Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005020.1 Hibiscus syriacus cultivar Beakdansim tig00011266_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: 64791
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2776 original size:135 final size:136
Alignment explanation
Indices: 2523--2785 Score: 363
Period size: 135 Copynumber: 1.9 Consensus size: 136
2513 CTATATACAT
*
2523 TTGTATATAAAGGTTATATATCGATTTTGTTTAATGCATATTTTGCATTTTCGTATCAATACTAT
1 TTGTATATAAAGGTTATAGATCGATTTTGTTTAATGCATATTTTGCATTTTCGTATCAATACTAT
* * * *
2588 GTGCACTTTCGACACTAGATGTGCAACCATAGTATTCATAATGAGTTTGTGAATTAT-CATTTCA
66 ATGCACTTTCGACACTAGATGTGCAACCATAGAATTCATAATAAGTTTATGAATT-TCCATTTCA
2652 ACATATA
130 ACATATA
* * * *
2659 TTGTGTATAAAGGTTATCGATCGATTTTGTTTAATGCATA-TTTGTATTTTCGTATCATTACTAT
1 TTGTATATAAAGGTTATAGATCGATTTTGTTTAATGCATATTTTGCATTTTCGTATCAATACTAT
* * *
2723 ATGTACTTTC-AGCACTATG-TGTGCATCCATGGAATTCATAATAAGTTTATGAATTTCCATTTC
66 ATGCACTTTCGA-CACTA-GATGTGCAACCATAGAATTCATAATAAGTTTATGAATTTCCATTTC
2786 GACACTTAGT
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
134 2 0.02
135 72 0.64
136 38 0.34
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (136 bp):
TTGTATATAAAGGTTATAGATCGATTTTGTTTAATGCATATTTTGCATTTTCGTATCAATACTAT
ATGCACTTTCGACACTAGATGTGCAACCATAGAATTCATAATAAGTTTATGAATTTCCATTTCAA
CATATA
Found at i:4596 original size:18 final size:18
Alignment explanation
Indices: 4573--4630 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
4563 AGAGTTTAGG
4573 AATTTAGGGTTCAAATCT
1 AATTTAGGGTTCAAATCT
* *
4591 AATTTA-GGTT-TAA--G
1 AATTTAGGGTTCAAATCT
4605 AATTTAGGGTTCAAATCT
1 AATTTAGGGTTCAAATCT
4623 AATTTAGG
1 AATTTAGG
4631 TTTAAGAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 6 0.19
15 4 0.12
16 4 0.12
17 4 0.12
18 14 0.44
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (18 bp):
AATTTAGGGTTCAAATCT
Found at i:4608 original size:32 final size:32
Alignment explanation
Indices: 4566--4656 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
4556 TAACCCTAGA
*
4566 GTTTAGGAATTTAGGGTTCAAATCTAATTTAG
1 GTTTAAGAATTTAGGGTTCAAATCTAATTTAG
4598 GTTTAAGAATTTAGGGTTCAAATCTAATTTAG
1 GTTTAAGAATTTAGGGTTCAAATCTAATTTAG
*
4630 GTTTAAGAATTTAGGGTTTTAAATCTA
1 GTTTAAGAATTTAGGG-TTCAAATCTA
4657 CTTTGGTGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 47 0.84
33 9 0.16
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (32 bp):
GTTTAAGAATTTAGGGTTCAAATCTAATTTAG
Found at i:4610 original size:14 final size:14
Alignment explanation
Indices: 4591--4644 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
4581 GTTCAAATCT
4591 AATTTAGGTTTAAG
1 AATTTAGGTTTAAG
* *
4605 AATTTAGGGTTCAAATCT
1 AATTTA-GGTT-TAA--G
4623 AATTTAGGTTTAAG
1 AATTTAGGTTTAAG
4637 AATTTAGG
1 AATTTAGG
4645 GTTTTAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 14 0.44
15 4 0.12
16 4 0.12
17 4 0.12
18 6 0.19
ACGTcount: A:0.35, C:0.04, G:0.20, T:0.41
Consensus pattern (14 bp):
AATTTAGGTTTAAG
Found at i:8450 original size:21 final size:19
Alignment explanation
Indices: 8400--8451 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
8390 TTAAATTTTA
8400 ATATTTTCTAAAAGATTAT
1 ATATTTTCTAAAAGATTAT
* * *
8419 CTATATT-TAAAATATATAT
1 ATATTTTCTAAAAGAT-TAT
8438 ATGATTTTCTAAAA
1 AT-ATTTTCTAAAA
8452 AAATGATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 4 0.16
21 5 0.20
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (19 bp):
ATATTTTCTAAAAGATTAT
Found at i:9681 original size:2 final size:2
Alignment explanation
Indices: 9676--9704 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9666 TATAAAACAA
9676 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 A
9705 AAGTATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11148 original size:30 final size:30
Alignment explanation
Indices: 11114--11194 Score: 108
Period size: 30 Copynumber: 2.7 Consensus size: 30
11104 CATATTCGAT
* *
11114 TTAAAGAACCAAAATAGAAAAAACAAAAAC
1 TTAAAGGACTAAAATAGAAAAAACAAAAAC
* * * *
11144 TTAAAGGACTAAAATAGCAAAAATATAAAT
1 TTAAAGGACTAAAATAGAAAAAACAAAAAC
11174 TTAAAGGACTAAAATAGAAAA
1 TTAAAGGACTAAAATAGAAAA
11195 TAGAAATTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.64, C:0.09, G:0.10, T:0.17
Consensus pattern (30 bp):
TTAAAGGACTAAAATAGAAAAAACAAAAAC
Found at i:13052 original size:134 final size:132
Alignment explanation
Indices: 12835--13186 Score: 413
Period size: 131 Copynumber: 2.7 Consensus size: 132
12825 GGTTGTTTAA
* * * * * *
12835 GGGTGACATGGCTCCTA-TATGATGAGGAGATATGGTCGATGGATGACACTGTTCCTACGCGACG
1 GGGTGACACGGCTCCTACT-TGATGAGGAGGTATGGTCGGTGGATGACACAGTTCCTACGTGATG
* * ** * * *
12899 AGGACGATTCTCCATCTTTAGGAAGGGTGGTAACACGGTTCCTACGAGATGAGGATGACTGGTTA
65 AGGATGGTTAGCCATCTTTAGG--GGATGATAACACGGTTCCTACGAGATGAGGATGACTGATTA
12964 TCTAG
128 TCTAG
* * *
12969 GGGTGACACGGCTCCTACTTGATGAGGAGGTATGGTTGGTGGATGACACGGTTCCTCCGTGATGA
1 GGGTGACACGGCTCCTACTTGATGAGGAGGTATGGTCGGTGGATGACACAGTTCCTACGTGATGA
** * * *
13034 GGATGGCAAGCCATCTTTA-GGGATGATAATATGGTTCCTACGTGATGAGGATGACTGATTATCT
66 GGATGGTTAGCCATCTTTAGGGGATGATAACACGGTTCCTACGAGATGAGGATGACTGATTATCT
13098 AG
131 AG
* * * *
13100 GGTTGACACGACTCCTACGTGATGAGGAGGTATGGTCGG-GTGATGACACAATTCCTACGTGATG
1 GGGTGACACGGCTCCTACTTGATGAGGAGGTATGGTCGGTG-GATGACACAGTTCCTACGTGATG
*
13164 AGGATGGTTGGCCATCTTTAGGG
65 AGGATGGTTAGCCATCTTTAGGG
13187 ATTTGTTTCA
Statistics
Matches: 185, Mismatches: 30, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
130 1 0.01
131 112 0.61
132 2 0.01
133 1 0.01
134 68 0.37
135 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (132 bp):
GGGTGACACGGCTCCTACTTGATGAGGAGGTATGGTCGGTGGATGACACAGTTCCTACGTGATGA
GGATGGTTAGCCATCTTTAGGGGATGATAACACGGTTCCTACGAGATGAGGATGACTGATTATCT
AG
Found at i:13320 original size:65 final size:66
Alignment explanation
Indices: 13190--13320 Score: 176
Period size: 67 Copynumber: 2.0 Consensus size: 66
13180 TTTAGGGATT
* *
13190 TGTTTCAAGAGAAACTATTTCAAGGGAGACAAAACTTTGTTTCAAGGAAAACAGACCCAAAGATT
1 TGTTTCAAGAGAAACGATCTCAAGGGAGACAAAAC-TTGTTTCAAGGAAAACAGACCCAAAGATT
13255 TG
65 TG
* * * *
13257 TGTTTCAAGAGAAACGGTCTCAAGGGAGACAAAA-TTGTTTTAAGGGAAAC-GATCTCAAAGATT
1 TGTTTCAAGAGAAACGATCTCAAGGGAGACAAAACTTGTTTCAAGGAAAACAGA-CCCAAAGATT
13320 T
65 T
13321 TACAAGAGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
64 2 0.04
65 24 0.42
67 31 0.54
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (66 bp):
TGTTTCAAGAGAAACGATCTCAAGGGAGACAAAACTTGTTTCAAGGAAAACAGACCCAAAGATTT
G
Found at i:14728 original size:16 final size:16
Alignment explanation
Indices: 14694--14742 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
14684 GTTTTTTGTC
*
14694 CTTTTTTTTCTTTGCTT
1 CTTTTTTTTCTTT-TTT
14711 CTTTTTTTTCTTTTTT
1 CTTTTTTTTCTTTTTT
* *
14727 CTTTTCTTTGTTTTTT
1 CTTTTTTTTCTTTTTT
14743 TCTCTTTGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 16 0.55
17 13 0.45
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (16 bp):
CTTTTTTTTCTTTTTT
Found at i:14729 original size:24 final size:24
Alignment explanation
Indices: 14697--14760 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
14687 TTTTGTCCTT
14697 TTTTTTCTTTGCTTCT-TTTTTTTC
1 TTTTTTCTTTGCTT-TGTTTTTTTC
*
14721 TTTTTTCTTTTCTTTGTTTTTTTC
1 TTTTTTCTTTGCTTTGTTTTTTTC
* * *
14745 TCTTTGCTTTGATTTG
1 TTTTTTCTTTGCTTTG
14761 ATCTTCGCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.02, C:0.14, G:0.08, T:0.77
Consensus pattern (24 bp):
TTTTTTCTTTGCTTTGTTTTTTTC
Found at i:14733 original size:12 final size:11
Alignment explanation
Indices: 14696--14745 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 11
14686 TTTTTGTCCT
14696 TTTTTTTCTTTGC
1 TTTTTTT-TTT-C
14709 TTCTTTTTTTTC
1 TT-TTTTTTTTC
14721 TTTTTTCTTTTC
1 TTTTTT-TTTTC
14733 TTTGTTTTTTTC
1 TTT-TTTTTTTC
14745 T
1 T
14746 CTTTGCTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.12
12 17 0.50
13 8 0.24
14 5 0.15
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:16804 original size:69 final size:69
Alignment explanation
Indices: 16720--16853 Score: 259
Period size: 69 Copynumber: 1.9 Consensus size: 69
16710 CTTTAATTTA
*
16720 AAAATTTGTTGATTTTGGATTAATTAGAATTAAATTGAAAAGGAGTCGCCATTGACCTTTGGGTT
1 AAAATTTGTTGATTTTGGATTAATTAGAATTAAATTGAAAAGGAGTCGCCATCGACCTTTGGGTT
16785 TTTG
66 TTTG
16789 AAAATTTGTTGATTTTGGATTAATTAGAATTAAATTGAAAAGGAGTCGCCATCGACCTTTGGGTT
1 AAAATTTGTTGATTTTGGATTAATTAGAATTAAATTGAAAAGGAGTCGCCATCGACCTTTGGGTT
16854 AGGTAGGTTG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (69 bp):
AAAATTTGTTGATTTTGGATTAATTAGAATTAAATTGAAAAGGAGTCGCCATCGACCTTTGGGTT
TTTG
Found at i:16911 original size:19 final size:19
Alignment explanation
Indices: 16884--16925 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
16874 AACGTCATTT
16884 AAAAACAATTTTAAGA-AA
1 AAAAACAATTTTAAGACAA
*
16902 AAAAATCAATTTTTAGACAA
1 AAAAA-CAATTTTAAGACAA
16922 AAAA
1 AAAA
16926 GTTGGTCTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 10 0.48
20 6 0.29
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAACAATTTTAAGACAA
Found at i:17743 original size:30 final size:29
Alignment explanation
Indices: 17678--17754 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 29
17668 ATCATATTCG
*
17678 ATTTAAAGGACCAAAATAGCAAAATAGAA
1 ATTTAAAGGACTAAAATAGCAAAATAGAA
* *
17707 ACTTAAAGGACTAAAATAGCAAAAATATAA
1 ATTTAAAGGACTAAAATAGC-AAAATAGAA
17737 ATTTAAAGGACTAAAATA
1 ATTTAAAGGACTAAAATA
17755 TAAAAAACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 18 0.42
30 25 0.58
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (29 bp):
ATTTAAAGGACTAAAATAGCAAAATAGAA
Found at i:22581 original size:21 final size:21
Alignment explanation
Indices: 22555--22610 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
22545 CGAGTTACCT
*
22555 GCGACGGCCGCAATAGCATTC
1 GCGACGGCCGCAATAGCATCC
*
22576 GCGACGACCGCAATAGCATCC
1 GCGACGGCCGCAATAGCATCC
**
22597 ATGACGGCCGCAAT
1 GCGACGGCCGCAAT
22611 CACGGTAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.34, G:0.27, T:0.12
Consensus pattern (21 bp):
GCGACGGCCGCAATAGCATCC
Found at i:41248 original size:32 final size:32
Alignment explanation
Indices: 41212--41397 Score: 203
Period size: 32 Copynumber: 5.8 Consensus size: 32
41202 GACGCTCTTT
* *
41212 TGCATTATCTGGATGCAACACTAACTTTGCTA
1 TGCATTATCTGAATGCAACACTGACTTTGCTA
* * * *
41244 TGCATTATTTGAACGCAACACTAACTTTTCTA
1 TGCATTATCTGAATGCAACACTGACTTTGCTA
* ** * *
41276 TGCATTATCTAAATATAATAGTGACTTTGCTA
1 TGCATTATCTGAATGCAACACTGACTTTGCTA
* *
41308 TGCATTATCTGAATGCAATATTGACTCTT-CTA
1 TGCATTATCTGAATGCAACACTGACT-TTGCTA
* *
41340 TACATTATCTGAATGCAACACTGACTCTGCTA
1 TGCATTATCTGAATGCAACACTGACTTTGCTA
* *
41372 TGTATTATCTAAATGCAACACTGACT
1 TGCATTATCTGAATGCAACACTGACT
41398 CTTTTGTGCA
Statistics
Matches: 128, Mismatches: 24, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
31 1 0.01
32 125 0.98
33 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (32 bp):
TGCATTATCTGAATGCAACACTGACTTTGCTA
Found at i:41284 original size:64 final size:64
Alignment explanation
Indices: 41212--41413 Score: 226
Period size: 64 Copynumber: 3.2 Consensus size: 64
41202 GACGCTCTTT
* * * * *
41212 TGCATTATCTGGATGCAACACTAACTTTGCTATGCATTATTTGAACGCAACACTAACTTTTCTA
1 TGCATTATCTGAATGCAACACTGACTTTGCTATGCATTATCTGAATGCAACACTGACTTTTCTA
* ** * * * * *
41276 TGCATTATCTAAATATAATAGTGACTTTGCTATGCATTATCTGAATGCAATATTGACTCTTCTA
1 TGCATTATCTGAATGCAACACTGACTTTGCTATGCATTATCTGAATGCAACACTGACTTTTCTA
* * * * *
41340 TACATTATCTGAATGCAACACTGACTCTGCTATGTATTATCTAAATGCAACACTGACTCTTT-TG
1 TGCATTATCTGAATGCAACACTGACTTTGCTATGCATTATCTGAATGCAACACTGACT-TTTCTA
41404 TGCATTATCT
1 TGCATTATCT
41414 AAATACAAAA
Statistics
Matches: 110, Mismatches: 27, Indels: 2
0.79 0.19 0.01
Matches are distributed among these distances:
64 108 0.98
65 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (64 bp):
TGCATTATCTGAATGCAACACTGACTTTGCTATGCATTATCTGAATGCAACACTGACTTTTCTA
Found at i:41398 original size:32 final size:32
Alignment explanation
Indices: 41183--41417 Score: 193
Period size: 32 Copynumber: 7.3 Consensus size: 32
41173 TCTGATGTGT
* * * *
41183 ATTATTTAAATGCAATACTGACGCT-CTTTTGC
1 ATTATCTAAATGCAACACTGACTCTGC-TATGC
** * *
41215 ATTATCTGGATGCAACACTAACTTTGCTATGC
1 ATTATCTAAATGCAACACTGACTCTGCTATGC
* * * * * *
41247 ATTATTTGAACGCAACACTAACTTTTCTATGC
1 ATTATCTAAATGCAACACTGACTCTGCTATGC
** * * *
41279 ATTATCTAAATATAATAGTGACTTTGCTATGC
1 ATTATCTAAATGCAACACTGACTCTGCTATGC
* * * * *
41311 ATTATCTGAATGCAATATTGACTCTTCTATAC
1 ATTATCTAAATGCAACACTGACTCTGCTATGC
* *
41343 ATTATCTGAATGCAACACTGACTCTGCTATGT
1 ATTATCTAAATGCAACACTGACTCTGCTATGC
** *
41375 ATTATCTAAATGCAACACTGACTCTTTTGTGC
1 ATTATCTAAATGCAACACTGACTCTGCTATGC
41407 ATTATCTAAAT
1 ATTATCTAAAT
41418 ACAAAATTGA
Statistics
Matches: 164, Mismatches: 38, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
32 163 0.99
33 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (32 bp):
ATTATCTAAATGCAACACTGACTCTGCTATGC
Found at i:41427 original size:96 final size:95
Alignment explanation
Indices: 41180--41427 Score: 248
Period size: 96 Copynumber: 2.6 Consensus size: 95
41170 TTATCTGATG
* * * * * *
41180 TGTATTATTTAAATGCAATACTGACGCTCTTTTGCATTATCTGGATGCAACACTAACTTTGCTAT
1 TGTATTATCTAAATGCAATACTGACTCT-TTTTGCATTATCTGAATGCAAAATTGACTTTGCTAT
* * * *
41245 GCATTATTTGAACGCAACACTAACTTTTCTA
65 ACATTATCTGAACGCAACACTAACTCTGCTA
* ** * * *
41276 TGCATTATCTAAATATAATAGTGACT-TTGCTATGCATTATCTGAATGCAATATTGACTCTT-CT
1 TGTATTATCTAAATGCAATACTGACTCTT--TTTGCATTATCTGAATGCAAAATTGACT-TTGCT
* *
41339 ATACATTATCTGAATGCAACACTGACTCTGCTA
63 ATACATTATCTGAACGCAACACTAACTCTGCTA
* * *
41372 TGTATTATCTAAATGCAACACTGACTCTTTTGTGCATTATCTAAATACAAAATTGA
1 TGTATTATCTAAATGCAATACTGACTCTTTT-TGCATTATCTGAATGCAAAATTGA
41428 TACTACTATA
Statistics
Matches: 121, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
94 1 0.01
95 2 0.02
96 114 0.94
97 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (95 bp):
TGTATTATCTAAATGCAATACTGACTCTTTTTGCATTATCTGAATGCAAAATTGACTTTGCTATA
CATTATCTGAACGCAACACTAACTCTGCTA
Found at i:43426 original size:3 final size:3
Alignment explanation
Indices: 43418--43463 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
43408 TTAATTGTTC
* * *
43418 ATT ATT ATT A-T ATT ATT ATT ATT A-T ATT AAT AAT ATT TTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43464 TTTTACAGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:43437 original size:14 final size:14
Alignment explanation
Indices: 43418--43463 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
43408 TTAATTGTTC
43418 ATTATTATTATATT
1 ATTATTATTATATT
43432 ATTATTATTATATT
1 ATTATTATTATATT
* *
43446 AATAATATT-T-TT
1 ATTATTATTATATT
43458 ATTATT
1 ATTATT
43464 TTTTACAGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
12 6 0.21
13 1 0.04
14 21 0.75
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATTATTATATT
Found at i:45048 original size:2 final size:2
Alignment explanation
Indices: 45041--45066 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45031 TTCGGTCATT
45041 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
45067 CATAATTATA
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):
TA
Found at i:45076 original size:12 final size:14
Alignment explanation
Indices: 45041--45083 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
45031 TTCGGTCATT
*
45041 TATATATATATATA
1 TATATATATATACA
45055 TATATATATATACA
1 TATATATATATACA
*
45069 TA-AT-TATACACA
1 TATATATATATACA
45081 TAT
1 TAT
45084 TGGTGATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 9 0.35
13 2 0.08
14 15 0.58
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATATATATACA
Found at i:49328 original size:26 final size:24
Alignment explanation
Indices: 49274--49329 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
49264 AAAAGGGCAC
*
49274 TTTTTTCAAAATTTTTGATTGAAG
1 TTTTTTCAAAATTTTTAATTGAAG
* *
49298 ATTTTTCAAAATTCTTTTAATTG-AT
1 TTTTTTCAAAA-T-TTTTAATTGAAG
49323 TTTTTTC
1 TTTTTTC
49330 CAATTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 10 0.38
25 8 0.31
26 8 0.31
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (24 bp):
TTTTTTCAAAATTTTTAATTGAAG
Found at i:52288 original size:104 final size:103
Alignment explanation
Indices: 52113--52337 Score: 299
Period size: 104 Copynumber: 2.2 Consensus size: 103
52103 TATTGAACAT
* ** * * ***
52113 ACTTCCTCAACGAGAAGGAATAACGTCATATGAAATAGGTAGAACTCTTCAGTTTGGATCAACAG
1 ACTTCCTCAACAAGAAAAAACAACGTCATAGGAAATAGGTAGAACTCTTCAACATGGATCAACAG
* * *
52178 TGTCGTCTTCAACACCATATTATCTCTGGATTGACCCG
66 TATCGTCTTCAACACCATATTATCTCTAGATTGACCCA
* *
52216 ATTTCCTCAACAAGAAAAAACAACGTCATAGGAAA-ACGGTCAGAACTCTTCAACATGGATGAAC
1 ACTTCCTCAACAAGAAAAAACAACGTCATAGGAAATA-GGT-AGAACTCTTCAACATGGATCAAC
*
52280 AGTATCGTCTTCAACACCATATTATCTCTAGATTGACTCA
64 AGTATCGTCTTCAACACCATATTATCTCTAGATTGACCCA
52320 ACTTCCTCAACAAGAAAA
1 ACTTCCTCAACAAGAAAA
52338 GAATAGTGTC
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
102 1 0.01
103 32 0.30
104 72 0.69
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (103 bp):
ACTTCCTCAACAAGAAAAAACAACGTCATAGGAAATAGGTAGAACTCTTCAACATGGATCAACAG
TATCGTCTTCAACACCATATTATCTCTAGATTGACCCA
Found at i:54246 original size:2 final size:2
Alignment explanation
Indices: 54167--54226 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
54157 TTCGGTCATT
54167 TA TA TA 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
54209 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
54227 CACATATGGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54428 original size:17 final size:16
Alignment explanation
Indices: 54388--54430 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
54378 ATAATCATAC
*
54388 ATATATTTTGTTTCGA
1 ATATATTTTATTTCGA
* *
54404 ATAAATTTTATTTGCTA
1 ATATATTTTATTT-CGA
54421 ATATATTTTA
1 ATATATTTTA
54431 ATATGTTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.56
Consensus pattern (16 bp):
ATATATTTTATTTCGA
Found at i:62602 original size:3 final size:3
Alignment explanation
Indices: 62594--62678 Score: 125
Period size: 3 Copynumber: 28.3 Consensus size: 3
62584 CCTGCAAGTC
* * *
62594 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AAA AAA ATA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
62642 ATA ATA ATA ATA ATA ATA ATA ATA ACA ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
62679 AGGGAAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:63238 original size:136 final size:135
Alignment explanation
Indices: 62893--63476 Score: 615
Period size: 135 Copynumber: 4.4 Consensus size: 135
62883 TTCAGGGTAG
* ** * *
62893 ATCAGATCTGGATACATTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGAAAAC---
1 ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
* ** *
62955 -T----TGTTCCT-ATAGAAGATCAAATCT---AAAAA-AGGGATCTATTCTGTTGCTTCTTGAG
66 TTCCACTGTTCCTCATGGAAGATCAAATCTGGAAAAAAGAGGGATCTATTCCATTGCTTCTTAAG
*
63010 GAAAA
131 GGAAA
* * *
63015 ATCAGATCTGAAAATGTTGATTCATTCCACTGTTCTT-ATGGAAGATTGAATCGAGGCAGACTTG
1 ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
* * * * * * *
63079 TTCAACTGTTCTTCAAGAAAGATCAAATCTAGAAAAAAGAGGGATATGTTCCATTGCTTCTTAAG
66 TTCCACTGTTCCTCATGGAAGATCAAATCTGGAAAAAAGAGGGATCTATTCCATTGCTTCTTAAG
63144 GGAAAA
131 GG-AAA
* *
63150 ATCAGATCTAGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCAAGGCAGACTTG
1 ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
* * * * *
63215 TTCCACTGTTCCTCATGGAAGATCAAATTTGGATAAAAGAGGGATTTGTT--ATGCTGCTTCTTG
66 TTCCACTGTTCCTCATGGAAGATCAAATCTGGAAAAAAGAGGGATCTATTCCAT--TGCTTCTTA
63278 AGGGAAA
129 AGGGAAA
* * * * * * *
63285 GTCAGATCTGGAAATGTTGATTTATTCCATTGTTCTTCAAGGAAGATTGAATCCAGGTAGACTTG
1 ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
* * * * * **
63350 TTCCACTGTTCCTCAGGGAAGATTAAATTTGGAAAAAAGAGAGATCTATTTCGCTGCTTCTTAAG
66 TTCCACTGTTCCTCATGGAAGATCAAATCTGGAAAAAAGAGGGATCTATTCCATTGCTTCTTAAG
63415 GGAAA
131 GGAAA
* * * * *
63420 ATCATATCTGGAAATGTTGATTCATTCCACTTTTCTTAAGGGAATATTGAATGGAGG
1 ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGG
63477 TAGATTTTTT
Statistics
Matches: 384, Mismatches: 59, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
121 21 0.05
122 32 0.08
125 1 0.00
129 6 0.02
130 13 0.03
133 5 0.01
134 24 0.06
135 203 0.53
136 79 0.21
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (135 bp):
ATCAGATCTGGAAATGTTGATTCATTCCACTATTCTTCAGGGAAGATTGAATCGAGGCAGACTTG
TTCCACTGTTCCTCATGGAAGATCAAATCTGGAAAAAAGAGGGATCTATTCCATTGCTTCTTAAG
GGAAA
Found at i:64715 original size:13 final size:12
Alignment explanation
Indices: 64670--64739 Score: 59
Period size: 13 Copynumber: 5.5 Consensus size: 12
64660 TCTTGAACCC
*
64670 TTTTTTATTCTCT
1 TTTTTTTTTCT-T
* *
64683 TTTCTTTATCTT
1 TTTTTTTTTCTT
*
64695 TCTTTTTTTCTT
1 TTTTTTTTTCTT
64707 TTATTTTTTTCATT
1 TT-TTTTTTTC-TT
*
64721 TTTTTCTTTCTT
1 TTTTTTTTTCTT
64733 TTCTTTT
1 TT-TTTT
64740 CCTTTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
12 15 0.33
13 26 0.58
14 4 0.09
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTTCTT
Found at i:64723 original size:9 final size:8
Alignment explanation
Indices: 64682--64739 Score: 50
Period size: 9 Copynumber: 7.1 Consensus size: 8
64672 TTTTATTCTC
64682 TTTTCTTT
1 TTTTCTTT
64690 ATCTTTCTTT
1 -T-TTTCTTT
64700 TTTTC---
1 TTTTCTTT
*
64705 TTTTATTT
1 TTTTCTTT
64713 TTTTCATTT
1 TTTTC-TTT
64722 TTTTCTTT
1 TTTTCTTT
64730 CTTTTCTTT
1 -TTTTCTTT
64739 T
1 T
64740 CCTTTTATTC
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
5 4 0.10
8 12 0.29
9 18 0.44
10 7 0.17
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTCTTT
Found at i:64739 original size:23 final size:22
Alignment explanation
Indices: 64683--64752 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 22
64673 TTTATTCTCT
64683 TTTCTTTATC-TTTCTTTTTTTC
1 TTTCTTT-TCTTTTCTTTTTTTC
64705 TTT-TATTT-TTTTCATTTTTTTC
1 TTTCT-TTTCTTTTC-TTTTTTTC
*
64727 TTTCTTTTCTTTTCCTTTTATTC
1 TTTCTTTTCTTTT-CTTTTTTTC
64750 TTT
1 TTT
64753 AGAAGAAACT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
21 6 0.15
22 19 0.46
23 15 0.37
24 1 0.02
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCTTTTCTTTTCTTTTTTTC
Done.