Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008436.1 Hibiscus syriacus cultivar Beakdansim tig00111234_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: 1066897
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 4
Found at i:223 original size:2 final size:2
Alignment explanation
Indices: 218--275 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
208 TATATACACA
*
218 AT AT AT A- AT AT TT AT AT AT AT A- 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
258 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
276 GTCTAAGAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4283 original size:21 final size:21
Alignment explanation
Indices: 4257--4301 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4247 GATTTCTGGG
* *
4257 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4278 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4299 CAA
1 CAA
4302 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:5399 original size:15 final size:14
Alignment explanation
Indices: 5360--5402 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
5350 ATAAGCAATG
5360 TGACTATAAGTATA
1 TGACTATAAGTATA
* *
5374 TGTGCTTTAAGTGATA
1 TG-ACTATAAGT-ATA
5390 TGACTATAAGTAT
1 TGACTATAAGTAT
5403 TTCTATTATA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
14 4 0.17
15 14 0.61
16 5 0.22
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.40
Consensus pattern (14 bp):
TGACTATAAGTATA
Found at i:5966 original size:149 final size:149
Alignment explanation
Indices: 5786--6090 Score: 574
Period size: 149 Copynumber: 2.0 Consensus size: 149
5776 AGAGTCGAGG
5786 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
1 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
* *
5851 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTAGGGACATCATT
5916 ACATGGCACTACGGTGCAA
131 ACATGGCACTACGGTGCAA
5935 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
1 GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
6000 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTAGGGACATCATT
66 TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTAGGGACATCATT
*
6065 ATATGGCACTACGGTGCAA
131 ACATGGCACTACGGTGCAA
*
6084 TTCTACG
1 GTCTACG
6091 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (149 bp):
GTCTACGCGGTTCTTAGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACA
TACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTAGGGACATCATT
ACATGGCACTACGGTGCAA
Found at i:6113 original size:23 final size:23
Alignment explanation
Indices: 6069--6113 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
6059 ATCATTATAT
*
6069 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
6092 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
6114 AGCTGTGGTG
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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:7885 original size:24 final size:24
Alignment explanation
Indices: 7851--7897 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
7841 CTGAAACATC
7851 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
7875 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
7898 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:8615 original size:20 final size:20
Alignment explanation
Indices: 8587--8816 Score: 250
Period size: 20 Copynumber: 11.5 Consensus size: 20
8577 AAATTTCAGT
* * * *
8587 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
* *
8607 GTTGCGATTTATGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
8627 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
8647 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
8667 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8687 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8707 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
8727 GTTGCGATTTACTGATACGC
1 GTTGCGATTTACGGATACGC
* *
8747 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
8767 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
8787 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
8807 GTTGCGATTT
1 GTTGCGATTT
8817 TTATATTCGC
Statistics
Matches: 181, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.02
20 175 0.97
21 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:8825 original size:20 final size:20
Alignment explanation
Indices: 8784--8835 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
8774 TTTACGGATA
* *
8784 CGCGTTGCGATTTATGTGTT
1 CGCGTTGCGATTTATATATT
*
8804 CGCGTTGCGATTTTTATATT
1 CGCGTTGCGATTTATATATT
8824 CGCGTTGCGATT
1 CGCGTTGCGATT
8836 CTTGAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.17, G:0.27, T:0.44
Consensus pattern (20 bp):
CGCGTTGCGATTTATATATT
Found at i:8896 original size:42 final size:42
Alignment explanation
Indices: 8803--8901 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
8793 ATTTATGTGT
* * *
8803 TCGCGTTGCG-ATTTTTATATTCGCGTTGCGATTCTTGAAAA
1 TCGCGTTGCGAATTTGTATATTCGCATTGCGATTCTTCAAAA
**
8844 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTA-TATTCGCATTGCGATTCTTCAA-AA
*
8886 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
8902 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 12 0.26
42 33 0.70
43 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.38
Consensus pattern (42 bp):
TCGCGTTGCGAATTTGTATATTCGCATTGCGATTCTTCAAAA
Found at i:9392 original size:2 final size:2
Alignment explanation
Indices: 9385--9412 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9375 TCATACATAC
9385 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
9413 GAACATAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38592 original size:15 final size:15
Alignment explanation
Indices: 38572--38610 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
38562 CATCATATAG
38572 TAATTTTTTTTTATT
1 TAATTTTTTTTTATT
** *
38587 TAATTTTAATTTCTT
1 TAATTTTTTTTTATT
38602 TAATTTTTT
1 TAATTTTTT
38611 ATATAAATTT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TAATTTTTTTTTATT
Found at i:39115 original size:37 final size:37
Alignment explanation
Indices: 39039--39115 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
39029 TTTTTATATT
*
39039 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
39076 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
39113 TTT
1 TTT
39116 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:51580 original size:63 final size:63
Alignment explanation
Indices: 51481--51609 Score: 258
Period size: 63 Copynumber: 2.0 Consensus size: 63
51471 CACCTGTTAA
51481 TTTAATAAAAAATATTCAAGCAGAAGGTCTATCCAAGACCCCAACATAAGTTGATAAAAATTC
1 TTTAATAAAAAATATTCAAGCAGAAGGTCTATCCAAGACCCCAACATAAGTTGATAAAAATTC
51544 TTTAATAAAAAATATTCAAGCAGAAGGTCTATCCAAGACCCCAACATAAGTTGATAAAAATTC
1 TTTAATAAAAAATATTCAAGCAGAAGGTCTATCCAAGACCCCAACATAAGTTGATAAAAATTC
51607 TTT
1 TTT
51610 GGAAACCCAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (63 bp):
TTTAATAAAAAATATTCAAGCAGAAGGTCTATCCAAGACCCCAACATAAGTTGATAAAAATTC
Found at i:56178 original size:29 final size:29
Alignment explanation
Indices: 56083--56166 Score: 150
Period size: 29 Copynumber: 2.9 Consensus size: 29
56073 TACCGGGGGT
56083 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCGGCGACCTACC
*
56112 AGGTCGCCATGCACGCCCGGCGAACTACC
1 AGGTCGCCATGCACGCCCGGCGACCTACC
*
56141 AGGTCGCCATGCACGCCCAGCGACCT
1 AGGTCGCCATGCACGCCCGGCGACCT
56167 GGTAGGTCGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.19, C:0.43, G:0.27, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCTACC
Found at i:56226 original size:30 final size:30
Alignment explanation
Indices: 56192--56298 Score: 178
Period size: 30 Copynumber: 3.6 Consensus size: 30
56182 ACCTACCTCA
*
56192 ACCTCCATGCACACCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
* *
56222 ACCTCCATGCATGCCCAGGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
*
56252 ACCTCCATGCACGGCCATGCACGCCCAACG
1 ACCTCCATGCACGCCCATGCACGCCCAACG
56282 ACCTCCATGCACGCCCA
1 ACCTCCATGCACGCCCA
56299 GCTCGCCAAA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 70 1.00
ACGTcount: A:0.24, C:0.49, G:0.17, T:0.10
Consensus pattern (30 bp):
ACCTCCATGCACGCCCATGCACGCCCAACG
Found at i:60107 original size:60 final size:59
Alignment explanation
Indices: 60035--60409 Score: 535
Period size: 60 Copynumber: 6.2 Consensus size: 59
60025 TTTATAAGAT
* * *
60035 TTAGTAATGATTAGTAATGATGAAATTATTATTAA-TATTTAATGATTTAATAGTAATTTGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAA--TGA
60096 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGA-TTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGA
*
60153 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAGGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGA
60213 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGA
* *
60273 TTTAGTAATGATTTGATAGTAATAATGAAATTATTATTAA-TATTTAATGATTTAATAGTAATTT
1 -TTAGTAATGA--T--TAGTAATAATGAAATTATTATTAATTATGT-ATGATTTGATAGTAA--T
60337 GA
58 GA
60339 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGA
60397 TTTAGTAATGATT
1 -TTAGTAATGATT
60410 TGATGATGAT
Statistics
Matches: 291, Mismatches: 9, Indels: 29
0.88 0.03 0.09
Matches are distributed among these distances:
57 3 0.01
58 3 0.01
59 52 0.18
60 169 0.58
61 8 0.03
62 2 0.01
63 4 0.01
64 47 0.16
66 3 0.01
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.45
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGA
Found at i:60160 original size:11 final size:10
Alignment explanation
Indices: 60144--60231 Score: 56
Period size: 10 Copynumber: 8.7 Consensus size: 10
60134 GTATGATTGA
60144 TAGTAATGATT
1 TAGTAATGA-T
60155 TAGTAATGAT
1 TAGTAATGAT
*
60165 TAGTAAT-AA
1 TAGTAATGAT
* *
60174 T-GAAATTAT
1 TAGTAATGAT
* *
60183 TATTAATTAT
1 TAGTAATGAT
* *
60193 GTAGGATTTGA-
1 -TAGTA-ATGAT
60204 TAGTAATGATT
1 TAGTAATGA-T
60215 TAGTAATGAT
1 TAGTAATGAT
60225 TAGTAAT
1 TAGTAAT
60232 AATGAAATTA
Statistics
Matches: 60, Mismatches: 11, Indels: 13
0.71 0.13 0.15
Matches are distributed among these distances:
8 4 0.07
9 7 0.12
10 26 0.43
11 21 0.35
12 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:60170 original size:21 final size:21
Alignment explanation
Indices: 60144--60231 Score: 67
Period size: 21 Copynumber: 4.3 Consensus size: 21
60134 GTATGATTGA
60144 TAGTAATGATTTAGTAATGAT
1 TAGTAATGATTTAGTAATGAT
* * *
60165 TAGTAAT-A-AT-GAAATTAT
1 TAGTAATGATTTAGTAATGAT
* * * * *
60183 TATTAATTATGTAGGATTTGA-
1 TAGTAATGATTTAGTA-ATGAT
60204 TAGTAATGATTTAGTAATGAT
1 TAGTAATGATTTAGTAATGAT
60225 TAGTAAT
1 TAGTAAT
60232 AATGAAATTA
Statistics
Matches: 49, Mismatches: 13, Indels: 10
0.68 0.18 0.14
Matches are distributed among these distances:
18 12 0.24
19 2 0.04
20 5 0.10
21 28 0.57
22 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (21 bp):
TAGTAATGATTTAGTAATGAT
Found at i:60274 original size:14 final size:14
Alignment explanation
Indices: 60255--60295 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
60245 TTAATTATGT
60255 ATGATTTGATAGTA
1 ATGATTTGATAGTA
60269 ATGA-TT--TAGTA
1 ATGATTTGATAGTA
60280 ATGATTTGATAGTA
1 ATGATTTGATAGTA
60294 AT
1 AT
60296 AATGAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
11 9 0.38
12 2 0.08
13 2 0.08
14 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.44
Consensus pattern (14 bp):
ATGATTTGATAGTA
Found at i:60371 original size:21 final size:21
Alignment explanation
Indices: 60289--60371 Score: 50
Period size: 21 Copynumber: 4.1 Consensus size: 21
60279 AATGATTTGA
60289 TAGTAATAATGAAATTATTAT
1 TAGTAATAATGAAATTATTAT
* * *
60310 TAATATTTAATG--A-T-TTAA
1 TAGTA-ATAATGAAATTATTAT
* * * *
60328 TAGTAAT-TTGATAGTAATGAT
1 TAGTAATAATGA-AATTATTAT
60349 TAGTAATAATGAAATTATTAT
1 TAGTAATAATGAAATTATTAT
60370 TA
1 TA
60372 ATTATGTATG
Statistics
Matches: 41, Mismatches: 14, Indels: 14
0.59 0.20 0.20
Matches are distributed among these distances:
16 2 0.05
17 1 0.02
18 7 0.17
19 1 0.02
20 1 0.02
21 21 0.51
22 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (21 bp):
TAGTAATAATGAAATTATTAT
Found at i:60404 original size:11 final size:11
Alignment explanation
Indices: 60388--60456 Score: 50
Period size: 11 Copynumber: 7.1 Consensus size: 11
60378 TATGATTTGA
60388 TAGTAATGATT
1 TAGTAATGATT
60399 TAGTAATGATT
1 TAGTAATGATT
*
60410 T-GATGATGATT
1 TAG-TAATGATT
60421 TA--AAT-A-T
1 TAGTAATGATT
60428 T--TAATGATT
1 TAGTAATGATT
60437 T-G--ATGATT
1 TAGTAATGATT
60445 TAGTAATGATT
1 TAGTAATGATT
60456 T
1 T
60457 GATAATATCA
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
7 5 0.11
8 9 0.19
9 5 0.11
10 1 0.02
11 27 0.57
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:60413 original size:124 final size:120
Alignment explanation
Indices: 60032--60409 Score: 629
Period size: 124 Copynumber: 3.1 Consensus size: 120
60022 GTATTTATAA
*
60032 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTAATAGTAATTTGAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTAATAGTAATTTGAT
60097 AGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGA-TTGATAGTAAT
66 AGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
* * *
60151 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGT-AGGATTTGATAGTAA--TGA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAA-TATTTAATGATTTAATAGTAATTTGA
60213 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
65 --TAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
60271 GATTTAGTAATGATTTGATAGTAATAATGAAATTATTATTAATATTTAATGATTTAATAGTAATT
1 GATTTAGTAATGA--T--TAGTAATAATGAAATTATTATTAATATTTAATGATTTAATAGTAATT
60336 TGATAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
62 TGATAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
60395 GATTTAGTAATGATT
1 GATTTAGTAATGATT
60410 TGATGATGAT
Statistics
Matches: 241, Mismatches: 7, Indels: 21
0.90 0.03 0.08
Matches are distributed among these distances:
117 3 0.01
119 94 0.39
120 29 0.12
122 2 0.01
123 4 0.02
124 106 0.44
126 3 0.01
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (120 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTAATAGTAATTTGAT
AGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
Found at i:60429 original size:19 final size:21
Alignment explanation
Indices: 60393--60435 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
60383 TTTGATAGTA
*
60393 ATGATTTAGTAATGATTTGATG
1 ATGATTTAG-AATGATTTAATG
60415 ATGATTTA-AAT-ATTTAATG
1 ATGATTTAGAATGATTTAATG
60434 AT
1 AT
60436 TTGATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 9 0.45
20 3 0.15
22 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (21 bp):
ATGATTTAGAATGATTTAATG
Found at i:60445 original size:184 final size:179
Alignment explanation
Indices: 60032--60456 Score: 510
Period size: 184 Copynumber: 2.3 Consensus size: 179
60022 GTATTTATAA
* * * * * *
60032 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAA-TATTTAATGATTTAATAGTAATTTGA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTAATAATTATGT-ATGATTTAGTAATGA-TT--
*
60096 TAGTAATGA--T--TAGTAATAATGAAATTATTATTAATTATGTATGATTGATAGTAATGATTTA
62 TAGTAATGATTTGATAGTAATAATGAAATTATTATTAATTATGTATGATTAATAGTAATGA-TTA
60157 GTAATGATTAGTAATAATGAAATTATTATTAATTATGTAGGATTTGATAGTAAT
126 GTAATGATTAGTAATAATGAAATTATTATTAATTATGTAGGATTTGATAGTAAT
*
60211 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTAATAATTATGTATGA-TT--TAGTAATGATTT
*
60276 AGTAATGATTTGATAGTAATAATGAAATTATTATTAA-TATTTAATGATTTAATAGTAATTTGA-
63 AGTAATGATTTGATAGTAATAATGAAATTATTATTAATTATGT-ATGA-TTAATAGTAA--TGAT
*
60339 TAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTATGATTTGATAGTAAT
124 TAGTAATGATTAGTAATAATGAAATTATTATTAATTATGTAGGATTTGATAGTAAT
* * * * *
60395 GATTTAGTAATGATTTGATGATGATTTAAA-TATTTAATGATT-TG-ATGATTTAGTAATGATTT
1 GATTTAGTAATGATTAG-TAAT-AATGAAATTA-TTAATAATTATGTATGATTTAGTAATGATTT
60457 GATAATATCA
Statistics
Matches: 217, Mismatches: 14, Indels: 28
0.84 0.05 0.11
Matches are distributed among these distances:
179 50 0.23
180 6 0.03
181 15 0.07
182 10 0.05
183 30 0.14
184 84 0.39
185 7 0.03
186 15 0.07
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.45
Consensus pattern (179 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTAATAATTATGTATGATTTAGTAATGATTTAGT
AATGATTTGATAGTAATAATGAAATTATTATTAATTATGTATGATTAATAGTAATGATTAGTAAT
GATTAGTAATAATGAAATTATTATTAATTATGTAGGATTTGATAGTAAT
Found at i:60504 original size:26 final size:26
Alignment explanation
Indices: 60448--60639 Score: 150
Period size: 26 Copynumber: 7.6 Consensus size: 26
60438 GATGATTTAG
*
60448 TAATGATTTGATAAT-ATCAAATTATAG
1 TAATGATTTGATAATAATC--ATTATAA
60475 TAATGATTTGATAATAATCATTATAA
1 TAATGATTTGATAATAATCATTATAA
*
60501 TAATGGTTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* * *
60527 AAATGATTTAATAATGAT--TTA-AA
1 TAATGATTTGATAATAATCATTATAA
* * * * * * *
60550 TATTTA-ATGAT-TTGATGATT-TAG
1 TAATGATTTGATAATAATCATTATAA
*
60573 TAATGATTTGATAATAATCATTATAG
1 TAATGATTTGATAATAATCATTATAA
60599 TAATGATTT-AGTAATAATCATTATAA
1 TAATGATTTGA-TAATAATCATTATAA
* *
60625 AAATGATTTAATAAT
1 TAATGATTTGATAAT
60640 GATTTAAATA
Statistics
Matches: 134, Mismatches: 20, Indels: 23
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.03
22 3 0.02
23 12 0.09
24 7 0.05
25 8 0.06
26 80 0.60
27 17 0.13
28 3 0.02
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (26 bp):
TAATGATTTGATAATAATCATTATAA
Found at i:60532 original size:98 final size:95
Alignment explanation
Indices: 60430--60706 Score: 315
Period size: 98 Copynumber: 2.8 Consensus size: 95
60420 TTAAATATTT
* *
60430 AATGATTTGATGATTTAGTAATGATTTGATAATATCA-AATTATAGTAATGATTTGATAATAATC
1 AATGATTTAATGATTTA--AAT-ATTTAATAATATCATAATT-TAGTAATGATTTGATAATAATC
*
60494 ATTATAATAATGGTTTAGTAATAATCATTATAAA
62 ATTATAATAATGATTTAGTAATAATCATTATAAA
* * * *
60528 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
1 AATGA-TT--TAATGATTTAAATATTTAATAATATCATAATTTAGTAATGATTTGATAATAATCA
*
60593 TTATAGTAATGATTTAGTAATAATCATTATAAA
63 TTATAATAATGATTTAGTAATAATCATTATAAA
* * * *
60626 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAAT-ATCA
1 AATGA-TT--TAATGATTTAAATATTTAATAATATCATAATTTAGTAATGATTTGATAATAATC-
*
60690 AATTATAGTAATGATTT
62 -ATTATAATAATGATTT
60707 GATAATTATT
Statistics
Matches: 165, Mismatches: 8, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
97 3 0.02
98 129 0.78
99 24 0.15
101 9 0.05
ACGTcount: A:0.42, C:0.02, G:0.12, T:0.44
Consensus pattern (95 bp):
AATGATTTAATGATTTAAATATTTAATAATATCATAATTTAGTAATGATTTGATAATAATCATTA
TAATAATGATTTAGTAATAATCATTATAAA
Found at i:60544 original size:11 final size:11
Alignment explanation
Indices: 60512--60646 Score: 60
Period size: 11 Copynumber: 11.3 Consensus size: 11
60502 AATGGTTTAG
*
60512 TAATAATCATT
1 TAATAATGATT
*
60523 ATAAAAATGATT
1 -TAATAATGATT
60535 TAATAATGATT
1 TAATAATGATT
60546 T-A-AAT-ATT
1 TAATAATGATT
60554 TAATGATTTGATGATT
1 TAAT-A----ATGATT
*
60570 TAGTAATGATTT
1 TAATAATGA-TT
*
60582 GATAATAATCATT
1 --TAATAATGATT
*
60595 ATAGTAATGATTT
1 -TAATAATGA-TT
*
60608 AGTAATAATCATT
1 --TAATAATGATT
*
60621 ATAAAAATGATT
1 -TAATAATGATT
60633 TAATAATGATT
1 TAATAATGATT
60644 TAA
1 TAA
60647 ATATTTAATG
Statistics
Matches: 95, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
8 4 0.04
9 4 0.04
10 1 0.01
11 29 0.31
12 28 0.29
13 6 0.06
14 14 0.15
15 3 0.03
16 6 0.06
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (11 bp):
TAATAATGATT
Found at i:60553 original size:125 final size:124
Alignment explanation
Indices: 60403--60639 Score: 388
Period size: 125 Copynumber: 1.9 Consensus size: 124
60393 ATGATTTAGT
* *
60403 AATGATTTGATGATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAAT-ATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATC-
* * *
60467 AATTATAGTAATGATTT-GATAATAATCATTATAATAATGGTTTAGTAATAATCATTATAAA
65 -ATTATAGTAATGATTTAG-TAATAATCATTATAAAAATGATTTAATAATAATCATTATAAA
60528 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
60593 TTATAGTAATGATTTAGTAATAATCATTATAAAAATGATTTAATAAT
66 TTATAGTAATGATTTAGTAATAATCATTATAAAAATGATTTAATAAT
60640 GATTTAAATA
Statistics
Matches: 105, Mismatches: 5, Indels: 5
0.91 0.04 0.04
Matches are distributed among these distances:
124 43 0.41
125 59 0.56
126 3 0.03
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.43
Consensus pattern (124 bp):
AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
TTATAGTAATGATTTAGTAATAATCATTATAAAAATGATTTAATAATAATCATTATAAA
Found at i:60640 original size:37 final size:37
Alignment explanation
Indices: 60564--60645 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
60554 TAATGATTTG
* * *
60564 ATGATTTAGTAATGATTTGATAATAATCATTATAGTA
1 ATGATTTAGTAATAATTTGATAAAAATCATTATAATA
*
60601 ATGATTTAGTAATAATCATT-ATAAAAATGATT-TAATA
1 ATGATTTAGTAATAAT--TTGATAAAAATCATTATAATA
60638 ATGATTTA
1 ATGATTTA
60646 AATATTTAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 27 0.69
38 10 0.26
39 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.43
Consensus pattern (37 bp):
ATGATTTAGTAATAATTTGATAAAAATCATTATAATA
Found at i:60833 original size:14 final size:14
Alignment explanation
Indices: 60814--60855 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
60804 TTTAAATATT
60814 TAATGATTTGATAC
1 TAATGATTTGATAC
60828 TAATGA-TT--TAC
1 TAATGATTTGATAC
*
60839 TAATTATTTGATAC
1 TAATGATTTGATAC
60853 TAA
1 TAA
60856 ACATCATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 8 0.33
12 2 0.08
13 2 0.08
14 12 0.50
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (14 bp):
TAATGATTTGATAC
Found at i:63162 original size:32 final size:34
Alignment explanation
Indices: 63087--63168 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
63077 CCAAACCCTT
* *
63087 AAAC-AACTAATAAAATATTTTTTTATATAACTA
1 AAACTAACTAATAAACTATTTTTTCATATAACTA
63120 AAACTAACTAATAAACTATTTTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTTTTTCA-TATAACTA
*
63153 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
63169 TACTAACTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 11 0.25
33 8 0.18
34 20 0.45
35 5 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTTTTTCATATAACTA
Found at i:63275 original size:42 final size:42
Alignment explanation
Indices: 63226--63336 Score: 120
Period size: 42 Copynumber: 2.6 Consensus size: 42
63216 AACTATTTAA
* *
63226 CTAACAAAAACTAATTAAATAATTTTTTTA-TATAACTAACTAT
1 CTAACAAAAACTAATTAAATAATTTTTTAACTAT-A-GAACTAT
*
63269 -TAACAAAAAACTAATT-AATTATTTTTTAACTATAGAACTAT
1 CTAAC-AAAAACTAATTAAATAATTTTTTAACTATAGAACTAT
* * *
63310 CAAACATATACTAATTAAATAATTTTT
1 CTAACAAAAACTAATTAAATAATTTTT
63337 AATTTATGTA
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
41 15 0.26
42 28 0.49
43 14 0.25
ACGTcount: A:0.49, C:0.11, G:0.01, T:0.40
Consensus pattern (42 bp):
CTAACAAAAACTAATTAAATAATTTTTTAACTATAGAACTAT
Found at i:63429 original size:16 final size:18
Alignment explanation
Indices: 63400--63438 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
63390 ACTAATTAAC
*
63400 ATTTATAATAATAAACTA
1 ATTTATAATAATAAACAA
63418 ATTTA-AAT-ATAAACAA
1 ATTTATAATAATAAACAA
63434 ATTTA
1 ATTTA
63439 CCTTATCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTATAATAATAAACAA
Found at i:63487 original size:16 final size:16
Alignment explanation
Indices: 63444--63494 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
63434 ATTTACCTTA
63444 TCTCCCTTTC-TTC-T
1 TCTCCCTTTCTTTCTT
**
63458 TCTTACTTTCCTTTCTT
1 TCTCCCTTT-CTTTCTT
63475 TCTCCCTTTCTTTCTT
1 TCTCCCTTTCTTTCTT
63491 TCTC
1 TCTC
63495 GGCTGCAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
14 7 0.23
15 1 0.03
16 14 0.47
17 8 0.27
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (16 bp):
TCTCCCTTTCTTTCTT
Found at i:63720 original size:50 final size:50
Alignment explanation
Indices: 63649--63757 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 50
63639 TAGGATCACA
*
63649 TGGCATGC-TGTAGGCATGCAGCGGGGAGCAGGAGCACGTGAAG-TTATCT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTAT-T
63698 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTATT
1 TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTATT
63748 TGGC-TGCATG
1 TGGCATGCATG
63758 TGCATGCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
49 14 0.25
50 39 0.68
51 4 0.07
ACGTcount: A:0.22, C:0.18, G:0.39, T:0.21
Consensus pattern (50 bp):
TGGCATGCATGCAGGCATGCAGCGGGGAGCAGGAGCACGTGAAGTTTATT
Found at i:63824 original size:29 final size:29
Alignment explanation
Indices: 63792--63886 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
63782 TGGACGCCGG
63792 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
63821 GGCGACCTACAAGGTCGCCGGGACTACAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
** *
63850 GGCGACCTACAAGGTCGCCCAGACTGCAT
1 GGCGACCTACAAGGTCGCCGGGACTACAT
63879 GGCGACCT
1 GGCGACCT
63887 CTCTATTGGC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.23, C:0.33, G:0.31, T:0.14
Consensus pattern (29 bp):
GGCGACCTACAAGGTCGCCGGGACTACAT
Found at i:63915 original size:32 final size:32
Alignment explanation
Indices: 63873--63944 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
63863 GTCGCCCAGA
*
63873 CTGCATGGCGACCTCTCTATTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
* *
63905 TTGCATGGCGACCTCTCCGTTGGCTGGCTCGT
1 CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
63937 CTGCATGG
1 CTGCATGG
63945 TGAGTATATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.08, C:0.31, G:0.31, T:0.31
Consensus pattern (32 bp):
CTGCATGGCGACCTCTCCATTGGCTGGCTCGT
Found at i:64009 original size:24 final size:19
Alignment explanation
Indices: 63959--63996 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
63949 TATATGGCTT
63959 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
63978 GTATGGCTCGTCTGCATGG
1 GTATGGCTCGTCTGCATGG
63997 TGAGTATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (19 bp):
GTATGGCTCGTCTGCATGG
Found at i:65743 original size:21 final size:21
Alignment explanation
Indices: 65699--65743 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
65689 TTGTATGACA
*
65699 TTTTTTCTTTTATGGAATTTT
1 TTTTTTCTTTTATGGAATTGT
*
65720 TTTTTTACTTTTATGGCA-TGT
1 TTTTTT-CTTTTATGGAATTGT
65741 TTT
1 TTT
65744 CGGTCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.13, C:0.07, G:0.11, T:0.69
Consensus pattern (21 bp):
TTTTTTCTTTTATGGAATTGT
Found at i:65743 original size:22 final size:21
Alignment explanation
Indices: 65699--65743 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
65689 TTGTATGACA
*
65699 TTTTTTCTTTTATGGAATTTT
1 TTTTTTCTTTTATGGAATGTT
*
65720 TTTTTTACTTTTATGGCATGTT
1 TTTTTT-CTTTTATGGAATGTT
65742 TT
1 TT
65744 CGGTCATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.13, C:0.07, G:0.11, T:0.69
Consensus pattern (21 bp):
TTTTTTCTTTTATGGAATGTT
Found at i:66475 original size:22 final size:22
Alignment explanation
Indices: 66444--66493 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
66434 ACCATTATCA
*
66444 TCGCCGCCATTGGTATCGTCTT
1 TCGCCACCATTGGTATCGTCTT
66466 TCGCCACCATTGGTATCGTCTT
1 TCGCCACCATTGGTATCGTCTT
66488 TCGCCA
1 TCGCCA
66494 ATGAGTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.12, C:0.34, G:0.20, T:0.34
Consensus pattern (22 bp):
TCGCCACCATTGGTATCGTCTT
Found at i:67800 original size:15 final size:16
Alignment explanation
Indices: 67772--67817 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
67762 TAATGTGATT
67772 AAAATA-AA-TTTTTA
1 AAAATACAATTTTTTA
67786 AAAAT-CAATTTTTTA
1 AAAATACAATTTTTTA
* *
67801 GAAATACAATATTTTA
1 AAAATACAATTTTTTA
67817 A
1 A
67818 TTAAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 7 0.27
15 10 0.38
16 9 0.35
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (16 bp):
AAAATACAATTTTTTA
Found at i:73363 original size:2 final size:2
Alignment explanation
Indices: 73356--73405 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
73346 CCGCCCCGAT
*
73356 TA TA TA TA TA TA TA TA TA TA TA -A TA TT TA TA T- TA -A T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73394 TA TA TA TA -A TA T
1 TA TA TA TA TA TA T
73406 TTTCGGATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
1 5 0.12
2 36 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79054 original size:15 final size:15
Alignment explanation
Indices: 79021--79064 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
79011 AATAAAACTG
* * *
79021 CAGCAGCAGCAGCAG
1 CAGCAGCAACAACAA
*
79036 CAGCATCAACAACAA
1 CAGCAGCAACAACAA
79051 CAGCAGCAACAACA
1 CAGCAGCAACAACA
79065 GCAACATTAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.45, C:0.34, G:0.18, T:0.02
Consensus pattern (15 bp):
CAGCAGCAACAACAA
Found at i:79056 original size:18 final size:18
Alignment explanation
Indices: 79033--79070 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
79023 GCAGCAGCAG
*
79033 CAGCAGCATCAACAACAA
1 CAGCAGCAACAACAACAA
*
79051 CAGCAGCAACAACAGCAA
1 CAGCAGCAACAACAACAA
79069 CA
1 CA
79071 TTATAACTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.34, G:0.13, T:0.03
Consensus pattern (18 bp):
CAGCAGCAACAACAACAA
Found at i:80894 original size:29 final size:29
Alignment explanation
Indices: 80852--80926 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
80842 AACCCAACCA
**
80852 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
80881 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
80910 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
80927 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:80932 original size:29 final size:29
Alignment explanation
Indices: 80853--80940 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
80843 ACCCAACCAT
* * ****
80853 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
80882 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
80911 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
80940 A
1 A
80941 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:81182 original size:29 final size:29
Alignment explanation
Indices: 81147--81233 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
81137 GTTGGCTGGT
*
81147 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
81176 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
81205 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
81234 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:84202 original size:17 final size:17
Alignment explanation
Indices: 84161--84205 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
84151 CCTCACTTGA
84161 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
84178 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
84195 TTAAATATTTA
1 TTAAATATTTA
84206 TTTTTACATA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:87456 original size:3 final size:3
Alignment explanation
Indices: 87450--87509 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
87440 ATTATTTTTT
* *
87450 TAA TAA TAA TAA T-A TATA TAA TAA TTA TAA TAA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
87495 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
87510 AACGAGTAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:100207 original size:60 final size:60
Alignment explanation
Indices: 100116--100271 Score: 172
Period size: 60 Copynumber: 2.6 Consensus size: 60
100106 TTTAAATTGA
* * * *
100116 TCCTCAAACTTTTGAATATTCCAATTTCATCCTCAAAACATGACTCTCATTCTAAATCAG
1 TCCTTAAACTTTTGAACATTCCAATTCCATCCTCAAAACATGACCCTCATTCTAAATCAG
* * * ** *
100176 TCCTTAAACTTTTGAACATTCTAATTCCATCCTTAAAATATGACCCTTTTTCTAAATTAG
1 TCCTTAAACTTTTGAACATTCCAATTCCATCCTCAAAACATGACCCTCATTCTAAATCAG
* * *
100236 TCATTAGACTTTTGAATC-TTCCAATTTCATCC-CAAA
1 TCCTTAAACTTTTGAA-CATTCCAATTCCATCCTCAAA
100272 TTTCATCCAA
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
59 3 0.04
60 76 0.95
61 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.38
Consensus pattern (60 bp):
TCCTTAAACTTTTGAACATTCCAATTCCATCCTCAAAACATGACCCTCATTCTAAATCAG
Found at i:105165 original size:7 final size:7
Alignment explanation
Indices: 105153--105186 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
105143 AGGATTTATA
105153 TAAACCC
1 TAAACCC
105160 TAAACCC
1 TAAACCC
105167 TAAACCC
1 TAAACCC
105174 TAAACCC
1 TAAACCC
105181 TAAACC
1 TAAACC
105187 AAAACAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.44, C:0.41, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:106508 original size:18 final size:18
Alignment explanation
Indices: 106460--106501 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
106450 TATCATTAAT
106460 AAAAATA-AACAAAAAATC
1 AAAAATATAA-AAAAAATC
*
106478 AAAAATATAAAAAAAATT
1 AAAAATATAAAAAAAATC
106496 AAAAAT
1 AAAAAT
106502 TTTAAAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.17
Consensus pattern (18 bp):
AAAAATATAAAAAAAATC
Found at i:106567 original size:17 final size:17
Alignment explanation
Indices: 106545--106578 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
106535 TAGAATCTAA
106545 CATTTAAATTTTTGATT
1 CATTTAAATTTTTGATT
106562 CATTTAAATTTTTGATT
1 CATTTAAATTTTTGATT
106579 TGTGTGCACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (17 bp):
CATTTAAATTTTTGATT
Found at i:110678 original size:23 final size:22
Alignment explanation
Indices: 110615--110672 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
110605 TCTGACGTTT
110615 TTTTA-AGATTTTTTCGAAATAC
1 TTTTAGAGATTTTTT-GAAATAC
110637 TTTTAGAGATTTTTTGAAATAC
1 TTTTAGAGATTTTTTGAAATAC
*
110659 TTTTAG-GTTTTTTT
1 TTTTAGAGATTTTTT
110673 ATGAAAACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 7 0.21
22 18 0.53
23 9 0.26
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTTAGAGATTTTTTGAAATAC
Found at i:116183 original size:55 final size:53
Alignment explanation
Indices: 116124--116255 Score: 124
Period size: 55 Copynumber: 2.4 Consensus size: 53
116114 GTCAGGATAA
*
116124 ATAAGACTTGAAAAATCTTCAAATGACGAGCCTGCTCCCTATTCCTTCAGGAAGT
1 ATAAGACTTGAAAAATCTTCAAA--ACGAGCCTGCTCCCTATTCATTCAGGAAGT
* * * * * *
116179 ATAAGACTCGAACAATCCTTTGC-AAACGTGTCTTCTCCCTATTCATTCAGGGAGT
1 ATAAGACTTGAAAAAT-C-TT-CAAAACGAGCCTGCTCCCTATTCATTCAGGAAGT
*
116234 ATAAGAC-TCAAACAATCTTCAA
1 ATAAGACTTGAAA-AATCTTCAA
116256 CAAACTTGTC
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
52 1 0.02
53 3 0.05
54 3 0.05
55 49 0.79
56 1 0.02
57 4 0.06
58 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.28
Consensus pattern (53 bp):
ATAAGACTTGAAAAATCTTCAAAACGAGCCTGCTCCCTATTCATTCAGGAAGT
Found at i:116306 original size:51 final size:51
Alignment explanation
Indices: 116213--116516 Score: 509
Period size: 51 Copynumber: 5.9 Consensus size: 51
116203 AACGTGTCTT
* * *
116213 CTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACTTGTCCG
1 CTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCG
*
116268 CTCCCTATTCATTTAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
116319 CTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
* *
116370 CTCCCTATCCATTCAGAGAGTATAGGACTCAATATTCAACGAACTTGTCCG
1 CTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
*
116421 CTCCCTATTCATTCAGAAAGTATAGGACTCAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
116472 CTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 CTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
116517 AATTTGCTTC
Statistics
Matches: 238, Mismatches: 11, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
51 212 0.89
55 26 0.11
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (51 bp):
CTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
Found at i:117858 original size:15 final size:15
Alignment explanation
Indices: 117827--117962 Score: 68
Period size: 15 Copynumber: 8.8 Consensus size: 15
117817 TGAACCCTCC
* *
117827 TTTT-ATTTCTCTTT
1 TTTTCATTTTTCTCT
117841 TTTTCATTTTTCTCT
1 TTTTCATTTTTCTCT
117856 TTTT-ATTTTTCTTTCCTTTT
1 TTTTCATTTTTC--T-C---T
* *
117876 TTTTCATTTTTATTT
1 TTTTCATTTTTCTCT
117891 TTTCTCATTTTT-TC-
1 TTT-TCATTTTTCTCT
*
117905 TTTTCTTCTTTTCTTCT
1 TTTTCAT-TTTTC-TCT
117922 TTTTC-TTTTTCTCAT
1 TTTTCATTTTTCTC-T
* * *
117937 TTTT-ATTATTATTT
1 TTTTCATTTTTCTCT
117951 TTTTCATTTTTC
1 TTTTCATTTTTC
117963 ATTTTTTTTT
Statistics
Matches: 95, Mismatches: 11, Indels: 31
0.69 0.08 0.23
Matches are distributed among these distances:
13 3 0.03
14 25 0.26
15 37 0.39
16 12 0.13
17 6 0.06
19 1 0.01
20 5 0.05
21 6 0.06
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCATTTTTCTCT
Found at i:117891 original size:16 final size:16
Alignment explanation
Indices: 117872--117989 Score: 72
Period size: 15 Copynumber: 7.6 Consensus size: 16
117862 TTTTCTTTCC
117872 TTTTTTTTCATTTTTA
1 TTTTTTTTCATTTTTA
*
117888 TTTTTTCTCATTTTT-
1 TTTTTTTTCATTTTTA
* *
117903 TCTTTTCTTC--TTTTC
1 T-TTTTTTTCATTTTTA
* *
117918 TTCTTTTTC-TTTTTC
1 TTTTTTTTCATTTTTA
** *
117933 TCATTTTT-ATTATTA
1 TTTTTTTTCATTTTTA
117948 -TTTTTTTCATTTTTCA
1 TTTTTTTTCATTTTT-A
117964 TTTTTTTT--TCTTTTA
1 TTTTTTTTCAT-TTTTA
117979 TTTTTTCTTCA
1 TTTTTT-TTCA
117990 AGCGAAACAT
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
14 15 0.19
15 30 0.38
16 27 0.34
17 7 0.09
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTTCATTTTTA
Found at i:117957 original size:21 final size:21
Alignment explanation
Indices: 117838--117983 Score: 68
Period size: 21 Copynumber: 6.7 Consensus size: 21
117828 TTTATTTCTC
*
117838 TTTTTTTCATTTTTCTCTTTTTA
1 TTTTTTTCA-TTTT-TCATTTTA
* *
117861 TTTTTCTTTCCTTTTT--TTTCA
1 -TTTT-TTTCATTTTTCATTTTA
*
117882 TTTTTATT--TTTTCTCATTTTT
1 TTTTT-TTCATTTT-TCATTTTA
* * *
117903 TCTTTTCTTCTTTTCTTCTTTTTC
1 T-TTTT-TTCATTT-TTCATTTTA
*
117927 TTTTTCTCATTTTT-ATTATTA
1 TTTTTTTCATTTTTCATT-TTA
*
117948 TTTTTTTCATTTTTCATTTTT
1 TTTTTTTCATTTTTCATTTTA
*
117969 TTTTCTTTTATTTTT
1 TTTT-TTTCATTTTT
117984 TCTTCAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
18 4 0.04
19 2 0.02
20 8 0.08
21 31 0.32
22 23 0.24
23 5 0.05
24 18 0.19
25 5 0.05
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTTCATTTTTCATTTTA
Found at i:117961 original size:22 final size:21
Alignment explanation
Indices: 117874--117984 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 21
117864 TTCTTTCCTT
117874 TTTTTTCATTTTTATTTTTTCTCA
1 TTTTTT-A-TTTTATTTTTT-TCA
* * *
117898 TTTTTTCTTTTCTTCTTTTC-
1 TTTTTTATTTTATTTTTTTCA
* * *
117918 --TTCT-TTTTCTTTTTCTCA
1 TTTTTTATTTTATTTTTTTCA
117936 -TTTTTATTATTATTTTTTTCA
1 TTTTTTATT-TTATTTTTTTCA
* * *
117957 TTTTTCATTTTTTTTTCTTTTA
1 TTTTTTATTTTATTTT-TTTCA
117979 TTTTTT
1 TTTTTT
117985 CTTCAAGCGA
Statistics
Matches: 68, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
17 11 0.16
18 3 0.04
19 3 0.04
20 2 0.03
21 18 0.26
22 25 0.37
24 6 0.09
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTTTATTTTATTTTTTTCA
Found at i:117969 original size:38 final size:39
Alignment explanation
Indices: 117838--117969 Score: 115
Period size: 38 Copynumber: 3.6 Consensus size: 39
117828 TTTATTTCTC
* *
117838 TTTTTTTCATTTTTC-TCTTTT-T-A-TTTTTCT-TTCCT
1 TTTTTTTCATTTTTCATTTTTTCTCATTTTTTCTATT-CA
* *
117873 TTTTTTTCATTTTT-ATTTTTTCTCATTTTTTCTTTTCT
1 TTTTTTTCATTTTTCATTTTTTCTCATTTTTTCTATTCA
117911 TCTTTTCTTC-TTTTTC--TTTTTCTCATTTTTAT-TATT-A
1 T-TTTT-TTCATTTTTCATTTTTTCTCATTTTT-TCTATTCA
117948 TTTTTTTCATTTTTCATTTTTT
1 TTTTTTTCATTTTTCATTTTTT
117970 TTTCTTTTAT
Statistics
Matches: 82, Mismatches: 3, Indels: 21
0.77 0.03 0.20
Matches are distributed among these distances:
35 22 0.27
36 11 0.13
37 2 0.02
38 32 0.39
39 12 0.15
40 3 0.04
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.77
Consensus pattern (39 bp):
TTTTTTTCATTTTTCATTTTTTCTCATTTTTTCTATTCA
Found at i:117977 original size:8 final size:8
Alignment explanation
Indices: 117836--117925 Score: 58
Period size: 8 Copynumber: 10.9 Consensus size: 8
117826 CTTTTATTTC
117836 TCTTTTTT
1 TCTTTTTT
*
117844 TCATTTTTC
1 TC-TTTTTT
117853 TCTTTTTAT
1 TCTTTTT-T
117862 T-TTTCTTT
1 TCTTT-TTT
*
117870 CCTTTTTTT
1 TC-TTTTTT
*
117879 TCATTTTTA
1 TC-TTTTTT
*
117888 T-TTTTTC
1 TCTTTTTT
*
117895 TCATTTTT
1 TCTTTTTT
*
117903 TCTTTTCT
1 TCTTTTTT
*
117911 TCTTTTCT
1 TCTTTTTT
117919 TCTTTTT
1 TCTTTTT
117926 CTTTTTCTCA
Statistics
Matches: 64, Mismatches: 12, Indels: 12
0.73 0.14 0.14
Matches are distributed among these distances:
7 6 0.09
8 35 0.55
9 20 0.31
10 3 0.05
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.78
Consensus pattern (8 bp):
TCTTTTTT
Found at i:131549 original size:18 final size:18
Alignment explanation
Indices: 131526--131566 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
131516 AGGATTACAC
131526 CATCATCA-AAGGCTGCAA
1 CATCATCACAA-GCTGCAA
131544 CATCATCACAAGCTGCAA
1 CATCATCACAAGCTGCAA
131562 CATCA
1 CATCA
131567 CAACCATCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.39, C:0.32, G:0.12, T:0.17
Consensus pattern (18 bp):
CATCATCACAAGCTGCAA
Found at i:132786 original size:30 final size:30
Alignment explanation
Indices: 132750--132819 Score: 131
Period size: 30 Copynumber: 2.3 Consensus size: 30
132740 AATAAACCGT
*
132750 CCATGTCATCGTCGTCATGGCATTCGAATG
1 CCATGTCATCGTCGTCACGGCATTCGAATG
132780 CCATGTCATCGTCGTCACGGCATTCGAATG
1 CCATGTCATCGTCGTCACGGCATTCGAATG
132810 CCATGTCATC
1 CCATGTCATC
132820 ACGCCGTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.20, C:0.30, G:0.21, T:0.29
Consensus pattern (30 bp):
CCATGTCATCGTCGTCACGGCATTCGAATG
Found at i:152206 original size:24 final size:24
Alignment explanation
Indices: 152178--152227 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
152168 TACGGTGCAT
*
152178 TTCTACGCGGCACTTCAGTGCAAA
1 TTCTACGCGGCACTACAGTGCAAA
* *
152202 TTCTACGTGGCACTACGGTGCAAA
1 TTCTACGCGGCACTACAGTGCAAA
152226 TT
1 TT
152228 TATACGAGCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (24 bp):
TTCTACGCGGCACTACAGTGCAAA
Found at i:152725 original size:11 final size:11
Alignment explanation
Indices: 152711--152744 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
152701 ATTTTACGAA
*
152711 AGTACTGTAGC
1 AGTATTGTAGC
152722 AGTATTGTAGC
1 AGTATTGTAGC
152733 AGTATTGTAGC
1 AGTATTGTAGC
152744 A
1 A
152745 AGGTATCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.32
Consensus pattern (11 bp):
AGTATTGTAGC
Found at i:159837 original size:32 final size:31
Alignment explanation
Indices: 159796--159904 Score: 130
Period size: 32 Copynumber: 3.4 Consensus size: 31
159786 TCAATATCAT
*
159796 ATCGATTGATTTTTGGATCGGGTTAATACCAG
1 ATCGATTGATTTTTGG-TCGGGTTAATACCGG
*
159828 ATCGATTGATTTTTGGGTTGGGTTAATACCGG
1 ATCGATTGATTTTT-GGTCGGGTTAATACCGG
* * *
159860 ATC-AGTTAGATTTATGGTCGGGTCAATATCGG
1 ATCGA-TT-GATTTTTGGTCGGGTTAATACCGG
159892 ATCGATTGATTTT
1 ATCGATTGATTTT
159905 CGGTTTAGGT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
31 6 0.09
32 51 0.77
33 9 0.14
ACGTcount: A:0.23, C:0.11, G:0.27, T:0.39
Consensus pattern (31 bp):
ATCGATTGATTTTTGGTCGGGTTAATACCGG
Found at i:160912 original size:9 final size:9
Alignment explanation
Indices: 160871--160923 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
160861 CTTTTCAGGA
*
160871 TCTTCCTCC
1 TCTTCCTCT
*
160880 TCTTCCTGT
1 TCTTCCTCT
160889 TCCTCCTCCTCT
1 T-CT--TCCTCT
160901 TCTTCCTCT
1 TCTTCCTCT
*
160910 TCTTCGTCT
1 TCTTCCTCT
160919 TCTTC
1 TCTTC
160924 AGGAGGATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
9 27 0.73
10 2 0.05
11 2 0.05
12 6 0.16
ACGTcount: A:0.00, C:0.45, G:0.04, T:0.51
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:168431 original size:20 final size:19
Alignment explanation
Indices: 168406--168449 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
168396 AAAGTTTGGG
*
168406 TTTTTTATAAATAAATTATT
1 TTTTTTATAAA-AAATAATT
*
168426 TTTTTTCTAAAAAATAATT
1 TTTTTTATAAAAAATAATT
168445 TTTTT
1 TTTTT
168450 ATTATTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTTATAAAAAATAATT
Found at i:184123 original size:29 final size:29
Alignment explanation
Indices: 184090--184150 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
184080 TTAAATGATG
**
184090 GGGAAAAATTGTTTATGTTAAACGGGAAC
1 GGGAAAAATCATTTATGTTAAACGGGAAC
*
184119 GGGAAAAATCATTTATGTTAAACGGGGAC
1 GGGAAAAATCATTTATGTTAAACGGGAAC
184148 GGG
1 GGG
184151 GACGGATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.36, C:0.08, G:0.31, T:0.25
Consensus pattern (29 bp):
GGGAAAAATCATTTATGTTAAACGGGAAC
Found at i:184295 original size:15 final size:15
Alignment explanation
Indices: 184273--184313 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
184263 TTAAATTTTA
184273 AAATATATATAATATT
1 AAATATATATAAT-TT
*
184289 -TATATATATAATTT
1 AAATATATATAATTT
184303 AAATATATATA
1 AAATATATATA
184314 CCGACCCGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 2 0.09
15 20 0.91
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AAATATATATAATTT
Found at i:188394 original size:13 final size:13
Alignment explanation
Indices: 188376--188400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
188366 AAATAAAATA
188376 AAATAAAAATTCT
1 AAATAAAAATTCT
188389 AAATAAAAATTC
1 AAATAAAAATTC
188401 GCCAAAAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAAAAATTCT
Found at i:191633 original size:2 final size:2
Alignment explanation
Indices: 191626--191651 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
191616 TCTTATGTTA
191626 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
191652 GGGTATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:193768 original size:2 final size:2
Alignment explanation
Indices: 193761--193788 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
193751 TAATCCTCAA
193761 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
193789 TATGCCCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:195437 original size:186 final size:186
Alignment explanation
Indices: 195123--195498 Score: 743
Period size: 186 Copynumber: 2.0 Consensus size: 186
195113 TGTAATAAAT
195123 TTTGAATTATTATTTGATATATAGTTCGTGTAAATTTTATTTTATGTAATTTTTCTATTAAAATT
1 TTTGAATTATTATTTGATATATAGTTCGTGTAAATTTTATTTTATGTAATTTTTCTATTAAAATT
*
195188 GTAAATTTTGAATGTTGGAGTCCATGCCCAACCCATATTTTTAAACATACCTAATTTTTTGTACA
66 GTAAATTTTGAATGTTGAAGTCCATGCCCAACCCATATTTTTAAACATACCTAATTTTTTGTACA
195253 AGTAATTTTCTGGACCAAATATTTGTATCTAAATCCTTCTAAACTTCGATTGGACC
131 AGTAATTTTCTGGACCAAATATTTGTATCTAAATCCTTCTAAACTTCGATTGGACC
195309 TTTGAATTATTATTTGATATATAGTTCGTGTAAATTTTATTTTATGTAATTTTTCTATTAAAATT
1 TTTGAATTATTATTTGATATATAGTTCGTGTAAATTTTATTTTATGTAATTTTTCTATTAAAATT
195374 GTAAATTTTGAATGTTGAAGTCCATGCCCAACCCATATTTTTAAACATACCTAATTTTTTGTACA
66 GTAAATTTTGAATGTTGAAGTCCATGCCCAACCCATATTTTTAAACATACCTAATTTTTTGTACA
195439 AGTAATTTTCTGGACCAAATATTTGTATCTAAATCCTTCTAAACTTCGATTGGACC
131 AGTAATTTTCTGGACCAAATATTTGTATCTAAATCCTTCTAAACTTCGATTGGACC
195495 TTTG
1 TTTG
195499 GGTTTGAGAA
Statistics
Matches: 189, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
186 189 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (186 bp):
TTTGAATTATTATTTGATATATAGTTCGTGTAAATTTTATTTTATGTAATTTTTCTATTAAAATT
GTAAATTTTGAATGTTGAAGTCCATGCCCAACCCATATTTTTAAACATACCTAATTTTTTGTACA
AGTAATTTTCTGGACCAAATATTTGTATCTAAATCCTTCTAAACTTCGATTGGACC
Found at i:203696 original size:5 final size:5
Alignment explanation
Indices: 203681--203711 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
203671 TTAATAAATG
*
203681 TCATT TTATT TCATT TCATT TCATT TCATT T
1 TCATT TCATT TCATT TCATT TCATT TCATT T
203712 AAAATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.65
Consensus pattern (5 bp):
TCATT
Found at i:206748 original size:2 final size:2
Alignment explanation
Indices: 206741--206768 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
206731 AAACAAATCT
206741 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
206769 GATTAGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:214855 original size:17 final size:19
Alignment explanation
Indices: 214835--214873 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
214825 TAAATGATCC
214835 AAATAAA-AGTAAA-TAAA
1 AAATAAAGAGTAAATTAAA
*
214852 AAATAAAGTGTAAATTAAA
1 AAATAAAGAGTAAATTAAA
214871 AAA
1 AAA
214874 AATAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.21
Consensus pattern (19 bp):
AAATAAAGAGTAAATTAAA
Found at i:215172 original size:6 final size:6
Alignment explanation
Indices: 215158--215193 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
215148 CAGGAGTGCT
* *
215158 CCACTA CCGCTA CCGCTA CCACTA CCACTA CCACTA
1 CCACTA CCACTA CCACTA CCACTA CCACTA CCACTA
215194 GACAAAAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.28, C:0.50, G:0.06, T:0.17
Consensus pattern (6 bp):
CCACTA
Found at i:224629 original size:36 final size:36
Alignment explanation
Indices: 224582--224654 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
224572 GGCTAAAAGG
224582 AGGTCCATTCCCATGGTTAAGCATCAGGAGGGAACA
1 AGGTCCATTCCCATGGTTAAGCATCAGGAGGGAACA
224618 AGGTCCATTCCCATGGTTAAGCATCAGGAGGGAACA
1 AGGTCCATTCCCATGGTTAAGCATCAGGAGGGAACA
224654 A
1 A
224655 TCATGAGCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (36 bp):
AGGTCCATTCCCATGGTTAAGCATCAGGAGGGAACA
Found at i:230465 original size:21 final size:18
Alignment explanation
Indices: 230441--230484 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
230431 AATTTTTATT
230441 TAAAATTATTTTAATTAAAAA
1 TAAAA-TATTTTAA--AAAAA
*
230462 TAAAATATTTTGAAAAAA
1 TAAAATATTTTAAAAAAA
230480 TAAAA
1 TAAAA
230485 ATTGATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
20 7 0.32
21 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAAATATTTTAAAAAAA
Found at i:230485 original size:24 final size:23
Alignment explanation
Indices: 230456--230503 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
230446 TTATTTTAAT
230456 TAAAAATAAAATATTTTGAAAAAA
1 TAAAAATAAAATATTTT-AAAAAA
** *
230480 TAAAAATTGATTATTTTAAAAAA
1 TAAAAATAAAATATTTTAAAAAA
230503 T
1 T
230504 GTTAGAGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (23 bp):
TAAAAATAAAATATTTTAAAAAA
Found at i:234066 original size:45 final size:44
Alignment explanation
Indices: 233994--234362 Score: 359
Period size: 45 Copynumber: 8.2 Consensus size: 44
233984 GTGCTATATC
233994 CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTT
1 CTTCCAAAACAGTATCATC-TTTGATGCAAGATCAATCCTCTTTT
* * *
234039 CATCCAAAACTGTATCAT-TTTCGGATGCAAGATCAATTCTCTTTT
1 CTTCCAAAACAGTATCATCTTT--GATGCAAGATCAATCCTCTTTT
* * *
234084 CTTCCAAAACAGTATCATCACTTGATCCAAGACCAATCCTCTTTT
1 CTTCCAAAACAGTATCATC-TTTGATGCAAGATCAATCCTCTTTT
* * *
234129 CATCCAAAACAGTGTCAT-TTTCGGATGCAAGATCAATTCTCTTTT
1 CTTCCAAAACAGTATCATCTTT--GATGCAAGATCAATCCTCTTTT
* * ** *
234174 CTTCCAAAACGGTAACATCATTCAATGCAAGATCAGTCCTCTTTT
1 CTTCCAAAACAGTATCATC-TTTGATGCAAGATCAATCCTCTTTT
* * * *
234219 CATCCAAAACTGTATC-GCTTTTGGATGCAAGATCAATTCTCTTTT
1 CTTCCAAAACAGTATCATC-TTT-GATGCAAGATCAATCCTCTTTT
* * *
234264 CTTCCAAAACAGTGTCATCGCTTGATCCAAGATCAA-CACTCTTTT
1 CTTCCAAAACAGTATCATC-TTTGATGCAAGATCAATC-CTCTTTT
* * * * * *
234309 CTTCCAAAACAGTATCATTTTCTGATACAATATTAATCTTCTTTC
1 CTTCCAAAACAGTATCATCTT-TGATGCAAGATCAATCCTCTTTT
234354 CTTCCAAAA
1 CTTCCAAAA
234363 TAACCTTATC
Statistics
Matches: 263, Mismatches: 48, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
43 5 0.02
44 4 0.02
45 246 0.94
46 4 0.02
47 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (44 bp):
CTTCCAAAACAGTATCATCTTTGATGCAAGATCAATCCTCTTTT
Found at i:234147 original size:90 final size:90
Alignment explanation
Indices: 233994--234362 Score: 494
Period size: 90 Copynumber: 4.1 Consensus size: 90
233984 GTGCTATATC
* * *
233994 CTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATCATTT
1 CTTCCAAAACAGTATCATCACTTGATCCAAGATCAATCCTCTTTTCATCCAAAACAGTATCATTT
234059 TCGGATGCAAGATCAATTCTCTTTT
66 TCGGATGCAAGATCAATTCTCTTTT
* *
234084 CTTCCAAAACAGTATCATCACTTGATCCAAGACCAATCCTCTTTTCATCCAAAACAGTGTCATTT
1 CTTCCAAAACAGTATCATCACTTGATCCAAGATCAATCCTCTTTTCATCCAAAACAGTATCATTT
234149 TCGGATGCAAGATCAATTCTCTTTT
66 TCGGATGCAAGATCAATTCTCTTTT
* * * * * * *
234174 CTTCCAAAACGGTAACATCA-TTCAATGCAAGATCAGTCCTCTTTTCATCCAAAACTGTATCGCT
1 CTTCCAAAACAGTATCATCACTT-GATCCAAGATCAATCCTCTTTTCATCCAAAACAGTATC-AT
234238 TTT-GGATGCAAGATCAATTCTCTTTT
64 TTTCGGATGCAAGATCAATTCTCTTTT
* * *
234264 CTTCCAAAACAGTGTCATCGCTTGATCCAAGATCAA-CACTCTTTTCTTCCAAAACAGTATCATT
1 CTTCCAAAACAGTATCATCACTTGATCCAAGATCAATC-CTCTTTTCATCCAAAACAGTATCATT
* * * * *
234328 TTCTGATACAATATTAA-TCTTCTTTC
65 TTCGGATGCAAGATCAATTC-TCTTTT
234354 CTTCCAAAA
1 CTTCCAAAA
234363 TAACCTTATC
Statistics
Matches: 244, Mismatches: 29, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
89 9 0.04
90 229 0.94
91 6 0.02
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (90 bp):
CTTCCAAAACAGTATCATCACTTGATCCAAGATCAATCCTCTTTTCATCCAAAACAGTATCATTT
TCGGATGCAAGATCAATTCTCTTTT
Found at i:234308 original size:180 final size:180
Alignment explanation
Indices: 233992--234362 Score: 550
Period size: 180 Copynumber: 2.1 Consensus size: 180
233982 CAGTGCTATA
* **
233992 TCCTTCCAAAACAGTATCATCATTTGATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATCAT
1 TCCTTCCAAAACAGTAACATCATTCAATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATCAT
234057 TTTCGGATGCAAGATCAATTCTCTTTTCTTCCAAAACAGTATCATCACTTGATCCAAGACCAATC
66 TTTCGGATGCAAGATCAATTCTCTTTTCTTCCAAAACAGTATCATCACTTGATCCAAGACCAATC
* *
234122 CTCTTTTCATCCAAAACAGTGTCATTTTCGGATGCAAGATCAAT-TCTCTT
131 CTCTTTTCATCCAAAACAGTATCATTTTCGGATACAAGATCAATCT-TCTT
* * * *
234172 TTCTTCCAAAACGGTAACATCATTCAATGCAAGATCAGTCCTCTTTTCATCCAAAACTGTATCGC
1 TCCTTCCAAAACAGTAACATCATTCAATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATC-A
* * *
234237 TTTT-GGATGCAAGATCAATTCTCTTTTCTTCCAAAACAGTGTCATCGCTTGATCCAAGATCAA-
65 TTTTCGGATGCAAGATCAATTCTCTTTTCTTCCAAAACAGTATCATCACTTGATCCAAGACCAAT
* * * *
234300 CACTCTTTTCTTCCAAAACAGTATCATTTTCTGATACAATATTAATCTTCTT
130 C-CTCTTTTCATCCAAAACAGTATCATTTTCGGATACAAGATCAATCTTCTT
234352 TCCTTCCAAAA
1 TCCTTCCAAAA
234363 TAACCTTATC
Statistics
Matches: 171, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
179 1 0.01
180 165 0.96
181 5 0.03
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (180 bp):
TCCTTCCAAAACAGTAACATCATTCAATGCAAGATCAATCCTCTTTTCATCCAAAACTGTATCAT
TTTCGGATGCAAGATCAATTCTCTTTTCTTCCAAAACAGTATCATCACTTGATCCAAGACCAATC
CTCTTTTCATCCAAAACAGTATCATTTTCGGATACAAGATCAATCTTCTT
Found at i:238388 original size:22 final size:21
Alignment explanation
Indices: 238353--238404 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
238343 GGTTCAACCT
**
238353 AATTTTTTTTTATTTTTATTA
1 AATTTTTTAGTATTTTTATTA
*
238374 AATATTTTTAGTATTTTTATTT
1 AAT-TTTTTAGTATTTTTATTA
238396 AATTTTTTA
1 AATTTTTTA
238405 AATAATTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
AATTTTTTAGTATTTTTATTA
Found at i:240947 original size:19 final size:20
Alignment explanation
Indices: 240925--240970 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
240915 TTTTTATAAG
*
240925 TTTATTAAT-TTTTTGAATT
1 TTTATTAATGTTTTGGAATT
*
240944 TTTAAT-ATGTTTTGGAATT
1 TTTATTAATGTTTTGGAATT
*
240963 TTCATTAA
1 TTTATTAA
240971 AAATATATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 2 0.10
19 18 0.86
20 1 0.05
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.61
Consensus pattern (20 bp):
TTTATTAATGTTTTGGAATT
Found at i:250784 original size:30 final size:30
Alignment explanation
Indices: 250748--250822 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
250738 CATTCCCCAC
*
250748 CATCTGCATCAAACATGCGGACAGGTTGTG
1 CATCTGCATCAAACATACGGACAGGTTGTG
250778 CATCTGCATCAAACATACGGACAGGTTGTG
1 CATCTGCATCAAACATACGGACAGGTTGTG
250808 CATCTGCATCTAAAC
1 CATCTGCATC-AAAC
250823 TACCACTTGC
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 39 0.91
31 4 0.09
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CATCTGCATCAAACATACGGACAGGTTGTG
Found at i:251743 original size:37 final size:36
Alignment explanation
Indices: 251678--251764 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 36
251668 TTATTCCATT
*
251678 ATCATTTTTC-AACAAACATCTACCAAACTTTGAAAA
1 ATCATTTTTCAAAGAAACATCTACCAAACTTTG-AAA
* * *
251714 ATTATTTTTCAAAGAAACATTTACTAAACTTTGAAA
1 ATCATTTTTCAAAGAAACATCTACCAAACTTTGAAA
251750 ATCATTTTTTCAAAG
1 ATCA-TTTTTCAAAG
251765 TTGGTTGCCA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
36 15 0.34
37 29 0.66
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.37
Consensus pattern (36 bp):
ATCATTTTTCAAAGAAACATCTACCAAACTTTGAAA
Found at i:265242 original size:16 final size:16
Alignment explanation
Indices: 265205--265243 Score: 55
Period size: 14 Copynumber: 2.6 Consensus size: 16
265195 ATAACCATGA
*
265205 AAATAATACATTTTAG
1 AAATAATATATTTTAG
265221 --ATAATATATTTTAG
1 AAATAATATATTTTAG
265235 AAATAATAT
1 AAATAATAT
265244 TAAACGATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
14 13 0.65
16 7 0.35
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
AAATAATATATTTTAG
Found at i:267316 original size:19 final size:18
Alignment explanation
Indices: 267274--267318 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
267264 TATTATATTT
* *
267274 TATTATATTTATCAATAA
1 TATTAAATTTAACAATAA
267292 TAATTAAATTTAACAATAAA
1 T-ATTAAATTTAACAAT-AA
267312 TATTAAA
1 TATTAAA
267319 ATAGAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 19 0.83
20 3 0.13
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
TATTAAATTTAACAATAA
Found at i:272394 original size:32 final size:30
Alignment explanation
Indices: 272358--272445 Score: 88
Period size: 30 Copynumber: 2.8 Consensus size: 30
272348 TTAGAAAATG
** * *
272358 TTTTATAATAATTTGATATCTTTTAATGATTA
1 TTTTATAAT-ATTTGA-AAATTTTAATAACTA
272390 TTTTATAATTATTT-AAAATTTTAATAACTA
1 TTTTATAA-TATTTGAAAATTTTAATAACTA
272420 TTTTATAATATTTGAAAGATTGTTAA
1 TTTTATAATATTTGAAA-ATT-TTAA
272446 CTACAGAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
29 5 0.10
30 22 0.46
31 4 0.08
32 16 0.33
33 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (30 bp):
TTTTATAATATTTGAAAATTTTAATAACTA
Found at i:273977 original size:2 final size:2
Alignment explanation
Indices: 273925--273959 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
273915 CTTGAACTTT
273925 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 T
273960 CCTCATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:285895 original size:21 final size:20
Alignment explanation
Indices: 285854--285909 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
285844 TCAGTTTCCA
285854 AAATCGCAATGCGATAGTAC
1 AAATCGCAATGCGATAGTAC
* **
285874 AAATTCGCATTGCGATTTTAC
1 AAA-TCGCAATGCGATAGTAC
*
285895 AGAATCGCAACGCGA
1 A-AATCGCAATGCGA
285910 ATATGAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 3 0.10
21 24 0.83
22 2 0.07
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
AAATCGCAATGCGATAGTAC
Found at i:285991 original size:20 final size:20
Alignment explanation
Indices: 285897--286104 Score: 242
Period size: 20 Copynumber: 10.4 Consensus size: 20
285887 GATTTTACAG
* ** *
285897 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
285917 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
285937 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
285957 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
285977 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
285997 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
286017 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
286037 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
286057 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
286077 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
286097 AATCGCAA
1 AATCGCAA
286105 TGAGAATCTG
Statistics
Matches: 163, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
19 2 0.01
20 159 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:286112 original size:20 final size:20
Alignment explanation
Indices: 285935--286125 Score: 233
Period size: 20 Copynumber: 9.6 Consensus size: 20
285925 CGCGAACACA
*
285935 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
*
285955 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACGAGTATCCG
*
285975 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
285995 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGAGTATCCG
* *
286015 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGAGTATCCG
286035 TAAATCGCAACGA-TAATCCG
1 TAAATCGCAACGAGT-ATCCG
* *
286055 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGAGTATCCG
286075 TAAATCGCAACGA-TAATCCG
1 TAAATCGCAACGAGT-ATCCG
* * *
286095 TAAATCGCAATGAGAATCTG
1 TAAATCGCAACGAGTATCCG
*
286115 TAAATCACAAC
1 TAAATCGCAAC
286126 ACTGAAATTT
Statistics
Matches: 151, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.01
20 150 0.99
ACGTcount: A:0.35, C:0.25, G:0.18, T:0.22
Consensus pattern (20 bp):
TAAATCGCAACGAGTATCCG
Found at i:286854 original size:24 final size:24
Alignment explanation
Indices: 286815--286861 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
286805 AAATTTGGTC
286815 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
286839 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
286862 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:287053 original size:12 final size:12
Alignment explanation
Indices: 287036--287060 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
287026 ATATAATCCT
287036 GAAGAAGAAAAA
1 GAAGAAGAAAAA
287048 GAAGAAGAAAAA
1 GAAGAAGAAAAA
287060 G
1 G
287061 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:289419 original size:53 final size:52
Alignment explanation
Indices: 289351--289573 Score: 358
Period size: 53 Copynumber: 4.2 Consensus size: 52
289341 GCAACGAGAG
* *
289351 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAA
* *
289404 AATCGCAATGTGAAATGAAAATCGCAACGAGGGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAA
289457 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
289509 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
289561 AATCGCATTGCGA
1 AATCGCAATGCGA
289574 TTCTCTCGTT
Statistics
Matches: 161, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
52 71 0.44
53 89 0.55
54 1 0.01
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:289420 original size:19 final size:19
Alignment explanation
Indices: 289351--289573 Score: 216
Period size: 19 Copynumber: 12.7 Consensus size: 19
289341 GCAACGAGAG
289351 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
289370 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
289384 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
289404 AATCGCAATGTGAAATGAA
1 AATCGCAATGCGAAATGAA
**
289423 AATCGCAA--CG--A-GGG
1 AATCGCAATGCGAAATGAA
289437 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
289457 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
289476 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
289490 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
289509 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
289528 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
289542 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
289561 AATCGCATTGCGA
1 AATCGCAATGCGA
289574 TTCTCTCGTT
Statistics
Matches: 168, Mismatches: 14, Indels: 44
0.74 0.06 0.19
Matches are distributed among these distances:
14 41 0.24
15 3 0.02
16 6 0.04
17 7 0.04
18 2 0.01
19 82 0.49
20 27 0.16
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:289494 original size:86 final size:84
Alignment explanation
Indices: 289337--289516 Score: 224
Period size: 86 Copynumber: 2.1 Consensus size: 84
289327 CGGAAATTAC
289337 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAA-GCGG-AATG
*
289402 AAAATCGCAATGTGAAATGAA
64 AAAATCGCAATGCGAAATGAA
* *
289423 AATCGCAACGAGGGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-C-G
1 AATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCCCAA--C---ATGAAAATCGCAAGCGG
*
289486 -A-GAGAATCGCAATGCGAAATGAA
60 AATGAAAATCGCAATGCGAAATGAA
289509 AATCGCAA
1 AATCGCAA
289517 TGCGAAATGA
Statistics
Matches: 84, Mismatches: 4, Indels: 12
0.84 0.04 0.12
Matches are distributed among these distances:
86 52 0.62
87 16 0.19
89 2 0.02
90 1 0.01
92 13 0.15
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (84 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAAGCGGAATGAA
AATCGCAATGCGAAATGAA
Found at i:289513 original size:33 final size:33
Alignment explanation
Indices: 289337--289516 Score: 152
Period size: 33 Copynumber: 5.2 Consensus size: 33
289327 CGGAAATTAC
*
289337 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
289370 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
* * * * * *
289404 AATCGCAATGTG-AAAT-GAAAAT-CGCAACGAGGG
1 AATCGCAACGAGAAAATCG-CAATGCGAAATGA--A
289437 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAAAATCGCAATGCGAAATGAA
*
289476 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
289509 AATCGCAA
1 AATCGCAA
289517 TGCGAAATGA
Statistics
Matches: 116, Mismatches: 16, Indels: 30
0.72 0.10 0.19
Matches are distributed among these distances:
31 5 0.04
32 3 0.03
33 65 0.56
34 17 0.15
36 2 0.02
37 1 0.01
39 9 0.08
40 7 0.06
41 7 0.06
ACGTcount: A:0.46, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:289546 original size:33 final size:33
Alignment explanation
Indices: 289404--289567 Score: 145
Period size: 33 Copynumber: 4.8 Consensus size: 33
289394 CGGAAATGAA
* *
289404 AATCGCAATGTGAAATGAAAATCGCAACGAGGG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
289437 AATCGCAATGCGGAAATGAAAATCGCAATGCGA-
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
* * * *
289470 AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAG
289509 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
289542 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
289568 TTGCGATTCT
Statistics
Matches: 105, Mismatches: 14, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
31 5 0.05
32 3 0.03
33 51 0.49
34 19 0.18
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:289622 original size:19 final size:19
Alignment explanation
Indices: 289582--289678 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
289572 GATTCTCTCG
289582 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
289602 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
289621 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
289635 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
289653 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
289672 TTGCGAT
1 TTGCGAT
289679 AGTCATTTTG
Statistics
Matches: 70, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 8 0.11
17 3 0.04
18 6 0.09
19 29 0.41
20 15 0.21
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:289674 original size:51 final size:53
Alignment explanation
Indices: 289563--289678 Score: 218
Period size: 51 Copynumber: 2.2 Consensus size: 53
289553 GAAATTAAAA
289563 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
289616 TCGCATTGCGATTCTCTCGTTGCGA-TTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
289667 TCGCATTGCGAT
1 TCGCATTGCGAT
289679 AGTCATTTTG
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
51 30 0.48
52 8 0.13
53 25 0.40
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:289686 original size:19 final size:18
Alignment explanation
Indices: 289563--289678 Score: 122
Period size: 19 Copynumber: 6.7 Consensus size: 18
289553 GAAATTAAAA
*
289563 TCGCATTGCGA-TTC-TC
1 TCGCATTGCGATTTCATT
289579 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
289596 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGA-TTTCATT
*
289616 TCGCATTGCGA-TTC-TC
1 TCGCATTGCGATTTCATT
289632 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
289648 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
289667 TCGCATTGCGAT
1 TCGCATTGCGAT
289679 AGTCATTTTG
Statistics
Matches: 86, Mismatches: 3, Indels: 20
0.79 0.03 0.18
Matches are distributed among these distances:
14 12 0.14
15 3 0.03
16 14 0.16
17 5 0.06
18 9 0.10
19 28 0.33
20 15 0.17
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:289802 original size:14 final size:14
Alignment explanation
Indices: 289783--289819 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
289773 CATCAATTAC
289783 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
289797 ACAAATCATCTTTT
1 ACAAATCAACTTTT
289811 ACAAATCAA
1 ACAAATCAA
289820 TTAAACAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:291777 original size:19 final size:19
Alignment explanation
Indices: 291735--291907 Score: 159
Period size: 19 Copynumber: 9.6 Consensus size: 19
291725 TAGTTTACTT
* *
291735 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
291755 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
291774 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
291793 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
291812 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
291831 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
291845 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
291864 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
291878 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
291897 TCGCAATGCGA
1 TCGCAACGCGA
291908 TTTTGGTTTC
Statistics
Matches: 128, Mismatches: 15, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
14 18 0.14
15 1 0.01
16 7 0.05
17 7 0.05
18 1 0.01
19 82 0.64
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:291848 original size:14 final size:14
Alignment explanation
Indices: 291829--291885 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
291819 GCGAAATGAA
*
291829 AATCGCAACGACAG
1 AATCGCAACGAAAG
291843 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
291860 AAAATCGCAACGAGAG
1 --AATCGCAACGAAAG
291876 AATCGCAACG
1 AATCGCAACG
291886 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:291856 original size:33 final size:33
Alignment explanation
Indices: 291810--291902 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
291800 GCGAAACCAA
291810 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* *
291843 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
291876 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
291903 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.22, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:291899 original size:52 final size:52
Alignment explanation
Indices: 291769--291907 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
291759 AACGCGAAAT
* * * *
291769 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * **
291821 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
291873 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
291908 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 43 0.63
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:291919 original size:19 final size:19
Alignment explanation
Indices: 291897--291938 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
291887 GAAATGAAAA
291897 TCGCAATGCGATTTTGGTT
1 TCGCAATGCGATTTTGGTT
**
291916 TCGCGTTGCGATTTTGGTT
1 TCGCAATGCGATTTTGGTT
291935 TCGC
1 TCGC
291939 GTTGCGATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.43
Consensus pattern (19 bp):
TCGCAATGCGATTTTGGTT
Found at i:291939 original size:19 final size:19
Alignment explanation
Indices: 291903--291947 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
291893 AAAATCGCAA
291903 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
291922 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
291941 TGCGATT
1 TGCGATT
291948 CTTTTGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.07, C:0.16, G:0.31, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:291962 original size:33 final size:33
Alignment explanation
Indices: 291919--292012 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 33
291909 TTTGGTTTCG
* *
291919 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTTT
1 CGTTGCGATTTTAGTTTCGCGTTGCGATTCTCT
* *
291952 TGTTGCGATTTTCA-TTTTGCGTTGCGATTCTCT
1 CGTTGCGATTTT-AGTTTCGCGTTGCGATTCTCT
*
291985 CGTTGCGATTTTAAGTTTCGTGTTGCGA
1 CGTTGCGATTTT-AGTTTCGCGTTGCGA
292013 AAGTAAACTA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
33 40 0.78
34 11 0.22
ACGTcount: A:0.10, C:0.17, G:0.26, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTAGTTTCGCGTTGCGATTCTCT
Found at i:291977 original size:19 final size:19
Alignment explanation
Indices: 291903--291980 Score: 76
Period size: 19 Copynumber: 4.4 Consensus size: 19
291893 AAAATCGCAA
*
291903 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCGTTTCGCGT
*
291922 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCGTTTCGCGT
*
291941 TGCGA--TTC-TTT--TGT
1 TGCGATTTTCGTTTCGCGT
* *
291955 TGCGATTTTCATTTTGCGT
1 TGCGATTTTCGTTTCGCGT
291974 TGCGATT
1 TGCGATT
291981 CTCTCGTTGC
Statistics
Matches: 51, Mismatches: 3, Indels: 10
0.80 0.05 0.16
Matches are distributed among these distances:
14 7 0.14
16 6 0.12
17 5 0.10
19 33 0.65
ACGTcount: A:0.08, C:0.15, G:0.27, T:0.50
Consensus pattern (19 bp):
TGCGATTTTCGTTTCGCGT
Found at i:292176 original size:93 final size:93
Alignment explanation
Indices: 292060--292807 Score: 1453
Period size: 93 Copynumber: 8.1 Consensus size: 93
292050 ATGTATTGCA
292060 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
292124 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
292152 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
292217 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
292245 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
292310 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
292338 TTACTTTCAATCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
292403 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
292431 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
292496 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
292524 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
292589 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
292617 TTACTTTCAATCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
292682 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
292710 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
* *
292775 TAGCAGAATTGGTAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
292803 TTACT
1 TTACT
292808 AAGCAATCTA
Statistics
Matches: 649, Mismatches: 6, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 645 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:294518 original size:20 final size:20
Alignment explanation
Indices: 294487--294583 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
294477 TTTTGGTTGA
294487 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
294507 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
294527 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
294546 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
294561 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
294581 AAT
1 AAT
294584 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:294539 original size:21 final size:21
Alignment explanation
Indices: 294485--294549 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
294475 TCTTTTGGTT
294485 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
294506 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
294526 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
294547 GAA
1 GAA
294550 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:294553 original size:14 final size:14
Alignment explanation
Indices: 294534--294590 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
294524 GAGAAATGAA
294534 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
294548 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
294567 AATCGCAACGAGAG
1 AATCGCAACGAGAG
294581 AATCGCAACG
1 AATCGCAACG
294591 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Done.