Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008422.1 Hibiscus syriacus cultivar Beakdansim tig00111203_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: 70002
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2352 original size:3 final size:3
Alignment explanation
Indices: 2344--2445 Score: 138
Period size: 3 Copynumber: 34.3 Consensus size: 3
2334 TCCGTTTTAA
2344 ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ACTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT
* *
2389 -TT TTT ATT ATAT ATT A-T ATT ATT ATT ACT ATT ATT ATT ATT ATT
1 ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
2433 ATT ATT ATC ATT A
1 ATT ATT ATT ATT A
2446 AATAAATATT
Statistics
Matches: 89, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
2 6 0.07
3 78 0.88
4 5 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3489 original size:21 final size:20
Alignment explanation
Indices: 3443--3485 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
3433 CTGATATTTT
*
3443 AATT-ATTTTTATTTTTTAC
1 AATTAATTTTTATATTTTAC
* *
3462 TATTAATTTTTATATTTTGC
1 AATTAATTTTTATATTTTAC
3482 AATT
1 AATT
3486 TAATCTTATA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTAATTTTTATATTTTAC
Found at i:11555 original size:75 final size:75
Alignment explanation
Indices: 11432--11601 Score: 220
Period size: 75 Copynumber: 2.3 Consensus size: 75
11422 ATAAAAAAAT
* *
11432 AAATGCTAGGGCATGCTGAAACCCCATTTCAATCATAATTAGGAATATTGATA-T-ATTTTGAAC
1 AAATGATAGGGCATGCTGAAACCCCATTTCAATCAAAATTAGGAATATT-A-ACTCATTTTGAAC
11495 GTTTGTATCAAC
64 GTTTGTATCAAC
* **
11507 AAATGATGGGGCATGCTGAAAGTCCATTTCAATCAGAAATT-GGAATATTAACTCATTTTGAACG
1 AAATGATAGGGCATGCTGAAACCCCATTTCAATCA-AAATTAGGAATATTAACTCATTTTGAACG
* *
11571 TTTGTATTAGC
65 TTTGTATCAAC
*
11582 AAATGTTAGGGCATGCTGAA
1 AAATGATAGGGCATGCTGAA
11602 GACTCATGTC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
73 1 0.01
74 2 0.02
75 76 0.92
76 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.32
Consensus pattern (75 bp):
AAATGATAGGGCATGCTGAAACCCCATTTCAATCAAAATTAGGAATATTAACTCATTTTGAACGT
TTGTATCAAC
Found at i:13758 original size:45 final size:45
Alignment explanation
Indices: 13702--14059 Score: 522
Period size: 45 Copynumber: 8.0 Consensus size: 45
13692 ATATTTAAAA
* * *
13702 CCTCC-GGTCATCTATAAGACCTACAGTGCTTGATGTTTTCAAAG
1 CCTCCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAG
* ** *
13746 CCTCCGGGTCATCTGTAAGCCCTTCAGTTTATGATGTTTTCAAAT
1 CCTCCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAG
*
13791 CCTCTGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAG
1 CCTCCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAG
*
13836 CCTCCGGGTCATCTGTAAGCCCTATAGTGCATGATGTTTTCAAAG
1 CCTCCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAG
* * * *
13881 CCTTCGGGTCATCTGTAATCCCTTCAGTGCAAGATGTTTTCAAAG
1 CCTCCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAG
* * *
13926 CCTCCGGGTCATTTGTAAGCCCTTCAGTGCATGATGTTTTTAAAG
1 CCTCCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAG
*
13971 CCTCCGGGTCATCTGTAAG-CCTGTCAGTGCATGATGTTTTCAAAG
1 CCTCCGGGTCATCTGTAAGCCCT-ACAGTGCATGATGTTTTCAAAG
* *
14016 CCTCCGGGTCATCTGTAAGACCTACAGTGCAGGATGTTTTCAAA
1 CCTCCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAA
14060 AAGCCTTCTG
Statistics
Matches: 283, Mismatches: 28, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
44 8 0.03
45 272 0.96
46 3 0.01
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.32
Consensus pattern (45 bp):
CCTCCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAG
Found at i:15136 original size:107 final size:107
Alignment explanation
Indices: 15010--15223 Score: 349
Period size: 107 Copynumber: 2.0 Consensus size: 107
15000 AACCCCAAAC
*
15010 GTCACCGAAGAACTAAAAATACCGAAGGTATTTTCTTAGATCTAGGAAATATC-GGGGATTTTTA
1 GTCACCGAAGAACTAAAAATACCGAAGGTATTTTCTTAGATCTAGGAAAT-TCTAGGGATTTTTA
*
15074 GGGGAAATAGAGGCCATATTCGGTCTTAGGGTTAAAAGAGGGA
65 GGGGAAATAGAGGCCATATTCGGCCTTAGGGTTAAAAGAGGGA
* * *
15117 GTCACCGGAGAACTGAAAATTCCGAAGGTATTTTCTTAGATCTAGGAAATTCTAGGGATTTTTAG
1 GTCACCGAAGAACTAAAAATACCGAAGGTATTTTCTTAGATCTAGGAAATTCTAGGGATTTTTAG
* *
15182 GGGGAATGGAGGCCATATTCGGCCTTAGGGTTAAAAGAGGGA
66 GGGAAATAGAGGCCATATTCGGCCTTAGGGTTAAAAGAGGGA
15224 AATTCGAAGC
Statistics
Matches: 99, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
106 2 0.02
107 97 0.98
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.27
Consensus pattern (107 bp):
GTCACCGAAGAACTAAAAATACCGAAGGTATTTTCTTAGATCTAGGAAATTCTAGGGATTTTTAG
GGGAAATAGAGGCCATATTCGGCCTTAGGGTTAAAAGAGGGA
Found at i:16011 original size:2 final size:2
Alignment explanation
Indices: 16004--16028 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15994 AAATATTATT
16004 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
16029 TTGATTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19351 original size:82 final size:83
Alignment explanation
Indices: 19166--19355 Score: 258
Period size: 82 Copynumber: 2.3 Consensus size: 83
19156 CAAAATGGTA
* * * * *
19166 ACTTTAGCGGCGTTTCTTTTCAAACGCCGCAATAGCGTTCACCTATAGTGGTGTTTTTTCAATAA
1 ACTTTAGCGGCGTTTCTATACAAACGACGCAATAGCATTCACCTATAGTGGCGTTTTTTCAATAA
19231 ATGCCTCAACAGATTAGT
66 ATGCCTCAACAGATTAGT
* * *
19249 ACTTTAGCGGCATTTTTATACAAACGACGTAATAGCATTCACCTATAGTGGCG-TTTTTCAATAA
1 ACTTTAGCGGCGTTTCTATACAAACGACGCAATAGCATTCACCTATAGTGGCGTTTTTTCAATAA
*
19313 ATGCCGT-AACATATTAGT
66 ATGCC-TCAACAGATTAGT
* *
19331 ACTTTAGCAGCGCTTCTATACAAAC
1 ACTTTAGCGGCGTTTCTATACAAAC
19356 ACCGCTAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
82 47 0.51
83 46 0.49
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (83 bp):
ACTTTAGCGGCGTTTCTATACAAACGACGCAATAGCATTCACCTATAGTGGCGTTTTTTCAATAA
ATGCCTCAACAGATTAGT
Found at i:19380 original size:82 final size:82
Alignment explanation
Indices: 19208--19388 Score: 190
Period size: 82 Copynumber: 2.2 Consensus size: 82
19198 TAGCGTTCAC
* * * *
19208 CTATAGTGGTGTTTTTTCAATAAATGCCTCAACAGATTAGTACTTTAGCGGCATTTTTATACAAA
1 CTATAGTGGCG-TTTTTCAATAAATGCCTCAACAGATTAGTACTTTAGCAGCACTTCTATACAAA
* * *
19273 CGACGTAATAGCATTCAC
65 CGACGTAATAGAACTCAA
* *
19291 CTATAGTGGCGTTTTTCAATAAATGCCGT-AACATATTAGTACTTTAGCAGCGCTTCTATACAAA
1 CTATAGTGGCGTTTTTCAATAAATGCC-TCAACAGATTAGTACTTTAGCAGCACTTCTATACAAA
19355 C-ACCGCTAA-A-AACTCATA
65 CGA-CG-TAATAGAACTCA-A
* *
19373 CTTTAGTGGCATTTTT
1 CTATAGTGGCGTTTTT
19389 ATACAAACAC
Statistics
Matches: 83, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
81 5 0.06
82 64 0.77
83 14 0.17
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (82 bp):
CTATAGTGGCGTTTTTCAATAAATGCCTCAACAGATTAGTACTTTAGCAGCACTTCTATACAAAC
GACGTAATAGAACTCAA
Found at i:20267 original size:42 final size:41
Alignment explanation
Indices: 20185--20280 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
20175 GCTAAAACTC
* ***
20185 ATACTTTAGTGGCGTTTATTTGACAAACGCCGTTACAAATA
1 ATACTTTAGTGGCGTTTATTTGAAAAACGCCACCACAAATA
* *
20226 AGTACTTTAGTGGCGTTTGTTT-AAAAACGCTACCACAAAATA
1 A-TACTTTAGTGGCGTTTATTTGAAAAACGCCACCAC-AAATA
*
20268 ATTCTTTAGTGGC
1 ATACTTTAGTGGC
20281 ATTTTTAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 21 0.46
42 25 0.54
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (41 bp):
ATACTTTAGTGGCGTTTATTTGAAAAACGCCACCACAAATA
Found at i:23239 original size:59 final size:58
Alignment explanation
Indices: 23147--23261 Score: 203
Period size: 59 Copynumber: 2.0 Consensus size: 58
23137 TATTCACACT
*
23147 ATGGATGAACCATATGTATTTTCTTCTCAAGTGAAACAAGTTTTTTACTATCACGATTG
1 ATGGATGAACCATATGCATTTTCTTCTCAAGTGAAACAAG-TTTTTACTATCACGATTG
*
23206 ATGGATGAACCATATGCATTTTCTTCTCAAGTGAAACAAGTTTTTACTGTCACGAT
1 ATGGATGAACCATATGCATTTTCTTCTCAAGTGAAACAAGTTTTTACTATCACGAT
23262 CCAATGGATG
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
58 15 0.28
59 39 0.72
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (58 bp):
ATGGATGAACCATATGCATTTTCTTCTCAAGTGAAACAAGTTTTTACTATCACGATTG
Found at i:24839 original size:99 final size:99
Alignment explanation
Indices: 24703--24898 Score: 374
Period size: 99 Copynumber: 2.0 Consensus size: 99
24693 GATTTGAATT
*
24703 ATGTTTTATTTATATATGTAGTATGCCATTTTTATTTGAATTAATTATTTACTTTATTATTAGGA
1 ATGTTTTATTTATATATGTAGTATGACATTTTTATTTGAATTAATTATTTACTTTATTATTAGGA
24768 AAAATTGAGGGAGAAAAGGGCGGAGTATGAAGCC
66 AAAATTGAGGGAGAAAAGGGCGGAGTATGAAGCC
*
24802 ATGTTTTATTTATATATGTAGTATGATATTTTTATTTGAATTAATTATTTACTTTATTATTAGGA
1 ATGTTTTATTTATATATGTAGTATGACATTTTTATTTGAATTAATTATTTACTTTATTATTAGGA
24867 AAAATTGAGGGAGAAAAGGGCGGAGTATGAAG
66 AAAATTGAGGGAGAAAAGGGCGGAGTATGAAG
24899 TTACGGCTTC
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.34, C:0.04, G:0.20, T:0.41
Consensus pattern (99 bp):
ATGTTTTATTTATATATGTAGTATGACATTTTTATTTGAATTAATTATTTACTTTATTATTAGGA
AAAATTGAGGGAGAAAAGGGCGGAGTATGAAGCC
Found at i:27615 original size:20 final size:21
Alignment explanation
Indices: 27590--27641 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
27580 TTTTCCCAAT
*
27590 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
27610 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
27631 TCGCAATGCGA
1 TCGCAATGCGA
27642 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:27655 original size:20 final size:20
Alignment explanation
Indices: 27630--27743 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
27620 AATTGGGAAA
*
27630 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
27650 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
** * *
27670 ATCGCAATACGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
27691 ATCGCAACGAGATACTAACT
1 ATCGCAACGCGATACTGACT
* *
27711 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
27731 TTCGCAACGCGAT
1 ATCGCAACGCGAT
27744 TTACATAGCG
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 62 0.79
21 12 0.15
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:28314 original size:19 final size:19
Alignment explanation
Indices: 28286--28470 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
28276 GAAATAACTA
28286 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
28305 TCGCGCTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
28324 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
28343 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
28363 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
28379 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
28396 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
28410 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
28429 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
* *
28449 ATCTCGTTACGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
28469 TC
1 TC
28471 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 48 0.35
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:28365 original size:39 final size:38
Alignment explanation
Indices: 28286--28375 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
28276 GAAATAACTA
28286 TCGCGTTGCGATTTTCATTTCGCGCTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGCTGCGATTTTCATT
* *
28324 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GCTGCGATTTTCATT
28363 TCGCGTTGCGATT
1 TCGCGTTGCGATT
28376 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 22 0.45
39 27 0.55
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGCTGCGATTTTCATT
Found at i:28395 original size:33 final size:33
Alignment explanation
Indices: 28358--28445 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
28348 GTTGCGATTT
* *
28358 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
28391 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
28424 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
28446 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:28447 original size:20 final size:20
Alignment explanation
Indices: 28413--28470 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
28403 GCGATTCTCT
**
28413 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
28433 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
* *
28453 CGTTACGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
28471 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:30553 original size:21 final size:21
Alignment explanation
Indices: 30529--30595 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
30519 TCATTCCTCG
30529 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
30550 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
30571 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
30592 AGAG
1 AGAG
30596 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:30553 original size:42 final size:42
Alignment explanation
Indices: 30473--30595 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
30463 GCCCGACTCG
* * * * * *
30473 CCTATCATCCCTCAAGAGTCCACTCCTATCATTGAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
*
30515 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
* * * *
30557 ACTGTCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 CCTATCATTCCTCG-AGA-GTCCCCTCCCACCATTCAAGAG
30596 CCCGATTCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 61 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
Found at i:31989 original size:14 final size:14
Alignment explanation
Indices: 31954--31980 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31944 ATTGTTTAAT
31954 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
31968 TGATTTGTAAAAG
1 TGATTTGTAAAAG
31981 TTGTTTTGTT
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:0.26, T:0.37
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:32140 original size:33 final size:34
Alignment explanation
Indices: 32097--32173 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 34
32087 AAAAGTACTA
* *
32097 TCGCAATGCGAAAT-TAGCGTTGTGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
* **
32130 TCGCATTGCG-ATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
32163 TCGCATTGCGA
1 TCGCATTGCGA
32174 TAGTAATTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
32 2 0.05
33 35 0.95
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (34 bp):
TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
Found at i:32173 original size:19 final size:19
Alignment explanation
Indices: 32120--32174 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
32110 TTAGCGTTGT
32120 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
*
32139 GA--TTC-TCTCG--TTGC
1 GATTTTCATTTCGCATTGC
32153 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
32172 GAT
1 GAT
32175 AGTAATTTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 6 0.21
16 7 0.24
17 7 0.24
19 9 0.31
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:35775 original size:20 final size:20
Alignment explanation
Indices: 35738--35775 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35728 ATTCATTTGA
*
35738 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
35758 CTATCGCAACGAGGAAAT
1 CTATCGCAACGAGAAAAT
35776 CGCAATGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:35835 original size:19 final size:19
Alignment explanation
Indices: 35794--35861 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
35784 GAAATGAAAA
35794 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
35810 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
35827 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
35846 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
35862 TCGTTGGGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:35881 original size:20 final size:20
Alignment explanation
Indices: 35856--35893 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35846 TCGCATTGCG
* *
35856 ATTTTCTCGTTGGGATAGCC
1 ATTTTCGCGTTGCGATAGCC
35876 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
35894 TCTGTTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:35998 original size:14 final size:14
Alignment explanation
Indices: 35979--36015 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
35969 CATCAATTAA
35979 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
35993 ACAAATCATCTTTT
1 ACAAATCAACATTT
36007 ACAAATCAA
1 ACAAATCAA
36016 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:37918 original size:20 final size:19
Alignment explanation
Indices: 37883--37949 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
37873 GAAACTTAAA
37883 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
37902 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
37922 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
37941 ATCGCAACG
1 ATCGCAACG
37950 ACAAAATTGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:37961 original size:14 final size:14
Alignment explanation
Indices: 37938--37995 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
37928 ATGCGAAATG
37938 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
37952 AAAATTGCAATGCGAA
1 AAAATCGCAA--CGAC
37968 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
37984 AAAATCGCAACG
1 AAAATCGCAACG
37996 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:37980 original size:32 final size:33
Alignment explanation
Indices: 37922--38000 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
37912 GGAAATGGCT
37922 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
37955 ATTGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
37987 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
38001 CACAAATCGC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 28 0.65
33 15 0.35
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:38048 original size:14 final size:14
Alignment explanation
Indices: 38029--38086 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
38019 TTTCATTTCG
38029 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
38043 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
38059 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
38075 CGTTGCGATTTT
1 CGTTGCGATTTT
38087 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:38093 original size:33 final size:33
Alignment explanation
Indices: 38012--38102 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
38002 ACAAATCGCA
*
38012 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
38045 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
38077 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
38103 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:38121 original size:20 final size:19
Alignment explanation
Indices: 38087--38141 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
38077 TTGCGATTTT
*
38087 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
38106 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
38126 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
38142 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:38649 original size:18 final size:18
Alignment explanation
Indices: 38623--38667 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
38613 GTCGATCAGA
*
38623 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
38641 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
38659 TGATGGCTC
1 TGATGGCTC
38668 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:40012 original size:20 final size:20
Alignment explanation
Indices: 39987--40024 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39977 AATGGTTTCT
39987 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
40007 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
40025 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:40314 original size:22 final size:22
Alignment explanation
Indices: 40287--40330 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40277 GATGGAGATA
40287 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
40309 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
40331 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:40543 original size:20 final size:20
Alignment explanation
Indices: 40518--40570 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
40508 GATTATGTAT
*
40518 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
40538 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
40558 TATCTCGTTGCGA
1 TATCGCGTTGCGA
40571 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:40625 original size:20 final size:20
Alignment explanation
Indices: 40581--40673 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
40571 TTTTTTATTA
* **
40581 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
40602 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
40622 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
40643 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
40663 TCGCATTGCGA
1 TCGCATTGCGA
40674 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:40626 original size:41 final size:41
Alignment explanation
Indices: 40563--40673 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
40553 GTAAGTATCT
*
40563 CGTTGCGATTT-TTTATTATCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTA-T-TCGCATTGCGATTTTCCCAATTCG
40605 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
1 CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
40646 CGTTGCGATTTACTTATTCGCATTGCGA
1 CGTTGCGATTTACTTATTCGCATTGCGA
40674 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
41 52 0.78
42 12 0.18
43 3 0.04
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
CGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCG
Found at i:46055 original size:19 final size:20
Alignment explanation
Indices: 46031--46076 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
46021 AATGATTTTC
* *
46031 TTTTGAAAGCTAAAAT-AGA
1 TTTTGAAAACTAAAATGAAA
46050 TTTTGAAAACTAAAATGAAA
1 TTTTGAAAACTAAAATGAAA
46070 TTTTGAA
1 TTTTGAA
46077 GAAGGATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (20 bp):
TTTTGAAAACTAAAATGAAA
Found at i:48690 original size:2 final size:2
Alignment explanation
Indices: 48683--48737 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
48673 CTTAACAAAT
48683 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48725 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
48738 GTTAAAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52642 original size:51 final size:51
Alignment explanation
Indices: 52576--52720 Score: 195
Period size: 51 Copynumber: 2.8 Consensus size: 51
52566 AAATAATAAT
52576 ATATGGTAATACACACATATATACAAGCATAAAATAAATGTTTAAAACAATA
1 ATATGGTAATACACACATATATACAAGCATAAAA-AAATGTTTAAAACAATA
52628 ATATGGT-ATACACACATATATACAAGCAT-AAAAAATGTTTAAAACAATA
1 ATATGGTAATACACACATATATACAAGCATAAAAAAATGTTTAAAACAATA
* * * * *
52677 ATAAATGGTAATACGCACGTATATCCACGCATAAAGAATATGTT
1 AT--ATGGTAATACACACATATATACAAGCATAAA-AAAATGTT
52721 AGACAATGAT
Statistics
Matches: 83, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
49 19 0.23
50 3 0.04
51 27 0.33
52 25 0.30
53 2 0.02
54 7 0.08
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (51 bp):
ATATGGTAATACACACATATATACAAGCATAAAAAAATGTTTAAAACAATA
Found at i:52664 original size:49 final size:51
Alignment explanation
Indices: 52576--52720 Score: 195
Period size: 52 Copynumber: 2.8 Consensus size: 51
52566 AAATAATAAT
*
52576 ATATGGTAATACACACATATATACAAGCATAAAATAAATGTTTAAAACAATA
1 ATATGGTAATACACACATATATACAAGCAT-AAAGAAATGTTTAAAACAATA
52628 ATATGGT-ATACACACATATATACAAGCATAAA-AAATGTTTAAAACAATA
1 ATATGGTAATACACACATATATACAAGCATAAAGAAATGTTTAAAACAATA
* * * *
52677 ATAAATGGTAATACGCACGTATATCCACGCATAAAGAATATGTT
1 AT--ATGGTAATACACACATATATACAAGCATAAAGAA-ATGTT
52721 AGACAATGAT
Statistics
Matches: 84, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
49 19 0.23
50 3 0.04
51 27 0.32
52 28 0.33
53 2 0.02
54 5 0.06
ACGTcount: A:0.50, C:0.13, G:0.10, T:0.27
Consensus pattern (51 bp):
ATATGGTAATACACACATATATACAAGCATAAAGAAATGTTTAAAACAATA
Found at i:54670 original size:23 final size:23
Alignment explanation
Indices: 54627--54671 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
54617 ATAATAATAA
54627 ATATAAAAAATTATTTAAAAACT
1 ATATAAAAAATTATTTAAAAACT
* *
54650 ATATAATATAATTTTTTAAAAA
1 ATATAA-AAAATTATTTAAAAA
54672 TGTTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
ATATAAAAAATTATTTAAAAACT
Found at i:54735 original size:31 final size:31
Alignment explanation
Indices: 54692--54789 Score: 139
Period size: 31 Copynumber: 3.2 Consensus size: 31
54682 CTATATATTA
54692 TATATAAATTTTCAAAAATGTTTTTTAAAAAC
1 TATAT-AATTTTCAAAAATGTTTTTTAAAAAC
54724 TATATAATTTTCAAAAAATG-TTTTTAAAAAC
1 TATATAATTTTC-AAAAATGTTTTTTAAAAAC
* *
54755 TATATAATTTTCTAAAA--TATTTTAAAAAC
1 TATATAATTTTCAAAAATGTTTTTTAAAAAC
54784 TATATA
1 TATATA
54790 TCATATACAT
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
29 16 0.26
30 4 0.06
31 30 0.48
32 12 0.19
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (31 bp):
TATATAATTTTCAAAAATGTTTTTTAAAAAC
Found at i:54802 original size:37 final size:37
Alignment explanation
Indices: 54756--54846 Score: 114
Period size: 37 Copynumber: 2.4 Consensus size: 37
54746 TTTAAAAACT
54756 ATATA-ATTTTCTAAAAT-ATTTTAAAAACTATATATC
1 ATATACATTTTC-AAAATGATTTTAAAAACTATATATC
* * *
54792 ATATACATTTTCAAAATGTTTTTAGAAACTATATATT
1 ATATACATTTTCAAAATGATTTTAAAAACTATATATC
54829 ATATACGTATTTTCAAAA
1 ATATAC--ATTTTCAAAA
54847 AACTGTTTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
36 10 0.21
37 28 0.58
39 10 0.21
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (37 bp):
ATATACATTTTCAAAATGATTTTAAAAACTATATATC
Found at i:54866 original size:40 final size:37
Alignment explanation
Indices: 54755--54873 Score: 102
Period size: 37 Copynumber: 3.2 Consensus size: 37
54745 TTTTAAAAAC
*
54755 TATATA-ATTTTCTAAAATA-T-TTTAAAAACTATATAT
1 TATATACATTTTC-AAAA-ACTGTTTAGAAACTATATAT
* ** *
54791 CATATACATTTTCAAAATGTTTTTAGAAACTATATAT
1 TATATACATTTTCAAAAACTGTTTAGAAACTATATAT
*
54828 TATATACGTATTTTCAAAAAACTGTTT-GCAAACTATATAA
1 TATATAC--ATTTTC-AAAAACTGTTTAG-AAACTATATAT
54868 TATATA
1 TATATA
54874 TATAGATATA
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
36 10 0.15
37 27 0.40
39 7 0.10
40 24 0.35
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (37 bp):
TATATACATTTTCAAAAACTGTTTAGAAACTATATAT
Found at i:55994 original size:25 final size:26
Alignment explanation
Indices: 55960--56021 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
55950 CAACAAGGGC
*
55960 TTTTAAAAGACAATATAGTCAACA-T
1 TTTTAGAAGACAATATAGTCAACATT
* * *
55985 TTTTAGAAGAATAATTTAGTCAGCATT
1 TTTTAGAAG-ACAATATAGTCAACATT
56012 TTTTAGAAGA
1 TTTTAGAAGA
56022 ATTTCGGACG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 8 0.26
26 13 0.42
27 10 0.32
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (26 bp):
TTTTAGAAGACAATATAGTCAACATT
Found at i:57048 original size:21 final size:21
Alignment explanation
Indices: 57024--57063 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
57014 AGTTTCTTAA
57024 GCTTATTTATTAGAAAATAGG
1 GCTTATTTATTAGAAAATAGG
*
57045 GCTTATTTATTTGAAAATA
1 GCTTATTTATTAGAAAATA
57064 CCAATGCTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (21 bp):
GCTTATTTATTAGAAAATAGG
Found at i:58568 original size:18 final size:20
Alignment explanation
Indices: 58542--58581 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
58532 CTCATTTACA
58542 TTTACATTTTTACAT-TTAT
1 TTTACATTTTTACATATTAT
*
58561 TTTA-ATTTTTGCATATTAT
1 TTTACATTTTTACATATTAT
58580 TT
1 TT
58582 CATTTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.25, C:0.07, G:0.03, T:0.65
Consensus pattern (20 bp):
TTTACATTTTTACATATTAT
Found at i:59051 original size:15 final size:14
Alignment explanation
Indices: 59032--59081 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
59022 CGATTGGTTT
*
59032 ATTTTCGTTATTTA
1 ATTTTTGTTATTTA
59046 ATTTTT-TCTATTTA
1 ATTTTTGT-TATTTA
*
59060 AATTTTGTTATTTTA
1 ATTTTTGTTA-TTTA
59075 ATTTTTG
1 ATTTTTG
59082 CCTTAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 1 0.03
14 18 0.60
15 11 0.37
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.68
Consensus pattern (14 bp):
ATTTTTGTTATTTA
Found at i:59672 original size:136 final size:139
Alignment explanation
Indices: 59405--59706 Score: 423
Period size: 136 Copynumber: 2.2 Consensus size: 139
59395 TGAATAATGC
*
59405 ATAATTG-CTTAAAATTAATTAGGATTAGTATTAGAGCCTTCACTTTAGGCCTAATTTAAAATAT
1 ATAATTGAC-TAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTAATTTAAAATAT
* * * ** *
59469 AATCCTTAAATTTATGCAAATTCTTAATTTGGTTCTCGCTTTTTCTTGATGTTCCATTTTAATTA
65 AATCCTTAAATTTAGGCAAATTCTTAATTTGGTCCTCGCTTTTGCTCAAGGTTCCATTTTAATTA
*
59534 TTCGAATCGT
130 TTCGAATCGA
* * *
59544 ATAATTGACTAAAATTAATTAGGATTAATATTAGAG-CTTCA-TTTGGGCCTAATTTTAAATTTA
1 ATAATTGACTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTAATTTAAAATATA
* * **
59607 TTCTTTAAATTTAGGTGAATTCTT-ATTTGGTCCTCGCTTTTGCTCAAGGTTCCATTTTAATTAT
66 ATCCTTAAATTTAGGCAAATTCTTAATTTGGTCCTCGCTTTTGCTCAAGGTTCCATTTTAATTAT
59671 TCGAATCGA
131 TCGAATCGA
*
59680 ATAATTGATTAAAATTAATTAGGATTA
1 ATAATTGACTAAAATTAATTAGGATTA
59707 TTAATGTTAG
Statistics
Matches: 146, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
136 69 0.47
137 38 0.26
138 5 0.03
139 33 0.23
140 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (139 bp):
ATAATTGACTAAAATTAATTAGGATTAATATTAGAGCCTTCACTTTAGGCCTAATTTAAAATATA
ATCCTTAAATTTAGGCAAATTCTTAATTTGGTCCTCGCTTTTGCTCAAGGTTCCATTTTAATTAT
TCGAATCGA
Found at i:59814 original size:142 final size:136
Alignment explanation
Indices: 59405--59865 Score: 401
Period size: 136 Copynumber: 3.3 Consensus size: 136
59395 TGAATAATGC
* * * *
59405 ATAATTGCTTAAAATTAATTAGGATTAGTATTAGAGCCTTCACTTTAGGCCTAATTTAAAATATA
1 ATAATTGATTAAAATTAATTAGGATTAATATTAGAACC-TCA-TTTAGGCCTAATTTCAAAT-TA
** * * * * ** *
59470 ATCC-TTAAATTTATGCA-AATTCTTAATTTGGTTCTCGCTTTTTCTTGATGTTCCATTTTAATT
63 ATCCTTTAAACCTA-GGAGAATTCTT-ATTTGGTACTCGCTTATGCTCAAGGTTCCATTTTAATT
*
59533 ATTCGAATCGT
126 ATTCGAATCGA
* * * * * * *
59544 ATAATTGACTAAAATTAATTAGGATTAATATTAGAGCTTCATTTGGGCCTAATTTTAAATTTATT
1 ATAATTGATTAAAATTAATTAGGATTAATATTAGAACCTCATTTAGGCCTAATTTCAAATTAATC
** * * *
59609 CTTTAAATTTAGGTGAATTCTTATTTGGTCCTCGCTTTTGCTCAAGGTTCCATTTTAATTATTCG
66 CTTTAAACCTAGGAGAATTCTTATTTGGTACTCGCTTATGCTCAAGGTTCCATTTTAATTATTCG
59674 AATCGA
131 AATCGA
* * *
59680 ATAATTGATTAAAATTAATTAGGATTATTAATGTTAGAACCTCTATTTTAGGCTTAATTTCAAGC
1 ATAATTGATTAAAATTAATTAGG---ATTAATATTAGAACCTC-A-TTTAGGCCTAATTTCAA-A
* * * *
59745 TTAATCCTTT-AACCTAGGAGAATTTTTGATTTGGTATTCGCTTATGCTCGAGGTTCCATTTTGA
60 TTAATCCTTTAAACCTAGGAGAATTCTT-ATTTGGTACTCGCTTATGCTCAAGGTTCCATTTTAA
* *
59809 CTATTCGACTC-A
124 TTATTCGAATCGA
* * * * *
59821 ATAATTTATTAAACATGACTT-GGACTAATATTAGATCCTACATTT
1 ATAATTGATTAAA-ATTAATTAGGATTAATATTAGAACCT-CATTT
59866 TTAGGTTTAA
Statistics
Matches: 268, Mismatches: 43, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
136 70 0.26
137 36 0.13
138 17 0.06
139 49 0.18
140 1 0.00
141 42 0.16
142 53 0.20
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (136 bp):
ATAATTGATTAAAATTAATTAGGATTAATATTAGAACCTCATTTAGGCCTAATTTCAAATTAATC
CTTTAAACCTAGGAGAATTCTTATTTGGTACTCGCTTATGCTCAAGGTTCCATTTTAATTATTCG
AATCGA
Found at i:60405 original size:19 final size:19
Alignment explanation
Indices: 60378--60426 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
60368 TTCGCAGACC
*
60378 AAATATTTTTAGTAAAATA
1 AAATGTTTTTAGTAAAATA
* *
60397 AAATG-TTTTATTAAAATT
1 AAATGTTTTTAGTAAAATA
*
60415 ACATGTTTTTAG
1 AAATGTTTTTAG
60427 GTGTTCCAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (19 bp):
AAATGTTTTTAGTAAAATA
Found at i:61123 original size:12 final size:12
Alignment explanation
Indices: 61106--61130 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61096 TAATTTTTTT
61106 GAGACCTTCATA
1 GAGACCTTCATA
61118 GAGACCTTCATA
1 GAGACCTTCATA
61130 G
1 G
61131 TTATGGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (12 bp):
GAGACCTTCATA
Done.