Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008117.1 Hibiscus syriacus cultivar Beakdansim tig00110656_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: 1567030
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 7
Found at i:1408584 original size:126 final size:124
Alignment explanation
Indices: 1408221--1408573 Score: 298
Period size: 126 Copynumber: 2.7 Consensus size: 124
1408211 GAGATAAAAT
* * * ** * * *
1408221 GATAATGTCTAATTATTTTCAATCGAGAATAAATGATATTTCATGCCTTAAAACATTCATTTATT
1 GATAATATCTAATGATTTCCAATCGAGAATAAAT-A-ACCTC-T-CATTAAAGCAGTCATTTATT
** * * *
1408286 AC-CTCAATTGAAATAAAGAGATATCACTATTTCGTCTTAAAATTCAATATTGATTCGAGCAAAA
62 ACTC-CAACCGAAATGAAGAGATATCACTA-TTC-TCTCAAAA-TCAATATTGACTCGAGCAAAA
1408350 GC
123 GC
* * *
1408352 GATAATATCTAATGATTTCCAATTGAGAATAAATAACCTCTCCTTAAAGTAGTCATTTATTACTC
1 GATAATATCTAATGATTTCCAATCGAGAATAAATAACCTCTCATTAAAGCAGTCATTTATTACTC
* *
1408417 CAATCGAAATGAAGAGATATCACTATTCCGTCTTAAAATCAATATTGACTCGAG-ATAAAGC
66 CAACCGAAATGAAGAGATATCACTATT-C-TCTCAAAATCAATATTGACTCGAGCA-AAAGC
* * * * * *
1408478 TG-TAATATCTGATTATTTCTAATCGAGAATAAATGACCTCTCATGAATTAAAGCATTCGTTTAT
1 -GATAATATCTAATGATTTCCAATCGAGAATAAATAACCTCTC----ATTAAAGCAGTCATTTAT
* * *
1408542 TACTCCGACCGAAATGATGAGATATTACTATT
61 TACTCCAACCGAAATGAAGAGATATCACTATT
1408574 TTCAATATCA
Statistics
Matches: 189, Mismatches: 25, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
125 1 0.01
126 57 0.30
127 53 0.28
128 2 0.01
129 3 0.02
130 43 0.23
131 30 0.16
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (124 bp):
GATAATATCTAATGATTTCCAATCGAGAATAAATAACCTCTCATTAAAGCAGTCATTTATTACTC
CAACCGAAATGAAGAGATATCACTATTCTCTCAAAATCAATATTGACTCGAGCAAAAGC
Found at i:1410673 original size:3 final size:3
Alignment explanation
Indices: 1410665--1410716 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
1410655 ACAAAAATTA
* * * *
1410665 AAT AAT AAT AAT AAT AAT AAT AAT ATT ATT AAA AAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1410713 AAT A
1 AAT A
1410717 TTGTTGGGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:1417279 original size:17 final size:17
Alignment explanation
Indices: 1417257--1417291 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1417247 TTTAGTATAC
1417257 AATAGAAAAAACTGTAT
1 AATAGAAAAAACTGTAT
1417274 AATAGAAAAAACTGTAT
1 AATAGAAAAAACTGTAT
1417291 A
1 A
1417292 TTAGTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.60, C:0.06, G:0.11, T:0.23
Consensus pattern (17 bp):
AATAGAAAAAACTGTAT
Found at i:1419871 original size:35 final size:34
Alignment explanation
Indices: 1419786--1419872 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 34
1419776 AATATAATTT
*
1419786 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
*
1419820 TAAATGATAA-ACAAATTACAATAACTGGTATTAAATGG
1 TAAAT-ACAACA-AAATTACAATAA---GTATTAAATGG
1419858 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
1419873 ACCAAAATAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
34 6 0.13
35 22 0.49
36 2 0.04
37 3 0.07
38 12 0.27
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Found at i:1422243 original size:17 final size:19
Alignment explanation
Indices: 1422223--1422264 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
1422213 ATTAATTAAA
1422223 TAAAATA-TTAAA-AAATT
1 TAAAATACTTAAATAAATT
1422240 T-AAATACTTAAATAAATT
1 TAAAATACTTAAATAAATT
*
1422258 AAAAATA
1 TAAAATA
1422265 AAATATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 5 0.24
17 6 0.29
18 5 0.24
19 5 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATACTTAAATAAATT
Found at i:1424700 original size:23 final size:22
Alignment explanation
Indices: 1424665--1424707 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1424655 ATAATTATTT
1424665 AAAAAATTAAATAAAAAATATC
1 AAAAAATTAAATAAAAAATATC
*
1424687 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
1424708 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATATC
Found at i:1425934 original size:19 final size:20
Alignment explanation
Indices: 1425910--1425960 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1425900 AATGACCAAT
1425910 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1425929 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1425949 AAAATCGCAACG
1 AAAATCGCAACG
1425961 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1425954 original size:20 final size:20
Alignment explanation
Indices: 1425910--1426214 Score: 130
Period size: 20 Copynumber: 14.6 Consensus size: 20
1425900 AATGACCAAT
* *
1425910 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1425929 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1425949 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1425969 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1425989 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1426010 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1426033 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1426053 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1426073 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1426093 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1426116 AAAATCGCAATGCGAGTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
1426136 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* *
1426156 AGAATCGCAATGCGATTTATAG
1 AAAATCGCAACGCGA-TT-TAG
*
1426178 AATCGCAAATCGCAACACGATTTAG
1 -A----AAATCGCAACGCGATTTAG
1426203 AAAATCGCAACG
1 AAAATCGCAACG
1426215 GTCAAAAGAA
Statistics
Matches: 223, Mismatches: 44, Indels: 37
0.73 0.14 0.12
Matches are distributed among these distances:
19 17 0.08
20 142 0.64
21 15 0.07
22 2 0.01
23 30 0.13
24 1 0.00
25 3 0.01
26 2 0.01
27 11 0.05
ACGTcount: A:0.40, C:0.19, G:0.22, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1426088 original size:40 final size:40
Alignment explanation
Indices: 1426014--1426185 Score: 191
Period size: 40 Copynumber: 4.2 Consensus size: 40
1426004 GCTTCCAAGT
* *
1426014 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAATGCGATTTA-AAG--AATCGCAATGCGATTGAGAGAA
* *
1426057 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAG
1 TCGCAATGCGATTTAAAGAATCGCAATGCGATTGAGAGAA
* *
1426097 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGAGTGAGAGAA
1 TCGCAATGCGATTTA-AAG--AATCGCAATGCGATTGAGAGAA
* * * * *
1426140 TCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAA
1 TCGCAATGCGATTTAAAGAATCGCAATGCGATTGAGAGAA
1426180 TCGCAA
1 TCGCAA
1426186 ATCGCAACAC
Statistics
Matches: 111, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
40 59 0.53
41 2 0.02
42 4 0.04
43 46 0.41
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGATTTAAAGAATCGCAATGCGATTGAGAGAA
Found at i:1426122 original size:63 final size:63
Alignment explanation
Indices: 1426055--1426174 Score: 186
Period size: 63 Copynumber: 1.9 Consensus size: 63
1426045 CGATTGATAG
* * * * *
1426055 AATCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGAGTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAGAA
*
1426118 AATCGCAATGCGAGTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTA
1 AATCGCAATGCGAGTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTA
1426175 TAGAATCGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.21
Consensus pattern (63 bp):
AATCGCAATGCGAGTGAGAGAATCGCAATGCGACTGAGAGAATCGCAACGCGATTTAGAAGAA
Found at i:1426124 original size:83 final size:83
Alignment explanation
Indices: 1426014--1426172 Score: 273
Period size: 83 Copynumber: 1.9 Consensus size: 83
1426004 GCTTCCAAGT
* * * * *
1426014 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGAGTGAGAGAATCGCAATGCGACTGAGAGAATC
1426079 GCAATGCGATTGAGAGAG
66 GCAATGCGATTGAGAGAG
1426097 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGAGTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGAGTGAGAGAATCGCAATGCGACTGAGAGAATC
1426162 GCAATGCGATT
66 GCAATGCGATT
1426173 TATAGAATCG
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 71 1.00
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (83 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGAGTGAGAGAATCGCAATGCGACTGAGAGAATC
GCAATGCGATTGAGAGAG
Found at i:1426198 original size:27 final size:27
Alignment explanation
Indices: 1426158--1426212 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
1426148 CGACTGAGAG
** * *
1426158 AATCGCAATGCGATTTATAGAATCGCA
1 AATCGCAACACGATTTAGAAAATCGCA
1426185 AATCGCAACACGATTTAGAAAATCGCA
1 AATCGCAACACGATTTAGAAAATCGCA
1426212 A
1 A
1426213 CGGTCAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (27 bp):
AATCGCAACACGATTTAGAAAATCGCA
Found at i:1426313 original size:6 final size:6
Alignment explanation
Indices: 1426302--1426345 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
1426292 GACACATATT
1426302 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1426346 CGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1426980 original size:21 final size:20
Alignment explanation
Indices: 1426954--1427051 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
1426944 ATCAGTTTCC
1426954 AAAATCGCAACGCGATTCTTA
1 AAAATCGCAACGCGATT-TTA
* **
1426975 AAAATCGCAATGCGATAGTA
1 AAAATCGCAACGCGATTTTA
* ** *
1426995 CAAATTCGCATTGCGATTTTCC
1 -AAAATCGCAACGCGATTTT-A
* * *
1427017 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTA
1427037 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1427052 ACACATAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTA
Found at i:1427080 original size:20 final size:20
Alignment explanation
Indices: 1427018--1427247 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
1427008 CGATTTTCCA
* ** *
1427018 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1427038 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
1427058 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1427078 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1427098 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1427118 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1427138 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1427158 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1427178 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1427198 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
1427218 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
1427238 AAATCACAAC
1 AAATCGCAAC
1427248 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1427968 original size:24 final size:24
Alignment explanation
Indices: 1427929--1427975 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1427919 AAATTTGGTC
1427929 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1427953 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1427976 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1428165 original size:12 final size:12
Alignment explanation
Indices: 1428148--1428172 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1428138 CTATAATCCT
1428148 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1428160 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1428172 G
1 G
1428173 TCCCGAAGAA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1430505 original size:34 final size:33
Alignment explanation
Indices: 1430437--1430537 Score: 141
Period size: 33 Copynumber: 3.0 Consensus size: 33
1430427 CGGAAATTAC
* *
1430437 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
1430470 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCCCAACGA-GAAAATCGCAATGC-GAAATGAA
* *
1430504 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCCCAACGAGAAAATCGCAATGCGAAATGAA
1430537 A
1 A
1430538 TCGCAATGCG
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
32 1 0.02
33 30 0.49
34 29 0.48
35 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
AATCCCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:1430523 original size:14 final size:15
Alignment explanation
Indices: 1430504--1430581 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 15
1430494 CGGAAATGAA
1430504 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
1430518 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
*
1430535 AAATCGCAATGCGAAATGAA
1 -AATCGCAA-GCG--A-GAG
1430555 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
1430569 AATCGCAATGCGA
1 AATCGCAA-GCGA
1430582 AATTAAAATC
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.14
17 3 0.06
18 12 0.24
19 8 0.16
20 1 0.02
21 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (15 bp):
AATCGCAAGCGAGAG
Found at i:1430560 original size:51 final size:52
Alignment explanation
Indices: 1430482--1430600 Score: 204
Period size: 51 Copynumber: 2.3 Consensus size: 52
1430472 TCCCAACATG
1430482 AAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAA-T
1 AAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATT
*
1430534 GAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATT
1 AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATT
*
1430586 AAAATCGCATTGCGA
1 AAAATCGCAATGCGA
1430601 TTCTCTCGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
51 37 0.59
52 26 0.41
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (52 bp):
AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATT
Found at i:1430703 original size:52 final size:53
Alignment explanation
Indices: 1430590--1430706 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1430580 GAAATTAAAA
1430590 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1430643 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1430695 TCGCATTGCGAT
1 TCGCATTGCGAT
1430707 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1430714 original size:19 final size:19
Alignment explanation
Indices: 1430609--1430706 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1430599 GATTCTCTCG
1430609 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1430629 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1430648 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1430662 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1430681 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1430700 TTGCGAT
1 TTGCGAT
1430707 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1430839 original size:14 final size:14
Alignment explanation
Indices: 1430822--1430848 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1430812 CATAAATTAA
1430822 CTTTTACAAATCAT
1 CTTTTACAAATCAT
1430836 CTTTTACAAATCA
1 CTTTTACAAATCA
1430849 ATTAACAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTTTACAAATCAT
Found at i:1432789 original size:19 final size:19
Alignment explanation
Indices: 1432750--1432837 Score: 67
Period size: 19 Copynumber: 4.6 Consensus size: 19
1432740 TAGTTTACTT
* *
1432750 TCGCAACACGAAATTAAAA
1 TCGCAACGCGAAATGAAAA
1432769 TCGCAACGCGAAATGATAATCAAA
1 TCGCAACGCGAAATG---A--AAA
*
1432793 TCGCAA--CGAAA--AGAA
1 TCGCAACGCGAAATGAAAA
1432808 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1432827 TCGCAATGCGA
1 TCGCAACGCGA
1432838 TTTTGGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
15 8 0.15
17 6 0.11
19 26 0.47
22 6 0.11
24 9 0.16
ACGTcount: A:0.47, C:0.22, G:0.18, T:0.14
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1432855 original size:19 final size:19
Alignment explanation
Indices: 1432833--1432942 Score: 84
Period size: 19 Copynumber: 6.5 Consensus size: 19
1432823 AAAATCGCAA
*
1432833 TGCGATTTTGGTTTCACGT
1 TGCGATTTTGGTTTCGCGT
*
1432852 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1432866 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1432885 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1432899 TGCGA-TTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1432917 TG-GA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1432934 TGCGATTTT
1 TGCGATTTT
1432943 AAGTTTCGTG
Statistics
Matches: 72, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
13 2 0.03
14 19 0.26
15 1 0.01
16 3 0.04
17 16 0.22
18 9 0.12
19 22 0.31
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1432875 original size:33 final size:33
Alignment explanation
Indices: 1432833--1432906 Score: 123
Period size: 33 Copynumber: 2.2 Consensus size: 33
1432823 AAAATCGCAA
1432833 TGCGATTTTGGTTTCACGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCACGTTGCGATTC-TGTCGT
*
1432866 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCACGTTGCGATTCTGTCGT
1432899 TGCGATTT
1 TGCGATTT
1432907 CATTTCGCGT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 37 0.95
34 2 0.05
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCACGTTGCGATTCTGTCGT
Found at i:1433343 original size:92 final size:94
Alignment explanation
Indices: 1433005--1433375 Score: 629
Period size: 91 Copynumber: 4.1 Consensus size: 94
1432995 ATGGATTGCA
*
1433005 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACT-TTTCACAGTGTT-AAGAAT--ATAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1433065 TAGCAGAATTGGCAGCAACCCGAACAAATT
66 TAGCAGAATTGGCAGCAACCCGAACAAA-T
1433095 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1433160 TAGCAGAATTGGCAGCAA-CCGAAC-AA-
66 TAGCAGAATTGGCAGCAACCCGAACAAAT
1433186 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1433250 TAGCAGAATTGGCAGCAA-CCGAACAAAT
66 TAGCAGAATTGGCAGCAACCCGAACAAAT
*
1433278 TTACTTTCAACCAAAAGACAACAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
1433342 TAGCAGAATTGGCAGCAACCCGAATAAAT
66 TAGCAGAATTGGCAGCAACCCGAACAAAT
1433371 TTACT
1 TTACT
1433376 AAGCAATCTA
Statistics
Matches: 269, Mismatches: 3, Indels: 15
0.94 0.01 0.05
Matches are distributed among these distances:
90 54 0.20
91 85 0.32
92 79 0.29
93 22 0.08
94 6 0.02
95 23 0.09
ACGTcount: A:0.45, C:0.20, G:0.13, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCCGAACAAAT
Found at i:1434946 original size:21 final size:21
Alignment explanation
Indices: 1434889--1434953 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
1434879 TCTTTTGGTT
1434889 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
*** *
1434910 G-AATGACTGTCTCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1434930 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1434951 GAA
1 GAA
1434954 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.48, C:0.15, G:0.25, T:0.12
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:1434976 original size:19 final size:19
Alignment explanation
Indices: 1434889--1435002 Score: 94
Period size: 19 Copynumber: 6.1 Consensus size: 19
1434879 TCTTTTGGTT
*
1434889 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** * *
1434908 GAGAATGACTGTCTCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
1434930 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1434947 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1434963 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1434982 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1435001 GA
1 GA
1435003 TTTTGGTTTC
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 1 0.01
18 1 0.01
19 35 0.47
20 11 0.15
21 10 0.13
22 4 0.05
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1435033 original size:14 final size:14
Alignment explanation
Indices: 1435014--1435070 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1435004 TTTGGTTTCG
1435014 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1435028 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1435047 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1435061 CGTTGCGATT
1 CGTTGCGATT
1435071 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1435046 original size:33 final size:33
Alignment explanation
Indices: 1434998--1435078 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
1434988 AAAATCGCAA
**
1434998 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1435031 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1435064 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
1435079 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1435081 original size:21 final size:21
Alignment explanation
Indices: 1435055--1435127 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
1435045 CGCGTTGCGA
1435055 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1435076 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1435096 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1435117 TTATCTCGTTG
1 TTCTCTCGTTG
1435128 TGACTCTTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.11, C:0.25, G:0.16, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1435251 original size:33 final size:33
Alignment explanation
Indices: 1435209--1435279 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1435199 AATACTAACT
*
1435209 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1435242 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1435275 TGAAA
1 TGAAA
1435280 TCTAAGTGAA
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:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1435511 original size:22 final size:22
Alignment explanation
Indices: 1435459--1435513 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1435449 TGGTTGTGAG
**
1435459 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1435481 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1435503 GGATTTCTTCG
1 GGATTTCTTCG
1435514 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1435693 original size:20 final size:20
Alignment explanation
Indices: 1435660--1435832 Score: 199
Period size: 20 Copynumber: 8.7 Consensus size: 20
1435650 CTTTAAATAT
1435660 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1435680 CGCG-TGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1435701 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1435720 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* * **
1435740 CGCATTACGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1435760 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1435780 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1435800 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
1435820 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1435833 TCATATTTGC
Statistics
Matches: 128, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
19 7 0.05
20 113 0.88
21 8 0.06
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1435852 original size:60 final size:60
Alignment explanation
Indices: 1435660--1435832 Score: 231
Period size: 60 Copynumber: 2.9 Consensus size: 60
1435650 CTTTAAATAT
**
1435660 CGCGTTGCGATTTACGGATACGCG-TGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * * *** *
1435720 CGCGTTGCGATATACGGATACGCATTACGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* *
1435780 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
1435833 TCATATTTGC
Statistics
Matches: 94, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 90 0.96
61 4 0.04
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1436304 original size:6 final size:6
Alignment explanation
Indices: 1436288--1436325 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
1436278 TCTCGTCTCG
1436288 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1436326 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1436411 original size:14 final size:14
Alignment explanation
Indices: 1436392--1436420 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1436382 GAAACAAAAT
1436392 TTTTTTAACTATTC
1 TTTTTTAACTATTC
1436406 TTTTTTAACTATTC
1 TTTTTTAACTATTC
1436420 T
1 T
1436421 CTCAGTCGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTTTAACTATTC
Found at i:1436441 original size:20 final size:20
Alignment explanation
Indices: 1436416--1436541 Score: 144
Period size: 20 Copynumber: 6.2 Consensus size: 20
1436406 TTTTTTAACT
*
1436416 ATTCTCTCAGTCGCATTGCG
1 ATTCTCTCAATCGCATTGCG
* *
1436436 ATTCTCTTAGTCGCATTGCG
1 ATTCTCTCAATCGCATTGCG
* *
1436456 ATTTTCTTCTAAATCGCGTTGCG
1 A--TTC-TCTCAATCGCATTGCG
*
1436479 ACTCTCTCAATCGCATTGCG
1 ATTCTCTCAATCGCATTGCG
* *
1436499 ATTCTATAAATCGCATTGCG
1 ATTCTCTCAATCGCATTGCG
*
1436519 ATTCTATCAATCGCATTGCG
1 ATTCTCTCAATCGCATTGCG
1436539 ATT
1 ATT
1436542 TTCTTCTAAA
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
20 73 0.79
21 2 0.02
22 3 0.03
23 14 0.15
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (20 bp):
ATTCTCTCAATCGCATTGCG
Found at i:1436529 original size:40 final size:41
Alignment explanation
Indices: 1436426--1436562 Score: 159
Period size: 43 Copynumber: 3.3 Consensus size: 41
1436416 ATTCTCTCAG
* * *
1436426 TCGCATTGCGATTCTCTTAGTCGCATTGCGATTTTCTTCTAAA
1 TCGCATTGCGATTCTCTCAATCGCATTGCGA--TTCTTATAAA
* *
1436469 TCGCGTTGCGACTCTCTCAATCGCATTGCGATTC-TATAAA
1 TCGCATTGCGATTCTCTCAATCGCATTGCGATTCTTATAAA
* *
1436509 TCGCATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAA
1 TCGCATTGCGATTCTCTCAATCGCATTGCGA--TTCTTATAAA
*
1436552 TCGCGTTGCGA
1 TCGCATTGCGA
1436563 ACTTGGAAGC
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
40 33 0.41
41 3 0.04
42 3 0.04
43 42 0.52
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (41 bp):
TCGCATTGCGATTCTCTCAATCGCATTGCGATTCTTATAAA
Found at i:1436554 original size:63 final size:61
Alignment explanation
Indices: 1436426--1436562 Score: 143
Period size: 63 Copynumber: 2.2 Consensus size: 61
1436416 ATTCTCTCAG
* * * * *
1436426 TCGCATTGCGATTCTCTTAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGACTCTCTCAA
1 TCGCATTGCGATTCTATAAATCGCATTGCGA-TTTCTTC-AAATCGCATTGCGACTCTCTAAA
*
1436489 TCGCATTGCGATTCTATAAATCGCATTGCGA-TTCTATC-AATCGCATTGCGATTTTCTTCTAAA
1 TCGCATTGCGATTCTATAAATCGCATTGCGATTTCT-TCAAATCGCATTGCGA--CTC-TCTAAA
*
1436552 TCGCGTTGCGA
1 TCGCATTGCGA
1436563 ACTTGGAAGC
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
60 12 0.19
61 4 0.06
62 4 0.06
63 43 0.68
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (61 bp):
TCGCATTGCGATTCTATAAATCGCATTGCGATTTCTTCAAATCGCATTGCGACTCTCTAAA
Found at i:1436603 original size:20 final size:20
Alignment explanation
Indices: 1436578--1436629 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1436568 GAAGCTCGCG
*
1436578 TTGCGATTTTCTTTTGACCA
1 TTGCGATTTTCTTTTGAACA
* *
1436598 TTGCGATTTTCTTTTTAACG
1 TTGCGATTTTCTTTTGAACA
1436618 TTGCGATTTTCT
1 TTGCGATTTTCT
1436630 AAATCGCGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.13, C:0.17, G:0.15, T:0.54
Consensus pattern (20 bp):
TTGCGATTTTCTTTTGAACA
Found at i:1436656 original size:19 final size:20
Alignment explanation
Indices: 1436616--1436666 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1436606 TTCTTTTTAA
*
1436616 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
1436636 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
1436655 CGTTGCGATTTT
1 CGTTGCGATTTT
1436667 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:1437518 original size:2 final size:2
Alignment explanation
Indices: 1437511--1437535 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1437501 TAAATTTAAT
1437511 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 T
1437536 GTAATATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1443585 original size:7 final size:7
Alignment explanation
Indices: 1443556--1443612 Score: 62
Period size: 7 Copynumber: 8.0 Consensus size: 7
1443546 GCCCTAAATT
1443556 GAAAAAA
1 GAAAAAA
1443563 GAGAAAAA
1 GA-AAAAA
*
1443571 AAATAAAA
1 GAA-AAAA
1443579 GAAAAAA
1 GAAAAAA
*
1443586 GAGAAAA
1 GAAAAAA
*
1443593 GAGAAAA
1 GAAAAAA
1443600 G-AAAAA
1 GAAAAAA
1443606 GAAAAAA
1 GAAAAAA
1443613 TAAGGTGGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
6 5 0.12
7 26 0.60
8 12 0.28
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (7 bp):
GAAAAAA
Found at i:1444789 original size:2 final size:2
Alignment explanation
Indices: 1444773--1444815 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
1444763 TATTACAAAC
1444773 TA TA TCA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1444815 T
1 T
1444816 TTGGGTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1445809 original size:16 final size:16
Alignment explanation
Indices: 1445775--1445830 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
1445765 ATTATTATTA
1445775 TATTTTTT-TCA-AAT
1 TATTTTTTATCATAAT
*
1445789 ATATTTTTATAT-ATATT
1 -TATTTTT-TATCATAAT
1445806 TATTTTTTATCATAAT
1 TATTTTTTATCATAAT
1445822 TATTATTTT
1 TATT-TTTT
1445831 TTTAAAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 10 0.29
16 17 0.50
17 7 0.21
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTTTTATCATAAT
Found at i:1447612 original size:28 final size:28
Alignment explanation
Indices: 1447580--1447657 Score: 113
Period size: 28 Copynumber: 2.8 Consensus size: 28
1447570 AATCGAGAAC
* *
1447580 CGTTGTTTAGTCCGATTCAATCATG-AAT
1 CGTTGTCTAGTCCGATTCAATC-GGAAAT
1447608 CGTTGTCTAGTCCGATTCAATCGGAAAT
1 CGTTGTCTAGTCCGATTCAATCGGAAAT
*
1447636 CGTTGTCTAGTCCGGTTCAATC
1 CGTTGTCTAGTCCGATTCAATC
1447658 TAGACCGATT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
27 1 0.02
28 45 0.98
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (28 bp):
CGTTGTCTAGTCCGATTCAATCGGAAAT
Found at i:1448466 original size:18 final size:18
Alignment explanation
Indices: 1448434--1448468 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1448424 CCGGTTCTTC
*
1448434 CGACCGGTCGGACCAGTT
1 CGACCGGTCGAACCAGTT
*
1448452 CGACCGGTTGAACCAGT
1 CGACCGGTCGAACCAGT
1448469 GAACCGGTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.31, G:0.31, T:0.17
Consensus pattern (18 bp):
CGACCGGTCGAACCAGTT
Found at i:1454384 original size:16 final size:17
Alignment explanation
Indices: 1454353--1454386 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1454343 TGTATCGCCG
*
1454353 ACAAAATTTTACTATTC
1 ACAAAATTTCACTATTC
1454370 ACAAAA-TTCACTATTC
1 ACAAAATTTCACTATTC
1454386 A
1 A
1454387 TGCAAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (17 bp):
ACAAAATTTCACTATTC
Found at i:1470774 original size:2 final size:2
Alignment explanation
Indices: 1470767--1470795 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1470757 ACTCATATTA
1470767 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 A
1470796 AAATACACTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1471435 original size:11 final size:12
Alignment explanation
Indices: 1471395--1471438 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
1471385 TATTTAAACG
*
1471395 GGTATTGGGCCA
1 GGTATTGGGTCA
*
1471407 GGTATTGGGTCG
1 GGTATTGGGTCA
1471419 GGTATTGGGTC-
1 GGTATTGGGTCA
1471430 GGTATTGGG
1 GGTATTGGG
1471439 CTGGGAATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 9 0.30
12 21 0.70
ACGTcount: A:0.11, C:0.09, G:0.48, T:0.32
Consensus pattern (12 bp):
GGTATTGGGTCA
Found at i:1471437 original size:23 final size:24
Alignment explanation
Indices: 1471393--1471438 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1471383 ATTATTTAAA
1471393 CGGGTATTGGGCCAGGTATTGGGT
1 CGGGTATTGGGCCAGGTATTGGGT
*
1471417 CGGGTATTGGGTC-GGTATTGGG
1 CGGGTATTGGGCCAGGTATTGGG
1471439 CTGGGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.11, C:0.11, G:0.48, T:0.30
Consensus pattern (24 bp):
CGGGTATTGGGCCAGGTATTGGGT
Found at i:1471516 original size:24 final size:25
Alignment explanation
Indices: 1471461--1471516 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
1471451 CCGGGTATAC
1471461 ATATATATTTAAATTAAATATATATT
1 ATAT-TATTTAAATTAAATATATATT
*
1471487 -TTTTATTTAAATTAAAT-T-TATT
1 ATATTATTTAAATTAAATATATATT
1471509 AATATTAT
1 -ATATTAT
1471517 ATATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 4 0.15
23 1 0.04
24 19 0.73
25 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATTATTTAAATTAAATATATATT
Found at i:1471635 original size:6 final size:6
Alignment explanation
Indices: 1471621--1471657 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1471611 AAATGGGTTT
*
1471621 TCCCCG TCCCTG TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG TCCCCG T
1471658 TTATCATCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.62, G:0.16, T:0.22
Consensus pattern (6 bp):
TCCCCG
Found at i:1474254 original size:21 final size:20
Alignment explanation
Indices: 1474225--1474266 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
1474215 TGTCGGTACG
1474225 TATCAATACTATTAA-AATATA
1 TATCAATAC-A-TAACAATATA
*
1474246 TATCGATACATAACAATATA
1 TATCAATACATAACAATATA
1474266 T
1 T
1474267 CAGATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 3 0.16
20 8 0.42
21 8 0.42
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (20 bp):
TATCAATACATAACAATATA
Found at i:1474611 original size:184 final size:183
Alignment explanation
Indices: 1474224--1474701 Score: 630
Period size: 184 Copynumber: 2.6 Consensus size: 183
1474214 TTGTCGGTAC
* * * *
1474224 GTATCAATACTATTA-AAATATATATCGATACATAACAATATATCA-GATAAAAATATGAGAAAA
1 GTATC-ATACT-TTATAAACATGTATCGATACATAACAATATAACAGGATAAAAATATGACAAAA
* * * *
1474287 CCTG-TTCA-ATATTATAAAACCGGTAAAGCGCTACAGGATATGTTGAAAGTATCAATTTCATTC
64 CCGGTTTCATA-ATGACAAAACCGGTAAAGCGATACAGGATATGTTGAAAGTATCAATTTCATTC
*
1474350 AAATAAGTATAGACACTTTTGAAATTTAAAATAAAAGCAATAATAAAGCCTATAAA
128 AAATAAGTATAGACACTTTTGAAATTTAAAAGAAAAGCAATAATAAAGCCTATAAA
* * *
1474406 GTATCAGTACTTTATAAACATGTATCGATACACAATAATATAACAGGAAAAAAATATGACAAAAC
1 GTATCA-TACTTTATAAACATGTATCGATACATAACAATATAACAGGATAAAAATATGACAAAAC
* *
1474471 CGGTTTCATAATGACAAAACCGGTAAAGCGATATTA-GATATGTTGAAGGTATCAATTTCATTCA
65 CGGTTTCATAATGACAAAACCGGTAAAGCGATA-CAGGATATGTTGAAAGTATCAATTTCATTCA
* * * **
1474535 AATAAGTATCGATACTTTTGGAATTTAAAAG-AAAGACAATAATAGCGCCTATAAA
129 AATAAGTATAGACACTTTTGAAATTTAAAAGAAAAG-CAATAATAAAGCCTATAAA
*
1474590 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAGG-TAAAAATATGACAAAAT
1 GTATC-ATACTTTATAAACATGTATCGATACATAACAATATAACAGGATAAAAATATGACAAAAC
* * *
1474654 CGGTTTCATAATGACAAAACCAGTAAAGCGCTACCGGATATGTT-AAAG
65 CGGTTTCATAATGACAAAACCGGTAAAGCGATACAGGATATGTTGAAAG
1474702 GTATAAATAC
Statistics
Matches: 259, Mismatches: 28, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
181 4 0.02
182 37 0.14
183 77 0.30
184 138 0.53
185 3 0.01
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (183 bp):
GTATCATACTTTATAAACATGTATCGATACATAACAATATAACAGGATAAAAATATGACAAAACC
GGTTTCATAATGACAAAACCGGTAAAGCGATACAGGATATGTTGAAAGTATCAATTTCATTCAAA
TAAGTATAGACACTTTTGAAATTTAAAAGAAAAGCAATAATAAAGCCTATAAA
Found at i:1476729 original size:22 final size:23
Alignment explanation
Indices: 1476681--1476731 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
1476671 TTTTTGTTTT
*
1476681 TTATATAAAATGATAGTATAATTA
1 TTATATAAAATGATAGCAT-ATTA
1476705 TTATATAAAATGATA-CAT-TTAA
1 TTATATAAAATGATAGCATATT-A
1476727 TTATA
1 TTATA
1476732 AATGCAGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 6 0.24
23 2 0.08
24 15 0.60
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (23 bp):
TTATATAAAATGATAGCATATTA
Found at i:1478159 original size:20 final size:20
Alignment explanation
Indices: 1478114--1478159 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1478104 GTTTATATAA
*
1478114 AGTATCGTTACTTTTTGTAC
1 AGTATCGATACTTTTTGTAC
*
1478134 ATGTATCGATACTTTTTGTCC
1 A-GTATCGATACTTTTTGTAC
1478155 AGTAT
1 AGTAT
1478160 GCTTCCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.48
Consensus pattern (20 bp):
AGTATCGATACTTTTTGTAC
Found at i:1480678 original size:14 final size:14
Alignment explanation
Indices: 1480661--1480688 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1480651 TTTAAATGTT
1480661 TGAGAACAAATGGA
1 TGAGAACAAATGGA
1480675 TGAGAACAAATGGA
1 TGAGAACAAATGGA
1480689 CCGCCTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.29, T:0.14
Consensus pattern (14 bp):
TGAGAACAAATGGA
Found at i:1485081 original size:43 final size:41
Alignment explanation
Indices: 1485009--1485101 Score: 159
Period size: 43 Copynumber: 2.2 Consensus size: 41
1484999 GGGCCTTACT
1485009 TGGTGTGTTGGTGGTTATGGTTCTAGGGAACCTACACATTA
1 TGGTGTGTTGGTGGTTATGGTTCTAGGGAACCTACACATTA
*
1485050 TGGTGTGTTGGTGGGTGTATGGTTCTGGGGAACCTACACATTA
1 TGGTGTGTTGGT-GGT-TATGGTTCTAGGGAACCTACACATTA
1485093 TGGTGTGTT
1 TGGTGTGTT
1485102 TGGTTGGAGG
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
41 12 0.24
42 3 0.06
43 34 0.69
ACGTcount: A:0.16, C:0.11, G:0.35, T:0.38
Consensus pattern (41 bp):
TGGTGTGTTGGTGGTTATGGTTCTAGGGAACCTACACATTA
Found at i:1487867 original size:3 final size:3
Alignment explanation
Indices: 1487849--1487908 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
1487839 TTTCATTAAA
* * *
1487849 ATT ATT CTT AATT ATT ATT TTT ATT ATT ATT ATT ATT AAT A-T ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1487894 ATT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT A
1487909 CAAATAAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
2 4 0.08
3 43 0.88
4 2 0.04
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1489355 original size:25 final size:25
Alignment explanation
Indices: 1489303--1489355 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
1489293 AATTTTGTTT
*
1489303 TATTATTAGTTTTATATATGTTTAA
1 TATTATTAGTTTTATATATATTTAA
1489328 TATTATTA-TTTTAT-TAGTATTTATA
1 TATTATTAGTTTTATATA-TATTTA-A
1489353 TAT
1 TAT
1489356 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 2 0.08
24 11 0.44
25 12 0.48
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (25 bp):
TATTATTAGTTTTATATATATTTAA
Found at i:1489356 original size:2 final size:2
Alignment explanation
Indices: 1489349--1489407 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1489339 TATTAGTATT
1489349 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
1489391 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1489408 TTATTTATCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1490245 original size:2 final size:2
Alignment explanation
Indices: 1490233--1490274 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
1490223 TATTTTCCTA
*
1490233 AT AT TT 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
1490275 TTAATGTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1491855 original size:12 final size:13
Alignment explanation
Indices: 1491838--1491866 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1491828 ACATTCACAT
1491838 ATTTACA-TTTGC
1 ATTTACATTTTGC
1491850 ATTTACATTTTGC
1 ATTTACATTTTGC
1491863 ATTT
1 ATTT
1491867 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:1494575 original size:9 final size:9
Alignment explanation
Indices: 1494561--1494593 Score: 52
Period size: 8 Copynumber: 3.9 Consensus size: 9
1494551 TATTATACTT
1494561 GAAAAAAAG
1 GAAAAAAAG
1494570 GAAAAAAAG
1 GAAAAAAAG
1494579 G-AAAAAA-
1 GAAAAAAAG
1494586 GAAAAAAA
1 GAAAAAAA
1494594 TTGAACCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.04
8 12 0.52
9 10 0.43
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
GAAAAAAAG
Found at i:1500126 original size:46 final size:46
Alignment explanation
Indices: 1500021--1500736 Score: 1118
Period size: 46 Copynumber: 15.6 Consensus size: 46
1500011 CTATTTCTAA
1500021 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAA-CCTTCGGGT
*
1500068 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGTGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
** * * * * *
1500114 CATCACTAAGTCCTTCAGTGTATGATGTTTTC-AAAACCTCCAGGA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
*
1500159 CATCTGTAAGTCTTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
*
1500205 CATCTGTAAGTCCTTTAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
*
1500251 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCAGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1500297 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
* * * *
1500343 CATCTGTAAGCCCTTCAGTGCATGTTGTTTTC-AAAACCTCCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
*
1500388 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
*
1500434 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTTGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
* *
1500480 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTATCAAAAACCTTCGGGT
*
1500526 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCAGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1500572 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
* *
1500618 CATCTGTAAGTCCTTCAATGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
* * * *
1500663 CATTTTTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
* * *
1500708 GATCTGTAAGCCCTTCAGTGCACGATGTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTT
1500737 TTTAAAACCT
Statistics
Matches: 617, Mismatches: 48, Indels: 10
0.91 0.07 0.01
Matches are distributed among these distances:
45 161 0.26
46 415 0.67
47 41 0.07
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (46 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
Found at i:1500423 original size:229 final size:229
Alignment explanation
Indices: 1500021--1500736 Score: 1141
Period size: 229 Copynumber: 3.1 Consensus size: 229
1500011 CTATTTCTAA
*
1500021 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCCTTCGGGTCATCTGTAAGTCCTTCAG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAA-CCTTCGGGTCATCTGTAAGTCCTTCAG
* ** *
1500086 TGCATGATGTTATCAAAAACCTTCGTGTCATCACTAAGTCCTTCAGTGTATGATGTTTTCAAAAC
65 TGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAC
* * *
1500151 CTCCAGGACATCTGTAAGTCTTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGT
130 CTCCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGT
*
1500216 CCTTTAGTGCATGATGTTATCAAAAACCTTCGGGT
195 CCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
* *
1500251 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCAGGTCATCTGTAAGTCCTTCAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
* *
1500316 GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGTTGTTTTCAAAACC
66 GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
*
1500381 TCCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTC
131 TCCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTC
*
1500446 CTTCAGTGCATGATGTTATCAAAAACCTTTGGGT
196 CTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
*
1500480 CATCTGTAAGCCCTTCAGTGCATGATGTTTTTC-AAAACCTTCGGGTCATCTGTAAGTCCTTCAG
1 CATCTGTAAGCCCTTCAGTGCATGATG-TTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAG
* *
1500544 TGCATGATGTTATCAAAAACCTTCAGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAA
65 TGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAA
* * * * *
1500609 CCTTCGGGTCATCTGTAAGTCCTTCAATGCATGATGTTTTC-AAAACCTTCGGGTCATTTTTAAG
129 CCTCCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAG
* *
1500673 CCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
194 TCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
* *
1500708 GATCTGTAAGCCCTTCAGTGCACGATGTT
1 CATCTGTAAGCCCTTCAGTGCATGATGTT
1500737 TTTAAAACCT
Statistics
Matches: 453, Mismatches: 31, Indels: 7
0.92 0.06 0.01
Matches are distributed among these distances:
227 2 0.00
228 37 0.08
229 332 0.73
230 82 0.18
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (229 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGT
GCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACC
TCCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTC
CTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
Found at i:1500566 original size:26 final size:26
Alignment explanation
Indices: 1500537--1500613 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
1500527 ATCTGTAAGT
1500537 CCTTCAGTGCATGATGTTATCAAAAA
1 CCTTCAGTGCATGATGTTATCAAAAA
* **
1500563 CCTTCAG-GTCAT-CTG---T--AAGT
1 CCTTCAGTG-CATGATGTTATCAAAAA
1500583 CCTTCAGTGCATGATGTTATCAAAAA
1 CCTTCAGTGCATGATGTTATCAAAAA
1500609 CCTTC
1 CCTTC
1500614 GGGTCATCTG
Statistics
Matches: 37, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
20 12 0.32
21 3 0.08
22 1 0.03
24 1 0.03
25 3 0.08
26 17 0.46
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (26 bp):
CCTTCAGTGCATGATGTTATCAAAAA
Found at i:1500702 original size:25 final size:25
Alignment explanation
Indices: 1500629--1500703 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
1500619 ATCTGTAAGT
*
1500629 CCTTCAATGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTCAAAA
* * **
1500654 CCTTC-G-G-GTCAT-TTTT-AAGC
1 CCTTCAGTGCATGATGTTTTCAAAA
1500674 CCTTCAGTGCATGATGTTTTCAAAA
1 CCTTCAGTGCATGATGTTTTCAAAA
1500699 CCTTC
1 CCTTC
1500704 GGGTGATCTG
Statistics
Matches: 36, Mismatches: 9, Indels: 10
0.65 0.16 0.18
Matches are distributed among these distances:
20 7 0.19
21 5 0.14
22 4 0.11
23 4 0.11
24 4 0.11
25 12 0.33
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (25 bp):
CCTTCAGTGCATGATGTTTTCAAAA
Found at i:1501004 original size:3 final size:3
Alignment explanation
Indices: 1500986--1501048 Score: 58
Period size: 3 Copynumber: 21.3 Consensus size: 3
1500976 TTTCATTAAA
* * * * *
1500986 ATT ATT CTT AATT ATT ATT TTT ATT ATT ATT ATT AAT A-T AAT AAT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1501031 ATT ATT ATT ATT -TT ATT A
1 ATT ATT ATT ATT ATT ATT A
1501049 CAAATAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 45 0.88
4 2 0.04
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1502456 original size:2 final size:2
Alignment explanation
Indices: 1502443--1502476 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1502433 ATCTTAAGTC
*
1502443 AT AT AA 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
1502477 TATCTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1505498 original size:23 final size:23
Alignment explanation
Indices: 1505472--1505522 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
1505462 AATGAGTATG
*
1505472 TTTATCGTTATTCTATAACGGTA
1 TTTATCGTTATTCTATAACAGTA
1505495 TTTATCGTTATTCTATAACAGTA
1 TTTATCGTTATTCTATAACAGTA
1505518 TTTAT
1 TTTAT
1505523 TATCACTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.10, T:0.51
Consensus pattern (23 bp):
TTTATCGTTATTCTATAACAGTA
Found at i:1509969 original size:177 final size:175
Alignment explanation
Indices: 1509664--1509993 Score: 624
Period size: 177 Copynumber: 1.9 Consensus size: 175
1509654 TTTATTTGAA
1509664 AAGTTTATTAATATAATCGAGTGTGATATAATTGATAAAATTTGAAAATGAGTACTCATTTTCAA
1 AAGTTTATTAATATAATCGAGTGTGATATAATTGATAAAATTTGAAAATGAGTACTCATTTTCAA
1509729 GTTTATTAATATAACTGATAAAATTTGAAATTTAATGGTATAAACAAATTAATGGACAAAATTTA
66 GTTTATTAATATAACTGATAAAATTTGAAATTTAATGGTATAAACAAATTAATGGACAAAATTTA
1509794 GTGGTATATGGTGTAATTTATTTGAAAATGAGCGTACTCATTTTC
131 GTGGTATATGGTGTAATTTATTTGAAAATGAGCGTACTCATTTTC
1509839 AAGTTTATTAATATAATCGAGTGTGATATAATTGATAAAATTTGAAAATGAGTGTACTCATTTTC
1 AAGTTTATTAATATAATCGAGTGTGATATAATTGATAAAATTTGAAAATGA--GTACTCATTTTC
* *
1509904 AAGTTTATTAATATAACTGATAAAATTTGAAATTTAATGGTATAAACAAATTCATGGATAAAATT
64 AAGTTTATTAATATAACTGATAAAATTTGAAATTTAATGGTATAAACAAATTAATGGACAAAATT
1509969 TAGTGGTATATGGTGTAATTTATTT
129 TAGTGGTATATGGTGTAATTTATTT
1509994 AATTTTTTTC
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
175 51 0.34
177 100 0.66
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (175 bp):
AAGTTTATTAATATAATCGAGTGTGATATAATTGATAAAATTTGAAAATGAGTACTCATTTTCAA
GTTTATTAATATAACTGATAAAATTTGAAATTTAATGGTATAAACAAATTAATGGACAAAATTTA
GTGGTATATGGTGTAATTTATTTGAAAATGAGCGTACTCATTTTC
Found at i:1511032 original size:2 final size:2
Alignment explanation
Indices: 1511025--1511064 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1511015 AGTCTAAATT
1511025 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
1511065 AAATAAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1515710 original size:3 final size:3
Alignment explanation
Indices: 1515702--1515727 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1515692 GGTCCTGTAA
1515702 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1515728 ACTCCGGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1522309 original size:75 final size:73
Alignment explanation
Indices: 1522215--1522423 Score: 226
Period size: 75 Copynumber: 2.8 Consensus size: 73
1522205 TTGGGTTTAA
* *
1522215 TATTTTTCTAGACTTAATATTATGATTTGAGTCTTAAGATTTGACACTTTACTATTATGATTTGA
1 TATTATTCTAGACTTAATATTATGGTTTGAGTCTTAA-ATTTGACACTTTA-TATTATGATTTGA
1522280 TTATGAATTT
64 TTATGAATTT
* * * * * * * *
1522290 TATTATTCTAGAGTTAATATTGTGGTTTGAATATTGAAATTTAACATTTTAATATTGTGATTTGT
1 TATTATTCTAGACTTAATATTATGGTTTGAGTCTT-AAATTTGACACTTT-ATATTATGATTTGA
*
1522355 TTATGGATTT
64 TTATGAATTT
* * *
1522365 TATTGTTCTAAACTTAATATTATGGTTTGAGTCTTGATATTTG--ACTTTAT-TTATGATTT
1 TATTATTCTAGACTTAATATTATGGTTTGAGTCTT-AAATTTGACACTTTATATTATGATTT
1522424 ATATATATAT
Statistics
Matches: 111, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
71 8 0.07
72 2 0.02
73 4 0.04
75 94 0.85
76 3 0.03
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (73 bp):
TATTATTCTAGACTTAATATTATGGTTTGAGTCTTAAATTTGACACTTTATATTATGATTTGATT
ATGAATTT
Found at i:1529793 original size:18 final size:18
Alignment explanation
Indices: 1529770--1529842 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
1529760 AGGGATTATC
1529770 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGATAT
* ** *
1529788 AGTGGTTCTTCGTAACAAT
1 AGTGGTCCTTCGGGA-TAT
* *
1529807 CAGTGGTCCTTCAGGACAT
1 -AGTGGTCCTTCGGGATAT
1529826 AGTGGTCCTTCGGGATA
1 AGTGGTCCTTCGGGATA
1529843 AATATTTAGT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
18 27 0.64
19 4 0.10
20 11 0.26
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.32
Consensus pattern (18 bp):
AGTGGTCCTTCGGGATAT
Found at i:1536642 original size:38 final size:38
Alignment explanation
Indices: 1536591--1536667 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
1536581 TCGAGGGATT
*
1536591 ATCAGTGGTCCTTCAGGACATAATGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCAGGACATAATGGTCCTTCGGAACA
* * *
1536629 ATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACA
1 ATCAGTGGTCCTTCAGGACATAATGGTCCTTCGGAACA
1536667 A
1 A
1536668 ATATTCAGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (38 bp):
ATCAGTGGTCCTTCAGGACATAATGGTCCTTCGGAACA
Found at i:1536655 original size:18 final size:18
Alignment explanation
Indices: 1536594--1536666 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
1536584 AGGGATTATC
*
1536594 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
* * *
1536612 AATGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
1536631 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
1536650 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1536667 AATATTCAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
18 29 0.63
19 4 0.09
20 13 0.28
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:1553522 original size:6 final size:6
Alignment explanation
Indices: 1553505--1553552 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
1553495 AAACAAGAAT
* *
1553505 AAAATAA AAAAAA GAAAAGA AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAAT-A AAAATA -AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
1553553 ATAGAAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
6 28 0.76
7 9 0.24
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.10
Consensus pattern (6 bp):
AAAATA
Found at i:1553534 original size:12 final size:12
Alignment explanation
Indices: 1553519--1553564 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1553509 TAAAAAAAAG
1553519 AAAAGAAAAATA
1 AAAAGAAAAATA
*
1553531 AAAATAAAAATA
1 AAAAGAAAAATA
*
1553543 AAAATAAAAAATA
1 AAAA-GAAAAATA
*
1553556 GAAAGAAAA
1 AAAAGAAAA
1553565 TGAGAGGTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.11
Consensus pattern (12 bp):
AAAAGAAAAATA
Found at i:1554250 original size:33 final size:33
Alignment explanation
Indices: 1554208--1554281 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
1554198 ACACACACCC
*
1554208 ATGCATACTCATGCATTCATTTAATAGGATCAA
1 ATGCATACTCATGCATTCATTTAATAGGAGCAA
*
1554241 ATGCATACTCATGCATTCATTTAATAGGAGCAT
1 ATGCATACTCATGCATTCATTTAATAGGAGCAA
1554274 ATGCATAC
1 ATGCATAC
1554282 ATCAAATTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (33 bp):
ATGCATACTCATGCATTCATTTAATAGGAGCAA
Found at i:1554489 original size:44 final size:44
Alignment explanation
Indices: 1554426--1554620 Score: 135
Period size: 44 Copynumber: 4.4 Consensus size: 44
1554416 AACTTTCAGC
*
1554426 TCGATTCTATCACAGAAGGAGGTAGATCAACACTAACATCTCAT
1 TCGATTCCATCACAGAAGGAGGTAGATCAACACTAACATCTCAT
* **** * *
1554470 TCGATTCCATCACAGAAGGAGGTGGATCAACA-TTTTTTGTTCGT
1 TCGATTCCATCACAGAAGGAGGTAGATCAACACTAACAT-CTCAT
* * * * * * * * *
1554514 TCAAATCCATCGCAGAAGGAGTTAGATCAGC-GTCAAC-TTTTAGC
1 TCGATTCCATCACAGAAGGAGGTAGATCAACACT-AACATCTCA-T
* * * * *
1554558 TCGATTCTATCACAGAATGAGGTAGATCAGCACCAACATCTCGT
1 TCGATTCCATCACAGAAGGAGGTAGATCAACACTAACATCTCAT
*
1554602 TCGATTCCATCACATAAGG
1 TCGATTCCATCACAGAAGG
1554621 GGGTGAATCG
Statistics
Matches: 110, Mismatches: 35, Indels: 12
0.70 0.22 0.08
Matches are distributed among these distances:
43 4 0.04
44 104 0.95
45 2 0.02
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (44 bp):
TCGATTCCATCACAGAAGGAGGTAGATCAACACTAACATCTCAT
Found at i:1554714 original size:133 final size:133
Alignment explanation
Indices: 1554414--1555597 Score: 1611
Period size: 133 Copynumber: 9.0 Consensus size: 133
1554404 AAGAACTTGT
* * ** *
1554414 TCAACTTTCAGCTCGATTCTATCACAGAAGGAGGTAGATCAACACTAACATCTCATTCGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * * *
1554479 TCACAGAAGGAGGTGGATCAACATTTTT-TGTTCGTTCAAATCCATCGCAGAAGGAGTTAGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
1554543 GCG
131 GCG
* *
1554546 TCAACTTTTAGCTCGATTCTATCACAGAATGAGGTAGATCAGCACCAACATCTCGTTCGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * * * * * *
1554611 TCACATAAGGGGGTGAATCGACATTTTTATTTTCACTCAAATTCATCGCAGAAGGAATTAGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
1554676 ACG
131 GCG
* * *
1554679 TCAACTTTTAGCTCGATTCTATCACATAAGAAGGTAGATCAGCACCGACATCTCGTTCGATTCTA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
** * * * **
1554744 TCACAGAAAAAGGTGGATCGACCTTTTTATTTTCACTTAAATCCATCATAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
*
1554809 ACG
131 GCG
* * *
1554812 TCAACTTTCAGCTTGATTCTGTCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * * *
1554877 TCACAGAAGGAGGTAGATCGACCTTTTTATTTTCGTTCAAATCCATCGCAGAAGGAGTTCGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
1554942 GCG
131 GCG
* * *
1554945 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCTGCACCAACATCTCGTTCGATTCTA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* *
1555010 TCACAGAAGGAGGAGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAATGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
1555075 GCG
131 GCG
* * *
1555078 TCAACTTTTAGCTCAATTCTATCACAGAAGAAAGTAGATCAGCACCGACATCTCGTTCGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * *
1555143 TCACAGAAGGAGGTGGATCGACCTCTTTATTTT-TCTCAAATCCATCGCAGAAGGAGTTGGATCA
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
1555207 GCG
131 GCG
* * * *
1555210 TCAACTTTCAGCTTGATTCTATCACAGAAGGAGGTAGATAAGCACCAACATCTCGTTCGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* *
1555275 TCATAGAAGGAGGTGGATCGACATTTTTTATTTTCGCTCAAATCCATTGCAGAAGGAGTTGGATC
66 TCACAGAAGGAGGTGGATCGACA-TTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
1555340 AGCG
130 AGCG
* *
1555344 TCAACTTTTAGCTCGATTCTATAATAGAAAGGAGGTAGAT---CACCGACATCTCGTTCGATTCC
1 TCAACTTTTAGCTCGATTCTATCACAG-AAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCC
* *
1555406 ATCACAGAATGAGGTGGATCGACA-TTTTATTTTCACTCAAATCCATCGCAGAAGGAGTTGGATC
65 ATCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATC
1555470 AGCG
130 AGCG
* * * ** * * *
1555474 TCAACTTTCAACTTGATTCTATCGTAGAATGAGGTAGATCAGCACCGATATCTCGTTAGATTCCA
1 TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
* * * * *
1555539 TCAAAAAAAGA-G-GGATCGACA---TT-TTTTCGCTCAAATCCATAC-CAGAAAGAGTTAGATC
66 TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCAT-CGCAGAAGGAGTTGGATC
1555597 A
130 A
1555598 TCATCATCAA
Statistics
Matches: 938, Mismatches: 106, Indels: 21
0.88 0.10 0.02
Matches are distributed among these distances:
127 31 0.03
128 3 0.00
129 11 0.01
130 73 0.08
131 1 0.00
132 267 0.28
133 485 0.52
134 55 0.06
135 12 0.01
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (133 bp):
TCAACTTTTAGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTCGATTCCA
TCACAGAAGGAGGTGGATCGACATTTTTATTTTCGCTCAAATCCATCGCAGAAGGAGTTGGATCA
GCG
Found at i:1554874 original size:44 final size:44
Alignment explanation
Indices: 1554826--1555293 Score: 200
Period size: 44 Copynumber: 10.6 Consensus size: 44
1554816 CTTTCAGCTT
* *
1554826 GATTCTGTCACAGAAGGAGGTAGATCAGCACCGACATCTCGTTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
* *** *
1554870 GATTCCATCACAGAAGGAGGTAGATC-G-ACCTTTTTATTTTCGTTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACC--AACA-TCTCGTTC
* * * * * * ** * * * *
1554915 AAATCCATCGCAGAAGGAGTTCGATCAGCGTCAACTTTTAGCTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
*
1554959 GATTCTATCACAGAAGGAGGTAGATCTGCACCAACATCTCGTTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
***** * *
1555003 GATTCTATCACAGAAGGAGG-AGGATC-GACATTTTTATTTTCGCTC
1 GATTCTATCACAGAAGGAGGTA-GATCAG-CACCAACA-TCTCGTTC
* * * * * * * ** * * * *
1555048 AAATCCATCGCAGAATGAGTTGGATCAGCGTCAACTTTTAGCTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
* * * *
1555092 AATTCTATCACAGAAGAAAGTAGATCAGCACCGACATCTCGTTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
* * * **
1555136 GATTCCATCACAGAAGGAGGTGGATC-G-ACC-TCTTTAT-TTTTCTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAAC---ATCTCGT-TC
* * * * * * ** *
1555180 AAATCCATCGCAGAAGGAGTTGGATCAGCGTCAAC-TTTCAGCTT-
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTC-G-TTC
*
1555224 GATTCTATCACAGAAGGAGGTAGATAAGCACCAACATCTCGTTC
1 GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
* * *
1555268 GATTCCATCATAGAAGGAGGTGGATC
1 GATTCTATCACAGAAGGAGGTAGATC
1555294 GACATTTTTT
Statistics
Matches: 303, Mismatches: 99, Indels: 44
0.68 0.22 0.10
Matches are distributed among these distances:
41 1 0.00
42 6 0.02
43 9 0.03
44 222 0.73
45 59 0.19
46 4 0.01
47 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.27
Consensus pattern (44 bp):
GATTCTATCACAGAAGGAGGTAGATCAGCACCAACATCTCGTTC
Found at i:1561121 original size:20 final size:20
Alignment explanation
Indices: 1561070--1561121 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
1561060 ATAGTTGTAG
**
1561070 GGGTATTGATACCTTAGGTA
1 GGGTATTGATACAGTAGGTA
**
1561090 GGGTATCAATACAGTAGAG-A
1 GGGTATTGATACAGTAG-GTA
1561110 GGGTATTGATAC
1 GGGTATTGATAC
1561122 TATAAGGCCA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.29
Consensus pattern (20 bp):
GGGTATTGATACAGTAGGTA
Done.