Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014446.1 Kokia drynarioides strain JFW-HI SEQ_129485, 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: 684930
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 166 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:630123 original size:30 final size:30
Alignment explanation
Indices: 630089--630149 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
630079 TTGGGCGCAT
* * *
630089 AATTTTAATTAAAGCTCAATTTAGTCCCTA
1 AATTTCAATAAAAGCTCAATTTAATCCCTA
* *
630119 AATTTCACTAAAAGTTCAATTTAATCCCTA
1 AATTTCAATAAAAGCTCAATTTAATCCCTA
630149 A
1 A
630150 TTAAATTAGG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.18, G:0.05, T:0.38
Consensus pattern (30 bp):
AATTTCAATAAAAGCTCAATTTAATCCCTA
Found at i:632137 original size:21 final size:21
Alignment explanation
Indices: 632096--632137 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
632086 AAAATTTATT
**
632096 TTTTAAAAAATTATAGCATCA
1 TTTTAAAAAATTATAAAATCA
632117 TTTTAAAAAA-TATTAAAATCA
1 TTTTAAAAAATTA-TAAAATCA
632138 AATATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTTAAAAAATTATAAAATCA
Found at i:632986 original size:15 final size:18
Alignment explanation
Indices: 632958--632997 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
632948 AGAGTTTTCA
*
632958 AAAAATGTACAAA-T-TT
1 AAAAATATACAAATTATT
632974 AAAAATATA-AAATTATT
1 AAAAATATACAAATTATT
632991 AAAAATA
1 AAAAATA
632998 ATATAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 9 0.43
17 9 0.43
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (18 bp):
AAAAATATACAAATTATT
Found at i:633002 original size:20 final size:21
Alignment explanation
Indices: 632977--633016 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
632967 CAAATTTAAA
*
632977 AATATAAAATTA-TTAAAAAT
1 AATATAAAAATATTTAAAAAT
632997 AATATAAAAATATTTAAAAA
1 AATATAAAAATATTTAAAAA
633017 AAAAAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATATAAAAATATTTAAAAAT
Found at i:633045 original size:26 final size:25
Alignment explanation
Indices: 633016--633075 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
633006 ATATTTAAAA
*
633016 AAAAAAATAGAATTTATAAAATTTAT
1 AAAAAAATAGAATTTATAAAA-ATAT
** *
633042 AAAAATTTAGAATTTTTAAAAATAT
1 AAAAAAATAGAATTTATAAAAATAT
*
633067 AAAATAATA
1 AAAAAAATA
633076 AAAAATTGCA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (25 bp):
AAAAAAATAGAATTTATAAAAATAT
Found at i:633116 original size:9 final size:9
Alignment explanation
Indices: 632968--633154 Score: 64
Period size: 9 Copynumber: 20.6 Consensus size: 9
632958 AAAAATGTAC
632968 AAATT-TAA
1 AAATTATAA
632976 AAA-TAT-A
1 AAATTATAA
632983 AAATTATTAA
1 AAATTA-TAA
632993 AAATAATATAA
1 AAAT--TATAA
*
633004 AAATATTTAA
1 AAAT-TATAA
** *
633014 AAAAAAAAA
1 AAATTATAA
633023 TAGAATTTATAA
1 -A-AA-TTATAA
*
633035 AATTTATAA
1 AAATTATAA
*
633044 AAATT-TAG
1 AAATTATAA
* *
633052 AATTTTTAA
1 AAATTATAA
633061 AAA-TAT-A
1 AAATTATAA
*
633068 AAATAATAAA
1 AAATTAT-AA
**
633078 AAATTGCAA
1 AAATTATAA
* *
633087 AAATAATTA
1 AAATTATAA
* *
633096 AAACTACAAA
1 AAATTA-TAA
633106 AAATTATAA
1 AAATTATAA
*
633115 AAATTATAG
1 AAATTATAA
* *
633124 AATTTTTAA
1 AAATTATAA
*
633133 AAAAT-TAA
1 AAATTATAA
*
633141 AAATTATAT
1 AAATTATAA
633150 AAATT
1 AAATT
633155 TATGAAAAAG
Statistics
Matches: 127, Mismatches: 37, Indels: 29
0.66 0.19 0.15
Matches are distributed among these distances:
7 9 0.07
8 23 0.18
9 54 0.43
10 26 0.20
11 10 0.08
12 5 0.04
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (9 bp):
AAATTATAA
Found at i:633162 original size:28 final size:28
Alignment explanation
Indices: 633103--633163 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
633093 TTAAAACTAC
* *
633103 AAAAAATTATAAAAATTATAGAATTTTT
1 AAAAAATTATAAAAATTATAAAATTTTG
633131 AAAAAA-T-TAAAAATTATATAAATTTATG
1 AAAAAATTATAAAAATTATA-AAATTT-TG
633159 AAAAA
1 AAAAA
633164 GAGTTTGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 11 0.38
27 6 0.21
28 12 0.41
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
AAAAAATTATAAAAATTATAAAATTTTG
Found at i:633414 original size:17 final size:17
Alignment explanation
Indices: 633392--633425 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
633382 TTTATATATA
*
633392 TATTTTTGCAATTTTTG
1 TATTTTTACAATTTTTG
*
633409 TATTTTTATAATTTTTG
1 TATTTTTACAATTTTTG
633426 AAAAAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.09, T:0.68
Consensus pattern (17 bp):
TATTTTTACAATTTTTG
Found at i:633557 original size:23 final size:23
Alignment explanation
Indices: 633531--633579 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
633521 ATAATTTTTG
*
633531 AAATTTCTATTTTTAAAAATTTA
1 AAATTTCCATTTTTAAAAATTTA
* *
633554 AAA-TTCCATTTTTAATAATTTT
1 AAATTTCCATTTTTAAAAATTTA
633576 AAAT
1 AAAT
633580 AATTTAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATTTCCATTTTTAAAAATTTA
Found at i:633969 original size:21 final size:19
Alignment explanation
Indices: 633922--633970 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 19
633912 TTATTATGTG
633922 TTATAAATTATATAATATA
1 TTATAAATTATATAATATA
* *
633941 TAAAAAATATATTATAATATA
1 TTATAAAT-TA-TATAATATA
633962 TTATAAATT
1 TTATAAATT
633971 TTAAAAATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 6 0.25
20 3 0.12
21 15 0.62
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTATAAATTATATAATATA
Found at i:635286 original size:52 final size:53
Alignment explanation
Indices: 635208--635314 Score: 146
Period size: 53 Copynumber: 2.0 Consensus size: 53
635198 TTTGAAATTC
* *
635208 ATCAGCATAAGAGTTGCATTCGTTC-TTTCCAACTCTACTTAGCATTTAAACT
1 ATCACCATAAGAGTTGCATTCGTTCTTTTCCAACTCTACTTAGCATCTAAACT
* * *
635260 ATCACCATAAGAGTTTCATT-GTTTCTTTTTCAACTTTACTTAGCATCTAAACT
1 ATCACCATAAGAGTTGCATTCG-TTCTTTTCCAACTCTACTTAGCATCTAAACT
635313 AT
1 AT
635315 ATATCTCTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
51 1 0.02
52 21 0.44
53 26 0.54
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.40
Consensus pattern (53 bp):
ATCACCATAAGAGTTGCATTCGTTCTTTTCCAACTCTACTTAGCATCTAAACT
Found at i:635476 original size:49 final size:49
Alignment explanation
Indices: 635404--635498 Score: 147
Period size: 49 Copynumber: 1.9 Consensus size: 49
635394 GCAGAGAAAT
*
635404 ACCAATTTAGCCACCTTTTCTTTATGCA-TACACTTATATCTAAGATGTA
1 ACCAATTTAGCCACCTTCTCTTTATGCACT-CACTTATATCTAAGATGTA
* *
635453 ACCAATTTAGCTACCTTCTCTTTATGCACTCACTTATTTCTAAGAT
1 ACCAATTTAGCCACCTTCTCTTTATGCACTCACTTATATCTAAGAT
635499 ATGGCCTTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
49 41 0.98
50 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.40
Consensus pattern (49 bp):
ACCAATTTAGCCACCTTCTCTTTATGCACTCACTTATATCTAAGATGTA
Found at i:640256 original size:24 final size:22
Alignment explanation
Indices: 640216--640261 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
640206 CATGCAGACT
*
640216 CCTATACATGTCATATGTGAAC
1 CCTATACATGTCATATGCGAAC
*
640238 CCTATATATGTCTATTATGCGAAC
1 CCTATACATGTC-A-TATGCGAAC
640262 TCATATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 1 0.05
24 8 0.40
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (22 bp):
CCTATACATGTCATATGCGAAC
Found at i:640279 original size:23 final size:23
Alignment explanation
Indices: 640253--640344 Score: 98
Period size: 23 Copynumber: 4.0 Consensus size: 23
640243 ATATGTCTAT
*
640253 TATGCGAACTCATATGATAGCAG
1 TATGTGAACTCATATGATAGCAG
* *
640276 TATGTGAACTCACATGTTAGCAG
1 TATGTGAACTCATATGATAGCAG
* *
640299 TATGTGAAC-CCTAT-ATATGCATT
1 TATGTGAACTCATATGATA-GCA-G
640322 TATGTGAACTCATATGATTAGCA
1 TATGTGAACTCATATGA-TAGCA
640345 ACATGCGATC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
21 2 0.04
22 6 0.11
23 38 0.68
24 4 0.07
25 4 0.07
26 2 0.04
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (23 bp):
TATGTGAACTCATATGATAGCAG
Found at i:640359 original size:47 final size:46
Alignment explanation
Indices: 640276--640365 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 46
640266 ATGATAGCAG
** *
640276 TATGTGAACTCACATGTTAGCAGTATGTGAACCCTATATATGCATT
1 TATGTGAACTCACATGTTAGCAACATGCGAACCCTATATATGCATT
* * *
640322 TATGTGAACTCATATGATTAGCAACATGCGATCCCTATGTATGC
1 TATGTGAACTCACATG-TTAGCAACATGCGAACCCTATATATGC
640366 GGACCCCTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 15 0.41
47 22 0.59
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (46 bp):
TATGTGAACTCACATGTTAGCAACATGCGAACCCTATATATGCATT
Found at i:642834 original size:2 final size:2
Alignment explanation
Indices: 642827--642855 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
642817 ACTTTACTTT
642827 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
642856 TGTTGGAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:643213 original size:12 final size:12
Alignment explanation
Indices: 643196--643248 Score: 54
Period size: 12 Copynumber: 4.4 Consensus size: 12
643186 CTGCAAAGAC
*
643196 AAAAAGACAGAG
1 AAAAAGACAAAG
*
643208 AAAAAGACAGAG
1 AAAAAGACAAAG
* *
643220 AAGAATGACAAAA
1 AA-AAAGACAAAG
643233 AAAAAGA-AAAG
1 AAAAAGACAAAG
643244 AAAAA
1 AAAAA
643249 AAAATATGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
11 8 0.23
12 18 0.51
13 9 0.26
ACGTcount: A:0.74, C:0.06, G:0.19, T:0.02
Consensus pattern (12 bp):
AAAAAGACAAAG
Found at i:644270 original size:30 final size:30
Alignment explanation
Indices: 644214--644380 Score: 101
Period size: 30 Copynumber: 5.6 Consensus size: 30
644204 TGTTTTATCG
**
644214 AAAAATTTGAATTTGACTTCTAAACTTGCC-
1 AAAAATTTGAATTTGACCCCTAAACTT-CCT
*
644244 AAAAATTTGAATTTGACCCCTTAACTTCCT
1 AAAAATTTGAATTTGACCCCTAAACTTCCT
* * ** **
644274 AAAAATTT-AGTTTTAACCCCCGAACTTTTT
1 AAAAATTTGA-ATTTGACCCCTAAACTTCCT
* * * *
644304 AAAAA-TTCAATTTTGACCCTTAAGCTTTCT
1 AAAAATTTGAA-TTTGACCCCTAAACTTCCT
** *
644334 -AAAATTACATTTTGACCCCTAAACTTTCC-
1 AAAAATTTGAATTTGACCCCTAAAC-TTCCT
* *
644363 AAAATTTTGATTTTGACC
1 AAAAATTTGAATTTGACC
644381 TCATTTTTCC
Statistics
Matches: 106, Mismatches: 24, Indels: 14
0.74 0.17 0.10
Matches are distributed among these distances:
29 21 0.20
30 85 0.80
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
AAAAATTTGAATTTGACCCCTAAACTTCCT
Found at i:644346 original size:29 final size:29
Alignment explanation
Indices: 644305--644368 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
644295 GAACTTTTTA
* * *
644305 AAAATTCAATTTTGACCCTTAAGCTTTCT
1 AAAATTCAATTTTGACCCCTAAACTTTCC
644334 AAAATT-ACATTTTGACCCCTAAACTTTCC
1 AAAATTCA-ATTTTGACCCCTAAACTTTCC
644363 AAAATT
1 AAAATT
644369 TTGATTTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAATTCAATTTTGACCCCTAAACTTTCC
Found at i:644376 original size:59 final size:59
Alignment explanation
Indices: 644233--644380 Score: 147
Period size: 59 Copynumber: 2.5 Consensus size: 59
644223 AATTTGACTT
* * *
644233 CTAAACTTGCCAAAAATTTGAATTTGACCCCTTAACTTCCTAAAAATTTAGTTTTAACCC
1 CTAAACTTTCCAAAAATTTGATTTTGA-CCCTTAACTTCCTAAAAATTTAATTTTAACCC
** ** ** * *
644293 CCGAACTTTTTAAAAATTCAATTTTGACCCTTAAGCTTTCT-AAAA-TTACATTTTGACCC
1 CTAAACTTTCCAAAAATTTGATTTTGACCCTTAA-CTTCCTAAAAATTTA-ATTTTAACCC
*
644352 CTAAACTTTCCAAAATTTTGATTTTGACC
1 CTAAACTTTCCAAAAATTTGATTTTGACC
644381 TCATTTTTCC
Statistics
Matches: 68, Mismatches: 18, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
58 3 0.04
59 41 0.60
60 24 0.35
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (59 bp):
CTAAACTTTCCAAAAATTTGATTTTGACCCTTAACTTCCTAAAAATTTAATTTTAACCC
Found at i:645730 original size:10 final size:10
Alignment explanation
Indices: 645711--645743 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
645701 TCACCCAAAA
*
645711 AAAAATAAAT
1 AAAAAGAAAT
645721 AAAAAGAAAT
1 AAAAAGAAAT
645731 AAAAAGAAA-
1 AAAAAGAAAT
645740 AAAA
1 AAAA
645744 TAAGGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (10 bp):
AAAAAGAAAT
Found at i:645730 original size:14 final size:13
Alignment explanation
Indices: 645707--645760 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
645697 AATTTCACCC
645707 AAAAAAAAATAAA
1 AAAAAAAAATAAA
*
645720 TAAAAAGAAATAAA
1 -AAAAAAAAATAAA
645734 AAGAAAAAAATAAGGA
1 AA-AAAAAAATAA--A
645750 AAAAGAAAAAT
1 AAAA-AAAAAT
645761 GAGAGGTCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 2 0.06
14 21 0.62
15 2 0.06
16 9 0.26
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.09
Consensus pattern (13 bp):
AAAAAAAAATAAA
Found at i:646224 original size:112 final size:115
Alignment explanation
Indices: 646071--646290 Score: 311
Period size: 112 Copynumber: 1.9 Consensus size: 115
646061 AATATTTGTC
* * ** *** *
646071 ATTTTTAATATTTTCATTCATACGAGCTTTGCCTTTAATAAAATTTAATTTTATCCACCTTACAA
1 ATTTGTAATATTTTCATTCATACGAGCTTTACCTCCAATAAAACACAATTTCATCCACCTTACAA
646136 CCTT-ATTCAAGCAT-TTTTGCA-TCGAAATAACGGTTAGTGGACCAATG
66 CCTTGATTCAAGCATATTTTGCATTCGAAATAACGGTTAGTGGACCAATG
* * *
646183 ATTTGTAATCTTTTCATTCATACGAGTTTTATCTCCAATAAAACACAATTTCATCCACCTTACAA
1 ATTTGTAATATTTTCATTCATACGAGCTTTACCTCCAATAAAACACAATTTCATCCACCTTACAA
*
646248 CCTTGATTCAAGCATATTTTGCATTTGAAATAACGGTTAGTGG
66 CCTTGATTCAAGCATATTTTGCATTCGAAATAACGGTTAGTGG
646291 TCTAACAATA
Statistics
Matches: 93, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
112 58 0.62
113 10 0.11
114 7 0.08
115 18 0.19
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (115 bp):
ATTTGTAATATTTTCATTCATACGAGCTTTACCTCCAATAAAACACAATTTCATCCACCTTACAA
CCTTGATTCAAGCATATTTTGCATTCGAAATAACGGTTAGTGGACCAATG
Found at i:646766 original size:49 final size:49
Alignment explanation
Indices: 646685--647308 Score: 418
Period size: 49 Copynumber: 12.7 Consensus size: 49
646675 TAGGTTTGAA
* * * * * * *
646685 GGGAAAGATTAAAGTCGCAACGGCAAACCTTGTACCTTAGAGATGTGAT
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAGAGATATGAT
* ** *
646734 GGGAAAGATTGAAGCCACAACGGTGAATCTTGTACCATGGAGATATGGA-
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAGAGATAT-GAT
* * * * * * * *
646783 GGGAAAGGTTGAATCTGCAATGACAAACCTTGTACCTTAGAGACATGAT
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAGAGATATGAT
* * *
646832 GCGAAAGATTGAAGCCGCAAC-AGCGAATCATGTACCATGGAGATATGGA-
1 GGGAAAGATTGAAGCCGCAACGA-CGAATCTTGTACCATAGAGATAT-GAT
* * * * * * * **
646881 GGGAAAGGTTGAAGTCGCAACAATGAACCTTGTACCTTAAAGACGTGAT
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAGAGATATGAT
* * * *
646930 GGGAAAGATTGAAGCCGCAACGGCGAATCATATACCAT-GCAGATATGAA
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAG-AGATATGAT
* * * * * * *
646979 GGGAAAGGTTAAAGCCGCAATGATGAAACTTGTACCTTAGAGATGTGAT
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAGAGATATGAT
* *
647028 GGGAAAGATTGAAGCCACAACGACGAATCTTGTACCAAAGAGATATTGA-
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAGAGATA-TGAT
* * * * * * *
647077 GGGAAAGGTTGAGGCCGCAACGACGAACCTTATACCTTTGAGATGTGAT
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAGAGATATGAT
* * * * *
647126 GGGAAAGATTGAAGTCACAAC-AGCGAATCTCGTACCATGGGGATATGGA-
1 GGGAAAGATTGAAGCCGCAACGA-CGAATCTTGTACCATAGAGATAT-GAT
* * * * * ** * * * *
647175 AGAAAAGGTTGAAGCCGCTATGGTGAACCTTATACCTTAGAGATGTGAT
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAGAGATATGAT
* * ** * *
647224 GGAAAAGATTGAAACCATAACGACGAATCTTATACCATGGAGATATGGA-
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAGAGATAT-GAT
* * * * *
647273 GGGAAAGGTTGAAGCTGTAACGACGAACCTTATACC
1 GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACC
647309 TTAAAGTTGT
Statistics
Matches: 429, Mismatches: 131, Indels: 30
0.73 0.22 0.05
Matches are distributed among these distances:
48 11 0.03
49 405 0.94
50 13 0.03
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (49 bp):
GGGAAAGATTGAAGCCGCAACGACGAATCTTGTACCATAGAGATATGAT
Found at i:646860 original size:98 final size:97
Alignment explanation
Indices: 646684--647311 Score: 734
Period size: 98 Copynumber: 6.4 Consensus size: 97
646674 ATAGGTTTGA
* * * * *
646684 AGGGAAAGATTAAAGTCGCAACGGCAAACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGC
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGC
*
646749 CACAACGGTGAATCTTGTACCATGGAGATATGG
66 CACAAC-GCGAATCTTGTACCATGGAGATATGG
* * * * ** *
646782 AGGGAAAGGTTGAATCTGCAATGACAAACCTTGTACCTTAGAGACATGATGCGAAAGATTGAAGC
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGC
* *
646847 CGCAACAGCGAATCATGTACCATGGAGATATGG
66 CACAAC-GCGAATCTTGTACCATGGAGATATGG
* * * * *
646880 AGGGAAAGGTTGAAGTCGCAACAATGAACCTTGTACCTTAAAGACGTGATGGGAAAGATTGAAGC
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGC
* * * * *
646945 CGCAACGGCGAATCATATACCATGCAGATATGA
66 CACAAC-GCGAATCTTGTACCATGGAGATATGG
* * * *
646978 AGGGAAAGGTTAAAGCCGCAATGATGAAACTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGC
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGC
** *
647043 CACAACGACGAATCTTGTACCAAAGAGATATTG
66 CACAACG-CGAATCTTGTACCATGGAGATATGG
* * * *
647076 AGGGAAAGGTTGAGGCCGCAACGACGAACCTTATACCTTTGAGATGTGATGGGAAAGATTGAAGT
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGC
* *
647141 CACAACAGCGAATCTCGTACCATGGGGATATGG
66 CACAAC-GCGAATCTTGTACCATGGAGATATGG
* * * * ** * * *
647174 AAGAAAAGGTTGAAGCCGCTATGGTGAACCTTATACCTTAGAGATGTGATGGAAAAGATTGAAAC
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGC
* *
647239 CATAACGACGAATCTTATACCATGGAGATATGG
66 CACAACG-CGAATCTTGTACCATGGAGATATGG
* * *
647272 AGGGAAAGGTTGAAGCTGTAACGACGAACCTTATACCTTA
1 AGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTA
647312 AAGTTGTAAA
Statistics
Matches: 448, Mismatches: 79, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
97 2 0.00
98 445 0.99
99 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (97 bp):
AGGGAAAGGTTGAAGCCGCAACGACGAACCTTGTACCTTAGAGATGTGATGGGAAAGATTGAAGC
CACAACGCGAATCTTGTACCATGGAGATATGG
Found at i:647758 original size:45 final size:46
Alignment explanation
Indices: 647678--647859 Score: 215
Period size: 45 Copynumber: 4.0 Consensus size: 46
647668 GAAGCACCAG
*
647678 AATCTTTTACCCCTAAAGTTAAGAGAGGCAGATTGAAGCCACCATCC
1 AATCTTTTACCCCTAAA-TCAAGAGAGGCAGATTGAAGCCACCATCC
* * * * * *
647725 AATCTTTTACCCCT-GATCAAGAAAGGTAGATTGAAGTCACCGTTC
1 AATCTTTTACCCCTAAATCAAGAGAGGCAGATTGAAGCCACCATCC
* * *
647770 GATCTTTTATCCCT-AATCAAGAGGGGCAGATTGAAGCCACCATCC
1 AATCTTTTACCCCTAAATCAAGAGAGGCAGATTGAAGCCACCATCC
* * * *
647815 AATCTTTTACCCTTAAATCAAGAGGGGAAGATTGAAGCTACCATC
1 AATCTTTTACCCCTAAATCAAGAGAGGCAGATTGAAGCCACCATC
647860 TCATAGAAGC
Statistics
Matches: 113, Mismatches: 21, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
45 70 0.62
46 29 0.26
47 14 0.12
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (46 bp):
AATCTTTTACCCCTAAATCAAGAGAGGCAGATTGAAGCCACCATCC
Found at i:649383 original size:30 final size:30
Alignment explanation
Indices: 649273--649420 Score: 133
Period size: 30 Copynumber: 4.9 Consensus size: 30
649263 TGTTTTATCG
* * *
649273 AAAAATTTGAATTTGA-CTTCTAAACTTGCC
1 AAAAATTTGATTTTGACCCTC-AAACTTTCC
* *
649303 AAAAATTTGAATTTGACCC-CTTAAC-TTCC
1 AAAAATTTGATTTTGACCCTC-AAACTTTCC
*
649332 TAAAAATTT-AGTTTTGACCCTCGAACTTTCC
1 -AAAAATTTGA-TTTTGACCCTCAAACTTTCC
* *
649363 AAAAATTTGATTTTGACCCTCAATCTTTCT
1 AAAAATTTGATTTTGACCCTCAAACTTTCC
* **
649393 AACAATTACATTTTGACCCTCAAACTTT
1 AAAAATTTGATTTTGACCCTCAAACTTT
649421 TTAAAAAGTA
Statistics
Matches: 100, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
29 4 0.04
30 89 0.89
31 7 0.07
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (30 bp):
AAAAATTTGATTTTGACCCTCAAACTTTCC
Found at i:649427 original size:60 final size:60
Alignment explanation
Indices: 649273--649420 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 60
649263 TGTTTTATCG
* * *
649273 AAAAATTTGAA-TTTGA-CTTCTAAACTTGCCAAAAATTTGAATTTGACCCCTTAACTTCCT
1 AAAAATTT-AATTTTGACCCTC-AAACTTTCCAAAAATTTGAATTTGACCCCTCAACTTCCT
* * * *
649333 AAAAATTTAGTTTTGACCCTCGAACTTTCCAAAAATTTGATTTTGA-CCCTCAATCTTTCT
1 AAAAATTTAATTTTGACCCTCAAACTTTCCAAAAATTTGAATTTGACCCCTCAA-CTTCCT
*
649393 AACAA-TTACATTTTGACCCTCAAACTTT
1 AAAAATTTA-ATTTTGACCCTCAAACTTT
649421 TTAAAAAGTA
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
59 10 0.14
60 61 0.82
61 3 0.04
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (60 bp):
AAAAATTTAATTTTGACCCTCAAACTTTCCAAAAATTTGAATTTGACCCCTCAACTTCCT
Found at i:649433 original size:30 final size:30
Alignment explanation
Indices: 649325--649530 Score: 159
Period size: 30 Copynumber: 6.9 Consensus size: 30
649315 TTGACCCCTT
* * *
649325 AACTTCCTAAAAATTTA-GTTTTGACCCTCG
1 AACTTTCTAAAAA-TTACATTTTGACCCTCA
* **
649355 AACTTTCCAAAAATTTGATTTTGACCCTCA
1 AACTTTCTAAAAATTACATTTTGACCCTCA
* *
649385 ATCTTTCTAACAATTACATTTTGACCCTCA
1 AACTTTCTAAAAATTACATTTTGACCCTCA
* * * *
649415 AACTTTTTAAAAAGTACATTTTAGA-TCTTA
1 AACTTTCTAAAAATTACATTTT-GACCCTCA
* * * *
649445 AAATTTTTAAAAATTGCATTTTGGCCC-CTA
1 AACTTTCTAAAAATTACATTTTGACCCTC-A
* *
649475 AACTTTCTAAAAAATACATTTTAACCACT-A
1 AACTTTCTAAAAATTACATTTTGACC-CTCA
* **
649505 AACTTTCTAAAATTTTGATTTTGACC
1 AACTTTCTAAAAATTACATTTTGACC
649531 TCATTTTTCC
Statistics
Matches: 137, Mismatches: 33, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
29 3 0.02
30 131 0.96
31 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (30 bp):
AACTTTCTAAAAATTACATTTTGACCCTCA
Found at i:651547 original size:136 final size:134
Alignment explanation
Indices: 651344--651597 Score: 348
Period size: 136 Copynumber: 1.9 Consensus size: 134
651334 TACTTAATGC
* * *
651344 TTTTAAATTTTCAATTTATTTTTTTAATATAATAGTTCTTTGGTTAGATGTTTAGATACTTGCAA
1 TTTTAAATTTTCAATTAATTTTTTTAACATAATAGTTCTTTGGTTAGATGGTTAGATACTTGCAA
* * * *
651409 TTACATCCTTGAGTCTTTAGTTTAATTCCTCTCCTACTTC-CATTTGTATTTTTTTTATTTCATG
66 TTACATCATTGAGTCTTGAGTTTAATTCCTCTACTAC-TCACATTTGCATTTTTTTTATTTCATG
651473 TTGCT
130 TTGCT
* * * * *
651478 TTTTAAATTTTTAATTAACGTTTTTTTAACATATTAGTTCTTTTGTTAGATGGTTAGATAGTTGT
1 TTTTAAATTTTCAATTAA--TTTTTTTAACATAATAGTTCTTTGGTTAGATGGTTAGATACTTGC
* *
651543 AATTACATCATTGAGTCTTGAGTTTGATTCTTCTACTACTCACATTTGCATTTTT
64 AATTACATCATTGAGTCTTGAGTTTAATTCCTCTACTACTCACATTTGCATTTTT
651598 ATTTCACGTT
Statistics
Matches: 103, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 16 0.16
135 2 0.02
136 85 0.83
ACGTcount: A:0.24, C:0.12, G:0.11, T:0.53
Consensus pattern (134 bp):
TTTTAAATTTTCAATTAATTTTTTTAACATAATAGTTCTTTGGTTAGATGGTTAGATACTTGCAA
TTACATCATTGAGTCTTGAGTTTAATTCCTCTACTACTCACATTTGCATTTTTTTTATTTCATGT
TGCT
Found at i:654835 original size:40 final size:40
Alignment explanation
Indices: 654780--654860 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
654770 GTAATAGGGA
654780 GTAAGCTCAGTTGGTTTTCTTGTCATCTTGATCGGCAATG
1 GTAAGCTCAGTTGGTTTTCTTGTCATCTTGATCGGCAATG
654820 GTAAGCTCAGTTGGTTTTCTTGTCATCTTGATCGGCAATG
1 GTAAGCTCAGTTGGTTTTCTTGTCATCTTGATCGGCAATG
654860 G
1 G
654861 CAGACGTCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (40 bp):
GTAAGCTCAGTTGGTTTTCTTGTCATCTTGATCGGCAATG
Found at i:661861 original size:20 final size:20
Alignment explanation
Indices: 661818--661861 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
661808 ATTATATTAT
* *
661818 TGTTTTGGTGCTTTTTTTAC
1 TGTTTTGGTGCTGTTTTCAC
661838 TGTTTTGGTTGCTGTTTTCA-
1 TGTTTTGG-TGCTGTTTTCAC
661858 TGTT
1 TGTT
661862 GTTTTTGCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.05, C:0.09, G:0.23, T:0.64
Consensus pattern (20 bp):
TGTTTTGGTGCTGTTTTCAC
Found at i:661873 original size:12 final size:12
Alignment explanation
Indices: 661858--661897 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
661848 GCTGTTTTCA
*
661858 TGTTGTTTTTGC
1 TGTTGTTTTTGT
*
661870 TGTTATTTTTGT
1 TGTTGTTTTTGT
*
661882 TGCTGTTTTTGT
1 TGTTGTTTTTGT
661894 TGTT
1 TGTT
661898 TAGATGTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.05, G:0.23, T:0.70
Consensus pattern (12 bp):
TGTTGTTTTTGT
Found at i:661879 original size:24 final size:24
Alignment explanation
Indices: 661852--661897 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
661842 TTGGTTGCTG
*
661852 TTTTCATGTTGTTTTTGCTGTTAT
1 TTTTCATGCTGTTTTTGCTGTTAT
** *
661876 TTTTGTTGCTGTTTTTGTTGTT
1 TTTTCATGCTGTTTTTGCTGTT
661898 TAGATGTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.04, C:0.07, G:0.20, T:0.70
Consensus pattern (24 bp):
TTTTCATGCTGTTTTTGCTGTTAT
Found at i:661886 original size:15 final size:16
Alignment explanation
Indices: 661865--661911 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
661855 TCATGTTGTT
661865 TTTGCTGTTATTTTTG
1 TTTGCTGTTATTTTTG
661881 -TTGCTGTT-TTTGTTG
1 TTTGCTGTTATTT-TTG
*
661896 TTTAGATGTTATTTTT
1 TTT-GCTGTTATTTTT
661912 TATGCGTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
14 3 0.12
15 11 0.42
16 2 0.08
17 7 0.27
18 3 0.12
ACGTcount: A:0.09, C:0.04, G:0.19, T:0.68
Consensus pattern (16 bp):
TTTGCTGTTATTTTTG
Found at i:661889 original size:35 final size:32
Alignment explanation
Indices: 661840--661911 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 32
661830 TTTTTTACTG
* * *
661840 TTTTGGTTGCTGTTTTCATGTTGTTTTTGCTGTTA
1 TTTTTGTTGCTGTTTT--TGTTG-TTTAGATGTTA
661875 TTTTTGTTGCTGTTTTTGTTGTTTAGATGTTA
1 TTTTTGTTGCTGTTTTTGTTGTTTAGATGTTA
661907 TTTTT
1 TTTTT
661912 TATGCGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 14 0.41
33 5 0.15
35 15 0.44
ACGTcount: A:0.07, C:0.06, G:0.21, T:0.67
Consensus pattern (32 bp):
TTTTTGTTGCTGTTTTTGTTGTTTAGATGTTA
Found at i:664169 original size:24 final size:21
Alignment explanation
Indices: 664142--664189 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
664132 TTAAAGGCAC
664142 AAAAAATATGACATATAAATAAAT
1 AAAAAATAT--CA-ATAAATAAAT
*
664166 -AAAAATATCAATGAATAAAT
1 AAAAAATATCAATAAATAAAT
664186 AAAA
1 AAAA
664190 TTAAATGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
23 8 0.36
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.23
Consensus pattern (21 bp):
AAAAAATATCAATAAATAAAT
Found at i:664454 original size:20 final size:21
Alignment explanation
Indices: 664431--664479 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
664421 AACAAACAAG
*
664431 ATAATAAATTAAATACCAA-A
1 ATAATAAATTAAATACAAATA
*
664451 ATAA-ACAATTAAATATAAATA
1 ATAATA-AATTAAATACAAATA
664472 ATAATAAA
1 ATAATAAA
664480 AAAGAATACG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 15 0.62
21 7 0.29
22 1 0.04
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (21 bp):
ATAATAAATTAAATACAAATA
Found at i:664633 original size:12 final size:12
Alignment explanation
Indices: 664616--664643 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
664606 TGTTAGTTTC
664616 AAAAGAAGAAAA
1 AAAAGAAGAAAA
664628 AAAAGAAGAAAA
1 AAAAGAAGAAAA
664640 AAAA
1 AAAA
664644 ATACAAATCG
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAAA
Found at i:666080 original size:76 final size:76
Alignment explanation
Indices: 665988--666246 Score: 288
Period size: 76 Copynumber: 3.4 Consensus size: 76
665978 ACATAAATCG
* * *
665988 TCGATTTATCCCACTAGCACTGGGCACAAAATATCGTTGGAATATCCAACTAGAGCTGGGCTCAC
1 TCGATTTATCCAACTAGCACTGGGCGCAAAATATCGTTGGAATATCCAACTAGAGATGGGCTCAC
666053 -TGTTGATATCA
66 AT-TTGATATCA
* * * * *
666064 TCGATTTATCCGACTAGGACTGAGCGC-AAATCATCGTTGGCATATCCAACTAGAGTTGGGCTCA
1 TCGATTTATCCAACTAGCACTGGGCGCAAAAT-ATCGTTGGAATATCCAACTAGAGATGGGCTCA
* **
666128 CATTCGATATTTT
65 CATTTGATA-TCA
* * * * * * *
666141 TCGGTTTATCCAAGTAGCGCTGGGTGCAAAATATTGTTGGTATATCCAACTAGAGATGAGCTCAC
1 TCGATTTATCCAACTAGCACTGGGCGCAAAATATCGTTGGAATATCCAACTAGAGATGGGCTCAC
*
666206 ATTTCATATCA
66 ATTTGATATCA
* *
666217 TCGGTTTATCCAACTAGCACTAGGCGCAAA
1 TCGATTTATCCAACTAGCACTGGGCGCAAA
666247 CTCTGTTACA
Statistics
Matches: 151, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
75 4 0.03
76 86 0.57
77 57 0.38
78 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (76 bp):
TCGATTTATCCAACTAGCACTGGGCGCAAAATATCGTTGGAATATCCAACTAGAGATGGGCTCAC
ATTTGATATCA
Found at i:673898 original size:61 final size:61
Alignment explanation
Indices: 673766--674090 Score: 370
Period size: 61 Copynumber: 5.3 Consensus size: 61
673756 TTTCAATTCA
* * * * * * *
673766 CATTTGATACTCACGATGTCATAGAGTCATCGGACC-TATAATCCAT-ATTCGGATTCATTT
1 CATTTAATACTCACGATGACACAAAGTCATCGGACCTTTTAATCCGTAATT-GGATTCATTG
* * *
673826 CATTTAATACTCACGATGACACAAAATCATCGGACCTTTTAATCTGTAATTGGATTCACTG
1 CATTTAATACTCACGATGACACAAAGTCATCGGACCTTTTAATCCGTAATTGGATTCATTG
* ** * * * *
673887 CATTTAGTACTCACGATGACACAAAGTCATCAAACCTTTTAATTCGTAAGTAGATTCATTT
1 CATTTAATACTCACGATGACACAAAGTCATCGGACCTTTTAATCCGTAATTGGATTCATTG
*
673948 CATTTAATACTC-CATATGACACAAAGTCATCGGACCTTTTAATCCGTAATTGGATTCATTG
1 CATTTAATACTCAC-GATGACACAAAGTCATCGGACCTTTTAATCCGTAATTGGATTCATTG
* * * * *
674009 CATTTAATACTCACGATAACACAAAGTCATCGAACC-TTTAATCCATAATAGGATTCATTTC
1 CATTTAATACTCACGATGACACAAAGTCATCGGACCTTTTAATCCGTAATTGGATTCA-TTG
* *
674070 CATGTAATACTTACGATGACA
1 CATTTAATACTCACGATGACA
674091 TAGAGAATCC
Statistics
Matches: 223, Mismatches: 37, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
60 51 0.23
61 168 0.75
62 4 0.02
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (61 bp):
CATTTAATACTCACGATGACACAAAGTCATCGGACCTTTTAATCCGTAATTGGATTCATTG
Found at i:673982 original size:122 final size:121
Alignment explanation
Indices: 673766--674090 Score: 411
Period size: 122 Copynumber: 2.7 Consensus size: 121
673756 TTTCAATTCA
* ** * * ** * * *
673766 CATTTGATACTCACGATGTCATAGAGTCATCGGACCTATAATCCATATTCGGATTCATTTCATTT
1 CATTTAATACTCACGATAACACAAAGTCATCAAACCTTTAATCCATAATAGGATTCATTTCATTT
*
673831 AATACTCACGATGACACAAAATCATCGGACCTTTTAATCTGTAATTGGATTCACTG
66 AATACTCACGATGACACAAAATCATCGGACCTTTTAATCCGTAATTGGATTCACTG
* * * *
673887 CATTTAGTACTCACGATGACACAAAGTCATCAAACCTTTTAATTCGTAAGTA-GATTCATTTCAT
1 CATTTAATACTCACGATAACACAAAGTCATCAAACC-TTTAATCCATAA-TAGGATTCATTTCAT
* * *
673951 TTAATACTC-CATATGACACAAAGTCATCGGACCTTTTAATCCGTAATTGGATTCATTG
64 TTAATACTCAC-GATGACACAAAATCATCGGACCTTTTAATCCGTAATTGGATTCACTG
* *
674009 CATTTAATACTCACGATAACACAAAGTCATCGAACCTTTAATCCATAATAGGATTCATTTCCATG
1 CATTTAATACTCACGATAACACAAAGTCATCAAACCTTTAATCCATAATAGGATTCATTT-CATT
*
674074 TAATACTTACGATGACA
65 TAATACTCACGATGACA
674091 TAGAGAATCC
Statistics
Matches: 174, Mismatches: 24, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
120 2 0.01
121 49 0.28
122 121 0.70
123 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (121 bp):
CATTTAATACTCACGATAACACAAAGTCATCAAACCTTTAATCCATAATAGGATTCATTTCATTT
AATACTCACGATGACACAAAATCATCGGACCTTTTAATCCGTAATTGGATTCACTG
Found at i:678442 original size:50 final size:49
Alignment explanation
Indices: 678374--678749 Score: 167
Period size: 50 Copynumber: 7.4 Consensus size: 49
678364 TTAAAAAAAC
* *
678374 AAGACAAAGTTTATATTTTTAAAATAAAAATATGTTTTTTAGTTATTTTA
1 AAGAAAAAGTTTAAATTTTT-AAATAAAAATATGTTTTTTAGTTATTTTA
* * * * *
678424 AAGAAAAATTTTAAATTTTTAAATAAAATTTTGATTTTTTAATTATTTCGA
1 AAGAAAAAGTTTAAATTTTTAAATAAAAATATG-TTTTTTAGTTATTT-TA
* ** * * ****
678475 AA-TAAAAGTTTGGATTTTTAAGT-AAAATAGTGATTTTCTT--TAAAAAAAA
1 AAGAAAAAGTTTAAATTTTTAAATAAAAATA-TG-TTTT-TTAGT-TATTTTA
* * *
678524 AAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTA
1 AAGAAAAAGTTTAAATTTTT--AAATAAAAATATGTTTTTTAGTTATTTTA
* ** * ** *
678575 AAGAAAAAATTTTAAATTTTTAAATAAAGTTTTAATTTTTTTTAACTATTTCA
1 AAG-AAAAAGTTTAAATTTTTAAATAAA--AAT-ATGTTTTTTAGTTATTTTA
** * ****
678628 AA-ATAAAAGTTTGGA-TTTTAAGT-AAAATAGTGATTTTTT--TTAAAAAAA
1 AAGA-AAAAGTTTAAATTTTTAAATAAAAATA-TG-TTTTTTAGTT-ATTTTA
*
678676 AAGAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTA
1 AAG-A-A-AAAGTTTAAATTTTT--AAATAAAAATATGTTTTTTAGTTATTTTA
*
678730 AAGAAAAAATTTTAAATTTT
1 AAG-AAAAAGTTTAAATTTT
678750 AAACAAAGTT
Statistics
Matches: 236, Mismatches: 62, Indels: 54
0.67 0.18 0.15
Matches are distributed among these distances:
47 2 0.01
48 6 0.03
49 25 0.11
50 80 0.34
51 30 0.13
52 45 0.19
53 28 0.12
54 12 0.05
55 8 0.03
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (49 bp):
AAGAAAAAGTTTAAATTTTTAAATAAAAATATGTTTTTTAGTTATTTTA
Found at i:678445 original size:21 final size:20
Alignment explanation
Indices: 678419--678465 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
678409 TTTTTAGTTA
678419 TTTTAAAGAAAAATTTTAAAT
1 TTTTAAA-AAAAATTTTAAAT
* * *
678440 TTTTAAATAAAATTTTGATT
1 TTTTAAAAAAAATTTTAAAT
678460 TTTTAA
1 TTTTAA
678466 TTATTTCGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTTAAAAAAAATTTTAAAT
Found at i:678493 original size:150 final size:152
Alignment explanation
Indices: 678296--678886 Score: 881
Period size: 150 Copynumber: 3.9 Consensus size: 152
678286 TGATTTTGGA
* * * *
678296 AAAGTTTTGGTTTTTTTAAACAATTTAGAAATAAAAAGTTTGGTTTTTTAAGTAAAATAGTGATT
1 AAAGTTTTGATTTTTTT-AACTATTTCGAAAT-AAAAGTTTGGATTTTTAAGTAAAATAGTGATT
* *
678361 TTCTTAAAAAAACAAGACAAAGTTTATATTTTT-AAAATAAAAATATGTTTTTTAGTTATTTTAA
64 TTCTTAAAAAAAGAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAA
678425 AG-AAAAATTTTAAATTTTTAAAT
129 AGAAAAAATTTTAAATTTTTAAAT
* *
678448 AAAATTTTGA-TTTTTTAATTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
* *
678512 CTTTAAAAAAAAAAGAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAA
66 C-TTAAAAAAAGAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAA
678577 GAAAAAATTTTAAATTTTTAAAT
130 GAAAAAATTTTAAATTTTTAAAT
* *
678600 AAAGTTTTAATTTTTTTTAACTATTTCAAAATAAAAGTTTGGA-TTTTAAGTAAAATAGTGATTT
1 AAAGTTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGA-TT
*
678664 TTTTTAAAAAAAAAGAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTT
64 TTCTT--AAAAAAAGAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTT
*
678729 AAAGAAAAAATTTTAAA-TTTTAAAC
127 AAAGAAAAAATTTTAAATTTTTAAAT
* *
678754 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAATAAAGTAGTGATTTT
1 AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
* * * *
678819 CATCAAAAAAGAA-AGAAAGTTTATATTTTAAAAAATAAAAATCA-GTTTTTTAGTGATTTTAAA
66 CTTAAAAAAAGAAGAGAAAGTTTATATTTTTAAAAATAAAAAT-ATGTTTTTTAGTTATTTTAAA
678882 GAAAA
130 GAAAA
678887 TTTTTTTGAT
Statistics
Matches: 403, Mismatches: 26, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
149 34 0.08
150 90 0.22
151 48 0.12
152 37 0.09
153 56 0.14
154 65 0.16
155 73 0.18
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (152 bp):
AAAGTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGTGATTTT
CTTAAAAAAAGAAGAGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTTAGTTATTTTAAAG
AAAAAATTTTAAATTTTTAAAT
Found at i:679460 original size:81 final size:81
Alignment explanation
Indices: 679358--679518 Score: 295
Period size: 81 Copynumber: 2.0 Consensus size: 81
679348 AATTTGATTT
679358 TCACTATCAAAATATATGGAATAACGGTCCTGATTACTATCCCTAATTAAAAAAGTGTCATCAGA
1 TCACTATCAAAATATATGGAATAACGGTCCTGATTACTATCCCTAATTAAAAAAGTGTCATCAGA
679423 AATGAAATTCCGAATC
66 AATGAAATTCCGAATC
* *
679439 TCACTATCAAAATATATGGAATAACGGTCCTGATTACTATCCCTAATTAAAAAGGTGTCATTAGA
1 TCACTATCAAAATATATGGAATAACGGTCCTGATTACTATCCCTAATTAAAAAAGTGTCATCAGA
*
679504 AATGAAATTTCGAAT
66 AATGAAATTCCGAAT
679519 GTCTTTGACG
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (81 bp):
TCACTATCAAAATATATGGAATAACGGTCCTGATTACTATCCCTAATTAAAAAAGTGTCATCAGA
AATGAAATTCCGAATC
Done.