Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014985.1 Kokia drynarioides strain JFW-HI SEQ_130029, whole genome shotgun sequence
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: 287700
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 300 characters in sequence are not A, C, G, or T
Found at i:2767 original size:2 final size:2
Alignment explanation
Indices: 2760--2791 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2750 TAAATAGGTA
2760 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
2792 TTGTTAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4101 original size:17 final size:17
Alignment explanation
Indices: 4081--4113 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4071 TCAAAAGGAA
4081 TTTGAGGGAAAAAAAGC
1 TTTGAGGGAAAAAAAGC
*
4098 TTTGAGGGAAATAAAG
1 TTTGAGGGAAAAAAAG
4114 AAGGATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.30, T:0.21
Consensus pattern (17 bp):
TTTGAGGGAAAAAAAGC
Found at i:14192 original size:26 final size:26
Alignment explanation
Indices: 14161--14226 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
14151 CTTAAATTAA
**
14161 ACTTTTTAAAAGTATTTTTCAAAATT
1 ACTTTTTAAAAGTATTTTTCAAAAGC
* *
14187 ACTTTTCTAAAA-CATTTTTTAAAAGC
1 ACTTTT-TAAAAGTATTTTTCAAAAGC
*
14213 ACTTTTGAAAAGTA
1 ACTTTTTAAAAGTA
14227 ATGCTAAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
25 4 0.12
26 23 0.72
27 5 0.16
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (26 bp):
ACTTTTTAAAAGTATTTTTCAAAAGC
Found at i:21764 original size:9 final size:9
Alignment explanation
Indices: 21750--21776 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
21740 ACCTTTTTTT
21750 TTCTTCCCC
1 TTCTTCCCC
21759 TTCTTCCCC
1 TTCTTCCCC
21768 TTCTTCCCC
1 TTCTTCCCC
21777 CCCTCCCACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (9 bp):
TTCTTCCCC
Found at i:41498 original size:80 final size:80
Alignment explanation
Indices: 41365--41525 Score: 268
Period size: 80 Copynumber: 2.0 Consensus size: 80
41355 AAAATCCGTT
*
41365 ATGCTCAAACCCGGTAGCTTAACCTTTGAAAGGACGAAAGATGCTGATGACAACAGGCTTGAAAC
1 ATGCTCAAACCCGGAAGCTTAACCTTTGAAAGGACGAAAGATGCTGATGACAACAGGCTTGAAAC
*
41430 TCCATGTTCCCCAAC
66 TCCATGATCCCCAAC
* * * *
41445 ATGCTTAAACCCTGAAGCTTAACCTTTGAAAGGACGGAAGATGTTGATGACAACAGGCTTGAAAC
1 ATGCTCAAACCCGGAAGCTTAACCTTTGAAAGGACGAAAGATGCTGATGACAACAGGCTTGAAAC
41510 TCCATGATCCCCAAC
66 TCCATGATCCCCAAC
41525 A
1 A
41526 AGTGGGCAGC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (80 bp):
ATGCTCAAACCCGGAAGCTTAACCTTTGAAAGGACGAAAGATGCTGATGACAACAGGCTTGAAAC
TCCATGATCCCCAAC
Found at i:52565 original size:8 final size:8
Alignment explanation
Indices: 52552--52576 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
52542 TCCATTAACC
52552 CAAAGATT
1 CAAAGATT
52560 CAAAGATT
1 CAAAGATT
52568 CAAAGATT
1 CAAAGATT
52576 C
1 C
52577 GATATCTTCT
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:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (8 bp):
CAAAGATT
Found at i:56322 original size:16 final size:17
Alignment explanation
Indices: 56277--56327 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
56267 TGAATTGTAT
*
56277 ATATT-TATTTTATAGTT
1 ATATTATATTTTATA-TC
56294 A-ATTATATTTTATATC
1 ATATTATATTTTATATC
*
56310 ATATTAT-TTTTATGTC
1 ATATTATATTTTATATC
56326 AT
1 AT
56328 TTGAAGTTCG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 15 0.50
17 15 0.50
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (17 bp):
ATATTATATTTTATATC
Found at i:60647 original size:30 final size:30
Alignment explanation
Indices: 60538--60640 Score: 145
Period size: 29 Copynumber: 3.4 Consensus size: 30
60528 CAAATGATTT
*
60538 TAAAATTATTAAAATTATTTTTTTTAAATA
1 TAAAATTATTAAAATTATTTTTTTAAAATA
* *
60568 TAAAATTTTTTAAATTA-TTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTTAAAATA
* *
60597 TAAAATTATTAAAATTATTTTTTTGAAGTAA
1 TAAAATTATTAAAATTATTTTTTTAAAAT-A
60628 TAAAATTATTAAA
1 TAAAATTATTAAA
60641 TAATTTTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
29 26 0.41
30 24 0.38
31 14 0.22
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
TAAAATTATTAAAATTATTTTTTTAAAATA
Found at i:61953 original size:17 final size:18
Alignment explanation
Indices: 61931--61965 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
61921 CCCAAAAAAT
61931 ATTTAACTAT-TTTTTAA
1 ATTTAACTATGTTTTTAA
*
61948 ATTTAATTATGTTTTTAA
1 ATTTAACTATGTTTTTAA
61966 GTTAAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (18 bp):
ATTTAACTATGTTTTTAA
Found at i:63404 original size:27 final size:28
Alignment explanation
Indices: 63374--63428 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
63364 TCTCTATGCA
63374 GTTTTTACATTT-AG-AATTTAATTTTTT
1 GTTTTTA-ATTTCAGAAATTTAATTTTTT
*
63401 GTTTTTATTTTCAGAAATTTAATTTTTT
1 GTTTTTAATTTCAGAAATTTAATTTTTT
63429 ACTTTTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 3 0.12
27 9 0.36
28 13 0.52
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (28 bp):
GTTTTTAATTTCAGAAATTTAATTTTTT
Found at i:75451 original size:9 final size:9
Alignment explanation
Indices: 75434--75520 Score: 72
Period size: 9 Copynumber: 9.9 Consensus size: 9
75424 GTATTTAATA
*
75434 AATAGTATT
1 AATAATATT
75443 AATAATATTT
1 AATAATA-TT
* *
75453 GATAATAAT
1 AATAATATT
*
75462 AATAATAAT
1 AATAATATT
*
75471 AATAATAAT
1 AATAATATT
*
75480 AATAATAAT
1 AATAATATT
75489 AATAA-A-T
1 AATAATATT
*
75496 -ATAACATT
1 AATAATATT
*
75504 AGTAATATT
1 AATAATATT
75513 AATAATAT
1 AATAATAT
75521 AAAAAAAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
6 4 0.06
7 2 0.03
8 2 0.03
9 51 0.76
10 8 0.12
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.38
Consensus pattern (9 bp):
AATAATATT
Found at i:75460 original size:3 final size:3
Alignment explanation
Indices: 75454--75493 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
75444 ATAATATTTG
75454 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
75494 ATATAACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:76695 original size:29 final size:29
Alignment explanation
Indices: 76662--76916 Score: 218
Period size: 29 Copynumber: 8.7 Consensus size: 29
76652 TAAAGAGTCA
76662 AAAAATTACATTTTGACCCCAAACTTTCC
1 AAAAATTACATTTTGACCCCAAACTTTCC
**
76691 AAAAATTACATTTTGACTCCCAAACTTTTT
1 AAAAATTACATTTTGAC-CCCAAACTTTCC
* *
76721 AAAAATTATATTTTGACTCCCAAACTTTTC
1 AAAAATTACATTTTGAC-CCCAAACTTTCC
* * *
76751 AAAAATTATATTTT-TCCCCTAAACTTTTC
1 AAAAATTACATTTTGACCCC-AAACTTTCC
* * *
76780 AAAAATCACAATTTTGCCCCCAAA-ATTCC
1 AAAAATTAC-ATTTTGACCCCAAACTTTCC
*
76809 AAAAATTACCATTTT-ACCCCTAAAC-ATCC
1 AAAAATTA-CATTTTGACCCC-AAACTTTCC
* *
76838 AAAAATTACCATTTT-ACCCTCGAA-TGTCC
1 AAAAATTA-CATTTTGACCC-CAAACTTTCC
* * * *
76867 AAAAATTACCATTTTGATCTCGAACTTTCT
1 AAAAATTA-CATTTTGACCCCAAACTTTCC
76897 AAAAATTACCATTTT-ACCCC
1 AAAAATTA-CATTTTGACCCC
76917 TGAACATAAA
Statistics
Matches: 194, Mismatches: 21, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.04
29 101 0.52
30 82 0.42
31 4 0.02
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCCAAACTTTCC
Found at i:76734 original size:59 final size:59
Alignment explanation
Indices: 76662--76943 Score: 224
Period size: 59 Copynumber: 4.8 Consensus size: 59
76652 TAAAGAGTCA
**
76662 AAAAATTA-CATTTTGACCCCAAACTTTCCAAAAATTA-CATTTTGACTCCC-AAACTTTTT
1 AAAAATTACCATTTTGACCCCAAA-TTTCCAAAAATTACCATTTT-AC-CCCTAAACTTTCC
* * * * *
76721 AAAAATTA-TATTTTGACTCCCAAACTTTTCAAAAATTA-TATTTTTCCCCTAAACTTTTC
1 AAAAATTACCATTTTGAC-CCCAAA-TTTCCAAAAATTACCATTTTACCCCTAAACTTTCC
* * * * *
76780 AAAAATCACAATTTTGCCCCCAAAATTCCAAAAATTACCATTTTACCCCTAAAC-ATCC
1 AAAAATTACCATTTTGACCCCAAATTTCCAAAAATTACCATTTTACCCCTAAACTTTCC
* * * * * *
76838 AAAAATTACCATTTT-ACCCTCGAATGTCCAAAAATTACCATTTTGATCTC-GAACTTTCT
1 AAAAATTACCATTTTGACCC-CAAATTTCCAAAAATTACCATTTT-ACCCCTAAACTTTCC
* ** *
76897 AAAAATTACCATTTT-ACCCCTGAACAT-AAAAAATTACCATTTTACCC
1 AAAAATTACCATTTTGACCCC-AAATTTCCAAAAATTACCATTTTACCC
76944 TTGGGTGTTC
Statistics
Matches: 185, Mismatches: 30, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
57 5 0.03
58 69 0.37
59 80 0.43
60 31 0.17
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTGACCCCAAATTTCCAAAAATTACCATTTTACCCCTAAACTTTCC
Found at i:76881 original size:87 final size:87
Alignment explanation
Indices: 76779--76944 Score: 226
Period size: 87 Copynumber: 1.9 Consensus size: 87
76769 CTAAACTTTT
*
76779 CAAAAATCACAATTTTG-CCCCCAAAATTCCAAAAATTACCATTTTACCCCTAAACATCCAAAAA
1 CAAAAATCACAATTTTGACCCCCAAAATTCCAAAAATTACCATTTTACCCCTAAACAT-AAAAAA
76843 TTACCATTTTACCCTCGAATGTC
65 TTACCATTTTACCCTCGAATGTC
* * * * * ** * *
76866 CAAAAATTACCATTTTGATCTCGAACTTTCTAAAAATTACCATTTTACCCCTGAACATAAAAAAT
1 CAAAAATCACAATTTTGACCCCCAAAATTCCAAAAATTACCATTTTACCCCTAAACATAAAAAAT
76931 TACCATTTTACCCT
66 TACCATTTTACCCT
76945 TGGGTGTTCG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
87 35 0.51
88 33 0.49
ACGTcount: A:0.39, C:0.27, G:0.04, T:0.31
Consensus pattern (87 bp):
CAAAAATCACAATTTTGACCCCCAAAATTCCAAAAATTACCATTTTACCCCTAAACATAAAAAAT
TACCATTTTACCCTCGAATGTC
Found at i:81521 original size:1 final size:1
Alignment explanation
Indices: 81515--81543 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
81505 AGAATTCAAG
81515 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
81544 CTATATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:82474 original size:5 final size:5
Alignment explanation
Indices: 82464--82498 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
82454 GGAAATTAAC
* *
82464 CAAAA CAAAA CAAAA CAAAA CAAAA TAAAA TAAAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA CAAAA
82499 ATTGTGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.80, C:0.14, G:0.00, T:0.06
Consensus pattern (5 bp):
CAAAA
Found at i:82926 original size:23 final size:23
Alignment explanation
Indices: 82891--82935 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
82881 ATACATCAAC
*
82891 ATTATATATAAAA-TATTATTAAA
1 ATTATATAAAAAATTA-TATTAAA
*
82914 ATTATGTAAAAAATTATATTAA
1 ATTATATAAAAAATTATATTAA
82936 TCATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTATATAAAAAATTATATTAAA
Found at i:84634 original size:19 final size:18
Alignment explanation
Indices: 84606--84642 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
84596 ATATTAAATT
84606 AATATTTTATAATTTAAA
1 AATATTTTATAATTTAAA
*
84624 AATATTTTTATTATTTAAA
1 AATA-TTTTATAATTTAAA
84643 TCGAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATATTTTATAATTTAAA
Found at i:97136 original size:23 final size:24
Alignment explanation
Indices: 97110--97165 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 24
97100 ATTCAAATTG
97110 CAAAATTCAACTTGATTCG-AACT
1 CAAAATTCAACTTGATTCGTAACT
97133 C-AAA--CAACTTGATTCGATTAACT
1 CAAAATTCAACTTGATTCG--TAACT
97156 CAAAATTCAA
1 CAAAATTCAA
97166 ATTTTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
20 12 0.44
22 3 0.11
23 6 0.22
24 3 0.11
26 3 0.11
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (24 bp):
CAAAATTCAACTTGATTCGTAACT
Found at i:97580 original size:9 final size:9
Alignment explanation
Indices: 97541--97609 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
97531 ATTATTTTTT
*
97541 AAAATTAAA
1 AAAATTATA
97550 AAAATTATA
1 AAAATTATA
*
97559 GAAATTATTTA
1 AAAATTA--TA
97570 AAAATTAT-
1 AAAATTATA
* *
97578 AAAATCATT
1 AAAATTATA
*
97587 AAAAGTATA
1 AAAATTATA
*
97596 AAAAATATA
1 AAAATTATA
97605 AAAAT
1 AAAAT
97610 ATTTTTTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
8 7 0.15
9 33 0.69
11 8 0.17
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:107133 original size:153 final size:152
Alignment explanation
Indices: 106831--107139 Score: 363
Period size: 153 Copynumber: 2.0 Consensus size: 152
106821 CTCCTTCCAC
* * * *
106831 TTGAAATCCCATTCAAGATGAAAGCCATTATAAATAGCTCAAAGTTCAGTTTGTTCAACACTACA
1 TTGAAATCCCATGCAAGATGAAAGCCATCATAAATAGCTCAAAGTTCAGCTTGATCAACACTACA
* * * ** *
106896 TCTTTCAACATTTCTTCCAATCACCCATTGCCACCTACCATACTCATCTCTTGCCATTATTGCCT
66 TCTTTCAACATTTCTTCCAATCACCCATTACCACCTACCATACTCATCTCTTACCACTACCGCCG
*
106961 AAGACGTAAAACCCGAAGACAGA
131 AAGAC-TAAAACCCAAAGACAGA
* * * * *
106984 TTGAAATCTCATGCTAGATGAAGGCCATCATAAATAGCTCAACGTTCAGCTTGATCAACACTATA
1 TTGAAATCCCATGCAAGATGAAAGCCATCATAAATAGCTCAAAGTTCAGCTTGATCAACACTACA
* * * *
107049 TC-TTCAAATATTTCTTCCAAT-ACCTCATTACCACCTACCATAGTCATCTCTTATCACTACCGT
66 TCTTTC-AACATTTCTTCCAATCACC-CATTACCACCTACCATACTCATCTCTTACCACTACCGC
*
107112 CGAAGA-TACAAGACCTAAAGACAGA
129 CGAAGACTA-AA-ACCCAAAGACAGA
107137 TTG
1 TTG
107140 CGAGCACCAT
Statistics
Matches: 131, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
151 2 0.02
152 8 0.06
153 121 0.92
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.29
Consensus pattern (152 bp):
TTGAAATCCCATGCAAGATGAAAGCCATCATAAATAGCTCAAAGTTCAGCTTGATCAACACTACA
TCTTTCAACATTTCTTCCAATCACCCATTACCACCTACCATACTCATCTCTTACCACTACCGCCG
AAGACTAAAACCCAAAGACAGA
Found at i:108055 original size:19 final size:18
Alignment explanation
Indices: 108012--108048 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
108002 TCTTCGATAT
* *
108012 TATTTTTTTTTATTTTTG
1 TATTATTTTTTATTTTAG
108030 TATTATTTTTTATTTTAG
1 TATTATTTTTTATTTTAG
108048 T
1 T
108049 CTATATTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.78
Consensus pattern (18 bp):
TATTATTTTTTATTTTAG
Found at i:112827 original size:17 final size:16
Alignment explanation
Indices: 112805--112907 Score: 61
Period size: 17 Copynumber: 6.3 Consensus size: 16
112795 TTAGACTTTC
*
112805 TAAATTTAATTTTATAA
1 TAAATTTAATTTCA-AA
112822 TAAATTTAAATTTCAAA
1 TAAATTT-AATTTCAAA
*
112839 TAAATTTAA---GAAA
1 TAAATTTAATTTCAAA
*
112852 TTTAAATTTAAATTTAAAA
1 --TAAATTT-AATTTCAAA
*
112871 TAAACTTAAATTT-AAA
1 TAAA-TTTAATTTCAAA
** *
112887 TAAATTCGATTTCCAA
1 TAAATTTAATTTCAAA
112903 TAAAT
1 TAAAT
112908 CCAGACAAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 19
0.73 0.07 0.20
Matches are distributed among these distances:
13 3 0.04
15 13 0.19
16 18 0.26
17 25 0.36
18 8 0.11
19 3 0.04
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (16 bp):
TAAATTTAATTTCAAA
Found at i:112831 original size:6 final size:6
Alignment explanation
Indices: 112805--112887 Score: 59
Period size: 6 Copynumber: 13.8 Consensus size: 6
112795 TTAGACTTTC
*
112805 TAAATT TAATTT TATAA-- TAAATT TAAATT TCAAA-- TAAATT TAAGAAATT
1 TAAATT TAAATT TA-AATT TAAATT TAAATT T-AAATT TAAATT T---AAATT
* *
112854 TAAATT TAAATT TAAA-A TAAACT TAAATT TAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAAT
112888 AAATTCGATT
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
4 5 0.08
5 7 0.11
6 40 0.65
7 4 0.06
9 6 0.10
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:113439 original size:24 final size:23
Alignment explanation
Indices: 113401--113469 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 23
113391 ATATATAGAT
113401 TATACTTTATAAATATATAGTAATAAA
1 TATA-TTTAT-AATATATA--AATAAA
113428 TAT-TTTATAATATA-AAATAAA
1 TATATTTATAATATATAAATAAA
113449 TATATTT-TAATAGTATAAATA
1 TATATTTATAATA-TATAAATA
113470 TGGGTATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
21 14 0.36
22 5 0.13
23 6 0.15
24 6 0.15
25 5 0.13
27 3 0.08
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (23 bp):
TATATTTATAATATATAAATAAA
Found at i:119866 original size:19 final size:20
Alignment explanation
Indices: 119822--119858 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
119812 TACCGAAATC
119822 TAAATTAATGATAGAAAAGA
1 TAAATTAATGATAGAAAAGA
119842 TAAATTAATGATA-AAAA
1 TAAATTAATGATAGAAAA
119859 TTACAATTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (20 bp):
TAAATTAATGATAGAAAAGA
Found at i:123504 original size:88 final size:87
Alignment explanation
Indices: 123370--123544 Score: 269
Period size: 88 Copynumber: 2.0 Consensus size: 87
123360 TACAACTAAA
*
123370 TAATGAAAGTATTCTGAAAATCGTACCCAAATAAGGTTTGTTTAAACTAAGGGTCCCATTAGATG
1 TAATGAAAGTATTCTGAAAATCGTACCCAAATAAGGCTTGTTTAAACTAAGGGTCCCATTAGATG
** *
123435 GGCATTTATTTTTAGAGCGTTG
66 AACATTTACTTTTAGAGCGTTG
* * *
123457 TAATGAAAGTATTCTGAAAATTGTAACCCAAGTAAGGCTTGTTTAAACTAAGGGTCCCCTTAGAT
1 TAATGAAAGTATTCTGAAAATCGT-ACCCAAATAAGGCTTGTTTAAACTAAGGGTCCCATTAGAT
*
123522 GAACATTTACTTTTAGAGTGTTG
65 GAACATTTACTTTTAGAGCGTTG
123545 CGTTTAGTTG
Statistics
Matches: 79, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 23 0.29
88 56 0.71
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (87 bp):
TAATGAAAGTATTCTGAAAATCGTACCCAAATAAGGCTTGTTTAAACTAAGGGTCCCATTAGATG
AACATTTACTTTTAGAGCGTTG
Found at i:127621 original size:2 final size:2
Alignment explanation
Indices: 127614--127661 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
127604 GACGTGAAGG
127614 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
127656 CT CT CT
1 CT CT CT
127662 ATTACATACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:139408 original size:6 final size:6
Alignment explanation
Indices: 139394--139433 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
139384 GCAGTGTCAT
* *
139394 TGCCAA TGCCGA TGCCAA TGCCGA TGCCGA TGCCGA TGCC
1 TGCCGA TGCCGA TGCCGA TGCCGA TGCCGA TGCCGA TGCC
139434 ATATGGTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.20, C:0.35, G:0.28, T:0.17
Consensus pattern (6 bp):
TGCCGA
Found at i:139411 original size:12 final size:12
Alignment explanation
Indices: 139394--139434 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
139384 GCAGTGTCAT
139394 TGCCAATGCCGA
1 TGCCAATGCCGA
139406 TGCCAATGCCGA
1 TGCCAATGCCGA
*
139418 TGCCGATGCCGA
1 TGCCAATGCCGA
139430 TGCCA
1 TGCCA
139435 TATGGTTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.22, C:0.34, G:0.27, T:0.17
Consensus pattern (12 bp):
TGCCAATGCCGA
Found at i:145475 original size:52 final size:52
Alignment explanation
Indices: 145371--145481 Score: 177
Period size: 52 Copynumber: 2.1 Consensus size: 52
145361 CTTTACACTA
*
145371 TTATATCAACATTTGTTATTAATGAAGTCAGGTTAATTACAAATGACATGCT
1 TTATATCAACATTTGTTATTAATGAAGTCAGGTTAATTACAAATCACATGCT
* * *
145423 TTATATCAACATTTGTTATTAATGAAGTCAGGTTAATTTCAAGTCACCTGCT
1 TTATATCAACATTTGTTATTAATGAAGTCAGGTTAATTACAAATCACATGCT
*
145475 TTCTATC
1 TTATATC
145482 CTTGCATCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (52 bp):
TTATATCAACATTTGTTATTAATGAAGTCAGGTTAATTACAAATCACATGCT
Found at i:155087 original size:2 final size:2
Alignment explanation
Indices: 155080--155118 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
155070 TTATTTCCAT
155080 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
155119 AATTTATCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:156816 original size:39 final size:41
Alignment explanation
Indices: 156762--156859 Score: 148
Period size: 39 Copynumber: 2.4 Consensus size: 41
156752 TATGCACTTA
156762 ATGGACACCTTTTGAAGAA-TCACAACCC-TTTCATATTGG
1 ATGGACACCTTTTGAAGAAGTCACAACCCTTTTCATATTGG
*
156801 ATGGACACCTTTTGAA-AAGTCACAACCCTTTTCATATTGT
1 ATGGACACCTTTTGAAGAAGTCACAACCCTTTTCATATTGG
*
156841 ATGGACACTTTTTGGAAGA
1 ATGGACACCTTTT-GAAGA
156860 GACTTGTCCC
Statistics
Matches: 53, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
38 2 0.04
39 25 0.47
40 22 0.42
41 3 0.06
42 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (41 bp):
ATGGACACCTTTTGAAGAAGTCACAACCCTTTTCATATTGG
Found at i:161740 original size:39 final size:40
Alignment explanation
Indices: 161686--161784 Score: 155
Period size: 40 Copynumber: 2.5 Consensus size: 40
161676 TATGCACTCA
*
161686 ATGGACACCTTTTGAAGAGTTACAA-CCATTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCATTTCATATTGG
* *
161725 ATGGACACCTTTTGAAAAGTCACAACCCTTTTCATATTGG
1 ATGGACACCTTTTGAAGAGTCACAACCCATTTCATATTGG
161765 ATGGACACCTTTTGGAAGAG
1 ATGGACACCTTTT-GAAGAG
161785 ACTTGTCTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 23 0.43
40 26 0.48
41 5 0.09
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (40 bp):
ATGGACACCTTTTGAAGAGTCACAACCCATTTCATATTGG
Found at i:161853 original size:20 final size:19
Alignment explanation
Indices: 161809--161846 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
161799 CATTGGATGA
*
161809 TAAATCATCATTTTTCAAT
1 TAAATCATCACTTTTCAAT
161828 TAAATCATCACTTTT-AAT
1 TAAATCATCACTTTTCAAT
161846 T
1 T
161847 TGAAATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.47
Consensus pattern (19 bp):
TAAATCATCACTTTTCAAT
Found at i:163298 original size:3 final size:3
Alignment explanation
Indices: 163292--163319 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
163282 TAATAATAAT
163292 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
163320 TGGATGTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:165265 original size:12 final size:12
Alignment explanation
Indices: 165248--165301 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 12
165238 TAAATATAAA
165248 TATTATTTTAAT
1 TATTATTTTAAT
165260 TATTATTTTAA-
1 TATTATTTTAAT
*
165271 TA-TATTTTTAT
1 TATTATTTTAAT
165282 TA-TA-TTTAAT
1 TATTATTTTAAT
*
165292 ATATAATTTT
1 -TATTATTTT
165302 TAATATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 12 0.34
11 8 0.23
12 12 0.34
13 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTATTTTAAT
Found at i:165300 original size:23 final size:21
Alignment explanation
Indices: 165244--165308 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 21
165234 ATTTTAAATA
*
165244 TAAATATTATTTTAATTATTATT
1 TAAATA-TATTTTTATTA-TATT
*
165267 TTAATATATTTTTATTATATT
1 TAAATATATTTTTATTATATT
*
165288 TAATATATAATTTTTAATATA
1 TAA-ATAT-ATTTTTATTATA
165309 AATCTAATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.17
22 14 0.39
23 16 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TAAATATATTTTTATTATATT
Found at i:172217 original size:2 final size:2
Alignment explanation
Indices: 172212--172251 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
172202 TCTCAATTAA
172212 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
172252 TAATCCTGTT
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:176617 original size:46 final size:46
Alignment explanation
Indices: 176564--176652 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
176554 GCTCTGTTCA
176564 GAAGCAGAAATAATTCTATATCACGTTATACATTAATGATCCTTAG
1 GAAGCAGAAATAATTCTATATCACGTTATACATTAATGATCCTTAG
* * * *
176610 GAAGCAGAAGTACTTCTTTATCACGTTATATATTAATGATCCT
1 GAAGCAGAAATAATTCTATATCACGTTATACATTAATGATCCT
176653 ACTGGTTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (46 bp):
GAAGCAGAAATAATTCTATATCACGTTATACATTAATGATCCTTAG
Found at i:179475 original size:2 final size:2
Alignment explanation
Indices: 179468--179523 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
179458 CAATTGTGAA
*
179468 CT CT CT CT TT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
179510 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
179524 ATTAAATTAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
CT
Found at i:187169 original size:6 final size:6
Alignment explanation
Indices: 187160--187254 Score: 56
Period size: 6 Copynumber: 15.8 Consensus size: 6
187150 GTTTATCTTC
* * *
187160 AGCATT AGCATC AGC-TT CAGCATT AGCATC AGC-TT CAGCATC AGC-TT
1 AGCATT AGCATT AGCATT -AGCATT AGCATT AGCATT -AGCATT AGCATT
* * *
187207 CAGCATT AGCATC AGC-TT CAGAATT AGCATC AGC-TT CAGCATT AGCAT
1 -AGCATT AGCATT AGCATT -AGCATT AGCATT AGCATT -AGCATT AGCAT
187255 CACTATCATC
Statistics
Matches: 67, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
5 5 0.07
6 53 0.79
7 9 0.13
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (6 bp):
AGCATT
Found at i:187179 original size:18 final size:18
Alignment explanation
Indices: 187156--187256 Score: 151
Period size: 18 Copynumber: 5.9 Consensus size: 18
187146 ATTGGTTTAT
187156 CTTCAGCATTAGCATCAG
1 CTTCAGCATTAGCATCAG
187174 CTTCAGCATTAGCATCAG
1 CTTCAGCATTAGCATCAG
187192 CTT---C---AGCATCAG
1 CTTCAGCATTAGCATCAG
187204 CTTCAGCATTAGCATCAG
1 CTTCAGCATTAGCATCAG
*
187222 CTTCAGAATTAGCATCAG
1 CTTCAGCATTAGCATCAG
187240 CTTCAGCATTAGCATCA
1 CTTCAGCATTAGCATCA
187257 CTATCATCAT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
12 11 0.15
15 2 0.03
18 62 0.83
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.28
Consensus pattern (18 bp):
CTTCAGCATTAGCATCAG
Found at i:187181 original size:12 final size:12
Alignment explanation
Indices: 187156--187248 Score: 91
Period size: 12 Copynumber: 7.8 Consensus size: 12
187146 ATTGGTTTAT
*
187156 CTTCAGCATTAG
1 CTTCAGCATCAG
* *
187168 CATCAGCTTCAG
1 CTTCAGCATCAG
187180 CATT-AGCATCAG
1 C-TTCAGCATCAG
187192 CTTCAGCATCAG
1 CTTCAGCATCAG
*
187204 CTTCAGCATTAG
1 CTTCAGCATCAG
* *
187216 CATCAGCTTCAG
1 CTTCAGCATCAG
*
187228 AATT-AGCATCAG
1 -CTTCAGCATCAG
187240 CTTCAGCAT
1 CTTCAGCAT
187249 TAGCATCACT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
11 4 0.06
12 58 0.91
13 2 0.03
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (12 bp):
CTTCAGCATCAG
Found at i:187200 original size:30 final size:30
Alignment explanation
Indices: 187158--187256 Score: 128
Period size: 30 Copynumber: 3.1 Consensus size: 30
187148 TGGTTTATCT
187158 TCAGCATT-AGCATCAGCTTCAGCATTAGCA
1 TCAGC-TTCAGCATCAGCTTCAGCATTAGCA
187188 TCAGCTTCAGCATCAGCTTCAGCATTAGCA
1 TCAGCTTCAGCATCAGCTTCAGCATTAGCA
187218 TCAGCTTCAGAATTAGCATCAGCTTCAGCATTAGCA
1 TCAGCTTC------AGCATCAGCTTCAGCATTAGCA
187254 TCA
1 TCA
187257 CTATCATCAT
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
29 2 0.03
30 35 0.56
36 25 0.40
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (30 bp):
TCAGCTTCAGCATCAGCTTCAGCATTAGCA
Found at i:191689 original size:157 final size:156
Alignment explanation
Indices: 191394--191691 Score: 395
Period size: 157 Copynumber: 1.9 Consensus size: 156
191384 AAACTGCTCG
* *
191394 ACAAAAGGGTGTGCTTAAAAAGAAATGAATTAACCGTTTGAAAAGTTAGTTGATCTATTAATAGA
1 ACAAAAGGGTGCGCTTAAAAAGAAATGAATTAACCGTTTGAAAAGTTAATTGATCTATTAATAGA
* * *
191459 TCAGATCGTTATATTCTTTTTACACGCACCACTTTCATTAAACTCTTATCCTCACCGTTTAACTA
66 TCAGATCCTTATATTCTTTTTACACGCACCACTTTCATTAAACTCTAATCCGCACCGTTTAACTA
*
191524 AAATAAAATGCTCTGTTTTACATCCA
131 AAACAAAATGCTCTGTTTTACATCCA
191550 ACAATAAGGGTGCGCTTAAAAAGAAATGAATTAACCGTTTGAAAAGTTAATTGA-CTTATTAATA
1 ACAA-AAGGGTGCGCTTAAAAAGAAATGAATTAACCGTTTGAAAAGTTAATTGATC-TATTAATA
* * * * * ** * **
191614 -ACTCAGGTCCTTGTCTTCTCTTTT-TACGCGCCGTTTTCATTAAATTCTAATCCGCATTGTTTA
64 GA-TCAGATCCTTATATTCT-TTTTACACGCACCACTTTCATTAAACTCTAATCCGCACCGTTTA
191677 ACTAAAACAAAATGC
127 ACTAAAACAAAATGC
191692 CATGTTATAC
Statistics
Matches: 122, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
156 6 0.05
157 112 0.92
158 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (156 bp):
ACAAAAGGGTGCGCTTAAAAAGAAATGAATTAACCGTTTGAAAAGTTAATTGATCTATTAATAGA
TCAGATCCTTATATTCTTTTTACACGCACCACTTTCATTAAACTCTAATCCGCACCGTTTAACTA
AAACAAAATGCTCTGTTTTACATCCA
Found at i:193672 original size:6 final size:6
Alignment explanation
Indices: 193661--193692 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
193651 TGGAAACATT
193661 AACTTA AACTTA AACTTA AACTTA AACTTA AA
1 AACTTA AACTTA AACTTA AACTTA AACTTA AA
193693 TAGAAGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (6 bp):
AACTTA
Found at i:194494 original size:13 final size:13
Alignment explanation
Indices: 194476--194500 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
194466 ACGATACCAC
194476 TCAACGGTATCAT
1 TCAACGGTATCAT
194489 TCAACGGTATCA
1 TCAACGGTATCA
194501 CTTAGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (13 bp):
TCAACGGTATCAT
Found at i:197214 original size:18 final size:18
Alignment explanation
Indices: 197193--197232 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
197183 CCAGTAGTAG
*
197193 TAGAATTGCCAGACACAA
1 TAGAATGGCCAGACACAA
* *
197211 TAGAATGGCCATACACAG
1 TAGAATGGCCAGACACAA
197229 TAGA
1 TAGA
197233 CGGTGCGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (18 bp):
TAGAATGGCCAGACACAA
Found at i:205466 original size:32 final size:33
Alignment explanation
Indices: 205420--205501 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 33
205410 CAAGCTTATT
* * *
205420 TAAAGTTGTTATTTTATTAA-TTTTGTTTTGGC
1 TAAATTTGTTATTTTATTAATTTTTATTTTGAC
*
205452 TAAATTTGTTATTTTTTTAATTTTTATTTTGAC
1 TAAATTTGTTATTTTATTAATTTTTATTTTGAC
205485 TAAAATTAT-TTATTTTA
1 T-AAATT-TGTTATTTTA
205502 AGTAAATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 18 0.43
33 11 0.26
34 12 0.29
35 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.09, T:0.62
Consensus pattern (33 bp):
TAAATTTGTTATTTTATTAATTTTTATTTTGAC
Found at i:213519 original size:6 final size:6
Alignment explanation
Indices: 213503--213532 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
213493 ATAGTTGGCA
*
213503 TCCATC GCCATC TCCATC TCCATC TCCATC
1 TCCATC TCCATC TCCATC TCCATC TCCATC
213533 ATCGAGATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.50, G:0.03, T:0.30
Consensus pattern (6 bp):
TCCATC
Found at i:220762 original size:20 final size:20
Alignment explanation
Indices: 220737--220774 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
220727 AGGAAAAGCT
220737 TTTACCAAAATATCTAAGGA
1 TTTACCAAAATATCTAAGGA
* *
220757 TTTACCAATATTTCTAAG
1 TTTACCAAAATATCTAAG
220775 ACCAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (20 bp):
TTTACCAAAATATCTAAGGA
Found at i:231699 original size:17 final size:19
Alignment explanation
Indices: 231665--231702 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
231655 ATATTAAGTA
231665 TATTACTTAAAATTTAAAAT
1 TATTACTTAAAA-TTAAAAT
231685 TATTA-TTAAAA-TAAAAT
1 TATTACTTAAAATTAAAAT
231702 T
1 T
231703 GTAATACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 6 0.33
20 5 0.28
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (19 bp):
TATTACTTAAAATTAAAAT
Found at i:233094 original size:23 final size:24
Alignment explanation
Indices: 233067--233125 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 24
233057 TGATAAATCA
233067 TTGTAT-TTAAATTTTA-AAATATC
1 TTGTATATT-AATTTTACAAATATC
*
233090 TTGTATCATTAATTTTACAAATA-A
1 TTGTAT-ATTAATTTTACAAATATC
233114 TT-TATATTAATT
1 TTGTATATTAATT
233126 ACTTAAAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
22 7 0.22
23 9 0.28
24 9 0.28
25 7 0.22
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (24 bp):
TTGTATATTAATTTTACAAATATC
Found at i:236077 original size:22 final size:21
Alignment explanation
Indices: 236029--236090 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
236019 AGTTGTGTGT
236029 AATTACACAAAATATTATC--C
1 AATTACACAAAATATTA-CAAC
*
236049 AATTACACAAATTATTACAAC
1 AATTACACAAAATATTACAAC
*
236070 AAATTACACAAAACATTACAA
1 -AATTACACAAAATATTACAA
236091 ATTATTACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 1 0.03
20 16 0.44
21 1 0.03
22 18 0.50
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (21 bp):
AATTACACAAAATATTACAAC
Found at i:244608 original size:19 final size:19
Alignment explanation
Indices: 244584--244628 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
244574 AAATCCCATA
* *
244584 AATTACTCCTAGCATCTCT
1 AATTACTCCTAACATCCCT
*
244603 AATTACTCCTAACTTCCCT
1 AATTACTCCTAACATCCCT
244622 AATTACT
1 AATTACT
244629 TGTAACACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.31, G:0.02, T:0.38
Consensus pattern (19 bp):
AATTACTCCTAACATCCCT
Found at i:249625 original size:19 final size:19
Alignment explanation
Indices: 249601--249646 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
249591 AAATCCCACA
*
249601 AATTACTCCTAACTTCTCG
1 AATTACTCCTAACTTCCCG
*
249620 AATTACTCCTAACTTCCCT
1 AATTACTCCTAACTTCCCG
249639 AATTACTC
1 AATTACTC
249647 GTAATAGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.28, C:0.33, G:0.02, T:0.37
Consensus pattern (19 bp):
AATTACTCCTAACTTCCCG
Found at i:252981 original size:235 final size:235
Alignment explanation
Indices: 252566--253025 Score: 785
Period size: 235 Copynumber: 2.0 Consensus size: 235
252556 CCTTCAAAAT
*
252566 GACTAGTTTTTTAGCCCTACCAACGTGTCTCCTTTGACTCATTTTGATCGACAACTTCTTCCGAC
1 GACTAGTTTTCTAGCCCTACCAACGTGTCTCCTTTGACTCATTTTGATCGACAACTTCTTCCGAC
* *
252631 ATCTTAATGATGTCTTCACAACTTGGCTTTGATACCAATTGTCACGAGGCTAAAACTTTAGTCTC
66 ATCTTAACGATGCCTTCACAACTTGGCTTTGATACCAATTGTCACGAGGCTAAAACTTTAGTCTC
** *
252696 GTAATCCATACGGCCTTAAGCAATCCTATCGATTCAAACACGTCTAAGTCAGCCTAACCACCAAT
131 ACAATCCATACGGCCTTAAGCAATCCTATCGATTCAAACACGTCTAAGTCAGCCTAACCACCAAC
252761 AATTAAAGATTCACACAAAAGTCCTTCAAGTTATCTCAAC
196 AATTAAAGATTCACACAAAAGTCCTTCAAGTTATCTCAAC
* *
252801 GACTAGTTTTCTGGCCCTACCAACGTGTCTCCTTTGACTCATTTTGATCGACAACTTCTTCTGAC
1 GACTAGTTTTCTAGCCCTACCAACGTGTCTCCTTTGACTCATTTTGATCGACAACTTCTTCCGAC
* * *
252866 ATCTTAGCGATGCCTTCACAACTTGGCTTTGATACCAATTGTCATGGGGCTAAAACTTTAGTCTC
66 ATCTTAACGATGCCTTCACAACTTGGCTTTGATACCAATTGTCACGAGGCTAAAACTTTAGTCTC
* * *
252931 ACAATCCGTACGGCCTTAAGCAATCCTATCGATTCAAACACGTTTAAGTCAGCTTAACCACCAAC
131 ACAATCCATACGGCCTTAAGCAATCCTATCGATTCAAACACGTCTAAGTCAGCCTAACCACCAAC
*
252996 AATTAAAGATTCACACGAAAGTCCTTCAAG
196 AATTAAAGATTCACACAAAAGTCCTTCAAG
253026 AAACCAAATT
Statistics
Matches: 210, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
235 210 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (235 bp):
GACTAGTTTTCTAGCCCTACCAACGTGTCTCCTTTGACTCATTTTGATCGACAACTTCTTCCGAC
ATCTTAACGATGCCTTCACAACTTGGCTTTGATACCAATTGTCACGAGGCTAAAACTTTAGTCTC
ACAATCCATACGGCCTTAAGCAATCCTATCGATTCAAACACGTCTAAGTCAGCCTAACCACCAAC
AATTAAAGATTCACACAAAAGTCCTTCAAGTTATCTCAAC
Found at i:263366 original size:29 final size:29
Alignment explanation
Indices: 263334--263421 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
263324 TCGAAGAATA
*
263334 TGGGGTTAAAATATAATTTTAGAAAAGTT
1 TGGGGTTAAAATGTAATTTTAGAAAAGTT
* *
263363 TGGGGATAAAAATGTAATTTT-GAGAATGTT
1 TGGGG-TTAAAATGTAATTTTAGA-AAAGTT
* * *
263393 T-GGATTAAAATGTGATTTTAGAGAAGTT
1 TGGGGTTAAAATGTAATTTTAGAAAAGTT
263421 T
1 T
263422 TAGGAAGCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
28 18 0.38
29 11 0.23
30 19 0.40
ACGTcount: A:0.38, C:0.00, G:0.24, T:0.39
Consensus pattern (29 bp):
TGGGGTTAAAATGTAATTTTAGAAAAGTT
Found at i:263410 original size:28 final size:28
Alignment explanation
Indices: 263341--263421 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 28
263331 ATATGGGGTT
* *
263341 AAAATATAATTTTAGAAAAGTTTGGGGATA
1 AAAATGTAATTTTAGAGAAGTTT--GGATA
*
263371 AAAATGTAATTTT-GAGAATGTTTGGATT
1 AAAATGTAATTTTAGAGAA-GTTTGGATA
*
263399 AAAATGTGATTTTAGAGAAGTTT
1 AAAATGTAATTTTAGAGAAGTTT
263422 TAGGAAGCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 20 0.44
29 9 0.20
30 16 0.36
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (28 bp):
AAAATGTAATTTTAGAGAAGTTTGGATA
Found at i:265135 original size:39 final size:39
Alignment explanation
Indices: 265083--265317 Score: 201
Period size: 39 Copynumber: 6.0 Consensus size: 39
265073 AAGATTAGTT
265083 GATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
1 GATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * *
265122 GATGGTTTAAATCTGCCACATGATCGGCGTAAGAGATTG
1 GATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * *
265161 GATGGTTTCAATCTGCCCCATGATCGAGGTAA-AAATCG
1 GATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
* * * *
265199 GATGGTTGCAATATGCCCCCT-ATCGCAAGGTAAGAGATTG
1 GATGGTTTCAATCTGCCCCATGATCG--GGGTAAGAGATTG
* *** * * *
265239 GCTGACAGT-GATCTGTCCCATGATCGGGGTAAAAGATCT-
1 GATG-GTTTCAATCTGCCCCATGATCGGGGTAAGAGAT-TG
** * *
265278 GATGGTTGT-AATCTGCCTTAAGCTCGGGGTAAGAGATTG
1 GATGGTT-TCAATCTGCCCCATGATCGGGGTAAGAGATTG
265317 G
1 G
265318 TTGATGGTGA
Statistics
Matches: 152, Mismatches: 36, Indels: 16
0.75 0.18 0.08
Matches are distributed among these distances:
37 4 0.03
38 23 0.15
39 105 0.69
40 16 0.11
41 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (39 bp):
GATGGTTTCAATCTGCCCCATGATCGGGGTAAGAGATTG
Found at i:265253 original size:78 final size:78
Alignment explanation
Indices: 265093--265626 Score: 352
Period size: 78 Copynumber: 6.8 Consensus size: 78
265083 GATGGTTTCA
* * * ** * *
265093 ATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTTAAATCTGCCAC-ATGATC-GGCGTAAGA
1 ATCTGCCCCATGATCGAGGTAAAAGATCGGATGGTTGCAATCTGCCCCTA-GCTCAGG-GTAAGA
* *** *
265156 GATTGGATG-GTTTCA
64 GATTGGCTGACAGT-G
* * * *
265171 ATCTGCCCCATGATCGAGGTAAAA-ATCGGATGGTTGCAATATGCCCCCTATCGCAAGGTAAGAG
1 ATCTGCCCCATGATCGAGGTAAAAGATCGGATGGTTGCAATCTG-CCCCTAGCTCAGGGTAAGAG
265235 ATTGGCTGACAGTG
65 ATTGGCTGACAGTG
* * * * * *
265249 ATCTGTCCCATGATCGGGGTAAAAGATCTGATGGTTGTAATCTG-CCTTAAGCTCGGGGTAAGAG
1 ATCTGCCCCATGATCGAGGTAAAAGATCGGATGGTTGCAATCTGCCCCT-AGCTCAGGGTAAGAG
* **
265313 ATTGGTTGATGGTG
65 ATTGGCTGACAGTG
* * * * *
265327 ATCTGCCCCAAGCTCG-GAGTAAAAGATCGGATGGCTACAATCT-ACCCTAGGCTCAGGGTAAGA
1 ATCTGCCCCATGATCGAG-GTAAAAGATCGGATGGTTGCAATCTGCCCCTA-GCTCAGGGTAAGA
* * **
265390 GATTGACTAATTGTG
64 GATTGGCTGACAGTG
* * * ** * * * * *
265405 ATCTG-CCCAGGCTCGGGGTAAAAGATCTAATGGCTGTAATCTGCCTCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCATGATCGAGGTAAAAGATCGGATGGTTGCAATCTGCCCCTAGCTCAGGGTAAGAGA
*
265469 TTGGCTGA-TGATG
66 TTGGCTGACAG-TG
* * * * * * *
265482 ATCTGCCCCAAGCTAGAGGTAAAAGATCAGATGGTTGCAATCTGCTCCTA-ATCGTGGAGTAAGA
1 ATCTGCCCCATGATCGAGGTAAAAGATCGGATGGTTGCAATCTGCCCCTAGCTC-AGG-GTAAGA
* *
265546 GATTGGCTGGCAATG
64 GATTGGCTGACAGTG
* * * * * *
265561 ATCTGCCTCATGATC-AGGGTAAAAGATCGAATGGTTGCAATCTACCCCAAGCTCAAGGTAAAAG
1 ATCTGCCCCATGATCGA-GGTAAAAGATCGGATGGTTGCAATCTGCCCCTAGCTCAGGGTAAGAG
265625 AT
65 AT
265627 CGGATGGCTG
Statistics
Matches: 357, Mismatches: 81, Indels: 36
0.75 0.17 0.08
Matches are distributed among these distances:
76 2 0.01
77 79 0.22
78 198 0.55
79 76 0.21
80 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (78 bp):
ATCTGCCCCATGATCGAGGTAAAAGATCGGATGGTTGCAATCTGCCCCTAGCTCAGGGTAAGAGA
TTGGCTGACAGTG
Found at i:265331 original size:39 final size:39
Alignment explanation
Indices: 265227--266488 Score: 565
Period size: 39 Copynumber: 32.3 Consensus size: 39
265217 CCTATCGCAA
** * * *
265227 GGTAAGAGATTGGCTGACAGTGATCTGTCCCATGATCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* **
265266 GGTAAAAGA-T--CTGATGGTTGTAATCTGCCTTAAGCTCGG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAAGCTCGG
*
265305 GGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * * * * * * *
265344 AGTAAAAGA-T--CGGATGGCTACAATCTACCCTAGGCTCAG
1 GGTAAGAGATTGGCTGATGG-T--GATCTGCCCCAAGCTCGG
* * * *
265383 GGTAAGAGATTGACTAATTGTGATCTG-CCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * *
265421 GGTAAAAGA-T--CTAATGGCTGTAATCTGCCTCAAGCTCGG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAAGCTCGG
* * *
265460 GGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTAGA
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * *
265499 GGTAAAAGA-T--CAGATGGTTGCAATCTGCTCCTAA--TCGTG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTGC-CCCAAGCTCG-G
**** * * * *
265538 GAGTAAGAGATTGGCTGGCAATGATCTGCCTCATGATCAG
1 G-GTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * ** * * ** * **
265578 GGTAAAAGATCGAATGGTTGCAATCTACCCCAAGCTCAA
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * ** *
265617 GGTAAAAGA-T--CGGATGGCTGCAATCTGGTCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAAGCTCGG
*
265656 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * * *
265695 GGTAAAAGA-T--CTAATGGCTGCAACCTACCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAAGCTCGG
* *
265734 GGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGA
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * * * * *
265773 GGAAAAAGATT-G--GATGGCTACAATCTGTCCCAGGCTCAG
1 GGTAAGAGATTGGCTGATGG-T--GATCTGCCCCAAGCTCGG
* * * *
265812 GGTAAGTGATTGGCTAATAGTGATCTGCCCCAGGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * *
265851 GGTAAAAGATT---TGATGGCTGCAATCTACCCCAAGCTCGA
1 GGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAAGCTCGG
* *
265890 GGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGA
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * *
265929 GGTAAAAGATT-G--GATGGCTGCAATCTGTCCCAAGCTTGG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAAGCTCGG
* * * * * * **
265968 GGTAATAGATTGGTTGATGGTAATTTCCCCCAAACTTAG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* ** * ** * * *
266007 GGTAAAAGATCAGATGACT-GCAATCTACCTCAGGCTCGG
1 GGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAAGCTCGG
* * *
266046 GGTAAGAGATTGGCTGATAGTGATCTGCCTCGAGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * * * **** * *
266085 GGTAAAAGATCGGATGGTTACAATTTGCCCCAAGCTTGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * *
266124 GGTAA-AGGATTGGTTAATGGTGATCTGCCCTAAGCTCGG
1 GGTAAGA-GATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * * ** * *
266163 GGTAAAAGATAGGATGACTACT-ATCTGCCCTAGGCTCGG
1 GGTAAGAGATTGGCTGA-TGGTGATCTGCCCCAAGCTCGG
*
266202 GGTAAGAGATTGACTGATGGTGATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * * * *
266241 GGTAAAAGA-T--CTGATGGTTGCAATCTGCACTAGGCTCTG
1 GGTAAGAGATTGGCTGATGG-TG--ATCTGCCCCAAGCTCGG
* * * *
266280 GGTAAGGAGATTGGCTGATTGTGATCTGTCTCAAGCTCGA
1 GGTAA-GAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * *
266320 GATAA-A-ATAT--CGGATGGCTGCAATCTACCCCAAGCTCGG
1 GGTAAGAGAT-TGGCTGATGG-TG--ATCTGCCCCAAGCTCGG
* * *
266359 GGTAAAAGATTGGTTAATGGTGATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
* * * * *
266398 GGTAAAAGATTAGAT-A-GCTGCAATCTACCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGGTG--ATCTGCCCCAAGCTCGG
*
266437 GGTAAGAGATTGGCTGATGGTAATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
*
266476 GGTAAAAGATTGG
1 GGTAAGAGATTGG
266489 ATGGATGTGA
Statistics
Matches: 910, Mismatches: 228, Indels: 170
0.70 0.17 0.13
Matches are distributed among these distances:
35 6 0.01
36 52 0.06
37 22 0.02
38 38 0.04
39 663 0.73
40 50 0.05
41 23 0.03
42 48 0.05
43 8 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (39 bp):
GGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGG
Found at i:265466 original size:155 final size:156
Alignment explanation
Indices: 265227--265524 Score: 438
Period size: 155 Copynumber: 1.9 Consensus size: 156
265217 CCTATCGCAA
* * * * *
265227 GGTAAGAGATTGGCTGACAGTGATCTGTCCCATGATCGGGGTAAAAGATCTGATGGTTGTAATCT
1 GGTAAGAGATTGACTAACAGTGATCTGTCCCAGGATCGGGGTAAAAGATCTAATGGCTGTAATCT
* * * * *
265292 GCCTTAAGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCG-GAGTAAAAGATCG
66 GCCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTAGAG-GTAAAAGATCA
265356 GATGGCTACAATCTACCCTAGGCTCAG
130 GATGGCTACAATCTACCCTAGGCTCAG
** *
265383 GGTAAGAGATTGACTAATTGTGATCTG-CCCAGGCTCGGGGTAAAAGATCTAATGGCTGTAATCT
1 GGTAAGAGATTGACTAACAGTGATCTGTCCCAGGATCGGGGTAAAAGATCTAATGGCTGTAATCT
265447 GCCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTAGAGGTAAAAGATCAG
66 GCCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTAGAGGTAAAAGATCAG
* *
265512 ATGGTTGCAATCT
131 ATGGCTACAATCT
265525 GCTCCTAATC
Statistics
Matches: 126, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
155 102 0.81
156 24 0.19
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.26
Consensus pattern (156 bp):
GGTAAGAGATTGACTAACAGTGATCTGTCCCAGGATCGGGGTAAAAGATCTAATGGCTGTAATCT
GCCTCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTGCCCCAAGCTAGAGGTAAAAGATCAG
ATGGCTACAATCTACCCTAGGCTCAG
Found at i:265687 original size:78 final size:77
Alignment explanation
Indices: 265600--266492 Score: 951
Period size: 78 Copynumber: 11.4 Consensus size: 77
265590 AATGGTTGCA
* ** ** *
265600 ATCTACCCCAAGCTCAAGGTAAAAGATCGGATGGCTGCAATCTGGTCCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAAGAGA
265665 TTGGCTGATGGTG
65 TTGGCTGATGGTG
* ** *
265678 ATCTGCCCCAGGCTCGGGGTAAAAGATCTAATGGCTGCAACCTACCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAAGAGA
*
265743 TTGGTTGATGGTG
65 TTGGCTGATGGTG
* * * * * * * *
265756 ATCTGCCCCAAGCTCGAGGAAAAAGATTGGATGGCTACAATCTGTCCCAGGCTCAGGGTAAGTGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAAGAGA
* *
265821 TTGGCTAATAGTG
65 TTGGCTGATGGTG
* ** *
265834 ATCTGCCCCAGGCTCGGGGTAAAAGATTTGATGGCTGCAATCTACCCCAAGCTCGAGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAAGAGA
*
265899 TTGGTTGATGGTG
65 TTGGCTGATGGTG
* * * * *
265912 ATCTGCCCCAAGCTCGAGGTAAAAGATTGGATGGCTGCAATCTGTCCCAAGCTTGGGGTAATAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAAGAGA
* *
265977 TTGGTTGATGGTA
65 TTGGCTGATGGTG
* * * ** * * * *
265990 ATTTCCCCCAAACTTAGGGTAAAAGATCAGATGACTGCAATCTACCTCAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAAGAGA
*
266055 TTGGCTGATAGTG
65 TTGGCTGATGGTG
* * * * * *
266068 ATCTGCCTCGAGCTCGGGGTAAAAGATCGGATGGTTACAATTTGCCCCAAGCTTGGGGTAA-AGG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAAGA-G
* *
266132 ATTGGTTAATGGTG
64 ATTGGCTGATGGTG
* * * * * * *
266146 ATCTGCCCTAAGCTCGGGGTAAAAGATAGGATGACTACTATCTGCCCTAGGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAAGAGA
*
266211 TTGACTGATGGTG
65 TTGGCTGATGGTG
* * * * * *
266224 ATCTGCCCCAAGCTCGGGGTAAAAGATCTGATGGTTGCAATCTGCACTAGGCTCTGGGTAAGGAG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAA-GAG
*
266289 ATTGGCTGATTGTG
64 ATTGGCTGATGGTG
* * * * * *
266303 ATCTGTCTCAAGCTCGAGATAAAATATCGGATGGCTGCAATCTACCCCAAGCTCGGGGTAAAAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAAGAGA
* *
266368 TTGGTTAATGGTG
65 TTGGCTGATGGTG
** *
266381 ATCTGCCCCAAGCTCGGGGTAAAAGATTAGATAGCTGCAATCTACCCCAAGCTCGGGGTAAGAGA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCT-CCCCAAGCTCGGGGTAAGAGA
*
266446 TTGGCTGATGGTA
65 TTGGCTGATGGTG
*
266459 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGATGG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGG
266493 ATGTGAGATC
Statistics
Matches: 669, Mismatches: 143, Indels: 6
0.82 0.17 0.01
Matches are distributed among these distances:
77 1 0.00
78 603 0.90
79 65 0.10
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (77 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCGGATGGCTGCAATCTCCCCAAGCTCGGGGTAAGAGAT
TGGCTGATGGTG
Found at i:267464 original size:106 final size:106
Alignment explanation
Indices: 267280--267474 Score: 266
Period size: 106 Copynumber: 1.8 Consensus size: 106
267270 ACTAACCGTC
* * * *
267280 ATTTCAATGCAAAAAATGCTTGAACAGGGTTGTAAGGTGGATAAAATTGAATTTTATTGGAGGTA
1 ATTTCAATGCAAAAAATGCTTGAACAAGGTTGTAAGGTGGATAAAATTGAACTGTATTGGAGGCA
* * **
267345 GAGCTTGCGTGAATGAAAAGAATTATTAGTCCACTGACTGTT
66 AAGCTAGAATGAATGAAAA-AATTATTAGTCCACTGACTGTT
** *
267387 ATTTCAATGC-AAACGTGCTTGAACAAGGTTGTAAGGTGGATAAAATTGAACTGTATTTGAGGCA
1 ATTTCAATGCAAAAAATGCTTGAACAAGGTTGTAAGGTGGATAAAATTGAACTGTATTGGAGGCA
*
267451 AAGGTAGAATGAATGAAAAAATTA
66 AAGCTAGAATGAATGAAAAAATTA
267475 AAAATCATTG
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
105 5 0.07
106 61 0.80
107 10 0.13
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (106 bp):
ATTTCAATGCAAAAAATGCTTGAACAAGGTTGTAAGGTGGATAAAATTGAACTGTATTGGAGGCA
AAGCTAGAATGAATGAAAAAATTATTAGTCCACTGACTGTT
Found at i:267905 original size:27 final size:29
Alignment explanation
Indices: 267875--267941 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
267865 CACCTCGACC
267875 TCTCTTTTTTCTT-TTTTTCTTTT-TTCT
1 TCTCTTTTTTCTTCTTTTTCTTTTCTTCT
*
267902 TCTCTTTTCTTTTTCTTTTTCTTTTCTTCT
1 TCTCTTTT-TTCTTCTTTTTCTTTTCTTCT
* *
267932 TTTTTTTTTT
1 TCTCTTTTTT
267942 AATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.24
28 4 0.12
29 12 0.35
30 10 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (29 bp):
TCTCTTTTTTCTTCTTTTTCTTTTCTTCT
Found at i:267914 original size:22 final size:19
Alignment explanation
Indices: 267879--267940 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
267869 TCGACCTCTC
*
267879 TTTTTTCTTTTTTTCTTTT
1 TTTTTTCTTTTCTTCTTTT
*
267898 TTCTTCTCTTTTC-T-TTTT
1 TT-TTTTCTTTTCTTCTTTT
*
267916 CTTTTTCTTTTCTTCTTTT
1 TTTTTTCTTTTCTTCTTTT
267935 TTTTTT
1 TTTTTT
267941 TAATTTATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 9 0.26
18 6 0.17
19 12 0.34
20 8 0.23
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTCTTTTCTTCTTTT
Found at i:267937 original size:17 final size:17
Alignment explanation
Indices: 267879--267938 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
267869 TCGACCTCTC
*
267879 TTTTTTCTTTTTTTCTTT
1 TTTTTTCTTTTCTTC-TT
267897 TTTCTTCTCTTTTCTT-TT
1 TTT-TT-TCTTTTCTTCTT
267915 TCTTTTTCTTTTCTTCTT
1 T-TTTTTCTTTTCTTCTT
267933 TTTTTT
1 TTTTTT
267939 TTTAATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 14 0.38
18 11 0.30
19 4 0.11
20 8 0.22
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTCTTTTCTTCTT
Found at i:268771 original size:15 final size:15
Alignment explanation
Indices: 268751--268804 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
268741 TTCATCTTGA
268751 CTTTCTTTTTTCTTC
1 CTTTCTTTTTTCTTC
*
268766 CTTTCTCTTTTCTT-
1 CTTTCTTTTTTCTTC
268780 C-TTCTTTTCTT-TTCC
1 CTTTCTTTT-TTCTT-C
268795 CTTT-TTTTTT
1 CTTTCTTTTTT
268805 TTTAAAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 8 0.24
14 5 0.15
15 18 0.55
16 2 0.06
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTCTTTTTTCTTC
Found at i:268783 original size:18 final size:16
Alignment explanation
Indices: 268752--268793 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
268742 TCATCTTGAC
268752 TTTCTTTT-TTCTTCCT
1 TTTCTTTTCTTCTT-CT
268768 TTCTCTTTTCTTCTTCT
1 TT-TCTTTTCTTCTTCT
268785 TTTCTTTTC
1 TTTCTTTTC
268794 CCTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.38
17 10 0.42
18 5 0.21
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTTTTCTTCTTCT
Found at i:270879 original size:13 final size:14
Alignment explanation
Indices: 270853--270890 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
270843 TTCTTGGAAA
*
270853 AATCAACGGTCAAC
1 AATCAACAGTCAAC
270867 AATCAA-AGTCAAC
1 AATCAACAGTCAAC
*
270880 GATCAACAGTC
1 AATCAACAGTC
270891 GATCAACGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.45, C:0.26, G:0.13, T:0.16
Consensus pattern (14 bp):
AATCAACAGTCAAC
Found at i:270945 original size:23 final size:22
Alignment explanation
Indices: 270915--270968 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
270905 CTTGGTTCAA
270915 TTGGGTTATTAGG-TCAAATGGGT
1 TTGGGTTATTAGGTTCAAAT--GT
* *
270938 TTGGGTTATTGGGTTTAAATGT
1 TTGGGTTATTAGGTTCAAATGT
270960 TTGGGTTAT
1 TTGGGTTAT
270969 GTTAGCTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 11 0.39
23 12 0.43
24 5 0.18
ACGTcount: A:0.19, C:0.02, G:0.33, T:0.46
Consensus pattern (22 bp):
TTGGGTTATTAGGTTCAAATGT
Found at i:279938 original size:41 final size:41
Alignment explanation
Indices: 279881--279972 Score: 157
Period size: 41 Copynumber: 2.2 Consensus size: 41
279871 TTATTCGTAG
**
279881 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGGTGACT
1 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGAAGACT
*
279922 AGAATTCTTGTTAAGGTGGAGATTGTTAGAATTGGAAGACT
1 AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGAAGACT
279963 AGAATTCTTG
1 AGAATTCTTG
279973 ATAAAATAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.35
Consensus pattern (41 bp):
AGAATTCTTGTCAAGGTGGAGATTGTTAGAATTGGAAGACT
Found at i:287109 original size:29 final size:29
Alignment explanation
Indices: 287036--287111 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
287026 TTATCTAATA
287036 TAATATAAATAT-TTTTATAATTTAATTT
1 TAATATAAATATATTTTATAATTTAATTT
* *
287064 TAATAAAAATAAAATTTTATAATTT-ATTT
1 TAATATAAAT-ATATTTTATAATTTAATTT
* *
287093 TAGTGTAAATATTATTTTA
1 TAATATAAATA-TATTTTA
287112 ATTTATATTG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 10 0.26
29 18 0.46
30 11 0.28
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (29 bp):
TAATATAAATATATTTTATAATTTAATTT
Found at i:287120 original size:29 final size:29
Alignment explanation
Indices: 287039--287127 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 29
287029 TCTAATATAA
*
287039 TATAAATATT-TTTATAATTTA-ATTTTAA
1 TATAAATATTATTT-TAATTTATATTTTAG
* ** *
287067 TAAAAATAAAATTTTATAATT-TATTTTAG
1 TATAAATATTATTTTA-ATTTATATTTTAG
* *
287096 TGTAAATATTATTTTAATTTATATTGTAG
1 TATAAATATTATTTTAATTTATATTTTAG
287125 TAT
1 TAT
287128 TTAATTTAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
28 12 0.27
29 33 0.73
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (29 bp):
TATAAATATTATTTTAATTTATATTTTAG
Found at i:287148 original size:20 final size:19
Alignment explanation
Indices: 287101--287150 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
287091 TTTAGTGTAA
*
287101 ATATTATTTTAATTTATATT
1 ATATTA-TTTAATTTAAATT
* *
287121 GTAGTATTTAATTTAAATCT
1 ATATTATTTAATTTAAAT-T
287141 ATATTATTTA
1 ATATTATTTA
287151 TAAAAAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
ATATTATTTAATTTAAATT
Done.