Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 88 of 171
Found at i:28819262 original size:14 final size:14
Alignment explanation
Indices: 28819243--28819272 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
28819233 TTTTGGTTGG
28819243 TTATGATTTATAGC
1 TTATGATTTATAGC
28819257 TTATGATTTATAGC
1 TTATGATTTATAGC
28819271 TT
1 TT
28819273 GTTACATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (14 bp):
TTATGATTTATAGC
Found at i:28819344 original size:21 final size:21
Alignment explanation
Indices: 28819302--28819346 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
28819292 TTGTGCCTTT
*
28819302 TTTGGTGTTGTTTTTATGTTG
1 TTTGGTGTTGTTTTTATATTG
28819323 TTTGGTGTTG-TTTTATTATTG
1 TTTGGTGTTGTTTTTA-TATTG
28819344 TTT
1 TTT
28819347 CAGAATTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.07, C:0.00, G:0.24, T:0.69
Consensus pattern (21 bp):
TTTGGTGTTGTTTTTATATTG
Found at i:28826495 original size:32 final size:32
Alignment explanation
Indices: 28826450--28826517 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
28826440 CAGTAGTATT
* *
28826450 TGTCGAGTTGATTTTCACTAATTGTGCAAATC
1 TGTCGAGTCGATTTTCACCAATTGTGCAAATC
28826482 TGTCGAGTCGATTTTCACCAATTGTGCAAATC
1 TGTCGAGTCGATTTTCACCAATTGTGCAAATC
28826514 TGTC
1 TGTC
28826518 AAAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (32 bp):
TGTCGAGTCGATTTTCACCAATTGTGCAAATC
Found at i:28826610 original size:15 final size:17
Alignment explanation
Indices: 28826590--28826621 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
28826580 TTTTAGCACA
28826590 AATTAA-TTAT-TTTTT
1 AATTAAGTTATATTTTT
28826605 AATTAAGTTATATTTTT
1 AATTAAGTTATATTTTT
28826622 CGATGTTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
AATTAAGTTATATTTTT
Found at i:28832027 original size:41 final size:41
Alignment explanation
Indices: 28831977--28832217 Score: 349
Period size: 41 Copynumber: 5.9 Consensus size: 41
28831967 GCAAAAGATT
**
28831977 GAGCAATAGCGGCGCTTATGGAGAAA-CGCCGCTAAATATCG
1 GAGCAATAGCGGCGCTTATGG-GAAAGCGCCGCTAAAGGTCG
* ** *
28832018 GAGCAATAGCGGCACTTATAAGAATGCGCCGCTAAAGGTCG
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
*
28832059 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCT
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
** *
28832100 GAGCAATAGCGGCGCTTATAAGAAAGCGCCGCCAAAGGTCG
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
* *
28832141 GAGCAATAGCGGCGCTTATGGGAAATCGCCACTAAAGGTCG
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
*
28832182 GAGAAATAGCGGCGCTTATGGGAAAGCGCCGCTAAA
1 GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAA
28832218 ATTTTTACAT
Statistics
Matches: 176, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 3 0.02
41 173 0.98
ACGTcount: A:0.31, C:0.22, G:0.32, T:0.16
Consensus pattern (41 bp):
GAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCG
Found at i:28835377 original size:10 final size:9
Alignment explanation
Indices: 28835334--28835507 Score: 53
Period size: 8 Copynumber: 18.9 Consensus size: 9
28835324 GTTAAAAGAT
28835334 TTAATTAT-
1 TTAATTATA
28835342 TTAATTATA
1 TTAATTATA
*
28835351 TTAAAGTA-A
1 TT-AATTATA
*
28835360 ATAATTATA
1 TTAATTATA
28835369 TTAAATTAT-
1 TT-AATTATA
*
28835378 TTAATTATGT
1 TTAATTAT-A
28835388 TTAATTATGTA
1 TTAATTA--TA
28835399 TTTAATTATA
1 -TTAATTATA
* *
28835409 -AACAGTATCGA
1 TTA-ATTAT--A
28835420 TTAATTA-A
1 TTAATTATA
* *
28835428 ATATTTA-A
1 TTAATTATA
*
28835436 GTTAA-TAGA
1 -TTAATTATA
28835445 TTTAATTAT-
1 -TTAATTATA
28835454 TTAATTATA
1 TTAATTATA
*
28835463 TTAAAGTA-A
1 TT-AATTATA
*
28835472 ATAATTATA
1 TTAATTATA
28835481 TTAAATTAT-
1 TT-AATTATA
*
28835490 TTAATTATGT
1 TTAATTAT-A
28835500 TTAATTAT
1 TTAATTAT
28835508 GTATTTAATT
Statistics
Matches: 125, Mismatches: 19, Indels: 42
0.67 0.10 0.23
Matches are distributed among these distances:
8 46 0.37
9 27 0.22
10 39 0.31
11 4 0.03
12 9 0.07
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (9 bp):
TTAATTATA
Found at i:28835382 original size:18 final size:18
Alignment explanation
Indices: 28835336--28835883 Score: 155
Period size: 18 Copynumber: 29.3 Consensus size: 18
28835326 TAAAAGATTT
28835336 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
28835354 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
*
28835372 AATTATTTAATTATGTTTA
1 AATTATTTAATTAT-ATTA
28835391 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* **
28835410 ACAGTA-TCGATTA-ATTA
1 A-ATTATTTAATTATATTA
*
28835427 AA-TATTTAAGTTAATAGATTT
1 AATTATTTAA-TT-AT--ATTA
28835448 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
28835466 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
*
28835484 AATTATTTAATTATGTTTA
1 AATTATTTAATTAT-ATTA
28835503 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* **
28835522 ACAGTA-TCGATTA-ATTA
1 A-ATTATTTAATTATATTA
*
28835539 AA-TATTTAAGTTAATAGATTT
1 AATTATTTAA-TT-AT--ATTA
28835560 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
28835578 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
* *
28835596 AATTATTTAATCATGTTTA
1 AATTATTTAATTAT-ATTA
28835615 ATTATGTATTTAATTATA--A
1 A--AT-TATTTAATTATATTA
* * ***
28835634 ACAGTAATCCTTTA-ATTA
1 A-ATTATTTAATTATATTA
* * *
28835652 AA-TATTTACGTTAAAAGATTT
1 AATTATTTA-ATT---ATATTA
28835673 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
* **
28835691 AAGTAAATAATTATATTA
1 AATTATTTAATTATATTA
*
28835709 AATTATTTAATTATGTTTA
1 AATTATTTAATTAT-ATTA
**
28835728 ATTATGTATTTAATTATAAACA
1 A--AT-TATTTAATTAT-ATTA
28835750 ATATTGA-TTAATTAT-TTA
1 A-ATT-ATTTAATTATATTA
* *
28835768 ATTATATTTAATTA-ACT-
1 AAT-TATTTAATTATATTA
* * *
28835785 ATTTAATTTAA-AATATTT
1 AATT-ATTTAATTATATTA
*** **
28835803 TCGTAAATAATTATA-TA
1 AATTATTTAATTATATTA
* *
28835820 TAATTATTTAATTTTATTT
1 -AATTATTTAATTATATTA
*
28835839 AATTATTTAATTGAAAATATTT
1 AATTATTTAATT----ATATTA
28835861 AATTATTTAATTATATTA
1 AATTATTTAATTATATTA
28835879 AATTA
1 AATTA
28835884 AATATTTAAT
Statistics
Matches: 385, Mismatches: 89, Indels: 112
0.66 0.15 0.19
Matches are distributed among these distances:
15 6 0.02
16 22 0.06
17 39 0.10
18 166 0.43
19 23 0.06
20 14 0.04
21 33 0.09
22 82 0.21
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
AATTATTTAATTATATTA
Found at i:28835446 original size:112 final size:112
Alignment explanation
Indices: 28835277--28835763 Score: 884
Period size: 112 Copynumber: 4.3 Consensus size: 112
28835267 AATAATTAAA
*
28835277 TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
28835342 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
66 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
*
28835389 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAATAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
28835454 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
66 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
*
28835501 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAATAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
*
28835566 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTT
66 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
** *
28835613 TAATTATGTATTTAATTATAAACAGTAATCCTTTAATTAAATATTTACGTTAAAAGATTTAATTA
1 TAATTATGTATTTAATTATAAACAGT-ATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTA
28835678 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
65 TTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
* *
28835726 TAATTATGTATTTAATTATAAACAATATTGATTAATTA
1 TAATTATGTATTTAATTATAAACAGTATCGATTAATTA
28835764 TTTAATTATA
Statistics
Matches: 362, Mismatches: 12, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
112 256 0.71
113 106 0.29
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (112 bp):
TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
Found at i:28835714 original size:10 final size:9
Alignment explanation
Indices: 28835671--28835903 Score: 54
Period size: 8 Copynumber: 25.8 Consensus size: 9
28835661 GTTAAAAGAT
28835671 TTAATTAT-
1 TTAATTATA
28835679 TTAATTATA
1 TTAATTATA
*
28835688 TTAAAGTA-A
1 TT-AATTATA
*
28835697 ATAATTATA
1 TTAATTATA
28835706 TTAAATTAT-
1 TT-AATTATA
*
28835715 TTAATTATGT
1 TTAATTAT-A
28835725 TTAATTATGTA
1 TTAATTA--TA
28835736 TTTAATTATA
1 -TTAATTATA
* *
28835746 -AACAATATTGA
1 TTA-ATTA-T-A
28835757 TTAATTAT-
1 TTAATTATA
28835765 TTAATTATA
1 TTAATTATA
28835774 TTTAATTA-A
1 -TTAATTATA
* *
28835783 CTATTTA-A
1 TTAATTATA
*
28835791 TTTAA-AATA
1 -TTAATTATA
*
28835800 TT--TTCGTAA
1 TTAATT-AT-A
*
28835809 ATAATTATA
1 TTAATTATA
28835818 TATAATTAT-
1 T-TAATTATA
*
28835827 TTAATTTTA
1 TTAATTATA
28835836 TTTAATTAT-
1 -TTAATTATA
28835845 TTAATTGA-A
1 TTAATT-ATA
28835854 --AA-TAT-
1 TTAATTATA
28835859 TTAATTAT-
1 TTAATTATA
28835867 TTAATTATA
1 TTAATTATA
28835876 TTAAATTAAATA
1 TT-AATT--ATA
28835888 TTTAATTAT-
1 -TTAATTATA
28835897 TTAATTA
1 TTAATTA
28835904 ATAAAAACAG
Statistics
Matches: 168, Mismatches: 21, Indels: 72
0.64 0.08 0.28
Matches are distributed among these distances:
5 1 0.01
6 1 0.01
7 4 0.02
8 67 0.40
9 22 0.13
10 49 0.29
11 6 0.04
12 16 0.10
13 2 0.01
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (9 bp):
TTAATTATA
Found at i:28835794 original size:113 final size:111
Alignment explanation
Indices: 28835277--28835894 Score: 565
Period size: 112 Copynumber: 5.6 Consensus size: 111
28835267 AATAATTAAA
* * * * * *
28835277 TAATTATGTATTTAATTATAAACAGTA--TCAATTAATTAAATAT-TTAAGTTAAAAGATTTAAT
1 TAATTATGTATTTAATTATAAACAATATTTTAATTATTTAATTATATTAAATT-AAATATTT-A-
28835339 TATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
63 -ATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
* ** * * * *
28835389 TAATTATGTATTTAATTATAAACAGTA--TCGATTAATTAAATAT-TTAAGTTAATAGATTTAAT
1 TAATTATGTATTTAATTATAAACAATATTTTAATTATTTAATTATATTAAATTAA-ATATTT-A-
28835451 TATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
63 -ATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
* ** * * * *
28835501 TAATTATGTATTTAATTATAAACAGTA--TCGATTAATTAAATAT-TTAAGTTAATAGATTTAAT
1 TAATTATGTATTTAATTATAAACAATATTTTAATTATTTAATTATATTAAATTAA-ATATTT-A-
*
28835563 TATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTT
63 -ATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
* ** * ** ** ** *
28835613 TAATTATGTATTTAATTATAAACAGTAATCCTTTAATTAAATATTTACGTTAAAAGATTTAATT-
1 TAATTATGTATTTAATTATAAACAAT-AT--TTTAATTATTTAATTATATTAAATTAAATATTTA
28835677 ATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
63 ATTTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
* *
28835726 TAATTATGTATTTAATTATAAACAATATTGATTAATTATTTAATTATATTTAATTAACTATTTAA
1 TAATTATGTATTTAATTATAAACAATATT--TTAATTATTTAATTATATTAAATTAAATATTTAA
* *** * *
28835791 TTTAA-AATATTTTCGTAAATAATTATA-TATAATTATTTAATTTTATT
64 TTTAATTATATTAAAGTAAATAATTATATTA-AATTATTTAATTATGTT
*
28835838 T-A--AT-TATTTAA-T-TGAA-AATA-TTTAATTATTTAATTATATTAAATTAAATATTTAATT
1 TAATTATGTATTTAATTATAAACAATATTTTAATTATTTAATTATATTAAATTAAATATTTAATT
28835895 ATTTAATTAA
Statistics
Matches: 458, Mismatches: 37, Indels: 32
0.87 0.07 0.06
Matches are distributed among these distances:
102 34 0.07
104 1 0.00
105 4 0.01
106 3 0.01
107 1 0.00
108 7 0.02
109 2 0.00
110 1 0.00
111 5 0.01
112 302 0.66
113 80 0.17
117 13 0.03
118 5 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (111 bp):
TAATTATGTATTTAATTATAAACAATATTTTAATTATTTAATTATATTAAATTAAATATTTAATT
TAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTT
Found at i:28835842 original size:225 final size:224
Alignment explanation
Indices: 28835277--28835844 Score: 838
Period size: 225 Copynumber: 2.5 Consensus size: 224
28835267 AATAATTAAA
* * * * *
28835277 TAATTATGTATTTAATTATAAACAGTATCAATTAATTAAATATTTAAGTTAAAAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAATATCGATTAATTAAATAATTAAGTTAATAGATCTAATTAT
*
28835342 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAATTA
66 TTAATAATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAATTA
* *
28835407 TAAACAGTATCGATTAATTAAATATTTAAGTTAATAGATTTAATTATTTAATTATATTAAAGTAA
131 TAAACAGTATCCATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
28835472 ATAATTATATTAAATTATTTAATTATGTT
196 ATAATTATATTAAATTATTTAATTATGTT
* * *
28835501 TAATTATGTATTTAATTATAAACAGTATCGATTAATTAAATATTTAAGTTAATAGATTTAATTAT
1 TAATTATGTATTTAATTATAAACAATATCGATTAATTAAATAATTAAGTTAATAGATCTAATTAT
* *
28835566 TTAATTATATTAAAGTAAATAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTA
66 TTAATAATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAATTA
* *
28835631 TAAACAGTAATCCTTTAATTAAATATTTACGTTAAAAGATTTAATTATTTAATTATATTAAAGTA
131 TAAACAGT-ATCCATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTA
28835696 AATAATTATATTAAATTATTTAATTATGTT
195 AATAATTATATTAAATTATTTAATTATGTT
* ** * *
28835726 TAATTATGTATTTAATTATAAACAATATTGATTAATTATTTAATTATATTTAATTA-A-CTATTT
1 TAATTATGTATTTAATTATAAACAATATCGATTAATTAAATAATTA-AGTTAA-TAGATCTAATT
*** * *
28835789 AATTTAA-AATATTTTCGTAAATAATTATA-TATAATTATTTAATTTTATTTAATTAT
64 -ATTTAATAATATTAAAGTAAATAATTATATTA-AATTATTTAATTATGTTTAATTAT
28835845 TTAATTGAAA
Statistics
Matches: 317, Mismatches: 22, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
224 137 0.43
225 166 0.52
226 12 0.04
227 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (224 bp):
TAATTATGTATTTAATTATAAACAATATCGATTAATTAAATAATTAAGTTAATAGATCTAATTAT
TTAATAATATTAAAGTAAATAATTATATTAAATTATTTAATTATGTTTAATTATGTATTTAATTA
TAAACAGTATCCATTAATTAAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAA
ATAATTATATTAAATTATTTAATTATGTT
Found at i:28835844 original size:8 final size:8
Alignment explanation
Indices: 28835810--28835903 Score: 74
Period size: 8 Copynumber: 11.8 Consensus size: 8
28835800 TTTTCGTAAA
28835810 TAATTATAT
1 TAATTAT-T
28835819 ATAATTATT
1 -TAATTATT
28835828 TAATTTTATT
1 TAA--TTATT
28835838 TAATTATT
1 TAATTATT
28835846 TAATTGA--
1 TAATT-ATT
*
28835853 -AAATATT
1 TAATTATT
28835860 TAATTATT
1 TAATTATT
28835868 TAATTATAT
1 TAATTAT-T
28835877 TAA--A-T
1 TAATTATT
*
28835882 TAAATATT
1 TAATTATT
28835890 TAATTATT
1 TAATTATT
28835898 TAATTA
1 TAATTA
28835904 ATAAAAACAG
Statistics
Matches: 71, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
5 5 0.07
6 3 0.04
7 2 0.03
8 40 0.56
9 6 0.08
10 15 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (8 bp):
TAATTATT
Found at i:28835869 original size:30 final size:30
Alignment explanation
Indices: 28835824--28835903 Score: 110
Period size: 30 Copynumber: 2.6 Consensus size: 30
28835814 TATATATAAT
28835824 TATTTAATTTTATTTAATTAT-TT-AATTGAAAA
1 TATTTAA--TTATTTAATTATATTAAATT--AAA
28835856 TATTTAATTATTTAATTATATTAAATTAAA
1 TATTTAATTATTTAATTATATTAAATTAAA
28835886 TATTTAATTATTTAATTA
1 TATTTAATTATTTAATTA
28835904 ATAAAAACAG
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
30 33 0.72
31 2 0.04
32 11 0.24
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (30 bp):
TATTTAATTATTTAATTATATTAAATTAAA
Found at i:28835884 original size:22 final size:21
Alignment explanation
Indices: 28835810--28835903 Score: 60
Period size: 18 Copynumber: 4.7 Consensus size: 21
28835800 TTTTCGTAAA
28835810 TAATTATATATAATTAT-TTAAT
1 TAATTAT-T-TAATTATATTAAT
28835832 T--TTATTTAATTAT-TTAAT
1 TAATTATTTAATTATATTAAT
*
28835850 TGAAAATATTTAATTAT-TTAAT
1 T--AATTATTTAATTATATTAAT
* * *
28835872 T-A-TATTAAATTA-AATATT
1 TAATTATTTAATTATATTAAT
28835890 TAATTATTTAATTA
1 TAATTATTTAATTA
28835904 ATAAAAACAG
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
18 26 0.43
19 3 0.05
20 13 0.22
22 18 0.30
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (21 bp):
TAATTATTTAATTATATTAAT
Found at i:28835981 original size:31 final size:33
Alignment explanation
Indices: 28835925--28835991 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
28835915 CCAACTATTT
28835925 AAGTAAAATGTTGTCACTAATATATATATTTTA
1 AAGTAAAATGTTGTCACTAATATATATATTTTA
28835958 AAGTAAAATGTTGTCACTAATATATAT-TTTTA
1 AAGTAAAATGTTGTCACTAATATATATATTTTA
28835990 AA
1 AA
28835992 TTTAAATCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 7 0.21
33 27 0.79
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (33 bp):
AAGTAAAATGTTGTCACTAATATATATATTTTA
Found at i:28841569 original size:66 final size:65
Alignment explanation
Indices: 28841423--28841579 Score: 206
Period size: 66 Copynumber: 2.4 Consensus size: 65
28841413 GCAAATTGCT
* *
28841423 CAACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAATATGATGAACTCCATCTA
1 CAACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAATATGAAGAACTCCACCTA
* * * * * * *
28841488 AAAATTAAAGAGGAGGTTGTAGTGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCTACCT
1 CAACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTC-AAAAAAATATGAAGAACTCCACCT
28841553 A
65 A
* *
28841554 CAACTTAAAGTGGAGGCAGCAGCGAG
1 CAACTTAAAGAGGAGGCTGCAGCGAG
28841580 GCAAGCGGAG
Statistics
Matches: 75, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
65 34 0.45
66 41 0.55
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.17
Consensus pattern (65 bp):
CAACTTAAAGAGGAGGCTGCAGCGAGAGAAGCAGAGGCTCAAAAAAATATGAAGAACTCCACCTA
Found at i:28841582 original size:11 final size:11
Alignment explanation
Indices: 28841566--28841603 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
28841556 ACTTAAAGTG
28841566 GAGGCAGCAGC
1 GAGGCAGCAGC
28841577 GAGGCA--AGC
1 GAGGCAGCAGC
28841586 GGAGGCAGCAGC
1 -GAGGCAGCAGC
28841598 GAGGCA
1 GAGGCA
28841604 AGCGAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
9 3 0.12
10 6 0.25
11 12 0.50
12 3 0.12
ACGTcount: A:0.29, C:0.24, G:0.47, T:0.00
Consensus pattern (11 bp):
GAGGCAGCAGC
Found at i:28841591 original size:21 final size:21
Alignment explanation
Indices: 28841565--28841617 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
28841555 AACTTAAAGT
28841565 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
28841586 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
* *
28841607 GAAGGAAGCAG
1 GGAGGCAGCAG
28841618 AGGCGACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.47, T:0.00
Consensus pattern (21 bp):
GGAGGCAGCAGCGAGGCAAGC
Found at i:28841838 original size:15 final size:15
Alignment explanation
Indices: 28841818--28841846 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28841808 ATTTGAAGTT
28841818 ATTGGTTGGATTTGC
1 ATTGGTTGGATTTGC
28841833 ATTGGTTGGATTTG
1 ATTGGTTGGATTTG
28841847 AATTTACAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.03, G:0.34, T:0.48
Consensus pattern (15 bp):
ATTGGTTGGATTTGC
Found at i:28842768 original size:18 final size:20
Alignment explanation
Indices: 28842736--28842772 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
28842726 AACATAAGAA
28842736 ATTTGTTTTTGATTTTTATG
1 ATTTGTTTTTGATTTTTATG
28842756 ATTT-TTTTT-ATTTTTAT
1 ATTTGTTTTTGATTTTTAT
28842773 TGACAAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (20 bp):
ATTTGTTTTTGATTTTTATG
Found at i:28846156 original size:12 final size:12
Alignment explanation
Indices: 28846107--28846166 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
28846097 TTGTTTATTA
*
28846107 TTCATTAACATTG
1 TTCATGAACA-TG
*
28846120 TTCGTGAACATG
1 TTCATGAACATG
* *
28846132 TTCAAT-TATATG
1 TTC-ATGAACATG
28846144 TTCATGAACATG
1 TTCATGAACATG
*
28846156 TTCGTGAACAT
1 TTCATGAACAT
28846167 TAAACAAACG
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
11 2 0.05
12 26 0.70
13 9 0.24
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (12 bp):
TTCATGAACATG
Found at i:28846222 original size:28 final size:28
Alignment explanation
Indices: 28846166--28846227 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
28846156 TTCGTGAACA
* * *
28846166 TTAAACAAACGAACATGAGCACATAATT
1 TTAAATAAACGAACATGAACACAAAATT
28846194 TTAAATAAACGAACATGAACA-AAACATT
1 TTAAATAAACGAACATGAACACAAA-ATT
*
28846222 TGAAAT
1 TTAAAT
28846228 TCTTAACGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.53, C:0.15, G:0.10, T:0.23
Consensus pattern (28 bp):
TTAAATAAACGAACATGAACACAAAATT
Found at i:28846435 original size:7 final size:7
Alignment explanation
Indices: 28846423--28846455 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
28846413 ATCTTGTCTT
28846423 CCATCCC
1 CCATCCC
28846430 CCAT-CC
1 CCATCCC
28846436 CCA-CCC
1 CCATCCC
28846442 CCATCCC
1 CCATCCC
28846449 CCATCCC
1 CCATCCC
28846456 GGCCCCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.42
7 14 0.58
ACGTcount: A:0.15, C:0.73, G:0.00, T:0.12
Consensus pattern (7 bp):
CCATCCC
Found at i:28849196 original size:22 final size:22
Alignment explanation
Indices: 28849171--28849220 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
28849161 AATTAACATC
28849171 TCTCGAAACAAATAAGTGTATG
1 TCTCGAAACAAATAAGTGTATG
*
28849193 TCTCGAAACAAATGAGTGTATG
1 TCTCGAAACAAATAAGTGTATG
28849215 TCTCGA
1 TCTCGA
28849221 GAGAAAAGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (22 bp):
TCTCGAAACAAATAAGTGTATG
Found at i:28852440 original size:28 final size:28
Alignment explanation
Indices: 28852408--28852479 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
28852398 GACGTCTTTT
** *
28852408 TTTACAAAGATAGTCACAAAGGCGTCCA
1 TTTACAAAGATAACCACAAAGGCATCCA
*
28852436 TTTACAAAGATAACCACACAGGCATCCA
1 TTTACAAAGATAACCACAAAGGCATCCA
28852464 TTTACAAAGATAACCA
1 TTTACAAAGATAACCA
28852480 TAAAAGCTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (28 bp):
TTTACAAAGATAACCACAAAGGCATCCA
Found at i:28855676 original size:30 final size:30
Alignment explanation
Indices: 28855642--28855699 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
28855632 ATTATTAAGT
28855642 CCTTAAAAGTTT-T-AAAAGTTTTAATTAAAC
1 CCTTAAAA-TTTATGAAAA-TTTTAATTAAAC
28855672 CCTTAAAATTTATGAAAATTTTAATTAA
1 CCTTAAAATTTATGAAAATTTTAATTAA
28855700 GCCCCCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 3 0.12
30 19 0.73
31 4 0.15
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (30 bp):
CCTTAAAATTTATGAAAATTTTAATTAAAC
Found at i:28858676 original size:23 final size:22
Alignment explanation
Indices: 28858634--28858685 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
28858624 GGAAAGTAAC
*
28858634 TAAAT-ATTTAATTTCGAAAAAT
1 TAAATAATTAAATTTC-AAAAAT
28858656 TAAATAATTAAATTTCAAAAAT
1 TAAATAATTAAATTTCAAAAAT
28858678 TAAA-AATT
1 TAAATAATT
28858686 TAGTGGTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.14
22 15 0.54
23 9 0.32
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (22 bp):
TAAATAATTAAATTTCAAAAAT
Found at i:28864420 original size:19 final size:19
Alignment explanation
Indices: 28864391--28864454 Score: 96
Period size: 19 Copynumber: 3.4 Consensus size: 19
28864381 TTTAATTTTC
28864391 ATTTC-AACTATAAGTTAA
1 ATTTCAAACTATAAGTTAA
28864409 ATTTCAAACTATAAGTTAA
1 ATTTCAAACTATAAGTTAA
*
28864428 ATTTCAAACTAGT-ATTTAA
1 ATTTCAAACTA-TAAGTTAA
28864447 ATTTCAAA
1 ATTTCAAA
28864455 TTAGCATTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
18 5 0.12
19 37 0.86
20 1 0.02
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.39
Consensus pattern (19 bp):
ATTTCAAACTATAAGTTAA
Found at i:28874374 original size:97 final size:97
Alignment explanation
Indices: 28874259--28874452 Score: 388
Period size: 97 Copynumber: 2.0 Consensus size: 97
28874249 GTCAATTTTA
28874259 TCATGGTTAGTCATTTAGGAAATATGGTGACTTTTTAGATAGATGAAAATGGAATTGATATGAAA
1 TCATGGTTAGTCATTTAGGAAATATGGTGACTTTTTAGATAGATGAAAATGGAATTGATATGAAA
28874324 TGAAATTGCATATATGATTTATGTATAAAAGG
66 TGAAATTGCATATATGATTTATGTATAAAAGG
28874356 TCATGGTTAGTCATTTAGGAAATATGGTGACTTTTTAGATAGATGAAAATGGAATTGATATGAAA
1 TCATGGTTAGTCATTTAGGAAATATGGTGACTTTTTAGATAGATGAAAATGGAATTGATATGAAA
28874421 TGAAATTGCATATATGATTTATGTATAAAAGG
66 TGAAATTGCATATATGATTTATGTATAAAAGG
28874453 ATATAACACT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.36
Consensus pattern (97 bp):
TCATGGTTAGTCATTTAGGAAATATGGTGACTTTTTAGATAGATGAAAATGGAATTGATATGAAA
TGAAATTGCATATATGATTTATGTATAAAAGG
Found at i:28879989 original size:58 final size:57
Alignment explanation
Indices: 28879895--28880040 Score: 181
Period size: 58 Copynumber: 2.5 Consensus size: 57
28879885 ATATATTATA
* * *
28879895 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAT-T-TTTATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATATATTAAATAAATTA-AT
*
28879952 ATTATTTTATTAAATTGTATTTAATAATAATTATATTAAAATATAATTAAATAAATTAAT
1 A-T-TTTTATTAAATTATATTTAATAATAATTATATTAAAATAT-ATTAAATAAATTAAT
28880012 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
28880041 CATTAAAATT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 1 0.01
58 50 0.64
59 10 0.13
60 7 0.09
61 10 0.13
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (57 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATATTAAATAAATTAAT
Found at i:28880037 original size:26 final size:26
Alignment explanation
Indices: 28879955--28880040 Score: 82
Period size: 26 Copynumber: 3.1 Consensus size: 26
28879945 ATTACATATT
*
28879955 ATTTTATTAAATTGTATTTAATAATA
1 ATTTTATTAAATTATATTTAATAATA
* *
28879981 ATTATATTAAAATATAATTAAATAAATTAATA
1 ATTTTATTAAATTAT-ATT---T-AA-TAATA
*
28880013 TTTTTATTAAATTATATTTAATAATA
1 ATTTTATTAAATTATATTTAATAATA
28880039 AT
1 AT
28880041 CATTAAAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
26 18 0.38
27 5 0.11
28 1 0.02
30 1 0.02
31 5 0.11
32 17 0.36
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (26 bp):
ATTTTATTAAATTATATTTAATAATA
Found at i:28880229 original size:16 final size:16
Alignment explanation
Indices: 28880204--28880248 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
28880194 AATTACTAAT
28880204 TACAGCTCTATTCCAG
1 TACAGCTCTATTCCAG
* *
28880220 TACAGTTCTATTCCAT
1 TACAGCTCTATTCCAG
*
28880236 TACACCTCTATTC
1 TACAGCTCTATTC
28880249 AATTATAGCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.07, T:0.38
Consensus pattern (16 bp):
TACAGCTCTATTCCAG
Found at i:28880253 original size:16 final size:16
Alignment explanation
Indices: 28880201--28880253 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
28880191 TTGAATTACT
28880201 AATTACAGCTCTATTC
1 AATTACAGCTCTATTC
* * *
28880217 CAGTACAGTTCTATTC
1 AATTACAGCTCTATTC
* *
28880233 CATTACACCTCTATTC
1 AATTACAGCTCTATTC
28880249 AATTA
1 AATTA
28880254 TAGCGAACCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.38
Consensus pattern (16 bp):
AATTACAGCTCTATTC
Found at i:28881901 original size:21 final size:21
Alignment explanation
Indices: 28881877--28881917 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28881867 GAGGAATTGT
*
28881877 GGGAAAAGAAGAAGGAAAGGC
1 GGGAAAAGAAAAAGGAAAGGC
* *
28881898 GGGAAAGGAAAAATGAAAGG
1 GGGAAAAGAAAAAGGAAAGG
28881918 TTAAAAAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.54, C:0.02, G:0.41, T:0.02
Consensus pattern (21 bp):
GGGAAAAGAAAAAGGAAAGGC
Found at i:28883308 original size:23 final size:23
Alignment explanation
Indices: 28883278--28883322 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
28883268 CCCATTTTAG
*
28883278 ATACACTCATATTTTTAATATAA
1 ATACACTCATATTTTAAATATAA
28883301 ATACACTCATATTTTAAATATA
1 ATACACTCATATTTTAAATATA
28883323 TATAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.42
Consensus pattern (23 bp):
ATACACTCATATTTTAAATATAA
Found at i:28884989 original size:15 final size:15
Alignment explanation
Indices: 28884966--28884996 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28884956 ATTTATGTAA
*
28884966 CATGGTTTAATTAAT
1 CATGATTTAATTAAT
28884981 CATGATTTAATTAAT
1 CATGATTTAATTAAT
28884996 C
1 C
28884997 TAATTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (15 bp):
CATGATTTAATTAAT
Found at i:28885722 original size:12 final size:12
Alignment explanation
Indices: 28885695--28885728 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
28885685 ATGATTATCA
*
28885695 TTTCTCTTTTTC
1 TTTCTTTTTTTC
28885707 -TTCTTTTTTTC
1 TTTCTTTTTTTC
28885718 TTTCTTTTTTT
1 TTTCTTTTTTT
28885729 TTTAATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:28890783 original size:3 final size:3
Alignment explanation
Indices: 28890775--28890806 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
28890765 TTGATCAAGA
28890775 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
28890807 GGGTAAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:28891969 original size:12 final size:12
Alignment explanation
Indices: 28891948--28891982 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28891938 TAAGCTAAAT
*
28891948 TATGAGTGAAAA
1 TATGATTGAAAA
28891960 TATGATTGAAAA
1 TATGATTGAAAA
*
28891972 TTTGATTGAAA
1 TATGATTGAAA
28891983 TGGTAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (12 bp):
TATGATTGAAAA
Found at i:28896497 original size:3 final size:3
Alignment explanation
Indices: 28896489--28896522 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
28896479 CCTTTCTCTT
28896489 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
28896523 CTTTTCCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28899845 original size:48 final size:48
Alignment explanation
Indices: 28899790--28899885 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
28899780 GAAGAGTTTC
28899790 AAATTTTACTCAAAGGTTTTACTGATAGGATTGTCTTATTTCATTTTA
1 AAATTTTACTCAAAGGTTTTACTGATAGGATTGTCTTATTTCATTTTA
28899838 AAATTTTACTCAAAGGTTTTACTGATAGGATTGTCTTATTTCATTTTA
1 AAATTTTACTCAAAGGTTTTACTGATAGGATTGTCTTATTTCATTTTA
28899886 CAAACATGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (48 bp):
AAATTTTACTCAAAGGTTTTACTGATAGGATTGTCTTATTTCATTTTA
Found at i:28904065 original size:17 final size:18
Alignment explanation
Indices: 28904043--28904084 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
28904033 CCCAATGAGA
*
28904043 TAAATTTGGTTTTAAA-T
1 TAAATTTGATTTTAAATT
28904060 TAAATTT-ATTTTAAATT
1 TAAATTTGATTTTAAATT
28904077 TAAATTTG
1 TAAATTTG
28904085 CACAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TAAATTTGATTTTAAATT
Found at i:28904118 original size:17 final size:17
Alignment explanation
Indices: 28904055--28904118 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
28904045 AATTTGGTTT
*
28904055 TAAA-TTAAATTTATTT
1 TAAATTTAAATTTATTA
*
28904071 TAAATTTAAATTTGCA-CA
1 TAAATTTAAATTT--ATTA
*
28904089 -AAATTTAAGTTTATTA
1 TAAATTTAAATTTATTA
*
28904105 TAAATATAAATTTA
1 TAAATTTAAATTTA
28904119 AAATTAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 30 0.81
19 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAATTTAAATTTATTA
Found at i:28906014 original size:29 final size:29
Alignment explanation
Indices: 28905967--28906081 Score: 128
Period size: 29 Copynumber: 4.0 Consensus size: 29
28905957 ATAGGTCCCT
28905967 AAACTATCCAAAAATTACATTTTAACCTCA
1 AAACT-TCCAAAAATTACATTTTAACCTCA
* * *
28905997 AAACTTCAAAAAACTACATTTTAACCTCG
1 AAACTTCCAAAAATTACATTTTAACCTCA
* *
28906026 AAACTTCCAAAAATTATCA-TTT-ACCCCC
1 AAACTTCCAAAAATTA-CATTTTAACCTCA
*
28906054 AAACATTCC-AAAATTCCATTTTAACCTC
1 AAAC-TTCCAAAAATTACATTTTAACCTC
28906082 GATTTCACCA
Statistics
Matches: 72, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
27 2 0.03
28 17 0.24
29 46 0.64
30 7 0.10
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.30
Consensus pattern (29 bp):
AAACTTCCAAAAATTACATTTTAACCTCA
Found at i:28906134 original size:29 final size:29
Alignment explanation
Indices: 28906045--28906199 Score: 75
Period size: 29 Copynumber: 5.3 Consensus size: 29
28906035 AAAATTATCA
*
28906045 TTTACCCCCAAACATTCCAAAATTCCATT
1 TTTACCCCCAAACCTTCCAAAATTCCATT
* * * *** * *
28906074 TTAACCTCGATTTC-ACCAAAAATTACC-GT
1 TTTACCCCCAAACCTTCC-AAAATT-CCATT
28906103 TTTACCCCCAAACCTTCCAAAATTCCATT
1 TTTACCCCCAAACCTTCCAAAATTCCATT
* ** **
28906132 TTTA-ACCCTGATTTTACCAAAAATTACCA-T
1 TTTACCCCCAAACCTT-CC-AAAATT-CCATT
* * *
28906162 TTTGCCCCCAAACCTTTCAAAATTTCATT
1 TTTACCCCCAAACCTTCCAAAATTCCATT
28906191 TTTGACCCC
1 TTT-ACCCC
28906200 AATTTCACCA
Statistics
Matches: 85, Mismatches: 31, Indels: 19
0.63 0.23 0.14
Matches are distributed among these distances:
28 12 0.14
29 45 0.53
30 19 0.22
31 9 0.11
ACGTcount: A:0.32, C:0.32, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTACCCCCAAACCTTCCAAAATTCCATT
Found at i:28906170 original size:59 final size:59
Alignment explanation
Indices: 28906032--28906256 Score: 285
Period size: 59 Copynumber: 3.8 Consensus size: 59
28906022 CTCGAAACTT
* *
28906032 CCAAAAATTATCA-TTTACCCCCAAACATTCCAAAATTCCA-TTTTAA-CCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCT-GATTTCA
* *
28906089 CCAAAAATTACCGTTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCTGATTTTA
1 CCAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCTGATTTCA
* * * * **
28906148 CCAAAAATTACCATTTTGCCCCCAAACCTTTCAAAATTTCATTTTTGACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCTGATTTCA
* * * * *
28906207 CCAAAAATTACCATTTCACCCTCGAACCTTACAAAATCCCATTTTTAACC
1 CCAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACC
28906257 ACGAATTTTC
Statistics
Matches: 145, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
57 11 0.08
58 26 0.18
59 105 0.72
60 3 0.02
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCTGATTTCA
Found at i:28906276 original size:118 final size:117
Alignment explanation
Indices: 28906032--28906287 Score: 290
Period size: 118 Copynumber: 2.2 Consensus size: 117
28906022 CTCGAAACTT
* * *
28906032 CCAAAAATTATCA--TTTACCCCCAAACATTCCAAAATTCCATTTTAACCTCGATTTCACCAAAA
1 CCAAAAATTA-CATTTTTGCCCCCAAACATTCCAAAATTCCATTTTAACCCCAATTTCACCAAAA
* * * *
28906095 ATTACCGTTTTACCCCCAAACCTTCCAAAATTCCATTTTTAACCCTGATTTTA
65 ATTACCATTTCACCCCCAAACCTTACAAAATCCCATTTTTAACCCTGATTTTA
* * * *
28906148 CCAAAAATTACCA-TTTTGCCCCCAAACCTTTCAAAATTTCATTTTTGACCCCAATTTCACCAAA
1 CCAAAAATTA-CATTTTTGCCCCCAAACATTCCAAAATTCCA-TTTTAACCCCAATTTCACCAAA
* *
28906212 AATTACCATTTCACCCTCGAACCTTACAAAATCCCATTTTTAACCAC-GAATTTT-
64 AATTACCATTTCACCCCCAAACCTTACAAAATCCCATTTTTAACC-CTG-ATTTTA
*
28906266 CTC-AAGATTACATTTTTGCCCC
1 C-CAAAAATTACATTTTTGCCCC
28906288 TCGAGAGTCA
Statistics
Matches: 119, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
116 12 0.10
117 25 0.21
118 75 0.63
119 7 0.06
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (117 bp):
CCAAAAATTACATTTTTGCCCCCAAACATTCCAAAATTCCATTTTAACCCCAATTTCACCAAAAA
TTACCATTTCACCCCCAAACCTTACAAAATCCCATTTTTAACCCTGATTTTA
Found at i:28918655 original size:200 final size:200
Alignment explanation
Indices: 28918305--28918946 Score: 1032
Period size: 200 Copynumber: 3.2 Consensus size: 200
28918295 ACAAAACATT
* *
28918305 GAGGCGATCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAGCGCTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
28918370 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* *
28918435 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCTAGAGAAGTGAATCAAAA
131 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
28918500 CAAGC
196 CAAGC
* * **
28918505 GAGGCGGTCATCTTCCTGATAAGATACAGAGAATAATACCAACTCAACATTCAACACGAGCCAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
28918570 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
28918635 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
131 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
28918700 CAAGC
196 CAAGC
* * * * * *
28918705 GAGACGGCCATCTTCCTGATGAGATACAGAGAAGAATATCAGCTCAACGCTCAACGCGAGCAAAT
1 GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
* * *
28918770 CTTCGAACCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTTC
66 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
* * * *
28918835 TGATGAGACACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGGATTAAAA
131 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
* **
28918900 AAAAT
196 CAAGC
* * *
28918905 GATCGCGGTCATCTTCCTGATGAGACACAGAGAAGAAGACCA
1 GA-GGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCA
28918947 GGTCAATGAA
Statistics
Matches: 407, Mismatches: 34, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
200 374 0.92
201 33 0.08
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (200 bp):
GAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAAT
CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
CAAGC
Found at i:28919302 original size:17 final size:18
Alignment explanation
Indices: 28919280--28919321 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
28919270 CCTAATGAGA
*
28919280 TAAATTTGGTTTTAAA-T
1 TAAATTTGATTTTAAATT
28919297 TAAATTT-ATTTTAAATT
1 TAAATTTGATTTTAAATT
28919314 TAAATTTG
1 TAAATTTG
28919322 CACAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TAAATTTGATTTTAAATT
Found at i:28919355 original size:17 final size:17
Alignment explanation
Indices: 28919292--28919355 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
28919282 AATTTGGTTT
*
28919292 TAAA-TTAAATTTATTT
1 TAAATTTAAATTTATTA
*
28919308 TAAATTTAAATTTGCA-CA
1 TAAATTTAAATTT--ATTA
*
28919326 -AAATTTAAGTTTATTA
1 TAAATTTAAATTTATTA
*
28919342 TAAATATAAATTTA
1 TAAATTTAAATTTA
28919356 AAATTAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
15 1 0.03
16 5 0.14
17 30 0.81
19 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (17 bp):
TAAATTTAAATTTATTA
Found at i:28921634 original size:21 final size:21
Alignment explanation
Indices: 28921605--28921659 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
28921595 CTTTAGGTTT
*
28921605 TTTA-ATTTGGATTTATAAAT
1 TTTATATTTGGATTTATAAAC
* *
28921625 TTTATGTTTGGATTTCTAAAC
1 TTTATATTTGGATTTATAAAC
28921646 TTTATATTTGGATT
1 TTTATATTTGGATT
28921660 ATGCTATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 4 0.13
21 26 0.87
ACGTcount: A:0.27, C:0.04, G:0.13, T:0.56
Consensus pattern (21 bp):
TTTATATTTGGATTTATAAAC
Found at i:28924401 original size:16 final size:16
Alignment explanation
Indices: 28924373--28924414 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
28924363 GGTTTGTATA
*
28924373 TATTTATTAATTT-TAT
1 TATTTATTTATTTGT-T
*
28924389 TATTTCTTTATTTGTT
1 TATTTATTTATTTGTT
28924405 TATTTATTTA
1 TATTTATTTA
28924415 ATAGATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
TATTTATTTATTTGTT
Found at i:28925293 original size:40 final size:40
Alignment explanation
Indices: 28925008--28925602 Score: 367
Period size: 39 Copynumber: 14.9 Consensus size: 40
28924998 GATCTGATGG
* * * *
28925008 TCTTCAA--TTGCCCTTTGGTTAGGGTTAAAGATTAGATT
1 TCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATT
* ** ** *
28925046 TCTTCAAT-TTG-CCTCATAATCGGGGTAAAAGATCAGATGG
1 TCTTCAATCTTGCCCTC-TAGTTAGGGTAAAAGATTGGAT-T
* *
28925086 TCTTTAATCTTGCCCTCTAGTTAGGGTAAAAGATTAGATT
1 TCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATT
* ** * * *
28925126 TCTTCAATC-TACCC-C-ATGATCGGGGTAAAAGATCGAATGG
1 TCTTCAATCTTGCCCTCTA-G-TTAGGGTAAAAGATTGGAT-T
* * *
28925166 TCTTTAATCTTGCCCTCTGGTTAGGGTAAAAGATTAGATT
1 TCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATT
* ** * *
28925206 TCTTCAAT-TTGCCC-CCATGATCGGGGTAAAAGATCGGATGG
1 TCTTCAATCTTGCCCTCTA-G-TTAGGGTAAAAGATTGGAT-T
*
28925247 TCTTCAATCCTGCCCTCTAGTTAGGGTAAAAGATTGGATT
1 TCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATT
* ** *
28925287 TTTTCAATC-TGCCC-C-ATGATCGGGGTAAAAG--TCGATT
1 TCTTCAATCTTGCCCTCTA-G-TTAGGGTAAAAGATTGGATT
28925324 GGTCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATT
1 --TCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATT
* * ** *
28925366 TTTTTAATC-TGCCC-C-ATGATCGGGGTAAAAG--TCGATT
1 TCTTCAATCTTGCCCTCTA-G-TTAGGGTAAAAGATTGGATT
*
28925403 GGTCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGATT
1 --TCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATT
** *
28925445 TCTTCAATC-TGCCC-C-ATGATCGGGGTAAAAGATTGGATGA
1 TCTTCAATCTTGCCCTCTA-G-TTAGGGTAAAAGATTGGAT-T
* * *
28925485 TCTTCAATCTTGCCCTTTGGTTAGGGTAAAAGATTAGATT
1 TCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATT
* * * * * *
28925525 TCTTCAATC-TACCC-C-ATGATCGAGGTAAAAGATCGGGTGG
1 TCTTCAATCTTGCCCTCTA-GTTAG-GGTAAAAGATTGGAT-T
*
28925565 TCTTCAATCTTGCCCTCTGGTTAGGGTAAAAGATTGGA
1 TCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGA
28925603 GGTTGTAACT
Statistics
Matches: 422, Mismatches: 89, Indels: 89
0.70 0.15 0.15
Matches are distributed among these distances:
37 13 0.03
38 22 0.05
39 127 0.30
40 126 0.30
41 104 0.25
42 28 0.07
43 2 0.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (40 bp):
TCTTCAATCTTGCCCTCTAGTTAGGGTAAAAGATTGGATT
Found at i:28925356 original size:79 final size:79
Alignment explanation
Indices: 28924947--28925599 Score: 902
Period size: 80 Copynumber: 8.2 Consensus size: 79
28924937 CTCTATAACT
* * * * *
28924947 TTAGAGGTAAAAGATTAGATTGT-TTCAATTTGCCTCATGGTCGAGGTAAGAGATCTGATGGTCT
1 TTAG-GGTAAAAGATTAGATT-TCTTCAATCTGCCCCATGATCGGGGTAAAAGATC-GATGGTCT
*
28925011 TCAA--TTGCCCTTTGG
63 TCAATCTTGCCCTCTGG
* * * * *
28925026 TTAGGGTTAAAGATTAGATTTCTTCAATTTGCCTCATAATCGGGGTAAAAGATCAGATGGTCTTT
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATC-GATGGTCTTC
*
28925091 AATCTTGCCCTCTAG
65 AATCTTGCCCTCTGG
* *
28925106 TTAGGGTAAAAGATTAGATTTCTTCAATCTACCCCATGATCGGGGTAAAAGATCGAATGGTCTTT
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCG-ATGGTCTTC
28925171 AATCTTGCCCTCTGG
65 AATCTTGCCCTCTGG
*
28925186 TTAGGGTAAAAGATTAGATTTCTTCAATTTGCCCCCATGATCGGGGTAAAAGATCGGATGGTCTT
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTG-CCCCATGATCGGGGTAAAAGATC-GATGGTCTT
* *
28925251 CAATCCTGCCCTCTAG
64 CAATCTTGCCCTCTGG
* *
28925267 TTAGGGTAAAAGATTGGATTTTTTCAATCTGCCCCATGATCGGGGTAAAAG-TCGATTGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGA-TGGTCTTC
*
28925331 AATCTTGCCCTCTAG
65 AATCTTGCCCTCTGG
* * *
28925346 TTAGGGTAAAAGATTGGATTTTTTTAATCTGCCCCATGATCGGGGTAAAAG-TCGATTGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGA-TGGTCTTC
28925410 AATCTTGCCCTCTGG
65 AATCTTGCCCTCTGG
* * *
28925425 TTAGGGTAAAAGATTGGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATTGGATGATCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGA-TCGATGGTCTTC
*
28925490 AATCTTGCCCTTTGG
65 AATCTTGCCCTCTGG
* * *
28925505 TTAGGGTAAAAGATTAGATTTCTTCAATCTACCCCATGATCGAGGTAAAAGATCGGGTGGTCTTC
1 TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATC-GATGGTCTTC
28925570 AATCTTGCCCTCTGG
65 AATCTTGCCCTCTGG
28925585 TTAGGGTAAAAGATT
1 TTAGGGTAAAAGATT
28925600 GGAGGTTGTA
Statistics
Matches: 526, Mismatches: 38, Indels: 19
0.90 0.07 0.03
Matches are distributed among these distances:
77 1 0.00
78 56 0.11
79 156 0.30
80 237 0.45
81 75 0.14
82 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (79 bp):
TTAGGGTAAAAGATTAGATTTCTTCAATCTGCCCCATGATCGGGGTAAAAGATCGATGGTCTTCA
ATCTTGCCCTCTGG
Found at i:28933851 original size:8 final size:8
Alignment explanation
Indices: 28933832--28933862 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
28933822 AATGTATGAT
28933832 AATGCAATG
1 AATGC-ATG
28933841 AATGCATG
1 AATGCATG
28933849 AATGCATG
1 AATGCATG
28933857 AATGCA
1 AATGCA
28933863 AATGCAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.77
9 5 0.23
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.23
Consensus pattern (8 bp):
AATGCATG
Found at i:28938477 original size:16 final size:16
Alignment explanation
Indices: 28938449--28938490 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
28938439 GGTTTGTATA
*
28938449 TATTTATTAATTT-TAT
1 TATTTATTTATTTGT-T
*
28938465 TATTTCTTTATTTGTT
1 TATTTATTTATTTGTT
28938481 TATTTATTTA
1 TATTTATTTA
28938491 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 21 0.95
17 1 0.05
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (16 bp):
TATTTATTTATTTGTT
Found at i:28939975 original size:19 final size:19
Alignment explanation
Indices: 28939936--28939973 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28939926 TATGACATTC
28939936 TAATTTTTGCCATGTTATT
1 TAATTTTTGCCATGTTATT
28939955 TAATTATTTG-CAT-TTATT
1 TAATT-TTTGCCATGTTATT
28939973 T
1 T
28939974 TACTTCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.61
Consensus pattern (19 bp):
TAATTTTTGCCATGTTATT
Found at i:28943166 original size:36 final size:36
Alignment explanation
Indices: 28943117--28943194 Score: 120
Period size: 36 Copynumber: 2.2 Consensus size: 36
28943107 TGATGACTGT
* * * *
28943117 TGTGAAAGTGAATATGTGGGTATGTTCTTCATGCCA
1 TGTGATAGAGAATATGTGAGTATATTCTTCATGCCA
28943153 TGTGATAGAGAATATGTGAGTATATTCTTCATGCCA
1 TGTGATAGAGAATATGTGAGTATATTCTTCATGCCA
28943189 TGTGAT
1 TGTGAT
28943195 TGATTATGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.37
Consensus pattern (36 bp):
TGTGATAGAGAATATGTGAGTATATTCTTCATGCCA
Found at i:28943238 original size:24 final size:24
Alignment explanation
Indices: 28943219--28943266 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
28943209 TAATAAAGTG
28943219 AATATGCAATGAATAT-ATAATAAA
1 AATATGCAATGAATATGATAA-AAA
*
28943243 AATATGTAATGAATATGATAAAAA
1 AATATGCAATGAATATGATAAAAA
28943267 TATGTAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.58, C:0.02, G:0.10, T:0.29
Consensus pattern (24 bp):
AATATGCAATGAATATGATAAAAA
Found at i:28943263 original size:22 final size:22
Alignment explanation
Indices: 28943219--28943278 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
28943209 TAATAAAGTG
*
28943219 AATATGCAATGAATATATAATAAA
1 AATATGTAATG-A-ATATAATAAA
*
28943243 AATATGTAATGAATATGATAAA
1 AATATGTAATGAATATAATAAA
28943265 AATATGTAAT-AATA
1 AATATGTAATGAATA
28943279 ATGTAGATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 19 0.56
23 1 0.03
24 10 0.29
ACGTcount: A:0.57, C:0.02, G:0.10, T:0.32
Consensus pattern (22 bp):
AATATGTAATGAATATAATAAA
Found at i:28950906 original size:14 final size:14
Alignment explanation
Indices: 28950887--28950914 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
28950877 TAGTAGTAGA
28950887 TTCATTTGACCTTT
1 TTCATTTGACCTTT
28950901 TTCATTTGACCTTT
1 TTCATTTGACCTTT
28950915 GTGTATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (14 bp):
TTCATTTGACCTTT
Found at i:28958987 original size:39 final size:38
Alignment explanation
Indices: 28958915--28958998 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 38
28958905 TTTATGTGCT
* * *
28958915 TATGCGCCAAGATGCACTTTGCGTGCCAGTATGCACT-
1 TATGTGCCAAGATGCACTTTGCGCGCCAATATGCACTA
* *
28958952 TCATGTGCCAAGAATGCGCTTTGTGCGCCAATATGCACTA
1 T-ATGTGCCAAG-ATGCACTTTGCGCGCCAATATGCACTA
28958992 TATGTGC
1 TATGTGC
28958999 TAGTTTTCCC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
37 1 0.03
38 9 0.23
39 28 0.72
40 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (38 bp):
TATGTGCCAAGATGCACTTTGCGCGCCAATATGCACTA
Found at i:28965492 original size:30 final size:30
Alignment explanation
Indices: 28965453--28965689 Score: 350
Period size: 30 Copynumber: 7.9 Consensus size: 30
28965443 TTAGGTGATT
* *
28965453 TTTTAGGGTCAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATATAATTTTGGAAAAG
*
28965483 TTTTGGGGTCAGAATATAATTTTGGAAAAG
1 TTTTGGGGTCAAAATATAATTTTGGAAAAG
28965513 TTTTGGGGTCAAAATATAATTTTGGAAAAG
1 TTTTGGGGTCAAAATATAATTTTGGAAAAG
* * *
28965543 TTTTAGGGTTAAAATGTAATTTTGGAAAAG
1 TTTTGGGGTCAAAATATAATTTTGGAAAAG
28965573 TTTTGGGGTCAAAATATAATTTTAGG-AAAG
1 TTTTGGGGTCAAAATATAATTTT-GGAAAAG
*
28965603 TTTTGGGGTCAAAATATAATTTTGTAAAAG
1 TTTTGGGGTCAAAATATAATTTTGGAAAAG
* * * *
28965633 TTTTAGGGTCAAAATGTAATTTTAGAGAAG
1 TTTTGGGGTCAAAATATAATTTTGGAAAAG
28965663 TTTTGGGGTCAAAATATAATTTCTGGA
1 TTTTGGGGTCAAAATATAATTT-TGGA
28965690 TTGTTTGGGG
Statistics
Matches: 185, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
29 1 0.01
30 179 0.97
31 5 0.03
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.38
Consensus pattern (30 bp):
TTTTGGGGTCAAAATATAATTTTGGAAAAG
Found at i:28965557 original size:90 final size:90
Alignment explanation
Indices: 28965453--28965689 Score: 404
Period size: 90 Copynumber: 2.6 Consensus size: 90
28965443 TTAGGTGATT
*
28965453 TTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAGAATATAATTTTGGAAAAGTTTTG
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTG
28965518 GGGTCAAAATATAATTTTGGAAAAG
66 GGGTCAAAATATAATTTTGGAAAAG
*
28965543 TTTTAGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTAGG-AAAGTTTT
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTT-GGAAAAGTTTT
*
28965607 GGGGTCAAAATATAATTTTGTAAAAG
65 GGGGTCAAAATATAATTTTGGAAAAG
* *
28965633 TTTTAGGGTCAAAATGTAATTTTAGAGAAGTTTTGGGGTCAAAATATAATTTCTGGA
1 TTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTT-TGGA
28965690 TTGTTTGGGG
Statistics
Matches: 138, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
90 135 0.98
91 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.38
Consensus pattern (90 bp):
TTTTAGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTTG
GGGTCAAAATATAATTTTGGAAAAG
Found at i:28966910 original size:16 final size:16
Alignment explanation
Indices: 28966889--28966937 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
28966879 ATTACCCATA
28966889 TTTATTAATGTTATTT
1 TTTATTAATGTTATTT
*
28966905 TTTATTAAAGGTTA-TT
1 TTTATT-AATGTTATTT
* *
28966921 ATTATTAATATTATTT
1 TTTATTAATGTTATTT
28966937 T
1 T
28966938 ACATTAGCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 5 0.19
16 15 0.58
17 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (16 bp):
TTTATTAATGTTATTT
Found at i:28967478 original size:18 final size:15
Alignment explanation
Indices: 28967445--28967475 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
28967435 ATGGTGGATG
28967445 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
28967460 GAGCTGGTGGTGGCA
1 GAGCTGGTGGTGGCA
28967475 G
1 G
28967476 CAGCATAGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.55, T:0.19
Consensus pattern (15 bp):
GAGCTGGTGGTGGCA
Found at i:28967661 original size:6 final size:6
Alignment explanation
Indices: 28967652--28967735 Score: 73
Period size: 6 Copynumber: 13.8 Consensus size: 6
28967642 ACTTTTAATG
* ** *
28967652 TTAAAT TTAATAT TTTAAT TTTTAT TTAAAT TTAAAT TCAAA- TTAAAT
1 TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* *
28967700 TTAAATAT TTAAAT TTAAA- ATAAAT CTAAAT TTAAA
1 TT-AA-AT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
28967736 ATCAATTTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
5 8 0.12
6 43 0.67
7 9 0.14
8 4 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (6 bp):
TTAAAT
Found at i:28967697 original size:17 final size:16
Alignment explanation
Indices: 28967677--28967742 Score: 73
Period size: 17 Copynumber: 4.1 Consensus size: 16
28967667 TAATTTTTAT
*
28967677 TTAAATTTAAATTCAAA
1 TTAAATTTAAAAT-AAA
*
28967694 TTAAATTT-AAAT-AT
1 TTAAATTTAAAATAAA
28967708 TTAAATTTAAAATAAA
1 TTAAATTTAAAATAAA
*
28967724 TCTAAATTTAAAATCAA
1 T-TAAATTTAAAATAAA
28967741 TT
1 TT
28967743 TAACTCAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.21
15 4 0.10
16 6 0.14
17 23 0.55
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:28967709 original size:25 final size:25
Alignment explanation
Indices: 28967681--28967730 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28967671 TTTTATTTAA
* *
28967681 ATTTAAATTCAAATTAAATTTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
*
28967706 ATTTAAATTTAAAATAAATCTAAAT
1 ATTTAAATTCAAAATAAATCTAAAT
28967731 TTAAAATCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAAATTCAAAATAAATCTAAAT
Found at i:28967709 original size:31 final size:31
Alignment explanation
Indices: 28967674--28967735 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
28967664 TTTTAATTTT
*
28967674 TATTTAAATTTAAATTCAAAT-TAAATTTAAA
1 TATTTAAATTTAAAAT-AAATCTAAATTTAAA
28967705 TATTTAAATTTAAAATAAATCTAAATTTAAA
1 TATTTAAATTTAAAATAAATCTAAATTTAAA
28967736 ATCAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TATTTAAATTTAAAATAAATCTAAATTTAAA
Found at i:28967724 original size:42 final size:43
Alignment explanation
Indices: 28967652--28967745 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 43
28967642 ACTTTTAATG
* * ** *
28967652 TTAAATTT-AATATTTTAATTTTTATTTAAATTTAAATTCAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
*
28967694 TTAAATTTAAATA-TTTAAATTTAAAATAAATCTAAATTTAAA
1 TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
* *
28967736 ATCAATTTAA
1 TTAAATTTAA
28967746 CTCAAAAGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.91
43 4 0.09
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (43 bp):
TTAAATTTAAATATTTTAAATTTAAAATAAATCTAAATTCAAA
Found at i:28968757 original size:2 final size:2
Alignment explanation
Indices: 28968750--28969145 Score: 764
Period size: 2 Copynumber: 200.0 Consensus size: 2
28968740 TAATGTAAGA
28968750 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28968792 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28968834 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28968875 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28968917 A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28968958 AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28968999 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28969041 AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28969082 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
28969124 AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG
28969146 TTTCCTTAGA
Statistics
Matches: 390, Mismatches: 0, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
1 4 0.01
2 386 0.99
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28969615 original size:19 final size:18
Alignment explanation
Indices: 28969583--28969626 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
28969573 GTTTGTTTGG
**
28969583 AATTTTATTTTTTTAAGAA
1 AATTTTATAATTTTAAG-A
*
28969602 AATTTTATAATTTTATGA
1 AATTTTATAATTTTAAGA
28969620 AATTTTA
1 AATTTTA
28969627 AAAGAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (18 bp):
AATTTTATAATTTTAAGA
Found at i:28970944 original size:22 final size:21
Alignment explanation
Indices: 28970909--28970954 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
28970899 ATGCACTTTG
*
28970909 AAAAATATTCATATACAGTATAA
1 AAAAACATTCATATA-A-TATAA
28970932 AAAAACATT-ATATAATATAA
1 AAAAACATTCATATAATATAA
28970952 AAA
1 AAA
28970955 CAATACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 1 0.05
22 5 0.23
23 8 0.36
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (21 bp):
AAAAACATTCATATAATATAA
Found at i:28985509 original size:62 final size:62
Alignment explanation
Indices: 28985337--28985525 Score: 185
Period size: 62 Copynumber: 3.0 Consensus size: 62
28985327 GTTTAACTAT
* * *
28985337 AATTAAATTTAATCACTTTAATATTAAATTAATATAAA-ACTTATCAAGATAAATATTGAATTAA
1 AATTAAA-ATAATCACATTAATATTAAATTAATA-AAATACTTATTAAGATAAATATT-AATTAA
* *
28985401 AATTAAAAT--T-AAATCT--TATTAAATTAATAAAATATTTATTTATAAGATAAATATTAATTT
1 AATTAAAATAATCACAT-TAATATTAAATTAATAAAATACTTA--T-TAAGATAAATATTAA-TT
28985461 AA
61 AA
* *
28985463 TATTAAAATAATCACATTAATATTAAATTAATAAAATA-TTATTAAGATAATTATTAAATTAA
1 AATTAAAATAATCACATTAATATTAAATTAATAAAATACTTATTAAGATAAATATT-AATTAA
28985525 A
1 A
28985526 TTTTTATAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 26
0.75 0.06 0.19
Matches are distributed among these distances:
58 3 0.03
59 17 0.16
60 2 0.02
61 5 0.05
62 40 0.38
63 4 0.04
64 9 0.09
65 6 0.06
66 18 0.17
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (62 bp):
AATTAAAATAATCACATTAATATTAAATTAATAAAATACTTATTAAGATAAATATTAATTAA
Found at i:28985548 original size:17 final size:17
Alignment explanation
Indices: 28985526--28985560 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28985516 TTAAATTAAA
28985526 TTTTTATAA-ATGCTTAT
1 TTTTTA-AATATGCTTAT
28985543 TTTTTAAATATGCTTAT
1 TTTTTAAATATGCTTAT
28985560 T
1 T
28985561 ATATTATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTAAATATGCTTAT
Found at i:28988869 original size:31 final size:31
Alignment explanation
Indices: 28988834--28988892 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
28988824 TAATGGAGAG
*
28988834 TGACCAAAATATAAACGATCTAAAATGTGAA
1 TGACCAAAATAAAAACGATCTAAAATGTGAA
*
28988865 TGACCAAAATAAAAATGATCTAAAATGT
1 TGACCAAAATAAAAACGATCTAAAATGT
28988893 TAGTGACTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (31 bp):
TGACCAAAATAAAAACGATCTAAAATGTGAA
Found at i:28993042 original size:141 final size:140
Alignment explanation
Indices: 28992781--28993063 Score: 417
Period size: 141 Copynumber: 2.0 Consensus size: 140
28992771 CCGAACTTCA
* * *
28992781 TGTTATCCGGTTCTGGTTCTGGCACAGTTCGGTTCTTAGTGCTATTTTCACCGTACAATCAGAGA
1 TGTTATCCGGTTCTGGTTCTGGCACAGTACGGTACTTAGTGCTATTTTCACCGTACAACCAGAGA
*
28992846 ATTGCAAGCGAAAATCAAAATTCAAGAGACGTCAATTTTGAAAATGAAGGCAAGTTGGGTTCATT
66 ATTGCAAGCGAAAATCAAAATTCAAGAGACGTCAATATTGAAAATGAAGGCAAGTTGGGTTCATT
28992911 GGAAAAAAGCT
131 GG-AAAAAGCT
* * * * * *
28992922 TGTTTTCCGGTTCTGGTTTTGGCACAGTAGGGTAGTTAGTGCTTTTTTCACTGTACAACCAGAGA
1 TGTTATCCGGTTCTGGTTCTGGCACAGTACGGTACTTAGTGCTATTTTCACCGTACAACCAGAGA
* *
28992987 ATTGCAAGCGAAAATCAAAATTCCAG-GAACGTCAATATTGAGAATGAAAGG-AAGTTGGGTTCA
66 ATTGCAAGCGAAAATCAAAATTCAAGAG-ACGTCAATATTGAAAATG-AAGGCAAGTTGGGTTCA
28993050 TTGGAAAAAGCT
129 TTGGAAAAAGCT
28993062 TG
1 TG
28993064 GTTCTATTTA
Statistics
Matches: 128, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
140 11 0.09
141 113 0.88
142 4 0.03
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (140 bp):
TGTTATCCGGTTCTGGTTCTGGCACAGTACGGTACTTAGTGCTATTTTCACCGTACAACCAGAGA
ATTGCAAGCGAAAATCAAAATTCAAGAGACGTCAATATTGAAAATGAAGGCAAGTTGGGTTCATT
GGAAAAAGCT
Found at i:28994927 original size:35 final size:35
Alignment explanation
Indices: 28994888--28994958 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 35
28994878 GTTTTGATAC
28994888 TGTTTTAG-TGCTGCTTTT-GCTGTTATTTTTGTTGT
1 TGTTTT-GCTGCTG-TTTTGGCTGTTATTTTTGTTGT
* *
28994923 TGTTTTGCTGCTGTTTTGGTTGTTGTTTTTGTTGT
1 TGTTTTGCTGCTGTTTTGGCTGTTATTTTTGTTGT
28994958 T
1 T
28994959 TGGTTGTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 5 0.16
35 27 0.84
ACGTcount: A:0.03, C:0.07, G:0.25, T:0.65
Consensus pattern (35 bp):
TGTTTTGCTGCTGTTTTGGCTGTTATTTTTGTTGT
Found at i:28994928 original size:23 final size:23
Alignment explanation
Indices: 28994902--28994951 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
28994892 TTAGTGCTGC
* *
28994902 TTTTGCTGTTATTTTTGTTGTTG
1 TTTTGCTGCTATTTTGGTTGTTG
*
28994925 TTTTGCTGCTGTTTTGGTTGTTG
1 TTTTGCTGCTATTTTGGTTGTTG
28994948 TTTT
1 TTTT
28994952 TGTTGTTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.02, C:0.06, G:0.24, T:0.68
Consensus pattern (23 bp):
TTTTGCTGCTATTTTGGTTGTTG
Found at i:28994960 original size:20 final size:21
Alignment explanation
Indices: 28994913--28994972 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 21
28994903 TTTGCTGTTA
*
28994913 TTTTTGTTGTTGTTTTGCTGCTG
1 TTTTGGTTGTTGTTTT--TGCTG
*
28994936 TTTTGGTTGTTGTTTTTGTTG
1 TTTTGGTTGTTGTTTTTGCTG
*
28994957 -TTTGGTTGTTATTTTT
1 TTTTGGTTGTTGTTTTT
28994973 ATGCGTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.44
21 4 0.12
23 15 0.44
ACGTcount: A:0.02, C:0.03, G:0.25, T:0.70
Consensus pattern (21 bp):
TTTTGGTTGTTGTTTTTGCTG
Found at i:28996304 original size:20 final size:21
Alignment explanation
Indices: 28996279--28996318 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
28996269 TCTTGGCCCA
28996279 TATATTTACT-TAT-AATTAAT
1 TATATTT-CTATATAAATTAAT
28996299 TATATTTCTATATAAATTAA
1 TATATTTCTATATAAATTAA
28996319 AAAATACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 10 0.56
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TATATTTCTATATAAATTAAT
Found at i:28997202 original size:2 final size:2
Alignment explanation
Indices: 28997195--28997235 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28997185 GATACTTCTA
28997195 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT A
28997236 ATGATTTGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28999349 original size:2 final size:2
Alignment explanation
Indices: 28999342--28999391 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
28999332 AAACATAACA
28999342 AT AT AT AT AT AT 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
28999384 AT AT AT AT
1 AT AT AT AT
28999392 TTGAAAGCAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29005465 original size:23 final size:23
Alignment explanation
Indices: 29005439--29005536 Score: 126
Period size: 23 Copynumber: 4.2 Consensus size: 23
29005429 ACACTAGCGC
*
29005439 GCTCTCTGATTAGCACTGTATGT
1 GCTCTCTGATTAGCACTGTGTGT
* *
29005462 GCTCTCTGTTTAGCAC-GTCTTGT
1 GCTCTCTGATTAGCACTGT-GTGT
29005485 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACTGTGTGT
*
29005510 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
29005533 GCTC
1 GCTC
29005537 AGTACTTTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.03
23 44 0.67
25 18 0.27
26 2 0.03
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:29007098 original size:21 final size:22
Alignment explanation
Indices: 29007074--29007114 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
29007064 AAAAATTAAT
*
29007074 TTTTTTTAT-TTTTTAAAAATA
1 TTTTTTTATAATTTTAAAAATA
29007095 TTTTTTTATAATTTTAAAAA
1 TTTTTTTATAATTTTAAAAA
29007115 AATTAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTTTTTATAATTTTAAAAATA
Found at i:29007099 original size:23 final size:24
Alignment explanation
Indices: 29007063--29007120 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 24
29007053 AAATTTTATA
* *
29007063 AAAAAATTAATTTTTTTTATTTTT
1 AAAAAATTAATTTTTTATAATTTT
* *
29007087 TAAAAA-TATTTTTTTATAATTTT
1 AAAAAATTAATTTTTTATAATTTT
29007110 AAAAAAATTAA
1 -AAAAAATTAA
29007121 GTTTGAAATG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
23 14 0.54
24 10 0.38
25 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AAAAAATTAATTTTTTATAATTTT
Found at i:29007115 original size:24 final size:23
Alignment explanation
Indices: 29007061--29007117 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
29007051 TAAAATTTTA
29007061 TAAAAAAATTAATTTTTTTTATTT
1 TAAAAAAA-TAATTTTTTTTATTT
**
29007085 TTTAAAAAT-ATTTTTTTATAATTT
1 TAAAAAAATAATTTTTTT-T-ATTT
29007109 TAAAAAAAT
1 TAAAAAAAT
29007118 TAAGTTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 8 0.30
23 2 0.07
24 17 0.63
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TAAAAAAATAATTTTTTTTATTT
Found at i:29011411 original size:23 final size:24
Alignment explanation
Indices: 29011362--29011412 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
29011352 TTGGGTCTGT
**
29011362 AATTTGGACATTTAATTTAAATTA
1 AATTTGGACATTTAATTTAAAAAA
*
29011386 AATTTGGGC-TTTAATTTAAAAAA
1 AATTTGGACATTTAATTTAAAAAA
29011409 AATT
1 AATT
29011413 ATTTTTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.43
Consensus pattern (24 bp):
AATTTGGACATTTAATTTAAAAAA
Found at i:29012066 original size:49 final size:47
Alignment explanation
Indices: 29011951--29012280 Score: 276
Period size: 49 Copynumber: 6.8 Consensus size: 47
29011941 ACACCTTTGT
* * *
29011951 GGTACTGGATTCGCCGTTGTGGCTTAAATCC-CTCCCTTCATTTTCAGA
1 GGTACTGGATTCGCCGTTGCGGCTTAAA-CCTTTCCCTTCATCTTC-GA
* * * *
29011999 GGTACAAGG-TTCACCGTTGCGGTTTAAACCTTTCCCTTGACATCTTCGT
1 GGTAC-TGGATTCGCCGTTGCGGCTTAAACCTTTCCCTT--CATCTTCGA
* *
29012048 GGTACTGGATTCGCCGTTGTGGCTTAAATCTTTCCCTTCATGCTTCTGA
1 GGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCAT-CTTC-GA
* * * *
29012097 GGTAC-GAGGTTCGTCGTTACGGCTTAAACCTTTCCCTTTGTATCCTTAC-A
1 GGTACTG-GATTCGCCGTTGCGGCTTAAACCTTTCCC-TT-CAT-CTT-CGA
*
29012147 -GTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCTGA
1 GGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCAT-CTTC-GA
* * * * *
29012195 GGTAC-GAGGTTCGTCATTGCGACTTAAACCTTTCCCTTCATATCTTCGT
1 GGTACTG-GATTCGCCGTTGCGGCTTAAACCTTTCCCTTC--ATCTTCGA
* *
29012244 GGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCCT
1 GGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCT
29012281 CCGTGCTTCT
Statistics
Matches: 225, Mismatches: 38, Indels: 37
0.75 0.13 0.12
Matches are distributed among these distances:
46 1 0.00
47 10 0.04
48 38 0.17
49 153 0.68
50 15 0.07
51 7 0.03
52 1 0.00
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (47 bp):
GGTACTGGATTCGCCGTTGCGGCTTAAACCTTTCCCTTCATCTTCGA
Found at i:29012071 original size:97 final size:98
Alignment explanation
Indices: 29011804--29012296 Score: 508
Period size: 98 Copynumber: 5.1 Consensus size: 98
29011794 TTCCCTTTGC
* * * *
29011804 GCTTTTGAGGTACAAGGTTCGCCGTTGTGACTTAAACCTTTTCCTCTG-TATGTTCGTGGTACTG
1 GCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCT-TGATATCTTCGTGGTACTG
** * *
29011868 GATTTACCGTCGTGACTTAAATCCTTCCCTTCAT
65 GATTCGCCGTTGTGGCTTAAATCCTTCCCTTCAT
* * * * * * *
29011902 -TTTCTGAGGTACTAGGTTCGCCGTT--G-C----AGCTTTCCTTTGACACCTTTGTGGTACTGG
1 GCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTGATATCTTCGTGGTACTGG
*
29011959 ATTCGCCGTTGTGGCTTAAATCCCTCCCTTCAT
66 ATTCGCCGTTGTGGCTTAAATCCTTCCCTTCAT
* * * ** *
29011992 -TTTCAGAGGTACAAGGTTCACCGTTGCGGTTTAAACCTTTCCCTTGACATCTTCGTGGTACTGG
1 GCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTGATATCTTCGTGGTACTGG
*
29012056 ATTCGCCGTTGTGGCTTAAATCTTTCCCTTCAT
66 ATTCGCCGTTGTGGCTTAAATCCTTCCCTTCAT
* * * * *
29012089 GCTTCTGAGGTACGAGGTTCGTCGTTACGGCTTAAACCTTTCCCTTTG-TATCCTTAC--AGTAC
1 GCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCC-TTGATAT-CTT-CGTGGTAC
* *
29012151 TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT
63 TGGATTCGCCGTTGTGGCTTAAATCCTTCCCTTCAT
* * * *
29012187 GCTTCTGAGGTACGAGGTTCGTCATTGCGACTTAAACCTTTCCCTTCATATCTTCGTGGTACTGG
1 GCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTGATATCTTCGTGGTACTGG
** * * *
29012252 ATTCGCCGTTACGGCTTAAATCTTTCCCTCCGT
66 ATTCGCCGTTGTGGCTTAAATCCTTCCCTTCAT
29012285 GCTTCTGAGGTA
1 GCTTCTGAGGTA
29012297 AAAAAATCTG
Statistics
Matches: 337, Mismatches: 43, Indels: 30
0.82 0.10 0.07
Matches are distributed among these distances:
89 2 0.01
90 70 0.21
92 1 0.00
94 1 0.00
95 1 0.00
96 1 0.00
97 84 0.25
98 170 0.50
99 6 0.02
100 1 0.00
ACGTcount: A:0.16, C:0.26, G:0.21, T:0.37
Consensus pattern (98 bp):
GCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTTGATATCTTCGTGGTACTGG
ATTCGCCGTTGTGGCTTAAATCCTTCCCTTCAT
Found at i:29012199 original size:147 final size:146
Alignment explanation
Indices: 29012012--29012280 Score: 330
Period size: 147 Copynumber: 1.8 Consensus size: 146
29012002 ACAAGGTTCA
* * * * *
29012012 CCGTTGCGGTTTAAACCTTTCCCTTGACATCTTCGTGGTACTG-GATTCGCCGTTGTGGCTTAAA
1 CCGTTGCGGCTTAAACCTTTCCCTT-ACATCTTCGAGGTAC-GAGATTCGCCATTGCGACTTAAA
* * *
29012076 TCTTTCCCTTCAT-GCTTCTGAGGTAC-GAGGTTCGTCGTTACGGCTTAAACCTTTCCCTTTGTA
64 CCTTTCCCTTCATAGCTTC-GAGGTACTG-GATTCGCCGTTACGGCTTAAACCTTTCCCTTTGTA
29012139 TCCTTACAGTACTGGATTCG
127 TCCTTACAGTACTGGATTCG
* * *
29012159 CCGTTGCGGCTTAAATCTTTCCCTT-CATGCTTCTGAGGTACGAGGTTCGTCATTGCGACTTAAA
1 CCGTTGCGGCTTAAACCTTTCCCTTACAT-CTTC-GAGGTACGAGATTCGCCATTGCGACTTAAA
* * *
29012223 CCTTTCCCTTCATATCTTCGTGGTACTGGATTCGCCGTTACGGCTTAAATCTTTCCCT
64 CCTTTCCCTTCATAGCTTCGAGGTACTGGATTCGCCGTTACGGCTTAAACCTTTCCCT
29012281 CCGTGCTTCT
Statistics
Matches: 103, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
145 3 0.03
146 5 0.05
147 90 0.87
148 5 0.05
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (146 bp):
CCGTTGCGGCTTAAACCTTTCCCTTACATCTTCGAGGTACGAGATTCGCCATTGCGACTTAAACC
TTTCCCTTCATAGCTTCGAGGTACTGGATTCGCCGTTACGGCTTAAACCTTTCCCTTTGTATCCT
TACAGTACTGGATTCG
Found at i:29023169 original size:29 final size:28
Alignment explanation
Indices: 29023122--29023191 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 28
29023112 ATTTTTTAAA
*
29023122 ATTTTAAGAATTCAAAAAAT-ATATATAAATT
1 ATTTTAAAAATT--AAAAATCAT-TA-AAATT
29023153 ATTTTTAAAAATTAAAAATCATTAAAATT
1 A-TTTTAAAAATTAAAAATCATTAAAATT
29023182 ATTTTAAAAA
1 ATTTTAAAAA
29023192 GTATTTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
28 9 0.25
29 6 0.17
30 8 0.22
31 3 0.08
32 10 0.28
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (28 bp):
ATTTTAAAAATTAAAAATCATTAAAATT
Found at i:29023625 original size:23 final size:21
Alignment explanation
Indices: 29023580--29023676 Score: 80
Period size: 23 Copynumber: 4.7 Consensus size: 21
29023570 TCAGCATCCT
* *
29023580 ATTTCATTACAAAACCCAATCA
1 ATTTCATTACAAAA-TCACTCA
29023602 AGTTTCATTACAAACATCACTCA
1 A-TTTCATTACAAA-ATCACTCA
*
29023625 A-TTCA-TACAAAA-C-CTGA
1 ATTTCATTACAAAATCACTCA
29023642 ATTTTCATTACAAACATCACTCA
1 A-TTTCATTACAAA-ATCACTCA
29023665 A-TTCA-TACAAAA
1 ATTTCATTACAAAA
29023677 CCTGTATACC
Statistics
Matches: 63, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
17 4 0.06
18 1 0.02
19 6 0.10
20 18 0.29
21 9 0.14
22 2 0.03
23 22 0.35
24 1 0.02
ACGTcount: A:0.44, C:0.25, G:0.02, T:0.29
Consensus pattern (21 bp):
ATTTCATTACAAAATCACTCA
Found at i:29023652 original size:40 final size:40
Alignment explanation
Indices: 29023604--29023680 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
29023594 CCCAATCAAG
29023604 TTTCATTACAAACATCACTCAATTCATACAAAACCTGAAT
1 TTTCATTACAAACATCACTCAATTCATACAAAACCTGAAT
29023644 TTTCATTACAAACATCACTCAATTCATACAAAACCTG
1 TTTCATTACAAACATCACTCAATTCATACAAAACCTG
29023681 TATACCATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.26, G:0.03, T:0.30
Consensus pattern (40 bp):
TTTCATTACAAACATCACTCAATTCATACAAAACCTGAAT
Found at i:29023677 original size:21 final size:21
Alignment explanation
Indices: 29023605--29023675 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 21
29023595 CCAATCAAGT
29023605 TTCATTACAAACATCACTCAA
1 TTCATTACAAACATCACTCAA
*
29023626 TTCA-TACAAA-A-C-CTGAA
1 TTCATTACAAACATCACTCAA
29023643 TTTTCATTACAAACATCACTCAA
1 --TTCATTACAAACATCACTCAA
29023666 TTCA-TACAAA
1 TTCATTACAAA
29023676 ACCTGTATAC
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
17 4 0.10
18 1 0.02
19 5 0.12
20 18 0.43
21 9 0.21
22 1 0.02
23 4 0.10
ACGTcount: A:0.44, C:0.25, G:0.01, T:0.30
Consensus pattern (21 bp):
TTCATTACAAACATCACTCAA
Found at i:29023775 original size:15 final size:15
Alignment explanation
Indices: 29023755--29023785 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29023745 AATTAAGTTG
29023755 TATATTTTAATAATT
1 TATATTTTAATAATT
*
29023770 TATATTTTTATAATT
1 TATATTTTAATAATT
29023785 T
1 T
29023786 TTAAAGTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATTTTAATAATT
Found at i:29024519 original size:41 final size:40
Alignment explanation
Indices: 29024474--29024557 Score: 150
Period size: 41 Copynumber: 2.1 Consensus size: 40
29024464 AATATATATG
29024474 ATTGTAGTATTTTAAAGATGAATTTTGGGTTTTTTTTTAGT
1 ATTGTAGTATTTTAAAGATGAATTTTGGG-TTTTTTTTAGT
*
29024515 ATTGTAGTATTTTAAGGATGAATTTTGGGTTTTTTTTAGT
1 ATTGTAGTATTTTAAAGATGAATTTTGGGTTTTTTTTAGT
29024555 ATT
1 ATT
29024558 TAATTTTGGA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 14 0.33
41 28 0.67
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (40 bp):
ATTGTAGTATTTTAAAGATGAATTTTGGGTTTTTTTTAGT
Found at i:29024572 original size:15 final size:14
Alignment explanation
Indices: 29024554--29024592 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
29024544 TTTTTTTTAG
29024554 TATTTAATTTTGGAA
1 TATTTAATTTT-GAA
*
29024569 TATTATGATTTTGAA
1 TATT-TAATTTTGAA
29024584 TATTTAATT
1 TATTTAATT
29024593 AAAACACGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 4 0.19
15 11 0.52
16 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (14 bp):
TATTTAATTTTGAA
Found at i:29025139 original size:16 final size:16
Alignment explanation
Indices: 29025115--29025156 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
29025105 TGACAATAAA
*
29025115 TAATTTAATTA-TATTT
1 TAATATAATTATTA-TT
29025131 TAATATAATTATTATT
1 TAATATAATTATTATT
*
29025147 AAATATAATT
1 TAATATAATT
29025157 TTAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATATAATTATTATT
Found at i:29025153 original size:26 final size:26
Alignment explanation
Indices: 29025119--29025197 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
29025109 AATAAATAAT
*
29025119 TTAATTATATTTTAATATAATTATTA
1 TTAAATATATTTTAATATAATTATTA
*
29025145 TTAAATATAATTTTAATAATAA--ATAA
1 TTAAATAT-ATTTTAAT-ATAATTATTA
* *
29025171 TTTAATAACATTCTTAATATAATTATT
1 TTAAAT-ATATT-TTAATATAATTATT
29025198 TTTATATTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
26 22 0.52
27 14 0.33
28 6 0.14
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (26 bp):
TTAAATATATTTTAATATAATTATTA
Found at i:29026169 original size:12 final size:12
Alignment explanation
Indices: 29026154--29026179 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29026144 AACCCAATAA
29026154 AAATTAAATTTT
1 AAATTAAATTTT
29026166 AAATTAAATTTT
1 AAATTAAATTTT
29026178 AA
1 AA
29026180 TTTTAAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAATTAAATTTT
Found at i:29026750 original size:16 final size:16
Alignment explanation
Indices: 29026730--29026763 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
29026720 CATATGCAAA
29026730 TATATAT-TC-ATATG
1 TATATATCTCTATATG
29026744 TATATATCTCTATATG
1 TATATATCTCTATATG
29026760 TATA
1 TATA
29026764 CGCACATCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 2 0.11
16 9 0.50
ACGTcount: A:0.35, C:0.09, G:0.06, T:0.50
Consensus pattern (16 bp):
TATATATCTCTATATG
Found at i:29039627 original size:208 final size:206
Alignment explanation
Indices: 29039256--29039770 Score: 701
Period size: 208 Copynumber: 2.5 Consensus size: 206
29039246 CAATGGAGAA
* * *
29039256 AAGTGAACTAAATCCGTCTTCCTGATGAGATACA-AAGAAGTGGATTAAAACAATGAGGCAATCA
1 AAGTGAACCAAATACGTCTTCCTGATGAGATACAGAA-AAGTGGATT-AAACAATGAGGCGATCA
* *
29039320 TCTTCCTGATGAGATACTGAGAAGTAAACCAAATCAATGAAATAAAGCTCAATTTGAGTGAAACT
64 TCTTCCT-ATGAGATACTGAGAAGT-AACCAAATCAATGAAACAAAGCTCAATGTGAGTGAAACT
* *
29039385 TCAAACCCCCATCTTCCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTTACCTTCC
127 TCAAACCCCCATCTTCCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCACCTTCC
29039450 TGATGAGATACAGAG
192 TGATGAGATACAGAG
* *
29039465 AAGTGAACCAAATACGTCTTCTTGATGAGATACAGAAAAGTGAATTAAACAATGAGGCGATCATC
1 AAGTGAACCAAATACGTCTTCCTGATGAGATACAGAAAAGTGGATTAAACAATGAGGCGATCATC
** *
29039530 TTTTTCATGAGATACTGAGAAGTAGACCAAATCAAT-AAAGCAAATCTCAATGTGAGTGAAACTT
66 TTCCT-ATGAGATACTGAGAAGTA-ACCAAATCAATGAAA-CAAAGCTCAATGTGAGTGAAACTT
* ** * *
29039594 CAAACCCCCATCTTCCTGATGAGATGTAGAGAAGTGGGTCAAAGCAATAAAACGGTCATCTTCTT
128 CAAACCCCCATCTTCCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCACCTTCCT
29039659 GATGAGATACAGAG
193 GATGAGATACAGAG
* * * * * * *
29039673 AAGTGAACCAAATTCGTCTTCCTAATGATATACAGAGAAGTGGATTAGACTAATGAAGCGGTCAT
1 AAGTGAACCAAATACGTCTTCCTGATGAGATACAGAAAAGTGGATTAAAC-AATGAGGCGATCAT
*
29039738 CTTCCTAGTGAGATACAGAGAAGTTAACCAAAT
65 CTTCCTA-TGAGATACTGAGAAG-TAACCAAAT
29039771 TAATCGATAG
Statistics
Matches: 270, Mismatches: 30, Indels: 12
0.87 0.10 0.04
Matches are distributed among these distances:
207 4 0.01
208 186 0.69
209 76 0.28
210 4 0.01
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (206 bp):
AAGTGAACCAAATACGTCTTCCTGATGAGATACAGAAAAGTGGATTAAACAATGAGGCGATCATC
TTCCTATGAGATACTGAGAAGTAACCAAATCAATGAAACAAAGCTCAATGTGAGTGAAACTTCAA
ACCCCCATCTTCCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAACGGTCACCTTCCTGAT
GAGATACAGAG
Found at i:29039990 original size:12 final size:12
Alignment explanation
Indices: 29039975--29040000 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29039965 AACCCAATAA
29039975 AAATTAAATTTT
1 AAATTAAATTTT
29039987 AAATTAAATTTT
1 AAATTAAATTTT
29039999 AA
1 AA
29040001 TTTTAAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
AAATTAAATTTT
Found at i:29051816 original size:9 final size:10
Alignment explanation
Indices: 29051791--29051823 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
29051781 TATATGGTAG
*
29051791 TATTTATTTA
1 TATTTTTTTA
29051801 TATTTTTTTA
1 TATTTTTTTA
29051811 -ATTTTTTTA
1 TATTTTTTTA
29051820 TATT
1 TATT
29051824 AAGGGAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TATTTTTTTA
Found at i:29056445 original size:19 final size:19
Alignment explanation
Indices: 29056423--29056466 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
29056413 ATTTTTCAAT
*
29056423 AATTTTAAA-ATATTTTTAC
1 AATTTTAAATA-ATTCTTAC
29056442 AATTTTAAATAATTCTTAC
1 AATTTTAAATAATTCTTAC
29056461 AATTTT
1 AATTTT
29056467 CAGTCAACGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 22 0.96
20 1 0.04
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTTAAATAATTCTTAC
Found at i:29057565 original size:30 final size:29
Alignment explanation
Indices: 29057531--29057613 Score: 80
Period size: 31 Copynumber: 2.7 Consensus size: 29
29057521 CGTAGATGAC
29057531 TTATTTTAATTAATTTTTTAAATTTCA-ATT
1 TTATTTT-ATTAATTTTTTAAATTT-AGATT
* *
29057561 TTATTTTTATTAGTTTTTTTAACTTTAGATT
1 TTA-TTTTATTA-ATTTTTTAAATTTAGATT
29057592 TT-TCTTTATTAATTTTTCTAAA
1 TTAT-TTTATTAATTTTT-TAAA
29057614 CGTAATGATT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
29 6 0.14
30 18 0.41
31 20 0.45
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (29 bp):
TTATTTTATTAATTTTTTAAATTTAGATT
Found at i:29057579 original size:31 final size:30
Alignment explanation
Indices: 29057531--29057613 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
29057521 CGTAGATGAC
* *
29057531 TTATTTTAATTAATTTTTTAAATTTCA-ATT
1 TTATTTTTATTATTTTTTTAAATTT-AGATT
*
29057561 TTATTTTTATTAGTTTTTTTAACTTTAGATT
1 TTATTTTTATTA-TTTTTTTAAATTTAGATT
* *
29057592 TT-TCTTTATTAATTTTTCTAAA
1 TTATTTTTATT-ATTTTTTTAAA
29057614 CGTAATGATT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 27 0.61
31 17 0.39
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (30 bp):
TTATTTTTATTATTTTTTTAAATTTAGATT
Found at i:29060254 original size:33 final size:32
Alignment explanation
Indices: 29060203--29060291 Score: 85
Period size: 33 Copynumber: 2.8 Consensus size: 32
29060193 ATGATCCAAG
* * * *
29060203 TTAAAAAATTTACCAAAATGATATGTCAATGA
1 TTAAAAAATATACTAAAATGATATGTAAATAA
*
29060235 TATAAAAAATATACTAAAATAATAT-TAAATAA
1 T-TAAAAAATATACTAAAATGATATGTAAATAA
29060267 TTAATAATAA-ATA-TAAAATGATATG
1 TTAA-AA-AATATACTAAAATGATATG
29060292 ACATCTCTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
31 13 0.28
32 12 0.26
33 22 0.47
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (32 bp):
TTAAAAAATATACTAAAATGATATGTAAATAA
Found at i:29060544 original size:23 final size:23
Alignment explanation
Indices: 29060518--29060569 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
29060508 TTCATTTAAC
29060518 TTAATCAAACATATTCACGAACA
1 TTAATCAAACATATTCACGAACA
* * * *
29060541 TTAAACGAACATGTTCATGAACA
1 TTAATCAAACATATTCACGAACA
29060564 TATAAT
1 T-TAAT
29060570 TGAACACGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
23 20 0.87
24 3 0.13
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (23 bp):
TTAATCAAACATATTCACGAACA
Found at i:29060652 original size:38 final size:38
Alignment explanation
Indices: 29060601--29060678 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
29060591 TTAATGAATA
29060601 ATAAACAAACAAACAATAAAAACATACACATAGATATT
1 ATAAACAAACAAACAATAAAAACATACACATAGATATT
29060639 ATAAACAAACAAACAATAAAAACATACACATAGATATT
1 ATAAACAAACAAACAATAAAAACATACACATAGATATT
29060677 AT
1 AT
29060679 TTTAATATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.63, C:0.15, G:0.03, T:0.19
Consensus pattern (38 bp):
ATAAACAAACAAACAATAAAAACATACACATAGATATT
Found at i:29060745 original size:23 final size:24
Alignment explanation
Indices: 29060711--29060755 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
29060701 ATCATTAATA
29060711 AATAAACAAGC-TATAAACGAGTT
1 AATAAACAAGCTTATAAACGAGTT
*
29060734 AATAAACGAGCTTATAAACGAG
1 AATAAACAAGCTTATAAACGAG
29060756 CCAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.51, C:0.13, G:0.16, T:0.20
Consensus pattern (24 bp):
AATAAACAAGCTTATAAACGAGTT
Found at i:29060761 original size:24 final size:23
Alignment explanation
Indices: 29060711--29060763 Score: 70
Period size: 24 Copynumber: 2.3 Consensus size: 23
29060701 ATCATTAATA
**
29060711 AATAAACAAGCTATAAACGAGTT
1 AATAAACAAGCTATAAACGAGCC
*
29060734 AATAAACGAGCTTATAAACGAGCC
1 AATAAACAAGC-TATAAACGAGCC
29060758 AATAAA
1 AATAAA
29060764 TTATCTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.19
Consensus pattern (23 bp):
AATAAACAAGCTATAAACGAGCC
Found at i:29060762 original size:12 final size:12
Alignment explanation
Indices: 29060711--29060763 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
29060701 ATCATTAATA
*
29060711 AATAAACAAGCT
1 AATAAACGAGCT
*
29060723 -ATAAACGAGTT
1 AATAAACGAGCT
29060734 AATAAACGAGCT
1 AATAAACGAGCT
* *
29060746 TATAAACGAGCC
1 AATAAACGAGCT
29060758 AATAAA
1 AATAAA
29060764 TTATCTTTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 9 0.26
12 25 0.74
ACGTcount: A:0.53, C:0.15, G:0.13, T:0.19
Consensus pattern (12 bp):
AATAAACGAGCT
Found at i:29061330 original size:28 final size:26
Alignment explanation
Indices: 29061293--29061348 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
29061283 AAATCAATTA
29061293 ATATAAAAAATAATAAAGTATTTTTTAT
1 ATATAAAAAAT-AT-AAGTATTTTTTAT
* *
29061321 ATATAAAAAATATGATTATTTTTTAT
1 ATATAAAAAATATAAGTATTTTTTAT
29061347 AT
1 AT
29061349 TTTTACATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 13 0.50
27 2 0.08
28 11 0.42
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
ATATAAAAAATATAAGTATTTTTTAT
Found at i:29063333 original size:27 final size:27
Alignment explanation
Indices: 29063284--29063335 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
29063274 AAAAATACCT
* *
29063284 GACACCAGTGGAGGAACACCAAGTGAC
1 GACACCAATGGAAGAACACCAAGTGAC
* *
29063311 GACACCAATGGAAGAATATCAAGTG
1 GACACCAATGGAAGAACACCAAGTG
29063336 GCGGCACTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.40, C:0.21, G:0.27, T:0.12
Consensus pattern (27 bp):
GACACCAATGGAAGAACACCAAGTGAC
Found at i:29063523 original size:4 final size:4
Alignment explanation
Indices: 29063514--29063583 Score: 81
Period size: 4 Copynumber: 17.2 Consensus size: 4
29063504 AAAAAAAGGG
*
29063514 GAAA GAAA GAGAG GAAA GAAA GAAA GAAA GAAA GAAA G-AA GAAGA GGAAA
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA-A -GAAA
*
29063564 GAAA G-AA GAAG GAAA GAAA G
1 GAAA GAAA GAAA GAAA GAAA G
29063584 GTAATGTGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
3 6 0.11
4 43 0.75
5 5 0.09
6 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:29063543 original size:25 final size:24
Alignment explanation
Indices: 29063514--29063583 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 24
29063504 AAAAAAAGGG
29063514 GAAAGAAAGAGAGGAAAGAAAGAAA
1 GAAAGAAAGA-AGGAAAGAAAGAAA
*
29063539 GAAAGAAAGAAAG-AAGAAGAGGAAA
1 GAAAGAAAGAAGGAAAGAA-A-GAAA
29063564 GAAAG-AAGAAGGAAAGAAAG
1 GAAAGAAAGAAGGAAAGAAAG
29063584 GTAATGTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
23 6 0.15
24 10 0.25
25 24 0.60
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (24 bp):
GAAAGAAAGAAGGAAAGAAAGAAA
Found at i:29063560 original size:33 final size:32
Alignment explanation
Indices: 29063514--29063583 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 32
29063504 AAAAAAAGGG
29063514 GAAAGAAAGAGAGGAAAGAAAGAAAGAAAGAAA
1 GAAAGAAAGAGAGGAAAGAAAG-AAGAAAGAAA
*
29063547 GAAAG-AAGAAGAGGAAAGAAAGAAGAAGGAAA
1 GAAAGAAAG-AGAGGAAAGAAAGAAGAAAGAAA
29063579 GAAAG
1 GAAAG
29063584 GTAATGTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
32 17 0.49
33 18 0.51
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (32 bp):
GAAAGAAAGAGAGGAAAGAAAGAAGAAAGAAA
Done.