Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005855.1 Hibiscus syriacus cultivar Beakdansim tig00013750_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: 71945
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:3462 original size:21 final size:21
Alignment explanation
Indices: 3427--3472 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3417 ATTTTAATAA
3427 TTCTATATGTATGATACAATTT
1 TTCTATATGTATGATAC-ATTT
*
3449 TTCTAT-TTTATGATACATTT
1 TTCTATATGTATGATACATTT
3469 TTCT
1 TTCT
3473 TTGCATTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 9 0.39
22 6 0.26
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.57
Consensus pattern (21 bp):
TTCTATATGTATGATACATTT
Found at i:3963 original size:13 final size:13
Alignment explanation
Indices: 3947--3971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3937 TTTATTAGAA
3947 AAATTAATTGATT
1 AAATTAATTGATT
3960 AAATTAATTGAT
1 AAATTAATTGAT
3972 ATGAATATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
AAATTAATTGATT
Found at i:5599 original size:51 final size:51
Alignment explanation
Indices: 5523--5628 Score: 194
Period size: 51 Copynumber: 2.1 Consensus size: 51
5513 TTTTTGGTGG
5523 GAAGACGGTCCAGAACAACCATCCAAGAAATAATGATATGCTTCGGTATGT
1 GAAGACGGTCCAGAACAACCATCCAAGAAATAATGATATGCTTCGGTATGT
* *
5574 GAAGACGGTCCATAACAACCATCCAAGAAATAATGATGTGCTTCGGTATGT
1 GAAGACGGTCCAGAACAACCATCCAAGAAATAATGATATGCTTCGGTATGT
5625 GAAG
1 GAAG
5629 GGGAAACCAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22
Consensus pattern (51 bp):
GAAGACGGTCCAGAACAACCATCCAAGAAATAATGATATGCTTCGGTATGT
Found at i:6614 original size:64 final size:64
Alignment explanation
Indices: 6563--6723 Score: 261
Period size: 65 Copynumber: 2.5 Consensus size: 64
6553 GTGCACTAAG
* *
6563 TGTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCCTGAGTGCATCGATGCATGGT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGT
* *
6626 TGGTGCATCGATGCATCAAATACATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGT
1 T-GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGT
6691 ATGTGCATCGATGCATAAAATGCATTCGATGTT
1 -TGTGCATCGATGCATAAAATGCATTCGATGTT
6724 CAATTTATTC
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
63 1 0.01
64 32 0.36
65 55 0.62
66 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGT
Found at i:6762 original size:65 final size:64
Alignment explanation
Indices: 6564--6765 Score: 243
Period size: 65 Copynumber: 3.1 Consensus size: 64
6554 TGCACTAAGT
* *
6564 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAA-AAAGCCTGAGTGCATCGATGCATGGTTG
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAATAAAACCTGAGTGCATCGATGCATGGTTG
* *
6628 GTGCATCGATGCATCAAATACATTCGATGTTTTC-ATAAAACCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAATAAAA-CCTGAGTGCATCGATGCATGGT-
6692 T-
63 TG
* **
6693 GTGCATCGATGCATAAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA-TAAAACC-TGAGTGCATCGATGCATGG-T
6756 TG
63 TG
6758 GTGCATCG
1 GTGCATCG
6766 GTGTATCACT
Statistics
Matches: 121, Mismatches: 9, Indels: 15
0.83 0.06 0.10
Matches are distributed among these distances:
63 4 0.03
64 54 0.45
65 62 0.51
66 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAACCTGAGTGCATCGATGCATGGTTG
Found at i:9609 original size:64 final size:63
Alignment explanation
Indices: 9514--9654 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 63
9504 TCTGGGCAAG
* * * *
9514 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAAATGGTGTATCGATGCATAAGGA
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAAATGATGTATCGATGCATAAGGA
* * * * * *
9577 GTGCATCGATGCATCCCTTTAAA-ATGAAAACATCAAAGGTAATTTATGTATCGATGCATGAGTA
1 GTGCATCGATGCA-CCCTTTAAAGAAG-AAACATCAAAGGCAAATGATGTATCGATGCATAAGGA
9641 GTGCATCGATGCAC
1 GTGCATCGATGCAC
9655 ATGTTAAAGA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
63 16 0.24
64 50 0.76
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCAAAGGCAAATGATGTATCGATGCATAAGGA
Found at i:9690 original size:20 final size:22
Alignment explanation
Indices: 9642--9699 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
9632 GCATGAGTAG
9642 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
*
9666 TGCATCGATGCACTG-T-AGCA
1 TGCATCGATGCACTGTTAAGAA
9686 TGCATCGATGCACT
1 TGCATCGATGCACT
9700 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:10618 original size:19 final size:19
Alignment explanation
Indices: 10594--10639 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
10584 ATATGTGACA
* * *
10594 TGATATATATGTGTTTATG
1 TGATATAAAAGTGTATATG
10613 TGATATAAAAGTGTATATG
1 TGATATAAAAGTGTATATG
*
10632 TGAAATAA
1 TGATATAA
10640 CATGATAGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (19 bp):
TGATATAAAAGTGTATATG
Found at i:11010 original size:30 final size:30
Alignment explanation
Indices: 10949--11020 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
10939 TTTCGAGACA
* *
10949 TATGGACAGCTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
*
10980 TATGGACAGTTACCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
11010 TCTGGATAGTT
1 TATGGACAGTT
11021 GTCGGGGTCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 27 0.75
31 9 0.25
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:11522 original size:2 final size:2
Alignment explanation
Indices: 11515--11555 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11505 TAATGACATA
11515 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
11556 TACATATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:18457 original size:14 final size:14
Alignment explanation
Indices: 18438--18465 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18428 TAAAATTCAA
18438 ATATTTTGACCGTT
1 ATATTTTGACCGTT
18452 ATATTTTGACCGTT
1 ATATTTTGACCGTT
18466 CGAACACTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.14, T:0.50
Consensus pattern (14 bp):
ATATTTTGACCGTT
Found at i:18559 original size:45 final size:46
Alignment explanation
Indices: 18495--18599 Score: 158
Period size: 45 Copynumber: 2.3 Consensus size: 46
18485 TGTACTAAGT
* *
18495 GTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AAAAGCCTAA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTAA
* * *
18540 GTGCATCGATGCATCAAATGCATTTGATGTTTTCATAAAAACCTGA
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTAA
18586 GTGCATCGATGCAT
1 GTGCATCGATGCAT
18600 GGTATGTGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 32 0.59
46 22 0.41
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (46 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCATAAAAACCTAA
Found at i:20458 original size:2 final size:2
Alignment explanation
Indices: 20453--20535 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
20443 TTAATCATTA
20453 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
20495 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT A
20536 ATGATATAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21417 original size:36 final size:37
Alignment explanation
Indices: 21333--21417 Score: 95
Period size: 38 Copynumber: 2.3 Consensus size: 37
21323 TTATTTTGTT
* **
21333 CGGGTC-GGGTTTTTTAAGTGTGATATTCTGGTCGAGT
1 CGGGTCAGGTTTTTTTAAGTGTGATATTCTGG-CGACC
*
21370 CGGGTCGGGTTTTTTTAAGTGTGATATTC-GG-GACC
1 CGGGTCAGGTTTTTTTAAGTGTGATATTCTGGCGACC
21405 CGGGTTCAGGTTT
1 CGGG-TCAGGTTT
21418 AGGGTGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 6 0.14
36 7 0.17
37 8 0.19
38 21 0.50
ACGTcount: A:0.13, C:0.13, G:0.35, T:0.39
Consensus pattern (37 bp):
CGGGTCAGGTTTTTTTAAGTGTGATATTCTGGCGACC
Found at i:21500 original size:256 final size:250
Alignment explanation
Indices: 21158--21617 Score: 751
Period size: 256 Copynumber: 1.8 Consensus size: 250
21148 GTCAGGTTTG
* *
21158 GGTTTAGGGTAAAAAAACCAGACTGACCCGAAAATATATAGAATTCAGGTCGGGTCGGATTAAGT
1 GGTTTAGGGTAAAAAAACCAGACCGACCCAAAAATATATAGAATTCAGGTCGGGTCGGATTAAGT
*
21223 CACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTC-AGGTTGAATTTCTAA
66 CACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCTA-GTCGAATTTCTAA
*
21287 TTCATATATTCGGGTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGT
130 TTCATATA-T----TCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGGTTTTTTAAGT
*
21352 GTGATATTCTGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGACCCGGGTTCA
190 GTGATATTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGACCCGGGTTCA
* * * *
21413 GGTTTAGGGTGAAAAAAATCGGACCGACCCAAAAATATATATAATTCGGGTCGGGTCGGATTAAG
1 GGTTTAGGGT-AAAAAAACCAGACCGACCCAAAAATATATAGAATTCAGGTCGGGTCGGATTAAG
* *
21478 TCACTGTTTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCTAGTCGTATTTCTAA
65 TCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCTAGTCGAATTTCTAA
21543 TTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGGTTTTTTAAGTGTGAT
130 TTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGGTTTTTTAAGTGTGAT
21608 ATTCGGGTCG
195 ATTCGGGTCG
21618 GGTTCGAGTT
Statistics
Matches: 192, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
251 64 0.33
255 11 0.06
256 116 0.60
257 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.37
Consensus pattern (250 bp):
GGTTTAGGGTAAAAAAACCAGACCGACCCAAAAATATATAGAATTCAGGTCGGGTCGGATTAAGT
CACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGTCTAGTCGAATTTCTAAT
TCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCAGGTCGGGTTTTTTAAGTGTGATA
TTCGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGACCCGGGTTCA
Found at i:22163 original size:17 final size:17
Alignment explanation
Indices: 22141--22173 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
22131 AAAATGAAAA
22141 TTTAATATTTTT-TAATT
1 TTTAAT-TTTTTATAATT
22158 TTTAATTTTTTATAAT
1 TTTAATTTTTTATAAT
22174 ATATTACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTAATTTTTTATAATT
Found at i:22367 original size:16 final size:18
Alignment explanation
Indices: 22346--22392 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
22336 ATATAGAATT
22346 AGATTCCAATTCC-T-AC
1 AGATTCCAATTCCTTCAC
*
22362 AGATTCTAATTCCTTCAC
1 AGATTCCAATTCCTTCAC
22380 AGATTCCAATTCC
1 AGATTCCAATTCC
22393 CTCATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 14 0.52
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.34
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAC
Found at i:24025 original size:19 final size:20
Alignment explanation
Indices: 24001--24040 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
23991 TAATATAGAA
* *
24001 TATTTTTGTT-TTATAATAT
1 TATTTTTATTATTAAAATAT
24020 TATTTTTATTATTAAAATAT
1 TATTTTTATTATTAAAATAT
24040 T
1 T
24041 TTTAATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
TATTTTTATTATTAAAATAT
Found at i:24051 original size:16 final size:17
Alignment explanation
Indices: 24020--24055 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
24010 TTTATAATAT
*
24020 TATTTTTATTATTAAAA
1 TATTTTTAATATTAAAA
*
24037 TATTTTTAATATAAAAA
1 TATTTTTAATATTAAAA
24054 TA
1 TA
24056 AGTGTCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTTTTAATATTAAAA
Found at i:31891 original size:41 final size:41
Alignment explanation
Indices: 31834--31918 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
31824 CAGGACATAA
31834 AAGAAAACTCACCATTGTAACCATCACTATAAATATGACCT
1 AAGAAAACTCACCATTGTAACCATCACTATAAATATGACCT
31875 AAGAAAACTCACCATTGTAACCATCACTATAAATATGACCT
1 AAGAAAACTCACCATTGTAACCATCACTATAAATATGACCT
31916 AAG
1 AAG
31919 CAACAACAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.24
Consensus pattern (41 bp):
AAGAAAACTCACCATTGTAACCATCACTATAAATATGACCT
Found at i:32379 original size:3 final size:3
Alignment explanation
Indices: 32371--32395 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
32361 GGTAAACAAA
32371 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
32396 CTAAATCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41679 original size:21 final size:21
Alignment explanation
Indices: 41654--41698 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
41644 ACCAAACGCA
41654 CCCTAAGAGAGAGAACCGATT
1 CCCTAAGAGAGAGAACCGATT
* * *
41675 CCCTATGAGAGGGTACCGATT
1 CCCTAAGAGAGAGAACCGATT
41696 CCC
1 CCC
41699 CCACGCTCCA
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:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (21 bp):
CCCTAAGAGAGAGAACCGATT
Found at i:41915 original size:13 final size:13
Alignment explanation
Indices: 41894--41948 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
41884 AAGTTCGATA
*
41894 AATTCAAATACTT
1 AATTGAAATACTT
41907 AATTGAAATACTT
1 AATTGAAATACTT
* *
41920 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
41934 AATTGAAATACTT
1 AATTGAAATACTT
41947 AA
1 AA
41949 ATACTTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:41979 original size:33 final size:33
Alignment explanation
Indices: 41934--42032 Score: 155
Period size: 33 Copynumber: 3.0 Consensus size: 33
41924 AACTCAACAT
* * *
41934 AATTGAAATACTTAAATACTTTCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
*
41967 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
42000 AATTCAAATACTTAAAAAC-TTCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTTCAAGTTCGATA
42032 A
1 A
42033 TTGAAACAAA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 13 0.21
33 48 0.79
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTTCAAGTTCGATA
Found at i:42051 original size:21 final size:21
Alignment explanation
Indices: 42027--42068 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
42017 ACTTCAAGTT
42027 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
42048 CGATAATTGAAATAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
42069 AAAATAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:44318 original size:12 final size:12
Alignment explanation
Indices: 44276--44319 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
44266 TTAAACCCAG
44276 ACCGGTTTTTTA
1 ACCGGTTTTTTA
*
44288 ACCGTTTTTTTCAA
1 ACCGGTTTTTT--A
44302 ACCGGTTTTTTA
1 ACCGGTTTTTTA
*
44314 TCCGGT
1 ACCGGT
44320 AAAAAAACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 16 0.59
14 11 0.41
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.48
Consensus pattern (12 bp):
ACCGGTTTTTTA
Found at i:44442 original size:28 final size:29
Alignment explanation
Indices: 44404--44462 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
44394 AAAAAACCGG
*
44404 TTTTTCCC-AAATCCGAT-TTCGGATATTT
1 TTTTTCCCAAAATCAGATATTCGGAT-TTT
*
44432 TTTTTCGCAAAATCAGATATTCGGATTTT
1 TTTTTCCCAAAATCAGATATTCGGATTTT
44461 TT
1 TT
44463 GTGCACCCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 7 0.26
29 13 0.48
30 7 0.26
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (29 bp):
TTTTTCCCAAAATCAGATATTCGGATTTT
Found at i:51598 original size:31 final size:31
Alignment explanation
Indices: 51563--51646 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
51553 GAGTACCTTG
* *
51563 GGGCCTGTAAGCCTACCCAAGAATATTCTCA
1 GGGCCTGTAAGCCTACCCAAGAAAAATCTCA
**
51594 GGGCCT-TCCTGGCCTACCCAAGAAAAATCTCA
1 GGGCCTGT--AAGCCTACCCAAGAAAAATCTCA
*
51626 GGGCC-GCAGAGCCTACCCAAG
1 GGGCCTGTA-AGCCTACCCAAG
51647 GGTCGCCTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
30 1 0.02
31 17 0.40
32 24 0.57
ACGTcount: A:0.27, C:0.33, G:0.23, T:0.17
Consensus pattern (31 bp):
GGGCCTGTAAGCCTACCCAAGAAAAATCTCA
Found at i:51814 original size:12 final size:12
Alignment explanation
Indices: 51791--51882 Score: 78
Period size: 12 Copynumber: 7.7 Consensus size: 12
51781 GATATATCAA
*
51791 AAATCTGAACAG
1 AAATCAGAACAG
*
51803 AACTCAGAACAG
1 AAATCAGAACAG
51815 AAATCAGAACAG
1 AAATCAGAACAG
*
51827 AAATCACAACAG
1 AAATCAGAACAG
* * * *
51839 AATTTAGAGCAT
1 AAATCAGAACAG
*
51851 AAATCA-AAGAAG
1 AAATCAGAA-CAG
* *
51863 AATTTAGAACAG
1 AAATCAGAACAG
51875 AAATCAGA
1 AAATCAGA
51883 TAAAATATTA
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
11 1 0.02
12 56 0.95
13 2 0.03
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (12 bp):
AAATCAGAACAG
Found at i:56893 original size:43 final size:44
Alignment explanation
Indices: 56832--57054 Score: 161
Period size: 43 Copynumber: 5.1 Consensus size: 44
56822 GAAAATCAAG
* * * * * *
56832 AAATTATGGGCCTAAATTATAAAGTTAAAAATTGATATT-AAAA
1 AAATTAAGGGTCTCAATTATAAAGGTAAAAAGTGAAATTAAAAA
*
56875 AAATTAGGGGTCTCAATTATAAAGGTAAAAAGTGAAATTAAAAA
1 AAATTAAGGGTCTCAATTATAAAGGTAAAAAGTGAAATTAAAAA
* ** * * *
56919 AAATTAAGAGTCTCAATTATAAAGACAAAAGGTGAAATTAGAAG
1 AAATTAAGGGTCTCAATTATAAAGGTAAAAAGTGAAATTAAAAA
* ** *
56963 AAACT-AGAACTCACAATTATAAAGGTAGAAAA-T-AAGATT-AAAA
1 AAATTAAG-GGTCTCAATTATAAAGGTA-AAAAGTGAA-ATTAAAAA
** * * * * *
57006 AAATTAAGCATCTTATTTATAAAGGTAAAATGTGAGA-TAAAGA
1 AAATTAAGGGTCTCAATTATAAAGGTAAAAAGTGAAATTAAAAA
57049 AAATTA
1 AAATTA
57055 GGGATTTTTA
Statistics
Matches: 142, Mismatches: 30, Indels: 16
0.76 0.16 0.09
Matches are distributed among these distances:
42 4 0.03
43 68 0.48
44 67 0.47
45 3 0.02
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (44 bp):
AAATTAAGGGTCTCAATTATAAAGGTAAAAAGTGAAATTAAAAA
Found at i:56934 original size:44 final size:45
Alignment explanation
Indices: 56846--57054 Score: 166
Period size: 44 Copynumber: 4.8 Consensus size: 45
56836 TATGGGCCTA
* * * **
56846 AATTATAAAGTTAAAAATTGATATT-AAAAAAATT-AGGGGTCTC
1 AATTATAAAGGTAAAAAGTGAAATTAAAAAAAATTAAGAAGTCTC
56889 AATTATAAAGGTAAAAAGTGAAATTAAAAAAAATTAAG-AGTCTC
1 AATTATAAAGGTAAAAAGTGAAATTAAAAAAAATTAAGAAGTCTC
** * * * * * *
56933 AATTATAAAGACAAAAGGTGAAATTAGAAGAAACT-AGAACTCAC
1 AATTATAAAGGTAAAAAGTGAAATTAAAAAAAATTAAGAAGTCTC
* *
56977 AATTATAAAGGTAGAAAA-T-AAGATT-AAAAAAATTAAGCA-TCTT
1 AATTATAAAGGTA-AAAAGTGAA-ATTAAAAAAAATTAAGAAGTCTC
* * * *
57020 ATTTATAAAGGTAAAATGTGAGA-TAAAGAAAATTA
1 AATTATAAAGGTAAAAAGTGAAATTAAAAAAAATTA
57055 GGGATTTTTA
Statistics
Matches: 132, Mismatches: 25, Indels: 18
0.75 0.14 0.10
Matches are distributed among these distances:
42 4 0.03
43 57 0.43
44 66 0.50
45 5 0.04
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.26
Consensus pattern (45 bp):
AATTATAAAGGTAAAAAGTGAAATTAAAAAAAATTAAGAAGTCTC
Found at i:61475 original size:24 final size:23
Alignment explanation
Indices: 61448--61497 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
61438 CCGGGTAGTG
*
61448 GGAGAGGTGGAA-GGAGTGGTGGAT
1 GGAGAGGAGGAAGGGA-TGGTGG-T
*
61472 GGAGTGGAGGAAGGGATGGTGGT
1 GGAGAGGAGGAAGGGATGGTGGT
61495 GGA
1 GGA
61498 CGTGGAGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 16 0.70
25 3 0.13
ACGTcount: A:0.24, C:0.00, G:0.60, T:0.16
Consensus pattern (23 bp):
GGAGAGGAGGAAGGGATGGTGGT
Found at i:61502 original size:24 final size:24
Alignment explanation
Indices: 61456--61505 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
61446 TGGGAGAGGT
61456 GGAAGGAGTGGTGGATGGAGTGGA
1 GGAAGGAGTGGTGGATGGAGTGGA
61480 GGAAGG-GATGGTGG-TGGACGTGGA
1 GGAAGGAG-TGGTGGATGGA-GTGGA
61504 GG
1 GG
61506 TCGTGGTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.22, C:0.02, G:0.60, T:0.16
Consensus pattern (24 bp):
GGAAGGAGTGGTGGATGGAGTGGA
Found at i:61544 original size:33 final size:33
Alignment explanation
Indices: 61475--61547 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
61465 GGTGGATGGA
** *
61475 GTGGAGGAAGGGATGGTGGTGGACGTGGAGGTC
1 GTGGAGGAAGGGATGGTGGCCGACGCGGAGGTC
* *
61508 GTGGTGGAAGGGATGGTGGCCGAGGCGGTAGG-C
1 GTGGAGGAAGGGATGGTGGCCGACGCGG-AGGTC
61541 GTGGAGG
1 GTGGAGG
61548 TGGCCGATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.16, C:0.08, G:0.59, T:0.16
Consensus pattern (33 bp):
GTGGAGGAAGGGATGGTGGCCGACGCGGAGGTC
Found at i:64741 original size:777 final size:761
Alignment explanation
Indices: 63222--64764 Score: 1911
Period size: 777 Copynumber: 2.0 Consensus size: 761
63212 GGCTAAAGAA
* * *
63222 ACTCATGAGAAACAAGTGGCTGCCAAAAGGCAGAAGAAAAGCGACGATGTTGCACAGGCTATTGT
1 ACTCATGAGAAACAAGTGGCTGCAAAAAGGCAGAAGAAAAACGACGATGTAGCACAGGCTATTGT
*
63287 AAAGAAGAAGGTTGAAGCTAAGACGAAGAGGAAATATGAAACTAGTAGTTCATCTAATGACTTCT
66 AAAGAAGAAGGTTGAAGCTAAGACGAAGAGGAAATATCAAACTAGTAGTTCATCTAATGACTTCT
*
63352 CTGATTCCGATTACATATGCGAGAGCCCACTACTGGTTGATGACTCTTCTAACTCCGATTATGTA
131 CTGATTCCGATTACATATGCGAAAGCCCACTACTGGTTGATGACTCTTCTAACTCCGATTATGTA
*
63417 TGCACAAACCCACTACTGGTTTACTTATGATGCTACATTTGTTGCTCTCGACATCCAAGTATGCT
196 TGCACAAACCCACTACTGGTTTACTTATGATGCTAAATTTGTTGCTCT---CATCCAAGTATGCT
* * * * *
63482 GATAGTTCACTTTTCATTACATGTTCTGCTTTGAATCGGTTCCTTATATCATTTAAGCTCTTAGT
258 GATAATTCACTATTCATTACATGTTCTGCTTTGAATAGGTTCCTTACATCATTTAAGCTCTAAGT
* *
63547 ACTCTTTAAGTATCGAGGCAATACATTCGTGTGATTGTAAAAATGGAGTAGATTAACGCATGTTT
323 ACTCTTTAAGTATCGAGGCAATACATTCGTGTGATTGTAAAAATGAAGCAGA-TAACGCATGTTT
* * * *
63612 GTATATGTTTTGCTTCTTTATGGTTATTTGTTTTCATCCAGAAACCTGCTCCTGTGAAGCAACAG
387 GTATATGTTTCGCTCCCTTATGGTAATTTGTTTTCATCCAGAAACCTGCTCCTGTGAAGCAACAG
* *
63677 CCGGCCGTTATGAAGAATGGTTCTGTACCTGCAAAGAAAGCAAAACAAGCTAGATATTCAGATTC
452 CC-GCCGTTACGAAGAATGGCTCTGTACCTGCAAAGAAAGCAAAACAAGCTAGATATTCAGATTC
* * *
63742 TTCAGACTCTAGTTGTGACTAAGATTTATCCTCCGATGAAGTGAATATTACGCTTATGCTTGTAA
516 TTCAGAC-CTAGTAGTGACTAAGATTTATCCTCCAATGAAGTGAATATTACGCTCATGCTTGTAA
* *
63807 CATTGTATGGTTGCAGATGTTATTTTTATGATTGTTAATGTTCAATGTTTTTGGCTTTCCAGGAA
580 CATTATATGGTTGCAGATGTTATTTTTATGATTGTTAATGTTCAATGTTTTTGACTTTCCAGGAA
63872 GCTCCTGCTCGGAATAAAAAACCTACAGTAGCTACAAAAGCCTCTGATCCAGCTGCAAAGACAGT
645 GCTCCTGCTCGGAATAAAAAACCTACAGTAGCTACAAAAGCCTCTGATCCAGCTGCAAAGACAGT
* *
63937 GAAATCTGATAGCAGTTCAGATTCTTCTTCTGACAATTATGTGTGTTTTGAG
710 GAAAGCTGATAACAGTTCAGATTCTTCTTCTGACAATTATGTGTGTTTTGAG
* * ** * *
63989 ACTCCTGAGAAACAAGTGGCTGCAAAAAGGCAGATGAAAAACGGTGGTGTAGCACGGGCTATTGT
1 ACTCATGAGAAACAAGTGGCTGCAAAAAGGCAGAAGAAAAACGACGATGTAGCACAGGCTATTGT
64054 AAAGAAGAAGGTTGAAGCTAAGACGACGACGACGACGACGACGAATAAATACAGAACTAGTAGTT
66 AAAGAAGAAGGTTGAAGCT-A-A-GACGA--A-GA-G--GA--AAT--AT-CA-AACTAGTAGTT
* * * * *
64119 CTTCTGATGAC-TCTTCTGATTCCGATTACATATGTGAAAGCTCAGC-ACTGGTTGATGATTCTT
116 CATCTAATGACTTC-TCTGATTCCGATTACATATGCGAAAGCCCA-CTACTGGTTGATGACTCTT
* * * * *
64182 CTAATTCTGATTATGTATGTGAC-AACCTACTATTGGTTTACTTAT-ATGCTAAATTTGTTGCTC
179 CTAACTCCGATTATGTATG-CACAAACCCACTACTGGTTTACTTATGATGCTAAATTTGTTGCTC
* * * * * *
64245 T-ATCGATGTCTGCTGATAATTCACTATTCATTATATGTTTTGCTTTGAATAGGTTCCTTACATG
243 TCATCCAAGTATGCTGATAATTCACTATTCATTACATGTTCTGCTTTGAATAGGTTCCTTACATC
* * * * *
64309 ATTTAAGCTCTAAGTTCTCTTTAAGTATCTAGTCAGTACATTTGTGTGATTGTAAAAATGAAGCA
308 ATTTAAGCTCTAAGTACTCTTTAAGTATCGAGGCAATACATTCGTGTGATTGTAAAAATGAAGCA
* * ** *
64374 GA-AGC-CATGTTTGTATCTG-TTCGC-CCACTTATGGTAATTT-TTTTGGTCCAGAAACCTGGT
373 GATAACGCATGTTTGTATATGTTTCGCTCC-CTTATGGTAATTTGTTTTCATCCAGAAACCTGCT
*
64434 CCTGTGAAG-AA-ATGCC-CCATTGTTGCGAAGAATGGCTCTGTACCTGCAAAGAAAGCAAAACA
437 CCTGTGAAGCAACA-GCCGCC---GTTACGAAGAATGGCTCTGTACCTGCAAAGAAAGCAAAACA
* * * *
64496 AGCTAGCA-ATTCGGGTTCTTCAGA-GTAGTAGTGAC-AGAGATTTATCCTCCAATGTAGTGAAT
498 AGCTAG-ATATTCAGATTCTTCAGACCTAGTAGTGACTA-AGATTTATCCTCCAATGAAGTGAAT
* * * * * *
64558 ATTTCGCTCATTCTTGTAACTATTTTATATGGTTGCAGTTGTTATTTTTGTGATTTTTTATCGTT
561 ATTACGCTCATGCTTGTAAC-A--TTATATGGTTGCAGATGTTATTTTTATGATTGTTAAT-GTT
* *
64623 CAATG-TTTTGACTTTCCAGCAGGAAGCTCCTGCTC-GAATAAAAAACCTGCAGTTGCTAC-AAA
622 CAATGTTTTTGACTTT-C--CAGGAAGCTCCTGCTCGGAATAAAAAACCTACAGTAGCTACAAAA
* * * *
64685 GCCTCTGTTCCAGCTGCTAAGACAGTGAGAGCTGATAACAGTTCAGATTCTTCTTCTGACAATGA
684 GCCTCTGATCCAGCTGCAAAGACAGTGAAAGCTGATAACAGTTCAGATTCTTCTTCTGACAATTA
* *
64750 -GTGAGTATTGAG
749 TGTGTGTTTTGAG
64762 ACT
1 ACT
64765 ATTACTAGAT
Statistics
Matches: 667, Mismatches: 77, Indels: 58
0.83 0.10 0.07
Matches are distributed among these distances:
767 75 0.11
768 1 0.00
769 4 0.01
770 55 0.08
771 6 0.01
772 86 0.13
773 72 0.11
774 85 0.13
775 24 0.04
776 18 0.03
777 112 0.17
778 3 0.00
780 2 0.00
781 21 0.03
782 100 0.15
783 3 0.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (761 bp):
ACTCATGAGAAACAAGTGGCTGCAAAAAGGCAGAAGAAAAACGACGATGTAGCACAGGCTATTGT
AAAGAAGAAGGTTGAAGCTAAGACGAAGAGGAAATATCAAACTAGTAGTTCATCTAATGACTTCT
CTGATTCCGATTACATATGCGAAAGCCCACTACTGGTTGATGACTCTTCTAACTCCGATTATGTA
TGCACAAACCCACTACTGGTTTACTTATGATGCTAAATTTGTTGCTCTCATCCAAGTATGCTGAT
AATTCACTATTCATTACATGTTCTGCTTTGAATAGGTTCCTTACATCATTTAAGCTCTAAGTACT
CTTTAAGTATCGAGGCAATACATTCGTGTGATTGTAAAAATGAAGCAGATAACGCATGTTTGTAT
ATGTTTCGCTCCCTTATGGTAATTTGTTTTCATCCAGAAACCTGCTCCTGTGAAGCAACAGCCGC
CGTTACGAAGAATGGCTCTGTACCTGCAAAGAAAGCAAAACAAGCTAGATATTCAGATTCTTCAG
ACCTAGTAGTGACTAAGATTTATCCTCCAATGAAGTGAATATTACGCTCATGCTTGTAACATTAT
ATGGTTGCAGATGTTATTTTTATGATTGTTAATGTTCAATGTTTTTGACTTTCCAGGAAGCTCCT
GCTCGGAATAAAAAACCTACAGTAGCTACAAAAGCCTCTGATCCAGCTGCAAAGACAGTGAAAGC
TGATAACAGTTCAGATTCTTCTTCTGACAATTATGTGTGTTTTGAG
Found at i:68152 original size:2 final size:2
Alignment explanation
Indices: 68145--68176 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
68135 TGTGTTGTTA
68145 AT AT AT AT AT AT AT AT A- AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68177 GCTCTCACCC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.