Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008372.1 Hibiscus syriacus cultivar Beakdansim tig00111128_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1214897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:214399 original size:6 final size:6
Alignment explanation
Indices: 214361--214423 Score: 63
Period size: 6 Copynumber: 9.5 Consensus size: 6
214351 ATTATTTTTT
*
214361 TAATAA TATATATA TATATATA TATATATA TAATAA TAATTA TAATAA
1 TAATAA TA-ATA-A TA-ATA-A TA-ATA-A TAATAA TAATAA TAATAA
214409 TAATAA TAATAA TAA
1 TAATAA TAATAA TAA
214424 ATAAATAAGT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
6 28 0.53
7 6 0.11
8 19 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
TAATAA
Found at i:214404 original size:12 final size:13
Alignment explanation
Indices: 214361--214431 Score: 78
Period size: 12 Copynumber: 5.5 Consensus size: 13
214351 ATTATTTTTT
214361 TAATAATATATATA
1 TAATAATA-ATATA
214375 TATATATATATATATA
1 TA-ATA-ATA-ATATA
214391 TAATAATAAT-TA
1 TAATAATAATATA
214403 TAATAATAATA-A
1 TAATAATAATATA
214415 TAATAATAA-ATA
1 TAATAATAATATA
214427 -AATAA
1 TAATAA
214432 GTAAAATGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.11
12 23 0.43
13 2 0.04
14 5 0.09
15 6 0.11
16 11 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAATAATATA
Found at i:214404 original size:18 final size:18
Alignment explanation
Indices: 214361--214431 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 18
214351 ATTATTTTTT
214361 TAATAA-TATATATAT-A
1 TAATAATTATATATATAA
214377 T-AT-ATATATATATATAA
1 TAATAAT-TATATATATAA
214394 TAATAATTATA-ATAATAA
1 TAATAATTATATAT-ATAA
* *
214412 TAATAATAATAAATA-AA
1 TAATAATTATATATATAA
214429 TAA
1 TAA
214432 GTAAAATGAG
Statistics
Matches: 47, Mismatches: 1, Indels: 13
0.77 0.02 0.21
Matches are distributed among these distances:
14 1 0.02
15 2 0.04
16 10 0.21
17 9 0.19
18 21 0.45
19 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATAATTATATATATAA
Found at i:214590 original size:76 final size:76
Alignment explanation
Indices: 214461--214604 Score: 216
Period size: 76 Copynumber: 1.9 Consensus size: 76
214451 AGTATCTTCA
* * * * *
214461 AACTTAACACGTAATTCCATTAGTTAAACTTAACATAGACTTACACCGGTGAAACTAACACTTAA
1 AACTTAACACATAATTCCATCAGTGAAACTTAACATAGACTTACACCAGTGAAACTAACACTGAA
214526 TTCTAGAACTG
66 TTCTAGAACTG
* * *
214537 AACTTAACACATAATTTCATCAGTGAAACTTAACATAGACTTACACTATTGAAACTAACACTGAA
1 AACTTAACACATAATTCCATCAGTGAAACTTAACATAGACTTACACCAGTGAAACTAACACTGAA
214602 TTC
66 TTC
214605 CAACATTGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
76 60 1.00
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (76 bp):
AACTTAACACATAATTCCATCAGTGAAACTTAACATAGACTTACACCAGTGAAACTAACACTGAA
TTCTAGAACTG
Found at i:214620 original size:76 final size:76
Alignment explanation
Indices: 214461--214634 Score: 215
Period size: 76 Copynumber: 2.3 Consensus size: 76
214451 AGTATCTTCA
* * * * * *
214461 AACTTAACACGTAATTCCATTAGTTAAACTTAACATAGACTTACACCGGTGAAACTAACACTTAA
1 AACTTAACACATAATTTCATCAGTGAAACTTAACATAGACTTACACCAGTGAAACTAACACTGAA
*
214526 TTCTAGAACTG
66 TTCCAGAACTG
* *
214537 AACTTAACACATAATTTCATCAGTGAAACTTAACATAGACTTACACTATTGAAACTAACACTGAA
1 AACTTAACACATAATTTCATCAGTGAAACTTAACATAGACTTACACCAGTGAAACTAACACTGAA
*
214602 TTCCA-ACATTG
66 TTCCAGA-ACTG
** *
214613 AGTTTAACACATAATTTTATCA
1 AACTTAACACATAATTTCATCA
214635 ATGGTATCCA
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
75 1 0.01
76 83 0.99
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.30
Consensus pattern (76 bp):
AACTTAACACATAATTTCATCAGTGAAACTTAACATAGACTTACACCAGTGAAACTAACACTGAA
TTCCAGAACTG
Found at i:215985 original size:23 final size:22
Alignment explanation
Indices: 215955--216018 Score: 76
Period size: 23 Copynumber: 2.9 Consensus size: 22
215945 GCATGGCCTT
215955 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
215977 AGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
215999 GTGTATCGATGCACATTCAA
1 GTGCATCGATGCACATTCAA
216019 AGGTATGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.44
22 3 0.09
23 16 0.47
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:216011 original size:21 final size:22
Alignment explanation
Indices: 215955--216017 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
215945 GCATGGCCTT
215955 GTGCATCGATGCACATTCAAGGA
1 GTGCATCGATGCACATTC-AGGA
* * *
215978 GTGCATCGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGA
*
215999 GTGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
216018 AAGGTATGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGA
Found at i:231238 original size:30 final size:30
Alignment explanation
Indices: 231158--231240 Score: 94
Period size: 32 Copynumber: 2.7 Consensus size: 30
231148 ATAAGGAATG
*
231158 ATATGAACATGTGATATGTGAACATAAGAGA
1 ATATG-ACATGAGATATGTGAACATAAGAGA
* * * *
231189 TTAAGTGATATGAGCTATGTGAACATATGAGA
1 AT-A-TGACATGAGATATGTGAACATAAGAGA
231221 ATATGACATGAGATATGTGA
1 ATATGACATGAGATATGTGA
231241 TATGTGAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
30 15 0.36
31 2 0.05
32 23 0.55
33 2 0.05
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (30 bp):
ATATGACATGAGATATGTGAACATAAGAGA
Found at i:234976 original size:70 final size:70
Alignment explanation
Indices: 234897--235057 Score: 198
Period size: 70 Copynumber: 2.3 Consensus size: 70
234887 GGTGTTACCA
* *** * *
234897 TACGAGTCACTCTAATCCTTCATGGCTCTGGTACGAGTCACCTAG-AATTAAATATAATTAGGTC
1 TACGAGTCACTCTAATCCTTCAGGGCTCCCATACAAGTCACC-AGAAATTAAATACAATTAGGTC
234961 CTCTCG
65 CTCTCG
* ** * *
234967 TACGTGTCACTCTAATCCTTTGGGGCTCCCATACAAGTCACCCGAAATTAAATACAATTAGGTGC
1 TACGAGTCACTCTAATCCTTCAGGGCTCCCATACAAGTCACCAGAAATTAAATACAATTAGGTCC
*
235032 TCTTG
66 TCTCG
235037 TACGAGTCACTCTAATCCTTC
1 TACGAGTCACTCTAATCCTTC
235058 CAAGCTCATG
Statistics
Matches: 76, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
69 1 0.01
70 75 0.99
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (70 bp):
TACGAGTCACTCTAATCCTTCAGGGCTCCCATACAAGTCACCAGAAATTAAATACAATTAGGTCC
TCTCG
Found at i:235502 original size:76 final size:75
Alignment explanation
Indices: 235373--235614 Score: 281
Period size: 76 Copynumber: 3.2 Consensus size: 75
235363 ATACTTACAC
* * *
235373 CAATGAAACTTAACATAGACATATACTGGTGAAACTAACACTTAATTCTAGCACTAAGCTTAACA
1 CAATGAAACTTAACATAGACTTACACTGGTGAAACTAACACTTAATTCCAGCACTAA-CTTAACA
* *
235438 CATAGTTCTAT
65 CATAATTCCAT
* * * *
235449 CAATGAAATTTAACATAGACTTGCATTGGTGAAACTAACACTTAATTCCAGCACCGAACTTAACA
1 CAATGAAACTTAACATAGACTTACACTGGTGAAACTAACACTTAATTCCAGCA-CTAACTTAACA
*
235514 CGTAATTCCAT
65 CATAATTCCAT
* * * * *
235525 CAGTGAAACTTAATATACACTTACACCT-GTGAAATTAACACTTAATTCCAGTACTGAACTTAAC
1 CAATGAAACTTAACATAGACTTACA-CTGGTGAAACTAACACTTAATTCCAGCACT-AACTTAAC
*
235589 ACATAATTTCAT
64 ACATAATTCCAT
*
235601 CAGTGAAAC-TAACA
1 CAATGAAACTTAACA
235615 CTTAATTTCA
Statistics
Matches: 141, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
75 5 0.04
76 132 0.94
77 4 0.03
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (75 bp):
CAATGAAACTTAACATAGACTTACACTGGTGAAACTAACACTTAATTCCAGCACTAACTTAACAC
ATAATTCCAT
Found at i:235512 original size:25 final size:25
Alignment explanation
Indices: 235484--235665 Score: 118
Period size: 25 Copynumber: 7.2 Consensus size: 25
235474 TTGGTGAAAC
*
235484 TAACACTTAATTCCAGCACCGAACT
1 TAACACTTAATTCCAGCACTGAACT
* * *
235509 TAACACGTAATTCCATCAGTGAAACT
1 TAACACTTAATTCCAGCACTG-AACT
* * * ** *
235535 TAATA--TACACTTACACCTGTGAAAT
1 TAACACTTA-A-TTCCAGCACTGAACT
*
235560 TAACACTTAATTCCAGTACTGAACT
1 TAACACTTAATTCCAGCACTGAACT
* * * *
235585 TAACACATAATTTCATCAGTGAAAC-
1 TAACACTTAATTCCAGCACTG-AACT
* *
235610 TAACACTTAATTTCAACACTGAACT
1 TAACACTTAATTCCAGCACTGAACT
* * *
235635 TAACACATAATTCCATCATTGAAACT
1 TAACACTTAATTCCAGCACTG-AACT
235661 TAACA
1 TAACA
235666 TAGACTTACA
Statistics
Matches: 121, Mismatches: 28, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
24 5 0.04
25 85 0.70
26 29 0.24
27 2 0.02
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (25 bp):
TAACACTTAATTCCAGCACTGAACT
Found at i:235607 original size:126 final size:126
Alignment explanation
Indices: 235477--235741 Score: 361
Period size: 126 Copynumber: 2.1 Consensus size: 126
235467 ACTTGCATTG
* * *
235477 GTGAAACTAACACTTAATTCCAGCACCGAACTTAACACGTAATTCCATCAGTGAAACTTAATATA
1 GTGAAACTAACACTTAATTCCAACACCGAACTTAACACATAATTCCATCAGTGAAACTTAACATA
* * ** *
235542 CACTTACACCTGTGAAATTAACACTTAATTCCAGTACTGAACTTAACACATAATT-TCATCA
66 CACTTACACCGGTGAAACTAACACTTAATTCCAACACTAAACTTAACACATAATTCT-ATCA
* * *
235603 GTGAAACTAACACTTAATTTCAACACTGAACTTAACACATAATTCCATCATTGAAACTTAACATA
1 GTGAAACTAACACTTAATTCCAACACCGAACTTAACACATAATTCCATCAGTGAAACTTAACATA
* * * * *
235668 GACTTACATCGGTGAAACTAACACTTAATTTCAACATTAAACTTAACACATTATTCTATCA
66 CACTTACACCGGTGAAACTAACACTTAATTCCAACACTAAACTTAACACATAATTCTATCA
235729 GTGAAACTTAACA
1 GTGAAAC-TAACA
235742 TAGACTTACA
Statistics
Matches: 121, Mismatches: 16, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
126 115 0.95
127 6 0.05
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.29
Consensus pattern (126 bp):
GTGAAACTAACACTTAATTCCAACACCGAACTTAACACATAATTCCATCAGTGAAACTTAACATA
CACTTACACCGGTGAAACTAACACTTAATTCCAACACTAAACTTAACACATAATTCTATCA
Found at i:235614 original size:50 final size:50
Alignment explanation
Indices: 235553--235665 Score: 163
Period size: 50 Copynumber: 2.2 Consensus size: 50
235543 ACTTACACCT
* ** *
235553 GTGAAATTAACACTTAATTCCAGTACTGAACTTAACACATAATTTCATCA
1 GTGAAACTAACACTTAATTCCAACACTGAACTTAACACATAATTCCATCA
*
235603 GTGAAACTAACACTTAATTTCAACACTGAACTTAACACATAATTCCATCA
1 GTGAAACTAACACTTAATTCCAACACTGAACTTAACACATAATTCCATCA
*
235653 TTGAAACTTAACA
1 GTGAAAC-TAACA
235666 TAGACTTACA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
50 51 0.91
51 5 0.09
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (50 bp):
GTGAAACTAACACTTAATTCCAACACTGAACTTAACACATAATTCCATCA
Found at i:235661 original size:76 final size:76
Alignment explanation
Indices: 235554--235773 Score: 246
Period size: 76 Copynumber: 2.9 Consensus size: 76
235544 CTTACACCTG
* * * *
235554 TGAAATTAACACTTAATTCCAGT-ACTG-AACTTAACACATAATTTCATCAGTGAAACTAACACT
1 TGAACTTAACACATAATTCCA-TCACTGAAACTTAACACAGAATTACATCAGTGAAACTAACACT
235617 TAATTTCAACAC
65 TAATTTCAACAC
* * * *
235629 TGAACTTAACACATAATTCCATCATTGAAACTTAACATAGACTTACATCGGTGAAACTAACACTT
1 TGAACTTAACACATAATTCCATCACTGAAACTTAACACAGAATTACATCAGTGAAACTAACACTT
*
235694 AATTTCAACAT
66 AATTTCAACAC
* * * * * * * * * *
235705 TAAACTTAACACATTATTCTATCAGTGAAACTTAACATAGACTTACACCGGTAAAATTAACACTT
1 TGAACTTAACACATAATTCCATCACTGAAACTTAACACAGAATTACATCAGTGAAACTAACACTT
235770 AATT
66 AATT
235774 CGAGCGTTGA
Statistics
Matches: 127, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
74 1 0.01
75 22 0.17
76 104 0.82
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.31
Consensus pattern (76 bp):
TGAACTTAACACATAATTCCATCACTGAAACTTAACACAGAATTACATCAGTGAAACTAACACTT
AATTTCAACAC
Found at i:235714 original size:25 final size:25
Alignment explanation
Indices: 235581--235741 Score: 112
Period size: 25 Copynumber: 6.4 Consensus size: 25
235571 TCCAGTACTG
*
235581 AACTTAACACATAATTTCATCAGTGA
1 AACTTAACACATAATTTCATCA-TTA
* * * *
235607 AAC-TAACACTTAATTTCAACACTG
1 AACTTAACACATAATTTCATCATTA
*
235631 AACTTAACACATAATTCCATCATTGA
1 AACTTAACACATAATTTCATCATT-A
* * * * * *
235657 AACTTAACATAGACTTACATCGGTGA
1 AACTTAACACATAATTTCATC-ATTA
* *
235683 AAC-TAACACTTAATTTCAACATTA
1 AACTTAACACATAATTTCATCATTA
* *
235707 AACTTAACACATTA-TTCTATCAGTGA
1 AACTTAACACATAATTTC-ATCA-TTA
235733 AACTTAACA
1 AACTTAACA
235742 TAGACTTACA
Statistics
Matches: 101, Mismatches: 28, Indels: 12
0.72 0.20 0.09
Matches are distributed among these distances:
24 11 0.11
25 54 0.53
26 35 0.35
27 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (25 bp):
AACTTAACACATAATTTCATCATTA
Found at i:235731 original size:202 final size:202
Alignment explanation
Indices: 235401--235774 Score: 545
Period size: 202 Copynumber: 1.9 Consensus size: 202
235391 ACATATACTG
* * * *
235401 GTGAAACTAACACTTAATTCTAGCACTAAGCTTAACACATAGTTCTATCAATGAAATTTAACATA
1 GTGAAACTAACACTTAATTCTAACACTAAGCTTAACACATAATTCCATCAATGAAACTTAACATA
* * * * *
235466 GACTTGCATTGGTGAAACTAACACTTAATTCCAGCACCGAACTTAACACGTAATTCCATCAGTGA
66 GACTTACATCGGTGAAACTAACACTTAATTCCAACACCAAACTTAACACATAATTCCATCAGTGA
* * *
235531 AACTTAATATACACTTACACCTGTGAAATTAACACTTAATTCCAGTACTGAACTTAACACATAAT
131 AACTTAACATACACTTACACCGGTAAAATTAACACTTAATTCCAGTACTGAACTTAACACATAAT
235596 TTCATCA
196 TTCATCA
*
235603 GTGAAACTAACACTTAATT-TCAACACTGAA-CTTAACACATAATTCCATCATTGAAACTTAACA
1 GTGAAACTAACACTTAATTCT-AACACT-AAGCTTAACACATAATTCCATCAATGAAACTTAACA
* ** * *
235666 TAGACTTACATCGGTGAAACTAACACTTAATTTCAACATTAAACTTAACACATTATTCTATCAGT
64 TAGACTTACATCGGTGAAACTAACACTTAATTCCAACACCAAACTTAACACATAATTCCATCAGT
*
235731 GAAACTTAACATAGACTTACACCGGTAAAATTAACACTTAATTC
129 GAAACTTAACATACACTTACACCGGTAAAATTAACACTTAATTC
235775 GAGCGTTGAA
Statistics
Matches: 151, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
201 1 0.01
202 148 0.98
203 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (202 bp):
GTGAAACTAACACTTAATTCTAACACTAAGCTTAACACATAATTCCATCAATGAAACTTAACATA
GACTTACATCGGTGAAACTAACACTTAATTCCAACACCAAACTTAACACATAATTCCATCAGTGA
AACTTAACATACACTTACACCGGTAAAATTAACACTTAATTCCAGTACTGAACTTAACACATAAT
TTCATCA
Found at i:235789 original size:76 final size:76
Alignment explanation
Indices: 235606--235773 Score: 264
Period size: 76 Copynumber: 2.2 Consensus size: 76
235596 TTCATCAGTG
* *
235606 AAACTAACACTTAATTTCAACACTGAACTTAACACATAATTCCATCATTGAAACTTAACATAGAC
1 AAACTAACACTTAATTTCAACATTGAACTTAACACATAATTCCATCAGTGAAACTTAACATAGAC
* *
235671 TTACATCGGTG
66 TTACACCGGTA
* * *
235682 AAACTAACACTTAATTTCAACATTAAACTTAACACATTATTCTATCAGTGAAACTTAACATAGAC
1 AAACTAACACTTAATTTCAACATTGAACTTAACACATAATTCCATCAGTGAAACTTAACATAGAC
235747 TTACACCGGTA
66 TTACACCGGTA
*
235758 AAATTAACACTTAATT
1 AAACTAACACTTAATT
235774 CGAGCGTTGA
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 84 1.00
ACGTcount: A:0.42, C:0.21, G:0.07, T:0.30
Consensus pattern (76 bp):
AAACTAACACTTAATTTCAACATTGAACTTAACACATAATTCCATCAGTGAAACTTAACATAGAC
TTACACCGGTA
Found at i:236060 original size:22 final size:21
Alignment explanation
Indices: 236026--236066 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
236016 ATAATTATTT
236026 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
236047 AAAAACATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
236067 TTTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:241472 original size:19 final size:16
Alignment explanation
Indices: 241447--241488 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
241437 TGTCATTTCT
241447 TAATATTTGAAAAATAAA
1 TAATATTT-AAAAAT-AA
241465 TAA-ATATTAAAAATAA
1 TAATAT-TTAAAAATAA
241481 TAATATTT
1 TAATATTT
241489 TCTAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 7 0.32
17 10 0.45
18 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAATATTTAAAAATAA
Found at i:241815 original size:20 final size:21
Alignment explanation
Indices: 241771--241815 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
241761 AAACTACAGT
*
241771 ATTAAAATACAAAATATATAA
1 ATTAAAATACAAAATATAGAA
* *
241792 ATTAATATACAAAA-ATGGAA
1 ATTAAAATACAAAATATAGAA
241812 ATTA
1 ATTA
241816 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (21 bp):
ATTAAAATACAAAATATAGAA
Found at i:244078 original size:2 final size:2
Alignment explanation
Indices: 244071--244124 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
244061 ATATTCATTC
244071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
244113 AT AT AC AT AT AT
1 AT AT AT AT AT AT
244125 TCATGTACAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:244401 original size:18 final size:18
Alignment explanation
Indices: 244372--244459 Score: 131
Period size: 18 Copynumber: 4.9 Consensus size: 18
244362 GCGTAGAATT
*
244372 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
244390 TGTCTCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
*
244408 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
244426 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
244444 TGTCCCAAAGGACCAC
1 TGTCCCGAAGGACCAC
244460 GTAGACCCTC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:245080 original size:20 final size:20
Alignment explanation
Indices: 245055--245092 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
245045 TTTCCCTTGA
245055 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
245075 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
245093 TTAACACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:245109 original size:24 final size:20
Alignment explanation
Indices: 245057--245112 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
245047 TCCCTTGAAG
*
245057 TGCATCGATGCATTCTACAG
1 TGCATCGATGCATTCTACAA
245077 TGCATCGATGCATTCTTTAACACA
1 TGCATCGATGCATTC--T-ACA-A
245101 TGCATCGATGCA
1 TGCATCGATGCA
245113 CTACCCATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (20 bp):
TGCATCGATGCATTCTACAA
Found at i:246432 original size:20 final size:20
Alignment explanation
Indices: 246409--246502 Score: 55
Period size: 20 Copynumber: 4.3 Consensus size: 20
246399 TTGGCATCTG
246409 TTCATGCCTTAATACATCCT
1 TTCATGCCTTAATACATCCT
*
246429 TTCATGCATTTTCAATTATGGCAT-CT
1 TTCATGC--CTT-AA-TA---CATCCT
* * *
246455 GTTCATGCCTTTATGCATCCG
1 -TTCATGCCTTAATACATCCT
* *
246476 TTCATGCCTTTATGCATCCT
1 TTCATGCCTTAATACATCCT
246496 TTCATGC
1 TTCATGC
246503 ATTTTCAATT
Statistics
Matches: 59, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
20 36 0.61
21 1 0.02
22 2 0.03
23 3 0.05
24 3 0.05
25 2 0.03
26 2 0.03
27 10 0.17
ACGTcount: A:0.19, C:0.27, G:0.12, T:0.43
Consensus pattern (20 bp):
TTCATGCCTTAATACATCCT
Found at i:246451 original size:47 final size:47
Alignment explanation
Indices: 246381--246482 Score: 141
Period size: 47 Copynumber: 2.2 Consensus size: 47
246371 AATACACCAT
* * *
246381 TTTCAAGCATTTCCAGTTTTGGCATCTGTTCATGCCTTAATACATCC
1 TTTCATGCATTTCCAATTATGGCATCTGTTCATGCCTTAATACATCC
* * *
246428 TTTCATGCATTTTCAATTATGGCATCTGTTCATGCCTTTATGCATCC
1 TTTCATGCATTTCCAATTATGGCATCTGTTCATGCCTTAATACATCC
*
246475 GTTCATGC
1 TTTCATGC
246483 CTTTATGCAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.20, C:0.25, G:0.14, T:0.42
Consensus pattern (47 bp):
TTTCATGCATTTCCAATTATGGCATCTGTTCATGCCTTAATACATCC
Found at i:246483 original size:67 final size:66
Alignment explanation
Indices: 246402--246682 Score: 272
Period size: 67 Copynumber: 4.2 Consensus size: 66
246392 TCCAGTTTTG
* * * * *
246402 GCATCTGTTCATGCCTTAATACATCCTTTCATGCATTTTCAATTATGGCATCTGTTCATGCCTTT
1 GCATCCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATGGCAT-TGTTCATTCCATT
246467 AT
65 AT
** *
246469 GCATCCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATGAAATTGATT--TTCAATT
1 GCATCCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATGGCATTG-TTCATTCCATT
246532 AT
65 AT
*
246534 GGCATCCGTTCATGCCTTTATGCATCCTTTCATGCCTTTATACATATTTTCAT-GCATT-TTCA-
1 -GCATCCGTTCATGCCTTTATGCATCCTTTCATGCATTT-T-CA-A--TT-ATGGCATTGTTCAT
246596 ---ATTAT
59 TCCATTAT
* ** * *
246601 GACATTCGTTCATGCCTTTATGCATTATTTCATGCATTTTCAATTATGGCATCCGTTCATTCCTT
1 G-CATCCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATGGCAT-TGTTCATTCCAT
246666 TAT
64 TAT
*
246669 GCATCCTTTCATGC
1 GCATCCGTTCATGC
246683 ATTTTCAATT
Statistics
Matches: 177, Mismatches: 19, Indels: 36
0.76 0.08 0.16
Matches are distributed among these distances:
61 2 0.01
62 6 0.03
64 5 0.03
65 8 0.05
66 41 0.23
67 98 0.55
68 7 0.04
69 3 0.02
71 5 0.03
72 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.44
Consensus pattern (66 bp):
GCATCCGTTCATGCCTTTATGCATCCTTTCATGCATTTTCAATTATGGCATTGTTCATTCCATTA
T
Found at i:246548 original size:86 final size:86
Alignment explanation
Indices: 246436--246705 Score: 310
Period size: 86 Copynumber: 3.0 Consensus size: 86
246426 CCTTTCATGC
*
246436 ATTTTCAATTATGGCATCTGTTCATGCCTTTATGCATCCGTTCATGCCTTTATGCATCCTTTCAT
1 ATTTTCAATTATGGCATCAGTTCATGCCTTTATGCATCCGTTCATGCCTTTATGCATCCTTTCAT
246501 GCATTTTCAATTATGAAATTG
66 GCATTTTCAATTATGAAATTG
* * * **
246522 ATTTTCAATTATGGCATCCGTTCATGCCTTTATGCATCCTTTCATGCCTTTATACATATTTTCAT
1 ATTTTCAATTATGGCATCAGTTCATGCCTTTATGCATCCGTTCATGCCTTTATGCATCCTTTCAT
*
246587 GCATTTTCAATTATGACATTCG
66 GCATTTTCAATTATGAAATT-G
* ** * * * *
246609 -TTCATGCCTTTAT-GCATTATTTCATGCATTTTCAATTATGGCATCCGTTCATTCCTTTATGCA
1 ATT--TTCAATTATGGCATCAGTTCATGC-----C-TTTAT-GCATCCGTTCATGCCTTTATGCA
246672 TCCTTTCATGCATTTTCAATTATGAAATTG
57 TCCTTTCATGCATTTTCAATTATGAAATTG
246702 ATTT
1 ATTT
246706 AGAGCAGTTC
Statistics
Matches: 154, Mismatches: 19, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
86 81 0.53
87 12 0.08
88 6 0.04
92 2 0.01
93 5 0.03
94 48 0.31
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.46
Consensus pattern (86 bp):
ATTTTCAATTATGGCATCAGTTCATGCCTTTATGCATCCGTTCATGCCTTTATGCATCCTTTCAT
GCATTTTCAATTATGAAATTG
Found at i:246560 original size:20 final size:21
Alignment explanation
Indices: 246530--246574 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
246520 TGATTTTCAA
246530 TTATGGCATCCGTTCATGCCT
1 TTATGGCATCCGTTCATGCCT
*
246551 TTAT-GCATCCTTTCATGCCT
1 TTATGGCATCCGTTCATGCCT
246571 TTAT
1 TTAT
246575 ACATATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.16, C:0.27, G:0.13, T:0.44
Consensus pattern (21 bp):
TTATGGCATCCGTTCATGCCT
Found at i:246584 original size:20 final size:20
Alignment explanation
Indices: 246542--246588 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
246532 ATGGCATCCG
* *
246542 TTCATGCCTTTATGCATCCT
1 TTCATGCCTTTATACATACT
*
246562 TTCATGCCTTTATACATATT
1 TTCATGCCTTTATACATACT
246582 TTCATGC
1 TTCATGC
246589 ATTTTCAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.26, G:0.09, T:0.47
Consensus pattern (20 bp):
TTCATGCCTTTATACATACT
Found at i:246619 original size:47 final size:46
Alignment explanation
Indices: 246551--246696 Score: 204
Period size: 47 Copynumber: 3.1 Consensus size: 46
246541 GTTCATGCCT
* *
246551 TTATG-CATCCTTTCATGCCTTTATACATATTTTCATGCATTTTCAA
1 TTATGACATCCGTTCATGCCTTTATGCAT-TTTTCATGCATTTTCAA
*
246597 TTATGACATTCGTTCATGCCTTTATGCATTATTTCATGCATTTTCAA
1 TTATGACATCCGTTCATGCCTTTATGCATT-TTTCATGCATTTTCAA
* * *
246644 TTATGGCATCCGTTCATTCCTTTATGCATCCTTTCATGCATTTTCAA
1 TTATGACATCCGTTCATGCCTTTATGCAT-TTTTCATGCATTTTCAA
246691 TTATGA
1 TTATGA
246697 AATTGATTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
46 6 0.07
47 83 0.93
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.47
Consensus pattern (46 bp):
TTATGACATCCGTTCATGCCTTTATGCATTTTTCATGCATTTTCAA
Found at i:246786 original size:2 final size:2
Alignment explanation
Indices: 246779--246805 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
246769 CAATATTATA
246779 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
246806 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:247165 original size:22 final size:21
Alignment explanation
Indices: 247119--247175 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
247109 CTGGCCCTTT
*
247119 GGTATTGATACCCCTGATTAT
1 GGTATTGATACCCCTGATTAG
247140 GGTATTGATACTACCCT-ATTAG
1 GGTATTGATAC--CCCTGATTAG
*
247162 GGTATCGATACCCC
1 GGTATTGATACCCC
247176 CTGCACGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 3 0.09
21 11 0.34
22 14 0.44
23 4 0.12
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (21 bp):
GGTATTGATACCCCTGATTAG
Found at i:247267 original size:95 final size:95
Alignment explanation
Indices: 247162--247341 Score: 247
Period size: 95 Copynumber: 1.9 Consensus size: 95
247152 ACCCTATTAG
* *
247162 GGTATCGATACCCCCTGC-ACGTATCGATACCAAAATTA-ACTTCGATGTAGCCTGGTATCGATA
1 GGTACCGATACCCCCT-CTACGTATCGATACCAAAATTAGA-TTCGATGTAGACTGGTATCGATA
247225 CCCTCACCATGGTATCGATACCCCTATGCTAT
64 CCCTCACCATGGTATCGATACCCCTATGCTAT
* * * * **
247257 GGTACCGATACCTCCTCTAGGTATCGATACCCAATTTAGATTCGATGTTTACTGGTATCGATACC
1 GGTACCGATACCCCCTCTACGTATCGATACCAAAATTAGATTCGATGTAGACTGGTATCGATACC
*
247322 CTTACCATGGTATCGATACC
66 CTCACCATGGTATCGATACC
247342 ACATTATTTG
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
94 1 0.01
95 72 0.97
96 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (95 bp):
GGTACCGATACCCCCTCTACGTATCGATACCAAAATTAGATTCGATGTAGACTGGTATCGATACC
CTCACCATGGTATCGATACCCCTATGCTAT
Found at i:247284 original size:19 final size:21
Alignment explanation
Indices: 247214--247288 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 21
247204 CGATGTAGCC
*
247214 TGGTATCGATACCCTCA--CCA
1 TGGTATCGATACCC-CATGCTA
247234 TGGTATCGATACCCCTATGCTA
1 TGGTATCGATACCCC-ATGCTA
*
247256 TGGTACCGATACCTCC-T-CTA
1 TGGTATCGATACC-CCATGCTA
247276 -GGTATCGATACCC
1 TGGTATCGATACCC
247289 AATTTAGATT
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.02
19 12 0.25
20 18 0.38
21 1 0.02
22 14 0.29
23 2 0.04
ACGTcount: A:0.23, C:0.32, G:0.17, T:0.28
Consensus pattern (21 bp):
TGGTATCGATACCCCATGCTA
Found at i:247356 original size:95 final size:95
Alignment explanation
Indices: 247138--247361 Score: 238
Period size: 95 Copynumber: 2.4 Consensus size: 95
247128 ACCCCTGATT
* * ** * *
247138 ATGGTATTGATACTACCCTATTAGGGTATCGATACCCCCTGCACGTATCGATACCAAAATTAACT
1 ATGGTATCGATACCACATTATTTGGGTACCGATACCCCCTGCACGTATCGATACCAAAATTAACT
*
247203 TCGATGTAGCCTGGTATCGATACCCTCACC
66 TCGATGTAGACTGGTATCGATACCCTCACC
* ** * * * * *
247233 ATGGTATCGATACCCCTATGCTAT-GGTACCGATACCTCCT-CTAGGTATCGATACCCAATTTAG
1 ATGGTATCGATACCAC-ATTATTTGGGTACCGATACCCCCTGC-ACGTATCGATACCAAAATTA-
** *
247296 A-TTCGATGTTTACTGGTATCGATACCCTTACC
63 ACTTCGATGTAGACTGGTATCGATACCCTCACC
247328 ATGGTATCGATACCACATTATTTGGGTACCGATA
1 ATGGTATCGATACCACATTATTTGGGTACCGATA
247362 TTAGTTGAAT
Statistics
Matches: 103, Mismatches: 22, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
94 5 0.05
95 96 0.93
96 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (95 bp):
ATGGTATCGATACCACATTATTTGGGTACCGATACCCCCTGCACGTATCGATACCAAAATTAACT
TCGATGTAGACTGGTATCGATACCCTCACC
Found at i:255069 original size:15 final size:15
Alignment explanation
Indices: 255049--255078 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
255039 CGAAGTATCA
*
255049 GAAGTCGGCAAGAGG
1 GAAGTCGACAAGAGG
255064 GAAGTCGACAAGAGG
1 GAAGTCGACAAGAGG
255079 AAAGAATTCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.43, T:0.07
Consensus pattern (15 bp):
GAAGTCGACAAGAGG
Found at i:272581 original size:18 final size:18
Alignment explanation
Indices: 272558--272628 Score: 115
Period size: 18 Copynumber: 3.9 Consensus size: 18
272548 ATTGAATATT
272558 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
272576 TGTCCCGAGGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
272594 TGTCCCGAATGACCATTA
1 TGTCCCGAAGGACCACTA
272612 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
272629 GATAATCCCT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:272801 original size:2 final size:2
Alignment explanation
Indices: 272790--272829 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
272780 CACTATAACA
272790 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
272830 AATGCATGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:274649 original size:24 final size:26
Alignment explanation
Indices: 274622--274700 Score: 78
Period size: 25 Copynumber: 3.2 Consensus size: 26
274612 AAACATGAAG
* *
274622 TAAAAAAAAGATA-AAACGAA-CAAA
1 TAAAAAAAAGATATAAACAAATAAAA
274646 T-AAAAAAAGATATAAACAAATAAAA
1 TAAAAAAAAGATATAAACAAATAAAA
* *
274671 TAAAAATAAACAAATAAAC-AAT-AAA
1 TAAAAA-AAAGATATAAACAAATAAAA
274696 TAAAA
1 TAAAA
274701 TAAATAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
23 11 0.23
24 7 0.15
25 12 0.26
26 7 0.15
27 10 0.21
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (26 bp):
TAAAAAAAAGATATAAACAAATAAAA
Found at i:274650 original size:23 final size:25
Alignment explanation
Indices: 274624--274676 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 25
274614 ACATGAAGTA
* *
274624 AAAAAAAGATA-AAACGAA-CAAAT
1 AAAAAAAGATATAAACAAATAAAAT
274647 AAAAAAAGATATAAACAAATAAAAT
1 AAAAAAAGATATAAACAAATAAAAT
274672 AAAAA
1 AAAAA
274677 TAAACAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 11 0.42
24 6 0.23
25 9 0.35
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (25 bp):
AAAAAAAGATATAAACAAATAAAAT
Found at i:274663 original size:20 final size:19
Alignment explanation
Indices: 274640--274737 Score: 74
Period size: 19 Copynumber: 4.8 Consensus size: 19
274630 AGATAAAACG
274640 AACAAATAAAA-AAAGATATA
1 AACAAATAAAATAAA-A-ATA
274660 AACAAATAAAATAAAAATA
1 AACAAATAAAATAAAAATA
274679 AACAAATAAACAATAAATAAAATA
1 AACAAAT-AA-AAT--A-AAAATA
* *
274703 AATAAATAAATTAGAAAA-A
1 AACAAATAAAATA-AAAATA
* *
274722 ACCAAACAAAATAAAA
1 AACAAATAAAATAAAA
274738 GAATAAAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.05
19 20 0.31
20 19 0.29
21 6 0.09
22 2 0.03
23 3 0.05
24 12 0.18
ACGTcount: A:0.76, C:0.07, G:0.02, T:0.15
Consensus pattern (19 bp):
AACAAATAAAATAAAAATA
Found at i:275011 original size:15 final size:14
Alignment explanation
Indices: 274991--275040 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
274981 TGTTAGGTTA
274991 ATAATATATATATAT
1 ATAATATA-ATATAT
275006 ATAATATAATA-AT
1 ATAATATAATATAT
*
275019 ACTAATGATAAAATAT
1 A-TAAT-ATAATATAT
275035 ATAATA
1 ATAATA
275041 AAACTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 3 0.10
14 8 0.26
15 17 0.55
16 3 0.10
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (14 bp):
ATAATATAATATAT
Found at i:276118 original size:2 final size:2
Alignment explanation
Indices: 276111--276157 Score: 55
Period size: 2 Copynumber: 24.5 Consensus size: 2
276101 CACAAACATA
*
276111 AT AT AT AT AT AT AT AT AT AT AT AT A- AGT AT GT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
276152 A- AT AT A
1 AT AT AT A
276158 GTTGGTAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
1 3 0.08
2 35 0.90
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:278254 original size:14 final size:13
Alignment explanation
Indices: 278217--278255 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
278207 CCACCTTATT
278217 TCTTTTCTTTTTC
1 TCTTTTCTTTTTC
*
278230 TTTTGTTCTTTTTC
1 TCTT-TTCTTTTTC
278244 TCTTTTCCTTTT
1 TCTTTT-CTTTT
278256 ATTTTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.77
Consensus pattern (13 bp):
TCTTTTCTTTTTC
Found at i:278263 original size:22 final size:20
Alignment explanation
Indices: 278212--278264 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
278202 TGAACCCACC
*
278212 TTATTTCTTTTCTTTTTCTT
1 TTATTTTTTTTCTTTTTCTT
* *
278232 TTGTTCTTTTTCTCTTTTCCTT
1 TTATT-TTTTT-TCTTTTTCTT
278254 TTATTTTTTTT
1 TTATTTTTTTT
278265 AAGTTAGGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 5 0.19
21 9 0.33
22 13 0.48
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.79
Consensus pattern (20 bp):
TTATTTTTTTTCTTTTTCTT
Found at i:278321 original size:16 final size:17
Alignment explanation
Indices: 278302--278338 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
278292 CCCTAAACGA
*
278302 TTTTCTCTTTTTTT-TT
1 TTTTCCCTTTTTTTCTT
278318 TTTTCCCTTTTTTTCTT
1 TTTTCCCTTTTTTTCTT
278335 TTTT
1 TTTT
278339 TAACTTAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTCCCTTTTTTTCTT
Found at i:288796 original size:33 final size:30
Alignment explanation
Indices: 288759--288824 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 30
288749 AAACAGGAAG
288759 TAAAAAAAAGATAAAAGGAACAAATAAAAAAAA
1 TAAAAAAAAGAT-AAA--AACAAATAAAAAAAA
* * *
288792 T-AAAATAAGATATAAACAAATAAATAAAA
1 TAAAAAAAAGATAAAAACAAATAAAAAAAA
288821 TAAA
1 TAAA
288825 CAAATAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
29 15 0.52
30 2 0.07
31 2 0.07
32 9 0.31
33 1 0.03
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (30 bp):
TAAAAAAAAGATAAAAACAAATAAAAAAAA
Found at i:288825 original size:17 final size:19
Alignment explanation
Indices: 288789--288832 Score: 65
Period size: 17 Copynumber: 2.4 Consensus size: 19
288779 CAAATAAAAA
288789 AAATAAAATAAGATATAAAC
1 AAAT-AAATAAGATATAAAC
288809 AAATAAATAA-A-ATAAAC
1 AAATAAATAAGATATAAAC
288826 AAATAAA
1 AAATAAA
288833 CAATAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.54
18 1 0.04
19 6 0.25
20 4 0.17
ACGTcount: A:0.75, C:0.05, G:0.02, T:0.18
Consensus pattern (19 bp):
AAATAAATAAGATATAAAC
Found at i:288837 original size:24 final size:24
Alignment explanation
Indices: 288777--288848 Score: 80
Period size: 24 Copynumber: 3.1 Consensus size: 24
288767 AGATAAAAGG
288777 AACAAATAAA-AA-AAATAAAAT-
1 AACAAATAAACAATAAATAAAATA
* *
288798 AAGATATAAACAAATAAATAAAATA
1 AACAAATAAAC-AATAAATAAAATA
288823 AACAAATAAACAATAAA-ATAAATA
1 AACAAATAAACAATAAATA-AAATA
288847 AA
1 AA
288849 TTAGAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
21 8 0.19
23 3 0.07
24 22 0.52
25 9 0.21
ACGTcount: A:0.76, C:0.06, G:0.01, T:0.17
Consensus pattern (24 bp):
AACAAATAAACAATAAATAAAATA
Found at i:288895 original size:12 final size:12
Alignment explanation
Indices: 288875--288924 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
288865 AAAATAAAAG
*
288875 AATAAAAATAAA
1 AATACAAATAAA
*
288887 AATACAAATACA
1 AATACAAATAAA
288899 AATACAAA-AATTA
1 AATACAAATAA--A
288912 AATA-AAATAAA
1 AATACAAATAAA
288923 AA
1 AA
288925 GTAGTTATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 4 0.12
12 21 0.66
13 7 0.22
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (12 bp):
AATACAAATAAA
Found at i:288901 original size:18 final size:17
Alignment explanation
Indices: 288786--288924 Score: 64
Period size: 17 Copynumber: 8.3 Consensus size: 17
288776 GAACAAATAA
* *
288786 AAAAAATAAAATAAGAT
1 AAAAAATCAAATAAAAT
*
288803 -ATAAA-CAAAT-AAAT
1 AAAAAATCAAATAAAAT
*
288817 AAAATAAACAAATAAACA-
1 AAAA-AATCAAATAAA-AT
* *
288835 ATAAAAT-AAATAAATT
1 AAAAAATCAAATAAAAT
*
288851 AGAAAAATCCAAACAAAAT
1 A-AAAAAT-CAAATAAAAT
288870 AAAAGAAT---A-AAAAT
1 AAAA-AATCAAATAAAAT
288884 -AAAAATACAAATACAAAT
1 AAAAAAT-CAAATA-AAAT
*
288902 ACAAAAATTAAATAAAAT
1 A-AAAAATCAAATAAAAT
288920 AAAAA
1 AAAAA
288925 GTAGTTATAA
Statistics
Matches: 93, Mismatches: 11, Indels: 36
0.66 0.08 0.26
Matches are distributed among these distances:
12 3 0.03
13 3 0.03
14 8 0.09
15 7 0.08
16 15 0.16
17 17 0.18
18 17 0.18
19 17 0.18
20 6 0.06
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.17
Consensus pattern (17 bp):
AAAAAATCAAATAAAAT
Found at i:291987 original size:35 final size:35
Alignment explanation
Indices: 291948--292031 Score: 159
Period size: 35 Copynumber: 2.4 Consensus size: 35
291938 CTTCCGACTT
291948 TAGTGAAGAAAGACCATAAATGAAACCTCTAGCAG
1 TAGTGAAGAAAGACCATAAATGAAACCTCTAGCAG
*
291983 TAGTGAAGAAAGACCATAAATGAAGCCTCTAGCAG
1 TAGTGAAGAAAGACCATAAATGAAACCTCTAGCAG
292018 TAGTGAAGAAAGAC
1 TAGTGAAGAAAGAC
292032 ATGATTATCT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (35 bp):
TAGTGAAGAAAGACCATAAATGAAACCTCTAGCAG
Found at i:292670 original size:18 final size:19
Alignment explanation
Indices: 292637--292674 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
292627 GTGAAGTATG
292637 AATGGCGTTGTCGTGGCAA
1 AATGGCGTTGTCGTGGCAA
*
292656 AATGG-GTTGTTGTGGCAA
1 AATGGCGTTGTCGTGGCAA
292674 A
1 A
292675 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.24, C:0.11, G:0.37, T:0.29
Consensus pattern (19 bp):
AATGGCGTTGTCGTGGCAA
Found at i:298428 original size:21 final size:21
Alignment explanation
Indices: 298404--298464 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
298394 AACTTTGAAA
298404 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
298425 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
298439 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
298460 AAATG
1 AAATG
298465 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:298495 original size:37 final size:37
Alignment explanation
Indices: 298396--298514 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
298386 TGGTAACCAA
298396 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
298433 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
298468 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
298505 -GTTGAAAAAT
1 CTTTGAAAAAT
298515 GATAATGAGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:298943 original size:16 final size:16
Alignment explanation
Indices: 298922--298954 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
298912 TACTATTCAT
*
298922 GTGAATAGTGAATTTC
1 GTGAATAGTGAAATTC
298938 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
298954 G
1 G
298955 GTCGGCGATA
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:0.33, C:0.06, G:0.27, T:0.33
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:303079 original size:36 final size:35
Alignment explanation
Indices: 302965--303084 Score: 170
Period size: 35 Copynumber: 3.3 Consensus size: 35
302955 TGGTAACCAA
302965 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAAT-GTTTTCAAAGTTTGGTAAATGTTT
*
303002 CTTTGAAAATTGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTCAAAGTTTGGTAAATGTTT
*
303037 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-G-TTTTCAAAGTTTGGTAAATGTTT
*
303074 -GTTGAAAAATG
1 CTTTGAAAAATG
303085 ATAATGAGAT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
35 35 0.45
36 15 0.19
37 27 0.35
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (35 bp):
CTTTGAAAAATGTTTTCAAAGTTTGGTAAATGTTT
Found at i:303605 original size:18 final size:18
Alignment explanation
Indices: 303562--303599 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
303552 GTGAAGTATG
*
303562 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
303580 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
303598 AA
1 AA
303600 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:309760 original size:15 final size:17
Alignment explanation
Indices: 309740--309783 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
309730 GTAAGGGTAT
*
309740 CCATAGCCATA-A-CCC
1 CCATAGCCATATAGCCA
309755 CCATAGCCATCATAGCCA
1 CCATAGCCAT-ATAGCCA
309773 CCATAGCCATA
1 CCATAGCCATA
309784 GTTGTAGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 10 0.40
16 1 0.04
17 2 0.08
18 12 0.48
ACGTcount: A:0.34, C:0.41, G:0.09, T:0.16
Consensus pattern (17 bp):
CCATAGCCATATAGCCA
Found at i:312322 original size:16 final size:16
Alignment explanation
Indices: 312298--312329 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
312288 AATTATTCAG
312298 GATTAACCCACAATTT
1 GATTAACCCACAATTT
*
312314 GATTGACCCACAATTT
1 GATTAACCCACAATTT
312330 ATGGATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.31
Consensus pattern (16 bp):
GATTAACCCACAATTT
Found at i:312372 original size:357 final size:356
Alignment explanation
Indices: 311713--312649 Score: 1527
Period size: 357 Copynumber: 2.6 Consensus size: 356
311703 TCTTCATTTT
* *
311713 TTTCTTGATTCACGCCATGGGAGTTCACGAAGGCAACCAAAGCATGGTACCCACCATTCTTGGTT
1 TTTCTTGATTCA-GTCATGGGAGTTCACGAAGGCAACCAAAGCATGATACCCACCATTCTTGGTT
* *
311778 CACTGAGATTGATACCCCAAGCCGACCACTGTGACGAGGTGTTTTTGGTGTATCGGTAAGCAATA
65 CACTGAGATTGATACCCCAAGCCGACCACTGTGACGAGGTGTTTTTGGTGCATCGGTAAGCTATA
*
311843 TAATAGAAGGATTTATCCTTTGTTTATGATGCTTAATCTTTCAAATAATGTAAATAATGAAATGG
130 TAATAGAAGGATTTATCTTTTGTTTATGATGCTTAATCTTTCAAATAATGTAAATAATGAAATGG
* *
311908 ATTTTTGTCTATTTGTGTAATGTAATTTGTCAGGATTAACCCACCATTTGATTGACCCACTATTT
195 ATTTTTGTCTATTTGTGTAATGTAATTTGTCAGGATTAACCCACAATTTGATTGACCCACAATTT
* * * *
311973 ACAGATTGATTAATGGAGGTTTTGAATGCTCATGACTTTTTTCATCCTTTGTTAAGTGCCAAATG
260 ACAGATTAATTAATAGAGGCTTTGAATGCTCATGACTTTTTTCATCCTTTGTTAAGTGCCAAAGG
312038 ATGATGGATTTTACCCT-ATTTCATCCTCAATG
325 ATGATGGATTTTA-CCTGATTTCATCCTCAATG
*
312070 TTTGTTGATTCATGTCATGGGAGTTCACGAAGGCAACCAAAGCATGATACCCACCATTCTTGGTT
1 TTTCTTGATTCA-GTCATGGGAGTTCACGAAGGCAACCAAAGCATGATACCCACCATTCTTGGTT
* *
312135 CACTAAGATTGATACCCCAAGCCGACCACTGTGACGAGGTGCTTTTGGTGCATCGGTAAGCTATA
65 CACTGAGATTGATACCCCAAGCCGACCACTGTGACGAGGTGTTTTTGGTGCATCGGTAAGCTATA
*
312200 TAATAGAAGGATTTATCTTTTGTTTATGATGCTTAATCTTTCAAATAATGTAACTAATGAAATGG
130 TAATAGAAGGATTTATCTTTTGTTTATGATGCTTAATCTTTCAAATAATGTAAATAATGAAATGG
312265 ATTTTTGTCTATTTGTGTAATGTAATTAT-TCAGGATTAACCCACAATTTGATTGACCCACAATT
195 ATTTTTGTCTATTTGTGTAATGTAATT-TGTCAGGATTAACCCACAATTTGATTGACCCACAATT
**
312329 TATGGATTAATTAATAGAGGCTTTGAATGCTCATGACTTTTTTCATCCTTTGTTAAGTGCCAAAG
259 TACAGATTAATTAATAGAGGCTTTGAATGCTCATGACTTTTTTCATCCTTTGTTAAGTGCCAAAG
312394 GATGATGGATTTTACCTGATTTCATCCTCAATG
324 GATGATGGATTTTACCTGATTTCATCCTCAATG
* *
312427 TTTCTTGATTCACTCTATAGGAGTTCACGAAGGCAACCAAAGCATGATACCCACCATTCTTGGTT
1 TTTCTTGATTCAGTC-ATGGGAGTTCACGAAGGCAACCAAAGCATGATACCCACCATTCTTGGTT
* * * * * *
312492 CACTGAGATTGATACCCCAAGCCAACCATTGTTACGAGGTTTTTTTGGGTGCGTTGGTAAGCTAT
65 CACTGAGATTGATACCCCAAGCCGACCACTGTGACGAGGTGTTTTT-GGTGCATCGGTAAGCTAT
* * *
312557 ATAATGGAGGGATTTATCTTTTTTGTTTATGATGCTTAATCTTTCAAATAATTTAAATAATGAAA
129 ATAATAGAAGGATTTATC--TTTTGTTTATGATGCTTAATCTTTCAAATAATGTAAATAATGAAA
*
312622 TGGATTTTTGTCTATTTTTGTAATGTAA
192 TGGATTTTTGTCTATTTGTGTAATGTAA
312650 CTCCAATGTT
Statistics
Matches: 540, Mismatches: 34, Indels: 9
0.93 0.06 0.02
Matches are distributed among these distances:
356 5 0.01
357 432 0.80
358 33 0.06
360 70 0.13
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (356 bp):
TTTCTTGATTCAGTCATGGGAGTTCACGAAGGCAACCAAAGCATGATACCCACCATTCTTGGTTC
ACTGAGATTGATACCCCAAGCCGACCACTGTGACGAGGTGTTTTTGGTGCATCGGTAAGCTATAT
AATAGAAGGATTTATCTTTTGTTTATGATGCTTAATCTTTCAAATAATGTAAATAATGAAATGGA
TTTTTGTCTATTTGTGTAATGTAATTTGTCAGGATTAACCCACAATTTGATTGACCCACAATTTA
CAGATTAATTAATAGAGGCTTTGAATGCTCATGACTTTTTTCATCCTTTGTTAAGTGCCAAAGGA
TGATGGATTTTACCTGATTTCATCCTCAATG
Found at i:313411 original size:357 final size:368
Alignment explanation
Indices: 312751--313607 Score: 1414
Period size: 357 Copynumber: 2.3 Consensus size: 368
312741 AATTTGTCAG
*
312751 GATTAACCCACTATTTATGGATTGATTAATGGAGGTTTTGAATGCTCATGACTTTTTTCATCCTT
1 GATTGACCCACTATTTATGGATTGATTAATGGAGGTTTTGAATGCTCATGACTTTTTTCATCCTT
*
312816 TGTTAAGTGTCAAAGGATGATGGATTTTACCCTATTTCATCCTTAATGTTTTTTGATTCACGCCA
66 TGTTAAGTGTCAAAGGATGATGGATTTTACCCTATTTCATCCTTAATGTTTGTTGATTCACGCCA
*
312881 TGGGAGTTCACGAAGGCAACCAAAGCATGGTACCCACCATTCTTGGTTCACTGAGATTGATACCC
131 TGGGAGTTCACAAAGGCAACCAAAGCATGGTACCCACCATTCTTGGTTCACTGAGATTGATACCC
312946 CAAGCCGACCACTGTGACGAGGTGCTTTTGGTGCATCGATAAGCTATATAATGGAAGGATTTATC
196 CAAGCCGACCACTGTGACGAGGTGCTTTTGGTGCATCGATAAGCTATATAATGGAAGGATTTATC
313011 TTTTGTTTATGATGCTTAATCTTTCAAATAATGTAAATAATGAAATGGATTTTTGTCTA-TT-TG
261 TTTTGTTTATGATGCTTAATCTTTCAAATAATGTAAATAATGAAATGGATTTTTGTCTATTTGTG
313074 -TGT-A-A-T-G-T-A-ATTTG-TCAGGATTAACCCACCATTT
326 ATGTAATATTAGATCACATTTGATCAGGATTAACCCACCATTT
* *
313108 GATTGACCCACTATTTATGGATTGATTAATGGAGGTTTTGAATGTTCGTGACTTTTTTCATCCTT
1 GATTGACCCACTATTTATGGATTGATTAATGGAGGTTTTGAATGCTCATGACTTTTTTCATCCTT
* * * * *
313173 TGTTAAGAGCCAAAGAATGGTGGATTTTACCCTATTTCATCCTCAATGTTTGTTGATTCACGCCA
66 TGTTAAGTGTCAAAGGATGATGGATTTTACCCTATTTCATCCTTAATGTTTGTTGATTCACGCCA
*
313238 TGGGAGTTCACAAAGGCAACCAAAGCATGGTACCCACCGTTCTTGGTTCACTGAGATTGATACCC
131 TGGGAGTTCACAAAGGCAACCAAAGCATGGTACCCACCATTCTTGGTTCACTGAGATTGATACCC
313303 CAAGCCGACCACTGTGACGAGGTGCTTTTGGTGCATCTG-TAAGCTATATAATGGAAGGATTTAT
196 CAAGCCGACCACTGTGACGAGGTGCTTTTGGTGCATC-GATAAGCTATATAATGGAAGGATTTAT
313367 CTTTTGTTTATGATGCTTAATCTTTCAAATAATGTAAATAATGAAATGGATTTTTGTCTATTTGT
260 CTTTTGTTTATGATGCTTAATCTTTCAAATAATGTAAATAATGAAATGGATTTTTGTCTATTTGT
313432 GTAATGTAATTATTCAGGATTAACCCACCATTTGATTCAGGATTAACCCACCATTT
325 G--ATGTAA-TATT-A-GA-T----CA-CATTTGA-TCAGGATTAACCCACCATTT
313488 GATTGACCCACTATTTATGGATTGATTAATGGAGGTTTTGAATGCTCATGACTTTTTTCATCCTT
1 GATTGACCCACTATTTATGGATTGATTAATGGAGGTTTTGAATGCTCATGACTTTTTTCATCCTT
313553 TGTTAAGTGTCAAAGGATGATGGATTTTACCCTATTTCATCCTTAATGTTTGTTG
66 TGTTAAGTGTCAAAGGATGATGGATTTTACCCTATTTCATCCTTAATGTTTGTTG
313608 TGGAAGCTAC
Statistics
Matches: 458, Mismatches: 18, Indels: 25
0.91 0.04 0.05
Matches are distributed among these distances:
357 306 0.67
358 3 0.01
359 2 0.00
362 3 0.01
363 1 0.00
365 1 0.00
366 1 0.00
369 1 0.00
371 1 0.00
376 1 0.00
378 5 0.01
380 133 0.29
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (368 bp):
GATTGACCCACTATTTATGGATTGATTAATGGAGGTTTTGAATGCTCATGACTTTTTTCATCCTT
TGTTAAGTGTCAAAGGATGATGGATTTTACCCTATTTCATCCTTAATGTTTGTTGATTCACGCCA
TGGGAGTTCACAAAGGCAACCAAAGCATGGTACCCACCATTCTTGGTTCACTGAGATTGATACCC
CAAGCCGACCACTGTGACGAGGTGCTTTTGGTGCATCGATAAGCTATATAATGGAAGGATTTATC
TTTTGTTTATGATGCTTAATCTTTCAAATAATGTAAATAATGAAATGGATTTTTGTCTATTTGTG
ATGTAATATTAGATCACATTTGATCAGGATTAACCCACCATTT
Found at i:313473 original size:23 final size:23
Alignment explanation
Indices: 313443--313491 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
313433 TAATGTAATT
313443 ATTCAGGATTAACCCACCATTTG
1 ATTCAGGATTAACCCACCATTTG
313466 ATTCAGGATTAACCCACCATTTG
1 ATTCAGGATTAACCCACCATTTG
313489 ATT
1 ATT
313492 GACCCACTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (23 bp):
ATTCAGGATTAACCCACCATTTG
Found at i:313932 original size:50 final size:49
Alignment explanation
Indices: 313822--313919 Score: 171
Period size: 48 Copynumber: 2.0 Consensus size: 49
313812 TTACTGGGAA
313822 AATGGAGAAGAGAAGATGGTGAAAAAAAAATAGAAGGTAGAAGAGAAGAC
1 AATGGAGAAGAGAAGATGGTG-AAAAAAAATAGAAGGTAGAAGAGAAGAC
*
313872 AATGGAGAAGAGAAGATGGTG-AAAAGAATAGAAGGTAGAAGAGAAGAC
1 AATGGAGAAGAGAAGATGGTGAAAAAAAATAGAAGGTAGAAGAGAAGAC
313920 GGTGGAGAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 26 0.55
50 21 0.45
ACGTcount: A:0.54, C:0.02, G:0.34, T:0.10
Consensus pattern (49 bp):
AATGGAGAAGAGAAGATGGTGAAAAAAAATAGAAGGTAGAAGAGAAGAC
Found at i:314263 original size:13 final size:12
Alignment explanation
Indices: 314247--314292 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
314237 AACATTTATT
314247 TTTAATTTAATAA
1 TTTAATTTAA-AA
314260 TTTAA-TTAAAA
1 TTTAATTTAAAA
*
314271 TTTAAAATTAAAA
1 TTT-AATTTAAAA
314284 TTT-ATTTAA
1 TTTAATTTAA
314293 GTTATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 10 0.33
12 6 0.20
13 14 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTAATTTAAAA
Found at i:315673 original size:37 final size:37
Alignment explanation
Indices: 315623--315693 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
315613 ACTTGAATAA
315623 TTCAAAACATTTAACAATTGTTGAGTTAATTTTTAAG
1 TTCAAAACATTTAACAATTGTTGAGTTAATTTTTAAG
*
315660 TTCAAAATATTTAACAATTGTTGAGTTAATTTTT
1 TTCAAAACATTTAACAATTGTTGAGTTAATTTTT
315694 TGACTCATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (37 bp):
TTCAAAACATTTAACAATTGTTGAGTTAATTTTTAAG
Found at i:319418 original size:19 final size:20
Alignment explanation
Indices: 319396--319433 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
319386 TTCCCCTTGT
*
319396 TGCT-GCCTTTTTTGTCCTC
1 TGCTAGCCTTTTTAGTCCTC
*
319415 TGCTATCCTTTTTAGTCCT
1 TGCTAGCCTTTTTAGTCCT
319434 GCAATAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.05, C:0.29, G:0.13, T:0.53
Consensus pattern (20 bp):
TGCTAGCCTTTTTAGTCCTC
Found at i:330360 original size:20 final size:22
Alignment explanation
Indices: 330335--330374 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
330325 TGTTGTATAT
330335 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
330355 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
330375 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:330597 original size:21 final size:21
Alignment explanation
Indices: 330571--330620 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
330561 ACTAGTGGCA
*
330571 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAAG
330592 GGTGCATGGATGCACTGCAAG
1 GGTGCATGGATGCACTGCAAG
330613 GGTGCATG
1 GGTGCATG
330621 TATGTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.18, G:0.42, T:0.20
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAAG
Found at i:330880 original size:21 final size:21
Alignment explanation
Indices: 330851--330890 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
330841 ATGTTTAATG
330851 AAAAAGATA-CTAATTGTTAAC
1 AAAAAGATATC-AATTGTTAAC
*
330872 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
330891 CCGATTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:332079 original size:23 final size:24
Alignment explanation
Indices: 332034--332079 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
332024 TTTGGCTTTC
*
332034 AAAATCTATTTTTGTTTTCAAAAG
1 AAAATCTATTTTCGTTTTCAAAAG
332058 AAAATC-ATTTTCGATTTT-AAAA
1 AAAATCTATTTTCG-TTTTCAAAA
332080 TTTGAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (24 bp):
AAAATCTATTTTCGTTTTCAAAAG
Found at i:333443 original size:23 final size:21
Alignment explanation
Indices: 333390--333485 Score: 79
Period size: 21 Copynumber: 4.5 Consensus size: 21
333380 TCGAAATGGA
* * *
333390 GTGCATGAATGCACTACA-TG
1 GTGCATGGATGCACTGCAGAG
* **
333410 GTGCATCGATGCACTAGTTGCAG
1 GTGCATGGATGCACT-GCAG-AG
*
333433 GTGCATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGAG
*
333454 GTGCATGGATGCACTGTA-AGG
1 GTGCATGGATGCACTGCAGA-G
333475 GTGCATGGATG
1 GTGCATGGATG
333486 GACTTTGACA
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.22
21 30 0.50
22 2 0.03
23 15 0.25
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.24
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGAG
Found at i:333458 original size:21 final size:21
Alignment explanation
Indices: 333432--333485 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
333422 ACTAGTTGCA
*
333432 GGTGCATGGATGCACTGCAGG
1 GGTGCATGGATGCACTGCAAG
*
333453 GGTGCATGGATGCACTGTAAG
1 GGTGCATGGATGCACTGCAAG
333474 GGTGCATGGATG
1 GGTGCATGGATG
333486 GACTTTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.15, G:0.43, T:0.22
Consensus pattern (21 bp):
GGTGCATGGATGCACTGCAAG
Found at i:336085 original size:23 final size:23
Alignment explanation
Indices: 336049--336138 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 23
336039 GAACATATAC
*
336049 GTGGTCCTTAGGGACAATTTTAT
1 GTGGTCCTTCGGGACAATTTTAT
* *
336072 GTGG-CCATTCGGGACAATTCTAC
1 GTGGTCC-TTCGGGACAATTTTAT
*
336095 GTGGTCCTTCGGGAC-A-TATAT
1 GTGGTCCTTCGGGACAATTTTAT
336116 GTGGTCCTTCGGGACAATTTTAT
1 GTGGTCCTTCGGGACAATTTTAT
336139 ATGGCACTCA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
21 18 0.32
22 4 0.07
23 33 0.58
24 2 0.04
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (23 bp):
GTGGTCCTTCGGGACAATTTTAT
Found at i:336098 original size:46 final size:44
Alignment explanation
Indices: 336046--336134 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
336036 TTTGAACATA
*
336046 TACGTGGTCCTTAGGGACAATTTTATGTGG-CCATTCGGGACAATTC
1 TACGTGGTCCTTAGGGAC-A-TATATGTGGTCC-TTCGGGACAATTC
*
336092 TACGTGGTCCTTCGGGACATATATGTGGTCCTTCGGGACAATT
1 TACGTGGTCCTTAGGGACATATATGTGGTCCTTCGGGACAATT
336135 TTATATGGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 20 0.50
45 3 0.08
46 17 0.43
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (44 bp):
TACGTGGTCCTTAGGGACATATATGTGGTCCTTCGGGACAATTC
Found at i:336121 original size:21 final size:21
Alignment explanation
Indices: 335967--336131 Score: 125
Period size: 21 Copynumber: 7.7 Consensus size: 21
335957 GGTTCTACTC
*
335967 GGTCATTCGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
* * * *
335988 GATCCTTTGGAACATATATGA
1 GGTCCTTCGGGACATATATGT
* * *
336009 GGTCCTTCGAGATATATATTT
1 GGTCCTTCGGGACATATATGT
* ** * *
336030 GGTCTTTTTGAACATATACGT
1 GGTCCTTCGGGACATATATGT
* *
336051 GGTCCTTAGGGACAATTTTATGT
1 GGTCCTTCGGGAC-A-TATATGT
* *
336074 GG-CCATTCGGGACAATTCTACGT
1 GGTCC-TTCGGGAC-A-TATATGT
336097 GGTCCTTCGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
336118 GGTCCTTCGGGACA
1 GGTCCTTCGGGACA
336132 ATTTTATATG
Statistics
Matches: 109, Mismatches: 31, Indels: 8
0.74 0.21 0.05
Matches are distributed among these distances:
21 71 0.65
22 4 0.04
23 32 0.29
24 2 0.02
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (21 bp):
GGTCCTTCGGGACATATATGT
Found at i:338397 original size:21 final size:21
Alignment explanation
Indices: 338373--338427 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
338363 CGATTTTCCC
*
338373 AATTCGCAATGCGAATAAGTA
1 AATTCGCAATGCGAATAAGGA
* **
338394 AATT-GCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGGA
*
338414 AAATCGCAATGCGA
1 AATTCGCAATGCGA
338428 TACTGACTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (21 bp):
AATTCGCAATGCGAATAAGGA
Found at i:338441 original size:20 final size:20
Alignment explanation
Indices: 338416--338529 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
338406 AATTGGGAAA
338416 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
338436 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
338456 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
338477 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
338497 TTCGCAATGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
338517 TTCGCAACGCGAT
1 ATCGCAATGCGAT
338530 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.78
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:338478 original size:61 final size:61
Alignment explanation
Indices: 338413--338529 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
338403 GCGAATTGGG
* * * *
338413 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
* * *
338474 AAAATCGCAACGAGATACTGACTTTCGCAATGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACTATCGCAACGCGAT
338530 TTACATAGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAATGCGATACTGACTATCGCAACGCGATAATAC
Found at i:339085 original size:19 final size:19
Alignment explanation
Indices: 339047--339113 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
339037 TTCGAGAATG
339047 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
339067 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
339086 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
339105 AAAATCGCA
1 AAAATCGCA
339114 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:339155 original size:20 final size:19
Alignment explanation
Indices: 339109--339274 Score: 109
Period size: 20 Copynumber: 9.1 Consensus size: 19
339099 GAAACCAAAA
*
339109 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
339128 TCGCGTTGCGATTTTTAAT
1 TCGCGTTGCGATTTTCATT
*
339147 TCGCGGTTGCAATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
339167 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
339183 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
339200 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * **
339214 TCTCATTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
339233 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
339253 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
339273 TC
1 TC
339275 AACCAAAAGA
Statistics
Matches: 113, Mismatches: 21, Indels: 26
0.71 0.13 0.16
Matches are distributed among these distances:
14 19 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 39 0.35
20 46 0.41
21 1 0.01
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:339244 original size:34 final size:33
Alignment explanation
Indices: 339162--339249 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
339152 GTTGCAATTT
* **
339162 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
*
339195 TCATTTCGCGTTGCGATTCTCTCATTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
339228 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
339250 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCATCGCGATAG
Found at i:342751 original size:14 final size:14
Alignment explanation
Indices: 342732--342767 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
342722 ATTGTTTAAT
342732 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
342746 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
342760 TGATTTGT
1 TGATTTGT
342768 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:342968 original size:19 final size:19
Alignment explanation
Indices: 342946--343096 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
342936 CGAAATTAAA
342946 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
342965 TTCGCATTACGA--TTCA-
1 TTCGCGTTGCGATTTTCAT
*
342981 --CTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
342998 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
343012 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
343031 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
343046 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
343064 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
343083 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
343097 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 27 0.28
16 7 0.07
17 7 0.07
19 44 0.46
20 10 0.11
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:342992 original size:33 final size:33
Alignment explanation
Indices: 342950--343076 Score: 195
Period size: 33 Copynumber: 3.8 Consensus size: 33
342940 ATTAAATTCG
*
342950 CGTTGCGATTTTCATTTCGCATTACGATTCACT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
*
342983 CGTTGCGATTTTCATTTCGCATTGCGAAATT-A-G
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCACT
*
343016 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
343049 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
343077 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 79 0.92
34 1 0.01
35 3 0.03
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:343044 original size:66 final size:66
Alignment explanation
Indices: 342943--343075 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
342933 ACGCGAAATT
*
342943 AAATTCGCGTTGCGATTTTCATTTCGCATTACGATTCACTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCACTCGTTGCGATTTTCATTTCGCATTGC
343008 G
66 G
* *
343009 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCACTCGTTGCGATTTTCATTTCGCATTGC
343074 G
66 G
343075 A
1 A
343076 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.18, C:0.22, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTACGATTCACTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:345386 original size:12 final size:12
Alignment explanation
Indices: 345369--345393 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
345359 TCTTCGGGGA
345369 CTTTTTCTTCTT
1 CTTTTTCTTCTT
345381 CTTTTTCTTCTT
1 CTTTTTCTTCTT
345393 C
1 C
345394 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:345607 original size:24 final size:24
Alignment explanation
Indices: 345580--345626 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
345570 CAAAATCCGT
*
345580 GTATTGACCAATATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
345604 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
345627 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:345635 original size:24 final size:24
Alignment explanation
Indices: 345584--345635 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
345574 ATCCGTGTAT
* ** *
345584 TGACCAATATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
345608 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
345632 TGAC
1 TGAC
345636 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:346570 original size:20 final size:20
Alignment explanation
Indices: 346545--346602 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
346535 AATCATTTGA
*
346545 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
346565 CTATCGCAACAAGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
346585 TTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
346603 CGCAATGCGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:346645 original size:14 final size:16
Alignment explanation
Indices: 346625--346698 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
346615 TGAAAATCGC
346625 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
346640 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
346657 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
346676 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
346692 -TTGCGAT
1 ATTGCGAT
346699 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:346662 original size:19 final size:19
Alignment explanation
Indices: 346621--346688 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
346611 GAAATGAAAA
346621 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
346637 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
346654 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
346673 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
346689 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:346824 original size:14 final size:14
Alignment explanation
Indices: 346805--346841 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
346795 CATCAATTAA
346805 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
346819 ACAAATCATCTTTT
1 ACAAATCAACATTT
346833 ACAAATCAA
1 ACAAATCAA
346842 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:348747 original size:20 final size:19
Alignment explanation
Indices: 348712--348778 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
348702 GAAACTTAAA
348712 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
348731 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
348751 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
348770 ATCGCAACG
1 ATCGCAACG
348779 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:348786 original size:14 final size:14
Alignment explanation
Indices: 348767--348824 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
348757 ATGCGAAATG
348767 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
348781 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
348797 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
348813 AAAATCGCAACG
1 AAAATCGCAACG
348825 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:348809 original size:32 final size:33
Alignment explanation
Indices: 348751--348829 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
348741 GGAAATGGCT
*
348751 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
348784 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
348816 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
348830 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:348877 original size:14 final size:14
Alignment explanation
Indices: 348858--348915 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
348848 TTTCATTTCG
348858 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
348872 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
348888 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
348904 CGTTGCGATTTT
1 CGTTGCGATTTT
348916 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:348926 original size:33 final size:33
Alignment explanation
Indices: 348841--348931 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
348831 ACAAATCGCA
*
348841 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
348874 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
348906 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
348932 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:348939 original size:19 final size:20
Alignment explanation
Indices: 348917--348959 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
348907 TGCGATTTTT
348917 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
348936 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
348956 ATTT
1 ATTT
348960 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:348950 original size:20 final size:20
Alignment explanation
Indices: 348925--348970 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
348915 TTATTTCGCA
348925 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
348945 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
348965 TTGCGA
1 TTGCGA
348971 AAGCAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:349478 original size:18 final size:18
Alignment explanation
Indices: 349452--349496 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
349442 GTCGATCAGA
*
349452 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
349470 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
349488 TGATGGCTC
1 TGATGGCTC
349497 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:350841 original size:20 final size:20
Alignment explanation
Indices: 350816--350853 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
350806 AATAGTTTCT
350816 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
350836 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
350854 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:351144 original size:22 final size:22
Alignment explanation
Indices: 351117--351160 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
351107 GATGGAGATA
351117 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
351139 GACGGATTTTGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
351161 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:351373 original size:20 final size:20
Alignment explanation
Indices: 351348--351441 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
351338 GATTATGTAT
351348 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
351368 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
351388 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
351409 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
351429 TATCGCATTGCGA
1 TATCGCGTTGCGA
351442 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:351442 original size:20 final size:20
Alignment explanation
Indices: 351328--351442 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
351318 CGCTTTGAAA
*
351328 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
351349 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
351369 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
351389 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
351410 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
351430 ATCGCATTGCGAT
1 ATCGCATTGCGAT
351443 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:351460 original size:21 final size:21
Alignment explanation
Indices: 351431--351523 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
351421 ATAGTCAGTA
351431 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
351452 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
351472 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
351493 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
351513 TCGCATTGCGA
1 TCGCATTGCGA
351524 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:351461 original size:41 final size:41
Alignment explanation
Indices: 351370--351504 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
351360 AAAGTCAGTA
* * * ** *
351370 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
351410 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
351452 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
351493 TCGCGTTGCGAT
1 TCGCGTTGCGAT
351505 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:351505 original size:41 final size:41
Alignment explanation
Indices: 351431--351523 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
351421 ATAGTCAGTA
351431 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
351472 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
351513 TCGCATTGCGA
1 TCGCATTGCGA
351524 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:354878 original size:2 final size:2
Alignment explanation
Indices: 354873--354904 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
354863 TCAAAAAATA
354873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
354905 GAAAAACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:355991 original size:3 final size:3
Alignment explanation
Indices: 355985--356048 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
355975 AACAATAATA
355985 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
356033 TGT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
356049 TTACACACTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:363792 original size:19 final size:19
Alignment explanation
Indices: 363768--363818 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
363758 AAATGACCAA
* *
363768 CAAATTTGCAACGTGATCT
1 CAAATTTGCAACGCGAACT
*
363787 CAAATTCGCAACGCGAACT
1 CAAATTTGCAACGCGAACT
*
363806 CCAATTTCGCAAC
1 CAAATTT-GCAAC
363819 CCAGTTTTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (19 bp):
CAAATTTGCAACGCGAACT
Found at i:363816 original size:20 final size:19
Alignment explanation
Indices: 363770--363818 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
363760 ATGACCAACA
* *
363770 AATTT-GCAACGTGATCTC
1 AATTTCGCAACGCGAACTC
*
363788 AAATTCGCAACGCGAACTCC
1 AATTTCGCAACGCGAACT-C
363808 AATTTCGCAAC
1 AATTTCGCAAC
363819 CCAGTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 4 0.16
19 10 0.40
20 11 0.44
ACGTcount: A:0.33, C:0.29, G:0.14, T:0.24
Consensus pattern (19 bp):
AATTTCGCAACGCGAACTC
Found at i:363916 original size:60 final size:59
Alignment explanation
Indices: 363852--364042 Score: 219
Period size: 60 Copynumber: 3.2 Consensus size: 59
363842 AATCTGTAAA
*
363852 TCGCAACGCGAATTTGTAAATCGCAACACAGAAGTCAAATTCGCAACATAGAAGTCAAAT
1 TCGCAACGCGAATTTGTAAATCGCAACAC-GAAGTCAAATTCGCAACACAGAAGTCAAAT
* * *
363912 TCGCAACGCG-A-TAGTCAAATTCGCAACACTGAAGTCAAATCCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATTTGT-AAA-TCGCAACAC-GAAGTCAAATTCGCAACACAGAAGTCAAAT
* * *
363972 TCGCAACGCGAATCTGTAAATCGCAACGCGAATTTGT-AAA-TCGTAACACAGAAGTCAAAT
1 TCGCAACGCGAATTTGTAAATCGCAACACGAA---GTCAAATTCGCAACACAGAAGTCAAAT
*
364032 TTGCAACGCGA
1 TCGCAACGCGA
364043 TAGTCAAATT
Statistics
Matches: 112, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
58 3 0.03
59 7 0.06
60 91 0.81
61 7 0.06
62 4 0.04
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (59 bp):
TCGCAACGCGAATTTGTAAATCGCAACACGAAGTCAAATTCGCAACACAGAAGTCAAAT
Found at i:364056 original size:60 final size:60
Alignment explanation
Indices: 363872--364120 Score: 233
Period size: 60 Copynumber: 4.2 Consensus size: 60
363862 AATTTGTAAA
* * *
363872 TCGCAACACAGAAGTCAAATTCGCAACATAGAAGTCAAATTCGCAACGCGATAGTCAAAT
1 TCGCAACACTGAAGTCAAATCCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
* *
363932 TCGCAACACTGAAGTCAAATCCGCAACACAAAAGTCAAATTCGCAACGCGAATCTGT-AAA-
1 TCGCAACACTGAAGTCAAATCCGCAACACAGAAGTCAAATTCGCAACGCG-AT-AGTCAAAT
* * *
363992 TCGCAACGC-GAATTTGT-AAAT-CGTAACACAGAAGTCAAATTTGCAACGCGATAGTCAAAT
1 TCGCAACACTGAA---GTCAAATCCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
* * * * * * * **
364052 TCGCAATACTGAATTTCAAATTCGC-A-ACTGAATTTTAAATTCGCAACTCGATTTTCAAAT
1 TCGCAACACTGAA-GTCAAATCCGCAACACAGAA-GTCAAATTCGCAACGCGATAGTCAAAT
364112 TCGCAACAC
1 TCGCAACAC
364121 GAATTTAATT
Statistics
Matches: 156, Mismatches: 22, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
58 2 0.01
59 15 0.10
60 121 0.78
61 14 0.09
62 4 0.03
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.23
Consensus pattern (60 bp):
TCGCAACACTGAAGTCAAATCCGCAACACAGAAGTCAAATTCGCAACGCGATAGTCAAAT
Found at i:364083 original size:19 final size:19
Alignment explanation
Indices: 364046--364137 Score: 105
Period size: 19 Copynumber: 4.7 Consensus size: 19
364036 AACGCGATAG
364046 TCAAATTCGCAATACTGAATT
1 TCAAATTCGC-A-ACTGAATT
364067 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
* *
364086 TTAAATTCGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
*
364106 TCAAATTCGCAACACGAATT
1 TCAAATTCGCAAC-TGAATT
*
364126 T-AATTTCGCAAC
1 TCAAATTCGCAAC
364138 AGGTTTTAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
19 31 0.49
20 22 0.35
21 10 0.16
ACGTcount: A:0.36, C:0.22, G:0.10, T:0.33
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:364138 original size:19 final size:20
Alignment explanation
Indices: 363786--364138 Score: 178
Period size: 20 Copynumber: 17.7 Consensus size: 20
363776 CAACGTGATC
* *
363786 TCAAATTCGCAACGCGAACT
1 TCAAATTCGCAACACGAATT
* * * *
363806 CCAATTTCGCAAC-CCAGTTT
1 TCAAATTCGCAACACGA-ATT
*
363826 TCAAATTCGCAACTCGAATCT
1 TCAAATTCGCAACACGAAT-T
*
363847 GT-AAA-TCGCAACGCGAATT
1 -TCAAATTCGCAACACGAATT
* *
363866 TGTAAA-TCGCAACACAGAA-G
1 T-CAAATTCGCAACAC-GAATT
* *
363886 TCAAATTCGCAACATAGAA-G
1 TCAAATTCGCAACA-CGAATT
* *
363906 TCAAATTCGCAACGCG-ATAG
1 TCAAATTCGCAACACGAAT-T
*
363926 TCAAATTCGCAACACTGAA-G
1 TCAAATTCGCAACAC-GAATT
* * **
363946 TCAAATCCGCAACACAAAAG
1 TCAAATTCGCAACACGAATT
*
363966 TCAAATTCGCAACGCGAATCT
1 TCAAATTCGCAACACGAAT-T
*
363987 GT-AAA-TCGCAACGCGAATT
1 -TCAAATTCGCAACACGAATT
* * *
364006 TGTAAA-TCGTAACACAGAA-G
1 T-CAAATTCGCAACAC-GAATT
* * *
364026 TCAAATTTGCAACGCG-ATAG
1 TCAAATTCGCAACACGAAT-T
*
364046 TCAAATTCGCAATACTGAATT
1 TCAAATTCGCAACAC-GAATT
*
364067 TCAAATTCGCAAC-TGAATT
1 TCAAATTCGCAACACGAATT
* * *
364086 TTAAATTCGCAACTCGATTT
1 TCAAATTCGCAACACGAATT
364106 TCAAATTCGCAACACGAATT
1 TCAAATTCGCAACACGAATT
*
364126 T-AATTTCGCAACA
1 TCAAATTCGCAACA
364139 GGTTTTAGTT
Statistics
Matches: 264, Mismatches: 44, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
18 4 0.02
19 42 0.16
20 184 0.70
21 29 0.11
22 5 0.02
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (20 bp):
TCAAATTCGCAACACGAATT
Found at i:364938 original size:12 final size:12
Alignment explanation
Indices: 364917--364950 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
364907 ACCACATTTC
*
364917 CAATACCAAACA
1 CAATATCAAACA
364929 CAATATCAAACA
1 CAATATCAAACA
*
364941 CAATCTCAAA
1 CAATATCAAA
364951 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:365127 original size:24 final size:24
Alignment explanation
Indices: 365076--365129 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
365066 GTATTCGAAA
*
365076 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCAGAC
* * *
365100 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATATTGGTCAATACCCAGAC
365124 TTTGAT
1 TTTGAT
365130 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCAGAC
Found at i:369251 original size:21 final size:21
Alignment explanation
Indices: 369222--369293 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
369212 GTGAATCGGG
369222 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGGTGGGAGGGAC
* ** *
369243 C-CATTGAACGATGACAGGGGC
1 CTC-TTGAACGGTGGGAGGGAC
*
369264 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGGTGGGAGGGAC
369285 CTCTTGAAC
1 CTCTTGAAC
369294 AATGAGATGA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.38, T:0.19
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGAC
Done.