Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009380.1 Hibiscus syriacus cultivar Beakdansim tig00113263_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: 73371
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1890 original size:50 final size:50
Alignment explanation
Indices: 1810--1940 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
1800 CACTCGTAGC
* * * *
1810 AGTAAAGCGCGCCCCCTGAACCGTGCTATACGCTGATTTGGCGCCACATG
1 AGTATAGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCGCCACATG
** * * *
1860 AGTATAGCGCGCCCCCTGCCCCGCGATATACGGTGATCTGGCGTCACGTG
1 AGTATAGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCGCCACATG
* *
1910 -GATATAGCGCGCCCCCTGATCCGCGCTATAC
1 AG-TATAGCGCGCCCCCTGAACCGCGATATAC
1941 CTAGTTATCT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 1 0.01
50 67 0.99
ACGTcount: A:0.19, C:0.34, G:0.27, T:0.20
Consensus pattern (50 bp):
AGTATAGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCGCCACATG
Found at i:2179 original size:17 final size:18
Alignment explanation
Indices: 2142--2182 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2132 CTATTATGTA
*
2142 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
2160 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
2177 TTTACT
1 TTTACT
2183 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:2526 original size:110 final size:111
Alignment explanation
Indices: 2282--2564 Score: 488
Period size: 109 Copynumber: 2.6 Consensus size: 111
2272 CATTTTAACG
2282 TTTAATTTAAATTATTAGTAAT-ATTAGTTGA-TTATTTAATGCATGATT-TTAGATTAAGAATT
1 TTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATT
* *
2344 AAATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAA
66 AAATATATCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAA
2390 -TTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATT
1 TTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATT
*
2454 AAA-ATATCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAA
66 AAATATATCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAA
*
2499 TTTAATTTAAATTATTAGTAATAATTAGTTGATTTATATAATGCATGA-TATTAGATTAAGAATT
1 TTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATT
2563 AA
66 AA
2565 TTTTGTAATT
Statistics
Matches: 167, Mismatches: 4, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
107 21 0.13
108 9 0.05
109 74 0.44
110 63 0.38
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.45
Consensus pattern (111 bp):
TTTAATTTAAATTATTAGTAATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATT
AAATATATCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAA
Found at i:8864 original size:2 final size:2
Alignment explanation
Indices: 8857--8909 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
8847 ATACTAATAA
8857 AT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8898 AT AT AT AT AT AT
1 AT AT AT AT AT AT
8910 TGACCTAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12204 original size:30 final size:29
Alignment explanation
Indices: 12164--12258 Score: 145
Period size: 30 Copynumber: 3.2 Consensus size: 29
12154 ACGTGGGGGC
* *
12164 ATGGTGGTGGCATGGGATATTGAATATAAA
1 ATGGTAGTGGCATGGGATGTTGAATA-AAA
12194 ATGGTAGTGGCATGGGATGTTGAATAAAAA
1 ATGGTAGTGGCATGGGATGTTGAAT-AAAA
12224 ATGGTAGTGGCATGGGATGTTGAATAAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAA
12253 TATGGT
1 -ATGGT
12259 GGAATAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
29 4 0.07
30 56 0.92
31 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.34, T:0.29
Consensus pattern (29 bp):
ATGGTAGTGGCATGGGATGTTGAATAAAA
Found at i:12650 original size:91 final size:91
Alignment explanation
Indices: 12461--12715 Score: 370
Period size: 91 Copynumber: 2.8 Consensus size: 91
12451 GTGATGCAAT
* * * *
12461 GTTGAATAAGTTCTTCTGATTATGAACTTCTTCTGCCTC-TATCGGATGAGTTATTCTCATTATG
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGT-T-GGATGAGTTCTTCTCATTATG
**
12525 AACTCTCCACTGTAAATATTGATGCAAG
64 AACTCTCCACTGTAAATATTGAACCAAG
* *
12553 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATAAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
* *
12618 CTTTCCACTAG-AAATCTTGAACCAAG
66 CTCTCCACT-GTAAATATTGAACCAAG
*
12644 GTTGAACAAGTTCTTCTCTTTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
12709 CTCTCCA
66 CTCTCCA
12716 TTTGAAATGT
Statistics
Matches: 147, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
91 109 0.74
92 37 0.25
93 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (91 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
CTCTCCACTGTAAATATTGAACCAAG
Found at i:16181 original size:30 final size:30
Alignment explanation
Indices: 16141--16229 Score: 144
Period size: 30 Copynumber: 3.0 Consensus size: 30
16131 ACGTGGGGGC
* *
16141 ATGGTGGTGGCATGGGATATTGAATATAAA-
1 ATGGTAGTGGCATGGGATGTTGAATA-AAAG
16171 ATGGTAGTGGCATGGGATGTTGAATAAAAG
1 ATGGTAGTGGCATGGGATGTTGAATAAAAG
16201 ATGGTAGTGGCATGGGATGTTGAATAAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAA
16230 TATGATGGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
29 3 0.05
30 53 0.95
ACGTcount: A:0.34, C:0.03, G:0.35, T:0.28
Consensus pattern (30 bp):
ATGGTAGTGGCATGGGATGTTGAATAAAAG
Found at i:16242 original size:15 final size:15
Alignment explanation
Indices: 16222--16252 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16212 ATGGGATGTT
*
16222 GAATAAAATATGATG
1 GAATAAAAAATGATG
16237 GAATAAAAAATGATG
1 GAATAAAAAATGATG
16252 G
1 G
16253 TGCTTACAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.23
Consensus pattern (15 bp):
GAATAAAAAATGATG
Found at i:16627 original size:91 final size:91
Alignment explanation
Indices: 16434--16692 Score: 376
Period size: 91 Copynumber: 2.8 Consensus size: 91
16424 ATATGTGATG
* * *
16434 CAAGGTTGAATAAGTTCTTCTGATTATGAACTTCTTCTGCCTC-TATCGGATGAGTTCTTCTCAT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGT-T-GGATGAGTTCTTCTCAT
* * **
16498 TATGAACTCTCCGCTATAAATATTGATG
64 TATGAACTCTCCACTAGAAATATTGAAC
* *
16526 CAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATAAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
* * *
16591 TGAACTTTCCACTGGAAATCTTGAAC
66 TGAACTCTCCACTAGAAATATTGAAC
*
16617 CAAGGTTGAACAAGTTCTTCTCTTTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
16682 TGAACTCTCCA
66 TGAACTCTCCA
16693 TTTGAAATGT
Statistics
Matches: 150, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
91 109 0.73
92 40 0.27
93 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (91 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
TGAACTCTCCACTAGAAATATTGAAC
Found at i:17252 original size:36 final size:36
Alignment explanation
Indices: 17212--17714 Score: 390
Period size: 36 Copynumber: 14.0 Consensus size: 36
17202 TGAGATAGAT
*
17212 TTTGTTTCAAGGGTAACTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
*
17248 TTTGTTTCAAGGGAAAC-GATCTCAA-AG-G-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGAAAAAA
* * * *
17277 TTGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
* * * *
17314 CTTATTTCAAGGAAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
* * *
17350 TTTGTTTCCAGGGAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGAAAAAA
* *
17379 TTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
*
17415 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
* * *
17451 TTTGTTTTAAGGGAAACTCTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
*
17487 TTTGTTTCAACGGAAACTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
* * **
17523 TTTGTTTCAAGGGAAATTATCTCAAGAGAGATAAATCT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA-AAA-AA
** * *
17561 TTTGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGA-AAAA-A
** * *
17599 TTATGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATC
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGA-AAAA-A
* * * * *
17638 TTCTGTTTCAAGTGAAACTATCTGAAGCGAGATAAAATC
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGA-AAAA-A
* * * * *
17677 TTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
17714 T
1 T
17715 CTTCTTTAAA
Statistics
Matches: 394, Mismatches: 50, Indels: 45
0.81 0.10 0.09
Matches are distributed among these distances:
28 1 0.00
29 21 0.05
30 20 0.05
31 3 0.01
32 3 0.01
33 2 0.01
34 2 0.01
35 4 0.01
36 194 0.49
37 6 0.02
38 37 0.09
39 101 0.26
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAAAAAA
Found at i:17299 original size:66 final size:66
Alignment explanation
Indices: 17214--17338 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
17204 AGATAGATTT
* * * * * *
17214 TGTTTCAAGGGTAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGAAAAAACTTATTTCAAGGAAAACTG-TCTCAAAGGTT
17278 TG
65 TG
* *
17280 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTATTTCAAGGAAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGAAAAAACTTATTTCAAGGAAAACTGTCTCAA
17339 GAGAGATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
66 49 0.98
67 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTAAAGAGAGAAAAAACTTATTTCAAGGAAAACTGTCTCAAAGGTTT
G
Found at i:17441 original size:101 final size:101
Alignment explanation
Indices: 17212--17577 Score: 446
Period size: 101 Copynumber: 3.5 Consensus size: 101
17202 TGAGATAGAT
* * *
17212 TTTGTTTCAAGGGTAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGGGAAACGATCTCAAAGGT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACGATCTCAAAGAT
* * *
17277 TTGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAA
66 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
17314 CTTATTTCAAGGAAAACTGTCTCAAGAGAGATAAAATTTGTTTCCAGGGAAACAGAT-TCAAAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGA
*
17378 TTTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
65 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* **
17415 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTTAAGGGAAACTCTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACGATCTC-A-A-A
* * *
17480 GACAAAATTTGTTTCAACGGAAACTGTCTCAAGAGAGAAAAAA
63 G----ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
17523 TTTGTTTCAAGGGAAATTATCTCAAGAGAGATAAATCTTTTGTTTCAAGGGAAAC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAA--ATTTGTTTCAAGGGAAAC
17578 TACCTCAAGC
Statistics
Matches: 227, Mismatches: 26, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
100 1 0.00
101 80 0.35
102 57 0.25
103 4 0.02
104 2 0.01
108 67 0.30
110 16 0.07
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (101 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACGATCTCAAAGAT
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:17688 original size:20 final size:20
Alignment explanation
Indices: 17626--17688 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
17616 CTACCTCAAG
17626 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
* * ***
17646 CAAG-TGAAA-CTATCTGAAG
1 CGAGATAAAATCT-TCTGTTT
17665 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
17685 CGAG
1 CGAG
17689 TGAAACTATC
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 2 0.07
19 11 0.37
20 15 0.50
21 2 0.07
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (20 bp):
CGAGATAAAATCTTCTGTTT
Found at i:17719 original size:39 final size:38
Alignment explanation
Indices: 17383--17717 Score: 391
Period size: 36 Copynumber: 8.9 Consensus size: 38
17373 AAAGATTTTT
* *
17383 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGATAAAATCTTTG
*
17419 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAA--TTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGATAAAATCTTTG
* * *
17455 TTTTAAGGGAAACTCTCTCAAGAGAGACAAAA--TTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGATAAAATCTTTG
* * *
17491 TTTCAACGGAAACTGTCTCAAGAGAGA-AAAA-ATTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGATAAAATCTTTG
*
17527 TTTCAAGGGAAATTATCTCAAGAGAGAT-AAATCTTTTG
1 TTTCAAGGGAAACTATCTCAAGAGAGATAAAATC-TTTG
* *
17565 TTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTATG
1 TTTCAAGGGAAACTATCTCAAGAGAGATAAAATCTT-TG
* *
17604 TTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTCTG
1 TTTCAAGGGAAACTATCTCAAGAGAGATAAAATCTT-TG
* * *
17643 TTTCAAGTGAAACTATCTGAAGCGAGATAAAATCTTCTG
1 TTTCAAGGGAAACTATCTCAAGAGAGATAAAATCTT-TG
* * *
17682 TTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTT
1 TTTCAAGGGAAACTATCTCAAGAGAGATAAAATCTT
17718 CTTTAAAAAC
Statistics
Matches: 273, Mismatches: 20, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
35 4 0.01
36 123 0.45
38 31 0.11
39 115 0.42
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (38 bp):
TTTCAAGGGAAACTATCTCAAGAGAGATAAAATCTTTG
Found at i:17839 original size:76 final size:73
Alignment explanation
Indices: 17672--17868 Score: 215
Period size: 76 Copynumber: 2.7 Consensus size: 73
17662 AAGCGAGATA
* * * *
17672 AAATCTTC-TGTTTCGAGTGAAACT-ATCTCAAGCGAGATAAAATCTTCTTTAAAAACAATATTG
1 AAATCTTCTTGTTTCGAGTAAAAATCGTCTCAAGCGAGA-CAAATCTTCTTTAAAAACAATATTG
17735 AGTGAAATG
65 AGTGAAATG
* * * * *
17744 AAATGTT-TTCTTTCAAGTAAAAATCGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATC
1 AAATCTTCTTGTTTCGAGTAAAAATCGTCTCAAGCGAGACAAATCTT-CTTT---AAAAACAATA
17808 TTGAGTGAAAT-
62 TTGAGTGAAATG
17819 AAATCTTCTTGTTTCGAGTAAAAA-CTGTCTCAAGCGAGACAGAATCTTCT
1 AAATCTTCTTGTTTCGAGTAAAAATC-GTCTCAAGCGAGACA-AATCTTCT
17869 GTTTCAAGGG
Statistics
Matches: 103, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
72 25 0.24
73 15 0.15
75 7 0.07
76 50 0.49
77 6 0.06
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (73 bp):
AAATCTTCTTGTTTCGAGTAAAAATCGTCTCAAGCGAGACAAATCTTCTTTAAAAACAATATTGA
GTGAAATG
Found at i:17896 original size:39 final size:39
Alignment explanation
Indices: 17840--17920 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 39
17830 TTTCGAGTAA
* * *
17840 AAACTGTCTCAAGCGAGACAGAATCTTCTGTTTCAAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGCG
*
17879 AAACTATCTCTAA-CGAGACAAAATTTTCTGTTTCAAGCG
1 AAACTATCTC-AAGCGAGACAAAATCTTCTGTTTCAAGCG
17918 AAA
1 AAA
17921 TAACTCTTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 35 0.95
40 2 0.05
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGCG
Found at i:22013 original size:29 final size:29
Alignment explanation
Indices: 21965--22020 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
21955 CAATAAGAGC
21965 AGACAAAAAGATCAATGTTAGTAGAAACA
1 AGACAAAAAGATCAATGTTAGTAGAAACA
* *
21994 AGACAACAAGAATCAA-GTTAGTTGAAA
1 AGACAAAAAG-ATCAATGTTAGTAGAAA
22021 AGATTAGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.18
Consensus pattern (29 bp):
AGACAAAAAGATCAATGTTAGTAGAAACA
Found at i:28362 original size:21 final size:21
Alignment explanation
Indices: 28336--28375 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28326 CCCCCTTTGA
*
28336 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
28357 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
28376 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:30657 original size:14 final size:14
Alignment explanation
Indices: 30638--30664 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30628 GGGGGAGTAA
30638 TTTCTAATTTCAAT
1 TTTCTAATTTCAAT
30652 TTTCTAATTTCAA
1 TTTCTAATTTCAA
30665 AACTTGATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTCTAATTTCAAT
Found at i:34287 original size:30 final size:30
Alignment explanation
Indices: 34253--34336 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
34243 ACATGTGGGC
* * *
34253 ATGGTGGTGGCATGGGATATTGAATATAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAAA
*
34283 ATGGTAGTGACATGGGATGTTGAATAAAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAAA
*
34313 ATGGTAGTGGAATGGGATGTTGAA
1 ATGGTAGTGGCATGGGATGTTGAA
34337 GAAACTATGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.35, C:0.02, G:0.35, T:0.29
Consensus pattern (30 bp):
ATGGTAGTGGCATGGGATGTTGAATAAAAA
Found at i:34739 original size:91 final size:90
Alignment explanation
Indices: 34550--34812 Score: 328
Period size: 91 Copynumber: 2.9 Consensus size: 90
34540 GTGATGCAAT
* * ** *
34550 GTTGAATAAGTTCTTCTGATTATGAACTTCTTCTGCCTCTATCAGATGAGTTCTTCTCATTATGT
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCT-TATTGGATGAGTTCTTCTCATTATGA
* * * * **
34615 ACTCTCCACTGTAAATGTTGATGCAAG
64 ACTCTCCATTGGAAATCTTAAACCAAG
* * *
34642 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCACTTTTTGGATAAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC-CTTATTGGATGAGTTCTTCTCATTATGAA
*
34707 CTCTCCATTGGAAATCTTAAACCCAG
65 CTCTCCATTGGAAATCTTAAACCAAG
**
34733 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCTTATTGGATGAGTTCTTCTCATTATGAA
*
34798 CTCTCCATTTGAAAT
65 CTCTCCATTGGAAAT
34813 GTCAATCCCT
Statistics
Matches: 149, Mismatches: 20, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
91 115 0.77
92 34 0.23
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (90 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTATTGGATGAGTTCTTCTCATTATGAAC
TCTCCATTGGAAATCTTAAACCAAG
Found at i:35441 original size:36 final size:36
Alignment explanation
Indices: 35327--35649 Score: 184
Period size: 39 Copynumber: 8.9 Consensus size: 36
35317 ATAGATTTTA
* *
35327 TTTCTAGGGAAACTGTCTAAAGAGAGACAAAA-TTCG
1 TTTCAAGGGAAACTATCTAAAGAGAGACAAAACTT-G
* * **
35363 TTTCAAGGGAAACCATCTCAA-AG-G-----TTTGTG
1 TTTCAAGGGAAACTATCTAAAGAGAGACAAAACT-TG
* * * *
35393 TTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTA
1 TTTCAAGGGAAACTATCTAAAGAGAGACAAAACTTG
*
35429 TTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTG
1 TTTCAAGGGAAACTATCTAAAGAGAGACAAAACTTG
*
35464 TTTTCAAGGGAAAC-AGTCTCAAA-AGAGACAAAATTTG
1 -TTTCAAGGGAAACTA-TCT-AAAGAGAGACAAAACTTG
* * *
35501 TTTCAAGGGAAATTATCTCAAGAGAGATAAAATCTTTTG
1 TTTCAAGGGAAACTATCTAAAGAGAGACAAAA-C--TTG
* * * *
35540 TTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTCTG
1 TTTCAAGGGAAACTATCTAAAGAGAGACAAAA-C-T-TG
* * * *
35579 TGTCAAGGGAAACTACCTCAAGCA-AGATAAAATCTTCTG
1 TTTCAAGGGAAACTATCTAAAG-AGAGACAAAA-C-T-TG
* * * *
35618 TTTCAAGTGAAACTATCTCAAGCGAGATAAAA
1 TTTCAAGGGAAACTATCTAAAGAGAGACAAAA
35650 TCTTCTGTTT
Statistics
Matches: 234, Mismatches: 32, Indels: 39
0.77 0.10 0.13
Matches are distributed among these distances:
30 19 0.08
31 2 0.01
32 1 0.00
34 1 0.00
35 7 0.03
36 96 0.41
37 7 0.03
38 2 0.01
39 99 0.42
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTATCTAAAGAGAGACAAAACTTG
Found at i:35495 original size:72 final size:74
Alignment explanation
Indices: 35388--35630 Score: 226
Period size: 72 Copynumber: 3.2 Consensus size: 74
35378 TCTCAAAGGT
* * *
35388 TTGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTATTTCAAGGGAAACTATCTCAAGAG
1 TTGTGTTTCAAGGGAAACAGTCTAAAGAGAGACAAAACTTATTTCAAGGGAAACTATCTCAAGAG
35453 AGACAAAA-
66 AGACAAAAC
* * *
35461 TTGT-TTTCAAGGGAAACAGTCTCAAA-AGAGACAAAATTTGTTTCAAGGGAAATTATCTCAAGA
1 TTGTGTTTCAAGGGAAACAGTCT-AAAGAGAGACAAAACTTATTTCAAGGGAAACTATCTCAAGA
*
35524 GAGATAAAATC
65 GAGACAAAA-C
* * * * * * *
35535 TTTTGTTTCAAGGGAAACTA-CCTCAAGCGAGATAAAATCTTCTGTGTCAAGGGAAACTACCTCA
1 TTGTGTTTCAAGGGAAAC-AGTCTAAAGAGAGACAAAA-CTTAT-T-TCAAGGGAAACTATCTCA
*
35599 AGCA-AGATAAAATC
62 AG-AGAGACAAAA-C
* *
35613 TTCTGTTTCAAGTGAAAC
1 TTGTGTTTCAAGGGAAAC
35631 TATCTCAAGC
Statistics
Matches: 142, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
72 57 0.40
73 7 0.05
74 5 0.04
75 23 0.16
76 4 0.03
77 1 0.01
78 44 0.31
79 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (74 bp):
TTGTGTTTCAAGGGAAACAGTCTAAAGAGAGACAAAACTTATTTCAAGGGAAACTATCTCAAGAG
AGACAAAAC
Found at i:35827 original size:76 final size:77
Alignment explanation
Indices: 35736--35880 Score: 222
Period size: 76 Copynumber: 1.9 Consensus size: 77
35726 AATCTTCTTT
* * *
35736 AAAAACAATCTTGAGTGAAATGAAATGTT-TTCTTTCGAGTAAAAATCGTCTCAAGCAAGACA-A
1 AAAAAAAATCTTGAGTGAAAT-AAATCTTCTTCTTTCGAGTAAAAACCGTCTCAAGCAAGACAGA
35799 ATCTTGTTTTAAG
65 ATCTTGTTTTAAG
* *
35812 AAAAAAAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACCGTCTCAAGCGAGACAGAA
1 AAAAAAAATCTTGAGTGAAATAAATCTTCTTCTTTCGAGTAAAAACCGTCTCAAGCAAGACAGAA
35877 TCTT
66 TCTT
35881 CTGTTTCAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
75 6 0.10
76 50 0.81
77 6 0.10
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (77 bp):
AAAAAAAATCTTGAGTGAAATAAATCTTCTTCTTTCGAGTAAAAACCGTCTCAAGCAAGACAGAA
TCTTGTTTTAAG
Found at i:35935 original size:39 final size:39
Alignment explanation
Indices: 35391--35960 Score: 347
Period size: 39 Copynumber: 15.0 Consensus size: 39
35381 CAAAGGTTTG
* * * *
35391 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAA-C-T-
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
* * * * *
35427 TATTTCAAGGGAAACTATCTCAAGAGAGACAAAA--TTG
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
* ** *
35464 T-TTTCAAGGGAAAC-AGTCTCAAAAGAGACAAAA--TT-
1 TGTTTCAAGAGAAACTA-TCTCAAGCGAGATAAAATCTTC
* * * *
35499 TGTTTCAAGGGAAATTATCTCAAGAGAGATAAAATCTTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
* *
35538 TGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
* * * *
35577 TGTGTCAAGGGAAACTACCTCAAGCAAGATAAAATCTTC
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
*
35616 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
35655 TGTTT-AGAGTGAAACTATCTGAAGCGAGATAAAATCATC
1 TGTTTCA-AGAGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
35694 TATTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
* ** * * * * *
35733 --TTT--A-A-AAACAATCTTGAGTGAAATGAAATGTTT
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
* * * * * *
35766 TCTTTCGAGTA-AAAATCGTCTCAAGCAAGA-CAAATC-T-
1 TGTTTCAAG-AGAAACT-ATCTCAAGCGAGATAAAATCTTC
* * ** ** * *
35803 TGTTTTAAGAAAAAAAATCTTGAGTGAAAT-AAATCTTC
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
* * ** * *
35841 TTGTTTCGAGTAAAAACCGTCTCAAGCGAGACAGAATCTTC
1 -TGTTTCAAG-AGAAACTATCTCAAGCGAGATAAAATCTTC
*
35882 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
** * * * *
35921 TGTTTTGAGAGAAACCATCTTAAGTGAGATAAAATATTC
1 TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
35960 T
1 T
35961 TTAAAAAAGA
Statistics
Matches: 431, Mismatches: 79, Indels: 45
0.78 0.14 0.08
Matches are distributed among these distances:
33 20 0.05
35 6 0.01
36 101 0.23
37 17 0.04
38 4 0.01
39 248 0.58
40 28 0.06
41 7 0.02
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (39 bp):
TGTTTCAAGAGAAACTATCTCAAGCGAGATAAAATCTTC
Found at i:39673 original size:31 final size:29
Alignment explanation
Indices: 39631--39688 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
39621 CAATAAAAGC
39631 AGACAAAAAGAAATCAATGTTAGTAGAAACA
1 AGACAAAAAG-AATCAA-GTTAGTAGAAACA
* *
39662 AGACAACAAGAATCAAGTTAGTTGAAA
1 AGACAAAAAGAATCAAGTTAGTAGAAA
39689 AGATTAGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 6 0.24
31 9 0.36
ACGTcount: A:0.55, C:0.10, G:0.17, T:0.17
Consensus pattern (29 bp):
AGACAAAAAGAATCAAGTTAGTAGAAACA
Found at i:42314 original size:29 final size:29
Alignment explanation
Indices: 42256--42338 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
42246 TCGTGGGGGT
*
42256 ATGGGATATTGAATATAAAATGGTAGTGGC
1 ATGGGATGTTGAATA-AAAATGGTAGTGGC
42286 ATGGGATGTTGAATAAAAATGGTAGTGGC
1 ATGGGATGTTGAATAAAAATGGTAGTGGC
*
42315 ATGGGATGTTTAATAAAATATGGT
1 ATGGGATGTTGAATAAAA-ATGGT
42339 GGAATAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
29 31 0.62
30 19 0.38
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.31
Consensus pattern (29 bp):
ATGGGATGTTGAATAAAAATGGTAGTGGC
Found at i:42730 original size:91 final size:91
Alignment explanation
Indices: 42537--42795 Score: 367
Period size: 91 Copynumber: 2.8 Consensus size: 91
42527 ATATGTGATG
* * * *
42537 CAAGGTTGAATAAGTTCTTCTGATTATGAACTTCTTCTGCCTC-TATCGGATGAGCTCTTCTCAT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGT-T-GGATGAGTTCTTCTCAT
** * * **
42601 TATGAACTCTCTGCTGTAAATGTTGATG
64 TATGAACTCTCCACTGGAAATCTTGAAC
* *
42629 CAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATAAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
42694 TGAACTCTCCACTGGAAATCTTGAAC
66 TGAACTCTCCACTGGAAATCTTGAAC
*
42720 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTATCCCTCGTTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
*
42785 TGAAATCTCCA
66 TGAACTCTCCA
42796 TTTGAAATGT
Statistics
Matches: 150, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
91 109 0.73
92 40 0.27
93 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (91 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
TGAACTCTCCACTGGAAATCTTGAAC
Found at i:43339 original size:36 final size:36
Alignment explanation
Indices: 43293--43885 Score: 352
Period size: 36 Copynumber: 16.6 Consensus size: 36
43283 TTAAAAAAAA
* * *
43293 AAACCATCTCAAGTGAGATAGATTTTGTTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* ** *
43329 AAACTATCTCAAGAAAGGCAAAATTTGTTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * * *
43365 AAACGATCTC-A-A-AGCT---TTGTGTTTCAAGAG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * * * ** *
43395 AAACTGTCTAAAGGGAGACAAAACTTATTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * *
43431 AAACTGTCTCAAGAAAGATAAAATTTGTTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
*
43467 AAACAAAT-TC-A-A-AG----ATTTTGTTTCAAGGG
1 AAAC-TATCTCAAGAGAGATAAATTTTGTTTCAAGGG
*
43496 AAACAGAT-TC-----A-A-AAATTTTGTTTCAAGGG
1 AAAC-TATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * *
43525 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
** * * * *
43561 AAACGGTCTCAAGAGAGACAAAATTTGTTTAAAAGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * * **
43597 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAACAG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* * * *
43633 AAACTGTCTCAAGAGAGACAAAATTTGCTTCAAGGG
1 AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
* *
43669 AAATTATCTCGAGAGAGATAAAATCTTTTGTTTCAAGGG
1 AAACTATCTCAAGAGAGAT-AAA--TTTTGTTTCAAGGG
* *
43708 AAACTACCTCAA-ATGAGATAAAATCGTCTGTTTCAAGGG
1 AAACTATCTCAAGA-GAGAT-AAAT--TTTGTTTCAAGGG
* * * *
43747 AAACTACCTCAAGCGAGATAAAATCTTCTGTTTGAAGTG
1 AAACTATCTCAAGAGAGAT-AAAT-TT-TGTTTCAAGGG
* *
43786 AAACTATCTCAAGCGAGATAAAATCTTCTGTTT-AGAGTG
1 AAACTATCTCAAGAGAGAT-AAAT-TT-TGTTTCA-AGGG
* * *
43825 AAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTG
1 AAACTATCTCAAGAGAGAT-AAAT-TT-TGTTTCAAGGG
*
43864 AAACTATCTCAAGCGAGATAAA
1 AAACTATCTCAAGAGAGATAAA
43886 ATCTTCTTTA
Statistics
Matches: 463, Mismatches: 66, Indels: 54
0.79 0.11 0.09
Matches are distributed among these distances:
27 1 0.00
28 1 0.00
29 44 0.10
30 18 0.04
31 1 0.00
33 6 0.01
34 3 0.01
35 3 0.01
36 212 0.46
37 5 0.01
38 6 0.01
39 163 0.35
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.27
Consensus pattern (36 bp):
AAACTATCTCAAGAGAGATAAATTTTGTTTCAAGGG
Found at i:43426 original size:66 final size:66
Alignment explanation
Indices: 43318--43442 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
43308 AGATAGATTT
* * * * *
43318 TGTTTCAAGGGAAACTATCTCAAGAAAGGCAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGCTT
1 TGTTTCAAGAGAAACTATCTAAAGAAAGACAAAACTTATTTCAAGGGAAACTG-TCTCAAAGCTT
43382 TG
65 TG
* **
43384 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTATTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTATCTAAAGAAAGACAAAACTTATTTCAAGGGAAACTGTCTCAA
43443 GAAAGATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
66 49 0.98
67 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTATCTAAAGAAAGACAAAACTTATTTCAAGGGAAACTGTCTCAAAGCTTT
G
Found at i:43494 original size:29 final size:29
Alignment explanation
Indices: 43450--43528 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
43440 CAAGAAAGAT
43450 AAAA-TTTGTTTCAAGGGAAACAAATTCA
1 AAAATTTTGTTTCAAGGGAAACAAATTCA
* *
43478 AAGATTTTGTTTCAAGGGAAACAGATTCA
1 AAAATTTTGTTTCAAGGGAAACAAATTCA
43507 AAAATTTTGTTTCAAGGGAAAC
1 AAAATTTTGTTTCAAGGGAAAC
43529 TGTCTCAAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 3 0.06
29 44 0.94
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (29 bp):
AAAATTTTGTTTCAAGGGAAACAAATTCA
Found at i:43556 original size:130 final size:131
Alignment explanation
Indices: 43352--43600 Score: 367
Period size: 130 Copynumber: 1.9 Consensus size: 131
43342 AAAGGCAAAA
** *
43352 TTTGTTTCAAGGGAAACGATCTCAAAGCTTTGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAA
1 TTTGTTTCAAGGGAAACGATCTCAAAAATTTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAA
* * * *
43417 ACTTATTTCAAGGGAAACTGTCTCAAGAAAGATAAAATTTGTTTCAAGGGAAACAAATTCAAAGA
66 ACTTATTTCAAGGGAAACGGTCTCAAGAAAGACAAAATTTGTTTAAAAGGAAACAAATTCAAAGA
43482 T
131 T
* *
43483 TTTGTTTCAAGGGAAACAGAT-TCAAAAATTT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTTGTTTCAAGGGAAAC-GATCTCAAAAATTTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAA
* * *
43546 AATTTGTTTCAAGGGAAACGGTCTCAAGAGAGACAAAATTTGTTTAAAAGGAAAC
65 AACTTATTTCAAGGGAAACGGTCTCAAGAAAGACAAAATTTGTTTAAAAGGAAAC
43601 TGTCTCAAGA
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
130 77 0.73
131 25 0.24
132 3 0.03
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (131 bp):
TTTGTTTCAAGGGAAACGATCTCAAAAATTTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAA
ACTTATTTCAAGGGAAACGGTCTCAAGAAAGACAAAATTTGTTTAAAAGGAAACAAATTCAAAGA
T
Found at i:43704 original size:39 final size:39
Alignment explanation
Indices: 43511--43890 Score: 356
Period size: 39 Copynumber: 10.1 Consensus size: 39
43501 GATTCAAAAA
* *
43511 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--
1 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATC
** *
43548 -TTTGTTTCAAGGGAAACGGTCTCAAGAGAGACAAAA--
1 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATC
* * * *
43584 -TTTGTTTAAAAGGAAACTGTCTCAAGAGAGACAAAA--
1 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATC
** * *
43620 -TTTGTTTCAACAGAAACTGTCTCAAGAGAGACAAAA--
1 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATC
* * *
43656 -TTTGCTTCAAGGGAAATTATCTCGAGAGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATC
*
43694 TTTTGTTTCAAGGGAAACTACCTCAA-ATGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGA-GAGATAAAATC
* * * *
43733 GTCTGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATC
* * * *
43772 TTCTGTTTGAAGTGAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATC
* * *
43811 TTCTGTTT-AGAGTGAAACTATCTCAAGTGAGATAAAATC
1 TTTTGTTTCA-AGGGAAACTATCTCAAGAGAGATAAAATC
* * * *
43850 TTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATC
43889 TT
1 TT
43891 CTTTAAAAAT
Statistics
Matches: 308, Mismatches: 28, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
36 130 0.42
38 2 0.01
39 176 0.57
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (39 bp):
TTTTGTTTCAAGGGAAACTATCTCAAGAGAGATAAAATC
Found at i:43889 original size:78 final size:77
Alignment explanation
Indices: 43507--44094 Score: 353
Period size: 78 Copynumber: 7.8 Consensus size: 77
43497 AACAGATTCA
* * * * * **
43507 AAAAT-TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TT-TGTTTCAAGGGAAACGG
1 AAAATCTTCTGTTT-AAGGGAAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTGAAACTA
* *
43567 TCTCAAGAGAGAC
65 TCTCAAGCGAGAT
* * * * * ** *
43580 AAAA--TT-TGTTTAAAAGGAAACTGTCTCAAGAGAGACAAAA--TT-TGTTTCAACAGAAACTG
1 AAAATCTTCTGTTT-AAGGGAAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTGAAACTA
* *
43639 TCTCAAGAGAGAC
65 TCTCAAGCGAGAT
* * * * * * *
43652 AAAA--TT-TGCTTCAAGGGAAATTATCTCGAGAGAGATAAAATCTTTTGTTTCAAGGGAAACTA
1 AAAATCTTCTG-TTTAAGGGAAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTGAAACTA
* **
43714 CCTCAAATGAGAT
65 TCTCAAGCGAGAT
* * *
43727 AAAATCGTCTGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTCTGTTT-GAAGTGAAACT
1 AAAATCTTCTGTTT-AAGGGAAACTATCTCAAGTGAGATAAAATCTTCTGTTTCG-AGTGAAACT
43791 ATCTCAAGCGAGAT
64 ATCTCAAGCGAGAT
*
43805 AAAATCTTCTGTTTAGAGTGAAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTGAAACTA
1 AAAATCTTCTGTTTA-AGGGAAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTGAAACTA
43870 TCTCAAGCGAGAT
65 TCTCAAGCGAGAT
** * * * * * *
43883 AAAATCTTC--TTTAA---AAA-TAATCTTGAGTGAAATAAAATGTTTTCTTTCGAGTAAAAACC
1 AAAATCTTCTGTTTAAGGGAAACT-ATCTCAAGTGAGATAAAATCTTCTGTTTCGAGT-GAAACT
*
43942 GTCTCAAGCGAGA-
64 ATCTCAAGCGAGAT
* * ** * ** * *
43955 CAAATCTTGT-TTTAAGAAAAACAATCTTGAGTGAAAT-AAATCTTCTTGTTTCGAGTAAAAACT
1 AAAATCTTCTGTTTAAGGGAAACTATCTCAAGTGAGATAAAATCTTC-TGTTTCGAGT-GAAACT
* *
44018 GTCTCAAGCGAGAC
64 ATCTCAAGCGAGAT
* * * * * * *
44032 AGAATCTTCTGTTTCAAGGGAAGCTATCTCCAA-CGAGACAAAATTTTCTGTTTCAAGCGAAAC
1 AAAATCTTCTGTTT-AAGGGAAACTATCT-CAAGTGAGATAAAATCTTCTGTTTCGAGTGAAAC
44095 AACTCTTGTT
Statistics
Matches: 425, Mismatches: 66, Indels: 43
0.80 0.12 0.08
Matches are distributed among these distances:
71 1 0.00
72 131 0.31
73 27 0.06
74 2 0.00
75 34 0.08
76 49 0.12
77 11 0.03
78 140 0.33
79 22 0.05
80 8 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (77 bp):
AAAATCTTCTGTTTAAGGGAAACTATCTCAAGTGAGATAAAATCTTCTGTTTCGAGTGAAACTAT
CTCAAGCGAGAT
Found at i:43992 original size:76 final size:77
Alignment explanation
Indices: 43895--44039 Score: 231
Period size: 76 Copynumber: 1.9 Consensus size: 77
43885 AATCTTCTTT
* *
43895 AAAAATAATCTTGAGTGAAATAAAATGTT-TTCTTTCGAGTAAAAACCGTCTCAAGCGAGACA-A
1 AAAAACAATCTTGAGTGAAAT-AAATCTTCTTCTTTCGAGTAAAAACCGTCTCAAGCGAGACAGA
43958 ATCTTGTTTTAAG
65 ATCTTGTTTTAAG
* *
43971 AAAAACAATCTTGAGTGAAATAAATCTTCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAGAA
1 AAAAACAATCTTGAGTGAAATAAATCTTCTTCTTTCGAGTAAAAACCGTCTCAAGCGAGACAGAA
44036 TCTT
66 TCTT
44040 CTGTTTCAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
75 6 0.10
76 51 0.81
77 6 0.10
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (77 bp):
AAAAACAATCTTGAGTGAAATAAATCTTCTTCTTTCGAGTAAAAACCGTCTCAAGCGAGACAGAA
TCTTGTTTTAAG
Found at i:44120 original size:60 final size:60
Alignment explanation
Indices: 44041--44154 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
44031 CAGAATCTTC
* * *
44041 TGTTTCAAGGGAAGCTATCTCCAA-CGAGACAAAATTTTCTGTTTCAAGCGAAACAACTCT
1 TGTTTCAAGGGAAACTATCT-CAAGCGAGACAAAATCTTCTGTTTCAAGAGAAACAACTCT
* * * *
44101 TGTTTTAAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGAGAAAC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGAGAAAC
44155 CATCTCATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 3 0.07
60 43 0.93
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (60 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGAGAAACAACTCT
Found at i:48855 original size:18 final size:18
Alignment explanation
Indices: 48813--48856 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
48803 AAAAACTGGG
*
48813 TGATTTTAATAAAACATT
1 TGATTTTAATAAAACATC
*
48831 TTATTTTAATAAAACA-C
1 TGATTTTAATAAAACATC
48848 TGAGTTTTA
1 TGA-TTTTA
48857 GGGTCTGCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (18 bp):
TGATTTTAATAAAACATC
Found at i:50737 original size:30 final size:29
Alignment explanation
Indices: 50697--50791 Score: 136
Period size: 30 Copynumber: 3.2 Consensus size: 29
50687 ACGTGGGGGC
* *
50697 ATGGTGGTGGCATGGGATATTGAATATAAA
1 ATGGTAGTGGCATGGGATGTTGAATA-AAA
50727 ATGGTAGTGGCATGGGATGTTGAATAAAAA
1 ATGGTAGTGGCATGGGATGTTGAAT-AAAA
*
50757 ATGGTAGTGGAATGGGATGTTGAATAAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAA
50786 TATGGT
1 -ATGGT
50792 GGAATAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
29 4 0.07
30 55 0.92
31 1 0.02
ACGTcount: A:0.35, C:0.02, G:0.34, T:0.29
Consensus pattern (29 bp):
ATGGTAGTGGCATGGGATGTTGAATAAAA
Found at i:51183 original size:91 final size:91
Alignment explanation
Indices: 50990--51248 Score: 376
Period size: 91 Copynumber: 2.8 Consensus size: 91
50980 ATATGTGATG
* * *
50990 CAAGGTTGAATAAGTTCTTCTGATTATGAACTTCTTCTGCCTC-TATCGGATGAGTTCTTCTCAT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGT-T-GGATGAGTTCTTCTCAT
* * **
51054 TATGAACTCTCCGCTGTAAATATTGATG
64 TATGAACTCTCCACTGGAAATATTGAAC
* *
51082 CAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATAAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
* *
51147 TGAACTTTCCACTGGAAATCTTGAAC
66 TGAACTCTCCACTGGAAATATTGAAC
* *
51173 CAAGGTTGAACAAGTTCTTCTCTTTATGAACTTCTTTTCCCTCGTTGGATGAGTTCTTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
51238 TGAACTCTCCA
66 TGAACTCTCCA
51249 TTTGAAATGT
Statistics
Matches: 150, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
91 109 0.73
92 40 0.27
93 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (91 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTA
TGAACTCTCCACTGGAAATATTGAAC
Found at i:51807 original size:36 final size:36
Alignment explanation
Indices: 51767--52234 Score: 340
Period size: 36 Copynumber: 13.0 Consensus size: 36
51757 TGAGATAGAT
* *
51767 TTTGTTTCAAGGGTAACTGTCTCAAGAGAGAGAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
51803 TTTGTTTCAAGGGAAAC-GATCTCAA-AG-G-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* * *
51832 TTGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
51869 CTTATTTCAAGGAAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
51905 TTTGTTTCCAGGGAAACAGAT-TC-A-A-AG----AT
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
*
51934 TTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
51970 TTTGTTTTAAGGGAAACTCTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
52006 TTTGTTTCAACGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
52042 TTTGTTTCAAGGGAAATTATCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
** * *
52078 TCTTTTGTTTCAAGGGAAACTACCTCAAGCGAGATAAAA
1 ---TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
** * *
52117 TCTTATGTTTCAAGGGAAACTACCTCAAGCGAGATAAAA
1 --TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
52156 TCTTCTGTTTCAAGTGAAACTATCTGAA-ACGAGATAAAA
1 --TT-TGTTTCAAGGGAAACTGTCTCAAGA-GAGACAAAA
* * * * *
52195 TCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAAA
1 --TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
52234 T
1 T
52235 CTTCTTTAAA
Statistics
Matches: 361, Mismatches: 46, Indels: 49
0.79 0.10 0.11
Matches are distributed among these distances:
28 1 0.00
29 21 0.06
30 20 0.06
31 3 0.01
32 3 0.01
33 2 0.01
34 2 0.01
35 4 0.01
36 165 0.46
37 3 0.01
38 2 0.01
39 135 0.37
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:51851 original size:66 final size:66
Alignment explanation
Indices: 51769--51893 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
51759 AGATAGATTT
* * * * * * *
51769 TGTTTCAAGGGTAACTGTCTCAAGAGAGAGAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGGTT
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTATTTCAAGGAAAACTG-TCTCAAAGGTT
51833 TG
65 TG
*
51835 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTATTTCAAGGAAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTATTTCAAGGAAAACTGTCTCAA
51894 GAGAGATAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
66 49 0.98
67 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAACTTATTTCAAGGAAAACTGTCTCAAAGGTTT
G
Found at i:52006 original size:101 final size:102
Alignment explanation
Indices: 51767--52030 Score: 354
Period size: 101 Copynumber: 2.6 Consensus size: 102
51757 TGAGATAGAT
* * *
51767 TTTGTTTCAAGGGTAACTGTCTCAAGAGAGAGAAAATTTGTTTCAAGGGAAACGATCTCAAAGGT
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGAT
*
51832 TTGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAA
66 TTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAA
* * * * *
51869 CTTATTTCAAGGAAAACTGTCTCAAGAGAGATAAAATTTGTTTCCAGGGAAACAGAT-TCAAAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGA
* * *
51933 TTT-TTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
65 TTTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAA
* * *
51970 TTTGTTTTAAGGGAAACTCTCTCAAGAGAGACAAAATTTGTTTCAACGGAAACTG-TCTCAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-GATCTCAA
52031 GAGAGACAAA
Statistics
Matches: 140, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
100 1 0.01
101 80 0.57
102 56 0.40
103 3 0.02
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGAT
TTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAA
Found at i:52208 original size:20 final size:20
Alignment explanation
Indices: 52146--52208 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
52136 CTACCTCAAG
52146 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
* * ***
52166 CAAG-TGAAA-CTATCTGAAA
1 CGAGATAAAATCT-TCTGTTT
52185 CGAGATAAAATCTTCTGTTT
1 CGAGATAAAATCTTCTGTTT
52205 CGAG
1 CGAG
52209 TGAAACTATC
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 2 0.07
19 11 0.37
20 15 0.50
21 2 0.07
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (20 bp):
CGAGATAAAATCTTCTGTTT
Found at i:52238 original size:39 final size:39
Alignment explanation
Indices: 51938--52239 Score: 343
Period size: 39 Copynumber: 8.0 Consensus size: 39
51928 AAAGATTTTT
* * *
51938 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--TT-TG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * * *
51974 TTTTAAGGGAAACTCTCTCAAGAGAGACAAAA--TT-TG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * * *
52010 TTTCAACGGAAACTGTCTCAAGAGAGACAAAA--TT-TG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * *
52046 TTTCAAGGGAAATTATCTCAAGAGAGATAAAATCTTTTG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* *
52085 TTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTATG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
*
52124 TTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTCTG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* * *
52163 TTTCAAGTGAAACTATCTGAAACGAGATAAAATCTTCTG
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
* *
52202 TTTCGAGTGAAACTATCTCAAGCGAGATAAAATCTTCT
1 TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCT
52240 TTAAAAACAA
Statistics
Matches: 242, Mismatches: 21, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
36 95 0.39
38 2 0.01
39 145 0.60
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (39 bp):
TTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTCTG
Found at i:52359 original size:76 final size:73
Alignment explanation
Indices: 52192--52388 Score: 215
Period size: 76 Copynumber: 2.7 Consensus size: 73
52182 AAACGAGATA
* * * *
52192 AAATCTTC-TGTTTCGAGTGAAACT-ATCTCAAGCGAGATAAAATCTTCTTTAAAAACAATATTG
1 AAATCTTCTTGTTTCGAGTAAAAATCGTCTCAAGCGAGA-CAAATCTTCTTTAAAAACAATATTG
52255 AGTGAAATG
65 AGTGAAATG
* * * * *
52264 AAATGTT-TTCTTTCGAGTAAAAATCGTCTCAAACGAGACAAATCTTGTTTTAAGAAAACCAATC
1 AAATCTTCTTGTTTCGAGTAAAAATCGTCTCAAGCGAGACAAATCTT-CTTT-A-AAAA-CAATA
52328 TTGAGTGAAAT-
62 TTGAGTGAAATG
52339 AAATCTTCTTGTTTCGAGTAAAAA-CTGTCTCAAGCGAGACAGAATCTTCT
1 AAATCTTCTTGTTTCGAGTAAAAATC-GTCTCAAGCGAGACA-AATCTTCT
52389 GTTTCAAGGG
Statistics
Matches: 103, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
72 26 0.25
73 14 0.14
74 1 0.01
75 11 0.11
76 45 0.44
77 6 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (73 bp):
AAATCTTCTTGTTTCGAGTAAAAATCGTCTCAAGCGAGACAAATCTTCTTTAAAAACAATATTGA
GTGAAATG
Found at i:52416 original size:39 final size:39
Alignment explanation
Indices: 52360--52441 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
52350 TTTCGAGTAA
* *
52360 AAACTGTCTCAAGCGAGACAGAATCTTCTGTTTCAAGGG
1 AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
* *
52399 AAACTATCTCTAA-CGAGACAAAATTTTCTGTTTCAAGTG
1 AAACTATCTC-AAGCGAGACAAAATCTTCTGTTTCAAGGG
52438 AAAC
1 AAAC
52442 AACTCTTGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 36 0.95
40 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (39 bp):
AAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGGG
Found at i:52466 original size:60 final size:60
Alignment explanation
Indices: 52388--52501 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
52378 CAGAATCTTC
* * *
52388 TGTTTCAAGGGAAACTATCTCTAA-CGAGACAAAATTTTCTGTTTCAAGTGAAACAACTCT
1 TGTTTCAAGGGAAACTATCTC-AAGCAAGACAAAATCTTCTGTTTCAAGAGAAACAACTCT
* * * *
52448 TGTTTTAAGTGAAACTATCTCAAGCAAGATAAAATCTTCTGTTTCGAGAGAAAC
1 TGTTTCAAGGGAAACTATCTCAAGCAAGACAAAATCTTCTGTTTCAAGAGAAAC
52502 CATCTCAAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
59 2 0.04
60 44 0.96
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (60 bp):
TGTTTCAAGGGAAACTATCTCAAGCAAGACAAAATCTTCTGTTTCAAGAGAAACAACTCT
Found at i:52491 original size:39 final size:39
Alignment explanation
Indices: 52448--52526 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
52438 AAACAACTCT
* * * *
52448 TGTTTTAAGTGAAACTATCTCAAGCAAGATAAAATCTTC
1 TGTTTCAAGAGAAACCATCTCAAGCAAGATAAAATATTC
* **
52487 TGTTTCGAGAGAAACCATCTCAAGTGAGATAAAATATTC
1 TGTTTCAAGAGAAACCATCTCAAGCAAGATAAAATATTC
52526 T
1 T
52527 TTAAAAAGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (39 bp):
TGTTTCAAGAGAAACCATCTCAAGCAAGATAAAATATTC
Found at i:56555 original size:29 final size:29
Alignment explanation
Indices: 56507--56562 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
56497 TAATAAGAGC
56507 AGACAAAAAGATCAATGTTAGTAGAAACA
1 AGACAAAAAGATCAATGTTAGTAGAAACA
* *
56536 AGACAACAAGAATCAA-GTTAGTTGAAA
1 AGACAAAAAG-ATCAATGTTAGTAGAAA
56563 AGATTAGTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.54, C:0.11, G:0.18, T:0.18
Consensus pattern (29 bp):
AGACAAAAAGATCAATGTTAGTAGAAACA
Found at i:59228 original size:30 final size:30
Alignment explanation
Indices: 59194--59277 Score: 123
Period size: 30 Copynumber: 2.8 Consensus size: 30
59184 ACATGGGGGC
* * *
59194 ATGGTGGTGGCATGGGATATTGAATATAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAAA
*
59224 ATGGTAGTGACATGGGATGTTGAATAAAAA
1 ATGGTAGTGGCATGGGATGTTGAATAAAAA
*
59254 ATGGTAGTGGAATGGGATGTTGAA
1 ATGGTAGTGGCATGGGATGTTGAA
59278 GAAACTATGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.35, C:0.02, G:0.35, T:0.29
Consensus pattern (30 bp):
ATGGTAGTGGCATGGGATGTTGAATAAAAA
Found at i:59680 original size:91 final size:91
Alignment explanation
Indices: 59491--59753 Score: 337
Period size: 91 Copynumber: 2.9 Consensus size: 91
59481 GTGATGCAAT
* * * * *
59491 GTTGAATAAGTTCTTCTGATTATGAACTTCTTCTGCCTCTATCGGATGAGTTCTTCTCATTATGT
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCT-TATTGGATGAGTTCTTCTCATTATGA
* * * * **
59556 ACTCTCCACTGTAAATGTTGATGCAAG
65 ACTCTCCATTGGAAATCTTAAACCAAG
* * *
59583 ATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTTTTGGATAAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATTGGATGAGTTCTTCTCATTATGAA
*
59648 CTCTCCATTGGAAATCTTAAACCCAG
66 CTCTCCATTGGAAATCTTAAACCAAG
* **
59674 GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAA
1 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATTGGATGAGTTCTTCTCATTATGAA
* *
59739 CACTCCATTTGAAAT
66 CTCTCCATTGGAAAT
59754 GTCAATCCCT
Statistics
Matches: 149, Mismatches: 22, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
91 115 0.77
92 34 0.23
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.40
Consensus pattern (91 bp):
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTTATTGGATGAGTTCTTCTCATTATGAA
CTCTCCATTGGAAATCTTAAACCAAG
Found at i:60312 original size:36 final size:36
Alignment explanation
Indices: 60262--60690 Score: 294
Period size: 36 Copynumber: 12.0 Consensus size: 36
60252 TGAGATAGAT
*
60262 TTTGTTTCTAGGGAAACTGTCTAAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* ** *
60298 TTCGTTTCAAGGGAAACCATCTCAAAG-GTG------
1 TTTGTTTCAAGGGAAACTGTCT-AAAGAGAGACAAAA
* * *
60328 TGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* * * * *
60364 CTTATTTCAAGGGAAACTATCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* * *
60400 TTTGTTTCAAGGGAAACAGAT-T-CA-A-AG----AT
1 TTTGTTTCAAGGGAAACTG-TCTAAAGAGAGACAAAA
*
60429 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* *
60465 TTTGTTTCAAGGGAAACTGCCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* *
60501 TTTGTTTCAAGGGAAACGGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* * * *
60537 TTTGTTTAAAGGGAAATTATCTAAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
** * * *
60573 TCTTTTGTTTCAAGGGAAACTACCTCAAGCGAGATAAAA
1 ---TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* ** * *
60612 TCTTATGTGTCAAGGGAAACTACCTCAAGCGAGACAAAA
1 --TT-TGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* * * * *
60651 TCTTCTGTTTCAAGTGAAACTATCTCAAGCGAGATAAAA
1 --TT-TGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
60690 T
1 T
60691 CTTCTGTTTA
Statistics
Matches: 321, Mismatches: 51, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
28 1 0.00
29 24 0.07
30 20 0.06
31 1 0.00
32 2 0.01
33 2 0.01
34 1 0.00
35 1 0.00
36 164 0.51
37 6 0.02
38 2 0.01
39 97 0.30
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
Found at i:60372 original size:66 final size:66
Alignment explanation
Indices: 60264--60388 Score: 189
Period size: 66 Copynumber: 1.9 Consensus size: 66
60254 AGATAGATTT
* * *
60264 TGTTTCTAGGGAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGGGAAACCATCTCAAAGGTGT
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAATTCATTTCAAGGGAAACCATCTCAAAGGTGT
60329 G
66 G
* *
60330 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTT-ATTTCAAGGGAAACTATCTCAA
1 TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAA-TTCATTTCAAGGGAAACCATCTCAA
60389 GAGAGATAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
66 51 0.96
67 2 0.04
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTGTCTAAAGAGAGACAAAATTCATTTCAAGGGAAACCATCTCAAAGGTGT
G
Found at i:60489 original size:101 final size:101
Alignment explanation
Indices: 60262--60631 Score: 373
Period size: 101 Copynumber: 3.5 Consensus size: 101
60252 TGAGATAGAT
* ** * * * *
60262 TTTGTTTCTAGGGAAACTGTCTAAAGAGAGACAAAATTCGTTTCAAGGGAAACCATCTCAAAGGT
1 TTTGTTTCAAGGGAAACTACCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGAT
* * *
60327 GTGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAA
66 -TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* * * *
60364 CTTATTTCAAGGGAAACTATCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACAGAT-TCAAAGA
1 TTTGTTTCAAGGGAAACTACCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGA
*
60428 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
65 TTTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* *
60465 TTTGTTTCAAGGGAAACTGCCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTACCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTC-A-A-A
* * * * *
60530 GACAAAATTTGTTTAAAGGGAAATTATCTAAAGAGAGATAAAA
63 G----ATTTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
* * *
60573 TCTTTTGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTATGTGTCAAGGGAAAC
1 ---TTTGTTTCAAGGGAAACTACCTCAAGAGAGACAAAA--TT-TGTTTCAAGGGAAAC
60632 TACCTCAAGC
Statistics
Matches: 224, Mismatches: 29, Indels: 18
0.83 0.11 0.07
Matches are distributed among these distances:
100 2 0.01
101 82 0.37
102 54 0.24
103 3 0.01
104 2 0.01
108 32 0.14
111 33 0.15
113 2 0.01
114 14 0.06
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (101 bp):
TTTGTTTCAAGGGAAACTACCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACGATCTCAAAGAT
TTTGTTTCAAGGGAAACTGTCTAAAGAGAGACAAAA
Found at i:60589 original size:39 final size:39
Alignment explanation
Indices: 60428--60995 Score: 357
Period size: 39 Copynumber: 15.0 Consensus size: 39
60418 GATTCAAAGA
* * *
60428 TTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
** * *
60465 -TTTGTTTCAAGGGAAACTGCCTCAAGAGAGACAAAA--
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
** * *
60501 -TTTGTTTCAAGGGAAACGGTCTCAAGAGAGACAAAA--
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
60537 -TTTGTTTAAAGGGAAATTATCTAAAGAGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
*
60575 TTTTGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
60614 TTATGTGTCAAGGGAAACTACCTCAAGCGAGACAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* *
60653 TTCTGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * *
60692 TTCTGTTT-AGAGTGAAACTATCTGAAGCGAGATAAAATC
1 TTTTGTTTCA-AGGGAAACTATCTCAAGCGAGATAAAATC
* * * *
60731 TTCTATTTCGAGTGAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* ** * * * *
60770 -TTT-TTT-AA---AAACAATCTTGAGTGAAATGAAATG
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * ** * * * *
60803 TTTTCTTTCGAGTAAAAATCGTCTCAAGCAAGA-CAAATC
1 TTTTGTTTCAAGGGAAACT-ATCTCAAGCGAGATAAAATC
* ** * ** * *
60842 --TTGTTTTAAGAAAAACAATCTTGAGTGAAAT-AAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* ** * ***
60878 TTCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACGGAATC
1 TT-TTGTTTCAAG-GGAAACTATCTCAAGCGAGATAAAATC
* *
60919 TTCTGTTTCAAGGAAAACTATCTCAAGCGAGATAAAATC
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
* * ** * *
60958 TTCTGTTTCGAGATAAACCATCTCAAGTGAGATAAAAT
1 TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
60996 ATTCTTTAAA
Statistics
Matches: 433, Mismatches: 80, Indels: 34
0.79 0.15 0.06
Matches are distributed among these distances:
33 18 0.04
34 3 0.01
35 3 0.01
36 113 0.26
37 14 0.03
38 3 0.01
39 244 0.56
40 29 0.07
41 6 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (39 bp):
TTTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATC
Found at i:64570 original size:15 final size:16
Alignment explanation
Indices: 64544--64573 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
64534 GATGAATGCA
64544 AATGTCATGCAAAATG
1 AATGTCATGCAAAATG
64560 AATGT-ATGCAAAAT
1 AATGTCATGCAAAAT
64574 ACATTGATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.27
Consensus pattern (16 bp):
AATGTCATGCAAAATG
Found at i:65060 original size:31 final size:29
Alignment explanation
Indices: 65018--65075 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
65008 CAATAAAAGC
65018 AGATAAAAAGAAATCAATGTTAGTAGAAACA
1 AGATAAAAAG-AATCAA-GTTAGTAGAAACA
* *
65049 AGATAACAAGAATCAAGTTAGTTGAAA
1 AGATAAAAAGAATCAAGTTAGTAGAAA
65076 AGATTAGTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 6 0.24
31 9 0.36
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.21
Consensus pattern (29 bp):
AGATAAAAAGAATCAAGTTAGTAGAAACA
Found at i:65876 original size:17 final size:18
Alignment explanation
Indices: 65841--65876 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
65831 AAATTGGATG
*
65841 ATTTTAATAAAACATTTT
1 ATTTTAATAAAACACTTT
65859 ATTTTAAT-AAACACTTT
1 ATTTTAATAAAACACTTT
65876 A
1 A
65877 GGATCTACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTTAATAAAACACTTT
Found at i:67682 original size:28 final size:28
Alignment explanation
Indices: 67628--67704 Score: 118
Period size: 28 Copynumber: 2.7 Consensus size: 28
67618 ACGTGGGGGT
*
67628 ATGGGATATTGAATATAAAATGGTAGTGGC
1 ATGGGATGTTG-A-ATAAAATGGTAGTGGC
67658 ATGGGATGTTGAATAAAATGGTAGTGGC
1 ATGGGATGTTGAATAAAATGGTAGTGGC
*
67686 ATGGGATGTTTAATAAAAT
1 ATGGGATGTTGAATAAAAT
67705 ATGGTGGAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 34 0.76
29 1 0.02
30 10 0.22
ACGTcount: A:0.36, C:0.03, G:0.30, T:0.31
Consensus pattern (28 bp):
ATGGGATGTTGAATAAAATGGTAGTGGC
Found at i:68105 original size:91 final size:90
Alignment explanation
Indices: 67905--68158 Score: 348
Period size: 91 Copynumber: 2.8 Consensus size: 90
67895 ATATGTGATG
* * *
67905 CAAGGTTGAATAAGTTCTTCTGATTATGAACTTCTTCTGCCTC-TATCGGATGAGCTCTTCTCAT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCTCGT-T-GGATGAGTTCTTCTCAT
* ** * * **
67969 TATGAAATCTCTGCTGTAAATGTTGATG
63 TATGAACTCTCCACTGGAAATCTTGAAC
* * *
67997 CAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATAAGTTATTCTCATTA
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCT-CCTCGTTGGATGAGTTCTTCTCATTA
68062 TGAACTCTCCACTGGAAATCTTGAAC
65 TGAACTCTCCACTGGAAATCTTGAAC
68088 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCGTTGGATGAGTTCTTCTCATTAT
1 CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCGTTGGATGAGTTCTTCTCATTAT
68153 GAACTC
66 GAACTC
68159 CATTTGAAAT
Statistics
Matches: 144, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
90 31 0.22
91 72 0.50
92 40 0.28
93 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (90 bp):
CAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTCGTTGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATCTTGAAC
Found at i:68788 original size:66 final size:65
Alignment explanation
Indices: 68680--68803 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 65
68670 AGATAGATTT
* * * *
68680 TGTTTCAAGTGAAACTATCTCAGAGAGACAAAATTTGTTTCAAGGGAAAC-GATCTCAAAGGTTT
1 TGTTTCAAGAGAAACTATCTAAGAGAGACAAAACTTATTTCAAGGGAAACTG-TCTCAAAGGTTT
68744 G
65 G
* *
68745 TGTTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTATTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTATCT-AAGAGAGACAAAACTTATTTCAAGGGAAACTGTCTCAA
68804 GAGAGATAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
65 18 0.35
66 32 0.63
67 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTATCTAAGAGAGACAAAACTTATTTCAAGGGAAACTGTCTCAAAGGTTTG
Found at i:68795 original size:36 final size:36
Alignment explanation
Indices: 68747--68831 Score: 116
Period size: 36 Copynumber: 2.4 Consensus size: 36
68737 AAGGTTTGTG
* *
68747 TTTCAAGAGAAACTGTCTAAAGGGAGACAAAACTTA
1 TTTCAAGGGAAACTGTCTAAAGAGAGACAAAACTTA
* * * *
68783 TTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTG
1 TTTCAAGGGAAACTGTCTAAAGAGAGACAAAACTTA
68819 TTTCAAGGGAAAC
1 TTTCAAGGGAAAC
68832 AGATTCAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTAAAGAGAGACAAAACTTA
Found at i:68855 original size:29 final size:29
Alignment explanation
Indices: 68811--68889 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
68801 CAAGAGAGAT
68811 AAAA-TTTGTTTCAAGGGAAACAGATTCA
1 AAAATTTTGTTTCAAGGGAAACAGATTCA
* *
68839 AAGATTTTGTTTCAAGGGAAAAAGATTCA
1 AAAATTTTGTTTCAAGGGAAACAGATTCA
68868 AAAATTTTGTTTCAAGGGAAAC
1 AAAATTTTGTTTCAAGGGAAAC
68890 TGTCTTAAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 3 0.07
29 43 0.93
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (29 bp):
AAAATTTTGTTTCAAGGGAAACAGATTCA
Found at i:68944 original size:129 final size:131
Alignment explanation
Indices: 68713--68958 Score: 372
Period size: 129 Copynumber: 1.9 Consensus size: 131
68703 AGAGACAAAA
* ** *
68713 TTTGTTTCAAGGGAAACGATCTCAAAGGTTTGTGTTTCAAGAGAAACTGTCTAAAGGGAGACAAA
1 TTTGTTTCAAGGGAAAAGATCTCAAAAATTTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAA
* * *
68778 ACTTATTTCAAGGGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACAGATTCAAAGA
66 ACTTATTTCAAGGGAAACGGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACAGATTCAAAGA
68843 T
131 T
* *
68844 TTTGTTTCAAGGGAAAAAGAT-TCAAAAATTT-TGTTTCAAGGGAAACTGTCTTAAGAGAGACAA
1 TTTGTTTCAAGGG-AAAAGATCTCAAAAATTTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAA
*
68907 AA-TTGTTTCAAGGGAAACGGTCTCAAGAGAGACAAAATTTATTTCAAGGGAA
65 AACTTATTTCAAGGGAAACGGTCTCAAGAGAGACAAAATTTATTTCAAGGGAA
68959 GCTGTCTCAA
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
129 46 0.44
130 31 0.30
131 21 0.20
132 6 0.06
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (131 bp):
TTTGTTTCAAGGGAAAAGATCTCAAAAATTTGTGTTTCAAGAGAAACTGTCTAAAGAGAGACAAA
ACTTATTTCAAGGGAAACGGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACAGATTCAAAGA
T
Found at i:68952 original size:36 final size:36
Alignment explanation
Indices: 68868--69169 Score: 284
Period size: 36 Copynumber: 8.1 Consensus size: 36
68858 AAAAGATTCA
*
68868 AAAATTTTGTTTCAAGGGAAACTGTCTTAAGAGAGAC
1 AAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
*
68905 AAAA-TTGTTTCAAGGGAAACGGTCTCAAGAGAGAC
1 AAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* *
68940 AAAATTTATTTCAAGGGAAGCTGTCTCAAGAGAGAC
1 AAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
*
68976 AAAATTTGTTTCAACGGAAACTGTCTCAAGAGAGAC
1 AAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
** * * * *
69012 AAAATTTGTTTCAACAGAAATTATCTCGAGAGAGAT
1 AAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* ** *
69048 AAAATCTTTTTTTTCAAGGGAAACTACCTCAA-ACGAGAT
1 AAAA---TTTGTTTCAAGGGAAACTGTCTCAAGA-GAGAC
** * *
69087 AAAATCGTCTGTTTCAAGGGAAACTACCTCAAGCGAGAT
1 AAAAT--T-TGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* * * *
69126 AAAATCTTCTGTTTCAAGTGAAACTATCTCAAGCGAGAT
1 AAAA--TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGAC
69165 AAAAT
1 AAAAT
69170 CTTCTGTTTA
Statistics
Matches: 231, Mismatches: 23, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
35 33 0.14
36 97 0.42
37 5 0.02
38 2 0.01
39 93 0.40
41 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (36 bp):
AAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
Found at i:69086 original size:39 final size:39
Alignment explanation
Indices: 68910--69454 Score: 281
Period size: 39 Copynumber: 14.4 Consensus size: 39
68900 GAGACAAAAT
* ** * *
68910 TGTTTCAAGGGAAACGGTCTCAAGAGAGACAAAA--TT-
1 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
* * * * * *
68946 TATTTCAAGGGAAGCTGTCTCAAGAGAGACAAAA--TT-
1 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
68982 TGTTTCAACG-GAAACTGTCTCAAGAGAGACAAAA--TT-
1 TGTTTCAA-GTGAAACTATCTCAAGCGAGATAAAATCTTC
** * * * *
69018 TGTTTCAACAGAAATTATCTCGAGAGAGATAAAATCTTT
1 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
* * * * *
69057 TTTTTCAAGGGAAACTACCTCAAACGAGATAAAATCGTC
1 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
* *
69096 TGTTTCAAGGGAAACTACCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
69135 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
1 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
* * *
69174 TGTTT-AGAGTAAAACTATCTCAAGTGATATAAAATCTTC
1 TGTTTCA-AGTGAAACTATCTCAAGCGAGATAAAATCTTC
* * * **
69213 TATTTCGAGTAAAACTATCTCAAATGAGATAAAATCTTC
1 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
** * * * *
69252 --TTT-AA---AAA-TAATCTTGAGTGAAATAAAATATTT
1 TGTTTCAAGTGAAACT-ATCTCAAGCGAGATAAAATCTTC
* * * ** * *
69285 TCTTTCGAGTAAAAACCGTCTCAATCGAGA-CAAATC-T-
1 TGTTTCAAGT-GAAACTATCTCAAGCGAGATAAAATCTTC
* ** * ** * *
69322 TGTTTTAAGAAAAACAATCTTGAGTGAAAT-AAATCTTC
1 TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
* * * * *
69360 TTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAGAATCTTC
1 -TGTTTCAAGT-GAAACTATCTCAAGCGAGATAAAATCTTC
* * *
69401 TGTTTCAAGGGAAACTATCTCCAA-CGAGACAAAATTTTC
1 TGTTTCAAGTGAAACTATCT-CAAGCGAGATAAAATCTTC
*
69440 TGTTTCAAGCGAAAC
1 TGTTTCAAGTGAAAC
69455 AACTTTTGTT
Statistics
Matches: 408, Mismatches: 78, Indels: 43
0.77 0.15 0.08
Matches are distributed among these distances:
32 1 0.00
33 20 0.05
35 3 0.01
36 112 0.27
37 11 0.03
38 4 0.01
39 216 0.53
40 34 0.08
41 7 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (39 bp):
TGTTTCAAGTGAAACTATCTCAAGCGAGATAAAATCTTC
Found at i:69320 original size:72 final size:73
Alignment explanation
Indices: 69196--69401 Score: 222
Period size: 76 Copynumber: 2.8 Consensus size: 73
69186 AACTATCTCA
* * * *
69196 AGTGATATAAAATCTTCTATTTCGAGT-AAAACTATCTCAAAT-GAGATAAAATCTTCTTT-AAA
1 AGTGAAATAAAATCTTTTATTTCGAGTAAAAACTGTCTC-AATCGAGA-CAAATCTTCTTTAAAA
*
69258 AATAATCTTG
64 AACAATCTTG
* * * *
69268 AGTGAAATAAAATATTTTCTTTCGAGTAAAAACCGTCTCAATCGAGACAAATCTTGTTTTAAGAA
1 AGTGAAATAAAATCTTTTATTTCGAGTAAAAACTGTCTCAATCGAGACAAATCTT-CTTT-A-AA
69333 AAACAATCTTG
63 AAACAATCTTG
* *
69344 AGTGAAAT-AAATCTTCTTGTTTCGAGTAAAAACTGTCTCAAGCGAGACAGAATCTTCT
1 AGTGAAATAAAATCTT-TTATTTCGAGTAAAAACTGTCTCAATCGAGACA-AATCTTCT
69402 GTTTCAAGGG
Statistics
Matches: 112, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
72 33 0.29
73 16 0.14
75 6 0.05
76 51 0.46
77 6 0.05
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (73 bp):
AGTGAAATAAAATCTTTTATTTCGAGTAAAAACTGTCTCAATCGAGACAAATCTTCTTTAAAAAA
CAATCTTG
Found at i:69477 original size:60 final size:60
Alignment explanation
Indices: 69401--69514 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
69391 CAGAATCTTC
* *
69401 TGTTTCAAGGGAAACTATCTCCAA-CGAGACAAAATTTTCTGTTTCAAGCGAAACAACTTT
1 TGTTTCAAGGGAAACTATCT-CAAGCGAGACAAAATCTTCTGTTTCAAGAGAAACAACTTT
* * * *
69461 TGTTTTAAGTGAAACTATCTCAAGCGAGATAAAATCTTCTGTTTCGAGAGAAAC
1 TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGAGAAAC
69515 CATCTCATGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 3 0.06
60 44 0.94
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (60 bp):
TGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATCTTCTGTTTCAAGAGAAACAACTTT
Done.