Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005043.1 Hibiscus syriacus cultivar Beakdansim tig00011321_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: 112405
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:2388 original size:12 final size:12
Alignment explanation
Indices: 2371--2404 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
2361 ACTCTTCTTA
2371 ACTTTCATATTC
1 ACTTTCATATTC
*
2383 ACTTTCCATATTT
1 ACTTT-CATATTC
2396 ACTTTCATA
1 ACTTTCATA
2405 GCCCAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.26, C:0.24, G:0.00, T:0.50
Consensus pattern (12 bp):
ACTTTCATATTC
Found at i:28251 original size:2 final size:2
Alignment explanation
Indices: 28244--28269 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
28234 TTTGAACTTA
28244 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
28270 TAGGTTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28548 original size:14 final size:14
Alignment explanation
Indices: 28515--28549 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
28505 AAGGGGAGTA
28515 ATTTTC-AAACTTG
1 ATTTTCAAAACTTG
28528 A-TTTCAAAACTTG
1 ATTTTCAAAACTTG
28541 ATTTTCAAA
1 ATTTTCAAA
28550 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 9 0.45
14 7 0.35
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (14 bp):
ATTTTCAAAACTTG
Found at i:34038 original size:29 final size:29
Alignment explanation
Indices: 33950--34040 Score: 101
Period size: 29 Copynumber: 3.0 Consensus size: 29
33940 CAAAAAATCT
* * *
33950 AACTTTTAAAAATTACCCTTTTGGTCGCTT
1 AACTTTTAAAAATTA-CATTTTGGTCACTA
* **
33980 AACTTTTCCAAACATTACATTTTGACCACTA
1 AACTTTT--AAAAATTACATTTTGGTCACTA
34011 AACTTTTAAAAATTACATTTTGGTCACTA
1 AACTTTTAAAAATTACATTTTGGTCACTA
34040 A
1 A
34041 CAAAAATTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
29 20 0.40
30 7 0.14
31 16 0.32
32 7 0.14
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.40
Consensus pattern (29 bp):
AACTTTTAAAAATTACATTTTGGTCACTA
Found at i:37739 original size:70 final size:70
Alignment explanation
Indices: 37622--37758 Score: 213
Period size: 70 Copynumber: 2.0 Consensus size: 70
37612 GTTAAAACCA
** *
37622 AATATAACACATAAGGACGTGCCAACCTTGCACACTAAGTGTCTTTTATATACACTCTAGTGCTA
1 AATATAACACATAAGGACGTGCCAACCTACCACACTAAGTGTATTTTATATACACTCTAGTGCTA
37687 AAGCG
66 AAGCG
* *
37692 AATATAACACATAAGGTCGTGCCCACC-ACCTACACTAAGTGTATTTTATATACACTCTAGTGCT
1 AATATAACACATAAGGACGTGCCAACCTACC-ACACTAAGTGTATTTTATATACACTCTAGTGCT
37756 AAA
65 AAA
37759 CCAGATATGT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 1 0.02
70 60 0.98
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (70 bp):
AATATAACACATAAGGACGTGCCAACCTACCACACTAAGTGTATTTTATATACACTCTAGTGCTA
AAGCG
Found at i:39134 original size:20 final size:20
Alignment explanation
Indices: 39099--39148 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
39089 AATATGGCCT
*
39099 AATTTC-ACATTCTAACATC
1 AATTTCAACACTCTAACATC
* *
39118 AATTTCAACACTCTAACCTT
1 AATTTCAACACTCTAACATC
39138 AATTTCCAACA
1 AATTT-CAACA
39149 TAATACATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 6 0.23
20 15 0.58
21 5 0.19
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.34
Consensus pattern (20 bp):
AATTTCAACACTCTAACATC
Found at i:40381 original size:29 final size:31
Alignment explanation
Indices: 40310--40381 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
40300 AAAATTACCC
* * *
40310 TTTTGGTCGCTAAACTTTTTTAAACTTTATA
1 TTTTGGTCACTAAACTTTTTAAAAATTTATA
*
40341 ATTTGG-CTACTAAAC-TTTTAAAAATTTA-A
1 TTTTGGTC-ACTAAACTTTTTAAAAATTTATA
40370 TTTTGGTCACTA
1 TTTTGGTCACTA
40382 CCCAAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
29 10 0.29
30 13 0.38
31 11 0.32
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (31 bp):
TTTTGGTCACTAAACTTTTTAAAAATTTATA
Found at i:41860 original size:16 final size:16
Alignment explanation
Indices: 41805--41860 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
41795 ACTTAATTCA
*
41805 AAGCATGTACTTCATTT
1 AAGCATGTA-GTCATTT
* *
41822 -AGCATATAGTTCATTA
1 AAGCATGTAG-TCATTT
*
41838 AATCATGTAGTCATTT
1 AAGCATGTAGTCATTT
41854 AAGCATG
1 AAGCATG
41861 CTACTTCTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
16 23 0.77
17 7 0.23
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (16 bp):
AAGCATGTAGTCATTT
Found at i:42476 original size:12 final size:13
Alignment explanation
Indices: 42453--42485 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
42443 AGCATTCAAG
*
42453 TCATTCTTTATCA
1 TCATTTTTTATCA
42466 TC-TTTTTTATCA
1 TCATTTTTTATCA
42478 TCATTTTT
1 TCATTTTT
42486 GAGAGACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (13 bp):
TCATTTTTTATCA
Found at i:43439 original size:16 final size:16
Alignment explanation
Indices: 43411--43444 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
43401 ATTCATATCG
43411 AAAATATTAATAAAAT
1 AAAATATTAATAAAAT
43427 AAAA-ATTATATAAAAT
1 AAAATATTA-ATAAAAT
43443 AA
1 AA
43445 TAGATCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATTAATAAAAT
Found at i:46207 original size:143 final size:144
Alignment explanation
Indices: 45973--46260 Score: 398
Period size: 143 Copynumber: 2.0 Consensus size: 144
45963 ACCTCTTTGT
* * * * *
45973 CTCGACCCCATGAGTCTGAAACTGACCTTCATTTTATTGGAACATGCTCTGAATCCGATCAAAAG
1 CTCGACCCCATGAGCCTGAAACCGACCTTCATTTTATTGAAACATGCTCTAAATCAGATCAAAAG
* * *
46038 TGAGAAAACCAAAACGTTGGTTATTGTCGACAACCATAGATGGTGCTTGTTCGATCTCATATTTC
66 TGAGAAAACCAAAACGTTGGTCATTGTCAACAACCATAGATGGTGCTTATTCGATCTCATATTTC
*
46103 ATGGGTCGTTTCAC
131 ATGGGTCGCTTCAC
* * * *
46117 CTCGA-CCCTTGAGCCTGAATCCGACCTTCATTTTGTTGAAACATGCTCTAAATCATATCAAAAG
1 CTCGACCCCATGAGCCTGAAACCGACCTTCATTTTATTGAAACATGCTCTAAATCAGATCAAAAG
** * * * *
46181 TGAGAAAACTGAAACGTTGGTCATTGTTAACCACCATAGATGGTGGTTATTCGGTCTCATATTTC
66 TGAGAAAACCAAAACGTTGGTCATTGTCAACAACCATAGATGGTGCTTATTCGATCTCATATTTC
46246 ATGGGTCGCTTCAC
131 ATGGGTCGCTTCAC
46260 C
1 C
46261 ATGACCTCTT
Statistics
Matches: 125, Mismatches: 19, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
143 120 0.96
144 5 0.04
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (144 bp):
CTCGACCCCATGAGCCTGAAACCGACCTTCATTTTATTGAAACATGCTCTAAATCAGATCAAAAG
TGAGAAAACCAAAACGTTGGTCATTGTCAACAACCATAGATGGTGCTTATTCGATCTCATATTTC
ATGGGTCGCTTCAC
Found at i:47161 original size:29 final size:29
Alignment explanation
Indices: 47140--47206 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
47130 AAAACTGAAC
*
47140 TTTAGGTATGATTTTGAAAAAATTAAAAA
1 TTTAGGTATGATTTTGAAAAAACTAAAAA
*
47169 TTTAGGTATGATTTTGAAAAAATTAAAAA
1 TTTAGGTATGATTTTGAAAAAACTAAAAA
47198 TTTAGGTAT
1 TTTAGGTAT
47207 TAAGACATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (29 bp):
TTTAGGTATGATTTTGAAAAAACTAAAAA
Found at i:47495 original size:22 final size:21
Alignment explanation
Indices: 47457--47501 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
47447 AAATTAAAAG
47457 TTTTAAATTAACATTTTTATC
1 TTTTAAATTAACATTTTTATC
*
47478 TTTTAAAATTTAAC-TTTTTTTC
1 TTTT-AAA-TTAACATTTTTATC
47500 TT
1 TT
47502 CTTTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 12 0.57
23 5 0.24
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTAAATTAACATTTTTATC
Found at i:47615 original size:17 final size:17
Alignment explanation
Indices: 47587--47631 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
47577 TTAATTTAAG
*
47587 TTTTATTTATTAATATTA
1 TTTTA-TTATTAATATCA
*
47605 TTTTATTATTATTATCA
1 TTTTATTATTAATATCA
*
47622 TATTATTATT
1 TTTTATTATT
47632 TTTTTAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 19 0.79
18 5 0.21
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTATTAATATCA
Found at i:49742 original size:64 final size:64
Alignment explanation
Indices: 49660--49893 Score: 337
Period size: 64 Copynumber: 3.7 Consensus size: 64
49650 TTCCTTTCTA
*
49660 TTATGATCTTCCATATTGGACTCCTAGATCATAGGGGTCTAGGGTAAGTCCTTACGGATGCCTG
1 TTATGATCTTCCATATTGGACTCCTAGATCCTAGGGGTCTAGGGTAAGTCCTTACGGATGCCTG
* *
49724 TTATGATCATT-CATATTGGACTCTTAGATCCTAGGGGTCTAGGGTAAGTCCTTACGGATGCTTG
1 TTATGATC-TTCCATATTGGACTCCTAGATCCTAGGGGTCTAGGGTAAGTCCTTACGGATGCCTG
** * * *
49788 TTATGATCTTGTATATTGGACTCCTAGATCCTAGGGGTCTAGGGTAAGTCTTTATGGATTCCTG
1 TTATGATCTTCCATATTGGACTCCTAGATCCTAGGGGTCTAGGGTAAGTCCTTACGGATGCCTG
* * * *
49852 TTATGATCTTTCATATTGAACTCC-ATATTCTAGGGGTCTAGG
1 TTATGATCTTCCATATTGGACTCCTAGATCCTAGGGGTCTAGG
49894 TTAATCCCTT
Statistics
Matches: 154, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
63 18 0.12
64 134 0.87
65 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.37
Consensus pattern (64 bp):
TTATGATCTTCCATATTGGACTCCTAGATCCTAGGGGTCTAGGGTAAGTCCTTACGGATGCCTG
Found at i:51951 original size:15 final size:15
Alignment explanation
Indices: 51931--51963 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
51921 ACCTTTAGGG
51931 TATGTAAGAGAGAAT
1 TATGTAAGAGAGAAT
51946 TATGTAAGAGAGAAT
1 TATGTAAGAGAGAAT
51961 TAT
1 TAT
51964 TTTGGACAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (15 bp):
TATGTAAGAGAGAAT
Found at i:63451 original size:19 final size:20
Alignment explanation
Indices: 63427--63477 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
63417 CGGCCAAGAG
*
63427 CATGTATTTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
63446 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
63466 CATGTATTTTCA
1 CATGTATTTTCA
63478 AAGGGATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:70287 original size:13 final size:14
Alignment explanation
Indices: 70269--70318 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 14
70259 CTTAGCATGT
70269 TTAAAAAT-AAAAC
1 TTAAAAATGAAAAC
70282 TT-AAAATGAAAAC
1 TTAAAAATGAAAAC
70295 --AAAAATGAAAAC
1 TTAAAAATGAAAAC
*
70307 TTGAAAA-GAAAA
1 TTAAAAATGAAAA
70319 GAAAAGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
12 16 0.50
13 12 0.38
14 4 0.12
ACGTcount: A:0.68, C:0.06, G:0.08, T:0.18
Consensus pattern (14 bp):
TTAAAAATGAAAAC
Found at i:70305 original size:25 final size:24
Alignment explanation
Indices: 70271--70323 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
70261 TAGCATGTTT
70271 AAAAATAAAACTT-AAAATGAAAAC
1 AAAAATAAAACTTGAAAA-GAAAAC
*
70295 AAAAATGAAAACTTGAAAAGAAAAG
1 AAAAAT-AAAACTTGAAAAGAAAAC
70320 AAAA
1 AAAA
70324 GAAATAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 6 0.23
25 16 0.62
26 4 0.15
ACGTcount: A:0.72, C:0.06, G:0.09, T:0.13
Consensus pattern (24 bp):
AAAAATAAAACTTGAAAAGAAAAC
Found at i:71194 original size:142 final size:142
Alignment explanation
Indices: 70938--71214 Score: 545
Period size: 142 Copynumber: 2.0 Consensus size: 142
70928 ATTGTATGTT
70938 GCATTGAGAGTCGTAGGTACAATTGGCATGCCATGAGGTAGAGTGATTATGATTATGATCTGGTA
1 GCATTGAGAGTCGTAGGTACAATTGGCATGCCATGAGGTAGAGTGATTATGATTATGATCTGGTA
71003 CATTTGTGTACATTATGTGTAGCACGTTGGTGCAAACAATATGACTTTAAATGGAGTGCATAGTT
66 CATTTGTGTACATTATGTGTAGCACGTTGGTGCAAACAATATGACTTTAAATGGAGTGCATAGTT
71068 TGATTATGTGTA
131 TGATTATGTGTA
*
71080 GCATTGAGAGTCGTAGGTACAATTGGCATGCCATGAGGTAGAGTGATTCTGATTATGATCTGGTA
1 GCATTGAGAGTCGTAGGTACAATTGGCATGCCATGAGGTAGAGTGATTATGATTATGATCTGGTA
71145 CATTTGTGTACATTATGTGTAGCACGTTGGTGCAAACAATATGACTTTAAATGGAGTGCATAGTT
66 CATTTGTGTACATTATGTGTAGCACGTTGGTGCAAACAATATGACTTTAAATGGAGTGCATAGTT
71210 TGATT
131 TGATT
71215 TTGATGATAG
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 134 1.00
ACGTcount: A:0.28, C:0.11, G:0.27, T:0.34
Consensus pattern (142 bp):
GCATTGAGAGTCGTAGGTACAATTGGCATGCCATGAGGTAGAGTGATTATGATTATGATCTGGTA
CATTTGTGTACATTATGTGTAGCACGTTGGTGCAAACAATATGACTTTAAATGGAGTGCATAGTT
TGATTATGTGTA
Found at i:71439 original size:20 final size:21
Alignment explanation
Indices: 71408--71460 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
71398 GAGTATTTTG
71408 ACAAGAAGTTTCAAAACTTCT
1 ACAAGAAGTTTCAAAACTTCT
71429 ACAAG-AGTTTCAAAACTT-T
1 ACAAGAAGTTTCAAAACTTCT
*
71448 CCAAGACAGTTTC
1 ACAAGA-AGTTTC
71461 CCAAAAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.17
20 13 0.45
21 11 0.38
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (21 bp):
ACAAGAAGTTTCAAAACTTCT
Found at i:72714 original size:20 final size:20
Alignment explanation
Indices: 72685--72735 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
72675 ATTTCTCGGA
72685 GGGA-ACCGATTCCCCCCAG
1 GGGATACCGATTCCCCCCAG
*
72704 GGGGTACCGATTCCCCCCAG
1 GGGATACCGATTCCCCCCAG
72724 GGGATACCGATT
1 GGGATACCGATT
72736 TCTCCCTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.20, C:0.35, G:0.29, T:0.16
Consensus pattern (20 bp):
GGGATACCGATTCCCCCCAG
Found at i:84460 original size:172 final size:173
Alignment explanation
Indices: 84141--84447 Score: 412
Period size: 172 Copynumber: 1.8 Consensus size: 173
84131 AATTGAGGAA
* * *
84141 TCATAATTTAATCTTTTTTCTATGATTTATTAATGTAATATTTAATTACTTTTTCAAAATAATAT
1 TCATAATTTAATCTATTTTCTATGATTCATTAATGTAATATTAAATTACTTTTTCAAAATAATAT
* * * ** * *
84206 AGTCTATTTTTGTTCTATAAGGCCTATTTTTGAGTTTTCGCTCAAGGTTTATAATTAAGGAGCCC
66 AATATAGTTTCATTCTATAAGGCCTATTTTTGAGTTTTCGATCAAGGTTTATAACTAAGGAGCCC
84271 TATTTTTTTAATTTTATATACTTTCTACTTTTATAAATAAGAG
131 TATTTTTTTAATTTTATATACTTTCTACTTTTATAAATAAGAG
* *
84314 TCATAATTTAATC-ATTTTCTATGGTTCATTAATGTAATATTAAATTAGTCTTTTC-AAATAAAT
1 TCATAATTTAATCTATTTTCTATGATTCATTAATGTAATATTAAATTACT-TTTTCAAAAT-AAT
* * *
84377 ATAATATAGTTTCATTCTAT-AGG-GT-TTTTT-AGTTTTC-ATCCAGGTTTATAACTAAGGGGC
64 ATAATATAGTTTCATTCTATAAGGCCTATTTTTGAGTTTTCGATCAAGGTTTATAACTAAGGAGC
84437 CCTATTTTTTT
129 CCTATTTTTTT
84448 TTTCAATTTT
Statistics
Matches: 117, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
168 30 0.26
169 7 0.06
170 5 0.04
171 1 0.01
172 38 0.32
173 36 0.31
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (173 bp):
TCATAATTTAATCTATTTTCTATGATTCATTAATGTAATATTAAATTACTTTTTCAAAATAATAT
AATATAGTTTCATTCTATAAGGCCTATTTTTGAGTTTTCGATCAAGGTTTATAACTAAGGAGCCC
TATTTTTTTAATTTTATATACTTTCTACTTTTATAAATAAGAG
Found at i:84761 original size:17 final size:17
Alignment explanation
Indices: 84739--84795 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 17
84729 CAAAGAAAAT
84739 ATTTAAGATATATAATA
1 ATTTAAGATATATAATA
* * *
84756 ATTTAAAATATAAAAAA
1 ATTTAAGATATATAATA
* *
84773 ATATAAGATATATACTA
1 ATTTAAGATATATAATA
84790 ATTTAA
1 ATTTAA
84796 AAAATTTTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (17 bp):
ATTTAAGATATATAATA
Found at i:84782 original size:34 final size:36
Alignment explanation
Indices: 84718--84797 Score: 110
Period size: 34 Copynumber: 2.2 Consensus size: 36
84708 ACAAATTATC
*
84718 AATTGAAAATACAAAGAAAATATTTAAGATATATAAT
1 AATTTAAAATACAAAGAAAATA-TTAAGATATATAAT
* *
84755 AATTTAAAATATAAA-AAAATA-TAAGATATATACT
1 AATTTAAAATACAAAGAAAATATTAAGATATATAAT
84789 AATTTAAAA
1 AATTTAAAA
84798 AATTTTTAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
34 21 0.52
36 6 0.15
37 13 0.32
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (36 bp):
AATTTAAAATACAAAGAAAATATTAAGATATATAAT
Found at i:87870 original size:20 final size:20
Alignment explanation
Indices: 87845--88056 Score: 91
Period size: 20 Copynumber: 9.4 Consensus size: 20
87835 TATGGCATCA
*
87845 TTTCATGCGTTAATGAATCC
1 TTTCATGCCTTAATGAATCC
*
87865 TTTCATGCATTTTAATTATGACATCC
1 TTTCATGC--CTT-A--ATGA-ATCC
*
87891 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGAATCC
* * *
87911 TTTCATGCATTTTAATTATGGCAGCC
1 TTTCATGC--CTT-A--AT-GAATCC
*
87937 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGAATCC
* *
87957 TTTCATGCATTTTAATTATGGCATCC
1 TTTCATGC--CTT-A--AT-GAATCC
*
87983 TTTCATGCCTTAATGGATCC
1 TTTCATGCCTTAATGAATCC
* *
88003 TTTCATGCATATTGATTATGGCATCC
1 TTTCATGC--CTT-A--AT-GAATCC
*
88029 TTTCATGCCTTAATGCATCC
1 TTTCATGCCTTAATGAATCC
88049 TTTCATGC
1 TTTCATGC
88057 ATTTTAATTA
Statistics
Matches: 155, Mismatches: 13, Indels: 48
0.72 0.06 0.22
Matches are distributed among these distances:
20 60 0.39
21 9 0.06
22 8 0.05
23 8 0.05
24 8 0.05
25 10 0.06
26 52 0.34
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.42
Consensus pattern (20 bp):
TTTCATGCCTTAATGAATCC
Found at i:87876 original size:46 final size:46
Alignment explanation
Indices: 87808--88108 Score: 462
Period size: 46 Copynumber: 6.5 Consensus size: 46
87798 TTTTCACGTT
* * *
87808 TTAATGCATCCATTT-ATACA-TTTACATTATGGCATCATTTCATGCG
1 TTAATGCATCC-TTTCATGCATTTTA-ATTATGGCATCCTTTCATGCC
* *
87854 TTAATGAATCCTTTCATGCATTTTAATTATGACATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
*
87900 TTAATGCATCCTTTCATGCATTTTAATTATGGCAGCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
87946 TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
* * *
87992 TTAATGGATCCTTTCATGCATATTGATTATGGCATCCTTTCATGCC
1 TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
* * *
88038 TTAATGCATCCTTTCATGCATTTTAATTATGTCATCCTTTAATGTC
1 TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
88084 TTAATGCATCCTTTCATGCATTTTA
1 TTAATGCATCCTTTCATGCATTTTA
88109 TATACTCTAA
Statistics
Matches: 235, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
45 3 0.01
46 228 0.97
47 4 0.02
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.44
Consensus pattern (46 bp):
TTAATGCATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCC
Found at i:88095 original size:20 final size:20
Alignment explanation
Indices: 87886--88101 Score: 117
Period size: 20 Copynumber: 9.6 Consensus size: 20
87876 TTAATTATGA
*
87886 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGTCTTAATG
*
87906 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATG--TCTT-A--AT-G
* *
87932 CAGCCTTTCATGCCTTAATG
1 CATCCTTTCATGTCTTAATG
*
87952 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATG--TCTT-A--AT-G
*
87978 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGTCTTAATG
* *
87998 GATCCTTTCATGCATATTGATTATGG
1 CATCCTTTCATG--TCTT-A--AT-G
*
88024 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGTCTTAATG
*
88044 CATCCTTTCATGCATTTTAATTATG
1 CATCCTTTCATG--TCTT-A--ATG
*
88069 TCATCCTTTAATGTCTTAATG
1 -CATCCTTTCATGTCTTAATG
88090 CATCCTTTCATG
1 CATCCTTTCATG
88102 CATTTTATAT
Statistics
Matches: 151, Mismatches: 21, Indels: 48
0.69 0.10 0.22
Matches are distributed among these distances:
20 60 0.40
21 9 0.06
22 8 0.05
23 8 0.05
24 9 0.06
25 9 0.06
26 48 0.32
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.43
Consensus pattern (20 bp):
CATCCTTTCATGTCTTAATG
Found at i:88508 original size:20 final size:22
Alignment explanation
Indices: 88483--88529 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
88473 CAATAGTATC
*
88483 GATACTACT-ATC-ATGGTACT
1 GATACTACTAAACTATGGTACT
*
88503 GATACTTCTAAACTATGGTACT
1 GATACTACTAAACTATGGTACT
88525 GATAC
1 GATAC
88530 CCCCTTCCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 13 0.57
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (22 bp):
GATACTACTAAACTATGGTACT
Found at i:88642 original size:19 final size:20
Alignment explanation
Indices: 88590--88644 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 20
88580 TACCCTTACC
*
88590 ATGGTATCGATACTACTATACT
1 ATGGTATCGATAC-CCTATA-T
88612 ATGGTA-CTGATACCCTAT-T
1 ATGGTATC-GATACCCTATAT
88631 ATGGTATCGATACC
1 ATGGTATCGATACC
88645 ATTTTTGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 13 0.43
20 1 0.03
21 5 0.17
22 11 0.37
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (20 bp):
ATGGTATCGATACCCTATAT
Found at i:93607 original size:43 final size:45
Alignment explanation
Indices: 93486--93706 Score: 163
Period size: 44 Copynumber: 5.3 Consensus size: 45
93476 AAAAAAATAT
* * *
93486 GATTGAAAAGATTA-GGGACCTCAATTATAT-AGGTAAAAAGTGA
1 GATTTAAAAAATTAGGGGACCTAAATTATATAAGGTAAAAAGTGA
* * *
93529 GA-TTAAAAAA--ATGGGACCTCAATTTTA-AAGGTAAAAAGTGA
1 GATTTAAAAAATTAGGGGACCTAAATTATATAAGGTAAAAAGTGA
* *
93570 GATTTAAAAAATTAGGGGA-CTAAATTATATGA-GTAAAAAATG-
1 GATTTAAAAAATTAGGGGACCTAAATTATATAAGGTAAAAAGTGA
* * *
93612 GTATTGAAAAAAATTAGGGG-TCTAAATTATATAA-GTAAAAAATGA
1 G-ATT-TAAAAAATTAGGGGACCTAAATTATATAAGGTAAAAAGTGA
* * *
93657 -A---AAAAAAATA-GGG-CCTCAATTATA-AAGGTGAAAAGTGA
1 GATTTAAAAAATTAGGGGACCTAAATTATATAAGGTAAAAAGTGA
*
93695 GATTGAAAAAAT
1 GATTTAAAAAAT
93707 CAAGAGCTTA
Statistics
Matches: 147, Mismatches: 16, Indels: 31
0.76 0.08 0.16
Matches are distributed among these distances:
37 2 0.01
38 21 0.14
39 9 0.06
40 1 0.01
41 29 0.20
42 21 0.14
43 23 0.16
44 41 0.28
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (45 bp):
GATTTAAAAAATTAGGGGACCTAAATTATATAAGGTAAAAAGTGA
Found at i:93609 original size:128 final size:125
Alignment explanation
Indices: 93450--93706 Score: 297
Period size: 128 Copynumber: 2.0 Consensus size: 125
93440 AAAAATGATT
* * *
93450 AAATTAGGGGCTTAAACTATAAAAGAAAAAAAAT-ATGATTG-AAAAGATTAGGGACCTCAATTA
1 AAATTAGGGGCTTAAACTATAAAAG-AAAAAAATGGT-ATTGAAAAAAATTAGGGACCTAAATTA
* * * *
93513 TATAGGTAAAAAGTGAGATTAAAAAAAT-GGGACCTCAATTTTAAAGGTAAAAAGTGAGATTTAA
64 TATAAGTAAAAAATGA-A--AAAAAAATAGGG-CCTCAATTATAAAGGTAAAAAGTGAGATTGAA
93577 A
125 A
* ** * **
93578 AAATTAGGGGAC-TAAATTATATGAGTAAAAAATGGTATTGAAAAAAATTAGGGGTCTAAATTAT
1 AAATTAGGGG-CTTAAACTATAAAAGAAAAAAATGGTATTGAAAAAAATTAGGGACCTAAATTAT
*
93642 ATAAGTAAAAAATGAAAAAAAAATAGGGCCTCAATTATAAAGGTGAAAAGTGAGATTGAAA
65 ATAAGTAAAAAATGAAAAAAAAATAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAA
93703 AAAT
1 AAAT
93707 CAAGAGCTTA
Statistics
Matches: 111, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
125 42 0.38
126 3 0.03
127 12 0.11
128 53 0.48
129 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.25
Consensus pattern (125 bp):
AAATTAGGGGCTTAAACTATAAAAGAAAAAAATGGTATTGAAAAAAATTAGGGACCTAAATTATA
TAAGTAAAAAATGAAAAAAAAATAGGGCCTCAATTATAAAGGTAAAAAGTGAGATTGAAA
Found at i:93705 original size:42 final size:42
Alignment explanation
Indices: 93486--93746 Score: 193
Period size: 42 Copynumber: 6.2 Consensus size: 42
93476 AAAAAAATAT
* * *
93486 GATTGAAAAGATTAGGGACCTCAATTATATAGGTAAAAAGTGA
1 GATTGAAAAAAATAGGG-CCTCAATTATAAAGGTAAAAAGTGA
*
93529 GATT-AAAAAAAT-GGGACCTCAATTTTAAAGGTAAAAAGTGA
1 GATTGAAAAAAATAGGG-CCTCAATTATAAAGGTAAAAAGTGA
* * * * * *
93570 GATTTAAAAAATTAGGGGACTAAATTAT-ATGAGTAAAAAATG-
1 GATTGAAAAAAATA-GGGCCTCAATTATAAAG-GTAAAAAGTGA
* * *
93612 GTATTGAAAAAAATTAGGGGTCTAAATTATATAA-GTAAAAAATGA
1 G-ATTGAAAAAAA-TA-GGGCCTCAATTATA-AAGGTAAAAAGTGA
*
93657 -A---AAAAAAATAGGGCCTCAATTATAAAGGTGAAAAGTGA
1 GATTGAAAAAAATAGGGCCTCAATTATAAAGGTAAAAAGTGA
* * * *
93695 GATTG-AAAAAATCAAGAG-CTTAATTATAAAGGTACAAAGTGG
1 GATTGAAAAAAAT--AGGGCCTCAATTATAAAGGTAAAAAGTGA
93737 GATTGAAAAA
1 GATTGAAAAA
93747 CTTAGGATTA
Statistics
Matches: 178, Mismatches: 23, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
37 2 0.01
38 21 0.12
39 3 0.02
40 7 0.04
41 38 0.21
42 41 0.23
43 37 0.21
44 28 0.16
46 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.25
Consensus pattern (42 bp):
GATTGAAAAAAATAGGGCCTCAATTATAAAGGTAAAAAGTGA
Found at i:95167 original size:19 final size:20
Alignment explanation
Indices: 95123--95168 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
95113 TAGATTGATA
95123 TTCCACGAATCCAAGCTTTT
1 TTCCACGAATCCAAGCTTTT
95143 TCTCCACGAATCCAAG-TTTT
1 T-TCCACGAATCCAAGCTTTT
95163 TTCCAC
1 TTCCAC
95169 AAGGAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.20
20 6 0.24
21 14 0.56
ACGTcount: A:0.24, C:0.33, G:0.09, T:0.35
Consensus pattern (20 bp):
TTCCACGAATCCAAGCTTTT
Found at i:96539 original size:2 final size:2
Alignment explanation
Indices: 96532--96561 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
96522 AATGAAGTAA
96532 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
96562 AGCATGATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:96712 original size:2 final size:2
Alignment explanation
Indices: 96705--96742 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
96695 CAAATCATTC
96705 AT AT 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
96743 TAATGTGACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99059 original size:2 final size:2
Alignment explanation
Indices: 99052--99088 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
99042 GCCAATTGAT
99052 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
99089 CTTAAGCTAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:99627 original size:18 final size:18
Alignment explanation
Indices: 99601--99651 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
99591 TATGGAGGTA
* * *
99601 TTTGATCCTCTGGTTGTG
1 TTTGTTCCTCTGCTCGTG
99619 TTTGTTCCTCTGCTCGTG
1 TTTGTTCCTCTGCTCGTG
*
99637 CTTGTTCCTCGTGCT
1 TTTGTTCCTC-TGCT
99652 ATTCTGGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.02, C:0.25, G:0.24, T:0.49
Consensus pattern (18 bp):
TTTGTTCCTCTGCTCGTG
Found at i:101272 original size:22 final size:21
Alignment explanation
Indices: 101214--101273 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
101204 CCAGAACCCC
101214 AGGGGGTATCGATTCCCCTAT
1 AGGGGGTATCGATTCCCCTAT
* *
101235 AGGGGGAATCGGTTCCCC-AT
1 AGGGGGTATCGATTCCCCTAT
*
101255 CAAGGGGGTATTGATTCCC
1 --AGGGGGTATCGATTCCC
101274 TCTGCACTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 2 0.06
21 16 0.50
22 14 0.44
ACGTcount: A:0.20, C:0.23, G:0.32, T:0.25
Consensus pattern (21 bp):
AGGGGGTATCGATTCCCCTAT
Found at i:107424 original size:3 final size:3
Alignment explanation
Indices: 107418--107458 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
107408 TTTTAGTAAC
107418 AAT AAT -AT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AA
107459 ACAAATAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:108439 original size:42 final size:42
Alignment explanation
Indices: 108361--108463 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 42
108351 AGGTCTTATG
* *
108361 GATGACCCGAAGGCAGCTTTATCATCATGCTCGAAAGGCTTACA
1 GATGACCCGAAGG-A-CTTTAGCATCATGCTCGAAAGACTTACA
*
108405 GATGACCCGAAGGA-TTTAAGCATCATGCTTGAAAGACTTACA
1 GATGACCCGAAGGACTTT-AGCATCATGCTCGAAAGACTTACA
* *
108447 GATGGCTCGAAGGACTT
1 GATGACCCGAAGGACTT
108464 ACGAATCAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 3 0.06
42 33 0.63
43 3 0.06
44 13 0.25
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (42 bp):
GATGACCCGAAGGACTTTAGCATCATGCTCGAAAGACTTACA
Found at i:109378 original size:44 final size:44
Alignment explanation
Indices: 109330--109415 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
109320 TTCAAAATTG
109330 TGACCTTGATGCCCCCATTTTATCCTGGATAACACCACCTTTCT
1 TGACCTTGATGCCCCCATTTTATCCTGGATAACACCACCTTTCT
*
109374 TGACCTTGATGCCCCCATTTTATCCTGGATAACACCAGCTTT
1 TGACCTTGATGCCCCCATTTTATCCTGGATAACACCACCTTT
109416 TTTGCCTAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.34
Consensus pattern (44 bp):
TGACCTTGATGCCCCCATTTTATCCTGGATAACACCACCTTTCT
Found at i:110810 original size:55 final size:54
Alignment explanation
Indices: 110605--110894 Score: 276
Period size: 55 Copynumber: 5.4 Consensus size: 54
110595 GTGTGCATTT
* * * * * **
110605 CACGGAATTCATCCT-ATGTGGATGAATAACCGTTTCAGCACTAAGTATATAAATC
1 CACGGAATTCATCATGA-GTTGATGAATAACCG-TACAGCACTATGTGTGCAAATC
* *
110660 CACGGAA-T--TCATGAGTTGATG---AACCGTACAAGAACTATGTGTGAAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTAC-AGCACTATGTGTGCAAATC
* * * * *
110709 CAC-AAAATAATCATGAGATGATGAAT-ATCGTACAGACACTATGTGTGCAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTACAG-CACTATGTGTGCAAATC
110762 CACGGAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTGCAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTACA-GCACTATGTGTGCAAATC
*
110817 CACAGAATTCATCATGAGTTGATGAACT-ACCGTACAGGCACTATGTGTGCAAATC
1 CACGGAATTCATCATGAGTTGATGAA-TAACCGTACA-GCACTATGTGTGCAAATC
* * * *
110872 CATGAAATTTATCATGAATTGAT
1 CACGGAATTCATCATGAGTTGAT
110895 TAATTACCAT
Statistics
Matches: 197, Mismatches: 25, Indels: 26
0.79 0.10 0.10
Matches are distributed among these distances:
48 4 0.02
49 23 0.12
51 12 0.06
52 11 0.06
53 25 0.13
54 20 0.10
55 100 0.51
56 2 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (54 bp):
CACGGAATTCATCATGAGTTGATGAATAACCGTACAGCACTATGTGTGCAAATC
Found at i:111221 original size:45 final size:45
Alignment explanation
Indices: 111161--111518 Score: 519
Period size: 45 Copynumber: 8.1 Consensus size: 45
111151 GATGGATATC
* * *
111161 AATGCATAATGGTGTATAAAAGGCATAAAAAGATGCCATAAATGA
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* *
111206 AAGGTATAATTGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
*
111251 AATGTATAATGGTGTATAAAAGGCATAAAAGGATGCCATAAATGA
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* * *
111296 AAGGTATAATGATGTATAAAAGTCATGAAAGGATGCCATAAATGA
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* * * *
111341 AATGTATAATGGTATGTAAAAGGCATGAAATGATGCCATAAATAA
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
*
111386 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCTATAAA-GA
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* * *
111430 AATG--TAATGGTGTATAAAATGCATGAAATGATGTCATAAATGA
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
*
111473 AATGTAT-ATGGTGTATAAAAGGCATGAAAGGATG-TATAAATGA
1 AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
111516 AAT
1 AAT
111519 TAATAATAAT
Statistics
Matches: 279, Mismatches: 31, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
42 32 0.11
43 17 0.06
44 30 0.11
45 200 0.72
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.26
Consensus pattern (45 bp):
AATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
Found at i:111470 original size:21 final size:20
Alignment explanation
Indices: 111303--111514 Score: 68
Period size: 21 Copynumber: 9.8 Consensus size: 20
111293 TGAAAGGTAT
*
111303 AATGATGTATAAAAGTCATGA
1 AATGATGTATAAATG-CATGA
* * *
111324 AAGGATGCCATAAATGAAATGTA
1 AATGATG-TATAAATG-CATG-A
*
111347 TAATGGTATGTA-AAAGGCATGA
1 -AAT-G-ATGTATAAATGCATGA
* **
111369 AATGATGCCATAAATAAAATGTA
1 AATGATG-TATAAAT-GCATG-A
* *
111392 TAATGGTGTATAAAAGGCATGA
1 -AATGATGTAT-AAATGCATGA
* * *
111414 AAGGATGCTATAAA-GAAATGT
1 AATGATG-TATAAATG-CATGA
*
111435 AATGGTGTATAAAATGCATGA
1 AATGATGTAT-AAATGCATGA
*
111456 AATGATGTCATAAATGAAATGTA
1 AATGATGT-ATAAATG-CATG-A
* * *
111479 TATGGTGTATAAAAGGCATGA
1 AATGATGTAT-AAATGCATGA
*
111500 AAGGATGTATAAATG
1 AATGATGTATAAATG
111515 AAATTAATAA
Statistics
Matches: 136, Mismatches: 36, Indels: 39
0.64 0.17 0.18
Matches are distributed among these distances:
19 3 0.02
20 10 0.07
21 54 0.40
22 28 0.21
23 21 0.15
24 15 0.11
25 2 0.01
26 3 0.02
ACGTcount: A:0.45, C:0.05, G:0.23, T:0.27
Consensus pattern (20 bp):
AATGATGTATAAATGCATGA
Done.