Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008676.1 Hibiscus syriacus cultivar Beakdansim tig00111693_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: 957917
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 4
Found at i:906892 original size:149 final size:149
Alignment explanation
Indices: 906622--906936 Score: 605
Period size: 149 Copynumber: 2.1 Consensus size: 149
906612 TATAATTGCA
906622 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
906686 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTT
906751 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
*
906771 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATGAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
906836 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
906901 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
906920 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
906937 CCCTCGACTC
Statistics
Matches: 164, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
148 1 0.01
149 163 0.99
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:907846 original size:18 final size:18
Alignment explanation
Indices: 907825--907859 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
907815 TCCCATCTAG
907825 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
907843 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
907860 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:908470 original size:21 final size:21
Alignment explanation
Indices: 908440--908484 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
908430 TGTTGTTTGT
* *
908440 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
908461 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
908482 TTG
1 TTG
908485 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:911704 original size:23 final size:23
Alignment explanation
Indices: 911678--911722 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
911668 CACCACAGCT
*
911678 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
911701 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
911723 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:911968 original size:149 final size:149
Alignment explanation
Indices: 911698--912004 Score: 587
Period size: 149 Copynumber: 2.1 Consensus size: 149
911688 CACCGAAGTG
911698 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
*
911763 AATCATATACATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATGCTAAGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAAT
*
911828 ATACATATGTCCTGAAGAA
131 ATACATATGTCCCGAAGAA
911847 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
1 CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
911912 AATCATATACATATGCTAAGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAAT
66 AATCATATACATATGCTAAGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAAT
*
911977 ATACATATGTCCCGAAGGA
131 ATACATATGTCCCGAAGAA
911996 CCGCGTAGA
1 CCGCGTAGA
912005 CCCTCGACTC
Statistics
Matches: 155, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 155 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAG
AATCATATACATATGCTAAGGATCATATATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAAT
ATACATATGTCCCGAAGAA
Found at i:912917 original size:18 final size:18
Alignment explanation
Indices: 912896--912930 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
912886 TCCCATCTAG
912896 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
912914 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
912931 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:913535 original size:21 final size:21
Alignment explanation
Indices: 913511--913553 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
913501 TGTTGTTCGT
* *
913511 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
913532 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
913553 T
1 T
913554 GCCCAGAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:921185 original size:29 final size:29
Alignment explanation
Indices: 921152--921243 Score: 80
Period size: 29 Copynumber: 3.0 Consensus size: 29
921142 AAATGTGTCT
921152 CTGATGTTTACTTGGCTTTCAAATTTTCA
1 CTGATGTTTACTTGGCTTTCAAATTTTCA
* *
921181 CTGATGTTCTAACTT--CTTTGAAGGAAATGTGTCA
1 CTGATGTT-T-ACTTGGCTTT----CAAAT-TTTCA
*
921215 CTGATGTTTACTTGGCTCTCAAATTTTCA
1 CTGATGTTTACTTGGCTTTCAAATTTTCA
921244 GCAAATAAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 18
0.68 0.07 0.25
Matches are distributed among these distances:
29 16 0.33
30 5 0.10
31 4 0.08
32 4 0.08
33 5 0.10
34 15 0.31
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.43
Consensus pattern (29 bp):
CTGATGTTTACTTGGCTTTCAAATTTTCA
Found at i:926212 original size:211 final size:205
Alignment explanation
Indices: 925800--926213 Score: 738
Period size: 211 Copynumber: 2.0 Consensus size: 205
925790 CTGCTACTCC
925800 TTGTGGATGATAGATACCAGAAAAGGAGCCAGGACCAACCTGTGTTGGAGCAAACGTCACATTCT
1 TTGTGGATGATAGATACCAGAAAAGGAGCCAGGACCAACCTGTGTTGGAGCAAACGTCACATTCT
* *
925865 GACTCTGAGGAGGAATAGAATGAACTAGATGGCAGCCTGGATGTGTCTCGACCAGGGGAGCAATC
66 GACTCTGAGGAGGAATAGAATGAACTAGATGGCAGACTGGATATGTCTCGACCAGGGGAGCAATC
925930 CACACAGCTGAACCTTCACTCTGCAGCAAAGAAAATATGTGAAAAAATGATAATAGAAGGAAAAG
131 CACACAGCTGAACCTTCACTCTGCAGCAAAGAAAATATGTGAAAAAATGATAATAGAAGGAAAAG
925995 AATTTTTTAA
196 AATTTTTTAA
926005 TTGTGGATGATAGATACCAGAAAAGGAGCCAGGACCAACCTGTGTTGGAGCAAACGTCACATTCT
1 TTGTGGATGATAGATACCAGAAAAGGAGCCAGGACCAACCTGTGTTGGAGCAAACGTCACATTCT
*
926070 GACTCTGAGGAGGAAGGTTATAGAATGAACTAGCTGGCAGACTGGATATGTCTCGACCAGGGGGA
66 GACTCTGAGGAGG-A----ATAGAATGAACTAGATGGCAGACTGGATATGTCTCGACCA-GGGGA
926135 GCAATCCACACAGCTGAACCTTCACTCTGCAGCAAAGAAAATATGTGAAAAAATGATAATAGAAG
125 GCAATCCACACAGCTGAACCTTCACTCTGCAGCAAAGAAAATATGTGAAAAAATGATAATAGAAG
*
926200 GAAAATAATTTTTT
190 GAAAAGAATTTTTT
926214 TTTAAAAAAT
Statistics
Matches: 199, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
205 78 0.39
206 1 0.01
210 37 0.19
211 83 0.42
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.21
Consensus pattern (205 bp):
TTGTGGATGATAGATACCAGAAAAGGAGCCAGGACCAACCTGTGTTGGAGCAAACGTCACATTCT
GACTCTGAGGAGGAATAGAATGAACTAGATGGCAGACTGGATATGTCTCGACCAGGGGAGCAATC
CACACAGCTGAACCTTCACTCTGCAGCAAAGAAAATATGTGAAAAAATGATAATAGAAGGAAAAG
AATTTTTTAA
Found at i:941214 original size:184 final size:184
Alignment explanation
Indices: 940922--941296 Score: 610
Period size: 184 Copynumber: 2.0 Consensus size: 184
940912 TATAAAAATT
*
940922 AAATGTTTTTAATTAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 AAAT-TTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
* *
940987 TTCAGATAAATTTGTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTAT
65 TTCAGATAAATTTGTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATATTAAATTAT
* *
941052 TAATTG-GATTTTAAATGGTTTGGACTTAGCCCATATGTTATATATAATATATATA
130 TAATTGTG-TTTTAAATGGTTTGGACTGAGCACATATGTTATATATAATATATATA
*
941107 ATATTTTTTAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 AAATTTTTTAATTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
* * *
941172 TTTATAT-AATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATATTAAATTAT
65 TTCAGATAAATTTGTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATATTAAATTAT
* *
941236 TAATTGTGTTTTAAATGGTTTGGGCTGAGCACATATGTTATATATAATATATTTA
130 TAATTGTGTTTTAAATGGTTTGGACTGAGCACATATGTTATATATAATATATATA
941291 AAATTT
1 AAATTT
941297 AATTTCGGTT
Statistics
Matches: 176, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
184 124 0.70
185 52 0.30
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (184 bp):
AAATTTTTTAATTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATT
TCAGATAAATTTGTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATATTAAATTATT
AATTGTGTTTTAAATGGTTTGGACTGAGCACATATGTTATATATAATATATATA
Found at i:942099 original size:21 final size:21
Alignment explanation
Indices: 942073--942167 Score: 93
Period size: 21 Copynumber: 4.6 Consensus size: 21
942063 GCGTTACATT
* *
942073 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTTAAAG
* * **
942094 TCGCGTTGCGAT-TTTTCATT
1 TCGCGTTGCGATAGTTTAAAG
* * *
942114 TCGCGTTACGATAGTCTATAG
1 TCGCGTTGCGATAGTTTAAAG
*
942135 TCGCGTTGCGATAGTTTACAG
1 TCGCGTTGCGATAGTTTAAAG
942156 TCGCGTTGCGAT
1 TCGCGTTGCGAT
942168 TTTTCATTAA
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 14 0.24
21 44 0.76
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTTAAAG
Found at i:942114 original size:41 final size:41
Alignment explanation
Indices: 942069--942146 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 41
942059 ATTTGCGTTA
*
942069 CATTTCGCGTTGCGATAGT-TGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTACGATAGTCT-AAAATCGCGTTGCGATTTTT
* *
942110 CATTTCGCGTTACGATAGTCTATAGTCGCGTTGCGAT
1 CATTTCGCGTTACGATAGTCTAAAATCGCGTTGCGAT
942147 AGTTTACAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 32 0.97
42 1 0.03
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTACGATAGTCTAAAATCGCGTTGCGATTTTT
Found at i:942263 original size:41 final size:41
Alignment explanation
Indices: 942216--942465 Score: 301
Period size: 41 Copynumber: 6.0 Consensus size: 41
942206 TCAACGAATT
* *
942216 TGGAAAATCGCAACGACAATTGT-AGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGATTTTCA-ACTATCGCAACGCGAAA
* *
942258 TGAAAAATCGTAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
* *
942299 TGGAAAATCACAACGCGATTTTCAACTATCGCAACGCGAATT
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAA-A
** *
942341 TGCGATGAT-GGAGATCGCG-TTTT-AACTATCGCAACGCGAAA
1 TG-GAAAATCGCA-A-CGCGATTTTCAACTATCGCAACGCGAAA
* *
942382 TGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
* *
942423 TGGAAAAACGCAACGCGATTTTCAACTATCGCAATGCGAAA
1 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
942464 TG
1 TG
942466 CAACGTGAAT
Statistics
Matches: 178, Mismatches: 22, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
39 4 0.02
40 7 0.04
41 120 0.67
42 34 0.19
43 9 0.05
44 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (41 bp):
TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
Found at i:942393 original size:20 final size:20
Alignment explanation
Indices: 942368--942440 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
942358 CGTTTTAACT
942368 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
942388 ATCGCAACGCGATCTCCAACT
1 ATCGCAACGCGAAATGGAA-A
942409 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
*
942429 AACGCAACGCGA
1 ATCGCAACGCGA
942441 TTTTCAACTA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.40, C:0.27, G:0.22, T:0.11
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:942469 original size:21 final size:21
Alignment explanation
Indices: 942241--942469 Score: 96
Period size: 21 Copynumber: 11.1 Consensus size: 21
942231 ACAATTGTAG
942241 ACTATCGCAACGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** * ** *
942261 AAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
942282 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
942303 A-AATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
* *
942323 ACTATCGCAACGCGAATTTGCG
1 ACTATCGCAACGCGAA-ATGCA
* * **
942345 A-TGAT-GGAGATCGCG--TTTTA
1 ACT-ATCGCA-A-CGCGAAATGCA
*
942365 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
942386 A-AATCGCAACGCGATCTCCA
1 ACTATCGCAACGCGAAATGCA
*
942406 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
942427 A-AAACGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
942447 ACTATCGCAATGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
942468 AC
1 AC
942470 GTGAATTTGC
Statistics
Matches: 143, Mismatches: 54, Indels: 23
0.65 0.25 0.10
Matches are distributed among these distances:
19 4 0.03
20 62 0.43
21 66 0.46
22 7 0.05
23 4 0.03
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:944093 original size:12 final size:12
Alignment explanation
Indices: 944038--944114 Score: 67
Period size: 12 Copynumber: 6.8 Consensus size: 12
944028 TGAAATGTAC
944038 ACATA-ATA-AT
1 ACATAGATATAT
944048 A-ATAGATATAT
1 ACATAGATATAT
* *
944059 AAATAAACTAT-T
1 ACATAGA-TATAT
944071 ACA-AG-TATAT
1 ACATAGATATAT
944081 ACATAGATATAT
1 ACATAGATATAT
*
944093 ACATATATATAT
1 ACATAGATATAT
*
944105 ACATATATAT
1 ACATAGATAT
944115 TAAAATATAA
Statistics
Matches: 56, Mismatches: 4, Indels: 12
0.78 0.06 0.17
Matches are distributed among these distances:
9 6 0.11
10 8 0.14
11 6 0.11
12 33 0.59
13 3 0.05
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (12 bp):
ACATAGATATAT
Found at i:944708 original size:63 final size:63
Alignment explanation
Indices: 944609--944734 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
944599 AAGGGAATTA
*
944609 AACCGATTTGGGGACCAAATTAAACGTTTTTTAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
* * *
944672 AACCGGTTTGGGGACCAAATTGAATGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
1 AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
944735 CTTTTAACAA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (63 bp):
AACCGATTTGGGGACCAAATTAAACGTTTTTCAAAACAGAGGGAGCCAAAATGAAGTTTACCC
Found at i:945689 original size:2 final size:2
Alignment explanation
Indices: 945682--945739 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
945672 CATATGTAAA
*
945682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT -T AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
945722 AT GT AA AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT A
945740 ATGTTAAAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
1 3 0.06
2 44 0.94
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:946254 original size:105 final size:104
Alignment explanation
Indices: 946086--946949 Score: 1410
Period size: 105 Copynumber: 8.2 Consensus size: 104
946076 GTCAACCTGT
* **
946086 TTGTGAAGTTGGAAA-TGGCTATGGAATTGAGAAAT-TATTCGTTGACAGTCAGTC-GTCCCTTC
1 TTGTGAAGTT-GAAATTGGCTCT-GAATTGAGAAATGT-TT-GTTGACAACCAG-CGGTCCCTTC
* * * * * * *
946148 GTTGTGAAGTCGAGCTTGTGCTGTCTTGAGTCCAATATCCTTTG
61 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
* *
946192 CTGTGAAGTTGAAATTGGCTCTGACATTGAGAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGA-ATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
946257 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
65 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
** ** *
946297 TTGCAAAGTTGAAATTGGCTCTGAAATTGAGAGGTGTTTATTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTG-AATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
*
946362 TGAAGTTGAACTTGCGTTGTCGGGAGTCCAATATCCTTCG
65 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
946402 CTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAA-TTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
946467 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
65 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
946507 TTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAATT-GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
946572 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
65 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
946612 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAA-TTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
946677 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
65 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
*
946717 TTGTGAAGTTGAAATTGGCTCTGAATTGGAGAAATGTTTGGTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAATT-GAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
946782 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
65 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
946822 TTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
1 TTGTGAAGTTGAAATTGGCTCTGAA-TTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCG
946887 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
65 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
946927 TTGTGAAGTTGAAATTGGCTCTG
1 TTGTGAAGTTGAAATTGGCTCTG
946950 GGTAAAACCT
Statistics
Matches: 718, Mismatches: 30, Indels: 21
0.93 0.04 0.03
Matches are distributed among these distances:
104 7 0.01
105 679 0.95
106 31 0.04
107 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (104 bp):
TTGTGAAGTTGAAATTGGCTCTGAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGT
GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
Done.