Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001622.1 Hibiscus syriacus cultivar Beakdansim tig00003223_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: 83462
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1017 original size:34 final size:34
Alignment explanation
Indices: 966--1038 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
956 ATTATTAGAT
* *
966 TTATCAAGTTAGGCGCATTCAAGTTCCAATCAAA
1 TTATTAAGTTAGACGCATTCAAGTTCCAATCAAA
*
1000 TTATTAAGTTAGACGCATTTAAGTTCCAATCAAA
1 TTATTAAGTTAGACGCATTCAAGTTCCAATCAAA
1034 TTATT
1 TTATT
1039 GTACGAAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (34 bp):
TTATTAAGTTAGACGCATTCAAGTTCCAATCAAA
Found at i:2108 original size:17 final size:17
Alignment explanation
Indices: 2079--2114 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2069 AATATAATTT
2079 AAAAATGAGAGAAAATAA
1 AAAAATGAGAGAAAA-AA
2097 AAAAATGA-AGAAAAAA
1 AAAAATGAGAGAAAAAA
2113 AA
1 AA
2115 GAAGTATTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 6 0.33
18 8 0.44
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.08
Consensus pattern (17 bp):
AAAAATGAGAGAAAAAA
Found at i:5457 original size:14 final size:15
Alignment explanation
Indices: 5438--5466 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5428 TAATGTAATT
5438 AATAATTTAT-TTTA
1 AATAATTTATGTTTA
5452 AATAATTTATGTTTA
1 AATAATTTATGTTTA
5467 GATTTTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
AATAATTTATGTTTA
Found at i:5673 original size:113 final size:111
Alignment explanation
Indices: 5465--5680 Score: 306
Period size: 113 Copynumber: 1.9 Consensus size: 111
5455 AATTTATGTT
*
5465 TAGATTTTTAACTAATTTATAATTATATGTTGAGTACTTTATAATTTCAAAGTTTTATAAATTAA
1 TAGATTTTTAACTAATTTATAATTATATGTTGAGTACTTTATAATTTCAAAATTTTATAAATTAA
* * * * *
5530 ATAAATGGTGCTTATATTTACTGGTATTCATCGGTGCTTGTCGAGC
66 ATAAACGATGCTCATAGTTACTAGTATTCATCGGTGCTTGTCGAGC
* *
5576 TAGATTTTTAACTAATTTATAATTATATGTTGAGAGTATTTTATAATTTTAAAATTTTATAAATT
1 TAGATTTTTAACTAATTTATAATTATATGTT--GAGTACTTTATAATTTCAAAATTTTATAAATT
* * * *
5641 AAATTAACGATGCTCATAGTTAGTAGTGTTCATTGGTGCT
64 AAATAAACGATGCTCATAGTTACTAGTATTCATCGGTGCT
5681 CGTCAAACGT
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
111 31 0.34
113 60 0.66
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.46
Consensus pattern (111 bp):
TAGATTTTTAACTAATTTATAATTATATGTTGAGTACTTTATAATTTCAAAATTTTATAAATTAA
ATAAACGATGCTCATAGTTACTAGTATTCATCGGTGCTTGTCGAGC
Found at i:5739 original size:2 final size:2
Alignment explanation
Indices: 5734--5762 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5724 ACACGCATAC
5734 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
5763 CACACACACA
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:5901 original size:17 final size:18
Alignment explanation
Indices: 5875--5908 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5865 GCCAACCAAA
5875 TAAAAATAAATA-AAAAG
1 TAAAAATAAATATAAAAG
*
5892 TAAAAGTAAATATAAAA
1 TAAAAATAAATATAAAA
5909 AAATATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (18 bp):
TAAAAATAAATATAAAAG
Found at i:7248 original size:21 final size:22
Alignment explanation
Indices: 7215--7255 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
7205 TTAAAAATTA
7215 TAAAGGTAGTACCGATACTCAT
1 TAAAGGTAGTACCGATACTCAT
7237 TAAAGG-AGTACCGATACTC
1 TAAAGGTAGTACCGATACTC
7256 CCTGTCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGTAGTACCGATACTCAT
Found at i:25523 original size:2 final size:2
Alignment explanation
Indices: 25518--25545 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25508 CGTGTGTGAG
25518 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
25546 GTGGTAGAAA
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:30526 original size:17 final size:16
Alignment explanation
Indices: 30490--30545 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
30480 ATGTTTATAG
30490 TTTTATATTATATGATA
1 TTTTATATTATATGA-A
*
30507 TTTTATATTTTATTGAA
1 TTTTATATTATA-TGAA
* *
30524 TTTTTTATTCTAAT-AA
1 TTTTATATTAT-ATGAA
30540 TTTTAT
1 TTTTAT
30546 GAATATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 7 0.21
17 22 0.67
18 4 0.12
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (16 bp):
TTTTATATTATATGAA
Found at i:32288 original size:21 final size:21
Alignment explanation
Indices: 32262--32301 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
32252 GAAGCTGGCG
32262 GATCGGATATCAGCAAAAAGT
1 GATCGGATATCAGCAAAAAGT
*
32283 GATCGGATATTAGCAAAAA
1 GATCGGATATCAGCAAAAA
32302 AGAAGGAATT
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:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (21 bp):
GATCGGATATCAGCAAAAAGT
Found at i:32919 original size:26 final size:25
Alignment explanation
Indices: 32880--32938 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
32870 AGAGTGTGTG
*
32880 AGAAGAAGAGGAGGAGGAAGAAGAA
1 AGAAGAAGAAGAGGAGGAAGAAGAA
*
32905 AGAAGGAAGAAGAGGAGGAGGAAG-A
1 AGAA-GAAGAAGAGGAGGAAGAAGAA
*
32930 AGTAGAAGA
1 AGAAGAAGA
32939 TGCCACGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.17
25 8 0.27
26 17 0.57
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02
Consensus pattern (25 bp):
AGAAGAAGAAGAGGAGGAAGAAGAA
Found at i:49365 original size:92 final size:91
Alignment explanation
Indices: 49245--49411 Score: 262
Period size: 92 Copynumber: 1.8 Consensus size: 91
49235 TCCCGAATAT
* * * * * *
49245 TTAATTTCAATTATTTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGATTAG
1 TTAAATTCAATTAATTAAATACAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
49310 GGTAACTTGGATAAAAAAAAGGATTA
66 GGTAACTTGGATAAAAAAAAGGATTA
49336 TTAAATTCTAATTAATTAAATACAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
1 TTAAATTC-AATTAATTAAATACAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTA
*
49401 TGGTAACTTGG
65 GGGTAACTTGG
49412 CTATAAAAGG
Statistics
Matches: 68, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
91 7 0.10
92 61 0.90
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (91 bp):
TTAAATTCAATTAATTAAATACAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGACTAG
GGTAACTTGGATAAAAAAAAGGATTA
Found at i:52252 original size:35 final size:35
Alignment explanation
Indices: 52200--52312 Score: 109
Period size: 35 Copynumber: 3.2 Consensus size: 35
52190 CAAAACAGTC
* * *
52200 TTTAATTTCATTCTAAACCCCAATTTCCAAAGTAA
1 TTTAATTTCATTATAAACCCCAAATTCCAAAATAA
* *
52235 TTTAATTTTATTATAAACCCTAAATTCCAAAATAA
1 TTTAATTTCATTATAAACCCCAAATTCCAAAATAA
** * * * * *
52270 TTTAATTAAATTTTAAATCCCAAACTCTAAAATAC
1 TTTAATTTCATTATAAACCCCAAATTCCAAAATAA
*
52305 TTCAATTT
1 TTTAATTT
52313 AAGGTTTAGA
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.42, C:0.18, G:0.01, T:0.40
Consensus pattern (35 bp):
TTTAATTTCATTATAAACCCCAAATTCCAAAATAA
Found at i:52376 original size:35 final size:35
Alignment explanation
Indices: 52315--52384 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
52305 TTCAATTTAA
* * *
52315 GGTTTAGAATGTAATTGAATTATTTTGGAATTTTG
1 GGTTTAGAATGAAATTGAAGTATTTTGAAATTTTG
*
52350 GGTTTAGAATGAAATT-AAGGTGTTTTGAAATTTTG
1 GGTTTAGAATGAAATTGAA-GTATTTTGAAATTTTG
52385 AACATGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 2 0.07
35 28 0.93
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (35 bp):
GGTTTAGAATGAAATTGAAGTATTTTGAAATTTTG
Found at i:53522 original size:64 final size:66
Alignment explanation
Indices: 53445--53606 Score: 174
Period size: 64 Copynumber: 2.5 Consensus size: 66
53435 TTTGTTTGAA
* * ** *
53445 AGTGTATCGATGCA-CAGGTAGTGCATCGATGCA-CTCTTTTAAAATAGAAACATCGAATGCA-A
1 AGTGCATCGATGCATCAGGTAGTGCATCGATGCATCCCAGTGAAAATA-AAACATCGAATGCATA
53507 TT
65 TT
* * * * *
53509 AGTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTGATAATACAACATCGAATGCATTT
1 AGTGCATCGATGCATCAGGTAGTGCATCGATGCATCCCAGTGAAAATAAAACATCGAATGCATAT
53573 T
66 T
*
53574 A-TGCACCGATGCATCA-GTAGTGCATCGATGCAT
1 AGTGCATCGATGCATCAGGTAGTGCATCGATGCAT
53607 ACTTTCATTG
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
63 2 0.02
64 64 0.79
65 15 0.19
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (66 bp):
AGTGCATCGATGCATCAGGTAGTGCATCGATGCATCCCAGTGAAAATAAAACATCGAATGCATAT
T
Found at i:54392 original size:19 final size:19
Alignment explanation
Indices: 54370--54417 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
54360 ATATGTGATG
*
54370 TGATATACGTTATGA-GAAA
1 TGATATACGTCAT-ATGAAA
*
54389 TGATATAAGTCATATGAAA
1 TGATATACGTCATATGAAA
*
54408 TGATTTACGT
1 TGATATACGT
54418 GAATACATGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (19 bp):
TGATATACGTCATATGAAA
Found at i:54643 original size:32 final size:31
Alignment explanation
Indices: 54607--54787 Score: 222
Period size: 32 Copynumber: 5.7 Consensus size: 31
54597 GTTCTACGGA
54607 ACATATGGACAGAATTACCTATGTCTTTTGAG
1 ACATATGGACAGAA-TACCTATGTCTTTTGAG
* * **
54639 ACATATGGACAGTATACCTATGT-TCTACAGG
1 ACATATGGACAGAATACCTATGTCTTTTGA-G
54670 ACATATGGACAGAATTACCTATGTCTTTTGAG
1 ACATATGGACAGAA-TACCTATGTCTTTTGAG
* ***
54702 ACATATGGACAGTATACCTATGTTCTACGGA-
1 ACATATGGACAGAATACCTATG-TCTTTTGAG
54733 ACATATGGACAGAATTACCTATGTCTTTTGAG
1 ACATATGGACAGAA-TACCTATGTCTTTTGAG
*
54765 ACATATGGACAGTATACCTATGT
1 ACATATGGACAGAATACCTATGT
54788 TCTAAGGAAC
Statistics
Matches: 126, Mismatches: 17, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
30 3 0.02
31 58 0.46
32 62 0.49
33 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (31 bp):
ACATATGGACAGAATACCTATGTCTTTTGAG
Found at i:54665 original size:63 final size:63
Alignment explanation
Indices: 54587--54804 Score: 411
Period size: 63 Copynumber: 3.5 Consensus size: 63
54577 AGAGTAGAGG
54587 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
54650 GTATACCTATGTTCTACAGG-ACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
1 GTATACCTATGTTCTAC-GGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
54713 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
*
54776 GTATACCTATGTTCTAAGGAACATATGGA
1 GTATACCTATGTTCTACGGAACATATGGA
54805 TAGTTTACCT
Statistics
Matches: 152, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
62 2 0.01
63 148 0.97
64 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
Found at i:54800 original size:31 final size:31
Alignment explanation
Indices: 54587--54843 Score: 238
Period size: 31 Copynumber: 8.2 Consensus size: 31
54577 AGAGTAGAGG
*
54587 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * *
54618 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTATGGA-ACATATGGACA
*
54650 GTATACCTATGTTCTACAGG-ACATATGGACA
1 GTATACCTATGTTCTA-TGGAACATATGGACA
* * *
54681 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTATGGA-ACATATGGACA
*
54713 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * *
54744 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTATGGA-ACATATGGACA
* *
54776 GTATACCTATGTTCTAAGGAACATATGGATA
1 GTATACCTATGTTCTATGGAACATATGGACA
* * * *
54807 GTTTACCTAGGTTC-ATCGGAACCTATAGACA
1 GTATACCTATGTTCTAT-GGAACATATGGACA
54838 GT-TACC
1 GTATACC
54844 GAGGATCTTT
Statistics
Matches: 183, Mismatches: 31, Indels: 25
0.77 0.13 0.10
Matches are distributed among these distances:
30 6 0.03
31 100 0.55
32 76 0.42
33 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (31 bp):
GTATACCTATGTTCTATGGAACATATGGACA
Found at i:59499 original size:32 final size:31
Alignment explanation
Indices: 59463--59643 Score: 204
Period size: 32 Copynumber: 5.7 Consensus size: 31
59453 GTTCTACGGA
59463 ACATATGGACAGAATTACCTATGTCTTTTGAG
1 ACATATGGACAGAA-TACCTATGTCTTTTGAG
* ** *
59495 ACATATGGACAGTATACCTATGT-TGTACGGG
1 ACATATGGACAGAATACCTATGTCT-TTTGAG
59526 ACATATGGACAGAATTACCTATGTCTTTTGAG
1 ACATATGGACAGAA-TACCTATGTCTTTTGAG
* ***
59558 ACATATGGACAGTATACCTATGTTCTACGGA-
1 ACATATGGACAGAATACCTATG-TCTTTTGAG
* *
59589 ACATATTGATAGAATTACCTATGTCTTTTGAG
1 ACATATGGACAGAA-TACCTATGTCTTTTGAG
*
59621 ACATATGGACAGTATACCTATGT
1 ACATATGGACAGAATACCTATGT
59644 TCTAAGGAAT
Statistics
Matches: 122, Mismatches: 21, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
30 1 0.01
31 58 0.48
32 62 0.51
33 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (31 bp):
ACATATGGACAGAATACCTATGTCTTTTGAG
Found at i:59658 original size:31 final size:31
Alignment explanation
Indices: 59443--59699 Score: 209
Period size: 31 Copynumber: 8.2 Consensus size: 31
59433 AGAGTCGAGG
59443 GTATACCTATGTTCTACGGAACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* ***
59474 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTACGGA-ACATATGGACA
* *
59506 GTATACCTATGTTGTACGGGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACA
* ***
59537 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTACGGA-ACATATGGACA
* *
59569 GTATACCTATGTTCTACGGAACATATTGATA
1 GTATACCTATGTTCTACGGAACATATGGACA
* ***
59600 GAATTACCTATG-TCTTTTGAGACATATGGACA
1 GTA-TACCTATGTTCTACGGA-ACATATGGACA
* * *
59632 GTATACCTATGTTCTAAGGAATATATGGATA
1 GTATACCTATGTTCTACGGAACATATGGACA
* * * *
59663 GTTTACCTAGGTTC-ATCGGAACCTATAGACA
1 GTATACCTATGTTCTA-CGGAACATATGGACA
59694 GT-TACC
1 GTATACC
59700 GAGGATCTTT
Statistics
Matches: 175, Mismatches: 41, Indels: 21
0.74 0.17 0.09
Matches are distributed among these distances:
30 5 0.03
31 96 0.55
32 74 0.42
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (31 bp):
GTATACCTATGTTCTACGGAACATATGGACA
Found at i:59663 original size:63 final size:63
Alignment explanation
Indices: 59443--59660 Score: 382
Period size: 63 Copynumber: 3.5 Consensus size: 63
59433 AGAGTCGAGG
59443 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
* *
59506 GTATACCTATGTTGTACGGGACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
* *
59569 GTATACCTATGTTCTACGGAACATATTGATAGAATTACCTATGTCTTTTGAGACATATGGACA
1 GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
* *
59632 GTATACCTATGTTCTAAGGAATATATGGA
1 GTATACCTATGTTCTACGGAACATATGGA
59661 TAGTTTACCT
Statistics
Matches: 146, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 146 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (63 bp):
GTATACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTTGAGACATATGGACA
Found at i:64042 original size:3 final size:3
Alignment explanation
Indices: 64034--64072 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
64024 TGTGGCAACG
64034 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
64073 GTAGTAGAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:65860 original size:2 final size:2
Alignment explanation
Indices: 65779--65840 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
65769 TACCCACTTT
*
65779 TA TA TT 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
65821 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
65841 CACACACACA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:74662 original size:20 final size:19
Alignment explanation
Indices: 74624--74660 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
74614 AGTATGTTCA
*
74624 GGGGGTATCGATTCCCCCT
1 GGGGGAATCGATTCCCCCT
*
74643 GGGGGAATCTATTCCCCC
1 GGGGGAATCGATTCCCCC
74661 CTAAAGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.32, G:0.30, T:0.24
Consensus pattern (19 bp):
GGGGGAATCGATTCCCCCT
Found at i:75432 original size:38 final size:38
Alignment explanation
Indices: 75389--75522 Score: 180
Period size: 38 Copynumber: 3.5 Consensus size: 38
75379 TATAAGATAT
*
75389 ATGACAGGTCTTTCGGGACACATATTACATCCTTCGGG
1 ATGACAGGTCTTTCGGGACACAGATTACATCCTTCGGG
*
75427 ATGACAGGTCCTTT-GGGACACAGATTACATCTTTCGGG
1 ATGACAGGT-CTTTCGGGACACAGATTACATCCTTCGGG
* * *
75465 ATGACAGGTCCTTCGGGACATAGATGACATCCTTCGGG
1 ATGACAGGTCTTTCGGGACACAGATTACATCCTTCGGG
* * *
75503 ATGATAGGTCATTCGAGACA
1 ATGACAGGTCTTTCGGGACA
75523 TTTATACGAG
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
37 3 0.04
38 78 0.92
39 4 0.05
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (38 bp):
ATGACAGGTCTTTCGGGACACAGATTACATCCTTCGGG
Found at i:75465 original size:21 final size:21
Alignment explanation
Indices: 75397--75465 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
75387 ATATGACAGG
*
75397 TCTTTCGGGACACATATTACA
1 TCTTTCGGGACACAGATTACA
* * *
75418 TCCTTCGGGATGACAG-GT-C-
1 TCTTTCGGGA-CACAGATTACA
75437 -CTTT-GGGACACAGATTACA
1 TCTTTCGGGACACAGATTACA
75456 TCTTTCGGGA
1 TCTTTCGGGA
75466 TGACAGGTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
16 4 0.11
17 5 0.14
18 4 0.11
20 5 0.14
21 14 0.40
22 3 0.09
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (21 bp):
TCTTTCGGGACACAGATTACA
Found at i:75481 original size:17 final size:17
Alignment explanation
Indices: 75418--75482 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
75408 ACATATTACA
75418 TCCTTCGGGATGACAGG
1 TCCTTCGGGATGACAGG
* * *
75435 TCCTTTGGGA-CACAGAT
1 TCCTTCGGGATGACAG-G
75452 TACATCTTTCGGGATGACAGG
1 T-C--C-TTCGGGATGACAGG
75473 TCCTTCGGGA
1 TCCTTCGGGA
75483 CATAGATGAC
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
16 4 0.11
17 17 0.47
18 2 0.06
20 2 0.06
21 7 0.19
22 4 0.11
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (17 bp):
TCCTTCGGGATGACAGG
Found at i:81466 original size:38 final size:38
Alignment explanation
Indices: 81424--81557 Score: 169
Period size: 38 Copynumber: 3.5 Consensus size: 38
81414 TATAAGACAT
**
81424 ATGACAGGTTATTCGGGACACAGATTACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATTACATCCTTCGGG
* * *
81462 ATGACAGGTCCTTCGGGACACATATTACATCATTCGAG
1 ATGACAGGTCCTTCGGGACACAGATTACATCCTTCGGG
* * * *
81500 ATGACAAGTCCTTCGGGACACAGATGATATTCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATTACATCCTTCGGG
* *
81538 ATGATAGGTCCTTCGTGACA
1 ATGACAGGTCCTTCGGGACA
81558 TTTATACGAG
Statistics
Matches: 81, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 81 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAGATTACATCCTTCGGG
Done.