Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000986.1 Hibiscus syriacus cultivar Beakdansim tig00001976_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: 69013
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:375 original size:26 final size:24
Alignment explanation
Indices: 304--375 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
294 TTATATTTGT
304 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
329 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
351 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
376 GTTGGACTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:4324 original size:15 final size:15
Alignment explanation
Indices: 4301--4330 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4291 TCCGAAAGTT
4301 TCGAATACCCAAAAA
1 TCGAATACCCAAAAA
*
4316 TCGAGTACCCAAAAA
1 TCGAATACCCAAAAA
4331 CCCGGATACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.10, T:0.13
Consensus pattern (15 bp):
TCGAATACCCAAAAA
Found at i:20755 original size:40 final size:41
Alignment explanation
Indices: 20698--20775 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 41
20688 CTTTATCCTT
*
20698 ATTTGAGGTTCAGGGATAAAACTCCCCT-ATCCTCATCTCC
1 ATTTGAGGTTCAGGGATAAAACTCCCCTCATCCCCATCTCC
*
20738 ATTTGAGGTTC-GAGGATAAAACTTCCCTCATCCCCATC
1 ATTTGAGGTTCAG-GGATAAAACTCCCCTCATCCCCATC
20776 CATGTGAGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 1 0.03
40 25 0.74
41 8 0.24
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (41 bp):
ATTTGAGGTTCAGGGATAAAACTCCCCTCATCCCCATCTCC
Found at i:21387 original size:2 final size:2
Alignment explanation
Indices: 21380--21415 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
21370 ATGAATACAA
21380 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
21416 TTAAATGCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21494 original size:10 final size:10
Alignment explanation
Indices: 21479--21505 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
21469 TTATGAATAA
21479 AAATACATTT
1 AAATACATTT
21489 AAATACATTT
1 AAATACATTT
21499 AAATACA
1 AAATACA
21506 AATATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (10 bp):
AAATACATTT
Found at i:21529 original size:101 final size:100
Alignment explanation
Indices: 21343--21534 Score: 233
Period size: 101 Copynumber: 1.9 Consensus size: 100
21333 TAAATATATT
* * * * * *
21343 TATATTTTAACAAAAATATTTAAATAGATGAATACAAATATATATATATATATATATATATATAT
1 TATATTTTAACAAAAATATTTAAATAGATGAATAAAAATATATAAATACATATAAATACAAATAT
21408 ATATATATTTAAATGCATTTAAATATGCGAATAAAA
66 ATATATATTTAAAT-CATTTAAATATGCGAATAAAA
** * *
21444 TATATTTTAACAAAAATATTTAAATTTATGAATAAAAATACATTTAAATACATTTAAATACAAAT
1 TATATTTTAACAAAAATATTTAAATAGATGAATAAAAAT--ATATAAATACATATAAATACAAAT
* * *
21509 ATTTATTTATTTATAT-ATTTAAATAT
64 ATATATATATTTAAATCATTTAAATAT
21535 TTTTATTAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
101 46 0.61
103 30 0.39
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (100 bp):
TATATTTTAACAAAAATATTTAAATAGATGAATAAAAATATATAAATACATATAAATACAAATAT
ATATATATTTAAATCATTTAAATATGCGAATAAAA
Found at i:21685 original size:18 final size:18
Alignment explanation
Indices: 21662--21696 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21652 TAATAAACAA
* *
21662 TAAAATTATTAATTAAAT
1 TAAAATAATCAATTAAAT
21680 TAAAATAATCAATTAAA
1 TAAAATAATCAATTAAA
21697 ATTATAGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATAATCAATTAAAT
Found at i:21687 original size:30 final size:30
Alignment explanation
Indices: 21653--21709 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
21643 TTTTATATTT
21653 AATAAACAA-TAAAATTATTAATTAAATTAA
1 AATAAACAATTAAAATTA-TAATTAAATTAA
* *
21683 AATAATCAATTAAAATTATAGTTAAAT
1 AATAAACAATTAAAATTATAATTAAAT
21710 ATTTTTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (30 bp):
AATAAACAATTAAAATTATAATTAAATTAA
Found at i:28348 original size:21 final size:21
Alignment explanation
Indices: 28315--28408 Score: 109
Period size: 21 Copynumber: 4.5 Consensus size: 21
28305 TCTGTCGATG
*
28315 CCGCATGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
28336 CCGCAGGGATACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
* *
28357 CCGCAGGGTTATATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* * *
28378 CCGCCA-GGTTATATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
28399 CCGCAGGGTT
1 CCGCAGGGTT
28409 TTATACCATA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
20 2 0.03
21 61 0.94
22 2 0.03
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:28981 original size:34 final size:34
Alignment explanation
Indices: 28931--29028 Score: 133
Period size: 34 Copynumber: 2.9 Consensus size: 34
28921 AAATGTTTTT
* *
28931 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
28965 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
28999 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
29029 CATTAAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:29654 original size:128 final size:128
Alignment explanation
Indices: 29426--29776 Score: 693
Period size: 128 Copynumber: 2.7 Consensus size: 128
29416 ACAATCCATC
*
29426 TAGTGTCCCCGAGGGACATGAGTAACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
29491 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
29554 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
29619 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
29682 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
29747 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
29777 TGTGAATAGT
Statistics
Matches: 222, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 222 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:29870 original size:8 final size:8
Alignment explanation
Indices: 29857--29897 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
29847 TCACAAGCTT
29857 TCAAATTC
1 TCAAATTC
29865 TCAAATTC
1 TCAAATTC
* *
29873 CCAAACTC
1 TCAAATTC
29881 T-AAATTC
1 TCAAATTC
29888 TCAAATTC
1 TCAAATTC
29896 TC
1 TC
29898 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:30976 original size:173 final size:173
Alignment explanation
Indices: 30687--31034 Score: 687
Period size: 173 Copynumber: 2.0 Consensus size: 173
30677 GGATTATTCG
30687 TTGAACCTGACTCACCACAGTTTAACGTACATTCTGATGATGACGAGGATGACGTTCTGATAAAT
1 TTGAACCTGACTCACCACAGTTTAACGTACATTCTGATGATGACGAGGATGACGTTCTGATAAAT
*
30752 ACAACACCAGCCGAACTTTCTGCACATATGTATGAGGCTGATTATGATGCAATGTATGAGCCTGA
66 ACAACACCAGCCGAACTTCCTGCACATATGTATGAGGCTGATTATGATGCAATGTATGAGCCTGA
30817 ATTTCCAGATCTTCCTGATGTTGGCAACTATGGACTTCAATCA
131 ATTTCCAGATCTTCCTGATGTTGGCAACTATGGACTTCAATCA
30860 TTGAACCTGACTCACCACAGTTTAACGTACATTCTGATGATGACGAGGATGACGTTCTGATAAAT
1 TTGAACCTGACTCACCACAGTTTAACGTACATTCTGATGATGACGAGGATGACGTTCTGATAAAT
30925 ACAACACCAGCCGAACTTCCTGCACATATGTATGAGGCTGATTATGATGCAATGTATGAGCCTGA
66 ACAACACCAGCCGAACTTCCTGCACATATGTATGAGGCTGATTATGATGCAATGTATGAGCCTGA
30990 ATTTCCAGATCTTCCTGATGTTGGCAACTATGGACTTCAATCA
131 ATTTCCAGATCTTCCTGATGTTGGCAACTATGGACTTCAATCA
31033 TT
1 TT
31035 AGTCATTGAC
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
173 174 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (173 bp):
TTGAACCTGACTCACCACAGTTTAACGTACATTCTGATGATGACGAGGATGACGTTCTGATAAAT
ACAACACCAGCCGAACTTCCTGCACATATGTATGAGGCTGATTATGATGCAATGTATGAGCCTGA
ATTTCCAGATCTTCCTGATGTTGGCAACTATGGACTTCAATCA
Found at i:37081 original size:33 final size:34
Alignment explanation
Indices: 37039--37114 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 34
37029 GTGGTAAGAA
* *
37039 ATTTATTTTTATGTTAGTAT-TTT-T-TAAATAGTT
1 ATTT-TTTTTATATTAATATATTTATGTAAATA-TT
37072 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTATATTAATATATTTATGTAAATATT
37107 ATTTTTTT
1 ATTTTTTT
37115 ATTAAAAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
33 16 0.43
34 9 0.24
35 6 0.16
36 6 0.16
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (34 bp):
ATTTTTTTTATATTAATATATTTATGTAAATATT
Found at i:37126 original size:21 final size:21
Alignment explanation
Indices: 37100--37159 Score: 57
Period size: 24 Copynumber: 2.7 Consensus size: 21
37090 ATATTTATGT
37100 AAATATTATTTTTTTATTAAA
1 AAATATTATTTTTTTATTAAA
* *
37121 AAATATTTATATTTATTTATTTAG
1 AAATA-TTAT-TTT-TTTATTAAA
* *
37145 AATTATTAATTTTTT
1 AAATATTATTTTTTT
37160 GCTAATTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
21 8 0.25
22 7 0.22
23 6 0.19
24 11 0.34
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
AAATATTATTTTTTTATTAAA
Found at i:38885 original size:21 final size:21
Alignment explanation
Indices: 38855--38902 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
38845 GTAGGGGTAC
* *
38855 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
38876 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
38897 ATGCCA
1 ATGCCA
38903 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:38932 original size:21 final size:21
Alignment explanation
Indices: 38906--38999 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
38896 TATGCCATCT
* *
38906 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
38927 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
38948 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
*
38969 CTGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
38990 CCGCAGGGTT
1 CCGCAGGGTT
39000 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:39581 original size:33 final size:34
Alignment explanation
Indices: 39522--39618 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
39512 AAATGTTTTT
*
39522 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
39556 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
39589 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
39619 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:39625 original size:34 final size:33
Alignment explanation
Indices: 39520--39625 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
39510 ATAAATGTTT
*
39520 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
39554 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
39586 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
39621 TTAAA
1 TTAAA
39626 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:40232 original size:126 final size:126
Alignment explanation
Indices: 40005--40484 Score: 926
Period size: 126 Copynumber: 3.8 Consensus size: 126
39995 TTTAAGTTAT
40005 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACGAAATAATGGAAG
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGAT-A-ATATTCTCTGACGAAATAATGGAAG
40070 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
64 GCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
40133 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
40198 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
40259 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
40324 GTGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
40385 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
40450 GCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
40485 CCGATTATAG
Statistics
Matches: 350, Mismatches: 2, Indels: 3
0.99 0.01 0.01
Matches are distributed among these distances:
125 32 0.09
126 280 0.80
127 1 0.00
128 37 0.11
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (126 bp):
TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:40565 original size:8 final size:8
Alignment explanation
Indices: 40552--40592 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
40542 TCACAATCTT
40552 TCAAATTC
1 TCAAATTC
40560 TCAAATTC
1 TCAAATTC
* *
40568 CCAAACTC
1 TCAAATTC
40576 T-AAATTC
1 TCAAATTC
40583 TCAAATTC
1 TCAAATTC
40591 TC
1 TC
40593 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:44259 original size:6 final size:6
Alignment explanation
Indices: 44243--44279 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
44233 TAAAAACCCC
44243 TCTCT- TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TC
1 TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TCTCTG TC
44280 CCCCAAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.00, C:0.35, G:0.14, T:0.51
Consensus pattern (6 bp):
TCTCTG
Found at i:46582 original size:5 final size:5
Alignment explanation
Indices: 46572--46597 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46562 TATTAGACTG
46572 AAATA AAATA AAATA AAATA AAATA A
1 AAATA AAATA AAATA AAATA AAATA A
46598 TGAAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:48638 original size:2 final size:2
Alignment explanation
Indices: 48631--48656 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48621 ACCAATCACA
48631 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
48657 GACTAATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54823 original size:2 final size:2
Alignment explanation
Indices: 54816--54840 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54806 TGCATGCGTC
54816 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 T
54841 CATTGTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56613 original size:2 final size:2
Alignment explanation
Indices: 56606--56630 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56596 ATATGTATTT
56606 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 T
56631 GTAATTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60131 original size:21 final size:20
Alignment explanation
Indices: 60107--60231 Score: 74
Period size: 21 Copynumber: 5.9 Consensus size: 20
60097 ACTTCGACTA
60107 TCGCATTGCGATAGTCCAAGT
1 TCGC-TTGCGATAGTCCAAGT
* *
60128 TCGCGTTGCGATAATCAAAGT
1 TCGC-TTGCGATAGTCCAAGT
* * *
60149 TCGCGTTGCGATTTATTTACAAAT
1 TCGC-TTGCGA--TA-GTCCAAGT
* *
60173 TCG-TTGTGATAGTCGAAGT
1 TCGCTTGCGATAGTCCAAGT
* *
60192 TCGCATTGCGATTTATTCCAAAT
1 TCGC-TTGCGA--TAGTCCAAGT
60215 TCG-TTGCGATAGTCCAA
1 TCGCTTGCGATAGTCCAA
60232 AATCGCAACG
Statistics
Matches: 80, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
19 14 0.17
20 2 0.03
21 40 0.50
22 5 0.06
23 12 0.15
24 7 0.09
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (20 bp):
TCGCTTGCGATAGTCCAAGT
Found at i:60227 original size:42 final size:43
Alignment explanation
Indices: 60131--60228 Score: 144
Period size: 43 Copynumber: 2.3 Consensus size: 43
60121 TCCAAGTTCG
* *
60131 CGTTGCGATAATCAAAGTTCGCGTTGCGATTTATTTACAAATT
1 CGTTGCGATAGTCAAAGTTCGCATTGCGATTTATTTACAAATT
* * *
60174 CGTTGTGATAGTCGAAGTTCGCATTGCGATTTA-TTCCAAATT
1 CGTTGCGATAGTCAAAGTTCGCATTGCGATTTATTTACAAATT
60216 CGTTGCGATAGTC
1 CGTTGCGATAGTC
60229 CAAAATCGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
42 20 0.41
43 29 0.59
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (43 bp):
CGTTGCGATAGTCAAAGTTCGCATTGCGATTTATTTACAAATT
Found at i:60232 original size:19 final size:19
Alignment explanation
Indices: 60168--60232 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
60158 GATTTATTTA
*
60168 CAAATTCGTTGTGATAGTC
1 CAAATTCGTTGCGATAGTC
* * *
60187 GAAGTTCGCATTGCGATTTATTC
1 CAAATTCG--TTGCGA--TAGTC
60210 CAAATTCGTTGCGATAGTC
1 CAAATTCGTTGCGATAGTC
60229 CAAA
1 CAAA
60233 ATCGCAACGA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
19 14 0.40
21 11 0.31
23 10 0.29
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (19 bp):
CAAATTCGTTGCGATAGTC
Found at i:60238 original size:42 final size:42
Alignment explanation
Indices: 60106--60238 Score: 119
Period size: 42 Copynumber: 3.1 Consensus size: 42
60096 AACTTCGACT
* * *
60106 ATCGCATTGCGA--TAGTCCAAGTTCGCGTTGCGATAAT-CAAA
1 ATCGCATTGCGATTTATTCCAAATT--CGTTGCGATAGTCCAAA
* * * * * *
60147 GTTCGCGTTGCGATTTATTTACAAATTCGTTGTGATAGTCGAAG
1 -ATCGCATTGCGATTTA-TTCCAAATTCGTTGCGATAGTCCAAA
*
60191 TTCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAA
1 ATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAA
60233 ATCGCA
1 ATCGCA
60239 ACGACTGGTG
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
42 37 0.51
43 25 0.35
44 4 0.06
45 6 0.08
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (42 bp):
ATCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAA
Found at i:60353 original size:21 final size:21
Alignment explanation
Indices: 60327--60366 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
60317 TATTACCACA
60327 ACCACGACCCGAGACGAGATG
1 ACCACGACCCGAGACGAGATG
60348 ACCACGACCCGAGACGAGA
1 ACCACGACCCGAGACGAGA
60367 CGAGACGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.35, G:0.28, T:0.03
Consensus pattern (21 bp):
ACCACGACCCGAGACGAGATG
Found at i:61015 original size:6 final size:6
Alignment explanation
Indices: 61004--61040 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
60994 TCTCGCCTTG
61004 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT G
61041 ATAATACGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:61164 original size:21 final size:20
Alignment explanation
Indices: 61132--61225 Score: 93
Period size: 21 Copynumber: 4.6 Consensus size: 20
61122 TGTTGCGATT
*
61132 TTGGACTATCGCAA-CGAAC
1 TTGGAATATCGCAACCGAAC
61151 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAAC-CGAAC
* *
61174 TTCGACTATCGCAA-CGAAC
1 TTGGAATATCGCAACCGAAC
*
61193 TTGGACTATCGCAACGCGAAC
1 TTGGAATATCGCAAC-CGAAC
*
61214 TTGGAAAATCGC
1 TTGGAATATCGC
61226 TGCGAATTTG
Statistics
Matches: 63, Mismatches: 6, Indels: 10
0.80 0.08 0.13
Matches are distributed among these distances:
19 24 0.38
21 29 0.46
23 10 0.16
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (20 bp):
TTGGAATATCGCAACCGAAC
Found at i:61193 original size:19 final size:19
Alignment explanation
Indices: 61132--61218 Score: 102
Period size: 19 Copynumber: 4.3 Consensus size: 19
61122 TGTTGCGATT
61132 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
*
61151 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
*
61174 TTCGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
61193 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
61214 TTGGA
1 TTGGA
61219 AAATCGCTGC
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
19 24 0.41
21 24 0.41
23 10 0.17
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:61194 original size:42 final size:40
Alignment explanation
Indices: 61135--61215 Score: 135
Period size: 42 Copynumber: 2.0 Consensus size: 40
61125 TGCGATTTTG
61135 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAAT--ATCGCAACGCGAACTTC
*
61177 GACTATCGCAACGAACTTGGACTATCGCAACGCGAACTT
1 GACTATCGCAACGAACTTGGAATATCGCAACGCGAACTT
61216 GGAAAATCGC
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 16 0.42
42 22 0.58
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (40 bp):
GACTATCGCAACGAACTTGGAATATCGCAACGCGAACTTC
Found at i:61225 original size:40 final size:41
Alignment explanation
Indices: 61139--61245 Score: 128
Period size: 40 Copynumber: 2.6 Consensus size: 41
61129 ATTTTGGACT
**
61139 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAACTTGGAAT-AATCGCAACGCGAACTTCGAAA
* *
61181 ATCGCAACGAACTTGGACT-ATCGCAACGCGAACTTGGAAA
1 ATCGCAACGAACTTGGAATAATCGCAACGCGAACTTCGAAA
** *
61221 ATCGCTGCGAATTTGGAA-AATCGCA
1 ATCGCAACGAACTTGGAATAATCGCA
61246 TTGCGGTAGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 38 0.68
42 18 0.32
ACGTcount: A:0.35, C:0.24, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGAACTTGGAATAATCGCAACGCGAACTTCGAAA
Found at i:61236 original size:19 final size:19
Alignment explanation
Indices: 61208--61244 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
61198 CTATCGCAAC
61208 GCGAACTTGGAAAATCGCT
1 GCGAACTTGGAAAATCGCT
*
61227 GCGAATTTGGAAAATCGC
1 GCGAACTTGGAAAATCGC
61245 ATTGCGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (19 bp):
GCGAACTTGGAAAATCGCT
Done.