Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 29
Found at i:230681 original size:12 final size:12
Alignment explanation
Indices: 230664--230688 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
230654 GTATCGATGC
230664 ACTGCTACAGTA
1 ACTGCTACAGTA
230676 ACTGCTACAGTA
1 ACTGCTACAGTA
230688 A
1 A
230689 TTTCAGCATT
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:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (12 bp):
ACTGCTACAGTA
Found at i:234543 original size:104 final size:105
Alignment explanation
Indices: 234362--234574 Score: 392
Period size: 104 Copynumber: 2.0 Consensus size: 105
234352 CATAAATAAT
234362 GTATATATATATATATATTATATAATATAATTTGAAATAACGTAACTATATTATATAATATAATA
1 GTATATATATATATATATTATATAATATAATTTGAAATAACGTAACTATATTATATAATATAATA
*
234427 ATTTTAATCGAATGGAAAGAGACGAAATTATGTGTCTTCA
66 ATTTTAATCGAATGGAAAGAGACGAAATTAGGTGTCTTCA
*
234467 GTATATATATATATATA-TATATTATATAATTTGAAATAACGTAACTATATTATATAATATAATA
1 GTATATATATATATATATTATATAATATAATTTGAAATAACGTAACTATATTATATAATATAATA
*
234531 ATTTTAATCGAATGGAAAGGGACGAAATTAGGTGTCTTCA
66 ATTTTAATCGAATGGAAAGAGACGAAATTAGGTGTCTTCA
234571 GTAT
1 GTAT
234575 GTAACAAATA
Statistics
Matches: 105, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
104 88 0.84
105 17 0.16
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.39
Consensus pattern (105 bp):
GTATATATATATATATATTATATAATATAATTTGAAATAACGTAACTATATTATATAATATAATA
ATTTTAATCGAATGGAAAGAGACGAAATTAGGTGTCTTCA
Found at i:234744 original size:30 final size:31
Alignment explanation
Indices: 234710--234768 Score: 93
Period size: 32 Copynumber: 1.9 Consensus size: 31
234700 TATTGGCTTA
*
234710 AAATAGAGTGA-TATATTTATTATAATTGTT
1 AAATAAAGTGATTATATTTATTATAATTGTT
234740 AAATAAAGTGATTTATATTTATTATAATT
1 AAATAAAGTGA-TTATATTTATTATAATT
234769 TAGATGAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 10 0.38
32 16 0.62
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (31 bp):
AAATAAAGTGATTATATTTATTATAATTGTT
Found at i:234924 original size:14 final size:15
Alignment explanation
Indices: 234897--234933 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
234887 ATAAATTAGT
234897 TAAAA-ATTTAAAAA
1 TAAAATATTTAAAAA
*
234911 TAAATTATTT-AAAA
1 TAAAATATTTAAAAA
234925 TAAAATATT
1 TAAAATATT
234934 AATTACATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAATATTTAAAAA
Found at i:241056 original size:21 final size:21
Alignment explanation
Indices: 241032--241073 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
241022 ATCAATATTT
241032 TTTTTTC-GCAGTAAAATAAAA
1 TTTTTTCTGC-GTAAAATAAAA
*
241053 TTTTTTCTGCTTAAAATAAAA
1 TTTTTTCTGCGTAAAATAAAA
241074 CTCATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (21 bp):
TTTTTTCTGCGTAAAATAAAA
Found at i:248154 original size:16 final size:16
Alignment explanation
Indices: 248133--248165 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
248123 TAATAAATAG
248133 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
248149 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
248165 A
1 A
248166 AAATTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:248246 original size:10 final size:10
Alignment explanation
Indices: 248231--248305 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
248221 CATTTAATAA
248231 ATAAACGAAC
1 ATAAACGAAC
248241 ATAAACGAAC
1 ATAAACGAAC
248251 ----ACGAAC
1 ATAAACGAAC
248257 ATAAACGAAC
1 ATAAACGAAC
** *
248267 ACGAAC-ATAA
1 ATAAACGA-AC
248277 ATGAACACGAAC
1 AT-AA-ACGAAC
248289 ATAAACGAAC
1 ATAAACGAAC
248299 ATAAACG
1 ATAAACG
248306 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 35 0.69
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:248256 original size:16 final size:16
Alignment explanation
Indices: 248235--248299 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
248225 TAATAAATAA
248235 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
248251 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
248267 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
248283 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
248299 A
1 A
248300 TAAACGTTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:249069 original size:14 final size:14
Alignment explanation
Indices: 249052--249107 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
249042 AATGAACATA
249052 AACGAACATAATCG
1 AACGAACATAATCG
249066 AACGAACAT-A---
1 AACGAACATAATCG
* *
249076 AACAAACATAACCG
1 AACGAACATAATCG
*
249090 AACAAACATAATCG
1 AACGAACATAATCG
249104 AACG
1 AACG
249108 TAAATGAACG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 8 0.23
11 1 0.03
13 1 0.03
14 25 0.71
ACGTcount: A:0.55, C:0.23, G:0.11, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:249072 original size:24 final size:24
Alignment explanation
Indices: 249032--249120 Score: 99
Period size: 24 Copynumber: 3.7 Consensus size: 24
249022 GATTGAGTTA
*
249032 AACATAAATGAATGAACATAAACG
1 AACATAAATGAACGAACATAAACG
*
249056 AACAT-AATCGAACGAACATAAACA
1 AACATAAAT-GAACGAACATAAACG
** * *
249080 AACATAACCGAACAAACATAATCG
1 AACATAAATGAACGAACATAAACG
*
249104 AACGTAAATGAACGAAC
1 AACATAAATGAACGAAC
249121 GAGACCTATG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
23 3 0.06
24 48 0.92
25 1 0.02
ACGTcount: A:0.56, C:0.19, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:252073 original size:23 final size:23
Alignment explanation
Indices: 252029--252073 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
252019 TCTTGAAAAA
* *
252029 TAAATATAATTCAATTTCTTTAT
1 TAAAAATAATTCAATTTATTTAT
* *
252052 TAAAAATAATTTATTTTATTTA
1 TAAAAATAATTCAATTTATTTA
252074 GTCAAAGATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
TAAAAATAATTCAATTTATTTAT
Found at i:252486 original size:74 final size:73
Alignment explanation
Indices: 252402--252539 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 73
252392 TAAATTTAGG
* ***
252402 ATTTTTAGTTTGATTATTTTATTATTATTATTATTTATTTAAGAATTA-GTTATTTACTTAGAAC
1 ATTTTTAGTTTGATTATATTATTA-TATT-TTATTTAGGAAAGAATTATGTTATTTACTTAGAAC
252466 TCTCGGTAGA
64 TCTCGGTAGA
* * *
252476 ATTTTTAGTTTGATTATATTATTATCTTTTATTTAGGAAATAATTATTTTATTTACTTAGAACT
1 ATTTTTAGTTTGATTATATTATTATATTTTATTTAGGAAAGAATTATGTTATTTACTTAGAACT
252540 GTATGGTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
72 14 0.25
73 19 0.34
74 23 0.41
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.55
Consensus pattern (73 bp):
ATTTTTAGTTTGATTATATTATTATATTTTATTTAGGAAAGAATTATGTTATTTACTTAGAACTC
TCGGTAGA
Found at i:252645 original size:13 final size:13
Alignment explanation
Indices: 252624--252657 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
252614 GAAGTTCTAT
* *
252624 TTTTATTTCTTTA
1 TTTTCTTTCATTA
252637 TTTTCTTTCATTA
1 TTTTCTTTCATTA
252650 TTTTCTTT
1 TTTTCTTT
252658 TCACAATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTCATTA
Found at i:253262 original size:18 final size:19
Alignment explanation
Indices: 253226--253262 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
253216 CTCTATTGAA
253226 TTCTCATACTTTATTTATT
1 TTCTCATACTTTATTTATT
253245 TTCTCAATA-TTT-TTTATT
1 TTCTC-ATACTTTATTTATT
253263 CAGTATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 8 0.47
20 3 0.18
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.65
Consensus pattern (19 bp):
TTCTCATACTTTATTTATT
Found at i:258208 original size:65 final size:65
Alignment explanation
Indices: 258079--258210 Score: 153
Period size: 65 Copynumber: 2.0 Consensus size: 65
258069 GGAAAATATC
* * *
258079 TTGTTTCAAGAGAAACAATCTTCAAGTTTATGTTTCAAGGGAAATAGTCTCACATGATACGAAAT
1 TTGTTTCAAGAGAAACAATCTTCAAGTTTATGTTTCAAGGAAAATAGTCTCACACGAGACGAAAT
* * * *
258144 TTGTTTCAAGAGGAATAATC-TCAAGGTTTGTGTTTCAAGGAAAACTA-TCTCA-AGCGAGATGA
1 TTGTTTCAAGAGAAACAATCTTCAA-GTTTATGTTTCAAGGAAAA-TAGTCTCACA-CGAGACGA
258206 AAT
63 AAT
258209 TT
1 TT
258211 TATTCCAAGG
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
64 5 0.09
65 50 0.88
66 2 0.04
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACAATCTTCAAGTTTATGTTTCAAGGAAAATAGTCTCACACGAGACGAAAT
Found at i:258541 original size:37 final size:38
Alignment explanation
Indices: 258474--258580 Score: 112
Period size: 37 Copynumber: 2.9 Consensus size: 38
258464 AATATTAAAG
* * *
258474 TTTGTGTTTCAAGAGAAACTATC-TCAAGTGAGACGAAA
1 TTTGT-TTTTAAGAAAAACAATCTTCAAGTGAGACGAAA
* ***
258512 TTTGTTTTTAAGAAAAATAAT-TTCAAGTGAGACGGGT
1 TTTGTTTTTAAGAAAAACAATCTTCAAGTGAGACGAAA
*
258549 TTTGTTTTTAAGAAAGACAATCTT-AAGTGAGA
1 TTTGTTTTTAAGAAAAACAATCTTCAAGTGAGA
258581 TACTTTTTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
37 51 0.88
38 7 0.12
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.35
Consensus pattern (38 bp):
TTTGTTTTTAAGAAAAACAATCTTCAAGTGAGACGAAA
Found at i:258678 original size:34 final size:34
Alignment explanation
Indices: 258633--258699 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
258623 AAATTGTCTA
* *
258633 AAGTGAGACG-AATTTTTTTAAGAAAAAAAATCTC
1 AAGTGAAACGAAATTTGTTTAA-AAAAAAAATCTC
*
258667 AAGTGAAACGAAATTTGTTTAAAAAAACAATCT
1 AAGTGAAACGAAATTTGTTTAAAAAAAAAATCT
258700 TAAGGGAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 19 0.66
35 10 0.34
ACGTcount: A:0.49, C:0.09, G:0.13, T:0.28
Consensus pattern (34 bp):
AAGTGAAACGAAATTTGTTTAAAAAAAAAATCTC
Found at i:260967 original size:108 final size:108
Alignment explanation
Indices: 260825--261075 Score: 358
Period size: 108 Copynumber: 2.3 Consensus size: 108
260815 TATAGCCACC
*
260825 AATAGCAAGCACATGTATATCATGCATATAATCATTAATATCAAGAACGTCTATATCATGTATAT
1 AATAGCAAGCACATGTATATCATGCATATTATCATTAATATCAAGAACGTCTATATCATGTATAT
* *
260890 AATCATCGTTAGCAAACATATGCATACCATGCATATAATCATT
66 AATCATCGGTAGCAAACACATGCATACCATGCATATAATCATT
* * * * * *
260933 AATAACAAGCACATGTATATCTTTCATATTATCATTAATATCAAGCATGTGTATATCATGTATAT
1 AATAGCAAGCACATGTATATCATGCATATTATCATTAATATCAAGAACGTCTATATCATGTATAT
** * * *
260998 AATCATCGGTATTAAACACATGTATATCATGCGTATAATCATT
66 AATCATCGGTAGCAAACACATGCATACCATGCATATAATCATT
* *
261041 AATAGTAAGCACATGTATATCCTGCATATTATCAT
1 AATAGCAAGCACATGTATATCATGCATATTATCAT
261076 CAGCAATAAT
Statistics
Matches: 125, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
108 125 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.34
Consensus pattern (108 bp):
AATAGCAAGCACATGTATATCATGCATATTATCATTAATATCAAGAACGTCTATATCATGTATAT
AATCATCGGTAGCAAACACATGCATACCATGCATATAATCATT
Found at i:261096 original size:108 final size:108
Alignment explanation
Indices: 260825--261168 Score: 316
Period size: 108 Copynumber: 3.2 Consensus size: 108
260815 TATAGCCACC
* * * * * ** *
260825 AATAGCAAGCACATGTATATCATGCATATAATCATTAATATCAAGAACGTCTATATCATGTATAT
1 AATAACAAGCACATGTATATCCTGCATATTATCATCAATATCAAGCATATATATATCATGTATAT
* *
260890 AATCATCGTTAGCAAACATATGCATACCATGCATATAATCATT
66 AATCATCGGTAGCAAACACATGCATACCATGCATATAATCATT
* * * * *
260933 AATAACAAGCACATGTATATCTTTCATATTATCATTAATATCAAGCATGTGTATATCATGTATAT
1 AATAACAAGCACATGTATATCCTGCATATTATCATCAATATCAAGCATATATATATCATGTATAT
** * * *
260998 AATCATCGGTATTAAACACATGTATATCATGCGTATAATCATT
66 AATCATCGGTAGCAAACACATGCATACCATGCATATAATCATT
** * *
261041 AATAGTAAGCACATGTATATCCTGCATATTATCATCAGCA-AT-AATCATATATATATCATGCAT
1 AATAACAAGCACATGTATATCCTGCATATTATCATCA--ATATCAAGCATATATATATCATGTAT
* * *** * ** * * * *
261104 AT-TTCAACACCAGCAAGCGTATGTATATCAGGCATATAATCATC
64 ATAATCATCGGTAGCAAACACATGCATACCATGCATATAATCATT
*
261148 AATAGCAAGCACATGTATATC
1 AATAACAAGCACATGTATATC
261169 GTTCATAGGA
Statistics
Matches: 197, Mismatches: 37, Indels: 5
0.82 0.15 0.02
Matches are distributed among these distances:
107 49 0.25
108 145 0.74
109 2 0.01
110 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (108 bp):
AATAACAAGCACATGTATATCCTGCATATTATCATCAATATCAAGCATATATATATCATGTATAT
AATCATCGGTAGCAAACACATGCATACCATGCATATAATCATT
Found at i:261164 original size:36 final size:36
Alignment explanation
Indices: 260824--261168 Score: 269
Period size: 36 Copynumber: 9.6 Consensus size: 36
260814 ATATAGCCAC
260824 CAATAGCAAGCACATGTATATCATGCATATAATCAT
1 CAATAGCAAGCACATGTATATCATGCATATAATCAT
* * * * * *
260860 TAATATCAAGAACGTCTATATCATGTATATAATCAT
1 CAATAGCAAGCACATGTATATCATGCATATAATCAT
** * * * *
260896 CGTTAGCAAACATATGCATACCATGCATATAATCAT
1 CAATAGCAAGCACATGTATATCATGCATATAATCAT
* * * * *
260932 TAATAACAAGCACATGTATATCTTTCATATTATCAT
1 CAATAGCAAGCACATGTATATCATGCATATAATCAT
* * ** *
260968 TAATATCAAGCATGTGTATATCATGTATATAATCAT
1 CAATAGCAAGCACATGTATATCATGCATATAATCAT
** ** * *
261004 CGGTATTAAACACATGTATATCATGCGTATAATCAT
1 CAATAGCAAGCACATGTATATCATGCATATAATCAT
* * * *
261040 TAATAGTAAGCACATGTATATCCTGCATATTATCAT
1 CAATAGCAAGCACATGTATATCATGCATATAATCAT
** ** * * * * *
261076 CAGCAATAATCATATATATATCATGCATAT-TTCAA
1 CAATAGCAAGCACATGTATATCATGCATATAATCAT
** ** *
261111 CACCAGCAAGCGTATGTATATCAGGCATATAATCAT
1 CAATAGCAAGCACATGTATATCATGCATATAATCAT
261147 CAATAGCAAGCACATGTATATC
1 CAATAGCAAGCACATGTATATC
261169 GTTCATAGGA
Statistics
Matches: 232, Mismatches: 76, Indels: 2
0.75 0.25 0.01
Matches are distributed among these distances:
35 26 0.11
36 206 0.89
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (36 bp):
CAATAGCAAGCACATGTATATCATGCATATAATCAT
Found at i:262042 original size:19 final size:19
Alignment explanation
Indices: 262018--262236 Score: 136
Period size: 19 Copynumber: 11.3 Consensus size: 19
262008 TGTTAACATA
262018 AAAATCTGGGTTGCAACCT
1 AAAATCTGGGTTGCAACCT
* * * *
262037 AAAATCTTGTTTCCATCCT
1 AAAATCTGGGTTGCAACCT
262056 AAAAATCTGGGTTGCAACCT
1 -AAAATCTGGGTTGCAACCT
* ** **
262076 AAAATATGTCTTATAACCT
1 AAAATCTGGGTTGCAACCT
*
262095 AAAATCTGGATTGCAACCT
1 AAAATCTGGGTTGCAACCT
* *
262114 AAAATCTAGGTTGCCACCT
1 AAAATCTGGGTTGCAACCT
* * * * *
262133 AAAATATGGATTCCATCAT
1 AAAATCTGGGTTGCAACCT
*
262152 AAAAATCTGGGATG-AGACCTT
1 -AAAATCTGGGTTGCA-ACC-T
* * *
262173 AAAATTTAGATT-CTAACCT
1 AAAATCTGGGTTGC-AACCT
* *
262192 AAAAATATGGGTTGCAACAT
1 -AAAATCTGGGTTGCAACCT
* *
262212 AAAATTATGGGTTGTAACCT
1 AAAA-TCTGGGTTGCAACCT
262232 AAAAT
1 AAAAT
262237 ATGGATTCCA
Statistics
Matches: 147, Mismatches: 44, Indels: 18
0.70 0.21 0.09
Matches are distributed among these distances:
19 78 0.53
20 66 0.45
21 3 0.02
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (19 bp):
AAAATCTGGGTTGCAACCT
Found at i:262059 original size:39 final size:40
Alignment explanation
Indices: 262016--262120 Score: 144
Period size: 39 Copynumber: 2.7 Consensus size: 40
262006 TTTGTTAACA
* *
262016 TAAAAATCTGGGTTGCAACCTAAAATCTTGT-TTCCATCC
1 TAAAAATCTGGGTTGCAACCTAAAATCTTGTCTTACAACC
* *
262055 TAAAAATCTGGGTTGCAACCTAAAAT-ATGTCTTATAACC
1 TAAAAATCTGGGTTGCAACCTAAAATCTTGTCTTACAACC
*
262094 T-AAAATCTGGATTGCAACCTAAAATCT
1 TAAAAATCTGGGTTGCAACCTAAAATCT
262121 AGGTTGCCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
38 26 0.45
39 32 0.55
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.31
Consensus pattern (40 bp):
TAAAAATCTGGGTTGCAACCTAAAATCTTGTCTTACAACC
Found at i:262076 original size:20 final size:20
Alignment explanation
Indices: 262016--262235 Score: 130
Period size: 20 Copynumber: 11.2 Consensus size: 20
262006 TTTGTTAACA
262016 TAAAAATCTGGGTTGCAACC
1 TAAAAATCTGGGTTGCAACC
* * * *
262036 T-AAAATCTTGTTTCCATCC
1 TAAAAATCTGGGTTGCAACC
262055 TAAAAATCTGGGTTGCAACC
1 TAAAAATCTGGGTTGCAACC
* ** **
262075 T-AAAATATGTCTTATAACC
1 TAAAAATCTGGGTTGCAACC
*
262094 T-AAAATCTGGATTGCAACC
1 TAAAAATCTGGGTTGCAACC
* *
262113 T-AAAATCTAGGTTGCCACC
1 TAAAAATCTGGGTTGCAACC
* * * * *
262132 T-AAAATATGGATTCCATCA
1 TAAAAATCTGGGTTGCAACC
*
262151 TAAAAATCTGGGATG-AGACC
1 TAAAAATCTGGGTTGCA-ACC
* * * *
262171 TTAAAATTTAGATT-CTAACC
1 TAAAAATCTGGGTTGC-AACC
* *
262191 TAAAAATATGGGTTGCAACA
1 TAAAAATCTGGGTTGCAACC
* * *
262211 TAAAATTATGGGTTGTAACC
1 TAAAAATCTGGGTTGCAACC
262231 TAAAA
1 TAAAA
262236 TATGGATTCC
Statistics
Matches: 147, Mismatches: 47, Indels: 12
0.71 0.23 0.06
Matches are distributed among these distances:
19 72 0.49
20 73 0.50
21 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
TAAAAATCTGGGTTGCAACC
Found at i:262138 original size:57 final size:58
Alignment explanation
Indices: 262032--262140 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 58
262022 TCTGGGTTGC
* * * *
262032 AACCTAAAATCTTGTTTCCATCCTAAAAATCTGGGTTGCAACCTAAAATATGTCTTAT
1 AACCTAAAATCTGGATTCCAACCTAAAAATCTAGGTTGCAACCTAAAATATGTCTTAT
* *
262090 AACCTAAAATCTGGATTGCAACCT-AAAATCTAGGTTGCCACCTAAAATATG
1 AACCTAAAATCTGGATTCCAACCTAAAAATCTAGGTTGCAACCTAAAATATG
262141 GATTCCATCA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
57 25 0.56
58 20 0.44
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (58 bp):
AACCTAAAATCTGGATTCCAACCTAAAAATCTAGGTTGCAACCTAAAATATGTCTTAT
Found at i:263941 original size:15 final size:15
Alignment explanation
Indices: 263923--263954 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
263913 TGATGTGATC
263923 CTACTTATTATCCTT
1 CTACTTATTATCCTT
*
263938 CTACTTATTATCTTT
1 CTACTTATTATCCTT
263953 CT
1 CT
263955 TTTTTCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (15 bp):
CTACTTATTATCCTT
Found at i:265439 original size:23 final size:25
Alignment explanation
Indices: 265392--265441 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
265382 GTAAAATTTG
265392 TTGTACGTTACTAAAATATATATAT
1 TTGTACGTTACTAAAATATATATAT
265417 TTGTACGTTACTAAAATATATATAT
1 TTGTACGTTACTAAAATATATATAT
265442 CTAGAGTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (25 bp):
TTGTACGTTACTAAAATATATATAT
Found at i:270016 original size:55 final size:55
Alignment explanation
Indices: 269812--270023 Score: 309
Period size: 55 Copynumber: 3.9 Consensus size: 55
269802 ACACACCTAA
269812 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAG-GTTGCACACACAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGTGTTGCACACACAG
* *
269866 TGCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGTGTTGCACACACAG
* * * *
269921 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTGTTGCACATACAG
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGTGTTGCACACACAG
* * * * * *
269976 TGCCCATACGGAAATTCATAAATTTATTATGAATTGCTTAGTTTTGCA
1 TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGTGTTGCA
270024 AACATATAGT
Statistics
Matches: 146, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
54 40 0.27
55 106 0.73
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (55 bp):
TGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAGTGTTGCACACACAG
Found at i:271512 original size:40 final size:40
Alignment explanation
Indices: 271450--271532 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
271440 CAATTAGAGG
*
271450 AATCATTTTGTTACGCGGTTTTCTTGATTTCTCGAGTCCA
1 AATCATTTTGTTACGCGATTTTCTTGATTTCTCGAGTCCA
*
271490 AATCATTTTGTTACGTGATTTTCTTGATTTCTCGAGTCCA
1 AATCATTTTGTTACGCGATTTTCTTGATTTCTCGAGTCCA
271530 AAT
1 AAT
271533 TTAACAAGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.20, C:0.18, G:0.16, T:0.46
Consensus pattern (40 bp):
AATCATTTTGTTACGCGATTTTCTTGATTTCTCGAGTCCA
Found at i:273474 original size:2 final size:2
Alignment explanation
Indices: 273467--273493 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
273457 CCATAAAAGT
273467 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 T
273494 CTTTCTGACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:275299 original size:45 final size:46
Alignment explanation
Indices: 275233--275320 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 46
275223 TTATTCATTC
275233 TTTTCATTTATGGAATCCTTTCAGGCCGATAATACACCGTTATGCA
1 TTTTCATTTATGGAATCCTTTCAGGCCGATAATACACCGTTATGCA
* * * *
275279 TTTT-ATTTAT-GACATCCTTTCATGCTGGTAATGCACCGTTAT
1 TTTTCATTTATGGA-ATCCTTTCAGGCCGATAATACACCGTTAT
275321 TCATCTAACT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 2 0.05
45 31 0.84
46 4 0.11
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (46 bp):
TTTTCATTTATGGAATCCTTTCAGGCCGATAATACACCGTTATGCA
Found at i:275368 original size:49 final size:49
Alignment explanation
Indices: 275308--275421 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 49
275298 TCATGCTGGT
** * * *
275308 AATGCACCGTTATTCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAA
1 AATGCACCGTTAGGCATCTAACTTGCATTAATGACACATTTCTGCCAAA
* *
275357 AATGCATCGTTAGGCATCTAACTTGCATTAATGACACATTTCTTCCAAA
1 AATGCACCGTTAGGCATCTAACTTGCATTAATGACACATTTCTGCCAAA
*
275406 AA-GCACAGTTAGGCAT
1 AATGCACCGTTAGGCAT
275422 TTATTCTTTC
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
48 12 0.21
49 44 0.79
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (49 bp):
AATGCACCGTTAGGCATCTAACTTGCATTAATGACACATTTCTGCCAAA
Found at i:275844 original size:55 final size:55
Alignment explanation
Indices: 275655--276467 Score: 1097
Period size: 55 Copynumber: 14.9 Consensus size: 55
275645 GGACACCAAA
* * * *
275655 TGCCAATATGGAAATTCATAAACTTATTATGAATTTCCTAG-GTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* * ** * *
275709 TTCCAATACAAAAATTCATAAACTCATTATGAATTTCTTAGTTTTGCACACAGAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* * * * *
275764 TG-TC-TATGAAAATTCATAGATTTATTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
** *
275817 TGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACATAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* * ** *
275872 TGCCTATACGAAAATTCATAAACTTATTATGAGCTTCTTAGTTTTTCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* *
275927 TGCCCATACGGAAATCCATAAACTTATTATGAATTTCTTAGTTTTGCAAACACTA-
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACAC-AG
* * * *
275982 TGCCCATACGAAAATTCATAAATTTATTACGAATTTCGTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* * * *
276037 TGCCCATACAGAAATTCATAAACTTATTATGAATTTCCTAGTTTTACACACACAT
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* * *
276092 TTCCCATA-TGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACATAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
*
276146 TGCCTATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* ** * *
276201 TGCCTATATAGAAATTCATAAACTTATTATG---TTCCTAGTTTTGCACACACAA
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
** *
276253 TGCCCATACAAAAATTCATAAACTTATTATGAATTTCTTAGTTTTGTACACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
*
276308 TGCCCATACGGAAATTCATAAACTTATTATGGATTTCTTAGTTTTG--CACACAG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* *
276361 TGCCCATACGGAAATTCATAAACTTATTATAAATTTCTTAGTTTTGCACACACGG
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
* *
276416 TGCCCATACAGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGGACACA
1 TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACA
276468 TATAGTGCCA
Statistics
Matches: 670, Mismatches: 78, Indels: 21
0.87 0.10 0.03
Matches are distributed among these distances:
52 47 0.07
53 96 0.14
54 84 0.13
55 442 0.66
56 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (55 bp):
TGCCCATACGGAAATTCATAAACTTATTATGAATTTCTTAGTTTTGCACACACAG
Found at i:289785 original size:27 final size:28
Alignment explanation
Indices: 289735--289787 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
289725 AACAAAGATT
289735 AAGAAAATGAAAAGATAAGGATAATGTA
1 AAGAAAATGAAAAGATAAGGATAATGTA
* *
289763 AAGACAATGAAGA-ATAAGGATAATG
1 AAGAAAATGAAAAGATAAGGATAATG
289788 AATGTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.58, C:0.02, G:0.23, T:0.17
Consensus pattern (28 bp):
AAGAAAATGAAAAGATAAGGATAATGTA
Found at i:290528 original size:19 final size:20
Alignment explanation
Indices: 290504--290549 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
290494 CAAATAATCA
290504 GTAATAATATTA-AAAAT-TC
1 GTAATAAT-TTACAAAATCTC
290523 GTAAT-ATTTACAAAATCTC
1 GTAATAATTTACAAAATCTC
*
290542 GTATTAAT
1 GTAATAAT
290550 CCTGTATAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 3 0.13
18 7 0.30
19 11 0.48
20 2 0.09
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (20 bp):
GTAATAATTTACAAAATCTC
Found at i:290529 original size:16 final size:19
Alignment explanation
Indices: 290508--290544 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
290498 TAATCAGTAA
290508 TAATA-TTA-AAAAT-TCG
1 TAATATTTACAAAATCTCG
290524 TAATATTTACAAAATCTCG
1 TAATATTTACAAAATCTCG
290543 TA
1 TA
290545 TTAATCCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 3 0.17
18 5 0.28
19 5 0.28
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (19 bp):
TAATATTTACAAAATCTCG
Found at i:294060 original size:20 final size:20
Alignment explanation
Indices: 294023--294061 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
294013 AATAAGAAGG
** *
294023 AATTGAAACTAAATTAAAAT
1 AATTGAAAAAAAACTAAAAT
294043 AATTGAAAAAAAACTAAAA
1 AATTGAAAAAAAACTAAAA
294062 ATGATGAACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (20 bp):
AATTGAAAAAAAACTAAAAT
Found at i:294962 original size:5 final size:6
Alignment explanation
Indices: 294934--294960 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
294924 CTAATGCTTG
294934 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
294961 TACTATCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:296370 original size:22 final size:21
Alignment explanation
Indices: 296344--296384 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
296334 TTAAAAATTA
296344 TAAAGTAACTATCGATACTCAT
1 TAAAG-AACTATCGATACTCAT
* *
296366 TAAAGGAGTATCGATACTC
1 TAAAGAACTATCGATACTC
296385 CCTATTCAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (21 bp):
TAAAGAACTATCGATACTCAT
Found at i:298544 original size:17 final size:15
Alignment explanation
Indices: 298517--298558 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
298507 AAAAAGGGGT
298517 ATAAA-AATAATAAA
1 ATAAATAATAATAAA
298531 ACTAATATAATAATAAA
1 A-TAA-ATAATAATAAA
298548 ATAAATAATAA
1 ATAAATAATAA
298559 ATAGAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 10 0.40
16 4 0.16
17 10 0.40
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
ATAAATAATAATAAA
Found at i:325352 original size:13 final size:13
Alignment explanation
Indices: 325331--325378 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
325321 TGATCAAAAT
*
325331 AAATAAATAATGCA
1 AAATAAATAAT-AA
325345 AAAT-AATAATAA
1 AAATAAATAATAA
325357 AAATAAATAATTAAA
1 AAATAAATAA-T-AA
325372 AAATAAA
1 AAATAAA
325379 ATAGGTTACC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 5 0.17
13 11 0.37
14 5 0.17
15 9 0.30
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (13 bp):
AAATAAATAATAA
Found at i:325364 original size:16 final size:15
Alignment explanation
Indices: 325345--325378 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
325335 AAATAATGCA
325345 AAATAATAATAAAAAT
1 AAATAATAA-AAAAAT
*
325361 AAATAATTAAAAAAT
1 AAATAATAAAAAAAT
325376 AAA
1 AAA
325379 ATAGGTTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAATAAAAAAAT
Found at i:325373 original size:26 final size:26
Alignment explanation
Indices: 325331--325381 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
325321 TGATCAAAAT
*
325331 AAATAAATAATG-CAAAATAATAATAA
1 AAATAAATAATGAAAAAATAA-AATAA
*
325357 AAATAAATAATTAAAAAATAAAATA
1 AAATAAATAATGAAAAAATAAAATA
325382 GGTTACCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (26 bp):
AAATAAATAATGAAAAAATAAAATAA
Found at i:325380 original size:16 final size:17
Alignment explanation
Indices: 325344--325381 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
325334 TAAATAATGC
325344 AAAATAATAATAAAAAT
1 AAAATAATAATAAAAAT
*
325361 -AAATAATTA-AAAAAT
1 AAAATAATAATAAAAAT
325376 AAAATA
1 AAAATA
325382 GGTTACCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAATAATAATAAAAAT
Found at i:342261 original size:28 final size:28
Alignment explanation
Indices: 342230--342307 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 28
342220 ATAAATACAA
342230 AAAATTAAATATTGGAAAATAAAGGAA-T
1 AAAATTAAATATTGGAAAATAAA-GAATT
342258 AAAATGTAAAT-TAT-GAAAATTAAAGAATT
1 AAAAT-TAAATAT-TGGAAAA-TAAAGAATT
* *
342287 GAAATTGAAATATTGAAAAAT
1 AAAATT-AAATATTGGAAAAT
342308 TAAAAGGCTG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
28 15 0.37
29 21 0.51
30 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.28
Consensus pattern (28 bp):
AAAATTAAATATTGGAAAATAAAGAATT
Found at i:344319 original size:22 final size:22
Alignment explanation
Indices: 344294--344344 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
344284 TGAGCACCTA
344294 ACTTGTAATTGTAGAGATAACC
1 ACTTGTAATTGTAGAGATAACC
*
344316 ACTTGTAATTGTAGAGATGACC
1 ACTTGTAATTGTAGAGATAACC
344338 AGCTTGT
1 A-CTTGT
344345 TAGAGCTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (22 bp):
ACTTGTAATTGTAGAGATAACC
Found at i:345443 original size:32 final size:32
Alignment explanation
Indices: 345382--345445 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
345372 AATTTCAATC
* *
345382 AGTTCGGGTTGCTTTCGGGCCGGGCTAAATTT
1 AGTTCGGGTTGCTTTCGGACCGGACTAAATTT
* * *
345414 AGTTTGGGTTGCTTTCGGATCGGATTAAATTT
1 AGTTCGGGTTGCTTTCGGACCGGACTAAATTT
345446 CAATTCAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.16, C:0.14, G:0.31, T:0.39
Consensus pattern (32 bp):
AGTTCGGGTTGCTTTCGGACCGGACTAAATTT
Found at i:345513 original size:32 final size:30
Alignment explanation
Indices: 345477--345545 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 30
345467 CATGTTAAAA
*
345477 TTCAGTTCGGGTTTCTTTCGATTCAGGTTAAT
1 TTCAGTTCGGGTTGCTTT-GATTC-GGTTAAT
* *
345509 TTCAGTTTGGGTTGCTTTGGTTCGGTTAAT
1 TTCAGTTCGGGTTGCTTTGATTCGGTTAAT
*
345539 TTTAGTT
1 TTCAGTT
345546 TCAGACCAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 13 0.39
31 4 0.12
32 16 0.48
ACGTcount: A:0.13, C:0.12, G:0.25, T:0.51
Consensus pattern (30 bp):
TTCAGTTCGGGTTGCTTTGATTCGGTTAAT
Found at i:347029 original size:79 final size:82
Alignment explanation
Indices: 346923--347118 Score: 224
Period size: 79 Copynumber: 2.4 Consensus size: 82
346913 TAGGACAATT
* * * * * * *
346923 ATATCCTTTT-AAATATCTCAAAGTAAAATATATTAATTATCTTTTTAAATTTGAATGTT-AAAA
1 ATATCTTTTTAAAATATTTTAAATTAAAAGATATTAATTATCTTTTTAAATTTAAATATTAAAAA
*
346986 CATATTA-AAAGGATA-TC
66 CATA-TACAAA-GATATTA
* * *
347003 ATATC-TTTTAGAATA-TTTAAGTTAAAAGATATTTATTATCTTTTTAAATTTAAATATTAAAAA
1 ATATCTTTTTAAAATATTTTAAATTAAAAGATATTAATTATCTTTTTAAATTTAAATATTAAAAA
*
347066 CATATACAAATATATTA
66 CATATACAAAGATATTA
347083 ATATCTTTTTAAAATATTTTAAATTAAAAGATATTA
1 ATATCTTTTTAAAATATTTTAAATTAAAAGATATTA
347119 TCCTTTAAGA
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
79 44 0.46
80 26 0.27
81 9 0.09
82 17 0.18
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (82 bp):
ATATCTTTTTAAAATATTTTAAATTAAAAGATATTAATTATCTTTTTAAATTTAAATATTAAAAA
CATATACAAAGATATTA
Found at i:348560 original size:57 final size:57
Alignment explanation
Indices: 348490--348630 Score: 169
Period size: 57 Copynumber: 2.5 Consensus size: 57
348480 TAGTAGAAGT
* ** * *
348490 AAATAAATTGTTGAATTTATTTATCT-AGAAACTTGTATGATTCTTTTTTGT-AAAAG
1 AAATAAATCGTTGAATTTATTTAT-TGAGAAACAAGCATGATTCTATTTTGTAAAAAG
* * *
348546 AAATAAAATCGTTGAATTTATTTCTTGAGCACCAAGCATGATTCTATTTTGTAAAAAG
1 AAAT-AAATCGTTGAATTTATTTATTGAGAAACAAGCATGATTCTATTTTGTAAAAAG
*
348604 AAATAAATCGTTGAATTTATTTCTTGA
1 AAATAAATCGTTGAATTTATTTATTGA
348631 AAATTTTGAT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
56 5 0.07
57 60 0.81
58 9 0.12
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.42
Consensus pattern (57 bp):
AAATAAATCGTTGAATTTATTTATTGAGAAACAAGCATGATTCTATTTTGTAAAAAG
Found at i:354040 original size:32 final size:32
Alignment explanation
Indices: 354004--354078 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
353994 GCCTGGGTTT
354004 GATTTTGAATGAACCATATTATCTTCGTTGAA
1 GATTTTGAATGAACCATATTATCTTCGTTGAA
* *
354036 GATTTTGAATGAACCATATTGTCTTGGTTGAA
1 GATTTTGAATGAACCATATTATCTTCGTTGAA
354068 GATTTTGAATG
1 GATTTTGAATG
354079 GAGAAAGCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.41
Consensus pattern (32 bp):
GATTTTGAATGAACCATATTATCTTCGTTGAA
Found at i:354154 original size:6 final size:6
Alignment explanation
Indices: 354145--354170 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
354135 GGAAAAGAAA
354145 AAGAGG AAGAGG AAGAGG AAGAGG AA
1 AAGAGG AAGAGG AAGAGG AAGAGG AA
354171 AGAAAGAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:354709 original size:40 final size:41
Alignment explanation
Indices: 354660--354892 Score: 234
Period size: 40 Copynumber: 5.8 Consensus size: 41
354650 TGCGATTTTC
* * *
354660 CAAATTCGCAACTCGAATTTGT-AAATT-GCAACACATAAGT
1 CAAATTCGCAACGCGAA-TAGTCAAATTCGCAACACAAAAGT
*
354700 CAAATTCGCAACGAG-ATAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATAGTCAAATTCGCAACACAAAAGT
* * *
354740 CAAATTCGCAACACG-ATAGTCAAATTCGCAACGC-GAA-T
1 CAAATTCGCAACGCGAATAGTCAAATTCGCAACACAAAAGT
* * * * *
354778 CTATAAATCGCAACGCAAATTTGT-AAA-TCGCAACACAGATGT
1 C-A-AATTCGCAACGCGAA-TAGTCAAATTCGCAACACAAAAGT
354820 CAAATTCGCAACGCG-ATAGTCAAATTCGCAACACAAAAGT
1 CAAATTCGCAACGCGAATAGTCAAATTCGCAACACAAAAGT
*
354860 CAAATTCGCAACGCGAA-ATTTCAAATTCGCAAC
1 CAAATTCGCAACGCGAATA-GTCAAATTCGCAAC
354893 TGAATTTCAA
Statistics
Matches: 161, Mismatches: 20, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
38 8 0.05
39 13 0.08
40 114 0.71
41 21 0.13
42 5 0.03
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.21
Consensus pattern (41 bp):
CAAATTCGCAACGCGAATAGTCAAATTCGCAACACAAAAGT
Found at i:354710 original size:20 final size:20
Alignment explanation
Indices: 354682--354871 Score: 155
Period size: 20 Copynumber: 9.6 Consensus size: 20
354672 TCGAATTTGT
354682 AAATT-GCAACACATAAGTC
1 AAATTCGCAACACATAAGTC
*
354701 AAATTCGCAACGAGAT-AGTC
1 AAATTCGCAAC-ACATAAGTC
*
354721 AAATTCGCAACACAAAAGTC
1 AAATTCGCAACACATAAGTC
354741 AAATTCGCAACACGAT-AGTC
1 AAATTCGCAACAC-ATAAGTC
* *
354761 AAATTCGCAACGC-GAA-TC
1 AAATTCGCAACACATAAGTC
* *
354779 TATAAATCGCAACGCA-AATTTGT-
1 -A-AATTCGCAACACATAA---GTC
* *
354802 AAA-TCGCAACACAGATGTC
1 AAATTCGCAACACATAAGTC
*
354821 AAATTCGCAACGCGAT-AGTC
1 AAATTCGCAACAC-ATAAGTC
*
354841 AAATTCGCAACACAAAAGTC
1 AAATTCGCAACACATAAGTC
354861 AAATTCGCAAC
1 AAATTCGCAAC
354872 GCGAAATTTC
Statistics
Matches: 140, Mismatches: 14, Indels: 33
0.75 0.07 0.18
Matches are distributed among these distances:
18 4 0.03
19 13 0.09
20 113 0.81
21 8 0.06
22 1 0.01
24 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (20 bp):
AAATTCGCAACACATAAGTC
Found at i:354751 original size:60 final size:60
Alignment explanation
Indices: 354682--354871 Score: 239
Period size: 60 Copynumber: 3.2 Consensus size: 60
354672 TCGAATTTGT
*
354682 AAATT-GCAACACATAAGTCAAATTCGCAACGAGATAGTCAAATTCGCAACACAAAAGTC
1 AAATTCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
* * *
354741 AAATTCGCAACACGAT-AGTCAAATTCGCAACGCGA-A-TCTATAAATCGCAACGCAAATTTGT-
1 AAATTCGCAACAC-ATAAGTCAAATTCGCAACGCGATAGTC-A-AATTCGCAACACAAA--AGTC
* *
354802 AAA-TCGCAACACAGATGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
1 AAATTCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
354861 AAATTCGCAAC
1 AAATTCGCAAC
354872 GCGAAATTTC
Statistics
Matches: 111, Mismatches: 9, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
58 4 0.04
59 11 0.10
60 85 0.77
61 7 0.06
62 4 0.04
ACGTcount: A:0.43, C:0.24, G:0.14, T:0.19
Consensus pattern (60 bp):
AAATTCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
Found at i:354900 original size:19 final size:19
Alignment explanation
Indices: 354859--354918 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
354849 AACACAAAAG
*
354859 TCAAATTCGCAACGCGAAATT
1 TCAAATTCGCAAC-TG-AATT
354880 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
*
354899 TCAAATTCGTAACTGAATT
1 TCAAATTCGCAACTGAATT
354918 T
1 T
354919 TTGAATTCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 23 0.62
20 1 0.03
21 13 0.35
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:354903 original size:60 final size:60
Alignment explanation
Indices: 354682--354907 Score: 213
Period size: 60 Copynumber: 3.8 Consensus size: 60
354672 TCGAATTTGT
354682 AAATT-GCAACAC-ATAA-GTCAAATTCGCAACGAGATAGTCAAATTCGCAACACAAAAGTC
1 AAATTCGCAACACGA-AATGTCAAATTCGCAACGA-ATAGTCAAATTCGCAACACAAAAGTC
* * *
354741 AAATTCGCAACACGATA-GTCAAATTCGCAACGCGAATCTA-T-AAA-TCGCAACGCAAATTTGT
1 AAATTCGCAACACGAAATGTCAAATTCGCAA--CGAA--TAGTCAAATTCGCAACACAAA--AGT
354802 -
60 C
* *
354802 AAA-TCGCAACAC-AGATGTCAAATTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTC
1 AAATTCGCAACACGAAATGTCAAATTCGCAACG-AATAGTCAAATTCGCAACACAAAAGTC
* * *
354861 AAATTCGCAACGCGAAATTTCAAATTCGCAACTGAAT-TTCAAATTCG
1 AAATTCGCAACACGAAATGTCAAATTCGCAAC-GAATAGTCAAATTCG
354908 TAACTGAATT
Statistics
Matches: 138, Mismatches: 12, Indels: 33
0.75 0.07 0.18
Matches are distributed among these distances:
57 2 0.01
58 5 0.04
59 14 0.10
60 82 0.59
61 26 0.19
62 7 0.05
63 2 0.01
ACGTcount: A:0.42, C:0.23, G:0.14, T:0.21
Consensus pattern (60 bp):
AAATTCGCAACACGAAATGTCAAATTCGCAACGAATAGTCAAATTCGCAACACAAAAGTC
Found at i:355126 original size:14 final size:15
Alignment explanation
Indices: 355107--355144 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
355097 TCCCCATCTC
355107 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
355121 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
355137 TAATTTTT
1 TAATTTTT
355145 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:355952 original size:24 final size:24
Alignment explanation
Indices: 355894--355940 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
355884 AGTCAGTATT
*
355894 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
355918 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
355941 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:358206 original size:6 final size:6
Alignment explanation
Indices: 358195--358241 Score: 76
Period size: 6 Copynumber: 7.8 Consensus size: 6
358185 AAGTAAAAGG
* *
358195 AAATCA AAATCA AAATCG CAATCA AAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
358242 CCAATCACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.62, C:0.19, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:358592 original size:20 final size:20
Alignment explanation
Indices: 358567--358622 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
358557 AAAATTGCAA
* * *
358567 TGCGAATTTGGCTTTCGCGT
1 TGCGAATTTGACTATCACGT
358587 TGCGAATTTGACTATCACGT
1 TGCGAATTTGACTATCACGT
358607 TGCGAATTTGACTATC
1 TGCGAATTTGACTATC
358623 GCAACGCTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.38
Consensus pattern (20 bp):
TGCGAATTTGACTATCACGT
Found at i:358691 original size:21 final size:20
Alignment explanation
Indices: 358639--358691 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
358629 CTTATTTCGT
* *
358639 ATTGCGAATTTGACTTTCGC
1 ATTGCGAATTTAACTTTCAC
*
358659 GTTGCGAATTTAACTTTCAC
1 ATTGCGAATTTAACTTTCAC
358679 ATTGCGAAATTTA
1 ATTGCG-AATTTA
358692 CATAATTGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (20 bp):
ATTGCGAATTTAACTTTCAC
Found at i:358874 original size:65 final size:65
Alignment explanation
Indices: 358788--358960 Score: 235
Period size: 65 Copynumber: 2.6 Consensus size: 65
358778 TTTAAAAAAC
358788 CAAAGCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATTAA
1 CAAAGCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATC-AATTAA
358853 A
65 A
* *
358854 CAAA-CAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTAAA
1 CAAAGCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAAA
*
358917 CAAATCAACCTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 CAAAGCAA-CTT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
358961 GTGTACCCCA
Statistics
Matches: 97, Mismatches: 2, Indels: 12
0.87 0.02 0.11
Matches are distributed among these distances:
63 11 0.11
64 26 0.27
65 30 0.31
66 4 0.04
68 4 0.04
69 16 0.16
70 6 0.06
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.27
Consensus pattern (65 bp):
CAAAGCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAATTAAA
Found at i:360149 original size:22 final size:22
Alignment explanation
Indices: 360119--360165 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
360109 GATGGAGATA
* *
360119 GACATATTTCACCGGAGATGGG
1 GACAAATTTCACCAGAGATGGG
**
360141 GACAAATTTCGTCAGAGATGGG
1 GACAAATTTCACCAGAGATGGG
360163 GAC
1 GAC
360166 GGATGTCACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.17, G:0.32, T:0.21
Consensus pattern (22 bp):
GACAAATTTCACCAGAGATGGG
Found at i:360313 original size:20 final size:20
Alignment explanation
Indices: 360283--360476 Score: 142
Period size: 20 Copynumber: 9.7 Consensus size: 20
360273 ATTGTGTTTA
*
360283 GCGTTGTGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
*
360303 ACGTTGCGAATTTGACTTTC
1 GCGTTGCGAATTTGACTTTC
* *
360323 GCGTTGTGAATTTGACTTTT
1 GCGTTGCGAATTTGACTTTC
* * **
360343 GTGTTACGAATTTGAAATTC
1 GCGTTGCGAATTTGACTTTC
** * *
360363 AGTATTGCGAATTTAACTTTT
1 -GCGTTGCGAATTTGACTTTC
** * * *
360384 ATGTTGCAAATTTTACTATC
1 GCGTTGCGAATTTGACTTTC
*
360404 GCGTTGCGAATTTGACTATC
1 GCGTTGCGAATTTGACTTTC
*
360424 GCGCTGCGAATTTGACTTAT-
1 GCGTTGCGAATTTGACTT-TC
* *
360444 GTGTTG-GAATTT-ACAAATTC
1 GCGTTGCGAATTTGAC--TTTC
360464 GCGTTGCGAATTT
1 GCGTTGCGAATTT
360477 TGAAAATCGC
Statistics
Matches: 135, Mismatches: 33, Indels: 11
0.75 0.18 0.06
Matches are distributed among these distances:
18 2 0.01
19 7 0.05
20 105 0.78
21 21 0.16
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (20 bp):
GCGTTGCGAATTTGACTTTC
Found at i:360434 original size:81 final size:81
Alignment explanation
Indices: 360290--360438 Score: 190
Period size: 81 Copynumber: 1.8 Consensus size: 81
360280 TTAGCGTTGT
* * * * * * * *
360290 GAATTTGACTTTCACGTTGCGAATTTGACTTTCGCGTTGTGAATTTGACTTTTGTGTTACGAATT
1 GAATTTAACTTTCACGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTATCGCGCTACGAATT
360355 TGAAATTCAGTATTGC
66 TGAAATTCAGTATTGC
* * * *
360371 GAATTTAACTTTTATGTTGCAAATTTTACTATCGCGTTGCGAATTTGACTATCGCGCTGCGAATT
1 GAATTTAACTTTCACGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTATCGCGCTACGAATT
360436 TGA
66 TGA
360439 CTTATGTGTT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 56 1.00
ACGTcount: A:0.23, C:0.15, G:0.20, T:0.42
Consensus pattern (81 bp):
GAATTTAACTTTCACGTTGCAAATTTGACTATCGCGTTGCGAATTTGACTATCGCGCTACGAATT
TGAAATTCAGTATTGC
Found at i:360512 original size:20 final size:20
Alignment explanation
Indices: 360452--360513 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
360442 ATGTGTTGGA
360452 ATTTACAAATTCGCGTTGCG
1 ATTTACAAATTCGCGTTGCG
** * **
360472 AATTTTGAAAATCGCAATGCG
1 -ATTTACAAATTCGCGTTGCG
*
360493 ATTTACATATTCGCGTTGCG
1 ATTTACAAATTCGCGTTGCG
360513 A
1 A
360514 AATTGGAGTT
Statistics
Matches: 30, Mismatches: 11, Indels: 1
0.71 0.26 0.02
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (20 bp):
ATTTACAAATTCGCGTTGCG
Found at i:360545 original size:19 final size:19
Alignment explanation
Indices: 360462--360575 Score: 95
Period size: 19 Copynumber: 5.8 Consensus size: 19
360452 ATTTACAAAT
*
360462 TCGCGTTGCGAATTTTGAAAA
1 TCGCGTTGCGAA-TTT-AAGA
** *
360483 TCGCAATGCG-ATTTACATA
1 TCGCGTTGCGAATTTA-AGA
** *
360502 TTCGCGTTGCGAAATTGGAGT
1 -TCGCGTTGCG-AATTTAAGA
*
360523 TCGCGTTGTGAATTTAAGA
1 TCGCGTTGCGAATTTAAGA
360542 TCGCGTTGCGAATTTAAGA
1 TCGCGTTGCGAATTTAAGA
*
360561 TCGGGTTGCGAATTT
1 TCGCGTTGCGAATTT
360576 GTTGGTCATT
Statistics
Matches: 74, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
18 1 0.01
19 43 0.58
20 18 0.24
21 9 0.12
22 3 0.04
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (19 bp):
TCGCGTTGCGAATTTAAGA
Found at i:367594 original size:17 final size:17
Alignment explanation
Indices: 367574--367665 Score: 87
Period size: 17 Copynumber: 5.3 Consensus size: 17
367564 TTTAACTAAG
367574 TAGTTCATTGATCAAAC
1 TAGTTCATTGATCAAAC
* *
367591 TAGTTCATTCGA-GATTAC
1 TAGTTCATT-GATCA-AAC
* *
367609 AAGTTCATTGAACAAAC
1 TAGTTCATTGATCAAAC
* *
367626 TTAGTTCATTAATTAAAC
1 -TAGTTCATTGATCAAAC
*
367644 TAGTTCATTCATCAAAC
1 TAGTTCATTGATCAAAC
367661 TAGTT
1 TAGTT
367666 AATTTATTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
17 34 0.57
18 26 0.43
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (17 bp):
TAGTTCATTGATCAAAC
Found at i:367616 original size:35 final size:33
Alignment explanation
Indices: 367575--367675 Score: 105
Period size: 35 Copynumber: 2.9 Consensus size: 33
367565 TTAACTAAGT
367575 AGTTCATTGATCAAACTAGTTCATTCGAGATT-ACA
1 AGTTCATTGATCAAACTAGTTCATT--A-ATTAACA
* *
367610 AGTTCATTGAACAAACTTAGTTCATTAATTAAACT
1 AGTTCATTGATCAAAC-TAGTTCATTAATT-AACA
* * *
367645 AGTTCATTCATCAAACTAGTTAATTTATTAA
1 AGTTCATTGATCAAACTAGTTCATTAATTAA
367676 ACAAACTCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
33 5 0.09
34 12 0.21
35 31 0.54
36 9 0.16
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (33 bp):
AGTTCATTGATCAAACTAGTTCATTAATTAACA
Found at i:367677 original size:17 final size:17
Alignment explanation
Indices: 367574--367677 Score: 70
Period size: 17 Copynumber: 6.0 Consensus size: 17
367564 TTTAACTAAG
* *
367574 TAGTTCATTGATCAAAC
1 TAGTTCATTAATTAAAC
367591 TAGTTCATTCGAGATT--AC
1 TAGTTCATT--A-ATTAAAC
* *
367609 AAGTTCATTGAA-CAAAC
1 TAGTTCATT-AATTAAAC
367626 TTAGTTCATTAATTAAAC
1 -TAGTTCATTAATTAAAC
* *
367644 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
367661 TAGTTAATTTATTAAAC
1 TAGTTCATTAATTAAAC
367678 AAACTCTTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
16 1 0.01
17 44 0.64
18 22 0.32
20 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:368115 original size:20 final size:20
Alignment explanation
Indices: 368090--368137 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
368080 ATCATCTAAA
*
368090 TTCAAGGGTTGTCCATATTC
1 TTCAAGGGTTCTCCATATTC
368110 TTCAAGGGTTCTCCATATTC
1 TTCAAGGGTTCTCCATATTC
368130 TTCAAGGG
1 TTCAAGGG
368138 AGCATGTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
TTCAAGGGTTCTCCATATTC
Found at i:369414 original size:30 final size:32
Alignment explanation
Indices: 369363--369424 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
369353 CTAGCATACA
* *
369363 TATCTTTCTTTGTATTTTTC-TT-TTTCCATT
1 TATCTTTCTTAGTATTATTCTTTATTTCCATT
369393 TATCTTT-TTAGTCATTATTCTTTATTTCCATT
1 TATCTTTCTTAGT-ATTATTCTTTATTTCCATT
369425 GAAAGCATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 4 0.15
30 13 0.48
31 2 0.07
32 8 0.30
ACGTcount: A:0.15, C:0.16, G:0.03, T:0.66
Consensus pattern (32 bp):
TATCTTTCTTAGTATTATTCTTTATTTCCATT
Found at i:369513 original size:47 final size:46
Alignment explanation
Indices: 369462--369553 Score: 121
Period size: 47 Copynumber: 2.0 Consensus size: 46
369452 AACATTATGT
* *
369462 ATTTTCACTTATGGAAACCGTTCATGCCTTTTTATATACTATTATAC
1 ATTTTCACTTATGGAAACCGTTCATG-CTTTTTATACACCATTATAC
* * * *
369509 ATTTTCATTTATGGCATCCTTTCATGCTTTTTATACACCATTATA
1 ATTTTCACTTATGGAAACCGTTCATGCTTTTTATACACCATTATA
369554 TGTTGTTATA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 17 0.44
47 22 0.56
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.47
Consensus pattern (46 bp):
ATTTTCACTTATGGAAACCGTTCATGCTTTTTATACACCATTATAC
Found at i:369655 original size:68 final size:68
Alignment explanation
Indices: 369578--369991 Score: 513
Period size: 68 Copynumber: 6.1 Consensus size: 68
369568 TAGTATTTTA
* * * * **
369578 CTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGTCAAATGCACAGCAA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
369643 GGC
66 GGC
* * * * * *
369646 TTCAAAGGCACTTAGTCTTTCATCTAACTCGCATAATTGACACCTTTCTTTCAAATGAACGGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
369711 GGC
66 GGC
* * * * * *
369714 ATCGAAGGCACTTAGCCTTTCACCTAACTGGCATAATTGACACCTTTCTATCGAATGCACAATTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
369779 GGC
66 GGC
* * * *
369782 CTCAAAGGCACTTAGCGTTTCATCTAATTGTCATAATTGACACCTTTCTGTCAAATGCACAATTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
369847 GGC
66 GGC
* * * * * * *
369850 CTTAAAGGAACTTATCCTTTAATCTAATTGGAATAATTGACACCTTTCTGTCAAATGCACAGTGA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
369915 GGC
66 GGC
* * * * *
369918 CTAAAAGGCACTTAGCCTTTCATCTAATTGGCATAATTGACACTTTTCTATAAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
*
369983 GGT
66 GGC
369986 CTCAAA
1 CTCAAA
369992 TATTTTATTT
Statistics
Matches: 297, Mismatches: 49, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 297 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
GGC
Found at i:370397 original size:59 final size:59
Alignment explanation
Indices: 370262--370777 Score: 678
Period size: 59 Copynumber: 8.8 Consensus size: 59
370252 ACTCATATTT
* * * *
370262 CCCATATGGAAATTCATACATTTAGTATGAATCTCTTAACAATTTT--CACACAAAGTGT
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAAC-ATTTTAGCACACAAAGTGC
* * **
370320 CCAATCCATAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGC
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGC
* * * *
370379 TCAATACGGAAATTCATACACTTAGTACGAATTTCTTAACATTTTAGCACACAAAATGC
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGC
** ** *
370438 CTAATACAAAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGAGC
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGC
* * * *
370497 CCCATACGAAAATTCATACACTTAGTATAAATTTCTTAACATTTTAGCATACAAAGCGC
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGC
* *
370556 CCCATATGGAAATTCATACACTTAGTATGATTTTCTTAACATTTTAGCACACAAAGTGC
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGC
* ** * *
370615 CCCGTATAGAAATTTATACACTTAGTATGAATTT-TATAACATTCTAGCACACAAAGTGC
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCT-TAACATTTTAGCACACAAAGTGC
* *
370674 CCCATACGGAAATTTATACACCTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGC
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGC
* ** * *
370733 CTCATACAAAAATTCATAAACTTAATATGAATTTCTTAACATTTT
1 CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTT
370778 TCACACTTAG
Statistics
Matches: 404, Mismatches: 50, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
57 5 0.01
58 34 0.08
59 364 0.90
60 1 0.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (59 bp):
CCCATACGGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGC
Found at i:371231 original size:20 final size:21
Alignment explanation
Indices: 371206--371274 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 21
371196 CAATGTTACC
* *
371206 TGGTATCATTACT-CTTACTA
1 TGGTATCAATACTACATACTA
371226 TGGTATCAATACTACCATACTA
1 TGGTATCAATACTA-CATACTA
* *
371248 TGGTATCGATACTACCATACGA
1 TGGTATCAATACTA-CATACTA
371270 TGGTA
1 TGGTA
371275 CCGATACCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.28
22 31 0.72
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (21 bp):
TGGTATCAATACTACATACTA
Found at i:371249 original size:22 final size:22
Alignment explanation
Indices: 371221--371274 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
371211 TCATTACTCT
371221 TACTATGGTATCAATACTACCA
1 TACTATGGTATCAATACTACCA
*
371243 TACTATGGTATCGATACTACCA
1 TACTATGGTATCAATACTACCA
*
371265 TACGATGGTA
1 TACTATGGTA
371275 CCGATACCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (22 bp):
TACTATGGTATCAATACTACCA
Found at i:371279 original size:22 final size:22
Alignment explanation
Indices: 371225--371281 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
371215 TACTCTTACT
* *
371225 ATGGTATCAATACTACCATACT
1 ATGGTATCGATACTACCATACG
371247 ATGGTATCGATACTACCATACG
1 ATGGTATCGATACTACCATACG
*
371269 ATGGTACCGATAC
1 ATGGTATCGATAC
371282 CCCCTTTCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (22 bp):
ATGGTATCGATACTACCATACG
Found at i:371285 original size:117 final size:113
Alignment explanation
Indices: 371123--371374 Score: 296
Period size: 116 Copynumber: 2.2 Consensus size: 113
371113 GTATCGATAC
* * * *
371123 TACTACC-C-TGGTATCGATACTTCTATACTATGGTACCGATACCCCC-TTCTGGTATCGATATC
1 TACTACCTCATGGTATCGATACTACCATACGATGGTACCGATACCCCCTTTC-GGTATCGAT-CC
* * *
371185 AATTTTAGGTTCAATGTTACCTGGTATC-ATTACTCTTACTATGGTATCAA
64 AATTTTAGCTTCAATGATACCTGGTATCGA-TACCCTTACTATGGTATCAA
371235 TACTACCATACTATGGTATCGATACTACCATACGATGGTACCGATACCCCCTTTCGGTATCGATC
1 TACTACC-T-C-ATGGTATCGATACTACCATACGATGGTACCGATACCCCCTTTCGGTATCGATC
* ** * * *
371300 CTATTTTAGCTTTGATGATGCTTGGTATCGATACCCTTACTATGGTATCGA
63 CAATTTTAGCTTCAATGATACCTGGTATCGATACCCTTACTATGGTATCAA
371351 TACTACCTCATCGGTATCGATACT
1 TACTACCTCAT-GGTATCGATACT
371375 GATTGATCAG
Statistics
Matches: 119, Mismatches: 13, Indels: 14
0.82 0.09 0.10
Matches are distributed among these distances:
112 7 0.06
113 2 0.02
114 13 0.11
115 2 0.02
116 47 0.39
117 45 0.38
118 3 0.03
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (113 bp):
TACTACCTCATGGTATCGATACTACCATACGATGGTACCGATACCCCCTTTCGGTATCGATCCAA
TTTTAGCTTCAATGATACCTGGTATCGATACCCTTACTATGGTATCAA
Found at i:371366 original size:20 final size:20
Alignment explanation
Indices: 371343--371396 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
371333 CCCTTACTAT
371343 GGTATCGATACTACCTCATC
1 GGTATCGATACTACCTCATC
* *
371363 GGTATCGATACTGA-TTGATC
1 GGTATCGATACT-ACCTCATC
*
371383 AGTATCGATACTAC
1 GGTATCGATACTAC
371397 TTAGCTAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 27 0.93
21 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
GGTATCGATACTACCTCATC
Found at i:375651 original size:203 final size:204
Alignment explanation
Indices: 375354--375872 Score: 722
Period size: 203 Copynumber: 2.5 Consensus size: 204
375344 TAGTATTTTA
* * * * *
375354 CTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACACTTTTCTGTCAAATGCACAACAA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGCTA
* * * * *
375419 GGCGTCAAAGGAACTTAGCCTTTCATCTAAGT-CATATAATTGACACCTTTGTATAAAATGCACA
66 GGCCTCAAAGGCACTTAGCCTTTCATCTAACTGCA-ATAATTGACACATTTCTATAAAATGCACA
*
375483 GTTAGGCATCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTG-ACACTTTCTATCAAATGC
130 GTTAGGCATCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGAACACTTTCCATCAAATGC
375547 ACAGCTAAGC
195 ACAGCTAAGC
* *
375557 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGTACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGCTA
* * * *
375622 GGCCTCAAAGGCTCTTAGCCTTTCATCTAACTGGAATAATTGACACATTTCTGTCAAATGCACAG
66 GGCCTCAAAGGCACTTAGCCTTTCATCTAACTGCAATAATTGACACATTTCTATAAAATGCACAG
* * * * *
375687 TTAGGCCTCAAAGGCACTTATCCTTTCATCTAACTGGCATAATTGATACCCTTTCCATCAAATGT
131 TTAGGCATCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGA-ACACTTTCCATCAAATGC
* *
375752 ACAGTTAGGC
195 ACAGCTAAGC
* * *
375762 CTCAAAGGCACTTAGCCTTTAATCTAACTGGCATAATTGACACCTTTT-TGTCAAATACACAGGT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACA-CTTTTCTGTCAAATGCACAGCT
*
375826 AGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGC-ATTATTGACAC
65 AGGCCTCAAAGGCACTTAGCCTTTCATCTAACT-GCAATAATTGACAC
375873 CTTCATGTTC
Statistics
Matches: 280, Mismatches: 31, Indels: 8
0.88 0.10 0.03
Matches are distributed among these distances:
203 154 0.55
204 1 0.00
205 119 0.43
206 6 0.02
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (204 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGCACAGCTA
GGCCTCAAAGGCACTTAGCCTTTCATCTAACTGCAATAATTGACACATTTCTATAAAATGCACAG
TTAGGCATCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGAACACTTTCCATCAAATGCA
CAGCTAAGC
Found at i:375804 original size:137 final size:135
Alignment explanation
Indices: 375354--375875 Score: 729
Period size: 137 Copynumber: 3.8 Consensus size: 135
375344 TAGTATTTTA
* * * * *
375354 CTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACACTTTTCTGTCAAATGCACAACAA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACAC-TTTCTGTCAAATGCACAGCTA
* * * *** * * *
375419 GGCGTCAAAGGAACTTAGCCTTTCATCTAAGTCATATAATTGACACCTTTGTATAAAATGCACAG
65 GGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGTACAG
375484 TTAGGC
130 TTAGGC
* * * *
375490 ATCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACACTTTCTATCAAATGCACAGCTAA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTCTGTCAAATGCACAGCTAG
* *
375555 GCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGTACAGT
66 GCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGTACAGT
375620 TAGGC
131 TAGGC
* * *
375625 CTCAAAGGCTCTTAGCCTTTCATCTAACTGGAATAATTGACACATTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACAC-TTTCTGTCAAATGCACAGCTA
* * *
375690 GGCCTCAAAGGCACTTATCCTTTCATCTAACTGGCATAATTGATACCCTTTCCATCAAATGTACA
65 GGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACA-CCTTTCTATCAAATGTACA
375755 GTTAGGC
129 GTTAGGC
* * * *
375762 CTCAAAGGCACTTAGCCTTTAATCTAACTGGCATAATTGACACCTTTTTGTCAAATACACAGGTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACA-CTTTCTGTCAAATGCACAGCTA
*
375827 GGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATTATTGACACCTT
65 GGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTT
375876 CATGTTCATT
Statistics
Matches: 342, Mismatches: 41, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
135 116 0.34
136 103 0.30
137 122 0.36
138 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (135 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTCTGTCAAATGCACAGCTAG
GCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGTACAGT
TAGGC
Found at i:375873 original size:68 final size:68
Alignment explanation
Indices: 375354--375875 Score: 704
Period size: 68 Copynumber: 7.7 Consensus size: 68
375344 TAGTATTTTA
* * * * ***
375354 CTCAAAGGCATTTAACCTTTCATCTAACTGGCATGATTGACACTTTTCTGTCAAATGCACAACAA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
375419 GGC
66 GGC
* * * *** * * *
375422 GTCAAAGGAACTTAGCCTTTCATCTAAGTCATATAATTGACACCTTTGTATAAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
375487 GGC
66 GGC
* * * *
375490 ATCAAAGGCACTTAGCCTTTCATCTAACTAGCATAATTGACA-CTTTCTATCAAATGCACAGCTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
*
375554 AGC
66 GGC
* *
375557 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACTTTTCTGTCAAATGTACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
375622 GGC
66 GGC
* * *
375625 CTCAAAGGCTCTTAGCCTTTCATCTAACTGGAATAATTGACACATTTCTGTCAAATGCACAGTTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
375690 GGC
66 GGC
* * ** *
375693 CTCAAAGGCACTTATCCTTTCATCTAACTGGCATAATTGATACCCTTTCCATCAAATGTACAGTT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACA-CCTTTCTGTCAAATGCACAGTT
375758 AGGC
65 AGGC
* * * *
375762 CTCAAAGGCACTTAGCCTTTAATCTAACTGGCATAATTGACACCTTTTTGTCAAATACACAGGTA
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
375827 GGC
66 GGC
*
375830 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATTATTGACACCTT
1 CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTT
375876 CATGTTCATT
Statistics
Matches: 396, Mismatches: 56, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
67 61 0.15
68 274 0.69
69 61 0.15
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (68 bp):
CTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAGTTA
GGC
Found at i:376153 original size:59 final size:59
Alignment explanation
Indices: 376025--376421 Score: 523
Period size: 59 Copynumber: 6.8 Consensus size: 59
376015 TTTCCCATAT
* * *
376025 GGAAATTCATACATTTAGTATGAATCTCTTAACAATTTT--CACACAAAGTGCCCAATCC
1 GGAAATTCATACACTTAGTATGAATTTCTTAAC-ATTTTAGCACACAAAGTGCCCAATAC
* * * *
376083 TGAAATTCATACACTTAGAATGAATTTCTTAACATTTTAGTACACAAAGTGCCTAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
* *
376142 GGAAATTCATACACTTAGTATGAATTTCTTAACATGTTAGCACACAAAGCGCCCAATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
* * * * *
376201 GGAAATTCATTCACTTGGTATGAATTTTTTAACATTTTGGCACACAAAGTGCCCCATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
* * * * *
376260 GAAAATTTATACAATTAGTACGAATTTCTTAACATTTTAGCACACAAAGTGCCCCATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
* *
376319 GCAAATTCATACACTTAGTACGAATTTCTTAACATTTTAGCACACAAAGTGACCC-ATAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTG-CCCAATAC
* * * *
376378 AGAAATTCATACACTTAATATAAAATTCTTAACATTTT-GCACAC
1 GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACAC
376422 TTAGTGCAAT
Statistics
Matches: 299, Mismatches: 37, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
57 5 0.02
58 35 0.12
59 256 0.86
60 3 0.01
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.31
Consensus pattern (59 bp):
GGAAATTCATACACTTAGTATGAATTTCTTAACATTTTAGCACACAAAGTGCCCAATAC
Found at i:377772 original size:15 final size:15
Alignment explanation
Indices: 377752--377785 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
377742 ATATATTTCA
377752 TTTTATCTTTTATTT
1 TTTTATCTTTTATTT
377767 TTTTATCTTTTATTT
1 TTTTATCTTTTATTT
377782 TTTT
1 TTTT
377786 GTATTGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTATCTTTTATTT
Found at i:377805 original size:32 final size:31
Alignment explanation
Indices: 377759--377829 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 31
377749 TCATTTTATC
* *
377759 TTTTATTTTTTTATC-T-TTTATTTTTTTGTA
1 TTTTATTTTATTATCTTCTTTA-TTTTATGTA
377789 TTGTTATTGTTATTATCTTCTTTATTTTATGTA
1 TT-TTATT-TTATTATCTTCTTTATTTTATGTA
377822 TTTTATTT
1 TTTTATTT
377830 ATATATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
30 2 0.06
31 6 0.17
32 12 0.34
33 11 0.31
34 4 0.11
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75
Consensus pattern (31 bp):
TTTTATTTTATTATCTTCTTTATTTTATGTA
Found at i:389618 original size:110 final size:110
Alignment explanation
Indices: 389424--389622 Score: 265
Period size: 110 Copynumber: 1.8 Consensus size: 110
389414 GTTTCATAGC
* * * * *
389424 CAATTTTAACTTCACAACGAGGGATATTGGACTCAAGATAACACAAACTCAACTTCACAACGAAG
1 CAATTTCAACTACACAACGAAGGATATTGAACTCAAGACAACACAAACTCAACTTCACAACGAAG
* *
389489 GGGTAACTGATTTTCAACAAACAACTTTTCAGTTTCATTCAGAGT
66 GGGCAACTGATGTTCAACAAACAACTTTTCAGTTTCATTCAGAGT
* * * *
389534 CAATTTCAACTACACAGCGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCACAGCGAAG
1 CAATTTCAACTACACAACGAAGGATATTGAACTCAAGACAACACAAACTCAACTTCACAACGAAG
**
389599 GGGCGGCTGACTGTT-AACAAACAA
66 GGGCAACTGA-TGTTCAACAAACAA
389623 TTTCCAGAGC
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
110 72 0.96
111 3 0.04
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (110 bp):
CAATTTCAACTACACAACGAAGGATATTGAACTCAAGACAACACAAACTCAACTTCACAACGAAG
GGGCAACTGATGTTCAACAAACAACTTTTCAGTTTCATTCAGAGT
Found at i:390402 original size:13 final size:13
Alignment explanation
Indices: 390384--390410 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
390374 TTTTCGTTCC
390384 ACGAAAAATGACA
1 ACGAAAAATGACA
390397 ACGAAAAATGACA
1 ACGAAAAATGACA
390410 A
1 A
390411 AGAGGGGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.15, G:0.15, T:0.07
Consensus pattern (13 bp):
ACGAAAAATGACA
Found at i:391119 original size:44 final size:41
Alignment explanation
Indices: 391071--391160 Score: 96
Period size: 44 Copynumber: 2.1 Consensus size: 41
391061 TTGGCTATTT
391071 TTTTATA-TATTTTTC-TATATTCTATTATATATATATATATATAC
1 TTTTATATTATTTTTCATATA-TC-ATTAT-TAT-TA-ATATATAC
* *
391115 TTTTA-ATTCTTTTTCATATATCATTATTATTAATATATAT
1 TTTTATATTATTTTTCATATATCATTATTATTAATATATAC
391155 TTTTAT
1 TTTTAT
391161 TACTATAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
40 12 0.29
41 2 0.05
42 3 0.07
43 6 0.15
44 14 0.34
45 4 0.10
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (41 bp):
TTTTATATTATTTTTCATATATCATTATTATTAATATATAC
Found at i:391162 original size:16 final size:17
Alignment explanation
Indices: 391130--391167 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
391120 ATTCTTTTTC
391130 ATATATCATTATTATTA
1 ATATATCATTATTATTA
*
391147 ATATAT-ATTTTTATTA
1 ATATATCATTATTATTA
*
391163 CTATA
1 ATATA
391168 ATTATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (17 bp):
ATATATCATTATTATTA
Found at i:391227 original size:16 final size:16
Alignment explanation
Indices: 391206--391238 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
391196 ATATATTTCA
*
391206 TTTTATCTTTTATTTT
1 TTTTATCTTCTATTTT
391222 TTTTATCTTCTATTTT
1 TTTTATCTTCTATTTT
391238 T
1 T
391239 ATTTTGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATCTTCTATTTT
Found at i:391254 original size:35 final size:32
Alignment explanation
Indices: 391213--391287 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 32
391203 TCATTTTATC
* * *
391213 TTTTATTTTTTTTATCTTCTATTTTTATTTTGTA
1 TTTTATTTTTATTATCTTCT-TTATT-TTATGTA
*
391247 TTGTTATTGTTATTATCTTCTTTATTTTATGTA
1 TT-TTATTTTTATTATCTTCTTTATTTTATGTA
391280 TTTTATTT
1 TTTTATTT
391288 ATATATATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 5 0.14
33 8 0.23
34 6 0.17
35 16 0.46
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (32 bp):
TTTTATTTTTATTATCTTCTTTATTTTATGTA
Found at i:391302 original size:31 final size:31
Alignment explanation
Indices: 391234--391308 Score: 77
Period size: 32 Copynumber: 2.4 Consensus size: 31
391224 TTATCTTCTA
391234 TTTTTA-TTTTGTATTGTTATTGTTATTATC
1 TTTTTATTTTTGTATTGTTATTGTTATTATC
391264 TTCTTTATTTTATGTATT-TTATT-TATATATAT-
1 TT-TTTATTTT-TGTATTGTTATTGT-TAT-TATC
*
391296 TTTTTATATTTGT
1 TTTTTATTTTTGT
391309 TTTTGTGCCT
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
30 5 0.13
31 12 0.31
32 13 0.33
33 9 0.23
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.71
Consensus pattern (31 bp):
TTTTTATTTTTGTATTGTTATTGTTATTATC
Found at i:404026 original size:35 final size:34
Alignment explanation
Indices: 403982--404086 Score: 95
Period size: 35 Copynumber: 3.0 Consensus size: 34
403972 AAGGATATCA
*
403982 ATATATTTTAGAATATTTAAATTAAATTATTTTATT
1 ATAT-TTTTA-AATATTTAAATTAAAATATTTTATT
* * * * *
404018 ATCTTTTTAAAT-TTAAAGATTAAAATGTTATCAAT
1 ATATTTTTAAATATTTAA-ATTAAAATATT-TTATT
*
404053 ATATTTTTAAATATTTCAAATTAAAATATATTAT
1 ATATTTTTAAATATTT-AAATTAAAATATTTTAT
404087 CTATTAAGAT
Statistics
Matches: 53, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
33 4 0.08
34 12 0.23
35 21 0.40
36 14 0.26
37 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (34 bp):
ATATTTTTAAATATTTAAATTAAAATATTTTATT
Found at i:416235 original size:12 final size:12
Alignment explanation
Indices: 416218--416242 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
416208 GTTGCCCTAT
416218 ATCCTCATGAGG
1 ATCCTCATGAGG
416230 ATCCTCATGAGG
1 ATCCTCATGAGG
416242 A
1 A
416243 GCATCACCAA
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:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (12 bp):
ATCCTCATGAGG
Found at i:422530 original size:26 final size:28
Alignment explanation
Indices: 422470--422530 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 28
422460 TCTTAAATAT
*
422470 CCAAATAACCAAATAAAAACATTCAAGTA
1 CCAAATAA-CAAATAAAAACATTCAAGGA
*
422499 CTAAATAA-AAAT-AAAACA-TCAAAGGA
1 CCAAATAACAAATAAAAACATTC-AAGGA
422525 CCAAAT
1 CCAAAT
422531 GTTATAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 2 0.07
26 15 0.54
27 4 0.14
29 7 0.25
ACGTcount: A:0.61, C:0.18, G:0.05, T:0.16
Consensus pattern (28 bp):
CCAAATAACAAATAAAAACATTCAAGGA
Found at i:426382 original size:26 final size:26
Alignment explanation
Indices: 426346--426421 Score: 143
Period size: 26 Copynumber: 2.9 Consensus size: 26
426336 AGTGCATATC
426346 GTGGGCACGACCTTATGTGTATTATG
1 GTGGGCACGACCTTATGTGTATTATG
426372 GTGGGCACGACCTTATGTGTATTATG
1 GTGGGCACGACCTTATGTGTATTATG
*
426398 GTGGGCACAACCTTATGTGTATTA
1 GTGGGCACGACCTTATGTGTATTA
426422 GCACTTCGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (26 bp):
GTGGGCACGACCTTATGTGTATTATG
Found at i:427827 original size:15 final size:15
Alignment explanation
Indices: 427807--427840 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
427797 AATTTTCAAA
427807 TCAAAATTTTATTTT
1 TCAAAATTTTATTTT
427822 TCAAAATTTTATTTT
1 TCAAAATTTTATTTT
427837 TCAA
1 TCAA
427841 TTTAGAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (15 bp):
TCAAAATTTTATTTT
Found at i:433299 original size:21 final size:22
Alignment explanation
Indices: 433275--433348 Score: 82
Period size: 21 Copynumber: 3.5 Consensus size: 22
433265 CCAGGAGGGT
*
433275 ATCGATTCCCCT-ATGGGGGGA
1 ATCGATTCCCCTCAAGGGGGGA
* *
433296 ATCGGTTCCCCTTCAAAGGGGGA
1 ATCGATTCCCC-TCAAGGGGGGA
*
433319 ATCGGTT-CCCTCAAGGGGGG-
1 ATCGATTCCCCTCAAGGGGGGA
433339 ATCGATTCCC
1 ATCGATTCCC
433349 TCTGCACCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 6 0.13
21 21 0.47
22 4 0.09
23 14 0.31
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.23
Consensus pattern (22 bp):
ATCGATTCCCCTCAAGGGGGGA
Found at i:433336 original size:20 final size:21
Alignment explanation
Indices: 433290--433350 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
433280 TTCCCCTATG
433290 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
433313 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
433333 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
433351 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:465551 original size:23 final size:23
Alignment explanation
Indices: 465500--465552 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
465490 AAGTATATAC
* *
465500 TAATATGTAAATGCATAATTATA
1 TAATATGTAAATGCATAATAAGA
465523 TCAATATGT-AATGCATAAATAAGA
1 T-AATATGTAAATGCAT-AATAAGA
465547 TAATAT
1 TAATAT
465553 ATGATGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (23 bp):
TAATATGTAAATGCATAATAAGA
Found at i:475271 original size:16 final size:16
Alignment explanation
Indices: 475245--475316 Score: 85
Period size: 16 Copynumber: 4.6 Consensus size: 16
475235 TTTGATTTGC
*
475245 TTTTATTTTTCTCTTT
1 TTTTCTTTTTCTCTTT
* *
475261 TCTTCTTTTTCTTTTT
1 TTTTCTTTTTCTCTTT
475277 TTTTCTTTTT-T-TTT
1 TTTTCTTTTTCTCTTT
*
475291 TTTTCTTTTTCCTTTTT
1 TTTTCTTTTT-CTCTTT
475308 TTTTCTTTT
1 TTTTCTTTT
475317 CTTTTGCACT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
14 13 0.27
15 1 0.02
16 23 0.47
17 12 0.24
ACGTcount: A:0.01, C:0.14, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTCTTTTTCTCTTT
Found at i:475277 original size:24 final size:24
Alignment explanation
Indices: 475250--475321 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 24
475240 TTTGCTTTTA
*
475250 TTTTTCTCTTTTCTTCTTTTTCTT
1 TTTTTCTCTTTTTTTCTTTTTCTT
* *
475274 TTTTTTTCTTTTTTTTTTTTTC-T
1 TTTTTCTCTTTTTTTCTTTTTCTT
* *
475297 TTTTCCTTTTTTTTTC-TTTTCTT
1 TTTTTCTCTTTTTTTCTTTTTCTT
475320 TT
1 TT
475322 GCACTTAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 5 0.12
23 16 0.40
24 19 0.47
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (24 bp):
TTTTTCTCTTTTTTTCTTTTTCTT
Found at i:475299 original size:30 final size:31
Alignment explanation
Indices: 475251--475321 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
475241 TTGCTTTTAT
475251 TTTTCTCTTTTCTTCTTTTT-CTTTTTTTTTC
1 TTTTCT-TTTTCTTCTTTTTCCTTTTTTTTTC
* *
475282 TTTTTTTTTTTTTCTTTTTCCTTTTTTTTTC
1 TTTTCTTTTTCTTCTTTTTCCTTTTTTTTTC
475313 TTTTCTTTT
1 TTTTCTTTT
475322 GCACTTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 12 0.33
31 24 0.67
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (31 bp):
TTTTCTTTTTCTTCTTTTTCCTTTTTTTTTC
Found at i:475307 original size:7 final size:7
Alignment explanation
Indices: 475250--475321 Score: 67
Period size: 7 Copynumber: 10.4 Consensus size: 7
475240 TTTGCTTTTA
475250 TTTTTCT
1 TTTTTCT
*
475257 CTTTTCT
1 TTTTTCT
*
475264 TCTTT-T
1 TTTTTCT
*
475270 TCTTT-T
1 TTTTTCT
475276 TTTTTCT
1 TTTTTCT
*
475283 TTTTTTT
1 TTTTTCT
475290 TTTTTCT
1 TTTTTCT
*
475297 TTTTCCT
1 TTTTTCT
*
475304 TTTTTTT
1 TTTTTCT
475311 TCTTTTCT
1 T-TTTTCT
475319 TTT
1 TTT
475322 GCACTTAAAT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
6 11 0.21
7 36 0.68
8 6 0.11
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:475321 original size:10 final size:10
Alignment explanation
Indices: 475256--475321 Score: 64
Period size: 10 Copynumber: 6.6 Consensus size: 10
475246 TTTATTTTTC
*
475256 TCTTTTCTTC
1 TCTTTTCTTT
475266 T-TTTTCTTT
1 TCTTTTCTTT
*
475275 TTTTTTCTTT
1 TCTTTTCTTT
*
475285 T-TTTTTTTT
1 TCTTTTCTTT
475294 TCTTTTTCCTTT
1 TC-TTTT-CTTT
*
475306 TTTTTTCTTT
1 TCTTTTCTTT
475316 TCTTTT
1 TCTTTT
475322 GCACTTAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
9 16 0.34
10 19 0.40
11 8 0.17
12 4 0.09
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TCTTTTCTTT
Found at i:476417 original size:17 final size:17
Alignment explanation
Indices: 476391--476424 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
476381 TAAGGTATGC
476391 ATGCTAAACATAAACAT
1 ATGCTAAACATAAACAT
* *
476408 ATGCTTAACATGAACAT
1 ATGCTAAACATAAACAT
476425 GAACATGTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.18, G:0.09, T:0.26
Consensus pattern (17 bp):
ATGCTAAACATAAACAT
Found at i:478919 original size:2 final size:2
Alignment explanation
Indices: 478912--478939 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
478902 TTTATTAATT
478912 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
478940 AGATATTTAT
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:479242 original size:149 final size:146
Alignment explanation
Indices: 478937--479242 Score: 318
Period size: 149 Copynumber: 2.0 Consensus size: 146
478927 ATATATATAT
* * *
478937 ATAAGATATTTATTTATTTAAAAATATCAGAAAATGACTTCTAGGTGCTTTAAGATAACTCTTTC
1 ATAA-ATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGTGCTTTAAGATAACCCTTTC
*
479002 CTTAATATTAAAAATAAATAAATATTAATAAAACATTTATCTAAAAATAATTAAAAAATATATTA
65 CTTAATATTAAAAATAAAT-AATATTAATAAAACATTTATCTAAAAATAATTAAAAAAGATATTA
* ***
479067 ATATATATAATTTATAAA
129 ATAGATATAACAAATAAA
* *
479085 AGTAAAATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGCTTTAAGACT-GCCCT
1 A-T-AAATATTTATTTATTTAAAAATATCAGAAAAT-GACATCCAGGTGCTTTAAGA-TAACCCT
* * *
479149 TT-CTTAATATTGAAAAATAAAT-ATATTAA-AATACGTTTATTTATAAAATTAAATTTATAAAT
62 TTCCTTAATATT-AAAAATAAATAATATTAATAAAACATTTATCTA-AAAA-T-AA-TTA-AAA-
* *
479211 AGGATTTTAATAGA-A-AACAAATAAA
120 AAGATATTAATAGATATAACAAATAAA
479236 ATAAATA
1 ATAAATA
479243 AATATTATTT
Statistics
Matches: 132, Mismatches: 15, Indels: 21
0.79 0.09 0.12
Matches are distributed among these distances:
147 11 0.08
148 12 0.09
149 46 0.35
150 37 0.28
151 12 0.09
152 4 0.03
153 10 0.08
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (146 bp):
ATAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAGGTGCTTTAAGATAACCCTTTCC
TTAATATTAAAAATAAATAATATTAATAAAACATTTATCTAAAAATAATTAAAAAAGATATTAAT
AGATATAACAAATAAA
Found at i:479820 original size:8 final size:8
Alignment explanation
Indices: 479807--479837 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
479797 ATATTTATTA
479807 TATTTTTT
1 TATTTTTT
479815 TATTTTTT
1 TATTTTTT
*
479823 TATTATTT
1 TATTTTTT
479831 TATTTTT
1 TATTTTT
479838 AGATATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
TATTTTTT
Found at i:480733 original size:36 final size:36
Alignment explanation
Indices: 480686--480758 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
480676 AGCTATGCAC
* * *
480686 ACAAATATCCTGTTATATTAATACCAAAAGTATTCT
1 ACAAAGATCCTGTTAGATTAATACCAAAAGCATTCT
*
480722 ACAAAGATCCTGTTAGATTGATACCAAAAGCATTCT
1 ACAAAGATCCTGTTAGATTAATACCAAAAGCATTCT
480758 A
1 A
480759 TGGTAAGAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.32
Consensus pattern (36 bp):
ACAAAGATCCTGTTAGATTAATACCAAAAGCATTCT
Found at i:481277 original size:43 final size:44
Alignment explanation
Indices: 481210--481293 Score: 116
Period size: 43 Copynumber: 1.9 Consensus size: 44
481200 TGGCTTTAGA
* * *
481210 GAAGTTAGGAGGGAAAGTTATCCCCTATATGT-AAAGTTTTGTT
1 GAAGTTAGGACGGAAAGATATCCCCTACATGTAAAAGTTTTGTT
* *
481253 GAAGTTAGGACTGAAAGATGTCCCCTACATGTAAAAGTTTT
1 GAAGTTAGGACGGAAAGATATCCCCTACATGTAAAAGTTTT
481294 ATTTGATGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
43 27 0.77
44 8 0.23
ACGTcount: A:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (44 bp):
GAAGTTAGGACGGAAAGATATCCCCTACATGTAAAAGTTTTGTT
Found at i:488412 original size:73 final size:73
Alignment explanation
Indices: 488291--488510 Score: 352
Period size: 73 Copynumber: 3.0 Consensus size: 73
488281 ATTTTCAAAT
* **
488291 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAACTGCGTCTCGCTTGAGACAGTTTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTAGTCTCGCTTGAGACAGTTTCA
488356 CTTGAAAC
66 CTTGAAAC
* * *
488364 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTTGTCTCACTTGAGACAGTGTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTAGTCTCGCTTGAGACAGTTTCA
*
488429 CTCGAAAC
66 CTTGAAAC
*
488437 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAGATTAGTCTCGCTTGAGACAGTTTCA
1 AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTAGTCTCGCTTGAGACAGTTTCA
488502 -TTAGAAAC
66 CTT-GAAAC
488510 A
1 A
488511 GAAATTTCCA
Statistics
Matches: 135, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
72 1 0.01
73 134 0.99
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (73 bp):
AACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAATTAGTCTCGCTTGAGACAGTTTCA
CTTGAAAC
Found at i:488414 original size:36 final size:36
Alignment explanation
Indices: 488294--488493 Score: 186
Period size: 36 Copynumber: 5.5 Consensus size: 36
488284 TTCAAATAAC
488294 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* *** * ** ** *
488330 ACTGCGTCTCGCTTGAGACAGTTTCACTTGAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
488366 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 -AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* ** * ** **
488403 AATTTGTCTCACTTGAGACAGTGTCACTCGAAACAA
1 AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
488439 CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
1 -AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
* *
488476 GA-TTAGTCTCGCTTGAGA
1 AATTTA-TCTCACTTGAGA
488494 CAGTTTCATT
Statistics
Matches: 123, Mismatches: 38, Indels: 6
0.74 0.23 0.04
Matches are distributed among these distances:
35 3 0.02
36 66 0.54
37 54 0.44
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (36 bp):
AATTTATCTCACTTGAGATTGTTTTTCTTAAAACAA
Found at i:488510 original size:36 final size:38
Alignment explanation
Indices: 488335--488510 Score: 140
Period size: 37 Copynumber: 4.8 Consensus size: 38
488325 AACAAACTGC
*
488335 GTCTCGCTTGAGACAGTTTCACTT-GAAACAACAATTTA
1 GTCTCACTTGAGACAGTTTCA-TTAGAAACAACAATTTA
**
488373 -TCTCACTTGAGATTGTTTTTC-TTA-AAACAA-AATTT-
1 GTCTCACTTGAGACAG--TTTCATTAGAAACAACAATTTA
* * *
488408 GTCTCACTTGAGACAGTGTCACTCGAAACAACAATTTA
1 GTCTCACTTGAGACAGTTTCATTAGAAACAACAATTTA
** *
488446 -TCTCACTTGAGATTGTTTTTC-TTA-AAACAA-GA-TTA
1 GTCTCACTTGAGACAG--TTTCATTAGAAACAACAATTTA
*
488481 GTCTCGCTTGAGACAGTTTCATTAGAAACA
1 GTCTCACTTGAGACAGTTTCATTAGAAACA
488511 GAAATTTCCA
Statistics
Matches: 108, Mismatches: 17, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
34 7 0.06
35 7 0.06
36 42 0.39
37 44 0.41
38 1 0.01
39 7 0.06
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.35
Consensus pattern (38 bp):
GTCTCACTTGAGACAGTTTCATTAGAAACAACAATTTA
Found at i:488809 original size:119 final size:121
Alignment explanation
Indices: 488532--488861 Score: 475
Period size: 119 Copynumber: 2.7 Consensus size: 121
488522 CACTCGATGG
* * * *
488532 ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGGAGAAGTTCATA
1 ATCAACATTTCCACAAGAAGTTCACAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
488597 ATGAGAAGAACTTGTTCAACCTTTTGCTTGATTCTATCATAGAAGGAGATAGATCAGC
66 AT--GAAGAACTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
* * * *
488655 ATCAACATTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATA
1 ATCAACATTTCCACAAGAAGTTCACAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
488720 AT-AAGAACTTGTTC-AGCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
66 ATGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
* * *
488774 ATCAACGTTTCCACAAGAAGTTTACGATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCACAAGAAGTTCACAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
*
488839 ATGAGAAGAACTTGTTCGACCTT
66 AT--GAAGAACTTGTTCAACCTT
488862 AGCTTGATTT
Statistics
Matches: 190, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
119 97 0.51
120 12 0.06
122 12 0.06
123 69 0.36
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (121 bp):
ATCAACATTTCCACAAGAAGTTCACAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAAGAACTTGTTCAACCTTTTGCTCGATTCTATCACAGAAGGAGATAGATCAGC
Found at i:488949 original size:137 final size:137
Alignment explanation
Indices: 488774--489125 Score: 442
Period size: 137 Copynumber: 2.6 Consensus size: 137
488764 ATAGATCAGC
* * * * *
488774 ATCAACGTTTCCACAAGAAGTTTACGATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCACAATGAGAATAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * * * *
488839 ATGAGAAGAACTTGTTCGACCTTAG-CTTGATTTATCATC-TATGGAGTTGAATGAAAGAAGCAT
66 ATGAGAAGAACTTGTTCAACCTT-GCCTTAATTCATCA-CATATGAAGTTGAATGAAAG-A-CAC
488902 CTCCCTGGAGG
127 CTCCCTGGAGG
* * *
488913 ATCAACATTTTCAG-AG-GGTTCATAATGAGAATAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCACAATGAGAATAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* * *
488976 ATGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATTAACGACACCTCT
66 ATGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATGAAAGACACCTCC
* *
489041 TTTGAGG
131 CTGGAGG
* *
489048 ATCAGCATTTCCAGAAGAAGTTCACAATGAGAATAACTCATTTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAAGTTCACAATGAGAATAACTCATCTGAAGAGGAAGAAGAAGTTCATA
**
489113 ATCTGAAGAACTT
66 ATGAGAAGAACTT
489126 ATTCTGCCTT
Statistics
Matches: 184, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
135 22 0.12
136 5 0.03
137 144 0.78
138 2 0.01
139 11 0.06
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (137 bp):
ATCAACATTTCCAGAAGAAGTTCACAATGAGAATAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGCCTTAATTCATCACATATGAAGTTGAATGAAAGACACCTCC
CTGGAGG
Found at i:491229 original size:3 final size:3
Alignment explanation
Indices: 491221--491269 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
491211 TATATTTAAC
491221 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
491269 T
1 T
491270 TAGTCATATA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:491623 original size:2 final size:2
Alignment explanation
Indices: 491616--491658 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
491606 AAATATCTTT
491616 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
491658 T
1 T
491659 TAATAAACTC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:492487 original size:20 final size:19
Alignment explanation
Indices: 492464--492508 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
492454 TAACATTAAA
492464 TAGTTTAAGTTAAAACTCAT
1 TAGTTTAA-TTAAAACTCAT
*
492484 TAGTGTTTATTAAAACTCAT
1 TAGT-TTAATTAAAACTCAT
492504 TAGTT
1 TAGTT
492509 GACATGATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.44
Consensus pattern (19 bp):
TAGTTTAATTAAAACTCAT
Done.