Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold565
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: 391512
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
File 3 of 3
Found at i:331526 original size:18 final size:18
Alignment explanation
Indices: 331478--331534 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
331468 GGCAAATTTG
331478 CCCAGATGTATCGATACA
1 CCCAGATGTATCGATACA
*
331496 -CTATGAAATGTATCGATACA
1 CCCA-G--ATGTATCGATACA
331516 CCCAGATGTATCGATACA
1 CCCAGATGTATCGATACA
331534 C
1 C
331535 TATGAAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
17 2 0.06
18 15 0.45
20 14 0.42
21 2 0.06
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (18 bp):
CCCAGATGTATCGATACA
Found at i:331529 original size:38 final size:38
Alignment explanation
Indices: 331478--331553 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
331468 GGCAAATTTG
331478 CCCAGATGTATCGATACACTATGAAATGTATCGATACA
1 CCCAGATGTATCGATACACTATGAAATGTATCGATACA
331516 CCCAGATGTATCGATACACTATGAAATGTATCGATACA
1 CCCAGATGTATCGATACACTATGAAATGTATCGATACA
331554 TGCAGGCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (38 bp):
CCCAGATGTATCGATACACTATGAAATGTATCGATACA
Found at i:338510 original size:2 final size:2
Alignment explanation
Indices: 338503--338527 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
338493 ATAGAAATAA
338503 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 A
338528 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:338532 original size:2 final size:2
Alignment explanation
Indices: 338527--338557 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
338517 ATATATATAT
338527 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
338558 TTTCAATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:338656 original size:2 final size:2
Alignment explanation
Indices: 338649--338679 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
338639 CAATAAAAAT
338649 TA 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 TA T
338680 TTACATATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:338878 original size:2 final size:2
Alignment explanation
Indices: 338871--338899 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
338861 ATCATTATGA
338871 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 A
338900 CACACGATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:339879 original size:80 final size:81
Alignment explanation
Indices: 339746--339908 Score: 247
Period size: 80 Copynumber: 2.0 Consensus size: 81
339736 TTAGTTGTCC
* * *
339746 ATCTATTTAGCTTTACAACCCACATGTCCGCCTTCAACCACAATAACATTATACTTTTCCTTACC
1 ATCTATTTAGCTTCACAACCCACATGTCCGCCTCCAACCACAATAACATTATACTTTTCCTGACC
*
339811 ATTCACCAGCT-CTCT
66 ATTCACAAGCTCCTCT
* ** *
339826 ATCTATTTAGCTTCACAGCCTGCGTGTCCGCCTCCAACCACAATAACATTATACTTTTCCTGACC
1 ATCTATTTAGCTTCACAACCCACATGTCCGCCTCCAACCACAATAACATTATACTTTTCCTGACC
339891 ATTCACAAGCTCCTCT
66 ATTCACAAGCTCCTCT
339907 AT
1 AT
339909 GCTGACTCCA
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 68 0.92
81 6 0.08
ACGTcount: A:0.26, C:0.34, G:0.07, T:0.33
Consensus pattern (81 bp):
ATCTATTTAGCTTCACAACCCACATGTCCGCCTCCAACCACAATAACATTATACTTTTCCTGACC
ATTCACAAGCTCCTCT
Found at i:341862 original size:18 final size:19
Alignment explanation
Indices: 341830--341867 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
341820 AAGGAAATTT
*
341830 TTTCATGCAAGTT-AAGTC
1 TTTCATGCAACTTAAAGTC
*
341848 TTTCATGTAACTTAAAGTC
1 TTTCATGCAACTTAAAGTC
341867 T
1 T
341868 AATGAGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (19 bp):
TTTCATGCAACTTAAAGTC
Found at i:342915 original size:15 final size:15
Alignment explanation
Indices: 342877--342915 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 15
342867 ATTGTGTTGG
342877 CTGCTGTGGTTGGAA
1 CTGCTGTGGTTGGAA
342892 CTG-T-T-GTTGGAA
1 CTGCTGTGGTTGGAA
342904 CTGCTGTGGTTG
1 CTGCTGTGGTTG
342916 TTGATTGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
12 10 0.48
13 2 0.10
14 2 0.10
15 7 0.33
ACGTcount: A:0.10, C:0.13, G:0.38, T:0.38
Consensus pattern (15 bp):
CTGCTGTGGTTGGAA
Found at i:346384 original size:2 final size:2
Alignment explanation
Indices: 346377--346431 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
346367 TGCTAGTCTA
346377 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
346418 AT AA AT AT AA AT AT
1 AT AT AT AT AT AT AT
346432 GGAGAATCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:348559 original size:35 final size:33
Alignment explanation
Indices: 348510--348575 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 33
348500 TTTTTAGTAA
*
348510 TTCAACATTTTTAACCTTTCGAAAATTATTTTACT
1 TTCAACATTTTTAA-CTCTCGAAAA-TATTTTACT
*
348545 TTCATACA-TTTTAACTCTCTAAAATATTTTA
1 TTCA-ACATTTTTAACTCTCGAAAATATTTTA
348576 TCTTAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 7 0.25
34 8 0.29
35 10 0.36
36 3 0.11
ACGTcount: A:0.33, C:0.17, G:0.02, T:0.48
Consensus pattern (33 bp):
TTCAACATTTTTAACTCTCGAAAATATTTTACT
Found at i:352135 original size:20 final size:20
Alignment explanation
Indices: 352110--352234 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
352100 AATTAACTAG
352110 ATGTATCGATACATTAAAAA
1 ATGTATCGATACATTAAAAA
352130 ATGTATCGATACATCTGGGTAAAAAAACTGA
1 ATGTATCGATACA--T---T---AAAA---A
* *
352161 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTAAAAA
* * *
352181 ATGTATCGATACATTCATAT
1 ATGTATCGATACATTAAAAA
*
352201 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTAAAAA
352221 ATGTATCGATACAT
1 ATGTATCGATACAT
352235 CTAGGTAAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 22
0.73 0.08 0.19
Matches are distributed among these distances:
20 61 0.72
22 1 0.01
23 3 0.04
25 1 0.01
26 1 0.01
28 4 0.05
29 1 0.01
31 13 0.15
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACATTAAAAA
Found at i:354419 original size:18 final size:17
Alignment explanation
Indices: 354387--354443 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
354377 ATTTAAATTC
*
354387 TATATTTGTCTTAATAAA
1 TATATTTATC-TAATAAA
354405 TAATATTTATCTAATAAA
1 T-ATATTTATCTAATAAA
* * *
354423 TATAATTATTTAATAAT
1 TATATTTATCTAATAAA
354440 TATA
1 TATA
354444 AAATTAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 17 0.50
18 9 0.26
19 8 0.24
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (17 bp):
TATATTTATCTAATAAA
Found at i:354820 original size:76 final size:76
Alignment explanation
Indices: 354739--354888 Score: 239
Period size: 76 Copynumber: 2.0 Consensus size: 76
354729 AGGACTTTTG
* * *
354739 TGTTGAAACATG-GCCATTAGGATTATTTTGGTAATAGTACCTTATAATCGAGTCTAGGATCATG
1 TGTTGAAACATGTG-CATTAGGATTATTTCGATAATAGTACCTTAAAATCGAGTCTAGGATCATG
*
354803 TGAAAACCTTCA
65 TAAAAACCTTCA
*
354815 TGTTGAAACATGTGCATTAGGATTATTTCGATAATAGTACCTTAAAATCGATTCTAGGATCATGT
1 TGTTGAAACATGTGCATTAGGATTATTTCGATAATAGTACCTTAAAATCGAGTCTAGGATCATGT
354880 AAAAACCTT
66 AAAAACCTT
354889 TGTGTCAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
76 67 0.99
77 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (76 bp):
TGTTGAAACATGTGCATTAGGATTATTTCGATAATAGTACCTTAAAATCGAGTCTAGGATCATGT
AAAAACCTTCA
Found at i:354910 original size:76 final size:75
Alignment explanation
Indices: 354753--354916 Score: 206
Period size: 76 Copynumber: 2.2 Consensus size: 75
354743 GAAACATGGC
* * * *
354753 CATTAGGATTATTTTGGTAATAGTACCTTATAATCGAGTCTAGGATCATGTGAAAACCTTCATGT
1 CATTAGGATTATTTCGATAATAGTACCTTAAAATCGAGTCTAGGATCATGTAAAAACCTT-ATGT
* *
354818 TGAAACATGTG
65 TCAAACATATG
*
354829 CATTAGGATTATTTCGATAATAGTACCTTAAAATCGATTCTAGGATCATGTAAAAACCTT-TGTG
1 CATTAGGATTATTTCGATAATAGTACCTTAAAATCGAGTCTAGGATCATGTAAAAACCTTATGT-
354893 TCAATACATAT-
65 TCAA-ACATATG
*
354904 CTATTAGGGTTAT
1 C-ATTAGGATTAT
354917 GTTAGAATTT
Statistics
Matches: 77, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
74 3 0.04
75 4 0.05
76 70 0.91
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (75 bp):
CATTAGGATTATTTCGATAATAGTACCTTAAAATCGAGTCTAGGATCATGTAAAAACCTTATGTT
CAAACATATG
Found at i:356207 original size:13 final size:13
Alignment explanation
Indices: 356189--356213 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
356179 CTATTCACAA
356189 TGTATCGATACAC
1 TGTATCGATACAC
356202 TGTATCGATACA
1 TGTATCGATACA
356214 TGAATAGTGA
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:356294 original size:24 final size:24
Alignment explanation
Indices: 356224--356294 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
356214 TGAATAGTGA
* * *
356224 TGAACAATAATGAATAGTGATACG
1 TGAACAGTAATGAACAGTGATATG
*
356248 TGAACAGTTAT-AAGCAGTGATATG
1 TGAACAGTAATGAA-CAGTGATATG
*
356272 TGAACAGTGATGAACAGTGATAT
1 TGAACAGTAATGAACAGTGATAT
356295 ATCGATACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 2 0.05
24 36 0.90
25 2 0.05
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (24 bp):
TGAACAGTAATGAACAGTGATATG
Found at i:356332 original size:19 final size:20
Alignment explanation
Indices: 356294--356332 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
356284 AACAGTGATA
**
356294 TATCGATACTATTCACAATG
1 TATCGATACTATGAACAATG
356314 TATCGATAC-ATGAACAATG
1 TATCGATACTATGAACAATG
356333 ATGAACAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (20 bp):
TATCGATACTATGAACAATG
Found at i:356399 original size:13 final size:13
Alignment explanation
Indices: 356381--356405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
356371 TGCCAGTTTT
356381 ATGTATCGATATA
1 ATGTATCGATATA
356394 ATGTATCGATAT
1 ATGTATCGATAT
356406 TAAGCAAAAT
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:0.08, G:0.16, T:0.40
Consensus pattern (13 bp):
ATGTATCGATATA
Found at i:360513 original size:29 final size:27
Alignment explanation
Indices: 360480--360569 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 27
360470 TGTCATACAT
360480 TTTAGGGTCATTTTAGTCATTTATCATGA
1 TTTAGGGTCA-TTTAGTCATTTATCAT-A
* *
360509 TTTAGGGACATTTATGTAATTTCATTCAT-
1 TTTAGGGTCATTTA-GTCATTT-A-TCATA
*
360538 TTTAGGGTCACTTTAGTCATTTACCATCA
1 TTTAGGGTCA-TTTAGTCATTTATCAT-A
360567 TTT
1 TTT
360570 GAGGACCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
27 3 0.06
28 5 0.10
29 33 0.66
30 5 0.10
31 4 0.08
ACGTcount: A:0.24, C:0.13, G:0.14, T:0.48
Consensus pattern (27 bp):
TTTAGGGTCATTTAGTCATTTATCATA
Found at i:360544 original size:58 final size:59
Alignment explanation
Indices: 360472--360757 Score: 298
Period size: 58 Copynumber: 4.9 Consensus size: 59
360462 TTATATCATG
* *
360472 TCATACATTTTAGGGTCATTTTAGTCATTTATCATGATTTAGGGA-CATTTATGTAATT
1 TCATACATTTTAGGGTCATTTTAGTAATTTTTCATGATTTAGGGATCATTTATGTAATT
* * * ** * * *
360530 TCATTCATTTTAGGGTCACTTTAGTCATTTACCATCATTT-GAGGA-CCTTTATGCAATT
1 TCATACATTTTAGGGTCATTTTAGTAATTTTTCATGATTTAG-GGATCATTTATGTAATT
* ** * * *
360588 TCATGCATTTTAATGCCATTTTAGT-TTTTTTGCCATGATTT-GGGATCATTTGTGTAATT
1 TCATACATTTTAGGGTCATTTTAGTAATTTTT--CATGATTTAGGGATCATTTATGTAATT
* *
360647 TCATACATTTTAAGGTCATTTTAGTAATTTTTCATGATTTA-GGATCGTTTATGTAATT
1 TCATACATTTTAGGGTCATTTTAGTAATTTTTCATGATTTAGGGATCATTTATGTAATT
* * * *
360705 TCTTGCATTTTAGGGTCATTTTATTAATTTTTCATGATTTA-GGACCATTTATG
1 TCATACATTTTAGGGTCATTTTAGTAATTTTTCATGATTTAGGGATCATTTATG
360758 GTTATTTTAA
Statistics
Matches: 192, Mismatches: 30, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
57 4 0.02
58 143 0.74
59 40 0.21
60 5 0.03
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (59 bp):
TCATACATTTTAGGGTCATTTTAGTAATTTTTCATGATTTAGGGATCATTTATGTAATT
Found at i:360698 original size:117 final size:117
Alignment explanation
Indices: 360504--360757 Score: 295
Period size: 117 Copynumber: 2.2 Consensus size: 117
360494 AGTCATTTAT
* * *
360504 CATGATTTAGGGACATTTATGTAATTTCATTCATTTTAGGGTCACTTTAGTCATTTACCATCATT
1 CATGATTTAGGGACATTTATGTAATTTCATACATTTTAAGGTCACTTTAGTAATTTACCATCATT
360569 TGAGGACCTTTATGCAATTTCATGCATTTTAATGCCATTTTAGTTTTTTTGC
66 TGAGGACCTTTATGCAATTTCATGCATTTTAATGCCATTTTAGTTTTTTTGC
* * ** *
360621 CATGATTT-GGGATCATTTGTGTAATTTCATACATTTTAAGGTCATTTTAGTAATTTTTCATGAT
1 CATGATTTAGGGA-CATTTATGTAATTTCATACATTTTAAGGTCACTTTAGTAATTTACCATCAT
* * * ** *
360685 TT-AGGATCGTTTATGTAATTTCTTGCATTTTAGGGTCATTTTA-TTAATTTTT--
65 TTGAGGA-CCTTTATGCAATTTCATGCATTTTAATGCCATTTTAGTT--TTTTTGC
360737 CATGATTTA-GGACCATTTATG
1 CATGATTTAGGGA-CATTTATG
360758 GTTATTTTAA
Statistics
Matches: 116, Mismatches: 16, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
116 28 0.24
117 83 0.72
118 5 0.04
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (117 bp):
CATGATTTAGGGACATTTATGTAATTTCATACATTTTAAGGTCACTTTAGTAATTTACCATCATT
TGAGGACCTTTATGCAATTTCATGCATTTTAATGCCATTTTAGTTTTTTTGC
Found at i:360753 original size:29 final size:29
Alignment explanation
Indices: 360662--360754 Score: 102
Period size: 29 Copynumber: 3.2 Consensus size: 29
360652 CATTTTAAGG
*
360662 TCATTTTAGTAATTTTTCATGATTTAGGA
1 TCATTTTATTAATTTTTCATGATTTAGGA
* *
360691 TC-GTTTATGTAATTTCTTGCAT--TTTAGGG
1 TCATTTTAT-TAATTT-TT-CATGATTTAGGA
360720 TCATTTTATTAATTTTTCATGATTTAGGA
1 TCATTTTATTAATTTTTCATGATTTAGGA
*
360749 CCATTT
1 TCATTT
360755 ATGGTTATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
27 3 0.06
28 6 0.12
29 33 0.63
30 7 0.13
31 3 0.06
ACGTcount: A:0.24, C:0.10, G:0.14, T:0.53
Consensus pattern (29 bp):
TCATTTTATTAATTTTTCATGATTTAGGA
Found at i:360765 original size:39 final size:39
Alignment explanation
Indices: 360713--360796 Score: 132
Period size: 39 Copynumber: 2.2 Consensus size: 39
360703 TTTCTTGCAT
* * *
360713 TTTAGGGTCATTTTATTAATTTTTCATGATTTAGGACCA
1 TTTATGGTCATTTTAATAACTTTTCATGATTTAGGACCA
*
360752 TTTATGGTTATTTTAATAACTTTTCATGATTTAGGACCA
1 TTTATGGTCATTTTAATAACTTTTCATGATTTAGGACCA
360791 TTTATG
1 TTTATG
360797 CATTTTCATG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (39 bp):
TTTATGGTCATTTTAATAACTTTTCATGATTTAGGACCA
Found at i:360793 original size:29 final size:29
Alignment explanation
Indices: 360761--360851 Score: 66
Period size: 29 Copynumber: 3.1 Consensus size: 29
360751 ATTTATGGTT
360761 ATTTTAATAACTTTTCATGATTTAGGACC
1 ATTTTAATAACTTTTCATGATTTAGGACC
* **
360790 A-TTT-AT-GCATTTTCATGTATTTTAGGTTC
1 ATTTTAATAAC-TTTTCATG-A-TTTAGGACC
*
360819 ATTTTAGA-AAGC-TTCCATGATTTAGGACC
1 ATTTTA-ATAA-CTTTTCATGATTTAGGACC
360848 ATTT
1 ATTT
360852 ATGCAATTTC
Statistics
Matches: 47, Mismatches: 7, Indels: 16
0.67 0.10 0.23
Matches are distributed among these distances:
26 1 0.02
27 10 0.21
28 4 0.09
29 20 0.43
30 4 0.09
31 6 0.13
32 1 0.02
33 1 0.02
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.46
Consensus pattern (29 bp):
ATTTTAATAACTTTTCATGATTTAGGACC
Found at i:360838 original size:97 final size:97
Alignment explanation
Indices: 360655--360854 Score: 256
Period size: 97 Copynumber: 2.1 Consensus size: 97
360645 TTTCATACAT
* * * * * * *
360655 TTTAAGGTCATTTTAGTAATTTTTCATGATTTAGGATCGTTTATGTAATTTCTTGCATTTTAGGG
1 TTTATGGTCATTTTAATAACTTTTCATGATTTAGGACCATTTATGCAATTTCATGCATTTTAGGG
** ** *
360720 TCATTTTATTAATTTTTCATGATTTAGGACCA
66 TCATTTTAGAAAGCTTCCATGATTTAGGACCA
* * * *
360752 TTTATGGTTATTTTAATAACTTTTCATGATTTAGGACCATTTATGCATTTTCATGTATTTTAGGT
1 TTTATGGTCATTTTAATAACTTTTCATGATTTAGGACCATTTATGCAATTTCATGCATTTTAGGG
360817 TCATTTTAGAAAGCTTCCATGATTTAGGACCA
66 TCATTTTAGAAAGCTTCCATGATTTAGGACCA
360849 TTTATG
1 TTTATG
360855 CAATTTCATG
Statistics
Matches: 87, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
97 87 1.00
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (97 bp):
TTTATGGTCATTTTAATAACTTTTCATGATTTAGGACCATTTATGCAATTTCATGCATTTTAGGG
TCATTTTAGAAAGCTTCCATGATTTAGGACCA
Found at i:360893 original size:58 final size:58
Alignment explanation
Indices: 360753--360902 Score: 164
Period size: 58 Copynumber: 2.6 Consensus size: 58
360743 TTAGGACCAT
* * *
360753 TTATGGTTATTTTAATAACTTTT-CATGATTTAGGACCATTTATGCATTTTCATGTATT
1 TTATGGTCATTTTAATAA-TTTTCCATGATTTAGGACCATTTATGCAATTTCATGTATG
**
360811 TTA-GGTTCATTTTAGA-AAGCTTCCATGATTTAGGACCATTTATGCAATTTCATGCT-TG
1 TTATGG-TCATTTTA-ATAATTTTCCATGATTTAGGACCATTTATGCAATTTCATG-TATG
* * *
360869 TTATGGTCACTTTAATCATTTTCCATGATCTAGG
1 TTATGGTCATTTTAATAATTTTCCATGATTTAGG
360903 GTCATTTAAG
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
57 5 0.07
58 67 0.88
59 4 0.05
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (58 bp):
TTATGGTCATTTTAATAATTTTCCATGATTTAGGACCATTTATGCAATTTCATGTATG
Found at i:360910 original size:155 final size:155
Alignment explanation
Indices: 360621--360902 Score: 343
Period size: 155 Copynumber: 1.8 Consensus size: 155
360611 GTTTTTTTGC
* * * * * ** *
360621 CATGATTTGGGATCATTTGTGTAATTTCATACATTTTAAGGTCATTTTAGTAATTTTTCATGATT
1 CATGATTTAGGACCATTTATGCAATTTCATACATTTTAAGGTCATTTTAGAAAGCTTCCATGATT
* * * * * * * *
360686 TAGGATCGTTTATGTAATTTCTTGCATTTTAGGGTCATTTTATTAATTTTTCATGATTTAGGACC
66 TAGGACCATTTATGCAATTTCATGCATTTTAGGGTCACTTTAATAATTTTCCATGATCTAGGACC
360751 ATTTATGGTTATTTTAATAACTTTT
131 ATTTATGGTTATTTTAATAACTTTT
* **
360776 CATGATTTAGGACCATTTATGCATTTTCATGTATTTT-AGGTTCATTTTAGAAAGCTTCCATGAT
1 CATGATTTAGGACCATTTATGCAATTTCATACATTTTAAGG-TCATTTTAGAAAGCTTCCATGAT
* *
360840 TTAGGACCATTTATGCAATTTCATGC-TTGTTATGGTCACTTTAATCATTTTCCATGATCTAGG
65 TTAGGACCATTTATGCAATTTCATGCATT-TTAGGGTCACTTTAATAATTTTCCATGATCTAGG
360903 GTCATTTAAG
Statistics
Matches: 104, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
154 5 0.05
155 99 0.95
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (155 bp):
CATGATTTAGGACCATTTATGCAATTTCATACATTTTAAGGTCATTTTAGAAAGCTTCCATGATT
TAGGACCATTTATGCAATTTCATGCATTTTAGGGTCACTTTAATAATTTTCCATGATCTAGGACC
ATTTATGGTTATTTTAATAACTTTT
Found at i:361079 original size:28 final size:27
Alignment explanation
Indices: 360983--361079 Score: 63
Period size: 28 Copynumber: 3.4 Consensus size: 27
360973 ATTTCTAATC
**
360983 TAAGGTCATTTTAGTATTTCCATGTATTT
1 TAAGGTCATTTT-GTATTT-CATACATTT
* * *
361012 TAAGGTCCTCTTGGTTATTTCATACATATG
1 TAAGGTCAT-TTTG-TATTTCATACAT-TT
*
361042 T--GGACTATTTTGTAATTTCATACATTT
1 TAAGGTC-ATTTTGT-ATTTCATACATTT
361069 TAAGGTCATTT
1 TAAGGTCATTT
361080 AGATTATATT
Statistics
Matches: 51, Mismatches: 10, Indels: 15
0.67 0.13 0.20
Matches are distributed among these distances:
27 3 0.06
28 21 0.41
29 18 0.35
30 9 0.18
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.48
Consensus pattern (27 bp):
TAAGGTCATTTTGTATTTCATACATTT
Found at i:361126 original size:58 final size:56
Alignment explanation
Indices: 360949--361128 Score: 158
Period size: 57 Copynumber: 3.2 Consensus size: 56
360939 TTGCAATTTT
*
360949 ATGCATTTT-AGAGTCATTTAGGTTATTTC-TAATCTAAGG-TCATTTTAGTATTTCC
1 ATGCATTTTAAG-GTCATTTAGGTTATTTCATAATCTAGGGATC-TTTTAGTATTTCC
* * * *
361004 ATGTATTTTAAGGTCCTCTT-GGTTATTTCATACATAT-GTGGA-CTATTTTGTAATTT-C
1 ATGCATTTTAAGGTCAT-TTAGGTTATTTCATA-ATCTAG-GGATCT-TTTAGT-ATTTCC
* * *
361061 ATACATTTTAAGGTCATTTAGATTATATTCATAATCTAGGGATCTTTTAGCATTTTCC
1 ATGCATTTTAAGGTCATTTAGGTTAT-TTCATAATCTAGGGATCTTTTAGTA-TTTCC
361119 ATGCATTTTA
1 ATGCATTTTA
361129 GGACTATTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
55 21 0.21
56 10 0.10
57 44 0.45
58 23 0.23
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (56 bp):
ATGCATTTTAAGGTCATTTAGGTTATTTCATAATCTAGGGATCTTTTAGTATTTCC
Found at i:364632 original size:14 final size:14
Alignment explanation
Indices: 364615--364686 Score: 51
Period size: 14 Copynumber: 5.2 Consensus size: 14
364605 AGGAGAGTAA
*
364615 AGAAAGAGAAAGAG
1 AGAAAAAGAAAGAG
364629 AGAAAAAGAAAGATG
1 AGAAAAAGAAAGA-G
*
364644 -G--AAAGAAAGAA
1 AGAAAAAGAAAGAG
* *
364655 AGAAAAGGAAAGAA
1 AGAAAAAGAAAGAG
* *
364669 AAAAAAATAAAAGAG
1 AGAAAAA-GAAAGAG
364684 AGA
1 AGA
364687 GATTTATGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
12 10 0.22
14 27 0.60
15 8 0.18
ACGTcount: A:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (14 bp):
AGAAAAAGAAAGAG
Found at i:364653 original size:36 final size:38
Alignment explanation
Indices: 364595--364671 Score: 97
Period size: 36 Copynumber: 2.1 Consensus size: 38
364585 TCTTATGAAG
* *
364595 AAAGAAAGAGAGGAGAGTAAAGAAAGAGAAA-GAGAGAA
1 AAAGAAAGAGAGGAAAGTAAAGAAAGA-AAAGGAAAGAA
*
364633 AAAGAAAGA-TGGAAAG-AAAGAAAGAAAAGGAAAGAA
1 AAAGAAAGAGAGGAAAGTAAAGAAAGAAAAGGAAAGAA
364669 AAA
1 AAA
364672 AAAATAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 3 0.09
36 18 0.51
37 5 0.14
38 9 0.26
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (38 bp):
AAAGAAAGAGAGGAAAGTAAAGAAAGAAAAGGAAAGAA
Found at i:364664 original size:18 final size:17
Alignment explanation
Indices: 364592--364669 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 17
364582 TTTTCTTATG
*
364592 AAGAAAGAAAGAGAGGA
1 AAGAAAGAAAGAAAGGA
*
364609 GAGTAAAGAAAGAGAAAGAGA
1 AAG-AAAG-AA-AGAAAG-GA
*
364630 GAA-AAAGAAAG-ATGGA
1 -AAGAAAGAAAGAAAGGA
364646 AAGAAAGAAAGAAAAGGA
1 AAGAAAGAAAG-AAAGGA
364664 AAGAAA
1 AAGAAA
364670 AAAAAATAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
15 2 0.04
16 10 0.21
17 4 0.08
18 16 0.33
19 4 0.08
20 9 0.19
21 2 0.04
22 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAAGAAAGGA
Found at i:366615 original size:16 final size:17
Alignment explanation
Indices: 366596--366639 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
366586 ATCTTTTTTG
366596 CTTTCCTTTTTT-CTCT
1 CTTTCCTTTTTTCCTCT
* *
366612 CTTTCTTTTTTTCCTTT
1 CTTTCCTTTTTTCCTCT
366629 CTTTCTCTTTT
1 CTTTC-CTTTT
366640 CTTTTCTCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
CTTTCCTTTTTTCCTCT
Found at i:366618 original size:28 final size:26
Alignment explanation
Indices: 366587--366644 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 26
366577 TCTCTTTTCA
366587 TCTTTTTTGCTTTCCTTT-TTTCTCTCTT
1 TCTTTTTT--TTTCCTTTCTTTCTCT-TT
366615 TC--TTTTTTTCCTTTCTTTCTCTTT
1 TCTTTTTTTTTCCTTTCTTTCTCTTT
366639 TCTTTT
1 TCTTTT
366645 CTCCTGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
24 12 0.44
25 7 0.26
26 6 0.22
28 2 0.07
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (26 bp):
TCTTTTTTTTTCCTTTCTTTCTCTTT
Found at i:366644 original size:23 final size:24
Alignment explanation
Indices: 366597--366644 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
366587 TCTTTTTTGC
366597 TTTCCTTTTTTCTCTCTTTCTTTT
1 TTTCCTTTTTTCTCTCTTTCTTTT
366621 TTTCCTTTCTTTCTCT-TTTCTTTT
1 TTTCCTTT-TTTCTCTCTTTCTTTT
366645 CTCCTGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTCCTTTTTTCTCTCTTTCTTTT
Found at i:367205 original size:17 final size:18
Alignment explanation
Indices: 367183--367223 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
367173 GAATAAAAAA
*
367183 TTAGATG-AAGTATAAAT
1 TTAGATGCAAATATAAAT
367200 TTAGATGCAAATATAAAT
1 TTAGATGCAAATATAAAT
*
367218 ATAGAT
1 TTAGAT
367224 ATTTTGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.49, C:0.02, G:0.15, T:0.34
Consensus pattern (18 bp):
TTAGATGCAAATATAAAT
Found at i:367518 original size:2 final size:2
Alignment explanation
Indices: 367511--367537 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
367501 GTGTTTTTGC
367511 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 A
367538 GAGGTTGGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:377112 original size:42 final size:42
Alignment explanation
Indices: 377056--377174 Score: 184
Period size: 42 Copynumber: 2.8 Consensus size: 42
377046 TTCTTCTCTC
* *
377056 CTCCTTCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
* *
377098 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
* *
377140 CTCCTCCTATCATCCCTCCTCTCTCTTTTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCT
377175 TTGAGGGCTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.08, C:0.45, G:0.03, T:0.45
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
Found at i:377115 original size:12 final size:11
Alignment explanation
Indices: 377089--377164 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
377079 TCTATTATCT
*
377089 CTCCTGTCTCTC
1 CTCCTATCTC-C
377101 CTCCTATCATCC
1 CTCCTATC-TCC
377113 CTCCTATCT--
1 CTCCTATCTCC
*
377122 CTACTATCT--
1 CTCCTATCTCC
*
377131 CTCCTGTCTCTC
1 CTCCTATCTC-C
377143 CTCCTATCATCC
1 CTCCTATC-TCC
*
377155 CTCCTCTCTC
1 CTCCTATCTC
377165 TTTTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:377116 original size:24 final size:24
Alignment explanation
Indices: 377080--377165 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
377070 CCTCCTCTCT
* *
377080 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
377104 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
377125 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
377146 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
377166 TTTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:377140 original size:18 final size:18
Alignment explanation
Indices: 377071--377141 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
377061 TCTGTCATCC
* *
377071 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
377089 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
377111 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
377131 CTCCTGTCTCT
1 CTCCTGTCTCT
377142 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:381292 original size:130 final size:128
Alignment explanation
Indices: 381039--381522 Score: 379
Period size: 130 Copynumber: 3.7 Consensus size: 128
381029 GATAATAACG
* * * *
381039 GGGTTGGAGTATCTCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGA-T
1 GGGTTGGAGTATCCCCT-GAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT-ATT
* * * * * * * * * *
381103 TTAGAAATAAGGCAA--GG-GTTGAAGTGTCTCCGATTATAGAAAAT-AGATGTTTCAAAAATAG
64 TTAAAAATAA---AATCGGAGTTGAAATATCCCCGATTATGGAGAATCA-ATATTTTAGAAATAA
381164 AATC
125 AATC
* * *
381168 GGGATTGGAGTATCCCCGTGAAAATAATGGGGTTAGAGTATCCCCAATTATGAGAAATCAATATT
1 GGG-TTGGAGTATCCCC-TGAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATT
** * ** ** * * *
381233 TTAAAAATAAGGTCGGGGTTGAGGTATCCTTGATTGT-GAGAAATCAATATTTTGGAAATAAAAC
64 TTAAAAATAAAATCGGAGTTGAAATATCCCCGATTATGGAG-AATCAATATTTTAGAAATAAAAT
381297 C
128 C
* * * *
381298 AGGGTTGGAGTATCCCCTTGAAAATAACT-GGGTTGGAGTATCCCCGATTGTGAAAAATTAGTGT
1 -GGGTTGGAGTATCCCC-TGAAAATAA-TGGGGTTGGAGTATCCCCGATTATGAAAAATCAATAT
** *** *
381362 TTTGGAAATAAAATCGGAGTTGAAATATCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAAT
63 TTTAAAAATAAAATCGGAGTTGAAATATCCCCGATTATGGAGAATCAATATTTTAGAAATAAAAT
381427 C
128 C
* ** *
381428 GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGTT
1 -GGGTTGGAGTATCCCCT-GAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATT
* * * * *
381493 TTAGAAATAAAACCGGGGTTGGAGTATCCC
64 TTAAAAATAAAATCGGAGTTGAAATATCCC
381523 TTCAAAAATA
Statistics
Matches: 285, Mismatches: 57, Indels: 25
0.78 0.16 0.07
Matches are distributed among these distances:
129 9 0.03
130 267 0.94
131 9 0.03
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (128 bp):
GGGTTGGAGTATCCCCTGAAAATAATGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTT
AAAAATAAAATCGGAGTTGAAATATCCCCGATTATGGAGAATCAATATTTTAGAAATAAAATC
Found at i:381392 original size:51 final size:51
Alignment explanation
Indices: 381336--381444 Score: 146
Period size: 51 Copynumber: 2.1 Consensus size: 51
381326 TGGGTTGGAG
* *
381336 TATCCCCGATTGTGAAAAATTAGTGTTTTGGAAATAAAATCGGAGTTGAAA
1 TATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGAGTTGAAA
* * * * * *
381387 TATCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAATCGGGGTTGGAG
1 TATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGAGTTGAAA
381438 TATCCCC
1 TATCCCC
381445 TCGAAAATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (51 bp):
TATCCCCGATTATGAAAAATTAGTGTTTTAGAAATAAAATCGGAGTTGAAA
Found at i:381512 original size:260 final size:258
Alignment explanation
Indices: 381039--381521 Score: 614
Period size: 260 Copynumber: 1.9 Consensus size: 258
381029 GATAATAACG
* *
381039 GGGTTGGAGTATCTCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATAGATGATT
* * * *
381104 TAGAAATAAGGCAAGGGTTGAAGTGTCTCCGATTATAGAAAATAGATGTTTCAAAAATAGAATCG
66 TAGAAATAA-G-AAGGGTTGAAATATCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAATCG
* *
381169 GGATTGGAGTATCCCCGTGAAAATAATGGGGTTAGAGTATCCCCAATTATGAGAAATCAATATTT
129 GGATTGGAGTATCCCCGTGAAAATAACGGGGTTAGAGTATCCCCAATTATGAAAAATCAATATTT
***
381234 TAAAAATAAGGTCGGGGTT-GAGGTATCCTTGATTGTGAGAAATCAATATTTTGGAAATAAAACC
194 TAAAAATAAAACCGGGGTTGGA-GTATCCTTGATTGTGAGAAATCAATATTTTGGAAATAAAACC
381298 A
258 A
* * *
381299 GGGTTGGAGTATCCCCTTGAAAATAACTGGGTTGGAGTATCCCCGATTGTGAAAAATTAG-TGTT
1 GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAA-TAGATGAT
* * * * * * *
381363 TTGGAAATAA-AATCGGAGTTGAAATATCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAAT
65 TTAGAAATAAGAA--GG-GTTGAAATATCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAAT
* * * ** *
381427 CGGGGTTGGAGTATCCCC-TCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATG
127 CGGGATTGGAGTATCCCCGT-GAAAATAACGGGGTTAGAGTATCCCCAATTATGAAAAATCAATA
*
381491 TTTTAGAAATAAAACCGGGGTTGGAGTATCC
191 TTTTAAAAATAAAACCGGGGTTGGAGTATCC
381522 CTTCAAAAAT
Statistics
Matches: 189, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
257 2 0.01
259 3 0.02
260 180 0.95
261 4 0.02
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (258 bp):
GGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATAGATGATT
TAGAAATAAGAAGGGTTGAAATATCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAATCGGG
ATTGGAGTATCCCCGTGAAAATAACGGGGTTAGAGTATCCCCAATTATGAAAAATCAATATTTTA
AAAATAAAACCGGGGTTGGAGTATCCTTGATTGTGAGAAATCAATATTTTGGAAATAAAACCA
Found at i:381518 original size:79 final size:79
Alignment explanation
Indices: 381387--381678 Score: 369
Period size: 79 Copynumber: 3.7 Consensus size: 79
381377 GGAGTTGAAA
* * * *
381387 TATCCCCGATTATGGAGAATTGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAA
1 TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAA
381452 TAACGGGGTTGGAG
66 TAACGGGGTTGGAG
* *
381466 TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCTTCAAAAA
1 TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAA
*
381531 TAACGGGGTTGGTG
66 TAACGGGGTTGGAG
* * *
381545 TATCCCCG---ATGAAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTGTTCCCTCGAAAA
1 TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAA
*
381607 TAACGAGGTTGGAG
66 TAACGGGGTTGGAG
* * * * ** *
381621 TATCCTCGATTGTG-AAAAGTCAGTGTTTT-GAAAATAAAATTGGAGTTGGAGTATCCCC
1 TATCCCCGATTATGAAAAATTGA-TGTTTTAG-AAATAAAACCGGGGTTGGAGTATCCCC
381679 GATTATGGAA
Statistics
Matches: 184, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
76 68 0.37
78 6 0.03
79 110 0.60
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (79 bp):
TATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAA
TAACGGGGTTGGAG
Found at i:381607 original size:76 final size:75
Alignment explanation
Indices: 381404--381630 Score: 328
Period size: 76 Copynumber: 2.9 Consensus size: 75
381394 GATTATGGAG
* *
381404 AATTGGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTAT
1 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGT-TTCCCTCGAAAATAACGGGGTTGGAGTAT
381469 CCCCGATTATGAAA
65 CCCCG---ATGAAA
* * * *
381483 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCTTCAAAAATAACGGGGTTGGTGTAT
1 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTTTCCC-TCGAAAATAACGGGGTTGGAGTAT
381548 CCCCGATGAAA
65 CCCCGATGAAA
*
381559 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTGTTCCCTCGAAAATAACGAGGTTGGAGTAT
1 AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGT-TTCCCTCGAAAATAACGGGGTTGGAGTAT
*
381624 CCTCGAT
65 CCCCGAT
381631 TGTGAAAAGT
Statistics
Matches: 134, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
76 67 0.50
77 4 0.03
78 3 0.02
79 60 0.45
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.28
Consensus pattern (75 bp):
AATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTTTCCCTCGAAAATAACGGGGTTGGAGTATC
CCCGATGAAA
Found at i:381742 original size:51 final size:50
Alignment explanation
Indices: 381614--381779 Score: 174
Period size: 51 Copynumber: 3.3 Consensus size: 50
381604 AAATAACGAG
* * * * *
381614 GTTGGAGTATCCTCGATTGTGAAAAGTCAGTGTTTTGAAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTG-AAATAAAATCGGA
* *
381665 GTTGGAGTATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTT-GAAATAAAATCGGA
* * * **
381716 GTTGGAGTATCCCCGATTAAGAAAAATTGAT-TTTTGGAAACGAAATCGG-
1 GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTT-GAAATAAAATCGGA
381765 GATTGGAGTATCCCC
1 G-TTGGAGTATCCCC
381780 AAGATGAAAA
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.01
50 28 0.28
51 69 0.70
52 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAAATCGGTGTTTTGAAATAAAATCGGA
Found at i:388592 original size:50 final size:51
Alignment explanation
Indices: 388528--388695 Score: 180
Period size: 51 Copynumber: 3.3 Consensus size: 51
388518 ATTTTTCATC
* * *
388528 TCGGGGATACTCCAA-TCCCGATTTCATTTCCAAAA-ATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTCATTTCCAAAACACCAATTTTCCATAA
* * *
388578 TCGGGGATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACACCAATTTTCCATAA
* * * * * *
388629 TCGGGGATACTCCAACTCCAATTTTATTTTCAAAACACTGACTTTT-CACAA
1 TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACAC-CAATTTTCCATAA
*
388680 TCGAGGATACTCCAAC
1 TCGGGGATACTCCAAC
388696 CTCGTTATTT
Statistics
Matches: 101, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
50 31 0.31
51 66 0.65
52 4 0.04
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTCATTTCCAAAACACCAATTTTCCATAA
Found at i:388878 original size:79 final size:79
Alignment explanation
Indices: 388631--388923 Score: 387
Period size: 79 Copynumber: 3.7 Consensus size: 79
388621 TTCCATAATC
* ** ** * * *
388631 GGGGATACTCCAACTCCAATTTTATTT-TCAAAACACTGACTTTTCACAATCGAGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTATTTCT-AAAACACCAATTTTTCATAATCGGGGATACTCCAA
*
388695 CCTCGTTATTTTCGA
65 CCCCGTTATTTTCGA
* * *
388710 GGGAACACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTC---ATCGGGGATACACCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
*
388772 CCCGTTATTTTTGA
66 CCCGTTATTTTCGA
* *
388786 AGGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
388851 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* *
388865 GGGGATACTCCAACCCCGAGTTTTATTTCTAAAACACCAATTCTCCATAATCGGGGATA
1 GGGGATACTCCAACCCCG-GTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATA
388924 TTTCAACTCC
Statistics
Matches: 187, Mismatches: 22, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
76 68 0.36
79 81 0.43
80 38 0.20
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:388943 original size:51 final size:52
Alignment explanation
Indices: 388865--388983 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 52
388855 TTATTTTCGA
* *
388865 GGGGATACTCCAACCCCGAGTTTTATTTCTAAAACACCAATTCTCCATAATC
1 GGGGATACTCCAACCCCGAGTTTTATTTCCAAAACACCAATTCTCCACAATC
* * * * * *
388917 GGGGATATTTCAACTCCGA-TTTTATTTCCAAAACACTAATTTTTCACAATC
1 GGGGATACTCCAACCCCGAGTTTTATTTCCAAAACACCAATTCTCCACAATC
388968 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
388984 AGTTATTTTC
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
51 40 0.71
52 16 0.29
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (52 bp):
GGGGATACTCCAACCCCGAGTTTTATTTCCAAAACACCAATTCTCCACAATC
Found at i:388968 original size:131 final size:130
Alignment explanation
Indices: 388787--389273 Score: 489
Period size: 130 Copynumber: 3.7 Consensus size: 130
388777 TATTTTTGAA
* * *
388787 GGGATACTCCAACCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAACC
1 GGGATACTTCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
*
388852 CCGTTATTTTCGAGGGGATACTCCAACCCCGAGTTTTATTTCTAAAACACCAATTCTCCATAATC
66 CCGTTATTTTCGAGGGGATACTCCAACCCCGAGTTTTATTTCTAAAACATCAATT-TCCATAATC
388917 G
130 G
* * *
388918 GGGATATTTCAACTCCGATTTTATTTCCAAAACA-CTAATTTTTCACAATCGGGGATACTCCAAC
1 GGGATACTTCAACCCCGATTTTATTTCTAAAACATC-AATTTTTCACAATCGGGGATACTCCAAC
* * * * * ** *
388982 CCAGTTATTTTCAAGGGGATACTCCAACCCTG-GTTTTATTTCCAAAATATTGATTTCTCACAAT
65 CCCGTTATTTTCGAGGGGATACTCCAACCCCGAGTTTTATTTCTAAAACATCAATTTC-CATAAT
*
389046 CA
129 CG
* * ** * * ** * * * *
389048 AGGATACCTCAACCCCGACCTTATTTTTAAAATATTGATTTCTCATAATTGGGGATACTCTAACC
1 GGGATACTTCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
* * * * * * *
389113 CCATTATTTTC-ACGGGGATACTCCAATCCCGA-TTCTATTTTTGAAACATCTATTTTCTATAAT
66 CCGTTATTTTCGA-GGGGATACTCCAACCCCGAGTTTTATTTCTAAAACATC-AATTTCCATAAT
389176 CG
129 CG
* * * ** * *
389178 GAGACACTTCAACCCTTG-CCTTATTTCTAAATCATCGATTTTTCACAATCGGGGATACTCCAAC
1 GGGATACTTCAACCC-CGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
* *
389242 CCCGTTATTTCCGAGGAGATACTCCAACCCCG
65 CCCGTTATTTTCGAGGGGATACTCCAACCCCG
389274 TTATTATCTC
Statistics
Matches: 285, Mismatches: 63, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
129 3 0.01
130 191 0.67
131 91 0.32
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (130 bp):
GGGATACTTCAACCCCGATTTTATTTCTAAAACATCAATTTTTCACAATCGGGGATACTCCAACC
CCGTTATTTTCGAGGGGATACTCCAACCCCGAGTTTTATTTCTAAAACATCAATTTCCATAATCG
Done.