Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009630.1 Hibiscus syriacus cultivar Beakdansim tig00117026_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: 1249403
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:305814 original size:42 final size:41
Alignment explanation
Indices: 305750--305868 Score: 148
Period size: 42 Copynumber: 2.8 Consensus size: 41
305740 GAATCTGGCA
* *
305750 CTTGAACAGTGGGAGGGACCTCTTGAACGATGACACGGGCCT
1 CTTGAACGGT-GGAGGGGCCTCTTGAACGATGACACGGGCCT
* * *
305792 CTTGAACGGTGTGAGGGGCCTCTTGAATGATGAGAGGGGCCT
1 CTTGAACGGTG-GAGGGGCCTCTTGAACGATGACACGGGCCT
* *
305834 CTTGAACGATAGGAGGCGCCTCTTGAACGATGACA
1 CTTGAACGGT-GGAGGGGCCTCTTGAACGATGACA
305869 GGTGAATCAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.02
42 64 0.97
43 1 0.02
ACGTcount: A:0.24, C:0.21, G:0.34, T:0.21
Consensus pattern (41 bp):
CTTGAACGGTGGAGGGGCCTCTTGAACGATGACACGGGCCT
Found at i:308076 original size:20 final size:20
Alignment explanation
Indices: 308051--308105 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
308041 TCGCGTTGCG
308051 ATTTTGGTGTTGCGATTTTC
1 ATTTTGGTGTTGCGATTTTC
*
308071 ATTTTGGTGTTACGATTTTC
1 ATTTTGGTGTTGCGATTTTC
*
308091 ATTTTCGTGTTGCGA
1 ATTTTGGTGTTGCGA
308106 ATTTAAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.13, C:0.11, G:0.24, T:0.53
Consensus pattern (20 bp):
ATTTTGGTGTTGCGATTTTC
Found at i:308476 original size:22 final size:22
Alignment explanation
Indices: 308449--308495 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
308439 GATGGAGATA
308449 GACGGATTTCACCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
**
308471 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCACCGGAGATGGG
308493 GAC
1 GAC
308496 ATATGTCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.43, T:0.19
Consensus pattern (22 bp):
GACGGATTTCACCGGAGATGGG
Found at i:308682 original size:20 final size:20
Alignment explanation
Indices: 308657--308699 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
308647 ACGTGCTTTA
308657 CGAATTTGACTTATGTGTTG
1 CGAATTTGACTTATGTGTTG
*
308677 CGAATTTGACTTCTGTGTTG
1 CGAATTTGACTTATGTGTTG
308697 CGA
1 CGA
308700 TTTACATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.42
Consensus pattern (20 bp):
CGAATTTGACTTATGTGTTG
Found at i:309895 original size:3 final size:3
Alignment explanation
Indices: 309882--309925 Score: 52
Period size: 3 Copynumber: 13.3 Consensus size: 3
309872 TTTCTAGCCA
309882 AAG AGAG AAG AAG AAG AATG AAG AAG AAG AATG AAAG AAG AAG A
1 AAG A-AG AAG AAG AAG AA-G AAG AAG AAG AA-G -AAG AAG AAG A
309926 CAAGGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 27 0.73
4 8 0.22
5 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.05
Consensus pattern (3 bp):
AAG
Found at i:309904 original size:13 final size:13
Alignment explanation
Indices: 309888--309925 Score: 67
Period size: 13 Copynumber: 2.8 Consensus size: 13
309878 GCCAAAGAGA
309888 GAAGAAGAAGAAT
1 GAAGAAGAAGAAT
309901 GAAGAAGAAGAAT
1 GAAGAAGAAGAAT
309914 GAAAGAAGAAGA
1 G-AAGAAGAAGA
309926 CAAGGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.32, T:0.05
Consensus pattern (13 bp):
GAAGAAGAAGAAT
Found at i:313290 original size:21 final size:21
Alignment explanation
Indices: 313266--313338 Score: 128
Period size: 21 Copynumber: 3.5 Consensus size: 21
313256 TTCCTCTCAC
*
313266 TTCTTCTTCTCCGTCCATTAT
1 TTCTTCTTCTCCGTCCATCAT
*
313287 TTCTTCTTCTCCATCCATCAT
1 TTCTTCTTCTCCGTCCATCAT
313308 TTCTTCTTCTCCGTCCATCAT
1 TTCTTCTTCTCCGTCCATCAT
313329 TTCTTCTTCT
1 TTCTTCTTCT
313339 TCCTCCTCTG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.10, C:0.36, G:0.03, T:0.52
Consensus pattern (21 bp):
TTCTTCTTCTCCGTCCATCAT
Found at i:317532 original size:33 final size:34
Alignment explanation
Indices: 317480--317555 Score: 129
Period size: 33 Copynumber: 2.3 Consensus size: 34
317470 TAGTCAGTGT
317480 TGAACCTACTATACAAGGAATTACCAACA-CTGAC
1 TGAACCTACTATACAAGGAATTACCAACATC-GAC
317514 TGAACCTAC-ATACAAGGAATTACCAACATCGAC
1 TGAACCTACTATACAAGGAATTACCAACATCGAC
317547 TGAACCTAC
1 TGAACCTAC
317556 CATAGTCTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
33 31 0.76
34 10 0.24
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.20
Consensus pattern (34 bp):
TGAACCTACTATACAAGGAATTACCAACATCGAC
Found at i:320306 original size:17 final size:17
Alignment explanation
Indices: 320279--320317 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
320269 ATCAGAACCG
320279 AAATT-TTAAATTTAAA
1 AAATTATTAAATTTAAA
*
320295 AAATTATTAAATTTAAT
1 AAATTATTAAATTTAAA
320312 AAATTA
1 AAATTA
320318 ATATATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTATTAAATTTAAA
Found at i:332388 original size:22 final size:23
Alignment explanation
Indices: 332360--332411 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
332350 TCCCTAAGGA
*
332360 CCACATA-GTTTACACCGAAGTG
1 CCACATAGGGTTACACCGAAGTG
*
332382 CCACATAGGGTTGCACCGAAGTG
1 CCACATAGGGTTACACCGAAGTG
*
332405 CAACATA
1 CCACATA
332412 ATTGTCCCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.33, C:0.27, G:0.21, T:0.19
Consensus pattern (23 bp):
CCACATAGGGTTACACCGAAGTG
Found at i:332423 original size:21 final size:21
Alignment explanation
Indices: 332397--332454 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
332387 TAGGGTTGCA
332397 CCGAAGTG-CAACATAATTGTC
1 CCGAAG-GACAACATAATTGTC
*
332418 CCGAAGGACCACATAATTGTC
1 CCGAAGGACAACATAATTGTC
* *
332439 CCGAAGAACCACATAA
1 CCGAAGGACAACATAA
332455 AACCCTTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (21 bp):
CCGAAGGACAACATAATTGTC
Found at i:333026 original size:19 final size:20
Alignment explanation
Indices: 332979--333029 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
332969 ATCCCTCCAA
*
332979 TACCGATACTTCTCTTCAAGGG
1 TACCGATAC--CTCCTCAAGGG
*
333001 TATCGATACCTCCTCAA-GG
1 TACCGATACCTCCTCAAGGG
333020 TACCGATACC
1 TACCGATACC
333030 AATCTGGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 11 0.42
20 7 0.27
22 8 0.31
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.27
Consensus pattern (20 bp):
TACCGATACCTCCTCAAGGG
Found at i:336966 original size:15 final size:17
Alignment explanation
Indices: 336948--336985 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
336938 TTAAAAACCT
*
336948 AACAAAA-AAAACT-CG
1 AACAAAATAAAAATACG
336963 AACAAAATAAAAATACG
1 AACAAAATAAAAATACG
336980 AACAAA
1 AACAAA
336986 TCTTACTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 7 0.35
16 5 0.25
17 8 0.40
ACGTcount: A:0.71, C:0.16, G:0.05, T:0.08
Consensus pattern (17 bp):
AACAAAATAAAAATACG
Found at i:338681 original size:12 final size:12
Alignment explanation
Indices: 338664--338688 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
338654 GTGGCATTAG
338664 TCTAATAATAGC
1 TCTAATAATAGC
338676 TCTAATAATAGC
1 TCTAATAATAGC
338688 T
1 T
338689 TTGGTCCCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCTAATAATAGC
Found at i:345206 original size:24 final size:24
Alignment explanation
Indices: 345179--345289 Score: 118
Period size: 24 Copynumber: 4.6 Consensus size: 24
345169 GTAAACGGAG
*
345179 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
345203 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
345227 AGATCAGAAATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* * * *
345251 ATGTAATG-TATCATAACAGAATTC
1 ATATCA-GAAATCAGAACAGAATTC
345275 A-AGTCAGAAATCAGA
1 ATA-TCAGAAATCAGA
345290 TAAAATATTT
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
23 1 0.01
24 67 0.97
25 1 0.01
ACGTcount: A:0.49, C:0.16, G:0.14, T:0.22
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:345210 original size:12 final size:12
Alignment explanation
Indices: 345183--345251 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
345173 ACGGAGATAT
* *
345183 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
345195 CAGAATTCATAT
1 CAGAATTCAGAA
345207 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
345219 CAGAATCCAGAT
1 CAGAATTCAGAA
*
345231 CAGAAATCAGAA
1 CAGAATTCAGAA
345243 CAGAATTCA
1 CAGAATTCA
345252 TGTAATGTAT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
11 2 0.05
12 40 0.91
13 2 0.05
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:345252 original size:48 final size:47
Alignment explanation
Indices: 345181--345289 Score: 139
Period size: 48 Copynumber: 2.3 Consensus size: 47
345171 AAACGGAGAT
* *
345181 ATCAGAAATCAAAACAGAATTCATATCA-GATATCAGAACAGAATCCA
1 ATCAGAAATCAGAACAGAATTCATATAATG-TATCAGAACAGAATCCA
* * *
345228 GATCAGAAATCAGAACAGAATTCATGTAATGTATCATAACAGAATTCA
1 -ATCAGAAATCAGAACAGAATTCATATAATGTATCAGAACAGAATCCA
345276 AGTCAGAAATCAGA
1 A-TCAGAAATCAGA
345290 TAAAATATTT
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
47 1 0.02
48 52 0.96
49 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.14, T:0.21
Consensus pattern (47 bp):
ATCAGAAATCAGAACAGAATTCATATAATGTATCAGAACAGAATCCA
Found at i:350697 original size:19 final size:19
Alignment explanation
Indices: 350673--350709 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
350663 GAATAATATA
350673 TTAAAAT-TATTTTATATTG
1 TTAAAATATA-TTTATATTG
350692 TTAAAATATATTTATATT
1 TTAAAATATATTTATATT
350710 AACAATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTAAAATATATTTATATTG
Found at i:351294 original size:38 final size:37
Alignment explanation
Indices: 351220--351295 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 37
351210 GTTGGAAAAT
* *
351220 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
351257 ATTTATATAATTTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-A-TTTTCTTTAAAAAATTGAAAATCATAAA
351295 A
1 A
351296 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 8 0.24
38 7 0.21
39 18 0.55
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:352062 original size:37 final size:36
Alignment explanation
Indices: 351987--352062 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
351977 TTTTATATTT
*
351987 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
352023 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
352060 TTT
1 TTT
352063 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:352929 original size:21 final size:20
Alignment explanation
Indices: 352903--353001 Score: 74
Period size: 21 Copynumber: 4.8 Consensus size: 20
352893 ATCAGTTTCC
352903 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTG
* **
352924 AAAATCGCAATGCGATAGT-
1 AAAATCGCAACGCGATTTTG
** *
352943 ACAAATTCGCATTGCGATTTTCCA
1 A-AAA-TCGCAACGCGATTTT--G
* *
352967 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTG
352987 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
353002 ACACATAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.31
21 27 0.44
22 11 0.18
23 3 0.05
24 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTG
Found at i:353017 original size:40 final size:40
Alignment explanation
Indices: 352968--353122 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
352958 GATTTTCCAA
* ** *
352968 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
353008 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
353048 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
353088 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
353123 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:353030 original size:20 final size:20
Alignment explanation
Indices: 352968--353121 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
352958 GATTTTCCAA
* ** *
352968 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
352988 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
353008 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
353028 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
353048 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
353068 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
353088 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
353109 AAATCGCAACGCG
1 AAATCGCAACGCG
353122 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:353543 original size:33 final size:33
Alignment explanation
Indices: 353504--353574 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
353494 TTCACTTAGA
*
353504 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
353537 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
353570 TTTCA
1 TTTCA
353575 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:353711 original size:41 final size:41
Alignment explanation
Indices: 353653--353730 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
353643 TTGCAGAAGA
*
353653 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
353694 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
353731 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:353727 original size:21 final size:21
Alignment explanation
Indices: 353654--353729 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
353644 TGCAGAAGAG
*
353654 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
353675 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
353695 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
353716 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
353730 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:353733 original size:14 final size:14
Alignment explanation
Indices: 353714--353770 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
353704 GAGAAATGAA
353714 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
353728 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
353747 AATCGCAACTAGAG
1 AATCGCAACGAGAG
353761 AATCGCAACG
1 AATCGCAACG
353771 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:353746 original size:33 final size:33
Alignment explanation
Indices: 353706--353784 Score: 131
Period size: 33 Copynumber: 2.4 Consensus size: 33
353696 CGCAACGAGA
353706 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
353739 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
353772 GAAACCAAAATCG
1 GAAATGAAAATCG
353785 TATTGCGATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:353809 original size:19 final size:19
Alignment explanation
Indices: 353787--353879 Score: 89
Period size: 19 Copynumber: 5.4 Consensus size: 19
353777 CAAAATCGTA
353787 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
353806 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
353820 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
353839 TTGCGA--TTC---TCTAG
1 TTGCGATTTTCATTTCGCG
353853 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
353872 TTGCGATT
1 TTGCGATT
353880 CTCTAGTTGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 19 0.33
16 6 0.10
17 6 0.10
19 27 0.47
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:353823 original size:14 final size:14
Alignment explanation
Indices: 353804--353893 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
353794 TTTCATTTCG
353804 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
353818 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
353837 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
353851 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
353870 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
353884 AGTTGCGATT
1 CGTTGCGATT
353894 TCATTTCAAC
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 28 0.47
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:353829 original size:33 final size:33
Alignment explanation
Indices: 353787--353900 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
353777 CAAAATCGTA
*
353787 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
353820 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
353853 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
353886 TTGCGA-TTTCATTTC
1 TTGCGATTTTCATTTC
353901 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
32 9 0.11
33 71 0.89
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
Found at i:355755 original size:93 final size:93
Alignment explanation
Indices: 355596--355966 Score: 710
Period size: 93 Copynumber: 4.0 Consensus size: 93
355586 ATTGCTTAGT
* *
355596 AATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTTAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
355661 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
355689 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
355754 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
355782 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
355847 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
355875 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
1 AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
355940 TCTTTGTTTTGTC-TTTGGTTG-AAGTA
66 TCTTTGTTTTGTCTTTTGGTTGAAAGTA
355966 A
1 A
355967 TGCAATCCAT
Statistics
Matches: 276, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
91 6 0.02
92 8 0.03
93 262 0.95
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTATTTG
TCTTTGTTTTGTCTTTTGGTTGAAAGTA
Found at i:356054 original size:19 final size:19
Alignment explanation
Indices: 356014--356142 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
356004 TAGTTTACTT
* *
356014 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
356034 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
356053 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
356072 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
356086 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
356105 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
356119 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
356138 TCGCA
1 TCGCA
356143 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:356093 original size:33 final size:32
Alignment explanation
Indices: 356050--356142 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
356040 CGCGAAACCA
**
356050 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
356082 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
356115 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
356143 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:356140 original size:52 final size:52
Alignment explanation
Indices: 356014--356142 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
356004 TAGTTTACTT
**
356014 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
356066 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
356119 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
356143 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:356160 original size:19 final size:19
Alignment explanation
Indices: 356138--356258 Score: 135
Period size: 19 Copynumber: 6.6 Consensus size: 19
356128 GAAACCAAAA
*
356138 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
356157 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
356176 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
356192 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
356209 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
356228 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
356248 TCGTGTTGCGA
1 TCGCGTTGCGA
356259 AAGTAAACTA
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
14 7 0.08
16 5 0.06
17 5 0.06
19 57 0.66
20 12 0.14
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:358339 original size:19 final size:19
Alignment explanation
Indices: 358315--358431 Score: 181
Period size: 19 Copynumber: 6.4 Consensus size: 19
358305 AAAATTGACT
358315 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
358334 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
358353 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
358372 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
358386 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
358405 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
358425 ATCGCAA
1 ATCGCAA
358432 CGGGAGAATC
Statistics
Matches: 90, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 58 0.64
20 16 0.18
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:358394 original size:33 final size:36
Alignment explanation
Indices: 358315--358431 Score: 159
Period size: 33 Copynumber: 3.2 Consensus size: 36
358305 AAAATTGACT
358315 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GCG-AATGAAA
*
358353 ATCGCAATGCGAAATGAAAATCGCAA-CG-A-GAGA
1 ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
358386 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA-GC-G-AATGAAA
358425 ATCGCAA
1 ATCGCAA
358432 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
33 29 0.41
34 1 0.01
35 1 0.01
36 3 0.04
38 27 0.38
39 10 0.14
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (36 bp):
ATCGCAATGCGAAATGAAAATCGCAAGCGAATGAAA
Found at i:358463 original size:53 final size:53
Alignment explanation
Indices: 358333--358450 Score: 220
Period size: 53 Copynumber: 2.2 Consensus size: 53
358323 GCGAAATGAA
358333 AATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
*
358385 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
358438 AATCGCAATGCGA
1 AATCGCAATGCGA
358451 TTTTAATTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAG
Found at i:358468 original size:19 final size:19
Alignment explanation
Indices: 358440--358627 Score: 201
Period size: 19 Copynumber: 10.7 Consensus size: 19
358430 AACGGGAGAA
* *
358440 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
358459 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
358475 TCG--TTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
358491 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
358510 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
358526 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
358543 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
358562 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
358581 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
358599 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
358615 TCGCATTGTGATT
1 TCGCATTGCGATT
358628 CTCTCGTTGC
Statistics
Matches: 145, Mismatches: 8, Indels: 32
0.78 0.04 0.17
Matches are distributed among these distances:
14 23 0.16
15 3 0.02
16 17 0.12
17 10 0.07
18 7 0.05
19 69 0.48
20 16 0.11
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:358503 original size:51 final size:51
Alignment explanation
Indices: 358440--358641 Score: 257
Period size: 51 Copynumber: 3.9 Consensus size: 51
358430 AACGGGAGAA
* *
358440 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATT
358491 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGA-TTTCATT
* * *
358543 TCGCATTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCCGCATTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCG-ATTTC-ATT
* * *
358595 T-TCATGTTGGGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATT
1 TCGCA--TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
358642 GTAATTTCCG
Statistics
Matches: 133, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
50 2 0.02
51 52 0.39
52 44 0.33
53 28 0.21
54 5 0.04
55 2 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (51 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTCATT
Found at i:358649 original size:33 final size:33
Alignment explanation
Indices: 358496--358641 Score: 186
Period size: 33 Copynumber: 4.2 Consensus size: 33
358486 TCATTTCGCA
358496 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
358529 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
358565 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
* *
358601 TTGGGATTTTCATTTCGCATTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
358634 TTGCGATT
1 TTGCGATT
358642 GTAATTTCCG
Statistics
Matches: 98, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
32 1 0.01
33 46 0.47
34 14 0.14
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:361094 original size:24 final size:24
Alignment explanation
Indices: 361060--361106 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
361050 CTGAAACATC
361060 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
361084 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
361107 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:361817 original size:20 final size:20
Alignment explanation
Indices: 361789--362058 Score: 290
Period size: 20 Copynumber: 13.5 Consensus size: 20
361779 AAATTTCAGT
* * *
361789 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
361809 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
361829 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
361849 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
361869 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
361889 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
361909 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
361929 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
361949 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
361969 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
361989 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
362009 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
362029 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
362049 GTTGCGATTT
1 GTTGCGATTT
362059 TGGAAAATCG
Statistics
Matches: 220, Mismatches: 28, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 219 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:362075 original size:21 final size:21
Alignment explanation
Indices: 362045--362127 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
362035 ATTTTCATAT
*
362045 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
362066 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
362087 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
362108 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
362128 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:362118 original size:42 final size:43
Alignment explanation
Indices: 362025--362123 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
362015 ATTTATGTGT
* *
362025 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
362066 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
362108 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
362124 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:376462 original size:6 final size:6
Alignment explanation
Indices: 376451--376972 Score: 995
Period size: 6 Copynumber: 88.2 Consensus size: 6
376441 AGTCATTCTC
376451 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376499 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376547 TATATG TATATG --TATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376593 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376641 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376689 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376737 TATATG TATATG TATATG T-TATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376784 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376832 --TATG TATATG TATATG TATATG --TATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376876 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376924 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
376972 T
1 T
376973 TTTGAACTGG
Statistics
Matches: 509, Mismatches: 0, Indels: 14
0.97 0.00 0.03
Matches are distributed among these distances:
4 12 0.02
5 5 0.01
6 492 0.97
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:390229 original size:24 final size:25
Alignment explanation
Indices: 390197--390259 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 25
390187 TATTCACAAA
*
390197 CAATCTCATTTACT-AACTCGTTTAT
1 CAAT-TCATTTACTCAACTCATTTAT
*
390222 CAATTCATTTA-TCAATTCATTTAT
1 CAATTCATTTACTCAACTCATTTAT
390246 CAATTCATTTACTC
1 CAATTCATTTACTC
390260 GGTTCTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 1 0.03
24 27 0.79
25 6 0.18
ACGTcount: A:0.30, C:0.22, G:0.02, T:0.46
Consensus pattern (25 bp):
CAATTCATTTACTCAACTCATTTAT
Found at i:390232 original size:12 final size:12
Alignment explanation
Indices: 390217--390256 Score: 80
Period size: 12 Copynumber: 3.3 Consensus size: 12
390207 TACTAACTCG
390217 TTTATCAATTCA
1 TTTATCAATTCA
390229 TTTATCAATTCA
1 TTTATCAATTCA
390241 TTTATCAATTCA
1 TTTATCAATTCA
390253 TTTA
1 TTTA
390257 CTCGGTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.53
Consensus pattern (12 bp):
TTTATCAATTCA
Found at i:393483 original size:32 final size:33
Alignment explanation
Indices: 393420--393483 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
393410 GATCTAATTA
* *
393420 AAAAAATACAGAGAGATTATTATAATTATCTCT
1 AAAAAATACAGAGAAATTATTATAATCATCTCT
*
393453 AAAAAATA-AGAGATAATTATT-TTATCATCTC
1 AAAAAATACAGAGA-AATTATTATAATCATCTC
393484 GGATCGGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.34
Consensus pattern (33 bp):
AAAAAATACAGAGAAATTATTATAATCATCTCT
Found at i:395091 original size:52 final size:52
Alignment explanation
Indices: 395008--395110 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 52
394998 GGATTTTGAT
* * * *
395008 TTTTGTTAATTTTAGAACTCTTATGAAATTGAAATTTTACGT-TTTGGAGGA
1 TTTTGTTAATTTTAGAAATCTAATGAAATTGAAATTTCAAGTCTTTGGAGGA
395059 TTTTGTTAATTTTAGAAAT-TGGAATGAAATTGAAATTTCAAGTCTTTGGAGG
1 TTTTGTTAATTTTAGAAATCT--AATGAAATTGAAATTTCAAGTCTTTGGAGG
395111 CTGAAATGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
50 1 0.02
51 18 0.40
52 18 0.40
53 8 0.18
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (52 bp):
TTTTGTTAATTTTAGAAATCTAATGAAATTGAAATTTCAAGTCTTTGGAGGA
Found at i:395124 original size:34 final size:32
Alignment explanation
Indices: 395081--395144 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 32
395071 TAGAAATTGG
395081 AATGAAATTGAAATTTCAAGTCTTTGGAGGCTGA
1 AATGAAATTGAAATTTCAAGTC--TGGAGGCTGA
*
395115 AATGAAATTGAAATTTTAAGTCTGGAGGCT
1 AATGAAATTGAAATTTCAAGTCTGGAGGCT
395145 TCCAAAATGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 8 0.28
34 21 0.72
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (32 bp):
AATGAAATTGAAATTTCAAGTCTGGAGGCTGA
Found at i:399122 original size:26 final size:26
Alignment explanation
Indices: 399092--399160 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
399082 AGGCTATAAA
399092 ATTTGTCCCGAAGGACCTATGACTGT
1 ATTTGTCCCGAAGGACCTATGACTGT
399118 ATTTGTCCCGAAGGACCTATGACTGT
1 ATTTGTCCCGAAGGACCTATGACTGT
*
399144 ATTTGTCCCGAATGACC
1 ATTTGTCCCGAAGGACC
399161 ACTCCTTAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (26 bp):
ATTTGTCCCGAAGGACCTATGACTGT
Found at i:408698 original size:22 final size:21
Alignment explanation
Indices: 408659--408720 Score: 72
Period size: 23 Copynumber: 2.9 Consensus size: 21
408649 TTTTGGTACA
*
408659 GAGGGAATCGA-TCCCCCTCAT
1 GAGGGAACCGATTCCCCCT-AT
*
408680 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCTAT
408701 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
408721 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.33
22 8 0.22
23 16 0.44
ACGTcount: A:0.23, C:0.34, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCTAT
Found at i:408729 original size:21 final size:21
Alignment explanation
Indices: 408703--408742 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
408693 CCCCCTTTGA
*
408703 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
408724 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
408743 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:409192 original size:2 final size:2
Alignment explanation
Indices: 409185--409223 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
409175 TATGAATAAC
409185 TA TA TA TA TA 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 TA TA TA TA TA T
409224 TTTTCAAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:411796 original size:18 final size:18
Alignment explanation
Indices: 411773--411809 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
411763 TGACAAGTCA
411773 AATTTGTCTTCCAATATG
1 AATTTGTCTTCCAATATG
411791 AATTTGTCTTCCAATATG
1 AATTTGTCTTCCAATATG
411809 A
1 A
411810 GTAATGAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (18 bp):
AATTTGTCTTCCAATATG
Found at i:412784 original size:15 final size:15
Alignment explanation
Indices: 412723--412801 Score: 63
Period size: 15 Copynumber: 5.2 Consensus size: 15
412713 TAATTTAAAA
*
412723 AAATATTTAAAATTAT
1 AAATA-TTAAAATAAT
* *
412739 AAATA-TAAATTATTT
1 AAATATTAAAATA-AT
412754 AAATATTTAAAA-AAT
1 AAATA-TTAAAATAAT
*
412769 AAATATAAAAATAAT
1 AAATATTAAAATAAT
* *
412784 AAAAATTAAATTAAT
1 AAATATTAAAATAAT
412799 AAA
1 AAA
412802 ATTTGGAATA
Statistics
Matches: 50, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
14 10 0.20
15 30 0.60
16 6 0.12
17 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATATTAAAATAAT
Found at i:413215 original size:25 final size:25
Alignment explanation
Indices: 413159--413218 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
413149 TTATATTTAC
* *
413159 TAGATTAATCGATATTTACAAAATT
1 TAGATTAGTCGATACTTACAAAATT
* *
413184 TAAATTAGTCGATACTTACAAATTT
1 TAGATTAGTCGATACTTACAAAATT
*
413209 TGGATTAGTC
1 TAGATTAGTC
413219 AAAATTTACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (25 bp):
TAGATTAGTCGATACTTACAAAATT
Found at i:413227 original size:25 final size:25
Alignment explanation
Indices: 413172--413227 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
413162 ATTAATCGAT
* *
413172 ATTTACAAAATTTAAATTAGTCGAT
1 ATTTACAAAATTTAAATTAGTCAAA
* * **
413197 ACTTACAAATTTTGGATTAGTCAAA
1 ATTTACAAAATTTAAATTAGTCAAA
413222 ATTTAC
1 ATTTAC
413228 TATGTATTCT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (25 bp):
ATTTACAAAATTTAAATTAGTCAAA
Found at i:413347 original size:25 final size:25
Alignment explanation
Indices: 413311--413364 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
413301 AAATTATTAG
413311 TAAAAATAATAAGT-TTCGACTAATC
1 TAAAAATAATAAGTCTT-GACTAATC
* *
413336 TAAAAATTATAAGTCTTGACTAATT
1 TAAAAATAATAAGTCTTGACTAATC
413361 TAAA
1 TAAA
413365 TTTTGTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (25 bp):
TAAAAATAATAAGTCTTGACTAATC
Found at i:415500 original size:23 final size:23
Alignment explanation
Indices: 415474--415542 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
415464 CACCACAGCT
*
415474 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
415497 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
415520 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
415543 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:416969 original size:21 final size:21
Alignment explanation
Indices: 416945--416989 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
416935 TTTTGTTCGT
* *
416945 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
416966 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
416987 TTG
1 TTG
416990 CCTAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:419055 original size:2 final size:2
Alignment explanation
Indices: 419048--419100 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
419038 ATCCTCCACT
419048 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
419090 TA TA TA TA TA T
1 TA TA TA TA TA T
419101 GTTTAGAGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:428042 original size:229 final size:228
Alignment explanation
Indices: 427631--428080 Score: 785
Period size: 229 Copynumber: 2.0 Consensus size: 228
427621 GTAAATTATC
* * *
427631 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
427696 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
*
427761 TGTGTAAATAAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
131 TGTGTAAATAAAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
427826 GAAACATAAATTACATAACTTTCAAAAAAGTATA
196 GAAACATAAATTACATAACTTT-AAAAAAGTATA
*
427860 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
427925 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
427990 TTGTGTAAAT-TAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAAT
130 TTGTGTAAATAAAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAAT
428054 TGAAACATAAATTACATAACTTTAAAA
195 TGAAACATAAATTACATAACTTTAAAA
428081 GCAGTTTTAA
Statistics
Matches: 210, Mismatches: 10, Indels: 3
0.94 0.04 0.01
Matches are distributed among these distances:
228 4 0.02
229 110 0.52
230 96 0.46
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATAAAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATT
GAAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:428169 original size:20 final size:19
Alignment explanation
Indices: 428146--428191 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
428136 CGATATACCA
428146 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
428166 GGTAACAAATGATAAAACC
1 GGTAAAAAATGATAAAACC
428185 GGTAAAA
1 GGTAAAA
428192 TTAAAAGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:430699 original size:33 final size:33
Alignment explanation
Indices: 430657--430722 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
430647 AAATAGATGG
*
430657 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
430690 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
430723 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:432564 original size:18 final size:19
Alignment explanation
Indices: 432518--432579 Score: 101
Period size: 19 Copynumber: 3.4 Consensus size: 19
432508 AATGTCGAGT
*
432518 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
432537 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
432556 TAA-TTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
432574 T-ATTTT
1 TAATTTT
432580 TTTATGTGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
17 1 0.02
18 19 0.46
19 21 0.51
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:433642 original size:200 final size:198
Alignment explanation
Indices: 432662--434674 Score: 3640
Period size: 200 Copynumber: 10.1 Consensus size: 198
432652 TTAAGGGTCA
*
432662 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
432727 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
432792 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
432857 ATG
196 ATG
432860 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
432924 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
432989 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
433054 ATG
196 ATG
433057 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
433122 ATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 ATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
433187 TAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
433251 AATG
195 AATG
433255 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
433320 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
433385 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
433450 ATG
196 ATG
* *** *
433453 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
*
433518 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
433583 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
433648 TAATG
194 TAATG
433653 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
433718 ATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
433782 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
433847 ATG
196 ATG
* *** *
433850 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
*
433915 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
433980 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
434045 TAATG
194 TAATG
434050 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
434115 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
434180 AATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAAATA
131 AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
434244 ATG
196 ATG
* *** *
434247 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
*
434312 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
434377 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
434442 TAATG
194 TAATG
* *** *
434447 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
*
434512 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
65 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
*
434577 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAA
129 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
434642 TAATG
194 TAATG
434647 TGTCGACACTAATATA-TTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
434675 CTAATTTAAA
Statistics
Matches: 1764, Mismatches: 40, Indels: 21
0.97 0.02 0.01
Matches are distributed among these distances:
197 486 0.28
198 475 0.27
199 240 0.14
200 563 0.32
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (198 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTGCATCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
ATG
Found at i:433842 original size:397 final size:398
Alignment explanation
Indices: 432662--434674 Score: 3763
Period size: 397 Copynumber: 5.1 Consensus size: 398
432652 TTAAGGGTCA
* * *** *
432662 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
432726 AATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
432790 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
432855 TAATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
432919 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
432984 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
433049 AAATAATG
391 AAATAATG
* *** *
433057 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
*
433121 AATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
433186 GTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
433250 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
433315 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
433380 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
433445 AAATAATG
391 AAATAATG
433453 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
433518 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
433583 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
433648 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
433713 CATCAATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
433777 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
433842 AAATAATG
391 AAATAATG
433850 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
433915 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
433980 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
434045 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
434110 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
261 CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
434175 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCT
326 AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
434239 AAATAATG
391 AAATAATG
434247 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
434312 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
66 CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
434377 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
131 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
* ***
434442 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGT
196 TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT-TTTACAAGGT
* *
434507 GCACCCATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
260 GCATCAATAAAGTGTCGATCCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGT
* *
434572 ATAATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGT
324 ATAATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGT
434637 CTAAATAATG
389 CTAAATAATG
434647 TGTCGACACTAATATA-TTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
434675 CTAATTTAAA
Statistics
Matches: 1595, Mismatches: 15, Indels: 12
0.98 0.01 0.01
Matches are distributed among these distances:
395 172 0.11
396 269 0.17
397 762 0.48
398 255 0.16
399 91 0.06
400 46 0.03
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (398 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACC
CATAAAGTGTCGATCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
TAATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATTTTTACAAGGTG
CATCAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTAT
AATGTAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCT
AAATAATG
Found at i:436162 original size:18 final size:18
Alignment explanation
Indices: 436139--436200 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
436129 ATCGGTCGCA
* * *
436139 GAAGATGAAGCTGACGAT
1 GAAGATGACGATGATGAT
436157 GAAGATGACGATGATGAT
1 GAAGATGACGATGATGAT
*
436175 GATGATGACGATGATGAT
1 GAAGATGACGATGATGAT
436193 GAAGATGA
1 GAAGATGA
436201 TGATCCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (18 bp):
GAAGATGACGATGATGAT
Found at i:436163 original size:6 final size:6
Alignment explanation
Indices: 436139--436200 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
436129 ATCGGTCGCA
* * * * * *
436139 GAAGAT GAAGCT GACGAT GAAGAT GACGAT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
*
436187 GATGAT GAAGAT GA
1 GAAGAT GAAGAT GA
436201 TGATCCAAAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.39, C:0.06, G:0.34, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:436174 original size:3 final size:3
Alignment explanation
Indices: 436154--436204 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
436144 TGAAGCTGAC
* * * *
436154 GAT GAA GAT GAC GAT GAT GAT GAT GAT GAC GAT GAT GAT GAA GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
436202 GAT
1 GAT
436205 CCAAACAAGT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.37, C:0.04, G:0.33, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:436201 original size:12 final size:12
Alignment explanation
Indices: 436142--436204 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
436132 GGTCGCAGAA
* *
436142 GATGAAGCTGAC
1 GATGAAGATGAT
*
436154 GATGAAGATGAC
1 GATGAAGATGAT
*
436166 GATGATGATGAT
1 GATGAAGATGAT
*
436178 GATGACGATGAT
1 GATGAAGATGAT
436190 GATGAAGATGAT
1 GATGAAGATGAT
436202 GAT
1 GAT
436205 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.37, C:0.06, G:0.33, T:0.24
Consensus pattern (12 bp):
GATGAAGATGAT
Found at i:439436 original size:23 final size:23
Alignment explanation
Indices: 439405--439467 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
439395 ATAGGTAAAC
*
439405 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* **
439428 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
439451 ATATAATGTAATAGGTA
1 ATATAATGTAATAGGTA
439468 ATGGTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:439475 original size:23 final size:23
Alignment explanation
Indices: 439405--439477 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
439395 ATAGGTAAAC
* * **
439405 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTATCGGTT
*
439428 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTATCGGTT
439451 ATATAATGTAATAGGTAAT-GGTT
1 ATATAATGTAATAGGT-ATCGGTT
439474 ATAT
1 ATAT
439478 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 42 0.95
24 2 0.05
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTATCGGTT
Found at i:451524 original size:12 final size:11
Alignment explanation
Indices: 451493--451526 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 11
451483 AGCAATATTA
451493 AAGCTAAGGAG
1 AAGCTAAGGAG
451504 AAGGCTAAGGAG
1 AA-GCTAAGGAG
451516 AAGCTTAAGGA
1 AAGC-TAAGGA
451527 TGAATTTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.44, C:0.09, G:0.35, T:0.12
Consensus pattern (11 bp):
AAGCTAAGGAG
Found at i:454651 original size:184 final size:183
Alignment explanation
Indices: 454343--454711 Score: 702
Period size: 184 Copynumber: 2.0 Consensus size: 183
454333 CGCTTAGTGA
454343 TAGTCTGATAAACAAAACAATTAATAAGTGGAGCAACGAAACCGAACACACCAACGACTTTGATG
1 TAGTCTGATAAACAAAACAATTAATAAGTGGAGCAACGAAACCGAACACACCAACGACTTTGATG
454408 CTCAAAACATGGAGGAGAGAAACTTGAAGAAGAACCAAAATTGCCAACGGAAAAAGTGATCTCCC
66 CTCAAAACATGGAGGAGAGAAACTTGAAGAAGAACCAAAATTGCCAACGGAAAAAGTGATCTCCC
* *
454473 CTTAACAGTAATCACATTCGACACATATATACGTTAGCCAACGAACCGTCTTG
131 CTTAACAGTAATCACATCCGACACATATATACGTTAGCAAACGAACCGTCTTG
*
454526 TAGTCTGATAAACAAAACAATTAATAAGTGGAGCAACGAAACTGACACACACCAACGACTTTGAT
1 TAGTCTGATAAACAAAACAATTAATAAGTGGAGCAACGAAACCGA-ACACACCAACGACTTTGAT
454591 GCTCAAAACATGGAGGAGAGAAACTTGAAGAAGAACCAAAATTGCCAACGGAAAAAGTGATCTCC
65 GCTCAAAACATGGAGGAGAGAAACTTGAAGAAGAACCAAAATTGCCAACGGAAAAAGTGATCTCC
454656 CCTTAACAGTAATCACATCCGACACATATATACGTTAGCAAACGAACCGTCTTG
130 CCTTAACAGTAATCACATCCGACACATATATACGTTAGCAAACGAACCGTCTTG
454710 TA
1 TA
454712 CAAACGAACA
Statistics
Matches: 182, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
183 44 0.24
184 138 0.76
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.19
Consensus pattern (183 bp):
TAGTCTGATAAACAAAACAATTAATAAGTGGAGCAACGAAACCGAACACACCAACGACTTTGATG
CTCAAAACATGGAGGAGAGAAACTTGAAGAAGAACCAAAATTGCCAACGGAAAAAGTGATCTCCC
CTTAACAGTAATCACATCCGACACATATATACGTTAGCAAACGAACCGTCTTG
Found at i:462058 original size:6 final size:6
Alignment explanation
Indices: 462047--462077 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
462037 GAGTCCTAAC
*
462047 AAAAAG AAAAAG AAAAAG AACAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG A
462078 CGCGAACCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:466550 original size:25 final size:25
Alignment explanation
Indices: 466522--466579 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
466512 TGAGCATGGT
466522 TTGATATGATTATATGCACTATATG
1 TTGATATGATTATATGCACTATATG
* *
466547 TTGATATGATTATATGCGCTGTATG
1 TTGATATGATTATATGCACTATATG
466572 TTGATATG
1 TTGATATG
466580 TTTTGTGTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (25 bp):
TTGATATGATTATATGCACTATATG
Found at i:466852 original size:3 final size:3
Alignment explanation
Indices: 466844--466876 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
466834 ACTCTAGGAA
466844 AAT AAT AAT AAT AAT AAT AAT AAT AAT ATAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA
466877 ATTAGGGGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:468082 original size:23 final size:23
Alignment explanation
Indices: 468049--468110 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
468039 AATCTTATAT
*
468049 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACAC
* * *
468072 GGCACTACGGTGCAATTCTACAT
1 GGCACTTCGGTGCATTTCTACAC
468095 GGCACTTCGGTGCATT
1 GGCACTTCGGTGCATT
468111 AATACGAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACAC
Found at i:468378 original size:18 final size:19
Alignment explanation
Indices: 468355--468391 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
468345 AAAGAAATCA
*
468355 ATAATAATGAT-AAGAATT
1 ATAATAAAGATAAAGAATT
468373 ATAATAAAGATAAAGAATT
1 ATAATAAAGATAAAGAATT
468392 GATATGCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.11, T:0.30
Consensus pattern (19 bp):
ATAATAAAGATAAAGAATT
Found at i:479416 original size:2 final size:2
Alignment explanation
Indices: 479411--479445 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
479401 ACACACACAC
479411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
479446 AACGAATTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:484789 original size:19 final size:20
Alignment explanation
Indices: 484765--484812 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
484755 TCTATATATT
* *
484765 ATTTTTTTTCAAT-TAAATC
1 ATTTTTATTCAATAAAAATC
*
484784 ATTTTTATTGAATAAAAATC
1 ATTTTTATTCAATAAAAATC
484804 ATTTTTATT
1 ATTTTTATT
484813 ATTTCGGGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTTTATTCAATAAAAATC
Found at i:486955 original size:30 final size:31
Alignment explanation
Indices: 486913--486970 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
486903 TTTACAATTT
*
486913 ATTTTATGTTATAT-TGCTATGTTTTATTCA
1 ATTTTATGTTATATAAGCTATGTTTTATTCA
486943 ATTTATAT-TTATATAAGCTATGTTTTAT
1 ATTT-TATGTTATATAAGCTATGTTTTAT
486971 GATCATATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.59
Consensus pattern (31 bp):
ATTTTATGTTATATAAGCTATGTTTTATTCA
Found at i:487788 original size:23 final size:23
Alignment explanation
Indices: 487751--487841 Score: 119
Period size: 23 Copynumber: 4.0 Consensus size: 23
487741 CACCACAGCT
* *
487751 CGTATAAATGTACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* * *
487774 CATAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCG
*
487797 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
*
487820 CGTAGAAATGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
487842 ATATAATGTC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:489314 original size:2 final size:2
Alignment explanation
Indices: 489309--489353 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
489299 CATCCTTATC
489309 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
489351 TA T
1 TA T
489354 CATTATTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:489707 original size:21 final size:21
Alignment explanation
Indices: 489681--489752 Score: 58
Period size: 21 Copynumber: 3.3 Consensus size: 21
489671 TCGAGGGTTT
489681 TATGTGGTCCTTCGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
489702 TATGTGG-CACTTCGGTG-CAAA
1 TATGTGGTC-CTTCGG-GACAAA
** * *
489723 CCTATGTGGTTTTTTGGGACAAT
1 --TATGTGGTCCTTCGGGACAAA
489746 TATGTGG
1 TATGTGG
489753 CACTTTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
20 1 0.02
21 24 0.59
22 2 0.05
23 14 0.34
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAA
Found at i:492062 original size:23 final size:23
Alignment explanation
Indices: 492032--492080 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
492022 TAATTTTATA
* *
492032 TTTGTGGCACATTTATCTCTGTC
1 TTTGTGGCACATTCATCTATGTC
*
492055 TTTGTGGCACGTTCATCTATGTC
1 TTTGTGGCACATTCATCTATGTC
492078 TTT
1 TTT
492081 TGGTAGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.12, C:0.20, G:0.18, T:0.49
Consensus pattern (23 bp):
TTTGTGGCACATTCATCTATGTC
Found at i:494487 original size:40 final size:40
Alignment explanation
Indices: 494432--494510 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
494422 CCATTAACTC
494432 TTCTTCTTCTTCTTCATACGACAAACCTGGAACAAGCTGG
1 TTCTTCTTCTTCTTCATACGACAAACCTGGAACAAGCTGG
494472 TTCTTCTTCTTCTTCATACGACAAACCTGGAACAAGCTG
1 TTCTTCTTCTTCTTCATACGACAAACCTGGAACAAGCTG
494511 ATATGGCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (40 bp):
TTCTTCTTCTTCTTCATACGACAAACCTGGAACAAGCTGG
Found at i:494796 original size:41 final size:40
Alignment explanation
Indices: 494746--494825 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
494736 AAATTATGAT
* * * * *
494746 TTTAGTGTAGGTTTTTTTTATGAAGAAATTATTATAATTCA
1 TTTAGTGTAGG-GTATTTTAGGAAGAAATGATTACAATTCA
*
494787 TTTATTGTAGGGTATTTTAGGAAGAAATGATTACAATTC
1 TTTAGTGTAGGGTATTTTAGGAAGAAATGATTACAATTC
494826 TTATTGAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
40 23 0.70
41 10 0.30
ACGTcount: A:0.33, C:0.04, G:0.17, T:0.46
Consensus pattern (40 bp):
TTTAGTGTAGGGTATTTTAGGAAGAAATGATTACAATTCA
Found at i:499237 original size:2 final size:2
Alignment explanation
Indices: 499230--499255 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
499220 AAATCTTCTT
499230 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
499256 ATTTTTTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:500007 original size:13 final size:12
Alignment explanation
Indices: 499988--500017 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
499978 TTTTAAAATA
499988 TAAAATATTATT
1 TAAAATATTATT
500000 TCAAAATATTATT
1 T-AAAATATTATT
500013 TAAAA
1 TAAAA
500018 GAATCTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (12 bp):
TAAAATATTATT
Found at i:510883 original size:25 final size:24
Alignment explanation
Indices: 510833--510884 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
510823 TTTATGTTTC
* *
510833 GAGAAAAAATCACAGACGAAAGAA
1 GAGAAAAAATCACACACCAAAGAA
510857 GAGAAAAAATCACTACACCCAAA-AA
1 GAGAAAAAATCAC-ACA-CCAAAGAA
510882 GAG
1 GAG
510885 TACATAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 13 0.54
25 7 0.29
26 4 0.17
ACGTcount: A:0.60, C:0.17, G:0.17, T:0.06
Consensus pattern (24 bp):
GAGAAAAAATCACACACCAAAGAA
Found at i:512714 original size:10 final size:10
Alignment explanation
Indices: 512696--512731 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
512686 ACGGGTATTC
512696 ATATATCTAT
1 ATATATCTAT
*
512706 ATATGTCTAT
1 ATATATCTAT
*
512716 ATATATATAT
1 ATATATCTAT
512726 ATATAT
1 ATATAT
512732 AACGTTATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.50
Consensus pattern (10 bp):
ATATATCTAT
Found at i:514510 original size:22 final size:22
Alignment explanation
Indices: 514485--514563 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
514475 AGAGGTACCG
514485 ATACCCCTATGAATGGGTATCA
1 ATACCCCTATGAATGGGTATCA
* *
514507 ATACCCCTATGAATGGGTACCG
1 ATACCCCTATGAATGGGTATCA
*
514529 ATACCCCTATGAATGGGTATTA
1 ATACCCCTATGAATGGGTATCA
514551 ATACCCCTATGAA
1 ATACCCCTATGAA
514564 GACTCAAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (22 bp):
ATACCCCTATGAATGGGTATCA
Found at i:514541 original size:44 final size:44
Alignment explanation
Indices: 514478--514563 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
514468 AATATTAAGA
514478 GGTACCGATACCCCTATGAATGGGTATCAATACCCCTATGAATG
1 GGTACCGATACCCCTATGAATGGGTATCAATACCCCTATGAATG
*
514522 GGTACCGATACCCCTATGAATGGGTATTAATACCCCTATGAA
1 GGTACCGATACCCCTATGAATGGGTATCAATACCCCTATGAA
514564 GACTCAAACA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (44 bp):
GGTACCGATACCCCTATGAATGGGTATCAATACCCCTATGAATG
Found at i:514631 original size:19 final size:19
Alignment explanation
Indices: 514585--514639 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
514575 CGAATGCAAA
*
514585 AAGGGTATATATACCATGC
1 AAGGGTATCTATACCATGC
514604 AAGGGTATCTATACCATGC
1 AAGGGTATCTATACCATGC
* *
514623 AATGGTATCGATACCAT
1 AAGGGTATCTATACCAT
514640 AGTGCAAAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (19 bp):
AAGGGTATCTATACCATGC
Found at i:516443 original size:24 final size:24
Alignment explanation
Indices: 516416--516473 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
516406 TTGGTACAAG
516416 TGATATGATTGCACTTGGAGTGCA
1 TGATATGATTGCACTTGGAGTGCA
516440 TGATATGATTGCACTTGGAGTGCA
1 TGATATGATTGCACTTGGAGTGCA
*
516464 TGATCTGATT
1 TGATATGATT
516474 TTGATGATAG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.24, C:0.12, G:0.28, T:0.36
Consensus pattern (24 bp):
TGATATGATTGCACTTGGAGTGCA
Found at i:516575 original size:19 final size:18
Alignment explanation
Indices: 516551--516612 Score: 72
Period size: 19 Copynumber: 3.4 Consensus size: 18
516541 TATGCATTGG
516551 GCTATGAACTTGAAAATAA
1 GCTATGAA-TTGAAAATAA
*
516570 GCTATGAATCTGAAATTAA
1 GCTATGAAT-TGAAAATAA
*
516589 GTTATGAATTG-AAATAA
1 GCTATGAATTGAAAATAA
*
516606 GTTATGA
1 GCTATGA
516613 GTCCGGAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
17 12 0.31
18 3 0.08
19 24 0.62
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (18 bp):
GCTATGAATTGAAAATAA
Found at i:516605 original size:36 final size:36
Alignment explanation
Indices: 516553--516644 Score: 96
Period size: 36 Copynumber: 2.4 Consensus size: 36
516543 TGCATTGGGC
* *
516553 TATGAACTTGAAAATAAGCTATGAAT-CTGAAATTAAGT
1 TATGAA-TTG-AAATAAGCTATGAATCCGGAAA-CAAGT
* *
516591 TATGAATTGAAATAAGTTATGAGTCCGGAAACAAGT
1 TATGAATTGAAATAAGCTATGAATCCGGAAACAAGT
516627 TATGAATATGAGAATAAG
1 TATGAAT-TGA-AATAAG
516645 TTGTGAAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
36 24 0.51
37 11 0.23
38 12 0.26
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.29
Consensus pattern (36 bp):
TATGAATTGAAATAAGCTATGAATCCGGAAACAAGT
Found at i:516645 original size:19 final size:18
Alignment explanation
Indices: 516564--516651 Score: 88
Period size: 19 Copynumber: 4.8 Consensus size: 18
516554 ATGAACTTGA
*
516564 AAATAAGCTATGAATCTG
1 AAATAAGTTATGAATCTG
516582 AAATTAAGTTATGAAT-TG
1 AAA-TAAGTTATGAATCTG
* *
516600 AAATAAGTTATGAGTCCGG
1 AAATAAGTTATGAAT-CTG
* *
516619 AAACAAGTTATGAATATG
1 AAATAAGTTATGAATCTG
*
516637 AGAATAAGTTGTGAA
1 A-AATAAGTTATGAA
516652 ATGTGAAAGT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
17 11 0.19
18 10 0.18
19 36 0.63
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.30
Consensus pattern (18 bp):
AAATAAGTTATGAATCTG
Found at i:516680 original size:6 final size:6
Alignment explanation
Indices: 516669--516786 Score: 76
Period size: 6 Copynumber: 18.7 Consensus size: 6
516659 AGTACATATC
* * * * * *
516669 ATGAAA ATGAAA TGTGAAA GTGAAT ATGAAA ATGAAA TGTGAAA GTGAAT
1 ATGAAA ATGAAA -ATGAAA ATGAAA ATGAAA ATGAAA -ATGAAA ATGAAA
* * * *
516719 ATGAAA ATGAAA TGTGAAA GTGAAT ATGAAA AT-AAA ATGTGAAA GTGAAA
1 ATGAAA ATGAAA -ATGAAA ATGAAA ATGAAA ATGAAA A--TGAAA ATGAAA
516769 GATGAAA GATGAAA ATGA
1 -ATGAAA -ATGAAA ATGA
516787 GATATGAAAG
Statistics
Matches: 91, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
5 4 0.04
6 56 0.62
7 28 0.31
8 3 0.03
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (6 bp):
ATGAAA
Found at i:516703 original size:25 final size:25
Alignment explanation
Indices: 516648--516782 Score: 198
Period size: 25 Copynumber: 5.2 Consensus size: 25
516638 GAATAAGTTG
*
516648 TGAAATGTGAAAGTACATATCATGAAAA
1 TGAAATGTGAAAGT-GA-AT-ATGAAAA
516676 TGAAATGTGAAAGTGAATATGAAAA
1 TGAAATGTGAAAGTGAATATGAAAA
516701 TGAAATGTGAAAGTGAATATGAAAA
1 TGAAATGTGAAAGTGAATATGAAAA
516726 TGAAATGTGAAAGTGAATATGAAAA
1 TGAAATGTGAAAGTGAATATGAAAA
* *
516751 TAAAATGTGAAAGTGAAAGATGAAAGA
1 TGAAATGTGAAAGTG-AATATGAAA-A
516778 TGAAA
1 TGAAA
516783 ATGAGATATG
Statistics
Matches: 101, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
25 71 0.70
26 10 0.10
27 6 0.06
28 14 0.14
ACGTcount: A:0.53, C:0.01, G:0.23, T:0.23
Consensus pattern (25 bp):
TGAAATGTGAAAGTGAATATGAAAA
Found at i:517312 original size:25 final size:25
Alignment explanation
Indices: 517275--517332 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
517265 TTGATGATCG
*
517275 TAGAACACGGCATGCAAAGAAATAA
1 TAGAACACAGCATGCAAAGAAATAA
517300 TAGAACACAGCATGCAAAGAAATAA
1 TAGAACACAGCATGCAAAGAAATAA
*
517325 TAAAACAC
1 TAGAACAC
517333 GGCACATTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.55, C:0.17, G:0.16, T:0.12
Consensus pattern (25 bp):
TAGAACACAGCATGCAAAGAAATAA
Found at i:522128 original size:24 final size:24
Alignment explanation
Indices: 522096--522141 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
522086 AACAAAACAG
522096 AAATATGCTCAATTTTTCCTAAGC
1 AAATATGCTCAATTTTTCCTAAGC
522120 AAATATGCTCAATTTTTCCTAA
1 AAATATGCTCAATTTTTCCTAA
522142 TCATTTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.39
Consensus pattern (24 bp):
AAATATGCTCAATTTTTCCTAAGC
Found at i:522226 original size:165 final size:165
Alignment explanation
Indices: 521951--522261 Score: 545
Period size: 165 Copynumber: 1.9 Consensus size: 165
521941 CTGTTAGACA
521951 CAAATATGCTCAATTTTTCCAAAGCATTTCTATACATTTAAAGGAGTATACCCCCATAACCATGT
1 CAAATATGCTCAATTTTTCCAAAGCATTTCTATACATTT-AAGGAGTATACCCCCATAACCATGT
*
522016 CCCAAATATGTGTTGAACACGTTACCTTAGGCAAAACCAAAGCTCGACATCTCAAAAAAAAATTA
65 CCCAAATATGTGTTGAACAAGTTACCTTAGGCAAAACCAAAGCTCGACATCTC-AAAAAAAATTA
522081 ATGAAAACAAAACAGAAATATGCTCAATTTTTCCTAAG
129 ATGAAAAC-AAACAGAAATATGCTCAATTTTTCCTAAG
* *
522119 CAAATATGCTCAATTTTTCCTAATCATTTCTATACATTT-A-GAGTATACCCCCATAACCATGTC
1 CAAATATGCTCAATTTTTCCAAAGCATTTCTATACATTTAAGGAGTATACCCCCATAACCATGTC
*
522182 CCAAATATGTGTTGAACAAGTTACCTTAGGGAAAACCAAAGCTCGACATCTCAAAAAAAATTAAT
66 CCAAATATGTGTTGAACAAGTTACCTTAGGCAAAACCAAAGCTCGACATCTCAAAAAAAATTAAT
522247 GAAAACAAACAGAAA
131 GAAAACAAACAGAAA
522262 AGGCAACAAG
Statistics
Matches: 139, Mismatches: 4, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
163 9 0.06
164 19 0.14
165 73 0.53
166 1 0.01
168 37 0.27
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (165 bp):
CAAATATGCTCAATTTTTCCAAAGCATTTCTATACATTTAAGGAGTATACCCCCATAACCATGTC
CCAAATATGTGTTGAACAAGTTACCTTAGGCAAAACCAAAGCTCGACATCTCAAAAAAAATTAAT
GAAAACAAACAGAAATATGCTCAATTTTTCCTAAG
Found at i:524224 original size:12 final size:12
Alignment explanation
Indices: 524207--524231 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
524197 CATAAATTTT
524207 AATAGTTAGAGG
1 AATAGTTAGAGG
524219 AATAGTTAGAGG
1 AATAGTTAGAGG
524231 A
1 A
524232 TTTAAAAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (12 bp):
AATAGTTAGAGG
Found at i:524295 original size:21 final size:22
Alignment explanation
Indices: 524271--524313 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
524261 AACATTTATG
*
524271 TACTCTACCC-AATTTTAATAA
1 TACTCTACCCTAATTTGAATAA
* *
524292 TACTTTTCCCTAATTTGAATAA
1 TACTCTACCCTAATTTGAATAA
524314 GTTTTTAAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (22 bp):
TACTCTACCCTAATTTGAATAA
Found at i:526411 original size:2 final size:2
Alignment explanation
Indices: 526404--526455 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
526394 CACGATTGCA
526404 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
526446 AT AT AT AT AT
1 AT AT AT AT AT
526456 GATTTAAAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526883 original size:2 final size:2
Alignment explanation
Indices: 526876--526925 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
526866 ACTTGTACTT
* * *
526876 TA TA TA TA TT TA TA -A AA AA 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
526917 TA TA TA TA T
1 TA TA TA TA T
526926 TAAAATATTT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:527022 original size:19 final size:20
Alignment explanation
Indices: 526974--527023 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 20
526964 GATTATATAG
526974 ATTTTAATTTATATAAATATGT
1 ATTTT-ATTTA-ATAAATATGT
*
526996 -TTAT-TTTAA-AAATATGT
1 ATTTTATTTAATAAATATGT
527013 ATTTTATTTAA
1 ATTTTATTTAA
527024 GATTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
17 8 0.33
18 4 0.17
19 9 0.38
21 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTTATTTAATAAATATGT
Found at i:541340 original size:60 final size:60
Alignment explanation
Indices: 541230--541360 Score: 149
Period size: 60 Copynumber: 2.2 Consensus size: 60
541220 ATAATATGTC
** * * *
541230 CCCAAAA-TATGACTTTCTTTTTAAATTAGTCCCTAAACTTTTAGATATTTTAATTTAAT
1 CCCAAAACTATGACTCCCATTTTAAATTAGACCCTAAACTTTTAGACATTTTAATTTAAT
* * * *
541289 TCCAAAACTATGACTCCCATTTTAAATTAGACCTTAAACTTTT-GAACATTTTATTTTCAT
1 CCCAAAACTATGACTCCCATTTTAAATTAGACCCTAAACTTTTAG-ACATTTTAATTTAAT
*
541349 CCCTAAACTATG
1 CCCAAAACTATG
541361 TCCATGTCTA
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 7 0.12
60 52 0.88
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (60 bp):
CCCAAAACTATGACTCCCATTTTAAATTAGACCCTAAACTTTTAGACATTTTAATTTAAT
Found at i:541644 original size:59 final size:60
Alignment explanation
Indices: 541564--541703 Score: 142
Period size: 59 Copynumber: 2.4 Consensus size: 60
541554 GGAATGCTCA
* * * * * *
541564 AAAAGTTGGGGGACCAATTTAGAAAGAGGGTCGTAGTTTGAT-GATGAAATTGAAA-ACTC
1 AAAAGTTTGAGGACTAATTTAGAAAGAGAGTCATAGCTT-ATGGATGAAATTGAAACACTC
* * * *
541623 AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGCTTATGGATGAAATTGAAACATTG
1 AAAAGTTTGAGGACTAATTTAGAAAGAGAGTCATAGCTTATGGATGAAATTGAAACACTC
*
541683 AGAAGTTT-AGGGACTAATTTA
1 AAAAGTTTGA-GGACTAATTTA
541704 AAATTAGGGT
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
58 2 0.03
59 45 0.67
60 20 0.30
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.29
Consensus pattern (60 bp):
AAAAGTTTGAGGACTAATTTAGAAAGAGAGTCATAGCTTATGGATGAAATTGAAACACTC
Found at i:542829 original size:2 final size:2
Alignment explanation
Indices: 542822--542849 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
542812 TGCTTAATTT
542822 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
542850 AAAAACGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:547143 original size:28 final size:28
Alignment explanation
Indices: 547103--547164 Score: 115
Period size: 28 Copynumber: 2.2 Consensus size: 28
547093 TGCTGAGGTT
547103 GCCATGTGATCCCATCCAACTGTAGCTC
1 GCCATGTGATCCCATCCAACTGTAGCTC
547131 GCCATGTGATCCCATCCAACTGTAGCTC
1 GCCATGTGATCCCATCCAACTGTAGCTC
*
547159 GTCATG
1 GCCATG
547165 CAAGCACCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (28 bp):
GCCATGTGATCCCATCCAACTGTAGCTC
Found at i:554929 original size:16 final size:16
Alignment explanation
Indices: 554905--554952 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
554895 TTCTTTTTCT
*
554905 TACACACATATATATA
1 TACATACATATATATA
*
554921 TACATACATATATACA
1 TACATACATATATATA
*
554937 TGCATACATATATATA
1 TACATACATATATATA
554953 CATACACACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (16 bp):
TACATACATATATATA
Found at i:555076 original size:12 final size:12
Alignment explanation
Indices: 555059--555093 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
555049 TTTTTCTTTA
*
555059 CATACATGCATG
1 CATACATACATG
555071 CATACATACATG
1 CATACATACATG
*
555083 CATGCATACAT
1 CATACATACAT
555094 ATGTCATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (12 bp):
CATACATACATG
Found at i:555078 original size:16 final size:16
Alignment explanation
Indices: 555057--555094 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
555047 TCTTTTTCTT
555057 TACATACATGCATGCA
1 TACATACATGCATGCA
555073 TACATACATGCATGCA
1 TACATACATGCATGCA
555089 TACATA
1 TACATA
555095 TGTCATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (16 bp):
TACATACATGCATGCA
Done.