATCCCACTAGTATTGGAAAT
1 CTCAAATTAGGTTTTTCCACTAGTATTGGAAAT
2385548 GATGATTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
35 8 0.13
36 39 0.64
37 14 0.23
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (36 bp):
CTCAAATTAGGTTTTTCCACTAGTATTGGAAATATG
Found at i:2390215 original size:21 final size:21
Alignment explanation
Indices: 2390186--2390245 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 21
2390176 ACAGGGTATC
* *
2390186 GATGCATCGGTGCACCTTCAT
1 GATGCATCGATGCACATTCAT
* *
2390207 GATGTATCGATGCACATTCAAAGG
1 GATGCATCGATGCACATTC--A-T
2390231 GATGCATCGATGCAC
1 GATGCATCGATGCAC
2390246 TGTTAAGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 16 0.52
23 1 0.03
24 14 0.45
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (21 bp):
GATGCATCGATGCACATTCAT
Found at i:2395438 original size:64 final size:65
Alignment explanation
Indices: 2395369--2395514 Score: 215
Period size: 64 Copynumber: 2.3 Consensus size: 65
2395359 CGGTGCACTA
* *
2395369 AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTGAAT-AAGCCT-AAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTGAA-TGCATCGATGCATG
2395432 G
65 G
* * *
2395433 TGTGTGCATCGATGCATAAAATGCATTCTATGTTTTCATTAAAACCTGAATGCATCGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTGAATGCATCGATGCATGG
*
2395498 AGAGTGCATCGATGCAT
1 AGTGTGCATCGATGCAT
2395515 GGAGAGTGCA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
64 36 0.49
65 35 0.48
66 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.31
Consensus pattern (65 bp):
AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTGAATGCATCGATGCATGG
Found at i:2395507 original size:19 final size:19
Alignment explanation
Indices: 2395483--2395533 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
2395473 AAAACCTGAA
2395483 TGCATCGATGCATGGAGAG
1 TGCATCGATGCATGGAGAG
2395502 TGCATCGATGCATGGAGAG
1 TGCATCGATGCATGGAGAG
2395521 TGCATCGATGCAT
1 TGCATCGATGCAT
2395534 AAACTATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAG
Found at i:2403584 original size:64 final size:65
Alignment explanation
Indices: 2403512--2403657 Score: 204
Period size: 65 Copynumber: 2.3 Consensus size: 65
2403502 AGGTGCACTA
* * *
2403512 AGTGTGCATCGATGCATAAAATGTATTCGATGTTTTGAAT-AAGCCTAAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
* * * * *
2403576 TGTGTGCATCGATGTATAAAATGCATTCGATTTTTTCATTAAAACCTGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
*
2403641 AGAGTGCATCGATGCAT
1 AGTGTGCATCGATGCAT
2403658 GGAGAGTGCA
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
64 34 0.49
65 36 0.51
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (65 bp):
AGTGTGCATCGATGCATAAAATGCATTCGATGTTTTCAATAAAACCTAAGTGCATCGATGCATGG
Found at i:2403647 original size:19 final size:19
Alignment explanation
Indices: 2403623--2403676 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
2403613 ATTAAAACCT
2403623 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
2403642 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
2403661 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
2403677 AAATTGCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.26, C:0.17, G:0.35, T:0.22
Consensus pattern (19 bp):
GAGTGCATCGATGCATGGA
Found at i:2403729 original size:20 final size:20
Alignment explanation
Indices: 2403704--2403741 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2403694 CAATTTATTC
2403704 ATTGGTGCATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
2403724 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
2403742 CCCTTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.34, T:0.32
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:2407739 original size:16 final size:17
Alignment explanation
Indices: 2407718--2407752 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
2407708 TTAGTGGGGG
2407718 AATGTTGATAATG-CTC
1 AATGTTGATAATGACTC
2407734 AATGTTGATAATGACTC
1 AATGTTGATAATGACTC
2407751 AA
1 AA
2407753 ATTAGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.34
Consensus pattern (17 bp):
AATGTTGATAATGACTC
Found at i:2407826 original size:36 final size:36
Alignment explanation
Indices: 2407748--2407851 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
2407738 TTGATAATGA
*
2407748 CTCAAATTAGG-TTTTCCAACTAGTATTGGAAATATG
1 CTCAAATTAGGTTTTTCC-ACTAGTATTGAAAATATG
* *
2407784 AT-AAATTAGGTTTTTCCACTAGTATTGCAAATATG
1 CTCAAATTAGGTTTTTCCACTAGTATTGAAAATATG
* *
2407819 CTCAAATTAGGTTATCCCACTAGTATTGAAAAT
1 CTCAAATTAGGTTTTTCCACTAGTATTGAAAAT
2407852 GACGATTTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
35 26 0.43
36 34 0.57
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (36 bp):
CTCAAATTAGGTTTTTCCACTAGTATTGAAAATATG
Found at i:2408687 original size:58 final size:58
Alignment explanation
Indices: 2408578--2408687 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 58
2408568 TAGAAAGAGG
* * * **
2408578 GTCATAGTTTAGGGATAAAATTAAACTGTTCAAAACTTTAAGGATTAATTTAGAATTA
1 GTCATAGTTTAGAGATAAAATTAAAATATTCAAAACTTTAAAAATTAATTTAGAATTA
* * *
2408636 GTCATAGTTTAGATATAAAATTAAAATATTCAAAAGTTTAAAAATTTATTTA
1 GTCATAGTTTAGAGATAAAATTAAAATATTCAAAACTTTAAAAATTAATTTA
2408688 AAATGAAAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (58 bp):
GTCATAGTTTAGAGATAAAATTAAAATATTCAAAACTTTAAAAATTAATTTAGAATTA
Found at i:2410724 original size:34 final size:32
Alignment explanation
Indices: 2410671--2410740 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
2410661 CCTTACAAAC
*
2410671 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
* * *
2410703 TCCCTAGCTTTTACACGGGCTAAGCTGGAACTTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
2410737 TCCC
1 TCCC
2410741 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:2411049 original size:21 final size:21
Alignment explanation
Indices: 2411023--2411064 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2411013 CCAGAATGGG
*
2411023 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2411044 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
2411065 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:2411217 original size:20 final size:20
Alignment explanation
Indices: 2411192--2411231 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2411182 ATCTGTTCCC
2411192 GGGGAATC-GATACCCCCTGG
1 GGGGAATCTG-TACCCCCTGG
2411212 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
2411232 ACAATCTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.17
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:2414270 original size:34 final size:32
Alignment explanation
Indices: 2414217--2414286 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
2414207 CCTTACAAAC
*
2414217 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
* *
2414249 TCCCTAGCTTTTACACGGGCTAAGCTATAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
2414283 TCCC
1 TCCC
2414287 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:2414778 original size:34 final size:35
Alignment explanation
Indices: 2414723--2414807 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 35
2414713 AAACCATGCA
*
2414723 GGGGGAATTTGTACCCAGGGAATCGATA-CCCCTG
1 GGGGGAATCTGTACCCAGGGAATCGATACCCCCTG
* *
2414757 GGGGGAATCTGTTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTACCCAGGGAATCGATACCCCCTG
2414792 GGGGGAATCTGTACCC
1 GGGGGAATCTGTACCC
2414808 CCTGAACAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 25 0.54
35 21 0.46
ACGTcount: A:0.20, C:0.26, G:0.34, T:0.20
Consensus pattern (35 bp):
GGGGGAATCTGTACCCAGGGAATCGATACCCCCTG
Found at i:2414798 original size:20 final size:20
Alignment explanation
Indices: 2414773--2414811 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2414763 ATCTGTTCCC
2414773 GGGGAATC-GATACCCCCTGG
1 GGGGAATCTG-TACCCCCTGG
2414793 GGGGAATCTGTACCCCCTG
1 GGGGAATCTGTACCCCCTG
2414812 AACAATCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.18, C:0.31, G:0.33, T:0.18
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:2415384 original size:16 final size:17
Alignment explanation
Indices: 2415365--2415398 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2415355 GTTATTTACA
2415365 TTTCT-TACCTTTAATT
1 TTTCTGTACCTTTAATT
*
2415381 TTTCTGTACTTTTAATT
1 TTTCTGTACCTTTAATT
2415398 T
1 T
2415399 ATGCCCTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.18, C:0.15, G:0.03, T:0.65
Consensus pattern (17 bp):
TTTCTGTACCTTTAATT
Found at i:2418179 original size:18 final size:18
Alignment explanation
Indices: 2418156--2418193 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2418146 TGATTCTTTT
2418156 GAAAAGTTGGATAATTTG
1 GAAAAGTTGGATAATTTG
2418174 GAAAAGTTGGATAATTTG
1 GAAAAGTTGGATAATTTG
2418192 GA
1 GA
2418194 TTATGGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (18 bp):
GAAAAGTTGGATAATTTG
Found at i:2420079 original size:44 final size:44
Alignment explanation
Indices: 2420031--2420132 Score: 102
Period size: 44 Copynumber: 2.3 Consensus size: 44
2420021 AAATGAAGGG
* **
2420031 TAAAAATTAAAAGACAGAAAA-TTAAA-GT-AATGCAATTAAATAAA
1 TAAAAA-TAAAAGA-AAAAAATTTAAATGTGAATAAAATTAAAT-AA
* *
2420075 TAAAAAGTAAAGGAAAAAAATTTAAATGTGCATAAAATTAAATAA
1 TAAAAA-TAAAAGAAAAAAATTTAAATGTGAATAAAATTAAATAA
2420120 TAAAAATAAAAGA
1 TAAAAATAAAAGA
2420133 GCAATAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
43 5 0.10
44 23 0.48
45 10 0.21
46 10 0.21
ACGTcount: A:0.65, C:0.03, G:0.10, T:0.23
Consensus pattern (44 bp):
TAAAAATAAAAGAAAAAAATTTAAATGTGAATAAAATTAAATAA
Found at i:2421767 original size:40 final size:40
Alignment explanation
Indices: 2421625--2421815 Score: 140
Period size: 40 Copynumber: 4.8 Consensus size: 40
2421615 TTGACCCAAG
* * * *
2421625 GTGATGCTGATTCAACTCCTTATGTGATGGA-TA-AGAAGA
1 GTGATGCTGATCCAACTCCTTATATGATGGACGAGCGAA-A
* * *
2421664 GGTGATACTGATCCAACT-ATTA-ATGTCATAGACGAGCGAAA
1 -GTGATGCTGATCCAACTCCTTATATG--ATGGACGAGCGAAA
* * * *
2421705 GTGATGATGACCCAACTTCTTATATGATGGATGAGCGAAA
1 GTGATGCTGATCCAACTCCTTATATGATGGACGAGCGAAA
* * *
2421745 GTGATGCTGATCCAACTCCTTAT-GGATGGACGAGTGAAG
1 GTGATGCTGATCCAACTCCTTATATGATGGACGAGCGAAA
* * * *
2421784 GTCGGTGTTGTTCCAACTCCTTATGTGATGGA
1 GT-GATGCTGATCCAACTCCTTATATGATGGA
2421816 ATCTAGCTAA
Statistics
Matches: 119, Mismatches: 24, Indels: 15
0.75 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 17 0.14
40 83 0.70
41 11 0.09
42 6 0.05
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (40 bp):
GTGATGCTGATCCAACTCCTTATATGATGGACGAGCGAAA
Found at i:2422483 original size:101 final size:101
Alignment explanation
Indices: 2422331--2422590 Score: 295
Period size: 101 Copynumber: 2.6 Consensus size: 101
2422321 TGGAAAGTTG
* * * * * * **
2422331 TCTCAAGCGAGACAAAAATGACTTTATGAAAAACAATCTCAATTGAGATAAATCTTGTTTTGAGT
1 TCTCAAGTGAAACAAAATTGATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTGTTTCAAGT
* * * * *
2422396 GAAGCATTTCTAGAACTTGTGCTGCAAAGGAAAGTG
66 GAAGCAATTCCAAAACTTGTGCTGCAAAGGAAACTA
** *
2422432 TCTCAAGTGAAATGAAATTGATTTTAAGAAAAACAATCTCAAGTGAAATAAATCTTGTTTCAAGT
1 TCTCAAGTGAAACAAAATTGATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTGTTTCAAGT
* ** *
2422497 GGAGCAATTCCAAAACTTGTGCTTTAACGGAAACTA
66 GAAGCAATTCCAAAACTTGTGCTGCAAAGGAAACTA
* * * * *
2422533 TCTCAAGTGAGACAAAATTGCTTTCAAGAAAAACAATATCAAGTGAGATAAATTTTGT
1 TCTCAAGTGAAACAAAATTGATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTGT
2422591 CGTATCAAAT
Statistics
Matches: 131, Mismatches: 28, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
101 131 1.00
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.29
Consensus pattern (101 bp):
TCTCAAGTGAAACAAAATTGATTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTGTTTCAAGT
GAAGCAATTCCAAAACTTGTGCTGCAAAGGAAACTA
Found at i:2424376 original size:21 final size:22
Alignment explanation
Indices: 2424352--2424400 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
2424342 CTTATTTCAA
2424352 TTTTATTTT-TTTCTCTTTC-TT
1 TTTTATTTTATTTCTC-TTCATT
*
2424373 TTTT-TTTTATTTTTCTTCATT
1 TTTTATTTTATTTCTCTTCATT
2424394 TTTTATT
1 TTTTATT
2424401 GGATCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 7 0.29
21 15 0.62
22 2 0.08
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTATTTTATTTCTCTTCATT
Found at i:2424387 original size:17 final size:17
Alignment explanation
Indices: 2424357--2424400 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
2424347 TTCAATTTTA
* * *
2424357 TTTTTTTCTCTTTCTTT
1 TTTTTTTATTTTTCTTC
2424374 TTTTTTTATTTTTCTTC
1 TTTTTTTATTTTTCTTC
*
2424391 ATTTTTTATT
1 TTTTTTTATT
2424401 GGATCATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTATTTTTCTTC
Found at i:2446252 original size:76 final size:76
Alignment explanation
Indices: 2446123--2446270 Score: 190
Period size: 76 Copynumber: 1.9 Consensus size: 76
2446113 CACTGAGGGC
* * * * * * * * *
2446123 CCTGAAACTCGAATTTTCTTCGGTTAGATACCTATTTTATTGATAGTATTCACCTTGAAATTTTA
1 CCTGAAACCCGAATTCTCTCCGGTTAGATACCTATTTTACTGAAAATACTCACCCTAAAATTTTA
2446188 TTTGTACTCAT
66 TTTGTACTCAT
*
2446199 CCTGAAACCCGAATTCTCTCCGGTTA-ATTACCTATTTTACTGAAAATGCTCACCCTAAAATTTT
1 CCTGAAACCCGAATTCTCTCCGGTTAGA-TACCTATTTTACTGAAAATACTCACCCTAAAATTTT
2446263 ATTTGTAC
65 ATTTGTAC
2446271 CCCTTATTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
75 1 0.02
76 60 0.98
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.41
Consensus pattern (76 bp):
CCTGAAACCCGAATTCTCTCCGGTTAGATACCTATTTTACTGAAAATACTCACCCTAAAATTTTA
TTTGTACTCAT
Found at i:2455172 original size:23 final size:23
Alignment explanation
Indices: 2455146--2455214 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
2455136 CACCACAGCT
*
2455146 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
2455169 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
2455192 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2455215 TATAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2456894 original size:64 final size:63
Alignment explanation
Indices: 2456785--2456946 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 63
2456775 TTCCCTTGAA
* * *
2456785 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * ** *
2456849 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
*
2456913 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
2456947 CTGAACAATT
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
63 2 0.02
64 73 0.87
65 9 0.11
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:2458897 original size:117 final size:117
Alignment explanation
Indices: 2458650--2459105 Score: 433
Period size: 117 Copynumber: 3.9 Consensus size: 117
2458640 CAAACTAAGG
* * * *
2458650 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTCTATCATCAGATGAGTTCTTCTCATTATTAA-
1 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCATCATCGGATGAGTTCTTCTCAATATGAAC
* * * * * * * * *
2458714 TTTCCACTAGAAAT-ATTGATTCATCTCCTTCTATGATGAAATCAAACCAAGG
66 TCTCCACTGGAAATGA-TGATCCACCTCCTTCTATGATGGATTCGAACAAAGA
* *
2458766 TTGAACAAGTTCTTCTCT-TTATGAAGTTCTTCTCCCTCATCGGATGAGTTCTTCTCAATATGAA
1 TTGAACAAGTTCTTCT-TATTATGAACTTCTTCTCCATCATCGGATGAGTTCTTCTCAATATGAA
* *
2458830 CTCTCCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGATTCGAACAAAGA
65 CTCTCCACTGGAAATGATGATCCACCTCCTTCTATGATGGATTCGAACAAAGA
* * * * * *
2458883 TTGAA-AATGTTCTTCTTATTGTGAAATTCTTCTCCCTCATCGGACGTGTTCTTAT-AATTATGA
1 TTGAACAA-GTTCTTCTTATTATGAACTTCTTCTCCATCATCGGATGAGTTCTTCTCAA-TATGA
* * * * * *
2458946 ACCTCTCCATTGGAAATGACGACCCACCTCCTTCTATGATAGATTTG-A-AAGGA
64 A-CTCTCCACTGGAAATGATGATCCACCTCCTTCTATGATGGATTCGAACAAAGA
* * * * * * * *
2458999 -CGAACAAGTTATTATCATTATGAACTTCTTCTTCATCCTCGAATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCATCATCGGATGAGTTCTTCTCAATATGAAC
** * *
2459063 TCCTCCTTTGGAAATGATGATCCACATCCTTTTATGATGGATT
66 T-CTCCACTGGAAATGATGATCCACCTCCTTCTATGATGGATT
2459106 TGACTCTGCA
Statistics
Matches: 280, Mismatches: 50, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
114 2 0.01
115 79 0.28
116 68 0.24
117 93 0.33
118 38 0.14
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (117 bp):
TTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCATCATCGGATGAGTTCTTCTCAATATGAAC
TCTCCACTGGAAATGATGATCCACCTCCTTCTATGATGGATTCGAACAAAGA
Found at i:2465400 original size:19 final size:19
Alignment explanation
Indices: 2465363--2465404 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2465353 AATAATTTGA
*
2465363 GATTAAAATAACTTGATTT
1 GATTAAAATAACATGATTT
2465382 GATTAAAATAAGCAT-ATTT
1 GATTAAAATAA-CATGATTT
2465401 GATT
1 GATT
2465405 TTTCAGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (19 bp):
GATTAAAATAACATGATTT
Found at i:2467493 original size:17 final size:15
Alignment explanation
Indices: 2467452--2467490 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
2467442 ATCACTCTCA
2467452 TTTCTCTCTTTTGCC
1 TTTCTCTCTTTTGCC
2467467 TTTCTCTCTTTTGCC
1 TTTCTCTCTTTTGCC
2467482 TTTCTCTCT
1 TTTCTCTCT
2467491 CTTAAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTCTCTCTTTTGCC
Found at i:2468245 original size:112 final size:113
Alignment explanation
Indices: 2468039--2468246 Score: 264
Period size: 112 Copynumber: 1.8 Consensus size: 113
2468029 TCTAAGCTAT
*
2468039 AAGTTCTTCTCATTATGAACTTTTCTCTCACTTCGGACGAGTTCTTATTATGAACTCTTCCACTA
1 AAGTTCTTCTCATTATGAAC-TTTCTCTCAC-TCGGACGAGTTCTTATTATGAAATCTTCCACTA
* *
2468104 GGAATGACGATCCATCTCCTTCTGTGATGGAATCTAGCAAAAGGTTGAAC
64 GGAAAGACGATCCACCTCCTTCTGTGATGGAATCTAGCAAAAGGTTGAAC
* *
2468154 AAGTTCTTCTTATTATGAAC-TTCT-TCA-TCGGATGAGTTCTTCTCATTATGAAATC-TCCA-T
1 AAGTTCTTCTCATTATGAACTTTCTCTCACTCGGACGAGTTC-T-T-ATTATGAAATCTTCCACT
* *
2468214 TGGAAAAGATGATCCACCTCCTTCTGTGATGGA
63 AGG-AAAGACGATCCACCTCCTTCTGTGATGGA
2468247 TTCGAATCTT
Statistics
Matches: 82, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
110 11 0.13
111 4 0.05
112 34 0.41
113 14 0.17
115 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (113 bp):
AAGTTCTTCTCATTATGAACTTTCTCTCACTCGGACGAGTTCTTATTATGAAATCTTCCACTAGG
AAAGACGATCCACCTCCTTCTGTGATGGAATCTAGCAAAAGGTTGAAC
Found at i:2469073 original size:42 final size:42
Alignment explanation
Indices: 2468983--2469064 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
2468973 GGTGTTTTAT
* *
2468983 CATCTTGCTCAAAAGACTTACAGATGACCTGAAGGATTTAAA
1 CATCATGCTCAAAAGACTTACAGATGACCTGAAGGACTTAAA
* * *
2469025 CATCATGCTCGAAATACTTACAGATGGCCTGAAGGACTTA
1 CATCATGCTCAAAAGACTTACAGATGACCTGAAGGACTTA
2469065 CGAATCATGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (42 bp):
CATCATGCTCAAAAGACTTACAGATGACCTGAAGGACTTAAA
Found at i:2469161 original size:243 final size:247
Alignment explanation
Indices: 2468733--2469586 Score: 1178
Period size: 260 Copynumber: 3.4 Consensus size: 247
2468723 TGAACTGAAG
* * *
2468733 GTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAATGATTTAAGCATCATGCTCAAAAGA
1 GTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGA
* *
2468798 CTTACAGATGGCTCGAAGGACTTACGAATCAAGAAACCCTCGAAA-ACTTAGTTTTTTAGTTGTC
66 CTTACAGATGGCCCGAAGGACTTACGAATCAAGAAACCCTCGAAAGA-TTAGTTTCTTAGTTGTC
* * *
2468862 AAGAAACCCCTTTATTAGGCTTAGCTTCCTTTAACAACTCTTTTGAGATAATTAGGAAACCCCCG
130 AAGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTTTTTTGAGATAATTAGGAAACCCCCG
*
2468927 AAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCTAGCACTG-A-A-GG-T
195 AAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGTATATGGAT
* * *
2468976 GTTTTATCATCTTGCTCAAAAGACTTACAGATGACCTGAAGGATTTAAACATCATGCTCGAAATA
1 GTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGA
* * *
2469041 CTTACAGATGGCCTGAAGGACTTACGAATCATGAAACCCTTGAAAGATTAGTTTCTTAGTTGTCA
66 CTTACAGATGGCCCGAAGGACTTACGAATCAAGAAACCCTCGAAAGATTAGTTTCTTAGTTGTCA
*
2469106 AGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTTTTTTGAGATAATTAGGAAACCCCCTA
131 AGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTTTTTTGAGATAATTAGGAAACCCCCGA
* * *
2469171 AAGGCTTAGTTTATAAAATCTCATTTGAAAACATCCAACACTAAAGGTCTTATGATGACCCGAAG
196 AAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACT----G---TAT-ATG----G-AT
* *
2469236 GTTTTATCATCTTGATCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAATA
1 GTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGA
**
2469301 CTTACAGATGGCCCGAAGGACTTACGAATCAAGAAACCCTCGAAAGCGTAGTTTCTTAGTTGTCA
66 CTTACAGATGGCCCGAAGGACTTACGAATCAAGAAACCCTCGAAAGATTAGTTTCTTAGTTGTCA
* *
2469366 AGGAACCCCTTTGTTAGGTTTAGCTTCCTTTAACAACTTTTTTGAGATAATTATGAAACCCCCGA
131 AGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTTTTTTGAGATAATTAGGAAACCCCCGA
2469431 AAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGACCCGAA
196 AAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACT----G---TAT--ATG----G-A
*
2469496 C
247 T
2469497 GTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGA
1 GTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGA
*
2469562 CTTACAGATAGCCCGAAGGACTTAC
66 CTTACAGATGGCCCGAAGGACTTAC
2469587 AAATTTGGGA
Statistics
Matches: 555, Mismatches: 37, Indels: 20
0.91 0.06 0.03
Matches are distributed among these distances:
243 217 0.39
244 1 0.00
247 1 0.00
251 1 0.00
253 1 0.00
254 1 0.00
258 1 0.00
260 234 0.42
261 98 0.18
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (247 bp):
GTTTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGGATTTAAACATCATGCTCGAAAGA
CTTACAGATGGCCCGAAGGACTTACGAATCAAGAAACCCTCGAAAGATTAGTTTCTTAGTTGTCA
AGGAACCCCTTTGTTAGGCTTAGCTTCCTTTAACAACTTTTTTGAGATAATTAGGAAACCCCCGA
AAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGTATATGGAT
Found at i:2469306 original size:42 final size:42
Alignment explanation
Indices: 2469224--2469320 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 42
2469214 AAGGTCTTAT
* * *
2469224 GATGACCCGAAGG-TTTTATCATCTTGATCGAAAGACTTACA
1 GATGACCCGAAGGATTTAAACATCATGATCGAAAGACTTACA
* *
2469265 GATGACCCGAAGGATTTAAACATCATGCTCGAAATACTTACA
1 GATGACCCGAAGGATTTAAACATCATGATCGAAAGACTTACA
*
2469307 GATGGCCCGAAGGA
1 GATGACCCGAAGGA
2469321 CTTACGAATC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
41 13 0.27
42 36 0.73
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (42 bp):
GATGACCCGAAGGATTTAAACATCATGATCGAAAGACTTACA
Found at i:2469561 original size:42 final size:42
Alignment explanation
Indices: 2469485--2469581 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
2469475 AGGTCTTATG
* * * *
2469485 GATGACCCGAACG-TTTTATCATCTTGCTCGAAAGACTTACA
1 GATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACA
2469526 GATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACA
1 GATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACA
2469568 GAT-AGCCCGAAGGA
1 GATGA-CCCGAAGGA
2469582 CTTACAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
41 13 0.26
42 37 0.74
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (42 bp):
GATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACA
Found at i:2469583 original size:20 final size:20
Alignment explanation
Indices: 2469513--2469587 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
2469503 TCATCTTGCT
2469513 CGAAAGACTTACAGAT-GACC
1 CGAAAGACTTACAGATAG-CC
* * * * *
2469533 CGAAGGATTTAAACATCATGCT
1 CGAAAGACTTACAGAT-A-GCC
2469555 CGAAAGACTTACAGATAGCC
1 CGAAAGACTTACAGATAGCC
*
2469575 CGAAGGACTTACA
1 CGAAAGACTTACA
2469588 AATTTGGGAA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
20 26 0.63
21 1 0.02
22 13 0.32
23 1 0.02
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.19
Consensus pattern (20 bp):
CGAAAGACTTACAGATAGCC
Found at i:2472235 original size:20 final size:21
Alignment explanation
Indices: 2472202--2472248 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2472192 ATTTATTTTC
*
2472202 TTCTTCTTC-TTTTTTTTCTT
1 TTCTTCTTCATTTTTTCTCTT
*
2472222 TTCTTTTTCATTTTTTCTCTT
1 TTCTTCTTCATTTTTTCTCTT
2472243 TT-TTCT
1 TTCTTCT
2472249 GATGGATGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (21 bp):
TTCTTCTTCATTTTTTCTCTT
Found at i:2478408 original size:2 final size:2
Alignment explanation
Indices: 2478401--2478442 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2478391 TGAATTTTTC
2478401 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2478443 TAATGTGACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2481043 original size:2 final size:2
Alignment explanation
Indices: 2481036--2481062 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2481026 CATATTAAAT
2481036 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 T
2481063 GAGATAGGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2482101 original size:22 final size:23
Alignment explanation
Indices: 2482056--2482112 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 23
2482046 ACATTACATG
* *
2482056 TTTATAAATTTAAAAATATATAT
1 TTTAAAAACTTAAAAATATATAT
*
2482079 TTTAAAAACTTAAAATTATTATTAT
1 TTTAAAAACTTAAAAATA-TA-TAT
2482104 TTCTAAAAA
1 TT-TAAAAA
2482113 AACCCAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.54
24 2 0.07
25 5 0.18
26 6 0.21
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAAAAACTTAAAAATATATAT
Found at i:2484755 original size:17 final size:18
Alignment explanation
Indices: 2484733--2484778 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
2484723 TATGAAATTG
*
2484733 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
2484750 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
2484768 -ATTCCAATTCC
1 GATTCCAATTCC
2484779 CTCAAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.28, C:0.33, G:0.07, T:0.33
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:2487104 original size:32 final size:32
Alignment explanation
Indices: 2487062--2487159 Score: 160
Period size: 32 Copynumber: 3.1 Consensus size: 32
2487052 TGAACAAACA
* * *
2487062 AATTAACGAACGTGCCCGAACGTAAATGAACG
1 AATTACCGAACGTTCACGAACGTAAATGAACG
*
2487094 AATTACCGAACGTTCACGAACGTAAATGAATG
1 AATTACCGAACGTTCACGAACGTAAATGAACG
2487126 AATTACCGAACGTTCACGAACGTAAATGAACG
1 AATTACCGAACGTTCACGAACGTAAATGAACG
2487158 AA
1 AA
2487160 CGAGCCCTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.18
Consensus pattern (32 bp):
AATTACCGAACGTTCACGAACGTAAATGAACG
Found at i:2488495 original size:14 final size:14
Alignment explanation
Indices: 2488476--2488507 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
2488466 TAAAATCAAT
2488476 TGGTAATAGGTGGA
1 TGGTAATAGGTGGA
2488490 TGGTAATAGGTGGA
1 TGGTAATAGGTGGA
2488504 -GGTA
1 TGGTA
2488508 CAAGATAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.28, C:0.00, G:0.44, T:0.28
Consensus pattern (14 bp):
TGGTAATAGGTGGA
Found at i:2489708 original size:15 final size:15
Alignment explanation
Indices: 2489684--2489718 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2489674 ACCTAAACCC
* *
2489684 TAAAACAAACCAAGA
1 TAAAAAAAACCAAAA
2489699 TAAAAAAAACCAAAA
1 TAAAAAAAACCAAAA
2489714 TAAAA
1 TAAAA
2489719 TTTTCAAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.14, G:0.03, T:0.09
Consensus pattern (15 bp):
TAAAAAAAACCAAAA
Found at i:2490558 original size:2 final size:2
Alignment explanation
Indices: 2490551--2490592 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2490541 TGTAAAATTA
2490551 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2490593 TGTGCAATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2490950 original size:19 final size:21
Alignment explanation
Indices: 2490923--2490966 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2490913 ATAATTTTAA
2490923 TTTAATTT-ATATTTAT-GTT
1 TTTAATTTAATATTTATAGTT
*
2490942 TTTATTTTAAATATTTATAGTT
1 TTTAATTT-AATATTTATAGTT
2490964 TTT
1 TTT
2490967 TAATGTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
21 8 0.38
22 6 0.29
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (21 bp):
TTTAATTTAATATTTATAGTT
Found at i:2496536 original size:21 final size:22
Alignment explanation
Indices: 2496495--2496537 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2496485 ATTTTATAAC
*
2496495 GTTTAATTCAATAATATTTTAT
1 GTTTAATTCAATAATAATTTAT
*
2496517 GTTTAATT-ATTAATAATTTAT
1 GTTTAATTCAATAATAATTTAT
2496538 TGGTATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (22 bp):
GTTTAATTCAATAATAATTTAT
Found at i:2498547 original size:2 final size:2
Alignment explanation
Indices: 2498540--2498567 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2498530 AACATATTTA
2498540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2498568 TAGATTTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2498924 original size:3 final size:3
Alignment explanation
Indices: 2498916--2498948 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2498906 AATCTCAAAT
2498916 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2498949 TACAAACTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2501382 original size:45 final size:45
Alignment explanation
Indices: 2501327--2501544 Score: 283
Period size: 45 Copynumber: 4.8 Consensus size: 45
2501317 TATATCACCA
2501327 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACT
* * * * * *
2501372 TCTATGTTGATAATGTACCCATATACATTTCAACCATAATATACT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACT
* * * * * *
2501417 TTTCTGTTGATAATGTACCCATATACATTTTAACTCTAGCATATT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACT
* *
2501462 TTTTTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATATCT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA-CT
* *
2501508 TTTCTGTTGATAATTCACCTATATGCATTTCAACTAT
1 TTTCTGTTGATAATGCACCCATATGCATTTCAACTAT
2501545 GGCATCCTTT
Statistics
Matches: 148, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
45 114 0.77
46 34 0.23
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.42
Consensus pattern (45 bp):
TTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATACT
Found at i:2502158 original size:19 final size:22
Alignment explanation
Indices: 2502107--2502162 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
2502097 TCGATTTAGC
*
2502107 ATGGTATCGATACCCCTATGTT
1 ATGGTATCGATACCCCTATGCT
*
2502129 ATGGTACCGATACCCC-AT-CT
1 ATGGTATCGATACCCCTATGCT
2502149 A-GGTATCGATACCC
1 ATGGTATCGATACCC
2502163 AATTTAGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.39
20 2 0.06
21 2 0.06
22 15 0.48
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.29
Consensus pattern (22 bp):
ATGGTATCGATACCCCTATGCT
Found at i:2508409 original size:45 final size:45
Alignment explanation
Indices: 2508354--2508571 Score: 301
Period size: 45 Copynumber: 4.8 Consensus size: 45
2508344 TCTAACATCA
*
2508354 TTTATGTTGATAATGCACCCATATGCATTTCAACTATAGTATACT
1 TTTATATTGATAATGCACCCATATGCATTTCAACTATAGTATACT
* * * *
2508399 TTTATATTGATAATGTACCCATATACATTTCAACCATAGTATATT
1 TTTATATTGATAATGCACCCATATGCATTTCAACTATAGTATACT
* * * * * *
2508444 TTTCTGTTGATAATGTACCCATATACATTTCAACTCTAGCATACT
1 TTTATATTGATAATGCACCCATATGCATTTCAACTATAGTATACT
* *
2508489 TTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGTATACTT
1 TTTATATTGATAATGCACCCATATGCATTTCAACTATAGTATAC-T
*
2508535 TTTTTATTGATAATGCACCCATATGCATTTCAACTAT
1 TTTATATTGATAATGCACCCATATGCATTTCAACTAT
2508572 GACATCTTTT
Statistics
Matches: 155, Mismatches: 17, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
45 119 0.77
46 36 0.23
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (45 bp):
TTTATATTGATAATGCACCCATATGCATTTCAACTATAGTATACT
Done.