Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002133.1 Hibiscus syriacus cultivar Beakdansim tig00004366_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: 76106
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:577 original size:37 final size:38
Alignment explanation
Indices: 527--602 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
517 ACTATATCAC
527 TAATCCTAAACGAT-ATCCATATGAAGTGTAAAAACTA
1 TAATCCTAAACGATAATCCATATGAAGTGTAAAAACTA
564 TAATCCTAAACGATAATCCATATGAAGTGTAAAAACTA
1 TAATCCTAAACGATAATCCATATGAAGTGTAAAAACTA
602 T
1 T
603 CTCAAGCGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 14 0.37
38 24 0.63
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.28
Consensus pattern (38 bp):
TAATCCTAAACGATAATCCATATGAAGTGTAAAAACTA
Found at i:14595 original size:19 final size:21
Alignment explanation
Indices: 14558--14600 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
14548 AACCATTCAG
*
14558 GGGGGGAATCGGTACCCCT-T
1 GGGGGGAATCGATACCCCTCT
*
14578 GGGGGGAATCGAT-TCCCTCT
1 GGGGGGAATCGATACCCCTCT
14598 GGG
1 GGG
14601 CAATCTGCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.14, C:0.23, G:0.42, T:0.21
Consensus pattern (21 bp):
GGGGGGAATCGATACCCCTCT
Found at i:21646 original size:2 final size:2
Alignment explanation
Indices: 21639--21717 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
21629 ATTTATTCTT
21639 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
21681 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
21718 GTTTTTTTAC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21792 original size:3 final size:3
Alignment explanation
Indices: 21777--21833 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
21767 TTTTATTTAT
* * *
21777 TTA TTA CTA TTA TTA TTTA TTA TTA TTT TTA TT- TTA ATA CTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
21823 TTA CTA TTA TT
1 TTA TTA TTA TT
21834 TTTTTATACC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.84
4 5 0.12
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:21794 original size:16 final size:16
Alignment explanation
Indices: 21773--21825 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
21763 TCTTTTTTAT
21773 TTATTTATTACTATTA
1 TTATTTATTACTATTA
* *
21789 TTATTTATTATTATTT
1 TTATTTATTACTATTA
*
21805 TTATTTTAATACTTATTA
1 TTA-TTTATTAC-TATTA
21823 TTA
1 TTA
21826 CTATTATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 17 0.57
17 6 0.20
18 7 0.23
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTATTACTATTA
Found at i:21795 original size:24 final size:22
Alignment explanation
Indices: 21769--21840 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 22
21759 TGTTTCTTTT
21769 TTATTTA-T-TTATTACTATTA
1 TTATTTATTATTATTACTATTA
**
21789 TTATTTATTATTATTTTTATT-
1 TTATTTATTATTATTACTATTA
*
21810 TTA-ATACTTATTATTACTATTA
1 TTATTTA-TTATTATTACTATTA
21832 TT-TTT-TTAT
1 TTATTTATTAT
21841 ACCTTGTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
20 13 0.32
21 16 0.39
22 12 0.29
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTTATTATTATTACTATTA
Found at i:37306 original size:24 final size:24
Alignment explanation
Indices: 37279--37324 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
37269 GTCTTAAGTA
37279 AAAAAAAAAAGAAAAAGAAAAAGG
1 AAAAAAAAAAGAAAAAGAAAAAGG
** *
37303 AAAAAAATGAGAAACAGAAAAA
1 AAAAAAAAAAGAAAAAGAAAAA
37325 TGTTTAGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAAAAAAAAGAAAAAGAAAAAGG
Found at i:37393 original size:11 final size:9
Alignment explanation
Indices: 37362--37410 Score: 66
Period size: 9 Copynumber: 5.6 Consensus size: 9
37352 CCCTAAATTG
37362 AAAAA-AGA
1 AAAAAGAGA
37370 AAAAAGAGA
1 AAAAAGAGA
37379 AAAAAGAGA
1 AAAAAGAGA
*
37388 ACAAA-AGA
1 AAAAAGAGA
37396 AAAAAGAGA
1 AAAAAGAGA
37405 AGAAAA
1 A-AAAA
37411 ATAAGGTGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
8 12 0.33
9 20 0.56
10 4 0.11
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:37396 original size:17 final size:16
Alignment explanation
Indices: 37361--37410 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 16
37351 GCCCTAAATT
37361 GAAAAAAGA-AAAAAGA
1 GAAAAAAGAGAAAAA-A
37377 GAAAAAAGAGAACAAAA
1 GAAAAAAGAGAA-AAAA
37394 GAAAAAAGAGAAGAAAA
1 GAAAAAAGAGAA-AAAA
37411 ATAAGGTGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 9 0.29
17 19 0.61
18 3 0.10
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (16 bp):
GAAAAAAGAGAAAAAA
Found at i:38740 original size:111 final size:111
Alignment explanation
Indices: 38541--38745 Score: 263
Period size: 111 Copynumber: 1.8 Consensus size: 111
38531 TCCCAGTTTC
*
38541 AGAGCCAATTTAGACTTCACAACAAAAGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
1 AGAGCCAATTTAGACTTCACAACAAAAGATATTAGACTCAAGACAACACAAGCTCAACTTCACAA
* *
38606 GGAAGGGGCGACTAATTGTCAACAAACAACTTTTTCAGTTTCATTT
66 GGAAGGGGCGACTAACTGACAACAAACAACTTTTTCAGTTTCATTT
* * * * * *
38652 AGAGTCAATTTCA-ACTTCACAGCTAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCAC-
1 AGAGCCAATTT-AGACTTCACAACAAAAGATATTAGACTCAAGACAACACAAGCTCAACTTCACA
**
38715 AGTGAAGGGGC-AGCTGGCTGACAACAAACAA
65 AG-GAAGGGGCGA-CTAACTGACAACAAACAA
38746 TTTACCAGTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
110 3 0.04
111 76 0.95
112 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (111 bp):
AGAGCCAATTTAGACTTCACAACAAAAGATATTAGACTCAAGACAACACAAGCTCAACTTCACAA
GGAAGGGGCGACTAACTGACAACAAACAACTTTTTCAGTTTCATTT
Found at i:40648 original size:28 final size:26
Alignment explanation
Indices: 40615--40705 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 26
40605 CCCCCACTAA
40615 TATTATATATGTTTAATTATATTTTCA-T
1 TATTATATAT-TTT-ATTATATTTT-ATT
40643 TATTAT-TATTTT-TTATATTTTATT
1 TATTATATATTTTATTATATTTTATT
* *
40667 TCATT-TATATTTTATTTATATATATATA
1 T-ATTATATATTTTA-TTATAT-TTTATT
40695 TATATATATAT
1 TAT-TATATAT
40706 ATATATATGT
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
23 1 0.02
24 12 0.23
25 9 0.17
26 3 0.06
27 11 0.21
28 12 0.23
29 5 0.09
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (26 bp):
TATTATATATTTTATTATATTTTATT
Found at i:40656 original size:17 final size:15
Alignment explanation
Indices: 40643--40683 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
40633 ATATTTTCAT
40643 TATTATTATTTTTTA
1 TATTATTATTTTTTA
40658 TATT-TTATTTCATTTA
1 TATTATTATTT--TTTA
40674 TATT-TTATTT
1 TATTATTATTT
40684 ATATATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.25
15 4 0.17
16 14 0.58
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTATTATTTTTTA
Found at i:40679 original size:24 final size:24
Alignment explanation
Indices: 40631--40681 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
40621 ATATGTTTAA
*
40631 TTATATTTTCATTATTATTATTTT
1 TTATATTTTCATTATCATTATTTT
*
40655 TTATATTTT-ATT-TCATTTATATT
1 TTATATTTTCATTATCA-TTATTTT
40678 TTAT
1 TTAT
40682 TTATATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 13 0.54
24 9 0.38
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (24 bp):
TTATATTTTCATTATCATTATTTT
Found at i:40690 original size:2 final size:2
Alignment explanation
Indices: 40683--40713 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40673 ATATTTTATT
40683 TA TA TA 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 TA TA TA T
40714 GTTTTTACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40734 original size:22 final size:23
Alignment explanation
Indices: 40709--40756 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
40699 TATATATATA
40709 TATATGTTTTTACTTATGTTT-T
1 TATATGTTTTTACTTATGTTTCT
* * *
40731 TATATTTTTTTATTTCTGTTTCT
1 TATATGTTTTTACTTATGTTTCT
40754 TAT
1 TAT
40757 TTATTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (23 bp):
TATATGTTTTTACTTATGTTTCT
Found at i:40777 original size:21 final size:24
Alignment explanation
Indices: 40753--40860 Score: 78
Period size: 25 Copynumber: 4.4 Consensus size: 24
40743 TTTCTGTTTC
*
40753 TTATT-TATTTA-TTTATTAC-TA
1 TTATTATATTTATTTTAATACTTA
*
40774 TTATTATTTTTATTTTAATACTTA
1 TTATTATATTTATTTTAATACTTA
* * *
40798 TTATTACTATTATTTTTTTATACCTTGT
1 TTATTA-TATT-TATTTTAATA-CTT-A
* *
40826 TTATACATATATATTTTAATACTTA
1 TTAT-TATATTTATTTTAATACTTA
40851 TTATATATAT
1 TTAT-TATAT
40861 ATATATATAT
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
21 5 0.07
22 5 0.07
23 7 0.10
24 8 0.12
25 12 0.18
26 11 0.16
27 11 0.16
28 7 0.10
29 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.62
Consensus pattern (24 bp):
TTATTATATTTATTTTAATACTTA
Found at i:40787 original size:30 final size:30
Alignment explanation
Indices: 40753--40818 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 30
40743 TTTCTGTTTC
40753 TTATTT-AT-TTATTTATTACTATTATTATTT
1 TTATTTAATATTA-TTATTACTATTATT-TTT
40783 TTATTTTAATACTTATTATTACTATTATTTTT
1 TTA-TTTAATA-TTATTATTACTATTATTTTT
40815 TTAT
1 TTAT
40819 ACCTTGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
30 3 0.09
31 4 0.12
32 8 0.25
33 14 0.44
34 3 0.09
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (30 bp):
TTATTTAATATTATTATTACTATTATTTTT
Found at i:40842 original size:27 final size:27
Alignment explanation
Indices: 40784--40866 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
40774 TTATTATTTT
40784 TATTTTAATACTTATTAT-TAC-TATTA
1 TATTTTAATACTTATTATATACATA-TA
* * *
40810 TTTTTTTATACCTTGTT-TATACATATA
1 TATTTTAATA-CTTATTATATACATATA
*
40837 TATTTTAATACTTATTATATATATATA
1 TATTTTAATACTTATTATATACATATA
40864 TAT
1 TAT
40867 ATATATATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
26 14 0.30
27 30 0.65
28 2 0.04
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (27 bp):
TATTTTAATACTTATTATATACATATA
Found at i:40857 original size:2 final size:2
Alignment explanation
Indices: 40852--40891 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
40842 TAATACTTAT
40852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40892 GACTATTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:40938 original size:57 final size:57
Alignment explanation
Indices: 40870--40980 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 57
40860 TATATATATA
* *
40870 TATATATATATATATATTATATGACTATTATTATTAGTAGTATTTTTACTATTAGCG
1 TATATACATATATATATTATATGACTATTATTATTAGTAGTATTATTACTATTAGCG
* * * * * * * *
40927 TATATACATATATTTTTTATTTTATTATTATTATTATTATTATTATTATTATTA
1 TATATACATATATATATTATATGACTATTATTATTAGTAGTATTATTACTATTA
40981 TTATTATTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
57 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.58
Consensus pattern (57 bp):
TATATACATATATATATTATATGACTATTATTATTAGTAGTATTATTACTATTAGCG
Found at i:40949 original size:7 final size:8
Alignment explanation
Indices: 40937--40990 Score: 65
Period size: 9 Copynumber: 6.4 Consensus size: 8
40927 TATATACATA
40937 TATTTT-T
1 TATTTTAT
40944 TATTTTAT
1 TATTTTAT
40952 TATTATTAT
1 TATT-TTAT
40961 TATTATTAT
1 TATT-TTAT
40970 TATTATTAT
1 TATT-TTAT
40979 TATTATTAT
1 TATT-TTAT
40988 TAT
1 TAT
40991 ATGTATATTC
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.13
8 5 0.11
9 34 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TATTTTAT
Found at i:40956 original size:3 final size:3
Alignment explanation
Indices: 40943--40990 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
40933 CATATATTTT
40943 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
40990 T
1 T
40991 ATGTATATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41067 original size:21 final size:20
Alignment explanation
Indices: 41042--41103 Score: 61
Period size: 23 Copynumber: 3.0 Consensus size: 20
41032 CTGCGTTTAC
*
41042 TTTTATTTTCTGTGTTTTTT
1 TTTTATTTTCTATGTTTTTT
* *
41062 TGTTTATTTAACATATGTTTTAT
1 T-TTTATTT-TC-TATGTTTTTT
*
41085 TTTTATTTTCTTTGTTTTT
1 TTTTATTTTCTATGTTTTT
41104 ATATAATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
20 8 0.24
21 8 0.24
22 8 0.24
23 9 0.27
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (20 bp):
TTTTATTTTCTATGTTTTTT
Found at i:41105 original size:21 final size:21
Alignment explanation
Indices: 41037--41105 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
41027 TTTTTCTGCG
* *
41037 TTTACTTTTATTTTCTGTGTT
1 TTTATTTTTATTTTCTATGTT
*
41058 TTT-TTGTTTATTTAACATATG-T
1 TTTATT-TTTATTT-TC-TATGTT
*
41080 TTTATTTTTATTTTCTTTGTT
1 TTTATTTTTATTTTCTATGTT
41101 TTTAT
1 TTTAT
41106 ATAATTTTCA
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 4 0.11
21 17 0.45
22 12 0.32
23 5 0.13
ACGTcount: A:0.14, C:0.06, G:0.07, T:0.72
Consensus pattern (21 bp):
TTTATTTTTATTTTCTATGTT
Found at i:44216 original size:22 final size:22
Alignment explanation
Indices: 44183--44241 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
44173 TAAAATCCAT
**
44183 GCAGCT-ACATCGTTAACAGCC
1 GCAGCTGACATCGCCAACAGCC
44204 GCAGCTGACATCGCCAACAGCC
1 GCAGCTGACATCGCCAACAGCC
44226 GCAGCTGACATCGCCA
1 GCAGCTGACATCGCCA
44242 TTCTTCCGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
21 6 0.17
22 29 0.83
ACGTcount: A:0.27, C:0.37, G:0.22, T:0.14
Consensus pattern (22 bp):
GCAGCTGACATCGCCAACAGCC
Found at i:45500 original size:89 final size:89
Alignment explanation
Indices: 45349--45532 Score: 350
Period size: 89 Copynumber: 2.1 Consensus size: 89
45339 CCACATAAAA
45349 CAACACTTCAATCTTCAGTTCCTGCAATGGGATATATAGCTTGTGAAATATAAGAATCTTACAAA
1 CAACACTTCAATCTTCAGTTCCTGCAATGGGATATATAGCTTGTGAAATATAAGAATCTTACAAA
45414 AAGATGCCTTTTAGTGACAACAAC
66 AAGATGCCTTTTAGTGACAACAAC
45438 CAACACTTCAATCTTCAGTTCCTGCAATGGGATATATAGCTTGTGAAATATAAGAATCTTACAAA
1 CAACACTTCAATCTTCAGTTCCTGCAATGGGATATATAGCTTGTGAAATATAAGAATCTTACAAA
* *
45503 AAGGTGCTTTTTAGTGACAACAAC
66 AAGATGCCTTTTAGTGACAACAAC
45527 CAACAC
1 CAACAC
45533 ATGCCACACA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 93 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (89 bp):
CAACACTTCAATCTTCAGTTCCTGCAATGGGATATATAGCTTGTGAAATATAAGAATCTTACAAA
AAGATGCCTTTTAGTGACAACAAC
Found at i:47753 original size:3 final size:3
Alignment explanation
Indices: 47745--47778 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
47735 GGTACGATGT
47745 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
47779 ATTTTTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:58026 original size:379 final size:381
Alignment explanation
Indices: 57319--58083 Score: 1417
Period size: 379 Copynumber: 2.0 Consensus size: 381
57309 CTGAGATTTC
* * *
57319 TGATATGCCGGAGATATGTGCAGCCCACCTTGGATGAGGGATCAACGGATTTGGTAGTTGGATCC
1 TGATATACCGGAGATATGTGCAGCCCACCTTGGACGAGGAATCAACGGATTTGGTAGTTGGATCC
57384 TAGTTTGAAACTAAGAAGGATGCCCAATTAGCAGTAAAGGAGTTTTTTTTATCAAAGCTCATATA
66 TAGTTTGAAACTAAGAAGGATGCCCAATTAGCAGTAAAGGAGTTTTTTTTATCAAAGCTCATATA
*
57449 TAATTCAATGTGGTTGAGTCTGATTAAAAGATATATTTTGTTAAGTGTATAAACAATAATGTCGG
131 GAATTCAATGTGGTTGAGTCTGATTAAAAGATATATTTTGTTAAGTGTATAAACAATAATGTCGG
*
57514 TTGTAAGTGAAGGATACATGTCTCATACCTATAATGAAAGATATTGTGGCAAGTGATAAGATTCC
196 TTGTAAGTGAAGGATACATGTCTCATACCTATAATGAAAGATATTGTGGCAAGTGACAAGATTCC
*
57579 ACTCCCAGTACAGTTGTACGTTGAGCTCCTTGACACAAGACCACAAACACTTAGATTCTGATGTC
261 ACTCCCAGTACAGTTGTACGTTGAGATCCTTGACACAAGACCACAAACACTTAGATTCTGATGTC
57644 ATATATGCACATGTCAAGC-TTTTTTTGGAGAAAAATCCAATGATCCTAGTTTCAA
326 ATATATGCACATGTCAAGCTTTTTTTTGGAGAAAAATCCAATGATCCTAGTTTCAA
57699 TGATATACCGGAGATATGTGCAGCCCACCTTGGACGAGGAATCAACGGATTTGGTAGTTGGATCC
1 TGATATACCGGAGATATGTGCAGCCCACCTTGGACGAGGAATCAACGGATTTGGTAGTTGGATCC
* *
57764 TAGTTTTAAACTAAGAAGGATGCCCAATTAGCAGTAAAGGAG-TTTTTTTATCAGAGCTCATATA
66 TAGTTTGAAACTAAGAAGGATGCCCAATTAGCAGTAAAGGAGTTTTTTTTATCAAAGCTCATATA
* *
57828 GAATTCAATGTGGTTGAGTCTGATTAAAAGATATATTTTTTTAAGTGTATAAACAATAATGTTGG
131 GAATTCAATGTGGTTGAGTCTGATTAAAAGATATATTTTGTTAAGTGTATAAACAATAATGTCGG
*
57893 TTGTAAGTGAAGGATACATGTCTCATACCTATAATGAAAGATATTGTGGCAAGTGACAAGGTTCC
196 TTGTAAGTGAAGGATACATGTCTCATACCTATAATGAAAGATATTGTGGCAAGTGACAAGATTCC
57958 ACTCCCAGTACAGTTGTACGTTGAGATCCTTGACACAAGACCACAAACACTTAGATTCTGATGTC
261 ACTCCCAGTACAGTTGTACGTTGAGATCCTTGACACAAGACCACAAACACTTAGATTCTGATGTC
58023 ATATATGCACATGTCAAGCTTTTTTTTGGAGAAAAATCCAATGATCCTAGTTTCAA
326 ATATATGCACATGTCAAGCTTTTTTTTGGAGAAAAATCCAATGATCCTAGTTTCAA
58079 TGATA
1 TGATA
58084 GTGGCATCAA
Statistics
Matches: 373, Mismatches: 11, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
379 229 0.61
380 144 0.39
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (381 bp):
TGATATACCGGAGATATGTGCAGCCCACCTTGGACGAGGAATCAACGGATTTGGTAGTTGGATCC
TAGTTTGAAACTAAGAAGGATGCCCAATTAGCAGTAAAGGAGTTTTTTTTATCAAAGCTCATATA
GAATTCAATGTGGTTGAGTCTGATTAAAAGATATATTTTGTTAAGTGTATAAACAATAATGTCGG
TTGTAAGTGAAGGATACATGTCTCATACCTATAATGAAAGATATTGTGGCAAGTGACAAGATTCC
ACTCCCAGTACAGTTGTACGTTGAGATCCTTGACACAAGACCACAAACACTTAGATTCTGATGTC
ATATATGCACATGTCAAGCTTTTTTTTGGAGAAAAATCCAATGATCCTAGTTTCAA
Found at i:61732 original size:2 final size:2
Alignment explanation
Indices: 61725--61758 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61715 CCAGAAACAA
61725 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
61759 GGGAAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62199 original size:16 final size:17
Alignment explanation
Indices: 62159--62202 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
62149 CCCTATTTGA
62159 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** *
62176 TTTTATATTT-TTAAAT
1 TTAAATATTTAATAAAT
62192 TTAAATATTTA
1 TTAAATATTTA
62203 GTTTTTGCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:63401 original size:153 final size:153
Alignment explanation
Indices: 63118--63432 Score: 567
Period size: 153 Copynumber: 2.1 Consensus size: 153
63108 ACATCGTTCT
* *
63118 CACATAATTTCTAATTGAAATTGGGTTTAGGTGGGAGTTATGACCCCCACTAATTTAGGGTATAA
1 CACA-AATTTCTAATTGAAATTGAGTTTAGGTGGGAGTTATGACCCCCACTAATTTAGAGTATAA
* *
63183 TAAAAATAAATTAATTAAATGCACCTGCACTGTTTTGGACAACAATTTCAATTAGAAATTATGTA
65 TAAAAATAAATTAATTAAATGCAACTACACTGTTTTGGACAACAATTTCAATTAGAAATTATGTA
63248 AGCACGATGTTGGTTTCTTTAGTA
130 AGCACGATGTTGGTTTCTTTAGTA
* *
63272 CACAAATTTCTAATTGAAATTGAGTTTAGGTGGGTGTTATGACCCCTACTAATTTAGAGTATAAT
1 CACAAATTTCTAATTGAAATTGAGTTTAGGTGGGAGTTATGACCCCCACTAATTTAGAGTATAAT
63337 AAAAATAAATTAATTAAATGCAACTACACTGTTTTGGACAACAATTTCAATTAGAAATTATGTAA
66 AAAAATAAATTAATTAAATGCAACTACACTGTTTTGGACAACAATTTCAATTAGAAATTATGTAA
63402 GCACGATGTTGGTTTCTTTAGTA
131 GCACGATGTTGGTTTCTTTAGTA
63425 CACAAATT
1 CACAAATT
63433 CAATACTTGG
Statistics
Matches: 155, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
153 151 0.97
154 4 0.03
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (153 bp):
CACAAATTTCTAATTGAAATTGAGTTTAGGTGGGAGTTATGACCCCCACTAATTTAGAGTATAAT
AAAAATAAATTAATTAAATGCAACTACACTGTTTTGGACAACAATTTCAATTAGAAATTATGTAA
GCACGATGTTGGTTTCTTTAGTA
Found at i:70323 original size:23 final size:23
Alignment explanation
Indices: 70297--70351 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
70287 ATGGCACTAT
70297 GGTGCATTTCTACACAGCACTTC
1 GGTGCATTTCTACACAGCACTTC
* **
70320 GGTGCAATTCTACATGGCACTTC
1 GGTGCATTTCTACACAGCACTTC
*
70343 GATGCATTT
1 GGTGCATTT
70352 ATACGAGTTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.33
Consensus pattern (23 bp):
GGTGCATTTCTACACAGCACTTC
Found at i:75738 original size:21 final size:22
Alignment explanation
Indices: 75699--75750 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
75689 CATCTTATAT
*
75699 GGCACTTCCGTGCATTTCTATC
1 GGCACTTCCGTGCAATTCTATC
* *
75721 GGCAC-TCGGTGCAATTCTATGT
1 GGCACTTCCGTGCAATTCTAT-C
75743 GGCACTTC
1 GGCACTTC
75751 GATGCATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 13 0.52
22 10 0.40
23 2 0.08
ACGTcount: A:0.15, C:0.29, G:0.23, T:0.33
Consensus pattern (22 bp):
GGCACTTCCGTGCAATTCTATC
Done.