Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002225.1 Hibiscus syriacus cultivar Beakdansim tig00004530_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: 121675
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2745 original size:196 final size:196
Alignment explanation
Indices: 2298--3222 Score: 988
Period size: 196 Copynumber: 4.8 Consensus size: 196
2288 GTTTAGATCT
*
2298 AAGTATCGATACCTATACAAAAGTATCGATACTTTATG-TTATCGCCTATTATCATTAAACCAGT
1 AAGTATCGATACCTATACAAAAGTATCAATACTTTATGTTTA-CGCCTATTATCATTAAACCAGT
* *
2362 AGAATTTTACCGTTTACATTGTAAGTTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTA-AC
65 AGACTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAT-GGTTTCGAAATTATA-
* * * * * * *
2426 AGTATATATGCTTG-TATACGTGTATCGATACTTTCTGCATGCAAATTGTTTGAGAAGCATATTG
128 AGTATAGATACTTGTTATACATGTATCGATACTTTGTGCTTGC-AATTG-TTGAGAAACATACTG
2490 GACTAA
191 GACTAA
* * * * * * * *
2496 AAGTATTGATACCTAAACAAAACGTAACGATGCTCTATGTTTACGCTTATTATCATTAAACCGGT
1 AAGTATCGATACCTATACAAAA-GTATCAATACTTTATGTTTACGCCTATTATCATTAAACCAGT
* * * *
2561 AGACTTTTACGGTTGACAATGT-AATTTACCTATAACTTT-AAGTAATCGGTTTCG-AATTATAA
65 AGACTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAT-GGTTTCGAAATTATAA
*
2623 GTATCGATACTTGTTATACATGTATCGATACTTTGTGCTTGCAAATTGTTGAGAAACATACTGGA
129 GTATAGATACTTGTTATACATGTATCGATACTTTGTGCTTGC-AATTGTTGAGAAACATACTGGA
2688 CTAA
193 CTAA
* *
2692 AAGTATCGATACCTATACAAAGAGTATCAATACTTTATGTTTACGCCTATTATCATTAAATCTGT
1 AAGTATCGATACCTATACAAA-AGTATCAATACTTTATGTTTACGCCTATTATCATTAAACCAGT
* * *
2757 AGATTTTTACAGTTTACACTGTAAATTTACCTATTACTTTAAAGTAATCGGTTTCGAAATTATAA
65 AGACTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAAT-GGTTTCGAAATTATAA
* *
2822 G--T--AT-C--G--AT--AT-TTTC--TAC---GTGC---AAATTGTTAGAGAAACATACTGGA
129 GTATAGATACTTGTTATACATGTATCGATACTTTGTGCTTGCAATTGTT-GAGAAACATACTGGA
2867 CTAA
193 CTAA
*
2871 AAGTATCGCA-ACCTATACAAAAAGTAT-AGATACTTTATG-TTACGCCTATTATCATTAAACTA
1 AAGTATCG-ATACCTATAC-AAAAGTATCA-ATACTTTATGTTTACGCCTATTATCATTAAACCA
* * * *
2933 GTAGACTTTTACCGTTTTCATTGTAAAATTACCTATTACTTT-AA--AAT-ATTTCAAAATTATA
63 GTAGACTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATGGTTTCGAAATTATA
* * *
2994 AGTATTGATACTTGTTATATATGTATCGATACTTTGTGCGTGCAATTGTTGAGAAACATACTGGA
128 AGTATAGATACTTGTTATACATGTATCGATACTTTGTGCTTGCAATTGTTGAGAAACATACTGGA
3059 CTAA
193 CTAA
* **
3063 AAGTATCGATACCTATACAAAGAGTATC--TACTTTATGTTTACGCATATTATCATTAAA-TTGA
1 AAGTATCGATACCTATACAAA-AGTATCAATACTTTATGTTTACGCCTATTATCATTAAACCAG-
* * * * * * * *
3125 TAGATTTTTATCATTT-CATTATAAAATTACCTATTACTTTAAAATAATAGTTTTGAAATTATAA
64 TAGACTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATGGTTTCGAAATTATAA
* *
3189 GTATAGATACTTGTTATGCGTGTATCGATACTTT
129 GTATAGATACTTGTTATACATGTATCGATACTTT
3223 TTTGCGTGCA
Statistics
Matches: 623, Mismatches: 63, Indels: 86
0.81 0.08 0.11
Matches are distributed among these distances:
173 14 0.02
175 4 0.01
177 4 0.01
178 66 0.11
179 50 0.08
180 5 0.01
182 6 0.01
184 2 0.00
185 6 0.01
187 6 0.01
188 2 0.00
190 40 0.06
191 38 0.06
192 41 0.07
193 10 0.02
194 43 0.07
195 2 0.00
196 107 0.17
197 64 0.10
198 50 0.08
199 60 0.10
200 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.38
Consensus pattern (196 bp):
AAGTATCGATACCTATACAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAACCAGTA
GACTTTTACCGTTTACATTGTAAATTTACCTATTACTTTAAAGTAATGGTTTCGAAATTATAAGT
ATAGATACTTGTTATACATGTATCGATACTTTGTGCTTGCAATTGTTGAGAAACATACTGGACTA
A
Found at i:2969 original size:178 final size:178
Alignment explanation
Indices: 2644--2977 Score: 514
Period size: 178 Copynumber: 1.9 Consensus size: 178
2634 TGTTATACAT
* * *
2644 GTATCGATACTTTGTGCTTGCAAATTGTTGAGAAACATACTGGACTAAAAGTATCGATACCTATA
1 GTATCGATACTTTCTACGTGCAAATTGTTGAGAAACATACTGGACTAAAAGTATCGATACCTATA
* *
2709 CAAAGAGTATCAATACTTTATGTTTACGCCTATTATCATTAAATCTGTAGATTTTTACAGTTTAC
66 CAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAATCTGTAGACTTTTACAGTTTAC
*
2774 ACTGTAAATTTACCTATTACTTTAAAGTAATCGGTTTCGAAATTATAA
131 ACTGTAAAATTACCTATTACTTTAAAGTAATCGGTTTCGAAATTATAA
*
2822 GTATCGATATTTTCTACGTGCAAATTGTTAGAGAAACATACTGGACTAAAAGTATCGCA-ACCTA
1 GTATCGATACTTTCTACGTGCAAATTGTT-GAGAAACATACTGGACTAAAAGTATCG-ATACCTA
*
2886 TACAAAAAGTAT-AGATACTTTATG-TTACGCCTATTATCATTAAA-CTAGTAGACTTTTACCGT
64 TACAAAAAGTATCA-ATACTTTATGTTTACGCCTATTATCATTAAATCT-GTAGACTTTTACAGT
* *
2948 TTTCATTGTAAAATTACCTATTACTTTAAA
127 TTACACTGTAAAATTACCTATTACTTTAAA
2978 ATATTTCAAA
Statistics
Matches: 142, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
177 2 0.01
178 86 0.61
179 53 0.37
180 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (178 bp):
GTATCGATACTTTCTACGTGCAAATTGTTGAGAAACATACTGGACTAAAAGTATCGATACCTATA
CAAAAAGTATCAATACTTTATGTTTACGCCTATTATCATTAAATCTGTAGACTTTTACAGTTTAC
ACTGTAAAATTACCTATTACTTTAAAGTAATCGGTTTCGAAATTATAA
Found at i:3165 original size:190 final size:195
Alignment explanation
Indices: 2817--3235 Score: 548
Period size: 194 Copynumber: 2.2 Consensus size: 195
2807 GTTTCGAAAT
* * *
2817 TATAAGTATCGATATTTTCTACGTGCAAATTGTTAGAGAAACATACTGGACTAAAAGTATCGCAA
1 TATATGTATCGATACTTTCTGCGTGC-AATTGTTAGAGAAACATACTGGACTAAAAGTATCGCAA
*
2882 CCTATACAAAAAGTATAGATACTTTATGTTACGCCTATTATCATTAAACTAGTAGACTTTTACCG
65 CCTATACAAAAAGTATA-ATACTTTATGTTACGCATATTATCATTAAACTAGTAGACTTTTACCG
* * *
2947 TTTTCATTGTAAAATTACCTATTACTTT-AA-AATA-TTTCAAAATTATAAGTATTGATACTTGT
129 ATTTCATTATAAAATTACCTATTACTTTAAATAATAGTTTCAAAATTATAAGTATAGATACTTGT
3009 TA
194 TA
*
3011 TATATGTATCGATACTTTGTGCGTGCAATTGTT-GAGAAACATACTGGACTAAAAGTATCG-ATA
1 TATATGTATCGATACTTTCTGCGTGCAATTGTTAGAGAAACATACTGGACTAAAAGTATCGCA-A
* * * * *
3074 CCTATACAAAGAGTAT-CTACTTTATGTTTACGCATATTATCATTAAA-TTGATAGATTTTTATC
65 CCTATACAAAAAGTATAATACTTTATG-TTACGCATATTATCATTAAACTAG-TAGACTTTTACC
**
3137 -ATTTCATTATAAAATTACCTATTACTTTAAAATAATAGTTTTGAAATTATAAGTATAGATACTT
128 GATTTCATTATAAAATTACCTATTACTTT-AAATAATAGTTTCAAAATTATAAGTATAGATACTT
3201 GTTA
192 GTTA
*** *
3205 TGCGTGTATCGATACTTTTTTGCGTGCAATT
1 TATATGTATCGATAC-TTTCTGCGTGCAATT
3236 ATTCATATGC
Statistics
Matches: 198, Mismatches: 19, Indels: 15
0.85 0.08 0.06
Matches are distributed among these distances:
190 37 0.19
191 30 0.15
192 45 0.23
193 11 0.06
194 61 0.31
195 14 0.07
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (195 bp):
TATATGTATCGATACTTTCTGCGTGCAATTGTTAGAGAAACATACTGGACTAAAAGTATCGCAAC
CTATACAAAAAGTATAATACTTTATGTTACGCATATTATCATTAAACTAGTAGACTTTTACCGAT
TTCATTATAAAATTACCTATTACTTTAAATAATAGTTTCAAAATTATAAGTATAGATACTTGTTA
Found at i:3230 original size:20 final size:21
Alignment explanation
Indices: 3189--3230 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3179 GAAATTATAA
3189 GTATAGATACTTGTTATGCGT
1 GTATAGATACTTGTTATGCGT
* *
3210 GTATCGATACTT-TTTTGCGT
1 GTATAGATACTTGTTATGCGT
3230 G
1 G
3231 CAATTATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.19, C:0.12, G:0.24, T:0.45
Consensus pattern (21 bp):
GTATAGATACTTGTTATGCGT
Found at i:4269 original size:65 final size:63
Alignment explanation
Indices: 4147--4355 Score: 215
Period size: 65 Copynumber: 3.2 Consensus size: 63
4137 ATTTATCAAA
* * * * ** *
4147 GATGCACCGATGCACCAATCCATGCATCGATGCACCATGAATTAAATTG-AACATCGAATGTATT
1 GATGCATCGATGCA-CAA-CCATGCATCGATGCACTAAGGA-TATTTTGAAACATCGAATGCATT
4211 T
63 T
* *
4212 CATGCATCGATGCACATACCATGCATCGATGCACTAAGGAT-TTTATGAAAACGTCGAATGCATT
1 GATGCATCGATGCACA-ACCATGCATCGATGCACTAAGGATATTT-TG-AAACATCGAATGCATT
4276 T
63 T
* ** * *
4277 GATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTT
1 GATGCATCGATGCA-CAACCATGCATCGATGCACTAAGGATATTTTGAAACATCGAATGCATTT
4341 GATGCATCGATGCAC
1 GATGCATCGATGCAC
4356 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 16, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 50 0.41
65 62 0.51
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
GATGCATCGATGCACAACCATGCATCGATGCACTAAGGATATTTTGAAACATCGAATGCATTT
Found at i:4355 original size:17 final size:19
Alignment explanation
Indices: 4327--4375 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
4317 TATTTTGAAA
4327 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
4345 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
4364 CACCGATGCACT
1 CATCGATGCACT
4376 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:7649 original size:22 final size:18
Alignment explanation
Indices: 7606--7675 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
7596 TTCAGTATTC
*
7606 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
7624 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
7646 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
7664 GTCCCGAAGGAC
1 GTCCCGAAGGAC
7676 TACTCCTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 28 0.62
22 17 0.38
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:9306 original size:64 final size:63
Alignment explanation
Indices: 9175--9329 Score: 165
Period size: 64 Copynumber: 2.4 Consensus size: 63
9165 TAATGAAGGT
* * * * *
9175 ATGCATCGATGCATACTGATGCAT-GGTGCATAAAATGCATTCGATGTTGTATTATTATAGGG
1 ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
9237 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
9299 G
63 G
*
9300 AGTGCATCGATGCATTACCAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
9330 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
62 14 0.18
63 11 0.14
64 46 0.58
65 8 0.10
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:13332 original size:20 final size:20
Alignment explanation
Indices: 13309--13351 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
13299 AATCCACCAT
*
13309 ATGCAACTAAATGCTTCTAA
1 ATGCAACTAAATGATTCTAA
* *
13329 ATGCATCTATATGATTCTAA
1 ATGCAACTAAATGATTCTAA
13349 ATG
1 ATG
13352 GTCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (20 bp):
ATGCAACTAAATGATTCTAA
Found at i:24295 original size:12 final size:12
Alignment explanation
Indices: 24280--24310 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
24270 CCCTCAATTC
24280 CACCACTTCTTT
1 CACCACTTCTTT
24292 CACCACTTCTTT
1 CACCACTTCTTT
24304 CACCACT
1 CACCACT
24311 CCATCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.45, G:0.00, T:0.35
Consensus pattern (12 bp):
CACCACTTCTTT
Found at i:27077 original size:40 final size:40
Alignment explanation
Indices: 27032--27126 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
27022 GCTCTTTATT
* * * *
27032 GGTTTTCTCAAATTGAAACCGGCTTTT-TTAATTTTCAATC
1 GGTTTTGTCAAATTCAAACCGG-TTTTGTCAATTTCCAATC
* * *
27072 GGTTTTGTCAATTTCCAATCGGTTTTGTCAATTTCCAATC
1 GGTTTTGTCAAATTCAAACCGGTTTTGTCAATTTCCAATC
27112 GGTTTTGTCAAATTC
1 GGTTTTGTCAAATTC
27127 GTTACCTGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.09
40 42 0.91
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (40 bp):
GGTTTTGTCAAATTCAAACCGGTTTTGTCAATTTCCAATC
Found at i:27090 original size:20 final size:20
Alignment explanation
Indices: 27061--27122 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
27051 CGGCTTTTTT
*
27061 AATTTTCAATCGGTTTTGTC
1 AATTTCCAATCGGTTTTGTC
27081 AATTTCCAATCGGTTTTGTC
1 AATTTCCAATCGGTTTTGTC
27101 AATTTCCAATCGGTTTTGTC
1 AATTTCCAATCGGTTTTGTC
27121 AA
1 AA
27123 ATTCGTTACC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.45
Consensus pattern (20 bp):
AATTTCCAATCGGTTTTGTC
Found at i:33953 original size:21 final size:21
Alignment explanation
Indices: 33921--33989 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
33911 AGATATTTCG
*
33921 ATGAAA-GAACTTAATCTTTTG
1 ATGAAATG-ACTTAATCTTTTA
* *
33942 ATTAAATGACTTATTCTTTTA
1 ATGAAATGACTTAATCTTTTA
* *
33963 ATGAAATGATTTAATCTTTTT
1 ATGAAATGACTTAATCTTTTA
33984 ATGAAA
1 ATGAAA
33990 AGAATTATTG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (21 bp):
ATGAAATGACTTAATCTTTTA
Found at i:34674 original size:20 final size:20
Alignment explanation
Indices: 34649--34722 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
34639 TTTTCCTAAT
34649 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
** ** *
34669 TCGCAACACGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
34690 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
34710 TCGCAATGCGAAT
1 TCGCAATGCGAAT
34723 CTGACTATCG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:34722 original size:41 final size:40
Alignment explanation
Indices: 34649--34742 Score: 125
Period size: 41 Copynumber: 2.3 Consensus size: 40
34639 TTTTCCTAAT
* *
34649 TCGCAATGCGAATACGTAAATCGCAACACGAATTTGGAAAA
1 TCGCAATGCGATTACGTAAATCGCAACACGAATCT-GAAAA
** **
34690 TCGCAATGCGATTACGTAAATCGCAATGCGAATCTGACTA
1 TCGCAATGCGATTACGTAAATCGCAACACGAATCTGAAAA
34730 TCGCAATGCGATT
1 TCGCAATGCGATT
34743 TACATAGCGC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 16 0.34
41 31 0.66
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.23
Consensus pattern (40 bp):
TCGCAATGCGATTACGTAAATCGCAACACGAATCTGAAAA
Found at i:34944 original size:22 final size:22
Alignment explanation
Indices: 34919--34980 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
34909 GGCGACATCC
34919 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
34941 GTCCCCA----CGACGATAA-CA
1 GTCCCCATCTCCGACGA-AATCA
* *
34959 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
34981 TTCACGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:35337 original size:20 final size:20
Alignment explanation
Indices: 35312--35359 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
35302 CAACGAGTGA
35312 ATCGCAACGCGAAAATGACC
1 ATCGCAACGCGAAAATGACC
** *
35332 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACC
35352 ATCGCAAC
1 ATCGCAAC
35360 AAGAGAATCG
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:0.29, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACC
Found at i:35432 original size:20 final size:20
Alignment explanation
Indices: 35403--35451 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
35393 GCGATTCTTA
*
35403 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
35423 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
35443 TGTTGCGAT
1 CGTTGCGAT
35452 TTTCATTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.18, C:0.16, G:0.27, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:35457 original size:20 final size:20
Alignment explanation
Indices: 35419--35473 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
35409 GATAGTCAAA
* **
35419 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
35439 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
35459 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
35474 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:35481 original size:20 final size:20
Alignment explanation
Indices: 35438--35481 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
35428 CGATAGTCAT
** *
35438 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
35458 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
35478 TTTC
1 TTTC
35482 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:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:37378 original size:20 final size:20
Alignment explanation
Indices: 37353--37496 Score: 192
Period size: 20 Copynumber: 7.5 Consensus size: 20
37343 AGAATAGTTT
37353 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
37373 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
37393 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
37409 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
37427 AATATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
37447 ACTATCGCAATACGAAAATG
1 ACTATCGCAATGCGAAAATG
**
37467 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
37487 ACTATCGCAA
1 ACTATCGCAA
37497 CGAAAGAATC
Statistics
Matches: 110, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
14 7 0.06
16 4 0.04
17 4 0.04
18 4 0.04
20 91 0.83
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:37514 original size:94 final size:93
Alignment explanation
Indices: 37353--37526 Score: 276
Period size: 94 Copynumber: 1.9 Consensus size: 93
37343 AGAATAGTTT
* * *
37353 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAAT
1 ACTATCGCAATACGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCACAAT
*
37418 GCGAAAATGAATATCGCAATGCGAAAATG
66 GCG-AAATGAAAATCGCAATGCGAAAATG
* **
37447 ACTATCGCAATACGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCACAAT
1 ACTATCGCAATACGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCACAAT
37512 GCGAAATGAAAATCG
66 GCGAAATGAAAATCG
37527 GATTGCGATT
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
93 11 0.15
94 62 0.85
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.18
Consensus pattern (93 bp):
ACTATCGCAATACGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCACAAT
GCGAAATGAAAATCGCAATGCGAAAATG
Found at i:37568 original size:20 final size:20
Alignment explanation
Indices: 37543--37648 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
37533 GATTCTCTCG
* *
37543 TTGCGATAGTCAAATTCACA
1 TTGCGATAGTCAATTTCGCA
37563 TTGCGATAGTC-ATTTCGCA
1 TTGCGATAGTCAATTTCGCA
*
37582 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAATTTCGCA
* *
37602 TTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCAATTTCGCA
* *
37622 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAATTTCGCA
37642 TTGCGAT
1 TTGCGAT
37649 TTTAAGTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
19 17 0.22
20 62 0.78
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCAATTTCGCA
Found at i:37604 original size:39 final size:40
Alignment explanation
Indices: 37543--37648 Score: 160
Period size: 40 Copynumber: 2.7 Consensus size: 40
37533 GATTCTCTCG
** *
37543 TTGCGATAGTCAAATTCACATTGCGATAGTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCA
*
37582 TTGCGATAGTCATTTTCGCATTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCA
*
37622 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
37649 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 28 0.47
40 32 0.53
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.39
Consensus pattern (40 bp):
TTGCGATAGTCATTTTCGCATTGCGATAGTCATTTTCGCA
Found at i:39611 original size:14 final size:14
Alignment explanation
Indices: 39592--39627 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39582 ATTGTTTAAT
39592 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
39606 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
39620 TGATTTGT
1 TGATTTGT
39628 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:40650 original size:64 final size:64
Alignment explanation
Indices: 40582--40746 Score: 194
Period size: 64 Copynumber: 2.6 Consensus size: 64
40572 TTGTTTGAAT
* * * **
40582 GTGCACCGATGCATTGGTGGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATT
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAA-T
40645 C-
63 CG
* * *
40646 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATCG
1 GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
40710 GTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCA
1 GTGCATCGATGCAT-AGGTAGTGCATCGATGCATCCCA
40747 ACAATAAAAC
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
63 2 0.02
64 79 0.90
65 7 0.08
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.25
Consensus pattern (64 bp):
GTGCATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
Found at i:40762 original size:64 final size:63
Alignment explanation
Indices: 40630--40806 Score: 196
Period size: 64 Copynumber: 2.8 Consensus size: 63
40620 TAAAATAAAG
* ** *
40630 ACATCGAATGCAATTCGTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAA
1 ACATCGAATGCAATTCGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAACAATAG-AAA
40694 ACATCGAATGCAA-TCGGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAACAATA-AAA
1 ACATCGAATGCAATTC-GTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAACAATAGAAA
* ** ** * * *
40756 CTACATCGAATACCTTTTATGCACCGATGCATCAGTAGTGCATCGATGCAT
1 --ACATCGAATGCAATTCGTGCATCGATGCATAAGGAGTGCATCGATGCAT
40807 ACCTTCATTA
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
62 2 0.02
63 2 0.02
64 92 0.95
65 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (63 bp):
ACATCGAATGCAATTCGTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAACAATAGAAA
Found at i:41132 original size:12 final size:12
Alignment explanation
Indices: 41114--41149 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
41104 TATATATGTT
41114 CATGTGATATGA
1 CATGTGATATGA
*
41126 TATGTGATATGA
1 CATGTGATATGA
*
41138 CCTGTGATATGA
1 CATGTGATATGA
41150 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:41312 original size:15 final size:15
Alignment explanation
Indices: 41294--41326 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
41284 GAGGGTATAA
41294 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
41309 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
41324 TAG
1 TAG
41327 GAGTCCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:47605 original size:64 final size:63
Alignment explanation
Indices: 47488--47630 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 63
47478 ATTGTTTGAA
* **
47488 TGTGCACCGATGCATTAATAGTGCATCGATGCACTCTTTTAAAATAAAGACATCGAATGCAAT-
1 TGTGCATCGATGCA-TAATAGTGCATCGATGCACTCCATTAAAATAAAGACATCGAATGCAATC
* *
47551 TCGTGCATCGATGCATAAGTAGTGCATCGATGCA-TCCCATTAATAGTGAA-ACATCGAATGCAA
1 T-GTGCATCGATGCATAA-TAGTGCATCGATGCACT-CCATTAA-AATAAAGACATCGAATGCAA
47614 TC
62 TC
47616 TGTGCATCGATGCAT
1 TGTGCATCGATGCAT
47631 CCCAACAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
63 5 0.07
64 60 0.86
65 5 0.07
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (63 bp):
TGTGCATCGATGCATAATAGTGCATCGATGCACTCCATTAAAATAAAGACATCGAATGCAATC
Found at i:48020 original size:12 final size:12
Alignment explanation
Indices: 48002--48037 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
47992 TATATATGTT
48002 CATGTGATATGA
1 CATGTGATATGA
*
48014 TATGTGATATGA
1 CATGTGATATGA
*
48026 CCTGTGATATGA
1 CATGTGATATGA
48038 GAAAATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:48200 original size:15 final size:15
Alignment explanation
Indices: 48182--48244 Score: 108
Period size: 15 Copynumber: 4.2 Consensus size: 15
48172 GAGGGTATAA
*
48182 TAGTCCTTTGGGACG
1 TAGTCCTTCGGGACG
48197 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
48212 TAGTCCTTCGGGACG
1 TAGTCCTTCGGGACG
*
48227 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGACG
48242 TAG
1 TAG
48245 GAGTCCTACG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.30
Consensus pattern (15 bp):
TAGTCCTTCGGGACG
Found at i:48942 original size:33 final size:34
Alignment explanation
Indices: 48886--48983 Score: 153
Period size: 33 Copynumber: 2.9 Consensus size: 34
48876 GTTACAGAGT
*
48886 GAATCACAATGCGAAAATGAAAATCGCAACGAGA
1 GAATCGCAATGCGAAAATGAAAATCGCAACGAGA
*
48920 GAATCGCAATGCG-AAATGAAAATCGCAACGAGT
1 GAATCGCAATGCGAAAATGAAAATCGCAACGAGA
* *
48953 GAATCGTAATGCGAAAATGAAAATTGCAACG
1 GAATCGCAATGCGAAAATGAAAATCGCAACG
48984 CGAAACTAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 31 0.53
34 28 0.47
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.15
Consensus pattern (34 bp):
GAATCGCAATGCGAAAATGAAAATCGCAACGAGA
Found at i:49018 original size:20 final size:20
Alignment explanation
Indices: 48993--49036 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
48983 GCGAAACTAA
48993 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
49013 TTTCGCGTTTCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
49033 TTTC
1 TTTC
49037 ATATTGCGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.09, C:0.20, G:0.16, T:0.55
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:49046 original size:20 final size:20
Alignment explanation
Indices: 49000--49047 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
48990 TAATTTCGCG
* *
49000 TTGCGATTTTCATTTTCGCG
1 TTGCGATTTTCATTTTCACA
* *
49020 TTTCGATTTTCATTTTCATA
1 TTGCGATTTTCATTTTCACA
49040 TTGCGATT
1 TTGCGATT
49048 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.54
Consensus pattern (20 bp):
TTGCGATTTTCATTTTCACA
Found at i:49077 original size:20 final size:20
Alignment explanation
Indices: 49052--49140 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
49042 GCGATTCTCT
49052 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
49072 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* *
49092 CATTGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
49112 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
49132 CGTTGCGAT
1 CGTTGCGAT
49141 TTTCGCGTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:49147 original size:14 final size:14
Alignment explanation
Indices: 49128--49154 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
49118 GATAGTCATA
49128 TTCGCGTTGCGATT
1 TTCGCGTTGCGATT
49142 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
49155 AGTCAAATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.30, T:0.41
Consensus pattern (14 bp):
TTCGCGTTGCGATT
Found at i:51601 original size:24 final size:24
Alignment explanation
Indices: 51567--51620 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
51557 CTGAAAAATC
51567 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
51591 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
51615 ATCAAA
1 ATCAAA
51621 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:51634 original size:24 final size:24
Alignment explanation
Indices: 51567--51634 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
51557 CTGAAAAATC
* * *
51567 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
51591 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
51615 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
51635 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:52489 original size:20 final size:20
Alignment explanation
Indices: 52464--52517 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
52454 AAATTCAGTA
52464 TTGCGATAGT-CAGAATCTCG
1 TTGCGAT-GTACAGAATCTCG
* *
52484 TTGCGATTTACAGATTCTCG
1 TTGCGATGTACAGAATCTCG
*
52504 TTGCGATTTACAGA
1 TTGCGATGTACAGA
52518 TTCGCATTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (20 bp):
TTGCGATGTACAGAATCTCG
Found at i:52518 original size:20 final size:20
Alignment explanation
Indices: 52474--52534 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
52464 TTGCGATAGT
*
52474 CAGAATCTCGTTGCGATTTA
1 CAGATTCTCGTTGCGATTTA
52494 CAGATTCTCGTTGCGATTTA
1 CAGATTCTCGTTGCGATTTA
* *
52514 CAGATTCGCATTGCGATTTA
1 CAGATTCTCGTTGCGATTTA
52534 C
1 C
52535 GTATTTGCAT
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:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (20 bp):
CAGATTCTCGTTGCGATTTA
Found at i:52544 original size:20 final size:20
Alignment explanation
Indices: 52484--52564 Score: 94
Period size: 20 Copynumber: 4.0 Consensus size: 20
52474 CAGAATCTCG
* *
52484 TTGCGATTTACAG-ATTCTCG
1 TTGCGATTTAC-GTATTCGCA
52504 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
52524 TTGCGATTTACGTATTTGCA
1 TTGCGATTTACGTATTCGCA
*
52544 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
52564 T
1 T
52565 CGCAACGCGA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 1 0.02
20 54 0.98
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:58762 original size:21 final size:20
Alignment explanation
Indices: 58738--58801 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
58728 AACTTTGAAA
58738 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
58759 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
58773 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
58794 AAATGTTT
1 AAATGTTT
58802 CTTTTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:58829 original size:37 final size:35
Alignment explanation
Indices: 58736--58851 Score: 160
Period size: 35 Copynumber: 3.3 Consensus size: 35
58726 CCAACTTTGA
58736 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTT
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTT
* *
58771 GAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTT
1 AAAAATGATTTTCAAAGTTTGGTAAATGTTTC-TTT
* * * *
58807 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTTGTTG
1 AAAAAT-GATTTTCAAAGTTTGGTAAATGTTTCTTT
58843 AAAAATGAT
1 AAAAATGAT
58852 AATGGGATAA
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
35 32 0.45
36 16 0.23
37 23 0.32
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (35 bp):
AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTT
Found at i:60866 original size:498 final size:499
Alignment explanation
Indices: 59929--60925 Score: 1640
Period size: 498 Copynumber: 2.0 Consensus size: 499
59919 GTGATCTGGT
* * *
59929 ACTGAGCGAAGAAATTCGACGGAGAGAATCGGGTGAAGCATTAATCTCCTCAGCCTTGCACACGA
1 ACTGAGCGAAGAAATTCGACGGAGAGAATCGGGTGAAGCATCAACCTCCTCAGCCTTGCAAACGA
*
59994 AGTCTAGAGGGAGAACTTCAGAAAGAAATTCAAATCGTGACAGATCGAAATCCAGAAGGGGCAAA
66 AGTCCAGAGGGAGAACTTCAGAAAGAAATTCAAATCGTGACAGATCGAAATCCAGAAGGGGCAAA
*
60059 TCAAGAACAGAAAAGAAAGATTTTACCTGTTATAATTGTGACAAGAAGGGTCATTTTAAAAGAGA
131 TCAAGAACAGAAAAGAAAGATTTTACCTGTTATAATTGTGACAAGAAGGGTCACTTTAAAAGAGA
* *
60124 TTGTCGAGCACTGAAGAAAGATACCGGTGCATAGGAATCTGCCAACATGACAGAGGAGACAGGTG
196 TTGTCGAACACTGAAGAAAGATACCGGTGCACAGGAATCTGCCAACATGACAGAGGAGACAGGTG
* * * * * * *
60189 ATGTCATGATTCTAAGCGTCAACACTCTGATTGAATCATGAATCTTGGATTCAGGGGCATTTTTT
261 ATGCCATGATTCTAAACGTCAACACTCCGATTGAATCATGAATCTTGAATTCAGGGGCATCTATC
* *
60254 CACTCCACCCCATGCCGAGAAATCATTGAGAACTATGTCAATGGTGATTTTGGGAATGCTCATCT
326 CACTCCACCCCATGCCGAGAAATCATTGAGAACTATGTCAATGGTGATTTTGAGAATACTCATCT
* *
60319 AGCTGATGATGAAACCTTGAAGATCGTTAGAAAAGAAGACATCCGATTAAAGTTGTCAAACCAGA
391 AGCTGATGATGAAACCTTGAAGATCGTCAGAAAAGAAGACATCCGATTAAAGTTGCCAAACCAGA
*
60384 CCACCTGGACGTTGAAAGGA-GAGACATATTCCTGGCCTCAAAC
456 CCACCTGGACGTTGAAAGGAGGAGACATATTCATGGCCTCAAAC
* * *
60427 ACTGAGCGAAGAAATTCGATGGAGAGAATCGGGTGAAGTATCAACCTCCTCAGCCTTGCAAACGG
1 ACTGAGCGAAGAAATTCGACGGAGAGAATCGGGTGAAGCATCAACCTCCTCAGCCTTGCAAACGA
* * *
60492 AGTCCAGAGGGAGAACTTCAGAAAGAAATTCAAATTGTGGCAGATCGAAATCTAGAAGGGGCAAA
66 AGTCCAGAGGGAGAACTTCAGAAAGAAATTCAAATCGTGACAGATCGAAATCCAGAAGGGGCAAA
* * *
60557 TCAAGAGCAGGAAATAAAGATTTTACCTGTTATAATTGTGACAAGAAGGGTCACTTTAAAAGAGA
131 TCAAGAACAGAAAAGAAAGATTTTACCTGTTATAATTGTGACAAGAAGGGTCACTTTAAAAGAGA
* * *
60622 TTGTTGAACACTGAAGAAATATACTGGTGCACAGGAATCTGCCAACATGACAGAGGAGACAGGTG
196 TTGTCGAACACTGAAGAAAGATACCGGTGCACAGGAATCTGCCAACATGACAGAGGAGACAGGTG
60687 ATGCCATGATTCTAAACGTCAACACTCCGATTGAATCATGAATCTTGAATTCAGGGGCATCTATC
261 ATGCCATGATTCTAAACGTCAACACTCCGATTGAATCATGAATCTTGAATTCAGGGGCATCTATC
*
60752 CACTCCACCCCATGCCGAGAAATCA-TGAAGAACTATGTCAATGGTGATTTTGAGAATATTCATC
326 CACTCCACCCCATGCCGAGAAATCATTG-AGAACTATGTCAATGGTGATTTTGAGAATACTCATC
* *
60816 TAGCTGATGATGAAACCTTGAAGATCGTCGGAAAAGGAA-ACATCCGATTAAAGTTGCCAAACTA
390 TAGCTGATGATGAAACCTTGAAGATCGTCAGAAAA-GAAGACATCCGATTAAAGTTGCCAAACCA
60880 GACCACCTGGACGTTGAAAGGAGTGAGACATATTCATGGCCTCAAA
454 GACCACCTGGACGTTGAAAGGAG-GAGACATATTCATGGCCTCAAA
60926 AGAAATTTGA
Statistics
Matches: 461, Mismatches: 34, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
497 2 0.00
498 435 0.94
499 3 0.01
500 21 0.05
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (499 bp):
ACTGAGCGAAGAAATTCGACGGAGAGAATCGGGTGAAGCATCAACCTCCTCAGCCTTGCAAACGA
AGTCCAGAGGGAGAACTTCAGAAAGAAATTCAAATCGTGACAGATCGAAATCCAGAAGGGGCAAA
TCAAGAACAGAAAAGAAAGATTTTACCTGTTATAATTGTGACAAGAAGGGTCACTTTAAAAGAGA
TTGTCGAACACTGAAGAAAGATACCGGTGCACAGGAATCTGCCAACATGACAGAGGAGACAGGTG
ATGCCATGATTCTAAACGTCAACACTCCGATTGAATCATGAATCTTGAATTCAGGGGCATCTATC
CACTCCACCCCATGCCGAGAAATCATTGAGAACTATGTCAATGGTGATTTTGAGAATACTCATCT
AGCTGATGATGAAACCTTGAAGATCGTCAGAAAAGAAGACATCCGATTAAAGTTGCCAAACCAGA
CCACCTGGACGTTGAAAGGAGGAGACATATTCATGGCCTCAAAC
Found at i:63914 original size:35 final size:34
Alignment explanation
Indices: 63829--63917 Score: 169
Period size: 34 Copynumber: 2.6 Consensus size: 34
63819 AAGTATTGTT
63829 AAAATGGTTTTCAAGTTTGACAACCAACTTTGAA
1 AAAATGGTTTTCAAGTTTGACAACCAACTTTGAA
63863 AAAATGGTTTTCAAGTTTGACAACCAACTTTGAA
1 AAAATGGTTTTCAAGTTTGACAACCAACTTTGAA
63897 AAAATGGTTTTCAAAGTTTGA
1 AAAATGGTTTTC-AAGTTTGA
63918 TAAATGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 46 0.85
35 8 0.15
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (34 bp):
AAAATGGTTTTCAAGTTTGACAACCAACTTTGAA
Found at i:63945 original size:37 final size:38
Alignment explanation
Indices: 63890--63973 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
63880 TGACAACCAA
63890 CTTTGAAAAA-ATGGTTTTCAAAGTTTGATAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGATAAATGTTT
* * *
63927 CTTTGAAAAATA-GTTTTTCAAAGTTTGTTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGATAAATGTTT
*
63964 -GTTGAAAAAT
1 CTTTGAAAAAT
63974 GATAATGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.21
37 32 0.76
38 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.44
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGATAAATGTTT
Found at i:73731 original size:20 final size:20
Alignment explanation
Indices: 73708--73751 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
73698 TTTCAAATTT
73708 GCAATGCGAATATGTAAATC
1 GCAATGCGAATATGTAAATC
*
73728 GCAATGCGAATTTGTAAATC
1 GCAATGCGAATATGTAAATC
73748 GCAA
1 GCAA
73752 CACAGAAGTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (20 bp):
GCAATGCGAATATGTAAATC
Found at i:73770 original size:40 final size:41
Alignment explanation
Indices: 73719--73833 Score: 114
Period size: 41 Copynumber: 2.9 Consensus size: 41
73709 CAATGCGAAT
**
73719 ATGT-AAA-TCGCAATGCGAATTTGTAAA-TCGCAACACAGA
1 ATGTCAAATTCGCAATGCG-ATTTCCAAATTCGCAACACAGA
*
73758 A-GTCAAATTCGCAATGCGATTTCCAAATTCGCAACACTGA
1 ATGTCAAATTCGCAATGCGATTTCCAAATTCGCAACACAGA
* * **
73798 ATTTCAAATTTGCAACT-CGATTTCTGAATTCGCAAC
1 ATGTCAAATTCGCAA-TGCGATTTCCAAATTCGCAAC
73834 GCGAATTTAG
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
38 2 0.03
39 11 0.17
40 22 0.34
41 28 0.44
42 1 0.02
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (41 bp):
ATGTCAAATTCGCAATGCGATTTCCAAATTCGCAACACAGA
Found at i:73819 original size:41 final size:40
Alignment explanation
Indices: 73657--73841 Score: 123
Period size: 40 Copynumber: 4.6 Consensus size: 40
73647 CGCAACGCAG
* * *
73657 TTTCCAAATTCGCAACGCGAATATAT-AAA-TCACATTGCGA
1 TTTCCAAATTCGCAACACGAAT-T-TCAAATTCGCAATGCGA
* * **
73697 TTTTCAAATTTGCAATGCGAATATGT-AAA-TCGCAATGCGAA
1 TTTCCAAATTCGCAACACGAAT-T-TCAAATTCGCAATGCG-A
** *
73738 TTTGTAAA-TCGCAACACAGAA-GTCAAATTCGCAATGCGA
1 TTTCCAAATTCGCAACAC-GAATTTCAAATTCGCAATGCGA
*
73777 TTTCCAAATTCGCAACACTGAATTTCAAATTTGCAACT-CGA
1 TTTCCAAATTCGCAACAC-GAATTTCAAATTCGCAA-TGCGA
** *
73818 TTTCTGAATTCGCAACGCGAATTT
1 TTTCCAAATTCGCAACACGAATTT
73842 AGAAAATCGC
Statistics
Matches: 118, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
38 1 0.01
39 10 0.08
40 67 0.57
41 39 0.33
42 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.30
Consensus pattern (40 bp):
TTTCCAAATTCGCAACACGAATTTCAAATTCGCAATGCGA
Found at i:73832 original size:20 final size:19
Alignment explanation
Indices: 73760--73833 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 19
73750 AACACAGAAG
73760 TCAAATTCGCAA-TGCGATT
1 TCAAATTCGCAACT-CGATT
*
73779 TCCAAATTCGCAACACTGAATT
1 T-CAAATTCGCAACTC-G-ATT
*
73801 TCAAATTTGCAACTCGATT
1 TCAAATTCGCAACTCGATT
*
73820 TCTGAATTCGCAAC
1 TC-AAATTCGCAAC
73834 GCGAATTTAG
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
19 6 0.13
20 22 0.49
21 13 0.29
22 4 0.09
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTCGATT
Found at i:73854 original size:41 final size:42
Alignment explanation
Indices: 73723--73854 Score: 105
Period size: 41 Copynumber: 3.2 Consensus size: 42
73713 GCGAATATGT
** * *
73723 AAATCGCAA-TGCGAATTTGTAAA-TCGCAACACAGAA-GTCA
1 AAATCGCAACTGCG-ATTTCCAAATTCGCAACACTGAATTTCA
*
73763 AATTCGCAA-TGCGATTTCCAAATTCGCAACACTGAATTTCA
1 AAATCGCAACTGCGATTTCCAAATTCGCAACACTGAATTTCA
* * ** * *
73804 AATTTGCAACT-CGATTTCTGAATTCGCAACGC-GAATTTAGA
1 AAATCGCAACTGCGATTTCCAAATTCGCAACACTGAATTT-CA
73845 AAATCGCAAC
1 AAATCGCAAC
73855 ACGAATTTTA
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
39 7 0.09
40 30 0.39
41 38 0.50
42 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (42 bp):
AAATCGCAACTGCGATTTCCAAATTCGCAACACTGAATTTCA
Found at i:74685 original size:12 final size:12
Alignment explanation
Indices: 74664--74697 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
74654 ACCACATTTC
*
74664 CAATACCAAACA
1 CAATATCAAACA
74676 CAATATCAAACA
1 CAATATCAAACA
*
74688 CAATCTCAAA
1 CAATATCAAA
74698 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:75068 original size:12 final size:12
Alignment explanation
Indices: 75051--75075 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75041 ATATAACCCT
75051 GAAGAAGAAAAA
1 GAAGAAGAAAAA
75063 GAAGAAGAAAAA
1 GAAGAAGAAAAA
75075 G
1 G
75076 TCCTCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:77912 original size:30 final size:30
Alignment explanation
Indices: 77876--77962 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
77866 CCCGAAGGAC
* * *
77876 CTATCCATAGGTCACAAGGAACCTCGGTAA
1 CTATCCATAGGTCACAAAGAACCTAGGCAA
* * *
77906 CTATCCAGAGGTCATAAAGATCCTAGGCAA
1 CTATCCATAGGTCACAAAGAACCTAGGCAA
* *
77936 CTGTCCATAGGTTC-CGAAGAACCTAGG
1 CTATCCATAGG-TCACAAAGAACCTAGG
77963 TAAACTGTCC
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
30 43 0.96
31 2 0.04
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (30 bp):
CTATCCATAGGTCACAAAGAACCTAGGCAA
Found at i:77970 original size:31 final size:31
Alignment explanation
Indices: 77934--78058 Score: 137
Period size: 31 Copynumber: 4.0 Consensus size: 31
77924 GATCCTAGGC
* *
77934 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
** *
77965 AACTGTCCATATGTTCCTTAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
77996 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
78027 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
78059 TACCCTCAAC
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
30 3 0.04
31 50 0.63
32 23 0.29
33 3 0.04
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:81981 original size:2 final size:2
Alignment explanation
Indices: 81963--82003 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
81953 ATCATCTATC
* *
81963 AT AT -T AT AT AA AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82004 CTCATAACTC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:82854 original size:30 final size:30
Alignment explanation
Indices: 82820--82891 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
82810 CCCGAAGGAC
* *
82820 CTATCCAGAGGTCACAATGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
82850 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
82880 CTGTCCATAGGT
1 CTATCCAGAGGT
82892 TCTGAAGAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:82916 original size:31 final size:31
Alignment explanation
Indices: 82878--83002 Score: 103
Period size: 31 Copynumber: 4.0 Consensus size: 31
82868 GATCCTCGGC
*
82878 AACTGTCCATAGGTT-CTGAAGAACCTAGGTA
1 AACTGTCCATAGGTTCCT-AAGAACATAGGTA
* *
82909 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTTCCTAAGAACATAGGTA
* ** **
82940 TACTGTCCATATATCTCGAAAG-ACATAGGTA
1 AACTGTCCATAGGT-TCCTAAGAACATAGGTA
* *
82971 ATTCTGTCCATATGTTCCGT-AGAACATAGGTA
1 A-ACTGTCCATAGGTTCC-TAAGAACATAGGTA
83003 TACCCTCAAC
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
31 50 0.66
32 26 0.34
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (31 bp):
AACTGTCCATAGGTTCCTAAGAACATAGGTA
Found at i:85196 original size:20 final size:20
Alignment explanation
Indices: 85163--85201 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
85153 TGTTGCAATT
85163 GTTGCAAAAGTCAAATTCGC
1 GTTGCAAAAGTCAAATTCGC
85183 GTTGCGAAAA-TCAAATTCG
1 GTTGC-AAAAGTCAAATTCG
85202 AAACACGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (20 bp):
GTTGCAAAAGTCAAATTCGC
Found at i:85255 original size:20 final size:20
Alignment explanation
Indices: 85230--85310 Score: 90
Period size: 20 Copynumber: 4.0 Consensus size: 20
85220 TGCAACGTGC
**
85230 ATTTGACTTTCGTGTTGCGA
1 ATTTGACTTTCGCATTGCGA
*
85250 ATTTGACTTTCTCATTGCGA
1 ATTTGACTTTCGCATTGCGA
* ***
85270 ATTTTACTTTCGCAACACGA
1 ATTTGACTTTCGCATTGCGA
*
85290 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCATTGCGA
85310 A
1 A
85311 AGTATACCTT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCATTGCGA
Found at i:87254 original size:21 final size:21
Alignment explanation
Indices: 87119--87279 Score: 71
Period size: 21 Copynumber: 7.7 Consensus size: 21
87109 TAGAGCGGCT
* ***
87119 ACCTCATCACGTAAAGTAGAT
1 ACCTCATCACGTAAAGCACCG
*
87140 ACCTCACCACGTAAAGCACC-
1 ACCTCATCACGTAAAGCACCG
** * * *
87160 ATTGTCATCGCGTAAAAC-CTCT
1 A-CCTCATCACGTAAAGCAC-CG
87182 ACCTCA-CTACGTAAAG-ACCG
1 ACCTCATC-ACGTAAAGCACCG
** *
87202 TACCTCATCACGCCATGCACC-
1 -ACCTCATCACGTAAAGCACCG
** *
87223 ATTATCATCACGTAAAGTACCG
1 A-CCTCATCACGTAAAGCACCG
* * *
87245 ACCTCCTCACGCAAAGCACTG
1 ACCTCATCACGTAAAGCACCG
87266 ACCTCATCACGTAA
1 ACCTCATCACGTAA
87280 CTCCCCTAAC
Statistics
Matches: 99, Mismatches: 31, Indels: 20
0.66 0.21 0.13
Matches are distributed among these distances:
20 5 0.05
21 88 0.89
22 6 0.06
ACGTcount: A:0.32, C:0.35, G:0.12, T:0.20
Consensus pattern (21 bp):
ACCTCATCACGTAAAGCACCG
Found at i:87460 original size:42 final size:42
Alignment explanation
Indices: 87394--87492 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
87384 GTGATGGAAT
* * *
87394 AGGTGATGGCTCTCGTTGTGGAGCTGTATAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
* *
87436 AGGTGATAGCTCTGGGTGTCGAGCTGTAGAATCGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
*
87478 AGGCGATGGCTCTCG
1 AGGTGATGGCTCTCG
87493 AAGTGGGGGG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.27
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATC
Found at i:89367 original size:22 final size:22
Alignment explanation
Indices: 89341--89391 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
89331 GATAGAGATA
89341 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
89363 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
89385 GACGGAT
1 GACGGAT
89392 GTCACCGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:89838 original size:13 final size:13
Alignment explanation
Indices: 89820--89845 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89810 CAATTGTTGG
89820 TAAATAAAAAAAT
1 TAAATAAAAAAAT
89833 TAAATAAAAAAAT
1 TAAATAAAAAAAT
89846 AATGAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAATAAAAAAAT
Found at i:91228 original size:22 final size:22
Alignment explanation
Indices: 91202--91252 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
91192 GATAGAGATA
91202 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
91224 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
91246 GACGGAT
1 GACGGAT
91253 GTCACCGTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.20, C:0.14, G:0.45, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:91699 original size:13 final size:13
Alignment explanation
Indices: 91681--91706 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
91671 CAATTGTTGG
91681 TAAATAAAAAAAT
1 TAAATAAAAAAAT
91694 TAAATAAAAAAAT
1 TAAATAAAAAAAT
91707 AATGAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAATAAAAAAAT
Found at i:93972 original size:34 final size:34
Alignment explanation
Indices: 93901--93974 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
93891 ATAACTGCAA
*
93901 AAAATAATAAAAAGTTAATATAATACAATTTAAT
1 AAAATAATAAAAAGTTAATATAATACAATATAAT
* * * *
93935 AAAATAATAAAATA-TTAATTTATTATAATATAGT
1 AAAATAATAAAA-AGTTAATATAATACAATATAAT
93969 AAAATA
1 AAAATA
93975 TTTTACCTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 33 0.97
35 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (34 bp):
AAAATAATAAAAAGTTAATATAATACAATATAAT
Found at i:97202 original size:31 final size:30
Alignment explanation
Indices: 97152--97215 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
97142 AAATAGATAT
*
97152 CTAATGTTTTCGACTTACACTTTTAGGTGC
1 CTAACGTTTTCGACTTACACTTTTAGGTGC
*
97182 CTAACGTTTTCTACGTTACACTTTTAGGTGC
1 CTAACGTTTTCGAC-TTACACTTTTAGGTGC
97213 CTA
1 CTA
97216 CGCAGTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (30 bp):
CTAACGTTTTCGACTTACACTTTTAGGTGC
Found at i:97703 original size:6 final size:6
Alignment explanation
Indices: 97692--98502 Score: 1484
Period size: 6 Copynumber: 136.2 Consensus size: 6
97682 ATGCATCAAA
97692 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
97740 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
97788 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
97834 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
97882 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
97928 ACATAT AC--AT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
97974 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATACAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACAT--AT
98024 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
98072 ACATAT AC--AT ACATAT ACATAT ACACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT --ACATAT ACATAT ACATAT ACATAT
98120 ACATAT AC--AT ACATAT ACATATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT AC--ATAT ACATAT ACATAT ACATAT ACATAT
98168 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
98216 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
98264 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
98312 ACATAT ACATAT ACATAT ACATAT AC--AT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
98358 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
98406 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
98454 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
98502 A
1 A
98503 ATTTCATTAT
Statistics
Matches: 787, Mismatches: 0, Indels: 36
0.96 0.00 0.04
Matches are distributed among these distances:
4 24 0.03
6 745 0.95
8 18 0.02
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:99095 original size:15 final size:16
Alignment explanation
Indices: 99064--99103 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
99054 CATGGAGTCT
*
99064 CATATCACAT-GTTCA
1 CATATCACATAGTGCA
99079 CATATCACATAG-GCA
1 CATATCACATAGTGCA
99094 CAT-TCACATA
1 CATATCACATA
99104 TACATGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 15 0.65
16 1 0.04
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (16 bp):
CATATCACATAGTGCA
Found at i:103934 original size:6 final size:6
Alignment explanation
Indices: 103916--103980 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
103906 ATGCATCAAA
* * * * *
103916 ACATAA ACATAT ACGTAT ACATAT ACATAC ACATAC ACATAC ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
* *
103964 ACATAC ACATAC ACATA
1 ACATAT ACATAT ACATA
103981 CGCATACGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.51, C:0.25, G:0.02, T:0.23
Consensus pattern (6 bp):
ACATAT
Found at i:103939 original size:12 final size:12
Alignment explanation
Indices: 103916--103986 Score: 88
Period size: 12 Copynumber: 5.9 Consensus size: 12
103906 ATGCATCAAA
*
103916 ACATAAACATAT
1 ACATACACATAT
* *
103928 ACGTATACATAT
1 ACATACACATAT
*
103940 ACATACACATAC
1 ACATACACATAT
103952 ACATACACATAT
1 ACATACACATAT
*
103964 ACATACACATAC
1 ACATACACATAT
*
103976 ACATACGCATA
1 ACATACACATA
103987 CGCATATGCA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 51 1.00
ACGTcount: A:0.49, C:0.25, G:0.03, T:0.23
Consensus pattern (12 bp):
ACATACACATAT
Found at i:103981 original size:6 final size:6
Alignment explanation
Indices: 103941--104154 Score: 248
Period size: 6 Copynumber: 35.7 Consensus size: 6
103931 TATACATATA
* * * ** * *
103941 CATACA CATACA CATACA CATATA CATACA CATACA CATACG CATACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
*
103989 CATATG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * * * *
104037 CATACG CATATG CATACG CATACC CATACA CATACC CATACC CATACA
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* * * *
104085 CATACC CATACG CATACC CATACG CATACC CATACG CATACG TATACG
1 CATACG CATACG CATACG CATACG CATACG CATACG CATACG CATACG
* *
104133 CATATG CATACG CATATG CATA
1 CATACG CATACG CATACG CATA
104155 TACATACACA
Statistics
Matches: 186, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 186 1.00
ACGTcount: A:0.37, C:0.33, G:0.10, T:0.20
Consensus pattern (6 bp):
CATACG
Found at i:104189 original size:12 final size:12
Alignment explanation
Indices: 104172--104204 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
104162 ACATATCATT
104172 TTATTATTCTTA
1 TTATTATTCTTA
104184 TTATTATTCTTA
1 TTATTATTCTTA
*
104196 TCATTATTC
1 TTATTATTC
104205 ATATGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (12 bp):
TTATTATTCTTA
Found at i:105510 original size:20 final size:20
Alignment explanation
Indices: 105485--105529 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
105475 AAGTGTACCG
105485 GTACACACTATAGGGTATCA
1 GTACACACTATAGGGTATCA
*
105505 GTACACACTATAGGGTATCG
1 GTACACACTATAGGGTATCA
105525 GTACA
1 GTACA
105530 TCCCTTCACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (20 bp):
GTACACACTATAGGGTATCA
Found at i:119847 original size:19 final size:19
Alignment explanation
Indices: 119819--119856 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
119809 CGATAAAATA
*
119819 TTATTTAAAATATTATTTT
1 TTATTAAAAATATTATTTT
119838 TTATTAAAAATATTATTTT
1 TTATTAAAAATATTATTTT
119857 ACTAACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTAAAAATATTATTTT
Found at i:119854 original size:12 final size:12
Alignment explanation
Indices: 119812--119836 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
119802 TAATATTCGA
119812 TAAAATATTATT
1 TAAAATATTATT
119824 TAAAATATTATT
1 TAAAATATTATT
119836 T
1 T
119837 TTTATTAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:120168 original size:24 final size:24
Alignment explanation
Indices: 120141--120188 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
120131 AATCATGGTT
120141 TAATACATTTGTGTTAAACTAATA
1 TAATACATTTGTGTTAAACTAATA
120165 TAATACATTTGTGTTAAACTAATA
1 TAATACATTTGTGTTAAACTAATA
120189 CTTAGAAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (24 bp):
TAATACATTTGTGTTAAACTAATA
Found at i:120843 original size:15 final size:15
Alignment explanation
Indices: 120823--120860 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
120813 GTTTACTTCA
*
120823 GAATGATTAAGTGTT
1 GAATGATTAAGCGTT
120838 GAATGATTAAGCGTT
1 GAATGATTAAGCGTT
120853 GAATGATT
1 GAATGATT
120861 CAGAGGATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (15 bp):
GAATGATTAAGCGTT
Done.