Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold340
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: 87735
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Found at i:2532 original size:39 final size:39
Alignment explanation
Indices: 2470--2609 Score: 155
Period size: 41 Copynumber: 3.6 Consensus size: 39
2460 CTCCGCATCG
*
2470 AATGCCTTC-GGACATAGCCCGGATATAGTAACTCGC-A
1 AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAA
*
2507 CATGCCTTCGGGATCTTAGCCCGGATATATGTAACTCGCAA
1 AATGCCTTCGGGA-CTTAGCCCGGATATA-GTAACTCGCAA
*
2548 AATGCCTTCGGGGACTCTAG-CCGGATATAGT-ACTCACACTA
1 AATGCCTTC-GGGACT-TAGCCCGGATATAGTAACTCGCA--A
*
2589 AATTCCTTC-GGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
2610 AACATAACAC
Statistics
Matches: 89, Mismatches: 5, Indels: 16
0.81 0.05 0.15
Matches are distributed among these distances:
37 8 0.09
38 6 0.07
39 28 0.31
40 11 0.12
41 29 0.33
42 7 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAA
Found at i:20216 original size:29 final size:29
Alignment explanation
Indices: 20182--20254 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
20172 AATCAACCAT
*
20182 GCACACTTAGTGCCATGTACTTT-AAACTC
1 GCACACTTAGTGCCATGCA-TTTCAAACTC
**
20211 GCACACTTAGTGCCATGCATTTCAAGTTC
1 GCACACTTAGTGCCATGCATTTCAAACTC
*
20240 GCACACCTAGTGCCA
1 GCACACTTAGTGCCA
20255 ATCTCACAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 36 0.92
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATGCATTTCAAACTC
Found at i:23953 original size:24 final size:24
Alignment explanation
Indices: 23902--24093 Score: 278
Period size: 24 Copynumber: 8.0 Consensus size: 24
23892 ACTTTATCAT
*
23902 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
23927 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
23951 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
23975 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
23999 ATAACTGGGGTAGAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
24023 ATAACTAGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
24047 ATAACTAGGGCAGAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
24071 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
24094 GCACTTCCTC
Statistics
Matches: 151, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
24 139 0.92
25 12 0.08
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:24169 original size:20 final size:20
Alignment explanation
Indices: 24144--24209 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
24134 TATGAATACC
24144 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
24164 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATA
24184 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
24204 CCATGT
1 TCATGT
24210 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:24174 original size:11 final size:11
Alignment explanation
Indices: 24144--24198 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
24134 TATGAATACC
24144 TCATGTGCATA
1 TCATGTGCATA
*
24155 TCA--TACATA
1 TCATGTGCATA
24164 TCATGTGCATA
1 TCATGTGCATA
* *
24175 TCA--TACATG
1 TCATGTGCATA
24184 TCATGTGCATA
1 TCATGTGCATA
24195 TCAT
1 TCAT
24199 ACATACCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:33356 original size:39 final size:41
Alignment explanation
Indices: 33255--33438 Score: 206
Period size: 39 Copynumber: 4.6 Consensus size: 41
33245 TTGAATGATG
* *
33255 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATA
*
33295 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT-
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAATA
*
33335 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAA-A
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
33374 TCCGGGTTAAGTCCCGAAGGCA-TTGTGCGAGTTACT-ATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
* *
33413 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
33439 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 9, Indels: 18
0.82 0.06 0.12
Matches are distributed among these distances:
38 1 0.01
39 69 0.55
40 43 0.34
41 12 0.10
42 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (41 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATA
Found at i:33391 original size:79 final size:80
Alignment explanation
Indices: 33255--33438 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
33245 TTGAATGATG
*
33255 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCA-T
33319 TGTGCGAGATACTA-A
65 TGTGCGAGATACTATA
* * * **
33334 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
33396 TTGTGCGAGTTACTATA
64 TTGTGCGAGATACTATA
* *
33413 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
33439 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
78 24 0.26
79 49 0.54
80 18 0.20
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
GTGCGAGATACTATA
Found at i:33461 original size:78 final size:79
Alignment explanation
Indices: 33308--33471 Score: 201
Period size: 78 Copynumber: 2.1 Consensus size: 79
33298 GGACTAAGAT
* **
33308 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
33373 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
33387 CCGAAGGCA-TTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
33449 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
33465 CCGAAGG
1 CCGAAGG
33472 TACGTGATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 38 0.51
79 34 0.46
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:41252 original size:40 final size:39
Alignment explanation
Indices: 41208--41284 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
41198 AGTGACCATA
* *
41208 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGACTAAG-CCCGAAGGCAATTGTGCGAGATACTAAT
* *
41248 TCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTACTA
1 TCCGGACTAAGCCCGAAGGCAATTGTGCGAGATACTA
41285 TAACCGGGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 23 0.70
40 10 0.30
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.23
Consensus pattern (39 bp):
TCCGGACTAAGCCCGAAGGCAATTGTGCGAGATACTAAT
Found at i:41319 original size:40 final size:39
Alignment explanation
Indices: 41169--41312 Score: 132
Period size: 40 Copynumber: 3.6 Consensus size: 39
41159 TGAATGATGT
* * *
41169 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 CCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAATA
* * * *
41208 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAATT
1 -CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAATA
*
41249 CCGGGCTAAGCCCGAAGGCAATTGTGCGAGTTACT-ATAA
1 CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAT-A
*
41288 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAG-CCCGAAGGCATTTG
41313 AACGAGTAGC
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
38 2 0.02
39 31 0.36
40 43 0.51
41 9 0.11
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:41331 original size:79 final size:80
Alignment explanation
Indices: 41168--41318 Score: 182
Period size: 79 Copynumber: 1.9 Consensus size: 80
41158 TTGAATGATG
* *
41168 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
41233 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * *
41248 TCCGGGCTAAG-CCCGAAGGCAATTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-ATTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
41310 TTGAACGAG
64 TTGAACGAG
41319 TAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.02
79 42 0.70
80 17 0.28
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:43067 original size:24 final size:24
Alignment explanation
Indices: 43003--43145 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
42993 GCTTTATCAT
*
43003 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
43028 ATAACTGGGG-AAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
43051 ATAACTAGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
43075 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
43099 ATAACTGGGGCAGAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
43123 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
43146 GCACTTCGCC
Statistics
Matches: 107, Mismatches: 9, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
23 15 0.14
24 84 0.79
25 8 0.07
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:43221 original size:20 final size:20
Alignment explanation
Indices: 43196--43261 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
43186 TATGAATACC
43196 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
43216 TCATGTGCATATCATACATG
1 TCATGTGCATATCATACATA
43236 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
*
43256 CCATGT
1 TCATGT
43262 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:43226 original size:11 final size:11
Alignment explanation
Indices: 43196--43250 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
43186 TATGAATACC
43196 TCATGTGCATA
1 TCATGTGCATA
*
43207 TCA--TACATA
1 TCATGTGCATA
43216 TCATGTGCATA
1 TCATGTGCATA
* *
43227 TCA--TACATG
1 TCATGTGCATA
43236 TCATGTGCATA
1 TCATGTGCATA
43247 TCAT
1 TCAT
43251 ACATACCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:43330 original size:25 final size:25
Alignment explanation
Indices: 43298--43345 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
43288 ATATATAAAC
* * *
43298 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
43323 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
43346 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:46613 original size:20 final size:20
Alignment explanation
Indices: 46588--46627 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
46578 CGTTCATCAT
46588 TATCATCAATTTTAGCCCTA
1 TATCATCAATTTTAGCCCTA
46608 TATCATCAATTTTAGCCCTA
1 TATCATCAATTTTAGCCCTA
46628 ACTTCTTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (20 bp):
TATCATCAATTTTAGCCCTA
Found at i:50827 original size:40 final size:40
Alignment explanation
Indices: 50790--51015 Score: 253
Period size: 40 Copynumber: 5.7 Consensus size: 40
50780 GCTACTCGTT
* *
50790 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
50830 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
50870 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** *
50910 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
** * * * * *
50950 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
50991 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
51016 CATCATTCAA
Statistics
Matches: 165, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 3 0.02
40 150 0.91
41 12 0.07
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:50902 original size:80 final size:80
Alignment explanation
Indices: 50790--51015 Score: 280
Period size: 80 Copynumber: 2.8 Consensus size: 80
50780 GCTACTCGTT
* * *
50790 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCTGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
50854 GATTTAGTAACTCGCA
65 GATTTAGTAACTCGCA
* * *
50870 CAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCACACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCTGGATTTAGTAACTCGCACAAATGCCTTCGGGA-CTTAGCCCG
*
50934 GATTTAGTAACTCGTA
65 GATTTAGTAACTCGCA
* * * * *
50950 CAAATGCCTTC-GGATCTTAGTCTGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCTGGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCC
51013 GGA
64 GGA
51016 CATCATTCAA
Statistics
Matches: 126, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
79 6 0.05
80 108 0.86
81 12 0.10
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCTGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGG
ATTTAGTAACTCGCA
Found at i:51003 original size:120 final size:120
Alignment explanation
Indices: 50790--51008 Score: 284
Period size: 120 Copynumber: 1.8 Consensus size: 120
50780 GCTACTCGTT
50790 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
50855 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCACA
66 ATATAGTAACTAGCACAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCACA
* * * **
50910 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTAACTCGTACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGA-CATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACC
* * *
50972 TGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTA
63 CGGATATAGTAAC-TAGCACAAATGCCTTCGGGACTTA
51009 GCCCGGACAT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
119 6 0.07
120 69 0.81
121 10 0.12
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (120 bp):
CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTAGCACAAATGCCTTCGGGACTTAACCTGGATTTAGTAACTCACA
Found at i:55792 original size:38 final size:38
Alignment explanation
Indices: 55695--55797 Score: 136
Period size: 38 Copynumber: 2.7 Consensus size: 38
55685 GGCTTAAAGA
** *
55695 CCCGCAGGCTTCGTGCTGGTAAAATATCCAGGTTAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAAT
55733 CCCGCAGGCTTCGTGCTGGTATTATAT-CAGGGATAAAT
1 CCCGCAGGCTTCGTGCTGGTATTATATCCA-GGATAAAT
* * *
55771 CTCGCAGGCCTAGTGCTGGTATTATAT
1 CCCGCAGGCTTCGTGCTGGTATTATAT
55798 TCGGGCCTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
37 2 0.03
38 56 0.97
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.29
Consensus pattern (38 bp):
CCCGCAGGCTTCGTGCTGGTATTATATCCAGGATAAAT
Found at i:55871 original size:42 final size:43
Alignment explanation
Indices: 55795--55875 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 43
55785 GCTGGTATTA
* **
55795 TATTCGGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTG
1 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGATGTG
*
55838 TATTC-GGCCTTCGTTCCTAGCAGGCGTAATGCCGGTGA
1 TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGA
55876 AATGATATGT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 29 0.85
43 5 0.15
ACGTcount: A:0.12, C:0.26, G:0.32, T:0.30
Consensus pattern (43 bp):
TATTCGGGCCTTCGTGCCTAGCAGGCGTAATGCCGGTGATGTG
Found at i:64964 original size:20 final size:20
Alignment explanation
Indices: 64941--64983 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
64931 TTTTTTATAG
*
64941 TTTTGTAAG-TTTTAAGATT
1 TTTTTTAAGATTTTAAGATT
* *
64960 TTTTTTTAGATTTTAATATT
1 TTTTTTAAGATTTTAAGATT
64980 TTTT
1 TTTT
64984 AATTTTTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTTTTAAGATTTTAAGATT
Found at i:66816 original size:19 final size:19
Alignment explanation
Indices: 66764--66817 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
66754 ATAGAATAGT
* *
66764 AAAAATTACGAG-GATATA
1 AAAAATTAAGAGAAATATA
66782 AAAAA--AATGAGAAAATATA
1 AAAAATTAA-GAG-AAATATA
66801 AAAAATTAAGAGAAATA
1 AAAAATTAAGAGAAATA
66818 CCAAAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 1 0.03
17 3 0.10
18 5 0.17
19 15 0.52
20 3 0.10
21 2 0.07
ACGTcount: A:0.67, C:0.02, G:0.13, T:0.19
Consensus pattern (19 bp):
AAAAATTAAGAGAAATATA
Found at i:66823 original size:19 final size:20
Alignment explanation
Indices: 66801--66839 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
66791 AGAAAATATA
66801 AAAAATTAAGAGAA-ATACC
1 AAAAATTAAGAGAATATACC
* *
66820 AAAATTTACGAGAATATACC
1 AAAAATTAAGAGAATATACC
66840 GATTATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.21
Consensus pattern (20 bp):
AAAAATTAAGAGAATATACC
Found at i:77699 original size:79 final size:81
Alignment explanation
Indices: 77597--77781 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
77587 GCTCCTCGTT
* *
77597 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
77660 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
77677 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
77741 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
77757 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
77782 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:77781 original size:40 final size:40
Alignment explanation
Indices: 77597--77781 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
77587 GCTCCTCGTT
* *
77597 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
77637 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
77677 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
77716 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
77757 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
77782 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:85414 original size:40 final size:40
Alignment explanation
Indices: 85368--85514 Score: 183
Period size: 40 Copynumber: 3.7 Consensus size: 40
85358 CCGGAAGTAA
*
85368 CACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCG
1 CACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCG
* *
85408 CACAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCG
1 CACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCG
* * * * *
85447 CACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAG
1 CACAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCG
85488 CACAAA-GCCTTCGGGACTTAGCCCGGA
1 CACAAATGCCTTCGGGACTTAGCCCGGA
85515 CATCATTCAA
Statistics
Matches: 92, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 33 0.36
40 46 0.50
41 11 0.12
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCG
Found at i:85499 original size:79 final size:80
Alignment explanation
Indices: 85368--85514 Score: 201
Period size: 79 Copynumber: 1.9 Consensus size: 80
85358 CCGGAAGTAA
* *
85368 CACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCC
1 CACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCC
85432 GGAATTAGTATCTCG
66 GGAATTAGTATCTCG
** * *
85447 CACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAGC
85510 CCGGA
64 CCGGA
85515 CATCATTCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
78 3 0.05
79 37 0.63
80 19 0.32
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
CACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCC
GGAATTAGTATCTCG
Done.