Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006094.1 Hibiscus syriacus cultivar Beakdansim tig00014445_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: 761529
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 5 of 5
Found at i:704355 original size:37 final size:38
Alignment explanation
Indices: 704201--704371 Score: 133
Period size: 37 Copynumber: 4.6 Consensus size: 38
704191 ACTATATATA
* * * *
704201 TATATATATATATATATTC-AAAA-TATGTTTTCAAAAC
1 TATATATATATATGTTTTCAAAAACCAT-TTTTAAAAAC
* * *
704238 TATAT-TATATATGTTTTCGAAAACCCTTTTT-TAAAC
1 TATATATATATATGTTTTCAAAAACCATTTTTAAAAAC
* * * *
704274 TATATA-CTATATGTTTTAAAAAAAACGTTTTTAAAAA-
1 TATATATATATATGTTTT-CAAAAACCATTTTTAAAAAC
* * *
704311 AACTATATAT-TATGTTTTCCAAAACCATTTTTAAAAAT
1 TA-TATATATATATGTTTTCAAAAACCATTTTTAAAAAC
704349 TATATAT-TATATGTTTTCAAAAA
1 TATATATATATATGTTTTCAAAAA
704372 AAATTGAAAA
Statistics
Matches: 106, Mismatches: 19, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
36 31 0.29
37 57 0.54
38 17 0.16
39 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.44
Consensus pattern (38 bp):
TATATATATATATGTTTTCAAAAACCATTTTTAAAAAC
Found at i:704767 original size:2 final size:2
Alignment explanation
Indices: 704760--704789 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
704750 ACCCAATTTC
704760 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
704790 TGTTCTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:707648 original size:35 final size:35
Alignment explanation
Indices: 707600--707783 Score: 242
Period size: 35 Copynumber: 5.1 Consensus size: 35
707590 AAAGATGAAC
*
707600 ACTTGAATTGAAAGTGCGATGCTTCCTTCCGTTCT
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCT
* **
707635 ACTTGAATCGAAAGTGTGATGCTTCCTTCCGTTAG
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCT
*
707670 ACTTGAATTGAAAGTGCGATGCTTCCTTCCATTCCGTTCT
1 ACTTGAATCGAAAGTGCGATG----CTTCC-TTCCGTTCT
* *
707710 ACTTGAATCGAAAGTGTGATGCTTTCTTCCGTTCT
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCT
* *
707745 ACTTGAATCGAAAGTGCAATGCTTCCTTCAGTTCT
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCT
707780 ACTT
1 ACTT
707784 TATTCACCTT
Statistics
Matches: 129, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
35 94 0.73
36 4 0.03
39 5 0.04
40 26 0.20
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (35 bp):
ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCT
Found at i:707725 original size:75 final size:74
Alignment explanation
Indices: 707600--707773 Score: 266
Period size: 75 Copynumber: 2.4 Consensus size: 74
707590 AAAGATGAAC
707600 ACTTGAATTGAAAGTGCGATG----CTTCCTTCCGTTCTACTTGAATCGAAAGTGTGATGCTTCC
1 ACTTGAATTGAAAGTGCGATGCTTCCTTCCTTCCGTTCTACTTGAATCGAAAGTGTGATGCTTCC
707661 TTCCGTTAG
66 TTCCGTTAG
*
707670 ACTTGAATTGAAAGTGCGATGCTTCCTTCCATTCCGTTCTACTTGAATCGAAAGTGTGATGCTTT
1 ACTTGAATTGAAAGTGCGATGCTTCCTTCC-TTCCGTTCTACTTGAATCGAAAGTGTGATGCTTC
**
707735 CTTCCGTTCT
65 CTTCCGTTAG
* *
707745 ACTTGAATCGAAAGTGCAATGCTTCCTTC
1 ACTTGAATTGAAAGTGCGATGCTTCCTTC
707774 AGTTCTACTT
Statistics
Matches: 94, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
70 21 0.22
74 5 0.05
75 68 0.72
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (74 bp):
ACTTGAATTGAAAGTGCGATGCTTCCTTCCTTCCGTTCTACTTGAATCGAAAGTGTGATGCTTCC
TTCCGTTAG
Found at i:711755 original size:29 final size:29
Alignment explanation
Indices: 711721--711812 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
711711 AATCTAGCTA
*
711721 AATAAATTAAAGCAAAATAAAAATAAAAT
1 AATAAAATAAAGCAAAATAAAAATAAAAT
* **
711750 AATAAAAGAAAAG-AAAA-AAATTTTAAAAT
1 AATAAAA-TAAAGCAAAATAAA-AATAAAAT
*
711779 AAGTAAAATAAAGACAACAATGAAAATAAAAT
1 AA-TAAAATAAAG-CAA-AATAAAAATAAAAT
711811 AA
1 AA
711813 ATAATGACAA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.06
29 22 0.46
30 9 0.19
31 2 0.04
32 10 0.21
33 2 0.04
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.18
Consensus pattern (29 bp):
AATAAAATAAAGCAAAATAAAAATAAAAT
Found at i:711757 original size:25 final size:25
Alignment explanation
Indices: 711720--711767 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
711710 AAATCTAGCT
* *
711720 AAATAAATTAAAGCAAAATAAAAATA
1 AAATAAATAAAAG-AAAAGAAAAATA
711746 AAAT-AATAAAAGAAAAGAAAAA
1 AAATAAATAAAAGAAAAGAAAAA
711768 AATTTTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 7 0.35
26 4 0.20
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (25 bp):
AAATAAATAAAAGAAAAGAAAAATA
Found at i:713636 original size:85 final size:86
Alignment explanation
Indices: 713530--714008 Score: 588
Period size: 86 Copynumber: 5.6 Consensus size: 86
713520 ATGTGTCATC
* * * * * ** ** * *
713530 GAGCTGAATGGAATCGAACTCGAAAGT-TTTCGTTGTCAGATAGCTTTTCTCGATTTAAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
713594 CTGTAAATTTGACATGCCCTT
66 CTGTAAATTTGATATGCCTTT
* * *
713615 GAGCTGAATGTAATCGAACTCGAAGATC-TTTGTTGACAGATAACCCTTCTCGCATTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
*
713679 CTGTAAATTGGATATGCCTTT
66 CTGTAAATTTGATATGCCTTT
* * * *
713700 GAGCTGAATATAATTGAACTCGAAGGTATTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
713765 CTAT-AATTTGGATATACCTTT
66 CTGTAAATTT-GATATGCCTTT
* * * * *
713786 GAGCTGAATATAATCAAACTCGAAGGTCTTTTGTTGACATATATCCCTTCTCTCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
713851 CTATAAATTTGATGTGCCTTT
66 CTGTAAATTTGATATGCCTTT
* *
713872 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTCTCGCCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
* *
713937 TTGTAAATTTGATGTGCCTTT
66 CTGTAAATTTGATATGCCTTT
* * *
713958 GAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGATGACAGATAACACTTCTC
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTC
714009 TCCTAGAGTT
Statistics
Matches: 348, Mismatches: 42, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
85 118 0.34
86 225 0.65
87 5 0.01
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (86 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATG
CTGTAAATTTGATATGCCTTT
Found at i:714282 original size:65 final size:65
Alignment explanation
Indices: 714146--714315 Score: 224
Period size: 65 Copynumber: 2.7 Consensus size: 65
714136 TTGAGCTTTG
* * * **
714146 AATTGGATATCCTTTGTTGTGAAGTTAAAATCCAA---GGA-T-TGTTTCACCAAATTGGTTTTG
1 AATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTGGTTTCA
* *
714206 AGTTGGATATCCTTTGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTGGTTTCA
1 AATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTGGTTTCA
* *
714271 AATTGGATATCCTTCGTTATGAAGTTGAAATCCAATCTTGAGTAA
1 AATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTTGAGTAA
714316 ATTGTGTCAC
Statistics
Matches: 94, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
60 32 0.34
63 2 0.02
64 1 0.01
65 59 0.63
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (65 bp):
AATTGGATATCCTTTGTTGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCACCAAATTGGTTTCA
Found at i:714549 original size:65 final size:59
Alignment explanation
Indices: 714423--714552 Score: 143
Period size: 59 Copynumber: 2.1 Consensus size: 59
714413 GAAGTTGAGC
* * * *
714423 TTTGAATTGGATATCCTTTGTTGTGAGTTGAAATCCAAGAGTTGTTTTACCAAATTGGT
1 TTTGAATTGGATATCCTTTGTCGTGAGTTGAAATCCAAGAGTAGTTTCACCAAATTAGT
* * *
714482 TTTGAGTTTGATATCCTTTGTCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCATCAAATTAGT
1 TTTGAATTGGATATCCTTTGTCGTG-AGTTGAAATCCAA----GAGT-AGTTTCACCAAATTAGT
714547 TTTGAA
1 TTTGAA
714553 GTTGAAATCC
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
59 22 0.39
60 13 0.23
64 4 0.07
65 18 0.32
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (59 bp):
TTTGAATTGGATATCCTTTGTCGTGAGTTGAAATCCAAGAGTAGTTTCACCAAATTAGT
Found at i:714757 original size:259 final size:258
Alignment explanation
Indices: 714290--714775 Score: 660
Period size: 259 Copynumber: 1.9 Consensus size: 258
714280 TCCTTCGTTA
* *
714290 TGAAGTTGAAATCCAATCTTGAGTAAATTGTGTCACTTCGAGTTCAATATCATTCGTTGTGAAGT
1 TGAAGTTGAAATCCAATCTTGAGTAAATTGTGTCACTTCGAGTTCAATATCATTCGCTATGAAGT
* * *
714355 TGAATTTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGACAATTGCTCATTCGCTGTGAAGTTG
66 TGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGACAATTACCCATTCGCTGTGAAGTTG
* * * * * *
714420 AGCTTTGAATTGGATATCCTTTGTTGTGAGTTGAAATCCAAGAGTTGTTTTACCAAATTGGTTTT
131 AGCTTTGAATTAGATATCATTCGTTGTGAGTTGAAATCCAAGAG-TGCTTGACCAAATTGGTTTC
** * *
714485 GAGTTTGATATCCTTTG-TCGTGAAGTTGAAATCCAATCTTGAGTAAGTTTCATCAAATTAGTTT
195 GAGTTCAATATCCTTCGCT-GTAAAGTTGAAATCCAATCTTGAGTAAGTTTCATCAAATTAGTTT
* * *
714549 TGAAGTTGAAATCCAATCTTGAGTAAATTGTGTCACTTTGAGTTCAATTTCCTTCGCTATGAAGT
1 TGAAGTTGAAATCCAATCTTGAGTAAATTGTGTCACTTCGAGTTCAATATCATTCGCTATGAAGT
* *
714614 TGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGAC-ATTCACCCCTTTGCTGTGAAGTT
66 TGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGACAATT-ACCCATTCGCTGTGAAGTT
**
714678 GAGCTTTGAATTAGATATCATTCGTTGTGAAGTTGAAATCC-A-A-T-CTTGAGTAAATTGGGTC
130 GAGCTTTGAATTAGATATCATTCGTTGTG-AGTTGAAATCCAAGAGTGCTTGACCAAATT-GGT-
714739 ACTTCGAGTTCAATATCCTTCGCTGTAAAGTTGAAAT
192 --TTCGAGTTCAATATCCTTCGCTGTAAAGTTGAAAT
714776 TGACTCTGTA
Statistics
Matches: 198, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
255 8 0.04
256 4 0.02
258 4 0.02
259 170 0.86
260 12 0.06
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (258 bp):
TGAAGTTGAAATCCAATCTTGAGTAAATTGTGTCACTTCGAGTTCAATATCATTCGCTATGAAGT
TGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTGACAATTACCCATTCGCTGTGAAGTTG
AGCTTTGAATTAGATATCATTCGTTGTGAGTTGAAATCCAAGAGTGCTTGACCAAATTGGTTTCG
AGTTCAATATCCTTCGCTGTAAAGTTGAAATCCAATCTTGAGTAAGTTTCATCAAATTAGTTT
Found at i:716319 original size:100 final size:99
Alignment explanation
Indices: 716147--716345 Score: 328
Period size: 100 Copynumber: 2.0 Consensus size: 99
716137 AGGATAACTC
* *
716147 AATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTTGAGGTGTTTAACCAAT
1 AATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTAGAGGCGTTTAACCAAT
* * *
716212 TGCTCTAGAGGGACGATTCAAGCTTTATTGTATA
66 TGCTCTAGAGGGACAACTCAAGCTTTATTATATA
716246 AATATTATAATCACCTTTATCAGGCTTAGCTGAATCTTATCCATAAAGTCAG-GGCGTTTAACCA
1 AATATTATAATCACCTTTATCAGGC-TAGCTGAATCTTATCCATAAAGT-AGAGGCGTTTAACCA
716310 ATTGCTCTAGAGGGACAACTCAAGCTTTATTATATA
64 ATTGCTCTAGAGGGACAACTCAAGCTTTATTATATA
716346 TATAAAATAT
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
99 25 0.27
100 67 0.72
101 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (99 bp):
AATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTAGAGGCGTTTAACCAAT
TGCTCTAGAGGGACAACTCAAGCTTTATTATATA
Found at i:720421 original size:19 final size:19
Alignment explanation
Indices: 720375--720422 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
720365 AACTAAATAA
* *
720375 ATTAAAACAAAATAAAAAT
1 ATTAAAATAAAAGAAAAAT
*
720394 A-AAATAATAAAAGAAAAAT
1 ATTAA-AATAAAAGAAAAAT
720413 ATTAAAATAA
1 ATTAAAATAA
720423 GTAAAATAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
18 2 0.09
19 19 0.83
20 2 0.09
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (19 bp):
ATTAAAATAAAAGAAAAAT
Found at i:720570 original size:27 final size:25
Alignment explanation
Indices: 720509--720571 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 25
720499 ATTAAATAAA
*
720509 AAAAATGAAAAGAAAAGAAAAAAAAT
1 AAAAAT-AAAAGAAAAGAAAAAAAAC
*
720535 AATGGAATAAAAGAAAAGAAACAAAAAGC
1 AA--AAATAAAAGAAAAGAAA-AAAAA-C
720564 AAAAATAA
1 AAAAATAA
720572 TATTAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
26 2 0.07
27 18 0.60
28 8 0.27
29 2 0.07
ACGTcount: A:0.76, C:0.03, G:0.13, T:0.08
Consensus pattern (25 bp):
AAAAATAAAAGAAAAGAAAAAAAAC
Found at i:720632 original size:20 final size:19
Alignment explanation
Indices: 720595--720644 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
720585 ATTATTAATG
720595 AAATAAAAAAATAGAAATAA
1 AAATAAAAAAATA-AAATAA
720615 CAAATAAAATAAAT-AAATAA
1 -AAATAAAA-AAATAAAATAA
720635 ATAATAAAAA
1 A-AATAAAAA
720645 TAACTAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 2 0.07
20 13 0.48
21 8 0.30
22 4 0.15
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (19 bp):
AAATAAAAAAATAAAATAA
Found at i:720652 original size:13 final size:13
Alignment explanation
Indices: 720595--720655 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
720585 ATTATTAATG
720595 AAATAA-AAAAAT
1 AAATAATAAAAAT
*
720607 AGA-AATAACAAAT
1 AAATAATAA-AAAT
*
720620 AAAATAA-ATAAAT
1 -AAATAATAAAAAT
720633 AAATAATAAAAAT
1 AAATAATAAAAAT
*
720646 AACTAATAAA
1 AAATAATAAA
720656 GAACAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
11 2 0.05
12 10 0.26
13 22 0.56
14 3 0.08
15 2 0.05
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (13 bp):
AAATAATAAAAAT
Found at i:720663 original size:20 final size:21
Alignment explanation
Indices: 720620--720664 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
720610 AATAACAAAT
* *
720620 AAAATAAATAAATAAATAATA
1 AAAATAAATAAATAAAGAACA
*
720641 AAAATAACT-AATAAAGAACA
1 AAAATAAATAAATAAAGAACA
720661 AAAA
1 AAAA
720665 AAGTAAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (21 bp):
AAAATAAATAAATAAAGAACA
Found at i:720709 original size:2 final size:2
Alignment explanation
Indices: 720702--720730 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
720692 TAATTAAATA
720702 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
720731 ATTATATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:720736 original size:8 final size:9
Alignment explanation
Indices: 720699--720737 Score: 53
Period size: 10 Copynumber: 4.2 Consensus size: 9
720689 ACTTAATTAA
720699 ATAATATAT
1 ATAATATAT
720708 ATATATATAT
1 ATA-ATATAT
720718 ATATATATAT
1 ATA-ATATAT
720728 ATAAT-TAT
1 ATAATATAT
720736 AT
1 AT
720738 TAGTAGTAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 5 0.17
9 5 0.17
10 19 0.66
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
ATAATATAT
Found at i:721830 original size:13 final size:14
Alignment explanation
Indices: 721812--721853 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
721802 TGAAGATGTA
721812 AATAAATA-ATATT
1 AATAAATATATATT
721825 AATAAATATATATAT
1 AATAAATATATAT-T
*
721840 ATATATATATATAT
1 A-ATAAATATATAT
721854 ATATATATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 4 0.16
15 2 0.08
16 11 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATAAATATATATT
Found at i:721837 original size:2 final size:2
Alignment explanation
Indices: 721830--721861 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
721820 ATATTAATAA
721830 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
721862 GTGTGTTAAG
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:726174 original size:29 final size:29
Alignment explanation
Indices: 726140--726198 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
726130 CCTAAATTAA
726140 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
726169 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
726198 T
1 T
726199 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:730858 original size:29 final size:29
Alignment explanation
Indices: 730824--730882 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
730814 CCTAAATTAA
730824 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
730853 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
730882 T
1 T
730883 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:734443 original size:20 final size:20
Alignment explanation
Indices: 734418--734531 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
734408 AATTGGGAAA
*
734418 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
734438 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
734458 ATCGTAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
734479 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
734499 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
734519 TTCGCAACGCGAT
1 ATCGCAACGCGAT
734532 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:734531 original size:61 final size:61
Alignment explanation
Indices: 734415--734531 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
734405 GCGAATTGGG
* * * * * *
734415 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGTAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
734476 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
734532 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:735119 original size:19 final size:19
Alignment explanation
Indices: 735095--735206 Score: 99
Period size: 20 Copynumber: 6.1 Consensus size: 19
735085 AGAATCGCAA
735095 CGCGTTGCGATTTTCATTT
1 CGCGTTGCGATTTTCATTT
**
735114 CGCGTTGCGATAGTCATTT
1 CGCGTTGCGATTTTCATTT
*
735133 CGCGTTCCGA--TTC---T
1 CGCGTTGCGATTTTCATTT
* **
735147 CTCGTTGCGATAGTCATTT
1 CGCGTTGCGATTTTCATTT
*
735166 CCGCGTTGCGATTCTCATTAT
1 -CGCGTTGCGATTTTCATT-T
*
735187 CTCGTTGCGATTTTCATTT
1 CGCGTTGCGATTTTCATTT
735206 C
1 C
735207 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 2 0.03
19 29 0.39
20 31 0.42
21 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42
Consensus pattern (19 bp):
CGCGTTGCGATTTTCATTT
Found at i:735158 original size:33 final size:34
Alignment explanation
Indices: 735116--735181 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
735106 TTTCATTTCG
735116 CGTTGCGATAGTCATTT-CGCGTTCCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTCCGATTCTCT
*
735149 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTCCGATTCTC
735182 ATTATCTCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.12, C:0.27, G:0.23, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTCCGATTCTCT
Found at i:735183 original size:20 final size:19
Alignment explanation
Indices: 735095--735206 Score: 99
Period size: 19 Copynumber: 6.1 Consensus size: 19
735085 AGAATCGCAA
*
735095 CGCGTTGCGATTTTCATTT
1 CGCGTTGCGATTCTCATTT
**
735114 CGCGTTGCGATAGTCATTT
1 CGCGTTGCGATTCTCATTT
*
735133 CGCGTTCCGATTCTC---T
1 CGCGTTGCGATTCTCATTT
**
735149 --CGTTGCGATAGTCATTT
1 CGCGTTGCGATTCTCATTT
735166 CCGCGTTGCGATTCTCATTAT
1 -CGCGTTGCGATTCTCATT-T
* *
735187 CTCGTTGCGATTTTCATTT
1 CGCGTTGCGATTCTCATTT
735206 C
1 C
735207 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
14 10 0.14
16 1 0.01
17 1 0.01
19 31 0.42
20 30 0.41
21 1 0.01
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42
Consensus pattern (19 bp):
CGCGTTGCGATTCTCATTT
Found at i:736534 original size:21 final size:20
Alignment explanation
Indices: 736463--736535 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
736453 CTCCACTTCG
736463 AGAGCCATCACCTCAC--CC
1 AGAGCCATCACCTCACAACC
*
736481 AGAGCCATCACCTGATCAACC
1 AGAGCCATCACCTCA-CAACC
* * *
736502 CGA-CTATACACCTCTACAACG
1 AGAGCCAT-CACCTC-ACAACC
736523 AGAGCCATCACCT
1 AGAGCCATCACCT
736536 ATCCCGTCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 14 0.33
19 1 0.02
20 3 0.07
21 20 0.48
22 4 0.10
ACGTcount: A:0.32, C:0.41, G:0.12, T:0.15
Consensus pattern (20 bp):
AGAGCCATCACCTCACAACC
Found at i:737375 original size:42 final size:42
Alignment explanation
Indices: 737329--737462 Score: 180
Period size: 42 Copynumber: 3.2 Consensus size: 42
737319 CCTATCGTTG
737329 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACTGTTC
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACTGTTC
* * * * * * *
737371 AAGAGGCCACTGTCATCCCTCAAGAGTCCACTCCTA-TCGTTG
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACT-GTTC
*
737413 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACCGTTC
1 AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACTGTTC
737455 AAGAGGCC
1 AAGAGGCC
737463 ACTGTCATCG
Statistics
Matches: 75, Mismatches: 15, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 1 0.01
42 74 0.99
ACGTcount: A:0.22, C:0.38, G:0.19, T:0.22
Consensus pattern (42 bp):
AAGAGGCCCCTATCATTCCTCGAGAGTCCCCTCCCACTGTTC
Found at i:737459 original size:21 final size:21
Alignment explanation
Indices: 737435--737501 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
737425 TCATTCCTCG
737435 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
737456 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
737477 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
737498 AGAG
1 AGAG
737502 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:737480 original size:84 final size:84
Alignment explanation
Indices: 737297--737471 Score: 341
Period size: 84 Copynumber: 2.1 Consensus size: 84
737287 CCGACTCGCT
737297 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
1 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
*
737362 CCACTGTTCAAGAGGCCAC
66 CCACCGTTCAAGAGGCCAC
737381 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
1 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
737446 CCACCGTTCAAGAGGCCAC
66 CCACCGTTCAAGAGGCCAC
737465 TGTCATC
1 TGTCATC
737472 GTTGAAGAGG
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (84 bp):
TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
CCACCGTTCAAGAGGCCAC
Found at i:737487 original size:42 final size:41
Alignment explanation
Indices: 737297--737501 Score: 162
Period size: 42 Copynumber: 4.9 Consensus size: 41
737287 CCGACTCGCT
* * * * * *
737297 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCC
1 TGTCATCCTTGAAGAGTCC-CTCCCACCGTTCAAGAGGCCAC
* * *
737339 TATCATTCCTCG-AGAGTCCCCTCCCACTGTTCAAGAGGCCAC
1 TGTCA-TCCTTGAAGAGT-CCCTCCCACCGTTCAAGAGGCCAC
* * * * * *
737381 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCC
1 TGTCATCCTTGAAGAGTCC-CTCCCACCGTTCAAGAGGCCAC
* *
737423 TATCATTCCTCG-AGAGTCCCCTCCCACCGTTCAAGAGGCCAC
1 TGTCA-TCCTTGAAGAGT-CCCTCCCACCGTTCAAGAGGCCAC
* *
737465 TGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TGTCATCCTTGAAGA-GTCCCTCCCACCGTTCAAGAG
737502 CCCGATTCAC
Statistics
Matches: 125, Mismatches: 30, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
41 9 0.07
42 104 0.83
43 12 0.10
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (41 bp):
TGTCATCCTTGAAGAGTCCCTCCCACCGTTCAAGAGGCCAC
Found at i:737501 original size:84 final size:84
Alignment explanation
Indices: 737297--737501 Score: 286
Period size: 84 Copynumber: 2.4 Consensus size: 84
737287 CCGACTCGCT
* * * *
737297 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
1 TGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
*
737362 CCACTGTTCAAGAGGCCAC
66 CCACCGTTCAAGAGGCCAC
* * * *
737381 TGTCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
1 TGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
737446 CCACCGTTCAAGAGGCCAC
66 CCACCGTTCAAGAGGCCAC
** *
737465 TGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 TGTCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
737502 CCCGATTCAC
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
84 108 0.96
85 4 0.04
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (84 bp):
TGTCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCCCCTATCATTCCTCGAGAGTCCCCTC
CCACCGTTCAAGAGGCCAC
Found at i:738879 original size:14 final size:14
Alignment explanation
Indices: 738860--738895 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
738850 ATTGTTTAAT
738860 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
738874 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
738888 TGATTTGT
1 TGATTTGT
738896 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:739060 original size:33 final size:33
Alignment explanation
Indices: 739013--739077 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
739003 TCGCAATGCG
*
739013 AAATGAAAATCGCAACGAGAGAATCACAACGCA
1 AAATAAAAATCGCAACGAGAGAATCACAACGCA
*
739046 AAATAAAAATCGCAACGAGAGAATCGCAACGC
1 AAATAAAAATCGCAACGAGAGAATCACAACGC
739078 GATTGCGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.51, C:0.22, G:0.18, T:0.09
Consensus pattern (33 bp):
AAATAAAAATCGCAACGAGAGAATCACAACGCA
Found at i:739118 original size:19 final size:19
Alignment explanation
Indices: 739094--739185 Score: 60
Period size: 19 Copynumber: 5.4 Consensus size: 19
739084 GATTCCCTCG
739094 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* * *
739113 TTGCGA-----AATTAGCG
1 TTGCGATTTTCATTTCGCA
739127 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
739146 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
739160 TTGAGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
739179 TTACGAT
1 TTGCGAT
739186 AGTAATTTCC
Statistics
Matches: 52, Mismatches: 11, Indels: 20
0.63 0.13 0.24
Matches are distributed among these distances:
14 16 0.31
16 7 0.13
17 7 0.13
19 22 0.42
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:739129 original size:33 final size:33
Alignment explanation
Indices: 739092--739180 Score: 126
Period size: 33 Copynumber: 2.7 Consensus size: 33
739082 GCGATTCCCT
739092 CGTTGCGATTTTCATTTCGCATTGCGAAAT-TAG
1 CGTTGCGATTTTCATTTCGCATTGCG-AATCTAG
* **
739125 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGAATCTAG
*
739158 CGTTGAGATTTTCATTTCGCATT
1 CGTTGCGATTTTCATTTCGCATT
739181 ACGATAGTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
32 2 0.04
33 49 0.96
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGAATCTAG
Found at i:741498 original size:12 final size:12
Alignment explanation
Indices: 741481--741505 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
741471 TCTTCGGGGA
741481 CTTTTTCTTCTT
1 CTTTTTCTTCTT
741493 CTTTTTCTTCTT
1 CTTTTTCTTCTT
741505 C
1 C
741506 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:741714 original size:24 final size:24
Alignment explanation
Indices: 741680--741733 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
741670 CTGAAACATC
*
741680 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
741704 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
741728 ATCAAA
1 ATCAAA
741734 TTCGAATACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:742517 original size:20 final size:21
Alignment explanation
Indices: 742492--742543 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
742482 TTTTCCTAAT
*
742492 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
742512 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
742533 TCGCAATGCGA
1 TCGCAATGCGA
742544 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:742617 original size:20 final size:20
Alignment explanation
Indices: 742570--742619 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
742560 GAGATAATAC
742570 AAAATCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
***
742590 ACTTTCGCAACGAGATTCTG
1 AAAATCGCAACGAGATTCTG
742610 AAAATCGCAA
1 AAAATCGCAA
742620 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (20 bp):
AAAATCGCAACGAGATTCTG
Found at i:742858 original size:20 final size:20
Alignment explanation
Indices: 742833--742900 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
742823 CAACGGGGAA
742833 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
742853 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
742873 ATCGCAATGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
742893 ATCGCAAC
1 ATCGCAAC
742901 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:742912 original size:34 final size:34
Alignment explanation
Indices: 742817--742920 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
742807 ATTCATTTGA
** * *
742817 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAATGCGAAAATGG
742851 CTATCGCAATTCGAAATGAAAAATCGCAATGCGAAAATGG
1 CTATCGCAA--C--AA-G-AAAATCGCAATGCGAAAATGG
*
742891 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACAAGAAAATCGCAATGCGAAA
742921 TGAAAATCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
34 26 0.44
35 1 0.02
36 2 0.03
38 1 0.02
39 1 0.02
40 28 0.47
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.16
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAATGCGAAAATGG
Found at i:742974 original size:19 final size:19
Alignment explanation
Indices: 742950--742994 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
742940 TTCTCGTTGT
*
742950 GATTTTCATTTTGCATTGC
1 GATTTTCATTTCGCATTGC
742969 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
742988 GATTTTC
1 GATTTTC
742995 TCGTTGCGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.51
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:743150 original size:14 final size:14
Alignment explanation
Indices: 743131--743167 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
743121 CATCAATTAA
743131 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
743145 ACAAATCATCTTTT
1 ACAAATCAACATTT
743159 ACAAATCAA
1 ACAAATCAA
743168 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:744939 original size:18 final size:18
Alignment explanation
Indices: 744913--744957 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
744903 GTCGATCGGA
*
744913 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
744931 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
744949 TGATGGCTC
1 TGATGGCTC
744958 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:746322 original size:20 final size:20
Alignment explanation
Indices: 746274--746332 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
746264 AATAGTTTCT
** *
746274 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
746294 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
746314 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
746333 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:746852 original size:20 final size:20
Alignment explanation
Indices: 746827--746878 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
746817 ATTATGTATT
746827 ATCGCGTTGCGAAAGTCAGA
1 ATCGCGTTGCGAAAGTCAGA
*
746847 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGA
*
746867 ATCTCGTTGCGA
1 ATCGCGTTGCGA
746879 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGA
Found at i:746912 original size:20 final size:20
Alignment explanation
Indices: 746887--746940 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
746877 GATTTTGTAT
746887 TATCGCATTGCGATAATAAG
1 TATCGCATTGCGATAATAAG
* *
746907 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAATAAG
746927 TATCGCATTGCGAT
1 TATCGCATTGCGAT
746941 TTTCCTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAATAAG
Found at i:746912 original size:61 final size:62
Alignment explanation
Indices: 746806--746961 Score: 201
Period size: 61 Copynumber: 2.5 Consensus size: 62
746796 CGCTTTGAAA
* * *
746806 ATCGCATTGCGATTATGTATTATCGCGTTGCGA-AAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
746867 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAA-TAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAAGTAAGAATCGCATTGCGAAAGTCAGT
*
746928 ATCGCATTGCGATTTTCCTATT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-GTATTATCGCGTTGCGAT
746962 TTACTTATTC
Statistics
Matches: 81, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
61 75 0.93
62 6 0.07
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (62 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:746978 original size:20 final size:21
Alignment explanation
Indices: 746929--746980 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
746919 ATAGTCAGTA
*
746929 TCGCATTGCGATTTTCCTATT
1 TCGCATTGCGATTTACCTATT
* *
746950 TCGCGTTGCGATTTACTTA-T
1 TCGCATTGCGATTTACCTATT
746970 TCGCATTGCGA
1 TCGCATTGCGA
746981 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTACCTATT
Found at i:747606 original size:29 final size:29
Alignment explanation
Indices: 747574--747680 Score: 119
Period size: 29 Copynumber: 3.7 Consensus size: 29
747564 TAAATACACA
747574 TTATTCTT-TTTGTAACTTAAAAATATATT
1 TTATTCTTATTT-TAACTTAAAAATATATT
*
747603 TTATTCTTATTTTAACTTAAAAATGTATT
1 TTATTCTTATTTTAACTTAAAAATATATT
* ** * *
747632 TTAATCTTAGCTTAAATT-AAAATATAAT
1 TTATTCTTATTTTAACTTAAAAATATATT
* *
747660 TTATTTTTATCTTAACTTAAA
1 TTATTCTTATTTTAACTTAAA
747681 TATTTATATT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 22 0.34
29 40 0.62
30 3 0.05
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.52
Consensus pattern (29 bp):
TTATTCTTATTTTAACTTAAAAATATATT
Found at i:747777 original size:25 final size:25
Alignment explanation
Indices: 747749--747830 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 25
747739 TTAGTTAAGA
747749 TAAAAATAAAATATATTTTTATAGT
1 TAAAAATAAAATATATTTTTATAGT
*
747774 T-AAAATAAAA-ATATTTTTAAATTAAGA
1 TAAAAATAAAATATATTTTT--A-T-AGT
*
747801 TAAGAATAAAATATATGTTTTA-AGT
1 TAAAAATAAAATATAT-TTTTATAGT
747826 TAAAA
1 TAAAA
747831 TAAGAATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
23 8 0.17
24 9 0.20
25 8 0.17
26 1 0.02
27 3 0.07
28 9 0.20
29 4 0.09
30 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
TAAAAATAAAATATATTTTTATAGT
Found at i:747798 original size:22 final size:23
Alignment explanation
Indices: 747751--747808 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
747741 AGTTAAGATA
*
747751 AAAATAAAATATATTTTTATAGTT
1 AAAATAAAA-ATATTTTTATAATT
747775 AAAATAAAAATATTTTTA-AATT
1 AAAATAAAAATATTTTTATAATT
* *
747797 AAGATAAGAATA
1 AAAATAAAAATA
747809 AAATATATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 13 0.42
23 9 0.29
24 9 0.29
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (23 bp):
AAAATAAAAATATTTTTATAATT
Found at i:747868 original size:82 final size:82
Alignment explanation
Indices: 747701--747855 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 82
747691 TTAATTTGAT
* * * * *
747701 AATATTTTAAATCTAAGATAAAAATATAATATGTTTTTTTAGTTAAGATAAAAATAAAATATATT
1 AATATTTTAAATCTAAGATAAAAATAAAATATATGTTTTAAGTTAAAATAAAAATAAAATATATT
*
747766 TTTATAGTTAAAATAAA
66 TTAATAGTTAAAATAAA
* * * *
747783 AATATTTTTAAAT-TAAGATAAGAATAAAATATATGTTTTAAGTTAAAATAAGAATTAATTATA-
1 AATA-TTTTAAATCTAAGATAAAAATAAAATATATGTTTTAAGTTAAAATAAAAATAAAATATAT
747846 TTTAATAGTT
65 TTTAATAGTT
747856 TAAGGTGAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 9 0.15
82 45 0.73
83 8 0.13
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.42
Consensus pattern (82 bp):
AATATTTTAAATCTAAGATAAAAATAAAATATATGTTTTAAGTTAAAATAAAAATAAAATATATT
TTAATAGTTAAAATAAA
Found at i:747941 original size:25 final size:28
Alignment explanation
Indices: 747913--748060 Score: 85
Period size: 29 Copynumber: 5.3 Consensus size: 28
747903 TTATGTAATT
747913 AGTTAAGAATAAGA-T-ATAT-TTTTTA
1 AGTTAAGAATAAGATTAATATATTTTTA
*
747938 AGTTGAG-ATAAAGATTAAAATATATTTTTA
1 AGTTAAGAAT-AAGATT--AATATATTTTTA
*
747968 AGTTAA-AATAAGAATAAAATATATTTTTA
1 AGTTAAGAATAAG-AT-TAATATATTTTTA
* * * * *
747997 GGTTAAG-ACAAGAGTAAAATATATTTA
1 AGTTAAGAATAAGATTAATATATTTTTA
* * * *
748024 AGTTAA-TATAAAAATAAAATATATTTTA
1 AGTTAAGAATAAGATTAATATAT-TTTTA
748052 ATGTTAAGA
1 A-GTTAAGA
748061 TGTAAAATTA
Statistics
Matches: 94, Mismatches: 15, Indels: 23
0.71 0.11 0.17
Matches are distributed among these distances:
24 2 0.02
25 10 0.11
26 1 0.01
27 27 0.29
28 6 0.06
29 33 0.35
30 15 0.16
ACGTcount: A:0.50, C:0.01, G:0.11, T:0.38
Consensus pattern (28 bp):
AGTTAAGAATAAGATTAATATATTTTTA
Found at i:747989 original size:27 final size:28
Alignment explanation
Indices: 747705--748061 Score: 202
Period size: 30 Copynumber: 12.5 Consensus size: 28
747695 TTTGATAATA
* * *
747705 TTTTAAATCTAAGATAAAAATATAATATGTT
1 TTTTAAGT-TAAGATAAGAATA-AATAT-AT
* *
747736 TTTTTAGTTAAGATAAAAATAAAATATAT
1 TTTTAAGTTAAGATAAGAAT-AAATATAT
* *
747765 TTTT-A--T-AGTTAA-AATAAAAATAT
1 TTTTAAGTTAAGATAAGAATAAATATAT
*
747788 TTTTAAATTAAGATAAGAATAAAATATAT
1 TTTTAAGTTAAGATAAGAAT-AAATATAT
* *
747817 GTTTTAAGTTAAAATAAGAATTAAT-TAT
1 -TTTTAAGTTAAGATAAGAATAAATATAT
* *
747845 ATTTAATAGTTTAAGGTGAA-AATAGAATATAT
1 -TTTTA-AG-TTAAGAT-AAGAATA-AATATAT
* * *
747877 TTAATAATTTAAGCTAAGAAT--ATA-AT
1 TT-TTAAGTTAAGATAAGAATAAATATAT
*
747903 TTATGTAA-TT-AGTTAAGAATAAGATATATT
1 TT-T-TAAGTTAAGATAAGAATAA-ATATA-T
* *
747933 TTTTAAGTTGAGATAAAGATTAAAATATAT
1 TTTTAAGTTAAGAT-AAGAAT-AAATATAT
*
747963 TTTTAAGTTAAAATAAGAATAAAATATAT
1 TTTTAAGTTAAGATAAGAAT-AAATATAT
* * *
747992 TTTTAGGTTAAGACAAGAGTAAA-ATAT
1 TTTTAAGTTAAGATAAGAATAAATATAT
* * *
748019 ATTTAAGTTAATATAAAAATAAA-ATAT
1 TTTTAAGTTAAGATAAGAATAAATATAT
748046 ATTTTAATGTTAAGAT
1 -TTTTAA-GTTAAGAT
748062 GTAAAATTAA
Statistics
Matches: 261, Mismatches: 38, Indels: 56
0.74 0.11 0.16
Matches are distributed among these distances:
23 11 0.04
24 4 0.02
25 14 0.05
26 9 0.03
27 36 0.14
28 25 0.10
29 60 0.23
30 71 0.27
31 25 0.10
32 6 0.02
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.40
Consensus pattern (28 bp):
TTTTAAGTTAAGATAAGAATAAATATAT
Found at i:748044 original size:56 final size:56
Alignment explanation
Indices: 747741--748060 Score: 226
Period size: 60 Copynumber: 5.7 Consensus size: 56
747731 ATGTTTTTTT
* *
747741 AGTTAAGATAAAAATAAAATATATTTTTATAGTT-A-A-AA-TA-AAAATATTTTTA
1 AGTTAAGATAAAAATAAAATATATTTTTA-AGTTAAGACAAGAATAAAATATATTTA
* * * * * *
747793 AATTAAGATAAGAATAAAATATATGTTTTAAGTTAAAATAAGAATTAATTATATTTAA
1 AGTTAAGATAAAAATAAAATATAT-TTTTAAGTTAAGACAAGAATAAAATATATTT-A
* * * * * * * *
747851 TAGTTTAAGGTGAAAATAGAATATATTTAATAATTTAAG-CTAAGAATATAATTTATGTA
1 -AG-TTAAGATAAAAATAAAATATATTT-TTAAGTTAAGAC-AAGAATAAAATATATTTA
* * * * * *
747910 A-TT-AGTTAAGAATAAGATATATTTTTTAAGTTGAGATAAAGATTAAAATATATTTTTA
1 AGTTAAGATAAAAATAAAATATA-TTTTTAAGTTAAGA-CAAGAATAAAATATA--TTTA
* * * *
747968 AGTTAAAATAAGAATAAAATATATTTTTAGGTTAAGACAAGAGTAAAATATATTTA
1 AGTTAAGATAAAAATAAAATATATTTTTAAGTTAAGACAAGAATAAAATATATTTA
*
748024 AGTTAATATAAAAATAAAATATA-TTTTAATGTTAAGA
1 AGTTAAGATAAAAATAAAATATATTTTTAA-GTTAAGA
748061 TGTAAAATTA
Statistics
Matches: 206, Mismatches: 43, Indels: 34
0.73 0.15 0.12
Matches are distributed among these distances:
52 26 0.13
53 6 0.03
54 1 0.00
55 27 0.13
56 49 0.24
57 8 0.04
58 19 0.09
59 18 0.09
60 52 0.25
ACGTcount: A:0.50, C:0.01, G:0.10, T:0.39
Consensus pattern (56 bp):
AGTTAAGATAAAAATAAAATATATTTTTAAGTTAAGACAAGAATAAAATATATTTA
Found at i:748050 original size:85 final size:83
Alignment explanation
Indices: 747705--748061 Score: 253
Period size: 85 Copynumber: 4.2 Consensus size: 83
747695 TTTGATAATA
* * * * * *
747705 TTTTAAATCTAAGATAAAAATATAATATGTTTTTTTAGTTAAGATAAAAATAAAATATATTT---
1 TTTTAAGT-TAAGATAAGAATAAAATAT-ATGTTTTAGTTAAGAT-AAGAT-AAATATATTTAAG
*
747767 TTATAG-TTAAAATAAAA-ATAT
62 TTA-AGATAAAAATAAAATATAT
* * *
747788 TTTTAAATTAAGATAAGAATAAAATATATGTTTTAAGTTAAAATAAGAATTAATTATATTTAATA
1 TTTTAAGTTAAGATAAGAATAAAATATATGTTTT-AGTTAAGATAAG-A-TAAATATATTT-A-A
* * *
747853 GTTTAAGGTGAAAATAGAATATAT
61 G-TTAAGATAAAAATAAAATATAT
* * * * * * * *
747877 TTAATAATTTAAGCTAAGAATATAATTTATGTAATTAGTTAAGAATAAGATATAT-TTTTTAAGT
1 TT-TTAAGTTAAGATAAGAATAAAATATATGT-TTTAGTTAAG-ATAAGATAAATATATTTAAGT
* *
747941 TGAGATAAAGATTAAAATATAT
63 TAAGATAAA-AATAAAATATAT
* *
747963 TTTTAAGTTAAAATAAGAATAAAATATAT-TTTTAGGTTAAGACAAGAGTAAAATATATTTAAGT
1 TTTTAAGTTAAGATAAGAATAAAATATATGTTTTA-GTTAAGATAAGA-T-AAATATATTTAAGT
*
748027 TAATATAAAAATAAAATATA-
63 TAAGATAAAAATAAAATATAT
748047 TTTTAATGTTAAGAT
1 TTTTAA-GTTAAGAT
748062 GTAAAATTAA
Statistics
Matches: 216, Mismatches: 38, Indels: 38
0.74 0.13 0.13
Matches are distributed among these distances:
81 7 0.03
82 35 0.16
83 17 0.08
84 14 0.06
85 48 0.22
86 29 0.13
87 3 0.01
88 16 0.07
89 9 0.04
90 31 0.14
91 7 0.03
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.40
Consensus pattern (83 bp):
TTTTAAGTTAAGATAAGAATAAAATATATGTTTTAGTTAAGATAAGATAAATATATTTAAGTTAA
GATAAAAATAAAATATAT
Found at i:748089 original size:18 final size:18
Alignment explanation
Indices: 748048--748097 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
748038 TAAAATATAT
748048 TTTAATGTTAAGATGTAAA
1 TTTAAT-TTAAGATGTAAA
* * *
748067 ATTAATTTAATATGTGAA
1 TTTAATTTAAGATGTAAA
*
748085 TTTAAGTTAAGAT
1 TTTAATTTAAGAT
748098 ATATAAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (18 bp):
TTTAATTTAAGATGTAAA
Found at i:750013 original size:29 final size:30
Alignment explanation
Indices: 749960--750022 Score: 69
Period size: 29 Copynumber: 2.1 Consensus size: 30
749950 AAACACCGGG
* *
749960 TTAGTGTCCAAATTGTAAAATTTTAGAA-T
1 TTAGTGACCAAATTGTAAAATTTTAAAAGT
749989 TTAGTGACCAAATTAG-ATAAA-TTTAAAAGT
1 TTAGTGACCAAATT-GTA-AAATTTTAAAAGT
750019 TTAG
1 TTAG
750023 GGACTTAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
29 20 0.69
30 9 0.31
ACGTcount: A:0.41, C:0.06, G:0.14, T:0.38
Consensus pattern (30 bp):
TTAGTGACCAAATTGTAAAATTTTAAAAGT
Found at i:750833 original size:20 final size:20
Alignment explanation
Indices: 750810--750864 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
750800 CCAAAAGAGT
*
750810 AGTACCGATACCATTATGCA
1 AGTACCGATACCATTATACA
*
750830 AGTACTGATACCATTATACA
1 AGTACCGATACCATTATACA
* *
750850 AGTATCAATACCATT
1 AGTACCGATACCATT
750865 TTTATAAGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (20 bp):
AGTACCGATACCATTATACA
Found at i:757965 original size:20 final size:19
Alignment explanation
Indices: 757921--758019 Score: 101
Period size: 20 Copynumber: 5.0 Consensus size: 19
757911 AAATAACCAA
757921 CGAATTCGCAACTCAATTT
1 CGAATTCGCAACTCAATTT
*
757940 CGAATTCGCAA-TACAGTTT
1 CGAATTCGCAACT-CAATTT
757959 CCGAATTCGCAACTCGAATTT
1 -CGAATTCGCAACTC-AATTT
* * **
757980 AGAATTCGCAACACAAAAGT
1 CGAATTCGCAACTC-AATTT
758000 CGAATTCGCAACTCGAATTT
1 CGAATTCGCAACTC-AATTT
758020 TTTTTTCGCA
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
18 1 0.02
19 16 0.25
20 42 0.66
21 5 0.08
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.27
Consensus pattern (19 bp):
CGAATTCGCAACTCAATTT
Found at i:757989 original size:40 final size:40
Alignment explanation
Indices: 757921--758019 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
757911 AAATAACCAA
* * ***
757921 CGAATTCGCAACTC-AATTTCGAATTCGCAATAC-AGTTT
1 CGAATTCGCAACTCGAATTTAGAATTCGCAACACAAAAGT
757959 CCGAATTCGCAACTCGAATTTAGAATTCGCAACACAAAAGT
1 -CGAATTCGCAACTCGAATTTAGAATTCGCAACACAAAAGT
758000 CGAATTCGCAACTCGAATTT
1 CGAATTCGCAACTCGAATTT
758020 TTTTTTCGCA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 14 0.26
40 37 0.70
41 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.27
Consensus pattern (40 bp):
CGAATTCGCAACTCGAATTTAGAATTCGCAACACAAAAGT
Found at i:758046 original size:40 final size:40
Alignment explanation
Indices: 758022--758100 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
758012 TCGAATTTTT
* *
758022 TTTTCGCAACTCGATT-TTTAAATTCGCAACACAAGTTTCG
1 TTTTCACAACTCGATTATCT-AATTCGCAACACAAGTTTCG
* *
758062 TTTTCACAACTCGATTATCTAATTCGCAACGCGAGTTTC
1 TTTTCACAACTCGATTATCTAATTCGCAACACAAGTTTC
758101 AATTTTGCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.94
41 2 0.06
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.37
Consensus pattern (40 bp):
TTTTCACAACTCGATTATCTAATTCGCAACACAAGTTTCG
Found at i:758047 original size:20 final size:20
Alignment explanation
Indices: 757962--758051 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
757952 ACAGTTTCCG
**
757962 AATTCGCAACTCGAATTTAG
1 AATTCGCAACTCGAATTTTT
* * ** **
757982 AATTCGCAACACAAAAGTCG
1 AATTCGCAACTCGAATTTTT
758002 AATTCGCAACTCGAATTTTT
1 AATTCGCAACTCGAATTTTT
**
758022 TTTTCGCAACTCG-ATTTTT
1 AATTCGCAACTCGAATTTTT
758041 AAATTCGCAAC
1 -AATTCGCAAC
758052 ACAAGTTTCG
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
19 6 0.11
20 48 0.89
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.32
Consensus pattern (20 bp):
AATTCGCAACTCGAATTTTT
Found at i:758088 original size:60 final size:58
Alignment explanation
Indices: 757962--758139 Score: 160
Period size: 60 Copynumber: 3.0 Consensus size: 58
757952 ACAGTTTCCG
* ** ** *
757962 AATTCGCAACTCGAATTTAGAATTCGCAACACAAAAGTCGAATTCGCAACTCGAATT-TTT
1 AATTCGCAACTCGATTTTA-AATTCGCAACAC-AATTTCGTTTTCGCAACTCG-ATTATCT
** *
758022 TTTTCGCAACTCGATTTTTAAATTCGCAACACAAGTTTCGTTTTCACAACTCGATTATCT
1 AATTCGCAACTCGA-TTTTAAATTCGCAACACAA-TTTCGTTTTCGCAACTCGATTATCT
* * * * *
758082 AATTCGCAACGCGAGTTTCAATTTTGCAACACGAATTTTGTTTTCGCAACTCGATTAT
1 AATTCGCAACTCGA-TTTTAAATTCGCAACAC-AATTTCGTTTTCGCAACTCGATTAT
758140 ACAGACTTGC
Statistics
Matches: 96, Mismatches: 18, Indels: 8
0.79 0.15 0.07
Matches are distributed among these distances:
59 5 0.05
60 85 0.89
61 6 0.06
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (58 bp):
AATTCGCAACTCGATTTTAAATTCGCAACACAATTTCGTTTTCGCAACTCGATTATCT
Found at i:758130 original size:20 final size:20
Alignment explanation
Indices: 758004--758135 Score: 74
Period size: 20 Copynumber: 6.6 Consensus size: 20
757994 AAAAGTCGAA
*
758004 TTCGCAACTCGAATTTTTTT
1 TTCGCAACTCGAATTTTATT
* **
758024 TTCGCAACTCGATTTTTAAA
1 TTCGCAACTCGAATTTTATT
* **
758044 TTCGCAACAC-AAGTTTCGTT
1 TTCGCAACTCGAA-TTTTATT
* *
758064 TTCACAACTCG-ATTATCTA-A
1 TTCGCAACTCGAATT-T-TATT
* * *
758084 TTCGCAACGCGAGTTTCAATT
1 TTCGCAACTCGAATTT-TATT
* *
758105 TT-GCAACACGAATTTTGTT
1 TTCGCAACTCGAATTTTATT
758124 TTCGCAACTCGA
1 TTCGCAACTCGA
758136 TTATACAGAC
Statistics
Matches: 80, Mismatches: 25, Indels: 14
0.67 0.21 0.12
Matches are distributed among these distances:
19 7 0.09
20 69 0.86
21 4 0.05
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.38
Consensus pattern (20 bp):
TTCGCAACTCGAATTTTATT
Found at i:758490 original size:20 final size:20
Alignment explanation
Indices: 758465--758595 Score: 156
Period size: 20 Copynumber: 6.6 Consensus size: 20
758455 TATATGCCAC
* * *
758465 TCGAGTTGTGAATTCGAAAT
1 TCGAGTTGCGAATTTGAATT
**
758485 TCGAGTTATGAATTTG-ATT
1 TCGAGTTGCGAATTTGAATT
*
758504 TCGAGTTGCGCATTTGAATT
1 TCGAGTTGCGAATTTGAATT
* *
758524 TCGAGTTGTGAATTTGAGTT
1 TCGAGTTGCGAATTTGAATT
758544 TCGAGTTGCGAATTTGAATT
1 TCGAGTTGCGAATTTGAATT
* *
758564 TCGAGTTGCGAATTCGATTT
1 TCGAGTTGCGAATTTGAATT
*
758584 TCAAGTTGCGAA
1 TCGAGTTGCGAA
758596 ATCCATATTC
Statistics
Matches: 96, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
19 15 0.16
20 81 0.84
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (20 bp):
TCGAGTTGCGAATTTGAATT
Found at i:758557 original size:59 final size:60
Alignment explanation
Indices: 758465--758683 Score: 176
Period size: 60 Copynumber: 3.6 Consensus size: 60
758455 TATATGCCAC
* * *
758465 TCGAGTTGTGAATTCGAAATTCGAGTTATGAATTTG-ATTTCGAGTTGCGCATTTGAATT
1 TCGAGTTGTGAATTCGAAATTCGAGTTACGAATTTGAATTTCGAGTTGCGAATTCGAATT
* ** * *
758524 TCGAGTTGTGAATTTGAGTTTCGAGTTGCGAATTTGAATTTCGAGTTGCGAATTCGATTT
1 TCGAGTTGTGAATTCGAAATTCGAGTTACGAATTTGAATTTCGAGTTGCGAATTCGAATT
* * * * * * * * * *
758584 TCAAGTTGCGAAATCCATATTCAAGTTACAAATTCGAAATT-GAGTTTGCGAAATTGACGGATT
1 TCGAGTTGTGAATTCGAAATTCGAGTTACGAATTTGAATTTCGAG-TTGCG-AATT--CGAATT
* * *
758647 T-GAGTTGCGAAATCCG-AATTCGAGTTGCGAATTTGAA
1 TCGAGTTGTG-AATTCGAAATTCGAGTTACGAATTTGAA
758684 AACTGAGTTG
Statistics
Matches: 123, Mismatches: 31, Indels: 9
0.75 0.19 0.06
Matches are distributed among these distances:
59 34 0.28
60 54 0.44
61 4 0.03
62 23 0.19
63 8 0.07
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.37
Consensus pattern (60 bp):
TCGAGTTGTGAATTCGAAATTCGAGTTACGAATTTGAATTTCGAGTTGCGAATTCGAATT
Found at i:758559 original size:40 final size:39
Alignment explanation
Indices: 758465--758595 Score: 172
Period size: 40 Copynumber: 3.3 Consensus size: 39
758455 TATATGCCAC
* * * *
758465 TCGAGTTGTGAATTCGAAATTCGAGTTATGAATTTGATT
1 TCGAGTTGCGAATTTGAATTTCGAGTTGTGAATTTGATT
*
758504 TCGAGTTGCGCATTTGAATTTCGAGTTGTGAATTTGAGTT
1 TCGAGTTGCGAATTTGAATTTCGAGTTGTGAATTTGA-TT
* *
758544 TCGAGTTGCGAATTTGAATTTCGAGTTGCGAATTCGATTT
1 TCGAGTTGCGAATTTGAATTTCGAGTTGTGAATTTGA-TT
*
758584 TCAAGTTGCGAA
1 TCGAGTTGCGAA
758596 ATCCATATTC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 32 0.40
40 49 0.60
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.40
Consensus pattern (39 bp):
TCGAGTTGCGAATTTGAATTTCGAGTTGTGAATTTGATT
Found at i:758673 original size:20 final size:20
Alignment explanation
Indices: 758465--758677 Score: 102
Period size: 20 Copynumber: 10.6 Consensus size: 20
758455 TATATGCCAC
*
758465 TCGAGTTGTG-AATTCGAAAT
1 TCGAGTTGCGAAATTCG-AAT
** * *
758485 TCGAGTTATG-AATTTGATT
1 TCGAGTTGCGAAATTCGAAT
* *
758504 TCGAGTTGCG-CATTTGAATT
1 TCGAGTTGCGAAATTCGAA-T
* * *
758524 TCGAGTTGTG-AATTTGAGTT
1 TCGAGTTGCGAAATTCGA-AT
*
758544 TCGAGTTGCG-AATTTGAATT
1 TCGAGTTGCGAAATTCGAA-T
*
758564 TCGAGTTGCG-AATTCGATTT
1 TCGAGTTGCGAAATTCGA-AT
* *
758584 TCAAGTTGCGAAA-TCCATAT
1 TCGAGTTGCGAAATTCGA-AT
* *
758604 TCAAGTTAC-AAATTCGAAAT
1 TCGAGTTGCGAAATTCG-AAT
*
758624 T-GAGTTTGCGAAATTGACGGAT
1 TCGAG-TTGCGAAATT--CGAAT
* *
758646 TTGAGTTGCGAAATCCGAAT
1 TCGAGTTGCGAAATTCGAAT
758666 TCGAGTTGCGAA
1 TCGAGTTGCGAA
758678 TTTGAAAACT
Statistics
Matches: 156, Mismatches: 25, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
19 21 0.13
20 110 0.71
21 8 0.05
22 12 0.08
23 5 0.03
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (20 bp):
TCGAGTTGCGAAATTCGAAT
Done.