Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000475.1 Hibiscus syriacus cultivar Beakdansim tig00000884_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: 86751
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1844 original size:20 final size:21
Alignment explanation
Indices: 1792--1847 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1782 GCACCTTCAT
1792 GGTGTATCGATGCACATTTAA
1 GGTGTATCGATGCACATTTAA
* *
1813 GAATGCATCGATGCAC-TGTT-A
1 G-GTGTATCGATGCACAT-TTAA
1834 GGTGTATCGATGCA
1 GGTGTATCGATGCA
1848 TGAAGCACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 11 0.38
21 4 0.14
22 14 0.48
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (21 bp):
GGTGTATCGATGCACATTTAA
Found at i:5426 original size:2 final size:2
Alignment explanation
Indices: 5419--5455 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5409 GATATAACAT
*
5419 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5456 CACACATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5816 original size:30 final size:30
Alignment explanation
Indices: 5757--5852 Score: 140
Period size: 30 Copynumber: 3.2 Consensus size: 30
5747 CCCGAAGGAC
* * *
5757 CTATCTAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
5786 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
5816 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
5846 CTGTCCA
1 CTATCCA
5853 TAAGGACTAC
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 18 0.29
30 44 0.71
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:6297 original size:15 final size:15
Alignment explanation
Indices: 6273--6307 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
6263 AACCATATAA
* *
6273 CTTATTATCACATAT
1 CTTATAATCACATAC
6288 CTTATAATCACATAC
1 CTTATAATCACATAC
6303 CTTAT
1 CTTAT
6308 TTCAATTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
CTTATAATCACATAC
Found at i:8293 original size:20 final size:21
Alignment explanation
Indices: 8254--8294 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8244 GAGTTTATTT
8254 TCATTTTTCAATTTTGAAAAA
1 TCATTTTTCAATTTTGAAAAA
8275 TCATTTTT-ATATTTT-AAAAA
1 TCATTTTTCA-ATTTTGAAAAA
8295 CAATTTCTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAAAA
Found at i:10273 original size:64 final size:63
Alignment explanation
Indices: 10205--10414 Score: 201
Period size: 65 Copynumber: 3.3 Consensus size: 63
10195 TGCACTAAGA
* * * *
10205 GTGCATCGATGCATCAAGTGTATTTGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
* **
10269 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
10333 T
63 G
* * ** *
10334 GTGCATCGATGCATGAAATGGATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG--
10397 TG
62 TG
*
10399 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
10415 CTCTGAAAAA
Statistics
Matches: 119, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 45 0.38
65 65 0.55
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:11966 original size:15 final size:16
Alignment explanation
Indices: 11941--11970 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11931 AATTGACATT
11941 TTTACACAAAAATCAC
1 TTTACACAAAAATCAC
11957 TTTA-ACAAAAATCA
1 TTTACACAAAAATCA
11971 ATTACATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.20, G:0.00, T:0.27
Consensus pattern (16 bp):
TTTACACAAAAATCAC
Found at i:12465 original size:3 final size:3
Alignment explanation
Indices: 12457--12492 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
12447 CGAGTAAAGT
*
12457 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AAA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
12493 CGAGACCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:19475 original size:24 final size:24
Alignment explanation
Indices: 19425--19475 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
19415 CCGAAGCATT
* * *
19425 TGAAGATGCTCACCAGCCAGCCAA
1 TGAAGAGGCTCACCAACCAACCAA
* *
19449 TGAAGAGGTTCACCAACCAACCGA
1 TGAAGAGGCTCACCAACCAACCAA
19473 TGA
1 TGA
19476 GGAAAAACCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.14
Consensus pattern (24 bp):
TGAAGAGGCTCACCAACCAACCAA
Found at i:24311 original size:725 final size:725
Alignment explanation
Indices: 22268--24445 Score: 3674
Period size: 726 Copynumber: 3.0 Consensus size: 725
22258 GACATTTACA
* * * *
22268 TCCAATTTGTCACAACATATCTATTTGCTACCATATTACCATCATTCCATTTCCACAACAACTAT
1 TCCAATTTGCCACAACATATCCATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCAT
* * *
22333 CTCATCTTGCTACATCATTATCATTTGTACATACTATTAGTAACTTTACTTAGGTGACAGAATAA
66 CTCATCTTGCTACATCATTATCATTTGTACATACCATAAGTAACTTTACTTAGGTGACAGAGTAA
22398 AGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCCTGTGGAGGCGATACTCACTTATCATTGT
131 AGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCCTGTGGAGGCGATACTCACTTATCATTGT
22463 ATTACTTATTCGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCGC
196 ATTACTTATTCGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCGC
22528 GGACACCTACCATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAAGC
261 GGACACCTACCATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAAGC
** * *
22593 GAGTGTTGTGTTAGCCATCCCTGTACAGCGACAACAAACCCTCGATAGTCAGGTTTCAAACCATG
326 GAGTGTTGTGTCGGCCATCCCTGTACAGCGACAACAAACCCTCGATAGTCGGGTCTCAAACCAT-
* *
22658 GACAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGCTGTCGGATCTAATTATGAAATTTTGT
390 GACAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGCTGTCGGATCTAATTCTGAAATTTTGC
*
22723 GGCATATCACCTTCACCTTGTGAAAGTATTGGGCAACCGCCATGTCGCATTGCGCCATTGATAGA
455 GGCATATCACCTTCACCTTGTGAAAGTATTGGGCAACCCCCATGTCGCATTGCGCCATTGATAGA
* * *
22788 AGTTCATTCTCGATAAGTTGCAATTGTGTATTTTTCCTCTTTGAAAAGAGTGTAGCAAAGGTGTC
520 AGTTCATTCTCGAGAAGTTGCAATTGTGTATTGTTCCTCTTCGAAAAGAGTGTAGCAAAGGTGTC
*
22853 TCATGATTCCTTCAGTGATTTAGCATCCCGAATATGCTCCAACATTTCTTCTTCTATTGTGGTCT
585 TCATGCTTCCTTCAGTGATTTAGCATCCCGAATATGCTCCAACATTTCTTCTTCTATTGTGGTCT
* *
22918 TTAAAGCAAACATTGCTTTGACTACCTTAATTTTCCACTTTCACAAGACACCGTTAGCATTTTCT
650 TTAAAGCAAACATTGCTTTGCCTACTTTAATTTTCCACTTTCACAAGACACCGTTAGCATTTTCT
* *
22983 GCTGCCGGTTA
715 GTTGCCGGTTG
* *
22994 TCCAATTTGCCATAACATATCCATTTGCTACCATATTACCATCATTTCATTTCCACAACATCCAT
1 TCCAATTTGCCACAACATATCCATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCAT
23059 CTCATCTTGCTACATCATTATCATTTGTACATACCATAAGTAACTTTACTTAGGTGACAGAGTAA
66 CTCATCTTGCTACATCATTATCATTTGTACATACCATAAGTAACTTTACTTAGGTGACAGAGTAA
23124 AGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCCTGTGGAGGCGATACTCACTTATCATTGT
131 AGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCCTGTGGAGGCGATACTCACTTATCATTGT
* * *
23189 ATTACTTATTTGATTGTGTATACTTGCACATATCTCTGCACCCATATATAGTACTAACACAGCAC
196 ATTACTTATTCGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCGC
* * * *
23254 GGACACCTACCATTTGCTTTGTCATGGCTTTTTAACCTGTAAGCATATTTTCGAACTCAACAAGC
261 GGACACCTACCATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAAGC
* *
23319 GAGTGTTGTGTCGGCCATCTCTGTACAGCGGCAACAAACCCTCGATAGTCGGGTCTCAAACCATG
326 GAGTGTTGTGTCGGCCATCCCTGTACAGCGACAACAAACCCTCGATAGTCGGGTCTCAAACCATG
*
23384 AACAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGCTGTCGGATCTAATTCTGAAATTTCGC
391 -ACAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGCTGTCGGATCTAATTCTGAAATTTTGC
* **
23449 GGCATATCACCTTCACCTTGTGAAAGTATTGGACAACATCCATGTCGCATTGCGCCATTGATAGA
455 GGCATATCACCTTCACCTTGTGAAAGTATTGGGCAACCCCCATGTCGCATTGCGCCATTGATAGA
* *
23514 AGTTCATTCTCAAGAAGTTGCAATTGTGTATTGTTCCTCTTCGAAAAGAGTGTAGCAAATGTGTC
520 AGTTCATTCTCGAGAAGTTGCAATTGTGTATTGTTCCTCTTCGAAAAGAGTGTAGCAAAGGTGTC
* *
23579 TCATGCTTTCTTCAGAGATTTAGCATCCCGAATATGCTCCAACATTTCTTCTTCTATTGTGGTCT
585 TCATGCTTCCTTCAGTGATTTAGCATCCCGAATATGCTCCAACATTTCTTCTTCTATTGTGGTCT
* * *
23644 TTAAAGCAAACATTGCTTTGCCTACTTTAATTTTCCACTTTCGCAAGACACTGTTAGCATTTTTT
650 TTAAAGCAAACATTGCTTTGCCTACTTTAATTTTCCACTTTCACAAGACACCGTTAGCATTTTCT
23709 GTTGCCGGTTG
715 GTTGCCGGTTG
*
23720 TCCAATTTGCCACAATATATCCATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCAT
1 TCCAATTTGCCACAACATATCCATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCAT
* * *
23785 CTCATCTTGCCACATCATTACCATTTGTACATACCATCAGTAACTTTACTTAGGTGACAGAGTAA
66 CTCATCTTGCTACATCATTATCATTTGTACATACCATAAGTAACTTTACTTAGGTGACAGAGTAA
* *
23850 AGTGCTTTGATCGAACTTATCAATTTCCTCCAATCCCTGTGGAGGCAATACTCACTTATCATTGT
131 AGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCCTGTGGAGGCGATACTCACTTATCATTGT
* *
23915 ATTACTT-TTCGATTGTGTATACTTGCACATATTTCCGCACCCATATATAGTACTCACACAGCGC
196 ATTACTTATTCGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCGC
* **
23979 GGACACCTACAATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAATT
261 GGACACCTACCATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAAGC
* * * *
24044 GAGTATTGTGTCGGTCATCCCTGTACAGTGACAACAAATCCTCGATAGTCGGGTCTCAAACCATA
326 GAGTGTTGTGTCGGCCATCCCTGTACAGCGACAACAAACCCTCGATAGTCGGGTCTCAAACCAT-
* *
24109 GACAATTATTCTTTTTATCCTAGCTTCCCCAATAGCAGCTGTCGGAACTAATTCTGAAATTTTGC
390 GACAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGCTGTCGGATCTAATTCTGAAATTTTGC
* * *
24174 GGCATATCGCCTTCACCTTGTAAAAGTATTGGGCAACCCCCATGTCACATTGCGCCATTGATAGA
455 GGCATATCACCTTCACCTTGTGAAAGTATTGGGCAACCCCCATGTCGCATTGCGCCATTGATAGA
* * * *
24239 AGTTCATTCTCGAGAAGTTACAATTTTGTATCGTTCCTCTTCGAAAAGAGTGTAGCGAAGGTGTC
520 AGTTCATTCTCGAGAAGTTGCAATTGTGTATTGTTCCTCTTCGAAAAGAGTGTAGCAAAGGTGTC
*
24304 CCATGCTTCCTTCAGTGATTTAGCATCCCGAATATGCTCCAACATTTCTTCTTCTATTGTGGTCT
585 TCATGCTTCCTTCAGTGATTTAGCATCCCGAATATGCTCCAACATTTCTTCTTCTATTGTGGTCT
* * *
24369 TTAAAGCAAACATTGCTTTGCCTATTTTAATTTTCCACTTTCACAAGACACCGTTAGCATCTTCC
650 TTAAAGCAAACATTGCTTTGCCTACTTTAATTTTCCACTTTCACAAGACACCGTTAGCATTTTCT
24434 GTTGCCGGTTG
715 GTTGCCGGTTG
24445 T
1 T
24446 GTAACTTCAC
Statistics
Matches: 1357, Mismatches: 93, Indels: 5
0.93 0.06 0.00
Matches are distributed among these distances:
725 481 0.35
726 876 0.65
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Consensus pattern (725 bp):
TCCAATTTGCCACAACATATCCATTTGCTACCATATTACCATCATTCCATTTCCACAACATCCAT
CTCATCTTGCTACATCATTATCATTTGTACATACCATAAGTAACTTTACTTAGGTGACAGAGTAA
AGTGTTTTGATCGAACTTATCAATTTCCTCCAATCCCTGTGGAGGCGATACTCACTTATCATTGT
ATTACTTATTCGATTGTGTATACTTGCACATATTTCTGCACCCATATATAGTACTAACACAGCGC
GGACACCTACCATTTGCTTGGCCATGGCTTTTTGACCTGTAAGCAAATTTTCGAACTCAACAAGC
GAGTGTTGTGTCGGCCATCCCTGTACAGCGACAACAAACCCTCGATAGTCGGGTCTCAAACCATG
ACAATTATTCTTTTTATCCTGGCTTCCCCAATAGCAGCTGTCGGATCTAATTCTGAAATTTTGCG
GCATATCACCTTCACCTTGTGAAAGTATTGGGCAACCCCCATGTCGCATTGCGCCATTGATAGAA
GTTCATTCTCGAGAAGTTGCAATTGTGTATTGTTCCTCTTCGAAAAGAGTGTAGCAAAGGTGTCT
CATGCTTCCTTCAGTGATTTAGCATCCCGAATATGCTCCAACATTTCTTCTTCTATTGTGGTCTT
TAAAGCAAACATTGCTTTGCCTACTTTAATTTTCCACTTTCACAAGACACCGTTAGCATTTTCTG
TTGCCGGTTG
Found at i:25068 original size:76 final size:77
Alignment explanation
Indices: 24941--25093 Score: 290
Period size: 76 Copynumber: 2.0 Consensus size: 77
24931 TCTAAACCAC
24941 TCATTAAAATAACCACAAAAATAATTTAAACCATTGAAATTAAAAATGAGAAAAATATCTAATTT
1 TCATTAAAATAACCACAAAAATAATTTAAACCATTGAAATTAAAAATGAGAAAAATATCTAATTT
25006 TTACCTAACTAA
66 TTACCTAACTAA
*
25018 TCATTAAAATAACCA-TAAAATAATTTAAACCATTGAAATTAAAAATGAGAAAAATATCTAATTT
1 TCATTAAAATAACCACAAAAATAATTTAAACCATTGAAATTAAAAATGAGAAAAATATCTAATTT
25082 TTACCTAACTAA
66 TTACCTAACTAA
25094 ATTAATGTAA
Statistics
Matches: 75, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
76 60 0.80
77 15 0.20
ACGTcount: A:0.53, C:0.12, G:0.04, T:0.31
Consensus pattern (77 bp):
TCATTAAAATAACCACAAAAATAATTTAAACCATTGAAATTAAAAATGAGAAAAATATCTAATTT
TTACCTAACTAA
Found at i:25080 original size:38 final size:38
Alignment explanation
Indices: 24962--25081 Score: 106
Period size: 38 Copynumber: 3.2 Consensus size: 38
24952 ACCACAAAAA
24962 TAATTTAAACCATTGAAATTAAAAATGAGAAAAATATC
1 TAATTTAAACCATTGAAATTAAAAATGAGAAAAATATC
** * * * *
25000 TAATTTTTACCTAACT-AATCATT-AAAATAACCATAAA-A--
1 TAATTTAAACC--ATTGAA--ATTAAAAATGA-GAAAAATATC
25038 TAATTTAAACCATTGAAATTAAAAATGAGAAAAATATC
1 TAATTTAAACCATTGAAATTAAAAATGAGAAAAATATC
25076 TAATTT
1 TAATTT
25082 TTACCTAACT
Statistics
Matches: 60, Mismatches: 12, Indels: 20
0.65 0.13 0.22
Matches are distributed among these distances:
35 7 0.12
36 9 0.15
37 2 0.03
38 24 0.40
39 2 0.03
40 9 0.15
41 7 0.12
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (38 bp):
TAATTTAAACCATTGAAATTAAAAATGAGAAAAATATC
Found at i:26058 original size:34 final size:34
Alignment explanation
Indices: 26019--26121 Score: 197
Period size: 34 Copynumber: 3.0 Consensus size: 34
26009 AAAAATTATC
*
26019 AGATTGTGTCACGTGTCACTTAACGGAGGAAATT
1 AGATTGTGTCACGTGTCACTTAACAGAGGAAATT
26053 AGATTGTGTCACGTGTCACTTAACAGAGGAAATT
1 AGATTGTGTCACGTGTCACTTAACAGAGGAAATT
26087 AGATTGTGTCACGTGTCACTTAACAGAGGAAATT
1 AGATTGTGTCACGTGTCACTTAACAGAGGAAATT
26121 A
1 A
26122 TCGCCTTTGA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 68 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (34 bp):
AGATTGTGTCACGTGTCACTTAACAGAGGAAATT
Found at i:26645 original size:88 final size:89
Alignment explanation
Indices: 26471--26652 Score: 321
Period size: 89 Copynumber: 2.1 Consensus size: 89
26461 ACTCGTCACG
*
26471 TCGAAGTGACGAGTTCCAATAAAAAATATTTTTTTATTCTAAATTTTTATCTCAATATAATAGAT
1 TCGAAGTGAAGAGTTCCAATAAAAAATATTTTTTTATTCTAAATTTTTATCTCAATATAATAGAT
26536 TTTAATAAAAAAATTATATTTTAT
66 TTTAATAAAAAAATTATATTTTAT
* * *
26560 TCGAAGTGAAGAGTTTCAATAAAAAATATTTTTTTATTCTAATTTTTTATCTCAATATGATAGAT
1 TCGAAGTGAAGAGTTCCAATAAAAAATATTTTTTTATTCTAAATTTTTATCTCAATATAATAGAT
26625 TTTAAT-AAAAAATTATATTTTAT
66 TTTAATAAAAAAATTATATTTTAT
26648 TCGAA
1 TCGAA
26653 CTCGTCATTT
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
88 22 0.25
89 67 0.75
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.45
Consensus pattern (89 bp):
TCGAAGTGAAGAGTTCCAATAAAAAATATTTTTTTATTCTAAATTTTTATCTCAATATAATAGAT
TTTAATAAAAAAATTATATTTTAT
Found at i:34592 original size:25 final size:25
Alignment explanation
Indices: 34563--34633 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
34553 TATTTAAATG
*
34563 ATATTAAATATTTAATACTTTATAT
1 ATATTTAATATTTAATACTTTATAT
* **
34588 ATATTTTAGTATTTTTTA-TTTATAT
1 ATA-TTTAATATTTAATACTTTATAT
34613 ATATTTAATACTTTAATACTT
1 ATATTTAATA-TTTAATACTT
34634 AATCAAATAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
24 6 0.17
25 18 0.50
26 12 0.33
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (25 bp):
ATATTTAATATTTAATACTTTATAT
Found at i:34840 original size:2 final size:2
Alignment explanation
Indices: 34691--34828 Score: 119
Period size: 2 Copynumber: 70.5 Consensus size: 2
34681 TCTAATAATT
* *
34691 TA TA TA T- TA -A TA TA TA CTA -A TA CA TA TA -A TT TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
** * *
34730 TA TA TA TA TA TA TA TA TA TA TA CG TA TA TG TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
34772 CTA TC TA CT- TA TA CTT TA TA TA -A T- TA TA TA TA TA TA TA TA
1 -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34812 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
34829 GATTAGTATA
Statistics
Matches: 109, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
1 7 0.06
2 96 0.88
3 6 0.06
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:43647 original size:2 final size:2
Alignment explanation
Indices: 43640--43665 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43630 TGAAATTGCA
43640 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
43666 CACTGTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45761 original size:31 final size:31
Alignment explanation
Indices: 45723--45817 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
45713 GAACCTCGGC
* *
45723 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
45754 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
45785 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
45816 AA
1 AA
45818 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:46527 original size:65 final size:66
Alignment explanation
Indices: 46415--46567 Score: 186
Period size: 65 Copynumber: 2.3 Consensus size: 66
46405 TCTTTCAATG
* * * * * * *
46415 AAGGTATGCATCGATGCACTA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTTTTTTATTTT
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCAATGTTCTTTATTTT
46479 AA
66 -A
* *
46481 AAGG-ATGCATCGATGCATTATC-TATGCATCGATGCATCAAAGGCATTCAATGTTCTTTCTTTT
1 AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCAATGTTCTTTATTTT
46544 A
66 A
46545 AAGGAATGCATCGATGCACTTAT
1 AAGGAATGCATCGATGCA-TTAT
46568 GAATGTGCAT
Statistics
Matches: 76, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
64 5 0.07
65 62 0.82
66 9 0.12
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (66 bp):
AAGGAATGCATCGATGCATTATCTTATGCATCGATGCATAAAAGGCATTCAATGTTCTTTATTTT
A
Found at i:50654 original size:64 final size:66
Alignment explanation
Indices: 50568--50694 Score: 188
Period size: 64 Copynumber: 2.0 Consensus size: 66
50558 GCACTACTTG
* *
50568 TGCATCGGTGCATAAAATGCATTCGATGTT-TTTATTTTAAAAGG-ATGCATCGATGCA-TTATC
1 TGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTT-AAAGGAATGCATCGATGCACTTATC
50630 TA
65 TA
* *
50632 TGCATCGATGCATCAAAGGCATTCGATGTTCTTTCTTTTAAAGGAATGCATCGATGCACTTAT
1 TGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTTAAAGGAATGCATCGATGCACTTAT
50695 GAATGTGCAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
64 32 0.57
65 20 0.36
66 4 0.07
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (66 bp):
TGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTTAAAGGAATGCATCGATGCACTTATCT
A
Found at i:54015 original size:31 final size:31
Alignment explanation
Indices: 53964--54071 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 31
53954 AAGAGGTCAT
* *
53964 AAAGAACCTCGG-CAACTGTCCATA-GATCCC
1 AAAGAACCTAGGTAAACTGTCCATATG-TCCC
*
53994 AAAGAACCTAGGTAAACTGTCCATATGTTCC
1 AAAGAACCTAGGTAAACTGTCCATATGTCCC
** * * *
54025 TTAGAACATAGGTATACTGTCCATATGTCTCG
1 AAAGAACCTAGGTAAACTGTCCATATGTC-CC
*
54057 AAAG-ACATAGGTAAA
1 AAAGAACCTAGGTAAA
54072 ACCCTCGACT
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
30 11 0.17
31 48 0.76
32 4 0.06
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (31 bp):
AAAGAACCTAGGTAAACTGTCCATATGTCCC
Found at i:54811 original size:65 final size:64
Alignment explanation
Indices: 54668--54818 Score: 184
Period size: 63 Copynumber: 2.3 Consensus size: 64
54658 TCTTTCAATG
* * * *
54668 AAGGTATGCACCGATGCAC-TA-CTTGTGCATCGGTGCATAAATGCATTCGATGTTTTTATTTTA
1 AAGG-ATGCATCGATGCACTTATC-TATGCATCGATGCATAAAGGCATTCGATGTTTTTATTTTA
54731 A
64 A
*
54732 AAGGATGCATCGATGCA-TTATCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTTCTTTT-
1 AAGGATGCATCGATGCACTTATCTATGCATCGATGCAT-AAAGGCATTCGATGTT-TTTATTTTA
54795 A
64 A
54796 AAGGAATGCATCGATGCACTTAT
1 AAGG-ATGCATCGATGCACTTAT
54819 GAATGTGCAT
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
63 27 0.36
64 25 0.33
65 20 0.26
66 4 0.05
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
AAGGATGCATCGATGCACTTATCTATGCATCGATGCATAAAGGCATTCGATGTTTTTATTTTAA
Found at i:56780 original size:421 final size:420
Alignment explanation
Indices: 55904--56926 Score: 1566
Period size: 421 Copynumber: 2.4 Consensus size: 420
55894 ATTTAAGAAT
*
55904 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTAATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAAC-A-ACACA--AA--AG
* * ** *
55969 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAAATTAAATTATACC
60 GGATCAAATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATA-AAAAAGTACTAAATTATACC
* * * *
56034 CATTTAAAAAGTTATGGGCCAATTAAAAAAATTGAATTAAGTAATAAGTATGGATCAATTTCATA
124 CATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGA
* *
56099 TGCAAATAAATTTTGGAGGATTAAATTAAACAAATATGAAATTACAAATAAAAATTTAAATAAAT
188 TGCAAATAAAATTTGGAGGACTAAATTAAACAAATATGAAATTACAAATAAAAATTTAAATAAAT
* * * * *
56164 TAAACAACACACATTGATGGGATCAAATCTAAATAATTTTAAATTGTGATGTTGAAATTAATACA
253 TAAACAACACACA-T-AAGGGATCAAATCAAAATAATTTTAAATTGTGAGGTTAAAAATAATACA
* *
56229 AAAAAGTACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTTAAAAATATAAATAAGAAATA
316 AAAAAGTACTAAATTATACCCATTAAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGAAATA
*
56294 AGTATGGGTCAATTTTAGATGCAAATAAAATTTGGAGGAC
381 AGTATGGGTCAATTTCAGATGCAAATAAAATTTGGAGGAC
56334 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
* *
56399 AATCAAAATAATTTTAAATTTTGAGGCTAAAATTAATATAATAAAGTACTAAATTATACCCATTT
66 AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATA-AA-AAAGTACTAAATTATACCCATTT
* *
56464 AAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTTAGATGCAAA
129 AAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGATGCAAA
* * *
56529 TAAAATTTGGAGGACTAAATTGAACAAATATGAAATTACAAATAAATATTTAAATATATTAAACA
194 TAAAATTTGGAGGACTAAATTAAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACA
*
56594 ACACA-A-AAGGGATCAAATCAAAATAATTTTAAATTTTGAGGTTAAAAATAATACAAAAAAAGT
259 ACACACATAAGGGATCAAATCAAAATAATTTTAAATTGTGAGGTTAAAAATAATAC-AAAAAAGT
*
56657 ACTAAATTATACCCATTAAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGG
323 ACTAAATTATACCCATTAAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGAAATAAGTATGG
*
56722 GTCAATTTCAGGTGCAAATAAAATTTGGAGGAC
388 GTCAATTTCAGATGCAAATAAAATTTGGAGGAC
*
56755 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAACATATTAAACAACACAAAAGGGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
* * *
56820 AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATAAAAAATGTTCTAAAATATACTCATTTA
66 AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATAAAAAA-GTACTAAATTATACCCATTTA
* *
56885 AAAAGTTATGAGCCAA-TTAATAAATATAAATAAGTAATAAGT
130 AAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGT
56927 TGAGAAAAAA
Statistics
Matches: 550, Mismatches: 39, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
419 7 0.01
420 97 0.18
421 201 0.37
423 1 0.00
424 149 0.27
425 39 0.07
426 2 0.00
428 5 0.01
429 1 0.00
430 48 0.09
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (420 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATAAAAAAGTACTAAATTATACCCATTTAA
AAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGATCAATTTCAGATGCAAATA
AAATTTGGAGGACTAAATTAAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAAC
ACACATAAGGGATCAAATCAAAATAATTTTAAATTGTGAGGTTAAAAATAATACAAAAAAGTACT
AAATTATACCCATTAAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGAAATAAGTATGGGTC
AATTTCAGATGCAAATAAAATTTGGAGGAC
Found at i:56784 original size:211 final size:211
Alignment explanation
Indices: 55904--56926 Score: 1556
Period size: 210 Copynumber: 4.8 Consensus size: 211
55894 ATTTAAGAAT
*
55904 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTAATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAAC-A-ACACA--AA--AG
* * *
55969 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAA--ATTAAATTATA
60 GGATCAAATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAAAGTACTAAATTATA
* * * *
56032 CCCATTTAAAAAGTTATGGGCCAATTAAAAAAATTGAATTAAGTAATAAGTATGGATCAATTTCA
125 CCCATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCA
* * *
56097 TATGCAAATAAATTTTGGAGGAT
189 GATGCAAATAAAATTTGGAGGAC
* * *
56120 TAAATTAAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGGG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACA-A---AAGGG
* * *
56185 ATCAAATCTAAATAATTTTAAATTGTGATGTTGAAATTAATAC-AAAAAAGTACTAAATTATACC
62 ATCAAATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAAAGTACTAAATTATACC
* * *
56249 CATTTAAAAAGTTATGGGCCAATTTAAAAATATAAATAAGAAATAAGTATGGGTCAATTTTAGAT
127 CATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGAT
56314 GCAAATAAAATTTGGAGGAC
192 GCAAATAAAATTTGGAGGAC
56334 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
* * * *
56399 AATCAAAATAATTTTAAATTTTGAGGCTAAAATTAATA-TAATAAAGTACTAAATTATACCCATT
66 AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAAAGTACTAAATTATACCCATT
*
56463 TAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTTAGATGCAA
131 TAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAA
56528 ATAAAATTTGGAGGAC
196 ATAAAATTTGGAGGAC
*
56544 TAAATTGAACAAATATGAAATTACAAATAAATATTTAAATATATTAAACAACACAAAAGGGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
* *
56609 AATCAAAATAATTTTAAATTTTGAGGTTAAAAATAATACAAAAAAAGTACTAAATTATACCCATT
66 AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAAAGTACTAAATTATACCCATT
* *
56674 AAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGGTGCAA
131 TAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAA
56739 ATAAAATTTGGAGGAC
196 ATAAAATTTGGAGGAC
*
56755 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAACATATTAAACAACACAAAAGGGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
* * * *
56820 AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAAT--AAAAAATGTTCTAAAATATACTCATT
66 AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAAAGTACTAAATTATACCCATT
* *
56883 TAAAAAGTTATGAGCCAA-TTAATAAATATAAATAAGTAATAAGT
131 TAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGT
56927 TGAGAAAAAA
Statistics
Matches: 753, Mismatches: 46, Indels: 23
0.92 0.06 0.03
Matches are distributed among these distances:
208 4 0.01
209 58 0.08
210 244 0.32
211 200 0.27
213 8 0.01
214 153 0.20
215 37 0.05
216 49 0.07
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (211 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
AATCAAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAAAGTACTAAATTATACCCATT
TAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAA
ATAAAATTTGGAGGAC
Found at i:56956 original size:2 final size:2
Alignment explanation
Indices: 56951--57064 Score: 99
Period size: 2 Copynumber: 56.5 Consensus size: 2
56941 AAAACAACTA
* *
56951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AGT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * *
56994 AT AT GT AT -T AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
* * *
57037 AT -T AT GT AT AA AGT AT AA AT -T AT AT AT A
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A
57065 CCAGGTATAA
Statistics
Matches: 89, Mismatches: 16, Indels: 14
0.75 0.13 0.12
Matches are distributed among these distances:
1 3 0.03
2 82 0.92
3 4 0.04
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:57054 original size:70 final size:70
Alignment explanation
Indices: 56954--57100 Score: 183
Period size: 70 Copynumber: 2.1 Consensus size: 70
56944 ACAACTAATA
* * * * *
56954 TATATATATATATATATATATATATATATAAAGTATATGTA-TATGTATTATATATATAA-ACTA
1 TATATATATATATATATATATATAAATATAAAGTATATATACCAGGTA-TAAAT-TATAATACTA
57017 TATAGTT
64 TATAGTT
* *
57024 TATATATATATATAT-TATGTATAAAGTATAAATTATATATACCAGGTATAAATTATAATACTAT
1 TATATATATATATATATATATATAAA-TATAAAGTATATATACCAGGTATAAATTATAATACTAT
57088 ATAGTT
65 ATAGTT
57094 TATATAT
1 TATATAT
57101 GAACTATTGA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
69 13 0.19
70 50 0.75
71 4 0.06
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (70 bp):
TATATATATATATATATATATATAAATATAAAGTATATATACCAGGTATAAATTATAATACTATA
TAGTT
Found at i:57255 original size:22 final size:22
Alignment explanation
Indices: 57203--57257 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
57193 ATATATTGTG
*
57203 TAAATTATATAGTTTATTGATA
1 TAAAGTATATAGTTTATTGATA
*
57225 TAAATTATATAGTTTATAT-ATA
1 TAAAGTATATAGTTTAT-TGATA
*
57247 TATAGTATATA
1 TAAAGTATATA
57258 TGGTTTAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (22 bp):
TAAAGTATATAGTTTATTGATA
Found at i:57269 original size:7 final size:7
Alignment explanation
Indices: 57259--57306 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
57249 TAGTATATAT
57259 GGTTTAG
1 GGTTTAG
57266 GGTTTAG
1 GGTTTAG
*
57273 GATTTAG
1 GGTTTAG
*
57280 GGTTTAA
1 GGTTTAG
*
57287 TGTTTAG
1 GGTTTAG
*
57294 GATTTAG
1 GGTTTAG
57301 GGTTTA
1 GGTTTA
57307 TATTTATATT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:57284 original size:21 final size:21
Alignment explanation
Indices: 57259--57306 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
57249 TAGTATATAT
*
57259 GGTTTAGGGTTTAGGATTTAG
1 GGTTTAAGGTTTAGGATTTAG
*
57280 GGTTTAATGTTTAGGATTTAG
1 GGTTTAAGGTTTAGGATTTAG
57301 GGTTTA
1 GGTTTA
57307 TATTTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (21 bp):
GGTTTAAGGTTTAGGATTTAG
Found at i:57354 original size:20 final size:20
Alignment explanation
Indices: 57329--57401 Score: 83
Period size: 20 Copynumber: 3.4 Consensus size: 20
57319 TATAAACTAC
57329 ATACTATAATTTATATTTAT
1 ATACTATAATTTATATTTAT
*
57349 ATACTATATTTTATCCTATTTAT
1 ATACTATAATTTA---TATTTAT
*
57372 ATAAACTATAGTTTATATTTAT
1 AT--ACTATAATTTATATTTAT
57394 ATACTATA
1 ATACTATA
57402 TATATATGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
20 18 0.39
22 9 0.20
23 9 0.20
25 10 0.22
ACGTcount: A:0.38, C:0.08, G:0.01, T:0.52
Consensus pattern (20 bp):
ATACTATAATTTATATTTAT
Found at i:57380 original size:25 final size:23
Alignment explanation
Indices: 57342--57401 Score: 72
Period size: 25 Copynumber: 2.7 Consensus size: 23
57332 CTATAATTTA
*
57342 TATTTATATACTATATTTTATCC
1 TATTTATATACTATAGTTTATCC
57365 TATTTATATAAACTATAGTTTA---
1 TATTTATAT--ACTATAGTTTATCC
57387 TATTTATATACTATA
1 TATTTATATACTATA
57402 TATATATGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 6 0.18
22 9 0.26
23 9 0.26
25 10 0.29
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (23 bp):
TATTTATATACTATAGTTTATCC
Found at i:57431 original size:18 final size:18
Alignment explanation
Indices: 57369--57514 Score: 111
Period size: 18 Copynumber: 7.7 Consensus size: 18
57359 TTATCCTATT
57369 TATATAAACTATAGTTTA
1 TATATAAACTATAGTTTA
*
57387 TATTTATATACTATA---TA
1 TA--TATAAACTATAGTTTA
*
57404 TATATGAACTATAGTTTA
1 TATATAAACTATAGTTTA
*
57422 CATATAAACTATATAGTTTA
1 TATATAAAC--TATAGTTTA
57442 TATACT-AACTATAGTTTA
1 TATA-TAAACTATAGTTTA
*
57460 AATATAAACTATAGTTAATA
1 TATATAAACTATAGTT--TA
57480 TTTATATATGAACTATAGTTTA
1 --TATATA--AACTATAGTTTA
* *
57502 CATATGAACTATA
1 TATATAAACTATA
57515 TATATAAACT
Statistics
Matches: 103, Mismatches: 10, Indels: 30
0.72 0.07 0.21
Matches are distributed among these distances:
15 9 0.09
17 5 0.05
18 40 0.39
20 31 0.30
21 1 0.01
22 7 0.07
24 10 0.10
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (18 bp):
TATATAAACTATAGTTTA
Found at i:57433 original size:33 final size:33
Alignment explanation
Indices: 57369--57554 Score: 124
Period size: 33 Copynumber: 5.2 Consensus size: 33
57359 TTATCCTATT
* * *
57369 TATATAAACTATAGTTTATATTTATATACTATATA
1 TATATGAACTATAGTTTACA--TATAAACTATATA
57404 TATATGAACTATAGTTTACATATAAACTATATA
1 TATATGAACTATAGTTTACATATAAACTATATA
* *
57437 GTTTATATACTAACTATAGTTTAAATATAAACTATAGTTAATATTTA
1 ---TATAT--GAACTATAGTTTACATATAAAC------T-ATA--TA
*
57484 TATATGAACTATAGTTTACATATGAACTATATA
1 TATATGAACTATAGTTTACATATAAACTATATA
* *
57517 TATA--AACTATATAGTTTACATATGACCTATATA
1 TATATGAAC--TATAGTTTACATATAAACTATATA
57550 TATAT
1 TATAT
57555 ATATATATAT
Statistics
Matches: 125, Mismatches: 9, Indels: 35
0.74 0.05 0.21
Matches are distributed among these distances:
31 3 0.02
33 45 0.36
35 21 0.17
36 6 0.05
38 20 0.16
42 19 0.15
44 6 0.05
45 3 0.02
47 2 0.02
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (33 bp):
TATATGAACTATAGTTTACATATAAACTATATA
Found at i:57516 original size:20 final size:20
Alignment explanation
Indices: 57405--57549 Score: 84
Period size: 18 Copynumber: 7.7 Consensus size: 20
57395 TACTATATAT
57405 ATATGAAC--TATAGTTTAC
1 ATATGAACTATATAGTTTAC
* *
57423 ATATAAACTATATAGTTTAT
1 ATATGAACTATATAGTTTAC
*
57443 ATACT-AAC--TATAGTTTAA
1 ATA-TGAACTATATAGTTTAC
* * *
57461 ATATAAACTATAGTTAATATTTAT
1 ATATGAACTATA--T-A-GTTTAC
57485 ATATGAAC--TATAGTTTAC
1 ATATGAACTATATAGTTTAC
57503 ATATGAACTATATA---T--
1 ATATGAACTATATAGTTTAC
57518 ATA--AACTATATAGTTTAC
1 ATATGAACTATATAGTTTAC
*
57536 ATATGACCTATATA
1 ATATGAACTATATA
57550 TATATATATA
Statistics
Matches: 99, Mismatches: 9, Indels: 36
0.69 0.06 0.25
Matches are distributed among these distances:
13 9 0.09
15 3 0.03
16 1 0.01
17 2 0.02
18 37 0.37
19 1 0.01
20 30 0.30
21 1 0.01
22 3 0.03
23 1 0.01
24 11 0.11
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (20 bp):
ATATGAACTATATAGTTTAC
Found at i:57529 original size:42 final size:40
Alignment explanation
Indices: 57391--57521 Score: 139
Period size: 38 Copynumber: 3.3 Consensus size: 40
57381 AGTTTATATT
57391 TATATACTAT-ATATATATGAACTATAGTTTACATATAAAC
1 TATATA-TATAATATATATGAACTATAGTTTACATATAAAC
*
57431 TATATAGT-T--TATATACT-AACTATAGTTTAAATATAAAC
1 TATATA-TATAATATATA-TGAACTATAGTTTACATATAAAC
* *
57469 TATAGT-TAATATTTATATATGAACTATAGTTTACATATGAAC
1 TATA-TAT-ATA-ATATATATGAACTATAGTTTACATATAAAC
57511 TATATATATAA
1 TATATATATAA
57522 ACTATATAGT
Statistics
Matches: 77, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
37 1 0.01
38 30 0.39
39 4 0.05
40 7 0.09
41 5 0.06
42 30 0.39
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (40 bp):
TATATATATAATATATATGAACTATAGTTTACATATAAAC
Found at i:57551 original size:2 final size:2
Alignment explanation
Indices: 57544--57671 Score: 93
Period size: 2 Copynumber: 62.0 Consensus size: 2
57534 ACATATGACC
*
57544 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GT- TGA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA
* * ** *
57587 TA TA CTA TA TA GTT TA CA TA TGA CC TA TA TA TA TA TA CTA TA GTT
1 TA TA -TA TA TA -TA TA TA TA T-A TA TA TA TA TA TA TA -TA TA -TA
*
57632 TA TA TT TA TA TA T- TA TA TA TA T- TA TA TA -A TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
57672 ATTTACATAT
Statistics
Matches: 100, Mismatches: 14, Indels: 24
0.72 0.10 0.17
Matches are distributed among these distances:
1 4 0.04
2 85 0.85
3 11 0.11
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:57566 original size:80 final size:82
Alignment explanation
Indices: 57385--57568 Score: 222
Period size: 80 Copynumber: 2.3 Consensus size: 82
57375 AACTATAGTT
*
57385 TATAT-TTATATACTATATATATATGAACTATAGTTTACATATAAACTATATAGTTTATATACTA
1 TATATATTATATA-TATATATATATGAACTATAGTTTACATATAAACTATATA--TTATAAACTA
57449 ACTATAGTTTAAATATAAAC
63 ACTATAGTTTAAATATAAAC
* *
57469 TATA-GTTA-ATAT-T-TATATATGAACTATAGTTTACATATGAACTATATA-TATAAACT-A-T
1 TATATATTATATATATATATATATGAACTATAGTTTACATATAAACTATATATTATAAACTAACT
* * *
57527 ATAGTTTACATATGACC
66 ATAGTTTAAATATAAAC
57544 TATATATATATATATATATATATAT
1 TATATAT-TATATATATATATATAT
57569 ATATATAGTT
Statistics
Matches: 88, Mismatches: 6, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
75 19 0.22
76 2 0.02
77 9 0.10
78 4 0.05
79 1 0.01
80 41 0.47
81 1 0.01
82 1 0.01
83 3 0.03
84 7 0.08
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (82 bp):
TATATATTATATATATATATATATGAACTATAGTTTACATATAAACTATATATTATAAACTAACT
ATAGTTTAAATATAAAC
Found at i:57595 original size:68 final size:70
Alignment explanation
Indices: 57511--57693 Score: 221
Period size: 68 Copynumber: 2.6 Consensus size: 70
57501 ACATATGAAC
* *
57511 TATATATATAAACTATATAGTTTACATATGACCTATATATATATA-TATA-TATATATATATATA
1 TATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGTATATATATATATA
57574 -TAGT-
66 TTA-TA
* *
57578 TGATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGTTTATATTTATAT
1 T-ATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGTATATATATATAT
57643 ATTATA
65 ATTATA
* * *
57649 TATATTATATAATATATAGTATAATTTACATATGAACTATATATA
1 TATATT-TAT-ATA-CTA-TATAGTTTACATATGACCTATATATA
57694 AAAATCCTAA
Statistics
Matches: 100, Mismatches: 7, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
67 1 0.01
68 42 0.42
69 4 0.04
70 18 0.18
71 6 0.06
72 3 0.03
73 2 0.02
74 24 0.24
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (70 bp):
TATATTTATATACTATATAGTTTACATATGACCTATATATATATACTATAGTATATATATATATA
TTATA
Found at i:57622 original size:33 final size:33
Alignment explanation
Indices: 57493--57628 Score: 159
Period size: 33 Copynumber: 4.1 Consensus size: 33
57483 ATATATGAAC
* *
57493 TATAGTTTACATATGAACTATATATATAAACTA
1 TATAGTTTACATATGACCTATATATATATACTA
57526 TATAGTTTACATATGACCTATATATATATA-TA
1 TATAGTTTACATATGACCTATATATATATACTA
* * ** *
57558 TATA-TATATATATATATAGTTGATATTTATATACTA
1 TATAGT-T-TACATAT-GACCT-ATATATATATACTA
57594 TATAGTTTACATATGACCTATATATATATACTA
1 TATAGTTTACATATGACCTATATATATATACTA
57627 TA
1 TA
57629 GTTTATATTT
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
31 1 0.01
32 7 0.08
33 49 0.58
34 4 0.05
35 16 0.19
36 7 0.08
37 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (33 bp):
TATAGTTTACATATGACCTATATATATATACTA
Found at i:57691 original size:101 final size:99
Alignment explanation
Indices: 57493--57674 Score: 239
Period size: 101 Copynumber: 1.8 Consensus size: 99
57483 ATATATGAAC
57493 TATAGTTTACATATGAACTATATATATAAACTATATAGTTTACATATGACCTATATATATATATA
1 TATAGTTTACATATGAACTATATATATAAAC-ATATAGTTTACATATGA-CTATATATATATATA
* *
57558 TATATATATATATATATAGTTGATATTTATATACTA
64 TATATATATATATATATAATTGATATCTATATACTA
* * * *
57594 TATAGTTTACATATGACCTATATATATATAC-TATAGTTTATAT-TTA-TATAT-TATATATAT-
1 TATAGTTTACATATGAACTATATATATAAACATATAGTTTACATATGACTATATATATATATATA
57654 TATATAATATATAGTATAATT
66 TATAT-ATATATA-TATAATT
57675 TACATATGAA
Statistics
Matches: 74, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
94 5 0.07
95 16 0.22
96 11 0.15
98 2 0.03
99 11 0.15
101 29 0.39
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (99 bp):
TATAGTTTACATATGAACTATATATATAAACATATAGTTTACATATGACTATATATATATATATA
TATATATATATATATAATTGATATCTATATACTA
Found at i:57754 original size:33 final size:33
Alignment explanation
Indices: 57715--57960 Score: 258
Period size: 33 Copynumber: 7.5 Consensus size: 33
57705 CCCTAAACCC
*
57715 TAAACTATACATTATATAGTTTATTAGTATATA
1 TAAACTATATATTATATAGTTTATTAGTATATA
** *
57748 TAAACTATATAATATATATAGACTATATGGTATATA
1 TAAACTATAT-AT-TATATAGTTTAT-TAGTATATA
*
57784 TAAACTATACATTATATA-TAATTCATTAGTATATA
1 TAAACTATATATTATATAGT--TT-ATTAGTATATA
*
57819 TAAACTATATATTATATAGTTCATTAGTATATA
1 TAAACTATATATTATATAGTTTATTAGTATATA
*
57852 TAAACTATATATTATATAGTTCATTAGTATATA
1 TAAACTATATATTATATAGTTTATTAGTATATA
* *
57885 TAACCTATATAGTATAT-G-------GTATATA
1 TAAACTATATATTATATAGTTTATTAGTATATA
* * *
57910 CAAACTATATATTTTATAGTTCATTAGTATATA
1 TAAACTATATATTATATAGTTTATTAGTATATA
*
57943 TAAACTATATAGTATATA
1 TAAACTATATATTATATA
57961 TAAACTATAT
Statistics
Matches: 179, Mismatches: 19, Indels: 30
0.79 0.08 0.13
Matches are distributed among these distances:
25 20 0.11
26 1 0.01
32 1 0.01
33 90 0.50
34 9 0.05
35 38 0.21
36 20 0.11
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (33 bp):
TAAACTATATATTATATAGTTTATTAGTATATA
Found at i:57765 original size:18 final size:18
Alignment explanation
Indices: 57739--57971 Score: 146
Period size: 18 Copynumber: 13.1 Consensus size: 18
57729 TATAGTTTAT
57739 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
* *
57757 TAATATATATAGACTATA
1 TAGTATATATAAACTATA
*
57775 TGGTATATATAAACTATA
1 TAGTATATATAAACTATA
* * *
57793 CATTATATAT-AATTCAT-
1 TAGTATATATAAACT-ATA
57810 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
**
57828 TA-T-TATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
57843 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
* ** *
57861 TATTATATAGTTCATTAGTA
1 TAGTATATA-TAAACTA-TA
* *
57881 TA-TATAACCTATATAGTATA
1 TAGTAT-A--TATAAACTATA
* *
57901 TGGTATATACAAACTATA
1 TAGTATATATAAACTATA
* **
57919 TA-T-TTTAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
57934 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
57952 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
57970 TA
1 TA
57972 TTAATTTATT
Statistics
Matches: 161, Mismatches: 35, Indels: 38
0.69 0.15 0.16
Matches are distributed among these distances:
15 8 0.05
16 14 0.09
17 28 0.17
18 86 0.53
19 7 0.04
20 9 0.06
21 7 0.04
22 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:57917 original size:58 final size:58
Alignment explanation
Indices: 57845--57959 Score: 203
Period size: 58 Copynumber: 2.0 Consensus size: 58
57835 TAGTTCATTA
* *
57845 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATG
*
57903 GTATATACAAACTATATATTTTATAGTTCATTAGTATATATAAACTATATAGTATAT
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATAT
57960 ATAAACTATA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (58 bp):
GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAGTATATG
Found at i:58015 original size:26 final size:25
Alignment explanation
Indices: 57958--58015 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
57948 TATATAGTAT
* **
57958 ATATAAACTATATATTAATTTATTA
1 ATATAAACTATATATTAATTAAAGA
57983 ATATAAACATATATATTAATTGAAAGA
1 ATATAAAC-TATATATTAATT-AAAGA
58010 AT-TAAA
1 ATATAAA
58016 AAAATATAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 8 0.29
26 16 0.57
27 4 0.14
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (25 bp):
ATATAAACTATATATTAATTAAAGA
Found at i:58097 original size:62 final size:61
Alignment explanation
Indices: 58030--58167 Score: 179
Period size: 62 Copynumber: 2.2 Consensus size: 61
58020 TATAAGGATC
* * *
58030 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATCATAA-CATTAAATTTGGATT
1 AAATTGAAAAAATTTGAAATATGAAGCTTAAATTAATAAATCA-AATCATTAAATTTGGACT
* * * *
58091 AAAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATATATTAAATTATTAAATTTGGACT
1 -AAATTGAAAAAATTTGAAATATGAAGCTTAAATTAATAAATCAAATCATTAAATTTGGACT
*
58153 AAATTGAATAAATTT
1 AAATTGAAAAAATTT
58168 AAAACTAAGA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
61 15 0.23
62 51 0.77
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.36
Consensus pattern (61 bp):
AAATTGAAAAAATTTGAAATATGAAGCTTAAATTAATAAATCAAATCATTAAATTTGGACT
Found at i:61399 original size:32 final size:31
Alignment explanation
Indices: 61327--61422 Score: 104
Period size: 31 Copynumber: 3.1 Consensus size: 31
61317 GAACCTCGGC
* *
61327 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
61358 AACTGTCCATATGTTCCTTAGAACATAGGGTA
1 AACTGTCCATATGTCCCAAAGAACATA-GGTA
* *
61390 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
61421 AA
1 AA
61423 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
31 27 0.52
32 22 0.42
33 3 0.06
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:62131 original size:64 final size:66
Alignment explanation
Indices: 62020--62171 Score: 188
Period size: 64 Copynumber: 2.3 Consensus size: 66
62010 TCTTTCAATG
* * * * *
62020 AAGGTATGTATCGATGCAC-TA-CTTGTGCATCGGTGCATAAAATGCATTCGATGTT-TTTATTT
1 AAGGAATGCATCGATGCACTTATC-TATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTT
62082 TAA
65 T-A
* *
62085 AAGG-ATGCATCGATGCA-TTATCTATGCATCGATGCATCAAAGGCATTCGATGTTCTTTCTTTT
1 AAGGAATGCATCGATGCACTTATCTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTT
62148 A
66 A
62149 AAGGAATGCATCGATGCACTTAT
1 AAGGAATGCATCGATGCACTTAT
62172 GAATGTGCAT
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
64 47 0.62
65 25 0.33
66 4 0.05
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (66 bp):
AAGGAATGCATCGATGCACTTATCTATGCATCGATGCATAAAAGGCATTCGATGTTCTTTATTTT
A
Found at i:63030 original size:23 final size:24
Alignment explanation
Indices: 63004--63053 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
62994 TTATTTTTTC
*
63004 TTTATATAAATTAAACTTTA-TAA
1 TTTATATAAATTAAACTATATTAA
63027 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
63051 TTT
1 TTT
63054 TTCTTTGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:63357 original size:16 final size:16
Alignment explanation
Indices: 63322--63377 Score: 94
Period size: 16 Copynumber: 3.4 Consensus size: 16
63312 CGGATCATTT
*
63322 ACAGGTCAGGTTAAAAA
1 ACAGGTCAGGTT-GAAA
63339 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
63355 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
63371 ACAGGTC
1 ACAGGTC
63378 GGGTAATACC
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
16 26 0.68
17 12 0.32
ACGTcount: A:0.39, C:0.14, G:0.29, T:0.18
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:63690 original size:24 final size:24
Alignment explanation
Indices: 63663--63720 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
63653 GCTTGCAAAT
* *
63663 GAACATGTTTGCGACCATATAAAC
1 GAACATGTTCGAGACCATATAAAC
63687 GAACATGTTCGAGACCATATAAAC
1 GAACATGTTCGAGACCATATAAAC
* *
63711 AAATATGTTC
1 GAACATGTTC
63721 TCGAACGTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
GAACATGTTCGAGACCATATAAAC
Found at i:72773 original size:7 final size:7
Alignment explanation
Indices: 72763--72849 Score: 54
Period size: 7 Copynumber: 12.7 Consensus size: 7
72753 TATATATATA
72763 ATATTTT
1 ATATTTT
72770 ATATTTT
1 ATATTTT
*
72777 -TATATT
1 ATATTTT
*
72783 A-ATTAT
1 ATATTTT
* *
72789 ATATATA
1 ATATTTT
72796 ATATTTT
1 ATATTTT
*
72803 TTATTTT
1 ATATTTT
*
72810 TTATTTT
1 ATATTTT
*
72817 A-ATTAT
1 ATATTTT
* *
72823 ATATATA
1 ATATTTT
*
72830 ATATTAT
1 ATATTTT
72837 ATATTTTT
1 ATA-TTTT
72845 ATATT
1 ATATT
72850 AATTATATAA
Statistics
Matches: 58, Mismatches: 18, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
6 14 0.24
7 38 0.66
8 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
ATATTTT
Found at i:72795 original size:33 final size:33
Alignment explanation
Indices: 72753--72858 Score: 176
Period size: 33 Copynumber: 3.2 Consensus size: 33
72743 CCTGATCATA
72753 TATATATATAATATTTTATATTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
* *
72786 TATATATATAATATTTTTTATTTTTTATTTTAAT
1 TATATATATAATATTTTATA-TTTTTATATTAAT
*
72820 TATATATATAATATTATATATTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTATATTAAT
72853 TATATA
1 TATATA
72859 ATACAAACCT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
33 37 0.55
34 30 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
TATATATATAATATTTTATATTTTTATATTAAT
Found at i:74044 original size:78 final size:79
Alignment explanation
Indices: 73914--74069 Score: 278
Period size: 78 Copynumber: 2.0 Consensus size: 79
73904 ATCATTAAAC
73914 AATTGTTTATATGGAAACTTATTCAAACATCAATTGCATTAAGTCATTGAACACATTATATAGTG
1 AATTGTTTATATGGAAACTTATTCAAACATCAATTGCATTAAGTCATTGAACACATTATATAGTG
73979 CATCTTTTCAACTT
66 CATCTTTTCAACTT
* *
73993 AATTGTTTATATGG-AACTTATTCAAACATCAATTGCATTGAGTCATTGAACACATTATGTAGTG
1 AATTGTTTATATGGAAACTTATTCAAACATCAATTGCATTAAGTCATTGAACACATTATATAGTG
*
74057 CATCTTTTGAACT
66 CATCTTTTCAACT
74070 AGTCCAAGTC
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
78 60 0.81
79 14 0.19
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (79 bp):
AATTGTTTATATGGAAACTTATTCAAACATCAATTGCATTAAGTCATTGAACACATTATATAGTG
CATCTTTTCAACTT
Found at i:78948 original size:19 final size:19
Alignment explanation
Indices: 78924--78961 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
78914 TTCTGGAGTT
78924 GCTAAATTGATCAAAGAAC
1 GCTAAATTGATCAAAGAAC
78943 GCTAAATTGATCAAAGAAC
1 GCTAAATTGATCAAAGAAC
78962 TTAAGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (19 bp):
GCTAAATTGATCAAAGAAC
Done.