Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008358.1 Hibiscus syriacus cultivar Beakdansim tig00111097_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: 729890
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:620179 original size:36 final size:36
Alignment explanation
Indices: 620081--620201 Score: 149
Period size: 36 Copynumber: 3.4 Consensus size: 36
620071 TTGAATATGT
* *
620081 TTTC-CTTGAAACAAATTTTGTCTCCCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* * * *
620116 TTTCTTTTAAAA-AAA-ATTGTCTCTCTTGAGATAT
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
620150 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
* *
620186 TTTCCCTTGAAACAAA
1 TTTCTCTTAAAACAAA
620202 ATCCTTGAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
34 26 0.37
35 10 0.14
36 35 0.49
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (36 bp):
TTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:620203 original size:135 final size:134
Alignment explanation
Indices: 619951--620532 Score: 916
Period size: 134 Copynumber: 4.3 Consensus size: 134
619941 AATTTACTCA
* *
619951 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTAAAACAAATTTTGTCTCTCTTGAGACATT
1 AAACAAA-TTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATT
*
620016 TTCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATATGT
65 TTCTCTT--AA-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGT
620081 TTTCCTTG
127 TTTCCTTG
* *
620089 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAAA-AAA-ATTGTCTCTCTTGAGATATTT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTT
*
620152 TCTCTTAAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCCTTGAATCTGTT
66 TCTCTT--AA-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTT
620217 TTCCTTG
128 TTCCTTG
** *
620224 AAACAAATTTCATCTCCATTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTT
*
620289 TCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAAATCTTTGAATCTGTTTTC
66 TCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTC
620354 CTTG
131 CTTG
** *
620358 AAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCATGAGACATTT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTT
* * *
620423 TCTCTTAAAAATTTTGTCTCTCTAGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTATTTCC
66 TCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTC
620488 CTTG
131 CTTG
* * *
620492 AAACAAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACA
620533 TAAAATCTTT
Statistics
Matches: 418, Mismatches: 24, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
134 223 0.53
135 127 0.30
136 6 0.01
137 55 0.13
138 7 0.02
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.41
Consensus pattern (134 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACATTT
TCTCTTAAAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATCTGTTTTC
CTTG
Found at i:620282 original size:36 final size:35
Alignment explanation
Indices: 620216--620323 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 35
620206 TTGAATCTGT
**
620216 TTTC-CTTGAAACAAATTTCATCTC-CATTGAGACAG
1 TTTCTCTT-AAACAAATTTTGTCTCTC-TTGAGACAG
* *
620251 TTTCTTTTAAAACAAATTTTGTCTCTCTTGAGACAT
1 TTTCTCTT-AAACAAATTTTGTCTCTCTTGAGACAG
620287 TTTCTCTT-AA-AAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTAAACAAATTTTGTCTCTCTTGAGACAG
620320 TTTC
1 TTTC
620324 CCTTGAAATA
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
33 26 0.41
34 2 0.03
35 4 0.06
36 31 0.48
37 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (35 bp):
TTTCTCTTAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:620417 original size:36 final size:34
Alignment explanation
Indices: 620350--620469 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 34
620340 TTGAATCTGT
** *
620350 TTTC-CTTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCTCTT-AAACAAATTTTGTCTCTC-TGAGACAG
* *
620385 TTTCTTTTAAAACAAATTTTGTCTCTCATGAGACAT
1 TTTCTCTT-AAACAAATTTTGTCTCTC-TGAGACAG
620421 TTTCTCTT-AA-AAATTTTGTCTCTCTAGAGACAG
1 TTTCTCTTAAACAAATTTTGTCTCTCT-GAGACAG
*
620454 TTTCCCTTGAAACAAA
1 TTTCTCTT-AAACAAA
620470 ATCTTTGAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
32 1 0.01
33 27 0.39
34 2 0.03
35 6 0.09
36 34 0.49
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (34 bp):
TTTCTCTTAAACAAATTTTGTCTCTCTGAGACAG
Found at i:620589 original size:67 final size:66
Alignment explanation
Indices: 620015--620623 Score: 336
Period size: 65 Copynumber: 9.1 Consensus size: 66
620005 CTTGAGACAT
* * *
620015 TTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAAATCTTTGAATA
1 TTTCCCTTAAAACAAAATTTTGTCTC-CTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAATC
*
620078 TG
65 TA
* * *
620080 TTTTCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAGTTTCT-TTTAAA-AAAAATTGTCTCTCT
1 TTTCCCTTAAAACAAAATTTTGTCT-CCTTGAGACAGTTTCTCTTGAAACAAAAA-----TCT-T
*
620142 TGAGATAT-
59 TGA-ATCTA
* * *
620150 TTTCTCTTAAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAAATCCTTGAATC
1 TTTCCCTTAAAACAAAATTTTGTCTC-CTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAATC
*
620213 TG
65 TA
* * ** * * **
620215 TTTTCCTTGAAAC-AAATTTCATCTCCATTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCT
1 TTTCCCTTAAAACAAAATTTTGTCTCC-TTGAGACAGTTTCTCTTGAAACAAA-----AATCT-T
620279 TGAGA-C-A
59 TGA-ATCTA
* * *
620286 TTTTCTCTT---A-AAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAA-TAAAATCTTTGAAT
1 -TTTCCCTTAAAACAAAATTTTGTCTC-CTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAAT
*
620346 CTG
64 CTA
* * ** * * **
620349 TTTTCCTTGAAAC-AAATTTCATCTCCCTTGAGACAGTTTCTTTTAAAACAAATTTTGTCTCTCA
1 TTTCCCTTAAAACAAAATTTTGTCT-CCTTGAGACAGTTTCTCTTGAAACAAA---AATCT-T--
620413 TGAGA-C-A
59 TGA-ATCTA
* * *
620420 TTTTCTCTT---A-AAAATTTTGTCTCTCTAGAGACAGTTTCCCTTGAAAC-AAAATCTTTGAAT
1 -TTTCCCTTAAAACAAAATTTTGTCTC-CTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAAT
620480 CTA
64 CTA
* *
620483 TTTCCCTTGAAAC-AAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAATCTTTGAAT
1 TTTCCCTTAAAACAAAATTTTGTCT-CCTTGAGACAGTTTCTCTTGAAACA-AAAATCTTTGAAT
*
620547 TTA
64 CTA
* *
620550 TTTCCCTTAAAACAAAATTTTGTTTGCCTTGAGAC-GTTTCTCATGAAACAACAAATATCTTTGA
1 TTTCCCTTAAAACAAAATTTTGTCT-CCTTGAGACAGTTTCTCTTGAAAC-A-AAA-ATCTTTGA
620614 GATCT-
62 -ATCTA
620619 TTTCC
1 TTTCC
620624 TTTGAAACGA
Statistics
Matches: 420, Mismatches: 68, Indels: 108
0.70 0.11 0.18
Matches are distributed among these distances:
61 2 0.00
62 22 0.05
63 4 0.01
64 14 0.03
65 142 0.34
66 9 0.02
67 40 0.10
68 27 0.06
69 78 0.19
70 44 0.10
71 15 0.04
72 21 0.05
73 2 0.00
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (66 bp):
TTTCCCTTAAAACAAAATTTTGTCTCCTTGAGACAGTTTCTCTTGAAACAAAAATCTTTGAATCT
A
Found at i:620651 original size:68 final size:66
Alignment explanation
Indices: 620432--620643 Score: 211
Period size: 67 Copynumber: 3.2 Consensus size: 66
620422 TTCTCTTAAA
* * *
620432 AATTTTGTCTCTCTAGAGACAGTTTCCCTTG--A-AACAAAATCTTTGAATCTATTTCCCTTGAA
1 AATTTTGTCTC-CTTGAGACAGTTTCTCATGAAACAACAAAATCTTTGAATCTATTTCCCTTGAA
620494 AC
65 AC
* * * *
620496 AAGTTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-ATAAAATCTTTGAATTTATTTCCCTTAA
1 AA-TTTTGTCT-CCTTGAGACAGTTTCTCATGAAACAACAAAATCTTTGAATCTATTTCCCTTGA
620560 AAC
64 AAC
* *
620563 AAAATTTTGTTTGCCTTGAGAC-GTTTCTCATGAAACAACAAATATCTTTGAGATCT-TTTCCTT
1 --AATTTTGTCT-CCTTGAGACAGTTTCTCATGAAACAACAAA-ATCTTTGA-ATCTATTTCCCT
620626 TGAAAC
61 TGAAAC
*
620632 GAATTCTGTCTC
1 -AATTTTGTCTC
620644 TTTTGAGATA
Statistics
Matches: 123, Mismatches: 15, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
64 2 0.02
65 25 0.20
66 1 0.01
67 43 0.35
68 28 0.23
69 21 0.17
70 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (66 bp):
AATTTTGTCTCCTTGAGACAGTTTCTCATGAAACAACAAAATCTTTGAATCTATTTCCCTTGAAA
C
Found at i:621359 original size:2 final size:2
Alignment explanation
Indices: 621339--621390 Score: 60
Period size: 2 Copynumber: 28.5 Consensus size: 2
621329 CACTGTTATT
*
621339 TA TA TA -A TA T- TA TA T- TA TA TA -A T- TA TA TA CA 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
621376 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
621391 TAACACATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
1 5 0.12
2 38 0.88
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:621363 original size:8 final size:9
Alignment explanation
Indices: 621335--621392 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
621325 CGTCCACTGT
621335 TATT-TATA
1 TATTATATA
*
621343 TAATAT-TA
1 TATTATATA
621351 TATTATATA
1 TATTATATA
621360 -ATTATATA
1 TATTATATA
*
621368 CATATATATA
1 TAT-TATATA
621378 TATATATATA
1 TAT-TATATA
621388 TATTA
1 TATTA
621393 ACACATATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
8 18 0.42
9 7 0.16
10 18 0.42
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (9 bp):
TATTATATA
Found at i:622658 original size:14 final size:13
Alignment explanation
Indices: 622614--622657 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
622604 TATTCCGTTG
*
622614 TTTATTTCATTTCT
1 TTTATTT-ATTTAT
622628 TTTATTTATCTTAT
1 TTTATTTAT-TTAT
622642 TTTATTTATTTAT
1 TTTATTTATTTAT
622655 TTT
1 TTT
622658 TCTTGTCTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (13 bp):
TTTATTTATTTAT
Found at i:631813 original size:3 final size:3
Alignment explanation
Indices: 631805--631846 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
631795 TGAAGATGTA
* *
631805 TTC TTC TTC TTC TT- TGTC TTC GTC ATC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC
631847 CTCGTCGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
2 1 0.03
3 32 0.94
4 1 0.03
ACGTcount: A:0.02, C:0.31, G:0.05, T:0.62
Consensus pattern (3 bp):
TTC
Found at i:635222 original size:29 final size:30
Alignment explanation
Indices: 635154--635210 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
635144 ATTTAAGGCA
635154 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
635184 AAAATGTTTTTGGACTT-AATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
635211 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.46
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:635338 original size:13 final size:13
Alignment explanation
Indices: 635322--635346 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
635312 AGTGCATCGA
635322 TGCATCCCTGCAG
1 TGCATCCCTGCAG
635335 TGCATCCCTGCA
1 TGCATCCCTGCA
635347 TCTGCACTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.40, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCCTGCAG
Found at i:635347 original size:21 final size:21
Alignment explanation
Indices: 635291--635348 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
635281 AGGGTGTCAA
*
635291 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
635312 AGTGCATCGATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
635333 AGTGCATCCCTGCATC
1 AGTGCATCCATGCATC
635349 TGCACTAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:635387 original size:20 final size:20
Alignment explanation
Indices: 635293--635465 Score: 65
Period size: 20 Copynumber: 8.8 Consensus size: 20
635283 GGTGTCAAAG
* * *
635293 TGCATCCATGCACCCCTGCAG
1 TGCATCCATGCA-TCATGCAA
* * *
635314 TGCATCGATGCATCCCTGCAG
1 TGCATCCATGCAT-CATGCAA
*
635335 TGCATCCCTGCATC-TGCACTAA
1 TGCATCCATGCATCATG--C-AA
* *
635357 TACATCGATGCATCATGCAA
1 TGCATCCATGCATCATGCAA
635377 TGCATCCATGCATC---CAA
1 TGCATCCATGCATCATGCAA
* * * *
635394 -ACATCGAATGCA--AT-TAG
1 TGCATC-CATGCATCATGCAA
* * *
635411 TGCATCGATGCATCTTGCTA
1 TGCATCCATGCATCATGCAA
* * *
635431 TGCATCGATGCATCCTGCGA
1 TGCATCCATGCATCATGCAA
635451 TGCATCCATGCATCA
1 TGCATCCATGCATCA
635466 AGGCTGCAAC
Statistics
Matches: 116, Mismatches: 24, Indels: 25
0.70 0.15 0.15
Matches are distributed among these distances:
16 4 0.03
17 14 0.12
18 4 0.03
19 3 0.03
20 46 0.40
21 31 0.27
22 12 0.10
23 2 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.25
Consensus pattern (20 bp):
TGCATCCATGCATCATGCAA
Found at i:636780 original size:19 final size:20
Alignment explanation
Indices: 636756--636803 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
636746 AAATGTTTTC
* *
636756 TTTTGAAAGCAAAAATG-GA
1 TTTTGAAAACAAAAATGAAA
*
636775 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
636795 TTTTGAAAA
1 TTTTGAAAA
636804 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:636846 original size:23 final size:22
Alignment explanation
Indices: 636811--636854 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
636801 AAAAGGATTT
636811 AGAGCTTTCAAAAATGAAAATTG
1 AGAGCTTTCAAAAA-GAAAATTG
* *
636834 AGAGTTTTGAAAAAGAAAATT
1 AGAGCTTTCAAAAAGAAAATT
636855 TTGATTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (22 bp):
AGAGCTTTCAAAAAGAAAATTG
Found at i:638127 original size:29 final size:30
Alignment explanation
Indices: 638059--638115 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
638049 ATTTAAGGCA
638059 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
638089 AAAATGTTTTTGGACTT-AATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
638116 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.46
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:638211 original size:8 final size:8
Alignment explanation
Indices: 638198--638284 Score: 50
Period size: 8 Copynumber: 12.0 Consensus size: 8
638188 GGTGTCAAAG
638198 TGCATCCA
1 TGCATCCA
638206 TGCATCCA
1 TGCATCCA
*
638214 TGCATCCC
1 TGCATCCA
*
638222 TGCA---G
1 TGCATCCA
638227 TGCATCCA
1 TGCATCCA
638235 TGCAT-C-
1 TGCATCCA
*
638241 TGCA-CTAA
1 TGCATC-CA
*
638249 TGCATCGA
1 TGCATCCA
638257 TGCAT-CA
1 TGCATCCA
638264 TGCA---A
1 TGCATCCA
638269 TGCATCCA
1 TGCATCCA
*
638277 TGAATCCA
1 TGCATCCA
638285 AACATCGAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
5 9 0.15
6 4 0.06
7 6 0.10
8 42 0.68
9 1 0.02
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.25
Consensus pattern (8 bp):
TGCATCCA
Found at i:638369 original size:20 final size:21
Alignment explanation
Indices: 638333--638378 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
638323 TGCATTTGAC
*
638333 GCATCCTTGCTATGCATCAAT
1 GCATCCTTGCGATGCATCAAT
*
638354 GCATCC-TGCGATGCATCTAT
1 GCATCCTTGCGATGCATCAAT
638374 GCATC
1 GCATC
638379 AAGGCTGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.30
Consensus pattern (21 bp):
GCATCCTTGCGATGCATCAAT
Found at i:639149 original size:2 final size:2
Alignment explanation
Indices: 639142--639174 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
639132 ATAATTTCAC
*
639142 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
639175 GTGATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:647787 original size:31 final size:31
Alignment explanation
Indices: 647715--647788 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
647705 AATGTAATCG
* * **
647715 TTAACATAA-ATGCGCATATATTTAATTTCT
1 TTAATATAATATGCGCATATATTAAATTAAT
*
647745 TTGATATAATATGCGCATATATTAAATTAAT
1 TTAATATAATATGCGCATATATTAAATTAAT
647776 TTAAT-TAAATATG
1 TTAATAT-AATATG
647789 AAATTAATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
30 8 0.22
31 28 0.78
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (31 bp):
TTAATATAATATGCGCATATATTAAATTAAT
Found at i:658249 original size:22 final size:22
Alignment explanation
Indices: 658146--658249 Score: 88
Period size: 22 Copynumber: 4.7 Consensus size: 22
658136 TTATATAACG
* * * *
658146 AAAGTGCCTTAGCACTAATACT
1 AAAGTGCCATCGCACTGATACA
*
658168 AAAGTGCCATAGCACTGATACA
1 AAAGTGCCATCGCACTGATACA
658190 AAAGTG-CATTCGCACTGA-ATCA
1 AAAGTGCCA-TCGCACTGATA-CA
* * *
658212 AAAGAG-CATTCACACTGATACT
1 AAAGTGCCA-TCGCACTGATACA
658234 AAAGTGCCATCGCACT
1 AAAGTGCCATCGCACT
658250 CGGGAAGAGA
Statistics
Matches: 69, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
21 3 0.04
22 63 0.91
23 3 0.04
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (22 bp):
AAAGTGCCATCGCACTGATACA
Found at i:658546 original size:18 final size:21
Alignment explanation
Indices: 658499--658551 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
658489 TATACAGGAC
658499 GTCAGTATCGATACTGAGCCT
1 GTCAGTATCGATACTGAGCCT
*
658520 GTCAGTATCGATACT-AGTCT
1 GTCAGTATCGATACTGAGCCT
658540 -T-AGTATCGATAC
1 GTCAGTATCGATAC
658552 CGGTTGAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 11 0.35
19 1 0.03
20 4 0.13
21 15 0.48
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
GTCAGTATCGATACTGAGCCT
Found at i:660260 original size:13 final size:13
Alignment explanation
Indices: 660242--660266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
660232 TAGGCATTTA
660242 TAAATATATAATT
1 TAAATATATAATT
660255 TAAATATATAAT
1 TAAATATATAAT
660267 ATAGTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TAAATATATAATT
Found at i:660663 original size:13 final size:13
Alignment explanation
Indices: 660645--660671 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
660635 ACAAACATCC
660645 TTCTTTATTTGTT
1 TTCTTTATTTGTT
660658 TTCTTTATTTGTT
1 TTCTTTATTTGTT
660671 T
1 T
660672 CATGTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (13 bp):
TTCTTTATTTGTT
Found at i:660704 original size:22 final size:23
Alignment explanation
Indices: 660665--660710 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
660655 GTTTTCTTTA
* *
660665 TTTGTTTCATGTATTTATTTATT
1 TTTGTTTAATGTATTTATATATT
660688 TTTGTTTAAT-TATTTATATATT
1 TTTGTTTAATGTATTTATATATT
660710 T
1 T
660711 CTCCAGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.22, C:0.02, G:0.07, T:0.70
Consensus pattern (23 bp):
TTTGTTTAATGTATTTATATATT
Found at i:662715 original size:3 final size:3
Alignment explanation
Indices: 662707--662731 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
662697 AATTAACAAA
662707 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
662732 GGATAACACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:666140 original size:135 final size:135
Alignment explanation
Indices: 665898--666166 Score: 430
Period size: 135 Copynumber: 2.0 Consensus size: 135
665888 CGGGATCGTT
*
665898 GCCATCACAAAGTGCTGCAACAGATTTAAGAACACACTGGCTGTTACGAACGAAACTCGGAATAT
1 GCCATCACAAAGTGCTGCAACAGATTTAAGAACACACTGGCTGTTACGAAAGAAACTCGGAATAT
* *
665963 ATGATTGGCGACTCAGTTGTGAAAGCTTACCGAAAATTTGTTTATTAGAAGATGGAACTATTGCC
66 ATGATTGGCAACTCAGTTATGAAAGCTTACCGAAAATTTGTTTATTAGAAGATGGAACTATTGCC
666028 TTCCG
131 TTCCG
* ** *
666033 GCCATCACAAAGTGCTGCAACTGATTTAAGAACACGTTGGCTGTTACGAAATAAACTCGGAATAT
1 GCCATCACAAAGTGCTGCAACAGATTTAAGAACACACTGGCTGTTACGAAAGAAACTCGGAATAT
* * * * *
666098 ATGATTGGCAATTCAGTTATGAAAGCTTACCTAAAGTTTGTTTTTTAGAAGATGGAACTATTGTC
66 ATGATTGGCAACTCAGTTATGAAAGCTTACCGAAAATTTGTTTATTAGAAGATGGAACTATTGCC
666163 TTCC
131 TTCC
666167 CATCCTTCGC
Statistics
Matches: 122, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
135 122 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (135 bp):
GCCATCACAAAGTGCTGCAACAGATTTAAGAACACACTGGCTGTTACGAAAGAAACTCGGAATAT
ATGATTGGCAACTCAGTTATGAAAGCTTACCGAAAATTTGTTTATTAGAAGATGGAACTATTGCC
TTCCG
Found at i:673531 original size:2 final size:2
Alignment explanation
Indices: 673524--673548 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
673514 TCCATACAAC
673524 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 A
673549 CATGCACAAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:677563 original size:66 final size:65
Alignment explanation
Indices: 677435--677566 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 65
677425 TGTATAAGGT
677435 AAGTGGGTCTTCAGTTGGTTAATTCTTTCGTTTAAAGCTTGTTTTGATTCTTGGGATGTTAAGAA
1 AAGTGGGTCTTCAGTTGGTTAATTCTTTCGTTTAAAGCTTGTTTTGATTCTTGGGATGTTAAGAA
677500 AAGTGGGTCTTCAGTTGGTTAATTCTTTCGTTTTAAAGCTTGTTTTGATTCTTGGGATGTTAAGA
1 AAGTGGGTCTTCAGTTGGTTAATTCTTTCG-TTTAAAGCTTGTTTTGATTCTTGGGATGTTAAGA
677565 A
65 A
677566 A
1 A
677567 GATTAAGGAA
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 30 0.45
66 36 0.55
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (65 bp):
AAGTGGGTCTTCAGTTGGTTAATTCTTTCGTTTAAAGCTTGTTTTGATTCTTGGGATGTTAAGAA
Found at i:677948 original size:21 final size:20
Alignment explanation
Indices: 677922--677965 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
677912 GATTTCTGGG
* *
677922 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCC-TT
677943 CAAGGGGAACCGATACCCTT
1 CAAGGGGAACCGATACCCTT
677963 CAA
1 CAA
677966 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAGGGGAACCGATACCCTT
Found at i:678805 original size:31 final size:31
Alignment explanation
Indices: 678767--678847 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
678757 AGGGTCGAGG
* *
678767 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGAACT
678798 GTTTACCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGAACT
* *
678829 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
678848 AATCTATGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGAACT
Found at i:679759 original size:16 final size:16
Alignment explanation
Indices: 679740--679773 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
679730 ATATGCACAC
679740 GTGATATGTGATAAAA
1 GTGATATGTGATAAAA
679756 GTGATATGTGATAAAA
1 GTGATATGTGATAAAA
679772 GT
1 GT
679774 AAGGATATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.32
Consensus pattern (16 bp):
GTGATATGTGATAAAA
Found at i:681681 original size:17 final size:17
Alignment explanation
Indices: 681646--681685 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
681636 GGTAATTAAA
681646 GATTGA-TAAGGAATTT
1 GATTGATTAAGGAATTT
* *
681662 GATTGATTAATGATTTT
1 GATTGATTAAGGAATTT
681679 GATTGAT
1 GATTGAT
681686 AAGAACTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.45
Consensus pattern (17 bp):
GATTGATTAAGGAATTT
Found at i:682600 original size:21 final size:21
Alignment explanation
Indices: 682574--682618 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
682564 GATTTCTGGG
* *
682574 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
682595 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
682616 CAA
1 CAA
682619 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:683469 original size:31 final size:31
Alignment explanation
Indices: 683431--683541 Score: 177
Period size: 31 Copynumber: 3.6 Consensus size: 31
683421 AGGGTCGAGG
683431 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
683462 GTTTACCTATGTTCTTCGGGACGTATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
683493 GTTTACCTATGTTTTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* **
683524 GATTACCTGGGTTCTTCG
1 GTTTACCTATGTTCTTCG
683542 AAATCTATAG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 73 1.00
ACGTcount: A:0.17, C:0.19, G:0.24, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:683555 original size:62 final size:62
Alignment explanation
Indices: 683431--683555 Score: 171
Period size: 62 Copynumber: 2.0 Consensus size: 62
683421 AGGGTCGAGG
* * ** *
683431 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACGTATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAACGTATAGACT
* *
683493 GTTTACCTATGTTTTTCGGGACATATGGACTGATTACCTGGGTTCTTCGAAATC-TATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAA-CGTATAGACT
683555 G
1 G
683556 GTCTTTCGGG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 54 0.98
63 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCGAAACGTATAGACT
Found at i:686340 original size:33 final size:33
Alignment explanation
Indices: 686276--686360 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 33
686266 ACAGTAGCCT
* * *
686276 CCTTCTGTTTCTTCCCAACAGCCAATCCAACAG
1 CCTTATGTTTCTTCCCAACAGCCAATACAACAA
* **
686309 CCTTTTGTTTCTTCCCAACAGTTAATACAACAA
1 CCTTATGTTTCTTCCCAACAGCCAATACAACAA
* *
686342 CCTTATGTTTTTTACCAAC
1 CCTTATGTTTCTTCCCAAC
686361 CTACCACCTT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.26, C:0.32, G:0.07, T:0.35
Consensus pattern (33 bp):
CCTTATGTTTCTTCCCAACAGCCAATACAACAA
Found at i:689049 original size:7 final size:7
Alignment explanation
Indices: 689039--689152 Score: 219
Period size: 7 Copynumber: 16.3 Consensus size: 7
689029 CATATTTTTA
*
689039 TTTTTCC
1 TTTTCCC
689046 TTTTCCC
1 TTTTCCC
689053 TTTTCCC
1 TTTTCCC
689060 TTTTCCC
1 TTTTCCC
689067 TTTTCCC
1 TTTTCCC
689074 TTTTCCC
1 TTTTCCC
689081 TTTTCCC
1 TTTTCCC
689088 TTTTCCC
1 TTTTCCC
689095 TTTTCCC
1 TTTTCCC
689102 TTTTCCC
1 TTTTCCC
689109 TTTTCCC
1 TTTTCCC
689116 TTTTCCC
1 TTTTCCC
689123 TTTTCCC
1 TTTTCCC
689130 TTTTCCC
1 TTTTCCC
689137 TTTTCCC
1 TTTTCCC
689144 TTTTCCC
1 TTTTCCC
689151 TT
1 TT
689153 CTTCTTCCTT
Statistics
Matches: 106, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
7 106 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTCCC
Found at i:689431 original size:24 final size:24
Alignment explanation
Indices: 689404--689453 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
689394 TGGTGGTTGA
*
689404 TTTAATGGT-TGTTTGAACTTTATT
1 TTTAATGGTATATTT-AACTTTATT
*
689428 TTTAATGGTATATTTAAGTTTATT
1 TTTAATGGTATATTTAACTTTATT
689452 TT
1 TT
689454 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.02, G:0.14, T:0.60
Consensus pattern (24 bp):
TTTAATGGTATATTTAACTTTATT
Found at i:696276 original size:19 final size:21
Alignment explanation
Indices: 696239--696281 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
696229 TAACTTTTTC
*
696239 TTTTCTCTTTCTTTATTAA-T
1 TTTTCTCTTTCATTATTAACT
696259 TTTTCTCTTTCATT-TTAACT
1 TTTTCTCTTTCATTATTAACT
696279 TTT
1 TTT
696282 ACTTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTCTCTTTCATTATTAACT
Found at i:700623 original size:96 final size:96
Alignment explanation
Indices: 700440--700624 Score: 207
Period size: 96 Copynumber: 1.9 Consensus size: 96
700430 AAATTTATTT
* * *
700440 ATTTAAAAATATCAGAAAAGAACTTCTAGGTGCCTTAAGACAGCTCTTTTCTTGATATTGATAAA
1 ATTTAAAAATATCAGAAAAGAACATCTAGGTGCATTAAGACAGCTCTTTTCTTGATATTGAAAAA
* *
700505 TATTAATTTAAATAATATTATTTACTTTTTA
66 TAATAATTTAAATAATACTATTTACTTTTTA
* * * * * *
700536 ATTTTAAAATATCAGAATAGGACATCTAGTTGTATTAAGACTG-TCCTTTTCTTCGATATT-AAA
1 ATTTAAAAATATCAGAAAAGAACATCTAGGTGCATTAAGACAGCT-CTTTTCTT-GATATTGAAA
700599 AATAA-ATATTTAAA-AATTACTATTTA
64 AATAATA-ATTTAAATAA-TACTATTTA
700625 TTATATATTT
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
95 4 0.05
96 64 0.86
97 6 0.08
ACGTcount: A:0.39, C:0.10, G:0.09, T:0.41
Consensus pattern (96 bp):
ATTTAAAAATATCAGAAAAGAACATCTAGGTGCATTAAGACAGCTCTTTTCTTGATATTGAAAAA
TAATAATTTAAATAATACTATTTACTTTTTA
Found at i:702087 original size:20 final size:19
Alignment explanation
Indices: 702064--702108 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
702054 TATTTTTTAT
* *
702064 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
702084 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
702103 TATTTA
1 TATTTA
702109 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:702098 original size:26 final size:30
Alignment explanation
Indices: 702059--702114 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
702049 AATTATATTT
*
702059 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
702086 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
702115 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:702115 original size:3 final size:3
Alignment explanation
Indices: 702107--702205 Score: 162
Period size: 3 Copynumber: 32.7 Consensus size: 3
702097 TTAATATATT
*
702107 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
702155 TAA TGA TAA TAG TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA
702201 TAA TA
1 TAA TA
702206 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
3 86 0.97
4 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:702916 original size:225 final size:226
Alignment explanation
Indices: 702521--703042 Score: 951
Period size: 225 Copynumber: 2.3 Consensus size: 226
702511 GAATTATGCC
* * *
702521 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
702585 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTCTCCGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATT
*
702649 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
702714 AAAGATGATCCATCAAGTGATGAATTCAGGT
196 AAAGATGATCCATCAAGTGATGAATTCAGGT
702745 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
702810 TATGAACTTTCTCTGG-AAAGATGATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTCTCCGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATT
702874 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
702939 AAAGATGATCCATCAAGTGATGAATTCAGGT
196 AAAGATGATCCATCAAGTGATGAATTCAGGT
702970 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
703035 TATGAACT
66 TATGAACT
703043 CGAACTGGAA
Statistics
Matches: 288, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
224 4 0.01
225 277 0.96
226 7 0.02
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (226 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCCGGAAAAGATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGATGATCCATCAAGTGATGAATTCAGGT
Found at i:703062 original size:113 final size:113
Alignment explanation
Indices: 702521--703042 Score: 951
Period size: 113 Copynumber: 4.6 Consensus size: 113
702511 GAATTATGCC
* * *
702521 AAAA-GTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
702585 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
702632 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
702697 TATGAACTTTTTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
702745 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
702810 TATGAACTTTCTCTGG-AAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
702857 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
702922 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
702970 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
703035 TATGAACT
66 TATGAACT
703043 CGAACTGGAA
Statistics
Matches: 399, Mismatches: 9, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
111 4 0.01
112 176 0.44
113 219 0.55
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCATCAAGTGATGAATTCAGGT
Found at i:704234 original size:250 final size:249
Alignment explanation
Indices: 703794--704332 Score: 990
Period size: 250 Copynumber: 2.2 Consensus size: 249
703784 CCTACTGAAT
*
703794 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGAACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
*
703859 TGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACA
66 TGATTGGATTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACA
*
703924 TTCATCTTCCAAATTCAATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCA
131 TTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCA
703989 GAAGATGCTATTGGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
196 GAAGATGCTATTGGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
*
704043 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT-GAACACATTCATCTTCCAAATTCA
*
704108 ATGATTGGATTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCA
65 ATGATTGGATTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACA
704172 CATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTC
129 CATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTC
*
704237 CAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAT
194 CAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
*
704293 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
704333 TGGTAAATTC
Statistics
Matches: 281, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
249 39 0.14
250 240 0.85
251 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (249 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
TGATTGGATTTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACA
TTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATTGGCACATTCATCTTCCAAATTCAATGATTGGTTTTGTCAAAC
Found at i:704333 original size:83 final size:83
Alignment explanation
Indices: 703794--704344 Score: 971
Period size: 83 Copynumber: 6.6 Consensus size: 83
703784 CCTACTGAAT
* *
703794 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTA-TGAACACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
703858 ATGATTGGTTTTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
*
703877 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
703941 ATGATTGGTTTTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
703960 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
704025 TGATTGGTTTTGTCAAAC
66 TGATTGGTTTTGTCAAAC
*
704043 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGAGCACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCACATTCATCTTCCAAATTCA
*
704108 ATGATTGGATTTGTCAAAC
65 ATGATTGGTTTTGTCAAAC
704127 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
*
704192 TGATTGGTTCTGTCAAAC
66 TGATTGGTTTTGTCAAAC
704210 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
*
704275 TGATTGGTTTTGTCAAAT
66 TGATTGGTTTTGTCAAAC
* * *
704293 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGGTAAATTCAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCAT
704345 TTGTTCTATT
Statistics
Matches: 454, Mismatches: 12, Indels: 4
0.97 0.03 0.01
Matches are distributed among these distances:
83 371 0.82
84 83 0.18
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCACATTCATCTTCCAAATTCAA
TGATTGGTTTTGTCAAAC
Found at i:705033 original size:19 final size:16
Alignment explanation
Indices: 705011--705056 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 16
705001 AATAGAAAAG
705011 AATAAATTGAATTTCCAAA
1 AATAAATTGAATTT-C--A
*
705030 AATAAATTTAATTTCA
1 AATAAATTGAATTTCA
705046 AATAAATTGAA
1 AATAAATTGAA
705057 CTTGAAATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.44
18 1 0.04
19 13 0.52
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (16 bp):
AATAAATTGAATTTCA
Found at i:718214 original size:20 final size:19
Alignment explanation
Indices: 718191--718235 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
718181 TATTTTTTAT
* *
718191 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
718211 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
718230 TATTTA
1 TATTTA
718236 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:718225 original size:26 final size:30
Alignment explanation
Indices: 718186--718241 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
718176 AATTATATTT
*
718186 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
718213 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
718242 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:718242 original size:3 final size:3
Alignment explanation
Indices: 718234--718346 Score: 163
Period size: 3 Copynumber: 37.7 Consensus size: 3
718224 TTAATATATT
* *
718234 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
718282 TAA TAA TAA TAA TGA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAT TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
718330 TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
718347 TGGATAAAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Done.