Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 45 of 145
Found at i:16003339 original size:50 final size:49
Alignment explanation
Indices: 16003276--16003720 Score: 205
Period size: 50 Copynumber: 8.9 Consensus size: 49
16003266 TGCAATTTCA
* *
16003276 GGAAGTAAGATTCACCGTCGTGGCTTCAATCTATTTACTTGCAATGTCGG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCT-TTTACTTGCAATGTCGG
* * * * * * * *
16003326 GGAAATGAGATTCACTGTCGTAGCTTCAATCTGTTCCGCTGCATTGCCTG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTTAC-TTGCAATGTCGG
* * * * * * *
16003376 GGAAGTAAGTTTCACCATTGTGGCTTCAATCTTTTGAGTTGCGATGTCGG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTT-ACTTGCAATGTCGG
* * * * * * *
16003426 GGAAGCGAGATTCACCGTCATAGCTTCAATCTGTTCCGCTGC-ATCGCCTG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTTAC-TTGCAAT-GTCGG
* * * * * * **
16003476 GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTTAG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATC-TTTTACTTGCAATGTCGG
* * * * * * * *
16003526 GGAAGTAAGATCCACTGTTGTAGCTTCAATCTGTTCCATTGCAACG-CTAG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTTAC-TTGCAATGTC-GG
* * * * * * * *
16003576 GAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATC-TTTTACTTGCAATGTCGG
* * * * * * *
16003626 GGAAGTGAGATCCGCTGTTGTAGCTTCAATCTGTTCCAC-TGCAACG-CTAG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCT-TT-TACTTGCAATGTC-GG
* * * * * *
16003676 GAAAGTAAGATCCACTGTTGTAGCTTCAATCTTTTAATTGCAATG
1 GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTTACTTGCAATG
16003721 CTAGGGAAGT
Statistics
Matches: 306, Mismatches: 75, Indels: 29
0.75 0.18 0.07
Matches are distributed among these distances:
48 1 0.00
49 18 0.06
50 277 0.91
51 10 0.03
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (49 bp):
GGAAGTGAGATTCACCGTCGTAGCTTCAATCTTTTACTTGCAATGTCGG
Found at i:16003450 original size:100 final size:99
Alignment explanation
Indices: 16003276--16003818 Score: 511
Period size: 100 Copynumber: 5.4 Consensus size: 99
16003266 TGCAATTTCA
* * *
16003276 GGAAGTAAGATTCACCGTCGTGGCTTCAATCTATTTACTTGCAATGTCGGGGAAATGAGATTCAC
1 GGAAGTAAGATTCACCGTTGTGGCTTCAATCT-TTTAATTGCAATGTCGGGGAAGTGAGATTCAC
*
16003341 TGTCGTAGCTTCAATCTGTTCCGCTGCATTGCCTG
65 TGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTG
* * * * *
16003376 GGAAGTAAGTTTCACCATTGTGGCTTCAATCTTTTGAGTTGCGATGTCGGGGAAGCGAGATTCAC
1 GGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTT-AATTGCAATGTCGGGGAAGTGAGATTCAC
* *
16003441 CGTCATAGCTTCAATCTGTTCCGCTGCATCGCCTG
65 TGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTG
* * * * ** * *
16003476 GGAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTTAGGGAAGTAAGATCCAC
1 GGAAGTAAGATTCACCGTTGTGGCTTCAATC-TTTTAATTGCAATGTCGGGGAAGTGAGATTCAC
* ** *
16003541 TGTTGTAGCTTCAATCTGTTCCATTGCAACG-CTAG
65 TGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-G
* * * * * * * *
16003576 GAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCAATGTCAGGGAAGTGAGATCCGC
1 GGAAGTAAGATTCACCGTTGTGGCTTCAATC-TTTTAATTGCAATGTCGGGGAAGTGAGATTCAC
* * *
16003641 TGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAG
65 TGTCGTAGCTTCAATCTGTTCCGCTGCATCGCCT-G
* * * * * * * *
16003676 GAAAGTAAGATCCACTGTTGTAGCTTCAATCTTTTAATTGCAATG-CTAGGGAAGTAAGATCCGC
1 GGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAATTGCAATGTC-GGGGAAGTGAGATTCAC
* * *
16003740 TATTGTAGCTTCAATCTGTTCCACTGCAAT-G-CTAG
65 TGTCGTAGCTTCAATCTGTTCCGCTGC-ATCGCCT-G
* * * * *
16003775 GAAAGTAAGATCCGCTGTTGTAGCTTCAATCATTTTAATTGCAA
1 GGAAGTAAGATTCACCGTTGTGGCTTCAATC-TTTTAATTGCAA
16003819 ACTATGGTTT
Statistics
Matches: 398, Mismatches: 39, Indels: 12
0.89 0.09 0.03
Matches are distributed among these distances:
98 1 0.00
99 96 0.24
100 297 0.75
101 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (99 bp):
GGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAGTGAGATTCACT
GTCGTAGCTTCAATCTGTTCCGCTGCATCGCCTG
Found at i:16003786 original size:50 final size:50
Alignment explanation
Indices: 16003446--16003805 Score: 467
Period size: 50 Copynumber: 7.2 Consensus size: 50
16003436 TTCACCGTCA
**
16003446 TAGCTTCAATCTGTTCCGCTGC-ATCGCCT-GGGAAGTAAGATCCGCTGTTG
1 TAGCTTCAATCTGTTCCATTGCAAT-G-CTAGGGAAGTAAGATCCGCTGTTG
* ** * *
16003496 TAGCTTCAATCTTTTTAATTGCAATGTTAGGGAAGTAAGATCCACTGTTG
1 TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
* *
16003546 TAGCTTCAATCTGTTCCATTGCAACGCTAGGAAAGTAAGATCCGCTGTTG
1 TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
* ** *
16003596 TAGCTTCAATCTTTTTAATTGCAATG-TCAGGGAAGTGAGATCCGCTGTTG
1 TAGCTTCAATCTGTTCCATTGCAATGCT-AGGGAAGTAAGATCCGCTGTTG
* * * *
16003646 TAGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCACTGTTG
1 TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
** *
16003696 TAGCTTCAATCT-TTTAATTGCAATGCTAGGGAAGTAAGATCCGCTATTG
1 TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
* *
16003745 TAGCTTCAATCTGTTCCACTGCAATGCTAGGAAAGTAAGATCCGCTGTTG
1 TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
16003795 TAGCTTCAATC
1 TAGCTTCAATC
16003806 ATTTTAATTG
Statistics
Matches: 265, Mismatches: 40, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
49 44 0.17
50 218 0.82
51 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.33
Consensus pattern (50 bp):
TAGCTTCAATCTGTTCCATTGCAATGCTAGGGAAGTAAGATCCGCTGTTG
Found at i:16004076 original size:44 final size:45
Alignment explanation
Indices: 16004026--16004352 Score: 191
Period size: 44 Copynumber: 7.4 Consensus size: 45
16004016 CAATGCAGGA
16004026 AGGCAAGATTTGTTGTCTTCAACCAGCTCCACT-ACAACCGAGAG
1 AGGCAAGATTTGTTGTCTTCAACCAGCTCCACTCACAACCGAGAG
* * * * * *** *
16004070 AGGCAAGGTTTG-TGTCTTCGACCTGCTTCGCTGTTAA-TGCAG-G
1 AGGCAAGATTTGTTGTCTTCAACCAGCTCCACTCACAACCG-AGAG
*
16004113 AAGGCAAGATCTGTTGTCTTCAACCAGCTCCA-TCACAACCGAGAG
1 -AGGCAAGATTTGTTGTCTTCAACCAGCTCCACTCACAACCGAGAG
* * * * * ** *
16004158 AGGCAAGGTTTG-TGTCTTCGACCTGCTTCGCTGTCAA-TGCAG-G
1 AGGCAAGATTTGTTGTCTTCAACCAGCTCCACTCACAACCG-AGAG
* *
16004201 AAGGCAAGATCTGTTGTCTTCAACCAACTCCA-TCACAACCGAGAG
1 -AGGCAAGATTTGTTGTCTTCAACCAGCTCCACTCACAACCGAGAG
* * * * * ** *
16004246 AGGCAAGGTTT-CTGTCTTCGATCTGCTTCGCTGTCA-ATACAG-GA-
1 AGGCAAGATTTGTTGTCTTCAACCAGC-TC-CACTCACA-ACCGAGAG
* *
16004290 AGGCAAGATCTT-TTGTCTTCAATCAGCTCCA-TCACAACTGAGAG
1 AGGCAAGAT-TTGTTGTCTTCAACCAGCTCCACTCACAACCGAGAG
*
16004334 AGGCAAGGTTTGTT-TCTTC
1 AGGCAAGATTTGTTGTCTTC
16004353 GACCTACTTC
Statistics
Matches: 209, Mismatches: 53, Indels: 43
0.69 0.17 0.14
Matches are distributed among these distances:
42 6 0.03
43 55 0.26
44 93 0.44
45 49 0.23
46 6 0.03
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (45 bp):
AGGCAAGATTTGTTGTCTTCAACCAGCTCCACTCACAACCGAGAG
Found at i:16004390 original size:88 final size:88
Alignment explanation
Indices: 16003928--16004388 Score: 701
Period size: 88 Copynumber: 5.2 Consensus size: 88
16003918 NCTTCCCTAC
* * * * *
16003928 CAATACAGGAAGGCAGGATCTGTTGTTTTCAACCAGCTCCATTACCACCGAGAGAGG-ATAGGTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCA-AGGTT
* * *
16003992 TGTGTATTCGACCTGCCTCGCTAT
65 TGTGTCTTCGACCTGCTTCGCTGT
*
16004016 CAATGCAGGAAGGCAAGATTTGTTGTCTTCAACCAGCTCCA-CTACAACCGAGAGAGGCAAGGTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATC-ACAACCGAGAGAGGCAAGGTT
16004080 TGTGTCTTCGACCTGCTTCGCTGT
65 TGTGTCTTCGACCTGCTTCGCTGT
*
16004104 TAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
16004169 GTGTCTTCGACCTGCTTCGCTGT
66 GTGTCTTCGACCTGCTTCGCTGT
*
16004192 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAACTCCATCACAACCGAGAGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* *
16004257 CTGTCTTCGATCTGCTTCGCTGT
66 GTGTCTTCGACCTGCTTCGCTGT
* * * *
16004280 CAATACAGGAAGGCAAGATCTTTTGTCTTCAATCAGCTCCATCACAACTGAGAGAGGCAAGGTTT
1 CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
* * *
16004345 GTTTCTTCGACCTACTTCACTGT
66 GTGTCTTCGACCTGCTTCGCTGT
*
16004368 TAATGCAGGAAGGCAAGATCT
1 CAATGCAGGAAGGCAAGATCT
16004389 TTAACTTCGT
Statistics
Matches: 343, Mismatches: 27, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
88 341 0.99
89 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (88 bp):
CAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCATCACAACCGAGAGAGGCAAGGTTT
GTGTCTTCGACCTGCTTCGCTGT
Found at i:16005600 original size:15 final size:15
Alignment explanation
Indices: 16005573--16005646 Score: 66
Period size: 15 Copynumber: 5.0 Consensus size: 15
16005563 TTAGCCTCTC
*
16005573 CATTTTT-ACTTTTT
1 CATTTTTCATTTTTT
*
16005587 CATTTTTTCATTTTCT
1 CA-TTTTTCATTTTTT
16005603 CATTTTTCATTTTTT
1 CATTTTTCATTTTTT
*
16005618 CA-TCTT--TTTTTT
1 CATTTTTCATTTTTT
16005630 CATTTTCATCATTTTTT
1 CATTTT--TCATTTTTT
16005647 TTGACTCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
12 8 0.17
13 2 0.04
14 5 0.10
15 20 0.42
16 7 0.15
17 6 0.12
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (15 bp):
CATTTTTCATTTTTT
Found at i:16005635 original size:8 final size:8
Alignment explanation
Indices: 16005582--16005626 Score: 65
Period size: 8 Copynumber: 5.6 Consensus size: 8
16005572 CCATTTTTAC
16005582 TTTTTCAT
1 TTTTTCAT
16005590 TTTTTCAT
1 TTTTTCAT
*
16005598 TTTCTCA-
1 TTTTTCAT
16005605 TTTTTCAT
1 TTTTTCAT
16005613 TTTTTCAT
1 TTTTTCAT
16005621 CTTTTT
1 -TTTTT
16005627 TTTCATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 6 0.18
8 22 0.67
9 5 0.15
ACGTcount: A:0.11, C:0.16, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTTCAT
Found at i:16005635 original size:9 final size:9
Alignment explanation
Indices: 16005582--16005647 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
16005572 CCATTTTTAC
16005582 TTTTTCA-T
1 TTTTTCATT
16005590 TTTTTCA-T
1 TTTTTCATT
*
16005598 TTTCTCA--
1 TTTTTCATT
16005605 TTTTTCATT
1 TTTTTCATT
*
16005614 TTTTCATCTTT
1 TTTT--TCATT
16005625 TTTTTCATT
1 TTTTTCATT
**
16005634 TTCATCATT
1 TTTTTCATT
16005643 TTTTT
1 TTTTT
16005648 TGACTCAAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
7 6 0.13
8 14 0.30
9 18 0.39
11 8 0.17
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTTCATT
Found at i:16005635 original size:18 final size:18
Alignment explanation
Indices: 16005589--16005648 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
16005579 TACTTTTTCA
16005589 TTTTTTCATTTTC-TC--
1 TTTTTTCATTTTCATCTT
*
16005604 ATTTTTCATTTTTTCATCTT
1 TTTTTTCA--TTTTCATCTT
16005624 TTTTTTCATTTTCATCATT
1 TTTTTTCATTTTCATC-TT
16005643 TTTTTT
1 TTTTTT
16005649 GACTCAAAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
15 7 0.19
17 5 0.14
18 10 0.27
19 8 0.22
20 7 0.19
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTTTCATTTTCATCTT
Found at i:16006501 original size:42 final size:41
Alignment explanation
Indices: 16006453--16006562 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 41
16006443 TCTTTTCTTT
*
16006453 TCTTTTCTTTTCATATTTTTATTTTGACTTTGATTGATTTCTC
1 TCTTTTCTTTTCAT-TTTTTATTTTGACTTTAATT-ATTTCTC
** * *
16006496 T-TTTTCTTTTTGTTTTTTTATTTTGATTTTAATTTTTTCTC
1 TCTTTTC-TTTTCATTTTTTATTTTGACTTTAATTATTTCTC
*
16006537 TCTTTTCATTTTCCTTTTTT-TTTTGA
1 TCTTTTC-TTTTCATTTTTTATTTTGA
16006563 ATCGGATCTG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
41 13 0.23
42 38 0.67
43 6 0.11
ACGTcount: A:0.11, C:0.12, G:0.05, T:0.72
Consensus pattern (41 bp):
TCTTTTCTTTTCATTTTTTATTTTGACTTTAATTATTTCTC
Found at i:16007041 original size:1 final size:1
Alignment explanation
Indices: 16007031--16007083 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
16007021 TGACCTCTCC
* * * * * *
16007031 TTTTTCTTTTTTTTTTCTTTTTTTTTTTTTCTTTTTTCTCTTTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16007084 AAATCTGAAC
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.02, C:0.09, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:16007045 original size:11 final size:11
Alignment explanation
Indices: 16007031--16007077 Score: 69
Period size: 11 Copynumber: 4.2 Consensus size: 11
16007021 TGACCTCTCC
16007031 TTTTTCTTTTT
1 TTTTTCTTTTT
16007042 TTTTTCTTTTT
1 TTTTTCTTTTT
16007053 TTTTT-TTTCTT
1 TTTTTCTTT-TT
16007064 TTTTCTCTTTTT
1 TTTT-TCTTTTT
16007076 TT
1 TT
16007078 ATTTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 3 0.09
11 22 0.67
12 5 0.15
13 3 0.09
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:16007056 original size:14 final size:14
Alignment explanation
Indices: 16007037--16007067 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
16007027 CTCCTTTTTC
16007037 TTTTTTTTTTCTTT
1 TTTTTTTTTTCTTT
16007051 TTTTTTTTTTCTTT
1 TTTTTTTTTTCTTT
16007065 TTT
1 TTT
16007068 CTCTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.06, G:0.00, T:0.94
Consensus pattern (14 bp):
TTTTTTTTTTCTTT
Found at i:16007058 original size:23 final size:23
Alignment explanation
Indices: 16007031--16007083 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
16007021 TGACCTCTCC
*
16007031 TTTTTCTTT-TTTTTT-TCTTTT
1 TTTTTTTTTCTTTTTTCTCTTTT
16007052 TTTTTTTTTCTTTTTTCTCTTTT
1 TTTTTTTTTCTTTTTTCTCTTTT
*
16007075 TTTATTTTT
1 TTTTTTTTT
16007084 AAATCTGAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 8 0.29
22 6 0.21
23 14 0.50
ACGTcount: A:0.02, C:0.09, G:0.00, T:0.89
Consensus pattern (23 bp):
TTTTTTTTTCTTTTTTCTCTTTT
Found at i:16007074 original size:14 final size:12
Alignment explanation
Indices: 16007031--16007082 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
16007021 TGACCTCTCC
16007031 TTTTTC-TTTTT
1 TTTTTCTTTTTT
16007042 TTTTTCTTTTTT
1 TTTTTCTTTTTT
*
16007054 TTTTT-TTCTTT
1 TTTTTCTTTTTT
*
16007065 TTTCTCTTTTTT
1 TTTTTCTTTTTT
16007077 TATTTT
1 T-TTTT
16007083 TAAATCTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
11 15 0.44
12 16 0.47
13 3 0.09
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:16010739 original size:3 final size:3
Alignment explanation
Indices: 16010731--16010795 Score: 51
Period size: 3 Copynumber: 21.7 Consensus size: 3
16010721 ATGTAGAAAC
* * ** * *
16010731 AAT AAT AAT AAT AAT AAC ATT AAT AAT AAT AGC AAT AAA AAC AAT GAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
16010780 TA- AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
16010796 AAAAGGGACT
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
2 1 0.02
3 43 0.91
4 3 0.06
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:16012279 original size:25 final size:27
Alignment explanation
Indices: 16012224--16012282 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
16012214 GTTTTAAAAT
* *
16012224 TTATTTTTATACAATAATAATAGTATT
1 TTATTTTTATAAAATAATAATAGTATG
16012251 TTATTTTT-TAAAAT-ATAATTA-TATG
1 TTATTTTTATAAAATAATAA-TAGTATG
16012276 TTATTTT
1 TTATTTT
16012283 ACTACTCCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 14 0.48
26 7 0.24
27 8 0.28
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (27 bp):
TTATTTTTATAAAATAATAATAGTATG
Found at i:16012414 original size:45 final size:47
Alignment explanation
Indices: 16012348--16012438 Score: 150
Period size: 45 Copynumber: 2.0 Consensus size: 47
16012338 CATTTTAACC
*
16012348 TACTAAATAATTAACTAAATTACATAGTATTTATTATAAATTATTTA
1 TACTAAATAATTAACTAAATTACATAGTACTTATTATAAATTATTTA
*
16012395 TACTAAAT-A-TAACTAAATTACATAGTACTTATTATTAATTATTT
1 TACTAAATAATTAACTAAATTACATAGTACTTATTATAAATTATTT
16012439 GTATTTGGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 33 0.79
46 1 0.02
47 8 0.19
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (47 bp):
TACTAAATAATTAACTAAATTACATAGTACTTATTATAAATTATTTA
Found at i:16021833 original size:18 final size:19
Alignment explanation
Indices: 16021795--16021835 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
16021785 CCGGAAAATG
16021795 AATAATTATGTTTATTAAA
1 AATAATTATGTTTATTAAA
*
16021814 AATAATTTAT-TTTATAAAA
1 AATAA-TTATGTTTATTAAA
16021833 AAT
1 AAT
16021836 GCAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (19 bp):
AATAATTATGTTTATTAAA
Found at i:16030707 original size:5 final size:5
Alignment explanation
Indices: 16030687--16030741 Score: 94
Period size: 5 Copynumber: 11.0 Consensus size: 5
16030677 CTTTCTTTCA
16030687 CCTT- CCTTC CCTTTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC
1 CCTTC CCTTC CC-TTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC CCTTC
16030737 CCTTC
1 CCTTC
16030742 TTTTTCTTTA
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.08
5 40 0.82
6 5 0.10
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (5 bp):
CCTTC
Found at i:16031666 original size:157 final size:157
Alignment explanation
Indices: 16031380--16031695 Score: 587
Period size: 157 Copynumber: 2.0 Consensus size: 157
16031370 CAGTTGAGTA
16031380 ATCTAAAGAGAACATCTAACCAAACTAAATGATGCAGAGAATGATACAACAATTACCACATAATT
1 ATCTAAAGAGAACATCTAACCAAACTAAATGATGCAGAGAATGATACAACAATTACCACATAATT
16031445 TGCTTCATTCACAAATATTTCCTCAAAGAACATACTTGCATCTCAATTCAATGCTTTTGAAGGCA
66 TGCTTCATTCACAAATATTTCCTCAAAGAACATACTTGCATCTCAATTCAATGCTTTTGAAGGCA
16031510 AACAAAAGTCCAGAACATTACAATGTC
131 AACAAAAGTCCAGAACATTACAATGTC
* *
16031537 ATCTAAAGAGCACATCTAACCAAACTAAATGATGCAGAGAATGATACGACAATTACCACATAATT
1 ATCTAAAGAGAACATCTAACCAAACTAAATGATGCAGAGAATGATACAACAATTACCACATAATT
*
16031602 TGCTTCATTCACAAATATTTCCTCAAAGAACATGCTTGCATCTCAATTCAATGCTTTTGAAGGCA
66 TGCTTCATTCACAAATATTTCCTCAAAGAACATACTTGCATCTCAATTCAATGCTTTTGAAGGCA
* *
16031667 AACAAAAGTCCAGATCATTGCAATGTC
131 AACAAAAGTCCAGAACATTACAATGTC
16031694 AT
1 AT
16031696 TTCCAAAAAT
Statistics
Matches: 154, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 154 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.27
Consensus pattern (157 bp):
ATCTAAAGAGAACATCTAACCAAACTAAATGATGCAGAGAATGATACAACAATTACCACATAATT
TGCTTCATTCACAAATATTTCCTCAAAGAACATACTTGCATCTCAATTCAATGCTTTTGAAGGCA
AACAAAAGTCCAGAACATTACAATGTC
Found at i:16036124 original size:73 final size:74
Alignment explanation
Indices: 16036004--16036150 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 74
16035994 TGGCTCTGAT
16036004 TTGAACATATTTATATGATAGAGTTTTAAGGAAATTTAGGGTCCGTTTGATTGCTAGTAAAATGT
1 TTGAACATATTTATATGATAGAGTTTTAAGGAAATTTAGGGTCCGTTTGATTGCTAGTAAAATGT
16036069 TTTCCGTAA
66 TTTCCGTAA
16036078 TTGAACATATTT-TATGATAGAGTTTTAAGGAAATTTAGGGTCCGTTTGATTGCTAGTAAAATGT
1 TTGAACATATTTATATGATAGAGTTTTAAGGAAATTTAGGGTCCGTTTGATTGCTAGTAAAATGT
16036142 TTTCCGTAA
66 TTTCCGTAA
16036151 AATAATTTCT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 61 0.84
74 12 0.16
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (74 bp):
TTGAACATATTTATATGATAGAGTTTTAAGGAAATTTAGGGTCCGTTTGATTGCTAGTAAAATGT
TTTCCGTAA
Found at i:16036181 original size:20 final size:20
Alignment explanation
Indices: 16036156--16036195 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16036146 CGTAAAATAA
*
16036156 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
16036176 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
16036196 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:16036185 original size:34 final size:35
Alignment explanation
Indices: 16036141--16036207 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16036131 TAGTAAAATG
*
16036141 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
* *
16036175 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGGAAAATATTTT
16036208 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGGAAAATATTTTAC
Found at i:16036319 original size:20 final size:20
Alignment explanation
Indices: 16036294--16036332 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16036284 GTTTTTACAT
16036294 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
16036314 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
16036333 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:16038317 original size:28 final size:27
Alignment explanation
Indices: 16038270--16038323 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
16038260 TTCTTAGTAA
* *
16038270 TGAAGAAGCTGAAGATGAGAACGGAGT
1 TGAAGAAGCTGAAGAAGAGAAAGGAGT
*
16038297 TGAAGAAGGTTGAAGAAGAGAAAGGAG
1 TGAAGAA-GCTGAAGAAGAGAAAGGAG
16038324 AAAGGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.44, C:0.04, G:0.39, T:0.13
Consensus pattern (27 bp):
TGAAGAAGCTGAAGAAGAGAAAGGAGT
Found at i:16077188 original size:47 final size:47
Alignment explanation
Indices: 16077137--16077245 Score: 173
Period size: 47 Copynumber: 2.3 Consensus size: 47
16077127 AGTAATGCAA
*
16077137 ATAAACTGCCAATAATCAAAATTGTGGACAAGCCACCAAAATCGCAG
1 ATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCGCAG
* *
16077184 ATAAACTGCCAATAATCAAAATCGTGGAGAAGCCACCAAAATCGTAG
1 ATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCGCAG
* *
16077231 AAAAAATGCCAATAA
1 ATAAACTGCCAATAA
16077246 CGTCCACCTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.17
Consensus pattern (47 bp):
ATAAACTGCCAATAATCAAAATCGTGGACAAGCCACCAAAATCGCAG
Found at i:16080652 original size:25 final size:27
Alignment explanation
Indices: 16080624--16080691 Score: 88
Period size: 25 Copynumber: 2.6 Consensus size: 27
16080614 AAAATTGGTA
*
16080624 AGACATTTTCCATTCT-TCTCT-A-AGT
1 AGACATTTTCCATTCTCT-TCTAACAGC
16080649 AGACATTTTCCATTCTCTTCTAAGCAGC
1 AGACATTTTCCATTCTCTTCTAA-CAGC
16080677 AGACATTTTCCATTC
1 AGACATTTTCCATTC
16080692 CTCAAAGCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
25 19 0.50
26 2 0.05
28 17 0.45
ACGTcount: A:0.25, C:0.26, G:0.09, T:0.40
Consensus pattern (27 bp):
AGACATTTTCCATTCTCTTCTAACAGC
Found at i:16086600 original size:32 final size:32
Alignment explanation
Indices: 16086564--16086648 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 32
16086554 AACTTTTCCG
* * *
16086564 GAAAATATTTTCAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTCAGCAAATCTACCAAACACCA
* *
16086596 GAAAATATTTTACA-CAGATTTACCAAACACCA
1 GAAAATATTTT-CAGCAAATCTACCAAACACCA
*
16086628 GAAAATATTTTTCAGTAAATC
1 GAAAATA-TTTTCAGCAAATC
16086649 ATTTTACAGA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
32 33 0.79
33 9 0.21
ACGTcount: A:0.45, C:0.18, G:0.11, T:0.27
Consensus pattern (32 bp):
GAAAATATTTTCAGCAAATCTACCAAACACCA
Found at i:16086666 original size:20 final size:20
Alignment explanation
Indices: 16086641--16086680 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16086631 AATATTTTTC
*
16086641 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
16086661 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
16086681 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:16086687 original size:14 final size:14
Alignment explanation
Indices: 16086664--16086703 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
16086654 ACAGAAAAGT
*
16086664 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
16086678 AAATCATTTTACGG
1 AAAACATTTTACAG
16086692 AAAACATTTTAC
1 AAAACATTTTAC
16086704 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:16116884 original size:35 final size:35
Alignment explanation
Indices: 16116838--16116908 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 35
16116828 ATTTTTGTTT
16116838 ATAAAAAAAAGAAGATGATG-AAAAAAATAAATAA
1 ATAAAAAAAAGAAGATGATGAAAAAAAATAAATAA
*
16116872 ATAAATAAAAAGATGATGATGAAAAAAAATAAATAA
1 ATAAA-AAAAAGAAGATGATGAAAAAAAATAAATAA
16116908 A
1 A
16116909 AAGCTGAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
34 5 0.15
35 14 0.41
36 15 0.44
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (35 bp):
ATAAAAAAAAGAAGATGATGAAAAAAAATAAATAA
Found at i:16117909 original size:44 final size:43
Alignment explanation
Indices: 16117770--16117927 Score: 138
Period size: 44 Copynumber: 3.6 Consensus size: 43
16117760 CTCGAATCAA
* * * ***
16117770 CTCCACTATAACTTCAGGGAGATAGGATTAGTAGCTTCAGTATG
1 CTCCACTACAACTTCAGGGAGATAAGATTA-TTGCTTCAACCTG
* * *
16117814 CTCCACTACAAGTTTAGGGAGATAAGAATTGTAT-CTTCAACCTG
1 CTCCACTACAACTTCAGGGAGATAAG-ATTAT-TGCTTCAACCTG
** *
16117858 CTCCACTGTAACTTCAGGGAGATAAGACTTATTGTTTCAACCTG
1 CTCCACTACAACTTCAGGGAGATAAGA-TTATTGCTTCAACCTG
* * *
16117902 CTCCACTGCGACTGCAGGGAGATAAG
1 CTCCACTACAACTTCAGGGAGATAAG
16117928 GTTCGATTTG
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
43 2 0.02
44 87 0.95
45 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.28
Consensus pattern (43 bp):
CTCCACTACAACTTCAGGGAGATAAGATTATTGCTTCAACCTG
Found at i:16118105 original size:41 final size:42
Alignment explanation
Indices: 16118060--16118171 Score: 127
Period size: 45 Copynumber: 2.6 Consensus size: 42
16118050 GATCCGCTCC
* * *
16118060 ACTGCAACTTTAGGGAGATAAGACTTATC-GTGATCTACTCT
1 ACTGCAACTTCAGAGAGATAAGACTTATCTGTAATCTACTCT
* *
16118101 ACTGCAACTTCAGAGAGATAAGATCTGTTATCTTTAATCTATTCT
1 ACTGCAACTTCAGAGAGATAAGA-C--TTATCTGTAATCTACTCT
* *
16118146 ACTGCAACCTCAGTGAGATAAGACTT
1 ACTGCAACTTCAGAGAGATAAGACTT
16118172 GTAGATTCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
41 21 0.35
42 3 0.05
44 6 0.10
45 30 0.50
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (42 bp):
ACTGCAACTTCAGAGAGATAAGACTTATCTGTAATCTACTCT
Found at i:16118268 original size:44 final size:45
Alignment explanation
Indices: 16118200--16118456 Score: 147
Period size: 44 Copynumber: 5.7 Consensus size: 45
16118190 GATGCGATCT
* * * *
16118200 GCTCTACTGCAAC-TTCGGAGAGATAAGATCTATCATTTTAATCC
1 GCTCCACTGCAACTTTAGGAGAGATAAGATCTATAATTTCAATCC
* * * *
16118244 GCTTCACTGCAACTTTAGGA-AGATAGGA-CTAGTAACTTCAATCT
1 GCTCCACTGCAACTTTAGGAGAGATAAGATCTA-TAATTTCAATCC
*
16118288 GCTCCACTGCAACTTTA-GAGAGATAAGATCTATAATTTATAGCCTTAATCT
1 GCTCCACTGCAACTTTAGGAGAGATAAGATCTATAA-TT-T---C--AATCC
* * * * * * *
16118339 GTTCCACTGCAACTTCAGGA-AAATAAGATTTGCT-ATCTTCAGTCT
1 GCTCCACTGCAACTTTAGGAGAGATAAGATCT-ATAAT-TTCAATCC
* * *
16118384 GCTCTACTGTAACTTCAGG-GAGATAAGA-CTCATAATTTCAA-CC
1 GCTCCACTGCAACTTTAGGAGAGATAAGATCT-ATAATTTCAATCC
* *
16118427 TGCCCCACTGCAACTTTAGG-GAGATGAGAT
1 -GCTCCACTGCAACTTTAGGAGAGATAAGAT
16118457 TTGATATGAT
Statistics
Matches: 164, Mismatches: 31, Indels: 35
0.71 0.13 0.15
Matches are distributed among these distances:
43 6 0.04
44 81 0.49
45 38 0.23
46 1 0.01
47 1 0.01
49 1 0.01
50 2 0.01
51 31 0.19
52 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (45 bp):
GCTCCACTGCAACTTTAGGAGAGATAAGATCTATAATTTCAATCC
Found at i:16118492 original size:85 final size:85
Alignment explanation
Indices: 16118381--16118677 Score: 247
Period size: 85 Copynumber: 3.4 Consensus size: 85
16118371 CTATCTTCAG
** * *
16118381 TCTGCTCTACTGTAACTTCAGGGAGATAAGACTCATAATTTCAACCTGCCCCACTGCAACTTTAG
1 TCTGCTCTACTACAACTTCAGAGAGATAAGACTCATAATTTCAACCTGCCCCACTGCAACTTCAG
16118446 GGAGATGAGATTTGATATGA
66 GGAGATGAGATTTGATATGA
* * * * * ***
16118466 TCTACTCTACTATAACTTCAGAGAGATAGGA-TCGGTATTTTATAGCTTCAATCTGTTTCACTGC
1 TCTGCTCTACTACAACTTCAGAGAGATAAGACTC---A---TA-A-TTTCAACCTGCCCCACTGC
* * * * *
16118530 AACTTCAGGGAAATAAGATTCGCTATCTTTA
58 AACTTCAGGGAGATGAGATTTG--AT-ATGA
* * * * * *
16118561 GTCTGCTCCACTGCAACTTCAGTGAGATAAGACTCGTAATTTCAACCTGCCCCATTACAACTTCA
1 -TCTGCTCTACTACAACTTCAGAGAGATAAGACTCATAATTTCAACCTGCCCCACTGCAACTTCA
16118626 GGGAGATGA-AGTTTGATATGA
65 GGGAGATGAGA-TTTGATATGA
*
16118647 TCTGCTCTACTACAACTTCAAAGAGATAAGA
1 TCTGCTCTACTACAACTTCAGAGAGATAAGA
16118678 TCGGTAATTT
Statistics
Matches: 160, Mismatches: 38, Indels: 28
0.71 0.17 0.12
Matches are distributed among these distances:
84 2 0.01
85 54 0.34
86 2 0.01
87 3 0.02
88 1 0.01
89 29 0.18
90 3 0.02
91 3 0.02
92 32 0.20
94 2 0.01
95 2 0.01
96 25 0.16
97 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (85 bp):
TCTGCTCTACTACAACTTCAGAGAGATAAGACTCATAATTTCAACCTGCCCCACTGCAACTTCAG
GGAGATGAGATTTGATATGA
Found at i:16118534 original size:181 final size:180
Alignment explanation
Indices: 16118297--16118775 Score: 674
Period size: 181 Copynumber: 2.6 Consensus size: 180
16118287 TGCTCCACTG
* ** *
16118297 CAACTTTAGAGAGATAAGATCTATAATTTATAGCCTT-AATCTGTTCCACTGCAACTTCAGGAAA
1 CAACTTCAGAGAGATAAGATCGGTAATTTATAG-CTTCAATCTGTTCCACTGCAACTTCAGGGAA
*
16118361 ATAAGATTTGCTATCTTCAGTCTGCTCTACTGTAACTTCAGGGAGATAAGACTCATAATTTCAAC
65 ATAAGATTTGCTATCTT-AGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTCATAATTTCAAC
* *
16118426 CTGCCCCACTGCAACTTTAGGGAGATG-AGATTTGATATGATCTACTCTACTA
129 CTGCCCCACTACAACTTCAGGGAGATGAAG-TTTGATATGATCTACTCTACTA
* * * *
16118478 TAACTTCAGAGAGATAGGATCGGTATTTTATAGCTTCAATCTGTTTCACTGCAACTTCAGGGAAA
1 CAACTTCAGAGAGATAAGATCGGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAA
* * * *
16118543 TAAGATTCGCTATCTTTAGTCTGCTCCACTGCAACTTCAGTGAGATAAGACTCGTAATTTCAACC
66 TAAGATTTGCTATC-TTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTCATAATTTCAACC
* *
16118608 TGCCCCATTACAACTTCAGGGAGATGAAGTTTGATATGATCTGCTCTACTA
130 TGCCCCACTACAACTTCAGGGAGATGAAGTTTGATATGATCTACTCTACTA
* *
16118659 CAACTTCAAAGAGATAAGATCGGTAATTTATATCTTCAATCTGTTCCACTGCAACTTCAGGGAAA
1 CAACTTCAGAGAGATAAGATCGGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAA
* * *
16118724 TAAGGTTTGATAAGATCTATAGTCTACTCCACTGTAACTTCAGGGAGATAAG
66 TAAGATTTGCT---ATCT-TAGTCTGCTCCACTGTAACTTCAGGGAGATAAG
16118776 GCTGGTGCTT
Statistics
Matches: 262, Mismatches: 29, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
180 3 0.01
181 221 0.84
182 4 0.02
183 1 0.00
184 33 0.13
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (180 bp):
CAACTTCAGAGAGATAAGATCGGTAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAA
TAAGATTTGCTATCTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTCATAATTTCAACCT
GCCCCACTACAACTTCAGGGAGATGAAGTTTGATATGATCTACTCTACTA
Found at i:16120502 original size:52 final size:52
Alignment explanation
Indices: 16120387--16120502 Score: 118
Period size: 52 Copynumber: 2.3 Consensus size: 52
16120377 TTCTTTTTAT
16120387 TCTTT-TTCCTTTTTTTTGACTCAAAGCGCCATTTGCAGGTTTTCACCTTAG
1 TCTTTCTTCCTTTTTTTTGACTCAAAGCGCCATTTGCAGGTTTTCACCTTAG
* ** *
16120438 TCTTTCTT--TTTTTTTTAGAACTCAATGCGTCC-TTTGCTTGTTTTTACCTT-G
1 TCTTTCTTCCTTTTTTTT-G-ACTCAAAGCG-CCATTTGCAGGTTTTCACCTTAG
*
16120489 -GTTTCTTCCTTTTT
1 TCTTTCTTCCTTTTT
16120503 AGGTAAAATC
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
50 14 0.26
51 7 0.13
52 31 0.57
53 2 0.04
ACGTcount: A:0.12, C:0.22, G:0.12, T:0.54
Consensus pattern (52 bp):
TCTTTCTTCCTTTTTTTTGACTCAAAGCGCCATTTGCAGGTTTTCACCTTAG
Found at i:16136212 original size:9 final size:9
Alignment explanation
Indices: 16136191--16136253 Score: 65
Period size: 9 Copynumber: 6.9 Consensus size: 9
16136181 TTTTGATCCA
16136191 TTTTATAATT
1 TTTTATAA-T
*
16136201 TTTTATGAT
1 TTTTATAAT
16136210 TTTTATAAT
1 TTTTATAAT
*
16136219 ATTTTAAAAT
1 -TTTTATAAT
*
16136229 TTTTAT-TT
1 TTTTATAAT
*
16136237 TTTTACAAT
1 TTTTATAAT
16136246 TTTTATAA
1 TTTTATAA
16136254 AAAAAATCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
8 6 0.14
9 22 0.51
10 15 0.35
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:16136213 original size:19 final size:19
Alignment explanation
Indices: 16136191--16136253 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
16136181 TTTTGATCCA
**
16136191 TTTTATAATTTTTTATGAT
1 TTTTATAATTTTTTAAAAT
*
16136210 TTTTATAATATTTTAAAAT
1 TTTTATAATTTTTTAAAAT
*
16136229 TTTTAT--TTTTTTACAAT
1 TTTTATAATTTTTTAAAAT
16136246 TTTTATAA
1 TTTTATAA
16136254 AAAAAATCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 15 0.41
19 22 0.59
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTATAATTTTTTAAAAT
Found at i:16136678 original size:27 final size:26
Alignment explanation
Indices: 16136647--16136711 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 26
16136637 GGGAATTAGA
*
16136647 GAAAAGGAAAAGAGAAAGGAAGGAATG
1 GAAAAGGAAAAGA-AAAGGAAGGAAAG
* *
16136674 GAAAAAGAGAAAGAAAGGGAAGGAAAG
1 GAAAAGGA-AAAGAAAAGGAAGGAAAG
*
16136701 AAAAAGGAAAA
1 GAAAAGGAAAA
16136712 ATAATAAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
26 3 0.09
27 24 0.75
28 5 0.16
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.02
Consensus pattern (26 bp):
GAAAAGGAAAAGAAAAGGAAGGAAAG
Found at i:16136681 original size:22 final size:22
Alignment explanation
Indices: 16136650--16136699 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
16136640 AATTAGAGAA
*
16136650 AAGG-AAAAGAGAAAGGAA-GG
1 AAGGAAAAAGAGAAAGAAAGGG
16136670 AATGGAAAAAGAGAAAGAAAGGG
1 AA-GGAAAAAGAGAAAGAAAGGG
16136693 AAGGAAA
1 AAGGAAA
16136700 GAAAAAGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 2 0.08
22 18 0.69
23 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (22 bp):
AAGGAAAAAGAGAAAGAAAGGG
Found at i:16137663 original size:21 final size:21
Alignment explanation
Indices: 16137639--16137703 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
16137629 TAATATATTT
16137639 TAATTTTTGATAAAAATAAAA
1 TAATTTTTGATAAAAATAAAA
* **
16137660 TAATTTTAG-T-TTAATAAAA
1 TAATTTTTGATAAAAATAAAA
*
16137679 TTAATTTTTAATAAAAATAAAA
1 -TAATTTTTGATAAAAATAAAA
16137701 TAA
1 TAA
16137704 AATAAATTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 7 0.21
20 8 0.24
21 12 0.35
22 7 0.21
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
TAATTTTTGATAAAAATAAAA
Found at i:16145187 original size:42 final size:43
Alignment explanation
Indices: 16145032--16145268 Score: 261
Period size: 43 Copynumber: 5.6 Consensus size: 43
16145022 TATAGACAAT
* * * * *
16145032 GTCGCTATAGAACATGACCTTTAGCGGCGCTTTTATAATAAAC
1 GTCGCTAAAGAACATGACCTTTAGCGACACTTTTATCACAAAC
*
16145075 GTCGCTAAAGAACATGACCTTTAACGACA-TTTTATCAACAAAC
1 GTCGCTAAAGAACATGACCTTTAGCGACACTTTTATC-ACAAAC
16145118 G-CTGCTAAAGAACATGACCTTTAGCGACACTTTTATCACAAAC
1 GTC-GCTAAAGAACATGACCTTTAGCGACACTTTTATCACAAAC
* ** * * *
16145161 GCCGCTAAA-AACATGATATTTAGCGACACTTTTAACCCAAAA
1 GTCGCTAAAGAACATGACCTTTAGCGACACTTTTATCACAAAC
* ***
16145203 GTTGCT-AA-AA-ATGACCTTTAGCGGTGCTTTTATCACAAAC
1 GTCGCTAAAGAACATGACCTTTAGCGACACTTTTATCACAAAC
*
16145243 GTCGCTAAAGAGCATGACCTTTAGCG
1 GTCGCTAAAGAACATGACCTTTAGCG
16145269 GCGTTTATGT
Statistics
Matches: 163, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
40 27 0.17
41 6 0.04
42 40 0.25
43 82 0.50
44 8 0.05
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (43 bp):
GTCGCTAAAGAACATGACCTTTAGCGACACTTTTATCACAAAC
Found at i:16147533 original size:1 final size:1
Alignment explanation
Indices: 16147527--16147564 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
16147517 GCACATATGT
16147527 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16147565 CCCTATCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16150151 original size:22 final size:23
Alignment explanation
Indices: 16150102--16150151 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
16150092 TCTTTCATAT
*
16150102 AAATTTTAAATAAATATTTTTAA
1 AAATTTTAAATAAATATTTTAAA
*
16150125 AAATTTTAAGT-AATA-TTTAAA
1 AAATTTTAAATAAATATTTTAAA
16150146 AGAATT
1 A-AATT
16150152 ATATAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.25
22 8 0.33
23 10 0.42
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
AAATTTTAAATAAATATTTTAAA
Found at i:16150396 original size:21 final size:21
Alignment explanation
Indices: 16150350--16150417 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
16150340 CCATAAATCA
* *
16150350 TAAAACATAAACCCTAAACCCC
1 TAAATCATAAACCCT-AACCCT
*
16150372 TAAATCTTAAACCCTAACCCT
1 TAAATCATAAACCCTAACCCT
* * *
16150393 TAAATCATAATCCATAAACCT
1 TAAATCATAAACCCTAACCCT
16150414 TAAA
1 TAAA
16150418 ATAGTAACTC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 26 0.67
22 13 0.33
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (21 bp):
TAAATCATAAACCCTAACCCT
Found at i:16150921 original size:40 final size:40
Alignment explanation
Indices: 16150866--16150970 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 40
16150856 TTTTTTGTGG
*
16150866 CGTTTTTCAAAAAGCGCCGCTAATGATCGATCTATAGCAA
1 CGTTTTTCAAAAAGCGCCGCTAATGATCAATCTATAGCAA
* * **
16150906 CGTTTTTTAAAAAGCGCCGCTAATGCTCAATCTATAGCGG
1 CGTTTTTCAAAAAGCGCCGCTAATGATCAATCTATAGCAA
* *
16150946 CATTTTTCAAAAAGCGCTGCTAATG
1 CGTTTTTCAAAAAGCGCCGCTAATG
16150971 CCACTAAAGC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (40 bp):
CGTTTTTCAAAAAGCGCCGCTAATGATCAATCTATAGCAA
Found at i:16151114 original size:40 final size:39
Alignment explanation
Indices: 16151018--16151119 Score: 152
Period size: 38 Copynumber: 2.6 Consensus size: 39
16151008 TTTTGTGGCG
* * *
16151018 TTTTTCAAAAAGCGCCGCTAGTACTCGATTTATAGCGGC
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
*
16151057 -TTTTCAAAAAGCACCGCTAATGCTCGATCTATAGCGGC
1 TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
16151095 ATTTTTCAAAAAGCGCCGCTAATGC
1 -TTTTTCAAAAAGCGCCGCTAATGC
16151120 CACTAAAACT
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
38 34 0.61
40 22 0.39
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (39 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
Found at i:16151165 original size:150 final size:146
Alignment explanation
Indices: 16150769--16151204 Score: 562
Period size: 150 Copynumber: 2.9 Consensus size: 146
16150759 CGTTTTTGAT
* **
16150769 AAAGCGCCGCTAAAGCTCGATCTATAGCGGCATTTTTCAAAAAGCATCGCTAATGCCACTAAAGC
1 AAAGCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGC
16150834 TCAAC--ACGGCTTTGTGCTTAACTTTTTTGTGGCGTTTTTCAAAAAGCGCCGCTAATGA-TCGA
66 TCAACAAAC-GCTTTGTGCTTAACTTTTTTGTGGCGTTTTTCAAAAAGCGCCGCTAAT-ACTCGA
* * *
16150896 TCTATAGCAACGTTTTTTAA
129 TCTATAGC--GGCTTTTCAA
* *
16150916 AAAGCGCCGCTAATGCTCAATCTATAGCGGCATTTTTCAAAAAGCGCTGCTAATGCCACTAAAGC
1 AAAGCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGC
*
16150981 TCAACACAACTG-TGTTGTGCTTAACTTTTTTGTGGCGTTTTTCAAAAAGCGCCGCTAGTACTCG
66 TCAACA-AAC-GCT-TTGTGCTTAACTTTTTTGTGGCGTTTTTCAAAAAGCGCCGCTAATACTCG
*
16151045 ATTTATAGCGGCTTTTCAA
128 ATCTATAGCGGCTTTTCAA
* *
16151064 AAAGCACCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAAC
1 AAAGCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGC
* * *
16151129 TCAACATAAAACGACATCATT-TGCTT-A-TTTTTTGTGGCGTTTTTTAAAAAGTGCCGCTAATG
66 TCAAC---AAACG-C-T--TTGTGCTTAACTTTTTTGTGGCGTTTTTCAAAAAGCGCCGCTAATA
16151191 CTCGATCTATAGCG
124 CTCGATCTATAGCG
16151205 TCATTTTTTA
Statistics
Matches: 256, Mismatches: 21, Indels: 21
0.86 0.07 0.07
Matches are distributed among these distances:
147 65 0.25
148 73 0.29
149 3 0.01
150 105 0.41
151 2 0.01
152 6 0.02
153 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (146 bp):
AAAGCGCCGCTAATGCTCGATCTATAGCGGCATTTTTCAAAAAGCGCCGCTAATGCCACTAAAGC
TCAACAAACGCTTTGTGCTTAACTTTTTTGTGGCGTTTTTCAAAAAGCGCCGCTAATACTCGATC
TATAGCGGCTTTTCAA
Found at i:16153556 original size:32 final size:32
Alignment explanation
Indices: 16153515--16153583 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
16153505 CAATAGTATA
*
16153515 ATTT-AACATATAATTTTCGTTTGAAATGATG
1 ATTTAAACATATAATTTTCATTTGAAATGATG
16153546 ATTTAAACATATAATTTTCATTTGAAATGATG
1 ATTTAAACATATAATTTTCATTTGAAATGATG
16153578 ATTTAA
1 ATTTAA
16153584 CATGCCATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (32 bp):
ATTTAAACATATAATTTTCATTTGAAATGATG
Found at i:16154701 original size:19 final size:20
Alignment explanation
Indices: 16154672--16154727 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
16154662 ACTGATTCCA
*
16154672 TTTAGTTTTATTTTTTATT-T
1 TTTACTTTTATTTTTT-TTAT
16154692 TTTA-TTTTATTTATTTTTAT
1 TTTACTTTTATTT-TTTTTAT
16154712 TTATACTTTTATTTTT
1 TT-TACTTTTATTTTT
16154728 ATTGTCAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
19 10 0.31
20 10 0.31
21 4 0.12
22 8 0.25
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTACTTTTATTTTTTTTAT
Found at i:16154721 original size:22 final size:23
Alignment explanation
Indices: 16154678--16154725 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
16154668 TCCATTTAGT
*
16154678 TTTATTTTTTATTTTTTATTTTA
1 TTTATTTTTTATTTTATATTTTA
16154701 TTTA-TTTTTA-TTTATACTTTTA
1 TTTATTTTTTATTTTATA-TTTTA
16154723 TTT
1 TTT
16154726 TTATTGTCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 5 0.22
22 14 0.61
23 4 0.17
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTATTTTTTATTTTATATTTTA
Found at i:16154748 original size:6 final size:6
Alignment explanation
Indices: 16154672--16154730 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
16154662 ACTGATTCCA
* * *
16154672 TTTAGT TTTATTT TTTATT TTT-TAT TTTA-- TTTATT TTTATT TATACT
1 TTTATT TTTA-TT TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT
16154719 TTTATT TTTATT
1 TTTATT TTTATT
16154731 GTCAGATGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
4 4 0.09
5 1 0.02
6 33 0.77
7 5 0.12
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:16155708 original size:9 final size:9
Alignment explanation
Indices: 16155694--16155719 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
16155684 TTATTCTCAA
16155694 AAAAAAAAG
1 AAAAAAAAG
16155703 AAAAAAAAG
1 AAAAAAAAG
16155712 AAAAAAAA
1 AAAAAAAA
16155720 AGAGATTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:16155708 original size:10 final size:10
Alignment explanation
Indices: 16155693--16155722 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
16155683 TTTATTCTCA
16155693 AAAAAAAAAG
1 AAAAAAAAAG
16155703 -AAAAAAAAG
1 AAAAAAAAAG
16155712 AAAAAAAAAG
1 AAAAAAAAAG
16155722 A
1 A
16155723 GATTGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:16159584 original size:14 final size:14
Alignment explanation
Indices: 16159561--16159592 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
16159551 TGTCGTTTTC
*
16159561 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
16159575 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
16159589 TTAG
1 TTAG
16159593 AACAATCATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:16164772 original size:27 final size:27
Alignment explanation
Indices: 16164742--16164795 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
16164732 CAATTATGTA
16164742 TACTTATTTCGTGCTTTAATATTTTAG
1 TACTTATTTCGTGCTTTAATATTTTAG
16164769 TACTTATTTCGTGCTTTAATATTTTAG
1 TACTTATTTCGTGCTTTAATATTTTAG
16164796 GGATATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (27 bp):
TACTTATTTCGTGCTTTAATATTTTAG
Found at i:16167893 original size:14 final size:14
Alignment explanation
Indices: 16167874--16167900 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16167864 TCAAACAAAA
16167874 TAACAATTAAATTG
1 TAACAATTAAATTG
16167888 TAACAATTAAATT
1 TAACAATTAAATT
16167901 AAAAACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (14 bp):
TAACAATTAAATTG
Found at i:16167918 original size:20 final size:20
Alignment explanation
Indices: 16167893--16167933 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
16167883 AATTGTAACA
*
16167893 ATTAAATTAAAAACAAAAAT
1 ATTAAAATAAAAACAAAAAT
*
16167913 ATTAAAATAAAAATAAAAAT
1 ATTAAAATAAAAACAAAAAT
16167933 A
1 A
16167934 AAAATGGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (20 bp):
ATTAAAATAAAAACAAAAAT
Found at i:16167925 original size:6 final size:6
Alignment explanation
Indices: 16167900--16167938 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
16167890 ACAATTAAAT
*
16167900 TAAAAA CAAAAA TATTAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TA--AAAA TAAAAA TAAAAA TAAAAA T
16167939 GGCTAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 23 0.79
8 6 0.21
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (6 bp):
TAAAAA
Found at i:16177399 original size:1 final size:1
Alignment explanation
Indices: 16177393--16177430 Score: 76
Period size: 1 Copynumber: 38.0 Consensus size: 1
16177383 TTACAACTAC
16177393 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16177431 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:16179081 original size:3 final size:3
Alignment explanation
Indices: 16179073--16179168 Score: 95
Period size: 3 Copynumber: 32.0 Consensus size: 3
16179063 GTGTATTGCA
** *
16179073 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TGT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * *
16179121 AGAC ACT -TT TAT AAC AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16179166 AAT
1 AAT
16179169 TGTAGTAGAC
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
2 1 0.01
3 76 0.97
4 1 0.01
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16179167 original size:54 final size:54
Alignment explanation
Indices: 16179085--16179192 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
16179075 TAATAATAAT
16179085 AATAATAATAATAATAATAATAATAATAATTGTAGTAGACACTTTTATAACAAA
1 AATAATAATAATAATAATAATAATAATAATTGTAGTAGACACTTTTATAACAAA
16179139 AATAATAATAATAATAATAATAATAATAATTGTAGTAGACACTTTTATAACAAA
1 AATAATAATAATAATAATAATAATAATAATTGTAGTAGACACTTTTATAACAAA
16179193 GCAATGTAAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (54 bp):
AATAATAATAATAATAATAATAATAATAATTGTAGTAGACACTTTTATAACAAA
Found at i:16183560 original size:13 final size:13
Alignment explanation
Indices: 16183542--16183620 Score: 61
Period size: 13 Copynumber: 6.0 Consensus size: 13
16183532 CATATATATC
16183542 CATATAAACATTT
1 CATATAAACATTT
* * *
16183555 CATATACATAATT
1 CATATAAACATTT
16183568 CATAT-AACTATTT
1 CATATAAAC-ATTT
* *
16183581 CCATATAACCAATT
1 -CATATAAACATTT
*
16183595 CATATAATCATTT
1 CATATAAACATTT
* *
16183608 TATATAATCATTT
1 CATATAAACATTT
16183621 TCCATATAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
12 1 0.02
13 41 0.79
14 8 0.15
15 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (13 bp):
CATATAAACATTT
Found at i:16183607 original size:27 final size:25
Alignment explanation
Indices: 16183542--16183613 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 25
16183532 CATATATATC
*
16183542 CATATAAACATTTCATATACATAATT
1 CATAT-AACATTTCATATACACAATT
16183568 CATATAACTATTTCCATATA-ACCAATT
1 CATATAAC-ATTT-CATATACA-CAATT
*
16183595 CATATAATCATTTTATATA
1 CATATAA-CATTTCATATA
16183614 ATCATTTTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 3 0.08
26 15 0.38
27 21 0.52
28 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (25 bp):
CATATAACATTTCATATACACAATT
Found at i:16183621 original size:13 final size:13
Alignment explanation
Indices: 16183596--16183662 Score: 73
Period size: 13 Copynumber: 5.0 Consensus size: 13
16183586 TAACCAATTC
16183596 ATATAATCATTTT
1 ATATAATCATTTT
16183609 ATATAATCATTTT
1 ATATAATCATTTT
* *
16183622 CCATATAATTGA-TTC
1 --ATATAA-TCATTTT
16183637 ATATAATCATTTT
1 ATATAATCATTTT
*
16183650 ATATATTCATTTT
1 ATATAATCATTTT
16183663 CCACTCGATT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
12 2 0.04
13 33 0.73
15 8 0.18
16 2 0.04
ACGTcount: A:0.36, C:0.10, G:0.01, T:0.52
Consensus pattern (13 bp):
ATATAATCATTTT
Found at i:16183628 original size:28 final size:27
Alignment explanation
Indices: 16183593--16183662 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
16183583 ATATAACCAA
16183593 TTCATATAATCATTTTATATAATCATT
1 TTCATATAATCATTTTATATAATCATT
* *
16183620 TTCCATATAATTGA-TTCATATAATCATT
1 TT-CATATAA-TCATTTTATATAATCATT
*
16183648 TT-ATATATTCATTTT
1 TTCATATAATCATTTT
16183663 CCACTCGATT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
25 2 0.06
26 7 0.20
27 2 0.06
28 22 0.63
29 2 0.06
ACGTcount: A:0.34, C:0.11, G:0.01, T:0.53
Consensus pattern (27 bp):
TTCATATAATCATTTTATATAATCATT
Found at i:16183637 original size:41 final size:41
Alignment explanation
Indices: 16183540--16183665 Score: 141
Period size: 41 Copynumber: 3.1 Consensus size: 41
16183530 TACATATATA
* * * *
16183540 TCCATATAAACATTTCATATACAT-AATTCATATAA-C-TATT
1 TCCATATAACCAATTCATATA-ATCATTTTATATAATCAT-TT
16183580 TCCATATAACCAATTCATATAATCATTTTATATAATCATTT
1 TCCATATAACCAATTCATATAATCATTTTATATAATCATTT
*** *
16183621 TCCATATAATTGATTCATATAATCATTTTATATATTCATTT
1 TCCATATAACCAATTCATATAATCATTTTATATAATCATTT
16183662 TCCA
1 TCCA
16183666 CTCGATTAAC
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
39 2 0.03
40 28 0.37
41 44 0.59
42 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.01, T:0.44
Consensus pattern (41 bp):
TCCATATAACCAATTCATATAATCATTTTATATAATCATTT
Found at i:16191016 original size:40 final size:39
Alignment explanation
Indices: 16190969--16191092 Score: 122
Period size: 40 Copynumber: 3.1 Consensus size: 39
16190959 GCGTTTGGAT
16190969 AAAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTA
1 AAAAAACGCCGCTAAAAAT-AAGCATTAGCGGCGCTTTTA
* * * * * *
16191009 AAAAAACGCCACTAAAGATTGAGTATTAGCGACGCTTTTT
1 AAAAAACGCCGCTAAA-AATAAGCATTAGCGGCGCTTTTA
** * * * *
16191049 GGAAAACACCGCTAAAAATTAGCATTAGCGGCGTTTTTC
1 AAAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTTA
16191088 AAAAA
1 AAAAA
16191093 GTGCCGCAAA
Statistics
Matches: 65, Mismatches: 18, Indels: 3
0.76 0.21 0.03
Matches are distributed among these distances:
39 20 0.31
40 43 0.66
41 2 0.03
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTTTA
Found at i:16191229 original size:40 final size:40
Alignment explanation
Indices: 16191137--16191313 Score: 237
Period size: 40 Copynumber: 4.3 Consensus size: 40
16191127 TTTTTAAATT
* *
16191137 TCAGGACTTTAGTGGCGTTTTTTAAAAAGCGCCGCTAATGC
1 TCAGG-CTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
* * * * *
16191178 GCAGGGTTTTAGTGGCATTTTTTAAAAAGCGCCGCTAATGC
1 TCA-GGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
16191219 TCAGGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
16191259 TCAGGCTTCAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCAGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
*
16191299 TCAGGGTTTTAGCGG
1 TCA-GGCTTTAGCGG
16191314 TGCTTTTTAA
Statistics
Matches: 121, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
40 73 0.60
41 46 0.38
42 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (40 bp):
TCAGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
Found at i:16191310 original size:81 final size:81
Alignment explanation
Indices: 16191137--16191321 Score: 246
Period size: 81 Copynumber: 2.3 Consensus size: 81
16191127 TTTTTAAATT
* * * * * * *
16191137 TCAGGACTTTAGTGGCGTTTTTTAAAAAGCGCCGCTAATGCGCAGGGTTTTAGTGGCATTTTTTA
1 TCAGG-CTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCGCAGGGCTTCAGCGGCATTTTTGA
16191202 AAAAGCGCCGCTAATGC
65 AAAAGCGCCGCTAATGC
* *
16191219 TCAGGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCA-GGCTTCAGCGGCGTTTTTGAA
1 TCAGGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCGCAGGGCTTCAGCGGCATTTTTGAA
16191283 AAAGCGCCGCTAATGC
66 AAAGCGCCGCTAATGC
*
16191299 TCAGGGTTTTAGCGGTGCTTTTT
1 TCA-GGCTTTAGCGGTG-TTTTT
16191322 AAGGATCGGG
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
80 35 0.38
81 46 0.51
82 10 0.11
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (81 bp):
TCAGGCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCGCAGGGCTTCAGCGGCATTTTTGAA
AAAGCGCCGCTAATGC
Found at i:16191422 original size:110 final size:109
Alignment explanation
Indices: 16191225--16191423 Score: 276
Period size: 110 Copynumber: 1.8 Consensus size: 109
16191215 ATGCTCAGGC
* * *
16191225 TTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCTTCAGCGGCGTTTTTGAAAAAGCGC
1 TTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATACTCAGGCTTCAGCGGCGTTTTTGAAAAAGCGC
**
16191290 CGCTAATGCTCAGGGTTTTAGCGGTGCTTTTTAAGGATCGGGTA
66 CGCTAATGCTCAGGGTAATAGCGGTGCTTTTTAAGGATCGGGTA
* * *
16191334 TTTAGCGGCGTTTCTGAGAAAGCGCCGCTAATACTCGGGGCTTTAGCGGCGTTTTT-AAAGAAGC
1 TTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATACTC-AGGCTTCAGCGGCGTTTTTGAAA-AAGC
*
16191398 GCTGCTAATGCTCA-GGTCAATAGCGG
64 GCCGCTAATGCTCAGGGT-AATAGCGG
16191424 CATTTTTGCT
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
109 38 0.49
110 40 0.51
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (109 bp):
TTTAGCGGCGTTTCTGAAAAAGCGCCGCTAATACTCAGGCTTCAGCGGCGTTTTTGAAAAAGCGC
CGCTAATGCTCAGGGTAATAGCGGTGCTTTTTAAGGATCGGGTA
Found at i:16195221 original size:43 final size:43
Alignment explanation
Indices: 16195158--16195328 Score: 234
Period size: 43 Copynumber: 4.0 Consensus size: 43
16195148 AAGGTTATGC
* **
16195158 TTGTGAGAAAATCGTTGCTAAAGGTCATGGTCTTTAGCGGCGT
1 TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGT
*
16195201 TTGTGAGAAAAGCGCCGCTAAAGGCCATGGTCTTTAGCGGCGT
1 TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGT
* * * *
16195244 TTGTGGGAAAAGTGCCACTAAAGGTCTTGGTCTTTAGCGGCGT
1 TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGT
* * * *
16195287 TTGTGGGAAAAGCACCGCTAAAGGTCTTGTTCTTTAGCGGCG
1 TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCG
16195329 CTTCTCGAAG
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 115 1.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.29
Consensus pattern (43 bp):
TTGTGAGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGT
Found at i:16197261 original size:27 final size:25
Alignment explanation
Indices: 16197223--16197291 Score: 75
Period size: 27 Copynumber: 2.7 Consensus size: 25
16197213 CGTTCCGACC
*
16197223 CACAACTCGTGTGAGCAGGCCCATTTT
1 CACAGCTCGTGTGAGCAGGCCCA--TT
** *
16197250 CACAGCTCGTGTGAGCATTCTCATT
1 CACAGCTCGTGTGAGCAGGCCCATT
*
16197275 CACAGCTTGTGTGAGCA
1 CACAGCTCGTGTGAGCA
16197292 TACATGTGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 18 0.49
27 19 0.51
ACGTcount: A:0.22, C:0.28, G:0.23, T:0.28
Consensus pattern (25 bp):
CACAGCTCGTGTGAGCAGGCCCATT
Found at i:16203244 original size:31 final size:30
Alignment explanation
Indices: 16203195--16203262 Score: 84
Period size: 31 Copynumber: 2.3 Consensus size: 30
16203185 TTTTTAAATG
*
16203195 TGTATA-ATTGAATCAAAATAAAAGTTTCA
1 TGTATATATTGAACCAAAATAAAAGTTTCA
**
16203224 TGTATATATATGAACCAAAATTCAAGTTTCA
1 TGTATATAT-TGAACCAAAATAAAAGTTTCA
*
16203255 TGTGTATA
1 TGTATATA
16203263 ATTAAAGTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 6 0.18
30 2 0.06
31 25 0.76
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.37
Consensus pattern (30 bp):
TGTATATATTGAACCAAAATAAAAGTTTCA
Found at i:16205493 original size:30 final size:30
Alignment explanation
Indices: 16205459--16205531 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 30
16205449 TGGTTAATAC
* *
16205459 ATCCCTTTTCGT-GATTCGATAACTAAAGTT
1 ATCCCTTTTCATAG-TTCGATAACTAAAGCT
*
16205489 ATCCCTTTTCATAGTTCGATAGCTAAAGCT
1 ATCCCTTTTCATAGTTCGATAACTAAAGCT
16205519 ATCCCTTTTCATA
1 ATCCCTTTTCATA
16205532 ATTTGATGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 38 0.97
31 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATAACTAAAGCT
Found at i:16205553 original size:30 final size:30
Alignment explanation
Indices: 16205519--16205620 Score: 143
Period size: 30 Copynumber: 3.4 Consensus size: 30
16205509 AGCTAAAGCT
16205519 ATCCCTTTTCATAATTTGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
** *
16205549 ATCCCTTTTCATTGTTCGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
* *
16205579 ATCCCTTTTCATAATTTGATAGTCG-AACC
1 ATCCCTTTTCATAATTTGATGGTCGTCACC
16205608 TATCCCTTTTCAT
1 -ATCCCTTTTCAT
16205621 TCGTCGATGA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
29 3 0.05
30 60 0.95
ACGTcount: A:0.20, C:0.27, G:0.12, T:0.41
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATGGTCGTCACC
Found at i:16205557 original size:60 final size:60
Alignment explanation
Indices: 16205488--16205620 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
16205478 TAACTAAAGT
* * *
16205488 TATCCCTTTTCATAGTTCGATAG-C-TAAAGCTATCCCTTTTCATAATTTGATGGTCGTCACC
1 TATCCCTTTTCATAGTTCGATAGTCGT-AA-CCATCCCTTTTCATAATTTGATAGTCG-AACC
* * *
16205549 -ATCCCTTTTCATTGTTCGATGGTCGTCACCATCCCTTTTCATAATTTGATAGTCGAACC
1 TATCCCTTTTCATAGTTCGATAGTCGTAACCATCCCTTTTCATAATTTGATAGTCGAACC
16205608 TATCCCTTTTCAT
1 TATCCCTTTTCAT
16205621 TCGTCGATGA
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
59 3 0.05
60 57 0.90
61 2 0.03
62 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (60 bp):
TATCCCTTTTCATAGTTCGATAGTCGTAACCATCCCTTTTCATAATTTGATAGTCGAACC
Found at i:16205621 original size:60 final size:60
Alignment explanation
Indices: 16205519--16205635 Score: 175
Period size: 60 Copynumber: 1.9 Consensus size: 60
16205509 AGCTAAAGCT
* * *
16205519 ATCCCTTTTCATAATTTGATGGTCGTCACCATCCCTTTTCATT-GTTCGATGGTCGTCACC
1 ATCCCTTTTCATAATTTGATAGTCGTAACCATCCCTTTTCATTCG-TCGATGATCGTCACC
16205579 ATCCCTTTTCATAATTTGATAGTCG-AACCTATCCCTTTTCATTCGTCGATGATCGTC
1 ATCCCTTTTCATAATTTGATAGTCGTAACC-ATCCCTTTTCATTCGTCGATGATCGTC
16205636 GTTACGTCGT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
59 3 0.06
60 48 0.92
61 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.14, T:0.40
Consensus pattern (60 bp):
ATCCCTTTTCATAATTTGATAGTCGTAACCATCCCTTTTCATTCGTCGATGATCGTCACC
Found at i:16208132 original size:21 final size:21
Alignment explanation
Indices: 16208106--16208146 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16208096 ACTTTTTCTT
16208106 TAATTAACTA-ACCAAAAATTG
1 TAATT-ACTAGACCAAAAATTG
16208127 TAATTACTAGACCAAAAATT
1 TAATTACTAGACCAAAAATT
16208147 AATTTGAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (21 bp):
TAATTACTAGACCAAAAATTG
Found at i:16212122 original size:50 final size:48
Alignment explanation
Indices: 16212052--16212238 Score: 169
Period size: 50 Copynumber: 3.7 Consensus size: 48
16212042 TATCATTCGA
*
16212052 TACACGTAGTTGCCTTCACATAGTACTACACACGTGATCAAACTTTCCGG
1 TACACGTAGTAGCC-TCACATAGTACTACACACGTGA-CAAACTTTCCGG
* * * * *
16212102 TTCACGTAGTAGCCTGCACATAGTACTACACATGTGACTAACGCCTTCTGG
1 TACACGTAGTAGCCT-CACATAGTACTACACACGTGAC-AA-ACTTTCCGG
* * * * * *
16212153 TACACATAGTAGCCTAACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACGTAGTAGCCTCACATAGTACTACACACGTGA-CA--AACTTTCCGG
*
16212203 TACACGTAGTAGCCTACACTTAGTACTACACACGTG
1 TACACGTAGTAGCCT-CACATAGTACTACACACGTG
16212239 TTTATAGGCA
Statistics
Matches: 112, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
49 2 0.02
50 70 0.62
51 39 0.35
52 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (48 bp):
TACACGTAGTAGCCTCACATAGTACTACACACGTGACAAACTTTCCGG
Found at i:16214097 original size:18 final size:18
Alignment explanation
Indices: 16214074--16214111 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
16214064 AAAAATCACT
16214074 TAATAA-AATACTTTTAAA
1 TAATAAGAATA-TTTTAAA
16214092 TAATAAGTAATATTTTAAA
1 TAATAAG-AATATTTTAAA
16214111 T
1 T
16214112 TTATAATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (18 bp):
TAATAAGAATATTTTAAA
Found at i:16217573 original size:41 final size:41
Alignment explanation
Indices: 16217512--16217590 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
16217502 ACAGACTTTA
* * *
16217512 AGCCTGCTAGACTTATAGTCTGAATTGTTTCACCAGCATTT
1 AGCCTGCTAGACGTAAAGTCTGAATGGTTTCACCAGCATTT
16217553 AGCCTGCTAGACGTAAAGTCTGAATGGTTTCACCAGCA
1 AGCCTGCTAGACGTAAAGTCTGAATGGTTTCACCAGCA
16217591 ATAAGTTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAATGGTTTCACCAGCATTT
Found at i:16235567 original size:15 final size:14
Alignment explanation
Indices: 16235536--16235564 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
16235526 ATTAGTGAAA
16235536 TATTAAAAATAAAT
1 TATTAAAAATAAAT
16235550 TATTAAAAATAAAT
1 TATTAAAAATAAAT
16235564 T
1 T
16235565 TATATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TATTAAAAATAAAT
Found at i:16243696 original size:19 final size:18
Alignment explanation
Indices: 16243663--16243698 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16243653 GTTAATAATT
16243663 TGAAAGTTTTAACTCGGA
1 TGAAAGTTTTAACTCGGA
*
16243681 TGAAATTTTGTAACTCGG
1 TGAAAGTTT-TAACTCGG
16243699 TTTAATACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (18 bp):
TGAAAGTTTTAACTCGGA
Found at i:16249758 original size:28 final size:29
Alignment explanation
Indices: 16249727--16249791 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
16249717 TTACTATTTC
* * *
16249727 TATATTTATACACGCATTTC-TTATATAG
1 TATATATATACACACATTTCTTTATATAA
* *
16249755 TATATATATATACATATTTCTTTATATAA
1 TATATATATACACACATTTCTTTATATAA
16249784 TATATATA
1 TATATATA
16249792 ACTTTTATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.49
Consensus pattern (29 bp):
TATATATATACACACATTTCTTTATATAA
Found at i:16251461 original size:13 final size:13
Alignment explanation
Indices: 16251443--16251468 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16251433 AAAGAGATTT
16251443 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
16251456 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
16251469 AAATTGAACA
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:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:16251538 original size:19 final size:19
Alignment explanation
Indices: 16251498--16251539 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
16251488 GTCTCTTGTC
* *
16251498 GCATTCATTTCATGCATTT
1 GCATTCATTACATGCATAT
16251517 GCATTACATTACAT-CATAT
1 GCATT-CATTACATGCATAT
16251536 GCAT
1 GCAT
16251540 CAAAGATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (19 bp):
GCATTCATTACATGCATAT
Found at i:16254439 original size:8 final size:7
Alignment explanation
Indices: 16254404--16254438 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
16254394 AAAAGTGATG
16254404 TGAAAAA
1 TGAAAAA
16254411 TGAAAAGA
1 TGAAAA-A
16254419 TG-AAAA
1 TGAAAAA
16254425 TGAAAAA
1 TGAAAAA
16254432 TGAAAAA
1 TGAAAAA
16254439 AGTAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 3 0.12
7 20 0.77
8 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
TGAAAAA
Found at i:16254829 original size:13 final size:13
Alignment explanation
Indices: 16254811--16254835 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16254801 TAAATCAATT
16254811 TCTTTGTTATCCA
1 TCTTTGTTATCCA
16254824 TCTTTGTTATCC
1 TCTTTGTTATCC
16254836 TCGACAATTT
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:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (13 bp):
TCTTTGTTATCCA
Found at i:16267103 original size:33 final size:33
Alignment explanation
Indices: 16267066--16267129 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
16267056 CTTGTACTTA
16267066 AATAAATGTATTTAAAGTAGATGTATCTAGTTT
1 AATAAATGTATTTAAAGTAGATGTATCTAGTTT
*
16267099 AATAAATGTATTTAGAGTAGATGTATCTAGT
1 AATAAATGTATTTAAAGTAGATGTATCTAGT
16267130 AGTCATGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.41
Consensus pattern (33 bp):
AATAAATGTATTTAAAGTAGATGTATCTAGTTT
Found at i:16273042 original size:33 final size:33
Alignment explanation
Indices: 16272970--16273066 Score: 110
Period size: 33 Copynumber: 3.0 Consensus size: 33
16272960 GAACTTGAGC
*
16272970 CAGGAGGAGTGGAGTACTACGGTGGATAC-GAGT
1 CAGGAGGAGTGGAGTACTGCGGTGGATACTG-GT
* *
16273003 CGGGAGGAGTGGAGTAATGCGGTGGATACTGG-
1 CAGGAGGAGTGGAGTACTGCGGTGGATACTGGT
**
16273035 CTAGGAGGAGTGTTGTACTGCGGTGG-TACTGG
1 C-AGGAGGAGTGGAGTACTGCGGTGGATACTGG
16273067 ACTGAAGATA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
32 7 0.13
33 47 0.85
34 1 0.02
ACGTcount: A:0.22, C:0.11, G:0.45, T:0.22
Consensus pattern (33 bp):
CAGGAGGAGTGGAGTACTGCGGTGGATACTGGT
Found at i:16274651 original size:49 final size:49
Alignment explanation
Indices: 16274576--16274706 Score: 217
Period size: 50 Copynumber: 2.6 Consensus size: 49
16274566 AATAATAATA
* *
16274576 ACATGCCAAATAAATTACATAAAAAAATAAATCTAATAAACCTAAAACAT
1 ACATGACAAATAAATTACAT-AAAAAATAAATCTAATAAACCTAAAACAC
16274626 ACATGACAAATAAATTACATAAAAAATAAATCTAATAAACCTAAAACAC
1 ACATGACAAATAAATTACATAAAAAATAAATCTAATAAACCTAAAACAC
*
16274675 ACATGACAAAATAAATTACATAAAAAAAAAAT
1 ACATGAC-AAATAAATTACATAAAAAATAAAT
16274707 AAAACATTCT
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
49 35 0.45
50 42 0.55
ACGTcount: A:0.63, C:0.15, G:0.02, T:0.21
Consensus pattern (49 bp):
ACATGACAAATAAATTACATAAAAAATAAATCTAATAAACCTAAAACAC
Found at i:16274663 original size:16 final size:17
Alignment explanation
Indices: 16274583--16274664 Score: 66
Period size: 16 Copynumber: 5.0 Consensus size: 17
16274573 ATAACATGCC
16274583 AAATAAAT-TACATAAAA
1 AAATAAATCTACAT-AAA
16274600 AAATAAATCTA-AT-AA
1 AAATAAATCTACATAAA
** * * *
16274615 ACCTAAAACATACATGAC
1 AAATAAATC-TACATAAA
16274633 AAATAAAT-TACATAAA
1 AAATAAATCTACATAAA
16274649 AAATAAATCTA-ATAAA
1 AAATAAATCTACATAAA
16274665 CCTAAAACAC
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
15 8 0.16
16 21 0.41
17 14 0.27
18 8 0.16
ACGTcount: A:0.65, C:0.11, G:0.01, T:0.23
Consensus pattern (17 bp):
AAATAAATCTACATAAA
Found at i:16275032 original size:31 final size:34
Alignment explanation
Indices: 16274965--16275050 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 34
16274955 AAATCCTTCT
* *
16274965 AACCCTAAATACAACCTCTTAATTAATTTTTTTCA
1 AACCCTAAACACAACCTCTTAATT-ATTTTTCTCA
16275000 AACCCTAAACACAACC-C-TAATT-TTTTTCTCA
1 AACCCTAAACACAACCTCTTAATTATTTTTCTCA
*
16275031 AATCCC-AAACACAACTTCTT
1 AA-CCCTAAACACAACCTCTT
16275051 CTCATTCCTT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
31 19 0.42
32 4 0.09
33 6 0.13
34 1 0.02
35 15 0.33
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (34 bp):
AACCCTAAACACAACCTCTTAATTATTTTTCTCA
Found at i:16275414 original size:11 final size:11
Alignment explanation
Indices: 16275399--16275431 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
16275389 CACCTCAATG
16275399 TCAGCGGGTCGA
1 TCAGCGGGTC-A
16275411 -CAGCGGGTCA
1 TCAGCGGGTCA
16275421 TCAGCGGGTCA
1 TCAGCGGGTCA
16275432 GGTTTTGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 19 0.95
ACGTcount: A:0.18, C:0.27, G:0.39, T:0.15
Consensus pattern (11 bp):
TCAGCGGGTCA
Found at i:16292369 original size:33 final size:33
Alignment explanation
Indices: 16292332--16292396 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
16292322 TATAAGAGTC
16292332 TAGCCTACAATGGAATACAATCTAAACCATACA
1 TAGCCTACAATGGAATACAATCTAAACCATACA
*
16292365 TAGCCTACAATGGAATACAATCTGAACCATAC
1 TAGCCTACAATGGAATACAATCTAAACCATAC
16292397 CCCAATGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.22
Consensus pattern (33 bp):
TAGCCTACAATGGAATACAATCTAAACCATACA
Found at i:16302071 original size:41 final size:41
Alignment explanation
Indices: 16301947--16302080 Score: 121
Period size: 40 Copynumber: 3.3 Consensus size: 41
16301937 ACTATGTTTA
* ** * * *
16301947 GCACTTAATGTGCGATTC-GAGATAGCTTCGTCTATTTCTG
1 GCACTTAGTGTGCGAGACTGAGATAGCTTCGGCTATATATG
* * * *
16301987 GCACTTAGTGT--GTGATTGGGAATAGCTTTGGCTATATATG
1 GCACTTAGTGTGCGAGACTGAG-ATAGCTTCGGCTATATATG
* *
16302027 GCACTTAGTGTGCGAGACTGAGATAGCTTCGGCTATGTAAG
1 GCACTTAGTGTGCGAGACTGAGATAGCTTCGGCTATATATG
*
16302068 GCACCTAGTGTGC
1 GCACTTAGTGTGC
16302081 AGGATTATAA
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
38 1 0.01
39 2 0.03
40 36 0.49
41 28 0.38
42 6 0.08
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (41 bp):
GCACTTAGTGTGCGAGACTGAGATAGCTTCGGCTATATATG
Found at i:16307617 original size:14 final size:14
Alignment explanation
Indices: 16307598--16307632 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16307588 GATATCACAG
16307598 TTGTATATATATAT
1 TTGTATATATATAT
*
16307612 TTGTATATGTATAT
1 TTGTATATATATAT
*
16307626 GTGTATA
1 TTGTATA
16307633 ATTAACATGG
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:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (14 bp):
TTGTATATATATAT
Found at i:16316633 original size:41 final size:41
Alignment explanation
Indices: 16316588--16316836 Score: 293
Period size: 41 Copynumber: 6.1 Consensus size: 41
16316578 AGAAAAGTAT
* * * *
16316588 ATTCAGGGGTATCGTAGTACTAACAGGGGCACGTATGTGCA
1 ATTCAGGGGTATCGAAGTACAAACAGGGGCACATAAGTGCA
16316629 ATTCAGGGGTA-CTGAAGTACAAACAGGGGCACATAAGTGCA
1 ATTCAGGGGTATC-GAAGTACAAACAGGGGCACATAAGTGCA
** * * *
16316670 ATTCAAAGGTACCGAAGTACAAAAAGGGGCACGTAAGTGCA
1 ATTCAGGGGTATCGAAGTACAAACAGGGGCACATAAGTGCA
* * * * *
16316711 ATTTAGGGGTACCAAAGTACAAATAGGGGCACATAAGTGTA
1 ATTCAGGGGTATCGAAGTACAAACAGGGGCACATAAGTGCA
* * * ** *
16316752 ATTCAAGGGTATCAAAGTACAAACAGGGGTATGTAAGTGTA
1 ATTCAGGGGTATCGAAGTACAAACAGGGGCACATAAGTGCA
*
16316793 ATTCAGGGGTATCGAAGTACAAACAAGGGCACATAAGTGCA
1 ATTCAGGGGTATCGAAGTACAAACAGGGGCACATAAGTGCA
16316834 ATT
1 ATT
16316837 GATCAATTTT
Statistics
Matches: 177, Mismatches: 29, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
40 1 0.01
41 175 0.99
42 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.28, T:0.20
Consensus pattern (41 bp):
ATTCAGGGGTATCGAAGTACAAACAGGGGCACATAAGTGCA
Found at i:16316666 original size:20 final size:20
Alignment explanation
Indices: 16316603--16316748 Score: 53
Period size: 20 Copynumber: 7.2 Consensus size: 20
16316593 GGGGTATCGT
* *
16316603 AGTACTAACAGGGGCACGTA
1 AGTACAAACAGGGGCACATA
* * * *
16316623 TGTGCAATTCAGGGGTAC-TGA
1 AGTACAA-ACAGGGGCACAT-A
16316644 AGTACAAACAGGGGCACATA
1 AGTACAAACAGGGGCACATA
* * ** * **
16316664 AGTGCAATTCAAAGGTACCGA
1 AGTACAA-ACAGGGGCACATA
* *
16316685 AGTACAAAAAGGGGCACGTA
1 AGTACAAACAGGGGCACATA
* ** *
16316705 AGTGCAATTTAGGGGTACCA-A
1 AGTACAA-ACAGGGGCA-CATA
*
16316726 AGTACAAATAGGGGCACATA
1 AGTACAAACAGGGGCACATA
16316746 AGT
1 AGT
16316749 GTAATTCAAG
Statistics
Matches: 87, Mismatches: 32, Indels: 14
0.65 0.24 0.11
Matches are distributed among these distances:
19 2 0.02
20 43 0.49
21 41 0.47
22 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.18
Consensus pattern (20 bp):
AGTACAAACAGGGGCACATA
Found at i:16316769 original size:21 final size:21
Alignment explanation
Indices: 16316745--16316810 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
16316735 AGGGGCACAT
*
16316745 AAGTGTAATTCAAGGGTATCA
1 AAGTGTAATTCAGGGGTATCA
** * **
16316766 AAGTACAA-ACAGGGGTATGT
1 AAGTGTAATTCAGGGGTATCA
*
16316786 AAGTGTAATTCAGGGGTATCG
1 AAGTGTAATTCAGGGGTATCA
16316807 AAGT
1 AAGT
16316811 ACAAACAAGG
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.36, C:0.09, G:0.29, T:0.26
Consensus pattern (21 bp):
AAGTGTAATTCAGGGGTATCA
Found at i:16316821 original size:21 final size:20
Alignment explanation
Indices: 16316758--16316817 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
16316748 TGTAATTCAA
*
16316758 GGGTATCAAAGTACAAACAG
1 GGGTATCGAAGTACAAACAG
** *
16316778 GGGTAT-GTAAGTGTAATTCAG
1 GGGTATCG-AAGTACAA-ACAG
16316799 GGGTATCGAAGTACAAACA
1 GGGTATCGAAGTACAAACA
16316818 AGGGCACATA
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
20 14 0.47
21 15 0.50
22 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (20 bp):
GGGTATCGAAGTACAAACAG
Found at i:16321144 original size:20 final size:20
Alignment explanation
Indices: 16321106--16321143 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16321096 CCTTAAAGTA
16321106 AAAATGAATGTCAAATTTTG
1 AAAATGAATGTCAAATTTTG
*
16321126 AAAATGTATGTC-AATTTT
1 AAAATGAATGTCAAATTTT
16321144 TATTTTGGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (20 bp):
AAAATGAATGTCAAATTTTG
Found at i:16323993 original size:25 final size:25
Alignment explanation
Indices: 16323957--16324034 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
16323947 TATATCCAAT
*
16323957 TTCATATAACATAATTCATACTATA
1 TTCATATCACATAATTCATACTATA
16323982 TTCATATCACAT-A-TCATA-TATCAA
1 TTCATATCACATAATTCATACTAT--A
* *
16324006 TT-ATATCACACTATTTTATACTATA
1 TTCATATCACA-TAATTCATACTATA
16324031 TTCA
1 TTCA
16324035 GTTCAGTCCA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
22 3 0.07
23 13 0.30
24 5 0.12
25 14 0.33
26 5 0.12
27 3 0.07
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (25 bp):
TTCATATCACATAATTCATACTATA
Found at i:16331674 original size:3 final size:3
Alignment explanation
Indices: 16331668--16331730 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
16331658 TGTCCAACAA
16331668 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
16331716 CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT
16331731 TTATTGCCCA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:16334531 original size:20 final size:19
Alignment explanation
Indices: 16334506--16334566 Score: 56
Period size: 20 Copynumber: 3.3 Consensus size: 19
16334496 TTTTATTTAT
16334506 ACTAAATTCACCAATATTAA
1 ACTAAATTC-CCAATATTAA
* * *
16334526 ACTAAATT-TC-AT-TCAT
1 ACTAAATTCCCAATATTAA
16334542 ACTAAATTCGCCAATATTAA
1 ACTAAATTC-CCAATATTAA
16334562 ACTAA
1 ACTAA
16334567 CATGTAGCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
16 10 0.32
17 2 0.06
18 2 0.06
19 2 0.06
20 15 0.48
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.33
Consensus pattern (19 bp):
ACTAAATTCCCAATATTAA
Found at i:16334544 original size:36 final size:36
Alignment explanation
Indices: 16334493--16334566 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
16334483 CATCCAAATC
* *
16334493 AAATTTTATTTATACTAAATTCACCAATATTAAACT
1 AAATTTCATTCATACTAAATTCACCAATATTAAACT
*
16334529 AAATTTCATTCATACTAAATTCGCCAATATTAAACT
1 AAATTTCATTCATACTAAATTCACCAATATTAAACT
16334565 AA
1 AA
16334567 CATGTAGCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.45, C:0.16, G:0.01, T:0.38
Consensus pattern (36 bp):
AAATTTCATTCATACTAAATTCACCAATATTAAACT
Found at i:16334672 original size:6 final size:6
Alignment explanation
Indices: 16334661--16334697 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
16334651 TCAACCACAA
16334661 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT A
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT A
16334698 TATAAATGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ACATAT
Found at i:16335886 original size:17 final size:17
Alignment explanation
Indices: 16335864--16335913 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
16335854 TAGTCATAAG
*
16335864 CTTTCTCTTTTTCTTTT
1 CTTTCTTTTTTTCTTTT
16335881 CTTTCTTTATTTTC-TTT
1 CTTTCTTT-TTTTCTTTT
16335898 CTTTCTTTTCTTTCTT
1 CTTTCTTTT-TTTCTT
16335914 AATGTTTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 1 0.03
17 22 0.76
18 6 0.21
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTCTTTTTTTCTTTT
Found at i:16335893 original size:13 final size:13
Alignment explanation
Indices: 16335877--16335913 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
16335867 TCTCTTTTTC
16335877 TTTTCTTTCTTTA
1 TTTTCTTTCTTTA
*
16335890 TTTTCTTTCTTTC
1 TTTTCTTTCTTTA
16335903 TTTTCTTTCTT
1 TTTTCTTTCTT
16335914 AATGTTTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTCTTTCTTTA
Found at i:16335954 original size:16 final size:16
Alignment explanation
Indices: 16335935--16335975 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
16335925 GTATTGGTTC
*
16335935 TATTATTTATTACTAT
1 TATTATTTATCACTAT
* *
16335951 TATTTTTTATCATTAT
1 TATTATTTATCACTAT
16335967 TATTATTTA
1 TATTATTTA
16335976 AGTTAACATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTATTTATCACTAT
Found at i:16337388 original size:43 final size:43
Alignment explanation
Indices: 16337341--16337446 Score: 110
Period size: 43 Copynumber: 2.5 Consensus size: 43
16337331 CTGGCAACGC
* **
16337341 AGTGCATCATCAGATAAATCC-AAGTGAATATACTA-GCACACAT
1 AGTGCATCATCAGACAAA-CCGAAGCAAATATAC-AGGCACACAT
* * *
16337384 AGTGCATCATCGGACGAACCGAAGCAAATATACAGGCACATAT
1 AGTGCATCATCAGACAAACCGAAGCAAATATACAGGCACACAT
16337427 AGTGCATCATCTA-ACAAACC
1 AGTGCATCATC-AGACAAACC
16337447 AAAGTATAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
42 3 0.06
43 49 0.94
ACGTcount: A:0.41, C:0.24, G:0.16, T:0.20
Consensus pattern (43 bp):
AGTGCATCATCAGACAAACCGAAGCAAATATACAGGCACACAT
Found at i:16342651 original size:28 final size:28
Alignment explanation
Indices: 16342611--16342664 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
16342601 TCGGATAAAA
*
16342611 CCGAAAAAATTCGGTTAACCGACCGATT
1 CCGAAAAAATTCGATTAACCGACCGATT
16342639 CCGAAAAAATTCGATTAACCGACCGA
1 CCGAAAAAATTCGATTAACCGACCGA
16342665 ATTAGGTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.19
Consensus pattern (28 bp):
CCGAAAAAATTCGATTAACCGACCGATT
Found at i:16343020 original size:9 final size:8
Alignment explanation
Indices: 16343000--16343048 Score: 53
Period size: 9 Copynumber: 5.5 Consensus size: 8
16342990 GTAGTGATTC
16343000 AATTCGGTT
1 AATTCGG-T
16343009 AATTCTGGT
1 AATTC-GGT
16343018 AATTCGGTT
1 AATTCGG-T
16343027 AATTCGGGT
1 AATTC-GGT
16343036 AATTCGGTT
1 AATTCGG-T
16343045 AATT
1 AATT
16343049 TTTGATCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 4 0.11
9 28 0.78
10 4 0.11
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.43
Consensus pattern (8 bp):
AATTCGGT
Found at i:16343023 original size:18 final size:18
Alignment explanation
Indices: 16343000--16343048 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
16342990 GTAGTGATTC
*
16343000 AATTCGGTTAATTCTGGT
1 AATTCGGTTAATTCGGGT
16343018 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
16343036 AATTCGGTTAATT
1 AATTCGGTTAATT
16343049 TTTGATCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.43
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:16349038 original size:53 final size:53
Alignment explanation
Indices: 16348958--16349071 Score: 210
Period size: 53 Copynumber: 2.2 Consensus size: 53
16348948 TACCACCGCA
* *
16348958 CTTGTTTTTCAGAGTCTATTTTGATTTTTCTCTCTATCATCTCTTCATGGCAT
1 CTTGTTTTTCAGAGCCTATTTTGATTTTTCTCTCCATCATCTCTTCATGGCAT
16349011 CTTGTTTTTCAGAGCCTATTTTGATTTTTCTCTCCATCATCTCTTCATGGCAT
1 CTTGTTTTTCAGAGCCTATTTTGATTTTTCTCTCCATCATCTCTTCATGGCAT
16349064 CTTGTTTT
1 CTTGTTTT
16349072 GCTAGATTAT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.14, C:0.22, G:0.11, T:0.53
Consensus pattern (53 bp):
CTTGTTTTTCAGAGCCTATTTTGATTTTTCTCTCCATCATCTCTTCATGGCAT
Found at i:16350922 original size:21 final size:21
Alignment explanation
Indices: 16350896--16350951 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
16350886 AACAGCGGTG
*
16350896 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
16350917 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
**
16350938 GTAGTGAGATTAGA
1 GCGGTGAGATTAGA
16350952 AACAATGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.07, G:0.36, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:16365476 original size:27 final size:27
Alignment explanation
Indices: 16365438--16365498 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
16365428 AGAATTTGAG
16365438 AGCCAAGTTGGGAGTTTGCAGCATGCA
1 AGCCAAGTTGGGAGTTTGCAGCATGCA
16365465 AGCCAAGTTGGGAGTTTGCAGCATGCA
1 AGCCAAGTTGGGAGTTTGCAGCATGCA
16365492 AGCCAAG
1 AGCCAAG
16365499 GAGGAGTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (27 bp):
AGCCAAGTTGGGAGTTTGCAGCATGCA
Done.