Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004069.1 Hibiscus syriacus cultivar Beakdansim tig00008910_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: 56427
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2596 original size:136 final size:137
Alignment explanation
Indices: 2356--2657 Score: 340
Period size: 136 Copynumber: 2.2 Consensus size: 137
2346 CTTTGCAGCA
* * **
2356 TTAAGAGTAGGCAGGGGGACAGAGTTCATGGCTAGCGCTTCTAGAGGGGAGTAAGCAAGATGACC
1 TTAAGAGTAGGCA-GGGGACAGAGTTCATAGCGAGCGCTTCTAGAGGAAAGTAAGCAAGATGACC
* ** * * * * *
2421 TAATCTTATGATGAACGCTCTAACGTATGTAATAGGCAGGGTGTT-TA-TGTTGCACGTCGAGCG
65 TAATCTTAAGACCAACACTCTAACGTATGGAATAAGCAGGGTGTTCTATTGTTCCACGCCGAGCG
2484 CTTCAACG
130 CTTCAACG
* *
2492 TTAAGAGTAGGCAGTGGGACAGAGTTCATATCGAGCGCTTCTAGAGGAAAGTAGGCAAGATGACC
1 TTAAGAGTAGGCAG-GGGACAGAGTTCATAGCGAGCGCTTCTAGAGGAAAGTAAGCAAGATGACC
** * *
2557 TGGTCTTAAG-CCAAGCACTCTAACGTATGGACTAAGCAGGGTGTTCCTATTTTTTCCACGCCGA
65 TAATCTTAAGACCAA-CACTCTAACGTATGGAATAAGCAGGGTGTT-CTA-TTGTTCCACGCCGA
2621 GCGCTTCAACG
127 GCGCTTCAACG
**
2632 TTGGGAGTAGGCAAGGGAGACAGAGT
1 TTAAGAGTAGGC-AGGG-GACAGAGT
2658 CATGCCGAGT
Statistics
Matches: 138, Mismatches: 20, Indels: 11
0.82 0.12 0.07
Matches are distributed among these distances:
135 3 0.02
136 90 0.65
138 2 0.01
140 33 0.24
141 10 0.07
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (137 bp):
TTAAGAGTAGGCAGGGGACAGAGTTCATAGCGAGCGCTTCTAGAGGAAAGTAAGCAAGATGACCT
AATCTTAAGACCAACACTCTAACGTATGGAATAAGCAGGGTGTTCTATTGTTCCACGCCGAGCGC
TTCAACG
Found at i:8250 original size:29 final size:30
Alignment explanation
Indices: 8216--8275 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 30
8206 AATATATATT
*
8216 TATACAT-ATTTTATAATAATTATTTTAAA
1 TATACATAATATTATAATAATTATTTTAAA
8245 TATACATAAAATATTATAATAATTATTTTAA
1 TATACAT--AATATTATAATAATTATTTTAA
8276 TACAGTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 7 0.26
32 20 0.74
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
TATACATAATATTATAATAATTATTTTAAA
Found at i:8902 original size:79 final size:79
Alignment explanation
Indices: 8807--8963 Score: 314
Period size: 79 Copynumber: 2.0 Consensus size: 79
8797 CAATAAACCC
8807 ATATTCCGACCACCATGCCGGCCACCACGTCAATCATCACGTCGGCCGCCCTTTTCACCACAGTA
1 ATATTCCGACCACCATGCCGGCCACCACGTCAATCATCACGTCGGCCGCCCTTTTCACCACAGTA
8872 TGTAATGAATAAAT
66 TGTAATGAATAAAT
8886 ATATTCCGACCACCATGCCGGCCACCACGTCAATCATCACGTCGGCCGCCCTTTTCACCACAGTA
1 ATATTCCGACCACCATGCCGGCCACCACGTCAATCATCACGTCGGCCGCCCTTTTCACCACAGTA
8951 TGTAATGAATAAA
66 TGTAATGAATAAA
8964 AGATATTTAG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.28, C:0.34, G:0.15, T:0.22
Consensus pattern (79 bp):
ATATTCCGACCACCATGCCGGCCACCACGTCAATCATCACGTCGGCCGCCCTTTTCACCACAGTA
TGTAATGAATAAAT
Found at i:22605 original size:18 final size:17
Alignment explanation
Indices: 22561--22612 Score: 54
Period size: 18 Copynumber: 3.1 Consensus size: 17
22551 TCATTACACA
22561 AATTTGATTAAA-TT-T
1 AATTTGATTAAACTTAT
* *
22576 AAATTAATTAAACTATAT
1 AATTTGATTAAACT-TAT
22594 AATTTGATTAAACTCTAT
1 AATTTGATTAAACT-TAT
22612 A
1 A
22613 GGAAGCGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 10 0.34
16 1 0.03
17 1 0.03
18 17 0.59
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (17 bp):
AATTTGATTAAACTTAT
Found at i:26294 original size:32 final size:32
Alignment explanation
Indices: 26245--26348 Score: 117
Period size: 32 Copynumber: 3.3 Consensus size: 32
26235 CTGCATGGCA
*
26245 CATGCACGTCCTCAACACCCCAACACAGGTCGC
1 CATGCAC-TCCCCAACACCCCAACACAGGTCGC
* *
26278 CATGCATTCCCCAACACCCCAACACAGGTTGC
1 CATGCACTCCCCAACACCCCAACACAGGTCGC
* *
26310 CATGCACT-CCCAGCGA--CCTACA-AGGTCGC
1 CATGCACTCCCCAAC-ACCCCAACACAGGTCGC
26339 CATGCACTCC
1 CATGCACTCC
26349 TAGCGACCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
29 14 0.23
30 6 0.10
31 5 0.08
32 31 0.50
33 6 0.10
ACGTcount: A:0.26, C:0.44, G:0.15, T:0.14
Consensus pattern (32 bp):
CATGCACTCCCCAACACCCCAACACAGGTCGC
Found at i:26340 original size:29 final size:29
Alignment explanation
Indices: 26303--26385 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 29
26293 ACCCCAACAC
*
26303 AGGTTGCCATGCACTCCCAGCGACCTACA
1 AGGTCGCCATGCACTCCCAGCGACCTACA
* ***
26332 AGGTCGCCATGCACTCCTAGCGACCTTGT
1 AGGTCGCCATGCACTCCCAGCGACCTACA
* * *
26361 AGGTCGCCAAGCAGTCCCGGCGACC
1 AGGTCGCCATGCACTCCCAGCGACC
26386 AAGCTTTCCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.20, C:0.37, G:0.25, T:0.17
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCAGCGACCTACA
Found at i:26671 original size:26 final size:26
Alignment explanation
Indices: 26638--26687 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
26628 ACATAAAAGA
*
26638 AAGAAAGGGAGAAGAGATTGCAGCAG
1 AAGAAAGGGAGAAGAAATTGCAGCAG
26664 AAGAAAGGGAGAAGAAATTGCAGC
1 AAGAAAGGGAGAAGAAATTGCAGC
26688 CCAGAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.36, T:0.08
Consensus pattern (26 bp):
AAGAAAGGGAGAAGAAATTGCAGCAG
Found at i:26717 original size:13 final size:13
Alignment explanation
Indices: 26694--26740 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
26684 CAGCCCAGAA
26694 AGAAA-GAAAGGG
1 AGAAAGGAAAGGG
*
26706 AGAAAGGAAAGGA
1 AGAAAGGAAAGGG
*
26719 AGAAGAAGAAAGGG
1 AGAA-AGGAAAGGG
26733 AGATAAGG
1 AGA-AAGG
26741 CTCTTGTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 5 0.18
13 10 0.36
14 12 0.43
15 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.02
Consensus pattern (13 bp):
AGAAAGGAAAGGG
Found at i:26867 original size:22 final size:21
Alignment explanation
Indices: 26842--26882 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
26832 GTTAATTAGT
*
26842 TTGTTAATTTAGGGTTATATGA
1 TTGTTAATTTA-AGTTATATGA
*
26864 TTGTTAGTTTAAGTTATAT
1 TTGTTAATTTAAGTTATAT
26883 TATACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (21 bp):
TTGTTAATTTAAGTTATATGA
Found at i:27215 original size:16 final size:16
Alignment explanation
Indices: 27183--27229 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
27173 TTTAAAAAGT
*
27183 TTAGTTTGTTAGT-TTA
1 TTAGTTTATTA-TATTA
27199 TTAGTTTATTATATTA
1 TTAGTTTATTATATTA
*
27215 TAAG-TTATTATATTA
1 TTAGTTTATTATATTA
27230 AAGTTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.60
Consensus pattern (16 bp):
TTAGTTTATTATATTA
Found at i:27224 original size:15 final size:14
Alignment explanation
Indices: 27204--27234 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
27194 GTTTATTAGT
27204 TTATTATATTATAAG
1 TTATTATATTA-AAG
27219 TTATTATATTAAAG
1 TTATTATATTAAAG
27233 TT
1 TT
27235 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:29464 original size:14 final size:14
Alignment explanation
Indices: 29445--29492 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
29435 TTCAAGTCGT
29445 AAATCATTACTATC
1 AAATCATTACTATC
29459 AAATCATTAC--T-
1 AAATCATTACTATC
*
29470 AAATCATTAATATC
1 AAATCATTACTATC
29484 AAATCATTA
1 AAATCATTA
29493 AATATTAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 9 0.30
12 1 0.03
13 1 0.03
14 19 0.63
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:29472 original size:25 final size:25
Alignment explanation
Indices: 29444--29492 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
29434 GTTCAAGTCG
*
29444 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATCATTAC
29469 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
29493 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAC
Found at i:29598 original size:21 final size:21
Alignment explanation
Indices: 29574--29778 Score: 64
Period size: 21 Copynumber: 10.2 Consensus size: 21
29564 TAATTTTATT
*
29574 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* *
29595 ATTAAT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* * *
29616 ATTAATAATAATT--T-CATT
1 ATTAATAATCATTACTAAATC
*
29634 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* * *
29655 ATT-ATTATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* *
29676 ATTAATAA-CAATT--T-CATT
1 ATTAATAATC-ATTACTAAATC
*
29694 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
* *
29715 ATTAAT-ATCAAATCATTAAAT-
1 ATTAATAATC--ATTACTAAATC
* * *
29736 ATTAATAATAATT--T-CATT
1 ATTAATAATCATTACTAAATC
*
29754 ATTACTAATCATTACTAAATC
1 ATTAATAATCATTACTAAATC
29775 ATTA
1 ATTA
29779 TTATAATTTC
Statistics
Matches: 132, Mismatches: 30, Indels: 44
0.64 0.15 0.21
Matches are distributed among these distances:
17 6 0.05
18 35 0.27
19 1 0.01
20 20 0.15
21 39 0.30
22 31 0.23
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAATAATCATTACTAAATC
Found at i:29598 original size:120 final size:119
Alignment explanation
Indices: 29460--30112 Score: 705
Period size: 120 Copynumber: 5.6 Consensus size: 119
29450 ATTACTATCA
*
29460 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATTA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* *
29525 TTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
66 TTACTAAATCATTAATAT-AAATCATTAAAAATTAATAATAATTTCATTATTACT
29580 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* * *
29645 TTACTAAATCATTATTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
66 TTACTAAATCATTAATAT-AAATCATTAAAAATTAATAATAATTTCATTATTACT
29700 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* * ** ** * *
29765 TTACTAAATCATTATTATAATTTCATTACGTAACGAA-AAT-ATGGTTAATTGA--ACCA
66 TTACTAAATCATTAATATAA-ATCATTA-AAAATTAATAATAAT--TTCATT-ATTA-CT
* * * * * * * *
29821 AAT-ATT-GT---TCATT-GT-TTAAGTC-GTAAATCATTACT-ATCAA-ATCATTACTA--AAT
1 AATCATTACTAAATCATTAATATCAAATCATTAAAT-ATTAATAAT-AATTTCATTATTACTAAT
* * * *
29874 CA-T--T-AAT-ATCAA-AT--A--ATTAAATATTAATAATAAATT-ATTATTATT
64 CATTACTAAATCATTAATATAAATCATTAAAAATTAATAATAATTTCATTATTACT
* *
29919 AATCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
* * *
29983 TTACTAAATCATTAATTTTAAATCATTAAATATTAATAATAATTTCATTATTATT
66 TTACTAAATCATTAA-TATAAATCATTAAAAATTAATAATAATTTCATTATTACT
* * *
30038 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATTA
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
30103 TTACTAAATC
66 TTACTAAATC
30113 TTATAAATAC
Statistics
Matches: 449, Mismatches: 48, Indels: 72
0.79 0.08 0.13
Matches are distributed among these distances:
97 1 0.00
98 6 0.01
99 9 0.02
100 8 0.02
101 1 0.00
102 5 0.01
103 1 0.00
104 12 0.03
105 16 0.04
106 3 0.01
107 8 0.02
108 2 0.00
110 2 0.00
111 8 0.02
112 4 0.01
113 15 0.03
114 13 0.03
115 1 0.00
116 6 0.01
118 20 0.04
119 24 0.05
120 271 0.60
121 12 0.03
122 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (119 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCA
TTACTAAATCATTAATATAAATCATTAAAAATTAATAATAATTTCATTATTACT
Found at i:29792 original size:60 final size:60
Alignment explanation
Indices: 29460--29778 Score: 584
Period size: 60 Copynumber: 5.3 Consensus size: 60
29450 ATTACTATCA
29460 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* * * *
29520 AATTATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTTATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
29580 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
29640 AATCATTACTAAATCATTATTATCAAATCATTAAATATTAATAACAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
29700 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
29760 AATCATTACTAAATCATTA
1 AATCATTACTAAATCATTA
29779 TTATAATTTC
Statistics
Matches: 247, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 247 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (60 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:29864 original size:14 final size:14
Alignment explanation
Indices: 29845--29892 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
29835 TTTAAGTCGT
29845 AAATCATTACTATC
1 AAATCATTACTATC
29859 AAATCATTAC--T-
1 AAATCATTACTATC
*
29870 AAATCATTAATATC
1 AAATCATTACTATC
*
29884 AAATAATTA
1 AAATCATTA
29893 AATATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
11 9 0.31
12 1 0.03
13 1 0.03
14 18 0.62
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (14 bp):
AAATCATTACTATC
Found at i:29872 original size:25 final size:25
Alignment explanation
Indices: 29844--29892 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
29834 GTTTAAGTCG
* *
29844 TAAATCATTACTATCAAATCATTAC
1 TAAATCATTAATATCAAATAATTAC
29869 TAAATCATTAATATCAAATAATTA
1 TAAATCATTAATATCAAATAATTA
29893 AATATTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (25 bp):
TAAATCATTAATATCAAATAATTAC
Found at i:30018 original size:60 final size:60
Alignment explanation
Indices: 29860--30112 Score: 393
Period size: 60 Copynumber: 4.2 Consensus size: 60
29850 ATTACTATCA
* * *
29860 AATCATTACTAAATCATTAATATCAAATAATTAAATATTAATAATAAATT-ATTATTATT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
29919 AATCATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* * *
29978 AATCATTACTAAATCATTAATTTTAAATCATTAAATATTAATAATAATTTCATTATTATT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
* *
30038 AATCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACT
1 AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
*
30098 AATTATTACTAAATC
1 AATCATTACTAAATC
30113 TTATAAATAC
Statistics
Matches: 176, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
58 35 0.20
59 28 0.16
60 113 0.64
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (60 bp):
AATCATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACT
Found at i:30127 original size:10 final size:10
Alignment explanation
Indices: 30114--30147 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
30104 TACTAAATCT
30114 TATAAATACA
1 TATAAATACA
*
30124 TATAAATTCA
1 TATAAATACA
*
30134 TAGAAATACA
1 TATAAATACA
30144 TATA
1 TATA
30148 TCATTACTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (10 bp):
TATAAATACA
Found at i:31004 original size:15 final size:16
Alignment explanation
Indices: 30955--31013 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
30945 ATAATATAAA
*
30955 TTAAACAAAATATTTT
1 TTAAACACAATATTTT
* *
30971 TAAAACAACACTAAATATTT
1 TTAAAC-ACA--ATAT-TTT
30991 TTAAACACAATATTTT
1 TTAAACACAATATTTT
31007 TTAAACA
1 TTAAACA
31014 GAAATTATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 15 0.44
17 5 0.15
19 6 0.18
20 8 0.24
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAACACAATATTTT
Found at i:31338 original size:28 final size:30
Alignment explanation
Indices: 31289--31350 Score: 101
Period size: 28 Copynumber: 2.1 Consensus size: 30
31279 ATTTTTAATA
31289 TAATATAATATATATCATAAACTAACAAAC
1 TAATATAATATATATCATAAACTAACAAAC
*
31319 TAATATAATATA-A-CTTAAACTAACAAAC
1 TAATATAATATATATCATAAACTAACAAAC
31347 TAAT
1 TAAT
31351 TAACTAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 18 0.58
29 1 0.03
30 12 0.39
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATATCATAAACTAACAAAC
Found at i:31805 original size:23 final size:23
Alignment explanation
Indices: 31775--31818 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
31765 GCTTGGCTAC
31775 AATCTCCCAGCTATGGATGCAGG
1 AATCTCCCAGCTATGGATGCAGG
31798 AATCTCCCAGCTATGGATGCA
1 AATCTCCCAGCTATGGATGCA
31819 ACCCATGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (23 bp):
AATCTCCCAGCTATGGATGCAGG
Found at i:31867 original size:22 final size:22
Alignment explanation
Indices: 31837--31896 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
31827 ACGAGGGAGT
* *
31837 AGGGTTAAGTTTGGTCGTCAGC
1 AGGGATAAGTTTGGTCGCCAGC
*
31859 AGGGATAAGTTTGGTCGCCAGT
1 AGGGATAAGTTTGGTCGCCAGC
31881 AGGGATAAGTTTGGTC
1 AGGGATAAGTTTGGTC
31897 CTAAGCTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.22, C:0.12, G:0.37, T:0.30
Consensus pattern (22 bp):
AGGGATAAGTTTGGTCGCCAGC
Found at i:31938 original size:29 final size:29
Alignment explanation
Indices: 31905--32016 Score: 170
Period size: 29 Copynumber: 3.9 Consensus size: 29
31895 TCCTAAGCTT
* * *
31905 GGTCGCCGGGACTGCTTGGCGACCTACAA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
***
31934 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
31963 GGTCGCTGGGAGTGCATGGCGACCTACAA
1 GGTCGCTGGGAGTGCATGGCGACCTACAA
31992 GGTCGCTGGGAGTGCATGGCGACCT
1 GGTCGCTGGGAGTGCATGGCGACCT
32017 GTGTTGGGGT
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 74 1.00
ACGTcount: A:0.16, C:0.25, G:0.39, T:0.20
Consensus pattern (29 bp):
GGTCGCTGGGAGTGCATGGCGACCTACAA
Found at i:31984 original size:58 final size:58
Alignment explanation
Indices: 31905--32016 Score: 197
Period size: 58 Copynumber: 1.9 Consensus size: 58
31895 TCCTAAGCTT
*
31905 GGTCGCCGGGACTGCTTGGCGACCTACAAGGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCCGGGACTGCATGGCGACCTACAAGGTCGCTGGGAGTGCATGGCGACCTTGTA
* *
31963 GGTCGCTGGGAGTGCATGGCGACCTACAAGGTCGCTGGGAGTGCATGGCGACCT
1 GGTCGCCGGGACTGCATGGCGACCTACAAGGTCGCTGGGAGTGCATGGCGACCT
32017 GTGTTGGGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.16, C:0.25, G:0.39, T:0.20
Consensus pattern (58 bp):
GGTCGCCGGGACTGCATGGCGACCTACAAGGTCGCTGGGAGTGCATGGCGACCTTGTA
Found at i:32045 original size:33 final size:33
Alignment explanation
Indices: 31999--32077 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
31989 CAAGGTCGCT
31999 GGGA-GTGCATGGCGACCTGTGTTGGGGTGTTG
1 GGGACGTGCATGGCGACCTGTGTTGGGGTGTTG
*
32031 GGGACGTGCATGGCGACCTGTGTTGGGGTTTTG
1 GGGACGTGCATGGCGACCTGTGTTGGGGTGTTG
32064 GGGACGTGCATGGC
1 GGGACGTGCATGGC
32078 ACATGCAGAC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 4 0.09
33 41 0.91
ACGTcount: A:0.10, C:0.15, G:0.48, T:0.27
Consensus pattern (33 bp):
GGGACGTGCATGGCGACCTGTGTTGGGGTGTTG
Found at i:36428 original size:14 final size:14
Alignment explanation
Indices: 36409--36436 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
36399 GTAAAATATG
36409 GTATGAACAGTACC
1 GTATGAACAGTACC
36423 GTATGAACAGTACC
1 GTATGAACAGTACC
36437 ATAAACAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (14 bp):
GTATGAACAGTACC
Found at i:37117 original size:30 final size:30
Alignment explanation
Indices: 37082--37198 Score: 139
Period size: 32 Copynumber: 3.8 Consensus size: 30
37072 GAAGGACCTA
* *
37082 TCCATATGTTCC-TAAGAACATAGGTAACTG
1 TCCATATGTCCCGAAAG-ACATAGGTAACTG
37112 TCCATATGTCCCGAAAGACATAGGTAATCT-
1 TCCATATGTCCCGAAAGACATAGGTAA-CTG
*
37142 TACCCATATGTCCCGAAAGACATAGGTAATCCTA
1 T--CCATATGTCCCGAAAGACATAGGTAA--CTG
37176 TCCATATGTCCCGAAAGACATAG
1 TCCATATGTCCCGAAAGACATAG
37199 ATAATCCTCG
Statistics
Matches: 78, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
30 22 0.28
31 5 0.06
32 48 0.62
33 2 0.03
34 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCCGAAAGACATAGGTAACTG
Found at i:37154 original size:32 final size:32
Alignment explanation
Indices: 37113--37206 Score: 161
Period size: 32 Copynumber: 2.9 Consensus size: 32
37103 AGGTAACTGT
*
37113 CCATATGTCCCGAAAGACATAGGTAATCTTAC
1 CCATATGTCCCGAAAGACATAGGTAATCCTAC
*
37145 CCATATGTCCCGAAAGACATAGGTAATCCTAT
1 CCATATGTCCCGAAAGACATAGGTAATCCTAC
*
37177 CCATATGTCCCGAAAGACATAGATAATCCT
1 CCATATGTCCCGAAAGACATAGGTAATCCT
37207 CGACTCTTAG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (32 bp):
CCATATGTCCCGAAAGACATAGGTAATCCTAC
Found at i:39946 original size:24 final size:24
Alignment explanation
Indices: 39913--39968 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
39903 CTATTCTTTC
*
39913 GCTTCGATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
39937 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
39961 GCTTCAAT
1 GCTTCAAT
39969 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:47514 original size:87 final size:87
Alignment explanation
Indices: 47368--47530 Score: 272
Period size: 87 Copynumber: 1.9 Consensus size: 87
47358 TATGTTATAT
* * *
47368 TATTTAACCGAAAATATTATCAAGTACAATAATATATTAGGTAACGCTTATATAATGTAATATAT
1 TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAC
47433 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
* * *
47455 TATTTAACCGGAAATATTATTAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGAC
1 TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAC
47520 AGCGCTTATAT
66 AGCGCTTATAT
47531 TGACATATTT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 70 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.34
Consensus pattern (87 bp):
TATTTAACCGAAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAC
AGCGCTTATATAATAAAATAGG
Found at i:47973 original size:182 final size:182
Alignment explanation
Indices: 47666--48549 Score: 1508
Period size: 182 Copynumber: 4.9 Consensus size: 182
47656 TGCGTTCACC
** *
47666 TTTTGTCATTTATAGACCGGTTTTATCATATTTTTACATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
47731 TTTATAAAGTATCGACACTTTATTGGCACTATAACTTCTTCTCTTATT-AATTCCAAAAGTGTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
*
47795 ATACTTATAATAAATTATCGACACTTTCAACATATCCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* * *
47848 TTTTGTCATTTCGAGACCGATTTTTTCATATTTTTACCTGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATT
47913 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
* *
47978 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGTGCTTTACCTA
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* * * *
48030 TTTTGTCATTTCGAGACCGGTTTTGTCATATTATTACCTGTTAGATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATT
48095 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
48160 TACTTATAATAAATTATCGACACTTTCAACATAACCAGTAGCGCTTTACCTG
131 TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
* * *
48212 TTTTATCATTTCGAGACCGGTTTTATCATATTTTTTCATGTTATATTATTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATT
* *
48277 TTTATAAAGTATTGACACGTTATTGGCGCTATAACTTCTTCTCTTATT-AATTCCAAAA--GTCG
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTT-TTAAATTCCAAAAGTGTCG
48339 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
130 ATACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
*
48392 TTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATACATT
1 TTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATT
*
48457 TTTATAAAGTATCGACACTTTATTGGCGCTATAAC-TCTTCTCTTTTAAATTCCAAAAGTGTTGA
66 TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
*
48521 TACGTATAATAAATTATCGACACTTTCAA
131 TACTTATAATAAATTATCGACACTTTCAA
48550 TTTTTTTAAT
Statistics
Matches: 662, Mismatches: 35, Indels: 11
0.94 0.05 0.02
Matches are distributed among these distances:
178 2 0.00
179 19 0.03
180 150 0.23
181 34 0.05
182 455 0.69
183 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (182 bp):
TTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATACATT
TTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAATAAATTATCGACACTTTCAACATAACCGGTAGCGCTTTACCTG
Found at i:50561 original size:184 final size:185
Alignment explanation
Indices: 50212--50561 Score: 605
Period size: 185 Copynumber: 1.9 Consensus size: 185
50202 GTTTTACTTA
*
50212 AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
1 AAAGTATGGACACAATATTAAAAAGTGTCGATATAGATTGTAGACCTATTCTCTCATAAAACCGG
* * *
50277 TATATTTATACCGGTTATATTAAAAAAAATACCTATTACATTATAATTGTGGGTTCCGATGTTTT
66 TATATCTATACCGATTATATTAAAAAAAATACCTATTACATTATAATTATGGGTTCCGATGTTTT
*
50342 TTCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
131 TTCAATCGACACTTTTTGAAAAGGTATCAACACTTTTTTCATCCATTCTGGACAT
*
50397 AAAGTA-GCGACACAATATTAAAAAGTGTCGATATAGATTGTATACCTATTCTCTCATAAAACCG
1 AAAGTATG-GACACAATATTAAAAAGTGTCGATATAGATTGTAGACCTATTCTCTCATAAAACCG
* *
50461 GTATATCTATACCGATTATATT-ACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTT
65 GTATATCTATACCGATTATATTAAAAAAAATACCTATTACATTATAATTATGGGTTCCGATGTTT
50525 TTTCAATCGACACTTTTTGAAAAGGTATCAACACTTT
130 TTTCAATCGACACTTTTTGAAAAGGTATCAACACTTT
50562 ATGCTGATAT
Statistics
Matches: 156, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
184 76 0.49
185 80 0.51
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (185 bp):
AAAGTATGGACACAATATTAAAAAGTGTCGATATAGATTGTAGACCTATTCTCTCATAAAACCGG
TATATCTATACCGATTATATTAAAAAAAATACCTATTACATTATAATTATGGGTTCCGATGTTTT
TTCAATCGACACTTTTTGAAAAGGTATCAACACTTTTTTCATCCATTCTGGACAT
Found at i:51853 original size:3 final size:3
Alignment explanation
Indices: 51845--51901 Score: 78
Period size: 3 Copynumber: 19.0 Consensus size: 3
51835 AATTGTTTGG
* * *
51845 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC GTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
*
51893 ATC TTC ATC
1 ATC ATC ATC
51902 GTCAGCTTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:51902 original size:12 final size:12
Alignment explanation
Indices: 51849--51918 Score: 86
Period size: 12 Copynumber: 5.8 Consensus size: 12
51839 GTTTGGATCA
* *
51849 TCATCATCATCA
1 TCATCGTCATCT
* *
51861 TCATCATCATCA
1 TCATCGTCATCT
51873 TCATCGTCATCT
1 TCATCGTCATCT
51885 TCATCGTCATCT
1 TCATCGTCATCT
*
51897 TCATCGTCAGCT
1 TCATCGTCATCT
*
51909 TCATCTTCAT
1 TCATCGTCAT
51919 TGACCGCTTG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 53 1.00
ACGTcount: A:0.23, C:0.33, G:0.06, T:0.39
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:53771 original size:200 final size:200
Alignment explanation
Indices: 53428--54014 Score: 1113
Period size: 200 Copynumber: 2.9 Consensus size: 200
53418 CGATATTTAA
*
53428 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCTG
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
53493 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
*
53558 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTAT
53623 GGACC
196 GGACC
*
53628 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACATATTCTCTCATAAATCCG
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
* *
53693 ATATACTTATACCAGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
*
53758 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTAT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTAT
53823 GGACC
196 GGACC
53828 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAAT-CG
1 AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
53892 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
66 GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
53957 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
54015 ATTGTAAATT
Statistics
Matches: 377, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
199 122 0.32
200 255 0.68
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (200 bp):
AATAGTATCGACACAAAATTAAAAAGTGTCGATACATATATTACACCTATTCTCTCATAAATCCG
GTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTC
TGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTAT
GGACC
Found at i:54273 original size:19 final size:19
Alignment explanation
Indices: 54249--54297 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
54239 TTACATTCAC
54249 ATACAAAATTATAAATCGT-
1 ATACAAAATTATAAATC-TA
54268 ATACAAAATTATAAATCTA
1 ATACAAAATTATAAATCTA
54287 ATACAAAATTA
1 ATACAAAATTA
54298 ACCTTACATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 1 0.03
19 28 0.97
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCTA
Found at i:55867 original size:15 final size:15
Alignment explanation
Indices: 55847--55899 Score: 65
Period size: 15 Copynumber: 3.5 Consensus size: 15
55837 TCCTCCTCAT
55847 TTCTTCCATCTCTTC
1 TTCTTCCATCTCTTC
55862 TTCTT-CATCCTCCCTT-
1 TTCTTCCAT-CT--CTTC
55878 TTCTTCCATCTCTTC
1 TTCTTCCATCTCTTC
55893 TTCTTCC
1 TTCTTCC
55900 TCCTCCCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 6 0.18
15 14 0.42
16 7 0.21
17 6 0.18
ACGTcount: A:0.06, C:0.42, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCTTCCATCTCTTC
Found at i:55884 original size:31 final size:32
Alignment explanation
Indices: 55837--55916 Score: 126
Period size: 31 Copynumber: 2.5 Consensus size: 32
55827 TCGACTTCCT
*
55837 TCCTCCTCATTTCTTCCATCTCTTCTTCTTCA
1 TCCTCCTCTTTTCTTCCATCTCTTCTTCTTCA
*
55869 TCCTCC-CTTTTCTTCCATCTCTTCTTCTTCC
1 TCCTCCTCTTTTCTTCCATCTCTTCTTCTTCA
55900 TCCTCCCTCTTTTCTTC
1 TCCT-CCTCTTTTCTTC
55917 TTCATATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
31 27 0.61
32 8 0.18
33 9 0.20
ACGTcount: A:0.05, C:0.44, G:0.00, T:0.51
Consensus pattern (32 bp):
TCCTCCTCTTTTCTTCCATCTCTTCTTCTTCA
Done.