Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001358.1 Hibiscus syriacus cultivar Beakdansim tig00002643_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: 107544
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:4081 original size:17 final size:18
Alignment explanation
Indices: 4048--4081 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4038 CCGCTACTGG
4048 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
4066 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
4082 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:5849 original size:31 final size:31
Alignment explanation
Indices: 5811--5998 Score: 290
Period size: 31 Copynumber: 6.1 Consensus size: 31
5801 CCCGAAGGAC
* * *
5811 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
5842 CAGTCCATATGTCCTGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5873 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
5904 TAGTCCAT-TAGTCCCGAAGAAGATAGGTAAA
1 CAGTCCATAT-GTCCCGAAGAACATAGGTAAA
5935 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5966 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5997 CA
1 CA
5999 CTCGACCCTT
Statistics
Matches: 145, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
30 1 0.01
31 142 0.98
32 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:6971 original size:18 final size:18
Alignment explanation
Indices: 6948--7015 Score: 72
Period size: 18 Copynumber: 3.9 Consensus size: 18
6938 ATTATTTAGG
6948 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
***
6966 GGGGAAT--ATGTTCCC-
1 GGGGAATCGATACCCCCA
6981 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
6999 GGGGAATCTG-TACCCCC
1 GGGGAATC-GATACCCCC
7016 TGGACATTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 7 0.17
16 5 0.12
17 5 0.12
18 22 0.55
19 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.16
Consensus pattern (18 bp):
GGGGAATCGATACCCCCA
Found at i:9986 original size:16 final size:16
Alignment explanation
Indices: 9965--9995 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9955 TCTAATTTTT
9965 TTTTTGAGTTCAAGTA
1 TTTTTGAGTTCAAGTA
9981 TTTTTGAGTTCAAGT
1 TTTTTGAGTTCAAGT
9996 TTCAATACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTTTGAGTTCAAGTA
Found at i:10409 original size:19 final size:19
Alignment explanation
Indices: 10385--10425 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
10375 CCTTGCACAT
10385 GGCGCCTTAGGTACACTTA
1 GGCGCCTTAGGTACACTTA
*
10404 GGCGCCTTAGGTACGCTTA
1 GGCGCCTTAGGTACACTTA
10423 GGC
1 GGC
10426 ACGTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.17, C:0.27, G:0.32, T:0.24
Consensus pattern (19 bp):
GGCGCCTTAGGTACACTTA
Found at i:14927 original size:94 final size:93
Alignment explanation
Indices: 14756--14944 Score: 236
Period size: 94 Copynumber: 2.0 Consensus size: 93
14746 GGTTTTAATG
* * **
14756 TAGTCTTACAATGTAGTTATTACAACCACGTATAAAAAATTAAAGTAAAACCAACATGTACATCA
1 TAGTCTTACAATATAGTTATAACAACCAAATATAAAAAATTAAAGTAAAACCAACATGTACATCA
* *
14821 TGCACGTGAAATGATAATATTAAAATATT
66 TACACGTCAAATGATAATATT-AAATATT
* * * **
14850 TAGTCTTGCAATATAGTTATAACAACCAAATATAAAATAATTGAAGT-AAATCAACATGTGGATC
1 TAGTCTTACAATATAGTTATAACAACCAAATATAAAA-AATTAAAGTAAAACCAACATGTACATC
* *
14914 GTACATGTCAAATGATAATATTAAATATT
65 ATACACGTCAAATGATAATATTAAATATT
14943 TA
1 TA
14945 CAGTAAAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
93 9 0.11
94 64 0.79
95 8 0.10
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (93 bp):
TAGTCTTACAATATAGTTATAACAACCAAATATAAAAAATTAAAGTAAAACCAACATGTACATCA
TACACGTCAAATGATAATATTAAATATT
Found at i:20913 original size:70 final size:70
Alignment explanation
Indices: 20800--20932 Score: 230
Period size: 70 Copynumber: 1.9 Consensus size: 70
20790 AAGAGCATAG
* *
20800 AAGAGCAAAAATAGGAGAACAAAACAATCCCACATGGCTAAGAAACTTAGAAGAGCATCCCAAAA
1 AAGAGCAAAAATAGGAGAACAAAACAATCCCACATGGATAAGAAACATAGAAGAGCATCCCAAAA
20865 GTCTA
66 GTCTA
* *
20870 AAGAGTAAAAATATGAGAACAAAACAATCCCACATGGATAAGAAACATAGAAGAGCATCCCAA
1 AAGAGCAAAAATAGGAGAACAAAACAATCCCACATGGATAAGAAACATAGAAGAGCATCCCAA
20933 CCGACTTCTA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 59 1.00
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.13
Consensus pattern (70 bp):
AAGAGCAAAAATAGGAGAACAAAACAATCCCACATGGATAAGAAACATAGAAGAGCATCCCAAAA
GTCTA
Found at i:21335 original size:30 final size:30
Alignment explanation
Indices: 21283--21340 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
21273 TAGAAACGAC
* *
21283 GGTTCACACCGGTTTTGCCGGTTTTCAGTT
1 GGTTCACACCGGTTTTACCGGTTCTCAGTT
* *
21313 GGTTCATACCGGTTTTATCGGTTCTCAG
1 GGTTCACACCGGTTTTACCGGTTCTCAG
21341 CCAGTTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.12, C:0.22, G:0.26, T:0.40
Consensus pattern (30 bp):
GGTTCACACCGGTTTTACCGGTTCTCAGTT
Found at i:22190 original size:22 final size:22
Alignment explanation
Indices: 22143--22184 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
22133 CTTTATCTCA
22143 ATTTATTTAATTAATTATTTTC
1 ATTTATTTAATTAATTATTTTC
*
22165 ATTTATTTAATT-CTTATTTT
1 ATTTATTTAATTAATTATTTT
22185 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTATTTAATTAATTATTTTC
Found at i:26009 original size:25 final size:26
Alignment explanation
Indices: 25981--26033 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
25971 AATCATTCAA
25981 TTATTACCAAAG-ATTATAAAAT-ATT
1 TTATTACCAAAGCATTA-AAAATCATT
* *
26006 TTATTTCCATAGCATTAAAAATCATT
1 TTATTACCAAAGCATTAAAAATCATT
26032 TT
1 TT
26034 CACTAGAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (26 bp):
TTATTACCAAAGCATTAAAAATCATT
Found at i:26659 original size:30 final size:30
Alignment explanation
Indices: 26625--26771 Score: 101
Period size: 30 Copynumber: 5.0 Consensus size: 30
26615 TCATATCAAA
26625 CATGTACCTTTCACTTTATTCATTTCATAG
1 CATGTACCTTTCACTTTATTCATTTCATAG
* * *
26655 CATGTTCCATTT-ACTTCATTTATTTCATAG
1 CATGTACC-TTTCACTTTATTCATTTCATAG
* * * *
26685 CATGTATCATTCA-TTTAATTGATTTCGTAG
1 CATGTACCTTTCACTTT-ATTCATTTCATAG
* * *
26715 CCTGTATCATTCAC--T-TTCATTTCATAG
1 CATGTACCTTTCACTTTATTCATTTCATAG
* * *
26742 CATATA-CTATTCA-TTTTTTTATTTCATAG
1 CATGTACCT-TTCACTTTATTCATTTCATAG
26771 C
1 C
26772 CCAATGTAAA
Statistics
Matches: 93, Mismatches: 16, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.01
27 18 0.19
28 1 0.01
29 17 0.18
30 53 0.57
31 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.48
Consensus pattern (30 bp):
CATGTACCTTTCACTTTATTCATTTCATAG
Found at i:27178 original size:25 final size:25
Alignment explanation
Indices: 27144--27200 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
27134 AATGCTCCAA
27144 ACATATGGCATGCCAATTATATTAT
1 ACATATGGCATGCCAATTATATTAT
27169 ACATATGGCATGCCAATTATATTAT
1 ACATATGGCATGCCAATTATATTAT
*
27194 ACCTATG
1 ACATATG
27201 ACTCTCAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (25 bp):
ACATATGGCATGCCAATTATATTAT
Found at i:29761 original size:23 final size:23
Alignment explanation
Indices: 29735--29829 Score: 64
Period size: 24 Copynumber: 3.7 Consensus size: 23
29725 ATATTTATTT
29735 ATTTATTTTTAAAATAATTTAAA
1 ATTTATTTTTAAAATAATTTAAA
*
29758 ATTTGTATTCTATTATAAATAAATATCATAA
1 A-TT-TATT-T-TTA-AAAT-AAT-TTA-AA
* *
29789 ATTTAATTTTTAAAATAAATTAAT
1 ATTT-ATTTTTAAAATAATTTAAA
*
29813 ATTAATTTTATAAAATA
1 ATTTATTTT-TAAAATA
29830 TATAACTTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 19
0.70 0.06 0.23
Matches are distributed among these distances:
23 6 0.11
24 13 0.23
25 6 0.11
26 3 0.05
27 7 0.12
28 7 0.12
29 5 0.09
30 7 0.12
31 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (23 bp):
ATTTATTTTTAAAATAATTTAAA
Found at i:30346 original size:64 final size:64
Alignment explanation
Indices: 30262--30412 Score: 151
Period size: 64 Copynumber: 2.4 Consensus size: 64
30252 CCACATAGAT
* * * * **
30262 AAATAATATCTCACCTCTAAGGTCATATGTATAAATAATC-TCTCAACATTAAGGCAGCATAAAC
1 AAATAATATATCACCACTAAGGTCACATGGATAAATAA-CATCTCAACATTAAAACAGCATAAAC
* * ** * *
30326 AAATAATATATCGCCACTAAGGTCGCATGGATAAATAACATCTCGCCATTAAAACCGCATAAAT
1 AAATAATATATCACCACTAAGGTCACATGGATAAATAACATCTCAACATTAAAACAGCATAAAC
* * *
30390 AAATAATATCTTACCAATAAGGT
1 AAATAATATATCACCACTAAGGT
30413 TGTTGAATAA
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
63 1 0.01
64 69 0.99
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (64 bp):
AAATAATATATCACCACTAAGGTCACATGGATAAATAACATCTCAACATTAAAACAGCATAAAC
Found at i:30362 original size:32 final size:32
Alignment explanation
Indices: 30308--30442 Score: 103
Period size: 32 Copynumber: 4.2 Consensus size: 32
30298 AATCTCTCAA
* *
30308 CATTAAGG-CAGCATAAACAAATAATATATCGC
1 CATTAAGGTC-GCATGAATAAATAATATATCGC
* * * *
30340 CACTAAGGTCGCATGGATAAATAACATCTCGC
1 CATTAAGGTCGCATGAATAAATAATATATCGC
*** * * **
30372 CATTAAAACCGCATAAATAAATAATATCTTAC
1 CATTAAGGTCGCATGAATAAATAATATATCGC
* * *
30404 CAATAAGGTTG-TTGAATAAATAATATATCGC
1 CATTAAGGTCGCATGAATAAATAATATATCGC
30435 CATTAAGG
1 CATTAAGG
30443 CCGTATATAT
Statistics
Matches: 76, Mismatches: 26, Indels: 3
0.72 0.25 0.03
Matches are distributed among these distances:
31 22 0.29
32 53 0.70
33 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (32 bp):
CATTAAGGTCGCATGAATAAATAATATATCGC
Found at i:30941 original size:18 final size:18
Alignment explanation
Indices: 30918--30962 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
30908 TAATACTAAC
30918 AATAATACAAG-TAAGAAT
1 AATAATA-AAGATAAGAAT
30936 AATAATAAAGATAAGAAT
1 AATAATAAAGATAAGAAT
30954 AATAATAAA
1 AATAATAAA
30963 ACATGTAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (18 bp):
AATAATAAAGATAAGAAT
Found at i:30971 original size:21 final size:20
Alignment explanation
Indices: 30927--30972 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
30917 CAATAATACA
*
30927 AGTAAGAATAATAAT-AAAG
1 AGTAAGAATAATAATAAAAC
30946 A-TAAGAATAATAATAAAAC
1 AGTAAGAATAATAATAAAAC
30965 ATGTAAGA
1 A-GTAAGA
30973 TCGATCAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 13 0.57
19 5 0.22
21 5 0.22
ACGTcount: A:0.63, C:0.02, G:0.13, T:0.22
Consensus pattern (20 bp):
AGTAAGAATAATAATAAAAC
Found at i:34381 original size:38 final size:38
Alignment explanation
Indices: 34330--34407 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
34320 ATCGCATCAG
34330 GAACGTACATCCAATACCCATTGATGATCAAGTACCTC
1 GAACGTACATCCAATACCCATTGATGATCAAGTACCTC
34368 GAACGTACATCCAATACCCATTGATGATCAAGTACCTC
1 GAACGTACATCCAATACCCATTGATGATCAAGTACCTC
34406 GA
1 GA
34408 GTGAGACCTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (38 bp):
GAACGTACATCCAATACCCATTGATGATCAAGTACCTC
Found at i:35161 original size:18 final size:18
Alignment explanation
Indices: 35138--35176 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
35128 TAGAGACAAA
35138 AGAAAAATAAACATTGTT
1 AGAAAAATAAACATTGTT
35156 AGAAAAATAAACATTGTT
1 AGAAAAATAAACATTGTT
35174 AGA
1 AGA
35177 GTTTGGCTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.26
Consensus pattern (18 bp):
AGAAAAATAAACATTGTT
Found at i:35314 original size:22 final size:22
Alignment explanation
Indices: 35289--35330 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
35279 TTTAGGGGTC
*
35289 AAAATTATAAGTTTTAGAAAAA
1 AAAATAATAAGTTTTAGAAAAA
*
35311 AAAATAATCAGTTTTAGAAA
1 AAAATAATAAGTTTTAGAAA
35331 GTTGTAGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.31
Consensus pattern (22 bp):
AAAATAATAAGTTTTAGAAAAA
Found at i:36098 original size:30 final size:30
Alignment explanation
Indices: 36057--36127 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 30
36047 CGGGTCAACT
* * *
36057 CGTTAACTTTGATCGAGTCAAACCGTTAAC
1 CGTTGACTTTGACCGAGTCAAACCATTAAC
* *
36087 CGTTGACTTTGACCGAGTCAACCCATTGAC
1 CGTTGACTTTGACCGAGTCAAACCATTAAC
36117 CGTTGACTTTG
1 CGTTGACTTTG
36128 TCTGAAAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (30 bp):
CGTTGACTTTGACCGAGTCAAACCATTAAC
Found at i:37122 original size:27 final size:28
Alignment explanation
Indices: 37084--37142 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 28
37074 ATTATAGAAT
*
37084 TACCCCTGAAGTGTAAAATGA-CTAAAA
1 TACCCCTAAAGTGTAAAATGACCTAAAA
* *
37111 TACCCCTAAAGTGTATAATGACCTAAAG
1 TACCCCTAAAGTGTAAAATGACCTAAAA
37139 TACC
1 TACC
37143 TCTGAACCCT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.24
Consensus pattern (28 bp):
TACCCCTAAAGTGTAAAATGACCTAAAA
Found at i:40783 original size:270 final size:270
Alignment explanation
Indices: 40294--40837 Score: 973
Period size: 270 Copynumber: 2.0 Consensus size: 270
40284 CTTGTGCTGC
*
40294 ATGAATCAACTAGCTCAAACTGTGTAAGAAAATGCAAGGGTTCTTCTAATAATATTAGAAGGGGT
1 ATGAATCAACTAGCTCAAACTGTGTAAGAAAATGCAAGCGTTCTTCTAATAATATTAGAAGGGGT
* *
40359 AGATAAAAATCTTCCAATCGTGGTAAAACTTGTCAGTTATGTAAAAAGGAATGTCATATTAAATC
66 AGATAAAAACCTTCCAATCATGGTAAAACTTGTCAGTTATGTAAAAAGGAATGTCATATTAAATC
40424 GGAGTATTACAAGTTACAGAATAAAATCAAAAGAGAAGTTGAATAACATAACTCTGGAAAATCTA
131 GGAGTATTACAAGTTACAGAATAAAATCAAAAGAGAAGTTGAATAACATAACTCTGGAAAATCTA
** *
40489 GTGAGGTTGATGTAGCAAAGGATTACAATGATAGAGAACTCATATTTGCGGCTGGCGATAACTTT
196 GTGAGGTCAATGTAGCAAAGGATTACAATGATAGAGAACTCATATTTGCGGCTGACGATAACTTT
40554 ATAACAAGTG
261 ATAACAAGTG
* * *
40564 ATGAATCGACTTGCTCAAACTGTGTAAGAAAATGCAAGCGTTCTTCTGATAATATTAGAAGGGGT
1 ATGAATCAACTAGCTCAAACTGTGTAAGAAAATGCAAGCGTTCTTCTAATAATATTAGAAGGGGT
*
40629 AGATAATAACCTTCCAATCATGGTAAAACTTGTCAGTTATGTAAAAAGGAATGTCATATTAAATC
66 AGATAAAAACCTTCCAATCATGGTAAAACTTGTCAGTTATGTAAAAAGGAATGTCATATTAAATC
*
40694 GGAGTATTACAAGTTACATAATAAAATCAAAAGAGAAGTTGAATAACATAACTCTGGAAAATCTA
131 GGAGTATTACAAGTTACAGAATAAAATCAAAAGAGAAGTTGAATAACATAACTCTGGAAAATCTA
40759 GTGAGGTCAATGTAG-AAGAGGATTACAATGATAGAGAACTCATATTTGCGGCTGACGATAACTT
196 GTGAGGTCAATGTAGCAA-AGGATTACAATGATAGAGAACTCATATTTGCGGCTGACGATAACTT
40823 TATAACAAGTG
260 TATAACAAGTG
40834 ATGA
1 ATGA
40838 GTGGATACCT
Statistics
Matches: 262, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
269 2 0.01
270 260 0.99
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (270 bp):
ATGAATCAACTAGCTCAAACTGTGTAAGAAAATGCAAGCGTTCTTCTAATAATATTAGAAGGGGT
AGATAAAAACCTTCCAATCATGGTAAAACTTGTCAGTTATGTAAAAAGGAATGTCATATTAAATC
GGAGTATTACAAGTTACAGAATAAAATCAAAAGAGAAGTTGAATAACATAACTCTGGAAAATCTA
GTGAGGTCAATGTAGCAAAGGATTACAATGATAGAGAACTCATATTTGCGGCTGACGATAACTTT
ATAACAAGTG
Found at i:43247 original size:35 final size:35
Alignment explanation
Indices: 43193--43290 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 35
43183 ATGGTATTTA
*
43193 AAGATTAGAGTAGG--T-ATTTTTTTTATTGATGTC
1 AAGATTAGAGT-GGATTAATTTTTTTTATTGAAGTC
43226 AAG-TTCAGAGTGGATTAATTTTTTTTAATTGAAGTC
1 AAGATT-AGAGTGGATTAATTTTTTTT-ATTGAAGTC
*
43262 TAGATTAGAGTGGATTAATTTTTTTTATT
1 AAGATTAGAGTGGATTAATTTTTTTTATT
43291 ATTAAAATCT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
32 4 0.07
33 8 0.14
34 1 0.02
35 12 0.21
36 30 0.53
37 2 0.04
ACGTcount: A:0.29, C:0.03, G:0.19, T:0.49
Consensus pattern (35 bp):
AAGATTAGAGTGGATTAATTTTTTTTATTGAAGTC
Found at i:45979 original size:53 final size:53
Alignment explanation
Indices: 45915--46106 Score: 366
Period size: 53 Copynumber: 3.6 Consensus size: 53
45905 ACTTGAGGAA
* *
45915 GCTACTTTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCAGGCACT
1 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
45968 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
1 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
46021 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
1 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
46074 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAAT
1 GCTACTCTTGCTTGATCTCCAAGTCTCGTCAAT
46107 TCTTGTTTTA
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
53 137 1.00
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (53 bp):
GCTACTCTTGCTTGATCTCCAAGTCTCGTCAATGATGATGATTAGCATGCACT
Found at i:47022 original size:16 final size:16
Alignment explanation
Indices: 46964--47026 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
46954 ATACAAAATC
*
46964 ATATCCAAAGAATTTTCG
1 ATATCC-AA-AATTTTAG
*
46982 ATATCTAAAATTTTAG
1 ATATCCAAAATTTTAG
* *
46998 -TGATACAAATTTTTAG
1 AT-ATCCAAAATTTTAG
47014 ATATCCAAAATTT
1 ATATCCAAAATTT
47027 CGGATCAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 1 0.03
16 27 0.75
17 3 0.08
18 5 0.14
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (16 bp):
ATATCCAAAATTTTAG
Found at i:48260 original size:60 final size:61
Alignment explanation
Indices: 48195--48310 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 61
48185 ATATTCTGAC
* *
48195 TTCAT-CTCTAAATTATGACAATT-ATTCTAAACTAATCCTCAAAC-TTTTGAACATTTTAAT
1 TTCATCCT-TAAACTATGAC-ATTAATTCTAAACTAATCCCCAAACTTTTTGAACATTTTAAT
* * **
48255 TTCATCCTTAAACTATGACCTTAATTCTAAATTGGTCCCCAAACTTTTTGAACATT
1 TTCATCCTTAAACTATGACATTAATTCTAAACTAATCCCCAAACTTTTTGAACATT
48311 CCAAATTCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
59 2 0.04
60 32 0.68
61 13 0.28
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.41
Consensus pattern (61 bp):
TTCATCCTTAAACTATGACATTAATTCTAAACTAATCCCCAAACTTTTTGAACATTTTAAT
Found at i:48640 original size:60 final size:58
Alignment explanation
Indices: 48455--48638 Score: 176
Period size: 60 Copynumber: 3.1 Consensus size: 58
48445 CTTGGATGAA
* * * * *
48455 TTTGGGGATTAAATTGGAATATTCAAAAGTTT-GGGGCCAATATAGA-AAGAGGTCATAG
1 TTTGGGGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTA-ATAAG-GGTTATAG
* * * * * *
48513 TGTAGGGATGAAATTAGAATATTCAAAATTTTAAGGACTAATTT-ATAATGGAATTCATAG
1 TTTGGGGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAATAA-GG-GTT-ATAG
* *
48573 TTTGGGGATGCAATTGGAATATTCAAAAGTTTAAGGACCAATTTAAATAAGGGTTATAT
1 TTTGGGGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTT-AATAAGGGTTATAG
48632 TTTGGGG
1 TTTGGGG
48639 GACACATGAA
Statistics
Matches: 100, Mismatches: 19, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
57 1 0.01
58 30 0.30
59 19 0.19
60 44 0.44
61 2 0.02
62 4 0.04
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.33
Consensus pattern (58 bp):
TTTGGGGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAATAAGGGTTATAG
Found at i:52611 original size:20 final size:20
Alignment explanation
Indices: 52586--52626 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
52576 TAAAATCAAT
52586 CCTAGAACCCCTAACCCAAC
1 CCTAGAACCCCTAACCCAAC
52606 CCTAGAACCCCTAACCCAAC
1 CCTAGAACCCCTAACCCAAC
52626 C
1 C
52627 TTACCATCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.51, G:0.05, T:0.10
Consensus pattern (20 bp):
CCTAGAACCCCTAACCCAAC
Found at i:52881 original size:167 final size:167
Alignment explanation
Indices: 52605--52939 Score: 616
Period size: 167 Copynumber: 2.0 Consensus size: 167
52595 CCTAACCCAA
* *
52605 CCCTAGAACCCCTAACCCAACCTTACCATCTTTCTTTCTGACCACGACCATCGTCAGCAACGTCT
1 CCCTAGAACCCCTAACCCAACCTTACCATCTCTCTTTCTGACCACGACCATCGTCAACAACGTCT
52670 CAATTACCTTCTCCTTTTTGGGACATCGACACTCATATCATCTCTCTTTTCGACCACAACCATCG
66 CAATTACCTTCTCCTTTTTGGGACATCGACACTCATATCATCTCTCTTTTCGACCACAACCATCG
*
52735 TCAGCGACGTCTTAATTGTCTTCTTCTTTTCGGACGT
131 TCAGCGACGTCTTAATTGTCTTCTTCTTTTCAGACGT
*
52772 CCCTAGAACCCCTAACCCAACCTTACCATGTCTCTTTCTGACCACGACCATCGTCAACAACGTCT
1 CCCTAGAACCCCTAACCCAACCTTACCATCTCTCTTTCTGACCACGACCATCGTCAACAACGTCT
**
52837 CAATTACCTTCTCCTTTTTGGGACATCGACACTCATATCATCTCTCTTTTCGACCATGACCATCG
66 CAATTACCTTCTCCTTTTTGGGACATCGACACTCATATCATCTCTCTTTTCGACCACAACCATCG
52902 TCAGCGACGTCTTAATTGTCTTCTTCTTTTCAGACGT
131 TCAGCGACGTCTTAATTGTCTTCTTCTTTTCAGACGT
52939 C
1 C
52940 GAAACTCATA
Statistics
Matches: 162, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
167 162 1.00
ACGTcount: A:0.22, C:0.35, G:0.11, T:0.32
Consensus pattern (167 bp):
CCCTAGAACCCCTAACCCAACCTTACCATCTCTCTTTCTGACCACGACCATCGTCAACAACGTCT
CAATTACCTTCTCCTTTTTGGGACATCGACACTCATATCATCTCTCTTTTCGACCACAACCATCG
TCAGCGACGTCTTAATTGTCTTCTTCTTTTCAGACGT
Found at i:52931 original size:77 final size:76
Alignment explanation
Indices: 52802--52958 Score: 190
Period size: 77 Copynumber: 2.1 Consensus size: 76
52792 CCTTACCATG
** *
52802 TCTCTTTCTGACCACGACCATCGTCAACAACGTCTCAATTACCTTCTCCTTTTTGGGACATCGAC
1 TCTCTTTCTGACCACGACCATCGTCAACAACGTCTCAATTACCTTCTCC-TTTTCAGACATCGAA
52867 ACTCATATCATC
65 ACTCATATCATC
* * * * ** * *
52879 TCTCTTT-TCGACCATGACCATCGTCAGCGACGTCTTAATTGTCTTCTTCTTTTCAGACGTCGAA
1 TCTCTTTCT-GACCACGACCATCGTCAACAACGTCTCAATTACCTTCTCCTTTTCAGACATCGAA
52943 ACTCATATCATC
65 ACTCATATCATC
52955 TCTC
1 TCTC
52959 GCGTCGTCGG
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
76 28 0.41
77 40 0.59
ACGTcount: A:0.22, C:0.32, G:0.11, T:0.35
Consensus pattern (76 bp):
TCTCTTTCTGACCACGACCATCGTCAACAACGTCTCAATTACCTTCTCCTTTTCAGACATCGAAA
CTCATATCATC
Found at i:57018 original size:30 final size:31
Alignment explanation
Indices: 56979--57051 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
56969 AATGGCTTTA
* *
56979 TTTA-GTGACCAAATTATAAA-TTTGGTAAAG
1 TTTAGGTGACCAAAGTATAAACTTT-GAAAAG
57009 TTT-GGTGACCAAAGTATAAACTTTGAAAAG
1 TTTAGGTGACCAAAGTATAAACTTTGAAAAG
57039 TTTAGG-GACCAAA
1 TTTAGGTGACCAAA
57052 ATGTAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
30 33 0.87
31 5 0.13
ACGTcount: A:0.40, C:0.10, G:0.19, T:0.32
Consensus pattern (31 bp):
TTTAGGTGACCAAAGTATAAACTTTGAAAAG
Found at i:58078 original size:32 final size:32
Alignment explanation
Indices: 58028--58097 Score: 99
Period size: 32 Copynumber: 2.2 Consensus size: 32
58018 GTATTTTTTT
*
58028 AAAAGTT--GGGGACCAATTCGATAACTTTGG
1 AAAAGTTGGGGGGACCAATTCGACAACTTTGG
* *
58058 AATAGTTGGGGGGACTAATTCGACAACTTTGG
1 AAAAGTTGGGGGGACCAATTCGACAACTTTGG
58090 AAAAGTTG
1 AAAAGTTG
58098 TGAATGGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 6 0.18
32 28 0.82
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (32 bp):
AAAAGTTGGGGGGACCAATTCGACAACTTTGG
Found at i:59239 original size:45 final size:45
Alignment explanation
Indices: 59124--59261 Score: 210
Period size: 45 Copynumber: 3.1 Consensus size: 45
59114 GATAAACTGG
59124 AAAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * *
59168 -AAATAAGCTTACGAGTTTATGAAATAAATGGTAAGAATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
59212 AAAATAAACTTATGAGCTTATGGAATAAATGGTAAGTATA-TGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
59256 AAAATA
1 AAAATA
59262 TTGGATATGC
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
43 23 0.27
44 27 0.32
45 34 0.40
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:59976 original size:13 final size:13
Alignment explanation
Indices: 59958--59993 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
59948 ACTTTTTGGT
*
59958 CAAAGTCAACGGA
1 CAAAGTCAACAGA
*
59971 CAAAGTCAACAGT
1 CAAAGTCAACAGA
59984 CAAAGTCAAC
1 CAAAGTCAAC
59994 TGGTTGACTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (13 bp):
CAAAGTCAACAGA
Found at i:61635 original size:2 final size:2
Alignment explanation
Indices: 61630--61663 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61620 ATCTAGATTA
61630 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
61664 TGAATTGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62388 original size:2 final size:2
Alignment explanation
Indices: 62381--62421 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
62371 AAATATCTAA
62381 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62422 ATCTTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65924 original size:4 final size:4
Alignment explanation
Indices: 65915--66001 Score: 56
Period size: 4 Copynumber: 21.5 Consensus size: 4
65905 GGACCTGAAA
* *
65915 AAAT AAAT AAAT -AAT AATAT ATAT AAAT ATAAT -AAT -AAT -AAT AAAG
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT AAAT AAAT AAAT
* * *
65961 AAAG AAAG AAAG AATAT AAAT AATAT AAAT AATAT AAAT AA
1 AAAT AAAT AAAT AA-AT AAAT AA-AT AAAT AA-AT AAAT AA
66002 TATTAATATA
Statistics
Matches: 72, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
3 12 0.17
4 43 0.60
5 17 0.24
ACGTcount: A:0.69, C:0.00, G:0.05, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:65958 original size:18 final size:19
Alignment explanation
Indices: 65916--66016 Score: 64
Period size: 21 Copynumber: 5.1 Consensus size: 19
65906 GACCTGAAAA
65916 AATAAATAAATAATAATAT
1 AATAAATAAATAATAATAT
65935 ATATAAATATAATAATAATAAT
1 A-ATAAATA-AATAATAAT-AT
* * * *
65957 AAAGAAAGAAAGAAAGAATAT
1 -AATAAATAAA-TAATAATAT
65978 AAATAATATAAATAAT-ATA-
1 -AATAA-ATAAATAATAATAT
*
65997 AATAATATTAAT-ATAATAT
1 AATAA-ATAAATAATAATAT
66016 A
1 A
66017 TAAGGTAATG
Statistics
Matches: 65, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
17 2 0.03
18 14 0.22
19 2 0.03
20 10 0.15
21 20 0.31
22 16 0.25
23 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (19 bp):
AATAAATAAATAATAATAT
Found at i:65987 original size:9 final size:9
Alignment explanation
Indices: 65917--66016 Score: 77
Period size: 9 Copynumber: 11.3 Consensus size: 9
65907 ACCTGAAAAA
65917 ATAAATAA-
1 ATAAATAAT
65925 AT-AATAAT
1 ATAAATAAT
*
65933 ATATATAA-
1 ATAAATAAT
65941 ATATAATAAT
1 ATA-AATAAT
65951 A-ATAATAA-
1 ATA-AATAAT
* *
65959 AGAAAGAA-
1 ATAAATAAT
* *
65967 AGAAAGAAT
1 ATAAATAAT
65976 ATAAATAAT
1 ATAAATAAT
65985 ATAAATAAT
1 ATAAATAAT
65994 ATAAATAAT
1 ATAAATAAT
66003 ATTAATATAAT
1 A-TAA-ATAAT
66014 ATA
1 ATA
66017 TAAGGTAATG
Statistics
Matches: 79, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
7 5 0.06
8 20 0.25
9 42 0.53
10 6 0.08
11 6 0.08
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (9 bp):
ATAAATAAT
Found at i:66074 original size:18 final size:18
Alignment explanation
Indices: 66045--66096 Score: 79
Period size: 18 Copynumber: 2.8 Consensus size: 18
66035 TGAACATATA
66045 ATATATAAGTATATTAACT
1 ATATA-AAGTATATTAACT
66064 ATATAAAGTATATTAACT
1 ATATAAAGTATATTAACT
66082 ATATAATA-TATATTA
1 ATATAA-AGTATATTA
66097 TGTTTTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 26 0.81
19 6 0.19
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (18 bp):
ATATAAAGTATATTAACT
Found at i:66155 original size:16 final size:16
Alignment explanation
Indices: 66134--66187 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
66124 TATTATATAC
66134 GTTTTCAAAACCATAT
1 GTTTTCAAAACCATAT
66150 GTTTTC-AAA--A-AT
1 GTTTTCAAAACCATAT
* *
66162 GTTTTCAAACCCATAC
1 GTTTTCAAAACCATAT
*
66178 GTTTTTAAAA
1 GTTTTCAAAA
66188 ATGTTTTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
12 8 0.27
13 3 0.10
15 4 0.13
16 15 0.50
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (16 bp):
GTTTTCAAAACCATAT
Found at i:66165 original size:12 final size:12
Alignment explanation
Indices: 66148--66199 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
66138 TCAAAACCAT
66148 ATGTTTTCAAAA
1 ATGTTTTCAAAA
66160 ATGTTTTCAAACCCA
1 ATGTTTTCAAA---A
* *
66175 TACGTTTTTAAAA
1 -ATGTTTTCAAAA
66188 ATGTTTTCAAAA
1 ATGTTTTCAAAA
66200 CTATATATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 21 0.66
13 1 0.03
15 1 0.03
16 9 0.28
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:66175 original size:28 final size:28
Alignment explanation
Indices: 66134--66200 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
66124 TATTATATAC
*
66134 GTTTTCAAAACCATATGTTTTCAAAAAT
1 GTTTTCAAAACCATACGTTTTCAAAAAT
* *
66162 GTTTTCAAACCCATACGTTTTTAAAAAT
1 GTTTTCAAAACCATACGTTTTCAAAAAT
66190 GTTTTCAAAAC
1 GTTTTCAAAAC
66201 TATATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.39
Consensus pattern (28 bp):
GTTTTCAAAACCATACGTTTTCAAAAAT
Found at i:67948 original size:20 final size:20
Alignment explanation
Indices: 67911--67948 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
67901 ACTTAACTTC
*
67911 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
67931 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
67949 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:70494 original size:22 final size:22
Alignment explanation
Indices: 70469--70510 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
70459 GTTTCAAGCC
70469 CTAGGTGTTTA-GCTCTGTTGGG
1 CTAGG-GTTTAGGCTCTGTTGGG
*
70491 CTAGGGTTTAGGCTTTGTTG
1 CTAGGGTTTAGGCTCTGTTG
70511 TTGGGTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.10, C:0.12, G:0.36, T:0.43
Consensus pattern (22 bp):
CTAGGGTTTAGGCTCTGTTGGG
Found at i:74128 original size:3 final size:3
Alignment explanation
Indices: 74114--74172 Score: 100
Period size: 3 Copynumber: 19.3 Consensus size: 3
74104 TTGTCTCGAC
*
74114 ATT ATC ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT
74160 ATT ATT ATT ATT A
1 ATT ATT ATT ATT A
74173 ATTTGTGCAG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:75540 original size:17 final size:16
Alignment explanation
Indices: 75503--75538 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
75493 GATTTGATTG
75503 TTTATATTTTAGTTCTA
1 TTTATATTTT-GTTCTA
*
75520 TTTATATTTTGTTTTA
1 TTTATATTTTGTTCTA
75536 TTT
1 TTT
75539 TAATTTTGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.19, C:0.03, G:0.06, T:0.72
Consensus pattern (16 bp):
TTTATATTTTGTTCTA
Found at i:76253 original size:131 final size:131
Alignment explanation
Indices: 76035--76367 Score: 533
Period size: 131 Copynumber: 2.5 Consensus size: 131
76025 ATTTCGGTTG
* * *
76035 GAGTAATAAATGACTGCTTTAGGGCATAAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
1 GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
* * * *
76100 TATCGTTTTCTCTCGAATCAATATTGA-TTTTCAAGACGGAATAGTGATATCTCTTCATTTCTAT
66 TATCGTTTTCACTCGAAGCAATATTGACTTTT-AAGACGAAATAGTGATATCTCTTCATTTCGAT
*
76164 TA
130 CA
* *
76166 GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTAGAAATCATTAGATAT
1 GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
*
76231 TATCGTTTTCACTCGAAGCAATATTGACTTTTAAGACGAAATAGTGATATCTCTTCTTTTCGATC
66 TATCGTTTTCACTCGAAGCAATATTGACTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATC
*
76296 G
131 A
*
76297 GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAAATAGATAT
1 GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
76362 TATCGT
66 TATCGT
76368 GTTTTAAAAA
Statistics
Matches: 186, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 182 0.98
132 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (131 bp):
GAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATAT
TATCGTTTTCACTCGAAGCAATATTGACTTTTAAGACGAAATAGTGATATCTCTTCATTTCGATC
A
Found at i:77280 original size:145 final size:145
Alignment explanation
Indices: 77017--77296 Score: 533
Period size: 145 Copynumber: 1.9 Consensus size: 145
77007 GATATCCGTT
*
77017 TTTTGTCATTTTTATTTAAAAATACAAAAATTATATATTTTTTCCTTCTTTGGTTGTTCATCTTT
1 TTTTGTCATTTTTATTTAAAAATACAAAAAATATATATTTTTTCCTTCTTTGGTTGTTCATCTTT
*
77082 TTTGAATTCTCCATCTTCTTTGAGTTGATGACTTTAATAAAATTATAAAGTGATTCGTTGTAGAT
66 TTTGAATTCTCCATCTTCTTTGAGTTGATGACTTTAATAAAATTATAAAGTGATTCGCTGTAGAT
77147 AATTTGTTTTAAAAA
131 AATTTGTTTTAAAAA
77162 TTTTGTCATTTTTATTTAAAAATACAAAAAATATATATTTTTTCCTTCTTTGGTTGTTCATCTTT
1 TTTTGTCATTTTTATTTAAAAATACAAAAAATATATATTTTTTCCTTCTTTGGTTGTTCATCTTT
*
77227 TTTGAATTCTCCATCTTCTTTGAGTTGATGATTTTAATAAAATTATAAAGTGATTCGCTGTAGAT
66 TTTGAATTCTCCATCTTCTTTGAGTTGATGACTTTAATAAAATTATAAAGTGATTCGCTGTAGAT
77292 AATTT
131 AATTT
77297 TTAAAAAAAA
Statistics
Matches: 132, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 132 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.50
Consensus pattern (145 bp):
TTTTGTCATTTTTATTTAAAAATACAAAAAATATATATTTTTTCCTTCTTTGGTTGTTCATCTTT
TTTGAATTCTCCATCTTCTTTGAGTTGATGACTTTAATAAAATTATAAAGTGATTCGCTGTAGAT
AATTTGTTTTAAAAA
Found at i:79367 original size:27 final size:27
Alignment explanation
Indices: 79335--79430 Score: 122
Period size: 27 Copynumber: 3.6 Consensus size: 27
79325 TATGGGGTTG
* *
79335 TGCATCATCTCGAAAGATGGAATACTA
1 TGCATCACCTCGAAAGATGAAATACTA
* *
79362 TGCATCACCTCGAAGGATGAAATATTA
1 TGCATCACCTCGAAAGATGAAATACTA
*
79389 TGCATCACCTTGAAATG-TGAAATACTA
1 TGCATCACCTCGAAA-GATGAAATACTA
*
79416 TGCATCACCTTGAAA
1 TGCATCACCTCGAAA
79431 TGTGGAACAA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 60 0.98
28 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (27 bp):
TGCATCACCTCGAAAGATGAAATACTA
Found at i:79572 original size:17 final size:17
Alignment explanation
Indices: 79546--79598 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
79536 TACAAACCTC
* *
79546 TATAATATTTAATAGCA
1 TATAACATTTAATAACA
* *
79563 TGTAACATTTAATAACT
1 TATAACATTTAATAACA
79580 TATAACATTTAAT-ACA
1 TATAACATTTAATAACA
79596 TAT
1 TAT
79599 GATCATGTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 5 0.17
17 25 0.83
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (17 bp):
TATAACATTTAATAACA
Found at i:86704 original size:29 final size:29
Alignment explanation
Indices: 86667--86726 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
86657 CATTTAATTT
*
86667 TGGATCTACGAAAATTGCAATAATCCTCA
1 TGGAGCTACGAAAATTGCAATAATCCTCA
*
86696 TGGAGCTACGACAATTGCAATAATCCTCA
1 TGGAGCTACGAAAATTGCAATAATCCTCA
86725 TG
1 TG
86727 AAACTCGTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (29 bp):
TGGAGCTACGAAAATTGCAATAATCCTCA
Found at i:92785 original size:70 final size:72
Alignment explanation
Indices: 92698--92843 Score: 219
Period size: 70 Copynumber: 2.1 Consensus size: 72
92688 ACTTTTGAAA
* *
92698 AAAATTTAAAAAATTTTAAAATTTCA-AAGTTAAAAATAATATGAAACTTTTAGAATTTTTTAA-
1 AAAATTTAAAAAATTTTAAAATTT-AGAAGTTAAAAATAATATGAAACTTGTAGAAATTTTTAAC
92761 AAATTT-G
65 AAATTTGG
*
92768 AAAATATT-AAAATTTTTAAAATTTAGAAGTTAAAAATAATATGAAACTTGTAGAAATTTTTAAC
1 AAAAT-TTAAAAAATTTTAAAATTTAGAAGTTAAAAATAATATGAAACTTGTAGAAATTTTTAAC
92832 AAATTTGG
65 AAATTTGG
92840 AAAA
1 AAAA
92844 AAAATAACAT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
69 1 0.01
70 55 0.80
71 8 0.12
72 5 0.07
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (72 bp):
AAAATTTAAAAAATTTTAAAATTTAGAAGTTAAAAATAATATGAAACTTGTAGAAATTTTTAACA
AATTTGG
Found at i:92825 original size:35 final size:35
Alignment explanation
Indices: 92711--92826 Score: 105
Period size: 34 Copynumber: 3.3 Consensus size: 35
92701 ATTTAAAAAA
*
92711 TTTTA-AAATTTCAAAGTTAAAAATAATATGAAAC
1 TTTTAGAAATTTAAAAGTTAAAAATAATATGAAAC
* * * * *
92745 TTTTAGAATTTTTTAAAAATTTGAAAAT-AT-TAAAAT
1 TTTTAGAA--ATTT-AAAAGTTAAAAATAATATGAAAC
*
92781 TTTTA-AAATTTAGAAGTTAAAAATAATATGAAAC
1 TTTTAGAAATTTAAAAGTTAAAAATAATATGAAAC
*
92815 TTGTAGAAATTT
1 TTTTAGAAATTT
92827 TTAACAAATT
Statistics
Matches: 62, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
32 10 0.16
33 5 0.08
34 13 0.21
35 10 0.16
36 9 0.15
37 5 0.08
38 10 0.16
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (35 bp):
TTTTAGAAATTTAAAAGTTAAAAATAATATGAAAC
Found at i:96103 original size:3 final size:3
Alignment explanation
Indices: 96095--96138 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
96085 CAAACCATAA
*
96095 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT TAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
96139 AGCTGAACTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
CAT
Found at i:96427 original size:32 final size:32
Alignment explanation
Indices: 96386--96455 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
96376 GTTTTTGCTT
* * *
96386 AGATGAAAGGAGTTTTTTGTGTAAGAGAATGA
1 AGATGAAAGGAGTATGTTATGTAAGAGAATGA
*
96418 AGATGAAAGGAGTATGTTATGTAAGAGATTGA
1 AGATGAAAGGAGTATGTTATGTAAGAGAATGA
96450 AGATGA
1 AGATGA
96456 TGTTCACAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (32 bp):
AGATGAAAGGAGTATGTTATGTAAGAGAATGA
Found at i:98869 original size:2 final size:2
Alignment explanation
Indices: 98864--98910 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
98854 TCTCTCTCTC
98864 TA TA TA TA TA TA TA TA TA TA TA TA TA 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 TA
98906 TA TA T
1 TA TA T
98911 GTGTGTGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:99276 original size:16 final size:16
Alignment explanation
Indices: 99255--99285 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
99245 GATAATTTTA
99255 ATCATTAAATTTTATG
1 ATCATTAAATTTTATG
*
99271 ATCATTATATTTTAT
1 ATCATTAAATTTTAT
99286 CGGTATGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
ATCATTAAATTTTATG
Found at i:100860 original size:12 final size:12
Alignment explanation
Indices: 100843--100868 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
100833 ACAAAAATCG
100843 CAATGCGATCTC
1 CAATGCGATCTC
100855 CAATGCGATCTC
1 CAATGCGATCTC
100867 CA
1 CA
100869 GTATCGCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (12 bp):
CAATGCGATCTC
Found at i:100957 original size:21 final size:21
Alignment explanation
Indices: 100911--100958 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
100901 GATTTTGACT
*
100911 ATCGCATTTCGATTTTCCAAA
1 ATCGCATTTCGATTTTACAAA
* *
100932 TTCGCATTGT-GATTTTAGAAA
1 ATCGCATT-TCGATTTTACAAA
100953 ATCGCA
1 ATCGCA
100959 ATGCGAATAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (21 bp):
ATCGCATTTCGATTTTACAAA
Found at i:101644 original size:14 final size:14
Alignment explanation
Indices: 101622--101653 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
101612 GCGATTTTAG
101622 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
*
101636 TTTCTCGTTGCGAT
1 TTTCGCGTTGCGAT
101650 TTTC
1 TTTC
101654 ATTTCGCGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.22, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTCGCGTTGCGAT
Found at i:101714 original size:20 final size:20
Alignment explanation
Indices: 101634--101731 Score: 90
Period size: 20 Copynumber: 5.0 Consensus size: 20
101624 TCGCGTTGCG
*
101634 ATTTTCTCGTTGCGATTTTC
1 ATTTTCGCGTTGCGATTTTC
**
101654 A-TTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATTTTC
** * **
101673 AAATTCGCGTTGCAATAGTC
1 ATTTTCGCGTTGCGATTTTC
*
101693 ATTTTCGTGTTGCGATTTTC
1 ATTTTCGCGTTGCGATTTTC
* *
101713 ATTTTCGTGTTGTGATTTT
1 ATTTTCGCGTTGCGATTTT
101732 AAGTTTCAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 16 0.25
20 49 0.75
ACGTcount: A:0.15, C:0.16, G:0.20, T:0.48
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATTTTC
Found at i:101738 original size:20 final size:20
Alignment explanation
Indices: 101695--101738 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
101685 CAATAGTCAT
* *
101695 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
*
101715 TTTCGTGTTGTGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
101735 TTTC
1 TTTC
101739 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:103651 original size:20 final size:20
Alignment explanation
Indices: 103628--103676 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
103618 GAAACTTAAA
103628 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
103648 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
103668 ATCGCAACG
1 ATCGCAACG
103677 GGATAATCGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.22, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:103781 original size:33 final size:34
Alignment explanation
Indices: 103724--103799 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 34
103714 ACTAAAATCG
*
103724 CGTTGCGATTTTCATTTTCGCATTGCGATTTTCA
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
* *
103758 CGTTGCGATTTTTA-TTTCGCATTGCGATTATCC
1 CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
103791 CGTTGCGAT
1 CGTTGCGAT
103800 AGTCAAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 26 0.67
34 13 0.33
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTATCA
Found at i:103816 original size:20 final size:20
Alignment explanation
Indices: 103791--103859 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
103781 GCGATTATCC
**
103791 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
103811 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCG
*
103831 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
103851 CGTTGCGAT
1 CGTTGCGAT
103860 TTTAAGTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:104397 original size:21 final size:21
Alignment explanation
Indices: 104371--104474 Score: 77
Period size: 21 Copynumber: 5.0 Consensus size: 21
104361 CTCACCTATC
*
104371 ATCGTTCAAGAGGCCTCTCCT
1 ATCGTTCAAGAGGCCCCTCCT
* *
104392 ATCGTTCAAGAGACCCCT-AT
1 ATCGTTCAAGAGGCCCCTCCT
** * *
104412 CATCCCTCAAGAGTCCCCTCCC
1 -ATCGTTCAAGAGGCCCCTCCT
* *
104434 ATCGTTCAAGAGGCCTCT-GT
1 ATCGTTCAAGAGGCCCCTCCT
* *
104454 CATCGTTGAAGAGGTCCCTCC
1 -ATCGTTCAAGAGGCCCCTCC
104475 CACCATTCAA
Statistics
Matches: 61, Mismatches: 18, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
20 1 0.02
21 60 0.98
ACGTcount: A:0.21, C:0.36, G:0.18, T:0.25
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCCT
Found at i:104424 original size:42 final size:42
Alignment explanation
Indices: 104365--104487 Score: 120
Period size: 42 Copynumber: 2.9 Consensus size: 42
104355 GCCCGACTCA
** * *
104365 CCTATCATCGTTCAAGAGGCCTCTCCTATCGTTCAAGAGACC
1 CCTATCATCCCTCAAGAGGCCCCTCCCATCGTTCAAGAGACC
* *
104407 CCTATCATCCCTCAAGAGTCCCCTCCCATCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGGCCCCTCCCATCGTTCAAGAGACC
* * ** * * * *
104449 TCTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGAGGCCCCTCCCATCGTTCAAGAG
104488 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGGCCCCTCCCATCGTTCAAGAGACC
Found at i:105983 original size:20 final size:20
Alignment explanation
Indices: 105960--106023 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
105950 AACATTAAAC
105960 TCAAAATCGCAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
*
105980 TCAAAATCACAATGCGAAAG
1 TCAAAATCGCAATGCGAAAG
* **
106000 CCAAAATCGCAACACGAAAG
1 TCAAAATCGCAATGCGAAAG
106020 TCAA
1 TCAA
106024 TTCGCGTTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.48, C:0.23, G:0.16, T:0.12
Consensus pattern (20 bp):
TCAAAATCGCAATGCGAAAG
Found at i:106055 original size:20 final size:20
Alignment explanation
Indices: 106018--106232 Score: 231
Period size: 20 Copynumber: 11.4 Consensus size: 20
106008 GCAACACGAA
106018 AGTC-AATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* * *
106037 AGTCTAATACGCTTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
106057 --T----TTCTCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
* *
106071 AGTCAAATTCTCATTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
106091 AGTCAAATTCTCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
106111 AGTCAAATTCCCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
106131 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
106151 AGTCAAATTCGTGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
106171 AGTCAAATTCGCGTTGTGAT
1 AGTCAAATTCGCGTTGCGAT
*
106191 --T----TTTGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
106205 AGTCAAATTCGCGTTGCGAT
1 AGTCAAATTCGCGTTGCGAT
*
106225 ATTCAAAT
1 AGTCAAAT
106233 GAATGTGTAA
Statistics
Matches: 167, Mismatches: 16, Indels: 25
0.80 0.08 0.12
Matches are distributed among these distances:
14 21 0.13
16 2 0.01
18 2 0.01
19 4 0.02
20 138 0.83
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (20 bp):
AGTCAAATTCGCGTTGCGAT
Found at i:106459 original size:140 final size:140
Alignment explanation
Indices: 106203--106485 Score: 521
Period size: 140 Copynumber: 2.0 Consensus size: 140
106193 TTGCGTTGCG
*
106203 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGAGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
*
106268 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATTTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
106333 AATACACATA
131 AATACACATA
* * *
106343 ATAGTCAAATTCGAGTTGCGATGTTCAAATGAATGTGTAATAAGTTATAACAACTTAACATATCA
1 ATAGTCAAATTCGAGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
106408 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
106473 AATACACATA
131 AATACACATA
106483 ATA
1 ATA
106486 CAACGTTTGC
Statistics
Matches: 138, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 138 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (140 bp):
ATAGTCAAATTCGAGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:106565 original size:17 final size:18
Alignment explanation
Indices: 106543--106576 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
106533 AAGCCGGTTG
*
106543 TGATTGGGA-TTTGATTT
1 TGATTGCGATTTTGATTT
106560 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
106577 GCCTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:106810 original size:20 final size:20
Alignment explanation
Indices: 106785--106875 Score: 104
Period size: 20 Copynumber: 4.8 Consensus size: 20
106775 GCCTTCTGTC
106785 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
106805 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
106825 CGTTGTGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
106839 CGTTGCGATAGTCAAATTCA
1 CGTTGCGATAGTCAAATTCG
*
106859 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
106876 GAATGTGTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
14 11 0.19
16 1 0.02
18 1 0.02
20 46 0.78
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:107102 original size:140 final size:140
Alignment explanation
Indices: 106846--107128 Score: 514
Period size: 140 Copynumber: 2.0 Consensus size: 140
106836 TTGCGTTGCG
106846 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
* *
106911 TAGCAATGTTCAAACACAAGTTACTAATACATGCCTAACTGAAAATTTTAAAAGTTTACACATAA
66 TAGCAATATTCAAACACAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
106976 AATACACATA
131 AATACACATA
*
106986 ATAGTCAAATTCGA-GTTGCGATGTTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATC
1 ATAGTCAAATTC-ACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATC
*
107050 ATAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
65 ATAGCAATATTCAAACACAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATA
107115 AAATACACATA
130 AAATACACATA
107126 ATA
1 ATA
107129 CAACGTTTGC
Statistics
Matches: 138, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
140 137 0.99
141 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
TAGCAATATTCAAACACAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:107208 original size:17 final size:18
Alignment explanation
Indices: 107186--107219 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
107176 AAGCCGGTTG
*
107186 TGATTGGGA-TTTGATTT
1 TGATTGCGATTTTGATTT
107203 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
107220 GCTTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:107368 original size:643 final size:643
Alignment explanation
Indices: 106142--107428 Score: 2466
Period size: 643 Copynumber: 2.0 Consensus size: 643
106132 GTCAAATTCG
*
106142 CGTTGCGATAGTCAAATTCGTGTTGCGATAGTCAAATTCGCGTTGTGATTTTTGCGTTGCGATAG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTTGCGTTGCGATAG
*
106207 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
66 TCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
*
106272 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATTTTAAAAGTTTACACATAAAATA
131 AATGTTCAAACACAAGTTACTAATACATGCCTAACTGAAAATTTTAAAAGTTTACACATAAAATA
* *
106337 CACATAATAGTCAAATTCGAGTTGCGATGTTCAAATGAATGTGTAATAAGTTATAACAACTTAAC
196 CACATAATAGTCAAATTCGAGTTGCGATGTTCAAATGAATGTGTAATAAGTGATAACAACTGAAC
*
106402 ATATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTAC
261 ATATCATAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTAC
*
106467 ACATAAAATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAATAGTCCTAAAAGGT
326 ACATAAAATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAATAGTCCCAAAAGGT
106532 GAAGCCGGTTGTGATTGGGATTTGATTTTGATTGCGATTTTGATTGCCTTTTTTTTGACACCATA
391 GAAGCCGGTTGTGATTGGGATTTGATTTTGATTGCGATTTTGATTGCCTTTTTTTTGACACCATA
106597 TGAGCTTTGGATTTTTATTTGGATCCATATTTTGGTAGAGGAAAAGATGATTGTGATAGCACTGG
456 TGAGCTTTGGATTTTTATTTGGATCCATATTTTGGTAGAGGAAAAGATGATTGTGATAGCACTGG
*
106662 TGATCTAAATGTCAACCATGTATGACCACTTTCCTTGCACCGACTACATGTTGATCTCTTCTTCT
521 TGATCTAAATGTCAACCATGTATGACCACTTTCCTTGCACCGACTACATGTCGATCTCTTCTTCT
*
106727 CTTCACCCTTGGACAGTATACGATCGTGACCTTTTGGTCGGTCAGGTAGCCTTCTGTC
586 CTTCACCCTTGGACAGTATACGATCGTGACCTTTTGGTCGGCCAGGTAGCCTTCTGTC
106785 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTTGCGTTGCGATAG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTTGCGTTGCGATAG
106850 TCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
66 TCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
106915 AATGTTCAAACACAAGTTACTAATACATGCCTAACTGAAAATTTTAAAAGTTTACACATAAAATA
131 AATGTTCAAACACAAGTTACTAATACATGCCTAACTGAAAATTTTAAAAGTTTACACATAAAATA
106980 CACATAATAGTCAAATTCGAGTTGCGATGTTCAAATGAATGTGTAATAAGTGATAACAACTGAAC
196 CACATAATAGTCAAATTCGAGTTGCGATGTTCAAATGAATGTGTAATAAGTGATAACAACTGAAC
107045 ATATCATAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTAC
261 ATATCATAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTAC
107110 ACATAAAATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAATAGTCCCAAAAGGT
326 ACATAAAATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAATAGTCCCAAAAGGT
*
107175 GAAGCCGGTTGTGATTGGGATTTGATTTTGATTGCGATTTTGATTGCTTTTTTTTTGACACCATA
391 GAAGCCGGTTGTGATTGGGATTTGATTTTGATTGCGATTTTGATTGCCTTTTTTTTGACACCATA
107240 TGAGCTTTGGATTTTTATTTGGATCCATATTTTGGTAGAGGAAAAGATGATTGTGATAGCACTGG
456 TGAGCTTTGGATTTTTATTTGGATCCATATTTTGGTAGAGGAAAAGATGATTGTGATAGCACTGG
107305 TGATCTAAATGTCAACCATGTATGACCACTTTCCTTGCACCGACTACATGTCGATCTCTTCTTCT
521 TGATCTAAATGTCAACCATGTATGACCACTTTCCTTGCACCGACTACATGTCGATCTCTTCTTCT
* *
107370 CTTCACCCTTGGACGGTATACGATCGTGACTTTTTGGTCGGCCAGGTAGCCTTCTGTC
586 CTTCACCCTTGGACAGTATACGATCGTGACCTTTTGGTCGGCCAGGTAGCCTTCTGTC
107428 C
1 C
107429 ATGGCTGGTG
Statistics
Matches: 632, Mismatches: 12, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
643 632 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (643 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTTGCGTTGCGATAG
TCAAATTCACGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
AATGTTCAAACACAAGTTACTAATACATGCCTAACTGAAAATTTTAAAAGTTTACACATAAAATA
CACATAATAGTCAAATTCGAGTTGCGATGTTCAAATGAATGTGTAATAAGTGATAACAACTGAAC
ATATCATAGCAATATTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTAC
ACATAAAATACACATAATACAACGTTTGCATTTAAAAATCACCTAAGTTAATAGTCCCAAAAGGT
GAAGCCGGTTGTGATTGGGATTTGATTTTGATTGCGATTTTGATTGCCTTTTTTTTGACACCATA
TGAGCTTTGGATTTTTATTTGGATCCATATTTTGGTAGAGGAAAAGATGATTGTGATAGCACTGG
TGATCTAAATGTCAACCATGTATGACCACTTTCCTTGCACCGACTACATGTCGATCTCTTCTTCT
CTTCACCCTTGGACAGTATACGATCGTGACCTTTTGGTCGGCCAGGTAGCCTTCTGTC
Done.