Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006510.1 Hibiscus syriacus cultivar Beakdansim tig00015854_pilon, 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: 80323
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:912 original size:3 final size:3
Alignment explanation
Indices: 904--938 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
894 GCATGTAAAT
904 TAA TAA TAA TAA TTAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA
939 TTAAAGACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:919 original size:13 final size:13
Alignment explanation
Indices: 901--942 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
891 CCTGCATGTA
901 AATTAATAATAAT
1 AATTAATAATAAT
914 AATTAATAATAAT
1 AATTAATAATAAT
927 AA-TAATAA-AAT
1 AATTAATAATAAT
938 -ATTAA
1 AATTAA
943 AGACATGACG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.04
11 6 0.21
12 6 0.21
13 15 0.54
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:1592 original size:16 final size:17
Alignment explanation
Indices: 1571--1606 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1561 AACTATAAAG
1571 ACGACGTATAATC-ATC
1 ACGACGTATAATCAATC
1587 ACGACGTATAATCAATC
1 ACGACGTATAATCAATC
1604 ACG
1 ACG
1607 GCCTGACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.22
Consensus pattern (17 bp):
ACGACGTATAATCAATC
Found at i:3346 original size:30 final size:30
Alignment explanation
Indices: 3302--3374 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 30
3292 GGGTTGAAAT
* * * *
3302 ATAAATATCA-AAAAATAAAGGGGATATAT
1 ATAAATAACAGAAAAATAAAGGGCATAGAA
* *
3331 GTAAATAACAGAAAAATAAAGTGCATAGAA
1 ATAAATAACAGAAAAATAAAGGGCATAGAA
3361 ATAAATAACAGAAA
1 ATAAATAACAGAAA
3375 TGTAAAATCG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 8 0.22
30 28 0.78
ACGTcount: A:0.62, C:0.05, G:0.14, T:0.19
Consensus pattern (30 bp):
ATAAATAACAGAAAAATAAAGGGCATAGAA
Found at i:6272 original size:20 final size:20
Alignment explanation
Indices: 6247--6284 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6237 TAAATTGATA
*
6247 AAATTAAAATACTGATAATG
1 AAATTAAAATACTCATAATG
*
6267 AAATTAGAATACTCATAA
1 AAATTAAAATACTCATAA
6285 ATTTTTCGAC
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:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (20 bp):
AAATTAAAATACTCATAATG
Found at i:18610 original size:2 final size:2
Alignment explanation
Indices: 18603--18645 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
18593 GAATTGCATC
18603 AT 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 AT
18645 A
1 A
18646 AGAACTGGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18837 original size:75 final size:75
Alignment explanation
Indices: 18693--18837 Score: 188
Period size: 75 Copynumber: 1.9 Consensus size: 75
18683 GTGCCCACCA
* *
18693 TGGAATCTGAATTTCTTTATACTAATTATTCATTTTATTGAAGATGCTCACCCTAAAATTTTGTT
1 TGGAATCTGAATTTCTTTATACTAATTATTCATTTTACTGAAGATGCTCACCCTAAAATTTTATT
18758 GTGTCCATCC
66 GTGTCCATCC
* * * *
18768 TGGAAT-TCGAATTTCTTTATATTAGTTATTCATTTTACT-AAGGTG-TCCACCCTGAAATTTTA
1 TGGAATCT-GAATTTCTTTATACTAATTATTCATTTTACTGAAGATGCT-CACCCTAAAATTTTA
18830 TTCGTGTC
64 TT-GTGTC
18838 TGTCCCATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
73 1 0.02
74 21 0.34
75 39 0.64
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.45
Consensus pattern (75 bp):
TGGAATCTGAATTTCTTTATACTAATTATTCATTTTACTGAAGATGCTCACCCTAAAATTTTATT
GTGTCCATCC
Found at i:19294 original size:23 final size:23
Alignment explanation
Indices: 19251--19294 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
19241 GATCAACTGA
**
19251 AAAATAATTTAGAACGTTAGAGT
1 AAAATAATTTAGAACAATAGAGT
19274 AAAATAATTTGAGAA-AATAGA
1 AAAATAATTT-AGAACAATAGA
19295 ATTTTAGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.55, C:0.02, G:0.16, T:0.27
Consensus pattern (23 bp):
AAAATAATTTAGAACAATAGAGT
Found at i:22031 original size:112 final size:112
Alignment explanation
Indices: 21831--22404 Score: 875
Period size: 112 Copynumber: 5.1 Consensus size: 112
21821 TTGTCGGTTT
* * *
21831 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
21896 AGTCTATAAATGACAAAACAGGTAAAACGCTACCGAATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
* * * * *
21943 GTATCGATATTTTATAAAAATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
22008 GGTCTATAAATGACAAAACAGGTAAAGCGCTATCGTATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
22055 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
22120 GGTCTATAAATCACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
* * * *
22167 GTGTCGATACTTTATAAAAATGTATCAATCCATAATAATATAACAGGT-AAAAAATTACAAAACT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* *
22231 GGTATATAAATGACAAAACATGTAAAGCGCTACC-AGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGA-ATATATTGAAA
* * *
22278 GTGTCGATACTTTATAAAATTGTATCGATTCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
22343 GGTCTATAAATGACAAAACAGGTAAAGGGCTACC-AGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGA-ATATATTGAAA
22390 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
22405 TATAAGTATC
Statistics
Matches: 424, Mismatches: 36, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
111 99 0.23
112 325 0.77
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGAATATATTGAAA
Found at i:22330 original size:223 final size:224
Alignment explanation
Indices: 21831--22404 Score: 918
Period size: 223 Copynumber: 2.6 Consensus size: 224
21821 TTGTCGGTTT
* *
21831 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
* * * * *
21896 AGTCTATAAATGACAAAACAGGTAAAACGCTACCGAATATATTGAAAGTATCGATATTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
** *
21961 AATATATTGATCCATAACAATATAACAGGTAAAAAAATGACAAAACTGGTCTATAAATGACAAAA
131 AATATATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACTGGTATATAAATGACAAAA
*
22026 CAGGTAAAGCGCTATCGTATATATTGAAA
196 CAGGTAAAGCGCTACCGTATATATTGAAA
*
22055 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
*
22120 GGTCTATAAATCACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* * *
22185 AATGTATCAATCCATAATAATATAACAGGT-AAAAAATTACAAAACTGGTATATAAATGACAAAA
131 AATATATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACTGGTATATAAATGACAAAA
*
22249 CATGTAAAGCGCTACCAG-ATATATTGAAA
196 CAGGTAAAGCGCTACC-GTATATATTGAAA
* *
22278 GTGTCGATACTTTATAAAATTGTATCGATTCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
* * * *
22343 GGTCTATAAATGACAAAACAGGTAAAGGGCTACCAGATATGTTGATAGTGTCGATACTTTAT
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
22405 TATAAGTATC
Statistics
Matches: 324, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
223 176 0.54
224 148 0.46
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.26
Consensus pattern (224 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
AATATATCAATCCATAACAATATAACAGGTAAAAAAATGACAAAACTGGTATATAAATGACAAAA
CAGGTAAAGCGCTACCGTATATATTGAAA
Found at i:22582 original size:182 final size:182
Alignment explanation
Indices: 22275--22722 Score: 700
Period size: 182 Copynumber: 2.5 Consensus size: 182
22265 AGATATATTG
* * * *
22275 AAAGTGTCGATACTTTATAAAATTGTATCGATTCATAACAATATAACATGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* ** * * *
22340 ACCGGTCTATAAATGACAAAACAGGTAAAGGGCTACCAGATATGTTGATAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACAGGAAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
*
22405 TATAAGTATCGACACTTTTGAAATTTAAAAGAGAATAAGTTATAGCGCAAAT
131 TATAAGTATCGACACTTTTGAAATTTAAAAGAAAATAAGTTATAGCGCAAAT
* * *
22457 AAAGTGTCAATACTTTATAAAAATGTGTCGATCCATTACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
22522 ATCGGTCTCGAAATGACAAAACCGGAAAAGAGCTACC-GAATATGTTGAAAGTGTCGATACTTTA
66 ATCGGTCTCGAAATGACAAAACAGGAAAAGAGCTACCAG-ATATGTTGAAAGTGTCGATACTTTA
* * *
22586 TTATAATTATCGACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCGCCAAT
130 TTATAAGTATCGACACTTTTGAAATTTAAAAGAAAATAAGTTATAGCGCAAAT
*
22639 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
*
22704 ATCGGTTTCGAAATGACAA
66 ATCGGTCTCGAAATGACAA
22723 CCAGTAGTAA
Statistics
Matches: 242, Mismatches: 23, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
181 1 0.00
182 241 1.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ATCGGTCTCGAAATGACAAAACAGGAAAAGAGCTACCAGATATGTTGAAAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGAAATTTAAAAGAAAATAAGTTATAGCGCAAAT
Found at i:23414 original size:23 final size:23
Alignment explanation
Indices: 23368--23414 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
23358 AAATAGGTCA
*
23368 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
23391 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
23414 A
1 A
23415 CTGTACTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:24143 original size:15 final size:15
Alignment explanation
Indices: 24123--24153 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
24113 CATAAATTTT
*
24123 ATTAAAAATATTAAA
1 ATTAAAAATAATAAA
24138 ATTAAAAATAATAAA
1 ATTAAAAATAATAAA
24153 A
1 A
24154 AATTATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTAAAAATAATAAA
Found at i:37432 original size:42 final size:42
Alignment explanation
Indices: 37381--37476 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
37371 ATTCTTTGAT
* *
37381 TATTAAAAATATAA-AAATTATTATATAATATATTATTTTAATAA
1 TATT-AAAATATAATAAATAATT-TAAAATATATTATTTTAA-AA
37425 T-TTAAAATATAATAAATAATTTAAAATATATTATTTTAAAA
1 TATTAAAATATAATAAATAATTTAAAATATATTATTTTAAAA
*
37466 TATTAATATAT
1 TATTAAAATAT
37477 TTGGGTTGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
41 3 0.06
42 34 0.72
43 9 0.19
44 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (42 bp):
TATTAAAATATAATAAATAATTTAAAATATATTATTTTAAAA
Found at i:37764 original size:25 final size:25
Alignment explanation
Indices: 37735--37782 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
37725 TCGTTACAGT
*
37735 GACTTAAAACTTGTCATGTCTAGGC
1 GACTTAAAACTCGTCATGTCTAGGC
* *
37760 GACTTGAAACTCGTTATGTCTAG
1 GACTTAAAACTCGTCATGTCTAG
37783 AATTTTGGGA
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:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (25 bp):
GACTTAAAACTCGTCATGTCTAGGC
Found at i:44219 original size:34 final size:36
Alignment explanation
Indices: 44176--44275 Score: 152
Period size: 34 Copynumber: 2.8 Consensus size: 36
44166 TCGTCCTACT
44176 AGGATTCAAACTCCTAAAAATAGGATAGAA-TT-TC
1 AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
*
44210 AGGATTCAAACTCCTAAAAATAGGAT-GAAATTTTGTT
1 AGGATTCAAACTCCTAAAAATAGGATAG-AA-TTTGTC
44247 AGGATTCAAACTCCTAAAAATAGGATAGA
1 AGGATTCAAACTCCTAAAAATAGGATAGA
44276 GTTCTACTAT
Statistics
Matches: 60, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
33 1 0.02
34 28 0.47
36 2 0.03
37 28 0.47
38 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (36 bp):
AGGATTCAAACTCCTAAAAATAGGATAGAATTTGTC
Found at i:44687 original size:14 final size:13
Alignment explanation
Indices: 44668--44706 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
44658 TATATGGATA
44668 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
44682 TTTTATTATTTAT
1 TTTTATTATTTAT
44695 GTTATTATTATT
1 -TT-TTATTATT
44707 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:44705 original size:18 final size:17
Alignment explanation
Indices: 44666--44708 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
44656 ATTATATGGA
44666 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
44682 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
44700 TATTATTAT
1 TATTATTAT
44709 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:44719 original size:2 final size:2
Alignment explanation
Indices: 44706--44748 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
44696 TTATTATTAT
*
44706 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44748 T
1 T
44749 TCTTTAATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45217 original size:9 final size:9
Alignment explanation
Indices: 45196--45229 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
45186 TATTTTTTCC
45196 TTTATCTTA-
1 TTTAT-TTAT
45205 TTTATTTAT
1 TTTATTTAT
45214 TTTATTTAT
1 TTTATTTAT
45223 TTTATTT
1 TTTATTT
45230 TTCCCTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:45218 original size:13 final size:14
Alignment explanation
Indices: 45196--45230 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
45186 TATTTTTTCC
*
45196 TTTATCTTATTTA-
1 TTTATTTTATTTAT
45209 TTTATTTTATTTAT
1 TTTATTTTATTTAT
45223 TTTATTTT
1 TTTATTTT
45231 TCCCTTGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:48288 original size:22 final size:22
Alignment explanation
Indices: 48265--48326 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
48255 CAAAAAGGGC
48265 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
48288 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
48309 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
48327 TAAAAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:48317 original size:20 final size:20
Alignment explanation
Indices: 48265--48334 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
48255 CAAAAAGGGC
*
48265 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
48288 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
48309 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
48329 AAAAAG
1 AAAAAG
48335 GGAATAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 18 0.43
21 7 0.17
22 6 0.14
23 10 0.24
24 1 0.02
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:49877 original size:36 final size:36
Alignment explanation
Indices: 49830--49934 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
49820 ATGCTCACCA
49830 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
49866 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
49903 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
49935 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:49924 original size:37 final size:37
Alignment explanation
Indices: 49830--49939 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
49820 ATGCTCACCA
49830 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
49866 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
49903 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
49940 ATTGAAAACA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 31 0.46
37 33 0.49
38 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:50024 original size:102 final size:102
Alignment explanation
Indices: 49848--50239 Score: 642
Period size: 102 Copynumber: 3.9 Consensus size: 102
49838 CTTGAGACAG
** * * *
49848 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
49913 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
49950 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
50015 TGAGACAGTTTCTCTTGAAATATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
50052 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
50117 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * * *
50154 TTTCCCTAGAAATGAATTTCGTATCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
50218 TGAGACAGCTTCTCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
50240 CAAAACCTTT
Statistics
Matches: 272, Mismatches: 18, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
101 35 0.13
102 237 0.87
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:50119 original size:37 final size:37
Alignment explanation
Indices: 50052--50138 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
50042 ATTGGAAACA
** * *
50052 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
50088 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
50125 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
50139 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:50208 original size:36 final size:36
Alignment explanation
Indices: 50153--50222 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
50143 CATTGAAAAC
** *
50153 ATTTCCCTAGAAATGAATTTCGTATCTCTTGAGATA
1 ATTTCCCTAGAAACAAATTTCGTATCCCTTGAGATA
* * *
50189 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGA
1 ATTTCCCTAGAAACAAATTTCGTATCCCTTGAGA
50223 CAGCTTCTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (36 bp):
ATTTCCCTAGAAACAAATTTCGTATCCCTTGAGATA
Found at i:50278 original size:21 final size:21
Alignment explanation
Indices: 50254--50304 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
50244 ACCTTTGAGA
*
50254 TTGTTTCCCTCGAAACAAATT
1 TTGTCTCCCTCGAAACAAATT
50275 TTGTCTCCCTCGAAACAAATT
1 TTGTCTCCCTCGAAACAAATT
50296 TTGTCTCCC
1 TTGTCTCCC
50305 ATGAGACAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.37
Consensus pattern (21 bp):
TTGTCTCCCTCGAAACAAATT
Found at i:50351 original size:88 final size:88
Alignment explanation
Indices: 50192--50360 Score: 252
Period size: 88 Copynumber: 1.9 Consensus size: 88
50182 TGAGATAATT
* *
50192 TCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGCTTCTCTTGAAACACAAAACCTTTGAGATTG
1 TCCCTCGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAACCTTTGAGATTG
*
50257 TTTCCCTCGAAACAAATTTTGTC
66 TTTCCCTCAAAACAAATTTTGTC
* *
50280 TCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAATCTTTGA-ATT-
1 TCCCTCGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAACCTTTGAGATTG
*
50343 TATCTCCCTTAAAACAAA
66 T-T-TCCCTCAAAACAAA
50361 ATTTCGTTTC
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
86 1 0.01
87 4 0.05
88 68 0.93
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (88 bp):
TCCCTCGAAACAAATTTTGTCTCCCATGAGACAGCTTCTCTTGAAACACAAAACCTTTGAGATTG
TTTCCCTCAAAACAAATTTTGTC
Found at i:51562 original size:105 final size:104
Alignment explanation
Indices: 51192--52264 Score: 1506
Period size: 105 Copynumber: 10.3 Consensus size: 104
51182 GCCATCCGCG
* * * * * *
51192 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
51257 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAAC-AACAACTTCCCAA-TTCAGAGCCA
51301 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
51366 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGCTTGTCAA-CAACAA-CTTCCCAA-TTCAGAGCCA
*
51408 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
51473 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
51513 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
51578 ACCACTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
51618 ATTTCAAATTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
51683 ACCGCTGCTTGCCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* * *
51718 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAAAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
51783 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGATCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
51823 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
51888 ACTGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* * *
51923 ATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
51988 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAAT-TCAGAGCCA
*
52028 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* ***
52093 ACCGCTGCTTGTCAACAA-AA-TT-TC-ATTCAGATTTA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
* * *
52128 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
52193 A-CGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
66 ACCG-CTGCTTGTCAAC-AACAACTTCCCAATT-CAGAGCCA
* *
52234 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
52265 TGGAATAATG
Statistics
Matches: 880, Mismatches: 64, Indels: 43
0.89 0.06 0.04
Matches are distributed among these distances:
99 2 0.00
100 251 0.29
101 12 0.01
102 9 0.01
103 10 0.01
104 12 0.01
105 371 0.42
106 92 0.10
107 99 0.11
109 22 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (104 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATTCAGAGCCA
Found at i:51783 original size:205 final size:205
Alignment explanation
Indices: 51192--52264 Score: 1576
Period size: 205 Copynumber: 5.2 Consensus size: 205
51182 GCCATCCGCG
* * * * * *
51192 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
51257 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACCGCTGCTTGTCAAC-AA-AA-TT-TC-A-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* * *
51322 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
122 ATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
* *
51387 ATTTTCCCAATTTCAGAGCCA
186 ACTTT-CCAATCTCAGAGCCA
*
51408 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
51473 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCAATTTCAACTTCACAACGAAGGATAT
*
51538 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAACAACTTT
126 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTT
51603 CCAATCTCAGAGCCA
191 CCAATCTCAGAGCCA
*
51618 ATTTCAAATTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
51683 ACCGCTGCTTGCCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
*
51748 TCCAGAAAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
*
51813 CTCAGATCCA
196 CTCAGAGCCA
51823 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
51888 ACTGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* *
51953 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTCCCAAT
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
*
52018 CCCAGAGCCA
196 CTCAGAGCCA
*
52028 ATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
***
52093 ACCGCTGCTTGTCAACAAAATTTCATTCAGATTTAATTTCAACTTCACAACGAAGGATATTGGAC
66 ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
* ** * *
52158 TCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAA-TTTCCC
131 TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCG-CTGCTTGTCAAC-AACAACTTT-CC
**
52221 GGT-TCCAGAGCCA
193 AATCT-CAGAGCCA
* *
52234 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
52265 TGGAATAATG
Statistics
Matches: 800, Mismatches: 52, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
204 2 0.00
205 474 0.59
206 46 0.06
207 1 0.00
208 2 0.00
209 2 0.00
210 93 0.12
211 9 0.01
212 98 0.12
213 49 0.06
214 3 0.00
216 21 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (205 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
TCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAAT
CTCAGAGCCA
Found at i:51806 original size:310 final size:311
Alignment explanation
Indices: 51192--52264 Score: 1542
Period size: 310 Copynumber: 3.4 Consensus size: 311
51182 GCCATCCGCG
* * * *
51192 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACACAAGTTCAACTTCACAACGAA
* * *
51257 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
63 GGGACGACTGCTTGTCAACAAACAATTTC-CAA-TTCAGAGCCAATTTCAACTTCACAACGAAGG
* *
51322 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
126 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAACA
*
51387 ATTTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
190 ACTTT--CAA-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAA
* *
51452 GTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
252 GTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-CCAATCTCAGATCCA
** *
51513 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
51578 ACCACTGCTTGTCAAC-AACAACTTTCCAATCTCAGAGCCAATTTCAAATTCACAACGAAGGATA
66 ACGACTGCTTGTCAACAAACAA-TTTCCAAT-TCAGAGCCAATTTCAACTTCACAACGAAGGATA
*
51642 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGCCAACAA-AA-TT
129 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT
* *
51705 TC-ATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGAAAATGCAAGTTCAAC
194 TCAATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAAC
51769 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGATCCA
259 TTCACGACGAAGGGACCGCTGCTTGTCAACAACAAC-TTCCAATCTCAGATCCA
* *
51823 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* *
51888 ACTG-CTGCTTGTCAAC-AA-AATTT-C-ATTCAGAGCCAATTTCAACTTCACAGCGAATGATAT
66 AC-GACTGCTTGTCAACAAACAATTTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
51948 TGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAACAACTTC
130 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTT-
* * * *
52013 CCAATCCCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAA
194 TCAAT-TCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAA
* **
52078 CTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTTC-AT-TCAGATTTA
258 CTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGATCCA
*
52128 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
* ** * *
52193 ACGACTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATA
66 ACGACTGCTTGTCAACAAACAATTT-CCAATT-CAGAGCCAATTTCAACTTCACAACGAAGGATA
52258 TTGGACT
129 TTGGACT
52265 TGGAATAATG
Statistics
Matches: 691, Mismatches: 45, Indels: 42
0.89 0.06 0.05
Matches are distributed among these distances:
304 1 0.00
305 168 0.24
306 8 0.01
307 11 0.02
308 4 0.01
309 7 0.01
310 277 0.40
311 38 0.05
312 1 0.00
314 3 0.00
315 2 0.00
316 3 0.00
317 94 0.14
318 49 0.07
319 3 0.00
321 22 0.03
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (311 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACAACGAAGGG
ACGACTGCTTGTCAACAAACAATTTCCAATTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTTC
AATTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCAATCTCAGATCCA
Found at i:53289 original size:14 final size:13
Alignment explanation
Indices: 53270--53308 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
53260 TATATGGATA
53270 TTTTATTCATTTAT
1 TTTTATT-ATTTAT
53284 TTTTATTATTTAT
1 TTTTATTATTTAT
53297 GTTATTATTATT
1 -TT-TTATTATT
53309 ATATGTATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTATTATTTAT
Found at i:53307 original size:18 final size:17
Alignment explanation
Indices: 53268--53310 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
53258 ATTATATGGA
53268 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
* *
53284 TTTTATTATTTATGTTAT
1 TATTATTATTCAT-TTAT
53302 TATTATTAT
1 TATTATTAT
53311 ATGTATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:53803 original size:9 final size:9
Alignment explanation
Indices: 53782--53815 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
53772 ATTTTTTTCC
53782 TTTATCTTA-
1 TTTAT-TTAT
53791 TTTATTTAT
1 TTTATTTAT
53800 TTTATTTAT
1 TTTATTTAT
53809 TTTATTT
1 TTTATTT
53816 TTCCCTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:53804 original size:13 final size:14
Alignment explanation
Indices: 53782--53816 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
53772 ATTTTTTTCC
*
53782 TTTATCTTATTTA-
1 TTTATTTTATTTAT
53795 TTTATTTTATTTAT
1 TTTATTTTATTTAT
53809 TTTATTTT
1 TTTATTTT
53817 TCCCTTGTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:56898 original size:39 final size:36
Alignment explanation
Indices: 56853--56938 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 36
56843 AACAAGTTGA
* *
56853 AAAATATTTATACATTTTATTTAAAAAATTTAAATTAAT
1 AAAATATTTATACA-TTT-TTTAAAAAATTAAAAAT-AT
* * *
56892 AAAATATATATATATTTTTTACAAAATTAAAAATAT
1 AAAATATTTATACATTTTTTAAAAAATTAAAAATAT
56928 AAAATGATTTA
1 AAAAT-ATTTA
56939 ATGAAATGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 7 0.17
37 18 0.45
38 3 0.08
39 12 0.30
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.43
Consensus pattern (36 bp):
AAAATATTTATACATTTTTTAAAAAATTAAAAATAT
Found at i:57457 original size:68 final size:65
Alignment explanation
Indices: 57354--57480 Score: 200
Period size: 68 Copynumber: 1.9 Consensus size: 65
57344 GGTTTAAAAT
* *
57354 AAAAACAAAAAAGATTCTCACAGAGATGACTTGATCACATCAAAATCCTGGATAACTTTTTATTT
1 AAAAACAAAAAAGATTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAA-TTTTTATTT
57419 A
65 A
*
57420 AAAAACAAAATAGATTTTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAATTTT
1 AAAAACAAAAAAGA--TTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAATTTT
57481 AAACTTAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
66 13 0.23
67 4 0.07
68 39 0.70
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.28
Consensus pattern (65 bp):
AAAAACAAAAAAGATTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAATTTTTATTTA
Found at i:57489 original size:68 final size:66
Alignment explanation
Indices: 57354--57495 Score: 196
Period size: 68 Copynumber: 2.1 Consensus size: 66
57344 GGTTTAAAAT
* * * *
57354 AAAAACAAAAAAGATTCTCACAGAGATGACTTGATCACATCAAAATCCTGGATAACTTTTTATTT
1 AAAAACAAAAAAGATTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAACTTTTAACTT
57419 A
66 A
*
57420 AAAAACAAAATAGATTTTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAA-TTTTAAA
1 AAAAACAAAAAAGA--TTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAACTTTT-AA
57484 CTTA
63 CTTA
*
57488 AAACACAA
1 AAAAACAA
57496 TTCATGATAT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
66 13 0.19
67 4 0.06
68 50 0.75
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (66 bp):
AAAAACAAAAAAGATTCGCACAGAGATGACTTGATCACATCAAAATCCAGGATAACTTTTAACTT
A
Found at i:58788 original size:26 final size:24
Alignment explanation
Indices: 58730--58788 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 24
58720 GTTTAATTGT
*
58730 TTTACTTTTTTATTTATTATTTAAA
1 TTTA-TTTTTTATTTATGATTTAAA
58755 TATATATTTTTTATTTATGATTATAAGA
1 T-T-TATTTTTTATTTATGATT-TAA-A
58783 TTTATT
1 TTTATT
58789 AAAGATTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 1 0.03
26 20 0.69
27 6 0.21
28 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (24 bp):
TTTATTTTTTATTTATGATTTAAA
Found at i:68042 original size:20 final size:19
Alignment explanation
Indices: 68014--68051 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
68004 TGCATGGATA
68014 TTTTTTTAAAATAATATTT
1 TTTTTTTAAAATAATATTT
*
68033 TTTTTATTAAAATATTATT
1 TTTTT-TTAAAATAATATT
68052 AAAAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTTTAAAATAATATTT
Found at i:69842 original size:21 final size:22
Alignment explanation
Indices: 69806--69846 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
69796 TTAAAATTTA
69806 TAAAGGAAGTACCGATACTCAT
1 TAAAGGAAGTACCGATACTCAT
*
69828 TAAAGG-AGTATCGATACTC
1 TAAAGGAAGTACCGATACTC
69847 CCTATCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (22 bp):
TAAAGGAAGTACCGATACTCAT
Found at i:71986 original size:26 final size:26
Alignment explanation
Indices: 71962--72046 Score: 134
Period size: 26 Copynumber: 3.3 Consensus size: 26
71952 CCTCGTTTGT
*
71962 CTCTGCGTATCTTCTTCTCCCTTTGC
1 CTCTGCGTATCTTCTTCTCCCCTTGC
* *
71988 CTTTGTGTATCTTCTTCTCCCCTTGC
1 CTCTGCGTATCTTCTTCTCCCCTTGC
*
72014 CTCTGTGTATCTTCTTCTCCCCTTGC
1 CTCTGCGTATCTTCTTCTCCCCTTGC
72040 CTCTGCG
1 CTCTGCG
72047 AAAAATTCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.04, C:0.38, G:0.13, T:0.46
Consensus pattern (26 bp):
CTCTGCGTATCTTCTTCTCCCCTTGC
Found at i:75727 original size:2 final size:2
Alignment explanation
Indices: 75720--75761 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
75710 TTAGGTCATT
75720 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
75762 AGAATGAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:78798 original size:15 final size:15
Alignment explanation
Indices: 78778--78811 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
78768 CAACAAATAA
78778 ATTTTTTATATAAAT
1 ATTTTTTATATAAAT
*
78793 ATTTTTTATTTAAAT
1 ATTTTTTATATAAAT
78808 ATTT
1 ATTT
78812 AGAATTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
ATTTTTTATATAAAT
Found at i:78990 original size:20 final size:20
Alignment explanation
Indices: 78957--79013 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
78947 CCAGTAACCC
78957 TATTCCC-C-GATAATCTTT
1 TATTCCCACTGATAATCTTT
78975 TATTCCCACTGATAATCTTT
1 TATTCCCACTGATAATCTTT
* *
78995 TATTCTCACTGGTAATCTT
1 TATTCCCACTGATAATCTT
79014 ACATCCCGTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.20
19 1 0.03
20 27 0.77
ACGTcount: A:0.23, C:0.25, G:0.07, T:0.46
Consensus pattern (20 bp):
TATTCCCACTGATAATCTTT
Done.