Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 122 of 167
Found at i:40822921 original size:26 final size:26
Alignment explanation
Indices: 40822892--40822995 Score: 172
Period size: 26 Copynumber: 4.0 Consensus size: 26
40822882 ATTCCCATCT
*
40822892 TGGAACATTTACCTAAACCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
40822918 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
* *
40822944 TGGAATATTTACCTAATCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
*
40822970 TGGAGCATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
40822996 ATTTGTACCA
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.33
Consensus pattern (26 bp):
TGGAACATTTACCTAACCCATTATCA
Found at i:40829566 original size:26 final size:26
Alignment explanation
Indices: 40829537--40829692 Score: 267
Period size: 26 Copynumber: 6.0 Consensus size: 26
40829527 ATTCCCATCT
*
40829537 TGGAACATTTACCTAAACCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
40829563 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
* *
40829589 TGGAATATTTACCTAATCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
40829615 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
* *
40829641 TGGAATATTTACCTAATCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
40829667 TGGAACATTTACCTAACCCATTATCA
1 TGGAACATTTACCTAACCCATTATCA
40829693 ATTTGTACAA
Statistics
Matches: 121, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 121 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (26 bp):
TGGAACATTTACCTAACCCATTATCA
Found at i:40829610 original size:52 final size:52
Alignment explanation
Indices: 40829537--40829692 Score: 294
Period size: 52 Copynumber: 3.0 Consensus size: 52
40829527 ATTCCCATCT
* *
40829537 TGGAACATTTACCTAAACCATTATCATGGAACATTTACCTAACCCATTATCA
1 TGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTATCA
40829589 TGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTATCA
1 TGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTATCA
40829641 TGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTATCA
1 TGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTATCA
40829693 ATTTGTACAA
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 102 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (52 bp):
TGGAATATTTACCTAATCCATTATCATGGAACATTTACCTAACCCATTATCA
Found at i:40844380 original size:35 final size:35
Alignment explanation
Indices: 40844334--40844404 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
40844324 CGACTGAAGG
40844334 TTTGAGGAACCAATTCCTAACTACGAAAGCAGGAA
1 TTTGAGGAACCAATTCCTAACTACGAAAGCAGGAA
*
40844369 TTTGAGGAACCAATTCCTGACTACGAAAGCAGGAA
1 TTTGAGGAACCAATTCCTAACTACGAAAGCAGGAA
40844404 T
1 T
40844405 GTATCTGTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (35 bp):
TTTGAGGAACCAATTCCTAACTACGAAAGCAGGAA
Found at i:40855275 original size:25 final size:26
Alignment explanation
Indices: 40855225--40855275 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
40855215 GAAAGGGAAA
*
40855225 AAAAAACAGAAACAAATATGGTTTTT
1 AAAAAACAGAAACAAATATGGATTTT
*
40855251 AAAAAA-A-AAACAACATATTGATTTT
1 AAAAAACAGAAACAA-ATATGGATTTT
40855276 GAATTGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
25 10 0.45
26 6 0.27
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (26 bp):
AAAAAACAGAAACAAATATGGATTTT
Found at i:40857406 original size:21 final size:21
Alignment explanation
Indices: 40857356--40857406 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
40857346 ATTTAAGAGA
40857356 TATTA-TTTGAATAATTATATC
1 TATTACTTT-AATAATTATATC
* *
40857377 TCTTACTTTAATAGTTATATC
1 TATTACTTTAATAATTATATC
*
40857398 TATTTCTTT
1 TATTACTTT
40857407 TTAAAATGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.29, C:0.10, G:0.04, T:0.57
Consensus pattern (21 bp):
TATTACTTTAATAATTATATC
Found at i:40867032 original size:12 final size:12
Alignment explanation
Indices: 40867010--40867038 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40867000 TTATTTAACT
40867010 TTTAA-ATTTAA
1 TTTAATATTTAA
40867021 TTTAATATTTAA
1 TTTAATATTTAA
40867033 TTTAAT
1 TTTAAT
40867039 GCTACATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTAATATTTAA
Found at i:40870099 original size:26 final size:26
Alignment explanation
Indices: 40870057--40870109 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
40870047 CAAGCTTCAC
*
40870057 CTCTCTGTCTTTGTCTCTCTTTATCA
1 CTCTCTGTCTTTATCTCTCTTTATCA
* *
40870083 CTCTCTGT-TCTTATCTCTGTTTCTCA
1 CTCTCTGTCT-TTATCTCTCTTTATCA
40870109 C
1 C
40870110 CTTGAGAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 1 0.04
26 22 0.96
ACGTcount: A:0.08, C:0.32, G:0.08, T:0.53
Consensus pattern (26 bp):
CTCTCTGTCTTTATCTCTCTTTATCA
Found at i:40877859 original size:43 final size:42
Alignment explanation
Indices: 40877798--40877906 Score: 150
Period size: 42 Copynumber: 2.6 Consensus size: 42
40877788 AATGCCAACT
40877798 TCCCAGAC-GTGGTCTTACATGTAATCAAATATCGATGCT-ACTG
1 TCCCAGACAG-GGTCTTACATGTAATCAAATA-CGATGCTGA-TG
*
40877841 TCCCAGACAGGGTCTTACATGAAATCAAATACGATGCTGATG
1 TCCCAGACAGGGTCTTACATGTAATCAAATACGATGCTGATG
* *
40877883 TCCCAGACATGGTCTTACACGTAA
1 TCCCAGACAGGGTCTTACATGTAA
40877907 ATCATCAGTC
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
42 30 0.50
43 29 0.48
44 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (42 bp):
TCCCAGACAGGGTCTTACATGTAATCAAATACGATGCTGATG
Found at i:40877909 original size:43 final size:41
Alignment explanation
Indices: 40877798--40877971 Score: 161
Period size: 43 Copynumber: 4.0 Consensus size: 41
40877788 AATGCCAACT
* * *
40877798 TCCCAGACGTGGTCTTACATGTAATCAAATATCGATGCTACTG
1 TCCCAGACATGGTCTTACACGAAATCAAATA-CGATGCTA-TG
* *
40877841 TCCCAGACAGGGTCTTACATGAAATCAAATACGATGCTGATG
1 TCCCAGACATGGTCTTACACGAAATCAAATACGATGCT-ATG
* * *
40877883 TCCCAGACATGGTCTTACACGTAAATCATCAGT-CGATGCCAACG
1 TCCCAGACATGGTCTTACACG-AAATCA--AATACGATG-CTATG
* * *
40877927 TTCCAGACATGGTCTTACACGAAAACAAATATCGAATCCTATG
1 TCCCAGACATGGTCTTACACGAAATCAAATA-CG-ATGCTATG
40877970 TC
1 TC
40877972 ATGACATATG
Statistics
Matches: 108, Mismatches: 15, Indels: 16
0.78 0.11 0.12
Matches are distributed among these distances:
41 2 0.02
42 28 0.26
43 46 0.43
44 29 0.27
45 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (41 bp):
TCCCAGACATGGTCTTACACGAAATCAAATACGATGCTATG
Found at i:40885853 original size:30 final size:30
Alignment explanation
Indices: 40885818--40885874 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
40885808 TGGGCAGGCC
40885818 GTGTGTCTCACACGGCCACTAGACATGTCT
1 GTGTGTCTCACACGGCCACTAGACATGTCT
* * *
40885848 GTGTGTCTTACATGGCCATTAGACATG
1 GTGTGTCTCACACGGCCACTAGACATG
40885875 CCCGTCTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (30 bp):
GTGTGTCTCACACGGCCACTAGACATGTCT
Found at i:40890108 original size:28 final size:28
Alignment explanation
Indices: 40890024--40890109 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 28
40890014 GAACATGCTA
* * *
40890024 GAAAATGAAAGCCTTTGTGGTAATTTAT
1 GAAAATGGAAGCCTTTGTGGCAATATAT
* **
40890052 AAAAATGGAAGCCTTTGTCACAATATAT
1 GAAAATGGAAGCCTTTGTGGCAATATAT
* *
40890080 GAAAATGGAAGCCTTTGTGGCGATCTAT
1 GAAAATGGAAGCCTTTGTGGCAATATAT
40890108 GA
1 GA
40890110 TGTAACACCC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (28 bp):
GAAAATGGAAGCCTTTGTGGCAATATAT
Found at i:40891449 original size:2 final size:2
Alignment explanation
Indices: 40891442--40891502 Score: 86
Period size: 2 Copynumber: 30.5 Consensus size: 2
40891432 ACAAGTAAAC
* * *
40891442 AT AT AT AT AT AA AT AT AT AT AA AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
40891484 AT TT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
40891503 CAAACCTTTC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:40891758 original size:43 final size:42
Alignment explanation
Indices: 40891709--40891854 Score: 159
Period size: 43 Copynumber: 3.4 Consensus size: 42
40891699 TATCCGAGAT
* * * *
40891709 ATGGTCTTACATGTTATTACATATGGATGCCATTGTCCCAGAC
1 ATGGTCTTACACGTAATTA-ATATCGATGCCAATGTCCCAGAC
* *
40891752 ATGGTCTTACACATAATTAATTAACGATGCCAATGTCCCAGAC
1 ATGGTCTTACACGTAATTAA-TATCGATGCCAATGTCCCAGAC
* * *
40891795 ATCGTCTTACACGTAATCTTAATA-CAATGCTAATGTCCCAGAC
1 ATGGTCTTACACGTAA--TTAATATCGATGCCAATGTCCCAGAC
*
40891838 ATGGTCTTACATGTAAT
1 ATGGTCTTACACGTAAT
40891855 CACATATCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 80 0.91
44 2 0.02
45 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGGTCTTACACGTAATTAATATCGATGCCAATGTCCCAGAC
Found at i:40891855 original size:43 final size:45
Alignment explanation
Indices: 40891735--40891855 Score: 160
Period size: 43 Copynumber: 2.8 Consensus size: 45
40891725 TTACATATGG
* * *
40891735 ATGCCATTGTCCCAGACATGGTCTTACACATAA--TTAATTAACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTTAATTAACA
*
40891778 ATGCCAATGTCCCAGACATCGTCTTACACGTAATCTTAA-T-ACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTTAATTAACA
* *
40891821 ATGCTAATGTCCCAGACATGGTCTTACATGTAATC
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATC
40891856 ACATATCAAT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 64 0.93
44 1 0.01
45 4 0.06
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (45 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCTTAATTAACA
Found at i:40892380 original size:29 final size:28
Alignment explanation
Indices: 40892339--40892404 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
40892329 CTTTCATTTA
*
40892339 TTTCACAAATTAACCCCTTAATTT-ACATT
1 TTTCTCAAATTAA-CCCTT-ATTTAACATT
* *
40892368 TTTCTCAATTTAATCCTTATTTAACATT
1 TTTCTCAAATTAACCCTTATTTAACATT
*
40892396 TTTGTCAAA
1 TTTCTCAAA
40892405 AATCACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
27 4 0.13
28 16 0.52
29 11 0.35
ACGTcount: A:0.32, C:0.20, G:0.02, T:0.47
Consensus pattern (28 bp):
TTTCTCAAATTAACCCTTATTTAACATT
Found at i:40892524 original size:20 final size:21
Alignment explanation
Indices: 40892481--40892525 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
40892471 AATCTCAAGC
40892481 ATTCATCAATGAAAAATCACAA
1 ATTCATCAA-GAAAAATCACAA
* *
40892503 ATTCATCAA-AAAATTCAGAA
1 ATTCATCAAGAAAAATCACAA
40892523 ATT
1 ATT
40892526 AGGGTACGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
22 9 0.43
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (21 bp):
ATTCATCAAGAAAAATCACAA
Found at i:40899326 original size:43 final size:43
Alignment explanation
Indices: 40899148--40899326 Score: 122
Period size: 43 Copynumber: 4.2 Consensus size: 43
40899138 ACTCAGAAAT
* * *
40899148 CACGTAAGCTC-ATACAATGCC-ATATCCCAGATATGGTCTTA
1 CACGTAATCTCAATACAATGCCAATGTCCCAGACATGGTCTTA
* * * * * *
40899189 CATGTTAT-T-ACATATCGATGCCACTGTTCTAGACA-GAGTCTTA
1 CACGTAATCTCA-ATA-CAATGCCAATGTCCCAGACATG-GTCTTA
* * *
40899232 CACATAA--TCAATTAACGATGCCATTGTCCC-GAACATGGTCTTA
1 CACGTAATCTCAA-T-ACAATGCCAATGTCCCAG-ACATGGTCTTA
*
40899275 CACATAATCTCAATACAATGCCAATGTCCCAGACATGGTCTTA
1 CACGTAATCTCAATACAATGCCAATGTCCCAGACATGGTCTTA
*
40899318 CATGTAATC
1 CACGTAATC
40899327 ACATATCAAT
Statistics
Matches: 106, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
40 1 0.01
41 8 0.08
42 10 0.09
43 79 0.75
44 4 0.04
45 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (43 bp):
CACGTAATCTCAATACAATGCCAATGTCCCAGACATGGTCTTA
Found at i:40902431 original size:22 final size:22
Alignment explanation
Indices: 40902400--40902454 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
40902390 GCCTTATGAA
40902400 TCTC-TTCCAAGGCTTTGAGTT
1 TCTCTTTCCAAGGCTTTGAGTT
40902421 TCTCTTTCCAAGGCTTTGAGTT
1 TCTCTTTCCAAGGCTTTGAGTT
*
40902443 TCTCTTCCCAAG
1 TCTCTTTCCAAG
40902455 CAAGTTTCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.12
22 28 0.88
ACGTcount: A:0.15, C:0.27, G:0.16, T:0.42
Consensus pattern (22 bp):
TCTCTTTCCAAGGCTTTGAGTT
Found at i:40905409 original size:51 final size:50
Alignment explanation
Indices: 40905343--40905830 Score: 784
Period size: 51 Copynumber: 9.9 Consensus size: 50
40905333 GAAATGATAG
40905343 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTG-TA
40905394 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTG-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGTA
*
40905443 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGAG-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGTA
40905490 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA-GATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG-TGT-A
*
40905541 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGT-A
*
40905592 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTG-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGTA
*
40905639 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGT-A
*
40905690 TAGGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTG-A
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGTA
40905737 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA-GATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATG-TGT-A
40905788 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
40905831 GTGACAGGGC
Statistics
Matches: 412, Mismatches: 10, Indels: 30
0.91 0.02 0.07
Matches are distributed among these distances:
47 118 0.29
48 2 0.00
49 79 0.19
51 213 0.52
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (50 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGTA
Found at i:40905558 original size:98 final size:97
Alignment explanation
Indices: 40905343--40905885 Score: 762
Period size: 98 Copynumber: 5.5 Consensus size: 97
40905333 GAAATGATAG
*
40905343 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATATAAGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATATA--TGAGATAAGGCCTAATGGC
40905408 CGATGTGATGAATGTGAAAGTGTATATATATGTGA
63 CGATGTGATGAATGTGAAAGTGTATATATATGTGA
40905443 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-TATATATGAGATAAGGCCTAATGGCCGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGAGATAAGGCCTAATGGCCGA
40905507 TGTGATGAATGTGAAAGTGTATATATAGATGTGA
66 TGTGATGAATGTGAAAGTGTATATAT--ATGTGA
* *
40905541 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAGGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG---ATATATATGAGATAAGGCCTAATGGC
40905606 CGATGTGATGAATGTGAAAGTG--TATATATGTGA
63 CGATGTGATGAATGTGAAAGTGTATATATATGTGA
* *
40905639 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAGGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG---ATATATATGAGATAAGGCCTAATGGC
40905704 CGATGTGATGAATGTGAAAGTG--TATATATGTGA
63 CGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
40905737 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAGATGTGATAAGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG-ATATAT--ATGAGATAAGGCCTAATGGC
40905802 CGATGTGATGAATGTGAAAGTG--TATATATGTGA
63 CGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * * *
40905835 -CAGGGCTGAGTGGCCAACGTGATGGATGTGAAAGTG-TATAAATGTGATAAG
1 TAAGGCCT-AATGGCCGATGTGATGAATGTGAAAGTGATATATATGAGATAAG
40905886 TCCCGAAGGG
Statistics
Matches: 423, Mismatches: 11, Indels: 24
0.92 0.02 0.05
Matches are distributed among these distances:
94 10 0.02
96 58 0.14
97 5 0.01
98 264 0.62
100 41 0.10
102 45 0.11
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (97 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGATATATATGAGATAAGGCCTAATGGCCGA
TGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:40905649 original size:149 final size:146
Alignment explanation
Indices: 40905343--40905885 Score: 843
Period size: 149 Copynumber: 3.7 Consensus size: 146
40905333 GAAATGATAG
40905343 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT-ATGTGATATAAGGCCTAATGG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAATGTG--ATAAGGCCTAATGG
40905407 CCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
64 CCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGT
*
40905472 GAAAGTGTATATATGAGA
129 GAAAGTGTATATATGTGA
40905490 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAGATGTGATAAGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA-ATGTGATAAGGCCTAATGGC
*
40905555 CGATGTGATGAATGTGAAAGTGTATATATATATGTGATAGGGCCTAATGGCCGATGTGATGAATG
65 CGATGTGATGAATGTGAAAGTG--TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATG
40905620 TGAAAGTGTATATATGTGA
128 TGAAAGTGTATATATGTGA
*
40905639 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAGGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA-ATGTGATAAGGCCTAATGGC
40905704 CGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
65 CGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
40905767 AAAGTGTATATATAGATGTGA
130 AAAGTG--TATAT--ATGTGA
* * *
40905788 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATAT-ATGTGA-CAGGGCTGAGTGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAATGTGATAAGGCCT-AATGGC
* * *
40905849 CAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
65 CGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
40905886 TCCCGAAGGG
Statistics
Matches: 373, Mismatches: 12, Indels: 24
0.91 0.03 0.06
Matches are distributed among these distances:
144 4 0.01
145 86 0.23
146 1 0.00
147 92 0.25
149 190 0.51
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (146 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAATGTGATAAGGCCTAATGGCC
GATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGA
AAGTGTATATATGTGA
Found at i:40906060 original size:37 final size:37
Alignment explanation
Indices: 40906004--40906082 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40905994 CCGAGCTCTA
* * *
40906004 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40906041 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40906078 AAGAC
1 AAGAC
40906083 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40914319 original size:28 final size:29
Alignment explanation
Indices: 40914263--40914342 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 29
40914253 GAACACGATA
40914263 GAAAATGGAAG-TGTTTGTGGCAATATAT
1 GAAAATGGAAGCTGTTTGTGGCAATATAT
* *
40914291 GAAAATGGAAGCT-TTCT-TGGTAATCTAT
1 GAAAATGGAAGCTGTT-TGTGGCAATATAT
* *
40914319 GAAAATAGAAGC-CTTTGTGGCAAT
1 GAAAATGGAAGCTGTTTGTGGCAAT
40914343 CTAAGGAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.02
28 41 0.93
29 2 0.05
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.31
Consensus pattern (29 bp):
GAAAATGGAAGCTGTTTGTGGCAATATAT
Found at i:40914528 original size:27 final size:27
Alignment explanation
Indices: 40914480--40914543 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 27
40914470 CATCTCCAAT
* **
40914480 GAACTCTAAACGGATAGCATGTATGGC
1 GAACTCTGAACGGATAAAATGTATGGC
* *
40914507 GAACTCTGAAGGGATAAAATGTGTGGC
1 GAACTCTGAACGGATAAAATGTATGGC
* *
40914534 AAACTTTGAA
1 GAACTCTGAA
40914544 ATAATGGTAG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.27, T:0.23
Consensus pattern (27 bp):
GAACTCTGAACGGATAAAATGTATGGC
Found at i:40916537 original size:26 final size:25
Alignment explanation
Indices: 40916501--40916556 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 25
40916491 ATTACATGTT
40916501 AGTTATTTAAATACATGATATCATCC
1 AGTTATTTAAATACATGAT-TCATCC
40916527 AGTTATTTAAATACATGATTCATCC
1 AGTTATTTAAATACATGATTCATCC
40916552 A-TTAT
1 AGTTAT
40916557 CTCAATGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
24 4 0.13
25 7 0.23
26 19 0.63
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (25 bp):
AGTTATTTAAATACATGATTCATCC
Found at i:40916890 original size:45 final size:47
Alignment explanation
Indices: 40916826--40916941 Score: 123
Period size: 46 Copynumber: 2.4 Consensus size: 47
40916816 TAGCTGATAG
*
40916826 ATAGTAAGCTC-TATTGAGCTGA-AAC-GATAAGCTCTAACGAGGTGA-
1 ATAGTAAGCTCATA-CGAGCTGAGAACAG-TAAGCTCTAACGAGGTGAT
* * *
40916871 ATAGTAAGCTCATACGAGCTAAGAACAGTAAGCTCTTACGAGTTGAT
1 ATAGTAAGCTCATACGAGCTGAGAACAGTAAGCTCTAACGAGGTGAT
40916918 ATATCGGTAAGCTCATACGAGCTG
1 ATA---GTAAGCTCATACGAGCTG
40916942 CGGTGAGTTC
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
45 17 0.29
46 21 0.36
47 4 0.07
50 17 0.29
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.25
Consensus pattern (47 bp):
ATAGTAAGCTCATACGAGCTGAGAACAGTAAGCTCTAACGAGGTGAT
Found at i:40916903 original size:24 final size:26
Alignment explanation
Indices: 40916873--40916941 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
40916863 CGAGGTGAAT
40916873 AGTAAGCTCATACGAGCT-A-AGAAC
1 AGTAAGCTCATACGAGCTGATAGAAC
* * * *
40916897 AGTAAGCTCTTACGAGTTGATATATC
1 AGTAAGCTCATACGAGCTGATAGAAC
*
40916923 GGTAAGCTCATACGAGCTG
1 AGTAAGCTCATACGAGCTG
40916942 CGGTGAGTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 16 0.44
25 1 0.03
26 19 0.53
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (26 bp):
AGTAAGCTCATACGAGCTGATAGAAC
Found at i:40923475 original size:18 final size:18
Alignment explanation
Indices: 40923452--40923487 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40923442 TTCCTGGGTG
40923452 ATAGTCGATTATCAACTC
1 ATAGTCGATTATCAACTC
**
40923470 ATAGTCTTTTATCAACTC
1 ATAGTCGATTATCAACTC
40923488 TAACCATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
ATAGTCGATTATCAACTC
Found at i:40942908 original size:13 final size:13
Alignment explanation
Indices: 40942890--40942915 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40942880 TCGACAAGGA
40942890 CACGCCCGTGTGC
1 CACGCCCGTGTGC
40942903 CACGCCCGTGTGC
1 CACGCCCGTGTGC
40942916 GATTGCTTCA
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:0.08, C:0.46, G:0.31, T:0.15
Consensus pattern (13 bp):
CACGCCCGTGTGC
Found at i:40950334 original size:23 final size:23
Alignment explanation
Indices: 40950252--40950338 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
40950242 CCTGATCAGT
*
40950252 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
40950274 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* *
40950294 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
40950317 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
40950339 TCGATAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
20 1 0.02
21 34 0.62
22 1 0.02
23 19 0.35
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:40950735 original size:15 final size:15
Alignment explanation
Indices: 40950715--40950766 Score: 86
Period size: 15 Copynumber: 3.5 Consensus size: 15
40950705 ATATTATATG
40950715 ATTCAATCAATATAA
1 ATTCAATCAATATAA
*
40950730 ATTCAATCAAAATAA
1 ATTCAATCAATATAA
*
40950745 TTTCAATCAATATAA
1 ATTCAATCAATATAA
40950760 ATTCAAT
1 ATTCAAT
40950767 AAATTCATCG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTCAATCAATATAA
Found at i:40956543 original size:23 final size:22
Alignment explanation
Indices: 40956482--40956543 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
40956472 CCTGATCAAT
*
40956482 ATACGGCACATAAAGTGCCTAA
1 ATACGACACATAAAGTGCCTAA
** *
40956504 A-ACGACACACGAGGTGCCTGAA
1 ATACGACACATAAAGTGCCT-AA
40956526 ATACGACACATAAAGTGC
1 ATACGACACATAAAGTGC
40956544 TTGATCGATA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 14 0.45
22 4 0.13
23 13 0.42
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTAA
Found at i:40956645 original size:54 final size:54
Alignment explanation
Indices: 40956563--40956670 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
40956553 AAAGCCGGTA
*
40956563 AATCCCGTACACTTCTAGATCCTATGGCATGCCAATTATATCCGACTCAGCCCG
1 AATCCCGTACACTTCTAGATCCTATGGCATGCCAATTATATCCGACTCAACCCG
40956617 AATCCCGTACACTTCTAGATCCTATGGCATGCCAATTATATCCGACTCAACCCG
1 AATCCCGTACACTTCTAGATCCTATGGCATGCCAATTATATCCGACTCAACCCG
40956671 GCTAGTTAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.26
Consensus pattern (54 bp):
AATCCCGTACACTTCTAGATCCTATGGCATGCCAATTATATCCGACTCAACCCG
Found at i:40956997 original size:15 final size:15
Alignment explanation
Indices: 40956972--40957029 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
40956962 TCATATATAT
40956972 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
40956988 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
40957003 AATAATTTCAATCAA
1 TATAAATTCAATCAA
40957018 TATAAATTCAAT
1 TATAAATTCAAT
40957030 AAACTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:40959623 original size:3 final size:3
Alignment explanation
Indices: 40959578--40959831 Score: 85
Period size: 3 Copynumber: 87.3 Consensus size: 3
40959568 GATTAAGTTT
* * *
40959578 TTA TTA TATA TTG TTA TT- TT- TTA -TA TTA TTA CTA TTA TCA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
40959621 TTA TT- TTA -TA TTA TTA TTA TTA TGTA -TA TTTA GTA TTA TTT TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA
* * * * * *
40959665 TTA ATA TTA -CA TT- TT- TTA CTA TCA -TA TTA CTA TTA TCT- TTG
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* * * * **
40959706 TTA CT- TTC TCTA TTA ATA TTTA TTA CTCTA TTT TTA ACA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA -TTA TTA -T-TA TTA TTA TTA TTA TTA TTA
* * * *
40959754 -TA TTA -TA TT- TGT- TTC TT- TT- TTA TATC TTA TTA TTA TTG CTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
*
40959795 TTA TTA TTA TTA TTA TTA TTA TTA GTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40959832 ATACACTATT
Statistics
Matches: 187, Mismatches: 40, Indels: 48
0.68 0.15 0.17
Matches are distributed among these distances:
2 30 0.16
3 139 0.74
4 16 0.09
5 2 0.01
ACGTcount: A:0.28, C:0.06, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:40959630 original size:28 final size:27
Alignment explanation
Indices: 40959591--40959643 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
40959581 TTATATATTG
40959591 TTATTTTTTATATTATTACTATTATCA
1 TTATTTTTTATATTATTACTATTATCA
*
40959618 TTATTATTTTATATTATTATTATTAT
1 TTATT-TTTTATATTATTACTATTAT
40959644 GTATATTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (27 bp):
TTATTTTTTATATTATTACTATTATCA
Found at i:40959650 original size:25 final size:24
Alignment explanation
Indices: 40959578--40959660 Score: 69
Period size: 25 Copynumber: 3.2 Consensus size: 24
40959568 GATTAAGTTT
* *
40959578 TTATTATATATTGTTATTTTTTATA
1 TTATTAT-TATTATTATATTTTATA
*
40959603 TTATTACTATTATCATTATTATTTTATA
1 TTA-T--TATTATTATTA-TATTTTATA
40959631 TTATTATTATTATGTATA-TTTAGTA
1 TTATTATTATTAT-TATATTTTA-TA
40959656 TTATT
1 TTATT
40959661 TTTTTTAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
24 4 0.08
25 20 0.42
26 3 0.06
27 7 0.15
28 14 0.29
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (24 bp):
TTATTATTATTATTATATTTTATA
Found at i:40959650 original size:28 final size:27
Alignment explanation
Indices: 40959578--40959651 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
40959568 GATTAAGTTT
40959578 TTATTATATATTGT-TATTTTTTATATTA
1 TTATTAT-TA-TGTATATTTTTTATATTA
* *
40959606 TTACTATTAT-CATTATTATTTTATATTA
1 TTATTATTATGTA-TATT-TTTTATATTA
40959634 TTATTATTATGTATATTT
1 TTATTATTATGTATATTT
40959652 AGTATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
26 1 0.03
27 7 0.18
28 29 0.76
29 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (27 bp):
TTATTATTATGTATATTTTTTATATTA
Found at i:40959657 original size:19 final size:19
Alignment explanation
Indices: 40959617--40959660 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
40959607 TACTATTATC
* *
40959617 ATTATTATTTTATATTATT
1 ATTATTATTATATATTAGT
40959636 ATTATTATGTATAT-TTAGT
1 ATTATTAT-TATATATTAGT
40959655 ATTATT
1 ATTATT
40959661 TTTTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (19 bp):
ATTATTATTATATATTAGT
Found at i:40960826 original size:9 final size:9
Alignment explanation
Indices: 40960812--40960837 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40960802 ATATATCTTT
40960812 TATTATTAC
1 TATTATTAC
40960821 TATTATTAC
1 TATTATTAC
40960830 TATTATTA
1 TATTATTA
40960838 TTAGTATATG
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:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (9 bp):
TATTATTAC
Found at i:40961257 original size:26 final size:26
Alignment explanation
Indices: 40961228--40961335 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
40961218 TGGTACAAAT
40961228 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
40961254 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40961280 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
40961306 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40961332 TGAT
1 TGAT
40961336 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40965182 original size:28 final size:27
Alignment explanation
Indices: 40965132--40965245 Score: 79
Period size: 28 Copynumber: 3.9 Consensus size: 27
40965122 CTATTCAGAA
*
40965132 ATCAGTGTTAA-CTGGGCCTTAGCCCAT
1 ATCAGTATTAATCTGGGCC-TAGCCCAT
40965159 ATCAGTATTAATCTGGGCCATAGCCC-T
1 ATCAGTATTAATCTGGGCC-TAGCCCAT
* *
40965186 ATTACAATATCAGAGCATACTGGGCCTAGCCCAT
1 A-T-CAGTAT--TA--AT-CTGGGCCTAGCCCAT
* *
40965220 ATCAGTATCAGTCTGGGCCGTAGCCC
1 ATCAGTATTAATCTGGGCC-TAGCCC
40965246 TATTACAAGT
Statistics
Matches: 70, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
27 19 0.27
28 21 0.30
29 5 0.07
30 1 0.01
31 1 0.01
32 5 0.07
33 9 0.13
34 9 0.13
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (27 bp):
ATCAGTATTAATCTGGGCCTAGCCCAT
Found at i:40965187 original size:62 final size:60
Alignment explanation
Indices: 40965109--40965253 Score: 177
Period size: 61 Copynumber: 2.4 Consensus size: 60
40965099 TCAAGCTTTA
* * *
40965109 CTGGGCCTAAGCCCTATT-CAGAAATCAGTG-TTAACTGGGCCTTAGCCCATATCAGTATTAAT
1 CTGGGCCT-AGCCCTATTACA-AAATCAGAGCAT-ACTGGGCC-TAGCCCATATCAGTATCAAT
* *
40965171 CTGGGCCATAGCCCTATTACAATATCAGAGCATACTGGGCCTAGCCCATATCAGTATCAGT
1 CTGGGCC-TAGCCCTATTACAAAATCAGAGCATACTGGGCCTAGCCCATATCAGTATCAAT
40965232 CTGGGCCGTAGCCCTATTACAA
1 CTGGGCC-TAGCCCTATTACAA
40965254 GTCGAGATAT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
61 39 0.53
62 31 0.42
63 4 0.05
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.26
Consensus pattern (60 bp):
CTGGGCCTAGCCCTATTACAAAATCAGAGCATACTGGGCCTAGCCCATATCAGTATCAAT
Found at i:40965317 original size:19 final size:20
Alignment explanation
Indices: 40965274--40965319 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
40965264 ATTGGGTCTT
40965274 GCCCATATTAACACAGTTGG
1 GCCCATATTAACACAGTTGG
* *
40965294 GCCCATTTTAATACAGTT-G
1 GCCCATATTAACACAGTTGG
40965313 GCCCATA
1 GCCCATA
40965320 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (20 bp):
GCCCATATTAACACAGTTGG
Found at i:40966697 original size:27 final size:27
Alignment explanation
Indices: 40966659--40966714 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
40966649 GTCGATCTCA
*
40966659 AAAATAACCGTAGATATGAATGGCCCC
1 AAAATAACCGTAGATATGAATAGCCCC
*
40966686 AAAATAATCGTAGATATGAATAGCCCC
1 AAAATAACCGTAGATATGAATAGCCCC
40966713 AA
1 AA
40966715 CCTAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.20
Consensus pattern (27 bp):
AAAATAACCGTAGATATGAATAGCCCC
Found at i:40968442 original size:12 final size:12
Alignment explanation
Indices: 40968427--40968538 Score: 51
Period size: 12 Copynumber: 9.3 Consensus size: 12
40968417 TTTTTACCCC
40968427 TATTATATTTAT
1 TATTATATTTAT
40968439 TATTA-A--TAT
1 TATTATATTTAT
40968448 TAGTGTATATCTTAT
1 TA-T-TATAT-TTAT
* *
40968463 TA-TACATGTA-
1 TATTATATTTAT
40968473 TATATATACTTT-T
1 TAT-TATA-TTTAT
40968486 TATATATAGTATTAT
1 TAT-TATA-T-TTAT
*
40968501 T-TT-TATATAT
1 TATTATATTTAT
*
40968511 CATTATATTTAT
1 TATTATATTTAT
*
40968523 TATTATACTTAT
1 TATTATATTTAT
40968535 TATT
1 TATT
40968539 TTCACTATTG
Statistics
Matches: 76, Mismatches: 10, Indels: 28
0.67 0.09 0.25
Matches are distributed among these distances:
9 5 0.07
10 6 0.08
11 8 0.11
12 35 0.46
13 12 0.16
14 3 0.04
15 7 0.09
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:40968505 original size:18 final size:18
Alignment explanation
Indices: 40968482--40968540 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 18
40968472 ATATATATAC
*
40968482 TTTTTATATATAGTATTA
1 TTTTTATATATATTATTA
40968500 TTTTTATATATCATTA-TA
1 TTTTTATATAT-ATTATTA
40968518 TTTATTAT-TATACTTATTA
1 TTT-TTATATATA-TTATTA
40968537 TTTT
1 TTTT
40968541 CACTATTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
17 1 0.03
18 23 0.64
19 12 0.33
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATATATATTATTA
Found at i:40975251 original size:14 final size:14
Alignment explanation
Indices: 40975234--40975260 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40975224 TAAATTCTTA
40975234 GAATTGCATTTCAG
1 GAATTGCATTTCAG
40975248 GAATTGCATTTCA
1 GAATTGCATTTCA
40975261 ACTTTCTATT
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:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (14 bp):
GAATTGCATTTCAG
Found at i:40975338 original size:13 final size:13
Alignment explanation
Indices: 40975320--40975344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40975310 TACAAATTAG
40975320 TTTTTCTATTAAT
1 TTTTTCTATTAAT
40975333 TTTTTCTATTAA
1 TTTTTCTATTAA
40975345 ATGATGATGT
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTTCTATTAAT
Found at i:40976230 original size:24 final size:22
Alignment explanation
Indices: 40976177--40976253 Score: 61
Period size: 24 Copynumber: 3.4 Consensus size: 22
40976167 TAGCAGATTT
40976177 ATTTTTTAAAAATATATTT-TTA
1 ATTTTTTAAAAATAT-TTTATTA
40976199 ATAATTTTTAAAAATATTTTACTGTA
1 AT--TTTTTAAAAATATTTTA-T-TA
* *
40976225 ATTTTTAAGAAAATTTTTTATT-
1 ATTTTTTA-AAAATATTTTATTA
40976247 -TTTTTTA
1 ATTTTTTA
40976254 GAATTATGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
21 6 0.13
22 2 0.04
23 4 0.09
24 19 0.41
25 11 0.24
26 4 0.09
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (22 bp):
ATTTTTTAAAAATATTTTATTA
Found at i:40976737 original size:12 final size:12
Alignment explanation
Indices: 40976720--40976744 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40976710 GGATTAGAAC
40976720 TAAAATGATAAA
1 TAAAATGATAAA
40976732 TAAAATGATAAA
1 TAAAATGATAAA
40976744 T
1 T
40976745 TTTGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (12 bp):
TAAAATGATAAA
Found at i:40977410 original size:18 final size:19
Alignment explanation
Indices: 40977383--40977424 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
40977373 ATGTCTCTAA
*
40977383 AATAATAACAAAAT-TAAC
1 AATAACAACAAAATATAAC
40977401 AATAACAACAAAATAGTAAC
1 AATAACAACAAAATA-TAAC
40977421 AATA
1 AATA
40977425 TAATAGTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
20 8 0.38
ACGTcount: A:0.67, C:0.12, G:0.02, T:0.19
Consensus pattern (19 bp):
AATAACAACAAAATATAAC
Found at i:40981446 original size:10 final size:10
Alignment explanation
Indices: 40981431--40981463 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
40981421 ATATATGTAT
40981431 AATAATATAA
1 AATAATATAA
40981441 AATAATA-AA
1 AATAATATAA
40981450 AATATATATAA
1 AATA-ATATAA
40981461 AAT
1 AAT
40981464 GTATAATACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.29
10 10 0.48
11 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
AATAATATAA
Found at i:40981484 original size:30 final size:29
Alignment explanation
Indices: 40981417--40981486 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 29
40981407 AGTTAAGGAT
40981417 AATAATATATGTATAATAATATAAAATAATA
1 AATAATATA--TATAATAATATAAAATAATA
* *
40981448 AA-AATATATATAA-AATGTATAATACATAA
1 AATAATATATATAATAATATAAAATA-AT-A
40981477 AATAATATAT
1 AATAATATAT
40981487 GAAAAGTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
27 9 0.26
28 7 0.21
29 3 0.09
30 13 0.38
31 2 0.06
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.34
Consensus pattern (29 bp):
AATAATATATATAATAATATAAAATAATA
Found at i:40981685 original size:15 final size:15
Alignment explanation
Indices: 40981668--40981724 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
40981658 AATAATCTAA
40981668 AAAGAAATAAAGTTA-
1 AAAGAAATAAA-TTAG
40981683 AAA-AAATAAAATTAG
1 AAAGAAAT-AAATTAG
* *
40981698 AAAGGATTAAATTAG
1 AAAGAAATAAATTAG
40981713 AATAGAAATAAA
1 AA-AGAAATAAA
40981725 AATGCAGATG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
14 7 0.21
15 18 0.53
16 9 0.26
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (15 bp):
AAAGAAATAAATTAG
Found at i:40982664 original size:13 final size:13
Alignment explanation
Indices: 40982646--40982670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40982636 CTAGATTCGA
40982646 GGCCTGGAATCAT
1 GGCCTGGAATCAT
40982659 GGCCTGGAATCA
1 GGCCTGGAATCA
40982671 CTGCGAGACA
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:0.24, C:0.24, G:0.32, T:0.20
Consensus pattern (13 bp):
GGCCTGGAATCAT
Found at i:40984008 original size:125 final size:125
Alignment explanation
Indices: 40983786--40984039 Score: 508
Period size: 125 Copynumber: 2.0 Consensus size: 125
40983776 TATATTCCAA
40983786 CAAAATCGAAGCTTATATACCTAACAATTTCTAACTTATCACAAACCTTTGATGGTGAACATGTA
1 CAAAATCGAAGCTTATATACCTAACAATTTCTAACTTATCACAAACCTTTGATGGTGAACATGTA
40983851 ATGTTTTATCTTCTAAAGATATCATAAGAATTATTTGATTGTTTTTCAATGATTTATATT
66 ATGTTTTATCTTCTAAAGATATCATAAGAATTATTTGATTGTTTTTCAATGATTTATATT
40983911 CAAAATCGAAGCTTATATACCTAACAATTTCTAACTTATCACAAACCTTTGATGGTGAACATGTA
1 CAAAATCGAAGCTTATATACCTAACAATTTCTAACTTATCACAAACCTTTGATGGTGAACATGTA
40983976 ATGTTTTATCTTCTAAAGATATCATAAGAATTATTTGATTGTTTTTCAATGATTTATATT
66 ATGTTTTATCTTCTAAAGATATCATAAGAATTATTTGATTGTTTTTCAATGATTTATATT
40984036 CAAA
1 CAAA
40984040 TTTCTCAAAT
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
125 129 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (125 bp):
CAAAATCGAAGCTTATATACCTAACAATTTCTAACTTATCACAAACCTTTGATGGTGAACATGTA
ATGTTTTATCTTCTAAAGATATCATAAGAATTATTTGATTGTTTTTCAATGATTTATATT
Found at i:41010967 original size:35 final size:35
Alignment explanation
Indices: 41010902--41010968 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
41010892 GGCAAAGGCT
* *
41010902 TTAGATGAGTAGCCTATCCCAGTTCGTGCTTTGCC
1 TTAGATGAGTAGCCTATCCCAGTGCATGCTTTGCC
41010937 TTAGATGAGTAGCCTATCCC-GATGCATGCTTT
1 TTAGATGAGTAGCCTATCCCAG-TGCATGCTTT
41010969 CATGATTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 1 0.03
35 28 0.97
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.34
Consensus pattern (35 bp):
TTAGATGAGTAGCCTATCCCAGTGCATGCTTTGCC
Found at i:41019918 original size:3 final size:3
Alignment explanation
Indices: 41019912--41019975 Score: 94
Period size: 3 Copynumber: 21.3 Consensus size: 3
41019902 AAGGTCTTAA
* *
41019912 AAT AAT AACT -AT AAC AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41019957 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
41019976 TTTCTAAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
2 1 0.02
3 54 0.96
4 1 0.02
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:41022422 original size:29 final size:28
Alignment explanation
Indices: 41022380--41022437 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 28
41022370 TTTAATATAA
41022380 ATATAAATATATAATTATTATT-TAACAT
1 ATATAAATATATAA-TATTATTATAACAT
* *
41022408 ATATAATTAATATAATATTTTTATAACAT
1 ATATAAAT-ATATAATATTATTATAACAT
41022437 A
1 A
41022438 ATATGTTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 13 0.50
29 13 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
ATATAAATATATAATATTATTATAACAT
Found at i:41025642 original size:27 final size:24
Alignment explanation
Indices: 41025612--41025672 Score: 61
Period size: 29 Copynumber: 2.4 Consensus size: 24
41025602 AAAACATTTT
41025612 AAAAATTAAAATTATTTAAAATATATAA
1 AAAAATTAAAATT-TTT-AAAT-T-TAA
*
41025640 AAAGAATTAATATTTTTAAATTT-A
1 AAA-AATTAAAATTTTTAAATTTAA
41025664 AAAAATTAA
1 AAAAATTAA
41025673 TTAAATACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
23 6 0.19
24 4 0.13
25 1 0.03
26 1 0.03
27 4 0.13
28 6 0.19
29 9 0.29
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AAAAATTAAAATTTTTAAATTTAA
Found at i:41027384 original size:20 final size:21
Alignment explanation
Indices: 41027349--41027387 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41027339 ATCATTTTCA
*
41027349 AATCGAGTTTTGAAAAATGGG
1 AATCGAGTTTTAAAAAATGGG
41027370 AATCGA-TTTTAAAAAATG
1 AATCGAGTTTTAAAAAATG
41027388 AAAACGGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.31
Consensus pattern (21 bp):
AATCGAGTTTTAAAAAATGGG
Found at i:41038461 original size:15 final size:15
Alignment explanation
Indices: 41038420--41038469 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
41038410 ATAACTTTGA
*
41038420 ATGCAAATG-ATGTG
1 ATGCAAATGCATGAG
41038434 ATG-AAATGCCATGAG
1 ATGCAAATG-CATGAG
41038449 ATGCAAATGCATGA-
1 ATGCAAATGCATGAG
41038463 ATGCAAA
1 ATGCAAA
41038470 AAGAATATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 12 0.38
16 5 0.16
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.22
Consensus pattern (15 bp):
ATGCAAATGCATGAG
Found at i:41041705 original size:30 final size:30
Alignment explanation
Indices: 41041667--41041737 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
41041657 AAACGTACAA
* *
41041667 ACATACAAAGTAA-TAATTAAATAATACATG
1 ACATACAAA-AAAGTAATAAAATAATACATG
* *
41041697 ATATACAAAAAAGTAATAAAATAATGCATG
1 ACATACAAAAAAGTAATAAAATAATACATG
41041727 ACATACAAAAA
1 ACATACAAAAA
41041738 GAATAATACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 2 0.06
30 33 0.94
ACGTcount: A:0.61, C:0.10, G:0.07, T:0.23
Consensus pattern (30 bp):
ACATACAAAAAAGTAATAAAATAATACATG
Found at i:41041712 original size:33 final size:31
Alignment explanation
Indices: 41041673--41041745 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
41041663 ACAAACATAC
*
41041673 AAAGTAATAATTAAATAATACATGATATACAAA
1 AAAGTAATAA-TAAATAATACATGACATAC-AA
*
41041706 AAAGTAAT-A-AAATAATGCATGACATACAA
1 AAAGTAATAATAAATAATACATGACATACAA
41041735 AAAG-AATAATA
1 AAAGTAATAATA
41041746 CAATGTCAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
28 3 0.08
29 7 0.19
30 17 0.47
32 1 0.03
33 8 0.22
ACGTcount: A:0.62, C:0.07, G:0.08, T:0.23
Consensus pattern (31 bp):
AAAGTAATAATAAATAATACATGACATACAA
Found at i:41041750 original size:28 final size:30
Alignment explanation
Indices: 41041667--41041750 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 30
41041657 AAACGTACAA
* * * *
41041667 ACATACAAAGTAA-TAATTAAATAATACATG
1 ACATACAAA-AAAGTAATAAAACAATGCATG
* *
41041697 ATATACAAAAAAGTAATAAAATAATGCATG
1 ACATACAAAAAAGTAATAAAACAATGCATG
*
41041727 ACATAC-AAAAAG-AATAATACAATG
1 ACATACAAAAAAGTAATAAAACAATG
41041751 TCAATGTACA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 10 0.22
29 8 0.17
30 28 0.61
ACGTcount: A:0.60, C:0.10, G:0.08, T:0.23
Consensus pattern (30 bp):
ACATACAAAAAAGTAATAAAACAATGCATG
Found at i:41042135 original size:8 final size:8
Alignment explanation
Indices: 41042122--41042146 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
41042112 AATATAATTT
41042122 AATTTTAA
1 AATTTTAA
41042130 AATTTTAA
1 AATTTTAA
41042138 AATTTTAA
1 AATTTTAA
41042146 A
1 A
41042147 TAATATAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:41042377 original size:21 final size:21
Alignment explanation
Indices: 41042333--41042378 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
41042323 TGTAAAAAAC
* *
41042333 AATATATATAAATAGTTAATA
1 AATATATATAAACAGGTAATA
41042354 AATATATATAATACAGGTAA-A
1 AATATATATAA-ACAGGTAATA
41042375 AATA
1 AATA
41042379 GAATAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (21 bp):
AATATATATAAACAGGTAATA
Found at i:41047137 original size:71 final size:71
Alignment explanation
Indices: 41047022--41047309 Score: 416
Period size: 71 Copynumber: 4.1 Consensus size: 71
41047012 GTAACAAATT
* * *
41047022 TTTGCGCCCAGCGCTAGTC-GGTAAACTGACAGTAGATGTGCCCTGCACTAGTCAAATAAATTGA
1 TTTGCGCCCAGCGCTAGTCGGGTAAACCGACAATAGATGTGCCCTGCACTAGTCAAATAAATCGA
41047086 TAAAGA
66 TAAAGA
* * * *
41047092 TTTGCGCCCAGCGCTAGTCGGGTAAACCGATAGTAGATGTGCCCTGCACTAATCAAATAAATGGA
1 TTTGCGCCCAGCGCTAGTCGGGTAAACCGACAATAGATGTGCCCTGCACTAGTCAAATAAATCGA
41047157 TAAAGA
66 TAAAGA
* *
41047163 TTTGCGCCCAGTGCTAGTCGGGTAAACCGACAATAGATGTGCCTTGCACTAGTCAAATAAATCGA
1 TTTGCGCCCAGCGCTAGTCGGGTAAACCGACAATAGATGTGCCCTGCACTAGTCAAATAAATCGA
41047228 TAAAGA
66 TAAAGA
* * ** * * *
41047234 TTTGTGCTCAGCGCTAGTCAAGTAAACCGACAATAGATGCGCCCTACACTAGTCGAATAAATCGA
1 TTTGCGCCCAGCGCTAGTCGGGTAAACCGACAATAGATGTGCCCTGCACTAGTCAAATAAATCGA
*
41047299 CAAAGA
66 TAAAGA
41047305 TTTGC
1 TTTGC
41047310 ATCTAAAGCT
Statistics
Matches: 196, Mismatches: 21, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
70 19 0.10
71 177 0.90
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (71 bp):
TTTGCGCCCAGCGCTAGTCGGGTAAACCGACAATAGATGTGCCCTGCACTAGTCAAATAAATCGA
TAAAGA
Found at i:41047251 original size:36 final size:36
Alignment explanation
Indices: 41047058--41047308 Score: 138
Period size: 36 Copynumber: 7.1 Consensus size: 36
41047048 TGACAGTAGA
* * *
41047058 TGTGCCCTGCACTAGTCAAATAAATTGATAAAGATT
1 TGTGCCCAGCGCTAGTCAAATAAATCGATAAAGATT
* *** * *
41047094 TGCGCCCAGCGCTAGTCGGGTAAACCGATAGTAGA--
1 TGTGCCCAGCGCTAGTCAAATAAATCGATA-AAGATT
* * * *
41047129 TGTGCCCTGCACTAATCAAATAAATGGATAAAGATT
1 TGTGCCCAGCGCTAGTCAAATAAATCGATAAAGATT
* * *** * *
41047165 TGCGCCCAGTGCTAGTCGGGTAAACCGACAATAGA--
1 TGTGCCCAGCGCTAGTCAAATAAATCGATAA-AGATT
** *
41047200 TGTGCCTTGCACTAGTCAAATAAATCGATAAAGATT
1 TGTGCCCAGCGCTAGTCAAATAAATCGATAAAGATT
* * * *
41047236 TGTGCTCAGCGCTAGTCAAGTAAACCGACAATAGA--
1 TGTGCCCAGCGCTAGTCAAATAAATCGATAA-AGATT
* * * *
41047271 TGCGCCCTA-CACTAGTCGAATAAATCGACAAAGATT
1 TGTGCCC-AGCGCTAGTCAAATAAATCGATAAAGATT
41047307 TG
1 TG
41047309 CATCTAAAGC
Statistics
Matches: 152, Mismatches: 53, Indels: 20
0.68 0.24 0.09
Matches are distributed among these distances:
34 9 0.06
35 65 0.43
36 69 0.45
37 9 0.06
ACGTcount: A:0.33, C:0.21, G:0.22, T:0.24
Consensus pattern (36 bp):
TGTGCCCAGCGCTAGTCAAATAAATCGATAAAGATT
Found at i:41047300 original size:35 final size:34
Alignment explanation
Indices: 41047176--41047331 Score: 100
Period size: 35 Copynumber: 4.4 Consensus size: 34
41047166 GCGCCCAGTG
** * *
41047176 CTAGTCGGGTAAACCGACAATAGATGTGCCTTGCA
1 CTAGTCGAATAAACCGACAA-AGATGTGCCCTACA
* * * * *
41047211 CTAGTCAAATAAATCGATAAAGATTTGTGCTC-AGCG
1 CTAGTCGAATAAACCGACAAAGA--TGTGCCCTA-CA
*
41047247 CTAGTC-AAGTAAACCGACAATAGATGCGCCCTACA
1 CTAGTCGAA-TAAACCGACAA-AGATGTGCCCTACA
* * * *
41047282 CTAGTCGAATAAATCGACAAAGATTTGCATCTAAA
1 CTAGTCGAATAAACCGACAAAGATGTGC-CCTACA
41047317 GCTAGTCGAATAAAC
1 -CTAGTCGAATAAAC
41047332 TGAAAATATT
Statistics
Matches: 92, Mismatches: 20, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
34 9 0.10
35 43 0.47
36 37 0.40
37 3 0.03
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (34 bp):
CTAGTCGAATAAACCGACAAAGATGTGCCCTACA
Found at i:41047469 original size:76 final size:75
Alignment explanation
Indices: 41047242--41047513 Score: 227
Period size: 76 Copynumber: 3.7 Consensus size: 75
41047232 GATTTGTGCT
* * * * * *
41047242 CAGCGCTAGTCAAGTAAACCGACA-A-TAGA--TGCGCCCTACACTAG-TCGAATAAATCGACAA
1 CAGCGCTAGTCAAATAAACCGACATATTAAATGTGTGCCCAACACTAGCT-GAATTAACCGACAA
* *
41047302 AGATTTGCATC
65 AGATTTGAACC
* ** * * * * **
41047313 TAAAGCTAGTCGAATAAACTGAAAATATTAAATGTGTTCCCAACACTAGCCAAATTAACCGACAA
1 CAGCGCTAGTCAAATAAACCG-ACATATTAAATGTGTGCCCAACACTAGCTGAATTAACCGACAA
*
41047378 AGATTT-ACACT
65 AGATTTGA-ACC
41047389 CAGCGCTAGTCAAATAAACCGACGATATTAAATGTGTGCCCAACACTAGCTGAATTAACCGACAA
1 CAGCGCTAGTCAAATAAACCGAC-ATATTAAATGTGTGCCCAACACTAGCTGAATTAACCGACAA
41047454 AGATTTGAACC
65 AGATTTGAACC
** * * * * *
41047465 CAGCGCTAAACAGATAAACCG--ATAGTAGATTTGTGCCCAGCACTAGCTG
1 CAGCGCTAGTCAAATAAACCGACATATTAAATGTGTGCCCAACACTAGCTG
41047514 GATAAATCGA
Statistics
Matches: 157, Mismatches: 35, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
71 15 0.10
72 2 0.01
73 25 0.16
74 3 0.02
75 1 0.01
76 110 0.70
77 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (75 bp):
CAGCGCTAGTCAAATAAACCGACATATTAAATGTGTGCCCAACACTAGCTGAATTAACCGACAAA
GATTTGAACC
Found at i:41048754 original size:3 final size:3
Alignment explanation
Indices: 41048746--41048774 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41048736 TACTTTAGTT
41048746 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
41048775 TTAATCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41052315 original size:26 final size:26
Alignment explanation
Indices: 41052285--41052366 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
41052275 TGAAATTCCC
41052285 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
41052311 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
41052337 ATCATGGAACATTTACCTAATCTATT
1 ATCATGGAACATTTACCTAACCCATT
41052363 ATCA
1 ATCA
41052367 ATTTGTATCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:41053805 original size:84 final size:84
Alignment explanation
Indices: 41053708--41053911 Score: 408
Period size: 84 Copynumber: 2.4 Consensus size: 84
41053698 TATTTTTTTA
41053708 AATTTTTCATACATTATTAATTTCATGCTATAATTATTCTCAAATCTACTTGTATATACATGTTT
1 AATTTTTCATACATTATTAATTTCATGCTATAATTATTCTCAAATCTACTTGTATATACATGTTT
41053773 TATGAATTTATTATGCTAT
66 TATGAATTTATTATGCTAT
41053792 AATTTTTCATACATTATTAATTTCATGCTATAATTATTCTCAAATCTACTTGTATATACATGTTT
1 AATTTTTCATACATTATTAATTTCATGCTATAATTATTCTCAAATCTACTTGTATATACATGTTT
41053857 TATGAATTTATTATGCTAT
66 TATGAATTTATTATGCTAT
41053876 AATTTTTCATACATTATTAATTTCATGCTATAATTA
1 AATTTTTCATACATTATTAATTTCATGCTATAATTA
41053912 GGAATTTGTG
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 120 1.00
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.50
Consensus pattern (84 bp):
AATTTTTCATACATTATTAATTTCATGCTATAATTATTCTCAAATCTACTTGTATATACATGTTT
TATGAATTTATTATGCTAT
Found at i:41055498 original size:16 final size:18
Alignment explanation
Indices: 41055462--41055499 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
41055452 CTGTCTTTTC
41055462 AAATAAAAATAAATATTA
1 AAATAAAAATAAATATTA
*
41055480 AAAT-AAAAT-AATCTTA
1 AAATAAAAATAAATATTA
41055496 AAAT
1 AAAT
41055500 CTAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 5 0.26
18 4 0.21
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATAAAAATAAATATTA
Found at i:41059231 original size:18 final size:18
Alignment explanation
Indices: 41059210--41059245 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41059200 CAAAGTACAT
*
41059210 AACTAATTTTTTGGCTCC
1 AACTAATTTTGTGGCTCC
41059228 AACTAATTTTGTGGCTCC
1 AACTAATTTTGTGGCTCC
41059246 TCTATTGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (18 bp):
AACTAATTTTGTGGCTCC
Found at i:41059312 original size:16 final size:16
Alignment explanation
Indices: 41059291--41059324 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41059281 TTAATTGTTT
41059291 CATTGAAGAAATATTA
1 CATTGAAGAAATATTA
*
41059307 CATTGAAGAACTATTA
1 CATTGAAGAAATATTA
41059323 CA
1 CA
41059325 ACACTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (16 bp):
CATTGAAGAAATATTA
Found at i:41061072 original size:40 final size:40
Alignment explanation
Indices: 41061009--41061086 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
41060999 TGTGGTACCT
* * *
41061009 TATGGTGTGTAGGGTTGGATGGGTCGATTATATCCCCATA
1 TATGGTGTGCAGGGATGGATGGGTCAATTATATCCCCATA
* *
41061049 TATGGTGTGCAGGGATGGGTGGGTCAATTTTATCCCCA
1 TATGGTGTGCAGGGATGGATGGGTCAATTATATCCCCA
41061087 CATGGTGTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.33
Consensus pattern (40 bp):
TATGGTGTGCAGGGATGGATGGGTCAATTATATCCCCATA
Found at i:41065428 original size:31 final size:31
Alignment explanation
Indices: 41065392--41065473 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
41065382 CAAGTTAAGC
**
41065392 CCTAAACTT-GACAATTGTTCTCACATTGGGA
1 CCTAAA-TTAGACAATTGTTCTCACACGGGGA
* *
41065423 CCTAAATTAGGCAATTGTTCTTACACGGGGA
1 CCTAAATTAGACAATTGTTCTCACACGGGGA
* * *
41065454 CCTAGATTAGGCAACTGTTC
1 CCTAAATTAGACAATTGTTC
41065474 CCGCTTTAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
30 2 0.05
31 42 0.95
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (31 bp):
CCTAAATTAGACAATTGTTCTCACACGGGGA
Found at i:41070169 original size:31 final size:31
Alignment explanation
Indices: 41070099--41070162 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
41070089 ATTTGATCCC
*
41070099 TGAACTATTCAAAATTTTTCATTTAAATCAT
1 TGAACTATTCAAAACTTTTCATTTAAATCAT
* *
41070130 TGAACTATTCAAAAACTTTT-ATTTTAGTCAT
1 TGAACTATTC-AAAACTTTTCATTTAAATCAT
41070161 TG
1 TG
41070163 GGCTATTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 21 0.72
32 8 0.28
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (31 bp):
TGAACTATTCAAAACTTTTCATTTAAATCAT
Found at i:41071481 original size:34 final size:30
Alignment explanation
Indices: 41071418--41071487 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 30
41071408 CAACATTTGG
41071418 AATTTAATTTTTTTTATTTTTATTATTAAA
1 AATTTAATTTTTTTTATTTTTATTATTAAA
41071448 AATTTAATTTTTATTTTATTTTT-TTAAATTTAAA
1 AATTTAA-TTTT-TTTTATTTTTATT--A-TTAAA
41071482 AATTTA
1 AATTTA
41071488 GGTTCAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
30 7 0.20
31 6 0.17
32 10 0.29
33 1 0.03
34 11 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (30 bp):
AATTTAATTTTTTTTATTTTTATTATTAAA
Found at i:41071523 original size:14 final size:15
Alignment explanation
Indices: 41071497--41071525 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41071487 AGGTTCAATT
41071497 ATTATTATTATTAAA
1 ATTATTATTATTAAA
41071512 ATTATT-TTATTAAA
1 ATTATTATTATTAAA
41071526 TTCACTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATTATTATTAAA
Found at i:41072351 original size:20 final size:19
Alignment explanation
Indices: 41072326--41072370 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
41072316 TTTTAATAAA
* *
41072326 TTTTAAAATTTTCAGATATT
1 TTTTAAAAATTT-AAATATT
41072346 TTTTAAAAATTTAAATATT
1 TTTTAAAAATTTAAATATT
41072365 TTTTAA
1 TTTTAA
41072371 CTTTTTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTTAAATATT
Found at i:41076706 original size:15 final size:14
Alignment explanation
Indices: 41076660--41076726 Score: 89
Period size: 14 Copynumber: 4.7 Consensus size: 14
41076650 GTTTGCAGGT
* *
41076660 AAAATGTTTTCCGG
1 AAAATGATTTCTGG
*
41076674 AAAATGATTTCCGG
1 AAAATGATTTCTGG
*
41076688 AAAATAATTTCTTGG
1 AAAATGATTTC-TGG
41076703 AAAATGATTTCTGG
1 AAAATGATTTCTGG
41076717 AAAATGATTT
1 AAAATGATTT
41076727 ACTTTTCTGG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
14 36 0.75
15 12 0.25
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (14 bp):
AAAATGATTTCTGG
Found at i:41089924 original size:44 final size:44
Alignment explanation
Indices: 41089857--41090241 Score: 287
Period size: 44 Copynumber: 8.9 Consensus size: 44
41089847 AAAAAATTTC
* *
41089857 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCCAG
* * **
41089901 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCCAG
* * * * *
41089945 TA-ATCCTATCTCCTTGAGATTACAATGGAGCGGAT-TAA---A-
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCCAG
* * * *
41089984 AGATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATC-ACA-TCAG
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGA-AGCCAG
* * * * *
41090027 -G-TCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTCC--
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATC---GAA-GCCAG
* *
41090071 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCCAG
* *
41090115 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCCAG
** * * * *** *
41090158 CTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATCAAAATGAT
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATCGAAGCCAG
*
41090202 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAG
41090242 ACACTANNNN
Statistics
Matches: 268, Mismatches: 51, Indels: 44
0.74 0.14 0.12
Matches are distributed among these distances:
38 2 0.01
39 25 0.09
40 2 0.01
41 26 0.10
42 5 0.02
43 37 0.14
44 137 0.51
45 4 0.01
46 30 0.11
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATCGAAGCCAG
Found at i:41090168 original size:87 final size:87
Alignment explanation
Indices: 41089857--41090247 Score: 291
Period size: 87 Copynumber: 4.5 Consensus size: 87
41089847 AAAAAATTTC
* * * * ** *
41089857 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTG-AGAT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-CTATCCTATCTCCCTGAAG-T
* *
41089921 TACAGCGGAGCAGATCAAAGA-TAG
64 TACAGTGGAGCAGATCAAA-ACCAG
* * ** * * * * *
41089945 TA-ATCCTATCTCCTTGAGATTACAATGGAGCGGAT-TAA-A-A-GATCTTATCTCTCTGAAGTT
1 -AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTT
* * * *
41090005 ACAGTAGAGAAGATC-ACATCAG
65 ACAGTGGAGCAGATCAAAACCAG
* * * * * * * * *
41090027 -G-TCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGA-ATTCCAGATCTTATCTCCCTGAG
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA---C-TATCCTATCTCCCTGAA
** *
41090089 GTTACAGTGGAGCAGATTGAAGCCAG
62 GTTACAGTGGAGCAGATCAAAACCAG
41090115 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
* ** *
41090180 CAGTGGAGCGGATCAAAATGAT
66 CAGTGGAGCAGATCAAAACCAG
41090202 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
41090248 NNNNNNNNNN
Statistics
Matches: 241, Mismatches: 47, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
80 24 0.10
81 2 0.01
82 5 0.02
83 28 0.12
84 2 0.01
85 1 0.00
87 111 0.46
88 33 0.14
89 2 0.01
90 32 0.13
91 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
CAGTGGAGCAGATCAAAACCAG
Found at i:41091510 original size:527 final size:527
Alignment explanation
Indices: 41090512--41091560 Score: 2046
Period size: 527 Copynumber: 2.0 Consensus size: 527
41090502 TGTTTGAAAA
*
41090512 ACAATAGAAATAAAAAATAAAATGGGTCCTTAAAAAATGGCAGAACCATTCAATAATTTTTAAAG
1 ACAATAGAAATAAAAAATAAAATGGGTCCTTAAAAAAGGGCAGAACCATTCAATAATTTTTAAAG
*
41090577 TGGTGGGGCCCACGTGTTTTGCCCTTAAAGGGTCAATTTGTGCATCAGGTCCCCGTACATTTTCT
66 TGGTGGGGCCCACGTGTTTTGCCCTTAAAGGGTCAATTTGGGCATCAGGTCCCCGTACATTTTCT
*
41090642 TGTTGCCCAAATCTGCTTCACTTTTGTTTTTGAATTTCACCCAGCAATTTTGTGCAGTTTTTAAT
131 TGTTGCCCAAATCTGCTTCACTTTTGTTTTTGAATTTCACCCAACAATTTTGTGCAGTTTTTAAT
41090707 TTGGTCCATATTAAATGCTAGGTTTAGGAATTTGGGTAAATTACATTTTTAAACCCCCTTGTTCC
196 TTGGTCCATATTAAATGCTAGGTTTAGGAATTTGGGTAAATTACATTTTTAAACCCCCTTGTTCC
41090772 ACGCACGCTTCAATGAGGTCCTCCTTTCCCCTTTTATTTGTGTTTTACCCCCGAACTTCCGTTTT
261 ACGCACGCTTCAATGAGGTCCTCCTTTCCCCTTTTATTTGTGTTTTACCCCCGAACTTCCGTTTT
41090837 GATTCCAATTAAGCCCTATTTTGTTTATTTTAAACACTTTTATCACAAAATTAAATTTTTTGGGT
326 GATTCCAATTAAGCCCTATTTTGTTTATTTTAAACACTTTTATCACAAAATTAAATTTTTTGGGT
41090902 ACTATTATTATTAATCTATTATTGCTATTTTATTTATTTATTTTTTTAGTTATTTTCCTGTTATT
391 ACTATTATTATTAATCTATTATTGCTATTTTATTTATTTATTTTTTTAGTTATTTTCCTGTTATT
41090967 TACTGTATTATTTTTTTTTTGCTTCCACTATTATTTATTATACTTATTATATCATTTTCGTTATT
456 TACTGTATTATTTTTTTTTTGCTTCCACTATTATTTATTATACTTATTATATCATTTTCGTTATT
41091032 TTTTATC
521 TTTTATC
*
41091039 ACAATAGAAATAAAAAATAAAATGGGTCCTTAAAAAAGGGCAGAACCATTCAATAGTTTTTAAAG
1 ACAATAGAAATAAAAAATAAAATGGGTCCTTAAAAAAGGGCAGAACCATTCAATAATTTTTAAAG
*
41091104 TGGTGGGGCCCACGTGTTTTGCCCTTAAAGGGTCAATTTGGGCATCAGGTCCCTGTACATTTTCT
66 TGGTGGGGCCCACGTGTTTTGCCCTTAAAGGGTCAATTTGGGCATCAGGTCCCCGTACATTTTCT
41091169 TGTTGCCCAAATCTGCTTCACTTTTGTTTTTGAATTTCACCCAACAATTTTGTGCAGTTTTTAAT
131 TGTTGCCCAAATCTGCTTCACTTTTGTTTTTGAATTTCACCCAACAATTTTGTGCAGTTTTTAAT
41091234 TTGGTCCATATTAAATGCTAGGTTTAGGAATTTGGGTAAATTACATTTTTAAACCCCCTTGTTCC
196 TTGGTCCATATTAAATGCTAGGTTTAGGAATTTGGGTAAATTACATTTTTAAACCCCCTTGTTCC
41091299 ACGCACGCTTCAATGAGGTCCTCCTTTCCCCTTTTATTTGTGTTTT-CCCCCGAACTTCCGTTTT
261 ACGCACGCTTCAATGAGGTCCTCCTTTCCCCTTTTATTTGTGTTTTACCCCCGAACTTCCGTTTT
41091363 GATTCCAATTAAGCCCTATTTTGTTTATTTTAAACACTTTTATCACAAAATTAAATTTTTTGGGT
326 GATTCCAATTAAGCCCTATTTTGTTTATTTTAAACACTTTTATCACAAAATTAAATTTTTTGGGT
41091428 ACTATTATTATTAATCTATTATTGCTATTTTATTTATTTATTTTTTTAGTTATTTTCCTGTTATT
391 ACTATTATTATTAATCTATTATTGCTATTTTATTTATTTATTTTTTTAGTTATTTTCCTGTTATT
41091493 TACTGTATTATTTTTTTTTTGCTTCCACTATTATTTATTATACTTATTATATCATTTTCGTTATT
456 TACTGTATTATTTTTTTTTTGCTTCCACTATTATTTATTATACTTATTATATCATTTTCGTTATT
41091558 TTT
521 TTT
41091561 ATCTATTTCC
Statistics
Matches: 517, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
526 216 0.42
527 301 0.58
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (527 bp):
ACAATAGAAATAAAAAATAAAATGGGTCCTTAAAAAAGGGCAGAACCATTCAATAATTTTTAAAG
TGGTGGGGCCCACGTGTTTTGCCCTTAAAGGGTCAATTTGGGCATCAGGTCCCCGTACATTTTCT
TGTTGCCCAAATCTGCTTCACTTTTGTTTTTGAATTTCACCCAACAATTTTGTGCAGTTTTTAAT
TTGGTCCATATTAAATGCTAGGTTTAGGAATTTGGGTAAATTACATTTTTAAACCCCCTTGTTCC
ACGCACGCTTCAATGAGGTCCTCCTTTCCCCTTTTATTTGTGTTTTACCCCCGAACTTCCGTTTT
GATTCCAATTAAGCCCTATTTTGTTTATTTTAAACACTTTTATCACAAAATTAAATTTTTTGGGT
ACTATTATTATTAATCTATTATTGCTATTTTATTTATTTATTTTTTTAGTTATTTTCCTGTTATT
TACTGTATTATTTTTTTTTTGCTTCCACTATTATTTATTATACTTATTATATCATTTTCGTTATT
TTTTATC
Found at i:41091822 original size:14 final size:14
Alignment explanation
Indices: 41091805--41091837 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
41091795 TTTATTATAC
41091805 TTATTATATTTTAT
1 TTATTATATTTTAT
41091819 TTATTATATTTTAT
1 TTATTATATTTTAT
41091833 TTATT
1 TTATT
41091838 TTTTTCCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TTATTATATTTTAT
Found at i:41091822 original size:23 final size:23
Alignment explanation
Indices: 41091795--41091839 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41091785 TTAAATATAG
41091795 TTTATTATA-CTTATTATATTTTA
1 TTTATTATATCTTATT-TATTTTA
*
41091818 TTTATTATATTTTATTTATTTT
1 TTTATTATATCTTATTTATTTT
41091840 TTTCCTACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTATTATATCTTATTTATTTTA
Found at i:41092010 original size:4 final size:4
Alignment explanation
Indices: 41092001--41092026 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41091991 TAAATTATTA
41092001 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
41092027 TCGCTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:41094987 original size:18 final size:17
Alignment explanation
Indices: 41094961--41094994 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41094951 AACATATATA
*
41094961 TTAGTTGAAGATTAATAG
1 TTAGATGAAGA-TAATAG
41094979 TTAGATGAAGATAATA
1 TTAGATGAAGATAATA
41094995 AATTTGGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (17 bp):
TTAGATGAAGATAATAG
Found at i:41097557 original size:2 final size:2
Alignment explanation
Indices: 41097550--41097582 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41097540 TTTCAAACAC
41097550 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
41097583 TGGTTACTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41102859 original size:21 final size:21
Alignment explanation
Indices: 41102830--41102870 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41102820 ATCTGCTCAA
* *
41102830 ACTCTACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
41102851 ACTCCACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
41102871 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:41106628 original size:15 final size:15
Alignment explanation
Indices: 41106608--41106661 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
41106598 ATACTACAAC
41106608 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
41106623 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
41106640 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
41106657 ATATT
1 ATATT
41106662 AATATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:41106725 original size:16 final size:16
Alignment explanation
Indices: 41106694--41106730 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
41106684 ATGTGAAGAA
41106694 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
41106710 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
41106726 TATTA
1 TATTA
41106731 AAATGAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:41106794 original size:14 final size:14
Alignment explanation
Indices: 41106746--41106797 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
41106736 AAATTGAAAT
41106746 ATTAAAT-TTAATAA
1 ATTAAATATTAAT-A
** *
41106760 ATTATTTATTATATG
1 ATTAAATATTA-ATA
41106775 ATTAAATATTAATA
1 ATTAAATATTAATA
41106789 ATTAAATAT
1 ATTAAATAT
41106798 GTATGTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 16 0.53
15 12 0.40
16 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTAAATATTAATA
Found at i:41108323 original size:8 final size:8
Alignment explanation
Indices: 41108310--41108338 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
41108300 ATATATACTC
41108310 TAACTTGA
1 TAACTTGA
41108318 TAACTTGA
1 TAACTTGA
41108326 TAACTTGA
1 TAACTTGA
41108334 TAACT
1 TAACT
41108339 CTAATTATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (8 bp):
TAACTTGA
Found at i:41108609 original size:43 final size:40
Alignment explanation
Indices: 41108454--41108660 Score: 155
Period size: 43 Copynumber: 4.9 Consensus size: 40
41108444 CGTTTATGTG
* * *
41108454 AAAAAACGCCACTAAAAGT-CATCACTTTTAGCGGCGTTTGAAC
1 AAAAAACGCCGCTAAAA-TACAT-ACCTTTAGCGGCGCTT--AC
** *
41108497 GGAAAACGCCGCTAAAAGTAGATACCTTTAGCGGCGCTTTAC
1 AAAAAACGCCGCTAAAA-TACATACCTTTAGCGGCGC-TTAC
* * * * * *
41108539 CATAAATGCCGCTAATAGTATAGACCTTTAGCGGCGCTTAGC
1 AAAAAACGCCGCTAA-AATACATACCTTTAGCGGCGCTTA-C
41108581 AAACAAACGCCGCTAAAATCACATACCTTTAGCGGCGCTTACCC
1 AAA-AAACGCCGCTAAAAT-ACATACCTTTAGCGGCGCTTA--C
* * *
41108625 AAAAAACGCCGCTAAAGGTGCAAACCTTTAGCGGCG
1 AAAAAACGCCGCTAAA-ATACATACCTTTAGCGGCG
41108661 TTTTATCCAC
Statistics
Matches: 133, Mismatches: 23, Indels: 16
0.77 0.13 0.09
Matches are distributed among these distances:
41 3 0.02
42 34 0.26
43 87 0.65
44 9 0.07
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (40 bp):
AAAAAACGCCGCTAAAATACATACCTTTAGCGGCGCTTAC
Found at i:41108683 original size:86 final size:85
Alignment explanation
Indices: 41108500--41108660 Score: 193
Period size: 85 Copynumber: 1.9 Consensus size: 85
41108490 TTTGAACGGA
* * * * * *
41108500 AAACGCCGCTAAAAGT-AGATACCTTTAGCGGCGCTTTACCATAAATGCCGCTAATAGTATAGAC
1 AAACGCCACTAAAA-TCACATACCTTTAGCGGCGCTTTACCAAAAACGCCGCTAATAGTACAAAC
41108564 CTTTAGCGGCGCTTAGCAAAC
65 CTTTAGCGGCGCTTAGCAAAC
* *
41108585 AAACGCCGCTAAAATCACATACCTTTAGCGGCGC-TTACCCAAAAAACGCCGCTAA-AGGTGCAA
1 AAACGCCACTAAAATCACATACCTTTAGCGGCGCTTTA-CC-AAAAACGCCGCTAATA-GTACAA
41108648 ACCTTTAGCGGCG
63 ACCTTTAGCGGCG
41108661 TTTTATCCAC
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
84 4 0.06
85 34 0.52
86 28 0.42
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (85 bp):
AAACGCCACTAAAATCACATACCTTTAGCGGCGCTTTACCAAAAACGCCGCTAATAGTACAAACC
TTTAGCGGCGCTTAGCAAAC
Found at i:41108811 original size:43 final size:43
Alignment explanation
Indices: 41108499--41108938 Score: 277
Period size: 43 Copynumber: 10.2 Consensus size: 43
41108489 GTTTGAACGG
* * *
41108499 AAAACGCCGCTAAAAGTAGATACCTTTAGCGGCGCTTTA-CCA
1 AAAACGCCGCCAAAAGTACAGACCTTTAGCGGCGCTTTACCCA
* * * * * * *
41108541 TAAATGCCGCTAATAGTATAGACCTTTAGCGGCGC-TTAGCAA
1 AAAACGCCGCCAAAAGTACAGACCTTTAGCGGCGCTTTACCCA
* *
41108583 ACAAACGCCGCTAAAA-TCACATACCTTTAGCGGCGC-TTACCCAA
1 A-AAACGCCGCCAAAAGT-ACAGACCTTTAGCGGCGCTTTACCC-A
* * * * * *
41108627 AAAACGCCGCTAAAGGTGCAAACCTTTAGCGGCGTTTTATCCA
1 AAAACGCCGCCAAAAGTACAGACCTTTAGCGGCGCTTTACCCA
* * * * * ** **
41108670 CAAATGCCACTAAAGGTGTAGACCTTTAGCGGCG-TTT-CCGGGG
1 AAAACGCCGCCAAAAGTACAGACCTTTAGCGGCGCTTTACC--CA
* ** * * * ***
41108713 AAAGCGCCGTTAAAAGTGCGGACCTTTAGCGGCGTTTGTTTGC-
1 AAAACGCCGCCAAAAGTACAGACCTTTAGCGGCGCTT-TACCCA
* * *
41108756 AAAGCGCCGCTAAAAGTACAGACCTTTAGCGGAGCTTTAGCCCA
1 AAAACGCCGCCAAAAGTACAGACCTTTAGCGGCGCTTTA-CCCA
* * * ** *
41108800 AAAA-ACTGCTAAATTTACAGACCTATAGCGGCGC-TTACACCA
1 AAAACGCCGCCAAAAGTACAGACCTTTAGCGGCGCTTTAC-CCA
*
41108842 AAAACGCCGCCAAAAGTACAGACCTTTTAGCGGCGCTTTATCCA
1 AAAACGCCGCCAAAAGTACAGACC-TTTAGCGGCGCTTTACCCA
* * * *
41108886 AAAATGCCGCCAAAAGTAGAGTCCTTTAGCGGCGCTTTCCCCA
1 AAAACGCCGCCAAAAGTACAGACCTTTAGCGGCGCTTTACCCA
*
41108929 CAAACGCCGC
1 AAAACGCCGC
41108939 TAAATTTACA
Statistics
Matches: 315, Mismatches: 66, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
41 5 0.02
42 47 0.15
43 212 0.67
44 47 0.15
45 4 0.01
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (43 bp):
AAAACGCCGCCAAAAGTACAGACCTTTAGCGGCGCTTTACCCA
Found at i:41108934 original size:87 final size:86
Alignment explanation
Indices: 41108755--41108938 Score: 208
Period size: 87 Copynumber: 2.1 Consensus size: 86
41108745 CGTTTGTTTG
* * * **
41108755 CAAAGCGCCGCTAAAAGTACAGACCTTTAGCGGAGCTTTAGCCCAAAAAACTGCTAAATTTACAG
1 CAAA-CGCCGCCAAAAGTACAGACCTTTAGCGGAGCTTTAGCCCAAAAAACCGCCAAAAGTACAG
41108820 ACCTATAGCGGCGCTTACACCA
65 ACCTATAGCGGCGCTTACACCA
* * * * *
41108842 AAAACGCCGCCAAAAGTACAGACCTTTTAGCGGCGCTTTA-TCCAAAAATGCCGCCAAAAGTAGA
1 CAAACGCCGCCAAAAGTACAGACC-TTTAGCGGAGCTTTAGCCCAAAAA-ACCGCCAAAAGTACA
* * * *
41108906 GTCCTTTAGCGGCGCTTTCCCCA
64 GACCTATAGCGGCGCTTACACCA
41108929 CAAACGCCGC
1 CAAACGCCGC
41108939 TAAATTTACA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
86 26 0.32
87 54 0.68
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (86 bp):
CAAACGCCGCCAAAAGTACAGACCTTTAGCGGAGCTTTAGCCCAAAAAACCGCCAAAAGTACAGA
CCTATAGCGGCGCTTACACCA
Found at i:41109294 original size:21 final size:21
Alignment explanation
Indices: 41109270--41109328 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
41109260 ACTCTGCTCC
* *
41109270 GCCTCTCTTGCTGCTGCCGCT
1 GCCTCCCTCGCTGCTGCCGCT
41109291 GCCTCCCTCGCTGCTGCCGCT
1 GCCTCCCTCGCTGCTGCCGCT
*
41109312 GCCTCCCTCTCTGCTGC
1 GCCTCCCTCGCTGCTGC
41109329 ATCGGCTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.22, T:0.29
Consensus pattern (21 bp):
GCCTCCCTCGCTGCTGCCGCT
Found at i:41113116 original size:83 final size:83
Alignment explanation
Indices: 41112977--41113141 Score: 312
Period size: 83 Copynumber: 2.0 Consensus size: 83
41112967 CTTATTAAAC
*
41112977 CTCAATTCCCCCGAATCAAAACAATAACTTTCAATCCAACAGAATAATATTCAACAAGAGAACTA
1 CTCAATTCCCCCGAATCAAAACAATAAATTTCAATCCAACAGAATAATATTCAACAAGAGAACTA
41113042 AAATTGGTTTTAATATTG
66 AAATTGGTTTTAATATTG
*
41113060 CTCAATTCCCCGGAATCAAAACAATAAATTTCAATCCAACAGAATAATATTCAACAAGAGAACTA
1 CTCAATTCCCCCGAATCAAAACAATAAATTTCAATCCAACAGAATAATATTCAACAAGAGAACTA
41113125 AAATTGGTTTTAATATT
66 AAATTGGTTTTAATATT
41113142 AACGTTAAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.28
Consensus pattern (83 bp):
CTCAATTCCCCCGAATCAAAACAATAAATTTCAATCCAACAGAATAATATTCAACAAGAGAACTA
AAATTGGTTTTAATATTG
Found at i:41114156 original size:7 final size:7
Alignment explanation
Indices: 41114144--41114193 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
41114134 ACAAAATCAG
41114144 ACCCTAA
1 ACCCTAA
41114151 ACCCTAA
1 ACCCTAA
* *
41114158 ATCTTAA
1 ACCCTAA
41114165 ACCCTAA
1 ACCCTAA
*
41114172 ACTCTAA
1 ACCCTAA
*
41114179 ACCATAA
1 ACCCTAA
41114186 ATCCCTAA
1 A-CCCTAA
41114194 CCTTATAAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
7 29 0.85
8 5 0.15
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (7 bp):
ACCCTAA
Found at i:41114167 original size:14 final size:15
Alignment explanation
Indices: 41114147--41114193 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 15
41114137 AAATCAGACC
41114147 CTAAACCCTAAATCT
1 CTAAACCCTAAATCT
41114162 -TAAACCCTAAA-CT
1 CTAAACCCTAAATCT
* *
41114175 CTAAACCATAAATCC
1 CTAAACCCTAAATCT
41114190 CTAA
1 CTAA
41114194 CCTTATAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 2 0.07
14 21 0.75
15 5 0.18
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.23
Consensus pattern (15 bp):
CTAAACCCTAAATCT
Found at i:41114169 original size:21 final size:21
Alignment explanation
Indices: 41114144--41114193 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
41114134 ACAAAATCAG
* *
41114144 ACCCTAAACCCTAAATCTTAA
1 ACCCTAAACCCTAAACCATAA
*
41114165 ACCCTAAACTCTAAACCATAA
1 ACCCTAAACCCTAAACCATAA
41114186 ATCCCTAA
1 A-CCCTAA
41114194 CCTTATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (21 bp):
ACCCTAAACCCTAAACCATAA
Found at i:41114810 original size:7 final size:7
Alignment explanation
Indices: 41114798--41114823 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41114788 ATTAAGATCA
41114798 TAAACAC
1 TAAACAC
41114805 TAAACAC
1 TAAACAC
41114812 TAAACAC
1 TAAACAC
41114819 TAAAC
1 TAAAC
41114824 CTCAAACCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.27, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACAC
Found at i:41114907 original size:35 final size:35
Alignment explanation
Indices: 41114842--41114923 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
41114832 CAAAATAACA
** *
41114842 AAACCCTAAACCATAAAATTAACATTTTAAATCTT
1 AAACCCTAAACCATAAAATTAACACCTTAAATATT
**
41114877 AAACCCTAAACCATAGACCTTAA-ACCTTAAATATT
1 AAACCCTAAACCATA-AAATTAACACCTTAAATATT
*
41114912 AAACCGTAAACC
1 AAACCCTAAACC
41114924 CAAAAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 35 0.88
36 5 0.12
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (35 bp):
AAACCCTAAACCATAAAATTAACACCTTAAATATT
Found at i:41115043 original size:41 final size:41
Alignment explanation
Indices: 41114977--41115112 Score: 184
Period size: 41 Copynumber: 3.3 Consensus size: 41
41114967 AATTCAAAAA
* * * *
41114977 AGACGTTTAGCGGCG-TTTCTCCAAAAACACCGCTAATGCTC
1 AGACTTTTGGCGGCGTTTTC-CCAAAAACGCCGCTAATACTC
*
41115018 AGACTTTTTGCGGCGTTTTCCCAAAAACGCCGCTAATACTC
1 AGACTTTTGGCGGCGTTTTCCCAAAAACGCCGCTAATACTC
* * *
41115059 AGACTTTTGGCGGTGTTTTTCCAAAAACGCAGCTAATACTC
1 AGACTTTTGGCGGCGTTTTCCCAAAAACGCCGCTAATACTC
41115100 AGACTTTTGGCGG
1 AGACTTTTGGCGG
41115113 ACTTTTGGCG
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
41 82 0.95
42 4 0.05
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.29
Consensus pattern (41 bp):
AGACTTTTGGCGGCGTTTTCCCAAAAACGCCGCTAATACTC
Found at i:41115122 original size:52 final size:52
Alignment explanation
Indices: 41115060--41115159 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
41115050 CTAATACTCA
* *
41115060 GACTTTTGGCGGTGTTTTTCCAAAAACGCAGCTAATACTCAGACTTTTGGCG
1 GACTTTTGGCGGCGTTTTTACAAAAACGCAGCTAATACTCAGACTTTTGGCG
* * *
41115112 GACTTTTGGCGGCGTTTTTATAAAAACGCCGCTAATGCTCAGACTTTT
1 GACTTTTGGCGGCGTTTTTACAAAAACGCAGCTAATACTCAGACTTTT
41115160 TACGGCGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (52 bp):
GACTTTTGGCGGCGTTTTTACAAAAACGCAGCTAATACTCAGACTTTTGGCG
Found at i:41116455 original size:88 final size:89
Alignment explanation
Indices: 41116348--41116550 Score: 243
Period size: 89 Copynumber: 2.3 Consensus size: 89
41116338 GTCCTTAATT
** * *
41116348 TTTTTCAAAAAAATTAATTAAG-CTCTTCATTTTTTTT-CACTCAATTGAGCACTTGAACTTTCA
1 TTTTTCAAAAAAAGCAATTAAGCCCCTAC-TTTTTTTTCCACTCAATTGAGCACTTGAACTTTCA
* *
41116411 AAATGCATAAAAAAGACCCTCAAAC
65 AAATACATAAAAAAGACCCTCAAAA
* * *
41116436 TTCTTT-AAAAAAAGCAATTAAGCCCCTACTTTTTTTTCCTCTCAATTGGGTACTTGAACTTTCA
1 TT-TTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTCCACTCAATTGAGCACTTGAACTTTCA
* *
41116500 AAATACATTAAAAAGCCCCTCAAAA
65 AAATACATAAAAAAGACCCTCAAAA
* *
41116525 TTTTTCAAAAAAA-TATTTAAGCCCCT
1 TTTTTCAAAAAAAGCAATTAAGCCCCT
41116551 GCTCTAATTA
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
88 38 0.39
89 60 0.61
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (89 bp):
TTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTCCACTCAATTGAGCACTTGAACTTTCAA
AATACATAAAAAAGACCCTCAAAA
Found at i:41116855 original size:9 final size:9
Alignment explanation
Indices: 41116841--41117007 Score: 51
Period size: 9 Copynumber: 18.0 Consensus size: 9
41116831 TTTTAGTACG
41116841 ATAATTTTT
1 ATAATTTTT
41116850 ATAATTTTTTT
1 ATAA--TTTTT
*
41116861 ATGAA-ATTT
1 AT-AATTTTT
*
41116870 ATATTTCTTT
1 ATAATT-TTT
* *
41116880 ACATTTTTTT
1 ATAAT-TTTT
41116890 ATAATTTTCTT
1 ATAA-TTT-TT
41116901 ATGAA--TTT
1 AT-AATTTTT
**
41116909 ATAAAATTT
1 ATAATTTTT
41116918 ATAATTTTT
1 ATAATTTTT
*
41116927 -TATATTTCT
1 ATA-ATTTTT
41116936 AT-ATATTTT
1 ATAAT-TTTT
41116945 ATAATATTTT
1 ATAAT-TTTT
*
41116955 ATGATTTTT
1 ATAATTTTT
* *
41116964 ATAAAATGTT
1 AT-AATTTTT
*
41116974 ACAATTTTT
1 ATAATTTTT
*
41116983 -TATTTTTT
1 ATAATTTTT
**
41116991 ACGATTTTT
1 ATAATTTTT
41117000 AT-ATTTTT
1 ATAATTTTT
41117008 TTTCTAATTT
Statistics
Matches: 118, Mismatches: 23, Indels: 35
0.67 0.13 0.20
Matches are distributed among these distances:
7 2 0.02
8 21 0.18
9 47 0.40
10 31 0.26
11 13 0.11
12 4 0.03
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:41116928 original size:19 final size:19
Alignment explanation
Indices: 41116906--41116985 Score: 60
Period size: 19 Copynumber: 4.3 Consensus size: 19
41116896 TTCTTATGAA
41116906 TTTATAAAATTTATAATTT
1 TTTATAAAATTTATAATTT
* *
41116925 TTTAT---ATTTCTATATAT
1 TTTATAAAATTTATA-ATTT
* *
41116942 TTTATAATATTTTATGA-TT
1 TTTATAA-AATTTATAATTT
*
41116961 TTTATAAAATGTTACAATTT
1 TTTATAAAAT-TTATAATTT
41116981 TTTAT
1 TTTAT
41116986 TTTTTACGAT
Statistics
Matches: 45, Mismatches: 9, Indels: 13
0.67 0.13 0.19
Matches are distributed among these distances:
16 6 0.13
17 8 0.18
18 2 0.04
19 17 0.38
20 8 0.18
21 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTATAAAATTTATAATTT
Found at i:41116946 original size:36 final size:39
Alignment explanation
Indices: 41116841--41116967 Score: 113
Period size: 36 Copynumber: 3.4 Consensus size: 39
41116831 TTTTAGTACG
* * **
41116841 ATAA-TTTTTATAATTTTTTTATGAAATTTATATTTCTTT
1 ATAATTTTTTATAATTTTCTTATG-AATTTATAATAATTT
* *
41116880 ACATTTTTTTATAATTTTCTTATGAATTTATAA-AATTT
1 ATAATTTTTTATAATTTTCTTATGAATTTATAATAATTT
* *
41116918 ATAATTTTTTAT-A-TTTCTATAT-ATTTTATAATATTTT
1 ATAATTTTTTATAATTTTCT-TATGAATTTATAATAATTT
*
41116955 ATGA-TTTTTATAA
1 ATAATTTTTTATAA
41116968 AATGTTACAA
Statistics
Matches: 73, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
36 20 0.27
37 12 0.16
38 13 0.18
39 10 0.14
40 18 0.25
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.61
Consensus pattern (39 bp):
ATAATTTTTTATAATTTTCTTATGAATTTATAATAATTT
Found at i:41116989 original size:27 final size:27
Alignment explanation
Indices: 41116887--41116991 Score: 106
Period size: 27 Copynumber: 3.8 Consensus size: 27
41116877 TTTACATTTT
*
41116887 TTTATAATTTTCTTATGA-ATTTATAAAA
1 TTTATAATTTT-TTAT-ATTTTTATAAAA
* * *
41116915 TTTATAATTTTTTATATTTCTATATAT
1 TTTATAATTTTTTATATTTTTATAAAA
*
41116942 TTTATAATATTTTATGATTTTTATAAAA
1 TTTATAATTTTTTAT-ATTTTTATAAAA
*
41116970 TGTTACAATTTTTTAT-TTTTTA
1 T-TTATAATTTTTTATATTTTTA
41116992 CGATTTTTAT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.02
27 30 0.47
28 21 0.33
29 12 0.19
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (27 bp):
TTTATAATTTTTTATATTTTTATAAAA
Found at i:41116997 original size:17 final size:18
Alignment explanation
Indices: 41116972--41117008 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
41116962 TTATAAAATG
41116972 TTACAATTTTT-TATTTT
1 TTACAATTTTTATATTTT
*
41116989 TTACGATTTTTATATTTT
1 TTACAATTTTTATATTTT
41117007 TT
1 TT
41117009 TTCTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (18 bp):
TTACAATTTTTATATTTT
Found at i:41117000 original size:55 final size:54
Alignment explanation
Indices: 41116885--41117002 Score: 141
Period size: 55 Copynumber: 2.1 Consensus size: 54
41116875 TCTTTACATT
* * *
41116885 TTTTTATAATTTTCTTATGAATTTATAAAATTTATAATTTTTTATATTTCTATA
1 TTTTTATAATATTCTTATGAATTTATAAAATTTACAATTTTTTATATTTCTAGA
* *
41116939 TATTTTATAATATT-TTATGATTTTTATAAAATGTTACAATTTTTTAT-TTTTTACGA
1 T-TTTTATAATATTCTTATGA-ATTTATAAAAT-TTACAATTTTTTATATTTCTA-GA
41116995 TTTTTATA
1 TTTTTATA
41117003 TTTTTTTTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
54 7 0.13
55 33 0.60
56 15 0.27
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.61
Consensus pattern (54 bp):
TTTTTATAATATTCTTATGAATTTATAAAATTTACAATTTTTTATATTTCTAGA
Found at i:41117129 original size:90 final size:89
Alignment explanation
Indices: 41117023--41117241 Score: 257
Period size: 90 Copynumber: 2.4 Consensus size: 89
41117013 AATTTTTAAT
* *
41117023 AAAAGTAGGGGATTAATT-TTCCTTTTTGAAAAAAATTGAGGGTCTTTTTT-ATACATTTTGAAA
1 AAAAGTAGGGGCTTAATTGTT--TTTTTGAAAAAAATTGA-GGACTTTTTTGATACATTTTGAAA
* *
41117086 GTTGAAATA-TCTAATTGAGTGCAAAAA
63 GTTCAAATACTC-AACTGAGTGCAAAAA
** ** *
41117113 AATGGTAGGGGCTTAATTGCTTTTTTTG-AAAAGGTTCGAGGACTTTTTTGATGCATTTTGAAAG
1 AAAAGTAGGGGCTTAATTG-TTTTTTTGAAAAAAATT-GAGGACTTTTTTGATACATTTTGAAAG
*
41117177 TTCAAGTACTCAACTGAGTGCAAAAA
64 TTCAAATACTCAACTGAGTGCAAAAA
41117203 AAAAGTAGGGGCTTAATTGTTTTTATTGAAAAAAATTGA
1 AAAAGTAGGGGCTTAATTGTTTTT-TTGAAAAAAATTGA
41117242 AGGCACCCTT
Statistics
Matches: 108, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
89 20 0.19
90 78 0.72
91 8 0.07
92 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (89 bp):
AAAAGTAGGGGCTTAATTGTTTTTTTGAAAAAAATTGAGGACTTTTTTGATACATTTTGAAAGTT
CAAATACTCAACTGAGTGCAAAAA
Done.