Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005914.1 Hibiscus syriacus cultivar Beakdansim tig00013888_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: 103218
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:890 original size:34 final size:33
Alignment explanation
Indices: 828--891 Score: 83
Period size: 34 Copynumber: 1.9 Consensus size: 33
818 ACTTACTTTG
***
828 TTTTTATGCCATTAATTCACTCGTAATCACCTT
1 TTTTTATGCCATTAATTCACTAAAAATCACCTT
*
861 TTTTTCATGCCATTAATTCTCTAAAAATCAC
1 TTTTT-ATGCCATTAATTCACTAAAAATCAC
892 TTAGTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 5 0.19
34 21 0.81
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.44
Consensus pattern (33 bp):
TTTTTATGCCATTAATTCACTAAAAATCACCTT
Found at i:1833 original size:53 final size:52
Alignment explanation
Indices: 1770--1871 Score: 152
Period size: 53 Copynumber: 1.9 Consensus size: 52
1760 TAACGGTACA
* *
1770 GTGAAGAGTGTTCATGTAAT-AATTTTTCGATTTAAAGACGATGAATCAAAATC
1 GTGAAGAGTGTTCATATAATAAATATTT-GATTTAAAGACGATG-ATCAAAATC
*
1823 GTGAAGAGTGTTCATATGATAAATATTTGATTTAAAGACGATGATCAAA
1 GTGAAGAGTGTTCATATAATAAATATTTGATTTAAAGACGATGATCAAA
1872 TCGCATCCGA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 6 0.13
53 33 0.73
54 6 0.13
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (52 bp):
GTGAAGAGTGTTCATATAATAAATATTTGATTTAAAGACGATGATCAAAATC
Found at i:5906 original size:67 final size:67
Alignment explanation
Indices: 5768--5916 Score: 192
Period size: 67 Copynumber: 2.2 Consensus size: 67
5758 AAAAATTTGT
* * *
5768 TGCTCGTTAAGCTCATTAAAATTTTGCTCAACTTGTGCTCGTTAAGAAAATTTGTTGCTAAACTC
1 TGCTCGTTAAGCTCATTAAAATTTTACTCAACTCGTGCTCGTTAAGAAAATTTGTTACTAAACTC
**
5833 TT
66 GC
* * **
5835 TGCTCGTTAAGCTCATTAAAATTTTATTCGAA-TCGTGCTCGTTAAGAAAATTTGTTATTCGACT
1 TGCTCGTTAAGCTCATTAAAATTTTACTC-AACTCGTGCTCGTTAAGAAAATTTGTTACTAAACT
5899 CGC
65 CGC
*
5902 TGCTCATTAAGCTCA
1 TGCTCGTTAAGCTCA
5917 CTGCTCGTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 69 0.97
68 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (67 bp):
TGCTCGTTAAGCTCATTAAAATTTTACTCAACTCGTGCTCGTTAAGAAAATTTGTTACTAAACTC
GC
Found at i:16391 original size:3 final size:3
Alignment explanation
Indices: 16383--16409 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
16373 GCAGATTCAG
16383 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
16410 AAGATTCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:26078 original size:3 final size:3
Alignment explanation
Indices: 26036--26065 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
26026 CTTAGTTTAC
26036 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
26066 AAATTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31218 original size:29 final size:29
Alignment explanation
Indices: 31176--31250 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
31166 AACCCAACCA
**
31176 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
31205 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
31234 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
31251 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:31256 original size:29 final size:29
Alignment explanation
Indices: 31177--31264 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
31167 ACCCAACCAT
* * ****
31177 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
31206 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
31235 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
31264 A
1 A
31265 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:32936 original size:36 final size:37
Alignment explanation
Indices: 32896--32976 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 37
32886 TTTTGTTCGG
*
32896 GTCGGGTCGGG-TTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGACGA
*
32932 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGACGG
1 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGACGA
32970 GTCGGGT
1 GTCGGGT
32977 TTAGGGTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
36 11 0.27
38 30 0.73
ACGTcount: A:0.12, C:0.11, G:0.41, T:0.36
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGACGA
Found at i:33199 original size:203 final size:202
Alignment explanation
Indices: 32651--33374 Score: 775
Period size: 203 Copynumber: 3.4 Consensus size: 202
32641 TTATTATTTC
* * * *
32651 GGGTCGGGTTTCTAATTCATATATTCGGGTCGAGTCGGGTGAAACTTTATTTTGGTCAGGTCGGA
1 GGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCA----GG-
*
32716 TCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAATCGGA
61 TCGGG-TTTTTTAAGTGTGATA------T----TCGGG-TCGGGTTTAGGGTGAAAAAAACCGGA
* *
32781 CCGACCCGAAAATATATATAATTCAGATCAGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAA
114 CCGACCCG-AAA-ATATATAATTCGGATCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAA
32846 TATTTTTTTATTATTTCGGGTCGGGT
177 TATTTTTTTATTATTTCGGGTCGGGT
* * * * * ** * *
32872 CGGAT-GAAACTT-T-ATT--T-TGTTCGGGTCGGGTCGGGTTTTTAAGTGTGATATTCGGGTCG
1 -GGGTCG-GATTTCTAATTCATATATTCGGGTCGGGTC-GG-ATGAAACT-T--TATT----TTG
* *
32931 AGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGACGGGTCGGGTTTAGGGTGAAAAAAACCGG
55 -TTCAGGTCGGG-TTTTTTAAGTGTGATATT-----CGGGTCGGGTTTAGGGTGAAAAAAACCGG
* * * *
32996 ACCGACTCGAAAATATATAATTCGGGTCGGGTCAGATTAAATCACTGTTTTTATTAAATAAAAAT
113 ACCGACCCGAAAATATATAATTCGGATCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAAT
33061 ATTTTTTTATTATTTCGGGTCGGGTT
178 ATTTTTTTATTATTTCGGGTCGGG-T
*
33087 GGGTCGGATTTCTAATTCATATATTCTGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGG
1 GGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGG
* *
33152 TTTTTTAAGAGTGATATTCGGGTCGGGTTTAGGGTGAAAACAACCGGACCGACCCGAAAATATAT
66 TTTTTTAAGTGTGATATTCGGGTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATAT
* * *
33217 AATTCGGTTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCGG
131 AATTCGGATCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTATTTCGG
33282 GTC----
196 GTCGGGT
*
33285 GGGTCGGATTTCTAATTCATATATTAGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGG
1 GGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGG
33350 TTTTTTAAGTGTGATATTCGGGTCG
66 TTTTTTAAGTGTGATATTCGGGTCG
33375 AGTCGGATCG
Statistics
Matches: 437, Mismatches: 42, Indels: 70
0.80 0.08 0.13
Matches are distributed among these distances:
198 87 0.20
203 108 0.25
208 17 0.04
209 9 0.02
210 2 0.00
212 1 0.00
214 82 0.19
215 6 0.01
216 37 0.08
217 21 0.05
218 6 0.01
219 17 0.04
220 4 0.01
221 2 0.00
222 31 0.07
223 2 0.00
226 2 0.00
227 3 0.01
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (202 bp):
GGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGG
TTTTTTAAGTGTGATATTCGGGTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATAT
AATTCGGATCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTATTTCGG
GTCGGGT
Found at i:33398 original size:38 final size:38
Alignment explanation
Indices: 33345--33427 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
33335 TTTGTTCAGG
33345 TCGGG-TTTTTTAAGTGTGATATTCGGGTC-GAGTCGGA
1 TCGGGTTTTTTTAAGTGTGATATTCGGGTCAG-GTCGGA
*
33382 TCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGG
1 TCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGA
33420 TCGGGTTT
1 TCGGGTTT
33428 AGGGTGAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
37 5 0.12
38 37 0.86
39 1 0.02
ACGTcount: A:0.13, C:0.11, G:0.36, T:0.40
Consensus pattern (38 bp):
TCGGGTTTTTTTAAGTGTGATATTCGGGTCAGGTCGGA
Found at i:39126 original size:17 final size:18
Alignment explanation
Indices: 39104--39138 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
39094 TTTTACATAT
39104 ATATT-AAATTAATTAAA
1 ATATTAAAATTAATTAAA
39121 ATATTAAAATTAATTAAA
1 ATATTAAAATTAATTAAA
39139 TTCAACTTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATTAAAATTAATTAAA
Found at i:39347 original size:18 final size:18
Alignment explanation
Indices: 39320--39367 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
39310 TAAATCACAC
39320 ATAT-TTATATGTTATAT
1 ATATATTATATGTTATAT
* *
39337 ATATATTATATATTGTAT
1 ATATATTATATGTTATAT
*
39355 AAATATTAT-TGTT
1 ATATATTATATGTT
39368 TTAGTAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
ATATATTATATGTTATAT
Found at i:40599 original size:2 final size:2
Alignment explanation
Indices: 40588--40620 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
40578 ACATTTAATG
40588 AT AT -T 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
40621 TTCTATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:41960 original size:5 final size:5
Alignment explanation
Indices: 41950--41977 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
41940 TCTTTTCATC
41950 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
41978 CATCACTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:43302 original size:8 final size:8
Alignment explanation
Indices: 43289--43327 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
43279 GAACATTTCA
*
43289 TGCATTCT
1 TGCATTTT
43297 TGCA-TTT
1 TGCATTTT
43304 TGCATTTT
1 TGCATTTT
*
43312 TGCCTTTT
1 TGCATTTT
43320 TGCATTTT
1 TGCATTTT
43328 CATCTACAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:44522 original size:9 final size:9
Alignment explanation
Indices: 44510--44549 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
44500 TAAAAAGGGC
44510 AAAAAGAAAA
1 AAAAAG-AAA
*
44520 AAAAAGCAA
1 AAAAAGAAA
*
44529 AAAAAGAAC
1 AAAAAGAAA
44538 AAAAAGAAA
1 AAAAAGAAA
44547 AAA
1 AAA
44550 GAAAAAGGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
9 20 0.77
10 6 0.23
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:45182 original size:22 final size:22
Alignment explanation
Indices: 45154--45197 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
45144 AGCTACCCCA
45154 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
45176 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
45198 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:46146 original size:36 final size:36
Alignment explanation
Indices: 46071--46148 Score: 102
Period size: 36 Copynumber: 2.2 Consensus size: 36
46061 GTTTTCCTTA
* ** *
46071 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTG
1 AAACAAATTTCGTCTCCCATGAGACAGTTTCGCTCG
* *
46107 AAACAAATTTTGTCTCCCATGAGGCAGTTTCGCTCG
1 AAACAAATTTCGTCTCCCATGAGACAGTTTCGCTCG
46143 AAACAA
1 AAACAA
46149 CACAATGTGC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.32
Consensus pattern (36 bp):
AAACAAATTTCGTCTCCCATGAGACAGTTTCGCTCG
Found at i:46591 original size:64 final size:65
Alignment explanation
Indices: 46490--46748 Score: 441
Period size: 64 Copynumber: 4.0 Consensus size: 65
46480 TTGGAACTCA
46490 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGTTTC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* *
46554 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCGACAAAAATTTCCCAGTATC
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* *
46619 AGACAACACAAGTTCAACTTCACAACGAATGGGCCGCTGGTTGTCAAC-AAAATTTCCCAGTTTA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
* *
46683 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAGTTT
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAA-AATTTCCCAGTTT
46748 C
65 C
46749 GGAGCCAATC
Statistics
Matches: 182, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
64 106 0.58
65 63 0.35
66 13 0.07
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.21
Consensus pattern (65 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTTC
Found at i:46720 original size:129 final size:130
Alignment explanation
Indices: 46490--46745 Score: 460
Period size: 129 Copynumber: 2.0 Consensus size: 130
46480 TTGGAACTCA
*
46490 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTTCA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTTAA
* *
46555 GACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCGACAAA-AATTTCCCAGTATC
66 GACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAGTATC
*
46619 AGACAACACAAGTTCAACTTCACAACGAATGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTTAA
1 AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTTAA
*
46684 GACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAGT
66 GACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAGT
46746 TTCGGAGCCA
Statistics
Matches: 121, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
129 110 0.91
130 11 0.09
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.21
Consensus pattern (130 bp):
AGACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAAATTTCCCAGTTTAA
GACAACACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAGTATC
Found at i:46869 original size:106 final size:106
Alignment explanation
Indices: 46691--46893 Score: 316
Period size: 106 Copynumber: 1.9 Consensus size: 106
46681 TAAGACAGCA
* * *
46691 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAGTTTCGGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACAATTTCCCAATTTCGGAACCA
46756 ATCTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACG
66 ATCTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACG
* * * *
46797 CAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAATAATTTCCCAATTTCGGAACCA
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACAATTTCCCAATTTCGGAACCA
* * *
46862 ATTTCAACTTCACGGCGGAGGATATTGGACTC
66 ATCTCAACTTCACAGCGAAGGATATTGGACTC
46894 GGAACAATAC
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 87 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.23
Consensus pattern (106 bp):
CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACAATTTCCCAATTTCGGAACCA
ATCTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACG
Found at i:47423 original size:18 final size:18
Alignment explanation
Indices: 47396--47443 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
47386 TAAATCACAC
47396 ATAT-TTATATGTTATAT
1 ATATATTATATGTTATAT
* *
47413 ATATATTATATATTGTAT
1 ATATATTATATGTTATAT
*
47431 AAATATTAT-TGTT
1 ATATATTATATGTT
47444 TTAGTAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
ATATATTATATGTTATAT
Found at i:48674 original size:2 final size:2
Alignment explanation
Indices: 48663--48701 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
48653 ACATTTAATG
48663 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48702 TTCTATTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:50408 original size:14 final size:15
Alignment explanation
Indices: 50374--50411 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
50364 GAAATCATTG
50374 AAAAATTATATATAA
1 AAAAATTATATATAA
*
50389 ATAAAATTATGTA-AA
1 A-AAAATTATATATAA
50404 AAAAATTA
1 AAAAATTA
50412 GAGATGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (15 bp):
AAAAATTATATATAA
Found at i:50621 original size:14 final size:15
Alignment explanation
Indices: 50584--50621 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
50574 AGAAATCATT
50584 AAAAAATTATATAGA
1 AAAAAATTATATAGA
* *
50599 AATAAATTATGTA-A
1 AAAAAATTATATAGA
50613 AAAAAATTA
1 AAAAAATTA
50622 GATATGAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAAATTATATAGA
Found at i:50704 original size:210 final size:211
Alignment explanation
Indices: 50340--50764 Score: 726
Period size: 210 Copynumber: 2.0 Consensus size: 211
50330 CCTTTATTAA
* * *
50340 GTTGATAGTTGATAATTTGGGAGAGAAATCATTGAAAAATTATATATAAATAAAATTATGTAAAA
1 GTTGATAGTTGATAATTTGAGAGAGAAATCATTAAAAAATTATATAGAAATAAAATTATGTAAAA
* * *
50405 AAAATTAGAGATGGGAAAGGATGTCGTTGGATATAGGAACGGATGTCGCCGGAGAGAGTGGGAGA
66 AAAATTAGAGATGAGAAAGGATATCGTTAGATATAGGAACGGATGTCGCCGGAGAGAGTGGGAGA
* * *
50470 TGGAGATGGAATGAGTTTCGATTTAGGGATTTTGGTTATGAGTTGTTGCTGTTGCGTAGTTTATA
131 TGGAGATGGAATGAGTTGCGATTTAGGGATTTTAGTTATGAGTTGTTGCTGCTGCGTAGTTTATA
*
50535 TATCCAAAACATTTGT
196 TACCCAAAACATTTGT
*
50551 GTTGATAGTTGATAGTTTGAGAGAGAAATCATTAAAAAATTATATAGAAAT-AAATTATGTAAAA
1 GTTGATAGTTGATAATTTGAGAGAGAAATCATTAAAAAATTATATAGAAATAAAATTATGTAAAA
* *
50615 AAAATTAGATATGAGAAAGGATATTGTTAGATATAGGAACGGATGTCGCCGGAGAGAGTGGGAGA
66 AAAATTAGAGATGAGAAAGGATATCGTTAGATATAGGAACGGATGTCGCCGGAGAGAGTGGGAGA
50680 TGGAGATGGAATGAGTTGCGATTTAGGGATTTTAGTTATGAGTTGTTGCTGCTGCGTAGTTTATA
131 TGGAGATGGAATGAGTTGCGATTTAGGGATTTTAGTTATGAGTTGTTGCTGCTGCGTAGTTTATA
50745 TACCCAAAACATTTGT
196 TACCCAAAACATTTGT
50761 GTTG
1 GTTG
50765 CGAAAATAAA
Statistics
Matches: 201, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
210 154 0.77
211 47 0.23
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (211 bp):
GTTGATAGTTGATAATTTGAGAGAGAAATCATTAAAAAATTATATAGAAATAAAATTATGTAAAA
AAAATTAGAGATGAGAAAGGATATCGTTAGATATAGGAACGGATGTCGCCGGAGAGAGTGGGAGA
TGGAGATGGAATGAGTTGCGATTTAGGGATTTTAGTTATGAGTTGTTGCTGCTGCGTAGTTTATA
TACCCAAAACATTTGT
Found at i:50787 original size:17 final size:19
Alignment explanation
Indices: 50760--50798 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
50750 AAAACATTTG
50760 TGTTGCGAAAA-TAAAAGT
1 TGTTGCGAAAATTAAAAGT
*
50778 TGTTGC-AAAATTAAAATT
1 TGTTGCGAAAATTAAAAGT
50796 TGT
1 TGT
50799 GTTGCGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.41, C:0.05, G:0.18, T:0.36
Consensus pattern (19 bp):
TGTTGCGAAAATTAAAAGT
Found at i:50813 original size:20 final size:20
Alignment explanation
Indices: 50786--50845 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
50776 GTTGTTGCAA
*
50786 AATT-AAAATTTGTGTTGCG
1 AATTCAAAATTCGTGTTGCG
* **
50805 AATTCAAAAATCAAGTTGCG
1 AATTCAAAATTCGTGTTGCG
**
50825 AAAACAAAATTCGTGTTGCG
1 AATTCAAAATTCGTGTTGCG
50845 A
1 A
50846 TTTAGAAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (20 bp):
AATTCAAAATTCGTGTTGCG
Found at i:50863 original size:40 final size:40
Alignment explanation
Indices: 50777--50868 Score: 98
Period size: 40 Copynumber: 2.3 Consensus size: 40
50767 AAAATAAAAG
* *
50777 TTGTTGCAAAATTAAAATTTGTGTTGCGAATTCAAAAATC
1 TTGTTGCAAAATCAAAATTCGTGTTGCGAATTCAAAAATC
** *
50817 AAGTTGCGAAAA-CAAAATTCGTGTTGCG-ATTTAGAAAATC
1 TTGTTGC-AAAATCAAAATTCGTGTTGCGAATTCA-AAAATC
50857 TTGTTGCTAAAA
1 TTGTTGC-AAAA
50869 GGAAACTTGT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
39 4 0.10
40 34 0.81
41 4 0.10
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (40 bp):
TTGTTGCAAAATCAAAATTCGTGTTGCGAATTCAAAAATC
Found at i:50915 original size:21 final size:20
Alignment explanation
Indices: 50889--50949 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
50879 ATTGCGAAAA
50889 AGAAATTCGCGTTGTGAATT
1 AGAAATTCGCGTTGTGAATT
* *
50909 CAGAAA-TCGAGTTGCGAATT
1 -AGAAATTCGCGTTGTGAATT
*
50929 TGAAATTC-CTTGTTGTGAATT
1 AGAAATTCGC--GTTGTGAATT
50950 TGGATATCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 4 0.12
20 14 0.44
21 14 0.44
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (20 bp):
AGAAATTCGCGTTGTGAATT
Found at i:50927 original size:20 final size:21
Alignment explanation
Indices: 50889--50936 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
50879 ATTGCGAAAA
* *
50889 AGAAATTCGCGTTGTGAATTC
1 AGAAATTCGAGTTGCGAATTC
50910 AGAAA-TCGAGTTGCGAATT-
1 AGAAATTCGAGTTGCGAATTC
*
50929 TGAAATTC
1 AGAAATTC
50937 CTTGTTGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 14 0.61
21 5 0.22
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.31
Consensus pattern (21 bp):
AGAAATTCGAGTTGCGAATTC
Found at i:55588 original size:22 final size:22
Alignment explanation
Indices: 55560--55602 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
55550 TTCTCTTTTT
55560 TCAAATATTAGTCTTCAATTTA
1 TCAAATATTAGTCTTCAATTTA
55582 TCAAATATTAGTCTTCAATTT
1 TCAAATATTAGTCTTCAATTT
55603 TTTTTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.47
Consensus pattern (22 bp):
TCAAATATTAGTCTTCAATTTA
Found at i:55862 original size:18 final size:19
Alignment explanation
Indices: 55826--55862 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
55816 CACGGAATGT
55826 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
55846 AAGATTACCAG-GGAATA
1 AAGATTACCAGAGGAATA
55863 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:56044 original size:37 final size:36
Alignment explanation
Indices: 56010--56079 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
56000 TACAAATTGT
56010 AAAATATTTATAT-ATTTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTAAAAAATTAAATTC
* *
56046 ATAATATTTATATAAATTTTTTTACAAAATTAAA
1 AAAATATTTATAT-AATTTTTTTAAAAAATTAAA
56080 AATATAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 12 0.40
37 13 0.43
38 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTAAAAAATTAAATTC
Found at i:59195 original size:23 final size:23
Alignment explanation
Indices: 59169--59234 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
59159 AACAATTCTA
59169 CCTTTATAGTACATTTATCTATG
1 CCTTTATAGTACATTTATCTATG
*
59192 CCTTTAT-G-ACACGTTTATATATG
1 CCTTTATAGTACA--TTTATCTATG
* * *
59215 TCTTTGTAGTACGTTTATCT
1 CCTTTATAGTACATTTATCT
59235 CTGACTTCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
21 3 0.09
22 1 0.03
23 27 0.79
24 1 0.03
25 2 0.06
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (23 bp):
CCTTTATAGTACATTTATCTATG
Found at i:65579 original size:21 final size:21
Alignment explanation
Indices: 65555--65603 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
65545 TTTTTTAGCC
65555 CAATGTATATGTAAGAGAATG
1 CAATGTATATGTAAGAGAATG
65576 CAATGTATATGTAAGAGAATG
1 CAATGTATATGTAAGAGAATG
65597 CAATGTA
1 CAATGTA
65604 CGTGATTCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (21 bp):
CAATGTATATGTAAGAGAATG
Found at i:67387 original size:78 final size:78
Alignment explanation
Indices: 67284--67440 Score: 271
Period size: 78 Copynumber: 2.0 Consensus size: 78
67274 TTTGGTTGCT
* *
67284 ATTTTTGTTTATTCTTTTTTTTAGGGTTTGATATCGCTTCGACTGATCAAGAT-GGATATTATTT
1 ATTTTTGTTTATTCTTTTTTCTAGGGTTTGATATCGCTTCAACTGATCAAGATGGGAT-TTATTT
67348 GTTACCATGCTAGG
65 GTTACCATGCTAGG
*
67362 ATTTTTGTTTATTCTTTTTTCTAGGGTTTGATATCGCTTCAACTGATCAAGATGGGCTTTATTTG
1 ATTTTTGTTTATTCTTTTTTCTAGGGTTTGATATCGCTTCAACTGATCAAGATGGGATTTATTTG
67427 TTACCATGCTAGG
66 TTACCATGCTAGG
67440 A
1 A
67441 CCATCAAATT
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
78 72 0.96
79 3 0.04
ACGTcount: A:0.20, C:0.13, G:0.19, T:0.48
Consensus pattern (78 bp):
ATTTTTGTTTATTCTTTTTTCTAGGGTTTGATATCGCTTCAACTGATCAAGATGGGATTTATTTG
TTACCATGCTAGG
Found at i:69288 original size:30 final size:30
Alignment explanation
Indices: 69252--69311 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
69242 TTTATAGGCC
69252 ACTAACGAAAGGACAAGAAAGAGATTATTA
1 ACTAACGAAAGGACAAGAAAGAGATTATTA
*
69282 ACTAACGAAAGGACAAGCAAGAGATTATTA
1 ACTAACGAAAGGACAAGAAAGAGATTATTA
69312 TACTGTGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.52, C:0.12, G:0.20, T:0.17
Consensus pattern (30 bp):
ACTAACGAAAGGACAAGAAAGAGATTATTA
Found at i:73433 original size:92 final size:91
Alignment explanation
Indices: 73269--73473 Score: 227
Period size: 92 Copynumber: 2.2 Consensus size: 91
73259 GTCATTCCCA
* * * * *
73269 GAAAAAGGA-CTGATCCCTTGACCAAAGGGATTGATCCCAAAGTTTCTATCTAGCAAAGGATCGA
1 GAAAAAGGATC-GATCCCTTCACCAAAAGGATCGATCCCAAACTTTCTATCTAACAAAGGATCGA
*
73333 TCCATTTT-CAAAATGATCCATCCCTTAG
65 ACCATTTTCCAAAA-GATCCATCCC-TAG
* * *
73361 GAAAAAGGATCGATCCATTCACCAAAAGGATCGATCCCAAACTTTCTGT-TATACATAGGATCGA
1 GAAAAAGGATCGATCCCTTCACCAAAAGGATCGATCCCAAACTTTCTATCTA-ACAAAGGATCGA
* * *
73425 ACCCTTTTCCAAAAGATCGATCCCTCG
65 ACCATTTTCCAAAAGATCCATCCCTAG
*
73452 AAAGAAAGGATCGATCCCTTCA
1 GAA-AAAGGATCGATCCCTTCA
73474 TTGTTTTGCT
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
91 6 0.06
92 83 0.87
93 6 0.06
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (91 bp):
GAAAAAGGATCGATCCCTTCACCAAAAGGATCGATCCCAAACTTTCTATCTAACAAAGGATCGAA
CCATTTTCCAAAAGATCCATCCCTAG
Found at i:74802 original size:55 final size:53
Alignment explanation
Indices: 74718--74826 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 53
74708 AACTTGTAAG
* *
74718 AGGGCTTATTTATGCACTGTAGTTGACTAATAGAATGTGTTTTTAGGAGATATAA
1 AGGGCTTATTTATGCACTGTAGTTGACTAATAG--TATGTATTTAGGAGATATAA
*
74773 AGGGCTTATTTATGCATTGTAGTTGACTAATAGTATGTATTTAGGAGATATAA
1 AGGGCTTATTTATGCACTGTAGTTGACTAATAGTATGTATTTAGGAGATATAA
74826 A
1 A
74827 TTAATCGAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
53 19 0.37
55 32 0.63
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (53 bp):
AGGGCTTATTTATGCACTGTAGTTGACTAATAGTATGTATTTAGGAGATATAA
Found at i:74872 original size:33 final size:33
Alignment explanation
Indices: 74830--74897 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
74820 ATATAAATTA
*
74830 ATCGAAATATGTGATAGAAGGAGAGATTTCTCG
1 ATCGAAATATATGATAGAAGGAGAGATTTCTCG
*
74863 ATCGGAATATATGATAGAAGGAGAGATTTCTCG
1 ATCGAAATATATGATAGAAGGAGAGATTTCTCG
74896 AT
1 AT
74898 ATATCTCTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.28
Consensus pattern (33 bp):
ATCGAAATATATGATAGAAGGAGAGATTTCTCG
Found at i:88692 original size:15 final size:15
Alignment explanation
Indices: 88672--88701 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
88662 TTATGCAGCT
*
88672 TGGAGCATTTCTGGC
1 TGGAGCATTACTGGC
88687 TGGAGCATTACTGGC
1 TGGAGCATTACTGGC
88702 AGAAACAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.20, G:0.33, T:0.30
Consensus pattern (15 bp):
TGGAGCATTACTGGC
Found at i:93748 original size:31 final size:31
Alignment explanation
Indices: 93699--93774 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
93689 CAAAAAAACA
* *
93699 TAAGATATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATGTGGTCATTTTCGTTTTTATTTAAT
* *
93730 TAAGATGTGATCATTTTCGTTTTTATTTAGT
1 TAAGATGTGGTCATTTTCGTTTTTATTTAAT
93761 TAAGATGTGGTCAT
1 TAAGATGTGGTCAT
93775 CACGGGTTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.25, C:0.08, G:0.17, T:0.50
Consensus pattern (31 bp):
TAAGATGTGGTCATTTTCGTTTTTATTTAAT
Found at i:93936 original size:27 final size:26
Alignment explanation
Indices: 93896--93978 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 26
93886 ATAAATTTTA
*
93896 ATATAAATAAATATTTTTAAATTTAGTT-
1 ATATAAA-AAATATTTTT-AA-TAAGTTC
*
93924 A-ATAATAAAATATATTTAATAAGTTC
1 ATATAA-AAAATATTTTTAATAAGTTC
*
93950 ATATAAAAAATATTTTT--TAAGTTA
1 ATATAAAAAATATTTTTAATAAGTTC
93974 ATATA
1 ATATA
93979 TATAAAAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
24 11 0.23
25 5 0.10
26 13 0.27
27 17 0.35
28 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.45
Consensus pattern (26 bp):
ATATAAAAAATATTTTTAATAAGTTC
Found at i:93962 original size:24 final size:24
Alignment explanation
Indices: 93893--93978 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 24
93883 TAAATAAATT
*
93893 TTAATATAAATAAATATTTTTAAATTTAG
1 TTAATATAAA-AAATA--TTT-AA-TAAG
*
93922 TTAATAATAAAATATATTTAATAAG
1 TTAAT-ATAAAAAATATTTAATAAG
* **
93947 TTCATATAAAAAATATTTTTTAAG
1 TTAATATAAAAAATATTTAATAAG
93971 TTAATATA
1 TTAATATA
93979 TATAAAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
24 23 0.47
25 7 0.14
26 2 0.04
27 3 0.06
29 9 0.18
30 5 0.10
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.45
Consensus pattern (24 bp):
TTAATATAAAAAATATTTAATAAG
Found at i:100323 original size:11 final size:12
Alignment explanation
Indices: 100283--100326 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
100273 TATTTAAACG
*
100283 GGTATTGGGCCA
1 GGTATTGGGTCA
*
100295 GGTATTGGGTCG
1 GGTATTGGGTCA
100307 GGTATTGGGTC-
1 GGTATTGGGTCA
100318 GGTATTGGG
1 GGTATTGGG
100327 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:100325 original size:23 final size:24
Alignment explanation
Indices: 100281--100326 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
100271 ATTATTTAAA
100281 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
100305 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
100327 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:100823 original size:5 final size:5
Alignment explanation
Indices: 100815--100840 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
100805 TATATAACTT
100815 GGTCG GGTCG GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTCG GGTCG GGTCG G
100841 ATAAGTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.62, T:0.19
Consensus pattern (5 bp):
GGTCG
Done.