Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 64 of 226
Found at i:24870194 original size:19 final size:18
Alignment explanation
Indices: 24870161--24870196 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24870151 TATAAATTTA
24870161 AAAAAAACTAAAAAATAT
1 AAAAAAACTAAAAAATAT
*
24870179 AAAAAAATTAATAAAATA
1 AAAAAAACTAA-AAAATA
24870197 ATAATTTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (18 bp):
AAAAAAACTAAAAAATAT
Found at i:24877761 original size:2 final size:2
Alignment explanation
Indices: 24877756--24877785 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24877746 TGAAAAAGAA
24877756 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24877786 AAGCTAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24884072 original size:21 final size:21
Alignment explanation
Indices: 24884028--24884072 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
24884018 GTCAAAAAAG
**
24884028 AAAAAAATATTTAAAATTTTA
1 AAAAAAATATTTAAAATTAGA
24884049 AAAAAAATCA-TTAAAATTAGA
1 AAAAAAAT-ATTTAAAATTAGA
24884070 AAA
1 AAA
24884073 TTAAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAAAAATATTTAAAATTAGA
Found at i:24884445 original size:26 final size:26
Alignment explanation
Indices: 24884416--24884468 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
24884406 TGCATACTAA
24884416 TATAATTGTCTGAGTTTTAAAATTTT
1 TATAATTGTCTGAGTTTTAAAATTTT
*
24884442 TATAATTGTCTGGGTTTTAAAATTTT
1 TATAATTGTCTGAGTTTTAAAATTTT
24884468 T
1 T
24884469 GGGGTTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.04, G:0.13, T:0.55
Consensus pattern (26 bp):
TATAATTGTCTGAGTTTTAAAATTTT
Found at i:24886504 original size:34 final size:35
Alignment explanation
Indices: 24886460--24886526 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
24886450 CAGTAAAATA
* *
24886460 TTTTCCGTAAAATGATTT-TTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
24886494 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
24886527 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.07, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:24886530 original size:14 final size:15
Alignment explanation
Indices: 24886454--24886530 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
24886444 GATTGCCAGT
* *
24886454 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
24886468 AAAATGATTTT-TGG
1 AAAATGATTTTCTGG
*
24886482 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
24886502 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
24886517 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
24886531 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 20 0.40
15 16 0.32
16 1 0.02
18 1 0.02
19 4 0.08
20 8 0.16
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:24886760 original size:22 final size:24
Alignment explanation
Indices: 24886735--24886778 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
24886725 TGAAAAAAAC
24886735 TAATT-AAAAAACAAG-TATTGAA
1 TAATTAAAAAAACAAGTTATTGAA
24886757 TAATTAAAAAAACAAGTTATTG
1 TAATTAAAAAAACAAGTTATTG
24886779 GAAAATCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.57, C:0.05, G:0.09, T:0.30
Consensus pattern (24 bp):
TAATTAAAAAAACAAGTTATTGAA
Found at i:24891067 original size:15 final size:15
Alignment explanation
Indices: 24891047--24891085 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
24891037 CAATAACAAT
24891047 GGCCCAAAATAACCA
1 GGCCCAAAATAACCA
24891062 GGCCCAAAATAACCA
1 GGCCCAAAATAACCA
24891077 GGCCCAAAA
1 GGCCCAAAA
24891086 AAATCAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.46, C:0.33, G:0.15, T:0.05
Consensus pattern (15 bp):
GGCCCAAAATAACCA
Found at i:24893134 original size:107 final size:106
Alignment explanation
Indices: 24892945--24893227 Score: 377
Period size: 107 Copynumber: 2.6 Consensus size: 106
24892935 AAAAAGAAAA
24892945 TTTTAAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
1 TTTTAAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* * *
24893010 CGATTTCTTGTTCGACCAAATAGCCAAATATCCTTTTTAAAC
66 CGACTTCTCGTTCGACCAAATAGCCAAATA-CCCTTTTAAAC
* *
24893052 TTTTAAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGTTGGGTTT
1 TTTTAAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
* *
24893117 CGACTTCTCGTTTGACCAAATGGCCAAATACCCTTTTAAAC
66 CGACTTCTCGTTCGACCAAATAGCCAAATACCCTTTTAAAC
* * * ** * * ** * *
24893158 TTTCAATAATGAAGCCAATATTCCGTATTTAGAAATTCGAGAAGTCGTGCCCTAACTTACTGGGT
1 TTTTAA-AAT-AAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGT
24893223 TTCGA
64 TTCGA
24893228 TCTTTTTTCG
Statistics
Matches: 154, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
106 15 0.10
107 92 0.60
108 47 0.31
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (106 bp):
TTTTAAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTT
CGACTTCTCGTTCGACCAAATAGCCAAATACCCTTTTAAAC
Found at i:24896466 original size:22 final size:22
Alignment explanation
Indices: 24896440--24896482 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24896430 TCGAAGTTAA
*
24896440 TAGATGACTC-ATACATAAATAG
1 TAGATGAC-CAATAAATAAATAG
24896462 TAGATGACCAATAAATAAATA
1 TAGATGACCAATAAATAAATA
24896483 CTCTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.26
Consensus pattern (22 bp):
TAGATGACCAATAAATAAATAG
Found at i:24902224 original size:31 final size:30
Alignment explanation
Indices: 24902144--24902232 Score: 81
Period size: 31 Copynumber: 3.0 Consensus size: 30
24902134 TTAATTAAAT
* *
24902144 GTGCAATTGTATACATGAAA-TTTAATTTG
1 GTGCAAATATATACATGAAACTTTAATTTG
* **
24902173 GTGCAATTATATACGGGAAACTTTAATTGTG
1 GTGCAAATATATACATGAAACTTTAATT-TG
* * * *
24902204 TTTCAAATATATACTTGAAACATTAATTT
1 GTGCAAATATATACATGAAACTTTAATTT
24902233 TGATTTAATC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
29 17 0.35
30 8 0.16
31 24 0.49
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (30 bp):
GTGCAAATATATACATGAAACTTTAATTTG
Found at i:24903109 original size:19 final size:20
Alignment explanation
Indices: 24903087--24903129 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
24903077 AAATATAATC
24903087 ATTTAATT-A-AATTATTAAA
1 ATTTAATTAATAATT-TTAAA
24903106 ATTT-ATTAATAATTTTAAA
1 ATTTAATTAATAATTTTAAA
24903125 ATTTA
1 ATTTA
24903130 TATTTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.14
19 14 0.67
20 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAATTAATAATTTTAAA
Found at i:24910820 original size:126 final size:123
Alignment explanation
Indices: 24910596--24910837 Score: 378
Period size: 126 Copynumber: 1.9 Consensus size: 123
24910586 TCGAGTAGAA
* * * *
24910596 GAGAAGAAAATTTATTATGTCGAATTCGAATGATTACAAAAGTAGACTATATCTATTTATAGGCT
1 GAGAAGAAAATTCACTATGTCGAATTCGAATAATTACAAAAGTAGACTATATATATTTATAGGCT
* *
24910661 TGCAAAACCATATTCTAATAGGAGTGTAGTAAAATTGAAACAGCTTATTCTGGCAGAG
66 TGCAAAACCATATTCTAATAGGAGTGTAATAAAATTGAAACACCTTATTCTGGCAGAG
24910719 GAGAAGAAAATTCACTATGTCGAATTCGAATAATTACAAGAGAAGTAGACTATATATATTTATAG
1 GAGAAGAAAATTCACTATGTCGAATTCGAATAATTAC-A-A-AAGTAGACTATATATATTTATAG
*
24910784 GCTTGTAAAACCATATTCTAATTA-GAGTGTAATAAAATTGAAACACCTTATTCT
63 GCTTGCAAAACCATATTCTAA-TAGGAGTGTAATAAAATTGAAACACCTTATTCT
24910838 AATCAATATT
Statistics
Matches: 108, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
123 34 0.31
124 1 0.01
125 1 0.01
126 70 0.65
127 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (123 bp):
GAGAAGAAAATTCACTATGTCGAATTCGAATAATTACAAAAGTAGACTATATATATTTATAGGCT
TGCAAAACCATATTCTAATAGGAGTGTAATAAAATTGAAACACCTTATTCTGGCAGAG
Found at i:24921130 original size:15 final size:16
Alignment explanation
Indices: 24921097--24921152 Score: 62
Period size: 15 Copynumber: 3.6 Consensus size: 16
24921087 CAATTAGTTT
* *
24921097 TTTATATTTATATTTA
1 TTTAAATTTATAATTA
24921113 TTTAAATTT-TAATTA
1 TTTAAATTTATAATTA
*
24921128 TTT-ATTTTATAATTA
1 TTTAAATTTATAATTA
24921143 TATTAAATTT
1 T-TTAAATTT
24921153 CTCTTGTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
14 4 0.12
15 15 0.45
16 10 0.30
17 4 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTAAATTTATAATTA
Found at i:24926785 original size:44 final size:45
Alignment explanation
Indices: 24926706--24926816 Score: 120
Period size: 44 Copynumber: 2.5 Consensus size: 45
24926696 TAATCCGCTC
* * * *
24926706 CACTGCAACTTCAGGGAGAT-AGGATTGATGGCTTCAACCTACTT
1 CACTGCAACTTCAGGAAGATAAGGACTGATGACTTCAACCTACTG
* ** *
24926750 CA-TAGCAACTTCAGGAAGATAAGG-CTGGTGACTTCAATTTGCTG
1 CACT-GCAACTTCAGGAAGATAAGGACTGATGACTTCAACCTACTG
24926794 CACTGCAACTTCAGGAAGATAAG
1 CACTGCAACTTCAGGAAGATAAG
24926817 ATTCGCCATA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
43 1 0.02
44 51 0.91
45 4 0.07
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (45 bp):
CACTGCAACTTCAGGAAGATAAGGACTGATGACTTCAACCTACTG
Found at i:24926947 original size:143 final size:143
Alignment explanation
Indices: 24926757--24927247 Score: 648
Period size: 143 Copynumber: 3.4 Consensus size: 143
24926747 CTTCATAGCA
* * * *
24926757 ACTTCAGGAAGATAAGGCTGGTGACTTCAATTTGCTGCACTGCAACTTCAGGAAGATAAGATTCG
1 ACTTCAGGGAGATAAGGCTGGTGGCTTCAATTTGCTCCACTGTAACTTCAGGAAGATAAGATTCG
* * * *
24926822 CCATAATTTGTAGCTTTAATCTGTTCCACTGCTACGCCAGGGAAATAAGATTCGATGTCTTCAAT
66 CCATAACTTGTAGCTTTAATCTGTTCCACTGCTACGCCAAGGAAATAAGATTCGCTGTCTTCAGT
*
24926887 ATGCTCCGCTGCT
131 CTGCTCCGCTGCT
* * * *
24926900 ACTTTAGGGAGATAAGGCTGGTGGCTACAATTTGCTCCACTATAACTTCAGGAAGATAAGATTCA
1 ACTTCAGGGAGATAAGGCTGGTGGCTTCAATTTGCTCCACTGTAACTTCAGGAAGATAAGATTCG
* * * * * *
24926965 CCATAGCTTGCAACTTTAATCTATTCCACTACTACACCAAGG-AA-AAGATTCGCTGTCTTCAGT
66 CCATAACTTGTAGCTTTAATCTGTTCCACTGCTACGCCAAGGAAATAAGATTCGCTGTCTTCAGT
*
24927028 CTGCTCCGCTGCA
131 CTGCTCCGCTGCT
* * * *
24927041 ACTTTAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGTAACTTCAGGAATATAAGATTCG
1 ACTTCAGGGAGATAAGGCTGGTGGCTTCAATTTGCTCCACTGTAACTTCAGGAAGATAAGATTCG
*
24927106 CCATAACTTGTAGCTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGATTCGCTGTCTTCAGT
66 CCATAACTTGTAGCTTTAATCTGTTCCACTGCTACGCCAAGGAAATAAGATTCGCTGTCTTCAGT
24927171 CTGCTCCGCTGCT
131 CTGCTCCGCTGCT
** ** * * *
24927184 ACTTCAGGGAGAT-AGAATTATTGGCTTTAATCTGCTCCACTGCAACTTCA-GAGAGATAAGATT
1 ACTTCAGGGAGATAAG-GCTGGTGGCTTCAATTTGCTCCACTGTAACTTCAGGA-AGATAAGATT
24927247 C
64 C
24927248 ACCAACTTCT
Statistics
Matches: 301, Mismatches: 43, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
141 122 0.41
142 8 0.03
143 171 0.57
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (143 bp):
ACTTCAGGGAGATAAGGCTGGTGGCTTCAATTTGCTCCACTGTAACTTCAGGAAGATAAGATTCG
CCATAACTTGTAGCTTTAATCTGTTCCACTGCTACGCCAAGGAAATAAGATTCGCTGTCTTCAGT
CTGCTCCGCTGCT
Found at i:24927610 original size:24 final size:24
Alignment explanation
Indices: 24927574--24927626 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
24927564 CAGATTGCCC
*
24927574 CCACTGTAGTCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTCAAT
*
24927598 CCACTGTAATCTTCTAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTCAAT
24927622 CCACT
1 CCACT
24927627 ATACTTTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGGTTCAAT
Found at i:24930329 original size:28 final size:28
Alignment explanation
Indices: 24930296--24930352 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
24930286 TTTACTGAGA
24930296 TAGTATATCACCCTTTCTTTCTTTCCTG
1 TAGTATATCACCCTTTCTTTCTTTCCTG
24930324 TAGTATATCACCCTTTCTTTCTTTCCTG
1 TAGTATATCACCCTTTCTTTCTTTCCTG
24930352 T
1 T
24930353 CTTATCATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.14, C:0.28, G:0.07, T:0.51
Consensus pattern (28 bp):
TAGTATATCACCCTTTCTTTCTTTCCTG
Found at i:24934275 original size:22 final size:22
Alignment explanation
Indices: 24934244--24934290 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
24934234 ATTATATGTA
24934244 CTTGTATTGTTCACCTCGTTTT
1 CTTGTATTGTTCACCTCGTTTT
* *
24934266 CTTGTGTTGTTCACTTCGTTTT
1 CTTGTATTGTTCACCTCGTTTT
24934288 CTT
1 CTT
24934291 TTTTCCTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.06, C:0.21, G:0.15, T:0.57
Consensus pattern (22 bp):
CTTGTATTGTTCACCTCGTTTT
Found at i:24940784 original size:2 final size:2
Alignment explanation
Indices: 24940777--24940815 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
24940767 AATTGATCCA
24940777 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24940816 CTTCCCTAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24941437 original size:31 final size:31
Alignment explanation
Indices: 24941401--24941466 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
24941391 TTTAAAAAAA
24941401 AATAGTCCAATGACTTAAATAAAAACTTTTG
1 AATAGTCCAATGACTTAAATAAAAACTTTTG
*** **
24941432 AATAGTTTGATGACTTAAATGGAAACTTTTG
1 AATAGTCCAATGACTTAAATAAAAACTTTTG
24941463 AATA
1 AATA
24941467 ATTCAGTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (31 bp):
AATAGTCCAATGACTTAAATAAAAACTTTTG
Found at i:24947503 original size:34 final size:34
Alignment explanation
Indices: 24947458--24947532 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
24947448 TGCTCATGAG
* *
24947458 CATGTTTGAGATACATTCTTTTAATGTTCGTGAA
1 CATGTTCGAGATACATTCGTTTAATGTTCGTGAA
* *
24947492 TATGTTCGAGATACGTTCGTTTAATGTTCGTGAA
1 CATGTTCGAGATACATTCGTTTAATGTTCGTGAA
24947526 CATGTTC
1 CATGTTC
24947533 AATTAAGTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (34 bp):
CATGTTCGAGATACATTCGTTTAATGTTCGTGAA
Found at i:24947742 original size:2 final size:2
Alignment explanation
Indices: 24947735--24947771 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
24947725 ATGGTATTTG
24947735 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24947772 CATGAATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24947959 original size:31 final size:31
Alignment explanation
Indices: 24947923--24947986 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
24947913 AGTATTTTTC
24947923 TTCTAATTTTCTCTTTTCAAATTTGAACATT
1 TTCTAATTTTCTCTTTTCAAATTTGAACATT
*
24947954 TTCTAATTTTCTTTTTTCAAATTTGAACATT
1 TTCTAATTTTCTCTTTTCAAATTTGAACATT
24947985 TT
1 TT
24947987 ACGGAGATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (31 bp):
TTCTAATTTTCTCTTTTCAAATTTGAACATT
Found at i:24952570 original size:15 final size:15
Alignment explanation
Indices: 24952550--24952579 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24952540 GAAACTTTAA
24952550 AATTATATATTTTTT
1 AATTATATATTTTTT
24952565 AATTATATATTTTTT
1 AATTATATATTTTTT
24952580 TTAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
AATTATATATTTTTT
Found at i:24952573 original size:17 final size:17
Alignment explanation
Indices: 24952553--24952585 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
24952543 ACTTTAAAAT
24952553 TATATATTTTTTAATTA
1 TATATATTTTTTAATTA
*
24952570 TATATTTTTTTTAATT
1 TATATATTTTTTAATT
24952586 TTTAAGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATATATTTTTTAATTA
Found at i:24953971 original size:32 final size:32
Alignment explanation
Indices: 24953930--24953990 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
24953920 ATCTACTTTC
24953930 ATTGTTCAACTCTTTGACAACACGAAAAATCT
1 ATTGTTCAACTCTTTGACAACACGAAAAATCT
*
24953962 ATTGTTCAACTCTTTGACAACATGAAAAA
1 ATTGTTCAACTCTTTGACAACACGAAAAA
24953991 ACCAAAAGCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (32 bp):
ATTGTTCAACTCTTTGACAACACGAAAAATCT
Found at i:24956722 original size:21 final size:20
Alignment explanation
Indices: 24956692--24956731 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
24956682 TTTAGTAAAA
*
24956692 ATTTAAAGAAGCATATTATAT
1 ATTTAAAGAA-AATATTATAT
*
24956713 ATTTAGAGAAAATATTATA
1 ATTTAAAGAAAATATTATA
24956732 AATAATTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.38
Consensus pattern (20 bp):
ATTTAAAGAAAATATTATAT
Found at i:24957175 original size:2 final size:2
Alignment explanation
Indices: 24957168--24957193 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24957158 GGAAGCGTGC
24957168 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
24957194 TCCCATCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:24962935 original size:29 final size:31
Alignment explanation
Indices: 24962888--24962949 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
24962878 TTGATTTAAT
* *
24962888 GTGTAATTATATACATG-AATTTTAATT-TG
1 GTGTAATTATACACATGAAACTTTAATTGTG
*
24962917 GTGTAATTATACACGTGAAACTTTAATTGTG
1 GTGTAATTATACACATGAAACTTTAATTGTG
24962948 GT
1 GT
24962950 TCAAATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.54
30 9 0.32
31 4 0.14
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (31 bp):
GTGTAATTATACACATGAAACTTTAATTGTG
Found at i:24976245 original size:19 final size:20
Alignment explanation
Indices: 24976212--24976267 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
24976202 TACTTGAAAT
*
24976212 TTATTTTAAATTTTTATAATA
1 TTATTTTCAATTTTTAT-ATA
24976233 TT-TTTTCAATTTTTATATA
1 TTATTTTCAATTTTTATATA
*
24976252 TTATTTTGAATTTTTA
1 TTATTTTCAATTTTTA
24976268 AAATTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 5 0.16
20 25 0.78
21 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TTATTTTCAATTTTTATATA
Found at i:24976796 original size:11 final size:12
Alignment explanation
Indices: 24976780--24976809 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
24976770 TAAAAAAATA
24976780 TTTTTTAAAACT
1 TTTTTTAAAACT
*
24976792 TTTTTTAGAACT
1 TTTTTTAAAACT
24976804 TTTTTT
1 TTTTTT
24976810 TACAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (12 bp):
TTTTTTAAAACT
Found at i:24976796 original size:13 final size:13
Alignment explanation
Indices: 24976780--24976820 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
24976770 TAAAAAAATA
24976780 TTTTTTAAAAC-T
1 TTTTTTAAAACTT
*
24976792 TTTTTTAGAACTT
1 TTTTTTAAAACTT
*
24976805 TTTTTTACAA-TT
1 TTTTTTAAAACTT
24976817 TTTT
1 TTTT
24976821 ATGATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (13 bp):
TTTTTTAAAACTT
Found at i:24976846 original size:19 final size:19
Alignment explanation
Indices: 24976806--24976848 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
24976796 TTAGAACTTT
* *
24976806 TTTTTACAATTTTTTATGA
1 TTTTTACAATTGTTTATCA
24976825 TTTTTACAATTCGTTTA-CA
1 TTTTTACAATT-GTTTATCA
24976844 TTTTT
1 TTTTT
24976849 CGCAATAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.23, C:0.09, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTTACAATTGTTTATCA
Found at i:24979605 original size:19 final size:19
Alignment explanation
Indices: 24979560--24979599 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
24979550 AGTTCATGTT
* *
24979560 TTCATTTCACATTTTCATA
1 TTCAATTCACATTTTCAAA
*
24979579 TTCAATTCACCTTTTCAAA
1 TTCAATTCACATTTTCAAA
24979598 TT
1 TT
24979600 ATATTCCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCAATTCACATTTTCAAA
Found at i:24979851 original size:45 final size:45
Alignment explanation
Indices: 24979787--24980185 Score: 281
Period size: 45 Copynumber: 9.2 Consensus size: 45
24979777 GTAACGGTAG
* * *
24979787 CAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAATCTGTAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAA
*
24979832 CAGTAACGGTAACAGTATTCGACACACAAAGTG-TCGAATCGGTAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTGCT-GAATCTGTAA
* * **
24979877 CAGTAA---T---AGTAGTCGGCAC-GTAAGTGCCT-AAT-TAGT-A
1 CAGTAACGGTAACAGTATTCGACACACAAAGTG-CTGAATCT-GTAA
* * *
24979914 -A-TTA--GTAACAGTATTCAACACACAAAGTGCTGAATCTGAAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAA
* * *
24979955 CAGTAATGGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAA
* * *
24980000 CAGTAATGGTAACAGCATTCAACACACAAAGTG-TCGAATC-GTAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTGCT-GAATCTGTAA
* * * *
24980044 C----A--GTAACAGTAGTCGGCACA-TAAGTGTCTG-ATCAGTAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTG-CTGAATCTGTAA
* *
24980082 TCAATAACGGTAGCAGTAACAGTATTCAACACACAAAGTGCTGAATCTGTAA
1 -CAGTAAC----G--GTAACAGTATTCGACACACAAAGTGCTGAATCTGTAA
* * *
24980134 CAGTAATGGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAA
1 CAGTAACGGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAA
24980179 CAGTAAC
1 CAGTAAC
24980186 AGTAGTTGGC
Statistics
Matches: 280, Mismatches: 39, Indels: 70
0.72 0.10 0.18
Matches are distributed among these distances:
35 2 0.01
36 2 0.01
37 9 0.03
38 29 0.10
39 23 0.08
40 11 0.04
41 2 0.01
42 2 0.01
43 3 0.01
44 6 0.02
45 155 0.55
47 1 0.00
51 23 0.08
52 12 0.04
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (45 bp):
CAGTAACGGTAACAGTATTCGACACACAAAGTGCTGAATCTGTAA
Found at i:24980114 original size:134 final size:135
Alignment explanation
Indices: 24979963--24980216 Score: 429
Period size: 134 Copynumber: 1.9 Consensus size: 135
24979953 AACAGTAATG
*
24979963 GTAACAGTATTCGACACACAAAGTGCCGAATCGGTAACAGTAATGGTAACAGCATTCAACACACA
1 GTAACAGTATTCAACACACAAAGTGCCGAATCGGTAACAGTAATGGTAACAGCATTCAACACACA
* *
24980028 AAGTGTCGAATC-GTAACAGTAACAGTAGTCGGCACATAAGTGTCTGATCAGTAATCAATAACGG
66 AAGTGCCGAATCAGTAACAGTAACAGTAGTCGGCACATAAGTGCCTGATCAGTAATCAATAACGG
24980092 TAGCA
131 TAGCA
* * * *
24980097 GTAACAGTATTCAACACACAAAGTGCTGAATCTGTAACAGTAATGGTAACAGTATTCGACACACA
1 GTAACAGTATTCAACACACAAAGTGCCGAATCGGTAACAGTAATGGTAACAGCATTCAACACACA
*
24980162 AAGTGCCGAATCAGTAACAGTAACAGTAGTTGGCACATAAGTGCCTGATCAGTAA
66 AAGTGCCGAATCAGTAACAGTAACAGTAGTCGGCACATAAGTGCCTGATCAGTAA
24980217 GCCGACAAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
134 71 0.64
135 40 0.36
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (135 bp):
GTAACAGTATTCAACACACAAAGTGCCGAATCGGTAACAGTAATGGTAACAGCATTCAACACACA
AAGTGCCGAATCAGTAACAGTAACAGTAGTCGGCACATAAGTGCCTGATCAGTAATCAATAACGG
TAGCA
Found at i:24980150 original size:51 final size:51
Alignment explanation
Indices: 24980040--24980150 Score: 118
Period size: 51 Copynumber: 2.2 Consensus size: 51
24980030 GTGTCGAATC
** *
24980040 GTAACAGTAACAGTAGTCGGCACATAAGTGTCTGATCAGTAATCAATAACG
1 GTAACAGTAACAGTAGTCAACACAAAAGTGTCTGATCAGTAATCAATAACG
* * * * *
24980091 GTAGCAGTAACAGTATTCAACACACAAAGTG-CTGAATCTGTAA-CAGTAATG
1 GTAACAGTAACAGTAGTCAACACA-AAAGTGTCTG-ATCAGTAATCAATAACG
24980142 GTAACAGTA
1 GTAACAGTA
24980151 TTCGACACAC
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
51 37 0.76
52 12 0.24
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (51 bp):
GTAACAGTAACAGTAGTCAACACAAAAGTGTCTGATCAGTAATCAATAACG
Found at i:24998817 original size:22 final size:20
Alignment explanation
Indices: 24998759--24998827 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
24998749 AATGCCTAGT
* *
24998759 CCGTGTGG-GGGTCAACACAC
1 CCGTGTGGAGGGGC-ACACGC
*
24998779 CCATGTGGAGGGGCACACGC
1 CCGTGTGGAGGGGCACACGC
*
24998799 CCGTGTGGAAGGAGGCACATGC
1 CCGTGTGG-AGG-GGCACACGC
24998821 CCGTGTG
1 CCGTGTG
24998828 ACCTAGGGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 19 0.46
21 7 0.17
22 15 0.37
ACGTcount: A:0.19, C:0.28, G:0.39, T:0.14
Consensus pattern (20 bp):
CCGTGTGGAGGGGCACACGC
Found at i:24999576 original size:17 final size:18
Alignment explanation
Indices: 24999550--24999594 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 18
24999540 TGCAAACAAC
24999550 AAAAAA-AAAAAGAAGA-
1 AAAAAATAAAAAGAAGAT
*
24999566 AAAAAAT-AAAATAAGAT
1 AAAAAATAAAAAGAAGAT
*
24999583 TAAAAATAAAAA
1 AAAAAATAAAAA
24999595 TAAAAATCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 14 0.58
17 6 0.25
18 4 0.17
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (18 bp):
AAAAAATAAAAAGAAGAT
Found at i:25002024 original size:22 final size:25
Alignment explanation
Indices: 25001998--25002048 Score: 81
Period size: 22 Copynumber: 2.2 Consensus size: 25
25001988 TTGTTTAACT
25001998 TTTAATTAG-TTTTA-GTTAA-CAA
1 TTTAATTAGATTTTATGTTAATCAA
25002020 TTTAATTAGATTTTATGTTAATCAA
1 TTTAATTAGATTTTATGTTAATCAA
25002045 TTTA
1 TTTA
25002049 CTATTAATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 9 0.35
23 5 0.19
24 5 0.19
25 7 0.27
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.53
Consensus pattern (25 bp):
TTTAATTAGATTTTATGTTAATCAA
Found at i:25003996 original size:24 final size:24
Alignment explanation
Indices: 25003962--25004015 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
25003952 ACTGACCTGG
*
25003962 AATATTATTTATCATTCACCAA-A
1 AATATTATTTATCATCCACCAACA
*
25003985 AAGTATTGTTTATCATCCACCAACA
1 AA-TATTATTTATCATCCACCAACA
25004010 AATATT
1 AATATT
25004016 TAATATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 22 0.81
25 3 0.11
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.37
Consensus pattern (24 bp):
AATATTATTTATCATCCACCAACA
Found at i:25004621 original size:27 final size:23
Alignment explanation
Indices: 25004591--25004638 Score: 60
Period size: 27 Copynumber: 1.9 Consensus size: 23
25004581 AATATGGTCT
25004591 ATATATACAAATATAATTATATATTTC
1 ATATAT-CAAA-AT-ATTA-ATATTTC
25004618 ATATATCAAAATATTAATATT
1 ATATATCAAAATATTAATATT
25004639 GAGTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 4 0.19
25 2 0.10
26 4 0.19
27 6 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATATCAAAATATTAATATTTC
Found at i:25031784 original size:20 final size:22
Alignment explanation
Indices: 25031755--25031795 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
25031745 TTCTTGTAAT
25031755 TTTATATTTT-A-AAAAATAAA
1 TTTATATTTTCATAAAAATAAA
*
25031775 TTTATTTTTTCATAAAAATAA
1 TTTATATTTTCATAAAAATAA
25031796 TAAAAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 1 0.06
22 8 0.44
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTATATTTTCATAAAAATAAA
Found at i:25033796 original size:24 final size:24
Alignment explanation
Indices: 25033762--25033813 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
25033752 TTTCTAGAAA
* **
25033762 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
25033786 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
25033810 ATTT
1 ATTT
25033814 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:25034004 original size:2 final size:2
Alignment explanation
Indices: 25033997--25034025 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
25033987 CATGAAATAG
25033997 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25034026 ATCTACCATC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25041468 original size:18 final size:18
Alignment explanation
Indices: 25041445--25041483 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
25041435 AGAATGAGGG
*
25041445 GAAAGGGAGGGAGACAAA
1 GAAAGGGAGGGAGAAAAA
25041463 GAAAGGGAGGGAGAAAAA
1 GAAAGGGAGGGAGAAAAA
25041481 GAA
1 GAA
25041484 GTGCTGCCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.54, C:0.03, G:0.44, T:0.00
Consensus pattern (18 bp):
GAAAGGGAGGGAGAAAAA
Found at i:25041518 original size:2 final size:2
Alignment explanation
Indices: 25041506--25041540 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
25041496 ATTAGCATTA
* *
25041506 TC TC TC GC TC TC TC TC TC TC TC TC TC CC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
25041541 GTGGACAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.51, G:0.03, T:0.46
Consensus pattern (2 bp):
TC
Found at i:25042928 original size:18 final size:18
Alignment explanation
Indices: 25042905--25042939 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
25042895 TATATCTTTA
25042905 AATATT-TATTTTAATTTT
1 AATATTGTA-TTTAATTTT
25042923 AATATTGTATTTAATTT
1 AATATTGTATTTAATTT
25042940 GTAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (18 bp):
AATATTGTATTTAATTTT
Found at i:25043597 original size:15 final size:15
Alignment explanation
Indices: 25043577--25043607 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
25043567 GCTTTTTAAA
25043577 ATTTTAAAATTATAT
1 ATTTTAAAATTATAT
*
25043592 ATTTTAAAATTTTAT
1 ATTTTAAAATTATAT
25043607 A
1 A
25043608 AAAAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTAAAATTATAT
Found at i:25043618 original size:22 final size:22
Alignment explanation
Indices: 25043570--25043626 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 22
25043560 TATTTTGGCT
*
25043570 TTTTAAAATTTTAAAATTATATA
1 TTTTAAAATTTTAAAA-TAAATA
25043593 TTTTAAAATTTTATAAA-AAATA
1 TTTTAAAATTTTA-AAATAAATA
25043615 TTTTAAAATTTT
1 TTTTAAAATTTT
25043627 TATATACTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 16 0.50
23 13 0.41
24 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAAAATTTTAAAATAAATA
Found at i:25043638 original size:23 final size:22
Alignment explanation
Indices: 25043570--25043638 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
25043560 TATTTTGGCT
* *
25043570 TTTTAAAATTTTAAAATTATATA
1 TTTTAAAATTTTTATA-TATATA
* *
25043593 TTTTAAAA-TTTTATAAAAAATA
1 TTTTAAAATTTTTAT-ATATATA
25043615 TTTTAAAATTTTTATATACTATA
1 TTTTAAAATTTTTATATA-TATA
25043638 T
1 T
25043639 ATGATTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 18 0.49
23 19 0.51
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAAATTTTTATATATATA
Found at i:25043996 original size:19 final size:18
Alignment explanation
Indices: 25043956--25044008 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
25043946 TTATATATTT
25043956 TAAAAATTGAAAATAATATA
1 TAAAAATTG-AAA-AATATA
*
25043976 TAAAAATTGAAAAATGGTA
1 TAAAAATTGAAAAAT-ATA
25043995 TAAAAATT-AAAAAT
1 TAAAAATTGAAAAAT
25044009 TAAATTTCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 9 0.29
19 13 0.42
20 9 0.29
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (18 bp):
TAAAAATTGAAAAATATA
Found at i:25044079 original size:15 final size:15
Alignment explanation
Indices: 25044059--25044088 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25044049 TTTTAGAATT
25044059 TTAGAATTATATATA
1 TTAGAATTATATATA
*
25044074 TTAGAATTTTATATA
1 TTAGAATTATATATA
25044089 AAAATTAAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (15 bp):
TTAGAATTATATATA
Found at i:25044260 original size:20 final size:20
Alignment explanation
Indices: 25044228--25044268 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
25044218 AATTTAAATA
*
25044228 TTTTCTAGATTTTATGTATT
1 TTTTCTAGATTTTATATATT
25044248 TTTTCTA-ATTTTTATATATT
1 TTTTCTAGA-TTTTATATATT
25044268 T
1 T
25044269 ATTTTCATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTCTAGATTTTATATATT
Found at i:25046065 original size:20 final size:20
Alignment explanation
Indices: 25046033--25046071 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25046023 ATTTAATGGT
25046033 TATATTTAAATATT-TAAAA
1 TATATTTAAATATTCTAAAA
*
25046052 TATAGTTTATATATTCTAAA
1 TATA-TTTAAATATTCTAAA
25046072 TAAATTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 9 0.53
21 4 0.24
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATTTAAATATTCTAAAA
Found at i:25052872 original size:15 final size:16
Alignment explanation
Indices: 25052843--25052875 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25052833 AATTACAATC
25052843 TTATCATTTTAATAAT
1 TTATCATTTTAATAAT
*
25052859 TTAT-ATTTTTATAAT
1 TTATCATTTTAATAAT
25052874 TT
1 TT
25052876 TTAAAATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTATCATTTTAATAAT
Found at i:25057574 original size:2 final size:2
Alignment explanation
Indices: 25057567--25057604 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
25057557 TTACCGGGAG
25057567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25057605 GATTTTTGTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25059790 original size:13 final size:13
Alignment explanation
Indices: 25059774--25059826 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
25059764 TTTAAACCAA
*
25059774 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
* *
25059787 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
* *
25059800 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
25059813 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
25059826 A
1 A
25059827 TTGCCAAACT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.34, C:0.30, G:0.06, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:25060170 original size:37 final size:39
Alignment explanation
Indices: 25060111--25060197 Score: 106
Period size: 37 Copynumber: 2.3 Consensus size: 39
25060101 TAAAAATTAT
* * *
25060111 TTATATTAAAAATACTGCCATAAATATAATAGATGTTTTA
1 TTATATTAAAAATAC-GACATAAATATAATAAATATTTTA
25060151 TTATATTAAAAA-AC-ACATAAATATAATAAATATTTTA
1 TTATATTAAAAATACGACATAAATATAATAAATATTTTA
* *
25060188 GTGTATTAAA
1 TTATATTAAA
25060198 TATGATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 28 0.67
39 2 0.05
40 12 0.29
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (39 bp):
TTATATTAAAAATACGACATAAATATAATAAATATTTTA
Found at i:25063463 original size:43 final size:43
Alignment explanation
Indices: 25063389--25063475 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
25063379 CACCTAGCAC
*
25063389 TAGCAGCCCCTGTATTCGCCCCAGCTTCATCAATATTTTAATA
1 TAGCAGCCCCTATATTCGCCCCAGCTTCATCAATATTTTAATA
*
25063432 TAGCAGCCCCTATATTC-CCCCTGCTTCCATCAATATTTTAATA
1 TAGCAGCCCCTATATTCGCCCCAGCTT-CATCAATATTTTAATA
25063475 T
1 T
25063476 GTTAGTGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 8 0.20
43 33 0.80
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.34
Consensus pattern (43 bp):
TAGCAGCCCCTATATTCGCCCCAGCTTCATCAATATTTTAATA
Found at i:25063798 original size:2 final size:2
Alignment explanation
Indices: 25063791--25063815 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25063781 AATAACCTAA
25063791 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
25063816 ATCGGTTGTG
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:25064881 original size:67 final size:68
Alignment explanation
Indices: 25064701--25064937 Score: 314
Period size: 68 Copynumber: 3.5 Consensus size: 68
25064691 ATTCGGTCAT
* * * *
25064701 GCACTTAATCCAACCGATTTTGTCTTACAATTTTCACATTGGACAGCATGTATAACCTCAACAAG
1 GCACTTAATTCAACCAAATTTGTCTTAAAATTTTCACATTGGACAGCATGTATAACCTCAACAAG
*
25064766 ATA
66 ACA
* * ** * *
25064769 GCACTTGATTCAAACAAATTTGTCTTAAAAAGTTCACGTTGGACAGCATGTATAACCTCAACGAG
1 GCACTTAATTCAACCAAATTTGTCTTAAAATTTTCACATTGGACAGCATGTATAACCTCAACAAG
25064834 ACA
66 ACA
* * **
25064837 GCA-TTAATTCAACCAAATTTGTCCTAACATTTTCGTATTGGACAGCATGTATAACCTCAACAAG
1 GCACTTAATTCAACCAAATTTGTCTTAAAATTTTCACATTGGACAGCATGTATAACCTCAACAAG
25064901 ACA
66 ACA
* *
25064904 ACACTTAATTCCACCAAATTTGTCTTAAAATTTT
1 GCACTTAATTCAACCAAATTTGTCTTAAAATTTT
25064938 TGTAACGCCT
Statistics
Matches: 143, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
67 56 0.39
68 87 0.61
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (68 bp):
GCACTTAATTCAACCAAATTTGTCTTAAAATTTTCACATTGGACAGCATGTATAACCTCAACAAG
ACA
Found at i:25074148 original size:136 final size:136
Alignment explanation
Indices: 25073904--25074176 Score: 546
Period size: 136 Copynumber: 2.0 Consensus size: 136
25073894 CAGCGGTGAC
25073904 CACTCGACAGGAAACTGTTTTCACTTATCATTATTTCATGGTTTTTACTTAAATTTTTGGCTTTT
1 CACTCGACAGGAAACTGTTTTCACTTATCATTATTTCATGGTTTTTACTTAAATTTTTGGCTTTT
25073969 GTGAGAGTTTTGTGATTTTTGGACTCTCCGGACTTTTTGACTGTTTGGTTTAAATTTTTTTGGTT
66 GTGAGAGTTTTGTGATTTTTGGACTCTCCGGACTTTTTGACTGTTTGGTTTAAATTTTTTTGGTT
25074034 TGGTTG
131 TGGTTG
25074040 CACTCGACAGGAAACTGTTTTCACTTATCATTATTTCATGGTTTTTACTTAAATTTTTGGCTTTT
1 CACTCGACAGGAAACTGTTTTCACTTATCATTATTTCATGGTTTTTACTTAAATTTTTGGCTTTT
25074105 GTGAGAGTTTTGTGATTTTTGGACTCTCCGGACTTTTTGACTGTTTGGTTTAAATTTTTTTGGTT
66 GTGAGAGTTTTGTGATTTTTGGACTCTCCGGACTTTTTGACTGTTTGGTTTAAATTTTTTTGGTT
25074170 TGGTTG
131 TGGTTG
25074176 C
1 C
25074177 GTTAGGATTT
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
136 137 1.00
ACGTcount: A:0.18, C:0.13, G:0.20, T:0.50
Consensus pattern (136 bp):
CACTCGACAGGAAACTGTTTTCACTTATCATTATTTCATGGTTTTTACTTAAATTTTTGGCTTTT
GTGAGAGTTTTGTGATTTTTGGACTCTCCGGACTTTTTGACTGTTTGGTTTAAATTTTTTTGGTT
TGGTTG
Found at i:25074575 original size:14 final size:14
Alignment explanation
Indices: 25074556--25074583 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25074546 TTAATCAAGG
25074556 AAATTAAAGCTCAA
1 AAATTAAAGCTCAA
25074570 AAATTAAAGCTCAA
1 AAATTAAAGCTCAA
25074584 TTTACTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATTAAAGCTCAA
Found at i:25078551 original size:23 final size:23
Alignment explanation
Indices: 25078521--25078568 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
25078511 CCTTATTTCA
25078521 TCTAACTCATTGGTAATTTCCCT
1 TCTAACTCATTGGTAATTTCCCT
25078544 TCTAACTCATTGGTAATTTCCCT
1 TCTAACTCATTGGTAATTTCCCT
25078567 TC
1 TC
25078569 CAAATCATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.44
Consensus pattern (23 bp):
TCTAACTCATTGGTAATTTCCCT
Found at i:25078576 original size:23 final size:23
Alignment explanation
Indices: 25078527--25078576 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
25078517 TTCATCTAAC
* *
25078527 TCATTGGTAATTTCCCTTCTAAC
1 TCATTGGTAATTTCCCTTCCAAA
25078550 TCATTGGTAATTTCCCTTCCAAA
1 TCATTGGTAATTTCCCTTCCAAA
25078573 TCAT
1 TCAT
25078577 GCATACCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.24, C:0.26, G:0.08, T:0.42
Consensus pattern (23 bp):
TCATTGGTAATTTCCCTTCCAAA
Found at i:25081004 original size:4 final size:4
Alignment explanation
Indices: 25080995--25081196 Score: 404
Period size: 4 Copynumber: 50.5 Consensus size: 4
25080985 AAAGAAGTAA
25080995 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
25081043 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
25081091 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
25081139 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
25081187 ATAC ATAC AT
1 ATAC ATAC AT
25081197 CAGATTACGG
Statistics
Matches: 198, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 198 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:25082922 original size:22 final size:22
Alignment explanation
Indices: 25082880--25082922 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
25082870 TGACATGTTT
* *
25082880 TGACCATTAAAAAAATGACATG
1 TGACAATTAAAAAAATAACATG
25082902 TGACAATTAAAATAAA-AACAT
1 TGACAATTAAAA-AAATAACAT
25082923 TAAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (22 bp):
TGACAATTAAAAAAATAACATG
Found at i:25083398 original size:6 final size:6
Alignment explanation
Indices: 25083387--25083413 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
25083377 AATATATTAA
25083387 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
25083414 TATAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:25099188 original size:3 final size:3
Alignment explanation
Indices: 25099175--25099223 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
25099165 TAAATACATA
* *
25099175 AAT AGAT AAT AAT AAT AAT AAT AAT AAC AGAT AA- GAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
25099221 AAT
1 AAT
25099224 GATAGTAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 1 0.03
3 33 0.85
4 5 0.13
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:25103279 original size:332 final size:331
Alignment explanation
Indices: 25102668--25103331 Score: 1148
Period size: 332 Copynumber: 2.0 Consensus size: 331
25102658 TTCATATTTT
*
25102668 GTTATTGAAATTAATATTATTGTAAAAGTATGAAAATTGAATTGAATGTTTAAAACGAGTAGAAC
1 GTTATTGAAATTAAGATTATTGTAAAAGTATGAAAATTGAATTGAATGTTTAAAACGAGTAGAAC
* * *
25102733 GTAGGATTGAGTATGATCGTTTCGTGGAAAAGAATGAATTGATGGGTAAGACCATGGTTGGACCA
66 GCAGGATTGAGTACGATCGTTTCGTGGAAAAGAATGAATTGATAGGTAAGACCATGGTTGGACCA
* * *
25102798 TGGATATGTTTAAATGTAATACCATAGTTGGGCTATGGCATTTTAATAAAAAGACCATAACTAGG
131 TGGATATGCTTAAATGTAAGACCATAGCTGGGCTATGGCATTTTAATAAAAAGACCATAACTAGG
*
25102863 TTATGACACCTTAAACATAAGATTATGGTTGGACAATGGCAATATAGATACATGCGTAAGACCAA
196 TTATGACACCTTAAACATAAGACTATGGTTGGACAATGGCAATATAGATACATGCGTAAGACCAA
* *
25102928 AGCTGGGCTATGGCATTCTGATGATAAGACTATAACTGGGTTATGGAACAACAAATGTAAGACCA
261 AGCTGGGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGAACAACAAATGTAAGACCA
25102993 TGGCAGG
326 TGG-AGG
25103000 GTTATTGAAATTAAGATTATTGTAAAAGTATGAAAATTGAATTGAATGTTTAAAACGAGTAGAAC
1 GTTATTGAAATTAAGATTATTGTAAAAGTATGAAAATTGAATTGAATGTTTAAAACGAGTAGAAC
*
25103065 GCATGATTGAGTACGATCGTTTCGTGGAAAAGAATGAATTGATAGGTAAGACCATGGTTGGACCA
66 GCAGGATTGAGTACGATCGTTTCGTGGAAAAGAATGAATTGATAGGTAAGACCATGGTTGGACCA
*
25103130 TGGATATGCTTAAATGTAAGACCATAGCTGGGCTATGGCATTTTAATGAAAAGACCATAACTAGG
131 TGGATATGCTTAAATGTAAGACCATAGCTGGGCTATGGCATTTTAATAAAAAGACCATAACTAGG
* * * * *
25103195 TTATGACATCTTGAACATAAGACTATGGTTGGACCATGGCAGTATAGATACATGCGTAAGACCAT
196 TTATGACACCTTAAACATAAGACTATGGTTGGACAATGGCAATATAGATACATGCGTAAGACCAA
* *
25103260 AGCTGGGCTATGACATTCTGATGATAATACCATAACTGGGTTATGGAACTACAAATGTAAGACCA
261 AGCTGGGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGAACAACAAATGTAAGACCA
25103325 TGGAGG
326 TGGAGG
25103331 G
1 G
25103332 CCATGGCAAT
Statistics
Matches: 313, Mismatches: 19, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
331 4 0.01
332 309 0.99
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.28
Consensus pattern (331 bp):
GTTATTGAAATTAAGATTATTGTAAAAGTATGAAAATTGAATTGAATGTTTAAAACGAGTAGAAC
GCAGGATTGAGTACGATCGTTTCGTGGAAAAGAATGAATTGATAGGTAAGACCATGGTTGGACCA
TGGATATGCTTAAATGTAAGACCATAGCTGGGCTATGGCATTTTAATAAAAAGACCATAACTAGG
TTATGACACCTTAAACATAAGACTATGGTTGGACAATGGCAATATAGATACATGCGTAAGACCAA
AGCTGGGCTATGACATTCTGATGATAAGACCATAACTGGGTTATGGAACAACAAATGTAAGACCA
TGGAGG
Found at i:25110967 original size:18 final size:18
Alignment explanation
Indices: 25110944--25110983 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
25110934 TTGATTTGTG
*
25110944 AATGTCTCCTTCACTTGA
1 AATGTCTCATTCACTTGA
25110962 AATGTCTCATTCACTTGA
1 AATGTCTCATTCACTTGA
25110980 AATG
1 AATG
25110984 CTTGCTCCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (18 bp):
AATGTCTCATTCACTTGA
Found at i:25112158 original size:57 final size:57
Alignment explanation
Indices: 25112070--25112183 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
25112060 GGGCTTAATG
25112070 AATCTATAGCTAAATAAGTAGCAAAGTAACAATCTAGAATATCAAGTAATTTCAGTA
1 AATCTATAGCTAAATAAGTAGCAAAGTAACAATCTAGAATATCAAGTAATTTCAGTA
25112127 AATCTATAGCTAAATAAGTAGCAAAGTAACAATCTAGAATATCAAGTAATTTCAGTA
1 AATCTATAGCTAAATAAGTAGCAAAGTAACAATCTAGAATATCAAGTAATTTCAGTA
25112184 GAACAAATTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (57 bp):
AATCTATAGCTAAATAAGTAGCAAAGTAACAATCTAGAATATCAAGTAATTTCAGTA
Found at i:25114473 original size:7 final size:7
Alignment explanation
Indices: 25114424--25114483 Score: 50
Period size: 7 Copynumber: 8.3 Consensus size: 7
25114414 TTAAAATAAT
25114424 AATATTA
1 AATATTA
25114431 AAT-TTA
1 AATATTA
*
25114437 AATTTTAA
1 AATATT-A
*
25114445 AAAATTA
1 AATATTA
* *
25114452 GAAAACTA
1 -AATATTA
25114460 TAATATTA
1 -AATATTA
25114468 AATATTA
1 AATATTA
25114475 AATATTA
1 AATATTA
25114482 AA
1 AA
25114484 AAAATACCTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
6 6 0.14
7 22 0.50
8 16 0.36
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (7 bp):
AATATTA
Found at i:25114619 original size:2 final size:2
Alignment explanation
Indices: 25114614--25114643 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25114604 AAAAATTATC
25114614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25114644 TAAATATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25114980 original size:21 final size:20
Alignment explanation
Indices: 25114937--25114981 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
25114927 ATTTTTTTCT
* *
25114937 TTATAAATTTTATGAATATA
1 TTATAAATTTTATAAACATA
*
25114957 TTATAAATATTTTTAAACATA
1 TTATAAAT-TTTATAAACATA
25114978 TTAT
1 TTAT
25114982 TTCAAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (20 bp):
TTATAAATTTTATAAACATA
Found at i:25118871 original size:15 final size:15
Alignment explanation
Indices: 25118830--25118871 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
25118820 ACATGCAATT
25118830 AGAAAAGAAAGAA-AA
1 AGAAAAG-AAGAAGAA
25118845 AGAAAAG-A-AAGAA
1 AGAAAAGAAGAAGAA
25118858 AGAAAAGAAGAAGA
1 AGAAAAGAAGAAGA
25118872 CTCACGCACA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.08
13 10 0.42
14 1 0.04
15 11 0.46
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAGAAGAA
Found at i:25119599 original size:25 final size:25
Alignment explanation
Indices: 25119551--25119599 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
25119541 TATAATTGAA
* * *
25119551 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
25119576 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
25119600 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:25121341 original size:42 final size:43
Alignment explanation
Indices: 25121248--25121397 Score: 144
Period size: 43 Copynumber: 3.5 Consensus size: 43
25121238 ATGTGATTTT
* * * *
25121248 GTGTAAGAACACGTCTGGGAC-GTTGGCATCGATTTGA-GATTTAC
1 GTGTAAGACCATGTCTGGGACAG-TGACATCGATAT-ATGA-TTAC
* * *
25121292 GTGTAAGACCATGTCTAGGACATTGACATC-ATATATGATTAT
1 GTGTAAGACCATGTCTGGGACAGTGACATCGATATATGATTAC
* * * *
25121334 GTGTAAGACCCTGTCTGGGACAGTGGCATCGTTATTTGATTAC
1 GTGTAAGACCATGTCTGGGACAGTGACATCGATATATGATTAC
*
25121377 ATGTAAGACCATGTCTGGGAC
1 GTGTAAGACCATGTCTGGGAC
25121398 GTTGGCATTG
Statistics
Matches: 87, Mismatches: 16, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
42 30 0.34
43 33 0.38
44 24 0.28
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGACAGTGACATCGATATATGATTAC
Found at i:25125417 original size:51 final size:51
Alignment explanation
Indices: 25125341--25125472 Score: 169
Period size: 51 Copynumber: 2.6 Consensus size: 51
25125331 TATGAAAACG
* * *
25125341 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-GATAG-ATAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGCACCGGATAGCAT--TGGTCACA
* * * *
25125392 TGTGTAGTACTATGTGCAGGCTACTATGTGCACCGGATGGCCTTGGTCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGCACCGGATAGCATTGGTCACA
25125443 TGTGTAGTACTATGTGCAGGCTACTACGTG
1 TGTGTAGTACTATGTGCAGGCTACTACGTG
25125473 AATCTAAAAG
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
51 66 0.93
52 4 0.06
53 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGCACCGGATAGCATTGGTCACA
Found at i:25128525 original size:34 final size:34
Alignment explanation
Indices: 25128478--25128542 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
25128468 TTTCAACCCC
*
25128478 AAACTTTTCGATCTTATCAATTAGAGGTCGTAAT
1 AAACTTTTCGATCTTATCAATTAAAGGTCGTAAT
25128512 AAAC-TTTCTGATCTTATCAATTAAAGGTCGT
1 AAACTTTTC-GATCTTATCAATTAAAGGTCGT
25128543 CATGCATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 4 0.14
34 25 0.86
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.38
Consensus pattern (34 bp):
AAACTTTTCGATCTTATCAATTAAAGGTCGTAAT
Found at i:25131776 original size:5 final size:5
Alignment explanation
Indices: 25131754--25131797 Score: 65
Period size: 5 Copynumber: 9.2 Consensus size: 5
25131744 AAATTATGTA
*
25131754 TGAGT T-AGT T-AAT TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT T
1 TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT TGAGT T
25131798 AATTATTTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
4 7 0.19
5 29 0.81
ACGTcount: A:0.23, C:0.00, G:0.34, T:0.43
Consensus pattern (5 bp):
TGAGT
Found at i:25140371 original size:51 final size:50
Alignment explanation
Indices: 25140259--25140384 Score: 125
Period size: 51 Copynumber: 2.5 Consensus size: 50
25140249 TTTATTTATT
*
25140259 ATTT-AATTAATTAGAGATAAAATAATAATTTAATATTATCACTTAATTA
1 ATTTAAATTAATTAGAGATAAAATAATAATTTAATATTACCACTTAATTA
* ** * * * *
25140308 TTTTATTTTTAATTAGTGTTAATAT-ATAATTTTAATACTTACCTCTTAATTA
1 ATTTA-AATTAATTAGAGATAAAATAATAA-TTTAATA-TTACCACTTAATTA
25140360 ATTTAAATTAATTAGA-A-AAAATAAT
1 ATTTAAATTAATTAGAGATAAAATAAT
25140385 TATGACACCT
Statistics
Matches: 58, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
49 7 0.12
50 6 0.10
51 29 0.50
52 16 0.28
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (50 bp):
ATTTAAATTAATTAGAGATAAAATAATAATTTAATATTACCACTTAATTA
Found at i:25140839 original size:22 final size:21
Alignment explanation
Indices: 25140796--25140846 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
25140786 TGAAGACGAC
25140796 TTTAATAAAAAAAATATTATAA
1 TTTAATAAAAAAAATA-TATAA
25140818 TTTAATAATTAAAAAATA-ATAA
1 TTTAATAA--AAAAAATATATAA
*
25140840 ATTAATA
1 TTTAATA
25140847 TAGTATCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 18 0.69
24 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TTTAATAAAAAAAATATATAA
Found at i:25146036 original size:22 final size:22
Alignment explanation
Indices: 25146008--25146049 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
25145998 CGGCTGGGTA
*
25146008 GATTTTTATAAT-TTTTATTTTT
1 GATTTTT-TAATAATTTATTTTT
25146030 GATTTTTTAATAATTTATTT
1 GATTTTTTAATAATTTATTT
25146050 GTTTTGAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
GATTTTTTAATAATTTATTTTT
Found at i:25146388 original size:19 final size:19
Alignment explanation
Indices: 25146363--25146454 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
25146353 AATTTTTGAG
25146363 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
25146382 TATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
25146401 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
25146420 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
25146439 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
25146455 ATATATGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:25147644 original size:98 final size:98
Alignment explanation
Indices: 25147527--25147724 Score: 342
Period size: 98 Copynumber: 2.0 Consensus size: 98
25147517 TTTAAAAATT
* *
25147527 GTAAAAGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCTCTAACGTATTGGGTGTGATTT
1 GTAAAAGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAAAGTATTGGGTGTGATTT
*
25147592 CTTAAATCTTGGATAAGCGGATGTTCTTTTAAA
66 CTTAAATCTTGGATAAGCGGATGTTCCTTTAAA
* *
25147625 GTAAAGGAAATATTTCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAAAGTATTGGGTGTGATTT
1 GTAAAAGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAAAGTATTGGGTGTGATTT
*
25147690 CTTAAATCTTGGATAAGTGGATGTTCCTTTAAA
66 CTTAAATCTTGGATAAGCGGATGTTCCTTTAAA
25147723 GT
1 GT
25147725 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.36
Consensus pattern (98 bp):
GTAAAAGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAAAGTATTGGGTGTGATTT
CTTAAATCTTGGATAAGCGGATGTTCCTTTAAA
Found at i:25153737 original size:44 final size:43
Alignment explanation
Indices: 25153683--25153968 Score: 212
Period size: 44 Copynumber: 6.7 Consensus size: 43
25153673 AAGATGGCAA
25153683 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-G
* * *
25153727 ATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAGCC--G
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAG
* * ** * * * *
25153768 ATCTTATCTCTCTAAAGTTGCAG-AAAGCAGATCACA-TC-TG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAG
* * **
25153808 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AGCCAAG
* ** * *
25153853 -TCTTATC-CTTCTGAAGTTGCAGT-GAGGCAGACCCAAGATGGCGA-
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAAG
* *
25153897 ATCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATA
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-G
* *
25153941 ATCCTATCTCCCTAAAGTTGCAGTGGAG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAG
25153969 TGGGTTAAAA
Statistics
Matches: 193, Mismatches: 34, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
39 1 0.01
40 29 0.15
41 29 0.15
42 3 0.02
43 5 0.03
44 91 0.47
45 32 0.17
46 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (43 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAG
Found at i:25153928 original size:45 final size:44
Alignment explanation
Indices: 25153808--25153928 Score: 133
Period size: 45 Copynumber: 2.7 Consensus size: 44
25153798 ATCACATCTG
* *
25153808 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAACAA
1 GTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACCAAGTAAACAA
**
25153852 GTCTTATC-CTTCTGAAGTTGCAGT-GAGGCAGACCCAAG-ATGGCGAA
1 GTCTTATCTC-TCTGAAGTTGCAGTGGA-GCAGA-CCAAGTA-AAC-AA
25153898 -TCTTATCTCTCTGAAGTTGCAGTGGAGCAGA
1 GTCTTATCTCTCTGAAGTTGCAGTGGAGCAGA
25153929 TTAAAGCCAA
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
43 3 0.05
44 27 0.41
45 31 0.47
46 5 0.08
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (44 bp):
GTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACCAAGTAAACAA
Found at i:25154140 original size:131 final size:131
Alignment explanation
Indices: 25153981--25154389 Score: 606
Period size: 132 Copynumber: 3.1 Consensus size: 131
25153971 GGTTAAAACT
* *
25153981 GATCTTAGCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTA
* *
25154046 TAGTGGAGTACATTGAAGCCAGTAATTCTACTTCTCTGGCAACAGTGGAATAGATTGAAGATTTC
66 CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGCAACAGTGGAATAGATTGAAGATTTC
25154111 A
131 A
* *
25154112 GATCTTATCTCCCTAAGAAGTAGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTA
* * *
25154177 CAGTGGAGTACGTTGAAGCTAGTAATTCTACTTCCCTAGGCAACAGTGGAATAGATTGAAGGTTT
66 CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCT-GGCAACAGTGGAATAGATTGAAGATTT
25154242 CA
130 CA
* * * *
25154244 GATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGGATTTTACCTCCCTGTCGTTA
1 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTA
* * * *
25154309 CAGTGGAGTACATTGAAGTCAGTAATCCTA-TCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT
66 CAGTGGAGTACATTGAAGCCAGTAATTCTACT-TCCCTGG-CAACAGTGGAATAGATTGAAGATT
*
25154373 GTAA
129 -TCA
25154377 G-TCTTATCTCCCT
1 GATCTTATCTCCCT
25154390 GCAGTTGCAA
Statistics
Matches: 251, Mismatches: 23, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
131 97 0.39
132 151 0.60
133 3 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (131 bp):
GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTA
CAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGCAACAGTGGAATAGATTGAAGATTTC
A
Found at i:25154663 original size:19 final size:19
Alignment explanation
Indices: 25154618--25154710 Score: 141
Period size: 19 Copynumber: 4.8 Consensus size: 19
25154608 AATTTTTGAG
*
25154618 GATATGCAATCTTATATAT
1 GATATGCAATCTTAGATAT
*
25154637 ATATATGCAATCTTAGATAT
1 -GATATGCAATCTTAGATAT
25154657 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
25154676 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
25154695 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
25154711 ATATATGATT
Statistics
Matches: 66, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
19 49 0.74
20 17 0.26
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:25154696 original size:38 final size:38
Alignment explanation
Indices: 25154618--25154716 Score: 157
Period size: 38 Copynumber: 2.6 Consensus size: 38
25154608 AATTTTTGAG
*
25154618 GATATGCAATCTTATATATATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATATATAT-CAATCTTAGATAT
25154657 GATATGCAATCTTAGATATGATATAT-AATCTTAGATAT
1 GATATGCAATCTTAGATAT-ATATATCAATCTTAGATAT
25154695 GATATGCAATCTTAGA-ATATAT
1 GATATGCAATCTTAGATATATAT
25154717 GATTTTGTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
36 4 0.07
37 2 0.03
38 28 0.48
39 18 0.31
40 6 0.10
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (38 bp):
GATATGCAATCTTAGATATATATATCAATCTTAGATAT
Found at i:25155889 original size:97 final size:98
Alignment explanation
Indices: 25155781--25155977 Score: 360
Period size: 97 Copynumber: 2.0 Consensus size: 98
25155771 TTTAAAAATT
*
25155781 GTAAAGGAAATATTCCTAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTT
1 GTAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTT
25155846 CTTAAATCTTGGATAAGCGGATGTT-CTTTAAA
66 CTTAAATCTTGGATAAGCGGATGTTCCTTTAAA
*
25155878 GTAAAGGAAATATTTCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTT
1 GTAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTT
*
25155943 CTTAAATCTTGGATAAGTGGATGTTCCTTTAAA
66 CTTAAATCTTGGATAAGCGGATGTTCCTTTAAA
25155976 GT
1 GT
25155978 TTTATTGTAC
Statistics
Matches: 96, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
97 87 0.91
98 9 0.09
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (98 bp):
GTAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTT
CTTAAATCTTGGATAAGCGGATGTTCCTTTAAA
Found at i:25158172 original size:2 final size:2
Alignment explanation
Indices: 25158165--25158195 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25158155 GAATCTTAAA
25158165 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25158196 AACATTTACT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25159028 original size:22 final size:22
Alignment explanation
Indices: 25159003--25159050 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
25158993 ACAAGAGCAA
*
25159003 AAACCCAATGTAAGATAACACC
1 AAACCCAATGTAAGACAACACC
25159025 AAACCCAATGTAAGACAACACC
1 AAACCCAATGTAAGACAACACC
25159047 AAAC
1 AAAC
25159051 TTAATTACCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.52, C:0.29, G:0.08, T:0.10
Consensus pattern (22 bp):
AAACCCAATGTAAGACAACACC
Found at i:25161720 original size:43 final size:43
Alignment explanation
Indices: 25161645--25161774 Score: 178
Period size: 43 Copynumber: 3.0 Consensus size: 43
25161635 CATGGGATTT
25161645 TCGATATGTGA-TATCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCA
*
25161688 TCGACT-TGTGTTTACGTGTAAGACC-CTGTCTGGGACAG-TGGCA
1 TCGA-TATGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
*
25161731 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
25161774 T
1 T
25161775 TGTACGAGTT
Statistics
Matches: 77, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
42 3 0.04
43 69 0.90
44 5 0.06
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.29
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:25162879 original size:47 final size:47
Alignment explanation
Indices: 25162822--25163209 Score: 594
Period size: 47 Copynumber: 8.4 Consensus size: 47
25162812 AATTTTGTAC
*
25162822 ATATGTTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
1 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
* * *
25162869 ATATGCTGTCAAATTTTTATGTATAAATGCAGTCCAATT-T-TGTAT
1 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
* *
25162914 ATATGCTGTCAAATTTTGATATATAAATGCAGTCTAATTATATATGT
1 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
* *
25162961 ATATGCTGTCAAATTTTGATGTATAAATGCAGTTCAATT-T-TATAT
1 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
25163006 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
1 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
* *
25163053 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATT-T-TGTAT
1 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
25163098 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
1 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
* *
25163145 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTGCTGTA--T
1 ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATT-ATATATGT
25163191 ATATGCTGTCCAAATTTTG
1 ATATGCTGT-CAAATTTTG
25163210 GTGTGAAAAT
Statistics
Matches: 312, Mismatches: 21, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
45 123 0.39
46 16 0.05
47 170 0.54
48 3 0.01
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.42
Consensus pattern (47 bp):
ATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGT
Found at i:25162965 original size:92 final size:92
Alignment explanation
Indices: 25162808--25163209 Score: 714
Period size: 92 Copynumber: 4.3 Consensus size: 92
25162798 AATATGTGCT
* *
25162808 GTCCAATTTTGTACATATGTTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTATAT
1 GTCCAATTTTGTATATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTATAT
*
25162873 GCTGTCAAATTTTTATGTATAAATGCA
66 GCTGTCAAATTTTGATGTATAAATGCA
* *
25162900 GTCCAATTTTGTATATATGCTGTCAAATTTTGATATATAAATGCAGTCTAATTATATATGTATAT
1 GTCCAATTTTGTATATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTATAT
25162965 GCTGTCAAATTTTGATGTATAAATGCA
66 GCTGTCAAATTTTGATGTATAAATGCA
* *
25162992 GTTCAATTTTATATATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTATAT
1 GTCCAATTTTGTATATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTATAT
25163057 GCTGTCAAATTTTGATGTATAAATGCA
66 GCTGTCAAATTTTGATGTATAAATGCA
25163084 GTCCAATTTTGTATATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTATAT
1 GTCCAATTTTGTATATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTATAT
25163149 GCTGTCAAATTTTGATGTATAAATGCA
66 GCTGTCAAATTTTGATGTATAAATGCA
*
25163176 GTCCAATTGCTGTATATATGCTGTCCAAATTTTG
1 GTCCAATT-TTGTATATATGCTGT-CAAATTTTG
25163210 GTGTGAAAAT
Statistics
Matches: 296, Mismatches: 12, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
92 273 0.92
93 14 0.05
94 9 0.03
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (92 bp):
GTCCAATTTTGTATATATGCTGTCAAATTTTGATGTATAAATGCAGTCCAATTATATATGTATAT
GCTGTCAAATTTTGATGTATAAATGCA
Found at i:25163189 original size:22 final size:22
Alignment explanation
Indices: 25162837--25163203 Score: 163
Period size: 24 Copynumber: 16.0 Consensus size: 22
25162827 TTGTCAAATT
25162837 TTGATGTATAAATGCAGTCCAA
1 TTGATGTATAAATGCAGTCCAA
* * * *
25162859 TT-ATATATGTATATGCTGTCAAA
1 TTGATGTA--TAAATGCAGTCCAA
*
25162882 TTTTTATGTATAAATGCAGTCCAA
1 --TTGATGTATAAATGCAGTCCAA
* * * *
25162906 TT-TTGTATATATGCTGTCAAA
1 TTGATGTATAAATGCAGTCCAA
* *
25162927 TTTTGATATATAAATGCAGTCTAA
1 --TTGATGTATAAATGCAGTCCAA
* * * *
25162951 TT-ATATATGTATATGCTGTCAAA
1 TTGATGTA--TAAATGCAGTCCAA
*
25162974 TTTTGATGTATAAATGCAGTTCAA
1 --TTGATGTATAAATGCAGTCCAA
* * * * *
25162998 TT-TTATATATATGCTGTCAAA
1 TTGATGTATAAATGCAGTCCAA
25163019 TTTTGATGTATAAATGCAGTCCAA
1 --TTGATGTATAAATGCAGTCCAA
* * * *
25163043 TT-ATATATGTATATGCTGTCAAA
1 TTGATGTA--TAAATGCAGTCCAA
25163066 TTTTGATGTATAAATGCAGTCCAA
1 --TTGATGTATAAATGCAGTCCAA
* * * *
25163090 TT-TTGTATATATGCTGTCAAA
1 TTGATGTATAAATGCAGTCCAA
25163111 TTTTGATGTATAAATGCAGTCCAA
1 --TTGATGTATAAATGCAGTCCAA
* * * *
25163135 TT-ATATATGTATATGCTGTCAAA
1 TTGATGTA--TAAATGCAGTCCAA
25163158 TTTTGATGTATAAATGCAGTCCAA
1 --TTGATGTATAAATGCAGTCCAA
* * *
25163182 TTGCTGTATATATGCTGTCCAA
1 TTGATGTATAAATGCAGTCCAA
25163204 ATTTTGGTGT
Statistics
Matches: 253, Mismatches: 63, Indels: 58
0.68 0.17 0.16
Matches are distributed among these distances:
21 60 0.24
22 33 0.13
23 50 0.20
24 86 0.34
25 8 0.03
26 16 0.06
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (22 bp):
TTGATGTATAAATGCAGTCCAA
Found at i:25163220 original size:47 final size:45
Alignment explanation
Indices: 25162808--25163263 Score: 585
Period size: 47 Copynumber: 9.9 Consensus size: 45
25162798 AATATGTGCT
* * * *
25162808 GTCCAATTTTGTACATATGTTGTCAAATTTTGATGTATAAATGCA
1 GTCCAATTATATATATATGCTGTCAAATTTTGATGTATAAATGCA
*
25162853 GTCCAATTATATATGTATATGCTGTCAAATTTTTATGTATAAATGCA
1 GTCCAATTATATA--TATATGCTGTCAAATTTTGATGTATAAATGCA
* * *
25162900 GTCCAATTTTGTATATATGCTGTCAAATTTTGATATATAAATGCA
1 GTCCAATTATATATATATGCTGTCAAATTTTGATGTATAAATGCA
*
25162945 GTCTAATTATATATGTATATGCTGTCAAATTTTGATGTATAAATGCA
1 GTCCAATTATATA--TATATGCTGTCAAATTTTGATGTATAAATGCA
* *
25162992 GTTCAATTTTATATATATGCTGTCAAATTTTGATGTATAAATGCA
1 GTCCAATTATATATATATGCTGTCAAATTTTGATGTATAAATGCA
25163037 GTCCAATTATATATGTATATGCTGTCAAATTTTGATGTATAAATGCA
1 GTCCAATTATATA--TATATGCTGTCAAATTTTGATGTATAAATGCA
* *
25163084 GTCCAATTTTGTATATATGCTGTCAAATTTTGATGTATAAATGCA
1 GTCCAATTATATATATATGCTGTCAAATTTTGATGTATAAATGCA
25163129 GTCCAATTATATATGTATATGCTGTCAAATTTTGATGTATAAATGCA
1 GTCCAATTATATA--TATATGCTGTCAAATTTTGATGTATAAATGCA
* * * *
25163176 GTCCAATTGCTGTATATATGCTGTCCAAATTTTGGTGTGA-AAATGCT
1 GTCCAATT-ATATATATATGCTGT-CAAATTTTGATGT-ATAAATGCA
* * *
25163223 GTCTAGTTTAGTATATAAATGCTGTCGAAA--TTGATGTATAA
1 GTCCA-ATTA-TATATATATGCTGTC-AAATTTTGATGTATAA
25163264 TAGTTGTCCA
Statistics
Matches: 364, Mismatches: 32, Indels: 29
0.86 0.08 0.07
Matches are distributed among these distances:
45 138 0.38
46 18 0.05
47 187 0.51
48 21 0.06
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (45 bp):
GTCCAATTATATATATATGCTGTCAAATTTTGATGTATAAATGCA
Found at i:25172822 original size:30 final size:30
Alignment explanation
Indices: 25172771--25172827 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
25172761 AAATAGATAA
* *
25172771 ATATAAATAAATATTTATATATATAATGAC
1 ATATAAATAAACAATTATATATATAATGAC
*
25172801 ATATAAATAGAACAATT-TATATTTAAT
1 ATATAAATA-AACAATTATATATATAAT
25172828 TTTCGAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 18 0.78
31 5 0.22
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (30 bp):
ATATAAATAAACAATTATATATATAATGAC
Found at i:25174266 original size:16 final size:16
Alignment explanation
Indices: 25174245--25174279 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
25174235 TATAAATAAA
25174245 TTTTATTTAA-ATTTAT
1 TTTTATTTAATA-TTAT
25174261 TTTTATTTAATATTAT
1 TTTTATTTAATATTAT
25174277 TTT
1 TTT
25174280 GTGAATTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 17 0.94
17 1 0.06
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTATTTAATATTAT
Found at i:25182401 original size:2 final size:2
Alignment explanation
Indices: 25182394--25182430 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
25182384 ATGTAGTTGG
*
25182394 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25182431 TTTTGGTTGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:25187348 original size:13 final size:13
Alignment explanation
Indices: 25187330--25187355 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
25187320 TAAGTTAATT
25187330 TACTTATCACATA
1 TACTTATCACATA
25187343 TACTTATCACATA
1 TACTTATCACATA
25187356 CAAGACCAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
TACTTATCACATA
Found at i:25190699 original size:11 final size:11
Alignment explanation
Indices: 25190683--25190707 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25190673 TTTCAAGCAT
25190683 TTAATTTTTAA
1 TTAATTTTTAA
25190694 TTAATTTTTAA
1 TTAATTTTTAA
25190705 TTA
1 TTA
25190708 TTGTTAAATA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTAATTTTTAA
Found at i:25190771 original size:17 final size:17
Alignment explanation
Indices: 25190739--25190772 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
25190729 TTTTTTAGTT
25190739 TTTAAATAATATATAAA
1 TTTAAATAATATATAAA
25190756 TTTAGAATAATA-ATAAA
1 TTTA-AATAATATATAAA
25190773 AAGTAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TTTAAATAATATATAAA
Found at i:25192193 original size:22 final size:23
Alignment explanation
Indices: 25192152--25192195 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
25192142 TAAATTTTTG
25192152 TCAATAATCAAGTAACATAACTT
1 TCAATAATCAAGTAACATAACTT
25192175 TCAATAAT-AA-TAAACATAACT
1 TCAATAATCAAGT-AACATAACT
25192196 CATTAGAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 1 0.05
22 11 0.55
23 8 0.40
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (23 bp):
TCAATAATCAAGTAACATAACTT
Found at i:25192744 original size:3 final size:3
Alignment explanation
Indices: 25192736--25192782 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
25192726 TACTTAGTGT
25192736 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
25192783 TTCTTTGACG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25200190 original size:12 final size:13
Alignment explanation
Indices: 25200175--25200227 Score: 67
Period size: 12 Copynumber: 4.3 Consensus size: 13
25200165 TTTCTAGGTC
*
25200175 TTTTCATTTTTCT
1 TTTTCATTTTTCA
25200188 TTTTC-TTTTTCA
1 TTTTCATTTTTCA
25200200 TTTTCA-TTTTCA
1 TTTTCATTTTTCA
*
25200212 TTTTTATTTTT-A
1 TTTTCATTTTTCA
25200224 TTTT
1 TTTT
25200228 TGAGAAAACC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
12 27 0.75
13 9 0.25
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:25200191 original size:7 final size:6
Alignment explanation
Indices: 25200175--25200228 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
25200165 TTTCTAGGTC
* * * *
25200175 TTTTCAT TTTTCT TTTTCT TTTTCA TTTTCA TTTTCAT TTTTAT TTTTAT
1 TTTTC-T TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT
25200225 TTTT
1 TTTT
25200229 GAGAAAACCA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
6 34 0.79
7 9 0.21
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTCT
Found at i:25200194 original size:18 final size:19
Alignment explanation
Indices: 25200175--25200228 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
25200165 TTTCTAGGTC
*
25200175 TTTTCATTTTTCTTTTTCT
1 TTTTCATTTTTCTTTTTCA
*
25200194 TTTTCA-TTTTCATTTTCA
1 TTTTCATTTTTCTTTTTCA
* *
25200212 TTTTTATTTTTATTTTT
1 TTTTCATTTTTCTTTTT
25200229 GAGAAAACCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCATTTTTCTTTTTCA
Found at i:25200278 original size:57 final size:58
Alignment explanation
Indices: 25200210--25200332 Score: 176
Period size: 57 Copynumber: 2.1 Consensus size: 58
25200200 TTTTCATTTT
* * ** *
25200210 CATTTTTATTTTTATTTTTGAGAAAACCACATTCATTTTCAAATGATT-CCATTTCTC
1 CATTTTCATTTTTATTTTGGAGAAAACCACAACCATTTCCAAATGATTCCCATTTCTC
* *
25200267 CATTTTCATTTTTATTTTGGAGAAAACCATAACCATTTCCAAATGTTTCCCATTTCTC
1 CATTTTCATTTTTATTTTGGAGAAAACCACAACCATTTCCAAATGATTCCCATTTCTC
25200325 CATTTTCA
1 CATTTTCA
25200333 CCATTTCTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 41 0.71
58 17 0.29
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.46
Consensus pattern (58 bp):
CATTTTCATTTTTATTTTGGAGAAAACCACAACCATTTCCAAATGATTCCCATTTCTC
Found at i:25208875 original size:19 final size:19
Alignment explanation
Indices: 25208851--25208921 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
25208841 TAATTTTTTC
*
25208851 CATAAAAATTATTAAAAAT
1 CATAAAAATTATAAAAAAT
* *
25208870 CATAAAAA-AAGGAAAAAAAT
1 CATAAAAATTA--TAAAAAAT
25208890 GCATAAAAATTATCAAAAAAT
1 -CATAAAAATTAT-AAAAAAT
*
25208911 -ATAAGAATTAT
1 CATAAAAATTAT
25208922 TAAATATTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
18 1 0.02
19 18 0.44
20 6 0.15
21 15 0.37
22 1 0.02
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (19 bp):
CATAAAAATTATAAAAAAT
Found at i:25208907 original size:10 final size:9
Alignment explanation
Indices: 25208892--25209018 Score: 53
Period size: 10 Copynumber: 13.7 Consensus size: 9
25208882 AAAAAAATGC
25208892 ATAAAAATT
1 ATAAAAATT
*
25208901 ATCAAAAAAT
1 AT-AAAAATT
*
25208911 ATAAGAATT
1 ATAAAAATT
*
25208920 AT-TAAA-T
1 ATAAAAATT
*
25208927 ATTAAAATAT
1 ATAAAAAT-T
* *
25208937 ATGAAAACTG
1 AT-AAAAATT
*
25208947 ATATAAACTT
1 ATA-AAAATT
25208957 ATAAATAATT
1 ATAAA-AATT
* *
25208967 -TCAATATT
1 ATAAAAATT
* *
25208975 ATTAGAATT
1 ATAAAAATT
*
25208984 ATCAAAATT
1 ATAAAAATT
*
25208993 CTAATAAATT
1 ATAA-AAATT
25209003 ATAAAAAATT
1 AT-AAAAATT
25209013 ATAAAA
1 ATAAAA
25209019 GTAATAAAAT
Statistics
Matches: 87, Mismatches: 21, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
7 3 0.03
8 8 0.09
9 33 0.38
10 37 0.43
11 6 0.07
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:25209487 original size:19 final size:18
Alignment explanation
Indices: 25209465--25209509 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
25209455 TATTTTTAAG
* *
25209465 AATTTTAATACGTTTTTTT
1 AATTTTAATAAG-TTTATT
25209484 AATTTTAAATAAGTTTATT
1 AATTTT-AATAAGTTTATT
25209503 AATTTTA
1 AATTTTA
25209510 TATTTTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (18 bp):
AATTTTAATAAGTTTATT
Found at i:25209515 original size:26 final size:27
Alignment explanation
Indices: 25209479--25209569 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 27
25209469 TTAATACGTT
25209479 TTTTTA-ATTTTAAATAAGTTTATT-AA
1 TTTTTATATTTTAAATAA-TTTATTAAA
*
25209505 -TTTTATATTTT-CATAATTTATTAAAA
1 TTTTTATATTTTAAATAATTTATT-AAA
* *
25209531 TTTTTATATTTTATAAT-ATTTA-CAAGT
1 TTTTTATATTTTA-AATAATTTATTAA-A
25209558 TTTTTATATTTT
1 TTTTTATATTTT
25209570 TTTATAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
24 6 0.11
25 9 0.17
26 9 0.17
27 23 0.43
28 5 0.09
29 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTTTATATTTTAAATAATTTATTAAA
Found at i:25209541 original size:27 final size:27
Alignment explanation
Indices: 25209505--25209569 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
25209495 AGTTTATTAA
*
25209505 TTTTATATTTTCATAATTTATTA-AA-AT
1 TTTTATATTTT-ATAATAT-TTACAAGAT
*
25209532 TTTTATATTTTATAATATTTACAAGTT
1 TTTTATATTTTATAATATTTACAAGAT
25209559 TTTTATATTTT
1 TTTTATATTTT
25209570 TTTATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 3 0.09
26 8 0.24
27 23 0.68
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTATATTTTATAATATTTACAAGAT
Found at i:25209580 original size:9 final size:9
Alignment explanation
Indices: 25209446--25209691 Score: 66
Period size: 9 Copynumber: 27.0 Consensus size: 9
25209436 ATTTTTTTCC
25209446 AATTTTTAT
1 AATTTTTAT
* *
25209455 TATTTTTAAG
1 AATTTTT-AT
*
25209465 AATTTTAAT
1 AATTTTTAT
* *
25209474 ACGTTTTTTT
1 A-ATTTTTAT
*
25209484 AATTTTAAAT
1 AATTTT-TAT
*
25209494 AA-GTTTATT
1 AATTTTTA-T
25209503 AA-TTTTAT
1 AATTTTTAT
*
25209511 -ATTTTCAT
1 AATTTTTAT
*
25209519 AATTTATTAA
1 AATTT-TTAT
25209529 AATTTTTAT
1 AATTTTTAT
25209538 -A-TTTTAT
1 AATTTTTAT
* *
25209545 AATATTTAC
1 AATTTTTAT
25209554 AAGTTTTTTAT
1 AA--TTTTTAT
*
25209565 ATTTTTTTAT
1 A-ATTTTTAT
*
25209575 AATTTTAAT
1 AATTTTTAT
*
25209584 AAGTTTATATT
1 AA-TTTTTA-T
* *
25209595 AATTCTAAT
1 AATTTTTAT
25209604 -ATTTTTA-
1 AATTTTTAT
*
25209611 AAGTTTT-T
1 AATTTTTAT
*
25209619 AATGTTTA-
1 AATTTTTAT
*
25209627 ATATATTTAT
1 A-ATTTTTAT
*
25209637 --TTTTAATT
1 AATTTTTA-T
**
25209645 CTTTTTTAT
1 AATTTTTAT
25209654 AATTTATTAT
1 AATTT-TTAT
25209664 AATTTTTA-
1 AATTTTTAT
25209672 ATATTTTTAAT
1 A-ATTTTT-AT
*
25209683 CATTTTTAT
1 AATTTTTAT
25209692 GACAAAAAAT
Statistics
Matches: 169, Mismatches: 42, Indels: 52
0.64 0.16 0.20
Matches are distributed among these distances:
7 11 0.07
8 27 0.16
9 64 0.38
10 58 0.34
11 9 0.05
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
AATTTTTAT
Found at i:25209610 original size:20 final size:19
Alignment explanation
Indices: 25209563--25209610 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
25209553 CAAGTTTTTT
* *
25209563 ATATTTTTTTATAATTTTA
1 ATATTTTTATATAATTCTA
**
25209582 ATAAGTTTATATTAATTCTA
1 ATATTTTTATA-TAATTCTA
25209602 ATATTTTTA
1 ATATTTTTA
25209611 AAGTTTTTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
ATATTTTTATATAATTCTA
Done.