Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015154.1 Kokia drynarioides strain JFW-HI SEQ_130198, 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: 822009
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 133 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:6996 original size:92 final size:89
Alignment explanation
Indices: 6810--7000 Score: 246
Period size: 89 Copynumber: 2.1 Consensus size: 89
6800 AGATAACGGA
* * * *
6810 GTATAGTTCAGGTACCACTTTGGGTAACAGAGTATAGTTTAGGTACTTGTGACCAACAGAAAGTT
1 GTATAGTTTAGGTACCACTTTGAGTAACAGAGTATAGTTTAAGTACTTGTGACCAAAAGAAAGTT
6875 TAGGTACTAACCTGGGAAAAAAGT
66 TAGGTACTAACCTGGGAAAAAAGT
*
6899 ATATAGTTTAGGTACCACTTTGAGTAAC-GAAGTATAGTTTAAGTACCACTTGTGA-CAAAAGAA
1 GTATAGTTTAGGTACCACTTTGAGTAACAG-AGTATAGTTTAAGT---ACTTGTGACCAAAAGAA
6962 AGGTTTAGGTAC-AACCTTGGGAAAAAAAG-
62 A-GTTTAGGTACTAACC-TGGG-AAAAAAGT
6991 GTATAGTTTA
1 GTATAGTTTA
7001 AGTCCATTTT
Statistics
Matches: 89, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
88 1 0.01
89 38 0.43
91 12 0.13
92 31 0.35
93 7 0.08
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (89 bp):
GTATAGTTTAGGTACCACTTTGAGTAACAGAGTATAGTTTAAGTACTTGTGACCAAAAGAAAGTT
TAGGTACTAACCTGGGAAAAAAGT
Found at i:12642 original size:6 final size:6
Alignment explanation
Indices: 12631--12663 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
12621 CCTCAATAAG
12631 TGGAAT TGGAAT TGGAAT TGGAAT TGGAAT TGG
1 TGGAAT TGGAAT TGGAAT TGGAAT TGGAAT TGG
12664 GTTAGGTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.33
Consensus pattern (6 bp):
TGGAAT
Found at i:27364 original size:28 final size:28
Alignment explanation
Indices: 27332--27486 Score: 109
Period size: 29 Copynumber: 5.4 Consensus size: 28
27322 TAAAAAATTC
*
27332 AATTTTTGGATGCTCGGGGTAAAATGGT
1 AATTTTTGGATGATCGGGGTAAAATGGT
* *
27360 TATTTTGGGATGATCGAGGGTAAAATGGT
1 AATTTTTGGATGATCG-GGGTAAAATGGT
* * *
27389 AATTTTTAGA-CATTCAAGGGTAAAATGGT
1 AATTTTTGGATGA-TC-GGGGTAAAATGGT
* * * *
27418 AATTTTTGGAAAGTTCAGGGTCAAAAATAG-
1 AATTTTTGG-ATGATCGGGGT--AAAATGGT
* *
27448 AATTTTTGGA-AATTCAGAGGTAAAATGGT
1 AATTTTTGGATGA-TC-GGGGTAAAATGGT
27477 AATTTTTGGA
1 AATTTTTGGA
27487 AAGTTCAGGG
Statistics
Matches: 100, Mismatches: 17, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
28 20 0.20
29 59 0.59
30 15 0.15
31 6 0.06
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (28 bp):
AATTTTTGGATGATCGGGGTAAAATGGT
Found at i:27408 original size:29 final size:28
Alignment explanation
Indices: 27348--27599 Score: 183
Period size: 29 Copynumber: 8.7 Consensus size: 28
27338 TGGATGCTCG
* * *
27348 GGGTAAAATGGTTATTTTGGGATGA-TCGA
1 GGGTAAAATGGTAATTTTTGGA-AATTC-A
* *
27377 GGGTAAAATGGTAATTTTTAGACATTCAA
1 GGGTAAAATGGTAATTTTTGGAAATTC-A
27406 GGGTAAAATGGTAATTTTTGGAAAGTTCA
1 GGGTAAAATGGTAATTTTTGGAAA-TTCA
*
27435 GGGTCAAAAATAG-AATTTTTGGAAATTCA
1 GGGT--AAAATGGTAATTTTTGGAAATTCA
27464 GAGGTAAAATGGTAATTTTTGGAAAGTTCA
1 G-GGTAAAATGGTAATTTTTGGAAA-TTCA
* * *
27494 GGGTTAAAAATGG-ATTTTTTGGAAGTTTA
1 GGG-T-AAAATGGTAATTTTTGGAAATTCA
** * *
27523 GGGGTAAAATGACAATTTTTGGAAGTTTAA
1 -GGGTAAAATGGTAATTTTTGGAA-ATTCA
* * *
27553 GGATAAAAAT-ATAA-TTTTGGAAGTTCA
1 GGGT-AAAATGGTAATTTTTGGAAATTCA
*
27580 GAGGCAAAAT-GTAATTTTTG
1 G-GGTAAAATGGTAATTTTTG
27600 TAAAGTTTGA
Statistics
Matches: 185, Mismatches: 23, Indels: 31
0.77 0.10 0.13
Matches are distributed among these distances:
27 12 0.06
28 27 0.15
29 88 0.48
30 45 0.24
31 13 0.07
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTGGAAATTCA
Found at i:27454 original size:30 final size:28
Alignment explanation
Indices: 27376--27627 Score: 158
Period size: 29 Copynumber: 8.6 Consensus size: 28
27366 GGGATGATCG
* * *
27376 AGGGTAAAATGGTAATTTTTAGACA-TTC
1 AGGGTAAAATAG-AATTTTTGGAAAGTTC
*
27404 AAGGGTAAAATGGTAATTTTTGGAAAGTTC
1 -AGGGTAAAATAG-AATTTTTGGAAAGTTC
27434 AGGGTCAAAAATAGAATTTTTGGAAA-TTC
1 AGGGT--AAAATAGAATTTTTGGAAAGTTC
*
27463 AGAGGTAAAATGGTAATTTTTGGAAAGTTC
1 AG-GGTAAAATAG-AATTTTTGGAAAGTTC
* * *
27493 AGGGTTAAAAATGGATTTTTTGG-AAGTTT
1 AGGG-T-AAAATAGAATTTTTGGAAAGTTC
* *
27522 AGGGGTAAAATGACAATTTTTGG-AAGTTTA
1 A-GGGTAAAAT-AGAATTTTTGGAAAG-TTC
* *
27552 AGGATAAAAATATAA-TTTTGG-AAGTTC
1 AGGGT-AAAATAGAATTTTTGGAAAGTTC
* * *
27579 AGAGGCAAAAT-GTAATTTTTGTAAAGTTTG
1 AG-GGTAAAATAG-AATTTTTGGAAAG-TTC
*
27609 AGGGTTAAAATATAATTTT
1 AGGG-TAAAATAGAATTTT
27628 AAGAAAATTT
Statistics
Matches: 184, Mismatches: 20, Indels: 37
0.76 0.08 0.15
Matches are distributed among these distances:
27 11 0.06
28 26 0.14
29 76 0.41
30 58 0.32
31 13 0.07
ACGTcount: A:0.38, C:0.04, G:0.23, T:0.35
Consensus pattern (28 bp):
AGGGTAAAATAGAATTTTTGGAAAGTTC
Found at i:27470 original size:59 final size:58
Alignment explanation
Indices: 27349--27627 Score: 246
Period size: 59 Copynumber: 4.8 Consensus size: 58
27339 GGATGCTCGG
* * * * * * *
27349 GGTAAAATGGTTA-TTTTGGGATGATCGAGGGT-AAAATGGTAATTTTTAGACATTCA-A
1 GGTAAAATGGTAATTTTTGGAAAGTTC-AGGGTAAAAATAG-AATTTTTGGAAATTCAGA
27406 GGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTCAAAAATAGAATTTTTGGAAATTCAGA
1 -GGTAAAATGGTAATTTTTGGAAAGTTCAGGGT-AAAAATAGAATTTTTGGAAATTCAGA
* * * * *
27466 GGTAAAATGGTAATTTTTGGAAAGTTCAGGGTTAAAAATGGATTTTTTGGAAGTTTAGG
1 GGTAAAATGGTAATTTTTGGAAAGTTCAGGG-TAAAAATAGAATTTTTGGAAATTCAGA
** * * * *
27525 GGTAAAATGACAATTTTTGG-AAGTTTAAGGATAAAAATATAA-TTTTGGAAGTTCAGA
1 GGTAAAATGGTAATTTTTGGAAAG-TTCAGGGTAAAAATAGAATTTTTGGAAATTCAGA
* * * * *
27582 GGCAAAAT-GTAATTTTTGTAAAGTTTGAGGGTTAAAATATAATTTT
1 GGTAAAATGGTAATTTTTGGAAAG-TTCAGGGTAAAAATAGAATTTT
27628 AAGAAAATTT
Statistics
Matches: 185, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
56 8 0.04
57 39 0.21
58 31 0.17
59 99 0.54
60 8 0.04
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (58 bp):
GGTAAAATGGTAATTTTTGGAAAGTTCAGGGTAAAAATAGAATTTTTGGAAATTCAGA
Found at i:27661 original size:116 final size:117
Alignment explanation
Indices: 27406--27649 Score: 280
Period size: 116 Copynumber: 2.1 Consensus size: 117
27396 AGACATTCAA
** * * *
27406 GGGTAAAATGGTAATTTTTGGAAAG-TTCAGGGTCAAAAATAGAATTTTTGGAAATTCAGAGGTA
1 GGGTAAAATGACAATTTTTGG-AAGTTTAAGGAT-AAAAATAGAATTTTTGGAAATTCAGAGGCA
* ** * *
27470 AAATGGTAATTTTTGGAAAGTTCAGGGTTAAAAATGGATTTTTTGGAAGTTTAG
64 AAATGGTAATTTTTGGAAAGTTCAGGGTTAAAAATGAATTTTAAGAAAATTTAG
* *
27524 GGGTAAAATGACAATTTTTGGAAGTTTAAGGATAAAAATATAA-TTTTGGAAGTTCAGAGGCAAA
1 GGGTAAAATGACAATTTTTGGAAGTTTAAGGATAAAAATAGAATTTTTGGAAATTCAGAGGCAAA
* *
27588 AT-GTAATTTTTGTAAAGTTTGAGGGTTAAAATAT-AATTTTAAGAAAATTTAAG
66 ATGGTAATTTTTGGAAAG-TTCAGGGTTAAAA-ATGAATTTTAAGAAAATTT-AG
*
27641 GGTTAAAAT
1 GGGTAAAAT
27650 ATGATTTTTG
Statistics
Matches: 107, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
115 14 0.13
116 44 0.41
117 24 0.22
118 25 0.23
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (117 bp):
GGGTAAAATGACAATTTTTGGAAGTTTAAGGATAAAAATAGAATTTTTGGAAATTCAGAGGCAAA
ATGGTAATTTTTGGAAAGTTCAGGGTTAAAAATGAATTTTAAGAAAATTTAG
Found at i:28675 original size:20 final size:20
Alignment explanation
Indices: 28650--28695 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
28640 CATTTTGTCA
28650 AAATTTGCATTTTGATTCAT
1 AAATTTGCATTTTGATTCAT
28670 AAATTTGCATTTTGATTCAT
1 AAATTTGCATTTTGATTCAT
28690 AAATTT
1 AAATTT
28696 CTCAGATCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
AAATTTGCATTTTGATTCAT
Found at i:28930 original size:3 final size:3
Alignment explanation
Indices: 28922--28947 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28912 TCTTTTTTAT
28922 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
28948 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:28952 original size:3 final size:3
Alignment explanation
Indices: 28946--28971 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28936 ATAATAATAA
28946 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
28972 ATTAATATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:29289 original size:21 final size:23
Alignment explanation
Indices: 29249--29294 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
29239 TTTTTGAATG
29249 TTCGAAAAAGTTTCTCTTTTTTT
1 TTCGAAAAAGTTTCTCTTTTTTT
29272 TTCGAAAAAGTTTCT-TTTTTTT
1 TTCGAAAAAGTTTCTCTTTTTTT
29294 T
1 T
29295 ATTATTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.59
Consensus pattern (23 bp):
TTCGAAAAAGTTTCTCTTTTTTT
Found at i:32485 original size:22 final size:21
Alignment explanation
Indices: 32444--32491 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
32434 TAATTTTTTT
*
32444 AAAAATCTATAATACATAAAA
1 AAAAATCTATAAAACATAAAA
*
32465 AAAAATACTA-AAAACATTAAA
1 AAAAAT-CTATAAAACATAAAA
*
32486 ATAAAT
1 AAAAAT
32492 GTTTCCCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAAATCTATAAAACATAAAA
Found at i:32688 original size:22 final size:21
Alignment explanation
Indices: 32663--32713 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
32653 AAATAGTAGC
*
32663 AAAATAGTGAG-AAAATAATAA
1 AAAATAGTG-GCAAAACAATAA
*
32684 GAAAATAGCGGCAAAACAATAA
1 -AAAATAGTGGCAAAACAATAA
32706 AAAATAGT
1 AAAATAGT
32714 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.63, C:0.06, G:0.16, T:0.16
Consensus pattern (21 bp):
AAAATAGTGGCAAAACAATAA
Found at i:33200 original size:79 final size:78
Alignment explanation
Indices: 33064--33690 Score: 353
Period size: 79 Copynumber: 8.2 Consensus size: 78
33054 CCTAGTGTCT
** * ** * ** *
33064 TTCCTAATTAATATGGAACTCACATAATTTTTTGACTCTATTGTACGTAGAATATATCAATTCCA
1 TTCCTAACCAATATGGAACTCACAT-GTTTTCCGACTCCATTGTACAAAGAACATATCAATTCCA
* *
33129 AAATCTCTTTGCCC
65 ATACCTCTTTGCCC
*
33143 TTCCTAACCAATATGGAACTCACATGATTTTCCGACTCCATTATACAAAGAACATATCAATTCC-
1 TTCCTAACCAATATGGAACTCACATG-TTTTCCGACTCCATTGTACAAAGAACATATCAATTCCA
*
33207 --ACCTCTTAGCCC
65 ATACCTCTTTGCCC
* * * *
33219 TTCCTAACCAATATAGG-ACCCACGTTGCTTTCCGACTCCA-T-T-----GAACATATCAA--CT
1 TTCCTAACCAATAT-GGAACTCAC-ATGTTTTCCGACTCCATTGTACAAAGAACATATCAATTCC
* *
33274 AAGACCTCTTT-ACC
64 AATACCTCTTTGCCC
* * * ** * * *
33288 TTCCAAATCAATATGGAACTTGTCACATCATTTTCTAACTCCACTGTACATAGAACATATCATTT
1 TTCCTAACCAATATGGAAC---TCACAT-GTTTTCCGACTCCATTGTACAAAGAACATATCAATT
*
33353 CCAATACCTCTTTGCAC
62 CCAATACCTCTTTGCCC
* * * *
33370 TTCCTAACCAATATAG-ACCCTACATCGCTTTCCGACT-C------CAATGAACATATCAA--CC
1 TTCCTAACCAATATGGAACTC-ACAT-GTTTTCCGACTCCATTGTACAAAGAACATATCAATTCC
**
33425 AAGGCCTCTTTG-CC
64 AATACCTCTTTGCCC
* * *** * * * ** * *
33439 TTCCTAATCAATACGGAACTCACATTGTTTTTTTATTCAATTGCATGTAA-AATATATAAATTCC
1 TTCCTAACCAATATGGAACTCACA-TGTTTTCCGACTCCATTGTA-CAAAGAACATATCAATTCC
*
33503 AATGCCTCTTTGCCC
64 AATACCTCTTTGCCC
* * * * **
33518 TTCCTAACCAATAT-GAGACTCGCATCATTTTTCGACTCCATTGTATTAAAGAACATATTGA--C
1 TTCCTAACCAATATGGA-ACTCACAT-GTTTTCCGACTCCATTGTA-CAAAGAACATATCAATTC
* *
33580 CAAAACCTCTTTTCCC
63 CAATACCTCTTTGCCC
*
33596 TTCCTAATCAATATGGAAACTCACATCGTTTTCCGACTCCATTGTACATAA-AACATATCAATTC
1 TTCCTAACCAATATGG-AACTCACAT-GTTTTCCGACTCCATTGTACA-AAGAACATATCAATTC
*
33660 CCATACCTCTTTGCCC
63 CAATACCTCTTTGCCC
*
33676 TT-CTTACCAATATGG
1 TTCCTAACCAATATGG
33691 GGCTCACACC
Statistics
Matches: 415, Mismatches: 90, Indels: 86
0.70 0.15 0.15
Matches are distributed among these distances:
67 1 0.00
68 2 0.00
69 50 0.12
70 23 0.06
71 1 0.00
72 25 0.06
73 1 0.00
74 2 0.00
75 1 0.00
76 49 0.12
77 5 0.01
78 54 0.13
79 150 0.36
80 24 0.06
81 13 0.03
82 14 0.03
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (78 bp):
TTCCTAACCAATATGGAACTCACATGTTTTCCGACTCCATTGTACAAAGAACATATCAATTCCAA
TACCTCTTTGCCC
Found at i:33415 original size:151 final size:146
Alignment explanation
Indices: 33141--33463 Score: 409
Period size: 151 Copynumber: 2.2 Consensus size: 146
33131 ATCTCTTTGC
* * * *
33141 CCTTCCTAACCAATATGGAAC-TCACATGATTTTCCGACTCCATTATACAAAGAACATATCAATT
1 CCTTCCTAATCAATATGGAACTTCACATCATTTTCCAACTCCACTATACAAAGAACATATCAATT
* * * *
33205 CCACCTCTTAGCCCTTCCTAACCAATATAGGACCCACGTTGCTTTCCGACTCCATTGAACATATC
66 CCACCTCTTAGCACTTCCTAACCAATATAGGACCCACATCGCTTTCCGACTCCAATGAACATATC
*
33270 AACTAAGACCTCTTTA
131 AACCAAGACCTCTTTA
* * * * *
33286 CCTTCCAAATCAATATGGAACTTGTCACATCATTTTCTAACTCCACTGTACATAGAACATATCAT
1 CCTTCCTAATCAATATGGAAC-T-TCACATCATTTTCCAACTCCACTATACAAAGAACATATCAA
*
33351 TTCCAATACCTCTTTGCACTTCCTAACCAATATA-GACCCTACATCGCTTTCCGACTCCAATGAA
64 TTCC---ACCTCTTAGCACTTCCTAACCAATATAGGACCC-ACATCGCTTTCCGACTCCAATGAA
* *
33415 CATATCAACCAAGGCCTCTTTG
125 CATATCAACCAAGACCTCTTTA
*
33437 CCTTCCTAATCAATACGGAAC-TCACAT
1 CCTTCCTAATCAATATGGAACTTCACAT
33464 TGTTTTTTTA
Statistics
Matches: 152, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
145 19 0.12
148 44 0.29
150 5 0.03
151 84 0.55
ACGTcount: A:0.31, C:0.31, G:0.09, T:0.29
Consensus pattern (146 bp):
CCTTCCTAATCAATATGGAACTTCACATCATTTTCCAACTCCACTATACAAAGAACATATCAATT
CCACCTCTTAGCACTTCCTAACCAATATAGGACCCACATCGCTTTCCGACTCCAATGAACATATC
AACCAAGACCTCTTTA
Found at i:33840 original size:130 final size:130
Alignment explanation
Indices: 33593--33841 Score: 313
Period size: 129 Copynumber: 1.9 Consensus size: 130
33583 AACCTCTTTT
* *
33593 CCCTTCCTAATCAATATGGAAACTCACATCGTTTTCCGACTCCATTGTACATAAAACATATCAAT
1 CCCTTCCTAATCAATATGGAAACTCACACCATTTTCCGACTCCATTGTACATAAAACATATCAAT
* ** * *
33658 TCCCATACCTCTTTGCCCTTCTTACCAATATGGGGCTCACACCGTTTTCCAACTTTATTAAAGAA
66 TCCAATACCTCTTCACCCTTCTAACCAATATGGGACTCACACCGTTTTCCAACTTTATTAAAGAA
* * * *
33723 CCCTTCCTAATGAATAT-GAAACTCACACCATTTTTCGACTTCATTGTATA-AAGAACATATCAA
1 CCCTTCCTAATCAATATGGAAACTCACACCATTTTCCGACTCCATTGTACATAA-AACATATCAA
* * * * * *
33786 TTTCAATGCCTCTTCATCCTTCCTAACTAATATGTGACTCACATCGTTTTCCAACT
65 TTCCAATACCTCTTCACCCTT-CTAACCAATATGGGACTCACACCGTTTTCCAACT
33842 CTACTATATT
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
128 2 0.02
129 53 0.53
130 45 0.45
ACGTcount: A:0.30, C:0.28, G:0.08, T:0.34
Consensus pattern (130 bp):
CCCTTCCTAATCAATATGGAAACTCACACCATTTTCCGACTCCATTGTACATAAAACATATCAAT
TCCAATACCTCTTCACCCTTCTAACCAATATGGGACTCACACCGTTTTCCAACTTTATTAAAGAA
Found at i:33968 original size:79 final size:78
Alignment explanation
Indices: 33723--33976 Score: 217
Period size: 79 Copynumber: 3.2 Consensus size: 78
33713 TATTAAAGAA
* * * * * *
33723 CCCTTCCTAATGAATATGAAACTCACACCATTTTTCGACTTCATTGTATAAAGAACATATCAATT
1 CCCTTCCTAATCAATATGTAACTCACATCGTTTTTCGACTCCATTGTATTAA-AACATATCAATT
* * **
33788 TCAATGCCTCTTCA
65 CCAATACCTCTTTG
* * * * * * * **
33802 TCCTTCCTAA-CTAATATGTGACTCACATCGTTTTCCAACTCTACTATATTAAAGAACATATTGA
1 CCCTTCCTAATC-AATATGTAACTCACATCGTTTTTCGACTCCATTGTATT-AA-AACATATCAA
* *
33866 --CCAAGACCTCATTG
63 TTCCAATACCTCTTTG
* * *
33880 CCCTCCCTAATCAATATGTAACTCACATTGTTTTTCGACTCCATTGTATGTAAAATATATCAATT
1 CCCTTCCTAATCAATATGTAACTCACATCGTTTTTCGACTCCATTGTAT-TAAAACATATCAATT
33945 CCAATACCTCTTTG
65 CCAATACCTCTTTG
*
33959 CCCTTCCTAACCAATATG
1 CCCTTCCTAATCAATATG
33977 GGACTCGCAT
Statistics
Matches: 132, Mismatches: 37, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
77 7 0.05
78 48 0.36
79 66 0.50
80 11 0.08
ACGTcount: A:0.31, C:0.26, G:0.08, T:0.35
Consensus pattern (78 bp):
CCCTTCCTAATCAATATGTAACTCACATCGTTTTTCGACTCCATTGTATTAAAACATATCAATTC
CAATACCTCTTTG
Found at i:37215 original size:3 final size:3
Alignment explanation
Indices: 37202--37246 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
37192 CAGGTACGAA
37202 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
37247 GAGTATAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:37528 original size:26 final size:26
Alignment explanation
Indices: 37498--37551 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
37488 AAAAGTCGGG
*
37498 TTAATATATCATTTAGTAGTTGAGTT
1 TTAATATATAATTTAGTAGTTGAGTT
* * *
37524 TTAATATTTAATTTGGTATTTGAGTT
1 TTAATATATAATTTAGTAGTTGAGTT
37550 TT
1 TT
37552 TTAAATCTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.15, T:0.56
Consensus pattern (26 bp):
TTAATATATAATTTAGTAGTTGAGTT
Found at i:48194 original size:5 final size:5
Alignment explanation
Indices: 48184--48210 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
48174 TATAGAGAGA
48184 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
48211 GAAACACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:63064 original size:26 final size:26
Alignment explanation
Indices: 63013--63065 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
63003 ACTAAGCATT
63013 GGTTGAAAGCATAATAATAATGAAAA
1 GGTTGAAAGCATAATAATAATGAAAA
63039 GGTTGGAAAGCACTAAT-ATAAT-AAAA
1 GGTT-GAAAGCA-TAATAATAATGAAAA
63065 G
1 G
63066 TTAAGAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 9 0.36
27 12 0.48
28 4 0.16
ACGTcount: A:0.51, C:0.06, G:0.21, T:0.23
Consensus pattern (26 bp):
GGTTGAAAGCATAATAATAATGAAAA
Found at i:66506 original size:13 final size:13
Alignment explanation
Indices: 66490--66519 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
66480 AAATAAGAGA
66490 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
*
66503 AAAAACAAAAAAC
1 AAAAAAAAAAAAC
66516 AAAA
1 AAAA
66520 TACTTGGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:69014 original size:21 final size:21
Alignment explanation
Indices: 68976--69015 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
68966 AAAAAAATTC
*
68976 TATATTATAAAAGTATTATAA
1 TATATTATAAAAGAATTATAA
68997 TATATTTATAAAA-AATTAT
1 TATA-TTATAAAAGAATTAT
69016 GGTGAAGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TATATTATAAAAGAATTATAA
Found at i:77107 original size:31 final size:31
Alignment explanation
Indices: 77048--77140 Score: 114
Period size: 31 Copynumber: 3.0 Consensus size: 31
77038 AAGGTTCAAA
* * *
77048 CTCCAATATGAAAACAATTGTCTAGTTTAAG
1 CTCCAATATAAAAATAATTATCTAGTTTAAG
* * *
77079 CTCTAATATAAAAATAATTATCTGGTTTAAA
1 CTCCAATATAAAAATAATTATCTAGTTTAAG
* *
77110 CTCCAATGTAAAAATAATTATCAAGTTTAAG
1 CTCCAATATAAAAATAATTATCTAGTTTAAG
77141 GCTTAACTTA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 51 1.00
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (31 bp):
CTCCAATATAAAAATAATTATCTAGTTTAAG
Found at i:85112 original size:69 final size:66
Alignment explanation
Indices: 85047--85171 Score: 180
Period size: 69 Copynumber: 1.9 Consensus size: 66
85037 CGAAAATCTG
* *
85047 AATAA-AAAAAGGTAAAACTACGTTGTTTTGATAAATGTTTACTTTTCTAAAGTTAAAAGTCAAA
1 AATAAGAAAAAGGTAAAACTACGTCGTTTTGATAAATGTTTACTTAT-T-AAGTTAAAAGTCAAA
85111 ATC
64 ATC
* *
85114 ATTAAGTTAAAAGGTAAAACTACGTCGTTTTGATAAATGTTTACTTATTAAGTTAAAA
1 AATAAG-AAAAAGGTAAAACTACGTCGTTTTGATAAATGTTTACTTATTAAGTTAAAA
85172 TGTAAAACCA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
67 13 0.25
68 1 0.02
69 38 0.73
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (66 bp):
AATAAGAAAAAGGTAAAACTACGTCGTTTTGATAAATGTTTACTTATTAAGTTAAAAGTCAAAAT
C
Found at i:86959 original size:20 final size:20
Alignment explanation
Indices: 86895--86965 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
86885 CAAATGATTT
86895 TAAAATTATTTTTTAAAAATA
1 TAAAATTATTTTTT-AAAATA
*
86916 TAAAATTA---TTTAAATTATTT
1 TAAAATTATTTTTTAAA--A-TA
86936 TAAAATTATTTTTTAAAATA
1 TAAAATTATTTTTTAAAATA
86956 TAAAATTATT
1 TAAAATTATT
86966 AAAATTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
17 3 0.07
18 3 0.07
19 1 0.02
20 20 0.48
21 9 0.21
23 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAATTATTTTTTAAAATA
Found at i:86959 original size:40 final size:41
Alignment explanation
Indices: 86886--86978 Score: 161
Period size: 40 Copynumber: 2.3 Consensus size: 41
86876 TTACATCAAC
* *
86886 AAATGATTTTAAAATTATTTTTTAAAAATATAAAATTATTT
1 AAATTATTTTAAAATTATTTTTTAAAAATATAAAATTATTA
86927 AAATTATTTTAAAATTATTTTTT-AAAATATAAAATTATTA
1 AAATTATTTTAAAATTATTTTTTAAAAATATAAAATTATTA
86967 AAATTATTTTAA
1 AAATTATTTTAA
86979 TATTTTAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 28 0.56
41 22 0.44
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (41 bp):
AAATTATTTTAAAATTATTTTTTAAAAATATAAAATTATTA
Found at i:87696 original size:51 final size:56
Alignment explanation
Indices: 87641--87777 Score: 158
Period size: 51 Copynumber: 2.5 Consensus size: 56
87631 ATAAAAAGAT
* **
87641 GGAAAATAAGAAGAAGGGGCAGGAGAACAG-AAAAA-AAAAAAACCAC-CA-A-AA
1 GGAAAATAAGAAGAAGGGGAAGGAGAACAGAAAAAACAAAAAAAAAACTCATAGAA
* * *
87692 GGAAAATAAAAAGAAAGGGAAGGGGAACAGAAAAAACCCAAAAAAAAAACTCATAGGAA
1 GGAAAATAAGAAGAAGGGGAAGGAGAACAGAAAAAA--CAAAAAAAAAACTCATA-GAA
87751 GGAAAATAAGAAGAAGGGGAAGGAGAA
1 GGAAAATAAGAAGAAGGGGAAGGAGAA
87778 AAAGGGAAGG
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
51 26 0.38
52 5 0.07
55 9 0.13
56 2 0.03
57 1 0.01
59 26 0.38
ACGTcount: A:0.61, C:0.09, G:0.26, T:0.04
Consensus pattern (56 bp):
GGAAAATAAGAAGAAGGGGAAGGAGAACAGAAAAAACAAAAAAAAAACTCATAGAA
Found at i:87853 original size:11 final size:10
Alignment explanation
Indices: 87830--87871 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 10
87820 ATATTTTAAA
*
87830 AAATAATTCT
1 AAATAATTTT
87840 AAATTAATTTT
1 AAA-TAATTTT
87851 AAAATAATTTT
1 -AAATAATTTT
87862 -AATAATTTT
1 AAATAATTTT
87871 A
1 A
87872 TATTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
9 9 0.32
10 3 0.11
11 13 0.46
12 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (10 bp):
AAATAATTTT
Found at i:87857 original size:22 final size:20
Alignment explanation
Indices: 87829--87871 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
87819 TATATTTTAA
87829 AAAATAATTCTAAATTAATTTT
1 AAAATAATT-TAAA-TAATTTT
*
87851 AAAATAATTTTAATAATTTT
1 AAAATAATTTAAATAATTTT
87871 A
1 A
87872 TATTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 3 0.15
22 9 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATAATTTAAATAATTTT
Found at i:87869 original size:20 final size:20
Alignment explanation
Indices: 87811--87871 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
87801 ATGATATTTT
87811 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTT--AA
*
87831 AATAATTCTAAATTAATTTTAA
1 AATAATT-TTAA-TAATTTTAA
87853 AATAATTTTAATAATTTTA
1 AATAATTTTAATAATTTTA
87872 TATTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 15 0.43
21 4 0.11
22 10 0.29
23 1 0.03
24 5 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
AATAATTTTAATAATTTTAA
Found at i:91274 original size:60 final size:60
Alignment explanation
Indices: 91181--91302 Score: 244
Period size: 60 Copynumber: 2.0 Consensus size: 60
91171 ACGGATTTAG
91181 AAATTCTTGCCGTAAGCCCTCCATTTCCCACAATAAATTACCGTTGTCCTGAAAATTAAA
1 AAATTCTTGCCGTAAGCCCTCCATTTCCCACAATAAATTACCGTTGTCCTGAAAATTAAA
91241 AAATTCTTGCCGTAAGCCCTCCATTTCCCACAATAAATTACCGTTGTCCTGAAAATTAAA
1 AAATTCTTGCCGTAAGCCCTCCATTTCCCACAATAAATTACCGTTGTCCTGAAAATTAAA
91301 AA
1 AA
91303 GGAAAAATGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 62 1.00
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (60 bp):
AAATTCTTGCCGTAAGCCCTCCATTTCCCACAATAAATTACCGTTGTCCTGAAAATTAAA
Found at i:98192 original size:78 final size:78
Alignment explanation
Indices: 98063--98221 Score: 318
Period size: 78 Copynumber: 2.0 Consensus size: 78
98053 GGTCTACAGT
98063 TTGATGAACTGAAATTGAGCAAACCGGTTAAAGGATTATTACATCGTCTATCAAGTTCAAATGGA
1 TTGATGAACTGAAATTGAGCAAACCGGTTAAAGGATTATTACATCGTCTATCAAGTTCAAATGGA
98128 GAGATATCTTGTC
66 GAGATATCTTGTC
98141 TTGATGAACTGAAATTGAGCAAACCGGTTAAAGGATTATTACATCGTCTATCAAGTTCAAATGGA
1 TTGATGAACTGAAATTGAGCAAACCGGTTAAAGGATTATTACATCGTCTATCAAGTTCAAATGGA
98206 GAGATATCTTGTC
66 GAGATATCTTGTC
98219 TTG
1 TTG
98222 GGTGTCGAAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (78 bp):
TTGATGAACTGAAATTGAGCAAACCGGTTAAAGGATTATTACATCGTCTATCAAGTTCAAATGGA
GAGATATCTTGTC
Found at i:99568 original size:6 final size:6
Alignment explanation
Indices: 99557--99601 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
99547 TCATGCATTT
* * * *
99557 GGAGCA GGAGCA GGAGCG GGCGCA GGCGCA GGAGCA GGAGTA GGA
1 GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA GGAGCA GGA
99602 CCACCTGTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.53, T:0.02
Consensus pattern (6 bp):
GGAGCA
Found at i:104826 original size:23 final size:22
Alignment explanation
Indices: 104772--104826 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
104762 TATTTTGAAA
104772 TTTAATTTTATACTTTTATTTT
1 TTTAATTTTATACTTTTATTTT
* *
104794 TTAAAATTTAGT-CATTTTATTTT
1 TTTAATTTTA-TAC-TTTTATTTT
104817 TTTAATTTTA
1 TTTAATTTTA
104827 AATTTTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTAATTTTATACTTTTATTTT
Found at i:114637 original size:31 final size:31
Alignment explanation
Indices: 114600--114658 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
114590 GTCTCTGTAT
114600 CTTTTATAAATTT-GAAATTTAGTC-CTTTTTA
1 CTTTTAT--ATTTAGAAATTTAGTCTCTTTTTA
*
114631 CTTTTATTTTTAGAAATTTAGTCTCTTT
1 CTTTTATATTTAGAAATTTAGTCTCTTT
114659 ATTTATCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 3 0.12
30 11 0.44
31 11 0.44
ACGTcount: A:0.25, C:0.10, G:0.07, T:0.58
Consensus pattern (31 bp):
CTTTTATATTTAGAAATTTAGTCTCTTTTTA
Found at i:125529 original size:21 final size:21
Alignment explanation
Indices: 125488--125529 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
125478 AGTAAAATAA
* *
125488 AAAAATTATTTCTAGTACAAT
1 AAAAATCATTTCTAATACAAT
125509 AAAAATCATTT-TAATATCAAT
1 AAAAATCATTTCTAATA-CAAT
125530 TATTAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAATCATTTCTAATACAAT
Found at i:126009 original size:15 final size:17
Alignment explanation
Indices: 125977--126013 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
125967 TAAAATATAA
125977 TTTTATTTATATTAATT
1 TTTTATTTATATTAATT
125994 TTTTATTT-TATT-ATT
1 TTTTATTTATATTAATT
126009 TTTTA
1 TTTTA
126014 AGTGAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.40
16 4 0.20
17 8 0.40
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTATTTATATTAATT
Found at i:129040 original size:21 final size:21
Alignment explanation
Indices: 129016--129056 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
129006 GTATACTCGA
*
129016 ATCAATTACAAAGTATCATGG
1 ATCAAGTACAAAGTATCATGG
*
129037 ATCAAGTACAAATTATCATG
1 ATCAAGTACAAAGTATCATG
129057 CGCTGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (21 bp):
ATCAAGTACAAAGTATCATGG
Found at i:132683 original size:41 final size:41
Alignment explanation
Indices: 132633--132715 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
132623 AAAAACTCTT
132633 CTCCTCTTTCAAATAAACAAATATTTTTTAAAACAAAATTC
1 CTCCTCTTTCAAATAAACAAATATTTTTTAAAACAAAATTC
132674 CTCCTCTTTCAAATAAACAAATATTTTTTAAAACAAAATTC
1 CTCCTCTTTCAAATAAACAAATATTTTTTAAAACAAAATTC
132715 C
1 C
132716 AACCTAAAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.36
Consensus pattern (41 bp):
CTCCTCTTTCAAATAAACAAATATTTTTTAAAACAAAATTC
Found at i:133396 original size:7 final size:7
Alignment explanation
Indices: 133384--133410 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
133374 AACTATTCAC
133384 AAATTTG
1 AAATTTG
133391 AAATTTG
1 AAATTTG
133398 AAATTTG
1 AAATTTG
133405 AAATTT
1 AAATTT
133411 AGTCTCTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (7 bp):
AAATTTG
Found at i:135712 original size:9 final size:9
Alignment explanation
Indices: 135698--135731 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
135688 TAATTATTTT
135698 TTAAAATTA
1 TTAAAATTA
135707 TTAAAATTA
1 TTAAAATTA
135716 TTAAAATTA
1 TTAAAATTA
*
135725 TAAAAAT
1 TTAAAAT
135732 ATATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TTAAAATTA
Found at i:136191 original size:131 final size:130
Alignment explanation
Indices: 136036--136282 Score: 320
Period size: 131 Copynumber: 1.9 Consensus size: 130
136026 TTAAGGATAC
* *
136036 TTTTGTCATCTCAACTAATATTAAACCCTTTACT-AAATTTGATGTCACGAGTCAATTATGCACC
1 TTTTGTCATCTCAACTAATATTAAACCCTTTACTGAAATTTG-TGTCACGAGTCAACTATACACC
* *
136100 AA-TTAATCTAAGTAATTAA-CAATATTACATTCATTTTACAAAGTAAATTATATAATCTTGAGA
65 AATTTAA-CTAAGTAA-TAATCAA-AATACATTCACTTTACAAAGTAAATTATATAATCTTGAGA
136163 GTAT
127 GTAT
* * * * * *
136167 TTTTGTCATCTCCACTAATATTAAATCCTTTAGTGAATTTTGTGTCATGAGTCAACTGTACACCA
1 TTTTGTCATCTCAACTAATATTAAACCCTTTACTGAAATTTGTGTCACGAGTCAACTATACACCA
* * *
136232 ATTTAACTAAGTAATAATGAAAATACCTTTACTTTACAAAGTAAATTATAT
66 ATTTAACTAAGTAATAATCAAAATACATTCACTTTACAAAGTAAATTATAT
136283 TACGTGGAGT
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
130 29 0.29
131 61 0.61
132 10 0.10
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (130 bp):
TTTTGTCATCTCAACTAATATTAAACCCTTTACTGAAATTTGTGTCACGAGTCAACTATACACCA
ATTTAACTAAGTAATAATCAAAATACATTCACTTTACAAAGTAAATTATATAATCTTGAGAGTAT
Found at i:149277 original size:125 final size:125
Alignment explanation
Indices: 149113--149490 Score: 659
Period size: 125 Copynumber: 3.0 Consensus size: 125
149103 CGATTATTGT
*
149113 TTGGATAATTGAATTTTAAGTAATGAATGCTTAGTGAATGATCCGATTTAAGTGTTTATTTCAAC
1 TTGGATAATTGAATTTTAAGTAATGAATGCTTAGTGAATGATCCAATTTAAGTGTTTATTTCAAC
* *
149178 AAATGAATGAAAATTTTATACATTTCTTAGATTCAATTGTAATGAACTGTTCTTTGTCGA
66 AAATGAATGAAAATTTTATACATTTCTTAGATTCAATTGTAATGAACTGTGCTTTGTTGA
*
149238 TTGGATAATTGAATTTTAAGTAATGAATGCTTAGTGAATGATTCAATTTAAGTGTTTATTTCAAC
1 TTGGATAATTGAATTTTAAGTAATGAATGCTTAGTGAATGATCCAATTTAAGTGTTTATTTCAAC
149303 AAATGAATGAAAATTTTATACATTTCTTAGATTCAATTGTAATGAACTGTGCTTTGTTGA
66 AAATGAATGAAAATTTTATACATTTCTTAGATTCAATTGTAATGAACTGTGCTTTGTTGA
* *
149363 TTGGATAATTGAATTTTAAGTAATGAATGCCTAGTGACTGATCCAATTTAAGTGTTTATTTCAAC
1 TTGGATAATTGAATTTTAAGTAATGAATGCTTAGTGAATGATCCAATTTAAGTGTTTATTTCAAC
* * * *
149428 AAATGAAAGAAAA-TTTATCCATTTCTCAGATTCAATTGCAATGAACTGTGCTTTGTTGA
66 AAATGAATGAAAATTTTATACATTTCTTAGATTCAATTGTAATGAACTGTGCTTTGTTGA
149487 TTGG
1 TTGG
149491 GAATTACAAT
Statistics
Matches: 242, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
124 47 0.19
125 195 0.81
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (125 bp):
TTGGATAATTGAATTTTAAGTAATGAATGCTTAGTGAATGATCCAATTTAAGTGTTTATTTCAAC
AAATGAATGAAAATTTTATACATTTCTTAGATTCAATTGTAATGAACTGTGCTTTGTTGA
Found at i:151500 original size:30 final size:30
Alignment explanation
Indices: 151446--151509 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
151436 TAGATTATAT
151446 TTTTTATAATTTTTAAAAAATTAAAT-TAAA
1 TTTTTATAATTTTTAAAAAATTAAATGT-AA
* ***
151476 TTTTTATAATTTTTGAAGGGTTAAATGTAA
1 TTTTTATAATTTTTAAAAAATTAAATGTAA
151506 TTTT
1 TTTT
151510 ACTATTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (30 bp):
TTTTTATAATTTTTAAAAAATTAAATGTAA
Found at i:151561 original size:15 final size:16
Alignment explanation
Indices: 151533--151562 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
151523 TAAATTTTTA
151533 TAAATTATAAAATATT
1 TAAATTATAAAATATT
151549 TAAATTA-AAAATAT
1 TAAATTATAAAATAT
151563 ACCATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATTATAAAATATT
Found at i:153557 original size:123 final size:123
Alignment explanation
Indices: 153394--154721 Score: 1727
Period size: 123 Copynumber: 10.8 Consensus size: 123
153384 AAACATAAGG
* * * * * *
153394 CCTATTCACTTC-AATGTCAGCTCATAGAAATTAACATTTAGCTGCCTCATTGAGTTCCATTTTG
1 CCTATTCACTTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCG
* * * *
153458 TATGGGTAGGTTAGAGGTAGCCAATTCATATTAGTTAAGAGCTACAGAAACATAAAAA
66 TATCGGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
* * *
153516 CCTATTCACTTCGGTTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTTCATTTTG
1 CCTATTCACTTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCG
* * * * *
153581 TAACAGTAGCTTAGAAGTAGCCAATTCATATTTGTCCAGAGCTGCAGAAACATAAAAA
66 TATCGGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
* * * *
153639 CCTATTCACTTTGATTTTTAGCTCATAGAAATGAACATTTAGCTGCCTCATTGAGTTCCATTTCG
1 CCTATTCACTTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCG
* *
153704 TATCAGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACAT-GAAA
66 TATCGGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
* * * * * * *
153761 TCTATTCATTTCGATTTTCAGCTCACAGGAATGAACATTCAGCTGGCTCATTGAGGTCCGTTTTG
1 CCTATTCACTTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCG
* * *
153826 TATTGGTAGGTTAGAAGTAGGC-ATTCATATTTGTTGAGAGCTACAGAAACAT-AAAA
66 TATCGGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
* * * * * * *
153882 CCTATTCACATCAATTTTCAGCTCACAGAAATTAACATTTTGCTGCCTCATTTAGGTCTATTTCA
1 CCTATTCACTTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCG
* * *
153947 TATCGGTTGGTTAGAAGTAGCCAATTCATTATTAGTTCAGTGCTACAGAAAACATAAAAA
66 TATCGGTAGGTTAGAAGTAGCCAATTCA-TATTTGTTCAGAGCTACAG-AAACATAAAAA
* * *
154007 CCTATTCACTTTCGATTTTCGGCTCACAGAAATGAACATTTAGCTGCTTCATTGAGGTACATTTC
1 CCTATTCAC-TTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTC
* * * * **
154072 GTATCGGTAGGTCAGAAGTAGGCAATTCATATTTGTTCAGTGTTATGGAAACATAAAAA
65 GTATCGGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
* ** *
154131 -CTATTCACTTTGATTTTCAGCTCATGGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTTG
1 CCTATTCACTTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCG
* *
154195 TACCGGTAGGTTAGAAGTAGGCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
66 TATCGGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
* * *
154253 CCTATTCACTTTGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGCTACATTTCG
1 CCTATTCACTTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCG
* * *
154318 TATCGGTAGGTCAGAAGTAGCCAATTCATATTTGTTCAGGGTTACAGAAACATAAAATA
66 TATCGGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAA-A
* ** * * *
154377 --TAATTCACTTTGATTTTCAGCTCATGGAAATGAACATTTGGCCGCCTCATTGAGGTCCATTTT
1 CCT-ATTCACTTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTC
* *
154440 GTATCGGTAGGTTAGAATTAGGCAATTCATATTTGTTCAGAGCTACAGAAACAT-AAAA
65 GTATCGGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
* * * *
154498 CCTATTCACTTTGATTTTCAGCTTACAGAAACGAACATTTAGCTGCCTCTTTGAGGTCCATTTCG
1 CCTATTCACTTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCG
* * * *
154563 TATTGGTATGTTATAACTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
66 TATCGGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
* * * *
154621 CCTATTCGCTCTCAATTTTCAGCTCAAAGAAATGAACATTTAGCTGCCTCATCGAGGTCCATTTC
1 CCTATTCACT-TCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTC
* * * * * *
154686 ATAGCAGTAGGTTAAAAGTAGCCGACTCATATTTGT
65 GTATCGGTAGGTTAGAAGTAGCCAATTCATATTTGT
154722 GTTTATTTCA
Statistics
Matches: 1047, Mismatches: 146, Indels: 24
0.86 0.12 0.02
Matches are distributed among these distances:
121 103 0.10
122 300 0.29
123 453 0.43
124 92 0.09
125 28 0.03
126 71 0.07
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (123 bp):
CCTATTCACTTCGATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCG
TATCGGTAGGTTAGAAGTAGCCAATTCATATTTGTTCAGAGCTACAGAAACATAAAAA
Found at i:154795 original size:90 final size:91
Alignment explanation
Indices: 154635--155036 Score: 488
Period size: 90 Copynumber: 4.5 Consensus size: 91
154625 TTCGCTCTCA
* * * *
154635 ATTTTCAGCTCAAAGAAATGAACATTTAGCTGCCTCATCGAGGTCCATTT--CATAGCAGTAGGT
1 ATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCGCATTG-AGTAGCT
* * *
154698 TAAAAGTAGCCGACTCATATTTGTGTTT
65 TAGAAGTAGCCAACTCATATTTGT-TTG
* *
154726 A-TTTCAGCTCACAGGAATGAACATTTAGCTGCCACATTGAGGTCCATTTCGCATTGA-TAGCTT
1 ATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCGCATTGAGTAGCTT
154789 AGAAGTAGCCAACTCATATTTGTGTTG
66 AGAAGTAGCCAACTCATATTTGT-TTG
*
154816 A-TTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCGTATTG-GTAGCTT
1 ATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCGCATTGAGTAGCTT
*
154879 AGAAGTAGCCAACTCATATTTGTTACG
66 AGAAGTAGCCAACTCATATTTGTT-TG
* * * * *
154906 ATTTTCAGCTCATAGAAATGAAC------CTGTCTCATTGAGGTCCATTTCGTA-TCAGTAGGTT
1 ATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCGCATTGAGTAGCTT
*
154964 AGAAGTAGCCAACTCATATTTGTTTCA
66 AGAAGTAGCCAACTCATATTTGTTT-G
* **
154991 ATTTTCAGCTCACAGAAATGAACATTTATCTGCCTTGTTGAGGTCC
1 ATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCC
155037 TACAGCGATG
Statistics
Matches: 275, Mismatches: 23, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
84 1 0.00
85 76 0.28
89 1 0.00
90 157 0.57
91 36 0.13
92 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (91 bp):
ATTTTCAGCTCACAGAAATGAACATTTAGCTGCCTCATTGAGGTCCATTTCGCATTGAGTAGCTT
AGAAGTAGCCAACTCATATTTGTTTG
Found at i:163611 original size:33 final size:33
Alignment explanation
Indices: 163569--163635 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
163559 TTGTGGAAGG
163569 TGCAAACCTATGCCATTCATCATTACAGAATGA
1 TGCAAACCTATGCCATTCATCATTACAGAATGA
163602 TGCAAACCTATGCCATTCATCATTACAGAATGA
1 TGCAAACCTATGCCATTCATCATTACAGAATGA
163635 T
1 T
163636 CAATCAAGCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (33 bp):
TGCAAACCTATGCCATTCATCATTACAGAATGA
Found at i:170466 original size:116 final size:116
Alignment explanation
Indices: 170259--170489 Score: 417
Period size: 116 Copynumber: 2.0 Consensus size: 116
170249 GTTTCTTGCC
* *
170259 TGTAGGCTTAGATTAGAAAAACTTAACTTGTAGCTTTTGTCATTGTTAAACTTAATAGATGACCA
1 TGTAGGCTTAAATCAGAAAAACTTAACTTGTAGCTTTTGTCATTGTTAAACTTAATAGATGACCA
* *
170324 GTTCAGTCTCTTGGTTACTATGATGACATATGCATCCTTGACATAGGGATA
66 GTTCAGTCTCTTGGTTACTATAATGACATATGCATCCTTCACATAGGGATA
170375 TGTAGGCTTAAATCAGAAAAACTTAACTTGTAGCTTTTGTCATTGTTAAACTTAATAGATGACCA
1 TGTAGGCTTAAATCAGAAAAACTTAACTTGTAGCTTTTGTCATTGTTAAACTTAATAGATGACCA
*
170440 GTTCAGTCTCTTGGTTACTATAATGACATATGCATCCTTCACTTAGGGAT
66 GTTCAGTCTCTTGGTTACTATAATGACATATGCATCCTTCACATAGGGAT
170490 GACATATCGG
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 110 1.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (116 bp):
TGTAGGCTTAAATCAGAAAAACTTAACTTGTAGCTTTTGTCATTGTTAAACTTAATAGATGACCA
GTTCAGTCTCTTGGTTACTATAATGACATATGCATCCTTCACATAGGGATA
Found at i:178264 original size:13 final size:13
Alignment explanation
Indices: 178248--178272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
178238 AATTTAATTA
178248 AAAATTAATTGAT
1 AAAATTAATTGAT
178261 AAAATTAATTGA
1 AAAATTAATTGA
178273 ACTCCTAAAT
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAAATTAATTGAT
Found at i:180398 original size:171 final size:172
Alignment explanation
Indices: 180050--180401 Score: 636
Period size: 171 Copynumber: 2.1 Consensus size: 172
180040 GGGCTGTAAG
* *
180050 AAAAA-GAGCTAAGAAATCTAATACAAGTTCTACTACAGATGTGGAAGTTGTTGAAATTAAAGAT
1 AAAAAGGAACTAAGAAATCTAATACAAGTTATACTACAGATGTGGAAGTTGTTGAAATTAAAGAT
**
180114 GGAGGAACTAAAAGGAAGTTTGGTAAGGCAATCACCTTGAACTAGATTGATTACTTATTTCGATG
66 GGAGGAACTAAAAGGAAGTTTGGTAAGGCAATCACCTCAAACTAGATTGATTACTTATTTCGATG
*
180179 TTGGATTTTACTTGAACATTACAAACTTTCTTCTCTATAGAA
131 TTCGATTTTACTTGAACATTACAAACTTTCTTCTCTATAGAA
180221 AAAAAGGAACTAAGAAATCTAATACAAGTTATACTACAGATGTGGAAGTTGTTGAAATTAAAGAT
1 AAAAAGGAACTAAGAAATCTAATACAAGTTATACTACAGATGTGGAAGTTGTTGAAATTAAAGAT
*
180286 GGAGGAACTAAAAGGAAGTTTGGT-AGGCAATCACCTCAAACTAGATTGATTACTTATTTCTATG
66 GGAGGAACTAAAAGGAAGTTTGGTAAGGCAATCACCTCAAACTAGATTGATTACTTATTTCGATG
180350 TTCGATTTTACTTGAACATTACAAACTTTCTTCTCTATAGAA
131 TTCGATTTTACTTGAACATTACAAACTTTCTTCTCTATAGAA
180392 AAAAAGGAAC
1 AAAAAGGAAC
180402 ACAAGGACTT
Statistics
Matches: 174, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
171 93 0.53
172 81 0.47
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (172 bp):
AAAAAGGAACTAAGAAATCTAATACAAGTTATACTACAGATGTGGAAGTTGTTGAAATTAAAGAT
GGAGGAACTAAAAGGAAGTTTGGTAAGGCAATCACCTCAAACTAGATTGATTACTTATTTCGATG
TTCGATTTTACTTGAACATTACAAACTTTCTTCTCTATAGAA
Found at i:191476 original size:29 final size:26
Alignment explanation
Indices: 191421--191492 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
191411 TCACATCAAC
*
191421 AAATAATTTTAAAA-T-TAA-T-TTA
1 AAATTATTTTAAAATTATAATTATTA
191443 AAATTATTTTTTAAAATATATAATTATTA
1 AAATTA--TTTTAAAAT-TATAATTATTA
191472 AAATTATTTTAAAATTATAAT
1 AAATTATTTTAAAATTATAAT
191493 CGTCATCATC
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
22 5 0.12
24 8 0.19
26 7 0.17
27 12 0.29
28 1 0.02
29 9 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
AAATTATTTTAAAATTATAATTATTA
Found at i:191485 original size:11 final size:11
Alignment explanation
Indices: 191421--191489 Score: 57
Period size: 11 Copynumber: 5.6 Consensus size: 11
191411 TCACATCAAC
*
191421 AAATAATTTTA
1 AAATTATTTTA
*
191432 AAATTAATTTA
1 AAATTATTTTA
191443 AAATTATTTTTTAA
1 AAATTA--TTTT-A
191457 AATATATAATTATTA
1 AA-AT-T-ATT-TTA
191472 AAATTATTTTA
1 AAATTATTTTA
191483 AAATTAT
1 AAATTAT
191490 AATCGTCATC
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
11 25 0.52
12 3 0.06
13 4 0.08
14 5 0.10
15 7 0.15
16 3 0.06
17 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:192786 original size:15 final size:14
Alignment explanation
Indices: 192762--192791 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
192752 AAATAAATAT
192762 AAGTATTTATTTAA
1 AAGTATTTATTTAA
192776 AAGTGATTTATTTAA
1 AAGT-ATTTATTTAA
192791 A
1 A
192792 TATAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
AAGTATTTATTTAA
Found at i:192893 original size:14 final size:14
Alignment explanation
Indices: 192874--192921 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
192864 AAATTATTTA
*
192874 TTTATATATATATT
1 TTTATATAAATATT
192888 TTTATATAAATA-T
1 TTTATATAAATATT
* *
192901 TATATTTAAATATT
1 TTTATATAAATATT
*
192915 TATATAT
1 TTTATAT
192922 TTATATGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 11 0.38
14 18 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTATATAAATATT
Found at i:192925 original size:8 final size:8
Alignment explanation
Indices: 192867--192927 Score: 54
Period size: 8 Copynumber: 7.8 Consensus size: 8
192857 TAAACAAAAA
*
192867 TTATTTAT
1 TTATATAT
192875 TTATATA-
1 TTATATAT
*
192882 -TATATTT
1 TTATATAT
*
192889 TTATATAA
1 TTATATAT
*
192897 ATATTATAT
1 TTA-TATAT
*
192906 TTAAATAT
1 TTATATAT
192914 TTATATAT
1 TTATATAT
192922 TTATAT
1 TTATAT
192928 GTATTCACTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
6 5 0.12
8 30 0.73
9 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATAT
Found at i:202059 original size:23 final size:21
Alignment explanation
Indices: 201999--202064 Score: 69
Period size: 23 Copynumber: 3.0 Consensus size: 21
201989 TTTCAAATAT
*
201999 TTTATATGCGAAATATTTTAA
1 TTTATATGTGAAATATTTTAA
* * *
202020 TTAATTATTTGAAATATTATTATG
1 TTTA-TATGTGAAATATT-TTA-A
202044 TTTATATGTGAAATATTTTAA
1 TTTATATGTGAAATATTTTAA
202065 ATATACATAC
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 3 0.09
22 14 0.40
23 15 0.43
24 3 0.09
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.52
Consensus pattern (21 bp):
TTTATATGTGAAATATTTTAA
Found at i:204783 original size:16 final size:16
Alignment explanation
Indices: 204762--204792 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
204752 ATAATGTGAA
204762 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
204778 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
204793 GGATTCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:205792 original size:37 final size:37
Alignment explanation
Indices: 205751--205829 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
205741 CCGAAAATAT
** *
205751 TCATGCGGTGACAATTTTGGGTGCAA-CTTAGAAGTGC
1 TCATGCGACGACAATTTTGGGCGCAATC-TAGAAGTGC
*
205788 TCATGCGACGACAGTTTTGGGCGCAATCTAGAAGTGC
1 TCATGCGACGACAATTTTGGGCGCAATCTAGAAGTGC
205825 TCATG
1 TCATG
205830 TAGCGACATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (37 bp):
TCATGCGACGACAATTTTGGGCGCAATCTAGAAGTGC
Found at i:205837 original size:37 final size:37
Alignment explanation
Indices: 205760--205837 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
205750 TTCATGCGGT
* *
205760 GACAATTTTGGGTGCAACTTAGAAGTGCTCATGCGAC
1 GACAATTTTGGGCGCAACTTAGAAGTGCTCATGAGAC
*
205797 GACAGTTTTGGGCGCAA-TCTAGAAGTGCTCATGTAG-C
1 GACAATTTTGGGCGCAACT-TAGAAGTGCTCATG-AGAC
205834 GACA
1 GACA
205838 TTAGTAGTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 1 0.03
37 34 0.94
38 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (37 bp):
GACAATTTTGGGCGCAACTTAGAAGTGCTCATGAGAC
Found at i:206930 original size:17 final size:17
Alignment explanation
Indices: 206875--206931 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
206865 AAGATATATG
*
206875 GAAATGCAATGACAAGA
1 GAAATGCAATGACAAAA
* * *
206892 TAGATGCAGTGACAATAA
1 GAAATGCAATGACAA-AA
206910 -AAATGCAATGACAAAA
1 GAAATGCAATGACAAAA
206926 GAAATG
1 GAAATG
206932 TGATGATAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.06
17 29 0.91
18 1 0.03
ACGTcount: A:0.53, C:0.11, G:0.21, T:0.16
Consensus pattern (17 bp):
GAAATGCAATGACAAAA
Found at i:209254 original size:16 final size:16
Alignment explanation
Indices: 209233--209263 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
209223 ATAATGTGAA
209233 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
209249 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
209264 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:210243 original size:37 final size:36
Alignment explanation
Indices: 210180--210255 Score: 98
Period size: 37 Copynumber: 2.1 Consensus size: 36
210170 TGCAATTGAA
* *
210180 GAAAATTTATGCGGCAACAGTCTTGGGTGCATTCTG
1 GAAAATTCATGCGGCAACAGTCTTGGGTGCAATCTG
* * *
210216 GAAATATTCATGCGGCGATAGTTTTGGGTGCAATCTG
1 GAAA-ATTCATGCGGCAACAGTCTTGGGTGCAATCTG
210253 GAA
1 GAA
210256 GTGCTCATAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 4 0.12
37 30 0.88
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.30
Consensus pattern (36 bp):
GAAAATTCATGCGGCAACAGTCTTGGGTGCAATCTG
Found at i:210276 original size:37 final size:37
Alignment explanation
Indices: 210196--210300 Score: 120
Period size: 37 Copynumber: 2.8 Consensus size: 37
210186 TTATGCGGCA
* * * ** * *
210196 ACAGTCTTGGGTGCATTCTGGAAATATTCATGCGGCG
1 ACAGTTTTGGGTGCAATCTGGAAGTGCTCATACGACG
*
210233 ATAGTTTTGGGTGCAATCTGGAAGTGCTCATACGACG
1 ACAGTTTTGGGTGCAATCTGGAAGTGCTCATACGACG
* *
210270 ACAGTTTTGGGCGCAATCTAGAAGTGCTCAT
1 ACAGTTTTGGGTGCAATCTGGAAGTGCTCAT
210301 GTAGCGACAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (37 bp):
ACAGTTTTGGGTGCAATCTGGAAGTGCTCATACGACG
Found at i:212210 original size:28 final size:25
Alignment explanation
Indices: 212146--212302 Score: 133
Period size: 24 Copynumber: 6.2 Consensus size: 25
212136 TTTAAACACG
*
212146 CGTTTACGCTCGCCAGTTTACACA-
1 CGTTTACGCTCGCCAGCTTACACAT
* * *
212170 CGTTTATGCTCGCCATCTTATACTTAT
1 CGTTTACGCTCGCCAGCTTACAC--AT
*
212197 GCGTTTACGCTCGCCAGCTTGCACAT
1 -CGTTTACGCTCGCCAGCTTACACAT
*
212223 -GTTTACGCTCGCCAGCTTGCACAT
1 CGTTTACGCTCGCCAGCTTACACAT
* *
212247 -GTTTACGCTCGTCAGCTTATACATAT
1 CGTTTACGCTCGCCAGC-T-TACACAT
* * *
212273 GCATTTACGCTCGCCAACTTGCACA-
1 -CGTTTACGCTCGCCAGCTTACACAT
212298 CGTTT
1 CGTTT
212303 TTGCTTATCA
Statistics
Matches: 108, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
24 62 0.57
25 1 0.01
26 12 0.11
27 1 0.01
28 32 0.30
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.33
Consensus pattern (25 bp):
CGTTTACGCTCGCCAGCTTACACAT
Found at i:212283 original size:52 final size:52
Alignment explanation
Indices: 212224--212501 Score: 178
Period size: 52 Copynumber: 5.4 Consensus size: 52
212214 CTTGCACATG
212224 TTTACGCTCGCCAGCTTGCACATGTTTACGCTCGTCAGCTTATACATATGCA
1 TTTACGCTCGCCAGCTTGCACATGTTTACGCTCGTCAGCTTATACATATGCA
* * ** ** * **
212276 TTTACGCTCGCCAACTTGCACACGTTTTTGCTTATCAGCTTATACACATGTG
1 TTTACGCTCGCCAGCTTGCACATGTTTACGCTCGTCAGCTTATACATATGCA
* * * * * * * * *
212328 TTTGCGCTCTCCAGCTTATACATATGCATTTATGCTCGCCAAC-T-TGCACATG--
1 TTTACGCTCGCCAGC-T-TGCACATG--TTTACGCTCGTCAGCTTATACATATGCA
* *** ** * *
212380 TTTATGCTCATTAGCTT----AT-ACTACACTCGCCAGCTTATACATATGCA
1 TTTACGCTCGCCAGCTTGCACATGTTTACGCTCGTCAGCTTATACATATGCA
* * * *
212427 TTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTAAACATATGCG
1 TTTACGCTCGCCAGCTTGCACATGTTTACGCTCGTCAGCTTATACATATGCA
*
212479 TTTACGCTCGCTAGCTTGCACAT
1 TTTACGCTCGCCAGCTTGCACAT
212502 ATGTATTGCA
Statistics
Matches: 167, Mismatches: 46, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
43 10 0.06
44 1 0.01
45 6 0.04
46 2 0.01
47 14 0.08
50 1 0.01
51 2 0.01
52 107 0.64
53 1 0.01
54 12 0.07
55 1 0.01
56 10 0.06
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (52 bp):
TTTACGCTCGCCAGCTTGCACATGTTTACGCTCGTCAGCTTATACATATGCA
Found at i:212355 original size:80 final size:77
Alignment explanation
Indices: 212177--212504 Score: 296
Period size: 80 Copynumber: 4.3 Consensus size: 77
212167 ACACGTTTAT
* * * * * * **
212177 GCTCGCCATCTTATACTTATGCGTTTACGCTCGCCAGCTTGCACATGTTTACGCTCGCCAGC-T-
1 GCTCGCCAGCTTATACATATGCATTTACGCTCGCCAACTTGCACACGTTTATGCTCATCAGCTTA
*
212240 TGCACATGTTTAC
66 TACACATGTTT-C
* * *
212253 GCTCGTCAGCTTATACATATGCATTTACGCTCGCCAACTTGCACACGTTTTTGCTTATCAGCTTA
1 GCTCGCCAGCTTATACATATGCATTTACGCTCGCCAACTTGCACACGTTTATGCTCATCAGCTTA
212318 TACACATGTGTTTGC
66 TACACA--TGTTT-C
* * * *
212333 GCTCTCCAGCTTATACATATGCATTTATGCTCGCCAACTTGCACATGTTTATGCTCATTAGCTTA
1 GCTCGCCAGCTTATACATATGCATTTACGCTCGCCAACTTGCACACGTTTATGCTCATCAGCTTA
212398 TACTACA------
66 TAC-ACATGTTTC
* * * *
212405 -CTCGCCAGCTTATACATATGCATTTATGCTCGCCAGCTTGCACACGTTTACGCTCGTCAGCTTA
1 GCTCGCCAGCTTATACATATGCATTTACGCTCGCCAACTTGCACACGTTTATGCTCATCAGCTTA
* *
212469 AACATATGCGTTTAC
66 TACACAT--GTTT-C
* **
212484 GCTCGCTAGCTTGCACATATG
1 GCTCGCCAGCTTATACATATG
212505 TATTGCATAT
Statistics
Matches: 206, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
70 2 0.01
71 60 0.29
76 51 0.25
77 1 0.00
78 5 0.02
80 84 0.41
81 3 0.01
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.34
Consensus pattern (77 bp):
GCTCGCCAGCTTATACATATGCATTTACGCTCGCCAACTTGCACACGTTTATGCTCATCAGCTTA
TACACATGTTTC
Found at i:212501 original size:28 final size:28
Alignment explanation
Indices: 212418--212504 Score: 85
Period size: 28 Copynumber: 3.2 Consensus size: 28
212408 GCCAGCTTAT
* * *
212418 ACATATGCATTTATGCTCGCCAGCTTGC
1 ACATATGCGTTTACGCTCGCTAGCTTGC
**
212446 AC--A--CGTTTACGCTCG-TCAGCTTAA
1 ACATATGCGTTTACGCTCGCT-AGCTTGC
212470 ACATATGCGTTTACGCTCGCTAGCTTGC
1 ACATATGCGTTTACGCTCGCTAGCTTGC
212498 ACATATG
1 ACATATG
212505 TATTGCATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
24 17 0.37
26 2 0.04
28 26 0.57
29 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (28 bp):
ACATATGCGTTTACGCTCGCTAGCTTGC
Found at i:220470 original size:52 final size:52
Alignment explanation
Indices: 220391--220724 Score: 246
Period size: 52 Copynumber: 6.3 Consensus size: 52
220381 TGCATTTACT
* *
220391 CTTGCCAACTTGCACACATTTATGCTCGTCAGCTTATACTTATGCGTTTATG
1 CTTGCCAGCTTGCACACATTTATGCTCGTCAGCTTATACATATGCGTTTATG
* * * **
220443 CTTGCCAGCTTGCACACATTTACGCTCGTTAGCTTCGCCA-ACTTGCACACGTTTATG
1 CTTGCCAGCTTGCACACATTTATGCTCGTCAGCTT----ATACAT--ATGCGTTTATG
* ** ** * * * *
220500 CTCGTTAGCTTATACATATTTTATGCTCGTTAGC-T-TGCACA--CGTTTATG
1 CTTGCCAGCTTGCACACA-TTTATGCTCGTCAGCTTATACATATGCGTTTATG
* * * * * **
220549 CTTGTCAGCTTATACATATGCGTTTATGCTCGCCAGCTTATACATATGCGTTTACA
1 CTTGCCAGC-T-TGCACA--CATTTATGCTCGTCAGCTTATACATATGCGTTTATG
* * *
220605 CTCGCCAGCTTGCACACATTTATGCTCGTCAACTTATACATACGCGTTTATG
1 CTTGCCAGCTTGCACACATTTATGCTCGTCAGCTTATACATATGCGTTTATG
* * * * *
220657 CTCGCTAGTTTGCACACGTTTATGCTCATCAGCTTATACATATGCGTTTATG
1 CTTGCCAGCTTGCACACATTTATGCTCGTCAGCTTATACATATGCGTTTATG
*
220709 CTTGCCGGCTTGCACA
1 CTTGCCAGCTTGCACA
220725 TATGTATTGT
Statistics
Matches: 219, Mismatches: 47, Indels: 32
0.73 0.16 0.11
Matches are distributed among these distances:
49 15 0.07
50 1 0.00
51 5 0.02
52 133 0.61
53 2 0.01
54 8 0.04
55 5 0.02
56 14 0.06
57 22 0.10
58 14 0.06
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (52 bp):
CTTGCCAGCTTGCACACATTTATGCTCGTCAGCTTATACATATGCGTTTATG
Found at i:220503 original size:33 final size:32
Alignment explanation
Indices: 220442--220510 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
220432 ATGCGTTTAT
*
220442 GCTTGCCAGCTTGCACACATTTACGCTCGTTA
1 GCTTGCCAACTTGCACACATTTACGCTCGTTA
* *
220474 GCTTCGCCAACTTGCACACGTTTATGCTCGTTA
1 GCTT-GCCAACTTGCACACATTTACGCTCGTTA
220507 GCTT
1 GCTT
220511 ATACATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 4 0.12
33 29 0.88
ACGTcount: A:0.17, C:0.30, G:0.19, T:0.33
Consensus pattern (32 bp):
GCTTGCCAACTTGCACACATTTACGCTCGTTA
Found at i:220558 original size:24 final size:24
Alignment explanation
Indices: 220484--220559 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
220474 GCTTCGCCAA
220484 CTTGCACACGTTTATGCTCGTTAG
1 CTTGCACACGTTTATGCTCGTTAG
** **
220508 CTTATACATATTTTATGCTCGTTAG
1 CTTGCACA-CGTTTATGCTCGTTAG
* *
220533 CTTGCACACGTTTATGCTTGTCAG
1 CTTGCACACGTTTATGCTCGTTAG
220557 CTT
1 CTT
220560 ATACATATGC
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
24 21 0.51
25 20 0.49
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.42
Consensus pattern (24 bp):
CTTGCACACGTTTATGCTCGTTAG
Found at i:220585 original size:28 final size:28
Alignment explanation
Indices: 220541--220728 Score: 149
Period size: 28 Copynumber: 7.0 Consensus size: 28
220531 AGCTTGCACA
* *
220541 CGTTTATGCTTGTCAGCTTATACATATG
1 CGTTTATGCTCGCCAGCTTATACATATG
220569 CGTTTATGCTCGCCAGCTTATACATATG
1 CGTTTATGCTCGCCAGCTTATACATATG
** * *
220597 CGTTTACACTCGCCAGC-T-TGCACA--
1 CGTTTATGCTCGCCAGCTTATACATATG
* * * *
220621 CATTTATGCTCGTCAACTTATACATACG
1 CGTTTATGCTCGCCAGCTTATACATATG
* * *
220649 CGTTTATGCTCGCTAG-TT-TGCACA--
1 CGTTTATGCTCGCCAGCTTATACATATG
**
220673 CGTTTATGCTCATCAGCTTATACATATG
1 CGTTTATGCTCGCCAGCTTATACATATG
* * **
220701 CGTTTATGCTTGCCGGCTTGCACATATG
1 CGTTTATGCTCGCCAGCTTATACATATG
220729 TATTGTATAT
Statistics
Matches: 122, Mismatches: 30, Indels: 16
0.73 0.18 0.10
Matches are distributed among these distances:
24 25 0.20
25 3 0.02
26 16 0.13
27 3 0.02
28 75 0.61
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (28 bp):
CGTTTATGCTCGCCAGCTTATACATATG
Found at i:220693 original size:132 final size:131
Alignment explanation
Indices: 220399--220728 Score: 414
Period size: 132 Copynumber: 2.5 Consensus size: 131
220389 CTCTTGCCAA
* * *
220399 CTTGCACACATTTATGCTCGTCAGCTTATACTTATGCGTTTATGCTTGCCAGCTTGCACACATTT
1 CTTGCACACGTTTATGCTCGTCAGCTTATACATATGCGTTTATGCTTGCCAGCTT--ACACATAT
* * * * * *
220464 ACGCTCGTTAGCTTCGCCAACTTGCACACGTTTATGCTCGTTAGCTTATACATATTTTATGCTCG
64 GCGCTC-TTAGCCTCGCCAACTTGCACACATTTATGCTCGTCAACTTATACATAGTTTATGCTCG
*
220529 TTAG
128 CTAG
* * *
220533 CTTGCACACGTTTATGCTTGTCAGCTTATACATATGCGTTTATGCTCGCCAGCTTATACATATGC
1 CTTGCACACGTTTATGCTCGTCAGCTTATACATATGCGTTTATGCTTGCCAGCTTACACATATGC
*
220598 G-T-TTA-CACTCGCCAGCTTGCACACATTTATGCTCGTCAACTTATACATACGCGTTTATGCTC
66 GCTCTTAGC-CTCGCCAACTTGCACACATTTATGCTCGTCAACTTATACATA---GTTTATGCTC
220660 GCTAG
127 GCTAG
* * * *
220665 TTTGCACACGTTTATGCTCATCAGCTTATACATATGCGTTTATGCTTGCCGGCTTGCACATATG
1 CTTGCACACGTTTATGCTCGTCAGCTTATACATATGCGTTTATGCTTGCCAGCTTACACATATG
220729 TATTGTATAT
Statistics
Matches: 171, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
128 1 0.01
129 40 0.23
131 1 0.01
132 78 0.46
134 51 0.30
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (131 bp):
CTTGCACACGTTTATGCTCGTCAGCTTATACATATGCGTTTATGCTTGCCAGCTTACACATATGC
GCTCTTAGCCTCGCCAACTTGCACACATTTATGCTCGTCAACTTATACATAGTTTATGCTCGCTA
G
Found at i:225632 original size:126 final size:126
Alignment explanation
Indices: 225407--225660 Score: 499
Period size: 126 Copynumber: 2.0 Consensus size: 126
225397 ACTTATTTAC
225407 ACTTGTTTTATTTGAAAATGAGTTGAATCAATCCGATATAATGAAATCGAGAAAGATGGATGATA
1 ACTTGTTTTATTTGAAAATGAGTTGAATCAATCCGATATAATGAAATCGAGAAAGATGGATGATA
*
225472 TGATGAAATTTTCAATTTGGAAATAAGAAAAATCCAGCAAATTTTTCAAAAGAAATAATAT
66 TGATGAAATTTTCAATTTGGAAATAAGAAAAATCCAGCAAAGTTTTCAAAAGAAATAATAT
225533 ACTTGTTTTATTTGAAAATGAGTTGAATCAATCCGATATAATGAAATCGAGAAAGATGGATGATA
1 ACTTGTTTTATTTGAAAATGAGTTGAATCAATCCGATATAATGAAATCGAGAAAGATGGATGATA
225598 TGATGAAATTTTCAATTTGGAAATAAGAAAAATCCAGCAAAGTTTTCAAAAGAAATAATAT
66 TGATGAAATTTTCAATTTGGAAATAAGAAAAATCCAGCAAAGTTTTCAAAAGAAATAATAT
225659 AC
1 AC
225661 GTAAATGTGA
Statistics
Matches: 127, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 127 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.31
Consensus pattern (126 bp):
ACTTGTTTTATTTGAAAATGAGTTGAATCAATCCGATATAATGAAATCGAGAAAGATGGATGATA
TGATGAAATTTTCAATTTGGAAATAAGAAAAATCCAGCAAAGTTTTCAAAAGAAATAATAT
Found at i:227066 original size:49 final size:49
Alignment explanation
Indices: 226994--227093 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
226984 GGCAATATAT
226994 ATATATATATATATTAAGTTGGTCGATGAGAATTTCATCTTTGTCATCC
1 ATATATATATATATTAAGTTGGTCGATGAGAATTTCATCTTTGTCATCC
227043 ATATATATATATATTAAGTTGGTCGATGAGAATTTCATCTTTGTCATCC
1 ATATATATATATATTAAGTTGGTCGATGAGAATTTCATCTTTGTCATCC
227092 AT
1 AT
227094 TCTCTCTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (49 bp):
ATATATATATATATTAAGTTGGTCGATGAGAATTTCATCTTTGTCATCC
Found at i:228423 original size:21 final size:21
Alignment explanation
Indices: 228385--228424 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
228375 ACATATAGCA
*
228385 TTTAAATATCAATTTAATTTC
1 TTTAAATATCAATATAATTTC
228406 TTTAAAT-TCAAATATAATT
1 TTTAAATATC-AATATAATT
228425 CGAAATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTAAATATCAATATAATTTC
Found at i:229289 original size:42 final size:37
Alignment explanation
Indices: 229249--229324 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
229239 TATATTCCTA
*
229249 TAGACAATCAACTTAACTCATATAAGTGACTTACCATTCC
1 TAGACAATCAA---AACACATATAAGTGACTTACCATTCC
*
229289 TAGGCAATCAAAACACATATAAGTGACTTACCATTC
1 TAGACAATCAAAACACATATAAGTGACTTACCATTC
229325 AAATCCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
37 24 0.71
40 10 0.29
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (37 bp):
TAGACAATCAAAACACATATAAGTGACTTACCATTCC
Found at i:234046 original size:30 final size:30
Alignment explanation
Indices: 233985--234052 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
233975 CACTTTGTGT
** * *
233985 GTGTTCACAACATGAGTGTTCGTAGCTCCA
1 GTGTTCACAACATGAGTGTTCACAACACCA
* *
234015 GTGTTCGCAACATTAGTGTTCACAACACCA
1 GTGTTCACAACATGAGTGTTCACAACACCA
*
234045 GTGCTCAC
1 GTGTTCAC
234053 TTCTTCCAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (30 bp):
GTGTTCACAACATGAGTGTTCACAACACCA
Found at i:240597 original size:15 final size:15
Alignment explanation
Indices: 240571--240620 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
240561 ATAGCTCCAA
*
240571 TGCTCGCAACATGAG
1 TGCTCACAACATGAG
*
240586 TGTTCACAACATGAG
1 TGCTCACAACATGAG
240601 TGCTCACAACACT-AG
1 TGCTCACAACA-TGAG
240616 TGCTC
1 TGCTC
240621 GCTTCTTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
15 30 0.97
16 1 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (15 bp):
TGCTCACAACATGAG
Found at i:242869 original size:27 final size:27
Alignment explanation
Indices: 242839--242901 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
242829 GGGAATGTGT
*
242839 AAAAAAACATAAATAT-AAAT-AGACATA
1 AAAAAAA-ATAAAGATGAAATAAGA-ATA
242866 AAAAAAAATAAAGATGAAATAAGAATA
1 AAAAAAAATAAAGATGAAATAAGAATA
*
242893 AATAAAAAT
1 AAAAAAAAT
242902 TATACATGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 7 0.22
27 22 0.69
28 3 0.09
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.17
Consensus pattern (27 bp):
AAAAAAAATAAAGATGAAATAAGAATA
Found at i:243464 original size:22 final size:22
Alignment explanation
Indices: 243422--243464 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
243412 ACGGTGGTCA
243422 AAAATTTTTTTTTTTGCAAAATT
1 AAAATTTTTTTTTTT-CAAAATT
243445 AAAATTTTCTTTTTTT-AAAA
1 AAAATTTT-TTTTTTTCAAAA
243465 CAAAATAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (22 bp):
AAAATTTTTTTTTTTCAAAATT
Found at i:243736 original size:21 final size:21
Alignment explanation
Indices: 243712--243760 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
243702 TTAAATTGAC
243712 TAAAAAATAAA-TTTTTATTTT
1 TAAAAAATAAACTTTTT-TTTT
**
243733 TAAAATCTAAACTTTTTTTTT
1 TAAAAAATAAACTTTTTTTTT
243754 TAAAAAA
1 TAAAAAA
243761 AAAAAAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAAAAATAAACTTTTTTTTT
Found at i:243754 original size:22 final size:21
Alignment explanation
Indices: 243719--243759 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
243709 GACTAAAAAA
*
243719 TAAATTTTTATTTTTAAAATC
1 TAAATTTTTATTTTAAAAATC
*
243740 TAAACTTTTTTTTTTAAAAA
1 TAAA-TTTTTATTTTAAAAA
243760 AAAAAAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (21 bp):
TAAATTTTTATTTTAAAAATC
Found at i:243885 original size:152 final size:157
Alignment explanation
Indices: 243614--244046 Score: 481
Period size: 156 Copynumber: 2.8 Consensus size: 157
243604 TTTTTTTTTT
* * *
243614 AAAATCAGTACTTTTCTTAAAAATAAAATATTTTATTTTAAAATAGTTAAAAATATCAAATTTTG
1 AAAATCACTACTTTTCTTAAAAATAAAATATTTTATTTCAAAATAGTTAAAAAAAT-AAATTTTG
*
243679 TCTAAAAATTTAAACCTTTTCCTTTAAATTGACTAAAAAATAAATTTTTATTTTT-AAAATCTAA
65 TCTAAAAATTTAAACATTTTCCTTTAAATTGACTAAAAAATAAATTTTTATTTTTAAAAATCTAA
*
243743 ACTT-TTTTTTTTAAAAAAAAAAAAACA
130 AATTATTTTTTTTAAAAAAAAAAAAACA
* *
243770 AAAATCACTACTTTTCTTAAAAATCAAATCTTTTATTTCAAAATAGTTAAAAAAAT-AATTTT-T
1 AAAATCACTACTTTTCTTAAAAATAAAATATTTTATTTCAAAATAGTTAAAAAAATAAATTTTGT
* ** *
243833 TTTTAAATTTAAA-ATTTTCCTTTAAATTGACTAAAAAATAGATTTTTATTTTTAAAAATCTAAA
66 CTAAAAATTTAAACATTTTCCTTTAAATTGACTAAAAAATAAATTTTTATTTTTAAAAATCTAAA
243897 ATTATTTTTTTT----------AAA-A
131 ATTATTTTTTTTAAAAAAAAAAAAACA
* * *
243913 AAAATCACTATTTTTCTTAAAAATTAAAAT-TTTTATTTCGAAATAGTTAAAAGAAAATCCAATT
1 AAAATCACTACTTTTCTTAAAAA-TAAAATATTTTATTTCAAAATAGTT-AAA-AAAAT-AAATT
* * ** * *
243977 TTGTTTAAAAATTTAAAC-TTTTTCTTTCAAAACGACTAAAAAAT-ATTTTATATATTTTTTAAA
62 TTGTCTAAAAATTTAAACATTTTCCTTT-AAATTGACTAAAAAATAAATTT-T-TATTTTTAAAA
244040 ATCTAAA
124 ATCTAAA
244047 CTTTCTCTTT
Statistics
Matches: 243, Mismatches: 22, Indels: 30
0.82 0.07 0.10
Matches are distributed among these distances:
143 40 0.16
144 11 0.05
145 5 0.02
147 6 0.02
148 23 0.09
149 15 0.06
150 17 0.07
152 38 0.16
153 23 0.09
154 14 0.06
156 51 0.21
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.43
Consensus pattern (157 bp):
AAAATCACTACTTTTCTTAAAAATAAAATATTTTATTTCAAAATAGTTAAAAAAATAAATTTTGT
CTAAAAATTTAAACATTTTCCTTTAAATTGACTAAAAAATAAATTTTTATTTTTAAAAATCTAAA
ATTATTTTTTTTAAAAAAAAAAAAACA
Found at i:243951 original size:23 final size:21
Alignment explanation
Indices: 243874--243946 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
243864 TAAAAAATAG
243874 ATTTTTATTTTTAAAAATCTAAA
1 ATTTTT-TTTTTAAAAAT-TAAA
243897 ATTATTTTTTTTAAAAA--AAA
1 ATT-TTTTTTTTAAAAATTAAA
* *
243917 TCACTATTTTTCTTAAAAATTAAA
1 --A-TTTTTTTTTTAAAAATTAAA
243941 ATTTTT
1 ATTTTT
243947 ATTTCGAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
20 3 0.07
21 4 0.10
22 14 0.34
23 14 0.34
24 6 0.15
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTTTTTTTTTAAAAATTAAA
Found at i:244968 original size:42 final size:42
Alignment explanation
Indices: 244935--245317 Score: 507
Period size: 42 Copynumber: 9.1 Consensus size: 42
244925 CTTTAAAGGG
* **
244935 AATGAAAAGTAAATGGACCTCTACAGTTGGGCCTCTAAATGC
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
* * * *
244977 ATTGATAAGTAAATGGACCTCCACACATGGGCCTCTAAATAC
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
* * *
245019 AATGGAAAGTAAATGGACCTCCACACTTGGGCCTCAAAATGC
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
* * *
245061 AATGAAAAGTAAATGGACCTCCACACCTGAGCCTCTAACTGT
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
* * * *
245103 GATGAAAAGTAAATGAACCTCCACACCTAGGCCTCTAAATGT
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
* * * * *
245145 GATGAAAAGTAAATAGACCTCCATAGCTGGGCCTTTAAATGC
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
* *
245187 AATG-AAAGTAAATTGACCTCCACACCTAGGCCTCTAAATGC
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
* * *
245228 GATGAAAAGTAAATGGACCTCCACACTTGGGCTTCTAAATGC
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
*
245270 AATGAAAAGTAAATGGACCTCCACACCTTGGCCTCTAAATGC
1 AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
245312 AATGAA
1 AATGAA
245318 TGCTTTCCTT
Statistics
Matches: 295, Mismatches: 45, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
41 35 0.12
42 260 0.88
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (42 bp):
AATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGC
Found at i:245745 original size:21 final size:21
Alignment explanation
Indices: 245721--245767 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
245711 TCTCTCTCTA
245721 TTTTTTCT-TCTTCTTTGTTG-
1 TTTTTTCTCTCTTCTTTG-TGC
*
245741 TTTTTTCTCTCTTTTTTGTGC
1 TTTTTTCTCTCTTCTTTGTGC
245762 TTTTTT
1 TTTTTT
245768 TATTCAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.77
Consensus pattern (21 bp):
TTTTTTCTCTCTTCTTTGTGC
Found at i:245765 original size:20 final size:20
Alignment explanation
Indices: 245722--245766 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
245712 CTCTCTCTAT
*
245722 TTTTTCTTCTTCTTTGTTGT
1 TTTTTCTTCTTCTTTGTTGC
*
245742 TTTTTCTCTCTTTTTTG-TGC
1 TTTTTCT-TCTTCTTTGTTGC
245762 TTTTT
1 TTTTT
245767 TTATTCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.76
Consensus pattern (20 bp):
TTTTTCTTCTTCTTTGTTGC
Found at i:251172 original size:17 final size:17
Alignment explanation
Indices: 251118--251172 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
251108 GACAAATGGA
* *
251118 AATGCAATGACAATGCG
1 AATGCAATAACAATGAG
* * *
251135 AATGCAGTAACAATTAA
1 AATGCAATAACAATGAG
*
251152 AATGCAATAAAAATGAG
1 AATGCAATAACAATGAG
251169 AATG
1 AATG
251173 TGATAACGAT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (17 bp):
AATGCAATAACAATGAG
Found at i:252354 original size:18 final size:18
Alignment explanation
Indices: 252327--252374 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
252317 AATACATCAG
* *
252327 GTTGCCTTGACATAGCTA
1 GTTGCGTTGACATAGATA
* *
252345 GTTGTGTTGACATTGATA
1 GTTGCGTTGACATAGATA
252363 GTTGCGTTGACA
1 GTTGCGTTGACA
252375 ATTTTGTCGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.27, T:0.38
Consensus pattern (18 bp):
GTTGCGTTGACATAGATA
Found at i:254148 original size:24 final size:23
Alignment explanation
Indices: 254121--254168 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
254111 TCCTGGTCAT
*
254121 AAAACATAAAA-AAAGTAGTCAAC
1 AAAAAATAAAACAAAGTAGT-AAC
*
254144 AAAAAATAAAACAAATTAGTAAC
1 AAAAAATAAAACAAAGTAGTAAC
254167 AA
1 AA
254169 GTAAAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.69, C:0.10, G:0.06, T:0.15
Consensus pattern (23 bp):
AAAAAATAAAACAAAGTAGTAAC
Found at i:263996 original size:17 final size:16
Alignment explanation
Indices: 263961--264002 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
263951 AGAATATAAA
263961 AAGAAA-AAATAAAAG
1 AAGAAATAAATAAAAG
*
263976 AAGAAATAAAGTAAAAT
1 AAGAAATAAA-TAAAAG
263993 AAGAAATAAA
1 AAGAAATAAA
264003 CATAAATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 6 0.25
16 3 0.12
17 15 0.62
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (16 bp):
AAGAAATAAATAAAAG
Found at i:272443 original size:17 final size:16
Alignment explanation
Indices: 272391--272462 Score: 65
Period size: 17 Copynumber: 4.3 Consensus size: 16
272381 ATTAGAATGG
* *
272391 AAATGCAACTACAATGT
1 AAATGCAACGACAAT-A
*
272408 AAATG-AACTAACAAGTA
1 AAATGCAAC-GACAA-TA
272425 AAATGCAACGACAACTA
1 AAATGCAACGACAA-TA
*
272442 AAATGCAATGACAATA
1 AAATGCAACGACAATA
272458 AAATG
1 AAATG
272463 AGATGCATGC
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
16 10 0.21
17 33 0.70
18 4 0.09
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.18
Consensus pattern (16 bp):
AAATGCAACGACAATA
Found at i:272446 original size:34 final size:33
Alignment explanation
Indices: 272391--272462 Score: 76
Period size: 34 Copynumber: 2.2 Consensus size: 33
272381 ATTAGAATGG
* *
272391 AAATGCAACTACAATGTAAATG-AACTAACAAGTA
1 AAATGCAACGACAATGAAAATGCAA-TAACAA-TA
*
272425 AAATGCAACGACAACT-AAAATGCAATGACAATA
1 AAATGCAACGACAA-TGAAAATGCAATAACAATA
272458 AAATG
1 AAATG
272463 AGATGCATGC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
33 7 0.21
34 23 0.70
35 3 0.09
ACGTcount: A:0.54, C:0.15, G:0.12, T:0.18
Consensus pattern (33 bp):
AAATGCAACGACAATGAAAATGCAATAACAATA
Found at i:279329 original size:15 final size:15
Alignment explanation
Indices: 279284--279338 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
279274 ACAACATATA
279284 TTTCTTTTTTCTTCT
1 TTTCTTTTTTCTTCT
279299 TTTCTGTTTTCCTCTTC-
1 TTTCT-TTTT--TCTTCT
279316 TTTCTTTCTTTCTT-T
1 TTTCTTT-TTTCTTCT
279331 TTT-TTTTT
1 TTTCTTTTT
279339 ATAAATGACT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 2 0.06
14 3 0.09
15 12 0.34
16 6 0.17
17 7 0.20
18 5 0.14
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTCTTTTTTCTTCT
Found at i:290341 original size:21 final size:21
Alignment explanation
Indices: 290329--290373 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
290319 CATCGCATGC
290329 TGTTGTGGCGGCATTCGAGCT
1 TGTTGTGGCGGCATTCGAGCT
**
290350 TGTTGTGGCTTCATTCGAGCT
1 TGTTGTGGCGGCATTCGAGCT
290371 TGT
1 TGT
290374 GGTTGCATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.18, G:0.33, T:0.40
Consensus pattern (21 bp):
TGTTGTGGCGGCATTCGAGCT
Found at i:293658 original size:16 final size:16
Alignment explanation
Indices: 293637--293676 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
293627 TTCTTGCAAC
293637 TTTTCAACCTCTAAGT
1 TTTTCAACCTCTAAGT
*
293653 TTTTCATCCTCTAAGT
1 TTTTCAACCTCTAAGT
*
293669 TCTTCAAC
1 TTTTCAAC
293677 AAAGTATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.28, G:0.05, T:0.45
Consensus pattern (16 bp):
TTTTCAACCTCTAAGT
Found at i:297428 original size:18 final size:18
Alignment explanation
Indices: 297389--297436 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
297379 CGTCTTCTAA
297389 TTTTTAATTTA--TTAAC
1 TTTTTAATTTATTTTAAC
* *
297405 TCTTTAATTTATTTTAAT
1 TTTTTAATTTATTTTAAC
*
297423 TTTTTAATATATTT
1 TTTTTAATTTATTT
297437 ACTAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 10 0.38
18 16 0.62
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTAATTTATTTTAAC
Found at i:298378 original size:30 final size:27
Alignment explanation
Indices: 298311--298385 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 27
298301 ACAGCAAGCT
* *
298311 GAAGAAGAAGAAAAAGA-CCT--TGAA
1 GAAGAAGAAGAAGAAGATCCTAAGGAA
*
298335 GAAGAAGAAGAAGAGGATCCTAAGGAA
1 GAAGAAGAAGAAGAAGATCCTAAGGAA
298362 GAAGAAGATATTGAAGAAGATCCT
1 GAAGAAGA-A--GAAGAAGATCCT
298386 GTGGAGATTG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
24 15 0.37
25 3 0.07
27 11 0.27
28 1 0.02
30 11 0.27
ACGTcount: A:0.52, C:0.08, G:0.28, T:0.12
Consensus pattern (27 bp):
GAAGAAGAAGAAGAAGATCCTAAGGAA
Found at i:305643 original size:19 final size:20
Alignment explanation
Indices: 305619--305657 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
305609 CGAAGGATAG
*
305619 AAAAAG-GAAGCACAAGGAC
1 AAAAAGAGAAACACAAGGAC
305638 AAAAAGAAGAAACACAAGGA
1 AAAAAG-AGAAACACAAGGA
305658 GGAAGGAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.64, C:0.13, G:0.23, T:0.00
Consensus pattern (20 bp):
AAAAAGAGAAACACAAGGAC
Found at i:306775 original size:77 final size:77
Alignment explanation
Indices: 306682--306834 Score: 297
Period size: 77 Copynumber: 2.0 Consensus size: 77
306672 TTGGGGGTGT
306682 GATAGCATTAGTAATGACACCTATTTTCTCCCTAAATTTGTGTATTATTTGTCTCTTTTGTACCA
1 GATAGCATTAGTAATGACACCTATTTTCTCCCTAAATTTGTGTATTATTTGTCTCTTTTGTACCA
306747 TATTTAGCATGA
66 TATTTAGCATGA
*
306759 GATAGCATTAGTAATGACACCTATTTTCTCCCTGAATTTGTGTATTATTTGTCTCTTTTGTACCA
1 GATAGCATTAGTAATGACACCTATTTTCTCCCTAAATTTGTGTATTATTTGTCTCTTTTGTACCA
306824 TATTTAGCATG
66 TATTTAGCATG
306835 CATGTTAGGC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 75 1.00
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (77 bp):
GATAGCATTAGTAATGACACCTATTTTCTCCCTAAATTTGTGTATTATTTGTCTCTTTTGTACCA
TATTTAGCATGA
Found at i:322988 original size:29 final size:29
Alignment explanation
Indices: 322955--323032 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
322945 ATGGTAAAAG
* ***
322955 TTTAGCTCGAATGAGTAACTTGATGTAAT
1 TTTAGCTCGAATGAGCAACCCAATGTAAT
*
322984 TTTAGCTCAAACT-AGCAACCCAATGTAAT
1 TTTAGCTCGAA-TGAGCAACCCAATGTAAT
* *
323013 TTTAGCTCGGATGAACAACC
1 TTTAGCTCGAATGAGCAACC
323033 TGGTGTGGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
28 1 0.03
29 37 0.95
30 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (29 bp):
TTTAGCTCGAATGAGCAACCCAATGTAAT
Found at i:327847 original size:17 final size:16
Alignment explanation
Indices: 327816--327849 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
327806 TTTAAAACCC
*
327816 TAAATTCTAACCATTA
1 TAAATTCTAAACATTA
327832 TAAATATCTAAACATTA
1 TAAAT-TCTAAACATTA
327849 T
1 T
327850 TTTAACTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAATTCTAAACATTA
Found at i:334508 original size:19 final size:18
Alignment explanation
Indices: 334479--334522 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
334469 TTAACTCATA
334479 ATTTTTACTAATCTGTTATC
1 ATTTTT-CTAAT-TGTTATC
*
334499 ATTTTTCTAATTGTTTTC
1 ATTTTTCTAATTGTTATC
334517 -TTTTTC
1 ATTTTTC
334523 AGATCCTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 5 0.22
20 6 0.26
ACGTcount: A:0.18, C:0.14, G:0.05, T:0.64
Consensus pattern (18 bp):
ATTTTTCTAATTGTTATC
Found at i:334521 original size:18 final size:19
Alignment explanation
Indices: 334480--334521 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
334470 TAACTCATAA
334480 TTTTTACTAATCTGTTATC
1 TTTTTACTAATCTGTTATC
*
334499 ATTTTT-CTAAT-TGTTTTC
1 -TTTTTACTAATCTGTTATC
334517 TTTTT
1 TTTTT
334522 CAGATCCTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 6 0.29
19 5 0.24
20 5 0.24
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.67
Consensus pattern (19 bp):
TTTTTACTAATCTGTTATC
Found at i:342016 original size:12 final size:12
Alignment explanation
Indices: 342001--342053 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
341991 AGAGGTGATC
*
342001 AAGAGAAGGATG
1 AAGAGAAGGAAG
* *
342013 AAGAAAAAGAAG
1 AAGAGAAGGAAG
342025 AAGAAGGAAAGGAAG
1 AAG-A-G-AAGGAAG
342040 AAGAGAAGGAAG
1 AAGAGAAGGAAG
342052 AA
1 AA
342054 ACTGAACCTT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
12 21 0.64
13 2 0.06
14 1 0.03
15 9 0.27
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (12 bp):
AAGAGAAGGAAG
Found at i:345562 original size:15 final size:15
Alignment explanation
Indices: 345542--345598 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
345532 TCGTTTGTGT
345542 GTGTTCGCAACATGA
1 GTGTTCGCAACATGA
* * *
345557 GTGTTCGCAGCTTCA
1 GTGTTCGCAACATGA
* *
345572 GTGTTTGCAATATGA
1 GTGTTCGCAACATGA
*
345587 GTGCTCGCAACA
1 GTGTTCGCAACA
345599 CCAGTGCTCG
Statistics
Matches: 31, Mismatches: 11, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (15 bp):
GTGTTCGCAACATGA
Found at i:345604 original size:30 final size:30
Alignment explanation
Indices: 345542--345609 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
345532 TCGTTTGTGT
* * **
345542 GTGTTCGCAACATGAGTGTTCGCAGCTTCA
1 GTGTTCGCAACATGAGTGCTCGCAACACCA
* *
345572 GTGTTTGCAATATGAGTGCTCGCAACACCA
1 GTGTTCGCAACATGAGTGCTCGCAACACCA
*
345602 GTGCTCGC
1 GTGTTCGC
345610 TTCTTTCAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (30 bp):
GTGTTCGCAACATGAGTGCTCGCAACACCA
Found at i:353670 original size:23 final size:23
Alignment explanation
Indices: 353632--353688 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
353622 TATTAAAGCT
* *
353632 AACAAATATGAAAGAAACAACTAAC
1 AACAAAGAT-AAAGAAACAA-GAAC
353657 -ACAAAGATAAAGAAACAAGAAC
1 AACAAAGATAAAGAAACAAGAAC
353679 AACAAAGATA
1 AACAAAGATA
353689 GGATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 3 0.10
23 19 0.66
24 7 0.24
ACGTcount: A:0.67, C:0.14, G:0.11, T:0.09
Consensus pattern (23 bp):
AACAAAGATAAAGAAACAAGAAC
Found at i:355626 original size:94 final size:94
Alignment explanation
Indices: 355460--355680 Score: 361
Period size: 94 Copynumber: 2.4 Consensus size: 94
355450 CAAATATTTT
* * * * *
355460 ATACCATACAATTAACCCTTCTTTAATTCATTTATTCTTGTTCAATTTGACAAATATTTTTGTTC
1 ATACCATACAATCAATCATTCTTAAATTCATTTATTCTTGTTCAATTTGACAAATATTTCTGTTC
*
355525 TTTTCAAAATGTTCTCTTCATTCATAATC
66 TTGTCAAAATGTTCTCTTCATTCATAATC
* *
355554 ATACCATATAATCAATCATTCTTCAATTCATTTATTCTTGTTCAATTTGACAAATATTTCTGTTC
1 ATACCATACAATCAATCATTCTTAAATTCATTTATTCTTGTTCAATTTGACAAATATTTCTGTTC
355619 TTGTCAAAATGTTCTCTTCATTCATAATC
66 TTGTCAAAATGTTCTCTTCATTCATAATC
*
355648 ATACCATACAATCAATCATTCTTAAAATCATTT
1 ATACCATACAATCAATCATTCTTAAATTCATTT
355681 GTTTCTGTGA
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
94 117 1.00
ACGTcount: A:0.31, C:0.19, G:0.04, T:0.45
Consensus pattern (94 bp):
ATACCATACAATCAATCATTCTTAAATTCATTTATTCTTGTTCAATTTGACAAATATTTCTGTTC
TTGTCAAAATGTTCTCTTCATTCATAATC
Found at i:360164 original size:51 final size:51
Alignment explanation
Indices: 360088--360193 Score: 194
Period size: 51 Copynumber: 2.1 Consensus size: 51
360078 GCTACACACC
*
360088 AATCTCTTACCACCGATCATGGGCAGAATGAAGCATTCAATCTTTCACCCT
1 AATCTCTTACCACCGATCATGGGCAGAATGAAGCATCCAATCTTTCACCCT
*
360139 AATCTCTTACCCCCGATCATGGGCAGAATGAAGCATCCAATCTTTCACCCT
1 AATCTCTTACCACCGATCATGGGCAGAATGAAGCATCCAATCTTTCACCCT
360190 AATC
1 AATC
360194 AGAGGGCAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.26
Consensus pattern (51 bp):
AATCTCTTACCACCGATCATGGGCAGAATGAAGCATCCAATCTTTCACCCT
Found at i:360268 original size:78 final size:77
Alignment explanation
Indices: 360139--360598 Score: 632
Period size: 78 Copynumber: 5.9 Consensus size: 77
360129 CTTTCACCCT
* *
360139 AATCTCTTACCCCCGATCATGGGCAGAATGAAGCATCCAATCTTTCACCCTAATCAGAGGGCAAA
1 AATCTCTTA-CCCCGATCATGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAAA
* *
360204 TTAAAGACACGCC
65 TTGAAGACACACC
* * * * *
360217 AATCTCTTACCCTGACCATGGGACAGATTGAAGCATCCAATCTTTTACCCTAATCAAAGGGTAGA
1 AATCTCTTACCCCGATCATGGG-CAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAAA
360282 TTGAAGACACACC
65 TTGAAGACACACC
* * *
360295 AATCTCTTACCCTGATCATGGGGCAGATTGAAGCATCTAATCTTTTACCCTAATTAGAGGGCAAA
1 AATCTCTTACCCCGATCAT-GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAAA
*
360360 TTGAAAACACACC
65 TTGAAGACACACC
* ** *
360373 AATCTCTTACCCCGATCATGGGACAGATTGAAGTATCCAATCTTTTATTCTAATCAGAGGGCAGA
1 AATCTCTTACCCCGATCATGGG-CAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAAA
*
360438 TTGAAGATACACC
65 TTGAAGACACACC
* * *
360451 AATCTCTTACCCCGATCATGGGGCAAATTGAAGCATCCAATCTTTTATCCTAATCAGAGGGAAAA
1 AATCTCTTACCCCGATCAT-GGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAAA
360516 TTGAAGACACACC
65 TTGAAGACACACC
* * * * *
360529 AATCTCTTACCTCGATTATGAGGCAGATTGAAGTAACCAATCTTTTACCCTAATCAGAGGGCAGA
1 AATCTCTTACCCCGATCATG-GGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAAA
360594 TTGAA
65 TTGAA
360599 AACGCTATTC
Statistics
Matches: 338, Mismatches: 39, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
77 15 0.04
78 317 0.94
79 6 0.02
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (77 bp):
AATCTCTTACCCCGATCATGGGCAGATTGAAGCATCCAATCTTTTACCCTAATCAGAGGGCAAAT
TGAAGACACACC
Found at i:381914 original size:19 final size:20
Alignment explanation
Indices: 381890--381931 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
381880 AGATTTTGGA
* *
381890 TAAAAAA-TAATATATCGGT
1 TAAAAAATTAATAAATCGAT
381909 TAAAAAATTAATAAATCGAT
1 TAAAAAATTAATAAATCGAT
381929 TAA
1 TAA
381932 TGAAGTGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (20 bp):
TAAAAAATTAATAAATCGAT
Found at i:382991 original size:3 final size:3
Alignment explanation
Indices: 382983--383015 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
382973 TTTGATCTTC
382983 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
383016 TTTTTAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:383786 original size:16 final size:16
Alignment explanation
Indices: 383747--383788 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
383737 GTGTAAAAAA
383747 AAACAT-AAATATAAAT
1 AAACATGAAA-ATAAAT
*
383763 AGACATGAAAATAAAT
1 AAACATGAAAATAAAT
*
383779 AAAGATGAAA
1 AAACATGAAA
383789 TAAGAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (16 bp):
AAACATGAAAATAAAT
Found at i:384364 original size:17 final size:18
Alignment explanation
Indices: 384342--384378 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
384332 TTTGAAATGA
384342 TTAAAAAA-TAAACTTTT
1 TTAAAAAATTAAACTTTT
384359 TTAAAAAATTTAAACTTTT
1 TTAAAAAA-TTAAACTTTT
384378 T
1 T
384379 CCTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.44
19 10 0.56
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (18 bp):
TTAAAAAATTAAACTTTT
Found at i:384417 original size:20 final size:20
Alignment explanation
Indices: 384392--384440 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
384382 TTAAAATCAC
*
384392 TAAAAAAAT-ATTTTTATTTT
1 TAAAAAAATAATTTTT-TTTA
**
384412 TAAAAATTTAATTTTTTTTA
1 TAAAAAAATAATTTTTTTTA
384432 TAAAAAAAT
1 TAAAAAAAT
384441 CACTACTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAAAAATAATTTTTTTTA
Found at i:384544 original size:147 final size:137
Alignment explanation
Indices: 384285--384562 Score: 371
Period size: 140 Copynumber: 2.0 Consensus size: 137
384275 TTCTTTTTTC
* * * * *
384285 TTTTTTAAAACAAAATCGCTATTTTTCTTAAAAATTAAAGCTTTTATTTTGAAATGATTAAAAAA
1 TTTTTTAAAACAAAATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAAATGATTAAAAAA
384350 TAAACTTTTTTAAAAAATTTAAACTTTTTCCTTTAAAATCACTAAAAAAATATTTTTATTTTTAA
66 TAAACTTTTTTAAAAAATTTAAACTTTTTCCTTTAAAATCACT-AAAAAA-A-TTTTATTTTTAA
384415 AAATTTAATT
128 AAATTTAATT
*
384425 TTTTTTATAAA-AAAATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAGAT-AGTTAAAA
1 TTTTTTA-AAACAAAATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAAATGA-TT----
*
384488 AAAAAATCAAAACTTTGTTTAAAAAATTTAAACTTTTTCCTTTAAAATGACTAAAAAAATTTTAT
60 AAAAAAT--AAACTTT-TTTAAAAAATTTAAACTTTTTCCTTTAAAATCACTAAAAAAATTTTAT
384553 TTTTAAAAAT
122 TTTTAAAAAT
384563 CTAAACTTTA
Statistics
Matches: 122, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
139 1 0.01
140 47 0.39
141 3 0.02
144 23 0.19
145 1 0.01
146 13 0.11
147 34 0.28
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (137 bp):
TTTTTTAAAACAAAATCACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAAATGATTAAAAAA
TAAACTTTTTTAAAAAATTTAAACTTTTTCCTTTAAAATCACTAAAAAAATTTTATTTTTAAAAA
TTTAATT
Found at i:386677 original size:12 final size:12
Alignment explanation
Indices: 386654--386686 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
386644 TACCAAGATG
386654 TTGTTG-TTGTT
1 TTGTTGATTGTT
386665 TTGTTGATTGTT
1 TTGTTGATTGTT
*
386677 TTGCTGATTG
1 TTGTTGATTG
386687 AAGATCGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.06, C:0.03, G:0.27, T:0.64
Consensus pattern (12 bp):
TTGTTGATTGTT
Done.