Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015089.1 Kokia drynarioides strain JFW-HI SEQ_130133, 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: 302494
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 460 characters in sequence are not A, C, G, or T
Found at i:5334 original size:20 final size:21
Alignment explanation
Indices: 5287--5334 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
5277 TAAAAAAATT
5287 AATTCAATTAGTTCGGTACATA
1 AATT-AATTAGTTCGGTACATA
* *
5309 AA-TAATTATTTCGGTAGA-A
1 AATTAATTAGTTCGGTACATA
5328 AATTAAT
1 AATTAAT
5335 AAAAACTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 3 0.13
20 17 0.74
21 1 0.04
22 2 0.09
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (21 bp):
AATTAATTAGTTCGGTACATA
Found at i:5534 original size:12 final size:11
Alignment explanation
Indices: 5517--5567 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
5507 CTACTCTACT
5517 AAATAAAAATAA
1 AAATAAAAAT-A
*
5529 AAATAACAAATT
1 AAATAA-AAATA
*
5541 AAATAAAAATT
1 AAATAAAAATA
*
5552 AAATTAAAA-A
1 AAATAAAAATA
5562 AAATAA
1 AAATAA
5568 TTTATAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
10 5 0.15
11 13 0.38
12 12 0.35
13 4 0.12
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:5546 original size:18 final size:18
Alignment explanation
Indices: 5523--5567 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
5513 TACTAAATAA
5523 AAATAAAAATAACAAATT
1 AAATAAAAATAACAAATT
*
5541 AAATAAAAAT--TAAATT
1 AAATAAAAATAACAAATT
5557 AAA-AAAAATAA
1 AAATAAAAATAA
5568 TTTATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.25
16 8 0.33
18 10 0.42
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (18 bp):
AAATAAAAATAACAAATT
Found at i:5557 original size:16 final size:15
Alignment explanation
Indices: 5536--5565 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
5526 TAAAAATAAC
5536 AAATTAAATAAAAATT
1 AAATTAAA-AAAAATT
5552 AAATTAAAAAAAAT
1 AAATTAAAAAAAAT
5566 AATTTATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATTAAAAAAAATT
Found at i:5919 original size:22 final size:22
Alignment explanation
Indices: 5894--5941 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
5884 CTTTCAATTA
* *
5894 CCCTTAATACCAAGGTCCCTCT
1 CCCTGAATACCAAGATCCCTCT
5916 CCCTGAATACCAAGATCCCTCT
1 CCCTGAATACCAAGATCCCTCT
5938 CCCT
1 CCCT
5942 CTTTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.44, G:0.08, T:0.25
Consensus pattern (22 bp):
CCCTGAATACCAAGATCCCTCT
Found at i:13241 original size:5 final size:5
Alignment explanation
Indices: 13233--13258 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13223 TGGAGGAGAG
13233 GGGAT GGGAT GGGAT GGGAT GGGAT G
1 GGGAT GGGAT GGGAT GGGAT GGGAT G
13259 AGAGAGGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.62, T:0.19
Consensus pattern (5 bp):
GGGAT
Found at i:22418 original size:12 final size:12
Alignment explanation
Indices: 22403--22465 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 12
22393 TTTAATTATA
22403 TTTAAAAATAAT
1 TTTAAAAATAAT
*
22415 TTT-AAATTAAT
1 TTTAAAAATAAT
*
22426 TTT-AAAATATT
1 TTTAAAAATAAT
22437 TTTAAAAAATTATAT
1 TTT-AAAAA-TA-AT
22452 TTTAAAAAATAAT
1 TTT-AAAAATAAT
22465 T
1 T
22466 AATTTTTACT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
11 19 0.44
12 3 0.07
13 7 0.16
14 4 0.09
15 10 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TTTAAAAATAAT
Found at i:22442 original size:22 final size:23
Alignment explanation
Indices: 22391--22465 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 23
22381 AATGATTATG
22391 ATTTT-AATTATATTTAAAAATA
1 ATTTTAAATTATATTTAAAAATA
*
22413 ATTTTAAATTA-ATTTTAAAATA
1 ATTTTAAATTATATTTAAAAATA
*
22435 TTTTTAAAAAATTATATTTTAAAAAATA
1 ATTTT---AAATTATA-TTT-AAAAATA
22463 ATT
1 ATT
22466 AATTTTTACT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
22 19 0.45
23 5 0.12
25 6 0.14
26 1 0.02
27 3 0.07
28 8 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTTTAAATTATATTTAAAAATA
Found at i:22453 original size:16 final size:15
Alignment explanation
Indices: 22418--22461 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
22408 AAATAATTTT
22418 AAATTA-ATTTT--A
1 AAATTATATTTTAAA
22430 AAA-TAT-TTTTAAA
1 AAATTATATTTTAAA
22443 AAATTATATTTTAAA
1 AAATTATATTTTAAA
22458 AAAT
1 AAAT
22462 AATTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 6 0.22
12 3 0.11
13 4 0.15
14 3 0.11
15 11 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATTATATTTTAAA
Found at i:23578 original size:22 final size:22
Alignment explanation
Indices: 23544--23590 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
23534 TGGATACTTT
*
23544 TGTAAGAATCATCATATATTCC
1 TGTAAGAACCATCATATATTCC
*
23566 TGTAATAACCATCATATATTCC
1 TGTAAGAACCATCATATATTCC
23588 TGT
1 TGT
23591 GTGTTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (22 bp):
TGTAAGAACCATCATATATTCC
Found at i:24776 original size:24 final size:25
Alignment explanation
Indices: 24749--24802 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
24739 GTTGCTATTG
*
24749 CATCTTGAATT-TCTCTTCCTTG-TT
1 CATCTTAAATTAT-TCTTCCTTGATT
*
24773 CATCTAAAATTATTCTTCCTTGATT
1 CATCTTAAATTATTCTTCCTTGATT
24798 -ATCTT
1 CATCTT
24803 TTTTTATTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.20, C:0.22, G:0.06, T:0.52
Consensus pattern (25 bp):
CATCTTAAATTATTCTTCCTTGATT
Found at i:26734 original size:11 final size:11
Alignment explanation
Indices: 26718--26748 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
26708 ATGAATGCTC
26718 ATAAAATTCAT
1 ATAAAATTCAT
26729 ATAAAATTCAT
1 ATAAAATTCAT
26740 ATAAAATTC
1 ATAAAATTC
26749 TTTGAATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAAAATTCAT
Found at i:29959 original size:19 final size:20
Alignment explanation
Indices: 29935--29972 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29925 ATTGAAGAAA
*
29935 TGGAAT-GAAGGGCATGTTG
1 TGGAATGGAAGAGCATGTTG
29954 TGGAATGGAAGAGCATGTT
1 TGGAATGGAAGAGCATGTT
29973 AGTTTTGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.29, C:0.05, G:0.39, T:0.26
Consensus pattern (20 bp):
TGGAATGGAAGAGCATGTTG
Found at i:38559 original size:69 final size:69
Alignment explanation
Indices: 38475--38607 Score: 185
Period size: 69 Copynumber: 1.9 Consensus size: 69
38465 CTGCAAAGAA
* * * *
38475 AAAAAACAAAGTGAACAGTGAGATTCCCTGACGTGAACAATGAGATTTTCTGACAATATTCTCTC
1 AAAAAACAAAATGAACAGTGAGATTCCCTGACGTGAACAATAAGATTCTCTGACAAGATTCTCTC
38540 CAAG
66 CAAG
* *** *
38544 AAAAAACAAAATGAACATTGAGATTTTTTGACGTGAACAGTAAGATTCTCTGACAAGATTCTCT
1 AAAAAACAAAATGAACAGTGAGATTCCCTGACGTGAACAATAAGATTCTCTGACAAGATTCTCT
38608 TATAATTTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
69 55 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (69 bp):
AAAAAACAAAATGAACAGTGAGATTCCCTGACGTGAACAATAAGATTCTCTGACAAGATTCTCTC
CAAG
Found at i:38827 original size:14 final size:14
Alignment explanation
Indices: 38808--38843 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
38798 TTTAACTTTC
*
38808 AATTTTAAAATTTA
1 AATTTTAAAATTCA
*
38822 AGTTTTAAAATTCA
1 AATTTTAAAATTCA
38836 AATTTTAA
1 AATTTTAA
38844 TTACATTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (14 bp):
AATTTTAAAATTCA
Found at i:47207 original size:39 final size:39
Alignment explanation
Indices: 47153--47230 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
47143 AATCTTCTTA
47153 TATGAATCTGCATGTATAAGTTCAT-CATATCTATGAATC
1 TATGAATCTGCATGTATAAG-TCATCCATATCTATGAATC
* * *
47192 TATGAATTTGCATGTATGAGTCCTCCATATCTATGAATC
1 TATGAATCTGCATGTATAAGTCATCCATATCTATGAATC
47231 CACATGTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 3 0.09
39 32 0.91
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (39 bp):
TATGAATCTGCATGTATAAGTCATCCATATCTATGAATC
Found at i:47227 original size:31 final size:31
Alignment explanation
Indices: 47202--47261 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
47192 TATGAATTTG
47202 CATGTATGAGTC-CTCCATATCTATGAATCCA
1 CATGTATGAGTCACT-CATATCTATGAATCCA
*
47233 CATGTATGAGTCAGTCATATCTATGAATC
1 CATGTATGAGTCACTCATATCTATGAATC
47262 TTCTACTATG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (31 bp):
CATGTATGAGTCACTCATATCTATGAATCCA
Found at i:47271 original size:45 final size:45
Alignment explanation
Indices: 47222--47400 Score: 220
Period size: 45 Copynumber: 4.0 Consensus size: 45
47212 TCCTCCATAT
* *
47222 CTATGAATCCACATGTATGAG-TCAGTCATATCTATGAATCTTCTA
1 CTATGAATCCACATATATGAGTTCA-CCATATCTATGAATCTTCTA
* **
47267 CTATGAGTCTGCATATATGAGTTCACCATATCTATGAATCTTCTA
1 CTATGAATCCACATATATGAGTTCACCATATCTATGAATCTTCTA
* * *
47312 CTATGAAT-CAGCATATTTGAGTTCGCCATATCCATGAATCTTCTA
1 CTATGAATCCA-CATATATGAGTTCACCATATCTATGAATCTTCTA
* *
47357 CCATGAA-CACACATGTATGAGTTCACCATATCTATGAATCTTCT
1 CTATGAATC-CACATATATGAGTTCACCATATCTATGAATCTTCT
47401 TTTACGAGTT
Statistics
Matches: 114, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
45 109 0.96
46 5 0.04
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (45 bp):
CTATGAATCCACATATATGAGTTCACCATATCTATGAATCTTCTA
Found at i:47272 original size:14 final size:15
Alignment explanation
Indices: 47247--47320 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 15
47237 TATGAGTCAG
47247 TCATATCTATGAATCT
1 TCATA-CTATGAATCT
*
47263 TC-TACTATGAGTCT
1 TCATACTATGAATCT
* * *
47277 GCATA-TATGAGTTCA
1 TCATACTATGA-ATCT
*
47292 CCATATCTATGAATCT
1 TCATA-CTATGAATCT
47308 TC-TACTATGAATC
1 TCATACTATGAATC
47321 AGCATATTTG
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
14 24 0.52
15 12 0.26
16 5 0.11
17 5 0.11
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (15 bp):
TCATACTATGAATCT
Found at i:47417 original size:45 final size:45
Alignment explanation
Indices: 47233--47424 Score: 210
Period size: 45 Copynumber: 4.3 Consensus size: 45
47223 TATGAATCCA
* *
47233 CATGTATGAG-TCAGTCATATCTATGAATCTTCTACTATGAGTCTG
1 CATGTATGAGTTCA-CCATATCTATGAATCTTCTACTATGAGTCAG
* *
47278 CATATATGAGTTCACCATATCTATGAATCTTCTACTATGAATCAG
1 CATGTATGAGTTCACCATATCTATGAATCTTCTACTATGAGTCAG
* * * * * * *
47323 CATATTTGAGTTCGCCATATCCATGAATCTTCTACCATGA-ACACA
1 CATGTATGAGTTCACCATATCTATGAATCTTCTACTATGAGTCA-G
** *
47368 CATGTATGAGTTCACCATATCTATGAATCTTCTTTTACGAGTTC-G
1 CATGTATGAGTTCACCATATCTATGAATCTTCTACTATGAG-TCAG
47413 CATGTATGAGTT
1 CATGTATGAGTT
47425 AGCAAATAAG
Statistics
Matches: 123, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
44 2 0.02
45 117 0.95
46 3 0.02
47 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (45 bp):
CATGTATGAGTTCACCATATCTATGAATCTTCTACTATGAGTCAG
Found at i:49071 original size:55 final size:54
Alignment explanation
Indices: 49006--49144 Score: 134
Period size: 58 Copynumber: 2.5 Consensus size: 54
48996 TCTTCTTAAT
* * * * *
49006 TGTTGGAATACTGCTTCTTTTGAATTAATTTTTTATATGTTTAAATCGATTGTTA
1 TGTT-GAATACTACTTCTTTTGAATCAATTATCTATATATTTAAATCGATTGTTA
* * * *
49061 TGTTAGAATACTACTTTTTTTTTTAAATCGATTATCTATATATTTAAATTGATTGTTA
1 TGTT-GAATACTAC---TTCTTTTGAATCAATTATCTATATATTTAAATCGATTGTTA
*
49119 TGTTGAAATATTACTTCTTTTGAATC
1 TGTTG-AATACTACTTCTTTTGAATC
49145 GATTGTTACA
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
55 22 0.33
57 1 0.01
58 44 0.66
ACGTcount: A:0.28, C:0.08, G:0.12, T:0.53
Consensus pattern (54 bp):
TGTTGAATACTACTTCTTTTGAATCAATTATCTATATATTTAAATCGATTGTTA
Found at i:50104 original size:6 final size:6
Alignment explanation
Indices: 50093--50178 Score: 85
Period size: 6 Copynumber: 15.2 Consensus size: 6
50083 GACCCAAATA
* *
50093 AAATTT AAATTT AAATTT -ATTTT AAGTTT AAATTT --ATTT GAAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT
* *
50139 AAATTT -ATTTT AAATTT AAGTTT AAATTT --ATTT AAATTT A
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT A
50179 TTAATGTCTC
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
4 8 0.12
5 8 0.12
6 46 0.70
7 4 0.06
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (6 bp):
AAATTT
Found at i:50116 original size:17 final size:17
Alignment explanation
Indices: 50096--50180 Score: 111
Period size: 17 Copynumber: 5.1 Consensus size: 17
50086 CCAAATAAAA
50096 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
50113 TTTAAGTTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
50130 TTGAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
* *
50147 TTTAAATTTAAGTTTAAA
1 TTTAAATTTAAATTT-AT
50165 TTT--ATTTAAATTTAT
1 TTTAAATTTAAATTTAT
50180 T
1 T
50181 AATGTCTCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
15 2 0.03
16 9 0.15
17 44 0.75
18 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.58
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:50137 original size:40 final size:39
Alignment explanation
Indices: 50093--50178 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 39
50083 GACCCAAATA
*
50093 AAATTTAAATTTAAATTT-ATTTTAAGTTTAAATTTATTT
1 AAATTTAAATTT-AATTTAAATTTAAGTTTAAATTTATTT
*
50132 GAAATTTAAATTTATTTTAAATTTAAGTTTAAATTTATTT
1 -AAATTTAAATTTAATTTAAATTTAAGTTTAAATTTATTT
50172 AAATTTA
1 AAATTTA
50179 TTAATGTCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
39 11 0.26
40 32 0.74
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (39 bp):
AAATTTAAATTTAATTTAAATTTAAGTTTAAATTTATTT
Found at i:50139 original size:23 final size:22
Alignment explanation
Indices: 50096--50178 Score: 79
Period size: 23 Copynumber: 3.9 Consensus size: 22
50086 CCAAATAAAA
*
50096 TTTAAATTTAAATTT-ATTTTAAG
1 TTTAAATTT--ATTTAAATTTAAG
*
50119 TTTAAATTTATTT-GA---AA-
1 TTTAAATTTATTTAAATTTAAG
50136 TTTAAATTTATTTTAAATTTAAG
1 TTTAAATTTA-TTTAAATTTAAG
50159 TTTAAATTTATTTAAATTTA
1 TTTAAATTTATTTAAATTTA
50179 TTAATGTCTC
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
17 10 0.20
18 5 0.10
19 1 0.02
21 4 0.08
22 12 0.24
23 19 0.37
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.57
Consensus pattern (22 bp):
TTTAAATTTATTTAAATTTAAG
Found at i:50573 original size:15 final size:17
Alignment explanation
Indices: 50548--50580 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
50538 ATCAATAGAA
50548 AAGCAAATCAA-TTTCC
1 AAGCAAATCAAGTTTCC
50564 AAGC-AATCAAGTTTCC
1 AAGCAAATCAAGTTTCC
50580 A
1 A
50581 TTCAAGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.42, C:0.24, G:0.09, T:0.24
Consensus pattern (17 bp):
AAGCAAATCAAGTTTCC
Found at i:51504 original size:20 final size:20
Alignment explanation
Indices: 51475--51515 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
51465 TAGTCAAAAA
*
51475 TTGTTATTTTCTTCTTTTTT
1 TTGTTATTTTCTTATTTTTT
* *
51495 TTGTTTTTTTTTTATTTTTT
1 TTGTTATTTTCTTATTTTTT
51515 T
1 T
51516 ATTTTTTAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.05, G:0.05, T:0.85
Consensus pattern (20 bp):
TTGTTATTTTCTTATTTTTT
Found at i:53615 original size:30 final size:29
Alignment explanation
Indices: 53353--53617 Score: 211
Period size: 30 Copynumber: 8.9 Consensus size: 29
53343 TCAGAAGGCC
* * *
53353 CCCT-AACTTTTCAAAAATCACATCTTGA
1 CCCTAAACTTTTCCAAAATCACATTTTAA
*
53381 CCTTTAAAC--TTCCAATAATCACATTTTGAA
1 CC-CTAAACTTTTCCAA-AATCACATTTT-AA
53411 -CCTCAAA-TTTTCCCAAAATCACATTTTAA
1 CCCT-AAACTTTT-CCAAAATCACATTTTAA
53440 CCCCTAAAC-TTTCCTAAAATCACATTTTAA
1 -CCCTAAACTTTTCC-AAAATCACATTTTAA
** * *
53470 CCCTAAAACTTTTCCATGATTATATTTTAA
1 CCCT-AAACTTTTCCAAAATCACATTTTAA
* * *
53500 CACCCAAACTTCTCCAAAATCACACTTTAA
1 C-CCTAAACTTTTCCAAAATCACATTTTAA
* * *
53530 CCCCCTAAAC-CTTCTCAAATTCACATTTCAA
1 --CCCTAAACTTTTC-CAAAATCACATTTTAA
*
53561 CCCTAAACTTATCCAAAATCACATTTTAA
1 CCCTAAACTTTTCCAAAATCACATTTTAA
* *
53590 CCCTAAACTTTTTCAAAAATTACATTTT
1 CCCTAAAC-TTTTCCAAAATCACATTTT
53618 TACCATTAAA
Statistics
Matches: 188, Mismatches: 29, Indels: 38
0.74 0.11 0.15
Matches are distributed among these distances:
28 8 0.04
29 53 0.28
30 93 0.49
31 33 0.18
32 1 0.01
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTTTCCAAAATCACATTTTAA
Found at i:65777 original size:39 final size:38
Alignment explanation
Indices: 65728--66017 Score: 167
Period size: 39 Copynumber: 7.4 Consensus size: 38
65718 ACCATTAACT
*
65728 AATCTCTTACCCCGAGCATGGGGCAGATTGAAGTCATCC
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGAA-TCATCC
* * * * * *
65767 GATCTTTTACCCCAAGCTTGAGGCA-AAT-CATCATCTGCC
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGAATCA--T-CC
* * * *
65806 AATCTCTTACCTCAAGCTTGGGGCAGATTTCG-ACCATTC
1 AATCTCTTACCCCGAGCTTGGGGCAGA-TT-GAATCATCC
* * * * *
65845 GATCTTTTATCCCAAGCTTGGGGCAGATTGCAATCATTC
1 AATCTCTTACCCCGAGCTTGGGGCAGATTG-AATCATCC
* * * * * *
65884 GATCTTTTACCCCGAGCCTGGGG-AAAATCACTATCAGT-C
1 AATCTCTTACCCCGAGCTTGGGGCAGATTGA--ATCA-TCC
* * * * *
65923 AATCTCTTACCCCGAGCCTAGGGCAAATTGTAGTCATCT
1 AATCTCTTACCCCGAGCTTGGGGCAGATTG-AATCATCC
* *
65962 AATCTCTTACCCCGAGCTTGGGGTAGATTGTAGTCATCC
1 AATCTCTTACCCCGAGCTTGGGGCAGATTG-AATCATCC
*
66001 AATCTCTTACCTCGAGC
1 AATCTCTTACCCCGAGC
66018 CAATCTCTTA
Statistics
Matches: 198, Mismatches: 38, Indels: 30
0.74 0.14 0.11
Matches are distributed among these distances:
36 3 0.02
37 3 0.02
38 9 0.05
39 171 0.86
40 7 0.04
41 2 0.01
42 3 0.02
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (38 bp):
AATCTCTTACCCCGAGCTTGGGGCAGATTGAATCATCC
Found at i:66017 original size:117 final size:117
Alignment explanation
Indices: 65726--66018 Score: 306
Period size: 117 Copynumber: 2.5 Consensus size: 117
65716 TCACCATTAA
* * * *
65726 CTAATCTCTTACCCCGAGCATGGGGCAGATTGAAGTCATCCGATCTTTTACCCCAAGCTTGAGGC
1 CTAATCTCTTACCCCGAGCTTGGGGCAGATTGAAGTCATCCGATCTTTTACCCCGAGCCTGAGGA
* * * * * *
65791 AAATCATCATCTGCCAATCTCTTACCTCAAGCTTGGGGCAGATTTCGACCAT
66 AAATCATCATCAGCCAATCTCTTACCCCAAGCCTAGGGCAAATTTAGACCAT
* * * * * *
65843 -TCGATCTTTTATCCCAAGCTTGGGGCAGATTGCAA-TCATTCGATCTTTTACCCCGAGCCTGGG
1 CT-AATCTCTTACCCCGAGCTTGGGGCAGATTG-AAGTCATCCGATCTTTTACCCCGAGCCTGAG
* * *
65906 GAAAATCA-CTATCAGTCAATCTCTTACCCCGAGCCTAGGGCAAATTGTAG-TCAT
64 GAAAATCATC-ATCAGCCAATCTCTTACCCCAAGCCTAGGGCAAATT-TAGACCAT
* * * * *
65960 CTAATCTCTTACCCCGAGCTTGGGGTAGATTGTAGTCATCCAATCTCTTACCTCGAGCC
1 CTAATCTCTTACCCCGAGCTTGGGGCAGATTGAAGTCATCCGATCTTTTACCCCGAGCC
66019 AATCTCTTAC
Statistics
Matches: 141, Mismatches: 29, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
116 3 0.02
117 133 0.94
118 5 0.04
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (117 bp):
CTAATCTCTTACCCCGAGCTTGGGGCAGATTGAAGTCATCCGATCTTTTACCCCGAGCCTGAGGA
AAATCATCATCAGCCAATCTCTTACCCCAAGCCTAGGGCAAATTTAGACCAT
Found at i:66022 original size:18 final size:18
Alignment explanation
Indices: 65999--66036 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
65989 TTGTAGTCAT
65999 CCAATCTCTTACCTCGAG
1 CCAATCTCTTACCTCGAG
66017 CCAATCTCTTACCTCGAG
1 CCAATCTCTTACCTCGAG
66035 CC
1 CC
66037 TGAGGCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.42, G:0.11, T:0.26
Consensus pattern (18 bp):
CCAATCTCTTACCTCGAG
Found at i:66146 original size:78 final size:78
Alignment explanation
Indices: 66056--66301 Score: 253
Period size: 78 Copynumber: 3.2 Consensus size: 78
66046 TCACCATCAG
* * *
66056 CCAATCTCTTACCCCGAGCCTAGGGTAGATCA-CTTCCAGCCAATCTCTTACCCCGAGCTTAGGG
1 CCAATCTTTTACCCCGAGCCTAGGGCAGATCACCAT-CAGCCAATCTCTTACCCCGAGCTTAGGG
* ** *
66120 CAGATTGTAGTCAT
65 CAAATTACAGCCAT
* * *
66134 CCGATCTTTTACCCCGAGCCTAGGGCAGGTCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
1 CCAATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTAGGGC
66199 AAATTACAGCCAT
66 AAATTACAGCCAT
* * * * * * * * *
66212 TCAATCTTTTACCCTGATCATGGGGCAGATCACCGTCAGCCAATCTTTTACCCCGCG-ATAGGGG
1 CCAATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTA-GGG
* * *
66276 CAGATTGCAACCAT
65 CAAATTACAGCCAT
*
66290 CCAATCTCTTAC
1 CCAATCTTTTAC
66302 AAAAAAAATC
Statistics
Matches: 139, Mismatches: 27, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
77 1 0.01
78 136 0.98
79 2 0.01
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.25
Consensus pattern (78 bp):
CCAATCTTTTACCCCGAGCCTAGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTAGGGC
AAATTACAGCCAT
Found at i:66258 original size:117 final size:117
Alignment explanation
Indices: 66015--66266 Score: 290
Period size: 117 Copynumber: 2.2 Consensus size: 117
66005 TCTTACCTCG
* *
66015 AGCCAATCTCTTACCTCGAGCCTGAGGCAGGTCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
1 AGCCAATCTTTTACCCCGAGCCTGAGGCAGGTCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
* * ** * ***
66080 GTAGATCACTTCCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTGTAGTC
66 GCAAATCACAGCCAGCCAATCTCTTACCCCGAGCATAGGGCAGATCACAGTC
* * * *
66132 ATCCGATCTTTTACCCCGAGCCT-AGGGCAGGTCACCATCAGCCAATCTCTTACCCCGAGCTTGG
1 AGCCAATCTTTTACCCCGAGCCTGA-GGCAGGTCACCATCAGCCAATCTCTTACCCCGAGCCTAG
* ** * * * * *
66196 GGCAAATTACAGCCATTCAATCTTTTACCCTGATCATGGGGCAGATCACCGTC
65 GGCAAATCACAGCCAGCCAATCTCTTACCCCGAGCATAGGGCAGATCACAGTC
66249 AGCCAATCTTTTACCCCG
1 AGCCAATCTTTTACCCCG
66267 CGATAGGGGC
Statistics
Matches: 110, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
116 1 0.01
117 109 0.99
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (117 bp):
AGCCAATCTTTTACCCCGAGCCTGAGGCAGGTCACCATCAGCCAATCTCTTACCCCGAGCCTAGG
GCAAATCACAGCCAGCCAATCTCTTACCCCGAGCATAGGGCAGATCACAGTC
Found at i:66280 original size:39 final size:39
Alignment explanation
Indices: 66015--66266 Score: 211
Period size: 39 Copynumber: 6.5 Consensus size: 39
66005 TCTTACCTCG
* * *
66015 AGCCAATCTCTTACCTCGAGCCT-GAGGCAGGTCACCATC
1 AGCCAATCTCTTACCCCGAGCCTAG-GGCAGATCACCGTC
* *
66054 AGCCAATCTCTTACCCCGAGCCTAGGGTAGATCA-CTTCC
1 AGCCAATCTCTTACCCCGAGCCTAGGGCAGATCACCGT-C
* ****
66093 AGCCAATCTCTTACCCCGAGCTTAGGGCAGATTGTAGTC
1 AGCCAATCTCTTACCCCGAGCCTAGGGCAGATCACCGTC
* * * * *
66132 ATCCGATCTTTTACCCCGAGCCTAGGGCAGGTCACCATC
1 AGCCAATCTCTTACCCCGAGCCTAGGGCAGATCACCGTC
* * * * * *
66171 AGCCAATCTCTTACCCCGAGCTTGGGGCAAATTACAGCC
1 AGCCAATCTCTTACCCCGAGCCTAGGGCAGATCACCGTC
** * * * * *
66210 ATTCAATCTTTTACCCTGATCATGGGGCAGATCACCGTC
1 AGCCAATCTCTTACCCCGAGCCTAGGGCAGATCACCGTC
*
66249 AGCCAATCTTTTACCCCG
1 AGCCAATCTCTTACCCCG
66267 CGATAGGGGC
Statistics
Matches: 166, Mismatches: 44, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
38 2 0.01
39 162 0.98
40 2 0.01
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.24
Consensus pattern (39 bp):
AGCCAATCTCTTACCCCGAGCCTAGGGCAGATCACCGTC
Found at i:66621 original size:86 final size:86
Alignment explanation
Indices: 66457--66622 Score: 212
Period size: 86 Copynumber: 1.9 Consensus size: 86
66447 TCAAACCCCA
* * *
66457 TCTTCCTGATGAGATACAGAGAAGTAGGTCAAAGTAATAAAGCGGTCACCTTCCTGATAAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTAGATCAAAGTAACAAAACGGTCACCTTCCTGATAAGATAC
*
66522 AGAGAATTGGACCAAAATTTG
66 AGAGAAATGGACCAAAATTTG
* * **
66543 TCTTCCTGATGAGATATAGAGAAGTTA-AT-TAAGTCAACAAAACGGTCATTTTCCTGATAAGAT
1 TCTTCCTGATGAGATACAGAGAAG-TAGATCAAAGT-AACAAAACGGTCACCTTCCTGATAAGAT
66606 ACAGAGAAGAT-GACCAA
64 ACAGAGAA-ATGGACCAA
66623 TTCAATGAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
85 4 0.06
86 62 0.90
87 3 0.04
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (86 bp):
TCTTCCTGATGAGATACAGAGAAGTAGATCAAAGTAACAAAACGGTCACCTTCCTGATAAGATAC
AGAGAAATGGACCAAAATTTG
Found at i:67140 original size:10 final size:10
Alignment explanation
Indices: 67125--67166 Score: 84
Period size: 10 Copynumber: 4.2 Consensus size: 10
67115 AGAATTTAAG
67125 TTTAAATTTA
1 TTTAAATTTA
67135 TTTAAATTTA
1 TTTAAATTTA
67145 TTTAAATTTA
1 TTTAAATTTA
67155 TTTAAATTTA
1 TTTAAATTTA
67165 TT
1 TT
67167 AATATCCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:67551 original size:15 final size:17
Alignment explanation
Indices: 67526--67558 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
67516 ATCAACAGAG
67526 AAGCAAATC-AATTTCC
1 AAGCAAATCAAATTTCC
67542 AAGC-AATCAAATTTCC
1 AAGCAAATCAAATTTCC
67558 A
1 A
67559 TTCAAGGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.45, C:0.24, G:0.06, T:0.24
Consensus pattern (17 bp):
AAGCAAATCAAATTTCC
Found at i:68814 original size:30 final size:30
Alignment explanation
Indices: 68778--68835 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
68768 AAGGCCTCCT
68778 AACTTTCCAAAAATCAC-ATCTTGACCCTCG
1 AACTTTCCAAAAATCACAATC-TGACCCTCG
68808 AACTTTCCAAAAATCACAATCTGACCCT
1 AACTTTCCAAAAATCACAATCTGACCCT
68836 TCCAAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.36, C:0.33, G:0.05, T:0.26
Consensus pattern (30 bp):
AACTTTCCAAAAATCACAATCTGACCCTCG
Found at i:68880 original size:30 final size:29
Alignment explanation
Indices: 68835--69008 Score: 206
Period size: 30 Copynumber: 5.8 Consensus size: 29
68825 AATCTGACCC
* *
68835 TTCCAAAAATCACATTTTAACACTAAAACT
1 TTCCCAAAATCACATTTTAACCCT-AAACT
*
68865 TTCCCAAAATTACATTTTAACCCCTAAACT
1 TTCCCAAAATCACATTTTAA-CCCTAAACT
68895 TTCCCAAAATCACATTTTAACCCTAAACCT
1 TTCCCAAAATCACATTTTAACCCTAAA-CT
* * *
68925 TTTCCAAAATTACATTTTAATCCCCAAAC-
1 TTCCCAAAATCACATTTTAA-CCCTAAACT
*
68954 TTCTCCAAAATCACATTTTGACCCTAAACT
1 TTC-CCAAAATCACATTTTAACCCTAAACT
* *
68984 TTCCCAAAAATTACATTTTTACCCT
1 TTCCC-AAAATCACATTTTAACCCT
69009 TAAATTTTTC
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
29 18 0.14
30 98 0.78
31 9 0.07
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (29 bp):
TTCCCAAAATCACATTTTAACCCTAAACT
Found at i:68932 original size:60 final size:58
Alignment explanation
Indices: 68834--69012 Score: 243
Period size: 60 Copynumber: 3.0 Consensus size: 58
68824 CAATCTGACC
* *
68834 CTTCCAAAAATCACATTTTAACACTAAAACTTTCCCAAAATTACATTTTAACCCCTAAA
1 CTTCCCAAAATCACATTTTAACCCT-AAACTTTCCCAAAATTACATTTTAACCCCTAAA
*
68893 CTTTCCCAAAATCACATTTTAACCCTAAACCTTTTCCAAAATTACATTTTAATCCCC-AAA
1 C-TTCCCAAAATCACATTTTAACCCTAAA-CTTTCCCAAAATTACATTTTAA-CCCCTAAA
* * *
68953 CTTCTCCAAAATCACATTTTGACCCTAAACTTTCCCAAAAATTACATTTTTACCCTTAAA
1 CTTC-CCAAAATCACATTTTAACCCTAAACTTTCCC-AAAATTACATTTTAACCCCTAAA
69013 TTTTTCTAAA
Statistics
Matches: 107, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
59 16 0.15
60 87 0.81
61 4 0.04
ACGTcount: A:0.38, C:0.28, G:0.01, T:0.33
Consensus pattern (58 bp):
CTTCCCAAAATCACATTTTAACCCTAAACTTTCCCAAAATTACATTTTAACCCCTAAA
Found at i:70389 original size:198 final size:198
Alignment explanation
Indices: 70046--70410 Score: 543
Period size: 198 Copynumber: 1.8 Consensus size: 198
70036 ATTATACTAG
* * * * *
70046 TAGTCGAATTGCATTTTACCTTCTCTATTCAAAAAATGGATAAACTAATCTTTATACATTAGATT
1 TAGTCGAATTGCATTTTACCTCCGCTATTAAAAAAATGGACAAACTAATCCTTATACATTAGATT
* * * * * *
70111 AAATAGCAAATTGATCCTTTCAGTTAAAAATTTTATCAATTTGTACTGTTAAAAACTGGCGTGGT
66 AAATAGCAAATTGATCATTTCAGTTAAAAATTTCAGCAATTTGTACTGTTAAAAACTGACATGAT
70176 TGATGGAATAACTAGACAGTGACATGTGACATGCCACATGTCCATTATGTTGACGTGCATGGACC
131 TGATGGAATAACTAGACAGTGACATGTGACATGCCACATGTCCATTATGTTGACGTGCATGGACC
70241 AAT
196 AAT
* * * *
70244 TAGTTGAATTGCATTTTGCCTCCGCTATTAAAAAAATGGGCAAACTAGTCCTTATACATTAGATT
1 TAGTCGAATTGCATTTTACCTCCGCTATTAAAAAAATGGACAAACTAATCCTTATACATTAGATT
* *
70309 AAATAGCAAATTGGTCATTTCTA-TTAAAAATTTCAGCCATTTGTACTGTTAAAAACTGACATGA
66 AAATAGCAAATTGATCATTTC-AGTTAAAAATTTCAGCAATTTGTACTGTTAAAAACTGACATGA
* *
70373 TTGATGGAATAACTAGATAGTGACATGTGATATGCCAC
130 TTGATGGAATAACTAGACAGTGACATGTGACATGCCAC
70411 GTGTACCTTA
Statistics
Matches: 147, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
198 146 0.99
199 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (198 bp):
TAGTCGAATTGCATTTTACCTCCGCTATTAAAAAAATGGACAAACTAATCCTTATACATTAGATT
AAATAGCAAATTGATCATTTCAGTTAAAAATTTCAGCAATTTGTACTGTTAAAAACTGACATGAT
TGATGGAATAACTAGACAGTGACATGTGACATGCCACATGTCCATTATGTTGACGTGCATGGACC
AAT
Found at i:74479 original size:54 final size:54
Alignment explanation
Indices: 74352--74462 Score: 213
Period size: 54 Copynumber: 2.1 Consensus size: 54
74342 CTTAATTAAC
*
74352 AGATGAGAGCGGGGACAAAAGCTAAAAGAAGTACAACACCTTAATTAGACGTTG
1 AGATGAGAGTGGGGACAAAAGCTAAAAGAAGTACAACACCTTAATTAGACGTTG
74406 AGATGAGAGTGGGGACAAAAGCTAAAAGAAGTACAACACCTTAATTAGACGTTG
1 AGATGAGAGTGGGGACAAAAGCTAAAAGAAGTACAACACCTTAATTAGACGTTG
74460 AGA
1 AGA
74463 GGTTTGGTAG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.43, C:0.14, G:0.26, T:0.17
Consensus pattern (54 bp):
AGATGAGAGTGGGGACAAAAGCTAAAAGAAGTACAACACCTTAATTAGACGTTG
Found at i:83819 original size:59 final size:57
Alignment explanation
Indices: 83754--83911 Score: 172
Period size: 59 Copynumber: 2.7 Consensus size: 57
83744 TTGGTAATTC
* * * * *
83754 AACTTGACACTTTTTTTTAATTTGATACTTAAATCTTTTTTTACCTAATTTGGCATCTG
1 AACTTGACA-TTTTTTTTAATTTGGTACCTAAA-CTTTTTTTACCCAATTTGACACCTG
* * * * *
83813 AACTTGACAAATTTTTCTAATTTGGTTCCTAAACTTTTTTGGACCCAATTTGATACCTG
1 AACTTGAC-ATTTTTTTTAATTTGGTACCTAAACTTTTTT-TACCCAATTTGACACCTG
* *
83872 AACTTGGCATTTTTTTTAATTTGGTACCTAAGCTTTTTTT
1 AACTTGACATTTTTTTTAATTTGGTACCTAAACTTTTTTT
83912 TTAAATTCAA
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
58 34 0.42
59 46 0.57
60 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.49
Consensus pattern (57 bp):
AACTTGACATTTTTTTTAATTTGGTACCTAAACTTTTTTTACCCAATTTGACACCTG
Found at i:87674 original size:14 final size:12
Alignment explanation
Indices: 87644--87674 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
87634 GGCCAACATT
*
87644 CGTGTGTTTGCC
1 CGTGTGTTAGCC
87656 CGTGTGTTAGCC
1 CGTGTGTTAGCC
87668 CGTGTGT
1 CGTGTGT
87675 CAAACACACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.03, C:0.23, G:0.35, T:0.39
Consensus pattern (12 bp):
CGTGTGTTAGCC
Found at i:98106 original size:24 final size:23
Alignment explanation
Indices: 98079--98141 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
98069 TTATTAACAT
98079 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* * *
98103 TGTTCATGAAAATGTTCATTTAA
1 TGTTCGTGAACATGTTCAATTAA
*
98126 TGTCCGTGAACATGTT
1 TGTTCGTGAACATGTT
98142 TGATTCAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:105003 original size:33 final size:32
Alignment explanation
Indices: 104929--105003 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
104919 AGAACAATTA
* * *
104929 TTCTAAATAAAAGCTATTATGAATGGCAGTTG
1 TTCTAAATAGAAGCTATTATGAATGACAGTTC
* *
104961 TTCTTAATAGAAGCTATTATCGAATGATAGTTAC
1 TTCTAAATAGAAGCTATTAT-GAATGACAGTT-C
104995 TT-TAAATAG
1 TTCTAAATAG
105004 CAATTGATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
32 18 0.51
33 15 0.43
34 2 0.06
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.37
Consensus pattern (32 bp):
TTCTAAATAGAAGCTATTATGAATGACAGTTC
Found at i:106446 original size:52 final size:52
Alignment explanation
Indices: 106383--106485 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
106373 TTGAATTGAT
*
106383 TTAAACCTAAAAGAGACCTGAAATTAACTCTGATTCAAAATAATCCGAACAG
1 TTAAACCTAAAACAGACCTGAAATTAACTCTGATTCAAAATAATCCGAACAG
*
106435 TTAAACTTAAAACAGACCTGAAATTAACTCTGATTCAAAATAATCCGAACA
1 TTAAACCTAAAACAGACCTGAAATTAACTCTGATTCAAAATAATCCGAACA
106486 AGTAATTTGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.47, C:0.19, G:0.10, T:0.24
Consensus pattern (52 bp):
TTAAACCTAAAACAGACCTGAAATTAACTCTGATTCAAAATAATCCGAACAG
Found at i:109540 original size:31 final size:31
Alignment explanation
Indices: 109505--109580 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
109495 GTTATATACC
*
109505 ATTTGGTACTTAAATTTGACTTTAATATTTA
1 ATTTGGTACTTAAATTTGACTTTAATATTCA
* * * ** *
109536 ATTTGGTATTTGAGTTTGGTTTTACTATTCA
1 ATTTGGTACTTAAATTTGACTTTAATATTCA
*
109567 ATTTGGTACCTAAA
1 ATTTGGTACTTAAA
109581 GCAAACAACA
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (31 bp):
ATTTGGTACTTAAATTTGACTTTAATATTCA
Found at i:110169 original size:3 final size:3
Alignment explanation
Indices: 110161--110187 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
110151 GCACACCCTC
110161 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
110188 ATATAGCAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:113186 original size:21 final size:21
Alignment explanation
Indices: 113141--113186 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
113131 TCGAGTTAAT
*
113141 ATTTACTATTTAAAAAATATC
1 ATTTACTATTTAAAAAATATA
113162 ATTTAC-ATTTTAATAAAAT-TA
1 ATTTACTA-TTTAA-AAAATATA
113183 ATTT
1 ATTT
113187 TTTAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 1 0.05
21 16 0.73
22 5 0.23
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTTACTATTTAAAAAATATA
Found at i:118628 original size:16 final size:16
Alignment explanation
Indices: 118609--118653 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
118599 TCAATTTAGT
118609 TTTAAATTATTTTAAG
1 TTTAAATTATTTTAAG
* **
118625 TTTAAATTAATTTGGG
1 TTTAAATTATTTTAAG
*
118641 TTTACATTATTTT
1 TTTAAATTATTTT
118654 TTAAGGAAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.31, C:0.02, G:0.09, T:0.58
Consensus pattern (16 bp):
TTTAAATTATTTTAAG
Found at i:121636 original size:6 final size:6
Alignment explanation
Indices: 121611--121655 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
121601 ACAATTCATA
* * *
121611 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
121656 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:137007 original size:133 final size:128
Alignment explanation
Indices: 136748--137055 Score: 372
Period size: 133 Copynumber: 2.3 Consensus size: 128
136738 GCAACGGGCA
* *
136748 GCCCCAAGGTTAGGTATAAATATCCAAGTACCAACTCTCACTCTCTCTTACTTCTTCTCTGCTAG
1 GCCCCAAGGCTAGGTATAAATATCCAAGTACC-ACTCT--CTCTCAC-TACTTCTTCTCTGCTAG
* *
136813 CTTGCTTTACCCATTACACAATCTCCTTTGCTAACTTAAGCATCAAAGAGCATTCCGGAGCATTG
62 CTTGCTTTACCCATTACACAATCTCCTTTGCTAACTTAAGCATCAAAGAGCACTCCAGAGCATTG
136878 AT
127 AT
136880 GCCCCAAGGCTAGGTATAAATATCCAAGTACCAGCTCTCTCTCAC-ACTT-TTCTGCTAGCTTAA
1 GCCCCAAGGCTAGGTATAAATATCCAAGTACCA-CTCTCTCTCACTACTTCTTCT-CT-GC-T-A
** * * * *
136943 GCTCTTTTTTTATCCATTACACATTCTCCTTTGCTAACTTAAGCATCACATAGCACTCCAGAGCA
61 G--CTTGCTTTACCCATTACACAATCTCCTTTGCTAACTTAAGCATCAAAGAGCACTCCAGAGCA
137008 TTGAT
124 TTGAT
* *
137013 GCCCCCAAGGCTAGGTATAAGTACCCAAGTA--ACTCTCTCTCAC
1 G-CCCCAAGGCTAGGTATAAATATCCAAGTACCACTCTCTCTCAC
137056 GATCTATACT
Statistics
Matches: 156, Mismatches: 12, Indels: 17
0.84 0.06 0.09
Matches are distributed among these distances:
127 4 0.03
128 6 0.04
129 2 0.01
130 7 0.04
131 14 0.09
132 36 0.23
133 60 0.38
134 27 0.17
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.31
Consensus pattern (128 bp):
GCCCCAAGGCTAGGTATAAATATCCAAGTACCACTCTCTCTCACTACTTCTTCTCTGCTAGCTTG
CTTTACCCATTACACAATCTCCTTTGCTAACTTAAGCATCAAAGAGCACTCCAGAGCATTGAT
Found at i:138813 original size:20 final size:19
Alignment explanation
Indices: 138776--138820 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
138766 ATTAATCCTA
*
138776 AATTTTATCATTAAATTTT
1 AATTTAATCATTAAATTTT
* *
138795 GAATTTAATCTTTATATTTT
1 -AATTTAATCATTAAATTTT
138815 AATTTA
1 AATTTA
138821 GTAATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
AATTTAATCATTAAATTTT
Found at i:139764 original size:21 final size:21
Alignment explanation
Indices: 139718--139764 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
139708 TTTAAATTTA
* *
139718 AAAATATTTTTTATATTGTTT
1 AAAATAATTTTAATATTGTTT
*
139739 TAAATAATTTTAATGATT-TTT
1 AAAATAATTTTAAT-ATTGTTT
139760 AAAAT
1 AAAAT
139765 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
AAAATAATTTTAATATTGTTT
Found at i:139782 original size:23 final size:23
Alignment explanation
Indices: 139754--139817 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
139744 AATTTTAATG
139754 ATTTTTAAAATTATAAAAAATAT
1 ATTTTTAAAATTATAAAAAATAT
139777 ATTTTTAAAATTATAAAAAATAT
1 ATTTTTAAAATTATAAAAAATAT
139800 ATTTTTAAAATT-TAAAAA
1 ATTTTTAAAATTATAAAAA
139818 TTAATTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 6 0.15
23 35 0.85
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTTTAAAATTATAAAAAATAT
Found at i:146340 original size:40 final size:39
Alignment explanation
Indices: 146291--146373 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 39
146281 TCAGTAAAAT
*
146291 ACCATTTCTAACAAGTTCAGATTTATAAAATAAACTAAA
1 ACCATTTCTAACAAGTTCAGATTTAGAAAATAAACTAAA
146330 ACCATATTCTAACAAGTTCAGATTTAGAAAATAAACTAAA
1 ACCAT-TTCTAACAAGTTCAGATTTAGAAAATAAACTAAA
146370 ACCA
1 ACCA
146374 GTGTTTGAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 5 0.12
40 37 0.88
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.28
Consensus pattern (39 bp):
ACCATTTCTAACAAGTTCAGATTTAGAAAATAAACTAAA
Found at i:149216 original size:7 final size:7
Alignment explanation
Indices: 149204--149292 Score: 74
Period size: 7 Copynumber: 13.0 Consensus size: 7
149194 CTCAAAAAAT
149204 TCAACGG
1 TCAACGG
149211 TCAACGG
1 TCAACGG
* *
149218 TTAACGA
1 TCAACGG
*
149225 TCAACTG
1 TCAACGG
*
149232 TCAACGA
1 TCAACGG
**
149239 TCAACTA
1 TCAACGG
149246 TCAACGG
1 TCAACGG
*
149253 TTAACGG
1 TCAACGG
*
149260 TCAACGA
1 TCAACGG
149267 TCAAC-G
1 TCAACGG
*
149273 TCAACAG
1 TCAACGG
*
149280 TCAA-AG
1 TCAACGG
149286 TCAACGG
1 TCAACGG
149293 GTCTGGTTTA
Statistics
Matches: 65, Mismatches: 15, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
6 11 0.17
7 54 0.83
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (7 bp):
TCAACGG
Found at i:149234 original size:21 final size:21
Alignment explanation
Indices: 149204--149292 Score: 101
Period size: 21 Copynumber: 4.3 Consensus size: 21
149194 CTCAAAAAAT
*
149204 TCAACGGTCAACGGTTAACGA
1 TCAACGGTCAACGGTCAACGA
* * *
149225 TCAACTGTCAACGATCAACTA
1 TCAACGGTCAACGGTCAACGA
*
149246 TCAACGGTTAACGGTCAACGA
1 TCAACGGTCAACGGTCAACGA
* *
149267 TCAAC-GTCAACAGTCAAAG-
1 TCAACGGTCAACGGTCAACGA
149286 TCAACGG
1 TCAACGG
149293 GTCTGGTTTA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.09
20 12 0.21
21 39 0.70
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (21 bp):
TCAACGGTCAACGGTCAACGA
Found at i:156051 original size:32 final size:31
Alignment explanation
Indices: 156015--156079 Score: 112
Period size: 32 Copynumber: 2.1 Consensus size: 31
156005 GAAAGAAAGT
156015 AAGACCATACAACACTGATTTAAAAAATGCAA
1 AAGACCATACAACACTGATTTAAAAAATG-AA
*
156047 AAGACCATACAACACTGATTTAGAAAATGAA
1 AAGACCATACAACACTGATTTAAAAAATGAA
156078 AA
1 AA
156080 TACTAAGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 4 0.12
32 28 0.88
ACGTcount: A:0.54, C:0.17, G:0.11, T:0.18
Consensus pattern (31 bp):
AAGACCATACAACACTGATTTAAAAAATGAA
Found at i:157082 original size:17 final size:17
Alignment explanation
Indices: 157046--157086 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
157036 AAATGTGAGA
*
157046 ACAACTAAAATGCAAAG
1 ACAATTAAAATGCAAAG
* *
157063 ACAATTAAAATGTAATG
1 ACAATTAAAATGCAAAG
157080 ACAATTA
1 ACAATTA
157087 GATGAAATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (17 bp):
ACAATTAAAATGCAAAG
Found at i:157526 original size:18 final size:16
Alignment explanation
Indices: 157483--157524 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
157473 ATCGGAACAA
157483 CTTCTTCTTCTTTTTC
1 CTTCTTCTTCTTTTTC
*
157499 CTT-TTCTTC-TCTTC
1 CTTCTTCTTCTTTTTC
*
157513 ATTCTTCTTCTT
1 CTTCTTCTTCTT
157525 CTTTAATACC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.27
15 12 0.55
16 4 0.18
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (16 bp):
CTTCTTCTTCTTTTTC
Found at i:162470 original size:29 final size:29
Alignment explanation
Indices: 162450--162719 Score: 199
Period size: 29 Copynumber: 9.3 Consensus size: 29
162440 TTTTAGCAAC
162450 TCGAGGGTAAAATGGTAA-TTTTGGAAGT
1 TCGAGGGTAAAATGGTAATTTTTGGAAGT
162478 TCG-GGGATAAAATGGTAATTTTTGGAAGT
1 TCGAGGG-TAAAATGGTAATTTTTGGAAGT
*
162507 TCGAGGGTAAGATGGTAATTTTTGGAAGCT
1 TCGAGGGTAAAATGGTAATTTTTGGAAG-T
*
162537 TC-AGGGTCAAAAATGG-GATTTTTAGGAA-T
1 TCGAGGGT--AAAATGGTAATTTTT-GGAAGT
* *
162566 TCG-GGAGTAAAACGATAA-TTTTGGAAGGT
1 TCGAGG-GTAAAATGGTAATTTTTGGAA-GT
* *
162595 TTG-GGGTCAAAAATGG-GATTTTTGGGAA-T
1 TCGAGGGT--AAAATGGTAATTTTT-GGAAGT
*
162624 TCGAGGGTAAAACGGTAATTTTTGGAAGGT
1 TCGAGGGTAAAATGGTAATTTTTGGAA-GT
* *
162654 TCG-GGGTTAAAAATGG-GATTTTTGGGAATT
1 TCGAGGG-T-AAAATGGTAATTTTT-GGAAGT
* * *
162684 TAG-GGGTAAAACGATAATTTTTGGAAGGT
1 TCGAGGGTAAAATGGTAATTTTTGGAA-GT
162713 TCG-GGGT
1 TCGAGGGT
162720 CCTCCGGGGT
Statistics
Matches: 195, Mismatches: 22, Indels: 49
0.73 0.08 0.18
Matches are distributed among these distances:
27 7 0.04
28 44 0.23
29 76 0.39
30 44 0.23
31 24 0.12
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (29 bp):
TCGAGGGTAAAATGGTAATTTTTGGAAGT
Found at i:162585 original size:59 final size:59
Alignment explanation
Indices: 162400--162720 Score: 345
Period size: 59 Copynumber: 5.5 Consensus size: 59
162390 ACGGAGTGGC
* * * ** * * *
162400 AAAATGGTAA-TTTTAGAATGTTCGGAATCAAAAATAGGATTTTTAGCAACTCGAGGGT
1 AAAACGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTAGGAATTCGAGGGT
* *
162458 AAAATGGTAA-TTTTGGAA-GTTCGGGG--ATAAAATGGTAATTTTT-GGAAGTTCGAGGGT
1 AAAACGGTAATTTTTGGAAGGTTCGGGGTCA-AAAATGG-GATTTTTAGGAA-TTCGAGGGT
* * * *
162515 AAGATGGTAATTTTTGGAAGCTTCAGGGTCAAAAATGGGATTTTTAGGAATTCG-GGAGT
1 AAAACGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTAGGAATTCGAGG-GT
* * *
162574 AAAACGATAA-TTTTGGAAGGTTTGGGGTCAAAAATGGGATTTTTGGGAATTCGAGGGT
1 AAAACGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTAGGAATTCGAGGGT
* * *
162632 AAAACGGTAATTTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGGAATT-TAGGGGT
1 AAAACGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTAGGAATTCGA-GGGT
*
162691 AAAACGATAATTTTTGGAAGGTTCGGGGTC
1 AAAACGGTAATTTTTGGAAGGTTCGGGGTC
162721 CTCCGGGGTA
Statistics
Matches: 227, Mismatches: 24, Indels: 23
0.83 0.09 0.08
Matches are distributed among these distances:
55 1 0.00
56 9 0.04
57 29 0.13
58 78 0.34
59 98 0.43
60 11 0.05
61 1 0.00
ACGTcount: A:0.32, C:0.06, G:0.30, T:0.32
Consensus pattern (59 bp):
AAAACGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTAGGAATTCGAGGGT
Found at i:162666 original size:117 final size:118
Alignment explanation
Indices: 162427--162720 Score: 375
Period size: 117 Copynumber: 2.5 Consensus size: 118
162417 ATGTTCGGAA
* * * * *
162427 TCAAAAATAGGATTTTTAGCAACTCGAGGGTAAAATGGTAATTTTGGAA-GTTCGGGG--ATAAA
1 TCAAAAATGGGATTTTTAGGAATTCG-GGGTAAAACGATAATTTTGGAAGGTTCGGGGTCATAAA
* *
162489 ATGGTAATTTTTGGAAGTTCGAGGGTAAGATGGTAATTTTTGGAAGCTTCAGGG
65 ATGGTAATTTTTGGAAGTTCGAGGGTAAAACGGTAATTTTTGGAAGCTTCAGGG
*
162543 TCAAAAATGGGATTTTTAGGAATTCGGGAGTAAAACGATAATTTTGGAAGGTTTGGGGTCA-AAA
1 TCAAAAATGGGATTTTTAGGAATTCGGG-GTAAAACGATAATTTTGGAAGGTTCGGGGTCATAAA
* * *
162607 ATGG-GATTTTTGGGAA-TTCGAGGGTAAAACGGTAATTTTTGGAAGGTTCGGGG
65 ATGGTAATTTTT-GGAAGTTCGAGGGTAAAACGGTAATTTTTGGAAGCTTCAGGG
* * *
162660 TTAAAAATGGGATTTTTGGGAATTTAGGGGTAAAACGATAATTTTTGGAAGGTTCGGGGTC
1 TCAAAAATGGGATTTTTAGGAA-TTCGGGGTAAAACGATAA-TTTTGGAAGGTTCGGGGTC
162721 CTCCGGGGTA
Statistics
Matches: 156, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
115 2 0.01
116 41 0.26
117 78 0.50
118 34 0.22
119 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.32
Consensus pattern (118 bp):
TCAAAAATGGGATTTTTAGGAATTCGGGGTAAAACGATAATTTTGGAAGGTTCGGGGTCATAAAA
TGGTAATTTTTGGAAGTTCGAGGGTAAAACGGTAATTTTTGGAAGCTTCAGGG
Found at i:163633 original size:18 final size:18
Alignment explanation
Indices: 163610--163652 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
163600 AAAAACATTA
163610 CCTTCTTTCCCTTCTTCT
1 CCTTCTTTCCCTTCTTCT
*
163628 CCTTCTTTTCCTTCTTCT
1 CCTTCTTTCCCTTCTTCT
*
163646 CATTCTT
1 CCTTCTT
163653 CCTTCTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.58
Consensus pattern (18 bp):
CCTTCTTTCCCTTCTTCT
Found at i:163651 original size:9 final size:9
Alignment explanation
Indices: 163610--163653 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
163600 AAAAACATTA
163610 CCTTCTT-T
1 CCTTCTTCT
163618 CCCTTCTTCT
1 -CCTTCTTCT
*
163628 CCTTCTTTT
1 CCTTCTTCT
163637 CCTTCTTCT
1 CCTTCTTCT
*
163646 CATTCTTC
1 CCTTCTTC
163654 CTTCTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
9 30 0.97
10 1 0.03
ACGTcount: A:0.02, C:0.41, G:0.00, T:0.57
Consensus pattern (9 bp):
CCTTCTTCT
Found at i:163677 original size:26 final size:26
Alignment explanation
Indices: 163639--163688 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
163629 CTTCTTTTCC
163639 TTCTTCTCATTCTTCCTTCTTTTTTAT
1 TTCTTCTCATTCTTCC-TCTTTTTTAT
* *
163666 TTCTT-TCTTTCTTTCTCTTTTTT
1 TTCTTCTCATTCTTCCTCTTTTTT
163689 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 8 0.38
27 5 0.24
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (26 bp):
TTCTTCTCATTCTTCCTCTTTTTTAT
Found at i:165098 original size:14 final size:15
Alignment explanation
Indices: 165079--165111 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
165069 GCTTAATCTT
*
165079 AAAAAGAA-AAAGAA
1 AAAAAGAATAAACAA
165093 AAAAAGAATAAACAA
1 AAAAAGAATAAACAA
165108 AAAA
1 AAAA
165112 GAGAGGAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.85, C:0.03, G:0.09, T:0.03
Consensus pattern (15 bp):
AAAAAGAATAAACAA
Found at i:171801 original size:24 final size:24
Alignment explanation
Indices: 171772--171818 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
171762 AGATATAAAG
* *
171772 TATAATTTTTAATCTATAAAAATA
1 TATAATTTTAAATATATAAAAATA
171796 TATAATTTTAAATATATAAAAAT
1 TATAATTTTAAATATATAAAAAT
171819 TAAAAGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
TATAATTTTAAATATATAAAAATA
Found at i:172184 original size:16 final size:17
Alignment explanation
Indices: 172163--172194 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
172153 TTTCTATAAC
172163 TATGTTTT-CCTTTCTA
1 TATGTTTTACCTTTCTA
172179 TATGTTTTACCTTTCT
1 TATGTTTTACCTTTCT
172195 TTTTTCATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.12, C:0.19, G:0.06, T:0.62
Consensus pattern (17 bp):
TATGTTTTACCTTTCTA
Found at i:188301 original size:17 final size:17
Alignment explanation
Indices: 188274--188316 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
188264 CCCTTTTTCC
*
188274 TTTCTTCATT-TCTTT-
1 TTTCTTCATTATTTTTA
188289 TTT-TTCATTATTTTTA
1 TTTCTTCATTATTTTTA
188305 TTTCTTCATTAT
1 TTTCTTCATTAT
188317 CAAAATGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
14 6 0.25
15 7 0.29
16 3 0.12
17 8 0.33
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCTTCATTATTTTTA
Found at i:189108 original size:2 final size:2
Alignment explanation
Indices: 189101--189149 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
189091 TTTTTATTTA
189101 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
189143 AT AT AT A
1 AT AT AT A
189150 ACATTCTCAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:201208 original size:12 final size:12
Alignment explanation
Indices: 201193--201217 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
201183 ATTTAGTTAT
201193 TAATTGAATCAA
1 TAATTGAATCAA
201205 TAATTGAATCAA
1 TAATTGAATCAA
201217 T
1 T
201218 GAGTCGAATC
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:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATTGAATCAA
Found at i:205890 original size:16 final size:15
Alignment explanation
Indices: 205869--205898 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
205859 CGTTTGGATT
205869 TTGGTGGGTCTCGTTG
1 TTGGTGGGT-TCGTTG
205885 TTGGTGGGTTCGTT
1 TTGGTGGGTTCGTT
205899 ATCGTTTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.10, G:0.43, T:0.47
Consensus pattern (15 bp):
TTGGTGGGTTCGTTG
Found at i:210906 original size:23 final size:23
Alignment explanation
Indices: 210880--210924 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
210870 AACCATTAAC
210880 TTTTCAAAAAAAATAAATTATTA
1 TTTTCAAAAAAAATAAATTATTA
* * *
210903 TTTTTAAATAAAATTAATTATT
1 TTTTCAAAAAAAATAAATTATT
210925 TTTAAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTCAAAAAAAATAAATTATTA
Found at i:210918 original size:19 final size:20
Alignment explanation
Indices: 210890--210937 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
210880 TTTTCAAAAA
210890 AAAT-AAATT-ATTATTTTT
1 AAATAAAATTAATTATTTTT
210908 AAATAAAATTAATTATTTTT
1 AAATAAAATTAATTATTTTT
210928 AAATAAAATT
1 AAATAAAATT
210938 TCTTACTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 4 0.14
19 5 0.18
20 19 0.68
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AAATAAAATTAATTATTTTT
Found at i:216254 original size:18 final size:18
Alignment explanation
Indices: 216231--216267 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
216221 TGGTACTTAG
216231 CTTTCCTTTCAGTGTTAA
1 CTTTCCTTTCAGTGTTAA
216249 CTTTCCTTTCAGTGTTAA
1 CTTTCCTTTCAGTGTTAA
216267 C
1 C
216268 ATGCGAAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.24, G:0.11, T:0.49
Consensus pattern (18 bp):
CTTTCCTTTCAGTGTTAA
Found at i:225128 original size:60 final size:60
Alignment explanation
Indices: 225026--225141 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
225016 AATATAGTTG
* * * *
225026 TGTGATCAAAAAAGATAAAAGTAAATAATTGAATGATCATTTTGTAATTTTTCATAATTA
1 TGTGATCAAAAAAAAAAAAACTAAATAATTGAATGATCATTTTATAATTTTTCATAATTA
*
225086 TGTGATCAAAAAAAAAAAAAACT-AATAATT-AAGTGA-CTATTTTATATTTTTTCATA
1 TGTGATC-AAAAAAAAAAAAACTAAATAATTGAA-TGATC-ATTTTATAATTTTTCATA
225142 GTCGAGTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
59 3 0.06
60 33 0.69
61 12 0.25
ACGTcount: A:0.47, C:0.06, G:0.09, T:0.38
Consensus pattern (60 bp):
TGTGATCAAAAAAAAAAAAACTAAATAATTGAATGATCATTTTATAATTTTTCATAATTA
Found at i:227541 original size:18 final size:19
Alignment explanation
Indices: 227509--227547 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
227499 CAATTTAATT
**
227509 TTTTTAATTCTTTATA-AA
1 TTTTTAATTAATTATATAA
227527 TTTTTAATTAATTATATAA
1 TTTTTAATTAATTATATAA
227546 TT
1 TT
227548 ATTATTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTAATTAATTATATAA
Found at i:237892 original size:18 final size:18
Alignment explanation
Indices: 237871--237905 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
237861 GACGAGACGG
*
237871 AGGAGGAGAAAAAGAAAA
1 AGGAGGAAAAAAAGAAAA
237889 AGGAGGAAAAAAAGAAA
1 AGGAGGAAAAAAAGAAA
237906 TCTTTTGAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AGGAGGAAAAAAAGAAAA
Found at i:238763 original size:60 final size:60
Alignment explanation
Indices: 238690--238833 Score: 245
Period size: 60 Copynumber: 2.4 Consensus size: 60
238680 TTATATATTT
* * *
238690 TTATCTCAAAACCTCCTTTTATTTGATG-TCATATATAATGTCGTTACAGTGAATTTTGAA
1 TTATCTCAAAACCTCATCTTATTTGATGCT-ATATATAATGTCGTTACAGTGAAATTTGAA
238750 TTATCTCAAAACCTCATCTTATTTGATGCTATATATAATGTCGTTACAGTGAAATTTGAA
1 TTATCTCAAAACCTCATCTTATTTGATGCTATATATAATGTCGTTACAGTGAAATTTGAA
238810 TTATCTCAAAACCTCATCTTATTT
1 TTATCTCAAAACCTCATCTTATTT
238834 TTATAAATAT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
60 79 0.99
61 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (60 bp):
TTATCTCAAAACCTCATCTTATTTGATGCTATATATAATGTCGTTACAGTGAAATTTGAA
Found at i:243726 original size:79 final size:80
Alignment explanation
Indices: 243585--243747 Score: 274
Period size: 79 Copynumber: 2.0 Consensus size: 80
243575 AGAGATTACT
* * * *
243585 AACTACGATTGAAAGGAATAAAAGATATCCTTCATTCCTCAACCACCCTCCCGCCTCTTTCCTTT
1 AACTACGACTGAAAGGAATAAAAGATATCCTTCATTCCTCAACAACCCTCCCGCCTCATTCCTTC
243650 CAAACTGCAAAACGA
66 CAAACTGCAAAACGA
*
243665 AACT-CGACTGAAAGGAATAAAAGATATCCTTCATTCCTCAACAACCCTCCTGCCTCATTCCTTC
1 AACTACGACTGAAAGGAATAAAAGATATCCTTCATTCCTCAACAACCCTCCCGCCTCATTCCTTC
243729 CAAACTGCAAAACGA
66 CAAACTGCAAAACGA
243744 AACT
1 AACT
243748 TGTCTAAGGA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 74 0.95
80 4 0.05
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.24
Consensus pattern (80 bp):
AACTACGACTGAAAGGAATAAAAGATATCCTTCATTCCTCAACAACCCTCCCGCCTCATTCCTTC
CAAACTGCAAAACGA
Found at i:246379 original size:20 final size:20
Alignment explanation
Indices: 246342--246382 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
246332 AATAAATAGA
*
246342 AAGCATAATAATAAAAAATC
1 AAGCAGAATAATAAAAAATC
*
246362 AAGCAGAATCATATAAAAATC
1 AAGCAGAATAATA-AAAAATC
246383 TATCGCAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.61, C:0.12, G:0.07, T:0.20
Consensus pattern (20 bp):
AAGCAGAATAATAAAAAATC
Found at i:246721 original size:23 final size:25
Alignment explanation
Indices: 246695--246752 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 25
246685 ATTCGTATTG
246695 ATTTCGAAT-T-TT-TTACAAATAAT
1 ATTTCGAATATCTTATT-CAAATAAT
* *
246718 ATTTAGAATATCTTAGTTCAAATATT
1 ATTTCGAATATCTTA-TTCAAATAAT
246744 ATTTCGAAT
1 ATTTCGAAT
246753 CTATAATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 8 0.29
24 1 0.04
25 2 0.07
26 15 0.54
27 2 0.07
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (25 bp):
ATTTCGAATATCTTATTCAAATAAT
Found at i:251082 original size:15 final size:17
Alignment explanation
Indices: 251048--251084 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
251038 GCCAAACCCG
251048 CTTCACTTCTCTAATTT
1 CTTCACTTCTCTAATTT
*
251065 CTTC-CTTCT-TATTTT
1 CTTCACTTCTCTAATTT
251080 CTTCA
1 CTTCA
251085 ATTTTTTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 9 0.50
16 5 0.28
17 4 0.22
ACGTcount: A:0.14, C:0.30, G:0.00, T:0.57
Consensus pattern (17 bp):
CTTCACTTCTCTAATTT
Found at i:261042 original size:20 final size:21
Alignment explanation
Indices: 261017--261058 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
261007 CAGTGGAGGG
*
261017 AAAAAAGAAAAAGAAA-AGAA
1 AAAAAACAAAAAGAAAGAGAA
*
261037 AAAAAACAAAGAGAAAGAGAA
1 AAAAAACAAAAAGAAAGAGAA
261058 A
1 A
261059 TGGGAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (21 bp):
AAAAAACAAAAAGAAAGAGAA
Found at i:284895 original size:18 final size:19
Alignment explanation
Indices: 284856--284895 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
284846 GATCGTTTAT
* *
284856 TTTCAATTATTTAATGATA
1 TTTCAATAATTTAATAATA
284875 TTTCAATAATTT-ATAATA
1 TTTCAATAATTTAATAATA
284893 TTT
1 TTT
284896 TTTTACACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTCAATAATTTAATAATA
Found at i:285294 original size:2 final size:2
Alignment explanation
Indices: 285287--285318 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
285277 TGCGATTTAA
285287 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
285319 GATTATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.