Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006876.1 Hibiscus syriacus cultivar Beakdansim tig00017513_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: 59293
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:5472 original size:18 final size:17
Alignment explanation
Indices: 5449--5482 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5439 CAGTCTGTTT
5449 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
5467 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
5483 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:16275 original size:18 final size:18
Alignment explanation
Indices: 16254--16322 Score: 67
Period size: 18 Copynumber: 3.9 Consensus size: 18
16244 AGAATATCCA
16254 GGGGGTA-CAGATTCCCCT
1 GGGGGTATC-GATTCCCCT
16272 GGGGGTATCGATTCCCC-
1 GGGGGTATCGATTCCCCT
*
16289 --GGG-AACAGATTCCCCT
1 GGGGGTATC-GATTCCCCT
16305 GGGGGGTATCGATTCCCC
1 -GGGGGTATCGATTCCCC
16323 CATAAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
14 2 0.05
15 11 0.26
18 15 0.36
19 12 0.29
20 2 0.05
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.22
Consensus pattern (18 bp):
GGGGGTATCGATTCCCCT
Found at i:17306 original size:31 final size:31
Alignment explanation
Indices: 17268--17472 Score: 365
Period size: 31 Copynumber: 6.6 Consensus size: 31
17258 AGGGTCGAGG
17268 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
17299 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
17330 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
17361 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
17392 GTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
17423 GTTTACATATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
17454 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
17473 AATCTATGAA
Statistics
Matches: 166, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 166 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:17991 original size:21 final size:21
Alignment explanation
Indices: 17966--18008 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
17956 AAAGAATATA
17966 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
17987 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
18008 T
1 T
18009 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:18868 original size:16 final size:16
Alignment explanation
Indices: 18843--18883 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
18833 AAAAAAATTT
18843 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
18859 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
18875 T-TT-ATTTAT
1 TGTTCATTTAT
18884 TAAATGAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 2 0.09
16 16 0.70
ACGTcount: A:0.12, C:0.10, G:0.17, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:20611 original size:20 final size:21
Alignment explanation
Indices: 20586--20624 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
20576 ACTTAAATTT
20586 AAATAGAAT-AAAATATCATA
1 AAATAGAATAAAAATATCATA
20606 AAATAGAATAAAAATATCA
1 AAATAGAATAAAAATATCA
20625 CCGTCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (21 bp):
AAATAGAATAAAAATATCATA
Found at i:22204 original size:30 final size:27
Alignment explanation
Indices: 22137--22208 Score: 76
Period size: 30 Copynumber: 2.6 Consensus size: 27
22127 TGCATAAAAT
* *
22137 ATAAATAAAATGATATTAGTAATAATA
1 ATAAATATAATCATATTAGTAATAATA
22164 AT-AATAATAATCATACTATAGTATATAATA
1 ATAAAT-ATAATCATA-T-TAGTA-ATAATA
22194 ATAAATATAAT-ATAT
1 ATAAATATAATCATAT
22209 ATTTTAATCC
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
26 3 0.08
27 9 0.24
28 2 0.05
29 8 0.21
30 13 0.34
31 3 0.08
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (27 bp):
ATAAATATAATCATATTAGTAATAATA
Found at i:22732 original size:91 final size:92
Alignment explanation
Indices: 22576--22750 Score: 255
Period size: 91 Copynumber: 1.9 Consensus size: 92
22566 GTTATAGGTC
*
22576 GAACAAGCTCTTCTTATTATGAACTTATTATCTCTCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTATTATCTCTCTTTCGGATGAGTTCTTCTCATTATGAACT
*
22641 CTCCATTGAAAATGTTGATGCGAAGTT
66 CTCCATTGAAAATATTGATGCGAAGTT
* * * *
22668 GAACAAGTTCTTCTCATTATGAACTTCTTCT-TC-CTTGTTGGATGAGTTCTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTATTATCTCTCTT-TCGGATGAGTTCTTCTCATTATGAAC
* *
22731 TCTCTATTGGAAATATTGAT
65 TCTCCATTGAAAATATTGAT
22751 CCATCTATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
90 3 0.04
91 44 0.59
92 27 0.36
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.42
Consensus pattern (92 bp):
GAACAAGCTCTTCTCATTATGAACTTATTATCTCTCTTTCGGATGAGTTCTTCTCATTATGAACT
CTCCATTGAAAATATTGATGCGAAGTT
Found at i:23091 original size:240 final size:240
Alignment explanation
Indices: 22669--23473 Score: 1369
Period size: 240 Copynumber: 3.4 Consensus size: 240
22659 TGCGAAGTTG
* * *
22669 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTGTTGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
* *
22734 CTATTGGAAATATTGATCCATCTATTTCTGTGATGGACTTGAAAAGAACAAGTTCTTCTCATTAT
66 CCATTGGAAATATTGATCCATCTATTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCATTAT
22799 GAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTTAGAAAATGTCAATCCCTCAAG
131 GAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTTAGAAAATGTCAATCCCTCAAG
* * *
22864 CGAGGTGTCACTGATTCAAAATACCGTGAATCGAGTGATAGGTCG
196 CGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCA
* *
22909 AACAAGCTCTTCTCATTTTGAGCTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
* * *
22974 CCATTAGAAATGTTGATCCATCTATTTCTATGATGGACTTGAAAGGAACAAGTTCTTCTCATTAT
66 CCATTGGAAATATTGATCCATCTATTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCATTAT
*
23039 GAACTTTCTCCTTTAGGACGAGTTCTTGTCATTATGAACTCTTTAGAAAATGTCAATCCCTCAAG
131 GAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTTAGAAAATGTCAATCCCTCAAG
*
23104 CGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGGTCA
196 CGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCA
*
23149 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGGGTTCTTCTCATTATGAACTCT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
* *
23214 CCATTGGAAATGTTGATCCATCTCTTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCATTAT
66 CCATTGGAAATATTGATCCATCTATTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCATTAT
23279 GAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTTTA-AAAATGTCAATCCCTCAA
131 GAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTC-TTTAGAAAATGTCAATCCCTCAA
* * *
23343 TCGAGGTGTGACGGATTCGAAATGCCGTGAATCGAGTGATAGGTCA
195 GCGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCA
* * *
23389 AACAAGCTATTCTCATTATAAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTC-GTTGGATGAGTTCTTCTCATTATGAACTC
23454 TCCATTGGAAATATTGATCC
65 TCCATTGGAAATATTGATCC
23474 CTCAAGCGAG
Statistics
Matches: 532, Mismatches: 31, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
240 482 0.91
241 50 0.09
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (240 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
CCATTGGAAATATTGATCCATCTATTTCTGTGATGGACTTGAAAGGAACAAGTTCTTCTCATTAT
GAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTTAGAAAATGTCAATCCCTCAAG
CGAGGTGTCACTGATTCGAAATGCCGTGAATCGAGTGATAGGTCA
Found at i:23507 original size:136 final size:135
Alignment explanation
Indices: 23298--23605 Score: 465
Period size: 136 Copynumber: 2.3 Consensus size: 135
23288 CCTTTAGGAC
* ** * ** * *
23298 GAGTTCTTCTCATTATGAACTCT-TTTAAAAATGTCAATCCCTCAATCGAGGTGTGACGGATTCG
1 GAGTTCTTCTCATTATGAACTCTCATTGGAAATATTGATCCCTCAAGCGAGGTGTCACGGATTCG
*
23362 AAATGCCGTGAATCGAGTGATAGGTCAAACAAGCTATTCTCATTATAAACTTCTTCTCCCTCTGT
66 AAATACCGTGAATCGAGTGATAGGTCAAACAAGCTATTCTCATTATAAACTTCTTCTCCCTCTGT
23427 CGGAT
131 CGGAT
* *
23432 GAGTTCTTCTCATTATGAACTCTCCATTGGAAATATTGATCCCTCAAGCGAGGTGTCACTGATTT
1 GAGTTCTTCTCATTATGAACTCT-CATTGGAAATATTGATCCCTCAAGCGAGGTGTCACGGATTC
* * *
23497 GAAATACCGTGAATCGAGTGATAGGTCAAACAAGCTCTTCTGATTATGAACTTCTTCTCCCTCTG
65 GAAATACCGTGAATCGAGTGATAGGTCAAACAAGCTATTCTCATTATAAACTTCTTCTCCCTCTG
23562 TCGGAT
130 TCGGAT
23568 GAGTTCTTCTCATTATGAACTCTCTATTGGAAATATTG
1 GAGTTCTTCTCATTATGAACTCTC-ATTGGAAATATTG
23606 GCTCACCTTC
Statistics
Matches: 157, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
134 23 0.15
135 1 0.01
136 133 0.85
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (135 bp):
GAGTTCTTCTCATTATGAACTCTCATTGGAAATATTGATCCCTCAAGCGAGGTGTCACGGATTCG
AAATACCGTGAATCGAGTGATAGGTCAAACAAGCTATTCTCATTATAAACTTCTTCTCCCTCTGT
CGGAT
Found at i:24499 original size:10 final size:10
Alignment explanation
Indices: 24484--24516 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
24474 TCTCTTTTCA
24484 TTTTTCATTT
1 TTTTTCATTT
24494 TTTTTCATTT
1 TTTTTCATTT
*
24504 TTTTTAATTT
1 TTTTTCATTT
24514 TTT
1 TTT
24517 CATCTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:31956 original size:6 final size:6
Alignment explanation
Indices: 31945--31969 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31935 TTATGCAAAG
31945 ATGCAA ATGCAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGCAA A
31970 AGGTATCGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGCAA
Found at i:38450 original size:3 final size:3
Alignment explanation
Indices: 38442--38489 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
38432 ATGATATTAG
* * *
38442 TAA TAA TAA TAA TAA TAA TAA TAA TCA TAC T-A TAC TATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
38487 TAA
1 TAA
38490 ATATAATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
2 1 0.03
3 34 0.92
4 2 0.05
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39450 original size:13 final size:13
Alignment explanation
Indices: 39434--39463 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
39424 TTTAATTGAG
39434 AAAATTAAAAATT
1 AAAATTAAAAATT
*
39447 AAAATTAAAATTT
1 AAAATTAAAAATT
39460 AAAA
1 AAAA
39464 ACCCGATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:41979 original size:85 final size:84
Alignment explanation
Indices: 41836--42078 Score: 315
Period size: 85 Copynumber: 2.9 Consensus size: 84
41826 ATATATCTTC
* * * ** * * *
41836 GAGCTAAATGAAATCGAACTCGAAAGTCTTCATTGACAGATAGCCTTTCTCGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGT-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
41901 CGTAAGTTTGATATGCCCTT
65 CGTAAATTTGATATGCCCTT
*
41921 GAGCTGAATGTAATCGAACTCGAAGGTTTTGGTTGACATATAACCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTTTT-GTTGACAGATAACCCTTCTCGCCTTGAGCTATGC
*
41986 TGTAAATTTGATATGCCCTT
65 CGTAAATTTGATATGCCCTT
* * * * **
42006 GAGTTGAATGTAATCGAACTCGAAGGTTTTGTTGGCAGATAACTCTTCTCACCTTGAGCTATGTT
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCC
42071 GTAAATTT
66 GTAAATTT
42079 CCTCTATATG
Statistics
Matches: 140, Mismatches: 17, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
84 40 0.29
85 100 0.71
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (84 bp):
GAGCTGAATGTAATCGAACTCGAAGGTTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCC
GTAAATTTGATATGCCCTT
Found at i:43726 original size:3 final size:3
Alignment explanation
Indices: 43720--43765 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
43710 TTTTATTTTA
*
43720 ATT ATT ATT ATT ATT ATAT ATT AGT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT
43765 A
1 A
43766 ATTCATTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:46259 original size:59 final size:59
Alignment explanation
Indices: 46186--46380 Score: 293
Period size: 59 Copynumber: 3.3 Consensus size: 59
46176 ACATATATTT
* *
46186 CCTATACGGAAATTCATACA-TGTAGTATGATTTCTTTATCATTTTAGCACACAAAGTGC
1 CCTATATGGAAATTCATACACT-TAGTATGATTTCATTATCATTTTAGCACACAAAGTGC
* * * *
46245 CCTATATGGAAATTCATACACTAAGTATGATTTCCTTATCATTTTAACACACAAACTGC
1 CCTATATGGAAATTCATACACTTAGTATGATTTCATTATCATTTTAGCACACAAAGTGC
* *
46304 CCTATCTGGAAATTCATACACTTAGTATGATTTCATTATCATTTTAGCACACAAAGTGT
1 CCTATATGGAAATTCATACACTTAGTATGATTTCATTATCATTTTAGCACACAAAGTGC
*
46363 CCTATCTGGAAATTCATA
1 CCTATATGGAAATTCATA
46381 ATTAAATTAT
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
59 123 0.99
60 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.35
Consensus pattern (59 bp):
CCTATATGGAAATTCATACACTTAGTATGATTTCATTATCATTTTAGCACACAAAGTGC
Found at i:46518 original size:54 final size:54
Alignment explanation
Indices: 46404--46793 Score: 584
Period size: 54 Copynumber: 7.2 Consensus size: 54
46394 TTTCGTGCTT
* * * * *
46404 TGCACACATAGTGTCGAAACGGTTATTCAT-CTCATAGGATTAATTCCGTAAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTCCGTGAAA
* *
46457 TACACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTCAGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTCCGTGAAA
* *
46511 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATATGATAAATTTCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTCCGTGAAA
* * * *
46565 TACACACTTACTGCCGAAACGGTTATTTATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTCCGTGAAA
* *
46619 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTAAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTCCGTGAAA
* *
46673 TACACACTTAGTGCCGAAACGGTTATTCATCCCCATAGGATAAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTCCGTGAAA
** * *
46727 TGCACACTTAGTGTTGAAATGGTTATTCATCCACATAGGATAAGTTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTCCGTGAAA
46781 TGCACACTTAGTG
1 TGCACACTTAGTG
46794 TCATTTGGTA
Statistics
Matches: 305, Mismatches: 31, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
53 27 0.09
54 278 0.91
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATAAATTCCGTGAAA
Found at i:47233 original size:20 final size:22
Alignment explanation
Indices: 47208--47262 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
47198 CGATGTTGCC
*
47208 TGGTATCGATA-T-CCTTACCA
1 TGGTATCGATACTACCATACCA
* *
47228 TGGTATTGATACTACCATACTA
1 TGGTATCGATACTACCATACCA
47250 TGGTATCGATACT
1 TGGTATCGATACT
47263 CCCTTCTAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 10 0.34
21 1 0.03
22 18 0.62
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (22 bp):
TGGTATCGATACTACCATACCA
Found at i:49104 original size:14 final size:12
Alignment explanation
Indices: 49087--49180 Score: 55
Period size: 14 Copynumber: 7.0 Consensus size: 12
49077 TTCTTATCCC
49087 TTTTTCTTTATTT
1 TTTTTCTTT-TTT
**
49100 ATTTTCTCTTTGCT
1 -TTTT-TCTTTTTT
49114 TTTTTCTTTTTTT
1 TTTTTC-TTTTTT
49127 TTTGTTCTTTTTTT
1 TTT-TTC-TTTTTT
49141 TATTTTCTCTTTGTT
1 T-TTTTCT-TTT-TT
49156 TTTTT-TTTTTT
1 TTTTTCTTTTTT
*
49167 GCTTCTTCTTTTTT
1 --TTTTTCTTTTTT
49181 GATTAAATCT
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
11 2 0.03
12 5 0.08
13 17 0.26
14 32 0.48
15 10 0.15
ACGTcount: A:0.03, C:0.12, G:0.04, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:49139 original size:23 final size:23
Alignment explanation
Indices: 49097--49164 Score: 83
Period size: 21 Copynumber: 3.1 Consensus size: 23
49087 TTTTTCTTTA
49097 TTTATTTTCTCTTTG--CTTTTT
1 TTTATTTTCTCTTTGTTCTTTTT
49118 TCTT-TTTT-T-TTTGTTCTTTTT
1 T-TTATTTTCTCTTTGTTCTTTTT
*
49139 TTTATTTTCTCTTTGTTTTTTTT
1 TTTATTTTCTCTTTGTTCTTTTT
49162 TTT
1 TTT
49165 TTGCTTCTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
19 4 0.10
20 3 0.08
21 16 0.40
22 3 0.08
23 14 0.35
ACGTcount: A:0.03, C:0.10, G:0.04, T:0.82
Consensus pattern (23 bp):
TTTATTTTCTCTTTGTTCTTTTT
Found at i:49141 original size:16 final size:15
Alignment explanation
Indices: 49087--49162 Score: 61
Period size: 14 Copynumber: 5.3 Consensus size: 15
49077 TTCTTATCCC
* *
49087 TTTT-TCTTTATTTA
1 TTTTCTCTTTTTTTT
**
49101 TTTTCTC-TTTGCTT
1 TTTTCTCTTTTTTTT
49115 TTTTCT-TTTTTTTT
1 TTTTCTCTTTTTTTT
* *
49129 TGTTCT-TTTTTTTA
1 TTTTCTCTTTTTTTT
49143 TTTTCTCTTTGTTTTT
1 TTTTCTCTTT-TTTTT
49159 TTTT
1 TTTT
49163 TTTTGCTTCT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
14 35 0.73
15 5 0.10
16 8 0.17
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.82
Consensus pattern (15 bp):
TTTTCTCTTTTTTTT
Found at i:49176 original size:41 final size:42
Alignment explanation
Indices: 49097--49180 Score: 127
Period size: 41 Copynumber: 2.0 Consensus size: 42
49087 TTTTTCTTTA
* *
49097 TTTATTTTCTCTTTGCTTTTTTCTTTTTTTTTTGTTCTTTTT
1 TTTATTTTCTCTTTGCTTTTTTCTTTTTTTCTTCTTCTTTTT
49139 TTTATTTTCTCTTTG-TTTTTT-TTTTTTTGCTTCTTCTTTTT
1 TTTATTTTCTCTTTGCTTTTTTCTTTTTTT-CTTCTTCTTTTT
49180 T
1 T
49181 GATTAAATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
40 7 0.18
41 17 0.44
42 15 0.38
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (42 bp):
TTTATTTTCTCTTTGCTTTTTTCTTTTTTTCTTCTTCTTTTT
Found at i:52168 original size:12 final size:13
Alignment explanation
Indices: 52153--52181 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
52143 TCTTAATTGC
52153 AAAATTAAAA-TT
1 AAAATTAAAATTT
52165 AAAATTAAAATTT
1 AAAATTAAAATTT
52178 AAAA
1 AAAA
52182 CCCGATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:55221 original size:9 final size:9
Alignment explanation
Indices: 55207--55239 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
55197 GATCTACAAA
55207 AATATTATT
1 AATATTATT
55216 AATATTATT
1 AATATTATT
55225 AAT-TTATT
1 AATATTATT
*
55233 ATTATTA
1 AATATTA
55240 ATTTACATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTATT
Found at i:55237 original size:14 final size:14
Alignment explanation
Indices: 55218--55244 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
55208 ATATTATTAA
55218 TATTATTAATTTAT
1 TATTATTAATTTAT
55232 TATTATTAATTTA
1 TATTATTAATTTA
55245 CATTTTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTATTAATTTAT
Found at i:55294 original size:18 final size:18
Alignment explanation
Indices: 55267--55305 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
55257 TTTTTAGGCC
55267 CCAATATGGAGCCCAAGA
1 CCAATATGGAGCCCAAGA
* *
55285 CCAATCTGGAGCTCAAGA
1 CCAATATGGAGCCCAAGA
55303 CCA
1 CCA
55306 TTACAAGCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.21, T:0.13
Consensus pattern (18 bp):
CCAATATGGAGCCCAAGA
Found at i:56718 original size:59 final size:59
Alignment explanation
Indices: 56653--56787 Score: 193
Period size: 59 Copynumber: 2.3 Consensus size: 59
56643 TTATTTGTTG
* * *
56653 TTTAGCCCTTTAAGTTTTTGTAATTACTATTTAGACCC-TTAAGTTT-TGATTTTTACTAT
1 TTTAGCCCTTTAAGTTTCTATAATTACTAGTTAG-CCCTTTAAGTTTATG-TTTTTACTAT
*
56712 TTTAGCCCTTTAAGTTTCTATAATTACTGGTTAGCCCTTTAAGTTTATGTTTTTACTAT
1 TTTAGCCCTTTAAGTTTCTATAATTACTAGTTAGCCCTTTAAGTTTATGTTTTTACTAT
*
56771 TTTAGTCCTTTAAGTTT
1 TTTAGCCCTTTAAGTTT
56788 ATGTGTTTGT
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
58 3 0.04
59 64 0.93
60 2 0.03
ACGTcount: A:0.22, C:0.14, G:0.11, T:0.53
Consensus pattern (59 bp):
TTTAGCCCTTTAAGTTTCTATAATTACTAGTTAGCCCTTTAAGTTTATGTTTTTACTAT
Found at i:56871 original size:59 final size:58
Alignment explanation
Indices: 56742--56929 Score: 159
Period size: 59 Copynumber: 3.2 Consensus size: 58
56732 TAATTACTGG
* * * * **
56742 TTAGCCCTTTAAGTTTATGTTTTTACTATTTTAGTCCTTTAAGTTTATGTGTTTGTTATT
1 TTAGCCCTTTAAGTTT-T-TTTTTGCTATTTTAGACCATTAAATTTATGTGTTTACTATT
* *
56802 TTAGTCCTTTAAGTTTCTATTTTTGCTA-TTTAGACCATTAAATTT-TGATTTTTACTATT
1 TTAGCCCTTTAAGTTT-T-TTTTTGCTATTTTAGACCATTAAATTTATG-TGTTTACTATT
* * * * * *
56861 TTAGCCCTTTAAGTTTTTTTTTG-TCATTTTGGTCCTTTAACTTTATGTATTTACT-GT
1 TTAGCCCTTTAAGTTTTTTTTTGCT-ATTTTAGACCATTAAATTTATGTGTTTACTATT
*
56918 TCAGCCCTTTAA
1 TTAGCCCTTTAA
56930 ATTTCTGTTA
Statistics
Matches: 106, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
56 1 0.01
57 19 0.18
58 23 0.22
59 39 0.37
60 24 0.23
ACGTcount: A:0.20, C:0.13, G:0.11, T:0.56
Consensus pattern (58 bp):
TTAGCCCTTTAAGTTTTTTTTTGCTATTTTAGACCATTAAATTTATGTGTTTACTATT
Found at i:56882 original size:29 final size:30
Alignment explanation
Indices: 56653--56876 Score: 190
Period size: 30 Copynumber: 7.6 Consensus size: 30
56643 TTATTTGTTG
* * **
56653 TTTAGCCCTTTAAGTTTTTGTAATTACTA-
1 TTTAGCCCTTTAAGTTTATATTTTTACTAT
56682 TTTAGACCC-TTAAGTTT-TGATTTTTACTAT
1 TTTAG-CCCTTTAAGTTTAT-ATTTTTACTAT
* ** *
56712 TTTAGCCCTTTAAGTTTCTATAATTACT-G
1 TTTAGCCCTTTAAGTTTATATTTTTACTAT
* *
56741 GTTAGCCCTTTAAGTTTATGTTTTTACTAT
1 TTTAGCCCTTTAAGTTTATATTTTTACTAT
* * * **
56771 TTTAGTCCTTTAAGTTTATGTGTTTGTTAT
1 TTTAGCCCTTTAAGTTTATATTTTTACTAT
* * *
56801 TTTAGTCCTTTAAGTTTCTATTTTTGCTA-
1 TTTAGCCCTTTAAGTTTATATTTTTACTAT
* * *
56830 TTTAGACCATTAAATTT-TGATTTTTACTAT
1 TTTAGCCCTTTAAGTTTAT-ATTTTTACTAT
56860 TTTAGCCCTTTAAGTTT
1 TTTAGCCCTTTAAGTTT
56877 TTTTTTGTCA
Statistics
Matches: 159, Mismatches: 28, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
28 2 0.01
29 69 0.43
30 87 0.55
31 1 0.01
ACGTcount: A:0.22, C:0.13, G:0.11, T:0.54
Consensus pattern (30 bp):
TTTAGCCCTTTAAGTTTATATTTTTACTAT
Done.