Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004719.1 Hibiscus syriacus cultivar Beakdansim tig00010645_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: 64168
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:3048 original size:2 final size:2
Alignment explanation
Indices: 3041--3070 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3031 TATATGTGAC
3041 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3071 GAACATATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3361 original size:21 final size:21
Alignment explanation
Indices: 3335--3391 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
3325 GGGTTTCATA
*
3335 GGTCCTTAAGGACAATACAGT
1 GGTCCTTCAGGACAATACAGT
*
3356 GGTCCTTCAGGACAATTCAGT
1 GGTCCTTCAGGACAATACAGT
*
3377 GGTCGTTCAGGACAA
1 GGTCCTTCAGGACAA
3392 ATTTCATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (21 bp):
GGTCCTTCAGGACAATACAGT
Found at i:3699 original size:16 final size:17
Alignment explanation
Indices: 3680--3713 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3670 TAAAATATTA
*
3680 ATGATAA-TAATAGGAT
1 ATGATAAGTAATAAGAT
3696 ATGATAAGTAATAAGAT
1 ATGATAAGTAATAAGAT
3713 A
1 A
3714 ATTATATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.18, T:0.29
Consensus pattern (17 bp):
ATGATAAGTAATAAGAT
Found at i:9127 original size:18 final size:17
Alignment explanation
Indices: 9100--9133 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
9090 TGACAGAAGA
9100 GAAAGAACAAATGATAT
1 GAAAGAACAAATGATAT
9117 GAAATGAACAAATGATA
1 GAAA-GAACAAATGATA
9134 ATGCCCATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.59, C:0.06, G:0.18, T:0.18
Consensus pattern (17 bp):
GAAAGAACAAATGATAT
Found at i:9543 original size:26 final size:24
Alignment explanation
Indices: 9514--9562 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
9504 TACGATGGGT
*
9514 ATAAATGATAAGTATATGATAATATG
1 ATAAAAGAT-AGTA-ATGATAATATG
*
9540 ATAAAAGATATTAATGATAATAT
1 ATAAAAGATAGTAATGATAATAT
9563 AGGATAATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 3 0.14
26 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (24 bp):
ATAAAAGATAGTAATGATAATATG
Found at i:10054 original size:21 final size:21
Alignment explanation
Indices: 10030--10070 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
10020 ATCAGTACTG
10030 TAGCA-GGATATCGATTCCCTA
1 TAGCAGGGA-ATCGATTCCCTA
10051 TAGCAGGGGAATCGATTCCC
1 TAGCA-GGGAATCGATTCCC
10071 CTTTTTGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 10 0.56
23 3 0.17
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
TAGCAGGGAATCGATTCCCTA
Found at i:10870 original size:18 final size:18
Alignment explanation
Indices: 10826--10874 Score: 82
Period size: 17 Copynumber: 2.8 Consensus size: 18
10816 CACATAGAAT
*
10826 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
10844 TGT-CCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
10861 TGTCCCGAAGGACC
1 TGTCCCGAAGGACC
10875 TCCTTAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 16 0.55
18 13 0.45
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:14935 original size:18 final size:18
Alignment explanation
Indices: 14912--14962 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
14902 GCGTAGAATT
*
14912 TGTCCCGTATGACCACTA
1 TGTCCCGAATGACCACTA
14930 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
14948 --TCCCGAAGGACCACT
1 TGTCCCGAATGACCACT
14963 CCTTAAGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 14 0.45
18 17 0.55
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.22
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:30797 original size:21 final size:21
Alignment explanation
Indices: 30758--30798 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
30748 TAAAAAAAAT
* * *
30758 TACTTAAAATATTATTATTTC
1 TACTTAAAAAATCAATATTTC
30779 TACTTAAAAAATCAATATTT
1 TACTTAAAAAATCAATATTT
30799 TTAATATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (21 bp):
TACTTAAAAAATCAATATTTC
Found at i:31454 original size:36 final size:37
Alignment explanation
Indices: 31403--31472 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
31393 ATTAATATAG
*
31403 TATAATTTTTGAAAAT-ACTTTTGAAAA-ATATAATA
1 TATAATTTTTAAAAATGACTTTTGAAAATATATAATA
**
31438 TATAATTTTTTAAAAATGGTTTTTGAAAATATATA
1 TATAA-TTTTTAAAAATGACTTTTGAAAATATATA
31473 TTTATTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 5 0.17
36 10 0.34
37 9 0.31
38 5 0.17
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (37 bp):
TATAATTTTTAAAAATGACTTTTGAAAATATATAATA
Found at i:31539 original size:23 final size:23
Alignment explanation
Indices: 31509--31555 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
31499 TTGAAAAAAT
*
31509 ATATATAATATATAGTTTTGAAA
1 ATATATAATATATAATTTTGAAA
31532 ATATATAATATATAATTTTGAAA
1 ATATATAATATATAATTTTGAAA
31555 A
1 A
31556 CATTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (23 bp):
ATATATAATATATAATTTTGAAA
Found at i:31657 original size:38 final size:38
Alignment explanation
Indices: 31529--31667 Score: 171
Period size: 37 Copynumber: 3.7 Consensus size: 38
31519 TATAGTTTTG
* *
31529 AAAATATATAATATATA-ATTTTGAAAACA-TTTTAAA
1 AAAATATATAATATATAGTTTTTGAAAATATTTTTAAA
* * **
31565 AATATATATAATATATAG-TTTTCAAAATATTTTTTGA
1 AAAATATATAATATATAGTTTTTGAAAATATTTTTAAA
31602 AAAATATATAATATATAGTTTTT-AAAATATTTTTAAA
1 AAAATATATAATATATAGTTTTTGAAAATATTTTTAAA
31639 AAAAGTATAT-ATAATATAGTTTTTGAAAA
1 AAAA-TATATAAT-ATATAGTTTTTGAAAA
31668 CATATGATAT
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
36 25 0.28
37 40 0.45
38 20 0.22
39 4 0.04
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.43
Consensus pattern (38 bp):
AAAATATATAATATATAGTTTTTGAAAATATTTTTAAA
Found at i:31666 original size:135 final size:133
Alignment explanation
Indices: 31403--31697 Score: 339
Period size: 135 Copynumber: 2.2 Consensus size: 133
31393 ATTAATATAG
* *
31403 TATAATTTTTGAAAATACTTTTGAAAAATATAATATATAATTTTTTAAAAATGGTTTTTGAAAAT
1 TATAA-TTTTGAAAATA-TTTT-AAAAATATAATATATAAGTTTTCAAAAAT-GTTTTTGAAAAT
* * * *
31468 ATATATTTATTATATAGTTTGCATATGATTTTTGAAAAAATATATATAATATATAGTTTTGAAAA
62 ATATA-TTAATATATAGTTTGAAAATGATTTTTAAAAAAATATATATAATATATA-TTTTGAAAA
*
31533 TATATAATA
125 CATATAATA
*
31542 TATAATTTTGAAAACATTTTAAAAATATATATAATATATAGTTTTCAAAATAT-TTTTTGAAAA-
1 TATAATTTTGAAAATATTTTAAAAATATA-AT-ATATA-AGTTTTCAAAA-ATGTTTTTGAAAAT
*
31605 ATATA-TAATATATAGTTTTTAAAAT-ATTTTTAAAAAAAGTATATATAATATAGT-TTTTGAAA
62 ATATATTAATATATAG-TTTGAAAATGATTTTTAAAAAAA-TATATATAATATA-TATTTTGAAA
*
31667 ACATATGATA
124 ACATATAATA
*
31677 TATAATTTTTAAAATATTTTA
1 TATAATTTTGAAAATATTTTA
31698 TTTTCTGAAA
Statistics
Matches: 137, Mismatches: 12, Indels: 18
0.82 0.07 0.11
Matches are distributed among these distances:
135 56 0.41
136 28 0.20
137 12 0.09
138 25 0.18
139 14 0.10
140 2 0.01
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (133 bp):
TATAATTTTGAAAATATTTTAAAAATATAATATATAAGTTTTCAAAAATGTTTTTGAAAATATAT
ATTAATATATAGTTTGAAAATGATTTTTAAAAAAATATATATAATATATATTTTGAAAACATATA
ATA
Found at i:33008 original size:8 final size:8
Alignment explanation
Indices: 32994--33175 Score: 61
Period size: 8 Copynumber: 22.4 Consensus size: 8
32984 TAAATTTTAA
32994 ATTTTTTT
1 ATTTTTTT
33002 -TTATTTTT
1 ATT-TTTTT
33010 A--TTTTT
1 ATTTTTTT
*
33016 ATTGTTTT
1 ATTTTTTT
*
33024 CTTTTTTT
1 ATTTTTTT
*** *
33032 CCCTTTTG
1 ATTTTTTT
*
33040 ATTTATTT
1 ATTTTTTT
* *
33048 AATATTTT
1 ATTTTTTT
*
33056 ACGTTTTTT
1 A-TTTTTTT
*
33065 ATTACTTTT
1 ATT-TTTTT
33074 A--TTTTT
1 ATTTTTTT
*
33080 ATGTTTTT
1 ATTTTTTT
*
33088 ATGTTTTT
1 ATTTTTTT
*
33096 ACTTAATTTT
1 A-TT-TTTTT
33106 ATTTATCTTT
1 ATTT-T-TTT
* *
33116 ATTTATCT
1 ATTTTTTT
33124 ATTTTATTT
1 ATTTT-TTT
*
33133 ATTTTATT
1 ATTTTTTT
*
33141 ATTATTTT
1 ATTTTTTT
33149 ATTATTTTT
1 ATT-TTTTT
*
33158 -TCTTTTT
1 ATTTTTTT
*
33165 CTTTTTTT
1 ATTTTTTT
33173 ATT
1 ATT
33176 ACTTCATTTT
Statistics
Matches: 126, Mismatches: 33, Indels: 30
0.67 0.17 0.16
Matches are distributed among these distances:
6 11 0.09
7 7 0.06
8 70 0.56
9 26 0.21
10 12 0.10
ACGTcount: A:0.17, C:0.06, G:0.03, T:0.74
Consensus pattern (8 bp):
ATTTTTTT
Found at i:33138 original size:28 final size:27
Alignment explanation
Indices: 33103--33156 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
33093 TTTACTTAAT
33103 TTTATTTATCT-TTA-TTTATCTATTTTA
1 TTTATTTAT-TATTATTTTAT-TATTTTA
33130 TTTATTTTATTATTATTTTATTATTTT
1 TTTA-TTTATTATTATTTTATTATTTT
33157 TTCTTTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 5 0.21
28 14 0.58
29 5 0.21
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (27 bp):
TTTATTTATTATTATTTTATTATTTTA
Found at i:33250 original size:18 final size:18
Alignment explanation
Indices: 33206--33252 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
33196 TTATTATCCC
*
33206 TTTTTAATTTTTAACTTA
1 TTTTTTATTTTTAACTTA
33224 TTTTATTATTTTTAACCTT-
1 TTTT-TTATTTTTAA-CTTA
33243 TTTTTTATTT
1 TTTTTTATTT
33253 GATATTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 10 0.38
19 13 0.50
20 3 0.12
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTATTTTTAACTTA
Found at i:37036 original size:32 final size:31
Alignment explanation
Indices: 36950--37058 Score: 157
Period size: 31 Copynumber: 3.5 Consensus size: 31
36940 AAAAGTGTTT
* *
36950 AAATTTTAATTTGACCCTTAAATTTTAGATA
1 AAATATTAATTTGACCCTTAAACTTTAGATA
*
36981 AAATACTAATTTGA-CCTTAAACTTTAGATAA
1 AAATATTAATTTGACCCTTAAACTTTAGAT-A
*
37012 AAATATTAATTTAACCCTTAAACTTTAGATA
1 AAATATTAATTTGACCCTTAAACTTTAGATA
*
37043 AAATATCAATTTGACC
1 AAATATTAATTTGACC
37059 AATGAATCTA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
30 14 0.20
31 40 0.58
32 15 0.22
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.39
Consensus pattern (31 bp):
AAATATTAATTTGACCCTTAAACTTTAGATA
Found at i:42238 original size:118 final size:120
Alignment explanation
Indices: 42060--42292 Score: 312
Period size: 119 Copynumber: 2.0 Consensus size: 120
42050 ATTAGGGTCT
* * * * * ** *
42060 CCAATTTTTTATTTTTTTTAATTAGAGTTCTTAATTTTTATAATTTGATAATTTTTTTAG-TTTT
1 CCAATTTTTTATTATTTATAATTAGAGATCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTT
*
42124 TACCATCTTTTTCTAAT-TCTCTTATTAATTCATTTAATTTTGAATTAAATTTTAA
66 TACCATCTTTTTC-AATCTCTCTTATTAATTCATTCAATTTTGAATTAAATTTTAA
42179 CCAATTTTTTA-TATTTATAATTA-AGAATCCTAATTTTTATAATTTCATAAAATGTTTAGTTTT
1 CCAATTTTTTATTATTTATAATTAGAG-ATCCTAATTTTTATAATTTCATAAAATGTTTAGTTTT
* * *
42242 TTACCCTCTTTTTCCATCTCTCTTATTTATTCATTCAATTTTGAATTAAAT
65 TTACCATCTTTTTCAATCTCTCTTATTAATTCATTCAATTTTGAATTAAAT
42293 CTAATCATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
117 2 0.02
118 39 0.39
119 58 0.59
ACGTcount: A:0.29, C:0.11, G:0.04, T:0.56
Consensus pattern (120 bp):
CCAATTTTTTATTATTTATAATTAGAGATCCTAATTTTTATAATTTCATAAAATGTTTAGTTTTT
TACCATCTTTTTCAATCTCTCTTATTAATTCATTCAATTTTGAATTAAATTTTAA
Found at i:42890 original size:19 final size:18
Alignment explanation
Indices: 42848--42899 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
42838 AACACGAACT
*
42848 ATTGACTATTGATGTTGATC
1 ATTGAC-ATTGAT-TAGATC
*
42868 ATTGACCTTGATTAGATC
1 ATTGACATTGATTAGATC
42886 TATTGACATTGATT
1 -ATTGACATTGATT
42900 CTGAAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 5 0.18
19 17 0.61
20 6 0.21
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (18 bp):
ATTGACATTGATTAGATC
Found at i:44226 original size:15 final size:15
Alignment explanation
Indices: 44206--44238 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
44196 TGAGACATTA
44206 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
44221 CCCGCCCCGCATCCG
1 CCCGCCCCGCATCCG
44236 CCC
1 CCC
44239 ACCCAGCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.70, G:0.18, T:0.06
Consensus pattern (15 bp):
CCCGCCCCGCATCCG
Found at i:47892 original size:18 final size:16
Alignment explanation
Indices: 47866--47946 Score: 72
Period size: 18 Copynumber: 4.6 Consensus size: 16
47856 TTTGACCTAC
47866 AATAAAATAAAAAAAA
1 AATAAAATAAAAAAAA
*
47882 GAATAAAAATAAAATAAATC
1 -AAT-AAAATAAAA-AAA-A
47902 AATAAAATAAATAAAATA
1 AATAAAATAAA-AAAA-A
*
47920 AATAAAATAAAAACGGAA
1 AATAAAATAAAAA--AAA
47938 AATAAAATA
1 AATAAAATA
47947 CTAATAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
17 5 0.09
18 42 0.76
19 8 0.15
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (16 bp):
AATAAAATAAAAAAAA
Found at i:47900 original size:9 final size:9
Alignment explanation
Indices: 47866--47930 Score: 73
Period size: 9 Copynumber: 7.2 Consensus size: 9
47856 TTTGACCTAC
47866 AATAAAATA
1 AATAAAATA
47875 AA-AAAA-A
1 AATAAAATA
47882 GAATAAAAATA
1 -AAT-AAAATA
*
47893 AA-ATAAATC
1 AATA-AAATA
47902 AATAAAATA
1 AATAAAATA
47911 AATAAAATA
1 AATAAAATA
47920 AATAAAATA
1 AATAAAATA
47929 AA
1 AA
47931 AACGGAAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
7 1 0.02
8 7 0.15
9 32 0.67
10 7 0.15
11 1 0.02
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (9 bp):
AATAAAATA
Found at i:47946 original size:5 final size:5
Alignment explanation
Indices: 47866--47931 Score: 63
Period size: 5 Copynumber: 14.4 Consensus size: 5
47856 TTTGACCTAC
* * *
47866 AATAA AATAA AA-AA AAGAA TA-AA AATAA AAT-A AAT-C AATAA AAT-A
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
47911 AATAA AAT-A AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AA
47932 ACGGAAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 22 0.42
5 30 0.58
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:48045 original size:81 final size:78
Alignment explanation
Indices: 47957--48168 Score: 248
Period size: 81 Copynumber: 2.6 Consensus size: 78
47947 CTAATAATAA
*
47957 TATATATTATATTTCAAAAATAATGTTTTCAAAGAAACTATATATATTATATATGTTTTC-AAAA
1 TATATATTATATTTCAAAAAT-ACGTTTTC-AA-AAACTATAT-TA-TATATATGTTTTCAAAAA
*
48021 A-CCGTTTTTAAAAAAAC
61 ACCCATTTTTAAAAAAAC
48038 TATATATTATATGTTTTCAAAAATACGTTTTCAAAAACTATATTATATATATGTTTTCAAAAAAC
1 TATATATTATA---TTTCAAAAATACGTTTTCAAAAACTATATTATATATATGTTTTCAAAAAAC
*
48103 CCATTTTTAAGAAAAC
63 CCATTTTTAAAAAAAC
*** *
48119 TATATATTATATGTTTTCAAAAACGTGTTTTCAAAAACTATACTATATAT
1 TATATATTATA---TTTCAAAAATACGTTTTCAAAAACTATATTATATAT
48169 TTTCAAAAAC
Statistics
Matches: 119, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
79 13 0.11
80 7 0.06
81 80 0.67
82 2 0.02
83 7 0.06
84 10 0.08
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (78 bp):
TATATATTATATTTCAAAAATACGTTTTCAAAAACTATATTATATATATGTTTTCAAAAAACCCA
TTTTTAAAAAAAC
Found at i:48085 original size:41 final size:39
Alignment explanation
Indices: 47956--48166 Score: 168
Period size: 40 Copynumber: 5.2 Consensus size: 39
47946 ACTAATAATA
*
47956 ATATATATTATA---TTTCAAAAATAATGTTTTCAAAGAAACT
1 ATATATATTATATGTTTTC-AAAA-AACGTTTTC-AA-AAACT
* * *
47996 ATATATATTATATATGTTTTCAAAAACCGTTTTTAAAAA-A
1 ATATATA-T-TATATGTTTTCAAAAAACGTTTTCAAAAACT
48036 ACTATATATTATATGTTTTCAAAAATACGTTTTCAAAAACT
1 A-TATATATTATATGTTTTCAAAAA-ACGTTTTCAAAAACT
* *
48077 ATAT-TATATATATGTTTTCAAAAAACCCATTTTTAAGAAA--
1 ATATATAT-TATATGTTTTCAAAAAA--CGTTTTCAA-AAACT
48117 ACTATATATTATATGTTTTC-AAAAACGTGTTTTCAAAAACT
1 A-TATATATTATATGTTTTCAAAAAAC--GTTTTCAAAAACT
48158 ATACTATAT
1 ATA-TATAT
48167 ATTTTCAAAA
Statistics
Matches: 141, Mismatches: 11, Indels: 37
0.75 0.06 0.20
Matches are distributed among these distances:
38 1 0.01
39 23 0.16
40 53 0.38
41 38 0.27
42 12 0.09
43 6 0.04
44 4 0.03
45 4 0.03
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (39 bp):
ATATATATTATATGTTTTCAAAAAACGTTTTCAAAAACT
Found at i:48149 original size:14 final size:14
Alignment explanation
Indices: 48130--48156 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
48120 ATATATTATA
48130 TGTTTTCAAAAACG
1 TGTTTTCAAAAACG
48144 TGTTTTCAAAAAC
1 TGTTTTCAAAAAC
48157 TATACTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (14 bp):
TGTTTTCAAAAACG
Found at i:51309 original size:20 final size:21
Alignment explanation
Indices: 51284--51325 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
51274 CCAACTTACA
51284 ATGCATTATG-AACCATTATT
1 ATGCATTATGCAACCATTATT
*
51304 ATGCATTATGCAACTATTATT
1 ATGCATTATGCAACCATTATT
51325 A
1 A
51326 GTTGCATGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (21 bp):
ATGCATTATGCAACCATTATT
Found at i:55620 original size:118 final size:118
Alignment explanation
Indices: 55431--55654 Score: 448
Period size: 118 Copynumber: 1.9 Consensus size: 118
55421 ATAAGCAGAT
55431 ATTACACACTCTAATCTGGCTCGGATACCAATTATTGCGGAAGACGACTATCGGATAGAGCAAAA
1 ATTACACACTCTAATCTGGCTCGGATACCAATTATTGCGGAAGACGACTATCGGATAGAGCAAAA
55496 TCGTAACTGATAATTTAAGAAAATAAAAATGAAGATAAAGACACAAAATAAGC
66 TCGTAACTGATAATTTAAGAAAATAAAAATGAAGATAAAGACACAAAATAAGC
55549 ATTACACACTCTAATCTGGCTCGGATACCAATTATTGCGGAAGACGACTATCGGATAGAGCAAAA
1 ATTACACACTCTAATCTGGCTCGGATACCAATTATTGCGGAAGACGACTATCGGATAGAGCAAAA
55614 TCGTAACTGATAATTTAAGAAAATAAAAATGAAGATAAAGA
66 TCGTAACTGATAATTTAAGAAAATAAAAATGAAGATAAAGA
55655 AGACACAAAA
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 106 1.00
ACGTcount: A:0.44, C:0.16, G:0.17, T:0.23
Consensus pattern (118 bp):
ATTACACACTCTAATCTGGCTCGGATACCAATTATTGCGGAAGACGACTATCGGATAGAGCAAAA
TCGTAACTGATAATTTAAGAAAATAAAAATGAAGATAAAGACACAAAATAAGC
Found at i:58039 original size:12 final size:12
Alignment explanation
Indices: 58020--58049 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
58010 TCCATTATGC
58020 TATATATGTATA
1 TATATATGTATA
*
58032 TGTATATGTATA
1 TATATATGTATA
58044 TATATA
1 TATATA
58050 ACCCTAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (12 bp):
TATATATGTATA
Found at i:58941 original size:13 final size:12
Alignment explanation
Indices: 58917--58950 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
58907 TGTAAGTTCA
58917 AAATAAATTTTT
1 AAATAAATTTTT
58929 AAATAACATTTTT
1 AAATAA-ATTTTT
*
58942 AAAAAAATT
1 AAATAAATT
58951 ATATATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
AAATAAATTTTT
Found at i:61836 original size:38 final size:36
Alignment explanation
Indices: 61769--62059 Score: 223
Period size: 37 Copynumber: 7.9 Consensus size: 36
61759 TTTGATTACC
* *
61769 TTTTGAAAATGTATATAATATATAGTTTTAAAAATATT
1 TTTTGAAAA-CTATATAATATATAGTTTTTAAAATA-T
* *
61807 TTTTGAAAACTATATAGTATATAGTTTTTAAAACAT
1 TTTTGAAAACTATATAATATATAGTTTTTAAAATAT
*
61843 TTTAGAAAA-TATACTAATATATAGTTTTTAAAATCAT
1 TTTTGAAAACTATA-TAATATATAGTTTTTAAAAT-AT
* *
61880 TTTTGAAAACTTATATAATATATAG-TTTT-GAATTT
1 TTTTGAAAAC-TATATAATATATAGTTTTTAAAATAT
* * * * *
61915 TTTTAAAACACTTAAATATTATATAATTTTTGAAAA-ACA
1 TTTTGAAA-AC-TATATAATATATAGTTTTT-AAAATA-T
* * * ***
61954 TTTTAAAAATATATATAATATATAATTTTTAAACCGT
1 TTTTGAAAA-CTATATAATATATAGTTTTTAAAATAT
* * * **
61991 TTCTGAAAA-TATATATTATAAAGTTTTTAAAACGT
1 TTTTGAAAACTATATAATATATAGTTTTTAAAATAT
* *
62026 TTTTAAAAACATGTATAATATATAGTTTTTAAAA
1 TTTTGAAAAC-TATATAATATATAGTTTTTAAAA
62060 GCATTTTGGA
Statistics
Matches: 206, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
35 41 0.20
36 44 0.21
37 70 0.34
38 37 0.18
39 14 0.07
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTTGAAAACTATATAATATATAGTTTTTAAAATAT
Found at i:61938 original size:74 final size:73
Alignment explanation
Indices: 61769--62071 Score: 230
Period size: 73 Copynumber: 4.1 Consensus size: 73
61759 TTTGATTACC
* * *
61769 TTTT-GAAAATGTATATAATATATAGTTTTAAAAAT-ATTTTTTGAAAAC-TATATAGTATATAG
1 TTTTAGAAAATATA-ATAATATATAGTTTTTAAAATCA-TTTTTGAAAACTTATATAATATATAG
61831 TTTTTAAAACA
64 -TTTTAAAACA
*
61842 TTTTAGAAAATATACTAATATATAGTTTTTAAAATCATTTTTGAAAACTTATATAATATATAGTT
1 TTTTAGAAAATATAATAATATATAGTTTTTAAAATCATTTTTGAAAACTTATATAATATATAGTT
* ***
61907 TTGAATTT
66 TTAAAACA
* * * *
61915 TTTTA-AAACACT-TAAATATTATATAATTTTTGAAAAACA-TTTT-AAAAATATATATAATATA
1 TTTTAGAAA-A-TAT-AATAATATATAGTTTTT-AAAATCATTTTTGAAAACT-TATATAATATA
* * *
61976 TAATTTTTAAACCG
61 T-AGTTTTAAAACA
* * * * * *
61990 TTTCT-GAAAATAT-ATATTATAAAGTTTTTAAAA-CGTTTTTAAAAACATGTATAATATATAGT
1 TTT-TAGAAAATATAATAATATATAGTTTTTAAAATCATTTTTGAAAACTTATATAATATATAG-
62052 TTTTAAAAGCA
64 TTTTAAAA-CA
*
62063 TTTTGGAAA
1 TTTTAGAAA
62072 TTTATATATA
Statistics
Matches: 186, Mismatches: 27, Indels: 34
0.75 0.11 0.14
Matches are distributed among these distances:
71 2 0.01
72 30 0.16
73 78 0.42
74 54 0.29
75 18 0.10
76 4 0.02
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.45
Consensus pattern (73 bp):
TTTTAGAAAATATAATAATATATAGTTTTTAAAATCATTTTTGAAAACTTATATAATATATAGTT
TTAAAACA
Found at i:61952 original size:29 final size:31
Alignment explanation
Indices: 61910--61972 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 31
61900 TATAGTTTTG
** *
61910 AATTTTTTTAAAACA-CTTAAATAT-TATAT
1 AATTTTTGAAAAACATCTTAAAAATATATAT
*
61939 AATTTTTGAAAAACATTTTAAAAATATATAT
1 AATTTTTGAAAAACATCTTAAAAATATATAT
61970 AAT
1 AAT
61973 ATATAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.46
30 7 0.25
31 8 0.29
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (31 bp):
AATTTTTGAAAAACATCTTAAAAATATATAT
Found at i:62081 original size:2 final size:2
Alignment explanation
Indices: 62074--62139 Score: 86
Period size: 2 Copynumber: 34.5 Consensus size: 2
62064 TTTGGAAATT
*
62074 TA TA TA TA TA CA TA T- TA TA TA TA 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
62115 TA TA TA TA GTA T- TA TA T- TA T- TA TA T
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA T
62140 TTTTTTTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
1 4 0.07
2 51 0.89
3 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Done.