Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007762.1 Hibiscus syriacus cultivar Beakdansim tig00110032_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: 314764
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:226706 original size:33 final size:33
Alignment explanation
Indices: 226649--226744 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
226639 AAAACAGACT
**
226649 ATCGCAATGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
226683 ATCGCAATGCGAAATAAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
226716 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
226745 CGAAACTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:226847 original size:52 final size:53
Alignment explanation
Indices: 226761--226862 Score: 170
Period size: 52 Copynumber: 1.9 Consensus size: 53
226751 TAATTTCGCG
**
226761 TTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCGTA
*
226814 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTC
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTC
226863 CGCGTTGCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 34 0.74
53 12 0.26
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (53 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCGTTGCGATAGTCATTTCGTA
Found at i:226870 original size:20 final size:20
Alignment explanation
Indices: 226845--226933 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
226835 GCGATTCTCT
226845 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
226865 CGTTGCGATAGTCAATTCTG
1 CGTTGCGATAGTCATTTCCG
*
226885 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
226905 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
226925 CGTTGCGAT
1 CGTTGCGAT
226934 TTCCGCGTTG
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 58 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:226894 original size:40 final size:40
Alignment explanation
Indices: 226847--226933 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
226837 GATTCTCTCG
226847 TTGCGATAGTCATTTCCGCGTTGCGATAGTCA-ATTCTGCA
1 TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTC-GCA
* *
226887 TTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCGCG
1 TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCGCA
226927 TTGCGAT
1 TTGCGAT
226934 TTCCGCGTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (40 bp):
TTGCGATAGTCATTTCCGCGTTGCGATAGTCATATTCGCA
Found at i:229397 original size:24 final size:24
Alignment explanation
Indices: 229363--229417 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
229353 CTGAAAAATC
229363 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
229387 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
229411 AT-AAAAT
1 ATCAAAAT
229418 TTCGAATACT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:230290 original size:20 final size:20
Alignment explanation
Indices: 230270--230482 Score: 340
Period size: 20 Copynumber: 10.7 Consensus size: 20
230260 CGATAGTTAG
*
230270 AATCTCGTTGCGATTTA--T
1 AATCGCGTTGCGATTTACGT
230288 AGATTCGCGTTGCGATTTACGT
1 A-A-TCGCGTTGCGATTTACGT
230310 AATCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
*
230330 ATTCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
230350 AATCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
*
230370 ATTCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
* *
230390 ATTCGCGTTGCGAATTACGT
1 AATCGCGTTGCGATTTACGT
230410 AATCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
230430 AATCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
*
230450 ATTCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
230470 AATCGCGTTGCGA
1 AATCGCGTTGCGA
230483 ATTAGGAAAA
Statistics
Matches: 182, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
18 1 0.01
19 1 0.01
20 177 0.97
21 1 0.01
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.37
Consensus pattern (20 bp):
AATCGCGTTGCGATTTACGT
Found at i:230503 original size:21 final size:21
Alignment explanation
Indices: 230479--230524 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
230469 TAATCGCGTT
230479 GCGAATTAGGA-AAATCGCAAC
1 GCGAATT-GGAGAAATCGCAAC
* *
230500 GCGAATTTGAGAAATCGCAAT
1 GCGAATTGGAGAAATCGCAAC
230521 GCGA
1 GCGA
230525 TAGTTAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTGGAGAAATCGCAAC
Found at i:230533 original size:21 final size:21
Alignment explanation
Indices: 230490--230537 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
230480 CGAATTAGGA
*
230490 AAATCGCAACGCGAATTTGAG
1 AAATCGCAACGCGAAGTTGAG
*
230511 AAATCGCAATGCGATAGTT-AG
1 AAATCGCAACGCGA-AGTTGAG
230532 -AATCGC
1 AAATCGC
230538 GTTGCGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (21 bp):
AAATCGCAACGCGAAGTTGAG
Found at i:231192 original size:10 final size:10
Alignment explanation
Indices: 231170--231216 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
231160 GGACCAGCTG
*
231170 AAAACCGGAA
1 AAAACCGGGA
*
231180 AAAACTGGGA
1 AAAACCGGGA
*
231190 AAAACCGAGA
1 AAAACCGGGA
*
231200 AAAACCGGAA
1 AAAACCGGGA
231210 AAAACCG
1 AAAACCG
231217 CCAATTTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.57, C:0.19, G:0.21, T:0.02
Consensus pattern (10 bp):
AAAACCGGGA
Found at i:231983 original size:18 final size:18
Alignment explanation
Indices: 231951--231985 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
231941 CCGGTTCTTC
*
231951 CGACCGGTCGGACCAGTT
1 CGACCGGTCGAACCAGTT
*
231969 CGACCGGTTGAACCAGT
1 CGACCGGTCGAACCAGT
231986 GAACCGATAG
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:246878 original size:31 final size:31
Alignment explanation
Indices: 246843--246902 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
246833 AATAGATACT
*
246843 AACATTTTCTAAGAGAATGCAATGAAGCTTG
1 AACATTTTCTAAGAAAATGCAATGAAGCTTG
246874 AACATTTTCTAAGAAAATGCAATGAAGCT
1 AACATTTTCTAAGAAAATGCAATGAAGCT
246903 GAAAAAGCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (31 bp):
AACATTTTCTAAGAAAATGCAATGAAGCTTG
Found at i:251599 original size:21 final size:21
Alignment explanation
Indices: 251569--251611 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
251559 ATATAAATTT
* *
251569 TGCATTGATGCACTGCTACAG
1 TGCATCGATGCAATGCTACAG
251590 TGCATCGATGCAATGCTACAG
1 TGCATCGATGCAATGCTACAG
251611 T
1 T
251612 ACTAATACAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
TGCATCGATGCAATGCTACAG
Found at i:252295 original size:31 final size:31
Alignment explanation
Indices: 252245--252322 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
252235 ATAGATTTCA
* *
252245 AAGAACCTAGGTAATCAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
252276 AAGAACATAGATAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
252307 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
252323 CCTCGACCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.19
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCG
Found at i:252542 original size:5 final size:5
Alignment explanation
Indices: 252527--252555 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
252517 TATGTGTAAA
252527 CATAT -ATAT CATAT CATAT CATAT CATAT
1 CATAT CATAT CATAT CATAT CATAT CATAT
252556 AACACCTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (5 bp):
CATAT
Found at i:256939 original size:33 final size:33
Alignment explanation
Indices: 256893--256966 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
256883 CCCAAAGTAT
*
256893 TGGGTA-AGTCCTTGGTACTACTTGACAAACGG
1 TGGGTAGAATCCTTGGTACTACTTGACAAACGG
*
256925 TGGGTAGAATCCTTGGTACTTCTTGACAAACGG
1 TGGGTAGAATCCTTGGTACTACTTGACAAACGG
256958 TGGGTAGAA
1 TGGGTAGAA
256967 GTCTTGATAT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 6 0.15
33 33 0.85
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (33 bp):
TGGGTAGAATCCTTGGTACTACTTGACAAACGG
Found at i:262647 original size:21 final size:20
Alignment explanation
Indices: 262621--262679 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 20
262611 ATTATCCAAT
262621 AAACTTGACATCCATAACAAC
1 AAACTTGA-ATCCATAACAAC
262642 AAACTTGAAATCCATAACAAC
1 AAACTTG-AATCCATAACAAC
*
262663 CAACTTGAACTCCATAA
1 AAACTTGAA-TCCATAA
262680 TAATAAATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 2 0.06
21 32 0.91
22 1 0.03
ACGTcount: A:0.47, C:0.27, G:0.05, T:0.20
Consensus pattern (20 bp):
AAACTTGAATCCATAACAAC
Found at i:274724 original size:12 final size:12
Alignment explanation
Indices: 274707--274798 Score: 78
Period size: 12 Copynumber: 7.7 Consensus size: 12
274697 ATGCTATATC
274707 TGATTTCTGTTA
1 TGATTTCTGTTA
* *
274719 TGATTTCTATTC
1 TGATTTCTGTTA
* *
274731 TAAATTCTGTTA
1 TGATTTCTGTTA
* *
274743 TGATTTCTGCTC
1 TGATTTCTGTTA
*
274755 TGAATTCTGTTA
1 TGATTTCTGTTA
*
274767 TGATTTCT-TCTC
1 TGATTTCTGT-TA
* *
274779 TAAATTCTGTTA
1 TGATTTCTGTTA
274791 TGATTTCT
1 TGATTTCT
274799 AATATCTATG
Statistics
Matches: 58, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
11 1 0.02
12 56 0.97
13 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.12, T:0.54
Consensus pattern (12 bp):
TGATTTCTGTTA
Found at i:274743 original size:24 final size:24
Alignment explanation
Indices: 274711--274799 Score: 135
Period size: 24 Copynumber: 3.7 Consensus size: 24
274701 TATATCTGAT
274711 TTCTGTTATGATTTCTATTCTAAA
1 TTCTGTTATGATTTCTATTCTAAA
** *
274735 TTCTGTTATGATTTCTGCTCTGAA
1 TTCTGTTATGATTTCTATTCTAAA
274759 TTCTGTTATGATTTCT-TCTCTAAA
1 TTCTGTTATGATTTCTAT-TCTAAA
274783 TTCTGTTATGATTTCTA
1 TTCTGTTATGATTTCTA
274800 ATATCTATGT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.20, C:0.15, G:0.11, T:0.54
Consensus pattern (24 bp):
TTCTGTTATGATTTCTATTCTAAA
Found at i:274763 original size:48 final size:48
Alignment explanation
Indices: 274705--274798 Score: 163
Period size: 48 Copynumber: 2.0 Consensus size: 48
274695 GAATGCTATA
*
274705 TCTGATTTCTGTTATGATTTCTAT-TCTAAATTCTGTTATGATTTCTGC
1 TCTGAATTCTGTTATGATTTCT-TCTCTAAATTCTGTTATGATTTCTGC
274753 TCTGAATTCTGTTATGATTTCTTCTCTAAATTCTGTTATGATTTCT
1 TCTGAATTCTGTTATGATTTCTTCTCTAAATTCTGTTATGATTTCT
274799 AATATCTATG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 1 0.02
48 43 0.98
ACGTcount: A:0.19, C:0.15, G:0.12, T:0.54
Consensus pattern (48 bp):
TCTGAATTCTGTTATGATTTCTTCTCTAAATTCTGTTATGATTTCTGC
Found at i:278493 original size:12 final size:12
Alignment explanation
Indices: 278476--278541 Score: 60
Period size: 12 Copynumber: 5.5 Consensus size: 12
278466 ATGCTATATC
278476 TGATTTCTGTTA
1 TGATTTCTGTTA
* *
278488 TGATTTCTATTC
1 TGATTTCTGTTA
* *
278500 TAAATTCTGTTA
1 TGATTTCTGTTA
* *
278512 TGATTTCTGCTC
1 TGATTTCTGTTA
* *
278524 TGAATTCTATTA
1 TGATTTCTGTTA
278536 TGATTT
1 TGATTT
278542 TTAATAATTA
Statistics
Matches: 39, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (12 bp):
TGATTTCTGTTA
Found at i:278512 original size:24 final size:24
Alignment explanation
Indices: 278480--278541 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
278470 TATATCTGAT
*
278480 TTCTGTTATGATTTCTATTCTAAA
1 TTCTGTTATGATTTCTACTCTAAA
* *
278504 TTCTGTTATGATTTCTGCTCTGAA
1 TTCTGTTATGATTTCTACTCTAAA
*
278528 TTCTATTATGATTT
1 TTCTGTTATGATTT
278542 TTAATAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (24 bp):
TTCTGTTATGATTTCTACTCTAAA
Found at i:284234 original size:24 final size:24
Alignment explanation
Indices: 284202--284264 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
284192 TATATCAAAA
* *
284202 ATCAAAACATAATTCAGGTCAGAT
1 ATCAAAACAGAATCCAGGTCAGAT
* *
284226 ATCATAACAGAATCCAGGTCAGGT
1 ATCAAAACAGAATCCAGGTCAGAT
* *
284250 ATTAGAACAGAATCC
1 ATCAAAACAGAATCC
284265 TACTCAGGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATCCAGGTCAGAT
Found at i:292243 original size:28 final size:28
Alignment explanation
Indices: 292209--292265 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
292199 CAGAATTTAA
292209 AGTTTATAATATAATTCATAGGATTTGG
1 AGTTTATAATATAATTCATAGGATTTGG
* * * *
292237 AGTTTATGATGTAATTTATAGGGTTTGG
1 AGTTTATAATATAATTCATAGGATTTGG
292265 A
1 A
292266 TTAAATTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.44
Consensus pattern (28 bp):
AGTTTATAATATAATTCATAGGATTTGG
Found at i:292744 original size:16 final size:16
Alignment explanation
Indices: 292723--292753 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
292713 TGAAGTTGAG
*
292723 TCAATATCATGTCAGT
1 TCAATATCAAGTCAGT
292739 TCAATATCAAGTCAG
1 TCAATATCAAGTCAG
292754 ATCATTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (16 bp):
TCAATATCAAGTCAGT
Found at i:293974 original size:31 final size:30
Alignment explanation
Indices: 293883--293985 Score: 188
Period size: 30 Copynumber: 3.4 Consensus size: 30
293873 TAGATGTTCA
293883 CGTGCAAGTCACTCTAATCCTTTGGGCTCC
1 CGTGCAAGTCACTCTAATCCTTTGGGCTCC
293913 CGTGCAAGTCACTCTAATCCTTTGGGCTCC
1 CGTGCAAGTCACTCTAATCCTTTGGGCTCC
*
293943 CGTGCAAGTCACTCTAATCCTTAGGGGCTCC
1 CGTGCAAGTCACTCTAATCCTT-TGGGCTCC
293974 CGTGCAAGTCAC
1 CGTGCAAGTCAC
293986 CCGAAATAAT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
30 52 0.73
31 19 0.27
ACGTcount: A:0.18, C:0.33, G:0.21, T:0.27
Consensus pattern (30 bp):
CGTGCAAGTCACTCTAATCCTTTGGGCTCC
Found at i:294063 original size:69 final size:69
Alignment explanation
Indices: 293938--294102 Score: 206
Period size: 69 Copynumber: 2.4 Consensus size: 69
293928 AATCCTTTGG
* * * *
293938 GCTCCCGTGCAAGTCACTCTAATCCTTAGGGGCTCCCGTGCAAGTCACCCGAAATAATTACAATT
1 GCTCCCGTGCGAGTCACTCTAATCCTTAGGGGCTCCCGTGCAAGTAACCAGAAATAATCACAATT
294003 AGGT
66 AGGT
* * * ** * *
294007 GCTCCCGTGTGATTCACTCTATTCCTTAGGGGCTTTCGTGCGAGTAACCA-AGAATAATCACGAT
1 GCTCCCGTGCGAGTCACTCTAATCCTTAGGGGCTCCCGTGCAAGTAACCAGA-AATAATCACAAT
294071 TAGGT
65 TAGGT
*
294076 GCTCCCTTGCGAGTCACTCTAATCCTT
1 GCTCCCGTGCGAGTCACTCTAATCCTT
294103 CAAGGCTCTT
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
68 1 0.01
69 79 0.99
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (69 bp):
GCTCCCGTGCGAGTCACTCTAATCCTTAGGGGCTCCCGTGCAAGTAACCAGAAATAATCACAATT
AGGT
Found at i:294380 original size:76 final size:76
Alignment explanation
Indices: 294288--294801 Score: 679
Period size: 76 Copynumber: 6.8 Consensus size: 76
294278 ATTCTAGCTG
* * * * *
294288 TGAAACATAACATTGACTTACACTAGTGAAATGAATACGTAATTCTAGCACTAAACTTATGACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
* *
294353 GATTTCAGCAA
66 AATTCCAGCAA
* * * *
294364 TGAAGCTTAACATTGACTTATACCAGTTAAATGAATATGTAATT-CAAGCACTAAACTTATCACA
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAA-CACTAAACTTATCACA
* * *
294428 TCATTTCAGCAG
65 TAATTCCAGCAA
* * * * *
294440 TGAAATTTAGCATTGACTTACACCAGTAAAATGAATATGTAATTCCAACGCTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
*
294505 AATTCCAGTAA
66 AATTCCAGCAA
* ** * *
294516 TGAAACTTAACATTAACTTACACCAACGAAATGAATACATAATTTCAACACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
*
294581 AATTCCAACAA
66 AATTCCAGCAA
* * * *
294592 TGAAACTTAACATTGACTTACACCAGTGAAATGAGTACATAATTCCAGCATTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
294657 AATTCCAGCAA
66 AATTCCAGCAA
* *
294668 TGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
*
294733 AATTCTAGCAA
66 AATTCCAGCAA
* * * *
294744 CGGAACTTAACATTGACTTACATCAGTGAAATGAATACGTAATTCCAACACTAGACTT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTT
294802 TGAAGCTTAA
Statistics
Matches: 382, Mismatches: 54, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
75 1 0.00
76 378 0.99
77 3 0.01
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (76 bp):
TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAAACTTATCACAT
AATTCCAGCAA
Found at i:294580 original size:25 final size:26
Alignment explanation
Indices: 294552--294672 Score: 83
Period size: 25 Copynumber: 4.8 Consensus size: 26
294542 CGAAATGAAT
* *
294552 ACATAATTTCAACACT-AAACTTATC
1 ACATAATTCCAACAATGAAACTTATC
294577 ACATAATTCCAACAATGAAACTTA--
1 ACATAATTCCAACAATGAAACTTATC
* * * * *
294601 ACATTGACTTACACCAGTGAAA-TGAGT-
1 ACA-T-AATTCCAACAATGAAACTTA-TC
* *
294628 ACATAATTCCAGC-ATTAAACTTATC
1 ACATAATTCCAACAATGAAACTTATC
*
294653 ACATAATTCCAGCAATGAAA
1 ACATAATTCCAACAATGAAA
294673 TTTAACATTG
Statistics
Matches: 74, Mismatches: 14, Indels: 15
0.72 0.14 0.15
Matches are distributed among these distances:
24 8 0.11
25 38 0.51
26 25 0.34
27 3 0.04
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.27
Consensus pattern (26 bp):
ACATAATTCCAACAATGAAACTTATC
Found at i:294854 original size:58 final size:58
Alignment explanation
Indices: 294749--294859 Score: 177
Period size: 58 Copynumber: 1.9 Consensus size: 58
294739 AGCAACGGAA
* *
294749 CTTAACATTGACTTACATCAGTGAAATGAATACGTAATTCCAACACTAGACTTTGAAG
1 CTTAACATTGACTTACATCAGTGAAATGAATACGTAATTACAACACTAAACTTTGAAG
* * *
294807 CTTAACATTGACTTACATCAGTGAAATGAATATGTAATTATAGCACTAAACTT
1 CTTAACATTGACTTACATCAGTGAAATGAATACGTAATTACAACACTAAACTT
294860 ATCACATAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.32
Consensus pattern (58 bp):
CTTAACATTGACTTACATCAGTGAAATGAATACGTAATTACAACACTAAACTTTGAAG
Found at i:294914 original size:134 final size:134
Alignment explanation
Indices: 294674--294930 Score: 397
Period size: 134 Copynumber: 1.9 Consensus size: 134
294664 GCAATGAAAT
* *
294674 TTAACATTGACTTACACCAGTAAAATGAATACGTAATTCCAACACTAAACTTATCACATAATTCT
1 TTAACATTGACTTACACCAGTAAAATGAATACGTAATTACAACACTAAACTTATCACATAATTCC
* *
294739 AGCAACGGAACTTAACATTGACTTACATCAGTGAAATGAATACGTAATTCCAACACTAGACTTTG
66 AGCAACGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAGACTTTG
294804 AAGC
131 AAGC
* * * * *
294808 TTAACATTGACTTACATCAGTGAAATGAATATGTAATTATAGCACTAAACTTATCACATAATTCC
1 TTAACATTGACTTACACCAGTAAAATGAATACGTAATTACAACACTAAACTTATCACATAATTCC
* * * *
294873 CGCAATGAAATTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCATCACTA
66 AGCAACGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTA
294931 AGCGTATCAC
Statistics
Matches: 110, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
134 110 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (134 bp):
TTAACATTGACTTACACCAGTAAAATGAATACGTAATTACAACACTAAACTTATCACATAATTCC
AGCAACGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAACACTAGACTTTG
AAGC
Found at i:294939 original size:76 final size:76
Alignment explanation
Indices: 294802--295165 Score: 462
Period size: 76 Copynumber: 4.8 Consensus size: 76
294792 CACTAGACTT
* * * **
294802 TGAAGCTTAACATTGACTTACATCAGTGAAATGAATATGTAATTATAGCACTAAACTTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
* *
294867 AATTCCCGCAA
66 AATTCCTGCAG
* * * *
294878 TGAAATTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCATCACTAAGCGTATCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
294943 AATTCCTGCAG
66 AATTCCTGCAG
* * * * * *
294954 TGAAACTTAACATTGACTTACACCAGCGAAATGAATACATAATTCCAGCATTAAATTTAACACCT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
*
295019 AATT-CTAGTAG
66 AATTCCT-GCAG
* * *
295030 TGAAACTTAACATTGACTTAAACCAGTGAAATGAATACGTAATTCCATCACTAAACTTTTCACAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
* *
295095 AAGTCAATG-AG
66 AATTC-CTGCAG
* * *
295106 TGAAACTGAACATTGACTTACACTAGTGAAATGAATACGTAATTCCAACACTAAACTTAT
1 TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTAT
295166 GGTTTCACAT
Statistics
Matches: 247, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
75 2 0.01
76 243 0.98
77 1 0.00
78 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (76 bp):
TGAAACTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCAGCACTAAACTTATCACAT
AATTCCTGCAG
Found at i:295039 original size:286 final size:286
Alignment explanation
Indices: 294516--295088 Score: 806
Period size: 286 Copynumber: 2.0 Consensus size: 286
294506 ATTCCAGTAA
294516 TGAAACTTAACATTAACTTACACCAACGAAATGAATACATAATTTCAACACTAAACTTATCACAT
1 TGAAACTTAACATTAACTTACACCAACGAAATGAATACATAATTTCAACACTAAACTTATCACAT
* *
294581 AATTCCAACAATGAAACTTAACATTGACTTACACCAGTGAAATGAGTACATAATTCCAGCATTAA
66 AATTCCAACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTCCAGCACTAA
* * * *
294646 ACTTATCACATAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAAT
131 ACGTATCACATAATTCCAGCAATGAAACTTAACATTGACTTACACCAGCAAAATGAATACATAAT
* * * *
294711 TCCAACACTAAACTTATCACATAATTCTAGCAACGGAACTTAACATTGACTTACATCAGTGAAAT
196 TCCAACACTAAACTTAACACATAATTCTAGCAACGAAACTTAACATTGACTTAAACCAGTGAAAT
*
294776 GAATACGTAATTCCAACACTAGACTT
261 GAATACGTAATTCCAACACTAAACTT
* * * ** ** *
294802 TGAAGCTTAACATTGACTTACATCAGTGAAATGAATATGTAATTAT-AGCACTAAACTTATCACA
1 TGAAACTTAACATTAACTTACACCAACGAAATGAATACATAATT-TCAACACTAAACTTATCACA
** * * *
294866 TAATTCCCGCAATGAAATTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCATCACTA
65 TAATTCCAACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTCCAGCACTA
* * * *
294931 AGCGTATCACATAATTCCTGCAGTGAAACTTAACATTGACTTACACCAGCGAAATGAATACATAA
130 AACGTATCACATAATTCCAGCAATGAAACTTAACATTGACTTACACCAGCAAAATGAATACATAA
* * * * * **
294996 TTCCAGCATTAAATTTAACACCTAATTCTAGTAGTGAAACTTAACATTGACTTAAACCAGTGAAA
195 TTCCAACACTAAACTTAACACATAATTCTAGCAACGAAACTTAACATTGACTTAAACCAGTGAAA
*
295061 TGAATACGTAATTCCATCACTAAACTT
260 TGAATACGTAATTCCAACACTAAACTT
295088 T
1 T
295089 TCACATAAGT
Statistics
Matches: 250, Mismatches: 36, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
286 249 1.00
287 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (286 bp):
TGAAACTTAACATTAACTTACACCAACGAAATGAATACATAATTTCAACACTAAACTTATCACAT
AATTCCAACAATGAAACTTAACATTGACTTACACCAGTGAAATGAATACATAATTCCAGCACTAA
ACGTATCACATAATTCCAGCAATGAAACTTAACATTGACTTACACCAGCAAAATGAATACATAAT
TCCAACACTAAACTTAACACATAATTCTAGCAACGAAACTTAACATTGACTTAAACCAGTGAAAT
GAATACGTAATTCCAACACTAAACTT
Found at i:295120 original size:362 final size:362
Alignment explanation
Indices: 294450--295163 Score: 1036
Period size: 362 Copynumber: 2.0 Consensus size: 362
294440 TGAAATTTAG
* * *
294450 CATTGACTTACACCAGTAAAATGAATATGTAATTCCAACGCTAAACTTATCACATAATTCCAGTA
1 CATTGACTTACACCAGTAAAATGAATATGTAATTACAACACTAAACTTATCACATAATTCCAGCA
* *
294515 ATGAAACTTAACATTAACTTACACCAACGAAATGAATACATAATTTCAACACTAAACTTATCACA
66 ATGAAACTTAACATTAACTTACACCAACGAAATGAATACATAATTCCAACACTAAACGTATCACA
* *
294580 TAATTCCAACAATGAAACTTAACATTGACTTACACCAGTGAAATGAGTACATAATTCCAGCATTA
131 TAATTCCAACAATGAAACTTAACATTGACTTACACCAGCGAAATGAATACATAATTCCAGCATTA
* * *
294645 AACTTATCACATAATTCCAGCAATGAAATTTAACATTGACTTACACCAGTAAAATGAATACGTAA
196 AACTTAACACATAATTCCAGCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAATACGTAA
* * * *
294710 TTCCAACACTAAACTTATCACATAATTCTAGCAACGGAACTTAACATTGACTTACA-TCAGTGAA
261 TTCCAACACTAAACTTATCACATAAGTCAAGCAACGAAACTGAACATTGACTTACACT-AGTGAA
*
294774 ATGAATACGTAATTCCAACACTAGACTTTGAAGCTTAA
325 ATGAATACGTAATTCCAACACTAAACTTTGAAGCTTAA
* * * * *
294812 CATTGACTTACATCAGTGAAATGAATATGTAATTATAGCACTAAACTTATCACATAATTCCCGCA
1 CATTGACTTACACCAGTAAAATGAATATGTAATTACAACACTAAACTTATCACATAATTCCAGCA
* * ** * * *
294877 ATGAAATTTAACATTGACTTACACCAGTGAAATGAATACGTAATTCCATCACTAAGCGTATCACA
66 ATGAAACTTAACATTAACTTACACCAACGAAATGAATACATAATTCCAACACTAAACGTATCACA
** *
294942 TAATTCCTGCAGTGAAACTTAACATTGACTTACACCAGCGAAATGAATACATAATTCCAGCATTA
131 TAATTCCAACAATGAAACTTAACATTGACTTACACCAGCGAAATGAATACATAATTCCAGCATTA
* * * * * *
295007 AATTTAACACCTAATTCTAGTAGTGAAACTTAACATTGACTTAAACCAGTGAAATGAATACGTAA
196 AACTTAACACATAATTCCAGCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAATACGTAA
* * **
295072 TTCCATCACTAAACTTTTCACATAAGTCAATG-AGTGAAACTGAACATTGACTTACACTAGTGAA
261 TTCCAACACTAAACTTATCACATAAGTCAA-GCAACGAAACTGAACATTGACTTACACTAGTGAA
295136 ATGAATACGTAATTCCAACACTAAACTT
325 ATGAATACGTAATTCCAACACTAAACTT
295164 ATGGTTTCAC
Statistics
Matches: 310, Mismatches: 40, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
362 308 0.99
363 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.28
Consensus pattern (362 bp):
CATTGACTTACACCAGTAAAATGAATATGTAATTACAACACTAAACTTATCACATAATTCCAGCA
ATGAAACTTAACATTAACTTACACCAACGAAATGAATACATAATTCCAACACTAAACGTATCACA
TAATTCCAACAATGAAACTTAACATTGACTTACACCAGCGAAATGAATACATAATTCCAGCATTA
AACTTAACACATAATTCCAGCAATGAAACTTAACATTGACTTAAACCAGTAAAATGAATACGTAA
TTCCAACACTAAACTTATCACATAAGTCAAGCAACGAAACTGAACATTGACTTACACTAGTGAAA
TGAATACGTAATTCCAACACTAAACTTTGAAGCTTAA
Found at i:296168 original size:43 final size:42
Alignment explanation
Indices: 296139--296363 Score: 125
Period size: 43 Copynumber: 5.2 Consensus size: 42
296129 ATTGTTCAAC
296139 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCATTA
1 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCA-TA
* * * * ** *
296182 AAACGCCGCAATAGGTGTTGATATTTAACGGCATTTGGCAGA
1 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCATA
* * * * *
296224 CAAACGCCGTAATA-GTCGTTGATGTTTAGCGGCGTTT-TCTACAA
1 -AAACGCCGCAAAAGGT-ATTGATATTTAGCGGCGTTTATC-A-TA
** * * * * * *
296268 AAACGCCGCAGTAGATTTTTATTTTTACCGGCGTTT-TCTTA
1 AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCATA
* * *
296309 CAAACGCCGCATAATATGTATTGAGATTTTGCGGCGTTTTTATCA-A
1 -AAACGCCGCA-AA-AGGTATTGATATTTAGCGGCG--TTTATCATA
296355 AAACGCCGC
1 AAACGCCGC
296364 TAACTGTATG
Statistics
Matches: 138, Mismatches: 33, Indels: 20
0.72 0.17 0.10
Matches are distributed among these distances:
41 1 0.01
42 14 0.10
43 93 0.67
44 15 0.11
45 9 0.07
46 4 0.03
47 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (42 bp):
AAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTATCATA
Found at i:296765 original size:21 final size:21
Alignment explanation
Indices: 296701--296809 Score: 103
Period size: 21 Copynumber: 5.2 Consensus size: 21
296691 TGATATATTA
* * *
296701 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* * *
296722 CCTCTCTCTGTGCTACCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
296743 CTTCTCTCTCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* **
296764 CTGCTCTAGCTGCTTCCGCTG
1 CTTCTCTCTCTGCTTCCGCTG
* *
296785 CTGCTCTCTCTGTTTCC-CTTG
1 CTTCTCTCTCTGCTTCCGC-TG
296806 CTTC
1 CTTC
296810 ATTTTCCGCT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 1 0.01
21 73 0.99
ACGTcount: A:0.02, C:0.40, G:0.17, T:0.40
Consensus pattern (21 bp):
CTTCTCTCTCTGCTTCCGCTG
Found at i:305287 original size:21 final size:21
Alignment explanation
Indices: 305261--305300 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
305251 CGAAACATCA
305261 TTCGTGTTCAGTAAAAAACAT
1 TTCGTGTTCAGTAAAAAACAT
305282 TTCGTGTTCAGTAAAAAAC
1 TTCGTGTTCAGTAAAAAAC
305301 TAATTGCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (21 bp):
TTCGTGTTCAGTAAAAAACAT
Found at i:306248 original size:41 final size:43
Alignment explanation
Indices: 306203--306297 Score: 108
Period size: 41 Copynumber: 2.3 Consensus size: 43
306193 TTTGTGATAT
* * *
306203 AAACGCCGCTAATTTAG-C-ACCCTATTGCGGCGTTTTT-CTAA
1 AAACGCCGCTAATAT-GTCAACCATATTGCAGCGTTTTTACTAA
**
306244 AAACGCCGC-AATATGTCAATTATATTGCAGCGTTTTTACTAA
1 AAACGCCGCTAATATGTCAACCATATTGCAGCGTTTTTACTAA
306286 AAACGCCGCTAA
1 AAACGCCGCTAA
306298 AGTATCAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
39 1 0.02
40 5 0.11
41 24 0.53
42 13 0.29
43 2 0.04
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (43 bp):
AAACGCCGCTAATATGTCAACCATATTGCAGCGTTTTTACTAA
Found at i:306254 original size:83 final size:83
Alignment explanation
Indices: 306036--306238 Score: 271
Period size: 83 Copynumber: 2.4 Consensus size: 83
306026 TTTTTTTGTC
* * * *
306036 AAAACGCCGCCAATTTACCGCTCTATTGCGGCGTTTTGACTCAATCACCGCAAAATTTATACTCT
1 AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAAAATTTATAATCT
** *
306101 ATTGTGGCGTTTGTGGTA
66 ATTGAAGCGTTTGTGATA
* * * *
306119 AAAACGCTGCCAGTTTACCACTATATTGCGGCGTTTTGGCTAAATCGCCGCAAAATTTATAATCT
1 AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAAAATTTATAATCT
306184 ATTGAAGCGTTTGTGATA
66 ATTGAAGCGTTTGTGATA
* * * *
306202 TAAACGCCGCTAATTTAGCACCCTATTGCGGCGTTTT
1 AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTT
306239 TCTAAAAACG
Statistics
Matches: 102, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
83 102 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (83 bp):
AAAACGCCGCCAATTTACCACTCTATTGCGGCGTTTTGACTAAATCGCCGCAAAATTTATAATCT
ATTGAAGCGTTTGTGATA
Found at i:311084 original size:86 final size:85
Alignment explanation
Indices: 310923--311174 Score: 274
Period size: 86 Copynumber: 3.0 Consensus size: 85
310913 TGTGAACGAA
* ** * *
310923 AAACGCCGCAATAGGTGTTGATATTTAGCGGC-GTTTTCATACAAACACCGCAATACGTGTTAAT
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGGTTTTCATACAAACGTCGCAATACGTCTT-GT
* *
310987 TTTTAGTGGCGTTTTTCCCAC
65 ATTTAGCGGCGTTTTTCCCAC
* * *
311008 AAACGCCGCAATAGGTGTTGAGATTTAGTGGCGGTTTT-ATCACAAATGTCGCAATATGTCTTGT
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGGTTTTCAT-ACAAACGTCGCAATACGTCTTGT
***
311072 GATTTAGCGGCGTTTTTCTTGC
65 -ATTTAGCGGCGTTTTTCCCAC
* * * * * * *
311094 AAATGCCGCAATAGGTGTTGAGATTTTGCGGCGTTTTTGATACAAACGTCGCAAAAGGTCTGGTA
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGGTTTTCATACAAACGTCGCAATACGTCTTGTA
*
311159 TATAGCGGCGTTTTTC
66 TTTAGCGGCGTTTTTC
311175 GGATATAAAC
Statistics
Matches: 141, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
85 49 0.35
86 90 0.64
87 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (85 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGGTTTTCATACAAACGTCGCAATACGTCTTGTA
TTTAGCGGCGTTTTTCCCAC
Found at i:311131 original size:43 final size:43
Alignment explanation
Indices: 310923--311174 Score: 217
Period size: 43 Copynumber: 5.9 Consensus size: 43
310913 TGTGAACGAA
*
310923 AAACGCCGCAATAGGTGTTGATATTTAGCGGCG-TTTTCAT-AC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTC-TCAC
* * * ** * *
310965 AAACACCGCAATACGTGTTAATTTTTAGTGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCAC
* * *
311008 AAACGCCGCAATAGGTGTTGAGATTTAGTGGCGGTTTTATCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCAC
* * * * * **
311051 AAATGTCGCAATATGTCTTGTGATTTAGCGGCGTTTTTCTTGC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCAC
* * *
311094 AAATGCCGCAATAGGTGTTGAGATTTTGCGGCGTTTTTGAT-AC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTT-CTCAC
* * * *
311137 AAACGTCGCAAAAGGT-CTG-GTATATAGCGGCGTTTTTC
1 AAACGCCGCAATAGGTGTTGAG-ATTTAGCGGCGTTTTTC
311175 GGATATAAAC
Statistics
Matches: 168, Mismatches: 38, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
41 1 0.01
42 44 0.26
43 122 0.73
44 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCAC
Done.