Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002220.1 Hibiscus syriacus cultivar Beakdansim tig00004517_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: 70239
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:2415 original size:15 final size:16
Alignment explanation
Indices: 2388--2418 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2378 TTCAAGAGCA
2388 AGGTGAGTTATTTGTT
1 AGGTGAGTTATTTGTT
2404 AGGTGA-TTATTTGTT
1 AGGTGAGTTATTTGTT
2419 GAATTTAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (16 bp):
AGGTGAGTTATTTGTT
Found at i:2988 original size:24 final size:24
Alignment explanation
Indices: 2961--3017 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
2951 GTATTGGTAT
2961 CGATACCCTCAGCTAGGGTAGTAC
1 CGATACCCTCAGCTAGGGTAGTAC
*
2985 CGATACCATCAGCTAGGGTAGTAC
1 CGATACCCTCAGCTAGGGTAGTAC
**
3009 TAATACCCT
1 CGATACCCT
3018 ATAGTGGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (24 bp):
CGATACCCTCAGCTAGGGTAGTAC
Found at i:4091 original size:20 final size:20
Alignment explanation
Indices: 4066--4110 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
4056 ATACAGTTGT
4066 ACGTGGACAGCTGGCTCTGC
1 ACGTGGACAGCTGGCTCTGC
4086 ACGTGGACAGCTGGCTCTGC
1 ACGTGGACAGCTGGCTCTGC
4106 ACGTG
1 ACGTG
4111 AAATGATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.29, G:0.36, T:0.20
Consensus pattern (20 bp):
ACGTGGACAGCTGGCTCTGC
Found at i:4515 original size:15 final size:15
Alignment explanation
Indices: 4492--4533 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
4482 CTCACTTCCC
4492 TTTGATGTTATTTTA
1 TTTGATGTTATTTTA
*
4507 TTTGCTGTTATTTTA
1 TTTGATGTTATTTTA
*
4522 TTT-ATTTTATTT
1 TTTGATGTTATTT
4534 GTGGGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (15 bp):
TTTGATGTTATTTTA
Found at i:4664 original size:24 final size:24
Alignment explanation
Indices: 4619--4668 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
4609 TGGTGGTTGG
4619 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
4643 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
4667 TT
1 TT
4669 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:10118 original size:15 final size:15
Alignment explanation
Indices: 10095--10136 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
10085 CTCACTTCCC
10095 TTTGATGTTATTTTA
1 TTTGATGTTATTTTA
*
10110 TTTGCTGTTATTTTA
1 TTTGATGTTATTTTA
*
10125 TTT-ATTTTATTT
1 TTTGATGTTATTT
10137 GTGGGTTGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (15 bp):
TTTGATGTTATTTTA
Found at i:10267 original size:24 final size:24
Alignment explanation
Indices: 10222--10271 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
10212 TGGTGGTTGG
10222 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
10246 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
10270 TT
1 TT
10272 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:15694 original size:20 final size:21
Alignment explanation
Indices: 15663--15701 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
15653 AAATATAGTG
15663 AGGAATAGATTTATCTTGCCA
1 AGGAATAGATTTATCTTGCCA
15684 AGGAA-AGATTTATCTTGC
1 AGGAATAGATTTATCTTGC
15702 AAGTCTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (21 bp):
AGGAATAGATTTATCTTGCCA
Found at i:27322 original size:21 final size:21
Alignment explanation
Indices: 27284--27344 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
27274 ATTATACAGT
*
27284 TTATATATAAATTATATATGAA
1 TTATATTTAAA-TATATATGAA
**
27306 TTATATTTAAATATATACAAA
1 TTATATTTAAATATATATGAA
*
27327 TTATATTTATATAT-TATG
1 TTATATTTAAATATATATG
27345 TATAATTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 2 0.06
21 21 0.64
22 10 0.30
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (21 bp):
TTATATTTAAATATATATGAA
Found at i:27348 original size:17 final size:17
Alignment explanation
Indices: 27328--27381 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
27318 ATATACAAAT
* * *
27328 TATATTTATATATTATG
1 TATAATTATAAATTATA
27345 TATAATTATAAATTATA
1 TATAATTATAAATTATA
27362 TATACTATGTATAAATTATA
1 TATA--AT-TATAAATTATA
27382 CAATTTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 18 0.58
19 2 0.06
20 11 0.35
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (17 bp):
TATAATTATAAATTATA
Found at i:27365 original size:11 final size:11
Alignment explanation
Indices: 27243--27354 Score: 74
Period size: 11 Copynumber: 10.4 Consensus size: 11
27233 ACTATTGCAC
27243 TATATATAAAT
1 TATATATAAAT
**
27254 TATATAGTTTAT
1 TATATA-TAAAT
27266 TA-ATATAAAT
1 TATATATAAAT
*
27276 TATACAGT---T
1 TATATA-TAAAT
27285 TATATATAAAT
1 TATATATAAAT
*
27296 TATATATGAAT
1 TATATATAAAT
*
27307 TATATTTAAA-
1 TATATATAAAT
*
27317 TATATACAAAT
1 TATATATAAAT
*
27328 TATATTTATATAT
1 TATA--TATAAAT
*
27341 TATGTAT-AAT
1 TATATATAAAT
27351 TATA
1 TATA
27355 AATTATATAT
Statistics
Matches: 76, Mismatches: 16, Indels: 19
0.68 0.14 0.17
Matches are distributed among these distances:
8 1 0.01
9 6 0.08
10 18 0.24
11 37 0.49
12 6 0.08
13 8 0.11
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (11 bp):
TATATATAAAT
Found at i:27463 original size:17 final size:16
Alignment explanation
Indices: 27443--27490 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
27433 ATTATATATT
27443 TTTATATATAATATACA
1 TTTATA-ATAATATACA
* *
27460 TTTAAAACATATATACA
1 TTTATAATA-ATATACA
*
27477 TATATAATAATATA
1 TTTATAATAATATA
27491 AAGTATAAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTATAATAATATACA
Found at i:27792 original size:68 final size:70
Alignment explanation
Indices: 27677--28162 Score: 211
Period size: 68 Copynumber: 7.1 Consensus size: 70
27667 TAAACTATAT
* * * **
27677 ATATATATATATATATAAAGTTTTAGTATAAAGCATATATATTATATAA-AGTATATAAGTGTGT
1 ATATATATATATATATAAAGTTTTAGTATAAAGCATATATATCATATAATAATATA-AAGTATAA
27741 GTATAT
65 GTATAT
27747 ATATATATATATATAT-AAGTTTTAGTATAAA-C-TATATATACATATAATAATATAAAGTATAA
1 ATATATATATATATATAAAGTTTTAGTATAAAGCATATATAT-CATATAATAATATAAAGTATAA
27809 GTATAT
65 GTATAT
* *
27815 ATATATATATAAAGTAT-AA-TTATAAAG-ACTAAA--ATATATA--AGTAT-ATAATATAAAGT
1 ATATATATATATA-TATAAAGTT-T-TAGTA-TAAAGCATATATATCA-TATAATAATATAAAG-
27872 ATATAAAGTATAT
60 -TAT-AAGTATAT
* * * * * *
27885 ATACATATA-A-AGTAT-AAG-TATA-TAT-AAGC-TATAAAGT-ATAT-AT-ATATATAGTTTT
1 ATATATATATATA-TATAAAGTTTTAGTATAAAGCATATATA-TCATATAATAATATAAAGTATA
27940 AGTATAT
64 AGTATAT
* * *
27947 A-ATATAAAT-TATA-AAAGTATATATACATATAAAG--TATA-AGCATAT-ATAAAGTATAAAG
1 ATATATATATATATATAAAGT-T-T-TA-GTATAAAGCATATATATCATATAAT-AA-TATAAAG
28005 TATAAGTATAT
60 TATAAGTATAT
** ** *
28016 ATATATATATATATATGGA-TATAAAGTATAAAGTATAAGTATAT-ATATATATATATATAAAGT
1 ATATATATATATATATAAAGT-TTTAGTATAAAGCAT-A-TATATCATATA-ATA-ATATAAAGT
* *
28079 TTTAGTATAT
61 ATAAGTATAT
* * * * *
28089 A-ATATA-A-AGTAT-TAAAATATATAATATAAAGTATATA-AGTACATAT-A-CATATAAAGTA
1 ATATATATATA-TATATAAAGT-TTTAGTATAAAGCATATATA-T-CATATAATAATATAAAGTA
28147 TAAGTATAT
62 TAAGTATAT
28156 ATATATA
1 ATATATA
28163 AACTATAAAG
Statistics
Matches: 331, Mismatches: 37, Indels: 98
0.71 0.08 0.21
Matches are distributed among these distances:
61 10 0.03
62 9 0.03
63 3 0.01
64 2 0.01
65 15 0.05
66 14 0.04
67 45 0.14
68 60 0.18
69 52 0.16
70 56 0.17
71 31 0.09
72 12 0.04
73 19 0.06
74 3 0.01
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (70 bp):
ATATATATATATATATAAAGTTTTAGTATAAAGCATATATATCATATAATAATATAAAGTATAAG
TATAT
Found at i:27877 original size:9 final size:9
Alignment explanation
Indices: 27863--27926 Score: 57
Period size: 9 Copynumber: 7.6 Consensus size: 9
27853 TAAGTATATA
27863 ATATAAAGT
1 ATATAAAGT
27872 ATATAAAGT
1 ATATAAAGT
* *
27881 ATATATA-C
1 ATATAAAGT
27889 ATATAAAG-
1 ATATAAAGT
27897 -TAT-AAGT
1 ATATAAAGT
27904 ATATATAAG-
1 ATATA-AAGT
*
27913 CTATAAAGT
1 ATATAAAGT
27922 ATATA
1 ATATA
27927 TATATATAGT
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
6 3 0.07
7 3 0.07
8 12 0.27
9 23 0.52
10 3 0.07
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.34
Consensus pattern (9 bp):
ATATAAAGT
Found at i:28089 original size:2 final size:2
Alignment explanation
Indices: 27066--28074 Score: 139
Period size: 2 Copynumber: 506.0 Consensus size: 2
27056 TAAAAACAAT
* *
27066 TA TA -A TA TA TA TA TA TA TA AA CTA TA TA GTT 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 TA TA TA
* * * * *
27108 TA AA TA TA TA TA -A TA TA TA AA AA CTA TA TA GTT TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA
* * *
27151 T- TA T- TA TA TA CTA TA TA AA AA T- TA TA TA TA TA T- TA TG TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
27190 TA AA CTA TA TA TA CCA TG TA TA AA CTA TA GA GTT TA TA TA TGA -A
1 TA TA -TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA T-A TA
* * * *
27234 CTA T- TG CA CTA TA TA TA AA T- TA TA TA GTT TA T- TA -A TA TA
1 -TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * *
27273 AA T- TA TA CA GTT TA TA TA TA AA T- TA TA TA TGA -A T- TA TA TT
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA
* * * * *
27313 TA AA TA TA TA CA AA T- TA TA TT TA TA TA T- TA TG TA TA -A T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
27351 TA TA AA T- TA TA TA TA CTA TG TA TA AA T- TA TA CA -A TT TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
27391 TA GTT TA AA TA TA AA GTA TA TA -A GTA TA TA TA TA AA CTA TA AA
1 TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * * * * *
27434 T- TA TA TA TT TT TA TA TA TA -A TA TA CA TT TA -A AA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
27473 TA CA TA TA TA -A TA -A TA TA AA GTA TA -A GTA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * * *
27514 TA TA TA TA TA TA TA AA TA TA TA AA GTA TA -A T- TA TA AA GA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
27554 TA AA GTA TA TA -A GCA TA TA -A TA TA AA GCA TA TA -A GTA TA TA
1 TA TA -TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA
* * * *
27595 -A TA TA -A AA TA TA TA AA TA TA TA AA TA T- TA AA TA TA -A GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
* * *
27634 TA TA -A GTA TA TA -A TA TA AA GTA TA TA TA AA CTA TA AA CTA TA
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA
* * * *
27676 TA TA TA TA TA TA TA TA TA AA GT- TT TA GTA TA AA GCA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA TA
* * * *
27718 T- TA TA TA AA GTA TA TA -A GTG TG TG TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
27760 TA TA -A GT- TT TA GTA TA AA CTA TA TA TA CA TA TA -A TA -A TA
1 TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* *
27799 TA AA GTA TA -A GTA TA TA TA TA TA TA TA AA GTA TA -A T- TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* * * * *
27839 AA GA CTA -A AA TA TA TA -A GTA TA TA -A TA TA AA GTA TA TA AA
1 TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA
* * ** *
27879 GTA TA TA TA CA TA TA AA GTA TA -A GTA TA TA TA -A GC TA TA AA
1 -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* *
27920 GTA TA TA TA TA TA TA GT- TT TA GTA TA TA -A TA TA AA T- TA TA
1 -TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * *
27960 -A AA GTA TA TA TA CA TA TA AA GTA TA -A GCA TA TA TA AA GTA TA
1 TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA
* * * *
28002 AA GTA TA -A GTA TA TA TA TA TA TA TA TA TA TG GA TA TA AA GTA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
*
28044 TA AA GTA TA -A GTA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
28075 AAGTTTTAGT
Statistics
Matches: 714, Mismatches: 168, Indels: 250
0.63 0.15 0.22
Matches are distributed among these distances:
1 64 0.09
2 589 0.82
3 61 0.09
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (2 bp):
TA
Found at i:28142 original size:164 final size:168
Alignment explanation
Indices: 27942--28291 Score: 428
Period size: 172 Copynumber: 2.1 Consensus size: 168
27932 ATAGTTTTAG
* * *
27942 TATATAATATAAATTATAAAAGTATATATACATATAAAGTATAAG-CATATATAAAGTATAAAGT
1 TATATAATATAAAGTATAAAAGTACATATACATATAAAGTATAAGACATATATAAACTATAAAGT
* ** *
28006 ATAAGTATATATAT-ATA-TAT-ATA-TATGGATATAAAGTATAAAGTATAAGTATATATA-TAT
66 ATAAGTATATATATAAAAGTATAATATTAAAG-TATAAACTATAAAGTATAAGT-TATA-AGTAT
* * *
28066 ATATATATAAAGT-TT-TAGTATATAATATAAAGTATTAAAA
128 -TAAATATAAAGTATTAAAGTATACAATATAAAGTATTAAAA
* *
28106 TATATAATATAAAGTATATAAGTACATATACATATAAAGTATAAGTATATATATATAAACTATAA
1 TATATAATATAAAGTATAAAAGTACATATACATATAAAGTATAAG---ACATATATAAACTATAA
*
28171 AGTATAAGTATATATATAAAAGTTATAATATTAAAGTATATACTATAAAGTATAAGTTATAAGTA
63 AGTATAAGTATATATATAAAAG-TATAATATTAAAGTATAAACTATAAAGTATAAGTTATAAGTA
* *
28236 TTAAATATAAAGTATTAAAGTATACCATATAAAGTATTAAAG
127 TTAAATATAAAGTATTAAAGTATACAATATAAAGTATTAAAA
28278 TATATAAATATAAA
1 TATAT-AATATAAA
28292 TATTAAATAT
Statistics
Matches: 158, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
164 42 0.27
168 31 0.20
169 2 0.01
170 12 0.08
171 12 0.08
172 48 0.30
173 11 0.07
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (168 bp):
TATATAATATAAAGTATAAAAGTACATATACATATAAAGTATAAGACATATATAAACTATAAAGT
ATAAGTATATATATAAAAGTATAATATTAAAGTATAAACTATAAAGTATAAGTTATAAGTATTAA
ATATAAAGTATTAAAGTATACAATATAAAGTATTAAAA
Found at i:28265 original size:22 final size:21
Alignment explanation
Indices: 27993--28359 Score: 180
Period size: 22 Copynumber: 17.0 Consensus size: 21
27983 TAAGCATATA
27993 TAAAGTATAAAGTAT-AAGTAT
1 TAAAGTATAAA-TATAAAGTAT
* * * *
28014 ATATA-TATATATATATATGGAT
1 -TAAAGTATAAATATA-AAGTAT
28036 ATAAAGTATAAAGTAT-AAGTAT
1 -TAAAGTATAAA-TATAAAGTAT
*
28058 ATATATA-TATATATATAAAGT-T
1 -TA-A-AGTATAAATATAAAGTAT
*
28080 T-TAGTATATAATATAAAGTAT
1 TAAAGTATA-AATATAAAGTAT
*
28101 TAAAATATATAATATAAAGTA-
1 TAAAGTATA-AATATAAAGTAT
28122 TATAAGTACATATACATATAAAGTA-
1 TA-AAGT--ATA-A-ATATAAAGTAT
*
28147 T-AAGTATATATATATAAACTA-
1 TAAAGTATA-A-ATATAAAGTAT
* *
28168 TAAAGTATAAGTATATA-TAT
1 TAAAGTATAAATATAAAGTAT
*
28188 AAAAGT-TATAATATTAAAGTA-
1 TAAAGTATA-AATA-TAAAGTAT
* *
28209 TATACTATAAAGTAT-AAG--T
1 TAAAGTATAAA-TATAAAGTAT
28228 TATAAGTATTAAATATAAAGTAT
1 TA-AAGTA-TAAATATAAAGTAT
*
28251 TAAAGTATACCATATAAAGTAT
1 TAAAGTATA-AATATAAAGTAT
28273 TAAAGTATATAAATATAAA-TAT
1 TAAAG--TATAAATATAAAGTAT
*
28295 TAAA-TATAAAGTATATATGTA-
1 TAAAGTATAAA-TATA-AAGTAT
28316 TATAAGTATATAATATAAAGTAT
1 TA-AAGTATA-AATATAAAGTAT
*
28339 TAAACTATATAATAT-AAGTAT
1 TAAAGTATA-AATATAAAGTAT
28360 ACAATATAAA
Statistics
Matches: 276, Mismatches: 31, Indels: 77
0.72 0.08 0.20
Matches are distributed among these distances:
18 1 0.00
19 16 0.06
20 38 0.14
21 53 0.19
22 103 0.37
23 39 0.14
24 15 0.05
25 11 0.04
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.37
Consensus pattern (21 bp):
TAAAGTATAAATATAAAGTAT
Found at i:28289 original size:101 final size:103
Alignment explanation
Indices: 28166--28410 Score: 286
Period size: 101 Copynumber: 2.5 Consensus size: 103
28156 ATATATAAAC
28166 TATAAAGTA-T-AAGTATAT--ATATAAAAGTTATAATATTAAAGTATATA-CTATA-AAGTATA
1 TATAAAGTATTAAAGTATATAAATATAAAAGTTATAATATTAAAGTATATATCTATATAAGTATA
* *
28225 -AGT-TATAAGTATTAAA-TATA-AAGTATTAAAGTATACCA
66 TAATATA-AAGTATTAAACTATATAA-TA-T-AAGTATACAA
*
28263 TATAAAGTATTAAAGTATATAAATATAAATA-TTA-AATA-TAAAGTATATATGTATATAAGTAT
1 TATAAAGTATTAAAGTATATAAATATAAA-AGTTATAATATTAAAGTATATATCTATATAAGTAT
28325 ATAATATAAAGTATTAAACTATATAATATAAGTATACAA
65 ATAATATAAAGTATTAAACTATATAATATAAGTATACAA
* * *
28364 TATAAAGTATTACAGTATATAAATAT-AGAGTTAT-ATATTAAATTATA
1 TATAAAGTATTAAAGTATATAAATATAAAAGTTATAATATTAAAGTATA
28411 AAATTCGTAG
Statistics
Matches: 128, Mismatches: 6, Indels: 24
0.81 0.04 0.15
Matches are distributed among these distances:
97 9 0.07
98 1 0.01
99 20 0.16
100 15 0.12
101 59 0.46
102 14 0.11
103 8 0.06
104 2 0.02
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.37
Consensus pattern (103 bp):
TATAAAGTATTAAAGTATATAAATATAAAAGTTATAATATTAAAGTATATATCTATATAAGTATA
TAATATAAAGTATTAAACTATATAATATAAGTATACAA
Found at i:28296 original size:58 final size:57
Alignment explanation
Indices: 28228--28382 Score: 168
Period size: 66 Copynumber: 2.6 Consensus size: 57
28218 AAGTATAAGT
* *
28228 TATAAGTATTAAATATAAAGTATTAAAGTATACCATATAAAGTATTAAAGTATATAAA
1 TATAAGTATTAAATATAAAGTATTAAAGTATACAATATAAAGTATTAAACTATAT-AA
* *
28286 TATAAATATTAAATATAAAGTATATATGTATATAAGTATATAATATAAAGTATTAAACTATATAA
1 TATAAGTATTAAATATAAAG----TA--T-TA-AAGTATACAATATAAAGTATTAAACTATATAA
*
28351 TATAAGTA-TACAATATAAAGTATTACAGTATA
1 TATAAGTATTA-AATATAAAGTATTAAAGTATA
28383 TAAATATAGA
Statistics
Matches: 82, Mismatches: 6, Indels: 19
0.77 0.06 0.18
Matches are distributed among these distances:
57 6 0.07
58 21 0.26
59 1 0.01
61 2 0.02
62 2 0.02
64 3 0.04
65 20 0.24
66 27 0.33
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (57 bp):
TATAAGTATTAAATATAAAGTATTAAAGTATACAATATAAAGTATTAAACTATATAA
Found at i:28318 original size:8 final size:8
Alignment explanation
Indices: 27494--28390 Score: 219
Period size: 8 Copynumber: 121.2 Consensus size: 8
27484 TAATATAAAG
27494 TATAAGTA
1 TATAAGTA
27502 TAT-A-TA
1 TATAAGTA
27508 TATATA-TA
1 TATA-AGTA
27516 TATATA-TA
1 TATA-AGTA
*
27524 TATAAATA
1 TATAAGTA
27532 TATAA--A
1 TATAAGTA
*
27538 GTATAATTA
1 -TATAAGTA
27547 TA-AAG-A
1 TATAAGTA
27553 T-TAAAGTA
1 TAT-AAGTA
*
27561 TATAAGCA
1 TATAAGTA
27569 TATAA-TA
1 TATAAGTA
*
27576 TA-AAGCA
1 TATAAGTA
27583 TATAAGTA
1 TATAAGTA
27591 TATAA-TA
1 TATAAGTA
*
27598 TA-AAATA
1 TATAAGTA
*
27605 TATAAATA
1 TATAAGTA
*
27613 TATAAATA
1 TATAAGTA
27621 T-TAA--A
1 TATAAGTA
27626 TATAAGTA
1 TATAAGTA
27634 TATAAGTA
1 TATAAGTA
27642 TATAA-TA
1 TATAAGTA
27649 TA-AAGTA
1 TATAAGTA
*
27656 TATATA-AA
1 TATA-AGTA
*
27664 CTATAAACTA
1 -TAT-AAGTA
27674 TATATA-TA
1 TATA-AGTA
27682 TATATA-TA
1 TATA-AGTA
27690 TATAAAGT-
1 TAT-AAGTA
*
27698 T-TTAGTA
1 TATAAGTA
*
27705 TA-AAGCA
1 TATAAGTA
*
27712 TATATATTA
1 TATA-AGTA
27721 TATAAAGTA
1 TAT-AAGTA
*
27730 TATAAGTG
1 TATAAGTA
*
27738 TGT--GTA
1 TATAAGTA
27744 TATATA-TA
1 TATA-AGTA
27752 TATATA-TA
1 TATA-AGTA
27760 TATAAGT-
1 TATAAGTA
*
27767 T-TTAGTA
1 TATAAGTA
*
27774 TA-AACTA
1 TATAAGTA
*
27781 TATATA-CA
1 TATA-AGTA
27789 TATAA-TAA
1 TATAAGT-A
27797 TATAA--A
1 TATAAGTA
27803 GTATAAGTA
1 -TATAAGTA
27812 TAT-A-TA
1 TATAAGTA
27818 TAT-A-TA
1 TATAAGTA
27824 TA-AAG--
1 TATAAGTA
*
27829 TATAATTA
1 TATAAGTA
27837 TA-AAG-A
1 TATAAGTA
*
27843 CTA-AAATA
1 -TATAAGTA
27851 TATAAGTA
1 TATAAGTA
27859 TATAA-TA
1 TATAAGTA
27866 TA-AAGTA
1 TATAAGTA
27873 TATAAAGTA
1 TAT-AAGTA
*
27882 TATATA-CA
1 TATA-AGTA
27890 TATAA--A
1 TATAAGTA
27896 GTATAAGTATA
1 -TATAAG--TA
27907 TATAAGCTA
1 TATAAG-TA
27916 TA-AAGTA
1 TATAAGTA
27923 TAT-A-TA
1 TATAAGTA
27929 TATATAGT-
1 TATA-AGTA
*
27937 T-TTAGTA
1 TATAAGTA
27944 TATAA-TA
1 TATAAGTA
*
27951 TA-AATTA
1 TATAAGTA
*
27958 TAAAAGTA
1 TATAAGTA
*
27966 TATATA-CA
1 TATA-AGTA
27974 TATAA--A
1 TATAAGTA
27980 GTATAAGCATA
1 -TATAAG--TA
27991 TATAAAGTA
1 TAT-AAGTA
28000 TA-AAG--
1 TATAAGTA
28005 TATAAGTA
1 TATAAGTA
28013 TAT-A-TA
1 TATAAGTA
28019 TATATA-TA
1 TATA-AGTA
* *
28027 TATATGGA
1 TATAAGTA
28035 TATAAAGTA
1 TAT-AAGTA
28044 TA-AAG--
1 TATAAGTA
28049 TATAAGTA
1 TATAAGTA
28057 TAT-A-TA
1 TATAAGTA
28063 TATATA-TA
1 TATA-AGTA
28071 TATAAAGT-
1 TAT-AAGTA
*
28079 T-TTAGTA
1 TATAAGTA
28086 TATAA-TA
1 TATAAGTA
28093 TA-AAGTA
1 TATAAGTA
*
28100 T-TAAAATA
1 TAT-AAGTA
28108 TATAA-TA
1 TATAAGTA
28115 TA-AAGTA
1 TATAAGTA
28122 TATAAGTACA
1 TATAAGT--A
28132 TATACA-TA
1 TATA-AGTA
28140 TA-AAG--
1 TATAAGTA
28145 TATAAGTA
1 TATAAGTA
28153 TAT-A-TA
1 TATAAGTA
*
28159 TATAAACTA
1 TAT-AAGTA
28168 TA-AAG--
1 TATAAGTA
28173 TATAAGTA
1 TATAAGTA
28181 TAT-A-TA
1 TATAAGTA
*
28187 TAAAAGT-
1 TATAAGTA
28194 TATAA-TA
1 TATAAGTA
28201 T-TAAAGTA
1 TAT-AAGTA
*
28209 TAT-ACTA
1 TATAAGTA
28216 TA-AAG--
1 TATAAGTA
28221 TATAAGT-
1 TATAAGTA
28228 TATAAGTA
1 TATAAGTA
*
28236 T-TAAATA
1 TATAAGTA
28243 TA-AAGTA
1 TATAAGTA
28250 T-TAAAGTA
1 TAT-AAGTA
**
28258 TACCA-TA
1 TATAAGTA
28265 TA-AAGTA
1 TATAAGTA
28272 T-TAAAGTA
1 TAT-AAGTA
28280 TATAA--A
1 TATAAGTA
*
28286 TATAAATA
1 TATAAGTA
*
28294 T-TAAATA
1 TATAAGTA
28301 TA-AAGTA
1 TATAAGTA
*
28308 TATATGTA
1 TATAAGTA
28316 TATAAGTA
1 TATAAGTA
28324 TATAA-TA
1 TATAAGTA
28331 TA-AAGTA
1 TATAAGTA
*
28338 T-TAAACTA
1 TAT-AAGTA
28346 TAT-A--A
1 TATAAGTA
28351 TATAAGTA
1 TATAAGTA
*
28359 TACAA-TA
1 TATAAGTA
28366 TA-AAGTA
1 TATAAGTA
28373 T-TACAGTA
1 TATA-AGTA
*
28381 TATAAATA
1 TATAAGTA
28389 TA
1 TA
28391 GAGTTATATA
Statistics
Matches: 690, Mismatches: 56, Indels: 286
0.67 0.05 0.28
Matches are distributed among these distances:
5 18 0.03
6 113 0.16
7 200 0.29
8 273 0.40
9 62 0.09
10 18 0.03
11 6 0.01
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (8 bp):
TATAAGTA
Found at i:28320 original size:150 final size:149
Alignment explanation
Indices: 27991--28373 Score: 329
Period size: 150 Copynumber: 2.6 Consensus size: 149
27981 TATAAGCATA
* * *
27991 TATAAAGTATAAAGTATAAGTATATATATAT--A-TAT-A-TATATGGATATAAAGTAT-AAAGT
1 TATAAA-TATAAAGTATAAATATATATATATAAACTATAAGTATAT-AATATAAAGTATAAAACT
* * * *
28050 ATA-AGTAT-A-TATA-TATATATA-TATAAAGTT-TTAGTA-TATAATATAAAGTATTAAAATA
64 ATATAATATAAGTATACAATATAAAGTAT-AAGTTATAAGTATTA-AATATAAAGTATTAAAATA
*
28108 TATAATATAAAGTATATAAGTACA
127 TACAATATAAAGTATATAAGTA-A
* * * * *
28132 TATACATATAAAGTATAAGTATATATATATAAACTATAAAGTATA-AGTATATA-TATAAAAGT-
1 TATAAATATAAAGTATAAATATATATATATAAACTAT-AAGTATATAATATAAAGTATAAAACTA
* * *
28194 TATAATATTAAAGTATATACTATAAAGTATAAGTTATAAGTATTAAATATAAAGTATTAAAGTAT
65 TATAATA-T-AAGTATACAATATAAAGTATAAGTTATAAGTATTAAATATAAAGTATTAAAATAT
*
28259 ACCATATAAAGTAT-TAAAGT-A
128 ACAATATAAAGTATAT-AAGTAA
** *
28280 TATAAATATAAA-TATTAAATATAAAGTATATATGTA-TATAAGTATATAATATAAAGTATTAAA
1 TATAAATATAAAGTA-TAAATAT--A-TATATATAAACTATAAGTATATAATATAAAGTATAAAA
28343 CTATATAATATAAGTATACAATATAAAGTAT
62 CTATATAATATAAGTATACAATATAAAGTAT
28374 TACAGTATAT
Statistics
Matches: 196, Mismatches: 22, Indels: 39
0.76 0.09 0.15
Matches are distributed among these distances:
140 24 0.12
141 5 0.03
142 1 0.01
143 8 0.04
144 13 0.07
145 2 0.01
146 4 0.02
147 3 0.02
148 22 0.11
149 18 0.09
150 71 0.36
151 18 0.09
152 7 0.04
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.37
Consensus pattern (149 bp):
TATAAATATAAAGTATAAATATATATATATAAACTATAAGTATATAATATAAAGTATAAAACTAT
ATAATATAAGTATACAATATAAAGTATAAGTTATAAGTATTAAATATAAAGTATTAAAATATACA
ATATAAAGTATATAAGTAA
Found at i:28651 original size:161 final size:155
Alignment explanation
Indices: 28395--28776 Score: 575
Period size: 161 Copynumber: 2.5 Consensus size: 155
28385 AATATAGAGT
28395 TATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATT
1 TATATATTAAATT-TAAAATTCGTAGGATCAAATTGAAAT-AAATAAAAATTTAAAGCCTAAATT
*
28460 AATACATTATATAGTTATATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAAT-AA
64 AATACATTATATAGTTATATATATTAAATTATAAAATTCATAGG-TCAAATTGAAATAAAATAAA
28524 AATTTAAAGCCTAAATTAATACATTATATAGTTA
128 AATTTAAAGCCTAAATTAAT--A-TAT-TA--TA
* *
28558 TATATATTAAAATTTAAAATTCGTAGGATCACATTGAAATAAA-AAAAACTTAAAGCCTAAATTA
1 TATATATT-AAATTTAAAATTCGTAGGATCAAATTGAAATAAATAAAAATTTAAAGCCTAAATTA
*
28622 ATATATTATATAGTTATATATATTAAATTATAAAATTCATAGGTCAAATTGAAATAAAATAAAAA
65 ATACATTATATAGTTATATATATTAAATTATAAAATTCATAGGTCAAATTGAAATAAAATAAAAA
28687 TTTAAAGCCTAAATTAATATATTATA
130 TTTAAAGCCTAAATTAATATATTATA
28713 T-TA-ATT--A--T-AAATTCGTAGGATCAAATTGAAATAAATAAAAATTTAAAGCCTAAATTAA
1 TATATATTAAATTTAAAATTCGTAGGATCAAATTGAAATAAATAAAAATTTAAAGCCTAAATTAA
28771 TACATT
66 TACATT
28777 TTTTGGACTA
Statistics
Matches: 209, Mismatches: 7, Indels: 21
0.88 0.03 0.09
Matches are distributed among these distances:
147 26 0.12
148 27 0.13
150 1 0.00
153 3 0.01
154 2 0.01
155 3 0.01
157 2 0.01
158 3 0.01
159 1 0.00
160 17 0.08
161 83 0.40
162 3 0.01
163 33 0.16
164 5 0.02
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.35
Consensus pattern (155 bp):
TATATATTAAATTTAAAATTCGTAGGATCAAATTGAAATAAATAAAAATTTAAAGCCTAAATTAA
TACATTATATAGTTATATATATTAAATTATAAAATTCATAGGTCAAATTGAAATAAAATAAAAAT
TTAAAGCCTAAATTAATATATTATA
Found at i:28713 original size:81 final size:82
Alignment explanation
Indices: 28395--28713 Score: 549
Period size: 81 Copynumber: 3.9 Consensus size: 82
28385 AATATAGAGT
28395 TATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATT
1 TATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATT
28460 AATACATTATATAGTTA
66 AATACATTATATAGTTA
28477 TATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAAT-AAAATTTAAAGCCTAAATT
1 TATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATT
28541 AATACATTATATAGTTA
66 AATACATTATATAGTTA
* *
28558 TATATATTAAAATT-TAAAATTCGTAGGATCACATTGAAAT-AAA-AAAAACTTAAAGCCTAAAT
1 TATATATT-AAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAAAGCCTAAAT
*
28620 TAATATATTATATAGTTA
65 TAATACATTATATAGTTA
*
28638 TATATATTAAATTATAAAATTCATAGG-TCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATT
1 TATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATT
*
28702 AATATATTATAT
66 AATACATTATAT
28714 TAATTATAAA
Statistics
Matches: 226, Mismatches: 6, Indels: 11
0.93 0.02 0.05
Matches are distributed among these distances:
79 16 0.07
80 60 0.27
81 100 0.44
82 50 0.22
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.36
Consensus pattern (82 bp):
TATATATTAAATTATAAAATTCGTAGGATCAAATTGAAATAAAATAAAAATTTAAAGCCTAAATT
AATACATTATATAGTTA
Found at i:28762 original size:67 final size:68
Alignment explanation
Indices: 28636--28772 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 68
28626 ATTATATAGT
28636 TATATATATTAAATTATAAAATTCATAGGTCAAATTGAAATAAAATAAAAATTTAAAGCCTAAAT
1 TATATATATTAAATTATAAAATTCATAGGTCAAATTGAAATAAAATAAAAATTTAAAGCCTAAAT
28701 TAA
66 TAA
*
28704 TATATTATATT-AATTAT-AAATTCGTAGGATCAAATTGAAAT-AAATAAAAATTTAAAGCCTAA
1 TATA-TATATTAAATTATAAAATTCATAGG-TCAAATTGAAATAAAATAAAAATTTAAAGCCTAA
28766 ATTAA
64 ATTAA
28771 TA
1 TA
28773 CATTTTTTGG
Statistics
Matches: 66, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
67 38 0.58
68 22 0.33
69 6 0.09
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.35
Consensus pattern (68 bp):
TATATATATTAAATTATAAAATTCATAGGTCAAATTGAAATAAAATAAAAATTTAAAGCCTAAAT
TAA
Found at i:30245 original size:32 final size:32
Alignment explanation
Indices: 30203--30273 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
30193 TGTAATATAA
*
30203 ATCAGGTAAATGTCAAGTTAGATAAATGTCA-
1 ATCAGGTAAATGTCAAGTCAGATAAATGTCAT
*
30234 AGTCAGGTAAATGTCAAGTCAGGTAAATGTCAT
1 A-TCAGGTAAATGTCAAGTCAGATAAATGTCAT
30267 ATCAGGT
1 ATCAGGT
30274 CAATAATAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
31 1 0.03
32 34 0.94
33 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.28
Consensus pattern (32 bp):
ATCAGGTAAATGTCAAGTCAGATAAATGTCAT
Found at i:30273 original size:16 final size:16
Alignment explanation
Indices: 30204--30265 Score: 106
Period size: 16 Copynumber: 3.9 Consensus size: 16
30194 GTAATATAAA
30204 TCAGGTAAATGTCAAG
1 TCAGGTAAATGTCAAG
* *
30220 TTAGATAAATGTCAAG
1 TCAGGTAAATGTCAAG
30236 TCAGGTAAATGTCAAG
1 TCAGGTAAATGTCAAG
30252 TCAGGTAAATGTCA
1 TCAGGTAAATGTCA
30266 TATCAGGTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (16 bp):
TCAGGTAAATGTCAAG
Found at i:34132 original size:15 final size:15
Alignment explanation
Indices: 34112--34141 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34102 TTCACAATAC
34112 GTAAAAAAATTCATA
1 GTAAAAAAATTCATA
34127 GTAAAAAAATTCATA
1 GTAAAAAAATTCATA
34142 CTCCATAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.27
Consensus pattern (15 bp):
GTAAAAAAATTCATA
Found at i:35097 original size:59 final size:61
Alignment explanation
Indices: 34985--35134 Score: 207
Period size: 59 Copynumber: 2.5 Consensus size: 61
34975 TGAGTCTTAT
*
34985 GACTATTAAAAGTTACAAAATGGTCCCTCAATGATATAAAATTACTTTATTGAGTCAC-TC
1 GACTATTAAAAGTTACAAAATGGTCCCTCGATGATATAAAATTACTTTATTGAGTCACTTC
** * * * *
35045 GACTATTAAAAGTTAC-AAATGGTCCCTCGATGATATGGAGTTATTTTGTTGAGTCCCTTC
1 GACTATTAAAAGTTACAAAATGGTCCCTCGATGATATAAAATTACTTTATTGAGTCACTTC
*
35105 -ACTATTAAAAGTTACAAAATGGTCACTCGA
1 GACTATTAAAAGTTACAAAATGGTCCCTCGA
35135 CTATTCGTTA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
59 49 0.61
60 31 0.39
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (61 bp):
GACTATTAAAAGTTACAAAATGGTCCCTCGATGATATAAAATTACTTTATTGAGTCACTTC
Found at i:40623 original size:20 final size:20
Alignment explanation
Indices: 40595--40687 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
40585 ACCCAGTTTC
*
40595 TAAATTCGCAATGCGAATATG
1 TAAA-TCGCAATGCGAATTTG
* * *
40616 TAAATCGCATTGCGATTTTC
1 TAAATCGCAATGCGAATTTG
* * *
40636 CAAATTCGCAACGCGAATCTG
1 TAAA-TCGCAATGCGAATTTG
*
40657 TAAATCGCAACGCGAATTTG
1 TAAATCGCAATGCGAATTTG
40677 TAAATCGCAAT
1 TAAATCGCAAT
40688 ATAGAAGTCA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 40 0.69
21 18 0.31
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (20 bp):
TAAATCGCAATGCGAATTTG
Found at i:40718 original size:20 final size:20
Alignment explanation
Indices: 40692--40740 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
40682 CGCAATATAG
*
40692 AAGTCAAATTCGTAACGCGA
1 AAGTCAAATTCGCAACGCGA
* *
40712 TAGTCAAATTTGCAACGCGA
1 AAGTCAAATTCGCAACGCGA
40732 AAGTCAAAT
1 AAGTCAAAT
40741 GTTTTTACGC
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:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (20 bp):
AAGTCAAATTCGCAACGCGA
Found at i:41306 original size:20 final size:20
Alignment explanation
Indices: 41255--41306 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
41245 ATCACAACGC
*
41255 AATTTTAGTTTCGCATTGCG
1 AATTTAAGTTTCGCATTGCG
* * * *
41275 ATTTTCATTTTCGCGTTGCG
1 AATTTAAGTTTCGCATTGCG
41295 AATTTAAGTTTC
1 AATTTAAGTTTC
41307 AGAAACTTCT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.15, G:0.17, T:0.48
Consensus pattern (20 bp):
AATTTAAGTTTCGCATTGCG
Found at i:43698 original size:66 final size:60
Alignment explanation
Indices: 43563--43702 Score: 181
Period size: 66 Copynumber: 2.2 Consensus size: 60
43553 TTTTACATTG
*
43563 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTTATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTA
* * * *
43623 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAG-A-T-TTATTTT--TTGATTAATTGATTTGT
43688 A
60 A
43689 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
43703 ATTTCTAAAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
60 17 0.25
61 14 0.20
62 1 0.01
63 1 0.01
64 6 0.09
66 30 0.43
ACGTcount: A:0.31, C:0.01, G:0.17, T:0.51
Consensus pattern (60 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGTA
Found at i:43787 original size:20 final size:20
Alignment explanation
Indices: 43761--43816 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
43751 GTTGAAGGTA
43761 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * * *
43781 TAAATTCGAAATGTGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
43801 CAAATTTGCAACGCGA
1 CAAATTCGCAACGCGA
43817 TTTTTGGTTT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:43863 original size:20 final size:20
Alignment explanation
Indices: 43825--43863 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
43815 GATTTTTGGT
*
43825 TTGCGAATTTGACTTTCGCG
1 TTGCGAATTTGACTATCGCG
*
43845 TTGCGAATTTGGCTATCGC
1 TTGCGAATTTGACTATCGC
43864 AACGCTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:44132 original size:39 final size:39
Alignment explanation
Indices: 44077--44163 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
44067 TCAAGTTGTA
*
44077 GATTTTGATTTTCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
44116 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
44155 GATTTTGAT
1 GATTTTGAT
44164 GAGTATGGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:44498 original size:18 final size:18
Alignment explanation
Indices: 44475--44511 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44465 CGAAATTGAT
44475 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
44493 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
44511 A
1 A
44512 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:44530 original size:24 final size:24
Alignment explanation
Indices: 44467--44519 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
44457 AGTGGAGCCG
*
44467 AAATTGATATTGAAATTCAAACTC
1 AAATTGAAATTGAAATTCAAACTC
*
44491 AAATTGAAATTTAAATTCAAACTC
1 AAATTGAAATTGAAATTCAAACTC
*
44515 CAATT
1 AAATT
44520 ACATATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (24 bp):
AAATTGAAATTGAAATTCAAACTC
Found at i:47432 original size:12 final size:12
Alignment explanation
Indices: 47415--47439 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47405 TCTTCGGGGA
47415 CTTTTTCTTCTT
1 CTTTTTCTTCTT
47427 CTTTTTCTTCTT
1 CTTTTTCTTCTT
47439 C
1 C
47440 AGGGTTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:47681 original size:24 final size:24
Alignment explanation
Indices: 47630--47681 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
47620 ATCTGAGTAT
** *
47630 TGACCAAGATCAAAGTCCGGGTAT
1 TGACCAAGATCAAAGTCCGAATAC
* *
47654 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTCCGAATAC
47678 TGAC
1 TGAC
47682 TAGTACTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (24 bp):
TGACCAAGATCAAAGTCCGAATAC
Found at i:47814 original size:12 final size:12
Alignment explanation
Indices: 47793--47827 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
47783 GGTTGTGGGT
*
47793 TTTGAGATTGTG
1 TTTGATATTGTG
47805 TTTGATATTGTG
1 TTTGATATTGTG
*
47817 TTTGGTATTGT
1 TTTGATATTGT
47828 AAATGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:48415 original size:14 final size:15
Alignment explanation
Indices: 48379--48416 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
48369 GAAATCATTG
48379 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
48394 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
48409 AAAAATTA
1 AAAAATTA
48417 GAGATGGGGA
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:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:48609 original size:20 final size:20
Alignment explanation
Indices: 48572--48744 Score: 70
Period size: 20 Copynumber: 8.7 Consensus size: 20
48562 AACTAAAACC
48572 TGTTGCGAAA-TT-AAATTCG
1 TGTTGC-AAATTTGAAATTCG
48591 TGTTGCAAATTTGAAATTC-
1 TGTTGCAAATTTGAAATTCG
* *
48610 AGTTGCGAATTTGAAATTCCG
1 TGTTGCAAATTTGAAATT-CG
** * ** *
48631 CATTGCGAATTTGACTTTTG
1 TGTTGCAAATTTGAAATTCG
* * *
48651 TGTTACGAATTTG-ACTTCTG
1 TGTTGCAAATTTGAAATTC-G
* *
48671 TGTTGC-GATTTACAAATTCG
1 TGTTGCAAATTT-GAAATTCG
* * *** *
48691 CGTTGCGAATTTGTCTTTTG
1 TGTTGCAAATTTGAAATTCG
*
48711 TGTTGCAAATTTG-ACTATCG
1 TGTTGCAAATTTGAAAT-TCG
*
48731 CGTTGCAAATTTGA
1 TGTTGCAAATTTGA
48745 CTTCCGTGTT
Statistics
Matches: 114, Mismatches: 30, Indels: 18
0.70 0.19 0.11
Matches are distributed among these distances:
18 3 0.03
19 31 0.27
20 58 0.51
21 22 0.19
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (20 bp):
TGTTGCAAATTTGAAATTCG
Found at i:48638 original size:21 final size:19
Alignment explanation
Indices: 48573--48644 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
48563 ACTAAAACCT
* *
48573 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTC-A
*
48592 GTTGCAAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
48611 GTTGCGAATTTGAAATTCC
1 GTTGCGAATTTGAAATTCA
48630 GCATTGCGAATTTGA
1 G--TTGCGAATTTGA
48645 CTTTTGTGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
19 27 0.60
20 6 0.13
21 12 0.27
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:48677 original size:40 final size:40
Alignment explanation
Indices: 48633--48779 Score: 131
Period size: 40 Copynumber: 3.7 Consensus size: 40
48623 AAATTCCGCA
* * *
48633 TTGCGAATTTGACTTTTGTGTTACGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTG
* * *
48673 TTGCG-ATTT-ACAAATTCGCGTTGCGAATTTGTCTTTTGTG
1 TTGCGAATTTGAC--TTTCGCGTTGCGAATTTGACTTCTGTG
* * * *
48713 TTGCAAATTTGACTATCGCGTTGCAAATTTGACTTCCGTG
1 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTG
*
48753 TTGCG-ATTT-ACAAATTCGCGTTGCGAA
1 TTGCGAATTTGAC--TTTCGCGTTGCGAA
48780 AATAGAAACT
Statistics
Matches: 84, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
38 4 0.05
39 8 0.10
40 66 0.79
41 4 0.05
42 2 0.02
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.41
Consensus pattern (40 bp):
TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCTGTG
Found at i:48736 original size:60 final size:61
Alignment explanation
Indices: 48590--48742 Score: 163
Period size: 60 Copynumber: 2.5 Consensus size: 61
48580 AATTAAATTC
* *
48590 GTGTTGCAAATTTGA-AATTC-AGTTGCGAATTTGAAATTCCGCATTGCGAATTTGACTTTT
1 GTGTTGCAAATTTGACTA-TCGAGTTGCGAATTTCAAATTCCGCATTGCGAATTTGACTTTT
* * * * *
48650 GTGTTACGAATTTGACT-TCTGTGTTGCG-ATTTACAAATT-CGCGTTGCGAATTTGTCTTTT
1 GTGTTGCAAATTTGACTATC-GAGTTGCGAATTT-CAAATTCCGCATTGCGAATTTGACTTTT
* *
48710 GTGTTGCAAATTTGACTATCGCGTTGCAAATTT
1 GTGTTGCAAATTTGACTATCGAGTTGCGAATTT
48743 GACTTCCGTG
Statistics
Matches: 76, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
59 2 0.03
60 57 0.75
61 17 0.22
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (61 bp):
GTGTTGCAAATTTGACTATCGAGTTGCGAATTTCAAATTCCGCATTGCGAATTTGACTTTT
Found at i:48745 original size:20 final size:20
Alignment explanation
Indices: 48688--48746 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
48678 ATTTACAAAT
* * *
48688 TCGCGTTGCGAATTTGTCTT
1 TCGCGTTGCAAATTTGACTA
* *
48708 TTGTGTTGCAAATTTGACTA
1 TCGCGTTGCAAATTTGACTA
48728 TCGCGTTGCAAATTTGACT
1 TCGCGTTGCAAATTTGACT
48747 TCCGTGTTGC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCAAATTTGACTA
Found at i:48755 original size:20 final size:20
Alignment explanation
Indices: 48710--48756 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
48700 TTTGTCTTTT
48710 GTGTTGCAAATTTGACTATC
1 GTGTTGCAAATTTGACTATC
*
48730 GCGTTGCAAATTTGACT-TCC
1 GTGTTGCAAATTTGACTAT-C
48750 GTGTTGC
1 GTGTTGC
48757 GATTTACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
GTGTTGCAAATTTGACTATC
Found at i:48796 original size:80 final size:80
Alignment explanation
Indices: 48658--48823 Score: 210
Period size: 80 Copynumber: 2.1 Consensus size: 80
48648 TTGTGTTACG
* * * **** *
48658 AATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAATTTGTCTTTTGTGTTGC-AAATT
1 AATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGCGAAATAGTAAACTGGGTTGCAAAATT
* *
48722 TGACTATCGCGTTGCA
66 GGA-GATCGCGTTGCA
48738 AATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGCGAAAATAG-AAACTGGGTTGCAAAAT
1 AATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGCG-AAATAGTAAACTGGGTTGCAAAAT
48802 TGGAGATCGCGTTGCA
65 TGGAGATCGCGTTGCA
48818 AATTTG
1 AATTTG
48824 TTGGTCATTT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 63 0.85
81 11 0.15
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.37
Consensus pattern (80 bp):
AATTTGACTTCCGTGTTGCGATTTACAAATTCGCGTTGCGAAATAGTAAACTGGGTTGCAAAATT
GGAGATCGCGTTGCA
Found at i:52316 original size:21 final size:21
Alignment explanation
Indices: 52292--52336 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
52282 TAAAAAGAAG
52292 GATAAAATAACAAAGTATGAT
1 GATAAAATAACAAAGTATGAT
52313 GATAAAATAACAAAGTATGAT
1 GATAAAATAACAAAGTATGAT
52334 GAT
1 GAT
52337 TAAACCCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (21 bp):
GATAAAATAACAAAGTATGAT
Found at i:54904 original size:25 final size:25
Alignment explanation
Indices: 54876--54969 Score: 179
Period size: 25 Copynumber: 3.8 Consensus size: 25
54866 GTACGGATGC
*
54876 TTAATGAGTTGAACAACTCATGTGT
1 TTAATGAGTTGAACAGCTCATGTGT
54901 TTAATGAGTTGAACAGCTCATGTGT
1 TTAATGAGTTGAACAGCTCATGTGT
54926 TTAATGAGTTGAACAGCTCATGTGT
1 TTAATGAGTTGAACAGCTCATGTGT
54951 TTAATGAGTTGAACAGCTC
1 TTAATGAGTTGAACAGCTC
54970 GTGAGTAATT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
25 68 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (25 bp):
TTAATGAGTTGAACAGCTCATGTGT
Found at i:55473 original size:16 final size:16
Alignment explanation
Indices: 55452--55485 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
55442 ATAAAAATTT
*
55452 CAATGAGTTTAACGAG
1 CAATGAGCTTAACGAG
55468 CAATGAGCTTAACGAG
1 CAATGAGCTTAACGAG
55484 CA
1 CA
55486 GCGAGTCGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (16 bp):
CAATGAGCTTAACGAG
Found at i:58491 original size:16 final size:16
Alignment explanation
Indices: 58472--58502 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58462 TATATGTAAC
*
58472 GTAAATAATATATAAA
1 GTAAATAATAAATAAA
58488 GTAAATAATAAATAA
1 GTAAATAATAAATAA
58503 TAAAATTGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
GTAAATAATAAATAAA
Found at i:62321 original size:21 final size:21
Alignment explanation
Indices: 62291--62331 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
62281 ATATGTGTTA
*
62291 TATGTGGTCATTCGAGACATC
1 TATGTAGTCATTCGAGACATC
*
62312 TATGTAGTCATTCGGGACAT
1 TATGTAGTCATTCGAGACAT
62332 TTCTACGCGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TATGTAGTCATTCGAGACATC
Found at i:63381 original size:19 final size:19
Alignment explanation
Indices: 63357--63423 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
63347 TTCAAGGTGT
* *
63357 ATCGATGCACATGAAGTGC
1 ATCGATGCACAAGTAGTGC
*
63376 ATCGATGCACAAGTAGGGC
1 ATCGATGCACAAGTAGTGC
63395 ATCGATGCACAAGTAGTGC
1 ATCGATGCACAAGTAGTGC
63414 ATCGATGCAC
1 ATCGATGCAC
63424 CCCCTTAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.19
Consensus pattern (19 bp):
ATCGATGCACAAGTAGTGC
Found at i:64135 original size:23 final size:23
Alignment explanation
Indices: 64109--64165 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
64099 AATCTTATAT
*
64109 GGCACTACGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
64132 GGCACTTCGGTGTAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
64155 GGCACTTCGGT
1 GGCACTTCGGT
64166 ACGTTTATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.18, C:0.26, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:67448 original size:16 final size:16
Alignment explanation
Indices: 67427--67460 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
67417 ATATGTTTGA
* *
67427 AAAGAATAGAGCAAGT
1 AAAGAATAAAGAAAGT
67443 AAAGAATAAAGAAAGT
1 AAAGAATAAAGAAAGT
67459 AA
1 AA
67461 GGATTTTGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.21, T:0.12
Consensus pattern (16 bp):
AAAGAATAAAGAAAGT
Found at i:69683 original size:19 final size:19
Alignment explanation
Indices: 69659--69711 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
69649 GAATGCCATC
69659 AGTGTATCGATGCACAAGT
1 AGTGTATCGATGCACAAGT
69678 AGTGTATCGATGCACAAGT
1 AGTGTATCGATGCACAAGT
*
69697 AGTGCATCGATGCAC
1 AGTGTATCGATGCAC
69712 CCCCTTAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (19 bp):
AGTGTATCGATGCACAAGT
Done.