Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold430
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: 426104
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
File 3 of 4
Found at i:261338 original size:28 final size:26
Alignment explanation
Indices: 261301--261352 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
261291 TTTTTTAATA
261301 TTTATATTATAATATTATATAATTATTT
1 TTTATATTATAA-ATTATAT-ATTATTT
261329 TTTATATTATAAATTATATATTAT
1 TTTATATTATAAATTATATATTAT
261353 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 5 0.21
27 7 0.29
28 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTATATTATAAATTATATATTATTT
Found at i:261354 original size:7 final size:7
Alignment explanation
Indices: 261298--261355 Score: 59
Period size: 7 Copynumber: 8.4 Consensus size: 7
261288 TATTTTTTTA
261298 ATATT-T
1 ATATTAT
261304 ATATTAT
1 ATATTAT
261311 AATATTAT
1 -ATATTAT
261319 ATAATTAT
1 AT-ATTAT
*
261327 -T-TTTT
1 ATATTAT
261332 ATATTAT
1 ATATTAT
*
261339 AAATTAT
1 ATATTAT
261346 ATATTAT
1 ATATTAT
261353 ATA
1 ATA
261356 AAAAATAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
5 3 0.07
6 6 0.14
7 22 0.51
8 12 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
ATATTAT
Found at i:263482 original size:2 final size:2
Alignment explanation
Indices: 263475--263504 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
263465 AGATTTCTTT
263475 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
263505 AGCCTAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:266448 original size:12 final size:12
Alignment explanation
Indices: 266431--266455 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
266421 TCGAGTTTTT
266431 TTATTTTCTTGA
1 TTATTTTCTTGA
266443 TTATTTTCTTGA
1 TTATTTTCTTGA
266455 T
1 T
266456 CGGGTCATTT
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:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TTATTTTCTTGA
Found at i:266494 original size:31 final size:31
Alignment explanation
Indices: 266459--266558 Score: 139
Period size: 31 Copynumber: 3.2 Consensus size: 31
266449 TCTTGATCGG
* *
266459 GTCATTTTAATTTTTGATAATTCGAGTTCGA
1 GTCATTTCAATTTTTGATTATTCGAGTTCGA
* *
266490 GTCATTTCAATTTTTTATTATTCGGGTTCGA
1 GTCATTTCAATTTTTGATTATTCGAGTTCGA
*
266521 GTCATTTCAATTTTTGGTTATTC-AGGTTCGA
1 GTCATTTCAATTTTTGATTATTCGA-GTTCGA
266552 GTCATTT
1 GTCATTT
266559 TAGGTCAAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.21, C:0.12, G:0.17, T:0.50
Consensus pattern (31 bp):
GTCATTTCAATTTTTGATTATTCGAGTTCGA
Found at i:266702 original size:24 final size:24
Alignment explanation
Indices: 266675--266721 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
266665 TCATATTTTA
* *
266675 TAAATATTATTTTCATTATAATTC
1 TAAATATTATTTTAAATATAATTC
*
266699 TAAATGTTATTTTAAATATAATT
1 TAAATATTATTTTAAATATAATT
266722 TATTAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (24 bp):
TAAATATTATTTTAAATATAATTC
Found at i:266998 original size:11 final size:10
Alignment explanation
Indices: 266975--267018 Score: 52
Period size: 11 Copynumber: 4.1 Consensus size: 10
266965 CTACGTAATA
266975 TCTATTCCTAT
1 TCTATT-CTAT
266986 TCTTATTCTAT
1 TC-TATTCTAT
266997 TCTATTTCTAT
1 TCTA-TTCTAT
*
267008 TCTATTTTAT
1 TCTATTCTAT
267018 T
1 T
267019 TTTATCGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 8 0.27
11 18 0.60
12 4 0.13
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (10 bp):
TCTATTCTAT
Found at i:266999 original size:5 final size:5
Alignment explanation
Indices: 266975--267018 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
266965 CTACGTAATA
*
266975 TCTAT TCCTAT TCTTAT TCTAT TCTATT TCTAT TCTAT TTTAT T
1 TCTAT T-CTAT TC-TAT TCTAT TCTA-T TCTAT TCTAT TCTAT T
267019 TTTATCGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
5 20 0.57
6 15 0.43
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (5 bp):
TCTAT
Found at i:268472 original size:36 final size:36
Alignment explanation
Indices: 268431--268500 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
268421 TAAATTATGA
268431 AGATTACAATCTAATAATCATAATCAGAACATTAAG
1 AGATTACAATCTAATAATCATAATCAGAACATTAAG
* * * *
268467 AGATTACGATCTTATAATCATAATTAGAATATTA
1 AGATTACAATCTAATAATCATAATCAGAACATTA
268501 GAAAATCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (36 bp):
AGATTACAATCTAATAATCATAATCAGAACATTAAG
Found at i:272628 original size:50 final size:51
Alignment explanation
Indices: 272574--272705 Score: 194
Period size: 50 Copynumber: 2.6 Consensus size: 51
272564 ATTTGCCTAC
* * * *
272574 ATGTATTGATACATTAAATAATGTATCGATACATCTGGGTAAAATCT-AGA
1 ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACTCAGA
* * *
272624 ATGTATCGATACAATGAAGAATATATCGATACATTTGGGTAAAAACTCAGA
1 ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACTCAGA
272675 ATGTATCGATACAATGAATAATGTATCGATA
1 ATGTATCGATACAATGAATAATGTATCGATA
272706 GAAACAGTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
50 40 0.56
51 32 0.44
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (51 bp):
ATGTATCGATACAATGAATAATGTATCGATACATCTGGGTAAAAACTCAGA
Found at i:273642 original size:52 final size:51
Alignment explanation
Indices: 273416--273826 Score: 285
Period size: 52 Copynumber: 8.0 Consensus size: 51
273406 ATGAAGATGA
* * * * *
273416 AAAGAGTGATAAAGATGTCAATATGCTGATTCGAGGCCAACGATATTGGGCTT
1 AAAGA-TG-TAAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * * * * * * * *
273469 AAAGATGCAACGAATGTCAATGTGCTAATTCATGGCCAGTGACGTTAGACTT
1 AAAGATGTAAAG-ATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * * * * * * **
273521 GAAGATGAAAAGAATGTCAATGTGTTGATTCATGACCAGCGACATTAAACTT
1 AAAGATGTAAAG-ATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * * * * *
273573 GAAGATGAGAAAAATGCCAATGTACTGATTCAAGGCCAGCGACATTGGGCTT
1 AAAGATG-TAAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* **
273625 -AAGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCAGACTT
1 AAAG-ATG-TAAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * *
273677 AAAGATG--AAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGACTT
1 AAAGATGTAAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * * *
273726 AAAGATGGTAAAGGTGCCAATATGCTGATTTAAGGCCAACGATATTGGACTT
1 AAAGAT-GTAAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * * * * * * *
273778 -AAGA--AAAAGGTGCTAATGTGCTAATTTAAGGCTAGCGGCATTGGACTT
1 AAAGATGTAAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
273826 A
1 A
273827 GAAAGAGATG
Statistics
Matches: 291, Mismatches: 59, Indels: 20
0.79 0.16 0.05
Matches are distributed among these distances:
48 36 0.12
49 42 0.14
50 1 0.00
51 10 0.03
52 191 0.66
53 11 0.04
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.26
Consensus pattern (51 bp):
AAAGATGTAAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
Found at i:273727 original size:101 final size:101
Alignment explanation
Indices: 273425--273826 Score: 346
Period size: 104 Copynumber: 3.9 Consensus size: 101
273415 AAAAGAGTGA
* * * * * *
273425 TAAAGATGTCAATATGCTGATTCGAGGCCAACGATATTGGGCTTAAAGATGCAACGAATGTCAAT
1 TAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAGATG-AAAG-ATGCCAAT
* * * *
273490 GTGCTAATTCATGGCCAGTGACGTTAGACTTGAAG-ATG
64 GTGCTAATTCAAGGCCAGCGACATTGGACTT-AAGAATG
* * * * * * * * * * *
273528 AAAAGAATGTCAATGTGTTGATTCATGACCAGCGACATTAAACTTGAAGATGAGAAAAATGCCAA
1 TAAAG-ATGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAGAT--GAAAGATGCCAA
* * *
273593 TGTACTGATTCAAGGCCAGCGACATTGGGCTTAAGAATG
63 TGTGCTAATTCAAGGCCAGCGACATTGGACTTAAGAATG
* * *
273632 TTAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATCAGACTTAAAGATG-AAGGTGCCAATG
1 -TAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAGATGAAAGATGCCAATG
* *
273696 TGCTGATTCAAGGCTAGCGACATTGGACTTAA-AGATGG
65 TGCTAATTCAAGGCCAGCGACATTGGACTTAAGA-AT-G
* * * * * *
273734 TAAAGGTGCCAATATGCTGATTTAAGGCCAACGATATTGGACTT-AAGA-AAAAGGTGCTAATGT
1 TAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAGATGAAAGATGCCAATGT
* * *
273797 GCTAATTTAAGGCTAGCGGCATTGGACTTA
66 GCTAATTCAAGGCCAGCGACATTGGACTTA
273827 GAAAGAGATG
Statistics
Matches: 244, Mismatches: 47, Indels: 19
0.79 0.15 0.06
Matches are distributed among these distances:
100 44 0.18
101 80 0.33
102 2 0.01
103 7 0.03
104 104 0.43
105 6 0.02
106 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (101 bp):
TAAAGATGCCAATATGCTGATTCAAGGCCAACGATATTAGACTTAAAGATGAAAGATGCCAATGT
GCTAATTCAAGGCCAGCGACATTGGACTTAAGAATG
Found at i:273938 original size:32 final size:30
Alignment explanation
Indices: 273902--274085 Score: 116
Period size: 32 Copynumber: 5.8 Consensus size: 30
273892 GATGCAACCA
*
273902 ACTTGTGTGGGCTTTTAAAAGGGTTACCACCG
1 ACTTGTGTGGGC-TTTAAAA-GGTTGCCACCG
* * *** **
273934 ACTTGTATGGGCTTTAGAAAAAGTCATCACTA
1 ACTTGTGTGGGCTTT--AAAAGGTTGCCACCG
* *
273966 ACGTGTGTGGGCTTTGAAGAAGGTTGCCACTG
1 ACTTGTGTGGGCTTT-AA-AAGGTTGCCACCG
*** ** *
273998 ACTTGTGTCAACTTTAGAAAGGGCCGCCACCA
1 ACTTGTGTGGGCTTTA-AAA-GGTTGCCACCG
*
274030 ACTTGTGTGGGCTTTAAGAAGGTTGTCACCG
1 ACTTGTGTGGGCTTTAA-AAGGTTGCCACCG
274061 ACTTGTGTGGGCTTTGAAGAAGGTT
1 ACTTGTGTGGGCTTT-AA-AAGGTT
274086 TCTCCACTGG
Statistics
Matches: 117, Mismatches: 28, Indels: 14
0.74 0.18 0.09
Matches are distributed among these distances:
31 32 0.27
32 81 0.69
33 4 0.03
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (30 bp):
ACTTGTGTGGGCTTTAAAAGGTTGCCACCG
Found at i:274001 original size:64 final size:63
Alignment explanation
Indices: 273898--274075 Score: 187
Period size: 64 Copynumber: 2.8 Consensus size: 63
273888 AGGAGATGCA
* * * * *
273898 ACCAACTTGTGTGGGCTTTTAA-AAGGGTTACCACCGACTTGTATGGGCTTTAGAAAAAGTCATC
1 ACCAACGTGTGTGGGC-TTTAAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAGCCACC
* * *** ** *
273962 ACTAACGTGTGTGGGCTTTGAAGAAGGTTGCCACTGACTTGTGTCAACTTTAGAAAGGGCCGCC
1 ACCAACGTGTGTGGGCTTT-AAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAGCCACC
* *
274026 ACCAACTTGTGTGGGCTTTAAGAAGGTTGTCACCGACTTGTGTGGGCTTT
1 ACCAACGTGTGTGGGCTTTAAGAAGGTTGCCACCGACTTGTGTGGGCTTT
274076 GAAGAAGGTT
Statistics
Matches: 92, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
63 29 0.32
64 61 0.66
65 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (63 bp):
ACCAACGTGTGTGGGCTTTAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAGCCACC
Found at i:274309 original size:28 final size:28
Alignment explanation
Indices: 274258--274322 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
274248 ATACAGCAAG
* * *
274258 TGCCACTGA-TTGTGGACTTTGAAGAGA
1 TGCCACTGACATGTGAACTTCGAAGAGA
*
274285 TGCCACTGACATGTGAACTTCGAAGAGG
1 TGCCACTGACATGTGAACTTCGAAGAGA
*
274313 TGCCATTGAC
1 TGCCACTGAC
274323 TAGGGAGCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 9 0.28
28 23 0.72
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (28 bp):
TGCCACTGACATGTGAACTTCGAAGAGA
Found at i:275678 original size:15 final size:14
Alignment explanation
Indices: 275655--275704 Score: 66
Period size: 15 Copynumber: 3.6 Consensus size: 14
275645 TTCTTCCCTC
*
275655 TTTTCTTGTTTGTT
1 TTTTTTTGTTTGTT
275669 GTTTTTTTGTTTGTT
1 -TTTTTTTGTTTGTT
*
275684 TTTTTTTGTGT-TT
1 TTTTTTTGTTTGTT
275697 TTTTTTTG
1 TTTTTTTG
275705 CGAAAGACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
13 10 0.30
14 10 0.30
15 13 0.39
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (14 bp):
TTTTTTTGTTTGTT
Found at i:275684 original size:12 final size:11
Alignment explanation
Indices: 275667--275704 Score: 58
Period size: 12 Copynumber: 3.3 Consensus size: 11
275657 TTCTTGTTTG
275667 TTGTTTTTTTGT
1 TTGTTTTTTT-T
275679 TTGTTTTTTTT
1 TTGTTTTTTTT
275690 TGTGTTTTTTTT
1 T-TGTTTTTTTT
275702 TTG
1 TTG
275705 CGAAAGACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (11 bp):
TTGTTTTTTTT
Found at i:292560 original size:21 final size:20
Alignment explanation
Indices: 292527--292567 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
292517 GAGGTGTTGG
292527 ACATACTAAAAATGCATGAA
1 ACATACTAAAAATGCATGAA
*
292547 ACATAGCTCAAAATGCATGAA
1 ACATA-CTAAAAATGCATGAA
292568 CATGGGCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (20 bp):
ACATACTAAAAATGCATGAA
Found at i:296759 original size:18 final size:19
Alignment explanation
Indices: 296738--296781 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
296728 AATACAATTA
*
296738 ATAAAACAA-TAGTAAAAG
1 ATAAAACAATTAATAAAAG
* *
296756 ATAAACCAATTAATATAAG
1 ATAAAACAATTAATAAAAG
296775 ATAAAAC
1 ATAAAAC
296782 TTTTGGTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (19 bp):
ATAAAACAATTAATAAAAG
Found at i:300724 original size:17 final size:17
Alignment explanation
Indices: 300686--300724 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
300676 TAAGACAATT
300686 GATAATAATATGAAAAA
1 GATAATAATATGAAAAA
* *
300703 AATAATAATATGAAGAA
1 GATAATAATATGAAAAA
300720 GATAA
1 GATAA
300725 ATAGCTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (17 bp):
GATAATAATATGAAAAA
Found at i:301340 original size:22 final size:20
Alignment explanation
Indices: 301310--301349 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
301300 ATTTTCATCT
301310 AATAAAATTATATAATATATAA
1 AATAAAATTA-AT-ATATATAA
*
301332 AATATAATTAATATATAT
1 AATAAAATTAATATATAT
301350 TAATGAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAAAATTAATATATATAA
Found at i:303014 original size:3 final size:3
Alignment explanation
Indices: 303006--303055 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
302996 GTTTGATCTG
303006 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
303054 TT
1 TT
303056 GTTGTTGTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:303060 original size:3 final size:3
Alignment explanation
Indices: 303054--303097 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
303044 ATTATTATTA
303054 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
303098 ATTTTACCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:304517 original size:42 final size:44
Alignment explanation
Indices: 304442--304532 Score: 107
Period size: 42 Copynumber: 2.1 Consensus size: 44
304432 ATTTAATTTG
* *
304442 ATAAATTAAATTTATTTATATTAAATTTTAATTAATATTT-TT-
1 ATAAATTAAATTGATTTATATTAAATTTAAATTAATATTTATTA
** *
304484 ATAAATTAATATTGATTTA-ATTTGATTTAAATTATTATTTATTA
1 ATAAATTAA-ATTGATTTATATTAAATTTAAATTAATATTTATTA
304528 ATAAA
1 ATAAA
304533 AATATTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 26 0.63
43 10 0.24
44 5 0.12
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (44 bp):
ATAAATTAAATTGATTTATATTAAATTTAAATTAATATTTATTA
Found at i:304941 original size:9 final size:9
Alignment explanation
Indices: 304911--304985 Score: 52
Period size: 9 Copynumber: 8.2 Consensus size: 9
304901 TATGATATAA
304911 TATTAAA-T
1 TATTAAATT
304919 T-TTAAA-T
1 TATTAAATT
304926 T-TTAAATT
1 TATTAAATT
304934 TATTAAATAT
1 TATTAAAT-T
304944 TATTATAA-T
1 TATTA-AATT
304953 TATATAAATT
1 TAT-TAAATT
*
304963 AATTAAATT
1 TATTAAATT
304972 AAATATTAAATT
1 ---TATTAAATT
304984 TA
1 TA
304986 AAAAAATATT
Statistics
Matches: 56, Mismatches: 2, Indels: 17
0.75 0.03 0.23
Matches are distributed among these distances:
7 12 0.21
8 3 0.05
9 20 0.36
10 11 0.20
11 2 0.04
12 8 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
TATTAAATT
Found at i:305332 original size:23 final size:23
Alignment explanation
Indices: 305281--305332 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
305271 AAGTTAATTT
305281 TTTTAATAAATTTTAAAATATAA
1 TTTTAATAAATTTTAAAATATAA
*
305304 TATTTAAT-AATTTTAAAATTTTAA
1 T-TTTAATAAATTTTAAAA-TATAA
305328 TTTTA
1 TTTTA
305333 TTATTCACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTAATAAATTTTAAAATATAA
Found at i:305668 original size:14 final size:14
Alignment explanation
Indices: 305649--305682 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
305639 AGTATTAAAA
*
305649 TATTATTTTTATAT
1 TATTATTTATATAT
305663 TATTATTTATATAT
1 TATTATTTATATAT
*
305677 TTTTAT
1 TATTAT
305683 AATTAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTATTTATATAT
Found at i:306503 original size:29 final size:28
Alignment explanation
Indices: 306467--306530 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
306457 AGTATTTCAC
*
306467 ATTT-TATAAAT-AATTCTCTATATTTTT
1 ATTTATATAAATAAATT-ACTATATTTTT
*
306494 ATTATATATAAATAAATTACTATCTTTTT
1 ATT-TATATAAATAAATTACTATATTTTT
306523 ATTTATAT
1 ATTTATAT
306531 TTAAAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 3 0.09
28 6 0.19
29 19 0.59
30 4 0.12
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTATATAAATAAATTACTATATTTTT
Found at i:306541 original size:30 final size:29
Alignment explanation
Indices: 306484--306541 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
306474 AAATAATTCT
*
306484 CTATATTTTTATTATATATAAATAAATTA
1 CTATATTTTTATTATATATAAAAAAATTA
* *
306513 CTATCTTTTTATTTATATTTAAAAAAATT
1 CTATATTTTTA-TTATATATAAAAAAATT
306542 TATTTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (29 bp):
CTATATTTTTATTATATATAAAAAAATTA
Found at i:306550 original size:15 final size:17
Alignment explanation
Indices: 306523--306556 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
306513 CTATCTTTTT
306523 ATTTATATTTAAA-AAA
1 ATTTATATTTAAATAAA
306539 ATTTAT-TTTAAATAAA
1 ATTTATATTTAAATAAA
306555 AT
1 AT
306557 GTTGATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTATATTTAAATAAA
Found at i:307695 original size:14 final size:14
Alignment explanation
Indices: 307676--307706 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
307666 CATATTTATA
307676 TAAAAAAGAATTAAG
1 TAAAAAA-AATTAAG
307691 TAAAAAAAATTAAG
1 TAAAAAAAATTAAG
307705 TA
1 TA
307707 GAGAAGTGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.68, C:0.00, G:0.10, T:0.23
Consensus pattern (14 bp):
TAAAAAAAATTAAG
Found at i:308096 original size:2 final size:2
Alignment explanation
Indices: 308091--308139 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
308081 ATAACGTGTG
*
308091 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
308133 TA TA TA T
1 TA TA TA T
308140 TGGGACAGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:308541 original size:18 final size:18
Alignment explanation
Indices: 308501--308542 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
308491 TATTTTGTGA
*
308501 GTTAAAAAAATCATAGAT
1 GTTAAAAAAATCATAAAT
*
308519 GTTAAAAAAATCTTAAAT
1 GTTAAAAAAATCATAAAT
*
308537 TTTAAA
1 GTTAAA
308543 TTATAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (18 bp):
GTTAAAAAAATCATAAAT
Found at i:308597 original size:22 final size:22
Alignment explanation
Indices: 308570--308613 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
308560 ATTATTTTTA
308570 AAAATAATTACATAAA-TTAATT
1 AAAATAA-TACATAAATTTAATT
*
308592 AAAATAATATATAAATTTAATT
1 AAAATAATACATAAATTTAATT
308614 TTTTATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATAATACATAAATTTAATT
Found at i:308959 original size:29 final size:30
Alignment explanation
Indices: 308921--309095 Score: 121
Period size: 30 Copynumber: 5.7 Consensus size: 30
308911 AAGTAATTTA
308921 AAATATTAAAA-TATATTTATATTAAATAAT
1 AAATA-TAAAACTATATTTATATTAAATAAT
* * *
308951 AAACAT-AAATTATATTTTTTATTAAATAAT
1 AAATATAAAACTATA-TTTATATTAAATAAT
* * *
308981 AATTA-AAAATTATATTTATATTAAA-AAC
1 AAATATAAAACTATATTTATATTAAATAAT
*
309009 AAATTATTAAAACTATATTTATAATAAATAAT
1 AAA-TA-TAAAACTATATTTATATTAAATAAT
* *
309041 AAAATACATATTAAACT-TACATTATGTTAAATAAT
1 -AAAT--ATA--AAACTATA-TTTATATTAAATAAT
309076 AAAT-TAAAA-TAATATTTATA
1 AAATATAAAACT-ATATTTATA
309096 CTATTTAATT
Statistics
Matches: 115, Mismatches: 15, Indels: 31
0.71 0.09 0.19
Matches are distributed among these distances:
28 8 0.07
29 24 0.21
30 31 0.27
31 20 0.17
32 3 0.03
33 5 0.04
34 7 0.06
35 17 0.15
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
AAATATAAAACTATATTTATATTAAATAAT
Found at i:309091 original size:95 final size:89
Alignment explanation
Indices: 308924--309095 Score: 213
Period size: 95 Copynumber: 1.9 Consensus size: 89
308914 TAATTTAAAA
* * *
308924 TATTAAAATATATTTATATTAAATAATAAACATAAATTATATTTTTTATTAAATAATAATTAAAA
1 TATTAAAATATATTTATAATAAATAATAAACATAAATTAAATTTTATATTAAATAATAATTAAAA
*
308989 ATTATATTTATATTAAAAACAAAT
66 ATAATATTTATATTAAAAACAAAT
*
309013 TATTAAAACTATATTTATAATAAATAATAAA-ATACATATTAAACTTACATTATGTTAAATAATA
1 TATTAAAA-TATATTTATAATAAATAATAAACATA-A-ATTAAA-TT---TTATATTAAATAAT-
309077 AATT-AAAATAATATTTATA
58 AATTAAAAATAATATTTATA
309096 CTATTTAATT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
89 11 0.16
90 22 0.31
91 5 0.07
92 2 0.03
95 26 0.37
96 4 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (89 bp):
TATTAAAATATATTTATAATAAATAATAAACATAAATTAAATTTTATATTAAATAATAATTAAAA
ATAATATTTATATTAAAAACAAAT
Found at i:310261 original size:22 final size:21
Alignment explanation
Indices: 310222--310263 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
310212 AATTTTTACT
310222 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
310243 TAAATATTAA-TATACAAATAT
1 TAAAT-TTAATTATA-AAATAT
310264 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:310464 original size:3 final size:3
Alignment explanation
Indices: 310456--310490 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
310446 CATAACTTAA
310456 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
310491 ATAACACTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:310766 original size:3 final size:3
Alignment explanation
Indices: 310760--310805 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
310750 ATAATAATTA
* *
310760 ATT ATT ATT ATT ATT ATT CTA ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
310806 AAAGGATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:310784 original size:21 final size:21
Alignment explanation
Indices: 310758--310798 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
310748 TAATAATAAT
310758 TAATTATTATTATTATTATTC
1 TAATTATTATTATTATTATTC
310779 TAATTATTATTATTATTATT
1 TAATTATTATTATTATTATT
310799 ATTATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TAATTATTATTATTATTATTC
Found at i:314415 original size:22 final size:21
Alignment explanation
Indices: 314390--314431 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
314380 TTTTTAAAAA
*
314390 ATATTTTTATATTAATATTTAT
1 ATATTTTTAAATTAA-ATTTAT
314412 ATATTTTTAAATTAAATTTA
1 ATATTTTTAAATTAAATTTA
314432 AGTAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATTTTTAAATTAAATTTAT
Found at i:316678 original size:19 final size:18
Alignment explanation
Indices: 316654--316691 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
316644 TTAAAAATCT
316654 ATAATTA-AAATATATAAAA
1 ATAATTATAAA-AT-TAAAA
316673 ATAATTATAAAATTAAAA
1 ATAATTATAAAATTAAAA
316691 A
1 A
316692 ACATTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 9 0.50
20 3 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAATTATAAAATTAAAA
Found at i:321322 original size:23 final size:22
Alignment explanation
Indices: 321291--321342 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
321281 AAAACCCTGA
*
321291 AAAAAAAAAAACCCAAAGAACG
1 AAAAAAAAAAACCCAAAGAAAG
* *
321313 AAAAAGAAAAACCCAAGGAAAG
1 AAAAAAAAAAACCCAAAGAAAG
321335 AAAAAAAA
1 AAAAAAAA
321343 TCAAAATTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.75, C:0.13, G:0.12, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAACCCAAAGAAAG
Found at i:321619 original size:4 final size:4
Alignment explanation
Indices: 321590--321662 Score: 78
Period size: 4 Copynumber: 18.5 Consensus size: 4
321580 AGAGAAATTT
* *
321590 GAGA GGGA GAGA GCA-A GAGC GAGA GAGA GAGA GAGA GAGA GAGA GAGA
1 GAGA GAGA GAGA G-AGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA GAGA
* * *
321638 GAGA GAAA GAGA AAGA AAG- GAGA GA
1 GAGA GAGA GAGA GAGA GAGA GAGA GA
321663 CACTTGATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
3 3 0.05
4 54 0.93
5 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.47, T:0.00
Consensus pattern (4 bp):
GAGA
Found at i:321619 original size:6 final size:6
Alignment explanation
Indices: 321590--321662 Score: 78
Period size: 6 Copynumber: 12.3 Consensus size: 6
321580 AGAGAAATTT
* *
321590 GAGAGG GAGAGA GCA-AGA GCGAGA GAGAGA GAGAGA GAGAGA GAGAGA
1 GAGAGA GAGAGA G-AGAGA GAGAGA GAGAGA GAGAGA GAGAGA GAGAGA
* * *
321638 GAGAGA AAGAGA AAGAAA G-GAGA GA
1 GAGAGA GAGAGA GAGAGA GAGAGA GA
321663 CACTTGATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
5 4 0.07
6 52 0.91
7 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.47, T:0.00
Consensus pattern (6 bp):
GAGAGA
Found at i:321623 original size:10 final size:10
Alignment explanation
Indices: 321590--321662 Score: 78
Period size: 10 Copynumber: 7.4 Consensus size: 10
321580 AGAGAAATTT
*
321590 GAGAGGGAGA
1 GAGAGAGAGA
*
321600 GAGCA-AGAGC
1 GAG-AGAGAGA
321610 GAGAGAGAGA
1 GAGAGAGAGA
321620 GAGAGAGAGA
1 GAGAGAGAGA
321630 GAGAGAGAGA
1 GAGAGAGAGA
*
321640 GAGAAAGAGA
1 GAGAGAGAGA
* *
321650 AAGAAAG-GA
1 GAGAGAGAGA
321659 GAGA
1 GAGA
321663 CACTTGATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
9 6 0.11
10 48 0.87
11 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.47, T:0.00
Consensus pattern (10 bp):
GAGAGAGAGA
Found at i:321649 original size:14 final size:14
Alignment explanation
Indices: 321591--321649 Score: 68
Period size: 14 Copynumber: 4.4 Consensus size: 14
321581 GAGAAATTTG
* *
321591 AGAGGGAGAGAGCA
1 AGAGAGAGAGAGAA
*
321605 AGAGCGAGAGAG--
1 AGAGAGAGAGAGAA
*
321617 AGAGAGAGAGAGAG
1 AGAGAGAGAGAGAA
321631 AGAGAGAGAGAGAA
1 AGAGAGAGAGAGAA
321645 AGAGA
1 AGAGA
321650 AAGAAAGGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.28
14 29 0.73
ACGTcount: A:0.49, C:0.03, G:0.47, T:0.00
Consensus pattern (14 bp):
AGAGAGAGAGAGAA
Found at i:323128 original size:20 final size:20
Alignment explanation
Indices: 323103--323169 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 20
323093 GTGTGAACAG
323103 TGATGTATCGATACTATTTA
1 TGATGTATCGATACTATTTA
323123 TGATGTATCGATAC-----A
1 TGATGTATCGATACTATTTA
*
323138 --CTGTATCGATACTATTTA
1 TGATGTATCGATACTATTTA
323156 TGATGTATCGATAC
1 TGATGTATCGATAC
323170 ACTGTATCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
13 11 0.29
15 1 0.03
18 1 0.03
20 25 0.66
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (20 bp):
TGATGTATCGATACTATTTA
Found at i:323143 original size:33 final size:33
Alignment explanation
Indices: 323106--323182 Score: 154
Period size: 33 Copynumber: 2.3 Consensus size: 33
323096 TGAACAGTGA
323106 TGTATCGATACTATTTATGATGTATCGATACAC
1 TGTATCGATACTATTTATGATGTATCGATACAC
323139 TGTATCGATACTATTTATGATGTATCGATACAC
1 TGTATCGATACTATTTATGATGTATCGATACAC
323172 TGTATCGATAC
1 TGTATCGATAC
323183 ATGAATAGTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (33 bp):
TGTATCGATACTATTTATGATGTATCGATACAC
Found at i:323144 original size:13 final size:12
Alignment explanation
Indices: 323125--323185 Score: 51
Period size: 13 Copynumber: 5.2 Consensus size: 12
323115 ACTATTTATG
323125 ATGTATCGATAC
1 ATGTATCGATAC
323137 ACTGTATCGATAC
1 A-TGTATCGATAC
*
323150 TAT-T-T--AT-G
1 -ATGTATCGATAC
323158 ATGTATCGATAC
1 ATGTATCGATAC
323170 ACTGTATCGATAC
1 A-TGTATCGATAC
323183 ATG
1 ATG
323186 AATAGTGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 16
0.68 0.04 0.28
Matches are distributed among these distances:
7 2 0.05
8 1 0.03
9 3 0.08
11 3 0.08
12 5 0.13
13 24 0.62
14 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:323277 original size:21 final size:21
Alignment explanation
Indices: 323252--323292 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
323242 CCTATGAACA
323252 GTGATGTATCGATACATGAAG
1 GTGATGTATCGATACATGAAG
323273 GTGATGTATCGATACATGAA
1 GTGATGTATCGATACATGAA
323293 CAGTGATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.29
Consensus pattern (21 bp):
GTGATGTATCGATACATGAAG
Found at i:323307 original size:10 final size:10
Alignment explanation
Indices: 323288--323318 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
323278 GTATCGATAC
323288 ATGAACAGTG
1 ATGAACAGTG
*
323298 ATGAATAGTG
1 ATGAACAGTG
323308 ATGAACAGTG
1 ATGAACAGTG
323318 A
1 A
323319 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:323406 original size:53 final size:53
Alignment explanation
Indices: 323342--323478 Score: 238
Period size: 53 Copynumber: 2.6 Consensus size: 53
323332 CTACTACCAA
*
323342 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACC
* *
323395 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTACCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACC
323448 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
323479 TATGCAATCT
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 66 0.84
54 13 0.16
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTACCAATGACC
Found at i:323511 original size:20 final size:20
Alignment explanation
Indices: 323448--323518 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
323438 ACCAATGTCC
**
323448 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
323468 TGTATCGATAC-TATGCAATC
1 TGTATCGATACATAT-TAATG
323488 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
323508 TGTATCGATAC
1 TGTATCGATAC
323519 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:323584 original size:21 final size:21
Alignment explanation
Indices: 323558--323598 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
323548 GTCAACCTTG
323558 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
323579 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
323599 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:325172 original size:27 final size:27
Alignment explanation
Indices: 325141--325202 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
325131 TGAGGTTGTG
* *
325141 GTATCCTTTCGAAGGAATAGGGTTGGA
1 GTATCCTCTCGAAGGAATAGGGCTGGA
* * *
325168 GTATCCCCTCGGAGGAATGGGGCTGGA
1 GTATCCTCTCGAAGGAATAGGGCTGGA
325195 GTATCCTC
1 GTATCCTC
325203 GATGGGTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.34, T:0.26
Consensus pattern (27 bp):
GTATCCTCTCGAAGGAATAGGGCTGGA
Found at i:330792 original size:83 final size:83
Alignment explanation
Indices: 330641--330806 Score: 253
Period size: 83 Copynumber: 2.0 Consensus size: 83
330631 AGCCATATGG
* * * *
330641 TGTAACTTTTTTGCATGGGCCATATCATGTAGTTACGTGACTAACAAACCTAGCATGAAAATGTC
1 TGTAACTTCTTTGCATGGGCCACATCATGTAGTTACATGACTAACAAACCTAGCATGAAAATGCC
330706 AGAA-ACCTACTTACACAA
66 AGAAGA-CTACTTACACAA
* *
330724 TGTAGCTTCTTTGCATGGGCCACATCATGTAGTTACATGACTAACAATCCTAGCATGAAAATGCC
1 TGTAACTTCTTTGCATGGGCCACATCATGTAGTTACATGACTAACAAACCTAGCATGAAAATGCC
*
330789 AGAAGATTACTTACACAA
66 AGAAGACTACTTACACAA
330807 CTAACACATT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
83 74 0.99
84 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (83 bp):
TGTAACTTCTTTGCATGGGCCACATCATGTAGTTACATGACTAACAAACCTAGCATGAAAATGCC
AGAAGACTACTTACACAA
Found at i:336256 original size:54 final size:54
Alignment explanation
Indices: 336174--336277 Score: 163
Period size: 54 Copynumber: 1.9 Consensus size: 54
336164 TTGACTCTAT
* * *
336174 AATTTTGTCAAAAAGTTTTTTACATAATAATGCTGATAAGTGCATTTACTTTTG
1 AATTTTGTCAAAAAGTTTTGTACATAATAATACTAATAAGTGCATTTACTTTTG
**
336228 AATTTTGTCAAATGGTTTTGTACATAATAATACTAATAAGTGCATTTACT
1 AATTTTGTCAAAAAGTTTTGTACATAATAATACTAATAAGTGCATTTACT
336278 CCAAATTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (54 bp):
AATTTTGTCAAAAAGTTTTGTACATAATAATACTAATAAGTGCATTTACTTTTG
Found at i:337886 original size:21 final size:20
Alignment explanation
Indices: 337861--337914 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
337851 GTGTATGTAG
*
337861 ATGAAATAATGTATTGGTTGA
1 ATGAAA-AATGCATTGGTTGA
**
337882 ATGAAAGAATGCATTTTTTGA
1 ATGAAA-AATGCATTGGTTGA
337903 ATGAAAAATGCA
1 ATGAAAAATGCA
337915 ACTTTTGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.43, C:0.04, G:0.20, T:0.33
Consensus pattern (20 bp):
ATGAAAAATGCATTGGTTGA
Found at i:337920 original size:20 final size:21
Alignment explanation
Indices: 337878--337921 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
337868 AATGTATTGG
**
337878 TTGAATGAAAGAATGCATTTT
1 TTGAATGAAAGAATGCAACTT
337899 TTGAATGAAA-AATGCAACTT
1 TTGAATGAAAGAATGCAACTT
337919 TTG
1 TTG
337922 TAACCATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (21 bp):
TTGAATGAAAGAATGCAACTT
Found at i:337920 original size:21 final size:21
Alignment explanation
Indices: 337878--337920 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
337868 AATGTATTGG
*
337878 TTGAATGAAAGAATGCATTTT
1 TTGAATGAAAGAATGCACTTT
337899 TTGAATGAAA-AATGCAACTTT
1 TTGAATGAAAGAATGC-ACTTT
337920 T
1 T
337921 GTAACCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (21 bp):
TTGAATGAAAGAATGCACTTT
Found at i:338647 original size:4 final size:4
Alignment explanation
Indices: 338638--338667 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
338628 AAACAATGTT
*
338638 TTTA TTTA TTTA TGTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
338668 AGAGTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:338657 original size:16 final size:16
Alignment explanation
Indices: 338633--338666 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
338623 AGCTCAAACA
*
338633 ATGTTTTTATTTATTT
1 ATGTATTTATTTATTT
338649 ATGTATTTATTTATTT
1 ATGTATTTATTTATTT
338665 AT
1 AT
338667 TAGAGTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (16 bp):
ATGTATTTATTTATTT
Found at i:338877 original size:15 final size:15
Alignment explanation
Indices: 338857--338907 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
338847 ATTTTTTATA
338857 TTAAAAATTTAAATT
1 TTAAAAATTTAAATT
**
338872 TTAAAAATAAAAAATT
1 TTAAAAAT-TTAAATT
*
338888 TT-AAATTTTAAAATT
1 TTAAAAATTT-AAATT
338903 TTAAA
1 TTAAA
338908 TCATAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAAAATTTAAATT
Found at i:338901 original size:8 final size:8
Alignment explanation
Indices: 338857--338907 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 8
338847 ATTTTTTATA
*
338857 TTAAAAAT
1 TTAAAATT
338865 TT-AAATT
1 TTAAAATT
*
338872 TTAAAAAT
1 TTAAAATT
**
338880 AAAAAATT
1 TTAAAATT
338888 TT-AAATT
1 TTAAAATT
338895 TTAAAATT
1 TTAAAATT
338903 TTAAA
1 TTAAA
338908 TCATAAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
7 13 0.38
8 21 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
TTAAAATT
Found at i:338914 original size:15 final size:15
Alignment explanation
Indices: 338882--338924 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
338872 TTAAAAATAA
**
338882 AAAATTTTAAATTTT
1 AAAATTTTAAATCAT
338897 AAAATTTTAAATCAT
1 AAAATTTTAAATCAT
*
338912 AAATTTATTAAAT
1 AAAATT-TTAAAT
338925 ATTATTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAATTTTAAATCAT
Found at i:339125 original size:29 final size:29
Alignment explanation
Indices: 339082--339165 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 29
339072 ATTAAAAAGG
* *
339082 AGATAATTATTATATAATTTTATAAAATA
1 AGATAAATATAATATAATTTTATAAAATA
* *
339111 AGATAAATATAATAT-ATTTAATAAATTA
1 AGATAAATATAATATAATTTTATAAAATA
* *
339139 A-AT-AATAATAATA-AATATTATATAATA
1 AGATAAAT-ATAATATAATTTTATAAAATA
339166 TATTTAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 3 0.07
27 17 0.38
28 12 0.27
29 13 0.29
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
AGATAAATATAATATAATTTTATAAAATA
Found at i:339134 original size:18 final size:19
Alignment explanation
Indices: 339113--339165 Score: 53
Period size: 18 Copynumber: 3.0 Consensus size: 19
339103 ATAAAATAAG
*
339113 ATAAATATAATATAT-TTA
1 ATAAATATAATATATAATA
339131 ATAAAT-TAA-ATAATAATA
1 ATAAATATAATAT-ATAATA
339149 ATAAATAT--TATATAATA
1 ATAAATATAATATATAATA
339166 TATTTAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
16 2 0.07
17 11 0.37
18 16 0.53
19 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATAAATATAATATATAATA
Found at i:339143 original size:27 final size:29
Alignment explanation
Indices: 339082--339151 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
339072 ATTAAAAAGG
* * *
339082 AGATAATTATTATATAATTTTATAAAATA
1 AGATAAATATAATATAATTTAATAAAATA
*
339111 AGATAAATATAATAT-ATTTAATAAATTA
1 AGATAAATATAATATAATTTAATAAAATA
339139 A-AT-AATAATAATA
1 AGATAAAT-ATAATA
339152 AATATTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 3 0.08
27 8 0.22
28 12 0.33
29 13 0.36
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (29 bp):
AGATAAATATAATATAATTTAATAAAATA
Found at i:339868 original size:27 final size:27
Alignment explanation
Indices: 339819--339885 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
339809 TTTATTTATT
*
339819 TATTT-TATTATATTATAAAATATTGTA
1 TATTTATATTATATTATAAAATATT-AA
* *
339846 TATTTATATTA-ATTTTAATATATTAA
1 TATTTATATTATATTATAAAATATTAA
339872 TAATTTATATTATA
1 T-ATTTATATTATA
339886 AAAATTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 2 0.06
27 26 0.76
28 6 0.18
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
TATTTATATTATATTATAAAATATTAA
Found at i:339924 original size:19 final size:19
Alignment explanation
Indices: 339900--339937 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
339890 TTTTAAAAAT
339900 ATATTTATATCATA-TTTTA
1 ATATTTATAT-ATAGTTTTA
339919 ATATTTATATATAGTTTTA
1 ATATTTATATATAGTTTTA
339938 TTTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (19 bp):
ATATTTATATATAGTTTTA
Found at i:340376 original size:19 final size:18
Alignment explanation
Indices: 340350--340401 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
340340 ATCATATAAA
340350 TATAAATATAGTATTAAT
1 TATAAATATAGTATTAAT
*
340368 TATTAAATAT-GT-TAAAAT
1 TA-TAAATATAGTAT-TAAT
340386 TATAAATATA-TATTAA
1 TATAAATATAGTATTAA
340402 ATTTATCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
17 11 0.39
18 10 0.36
19 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
TATAAATATAGTATTAAT
Found at i:340403 original size:18 final size:18
Alignment explanation
Indices: 340346--340404 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
340336 GTTAATCATA
340346 TAAA-TATAAATATAGTAT
1 TAAATTATAAATATA-TAT
*
340364 T-AATTATTAAATATGT-T
1 TAAATTA-TAAATATATAT
*
340381 AAAATTATAAATATATAT
1 TAAATTATAAATATATAT
340399 TAAATT
1 TAAATT
340405 TATCATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 11 0.33
18 15 0.45
19 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TAAATTATAAATATATAT
Found at i:341078 original size:17 final size:18
Alignment explanation
Indices: 341052--341093 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
341042 TTTACCTAAA
341052 TTATTATTTATTAAAATT
1 TTATTATTTATTAAAATT
*
341070 TTATT-TTTATTTAAATT
1 TTATTATTTATTAAAATT
*
341087 TAATTAT
1 TTATTAT
341094 AAATAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTATTTATTAAAATT
Found at i:341754 original size:23 final size:24
Alignment explanation
Indices: 341725--341786 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
341715 AATTTTAAAA
*
341725 TATTTATTTATTTTTGTCATTTTT
1 TATTTATTTATTTTTGTCATATTT
* ** *
341749 TA-TTATGTATTAATGTTATATTT
1 TATTTATTTATTTTTGTCATATTT
341772 TATTTATTTATTTTT
1 TATTTATTTATTTTT
341787 TGTCTAACAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.71
Consensus pattern (24 bp):
TATTTATTTATTTTTGTCATATTT
Found at i:342738 original size:16 final size:16
Alignment explanation
Indices: 342717--342747 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
342707 AAACCCCAAA
342717 CTACCAACAGCAAGCC
1 CTACCAACAGCAAGCC
342733 CTACCAACAGCAAGC
1 CTACCAACAGCAAGC
342748 TTAGTGTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.42, G:0.13, T:0.06
Consensus pattern (16 bp):
CTACCAACAGCAAGCC
Found at i:345629 original size:2 final size:2
Alignment explanation
Indices: 345622--345670 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
345612 AAATATAGAG
*
345622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT 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
*
345664 AT GT AT A
1 AT AT AT A
345671 CATTTTTGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:346188 original size:24 final size:24
Alignment explanation
Indices: 346161--346207 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
346151 AATAATGACC
*
346161 TCAGGCTCTTCTTCTAT-TTCCTCT
1 TCAGACTCTTCTTCT-TCTTCCTCT
346185 TCAGACTCTTCTTCTTCTTCCTC
1 TCAGACTCTTCTTCTTCTTCCTC
346208 CATTTCGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.09, C:0.36, G:0.06, T:0.49
Consensus pattern (24 bp):
TCAGACTCTTCTTCTTCTTCCTCT
Found at i:351722 original size:88 final size:86
Alignment explanation
Indices: 351483--351723 Score: 221
Period size: 88 Copynumber: 2.7 Consensus size: 86
351473 ATCAATTTTT
* ** * * * *
351483 TTTCTATCGTGTAAGAAAAAATCTAATACCATATGCATTTATCTCATCTTTTGGGTTTTAAAAAA
1 TTTCTATAGTGTAAG-AAAAATCTAATACCCCATGCATCTATCACATC-TTTCGGTTTTAAGAAA
351548 TTTATTAGGCATTAGTCAAATAC
64 TTTATTAGGCATTAGTCAAATAC
* * * ** * * *
351571 TTTCTATAATGTAAGAAAGAATCTGATATCCCATATATCTGTCACATCTTTCGCATTTCAAGAAA
1 TTTCTATAGTGTAAGAAA-AATCTAATACCCCATGCATCTATCACATCTTTCG-GTTTTAAGAAA
* *
351636 TTTATTAGGCTTTAGTCAAATAT
64 TTTATTAGGCATTAGTCAAATAC
* * * * * *
351659 TTTTTGTTGTGTTAGAAGAAATCTTATACCCCATGCATCCATCACATCTTTCCGGTTTTAAGAAA
1 TTTCTATAGTGTAAGAA-AAATCTAATACCCCATGCATCTATCACATCTTT-CGGTTTTAAGAAA
351724 AATATTATGC
Statistics
Matches: 119, Mismatches: 30, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
87 7 0.06
88 109 0.92
89 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (86 bp):
TTTCTATAGTGTAAGAAAAATCTAATACCCCATGCATCTATCACATCTTTCGGTTTTAAGAAATT
TATTAGGCATTAGTCAAATAC
Found at i:355010 original size:13 final size:13
Alignment explanation
Indices: 354979--355015 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
354969 GATTTTTATT
354979 TAATA-TTTT-AA
1 TAATATTTTTAAA
*
354990 TTATATTTTTAAA
1 TAATATTTTTAAA
355003 TAATATTTTTAAA
1 TAATATTTTTAAA
355016 AAACTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 4 0.18
12 4 0.18
13 14 0.64
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TAATATTTTTAAA
Found at i:355660 original size:3 final size:3
Alignment explanation
Indices: 355652--355684 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
355642 CTCAAATTTT
*
355652 ATA ATA ATA ATA ATA ATA ATA ATA TTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
355685 TTATTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:356011 original size:16 final size:16
Alignment explanation
Indices: 355987--356035 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
355977 GCACTAATAT
*
355987 TATTAAATTATATTAA
1 TATTTAATTATATTAA
356003 TATTTAATTA-A--AA
1 TATTTAATTATATTAA
356016 TATTT--TTATATTAA
1 TATTTAATTATATTAA
356030 TATTTA
1 TATTTA
356036 TCATTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
11 3 0.11
12 1 0.04
13 7 0.25
14 7 0.25
15 1 0.04
16 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTAATTATATTAA
Found at i:356026 original size:21 final size:21
Alignment explanation
Indices: 355981--356027 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
355971 CTTATAGCAC
*
355981 TAATA-TT-ATTAAATTATAT
1 TAATATTTAATTAAAATATAT
*
356000 TAATATTTAATTAAAATATTT
1 TAATATTTAATTAAAATATAT
*
356021 TTATATT
1 TAATATT
356028 AATATTTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 5 0.22
20 2 0.09
21 16 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TAATATTTAATTAAAATATAT
Found at i:356053 original size:27 final size:27
Alignment explanation
Indices: 355996--356054 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
355986 TTATTAAATT
**
355996 ATATTAATATTTAATTAAAATATTTTT
1 ATATTAATATTTAATTAAAATATTTAA
356023 ATATTAATATTTATCATT-AAAT-TTTAA
1 ATATTAATATTTA--ATTAAAATATTTAA
356050 ATATT
1 ATATT
356055 TTTTATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 21 0.75
28 4 0.14
29 3 0.11
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
ATATTAATATTTAATTAAAATATTTAA
Found at i:356669 original size:206 final size:206
Alignment explanation
Indices: 356314--356715 Score: 606
Period size: 206 Copynumber: 2.0 Consensus size: 206
356304 TGTCTTTCGA
* * * *
356314 TTACTTTTACATTACGTTTGGTTGGAGTGAATAAGCATTCTATTTCATGCCTATATATTGTGGGA
1 TTACTTTTACATTACGTTTGGTTGGAGTGAATAAGCATTCTATTCCATGCCTATACATTATAGGA
* *
356379 CTACCATTCACATGTTTGGTTCAATTTTGATTTTTGAATTACAATTCTTCATTCTTACTTTATTC
66 CCACCATTAACATGTTTGGTTCAATTTTGATTTTTGAATTACAATTCTTCATTCTTACTTTATTC
* * * * * *
356444 AGTAAAAGCTTTGAATTGAAATTCAGTGACTCCCACCGTAATAGCAATTCCATGGAGATAAGGAA
131 AGTAAAAACCTTCAATTGAAATTCAGTGACTCCCACCATAATAGCAATTCCACGAAGATAAGGAA
356509 TCATCATTTGG
196 TCATCATTTGG
* *
356520 TTACTTTTACGTTATGTTTGGTTGGAGTGAATAAGCATTCTATTCCATGCCTATACATTATAGGA
1 TTACTTTTACATTACGTTTGGTTGGAGTGAATAAGCATTCTATTCCATGCCTATACATTATAGGA
* * * * *
356585 CCATCATTAACGTGTTTGGTTTAATTTTGCTTTTTGAATTACAATTCTTCATTCTTGCTTTATTC
66 CCACCATTAACATGTTTGGTTCAATTTTGATTTTTGAATTACAATTCTTCATTCTTACTTTATTC
* * *
356650 AGTAAAAACCTTCAATTGAAATTTAGTGGCTCCTACCATAATAGCAATTCCACGAAGATAAGGAA
131 AGTAAAAACCTTCAATTGAAATTCAGTGACTCCCACCATAATAGCAATTCCACGAAGATAAGGAA
356715 T
196 T
356716 AGCTCAATTT
Statistics
Matches: 174, Mismatches: 22, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
206 174 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (206 bp):
TTACTTTTACATTACGTTTGGTTGGAGTGAATAAGCATTCTATTCCATGCCTATACATTATAGGA
CCACCATTAACATGTTTGGTTCAATTTTGATTTTTGAATTACAATTCTTCATTCTTACTTTATTC
AGTAAAAACCTTCAATTGAAATTCAGTGACTCCCACCATAATAGCAATTCCACGAAGATAAGGAA
TCATCATTTGG
Found at i:363262 original size:84 final size:84
Alignment explanation
Indices: 363121--363288 Score: 336
Period size: 84 Copynumber: 2.0 Consensus size: 84
363111 AACTTGGACC
363121 ACATGGTTTTGGCATTCAATGCCATGCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATGT
1 ACATGGTTTTGGCATTCAATGCCATGCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATGT
363186 GGCAATTGAGATTTGACAT
66 GGCAATTGAGATTTGACAT
363205 ACATGGTTTTGGCATTCAATGCCATGCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATGT
1 ACATGGTTTTGGCATTCAATGCCATGCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATGT
363270 GGCAATTGAGATTTGACAT
66 GGCAATTGAGATTTGACAT
363289 GAATCCTGAT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (84 bp):
ACATGGTTTTGGCATTCAATGCCATGCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATGT
GGCAATTGAGATTTGACAT
Found at i:363457 original size:13 final size:13
Alignment explanation
Indices: 363439--363463 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
363429 TAAAGATCAG
363439 TGTATCGATACAA
1 TGTATCGATACAA
363452 TGTATCGATACA
1 TGTATCGATACA
363464 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:363476 original size:21 final size:21
Alignment explanation
Indices: 363450--363508 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
363440 GTATCGATAC
363450 AATGTATCGATACATTTGAGT
1 AATGTATCGATACATTTGAGT
363471 AATGTATCGATACATTTGAGT
1 AATGTATCGATACATTTGAGT
363492 AATGTATCGATACATTT
1 AATGTATCGATACATTT
363509 TTTGGCAGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (21 bp):
AATGTATCGATACATTTGAGT
Found at i:363566 original size:13 final size:13
Alignment explanation
Indices: 363548--363572 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
363538 AAAAAAAATA
363548 TGTATCGATACAT
1 TGTATCGATACAT
363561 TGTATCGATACA
1 TGTATCGATACA
363573 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:365974 original size:2 final size:2
Alignment explanation
Indices: 365967--366003 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
365957 ATACACGCAT
365967 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
366004 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:367004 original size:31 final size:31
Alignment explanation
Indices: 366969--367030 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
366959 CTCTCTTTCC
366969 CTGTCTAGTTTGGAATTCTTATTCTTACGGT
1 CTGTCTAGTTTGGAATTCTTATTCTTACGGT
367000 CTGTCTAGTTTGGAATTCTTATTCTTACGGT
1 CTGTCTAGTTTGGAATTCTTATTCTTACGGT
367031 TTTAATAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.48
Consensus pattern (31 bp):
CTGTCTAGTTTGGAATTCTTATTCTTACGGT
Found at i:369466 original size:23 final size:23
Alignment explanation
Indices: 369440--369483 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
369430 ATATGATGTT
*
369440 ATGGTCAATATTTTATGGTTTCA
1 ATGGTCAATATTTAATGGTTTCA
*
369463 ATGGTCGATATTTAATGGTTT
1 ATGGTCAATATTTAATGGTTT
369484 TGACCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.48
Consensus pattern (23 bp):
ATGGTCAATATTTAATGGTTTCA
Found at i:370694 original size:17 final size:15
Alignment explanation
Indices: 370655--370692 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
370645 TTGATAATTT
*
370655 TAAATATTA-TTATA
1 TAAATATAATTTATA
370669 TAAATATAATTTATA
1 TAAATATAATTTATA
370684 TAAA-ATAAT
1 TAAATATAAT
370693 AAAAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATATAATTTATA
Found at i:370750 original size:18 final size:17
Alignment explanation
Indices: 370727--370790 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 17
370717 ATATATTAAA
370727 TTAATATAATACAAATTT
1 TTAATATAATA-AAATTT
*
370745 TTAATATATTAAAATTT
1 TTAATATAATAAAATTT
370762 ATATAA-AT-ATAAAATATT
1 -T-TAATATAATAAAAT-TT
370780 TTAAGTATAAT
1 TTAA-TATAAT
370791 TATGATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
16 3 0.08
17 13 0.34
18 17 0.45
19 5 0.13
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TTAATATAATAAAATTT
Found at i:372120 original size:14 final size:15
Alignment explanation
Indices: 372080--372128 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
372070 AACTTAATCT
372080 AATTAATTTATATAATTA
1 AATTAATTT-T-TAA-TA
372098 AA-T-ATTTTTAA-A
1 AATTAATTTTTAATA
372110 AATTAATTTTTAATA
1 AATTAATTTTTAATA
372125 AATT
1 AATT
372129 TAAGATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 3 0.11
13 1 0.04
14 11 0.39
15 6 0.21
16 4 0.14
17 1 0.04
18 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTAATTTTTAATA
Found at i:372448 original size:16 final size:16
Alignment explanation
Indices: 372427--372461 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
372417 TTTTTAATTT
*
372427 TAATTAATTATTTTAA
1 TAATTAATTATATTAA
372443 TAATTAATTATATTAA
1 TAATTAATTATATTAA
372459 TAA
1 TAA
372462 ATATTAAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTAATTATATTAA
Found at i:380678 original size:18 final size:18
Alignment explanation
Indices: 380631--380681 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
380621 ATTAATATAA
*
380631 AAAAATTAT-TAACATATC
1 AAAATTTATATAA-ATATC
*
380649 AAAATTTATATAAATATA
1 AAAATTTATATAAATATC
380667 AAATATTTTATATAA
1 AAA-A-TTTATATAA
380682 TTATAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 15 0.54
19 4 0.14
20 9 0.32
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAATTTATATAAATATC
Found at i:380694 original size:23 final size:22
Alignment explanation
Indices: 380653--380719 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
380643 CATATCAAAA
380653 TTTATATAA-AT-ATAAAATAT
1 TTTATATAATATAATAAAATAT
*
380673 TTTATATAATTATAATAAAATAA
1 TTTATATAA-TATAATAAAATAT
**
380696 AATATATAAATATAATACAAATAT
1 TTTATAT-AATATAATA-AAATAT
380720 ATTAATTATC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
20 9 0.24
22 2 0.05
23 20 0.53
24 7 0.18
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTATATAATATAATAAAATAT
Found at i:380719 original size:19 final size:18
Alignment explanation
Indices: 380686--380721 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
380676 ATATAATTAT
380686 AATAAAATAAAATATATA
1 AATAAAATAAAATATATA
*
380704 AATATAATACAAATATAT
1 AATAAAATA-AAATATAT
380722 TAATTATCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAAATAAAATATATA
Found at i:385562 original size:2 final size:2
Alignment explanation
Indices: 385555--385592 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
385545 AGCAACTTTG
385555 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
385593 GAAATCATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:386453 original size:33 final size:32
Alignment explanation
Indices: 386410--386481 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
386400 TATCTTTTAT
* ** *
386410 ATTTTAATTTTAGTAATATTAAAAGTTAATATC
1 ATTTTTATTTTAACAATATT-AAAGGTAATATC
* *
386443 ATTTTTATTTTAACAGTATTAGAGGTAATATC
1 ATTTTTATTTTAACAATATTAAAGGTAATATC
386475 ATTTTTA
1 ATTTTTA
386482 AAATATTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (32 bp):
ATTTTTATTTTAACAATATTAAAGGTAATATC
Found at i:387865 original size:4 final size:4
Alignment explanation
Indices: 387858--387884 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
387848 TAAGAATCAG
387858 TAAA TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAA
387885 GCATTTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:388142 original size:5 final size:5
Alignment explanation
Indices: 388134--388204 Score: 52
Period size: 5 Copynumber: 13.8 Consensus size: 5
388124 GATTTGATTC
* * ** * *
388134 AAATT AAATT AAATTT AAAAT AAAAT ATTTT TAATT AAATT AAATT AATTT
1 AAATT AAATT AAA-TT AAATT AAATT AAATT AAATT AAATT AAATT AAATT
* *
388185 AAATT ATTATT TAATT AAAT
1 AAATT A-AATT AAATT AAAT
388205 AAAAATATTT
Statistics
Matches: 50, Mismatches: 14, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
5 42 0.84
6 8 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (5 bp):
AAATT
Found at i:388171 original size:31 final size:31
Alignment explanation
Indices: 388135--388204 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
388125 ATTTGATTCA
388135 AATTAAATTAAATTTAAAATAAAATATT-TTT
1 AATTAAATTAAA-TTAAAATAAAATATTATTT
** *
388166 AATTAAATTAAATTAATTTAAATTATTATTT
1 AATTAAATTAAATTAAAATAAAATATTATTT
388197 AATTAAAT
1 AATTAAAT
388205 AAAAATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
30 12 0.34
31 23 0.66
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
AATTAAATTAAATTAAAATAAAATATTATTT
Found at i:388269 original size:21 final size:21
Alignment explanation
Indices: 388231--388289 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
388221 ATTAATTATA
*
388231 AAATAAATAATATT-AATATAT-
1 AAATAAAT-ATTTTAAATA-ATG
*
388252 AAATTAATATTTTAAATAATG
1 AAATAAATATTTTAAATAATG
*
388273 AAATAAATTTTTTAAAT
1 AAATAAATATTTTAAAT
388290 TTTATAGATC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.19
21 26 0.81
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
AAATAAATATTTTAAATAATG
Found at i:389958 original size:22 final size:22
Alignment explanation
Indices: 389899--389960 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
389889 TTGATAAATT
*
389899 ATATTTTTAAATATA-ATATAA
1 ATATTTTAAAATATATATATAA
* *
389920 TTA-TTTAACATGA-ATATATAA
1 ATATTTTAAAAT-ATATATATAA
*
389941 ATATTTTAAAATTTATATAT
1 ATATTTTAAAATATATATAT
389961 TATAAATTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
20 7 0.23
21 11 0.35
22 13 0.42
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATTTTAAAATATATATATAA
Found at i:389966 original size:16 final size:17
Alignment explanation
Indices: 389941--390012 Score: 64
Period size: 16 Copynumber: 4.5 Consensus size: 17
389931 GAATATATAA
*
389941 ATATTTTAAAAT-TTAT
1 ATATTATAAAATATTAT
*
389957 ATATTATAAATTATTA-
1 ATATTATAAAATATTAT
*
389973 AT-TTATAATAT-TTAT
1 ATATTATAAAATATTAT
* *
389988 AAATTATAAAATATTTT
1 ATATTATAAAATATTAT
390005 ATA-TATAA
1 ATATTATAA
390013 TTTTAACATA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
14 3 0.07
15 8 0.18
16 25 0.57
17 8 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATAAAATATTAT
Found at i:389986 original size:31 final size:30
Alignment explanation
Indices: 389943--390002 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
389933 ATATATAAAT
* *
389943 ATTTTAAAATTTATATATTATAAATTATTA
1 ATTTTAAAATTTATAAATTATAAAATATTA
*
389973 ATTTATAATATTTATAAATTATAAAATATT
1 ATTT-TAAAATTTATAAATTATAAAATATT
390003 TTATATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTTTAAAATTTATAAATTATAAAATATTA
Found at i:390838 original size:31 final size:31
Alignment explanation
Indices: 390803--390870 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
390793 TATAAGCATC
* *
390803 ATTTTTGAATTATTTAAT-TATTATTTTATAA
1 ATTTTTGAA-CATGTAATATATTATTTTATAA
**
390834 ATTTTTTTACATGTAATATATTATTTTATAA
1 ATTTTTGAACATGTAATATATTATTTTATAA
*
390865 AATTTT
1 ATTTTT
390871 AAAAATTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.60
Consensus pattern (31 bp):
ATTTTTGAACATGTAATATATTATTTTATAA
Found at i:391447 original size:24 final size:23
Alignment explanation
Indices: 391420--391474 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
391410 TATTTTTATT
* *
391420 TAAATTTATTTATAAATATTAATA
1 TAAATTTATTT-TAAATAATAAAA
* *
391444 TAAATAATATTTTAAGTAATAAAA
1 TAAAT-TTATTTTAAATAATAAAA
391468 TAAATTT
1 TAAATTT
391475 TTAGATTAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 1 0.04
24 19 0.76
25 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATTTATTTTAAATAATAAAA
Found at i:391687 original size:21 final size:21
Alignment explanation
Indices: 391634--391676 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
391624 ATATAATATT
391634 TAATAAATTTTAAAATTTAAA
1 TAATAAATTTTAAAATTTAAA
391655 TAATAAATTTTAAAATTTAAA
1 TAATAAATTTTAAAATTTAAA
391676 T
1 T
391677 CTAAATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TAATAAATTTTAAAATTTAAA
Found at i:392234 original size:16 final size:16
Alignment explanation
Indices: 392215--392250 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
392205 TTCGAAACCA
*
392215 AAATAACTCAAATTCG
1 AAATAACTCAAACTCG
*
392231 AAATAATTCAAACTCG
1 AAATAACTCAAACTCG
392247 AAAT
1 AAAT
392251 GATCTACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.17, G:0.06, T:0.25
Consensus pattern (16 bp):
AAATAACTCAAACTCG
Found at i:393597 original size:20 final size:19
Alignment explanation
Indices: 393572--393612 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
393562 GATATAAATC
* *
393572 AATATTTCATTTAATATAAA
1 AATATTTAAATTAA-ATAAA
393592 AATATTTAAATTAAATAAA
1 AATATTTAAATTAAATAAA
393611 AA
1 AA
393613 ATAAATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATTTAAATTAAATAAA
Found at i:395454 original size:23 final size:23
Alignment explanation
Indices: 395410--395453 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
395400 TATAAAATTA
395410 TTTTTATATTAATATTTATATAT
1 TTTTTATATTAATATTTATATAT
*
395433 TTTTTA-ATTAA-ATTTAAATAT
1 TTTTTATATTAATATTTATATAT
395454 AAAATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 5 0.25
23 6 0.30
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTTTATATTAATATTTATATAT
Found at i:395868 original size:22 final size:20
Alignment explanation
Indices: 395843--395885 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 20
395833 TAATATTTTT
395843 TAATTTAAATAAAATAAAATTA
1 TAATTT-AATAAAA-AAAATTA
*
395865 TAATTTAATAATAAAAATTA
1 TAATTTAATAAAAAAAATTA
395885 T
1 T
395886 TTTTTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 6 0.30
22 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATTTAATAAAAAAAATTA
Found at i:395933 original size:51 final size:48
Alignment explanation
Indices: 395836--395972 Score: 138
Period size: 51 Copynumber: 2.8 Consensus size: 48
395826 TTAAACATAA
*
395836 TATTTTTTAATTTAAA-TAA-AATAAAATTATAATTTAATAATAAAAAT
1 TATTTTTT-ATTTAAATTAATTATAAAATTATAATTTAATAATAAAAAT
395883 TATTTTTTATTTAAATTTAATTATAAAATATATAAATATTAAT-ATAAAAAT
1 TATTTTTTATTTAAA-TTAATTATAAAAT-TAT-AAT-TTAATAATAAAAAT
* * * *
395934 AATTTTTTACTTTTAATTAATT-TATGAATAATAATTTAA
1 TATTTTTTA-TTTAAATTAATTATA-AAATTATAATTTAA
395973 ACTTCTGAGG
Statistics
Matches: 77, Mismatches: 5, Indels: 15
0.79 0.05 0.15
Matches are distributed among these distances:
46 7 0.09
47 8 0.10
48 7 0.09
49 10 0.13
50 7 0.09
51 28 0.36
52 10 0.13
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (48 bp):
TATTTTTTATTTAAATTAATTATAAAATTATAATTTAATAATAAAAAT
Found at i:396758 original size:2 final size:2
Alignment explanation
Indices: 396751--396779 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
396741 AAACAAATTT
396751 TA TA 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 TA TA T
396780 TATCAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:397961 original size:18 final size:18
Alignment explanation
Indices: 397936--397973 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
397926 TAAAAATTTA
397936 ATAAATTATC-ATTTTTT
1 ATAAATTATCAATTTTTT
397953 ATAATATTATCTAATTTTTT
1 ATAA-ATTATC-AATTTTTT
397973 A
1 A
397974 GAATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
20 8 0.44
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (18 bp):
ATAAATTATCAATTTTTT
Found at i:399202 original size:3 final size:3
Alignment explanation
Indices: 399194--399219 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
399184 GAAAAGGGAG
399194 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
399220 GTGGGGCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:399967 original size:6 final size:6
Alignment explanation
Indices: 399958--399991 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
399948 GAAGCTGCAG
399958 CTGAGA CTGAGA CTGAGA CTGAGA CTGAGA CTGA
1 CTGAGA CTGAGA CTGAGA CTGAGA CTGAGA CTGA
399992 AGAAGGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.32, C:0.18, G:0.32, T:0.18
Consensus pattern (6 bp):
CTGAGA
Done.