Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003867.1 Hibiscus syriacus cultivar Beakdansim tig00008320_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: 54361
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:2651 original size:2 final size:2
Alignment explanation
Indices: 2644--2669 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2634 GTTCAATTTC
2644 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
2670 GAAATTGGAC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13048 original size:36 final size:35
Alignment explanation
Indices: 12993--13074 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 35
12983 ATCGAATTAA
* *
12993 ACGGGGACGGGAAACACTGTTTATGTTGAACGGGG
1 ACGGGGACGGGAAAAACTGTTTATGTTAAACGGGG
*
13028 ACGGGGATGGGGAAAAACTGTTTATGTTAAACGGGG
1 ACGGGGA-CGGGAAAAACTGTTTATGTTAAACGGGG
13064 ACGGGGACGGG
1 ACGGGGACGGG
13075 TTTAGTAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 10 0.24
36 32 0.76
ACGTcount: A:0.27, C:0.12, G:0.43, T:0.18
Consensus pattern (35 bp):
ACGGGGACGGGAAAAACTGTTTATGTTAAACGGGG
Found at i:16055 original size:39 final size:39
Alignment explanation
Indices: 15994--16077 Score: 114
Period size: 39 Copynumber: 2.2 Consensus size: 39
15984 TTGTAAGACC
* * *
15994 TTACCACAGGCTCATCTGCTTTGTGCTCATGGTAAGTCA
1 TTACCACAGCCTCATCTACTTTGTGCTCAGGGTAAGTCA
* * *
16033 TTACCGCAGCCTCCTCTACTTTGTGCTCAGGGTAAGTCC
1 TTACCACAGCCTCATCTACTTTGTGCTCAGGGTAAGTCA
16072 TTACCA
1 TTACCA
16078 AAGGTCCTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.32
Consensus pattern (39 bp):
TTACCACAGCCTCATCTACTTTGTGCTCAGGGTAAGTCA
Found at i:16242 original size:16 final size:16
Alignment explanation
Indices: 16209--16245 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
16199 GATAAATTGA
16209 TTTATACTGAAGTATT
1 TTTATACTGAAGTATT
16225 TTTAT-CTGAATGT-TT
1 TTTATACTGAA-GTATT
16240 TTTATA
1 TTTATA
16246 TACACTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTATACTGAAGTATT
Found at i:23151 original size:29 final size:28
Alignment explanation
Indices: 23091--23165 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
23081 CGTGTCACCA
* **
23091 TAAAATAATGTCACATCATCATTGAATTT
1 TAAAA-AATATCACATCATCATTGAAAAT
*
23120 TAAAAAATATCACATTATCATTGAAAAAT
1 TAAAAAATATCACATCATCATTG-AAAAT
* *
23149 TAAAACATATCAGATCA
1 TAAAAAATATCACATCA
23166 GTAATTCTGT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 16 0.42
29 22 0.58
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.32
Consensus pattern (28 bp):
TAAAAAATATCACATCATCATTGAAAAT
Found at i:25781 original size:3 final size:3
Alignment explanation
Indices: 25762--25810 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
25752 TCAGTTTGTT
25762 TTA TTA TT- TT- TTA -TA TTA TTA TTA TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
25805 TTA TTA
1 TTA TTA
25811 AATAAATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.14
3 34 0.79
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:27072 original size:31 final size:29
Alignment explanation
Indices: 27002--27089 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 29
26992 TAATTTAATC
* *
27002 ACTAATTTTAATACTTTTATTTATTTTTAACT
1 ACTAAGTTTTATA-TTTTATTTA-TTTTAA-T
27034 AC-AAGTTTTATTATTTT-TTATATTTTAAT
1 ACTAAGTTTTA-TATTTTATT-TATTTTAAT
27063 ACTATAGTTTTA-ATTTTATTTATTTTA
1 ACTA-AGTTTTATATTTTATTTATTTTA
27090 GTCGCTATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
29 15 0.31
30 11 0.22
31 19 0.39
32 4 0.08
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (29 bp):
ACTAAGTTTTATATTTTATTTATTTTAAT
Found at i:27089 original size:29 final size:29
Alignment explanation
Indices: 27007--27089 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 29
26997 TAATCACTAA
27007 TTTTAATACTTTTATTTATTTTTAACTACAAG
1 TTTT-ATA-TTTTATTTA-TTTTAACTACAAG
27039 TTTTATTATTTT-TTATATTTTAA-TACTATAG
1 TTTTA-TATTTTATT-TATTTTAACTAC-A-AG
27070 TTTTA-ATTTTATTTATTTTA
1 TTTTATATTTTATTTATTTTA
27090 GTCGCTATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
29 15 0.33
30 11 0.24
31 14 0.30
32 6 0.13
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (29 bp):
TTTTATATTTTATTTATTTTAACTACAAG
Found at i:27276 original size:15 final size:16
Alignment explanation
Indices: 27245--27277 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
27235 AAATCCTATT
27245 TATAAATTTAATTTTA
1 TATAAATTTAATTTTA
*
27261 TATAAA-TTACTTTTA
1 TATAAATTTAATTTTA
27276 TA
1 TA
27278 AACATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAAATTTAATTTTA
Found at i:28945 original size:36 final size:36
Alignment explanation
Indices: 28898--28969 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
28888 CAGCTATGCA
* *
28898 CACAAAGATCCTGTTATATT-AATACCAAAAGTATTC
1 CACAAAGATCCTGTTAGATTGAA-ACCAAAAGCATTC
28934 CACAAAGATCCTGTTAGATTGAAACCAAAAGCATTC
1 CACAAAGATCCTGTTAGATTGAAACCAAAAGCATTC
28970 TATGGTAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
36 31 0.94
37 2 0.06
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (36 bp):
CACAAAGATCCTGTTAGATTGAAACCAAAAGCATTC
Found at i:29431 original size:43 final size:44
Alignment explanation
Indices: 29354--29440 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 44
29344 TGGCTTTAGA
* *
29354 GAAGTTAGGAGGTAAAGTTATCACCTATAGGT-AAAGTTTTGTT
1 GAAGTTAGGAGGTAAAGCTATCACCTACAGGTAAAAGTTTTGTT
* *
29397 GAAGTTAGGA-GTGAAAGCTATCCCCTACATGTAAAAGTTTTGTT
1 GAAGTTAGGAGGT-AAAGCTATCACCTACAGGTAAAAGTTTTGTT
29441 TGATGCACGG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.05
43 25 0.66
44 11 0.29
ACGTcount: A:0.32, C:0.10, G:0.24, T:0.33
Consensus pattern (44 bp):
GAAGTTAGGAGGTAAAGCTATCACCTACAGGTAAAAGTTTTGTT
Found at i:29531 original size:7 final size:7
Alignment explanation
Indices: 29515--29555 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
29505 TTTTCATACA
29515 TGCA-TT
1 TGCATTT
29521 TGCATTT
1 TGCATTT
29528 TGCATTT
1 TGCATTT
*
29535 TGTATCTT
1 TGCAT-TT
29543 TGCATTT
1 TGCATTT
29550 T-CATTT
1 TGCATTT
29556 ATACTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 9 0.29
7 16 0.52
8 6 0.19
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:36542 original size:54 final size:54
Alignment explanation
Indices: 36421--36581 Score: 243
Period size: 54 Copynumber: 3.0 Consensus size: 54
36411 TGATTGAGAA
* ** *
36421 ATCTGGGCAGAAGCCATAGGAAAGGATGAATGTGTTGTC-AATGCTTTACGAAC
1 ATCTGGGCAGAAGCCACAATAAAGAATGAATGTGTTGTCAAATGCTTTACGAAC
36474 ATCTGGGCAGAAGCCACAATAAAGAATGAATGTGTTGTCAAATGCTTTACGAAC
1 ATCTGGGCAGAAGCCACAATAAAGAATGAATGTGTTGTCAAATGCTTTACGAAC
* * **
36528 ATCTGGGCAGAAGCCACAATAAAAAATGAATGTGTTATCAAATATTTTACGAAC
1 ATCTGGGCAGAAGCCACAATAAAGAATGAATGTGTTGTCAAATGCTTTACGAAC
36582 CAGTTATTCT
Statistics
Matches: 99, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 35 0.35
54 64 0.65
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (54 bp):
ATCTGGGCAGAAGCCACAATAAAGAATGAATGTGTTGTCAAATGCTTTACGAAC
Found at i:37715 original size:45 final size:45
Alignment explanation
Indices: 37651--38222 Score: 821
Period size: 45 Copynumber: 12.8 Consensus size: 45
37641 CTATTTCCCA
37651 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
*
37696 CATCTATAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* *
37741 CATCTGTAATCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* * * *
37786 CTTCTGTAAGCCCTTCAGTTCAGGATGTTTTCAAAGCCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* * *
37831 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* *
37876 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
37921 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* * * *
37966 AATCTGTAAGCCTTTCAGTGCAGGATGTTTTCAAAAGCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* *
38011 CAT-TAGTAAGCCCTTCCGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCT-GTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* * * *
38056 CATCTGTAAGCCCTTCAGGGCAGTATGTTTTCAAAGCCTCCGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* *
38101 CATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTTC-GGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
* * *
38145 CATCTGTAAGCTCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
** *
38190 CATCCATAAG-ACTTACAGTG--GGATGTTTTCAAA
1 CATCTGTAAGCCCTT-CAGTGCAGGATGTTTTCAAA
38223 TGAGATTTAA
Statistics
Matches: 472, Mismatches: 51, Indels: 10
0.89 0.10 0.02
Matches are distributed among these distances:
43 12 0.03
44 45 0.10
45 414 0.88
46 1 0.00
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCAGGATGTTTTCAAAACCTTCGGGT
Found at i:38479 original size:3 final size:3
Alignment explanation
Indices: 38471--38531 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
38461 TTAGTTTGTT
* *
38471 TTA TTA TTA TTT TTA -TA TTA TTA TTA TACA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
38516 TTA TTA -TA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA
38532 AATAAATATT
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 6 0.12
3 42 0.84
4 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:38520 original size:25 final size:24
Alignment explanation
Indices: 38476--38523 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
38466 TTGTTTTATT
*
38476 ATTATTTTTATATTATTATTATAC
1 ATTATTATTATATTATTATTATAC
38500 ATTATTATTATTATTATTATTATA
1 ATTATTATTA-TATTATTATTATA
38524 TTTTATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTATTATTATATTATTATTATAC
Found at i:38529 original size:25 final size:24
Alignment explanation
Indices: 38472--38531 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
38462 TAGTTTGTTT
*
38472 TATTATTATTTTTATATTATTATTA
1 TATT-TTATTATTATATTATTATTA
**
38497 TACATTATTATTATTATTATTATTA
1 TATTTTATTATTA-TATTATTATTA
38522 TATTTTATTA
1 TATTTTATTA
38532 AATAAATATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TATTTTATTATTATATTATTATTA
Found at i:38542 original size:33 final size:36
Alignment explanation
Indices: 38471--38543 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
38461 TTAGTTTGTT
* * *
38471 TTATTATTATTTTTATATTATTATTATACATTATTA
1 TTATTATTATTATTATATTATTATTATACATAAATA
38507 TTATTATTATTATTATATT-TTATTA-A-ATAAATA
1 TTATTATTATTATTATATTATTATTATACATAAATA
38540 TTAT
1 TTAT
38544 AAAGCCCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 9 0.26
34 1 0.03
35 6 0.18
36 18 0.53
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (36 bp):
TTATTATTATTATTATATTATTATTATACATAAATA
Found at i:39713 original size:28 final size:30
Alignment explanation
Indices: 39676--39747 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
39666 ATTTTAATAC
39676 TTTTATTTATTTTTAACTAC-A-AGTTTT-A
1 TTTTATTTATTTTTAA-TACTATAGTTTTAA
39704 TATTT-TTTATATTTTAATACTATAGTTTTAA
1 T-TTTATTTAT-TTTTAATACTATAGTTTTAA
39735 TTTTATTTATTTT
1 TTTTATTTATTTT
39748 AGTCACTATT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
28 9 0.24
29 10 0.26
30 12 0.32
31 7 0.18
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTTATTTATTTTTAATACTATAGTTTTAA
Found at i:39719 original size:29 final size:29
Alignment explanation
Indices: 39639--39748 Score: 86
Period size: 29 Copynumber: 3.7 Consensus size: 29
39629 GTGCATTTGA
* *
39639 TTTTAATATTTTATAATTTAATCACTA-A-
1 TTTTAATTTTTTATATTTTAAT-ACTATAG
*
39667 TTTTAATACTTTTATTTATTTTTAACTAC-A-AG
1 TTTTAAT--TTTT-TATA-TTTTAA-TACTATAG
39699 TTTTATATTTTTTATATTTTAATACTATAG
1 TTTTA-ATTTTTTATATTTTAATACTATAG
39729 TTTTAATTTTATT-TATTTTA
1 TTTTAATTTT-TTATATTTTA
39749 GTCACTATTT
Statistics
Matches: 68, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
28 10 0.15
29 19 0.28
30 15 0.22
31 9 0.13
32 12 0.18
33 3 0.04
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (29 bp):
TTTTAATTTTTTATATTTTAATACTATAG
Found at i:39756 original size:30 final size:29
Alignment explanation
Indices: 39667--39748 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 29
39657 TAATCACTAA
*
39667 TTTTAATACTTTTATTTATTTT-TAACTACAAG
1 TTTT-ATA-TTTTATTTATTTTAT-ACTA-TAG
39699 TTTTATATTTT-TTATATTTTAATACTATAG
1 TTTTATATTTTATT-TATTTT-ATACTATAG
39729 TTTTA-ATTTTATTTATTTTA
1 TTTTATATTTTATTTATTTTA
39749 GTCACTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
28 1 0.02
29 13 0.29
30 19 0.42
31 7 0.16
32 5 0.11
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTATATTTTATTTATTTTATACTATAG
Found at i:39931 original size:15 final size:16
Alignment explanation
Indices: 39900--39932 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
39890 AAATCCTATT
39900 TATAAATTTAATTTTA
1 TATAAATTTAATTTTA
*
39916 TATAAA-TTACTTTTA
1 TATAAATTTAATTTTA
39931 TA
1 TA
39933 AACATATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TATAAATTTAATTTTA
Found at i:40855 original size:2 final size:2
Alignment explanation
Indices: 40817--40844 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40807 TTCAAGTAAT
40817 TA 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
40845 CTTTTTATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41370 original size:59 final size:59
Alignment explanation
Indices: 41276--41448 Score: 172
Period size: 59 Copynumber: 2.9 Consensus size: 59
41266 AGGGGATATT
* * * *
41276 ATTGGAAAGTTGAAAAGTTTTGGGACTAATTTAGAATAAGGGTCATAGTTTGAGGATGAA
1 ATTGGAATGTTCAAAAGTTTTGGGACCAAATTAGAATAAGGGTCATAGTTTG-GGATGAA
* * * *
41336 TTTGGAATGTTTAAAA-TTTTGGGACCAAATTAGAAT-GGGAGTCATAATTTGGGATGAA
1 ATTGGAATGTTCAAAAGTTTTGGGACCAAATTAGAATAAGG-GTCATAGTTTGGGATGAA
** * * * *
41394 ATTAAAATGCTCAAAAGTTTAT-TGACCAAATTAGAATAAGAGTAATAGTTTGGGA
1 ATTGGAATGTTCAAAAGTTT-TGGGACCAAATTAGAATAAGGGTCATAGTTTGGGA
41449 ATGTATGTTA
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
58 20 0.22
59 57 0.62
60 15 0.16
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.32
Consensus pattern (59 bp):
ATTGGAATGTTCAAAAGTTTTGGGACCAAATTAGAATAAGGGTCATAGTTTGGGATGAA
Found at i:42520 original size:11 final size:11
Alignment explanation
Indices: 42504--42540 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
42494 GAAAACTTTT
42504 AAAGAAAAATA
1 AAAGAAAAATA
42515 AAAGAAAAATA
1 AAAGAAAAATA
42526 AAAGAAAAAGTA
1 AAAGAAAAA-TA
42538 AAA
1 AAA
42541 ATTTATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 20 0.80
12 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (11 bp):
AAAGAAAAATA
Found at i:45014 original size:2 final size:2
Alignment explanation
Indices: 45003--45044 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
44993 TGTTTTGTAT
45003 TA TA -A TA TA TA TA TA 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
45044 T
1 T
45045 TTAGGGTTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48710 original size:20 final size:21
Alignment explanation
Indices: 48666--48712 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
48656 CAAAATCTAT
*
48666 TTTTAAGTGAAAGTGTTTTGA
1 TTTTAAGTGAAAGCGTTTTGA
48687 -TTTAAGTGAAAGCGTTTT-A
1 TTTTAAGTGAAAGCGTTTTGA
48706 TTTTAAG
1 TTTTAAG
48713 AAAGACTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.30, C:0.02, G:0.21, T:0.47
Consensus pattern (21 bp):
TTTTAAGTGAAAGCGTTTTGA
Found at i:49898 original size:2 final size:2
Alignment explanation
Indices: 49891--49917 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49881 TTAATTAGTA
49891 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
49918 ATTCTTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52964 original size:21 final size:21
Alignment explanation
Indices: 52938--52977 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
52928 TTACCTTCTT
52938 TTTTTATTTTTTCATTTTTCA
1 TTTTTATTTTTTCATTTTTCA
*
52959 TTTTTATTTTTTTATTTTT
1 TTTTTATTTTTTCATTTTT
52978 AAAAAGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTATTTTTTCATTTTTCA
Done.