Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004538.1 Hibiscus syriacus cultivar Beakdansim tig00010029_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: 76258
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1625 original size:13 final size:13
Alignment explanation
Indices: 1603--1667 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 13
1593 CAAAGATGCC
1603 AAATGCAAATGTA
1 AAATGCAAATGTA
*
1616 AAATGTAAATGT-
1 AAATGCAAATGTA
* *
1628 AAATACAAACGTAA
1 AAATGCAAATGT-A
*
1642 AAATGTACAAATGCA
1 AAATG--CAAATGTA
*
1657 AAATACAAATG
1 AAATGCAAATG
1668 CATGTATGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
12 9 0.22
13 17 0.43
14 4 0.10
15 5 0.12
16 5 0.12
ACGTcount: A:0.57, C:0.09, G:0.12, T:0.22
Consensus pattern (13 bp):
AAATGCAAATGTA
Found at i:3797 original size:17 final size:18
Alignment explanation
Indices: 3774--3825 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 18
3764 GATATTAATA
3774 AATATTATAATTTAAAAT
1 AATATTATAATTTAAAAT
**
3792 AA-ATTATAATTT-TTAT
1 AATATTATAATTTAAAAT
3808 AATATT-TAATTTAAAAT
1 AATATTATAATTTAAAAT
3825 A
1 A
3826 CCAGAATAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 10 0.36
17 16 0.57
18 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATATTATAATTTAAAAT
Found at i:5475 original size:9 final size:9
Alignment explanation
Indices: 5455--5513 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
5445 TTGGGCTTTG
5455 TAATATTTAA
1 TAATA-TTAA
5465 TAATATTAA
1 TAATATTAA
*
5474 TAATAATAA
1 TAATATTAA
*
5483 TAATAATAAA
1 TAAT-ATTAA
5493 TAATGA-TAA
1 TAAT-ATTAA
*
5502 TAATAATAA
1 TAATATTAA
5511 TAA
1 TAA
5514 ATATATAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
8 1 0.02
9 28 0.67
10 13 0.31
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (9 bp):
TAATATTAA
Found at i:5477 original size:3 final size:3
Alignment explanation
Indices: 5462--5513 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
5452 TTGTAATATT
* *
5462 TAA TAA TAT TAA TAA TAA TAA TAA TAA TAAA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
5508 TAA TAA
1 TAA TAA
5514 ATATATAAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5523 original size:8 final size:7
Alignment explanation
Indices: 5472--5525 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 7
5462 TAATAATATT
5472 AATAAT-
1 AATAATA
5478 AATAAT-
1 AATAATA
5484 AATAATA
1 AATAATA
5491 AATAATGA
1 AATAAT-A
5499 TAATAAT-
1 -AATAATA
5506 AATAATA
1 AATAATA
5513 AATATATA
1 AATA-ATA
5521 AATAA
1 AATAA
5526 AATGGGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
6 18 0.42
7 11 0.26
8 8 0.19
9 6 0.14
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (7 bp):
AATAATA
Found at i:5822 original size:22 final size:22
Alignment explanation
Indices: 5797--5876 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
5787 AATAAAGCTT
* * *
5797 TCATCTTTGAAAAGAGAAACTA
1 TCATCTTTGAAGAGATAATCTA
5819 TCATCTTTGAAGAGATAATCTA
1 TCATCTTTGAAGAGATAATCTA
5841 TCATCTTTGAAGAGATAATCTA
1 TCATCTTTGAAGAGATAATCTA
5863 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
5877 TGTAGATGTA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGATAATCTA
Found at i:6346 original size:54 final size:54
Alignment explanation
Indices: 6240--6346 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 54
6230 ATAATCACTG
* **
6240 GTTCGGAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGTCCAGAT
1 GTTCGGAAAACATTTGACAACACATTCATCATTTCTTGTGGCTTCTACCCAGAT
* * *
6294 GTTCGTAAAACATTTGGCAACACATTCATTATTTCTTGTGGCTTCTACCCAGA
1 GTTCGGAAAACATTTGACAACACATTCATCATTTCTTGTGGCTTCTACCCAGA
6347 GTTTTCATCG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (54 bp):
GTTCGGAAAACATTTGACAACACATTCATCATTTCTTGTGGCTTCTACCCAGAT
Found at i:7478 original size:35 final size:35
Alignment explanation
Indices: 7416--7482 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
7406 TCTTATTGAG
7416 ATGAGCCTCCAAGAATGCCCAAATATTCATATTACT
1 ATGAGCCTCCAAGAATGCCCAAATATTC-TATTACT
* * *
7452 ATGAGCCTTCAA-AATGCCCCACTATTCTATT
1 ATGAGCCTCCAAGAATGCCCAAATATTCTATT
7483 TCTGGTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 4 0.14
35 13 0.46
36 11 0.39
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (35 bp):
ATGAGCCTCCAAGAATGCCCAAATATTCTATTACT
Found at i:10538 original size:72 final size:72
Alignment explanation
Indices: 10420--10627 Score: 328
Period size: 73 Copynumber: 2.9 Consensus size: 72
10410 TATAATATGT
*
10420 TAGCTGAATATTATCCATAAAGTCAGGGCTATTAACCAATTGCTTTAGGGGGACAACTTAAGCAT
1 TAGCTGAATATTATCCATAAAGTCGGGGCTATTAACCAATTGCTTTAGGGGGACAACTTAAGCAT
10485 AACAAAC
66 AACAAAC
* *
10492 TAGCTGAATATTATCCATAAAGTCGGGGCTATTAACCAATTACTTTAGGGGGACAAATTCAAGCA
1 TAGCTGAATATTATCCATAAAGTCGGGGCTATTAACCAATTGCTTTAGGGGGACAACTT-AAGCA
10557 TAACAAAC
65 TAACAAAC
* * * *
10565 TAGCT-AAGTATTATCCATAAAGCCGAGGCTATTAACCAATTGCTTTAGGGGGATAACTCAAGC
1 TAGCTGAA-TATTATCCATAAAGTCGGGGCTATTAACCAATTGCTTTAGGGGGACAACTTAAGC
10628 TTTATTGTAT
Statistics
Matches: 125, Mismatches: 9, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
72 62 0.50
73 63 0.50
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (72 bp):
TAGCTGAATATTATCCATAAAGTCGGGGCTATTAACCAATTGCTTTAGGGGGACAACTTAAGCAT
AACAAAC
Found at i:12330 original size:34 final size:32
Alignment explanation
Indices: 12291--12360 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
12281 TTTTGTAAAG
* * *
12291 GGGAAATGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCACG-G-AAAAACTA
*
12325 GGGAAAGGTTCTAGTTTAGCACGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCACGGAAAAACTA
12357 GGGA
1 GGGA
12361 GTTTGTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCACGGAAAAACTA
Found at i:13580 original size:16 final size:16
Alignment explanation
Indices: 13559--13590 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13549 AAATGTAATG
*
13559 TAAATGCGAAAATGCA
1 TAAATGCAAAAATGCA
13575 TAAATGCAAAAATGCA
1 TAAATGCAAAAATGCA
13591 AACTGTGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.16, T:0.19
Consensus pattern (16 bp):
TAAATGCAAAAATGCA
Found at i:15935 original size:27 final size:26
Alignment explanation
Indices: 15897--15949 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
15887 TGAAAATAAA
15897 ATAAAAACATTAATAA-TAATAAAAAT
1 ATAAAAACATT-ATAAGTAATAAAAAT
*
15923 ATAATAAATATTATAAGTAATAAAAAT
1 ATAA-AAACATTATAAGTAATAAAAAT
15950 TTTGAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (26 bp):
ATAAAAACATTATAAGTAATAAAAAT
Found at i:16625 original size:22 final size:22
Alignment explanation
Indices: 16600--16642 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
16590 ATAGATTAAT
16600 ATATATAATTTA-TAAAAATAGA
1 ATAT-TAATTTATTAAAAATAGA
*
16622 ATATTTATTTATTTAAAAATA
1 ATATTAATTTA-TTAAAAATA
16643 TCAGAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.33
22 4 0.22
23 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATTAATTTATTAAAAATAGA
Found at i:16641 original size:137 final size:134
Alignment explanation
Indices: 16450--16703 Score: 314
Period size: 137 Copynumber: 1.9 Consensus size: 134
16440 TAACTTTAAG
* * * * * * *
16450 AAAATATATTAATTTTTATATTTTATAAATAAGATATTTATTTATTTTTTAAAATACCATAATAA
1 AAAATAGATTAATATATATAATTTATAAAAAAGATATTTATTTA-TTTTAAAAATACCAGAA-AA
* * * *
16515 -GACATCTAGTTGCTTTAAGACTGTCATTTTCTTAATATTAAAAATAAATAAATATTAAAACATT
64 TGACATCCAGTTACGTTAAGACTGCCA-TTTCTTAATATT-AAAATAAATAAATATTAAAACATT
16579 TTTCTAAA
127 TTTCTAAA
*
16587 AAAATAGATTAATATATATAATTTATAAAAATAGAATATTTATTTA-TTTAAAAATATCAGAAAA
1 AAAATAGATTAATATATATAATTTATAAAAA-AG-ATATTTATTTATTTTAAAAATACCAGAAAA
* *
16651 TGACATCCAGTTACGTTAAGACTGCCATTTCTTAATATTGAAATAAGTAAATA
64 TGACATCCAGTTACGTTAAGACTGCCATTTCTTAATATTAAAATAAATAAATA
16704 CTATTATTAA
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
135 12 0.12
136 14 0.14
137 61 0.61
138 2 0.02
139 11 0.11
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (134 bp):
AAAATAGATTAATATATATAATTTATAAAAAAGATATTTATTTATTTTAAAAATACCAGAAAATG
ACATCCAGTTACGTTAAGACTGCCATTTCTTAATATTAAAATAAATAAATATTAAAACATTTTTC
TAAA
Found at i:18320 original size:3 final size:3
Alignment explanation
Indices: 18312--18348 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
18302 TGTAATTAAA
18312 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
18349 AAAAATTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18361 original size:14 final size:14
Alignment explanation
Indices: 18344--18370 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18334 ATAATAATAT
18344 AATAAAAAAATTAA
1 AATAAAAAAATTAA
18358 AATAAAAAAATTA
1 AATAAAAAAATTA
18371 GTGTCTACAT
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAAAAATTAA
Found at i:27424 original size:57 final size:57
Alignment explanation
Indices: 27331--27503 Score: 328
Period size: 57 Copynumber: 3.0 Consensus size: 57
27321 TCCGTGTAGG
*
27331 AATGTGATTATGAGGAAGGGTATTAATGTTGCTTGGATTATCAATATCTTTTCTTTT
1 AATGTGATTATGAGGAAGGGTATTAATGTTGTTTGGATTATCAATATCTTTTCTTTT
27388 AATGTGATTATGAGGAAGGGTATTAATGTTGTTTGGATTATCAATATCTTTTCTTTT
1 AATGTGATTATGAGGAAGGGTATTAATGTTGTTTGGATTATCAATATCTTTTCTTTT
*
27445 AATGTGATTATGAGGAAGGGTATTAATGTTGTTTGGATTCTCAATATCTTTTCTTTT
1 AATGTGATTATGAGGAAGGGTATTAATGTTGTTTGGATTATCAATATCTTTTCTTTT
27502 AA
1 AA
27504 GTGCATTGAA
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 114 1.00
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (57 bp):
AATGTGATTATGAGGAAGGGTATTAATGTTGTTTGGATTATCAATATCTTTTCTTTT
Found at i:37204 original size:20 final size:21
Alignment explanation
Indices: 37176--37214 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
37166 ATTTTATCCA
37176 TTTACTTTTAAAAT-TTTAAG
1 TTTACTTTTAAAATGTTTAAG
*
37196 TTTATTTTTAAAATGTTTA
1 TTTACTTTTAAAATGTTTA
37215 TTATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTACTTTTAAAATGTTTAAG
Found at i:37489 original size:24 final size:24
Alignment explanation
Indices: 37462--37534 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
37452 CGTTCATTTA
37462 CGTTC-GTGAACGTTCGATTATGTT
1 CGTTCGGT-AACGTTCGATTATGTT
* * * *
37486 CGTTAGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGATTATGTT
* * *
37510 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGATTATGTT
37534 C
1 C
37535 ATTCATTTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 41 0.95
25 2 0.05
ACGTcount: A:0.12, C:0.14, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGATTATGTT
Found at i:37496 original size:14 final size:13
Alignment explanation
Indices: 37479--37527 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
37469 GAACGTTCGA
37479 TTATGTTCGTTAGG
1 TTATGTTCGTT-GG
37493 TTATGTTCG-T--
1 TTATGTTCGTTGG
37503 TTATGTTCGTTCGG
1 TTATGTTCGTT-GG
37517 TTATGTTCGTT
1 TTATGTTCGTT
37528 TATGTTCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.29
11 1 0.03
13 1 0.03
14 20 0.65
ACGTcount: A:0.10, C:0.10, G:0.24, T:0.55
Consensus pattern (13 bp):
TTATGTTCGTTGG
Found at i:37544 original size:24 final size:24
Alignment explanation
Indices: 37473--37547 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
37463 GTTCGTGAAC
* *
37473 GTTCGATTATGTTCGTT-AGGTTAT
1 GTTCGTTTATGTTCATTCA-GTTAT
* *
37497 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
*
37521 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCATTCAGTTAT
37545 GTT
1 GTT
37548 TAACCCAATC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.13, C:0.11, G:0.21, T:0.55
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCAGTTAT
Found at i:37933 original size:16 final size:16
Alignment explanation
Indices: 37914--37980 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
37904 TTTATGTTTG
37914 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
**
37930 TTTATGTTCGTGTTTG
1 TTTATGTTCGTGTTCA
* *
37946 TTTATGTTTGTGTTCG
1 TTTATGTTCGTGTTCA
37962 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
37976 TTTAT
1 TTTAT
37981 TAAATGAACG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 38 0.84
ACGTcount: A:0.10, C:0.07, G:0.19, T:0.63
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:37949 original size:32 final size:32
Alignment explanation
Indices: 37908--37972 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
37898 CTAACGTTTA
37908 TGTTTGTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTTGTTTATGTTCGTGTTCATTTATGTTCG
* *
37940 TGTTTGTTTATGTTTGTGTTCGTTTATGTTCG
1 TGTTTGTTTATGTTCGTGTTCATTTATGTTCG
37972 T
1 T
37973 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.08, C:0.08, G:0.23, T:0.62
Consensus pattern (32 bp):
TGTTTGTTTATGTTCGTGTTCATTTATGTTCG
Found at i:43056 original size:23 final size:23
Alignment explanation
Indices: 42983--43067 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
42973 TCATATAAAT
*
42983 TTGCACCGAAGTGCCACATAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
43006 TTGTACCGAAG-GACCGCGTA-AA
1 TTGCACCGAAGTG-CCACGTAGAA
* *
43028 GATGCACTGAAGTGCCACGTAGAA
1 -TTGCACCGAAGTGCCACGTAGAA
*
43052 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
43068 TATAATATGT
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
22 3 0.06
23 42 0.88
24 3 0.06
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:43787 original size:19 final size:20
Alignment explanation
Indices: 43747--43800 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
43737 TTTCCTTTAG
* *
43747 GGGGAATCGATTCCCACCCA
1 GGGGTATCGGTTCCCACCCA
43767 GGGGTATCGGTTCCC-CCCA
1 GGGGTATCGGTTCCCACCCA
43786 GGGGTATCGGTTCCC
1 GGGGTATCGGTTCCC
43801 TCTGCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.15, C:0.33, G:0.31, T:0.20
Consensus pattern (20 bp):
GGGGTATCGGTTCCCACCCA
Found at i:46656 original size:13 final size:13
Alignment explanation
Indices: 46638--46665 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
46628 CATTTATGCG
46638 TACTTATGGCTTA
1 TACTTATGGCTTA
46651 TACTTATGGCTTA
1 TACTTATGGCTTA
46664 TA
1 TA
46666 TAATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (13 bp):
TACTTATGGCTTA
Found at i:51015 original size:18 final size:19
Alignment explanation
Indices: 50992--51028 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
50982 TGAGTAATAA
50992 ATTTAATT-TTTATATTTT
1 ATTTAATTATTTATATTTT
*
51010 ATTTAATTATTTTTATTTT
1 ATTTAATTATTTATATTTT
51029 TCATATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
ATTTAATTATTTATATTTT
Found at i:51449 original size:19 final size:19
Alignment explanation
Indices: 51427--51504 Score: 52
Period size: 19 Copynumber: 4.0 Consensus size: 19
51417 TTAATAACTT
51427 ATTTTAATTTTAATTATTA
1 ATTTTAATTTTAATTATTA
* * *
51446 ATTTCAA--TAAATTATATT
1 ATTTTAATTTTAATTAT-TA
* *
51464 ATATTTAATATTATAATGATTG
1 AT-TTTAAT-TT-TAATTATTA
*
51486 ATTTTAATTATAATTATTA
1 ATTTTAATTTTAATTATTA
51505 GTCAAATTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
17 7 0.16
18 3 0.07
19 17 0.40
20 1 0.02
21 6 0.14
22 4 0.09
23 5 0.12
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTTTAATTTTAATTATTA
Found at i:52907 original size:29 final size:25
Alignment explanation
Indices: 52867--52926 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 25
52857 GTATTTTTAT
52867 TTTAAATCATTTAAAATTATAAAAATATA
1 TTTAAATCATTT--AATTAT-AAAATA-A
* *
52896 TTTAAATTATTTTATTATAAAATAA
1 TTTAAATCATTTAATTATAAAATAA
52921 TTTAAA
1 TTTAAA
52927 GTGACATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 7 0.24
26 6 0.21
27 5 0.17
29 11 0.38
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TTTAAATCATTTAATTATAAAATAA
Found at i:53295 original size:23 final size:24
Alignment explanation
Indices: 53246--53295 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
53236 TAATAAAACT
*
53246 TAATTATATTTTATAATAATTTAA
1 TAATTATATTTTATAATAATGTAA
* *
53270 TAATTAT-TTTTATAATGATGTGA
1 TAATTATATTTTATAATAATGTAA
53293 TAA
1 TAA
53296 AATAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (24 bp):
TAATTATATTTTATAATAATGTAA
Found at i:59915 original size:3 final size:3
Alignment explanation
Indices: 59895--59959 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
59885 CTGCAAAAAA
* * * *
59895 AAT ATT AAT AGT ATT AAT AAT -AT AAT AAT AAT AATT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
59940 AATT ATT AAT AAT AAT AAT A
1 AA-T AAT AAT AAT AAT AAT A
59960 TATATATATA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.88
4 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (3 bp):
AAT
Found at i:59938 original size:13 final size:13
Alignment explanation
Indices: 59906--59955 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
59896 ATATTAATAG
59906 TATTAATAAT-A-
1 TATTAATAATAAT
*
59917 TAATAATAATAAT
1 TATTAATAATAAT
59930 TATTAATAATAAT
1 TATTAATAATAAT
59943 TATTAATAATAAT
1 TATTAATAATAAT
59956 AATATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 9 0.26
12 1 0.03
13 25 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATTAATAATAAT
Found at i:61587 original size:2 final size:2
Alignment explanation
Indices: 61578--61607 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
61568 AATAGTAATA
61578 AT AT -T 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 AT A
61608 CAGTGAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74657 original size:55 final size:54
Alignment explanation
Indices: 74529--74767 Score: 253
Period size: 54 Copynumber: 4.5 Consensus size: 54
74519 AAATGACAGC
* *
74529 CTGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTC-ATAAATGTGT
1 CTGCTCTCTATTCCTTCAGAG-AGTATAAGACTCGAACAATCTTCAATAAACG-GT
* * *
74583 ATGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACGGT
1 CTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAAT-AAACGGT
74638 CTGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGGAA-AATCTTCAATAAACAGGT
1 CTGCTCTCTATTCCTTCAGAGAGTATAAG-ACTC-GAACAATCTTCAATAAAC-GGT
* * * *
74693 CCGCTC-CTATTCCTTCAGAGAGTATAAGACT----CAATCTTTAACAAACTTGT
1 CTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAAC-GGT
* *
74743 CTGCTCCCTATTCCTTTAGAGAGTA
1 CTGCTCTCTATTCCTTCAGAGAGTA
74768 GACTCGATCT
Statistics
Matches: 161, Mismatches: 15, Indels: 21
0.82 0.08 0.11
Matches are distributed among these distances:
50 19 0.12
51 17 0.11
54 66 0.41
55 52 0.32
56 7 0.04
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (54 bp):
CTGCTCTCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGT
Found at i:74800 original size:45 final size:47
Alignment explanation
Indices: 74693--74835 Score: 134
Period size: 48 Copynumber: 3.0 Consensus size: 47
74683 ATAAACAGGT
* * * *
74693 CCGCT-CCTATTCCTTCAGAGAGTATAAGACTCAATCTTTA-ACAAACTTG
1 CCGCTCCCTATTCCTT-ATAGAGTATATGACTCGATCTTCATA-AAA--TG
*
74742 TCTGCTCCCTATTCCTT-TAGAG-AGTA-GACTCGATCTTCATAAAATG
1 -CCGCTCCCTATTCCTTATAGAGTA-TATGACTCGATCTTCATAAAATG
*
74788 CCGCTCCCTATTCCTTCATAGAGTATATGACTCGATTTTCATAAAATG
1 CCGCTCCCTATTCCTT-ATAGAGTATATGACTCGATCTTCATAAAATG
74836 AGTTTGCTTC
Statistics
Matches: 80, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
45 15 0.19
46 2 0.03
47 7 0.09
48 35 0.44
49 7 0.09
50 4 0.05
51 10 0.12
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (47 bp):
CCGCTCCCTATTCCTTATAGAGTATATGACTCGATCTTCATAAAATG
Found at i:74898 original size:35 final size:36
Alignment explanation
Indices: 74837--74906 Score: 108
Period size: 35 Copynumber: 2.0 Consensus size: 36
74827 CATAAAATGA
74837 GTTTGCTTCACTAATCTTCCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTA-AGATG
*
74874 GTTTGCTT-ACTACTCTT-CGTGAAGGCTTAAGAT
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGAT
74907 TGACCTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 4 0.12
35 12 0.38
36 8 0.25
37 8 0.25
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGATG
Found at i:75204 original size:19 final size:20
Alignment explanation
Indices: 75180--75221 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
75170 GTCATCATGC
75180 AATTATGAATGT-TGATCCT
1 AATTATGAATGTATGATCCT
75199 AATTATGAATGTATGATCCT
1 AATTATGAATGTATGATCCT
75219 AAT
1 AAT
75222 CATGCCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (20 bp):
AATTATGAATGTATGATCCT
Found at i:76198 original size:6 final size:6
Alignment explanation
Indices: 76180--76254 Score: 51
Period size: 6 Copynumber: 11.5 Consensus size: 6
76170 CTTTTATTTC
* * * *
76180 TTCTTT TTTTTT TTCTTTT TTCTTT TTCCATTT TCCATT TTCATTT TTATTT
1 TTCTTT TTCTTT TTC-TTT TTCTTT TT-C-TTT TTCTTT TTC-TTT TTCTTT
*
76232 TTCATTT TTCATTT TTCATT TTC
1 TTC-TTT TTC-TTT TTCTTT TTC
76255 ATTT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
6 26 0.47
7 25 0.45
8 4 0.07
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (6 bp):
TTCTTT
Found at i:76199 original size:13 final size:13
Alignment explanation
Indices: 76180--76253 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
76170 CTTTTATTTC
76180 TTCTTTTTT-TTT
1 TTCTTTTTTCTTT
76192 TTCTTTTTTCTTT
1 TTCTTTTTTCTTT
* * *
76205 TTCCATTTTCCATT
1 TT-CTTTTTTCTTT
* *
76219 TTCATTTTTATTT
1 TTCTTTTTTCTTT
*
76232 TTCATTTTTCATTT
1 TTCTTTTTTC-TTT
76246 TTCATTTT
1 TTC-TTTT
76254 CATTT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
12 9 0.18
13 22 0.44
14 16 0.32
15 3 0.06
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCTTTTTTCTTT
Found at i:76213 original size:7 final size:6
Alignment explanation
Indices: 76197--76258 Score: 61
Period size: 7 Copynumber: 9.5 Consensus size: 6
76187 TTTTTTTCTT
* *
76197 TTTTCT TTTTCCA TTTTCCA TTTTCA TTTTTA TTTTTCA TTTTTCA TTTTTCA
1 TTTTCA TTTT-CA TTTT-CA TTTTCA TTTTCA -TTTTCA -TTTTCA -TTTTCA
76250 TTTTCA TTT
1 TTTTCA TTT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
6 20 0.39
7 31 0.61
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCA
Found at i:76254 original size:13 final size:13
Alignment explanation
Indices: 76197--76258 Score: 74
Period size: 13 Copynumber: 4.7 Consensus size: 13
76187 TTTTTTTCTT
76197 TTTTC-TTTTTCCA
1 TTTTCATTTTT-CA
76210 TTTTCCA-TTTTCA
1 TTTT-CATTTTTCA
*
76223 TTTTTATTTTTCA
1 TTTTCATTTTTCA
76236 TTTTTCATTTTTCA
1 -TTTTCATTTTTCA
76250 TTTTCATTT
1 TTTTCATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
12 1 0.02
13 25 0.58
14 17 0.40
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTCATTTTTCA
Done.