Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004095.1 Hibiscus syriacus cultivar Beakdansim tig00008956_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: 151178
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:4973 original size:30 final size:30
Alignment explanation
Indices: 4937--5000 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 30
4927 CTGATTAGAC
*
4937 TAAGAGTTAAAGTAAATCATAATTGAAAAT
1 TAAGAGTCAAAGTAAATCATAATTGAAAAT
4967 TAAGAGTCAAAGTAAATCATAATTGAAAAT
1 TAAGAGTCAAAGTAAATCATAATTGAAAAT
4997 TAAG
1 TAAG
5001 GCATAAACCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (30 bp):
TAAGAGTCAAAGTAAATCATAATTGAAAAT
Found at i:16408 original size:18 final size:18
Alignment explanation
Indices: 16385--16423 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
16375 TGGTAAAATA
16385 TTTTTATATCTTAATAAT
1 TTTTTATATCTTAATAAT
* * *
16403 TTTTTATTTTTTAATTAT
1 TTTTTATATCTTAATAAT
16421 TTT
1 TTT
16424 AGTAATTTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATATCTTAATAAT
Found at i:16533 original size:20 final size:20
Alignment explanation
Indices: 16475--16534 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 20
16465 AATTTAGAAG
16475 TTTTTATGTATTTAATTATATAT
1 TTTTTAT-T-TTTAATTA-ATAT
*
16498 TTTTTAGTTTTT--TTAATCT
1 TTTTTA-TTTTTAATTAATAT
16517 TTTTTATTTTTAATTAAT
1 TTTTTATTTTTAATTAAT
16535 TTATATTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
18 5 0.15
19 9 0.27
20 8 0.24
22 3 0.09
23 7 0.21
24 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTTATTTTTAATTAATAT
Found at i:16798 original size:21 final size:20
Alignment explanation
Indices: 16772--16815 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
16762 GTTGATCATT
*
16772 ACGGTGATGATATGACAGTCC
1 ACGGTGATAAT-TGACAGTCC
* *
16793 ACGGTGCTAATTGACAGTTC
1 ACGGTGATAATTGACAGTCC
16813 ACG
1 ACG
16816 ATGGTTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.25
Consensus pattern (20 bp):
ACGGTGATAATTGACAGTCC
Found at i:17049 original size:21 final size:17
Alignment explanation
Indices: 16996--17035 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
16986 ATACTAAAAA
16996 TAAAAATT-AA-ATTAT
1 TAAAAATTAAATATTAT
17011 TAAAAATTAAATATTTAT
1 TAAAAATTAAATA-TTAT
17029 TAAAAAT
1 TAAAAAT
17036 ACTAAAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.36
16 2 0.09
17 1 0.05
18 11 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAAAATTAAATATTAT
Found at i:27575 original size:20 final size:21
Alignment explanation
Indices: 27526--27575 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
27516 AAGACCAAAT
27526 AAGA-AGACAAAATGTGCTACA
1 AAGACAGA-AAAATGTGCTACA
*
27547 AAGATAGAAAAATGTG-TCACA
1 AAGACAGAAAAATGTGCT-ACA
27568 AA-ACAGAA
1 AAGACAGAA
27576 TTATTCTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 17 0.65
22 3 0.12
ACGTcount: A:0.56, C:0.12, G:0.18, T:0.14
Consensus pattern (21 bp):
AAGACAGAAAAATGTGCTACA
Found at i:27841 original size:31 final size:31
Alignment explanation
Indices: 27806--27870 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
27796 TCAAAAAACA
*
27806 TAATATATGAG-CACTTTCGCTTTTATTTAAT
1 TAATATATG-GTCACTTTCGCTTTTATATAAT
*
27837 TAATATATGGTCACTTTCGTTTTTATATAAT
1 TAATATATGGTCACTTTCGCTTTTATATAAT
27868 TAA
1 TAA
27871 GATGTGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (31 bp):
TAATATATGGTCACTTTCGCTTTTATATAAT
Found at i:27882 original size:31 final size:31
Alignment explanation
Indices: 27810--27882 Score: 92
Period size: 31 Copynumber: 2.4 Consensus size: 31
27800 AAAACATAAT
* * *
27810 ATATGAGCACTTTCGCTTTTATTTAATTAAT
1 ATATGATCACTTTCGCTTTTATATAATTAAG
* *
27841 ATATGGTCACTTTCGTTTTTATATAATTAAG
1 ATATGATCACTTTCGCTTTTATATAATTAAG
*
27872 ATGTGATCACT
1 ATATGATCACT
27883 ACAGGTTAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (31 bp):
ATATGATCACTTTCGCTTTTATATAATTAAG
Found at i:30910 original size:27 final size:27
Alignment explanation
Indices: 30879--30967 Score: 169
Period size: 27 Copynumber: 3.3 Consensus size: 27
30869 AGATGCCATG
30879 TACATATACACATGTACACACGTGTTT
1 TACATATACACATGTACACACGTGTTT
30906 TACATATACACATGTACACACGTGTTT
1 TACATATACACATGTACACACGTGTTT
30933 TACATATACACATGTACACACGTGTTT
1 TACATATACACATGTACACACGTGTTT
*
30960 TATATATA
1 TACATATA
30968 TAAGAAAGAC
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (27 bp):
TACATATACACATGTACACACGTGTTT
Found at i:47504 original size:33 final size:33
Alignment explanation
Indices: 47464--47529 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
47454 GGTTTTTGTT
*
47464 TTTGGTGTAGTTGTTAAGTCTTATGTAATTTTG
1 TTTGGTGTAATTGTTAAGTCTTATGTAATTTTG
* *
47497 TTTGGTGTAATTTTTAAGTCTTATGTACTTTTG
1 TTTGGTGTAATTGTTAAGTCTTATGTAATTTTG
47530 GTATATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.56
Consensus pattern (33 bp):
TTTGGTGTAATTGTTAAGTCTTATGTAATTTTG
Found at i:51239 original size:21 final size:21
Alignment explanation
Indices: 51190--51250 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 21
51180 TATATATATA
*
51190 TTATTCTTAAATTCATATTTT
1 TTATTTTTAAATTCATATTTT
* *
51211 TATTTTTTTAAATTCATGTTTT
1 T-TATTTTTAAATTCATATTTT
*
51233 TTATTTTTAAATTAATAT
1 TTATTTTTAAATTCATAT
51251 CTTAAATTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 15 0.45
22 18 0.55
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (21 bp):
TTATTTTTAAATTCATATTTT
Found at i:51257 original size:13 final size:13
Alignment explanation
Indices: 51239--51263 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51229 TTTTTTATTT
51239 TTAAATTAATATC
1 TTAAATTAATATC
51252 TTAAATTAATAT
1 TTAAATTAATAT
51264 GAATTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (13 bp):
TTAAATTAATATC
Found at i:51332 original size:34 final size:35
Alignment explanation
Indices: 51294--51376 Score: 132
Period size: 35 Copynumber: 2.4 Consensus size: 35
51284 TTAATTTAAG
*
51294 ATATGAATTTAAGATATAAATTT-AAAGAATAAAA
1 ATATGAATTTAAGATATAAATTTAAAAAAATAAAA
*
51328 ATATGAATTTAAGATATGAATTTAAAAAAATAAAA
1 ATATGAATTTAAGATATAAATTTAAAAAAATAAAA
*
51363 ATATGGATTTAAGA
1 ATATGAATTTAAGA
51377 CTAAAATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 22 0.49
35 23 0.51
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.33
Consensus pattern (35 bp):
ATATGAATTTAAGATATAAATTTAAAAAAATAAAA
Found at i:51344 original size:13 final size:13
Alignment explanation
Indices: 51279--51352 Score: 79
Period size: 13 Copynumber: 6.1 Consensus size: 13
51269 TATATTTTTT
*
51279 AGATATTAATTTA
1 AGATATGAATTTA
51292 AGATATGAATTTA
1 AGATATGAATTTA
*
51305 AGATATAAATTTAA
1 AGATATGAATTT-A
51319 AGA-AT-AA---A
1 AGATATGAATTTA
51327 A-ATATGAATTTA
1 AGATATGAATTTA
51339 AGATATGAATTTA
1 AGATATGAATTTA
51352 A
1 A
51353 AAAAATAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
7 1 0.02
8 4 0.08
9 2 0.04
12 4 0.08
13 37 0.71
14 4 0.08
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (13 bp):
AGATATGAATTTA
Found at i:51461 original size:2 final size:2
Alignment explanation
Indices: 51454--51490 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
51444 AATTTAAGTT
51454 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51491 TTAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55211 original size:26 final size:26
Alignment explanation
Indices: 55173--55226 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
55163 ATCATAAATC
*
55173 TATGACACGCATTTATGACACGCATT
1 TATGACACACATTTATGACACGCATT
* *
55199 TATGACACACATTTATGACGCGTATT
1 TATGACACACATTTATGACACGCATT
55225 TA
1 TA
55227 GCGTCATTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (26 bp):
TATGACACACATTTATGACACGCATT
Found at i:55226 original size:13 final size:13
Alignment explanation
Indices: 55173--55217 Score: 81
Period size: 13 Copynumber: 3.5 Consensus size: 13
55163 ATCATAAATC
55173 TATGACACGCATT
1 TATGACACGCATT
55186 TATGACACGCATT
1 TATGACACGCATT
*
55199 TATGACACACATT
1 TATGACACGCATT
55212 TATGAC
1 TATGAC
55218 GCGTATTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (13 bp):
TATGACACGCATT
Found at i:55388 original size:2 final size:2
Alignment explanation
Indices: 55381--55405 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
55371 TGTCGTAAAT
55381 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
55406 TGTAGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64964 original size:34 final size:34
Alignment explanation
Indices: 64911--65014 Score: 158
Period size: 34 Copynumber: 3.1 Consensus size: 34
64901 CCTTACAGAC
* *
64911 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACATT
1 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
*
64943 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
*
64977 TCCCTAGCTTTTACACGGGCTAAGCTAAAACATT
1 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
65011 TCCC
1 TCCC
65015 CTTTACAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 7 0.11
33 5 0.08
34 53 0.82
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
Found at i:65446 original size:20 final size:20
Alignment explanation
Indices: 65421--65481 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
65411 AAACCATTCA
*
65421 GGGGGAATCGGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
*
65441 GGGGGAATCTGTACCTCCTG
1 GGGGGAATCTGTACCCCCTG
65461 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
65481 G
1 G
65482 AGAATCTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.15, C:0.28, G:0.38, T:0.20
Consensus pattern (20 bp):
GGGGGAATCTGTACCCCCTG
Found at i:66406 original size:20 final size:20
Alignment explanation
Indices: 66381--66425 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
66371 AGAAAATTAA
66381 AGTTGAGGGGTGAGATTTGT
1 AGTTGAGGGGTGAGATTTGT
66401 AGTTGAGGGGTGAGATTTGT
1 AGTTGAGGGGTGAGATTTGT
66421 AGTTG
1 AGTTG
66426 CAATATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (20 bp):
AGTTGAGGGGTGAGATTTGT
Found at i:76505 original size:75 final size:76
Alignment explanation
Indices: 76390--76541 Score: 234
Period size: 75 Copynumber: 2.0 Consensus size: 76
76380 TTGATTTATT
* *
76390 AAAAAATGACACATGGATTGTTGATGTGAAAGGAGCAATGAAATTCAAAATAAAAAATAGAAGAA
1 AAAAAATGACACATGGATTGTTGATGTGAAAGGAGAAATGAAATGCAAAATAAAAAATAGAAGAA
76455 AAAAAAACTAC
66 AAAAAAACTAC
* * * * *
76466 AAAAAA-GACACATGGCTTGTTGATGTGAAATGATAAATGAAATGGAAAATAAAAAATAGAAGGA
1 AAAAAATGACACATGGATTGTTGATGTGAAAGGAGAAATGAAATGCAAAATAAAAAATAGAAGAA
76530 AAAAAAACTAC
66 AAAAAAACTAC
76541 A
1 A
76542 TCAATACGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 63 0.91
76 6 0.09
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.18
Consensus pattern (76 bp):
AAAAAATGACACATGGATTGTTGATGTGAAAGGAGAAATGAAATGCAAAATAAAAAATAGAAGAA
AAAAAAACTAC
Found at i:76705 original size:30 final size:30
Alignment explanation
Indices: 76669--76727 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
76659 ACAATACAGT
*
76669 CCCAATATTTAATAC-GTTTGCAATATGGTC
1 CCCAATATTTAAT-CTATTTGCAATATGGTC
*
76699 CCCAATATTTAGTCTATTTGCAATATGGT
1 CCCAATATTTAATCTATTTGCAATATGGT
76728 TCCCGACCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (30 bp):
CCCAATATTTAATCTATTTGCAATATGGTC
Found at i:78739 original size:31 final size:30
Alignment explanation
Indices: 78676--78739 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
78666 TCAAACGGTC
* *
78676 GGGGACCATATTGCAAACAGACTAAATTTT
1 GGGGACCATATTGCAAACAGACGAAATGTT
*
78706 GGGGAACCATATTGTAAAC-GAACGAAATGTT
1 GGGG-ACCATATTGCAAACAG-ACGAAATGTT
78737 GGG
1 GGG
78740 AGACTGTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (30 bp):
GGGGACCATATTGCAAACAGACGAAATGTT
Found at i:83743 original size:2 final size:2
Alignment explanation
Indices: 83736--83771 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
83726 ATGTACTTAA
83736 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
83772 GCGCGCGCGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:88744 original size:226 final size:226
Alignment explanation
Indices: 88343--88786 Score: 656
Period size: 226 Copynumber: 2.0 Consensus size: 226
88333 TGATTCTAAT
* *
88343 TTATCGAACCATAATAACATAACAAGTAACGTTTATTTAATGTAATAGGTAGCACATTTTTAAAG
1 TTATCGAACCATAATAACATAACAAGTAACGCTTATTTAATGTAATAGGTAACACATTTTTAAAG
** *
88408 CCAATGGGGTCTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTAAAAATATT
66 CCAATGGGACCTTAAAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTAAAAATATT
* * *
88473 ATCAACATATTAAATAGCGCCTAAAATGTTACCAAATTTTAAGCTGATAGAGCCTTAGAAATTCA
131 ATCAACATATTAAATAGCGCCTAAAATATTACCAAAGTTTAAGCTGATAGA-CCTTAGAAATCCA
* *
88538 ACGATGACAAAATAGGTTAATTACCGAAAACA
195 ACAATAACAAAATAGGTTAATTACCGAAAACA
* * *
88570 TTATCG-ACCATAATAACATAACAAGTAACGCTTATTTAATGTAATATGTAACGCCTTTTTAAAG
1 TTATCGAACCATAATAACATAACAAGTAACGCTTATTTAATGTAATAGGTAACACATTTTTAAAG
** * * * **
88634 CTGATGTGACCTTAAAAATCCGACGATAATAAAATATGTTAATTACTTAATTTGTTATCAATATT
66 CCAATGGGACCTTAAAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTAAAAATATT
** * *
88699 ATCAACATATTAGGTAGCGCCTAAAATATTACCAAAGTTTAAGCTGATCGACCTTAGAAATCCGA
131 ATCAACATATTAAATAGCGCCTAAAATATTACCAAAGTTTAAGCTGATAGACCTTAGAAATCCAA
88764 CAATAACAAAATAGGTTAATTAC
196 CAATAACAAAATAGGTTAATTAC
88787 TTATTTTGTT
Statistics
Matches: 193, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
225 33 0.17
226 154 0.80
227 6 0.03
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (226 bp):
TTATCGAACCATAATAACATAACAAGTAACGCTTATTTAATGTAATAGGTAACACATTTTTAAAG
CCAATGGGACCTTAAAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTAAAAATATT
ATCAACATATTAAATAGCGCCTAAAATATTACCAAAGTTTAAGCTGATAGACCTTAGAAATCCAA
CAATAACAAAATAGGTTAATTACCGAAAACA
Found at i:88831 original size:107 final size:108
Alignment explanation
Indices: 88418--88926 Score: 414
Period size: 108 Copynumber: 4.6 Consensus size: 108
88408 CCAATGGGGT
*
88418 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTAAAAATATTATCAACATAT
1 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATAAATATTATCAACATAT
*
88483 TAAATAGCGCCTAAAATGTTACCAAATTTTAAGCTGAT-AGAGC
66 TAAATAGCGCCTAAAATATTACCAAATTTTAAGCTGATGAGA-C
* * * ** **** * ** *
88526 CTTAGAAATTCAACGATGACAAAATAGGTTAATTACCGAAAACATTATCGACCATAAT-AACATA
1 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTAT-AAATATTATCAACATA
** * * * ** *
88590 ACAAGTAACGCTTATTTAATGTAATATGTAACGC-CTTTTTAAAGCTGATGTGAC
65 TTAAATAGCGC----CTAA---AATAT-T-AC-CAAATTTT-AAGCTGATGAGAC
* * * *
88644 CTTAAAAATCCGACGATAATAAAATATGTTAATTACTTAATTTGTTATCAATATTATCAACATAT
1 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATAAATATTATCAACATAT
** * *
88709 TAGGTAGCGCCTAAAATATTACCAAAGTTTAAGCTGAT-CGAC
66 TAAATAGCGCCTAAAATATTACCAAATTTTAAGCTGATGAGAC
* * *
88751 CTTAGAAATCCGACAATAACAAAATAGGTTAATTACTTATTTTGTTATTAATATTATCAACATAT
1 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATAAATATTATCAACATAT
* * * * **
88816 TAAATATCGCTTAAAATATTACCAAAATTTAAGCTGATGGGGT
66 TAAATAGCGCCTAAAATATTACCAAATTTTAAGCTGATGAGAC
* * ** * ** * * *
88859 CTTCGAAATCCTACGACGACAAAATAAGTTAATTTTTTATTTTGTTATAAATAAATATTAACATA
1 CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATAAAT-ATTATCAACATA
88924 TTA
65 TTA
88927 GGTTGCACCC
Statistics
Matches: 311, Mismatches: 73, Indels: 33
0.75 0.18 0.08
Matches are distributed among these distances:
107 95 0.31
108 104 0.33
109 23 0.07
110 1 0.00
111 5 0.02
112 3 0.01
114 3 0.01
115 4 0.01
116 1 0.00
117 11 0.04
118 59 0.19
119 2 0.01
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (108 bp):
CTTAGAAATCCGACGATAACAAAATAGGTTAATTACTTAATTTGTTATAAATATTATCAACATAT
TAAATAGCGCCTAAAATATTACCAAATTTTAAGCTGATGAGAC
Found at i:89474 original size:23 final size:23
Alignment explanation
Indices: 89437--89508 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
89427 CGATAGCTAG
* * * *
89437 TTTAACGTAAGAGGTAACACTTA
1 TTTAACATAATAGGTAGCACCTA
*
89460 TTTAACATAATAGGTAGCGCCTA
1 TTTAACATAATAGGTAGCACCTA
*
89483 TTTAACTTAATAGGTAGCACCTA
1 TTTAACATAATAGGTAGCACCTA
89506 TTT
1 TTT
89509 TATTTTACCA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (23 bp):
TTTAACATAATAGGTAGCACCTA
Found at i:96055 original size:75 final size:74
Alignment explanation
Indices: 95808--96065 Score: 277
Period size: 75 Copynumber: 3.4 Consensus size: 74
95798 CAACAGCCTA
* * *
95808 TTTAACCTAATAGGTAGCGCCTATTTTATTTTACCATTTACATTATTATTAATCTTTAAACAAAC
1 TTTAACGTAATAGGTAACGCCTATTTTATTTTACCATTTACATTATTAGTAATCTTTAAACAAAC
*
95873 ATGTAGCTAG
66 -TGTAGATAG
*** *
95883 TTTAACGTAATAGGTAATTTCTATTTTATTTTACCATTTATATTATTAGTAA-CATTTAAACAAA
1 TTTAACGTAATAGGTAACGCCTATTTTATTTTACCATTTACATTATTAGTAATC-TTTAAACAAA
* * *
95947 CCGGTATATAT
65 -CTGTAGATAG
* * * *
95958 TTTAACGTAATAGGTAGA-GCCTATTTTATTTTACCGTTTGCATTATCAGTAATCTTCAAACAAA
1 TTTAACGTAATAGGTA-ACGCCTATTTTATTTTACCATTTACATTATTAGTAATCTTTAAACAAA
*
96022 CTGATAGGTAG
65 CTG-TAGATAG
* ** *
96033 TTTAACATAATAGACAACGCCTATTTTACTTTA
1 TTTAACGTAATAGGTAACGCCTATTTTATTTTA
96066 ACCGATTAAT
Statistics
Matches: 151, Mismatches: 26, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
74 4 0.03
75 144 0.95
76 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (74 bp):
TTTAACGTAATAGGTAACGCCTATTTTATTTTACCATTTACATTATTAGTAATCTTTAAACAAAC
TGTAGATAG
Found at i:96605 original size:21 final size:21
Alignment explanation
Indices: 96575--96638 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
96565 GATTTACATA
*
96575 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
96596 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
96617 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
96636 TTC
1 TTC
96639 ACGACTGGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:96742 original size:6 final size:6
Alignment explanation
Indices: 96721--96789 Score: 87
Period size: 5 Copynumber: 12.5 Consensus size: 6
96711 GACACGTATT
*
96721 ACCACG ACCACG ACCACA ACCACG ACC-CG ACC-CG ACC-CG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
96766 ACC-CG ACC-CG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
96790 CAACCTGAGA
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
5 30 0.51
6 29 0.49
ACGTcount: A:0.29, C:0.55, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:96765 original size:21 final size:22
Alignment explanation
Indices: 96725--96790 Score: 100
Period size: 21 Copynumber: 3.0 Consensus size: 22
96715 CGTATTACCA
*
96725 CGACCACGACCACAACCACGACC
1 CGACC-CGACCACGACCACGACC
96748 CGACCCGACC-CGACCACGACC
1 CGACCCGACCACGACCACGACC
96769 CGACCCGACCACGACC-CGACC
1 CGACCCGACCACGACCACGACC
96790 C
1 C
96791 AACCTGAGAC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
21 26 0.63
22 10 0.24
23 5 0.12
ACGTcount: A:0.27, C:0.56, G:0.17, T:0.00
Consensus pattern (22 bp):
CGACCCGACCACGACCACGACC
Found at i:96769 original size:16 final size:16
Alignment explanation
Indices: 96725--96790 Score: 98
Period size: 16 Copynumber: 4.1 Consensus size: 16
96715 CGTATTACCA
*
96725 CGACCACGACCACAACC
1 CGACCACGACC-CGACC
96742 ACGACC-CGACCCGACC
1 -CGACCACGACCCGACC
96758 CGACCACGACCCGACC
1 CGACCACGACCCGACC
96774 CGACCACGACCCGACC
1 CGACCACGACCCGACC
96790 C
1 C
96791 AACCTGAGAC
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
15 5 0.11
16 31 0.67
17 5 0.11
18 5 0.11
ACGTcount: A:0.27, C:0.56, G:0.17, T:0.00
Consensus pattern (16 bp):
CGACCACGACCCGACC
Found at i:97440 original size:42 final size:42
Alignment explanation
Indices: 97392--97528 Score: 220
Period size: 42 Copynumber: 3.3 Consensus size: 42
97382 TACGATTTTG
* *
97392 GACTATCGCAACAAATTTGAAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
97434 GACTATCGCAATGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
97476 GACTATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
97518 GACTATCGCAA
1 GACTATCGCAA
97529 TGCGAATATG
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:97441 original size:21 final size:21
Alignment explanation
Indices: 97417--97534 Score: 100
Period size: 21 Copynumber: 5.6 Consensus size: 21
97407 TTTGAAATAA
*
97417 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* *
97438 ATCGCAA--TGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
97457 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
* * *
97480 ATCGTAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTGGACT
*
97499 AAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTGGACT
*
97522 ATCGCAATGCGAA
1 ATCGCAACGCGAA
97535 TATGTAAATC
Statistics
Matches: 76, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
19 19 0.25
21 38 0.50
23 19 0.25
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:114858 original size:24 final size:21
Alignment explanation
Indices: 114816--114859 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
114806 ATATAAAAAA
114816 AATAAATTTTAAAATATAATT
1 AATAAATTTTAAAATATAATT
114837 AATATAATATTTAAAATGATAAT
1 AATA-AAT-TTTAAAAT-ATAAT
114860 AAATTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 3 0.15
23 8 0.40
24 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATAAATTTTAAAATATAATT
Found at i:114870 original size:24 final size:23
Alignment explanation
Indices: 114815--114893 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 23
114805 TATATAAAAA
114815 AAATA-AAT-TTTAAAATATAAT
1 AAATATAATATTTAAAATATAAT
*
114836 TAATATAATATTTAAAATGATAAT
1 AAATATAATATTTAAAAT-ATAAT
* * * *
114860 AAATTTTATATGTACAA-A-AAT
1 AAATATAATATTTAAAATATAAT
*
114881 AAATTTAATATTT
1 AAATATAATATTT
114894 TTAAAATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 18 0.38
22 4 0.09
23 8 0.17
24 17 0.36
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (23 bp):
AAATATAATATTTAAAATATAAT
Found at i:114899 original size:21 final size:20
Alignment explanation
Indices: 114857--114907 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
114847 TTAAAATGAT
*
114857 AATAAATTTTATATGTACAAA
1 AATAAATTTAATATGTAC-AA
* **
114878 AATAAATTTAATATTTTTAA
1 AATAAATTTAATATGTACAA
114898 AATAAATTTA
1 AATAAATTTA
114908 TAAATTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AATAAATTTAATATGTACAA
Found at i:114904 original size:24 final size:25
Alignment explanation
Indices: 114822--114901 Score: 64
Period size: 23 Copynumber: 3.4 Consensus size: 25
114812 AAAAAATAAA
* *
114822 TTTTAAAATATAATTAATATAATA-
1 TTTTAAAATATAATAAATTTAATAT
114846 -TTTAAAATGATAATAAATTT--TAT
1 TTTTAAAAT-ATAATAAATTTAATAT
* * *
114869 ATGTACAA-A-AATAAATTTAATAT
1 TTTTAAAATATAATAAATTTAATAT
114892 TTTTAAAATA
1 TTTTAAAATA
114902 AATTTATAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 12
0.69 0.11 0.19
Matches are distributed among these distances:
21 9 0.21
22 3 0.07
23 16 0.37
24 15 0.35
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (25 bp):
TTTTAAAATATAATAAATTTAATAT
Found at i:114917 original size:19 final size:20
Alignment explanation
Indices: 114876--114925 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
114866 TATATGTACA
**
114876 AAAATAAATTTAATATTTTT
1 AAAATAAATTTAATAAATTT
114896 AAAATAAATTT-ATAAATTT
1 AAAATAAATTTAATAAATTT
*
114915 AAAATTAATTT
1 AAAATAAATTT
114926 TATCAAACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AAAATAAATTTAATAAATTT
Found at i:115551 original size:12 final size:12
Alignment explanation
Indices: 115534--115558 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
115524 TATTGTTCAT
115534 TGCTACAGTAAC
1 TGCTACAGTAAC
115546 TGCTACAGTAAC
1 TGCTACAGTAAC
115558 T
1 T
115559 TTCGAAAATA
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:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (12 bp):
TGCTACAGTAAC
Found at i:117107 original size:29 final size:30
Alignment explanation
Indices: 117062--117131 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
117052 AACCCCTCAA
* * *
117062 TTTTCCAAAATTTACGAATTGAT-CTCCAAC
1 TTTT-CAAAAATTACGAAATGATCCTCAAAC
* *
117092 TTTTCAAAAATTACGAAATGGTCCTCAAAT
1 TTTTCAAAAATTACGAAATGATCCTCAAAC
117122 TTTTCAAAAA
1 TTTTCAAAAA
117132 CTTGTATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 15 0.44
30 19 0.56
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (30 bp):
TTTTCAAAAATTACGAAATGATCCTCAAAC
Found at i:118676 original size:22 final size:19
Alignment explanation
Indices: 118646--118696 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 19
118636 ATTAAATACA
118646 TAAA-TAATATCATTTATAAT
1 TAAATTAATAT-ATTT-TAAT
*
118666 TAAATTTAATAATATTTTTAT
1 TAAA-TTAAT-ATATTTTAAT
118687 TAAATTAATA
1 TAAATTAATA
118697 AATAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.04
20 9 0.33
21 7 0.26
22 8 0.30
23 2 0.07
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTAATATATTTTAAT
Found at i:118700 original size:24 final size:26
Alignment explanation
Indices: 118627--118705 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 26
118617 ATTAGATTAT
*
118627 TATATTAATATTAAA-TACATAAATAA
1 TATATTTATATTAAATTA-ATAAATAA
118653 TATCATTTATAATTAAATT--T-AATAA
1 TAT-ATTTAT-ATTAAATTAATAAATAA
118678 TAT-TTT-TATTAAATTAATAAATAA
1 TATATTTATATTAAATTAATAAATAA
118702 TATA
1 TATA
118706 AATTTTATTA
Statistics
Matches: 45, Mismatches: 1, Indels: 15
0.74 0.02 0.25
Matches are distributed among these distances:
21 8 0.18
22 1 0.02
23 4 0.09
24 8 0.18
25 8 0.18
26 4 0.09
27 5 0.11
28 6 0.13
29 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.46
Consensus pattern (26 bp):
TATATTTATATTAAATTAATAAATAA
Found at i:118915 original size:21 final size:20
Alignment explanation
Indices: 118829--118986 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
118819 AAATGACCAA
**
118829 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
118848 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
118868 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
118888 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
118909 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
118930 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
118950 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
118971 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
118987 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:119015 original size:20 final size:20
Alignment explanation
Indices: 118953--119146 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
118943 CGATTTTCCA
* ** *
118953 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
118973 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
118993 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
119013 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
119033 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
119053 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
119073 ATATCGCAACGCGTATCCAT
1 AAATCGCAACGCGTATCCGT
* * *
119093 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
119113 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
119134 AAATCGCAACGCG
1 AAATCGCAACGCG
119147 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:119037 original size:60 final size:60
Alignment explanation
Indices: 118973--119146 Score: 240
Period size: 60 Copynumber: 2.9 Consensus size: 60
118963 GCGAATATGA
* * *
118973 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCAT
* *** * *
119033 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAACGCGTATCCAT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCAT
**
119093 AAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCG
119147 ATATTTAAAG
Statistics
Matches: 96, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 65 0.68
61 31 0.32
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCAT
Found at i:119566 original size:33 final size:33
Alignment explanation
Indices: 119527--119597 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
119517 TTCACTTAGA
*
119527 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
119560 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
119593 TTTCA
1 TTTCA
119598 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.25, G:0.15, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:119703 original size:21 final size:20
Alignment explanation
Indices: 119677--119780 Score: 87
Period size: 21 Copynumber: 5.5 Consensus size: 20
119667 TGCAGAAGAG
119677 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
119698 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
119718 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
119739 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
119753 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
119772 TCGCAACGA
1 TCGCAACGA
119781 CAGAATCGCA
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 10 0.15
20 16 0.25
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.11
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:119721 original size:20 final size:21
Alignment explanation
Indices: 119675--119753 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
119665 TTTGCAGAAG
*
119675 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
119697 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
119716 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
119738 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
119754 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:119734 original size:41 final size:41
Alignment explanation
Indices: 119676--119753 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
119666 TTGCAGAAGA
* *
119676 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
119717 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAAT
119754 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.45, C:0.17, G:0.27, T:0.12
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAAGCGCAACGAGAGAATGACT
Found at i:119769 original size:33 final size:33
Alignment explanation
Indices: 119729--119798 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
119719 CGCAACGAGA
*
119729 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGACAGAATCGCAACGC
*
119762 GAAATGAAAATCGCAACGACAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGACAGAATCGCAACGC
119795 GAAA
1 GAAA
119799 CCAAAATCGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.21, G:0.24, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGACAGAATCGCAACGC
Found at i:119805 original size:33 final size:33
Alignment explanation
Indices: 119735--119809 Score: 114
Period size: 33 Copynumber: 2.3 Consensus size: 33
119725 GAGAGAAATG
* * **
119735 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
119768 AAAATCGCAACGACAGAATCGCAACGCGAAACC
1 AAAATCGCAACGACAGAATCGCAACGCGAAACC
119801 AAAATCGCA
1 AAAATCGCA
119810 TTGCGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.47, C:0.25, G:0.21, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGACAGAATCGCAACGCGAAACC
Found at i:119808 original size:19 final size:18
Alignment explanation
Indices: 119751--119809 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
119741 GCAACGAGAG
*
119751 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-CAA
*
119770 AATCGCAA--CG--ACAG
1 AATCGCAACGCGAAACAA
119784 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-CAA
119803 AATCGCA
1 AATCGCA
119810 TTGCGATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 9 0.28
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.46, C:0.27, G:0.19, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAACAA
Found at i:119827 original size:19 final size:19
Alignment explanation
Indices: 119805--119907 Score: 100
Period size: 19 Copynumber: 5.9 Consensus size: 19
119795 GAAACCAAAA
* *
119805 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATC
119824 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
*
119840 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATC
*
119857 TCGCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATC
119876 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
119892 T--CGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
119908 TTCAACCAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
14 16 0.23
16 11 0.16
17 8 0.11
19 35 0.50
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATC
Found at i:119888 original size:52 final size:52
Alignment explanation
Indices: 119805--119910 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
119795 GAAACCAAAA
* *
119805 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
119857 TCGCGTTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
119909 TC
1 TC
119911 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:121195 original size:18 final size:18
Alignment explanation
Indices: 121172--121219 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
121162 CTCCAATTCG
121172 AGAGCCATCACCTCACCT
1 AGAGCCATCACCTCACCT
121190 AGAGCCATCACCTCACCT
1 AGAGCCATCACCTCACCT
121208 AGAGCCATCACC
1 AGAGCCATCACC
121220 CGATCGACCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.29, C:0.44, G:0.12, T:0.15
Consensus pattern (18 bp):
AGAGCCATCACCTCACCT
Found at i:121791 original size:93 final size:93
Alignment explanation
Indices: 121632--122198 Score: 1098
Period size: 93 Copynumber: 6.1 Consensus size: 93
121622 TAGATTGCTT
*
121632 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
121697 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
121725 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
121790 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
121818 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
121883 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
121911 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
121976 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
122004 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAATTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
122069 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
122097 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
122162 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
122190 AGTAAATTT
1 AGTAAATTT
122199 ATCCATTCAA
Statistics
Matches: 469, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 469 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:122282 original size:19 final size:19
Alignment explanation
Indices: 122242--122370 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
122232 TAGTTTACTT
* *
122242 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
122262 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
122281 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
122300 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
122314 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
* *
122333 TCGCAA--CG--A-TAAGA
1 TCGCAACGCGAAACCAAAA
122347 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
122366 TCGCA
1 TCGCA
122371 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 18 0.20
15 2 0.02
16 4 0.05
17 4 0.05
18 2 0.02
19 45 0.51
20 13 0.15
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:122321 original size:33 final size:32
Alignment explanation
Indices: 122278--122370 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
122268 CGCGAAACCA
**
122278 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
122310 AGAATCGCAACGCGAAACCAAAATCGCAACGAT
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
122343 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
122371 TTGCGATTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
32 2 0.04
33 54 0.96
ACGTcount: A:0.46, C:0.27, G:0.18, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:122368 original size:52 final size:52
Alignment explanation
Indices: 122242--122370 Score: 138
Period size: 52 Copynumber: 2.5 Consensus size: 52
122232 TAGTTTACTT
** *
122242 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
* * * *
122294 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGATAAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAA-A
*
122347 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
122371 TTGCGATTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.69
53 2 0.03
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGAGAAA
Found at i:122388 original size:19 final size:19
Alignment explanation
Indices: 122366--122500 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
122356 GAAACCAAAA
*
122366 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
122385 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
122401 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
122418 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
122434 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
122451 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
122470 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
122490 TCGTGTTGCGA
1 TCGCGTTGCGA
122501 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:122407 original size:14 final size:14
Alignment explanation
Indices: 122388--122444 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
122378 TTTCATTTCG
122388 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
122402 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
122419 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
122435 CGTTGCGATT
1 CGTTGCGATT
122445 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:122413 original size:33 final size:33
Alignment explanation
Indices: 122371--122463 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
122361 CAAAATCGCA
*
122371 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
122404 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
122437 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
122464 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:124447 original size:14 final size:14
Alignment explanation
Indices: 124428--124463 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
124418 ATTGTTTAAT
124428 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
124442 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
124456 TGATTTGT
1 TGATTTGT
124464 GTAATTGATG
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:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:124663 original size:20 final size:19
Alignment explanation
Indices: 124570--124667 Score: 125
Period size: 19 Copynumber: 5.4 Consensus size: 19
124560 AAAATTGACT
124570 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
124589 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
124608 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
124622 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
124641 ATCGCAATGCGGAAATTACA
1 ATCGCAATGC-GAAATGAAA
124661 ATCGCAA
1 ATCGCAA
124668 CGAGAGAATC
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.57
20 14 0.20
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:124699 original size:53 final size:53
Alignment explanation
Indices: 124570--124686 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
124560 AAAATTGACT
124570 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
124622 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATTACAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
124675 ATCGCAATGCGA
1 ATCGCAATGCGA
124687 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:124704 original size:19 final size:19
Alignment explanation
Indices: 124676--124843 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
124666 AACGAGAGAA
* *
124676 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
124695 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
124711 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
124728 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
124747 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
124763 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
124780 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
124799 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
124815 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
124832 TCCGCATTGCGA
1 T-CGCATTGCGA
124844 AATGTAATGG
Statistics
Matches: 125, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 18 0.14
16 21 0.17
17 18 0.14
18 2 0.02
19 60 0.48
20 6 0.05
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:124719 original size:33 final size:33
Alignment explanation
Indices: 124682--124843 Score: 159
Period size: 33 Copynumber: 4.7 Consensus size: 33
124672 AGAATCGCAA
*
124682 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
124715 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
124753 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
124786 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
124819 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
124844 AATGTAATGG
Statistics
Matches: 104, Mismatches: 13, Indels: 23
0.74 0.09 0.16
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 49 0.47
34 10 0.10
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:124739 original size:52 final size:52
Alignment explanation
Indices: 124676--124843 Score: 309
Period size: 52 Copynumber: 3.2 Consensus size: 52
124666 AACGAGAGAA
* *
124676 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
124728 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
124780 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
124832 TCCGCATTGCGA
1 T-CGCATTGCGA
124844 AATGTAATGG
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 103 0.91
53 10 0.09
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:124926 original size:19 final size:19
Alignment explanation
Indices: 124902--124999 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
124892 AAAATTGACT
124902 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
124921 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
124940 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
124954 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
124973 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
124993 ATCGCAA
1 ATCGCAA
125000 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:125031 original size:53 final size:53
Alignment explanation
Indices: 124902--125018 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
124892 AAAATTGACT
124902 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
124954 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
125007 ATCGCAATGCGA
1 ATCGCAATGCGA
125019 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:127567 original size:24 final size:24
Alignment explanation
Indices: 127533--127579 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
127523 CTGAAACATC
127533 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
127557 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
127580 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:128290 original size:20 final size:20
Alignment explanation
Indices: 128262--128491 Score: 264
Period size: 20 Copynumber: 11.5 Consensus size: 20
128252 AAATTTCAGT
* *
128262 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
128282 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
128302 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
128322 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
128342 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
128362 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
128382 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
128402 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
128422 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
128442 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
128462 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
128482 GTTGCGATTT
1 GTTGCGATTT
128492 TTATATTCGC
Statistics
Matches: 185, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
20 184 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:128500 original size:20 final size:20
Alignment explanation
Indices: 128461--128512 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
128451 TACGGATACA
* * *
128461 CGTTGCGATTTATGTGTTCG
1 CGTTGCGATTTTTATATTCG
128481 CGTTGCGATTTTTATATTCG
1 CGTTGCGATTTTTATATTCG
128501 CGTTGCGATTTT
1 CGTTGCGATTTT
128513 GGAAAATCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (20 bp):
CGTTGCGATTTTTATATTCG
Found at i:128528 original size:21 final size:21
Alignment explanation
Indices: 128498--128580 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
128488 ATTTTTATAT
*
128498 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
128519 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
128540 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
128561 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
128581 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:128571 original size:42 final size:42
Alignment explanation
Indices: 128478--128576 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
128468 ATTTATGTGT
* * *
128478 TCGCGTTGCG-ATTTTTATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTATATTCGCATTGCGATTTTGCAAAA
**
128519 TCGCAATGCGAATTTGTACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTA-TATTCGCATTGCGATTTTGCAA-AA
*
128561 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
128577 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 10 0.21
42 35 0.74
43 2 0.04
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (42 bp):
TCGCGTTGCGAATTTGTATATTCGCATTGCGATTTTGCAAAA
Found at i:133669 original size:6 final size:6
Alignment explanation
Indices: 133658--133695 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
133648 TTAGAATTGC
133658 CCCAAG CCCAAG CCCAAG CCCAAG CCCAAG CCCAAG CC
1 CCCAAG CCCAAG CCCAAG CCCAAG CCCAAG CCCAAG CC
133696 AAAATCTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
CCCAAG
Found at i:141088 original size:19 final size:19
Alignment explanation
Indices: 141064--141113 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
141054 TCGACCCTCC
*
141064 AGTATCGGTACCTACCCTT
1 AGTATCGATACCTACCCTT
141083 AGTATCGATACCTACCCTT
1 AGTATCGATACCTACCCTT
*
141102 AGTATTGATACC
1 AGTATCGATACC
141114 GAAATTGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (19 bp):
AGTATCGATACCTACCCTT
Found at i:141211 original size:18 final size:18
Alignment explanation
Indices: 141188--141236 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
141178 ACCTTGTTAG
141188 GGTATCGATACCATCCTA
1 GGTATCGATACCATCCTA
141206 GGTATCGATACCATCCTA
1 GGTATCGATACCATCCTA
141224 GGTATCGATACCA
1 GGTATCGATACCA
141237 AAATTGGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (18 bp):
GGTATCGATACCATCCTA
Found at i:141328 original size:20 final size:21
Alignment explanation
Indices: 141289--141341 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
141279 CCCTATCCTC
*
141289 AGTATCGGTACCCCAAGAAT-
1 AGTATCGATACCCCAAGAATA
* *
141309 AGTATCGATACCCTATGAATA
1 AGTATCGATACCCCAAGAATA
141330 GAGTATCGATAC
1 -AGTATCGATAC
141342 TACTGACCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.61
22 11 0.39
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.25
Consensus pattern (21 bp):
AGTATCGATACCCCAAGAATA
Found at i:143450 original size:29 final size:30
Alignment explanation
Indices: 143399--143459 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
143389 AAATTTTATC
* **
143399 TAGTGACTAAAGTGTAAGTTTTG-AAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
*
143428 TAGTGGCTAAAGTATAAACTTTGAAAAGTT
1 TAGTGACTAAAGTATAAACTTTGAAAAGTT
143458 TA
1 TA
143460 AAGAATGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 19 0.70
30 8 0.30
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (30 bp):
TAGTGACTAAAGTATAAACTTTGAAAAGTT
Found at i:144993 original size:17 final size:17
Alignment explanation
Indices: 144971--145013 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
144961 TGATTATGGA
*
144971 ATTTATTTTGGAAATGT
1 ATTTATGTTGGAAATGT
144988 ATTTATGTTGGAAATGT
1 ATTTATGTTGGAAATGT
145005 ATTTATGTT
1 ATTTATGTT
145014 AGTACAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (17 bp):
ATTTATGTTGGAAATGT
Found at i:145209 original size:24 final size:24
Alignment explanation
Indices: 145182--145230 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
145172 TGCATGACAT
*
145182 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGATTTATACATCA
145206 TGTACATAGATGATTTATACATCA
1 TGTACATAGATGATTTATACATCA
145230 T
1 T
145231 CAGGAAGACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (24 bp):
TGTACATAGATGATTTATACATCA
Found at i:146315 original size:20 final size:20
Alignment explanation
Indices: 146290--146337 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
146280 ATGAACAGTA
* * *
146290 GTGAACATTACCGATACTGT
1 GTGAACAGTACCAATAATGT
146310 GTGAACAGTACCAATAATGT
1 GTGAACAGTACCAATAATGT
146330 GTGAACAG
1 GTGAACAG
146338 CAATGAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (20 bp):
GTGAACAGTACCAATAATGT
Found at i:146535 original size:21 final size:20
Alignment explanation
Indices: 146502--146540 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
146492 ATTTTTGTAG
*
146502 AAAAAATCTCCAAACGGCTCC
1 AAAAAATC-CCCAACGGCTCC
*
146523 AAAACATCCCCAACGGCT
1 AAAAAATCCCCAACGGCT
146541 ATATACGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.41, C:0.36, G:0.10, T:0.13
Consensus pattern (20 bp):
AAAAAATCCCCAACGGCTCC
Found at i:147108 original size:14 final size:14
Alignment explanation
Indices: 147091--147131 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
147081 GTAAAATATG
*
147091 GTATGAACAGTGTC
1 GTATGAACAGTGCC
147105 GTATGAACAGTGCC
1 GTATGAACAGTGCC
147119 G--TGAACAGTGCC
1 GTATGAACAGTGCC
147131 G
1 G
147132 AATTCTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 12 0.46
14 14 0.54
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.22
Consensus pattern (14 bp):
GTATGAACAGTGCC
Found at i:147125 original size:12 final size:13
Alignment explanation
Indices: 147093--147132 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
147083 AAAATATGGT
*
147093 ATGAACAGTGTCG
1 ATGAACAGTGCCG
147106 TATGAACAGTGCCG
1 -ATGAACAGTGCCG
147120 -TGAACAGTGCCG
1 ATGAACAGTGCCG
147132 A
1 A
147133 ATTCTAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 12 0.50
14 12 0.50
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (13 bp):
ATGAACAGTGCCG
Found at i:147969 original size:31 final size:31
Alignment explanation
Indices: 147931--148058 Score: 141
Period size: 31 Copynumber: 4.1 Consensus size: 31
147921 GAACCTCGAC
*
147931 AACTGTCCATATGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
** **
147962 AACTGTCCATATGTTTCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
*
147993 TACTGTCCATATGTCCCGAA-AGACATAGGTTA
1 AACTGTCCATATGTCCCGAAGA-ACATAGG-TA
** * *
148025 TTCTGTCCATATGTTCCGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
148056 AAC
1 AAC
148059 CCTCGACTCT
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
30 1 0.01
31 51 0.65
32 26 0.33
33 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:148053 original size:63 final size:62
Alignment explanation
Indices: 147932--148055 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 62
147922 AACCTCGACA
* * *
147932 ACTGTCCATATGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTTCTTAGAACATAGGTAT
1 ACTGTCCATATGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
**
147994 ACTGTCCATATGTCCCGAA-AGACATAGGTTATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGTCCCGAAGA-ACATAGG-TAAACTGTCCATATGTTCCGTAGAACATAGGTA
148056 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
61 1 0.02
62 25 0.45
63 29 0.53
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (62 bp):
ACTGTCCATATGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:148404 original size:29 final size:30
Alignment explanation
Indices: 148321--148405 Score: 77
Period size: 29 Copynumber: 2.9 Consensus size: 30
148311 ATATTCATAT
* *
148321 ATATAGTTCAC-TTCACATATCATATTAATC
1 ATATGGTTCACTTTCACATATCACATT-ATC
* * * *
148351 ATATGGTTTACTTGCACGTAGCACATT-TC
1 ATATGGTTCACTTTCACATATCACATTATC
148380 ATA-GGATTCACTTTCACATATCACAT
1 ATATGG-TTCACTTTCACATATCACAT
148406 ATTCCTTTTC
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
28 2 0.05
29 21 0.49
30 9 0.21
31 11 0.26
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (30 bp):
ATATGGTTCACTTTCACATATCACATTATC
Done.