Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014742.1 Kokia drynarioides strain JFW-HI SEQ_129781, 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: 219017
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:1257 original size:21 final size:20
Alignment explanation
Indices: 1233--1298 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
1223 TAGGTAAAGT
*
1233 AATATATAATTATATTTTAAA
1 AATATA-AAATATATTTTAAA
*
1254 AATA-AAAATATATATCTAAA
1 AATATAAAATATAT-TTTAAA
1274 AAT-TAAAATATTATTATTAAA
1 AATATAAAATA-TATT-TTAAA
1295 AATA
1 AATA
1299 ATTCCTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 7 0.19
20 16 0.43
21 14 0.38
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATAAAATATATTTTAAA
Found at i:1275 original size:20 final size:21
Alignment explanation
Indices: 1245--1299 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
1235 TATATAATTA
1245 TATT-TTAAAAATAAAAATA-
1 TATTATTAAAAATAAAAATAT
*
1264 TA-TATCTAAAAATTAAAATAT
1 TATTAT-TAAAAATAAAAATAT
1285 TATTATTAAAAATAA
1 TATTATTAAAAATAA
1300 TTCCTTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 3 0.10
20 13 0.43
21 10 0.33
22 3 0.10
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TATTATTAAAAATAAAAATAT
Found at i:2444 original size:20 final size:20
Alignment explanation
Indices: 2421--2462 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2411 TCACTAATAA
*
2421 AAATTTTAGA-TGATTTAAAT
1 AAATATTAGAGTGA-TTAAAT
2441 AAATATTAGAGTGATTAAAT
1 AAATATTAGAGTGATTAAAT
2461 AA
1 AA
2463 TTCTTAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (20 bp):
AAATATTAGAGTGATTAAAT
Found at i:3769 original size:29 final size:29
Alignment explanation
Indices: 3737--4139 Score: 323
Period size: 30 Copynumber: 13.7 Consensus size: 29
3727 GTTCGGAATC
3737 AAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
3766 AAAAA-GGGTAATTTATGGAAAGTTTG-GGGT
1 AAAAATGGG--ATTTTTGG-AAGTTCGAGGGT
3796 CAAAAATGGGATTTTTGGAAGTTCGAGGGGT
1 -AAAAATGGGATTTTTGGAAGTTCGA-GGGT
* *
3827 -AAAATGGTAATTTATGGAAAGTTCGA-GGT
1 AAAAATGG-GATTTTTGG-AAGTTCGAGGGT
*
3856 CAAAAATGGGAATTTTGGAAGTTCGAGGGT
1 -AAAAATGGGATTTTTGGAAGTTCGAGGGT
*
3886 -AAAATGGTAATTTTTGGAAGGTTCG-GGGT
1 AAAAATGG-GATTTTTGGAA-GTTCGAGGGT
* * *
3915 CAAAAATGGAATTTTGGGATGTTC-AGGGGT
1 -AAAAATGGGATTTTTGGAAGTTCGA-GGGT
* * *
3945 -AAAATGGTAATTTTGGAAGGTTTG-GGGT
1 AAAAATGGGATTTTTGGAA-GTTCGAGGGT
* * *
3973 CAAAAATGAGATTTTGGGAAGTT-TAGGGGT
1 -AAAAATGGGATTTTTGGAAGTTCGA-GGGT
* *
4003 -AAAATGGTAATTTTGGAAGGTTCG-GGGTT
1 AAAAATGGGATTTTTGGAA-GTTCGAGGG-T
*
4032 AAAAATGGGATTTTTGGAAGTTCAAGGGT
1 AAAAATGGGATTTTTGGAAGTTCGAGGGT
* *
4061 -AAAATGGTAATTCTTGGAAGATTC-AGGGT
1 AAAAATGG-GATTTTTGGAAG-TTCGAGGGT
4090 CAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 -AAAAATGGGATTTTTGGAAGTTCGAGGGT
*
4120 -AAAATGGTAATTTTTGGAAG
1 AAAAATGG-GATTTTTGGAAG
4140 GTTTAGGAAC
Statistics
Matches: 303, Mismatches: 36, Indels: 70
0.74 0.09 0.17
Matches are distributed among these distances:
28 59 0.19
29 90 0.30
30 107 0.35
31 44 0.15
32 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.33, T:0.31
Consensus pattern (29 bp):
AAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:3916 original size:59 final size:59
Alignment explanation
Indices: 3708--4142 Score: 583
Period size: 59 Copynumber: 7.4 Consensus size: 59
3698 GCACGGGGGC
* * **
3708 AAAATGGTAGTTTTT-GAATGTTCGGAATCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * * *
3766 AAAAAGGGTAATTTATGGAAAGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGGT
1 -AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGT
* * * *
3827 AAAATGGTAATTTATGGAAAGTTCGAGGTCAAAAATGGGAATTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
3886 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGAATTTTGGGATGTTC-AGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGT
* * * *
3945 AAAATGGTAA-TTTTGGAAGGTTTGGGGTCAAAAATGAGATTTTGGGAAGTT-TAGGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGA-GGGT
* *
4003 AAAATGGTAA-TTTTGGAAGGTTCGGGGTTAAAAATGGGATTTTTGGAAGTTCAAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* * *
4061 AAAATGGTAATTCTTGGAAGATTCAGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
4120 AAAATGGTAATTTTTGGAAGGTT
1 AAAATGGTAATTTTTGGAAGGTT
4143 TAGGAACCTC
Statistics
Matches: 336, Mismatches: 34, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
58 105 0.31
59 141 0.42
60 86 0.26
61 4 0.01
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
Found at i:5357 original size:24 final size:24
Alignment explanation
Indices: 5329--5375 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5319 ACTTATTTAA
*
5329 TATTAATAGAGTCATTAATATTAT
1 TATTAATACAGTCATTAATATTAT
* * *
5353 TATTAGTACATTTATTAATATTA
1 TATTAATACAGTCATTAATATTA
5376 ATAAAAGCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (24 bp):
TATTAATACAGTCATTAATATTAT
Found at i:5927 original size:15 final size:15
Alignment explanation
Indices: 5907--5977 Score: 106
Period size: 15 Copynumber: 4.7 Consensus size: 15
5897 TTTTTGGTAG
5907 TTTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
*
5922 TTTGTATTTGGGCCA
1 TTTGTAATTGGGCCA
*
5937 TCTGTAATTGGGCCA
1 TTTGTAATTGGGCCA
* *
5952 TTTGTTATTGGGTCA
1 TTTGTAATTGGGCCA
5967 TTTGTAATTGG
1 TTTGTAATTGG
5978 ACTTTGTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 49 1.00
ACGTcount: A:0.17, C:0.11, G:0.27, T:0.45
Consensus pattern (15 bp):
TTTGTAATTGGGCCA
Found at i:6014 original size:14 final size:13
Alignment explanation
Indices: 5971--6011 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
5961 GGGTCATTTG
5971 TAATTGGACTTTGT
1 TAATTGGACTTT-T
5985 T--TTGGACTTTT
1 TAATTGGACTTTT
*
5996 TAATTGGATTTTT
1 TAATTGGACTTTT
6009 TAA
1 TAA
6012 ATTTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
11 2 0.08
12 9 0.38
13 12 0.50
14 1 0.04
ACGTcount: A:0.22, C:0.05, G:0.17, T:0.56
Consensus pattern (13 bp):
TAATTGGACTTTT
Found at i:6031 original size:17 final size:16
Alignment explanation
Indices: 6009--6064 Score: 67
Period size: 17 Copynumber: 3.4 Consensus size: 16
5999 TTGGATTTTT
*
6009 TAAATTTAATTTTATAA
1 TAAATTTAAATTTA-AA
*
6026 TAAATTGAAATTTAAAA
1 TAAATTTAAATTT-AAA
*
6043 TAAACTTAAATTTAAA
1 TAAATTTAAATTTAAA
6059 TAAATT
1 TAAATT
6065 CAATTTCCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
16 8 0.24
17 24 0.73
18 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:6280 original size:25 final size:26
Alignment explanation
Indices: 6252--6310 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
6242 TTTTGATCAC
*
6252 TTATTTTATATTTT-TAAAATTTATT
1 TTATTTTATATTTTATAAAATTAATT
* * *
6277 TTATTTTTTCTTTTATAATATTAATT
1 TTATTTTATATTTTATAAAATTAATT
6303 TTAGTTTT
1 TTA-TTTT
6311 TTCCGTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 12 0.43
26 12 0.43
27 4 0.14
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (26 bp):
TTATTTTATATTTTATAAAATTAATT
Found at i:6284 original size:26 final size:27
Alignment explanation
Indices: 6255--6312 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
6245 TGATCACTTA
* *
6255 TTTTATATTTT-TAAAATTTATTTTA-
1 TTTTTTATTTTATAAAATTAATTTTAG
* *
6280 TTTTTTCTTTTATAATATTAATTTTAG
1 TTTTTTATTTTATAAAATTAATTTTAG
6307 TTTTTT
1 TTTTTT
6313 CCGTAAAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.33
26 12 0.44
27 6 0.22
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTTTATTTTATAAAATTAATTTTAG
Found at i:7641 original size:41 final size:41
Alignment explanation
Indices: 7591--7697 Score: 187
Period size: 41 Copynumber: 2.6 Consensus size: 41
7581 GACTTCTATA
* *
7591 GATACCTTGGCCGAGATTACCGAAACAACTTCAGTTCTACC
1 GATACCTTGGCCAAGATTATCGAAACAACTTCAGTTCTACC
7632 GATACCTTGGCCAAGATTATCGAAACAACTTCAGTTCTACC
1 GATACCTTGGCCAAGATTATCGAAACAACTTCAGTTCTACC
*
7673 GATACATTGGCCAAGATTATCGAAA
1 GATACCTTGGCCAAGATTATCGAAA
7698 TGAAGACTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
GATACCTTGGCCAAGATTATCGAAACAACTTCAGTTCTACC
Found at i:8144 original size:21 final size:21
Alignment explanation
Indices: 8118--8160 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
8108 CTTGTACACA
8118 CTTATGGGTTAAGTTTCCAAT
1 CTTATGGGTTAAGTTTCCAAT
8139 CTTATGGGTTAAGTTTCCAAT
1 CTTATGGGTTAAGTTTCCAAT
8160 C
1 C
8161 ATTCTTTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (21 bp):
CTTATGGGTTAAGTTTCCAAT
Found at i:10106 original size:22 final size:21
Alignment explanation
Indices: 10081--10146 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
10071 TTAAAAATCC
*
10081 AAATATTTATAAAAATTATAAA
1 AAATATATATAAAAATT-TAAA
* *
10103 AAATAAAAATAAAAATTCTAAA
1 AAATATATATAAAAATT-TAAA
* *
10125 GAATATATA-AAAAAGTTAAA
1 AAATATATATAAAAATTTAAA
10145 AA
1 AA
10147 TTCTAAAATA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 5 0.14
21 6 0.17
22 24 0.69
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (21 bp):
AAATATATATAAAAATTTAAA
Found at i:30604 original size:21 final size:21
Alignment explanation
Indices: 30576--30649 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
30566 GGAGTTTTTT
30576 TATCGGTAGAAG-CATGACTTG
1 TATCGGTAGAAGTCAT-ACTTG
*
30597 TTTCGGTAGAAGTCATACTTG
1 TATCGGTAGAAGTCATACTTG
* * *
30618 TATCAGTAGAACT-ATCACATG
1 TATCGGTAGAAGTCAT-ACTTG
30639 TATCGGTAGAA
1 TATCGGTAGAA
30650 ATCTGCACTG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.04
21 40 0.89
22 3 0.07
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (21 bp):
TATCGGTAGAAGTCATACTTG
Found at i:39253 original size:24 final size:24
Alignment explanation
Indices: 39216--39296 Score: 135
Period size: 24 Copynumber: 3.4 Consensus size: 24
39206 TAAACTAATA
* * *
39216 AGAGTTTGACTTAAACAAATAAAG
1 AGAGTTTAATTTAAACAAATAAAC
39240 AGAGTTTAATTTAAACAAATAAAC
1 AGAGTTTAATTTAAACAAATAAAC
39264 AGAGTTTAATTTAAACAAATAAAC
1 AGAGTTTAATTTAAACAAATAAAC
39288 AGAGTTTAA
1 AGAGTTTAA
39297 CTGAAAGATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.28
Consensus pattern (24 bp):
AGAGTTTAATTTAAACAAATAAAC
Found at i:39666 original size:109 final size:108
Alignment explanation
Indices: 39511--39713 Score: 259
Period size: 109 Copynumber: 1.9 Consensus size: 108
39501 AAAAAGAGGC
* *
39511 AATGTTCTTTTATTTGAGAGATTCGAAAAAATATGTCATAACGTATTGGTTATGAATTTTCGTT-
1 AATGTTCTTTTATTTAAGAGATTCGAAAAAATATGTCATAACGTATTGGGTATGAATTTTCGTTG
*
39575 AACCTTACA-TAATTAAATATCCTATTTAAAGTAGGTAAATATTT
66 AACC-TA-AGTAATTAAACATCCTATTTAAAGTAGGTAAATATTT
* * * * * *
39619 AATGTTCTTTTATTTTAAG-GAATTCGAGAAATTGTGTCCTAACGTATTGGGTATGATTTTTCTT
1 AATGTTCTTTTA-TTTAAGAG-ATTCGAAAAAATATGTCATAACGTATTGGGTATGAATTTTCGT
*
39683 TGAACCTAAGTAATTGAACATCCTATTTAAA
64 TGAACCTAAGTAATTAAACATCCTATTTAAA
39714 AATCGATAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
108 14 0.17
109 63 0.78
110 4 0.05
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.42
Consensus pattern (108 bp):
AATGTTCTTTTATTTAAGAGATTCGAAAAAATATGTCATAACGTATTGGGTATGAATTTTCGTTG
AACCTAAGTAATTAAACATCCTATTTAAAGTAGGTAAATATTT
Found at i:41621 original size:39 final size:39
Alignment explanation
Indices: 41573--41835 Score: 276
Period size: 39 Copynumber: 6.7 Consensus size: 39
41563 GTTATCAAAA
* * * * *
41573 TACTTAACTGGCAGTGACATTGTAAACACTACAATGCAT
1 TACTGAACTGACAGTGACACTGTAAACACTGCAATACAT
* *
41612 TACTGAACTGACAGTGACATTGTAAACACT-CAAATAAAT
1 TACTGAACTGACAGTGACACTGTAAACACTGC-AATACAT
* ** * *
41651 GACTGAACTGGTAGTGACACTGTAAACATTGTAATACAT
1 TACTGAACTGACAGTGACACTGTAAACACTGCAATACAT
* * * *
41690 TACTGAACTGACAGTGATACTGTGAACATTGTAATACAT
1 TACTGAACTGACAGTGACACTGTAAACACTGCAATACAT
* *
41729 TACTGAACTGACAGTGACACTGTAAACACTGCAATGCAA
1 TACTGAACTGACAGTGACACTGTAAACACTGCAATACAT
* * * * * *
41768 CACTGAACTGACAGTAACACAGTAAACACTGCAAAAAAA
1 TACTGAACTGACAGTGACACTGTAAACACTGCAATACAT
* *
41807 TACTGAACTGACAGTGATATTGTAAACAC
1 TACTGAACTGACAGTGACACTGTAAACAC
41836 CGAATGTTGT
Statistics
Matches: 189, Mismatches: 33, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
38 1 0.01
39 188 0.99
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (39 bp):
TACTGAACTGACAGTGACACTGTAAACACTGCAATACAT
Found at i:41709 original size:22 final size:22
Alignment explanation
Indices: 41684--41745 Score: 53
Period size: 22 Copynumber: 3.0 Consensus size: 22
41674 AAACATTGTA
41684 ATACATTACTGAACTGACAGTG
1 ATACATTACTGAACTGACAGTG
* ** *
41706 ATAC--T-GTGAAC--ATTGTA
1 ATACATTACTGAACTGACAGTG
41723 ATACATTACTGAACTGACAGTG
1 ATACATTACTGAACTGACAGTG
41745 A
1 A
41746 CACTGTAAAC
Statistics
Matches: 27, Mismatches: 8, Indels: 10
0.60 0.18 0.22
Matches are distributed among these distances:
17 7 0.26
19 6 0.22
20 6 0.22
22 8 0.30
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (22 bp):
ATACATTACTGAACTGACAGTG
Found at i:42050 original size:25 final size:26
Alignment explanation
Indices: 42021--42070 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
42011 TTAAATTGTA
42021 ATAACAAAC-TACCCTAAAAGTATAT
1 ATAACAAACATACCCTAAAAGTATAT
*
42046 ATAACAAACATAGCCTAAAAGTATA
1 ATAACAAACATACCCTAAAAGTATA
42071 CTCATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.54, C:0.18, G:0.06, T:0.22
Consensus pattern (26 bp):
ATAACAAACATACCCTAAAAGTATAT
Found at i:43332 original size:52 final size:52
Alignment explanation
Indices: 43251--43487 Score: 370
Period size: 52 Copynumber: 4.6 Consensus size: 52
43241 TTCTCATTTA
*
43251 ATACTCACGATGACAC--AGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
43301 ACACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAAGATTCAT
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * * *
43353 ATACTCACAATGACACATAGTCATCAGACCTTATAATTCATAAAGGATTCAT
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
*
43405 ATACACACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
43457 ATACTCACGATGACACATATTCATCGGACCT
1 ATACTCACAATGACACATAGTCATCGGACCT
43488 TTTGCATTTA
Statistics
Matches: 168, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
50 14 0.08
52 154 0.92
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (52 bp):
ATACTCACAATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:44458 original size:16 final size:16
Alignment explanation
Indices: 44434--44466 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
44424 TCCTTACAAA
*
44434 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
44450 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
44466 T
1 T
44467 AAAATCATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.03, T:0.55
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:45028 original size:28 final size:28
Alignment explanation
Indices: 44995--45053 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
44985 ATTGACTATC
44995 TAAACTATTAAATTTCATAACCAAATTT
1 TAAACTATTAAATTTCATAACCAAATTT
45023 TAAACTATTAAATTTCATAACCAAATTT
1 TAAACTATTAAATTTCATAACCAAATTT
45051 TAA
1 TAA
45054 TACAATACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (28 bp):
TAAACTATTAAATTTCATAACCAAATTT
Found at i:48949 original size:20 final size:20
Alignment explanation
Indices: 48926--48989 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
48916 AGTGAAACTG
48926 TAAACACTGCAATACATTAC
1 TAAACACTGCAATACATTAC
* *
48946 T-AA-ACTGACAGTGACATT-G
1 TAAACACTG-CAAT-ACATTAC
*
48965 TAAACACTCCAATACATTAC
1 TAAACACTGCAATACATTAC
48985 TAAAC
1 TAAAC
48990 TGGCAGTGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
18 4 0.12
19 11 0.32
20 16 0.47
21 3 0.09
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (20 bp):
TAAACACTGCAATACATTAC
Found at i:49001 original size:20 final size:20
Alignment explanation
Indices: 48939--49002 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
48929 ACACTGCAAT
48939 ACATTACTAAACTGACAGTG
1 ACATTACTAAACTGACAGTG
* * *
48959 ACATT-GTAAACACT-CCAAT-
1 ACATTACT-AA-ACTGACAGTG
*
48978 ACATTACTAAACTGGCAGTG
1 ACATTACTAAACTGACAGTG
48998 ACATT
1 ACATT
49003 GTAAACACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (20 bp):
ACATTACTAAACTGACAGTG
Found at i:49057 original size:74 final size:76
Alignment explanation
Indices: 48905--49124 Score: 239
Period size: 74 Copynumber: 2.9 Consensus size: 76
48895 GTTATCAAAA
* * * *
48905 TACTAAACT-GCAGTGAAACTGTAAACACTGCAATACATTACTAAACTGACAGTGACATTGTAAA
1 TACTAAACTGGCAGTGACATTGTAAACACT--AATACATTACTAAACTGACAGTGACACTATAAA
48969 CACTCCAATACAT
64 CACTCCAATACAT
* * * *
48982 TACTAAACTGGCAGTGACATTGTAAACACT-ATACATTATTGAACTG-GAGTGACACTATAGACA
1 TACTAAACTGGCAGTGACATTGTAAACACTAATACATTACTAAACTGACAGTGACACTATAAACA
* *
49045 TTGCAATACAT
66 CTCCAATACAT
* * * * * *
49056 TACTGAACTGGCAGTGACATTGTAAACACTGTAATGCAATACTGAACTGTCAGTGACACTGTAAA
1 TACTAAACTGGCAGTGACATTGTAAACAC--TAATACATTACTAAACTGACAGTGACACTATAAA
49121 CACT
64 CACT
49125 GCAAAGAAAT
Statistics
Matches: 120, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
74 50 0.42
75 14 0.12
76 1 0.01
77 22 0.18
78 33 0.28
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.26
Consensus pattern (76 bp):
TACTAAACTGGCAGTGACATTGTAAACACTAATACATTACTAAACTGACAGTGACACTATAAACA
CTCCAATACAT
Found at i:49110 original size:113 final size:113
Alignment explanation
Indices: 48910--49124 Score: 304
Period size: 113 Copynumber: 1.9 Consensus size: 113
48900 CAAAATACTA
*
48910 AACTGCAGTGAAACTGTAAACACTGCAATACATTACTAAACTGACAGTGACATTGTAAACACTCC
1 AACTGCAGTGAAACTATAAACACTGCAATACATTACTAAACTGACAGTGACATTGTAAACACTCC
* *
48975 AATACATTACTAAACTGGCAGTGACATTGTAAACACTATACATTATTG
66 AATACAATACTAAACTGGCAGTGACACTGTAAACACTATACATTATTG
* * * * * * **
49023 AACTGGAGTGACACTATAGACATTGCAATACATTACTGAACTGGCAGTGACATTGTAAACACTGT
1 AACTGCAGTGAAACTATAAACACTGCAATACATTACTAAACTGACAGTGACATTGTAAACACTCC
* * *
49088 AATGCAATACTGAACTGTCAGTGACACTGTAAACACT
66 AATACAATACTAAACTGGCAGTGACACTGTAAACACT
49125 GCAAAGAAAT
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
113 88 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (113 bp):
AACTGCAGTGAAACTATAAACACTGCAATACATTACTAAACTGACAGTGACATTGTAAACACTCC
AATACAATACTAAACTGGCAGTGACACTGTAAACACTATACATTATTG
Found at i:49136 original size:39 final size:38
Alignment explanation
Indices: 48905--49162 Score: 247
Period size: 39 Copynumber: 6.7 Consensus size: 38
48895 GTTATCAAAA
* *
48905 TACTAAACTGCAGTGAAACTGTAAACACTGCAATACAT
1 TACTGAACTGCAGTGACACTGTAAACACTGCAATACAT
* * *
48943 TACTAAACTGACAGTGACATTGTAAACACTCCAATACAT
1 TACTGAACTG-CAGTGACACTGTAAACACTGCAATACAT
* *
48982 TACTAAACTGGCAGTGACATTGTAAACACT---ATACAT
1 TACTGAACT-GCAGTGACACTGTAAACACTGCAATACAT
* * * * *
49018 TATTGAACTGGAGTGACACTATAGACATTGCAATACAT
1 TACTGAACTGCAGTGACACTGTAAACACTGCAATACAT
* * * *
49056 TACTGAACTGGCAGTGACATTGTAAACACTGTAATGCAA
1 TACTGAACT-GCAGTGACACTGTAAACACTGCAATACAT
* *
49095 TACTGAACTGTCAGTGACACTGTAAACACTGCAA-AGAAA
1 TACTGAACTG-CAGTGACACTGTAAACACTGCAATA-CAT
*
49134 TACTGAACT-AACGTTGACACTGTAAACAC
1 TACTGAACTGCA-G-TGACACTGTAAACAC
49163 CGTAATGTTG
Statistics
Matches: 186, Mismatches: 24, Indels: 19
0.81 0.10 0.08
Matches are distributed among these distances:
35 15 0.08
36 13 0.07
37 1 0.01
38 26 0.14
39 130 0.70
40 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (38 bp):
TACTGAACTGCAGTGACACTGTAAACACTGCAATACAT
Found at i:65000 original size:29 final size:29
Alignment explanation
Indices: 64968--65032 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
64958 AAGTAGAGGG
*
64968 ACTAAATTCTTAAAAATAAAAGTATAGAA
1 ACTAAATTCTTAAAAATAAAAATATAGAA
*
64997 ACTAAATTCTTGAAAATAAAAATATAGAA
1 ACTAAATTCTTAAAAATAAAAATATAGAA
65026 ACTAAAT
1 ACTAAAT
65033 GATGTATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (29 bp):
ACTAAATTCTTAAAAATAAAAATATAGAA
Found at i:65642 original size:22 final size:22
Alignment explanation
Indices: 65617--65665 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
65607 AGTTTAGCCC
*
65617 TTATTCCAAAAAGATTTGACTT
1 TTATTCCAAAAAGATTTGACTA
* * *
65639 TTATTTCTAAAAGATTTTACTA
1 TTATTCCAAAAAGATTTGACTA
65661 TTATT
1 TTATT
65666 TGAGCATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (22 bp):
TTATTCCAAAAAGATTTGACTA
Found at i:65666 original size:22 final size:22
Alignment explanation
Indices: 65625--65666 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
65615 CCTTATTCCA
*
65625 AAAAGATTTGACTTTTATTTCT
1 AAAAGATTTGACTATTATTTCT
*
65647 AAAAGATTTTACTATTATTT
1 AAAAGATTTGACTATTATTT
65667 GAGCATTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (22 bp):
AAAAGATTTGACTATTATTTCT
Found at i:69618 original size:69 final size:69
Alignment explanation
Indices: 69503--69710 Score: 299
Period size: 69 Copynumber: 3.0 Consensus size: 69
69493 TCTCTGAGTA
* *
69503 TTTCAACATGTCCATCGAACCCTATGGATAGACAGGTTGATGCTGGTGTTGTTTTAGCTTCTCCG
1 TTTCAACATGTCCATCGAACCCTATGGAAAGACAGGTTGATGCTGGTGCTGTTTTAGCTTCTCCG
69568 TGTG
66 TGTG
* * * * * *
69572 TTTCAACATGTCCATCGAACCCTTTAGACAGACAGGTTGATACTGGTGCTGTTTTAACTTCTCTG
1 TTTCAACATGTCCATCGAACCCTATGGAAAGACAGGTTGATGCTGGTGCTGTTTTAGCTTCTCCG
*
69637 AGTG
66 TGTG
* * * *
69641 TTTCAACATGTCCATCGAATCCTGTGGAAAGATAGGTTGATGCTGGTACTGTTTTAGCTTCTCCG
1 TTTCAACATGTCCATCGAACCCTATGGAAAGACAGGTTGATGCTGGTGCTGTTTTAGCTTCTCCG
69706 TGTG
66 TGTG
69710 T
1 T
69711 GGATGTAGAG
Statistics
Matches: 121, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 121 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (69 bp):
TTTCAACATGTCCATCGAACCCTATGGAAAGACAGGTTGATGCTGGTGCTGTTTTAGCTTCTCCG
TGTG
Found at i:72885 original size:26 final size:25
Alignment explanation
Indices: 72841--72894 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
72831 GAAAAATTTC
* * * *
72841 ACTCGACTCAATTTGATTTGATTCG
1 ACTCGACTAAATTTCATTTCACTCG
72866 ACTCGACTTAAATTTCATTTCACTCG
1 ACTCGAC-TAAATTTCATTTCACTCG
72892 ACT
1 ACT
72895 TGATTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (25 bp):
ACTCGACTAAATTTCATTTCACTCG
Found at i:74482 original size:14 final size:15
Alignment explanation
Indices: 74445--74482 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
74435 ACTATATAGA
74445 TGAATTAAATTTTAAC
1 TGAATT-AATTTTAAC
74461 TGAA-TAATTTT-AC
1 TGAATTAATTTTAAC
74474 TGAATTAAT
1 TGAATTAAT
74483 GATTAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.29
14 10 0.48
15 1 0.05
16 4 0.19
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (15 bp):
TGAATTAATTTTAAC
Found at i:78171 original size:23 final size:22
Alignment explanation
Indices: 78141--78264 Score: 126
Period size: 23 Copynumber: 5.5 Consensus size: 22
78131 ACGCTAGCGC
78141 GCTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTT-GCACTTTGTGT
78164 GCTTACTGTTT-CACATTTCGTGT
1 GCTTACTGTTTGCAC-TTT-GTGT
* * *
78187 GCTTACTGATTTGCGCTATGTGC
1 GCTTACTG-TTTGCACTTTGTGT
* * *
78210 GCCTACTGATTGCACTGTGTGT
1 GCTTACTGTTTGCACTTTGTGT
*
78232 GCTTACTAGATTGCAC-TTGTGT
1 GCTTACT-GTTTGCACTTTGTGT
78254 GCTTACTGTTT
1 GCTTACTGTTT
78265 CCTCAGCACT
Statistics
Matches: 85, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
21 6 0.07
22 31 0.36
23 41 0.48
24 5 0.06
25 2 0.02
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.44
Consensus pattern (22 bp):
GCTTACTGTTTGCACTTTGTGT
Found at i:78230 original size:22 final size:22
Alignment explanation
Indices: 78190--78255 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
78180 TTCGTGTGCT
* *
78190 TACTGATTTGCGCTATGTGCGCC
1 TACTGA-TTGCACTGTGTGCGCC
* *
78213 TACTGATTGCACTGTGTGTGCT
1 TACTGATTGCACTGTGTGCGCC
78235 TACTAGATTGCACTTGTGTGC
1 TACT-GATTGCAC-TGTGTGC
78256 TTACTGTTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 16 0.44
23 14 0.39
24 6 0.17
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (22 bp):
TACTGATTGCACTGTGTGCGCC
Found at i:83780 original size:23 final size:23
Alignment explanation
Indices: 83745--83794 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
83735 CAAGTGCGCC
*
83745 TACT-GATTGCACTATGTGTGCT
1 TACTGGATTACACTATGTGTGCT
*
83767 TACTGGATTACACTGTGTGTGCT
1 TACTGGATTACACTATGTGTGCT
83790 TACTG
1 TACTG
83795 TTTCCCTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.40
Consensus pattern (23 bp):
TACTGGATTACACTATGTGTGCT
Found at i:91500 original size:17 final size:17
Alignment explanation
Indices: 91463--91564 Score: 123
Period size: 17 Copynumber: 5.9 Consensus size: 17
91453 TTGAGCTCAA
*
91463 ATTTTAAATTTTAATTTT
1 ATTTTAAA-TTTAAATTT
* *
91481 ATTTTAAGTTTGAATTT
1 ATTTTAAATTTAAATTT
* *
91498 ATTTTAATTTTAAACTT
1 ATTTTAAATTTAAATTT
*
91515 ATTTTAAATTTGAATTT
1 ATTTTAAATTTAAATTT
*
91532 ACTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
91549 ATTTTAAATTAAAATT
1 ATTTTAAATTTAAATT
91565 AATTAAGGAA
Statistics
Matches: 71, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
17 64 0.90
18 7 0.10
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:91509 original size:34 final size:34
Alignment explanation
Indices: 91463--91558 Score: 138
Period size: 34 Copynumber: 2.8 Consensus size: 34
91453 TTGAGCTCAA
* *
91463 ATTTTAAATTTTAATTTTATTTTAAGTTTGAATTT
1 ATTTT-AATTTTAAATTTATTTTAAATTTGAATTT
*
91498 ATTTTAATTTTAAACTTATTTTAAATTTGAATTT
1 ATTTTAATTTTAAATTTATTTTAAATTTGAATTT
* *
91532 ACTTTAAATTTAAATTTATTTTAAATT
1 ATTTTAATTTTAAATTTATTTTAAATT
91559 AAAATTAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
34 50 0.91
35 5 0.09
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.59
Consensus pattern (34 bp):
ATTTTAATTTTAAATTTATTTTAAATTTGAATTT
Found at i:91543 original size:6 final size:6
Alignment explanation
Indices: 91465--91564 Score: 55
Period size: 6 Copynumber: 17.3 Consensus size: 6
91455 GAGCTCAAAT
* * * * * * *
91465 TTTAAA TTTTAA TTTTAT TTTAAG TTTGAA TTT-AT TTTAAT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
91512 CTT-AT TTTAAA TTTGAA TTT-AC TTTAAA TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
91557 TTAAAA TT
1 TTTAAA TT
91565 AATTAAGGAA
Statistics
Matches: 72, Mismatches: 18, Indels: 8
0.73 0.18 0.08
Matches are distributed among these distances:
5 15 0.21
6 57 0.79
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:91556 original size:11 final size:12
Alignment explanation
Indices: 91469--91558 Score: 59
Period size: 11 Copynumber: 7.9 Consensus size: 12
91459 TCAAATTTTA
91469 AATTTT-AATTT
1 AATTTTAAATTT
* *
91480 TATTTTAAGTTT
1 AATTTTAAATTT
*
91492 GAA-TTT-ATTTT
1 -AATTTTAAATTT
*
91503 AATTTTAAACTT
1 AATTTTAAATTT
91515 -ATTTTAAATTT
1 AATTTTAAATTT
*
91526 GAA-TTT-ACTTT
1 -AATTTTAAATTT
*
91537 AAATTTAAATTT
1 AATTTTAAATTT
91549 -ATTTTAAATT
1 AATTTTAAATT
91559 AAAATTAATT
Statistics
Matches: 61, Mismatches: 10, Indels: 16
0.70 0.11 0.18
Matches are distributed among these distances:
10 4 0.07
11 38 0.62
12 17 0.28
13 2 0.03
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (12 bp):
AATTTTAAATTT
Found at i:91637 original size:85 final size:85
Alignment explanation
Indices: 91538--91709 Score: 335
Period size: 85 Copynumber: 2.0 Consensus size: 85
91528 ATTTACTTTA
*
91538 AATTTAAATTTATTTTAAATTAAAATTAATTAAGGAATGTCCAAAATACAAATTGAACGGCCCAA
1 AATTTAAATTTATTTTAAATTAAAATTAATTAAGGAATGTCCAAAATACAAATTGAAAGGCCCAA
91603 ATTACTTGTCCCTAAAGCCC
66 ATTACTTGTCCCTAAAGCCC
91623 AATTTAAATTTATTTTAAATTAAAATTAATTAAGGAATGTCCAAAATACAAATTGAAAGGCCCAA
1 AATTTAAATTTATTTTAAATTAAAATTAATTAAGGAATGTCCAAAATACAAATTGAAAGGCCCAA
91688 ATTACTTGTCCCTAAAGCCC
66 ATTACTTGTCCCTAAAGCCC
91708 AA
1 AA
91710 CTACAAAAAG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (85 bp):
AATTTAAATTTATTTTAAATTAAAATTAATTAAGGAATGTCCAAAATACAAATTGAAAGGCCCAA
ATTACTTGTCCCTAAAGCCC
Found at i:93603 original size:30 final size:30
Alignment explanation
Indices: 93428--93732 Score: 223
Period size: 29 Copynumber: 10.5 Consensus size: 30
93418 AAAAATCATG
* *
93428 TTTTCACCC-CAAACTT-TCTAAAAATTATA
1 TTTTGACCCTCAAACTTCTC-AAAAATTACA
*
93457 TTTTAACCC-CTAAACTTC-CAAAAATTACA
1 TTTTGACCCTC-AAACTTCTCAAAAATTACA
* *
93486 TTTTGA-CCTTAAACTTCTCAAAATTTACA
1 TTTTGACCCTCAAACTTCTCAAAAATTACA
* *
93515 TTTTG-CCCTCGAACTT-TCAAAAATTACT
1 TTTTGACCCTCAAACTTCTCAAAAATTACA
* * * * *
93543 TTTTTATCC-CGAACTATCT-AGAAATCACA
1 TTTTGACCCTCAAACT-TCTCAAAAATTACA
93572 TTTTGACCCTCAAACTTCTCAAAAATTACA
1 TTTTGACCCTCAAACTTCTCAAAAATTACA
*
93602 TTTTTACCCT-AAACTT-TCCAAAAATTACCA
1 TTTTGACCCTCAAACTTCT-CAAAAATTA-CA
*
93632 TTTT-ACCCTCAAACTTTTC-AAAATTAGCA
1 TTTTGACCCTCAAACTTCTCAAAAATTA-CA
* *
93661 TTTTGACCAT-GAACTT-TCTAAAAATTATCA
1 TTTTGACCCTCAAACTTCTC-AAAAATTA-CA
* * * *
93691 TTTT-ACCCCCGAACATC-CAAAAATCACCA
1 TTTTGACCCTCAAACTTCTCAAAAATTA-CA
93720 TTTT-ACCCTCAAA
1 TTTTGACCCTCAAA
93733 TTTTCCAAAA
Statistics
Matches: 226, Mismatches: 31, Indels: 38
0.77 0.11 0.13
Matches are distributed among these distances:
28 32 0.14
29 127 0.56
30 66 0.29
31 1 0.00
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (30 bp):
TTTTGACCCTCAAACTTCTCAAAAATTACA
Found at i:93676 original size:59 final size:56
Alignment explanation
Indices: 93438--93698 Score: 249
Period size: 59 Copynumber: 4.5 Consensus size: 56
93428 TTTTCACCCC
* *
93438 AAACTTTCTAAAAATTATATTTTAACCC-CTAAACTTCCAAAAATTACATTTTGACCTT
1 AAACTTTCTAAAAATTACATTTT-ACCCTC-AAACTTTCAAAAATTACATTTTGACC-T
* * * * * *
93496 AAAC-TTCTCAAAATTTACATTTTGCCCTCGAACTTTCAAAAATTACTTTTTTATCCC
1 AAACTTTCT-AAAAATTACATTTTACCCTCAAACTTTCAAAAATTACATTTTGA-CCT
* * * * *
93553 GAACTATCTAGAAATCACATTTTGACCCTCAAACTTCTCAAAAATTACATTTTTACCCT
1 AAACTTTCTAAAAATTACATTTT-ACCCTCAAACTT-TCAAAAATTACATTTTGA-CCT
*
93612 AAACTTTCCAAAAATTACCATTTTACCCTCAAACTTTTC-AAAATTAGCATTTTGACCAT
1 AAACTTTCTAAAAATTA-CATTTTACCCTCAAAC-TTTCAAAAATTA-CATTTTGACC-T
*
93671 GAACTTTCTAAAAATTATCATTTTACCC
1 AAACTTTCTAAAAATTA-CATTTTACCC
93699 CCGAACATCC
Statistics
Matches: 166, Mismatches: 27, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
57 41 0.25
58 41 0.25
59 76 0.46
60 8 0.05
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.37
Consensus pattern (56 bp):
AAACTTTCTAAAAATTACATTTTACCCTCAAACTTTCAAAAATTACATTTTGACCT
Found at i:95207 original size:66 final size:66
Alignment explanation
Indices: 95101--95247 Score: 240
Period size: 66 Copynumber: 2.2 Consensus size: 66
95091 AAACTACTCC
* * *
95101 TTCGTGAGGTTTTCATCTCCGTGCAAGATAGTGGATCGCTTTCGGGATTACATCTGTACTCATGT
1 TTCGTGAGGTTTTCACCTCCATGCAAGATAGTGGATCGCTTTCGGGATTACATCTGTACCCATGT
95166 T
66 T
* *
95167 TTCGTGAGGTTTTCACCTCCATGTAGGATAGTGGATCGCTTTCGGGATTACATCTGTACCCATGT
1 TTCGTGAGGTTTTCACCTCCATGCAAGATAGTGGATCGCTTTCGGGATTACATCTGTACCCATGT
95232 T
66 T
*
95233 TTCGTGAAGTTTTCA
1 TTCGTGAGGTTTTCA
95248 TTTCCGTGCA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 75 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (66 bp):
TTCGTGAGGTTTTCACCTCCATGCAAGATAGTGGATCGCTTTCGGGATTACATCTGTACCCATGT
T
Found at i:102294 original size:61 final size:61
Alignment explanation
Indices: 102199--102326 Score: 220
Period size: 61 Copynumber: 2.1 Consensus size: 61
102189 TTACCTCACA
* *
102199 TCGATACCTTAGTGGATAATACAGCAGGTCATTCCCTATTTTCATTCATGGATGGTTTCTC
1 TCGATACCTTAGTAGATAATACAGCAGGTCATTCCCTATTTTCATTCATGGATGATTTCTC
*
102260 TCGATACCTTAGTAGATAATACAGTAGGTCATTCCCTATTTTCATTCATGGATGATTTCTC
1 TCGATACCTTAGTAGATAATACAGCAGGTCATTCCCTATTTTCATTCATGGATGATTTCTC
*
102321 TAGATA
1 TCGATA
102327 TAACCAGACA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (61 bp):
TCGATACCTTAGTAGATAATACAGCAGGTCATTCCCTATTTTCATTCATGGATGATTTCTC
Found at i:106438 original size:209 final size:209
Alignment explanation
Indices: 106067--107155 Score: 1348
Period size: 208 Copynumber: 5.2 Consensus size: 209
106057 TTGCAGTCAT
* *
106067 TCGAAGCAATAAAATGTTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTG
1 TCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTG
* * *
106132 ATGAGATACAGAGAAGCGGATTAAAACAAGTGAGGCAGTCATCTTCCTGATGAGATACAGAAAAG
66 ATGAGATACAGAGAAGCGGATTAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACTGAGAAG
* * * *
106197 TATACCAAATCAATGAAAAAAAGCTTAATGTGAGCAAAACTTTGAACCCTAGCTTCCTGATGAGA
131 TAGACCAAATCAATGAAACAAAGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGA
* *
106262 TATTGAGAAGTAGG
196 TACTGAGAAGCAGG
* * * * *
106276 TCGAAGCAATAAAATTGTCAGCTTCCTGATGAGATATAGAGAAATGAACCAAATTCGTCTTTCTG
1 TCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTG
* * * *
106341 ATGAGATACAAAGAAGCGGATTAAAATAAGTGAGGCGGTTATCTTCCTGATGAGATACAGAGAAG
66 ATGAGATACAGAGAAGCGGATTAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACTGAGAAG
* * *
106406 TATACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAA-CCTCAGCTTCCTAATGAG
131 TAGACCAAATCAATGAAACAAAGCTCAATGTGAGCAAAACTTCGAACCCT-AGCTTCCTGATGAG
* **
106470 ATACTAAGAAGCAAA
195 ATACTGAGAAGCAGG
* *
106485 TCGAAGCAATAAAATGGTCAGCTTCCTAATGAGATACAGAGAAGCGGACCAAATTCGTCTTCCTG
1 TCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTG
* * ** **
106550 ATGAGATATAGAGAAGCGGATTGAAACAA-CAAGGCTATCATCTTCCTGATGAGATACTGAGAAG
66 ATGAGATACAGAGAAGCGGATTAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACTGAGAAG
* * * * *
106614 TAGACCAAATCAATGAAAC-CAGTCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAG
131 TAGACCAAATCAATGAAACAAAG-CTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAG
106678 ATACTGAGAAGCAGG
195 ATACTGAGAAGCAGG
* * * * ** * *
106693 TCGAAGCAATAAAACGGTTACCTTCCTGTTGAGATACAGAGAAGTAAACCAGATTCGTCTTTCTG
1 TCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTG
* ** * * * *
106758 ATGAGATACGGAGAAGTAGATCAAAATAA-CGAGGCGGTCATCTTCCTGATGAGATACTGAAAAG
66 ATGAGATACAGAGAAGCGGATTAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACTGAGAAG
* * * * * * * *
106822 TGGACCAAATCAATGAAACTAGGCTCAAAGTGAGCAAATCTTTGAACCCTAACTTCCTGATTAGA
131 TAGACCAAATCAATGAAACAAAGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGA
*
106887 TACTGAGAAGTAGG
196 TACTGAGAAGCAGG
* * * * *
106901 TCGAAGCAATAAAGTGGT-TGTCTTCCTGATAAGATACAGAGAAGTGGACCAAATCCATCTTCCT
1 TCGAAGCAATAAAATGGTCAG-CTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCT
* * * ** *
106965 GATGAGATACAAAGAAACGGATTAAAACAAGTGATGCGGTTGTTTTCCTGATGAGATACTGAGAA
65 GATGAGATACAGAGAAGCGGATTAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACTGAGAA
* *
107030 GTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCGAAACTTCGAACCCCTAGCTTCCTGATGA
130 GTAGACCAAATCAATGAAACAAAGCTCAATGTGAGCAAAACTTCGAA-CCCTAGCTTCCTGATGA
107095 GATACTGAGAAGC-GAG
194 GATACTGAGAAGCAG-G
* * *
107111 TTGAAGCAAT--AATGCGATCATCTTCCTGATGAGATATAGAGAAGT
1 TCGAAGCAATAAAATG-G-TCAGCTTCCTGATGAGATACAGAGAAGT
107156 ATGTCAAATC
Statistics
Matches: 748, Mismatches: 121, Indels: 21
0.84 0.14 0.02
Matches are distributed among these distances:
207 2 0.00
208 347 0.46
209 339 0.45
210 60 0.08
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (209 bp):
TCGAAGCAATAAAATGGTCAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTG
ATGAGATACAGAGAAGCGGATTAAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACTGAGAAG
TAGACCAAATCAATGAAACAAAGCTCAATGTGAGCAAAACTTCGAACCCTAGCTTCCTGATGAGA
TACTGAGAAGCAGG
Found at i:107394 original size:124 final size:124
Alignment explanation
Indices: 106959--107401 Score: 536
Period size: 124 Copynumber: 3.6 Consensus size: 124
106949 CCAAATCCAT
** * * * * * * * * *
106959 CTTCCTGATGAGATACAAAGAAACGGATTAAAACAAGTGATGCGGTTGTTTTCCTGATGAGATAC
1 CTTCCTGATGAGATACTGAGAAGCGGGTTAAAGCAA-TAAAGTGGTAGTCTTCTTGATGAGATAC
* *
107024 TGAGAAGTAGACCAAATCAATGAAACCAAGCTCAATGTGAGCGAAACTTCGAACCCCTAG
65 AGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCCTAG
* * * * * * *
107084 CTTCCTGATGAGATACTGAGAAGCGAGTTGAAGCAATAATGCGATCA-TCTTCCTGATGAGATAT
1 CTTCCTGATGAGATACTGAGAAGCGGGTTAAAGCAATAAAGTGGT-AGTCTTCTTGATGAGATAC
* *
107148 AGAGAAGTATG-TCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAATCCC-AG
65 AGAGAAGTA-GACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCCTAG
* * * *
107207 CTTCCTGATGAGATACTGAGAAGCAGGTCAAAGTC-ATAAAGTGGTTGTCTT-TCGGATGAGATA
1 CTTCCTGATGAGATACTGAGAAGCGGGTTAAAG-CAATAAAGTGGTAGTCTTCT-TGATGAGATA
* *
107270 CAGAGAAGTAGACCAAATCAAGGAAACAAAGCTCAATGTGAGTGAAACTTCGAACCCCTAG
64 CAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCCTAG
*
107331 CTTCCTGATAAGATACTGAGAAGCGGGTTAAAGCAATAAAGTGGTAGTCTTCTTGATGAGATACA
1 CTTCCTGATGAGATACTGAGAAGCGGGTTAAAGCAATAAAGTGGTAGTCTTCTTGATGAGATACA
*
107396 AAGAAG
66 GAGAAG
107402 CGGATTAAAA
Statistics
Matches: 272, Mismatches: 37, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
122 1 0.00
123 103 0.38
124 137 0.50
125 31 0.11
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (124 bp):
CTTCCTGATGAGATACTGAGAAGCGGGTTAAAGCAATAAAGTGGTAGTCTTCTTGATGAGATACA
GAGAAGTAGACCAAATCAATGAAACAAAGCTCAATGTGAGCGAAACTTCGAACCCCTAG
Found at i:107869 original size:17 final size:17
Alignment explanation
Indices: 107832--107933 Score: 123
Period size: 17 Copynumber: 5.9 Consensus size: 17
107822 TTGAGCCCAA
*
107832 ATTTTAAATTTTAATTTT
1 ATTTTAAA-TTTAAATTT
* *
107850 ATTTTAAGTTTGAATTT
1 ATTTTAAATTTAAATTT
*
107867 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
107884 ATTTTAAGTTTGAATTT
1 ATTTTAAATTTAAATTT
*
107901 ACTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
107918 ATTTTAAATTAAAATT
1 ATTTTAAATTTAAATT
107934 AATTAAGGAA
Statistics
Matches: 70, Mismatches: 14, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
17 63 0.90
18 7 0.10
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:107880 original size:6 final size:6
Alignment explanation
Indices: 107834--107933 Score: 55
Period size: 6 Copynumber: 17.3 Consensus size: 6
107824 GAGCCCAAAT
* * * * * *
107834 TTTAAA TTTTAA TTTTAT TTTAAG TTTGAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * * *
107881 CTT-AT TTTAAG TTTGAA TTT-AC TTTAAA TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
107926 TTAAAA TT
1 TTTAAA TT
107934 AATTAAGGAA
Statistics
Matches: 71, Mismatches: 19, Indels: 8
0.72 0.19 0.08
Matches are distributed among these distances:
5 15 0.21
6 56 0.79
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:107886 original size:34 final size:34
Alignment explanation
Indices: 107832--107924 Score: 150
Period size: 34 Copynumber: 2.7 Consensus size: 34
107822 TTGAGCCCAA
*
107832 ATTTTAAATTTTAATTTTATTTTAAGTTTGAATTT
1 ATTTTAAA-TTTAAATTTATTTTAAGTTTGAATTT
*
107867 ATTTTAAATTTAAACTTATTTTAAGTTTGAATTT
1 ATTTTAAATTTAAATTTATTTTAAGTTTGAATTT
*
107901 ACTTTAAATTTAAATTTATTTTAA
1 ATTTTAAATTTAAATTTATTTTAA
107925 ATTAAAATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
34 46 0.85
35 8 0.15
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (34 bp):
ATTTTAAATTTAAATTTATTTTAAGTTTGAATTT
Found at i:109807 original size:29 final size:29
Alignment explanation
Indices: 109747--109843 Score: 149
Period size: 29 Copynumber: 3.3 Consensus size: 29
109737 AAAATCACAT
* * *
109747 TTTTCACCCCTAAACTTTCCAAAAATTACA
1 TTTTAACCCCTAAA-ATTCCAAAAATTTCA
*
109777 TTTTAACCTCTAAAATTCCAAAAATTTCA
1 TTTTAACCCCTAAAATTCCAAAAATTTCA
109806 TTTTAACCCCTAAAATTCCAAAAATTTCA
1 TTTTAACCCCTAAAATTCCAAAAATTTCA
109835 TTTTAACCC
1 TTTTAACCC
109844 TCGAACTTCT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
29 50 0.81
30 12 0.19
ACGTcount: A:0.38, C:0.26, G:0.00, T:0.36
Consensus pattern (29 bp):
TTTTAACCCCTAAAATTCCAAAAATTTCA
Found at i:109860 original size:30 final size:30
Alignment explanation
Indices: 109736--109870 Score: 143
Period size: 29 Copynumber: 4.5 Consensus size: 30
109726 TAAATTATCA
* * *
109736 AAAAATCACATTTTTCACCC-CTAAACTTTCC
1 AAAAATTACA-TTTTAACCCTCTAAA-ATTCC
109767 AAAAATTACATTTTAA-CCTCTAAAATTCC
1 AAAAATTACATTTTAACCCTCTAAAATTCC
*
109796 AAAAATTTCATTTTAACCC-CTAAAATTCC
1 AAAAATTACATTTTAACCCTCTAAAATTCC
* * *
109825 AAAAATTTCATTTTAACCCTC-GAACTTCTC
1 AAAAATTACATTTTAACCCTCTAAAATTC-C
109855 AAAAATTACATATTTA
1 AAAAATTACAT-TTTA
109871 CCCCCGAACT
Statistics
Matches: 92, Mismatches: 7, Indels: 10
0.84 0.06 0.09
Matches are distributed among these distances:
29 55 0.60
30 24 0.26
31 13 0.14
ACGTcount: A:0.41, C:0.24, G:0.01, T:0.35
Consensus pattern (30 bp):
AAAAATTACATTTTAACCCTCTAAAATTCC
Found at i:109874 original size:59 final size:58
Alignment explanation
Indices: 109736--109889 Score: 159
Period size: 59 Copynumber: 2.6 Consensus size: 58
109726 TAAATTATCA
* * *
109736 AAAAATCACATTTTTCACCCCTAAACTTTCCAAAAATTACATTTTAACCTCTAAAATTCC
1 AAAAATTACA-TTTTAACCCCTAAA-ATTCCAAAAATTACATTTTAACCTCTAAAATTCC
* * * *
109796 AAAAATTTCATTTTAACCCCTAAAATTCCAAAAATTTCATTTTAACC-CTCGAACTTCTC
1 AAAAATTACATTTTAACCCCTAAAATTCCAAAAATTACATTTTAACCTCT-AAAATTC-C
** *
109855 AAAAATTACATATTT-ACCCCCGAACTTCCAAAAAT
1 AAAAATTACAT-TTTAACCCCTAAAATTCCAAAAAT
109890 ATATTGTTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 2 0.03
58 26 0.32
59 41 0.51
60 11 0.14
ACGTcount: A:0.40, C:0.26, G:0.01, T:0.32
Consensus pattern (58 bp):
AAAAATTACATTTTAACCCCTAAAATTCCAAAAATTACATTTTAACCTCTAAAATTCC
Found at i:109879 original size:30 final size:29
Alignment explanation
Indices: 109736--109889 Score: 139
Period size: 29 Copynumber: 5.2 Consensus size: 29
109726 TAAATTATCA
* * **
109736 AAAAATCACATTTTTCACCCCTAAACTTTCC
1 AAAAATTACA-TTTTAACCCCCGAAC-TTCC
* ** *
109767 AAAAATTACATTTTAACCTCTAAAATTCC
1 AAAAATTACATTTTAACCCCCGAACTTCC
* ** *
109796 AAAAATTTCATTTTAACCCCTAAAATTCC
1 AAAAATTACATTTTAACCCCCGAACTTCC
* *
109825 AAAAATTTCATTTTAACCCTCGAACTTCTC
1 AAAAATTACATTTTAACCCCCGAACTTC-C
109855 AAAAATTACATATTT-ACCCCCGAACTTCC
1 AAAAATTACAT-TTTAACCCCCGAACTTCC
109884 AAAAAT
1 AAAAAT
109890 ATATTGTTAA
Statistics
Matches: 109, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
29 62 0.57
30 35 0.32
31 12 0.11
ACGTcount: A:0.40, C:0.26, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCCCGAACTTCC
Found at i:116981 original size:17 final size:17
Alignment explanation
Indices: 116943--116981 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
116933 AGGTGGAGAA
* *
116943 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
*
116960 ATTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
116977 CTTGT
1 CTTGT
116982 CAAGTTGGAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:119564 original size:11 final size:11
Alignment explanation
Indices: 119550--119580 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
119540 CTATTTTAAA
119550 AATATTTTTTC
1 AATATTTTTTC
119561 AATA-TTTTTC
1 AATATTTTTTC
119571 AATATTTTTT
1 AATATTTTTT
119581 AGCCCGACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (11 bp):
AATATTTTTTC
Found at i:121718 original size:15 final size:16
Alignment explanation
Indices: 121687--121727 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
121677 TTTATATATT
*
121687 TTTAAGTTTTTTAAAA
1 TTTAAATTTTTTAAAA
*
121703 TTTATATTTTTT-AAA
1 TTTAAATTTTTTAAAA
121718 TTTAAATTTT
1 TTTAAATTTT
121728 GAAATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTAAATTTTTTAAAA
Found at i:121799 original size:19 final size:20
Alignment explanation
Indices: 121755--121794 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
121745 CTTAAATTTA
*
121755 AAAATTATTCTGGATTTTTT
1 AAAATTATTCTGAATTTTTT
*
121775 AAAATTATTTTGAATTTTTT
1 AAAATTATTCTGAATTTTTT
121795 TAATTTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (20 bp):
AAAATTATTCTGAATTTTTT
Found at i:127066 original size:21 final size:20
Alignment explanation
Indices: 127036--127088 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
127026 TTATTTTTTA
127036 AATT-TTTTATAAAATATTT
1 AATTATTTTATAAAATATTT
**
127055 ATATTATTTTATTTTAATATTT
1 A-ATTATTTTA-TAAAATATTT
*
127077 AATAATTTTATA
1 AATTATTTTATA
127089 CATTTTTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.04
20 4 0.15
21 13 0.48
22 9 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTATTTTATAAAATATTT
Found at i:142371 original size:3 final size:3
Alignment explanation
Indices: 142363--142394 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
142353 ATTTAACCCT
142363 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
142395 GGTGAGTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:148348 original size:31 final size:30
Alignment explanation
Indices: 148286--148357 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 30
148276 TGTATACACG
*
148286 AACTTTAATTTGGTGCAAATATGCACGTGA
1 AACTTTAATTTGGTGCAAATATACACGTGA
* * *
148316 AACTTTAATTGTGGTTCAAATATATACTTGA
1 AACTTTAATT-TGGTGCAAATATACACGTGA
148347 AACTTTAATTT
1 AACTTTAATTT
148358 TGATTTAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (30 bp):
AACTTTAATTTGGTGCAAATATACACGTGA
Found at i:148547 original size:28 final size:29
Alignment explanation
Indices: 148500--148555 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
148490 GAATTAGATC
148500 AAATCAAAATTCCATGTATAAAATTGCAA
1 AAATCAAAATTCCATGTATAAAATTGCAA
* *
148529 AAATCAAAGTT-CATGTATACAATTGCA
1 AAATCAAAATTCCATGTATAAAATTGCA
148556 CATTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (29 bp):
AAATCAAAATTCCATGTATAAAATTGCAA
Found at i:155706 original size:24 final size:21
Alignment explanation
Indices: 155678--155721 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
155668 TTTATCAAGA
155678 TAAATATTAGATTAAATTTAATAT
1 TAAATATTA-A-TAAA-TTAATAT
155702 TAAATATTAATAAATTAATA
1 TAAATATTAATAAATTAATA
155722 GAATATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 1 0.05
24 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TAAATATTAATAAATTAATAT
Found at i:155727 original size:59 final size:61
Alignment explanation
Indices: 155653--155769 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 61
155643 CCTTTAATAT
* * * *
155653 TAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATATTAA
1 TAAATTAATAGAATATTTACTACAAAATAAATATTAAATTAAATTAAATATTAAATATTAA
*
155712 TAAATTAATAGAATATTTATCTACAAAATAAATATTAAATTTAATTAAATATTAAATA
1 TAAATTAATAGAATATTTA-CTACAAAATAAATATTAAATTAAATTAAATATTAAATA
155770 ATCACTTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 18 0.36
61 1 0.02
62 31 0.62
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (61 bp):
TAAATTAATAGAATATTTACTACAAAATAAATATTAAATTAAATTAAATATTAAATATTAA
Found at i:157445 original size:51 final size:51
Alignment explanation
Indices: 157365--157653 Score: 391
Period size: 51 Copynumber: 5.7 Consensus size: 51
157355 ACTCGCAATT
* ** * ** * * *
157365 ATTT-CTCACGATAACACAAAGTCATCGGACTTTTAATTTGTCATGAATTC
1 ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTC
*
157415 ATTCACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTC
1 ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTC
*
157466 ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTC
1 ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTC
* * * *
157517 ATTTACTCACGATAACACTTAGTCACCGGACCTTTAATCTGTAAAAGATTC
1 ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTC
* * * *
157568 ATTTACTCATGATGCCACCTAGTCATCGGAACTTTAATCCGTAAAGGATTC
1 ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTC
*
157619 ATTTACTCACGATGACACTTAGTCACCGGACCTTT
1 ATTTACTCACGATGACACTTAGTCATCGGACCTTT
157654 TCGTTTATAG
Statistics
Matches: 208, Mismatches: 30, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
50 3 0.01
51 205 0.99
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (51 bp):
ATTTACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTC
Found at i:157649 original size:153 final size:152
Alignment explanation
Indices: 157365--157653 Score: 436
Period size: 153 Copynumber: 1.9 Consensus size: 152
157355 ACTCGCAATT
* * * * *
157365 ATTTCTCACGATAACACAAAGTCATCGGACTTTTAATTTGTCATGAATTCATTCACTCACGATGA
1 ATTTCTCACGATAACACAAAGTCACCGGACCTTTAATCTGTAAAGAATTCATTCACTCACGATGA
* * *
157430 CACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCATCGG
66 CACCTAGTCATCGGAACTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCACCGG
157495 ACCTTTAATCCATAAAGGATTC
131 ACCTTTAATCCATAAAGGATTC
** * *
157517 ATTTACTCACGATAACACTTAGTCACCGGACCTTTAATCTGTAAA-AGATTCATTTACTCATGAT
1 ATTT-CTCACGATAACACAAAGTCACCGGACCTTTAATCTGTAAAGA-ATTCATTCACTCACGAT
*
157581 GCCACCTAGTCATCGGAACTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCACC
64 GACACCTAGTCATCGGAACTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCACC
157646 GGACCTTT
129 GGACCTTT
157654 TCGTTTATAG
Statistics
Matches: 122, Mismatches: 13, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
152 5 0.04
153 117 0.96
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (152 bp):
ATTTCTCACGATAACACAAAGTCACCGGACCTTTAATCTGTAAAGAATTCATTCACTCACGATGA
CACCTAGTCATCGGAACTTTAATCCGTAAAGGATTCATTTACTCACGATGACACTTAGTCACCGG
ACCTTTAATCCATAAAGGATTC
Found at i:173249 original size:69 final size:69
Alignment explanation
Indices: 173134--173279 Score: 184
Period size: 69 Copynumber: 2.1 Consensus size: 69
173124 CTCTCTTTGC
* * *
173134 AATTTGTATATCTACTACTGTCCCAACCTCCAATCCATGCCCCCAAACATGCTTCCACACTCCCT
1 AATTTGTATATCTACAACTGTCCCAACCTCCAATCCATACCCCCAAACATGCTCCCACACTCCCT
173199 TTCT
66 TTCT
* * * * * * * *
173203 AATTTGTCTATCTACAATTGTCCCAAGCTCCAATCCATATCGCCAAACATGCTCCCTCCCTCTCT
1 AATTTGTATATCTACAACTGTCCCAACCTCCAATCCATACCCCCAAACATGCTCCCACACTCCCT
173268 TTCT
66 TTCT
*
173272 CATTTGTA
1 AATTTGTA
173280 CATTCGAAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.24, C:0.36, G:0.07, T:0.33
Consensus pattern (69 bp):
AATTTGTATATCTACAACTGTCCCAACCTCCAATCCATACCCCCAAACATGCTCCCACACTCCCT
TTCT
Found at i:176297 original size:22 final size:22
Alignment explanation
Indices: 176254--176299 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
176244 TTGGGTTTTC
**
176254 TTTGAAGAGAAAAATATTGGGT
1 TTTGAAGAGAAAAATAACGGGT
* *
176276 TTTGATGAGAAAATTAACGGGT
1 TTTGAAGAGAAAAATAACGGGT
176298 TT
1 TT
176300 AGAGGGAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (22 bp):
TTTGAAGAGAAAAATAACGGGT
Found at i:179873 original size:38 final size:38
Alignment explanation
Indices: 179822--179898 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
179812 TTTCCTAAAG
179822 ATCCGTATTGGCTCTTTAGCAAAGCAACATTCAGCTGA
1 ATCCGTATTGGCTCTTTAGCAAAGCAACATTCAGCTGA
179860 ATCCGTATTGGCTCTTTAGCAAAGCAACATTCAGCTGA
1 ATCCGTATTGGCTCTTTAGCAAAGCAACATTCAGCTGA
179898 A
1 A
179899 CTTTAAGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (38 bp):
ATCCGTATTGGCTCTTTAGCAAAGCAACATTCAGCTGA
Found at i:184686 original size:306 final size:304
Alignment explanation
Indices: 184096--184708 Score: 1122
Period size: 306 Copynumber: 2.0 Consensus size: 304
184086 TTTACAGACA
184096 AACCAAATGAAACCAAGAACCGTAAACTGATTCCTCTAGTTATATGCACGCACACACACACATAT
1 AACCAAATGAAACCAAGAACCGTAAACTGATTCCTCTAGTTATATGCACGCACACACACACATAT
184161 ATGTTTCCATGTGTTCTAGTTTGTATGATCTAAATTCTAACTAACTAACAACCAGAAGAACCACC
66 ATGTTTCCATGTGTTCTAGTTTGTATGATCTAAATTCTAACTAACTAACAACCAGAAGAACCACC
*
184226 ATAGATATCGTCAAGGATTCAAAATAACATACAGAACTCTTCAACCTAGTAGAAAAGAATCAGAG
131 AGAGATATCGTCAAGGATTCAAAATAACATACAGAACTCTTCAACCTAGTAGAAAAGAATCAGAG
*
184291 GAAGACAAACGAAAATGATGTTTCCCCATTTTCATTGTTTTAGAAGTCTGTACAAATTCAGGGTC
196 GAAGACAAACGAAAATGATGTTTCCCCATTTTCATTGTTTTAGAAGTCTGTAAAAATTCAGGGTC
184356 AAACTGTTGGCATTTGAATACTGTGGATGTTTACCACAT-CACT
261 AAACTGTTGGCATTTGAATACTGTGGATGTTTACCACATCCACT
*
184399 AACCAAATGAAACCAAGAACTGTAAACTGATTCCTCTAGTTATATGAACGCACGCACACACACAC
1 AACCAAATGAAACCAAGAACCGTAAACTGATTCCTCTAGTTATAT----GCACGCACACACACAC
* * *
184464 ATATATGTTTCCATGTGTTCTAGTTTGTATGATCTAAATTCTAAGTTACTAACAACCAGAAGACC
62 ATATATGTTTCCATGTGTTCTAGTTTGTATGATCTAAATTCTAACTAACTAACAACCAGAAGAAC
184529 CACCAGAGATATCGTCAAGGATTCAAAATAACATACAGAACTC-TCAACCTAGTAGAAAAGAATC
127 CACCAGAGATATCGTCAAGGATTCAAAATAACATACAGAACTCTTCAACCTAGTAGAAAAGAATC
184593 AGAGGAAGACAAACGAAAATGATGTTTCCCCATTTTCATTGTTTTAGAAGTCTGTAAAAATTCAG
192 AGAGGAAGACAAACGAAAATGATGTTTCCCCATTTTCATTGTTTTAGAAGTCTGTAAAAATTCAG
184658 GGTCAAACTGTTGGCATTTGAATACTGTGGATGTTTACCACATCCACT
257 GGTCAAACTGTTGGCATTTGAATACTGTGGATGTTTACCACATCCACT
184706 AAC
1 AAC
184709 TTGTGAACAG
Statistics
Matches: 299, Mismatches: 6, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
303 44 0.15
306 128 0.43
307 127 0.42
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (304 bp):
AACCAAATGAAACCAAGAACCGTAAACTGATTCCTCTAGTTATATGCACGCACACACACACATAT
ATGTTTCCATGTGTTCTAGTTTGTATGATCTAAATTCTAACTAACTAACAACCAGAAGAACCACC
AGAGATATCGTCAAGGATTCAAAATAACATACAGAACTCTTCAACCTAGTAGAAAAGAATCAGAG
GAAGACAAACGAAAATGATGTTTCCCCATTTTCATTGTTTTAGAAGTCTGTAAAAATTCAGGGTC
AAACTGTTGGCATTTGAATACTGTGGATGTTTACCACATCCACT
Found at i:187810 original size:21 final size:21
Alignment explanation
Indices: 187786--187825 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
187776 CTAAAAAAAA
187786 AAAAAAGATAACT-AAATAATT
1 AAAAAA-ATAACTGAAATAATT
*
187807 AAAAAAATACCTGAAATAA
1 AAAAAAATAACTGAAATAA
187826 AACGATAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (21 bp):
AAAAAAATAACTGAAATAATT
Found at i:194534 original size:19 final size:20
Alignment explanation
Indices: 194500--194539 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
194490 AAATCTTGCA
* *
194500 AAATTATCTCTAAAATTATC
1 AAATTATCTATAAAATGATC
194520 AAATTAT-TATAAAATGATC
1 AAATTATCTATAAAATGATC
194539 A
1 A
194540 CCCAATCGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATTATCTATAAAATGATC
Found at i:200048 original size:27 final size:28
Alignment explanation
Indices: 200010--200116 Score: 90
Period size: 29 Copynumber: 3.6 Consensus size: 28
200000 ACACTTTTTT
*
200010 AATTTGATACTTAAAC-TTTTTTTACTC
1 AATTTGGTACTTAAACTTTTTTTTACTC
* **
200037 AATTTGGTACTTGAACTTGATAATTTTTTTTC
1 AATTTGGTACTTAAACTT--T--TTTTTACTC
* *
200069 TAATTTGGCACTTAAACTTTTTTTTGACCC
1 -AATTTGGTACTTAAACTTTTTTTT-ACTC
*
200099 AATTTGGTACCTAAACTT
1 AATTTGGTACTTAAACTT
200117 GACATTTTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
27 14 0.23
28 1 0.02
29 21 0.34
30 2 0.03
31 1 0.02
32 7 0.11
33 16 0.26
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (28 bp):
AATTTGGTACTTAAACTTTTTTTTACTC
Found at i:200082 original size:60 final size:59
Alignment explanation
Indices: 200004--200135 Score: 169
Period size: 60 Copynumber: 2.2 Consensus size: 59
199994 AATTTTACAC
** * * *
200004 TTTTTTAATTTGATACTTAAAC-TTTTTTT-ACTCAATTTGGTACTTGAACTTGATAATTT
1 TTTTTTAATTTGGCACTTAAACTTTTTTTTGACCCAATTTGGTACCTAAACTTGA-AA-TT
*
200063 TTTTTCTAATTTGGCACTTAAACTTTTTTTTGACCCAATTTGGTACCTAAACTTGACATT
1 TTTTT-TAATTTGGCACTTAAACTTTTTTTTGACCCAATTTGGTACCTAAACTTGAAATT
200123 TTTTTTAATTTGG
1 TTTTTTAATTTGG
200136 TACCCAAGCT
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
59 13 0.20
60 22 0.34
61 8 0.12
62 21 0.33
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (59 bp):
TTTTTTAATTTGGCACTTAAACTTTTTTTTGACCCAATTTGGTACCTAAACTTGAAATT
Found at i:200439 original size:35 final size:34
Alignment explanation
Indices: 200373--200467 Score: 124
Period size: 35 Copynumber: 2.9 Consensus size: 34
200363 GGACTTCAAA
* *
200373 AAGTTTAAGTACCAACTT---AAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTGGAAAAAAAAAATGTC
200404 AAGTTTAAGTACCAAATTAGGAAAAAAAAAATGTC
1 AAGTTTAAGTACCAAATT-GGAAAAAAAAAATGTC
* *
200439 AAGTTTGAGTACCAAATTGGACAAAAAAA
1 AAGTTTAAGTACCAAATTGGAAAAAAAAA
200468 GTATAGGTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
31 17 0.30
34 10 0.18
35 29 0.52
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.23
Consensus pattern (34 bp):
AAGTTTAAGTACCAAATTGGAAAAAAAAAATGTC
Found at i:200455 original size:94 final size:93
Alignment explanation
Indices: 200342--200513 Score: 227
Period size: 93 Copynumber: 1.8 Consensus size: 93
200332 AGTAAAAAGA
* ** * *
200342 GTCAAGTTCAAGTGCCAAATTGGACTTCAAAAAGTTTAAGTACCAACTTAAAAAAAAGTGTCAAG
1 GTCAAGTTCAAGTACCAAATTGGAC-AAAAAAAGTATAAGTACCAAATTAAAAAAAAGTGTCAAG
200407 TTTAAGTACCAAATTAGGAAAAAAAAAAT
65 TTTAAGTACCAAATTAGGAAAAAAAAAAT
** * * **
200436 GTCAAGTTTGAGTACCAAATTGGACAAAAAAAGTATAGGTATCAAATTAGGAAAAAGTGTCAAGT
1 GTCAAGTTCAAGTACCAAATTGGACAAAAAAAGTATAAGTACCAAATTAAAAAAAAGTGTCAAGT
*
200501 TTAGGTACCAAAT
66 TTAAGTACCAAAT
200514 GTTATATTAA
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
93 44 0.67
94 22 0.33
ACGTcount: A:0.46, C:0.12, G:0.17, T:0.25
Consensus pattern (93 bp):
GTCAAGTTCAAGTACCAAATTGGACAAAAAAAGTATAAGTACCAAATTAAAAAAAAGTGTCAAGT
TTAAGTACCAAATTAGGAAAAAAAAAAT
Found at i:200513 original size:31 final size:31
Alignment explanation
Indices: 200373--200513 Score: 105
Period size: 31 Copynumber: 4.5 Consensus size: 31
200363 GGACTTCAAA
* * **
200373 AAGTTTAAGTACCAACTTAAAAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGGAAAAAGTGTC
* *
200404 AAGTTTAAGTACCAAATTAGGAAAAAAAAAATGTC
1 AAGTTTAGGTACCAAATTAGG----AAAAAGTGTC
*
200439 AAGTTT-GAGTACCAAATT-GGACAAAA----A
1 AAGTTTAG-GTACCAAATTAGGA-AAAAGTGTC
* *
200466 AAGTATAGGTATCAAATTAGGAAAAAGTGTC
1 AAGTTTAGGTACCAAATTAGGAAAAAGTGTC
200497 AAGTTTAGGTACCAAAT
1 AAGTTTAGGTACCAAAT
200514 GTTATATTAA
Statistics
Matches: 87, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
27 18 0.21
28 4 0.05
30 1 0.01
31 37 0.43
34 2 0.02
35 25 0.29
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.25
Consensus pattern (31 bp):
AAGTTTAGGTACCAAATTAGGAAAAAGTGTC
Found at i:200803 original size:18 final size:19
Alignment explanation
Indices: 200760--200821 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 19
200750 AATATAATTT
* *
200760 TTAAAAAATAAAAAATC-A
1 TTAAAATATATAAAATCAA
*
200778 TTAAAA-ATTTTAAAATCAA
1 TTAAAATA-TATAAAATCAA
*
200797 TTAAAATATATCAAA-CAA
1 TTAAAATATATAAAATCAA
200815 TTAAAAT
1 TTAAAAT
200822 CTAAAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
17 1 0.03
18 23 0.62
19 12 0.32
20 1 0.03
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
TTAAAATATATAAAATCAA
Found at i:201607 original size:49 final size:48
Alignment explanation
Indices: 201544--201639 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 48
201534 AATTGGCATA
* * *
201544 ATAGAAACTTTAACCTTCAACATTTATACATTGTGTCAATTTAATATTG
1 ATAGAAAATCTAACCTTCAACATTTACACATTGTGT-AATTTAATATTG
* *
201593 ATAGAAAATCTAACCTTTAACATTTACACATTGTGTAATTTAGTATT
1 ATAGAAAATCTAACCTTCAACATTTACACATTGTGTAATTTAATATT
201640 TTTTTTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 10 0.24
49 32 0.76
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (48 bp):
ATAGAAAATCTAACCTTCAACATTTACACATTGTGTAATTTAATATTG
Found at i:211358 original size:60 final size:59
Alignment explanation
Indices: 211253--211449 Score: 179
Period size: 60 Copynumber: 3.3 Consensus size: 59
211243 TTAATATAAC
* * * *
211253 ATTTAGTACCTGAATTTTGTATTTTTTACTAATTTGGAACTTAAACCTTTTTTT-GATTCA
1 ATTTGGTACTTGAA-TTTGTATTTTTTACTAATTTGGTACCTAAA-CTTTTTTTAGATTCA
*
211313 ATTTGGTACTTGAATTTGATATTTTTT-CTTAATTTGGTACCTAAACTTTTTTTGGACTT-A
1 ATTTGGTACTTGAATTTG-TATTTTTTAC-TAATTTGGTACCTAAACTTTTTTTAGA-TTCA
* * * **
211373 ATTTGGTA-TCTGAACTTGGCATTTTTTACT-ATTTGATACCTAAGGTTTTTTTTAGATTCA
1 ATTTGGTACT-TGAA-TTTGTATTTTTTACTAATTTGGTACCTAA-ACTTTTTTTAGATTCA
* *
211433 ATTTGATACTTAAATTT
1 ATTTGGTACTTGAATTT
211450 ATTAAAATTA
Statistics
Matches: 114, Mismatches: 13, Indels: 21
0.77 0.09 0.14
Matches are distributed among these distances:
59 30 0.26
60 77 0.68
61 7 0.06
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.52
Consensus pattern (59 bp):
ATTTGGTACTTGAATTTGTATTTTTTACTAATTTGGTACCTAAACTTTTTTTAGATTCA
Found at i:211928 original size:26 final size:23
Alignment explanation
Indices: 211899--211964 Score: 62
Period size: 26 Copynumber: 2.8 Consensus size: 23
211889 ATTTTTGAAA
211899 GATTAATTTAAAATTTTATTTTT
1 GATTAATTTAAAATTTTATTTTT
** **
211922 AGGGATTAAAATGTAATTTTATTTTT
1 ---GATTAATTTAAAATTTTATTTTT
211948 -ATTAATTTAAAATTTTA
1 GATTAATTTAAAATTTTA
211965 AATTTTTAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 13 0.41
26 19 0.59
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (23 bp):
GATTAATTTAAAATTTTATTTTT
Found at i:212468 original size:21 final size:20
Alignment explanation
Indices: 212444--212483 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
212434 TTTTTCTTTT
212444 TTTTGTAGTTTTATATTTATA
1 TTTTGTAGTTTTAT-TTTATA
*
212465 TTTTTTAGTTTTATTTTAT
1 TTTTGTAGTTTTATTTTAT
212484 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTTGTAGTTTTATTTTATA
Found at i:213207 original size:7 final size:7
Alignment explanation
Indices: 213185--213231 Score: 53
Period size: 7 Copynumber: 6.6 Consensus size: 7
213175 TTTATTAAAT
213185 AAATA-A
1 AAATATA
213191 AAACTATA
1 AAA-TATA
213199 AAATAT-
1 AAATATA
213205 AAATATA
1 AAATATA
213212 AAACTATTA
1 AAA-TA-TA
213221 AAATATA
1 AAATATA
213228 AAAT
1 AAAT
213232 TTATTTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
6 9 0.25
7 14 0.39
8 8 0.22
9 5 0.14
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATATA
Found at i:213222 original size:22 final size:20
Alignment explanation
Indices: 213183--213229 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 20
213173 TTTTTATTAA
213183 ATAAATAAAAACTATAAAAT
1 ATAAATAAAAACTATAAAAT
213203 ATAAATATAAAACTATTAAAAT
1 ATAAATA-AAAACTA-TAAAAT
213225 ATAAA
1 ATAAA
213230 ATTTATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 7 0.28
21 7 0.28
22 11 0.44
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (20 bp):
ATAAATAAAAACTATAAAAT
Found at i:213253 original size:21 final size:22
Alignment explanation
Indices: 213220--213283 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 22
213210 TAAAACTATT
*
213220 AAAA-TATAAAATT-TATTTTA
1 AAAAGTATAAAATTAAATTTTA
*
213240 AAAAGTATATAATTAAATTTTA
1 AAAAGTATAAAATTAAATTTTA
213262 AAAAGT-TAAAATAATAAATTTT
1 AAAAGTATAAAAT--TAAATTTT
213284 TATTTATTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.11
21 13 0.35
22 12 0.32
23 8 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
AAAAGTATAAAATTAAATTTTA
Found at i:213279 original size:23 final size:22
Alignment explanation
Indices: 213234--213283 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
213224 TATAAAATTT
*
213234 ATTTTAAAAAGTATATAATTAA
1 ATTTTAAAAAGTAAATAATTAA
213256 ATTTTAAAAAGTTAAAATAA-TAA
1 ATTTTAAAAAG-T-AAATAATTAA
213279 ATTTT
1 ATTTT
213284 TATTTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 11 0.44
23 9 0.36
24 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (22 bp):
ATTTTAAAAAGTAAATAATTAA
Found at i:214168 original size:19 final size:19
Alignment explanation
Indices: 214123--214168 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
214113 GTATGATATC
*
214123 TTTTTAAAATCGTATTTTA
1 TTTTTAAAATCGTATTTAA
**
214142 TTTATTAAAATTTTATTTAA
1 TTT-TTAAAATCGTATTTAA
214162 TTTTTAA
1 TTTTTAA
214169 CAGATTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTTAAAATCGTATTTAA
Found at i:217601 original size:45 final size:45
Alignment explanation
Indices: 217491--217609 Score: 166
Period size: 45 Copynumber: 2.6 Consensus size: 45
217481 TGATGGCTCG
* * * ** * *
217491 TCAAACTCAGTCTGATATCCCTCCCTTGAGTATTGCGGTGGCTCG
1 TCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGGTGACTCA
*
217536 TCAAATTGAGGCTGATATCCTTGGCTTGAGTATTGCGGTGACTCA
1 TCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGGTGACTCA
217581 TCAAACTGAGGCTGATATCCTTGGCTTGA
1 TCAAACTGAGGCTGATATCCTTGGCTTGA
217610 TGAGATATGC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.32
Consensus pattern (45 bp):
TCAAACTGAGGCTGATATCCTTGGCTTGAGTATTGCGGTGACTCA
Found at i:218250 original size:43 final size:42
Alignment explanation
Indices: 218177--218260 Score: 123
Period size: 43 Copynumber: 2.0 Consensus size: 42
218167 GCACAATTAA
* *
218177 TAACATGCAAGATATTAATAAGAGTAAAGTAATATAATTTAG
1 TAACATGCAACATATTAACAAGAGTAAAGTAATATAATTTAG
* *
218219 TAACATGCAACCATATTAACACGAGTCAAGTAATATAATTTA
1 TAACATGCAA-CATATTAACAAGAGTAAAGTAATATAATTTA
218261 ACATGTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 10 0.27
43 27 0.73
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.30
Consensus pattern (42 bp):
TAACATGCAACATATTAACAAGAGTAAAGTAATATAATTTAG
Done.