Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000418.1 Hibiscus syriacus cultivar Beakdansim tig00000765_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: 909013
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:92 original size:52 final size:54
Alignment explanation
Indices: 1--193 Score: 191
Period size: 55 Copynumber: 3.6 Consensus size: 54
* * * * *
1 CTGCTCCCTATTCCCTCAGA-AGTATAAGACTCGAGCAATCTTC-TAAATGTGT
1 CTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAAGGGT
* *
53 -TGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAAGGGT
1 CTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTC-ATAAAAGGGT
* *
107 CCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAATAAACA-GGT
1 CTGCTCTCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTC-ATAAA-AGGGT
* * * *
162 CCGCTCCCTATT-CTTCAGGGAGTATAGGACTC
1 CTGCTCTCTATTCCTTCAGAGAGTATAAGACTC
194 AATCTTCAAC
Statistics
Matches: 120, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
51 16 0.13
52 21 0.17
54 25 0.21
55 57 0.47
56 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (54 bp):
CTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATAAAAGGGT
Found at i:128 original size:55 final size:55
Alignment explanation
Indices: 3--392 Score: 210
Period size: 50 Copynumber: 7.6 Consensus size: 55
1 CT
* * * * *
3 GCTCCCTATTCCCTCAGA-AGTATAAGACTCGAGCAATCTTC--TAAATGTGT-T
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAAGGGTCC
* * *
54 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAAGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAAGGGTCC
* *
109 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCAATAAACA-GGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAA-AGGGTCC
* * ** ***
164 GCTCCCTATT-CTTCAGGGAGTATAGGACT----CAATCTTCAACGAACTAGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAAGGGTCC
** * * * ***
214 GCTCCCTATTTATTCAGAGAGTATAGGACT----TAATCTTCAACGAAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-TAAAAGGGTCC
* * ** ***
266 G--CCCTATTCATTCAGAGAG--TAGGACT----CAAT-TTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAAGGGTCC
* **
312 GCTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACT--AACTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAA-TAAAAGGGTCC
*
362 GCTCCCTATTCCTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCCTTCAGAGAGTATAAGACTC
393 ATCTTCAACA
Statistics
Matches: 289, Mismatches: 33, Indels: 34
0.81 0.09 0.10
Matches are distributed among these distances:
46 10 0.03
47 5 0.02
48 27 0.09
50 89 0.31
51 46 0.16
52 30 0.10
54 24 0.08
55 57 0.20
56 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAAGGGTCC
Found at i:215 original size:50 final size:51
Alignment explanation
Indices: 105--401 Score: 369
Period size: 50 Copynumber: 5.9 Consensus size: 51
95 CAATAAAAGG
* * **
105 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAAC-A
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTA
*
159 GGTCCGCTCCCTATT-CTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
1 -GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTA
** * *
210 GTCCGCTCCCTATTTATTCAGAGAGTATAGGACTTAATCTTCAACGAAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACG-AACTA
* *
262 GTCCG--CCCTATTCATTCAGAGAG--TAGGACTCAAT-TTCAACGAACTT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTA
*
308 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACTAACT-
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTA
358 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC-ATCTTCAAC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAAC
402 AAACGAATTG
Statistics
Matches: 221, Mismatches: 13, Indels: 22
0.86 0.05 0.09
Matches are distributed among these distances:
46 10 0.05
47 7 0.03
48 27 0.12
49 9 0.04
50 89 0.40
51 39 0.18
52 9 0.04
54 18 0.08
55 13 0.06
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (51 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTA
Found at i:328 original size:98 final size:98
Alignment explanation
Indices: 105--401 Score: 350
Period size: 98 Copynumber: 2.9 Consensus size: 98
95 CAATAAAAGG
* * * *
105 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAGGTCCGCTCCC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT----AAATCTTCAACAAAC-TGTCCGC-CCC
*
170 TATTCTTCAGGGAGTATAGGACTCAATCTTCAACGAACTA
60 TATTCTTCAGAGAG-ATAGGACTCAATCTTCAACGAACTA
** *
210 GTCCGCTCCCTATTTATTCAGAGAGTATAGGACTTAATCTTCAACGAAACTTGTCCG-CCCTATT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTAAATCTTCAAC-AAAC-TGTCCGCCCCTATT
*
274 CATTCAGAGAG-TAGGACTCAAT-TTCAACGAACTT
64 C-TTCAGAGAGATAGGACTCAATCTTCAACGAACTA
* *
308 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACTAACTGTCCGCTCCCTATTC
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAACTGTCCGC-CCCTATT-
373 CTTCAGAGAGTATAGGACTC-ATCTTCAAC
64 CTTCAGAGAG-ATAGGACTCAATCTTCAAC
402 AAACGAATTG
Statistics
Matches: 170, Mismatches: 14, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
96 6 0.04
97 3 0.02
98 69 0.41
99 14 0.08
100 22 0.13
101 17 0.10
102 9 0.05
105 30 0.18
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (98 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTAAATCTTCAACAAACTGTCCGCCCCTATTCT
TCAGAGAGATAGGACTCAATCTTCAACGAACTA
Found at i:1564 original size:26 final size:25
Alignment explanation
Indices: 1526--1591 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
1516 TTTATTTCTC
1526 TTTTTTTCATTTTTCTCT-TTTTAA
1 TTTTTTTCATTTTTCTCTCTTTTAA
*
1550 TTTTTTTCCATTTTTTCTCTCTTTT-T
1 TTTTTTT-CA-TTTTTCTCTCTTTTAA
*
1576 TTTCTTTTCGTTTTTC
1 TTT-TTTTCATTTTTC
1592 CATCATTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
24 7 0.19
25 8 0.22
26 13 0.36
27 8 0.22
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.76
Consensus pattern (25 bp):
TTTTTTTCATTTTTCTCTCTTTTAA
Found at i:1617 original size:10 final size:9
Alignment explanation
Indices: 1520--1640 Score: 69
Period size: 8 Copynumber: 13.6 Consensus size: 9
1510 CCTCCTTTTA
1520 TTTCTCTTT
1 TTTCTCTTT
*
1529 TTT-TCATT
1 TTTCTCTTT
1537 TTTCTCTTT
1 TTTCTCTTT
**
1546 TTAAT-TTT
1 TTTCTCTTT
1554 TTTC-CATTT
1 TTTCTC-TTT
1563 TTTCTCTCTT
1 TTTCTCT-TT
1573 TTT-T-TTCT
1 TTTCTCTT-T
*
1581 TTTC-GTTT
1 TTTCTCTTT
* *
1589 TTCCATCATT
1 TTTC-TCTTT
1599 TTT-TCTTT
1 TTTCTCTTT
1607 TTTCTCATTT
1 TTTCTC-TTT
1617 TTTC-CTTCT
1 TTTCTCTT-T
1626 TTTCTCTTT
1 TTTCTCTTT
1635 ATTTCT
1 -TTTCT
1641 TCTTCAAGCA
Statistics
Matches: 86, Mismatches: 11, Indels: 29
0.68 0.09 0.23
Matches are distributed among these distances:
7 1 0.01
8 30 0.35
9 30 0.35
10 25 0.29
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.73
Consensus pattern (9 bp):
TTTCTCTTT
Found at i:1644 original size:18 final size:18
Alignment explanation
Indices: 1520--1644 Score: 77
Period size: 17 Copynumber: 7.1 Consensus size: 18
1510 CCTCCTTTTA
* *
1520 TTTCTCTTTTTTTCAT-T
1 TTTCTCATTTTTTCTTCT
** *
1537 TTTCTC-TTTTTAATTTT
1 TTTCTCATTTTTTCTTCT
1554 TTTC-CATTTTTTCTCTCT
1 TTTCTCATTTTTTCT-TCT
*
1572 TTT-T-TTTCTTTTCGTT-T
1 TTTCTCATT-TTTTC-TTCT
*
1589 TTCCATCATTTTTTCTT-T
1 TTTC-TCATTTTTTCTTCT
1607 TTTCTCATTTTTTCCTTCT
1 TTTCTCATTTTTT-CTTCT
1626 TTTCTC-TTTATTTCTTCT
1 TTTCTCATTT-TTTCTTCT
1644 T
1 T
1645 CAAGCAAATA
Statistics
Matches: 86, Mismatches: 10, Indels: 23
0.72 0.08 0.19
Matches are distributed among these distances:
16 7 0.08
17 31 0.36
18 29 0.34
19 17 0.20
20 2 0.02
ACGTcount: A:0.06, C:0.20, G:0.01, T:0.73
Consensus pattern (18 bp):
TTTCTCATTTTTTCTTCT
Found at i:1645 original size:21 final size:22
Alignment explanation
Indices: 1596--1645 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 22
1586 TTTTTCCATC
*
1596 ATTTTTTCTT-TTTTCTCATTT
1 ATTTCTTCTTCTTTTCTCATTT
1617 -TTTC--CTTCTTTTCTC-TTT
1 ATTTCTTCTTCTTTTCTCATTT
1635 ATTTCTTCTTC
1 ATTTCTTCTTC
1646 AAGCAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 8
0.73 0.03 0.24
Matches are distributed among these distances:
18 6 0.25
19 11 0.46
20 3 0.12
21 4 0.17
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (22 bp):
ATTTCTTCTTCTTTTCTCATTT
Found at i:15011 original size:64 final size:64
Alignment explanation
Indices: 14939--15091 Score: 161
Period size: 64 Copynumber: 2.4 Consensus size: 64
14929 TTCCTTATCG
* * **
14939 GTGCATCGATGCACTACCTGTGCATCGGTGCA-TAAAATACATTCGATGTTTGTT-TATT-ACTG
1 GTGCATCGATGCACTACCTGTGCATCGATGCACT-AAATACATTCGATGTTT-TTAGATTAAAAG
*
15001 G
64 C
* * * *
15002 GATGCATCGATTCA-TGCCTTATGCATCGATGCACTAATTACATTCGATGTTTTTAGATTAAAAG
1 G-TGCATCGATGCACTACC-TGTGCATCGATGCACTAAATACATTCGATGTTTTTAGATTAAAAG
15066 C
64 C
15067 GTGCATCGATGCACTACCTGTGCAT
1 GTGCATCGATGCACTACCTGTGCAT
15092 TGATACACCT
Statistics
Matches: 72, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
63 6 0.08
64 59 0.82
65 7 0.10
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTGTGCATCGATGCACTAAATACATTCGATGTTTTTAGATTAAAAGC
Found at i:16224 original size:15 final size:15
Alignment explanation
Indices: 16204--16238 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
16194 ATTGGACCTG
*
16204 AAAAATAAATAAATA
1 AAAAATAAAAAAATA
16219 AAAAATAAAAAAATA
1 AAAAATAAAAAAATA
16234 AAAAA
1 AAAAA
16239 GAATACTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Found at i:16226 original size:7 final size:7
Alignment explanation
Indices: 16204--16238 Score: 52
Period size: 8 Copynumber: 4.7 Consensus size: 7
16194 ATTGGACCTG
16204 AAAAATA
1 AAAAATA
16211 AATAAATA
1 AA-AAATA
16219 AAAAATAA
1 AAAAAT-A
16227 AAAAATA
1 AAAAATA
16234 AAAAA
1 AAAAA
16239 GAATACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 12 0.46
8 14 0.54
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:16397 original size:76 final size:73
Alignment explanation
Indices: 16294--16576 Score: 304
Period size: 76 Copynumber: 3.8 Consensus size: 73
16284 AATCTCAAAA
* *
16294 TTTCAAAAACGTTTTCAAAACTTATATATTATATATATTTTAGAAAAATGTTTTCAAAAAATATA
1 TTTC-AAAATGTTTTCAAAAC-TATATATTATATATATTTT--AAAAATGTTTTCAAAAATTATA
16359 TATTATATATAT
62 TATTATATATAT
* *
16371 TTTCAAAATGTTTTCATAAACTATATATTATATATATGTTTTCAAAATATTTTC-AAAATTATAT
1 TTTCAAAATGTTTTCA-AAACTATATATTATATATA--TTTTAAAAATGTTTTCAAAAATTATAT
16435 ATTATATATATGT
63 ATTATATATA--T
** * *
16448 TTTCAAAATGTTTTCAAAACTATATATTATATA-CCTTTAAAAATGATTTCAAAAATTATATAAT
1 TTTCAAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAAATTATATATT
16512 ATATATAT
66 ATATATAT
* * * * *
16520 TTTCAAAAATCATTTTAAAAGACTATATA--ATTTATATTTCAAAAATCGCTTTCAAAA
1 TTTC-AAAAT-GTTTTCAAA-ACTATATATTATATATATTTTAAAAAT-GTTTTCAAAA
16577 CTATATAATA
Statistics
Matches: 178, Mismatches: 17, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
72 5 0.03
73 21 0.12
74 34 0.19
75 36 0.20
76 53 0.30
77 25 0.14
78 4 0.02
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (73 bp):
TTTCAAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCAAAAATTATATATT
ATATATAT
Found at i:16443 original size:38 final size:37
Alignment explanation
Indices: 16294--16583 Score: 263
Period size: 38 Copynumber: 7.7 Consensus size: 37
16284 AATCTCAAAA
*
16294 TTTCAAAAACGTTTTCAAAACTTATATATTATATATATT
1 TTTC-AAAATGTTTTCAAAAC-TATATATTATATATATT
** *
16333 TTAGAAAAATGTTTTCAAAAAATATATATTATATATA-T
1 TT-TCAAAATGTTTTC-AAAACTATATATTATATATATT
16371 TTTCAAAATGTTTTCATAAACTATATATTATATATATGT
1 TTTCAAAATGTTTTCA-AAACTATATATTATATATAT-T
* *
16410 TTTCAAAATATTTTCAAAATTATATATTATATATATGT
1 TTTCAAAATGTTTTCAAAACTATATATTATATATAT-T
**
16448 TTTCAAAATGTTTTCAAAACTATATA-T-TATATACC
1 TTTCAAAATGTTTTCAAAACTATATATTATATATATT
* * * *
16483 TTTAAAAATGATTTCAAAAAT-TATATAATATATATAT
1 TTTCAAAATGTTTTCAAAACTATATATTATATATAT-T
* * *
16520 TTTCAAAAATCATTTTAAAAGACTATATA--AT-T-TATA
1 TTTC-AAAAT-GTTTTCAAA-ACTATATATTATATATATT
*
16556 TTTCAAAAATCGCTTTCAAAACTATATA
1 TTTC-AAAAT-GTTTTCAAAACTATATA
16584 ATATTTTCAA
Statistics
Matches: 211, Mismatches: 28, Indels: 28
0.79 0.10 0.10
Matches are distributed among these distances:
34 4 0.02
35 26 0.12
36 30 0.14
37 36 0.17
38 54 0.26
39 51 0.24
40 6 0.03
41 4 0.02
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (37 bp):
TTTCAAAATGTTTTCAAAACTATATATTATATATATT
Found at i:22343 original size:31 final size:32
Alignment explanation
Indices: 22285--22350 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 32
22275 AAAAGATTGA
22285 AATGACTCATCGACAGCCAAAAAGGGAGAACCT
1 AATGACTCATCGACAGCC-AAAAGGGAGAACCT
* * *
22318 AATGACTCTTTGACAGCC-AAAGGGAGAAGCT
1 AATGACTCATCGACAGCCAAAAGGGAGAACCT
22349 AA
1 AA
22351 CTACACCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 14 0.47
33 16 0.53
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.15
Consensus pattern (32 bp):
AATGACTCATCGACAGCCAAAAGGGAGAACCT
Found at i:27080 original size:28 final size:28
Alignment explanation
Indices: 27041--27102 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
27031 ATTTGACTTC
*
27041 TTTTTTTATGCAATTAGATACTTAAGAT
1 TTTTTTTATGCAATTAGATACCTAAGAT
* *
27069 TTTTTTTGTGCAATTAGATACCTAATAT
1 TTTTTTTATGCAATTAGATACCTAAGAT
27097 TTTTTT
1 TTTTTT
27103 AATTACTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (28 bp):
TTTTTTTATGCAATTAGATACCTAAGAT
Found at i:28194 original size:23 final size:23
Alignment explanation
Indices: 28168--28219 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
28158 TAAACAAACT
* *
28168 TTAAACGAACATTTTTGTGAACG
1 TTAAACGAACATATTCGTGAACG
*
28191 TTAAACGAATATATTCGTGAACG
1 TTAAACGAACATATTCGTGAACG
*
28214 CTAAAC
1 TTAAAC
28220 TAATGAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (23 bp):
TTAAACGAACATATTCGTGAACG
Found at i:29383 original size:31 final size:31
Alignment explanation
Indices: 29345--29469 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
29335 CCCGAAGGAC
* * *
29345 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
29376 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
29407 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
29438 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
29469 C
1 C
29470 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:30288 original size:21 final size:21
Alignment explanation
Indices: 30264--30308 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
30254 TGTTGTTCGA
* *
30264 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
30285 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
30306 TTG
1 TTG
30309 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:33496 original size:31 final size:31
Alignment explanation
Indices: 33458--33582 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
33448 CCCGAAGGAC
* * *
33458 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
33489 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
33520 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
33551 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
33582 C
1 C
33583 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:34400 original size:21 final size:21
Alignment explanation
Indices: 34376--34420 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
34366 TGTTGTTCGT
* *
34376 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
34397 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
34418 TTG
1 TTG
34421 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:35717 original size:31 final size:31
Alignment explanation
Indices: 35679--35749 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
35669 GGATTAAGGG
35679 TCATTTTTGTCCATGTAGTAGACCCAATTTA
1 TCATTTTTGTCCATGTAGTAGACCCAATTTA
*
35710 TCATTTTTGTCCCTGTAGTAGACCCAATTTA
1 TCATTTTTGTCCATGTAGTAGACCCAATTTA
35741 TCATTTTTG
1 TCATTTTTG
35750 ACCCTATTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.45
Consensus pattern (31 bp):
TCATTTTTGTCCATGTAGTAGACCCAATTTA
Found at i:42310 original size:27 final size:28
Alignment explanation
Indices: 42272--42326 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
42262 TTGATTATTC
*
42272 ATTGTT-AAAAAATAAACTGTAATGTTA
1 ATTGTTAAAAAAATAAACTATAATGTTA
42299 ATTGTTAAAAAAATAAACTATAATGTTA
1 ATTGTTAAAAAAATAAACTATAATGTTA
42327 GTATGTCATC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 6 0.23
28 20 0.77
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (28 bp):
ATTGTTAAAAAAATAAACTATAATGTTA
Found at i:43145 original size:142 final size:142
Alignment explanation
Indices: 42889--43187 Score: 553
Period size: 142 Copynumber: 2.1 Consensus size: 142
42879 TTCGCTCATA
* *
42889 AATGGAAAAATTATTATGGGTGATTATAATGTAGTATATGTTTATGATATTTCTTAATTATTGAC
1 AATGGGAAAATTATTATGGGTGATTATAATGTAGTATATATTTATGATATTTCTTAATTATTGAC
*
42954 AATGTACACATGTTTGAATCTAGAACATCAGGAGAGAATAACACTTTTTTAAACCATTGAAGCGA
66 AATGTACACATGTTTGAATCTAGAACATCAAGAGAGAATAACACTTTTTTAAACCATTGAAGCGA
43019 CTCAATAAATTT
131 CTCAATAAATTT
*
43031 AATGGGAAAATTATTATGGGTGATTATAATGTAGTATATATTTATGATCTTTCTTAATTATTGAC
1 AATGGGAAAATTATTATGGGTGATTATAATGTAGTATATATTTATGATATTTCTTAATTATTGAC
*
43096 AATGTACACATGTTTGAATCTAGAACATCAAGAGAGAATAACACTTTTTTTAACCATTGAAGCGA
66 AATGTACACATGTTTGAATCTAGAACATCAAGAGAGAATAACACTTTTTTAAACCATTGAAGCGA
43161 CTCAATAAATTT
131 CTCAATAAATTT
43173 AATGGGAAAATTATT
1 AATGGGAAAATTATT
43188 CTCTATTTGC
Statistics
Matches: 152, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 152 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (142 bp):
AATGGGAAAATTATTATGGGTGATTATAATGTAGTATATATTTATGATATTTCTTAATTATTGAC
AATGTACACATGTTTGAATCTAGAACATCAAGAGAGAATAACACTTTTTTAAACCATTGAAGCGA
CTCAATAAATTT
Found at i:53882 original size:2 final size:2
Alignment explanation
Indices: 53875--53911 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
53865 TTTCCTATGT
53875 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53912 GTAATATGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57061 original size:10 final size:10
Alignment explanation
Indices: 57021--57059 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
57011 ATCATGTTCC
57021 AAAAAAACCA
1 AAAAAAACCA
57031 AAAAAAACCAA
1 AAAAAAACC-A
*
57042 AAACAAAATCA
1 AAA-AAAACCA
57053 AAAAAAA
1 AAAAAAA
57060 TCCCTCGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
10 13 0.50
11 8 0.31
12 5 0.19
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (10 bp):
AAAAAAACCA
Found at i:57456 original size:2 final size:2
Alignment explanation
Indices: 57449--57503 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
57439 TCCATTTATG
57449 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57491 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
57504 CCCTTGTTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59293 original size:61 final size:60
Alignment explanation
Indices: 59189--59314 Score: 191
Period size: 61 Copynumber: 2.1 Consensus size: 60
59179 TCCCAGTTTT
* *
59189 ATTT-AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCTA
1 ATTTCAGAGTCAATTTCAACTTCACAACGAACGATATTGGACTCAACAAACAACTTTCCA
* * *
59248 ACTTTCAGAGTCAATTTCAACTTCACAGCGAACGATATTGTACTCAACAAACAATTTTCCA
1 A-TTTCAGAGTCAATTTCAACTTCACAACGAACGATATTGGACTCAACAAACAACTTTCCA
59309 ATTTCA
1 ATTTCA
59315 ACTTCACAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
59 1 0.02
60 8 0.13
61 51 0.85
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.30
Consensus pattern (60 bp):
ATTTCAGAGTCAATTTCAACTTCACAACGAACGATATTGGACTCAACAAACAACTTTCCA
Found at i:59637 original size:43 final size:41
Alignment explanation
Indices: 59546--59655 Score: 121
Period size: 43 Copynumber: 2.6 Consensus size: 41
59536 ACGAAGAGGC
* *
59546 CATCCACGATTTCAATTCCACGACGGAGGATATCGTACCAA
1 CATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAA
* *
59587 CGGATCCACGATTTCAACTCCACGACAGAGGATATTGTGCCCATA
1 C--ATCCACGATTTCAACTCCACGACAGAGGATATCGT-ACCA-A
* * *
59632 CATCCACGGTTTTAACTTCACGAC
1 CATCCACGATTTCAACTCCACGAC
59656 GAAGGGAATC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
41 1 0.02
43 52 0.90
44 3 0.05
45 2 0.03
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (41 bp):
CATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAA
Found at i:60091 original size:84 final size:84
Alignment explanation
Indices: 59957--60751 Score: 837
Period size: 84 Copynumber: 9.6 Consensus size: 84
59947 GGGCTATCTG
* * * *
59957 CCAAAGACCTTCGAGTTCTATTACACTCAGCTCAAAGGCACTAACA-TTGCAACATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCAC-ATCATTTGCAGCATAACTTAAGT
*
60021 CGAGAAGGGTTATCTTCCAA
65 CGAGAAGGGTTATCTGCCAA
* * * * *
60041 CTAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
60106 AAGAAGGGCTATCT----A
66 GAGAAGGGTTATCTGCCAA
* * * * * *
60121 CCAAAGACCTTCGAGTTTGATTACATTCAGCTCAAAGGCCCCAACATTTGCAGCATACCTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGG-CACATCATTTGCAGCATAACTTAAGT
60186 CGAGAA-GGTTATCTGCCAA
65 CGAGAAGGGTTATCTGCCAA
* * * * * *
60205 CCAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCATATCATTTGTAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTC
* **
60270 GAGAATGACTATCT----A
66 GAGAAGGGTTATCTGCCAA
* * * * *
60285 CCAAATACCTTCGAGTTCGAATACACTCACCTCAAAGGCATCAACATTTACAGCATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCA-CATCATTTGCAGCATAACTTAAGT
*
60350 CGAGAAGGGTTATCTGACAA
65 CGAGAAGGGTTATCTGCCAA
* ** * *
60370 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATATTATTTGCAGCATAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTC
*
60435 GAGAAGGGCTATCTG----
66 GAGAAGGGTTATCTGCCAA
* * * * * *
60450 CCAAAGACCTTCGAGTTCGATTACACTTAGCTCAAAGGTACCAAT-ATTTACAGCATAACGTAAC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCA-C-ATCATTTGCAGCATAACTTAAG
* *
60514 TCGAAAAGGGTTATATGCCAA
64 TCGAGAAGGGTTATCTGCCAA
* * * * * *
60535 CTAAAGACCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAATTC
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
60600 AAGAAGGGCTATCTGCCAA
66 GAGAAGGGTTATCTGCCAA
* * * * * * *
60619 CCAAAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTTGTAACATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCA-TTTGCAGCATAACTTAAGT
*
60684 CCAGAAGGGTTATCTGCCAA
65 CGAGAAGGGTTATCTGCCAA
* * *
60704 CAAAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACATCATTT
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTT
60752 ATAGTAATTC
Statistics
Matches: 585, Mismatches: 106, Indels: 40
0.80 0.15 0.05
Matches are distributed among these distances:
80 109 0.19
81 88 0.15
82 2 0.00
83 32 0.05
84 216 0.37
85 138 0.24
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (84 bp):
CCAAAGACCTTCGAGTTCGACTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTTAAGTC
GAGAAGGGTTATCTGCCAA
Found at i:60198 original size:164 final size:165
Alignment explanation
Indices: 59919--60751 Score: 1053
Period size: 165 Copynumber: 5.0 Consensus size: 165
59909 GATATCGTGC
* * * * *
59919 TCATTTGTAGCTTAGCTCAAGGCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCT-ATTACAC
1 TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCTTCGAGTT-TGATTACAC
* * * *
59983 TCAGCTCAAAGGCACTAACA-TTGCAACATAACTTAAGTCGAGAAGGGTTATCTTCCAACTAAAG
65 TCAGCTCAAAGGCACCAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAG
*
60047 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTACA
130 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
* *
60083 TCATTTGCAGCATAGCTTAAGTCAAGAAGGGCTATCTACCAAAGACCTTCGAGTTTGATTACATT
1 TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCTTCGAGTTTGATTACACT
* *
60148 CAGCTCAAAGGCCCCAACATTTGCAGCATACCTTAAGTCGAGAA-GGTTATCTGCCAACCAAAGA
66 CAGCTCAAAGGCACCAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA
* * *
60212 CCTTTGAGTTCGACTACGCTCAGCTCTAAGGCATA
131 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
* * * * * *
60247 TCATTTGTAGCATAGCTTAAGTCGAGAATGACTATCTACCAAATACCTTCGAGTTCGAATACACT
1 TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCTTCGAGTTTGATTACACT
* * * *
60312 CACCTCAAAGGCATCAACATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGACAACCAAAGA
66 CAGCTCAAAGGCACCAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA
* *
60377 CCTTCGAGTTCGACTACGCTCAGCTCCTAGGCATA
131 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
* * * *
60412 TTATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGATTACACT
1 TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCTTCGAGTTTGATTACACT
* * * * * * * * *
60477 TAGCTCAAAGGTACCAATATTTACAGCATAACGTAACTCGAAAAGGGTTATATGCCAACTAAAGA
66 CAGCTCAAAGGCACCAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA
*
60542 CCTTCGAGTTCAACTACGCTCAGCTCCAAGGCACA
131 CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
* * *
60577 TCATTTGCAGCATAGCTTAATTCAAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTTGACTA
1 TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT----ACCAAAGACCTTCGAGTTTGATTA
* * * * * * * * *
60642 CGCTCAGCTCCAAGGCA-CATCATTTTGTAACATAACTCAAGGCCAGAAGGGTTATCTGCCAACA
62 CACTCAGCTCAAAGGCACCAACA-TTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC
* ** *
60706 AAAGACCTTCGAGTTCGATTACATTCAGCTCAAAGGCACA
126 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
60746 TCATTT
1 TCATTT
60752 ATAGTAATTC
Statistics
Matches: 576, Mismatches: 85, Indels: 11
0.86 0.13 0.02
Matches are distributed among these distances:
163 1 0.00
164 218 0.38
165 249 0.43
168 3 0.01
169 105 0.18
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (165 bp):
TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCTTCGAGTTTGATTACACT
CAGCTCAAAGGCACCAACATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA
CCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
Found at i:61009 original size:43 final size:43
Alignment explanation
Indices: 60944--61140 Score: 136
Period size: 43 Copynumber: 4.5 Consensus size: 43
60934 CGACCTGATC
*
60944 TCCTCATCACGTAGGAGA-CGTGTCAACCTTAGATAACCAGTCG
1 TCCTCATCACGTAGGA-ACCGTGTCAACCTTAGATAACCAGCCG
* * ** * *
60987 TCCTCATCACGTAGGAACCGTGTTATCATCCCTAATGATGGCCTGCCA
1 TCCTCATCACGTAGGAACCGTG---TCA-ACCTTA-GATAACCAGCCG
* * * * *
61035 TCCTCATCACGTAGGAACCATGTCATCCCTCG---ACCAGATC-
1 TCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAG-CCG
* * * *
61075 TCATCATCACGTCA-GAGCAGTGTCAGCCTTAGATAACCAGCCG
1 TCCTCATCACGT-AGGAACCGTGTCAACCTTAGATAACCAGCCG
61118 TCCTCATCACGTAGGAACCGTGT
1 TCCTCATCACGTAGGAACCGTGT
61141 TATCATCCTT
Statistics
Matches: 115, Mismatches: 26, Indels: 26
0.69 0.16 0.16
Matches are distributed among these distances:
40 26 0.23
41 2 0.02
42 3 0.03
43 44 0.38
44 2 0.02
45 3 0.03
46 3 0.03
47 4 0.03
48 28 0.24
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (43 bp):
TCCTCATCACGTAGGAACCGTGTCAACCTTAGATAACCAGCCG
Found at i:61136 original size:131 final size:130
Alignment explanation
Indices: 60876--61148 Score: 392
Period size: 131 Copynumber: 2.1 Consensus size: 130
60866 CGAATGATAT
* * * * *
60876 CGTGTTATCA-CCCTTAGATGACCTGTCATCCTCATTACGTAGGAACCGTGTCATTACCCGACCT
1 CGTGTTATCATCCCTAAGATGACCTGCCATCCTCATCACGTAGGAACCATGTCATTACCCGACCA
* *
60940 GATCTCCTCATCACGTAGGAGACGTGTCAACCTTAGATAACCAGTCGTCCTCATCACGTAGGAAC
66 GATCTCATCATCACGTAGGAGACGTGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAGGAAC
* *
61005 CGTGTTATCATCCCTAATGATGGCCTGCCATCCTCATCACGTAGGAACCATGTCA-TCCCTCGAC
1 CGTGTTATCATCCCTAA-GATGACCTGCCATCCTCATCACGTAGGAACCATGTCATTACC-CGAC
*
61069 CAGATCTCATCATCACGTCA-GAG-CAGTGTCAGCCTTAGATAACCAGCCGTCCTCATCACGTAG
64 CAGATCTCATCATCACGT-AGGAGAC-GTGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAG
61132 GAAC
127 GAAC
61136 CGTGTTATCATCC
1 CGTGTTATCATCC
61149 TTAGACAATC
Statistics
Matches: 129, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
129 10 0.08
130 9 0.07
131 109 0.84
132 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.26
Consensus pattern (130 bp):
CGTGTTATCATCCCTAAGATGACCTGCCATCCTCATCACGTAGGAACCATGTCATTACCCGACCA
GATCTCATCATCACGTAGGAGACGTGTCAACCTTAGATAACCAGCCGTCCTCATCACGTAGGAAC
Found at i:65957 original size:23 final size:23
Alignment explanation
Indices: 65931--65999 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
65921 CACCACAGCT
* *
65931 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
* *
65954 CGTAGAATTGCACCGGAGTTCCG
1 CGTAGAATTGCACCGGAGTGCCA
*
65977 CGTAGAATTACACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
66000 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:66704 original size:19 final size:19
Alignment explanation
Indices: 66656--66706 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
66646 TTTAATGGGG
*
66656 ATGCATCGAAGCACTCCTT
1 ATGCATCGATGCACTCCTT
*
66675 ATACATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
*
66694 ATGCATTGATGCA
1 ATGCATCGATGCA
66707 TTAATTGCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:76258 original size:23 final size:23
Alignment explanation
Indices: 76232--76286 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
76222 CCCTTATGAA
*
76232 CAATTTTATGTGGCACTACGGTG
1 CAATTTTATGCGGCACTACGGTG
* * *
76255 CAATTCTACGCGGCACTTCGGTG
1 CAATTTTATGCGGCACTACGGTG
* *
76278 AAAATTTAT
1 CAATTTTAT
76287 ACGAGCTGTG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (23 bp):
CAATTTTATGCGGCACTACGGTG
Found at i:78938 original size:90 final size:89
Alignment explanation
Indices: 78817--78993 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
78807 TAATCCCGAA
* *
78817 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCCTAATATGAT
78882 TAGGGTAACTTGGATATAAAAGGAT
65 TAGGGTAACTTGGATATAAAAGGAT
78907 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
* *
78972 AGGGTGACTTGGCTATAAAAGG
66 AGGGTAACTTGGATATAAAAGG
78994 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 33 0.40
90 50 0.60
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAAAGGAT
Found at i:81474 original size:44 final size:44
Alignment explanation
Indices: 81425--81519 Score: 145
Period size: 44 Copynumber: 2.2 Consensus size: 44
81415 AGTCACATCT
* *
81425 TTTAAATTTTTAAATAATTTAAATATTTTTACACTTTATTTATC
1 TTTAAATTTTTAAATAATTTAAATATTTTTACACTTCATATATC
* *
81469 TTTAAAATTTTATATAATTTAAATATTTTTACACTTCATATATC
1 TTTAAATTTTTAAATAATTTAAATATTTTTACACTTCATATATC
*
81513 CTTAAAT
1 TTTAAAT
81520 GTGATAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (44 bp):
TTTAAATTTTTAAATAATTTAAATATTTTTACACTTCATATATC
Found at i:84078 original size:2 final size:2
Alignment explanation
Indices: 84071--84115 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
84061 TCTCAACATG
84071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84113 AT A
1 AT A
84116 GAGGCTTAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:99302 original size:21 final size:21
Alignment explanation
Indices: 99231--99315 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
99221 ATTTTGGTAC
*
99231 AGAGGGAATCGA-TCCCCCCA
1 AGAGGGAACCGATTCCCCCCA
*
99251 ATGAGGGAACCGATTCCCCCTTTGA
1 A-GAGGGAACCGATTCCCCC---CA
99276 AG-GGGAACCGATTCCCCCCA
1 AGAGGGAACCGATTCCCCCCA
* *
99296 CAG-GGGAATCGATACCCCCC
1 -AGAGGGAACCGATTCCCCCC
99316 TGGGGTTCTG
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
20 2 0.04
21 27 0.50
22 6 0.11
23 16 0.30
24 1 0.02
25 2 0.04
ACGTcount: A:0.26, C:0.35, G:0.25, T:0.14
Consensus pattern (21 bp):
AGAGGGAACCGATTCCCCCCA
Found at i:102854 original size:15 final size:15
Alignment explanation
Indices: 102834--102878 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
102824 GTTCAGTATT
102834 CGTCCCGAAGGACTA
1 CGTCCCGAAGGACTA
102849 CGTCCCGAAGGACTA
1 CGTCCCGAAGGACTA
*
102864 CGTCCCGAATGACTA
1 CGTCCCGAAGGACTA
102879 TTATACCCTC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.27, C:0.33, G:0.24, T:0.16
Consensus pattern (15 bp):
CGTCCCGAAGGACTA
Found at i:103481 original size:64 final size:64
Alignment explanation
Indices: 103369--103509 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 64
103359 TAATGAAGGT
* * * **
103369 ATGCATCGATGCACTACTGATGCATCGATGCATAAAAGGTATTTGATGTAGT-ATTATTGCTGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGT-GTCATTATTAATGGG
* * * ** *
103433 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTGTCATTATTAATGGG
103497 ATGCATCGATGCA
1 ATGCATCGATGCA
103510 TGAATTGCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
63 1 0.02
64 64 0.98
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTGATGCATCGATGCACAAAAGGCATTCGATGTGTCATTATTAATGGG
Found at i:103547 original size:45 final size:45
Alignment explanation
Indices: 103452--103555 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
103442 TGCACTCCTT
* *
103452 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** *
103497 ATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-AG
1 ATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
103541 AGTGCATCGATGCAC
1 A-TGCATCGATGCAC
103556 TACCAATGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
44 2 0.04
45 44 0.86
46 5 0.10
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (45 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:109768 original size:15 final size:15
Alignment explanation
Indices: 109745--109792 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
109735 CGTATGACTC
*
109745 CTACATCCCGAAGGA
1 CTACGTCCCGAAGGA
109760 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
109775 CTACGTCCCGAAGGA
1 CTACGTCCCGAAGGA
109790 CTA
1 CTA
109793 TTATACCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.29, C:0.33, G:0.23, T:0.15
Consensus pattern (15 bp):
CTACGTCCCGAAGGA
Found at i:109971 original size:12 final size:12
Alignment explanation
Indices: 109937--109971 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
109927 TATCATGTTC
**
109937 TCATATCACAGG
1 TCATATCACATA
109949 TCATATCACATA
1 TCATATCACATA
109961 TCATATCACAT
1 TCATATCACAT
109972 GAACAAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (12 bp):
TCATATCACATA
Found at i:110390 original size:64 final size:64
Alignment explanation
Indices: 110282--110458 Score: 196
Period size: 64 Copynumber: 2.8 Consensus size: 64
110272 TAATGAAGGT
* * ** **
110282 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGT-ATTCGATGTAGT-ATTATTGCTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-AAAATTTCATTCGATGT-GTCATTATTAATGG
110345 G
64 G
* ** *
110346 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTTCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCAAAAATTTCATTCGATGTGTCATTATTAATGGG
* ** *
110410 ATGCATCGATGCAATACTTATGCATCGATGCATGAATTACATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCAAAAATTTCATTCGATGT
110459 CTTTATTTTA
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
63 4 0.04
64 92 0.96
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCAAAAATTTCATTCGATGTGTCATTATTAATGGG
Found at i:110479 original size:64 final size:64
Alignment explanation
Indices: 110345--110500 Score: 190
Period size: 64 Copynumber: 2.4 Consensus size: 64
110335 TTATTGCTGG
* * * *
110345 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTTCATTCGATGTTTCATTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTTCATTATTAAAGA
* ** *
110409 GATGCATCGATGCAATACTTATGCATCGATGCATGAATTACATTCGATGTCTTTATT-TTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGT-TTCATTATTAAAGA
**
110472 GAGTGCATCGATGCACTACCAATGCATCG
1 GA-TGCATCGATGCACTACTTATGCATCG
110501 GTGTACATTC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 2 0.03
64 72 0.91
65 5 0.06
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (64 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACCAATTACATTCGATGTTTCATTATTAAAGA
Found at i:113094 original size:35 final size:35
Alignment explanation
Indices: 113048--113126 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
113038 TGATTATAAG
* *
113048 TGATATGATTACATGATTACAAGAGATAATCCATA
1 TGATATGATTACATGATCACAAGAGATAAGCCATA
*
113083 TGATATGATTACATGATCACATGAGATAAGCCATA
1 TGATATGATTACATGATCACAAGAGATAAGCCATA
113118 TGATATGAT
1 TGATATGAT
113127 AAGAAACTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (35 bp):
TGATATGATTACATGATCACAAGAGATAAGCCATA
Found at i:117282 original size:35 final size:35
Alignment explanation
Indices: 117236--117312 Score: 136
Period size: 35 Copynumber: 2.2 Consensus size: 35
117226 ATTATAAGTA
*
117236 ATATGATTACATGATCATAAGAGATAAGCCATATG
1 ATATGATTACATGATCACAAGAGATAAGCCATATG
*
117271 ATATGATTACATGATCACAAGAGATAAGTCATATG
1 ATATGATTACATGATCACAAGAGATAAGCCATATG
117306 ATATGAT
1 ATATGAT
117313 AAGAAGCTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (35 bp):
ATATGATTACATGATCACAAGAGATAAGCCATATG
Found at i:123789 original size:4 final size:4
Alignment explanation
Indices: 123780--123817 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
123770 AAGAAATTAT
123780 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
123818 TAAGGAAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:124198 original size:2 final size:2
Alignment explanation
Indices: 124191--124243 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
124181 CTATCTATCA
124191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124233 AT AT AT AT AT A
1 AT AT AT AT AT A
124244 AAAGTAATAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:131670 original size:29 final size:29
Alignment explanation
Indices: 131638--131728 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
131628 TATGTCTTTT
131638 CAGCTAATTTGCATGAATTATAACTAATC
1 CAGCTAATTTGCATGAATTATAACTAATC
* ** * * *
131667 CAGC-ACATTGTTCATTCATT-TCCACT-TTT
1 CAGCTA-ATT-TGCATGAATTAT-AACTAATC
131696 CAGCTAATTTGCATGAATTATAACTAATC
1 CAGCTAATTTGCATGAATTATAACTAATC
131725 CAGC
1 CAGC
131729 ACATTGTTCA
Statistics
Matches: 44, Mismatches: 12, Indels: 12
0.65 0.18 0.18
Matches are distributed among these distances:
28 11 0.25
29 22 0.50
30 11 0.25
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (29 bp):
CAGCTAATTTGCATGAATTATAACTAATC
Found at i:131723 original size:58 final size:58
Alignment explanation
Indices: 131633--131748 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
131623 GATATTATGT
131633 CTTTTCAGCTAATTTGCATGAATTATAACTAATCCAGCACATTGTTCATTCATTTCCA
1 CTTTTCAGCTAATTTGCATGAATTATAACTAATCCAGCACATTGTTCATTCATTTCCA
131691 CTTTTCAGCTAATTTGCATGAATTATAACTAATCCAGCACATTGTTCATTCATTTCCA
1 CTTTTCAGCTAATTTGCATGAATTATAACTAATCCAGCACATTGTTCATTCATTTCCA
131749 GATAAAGTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (58 bp):
CTTTTCAGCTAATTTGCATGAATTATAACTAATCCAGCACATTGTTCATTCATTTCCA
Found at i:132060 original size:194 final size:196
Alignment explanation
Indices: 131713--132104 Score: 761
Period size: 194 Copynumber: 2.0 Consensus size: 196
131703 TTTGCATGAA
131713 TTATAACTAATCCAGCACATTGTTCATTCATTTCCAGATAAAGTATTCTTATCATCAGAATAGAA
1 TTATAACTAATCCAGCACATTGTTCATTCATTTCCAGATAAAGTATTCTTATCATCAGAATAGAA
131778 GGGATACCATATTATAAGTAAAATCGTGTATTCCTCATGAAGCAAATAAATGCACAAGTATTTTG
66 GGGATACCA-ATTATAAGTAAAATCGTGTATTCCTCATGAAGCAAATAAATGCACAAGTATTTTG
131843 ACAATAAGTGATACCTCCAGGTCTGAATTGTATAAATCCAAAATTTTCCAATCTTTTAGCTGTAT
130 ACAATAAGTGATACCTCCAGGTCTGAATTGTATAAATCCAAAATTTTCCAATCTTTTAGCTGTAT
131908 CT
195 CT
131910 TTATAACTAATCCAGCACATTGTTCATTCATTTCCAGATAAAGTATTCTTATCATCAGAATAGAA
1 TTATAACTAATCCAGCACATTGTTCATTCATTTCCAGATAAAGTATTCTTATCATCAGAATAGAA
131975 GGGATACC-A-TATAAGTAAAATCGTGTATTCCTCATGAAGCAAATAAATGCACAAGTATTTTGA
66 GGGATACCAATTATAAGTAAAATCGTGTATTCCTCATGAAGCAAATAAATGCACAAGTATTTTGA
132038 CAATAAGTGATACCTCCAGGTCTGAATTGTATAAATCCAAAATTTTCCAATCTTTTAGCTGTATC
131 CAATAAGTGATACCTCCAGGTCTGAATTGTATAAATCCAAAATTTTCCAATCTTTTAGCTGTATC
132103 T
196 T
132104 T
1 T
132105 CAGAGAATGC
Statistics
Matches: 195, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
194 121 0.62
195 1 0.01
197 73 0.37
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (196 bp):
TTATAACTAATCCAGCACATTGTTCATTCATTTCCAGATAAAGTATTCTTATCATCAGAATAGAA
GGGATACCAATTATAAGTAAAATCGTGTATTCCTCATGAAGCAAATAAATGCACAAGTATTTTGA
CAATAAGTGATACCTCCAGGTCTGAATTGTATAAATCCAAAATTTTCCAATCTTTTAGCTGTATC
T
Found at i:133726 original size:104 final size:104
Alignment explanation
Indices: 133546--133737 Score: 312
Period size: 104 Copynumber: 1.8 Consensus size: 104
133536 TCCGTCAAAT
*
133546 TGATCAAACATGTTGAACCAGGTTAAACCGCACTAGTTCAATGTTGAACCAGTTTAGAGATTCTT
1 TGATCAAACATGTTGAACCAGGCTAAACCGCACTAGTTCAATGTTGAACCAGTTTAGAGATTCTT
* *
133611 TTATTATTTTAAGTTTCAAAAATTTAGAGTGCATTGAAC
66 TTATTATTTTAAGTATAAAAAATTTAGAGTGCATTGAAC
* *** *
133650 TGATCAAGCATGTTGAATTGGGCTAAACCGCACTAGTTCAATGTTGAACTAGTTTAGAGATTCTT
1 TGATCAAACATGTTGAACCAGGCTAAACCGCACTAGTTCAATGTTGAACCAGTTTAGAGATTCTT
133715 TTATTATTTTAAGTATAAAAAAT
66 TTATTATTTTAAGTATAAAAAAT
133738 ATACAGAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 80 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (104 bp):
TGATCAAACATGTTGAACCAGGCTAAACCGCACTAGTTCAATGTTGAACCAGTTTAGAGATTCTT
TTATTATTTTAAGTATAAAAAATTTAGAGTGCATTGAAC
Found at i:134013 original size:20 final size:20
Alignment explanation
Indices: 133988--134078 Score: 72
Period size: 20 Copynumber: 5.0 Consensus size: 20
133978 TAAATTAAAT
*
133988 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
134008 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
*
134028 ATT--AT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* * *
134040 ATCAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
134060 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
134079 TTATTTTGTT
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
12 2 0.04
13 2 0.04
14 2 0.04
15 4 0.07
17 3 0.06
18 2 0.04
19 2 0.04
20 37 0.69
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.44
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:138165 original size:168 final size:165
Alignment explanation
Indices: 137890--138223 Score: 641
Period size: 168 Copynumber: 2.0 Consensus size: 165
137880 CACTCCAGGC
137890 TGTTTACCGGATTCTTCATTACTTGAAAGGGTCATGGTAAAGGAATCATGTTTTCGAAGATGGAA
1 TGTTTACCGGATTCTTCATTACTTGAAAGGGTCATGGTAAAGGAATCATGTTTTCGAAGATGGAA
137955 GTCGAAGAGTGGAGATCTTCACTGATGCTGATTAGGGCGGAAGTTCTACAGACAGAAGATCTACT
66 GTCGAAGAGTGGAGATCTTCACTGATGCTGATTAGGGCGGAAGTTCTACAGACAGAAGATCTACT
138020 ACCGGTTATTGCTCCTTTGTCTGGGGCAACTTAGT
131 ACCGGTTATTGCTCCTTTGTCTGGGGCAACTTAGT
138055 TGTTTACCGGATTCTTCATTACTTGAAAGGGAGTCATGGTAAAGGAATCATGTTTTCGAAGAATG
1 TGTTTACCGGATTCTTCATTACTTGAAA-GG-GTCATGGTAAAGGAATCATGTTTTCGAAG-ATG
138120 GAAGTCGAAGAGTGGAGATCTTCACTGATGCTGATTAGGGCGGAAGTTCTACAGACAGAAGATCT
63 GAAGTCGAAGAGTGGAGATCTTCACTGATGCTGATTAGGGCGGAAGTTCTACAGACAGAAGATCT
138185 ACTACCGGTTATTGCTCCTTTGTCTGGGGCAACTTAGT
128 ACTACCGGTTATTGCTCCTTTGTCTGGGGCAACTTAGT
138223 T
1 T
138224 ACTTGGAGGA
Statistics
Matches: 166, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
165 28 0.17
166 2 0.01
167 29 0.17
168 107 0.64
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (165 bp):
TGTTTACCGGATTCTTCATTACTTGAAAGGGTCATGGTAAAGGAATCATGTTTTCGAAGATGGAA
GTCGAAGAGTGGAGATCTTCACTGATGCTGATTAGGGCGGAAGTTCTACAGACAGAAGATCTACT
ACCGGTTATTGCTCCTTTGTCTGGGGCAACTTAGT
Found at i:138665 original size:20 final size:20
Alignment explanation
Indices: 138640--138730 Score: 81
Period size: 20 Copynumber: 5.0 Consensus size: 20
138630 TAAATTAAAT
*
138640 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
*
138660 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTA
*
138680 ATT--AT---ATTAG--TT-
1 ATTAGATAGAATCAGTTTTA
* *
138692 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCAGTTTTA
138712 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
138731 TTATTTTGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
12 3 0.05
13 2 0.04
14 2 0.04
15 4 0.07
17 3 0.05
18 2 0.04
19 2 0.04
20 38 0.68
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:140047 original size:18 final size:16
Alignment explanation
Indices: 140024--140094 Score: 60
Period size: 16 Copynumber: 4.4 Consensus size: 16
140014 AGAAATTTAT
140024 TTAAAAATCATAAAAATA
1 TTAAAAAT-AT-AAAATA
140042 TTAAAAATATAAAATA
1 TTAAAAATATAAAATA
* *
140058 TTCAAAAT-T---ATT
1 TTAAAAATATAAAATA
140070 TTAAAAATTATAAAATA
1 TTAAAAA-TATAAAATA
140087 TTACAAAA
1 TTA-AAAA
140095 CTATTCTACA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
12 8 0.19
13 1 0.02
14 1 0.02
15 1 0.02
16 13 0.30
17 7 0.16
18 12 0.28
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (16 bp):
TTAAAAATATAAAATA
Found at i:140081 original size:29 final size:29
Alignment explanation
Indices: 140042--140099 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
140032 CATAAAAATA
*
140042 TTAAAAATATAAAATATT-CAAAATTATT
1 TTAAAAATATAAAATATTACAAAACTATT
140070 TTAAAAATTATAAAATATTACAAAACTATT
1 TTAAAAA-TATAAAATATTACAAAACTATT
140100 CTACAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 7 0.26
29 11 0.41
30 9 0.33
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (29 bp):
TTAAAAATATAAAATATTACAAAACTATT
Found at i:140112 original size:29 final size:27
Alignment explanation
Indices: 140046--140112 Score: 64
Period size: 29 Copynumber: 2.4 Consensus size: 27
140036 AAAATATTAA
* *
140046 AAATA-TAAAATATTCAAAATTATTTT
1 AAATATTAAAATATTCAAAACTATTCT
*
140072 AAAAATTATAAAATATTACAAAACTATTCT
1 AAATA-T-TAAAATATT-CAAAACTATTCT
140102 ACAATATTAAA
1 A-AATATTAAA
140113 GAATTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
26 4 0.12
29 13 0.41
30 12 0.38
31 3 0.09
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATATTAAAATATTCAAAACTATTCT
Found at i:140436 original size:28 final size:27
Alignment explanation
Indices: 140405--140472 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
140395 ATAATTATTT
140405 TTTTACAAAT-TTTAATAATATTTAATAA
1 TTTTA-AAATATTT-ATAATATTTAATAA
* *
140433 TTTTAAAATAATTTTTAATATTTTATAA
1 TTTTAAAAT-ATTTATAATATTTAATAA
*
140461 TTTT-TAATATTT
1 TTTTAAAATATTT
140473 TTTATAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
26 4 0.11
27 7 0.20
28 21 0.60
29 3 0.09
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTTAAAATATTTATAATATTTAATAA
Found at i:140444 original size:21 final size:20
Alignment explanation
Indices: 140418--140473 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 20
140408 TACAAATTTT
140418 AATAATATTTAATAATTTTAA
1 AATAATATTTAAT-ATTTTAA
*
140439 AATAATTTTTAATATTTT--
1 AATAATATTTAATATTTTAA
*
140457 -ATAATTTTTAATATTTT
1 AATAATATTTAATATTTT
140474 TTATAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
17 17 0.50
20 5 0.15
21 12 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATAATATTTAATATTTTAA
Found at i:140462 original size:17 final size:18
Alignment explanation
Indices: 140440--140483 Score: 72
Period size: 17 Copynumber: 2.4 Consensus size: 18
140430 TAATTTTAAA
140440 ATAATTTTTAATA-TTTT
1 ATAATTTTTAATATTTTT
140457 ATAATTTTTAATATTTTTT
1 ATAATTTTTAATA-TTTTT
140476 ATAATTTT
1 ATAATTTT
140484 AAGATGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 13 0.52
19 12 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATAATTTTTAATATTTTT
Found at i:140474 original size:10 final size:10
Alignment explanation
Indices: 140414--140483 Score: 76
Period size: 10 Copynumber: 7.3 Consensus size: 10
140404 TTTTTACAAA
140414 TTTTAATAAT
1 TTTTAATAAT
*
140424 ATTTAATAAT
1 TTTTAATAAT
*
140434 TTTAAAATAAT
1 TTT-TAATAAT
140445 TTTTAAT-A-
1 TTTTAATAAT
140453 TTTT-ATAAT
1 TTTTAATAAT
140462 TTTTAAT-AT
1 TTTTAATAAT
*
140471 TTTTTATAAT
1 TTTTAATAAT
140481 TTT
1 TTT
140484 AAGATGGTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
7 2 0.04
8 5 0.10
9 13 0.26
10 21 0.42
11 9 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:140494 original size:19 final size:19
Alignment explanation
Indices: 140440--140495 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
140430 TAATTTTAAA
*
140440 ATAATTTTT-A-ATATTTT
1 ATAATTTTTAAGATGTTTT
* *
140457 ATAATTTTTAATATTTTTT
1 ATAATTTTTAAGATGTTTT
140476 ATAA-TTTTAAGATGGTTTT
1 ATAATTTTTAAGAT-GTTTT
140495 A
1 A
140496 AAAAATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 9 0.27
18 9 0.27
19 15 0.45
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
ATAATTTTTAAGATGTTTT
Found at i:140521 original size:24 final size:25
Alignment explanation
Indices: 140477--140526 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
140467 ATATTTTTTA
*
140477 TAATTTTAAGATGGTTTTAAAAAAT
1 TAATTTTAAGATGATTTTAAAAAAT
* *
140502 TAATTTTTAGA-GATTTTAAATAAT
1 TAATTTTAAGATGATTTTAAAAAAT
140526 T
1 T
140527 TTAAAACTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (25 bp):
TAATTTTAAGATGATTTTAAAAAAT
Found at i:148268 original size:60 final size:55
Alignment explanation
Indices: 148183--148302 Score: 168
Period size: 60 Copynumber: 2.1 Consensus size: 55
148173 AATAATTATT
*
148183 TTTTTTACTTTTAATGTTTTAGGTTTGGGCCAAAACAAACCCAATAATAAGTTAATTAA
1 TTTTTTACTTTTAATGTTTTAGGTTTGGACCAAAACAAA-CC--TAATAAGTTAATT-A
* *
148242 TTTTTTACTTTTTAATGTTTTGGGTTTGGACCAAAACAGACCTAATAAGTTAATTA
1 TTTTTTAC-TTTTAATGTTTTAGGTTTGGACCAAAACAAACCTAATAAGTTAATTA
148298 TTTTT
1 TTTTT
148303 GTGATTTAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
56 6 0.11
57 13 0.23
59 10 0.18
60 28 0.49
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (55 bp):
TTTTTTACTTTTAATGTTTTAGGTTTGGACCAAAACAAACCTAATAAGTTAATTA
Found at i:154897 original size:22 final size:22
Alignment explanation
Indices: 154872--154938 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 22
154862 CACATTTTTA
154872 AGAAAAGTCTAATCTTCTATTC
1 AGAAAAGTCTAATCTTCTATTC
* ** * *
154894 AGAACA-TAAAAT-TT-TTTTA
1 AGAAAAGTCTAATCTTCTATTC
154913 AGAAAAGTCTAATCTTCTATTC
1 AGAAAAGTCTAATCTTCTATTC
154935 AGAA
1 AGAA
154939 CATAAAAAAT
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
19 8 0.25
20 6 0.19
21 6 0.19
22 12 0.38
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (22 bp):
AGAAAAGTCTAATCTTCTATTC
Found at i:154920 original size:41 final size:41
Alignment explanation
Indices: 154866--154945 Score: 160
Period size: 41 Copynumber: 2.0 Consensus size: 41
154856 AAGTTTCACA
154866 TTTTTAAGAAAAGTCTAATCTTCTATTCAGAACATAAAATT
1 TTTTTAAGAAAAGTCTAATCTTCTATTCAGAACATAAAATT
154907 TTTTTAAGAAAAGTCTAATCTTCTATTCAGAACATAAAA
1 TTTTTAAGAAAAGTCTAATCTTCTATTCAGAACATAAAA
154946 AATAAAGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (41 bp):
TTTTTAAGAAAAGTCTAATCTTCTATTCAGAACATAAAATT
Found at i:156460 original size:137 final size:139
Alignment explanation
Indices: 156214--156494 Score: 539
Period size: 137 Copynumber: 2.0 Consensus size: 139
156204 AAGAAGATTC
156214 ATTGGGTTAATTGGTCAACCATATGCCAACCTAAATATTTAGGAGGTCTTGGTAATTTAGATTTA
1 ATTGGGTTAATTGGTCAACCATATGCCAACCTAAATATTTAGGAGGTCTTGGTAATTTAGATTTA
156279 AATCTTCTGAATCGAGCACTCCTTGGGAAATGGTCTTGGAAATTTGCGACAAAAAGGGAC-CTTG
66 AATCTTCTGAATCGAGCACTCCTTGGGAAATGGTCTTGGAAATTTGCGACAAAAAGGGACACTTG
156343 GTGGAAAA-
131 GTGGAAAAG
*
156351 ATTGGGTTAATTGGTCAACCATATGCCAACCTAAATATTTAGGAGGTCTTGGTATTTTAGATTTA
1 ATTGGGTTAATTGGTCAACCATATGCCAACCTAAATATTTAGGAGGTCTTGGTAATTTAGATTTA
156416 AATCTTCTGAATCGAGCACTCCTTGGGAAATGGTCTTGGAAATTTGCGACAAAAAGGGACACTTG
66 AATCTTCTGAATCGAGCACTCCTTGGGAAATGGTCTTGGAAATTTGCGACAAAAAGGGACACTTG
156481 GTGGAAAAG
131 GTGGAAAAG
156490 ATTGG
1 ATTGG
156495 TGTGCAGAAA
Statistics
Matches: 141, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
137 124 0.88
138 12 0.09
139 5 0.04
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (139 bp):
ATTGGGTTAATTGGTCAACCATATGCCAACCTAAATATTTAGGAGGTCTTGGTAATTTAGATTTA
AATCTTCTGAATCGAGCACTCCTTGGGAAATGGTCTTGGAAATTTGCGACAAAAAGGGACACTTG
GTGGAAAAG
Found at i:161988 original size:309 final size:311
Alignment explanation
Indices: 161429--162048 Score: 1226
Period size: 309 Copynumber: 2.0 Consensus size: 311
161419 TAGCTCTAAG
161429 TTCACCAATCATGACACAGTATAATTCCAATGGTATACTACAACATTAATCAAGTTTATAGCCCA
1 TTCACCAATCATGACACAGTATAATTCCAATGGTATACTACAACATTAATCAAGTTTATAGCCCA
161494 TACTTCAGCTGCACTATCAAGATTTGCCGAGTCAGATGCCTTTGGGTTACCAAACGGCCGAATTT
66 TACTTCAGCTGCACTATCAAGATTTGCCGAGTCAGATGCCTTTGGGTTACCAAACGGCCGAATTT
161559 CATTTTCCCTTCCACGCCAAACAGGGGACTTCAGTGAGGTTTCACGAGATCGCATCCAATTCAAG
131 CATTTTCCCTTCCACGCCAAACAGGGGACTTCAGTGAGGTTTCACGAGATCGCATCCAATTCAAG
161624 TTCCCCTGCATAAGGTTCAGAGTAGAACGCAAAGAACAAACTGAGCTCATTAATCATATTTTTCA
196 TTCCCCTGCATAAGGTTCAGAGTAGAACGCAAAGAACAAACTGAGCTCATTAATCATATTTTTCA
161689 TAATGAAAT-ATATTATTAGAC-AACATGATATTTGTAGCGAAACTAACCT
261 TAATGAAATAATATTATTAGACAAACATGATATTTGTAGCGAAACTAACCT
161738 TTCACCAATCATGACACAGTATAATTCCAATGGTATACTACAACATTAATCAAGTTTATAGCCCA
1 TTCACCAATCATGACACAGTATAATTCCAATGGTATACTACAACATTAATCAAGTTTATAGCCCA
161803 TACTTCAGCTGCACTATCAAGATTTGCCGAGTCAGATGCCTTTGGGTTACCAAACGGCCGAATTT
66 TACTTCAGCTGCACTATCAAGATTTGCCGAGTCAGATGCCTTTGGGTTACCAAACGGCCGAATTT
161868 CATTTTCCCTTCCACGCCAAACAGGGGACTTCAGTGAGGTTTCACGAGATCGCATCCAATTCAAG
131 CATTTTCCCTTCCACGCCAAACAGGGGACTTCAGTGAGGTTTCACGAGATCGCATCCAATTCAAG
161933 TTCCCCTGCATAAGGTTCAGAGTAGAACGCAAAGAACAAACTGAGCTCATTAATCATATTTTTCA
196 TTCCCCTGCATAAGGTTCAGAGTAGAACGCAAAGAACAAACTGAGCTCATTAATCATATTTTTCA
161998 TAATGAAATAATATTATTAGACAAACATGATATTTGTAGCGAAACTAACCT
261 TAATGAAATAATATTATTAGACAAACATGATATTTGTAGCGAAACTAACCT
162049 GTACAGTATT
Statistics
Matches: 309, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
309 269 0.87
310 12 0.04
311 28 0.09
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (311 bp):
TTCACCAATCATGACACAGTATAATTCCAATGGTATACTACAACATTAATCAAGTTTATAGCCCA
TACTTCAGCTGCACTATCAAGATTTGCCGAGTCAGATGCCTTTGGGTTACCAAACGGCCGAATTT
CATTTTCCCTTCCACGCCAAACAGGGGACTTCAGTGAGGTTTCACGAGATCGCATCCAATTCAAG
TTCCCCTGCATAAGGTTCAGAGTAGAACGCAAAGAACAAACTGAGCTCATTAATCATATTTTTCA
TAATGAAATAATATTATTAGACAAACATGATATTTGTAGCGAAACTAACCT
Found at i:170897 original size:12 final size:12
Alignment explanation
Indices: 170880--170904 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
170870 TGCCTTTCCT
170880 TCCGTTCATTCG
1 TCCGTTCATTCG
170892 TCCGTTCATTCG
1 TCCGTTCATTCG
170904 T
1 T
170905 TCGTCAGTGG
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:0.08, C:0.32, G:0.16, T:0.44
Consensus pattern (12 bp):
TCCGTTCATTCG
Found at i:171166 original size:17 final size:18
Alignment explanation
Indices: 171125--171166 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
171115 TGCTCAAACC
*
171125 ATTTAAAATCAATTAATT
1 ATTTAAAATCAATTAACT
171143 ATTTAAAATCTAA-TAACT
1 ATTTAAAATC-AATTAACT
171161 -TTTAAA
1 ATTTAAA
171167 CTTATATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 6 0.27
18 14 0.64
19 2 0.09
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTAAAATCAATTAACT
Found at i:172053 original size:2 final size:2
Alignment explanation
Indices: 172048--172087 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
172038 TTTTTAGTTT
172048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
172088 TTTTTGTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:174368 original size:17 final size:17
Alignment explanation
Indices: 174346--174380 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
174336 TTCTTTCGAC
174346 TCTTGCCTGCATGTTGG
1 TCTTGCCTGCATGTTGG
174363 TCTTGCCTGCATGTTGG
1 TCTTGCCTGCATGTTGG
174380 T
1 T
174381 GCCTAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.23, G:0.29, T:0.43
Consensus pattern (17 bp):
TCTTGCCTGCATGTTGG
Found at i:182175 original size:18 final size:19
Alignment explanation
Indices: 182142--182177 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
182132 GATTAAAACA
182142 ATATATTTTATAATAATTT
1 ATATATTTTATAATAATTT
182161 ATATATTTT-TAATAATT
1 ATATATTTTATAATAATT
182178 AAAGAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATATATTTTATAATAATTT
Found at i:182191 original size:21 final size:21
Alignment explanation
Indices: 182120--182202 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
182110 AATTATTTAT
*
182120 TATATTTTAAATGATTAAAACAA
1 TATATTTT-AATAATT-AAACAA
***
182143 TATATTTT-ATAA-TAATTTA
1 TATATTTTAATAATTAAACAA
*
182162 TATATTTTTAATAATTAAAGAA
1 TATA-TTTTAATAATTAAACAA
182184 TATATTTTAATAATATAAA
1 TATATTTTAATAAT-TAAA
182203 ATTAAAATTC
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 7 0.14
20 5 0.10
21 17 0.35
22 12 0.24
23 8 0.16
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (21 bp):
TATATTTTAATAATTAAACAA
Found at i:182203 original size:64 final size:64
Alignment explanation
Indices: 182080--182227 Score: 144
Period size: 64 Copynumber: 2.3 Consensus size: 64
182070 AAATATATTA
* *** * *
182080 ATATTTTAAAATAATTAAATAATTTTTTATAATTATTTATTATATTTTAAATGATTAAAACAAT
1 ATATTTTAAAATAATTAAATAATTTTTAATAATTAAAGAATATATTTTAAATAATTAAAACAAT
* * *
182144 ATATTTTATAATAATT-TATATATTTTTAATAATTAAAGAATATATTTT-AATAATATAAAATTA
1 ATATTTTAAAATAATTAAATA-ATTTTTAATAATTAAAGAATATATTTTAAATAAT-TAAAA-CA
182207 A-
63 AT
182208 A-ATTCTTAAAAT-ATTAAATA
1 ATATT-TTAAAATAATTAAATA
182228 TATTATATAT
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
63 14 0.21
64 52 0.76
65 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (64 bp):
ATATTTTAAAATAATTAAATAATTTTTAATAATTAAAGAATATATTTTAAATAATTAAAACAAT
Found at i:182624 original size:32 final size:32
Alignment explanation
Indices: 182583--182643 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
182573 TAAAATACAC
*
182583 TTTATATTCAGTTTAGTCACTATTTTCACATA
1 TTTATATTCAATTTAGTCACTATTTTCACATA
182615 TTTATATTCAATTTAGTCACTATTTTCAC
1 TTTATATTCAATTTAGTCACTATTTTCAC
182644 CAATATCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.05, T:0.51
Consensus pattern (32 bp):
TTTATATTCAATTTAGTCACTATTTTCACATA
Found at i:182675 original size:46 final size:45
Alignment explanation
Indices: 182606--182693 Score: 140
Period size: 46 Copynumber: 1.9 Consensus size: 45
182596 TAGTCACTAT
182606 TTTCACATATTTATATTCAATTTAGTCACTATTTTCACCAATATC
1 TTTCACATATTTATATTCAATTTAGTCACTATTTTCACCAATATC
* * *
182651 TTTCAACATGTTTATGTTCGATTTAGTCACTATTTTCACCAAT
1 TTTC-ACATATTTATATTCAATTTAGTCACTATTTTCACCAAT
182694 TTAGGCTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 4 0.10
46 35 0.90
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (45 bp):
TTTCACATATTTATATTCAATTTAGTCACTATTTTCACCAATATC
Found at i:185058 original size:10 final size:10
Alignment explanation
Indices: 185034--185068 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
185024 AGGGTTAGAA
*
185034 TAAAATAAAT
1 TAAATTAAAT
185044 ATAAATTAAAT
1 -TAAATTAAAT
185055 TAAATTAAAT
1 TAAATTAAAT
185065 TAAA
1 TAAA
185069 AAAGAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
TAAATTAAAT
Found at i:185063 original size:15 final size:16
Alignment explanation
Indices: 185034--185069 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
185024 AGGGTTAGAA
185034 TAAAATAAATATAAAT
1 TAAAATAAATATAAAT
*
185050 TAAATTAAAT-TAAAT
1 TAAAATAAATATAAAT
185065 TAAAA
1 TAAAA
185070 AAGAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATAAATATAAAT
Found at i:186273 original size:22 final size:24
Alignment explanation
Indices: 186225--186280 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
186215 AACCCTAAAA
186225 AAAT-AACAAAAAATAACAAAATG
1 AAATAAACAAAAAATAACAAAATG
*
186248 -AATAAACAAATAAT-A-AAAATG
1 AAATAAACAAAAAATAACAAAATG
*
186269 AAATAAATAAAA
1 AAATAAACAAAA
186281 TGAAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 6 0.21
22 13 0.46
23 9 0.32
ACGTcount: A:0.75, C:0.05, G:0.04, T:0.16
Consensus pattern (24 bp):
AAATAAACAAAAAATAACAAAATG
Found at i:186281 original size:23 final size:21
Alignment explanation
Indices: 186232--186286 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
186222 AAAAAATAAC
*
186232 AAAAAATAACAAAATG-AATA
1 AAAAAATAAAAAAATGAAATA
*
186252 AACAAATAATAAAAATGAAATA
1 AAAAAATAA-AAAAATGAAATA
*
186274 AATAAAATGAAAA
1 AA-AAAATAAAAA
186287 TAAAAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.29
21 6 0.21
22 9 0.32
23 5 0.18
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (21 bp):
AAAAAATAAAAAAATGAAATA
Found at i:186409 original size:37 final size:36
Alignment explanation
Indices: 186304--186611 Score: 384
Period size: 36 Copynumber: 8.3 Consensus size: 36
186294 TATAAAAATA
** *
186304 ATATTATATATTTTCGAAAAAAATGTTTTCAAAATTAT
1 ATATTATATATTTT--TTAAAAATGTTTTCAAAACTAT
* *
186342 ATATTATATATATTTTCAAAATGTTTTCAAAACTAT
1 ATATTATATATTTTTTAAAAATGTTTTCAAAACTAT
* * *
186378 ACATCATATATGTTTTTAAAAATATTTTCAAAACTAT
1 ATATTATATAT-TTTTTAAAAATGTTTTCAAAACTAT
*
186415 ATATTATATATATATTTTCAAAAATGCTTTCAAAACTAT
1 ATATTATATAT-T-TTTT-AAAAATGTTTTCAAAACTAT
* *
186454 ATATTATATATGTTTTCAAAAATATTTTCAAAACTAT
1 ATATTATATAT-TTTTTAAAAATGTTTTCAAAACTAT
*
186491 ATATTATATATTTTCTAAAAATGTTTTCAAAACTAT
1 ATATTATATATTTTTTAAAAATGTTTTCAAAACTAT
* *
186527 ATATTATATATTTTCTAAAAATGTTTTTAAAACTAT
1 ATATTATATATTTTTTAAAAATGTTTTCAAAACTAT
186563 ATATTATTATATATTTTCTAAAAATGTTTTCAAAA-TAAT
1 ATATTA-TATAT-TTTT-TAAAAATGTTTTCAAAACT-AT
186602 ATATTATATA
1 ATATTATATA
186612 GATATTATGT
Statistics
Matches: 238, Mismatches: 25, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
36 90 0.38
37 66 0.28
38 28 0.12
39 54 0.23
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (36 bp):
ATATTATATATTTTTTAAAAATGTTTTCAAAACTAT
Found at i:187426 original size:19 final size:19
Alignment explanation
Indices: 187402--187453 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
187392 ATTGTTCAAG
187402 GTGTATCGATGCACATGAA
1 GTGTATCGATGCACATGAA
187421 GTGTATCGATGCACATGAA
1 GTGTATCGATGCACATGAA
187440 GTGTATCGATGCAC
1 GTGTATCGATGCAC
187454 TCCTTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (19 bp):
GTGTATCGATGCACATGAA
Found at i:188311 original size:18 final size:18
Alignment explanation
Indices: 188288--188339 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
188278 GGGTCTATGC
188288 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
188306 GGTCCTTTGGGACATAGT
1 GGTCCTTCGGGACATAGT
188324 GGTCCTTCGGGACATA
1 GGTCCTTCGGGACATA
188340 TGTGTTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.17, C:0.21, G:0.33, T:0.29
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:194060 original size:21 final size:20
Alignment explanation
Indices: 194029--194075 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
194019 AATTCAAAAG
194029 GAAATGAAATGAAGTACAGAA
1 GAAATGAAATGAAGTA-AGAA
194050 TGAAA-GAAATGAAGTAAGAA
1 -GAAATGAAATGAAGTAAGAA
194070 GAAATG
1 GAAATG
194076 TTTGTCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.17
20 5 0.21
21 11 0.46
22 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.26, T:0.15
Consensus pattern (20 bp):
GAAATGAAATGAAGTAAGAA
Found at i:197171 original size:45 final size:44
Alignment explanation
Indices: 197108--197192 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 44
197098 TTCATAAAAA
*
197108 TTTTCCAATTTTTTTAAGTATAAAAAACATACAAATCGTGATTT
1 TTTTCCAATTTTTCTAAGTATAAAAAACATACAAATCGTGATTT
* *
197152 TTTTCCCAATTTTTCTAAGTATAGAGAACATACAAATCGTG
1 TTTT-CCAATTTTTCTAAGTATAAAAAACATACAAATCGTG
197193 TAAAAAGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 4 0.11
45 33 0.89
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.40
Consensus pattern (44 bp):
TTTTCCAATTTTTCTAAGTATAAAAAACATACAAATCGTGATTT
Found at i:206436 original size:23 final size:23
Alignment explanation
Indices: 206410--206458 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
206400 ATAAAGAACC
*
206410 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
206433 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
206456 AAA
1 AAA
206459 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:206777 original size:17 final size:17
Alignment explanation
Indices: 206757--206798 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
206747 CTCTGTGCGT
206757 GTGTCTCCTCTTCTCCA
1 GTGTCTCCTCTTCTCCA
206774 GTGTCTCCTCTTCTCCA
1 GTGTCTCCTCTTCTCCA
206791 GTGTCTCC
1 GTGTCTCC
206799 CTTGAGGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.05, C:0.40, G:0.14, T:0.40
Consensus pattern (17 bp):
GTGTCTCCTCTTCTCCA
Found at i:207129 original size:13 final size:13
Alignment explanation
Indices: 207111--207136 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
207101 TCAATATTTC
207111 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
207124 TCTTCTTCTTCTT
1 TCTTCTTCTTCTT
207137 CATCGTGAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (13 bp):
TCTTCTTCTTCTT
Found at i:207728 original size:65 final size:63
Alignment explanation
Indices: 207657--207778 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 63
207647 ATTGTTCAAG
207657 GTGTATCGATGCA-CATGAAGTGCATCGATGCACTCCTT-TAAAATAAAAAACATCGAATGTCAT
1 GTGTATCGATGCACCA-GAAGTGCATCGATGCA--CCTTATAAAAT-AAAAACATCGAATGTCAT
207720 TA
62 TA
* * *
207722 GTGTATCGATGCACCAGTAGTGCATCGATGCACCTTATTAAATATAAACATCGAATG
1 GTGTATCGATGCACCAGAAGTGCATCGATGCACCTTATAAAATAAAAACATCGAATG
207779 GGACTTATGC
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
63 17 0.33
64 5 0.10
65 28 0.54
66 2 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (63 bp):
GTGTATCGATGCACCAGAAGTGCATCGATGCACCTTATAAAATAAAAACATCGAATGTCATTA
Found at i:207930 original size:24 final size:24
Alignment explanation
Indices: 207876--207930 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
207866 TCAATATATG
* *
207876 GATGCATGATTCATTTCATATTGT
1 GATGCATGATTCAATTCATATTAT
* *
207900 GAAGCATGATATGAATTCATATTAT
1 GATGCATGAT-TCAATTCATATTAT
207925 -ATGCAT
1 GATGCAT
207931 TATGTAACAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 14 0.56
25 11 0.44
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (24 bp):
GATGCATGATTCAATTCATATTAT
Found at i:208279 original size:23 final size:23
Alignment explanation
Indices: 208227--208287 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
208217 CAATTTTATA
*
208227 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * * *
208250 CGACACTTTGGTGCAATTCTACT
1 TGGCACTTCGGTGCAATTCTACG
208273 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
208288 TTTATACGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:208514 original size:3 final size:3
Alignment explanation
Indices: 208506--208533 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
208496 TGATATTTCT
208506 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
208534 ATTGCCTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:213436 original size:14 final size:14
Alignment explanation
Indices: 213417--213443 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
213407 CACAACTTCA
213417 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
213431 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
213444 TTTACAAAGT
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:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:215246 original size:28 final size:28
Alignment explanation
Indices: 215206--215270 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
215196 GAAAAATCAT
*
215206 TAGGCTCTCTGGCCTTTAAGTCTTCAAA
1 TAGGCTCTCTGGCCTTTAAGTATTCAAA
* *
215234 TAGGCTTTTTGGCCTTTAAGTATTCAAA
1 TAGGCTCTCTGGCCTTTAAGTATTCAAA
*
215262 TAGCCTCTC
1 TAGGCTCTC
215271 ATCAGTTTCC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.38
Consensus pattern (28 bp):
TAGGCTCTCTGGCCTTTAAGTATTCAAA
Found at i:222818 original size:16 final size:16
Alignment explanation
Indices: 222799--222845 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
222789 TAAAACAAAC
222799 AAAAATTAAATTAAAT
1 AAAAATTAAATTAAAT
*
222815 AAAAATTAAATAAAAT
1 AAAAATTAAATTAAAT
*
222831 -AACATTCAAATTAAA
1 AAAAATT-AAATTAAA
222846 AGGGTTAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
15 5 0.19
16 22 0.81
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAATTAAATTAAAT
Found at i:224136 original size:2 final size:2
Alignment explanation
Indices: 224080--224121 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
224070 TTTATATTCT
224080 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
224122 TCAAAATGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:224233 original size:37 final size:36
Alignment explanation
Indices: 224147--224396 Score: 322
Period size: 37 Copynumber: 6.8 Consensus size: 36
224137 CATATTTTCC
* * * *
224147 AAAACGTTTTCAAAATTATATATTATATATATTTTC
1 AAAATGTTTTCAAAACTATATATTATATATTTTTTA
*
224183 AAAATGTTTTCAAAACTATACATTATATATGTTTTTA
1 AAAATGTTTTCAAAACTATATATTATATAT-TTTTTA
*
224220 AAAATATTTTCAAAACTATATATTATATATATTTTTA
1 AAAATGTTTTCAAAACTATATATTATATAT-TTTTTA
* *
224257 AAAATGCTTTCAAAACTATATATTATATATGTTTTCA
1 AAAATGTTTTCAAAACTATATATTATATAT-TTTTTA
*
224294 AAAATGTTTTCAAAACTATATATATTATATATTTTCTA
1 AAAATGTTTTCAAAAC--TATATATTATATATTTTTTA
** *
224332 AAAACATTTTCAAAACTATATATTATATATTTTCTA
1 AAAATGTTTTCAAAACTATATATTATATATTTTTTA
*
224368 AAAACGTTTTCAAAA-TAATATATTATATA
1 AAAATGTTTTCAAAACT-ATATATTATATA
224397 CATATTATGT
Statistics
Matches: 192, Mismatches: 18, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
35 1 0.01
36 73 0.38
37 86 0.45
38 18 0.09
39 14 0.07
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (36 bp):
AAAATGTTTTCAAAACTATATATTATATATTTTTTA
Found at i:226615 original size:2 final size:2
Alignment explanation
Indices: 226608--226639 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
226598 AAAATATGAG
226608 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
226640 GGATGGTTTA
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):
TA
Found at i:231875 original size:149 final size:145
Alignment explanation
Indices: 231597--232586 Score: 979
Period size: 149 Copynumber: 6.9 Consensus size: 145
231587 CCTAAATCAT
*
231597 TTTATTTCACCCGGCCTACTCCACACGTTA-AGGCGCTCGGCGTAAGATCAGGTCATCCTGCCTA
1 TTTATTTCACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
* * * *
231661 CTCCCCTCTGGAAGCGCTCGGCATAAACTCTGTCTACCCTGCCTACCCCACACGTTGAGGCGCTC
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCT-CCCTGCCTACTCTACACGTTGA-ACGCTC
* * * *
231726 GACCTGATATTAAAGCGCA
128 GGCGTGACATT-AAGCACA
* *
231745 TTATATTTCACCCGACCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
1 TT-TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
* * * * *
231810 CTCCCCTCTAGAAGCGCTAGGCATGAACTCTGTCTACCCTGCTTACCCTACACGTTGAGATGCTC
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCT-CCCTGCCTACTCTACACGTTGA-ACGCTC
231875 GGCGTGA-A-T-----C-
128 GGCGTGACATTAAGCACA
** * * * *
231885 TGGGA---CACCCTGCCTACTCCATACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTA
1 T-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
* * * *
231947 CTCCCCTTTGGAAGCGCTCGACATGCACTCTGTCTCCTCTGCCTACTCT-CAACGTTGAAGCGTT
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCC-CTGCCTACTCTAC-ACGTTGAA-CGCT
232011 CGGCGTGACATTAAGGCACA
127 CGGCGTGACATTAA-GCACA
232031 TCTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
1 T-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
* * *
232096 CTTCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTC
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCC-CTGCCTACTCTACACGTTGAA-CGCTC
232161 GGCGTGACATTAAGGCACA
128 GGCGTGACATTAA-GCACA
*
232180 TCTTGTTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
1 T-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTA
* * *
232245 CTCCCCTCTGGAAGCGCTCGGCATGTACTCTGTCCCCCCTGCCTACTCT-CAACGTTGAAGTGCT
65 CTCCCCTCTGGAAGCGCTCGGCATGAACTCTGT-CTCCCTGCCTACTCTAC-ACGTTGAA-CGCT
232309 CGGCGTG--A-T------A
127 CGGCGTGACATTAAGCACA
** * * * *
232319 -TTATAACACCCTGCCTACTCCACACGTTAGAGCGCCCGGCGTAAGATCAAGTCATCCTGCCTAC
1 TTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTAC
* * * * * *
232383 TCCCCACTGGAAGCGCTCGGCATGAACTCTATCCCCCTTCCAACTCTTA-ACGGTGAAGCGCTCG
66 TCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACTC-TACACGTTGAA-CGCTCG
* * *
232447 GCGTGAAAAT-AG--GA
129 GCGTGACATTAAGCACA
* * * * * * *
232461 ---A--T-ACCCTGCCTACCCCATACATTAGAGCGCCCGGCGTAAGATCAGGTCATCCGGCCTAC
1 TTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTAC
* * * * *
232520 TCCCCACTGGAAGCGCTCGGCATGAACTCTGTCCCCCTTCCAACTCTTA-ATGTTGAAGCGCTCG
66 TCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACTC-TACACGTTGAA-CGCTCG
232584 GCG
129 GCG
232587 AAATTCCTTA
Statistics
Matches: 743, Mismatches: 70, Indels: 69
0.84 0.08 0.08
Matches are distributed among these distances:
136 34 0.05
137 310 0.42
138 2 0.00
139 3 0.00
140 3 0.00
141 1 0.00
142 1 0.00
145 1 0.00
146 3 0.00
147 2 0.00
148 3 0.00
149 377 0.51
150 3 0.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (145 bp):
TTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTAC
TCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACTCTACACGTTGAACGCTCGGC
GTGACATTAAGCACA
Found at i:232002 original size:137 final size:138
Alignment explanation
Indices: 231760--232586 Score: 930
Period size: 137 Copynumber: 5.9 Consensus size: 138
231750 TTTCACCCGA
* *
231760 CCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTAGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * *
231825 GCTAGGCATGAACTCTGTCTACCCTGCTTACCCT-ACACGTTG-AGATGCTCGGCGTGA-ATCT-
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCA-ACGTTGAAG-CGCTCGGCGTGACAT-TA
*
231886 GGGACACCCTG
128 GGAACACCCTG
* * * *
231897 CCTACTCCATACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTTTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * *
231962 GCTCGACATGCACTCTGTCTCCTCTGCCTACTCTCAACGTTGAAGCGTTCGGCGTGACATTAAGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCGTGACATT-AGG
*
232027 CACATCTTATTTCACCCGG
130 ---A----A---CACCCTG
*
232046 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTTCCCTCTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * *
232111 GCTCGGCATGTACTCTGTCTCCTCTGCCTACTCTAAACGTTGAAGCGCTCGGCGTGACATTAAGG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCGTGACATT-AGG
*
232176 CACATCTTGTTTCACCCGG
130 -A-A--------CACCCTG
232195 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * *
232260 GCTCGGCATGTACTCTGTCCCCCCTGCCTACTCTCAACGTTGAAGTGCTCGGCGTGATATTA-TA
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCGTGACATTAGGA
232324 ACACCCTG
131 ACACCCTG
* * * *
232332 CCTACTCCACACGTTAGAGCGCCCGGCGTAAGATCAAGTCATCCTGCCTACTCCCCACTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * * * * *
232397 GCTCGGCATGAACTCTATC-CCCCTTCCAACTCTTAACGGTGAAGCGCTCGGCGTGAAAATAGGA
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCGTGACATTAGGA
*
232461 ATACCCTG
131 ACACCCTG
* * * * * * *
232469 CCTACCCCATACATTAGAGCGCCCGGCGTAAGATCAGGTCATCCGGCCTACTCCCCACTGGAAGC
1 CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
* * * *
232534 GCTCGGCATGAACTCTGTC-CCCCTTCCAACTCTTAATGTTGAAGCGCTCGGCG
66 GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCG
232587 AAATTCCTTA
Statistics
Matches: 611, Mismatches: 58, Indels: 42
0.86 0.08 0.06
Matches are distributed among these distances:
136 35 0.06
137 305 0.50
138 5 0.01
139 2 0.00
144 1 0.00
145 1 0.00
146 2 0.00
147 2 0.00
148 1 0.00
149 257 0.42
ACGTcount: A:0.20, C:0.34, G:0.22, T:0.24
Consensus pattern (138 bp):
CCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTCTGGAAGC
GCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCGTGACATTAGGA
ACACCCTG
Found at i:232128 original size:286 final size:280
Alignment explanation
Indices: 231604--232586 Score: 1110
Period size: 286 Copynumber: 3.5 Consensus size: 280
231594 CATTTTATTT
231604 CACCCGGCCTACTCCACACGTTA-AGGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCT
1 CACCCGGCCTACTCCACACGTTAGA-GCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCT
* * * * * *
231668 CTGGAAGCGCTCGGCATAAACTCTGTCTACCCTGCCTAC-CCCACACGTTGAGGCGCTCGACCTG
65 CTGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCA-ACGTTGAAGCGCTCGGCGTG
* *
231732 ATATTAAAGCGCATTATATTTCACCCGACCTACTCCACACGTTAGGGCGCTCGGCGTAAGACCAG
129 A-ATT-AAGC-CATT-TATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAG
* * *
231797 GTCATCCTGCCTACTCCCCTCTAGAAGCGCTAGGCATGAACTCTGTCTACCCTGCTTACCCTACA
190 GTCATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCT-CCCTGCCTACCCTA-A
*
231862 CGTTG-AGATGCTCGGCGTGAATCT-GGGA
253 CGTTGAAG-CGCTCGGCGTGAAT-TAGGGA
* * * *
231890 CACCCTGCCTACTCCATACGTTAGAGCGCTCGACGTAAGATCAGGTCATCCTGCCTACTCCCCTT
1 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
* * * *
231955 TGGAAGCGCTCGACATGCACTCTGTCTCCTCTGCCTACTCTCAACGTTGAAGCGTTCGGCGTGAC
66 TGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCGTGA-
232020 ATTAAGGCACATCTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGT
130 ATTAA-GC-CAT-TTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGT
* * *
232085 CATCCTGCCTACTTCCCTCTGGAAGCGCTCGGCATGTACTCTGTCTCCTCTGCCTACTCTAAACG
192 CATCCTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCC-CTGCCTACCCT-AACG
*
232150 TTGAAGCGCTCGGCGTGACATTAAGGCACATCTTGTTT
255 TTGAAGCGCTCGGCGTGA-ATT-AGG--------G--A
*
232188 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATCCTGCCTACTCCCCTC
1 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
* * *
232253 TGGAAGCGCTCGGCATGTACTCTGTCCCCCCTGCCTACTCTCAACGTTGAAGTGCTCGGCGTG-A
66 TGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCGTGAA
** * * * *
232317 -T-----A-TTATAACACCCTGCCTACTCCACACGTTAGAGCGCCCGGCGTAAGATCAAGTCATC
131 TTAAGCCATTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATC
* * * * * * *
232375 CTGCCTACTCCCCACTGGAAGCGCTCGGCATGAACTCTATCCCCCTTCCAACTCTTAACGGTGAA
196 CTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTAC-CCTAACGTTGAA
* *
232440 GCGCTCGGCGTGAAAATAGGAA
260 GCGCTCGGCGTG-AATTAGGGA
* * * * * * * *
232462 TACCCTGCCTACCCCATACATTAGAGCGCCCGGCGTAAGATCAGGTCATCCGGCCTACTCCCCAC
1 CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
* * * *
232527 TGGAAGCGCTCGGCATGAACTCTGTC-CCCCTTCCAACTCTTAATGTTGAAGCGCTCGGCG
66 TGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCG
232587 AAATTCCTTA
Statistics
Matches: 604, Mismatches: 71, Indels: 57
0.83 0.10 0.08
Matches are distributed among these distances:
273 29 0.05
274 81 0.13
284 3 0.00
285 32 0.05
286 326 0.54
287 10 0.02
288 3 0.00
295 1 0.00
296 2 0.00
298 117 0.19
ACGTcount: A:0.21, C:0.35, G:0.21, T:0.23
Consensus pattern (280 bp):
CACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGATCAGGTCATCCTGCCTACTCCCCTC
TGGAAGCGCTCGGCATGAACTCTGTCTCCCCTGCCTACTCTCAACGTTGAAGCGCTCGGCGTGAA
TTAAGCCATTTATTTCACCCGGCCTACTCCACACGTTAGAGCGCTCGGCGTAAGACCAGGTCATC
CTGCCTACTCCCCTCTGGAAGCGCTCGGCATGAACTCTGTCTCCCTGCCTACCCTAACGTTGAAG
CGCTCGGCGTGAATTAGGGA
Found at i:253094 original size:63 final size:63
Alignment explanation
Indices: 253022--253180 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 63
253012 GGTGCACCAA
* * *
253022 GTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGCGTGCATCGATGCATG
1 GTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGCGCATCGATGCATG
* **
253084 GCTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGCGCATCGATGCATG
1 G-TGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGCGCATCGATGCATG
* * *
253148 GAGAATGCATCGGTGCATGGAATGCATTCGATG
1 GTG--TGCATCGATGCATGAAATGCATTCGATG
253181 ATTCAATTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
62 1 0.01
63 30 0.36
64 27 0.33
65 25 0.30
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (63 bp):
GTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGCGCATCGATGCATG
Found at i:253172 original size:17 final size:19
Alignment explanation
Indices: 253135--253180 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
253125 TATTCAGAGC
253135 GCATCGATGCATGGAGAAT
1 GCATCGATGCATGGAGAAT
*
253154 GCATCGGTGCAT-G-GAAT
1 GCATCGATGCATGGAGAAT
253171 GCATTCGATG
1 GCA-TCGATG
253181 ATTCAATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.29
18 6 0.25
19 11 0.46
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (19 bp):
GCATCGATGCATGGAGAAT
Found at i:261341 original size:64 final size:65
Alignment explanation
Indices: 261273--261413 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 65
261263 GAACACTTGA
* *
261273 TGCATCGGTGCACCAAGTGTGCATCGATGCATGAAATGCATTCAATG-TTTGAAAATAGCCTGCG
1 TGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAATAGCCTGCG
***** * ** * *
261337 TGCATCGATGCATGGCTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAATAGCCTGCG
261402 TGCATCGATGCA
1 TGCATCGATGCA
261414 TGGAGAATGC
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 39 0.61
65 25 0.39
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (65 bp):
TGCATCGATGCACCAAGTGTGCATCGATGCATCAAATGCATTCAATGTTTTGAAAATAGCCTGCG
Found at i:261425 original size:65 final size:65
Alignment explanation
Indices: 261292--261451 Score: 205
Period size: 65 Copynumber: 2.5 Consensus size: 65
261282 GCACCAAGTG
* * * ****
261292 TGCATCGATGCATGAAATGCATTCAATG-TTTGAAAATAGCCTGCGTGCATCGATGCATGGCTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* **
261356 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* *
261421 TGCATCGGTGCATGGAATGCATTCGATGTTT
1 TGCATCGATGCATGAAATGCATTCGATGTTT
261452 CAATTAATTC
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 26 0.32
65 56 0.68
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.31
Consensus pattern (65 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
Found at i:261440 original size:17 final size:19
Alignment explanation
Indices: 261402--261448 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
261392 ATATTCAGAG
261402 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
261421 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
261438 TGCATTCGATG
1 TGCA-TCGATG
261449 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:262540 original size:18 final size:18
Alignment explanation
Indices: 262517--262559 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
262507 CTCATTCTTT
262517 GAAGTCTATCTCTTGTAG
1 GAAGTCTATCTCTTGTAG
262535 GAAGTCTATCTCTTGTAG
1 GAAGTCTATCTCTTGTAG
*
262553 AAAGTCT
1 GAAGTCT
262560 GTCCAAGTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (18 bp):
GAAGTCTATCTCTTGTAG
Found at i:267235 original size:23 final size:23
Alignment explanation
Indices: 267180--267236 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
267170 TCGATTAACA
* *
267180 TTCATTAACATATTCTTTTAGTG
1 TTCATCAACATATTCATTTAGTG
**
267203 TTTGTCAACATATTCATTTAGTG
1 TTCATCAACATATTCATTTAGTG
*
267226 TTCATGAACAT
1 TTCATCAACAT
267237 TTTCCATTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.14, G:0.11, T:0.47
Consensus pattern (23 bp):
TTCATCAACATATTCATTTAGTG
Found at i:272475 original size:29 final size:29
Alignment explanation
Indices: 272420--272581 Score: 202
Period size: 29 Copynumber: 5.6 Consensus size: 29
272410 ACCCGACCCA
* *
272420 GTGATATTCTGGG-AATTTTTGTGAAAAAG
1 GTGACATTCTGGGAAATATTT-TGAAAAAG
** * *
272449 AAGACATTCTGGGAAATATTTTAAAAAAT
1 GTGACATTCTGGGAAATATTTTGAAAAAG
*
272478 GTGACATTATGGGAAATATTTTGAAAAAG
1 GTGACATTCTGGGAAATATTTTGAAAAAG
272507 GTGACATTCTGGGAAATATTTTGAAAAAG
1 GTGACATTCTGGGAAATATTTTGAAAAAG
*
272536 GTGACATGT-TGGGAATTATTTTGAAAAAG
1 GTGACAT-TCTGGGAAATATTTTGAAAAAG
* *
272565 GTGATATTTTGGGAAAT
1 GTGACATTCTGGGAAAT
272582 TTTGAATGTT
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
28 1 0.01
29 107 0.93
30 7 0.06
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.34
Consensus pattern (29 bp):
GTGACATTCTGGGAAATATTTTGAAAAAG
Found at i:279391 original size:17 final size:18
Alignment explanation
Indices: 279366--279410 Score: 74
Period size: 17 Copynumber: 2.6 Consensus size: 18
279356 GAACCGGTCA
279366 GACCCGACCCGACCAGTT
1 GACCCGACCCGACCAGTT
*
279384 GA-CCGACCCGACCCGTT
1 GACCCGACCCGACCAGTT
279401 GACCCGACCC
1 GACCCGACCC
279411 AGTGACATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.20, C:0.49, G:0.22, T:0.09
Consensus pattern (18 bp):
GACCCGACCCGACCAGTT
Found at i:279517 original size:57 final size:56
Alignment explanation
Indices: 279411--279555 Score: 143
Period size: 57 Copynumber: 2.5 Consensus size: 56
279401 GACCCGACCC
** * *
279411 AGTGACATTCTGGGAATTTTTGTGAAAAGGTGACATTTTGGGACATATTTTGAAAA
1 AGTGACATTCTGGGAATTTTTGTGAAAAAATGACATTCTGGGACATATTTTAAAAA
* *
279467 AGTGACATTTTGGGAAATATTTT-TTAAAAAATGACATTCTGGGA-ATTATTTTAAAAAAA
1 AGTGACATTCTGGG-AAT-TTTTGTGAAAAAATGACATTCTGGGACA-TATTTT--AAAAA
*
279526 AGGTGACATGCTGGGAATTATTT-TGAAAAA
1 A-GTGACATTCTGGGAATT-TTTGTGAAAAA
279556 GGTGATATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
56 14 0.19
57 26 0.36
58 5 0.07
59 17 0.23
60 11 0.15
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.35
Consensus pattern (56 bp):
AGTGACATTCTGGGAATTTTTGTGAAAAAATGACATTCTGGGACATATTTTAAAAA
Found at i:279572 original size:29 final size:29
Alignment explanation
Indices: 279412--279573 Score: 163
Period size: 29 Copynumber: 5.6 Consensus size: 29
279402 ACCCGACCCA
279412 GTGACATTCTGGGAATT-TTTGTG-AAAAG
1 GTGACATTCTGGGAATTATTT-TGAAAAAG
*
279440 GTGACATTTTGGGACA-TATTTTGAAAAA-
1 GTGACATTCTGGGA-ATTATTTTGAAAAAG
* * *
279468 GTGACATTTTGGGAAATATTTTTTAAAAA-
1 GTGACATTCTGGGAATTA-TTTTGAAAAAG
* *
279497 ATGACATTCTGGGAATTATTTTAAAAAAAAG
1 GTGACATTCTGGGAATTATTTT--GAAAAAG
*
279528 GTGACATGCTGGGAATTATTTTGAAAAAG
1 GTGACATTCTGGGAATTATTTTGAAAAAG
* *
279557 GTGATATTTTGGGAATT
1 GTGACATTCTGGGAATT
279574 TTCAAATGTG
Statistics
Matches: 114, Mismatches: 12, Indels: 15
0.81 0.09 0.11
Matches are distributed among these distances:
27 1 0.01
28 36 0.32
29 52 0.46
30 5 0.04
31 20 0.18
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.36
Consensus pattern (29 bp):
GTGACATTCTGGGAATTATTTTGAAAAAG
Found at i:284175 original size:22 final size:22
Alignment explanation
Indices: 284149--284208 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
284139 TTGGCGCAGA
*
284149 GGGAATCAATACCCCCTTGA-AG
1 GGGAATCGATACCCCCTT-ATAG
* *
284171 GGGAACCGATTCCCCC-TATAG
1 GGGAATCGATACCCCCTTATAG
284192 GGGAATCGATACCCCCT
1 GGGAATCGATACCCCCT
284209 GAGGGTTCTG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 17 0.55
22 13 0.42
ACGTcount: A:0.27, C:0.32, G:0.23, T:0.18
Consensus pattern (22 bp):
GGGAATCGATACCCCCTTATAG
Found at i:287254 original size:22 final size:22
Alignment explanation
Indices: 287224--287267 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
287214 TAATGGTTAC
*
287224 TTTTTTTCTTATATTAATATTA
1 TTTTCTTCTTATATTAATATTA
287246 TTTTCTTCTTATATTAATATTA
1 TTTTCTTCTTATATTAATATTA
287268 ATGTACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTCTTCTTATATTAATATTA
Found at i:287570 original size:12 final size:12
Alignment explanation
Indices: 287553--287603 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
287543 TTCAAAGAGG
287553 TTTTATATTTAA
1 TTTTATATTTAA
287565 TTTTATA-TTATA
1 TTTTATATTTA-A
*
287577 TTTGAT-TTTAA
1 TTTTATATTTAA
287588 TTTTA-ATTTTAA
1 TTTTATA-TTTAA
287600 TTTT
1 TTTT
287604 TTTAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 8 0.24
12 25 0.76
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATATTTAA
Found at i:287596 original size:17 final size:17
Alignment explanation
Indices: 287553--287603 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
287543 TTCAAAGAGG
287553 TTTTATATTTAATTTTA
1 TTTTATATTTAATTTTA
* *
287570 TATTATATTTGATTTTAA
1 TTTTATATTTAATTTT-A
287588 TTTTA-ATTTTAATTTT
1 TTTTATA-TTTAATTTT
287604 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 15 0.54
18 13 0.46
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTATATTTAATTTTA
Done.