Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005457.1 Hibiscus syriacus cultivar Beakdansim tig00012498_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: 56495
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:5212 original size:20 final size:20
Alignment explanation
Indices: 5189--5237 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 20
5179 TATTAAAAAT
*
5189 AATATTAATA-CTATTTTAAA
1 AATATTAATATC-AATTTAAA
5209 AATATTAATATCAATTTAAA
1 AATATTAATATCAATTTAAA
5229 AATAATTAA
1 AAT-ATTAA
5238 ACCCTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATTAATATCAATTTAAA
Found at i:5214 original size:11 final size:11
Alignment explanation
Indices: 5171--5213 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
5161 ATCCTTTTTA
5171 TAAAAATATAT
1 TAAAAATATAT
5182 TAAAAATAATAT
1 TAAAAAT-ATAT
* * *
5194 TAATACTATTT
1 TAAAAATATAT
5205 TAAAAATAT
1 TAAAAATAT
5214 TAATATCAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAAAATATAT
Found at i:5837 original size:20 final size:19
Alignment explanation
Indices: 5791--5851 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 19
5781 TAATATGTGG
5791 TTTTGAATATATATATATAATGGT
1 TTTTGAA-A-ATATATATAA---T
5815 TTTTGAAAATATAGTATAAT
1 TTTTGAAAATATA-TATAAT
* *
5835 TTTTTAATATATATATA
1 TTTTGAAAATATATATA
5852 TATATATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.12
20 12 0.35
22 5 0.15
23 6 0.18
24 7 0.21
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (19 bp):
TTTTGAAAATATATATAAT
Found at i:5846 original size:2 final size:2
Alignment explanation
Indices: 5841--5884 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
5831 TAATTTTTTA
5841 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5883 AT
1 AT
5885 TTTTAAAAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5951 original size:16 final size:17
Alignment explanation
Indices: 5920--5957 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5910 GTAATATATT
5920 ATATAGTTTTTGAAAAG
1 ATATAGTTTTTGAAAAG
*
5937 ATATAGTTTTT-AAAAT
1 ATATAGTTTTTGAAAAG
5953 ATATA
1 ATATA
5958 TAGTATACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (17 bp):
ATATAGTTTTTGAAAAG
Found at i:5958 original size:18 final size:17
Alignment explanation
Indices: 5919--5961 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5909 CGTAATATAT
*
5919 TATATAGTTTTTGAAAA
1 TATATAGTTTTTAAAAA
*
5936 GATATAGTTTTTAAAATA
1 TATATAGTTTTTAAAA-A
5954 TATATAGT
1 TATATAGT
5962 ATACATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
TATATAGTTTTTAAAAA
Found at i:5959 original size:42 final size:40
Alignment explanation
Indices: 5867--5964 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 40
5857 ATATATATAT
5867 ATATATATATATATATATTTTTAAAAACATAATTTTTGAAA
1 ATATATATAT-TATATATTTTTAAAAACATAATTTTTGAAA
* *
5908 ACGTA-ATATATTATATAGTTTTTGAAAAGATATAGTTTTT-AAA
1 A--TATATATATTATATA-TTTTT-AAAA-ACATAATTTTTGAAA
*
5951 ATATATATAGTATA
1 ATATATATATTATA
5965 CATATTATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
41 9 0.19
42 20 0.42
43 10 0.21
44 9 0.19
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (40 bp):
ATATATATATTATATATTTTTAAAAACATAATTTTTGAAA
Found at i:9938 original size:68 final size:68
Alignment explanation
Indices: 9854--9989 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
9844 TTTGAATGCA
9854 GAAATGGAGCAACAAAAAGGGTCTCAAAAGACTCTTCAATTGTTGGTTGTACGAAGTAAGTTACT
1 GAAATGGAGCAACAAAAAGGGTCTCAAAAGACTCTTCAATTGTTGGTTGTACGAAGTAAGTTACT
9919 CTT
66 CTT
9922 GAAATGGAGCAACAAAAAGGGTCTCAAAAGACTCTTCAATTGTTGGTTGTACGAAGTAAGTTACT
1 GAAATGGAGCAACAAAAAGGGTCTCAAAAGACTCTTCAATTGTTGGTTGTACGAAGTAAGTTACT
9987 CTT
66 CTT
9990 TGACGCGATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (68 bp):
GAAATGGAGCAACAAAAAGGGTCTCAAAAGACTCTTCAATTGTTGGTTGTACGAAGTAAGTTACT
CTT
Found at i:10236 original size:2 final size:2
Alignment explanation
Indices: 10223--10280 Score: 73
Period size: 2 Copynumber: 28.5 Consensus size: 2
10213 GTCACTCAAC
* *
10223 TA TA TA TGA TA TA TA TA TA TCA CA TA TA -A AA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
10266 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
10281 CTATTGAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.02
2 46 0.92
3 3 0.06
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:25490 original size:39 final size:40
Alignment explanation
Indices: 25440--25540 Score: 159
Period size: 39 Copynumber: 2.5 Consensus size: 40
25430 AAAAGGTTGA
* *
25440 ACAAATTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAG
1 ACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
25479 ATAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 ACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
*
25519 ACGAGTTCTTCTCATTATGAAC
1 ACAAGTTCTTCTCATTATGAAC
25541 ACTTCTGGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 29 0.52
40 27 0.48
ACGTcount: A:0.23, C:0.25, G:0.08, T:0.45
Consensus pattern (40 bp):
ACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
Found at i:25638 original size:152 final size:152
Alignment explanation
Indices: 25333--25654 Score: 497
Period size: 152 Copynumber: 2.1 Consensus size: 152
25323 TTGAACAAGC
**
25333 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAGTTCTTCTCATTATGAACTTTCTCTGG
1 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAGTTCTTCTCATTATGAACACTCTCTGG
*
25398 AAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAATT
66 AAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
* *
25463 TCTTCTTCCTCTTCAGATAAGT
131 TCCTCTTCCTCTTCAAATAAGT
*
25485 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACACT-TCTGG
1 TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAGTTCTTCTCATTATGAACACTCTCTGG
* * * *
25549 AAATA-TTGATCCATCAAGTGATGGATT-TGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAA
66 AAA-AGTTAATCCATCAAGTGATGAATTCAG-GCAAAAGGTTGAACAAATTCTTCTCATTATGAA
*
25612 CTTCCTCTTCCTTCTTCAAATGAGT
129 CTTCCTCTTCC-TCTTCAAATAAGT
25637 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
25655 TCTCTGGCAA
Statistics
Matches: 156, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
150 1 0.01
151 69 0.44
152 86 0.55
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (152 bp):
TCTTCTCATTATGAACTTCTTCTTCATTCTTCAGACGAGTTCTTCTCATTATGAACACTCTCTGG
AAAAGTTAATCCATCAAGTGATGAATTCAGGCAAAAGGTTGAACAAATTCTTCTCATTATGAACT
TCCTCTTCCTCTTCAAATAAGT
Found at i:25829 original size:226 final size:226
Alignment explanation
Indices: 25484--26013 Score: 929
Period size: 226 Copynumber: 2.4 Consensus size: 226
25474 TTCAGATAAG
* * *
25484 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACACT-TCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
* * *
25548 GAAATATTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 GCAATGTTGATCCATAAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
25613 TTCCTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGCAATGCTAATCCATCG
131 TTCCTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGCAATGCTAATCCATCA
* *
25678 GGTGATGAATTAAAGCAAAAGGTTGAGCAAA
196 GGTGATGAATTAAAGCAAAAAGTTGAACAAA
25709 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
25774 GCAATGTTGATCCATAAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 GCAATGTTGATCCATAAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* *
25839 TTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATTAACTTTCTCTGGCAATGCTAATCCATCA
131 TTCCTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGCAATGCTAATCCATCA
*
25904 GGTGATGAATTAAAGCAAAAAGTTGAACACA
196 GGTGATGAATTAAAGCAAAAAGTTGAACAAA
*
25935 TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
26000 GC-ATGTTGATCCAT
66 GCAATGTTGATCCAT
26014 TGAGTAATGG
Statistics
Matches: 291, Mismatches: 13, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
225 70 0.24
226 221 0.76
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (226 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACCTG
GCAATGTTGATCCATAAAGTGATGGATTTGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
TTCCTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTGGCAATGCTAATCCATCA
GGTGATGAATTAAAGCAAAAAGTTGAACAAA
Found at i:26001 original size:113 final size:113
Alignment explanation
Indices: 25481--26002 Score: 728
Period size: 113 Copynumber: 4.6 Consensus size: 113
25471 CTCTTCAGAT
* * *
25481 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGAACACT-T
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* ** * * **
25545 CTGGAAATATTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAAC
66 CTGGCAATGCTAATCCATCAAGTGATGAATTAAAGCAAAAGGTTGAAC
* * *
25593 AAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACT-TTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
** *
25657 TCTGGCAATGCTAATCCATCGGGTGATGAATTAAAGCAAAAGGTTGAGC
66 -CTGGCAATGCTAATCCATCAAGTGATGAATTAAAGCAAAAGGTTGAAC
*
25706 AAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* * * * **
25771 CTGGCAATGTTGATCCATAAAGTGATGGATTTGAGCAAAAGGTTGAAC
66 CTGGCAATGCTAATCCATCAAGTGATGAATTAAAGCAAAAGGTTGAAC
* * *
25819 AAGTTCTTCTCATTATGAACTTCCTCTTCCTTCTTCAGATGAGTTCTTCTCATTATTAACT-TTC
1 AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
* *
25883 TCTGGCAATGCTAATCCATCAGGTGATGAATTAAAGCAAAAAGTTGAAC
66 -CTGGCAATGCTAATCCATCAAGTGATGAATTAAAGCAAAAGGTTGAAC
*
25932 ACA-TTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTA
1 A-AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTA
25996 CCTGGCA
65 CCTGGCA
26003 TGTTGATCCA
Statistics
Matches: 360, Mismatches: 44, Indels: 11
0.87 0.11 0.03
Matches are distributed among these distances:
111 1 0.00
112 59 0.16
113 295 0.82
114 5 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.38
Consensus pattern (113 bp):
AAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTAC
CTGGCAATGCTAATCCATCAAGTGATGAATTAAAGCAAAAGGTTGAAC
Found at i:31075 original size:14 final size:14
Alignment explanation
Indices: 31056--31093 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
31046 CAAAGATTCC
31056 AAATGTAAATATGA
1 AAATGTAAATATGA
* *
31070 AAATGTAAAAATGT
1 AAATGTAAATATGA
31084 AAATGTAAAT
1 AAATGTAAAT
31094 TATTTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (14 bp):
AAATGTAAATATGA
Found at i:31410 original size:43 final size:44
Alignment explanation
Indices: 31331--31415 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 44
31321 ATGCATTAAA
* ** *
31331 CAAAACTTTTACATATAGGGGACATCTTTTAGTCCTAACTTCAG
1 CAAAACTTTTACATATAGGGGACAACTTCCACTCCTAACTTCAG
* *
31375 CAAAAC-TTTACATATAGGGGATAACTTCCCCTCCTAACTTC
1 CAAAACTTTTACATATAGGGGACAACTTCCACTCCTAACTTC
31416 TCTAAAGCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
43 29 0.83
44 6 0.17
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.32
Consensus pattern (44 bp):
CAAAACTTTTACATATAGGGGACAACTTCCACTCCTAACTTCAG
Found at i:33591 original size:33 final size:35
Alignment explanation
Indices: 33514--33581 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
33504 TTTCATAAAA
* **
33514 TAAATGAATATTATTTATATATATATTTATAAGAC
1 TAAATAAATATTATTTATATATATATACATAAGAC
33549 TAAATAAATATTATTTATATATATATGACATAA
1 TAAATAAATATTATTTATATATATAT-ACATAA
33582 CTAATAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 25 0.86
36 4 0.14
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (35 bp):
TAAATAAATATTATTTATATATATATACATAAGAC
Found at i:35148 original size:3 final size:3
Alignment explanation
Indices: 35140--35183 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
35130 ATTAATTATT
*
35140 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAA -AA CAA -AA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
35184 ATAAAACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 8 0.22
3 29 0.78
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:35163 original size:16 final size:15
Alignment explanation
Indices: 35141--35189 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
35131 TTAATTATTT
35141 AATAATAATAATATAA
1 AATAATAATAA-ATAA
* *
35157 TATAATAATAAAACAA
1 AATAATAAT-AAATAA
35173 AATAATAATAAATAA
1 AATAATAATAAATAA
35188 AA
1 AA
35190 CAAATGAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 7 0.25
16 19 0.68
17 2 0.07
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATAATAAATAA
Found at i:35194 original size:19 final size:19
Alignment explanation
Indices: 35140--35193 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
35130 ATTAATTATT
* *
35140 TAATAATAATAATATAAT-A
1 TAATAATAA-AACAAAATAA
35159 TAATAATAAAACAAAATAA
1 TAATAATAAAACAAAATAA
35178 TAATAAATAAAACAAA
1 TAAT-AATAAAACAAA
35194 TGAAATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 6 0.19
19 14 0.45
20 11 0.35
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (19 bp):
TAATAATAAAACAAAATAA
Found at i:44781 original size:35 final size:35
Alignment explanation
Indices: 44734--44811 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
44724 ATGTAATCGA
44734 AAAATAAGAGTTGGATTAGGACTCAAATACTAGTCT
1 AAAAT-AGAGTTGGATTAGGACTCAAATACTAGTCT
44770 AAAATAGAGTTGGATTAGGACTCAAATACTAGTCT
1 AAAATAGAGTTGGATTAGGACTCAAATACTAGTCT
44805 AAAATAG
1 AAAATAG
44812 GGTGTTTAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 37 0.88
36 5 0.12
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (35 bp):
AAAATAGAGTTGGATTAGGACTCAAATACTAGTCT
Found at i:45211 original size:17 final size:18
Alignment explanation
Indices: 45185--45224 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
45175 ATTATATGGA
45185 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
45201 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
45219 TATTAT
1 TATTAT
45225 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:45284 original size:2 final size:2
Alignment explanation
Indices: 45270--45303 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
45260 ATTTTTTTAC
*
45270 TA TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45304 TTCTTTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:45421 original size:2 final size:2
Alignment explanation
Indices: 45416--45445 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
45406 ATTATTAATA
45416 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
45446 TCTTAATTAT
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:45784 original size:38 final size:40
Alignment explanation
Indices: 45733--45812 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 40
45723 AGTGAGAGGG
**
45733 TAGCTTTTCTATTTT-TAAATA-TTTTTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
45771 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
45811 TA
1 TA
45813 TATATATTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 12 0.33
39 7 0.19
40 17 0.47
ACGTcount: A:0.31, C:0.05, G:0.06, T:0.57
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:53987 original size:104 final size:104
Alignment explanation
Indices: 53808--54557 Score: 923
Period size: 105 Copynumber: 7.3 Consensus size: 104
53798 GCTAGAGTCC
* *
53808 ATTTCAACTTCA-CAGTAAAGGATATT-GACTCAAGAC-A-ACAAGTTCAACTTCACAACGAATG
1 ATTTCAACTTCAGC-G--AAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
*
53869 GACGACTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
63 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * *
53911 ATTTCAACTTCATCGAAGGATGTTGGACTCGGGACAACACAAGTTCAACTTCACAACGAAGGGAC
1 ATTTCAACTTCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAC
* *
53976 GGCTAGTTGTCAACAAACAATTTCCCAATTTCAGAGTCA
66 GGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
54015 ATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTT--CAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
*
54080 AC-GCTGGTTGTCAAC-AACAATCTCCCAATTTCAGAG---
64 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
54116 ------A--T-AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGAC
1 ATTTCAACTTCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAC
* * * *
54172 GGCTGGTTGTCAATAAATAATTTCCCAATTT-AGGGTCA
66 GGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
54210 ATTTCAACTTCACACGAAGGATATTGGACTCGAGAC--CACAAGTTCAACTTCACAACGAAGGGA
1 ATTTCAACTTCA-GCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA
*
54273 CGGCTGGTTGTCAACAAATAATTTCCCAATTTCAGAGCCA
65 CGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
54313 ATTTCAACTTCACAGCGAAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGG
1 ATTTCAACTT--CAGCG-AAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGG
* * *
54378 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTTAGGGTCA
63 GACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
* * * * * *
54420 ATTTCAACTTCA-CATGAAGGATATTAGACTCAAGACAGCATAAGCTCAACTTCACAGCGAAGGG
1 ATTTCAACTTCAGC--GAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
* * * * * *
54484 GCGGTTGGCTGTCAACAAACAATTTTCCAGTTCCAGAGCCA
64 ACGGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
*
54525 ATTTCAACTTCACGACGGAGGATATTGGACTCG
1 ATTTCAACTTCA-G-CGAAGGATATTGGACTCG
54558 GAACAATACA
Statistics
Matches: 568, Mismatches: 47, Indels: 61
0.84 0.07 0.09
Matches are distributed among these distances:
90 52 0.09
91 15 0.03
92 14 0.02
93 1 0.00
95 1 0.00
100 1 0.00
101 8 0.01
102 67 0.12
103 30 0.05
104 118 0.21
105 121 0.21
106 66 0.12
107 73 0.13
108 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (104 bp):
ATTTCAACTTCAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGAC
GGCTGGTTGTCAACAAACAATTTCCCAATTTCAGAGCCA
Found at i:54133 original size:90 final size:92
Alignment explanation
Indices: 53825--54309 Score: 426
Period size: 104 Copynumber: 4.9 Consensus size: 92
53815 CTTCACAGTA
* * *
53825 AAGGATATT-GACTCAAGACA-ACAAGTTCAACTTCACAACGAATGGACGACTGGTTGTCAACAA
1 AAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-A
* *
53888 ACAATTTCCCAATTTCAGAGCCAATTTCAACTTCATCG
65 ATAATTTCCCAATTTCAGAG---------AC-TCAGCG
* * *
53926 AAGGATGTTGGACTCGGGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACA
1 AAGGATATTGGACTCGAGAC-ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-
*
53991 AACAATTTCCCAATTTCAGAGTCAATTTCAACTTCACAGCG
64 AATAATTTCCCAATTTCAGAG---------AC-T--CAGCG
*
54032 AAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGAC-GCTGGTTGTCAACA
1 AAGGATATTGGACTCGAGAC-ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACA
* *
54096 ACAATCTCCCAATTTCAGAGA-T-AGCG
65 ATAATTTCCCAATTTCAGAGACTCAGCG
*
54122 AAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAATA
1 AAGGATATTGGACTCGAGAC-ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-C
* *
54187 AATAATTTCCCAATTT-AGGGTCAATTTCAACTTCACACG
64 AATAATTTCCCAATTTCA--G---A----GAC-TCA-GCG
54226 AAGGATATTGGACTCGAGAC-CACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAA
1 AAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-A
54290 ATAATTTCCCAATTTCAGAG
65 ATAATTTCCCAATTTCAGAG
54310 CCAATTTCAA
Statistics
Matches: 340, Mismatches: 22, Indels: 51
0.82 0.05 0.12
Matches are distributed among these distances:
90 52 0.15
91 13 0.04
92 14 0.04
93 2 0.01
95 1 0.00
96 1 0.00
98 1 0.00
100 1 0.00
101 9 0.03
102 66 0.19
103 3 0.01
104 114 0.34
105 12 0.04
106 51 0.15
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (92 bp):
AAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAA
TAATTTCCCAATTTCAGAGACTCAGCG
Found at i:55455 original size:14 final size:15
Alignment explanation
Indices: 55436--55470 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
55426 TATATGGATA
55436 TTTTATTCAT-TTAT
1 TTTTATTCATGTTAT
55450 TTTTATTCATGTTAT
1 TTTTATTCATGTTAT
*
55465 TATTAT
1 TTTTAT
55471 ACGTATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.69
Consensus pattern (15 bp):
TTTTATTCATGTTAT
Found at i:55901 original size:42 final size:39
Alignment explanation
Indices: 55838--55915 Score: 102
Period size: 42 Copynumber: 1.9 Consensus size: 39
55828 GAGGGCCATT
* *
55838 TTTTTGTTTTATTTCTAACTAAAGTCTCTCCCCACTTTCCTC
1 TTTTTGTCTTATTTATAACTAAAG-C-C-CCCCACTTTCCTC
*
55880 TTTTTGTCTTATTTATGACTAAAGCCCCCCACTTTC
1 TTTTTGTCTTATTTATAACTAAAGCCCCCCACTTTC
55916 GGTAAGTGAG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 10 0.30
40 1 0.03
41 1 0.03
42 21 0.64
ACGTcount: A:0.18, C:0.28, G:0.06, T:0.47
Consensus pattern (39 bp):
TTTTTGTCTTATTTATAACTAAAGCCCCCCACTTTCCTC
Found at i:56069 original size:5 final size:5
Alignment explanation
Indices: 56062--56125 Score: 51
Period size: 5 Copynumber: 13.2 Consensus size: 5
56052 TTTTTTTTCC
* ** * * *
56062 TTATC TTATT TTATT TTATT TTA-T TCCTT TTATT TTATT CT-CT TTATC
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT TTATT
*
56110 TTATT TTGTT TTATT T
1 TTATT TTATT TTATT T
56126 CCTTGTTTAT
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
4 4 0.09
5 40 0.91
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:56092 original size:14 final size:15
Alignment explanation
Indices: 56075--56125 Score: 61
Period size: 14 Copynumber: 3.5 Consensus size: 15
56065 TCTTATTTTA
56075 TTTTATTTTATTC-C
1 TTTTATTTTATTCTC
56089 TTTTATTTTATTCTC
1 TTTTATTTTATTCTC
* * *
56104 -TTTATCTTATTTTG
1 TTTTATTTTATTCTC
56118 TTTTATTT
1 TTTTATTT
56126 CCTTGTTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 24 0.77
15 7 0.23
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTTATTTTATTCTC
Done.