Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015266.1 Kokia drynarioides strain JFW-HI SEQ_130311, 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: 514914
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 275 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:450859 original size:25 final size:23
Alignment explanation
Indices: 450831--450876 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
450821 GTTGGATCCA
450831 AATTAAATTCTAAAAAGATAATTAG
1 AATTAAA-TCTAAAAA-ATAATTAG
*
450856 AATTAAATCTAAACAATAATT
1 AATTAAATCTAAAAAATAATT
450877 TCCTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.33
Consensus pattern (23 bp):
AATTAAATCTAAAAAATAATTAG
Found at i:451914 original size:11 final size:11
Alignment explanation
Indices: 451898--451964 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 11
451888 CACACCTTTG
451898 TCTTTTTTTTT
1 TCTTTTTTTTT
*
451909 TCTTTTTTTTC
1 TCTTTTTTTTT
451920 TCATTTTTTTTTCAAT
1 TC--TTTTTTTT---T
451936 TCTTTTTTTTT
1 TCTTTTTTTTT
451947 T-TTTCATTTTTT
1 TCTTT--TTTTTT
451959 TCTTTT
1 TCTTTT
451965 CGACTTTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
10 3 0.07
11 15 0.33
12 7 0.15
13 11 0.24
14 8 0.17
16 2 0.04
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:451945 original size:19 final size:17
Alignment explanation
Indices: 451923--451964 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 17
451913 TTTTTTCTCA
451923 TTTTTTTTTCAATTCTTTT
1 TTTTTTTTTC-ATT-TTTT
451942 TTTTTTTTTCATTTTTT
1 TTTTTTTTTCATTTTTT
451959 TCTTTT
1 T-TTTT
451965 CGACTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.23
18 7 0.32
19 10 0.45
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTCATTTTTT
Found at i:451972 original size:16 final size:14
Alignment explanation
Indices: 451900--451975 Score: 50
Period size: 14 Copynumber: 5.4 Consensus size: 14
451890 CACCTTTGTC
*
451900 TTTTTT-TTTTCTT
1 TTTTTTCTTTTCAT
*
451913 TTTTTTCTCATT--T
1 TTTTTTCT-TTTCAT
** *
451926 TTTTTTCAATTCTT
1 TTTTTTCTTTTCAT
*
451940 TTTTTTTTTTTCAT
1 TTTTTTCTTTTCAT
451954 TTTTTTCTTTTCGACT
1 TTTTTTCTTTTC-A-T
451970 TTTTTT
1 TTTTTT
451976 TCTAAATAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
12 3 0.06
13 14 0.28
14 23 0.46
15 3 0.06
16 7 0.14
ACGTcount: A:0.07, C:0.12, G:0.01, T:0.80
Consensus pattern (14 bp):
TTTTTTCTTTTCAT
Found at i:451973 original size:17 final size:16
Alignment explanation
Indices: 451937--451978 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
451927 TTTTTCAATT
*
451937 CTTTTTTTTTTTTTCA
1 CTTTTTTTTCTTTTCA
451953 --TTTTTTTCTTTTCGA
1 CTTTTTTTTCTTTTC-A
451968 CTTTTTTTTCT
1 CTTTTTTTTCT
451979 AAATAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 12 0.55
15 1 0.05
17 9 0.41
ACGTcount: A:0.05, C:0.14, G:0.02, T:0.79
Consensus pattern (16 bp):
CTTTTTTTTCTTTTCA
Found at i:452921 original size:17 final size:17
Alignment explanation
Indices: 452901--452950 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
452891 AGTGCATAAT
*
452901 TAAAATAAAATTAAAAA
1 TAAAATAAAATAAAAAA
*
452918 TAAAATAAGATAAAAAA
1 TAAAATAAAATAAAAAA
452935 TAAAATTGAAAATAAA
1 TAAAA-T-AAAATAAA
452951 TATACTAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 20 0.71
18 1 0.04
19 7 0.25
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (17 bp):
TAAAATAAAATAAAAAA
Found at i:452995 original size:15 final size:15
Alignment explanation
Indices: 452977--453006 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
452967 ATTTTTCAAT
452977 TTTTTTTCAAATTAA
1 TTTTTTTCAAATTAA
*
452992 TTTTTTTCAATTTAA
1 TTTTTTTCAAATTAA
453007 AAAAAAACAT
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:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTTCAAATTAA
Found at i:463927 original size:21 final size:22
Alignment explanation
Indices: 463894--463934 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
463884 ATAAAATATT
*
463894 ATTTTTATTAAATTGGATTTTA
1 ATTTTTATCAAATTGGATTTTA
*
463916 ATTTTTA-CAAATTGTATTT
1 ATTTTTATCAAATTGGATTT
463935 GGATATTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.59
Consensus pattern (22 bp):
ATTTTTATCAAATTGGATTTTA
Found at i:465090 original size:16 final size:17
Alignment explanation
Indices: 465038--465099 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
465028 GGCCCAACAG
*
465038 AATTTAAATTTATTTTA
1 AATTTAAATTTATTATA
465055 AATTTAAATTTATTGA-A
1 AATTTAAATTTATT-ATA
*
465072 AATTT-AATCTATTATA
1 AATTTAAATTTATTATA
465088 AATTTAAATTTA
1 AATTTAAATTTA
465100 AATTCATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
15 1 0.03
16 13 0.33
17 25 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
AATTTAAATTTATTATA
Found at i:465134 original size:13 final size:13
Alignment explanation
Indices: 465116--465141 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
465106 TTTAAATAAT
465116 GTCCAATTACAAA
1 GTCCAATTACAAA
465129 GTCCAATTACAAA
1 GTCCAATTACAAA
465142 TTGGGTCCAA
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:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GTCCAATTACAAA
Found at i:465767 original size:3 final size:3
Alignment explanation
Indices: 465761--465829 Score: 61
Period size: 3 Copynumber: 23.0 Consensus size: 3
465751 TAATTTTTTT
* ** *
465761 TAA TAA TAA TAAA TAT TTT TAA TAA TAA TAA TAA TAA -ATA TAA TAT
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
*
465807 TAA TAA TAT TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
465830 AAAAGGGATA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 3 0.06
3 47 0.87
4 4 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:465772 original size:19 final size:19
Alignment explanation
Indices: 465748--465792 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
465738 ATAGTGATAG
*
465748 TAATAATTTTTTTTAATAA
1 TAATAATTATTTTTAATAA
*
465767 TAATAAATATTTTTAATAA
1 TAATAATTATTTTTAATAA
465786 TAATAAT
1 TAATAAT
465793 AATAAATATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAATTATTTTTAATAA
Found at i:467000 original size:29 final size:28
Alignment explanation
Indices: 466946--467294 Score: 201
Period size: 29 Copynumber: 12.0 Consensus size: 28
466936 AGAAATCATG
* *
466946 TTTTGACCCCTAAAATTTCCATAAATTACA
1 TTTTTACCCC-AAACTTTCCA-AAATTACA
*
466976 TTTTTACCCTCGAACTTTCCAAAATT-CTA
1 TTTTTACCC-CAAACTTTCCAAAATTAC-A
* *
467005 TTCTTAACCCCAAATTTTCCAAAAATTACA
1 TT-TTTACCCCAAACTTTCC-AAAATTACA
* *
467035 TTTTTACCCCTAAACTTTCTAAAATTCCA
1 TTTTTACCCC-AAACTTTCCAAAATTACA
* * * * *
467064 TTTTTGTCCTCGAATTTTCCAAAA-AATCA
1 TTTTT-ACCCCAAACTTTCCAAAATTA-CA
* * *
467093 TTTTTAACCTCAAATTTTCAAAAATT--A
1 TTTTT-ACCCCAAACTTTCCAAAATTACA
* *
467120 TTTCTTACGCTCGAACTTTCCAAAATT-CTA
1 TTT-TTAC-CCCAAACTTTCCAAAATTAC-A
*
467150 TTTTTGACCCCAAATTTTCCAAAAATTACA
1 TTTTT-ACCCCAAACTTTCC-AAAATTACA
* *
467180 -TTTTACTCCCGAACTTTCCAAAATTCCA
1 TTTTTAC-CCCAAACTTTCCAAAATTACA
* * *
467208 TTTTGACCCCGAACTTCCCAAAAATTACCA
1 TTTTTACCCCAAACTTTCC-AAAATTA-CA
*
467238 -TTTTATCCCCAAAC-TTCCAAAGATTCCA
1 TTTTTA-CCCCAAACTTTCCAAA-ATTACA
* * *
467266 TTTTTTTACCTCAAAGTGTCCAAAATTAC
1 --TTTTTACCCCAAACTTTCCAAAATTAC
467295 CGTTTTGCCC
Statistics
Matches: 251, Mismatches: 42, Indels: 52
0.73 0.12 0.15
Matches are distributed among these distances:
27 6 0.02
28 44 0.18
29 114 0.45
30 73 0.29
31 14 0.06
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.38
Consensus pattern (28 bp):
TTTTTACCCCAAACTTTCCAAAATTACA
Found at i:467143 original size:57 final size:59
Alignment explanation
Indices: 467072--467242 Score: 165
Period size: 57 Copynumber: 3.0 Consensus size: 59
467062 CATTTTTGTC
* * *
467072 CTCGAATTTTCCAAAAAATC-ATTTTTAACCTCAAATTTT-CAAAAATTA-TTTCTTACG
1 CTCGAACTTTCCAAAAAATCTATTTTTAACCCCAAATTTTCCAAAAATTACATT-TTACG
* * *
467129 CTCGAACTTTCC-AAAATTCTATTTTTGACCCCAAATTTTCCAAAAATTACATTTTACT
1 CTCGAACTTTCCAAAAAATCTATTTTTAACCCCAAATTTTCCAAAAATTACATTTTACG
* * * * * * *
467187 CCCGAACTTTCC-AAAATTCCA-TTTTGACCCCGAACTTCCCAAAAATTACCATTTTA
1 CTCGAACTTTCCAAAAAATCTATTTTTAACCCCAAATTTTCCAAAAATTA-CATTTTA
467243 TCCCCAAACT
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
56 6 0.06
57 52 0.53
58 39 0.39
59 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (59 bp):
CTCGAACTTTCCAAAAAATCTATTTTTAACCCCAAATTTTCCAAAAATTACATTTTACG
Found at i:467221 original size:86 final size:85
Alignment explanation
Indices: 466961--467241 Score: 230
Period size: 86 Copynumber: 3.2 Consensus size: 85
466951 ACCCCTAAAA
* * * * * *
466961 TTTCCATAAATTACATTTTT-ACCCTCGAACTTTCC-AAAATTCTATTCTTAACCCCAAATTTTC
1 TTTCCA-AAATTCCATTTTTGACCC-CAAATTTTCCAAAAAATC-ATTTTTAACCCCAAACTTTC
*
467024 CAAAAATTACATTTTTACCCCTAAAC
63 C-AAAATT-CATTTTTACCCC-GAAC
* * * * * * *
467050 TTTCTAAAATTCCATTTTTGTCCTCGAATTTTCCAAAAAATCATTTTTAACCTCAAATTTTCAAA
1 TTTCCAAAATTCCATTTTTGACCCCAAATTTTCCAAAAAATCATTTTTAACCCCAAACTTTCCAA
*
467115 AATT-ATTTCTTACGCTCGAAC
66 AATTCATTT-TTAC-CCCGAAC
* * *
467136 TTTCCAAAATTCTATTTTTGACCCCAAATTTTCCAAAAATTACA-TTTT-ACTCCCGAACTTTCC
1 TTTCCAAAATTCCATTTTTGACCCCAAATTTTCCAAAAAAT-CATTTTTAAC-CCCAAACTTTCC
*
467199 AAAATTCCATTTTGACCCCGAAC
64 AAAATT-CATTTTTACCCCGAAC
*
467222 TTCCCAAAAATTACCATTTT
1 TTTCC-AAAATT-CCATTTT
467242 ATCCCCAAAC
Statistics
Matches: 157, Mismatches: 25, Indels: 21
0.77 0.12 0.10
Matches are distributed among these distances:
85 6 0.04
86 70 0.45
87 19 0.12
88 49 0.31
89 13 0.08
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (85 bp):
TTTCCAAAATTCCATTTTTGACCCCAAATTTTCCAAAAAATCATTTTTAACCCCAAACTTTCCAA
AATTCATTTTTACCCCGAAC
Found at i:478573 original size:17 final size:17
Alignment explanation
Indices: 478535--478573 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
478525 AGGTGGAGAA
* *
478535 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
478552 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
*
478569 TTTGT
1 CTTGT
478574 CAAGGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.10, G:0.26, T:0.49
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:480711 original size:24 final size:24
Alignment explanation
Indices: 480666--480712 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
480656 ATTTAGTAGT
*
480666 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
480690 ATAATATATTTTA-CATTGATTAG
1 ATAATATA-TTTAGCATTGATTAG
480713 ATTTAGGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:484356 original size:25 final size:25
Alignment explanation
Indices: 484328--484375 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
484318 CTTTCTAAAA
*
484328 CATTTAGTAGTATAATATATTTTGT
1 CATTTAGTAGCATAATATATTTTGT
*
484353 CATTTATTAGCATAATATATTTT
1 CATTTAGTAGCATAATATATTTT
484376 ACATTGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (25 bp):
CATTTAGTAGCATAATATATTTTGT
Found at i:484385 original size:24 final size:25
Alignment explanation
Indices: 484339--484386 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
484329 ATTTAGTAGT
* *
484339 ATAATATATTTTGTCATTTATTAGC
1 ATAATATATTTTGACATTGATTAGC
484364 ATAATATATTTT-ACATTGATTAG
1 ATAATATATTTTGACATTGATTAG
484387 AATTAGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.50
Consensus pattern (25 bp):
ATAATATATTTTGACATTGATTAGC
Found at i:485542 original size:3 final size:3
Alignment explanation
Indices: 485536--485570 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
485526 TATTAAAATA
485536 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
485571 TTAGGTCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:485562 original size:20 final size:19
Alignment explanation
Indices: 485532--485570 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
485522 AAATTATTAA
485532 AATAAATAATAATAATAAT
1 AATAAATAATAATAATAAT
485551 AATAATATAATAATAATAAT
1 AATAA-ATAATAATAATAAT
485571 TTAGGTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AATAAATAATAATAATAAT
Found at i:491020 original size:8 final size:9
Alignment explanation
Indices: 491000--491028 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
490990 TTAATAATTT
491000 AAAATTTTA
1 AAAATTTTA
491009 AAAATTTTA
1 AAAATTTTA
491018 AAAATTTTA
1 AAAATTTTA
491027 AA
1 AA
491029 TCATCTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
AAAATTTTA
Found at i:491029 original size:16 final size:16
Alignment explanation
Indices: 490989--491028 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
490979 TAATTTTTCA
*
490989 TTTAATAATTTAAAAT
1 TTTAAAAATTTAAAAT
491005 TTTAAAAATTTTAAAAAT
1 TTTAAAAA-TTT-AAAAT
491023 TTTAAA
1 TTTAAA
491029 TCATCTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 3 0.14
18 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAAATTTAAAAT
Found at i:491896 original size:4 final size:4
Alignment explanation
Indices: 491887--491946 Score: 75
Period size: 4 Copynumber: 14.5 Consensus size: 4
491877 AATAAACGGA
* * *
491887 AAAG AAAG AAAGG AAAG AAAG AAAG AAAG AAAG AAAG GAAG AAGG AGAGG
1 AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG A-AAG
491937 AAAG AAAG AA
1 AAAG AAAG AA
491947 GAAGGAGAGG
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
4 42 0.84
5 8 0.16
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:491917 original size:25 final size:25
Alignment explanation
Indices: 491887--491946 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
491877 AATAAACGGA
491887 AAAGAAAGAAAGGAAAGAAAGA-AAG
1 AAAGAAAGAAAGG-AAGAAAGAGAAG
* *
491912 AAAGAAAGAAAGGAAGAAGGAGAGG
1 AAAGAAAGAAAGGAAGAAAGAGAAG
491937 AAAGAAAGAA
1 AAAGAAAGAA
491947 GAAGGAGAGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 7 0.22
25 25 0.78
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (25 bp):
AAAGAAAGAAAGGAAGAAAGAGAAG
Found at i:491950 original size:20 final size:21
Alignment explanation
Indices: 491915--491959 Score: 83
Period size: 20 Copynumber: 2.2 Consensus size: 21
491905 AAGAAAGAAA
491915 GAAAGAAAGGAAGAAGGAGAG
1 GAAAGAAAGGAAGAAGGAGAG
491936 GAAAGAAA-GAAGAAGGAGAG
1 GAAAGAAAGGAAGAAGGAGAG
491956 GAAA
1 GAAA
491960 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGGAAGAAGGAGAG
Found at i:495008 original size:4 final size:4
Alignment explanation
Indices: 494999--495085 Score: 79
Period size: 4 Copynumber: 21.5 Consensus size: 4
494989 AAACACATTA
* * *
494999 TCTT TCTT TCCT TC-T TCTT TCTT TCCTC TCCT TC-T TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT T-CTT TCTT TCTT TCTT TCTT TCTT
* * *
495046 CTCCT TCTT CCTT TCTT TCCT TCTTT TCTT TCTT TCTT TC
1 -TCTT TCTT TCTT TCTT TCTT TC-TT TCTT TCTT TCTT TC
495086 CCGTTTATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
3 6 0.09
4 53 0.78
5 9 0.13
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
TCTT
Found at i:495034 original size:17 final size:17
Alignment explanation
Indices: 494999--495077 Score: 74
Period size: 17 Copynumber: 4.6 Consensus size: 17
494989 AAACACATTA
494999 TCTTTCTTTCCT-T-CT
1 TCTTTCTTTCCTCTCCT
495014 TCTTTCTTTCCTCTCCTTCT
1 TCTTTCTTTCCTCT-C--CT
*
495034 TCTTTCTTTCTTCTCCT
1 TCTTTCTTTCCTCTCCT
* *
495051 TCTTCCTTT-CTTTCCT
1 TCTTTCTTTCCTCTCCT
495067 TCTTTTCTTTC
1 TC-TTTCTTTC
495078 TTTCTTTCCC
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
15 12 0.23
16 8 0.15
17 16 0.31
19 1 0.02
20 15 0.29
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (17 bp):
TCTTTCTTTCCTCTCCT
Found at i:495078 original size:17 final size:19
Alignment explanation
Indices: 494999--495086 Score: 117
Period size: 20 Copynumber: 4.6 Consensus size: 19
494989 AAACACATTA
494999 TCTTTCTTTCCTTCTTCTT
1 TCTTTCTTTCCTTCTTCTT
*
495018 TCTTTCCTCTCCTTCTTCTT
1 TCTTT-CTTTCCTTCTTCTT
495038 TCTTTCTTCTCCTTCTTCCTT
1 TCTTTCTT-TCCTTCTT-CTT
*
495059 TCTTTCCTT-CTT-TTCTT
1 TCTTTCTTTCCTTCTTCTT
495076 TCTTTCTTTCC
1 TCTTTCTTTCC
495087 CGTTTATTTG
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
17 11 0.18
18 3 0.05
19 10 0.16
20 27 0.44
21 10 0.16
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (19 bp):
TCTTTCTTTCCTTCTTCTT
Found at i:495341 original size:13 final size:13
Alignment explanation
Indices: 495323--495347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
495313 TGGGTGTCAG
495323 GTATTTTTTTGTC
1 GTATTTTTTTGTC
495336 GTATTTTTTTGT
1 GTATTTTTTTGT
495348 ATTTTTCTGA
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:0.08, C:0.04, G:0.16, T:0.72
Consensus pattern (13 bp):
GTATTTTTTTGTC
Found at i:495679 original size:18 final size:18
Alignment explanation
Indices: 495646--495680 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
495636 TAAATAGTTT
* *
495646 GAGTTATTTGAGTTAATC
1 GAGTTATTCGAATTAATC
495664 GAGTTATTCGAATTAAT
1 GAGTTATTCGAATTAAT
495681 TCGAATAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (18 bp):
GAGTTATTCGAATTAATC
Found at i:499117 original size:19 final size:20
Alignment explanation
Indices: 499080--499120 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
499070 TATAAATTTT
* *
499080 TATAACATATATTTGTAATA
1 TATAACATAAATTTATAATA
499100 TATAACA-AAATTTATAATA
1 TATAACATAAATTTATAATA
499119 TA
1 TA
499121 AATTTTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (20 bp):
TATAACATAAATTTATAATA
Found at i:499133 original size:15 final size:15
Alignment explanation
Indices: 499070--499134 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 15
499060 AACTTTTATT
*
499070 TATAAATTTTTATAA
1 TATAAATTTTAATAA
* *
499085 CATATATTTGTAATATA
1 TATAAATTT-TAATA-A
* *
499102 TAACAAAATTT-ATAA
1 T-ATAAATTTTAATAA
499117 TATAAATTTTAATAA
1 TATAAATTTTAATAA
499132 TAT
1 TAT
499135 TTTTTTCGTA
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
14 7 0.19
15 16 0.43
16 7 0.19
17 2 0.05
18 5 0.14
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (15 bp):
TATAAATTTTAATAA
Found at i:499305 original size:6 final size:7
Alignment explanation
Indices: 499289--499315 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
499279 AAAAAATTTG
499289 AAAAATA
1 AAAAATA
499296 AAAAATA
1 AAAAATA
499303 AAAAATA
1 AAAAATA
499310 AAAAAT
1 AAAAAT
499316 TATTACAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:500299 original size:41 final size:41
Alignment explanation
Indices: 500253--500384 Score: 169
Period size: 40 Copynumber: 3.3 Consensus size: 41
500243 AACAGGTTAT
*** *
500253 TAGCGGCGTTTGGACAGTAAACGCCGCAAAAGATAAAGCAA
1 TAGCGGCGTTTTTTCAGTAAACGCCGCAAAAGATAAAACAA
* *
500294 TAGCGGCGTTTTTTCA-TAAACGCCGCAAAACATAAATCAA
1 TAGCGGCGTTTTTTCAGTAAACGCCGCAAAAGATAAAACAA
** *
500334 TAGCGGTATTTTTTC-GTAAACGCCGCAAAAGGTAAAACAA
1 TAGCGGCGTTTTTTCAGTAAACGCCGCAAAAGATAAAACAA
500374 TAGCGGCGTTT
1 TAGCGGCGTTT
500385 ATAGAAAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
40 65 0.83
41 13 0.17
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (41 bp):
TAGCGGCGTTTTTTCAGTAAACGCCGCAAAAGATAAAACAA
Found at i:500483 original size:41 final size:38
Alignment explanation
Indices: 500432--500612 Score: 158
Period size: 36 Copynumber: 4.7 Consensus size: 38
500422 CGCTTCCCAT
* *
500432 AAGCGCCGCTAAAGGTCAGAGCATTAGCGATGCTTATGGGA
1 AAGCGTCGCTAAAGGTCAGAGCATTAG-G-TG-TTATAGGA
* * * *
500473 AAGCGTCGCTAAAAGTCAGAGCATTA-GT-TTCTTGCA
1 AAGCGTCGCTAAAGGTCAGAGCATTAGGTGTTATAGGA
* *
500509 AAAC-ACTGCTAAAGGTCAGAGCATTAGTGGTGCTTATAGGA
1 AAGCGTC-GCTAAAGGTCAGAGCATTA--GGTG-TTATAGGA
* *
500550 AAGCGTCGCTAAAGGTCAGAGCATTA-GT-TTCTAGCA
1 AAGCGTCGCTAAAGGTCAGAGCATTAGGTGTTATAGGA
500586 AAGCG-CTGCTAAAGGTCAGAGCATTAG
1 AAGCGTC-GCTAAAGGTCAGAGCATTAG
500613 CGGTGTTTAT
Statistics
Matches: 116, Mismatches: 15, Indels: 22
0.76 0.10 0.14
Matches are distributed among these distances:
35 2 0.02
36 56 0.48
38 3 0.03
39 3 0.03
41 51 0.44
42 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.23
Consensus pattern (38 bp):
AAGCGTCGCTAAAGGTCAGAGCATTAGGTGTTATAGGA
Found at i:500531 original size:77 final size:77
Alignment explanation
Indices: 500439--500629 Score: 301
Period size: 77 Copynumber: 2.5 Consensus size: 77
500429 CATAAGCGCC
*
500439 GCTAAAGGTCAGAGCATTAGCGATGCTTATGGGAAAGCGTCGCTAAAAGTCAGAGCATTAGTTTC
1 GCTAAAGGTCAGAGCATTAGCGGTGCTTATGGGAAAGCGTCGCTAAAAGTCAGAGCATTAGTTTC
*
500504 TTGCAAAACACT
66 TAGCAAAACACT
* * *
500516 GCTAAAGGTCAGAGCATTAGTGGTGCTTATAGGAAAGCGTCGCTAAAGGTCAGAGCATTAGTTTC
1 GCTAAAGGTCAGAGCATTAGCGGTGCTTATGGGAAAGCGTCGCTAAAAGTCAGAGCATTAGTTTC
* *
500581 TAGCAAAGCGCT
66 TAGCAAAACACT
*
500593 GCTAAAGGTCAGAGCATTAGCGGTGTTTATGGAGAAA
1 GCTAAAGGTCAGAGCATTAGCGGTGCTTATGG-GAAA
500630 CCGCCACTAA
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
77 99 0.96
78 4 0.04
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (77 bp):
GCTAAAGGTCAGAGCATTAGCGGTGCTTATGGGAAAGCGTCGCTAAAAGTCAGAGCATTAGTTTC
TAGCAAAACACT
Found at i:501458 original size:57 final size:58
Alignment explanation
Indices: 501366--501482 Score: 141
Period size: 57 Copynumber: 2.0 Consensus size: 58
501356 AATTAATTAT
* * * * *
501366 TTGACTCAAATCTCCTTATATAGTAATAATGTATATTAAT-CAATATTTAATAGTTAA
1 TTGACTCAAATCTCCTTATAGACTAATAATATATATTAATGCAATATTTAAGAGGTAA
*
501423 TTGACTC-AATCTCCTCT-TAGACTAATATATATATATTAATGTAATATTTAAGAGGTAA
1 TTGACTCAAATCTCCT-TATAGACTAATA-ATATATATTAATGCAATATTTAAGAGGTAA
501481 TT
1 TT
501483 CACTGAAACT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
56 16 0.31
57 19 0.37
58 16 0.31
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (58 bp):
TTGACTCAAATCTCCTTATAGACTAATAATATATATTAATGCAATATTTAAGAGGTAA
Found at i:502216 original size:18 final size:20
Alignment explanation
Indices: 502195--502235 Score: 50
Period size: 18 Copynumber: 2.1 Consensus size: 20
502185 GTTTTGGATG
*
502195 AAATTCAAACAT-TAT-TAA
1 AAATGCAAACATATATATAA
*
502213 AAATGCAAATATATATATAA
1 AAATGCAAACATATATATAA
502233 AAA
1 AAA
502236 GATTATATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.29
Consensus pattern (20 bp):
AAATGCAAACATATATATAA
Found at i:504748 original size:8 final size:8
Alignment explanation
Indices: 504712--504750 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
504702 TAATAACATT
*
504712 TAATTAAA
1 TAATTTAA
*
504720 TAATTAAA
1 TAATTTAA
504728 T-ATTTAA
1 TAATTTAA
504735 TAATTTAA
1 TAATTTAA
504743 TAATTTAA
1 TAATTTAA
504751 AACAACTCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
TAATTTAA
Found at i:504748 original size:16 final size:16
Alignment explanation
Indices: 504712--504750 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
504702 TAATAACATT
*
504712 TAATTAAATAATTAAA
1 TAATTTAATAATTAAA
*
504728 T-ATTTAATAATTTAA
1 TAATTTAATAATTAAA
504743 TAATTTAA
1 TAATTTAA
504751 AACAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
TAATTTAATAATTAAA
Found at i:504776 original size:26 final size:26
Alignment explanation
Indices: 504737--504831 Score: 77
Period size: 26 Copynumber: 3.5 Consensus size: 26
504727 ATATTTAATA
* * *
504737 ATTTAATAATTTAAAACAACTCAAAT
1 ATTTAATTAGTTAAAATAACTCAAAT
*
504763 ATTTAATTAGTTAATTATATTTAA-TTAAAT
1 ATTTAATTAGTTAA--A-A--TAACTCAAAT
*
504793 ATTTAATTA-TTAAAAATAACCCAAAT
1 ATTTAATTAGTT-AAAATAACTCAAAT
504819 ATTTAATTAGTTA
1 ATTTAATTAGTTA
504832 TTTATTAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
25 3 0.05
26 26 0.47
27 3 0.05
28 2 0.04
29 3 0.05
30 16 0.29
31 2 0.04
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTTAATTAGTTAAAATAACTCAAAT
Found at i:504798 original size:22 final size:23
Alignment explanation
Indices: 504773--504900 Score: 86
Period size: 22 Copynumber: 5.4 Consensus size: 23
504763 ATTTAATTAG
504773 TTAATTA-TATTTAATTAAATAT
1 TTAATTATTATTTAATTAAATAT
** **
504795 TTAATTATTAAAAATAACCCAAATAT
1 TTAATTATT--ATTTAA-TTAAATAT
504821 TTAATTAGTTATTT-ATTAAA-A-
1 TTAATTA-TTATTTAATTAAATAT
** *
504842 ACAATTCAAATATTTAATTAAAATTAT
1 TTAATT--ATTATTTAATT-AAA-TAT
504869 TTAATTA-TATTTAATTAAATAT
1 TTAATTATTATTTAATTAAATAT
504891 TTAATTATTA
1 TTAATTATTA
504901 AAAACAATCC
Statistics
Matches: 80, Mismatches: 13, Indels: 25
0.68 0.11 0.21
Matches are distributed among these distances:
21 4 0.05
22 23 0.29
23 13 0.16
24 13 0.16
25 7 0.09
26 14 0.17
27 6 0.08
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.48
Consensus pattern (23 bp):
TTAATTATTATTTAATTAAATAT
Found at i:504871 original size:14 final size:12
Alignment explanation
Indices: 504815--504897 Score: 68
Period size: 12 Copynumber: 7.1 Consensus size: 12
504805 AAAATAACCC
504815 AAATATTTAATT
1 AAATATTTAATT
**
504827 AGTTATTT-ATT
1 AAATATTTAATT
**
504838 AAA-A-ACAATT
1 AAATATTTAATT
504848 CAAATATTTAATT
1 -AAATATTTAATT
504861 AAAATTATTTAATT
1 -AAA-TATTTAATT
504875 --ATATTTAATT
1 AAATATTTAATT
504885 AAATATTTAATT
1 AAATATTTAATT
504897 A
1 A
504898 TTAAAAACAA
Statistics
Matches: 55, Mismatches: 9, Indels: 14
0.71 0.12 0.18
Matches are distributed among these distances:
10 13 0.24
11 8 0.15
12 18 0.33
13 7 0.13
14 9 0.16
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (12 bp):
AAATATTTAATT
Found at i:504892 original size:58 final size:57
Alignment explanation
Indices: 504817--505046 Score: 199
Period size: 62 Copynumber: 4.0 Consensus size: 57
504807 AATAACCCAA
* **
504817 ATATTTAATTAGTTATTTATTAAAAACAATTCAAATATTTAATTAAAATTATTTAATT
1 ATATTTAATTAATTATTTATTAAAAACAACCCAAATATTTAATTAAAATTATTTAA-T
* * * *
504875 ATATTTAATTAAATATTTAATTATTAAAAACAATCCAAATATTTAATT--ATTTAGTT--T
1 ATATTTAATT--A-A-TTATTTATTAAAAACAACCCAAATATTTAATTAAAATTATTTAAT
* *
504932 A-A--TAATTAGTTATTTATTAACAACAACCCAAATATTTAATTCAAAA-TATTTAAT
1 ATATTTAATTAATTATTTATTAAAAACAACCCAAATATTTAATT-AAAATTATTTAAT
* *
504986 -TATTTAATTATATTTAATTATTAAAAACAACCCAAAATATTTAATTACTTAATTATTTAAT
1 ATATTTAATTA-A-TTATTTATTAAAAACAACCC-AAATATTTAATTA--AAATTATTTAAT
505047 TAGTTATTTA
Statistics
Matches: 139, Mismatches: 15, Indels: 33
0.74 0.08 0.18
Matches are distributed among these distances:
50 29 0.21
52 5 0.04
53 1 0.01
54 7 0.05
56 7 0.05
57 2 0.01
58 29 0.21
59 12 0.09
60 9 0.06
61 8 0.06
62 30 0.22
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (57 bp):
ATATTTAATTAATTATTTATTAAAAACAACCCAAATATTTAATTAAAATTATTTAAT
Found at i:504944 original size:112 final size:109
Alignment explanation
Indices: 504822--505058 Score: 336
Period size: 112 Copynumber: 2.1 Consensus size: 109
504812 CCCAAATATT
**
504822 TAATTAGTTATTTATTAAAAACAATTCAAATATTTAATT-AAAATTATTTAATTATATTTAATTA
1 TAATTAGTTATTTATTAAAAACAACCCAAATATTTAATTCAAAA-TATTTAA-T-TATTTAATT-
* * *
504886 AATATTTAATTATTAAAAACAATCC-AAATATTTAATTATTTAGTT-TAA
62 -ATATTTAATTATTAAAAACAACCCAAAATATTTAATTACTTAATTAT-A
*
504934 TAATTAGTTATTTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATTATAT
1 TAATTAGTTATTTATTAAAAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATTATAT
*
504999 TTAATTATTAAAAACAACCCAAAATATTTAATTACTTAATTATT
66 TTAATTATTAAAAACAACCCAAAATATTTAATTACTTAATTATA
505043 TAATTAGTTATTTATT
1 TAATTAGTTATTTATT
505059 TGCAACTATG
Statistics
Matches: 115, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
108 23 0.20
109 34 0.30
110 10 0.09
111 1 0.01
112 43 0.37
113 4 0.03
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (109 bp):
TAATTAGTTATTTATTAAAAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATTATAT
TTAATTATTAAAAACAACCCAAAATATTTAATTACTTAATTATA
Found at i:505044 original size:16 final size:16
Alignment explanation
Indices: 505023--505059 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
505013 CAACCCAAAA
505023 TATTTAATTACTTAAT
1 TATTTAATTACTTAAT
* *
505039 TATTTAATTAGTTATT
1 TATTTAATTACTTAAT
505055 TATTT
1 TATTT
505060 GCAACTATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
TATTTAATTACTTAAT
Found at i:507832 original size:43 final size:43
Alignment explanation
Indices: 507792--507910 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 43
507782 AGAAAGCACT
*
507792 GTTAAAGATAATGTTTTTTAGCGGTGTTTGTGGGAGAAGCATC
1 GTTAAAGATAATGCTTTTTAGCGGTGTTTGTGGGAGAAGCATC
* ** * *
507835 GCTAAATG-TTGTGCTCTTTAGCGGTGTTTGTGGGAGAAGCGTC
1 GTTAAA-GATAATGCTTTTTAGCGGTGTTTGTGGGAGAAGCATC
* * *
507878 GTTAAAGATCATGGTTTTTAGCGGCGTTTGTGG
1 GTTAAAGATAATGCTTTTTAGCGGTGTTTGTGG
507911 AAAAAATGCT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
42 1 0.02
43 60 0.97
44 1 0.02
ACGTcount: A:0.20, C:0.10, G:0.33, T:0.37
Consensus pattern (43 bp):
GTTAAAGATAATGCTTTTTAGCGGTGTTTGTGGGAGAAGCATC
Found at i:508115 original size:22 final size:22
Alignment explanation
Indices: 508090--508135 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
508080 TAAAGGTGCT
508090 CTAATGTCATTCACAACAATGA
1 CTAATGTCATTCACAACAATGA
508112 CTAATGTCATTCACAACAATGA
1 CTAATGTCATTCACAACAATGA
508134 CT
1 CT
508136 TTCATTCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (22 bp):
CTAATGTCATTCACAACAATGA
Found at i:508140 original size:19 final size:21
Alignment explanation
Indices: 508093--508144 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
508083 AGGTGCTCTA
508093 ATGTCATTCACAACAATGACT
1 ATGTCATTCACAACAATGACT
508114 AATGTCATTCACAACAATGACT
1 -ATGTCATTCACAACAATGACT
508136 -T-TCATTCAC
1 ATGTCATTCAC
508145 TACTAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.27
20 1 0.03
22 21 0.70
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.31
Consensus pattern (21 bp):
ATGTCATTCACAACAATGACT
Found at i:511748 original size:12 final size:12
Alignment explanation
Indices: 511731--511766 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
511721 ATATACAATT
511731 CCGTTTCTTTCA
1 CCGTTTCTTTCA
511743 CCGTTTCTTTCA
1 CCGTTTCTTTCA
511755 CCGTTTCTTTCA
1 CCGTTTCTTTCA
511767 TATGAAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.33, G:0.08, T:0.50
Consensus pattern (12 bp):
CCGTTTCTTTCA
Done.