Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004811.1 Hibiscus syriacus cultivar Beakdansim tig00010841_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: 67616
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:2394 original size:6 final size:6
Alignment explanation
Indices: 2378--2462 Score: 70
Period size: 6 Copynumber: 14.2 Consensus size: 6
2368 TAATTGGACC
*
2378 TAAAAA T-AAAA TAAAAA TAAAAA T-AAAA -AAAAA TAAAAAA TAGAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA T-AAAAA TAAAAA
* * *
2424 TAGAAA TAGAAA TAAATAAA TAAATAA -ATAAA TAAAAA T
1 TAAAAA TAAAAA T-AA-AAA TAAA-AA TAAAAA TAAAAA T
2463 GTATATATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
5 15 0.22
6 37 0.55
7 11 0.16
8 4 0.06
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.19
Consensus pattern (6 bp):
TAAAAA
Found at i:2424 original size:29 final size:29
Alignment explanation
Indices: 2385--2462 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
2375 ACCTAAAAAT
2385 AAAATAAAAATAAAAATAAAAAAAAATAA
1 AAAATAAAAATAAAAATAAAAAAAAATAA
* * * *
2414 AAAATAGAAATAGAAATAGAAATAAATAA
1 AAAATAAAAATAAAAATAAAAAAAAATAA
2443 ATAAATAAATAAATAAAAAT
1 A-AAAT-AA-AAATAAAAAT
2463 GTATATATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 26 0.65
30 4 0.10
31 1 0.03
32 9 0.22
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (29 bp):
AAAATAAAAATAAAAATAAAAAAAAATAA
Found at i:2442 original size:4 final size:4
Alignment explanation
Indices: 2433--2459 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2423 ATAGAAATAG
2433 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
2460 AATGTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2684 original size:37 final size:37
Alignment explanation
Indices: 2591--2780 Score: 210
Period size: 37 Copynumber: 5.2 Consensus size: 37
2581 TTTTTAAACC
* *
2591 ATATATTTT-TAAAACGTTTTCAAAACTATATA-T-T
1 ATATATTTTCAAAAATGTTTTCAAAACTATATATTAT
* * *
2625 ATATACTTT-AAAAATATTTTCAAAATTATATATTAT
1 ATATATTTTCAAAAATGTTTTCAAAACTATATATTAT
*
2661 ATATATTTTCAAAAATGTTTTCAAAATTATATATTAT
1 ATATATTTTCAAAAATGTTTTCAAAACTATATATTAT
* * *
2698 ATATATTTTCGAACAATATTTTCAAAACTATATACTAT
1 ATATATTTTC-AAAAATGTTTTCAAAACTATATATTAT
* *
2736 ATATATTTTTC-AAAACGTATTCAAAACTATATTATATAT
1 ATATA-TTTTCAAAAATGTTTTCAAAACTATA-TAT-TAT
2775 ATATAT
1 ATATAT
2781 ATATATCAAA
Statistics
Matches: 133, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
34 27 0.20
35 1 0.01
36 9 0.07
37 52 0.39
38 31 0.23
39 13 0.10
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (37 bp):
ATATATTTTCAAAAATGTTTTCAAAACTATATATTAT
Found at i:2717 original size:75 final size:72
Alignment explanation
Indices: 2591--2780 Score: 240
Period size: 75 Copynumber: 2.6 Consensus size: 72
2581 TTTTTAAACC
* * *
2591 ATATATTTTTAAAACGTTTTCAAAACTATATA-T-TATATACTTTAAAAATATTTTCAAAATTAT
1 ATATATTTTCAAAACGTTTTCAAAACTATATATTATATATATTTTAAAAATATTTTCAAAACTAT
*
2654 ATATTAT
66 ATACTAT
* * *
2661 ATATATTTTCAAAAATGTTTTCAAAATTATATATTATATATATTTTCGAACAATATTTTCAAAAC
1 ATATATTTTC-AAAACGTTTTCAAAACTATATATTATATATATTTT--AAAAATATTTTCAAAAC
2726 TATATACTAT
63 TATATACTAT
*
2736 ATATATTTTTCAAAACGTATTCAAAACTATATTATATATATATAT
1 ATATA-TTTTCAAAACGTTTTCAAAACTATA-TAT-TATATATAT
2781 ATATATCAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 9
0.84 0.08 0.07
Matches are distributed among these distances:
70 9 0.09
71 20 0.20
72 1 0.01
73 9 0.09
75 46 0.45
76 8 0.08
77 9 0.09
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (72 bp):
ATATATTTTCAAAACGTTTTCAAAACTATATATTATATATATTTTAAAAATATTTTCAAAACTAT
ATACTAT
Found at i:3141 original size:3 final size:3
Alignment explanation
Indices: 3125--3197 Score: 73
Period size: 3 Copynumber: 25.0 Consensus size: 3
3115 TTGAAAAAAC
* *
3125 ATT ATT A-T ATTT ATT ATT ATA ATT AATT A-A ATT ATT ATT ATT ATT
1 ATT ATT ATT A-TT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT
*
3170 A-T ATT ATT -TT ATT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3198 TAATACATTG
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
2 7 0.12
3 46 0.79
4 5 0.09
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:3153 original size:22 final size:23
Alignment explanation
Indices: 3127--3187 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
3117 GAAAAAACAT
3127 TATTATATTTATTATTATAATTA
1 TATTATATTTATTATTATAATTA
* *
3150 -ATTA-AATTATTATTATTATTA
1 TATTATATTTATTATTATAATTA
3171 TATTAT-TTTATTATTAT
1 TATTATATTTATTATTAT
3188 TGTTATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 15 0.45
22 18 0.55
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TATTATATTTATTATTATAATTA
Found at i:6058 original size:13 final size:13
Alignment explanation
Indices: 6023--6077 Score: 76
Period size: 13 Copynumber: 4.3 Consensus size: 13
6013 ACCGGTCACA
6023 ACCCGACCCGTTG
1 ACCCGACCCGTTG
* *
6036 ACCC-AACCGTTA
1 ACCCGACCCGTTG
6048 ACCCGACCCGTTG
1 ACCCGACCCGTTG
*
6061 ACTCGACCCGTTG
1 ACCCGACCCGTTG
6074 ACCC
1 ACCC
6078 ATTGACCGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 10 0.29
13 25 0.71
ACGTcount: A:0.20, C:0.45, G:0.18, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTG
Found at i:6088 original size:15 final size:15
Alignment explanation
Indices: 6068--6106 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
6058 TTGACTCGAC
6068 CCGTTGACCCATTGA
1 CCGTTGACCCATTGA
6083 CCGTTGACCCATTGA
1 CCGTTGACCCATTGA
6098 CCGTTGACC
1 CCGTTGACC
6107 GGCGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.18, C:0.36, G:0.21, T:0.26
Consensus pattern (15 bp):
CCGTTGACCCATTGA
Found at i:7419 original size:18 final size:18
Alignment explanation
Indices: 7393--7428 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
7383 TCGAAAGGAC
*
7393 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
7411 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
7429 CGGATGGCAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:8590 original size:24 final size:23
Alignment explanation
Indices: 8561--8643 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
8551 CCGACTTGAG
* *
8561 TCTGTTCTGATACAGTACCTGAAT
1 TCTGTTCTGATACTG-ATCTGAAT
* * *
8585 TCTGTTATGATTTCTGATCTGGAT
1 TCTGTTCTGA-TACTGATCTGAAT
8609 TCTGTTCTGATATCTGATCTGAAT
1 TCTGTTCTGATA-CTGATCTGAAT
*
8633 TCTGTTTTGAT
1 TCTGTTCTGAT
8644 TTCTGATATC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
23 1 0.02
24 44 0.92
25 3 0.06
ACGTcount: A:0.19, C:0.16, G:0.18, T:0.47
Consensus pattern (23 bp):
TCTGTTCTGATACTGATCTGAAT
Found at i:8599 original size:12 final size:12
Alignment explanation
Indices: 8579--8648 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
8569 GATACAGTAC
*
8579 CTGAATTCTGTT
1 CTGATTTCTGTT
* *
8591 ATGATTTCTGAT
1 CTGATTTCTGTT
8603 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
* *
8615 CTGATATCTGAT
1 CTGATTTCTGTT
*
8627 CTGAATTCTGTT
1 CTGATTTCTGTT
*
8639 TTGATTTCTG
1 CTGATTTCTG
8649 ATATCTCCGT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:8648 original size:24 final size:24
Alignment explanation
Indices: 8579--8650 Score: 108
Period size: 24 Copynumber: 3.0 Consensus size: 24
8569 GATACAGTAC
8579 CTGAATTCTGTTATGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
* * *
8603 CTGGATTCTGTTCTGATATCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
*
8627 CTGAATTCTGTTTTGATTTCTGAT
1 CTGAATTCTGTTATGATTTCTGAT
8651 ATCTCCGTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.18, C:0.14, G:0.18, T:0.50
Consensus pattern (24 bp):
CTGAATTCTGTTATGATTTCTGAT
Found at i:10422 original size:144 final size:149
Alignment explanation
Indices: 10223--10538 Score: 443
Period size: 144 Copynumber: 2.2 Consensus size: 149
10213 CAGGTGAAAC
* * * *
10223 TTTATTTT--GGTCGGATCGGGTTTTTTGTAAGTGTGATATTCGGATCGGGTTCGGTTTAGGGTG
1 TTTATTTTCGGGTCGGGTC-GGATTTTTGTAAGTGTGATATTCGGATCGAGTTCGGTTTAAGGTG
* *
10286 AAAAAAACCGTACCGAGACG-AAA-ATATATAATTCAGGTCGGATCGGATTAAGTCACTATTTTT
65 AAAAAAACCGGACCGACACGAAAATATATATAATTCAGGTCGGATCGGATTAAGTCACTATTTTT
10349 -TTAA-ATAAAATA-TTTTTT
130 ATTAATA-AAAATACTTTTTT
*
10367 TTTATTTTCGGGTCGGGTCGGATTTTT-TAAGTGTGATATTCGGGTCGAGTTCGGTTTAAGGTGA
1 TTTATTTTCGGGTCGGGTCGGATTTTTGTAAGTGTGATATTCGGATCGAGTTCGGTTTAAGGTGA
* * * *
10431 AAAAAACCGGACCGACCCGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTGTTTTTA
66 AAAAAACCGGACCGACACGAAAATATATATAATTCAGGTCGGATCGGATTAAGTCACTATTTTTA
10496 TTAATAAAAATACTTTTTT
131 TTAATAAAAATACTTTTTT
*
10515 ATTA-TTTCGGGTCGGGTCGGATTT
1 TTTATTTTCGGGTCGGGTCGGATTT
10539 CTAATTCATA
Statistics
Matches: 153, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
144 58 0.38
145 10 0.07
146 45 0.29
147 30 0.20
148 10 0.07
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.38
Consensus pattern (149 bp):
TTTATTTTCGGGTCGGGTCGGATTTTTGTAAGTGTGATATTCGGATCGAGTTCGGTTTAAGGTGA
AAAAAACCGGACCGACACGAAAATATATATAATTCAGGTCGGATCGGATTAAGTCACTATTTTTA
TTAATAAAAATACTTTTTT
Found at i:10627 original size:29 final size:30
Alignment explanation
Indices: 10589--10648 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
10579 TTGTTCGGTC
10589 GGGTCGGG-TTTTTTAAGTCTGATATTCGG
1 GGGTCGGGTTTTTTTAAGTCTGATATTCGG
*
10618 GGGTCGGGTTTTTTTAAGTGTGATATTCGG
1 GGGTCGGGTTTTTTTAAGTCTGATATTCGG
10648 G
1 G
10649 TCGAGTCGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 8 0.28
30 21 0.72
ACGTcount: A:0.13, C:0.08, G:0.37, T:0.42
Consensus pattern (30 bp):
GGGTCGGGTTTTTTTAAGTCTGATATTCGG
Found at i:10797 original size:27 final size:27
Alignment explanation
Indices: 10765--10828 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
10755 AACTTTATTT
10765 TATTCGGGTCGGGTTTTTTAAGTGTGA
1 TATTCGGGTCGGGTTTTTTAAGTGTGA
10792 TATTCGGGTCGGGTTTTTTAAGTGTGA
1 TATTCGGGTCGGGTTTTTTAAGTGTGA
10819 TATTCGGGTC
1 TATTCGGGTC
10829 AGGTCGGTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.14, C:0.09, G:0.33, T:0.44
Consensus pattern (27 bp):
TATTCGGGTCGGGTTTTTTAAGTGTGA
Found at i:11382 original size:16 final size:18
Alignment explanation
Indices: 11358--11402 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
11348 TATGAAATTG
11358 GATTTCAATTCC-T-ACA
1 GATTTCAATTCCTTCACA
*
11374 GATTCCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
11392 GATTTCAATTC
1 GATTTCAATTC
11403 TCTCATAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 13 0.52
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.38
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:15812 original size:19 final size:20
Alignment explanation
Indices: 15781--15833 Score: 51
Period size: 19 Copynumber: 2.8 Consensus size: 20
15771 AATAACACTA
15781 TAAAT-ATATTTTATAATT-T
1 TAAATAATA-TTTATAATTAT
*
15800 TAAATAATATTTA-ATTTAT
1 TAAATAATATTTATAATTAT
*
15819 TCAATAATA-TTATAA
1 TAAATAATATTTATAA
15834 ATCTTACTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 6 0.21
19 19 0.68
20 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAATAATATTTATAATTAT
Found at i:23651 original size:24 final size:24
Alignment explanation
Indices: 23624--23733 Score: 77
Period size: 24 Copynumber: 4.6 Consensus size: 24
23614 GTAAACGGAG
*
23624 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
23648 ATATCA-AATATCAGAATAGAATCC
1 ATATCAGAA-ATCAGAACAGAATTC
* *
23672 AGATCAG-AATTAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
23695 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
*
23719 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
23734 TAAAATATTT
Statistics
Matches: 66, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 16 0.24
24 46 0.70
25 2 0.03
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:24838 original size:18 final size:18
Alignment explanation
Indices: 24817--24851 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24807 TGCCATCCGG
*
24817 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
24835 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
24852 GTCCTTTTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:26175 original size:13 final size:13
Alignment explanation
Indices: 26157--26212 Score: 94
Period size: 13 Copynumber: 4.3 Consensus size: 13
26147 AGTGGTCAAC
26157 GGTCAACGGGTCG
1 GGTCAACGGGTCG
26170 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
26183 GGTCAACGGTTCG
1 GGTCAACGGGTCG
*
26196 GGTCAACAGGTCG
1 GGTCAACGGGTCG
26209 GGTC
1 GGTC
26213 GGGTTGGGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.16, C:0.23, G:0.43, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:28325 original size:24 final size:24
Alignment explanation
Indices: 28298--28369 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
28288 GTAAACGGAG
*
28298 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
28322 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
28346 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
28369 A
1 A
28370 GGTAACGTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 15 0.36
24 27 0.64
ACGTcount: A:0.50, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:28329 original size:12 final size:12
Alignment explanation
Indices: 28302--28370 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
28292 ACGGAGATAT
* *
28302 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
28314 CAGAATTCATAT
1 CAGAATTCAGAA
28326 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
28338 CAGAATCCAGAT
1 CAGAATTCAGAA
28350 CAGAA-TCAGAA
1 CAGAATTCAGAA
28361 CAGAATTCAG
1 CAGAATTCAG
28371 GTAACGTATC
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
11 11 0.24
12 32 0.71
13 2 0.04
ACGTcount: A:0.49, C:0.19, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:28386 original size:24 final size:23
Alignment explanation
Indices: 28307--28393 Score: 84
Period size: 24 Copynumber: 3.7 Consensus size: 23
28297 GATATCAGAA
* * *
28307 ATCAAAACAGAATTCATATCAGAT
1 ATCAGAACAGAATTCAGATAAG-T
* * *
28331 ATCAGAACAGAATCCAGATCAGA
1 ATCAGAACAGAATTCAGATAAGT
*
28354 ATCAGAACAGAATTCAGGTAACGT
1 ATCAGAACAGAATTCAGATAA-GT
*
28378 ATCAGAACATAATTCA
1 ATCAGAACAGAATTCA
28394 ATTCGGAAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.34
24 35 0.66
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (23 bp):
ATCAGAACAGAATTCAGATAAGT
Found at i:29722 original size:18 final size:18
Alignment explanation
Indices: 29696--29740 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
29686 TCAGGTCAAC
29696 GGTTCGGGTCAACAGGTCG
1 GGTT-GGGTCAACAGGTCG
*
29715 GGTTGGGTCAACGGGTCG
1 GGTTGGGTCAACAGGTCG
*
29733 GGTCGGGT
1 GGTTGGGT
29741 TATGACCGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.11, C:0.18, G:0.49, T:0.22
Consensus pattern (18 bp):
GGTTGGGTCAACAGGTCG
Found at i:34307 original size:81 final size:81
Alignment explanation
Indices: 34221--34389 Score: 214
Period size: 81 Copynumber: 2.1 Consensus size: 81
34211 ATTCCTTTAG
* * * *
34221 TCTTTTACCCAAAAGCATTTAGCCTTTCATCTAACT-TGCATGATTGACACTTTTATGCCAAATG
1 TCTTTTACCCAAAAGCATTTAACCTTTCATCTAACTGT-CATAATTGACACATTTATGCCAAATA
*
34285 CACAGCTAGGCCATTAA
65 CACAACTAGGCCATTAA
** * * * *
34302 TCTTTTACTTAAAGGTATTTAACCTTTCATCTAACTGTCATAATTGATACATTTCTGCCAAATAC
1 TCTTTTACCCAAAAGCATTTAACCTTTCATCTAACTGTCATAATTGACACATTTATGCCAAATAC
*
34367 ATAACTAGGCCATTAA
66 ACAACTAGGCCATTAA
34383 TCTTTTA
1 TCTTTTA
34390 TTTTAGAACA
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
81 74 0.99
82 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (81 bp):
TCTTTTACCCAAAAGCATTTAACCTTTCATCTAACTGTCATAATTGACACATTTATGCCAAATAC
ACAACTAGGCCATTAA
Found at i:34802 original size:26 final size:26
Alignment explanation
Indices: 34768--34910 Score: 103
Period size: 26 Copynumber: 6.0 Consensus size: 26
34758 TGCCTTAATG
*
34768 CATCATTTCATGCATTTCATTTATGT
1 CATCCTTTCATGCATTTCATTTATGT
*
34794 CATCCTTTCATGCATTTCATTTATGG
1 CATCCTTTCATGCATTTCATTTATGT
* * *
34820 CTTTCTTTCATGC----C-TTAATGT
1 CATCCTTTCATGCATTTCATTTATGT
* * * *
34841 -ATCATTTCATGAATTTTATTTATGA
1 CATCCTTTCATGCATTTCATTTATGT
*
34866 CATCCTTTCATGC----C-TTAATG-
1 CATCCTTTCATGCATTTCATTTATGT
*
34886 CATCCTTTCATTCATTTCATTTATG
1 CATCCTTTCATGCATTTCATTTATG
34911 GATTCATTTT
Statistics
Matches: 87, Mismatches: 19, Indels: 23
0.67 0.15 0.18
Matches are distributed among these distances:
20 20 0.23
21 10 0.11
22 1 0.01
24 1 0.01
25 10 0.11
26 45 0.52
ACGTcount: A:0.22, C:0.21, G:0.08, T:0.49
Consensus pattern (26 bp):
CATCCTTTCATGCATTTCATTTATGT
Found at i:34819 original size:72 final size:72
Alignment explanation
Indices: 34735--34878 Score: 227
Period size: 72 Copynumber: 2.0 Consensus size: 72
34725 TTATTCTGTA
* *
34735 ATTTCATTTATGGCATCT-TTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGTCATCC
1 ATTTCATTTATGGC-TCTCTTTCATGCCTTAATGCATCATTTCATGAATTTCATTTATGACATCC
34799 TTTCATGC
65 TTTCATGC
* * *
34807 ATTTCATTTATGGCTTTCTTTCATGCCTTAATGTATCATTTCATGAATTTTATTTATGACATCCT
1 ATTTCATTTATGGCTCTCTTTCATGCCTTAATGCATCATTTCATGAATTTCATTTATGACATCCT
34872 TTCATGC
66 TTCATGC
34879 CTTAATGCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 2 0.03
72 64 0.97
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (72 bp):
ATTTCATTTATGGCTCTCTTTCATGCCTTAATGCATCATTTCATGAATTTCATTTATGACATCCT
TTCATGC
Found at i:34849 original size:46 final size:46
Alignment explanation
Indices: 34790--34911 Score: 163
Period size: 46 Copynumber: 2.6 Consensus size: 46
34780 CATTTCATTT
* *
34790 ATGTCATCCTTTCATGCATTTCATTTATGGCTTTCTTTCATGCCTTA
1 ATGT-ATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTA
* * * *
34837 ATGTATCATTTCATGAATTTTATTTATGACATCCTTTCATGCCTTA
1 ATGTATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTA
* *
34883 ATGCATCCTTTCATTCATTTCATTTATGG
1 ATGTATCCTTTCATGCATTTCATTTATGG
34912 ATTCATTTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
46 59 0.94
47 4 0.06
ACGTcount: A:0.21, C:0.20, G:0.10, T:0.48
Consensus pattern (46 bp):
ATGTATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTA
Found at i:39530 original size:81 final size:81
Alignment explanation
Indices: 39429--39595 Score: 219
Period size: 81 Copynumber: 2.1 Consensus size: 81
39419 ATTCCTTTAG
* * * *
39429 TCTTTTACCCAAAGGCATTTAGAC-TTTCATCTAACTTGCATGATTGACACTTTTAAGCCAAATG
1 TCTTTTACCCAAAGGCATTTA-ACATTTCATCTAACTGGCATAATTGACACATTTAAGCCAAATA
* *
39493 CACAGCTAGGCCATTAA
65 AACAGCTAGACCATTAA
* * * **
39510 TCTTTTACTCAAATGTATTTAACATTTCATCTAACTGGCATAATTGACACATTTCTGCCAAATAA
1 TCTTTTACCCAAAGGCATTTAACATTTCATCTAACTGGCATAATTGACACATTTAAGCCAAATAA
39575 ACAGCTAGACCATTAA
66 ACAGCTAGACCATTAA
39591 TCTTT
1 TCTTT
39596 ATTTTAGAAC
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 2 0.03
81 72 0.97
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (81 bp):
TCTTTTACCCAAAGGCATTTAACATTTCATCTAACTGGCATAATTGACACATTTAAGCCAAATAA
ACAGCTAGACCATTAA
Found at i:39979 original size:20 final size:20
Alignment explanation
Indices: 39954--40079 Score: 81
Period size: 20 Copynumber: 5.7 Consensus size: 20
39944 TTCATTTATG
39954 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
* *
39974 GCATCCTTTCATGTATTTCATTTAT
1 GCATCCTTTCATG-----CCTTAAT
* *
39999 GGCATCTTTTCATGCCTTAAA
1 -GCATCCTTTCATGCCTTAAT
* *
40020 GCATCATTTCATGCATTTTATTTAT
1 GCATCCTTTCATGC--CTTA---AT
*
40045 GGTATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
40066 GCATCCTTTCATGC
1 GCATCCTTTCATGC
40080 ATTTCATTTA
Statistics
Matches: 81, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
20 39 0.48
21 6 0.07
22 3 0.04
24 3 0.04
25 6 0.07
26 24 0.30
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:39996 original size:46 final size:46
Alignment explanation
Indices: 39942--40092 Score: 248
Period size: 46 Copynumber: 3.3 Consensus size: 46
39932 TTATTCGTCA
*
39942 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGT
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
39988 ATTTCATTTATGGCATCTTTTCATGCCTTAAAGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
40034 ATTTTATTTATGGTATCCTTTCATGCCTTAATGCATCCTTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
40080 ATTTCATTTATGG
1 ATTTCATTTATGG
40093 ATTCGTTATA
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 95 1.00
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.46
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:40890 original size:22 final size:21
Alignment explanation
Indices: 40837--40887 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
40827 GATACCCATA
*
40837 CCCGGATTTACCATTTTTCAG
1 CCCGGTTTTACCATTTTTCAG
* *
40858 CCTGGTTTTACCATTTTTTAG
1 CCCGGTTTTACCATTTTTCAG
40879 CCCGGTTTT
1 CCCGGTTTT
40888 TACTATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.25, G:0.16, T:0.45
Consensus pattern (21 bp):
CCCGGTTTTACCATTTTTCAG
Found at i:46218 original size:40 final size:40
Alignment explanation
Indices: 46163--46284 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
46153 TGCAGGTTTA
*
46163 TAATACACTTCGGTGTATATGGTGGGTACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
46203 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
46243 TAATACACTTCGGTGTATATGCTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
46283 TA
1 TA
46285 GCACTACAGG
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:52531 original size:40 final size:40
Alignment explanation
Indices: 52476--52597 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
52466 TGCAGGTTTA
52476 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
52516 TAATACACTTCGGTGTATATGATGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
52556 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
52596 TA
1 TA
52598 GCACTACGGT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:52796 original size:47 final size:45
Alignment explanation
Indices: 52702--52827 Score: 157
Period size: 47 Copynumber: 2.8 Consensus size: 45
52692 GTAACCAGGC
* *
52702 AAATAAGCTTATGAGCTTACT-GAAT-AATGGCAAGTATATAGGAA
1 AAATAAGCTTACGAGCTTA-TGGAATAAATGGTAAGTATATAGGAA
* * *
52746 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGGAA
*
52793 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
52828 AGATTTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
43 1 0.01
44 21 0.29
45 11 0.15
46 1 0.01
47 38 0.53
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.30
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGGAA
Found at i:56478 original size:19 final size:19
Alignment explanation
Indices: 56454--56492 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
56444 GTAATCATCG
56454 ATGGTTCTCCTAACCCTCC
1 ATGGTTCTCCTAACCCTCC
56473 ATGGTTCTCCTAACCCTCC
1 ATGGTTCTCCTAACCCTCC
56492 A
1 A
56493 AGAAACTAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.18, C:0.41, G:0.10, T:0.31
Consensus pattern (19 bp):
ATGGTTCTCCTAACCCTCC
Found at i:56976 original size:18 final size:18
Alignment explanation
Indices: 56953--56993 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
56943 AGACTCCAAA
*
56953 AGAAGAAGGAAGAAAAA-G
1 AGAAGAACG-AGAAAAAGG
56971 AGAAGAACGAGAAAAAGG
1 AGAAGAACGAGAAAAAGG
56989 AGAAG
1 AGAAG
56994 GTGAGAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.63, C:0.02, G:0.34, T:0.00
Consensus pattern (18 bp):
AGAAGAACGAGAAAAAGG
Found at i:62689 original size:22 final size:22
Alignment explanation
Indices: 62637--62689 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
62627 TTAGCAATGA
*
62637 TACTAAAGTGCCTTGGCATCAT
1 TACTAAAGTGCATTGGCATCAT
** * **
62659 TACGGAAGTGCATTTGCATTGT
1 TACTAAAGTGCATTGGCATCAT
62681 TACTAAAGT
1 TACTAAAGT
62690 ATCTTAGCAC
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (22 bp):
TACTAAAGTGCATTGGCATCAT
Found at i:64038 original size:19 final size:19
Alignment explanation
Indices: 64014--64051 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
64004 ATGTCACTCA
64014 TTGTTTGTAATATTAGAAT
1 TTGTTTGTAATATTAGAAT
64033 TTGTTTGTAATATTAGAAT
1 TTGTTTGTAATATTAGAAT
64052 GGTTATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.53
Consensus pattern (19 bp):
TTGTTTGTAATATTAGAAT
Found at i:64188 original size:2 final size:2
Alignment explanation
Indices: 64181--64227 Score: 76
Period size: 2 Copynumber: 23.0 Consensus size: 2
64171 ATTAATGTTA
*
64181 AT AT AT AT TT GAT 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 AT AT AT AT
64224 AT AT
1 AT AT
64228 TTTTAATTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 41 0.98
3 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Done.