Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004427.1 Hibiscus syriacus cultivar Beakdansim tig00009708_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: 54862
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1171 original size:19 final size:20
Alignment explanation
Indices: 1127--1176 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1117 TACTGTTCAT
* * *
1127 TACTGTTCACACAATATCAG
1 TACTATTCATACAATATCAA
1147 TACTATTCATACAATA-CAA
1 TACTATTCATACAATATCAA
1166 TACTATTCATA
1 TACTATTCATA
1177 AAAACATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 13 0.48
20 14 0.52
ACGTcount: A:0.40, C:0.22, G:0.04, T:0.34
Consensus pattern (20 bp):
TACTATTCATACAATATCAA
Found at i:2432 original size:14 final size:14
Alignment explanation
Indices: 2409--2438 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2399 TAAATATCCG
*
2409 AAAAAGAAAAAGGA
1 AAAAACAAAAAGGA
2423 AAAAACAAAAAGGA
1 AAAAACAAAAAGGA
2437 AA
1 AA
2439 GTAAAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAACAAAAAGGA
Found at i:17046 original size:108 final size:111
Alignment explanation
Indices: 16834--17466 Score: 306
Period size: 112 Copynumber: 5.7 Consensus size: 111
16824 TGAGACAGTC
16834 TCATTTAATACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTG
1 TCATTTAATACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTG
* ***
16899 AGATAATTTCATTAGAAGAAATTTTTTTATCTAGCTTGAGATAATT
66 AGATAATTTCACTAGAAGAAATAGATTTATCTAGCTTGAGATAATT
* ** *
16945 TCATTTAATACGAGGATTTATCTCACTTGAGATT-TTTTT-TTAAAAC-AGATTCATCTCGTTTG
1 TCATTTAATACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTG
* * **
17007 AGATAGTTTCACTCGAA-ACAGA-AGATTTATCTCA-CTTGAGATTGTT
66 AGATAATTTCACTAGAAGA-A-ATAGATTTATCT-AGCTTGAGATAATT
* * * * * ** * * *
17053 T-TTATTAAAACAAGATTTTATCT-AGCTTGAGATAGTTTCACTTGAAACAGAAGATTTATCTCA
1 TCAT-TTAATACAAAAATTTATCTCA-CTTGAGATTGTTTTTCTT-AAA-ACAAGATTCATCTCG
* ** ** * * * *
17116 CTTAAGATTGTTTTTTCGTAAAACAAAT---TTTATCTCGCTTGAGATAGTT
62 CTTGAGA-TAATTTCAC-TAGAAGAAATAGATTTATCTAGCTTGAGATAATT
* ** *
17165 TCGCTCGAA-ACAAAATATTTATCTCACTTGAGATTAG-TTTTCTTAAAACAA-ATTTTATCTCG
1 TC-ATTTAATACAAAA-ATTTATCTCACTTGAGATT-GTTTTTCTTAAAACAAGA-TTCATCTCG
* * * * **
17227 CTTGAGATAGTGTCACTCGAA-ACGAA-AGATTTATCTCA-CTTGATATTGTT
62 CTTGAGATAATTTCACTAGAAGA--AATAGATTTATCT-AGCTTGAGATAATT
* * * * * ** * * * *
17277 T-TTCTTAAAAC-AAGATTAATCT-AGCTTGAGATAGTTTAACTCAAAACATAAATTTTATCTCA
1 TCAT-TTAATACAAAAATTTATCTCA-CTTGAGATTGTTTTTCTTAAAACA-AGA-TTCATCTCG
** ** * * * *
17339 CTTGAGATTGTTTTTCTTA-AA-ACA-AGATTTATCTCGCTTGAGACAGTT
62 CTTGAGATAATTTCAC-TAGAAGAAATAGATTTATCTAGCTTGAGATAATT
** *
17387 TCACTCGAA-ACATAAGATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCT
1 TCA-TTTAATACA-AAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCT
*
17451 TGAGATAGTTTTCACT
64 TGAGATA-ATTTCACT
17467 CAAAATAGAA
Statistics
Matches: 392, Mismatches: 89, Indels: 83
0.70 0.16 0.15
Matches are distributed among these distances:
107 3 0.01
108 72 0.18
109 17 0.04
110 79 0.20
111 64 0.16
112 104 0.27
113 39 0.10
114 9 0.02
115 4 0.01
116 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (111 bp):
TCATTTAATACAAAAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTCATCTCGCTTG
AGATAATTTCACTAGAAGAAATAGATTTATCTAGCTTGAGATAATT
Found at i:17104 original size:75 final size:75
Alignment explanation
Indices: 16923--17613 Score: 806
Period size: 74 Copynumber: 9.3 Consensus size: 75
16913 GAAGAAATTT
* * ** *
16923 TTTTATCTAGCTTGAGATAATTTCA-TTTAATAC-GAGGATTTATCTCACTTGAGATT-TTTTT-
1 TTTTATCTCGCTTGAGATAGTTTCACTCGAA-ACAGAAGATTTATCTCACTTGAGATTGTTTTTC
16984 TTAAAAC-AGA
65 TTAAAACAAGA
* * *
16994 -TTCATCTCGTTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTTTAT
1 TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTTTCT
17058 TAAAACAAGA
66 TAAAACAAGA
* * *
17068 TTTTATCTAGCTTGAGATAGTTTCACTTGAAACAGAAGATTTATCTCACTTAAGATTGTTTTTTC
1 TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTG-TTTTTC
*
17133 GTAAAACAA-A
65 TTAAAACAAGA
* * *
17143 TTTTATCTCGCTTGAGATAGTTTCGCTCGAAACAAAATATTTATCTCACTTGAGATTAG-TTTTC
1 TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATT-GTTTTTC
17207 TTAAAACAA-A
65 TTAAAACAAGA
* *
17217 TTTTATCTCGCTTGAGATAGTGTCACTCGAAAC-GAAAGATTTATCTCACTTGATATTGTTTTTC
1 TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG-AAGATTTATCTCACTTGAGATTGTTTTTC
17281 TTAAAACAAGA
65 TTAAAACAAGA
* * * * *
17292 -TTAATCTAGCTTGAGATAGTTTAACTCAAAACATAA-ATTTTATCTCACTTGAGATTGTTTTTC
1 TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTATCTCACTTGAGATTGTTTTTC
17355 TTAAAACAAGA
65 TTAAAACAAGA
* *
17366 -TTTATCTCGCTTGAGACAGTTTCACTCGAAACATAAGATTTATCTCACTTGAGATTGTTTTTCT
1 TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTTTCT
17430 TAAAACAAGA
66 TAAAACAAGA
* * * **
17440 -TTCATCTCGCTTGAGATAGTTTTCACTCAAAATAGAA-ATTTTATCTCACTTGATTTTGTTTTT
1 TTTTATCTCGCTTGAGATAG-TTTCACTCGAAACAGAAGA-TTTATCTCACTTGAGATTGTTTTT
*
17503 CTAAAAACAA-A
64 CTTAAAACAAGA
* * * * * ** *
17514 CTTTGTCTCGCTTGAGACAGTTTTTACTCGAAACAAGAA-ATTTTATTTCACTAAAGATTATTTT
1 TTTTATCTCGCTTGAGATAG-TTTCACTCGAAAC-AGAAGA-TTTATCTCACTTGAGATTGTTTT
17578 TCTTAAAACAA-A
63 TCTTAAAACAAGA
* *
17590 TTTCATCTCGCTTGAGAAAGTTTC
1 TTTTATCTCGCTTGAGATAGTTTC
17614 CCTTGAAATA
Statistics
Matches: 538, Mismatches: 64, Indels: 32
0.85 0.10 0.05
Matches are distributed among these distances:
70 22 0.04
71 25 0.05
72 5 0.01
73 9 0.02
74 232 0.43
75 181 0.34
76 64 0.12
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (75 bp):
TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTATCTCACTTGAGATTGTTTTTCT
TAAAACAAGA
Found at i:18085 original size:91 final size:91
Alignment explanation
Indices: 17923--18159 Score: 262
Period size: 91 Copynumber: 2.6 Consensus size: 91
17913 CTTTGCTCTT
* ** * * *
17923 TTCACGACATTTCGAATTAGTGTCGCCTCACAT-GAGGGACTAAAATTTCCAATAGAGAATTCAT
1 TTCACG-CATTTTGAATTAGTAACGCCTCAC-TCGAGGGACCAAAATTTCTAGTAGAGAATTCAT
*
17987 CAGAAGAACTTGTTCAACCATAGCTCAA
64 CAGAAGAACTTATTCAACCATAGCTCAA
* *
18015 TTCACGCATTTTGAATTAGCAACGCCTCACTCGAGGGACCAAAATTTCTAGTAGAGAATTCATGA
1 TTCACGCATTTTGAATTAGTAACGCCTCACTCGAGGGACCAAAATTTCTAGTAGAGAATTCATCA
* * *
18080 GAAGAACTTATTCAACCTTGGCTCGA
66 GAAGAACTTATTCAACCATAGCTCAA
* * * * * *
18106 TTCATG-ATATTTCAAATCAGTAATGCCTCATTCGAGGGACCAATATTTCTAGTA
1 TTCACGCAT-TTT-GAATTAGTAACGCCTCACTCGAGGGACCAAAATTTCTAGTA
18160 AAAAGATCAT
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
90 3 0.02
91 79 0.64
92 41 0.33
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (91 bp):
TTCACGCATTTTGAATTAGTAACGCCTCACTCGAGGGACCAAAATTTCTAGTAGAGAATTCATCA
GAAGAACTTATTCAACCATAGCTCAA
Found at i:19389 original size:22 final size:21
Alignment explanation
Indices: 19347--19402 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
19337 TCTAATTTAT
19347 TTTATTTTAATTTAGTCACTG
1 TTTATTTTAATTTAGTCACTG
*
19368 TTTATTTCTGATTTAG-CTACTG
1 TTTATTT-TAATTTAGTC-ACTG
19390 -TTATTTTAATTTA
1 TTTATTTTAATTTA
19403 TGCAATTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 6 0.19
21 14 0.45
22 11 0.35
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.59
Consensus pattern (21 bp):
TTTATTTTAATTTAGTCACTG
Found at i:36801 original size:38 final size:38
Alignment explanation
Indices: 36759--37479 Score: 682
Period size: 38 Copynumber: 19.0 Consensus size: 38
36749 CAATCCAATC
* * ** *
36759 TTATTCTCGACTCCCTCACGAAGAGGAGTCACTCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * *
36797 TTATTATTGACTTCCTCATGAAGAGAAATCAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* *** * *
36835 TTATTCCTGACTTCCTCACAAAGATGATTCAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * *
36873 TTATTCTTGACTTCCTCATGAAAAGAAGTCAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* *
36911 TTATTCCTT-ACTCCCTCGCGAAGAGGAGTCAATCTTTG
1 TTATT-CTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * * *
36949 TTATTCTTGACTTCTTCGTAAAGAGAAGTCAATTTTTA
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
** * * * *
36987 TTATTAC-CAACTCCCTTGTGAAGAGGAGTCAGTCTTTT
1 TTATT-CTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * *
37025 TTATCCTTGACTTCCTCGTGAAAAGAATTCAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * *
37063 TTATTCCTGACTCCCTCATGAAGAGGAGTCAATCTTAG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * * *
37101 TTATTGTTGACTTCATCATGAAGAGAAGTAAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * * *
37139 TTATTCCTGACTCCCTCGCG-AGTTA-GAGTCATTTTTTG
1 TTATTCTTGACTTCCTCGTGAAG--AGGAGTCAATCTTTG
* * *
37177 TTATCCTTGACTTCCTTGTGAAGAGAAGTCAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * **
37215 TTATTCCTGACTCCCTTGCAAAGAGGAGTCAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * *
37253 TTATTCTTGACTTCCTCGTGAAGAGAAATCAATCTTTA
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * *
37291 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* * * * *
37329 TTATTATTTACTTCCTCGTGAAGAGAATTCAATCTCTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* *
37367 TTATTCTTGACTCCCTCGTGAAGAGGTGTCAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
* *
37405 TTATTCTTGACTTCCACATGAAGAGGAGTCAATCTTTG
1 TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
37443 TTATAT-TTGACTTCCTCGTGCGAAGA--AGTCAATCTTT
1 TTAT-TCTTGACTTCCTCGT--GAAGAGGAGTCAATCTTT
37480 TAGTTTTGTC
Statistics
Matches: 545, Mismatches: 127, Indels: 22
0.79 0.18 0.03
Matches are distributed among these distances:
37 7 0.01
38 525 0.96
39 8 0.01
40 5 0.01
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (38 bp):
TTATTCTTGACTTCCTCGTGAAGAGGAGTCAATCTTTG
Found at i:36852 original size:76 final size:76
Alignment explanation
Indices: 36759--37479 Score: 862
Period size: 76 Copynumber: 9.5 Consensus size: 76
36749 CAATCCAATC
* * * *
36759 TTATT-CTCGACTCCCTCACGAAGAGGAGTCACTCTTTGTTATTATTGACTTCCTCATGAAGAGA
1 TTATTCCT-GACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGA
*
36823 AATCAATCTTTG
65 AGTCAATCTTTG
* * * * * * *
36835 TTATTCCTGACTTCCTCACAAAGATGATTCAATCTTTGTTATTCTTGACTTCCTCATGAAAAGAA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
36900 GTCAATCTTTG
66 GTCAATCTTTG
* * *
36911 TTATTCCTTACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCTTCGTAAAGAGAA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
* *
36976 GTCAATTTTTA
66 GTCAATCTTTG
* * * * * * *
36987 TTATTACC-AACTCCCTTGTGAAGAGGAGTCAGTCTTTTTTATCCTTGACTTCCTCGTGAAAAGA
1 TTATT-CCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGA
*
37051 ATTCAATCTTTG
65 AGTCAATCTTTG
** * * * *
37063 TTATTCCTGACTCCCTCATGAAGAGGAGTCAATCTTAGTTATTGTTGACTTCATCATGAAGAGAA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
*
37128 GTAAATCTTTG
66 GTCAATCTTTG
* * * *
37139 TTATTCCTGACTCCCTCGCG-AGTTA-GAGTCATTTTTTGTTATCCTTGACTTCCTTGTGAAGAG
1 TTATTCCTGACTCCCTCGCGAAG--AGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAG
37202 AAGTCAATCTTTG
64 AAGTCAATCTTTG
* *
37215 TTATTCCTGACTCCCTTGCAAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
* *
37280 ATCAATCTTTA
66 GTCAATCTTTG
* *
37291 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTATTTACTTCCTCGTGAAGAGAA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
* *
37356 TTCAATCTCTG
66 GTCAATCTTTG
* * * * * *
37367 TTATTCTTGACTCCCTCGTGAAGAGGTGTCAATCTTTGTTATTCTTGACTTCCACATGAAGAGGA
1 TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
37432 GTCAATCTTTG
66 GTCAATCTTTG
* *
37443 TTATAT-TTGACTTCCTCGTGCGAAGA--AGTCAATCTTT
1 TTAT-TCCTGACTCCCTC--GCGAAGAGGAGTCAATCTTT
37480 TAGTTTTGTC
Statistics
Matches: 551, Mismatches: 84, Indels: 20
0.84 0.13 0.03
Matches are distributed among these distances:
75 5 0.01
76 532 0.97
77 8 0.01
78 6 0.01
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (76 bp):
TTATTCCTGACTCCCTCGCGAAGAGGAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAA
GTCAATCTTTG
Found at i:37672 original size:45 final size:46
Alignment explanation
Indices: 37469--37705 Score: 175
Period size: 45 Copynumber: 5.3 Consensus size: 46
37459 CGTGCGAAGA
** * *
37469 AGTCAATCTTTTAGT-TTTGTCCTT-CTTGACTTTCTCGCGAATAGA
1 AGTCAATCTTTTAGTGTTT-TCCTTCCTTGACTTTCTCATGAAGAGG
* * ** *
37514 ATTCAATCGTTCGGTGTTTT-CTTCCTAGACTTTCTCATGAAGAGG
1 AGTCAATCTTTTAGTGTTTTCCTTCCTTGACTTTCTCATGAAGAGG
* * * * **
37559 AGTCAATATTTTAGTGGTGT-CTTCCTTGACTTTCTCGTGAAGAAT
1 AGTCAATCTTTTAGTGTTTTCCTTCCTTGACTTTCTCATGAAGAGG
* * * *
37604 AGTCAATATTTTAGTGTTGTCCTT-CTTGATTTTCTC-TCAAAGAGG
1 AGTCAATCTTTTAGTGTTTTCCTTCCTTGACTTTCTCAT-GAAGAGG
* * * * *
37649 AGTCAATCTTTTGGTGTTTTCCTT-TTTCGACTTTGTCGTGGAGAGG
1 AGTCAATCTTTTAGTGTTTTCCTTCCTT-GACTTTCTCATGAAGAGG
37695 AGTCAA-CTTTT
1 AGTCAATCTTTT
37706 CAGTAGTATC
Statistics
Matches: 153, Mismatches: 33, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
44 4 0.03
45 124 0.81
46 24 0.16
47 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.19, T:0.43
Consensus pattern (46 bp):
AGTCAATCTTTTAGTGTTTTCCTTCCTTGACTTTCTCATGAAGAGG
Found at i:38678 original size:45 final size:45
Alignment explanation
Indices: 38566--39002 Score: 567
Period size: 45 Copynumber: 9.7 Consensus size: 45
38556 TTCATTAATA
* ** * *
38566 GCATCCATTCATGCTTATAATGTA-CCATTATGCATTTTCAATTATA
1 GCATCCTTTCATGCCAATAATGCACCCA-TATGCA-TTTCAATTATG
* *
38612 GCATCCTTTCATGCTAATAATGCACCCATATGCATTTCAATTGTG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
* * * * * * *
38657 GCATCATTTCTTGTCACTAATGCACCCATATACATTTTAATTATT
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
38702 GCATCCTTTCATGCCAAT-ATGCACCCATATGCATTTCAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
* * * * *
38746 GCATCATTT-ATTGTCAATAATACACCCATATGCATTTTAATTATA
1 GCATCCTTTCA-TGCCAATAATGCACCCATATGCATTTCAATTATG
* * *
38791 GCATCCTTTCATGCCAATAATTCACCCATATTCATTTTTAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCA-TTTCAATTATG
*
38837 GCATCATTTCATGCCAATAATGCA-CCATATGCATTTCAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
38881 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
* *
38926 GCATCTTTTCATGCCAATAATGCACCCATATGAATTTCAATTATG
1 GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
* *
38971 TCATCTTTTCATGCCAATAATGCACCCATATG
1 GCATCCTTTCATGCCAATAATGCACCCATATG
39003 TATTATTTAA
Statistics
Matches: 346, Mismatches: 39, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
43 1 0.00
44 70 0.20
45 212 0.61
46 60 0.17
47 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (45 bp):
GCATCCTTTCATGCCAATAATGCACCCATATGCATTTCAATTATG
Found at i:49946 original size:17 final size:17
Alignment explanation
Indices: 49924--49956 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
49914 TAAAAATATA
49924 TTTAAA-TAATAATAAAT
1 TTTAAAGTAA-AATAAAT
49941 TTTAAAGTAAAATAAA
1 TTTAAAGTAAAATAAA
49957 GAAAAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TTTAAAGTAAAATAAAT
Found at i:52071 original size:20 final size:19
Alignment explanation
Indices: 52038--52079 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
52028 AAGTTCTCTC
52038 TTTTCTTTTCATTTCAAGT
1 TTTTCTTTTCATTTCAAGT
* *
52057 TTTTCGTTTTTATTTTAAGT
1 TTTTC-TTTTCATTTCAAGT
52077 TTT
1 TTT
52080 ATTTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.14, C:0.10, G:0.07, T:0.69
Consensus pattern (19 bp):
TTTTCTTTTCATTTCAAGT
Done.