Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008463.1 Hibiscus syriacus cultivar Beakdansim tig00111276_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: 1833679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:935558 original size:19 final size:19
Alignment explanation
Indices: 935534--935571 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
935524 GTGGGCGGGT
935534 GGTAGATTGCAAAATATTA
1 GGTAGATTGCAAAATATTA
935553 GGTAGATTGCAAAATATTA
1 GGTAGATTGCAAAATATTA
935572 AGTGGGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (19 bp):
GGTAGATTGCAAAATATTA
Found at i:939846 original size:19 final size:20
Alignment explanation
Indices: 939812--939849 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
939802 TTATAACCGG
*
939812 ACTAAAAAGTTTTTTTTAAT
1 ACTAAAAAGTTATTTTTAAT
939832 ACTAAAAAG-TATTTTTAA
1 ACTAAAAAGTTATTTTTAA
939850 GATTAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
ACTAAAAAGTTATTTTTAAT
Found at i:943841 original size:24 final size:24
Alignment explanation
Indices: 943814--943873 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
943804 AGAAGAAAAG
* * *
943814 TGAAGAAAAAGATGGGGAATGGGT
1 TGAAGAAGAAGATGAGGAATGAGT
943838 TGAAGAAGAAGATGAGGAATGAGT
1 TGAAGAAGAAGATGAGGAATGAGT
*
943862 TTAAGAAGAAGA
1 TGAAGAAGAAGA
943874 AGAAGAAGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.37, T:0.17
Consensus pattern (24 bp):
TGAAGAAGAAGATGAGGAATGAGT
Found at i:945448 original size:100 final size:99
Alignment explanation
Indices: 945314--945497 Score: 228
Period size: 101 Copynumber: 1.8 Consensus size: 99
945304 CCAAATTATG
* * * * ** * *
945314 AAAATTAGAAATAAATAGGGGTTATTTTATACTAAATAGT-TTCTT-GGGATTAAATTGAATAAA
1 AAAAATAGAAACAAATAGAGGTTATTTTAGACTAAATA-TATT-TTAAAGACTAAATTAAATAAA
945377 AATATTATAATATCAAAAATATTTGACCAAGTTAAA
64 AATATTATAATATCAAAAATATTTGACCAAGTTAAA
*
945413 AAAAATAGAAACAAATAGAGTTTAATTTTAGACTAAATATAATTTTAAAGACTAAATTAAATAAA
1 AAAAATAGAAACAAATAGAGGTT-ATTTTAGACTAAATAT-ATTTTAAAGACTAAATTAAATAAA
*
945478 AATATTATAATATTAAAAAT
64 AATATTATAATATCAAAAAT
945498 GTCGAACTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
99 20 0.28
100 16 0.23
101 35 0.49
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.34
Consensus pattern (99 bp):
AAAAATAGAAACAAATAGAGGTTATTTTAGACTAAATATATTTTAAAGACTAAATTAAATAAAAA
TATTATAATATCAAAAATATTTGACCAAGTTAAA
Found at i:945457 original size:17 final size:18
Alignment explanation
Indices: 945435--945469 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
945425 AAATAGAGTT
945435 TAATTTT-AGACTAAATA
1 TAATTTTAAGACTAAATA
945452 TAATTTTAAAGACTAAAT
1 TAATTTT-AAGACTAAAT
945470 TAAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (18 bp):
TAATTTTAAGACTAAATA
Found at i:948377 original size:17 final size:17
Alignment explanation
Indices: 948357--948403 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
948347 ACATTATCAT
948357 TAAT-TTTATTTTATTTA
1 TAATATTTATTTTA-TTA
948374 TAATATTTA-TTTATTA
1 TAATATTTATTTTATTA
*
948390 TAATATTAATTTTA
1 TAATATTTATTTTA
948404 AAAATATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 11 0.41
17 12 0.44
18 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TAATATTTATTTTATTA
Found at i:948392 original size:16 final size:17
Alignment explanation
Indices: 948357--948401 Score: 58
Period size: 16 Copynumber: 2.7 Consensus size: 17
948347 ACATTATCAT
948357 TAAT-TTTATTTTATTTA
1 TAATATTTA-TTTATTTA
948374 TAATATTTATTTA-TTA
1 TAATATTTATTTATTTA
*
948390 TAATATTAATTT
1 TAATATTTATTT
948402 TAAAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 14 0.54
17 8 0.31
18 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TAATATTTATTTATTTA
Found at i:948425 original size:18 final size:18
Alignment explanation
Indices: 948402--948436 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
948392 ATATTAATTT
*
948402 TAAAAATATAAAAAAATC
1 TAAAAAAATAAAAAAATC
*
948420 TAAAAAAATACAAAAAT
1 TAAAAAAATAAAAAAAT
948437 TTCGAAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (18 bp):
TAAAAAAATAAAAAAATC
Found at i:948840 original size:2 final size:2
Alignment explanation
Indices: 948833--948873 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
948823 CAAGATGGGT
948833 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
948874 GTGTGTGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:950453 original size:16 final size:15
Alignment explanation
Indices: 950432--950464 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
950422 AAATATTTTG
*
950432 ATATATAT-TCATAA
1 ATATATATATAATAA
950446 ATATATATATAATAA
1 ATATATATATAATAA
950461 ATAT
1 ATAT
950465 TAACTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATATATAATAA
Found at i:952664 original size:4 final size:4
Alignment explanation
Indices: 952655--952729 Score: 61
Period size: 4 Copynumber: 19.0 Consensus size: 4
952645 TGCTTGAAGA
*
952655 AAAG AAAG -AA- AAAG AAAG AAAAG AAAG AAAG AAAG AAA- AAAA AAAG
1 AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG
*
952701 TAAAAG AAAAA AAAG AAA- AAAG AAA- AAAG
1 --AAAG -AAAG AAAG AAAG AAAG AAAG AAAG
952730 GAGGGTCAAG
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
3 13 0.22
4 35 0.58
5 8 0.13
6 4 0.07
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (4 bp):
AAAG
Found at i:952665 original size:9 final size:9
Alignment explanation
Indices: 952651--952718 Score: 75
Period size: 9 Copynumber: 7.2 Consensus size: 9
952641 ATTATGCTTG
952651 AAGAAAAGA
1 AAGAAAAGA
952660 AAGAAAAAGA
1 AAG-AAAAGA
952670 AAGAAAAGA
1 AAGAAAAGA
952679 AAG-AAAGA
1 AAGAAAAGA
*
952687 AAGAAAAAAAA
1 AAG--AAAAGA
952698 AAGTAAAAGA
1 AAG-AAAAGA
*
952708 AAAAAAAGA
1 AAGAAAAGA
952717 AA
1 AA
952719 AAAGAAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
8 8 0.16
9 20 0.39
10 16 0.31
11 7 0.14
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:952683 original size:23 final size:22
Alignment explanation
Indices: 952655--952729 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 22
952645 TGCTTGAAGA
952655 AAAGAAAGAAAAAGAAAGAAAAG
1 AAAGAAAGAAAAAGAAA-AAAAG
*
952678 AAAGAAAGAAAGAAAAAAAAAAG
1 AAAGAAAGAAA-AAGAAAAAAAG
952701 TAAAAGAAA-AAAAAG-AAAAAAG
1 --AAAGAAAGAAAAAGAAAAAAAG
952723 AAA-AAAG
1 AAAGAAAG
952730 GAGGGTCAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
19 3 0.07
20 3 0.07
22 7 0.15
23 18 0.39
24 8 0.17
25 7 0.15
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.01
Consensus pattern (22 bp):
AAAGAAAGAAAAAGAAAAAAAG
Found at i:952715 original size:38 final size:37
Alignment explanation
Indices: 952654--952725 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
952644 ATGCTTGAAG
* *
952654 AAAAGAAAGAAAAAGAAAGAAAAGAAAGAAAGAAAGAA
1 AAAAAAAAGAAAAAGAAAAAAAAGAAA-AAAGAAAGAA
*
952692 AAAAAAAAGTAAAAGAAAAAAAAGAAAAAAGAAA
1 AAAAAAAAGAAAAAGAAAAAAAAGAAAAAAGAAA
952726 AAAGGAGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 7 0.23
38 24 0.77
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (37 bp):
AAAAAAAAGAAAAAGAAAAAAAAGAAAAAAGAAAGAA
Found at i:953745 original size:51 final size:51
Alignment explanation
Indices: 953676--954532 Score: 1579
Period size: 51 Copynumber: 16.7 Consensus size: 51
953666 TGCTCAATAA
953676 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
953727 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
953778 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
953829 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
953881 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
953933 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
953984 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
954035 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
954086 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
954137 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
954189 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
954240 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
954292 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
954343 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
954394 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
954446 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
954497 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
954533 ATTGGACAGA
Statistics
Matches: 785, Mismatches: 17, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
51 536 0.68
52 249 0.32
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (51 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
Found at i:954289 original size:308 final size:308
Alignment explanation
Indices: 953676--954551 Score: 1614
Period size: 308 Copynumber: 2.8 Consensus size: 308
953666 TGCTCAATAA
953676 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
953741 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
953806 CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
131 CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
*
953871 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCAT
196 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCAT
*
953936 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
261 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
953984 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
954049 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
954114 CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
131 CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
954179 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCAT
196 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCAT
*
954243 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
261 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
954292 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
*
954357 GTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* * *
954422 CTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAG
131 CTGATCTGGTTAGA-AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
* *
954487 A-AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA-AGC
195 ACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA-CATAGC
954550 AT
259 AT
954552 TTAATTTGGA
Statistics
Matches: 554, Mismatches: 10, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
307 49 0.09
308 445 0.80
309 58 0.10
310 2 0.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (308 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCAT
CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
Found at i:954543 original size:257 final size:256
Alignment explanation
Indices: 953676--954532 Score: 1642
Period size: 257 Copynumber: 3.3 Consensus size: 256
953666 TGCTCAATAA
953676 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
*
953741 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 GTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
953806 CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
131 CTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
953871 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
196 -AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
*
953933 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
953998 GTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 GTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
954063 CTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
131 CTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
954128 AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
196 AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
954189 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
*
954254 GTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
66 GTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
954319 TCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAG
130 TCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAG
954384 AAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
195 AAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
*
954446 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
954511 GTTCTTTGAGTTATCTGATCTG
66 GTTCTTTGAGTTATCTGATCTG
954533 ATTGGACAGA
Statistics
Matches: 592, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
256 152 0.26
257 440 0.74
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (256 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
GTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
Found at i:956322 original size:3 final size:3
Alignment explanation
Indices: 956314--956390 Score: 100
Period size: 3 Copynumber: 25.0 Consensus size: 3
956304 TATCCATATC
* *
956314 ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT ATT ATT ATT AGT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* *
956360 ATT ATT AAT ATT AAT ATT ATAT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
956391 TAATAAATAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 59 0.92
4 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:956653 original size:114 final size:114
Alignment explanation
Indices: 956453--957081 Score: 1120
Period size: 114 Copynumber: 5.5 Consensus size: 114
956443 CCAGCCAACC
956453 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
956518 CAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGA
66 CAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGA
956567 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
956632 CAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGA
66 CAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGA
956681 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
956746 CAACCTTTTGCTTGAATTCATCACTTGATGAATCATTCTTTTCCAGAGA
66 CAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGA
*
956795 AAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
956860 CAACCTTTTGCTTGAATTCATCATTTGATGGATCA-TCTTTTCCCGAGA
66 CAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGA
*
956908 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * *
956973 CAACCTTTTGCGTGAATTCATCATTTGATGGATCA-ACATTACCAG-GTA
66 CAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAG-A
* *
957021 AAGTTCATAATGAGAAGAACTCATTTGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
957082 CATCAAGAGC
Statistics
Matches: 499, Mismatches: 15, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
112 1 0.00
113 174 0.35
114 324 0.65
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (114 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGA
Found at i:957079 original size:113 final size:114
Alignment explanation
Indices: 955175--956064 Score: 1610
Period size: 114 Copynumber: 7.8 Consensus size: 114
955165 AAAGATTTGG
*
955175 ATTCATCAAATTGATGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 ATTCATC-ACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
955239 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTTGCTTGA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
955288 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
955353 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
955402 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
955467 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
955516 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
955581 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
955630 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
955695 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
*
955744 ATTCATCACTTGATGAATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
955809 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
* *
955858 ATTCATCATTTGATGGATCA-TCTTTTCCCGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
955922 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCGTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
* * * * *
955971 ATTCATCATTTGATGGATCA-ACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATTTGAAG
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
*
956034 AAGGAAGAAAAAGTTCATAATGAGAAGAACT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACT
956065 CATCAAGAGC
Statistics
Matches: 758, Mismatches: 16, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
112 13 0.02
113 264 0.35
114 481 0.63
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (114 bp):
ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
Found at i:957333 original size:3 final size:3
Alignment explanation
Indices: 957325--957554 Score: 299
Period size: 3 Copynumber: 77.3 Consensus size: 3
957315 TTTTTATCCA
* *
957325 TAT TAT TAT TAT TAT TAT TAT TAT TAAT TAT GAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
* *
957371 TAT TAT TAT TAT TAA TAT TAT TAT TA- TAT TAT TAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
957418 TAT TAT TAT TAT TAT TA- TAA TAT TAT TA- TAT TAT TA- TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
957463 TAT TAT TAT TAT TAT TAT TAT CAG TAT TAT TAT TAT TAT TAG CAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
957511 TAT TAT TAT TAT TAT ATAT TAT TAT TAG TAT T-T ATAT TAT TAT T
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT -TAT TAT TAT T
957555 TAATAAATAA
Statistics
Matches: 198, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
2 9 0.05
3 182 0.92
4 7 0.04
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:958244 original size:13 final size:13
Alignment explanation
Indices: 958226--958254 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
958216 ACCACCGTTA
958226 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
958239 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
958252 CGG
1 CGG
958255 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:958741 original size:19 final size:19
Alignment explanation
Indices: 958703--958738 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
958693 CAATTTAGTC
958703 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
958722 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
958739 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:970006 original size:4 final size:4
Alignment explanation
Indices: 969997--970067 Score: 73
Period size: 4 Copynumber: 19.0 Consensus size: 4
969987 TGCTTGAAGA
969997 AAAG AAAG AAA- AAAG AAAG AAAAG AAAG AAAG AAAG AAA- AAA- AAA-
1 AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* *
970042 AAAA AAAA AAAG AAA- AAAG AAA- AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG
970068 GAGGGTCAAG
Statistics
Matches: 61, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
3 18 0.30
4 39 0.64
5 4 0.07
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:970007 original size:9 final size:9
Alignment explanation
Indices: 969993--970056 Score: 71
Period size: 9 Copynumber: 7.2 Consensus size: 9
969983 ATTATGCTTG
969993 AAGAAAAGA
1 AAGAAAAGA
970002 AAGAAAAAAGA
1 AAG--AAAAGA
970013 AAGAAAAGA
1 AAGAAAAGA
970022 AAG-AAAGA
1 AAGAAAAGA
970030 AAGAAAA-A
1 AAGAAAAGA
*
970038 AA-AAAAAA
1 AAGAAAAGA
*
970046 AAAAAAAGA
1 AAGAAAAGA
970055 AA
1 AA
970057 AAAGAAAAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 10
0.82 0.02 0.17
Matches are distributed among these distances:
7 4 0.08
8 14 0.29
9 22 0.45
11 9 0.18
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:970018 original size:20 final size:19
Alignment explanation
Indices: 969993--970067 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 19
969983 ATTATGCTTG
969993 AAGAAAAGAAAGAAAAAAGA
1 AAGAAAA-AAAGAAAAAAGA
970013 AAGAAAAGAAAGAAAGAAAGA
1 AAGAAAA-AAAGAAA-AAAGA
*
970034 AA-AAAAAAA-AAAAAAAA
1 AAGAAAAAAAGAAAAAAGA
970051 AAG-AAAAAAGAAAAAAG
1 AAGAAAAAAAGAAAAAAG
970068 GAGGGTCAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
17 12 0.24
18 9 0.18
19 3 0.06
20 19 0.38
21 7 0.14
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAGAAAAAAGA
Found at i:970030 original size:8 final size:7
Alignment explanation
Indices: 970001--970067 Score: 82
Period size: 7 Copynumber: 9.6 Consensus size: 7
969991 TGAAGAAAAG
970001 AAAGAAA
1 AAAGAAA
970008 AAAGAAA
1 AAAGAAA
* *
970015 GAA-AAG
1 AAAGAAA
970021 AAAGAAA
1 AAAGAAA
970028 GAAAGAAA
1 -AAAGAAA
*
970036 AAAAAAA
1 AAAGAAA
*
970043 AAAAAAA
1 AAAGAAA
970050 AAAGAAA
1 AAAGAAA
970057 AAAGAAA
1 AAAGAAA
970064 AAAG
1 AAAG
970068 GAGGGTCAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 4 0.08
7 41 0.79
8 7 0.13
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:970030 original size:28 final size:28
Alignment explanation
Indices: 969997--970067 Score: 99
Period size: 29 Copynumber: 2.5 Consensus size: 28
969987 TGCTTGAAGA
* *
969997 AAAGAAAGAAAAAAGAAAGAAAAGAAAG
1 AAAGAAAGAAAAAAGAAAAAAAAAAAAG
*
970025 AAAGAAAGAAAAAAAAAAAAAAAAAAAAG
1 AAAGAAAG-AAAAAAGAAAAAAAAAAAAG
970054 AAA-AAAGAAAAAAG
1 AAAGAAAGAAAAAAG
970068 GAGGGTCAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
27 6 0.16
28 12 0.32
29 20 0.53
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (28 bp):
AAAGAAAGAAAAAAGAAAAAAAAAAAAG
Found at i:970039 original size:1 final size:1
Alignment explanation
Indices: 970005--970066 Score: 52
Period size: 1 Copynumber: 62.0 Consensus size: 1
969995 GAAAAGAAAG
* * * * * * * *
970005 AAAAAAGAAAGAAAAGAAAGAAAGAAAGAAAAAAAAAAAAAAAAAAAAGAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
970067 GGAGGGTCAA
Statistics
Matches: 45, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:971084 original size:51 final size:51
Alignment explanation
Indices: 971015--971871 Score: 1579
Period size: 51 Copynumber: 16.7 Consensus size: 51
971005 TGCTCAATAA
971015 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
971066 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
971117 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
971168 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
971220 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
971272 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
971323 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
971374 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
971425 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
971476 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
971528 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
971579 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
971631 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
971682 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
*
971733 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
971785 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
971836 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
971872 ATTGGACAGA
Statistics
Matches: 785, Mismatches: 17, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
51 536 0.68
52 249 0.32
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (51 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
Found at i:971628 original size:308 final size:308
Alignment explanation
Indices: 971015--971890 Score: 1614
Period size: 308 Copynumber: 2.8 Consensus size: 308
971005 TGCTCAATAA
971015 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
971080 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
971145 CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
131 CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
*
971210 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCAT
196 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCAT
*
971275 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAG
261 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
971323 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
971388 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
971453 CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
131 CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
971518 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCAT
196 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCAT
*
971582 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
261 CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAG
*
971631 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
*
971696 GTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* * *
971761 CTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAG
131 CTGATCTGGTTAGA-AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGG
* *
971826 A-AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACAGAATCA-AGC
195 ACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA-CATAGC
971889 AT
259 AT
971891 TTAATTTGGA
Statistics
Matches: 554, Mismatches: 10, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
307 49 0.09
308 445 0.80
309 58 0.10
310 2 0.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (308 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAACATAGCAT
CTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAG
Found at i:971882 original size:257 final size:256
Alignment explanation
Indices: 971015--971871 Score: 1642
Period size: 257 Copynumber: 3.3 Consensus size: 256
971005 TGCTCAATAA
971015 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
*
971080 GTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 GTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
971145 CTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA
131 CTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
971210 CAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
196 -AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
*
971272 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
971337 GTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
66 GTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
971402 CTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
131 CTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
971467 AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
196 AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
971528 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
*
971593 GTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
66 GTTCTTTGAGTTATCTGATCTGGTTAGA-AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
971658 TCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAG
130 TCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAG
971723 AAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
195 AAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
*
971785 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGT
1 CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
971850 GTTCTTTGAGTTATCTGATCTG
66 GTTCTTTGAGTTATCTGATCTG
971872 ATTGGACAGA
Statistics
Matches: 592, Mismatches: 7, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
256 152 0.26
257 440 0.74
ACGTcount: A:0.24, C:0.14, G:0.23, T:0.38
Consensus pattern (256 bp):
CATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGT
GTTCTTTGAGTTATCTGATCTGGTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGTTTAGAAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGA
AGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAACATAG
Found at i:972714 original size:114 final size:114
Alignment explanation
Indices: 972514--973404 Score: 1610
Period size: 114 Copynumber: 7.8 Consensus size: 114
972504 AAAGATTTGG
*
972514 ATTCATCAAATTGATGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 ATTCATC-ACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
972578 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
972628 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
972693 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
972742 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
972807 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
972856 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
972921 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
972970 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
973035 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
* *
973084 ATTCATCACTTGATGAATCATTCTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
*
973149 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
* *
973198 ATTCATCATTTGATGGATCA-TCTTTTCCCGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
973262 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCGTGA
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
* * * * *
973311 ATTCATCATTTGATGGATCA-ACATTACCAG-GTAAAGTTCATAATGAGAAGAACTCATTTGAAG
1 ATTCATCACTTGATGGATCATTCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAG
*
973374 AAGGAAGAAAAAGTTCATAATGAGAAGAACT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAACT
973405 CATCAAGAGC
Statistics
Matches: 757, Mismatches: 18, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
112 1 0.00
113 185 0.24
114 571 0.75
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.29
Consensus pattern (114 bp):
ATTCATCACTTGATGGATCATTCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA
Found at i:973658 original size:3 final size:3
Alignment explanation
Indices: 973650--973891 Score: 367
Period size: 3 Copynumber: 80.3 Consensus size: 3
973640 TTTTTATCCA
* * *
973650 TAT TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT GAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
973698 TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
973746 TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
973794 TAA TAT TAT TAT TAT TAT TAT TAT CAG TAT TAT TAT TAT TAT TAG CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
973842 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TATT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
973888 TAT T
1 TAT T
973892 TAATAAATAA
Statistics
Matches: 214, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
3 212 0.99
4 2 0.01
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:974579 original size:13 final size:13
Alignment explanation
Indices: 974561--974589 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
974551 ACCACCGTTA
974561 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
974574 CGGTGGCCGGCGG
1 CGGTGGCCGGCGG
974587 CGG
1 CGG
974590 AGTACGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.31, G:0.62, T:0.07
Consensus pattern (13 bp):
CGGTGGCCGGCGG
Found at i:975076 original size:19 final size:19
Alignment explanation
Indices: 975038--975073 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
975028 CAATTTAGTC
975038 ATTTATTTTATATGTTTTA
1 ATTTATTTTATATGTTTTA
975057 ATTTATTTTAT-TGTTTT
1 ATTTATTTTATATGTTTT
975074 TAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTATTTTATATGTTTTA
Found at i:975149 original size:16 final size:15
Alignment explanation
Indices: 975128--975160 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
975118 AAATATTTTG
*
975128 ATATATAT-TCATAA
1 ATATATATATAATAA
975142 ATATATATATAATAA
1 ATATATATATAATAA
975157 ATAT
1 ATAT
975161 TAACTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATATATAATAA
Found at i:979215 original size:3 final size:3
Alignment explanation
Indices: 979207--979236 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
979197 TCTTGAAAAT
979207 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
979237 ACTACGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:980864 original size:59 final size:59
Alignment explanation
Indices: 980800--980927 Score: 177
Period size: 59 Copynumber: 2.2 Consensus size: 59
980790 TATCTTCTAA
* *
980800 CTCCTATTTTGGTACTAAAGTTTAAAAATTTTCAATCT-AACTACTCAACTATCAAATTG
1 CTCCTATTTTGGTACTAAAATTTAAAAATTTTCAAT-TAAACCACTCAACTATCAAATTG
* * * * *
980859 TTCCTATTTGGGTACTAAAATTTTAAAATTTTCAGTTAAACCACTCAACTTTCAAATTG
1 CTCCTATTTTGGTACTAAAATTTAAAAATTTTCAATTAAACCACTCAACTATCAAATTG
980918 CTCCTATTTT
1 CTCCTATTTT
980928 AACCACTCTG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 1 0.02
59 58 0.98
ACGTcount: A:0.33, C:0.19, G:0.07, T:0.41
Consensus pattern (59 bp):
CTCCTATTTTGGTACTAAAATTTAAAAATTTTCAATTAAACCACTCAACTATCAAATTG
Found at i:1015005 original size:21 final size:21
Alignment explanation
Indices: 1014974--1015022 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1014964 AGTCGTGTAT
*
1014974 AGCCG-TTGGGGATGTTTTGG
1 AGCCGTTTGGGGATATTTTGG
1014994 AGCCGTTTGGGGATATTTTGG
1 AGCCGTTTGGGGATATTTTGG
*
1015015 AGTCGTTT
1 AGCCGTTT
1015023 ATGGATGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.12, C:0.10, G:0.39, T:0.39
Consensus pattern (21 bp):
AGCCGTTTGGGGATATTTTGG
Found at i:1015028 original size:21 final size:21
Alignment explanation
Indices: 1014974--1015034 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
1014964 AGTCGTGTAT
* *
1014974 AGCCG-TTGGGGATGTTTTGG
1 AGCCGTTTAGGGATATTTTGG
*
1014994 AGCCGTTTGGGGATATTTTGG
1 AGCCGTTTAGGGATATTTTGG
* *
1015015 AGTCGTTTATGGATGATTTT
1 AGCCGTTTAGGGAT-ATTTT
1015035 TTTTTGTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.14
21 25 0.71
22 5 0.14
ACGTcount: A:0.15, C:0.08, G:0.36, T:0.41
Consensus pattern (21 bp):
AGCCGTTTAGGGATATTTTGG
Found at i:1015197 original size:18 final size:17
Alignment explanation
Indices: 1015147--1015205 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
1015137 AGGGTATATT
1015147 GATACCCACAGGGGGTATC
1 GATACCCA-A-GGGGTATC
* *
1015166 GGTACCC-A-GGGTATT
1 GATACCCAAGGGGTATC
1015181 GATACCCATAGGGGTATC
1 GATACCCA-AGGGGTATC
1015199 GATACCC
1 GATACCC
1015206 TTTTTGCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
15 12 0.36
17 2 0.06
18 13 0.39
19 6 0.18
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (17 bp):
GATACCCAAGGGGTATC
Found at i:1015255 original size:22 final size:22
Alignment explanation
Indices: 1015230--1015272 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1015220 GTTTGAGCCT
*
1015230 TCATAGGGGTATTGATACCCAG
1 TCATAGGGGTATCGATACCCAG
1015252 TCATAGGGGTATCGATACCCA
1 TCATAGGGGTATCGATACCCA
1015273 TTAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (22 bp):
TCATAGGGGTATCGATACCCAG
Found at i:1015530 original size:18 final size:19
Alignment explanation
Indices: 1015493--1015545 Score: 72
Period size: 18 Copynumber: 2.7 Consensus size: 19
1015483 AAAAATATAT
1015493 CAATTGTTTACAAAAGGATAC
1 CAATTG-TTACAAAA-GATAC
1015514 CAATTGTTA-AAAAGATAC
1 CAATTGTTACAAAAGATAC
*
1015532 CAATTGTTAGAAAA
1 CAATTGTTACAAAA
1015546 TATATGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.45
19 8 0.26
20 3 0.10
21 6 0.19
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.28
Consensus pattern (19 bp):
CAATTGTTACAAAAGATAC
Found at i:1022686 original size:41 final size:41
Alignment explanation
Indices: 1022509--1022784 Score: 218
Period size: 41 Copynumber: 6.8 Consensus size: 41
1022499 CCTTTATTTA
** * ** *
1022509 AATTGAATTGGATTGTGAATTAATATATG-TTACCATGATCT
1 AATTGAATTAAATTGTGAATTATTGCATGCTT-CCATGATCG
*** * * * *
1022550 AATTGAATTGGTTTGTGAATAAATGCATG-TTTCATGACCG
1 AATTGAATTAAATTGTGAATTATTGCATGCTTCCATGATCG
* * * *
1022590 AATTGAATTGAATTATGGATTACTGCATGCTGT-CATGATCG
1 AATTGAATTAAATTGTGAATTATTGCATGCT-TCCATGATCG
* * *
1022631 AATTAAATTGAATTGTGAATTATTGCATGCTTCCATGATTG
1 AATTGAATTAAATTGTGAATTATTGCATGCTTCCATGATCG
* *
1022672 AATTGAATCAAATTGTGAATTATTGCATG-TTGCCATAATCG
1 AATTGAATTAAATTGTGAATTATTGCATGCTT-CCATGATCG
* * * * * *
1022713 AATTGAGTTTAATGGTGAATTATTGCATGTTTCTATGATTG
1 AATTGAATTAAATTGTGAATTATTGCATGCTTCCATGATCG
* * *
1022754 AACTGAATCAAATTGTGAATTAGTGCATGCT
1 AATTGAATTAAATTGTGAATTATTGCATGCT
1022785 AATAAGATCG
Statistics
Matches: 192, Mismatches: 38, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
40 32 0.17
41 157 0.82
42 3 0.02
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.39
Consensus pattern (41 bp):
AATTGAATTAAATTGTGAATTATTGCATGCTTCCATGATCG
Found at i:1022713 original size:82 final size:81
Alignment explanation
Indices: 1022520--1022782 Score: 265
Period size: 82 Copynumber: 3.2 Consensus size: 81
1022510 ATTGAATTGG
** * * ** * * *
1022520 ATTGTGAATTAATATATGTTACCATGATCTAATTGAATTGGTTTGTGAATAAATGCATGTTTCAT
1 ATTGTGAATTAATGCATGTTGCCATGATCGAATTGAATTGAATTGTGAATTATTGCATGTTCCAT
** **
1022585 GACCGAATTGAATTGA
66 GATTGAATTGAATCAA
* * * * * *
1022601 ATTATGGATTACTGCATGCTGTCATGATCGAATTAAATTGAATTGTGAATTATTGCATGCTTCCA
1 ATTGTGAATTAATGCATGTTGCCATGATCGAATTGAATTGAATTGTGAATTATTGCATG-TTCCA
1022666 TGATTGAATTGAATCAA
65 TGATTGAATTGAATCAA
* * * * * *
1022683 ATTGTGAATTATTGCATGTTGCCATAATCGAATTGAGTTTAATGGTGAATTATTGCATGTTTCTA
1 ATTGTGAATTAATGCATGTTGCCATGATCGAATTGAATTGAATTGTGAATTATTGCATG-TTCCA
*
1022748 TGATTGAACTGAATCAA
65 TGATTGAATTGAATCAA
*
1022765 ATTGTGAATTAGTGCATG
1 ATTGTGAATTAATGCATG
1022783 CTAATAAGAT
Statistics
Matches: 148, Mismatches: 33, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
81 45 0.30
82 103 0.70
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (81 bp):
ATTGTGAATTAATGCATGTTGCCATGATCGAATTGAATTGAATTGTGAATTATTGCATGTTCCAT
GATTGAATTGAATCAA
Found at i:1022795 original size:82 final size:82
Alignment explanation
Indices: 1022626--1022807 Score: 226
Period size: 82 Copynumber: 2.2 Consensus size: 82
1022616 ATGCTGTCAT
* * *
1022626 GATCGAATTAAATTGAATTGTGAATTATTGCATGCTTCCATGATTGAATTGAATCAAATTGTGAA
1 GATCGAATTGAATTGAATGGTGAATTATTGCATGCTTCCATGATTGAACTGAATCAAATTGTGAA
* * *
1022691 TTATTGCATGTTGCCATA
66 TTAGTGCATGCT-CAATA
* * * *
1022709 -ATCGAATTGAGTTTAATGGTGAATTATTGCATGTTTCTATGATTGAACTGAATCAAATTGTGAA
1 GATCGAATTGAATTGAATGGTGAATTATTGCATGCTTCCATGATTGAACTGAATCAAATTGTGAA
1022773 TTAGTGCATGCT-AATAA
66 TTAGTGCATGCTCAAT-A
1022790 GATCGAACTTG-ATTGAAT
1 GATCGAA-TTGAATTGAAT
1022808 TGAAATCTTG
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
80 2 0.02
81 1 0.01
82 78 0.93
83 3 0.04
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (82 bp):
GATCGAATTGAATTGAATGGTGAATTATTGCATGCTTCCATGATTGAACTGAATCAAATTGTGAA
TTAGTGCATGCTCAATA
Found at i:1025774 original size:4 final size:4
Alignment explanation
Indices: 1025765--1025797 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1025755 ATTCAAGAGC
1025765 TATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
1025798 TCTCTCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1026352 original size:54 final size:53
Alignment explanation
Indices: 1026293--1026405 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 53
1026283 GCTGCCGTTG
* *
1026293 TTCACATCCCTTCCGAACAA-CAAGTTTCACCGGAGACAACCGCTACTGAAGCTA
1 TTCACATCCCTTCCGAACAAGCAA--TTCACCGGAGAAAACCGCTACTGAAACTA
* * * * *
1026347 TTCACATCGCTTCCGTACAAGGCAATTCACCTGAGAAAACGGCTACTGAAACTG
1 TTCACATCCCTTCCGAACAA-GCAATTCACCGGAGAAAACCGCTACTGAAACTA
1026401 TTCAC
1 TTCAC
1026406 GCCGCTTCCG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 47 0.94
56 3 0.06
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.22
Consensus pattern (53 bp):
TTCACATCCCTTCCGAACAAGCAATTCACCGGAGAAAACCGCTACTGAAACTA
Found at i:1026412 original size:54 final size:54
Alignment explanation
Indices: 1026323--1026883 Score: 505
Period size: 54 Copynumber: 10.4 Consensus size: 54
1026313 CAAGTTTCAC
* * ** * *
1026323 CGGAGACAACCGCTACTGAAGCTATTCACATCGCTTCCGTACAAGGCAATTCAC
1 CGGAGAAAACCGCTACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAT
* * * * *
1026377 CTGAGAAAACGGCTACTGAAACTGTTCACGCCGCTTCCGTACTAGGAAAATCAT
1 CGGAGAAAACCGCTACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAT
* * * * * *
1026431 CGGAGAAGACCACTAATGAAGCTG-TCAACGTCGCTTTCGTACAAGGCAAATCCT
1 CGGAGAAAACCGCTACTGAAGCTGTTC-ACGCCGCTTCCGTACAAGGCAAATCAT
* * * * * *
1026485 CGGAGAAAGCCG-TAACTGAAGCTATCCACGTCGCTTCTGTTCAAGGCAAATCAT
1 CGGAGAAAACCGCT-ACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAT
* * * * *
1026539 CGGGGAAAGCTGTTACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAC
1 CGGAGAAAACCGCTACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAT
* * * * * *
1026593 CGGAGAAGACCACTACTGAAGCTGTCCACGTCGCTTCCGCACAACGCAAATCAT
1 CGGAGAAAACCGCTACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAT
* * * * * * *
1026647 CGGAGAAAGCCACTACTGAAGCTGTGCATGCCGTTTCCGCACAACGCAAATCAT
1 CGGAGAAAACCGCTACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAT
* * * * * ** * *
1026701 CGGAGAAAGCCGCTACCGAAGCTGTACATGCCGCTTTCACACAACGCAAATCGT
1 CGGAGAAAACCGCTACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAT
* * * * * *
1026755 CGGAGAAAACCGCTACTGAAGCTGTTCACACCGTTTCCGCAAAATGTAAATCAT
1 CGGAGAAAACCGCTACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAT
* * ** * *
1026809 CGCATAAAACCGCTGTTGAAGCTGTTCACGCCGCTTCCGTTCAACGCAAATCAT
1 CGGAGAAAACCGCTACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAT
* * *
1026863 CGCATAAAACCGCCACTGAAG
1 CGGAGAAAACCGCTACTGAAG
1026884 TTGCTCAGGC
Statistics
Matches: 413, Mismatches: 90, Indels: 8
0.81 0.18 0.02
Matches are distributed among these distances:
53 3 0.01
54 408 0.99
55 2 0.00
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.20
Consensus pattern (54 bp):
CGGAGAAAACCGCTACTGAAGCTGTTCACGCCGCTTCCGTACAAGGCAAATCAT
Found at i:1027887 original size:183 final size:181
Alignment explanation
Indices: 1027361--1028021 Score: 887
Period size: 182 Copynumber: 3.6 Consensus size: 181
1027351 GATACAAATG
* * *
1027361 AAAAATGTATCGCTCCATAACAATATTACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACA-GTAAAAATATGACAAAACCGGTCTCAAAATGACA
* *
1027426 AAACCGGTAAAATGCTACCAGATATGTTGAAAGTGTCGATACA-TTAATCTAAGTATCGACACTT
65 AAACCGGTAAAAAGCTACCAGATATGTTGAAAGTGTCGATA-ATTTAATATAAGTATCGACACTT
* * *
1027490 TCT-GAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAATGTCGATACTTTAT
129 T-TGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
* * *
1027543 GAAAATGTATCGACCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAAC-AGTAAAAATATGACAAAACCGGTCTCAAAATGACA
* * * * *
1027608 AAACAGGTAAATAA-CTATCGGATATGTTGAAAGTGTCGATACTTTAATACAAGTATCGACACTT
65 AAACCGGTAAA-AAGCTACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
1027672 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
129 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
* * * *
1027725 AAAAATGTATCGATCAATAACAATATAATATGTAAAAATATGACAAAACAGGTCTCAAAAATGAA
1 AAAAATGTATCGATCCATAACAATATAACA-GTAAAAATATGACAAAACCGGTCTC-AAAATGAC
* * * * * *
1027790 AAAACCGATAAAAAGATATCAGATATGTTGAAAGTATCGATAATTTAATATAAGTATAGATACTT
64 AAAACCGGTAAAAAGCTACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTT
*
1027855 TTGGAATTTAAAAGAGAATAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
129 TTGGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
* * ** * *
1027908 AAATATATATTAATCCATAATAATATAACAGATAAAAATATGACAAATCCGGTCTCAAAATGACA
1 AAAAATGTATCGATCCATAACAATATAACAG-TAAAAATATGACAAAACCGGTCTCAAAATGACA
* ** * *
1027973 AAACTGGTAAAGCGCTACCAAATATGTTGAAAGTGTCGATACTTTAATA
65 AAACCGGTAAAAAGCTACCAGATATGTTGAAAGTGTCGATAATTTAATA
1028022 AGTACGTATA
Statistics
Matches: 419, Mismatches: 52, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
181 2 0.00
182 258 0.62
183 159 0.38
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (181 bp):
AAAAATGTATCGATCCATAACAATATAACAGTAAAAATATGACAAAACCGGTCTCAAAATGACAA
AACCGGTAAAAAGCTACCAGATATGTTGAAAGTGTCGATAATTTAATATAAGTATCGACACTTTT
GGAATTTAAAAGAGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:1028016 original size:365 final size:364
Alignment explanation
Indices: 1027361--1028021 Score: 952
Period size: 365 Copynumber: 1.8 Consensus size: 364
1027351 GATACAAATG
* * * * * *
1027361 AAAAATGTATCGCTCCATAACAATATTACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
1 AAAAATGTATCGATCAATAACAATATAACAGGTAAAAATATGACAAAACAGGTCTCAAAATGAAA
* * * * * *
1027426 AAACCGGTAAAATGCTACCAGATATGTTGAAAGTGTCGATACATTAATCTAAGTATCGACACTTT
66 AAACCGATAAAAAGATACCAGATATGTTGAAAGTATCGATACATTAATATAAGTATAGACACTTT
* * *
1027491 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAATGTCGATACTTTATGAAAATGTATCGA
131 CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAATGTCGATACTTTATAAAAATATATCAA
*
1027556 CCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAATA
196 CCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAAGA
* **
1027621 ACTATCGGATATGTTGAAAGTGTCGATACTTTAATACAAGTATCGACACTTTTGGAATTTAAAAG
261 ACTACCAAATATGTTGAAAGTGTCGATACTTTAATACAAGTATCGACACTTTTGGAATTTAAAAG
1027686 AGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
326 AGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
* *
1027725 AAAAATGTATCGATCAATAACAATATAATATGTAAAAATATGACAAAACAGGTCTCAAAAATGAA
1 AAAAATGTATCGATCAATAACAATATAACAGGTAAAAATATGACAAAACAGGTCTC-AAAATGAA
* *
1027790 AAAACCGATAAAAAGATATCAGATATGTTGAAAGTATCGATA-ATTTAATATAAGTATAGATACT
65 AAAACCGATAAAAAGATACCAGATATGTTGAAAGTATCGATACA-TTAATATAAGTATAGACACT
* * *
1027854 TT-TGGAATTTAAAAGAGAATAAGTTATAGCGCCTATAAAGTGTCGATACTTTA-AAAATATATA
129 TTCT-GAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAATGTCGATACTTTATAAAA-ATATA
* * * * *
1027917 TTAATCCATAATAATATAACAGA-TAAAAATATGACAAATCCGGTCTCAAAATGACAAAACTGGT
192 TCAACCCATAACAATATAACA-ACTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGT
**
1027981 AAAGCGCTACCAAATATGTTGAAAGTGTCGATACTTTAATA
256 AAAGAACTACCAAATATGTTGAAAGTGTCGATACTTTAATA
1028022 AGTACGTATA
Statistics
Matches: 259, Mismatches: 33, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
364 55 0.21
365 203 0.78
366 1 0.00
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (364 bp):
AAAAATGTATCGATCAATAACAATATAACAGGTAAAAATATGACAAAACAGGTCTCAAAATGAAA
AAACCGATAAAAAGATACCAGATATGTTGAAAGTATCGATACATTAATATAAGTATAGACACTTT
CTGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAATGTCGATACTTTATAAAAATATATCAA
CCCATAACAATATAACAACTAAAAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAAGA
ACTACCAAATATGTTGAAAGTGTCGATACTTTAATACAAGTATCGACACTTTTGGAATTTAAAAG
AGAAGAAGTTATAGCGCCTATAAAGTGTCGATACTTTAA
Found at i:1028464 original size:199 final size:198
Alignment explanation
Indices: 1028259--1029154 Score: 735
Period size: 200 Copynumber: 4.6 Consensus size: 198
1028249 AGCGCACAAA
* * * * * * *
1028259 AAAGTGTCGATACATTTATAACATGTGTCGATCCCAAATACGTCGA-AACTATAATTATAATGTA
1 AAAGTGTCGATACATTTATAA-AAGTATCGACCCCAAATACATCGAGACCGAAAATTATAATGTA
* *
1028323 ATAGGTCACTTTACAATGTAACCGGTTTAAGTTTACCGGTTTATGAGAAAATATGTCTAAATAAT
65 ATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTATGAGAAAATAGGTCTAAATAAT
** * * *
1028388 GTATCGACATTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTATGTGCA
130 GTATCGACATTTTATACATTTGTGTCGATACTTTATATCCATAATGAA-TCCCAAACGATGTCCA
**
1028453 CTTAT
194 CGCAT
1028458 AAAGTGTCGATACATTTATTAAAAGTATCGACCCCAAATACATCGAGACCGAAAATTATAATGTA
1 AAAGTGTCGATACATTTA-TAAAAGTATCGACCCCAAATACATCGAGACCGAAAATTATAATGTA
* ** * *
1028523 ATAGGTCACTTTACAATGTAACCGATTTAAATTTACCAATTTTATGAGCAAATAGGTCTACATAA
65 ATAGGTCACTTTACAATGTAACCGGTTTAAATTTACC-GGTTTATGAGAAAATAGGTCTAAATAA
* * * *
1028588 TGTATCGATATTTTGTACATTTGTGTCGATACTTTATGTCCATAATGAATGCCAAACGATGTCCA
129 TGTATCGACATTTTATACATTTGTGTCGATACTTTATATCCATAATGAATCCCAAACGATGTCCA
1028653 CGCAT
194 CGCAT
* *
1028658 AAAATGTCGATGCATTTATAAAAAGTATCGACCCCAAATACATCGAGACCGAAAATTATAATGTA
1 AAAGTGTCGATACATTTAT-AAAAGTATCGACCCCAAATACATCGAGACCGAAAATTATAATGTA
* * * * *
1028723 ATATGTCAATTTACAATGGAACCGGTTGAAATTTACCGGTGTAAAT-AGAAAATAGGTC-AACAT
65 ATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGT-T-TATGAGAAAATAGGTCTAA-AT
* * * * *
1028786 AATGTGTCGACAGTTTT-TA-A-ATGTGTTGATAC-----AT---T--TG--T-CCAGACGAGGT
127 AATGTATCGACA-TTTTATACATTTGTGTCGATACTTTATATCCATAATGAATCCCAAACGATGT
**
1028835 GTACGCAT
191 CCACGCAT
* * * * * * * *
1028843 AAACTGTCGATATATTTATAAAAAGTATCGA-TCCTAATACATTGAAATCGATAA-T-T-AT-TA
1 AAAGTGTCGATACATTTAT-AAAAGTATCGACCCCAAATACATCGAGACCGAAAATTATAATGTA
* * * * * * * * * *
1028903 ACAGG-----TTACAATGTAACCGG-TAAAAGTATACCCGTTAATTAGCAAATATGTCTACATTA
65 ATAGGTCACTTTACAATGTAACCGGTTTAAA-TTTACCGGTTTATGAGAAAATAGGTCTAAATAA
* * * * * ** *
1028962 TGTATCGACACTCTTTA-A-ATATGTGTCGATACTTTTTTTTCCAAAATGAAAGCAAAAAC-AGG
129 TGTATCGACA-T-TTTATACATTTGTGTCGATAC-TTTATATCCATAATG-AATCCCAAACGATG
*
1029024 TGCACGCAT
190 TCCACGCAT
* * * * *
1029033 AAAGTGTCGATACATTTA-AAATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
1 AAAGTGTCGATACATTTATAAA-AGTATCGACCCCAAATACATCGAGACCGAAAATTATAATGTA
* * *
1029097 ATAGGTCAATTTACAATGTAATCGGTTGAAATTTACCGGTTTTATGAGAAAATAGGTC
65 ATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGG-TTTATGAGAAAATAGGTC
1029155 AATATAAGCG
Statistics
Matches: 563, Mismatches: 92, Indels: 83
0.76 0.12 0.11
Matches are distributed among these distances:
173 3 0.01
174 28 0.05
175 27 0.05
176 11 0.02
180 5 0.01
181 2 0.00
182 2 0.00
183 1 0.00
184 17 0.03
185 43 0.08
186 1 0.00
187 2 0.00
188 5 0.01
189 7 0.01
190 46 0.08
191 4 0.01
192 1 0.00
193 3 0.01
194 6 0.01
198 10 0.02
199 62 0.11
200 206 0.37
201 71 0.13
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (198 bp):
AAAGTGTCGATACATTTATAAAAGTATCGACCCCAAATACATCGAGACCGAAAATTATAATGTAA
TAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTATGAGAAAATAGGTCTAAATAATG
TATCGACATTTTATACATTTGTGTCGATACTTTATATCCATAATGAATCCCAAACGATGTCCACG
CAT
Found at i:1033959 original size:324 final size:324
Alignment explanation
Indices: 1033370--1034020 Score: 1167
Period size: 324 Copynumber: 2.0 Consensus size: 324
1033360 TCAAATCAGA
* *
1033370 TCTCAAGCAGTCTTCCCACTTCCGCCTTGGTCGTCCTCTTCTTCTGACACCGTCAATTGTGATCG
1 TCTCAAGCAGTCTTCCCACTTCCGCCTTGGTCGTCCTCTCCTTCTGACACCGTCAATTGTGATCA
1033435 ACTCTACCCTCCTGACCGCATCCGACGGTTGTCGCCTAAGGACATGCCCAAACCACCGTAGTCTT
66 ACTCTACCCTCCTGACCGCATCCGACGGTTGTCGCCTAAGGACATGCCCAAACCACCGTAGTCTT
*
1033500 CTCTCCCTCAATTTTTCGGATACAGGCACCACCCCCAAAGACATCCTAATAGAAGAGTTTGATGT
131 CCCTCCCTCAATTTTTCGGATACAGGCACCACCCCCAAAGACATCCTAATAGAAGAGTTTGATGT
*
1033565 CATGTCCCACAGAGTCTTACCACATGCCCATCGAAGCATTCTCATTTCTGCGGCCTCCATCTTCC
196 CATGTCCCACAGAGTCTTACCACATGCCCATCGAAGCATTCTCATTTCTGCGGCCTCCATCCTCC
* * *
1033630 TTATGTGATCCTTCTTGATTGCCCAACATTTTGATCCATACAACAGCGCTGATCTTTTTGCCAT
261 TTATGTGATCATTCTTGATTGCCCAACATTCTGATCCATACAACAGCGCTGATCTTATTGCCAT
* *
1033694 TCTCAAGCAGTCTTCCCACTTCCGCCTTGGTCGTCCTCTCCTTCTGGCACCGTCGATTGTGATCA
1 TCTCAAGCAGTCTTCCCACTTCCGCCTTGGTCGTCCTCTCCTTCTGACACCGTCAATTGTGATCA
*
1033759 ACTCTACCCTCCTGACCGCATCCGACGGTTGTTGCCTAAGGACATGCCCAAACCACCGTAGTCTT
66 ACTCTACCCTCCTGACCGCATCCGACGGTTGTCGCCTAAGGACATGCCCAAACCACCGTAGTCTT
* * *
1033824 CCCTCCCTCAATTTTTCGGATACAGGCACCACCCCCAAGGACATCTTAATAGAAGAGTTTGGTGT
131 CCCTCCCTCAATTTTTCGGATACAGGCACCACCCCCAAAGACATCCTAATAGAAGAGTTTGATGT
1033889 CATGTCCCACAGAGTCTTACCACATGCCCATCGAAGCATTCTCATTTCTGCGGCCTCCATCCTCC
196 CATGTCCCACAGAGTCTTACCACATGCCCATCGAAGCATTCTCATTTCTGCGGCCTCCATCCTCC
* *
1033954 TTATGTGATCATTCTTGATTGCCCAACATTCTGATCCATACAGCAGCGCTGGTCTTATTGCCAT
261 TTATGTGATCATTCTTGATTGCCCAACATTCTGATCCATACAACAGCGCTGATCTTATTGCCAT
1034018 TCT
1 TCT
1034021 ATAAAATTTT
Statistics
Matches: 312, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
324 312 1.00
ACGTcount: A:0.21, C:0.33, G:0.16, T:0.29
Consensus pattern (324 bp):
TCTCAAGCAGTCTTCCCACTTCCGCCTTGGTCGTCCTCTCCTTCTGACACCGTCAATTGTGATCA
ACTCTACCCTCCTGACCGCATCCGACGGTTGTCGCCTAAGGACATGCCCAAACCACCGTAGTCTT
CCCTCCCTCAATTTTTCGGATACAGGCACCACCCCCAAAGACATCCTAATAGAAGAGTTTGATGT
CATGTCCCACAGAGTCTTACCACATGCCCATCGAAGCATTCTCATTTCTGCGGCCTCCATCCTCC
TTATGTGATCATTCTTGATTGCCCAACATTCTGATCCATACAACAGCGCTGATCTTATTGCCAT
Found at i:1036113 original size:32 final size:30
Alignment explanation
Indices: 1036072--1036277 Score: 130
Period size: 32 Copynumber: 6.9 Consensus size: 30
1036062 TAAATTTCAA
1036072 AATATATTATAATTATATATTATTAATTATTT
1 AATATATTATAA-TATATATTATTAATTA-TT
* *
1036104 AATATATTATACATATA-ATTTTTTATTATTT
1 AATATATTATA-ATATATATTATTAATTA-TT
* *
1036135 CAAAAT-TTATAAAATATATTA-TAATTATT
1 -AATATATTATAATATATATTATTAATTATT
* * *
1036164 -ATTTA-TAAAATATCTATT-TTAATTATT
1 AATATATTATAATATATATTATTAATTATT
*
1036191 ATATTTATT-TAAT-TATATT-TTAATTATTT
1 A-ATATATTATAATATATATTATTAATTA-TT
*
1036220 ATTATATT-TAATAATTAATATTATTAATTATT
1 AATATATTATAAT-A-T-ATATTATTAATTATT
* *
1036252 -AT-TATTATATTTATTTATTATTAATT
1 AATATATTATA-ATATATATTATTAATT
1036278 TCAATTTAAA
Statistics
Matches: 140, Mismatches: 18, Indels: 35
0.73 0.09 0.18
Matches are distributed among these distances:
27 20 0.14
28 21 0.15
29 24 0.17
30 15 0.11
31 25 0.18
32 27 0.19
33 8 0.06
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (30 bp):
AATATATTATAATATATATTATTAATTATT
Found at i:1036167 original size:25 final size:26
Alignment explanation
Indices: 1036139--1036192 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
1036129 TTATTTCAAA
1036139 ATTTATAAAATA-TATTATAATTATT
1 ATTTATAAAATACTATTATAATTATT
*
1036164 ATTTATAAAATATCTATTTTAATTATT
1 ATTTATAAAATA-CTATTATAATTATT
1036191 AT
1 AT
1036193 ATTTATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 12 0.46
27 14 0.54
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
ATTTATAAAATACTATTATAATTATT
Found at i:1036238 original size:35 final size:33
Alignment explanation
Indices: 1036182--1036274 Score: 103
Period size: 28 Copynumber: 3.0 Consensus size: 33
1036172 AATATCTATT
1036182 TTAATTATTA-TATT-TATTTAA-TT-ATATT-
1 TTAATTATTATTATTATATTTAATTTAATATTA
1036210 TTAATTA-T-TTATTATATTTAATAATTAATATTA
1 TTAATTATTATTATTATATTTAAT--TTAATATTA
*
1036243 TTAATTATTATTATTATATTT-ATTTATTATTA
1 TTAATTATTATTATTATATTTAATTTAATATTA
1036275 ATTTCAATTT
Statistics
Matches: 55, Mismatches: 1, Indels: 14
0.79 0.01 0.20
Matches are distributed among these distances:
27 5 0.09
28 14 0.25
31 2 0.04
32 13 0.24
33 7 0.13
34 3 0.05
35 11 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (33 bp):
TTAATTATTATTATTATATTTAATTTAATATTA
Found at i:1036252 original size:16 final size:15
Alignment explanation
Indices: 1036149--1036277 Score: 87
Period size: 13 Copynumber: 8.9 Consensus size: 15
1036139 ATTTATAAAA
1036149 TATATTA-TAATTAT
1 TATATTATTAATTAT
* *
1036163 TAT-TTATAAAATA-
1 TATATTATTAATTAT
*
1036176 TCTATT-TTAATTAT
1 TATATTATTAATTAT
1036190 TATATTTATTTAATTA-
1 TATA-TTA-TTAATTAT
* *
1036206 TATTTTAATTATTTAT
1 TATATT-ATTAATTAT
*
1036222 TATA-T-TTAATAAT
1 TATATTATTAATTAT
1036235 TAATATTATTAATTAT
1 T-ATATTATTAATTAT
*
1036251 TATTATTA-TATTTAT
1 TA-TATTATTAATTAT
1036266 T-TATTATTAATT
1 TATATTATTAATT
1036278 TCAATTTAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
13 22 0.25
14 19 0.22
15 20 0.23
16 20 0.23
17 7 0.08
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (15 bp):
TATATTATTAATTAT
Found at i:1036269 original size:19 final size:19
Alignment explanation
Indices: 1036185--1036274 Score: 81
Period size: 16 Copynumber: 5.2 Consensus size: 19
1036175 ATCTATTTTA
*
1036185 ATTATTATATTT-ATT-TA
1 ATTATTATATTTAATTATT
1036202 ATTA-TAT-TTTAATTA-T
1 ATTATTATATTTAATTATT
*
1036218 -TTATTATATTTAATAATT
1 ATTATTATATTTAATTATT
*
1036236 AATA-T-TA-TTAATTATT
1 ATTATTATATTTAATTATT
*
1036252 ATTATTATATTTATTTATT
1 ATTATTATATTTAATTATT
1036271 ATTA
1 ATTA
1036275 ATTTCAATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
15 6 0.10
16 20 0.34
17 14 0.24
18 4 0.07
19 14 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTATATTTAATTATT
Found at i:1039872 original size:2 final size:2
Alignment explanation
Indices: 1039865--1039896 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1039855 TTGATACTCA
1039865 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
1039897 CTTTCTTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1040301 original size:5 final size:5
Alignment explanation
Indices: 1040291--1040325 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
1040281 TCGAATAAAA
1040291 TGACT TGACT TGACT TGACT TGACT TGACT TGACT
1 TGACT TGACT TGACT TGACT TGACT TGACT TGACT
1040326 GAGATTTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
TGACT
Found at i:1044592 original size:19 final size:20
Alignment explanation
Indices: 1044570--1044613 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1044560 GAGAAAAGGT
1044570 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
1044589 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
1044609 AAAAG
1 AAAAG
1044614 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Found at i:1050983 original size:17 final size:16
Alignment explanation
Indices: 1050961--1050994 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1050951 TAAAAACAGT
1050961 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1050978 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1050994 A
1 A
1050995 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1056952 original size:19 final size:19
Alignment explanation
Indices: 1056909--1056959 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
1056899 AAATGACCAA
* * *
1056909 CAAATTCGCAATGCGATCT
1 CAAATTCGCAACGCAAACT
1056928 CAAATTCGCAACGCAAACT
1 CAAATTCGCAACGCAAACT
*
1056947 CCAATTTCGCAAC
1 -CAAATTCGCAAC
1056960 CCAGTTTCCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.35, C:0.31, G:0.12, T:0.22
Consensus pattern (19 bp):
CAAATTCGCAACGCAAACT
Found at i:1057053 original size:20 final size:20
Alignment explanation
Indices: 1057030--1057088 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
1057020 AATTTGTAAA
*
1057030 TCGCAACATATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
1057050 TCGCAACACATAAGTCAAAT
1 TCGCAACACATAAGTCAAAT
*
1057070 TCGCAACACAGAAGTCAAA
1 TCGCAACACATAAGTCAAA
1057089 GCGCGTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.46, C:0.24, G:0.12, T:0.19
Consensus pattern (20 bp):
TCGCAACACATAAGTCAAAT
Found at i:1057420 original size:24 final size:24
Alignment explanation
Indices: 1057386--1057439 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1057376 CTGAAACATA
1057386 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1057410 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1057434 ATCAAA
1 ATCAAA
1057440 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1058215 original size:16 final size:16
Alignment explanation
Indices: 1058194--1058224 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1058184 AAATCATTGA
1058194 AAAATTATATAAAAAT
1 AAAATTATATAAAAAT
*
1058210 AAAATTATGTAAAAA
1 AAAATTATATAAAAA
1058225 CAATTAGAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:1058295 original size:16 final size:16
Alignment explanation
Indices: 1058274--1058306 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1058264 ATATGTCGCC
1058274 GGAGAGAGTGATAGAT
1 GGAGAGAGTGATAGAT
1058290 GGAGAGAGTGATAGAT
1 GGAGAGAGTGATAGAT
1058306 G
1 G
1058307 TAGATAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.45, T:0.18
Consensus pattern (16 bp):
GGAGAGAGTGATAGAT
Found at i:1058426 original size:19 final size:20
Alignment explanation
Indices: 1058403--1058508 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 20
1058393 ACTAAAACCT
*
1058403 GTTGCGAAATT-AAATTCGT
1 GTTGCGAAATTGAAATTCGA
* *
1058422 GTTGCG-AATTCAAAAATCGA
1 GTTGCGAAATT-GAAATTCGA
*
1058442 GTTGCGAATTTGAAATTC-A
1 GTTGCGAAATTGAAATTCGA
1058461 GTTGC-AAATTTGAAATTC-A
1 GTTGCGAAA-TTGAAATTCGA
* * *
1058480 GTTGTGAATTTGAAATTCAGT
1 GTTGCGAAATTGAAATTC-GA
1058501 GTTGCGAA
1 GTTGCGAA
1058509 TTTGGCAAAC
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
18 6 0.09
19 35 0.50
20 19 0.27
21 10 0.14
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.35
Consensus pattern (20 bp):
GTTGCGAAATTGAAATTCGA
Found at i:1058447 original size:39 final size:39
Alignment explanation
Indices: 1058403--1058510 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 39
1058393 ACTAAAACCT
*
1058403 GTTGCGAAATT-AAATTCGTGTTGCGAATTCAAAAATCGA
1 GTTGCGAATTTGAAATTCGTGTTGCGAATTCAAAAATC-A
* * ** *
1058442 GTTGCGAATTTGAAATTC-AGTTGCAAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCGTGTTGCGAATTCAAAAATCA
*
1058480 GTTGTGAATTTGAAATTCAGTGTTGCGAATT
1 GTTGCGAATTTGAAATTC-GTGTTGCGAATT
1058511 TGGCAAACGC
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
38 18 0.32
39 24 0.42
40 15 0.26
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.36
Consensus pattern (39 bp):
GTTGCGAATTTGAAATTCGTGTTGCGAATTCAAAAATCA
Found at i:1059486 original size:31 final size:31
Alignment explanation
Indices: 1059446--1059515 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
1059436 TCGGGGACCA
* * * *
1059446 TATTACAAATGGACTAAATGTTTGGGGACTG
1 TATTGCAAATGAACTAAATATTAGGGGACTG
1059477 TATTGCAAATGAACTAAATATTAGGGGACTG
1 TATTGCAAATGAACTAAATATTAGGGGACTG
1059508 TATTGCAA
1 TATTGCAA
1059516 GTTTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (31 bp):
TATTGCAAATGAACTAAATATTAGGGGACTG
Found at i:1060505 original size:22 final size:21
Alignment explanation
Indices: 1060480--1060535 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
1060470 AAATATATTC
1060480 TAAAAATATTTTTTAAATATA
1 TAAAAATATTTTTTAAATATA
* * *
1060501 GTAAATATATGATTTTCAATATA
1 -TAAAAATAT-TTTTTAAATATA
1060524 -AAATAATATTTT
1 TAAA-AATATTTT
1060536 AAATTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
21 5 0.19
22 12 0.44
23 10 0.37
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (21 bp):
TAAAAATATTTTTTAAATATA
Found at i:1062676 original size:2 final size:2
Alignment explanation
Indices: 1062671--1062717 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1062661 ACACACACAC
1062671 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1062713 AG AG A
1 AG AG A
1062718 ATTACTTGGG
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1065265 original size:198 final size:199
Alignment explanation
Indices: 1064913--1065310 Score: 780
Period size: 198 Copynumber: 2.0 Consensus size: 199
1064903 ATCAAAAACG
1064913 AGATTTAAATCCAAAATTTTCAAATTCATGTTTCCAAACATACTATAATGTTATAATCCAAAATC
1 AGATTTAAATCC-AAATTTTCAAATTCATGTTTCCAAACATACTATAATGTTATAATCCAAAATC
1064978 CTATGACCCTACTAACTCCAATCAACTAATTCCCAGCTTAAGCATTTTCCTAAAAAAGCACCAAA
65 CTATGACCCTACTAACTCCAATCAACTAATTCCCAGCTTAAGCATTTTCCTAAAAAAGCACCAAA
1065043 TGTTGCAACATAAAACACATAGTCTACTTTCTCATACACACTAAACTATGTTATTCTGACTTCAT
130 TGTTGCAACATAAAACACATAGTCTACTTTCTCATACACACTAAACTATGTTATTCTGACTTCAT
1065108 TTTTA
195 TTTTA
1065113 AGATTTAAATCC-AATTTTCAAATTCATGTTTCCAAACATACTATAATGTTATAATCCAAAATCC
1 AGATTTAAATCCAAATTTTCAAATTCATGTTTCCAAACATACTATAATGTTATAATCCAAAATCC
1065177 TATGACCCTACTAACTCCAATCAACTAATTCCCAGCTTAAGCATTTTCCTAAAAAAGCACCAAAT
66 TATGACCCTACTAACTCCAATCAACTAATTCCCAGCTTAAGCATTTTCCTAAAAAAGCACCAAAT
1065242 GTTGCAACATAAAACACATAGTCTACTTTCTCATACACACTAAACTATGTTATTCTGACTTCATT
131 GTTGCAACATAAAACACATAGTCTACTTTCTCATACACACTAAACTATGTTATTCTGACTTCATT
1065307 TTTA
196 TTTA
1065311 TATAAGTACC
Statistics
Matches: 198, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
198 186 0.94
200 12 0.06
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (199 bp):
AGATTTAAATCCAAATTTTCAAATTCATGTTTCCAAACATACTATAATGTTATAATCCAAAATCC
TATGACCCTACTAACTCCAATCAACTAATTCCCAGCTTAAGCATTTTCCTAAAAAAGCACCAAAT
GTTGCAACATAAAACACATAGTCTACTTTCTCATACACACTAAACTATGTTATTCTGACTTCATT
TTTA
Found at i:1073341 original size:21 final size:21
Alignment explanation
Indices: 1073315--1073368 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
1073305 GTTTTCAGAT
*
1073315 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1073336 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
1073357 TCGCAATGCGAA
1 TCGCAATGCGAA
1073369 TATGTAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:1073380 original size:41 final size:41
Alignment explanation
Indices: 1073335--1073433 Score: 146
Period size: 41 Copynumber: 2.4 Consensus size: 41
1073325 AACTTGGACT
* * *
1073335 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCAAATATGTAA
*
1073376 ATCGCAATGCGATAGTCGATTATCGCAATGCAAATATGTAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCAAATATGTAA
1073417 ATCGCAATGCGATAGTC
1 ATCGCAATGCGATAGTC
1073434 CAAGTTCGCA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 52 0.98
42 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.25
Consensus pattern (41 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCAAATATGTAA
Found at i:1073381 original size:20 final size:20
Alignment explanation
Indices: 1073356--1073428 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
1073346 AACTTGGACT
1073356 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
1073376 ATCGCAATGCG-ATA-GTCGATT
1 ATCGCAATGCGAATATGT--A-A
*
1073397 ATCGCAATGCAAATATGTAA
1 ATCGCAATGCGAATATGTAA
1073417 ATCGCAATGCGA
1 ATCGCAATGCGA
1073429 TAGTCCAAGT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.05
19 3 0.07
20 23 0.52
21 11 0.25
22 3 0.07
23 2 0.05
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:1073443 original size:41 final size:41
Alignment explanation
Indices: 1073355--1073443 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
1073345 GAACTTGGAC
* * *
1073355 TATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAT
1 TATCGCAATGCAAATATGTAAATCGCAATGCGATAGTCAAG
1073396 TATCGCAATGCAAATATGTAAATCGCAATGCGATAGTCCAAG
1 TATCGCAATGCAAATATGTAAATCGCAATGCGATAGT-CAAG
1073438 T-TCGCA
1 TATCGCA
1073444 TTGCGATAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
41 41 0.93
42 3 0.07
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (41 bp):
TATCGCAATGCAAATATGTAAATCGCAATGCGATAGTCAAG
Found at i:1073463 original size:21 final size:21
Alignment explanation
Indices: 1073374--1073465 Score: 82
Period size: 21 Copynumber: 4.4 Consensus size: 21
1073364 GCGAATATGT
*
1073374 AAATCGCAATGCGATAGTCGA
1 AAATCGCAATGCGATAGTCCA
** *
1073395 TTATCGCAATGCAAATATGT---
1 AAATCGCAATGC-GATA-GTCCA
1073415 AAATCGCAATGCGATAGTCCA
1 AAATCGCAATGCGATAGTCCA
** *
1073436 AGTTCGCATTGCGATAGTCCA
1 AAATCGCAATGCGATAGTCCA
1073457 AAATCGCAA
1 AAATCGCAA
1073466 CGACTGGTGG
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
18 2 0.04
19 3 0.06
20 10 0.19
21 34 0.63
22 3 0.06
23 2 0.04
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (21 bp):
AAATCGCAATGCGATAGTCCA
Found at i:1074717 original size:2 final size:2
Alignment explanation
Indices: 1074712--1074736 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1074702 AAAACGCCAT
1074712 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 T
1074737 TTAACTATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1077137 original size:11 final size:12
Alignment explanation
Indices: 1077097--1077140 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1077087 TATTTAAACG
*
1077097 GGTATTGGGCCA
1 GGTATTGGGTCA
*
1077109 GGTATTGGGTCG
1 GGTATTGGGTCA
1077121 GGTATTGGGTC-
1 GGTATTGGGTCA
1077132 GGTATTGGG
1 GGTATTGGG
1077141 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:1077139 original size:23 final size:24
Alignment explanation
Indices: 1077095--1077140 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1077085 ATTATTTAAA
1077095 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
1077119 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
1077141 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:1077218 original size:24 final size:25
Alignment explanation
Indices: 1077158--1077218 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
1077148 TCGGGCCGGG
1077158 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
1077181 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
1077205 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
1077219 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:1077268 original size:13 final size:13
Alignment explanation
Indices: 1077252--1077284 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1077242 TTTAATATTT
1077252 ATCGGGTCGGGTA
1 ATCGGGTCGGGTA
*
1077265 ATCGGGGCGGGTA
1 ATCGGGTCGGGTA
1077278 ATCGGGT
1 ATCGGGT
1077285 AATCGGGGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.48, T:0.21
Consensus pattern (13 bp):
ATCGGGTCGGGTA
Found at i:1077358 original size:6 final size:6
Alignment explanation
Indices: 1077347--1077383 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
1077337 AAATGGGTTT
1077347 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG T
1077384 TTATCATCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.65, G:0.16, T:0.19
Consensus pattern (6 bp):
TCCCCG
Found at i:1077836 original size:30 final size:32
Alignment explanation
Indices: 1077765--1077845 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
1077755 ATCTTTTAGT
* *
1077765 ATTCGGATCGGATTTTTTTTAAAAAATTGAGG
1 ATTCGGGTCGGATTTTTTTTAAAAAATCGAGG
*
1077797 AATT-AGGTCGGATTTTTTTTAAAAAATCG-GG
1 -ATTCGGGTCGGATTTTTTTTAAAAAATCGAGG
1077828 -TTCGGGTCGGATTTTTTT
1 ATTCGGGTCGGATTTTTTT
1077846 AAGTTTGATA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 14 0.33
31 2 0.05
32 22 0.51
33 3 0.07
ACGTcount: A:0.26, C:0.07, G:0.23, T:0.43
Consensus pattern (32 bp):
ATTCGGGTCGGATTTTTTTTAAAAAATCGAGG
Found at i:1077859 original size:28 final size:28
Alignment explanation
Indices: 1077828--1078016 Score: 139
Period size: 28 Copynumber: 6.4 Consensus size: 28
1077818 AAAAATCGGG
*
1077828 TTCGGGTCGGATTTTTTTAAGTTTGATA
1 TTCGGGTCGGATTTTTTTAAGTGTGATA
1077856 TTCGGGTCGGGTCATGTTTTTTTAAGTGTGATA
1 TTCGGGTC-GG--A--TTTTTTTAAGTGTGATA
***** *
1077889 TTCGGGTCAGGTCGGATTTTTTTAAAAAAAATTGGG
1 TTC--G---GGTCGGATTTTTTTAAGTGTGA-T--A
* * *
1077925 TTCGGGTTGG-GTTTTTTAAGTTTGATA
1 TTCGGGTCGGATTTTTTTAAGTGTGATA
* *
1077952 TCCGGGTCGG-GTTTTTTAAGTGTGATA
1 TTCGGGTCGGATTTTTTTAAGTGTGATA
1077979 TTCGGGTCGGATTTTTTTAAGTGTGATA
1 TTCGGGTCGGATTTTTTTAAGTGTGATA
1078007 TTCGGGTCGG
1 TTCGGGTCGG
1078017 GTTCGGGTTT
Statistics
Matches: 127, Mismatches: 20, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
27 33 0.26
28 34 0.27
29 3 0.02
30 9 0.07
31 6 0.05
33 29 0.23
34 2 0.02
35 2 0.02
36 3 0.02
37 2 0.02
38 4 0.03
ACGTcount: A:0.17, C:0.08, G:0.30, T:0.44
Consensus pattern (28 bp):
TTCGGGTCGGATTTTTTTAAGTGTGATA
Found at i:1077876 original size:33 final size:30
Alignment explanation
Indices: 1077839--1078018 Score: 133
Period size: 33 Copynumber: 6.0 Consensus size: 30
1077829 TCGGGTCGGA
*
1077839 TTTTTTTAAGTTTGATATTCGGGTCGGGTCATG
1 TTTTTTTAAGTGTGATATTCGGGTCGGG---TG
*
1077872 TTTTTTTAAGTGTGATATTCGGGTCAGGTCGG
1 TTTTTTTAAGTGTGATATTCGGGTCGGGT--G
*** *
1077904 ATTTTTTTAA--AAAAAATT-GGGTTCGGGTTGG
1 -TTTTTTTAAGTGTGATATTCGGG-TCGGG-T-G
* * *
1077935 GTTTTTTAAGTTTGATATCCGGGTC-GG-G
1 TTTTTTTAAGTGTGATATTCGGGTCGGGTG
*
1077963 -TTTTTTAAGTGTGATATTCGGGTC-GG-A
1 TTTTTTTAAGTGTGATATTCGGGTCGGGTG
1077990 TTTTTTTAAGTGTGATATTCGGGTCGGGT
1 TTTTTTTAAGTGTGATATTCGGGTCGGGT
1078019 TCGGGTTTAG
Statistics
Matches: 120, Mismatches: 16, Indels: 25
0.75 0.10 0.16
Matches are distributed among these distances:
27 24 0.20
28 25 0.21
29 2 0.02
30 12 0.10
31 12 0.10
32 7 0.06
33 38 0.32
ACGTcount: A:0.18, C:0.08, G:0.29, T:0.45
Consensus pattern (30 bp):
TTTTTTTAAGTGTGATATTCGGGTCGGGTG
Found at i:1077940 original size:96 final size:90
Alignment explanation
Indices: 1077801--1077986 Score: 257
Period size: 96 Copynumber: 2.0 Consensus size: 90
1077791 TTGAGGAATT
* * *
1077801 AGGTCGGATTTTTTTTAAAAAATCGGGTTCGGGTCGGATTTTTTTAAGTTTGATATTCGGGTCGG
1 AGGTCGGATTTTTTTAAAAAAATCGGGTTCGGGTCGGAGTTTTTTAAGTTTGATATCCGGGTC-G
1077866 GTCATGTTTTTTTAAGTGTGATATTCGGGTC
65 G----G-TTTTTTAAGTGTGATATTCGGGTC
* *
1077897 AGGTCGGATTTTTTTAAAAAAAATTGGGTTCGGGTTGG-GTTTTTTAAGTTTGATATCCGGGTCG
1 AGGTCGGATTTTTTT-AAAAAAATCGGGTTCGGGTCGGAGTTTTTTAAGTTTGATATCCGGGTCG
1077961 GGTTTTTTAAGTGTGATATTCGGGTC
65 GGTTTTTTAAGTGTGATATTCGGGTC
1077987 GGATTTTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
90 24 0.29
91 1 0.01
95 2 0.02
96 38 0.45
97 19 0.23
ACGTcount: A:0.19, C:0.09, G:0.29, T:0.43
Consensus pattern (90 bp):
AGGTCGGATTTTTTTAAAAAAATCGGGTTCGGGTCGGAGTTTTTTAAGTTTGATATCCGGGTCGG
GTTTTTTAAGTGTGATATTCGGGTC
Found at i:1077963 original size:27 final size:27
Alignment explanation
Indices: 1077925--1078019 Score: 145
Period size: 27 Copynumber: 3.5 Consensus size: 27
1077915 AAAAATTGGG
* *
1077925 TTCGGGTTGGGTTTTTTAAGTTTGATA
1 TTCGGGTCGGGTTTTTTAAGTGTGATA
*
1077952 TCCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTAAGTGTGATA
*
1077979 TTCGGGTCGGATTTTTTTAAGTGTGATA
1 TTCGGGTCGG-GTTTTTTAAGTGTGATA
1078007 TTCGGGTCGGGTT
1 TTCGGGTCGGGTT
1078020 CGGGTTTAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 35 0.57
28 26 0.43
ACGTcount: A:0.14, C:0.08, G:0.33, T:0.45
Consensus pattern (27 bp):
TTCGGGTCGGGTTTTTTAAGTGTGATA
Found at i:1078082 original size:16 final size:16
Alignment explanation
Indices: 1078061--1078094 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1078051 AGATTTCAGA
1078061 TTCAGATTCAAATTCC
1 TTCAGATTCAAATTCC
*
1078077 TTCAGATTCCAATTCC
1 TTCAGATTCAAATTCC
1078093 TT
1 TT
1078095 TACAGATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.41
Consensus pattern (16 bp):
TTCAGATTCAAATTCC
Found at i:1086070 original size:2 final size:2
Alignment explanation
Indices: 1086063--1086643 Score: 82
Period size: 2 Copynumber: 293.5 Consensus size: 2
1086053 TGGTGTATTA
* *
1086063 AT AT AT AT AT AT AT AT AT A- AT TT AT AT -T A- AT AA ACT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
1086103 A- AT -T CAT -T AGT AT AT AT AA ACT AT AT AT -T AT AT AGT TT AT
1 AT AT AT -AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT A-T AT AT
*
1086143 -T AGT AT A- ACT AT AT AGT AT AT AGT -T CAT -T A- AT AT AT AT AA
1 AT A-T AT AT A-T AT AT A-T AT AT A-T AT -AT AT AT AT AT AT AT AT
* *
1086183 ACT AT AT A- AT AT AT AT AA ACT AT AT GAT AT AT AT AA AT -T AT
1 A-T AT AT AT AT AT AT AT AT A-T AT AT -AT AT AT AT AT AT AT AT
*
1086224 AT AT -T A- AT AT AT -T AT AT AGT -T CAT -T AGT AT AT AT AA ACT
1 AT AT AT AT AT AT AT AT AT AT A-T AT -AT AT A-T AT AT AT AT A-T
* * * *
1086263 AT AT GGT AT AT AT AA ACT AT AT AT -T A- AT AT AT -T AT GT AT AA
1 AT AT -AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
1086304 ACT AT AT A- AT TT AT -T AT AGT TT AT AT AT AA AGT AT AT AT GA-
1 A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT -AT
* * * * *
1086345 ACT AT AT AT AA ACT AT AC A- ACT AT AT TT AT AT TT GT AT A- AT
1 A-T AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * * *
1086386 -T AA AT -T AT AT AA AT -T AT GT AT AA AT -T AT AT A- AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1086423 -T A- AT AT AA AT -T AT AT AT AA ACT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * * * *
1086462 AT AT AT AT AT GAT TT AGG GT -T A- AT TT AT GT A- AT -T AT AT GT
1 AT AT AT AT AT -AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1086502 AGT TT AT AT AT AT AC AT AA ACT AT AT AT ACT AT AT AGT TT AT AT
1 A-T AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT A-T AT AT AT
* * * * *
1086546 AT A- AA AT AT AT TT AA AA AT -T AT AT AT AT AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * *
1086587 AGT TT AT AT AT AA AT -T AT AT ACT AT AGT -T GAT AC AT AT AA ACT
1 A-T AT AT AT AT AT AT AT AT AT A-T AT A-T AT -AT AT AT AT AT A-T
1086630 AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT A
1086644 GTTTACATTA
Statistics
Matches: 409, Mismatches: 86, Indels: 168
0.62 0.13 0.25
Matches are distributed among these distances:
1 45 0.11
2 318 0.78
3 46 0.11
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1086116 original size:28 final size:28
Alignment explanation
Indices: 1086085--1086341 Score: 112
Period size: 26 Copynumber: 9.7 Consensus size: 28
1086075 ATATATAATT
1086085 TATATTAATAAACTATATAATTCAT-TAG
1 TATATTAATAAACTATATAATT-ATATAG
1086113 TATA-T-ATAAACTATAT-ATTATATAG
1 TATATTAATAAACTATATAATTATATAG
* * *
1086138 TTTATTAGTATAACTATAT-AGTATATAG
1 TATATTAATA-AACTATATAATTATATAG
* * *
1086166 T-TCATTAATATA-TATA-AACTATATAA
1 TAT-ATTAATAAACTATATAATTATATAG
*
1086192 TATA-T-ATAAACTATATGA-TATATA-
1 TATATTAATAAACTATATAATTATATAG
* * *
1086216 TAAATT-ATATATTA-ATATATTATATAG
1 TATATTAATAAACTATATA-ATTATATAG
* * * *
1086243 T-TCATTAGTATA-TATA-AACTATATGG
1 TAT-ATTAATAAACTATATAATTATATAG
1086269 TATA-TA-TAAACTATAT-ATTA-ATA-
1 TATATTAATAAACTATATAATTATATAG
1086292 TATTATGT-ATAAACTATATAATTTATTATAG
1 TA-TAT-TAATAAACTATATAA-TTA-TATAG
* *
1086323 TTTA-TATATAAAGTATATA
1 TATATTA-ATAAACTATATA
1086342 TGAACTATAT
Statistics
Matches: 177, Mismatches: 22, Indels: 58
0.69 0.09 0.23
Matches are distributed among these distances:
23 2 0.01
24 18 0.10
25 37 0.21
26 52 0.29
27 15 0.08
28 36 0.20
30 16 0.09
31 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (28 bp):
TATATTAATAAACTATATAATTATATAG
Found at i:1086121 original size:26 final size:24
Alignment explanation
Indices: 1086038--1086133 Score: 76
Period size: 26 Copynumber: 3.9 Consensus size: 24
1086028 ATATATGAAC
**
1086038 TATATATAAACTATATGGTGTATTAA
1 TATATATAAACTATATAAT-TATT-A
1086064 TATATATATATA-TATATAA-T-TTA
1 TATATATA-A-ACTATATAATTATTA
1086087 TAT-TAATAAACTATATAATTCATTA
1 TATAT-ATAAACTATATAATT-ATTA
1086112 GTATATATAAACTATAT-ATTAT
1 -TATATATAAACTATATAATTAT
1086134 ATAGTTTATT
Statistics
Matches: 59, Mismatches: 2, Indels: 20
0.73 0.02 0.25
Matches are distributed among these distances:
21 1 0.02
22 9 0.15
23 8 0.14
24 4 0.07
25 7 0.12
26 22 0.37
27 7 0.12
28 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (24 bp):
TATATATAAACTATATAATTATTA
Found at i:1086136 original size:33 final size:33
Alignment explanation
Indices: 1086098--1086197 Score: 120
Period size: 33 Copynumber: 3.2 Consensus size: 33
1086088 ATTAATAAAC
* *
1086098 TATATAATTCATTAGTATATATAAACTATATAT
1 TATATAGTTCATTAGTATATATAAACTATATAA
* *
1086131 TATATAGTTTATTAG----TAT-AACTATATAG
1 TATATAGTTCATTAGTATATATAAACTATATAA
*
1086159 TATATAGTTCATTAATATATATAAACTATATAA
1 TATATAGTTCATTAGTATATATAAACTATATAA
1086192 TATATA
1 TATATA
1086198 TAAACTATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
28 22 0.39
29 3 0.05
32 3 0.05
33 28 0.50
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (33 bp):
TATATAGTTCATTAGTATATATAAACTATATAA
Found at i:1086213 original size:77 final size:75
Alignment explanation
Indices: 1086113--1086311 Score: 215
Period size: 77 Copynumber: 2.5 Consensus size: 75
1086103 AATTCATTAG
1086113 TATATATAAACTATATATTATATAGTTTATTAGTATAACTATATAGTATATAGTTCATTAATATA
1 TATATATAAAC--TATA-TATATA-TTTATTAGTATAACTATATAGTATATAGTTCATTAATATA
1086178 TATAAACTATATAA
62 TATAAACTATATAA
* * * *
1086192 TATATATAAACTATATGATATATATAAATTA-TAT-ATTAATATATTATATAGTTCATTAGTATA
1 TATATATAAACTATAT-ATATAT-T-TATTAGTATAACT-ATATAGTATATAGTTCATTAATATA
**
1086255 TATAAACTATATGG
62 TATAAACTATATAA
*
1086269 TATATATAAACTATATAT-TAATATATTATGTATAAACTATATA
1 TATATATAAACTATATATAT-ATTTATTA-GTAT-AACTATATA
1086312 ATTTATTATA
Statistics
Matches: 102, Mismatches: 9, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
74 4 0.04
75 1 0.01
76 11 0.11
77 69 0.68
78 6 0.06
79 11 0.11
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (75 bp):
TATATATAAACTATATATATATTTATTAGTATAACTATATAGTATATAGTTCATTAATATATATA
AACTATATAA
Found at i:1086339 original size:11 final size:11
Alignment explanation
Indices: 1086325--1086361 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
1086315 TATTATAGTT
*
1086325 TATATATAAAG
1 TATATATAAAC
*
1086336 TATATATGAAC
1 TATATATAAAC
1086347 TATATATAAAC
1 TATATATAAAC
1086358 TATA
1 TATA
1086362 CAACTATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (11 bp):
TATATATAAAC
Found at i:1086441 original size:11 final size:11
Alignment explanation
Indices: 1086391--1086464 Score: 69
Period size: 11 Copynumber: 6.5 Consensus size: 11
1086381 ATAATTAAAT
1086391 TATATAAATTA
1 TATATAAATTA
*
1086402 TGTATAAATTA
1 TATATAAATTA
**
1086413 TATAATTTATTA
1 TAT-ATAAATTA
1086425 -ATATAAATTA
1 TATATAAATTA
*
1086435 TATATAAACTA
1 TATATAAATTA
*
1086446 TATAATATATATA
1 TAT-ATAAAT-TA
1086459 TATATA
1 TATATA
1086465 TATATATGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
10 6 0.12
11 26 0.52
12 13 0.26
13 5 0.10
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (11 bp):
TATATAAATTA
Found at i:1086462 original size:33 final size:32
Alignment explanation
Indices: 1086380--1086471 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 32
1086370 TTTATATTTG
* * *
1086380 TATAATTAAATTATATAAATTATGTATAAATTA
1 TATAA-TATATTATATAAATTATATATAAACTA
*
1086413 TATAATTTATTAATATAAATTATATATAAACTA
1 TATAATATATT-ATATAAATTATATATAAACTA
*
1086446 TATAATATA-TATATATATATATATAT
1 TATAATATATTATATAAAT-TATATAT
1086472 GATTTAGGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
31 7 0.14
32 12 0.24
33 32 0.63
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (32 bp):
TATAATATATTATATAAATTATATATAAACTA
Found at i:1086596 original size:20 final size:20
Alignment explanation
Indices: 1086571--1086632 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 20
1086561 AAATTATATA
1086571 TATATATATAAACTATAGTT
1 TATATATATAAACTATAGTT
1086591 TATATATAAATTATATACTATAGTT
1 TATATAT--A-TA-A-ACTATAGTT
* *
1086616 GATACATATAAACTATA
1 TATATATATAAACTATA
1086633 TAATATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
20 13 0.37
21 1 0.03
22 3 0.09
23 3 0.09
24 1 0.03
25 14 0.40
ACGTcount: A:0.47, C:0.06, G:0.05, T:0.42
Consensus pattern (20 bp):
TATATATATAAACTATAGTT
Found at i:1086612 original size:18 final size:18
Alignment explanation
Indices: 1086066--1086612 Score: 147
Period size: 18 Copynumber: 28.6 Consensus size: 18
1086056 TGTATTAATA
*
1086066 TATATATATATATATAATT
1 TATATA-ATATATATAAAT
*
1086085 TATATTAATAAACTATATAAT
1 TATA-TAATATA-TATA-AAT
* *
1086106 TCAT-TAGTATATATAAAC
1 T-ATATAATATATATAAAT
* **
1086124 TATATATTATATAGTTTAT
1 TATATAATATATA-TAAAT
1086143 TAGTATAACTATATAGTATATAGT
1 TA-TATAA-TATATA-TA-A-A-T
*
1086167 TCAT-TAATATATATAAAC
1 T-ATATAATATATATAAAT
*
1086185 TATATAATATATATAAAC
1 TATATAATATATATAAAT
*
1086203 TATATGATATATATAAATT
1 TATATAATATATATAAA-T
*
1086222 ATATATTAATATATTATATAGT
1 -TATA-TAATATA-TATA-AAT
* *
1086244 TCAT-TAGTATATATAAAC
1 T-ATATAATATATATAAAT
** *
1086262 TATATGGTATATATAAAC
1 TATATAATATATATAAAT
*
1086280 TATAT-AT-TA-ATATAT
1 TATATAATATATATAAAT
*
1086295 TATGTATAA-ACTATATAATT
1 TA--TATAATA-TATATAAAT
*
1086315 TATTATAGTTTATATATAAAGT
1 TA-TATA--ATATATATAAA-T
*
1086337 ATATATGAACTATATATAAAC
1 -TATAT-AA-TATATATAAAT
* * *
1086358 TATACAACTATATTTATAT
1 TATATAA-TATATATAAAT
*
1086377 T-TGT-ATA-AT-TAAAT
1 TATATAATATATATAAAT
*
1086391 TATATAAATTATGTATAAAT
1 TATAT-AA-TATATATAAAT
*
1086411 TATATAAT-T-TATTAA-
1 TATATAATATATATAAAT
*
1086426 TATA-AATTATATATAAAC
1 TATATAA-TATATATAAAT
*
1086444 TATATAATATATATATAT
1 TATATAATATATATAAAT
* *
1086462 ATATATATATGATTTAGGGTTAATT
1 -TATATA-AT-ATATA----TAAAT
* * **
1086487 TATGTAATTATATGTAGTT
1 TATATAA-TATATATAAAT
*
1086506 TATAT-ATATACATAAACT
1 TATATAATATATATAAA-T
* **
1086524 ATATATACTATATAGTTTAT
1 -TATATAATATATA-TAAAT
* *
1086544 ATATAAAATATATTTAAAAAT
1 -TATATAATATA--TATAAAT
*
1086565 TATATATATATATATAAAC
1 TATATA-ATATATATAAAT
*
1086584 TATAGT-TTATATATAAAT
1 TATA-TAATATATATAAAT
*
1086602 TATATACTATA
1 TATATAATATA
1086613 GTTGATACAT
Statistics
Matches: 396, Mismatches: 71, Indels: 123
0.67 0.12 0.21
Matches are distributed among these distances:
14 7 0.02
15 15 0.04
16 10 0.03
17 25 0.06
18 100 0.25
19 72 0.18
20 70 0.18
21 40 0.10
22 32 0.08
23 12 0.03
24 9 0.02
25 4 0.01
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (18 bp):
TATATAATATATATAAAT
Found at i:1086624 original size:27 final size:25
Alignment explanation
Indices: 1086568--1086639 Score: 72
Period size: 27 Copynumber: 2.8 Consensus size: 25
1086558 TAAAAATTAT
* * *
1086568 ATATATATATATAAACTATAGTTTAT
1 ATATAAAT-TATATACTATAGTTTAC
1086594 ATATAAATTATATACTATAGTTGATAC
1 ATATAAATTATATACTATAGTT--TAC
* *
1086621 ATATAAACTATATAATATA
1 ATATAAATTATATACTATA
1086640 TATAGTTTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
25 13 0.33
26 7 0.18
27 19 0.49
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.42
Consensus pattern (25 bp):
ATATAAATTATATACTATAGTTTAC
Found at i:1086904 original size:21 final size:22
Alignment explanation
Indices: 1086862--1086913 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
1086852 CTGACTATCA
1086862 CATTGCGA-TTTCCCAAATTCG
1 CATTGCGATTTTCCCAAATTCG
* *
1086883 CGTTGCGATTTTCCTAAA-TCG
1 CATTGCGATTTTCCCAAATTCG
*
1086904 CAATGCGATT
1 CATTGCGATT
1086914 ACGTAAATCG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (22 bp):
CATTGCGATTTTCCCAAATTCG
Found at i:1086922 original size:20 final size:20
Alignment explanation
Indices: 1086897--1086946 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1086887 GCGATTTTCC
1086897 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
1086917 TAAATCGCAATGCGATTACG
1 TAAATCGCAATGCGATTACG
1086937 TAAATCGCAA
1 TAAATCGCAA
1086947 CGATATTCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (20 bp):
TAAATCGCAATGCGATTACG
Found at i:1087215 original size:19 final size:19
Alignment explanation
Indices: 1087191--1087237 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1087181 ACGATTTTGT
1087191 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
1087210 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1087229 CATTGCGAT
1 CGTTGCGAT
1087238 AGTCATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1087243 original size:19 final size:19
Alignment explanation
Indices: 1087202--1087245 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1087192 GTTGCGATTT
* **
1087202 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATAG
1087221 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
1087240 TCATTT
1 TCATTT
1087246 TTGCCTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:1087362 original size:14 final size:14
Alignment explanation
Indices: 1087343--1087379 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1087333 CATCAATTAA
1087343 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1087357 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1087371 ACAAATCAA
1 ACAAATCAA
1087380 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1088801 original size:42 final size:42
Alignment explanation
Indices: 1088755--1088834 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
1088745 CGATGACAGT
* * *
1088755 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
1088797 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
1088835 CAGGCGAGTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:1089276 original size:19 final size:19
Alignment explanation
Indices: 1089236--1089361 Score: 136
Period size: 19 Copynumber: 6.8 Consensus size: 19
1089226 TCTGGAACTT
*
1089236 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
1089257 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
1089276 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAATG
1089295 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
*
1089314 AAAATCTCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
1089328 AGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
1089347 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1089362 TTATAGTTTC
Statistics
Matches: 88, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
14 9 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 62 0.70
21 11 0.12
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1089334 original size:33 final size:35
Alignment explanation
Indices: 1089260--1089358 Score: 130
Period size: 33 Copynumber: 2.8 Consensus size: 35
1089250 AAAAATGACT
1089260 ATCGCAACGCGAAATGAAAATCGCAACGCGAAACGAAA
1 ATCGCAACGCGAAATGAAAATCGCAA--CG-AACGAAA
* *
1089298 ATCGCAACGCGAAATGAAAATCTCAACG-A-GAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAACGAAA
*
1089331 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
1089359 CGATTATAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
33 29 0.51
34 1 0.02
36 2 0.04
38 25 0.44
ACGTcount: A:0.45, C:0.22, G:0.21, T:0.11
Consensus pattern (35 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAACGAAA
Found at i:1089380 original size:19 final size:19
Alignment explanation
Indices: 1089358--1089442 Score: 118
Period size: 19 Copynumber: 4.4 Consensus size: 19
1089348 AAATCGCAAC
*
1089358 GCGATTATAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
*
1089377 GCGATTTTTGGTTTCGCGTT
1 GCGA-TTTTAGTTTCGCGTT
1089397 GCGATTTTCA-TTTCGCGTT
1 GCGATTTT-AGTTTCGCGTT
*
1089416 GCGATTTTTGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
1089435 GCGATTTT
1 GCGATTTT
1089443 CATTCTCTCG
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
19 42 0.71
20 17 0.29
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1089401 original size:39 final size:38
Alignment explanation
Indices: 1089358--1089462 Score: 140
Period size: 39 Copynumber: 2.7 Consensus size: 38
1089348 AAATCGCAAC
1089358 GCGATTAT-AGTTTCGCGTTGCGATTTTTGGTTTCGCGTT
1 GCGATTATCA-TTTCGCGTTGCGATTTTT-GTTTCGCGTT
*
1089397 GCGATTTTCATTTCGCGTTGCGATTTTTGTTTCGCGTT
1 GCGATTATCATTTCGCGTTGCGATTTTTGTTTCGCGTT
* * *
1089435 GCGATTTTCATTCTCTCGATGCGATTTT
1 GCGATTATCATT-TCGCGTTGCGATTTT
1089463 CATTTCAACC
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
38 22 0.36
39 38 0.62
40 1 0.02
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (38 bp):
GCGATTATCATTTCGCGTTGCGATTTTTGTTTCGCGTT
Found at i:1089431 original size:58 final size:58
Alignment explanation
Indices: 1089358--1089468 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
1089348 AAATCGCAAC
** *
1089358 GCGATTATAGTTTCGCGTTGCGATTTTTGGTT-TCGCGTTGCGATTTTCATTTCGCGTT
1 GCGATTATAGTTTCGCGTTGCGA-TTTTCATTCTCGCGATGCGATTTTCATTTCGCGTT
* * *
1089416 GCGATTTTTGTTTCGCGTTGCGATTTTCATTCTCTCGATGCGATTTTCATTTC
1 GCGATTATAGTTTCGCGTTGCGATTTTCATTCTCGCGATGCGATTTTCATTTC
1089469 AACCAAAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 6 0.13
58 40 0.87
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.48
Consensus pattern (58 bp):
GCGATTATAGTTTCGCGTTGCGATTTTCATTCTCGCGATGCGATTTTCATTTCGCGTT
Found at i:1089459 original size:20 final size:19
Alignment explanation
Indices: 1089368--1089468 Score: 130
Period size: 19 Copynumber: 5.2 Consensus size: 19
1089358 GCGATTATAG
**
1089368 TTTCGCGTTGCGATTTTTGG
1 TTTCGCGTTGCGA-TTTTCA
1089388 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
**
1089407 TTTCGCGTTGCGATTTTTG
1 TTTCGCGTTGCGATTTTCA
1089426 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
1089445 TTCTCTCGATGCGATTTTCA
1 TT-TCGCGTTGCGATTTTCA
1089465 TTTC
1 TTTC
1089469 AACCAAAAGA
Statistics
Matches: 72, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
19 42 0.58
20 30 0.42
ACGTcount: A:0.09, C:0.20, G:0.22, T:0.50
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1089788 original size:189 final size:182
Alignment explanation
Indices: 1089559--1089933 Score: 536
Period size: 189 Copynumber: 2.0 Consensus size: 182
1089549 ATGGATTGCA
* *
1089559 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACCGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
*
1089623 TTAGCAGAATTGGCAGCAAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA
66 TTAGCAGAATTGGCAGC-AAACAAACAAATTTAC-TTCAACCAAAAGACAAAA-AAAGACAAATA
* * *
1089688 CTAACTTCACAGTGTTAAAGAATAGACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
128 CTAACTTCACAATGTT----AATAAACAGTTTAGCACAATTGGCAGCAACCGAACAAAT
* *
1089747 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
* * * *
1089812 TTAGCAGAATTGGCAGCAACCAAATAAATTTACTTCAATCAAAAGACAACAAAAGACAAATACTA
66 TTAGCAGAATTGGCAGCAAACAAACAAATTTACTTCAACCAAAAGACAAAAAAAGACAAATACTA
* * * *
1089877 ACTTCACAATGTTAATAAACAGTTTAGCACTATTGGCAGCGACTGAATAAAT
131 ACTTCACAATGTTAATAAACAGTTTAGCACAATTGGCAGCAACCGAACAAAT
1089929 TTACT
1 TTACT
1089934 AAGCAATCTA
Statistics
Matches: 170, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
182 38 0.22
186 26 0.15
187 16 0.09
188 17 0.10
189 73 0.43
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (182 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAAACAAACAAATTTACTTCAACCAAAAGACAAAAAAAGACAAATACTA
ACTTCACAATGTTAATAAACAGTTTAGCACAATTGGCAGCAACCGAACAAAT
Found at i:1089791 original size:94 final size:94
Alignment explanation
Indices: 1089559--1089933 Score: 539
Period size: 94 Copynumber: 4.1 Consensus size: 94
1089549 ATGGATTGCA
* * *
1089559 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACCGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1089623 TTAGCAGAATTGGCAGCAAAACGAACAAAT
66 TTAGCAGAATTGGCAGC-AACCGAACAAAT
*
1089653 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATAGACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1089718 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
1089747 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
1089812 TTAGCAGAATTGGCAGCAACCAAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * * *
1089841 TTAC-TTCAATCAAAAGACAACA-AAAGACAAATACTAACTTCACAATGTT----AATAAACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
** * * *
1089900 TTAGCACTATTGGCAGCGACTGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1089929 TTACT
1 TTACT
1089934 AAGCAATCTA
Statistics
Matches: 260, Mismatches: 19, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
88 37 0.14
92 26 0.10
93 15 0.06
94 109 0.42
95 73 0.28
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1092749 original size:39 final size:38
Alignment explanation
Indices: 1092680--1092823 Score: 145
Period size: 39 Copynumber: 3.8 Consensus size: 38
1092670 TCTGGAACTT
* ** *
1092680 AAAATCGCAACGTGAAAAATGACTATCGCAACGCAAAATG
1 AAAATCGCAAC--GAGAAATGAAAATCGCAACGCAAAACG
*
1092720 AAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAACG
1 AAAATCGCAACGAGA-AATGAAAATCGCAACGCAAAACG
*
1092759 AAAATCGCAACGCGAAATGAAAATCGCAACG----A-G
1 AAAATCGCAACGAGAAATGAAAATCGCAACGCAAAACG
* * *
1092792 AGAATCGCAATGCGAAATGAAAATCGCAACGC
1 AAAATCGCAACGAGAAATGAAAATCGCAACGC
1092824 GATTATAGTT
Statistics
Matches: 94, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
33 30 0.32
34 1 0.01
38 19 0.20
39 33 0.35
40 11 0.12
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (38 bp):
AAAATCGCAACGAGAAATGAAAATCGCAACGCAAAACG
Found at i:1092798 original size:33 final size:35
Alignment explanation
Indices: 1092719--1092822 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 35
1092709 AACGCAAAAT
*
1092719 GAAAATCGCAACGAGAGAATGAAAATCGCAACGCGAAAC
1 GAAAATCGCAACGCGA-AATGAAAATCGCAA--CG-AAC
1092758 GAAAATCGCAACGCGAAATGAAAATCGCAACG-A-
1 GAAAATCGCAACGCGAAATGAAAATCGCAACGAAC
* *
1092791 GAGAATCGCAATGCGAAATGAAAATCGCAACG
1 GAAAATCGCAACGCGAAATGAAAATCGCAACG
1092823 CGATTATAGT
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
33 30 0.48
34 1 0.02
36 2 0.03
38 14 0.23
39 15 0.24
ACGTcount: A:0.47, C:0.20, G:0.23, T:0.10
Consensus pattern (35 bp):
GAAAATCGCAACGCGAAATGAAAATCGCAACGAAC
Found at i:1092825 original size:19 final size:19
Alignment explanation
Indices: 1092680--1092825 Score: 158
Period size: 19 Copynumber: 7.8 Consensus size: 19
1092670 TCTGGAACTT
*
1092680 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
** *
1092701 ACTATCGCAACGCAAAATG
1 AAAATCGCAACGCGAAATG
*
1092720 AAAATCGCAACGAGAGAATG
1 AAAATCGCAACGCGA-AATG
*
1092740 AAAATCGCAACGCGAAACG
1 AAAATCGCAACGCGAAATG
1092759 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
1092778 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
1092792 AGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
1092811 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1092826 TTATAGTTTC
Statistics
Matches: 105, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
14 10 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 61 0.58
20 18 0.17
21 10 0.10
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:1092868 original size:13 final size:14
Alignment explanation
Indices: 1092852--1092882 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1092842 CGATTTTTGG
1092852 TTTT-TCGTTGCGA
1 TTTTGTCGTTGCGA
1092865 TTTTGTCGTTGCGA
1 TTTTGTCGTTGCGA
1092879 TTTT
1 TTTT
1092883 CATTTCGCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (14 bp):
TTTTGTCGTTGCGA
Done.