Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 140 of 335
Found at i:41035515 original size:20 final size:20
Alignment explanation
Indices: 41035392--41035508 Score: 90
Period size: 20 Copynumber: 5.8 Consensus size: 20
41035382 AGTTTATCTG
* *
41035392 CATTTCTGGTGGCTTGTCCA
1 CATTACTGGTGGCTTGTCTA
* * **
41035412 TAATACTGGCAGCTTGTCTA
1 CATTACTGGTGGCTTGTCTA
* ** * *
41035432 CAATACTGGCAGTTTATCTA
1 CATTACTGGTGGCTTGTCTA
*
41035452 CATTACTGGTGGTTTGTCTA
1 CATTACTGGTGGCTTGTCTA
* ** *
41035472 CATTATTGGTATCTTGTCTG
1 CATTACTGGTGGCTTGTCTA
41035492 CATTACTGGTGGCTTGT
1 CATTACTGGTGGCTTGT
41035509 TCACATTTAT
Statistics
Matches: 76, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
CATTACTGGTGGCTTGTCTA
Found at i:41038187 original size:10 final size:10
Alignment explanation
Indices: 41038166--41038200 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
41038156 AATTAAATTC
41038166 TAAAAGATAAA
1 TAAAA-ATAAA
41038177 TAAAAATAAA
1 TAAAAATAAA
*
41038187 TAAAGATAAA
1 TAAAAATAAA
41038197 TAAA
1 TAAA
41038201 TATTAAATCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.78
11 5 0.22
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (10 bp):
TAAAAATAAA
Found at i:41039453 original size:26 final size:26
Alignment explanation
Indices: 41039417--41039469 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
41039407 AACCACCAAG
41039417 TATATCCCATTGTGATTAAAATAATT
1 TATATCCCATTGTGATTAAAATAATT
* *
41039443 TATATCTCATTGTGATTGAAATAATT
1 TATATCCCATTGTGATTAAAATAATT
41039469 T
1 T
41039470 TGCAAGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (26 bp):
TATATCCCATTGTGATTAAAATAATT
Found at i:41043549 original size:21 final size:21
Alignment explanation
Indices: 41043523--41043563 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
41043513 ATCTGCTCAA
*
41043523 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
41043544 ACTCCACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
41043564 TCGCTCGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:41046384 original size:16 final size:16
Alignment explanation
Indices: 41046359--41046389 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41046349 CACCACTTGG
*
41046359 ATTGTTTGCCATTAAA
1 ATTGTCTGCCATTAAA
41046375 ATTGTCTGCCATTAA
1 ATTGTCTGCCATTAA
41046390 TCATAATGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (16 bp):
ATTGTCTGCCATTAAA
Found at i:41049453 original size:31 final size:31
Alignment explanation
Indices: 41049417--41049482 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
41049407 TTTTTTAGCT
*
41049417 AAATTTGACCATAAATCTTTTAAAAACAGTC
1 AAATTTGACCATAAACCTTTTAAAAACAGTC
* **
41049448 AAATTTGACTATAAACCTTTTAAAAGGAGTC
1 AAATTTGACCATAAACCTTTTAAAAACAGTC
41049479 AAAT
1 AAAT
41049483 AGTTGCTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (31 bp):
AAATTTGACCATAAACCTTTTAAAAACAGTC
Found at i:41049599 original size:16 final size:17
Alignment explanation
Indices: 41049574--41049612 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
41049564 TTTATACTTT
*
41049574 TTTTTTAATTTTT-ATA
1 TTTTTAAATTTTTAATA
41049590 TTTTTAAATTTTTGAATA
1 TTTTTAAATTTTT-AATA
41049608 TTTTT
1 TTTTT
41049613 TTATCATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
18 8 0.40
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTTAAATTTTTAATA
Found at i:41050725 original size:6 final size:6
Alignment explanation
Indices: 41050714--41050744 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
41050704 CAACCAACTT
41050714 TTAGAA TTAGAA TTAGAA TTAGAA TTA-AA TT
1 TTAGAA TTAGAA TTAGAA TTAGAA TTAGAA TT
41050745 GATAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (6 bp):
TTAGAA
Found at i:41051568 original size:12 final size:12
Alignment explanation
Indices: 41051551--41051580 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
41051541 GGAAAAGCTT
41051551 AAATAATGACAA
1 AAATAATGACAA
*
41051563 AAATAATTACAA
1 AAATAATGACAA
41051575 AAATAA
1 AAATAA
41051581 AAATAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.70, C:0.07, G:0.03, T:0.20
Consensus pattern (12 bp):
AAATAATGACAA
Found at i:41052394 original size:16 final size:16
Alignment explanation
Indices: 41052360--41052392 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41052350 TAAATGATGA
41052360 TTAATAATTTATATTT
1 TTAATAATTTATATTT
*
41052376 TTAATGATTTA-ATTT
1 TTAATAATTTATATTT
41052391 TT
1 TT
41052393 TATACATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (16 bp):
TTAATAATTTATATTT
Found at i:41057059 original size:19 final size:19
Alignment explanation
Indices: 41057035--41057072 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41057025 CCACATGGCT
* *
41057035 ATGTGCCTCGGCCGTGTGG
1 ATGTGCCTAGGCCATGTGG
41057054 ATGTGCCTAGGCCATGTGG
1 ATGTGCCTAGGCCATGTGG
41057073 GGGACTACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.24, G:0.39, T:0.26
Consensus pattern (19 bp):
ATGTGCCTAGGCCATGTGG
Found at i:41059653 original size:46 final size:46
Alignment explanation
Indices: 41059539--41059779 Score: 204
Period size: 46 Copynumber: 5.1 Consensus size: 46
41059529 GAAATCTTAC
* *
41059539 ACATATCGATGCCGATGCTATATCCCAGATATGGTCTTACACTGGCTCTT
1 ACATATCGATGCCGATGC-ATGTCCCAGACAT-GTCTTACACTGG--CTT
* *
41059589 ACATATCCG-TGTCGATGCATGTCCCAAACATGTCTTACACTGGCTT
1 ACATAT-CGATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
* * *
41059635 ACATCTCGAGGCCGATGCATGTCCCAGACATGTCTTACACTAG--T
1 ACATATCGATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
* * * * * *
41059679 ACTCGTCTCAATGTCGATGCCATGTCCCAGGCAATGTCTTACATTGGCTT
1 A--CATATCGATGCCGATG-CATGTCCCAGAC-ATGTCTTACACTGGCTT
* * *
41059729 TCATAAT--ATGGCCGATGCATGTCCCAGACATGTCTTGCACTGGCTC
1 ACAT-ATCGAT-GCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
41059775 ACATA
1 ACATA
41059780 ATAGCAGTGT
Statistics
Matches: 156, Mismatches: 25, Indels: 25
0.76 0.12 0.12
Matches are distributed among these distances:
44 2 0.01
45 3 0.02
46 67 0.43
47 24 0.15
48 32 0.21
49 11 0.07
50 15 0.10
51 2 0.01
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (46 bp):
ACATATCGATGCCGATGCATGTCCCAGACATGTCTTACACTGGCTT
Found at i:41059716 original size:94 final size:92
Alignment explanation
Indices: 41059598--41059769 Score: 240
Period size: 94 Copynumber: 1.8 Consensus size: 92
41059588 TACATATCCG
*
41059598 TGTCGATGCATGTCCCAAACATGTCTTACACTGGCTTACAT-CTCGA-GGCCGATGCATGTCCCA
1 TGTCGATGCATGTCCCAAACATGTCTTACACTGGCTTACATAAT--ATGGCCGATGCATGTCCCA
41059661 GACATGTCTTACACTAGTACTCGTCTCAA
64 GACATGTCTTACACTAGTACTCGTCTCAA
** * *
41059690 TGTCGATGCCATGTCCCAGGCAATGTCTTACATTGGCTTTCATAATATGGCCGATGCATGTCCCA
1 TGTCGATG-CATGTCCCAAAC-ATGTCTTACACTGGCTTACATAATATGGCCGATGCATGTCCCA
*
41059755 GACATGTCTTGCACT
64 GACATGTCTTACACT
41059770 GGCTCACATA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
92 8 0.11
93 11 0.16
94 50 0.71
95 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (92 bp):
TGTCGATGCATGTCCCAAACATGTCTTACACTGGCTTACATAATATGGCCGATGCATGTCCCAGA
CATGTCTTACACTAGTACTCGTCTCAA
Found at i:41064901 original size:19 final size:19
Alignment explanation
Indices: 41064877--41064915 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41064867 AATAATAATT
*
41064877 AATTTATCAATATGTTTTC
1 AATTTATCAATATGCTTTC
41064896 AATTTATCAATATGCTTTC
1 AATTTATCAATATGCTTTC
41064915 A
1 A
41064916 CCAATTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (19 bp):
AATTTATCAATATGCTTTC
Found at i:41066124 original size:46 final size:46
Alignment explanation
Indices: 41065985--41066246 Score: 266
Period size: 46 Copynumber: 5.6 Consensus size: 46
41065975 CGACGCCATA
* * * *
41065985 TCCCAGATATGGTCTTACACTGGCTCTTACATATCCATGCCGATGCATG
1 TCCCAGACAT-GTCTTACACTGG--CTTACATCTCGAGGCCGATGCATG
* *
41066034 TCCCAAACATGTCTTACACTAGC--ACATCTCGTA-GCCGATGCATG
1 TCCCAGACATGTCTTACACTGGCTTACATCTCG-AGGCCGATGCATG
*
41066078 TCCCAAACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATG
1 TCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATG
* * * *
41066124 TCCCAGACATGTCTTACACCGGCACT-CATCTCAATGCCGATGCCATG
1 TCCCAGACATGTCTTACACTGGC-TTACATCTCGAGGCCGATG-CATG
* *
41066171 TCCCAGACATGGTCTTACACTGGCTTTCATAAT--ATGGCCGATGCATG
1 TCCCAGACAT-GTCTTACACTGGCTTACAT-CTCGA-GGCCGATGCATG
* *
41066218 TCCCAGACATGTCTTGCACTGGCTCACAT
1 TCCCAGACATGTCTTACACTGGCTTACAT
41066247 AACAGCAGTG
Statistics
Matches: 185, Mismatches: 18, Indels: 23
0.82 0.08 0.10
Matches are distributed among these distances:
44 39 0.21
45 2 0.01
46 71 0.38
47 31 0.17
48 33 0.18
49 9 0.05
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (46 bp):
TCCCAGACATGTCTTACACTGGCTTACATCTCGAGGCCGATGCATG
Found at i:41066218 original size:94 final size:91
Alignment explanation
Indices: 41065962--41066232 Score: 318
Period size: 94 Copynumber: 2.9 Consensus size: 91
41065952 GGAAATCTTA
* * * *
41065962 CACATATCGATGCCGACGCCATATCCCAGATATGGTCTTACACTGGCTCTTACATATCCAT-GCC
1 CACATCTC-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCT-TT-CATAT-CATGGCC
* *
41066026 GATGCATGTCCCAAACATGTCTTACACTAG
62 GATGCATGTCCCAGACATGTCTTACACCAG
* * * *
41066056 CACATCTCGTAGCCGATG-CATGTCCCAAACAT-GTCTTACACTGGCTTACATCTCGA-GGCCGA
1 CACATCTCAT-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATC-ATGGCCGA
*
41066118 TGCATGTCCCAGACATGTCTTACACCGG
64 TGCATGTCCCAGACATGTCTTACACCAG
41066146 CACTCATCTCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATAAT-ATGGCC
1 CA--CATCTC-ATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCAT-ATCATGGCC
41066210 GATGCATGTCCCAGACATGTCTT
62 GATGCATGTCCCAGACATGTCTT
41066233 GCACTGGCTC
Statistics
Matches: 152, Mismatches: 15, Indels: 20
0.81 0.08 0.11
Matches are distributed among these distances:
89 1 0.01
90 37 0.24
91 1 0.01
92 27 0.18
93 27 0.18
94 58 0.38
95 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (91 bp):
CACATCTCATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTTTCATATCATGGCCGATG
CATGTCCCAGACATGTCTTACACCAG
Found at i:41086275 original size:46 final size:46
Alignment explanation
Indices: 41086131--41086256 Score: 225
Period size: 46 Copynumber: 2.7 Consensus size: 46
41086121 AACCCGCCCC
* *
41086131 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
*
41086177 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
41086223 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
41086257 TGCTCAACTA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 77 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:41090112 original size:27 final size:28
Alignment explanation
Indices: 41090055--41090122 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 28
41090045 AAATTTGTAC
**
41090055 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
41090083 AGCACTAAGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
41090110 AGCACTAAGTGTG
1 AGCACTAAGTGTG
41090123 TGGACTCACT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:41090135 original size:27 final size:27
Alignment explanation
Indices: 41090055--41090136 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
41090045 AAATTTGTAC
** * *
41090055 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCG-AGCTCACTATAT
* *
41090083 AGCACTAAGTGTGCGAGCTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
*
41090110 AGCACTAAGTGTGTG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
41090137 GCTTTTGCAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
26 1 0.02
27 32 0.67
28 15 0.31
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:41094709 original size:24 final size:26
Alignment explanation
Indices: 41094649--41094714 Score: 91
Period size: 24 Copynumber: 2.6 Consensus size: 26
41094639 CTCATCGTAG
*
41094649 CTCGTATGAGCTTACTGATATATCAT
1 CTCGTATGAGCTTACTGATATATCAA
* *
41094675 CTCGTAAGAGCTTACTG-T-TCTCAA
1 CTCGTATGAGCTTACTGATATATCAA
41094699 CTCGTATGAGCTTACT
1 CTCGTATGAGCTTACT
41094715 AATTCAGCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
24 19 0.53
25 1 0.03
26 16 0.44
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (26 bp):
CTCGTATGAGCTTACTGATATATCAA
Found at i:41095761 original size:13 final size:13
Alignment explanation
Indices: 41095715--41095761 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
41095705 AGACACCGGC
41095715 GTGTGTCTCAGCAA
1 GTGTGTCTCAGC-A
*
41095729 TGTGTGACATCAGC-
1 -GTGTGTC-TCAGCA
41095743 GTGTGTCTCAGCA
1 GTGTGTCTCAGCA
41095756 GTGTGT
1 GTGTGT
41095762 GACACACGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 5 0.18
13 12 0.43
15 6 0.21
16 5 0.18
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (13 bp):
GTGTGTCTCAGCA
Found at i:41103340 original size:109 final size:107
Alignment explanation
Indices: 41103156--41103550 Score: 464
Period size: 109 Copynumber: 3.7 Consensus size: 107
41103146 TTACCATTGC
* * *
41103156 CATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATACCTTGGCA
1 CATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGCA
* *
41103221 TGGTCTTACATGGGACCTTTGTCTTATAGTAACTCTTTAATGT
66 TGGTCTTACATGGGACCTTTGCCTTATAGTAACTC-TAAATGT
* * * *
41103264 CATGTCTTGACATGGTCTTACATGATTTCCTAGCCTTATAGAACTTATCAATGCCATGCCTTGGC
1 CATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTTGGC
* * * *
41103329 ATGGTCTTACAT--GA--TAT-CCTTAT-CTTAC-C-AAATGC
65 ATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCTAAATGT
*** * * *
41103364 CATGTTCCAAACATGGTCTTAGATGGTATCCTTGCTTTATGAACTCACCAATGCCATGCCTTGGC
1 CATG-TCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGC
*
41103429 ATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAATGT
65 ATGGTCTTACATGGGACCTTTGCCTTATAGTAACTC-TAAATGT
* * * * *
41103473 CATGTCTTGACATAGTTTTACATGATTTCCTTGCCTTATAGAACTTATCAATGCCATGCCTTGGC
1 CATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAT-GAACTCACCAATGCCATGCCTTGGC
41103538 ATGGTCTTACATG
65 ATGGTCTTACATG
41103551 ATATCCTTAT
Statistics
Matches: 236, Mismatches: 39, Indels: 23
0.79 0.13 0.08
Matches are distributed among these distances:
100 43 0.18
101 27 0.11
102 3 0.01
103 3 0.01
104 7 0.03
105 8 0.03
106 3 0.01
107 3 0.01
108 61 0.26
109 78 0.33
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.36
Consensus pattern (107 bp):
CATGTCTTGACATGGTCTTACATGATATCCTTGCCTTATGAACTCACCAATGCCATGCCTTGGCA
TGGTCTTACATGGGACCTTTGCCTTATAGTAACTCTAAATGT
Found at i:41103342 original size:54 final size:54
Alignment explanation
Indices: 41103142--41103558 Score: 333
Period size: 55 Copynumber: 7.9 Consensus size: 54
41103132 TTTCCTTTTT
* * * *
41103142 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * * ** *
41103195 GAACTCACCAATGCCATACCTTGGCATGGTCTTACATGGGA-CCTTTGTCTTATA
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATA
** * * * *
41103249 GTAACTCT-TTAATGTCATGTCTTGACATGGTCTTACATGATTTCCTAGCCTTATA
1 G-AACT-TACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* *
41103304 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATA----T-CCTTAT-
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
** * * *
41103352 ---CTTACCAAATGCCATGTTCC-AAACATGGTCTTAGATGGTATCCTTGCTTTAT-
1 GAACTTACC-AATGCCATG--CCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* * **
41103404 GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATA
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCC-TTGCCTTATA
* * * * * * *
41103458 GTAACTCATCAATGTCATGTCTTGACATAGTTTTACATGATTTCCTTGCCTTATA
1 G-AACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
* *
41103513 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTT
41103559 ATCTTACCAA
Statistics
Matches: 286, Mismatches: 56, Indels: 43
0.74 0.15 0.11
Matches are distributed among these distances:
45 5 0.02
46 9 0.03
47 15 0.05
48 2 0.01
49 6 0.02
51 1 0.00
52 11 0.04
53 66 0.23
54 82 0.29
55 85 0.30
56 4 0.01
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.36
Consensus pattern (54 bp):
GAACTTACCAATGCCATGCCTTGACATGGTCTTACATGATATCCTTGCCTTATA
Found at i:41103525 original size:209 final size:209
Alignment explanation
Indices: 41103165--41103611 Score: 779
Period size: 209 Copynumber: 2.1 Consensus size: 209
41103155 CCATGTCTTG
41103165 ACATGGTCTTACG-TGGTATCCTTGCCTTATGAACTCACCAATGCCATACCTTGGCATGGTCTTA
1 ACATGGTCTTA-GATGGTATCCTTGCCTTATGAACTCACCAATGCCATACCTTGGCATGGTCTTA
* * * *
41103229 CATGGGACCTTTGTCTTATAGTAACTCTTTAATGTCATGTCTTGACATGGTCTTACATGATTTCC
65 CATGGGACCTTTGCCTTATAGTAACTCATCAATGTCATGTCTTGACATAGTCTTACATGATTTCC
41103294 TAGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCA
130 TAGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCA
41103359 AATGCCATGTTCCAA
195 AATGCCATGTTCCAA
* *
41103374 ACATGGTCTTAGATGGTATCCTTGCTTTATGAACTCACCAATGCCATGCCTTGGCATGGTCTTAC
1 ACATGGTCTTAGATGGTATCCTTGCCTTATGAACTCACCAATGCCATACCTTGGCATGGTCTTAC
*
41103439 ATGGGACCTTTGCCTTATAGTAACTCATCAATGTCATGTCTTGACATAGTTTTACATGATTTCCT
66 ATGGGACCTTTGCCTTATAGTAACTCATCAATGTCATGTCTTGACATAGTCTTACATGATTTCCT
*
41103504 TGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAA
131 AGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAA
*
41103569 ATGTCATGTTCCAA
196 ATGCCATGTTCCAA
* *
41103583 ACATGGTCTTACATGGTATCCTTGTCTTA
1 ACATGGTCTTAGATGGTATCCTTGCCTTA
41103612 GTGCCAATGC
Statistics
Matches: 225, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
208 1 0.00
209 224 1.00
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (209 bp):
ACATGGTCTTAGATGGTATCCTTGCCTTATGAACTCACCAATGCCATACCTTGGCATGGTCTTAC
ATGGGACCTTTGCCTTATAGTAACTCATCAATGTCATGTCTTGACATAGTCTTACATGATTTCCT
AGCCTTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTACCAA
ATGCCATGTTCCAA
Found at i:41105240 original size:21 final size:21
Alignment explanation
Indices: 41105211--41105318 Score: 89
Period size: 21 Copynumber: 5.3 Consensus size: 21
41105201 ATGTTTTACT
* *
41105211 TTCTATTTAGCTCTTTCGTGC
1 TTCTGTTTAGCTCTTTCGAGC
* * *
41105232 TTTTGTTTAGCTTTTTCAAG-
1 TTCTGTTTAGCTCTTTCGAGC
*
41105252 TTCTGTTCAGCTCTTTCGAGC
1 TTCTGTTTAGCTCTTTCGAGC
* * *
41105273 TTCTGTTCAACTCTTAT-GAGT
1 TTCTGTTTAGCTCTT-TCGAGC
*
41105294 TTCTGTTAAGCT-TTT-GAGC
1 TTCTGTTTAGCTCTTTCGAGC
41105313 TTCTGT
1 TTCTGT
41105319 CGGTGTATCT
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
19 10 0.14
20 18 0.25
21 42 0.59
22 1 0.01
ACGTcount: A:0.13, C:0.19, G:0.17, T:0.51
Consensus pattern (21 bp):
TTCTGTTTAGCTCTTTCGAGC
Found at i:41107991 original size:28 final size:28
Alignment explanation
Indices: 41107943--41108033 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
41107933 GTGACAGAGT
*
41107943 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
*
41107972 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGTGC
41108000 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
41108028 CACCAG
1 CACCAG
41108034 GACGCTTCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:41108185 original size:27 final size:27
Alignment explanation
Indices: 41108142--41108198 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
41108132 TTAACCCTAG
*
41108142 GGGTATAGAGGTCATTTTGCATACATA
1 GGGTATAGAGGTAATTTTGCATACATA
41108169 GGGTATA-ATGGTAATTTTGCATACATA
1 GGGTATAGA-GGTAATTTTGCATACATA
41108196 GGG
1 GGG
41108199 GTATTCTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (27 bp):
GGGTATAGAGGTAATTTTGCATACATA
Found at i:41109497 original size:24 final size:24
Alignment explanation
Indices: 41109470--41109516 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
41109460 CTAGATTTCC
*
41109470 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAGCTCCTAAATCCTA
41109494 TCCCTTATCAGCTCCTAAATCCT
1 TCCCTTATCAGCTCCTAAATCCT
41109517 CTCCTGACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.38, G:0.04, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAGCTCCTAAATCCTA
Found at i:41110433 original size:15 final size:15
Alignment explanation
Indices: 41110413--41110444 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41110403 CTATCAGACG
41110413 CTTCCTTTAACCGAT
1 CTTCCTTTAACCGAT
41110428 CTTCCTTTAACCGAT
1 CTTCCTTTAACCGAT
41110443 CT
1 CT
41110445 CTAATTAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.34, G:0.06, T:0.41
Consensus pattern (15 bp):
CTTCCTTTAACCGAT
Found at i:41115816 original size:28 final size:28
Alignment explanation
Indices: 41115777--41115866 Score: 130
Period size: 27 Copynumber: 3.2 Consensus size: 28
41115767 TGTGACGAGT
*
41115777 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
*
41115806 CACCAGAACAGATAATTTGT-GCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGTGC
41115833 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
41115861 CACCAG
1 CACCAG
41115867 GACGCTTCCT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
27 26 0.46
28 23 0.41
29 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:41116022 original size:28 final size:27
Alignment explanation
Indices: 41115973--41116033 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 27
41115963 ATTAACCCTA
* *
41115973 GGGTATAAGGTCATTTTGCATACATAG
1 GGGTATAAGGTAATTTTACATACATAG
41116000 GGGTATAATGGTAATTTTACATACATAG
1 GGGTATAA-GGTAATTTTACATACATAG
41116028 GGGTAT
1 GGGTAT
41116034 TCTAGTACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 8 0.26
28 23 0.74
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.34
Consensus pattern (27 bp):
GGGTATAAGGTAATTTTACATACATAG
Found at i:41123093 original size:28 final size:28
Alignment explanation
Indices: 41123045--41123135 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
41123035 GTGACAGAGT
*
41123045 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
*
41123074 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGTGC
41123102 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
41123130 CACCAG
1 CACCAG
41123136 GACGCTTCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:41123288 original size:28 final size:28
Alignment explanation
Indices: 41123241--41123305 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
41123231 AAATTAACCC
* *
41123241 TAGGGGTATAGAGGTCATTTTGCATACA
1 TAGGGGTATAGAGGTAATTTTACATACA
41123269 TAGGGGTATA-ATGGTAATTTTACATACA
1 TAGGGGTATAGA-GGTAATTTTACATACA
41123297 TAGGGGTAT
1 TAGGGGTAT
41123306 TCTAGTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
27 1 0.03
28 33 0.97
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAGAGGTAATTTTACATACA
Found at i:41123574 original size:16 final size:16
Alignment explanation
Indices: 41123553--41123616 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
41123543 CCAAAATACC
41123553 GGCTTTTCGGCATTTT
1 GGCTTTTCGGCATTTT
41123569 GGCTTTTCGGCATTTT
1 GGCTTTTCGGCATTTT
*
41123585 GGCTTTTCGGCATTTC
1 GGCTTTTCGGCATTTT
41123601 GGCTTTTCGGC-TTTT
1 GGCTTTTCGGCATTTT
41123616 G
1 G
41123617 CCGATCTAGC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
15 4 0.09
16 42 0.91
ACGTcount: A:0.05, C:0.20, G:0.27, T:0.48
Consensus pattern (16 bp):
GGCTTTTCGGCATTTT
Found at i:41123602 original size:8 final size:8
Alignment explanation
Indices: 41123552--41123615 Score: 87
Period size: 8 Copynumber: 8.0 Consensus size: 8
41123542 CCCAAAATAC
41123552 CGGCTTTT
1 CGGCTTTT
41123560 CGGCATTTT
1 CGGC-TTTT
41123569 -GGCTTTT
1 CGGCTTTT
41123576 CGGCATTTT
1 CGGC-TTTT
41123585 -GGCTTTT
1 CGGCTTTT
*
41123592 CGGCATTT
1 CGGCTTTT
41123600 CGGCTTTT
1 CGGCTTTT
41123608 CGGCTTTT
1 CGGCTTTT
41123616 GCCGATCTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
7 8 0.16
8 34 0.68
9 8 0.16
ACGTcount: A:0.05, C:0.22, G:0.25, T:0.48
Consensus pattern (8 bp):
CGGCTTTT
Found at i:41124633 original size:24 final size:24
Alignment explanation
Indices: 41124606--41124652 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
41124596 CTAGATTTCC
*
41124606 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAGCTCCTAAATCCTA
41124630 TCCCTTATCAGCTCCTAAATCCT
1 TCCCTTATCAGCTCCTAAATCCT
41124653 CTCCTGACAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.38, G:0.04, T:0.36
Consensus pattern (24 bp):
TCCCTTATCAGCTCCTAAATCCTA
Found at i:41131241 original size:20 final size:20
Alignment explanation
Indices: 41131216--41131269 Score: 90
Period size: 20 Copynumber: 2.6 Consensus size: 20
41131206 GGGATTGCAC
41131216 TTTGGTGTCTCTATTAGCAT
1 TTTGGTGTCTCTATTAGCAT
41131236 TTTGGTGTCTCTATTAGCAT
1 TTTGGTGTCTCTATTAGCAT
*
41131256 TTTGATGCTCTCTA
1 TTTGGTG-TCTCTA
41131270 GTGTGTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 26 0.81
21 6 0.19
ACGTcount: A:0.15, C:0.17, G:0.19, T:0.50
Consensus pattern (20 bp):
TTTGGTGTCTCTATTAGCAT
Found at i:41133057 original size:24 final size:23
Alignment explanation
Indices: 41133030--41133076 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41133020 ATTTTTTTGA
* *
41133030 ATATTAATTATTTTTAAATTGTTT
1 ATATTAATTA-CTTTAAACTGTTT
*
41133054 ATATTATTTACTTTAAACTGTTT
1 ATATTAATTACTTTAAACTGTTT
41133077 TTATAGTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.60
Consensus pattern (23 bp):
ATATTAATTACTTTAAACTGTTT
Found at i:41137172 original size:49 final size:49
Alignment explanation
Indices: 41137108--41137204 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
41137098 TCCATATAGA
* * *
41137108 ACTATACTTCTTTTATTTTACATTGATTAGAATAAGGTTTTTCAACCTT
1 ACTACACTTCATTTATTTGACATTGATTAGAATAAGGTTTTTCAACCTT
41137157 ACTACACTTCATTTATTTGACATTGATTAGAATAAGGTTTTTCAACCT
1 ACTACACTTCATTTATTTGACATTGATTAGAATAAGGTTTTTCAACCT
41137205 ATAAATAGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.45
Consensus pattern (49 bp):
ACTACACTTCATTTATTTGACATTGATTAGAATAAGGTTTTTCAACCTT
Found at i:41141226 original size:20 final size:20
Alignment explanation
Indices: 41141201--41141241 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41141191 ACACTTTAAT
41141201 TACATAGTATTTTCAACCAA
1 TACATAGTATTTTCAACCAA
41141221 TACATAGTATTTTCAACCAA
1 TACATAGTATTTTCAACCAA
41141241 T
1 T
41141242 TTCAAACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.37
Consensus pattern (20 bp):
TACATAGTATTTTCAACCAA
Found at i:41142149 original size:43 final size:43
Alignment explanation
Indices: 41142088--41142238 Score: 166
Period size: 43 Copynumber: 3.6 Consensus size: 43
41142078 TCTTAGACGT
* * * *
41142088 GGTCTTACATGTAATCAAATATCGATGTCACTGTCCCAGACAG
1 GGTCTTACACGAAATCAAATATCGATGACAATGTCCCAGACAG
*
41142131 GGTCTTACACGAAATCAAATA-CGATGACAATGTCCCAGACAT
1 GGTCTTACACGAAATCAAATATCGATGACAATGTCCCAGACAG
* * *
41142173 GGTCTTACACGTAAATCATAA-GTCGATGCCAAAGTCCCAGAC-G
1 GGTCTTACACG-AAATCA-AATATCGATGACAATGTCCCAGACAG
* *
41142216 TGTCTTACACGAAA-CACATATCG
1 GGTCTTACACGAAATCAAATATCG
41142239 GATCCTATGT
Statistics
Matches: 92, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
40 1 0.01
41 5 0.05
42 32 0.35
43 35 0.38
44 19 0.21
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
GGTCTTACACGAAATCAAATATCGATGACAATGTCCCAGACAG
Found at i:41147801 original size:29 final size:29
Alignment explanation
Indices: 41147768--41147827 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
41147758 GGACAAAGAG
41147768 GTTCCCTACGTCTCCAAGGGTACTTTATA
1 GTTCCCTACGTCTCCAAGGGTACTTTATA
*
41147797 GTTCCTTACGTCTCCAAGGGTACTTTATA
1 GTTCCCTACGTCTCCAAGGGTACTTTATA
41147826 GT
1 GT
41147828 GTATGAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (29 bp):
GTTCCCTACGTCTCCAAGGGTACTTTATA
Found at i:41149027 original size:67 final size:67
Alignment explanation
Indices: 41148919--41149054 Score: 263
Period size: 67 Copynumber: 2.0 Consensus size: 67
41148909 GTCATACTTG
*
41148919 TCACCTTCAAAATAGTCATTTAGTAAACCTTTGTATTCCACCCGTTGAATCTTATCTTTAATTGT
1 TCACCTTCAAAATAGTCATTCAGTAAACCTTTGTATTCCACCCGTTGAATCTTATCTTTAATTGT
41148984 AA
66 AA
41148986 TCACCTTCAAAATAGTCATTCAGTAAACCTTTGTATTCCACCCGTTGAATCTTATCTTTAATTGT
1 TCACCTTCAAAATAGTCATTCAGTAAACCTTTGTATTCCACCCGTTGAATCTTATCTTTAATTGT
41149051 AA
66 AA
41149053 TC
1 TC
41149055 TTGTATATTA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 68 1.00
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (67 bp):
TCACCTTCAAAATAGTCATTCAGTAAACCTTTGTATTCCACCCGTTGAATCTTATCTTTAATTGT
AA
Found at i:41149613 original size:13 final size:14
Alignment explanation
Indices: 41149571--41149615 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
41149561 TAATAATGAT
41149571 TAAAGTATATTATAA
1 TAAAGTA-ATTATAA
41149586 TAATA-TAA-TATAA
1 TAA-AGTAATTATAA
41149599 TAAAGTAATTA-AA
1 TAAAGTAATTATAA
41149612 TAAA
1 TAAA
41149616 AAATAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.04
13 17 0.63
14 3 0.11
15 5 0.19
16 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
TAAAGTAATTATAA
Found at i:41149707 original size:16 final size:19
Alignment explanation
Indices: 41149666--41149708 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
41149656 GAAACAAAGC
41149666 AAGGAAAGAAAGAAAGAAA
1 AAGGAAAGAAAGAAAGAAA
41149685 AAGGGAAAG-AA-AAAG-AA
1 AA-GGAAAGAAAGAAAGAAA
41149702 AAGGAAA
1 AAGGAAA
41149709 ATTTAGGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 5 0.22
17 4 0.17
18 4 0.17
19 4 0.17
20 6 0.26
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (19 bp):
AAGGAAAGAAAGAAAGAAA
Found at i:41151496 original size:20 final size:20
Alignment explanation
Indices: 41151473--41151513 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41151463 GCCCCACGAC
41151473 CATGTCCCAAGCCACACGGG
1 CATGTCCCAAGCCACACGGG
*
41151493 CATGTCCCAGGCCACACGGG
1 CATGTCCCAAGCCACACGGG
41151513 C
1 C
41151514 GTGTGCCCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.22, C:0.41, G:0.27, T:0.10
Consensus pattern (20 bp):
CATGTCCCAAGCCACACGGG
Found at i:41154852 original size:38 final size:38
Alignment explanation
Indices: 41154801--41154877 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
41154791 AATGGGATTA
**
41154801 TACAAATTTTGCTGAGTTGGAGATTGCTTCCTGGATGT
1 TACAAATTTTGCTGAGTTGGAGATCACTTCCTGGATGT
*
41154839 TACAAATTTTGCTGAGTTGGAGATCATTTCCTGGATGT
1 TACAAATTTTGCTGAGTTGGAGATCACTTCCTGGATGT
41154877 T
1 T
41154878 GGATCAACTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.13, G:0.25, T:0.40
Consensus pattern (38 bp):
TACAAATTTTGCTGAGTTGGAGATCACTTCCTGGATGT
Found at i:41159872 original size:27 final size:27
Alignment explanation
Indices: 41159821--41159910 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 27
41159811 GTGACAGAGT
*
41159821 CACCAGATACAGAAATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
*
41159850 CACCAGAACAGATATATGTGGCAAG-GC
1 CACCAGAACAGATATTTGTGGC-AGTGC
*
41159877 CACTAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
41159905 CACCAG
1 CACCAG
41159911 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:41159906 original size:28 final size:28
Alignment explanation
Indices: 41159821--41159910 Score: 98
Period size: 27 Copynumber: 3.2 Consensus size: 28
41159811 GTGACAGAGT
41159821 CACCAGATACAGA-AATTTTGTGGCAGT-GC
1 CACCAGA-ACAGATAA-TTTGTGGCA-TAGC
*
41159850 CACCAGAACAGAT-ATATGTGGCA-AGGC
1 CACCAGAACAGATAATTTGTGGCATA-GC
*
41159877 CACTAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCATAGC
41159905 CACCAG
1 CACCAG
41159911 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
27 22 0.42
28 22 0.42
29 8 0.15
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCATAGC
Found at i:41160063 original size:28 final size:28
Alignment explanation
Indices: 41160019--41160080 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
41160009 TTAACCCTAA
*
41160019 GGGTATAAAGGTCATTTTGCATACATAG
1 GGGTATAAAGGTAATTTTGCATACATAG
*
41160047 GGGTATAATGGTAATTTTGCATACATAG
1 GGGTATAAAGGTAATTTTGCATACATAG
41160075 GGGTAT
1 GGGTAT
41160081 TCTAGTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (28 bp):
GGGTATAAAGGTAATTTTGCATACATAG
Found at i:41164281 original size:60 final size:60
Alignment explanation
Indices: 41164200--41164338 Score: 165
Period size: 60 Copynumber: 2.3 Consensus size: 60
41164190 CCAACTGTGT
* * *
41164200 TAATATGGGCAAGGCCCAATATA-TCTCGA-ATTGTAATAGGGCTACGGCCCAGATTGATAC
1 TAATATGGGCTAGGCCCAATATACTCT-GATACTGTAA-AGGGCTACGGCCCAGATTAATAC
* * * *
41164260 TAATATGGGCTAGGCCTAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATAT
1 TAATATGGGCTAGGCCCAATATACTCTGATACTGTAAAGGGCTACGGCCCAGATTAATAC
*
41164320 TGATATGGGCTAAGGCCCA
1 TAATATGGGCT-AGGCCCA
41164339 GTTAACTCTG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
60 52 0.78
61 15 0.22
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (60 bp):
TAATATGGGCTAGGCCCAATATACTCTGATACTGTAAAGGGCTACGGCCCAGATTAATAC
Found at i:41173408 original size:14 final size:14
Alignment explanation
Indices: 41173389--41173417 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41173379 GATAAATAAT
41173389 AATCTATATAACAA
1 AATCTATATAACAA
41173403 AATCTATATAACAA
1 AATCTATATAACAA
41173417 A
1 A
41173418 GTAAAAAGGG
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:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
AATCTATATAACAA
Found at i:41175651 original size:17 final size:17
Alignment explanation
Indices: 41175631--41175664 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41175621 TTCGTATATT
*
41175631 ATACTAATTATATCTAA
1 ATACTAAGTATATCTAA
41175648 ATACTAAGTATATCTAA
1 ATACTAAGTATATCTAA
41175665 GCGAATCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (17 bp):
ATACTAAGTATATCTAA
Found at i:41183828 original size:29 final size:28
Alignment explanation
Indices: 41183790--41183892 Score: 134
Period size: 29 Copynumber: 3.6 Consensus size: 28
41183780 GTGACGAGAT
*
41183790 TGGCACTAAGTGTGCAAGCTTGAAATGTA
1 TGGCACTAAGTGTGCAAGCTT-AAATATA
*
41183819 TGGCACTAAGTGTGCGAGCTTAAATTATA
1 TGGCACTAAGTGTGCAAGCTTAAA-TATA
* * *
41183848 TGGCACTATGTGTGCGAGCTTAAATCACA
1 TGGCACTAAGTGTGCAAGCTTAAAT-ATA
41183877 TGGCACTAAGTGTGCA
1 TGGCACTAAGTGTGCA
41183893 TGATCGATTA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
28 4 0.06
29 62 0.94
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (28 bp):
TGGCACTAAGTGTGCAAGCTTAAATATA
Found at i:41195170 original size:6 final size:6
Alignment explanation
Indices: 41195159--41195185 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41195149 TCCTCCTATC
41195159 TTTTTA TTTTTA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTT
41195186 CAATTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:41197019 original size:21 final size:22
Alignment explanation
Indices: 41196979--41197019 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41196969 TACTTAGCAT
*
41196979 ATTTATGGATGTTTATTACTAG
1 ATTTATGGATGTTTAGTACTAG
*
41197001 ATTTGTGGAT-TTTAGTACT
1 ATTTATGGATGTTTAGTACT
41197020 CTTAATCCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.24, C:0.05, G:0.20, T:0.51
Consensus pattern (22 bp):
ATTTATGGATGTTTAGTACTAG
Found at i:41198147 original size:13 final size:13
Alignment explanation
Indices: 41198129--41198157 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
41198119 TTTAGTATAA
41198129 TTAGTTAATTAGT
1 TTAGTTAATTAGT
41198142 TTAGTTAATTAGT
1 TTAGTTAATTAGT
41198155 TTA
1 TTA
41198158 ATAAACAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (13 bp):
TTAGTTAATTAGT
Found at i:41201886 original size:27 final size:26
Alignment explanation
Indices: 41201838--41201889 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
41201828 GCGAGGCTGC
*
41201838 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
41201864 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
41201890 TTGCAGCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:41206705 original size:26 final size:24
Alignment explanation
Indices: 41206676--41206737 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
41206666 TAGTTTACTC
*
41206676 TTTTCTTTTTTTTAAGTTATATTGAT
1 TTTTCTTTTTTTTAAGTT-TA-AGAT
* *
41206702 TTTTATTTTCTTTTAGGTTTAAGAT
1 TTTTCTTTT-TTTTAAGTTTAAGAT
*
41206727 TTTTCATTTTT
1 TTTTCTTTTTT
41206738 AGTTATAATC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
24 2 0.07
25 10 0.33
26 10 0.33
27 8 0.27
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (24 bp):
TTTTCTTTTTTTTAAGTTTAAGAT
Found at i:41208468 original size:24 final size:24
Alignment explanation
Indices: 41208441--41208492 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
41208431 AATCAAAGTC
* *
41208441 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
*
41208465 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
41208489 AAAT
1 AAAT
41208493 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:41211833 original size:23 final size:23
Alignment explanation
Indices: 41211803--41211848 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
41211793 CCCAAAAATG
41211803 ATAGTTTGATAGTGTGATTTTGC
1 ATAGTTTGATAGTGTGATTTTGC
41211826 ATAGTTTGATAGTGTGATTTTGC
1 ATAGTTTGATAGTGTGATTTTGC
41211849 CTCCAACGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.04, G:0.26, T:0.48
Consensus pattern (23 bp):
ATAGTTTGATAGTGTGATTTTGC
Found at i:41212860 original size:49 final size:49
Alignment explanation
Indices: 41212803--41212976 Score: 244
Period size: 49 Copynumber: 3.5 Consensus size: 49
41212793 CTAGTACGCA
*
41212803 TAGTAGCCTGCACTTAGTACTACACATACGACCAATTATCCGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATACGACCAATTATCAGATACACG
** *
41212852 TAGTAGCCTGCACTTAGTACT--ACATACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACATAC--GACC-AATTATCAGATACACG
* * *
41212902 TAGTAGCCTGCACTTAGTACTACAAATGCGACCAATTATCAGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATACGACCAATTATCAGATACACG
41212951 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
41212977 CGTGACCTCA
Statistics
Matches: 110, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
47 6 0.05
49 62 0.56
50 38 0.35
52 4 0.04
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACATACGACCAATTATCAGATACACG
Found at i:41212974 original size:99 final size:99
Alignment explanation
Indices: 41212803--41212984 Score: 319
Period size: 99 Copynumber: 1.8 Consensus size: 99
41212793 CTAGTACGCA
* *
41212803 TAGTAGCCTGCACTTAGTACTACACATACGACCAATTATCCGATACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACAAATACGACCAATTATCAGATACACGTAGTAGCCTGCACTTA
*
41212868 GTACTACATACGTGACCTAACCATCTGATACACG
66 GTACTACACACGTGACCTAACCATCTGATACACG
* *
41212902 TAGTAGCCTGCACTTAGTACTACAAATGCGACCAATTATCAGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACAAATACGACCAATTATCAGATACACGTAGTAGCCTGCACTTA
41212967 GTACTACACACGTGACCT
66 GTACTACACACGTGACCT
41212985 CACAATAGAT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 78 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACAAATACGACCAATTATCAGATACACGTAGTAGCCTGCACTTA
GTACTACACACGTGACCTAACCATCTGATACACG
Found at i:41213251 original size:29 final size:30
Alignment explanation
Indices: 41213209--41213270 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
41213199 GGTACAACCA
* *
41213209 ATGTAATAGTAATTTAACATTCAA-TTCAC
1 ATGTAACAATAATTTAACATTCAATTTCAC
**
41213238 ATGTAACAATAATTTGTCATTCAATTTCAC
1 ATGTAACAATAATTTAACATTCAATTTCAC
41213268 ATG
1 ATG
41213271 ACACAACAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (30 bp):
ATGTAACAATAATTTAACATTCAATTTCAC
Found at i:41215999 original size:13 final size:14
Alignment explanation
Indices: 41215978--41216006 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41215968 TATTTATAAG
41215978 TTAAAAAAACCTAA
1 TTAAAAAAACCTAA
41215992 TTAAAAAAACCTAA
1 TTAAAAAAACCTAA
41216006 T
1 T
41216007 CCTAATCAAA
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:0.14, G:0.00, T:0.24
Consensus pattern (14 bp):
TTAAAAAAACCTAA
Found at i:41216062 original size:24 final size:24
Alignment explanation
Indices: 41216020--41216071 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
41216010 AATCAAAGTC
** *
41216020 AAATATATTATTTTAATAAATTCT
1 AAATATATTATACTAATAAATACT
*
41216044 AAATATATTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
41216068 AAAT
1 AAAT
41216072 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:41217458 original size:21 final size:21
Alignment explanation
Indices: 41217428--41217480 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
41217418 TATTTATATC
*
41217428 TTTTGGGTTTTAGG-TTCTAAA
1 TTTTGAGTTTTAGGATT-TAAA
**
41217449 TTTTGAGTTTTAGGATTTTTA
1 TTTTGAGTTTTAGGATTTAAA
41217470 TTTTGAGTTTT
1 TTTTGAGTTTT
41217481 GAGTTTTAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.17, C:0.02, G:0.21, T:0.60
Consensus pattern (21 bp):
TTTTGAGTTTTAGGATTTAAA
Found at i:41217548 original size:13 final size:13
Alignment explanation
Indices: 41217510--41217548 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
41217500 TTTTTTCATT
41217510 TATTTATTTTTAA
1 TATTTATTTTTAA
* **
41217523 TAATTATAATTAA
1 TATTTATTTTTAA
41217536 TATTTATTTTTAA
1 TATTTATTTTTAA
41217549 AACAAATTTA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTTATTTTTAA
Found at i:41218861 original size:22 final size:22
Alignment explanation
Indices: 41218836--41218878 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41218826 TATCCAAACA
41218836 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
41218858 ATAATAGTAAAATTGTAGCAA
1 ATAACAATAAAATAGTAGCAA
41218879 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.12, T:0.23
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:41220600 original size:21 final size:20
Alignment explanation
Indices: 41220559--41220602 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
41220549 GACGTTTTAT
* *
41220559 GTTTAGGTTCGGGATTTAAG
1 GTTTAGGTTCGAGATTCAAG
*
41220579 GTTTAGGGTTCGAGCTTCAAG
1 GTTTA-GGTTCGAGATTCAAG
41220600 GTT
1 GTT
41220603 CAAAGGTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.18, C:0.09, G:0.34, T:0.39
Consensus pattern (20 bp):
GTTTAGGTTCGAGATTCAAG
Found at i:41221872 original size:14 final size:14
Alignment explanation
Indices: 41221812--41221872 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
41221802 TCAATATTGT
41221812 GATTTAG-GATTTAA
1 GATTTAGAG-TTTAA
*
41221826 GGTTTAGAGTTTAA
1 GATTTAGAGTTTAA
* * *
41221840 AATTCAAAGTTTAA
1 GATTTAGAGTTTAA
*
41221854 TGATTTAGGGTTTAA
1 -GATTTAGAGTTTAA
41221869 GATT
1 GATT
41221873 CAATGATTTA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.34, C:0.02, G:0.21, T:0.43
Consensus pattern (14 bp):
GATTTAGAGTTTAA
Found at i:41222477 original size:13 final size:12
Alignment explanation
Indices: 41222455--41222479 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41222445 CAGAAACATC
41222455 ATAGAAAAAAAA
1 ATAGAAAAAAAA
41222467 ATAGAAAAAAAA
1 ATAGAAAAAAAA
41222479 A
1 A
41222480 GAGAGTCATT
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:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
ATAGAAAAAAAA
Found at i:41223890 original size:12 final size:12
Alignment explanation
Indices: 41223875--41223902 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41223865 TTTTGTTTCC
41223875 TTTAGCATACAT
1 TTTAGCATACAT
41223887 TTTAGCATACAT
1 TTTAGCATACAT
41223899 TTTA
1 TTTA
41223903 ATTTTGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.46
Consensus pattern (12 bp):
TTTAGCATACAT
Found at i:41230594 original size:42 final size:42
Alignment explanation
Indices: 41230548--41230642 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
41230538 TTCGATTGTT
*
41230548 ACATGGCCTGGGACATGGGCATGTGTCTCAGCCATGTCAGTC
1 ACATGGCCTGGGACATGGGCATGTGTCTCAACCATGTCAGTC
** * *
41230590 ACATGGATTGAGACATGGGCATGTGTCTCAACCATGTGAGTC
1 ACATGGCCTGGGACATGGGCATGTGTCTCAACCATGTCAGTC
*
41230632 ACACGGCCTGG
1 ACATGGCCTGG
41230643 CCACATGGCC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.23
Consensus pattern (42 bp):
ACATGGCCTGGGACATGGGCATGTGTCTCAACCATGTCAGTC
Found at i:41240296 original size:26 final size:26
Alignment explanation
Indices: 41240261--41240310 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
41240251 TCCTGTACAT
* *
41240261 ATATGTTCACATGAGCTGTGAAATCA
1 ATATGCTCACACGAGCTGTGAAATCA
41240287 ATATGCTCACACGAGCTGTGAAAT
1 ATATGCTCACACGAGCTGTGAAAT
41240311 GGGCTTGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (26 bp):
ATATGCTCACACGAGCTGTGAAATCA
Found at i:41240566 original size:2 final size:2
Alignment explanation
Indices: 41240559--41240588 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41240549 GTATAATAAC
41240559 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41240589 TGATTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41247558 original size:11 final size:11
Alignment explanation
Indices: 41247531--41247583 Score: 81
Period size: 11 Copynumber: 4.9 Consensus size: 11
41247521 TGACCTTTCC
41247531 AAGGTATGGG-
1 AAGGTATGGGA
*
41247541 TAGGTATGGGA
1 AAGGTATGGGA
41247552 AAGGTATGGGA
1 AAGGTATGGGA
*
41247563 AAGGTATGGGT
1 AAGGTATGGGA
41247574 AAGGTATGGG
1 AAGGTATGGG
41247584 GTATATTCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
10 9 0.23
11 30 0.77
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (11 bp):
AAGGTATGGGA
Found at i:41251648 original size:18 final size:18
Alignment explanation
Indices: 41251625--41251693 Score: 102
Period size: 18 Copynumber: 3.8 Consensus size: 18
41251615 CCCAACTACT
*
41251625 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
41251643 GTATACGTGAATAGTATC
1 GTATACGTGAATAGTACC
* *
41251661 GTATATGTAAATAGTACC
1 GTATACGTGAATAGTACC
41251679 GTATACGTGAATAGT
1 GTATACGTGAATAGT
41251694 GTTATAAACG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:41266048 original size:14 final size:14
Alignment explanation
Indices: 41266029--41266062 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
41266019 GCTCTAAAAG
41266029 TTGATGATTTCATT
1 TTGATGATTTCATT
41266043 TTGATGATTTCATT
1 TTGATGATTTCATT
41266057 TTGATG
1 TTGATG
41266063 GTGTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.21, C:0.06, G:0.18, T:0.56
Consensus pattern (14 bp):
TTGATGATTTCATT
Found at i:41274850 original size:39 final size:39
Alignment explanation
Indices: 41274769--41274931 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
41274759 TATGGTAACC
* *
41274769 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
41274809 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
41274848 CGCACCATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
41274887 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
41274926 CGCACA
1 CGCACA
41274932 TTCATACACA
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
39 97 0.85
40 17 0.15
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:41283203 original size:2 final size:2
Alignment explanation
Indices: 41283196--41283235 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
41283186 AAAAACTTGC
41283196 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41283236 GTGTGTGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41284022 original size:31 final size:31
Alignment explanation
Indices: 41283960--41284022 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
41283950 ACAACATTTC
**
41283960 AAAAAGAAAATCTAAAAAATGAAATCTTGAG
1 AAAAAGAAAATCTAAAAAATGAAATAATGAG
* *
41283991 AAAAAGAAAATTTAATAAATG-AATAAATGAG
1 AAAAAGAAAATCTAAAAAATGAAAT-AATGAG
41284022 A
1 A
41284023 CATTTATCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.63, C:0.03, G:0.13, T:0.21
Consensus pattern (31 bp):
AAAAAGAAAATCTAAAAAATGAAATAATGAG
Found at i:41287388 original size:30 final size:29
Alignment explanation
Indices: 41287322--41287395 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
41287312 ATGAATTTTG
* *
41287322 GTGATGTTATATATAAATTTTAATTTTAT
1 GTGATTTTATAAATAAATTTTAATTTTAT
*
41287351 GTAATTTTATAAATAAAATTTT-ATTTTAAT
1 GTGATTTTATAAAT-AAATTTTAATTTT-AT
*
41287381 TTGATTTTCATAAAT
1 GTGATTTT-ATAAAT
41287396 TTTCGATATC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 16 0.43
30 15 0.41
31 6 0.16
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (29 bp):
GTGATTTTATAAATAAATTTTAATTTTAT
Found at i:41287859 original size:2 final size:2
Alignment explanation
Indices: 41287852--41287893 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
41287842 TGAACATTGT
41287852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41287894 ATTTGTTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41287984 original size:2 final size:2
Alignment explanation
Indices: 41287977--41288006 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41287967 CTAAGAAATA
41287977 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
41288007 TTCACCGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41291962 original size:21 final size:21
Alignment explanation
Indices: 41291921--41291963 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41291911 GTATTTTGTT
* * *
41291921 TATTTTTATTTTATTATAAAA
1 TATTTTTATATTATAAAAAAA
41291942 TATTTTTATATTATAAAAAAA
1 TATTTTTATATTATAAAAAAA
41291963 T
1 T
41291964 TAAGGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTTTATATTATAAAAAAA
Found at i:41292462 original size:16 final size:15
Alignment explanation
Indices: 41292436--41292474 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
41292426 ATTGAATTAT
* *
41292436 TTATATTTTATATAA
1 TTATATATTATAAAA
41292451 TTGATATATTATAAAA
1 TT-ATATATTATAAAA
41292467 TTATATAT
1 TTATATAT
41292475 GATTTAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (15 bp):
TTATATATTATAAAA
Found at i:41297217 original size:30 final size:30
Alignment explanation
Indices: 41297172--41297238 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
41297162 TAAATTACCA
* *
41297172 GTGACACCCAGCCGTGTCAACCGA-CTGTGG
1 GTGACACCCAACCGTGTCAACCAATC-GTGG
*
41297202 GTGACATCCAACCGTGTCAACCAATCGTGG
1 GTGACACCCAACCGTGTCAACCAATCGTGG
41297232 GTGACAC
1 GTGACAC
41297239 ACGATTGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (30 bp):
GTGACACCCAACCGTGTCAACCAATCGTGG
Found at i:41298320 original size:20 final size:20
Alignment explanation
Indices: 41298278--41298325 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
41298268 AGGGTATCAA
*
41298278 AGTGCAAATAGCGGCACCAT
1 AGTGCAAATAGCGGAACCAT
* **
41298298 AGTGCAAATAGGGGAACTGT
1 AGTGCAAATAGCGGAACCAT
41298318 AGTGCAAA
1 AGTGCAAA
41298326 CAAGGGCAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.29, T:0.17
Consensus pattern (20 bp):
AGTGCAAATAGCGGAACCAT
Found at i:41298336 original size:21 final size:20
Alignment explanation
Indices: 41298297--41298336 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
41298287 AGCGGCACCA
* *
41298297 TAGTGCAAATAGGGGAACTG
1 TAGTGCAAAAAGGGCAACTG
41298317 TAGTGCAAACAAGGGCAACT
1 TAGTGCAAA-AAGGGCAACT
41298337 AAGTGTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.15, G:0.30, T:0.17
Consensus pattern (20 bp):
TAGTGCAAAAAGGGCAACTG
Found at i:41299237 original size:35 final size:35
Alignment explanation
Indices: 41299198--41299265 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
41299188 AGCTCCTGAG
41299198 TTAGCTAGATTAAGCTACAATGATCGCAAAAACAC
1 TTAGCTAGATTAAGCTACAATGATCGCAAAAACAC
41299233 TTAGCTAGATTAAGCTACAATGATCGCAAAAAC
1 TTAGCTAGATTAAGCTACAATGATCGCAAAAAC
41299266 CTAAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.43, C:0.19, G:0.15, T:0.24
Consensus pattern (35 bp):
TTAGCTAGATTAAGCTACAATGATCGCAAAAACAC
Found at i:41303483 original size:25 final size:25
Alignment explanation
Indices: 41303435--41303483 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41303425 CATTATTCTA
* *
41303435 AATATTCAAAAATTTATAATTATAG
1 AATATTAAAAAATTTATAAATATAG
41303460 AATATTAAATAAATTTA-AAATATA
1 AATATTAAA-AAATTTATAAATATA
41303484 AAAACAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (25 bp):
AATATTAAAAAATTTATAAATATAG
Found at i:41303573 original size:16 final size:18
Alignment explanation
Indices: 41303546--41303585 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
41303536 AACTCAACCA
41303546 TTAATAATTTTA-TATTT
1 TTAATAATTTTAGTATTT
41303563 TTAAT-ATTTTAGTATTT
1 TTAATAATTTTAGTATTT
41303580 TATAAT
1 T-TAAT
41303586 TATAATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 11 0.52
18 4 0.19
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TTAATAATTTTAGTATTT
Found at i:41303602 original size:24 final size:24
Alignment explanation
Indices: 41303552--41303603 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
41303542 ACCATTAATA
* * * *
41303552 ATTTTATATTTTTAATATTTTAGT
1 ATTTTATAATTATAATATTTAAAT
*
41303576 ATTTTATAATTATAATTTTTAAAT
1 ATTTTATAATTATAATATTTAAAT
41303600 ATTT
1 ATTT
41303604 AGAATAATGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTTATAATTATAATATTTAAAT
Found at i:41304067 original size:15 final size:15
Alignment explanation
Indices: 41304049--41304096 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
41304039 TTAAATTATG
41304049 AAAATTATAAAATAT
1 AAAATTATAAAATAT
*
41304064 AAAATTATAAAACA-
1 AAAATTATAAAATAT
*
41304078 AAAATAAATAAAAT-T
1 AAAAT-TATAAAATAT
41304093 AAAA
1 AAAA
41304097 AAAAAGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
14 5 0.18
15 23 0.82
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATTATAAAATAT
Found at i:41304072 original size:8 final size:8
Alignment explanation
Indices: 41304041--41304075 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
41304031 AATAAAAATT
41304041 AAATTATGA
1 AAATTAT-A
41304050 AAATTATA
1 AAATTATA
41304058 AAA-TATA
1 AAATTATA
41304065 AAATTATA
1 AAATTATA
41304073 AAA
1 AAA
41304076 CAAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.28
8 11 0.44
9 7 0.28
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (8 bp):
AAATTATA
Found at i:41304083 original size:21 final size:20
Alignment explanation
Indices: 41304057--41304101 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
41304047 TGAAAATTAT
41304057 AAAAT-ATAAAATTATAAAACA
1 AAAATAATAAAATTA-AAAA-A
41304078 AAAATAAATAAAATTAAAAAA
1 AAAAT-AATAAAATTAAAAAA
41304099 AAA
1 AAA
41304102 GTAAAGGTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 9 0.41
22 4 0.18
23 9 0.41
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAATAATAAAATTAAAAAA
Found at i:41304106 original size:21 final size:23
Alignment explanation
Indices: 41304062--41304106 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
41304052 ATTATAAAAT
41304062 ATAAAATTATAAAACAAAAATAA
1 ATAAAATTATAAAACAAAAATAA
*
41304085 ATAAAATTA-AAAA-AAAAGTAA
1 ATAAAATTATAAAACAAAAATAA
41304106 A
1 A
41304107 GGTGGAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 4 0.19
23 9 0.43
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (23 bp):
ATAAAATTATAAAACAAAAATAA
Found at i:41304362 original size:5 final size:5
Alignment explanation
Indices: 41304325--41304359 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
41304315 AAAACTAAAA
41304325 TTCTT TTCTT TTCTT TTCTT TTCTT TT-TT TT-TT TT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TT
41304360 TTTGCTTGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (5 bp):
TTCTT
Found at i:41315107 original size:178 final size:177
Alignment explanation
Indices: 41314798--41315155 Score: 689
Period size: 178 Copynumber: 2.0 Consensus size: 177
41314788 ACAAAATTAA
*
41314798 GCATACATGCATACAGATTTAGATACATAATCAAAAGCAGATATAGCTTTAGATTCAGAATCAGA
1 GCATACATGCATACAGATTTAGATACATAATCAAAAGCAGATATAGCTTTAGATTCAAAATCAGA
41314863 TCAGATTCATATTATAGATACAGATATGCATAAATCCTACCCCATCCTCTACACACCATCTCCGT
66 TCAGATTCATATTATAGATACAGATATGCATAAATCCTACCCCATCCTCTACACACCATCTCCGT
*
41314928 CCATCCCATCACACCATGTGAGGTTTAAAACACTCATCCATCCCTAC
131 CCATCCCATCACACCATGTGAGGTTTAAAACACCCATCCATCCCTAC
41314975 GCATACATGCATACAGATTTAGATACATAATCAAAAGCAGATATAGCTTTAGATTCAAAATCAGA
1 GCATACATGCATACAGATTTAGATACATAATCAAAAGCAGATATAGCTTTAGATTCAAAATCAGA
41315040 TCCAGATTCATATTATAGATACAGATATGCATAAATCCTACCCCATCCTCTACACACCATCTCCG
66 T-CAGATTCATATTATAGATACAGATATGCATAAATCCTACCCCATCCTCTACACACCATCTCCG
41315105 TCCATCCCATCACACCATGTGAGGTTTAAAACACCCATCCATCCCTAC
130 TCCATCCCATCACACCATGTGAGGTTTAAAACACCCATCCATCCCTAC
41315153 GCA
1 GCA
41315156 CCACATTGTG
Statistics
Matches: 178, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
177 65 0.37
178 113 0.63
ACGTcount: A:0.36, C:0.28, G:0.11, T:0.26
Consensus pattern (177 bp):
GCATACATGCATACAGATTTAGATACATAATCAAAAGCAGATATAGCTTTAGATTCAAAATCAGA
TCAGATTCATATTATAGATACAGATATGCATAAATCCTACCCCATCCTCTACACACCATCTCCGT
CCATCCCATCACACCATGTGAGGTTTAAAACACCCATCCATCCCTAC
Found at i:41321165 original size:13 final size:13
Alignment explanation
Indices: 41321147--41321172 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41321137 CCATGGCCCA
41321147 CATTCACTCACGC
1 CATTCACTCACGC
41321160 CATTCACTCACGC
1 CATTCACTCACGC
41321173 GAGTGAATAT
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:0.23, C:0.46, G:0.08, T:0.23
Consensus pattern (13 bp):
CATTCACTCACGC
Found at i:41325050 original size:16 final size:16
Alignment explanation
Indices: 41325026--41325067 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
41325016 TAATAAAAAA
*
41325026 TAATTTAATTA-TATTT
1 TAATATAATTATTA-TT
41325042 TAATATAATTATTATT
1 TAATATAATTATTATT
*
41325058 AAATATAATT
1 TAATATAATT
41325068 TAATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 21 0.91
17 2 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAATATAATTATTATT
Found at i:41325073 original size:24 final size:23
Alignment explanation
Indices: 41325052--41325113 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
41325042 TAATATAATT
41325052 ATTATTAAATATAATTTAATAAAA
1 ATTATTAAATATAATTTAAT-AAA
* * *
41325076 ATAATCAAAAATAATTTAATAAA
1 ATTATTAAATATAATTTAATAAA
*
41325099 ATT-TTTAATATAATT
1 ATTATTAAATATAATT
41325114 ATTTTATATT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
22 9 0.29
23 5 0.16
24 17 0.55
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTATTAAATATAATTTAATAAA
Found at i:41325136 original size:13 final size:13
Alignment explanation
Indices: 41325036--41325134 Score: 53
Period size: 12 Copynumber: 7.6 Consensus size: 13
41325026 TAATTTAATT
*
41325036 ATATTTTAATATA
1 ATATTTTAATAAA
* *
41325049 AT-TATTATTAAA
1 ATATTTTAATAAA
*
41325061 TATAATTTAATAAA
1 -ATATTTTAATAAA
** *
41325075 A-ATAATCA-AAA
1 ATATTTTAATAAA
*
41325086 ATAATTTAATAAA
1 ATATTTTAATAAA
41325099 AT-TTTTAATATAA
1 ATATTTTAATA-AA
*
41325112 TTATTTTATATTAAA
1 ATATTTTA-A-TAAA
41325127 ATATTTTA
1 ATATTTTA
41325135 TTTTTATATT
Statistics
Matches: 61, Mismatches: 17, Indels: 14
0.66 0.18 0.15
Matches are distributed among these distances:
11 4 0.07
12 20 0.33
13 13 0.21
14 12 0.20
15 10 0.16
16 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATTTTAATAAA
Found at i:41328103 original size:25 final size:26
Alignment explanation
Indices: 41328068--41328172 Score: 180
Period size: 25 Copynumber: 4.2 Consensus size: 26
41328058 ATGAAATTCC
41328068 ATCAT-GAACATTTACCTAA-CCATT
1 ATCATGGAACATTTACCTAACCCATT
41328092 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
41328118 ATCATGAAACATTTACCTAA-CCATT
1 ATCATGGAACATTTACCTAACCCATT
41328143 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41328169 ATCA
1 ATCA
41328173 ATTTGTATCA
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
24 5 0.07
25 38 0.50
26 33 0.43
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:41328132 original size:51 final size:50
Alignment explanation
Indices: 41328068--41328172 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 50
41328058 ATGAAATTCC
41328068 ATCATGAACATTTACCTAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATGAACATTTACCTAACCATTATCATGGAACATTTACCTAACCCATT
41328118 ATCATGAAACATTTACCTAACCATTATCATGGAACATTTACCTAACCCATT
1 ATCATG-AACATTTACCTAACCATTATCATGGAACATTTACCTAACCCATT
41328169 ATCA
1 ATCA
41328173 ATTTGTATCA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 6 0.11
51 48 0.89
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.31
Consensus pattern (50 bp):
ATCATGAACATTTACCTAACCATTATCATGGAACATTTACCTAACCCATT
Found at i:41335163 original size:25 final size:26
Alignment explanation
Indices: 41335097--41335202 Score: 180
Period size: 25 Copynumber: 4.2 Consensus size: 26
41335087 TGAAATTCCA
*
41335097 ATCATAGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
41335123 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
41335149 ATCAT-GAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41335174 A-CATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
41335199 ATCA
1 ATCA
41335203 ATTTGTATCA
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
24 3 0.04
25 41 0.55
26 31 0.41
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:41340084 original size:29 final size:30
Alignment explanation
Indices: 41340049--41340123 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
41340039 GACCAAATTA
*
41340049 AAATTTCATGTATAAAATTGTACA-AAATC
1 AAATTTCATGTATAAAATTGCACATAAATC
*
41340078 AAATTTCATGTATAGAATTGCACATTAAATC
1 AAATTTCATGTATAAAATTGCACA-TAAATC
* *
41340109 AAAGTTCATGGATAA
1 AAATTTCATGTATAA
41340124 TTTTGAGATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 22 0.56
31 17 0.44
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (30 bp):
AAATTTCATGTATAAAATTGCACATAAATC
Found at i:41342027 original size:63 final size:60
Alignment explanation
Indices: 41341946--41342065 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 60
41341936 TAAAAAAATT
* *
41341946 TAAAATTTAAAATTTTTATATATATATTTTAGAATTTTTAAGAATTTTTAT-ATTTTTTAAAAA
1 TAAAATTTAAAATTTTTATA-A-ATATTTTA-AA-TTTTAAAAATTATTATAATTTTTTAAAAA
*
41342009 TAAAATTTGAAATTTTTATAAATATTTTAAATTTTAAAAATTATTATGAATTTTTTA
1 TAAAATTTAAAATTTTTATAAATATTTTAAATTTTAAAAATTATTAT-AATTTTTTA
41342066 GAATTATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
59 14 0.27
60 2 0.04
61 16 0.31
62 1 0.02
63 19 0.37
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (60 bp):
TAAAATTTAAAATTTTTATAAATATTTTAAATTTTAAAAATTATTATAATTTTTTAAAAA
Found at i:41342043 original size:18 final size:19
Alignment explanation
Indices: 41342008--41342065 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 19
41341998 TTTTTTAAAA
41342008 ATAAA-ATTTGAAATTTTT
1 ATAAATATTTGAAATTTTT
*
41342026 ATAAATATTTTAAA-TTTT
1 ATAAATATTTGAAATTTTT
* *
41342044 AAAAATTATTATGAATTTTTT
1 ATAAA-TATT-TGAAATTTTT
41342065 A
1 A
41342066 GAATTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 13 0.41
19 11 0.34
20 3 0.09
21 5 0.16
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
ATAAATATTTGAAATTTTT
Found at i:41342084 original size:20 final size:20
Alignment explanation
Indices: 41342047--41342083 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41342037 AAATTTTAAA
41342047 AATTATTATGAATTTTTTAG
1 AATTATTATGAATTTTTTAG
*
41342067 AATTATTTTG-ATTTTTT
1 AATTATTATGAATTTTTT
41342084 TTAAAGAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (20 bp):
AATTATTATGAATTTTTTAG
Found at i:41343825 original size:44 final size:44
Alignment explanation
Indices: 41343729--41343876 Score: 154
Period size: 44 Copynumber: 3.4 Consensus size: 44
41343719 GCCTTATATT
* **
41343729 CCTGAAGTTGTAGTGGAGCAGATTGAAGCTACGAATCTTATCTA
1 CCTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCCC
** *
41343773 CC-GTAAGTTGTAGTGGAGCAGATTGAATTTATAAATCTTATCCC
1 CCTG-AAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCCC
* * * * * * *
41343817 CCTGAAGTTGCAATAGAGCAAATTGAAGCTACAATTCCTATACC
1 CCTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCCC
*
41343861 CCTGAAGTTGTTGTGG
1 CCTGAAGTTGTAGTGG
41343877 GTTAGAACGA
Statistics
Matches: 82, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
43 1 0.01
44 80 0.98
45 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (44 bp):
CCTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCTTATCCC
Found at i:41345736 original size:15 final size:15
Alignment explanation
Indices: 41345718--41345747 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41345708 ATTAATCATG
41345718 TTATAATTATCATTA
1 TTATAATTATCATTA
*
41345733 TTATTATTATCATTA
1 TTATAATTATCATTA
41345748 ACTTGTGTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATAATTATCATTA
Found at i:41347646 original size:14 final size:14
Alignment explanation
Indices: 41347619--41347658 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
41347609 TGAGAATCAT
41347619 TTTATATAATTTTTA
1 TTTAT-TAATTTTTA
* *
41347634 TTTATTTATTTTTG
1 TTTATTAATTTTTA
41347648 TTTATTAATTT
1 TTTATTAATTT
41347659 GGTGAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTTATTAATTTTTA
Found at i:41348264 original size:142 final size:141
Alignment explanation
Indices: 41348013--41348354 Score: 303
Period size: 142 Copynumber: 2.5 Consensus size: 141
41348003 AGATAGGTAT
* * ** * * *
41348013 TTTTACTATTTAGTTTTTAATCCGAAAGCATAAAGTGAAAATTGC-TTTGAGATGAAAT--AATA
1 TTTTACTACTTAGTTTTAAATAAGGAAGCATAAAGTAAAAACTGCATTTGAGATGAAATCAAATA
* * * *
41348075 GATCTGAATATATGTCGAACACAGGTCTCATACACATAGGCTATAGGAGAAAGTGAAGAGATCT-
66 GATCTAAATATATGTCAAACACAGGTCTCATACACATAGGCTATAGGAAAAAAT-AA-AGAT-TG
41348139 AATAATATAGATTAA
128 AATAATATA-ATTAA
*
41348154 TTTTACTACTTAGTTTTAAATATGGAAGCATAAAGTAAAAACTGCATTTGAGATGAAATCAAAT-
1 TTTTACTACTTAGTTTTAAATAAGGAAGCATAAAGTAAAAACTGCATTTGAGATGAAATCAAATA
* * * * * * * *
41348218 G-TCTAAATCTATGTCAAACATAGGTCTTGAGTGCATAT-GTCT-TAGGAAAAAATAAAGGTTGG
66 GATCTAAATATATGTCAAACACAGGTC-TCA-TACACATAGGCTATAGGAAAAAATAAAGATTGA
*
41348280 ATAATATAATTTA
129 ATAATATAATTAA
* * * *
41348293 TTTT-C-ACTTAG-CTTAAA-AACGATAGCATGAAGTAAAAACTGCTATTGGAGATGAAATCAAA
1 TTTTACTACTTAGTTTTAAATAAGGA-AGCATAAAGTAAAAACTGC-ATTTGAGATGAAATCAAA
41348354 T
64 T
41348355 TGTTTTTAGA
Statistics
Matches: 168, Mismatches: 25, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
135 3 0.02
136 23 0.14
137 24 0.14
138 1 0.01
139 9 0.05
140 11 0.07
141 40 0.24
142 43 0.26
143 6 0.04
144 8 0.05
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.32
Consensus pattern (141 bp):
TTTTACTACTTAGTTTTAAATAAGGAAGCATAAAGTAAAAACTGCATTTGAGATGAAATCAAATA
GATCTAAATATATGTCAAACACAGGTCTCATACACATAGGCTATAGGAAAAAATAAAGATTGAAT
AATATAATTAA
Found at i:41352320 original size:14 final size:15
Alignment explanation
Indices: 41352303--41352331 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41352293 CTTAAAAAGG
41352303 ACAAAAAA-AAAAAA
1 ACAAAAAACAAAAAA
41352317 ACAAAAAACAAAAAA
1 ACAAAAAACAAAAAA
41352332 TCTAAATACA
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:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (15 bp):
ACAAAAAACAAAAAA
Found at i:41361361 original size:30 final size:30
Alignment explanation
Indices: 41361290--41361372 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 30
41361280 AAGTTGTGAA
* *
41361290 TTTAGTTTATATA-TTTT-AATTTGATCAAT
1 TTTAGTTT-TATACTTTTGAATTAGATCAAC
41361319 TTTAGTTCTTATACTTTTAGAATTAG-TCAAC
1 TTTAGTT-TTATACTTTT-GAATTAGATCAAC
41361350 TTTAGTTTTATACTTTTTGAATT
1 TTTAGTTTTATAC-TTTTGAATT
41361373 TTAAAATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
29 11 0.23
30 16 0.34
31 15 0.32
32 5 0.11
ACGTcount: A:0.28, C:0.07, G:0.08, T:0.57
Consensus pattern (30 bp):
TTTAGTTTTATACTTTTGAATTAGATCAAC
Found at i:41364633 original size:25 final size:25
Alignment explanation
Indices: 41364604--41364670 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 25
41364594 TTAATATTAA
*
41364604 ATTAATATAATATTAAGATAATCACT
1 ATTAATATAATATTAAGAAAAT-ACT
*
41364630 -TTAATATTAA-ATTAATAAAATACT
1 ATTAATA-TAATATTAAGAAAATACT
*
41364654 ATTAAGATAAGTATTAA
1 ATTAATATAA-TATTAA
41364671 ATTTAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
24 6 0.18
25 20 0.59
26 8 0.24
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (25 bp):
ATTAATATAATATTAAGAAAATACT
Found at i:41364645 original size:20 final size:20
Alignment explanation
Indices: 41364585--41364645 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
41364575 AAACTAGCCC
*
41364585 TTAACCACTTTAATATTAAA
1 TTAATCACTTTAATATTAAA
41364605 TTAAT-A---TAATATTAAGA
1 TTAATCACTTTAATATTAA-A
41364622 -TAATCACTTTAATATTAAA
1 TTAATCACTTTAATATTAAA
41364641 TTAAT
1 TTAAT
41364646 AAAATACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
16 13 0.38
17 2 0.06
19 2 0.06
20 17 0.50
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAATCACTTTAATATTAAA
Found at i:41368806 original size:40 final size:40
Alignment explanation
Indices: 41368760--41368942 Score: 253
Period size: 40 Copynumber: 4.6 Consensus size: 40
41368750 CTACTCGCTC
* *
41368760 AATGCCTTCGGGACATAGCCCGGATATAATAACTAGCACC
1 AATGCCTTCGGGACTTAGCCCGGATATAATAACTAGCACA
* * *
41368800 AATGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGATATAATAACTAGCACA
*
41368840 AATGCCTTCGGGACTTAGCCCGGATGTAATAACTCA-CACA
1 AATGCCTTCGGGACTTAGCCCGGATATAATAACT-AGCACA
* * *
41368880 AATGCCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA
1 AATGCCTTCGGGACTTAGCCCGGATA-TAATAACTAGCACA
41368920 AATGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGACTTAGCCCGG
41368943 TTATCATCCG
Statistics
Matches: 127, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
39 1 0.01
40 126 0.99
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.21
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGATATAATAACTAGCACA
Done.