Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004950.1 Hibiscus syriacus cultivar Beakdansim tig00011126_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: 80259
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:442 original size:22 final size:23
Alignment explanation
Indices: 391--446 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
381 ATCTACACTC
* *
391 TTCAAAGATGATAGATTCCCTTT
1 TTCAAAGATGACAAATTCCCTTT
* *
414 TTAAAAGATGACAAATTCTC-TT
1 TTCAAAGATGACAAATTCCCTTT
436 TTCAAAGATGA
1 TTCAAAGATGA
447 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (23 bp):
TTCAAAGATGACAAATTCCCTTT
Found at i:1215 original size:111 final size:111
Alignment explanation
Indices: 873--1588 Score: 891
Period size: 109 Copynumber: 6.6 Consensus size: 111
863 ATTTCTAGAA
*
873 GAGTTCATAATGAGAAGAA-TCATCTGAAGAAGGAAGAAGAAGTTCATATAAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA-ATGAAGAACTTGTTC
* * * *
937 AACTTTTCACTTGAATTTATCATTCGATGGATCAGTATTACCAGGTC
65 AACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
984 GAGTTCATAATG-GAAGAACTCATCT---GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT--GAAGAACTTGTT
1045 CAACTTTTCGCTTGAATTCATCATTCGATGGATCA-CA-TGCCAGGTC
64 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
1091 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAACTTGTTCA
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAACTTGTTCA
*
1156 ACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGTCAGGTC
66 ACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
* *
1202 GAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATG-AGAACTTGTTTA
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAACTTGTTCA
* * *
1266 ACTTTTCGCTTGAATTTATCATTCG-TGGACCAGCATTGCCAGGGC
66 ACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
*
1311 GAGTTCATAATAAGAAGAACTCATC----GAA-GAAGAAGAAGTTCATAATGATAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG--AAGAACTTGTT
* * **
1371 CAAC-TTTCGCTTGAATT-ATCATTCGATAGACCAGCATTGCCAGGGG
64 CAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
* * *
1417 GAGTTCATAATAAGAAGAACTCATCTGAAGAAAGAAGAAGAAATTCATAATG-AGAA---G---A
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAACTTGTTCA
* * * * * *
1475 ACTTGTT-GCTCGAATTCATCACTCGATGGATCAACTTTTCCA-G-A
66 ACTT-TTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
*
1519 GAGTTC--AATGAGAAGAATTCATCTGAAGAGAGG-AG--GAAGTTCATAATTAGAAGAACTTGT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGA-AGGAAGAAGAAGTTCATAA-T-GAAGAACTTGT
1579 TCAATCTTTT
63 TCAA-CTTTT
1589 GCATGATTCT
Statistics
Matches: 544, Mismatches: 29, Indels: 68
0.85 0.05 0.11
Matches are distributed among these distances:
98 10 0.02
99 1 0.00
100 24 0.04
101 6 0.01
102 9 0.02
103 10 0.02
104 41 0.08
105 12 0.02
106 56 0.10
107 38 0.07
108 41 0.08
109 133 0.24
110 46 0.08
111 117 0.22
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (111 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAACTTGTTCA
ACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGTC
Found at i:1348 original size:218 final size:218
Alignment explanation
Indices: 873--1588 Score: 890
Period size: 215 Copynumber: 3.3 Consensus size: 218
863 ATTTCTAGAA
*
873 GAGTTCATAATGAGAAGAA-TCATCTGAAGAAGGAAGAAGAAGTTCATATAAGAAGAACTTGTTC
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATA-ATGAAGAACTTGTTC
* * *
937 AACTTTTCACTTGAATTTATCATTCGATGGATCAGTATTACCAGGTCGAGTTCATAATG-GAAGA
65 AACTTTTCGCTTGAA-TTATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGA
1001 ACTCATCTGAAG---GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATT
129 ACTCATCTGAAGAAAGAAGAAGAAGTTCATAAT--G-AGAACTTGTTCAACTTTTCGCTTGAATT
* *
1063 CATCATTCGATGGATCACATGCCAGGTC
191 CATCATTCGATGGACCACATGCCAGGGC
1091 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAACTTGTTCA
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAACTTGTTCA
*
1156 ACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGTCAGGTCGAGTTCATAATGAGAAGAA
66 ACTTTTCGCTTGAATT-ATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAA
* *
1221 CTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAACTTGTTTAACTTTTCGCTTGAATTTATC
130 CTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAACTTGTTCAACTTTTCGCTTGAATTCATC
1286 ATTCG-TGGACCAGCATTGCCAGGGC
195 ATTCGATGGACCA-CA-TGCCAGGGC
*
1311 GAGTTCATAATAAGAAGAACTCATC----GAA-GAAGAAGAAGTTCATAATGATAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG--AAGAACTTGTT
* * ** *
1371 CAAC-TTTCGCTTGAATTATCATTCGATAGACCAGCATTGCCAGGGGGAGTTCATAATAAGAAGA
64 CAACTTTTCGCTTGAATTATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGA
* *
1435 ACTCATCTGAAGAAAGAAGAAGAAATTCATAATGAGAA---G---AACTTGTT-GCTCGAATTCA
129 ACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAACTTGTTCAACTT-TTCGCTTGAATTCA
* * * * *
1493 TCACTCGATGGATCAACTTTTCCA--GA
193 TCATTCGATGGA-CCAC-ATGCCAGGGC
*
1519 GAGTTC--AATGAGAAGAATTCATCTGAAGAGAGG-AG--GAAGTTCATAATTAGAAGAACTTGT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGA-AGGAAGAAGAAGTTCATAA-T-GAAGAACTTGT
1579 TCAATCTTTT
63 TCAA-CTTTT
1589 GCATGATTCT
Statistics
Matches: 448, Mismatches: 26, Indels: 55
0.85 0.05 0.10
Matches are distributed among these distances:
206 15 0.03
208 7 0.02
209 45 0.10
210 15 0.03
211 9 0.02
212 2 0.00
215 97 0.22
216 16 0.04
217 17 0.04
218 91 0.20
219 83 0.19
220 33 0.07
222 18 0.04
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (218 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAGAACTTGTTCA
ACTTTTCGCTTGAATTATCATTCGATGGATCAGCATTGCCAGGTCGAGTTCATAATGAGAAGAAC
TCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAACTTGTTCAACTTTTCGCTTGAATTCATCA
TTCGATGGACCACATGCCAGGGC
Found at i:1881 original size:19 final size:20
Alignment explanation
Indices: 1854--1910 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
1844 ATTTGTTTTA
* *
1854 TTTATTATTATTATT-TTGT
1 TTTAATATTATTATTATTAT
*
1873 TTTAATATTAATATTATTAT
1 TTTAATATTATTATTATTAT
*
1893 ATT-ATATTATTATTATTA
1 TTTAATATTATTATTATTA
1911 AATAAATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 27 0.84
20 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTAATATTATTATTATTAT
Found at i:1881 original size:22 final size:22
Alignment explanation
Indices: 1845--1910 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
1835 TTTTATTTCA
1845 TTTGTTTTATTTATTATTATTAT
1 TTTGTTTTA-TTATTATTATTAT
* *
1868 TTTGTTTTAATATTAATATTAT
1 TTTGTTTTATTATTATTATTAT
* * *
1890 TATATTATATTATTATTATTA
1 TTTGTTTTATTATTATTATTA
1911 AATAAATAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 27 0.75
23 9 0.25
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (22 bp):
TTTGTTTTATTATTATTATTAT
Found at i:1906 original size:25 final size:25
Alignment explanation
Indices: 1859--1907 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1849 TTTTATTTAT
* * *
1859 TATTATTATTTTGTTTTAATATTAA
1 TATTATTATATTATATTAATATTAA
*
1884 TATTATTATATTATATTATTATTA
1 TATTATTATATTATATTAATATTA
1908 TTAAATAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (25 bp):
TATTATTATATTATATTAATATTAA
Found at i:1930 original size:3 final size:3
Alignment explanation
Indices: 1855--1910 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
1845 TTTGTTTTAT
* * *
1855 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA ATA TTA TTA -TA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1899 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1911 AATAAATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 8 0.18
3 37 0.82
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:3238 original size:12 final size:11
Alignment explanation
Indices: 3221--3269 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
3211 TTAATTCCTT
3221 TTATTTTAATTA
1 TTATTTT-ATTA
* *
3233 TTATTTGCAATA
1 TTATTT-TATTA
3245 TTATTTTATTA
1 TTATTTTATTA
3256 TTATTCTTATTA
1 TTATT-TTATTA
3268 TT
1 TT
3270 TATATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 8 0.26
12 23 0.74
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:3288 original size:15 final size:14
Alignment explanation
Indices: 3270--3301 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
3260 TCTTATTATT
3270 TATATAATAAATATA
1 TATATAATAAATA-A
3285 TATATAATAAATAA
1 TATATAATAAATAA
3299 TAT
1 TAT
3302 TTGTTTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATATAATAAATAA
Found at i:3582 original size:22 final size:22
Alignment explanation
Indices: 3541--3582 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
3531 TTGATATTTC
**
3541 TAAATAAATAAATTTTTTTTTA
1 TAAATAAATAAATTAATTTTTA
*
3563 TAAATATATAAATTAATTTT
1 TAAATAAATAAATTAATTTT
3583 CCATAATTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAATAAATAAATTAATTTTTA
Found at i:8366 original size:20 final size:20
Alignment explanation
Indices: 8341--8391 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
8331 CAGGGTTGTA
*
8341 GTATCGATACCAGAAGCTCG
1 GTATCGAGACCAGAAGCTCG
8361 GTATCGAGACCAGAAGCTCG
1 GTATCGAGACCAGAAGCTCG
* *
8381 ATATCAAGACC
1 GTATCGAGACC
8392 TAATGACTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (20 bp):
GTATCGAGACCAGAAGCTCG
Found at i:9307 original size:20 final size:20
Alignment explanation
Indices: 9278--9328 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
9268 GTTATTTTTG
*
9278 GTATCGATACTCAGGGGTCA
1 GTATCGATACTCAAGGGTCA
* *
9298 TTATCAATACTCAAGGGTCA
1 GTATCGATACTCAAGGGTCA
9318 GTATCGATACT
1 GTATCGATACT
9329 GCTGATATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (20 bp):
GTATCGATACTCAAGGGTCA
Found at i:19030 original size:17 final size:17
Alignment explanation
Indices: 18982--19031 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
18972 TTCCTTTCAT
18982 TATATTGTATCTTTTAC
1 TATATTGTATCTTTTAC
** * * *
18999 TGCACTATATATTTTAC
1 TATATTGTATCTTTTAC
19016 TATATTGTATCTTTTA
1 TATATTGTATCTTTTA
19032 GTTTCATTTC
Statistics
Matches: 23, Mismatches: 10, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (17 bp):
TATATTGTATCTTTTAC
Found at i:19359 original size:21 final size:21
Alignment explanation
Indices: 19308--19364 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 21
19298 CGTGAAACCC
*
19308 ATAATGCACATATAGTGTCAG
1 ATAATGCACATAAAGTGTCAG
*
19329 A-ACT-CACATAAAGT-TCTAG
1 ATAATGCACATAAAGTGTC-AG
*
19348 ATAATGCACATATAGTG
1 ATAATGCACATAAAGTG
19365 CATGACAGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
18 2 0.07
19 12 0.43
20 4 0.14
21 10 0.36
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (21 bp):
ATAATGCACATAAAGTGTCAG
Found at i:21730 original size:18 final size:19
Alignment explanation
Indices: 21695--21731 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21685 TTTGACCTTC
21695 TTTTATTAAGTCTCTGATG
1 TTTTATTAAGTCTCTGATG
*
21714 TTTTATTACGT-TCTGATG
1 TTTTATTAAGTCTCTGATG
21732 ATTCAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.19, C:0.11, G:0.16, T:0.54
Consensus pattern (19 bp):
TTTTATTAAGTCTCTGATG
Found at i:22630 original size:21 final size:21
Alignment explanation
Indices: 22604--22683 Score: 108
Period size: 21 Copynumber: 3.7 Consensus size: 21
22594 AAAATACCAT
*
22604 AGTACACGAAGTACTACTCCA
1 AGTACACAAAGTACTACTCCA
*
22625 AGTACACAAAGTACT-CTTGACA
1 AGTACACAAAGTACTAC-T-CCA
22647 CAGTACACAAAGTACTACTCCA
1 -AGTACACAAAGTACTACTCCA
22669 AGTACACAAAGTACT
1 AGTACACAAAGTACT
22684 CTTACAAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
20 1 0.02
21 30 0.58
22 4 0.08
23 16 0.31
24 1 0.02
ACGTcount: A:0.41, C:0.26, G:0.12, T:0.20
Consensus pattern (21 bp):
AGTACACAAAGTACTACTCCA
Found at i:32222 original size:19 final size:20
Alignment explanation
Indices: 32198--32241 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
32188 GCTATTTTTG
*
32198 GTATCGATACTC-AAGGTTA
1 GTATCGATACTCAAAGGTCA
32217 GTATCGATACTCAAAGGTCA
1 GTATCGATACTCAAAGGTCA
32237 GTATC
1 GTATC
32242 AATAATGCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (20 bp):
GTATCGATACTCAAAGGTCA
Found at i:40191 original size:36 final size:36
Alignment explanation
Indices: 40144--40217 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
40134 GAGTCAGAGG
40144 ATGCAGCCTTAGAAACAACCTCAACAGAGGTTGGGA
1 ATGCAGCCTTAGAAACAACCTCAACAGAGGTTGGGA
40180 ATGCAGCCTTAGAAACAACCTCAACAGAGGTTGGGA
1 ATGCAGCCTTAGAAACAACCTCAACAGAGGTTGGGA
40216 AT
1 AT
40218 ACCATCATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (36 bp):
ATGCAGCCTTAGAAACAACCTCAACAGAGGTTGGGA
Found at i:40385 original size:18 final size:18
Alignment explanation
Indices: 40362--40398 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40352 GAAATGTGCT
*
40362 AGAGTCCTAGTTAAGTTA
1 AGAGTCCTAGCTAAGTTA
40380 AGAGTCCTAGCTAAGTTA
1 AGAGTCCTAGCTAAGTTA
40398 A
1 A
40399 CCTTATCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.30
Consensus pattern (18 bp):
AGAGTCCTAGCTAAGTTA
Found at i:42982 original size:116 final size:116
Alignment explanation
Indices: 42751--42975 Score: 396
Period size: 116 Copynumber: 1.9 Consensus size: 116
42741 TATAGTAGGT
* *
42751 GGTCGTCTCCCGAGGTTAACACGATAGCTCCGAAAATCGTACACCCAAAGATCGGAGTGGACAAC
1 GGTCGTCTCCCGAGATTAACACGATAGCTCCGAAAATCATACACCCAAAGATCGGAGTGGACAAC
*
42816 AATGGTACTACTATTCTCTTAGTACCGAAAAGAAAGCTTAGAAATCTTTAG
66 AATGGTACTACTATTCTCTTAGCACCGAAAAGAAAGCTTAGAAATCTTTAG
* *
42867 GGTCGTTTCCCGAGATTAACACGATAGTTCCGAAAATCATACACCCAAAGATCGGAGTGGACAAC
1 GGTCGTCTCCCGAGATTAACACGATAGCTCCGAAAATCATACACCCAAAGATCGGAGTGGACAAC
*
42932 AATGGTACTACTCTTCTCTTAGCACCGAAAAGAAAGCTTAGAAA
66 AATGGTACTACTATTCTCTTAGCACCGAAAAGAAAGCTTAGAAA
42976 GTTTTAGAGG
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
116 103 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (116 bp):
GGTCGTCTCCCGAGATTAACACGATAGCTCCGAAAATCATACACCCAAAGATCGGAGTGGACAAC
AATGGTACTACTATTCTCTTAGCACCGAAAAGAAAGCTTAGAAATCTTTAG
Found at i:48949 original size:21 final size:21
Alignment explanation
Indices: 48920--48964 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
48910 CCCATACCAA
*
48920 ACCAGACCCGACCCGCACCTG
1 ACCAAACCCGACCCGCACCTG
48941 ACCAAACCCGACCCGCACCTG
1 ACCAAACCCGACCCGCACCTG
48962 ACC
1 ACC
48965 CTAGCTCTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.53, G:0.16, T:0.04
Consensus pattern (21 bp):
ACCAAACCCGACCCGCACCTG
Found at i:50023 original size:17 final size:16
Alignment explanation
Indices: 49981--50023 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
49971 TTCGATTACA
*
49981 TGTTTAATTTTGCATT
1 TGTTTAATTTAGCATT
*
49997 TATTTCAATTTAGTCATT
1 TGTTT-AATTTAG-CATT
50015 TGTTTAATT
1 TGTTTAATT
50024 CACATAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
18 8 0.36
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.60
Consensus pattern (16 bp):
TGTTTAATTTAGCATT
Found at i:50120 original size:28 final size:29
Alignment explanation
Indices: 50069--50135 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
50059 CTATAAATTT
*
50069 CAATTTAGTCCCTAATTCTAA-TTTATTG
1 CAATTTAGTTCCTAATTCTAATTTTATTG
* * * *
50097 CAATTTAGTTCCTATTTTTTATTTTATTT
1 CAATTTAGTTCCTAATTCTAATTTTATTG
*
50126 TAATTTAGTT
1 CAATTTAGTT
50136 TTCACTTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 17 0.53
29 15 0.47
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.57
Consensus pattern (29 bp):
CAATTTAGTTCCTAATTCTAATTTTATTG
Found at i:54769 original size:22 final size:22
Alignment explanation
Indices: 54744--54788 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
54734 CATTATCATT
54744 TTACCTATTGAACATGCTGTCA
1 TTACCTATTGAACATGCTGTCA
54766 TTACCTATTGAACATGCTGTCA
1 TTACCTATTGAACATGCTGTCA
54788 T
1 T
54789 AAGTTTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (22 bp):
TTACCTATTGAACATGCTGTCA
Found at i:56672 original size:9 final size:9
Alignment explanation
Indices: 56640--56699 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
56630 CTGCTGGAAA
56640 ACCGGTTTG
1 ACCGGTTTG
*
56649 ACCAGTTTTG
1 ACC-GGTTTG
56659 AACCGGTTTG
1 -ACCGGTTTG
*
56669 ACCGGTTCG
1 ACCGGTTTG
56678 AACCGGTTTG
1 -ACCGGTTTG
*
56688 ACCGGTCTG
1 ACCGGTTTG
56697 ACC
1 ACC
56700 CGACCCGTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 22 0.51
10 18 0.42
11 3 0.07
ACGTcount: A:0.17, C:0.27, G:0.28, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:56682 original size:19 final size:19
Alignment explanation
Indices: 56639--56693 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 19
56629 GCTGCTGGAA
* *
56639 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
56659 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
56678 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
56694 CTGACCCGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 20 0.61
20 13 0.39
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:56709 original size:14 final size:14
Alignment explanation
Indices: 56687--56720 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
56677 GAACCGGTTT
*
56687 GACCGGTCTGACCC
1 GACCCGTCTGACCC
56701 GACCCGTCTGACCC
1 GACCCGTCTGACCC
56715 GACCCG
1 GACCCG
56721 ACCCGACCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.47, G:0.26, T:0.12
Consensus pattern (14 bp):
GACCCGTCTGACCC
Found at i:63955 original size:9 final size:9
Alignment explanation
Indices: 63923--63982 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
63913 CTGCTGGAAA
63923 ACCGGTTTG
1 ACCGGTTTG
*
63932 ACCAGTTTTG
1 ACC-GGTTTG
63942 AACCGGTTTG
1 -ACCGGTTTG
*
63952 ACCGGTCTGG
1 ACCGGT-TTG
63962 ACCGGTTTG
1 ACCGGTTTG
*
63971 ACCGGTCTG
1 ACCGGTTTG
63980 ACC
1 ACC
63983 CGACCCGTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 22 0.51
10 18 0.42
11 3 0.07
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:63967 original size:19 final size:19
Alignment explanation
Indices: 63922--63980 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
63912 GCTGCTGGAA
* *
63922 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
63942 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
63961 GACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
63980 A
1 A
63981 CCCGACCCGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 22 0.63
20 13 0.37
ACGTcount: A:0.17, C:0.24, G:0.31, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:63992 original size:14 final size:14
Alignment explanation
Indices: 63970--64016 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
63960 GGACCGGTTT
*
63970 GACCGGTCTGACCC
1 GACCCGTCTGACCC
63984 GACCCGTCTGACCC
1 GACCCGTCTGACCC
63998 GACCCGTCTGACCC
1 GACCCGTCTGACCC
64012 GACCC
1 GACCC
64017 AACCCGACTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.15, C:0.49, G:0.23, T:0.13
Consensus pattern (14 bp):
GACCCGTCTGACCC
Found at i:64038 original size:17 final size:17
Alignment explanation
Indices: 64012--64049 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
64002 CGTCTGACCC
*
64012 GACCCAACCCGACTGTT
1 GACCCAACCCGACCGTT
*
64029 GACCCGACCCGACCGTT
1 GACCCAACCCGACCGTT
64046 GACC
1 GACC
64050 GTTGACCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.13
Consensus pattern (17 bp):
GACCCAACCCGACCGTT
Found at i:65033 original size:63 final size:63
Alignment explanation
Indices: 64931--65054 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
64921 CTAATGTGAC
* ** * *
64931 TCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCAACGGCCCCGAAATCATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
64994 TCTTAGGTAGGCCCAACGGCCCCGAAATC-TATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCAACGGCCCCGAAATCAT-TCTCGGGTAGGCCCTCAGGCCCTAAGATGT
65055 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.26
Consensus pattern (63 bp):
TCTTAGGTAGGCCCAACGGCCCCGAAATCATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:69037 original size:2 final size:2
Alignment explanation
Indices: 69030--69062 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
69020 TATAATTTTC
69030 TA TA TA TA 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 T
69063 GGGTTAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76066 original size:31 final size:32
Alignment explanation
Indices: 76003--76081 Score: 133
Period size: 31 Copynumber: 2.5 Consensus size: 32
75993 ATTCAAAAAA
*
76003 TAAGTTTTGCTCACTTACGTTATCAATTTTAT
1 TAAGTTTTGATCACTTACGTTATCAATTTTAT
*
76035 TAAGTTTTAATCACTTACGTTATC-ATTTTAT
1 TAAGTTTTGATCACTTACGTTATCAATTTTAT
76066 TAAGTTTTGATCACTT
1 TAAGTTTTGATCACTT
76082 GGACTTTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
31 22 0.50
32 22 0.50
ACGTcount: A:0.27, C:0.14, G:0.09, T:0.51
Consensus pattern (32 bp):
TAAGTTTTGATCACTTACGTTATCAATTTTAT
Done.