Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001316.1 Hibiscus syriacus cultivar Beakdansim tig00002567_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: 63924
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:1764 original size:16 final size:16
Alignment explanation
Indices: 1743--1774 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1733 TTGGGGATGA
1743 TAATGTACTTTTGCCC
1 TAATGTACTTTTGCCC
1759 TAATGTACTTTTGCCC
1 TAATGTACTTTTGCCC
1775 ACTAGTCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (16 bp):
TAATGTACTTTTGCCC
Found at i:2140 original size:8 final size:9
Alignment explanation
Indices: 2120--2157 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
2110 CTGTTTATTT
*
2120 TTATTATTA
1 TTATAATTA
2129 TTATAA-TA
1 TTATAATTA
*
2137 TTATAATTG
1 TTATAATTA
2146 TTATAATTA
1 TTATAATTA
2155 TTA
1 TTA
2158 CTATATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
8 8 0.32
9 17 0.68
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (9 bp):
TTATAATTA
Found at i:2178 original size:26 final size:26
Alignment explanation
Indices: 2115--2178 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
2105 TTTGCCTGTT
2115 TATTTTTATT-ATTATTATAATATTA
1 TATTTTTATTAATTATTATAATATTA
*
2140 TAATTGTTA-TAATTATTACT-ATATTA
1 T-ATTTTTATTAATTATTA-TAATATTA
2166 TATTTTTATTAAT
1 TATTTTTATTAAT
2179 AAATATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 8 0.24
26 24 0.73
27 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
TATTTTTATTAATTATTATAATATTA
Found at i:15058 original size:26 final size:28
Alignment explanation
Indices: 15029--15080 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
15019 ATGCTTGAAG
*
15029 AAAAAAATGATGAA-AAAAA-TAATACT
1 AAAAAAATAATGAAGAAAAATTAATACT
15055 AAAAAAATAATGAAGAAAAATTAATA
1 AAAAAAATAATGAAGAAAAATTAATA
15081 AAAGAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 13 0.57
27 5 0.22
28 5 0.22
ACGTcount: A:0.71, C:0.02, G:0.08, T:0.19
Consensus pattern (28 bp):
AAAAAAATAATGAAGAAAAATTAATACT
Found at i:15097 original size:30 final size:31
Alignment explanation
Indices: 15055--15123 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
15045 AAATAATACT
* *
15055 AAAAA-AATAATGAAGAAAAATTAATAAAAG
1 AAAAATAATAATGAAAAAAAATGAATAAAAG
* *
15085 AAAAATAA-AATGAAAAAAAATGAGTGAAAG
1 AAAAATAATAATGAAAAAAAATGAATAAAAG
15115 AGAAAATAA
1 A-AAAATAA
15124 GGGTCAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.14
Consensus pattern (31 bp):
AAAAATAATAATGAAAAAAAATGAATAAAAG
Found at i:15103 original size:15 final size:13
Alignment explanation
Indices: 15029--15105 Score: 59
Period size: 14 Copynumber: 5.6 Consensus size: 13
15019 ATGCTTGAAG
*
15029 AAAAAAATGATG-
1 AAAAAAATAATGA
15041 AAAAAAATAAT-A
1 AAAAAAATAATGA
15053 CTAAAAAAATAATGA
1 --AAAAAAATAATGA
* *
15068 AGAAAAATTAATAA
1 A-AAAAAATAATGA
15082 AAGAAAAATAAAATGA
1 AA-AAAAAT--AATGA
15098 AAAAAAAT
1 AAAAAAAT
15106 GAGTGAAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
12 10 0.19
13 2 0.04
14 27 0.52
15 7 0.13
16 6 0.12
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (13 bp):
AAAAAAATAATGA
Found at i:15490 original size:18 final size:18
Alignment explanation
Indices: 15467--15501 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
15457 CAAGTTTATC
15467 TTTTTGAAATTCAATTTA
1 TTTTTGAAATTCAATTTA
15485 TTTTTGAAATTCAATTT
1 TTTTTGAAATTCAATTT
15502 GTTTCATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (18 bp):
TTTTTGAAATTCAATTTA
Found at i:16910 original size:124 final size:124
Alignment explanation
Indices: 16673--17338 Score: 1009
Period size: 124 Copynumber: 5.4 Consensus size: 124
16663 CATTCGATGG
* * * * *
16673 ATCAACATTTCC-GGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
*
16737 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACAGAAGGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
*
16796 ATCAACTTTTCCATAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * *
16861 AATGAGAAGAGCTTGTTCAACCTTTTGCATGCCTCTATCACAGAAGGAGATAGATTAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* *
16920 ATCAACTTTTCCAGAAAAAGTTCATAATAAAAAGAACTCATCTGAAGAATGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
16985 AATGAGAAGAGCTTGTTCAACCTTTTGCATAACTCTATCACATAAGGAGATAGATCAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
17044 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* *
17109 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTTTATCACAGAAGGAGATAGATCAAC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
* * * *
17168 ATCAACTTTTCCAGAGAAAGTTTATAATGAGAAGAACTCATCTAAAGAA-GAAGAAGAAGTTCAT
1 ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
* * * * * *
17232 AATGAGAAGAACTTATTCAACCTTTTGTATGA-TCTATCTCAGAAGAAGATAGATTAGC
66 AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
** * * *
17290 ATCAACATTTT-CAG-AAGTGTTTATAATGAGAAGAACTCATCTAAAGAAG
1 ATCAAC-TTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAG
17339 AAGGAGCAGA
Statistics
Matches: 501, Mismatches: 39, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
121 31 0.06
122 30 0.06
123 59 0.12
124 381 0.76
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (124 bp):
ATCAACTTTTCCAGAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAGCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:17579 original size:3 final size:3
Alignment explanation
Indices: 17566--17654 Score: 65
Period size: 3 Copynumber: 30.0 Consensus size: 3
17556 TTTGCCTGTT
* * * * *
17566 TTA TT- TTA TTA TTA TTA TAA TTA TTA TAA TTG TTA TAA TTA TTA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
17613 TTA TTA CTG TTA TTA -TA TTT TTA TTAA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
17655 CATATTACAG
Statistics
Matches: 63, Mismatches: 20, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
2 4 0.06
3 57 0.90
4 2 0.03
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:17626 original size:36 final size:36
Alignment explanation
Indices: 17586--17655 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
17576 ATTATTATAA
* *
17586 TTATTATAATTGTTA-TAATTATTATAATTATTACTG
1 TTATTAT-ATTGTTATTAATAAATATAATTATTACTG
* *
17622 TTATTATATTTTTATTAATAAATATTATTATTAC
1 TTATTATATTGTTATTAATAAATATAATTATTAC
17656 ATATTACAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 6 0.21
36 23 0.79
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (36 bp):
TTATTATATTGTTATTAATAAATATAATTATTACTG
Found at i:17629 original size:18 final size:18
Alignment explanation
Indices: 17571--17618 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
17561 CTGTTTTATT
*
17571 TTATTATTATTATAATTA
1 TTATAATTATTATAATTA
*
17589 TTATAATTGTTATAATTA
1 TTATAATTATTATAATTA
17607 TTATAATTATTA
1 TTATAATTATTA
17619 CTGTTATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TTATAATTATTATAATTA
Found at i:32956 original size:30 final size:29
Alignment explanation
Indices: 32905--32975 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
32895 AAACTTTCAC
*
32905 ACAACAA-CCTTTCAACCGTAAACATCAA
1 ACAACAATCCTCTCAACCGTAAACATCAA
* * *
32933 ACAATAATCCTCTCAACCCGTAAATATCAC
1 ACAACAATCCTCTCAA-CCGTAAACATCAA
*
32963 CCAACAATCCTCT
1 ACAACAATCCTCT
32976 TATCTTTTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 6 0.17
29 7 0.20
30 22 0.63
ACGTcount: A:0.41, C:0.35, G:0.03, T:0.21
Consensus pattern (29 bp):
ACAACAATCCTCTCAACCGTAAACATCAA
Found at i:37391 original size:12 final size:13
Alignment explanation
Indices: 37374--37402 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
37364 TGATATATTG
37374 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
37386 GAAATAAAGAAAT
1 GAAATAAAGAAAT
37399 GAAA
1 GAAA
37403 GGATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:37553 original size:22 final size:22
Alignment explanation
Indices: 37528--37569 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
37518 TATGATAAAT
**
37528 GAATGATAATTTAATGGTGAAG
1 GAATGATAATGAAATGGTGAAG
37550 GAATGATAATGAAATGGTGA
1 GAATGATAATGAAATGGTGA
37570 TGATGATGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (22 bp):
GAATGATAATGAAATGGTGAAG
Found at i:40908 original size:16 final size:16
Alignment explanation
Indices: 40875--40923 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
40865 TAAGGCAATG
40875 GAATAAGAATAGATGAAA
1 GAATAAGAA-A-ATGAAA
40893 GAATAAGAAAATGAAA
1 GAATAAGAAAATGAAA
* * *
40909 TAGTAAGAAAGTGAA
1 GAATAAGAAAATGAA
40924 GATAACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 18 0.64
17 1 0.04
18 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.16
Consensus pattern (16 bp):
GAATAAGAAAATGAAA
Found at i:41351 original size:12 final size:13
Alignment explanation
Indices: 41334--41362 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41324 TGATATATTG
41334 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
41346 GAAATAAAGAAAT
1 GAAATAAAGAAAT
41359 GAAA
1 GAAA
41363 GGATAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:44404 original size:17 final size:18
Alignment explanation
Indices: 44371--44405 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44361 AATAATTAAA
44371 TAAATACTAACAAAATAT
1 TAAATACTAACAAAATAT
*
44389 TAAATA-TAATAAAATAT
1 TAAATACTAACAAAATAT
44406 ATCTTAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAATACTAACAAAATAT
Found at i:44445 original size:20 final size:20
Alignment explanation
Indices: 44422--44461 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
44412 AAGAGCTATA
* *
44422 AGAGAATTTAAGAGTATTTG
1 AGAGAAGTTAAGAGGATTTG
*
44442 AGAGAAGTTGAGAGGATTTG
1 AGAGAAGTTAAGAGGATTTG
44462 GTGTGATGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.30
Consensus pattern (20 bp):
AGAGAAGTTAAGAGGATTTG
Found at i:44615 original size:32 final size:32
Alignment explanation
Indices: 44574--44636 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
44564 CTATTCTGAT
44574 GCGTGTCAAAATGTCAGAAAAGCGCGACCCAC
1 GCGTGTCAAAATGTCAGAAAAGCGCGACCCAC
44606 GCGTGTCAAAATGTCAGAAAAGCGCGACCCA
1 GCGTGTCAAAATGTCAGAAAAGCGCGACCCA
44637 TGCATCGCGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.27, G:0.25, T:0.13
Consensus pattern (32 bp):
GCGTGTCAAAATGTCAGAAAAGCGCGACCCAC
Found at i:45579 original size:3 final size:3
Alignment explanation
Indices: 45573--45623 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
45563 ATTTATTTAT
* * *
45573 TTA TTA TTA TTA GTA TTA TTA TTA TTA TTA TTTA TTA ATA TTT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
45619 TTA TT
1 TTA TT
45624 TTGCAGGGTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:45579 original size:15 final size:14
Alignment explanation
Indices: 45555--45624 Score: 60
Period size: 15 Copynumber: 5.1 Consensus size: 14
45545 TTAAAAAATA
45555 TATTATTTATTTATT
1 TATTATTTA-TTATT
45570 TATT-TATTATTATT
1 TATTAT-TTATTATT
45584 AGTATTA-TTATTA-T
1 --TATTATTTATTATT
*
45598 TATTATTTATTA-A
1 TATTATTTATTATT
45611 TATT-TTTATTATT
1 TATTATTTATTATT
45624 T
1 T
45625 TGCAGGGTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
12 12 0.26
13 11 0.23
14 7 0.15
15 13 0.28
16 4 0.09
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (14 bp):
TATTATTTATTATT
Found at i:45604 original size:31 final size:33
Alignment explanation
Indices: 45555--45623 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 33
45545 TTAAAAAATA
*
45555 TATTATTTATTTATTTATTTATTATTATTAGTAT
1 TATTATTTA-TTATTTATTTATTAATATTAGTAT
**
45589 TATTA-TTATTA-TTATTTATTAATATTTTTAT
1 TATTATTTATTATTTATTTATTAATATTAGTAT
45620 TATT
1 TATT
45624 TTGCAGGGTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 21 0.66
32 3 0.09
33 3 0.09
34 5 0.16
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (33 bp):
TATTATTTATTATTTATTTATTAATATTAGTAT
Found at i:56334 original size:43 final size:43
Alignment explanation
Indices: 56260--56341 Score: 110
Period size: 43 Copynumber: 1.9 Consensus size: 43
56250 CGAAGAGGCC
**
56260 ATCCACGATTTCAACTCCACAACGGAGGATATCGTGCCCTCAA
1 ATCCACGATTTCAACTCCACAACAAAGGATATCGTGCCCTCAA
* ** *
56303 ATCCACGATTTCAACTTCACGGCAAATGATATCGTGCCC
1 ATCCACGATTTCAACTCCACAACAAAGGATATCGTGCCC
56342 ATCTACACAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 33 1.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (43 bp):
ATCCACGATTTCAACTCCACAACAAAGGATATCGTGCCCTCAA
Found at i:56631 original size:240 final size:246
Alignment explanation
Indices: 56303--56814 Score: 696
Period size: 240 Copynumber: 2.1 Consensus size: 246
56293 GTGCCCTCAA
56303 ATCCACGATTTCAACTTCACGGCAAATGATATCGTGCCCATCTACACAAGAATGGATTTCAACTT
1 ATCCACGATTTCAACTTCACGGCAAATGATATCGTGCCCA--TACACAAGAATGGATTTCAACTT
* *
56368 CACGACGAAGGATATCCAATTCAAAGCTCAACTTCACGGCGAA-TGGGCTTCCTAGTTGCATTCA
64 CACGACGAAGGATATCCAATTCAAAACTCAACTTCACGGCGAAGT-GGCTTCCCAGTTGCATTCA
* * * *
56432 GAGCCAATTTCAACTTCATGACGAATGATATTGGACTCG-A-AACA-ATA-CAAGTTTGGATTTT
128 GAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAACAACATATATCAAGATTGGATTTC
* *
56493 AACTTCACGACGAAGGATATTCAAGTCAAGGATCAACTTTACAACGAAGAGGCC
193 AACTTCACGACGAAGGATATCCAAGTCAAGGATCAACTTCACAACGAAGAGGCC
** * * * *
56547 ATCCACGATTTCAACTTCACGGTGAATGATATCGTG-CCA-ACTCTATATTGGATTTCAACTTCA
1 ATCCACGATTTCAACTTCACGGCAAATGATATCGTGCCCATACACAAGAATGGATTTCAACTTCA
* * *
56610 CGACGAATGATATCCAATTCAAAACTCAACTTCAGGGCGAAGTGGCTTCCCAGTTTCATTCAGAG
66 CGACGAAGGATATCCAATTCAAAACTCAACTTCACGGCGAAGTGGCTTCCCAGTTGCATTCAGAG
* **
56675 CCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAGCAACATTCATATTTAGATTGGATTTC
131 CCAATTTCAACTTCACGACGAAGGATATTGGACTCGAA-CAACA-T-ATATCAAGATTGGATTTC
* * * *
56740 AACTTCACGTCGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCC
193 AACTTCACGACGAAGGATATCCAAGTCAAGGATCAACTTCACAACGAAGAGGCC
*
56794 ATCCACGGTTTCAACTTCACG
1 ATCCACGATTTCAACTTCACG
56815 ACGAAAGGAA
Statistics
Matches: 235, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
240 111 0.47
241 2 0.01
243 7 0.03
244 34 0.14
246 3 0.01
247 78 0.33
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (246 bp):
ATCCACGATTTCAACTTCACGGCAAATGATATCGTGCCCATACACAAGAATGGATTTCAACTTCA
CGACGAAGGATATCCAATTCAAAACTCAACTTCACGGCGAAGTGGCTTCCCAGTTGCATTCAGAG
CCAATTTCAACTTCACGACGAAGGATATTGGACTCGAACAACATATATCAAGATTGGATTTCAAC
TTCACGACGAAGGATATCCAAGTCAAGGATCAACTTCACAACGAAGAGGCC
Found at i:56920 original size:123 final size:124
Alignment explanation
Indices: 56678--56953 Score: 400
Period size: 123 Copynumber: 2.2 Consensus size: 124
56668 TTCAGAGCCA
* *
56678 ATTTCAACTTCACGGCGAAGGATATTG-GACTCGA--AGCAACATTCATATTTAGATTGGATTTC
1 ATTTCAACTTCACGACGAAGGATATCGTG-CTC-ACCAGCAACATTCATATTTAGATTGGATTTC
** * *
56740 AACTTCACGTCGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACG
64 AACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCACG
* *
56801 GTTTCAACTTCACGACGAAAGGA-ATCGTGCTCACCAGCAACATTCATCTTTAGATTGGATTTCA
1 ATTTCAACTTCACGACG-AAGGATATCGTGCTCACCAGCAACATTCATATTTAGATTGGATTTCA
* *
56865 ACTTCACAACGAATGATAT-CAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACG
65 ACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCACG
56924 ATTTCAACTTCACGACGAAGGATATCGTGC
1 ATTTCAACTTCACGACGAAGGATATCGTGC
56954 CCAACGGATC
Statistics
Matches: 137, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
122 6 0.04
123 81 0.59
124 50 0.36
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (124 bp):
ATTTCAACTTCACGACGAAGGATATCGTGCTCACCAGCAACATTCATATTTAGATTGGATTTCAA
CTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCACG
Found at i:57182 original size:3 final size:3
Alignment explanation
Indices: 57170--57224 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
57160 GGTTTAAATA
* * *
57170 TAT TATT TAT TATT TAT TAT TAT TAT TAG TATT TAT TAT TAA TAT TTT
1 TAT TA-T TAT TA-T TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
57218 TAT TAT T
1 TAT TAT T
57225 TTGCAGGGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 35 0.81
4 8 0.19
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:57182 original size:7 final size:7
Alignment explanation
Indices: 57170--57225 Score: 64
Period size: 7 Copynumber: 8.1 Consensus size: 7
57160 GGTTTAAATA
57170 TATTATT
1 TATTATT
57177 TATTATT
1 TATTATT
57184 TATTA-T
1 TATTATT
57190 TATTA-T
1 TATTATT
*
57196 TAGTATT
1 TATTATT
57203 TATTATT
1 TATTATT
57210 AATATT-TT
1 --TATTATT
57218 TATTATT
1 TATTATT
57225 T
1 T
57226 TGCAGGGCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 15 0.35
7 22 0.51
8 2 0.05
9 4 0.09
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (7 bp):
TATTATT
Found at i:57221 original size:19 final size:19
Alignment explanation
Indices: 57173--57221 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
57163 TTAAATATAT
*
57173 TATTTATTATTTATTATTAT
1 TATTT-TTATTTATTATTAA
**
57193 TATTAGTATTTATTATTAA
1 TATTTTTATTTATTATTAA
57212 TATTTTTATT
1 TATTTTTATT
57222 ATTTTGCAGG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TATTTTTATTTATTATTAA
Found at i:57599 original size:3 final size:3
Alignment explanation
Indices: 57579--57637 Score: 57
Period size: 3 Copynumber: 19.0 Consensus size: 3
57569 ATCCACAAGC
* *
57579 ATT A-T ATT ATTT ATTT ATT ATT ATT AGT ATT ATT ATTT ATT ATT AAT
1 ATT ATT ATT A-TT A-TT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
*
57626 ATT TTT ATT ATT
1 ATT ATT ATT ATT
57638 TTACAGGGCC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.04
3 35 0.74
4 10 0.21
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:57611 original size:19 final size:19
Alignment explanation
Indices: 57589--57637 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
57579 ATTATATTAT
*
57589 TTATTTATTATTATTAGTA
1 TTATTTATTATTATTAATA
57608 TTA-TTATTTATTATTAATA
1 TTATTTA-TTATTATTAATA
57627 TT-TTTATTATT
1 TTATTTATTATT
57638 TTACAGGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.30
19 19 0.70
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTATTTATTATTATTAATA
Found at i:57614 original size:22 final size:21
Alignment explanation
Indices: 57579--57638 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
57569 ATCCACAAGC
57579 ATTATATTATTTATTTATTATT
1 ATTATATTA-TTATTTATTATT
57601 ATTAGTATTATTATTTATTATT
1 ATTA-TATTATTATTTATTATT
* *
57623 AATATTTTTATTATTT
1 ATTA-TATTATTATTT
57639 TACAGGGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 29 0.85
23 5 0.15
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTATATTATTATTTATTATT
Found at i:57940 original size:419 final size:413
Alignment explanation
Indices: 57168--58000 Score: 1366
Period size: 419 Copynumber: 2.0 Consensus size: 413
57158 CTGGTTTAAA
* *
57168 TATATTATTTATTATTTATTATTATTATTAGTATTTATTATTAATATTTTTATTATTTTGCAGGG
1 TATATTATTTATTATTTATTATTAGTATTAGTATTTATTATTAATATTTTTATTATTTTACAGGG
*
57233 CCATTTCCAACAAACTACCCAACATCTTCCACTACTCCCACAACCACCTTAACTTCAACTCCTCA
66 CCATTTCCAACAAACTACCCAACATCTTCCACTACTCCCACAACCACCTTAACTTCAACGCCTCA
* * *
57298 TCTCACATTTTTTGCAGGGGAAATGGGGTGAGGTTTTCAGTTGAATAAAAGACCTTGGGAGCACA
131 TCTCACATTTTTTGCAGGGAAAATGGGGTGAGGTTTTCAGCTGAAGAAAAGACCTTGGGAGCACA
*
57363 AGTTTTTTTATTTAAAGGGGACATGCACAAATGAGACGGGGTCACACTTATGGATCTTCATCGAA
196 AGTTTTTTTATTTAAAGGGGACATGCACAAATGAGACGGGGTCACACTTATGGATCTTCATCAAA
* *
57428 ACGTCTCGAATTAACCAAACACCAACAGTCCATGCTCTCTTTAATTTCTTATCAAGTTTCGATCC
261 ACGTCTCGAATTAACCAAACACCAACAGTCCATGCTCTCTTTAATTTCTTACCAAGTTCCGATCC
57493 TCCAATCAACTTACGGAGCTCTAAAACAAAAGAAAACCGAAAGAAACTTTCGCCTCCGCTACTTC
326 TCCAATCAACTTACGGAGCTCTAAAACAAAAGAAAACCGAAAGAAACTTTCGCCTCCGCTACTTC
*
57558 TATTGAAGCATATCCACAAGCAT
391 CATTGAAGCATATCCACAAGCAT
*
57581 TATATTATTTATT-TATTATTATTAGTATTATTATTTATTATTAATATTTTTATTATTTTACAGG
1 TATATTATTTATTAT-TTATTATTAGTATTAGTATTTATTATTAATATTTTTATTATTTTACAGG
* *
57645 GCCCATTTCTAACAAACTACCCAACATCTTCCACTACTCCTACAACCACCTTAACTTCAACGCCT
65 G-CCATTTCCAACAAACTACCCAACATCTTCCACTACTCCCACAACCACCTTAACTTCAACGCCT
* **
57710 CATCTCACGTTTTTTTGTTGGAGAAAATGGGGTGAGGTTTTCAGCTGAAGAAAAGGACCTTGGGA
129 CATCTCAC-ATTTTTTGCAGG-GAAAATGGGGTGAGGTTTTCAGCTGAAGAAAA-GACCTTGGGA
57775 GCACAAGTTTTTTTATTTAAAGGGGAGGACATGCAC-AATCGAGA-GGGGTCACACTTATGGATC
191 GCACAAGTTTTTTTATTTAAA--GG-GGACATGCACAAAT-GAGACGGGGTCACACTTATGGATC
* * *
57838 TTCATCAAAACGTCTTGAATTAACCAAACACCAAGAGTCCATGCTCTCTTTAATTTCTTACCTAG
252 TTCATCAAAACGTCTCGAATTAACCAAACACCAACAGTCCATGCTCTCTTTAATTTCTTACCAAG
* **
57903 TTCCGATCCTCCAATCAACTTACGGAGCTCTAAAACAAAAGGAAATTGAAAGAAACTTTCGCCTC
317 TTCCGATCCTCCAATCAACTTACGGAGCTCTAAAACAAAAGAAAACCGAAAGAAACTTTCGCCTC
57968 CGCTACTTCCATTGAAGCATATCCACAAGCAT
382 CGCTACTTCCATTGAAGCATATCCACAAGCAT
58000 T
1 T
58001 TGGCAGCCAT
Statistics
Matches: 389, Mismatches: 22, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
412 1 0.00
413 60 0.15
414 68 0.17
415 9 0.02
416 29 0.07
417 31 0.08
419 177 0.46
420 14 0.04
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (413 bp):
TATATTATTTATTATTTATTATTAGTATTAGTATTTATTATTAATATTTTTATTATTTTACAGGG
CCATTTCCAACAAACTACCCAACATCTTCCACTACTCCCACAACCACCTTAACTTCAACGCCTCA
TCTCACATTTTTTGCAGGGAAAATGGGGTGAGGTTTTCAGCTGAAGAAAAGACCTTGGGAGCACA
AGTTTTTTTATTTAAAGGGGACATGCACAAATGAGACGGGGTCACACTTATGGATCTTCATCAAA
ACGTCTCGAATTAACCAAACACCAACAGTCCATGCTCTCTTTAATTTCTTACCAAGTTCCGATCC
TCCAATCAACTTACGGAGCTCTAAAACAAAAGAAAACCGAAAGAAACTTTCGCCTCCGCTACTTC
CATTGAAGCATATCCACAAGCAT
Found at i:62802 original size:34 final size:34
Alignment explanation
Indices: 62739--62829 Score: 103
Period size: 34 Copynumber: 2.6 Consensus size: 34
62729 TAAGTTTCAC
*
62739 TTTATCTTAATTATTTTAAATTTAAATTATTTATTTAT
1 TTTATCTT-A-TATTTT--ATTTAAATTATTTATTAAT
*
62777 TTTATCCTTATCTTTTATTT-AATTATTTATTAAT
1 TTTAT-CTTATATTTTATTTAAATTATTTATTAAT
*
62811 TTTATCTTTTATTTTATTT
1 TTTATCTTATATTTTATTT
62830 TTAAACCCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
33 12 0.25
34 18 0.38
35 4 0.08
37 5 0.10
38 6 0.12
39 3 0.06
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.67
Consensus pattern (34 bp):
TTTATCTTATATTTTATTTAAATTATTTATTAAT
Done.