Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold250
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: 1171037
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 53818 characters in sequence are not A, C, G, or T
File 3 of 5
Found at i:402154 original size:101 final size:100
Alignment explanation
Indices: 401880--402189 Score: 462
Period size: 100 Copynumber: 3.1 Consensus size: 100
401870 ACAGTGGAGC
* * * * *
401880 AGATTAAAGCCGCAATGGCGGATCTTACTCCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
1 AGATTGAAGCCGCAACGGCGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
**
401945 CAGCGAATCTAGTTTCCCCAACATTGCAATTAAAA
66 TGGCGAATCTAGTTTCCCCAACATTGCAATTAAAA
* * *
401980 AGATTGAAGCCGCAACTGCAAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACAA
1 AGATTGAAGCCGCAACGGCGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
*
402045 TGGCGAATCTCGTTTCCCCAACATTGCAATTAAAA
66 TGGCGAATCTAGTTTCCCCAACATTGCAATTAAAA
*
402080 AGATTGAAGCCGCAAACGGCGAATTTTACTTCCCTGGCAGTGTAGTGGAACAGATTGAAGCTACG
1 AGATTGAAGCCGC-AACGGCGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACG
*
402145 ATGGTGAATCTTA-TTTCCCCAACATTGCAATGT-AAA
65 ATGGCGAATC-TAGTTTCCCCAACATTGCAAT-TAAAA
402181 AGATTGAAG
1 AGATTGAAG
402190 ATGGCGAGTC
Statistics
Matches: 190, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
100 102 0.54
101 86 0.45
102 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (100 bp):
AGATTGAAGCCGCAACGGCGAATTTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGA
TGGCGAATCTAGTTTCCCCAACATTGCAATTAAAA
Found at i:402185 original size:50 final size:50
Alignment explanation
Indices: 402030--402189 Score: 142
Period size: 50 Copynumber: 3.2 Consensus size: 50
402020 GTAGTGGAAC
**
402030 AGATTGAAGCTACAATGGCGAATCTCGTTTCCCCAACATTGCAAT-TAAAA
1 AGATTGAAGCTACAATGGCGAATCTTATTTCCCCAACATTGCAATGT-AAA
** * * * *** * * * * *
402080 AGATTGAAGCCGCAAACGGCGAATTTTACTTCCCTGGCAGTGTAGTGGAAC
1 AGATTGAAGCTAC-AATGGCGAATCTTATTTCCCCAACATTGCAATGTAAA
* *
402131 AGATTGAAGCTACGATGGTGAATCTTATTTCCCCAACATTGCAATGTAAA
1 AGATTGAAGCTACAATGGCGAATCTTATTTCCCCAACATTGCAATGTAAA
402181 AGATTGAAG
1 AGATTGAAG
402190 ATGGCGAGTC
Statistics
Matches: 78, Mismatches: 30, Indels: 4
0.70 0.27 0.04
Matches are distributed among these distances:
50 44 0.56
51 34 0.44
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (50 bp):
AGATTGAAGCTACAATGGCGAATCTTATTTCCCCAACATTGCAATGTAAA
Found at i:402823 original size:19 final size:19
Alignment explanation
Indices: 402799--402836 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
402789 AATCTTCAAG
*
402799 GATATGCAATTTTAGATAT
1 GATATGCAATCTTAGATAT
*
402818 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
402837 TTAAGGTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:403014 original size:22 final size:20
Alignment explanation
Indices: 402989--403033 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
402979 TTTACTCAAA
*
402989 TTTCTCTCTCTTGCGTTCTTAT
1 TTTCTCTCACTT--GTTCTTAT
*
403011 TTTCTCTGACTTGTTCTTAT
1 TTTCTCTCACTTGTTCTTAT
403031 TTT
1 TTT
403034 GTTGATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 11 0.52
22 10 0.48
ACGTcount: A:0.07, C:0.22, G:0.09, T:0.62
Consensus pattern (20 bp):
TTTCTCTCACTTGTTCTTAT
Found at i:405903 original size:68 final size:68
Alignment explanation
Indices: 405753--405916 Score: 177
Period size: 68 Copynumber: 2.4 Consensus size: 68
405743 TTAAAATTTC
* * * *
405753 TTTAGAAGTAAAAGAATAAATAAGTGAATAATAGATAAAACAAATGTAAACATTATTAAATTTAA
1 TTTAAAAGTAAAAGAAT-AATAAATAAATAATAGATAAAACAAATGTAAACAATATTAAATTTAA
*
405818 GCAT
65 ACAT
* * ** ** *
405822 TTGAAAAGTAAAAGAATCATAAATAAATAAATAGATAAAGTAAATGTTCATAATATT-AATTTAA
1 TTTAAAAGTAAAAGAATAATAAATAAAT-AATAGATAAAACAAATGTAAACAATATTAAATTTAA
*
405886 ATAT
65 ACAT
*
405890 TTTAAAAGTAAAAGAATGATAAATAAA
1 TTTAAAAGTAAAAGAATAATAAATAAA
405917 AGTAAAAAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
68 42 0.53
69 37 0.47
ACGTcount: A:0.57, C:0.03, G:0.10, T:0.30
Consensus pattern (68 bp):
TTTAAAAGTAAAAGAATAATAAATAAATAATAGATAAAACAAATGTAAACAATATTAAATTTAAA
CAT
Found at i:407729 original size:143 final size:143
Alignment explanation
Indices: 407502--408341 Score: 1063
Period size: 143 Copynumber: 5.9 Consensus size: 143
407492 GGTTTGCAAA
* * * **
407502 TTGTAGCTTTAATATGTTCCACAGTAACGTTAGGGAAATAAGATTCGC--TCTTCAGTCTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * * *
407565 ACTGCAATTTCAGGGAGATAAGGCTGGTGGCTTCAATTTGCTCCACTACAACTTCAGAAAGGTAA
66 GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAA
*
407630 GATCTACCATAAT
131 GATCCACCATAAT
** * * * *
407643 TTGTAGCTTTAATCTGTTCTGCTACAATGCCAGGGAAATAACATTCGTTGTCTTCAGTCTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * * *
407708 GCTGCAACTTCAGGGAAATAAGGCTGGTGACTTCAATCTACTCCACTGCAACTTCAGGAAGATAT
66 GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAA
*
407773 GATCCGCCATAAT
131 GATCCACCATAAT
* * *
407786 TTGTAGCTTTAATTTGTTCCACTGCAACGCCAGGGAGATAAGATTCGTTGTCTTCAGTCTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * *
407851 GCTGCAACTTTAGGGAGATAAGTCTGGTGGCTTCAATTTGCTCCACTACAACTTCAGAAAGATAA
66 GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAA
407916 GATCCACCATAAT
131 GATCCACCATAAT
* * * * * *
407929 TTGTAGCTTTAAACTGTTCCACTACAACGCTAGGGAAATTAGATTCACTGTCTTCAGTTTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * * * * *
407994 GCAGCAACTTTAGGGAGATAAGGCCGGTGGCTTCAATCTACTCCATTGCAAATTCAGGAAGATAA
66 GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAA
*
408059 GATCCACCGTAAT
131 GATCCACCATAAT
* * * * * * * *
408072 TTTTAGCTTTAATCTCTTCCACTGTAACGCTAGGGAAATAAGATCCGCTATCTTCAGTCTACTTC
1 TTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * * *
408137 GCTGTAACTTCAGGGAGATAAGGTTGGTGGCTTTAATCTGCTCCACTGCAGCTTCAGGAAGATAA
66 GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAA
408202 GATCCACCATAAT
131 GATCCACCATAAT
* ** * * *
408215 TTGTAACTTTAATCTGTTCCACTGCAACGTGAAGGAAATAAGATTTGCTATCTTCAGTCTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
* * * *
408280 ACTGCAACTTTAGGGAGATAAGGCTGGTGGCTTCAATTTGCTCCACTACAACTTCAAGAAGA
66 GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGA
408342 AAATATCTTC
Statistics
Matches: 595, Mismatches: 102, Indels: 2
0.85 0.15 0.00
Matches are distributed among these distances:
141 37 0.06
143 558 0.94
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (143 bp):
TTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCC
GCTGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAGGAAGATAA
GATCCACCATAAT
Found at i:409706 original size:1 final size:1
Alignment explanation
Indices: 409696--409753 Score: 62
Period size: 1 Copynumber: 58.0 Consensus size: 1
409686 CTAGTAGAGG
* ** * * *
409696 TTTTTATTTTTTTGCTTTTTGTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
409754 GTCCTCTACT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.90
Consensus pattern (1 bp):
T
Found at i:409737 original size:29 final size:29
Alignment explanation
Indices: 409696--409753 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
409686 CTAGTAGAGG
409696 TTTTTATTTTTTTGCTTTTTGTTGTTTTT
1 TTTTTATTTTTTTGCTTTTTGTTGTTTTT
* ** *
409725 TTTTTTTTTTTTTTTTTTTTTTTGTTTTT
1 TTTTTATTTTTTTGCTTTTTGTTGTTTTT
409754 GTCCTCTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.02, C:0.02, G:0.07, T:0.90
Consensus pattern (29 bp):
TTTTTATTTTTTTGCTTTTTGTTGTTTTT
Found at i:412780 original size:20 final size:23
Alignment explanation
Indices: 412741--412784 Score: 67
Period size: 20 Copynumber: 2.0 Consensus size: 23
412731 GTAAATCATG
412741 TTATTCTTAGATTATTGAATGTT
1 TTATTCTTAGATTATTGAATGTT
412764 TTATTCTTA-A-T-TTGAATGTT
1 TTATTCTTAGATTATTGAATGTT
412784 T
1 T
412785 AAAACTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.48
21 1 0.05
22 1 0.05
23 9 0.43
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.59
Consensus pattern (23 bp):
TTATTCTTAGATTATTGAATGTT
Found at i:418581 original size:168 final size:168
Alignment explanation
Indices: 418298--418639 Score: 585
Period size: 168 Copynumber: 2.0 Consensus size: 168
418288 TGAAGTCGAT
* ** * * *
418298 AAAGTAAAGGTGGATTTAATTGAAAGATTACCAGCCCCAATTACTGTGAAAGGAGTTAGAAGTTT
1 AAAGCAAAGGTGGACGTAATTGAAAGATTACCAGCCCCAATGAATGTGAAAGGAGTCAGAAGTTT
*
418363 CTTAGGCCATGCCGGTTTTTACCGAAGGTTTATCAAGGATTTCTCAAAAATTTCTAAGCCGCTGT
66 CTTAGGCCATGCCGGTTTTTACCGAAGGTTTATCAAGGATTTCTCAAAAATTTCTAAGCCGCTAT
*
418428 GTTTGTTGTTAGAGAAAGATACAATGTTCAATTTCAAC
131 GTTTGTTGTTAGAGAAAGATACAATGTTCAATTTCAAA
418466 AAAGCAAAGGTGGACGTAATTGAAAGATTACCAGCCCCAATGAATGTGAAAGGAGTCAGAAGTTT
1 AAAGCAAAGGTGGACGTAATTGAAAGATTACCAGCCCCAATGAATGTGAAAGGAGTCAGAAGTTT
* * *
418531 CTTAGGCCATGCCGGTTTTTACCGAAGGTTTATTAAGGATTTCTCAAAAATTTCTATGCCGTTAT
66 CTTAGGCCATGCCGGTTTTTACCGAAGGTTTATCAAGGATTTCTCAAAAATTTCTAAGCCGCTAT
418596 GTTTGTTGTTAGAGAAAGATACAATGTTCAATTTCAAA
131 GTTTGTTGTTAGAGAAAGATACAATGTTCAATTTCAAA
418634 AAAGCA
1 AAAGCA
418640 TGTTTAGAAG
Statistics
Matches: 163, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
168 163 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (168 bp):
AAAGCAAAGGTGGACGTAATTGAAAGATTACCAGCCCCAATGAATGTGAAAGGAGTCAGAAGTTT
CTTAGGCCATGCCGGTTTTTACCGAAGGTTTATCAAGGATTTCTCAAAAATTTCTAAGCCGCTAT
GTTTGTTGTTAGAGAAAGATACAATGTTCAATTTCAAA
Found at i:427863 original size:23 final size:22
Alignment explanation
Indices: 427811--427863 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
427801 AAATAACAAG
*
427811 ATAAGAAATAACATACAAAAAT
1 ATAAGAAATAACAAACAAAAAT
*
427833 -TGCA-AAATAACACAACAAAAAT
1 AT-AAGAAATAACA-AACAAAAAT
427855 ATAAGAAAT
1 ATAAGAAAT
427864 TAAAGCGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 7
0.71 0.09 0.21
Matches are distributed among these distances:
21 9 0.38
22 10 0.42
23 5 0.21
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (22 bp):
ATAAGAAATAACAAACAAAAAT
Found at i:428092 original size:17 final size:17
Alignment explanation
Indices: 428072--428120 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
428062 TTAAATATCT
*
428072 AAAATAAATAAACAAGA
1 AAAATAAATAAACAACA
* *
428089 AAAATAAACAAACAACT
1 AAAATAAATAAACAACA
428106 AAAATAAATAAACAA
1 AAAATAAATAAACAA
428121 ATAAGGATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.76, C:0.10, G:0.02, T:0.12
Consensus pattern (17 bp):
AAAATAAATAAACAACA
Found at i:430711 original size:27 final size:27
Alignment explanation
Indices: 430650--430716 Score: 66
Period size: 27 Copynumber: 2.4 Consensus size: 27
430640 TTACCGTATA
430650 ACATAATTGTGGAAAGTCTGTCAAGACT
1 ACATAA-TGTGGAAAGTCTGTCAAGACT
* *
430678 ATC-TAATGTGGAAAG-CTCGTGAGGACT
1 A-CATAATGTGGAAAGTCT-GTCAAGACT
*
430705 ACATAATATGGA
1 ACATAATGTGGA
430717 GAAAGTCCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 3 0.09
27 25 0.76
28 4 0.12
29 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (27 bp):
ACATAATGTGGAAAGTCTGTCAAGACT
Found at i:434044 original size:42 final size:42
Alignment explanation
Indices: 433975--434102 Score: 161
Period size: 42 Copynumber: 3.1 Consensus size: 42
433965 TCTCATAAGC
* * * *
433975 TTCAGTT-AACTCATATGAGTTTCAGTTTAACCCTAATGGGT
1 TTCAGTTCAGCTCTTATGAGCTTCAGTTTAACCCTTATGGGT
*
434016 TTCAGTTCAGCTCTT-TCGAGCTTCAGTTTAACCCTTCTGGGT
1 TTCAGTTCAGCTCTTAT-GAGCTTCAGTTTAACCCTTATGGGT
* * *
434058 TTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGGT
1 TTCAGTTCAGCTCTTATGAGCTTCAGTTTAACCCTTATGGGT
434100 TTC
1 TTC
434103 TGTTTAGCAC
Statistics
Matches: 75, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
41 8 0.11
42 66 0.88
43 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.18, T:0.41
Consensus pattern (42 bp):
TTCAGTTCAGCTCTTATGAGCTTCAGTTTAACCCTTATGGGT
Found at i:434094 original size:21 final size:21
Alignment explanation
Indices: 434033--434106 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
434023 CAGCTCTTTC
* * *
434033 GAGCTTCAGTTTAACCCTTCT
1 GAGCTTCTGTTCAACCCTTAT
* * * * *
434054 GGGTTTCCGTTCAGCTCTTAT
1 GAGCTTCTGTTCAACCCTTAT
434075 GAGCTTCTGTTCAACCCTTAT
1 GAGCTTCTGTTCAACCCTTAT
* *
434096 GGGTTTCTGTT
1 GAGCTTCTGTT
434107 TAGCACTTAA
Statistics
Matches: 39, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (21 bp):
GAGCTTCTGTTCAACCCTTAT
Found at i:434115 original size:21 final size:21
Alignment explanation
Indices: 434053--434115 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
434043 TTAACCCTTC
* *
434053 TGGGTTTCCGTTCAGCTCTTA
1 TGGGTTTCTGTTCAGCACTTA
* * * *
434074 TGAGCTTCTGTTCAACCCTTA
1 TGGGTTTCTGTTCAGCACTTA
*
434095 TGGGTTTCTGTTTAGCACTTA
1 TGGGTTTCTGTTCAGCACTTA
434116 AGTGCTTCTG
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.43
Consensus pattern (21 bp):
TGGGTTTCTGTTCAGCACTTA
Found at i:434123 original size:42 final size:42
Alignment explanation
Indices: 434003--434126 Score: 140
Period size: 42 Copynumber: 3.0 Consensus size: 42
433993 GTTTCAGTTT
* ** * *
434003 AACCCTAATGGGTTTCAGTTCAGCTCTTTCGAGCTTCAGTTT
1 AACCCTTATGGGTTTCAGTTCAGCTCTTAAGAGCTTCTGTTC
* * *
434045 AACCCTTCTGGGTTTCCGTTCAGCTCTTATGAGCTTCTGTTC
1 AACCCTTATGGGTTTCAGTTCAGCTCTTAAGAGCTTCTGTTC
* * * *
434087 AACCCTTATGGGTTTCTGTTTAGCACTTAAGTGCTTCTGT
1 AACCCTTATGGGTTTCAGTTCAGCTCTTAAGAGCTTCTGT
434127 GCAGCCTTTG
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.40
Consensus pattern (42 bp):
AACCCTTATGGGTTTCAGTTCAGCTCTTAAGAGCTTCTGTTC
Found at i:435134 original size:20 final size:22
Alignment explanation
Indices: 435105--435146 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
435095 ATGTCCCTTA
435105 ATTTTAAG-AAAATTT-TTGAG
1 ATTTTAAGAAAAATTTCTTGAG
*
435125 ATTTTGAGAAAAATTTCTTGAG
1 ATTTTAAGAAAAATTTCTTGAG
435147 TATCCAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 7 0.37
22 5 0.26
ACGTcount: A:0.38, C:0.02, G:0.17, T:0.43
Consensus pattern (22 bp):
ATTTTAAGAAAAATTTCTTGAG
Found at i:435790 original size:17 final size:18
Alignment explanation
Indices: 435763--435796 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
435753 TATTATAATA
*
435763 ATAATTAAAATGAAAGAT
1 ATAATTAAAATAAAAGAT
435781 ATAA-TAAAATAAAAGA
1 ATAATTAAAATAAAAGA
435797 AAGTGGAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (18 bp):
ATAATTAAAATAAAAGAT
Found at i:435798 original size:21 final size:24
Alignment explanation
Indices: 435756--435799 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
435746 TATATATTAT
435756 TATAATAATAATTAAAATGAAAGA
1 TATAATAATAATTAAAATGAAAGA
435780 TATAATAA-AA-TAAAA-GAAAG
1 TATAATAATAATTAAAATGAAAG
435800 TGGAGACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 5 0.25
23 2 0.10
24 8 0.40
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.25
Consensus pattern (24 bp):
TATAATAATAATTAAAATGAAAGA
Found at i:436586 original size:24 final size:24
Alignment explanation
Indices: 436536--436583 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
436526 CATAATTGAA
* *
436536 ATGAAATGGATTGATTTGTATATT
1 ATGAAATAGATTGATTTGAATATT
*
436560 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATT-TGAATAT
436584 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.44
Consensus pattern (24 bp):
ATGAAATAGATTGATTTGAATATT
Found at i:437039 original size:43 final size:43
Alignment explanation
Indices: 436975--437060 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
436965 TATGTGATTG
436975 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
* *
437018 ATATTGAAATGGCAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
437061 TGAGATATGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.50, C:0.02, G:0.24, T:0.23
Consensus pattern (43 bp):
ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
Found at i:437044 original size:16 final size:16
Alignment explanation
Indices: 436980--437044 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
436970 GATTGATATT
*
436980 GAAATGGCAAAGATGA
1 GAAATGGCAAATATGA
436996 GAAAT-G--AATATGA
1 GAAATGGCAAATATGA
* *
437009 G--ATGAGAAAATAT-T
1 GAAATG-GCAAATATGA
437023 GAAATGGCAAATATGA
1 GAAATGGCAAATATGA
437039 GAAATG
1 GAAATG
437045 ATTATGAGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
11 2 0.05
13 8 0.21
14 1 0.03
15 13 0.34
16 14 0.37
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.20
Consensus pattern (16 bp):
GAAATGGCAAATATGA
Found at i:438429 original size:49 final size:49
Alignment explanation
Indices: 438357--438457 Score: 175
Period size: 49 Copynumber: 2.1 Consensus size: 49
438347 TCTAGAAGGG
* *
438357 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGAAATGT
*
438406 ATAAATAGTGATAAGAGTGTAGACAGTGGAATACCAAGTTTAGAAATGT
1 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGAAATGT
438455 ATA
1 ATA
438458 GCATAATTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.27
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGAAATGT
Found at i:439844 original size:88 final size:89
Alignment explanation
Indices: 439690--439944 Score: 398
Period size: 88 Copynumber: 2.9 Consensus size: 89
439680 GAGGGGGGGA
439690 GGGGAAGCCGACAATTGAGGTCTCTATTGATGTTAAC---AAAAAAAAACTCATTTTTCCAGGTT
1 GGGGAAGCCGACAATTGAGG--TCTATTGATGTTAACAATAAAAAAAAACTCATTTTTCCAGGTT
439752 GATTTTGGGACGTGGGTAAATTA-GG
64 GATTTTGGGACGTGGGTAAATTAGGG
*
439777 GGGGAAGCCGACAATTAAGGTCTATTGATGTTAACAATAAAAAAAAACTCATTTTTCCAGGTTGA
1 GGGGAAGCCGACAATTGAGGTCTATTGATGTTAACAATAAAAAAAAACTCATTTTTCCAGGTTGA
*
439842 TTTTAGGACGTGGGTAAATTAGGGG
66 TTTTGGGACGTGGGTAAATTA-GGG
*
439867 GGTGGAAGCCGACAATTGAGGTCTATTGATGTTAACAAT---AAAAAACCCATTTTTCCAGGTTG
1 GG-GGAAGCCGACAATTGAGGTCTATTGATGTTAACAATAAAAAAAAACTCATTTTTCCAGGTTG
439929 ATTTTGGGACGTGGGT
65 ATTTTGGGACGTGGGT
439945 TTCAACATTG
Statistics
Matches: 157, Mismatches: 5, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
85 15 0.10
87 19 0.12
88 84 0.54
90 4 0.03
91 35 0.22
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.30
Consensus pattern (89 bp):
GGGGAAGCCGACAATTGAGGTCTATTGATGTTAACAATAAAAAAAAACTCATTTTTCCAGGTTGA
TTTTGGGACGTGGGTAAATTAGGG
Found at i:440817 original size:29 final size:30
Alignment explanation
Indices: 440783--440868 Score: 111
Period size: 31 Copynumber: 2.9 Consensus size: 30
440773 ATTTAATGTA
440783 CAATTGTATACAT-AAACTTTAATTTGGTG
1 CAATTGTATACATGAAACTTTAATTTGGTG
* * *
440812 CAATTGTACACATGAAACTCTAATTGTGGTT
1 CAATTGTATACATGAAACTTTAATT-TGGTG
* *
440843 CAAATGTATACTTGAAACTTTAATTT
1 CAATTGTATACATGAAACTTTAATTT
440869 TGATTTGATC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
29 12 0.25
30 11 0.23
31 25 0.52
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (30 bp):
CAATTGTATACATGAAACTTTAATTTGGTG
Found at i:445063 original size:19 final size:18
Alignment explanation
Indices: 445030--445065 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
445020 ATTAGATTCT
445030 ATAATTTAATTTAATTTA
1 ATAATTTAATTTAATTTA
*
445048 ATAATTATAGTTTAATTT
1 ATAATT-TAATTTAATTT
445066 TAAATGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATAATTTAATTTAATTTA
Found at i:466646 original size:3 final size:3
Alignment explanation
Indices: 466638--466672 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
466628 TTTAGATTTC
466638 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
466673 AATTTTTTTA
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):
TAT
Found at i:469381 original size:19 final size:19
Alignment explanation
Indices: 469357--469393 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
469347 ATGTTATATA
*
469357 AGAAAATGATGAGATTATG
1 AGAAAATGATGAAATTATG
469376 AGAAAATGATGAAATTAT
1 AGAAAATGATGAAATTAT
469394 AGAGGGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (19 bp):
AGAAAATGATGAAATTATG
Found at i:469744 original size:24 final size:23
Alignment explanation
Indices: 469700--469744 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
469690 GATTTATGGC
*
469700 TTTTAGGGTTTAGGGTGCAGGCT
1 TTTTAGGGTTTAGGGTCCAGGCT
469723 TTTTAGGAG-TTAGGGGTCCAGG
1 TTTTAGG-GTTTA-GGGTCCAGG
469745 AAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.36
Consensus pattern (23 bp):
TTTTAGGGTTTAGGGTCCAGGCT
Found at i:469905 original size:124 final size:125
Alignment explanation
Indices: 469761--470031 Score: 370
Period size: 124 Copynumber: 2.2 Consensus size: 125
469751 TTTTTTCGAG
* * * ** * *
469761 TTGACGTTTCTG-GTTAAATAGTGGGAAATCGCTTCTACTAGGATGCTATTTAAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTAGAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
* *
469825 GAAATAGTGGCCTCGTGGACGCGATTTCGCTACAG-TGGTCATGT-GAGAAATAA-TTTTTT
65 GAAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAG-GAAATAATTTTTTT
* * *
469884 TTGACGTTTTCTGAGGAAATAGTATAAAATCGCTGATACCAGGATGCTATATGAGAAGAAATTGT
1 TTGACG-TTTCTGAGCAAATAGTAGAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGT
*
469949 GAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTT
65 GAAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTT
470010 TTGACGTTTCTGAGCAAATAGT
1 TTGACGTTTCTGAGCAAATAGT
470032 NNNNNNNNNN
Statistics
Matches: 130, Mismatches: 13, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
123 6 0.05
124 79 0.61
125 32 0.25
126 13 0.10
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.33
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTAGAAAATCGCTGATACCAGGATGCTATATAAGAAGAAATTGTG
AAATAGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAATTTTTTT
Found at i:478688 original size:11 final size:11
Alignment explanation
Indices: 478672--478696 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
478662 AATTTACGCC
478672 GAAAAAAAAAA
1 GAAAAAAAAAA
478683 GAAAAAAAAAA
1 GAAAAAAAAAA
478694 GAA
1 GAA
478697 TGAGTGGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:479431 original size:12 final size:13
Alignment explanation
Indices: 479409--479433 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
479399 AAAATTCAGA
479409 ATTAAATTTTTTT
1 ATTAAATTTTTTT
479422 ATTAAATTTTTT
1 ATTAAATTTTTT
479434 GATGCGACAT
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTAAATTTTTTT
Found at i:482629 original size:42 final size:42
Alignment explanation
Indices: 482562--482642 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
482552 AAGCTTTTCA
* *
482562 AAGTTGGAATCTTCATTCTATTGATGTAATCAAAGAGTTAGG
1 AAGTTGGAATCTTCATTCTAATGATGCAATCAAAGAGTTAGG
*
482604 AAGTTGGAATCTTCATTTTAATGATGCAATCAAAGAGTT
1 AAGTTGGAATCTTCATTCTAATGATGCAATCAAAGAGTT
482643 TGGTTTTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.36
Consensus pattern (42 bp):
AAGTTGGAATCTTCATTCTAATGATGCAATCAAAGAGTTAGG
Found at i:504653 original size:8 final size:7
Alignment explanation
Indices: 504637--504691 Score: 85
Period size: 7 Copynumber: 7.7 Consensus size: 7
504627 TTTTTATTAC
504637 ATGAAAA
1 ATGAAAA
504644 ATGAAAAA
1 ATG-AAAA
504652 ATGAAAAA
1 ATG-AAAA
504660 ATGAAAA
1 ATGAAAA
504667 ATGAAAA
1 ATGAAAA
504674 AT-AAAA
1 ATGAAAA
504680 ATGAAAA
1 ATGAAAA
504687 ATGAA
1 ATGAA
504692 TATTTAATTC
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.13
7 25 0.54
8 15 0.33
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:504657 original size:15 final size:14
Alignment explanation
Indices: 504637--504691 Score: 85
Period size: 13 Copynumber: 3.9 Consensus size: 14
504627 TTTTTATTAC
504637 ATGAAAAATGAAAAA
1 ATGAAAAATG-AAAA
504652 ATGAAAAAATGAAAA
1 ATG-AAAAATGAAAA
504667 ATGAAAAAT-AAAA
1 ATGAAAAATGAAAA
504680 ATGAAAAATGAA
1 ATGAAAAATGAA
504692 TATTTAATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
13 13 0.34
14 8 0.21
15 10 0.26
16 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.15
Consensus pattern (14 bp):
ATGAAAAATGAAAA
Found at i:509219 original size:8 final size:8
Alignment explanation
Indices: 509206--509230 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
509196 GCAAAATTAC
509206 ATTTTAAA
1 ATTTTAAA
509214 ATTTTAAA
1 ATTTTAAA
509222 ATTTTAAA
1 ATTTTAAA
509230 A
1 A
509231 CGGTCATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTTAAA
Found at i:510355 original size:15 final size:16
Alignment explanation
Indices: 510322--510357 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
510312 GAATAATCAT
*
510322 TATTTGGAACAAGTTG
1 TATTTAGAACAAGTTG
510338 TATTTAGAACAA-TTG
1 TATTTAGAACAAGTTG
510353 TATTT
1 TATTT
510358 TTTAGAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (16 bp):
TATTTAGAACAAGTTG
Found at i:510515 original size:17 final size:17
Alignment explanation
Indices: 510490--510525 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
510480 AAGTCTAAAT
510490 AACTATTATTCAAGAAC
1 AACTATTATTCAAGAAC
* *
510507 AACTTTTATTTAAGAAC
1 AACTATTATTCAAGAAC
510524 AA
1 AA
510526 TCATCATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (17 bp):
AACTATTATTCAAGAAC
Found at i:512598 original size:28 final size:27
Alignment explanation
Indices: 512541--512592 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
512531 TACAAATGAT
*
512541 CCAAAGAGAATATTCAAAGTAGCATTAA
1 CCAAAGAGAACATTCAAAG-AGCATTAA
*
512569 CCAAAGATAACATTCAAA-AGCATT
1 CCAAAGAGAACATTCAAAGAGCATT
512593 GTAACCTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 6 0.27
28 16 0.73
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (27 bp):
CCAAAGAGAACATTCAAAGAGCATTAA
Found at i:515413 original size:21 final size:21
Alignment explanation
Indices: 515389--515428 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
515379 TTAGGATGGA
*
515389 TGTTTTAGCATGTTTTGAGCT
1 TGTTTAAGCATGTTTTGAGCT
*
515410 TGTTTAATCATGTTTTGAG
1 TGTTTAAGCATGTTTTGAG
515429 TAGGTATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.07, G:0.23, T:0.53
Consensus pattern (21 bp):
TGTTTAAGCATGTTTTGAGCT
Found at i:515438 original size:21 final size:21
Alignment explanation
Indices: 515397--515438 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
515387 GATGTTTTAG
* *
515397 CATGTTTTGAGCTTGTTTAAT
1 CATGTTTTGAGCTGGTATAAT
515418 CATGTTTTGAG-TAGGTATAAT
1 CATGTTTTGAGCT-GGTATAAT
515439 TGATGGTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.24, C:0.07, G:0.21, T:0.48
Consensus pattern (21 bp):
CATGTTTTGAGCTGGTATAAT
Found at i:516368 original size:18 final size:18
Alignment explanation
Indices: 516345--516379 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
516335 CCCAGCCGTC
516345 TTCTCATTTCTTTCTCAT
1 TTCTCATTTCTTTCTCAT
516363 TTCTCATTTCTTTCTCA
1 TTCTCATTTCTTTCTCA
516380 CGTCTGAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.29, G:0.00, T:0.60
Consensus pattern (18 bp):
TTCTCATTTCTTTCTCAT
Found at i:517609 original size:7 final size:7
Alignment explanation
Indices: 517597--517638 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
517587 ATATGTGGAA
517597 ATCAAGT
1 ATCAAGT
517604 ATCAAGT
1 ATCAAGT
517611 ATCAAGT
1 ATCAAGT
517618 ATCAAGT
1 ATCAAGT
517625 ATCAAGT
1 ATCAAGT
517632 ATCAAGT
1 ATCAAGT
517639 TTCGAATTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (7 bp):
ATCAAGT
Found at i:519578 original size:16 final size:16
Alignment explanation
Indices: 519559--519610 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
519549 GATTTGCTAT
* *
519559 TACACCTCTATTCCAT
1 TACACCTCTAATCCAA
519575 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
519591 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
519607 TACA
1 TACA
519611 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:543394 original size:8 final size:7
Alignment explanation
Indices: 543370--543408 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
543360 AAAGTATTTT
543370 AAAATTA
1 AAAATTA
543377 AAAATTA
1 AAAATTA
543384 AAAATTA
1 AAAATTA
* *
543391 AAAAATG
1 AAAATTA
543398 AAAA-TA
1 AAAATTA
543404 AAAAT
1 AAAAT
543409 ATATTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (7 bp):
AAAATTA
Found at i:561699 original size:17 final size:17
Alignment explanation
Indices: 561679--561733 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
561669 TTAGGAATTA
*
561679 TATTTACATTA-TTATT
1 TATTTACATCATTTATT
561695 CTATTTAC-TCATTTATT
1 -TATTTACATCATTTATT
**
561712 TATTTACAAAATTTATT
1 TATTTACATCATTTATT
561729 TATTT
1 TATTT
561734 TATTTAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 9 0.27
17 24 0.73
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTACATCATTTATT
Found at i:570919 original size:20 final size:20
Alignment explanation
Indices: 570894--570931 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
570884 CATATGCATC
*
570894 AACATTTTCATAAAATTATG
1 AACATTTCCATAAAATTATG
*
570914 AACATTTCCATTAAATTA
1 AACATTTCCATAAAATTA
570932 CCATTCTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (20 bp):
AACATTTCCATAAAATTATG
Found at i:572247 original size:21 final size:21
Alignment explanation
Indices: 572221--572278 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
572211 TTAGGGTGGA
* *
572221 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTAT
*
572242 TCAGCTCTTTTGAGCTTCTAT
1 TCAGCTCTTATGAGCTTCTAT
*
572263 T-AACTCTTATGAGCTT
1 TCAGCTCTTATGAGCTT
572279 TCGTTGGTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 13 0.41
21 19 0.59
ACGTcount: A:0.17, C:0.24, G:0.16, T:0.43
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTAT
Found at i:574210 original size:29 final size:29
Alignment explanation
Indices: 574161--574217 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
574151 GGACCTTGAA
*
574161 AAAACCCATATTTACTAACATTTCACAAC
1 AAAACCCATATTTACTAACATTTAACAAC
574190 AAAACCCATAGATTTA-T-ACATTTAACAA
1 AAAACCCAT--ATTTACTAACATTTAACAA
574218 TTTAATCCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 19 0.76
30 1 0.04
31 5 0.20
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (29 bp):
AAAACCCATATTTACTAACATTTAACAAC
Found at i:582400 original size:19 final size:21
Alignment explanation
Indices: 582364--582402 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
582354 TTTTCACATG
*
582364 GCCTCCTCAAGCTCCCATGCA
1 GCCTCATCAAGCTCCCATGCA
582385 GCCTCATCAA-CT-CCATGC
1 GCCTCATCAAGCTCCCATGC
582403 CTATTCCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.21, C:0.46, G:0.13, T:0.21
Consensus pattern (21 bp):
GCCTCATCAAGCTCCCATGCA
Found at i:587252 original size:50 final size:50
Alignment explanation
Indices: 587134--587376 Score: 204
Period size: 50 Copynumber: 4.8 Consensus size: 50
587124 TGATAATAAC
* * *
587134 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTT-TCCTGT--
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GTTCTCATATCG
* * * *
587182 ACTGCCAATGCCATATCCCAGATACGGTCTGACATGGGAGTTCTCATATCG
1 A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCG
* ** ** *
587233 ATGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCG
* * **
587283 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCAT-A--TC---G
* * * *
587339 ATGCAAATGCCATGTTCCAAACATGGTTTTACATGGGA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
587377 TCTCATCACC
Statistics
Matches: 156, Mismatches: 29, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
48 4 0.03
49 36 0.23
50 80 0.51
51 1 0.01
53 2 0.01
56 33 0.21
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGTTCTCATATCG
Found at i:594518 original size:15 final size:15
Alignment explanation
Indices: 594498--594528 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
594488 GTTATGTAAG
594498 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
594513 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
594528 T
1 T
594529 ATGTTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:603028 original size:129 final size:128
Alignment explanation
Indices: 602799--603053 Score: 465
Period size: 129 Copynumber: 2.0 Consensus size: 128
602789 TGAGGGCTCC
*
602799 ACCATGGACAACAGGAGTTATTGCAACTAAGGTATGTGTCAAACCACAAAAATATTTGCTTTCTA
1 ACCATGGACAACAGGAGTTATTGCAACTAAGGTATGTGTCAAACCAAAAAAATATTTGCTTTCTA
* * *
602864 AATAATGTAATAAAGTAATTAACAAAAATTGCCTTCAGGAAAATTTTCACACTTTTACAGCCA
66 AAAAATGTAATAAAGTAACTAACAAAAATTGCCTTCAAGAAAATTTTCACACTTTTACAGCCA
602927 ACCATGGACAACAGGAGTTATTGCAACTAAGGTATGTGTCAAAACCAAAAAAATATTTGCTTTCT
1 ACCATGGACAACAGGAGTTATTGCAACTAAGGTATGTGTC-AAACCAAAAAAATATTTGCTTTCT
602992 AAAAAATGTAATAAAGTAACTAACAAAAATTGCCTTCAAGAAAATTTTCACACTTTTACAGC
65 AAAAAATGTAATAAAGTAACTAACAAAAATTGCCTTCAAGAAAATTTTCACACTTTTACAGC
603054 AAGGTTCAGA
Statistics
Matches: 122, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
128 40 0.33
129 82 0.67
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (128 bp):
ACCATGGACAACAGGAGTTATTGCAACTAAGGTATGTGTCAAACCAAAAAAATATTTGCTTTCTA
AAAAATGTAATAAAGTAACTAACAAAAATTGCCTTCAAGAAAATTTTCACACTTTTACAGCCA
Found at i:606093 original size:2 final size:2
Alignment explanation
Indices: 606086--606137 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
606076 ATAGGTAGGT
*
606086 AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
606128 AG AG AG AG AG
1 AG AG AG AG AG
606138 CAAACGAGCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:613978 original size:15 final size:15
Alignment explanation
Indices: 613960--613990 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
613950 AATAAATAGG
613960 ATAATATGAACAAAA
1 ATAATATGAACAAAA
613975 ATAATATGAACAAAA
1 ATAATATGAACAAAA
613990 A
1 A
613991 CGAACAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
ATAATATGAACAAAA
Found at i:614526 original size:2 final size:2
Alignment explanation
Indices: 614514--614543 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
614504 CATAAAAATG
*
614514 TA TA TA CA 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
614544 ACTGCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:615326 original size:17 final size:17
Alignment explanation
Indices: 615304--615347 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
615294 ACAAGTAGTT
615304 AGAAAAAAAATA-AAGAA
1 AGAAAAAAAATAGAA-AA
615321 AGAAAAAAAA-AGAAAA
1 AGAAAAAAAATAGAAAA
*
615337 AGAAAATAAAT
1 AGAAAAAAAAT
615348 GTACCGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAATAGAAAA
Found at i:615328 original size:16 final size:15
Alignment explanation
Indices: 615306--615346 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
615296 AAGTAGTTAG
615306 AAAAAAAATAAAGAA
1 AAAAAAAATAAAGAA
*
615321 AGAAAAAA-AAAGAA
1 AAAAAAAATAAAGAA
*
615335 AAAGAAAATAAA
1 AAAAAAAATAAA
615347 TGTACCGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.85, C:0.00, G:0.10, T:0.05
Consensus pattern (15 bp):
AAAAAAAATAAAGAA
Found at i:616052 original size:44 final size:43
Alignment explanation
Indices: 615980--616320 Score: 201
Period size: 44 Copynumber: 7.8 Consensus size: 43
615970 ATCTGATGTG
* * *
615980 ATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGAT-CTTTATTTCA
* * * *
616024 ATCCACTCCACTGTAACTTCAGAGAGATAAGAT-TACTAGCTTCA
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCT-TTA-TTTCA
* * *
616068 ATCTACTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTAGCTTCA
1 ATCTACTCCACTGTAACT-TCAGGGAGATAAGATCTTTA-TTTCA
* * ** *
616112 ATCTGCTCAACTGTAACCTT-AGGGAGATAAGATCTGAAATTCTTCG
1 ATCTACTCCACTGTAA-CTTCAGGGAGATAAGATCT-TTA-T-TTCA
* * * * * * * *
616158 GTCTACTCTACTATAACCTCAGGGAGATAAGA-CCTGA-TGCG
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCTTTATTTCA
* * * *
616199 ATCTACTCTACTGTAACTTTAGAGAGATGAA-ATCCTTTATTTTA
1 ATCTACTCCACTGTAACTTCAGGGAGAT-AAGAT-CTTTATTTCA
** * * * *
616243 ATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-TATGTCTTCG
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCTTTAT-TTCA
* * *
616286 ATCTGCTCCGCTGTAACCTCAGGGAGATAAGATCT
1 ATCTACTCCACTGTAACTTCAGGGAGATAAGATCT
616321 GAAAGTCNNN
Statistics
Matches: 232, Mismatches: 49, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
41 27 0.12
42 6 0.03
43 38 0.16
44 127 0.55
45 6 0.03
46 28 0.12
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (43 bp):
ATCTACTCCACTGTAACTTCAGGGAGATAAGATCTTTATTTCA
Found at i:616692 original size:44 final size:44
Alignment explanation
Indices: 616628--616731 Score: 172
Period size: 44 Copynumber: 2.4 Consensus size: 44
616618 NNNNNNNNNN
** *
616628 CTTAGGGAGATAAAACCTACCATCTTTGACCTGCTCCACTACTG
1 CTTAGGGAGATAGGACCTACCATCTTCGACCTGCTCCACTACTG
*
616672 CTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTG
1 CTTAGGGAGATAGGACCTACCATCTTCGACCTGCTCCACTACTG
616716 CTTAGGGAGATAGGAC
1 CTTAGGGAGATAGGAC
616732 TGGTGGCTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (44 bp):
CTTAGGGAGATAGGACCTACCATCTTCGACCTGCTCCACTACTG
Found at i:617231 original size:170 final size:171
Alignment explanation
Indices: 616940--617280 Score: 675
Period size: 170 Copynumber: 2.0 Consensus size: 171
616930 TTTTCTAGGG
616940 AACATGACCTGTATAATGAACCTAATTATGCCTAATGATTAGGATGACATGATCAAAATGAATCA
1 AACATGACCTGTATAATGAACCTAATTATGCCTAATGATTAGGATGACATGATCAAAATGAATCA
617005 AATGCTCCTAACAAGACATGTGTGAATGGTGTTTGCATGAATGCAGAATTTTTTTTTTGAGAATG
66 AATGCTCCTAACAAGACATGTGTGAATGGTGTTTGCATGAATGCAGAATTTTTTTTTTGAGAATG
617070 ATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAAGCTT
131 ATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAAGCTT
617111 AACATGACCT-TATAATGAACCTAATTATGCCTAATGATTAGGATGACATGATCAAAATGAATCA
1 AACATGACCTGTATAATGAACCTAATTATGCCTAATGATTAGGATGACATGATCAAAATGAATCA
617175 AATGCTCCTAACAAGACATGTGTGAATGGTGTTTGCATGAATGCAGAATTTTTTTTTTGAGAATG
66 AATGCTCCTAACAAGACATGTGTGAATGGTGTTTGCATGAATGCAGAATTTTTTTTTTGAGAATG
617240 ATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAAGCTT
131 ATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAAGCTT
617281 TGCGACTGAC
Statistics
Matches: 170, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
170 160 0.94
171 10 0.06
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (171 bp):
AACATGACCTGTATAATGAACCTAATTATGCCTAATGATTAGGATGACATGATCAAAATGAATCA
AATGCTCCTAACAAGACATGTGTGAATGGTGTTTGCATGAATGCAGAATTTTTTTTTTGAGAATG
ATCCCGCTTAGGTTGTCATTACTCGAAGTTTATTAAAGCTT
Found at i:622053 original size:14 final size:15
Alignment explanation
Indices: 622024--622055 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
622014 AAAAACATCA
622024 TAATTTTATCTATTT
1 TAATTTTATCTATTT
622039 TAATTTTAT-TATTT
1 TAATTTTATCTATTT
622053 TAA
1 TAA
622056 CTATAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTATCTATTT
Found at i:623226 original size:7 final size:6
Alignment explanation
Indices: 623210--623257 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
623200 TGGCCTCTCC
* *
623210 TTTTCT TTTTCCT TTTTCT TTTTCT TTTCTCT TCTTCA TTTTCAT TTT
1 TTTTCT TTTT-CT TTTTCT TTTTCT TTT-TCT TTTTCT TTTTC-T TTT
623258 GACTTTGATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
6 21 0.60
7 14 0.40
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTCT
Found at i:623228 original size:13 final size:12
Alignment explanation
Indices: 623210--623257 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
623200 TGGCCTCTCC
623210 TTTTCTTTTTCCT
1 TTTTCTTTTT-CT
623223 TTTTCTTTTTCT
1 TTTTCTTTTTCT
* *
623235 TTTCTCTTCTTCA
1 TTT-TCTTTTTCT
623248 TTTTCATTTT
1 TTTTC-TTTT
623258 GACTTTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 7 0.23
13 23 0.77
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:623251 original size:19 final size:19
Alignment explanation
Indices: 623210--623257 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
623200 TGGCCTCTCC
* *
623210 TTTTCTTTTTCCTTTTTCT
1 TTTTCTTTTTCCTTCTTCA
623229 TTTTC-TTTTCTCTTCTTCA
1 TTTTCTTTTTC-CTTCTTCA
623248 TTTTCATTTT
1 TTTTC-TTTT
623258 GACTTTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 5 0.21
19 16 0.67
21 3 0.12
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTCTTTTTCCTTCTTCA
Found at i:626991 original size:109 final size:109
Alignment explanation
Indices: 626620--627012 Score: 621
Period size: 109 Copynumber: 3.6 Consensus size: 109
626610 AAATTTGGCA
** * * * * *
626620 ATTTGGTTAAACGTGAAATCGAAACCCAGCACCTTAGGGCATGTTTCTTGAATTTCCAAACGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* *
626685 AACATGGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCT
66 AATATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCT
* *
626729 AGTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGTAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
*
626794 AATATTGCCTT-TTTTTGAAAA-TTTTTGAAAAGGATATTAAG-T
66 AATATTGCCTTATTTTTGAAAAGTTTTT-AAAAGGATATTTAGCT
* *
626836 CATTTGGTGGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTTCAAACGCA
1 -ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCA
626901 AAATATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCT
65 AAATATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCT
626946 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
1 ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
627011 AA
66 AA
627013 NNNNNNNNNN
Statistics
Matches: 260, Mismatches: 19, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
107 6 0.02
108 95 0.37
109 153 0.59
110 6 0.02
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (109 bp):
ATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
AATATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCT
Found at i:626995 original size:217 final size:217
Alignment explanation
Indices: 626620--627012 Score: 678
Period size: 217 Copynumber: 1.8 Consensus size: 217
626610 AAATTTGGCA
* * * * *
626620 ATTTGGTTAAACGTGAAATCGAAACCCAGCACCTTAGGGCATGTTTCTTGAATTTCCAAACGCAA
1 ATTTGGTGAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
626685 AACATGGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTAGTTGGTCGAACGAGAAATCG
66 AACATGGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTAGTTGGTCGAACGAGAAATCG
*
626750 AAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGTAAAATATTGCCTTTTTTTGAAAA
131 AAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTTTTTTGAAAA
626815 TTTTTGAAAAGGATATTAAGTC
196 TTTTTGAAAAGGATATTAAGTC
* * *
626837 ATTTGGTGGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTTCAAACGCAA
1 ATTTGGTGAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
* * *
626902 AATATTGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAATCG
66 AACATGGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTAGTTGGTCGAACGAGAAATCG
626967 AAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAA
131 AAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAA
627013 NNNNNNNNNN
Statistics
Matches: 164, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 164 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (217 bp):
ATTTGGTGAAACGAGAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAA
AACATGGCCTTATTTTTGAAAAGTTTTTAAAAGGATATTTAGCTAGTTGGTCGAACGAGAAATCG
AAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAATATTGCCTTTTTTTGAAAA
TTTTTGAAAAGGATATTAAGTC
Found at i:627481 original size:2 final size:2
Alignment explanation
Indices: 627469--627498 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
627459 CATAAAAATG
*
627469 TA TA TA CA 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
627499 ACTGCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:628282 original size:14 final size:14
Alignment explanation
Indices: 628259--628300 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
628249 ACAAGTAGTT
*
628259 AGAAAAAAAAATAA
1 AGAAAGAAAAATAA
*
628273 AGAAAGAAAAAAAA
1 AGAAAGAAAAATAA
*
628287 AAAAAG-AAAATAA
1 AGAAAGAAAAATAA
628300 A
1 A
628301 TGTACCGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 7 0.29
14 17 0.71
ACGTcount: A:0.86, C:0.00, G:0.10, T:0.05
Consensus pattern (14 bp):
AGAAAGAAAAATAA
Found at i:628282 original size:18 final size:18
Alignment explanation
Indices: 628259--628295 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
628249 ACAAGTAGTT
*
628259 AGAAAAAAAAATAAAGAA
1 AGAAAAAAAAAAAAAGAA
628277 AGAAAAAAAAAAAAAGAA
1 AGAAAAAAAAAAAAAGAA
628295 A
1 A
628296 ATAAATGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (18 bp):
AGAAAAAAAAAAAAAGAA
Found at i:629551 original size:41 final size:42
Alignment explanation
Indices: 629468--629552 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
629458 GTACATATCT
*
629468 TTTACTTTCTTTATTAAAGAGATAATTTTTTAAATTTATAAA
1 TTTACTTTCTATATTAAAGAGATAATTTTTTAAATTTATAAA
629510 TTTACTTTCTATATTAAAGAGATAATTTTTT-AATTTATAAA
1 TTTACTTTCTATATTAAAGAGATAATTTTTTAAATTTATAAA
629551 TT
1 TT
629553 ACTCTTTATA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
41 12 0.29
42 30 0.71
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (42 bp):
TTTACTTTCTATATTAAAGAGATAATTTTTTAAATTTATAAA
Found at i:629565 original size:42 final size:42
Alignment explanation
Indices: 629468--629568 Score: 143
Period size: 42 Copynumber: 2.4 Consensus size: 42
629458 GTACATATCT
* *
629468 TTTACTTTCTTTATTAAAGAGATAATTTTTTAAATTTATAAA
1 TTTACTTTATATATTAAAGAGATAATTTTTTAAATTTATAAA
*
629510 TTTACTTTCTATATTAAAGAGATAATTTTTT-AATTTATAAA
1 TTTACTTTATATATTAAAGAGATAATTTTTTAAATTTATAAA
629551 -TTACTCTTTATATATTAA
1 TTTA--CTTTATATATTAA
629569 TTATATACAT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
40 3 0.05
41 10 0.18
42 42 0.76
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (42 bp):
TTTACTTTATATATTAAAGAGATAATTTTTTAAATTTATAAA
Found at i:630508 original size:15 final size:16
Alignment explanation
Indices: 630478--630523 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
630468 AATACAATAG
630478 AAAAAAGATAAGTAAT
1 AAAAAAGATAAGTAAT
*
630494 AAAAAAGATTA-TAAT
1 AAAAAAGATAAGTAAT
*
630509 AAAAAACATAAGTAA
1 AAAAAAGATAAGTAA
630524 AAGTCTAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.20
Consensus pattern (16 bp):
AAAAAAGATAAGTAAT
Found at i:635094 original size:14 final size:14
Alignment explanation
Indices: 635077--635111 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
635067 GTGGAGGACC
635077 GGAGGTGGATCAGT
1 GGAGGTGGATCAGT
**
635091 GGAGGTGGATTGGT
1 GGAGGTGGATCAGT
635105 GGAGGTG
1 GGAGGTG
635112 AAGGTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.57, T:0.23
Consensus pattern (14 bp):
GGAGGTGGATCAGT
Found at i:638385 original size:20 final size:20
Alignment explanation
Indices: 638360--638400 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
638350 CGTATATGTG
638360 TGGGATATGAATTTTGGCGA
1 TGGGATATGAATTTTGGCGA
638380 TGGGATATGAATTTTGGCGA
1 TGGGATATGAATTTTGGCGA
638400 T
1 T
638401 TTCAAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.34, T:0.37
Consensus pattern (20 bp):
TGGGATATGAATTTTGGCGA
Found at i:642286 original size:27 final size:27
Alignment explanation
Indices: 642244--642311 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
642234 AACACACTAG
*
642244 GAAAGGAATGCTTTTGTGGCAATACAT
1 GAAAGGAATGCCTTTGTGGCAATACAT
*
642271 TAAAGGAATGCCTTTGTGGCAATACAT
1 GAAAGGAATGCCTTTGTGGCAATACAT
*
642298 GAAAGGAGTGCCTT
1 GAAAGGAATGCCTT
642312 CATTGCGGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (27 bp):
GAAAGGAATGCCTTTGTGGCAATACAT
Found at i:653073 original size:5 final size:5
Alignment explanation
Indices: 653063--653090 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
653053 TCCATACAAA
653063 CATAT CATAT CATAT CATAT CATAT CAT
1 CATAT CATAT CATAT CATAT CATAT CAT
653091 GCCATGGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
CATAT
Found at i:658894 original size:27 final size:27
Alignment explanation
Indices: 658877--659018 Score: 207
Period size: 27 Copynumber: 5.3 Consensus size: 27
658867 GTATAACAGC
*
658877 CATTTTACCCTATGGGGGTATTTTGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
658904 CATTTTACCCTAT-GGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
*
658930 CATTTTACCCTATAGGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
*
658957 CATTTTATCCTATGGGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
** *
658984 CATTTTATTCTAT-GGGGTATTTTGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
*
659010 TATTTTACC
1 CATTTTACC
659019 TATTTTGGGG
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
26 43 0.41
27 63 0.59
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.46
Consensus pattern (27 bp):
CATTTTACCCTATGGGGGTATTTCGGT
Found at i:658934 original size:53 final size:53
Alignment explanation
Indices: 658877--659018 Score: 214
Period size: 53 Copynumber: 2.7 Consensus size: 53
658867 GTATAACAGC
658877 CATTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTAT-GGGGTATTTCGGT
1 CATTTTACCCTAT-GGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGT
* *
658930 CATTTTACCCTATAGGGGTATTTCGGTCATTTTATCCTATGGGGGTATTTCGGT
1 CATTTTACCCTAT-GGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGT
** *
658984 CATTTTATTCTATGGGGTATTTTGGTTATTTTACC
1 CATTTTACCCTATGGGGTATTTTGGTCATTTTACC
659019 TATTTTGGGG
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 56 0.70
54 24 0.30
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.46
Consensus pattern (53 bp):
CATTTTACCCTATGGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGGT
Found at i:661370 original size:8 final size:8
Alignment explanation
Indices: 661357--661381 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
661347 CAAAATACAA
661357 ATGAATGC
1 ATGAATGC
661365 ATGAATGC
1 ATGAATGC
661373 ATGAATGC
1 ATGAATGC
661381 A
1 A
661382 CAAATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (8 bp):
ATGAATGC
Found at i:661693 original size:3 final size:3
Alignment explanation
Indices: 661685--661710 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
661675 TTTTTTCTCT
661685 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
661711 TCCTTTTCCT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:667727 original size:69 final size:69
Alignment explanation
Indices: 667645--667783 Score: 206
Period size: 69 Copynumber: 2.0 Consensus size: 69
667635 TTATAATCTT
* * * *
667645 CGTGTTTATTGTCCCGAAAGACTCTATTAGTCGCCATAGCCAAACTATGGTCTTACACCTCGTAA
1 CGTGTTTACTGTCCCGAAAGACTATATTAGTCGCCATAGCCAAAATATGGTCTTACACCTCATAA
667710 TTCC
66 TTCC
* * * *
667714 CGTGTTTACTGTCCCGATAGACTATATTGGTTGCCATAGCTAAAATATGGTCTTACACCTCATAA
1 CGTGTTTACTGTCCCGAAAGACTATATTAGTCGCCATAGCCAAAATATGGTCTTACACCTCATAA
667779 TTCC
66 TTCC
667783 C
1 C
667784 CTATTTATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 62 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.33
Consensus pattern (69 bp):
CGTGTTTACTGTCCCGAAAGACTATATTAGTCGCCATAGCCAAAATATGGTCTTACACCTCATAA
TTCC
Found at i:667811 original size:69 final size:69
Alignment explanation
Indices: 667663--667821 Score: 174
Period size: 69 Copynumber: 2.3 Consensus size: 69
667653 TTGTCCCGAA
* * * * * *
667663 AGACTCTATTAGTCGCCATAGCCAAACTATGGTCTTACACCTCGTAATTCCCGTGTTTACTGTCC
1 AGACTCTATTGGTCGCCATAGCCAAAATATGGTCTTACACCTCATAATTCCCCTATTTACTATCC
* *
667728 CGAT
66 CAAC
* * * *
667732 AGACTATATTGGTTGCCATAGCTAAAATATGGTCTTACACCTCATAATTCCCCTATTTATTATCC
1 AGACTCTATTGGTCGCCATAGCCAAAATATGGTCTTACACCTCATAATTCCCCTATTTACTATCC
*
667797 TAAC
66 CAAC
** *
667801 AGGTTCTATTGGTCGTCATAG
1 AGACTCTATTGGTCGCCATAG
667822 TCGAGCTATG
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.35
Consensus pattern (69 bp):
AGACTCTATTGGTCGCCATAGCCAAAATATGGTCTTACACCTCATAATTCCCCTATTTACTATCC
CAAC
Found at i:669720 original size:32 final size:32
Alignment explanation
Indices: 669675--669736 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
669665 GAAGATAAAT
* *
669675 CTTGGGTTGTTTGAATTATCCTGAAAAAAAAC
1 CTTGGGCTATTTGAATTATCCTGAAAAAAAAC
669707 CTTGGGCTATTTGAATTATCCTGAAAAAAA
1 CTTGGGCTATTTGAATTATCCTGAAAAAAA
669737 GAATAAAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (32 bp):
CTTGGGCTATTTGAATTATCCTGAAAAAAAAC
Found at i:671121 original size:27 final size:27
Alignment explanation
Indices: 671091--671142 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
671081 AATGACCCTG
*
671091 GTCTCAACGATAATCTAAATGGTCATA
1 GTCTCAACGATAATCCAAATGGTCATA
* *
671118 GTCTTAATGATAATCCAAATGGTCA
1 GTCTCAACGATAATCCAAATGGTCA
671143 GAATGTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (27 bp):
GTCTCAACGATAATCCAAATGGTCATA
Found at i:671151 original size:27 final size:27
Alignment explanation
Indices: 671099--671152 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
671089 TGGTCTCAAC
* * *
671099 GATAATCTAAATGGTCATAGTCTTAAT
1 GATAATCCAAATGGTCAGAATCTTAAT
*
671126 GATAATCCAAATGGTCAGAATGTTAAT
1 GATAATCCAAATGGTCAGAATCTTAAT
671153 TCTCCTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (27 bp):
GATAATCCAAATGGTCAGAATCTTAAT
Found at i:676829 original size:27 final size:26
Alignment explanation
Indices: 676790--677048 Score: 259
Period size: 27 Copynumber: 9.6 Consensus size: 26
676780 AGGTCGATAT
* * *
676790 ATGATCGAAATACCCCTATTGGGTAAA
1 ATGACCGAAATACCCCGA-AGGGTAAA
*
676817 ATGACCGAGATACCCTCGAAGGGTAAA
1 ATGACCGAAATACCC-CGAAGGGTAAA
676844 ATGACCGAAATACCCCCGAAGGGTAAA
1 ATGACCGAAATA-CCCCGAAGGGTAAA
* **
676871 ATGATCGAAATACCCTTAAAGGGTAAA
1 ATGACCGAAATACCC-CGAAGGGTAAA
**
676898 ATGACTAAAATACCCTCGAAGGGTAAA
1 ATGACCGAAATACCC-CGAAGGGTAAA
* * *
676925 ATAACCAAAATACCCTCGAGGGGTAAA
1 ATGACCGAAATACCC-CGAAGGGTAAA
**
676952 ATGATTGAAATACCCCCGAAGGGTAAA
1 ATGACCGAAATA-CCCCGAAGGGTAAA
*
676979 ATGATC-AAATTACCCTCGAAGGGTAAA
1 ATGACCGAAA-TACCC-CGAAGGGTAAA
*
677006 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCGA-AGGGTAAA
* *
677033 ATGACTGATATACCCC
1 ATGACCGAAATACCCC
677049 TAAGAATTGA
Statistics
Matches: 198, Mismatches: 26, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
26 11 0.06
27 176 0.89
28 11 0.06
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.19
Consensus pattern (26 bp):
ATGACCGAAATACCCCGAAGGGTAAA
Found at i:676884 original size:54 final size:54
Alignment explanation
Indices: 676810--677047 Score: 309
Period size: 54 Copynumber: 4.4 Consensus size: 54
676800 TACCCCTATT
*
676810 GGGTAAAATGACCGAGATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
1 GGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
* ** ** *
676864 GGGTAAAATGATCGAAATACCCTTAAAGGGTAAAATGACTAAAATACCCTCGAA
1 GGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
* * * **
676918 GGGTAAAATAACCAAAATACCCTCGAGGGGTAAAATGATTGAAATACCCCCGAA
1 GGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
*
676972 GGGTAAAATGATC-AAATTACCCTCGAAGGGTAAAATGACCGAAATACCCCC-ATA
1 GGGTAAAATGACCGAAA-TACCCTCGAAGGGTAAAATGACCGAAATACCCCCGA-A
* *
677026 GGGTAAAATGACTGATATACCC
1 GGGTAAAATGACCGAAATACCC
677048 CTAAGAATTG
Statistics
Matches: 157, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
53 4 0.03
54 151 0.96
55 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.18
Consensus pattern (54 bp):
GGGTAAAATGACCGAAATACCCTCGAAGGGTAAAATGACCGAAATACCCCCGAA
Found at i:676925 original size:81 final size:81
Alignment explanation
Indices: 676790--677051 Score: 341
Period size: 81 Copynumber: 3.2 Consensus size: 81
676780 AGGTCGATAT
** ** *
676790 ATGATCGAAATACCCCTATTGGGTAAAATGACCGAGATACCCTCGAAGGGTAAAATGACCGAAAT
1 ATGATCGAAATACCCCTAAAGGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCGAAAT
676855 ACCCCCGAAGGGTAAA
66 ACCCCCGAAGGGTAAA
* * *
676871 ATGATCGAAATACCCTTAAAGGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATAACCAAAAT
1 ATGATCGAAATACCCCTAAAGGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCGAAAT
* *
676936 ACCCTCGAGGGGTAAA
66 ACCCCCGAAGGGTAAA
* ** *
676952 ATGATTGAAATACCCCCGAAGGGTAAAATGA-TCAAATTACCCTCGAAGGGTAAAATGACCGAAA
1 ATGATCGAAATACCCCTAAAGGGTAAAATGACT-AAAATACCCTCGAAGGGTAAAATGACCGAAA
677016 TACCCCC-ATAGGGTAAA
65 TACCCCCGA-AGGGTAAA
*
677033 ATGA-CTGATATACCCCTAA
1 ATGATC-GAAATACCCCTAA
677052 GAATTGAAAT
Statistics
Matches: 155, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
80 2 0.01
81 153 0.99
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.19
Consensus pattern (81 bp):
ATGATCGAAATACCCCTAAAGGGTAAAATGACTAAAATACCCTCGAAGGGTAAAATGACCGAAAT
ACCCCCGAAGGGTAAA
Found at i:677386 original size:28 final size:28
Alignment explanation
Indices: 677346--677431 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
677336 CATTGTACTG
*
677346 ATTACTATATTGGGCTAAGGCCCACACT
1 ATTACTGTATTGGGCTAAGGCCCACACT
* *
677374 ATTACTGTATTGGGCTACGACTCACACACT
1 ATTACTGTATTGGGCTAAGGC-C-CACACT
* * *
677404 GTTACTGTAATGGGATAAGGCCCACACT
1 ATTACTGTATTGGGCTAAGGCCCACACT
677432 GCACTGATAC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 24 0.50
29 2 0.04
30 22 0.46
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (28 bp):
ATTACTGTATTGGGCTAAGGCCCACACT
Found at i:678691 original size:43 final size:42
Alignment explanation
Indices: 678581--678805 Score: 292
Period size: 43 Copynumber: 5.3 Consensus size: 42
678571 TTCTAGAAAT
*
678581 AAACACCACTAAAGGTCATGTTCTTTAGCGGCGC-TTT-CAC
1 AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCAC
*
678621 AAAAATGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCTAC
1 AAACA--CCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCC-AC
* * *
678666 AAACACCGCTAAAGGTCATGCTCTTTAGCGGAGGTTTTCCTAC
1 AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCC-AC
* *
678709 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTATTCCCAC
1 AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGCT-TTTCCAC
* * *
678752 AAACGCCGCTAAAGGTCATGTTCTTTCGCGACGCTTTTTCCAC
1 AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTTTCCAC
678795 AAACACCGCTA
1 AAACACCGCTA
678806 TTGTTTGGTG
Statistics
Matches: 163, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
40 4 0.02
42 28 0.17
43 119 0.73
44 6 0.04
45 6 0.04
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (42 bp):
AAACACCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTTCCAC
Found at i:679180 original size:21 final size:21
Alignment explanation
Indices: 679154--679203 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
679144 TTTTGCTCTG
*
679154 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCACC
* *
679175 CTCTGCTTCCTTCGCTGCCCC
1 CTCTGCTTCCCTCGCTGCACC
679196 CTCTGCTT
1 CTCTGCTT
679204 TAATTAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.02, C:0.48, G:0.16, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCACC
Found at i:679580 original size:8 final size:8
Alignment explanation
Indices: 679567--679592 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
679557 GGCCTATAAT
679567 GCAACAAG
1 GCAACAAG
679575 GCAACAAG
1 GCAACAAG
679583 GCAACAAG
1 GCAACAAG
679591 GC
1 GC
679593 CTTCATGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.46, C:0.27, G:0.27, T:0.00
Consensus pattern (8 bp):
GCAACAAG
Found at i:682631 original size:2 final size:2
Alignment explanation
Indices: 682624--682668 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
682614 TAATTACTCG
*
682624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
682665 TA TA
1 TA TA
682669 AAAAATATGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:683374 original size:41 final size:40
Alignment explanation
Indices: 683302--683543 Score: 304
Period size: 41 Copynumber: 5.9 Consensus size: 40
683292 TTTTTTTATT
* *
683302 ATTAGCGGCGCTTTCTCAAAAACACCGCTAAAGGCCTGAGC
1 ATTAGCGGCGCTTT-TCAAAAACGCCGCTAAAGGCCCGAGC
* *
683343 ATTAGCGGCGCTATTTCAACAACGCCACTAAAGGCCCGAGC
1 ATTAGCGGCGCT-TTTCAAAAACGCCGCTAAAGGCCCGAGC
**
683384 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGAACGAGC
1 ATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCCGAGC
**
683425 ATTAGCGGCGCATTTTCAAAAACGCCGCTAAAGGCTTGAGC
1 ATTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
683466 ATTAGGGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGATC
1 ATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCCCGAGC
* * * *
683507 ATTAGTGGTGCTTCTTCAAAAACGTCGCTAAAAGCCC
1 ATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCCC
683544 CCAAAACTCA
Statistics
Matches: 178, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
40 2 0.01
41 173 0.97
42 3 0.02
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (40 bp):
ATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:683525 original size:123 final size:123
Alignment explanation
Indices: 683302--683538 Score: 352
Period size: 123 Copynumber: 1.9 Consensus size: 123
683292 TTTTTTTATT
*
683302 ATTAGCGGCGCTTTCTCAAAAACACCGCTAAAGGCCTGAGCATTAGCGGCGCTATTTCAACAACG
1 ATTAGCGGCGCTTTCTCAAAAACACCGCTAAAGGCCTGAGCATTAGCGGCGCTATTTCAAAAACG
*
683367 CCACTAAAGGCCCGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGAACGAGC
66 CCACTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGAACGAGC
* * *
683425 ATTAGCGGCGCATTT-TCAAAAACGCCGCTAAAGGCTTGAGCATTAGGGGCGCT-TCTTCAAAAA
1 ATTAGCGGCGC-TTTCTCAAAAACACCGCTAAAGGCCTGAGCATTAGCGGCGCTAT-TTCAAAAA
* * * * *
683488 CGCCGCTAAAGGCCCGATCATTAGTGGTGCTTCTTCAAAAACGTCGCTAAA
64 CGCCACTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAA
683539 AGCCCCCAAA
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
122 1 0.01
123 98 0.96
124 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.21
Consensus pattern (123 bp):
ATTAGCGGCGCTTTCTCAAAAACACCGCTAAAGGCCTGAGCATTAGCGGCGCTATTTCAAAAACG
CCACTAAAGGCCCGAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGAACGAGC
Found at i:684869 original size:138 final size:139
Alignment explanation
Indices: 684704--684967 Score: 326
Period size: 138 Copynumber: 1.9 Consensus size: 139
684694 TATGAACCCA
* ** * *
684704 TGTTTATTGTCCAAGCAAACTCTTATTGGTTGCCATAGTTG-ACTTATGGTTTTACACCT-TGTA
1 TGTTTACTGTCCAAGCAAACTCTTATTGGTCACCATAGTCGAAC-TATGGTCTTACACCTCT-TA
* * *
684767 ATCCTTGTG-TTTACTGTCCCA-G-TGGACTCTATTGATCGCCATAGCCAAACTATAGTCTTACA
64 ATCCTTGTGCTTTA-TGT--CATGACGGACTCTATTGATCACCATAGCCAAACTATAGTCTCACA
684829 CATTGTAATTCATG
126 CATTGTAATTCATG
684843 TGTTTACTGTCCCAA-CAAACTC-TATTGGTCACCATAGTCGAACTATGGTCTTACACCTCTTAA
1 TGTTTACTGT-CCAAGCAAACTCTTATTGGTCACCATAGTCGAACTATGGTCTTACACCTCTTAA
* * *
684906 TTCTTGTGCTTTATGTCATGACGGACTCTATTGATCACCATAGCCAAGCTATGGTCTCACAC
65 TCCTTGTGCTTTATGTCATGACGGACTCTATTGATCACCATAGCCAAACTATAGTCTCACAC
684968 TCTAAACCTC
Statistics
Matches: 108, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
136 2 0.02
137 1 0.01
138 78 0.72
139 23 0.21
140 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (139 bp):
TGTTTACTGTCCAAGCAAACTCTTATTGGTCACCATAGTCGAACTATGGTCTTACACCTCTTAAT
CCTTGTGCTTTATGTCATGACGGACTCTATTGATCACCATAGCCAAACTATAGTCTCACACATTG
TAATTCATG
Found at i:684958 original size:69 final size:68
Alignment explanation
Indices: 684748--684967 Score: 210
Period size: 69 Copynumber: 3.2 Consensus size: 68
684738 ATAGTTGACT
* * * * * ** *
684748 TATGGTTTTACACCTTGTAATCCTTGTGTTTACTGTCCCAGTGGACTCTATTGATCGCCATAGCC
1 TATGGTCTTACACATTGTAATTCATGTGTTTACTGTCACAACGGACTCTATTGATCACCATAGCC
684813 AAAC
66 -AAC
* * ** *
684817 TATAGTCTTACACATTGTAATTCATGTGTTTACTGTCCCAACAAACTCTATTGGTCACCATAGTC
1 TATGGTCTTACACATTGTAATTCATGTGTTTACTGTCACAACGGACTCTATTGATCACCATAG-C
*
684882 GAAC
65 CAAC
* * **
684886 TATGGTCTTACACCTCT-TAATTCTTGTGCTTTA-TGTCATGACGGACTCTATTGATCACCATAG
1 TATGGTCTTACACAT-TGTAATTCATGTG-TTTACTGTCACAACGGACTCTATTGATCACCATAG
684949 CCAAGC
64 CCAA-C
*
684955 TATGGTCTCACAC
1 TATGGTCTTACAC
684968 TCTAAACCTC
Statistics
Matches: 124, Mismatches: 23, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
68 3 0.02
69 115 0.93
70 6 0.05
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (68 bp):
TATGGTCTTACACATTGTAATTCATGTGTTTACTGTCACAACGGACTCTATTGATCACCATAGCC
AAC
Found at i:689766 original size:29 final size:29
Alignment explanation
Indices: 689719--689968 Score: 229
Period size: 29 Copynumber: 8.6 Consensus size: 29
689709 ATGGCGATCT
* *
689719 TCGAATATGATAAGGGATAGCTTCGGCTA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
* *
689748 TTGATTATGAAAAGGGATAGCTTCGACTA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
* * *
689777 TCGAATATGAAAAGGGATAGATTTGGCTA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
* * * ** * *
689806 TTGATTATGAAAAGGGATGGCGACAACCA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
* * *
689835 TC-AACTATGGAAAGGGAT-GGTGAT-GACCA
1 TCGAA-TATGAAAAGGGATAGCT--TCGACTA
*
689864 TCGAATATGAAAATGGATAGCTTCGACTA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
* * *
689893 TCAAATATAAAAAGGGATAGCTTCGGCTA
1 TCGAATATGAAAAGGGATAGCTTCGACTA
*
689922 TCGAATATGAAAAGGAATAGCTTC-AGCTA
1 TCGAATATGAAAAGGGATAGCTTCGA-CTA
*
689951 TCGATTATGAAAAGGGAT
1 TCGAATATGAAAAGGGAT
689969 GGTGACGACC
Statistics
Matches: 174, Mismatches: 40, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
28 3 0.02
29 167 0.96
30 4 0.02
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (29 bp):
TCGAATATGAAAAGGGATAGCTTCGACTA
Found at i:689934 original size:116 final size:116
Alignment explanation
Indices: 689753--689997 Score: 321
Period size: 116 Copynumber: 2.1 Consensus size: 116
689743 GGCTATTGAT
* * * * *
689753 TATGAAAAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGATTTGGCTATTGATTATGAAA
1 TATGAAAAGGGATAGCTTCGACTATCAAATATAAAAAGGGATAGATTCGGCTATCGAATATGAAA
* * * *
689818 AGGGATGGCGACAACCATCAACTATGGAAAGGGATGGTGATGACCATCGAA-
66 AGGAATAGCGACAACCATCAACTATGAAAAGGGATGGTGACGACCATC-AAC
* *
689869 TATGAAAATGGATAGCTTCGACTATCAAATATAAAAAGGGATAGCTTCGGCTATCGAATATGAAA
1 TATGAAAAGGGATAGCTTCGACTATCAAATATAAAAAGGGATAGATTCGGCTATCGAATATGAAA
** * * * *
689934 AGGAATAGCTTCAGCTATCGATTATGAAAAGGGATGGTGACGACCATCAAC
66 AGGAATAGCGACAACCATCAACTATGAAAAGGGATGGTGACGACCATCAAC
689985 TATGAAAAGGGAT
1 TATGAAAAGGGAT
689998 GGTGACAACC
Statistics
Matches: 110, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
115 2 0.02
116 108 0.98
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.24
Consensus pattern (116 bp):
TATGAAAAGGGATAGCTTCGACTATCAAATATAAAAAGGGATAGATTCGGCTATCGAATATGAAA
AGGAATAGCGACAACCATCAACTATGAAAAGGGATGGTGACGACCATCAAC
Found at i:689982 original size:145 final size:145
Alignment explanation
Indices: 689719--690054 Score: 447
Period size: 145 Copynumber: 2.3 Consensus size: 145
689709 ATGGCGATCT
* * ** *
689719 TCGAATATGATAAGGGATAGCTTCGGCTATTGATTATGAAAAGGGATAGCTTCGACTATCGAATA
1 TCGAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGACTATCGAATA
* ** * *
689784 TGAAAAGGGATAGATTTGGCTATTGATTATGAAAAGGGATGGCGACAACCATCAACTATGGAAAG
66 TGAAAAGGAATAGATTCAGCTATCGATTATGAAAAGGGATGGCGACAACCATCAACTATGAAAAG
**
689849 GGATGGTGATGACCA
131 GGATGGTGACAACCA
* * *
689864 TCGAATATGAAAATGGATAGCTTCGACTATCAAATATAAAAAGGGATAGCTTCGGCTATCGAATA
1 TCGAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGACTATCGAATA
* * *
689929 TGAAAAGGAATAGCTTCAGCTATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAG
66 TGAAAAGGAATAGATTCAGCTATCGATTATGAAAAGGGATGGCGACAACCATCAACTATGAAAAG
689994 GGATGGTGACAACCA
131 GGATGGTGACAACCA
* * * * * *
690009 TCGATTAATGAAAAGGGATGGTTTCAACCATCAAGTATGAAAAGGG
1 TCGAAT-ATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGG
690055 CCGGTTACAA
Statistics
Matches: 164, Mismatches: 26, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
145 132 0.80
146 32 0.20
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.24
Consensus pattern (145 bp):
TCGAATATGAAAAGGGATAGCTTCGACTATCAAATATGAAAAGGGATAGCTTCGACTATCGAATA
TGAAAAGGAATAGATTCAGCTATCGATTATGAAAAGGGATGGCGACAACCATCAACTATGAAAAG
GGATGGTGACAACCA
Found at i:689989 original size:58 final size:57
Alignment explanation
Indices: 689840--690053 Score: 168
Period size: 58 Copynumber: 3.7 Consensus size: 57
689830 AACCATCAAC
* * * *
689840 TATGGAAAGGGATGGTGATGACCATCGAATATGAAAATGGATAGCTTC-GACTATCAAA
1 TATGAAAAGGGATGGTGACGACCATCGAATATGAAAA-GGATAGCTTCAG-CTATCGAT
* * * * *
689898 TATAAAAAGGGATAGCT-TCGGCTATCGAATATGAAAAGGAATAGCTTCAGCTATCGAT
1 TATGAAAAGGGAT-GGTGACGACCATCGAATATGAAAAGG-ATAGCTTCAGCTATCGAT
* * * *
689956 TATGAAAAGGGATGGTGACGACCATC-AACTATGAAAAGGGAT-GGTGACAACCATCGAT
1 TATGAAAAGGGATGGTGACGACCATCGAA-TATGAAAA-GGATAGCT-TCAGCTATCGAT
** *
690014 TAATGAAAAGGGATGGTTTCAACCATC-AAGTATGAAAAGG
1 T-ATGAAAAGGGATGGTGACGACCATCGAA-TATGAAAAGG
690054 GCCGGTTACA
Statistics
Matches: 126, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
57 8 0.06
58 81 0.64
59 37 0.29
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (57 bp):
TATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGATAGCTTCAGCTATCGAT
Found at i:690022 original size:30 final size:29
Alignment explanation
Indices: 689808--690070 Score: 145
Period size: 29 Copynumber: 9.0 Consensus size: 29
689798 TTTGGCTATT
*
689808 GATTATGAAAAGGGATGGCGACAACCATC
1 GATTATGAAAAGGGATGGTGACAACCATC
* * * **
689837 AACTATGGAAAGGGATGGTGATGACCATC
1 GATTATGAAAAGGGATGGTGACAACCATC
* * * * * *
689866 GAATATGAAAATGGATAGCT-TCGACTATC
1 GATTATGAAAAGGGAT-GGTGACAACCATC
* * * * * ** *
689895 AAATATAAAAAGGGATAGCT-TCGGCTATC
1 GATTATGAAAAGGGAT-GGTGACAACCATC
* * * * * *
689924 GAATATGAAAAGGAATAGCT-TCAGCTATC
1 GATTATGAAAAGGGAT-GGTGACAACCATC
*
689953 GATTATGAAAAGGGATGGTGACGACCATC
1 GATTATGAAAAGGGATGGTGACAACCATC
* *
689982 AACTATGAAAAGGGATGGTGACAACCATC
1 GATTATGAAAAGGGATGGTGACAACCATC
**
690011 GATTAATGAAAAGGGATGGTTTCAACCATC
1 GATT-ATGAAAAGGGATGGTGACAACCATC
* * ** *
690041 AAGTATGAAAAGGGCCGGTTACAACCATC
1 GATTATGAAAAGGGATGGTGACAACCATC
690070 G
1 G
690071 TTTAGCACAC
Statistics
Matches: 189, Mismatches: 42, Indels: 6
0.80 0.18 0.03
Matches are distributed among these distances:
28 2 0.01
29 160 0.85
30 27 0.14
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (29 bp):
GATTATGAAAAGGGATGGTGACAACCATC
Found at i:690039 original size:59 final size:58
Alignment explanation
Indices: 689950--690070 Score: 170
Period size: 59 Copynumber: 2.1 Consensus size: 58
689940 AGCTTCAGCT
* *
689950 ATCGATTATGAAAAGGGATGGTGACGACCATCAACTATGAAAAGGGATGGTGACAACC
1 ATCGATTATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGACGGTGACAACC
** * * *
690008 ATCGATTAATGAAAAGGGATGGTTTCAACCATCAAGTATGAAAAGGGCCGGTTACAACC
1 ATCGATT-ATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGACGGTGACAACC
690067 ATCG
1 ATCG
690071 TTTAGCACAC
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 7 0.13
59 48 0.87
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.21
Consensus pattern (58 bp):
ATCGATTATGAAAAGGGATGGTGACAACCATCAACTATGAAAAGGGACGGTGACAACC
Found at i:694074 original size:40 final size:39
Alignment explanation
Indices: 694019--694106 Score: 158
Period size: 40 Copynumber: 2.2 Consensus size: 39
694009 AGTTGCGTGA
694019 TTGAATTTGGGCTAAACTAGGAAAGGCATCTTTCTTTGG
1 TTGAATTTGGGCTAAACTAGGAAAGGCATCTTTCTTTGG
*
694058 TTTGAATTTGGGCTAAACTAGGAAAGGTATCTTTCTTTGG
1 -TTGAATTTGGGCTAAACTAGGAAAGGCATCTTTCTTTGG
694098 TTGAATTTG
1 TTGAATTTG
694107 TGTATAATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 9 0.19
40 38 0.81
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (39 bp):
TTGAATTTGGGCTAAACTAGGAAAGGCATCTTTCTTTGG
Found at i:706116 original size:22 final size:21
Alignment explanation
Indices: 706091--706132 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
706081 CCTGGGATGT
706091 CTCAGTATCACAATACTCATTA
1 CTCAGTATCACAATA-TCATTA
*
706113 CTCAGTATCACGATATCATT
1 CTCAGTATCACAATATCATT
706133 GTATATGTCC
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:0.33, C:0.26, G:0.07, T:0.33
Consensus pattern (21 bp):
CTCAGTATCACAATATCATTA
Found at i:708638 original size:13 final size:13
Alignment explanation
Indices: 708615--708650 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
708605 AATGCATGTG
708615 TAATG-TAATGGT
1 TAATGTTAATGGT
708627 TAATGTTAATGGT
1 TAATGTTAATGGT
708640 TAATGTGTAAT
1 TAATGT-TAAT
708651 CGTGAATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 5 0.23
13 13 0.59
14 4 0.18
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (13 bp):
TAATGTTAATGGT
Found at i:711936 original size:14 final size:14
Alignment explanation
Indices: 711897--711936 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
711887 AGAAATTTAT
711897 TTAATTTAA-AAAA
1 TTAATTTAATAAAA
711910 TTAA-TTAATTAAAA
1 TTAATTTAA-TAAAA
711924 TTAATTTAATAAA
1 TTAATTTAATAAA
711937 TAATATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 4 0.17
13 4 0.17
14 12 0.50
15 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAATTTAATAAAA
Found at i:717030 original size:22 final size:22
Alignment explanation
Indices: 717003--717046 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
716993 GAAAAACAAG
*
717003 TCCCTACAAATCAATTCTATGA
1 TCCCTACAAATCAACTCTATGA
*
717025 TCCCTACAAATCAGCTCTATGA
1 TCCCTACAAATCAACTCTATGA
717047 ATCAGCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.30
Consensus pattern (22 bp):
TCCCTACAAATCAACTCTATGA
Found at i:719410 original size:17 final size:17
Alignment explanation
Indices: 719388--719441 Score: 55
Period size: 17 Copynumber: 3.5 Consensus size: 17
719378 TTGATACCAT
719388 GAAAGCAAGCTGTTTCA
1 GAAAGCAAGCTGTTTCA
**
719405 GAAAGCAA-C-AATT--
1 GAAAGCAAGCTGTTTCA
719418 -AAAGCAAGCTGTTTCA
1 GAAAGCAAGCTGTTTCA
719434 GAAAGCAA
1 GAAAGCAA
719442 TAATTAATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 10
0.67 0.10 0.24
Matches are distributed among these distances:
12 7 0.25
13 1 0.04
14 2 0.07
15 2 0.07
16 1 0.04
17 15 0.54
ACGTcount: A:0.44, C:0.17, G:0.20, T:0.19
Consensus pattern (17 bp):
GAAAGCAAGCTGTTTCA
Found at i:719422 original size:29 final size:29
Alignment explanation
Indices: 719389--719448 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
719379 TGATACCATG
719389 AAAGCAAGCTGTTTCAGAAAGCAACAATT
1 AAAGCAAGCTGTTTCAGAAAGCAACAATT
*
719418 AAAGCAAGCTGTTTCAGAAAGCAATAATT
1 AAAGCAAGCTGTTTCAGAAAGCAACAATT
719447 AA
1 AA
719449 TCAGAAACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.22
Consensus pattern (29 bp):
AAAGCAAGCTGTTTCAGAAAGCAACAATT
Found at i:720695 original size:158 final size:158
Alignment explanation
Indices: 720407--721195 Score: 1215
Period size: 158 Copynumber: 5.0 Consensus size: 158
720397 TATTATTGAG
* *
720407 TTAAAGAATATATATTGAGAGCATTTACTCAAAC-CATTGGTGTGCATTGCTTCCTTGTGACTTT
1 TTAAAGAATATATATTGAGAACATTTACTCAAACAC-TTGGTGTGCATTGCTTCCTTGTGGCTTT
* *
720471 TCAATTCTCTTGTTGCTCTTTCATTTCGAGTTGCTTCTGCTTTATTTTCAGTGCTTGAAGAGAAT
65 TCAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCTGCTTTATTTTCAGTGCTTGAAGAGAAT
720536 TTCTATTGAGAATTCTCACTTTGTGAGAA
130 TTCTATTGAGAATTCTCACTTTGTGAGAA
* * *
720565 TTAAAGAATATATATTGAGAACATTTACTTAAACACTTGGTGTGCATTGCTTCTTTGTGACTTTT
1 TTAAAGAATATATATTGAGAACATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
* * * *
720630 CAGTTCTCTCATTTCTTTTTCATTTCGAGTTGCTTCTGCTTTATTTTCTGTGCTTGAAGAGAATT
66 CAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCTGCTTTATTTTCAGTGCTTGAAGAGAATT
*
720695 TCTATTGAGAATTCTCACTTTGTAAGAA
131 TCTATTGAGAATTCTCACTTTGTGAGAA
* *
720723 TTAAAGAATATATATCGA-AAGCATTTACTCAAACACTTGGTGTGCTTTGCTTCCTTGTGGCTTT
1 TTAAAGAATATATATTGAGAA-CATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTT
* *
720787 TCAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGATCCCT-CTTTATTTTCAGTGCTTGAAGAGAA
65 TCAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCT-TCTGCTTTATTTTCAGTGCTTGAAGAGAA
720851 TTTCTATTGAGAATTCTCACTTTGTGAGAA
129 TTTCTATTGAGAATTCTCACTTTGTGAGAA
* * * * *
720881 TTAAAGAAAATATATTGAGAATATTTACTTAAACACTTGGTGTGGATTGCTTCCTTATGGCTTTT
1 TTAAAGAATATATATTGAGAACATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
* * * *
720946 CAGTTCTCTCGTTACTTTTTCATTTCGAGTTGCTTCCGCTTTATTTTCTGTGCTTGAAGAGAATT
66 CAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCTGCTTTATTTTCAGTGCTTGAAGAGAATT
*
721011 TCTATTGAGAATTCTCACTTTGCGAGAA
131 TCTATTGAGAATTCTCACTTTGTGAGAA
**
721039 TTAAAGAATATATATTGAGAGTATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
1 TTAAAGAATATATATTGAGAACATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
* * * * * *
721104 TAGTTCTCTCGTTTCTCTTTCATTTTGAGTTGCTCCCGCTTTATTTTCAGTGCGTGAAGAGAATT
66 CAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCTGCTTTATTTTCAGTGCTTGAAGAGAATT
*
721169 TCTATTGAGAATTCTCACTTTGCGAGA
131 TCTATTGAGAATTCTCACTTTGTGAGA
721196 GCTAGATCGA
Statistics
Matches: 578, Mismatches: 48, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
157 3 0.01
158 570 0.99
159 5 0.01
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.43
Consensus pattern (158 bp):
TTAAAGAATATATATTGAGAACATTTACTCAAACACTTGGTGTGCATTGCTTCCTTGTGGCTTTT
CAGTTCTCTCGTTGCTCTTTCATTTCGAGTTGCTTCTGCTTTATTTTCAGTGCTTGAAGAGAATT
TCTATTGAGAATTCTCACTTTGTGAGAA
Found at i:723108 original size:18 final size:18
Alignment explanation
Indices: 723085--723122 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
723075 AAATAACGAC
723085 ATTGAAAT-AAGAAATGAT
1 ATTGAAATGAA-AAATGAT
723103 ATTGAAATGAAAAATGAT
1 ATTGAAATGAAAAATGAT
723121 AT
1 AT
723123 GGAATGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (18 bp):
ATTGAAATGAAAAATGAT
Found at i:729987 original size:17 final size:18
Alignment explanation
Indices: 729965--730000 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
729955 ACCACTGTAT
729965 TTGGGCCA-TATTTGAAA
1 TTGGGCCACTATTTGAAA
*
729982 TTGGGCCACTATTTTAAA
1 TTGGGCCACTATTTGAAA
730000 T
1 T
730001 CGGTTTGGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (18 bp):
TTGGGCCACTATTTGAAA
Found at i:731666 original size:21 final size:20
Alignment explanation
Indices: 731635--731688 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
731625 ATTGGAGTAG
* * *
731635 AAATATTGATATCTTAGGAA
1 AAATATCGATACCTTAAGAA
731655 AATATATCGATACCTTAAGAA
1 AA-ATATCGATACCTTAAGAA
*
731676 AAGTATCGATACC
1 AAATATCGATACC
731689 GGATCGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (20 bp):
AAATATCGATACCTTAAGAA
Found at i:738303 original size:26 final size:27
Alignment explanation
Indices: 738272--738328 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
738262 CCACAAAATT
*
738272 TATTCTTTCAGAG-TCTGCCAC-AAGGC
1 TATTCTTTCAAAGTTC-GCCACAAAGGC
738298 TATTCTTTCAAAGTTCGCCACAAAGGC
1 TATTCTTTCAAAGTTCGCCACAAAGGC
738325 TATT
1 TATT
738329 TCTTAGCTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (27 bp):
TATTCTTTCAAAGTTCGCCACAAAGGC
Found at i:742151 original size:35 final size:36
Alignment explanation
Indices: 742112--742214 Score: 111
Period size: 35 Copynumber: 2.9 Consensus size: 36
742102 TGTGATTTAG
* * *
742112 AATCAGTACAGTGGCATACTTAACATGCGAATC-AA
1 AATCAGTATAATGGCATGCTTAACATGCGAATCAAA
* * *
742147 AATCAATATAACGCCATGCTTAACATGCGAA-CAAA
1 AATCAGTATAATGGCATGCTTAACATGCGAATCAAA
* *
742182 AATAAGTAATAATGGCATGCTTAACATGAGAAT
1 AATCAGT-ATAATGGCATGCTTAACATGCGAAT
742215 TAGAATATCA
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
34 1 0.02
35 32 0.59
36 21 0.39
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (36 bp):
AATCAGTATAATGGCATGCTTAACATGCGAATCAAA
Found at i:745127 original size:8 final size:8
Alignment explanation
Indices: 745114--745143 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
745104 CTGTAGTTAA
*
745114 AATTTTAC
1 AATTTTGC
745122 AATTTTGC
1 AATTTTGC
745130 AATTTTGC
1 AATTTTGC
745138 AATTTT
1 AATTTT
745144 TTCCTGTACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (8 bp):
AATTTTGC
Found at i:748093 original size:32 final size:30
Alignment explanation
Indices: 748057--748126 Score: 77
Period size: 33 Copynumber: 2.2 Consensus size: 30
748047 GTTTCACTAT
* *
748057 AGTTTCAAAATTTATGGTTTTCAGAATCTTAA
1 AGTTTCAAAATTTATAG-TTTCACAATC-TAA
* *
748089 AGTTTTCACAGTTTATAGTTTCACAATCTAA
1 AG-TTTCAAAATTTATAGTTTCACAATCTAA
748120 AGTTTCA
1 AGTTTCA
748127 GTGCGTAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 5 0.15
31 5 0.15
32 11 0.33
33 12 0.36
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (30 bp):
AGTTTCAAAATTTATAGTTTCACAATCTAA
Done.