Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009583.1 Hibiscus syriacus cultivar Beakdansim tig00116960_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: 1341443
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:426680 original size:15 final size:15
Alignment explanation
Indices: 426660--426730 Score: 79
Period size: 15 Copynumber: 4.7 Consensus size: 15
426650 GAATTTATTA
426660 ATATGTGAATATGTT
1 ATATGTGAATATGTT
*
426675 ATATGTAAATATGTT
1 ATATGTGAATATGTT
* * *
426690 CTATATGAAAATGTT
1 ATATGTGAATATGTT
* *
426705 TTATGTGAATGTGTT
1 ATATGTGAATATGTT
*
426720 CTATGTGAATA
1 ATATGTGAATA
426731 AATGATACTT
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.45
Consensus pattern (15 bp):
ATATGTGAATATGTT
Found at i:438967 original size:132 final size:133
Alignment explanation
Indices: 438787--439047 Score: 305
Period size: 132 Copynumber: 2.0 Consensus size: 133
438777 ATCAACTATG
*
438787 ATTTAGCTAAACTCAACAACGAGGAGCTACTTCCCAATTCAGACTTTGAGCT-ATATTTCAACTT
1 ATTTAGCTAAACTCAACAACGAGGAGCTACTTCCCAATTCAGACTTTGAG-TAAGATTTCAACTT
** * *
438851 AACAATAAAGGATATCATGCTAAAG-CATTCGAGATCGACTCAACTTCACGAAGAAGGAGTCATC
65 AACAATAAAGGATATCAACCTAAAGTCATCCGAGATCGACTCAACTTCACAAAGAAGGAGTCATC
438915 TACA
130 TACA
* * ** * *
438919 ATTTAGCTTAACTCAACAACGAGGAGCTATTTTTCAGCA-T-AGATTTTGAGTAAGATTTTAACT
1 ATTTAGCTAAACTCAACAACGAGGAGCTACTTCCCA--ATTCAGACTTTGAGTAAGATTTCAACT
** * * ** *
438982 TCTCGATGAAGGATATCAACCTCGAGTCATCCGAGATCGACTCAACTTCACAAAGAATGAGTCAT
64 TAACAATAAAGGATATCAACCTAAAGTCATCCGAGATCGACTCAACTTCACAAAGAAGGAGTCAT
439047 C
129 C
439048 CATGACATGG
Statistics
Matches: 107, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
131 1 0.01
132 68 0.64
133 37 0.35
134 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (133 bp):
ATTTAGCTAAACTCAACAACGAGGAGCTACTTCCCAATTCAGACTTTGAGTAAGATTTCAACTTA
ACAATAAAGGATATCAACCTAAAGTCATCCGAGATCGACTCAACTTCACAAAGAAGGAGTCATCT
ACA
Found at i:439607 original size:5 final size:5
Alignment explanation
Indices: 439576--439720 Score: 61
Period size: 5 Copynumber: 28.0 Consensus size: 5
439566 TGATGTTTTC
* * *
439576 ATATT ATA-T GTATT ATCTT AT-TAT ATATT ATATT GTATTT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATAT-T ATATT ATATT ATA-TT ATATT ATATT
* * *
439626 -TATT ATA-T AGTATTT ATCTT ATATA ATA-T AGTATTT ATGTT ATA-T
1 ATATT ATATT A-TA-TT ATATT ATATT ATATT A-TA-TT ATATT ATATT
* *
439671 ATA-T AGTATT ATATAGT ATATA ACATTT ATAGTAT ATATT ATATT ATATT
1 ATATT A-TATT ATAT--T ATATT ATA-TT ATA-T-T ATATT ATATT ATATT
439721 TTATGGCATG
Statistics
Matches: 107, Mismatches: 16, Indels: 34
0.68 0.10 0.22
Matches are distributed among these distances:
4 17 0.16
5 63 0.59
6 14 0.13
7 13 0.12
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (5 bp):
ATATT
Found at i:439612 original size:25 final size:26
Alignment explanation
Indices: 439576--439675 Score: 99
Period size: 25 Copynumber: 4.1 Consensus size: 26
439566 TGATGTTTTC
439576 ATATTATA-TGTA-TTATCTTATTAT
1 ATATTATATTGTATTTATCTTATTAT
*
439600 ATATTATATTGTATTTATATTA-TAT
1 ATATTATATTGTATTTATCTTATTAT
* *
439625 TTATTATATAGTATTTATCTTA-TAT
1 ATATTATATTGTATTTATCTTATTAT
*
439650 A-A-TATA--GTATTTATGTTATATAT
1 ATATTATATTGTATTTATCTTAT-TAT
439673 ATA
1 ATA
439676 GTATTATATA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
21 11 0.17
23 8 0.12
24 10 0.15
25 29 0.45
26 7 0.11
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (26 bp):
ATATTATATTGTATTTATCTTATTAT
Found at i:439620 original size:16 final size:15
Alignment explanation
Indices: 439579--439670 Score: 71
Period size: 16 Copynumber: 5.7 Consensus size: 15
439569 TGTTTTCATA
439579 TTATATGTATTATCTTAT
1 TTATAT-TA-TAT-TTAT
439597 TATATATTATATTGTAT
1 T-TATATTATATT-TAT
439614 TTATATTATATTTA-
1 TTATATTATATTTAT
439628 TTATA-TAGTATTTAT
1 TTATATTA-TATTTAT
* *
439643 CTTATATAATATAGTAT
1 -TTATATTATAT-TTAT
*
439660 TTATGTTATAT
1 TTATATTATAT
439671 ATATAGTATT
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
13 2 0.03
14 11 0.17
15 2 0.03
16 29 0.46
17 11 0.17
18 3 0.05
19 5 0.08
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (15 bp):
TTATATTATATTTAT
Found at i:439648 original size:14 final size:14
Alignment explanation
Indices: 439601--439642 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
439591 TCTTATTATA
*
439601 TATTATATTGTATT
1 TATTATATAGTATT
439615 TA-TAT-TA-TATT
1 TATTATATAGTATT
439626 TATTATATAGTATT
1 TATTATATAGTATT
439640 TAT
1 TAT
439643 CTTATATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
11 6 0.25
12 4 0.17
13 5 0.21
14 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (14 bp):
TATTATATAGTATT
Found at i:439670 original size:51 final size:51
Alignment explanation
Indices: 439577--439721 Score: 140
Period size: 51 Copynumber: 2.8 Consensus size: 51
439567 GATGTTTTCA
*
439577 TATTATAT-GTA-TTATCTTATTATATATTATATTGTATTTATAT-TATATT
1 TATTATATAGTATTTATCTTATTATATATTATATTGTATTTATATATATA-G
439626 TATTATATAGTATTTATCTTA-TATA-ATATAGTATT-TATGTTATATATATAG
1 TATTATATAGTATTTATCTTATTATATAT-TA-TATTGTAT-TTATATATATAG
* * *
439677 TATTATATAGTATATAACATTTATAGTATATATTATATTATATTT
1 TATTATATAGTATTTATC--TTAT--TATATATTATATTGTATTT
439722 TATGGCATGT
Statistics
Matches: 80, Mismatches: 3, Indels: 20
0.78 0.03 0.19
Matches are distributed among these distances:
49 10 0.12
50 12 0.15
51 34 0.43
52 4 0.05
53 3 0.04
55 6 0.08
56 9 0.11
57 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (51 bp):
TATTATATAGTATTTATCTTATTATATATTATATTGTATTTATATATATAG
Found at i:439683 original size:35 final size:37
Alignment explanation
Indices: 439644--439792 Score: 129
Period size: 35 Copynumber: 4.2 Consensus size: 37
439634 AGTATTTATC
*
439644 TTATATA-ATATAGTATTTAT-GTTATATATATAGTA
1 TTATATATATATAGCATTTATAGTTATATATATAGTA
*
439679 TTATATAGTATATAACATTTATAG-TATATAT-TA-TA
1 TTATATA-TATATAGCATTTATAGTTATATATATAGTA
* * * *
439714 TTATAT-TTTATGGCATGTAGTA-TATATATTTTATAGTA
1 TTATATATATATAGCATTTA-TAGT-TATA-TATATAGTA
*
439752 TTA-ATATATATAGCATTTATAGTT-TATATGTAGTA
1 TTATATATATATAGCATTTATAGTTATATATATAGTA
439787 -TATATA
1 TTATATA
439793 GTATTATTAT
Statistics
Matches: 90, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
33 9 0.10
34 4 0.04
35 29 0.32
36 6 0.07
37 25 0.28
38 17 0.19
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.50
Consensus pattern (37 bp):
TTATATATATATAGCATTTATAGTTATATATATAGTA
Found at i:439779 original size:20 final size:21
Alignment explanation
Indices: 439756--439803 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
439746 ATAGTATTAA
*
439756 TATATATAGCATTTATAGT-T
1 TATATATAGCATATATAGTAT
* *
439776 TATATGTAGTATATATAGTAT
1 TATATATAGCATATATAGTAT
439797 TAT-TATA
1 TATATATA
439804 ATATTATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (21 bp):
TATATATAGCATATATAGTAT
Found at i:440593 original size:2 final size:2
Alignment explanation
Indices: 440586--440624 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
440576 CCAAAAATCA
440586 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
440625 ATTAGTTTCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:445320 original size:21 final size:21
Alignment explanation
Indices: 445274--445321 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
445264 AAACTCTAAA
*
445274 TATTTTCTCAAAATTTAATTT
1 TATTTTCTCAAAATATAATTT
* *
445295 AATTTT-TCAAAATATATTTTT
1 TATTTTCTCAAAATATA-ATTT
445316 TATTTT
1 TATTTT
445322 AAAAGTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.60
Consensus pattern (21 bp):
TATTTTCTCAAAATATAATTT
Found at i:448829 original size:20 final size:21
Alignment explanation
Indices: 448789--448832 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
448779 TCAAAATCAT
* *
448789 TTTTCAAAATTTCATTTTTGC
1 TTTTCAAAATTCCAATTTTGC
448810 TTTTCAAAA-TCCAATTTTGC
1 TTTTCAAAATTCCAATTTTGC
448830 TTT
1 TTT
448833 CAAGAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.25, C:0.16, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTTCAAAATTCCAATTTTGC
Found at i:450329 original size:17 final size:17
Alignment explanation
Indices: 450307--450345 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
450297 ATAACCTTTA
450307 CAAAGTCCCTAGTTTTT
1 CAAAGTCCCTAGTTTTT
*
450324 CAAAGTCTCTAGTTTTT
1 CAAAGTCCCTAGTTTTT
450341 CAAAG
1 CAAAG
450346 GCTCAGCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (17 bp):
CAAAGTCCCTAGTTTTT
Found at i:452332 original size:15 final size:17
Alignment explanation
Indices: 452300--452346 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
452290 AATGATTTTC
452300 TTTTGAAAAAAAATAAA
1 TTTTGAAAAAAAATAAA
*
452317 TTTTAAAAAACAAAATGAAA
1 TTTT-GAAAA-AAAAT-AAA
452337 TTTTGAAAAA
1 TTTTGAAAAA
452347 TGATTTTGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.16
18 5 0.20
19 9 0.36
20 7 0.28
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (17 bp):
TTTTGAAAAAAAATAAA
Found at i:452337 original size:20 final size:19
Alignment explanation
Indices: 452305--452346 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
452295 TTTTCTTTTG
452305 AAAAAAAATAAATTTT-AA
1 AAAAAAAATAAATTTTGAA
452323 AAAACAAAATGAAATTTTGAA
1 AAAA-AAAAT-AAATTTTGAA
452344 AAA
1 AAA
452347 TGATTTTGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 5 0.24
20 7 0.33
21 5 0.24
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAAAAATAAATTTTGAA
Found at i:456429 original size:16 final size:16
Alignment explanation
Indices: 456399--456428 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
456389 TTTCAAGATA
456399 AAAATATAAATAAAAT
1 AAAATATAAATAAAAT
456415 AAAATAT-AATAAAA
1 AAAATATAAATAAAA
456429 AAGGTGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATATAAATAAAAT
Found at i:458924 original size:244 final size:243
Alignment explanation
Indices: 458317--458929 Score: 684
Period size: 244 Copynumber: 2.5 Consensus size: 243
458307 AGTTAATTTA
*
458317 GGGTCTTCTTCTAGTCCAATATCATTCATT-GTGAAGTTGAAATTTGACTTGAAAACCTTGGTTA
1 GGGTCTTATTCTAGTCCAATATC-TTCATTCGTGAAGTTGAAATTTGACTTG-AAACCTTGGTTA
* *
458381 GAAAATAACT-TGT-AGC-TGTTGAGTTAAGCTATGTTGTGGATGACTC---CATT-A-CAAGTT
64 GAAAATAACTCT-TCA-CTTGTTGAGTTAAGCTATGTTGTGTATGACTCATTC-TTCATGAAGTT
* * * **
458438 AAGTCACTCTTGGATGACTCGAGACTGATATCCTTCGTCGTGAAGTTGAAATTTGGCTCAAAATA
126 AAGTCACTCTCGGATGACTCGAGACTGATATCCTTCATCGTGAAGTTGAAATCTAACTCAAAATA
* * * * *
458503 TGGTTGGAAAATAGCTCATTGTTGTTGAGTTAAGCTAAATCGCAGTCGATTTT
191 TGGCTGGAAAATAACTCATTGTTGTTGAGTTAAACTAAATCACAGTCGACTTT
* * *
458556 GGATCTTATTCTAGTCCAATATCCTTCA-TCGTGAAGTTGAAATTTGACTTGATAACCTTTGTTG
1 GGGTCTTATTCTAGTCCAATAT-CTTCATTCGTGAAGTTGAAATTTGACTTGA-AACCTTGGTTA
** * * ** *
458620 GAAAATATTTCCTCACTT-TTGAGTTAAGCTATGTTATGTATGACT-ATTTCGGCGTGAAGTTAA
64 GAAAATAACTCTTCACTTGTTGAGTTAAGCTATGTTGTGTATGACTCA-TTCTTCATGAAGTTAA
* *
458683 GTCGA-TCTCGGATGGCTCGAG-CTTGATATCCTTCATCGTGAAGTTGAAATCTAACTCAAAATC
128 GTC-ACTCTCGGATGACTCGAGAC-TGATATCCTTCATCGTGAAGTTGAAATCTAACTCAAAATA
*
458746 TAGGCT-GAAAATTAACTTC-TTGTTGTTGAGTTAAACTAAATCACATTCGACTTT
191 T-GGCTGGAAAA-TAAC-TCATTGTTGTTGAGTTAAACTAAATCACAGTCGACTTT
* * * * * *
458800 GGGTCTTATTCTAGTCTAATATCTTTATTCATGAAGTTGAAATTTGACTTGAAGATCTTGGATCG
1 GGGTCTTATTCTAGTCCAATATCTTCATTCGTGAAGTTGAAATTTGACTTGAA-ACCTTGGTTAG
*
458865 AAAATAACTCTTCA-TTGTTGAGTTGAGCTATGTTGTGTATGACTCATTCTTCATGAAGTTAAGT
65 AAAATAACTCTTCACTTGTTGAGTTAAGCTATGTTGTGTATGACTCATTCTTCATGAAGTTAAGT
458929 C
130 C
458930 CAGGTTGAAT
Statistics
Matches: 311, Mismatches: 42, Indels: 37
0.80 0.11 0.09
Matches are distributed among these distances:
238 2 0.01
239 89 0.29
240 3 0.01
242 2 0.01
243 72 0.23
244 140 0.45
245 3 0.01
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (243 bp):
GGGTCTTATTCTAGTCCAATATCTTCATTCGTGAAGTTGAAATTTGACTTGAAACCTTGGTTAGA
AAATAACTCTTCACTTGTTGAGTTAAGCTATGTTGTGTATGACTCATTCTTCATGAAGTTAAGTC
ACTCTCGGATGACTCGAGACTGATATCCTTCATCGTGAAGTTGAAATCTAACTCAAAATATGGCT
GGAAAATAACTCATTGTTGTTGAGTTAAACTAAATCACAGTCGACTTT
Found at i:465266 original size:3 final size:3
Alignment explanation
Indices: 465258--465284 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
465248 ATCAAACAAT
465258 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
465285 ATTGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:466397 original size:23 final size:23
Alignment explanation
Indices: 466370--466418 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
466360 ATTATTTTTA
466370 ATATATATACTTTTTAATAAAATTT
1 ATATA-AT-CTTTTTAATAAAATTT
* *
466395 ATATAATTTTTTTTATAAAATTT
1 ATATAATCTTTTTAATAAAATTT
466418 A
1 A
466419 AAAGATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 2 0.09
25 5 0.23
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATATAATCTTTTTAATAAAATTT
Found at i:481214 original size:21 final size:21
Alignment explanation
Indices: 481190--481232 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
481180 GAAAATAAAG
481190 AACTTCTGCAGAAACCATGGC
1 AACTTCTGCAGAAACCATGGC
481211 AACTTCTGCAGAAACCATGGC
1 AACTTCTGCAGAAACCATGGC
481232 A
1 A
481233 TGCTCGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.28, G:0.19, T:0.19
Consensus pattern (21 bp):
AACTTCTGCAGAAACCATGGC
Found at i:483938 original size:21 final size:21
Alignment explanation
Indices: 483908--483964 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
483898 TATGTGCAAT
483908 TAAA-ATTTATAAAAATAATA
1 TAAATATTTATAAAAATAATA
* * *
483928 TAAATATTTATATATATATTA
1 TAAATATTTATAAAAATAATA
483949 TAAAACTATTTATAAA
1 T-AAA-TATTTATAAA
483965 TTAAAAGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 4 0.13
21 14 0.47
22 3 0.10
23 9 0.30
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TAAATATTTATAAAAATAATA
Found at i:484660 original size:20 final size:20
Alignment explanation
Indices: 484635--484679 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
484625 TACCTCCAGA
484635 AGTCACCTCCTGAAACTGCC
1 AGTCACCTCCTGAAACTGCC
484655 AGTCACCTCCTGAAACTGCC
1 AGTCACCTCCTGAAACTGCC
484675 AGTCA
1 AGTCA
484680 AGACCTCTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.38, G:0.16, T:0.20
Consensus pattern (20 bp):
AGTCACCTCCTGAAACTGCC
Found at i:488230 original size:20 final size:20
Alignment explanation
Indices: 488205--488248 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
488195 AGTTATTTTT
*
488205 TTTACTTTTGGTTATCATAA
1 TTTACTTTTGGATATCATAA
* *
488225 TTTACTTTTTGATATTATAA
1 TTTACTTTTGGATATCATAA
488245 TTTA
1 TTTA
488249 TGATTCTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.07, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTACTTTTGGATATCATAA
Found at i:490944 original size:17 final size:18
Alignment explanation
Indices: 490906--490951 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
490896 TTTTGGTAAG
490906 AAAATATT-AA-AATAAT
1 AAAATATTAAATAATAAT
490922 AAAATATTAAATAATAA-
1 AAAATATTAAATAATAAT
490939 AAAATATTAAATA
1 AAAATATTAAATA
490952 CGTAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.29
17 15 0.54
18 5 0.18
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAATATTAAATAATAAT
Found at i:496503 original size:18 final size:19
Alignment explanation
Indices: 496480--496525 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
496470 GTAAGAAAAT
*
496480 ATTAAAGTAA-TAAAAACG
1 ATTAAAGTAAGTAAAAACA
*
496498 ATTAAA-TAAGTAAAAGCA
1 ATTAAAGTAAGTAAAAACA
496516 ATTAAAGTAA
1 ATTAAAGTAA
496526 AAATAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 18 0.75
19 3 0.12
ACGTcount: A:0.61, C:0.04, G:0.11, T:0.24
Consensus pattern (19 bp):
ATTAAAGTAAGTAAAAACA
Found at i:502198 original size:24 final size:24
Alignment explanation
Indices: 502166--502222 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
502156 CTATCTACGA
*
502166 CTGAAGCTGAGTACATGGCAGCGG
1 CTGAAGCTGAGTACATGACAGCGG
*
502190 CTGAAGCTGAGTACATGACAGTGG
1 CTGAAGCTGAGTACATGACAGCGG
502214 CTGAAGCTG
1 CTGAAGCTG
502223 CAAAAAAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.26, C:0.19, G:0.35, T:0.19
Consensus pattern (24 bp):
CTGAAGCTGAGTACATGACAGCGG
Found at i:504663 original size:3 final size:3
Alignment explanation
Indices: 504655--504696 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
504645 TTTCATTCCG
504655 TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TT
504697 TGTTTCTCGG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:504876 original size:31 final size:31
Alignment explanation
Indices: 504838--504928 Score: 146
Period size: 31 Copynumber: 2.9 Consensus size: 31
504828 TCTCAGCTGC
*
504838 CGCCGCCATTGGAACCAACCTAATATGCCGT
1 CGCCGCCATTGGAGCCAACCTAATATGCCGT
*
504869 CGCCGCCATTGGAGCCAACCTAATATGCTGT
1 CGCCGCCATTGGAGCCAACCTAATATGCCGT
* *
504900 CGCCACCATTGGAGCCAACCTAATCTGCC
1 CGCCGCCATTGGAGCCAACCTAATATGCC
504929 ACCCATCTCC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.24, C:0.36, G:0.20, T:0.20
Consensus pattern (31 bp):
CGCCGCCATTGGAGCCAACCTAATATGCCGT
Found at i:506365 original size:131 final size:130
Alignment explanation
Indices: 506214--506521 Score: 418
Period size: 131 Copynumber: 2.4 Consensus size: 130
506204 GGCATGGGAT
* * *
506214 GTCATTTATTCTCGATTGGAAATAATTTGATATTATCATTTTCTCTCGAATTAATATTGATTTTT
1 GTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATTAATATTGAATTTT
** *
506279 AAGATGGAATAGTGATATATCTTCATTTTGATTGGAGCAATAAATGACTGCTTCAAGGTATGAGA
66 AAGAAAGAATAGTGATATATCTTCA-TTCGATTGGAGCAATAAATGACTGCTTCAAGGTATGAGA
506344 G
130 G
* * * *
506345 GTCACTTATTCTCAATTGGAAATCATTAGATATTATCATTTTCACTCGAATTGATATTGAATTTT
1 GTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATTAATATTGAATTTT
* * * * * * * *
506410 AGGAAAGAATAGTGATATCTTTTTATTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGATAG
66 AAGAAAGAATAGTGATATATCTTCATTCGATTGGAGCAATAAATGACTGCTTCAAGGTATGAGAG
* * *
506475 ATCATTTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCACTC
1 GTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTC
506522 TAAAAATTAT
Statistics
Matches: 153, Mismatches: 24, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
130 76 0.50
131 77 0.50
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (130 bp):
GTCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATTAATATTGAATTTT
AAGAAAGAATAGTGATATATCTTCATTCGATTGGAGCAATAAATGACTGCTTCAAGGTATGAGAG
Found at i:506503 original size:130 final size:131
Alignment explanation
Indices: 506215--506521 Score: 418
Period size: 130 Copynumber: 2.4 Consensus size: 131
506205 GCATGGGATG
* * *
506215 TCATTTATTCTCGATTGGAAATAATTTGATATTATCATTTTCTCTCGAATTAATATTGATTTTTA
1 TCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATTAATATTGAATTTTA
** *
506280 AGATGGAATAGTGATATATCTTCATTTTGATTGGAGCAATAAATGACTGCTTCAAGGTATGAGAG
66 AGAAAGAATAGTGATATATCTTCATTTCGATTGGAGCAATAAATGACTGCTTCAAGGTATGAGAG
*
506345 G
131 A
* * * *
506346 TCACTTATTCTCAATTGGAAATCATTAGATATTATCATTTTCACTCGAATTGATATTGAATTTTA
1 TCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATTAATATTGAATTTTA
* * * * * * * *
506411 GGAAAGAATAGTGATATCTTTTTA-TTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGATAG
66 AGAAAGAATAGTGATATATCTTCATTTCGATTGGAGCAATAAATGACTGCTTCAAGGTATGAGAG
506475 A
131 A
* *
506476 TCATTTATTCTCGATTAGAAATAATTAGATATTATCGTTTTCACTC
1 TCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTC
506522 TAAAAATTAT
Statistics
Matches: 152, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
130 76 0.50
131 76 0.50
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (131 bp):
TCATTTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATTAATATTGAATTTTA
AGAAAGAATAGTGATATATCTTCATTTCGATTGGAGCAATAAATGACTGCTTCAAGGTATGAGAG
A
Found at i:512816 original size:20 final size:20
Alignment explanation
Indices: 512793--512840 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
512783 ACTTTTAAGG
512793 ACTTTGAATTATTTTTGAGA
1 ACTTTGAATTATTTTTGAGA
512813 ACTTTGAATTATTTTTGAGA
1 ACTTTGAATTATTTTTGAGA
512833 ACTTTGAA
1 ACTTTGAA
512841 AACTTTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (20 bp):
ACTTTGAATTATTTTTGAGA
Found at i:519185 original size:232 final size:232
Alignment explanation
Indices: 518779--519899 Score: 1308
Period size: 232 Copynumber: 4.8 Consensus size: 232
518769 TTCTTACTTT
* * * * *
518779 GTAAGTCCTTCGGGCCATCAATAAGTATTTCAAGCATGATGTTTAAAT-TCATCGGGTCATCTGT
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCT-TTCGGGTCATCTGT
* * * * *
518843 AAGTCTTTCGAGCAAGATGATAAGTCTTTTGGGCCATCTATAAGACATTCGGGCAGGATATTTTC
65 AAGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTC
* * * *
518908 ACGTATCTTTCGAAAAATGAG-AAAGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGT
130 ACATGTCTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTAAAAAGT
*
518972 AAGAGAAA-TTTCTTACTTAGTAAACTATTCCTAAATTTG
195 AAGA-AAAGTTTCTTACCTAGTAAACTATTCC-AAATTTG
* * * *
519011 GTAAGTCTTTCGGGTCATCAGTAAGTCTTTCAAGTATGATGCTTAAATCTTTCGGGTCATCTGTA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTA
* * * *
519076 AGTATTTCGTGCAAGATGATAAGTCATTCGGGCCACCCATAAGACCTTCGGGTAGGATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
* * * *
519141 CATGCCTTTC-AAAAATGAGAAATGTTTCTCATTTAAATATGAAAATTGAAATTTTTGAAAAGTA
131 CATGTCTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTAAAAAGTA
*
519205 AGAAAAGTTTCTTACCTAGTAAACTATTCCCAATTTTG
196 AGAAAAGTTTCTTACCTAGTAAACTATT-CCAAATTTG
* * * *
519243 GTAAGTCCTTCGAGCCATCTGTAAGTCTTTCGAGCATGATGCTTAAAACCTTCGGGTCATCTGTA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTA
* * * * * * ***
519308 AGTTTTTCGAGTAAGATAATAAGT-ACTTTGGGCCATTCATAAGACTTTCGATTAGGATGTTTTC
66 AGTCTTTCGAGCAAGATGATAAGTCA-TTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTC
* * * *
519372 ACGTGTCTTTCAAAAAAGGA-AAAAGATTACTCATTTAAATCTGAAAATTGAAATTTTTAAAAAG
130 ACATGTCTTTCGAAAAATGAGAAAAG-TTTCTCATTTAAATCTGAAAATTGAAATTTTTAAAAAG
*
519436 TAAGAAAAGTTTTTTACCTAGTAAACTATTCCAAAATTTG
194 TAAGAAAAGTTTCTTACCTAGTAAACTATTCC-AAATTTG
* * * * ** *
519476 GTAAGTCCTTTGGGCCATTATTAAGTCTTTCGAGCATGATACTTAAATCTTTCAAGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTA
* * * * * * *
519541 AGTCTTTCGAGCAAGATGATAAGTCTTTCAGCCCATCCACAAGACCTTCAGGAAAGATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
* * *
519606 CATGTTTTTCGAAAAAGGAGAAAGGTATT-TCATTTAAATCTGAAAAATTG-AATTTTTCAAAAA
131 CATGTCTTTCGAAAAATGAGAAAAGT-TTCTCATTTAAATCTG-AAAATTGAAATTTTT----AA
*
519669 AAAGTAAGAAAAGTTTCTTACCTAGCAAACTATTTCCAAGA-TTG
190 AAAGTAAGAAAAGTTTCTTACCTAGTAAACTA-TTCCAA-ATTTG
* * ** * * *
519713 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTTGAGCATGTTGAGTAAATCCTTCGAGTCATCTATA
1 GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTA
* * * *
519778 AGCCTTTCGAGCAAGATGATAAGTCCTTCGGTCCATCCATAAGACCTTCGAGCAGGATGTTTTCA
66 AGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
* * *
519843 CATATTTTTTTTCGAAAAATGAGAAAAATTTCTCATTT-AATCTGAAAATTGAAATTT
131 C--A-TGTCTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTT
519900 AGAATAAAGG
Statistics
Matches: 761, Mismatches: 105, Indels: 39
0.84 0.12 0.04
Matches are distributed among these distances:
231 13 0.02
232 315 0.41
233 220 0.29
234 12 0.02
237 149 0.20
238 12 0.02
239 14 0.02
240 26 0.03
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (232 bp):
GTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTA
AGTCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGGGCAGGATGTTTTCA
CATGTCTTTCGAAAAATGAGAAAAGTTTCTCATTTAAATCTGAAAATTGAAATTTTTAAAAAGTA
AGAAAAGTTTCTTACCTAGTAAACTATTCCAAATTTG
Found at i:519790 original size:42 final size:41
Alignment explanation
Indices: 519718--519836 Score: 109
Period size: 41 Copynumber: 2.9 Consensus size: 41
519708 GATTGGTAAG
* * * * *
519718 TCCTTCGGGCCAT-CAGTAAGTCTTTTGAGCATGTTGAGTAAA
1 TCCTTCGGTCCATCCA-TAAGCCTTTCGAGCAAGATGA-TAAA
* *
519760 TCCTTCGAGT-CATCTATAAGCCTTTCGAGCAAGATGATAAG
1 TCCTTCG-GTCCATCCATAAGCCTTTCGAGCAAGATGATAAA
*
519801 TCCTTCGGTCCATCCATAAGACC-TTCGAGCAGGATG
1 TCCTTCGGTCCATCCATAAG-CCTTTCGAGCAAGATG
519837 TTTTCACATA
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
40 2 0.03
41 31 0.48
42 29 0.45
43 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (41 bp):
TCCTTCGGTCCATCCATAAGCCTTTCGAGCAAGATGATAAA
Found at i:519820 original size:41 final size:41
Alignment explanation
Indices: 519705--519836 Score: 117
Period size: 42 Copynumber: 3.2 Consensus size: 41
519695 AAACTATTTC
* * * *
519705 CAAGATTGGTAAGTCCTTCGGGCCAT-CAGTAAGTCTTTTGAG
1 CAAGA-TGATAAGTCCTTCGGTCCATCCA-TAAGCCTTTCGAG
* * * *
519747 CATGTTGAGTAAATCCTTCGAGT-CATCTATAAGCCTTTCGAG
1 CAAGATGA-TAAGTCCTTCG-GTCCATCCATAAGCCTTTCGAG
519789 CAAGATGATAAGTCCTTCGGTCCATCCATAAGACC-TTCGAG
1 CAAGATGATAAGTCCTTCGGTCCATCCATAAG-CCTTTCGAG
*
519830 CAGGATG
1 CAAGATG
519837 TTTTCACATA
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
40 2 0.03
41 33 0.46
42 35 0.49
43 2 0.03
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (41 bp):
CAAGATGATAAGTCCTTCGGTCCATCCATAAGCCTTTCGAG
Found at i:520531 original size:133 final size:133
Alignment explanation
Indices: 520164--520700 Score: 481
Period size: 133 Copynumber: 4.0 Consensus size: 133
520154 TAATGTTTAA
* ** * * * *
520164 TTTCCATATATGATTTTCCCTCAAGAAGTAGCAGAATAGATCCCTCTTTTTTCCAGATTTGATCT
1 TTTCCATATATGATTTTCCCTCAAGAAGAAGTGGAACAAAT-CCTC-TCTTTCAAGATTTGATCT
** * * ** * * * ** * *
520229 TCCAAGAGGAATAGTGGAATGAGTCTGCCTCGATTCAATCTTCCCTTAAGAGCAATGAAATGAAT
64 TCCTTGAGTAACAGTGGAACAAGTATGCCTCGTTTCAATCTTCCCTGAAGAATAGTGGAATGAAT
*
520294 CAACA
129 CAACG
* * * * * *
520299 TTTCCATATATGATTTTCCCTCAATAAGAAATGGAATAGATCC-CTCTTTCAATATTTGATATT-
1 TTTCCATATATGATTTTCCCTCAAGAAGAAGTGGAACAAATCCTCTCTTTCAAGATTTGATCTTC
* * * * * * *
520362 CTCTGAGTAATAGTGAAACAAGTTTGCCTCGATTCAAACTTCCTTGAATAATAGTGGAATGAATC
66 CT-TGAGTAACAGTGGAACAAGTATGCCTCGTTTCAATCTTCCCTGAAGAATAGTGGAATGAATC
520427 AACG
130 AACG
** * * * *
520431 TCCCCATATATGATTTACCCTTAAGAATAAGTGGAACAAATCCTCCCTTTCAAGATTTGATCTTC
1 TTTCCATATATGATTTTCCCTCAAGAAGAAGTGGAACAAATCCTCTCTTTCAAGATTTGATCTTC
* * * *
520496 CTTGAGTAACAATGGAACAAGTATGCCTCGTTTCAATCTTCCCTGAAGAACAGTTGAATGAATTA
66 CTTGAGTAACAGTGGAACAAGTATGCCTCGTTTCAATCTTCCCTGAAGAATAGTGGAATGAATCA
520561 ACG
131 ACG
* * * ** *
520564 TTTCCAGATCTGATTTTCCCTCAAGAAGAAGTGCAACATGTCCTTCTCTTTCAAGACTTGATCTT
1 TTTCCATATATGATTTTCCCTCAAGAAGAAGTGGAACAAATCC-TCTCTTTCAAGATTTGATCTT
* * * * *
520629 CCCT-AGATAGCAGTGGAACAA-TCTACCTCAATTT-AATCTTCCCTGAAGAATAGTGGAATGAA
65 CCTTGAG-TAACAGTGGAACAAGTATGCCTC-GTTTCAATCTTCCCTGAAGAATAGTGGAATGAA
*
520691 TCAATG
128 TCAACG
520697 TTTC
1 TTTC
520701 TCGATTTGAT
Statistics
Matches: 326, Mismatches: 70, Indels: 14
0.80 0.17 0.03
Matches are distributed among these distances:
131 1 0.00
132 100 0.31
133 148 0.45
134 41 0.13
135 36 0.11
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (133 bp):
TTTCCATATATGATTTTCCCTCAAGAAGAAGTGGAACAAATCCTCTCTTTCAAGATTTGATCTTC
CTTGAGTAACAGTGGAACAAGTATGCCTCGTTTCAATCTTCCCTGAAGAATAGTGGAATGAATCA
ACG
Found at i:522966 original size:131 final size:131
Alignment explanation
Indices: 522765--523122 Score: 518
Period size: 131 Copynumber: 2.7 Consensus size: 131
522755 TCGATATTGA
* * * * *
522765 GAATAGTAATATCTTTTCATTTCGGTTTGAGTAATAAATGACTGCTCTAAGGAATGAGAGGTCAT
1 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGAATGAGAGGTCAT
* * * * * * *
522830 TTATTCTTGATTGGAAATAATTCGGTATTATCATTTTCTCTCGAATTAATATTGATTTTTAAGAT
66 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAGAC
522895 G
131 G
* *
522896 GAATAGTGATATCTCTTCATTTCGATTGGAGCAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
1 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGAATGAGAGGTCAT
* * *
522961 TTATTCTCGATTGGAAATCATTAGATATTATCGTTTTCACTCGAATCGATATTGAATTTTAAGAC
66 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAGAC
523026 G
131 G
* * * *
523027 GAATAATGATATATCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGTATGAGAGGTCAT
1 GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGAATGAGAGGTCAT
*
523092 TTATTCTCGATTAGAAATAATTAGATATTAT
66 TTATTCTCGATTGGAAATAATTAGATATTAT
523123 TGTTTTTATT
Statistics
Matches: 203, Mismatches: 24, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
131 203 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (131 bp):
GAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGAATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAGAC
G
Found at i:524977 original size:167 final size:166
Alignment explanation
Indices: 524599--525068 Score: 683
Period size: 167 Copynumber: 2.8 Consensus size: 166
524589 ATAAAAAATT
* * *
524599 ATAATTTTTTTTATCAATTTTCATGTATAGTGTCATTTTGGTAATTGCATAACTAGAAAGAATTA
1 ATAA-TTTTTTTATCAATTTTCATGTATTGTGTCATTTTGGTAATTGCATATCTAAAAAGAATTA
* * *
524664 TAATTAATAAAAAAT-ATTATAATCTAATTAAAATATCCCTAAAAGTATGTCATATTATAAAAGA
65 TAATTAATAAAAATTCATTATAATCTAATTAAAATATCCCTAAAAGTATGTAATATTATAAAAAA
*
524728 AAATCATTTTTAACAAAATAATATGAAAAACTCTACA
130 AAATCATTTTTAACAAAATAATATGAAAAACTCTAAA
** * * * *
524765 ATTGTTTTTTTCTCAATTTTCATGTATTGTGTCGTTTTCGTAATTGCATATCTAAAAAGAATCAT
1 ATAATTTTTTTATCAATTTTCATGTATTGTGTCATTTTGGTAATTGCATATCTAAAAAGAATTAT
* *
524830 AATTAATAAAAATTCATTATAATATAATTAAAATATCCCTAAAAGTATATAATATTATAAAATAA
66 AATTAATAAAAATTCATTATAATCTAATTAAAATATCCCTAAAAGTATGTAATATTATAAAA-AA
* * * * * *
524895 AAATTATTTTTAATAAAGTAATATGAACAATTTTATAA
130 AAATCATTTTTAACAAAATAATATGAAAAACTCTA-AA
*
524933 ATAATTTTTTT-TCAATTTTCATGTATTGTGTCATTTTGGTAATTGCATATCTAAAACGAATTAT
1 ATAATTTTTTTATCAATTTTCATGTATTGTGTCATTTTGGTAATTGCATATCTAAAAAGAATTAT
*
524997 AATTAATACAAATTCATTATAATCTAATTAAAATATCCCTAAAAGTATGTAATATTATAAAAGAA
66 AATTAATAAAAATTCATTATAATCTAATTAAAATATCCCTAAAAGTATGTAATATTATAAAA-AA
525062 AAATCAT
130 AAATCAT
525069 AAAAAAACAT
Statistics
Matches: 269, Mismatches: 32, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
165 67 0.25
166 46 0.17
167 146 0.54
168 10 0.04
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (166 bp):
ATAATTTTTTTATCAATTTTCATGTATTGTGTCATTTTGGTAATTGCATATCTAAAAAGAATTAT
AATTAATAAAAATTCATTATAATCTAATTAAAATATCCCTAAAAGTATGTAATATTATAAAAAAA
AATCATTTTTAACAAAATAATATGAAAAACTCTAAA
Found at i:531550 original size:20 final size:22
Alignment explanation
Indices: 531527--531584 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
531517 ATCATTTCTT
531527 AGTGCATCGATGCATTC-TA-C
1 AGTGCATCGATGCATTCTTATC
531547 AGTGCATCGATGCATTCTTTATC
1 AGTGCATCGATGCATTC-TTATC
531570 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
531585 CTACTCATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 2 0.06
23 2 0.06
24 13 0.38
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTATC
Found at i:531715 original size:64 final size:64
Alignment explanation
Indices: 531575--531733 Score: 194
Period size: 64 Copynumber: 2.5 Consensus size: 64
531565 TTATCATGTG
* * * * * *
531575 CATCGATGCACTACTCATGTATCGATACACAAATCACCTTCGATGTTTTCATTTTAAGGGGGTG
1 CATCGATGCACTTCTTATGTATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGGGGGTA
* * *
531639 CATCGATGCACTTCTTATGTATCGATGCACTAATTACATTCGATGTTTCCATTTTTAA-TGGGTA
1 CATCGATGCACTTCTTATGTATCGATGCACAAATCACATTCGATGTTTCCA-TTTTAAGGGGGTA
* * *
531703 CATCGATGCACTTCCTGTGCATCGATGCACA
1 CATCGATGCACTTCTTATGTATCGATGCACA
531734 CTAAACAATT
Statistics
Matches: 81, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 75 0.93
65 6 0.07
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.35
Consensus pattern (64 bp):
CATCGATGCACTTCTTATGTATCGATGCACAAATCACATTCGATGTTTCCATTTTAAGGGGGTA
Found at i:535052 original size:26 final size:26
Alignment explanation
Indices: 534993--535044 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
534983 AGGACCGCGT
534993 AGACCCTCGACTCTTGGCATGCCAAC
1 AGACCCTCGACTCTTGGCATGCCAAC
535019 AGACCCTCGACTCTTGGCATGCCAAC
1 AGACCCTCGACTCTTGGCATGCCAAC
535045 TATACCTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.19, T:0.19
Consensus pattern (26 bp):
AGACCCTCGACTCTTGGCATGCCAAC
Found at i:536068 original size:26 final size:27
Alignment explanation
Indices: 536032--536084 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
536022 TCCTATTCTC
536032 CATATGTAATTCAAGAATTACACTAAA
1 CATATGTAATTCAAGAATTACACTAAA
536059 CATATG-AATTCAAGAATTACACTAAA
1 CATATGTAATTCAAGAATTACACTAAA
536085 TTTTTAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (27 bp):
CATATGTAATTCAAGAATTACACTAAA
Found at i:539025 original size:21 final size:21
Alignment explanation
Indices: 538999--539047 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
538989 AGGTACCTAT
538999 CTAGCTACCTAAACTACATAG
1 CTAGCTACCTAAACTACATAG
* ** *
539020 CTAGCTATCTATGCTACCTAG
1 CTAGCTACCTAAACTACATAG
539041 CTAGCTA
1 CTAGCTA
539048 AGTGACCTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (21 bp):
CTAGCTACCTAAACTACATAG
Found at i:551140 original size:31 final size:31
Alignment explanation
Indices: 551105--551168 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
551095 AAACACATTT
* *
551105 TTGTTTCTTCAGCAAGAATGTTTGCCACCAA
1 TTGTTTCTTCAACAAGAATGTCTGCCACCAA
551136 TTGTTTCTTCAACAAGAATGTCTGCCACCAA
1 TTGTTTCTTCAACAAGAATGTCTGCCACCAA
551167 TT
1 TT
551169 TCTCATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (31 bp):
TTGTTTCTTCAACAAGAATGTCTGCCACCAA
Found at i:552689 original size:41 final size:41
Alignment explanation
Indices: 552600--552680 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
552590 AACTAATTCC
552600 TAAATAAA-TAATAATAAAATAATCAAACTAAAAATCCTAAA
1 TAAA-AAAGTAATAATAAAATAATCAAACTAAAAATCCTAAA
552641 TAAAAAAGTAATAATAAAATAATCAAACTAAAAATCCTAA
1 TAAAAAAGTAATAATAAAATAATCAAACTAAAAATCCTAA
552681 TTCTAAAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
40 3 0.08
41 36 0.92
ACGTcount: A:0.65, C:0.10, G:0.01, T:0.23
Consensus pattern (41 bp):
TAAAAAAGTAATAATAAAATAATCAAACTAAAAATCCTAAA
Found at i:553276 original size:44 final size:44
Alignment explanation
Indices: 553208--553291 Score: 141
Period size: 44 Copynumber: 1.9 Consensus size: 44
553198 GATGAAATTT
* *
553208 AACCAAGTTTAGTTTCCTCGTGAGAAGCGATTGGTGGAGTATAA
1 AACCAAGTTTAGTTTCCTCATGAGAAGCGATTGGCGGAGTATAA
*
553252 AACCAAGTTTATTTTCCTCATGAGAAGCGATTGGCGGAGT
1 AACCAAGTTTAGTTTCCTCATGAGAAGCGATTGGCGGAGT
553292 GTGAGTTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (44 bp):
AACCAAGTTTAGTTTCCTCATGAGAAGCGATTGGCGGAGTATAA
Found at i:554019 original size:17 final size:17
Alignment explanation
Indices: 553990--554034 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
553980 CTAAAATAAA
553990 AAAATAAAT-AAATAGCT
1 AAAATAAATAAAATAG-T
*
554007 AGAA-AAATAAAATAGT
1 AAAATAAATAAAATAGT
554023 AAAATAAATAAA
1 AAAATAAATAAA
554035 TTGAGCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.20
Consensus pattern (17 bp):
AAAATAAATAAAATAGT
Found at i:556763 original size:19 final size:19
Alignment explanation
Indices: 556719--556765 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
556709 AAAGAGGTTT
*
556719 AGAAAAATAAATTGAAAAA
1 AGAAAAATAAATTAAAAAA
**
556738 ATTAAAATAAA-TAAAAATA
1 AGAAAAATAAATTAAAAA-A
556757 AGAAAAATA
1 AGAAAAATA
556766 GATGATTGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (19 bp):
AGAAAAATAAATTAAAAAA
Found at i:557391 original size:14 final size:14
Alignment explanation
Indices: 557366--557401 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
557356 AGCATTGTGA
557366 AAAGAAAA-TAATG
1 AAAGAAAAGTAATG
557379 AAAGAAAAGTAATG
1 AAAGAAAAGTAATG
557393 --AGAAAAGTA
1 AAAGAAAAGTA
557402 GAACTTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 9 0.41
13 8 0.36
14 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (14 bp):
AAAGAAAAGTAATG
Found at i:558840 original size:70 final size:70
Alignment explanation
Indices: 558727--558866 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
558717 TCGTGATTGG
558727 ATTGCCAACTTGTTGTTTTTCCAGGAACCCAAGATGAATTGCACATCCTTTCCTCCTTAATATGA
1 ATTGCCAACTTGTTGTTTTTCCAGGAACCCAAGATGAATTGCACATCCTTTCCTCCTTAATATGA
558792 TTTTT
66 TTTTT
558797 ATTGCCAACTTGTTGTTTTTCCAGGAACCCAAGATGAATTGCACATCCTTTCCTCCTTAATATGA
1 ATTGCCAACTTGTTGTTTTTCCAGGAACCCAAGATGAATTGCACATCCTTTCCTCCTTAATATGA
558862 TTTTT
66 TTTTT
558867 CGTACATGGG
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (70 bp):
ATTGCCAACTTGTTGTTTTTCCAGGAACCCAAGATGAATTGCACATCCTTTCCTCCTTAATATGA
TTTTT
Found at i:563609 original size:3 final size:3
Alignment explanation
Indices: 563601--563661 Score: 74
Period size: 3 Copynumber: 20.7 Consensus size: 3
563591 TTTTTCATTC
*
563601 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT T-T ATAT TAC TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
563644 TAT ATAT TAT TAT TAT TA
1 TAT -TAT TAT TAT TAT TA
563662 AATAAAAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
2 5 0.10
3 43 0.83
4 4 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:565071 original size:22 final size:21
Alignment explanation
Indices: 565035--565105 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 21
565025 TATAGTTCAA
* *
565035 TATTTTAATTTATTTTAGTTAT
1 TATTTCAATATATTTTA-TTAT
* *
565057 TGTTTCAATATATTTTAATATGTT
1 TATTTCAATATATTTT-AT-T-AT
565081 TATTTCAATATATTTTATTAT
1 TATTTCAATATATTTTATTAT
565102 TATT
1 TATT
565106 ATTATTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
21 5 0.12
22 15 0.38
23 4 0.10
24 16 0.40
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (21 bp):
TATTTCAATATATTTTATTAT
Found at i:565107 original size:24 final size:24
Alignment explanation
Indices: 565053--565108 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
565043 TTTATTTTAG
*
565053 TTATTGTTTCAATATATTTTAATA
1 TTATTATTTCAATATATTTTAATA
*
565077 TGT-TTATTTCAATATATTTTATTA
1 T-TATTATTTCAATATATTTTAATA
565101 TTATTATT
1 TTATTATT
565109 ATTATTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 26 0.93
25 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (24 bp):
TTATTATTTCAATATATTTTAATA
Found at i:565110 original size:27 final size:27
Alignment explanation
Indices: 565043--565111 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 27
565033 AATATTTTAA
*
565043 TTTATT-TTAGTTATTGTTTCAATATAT
1 TTTATTATTA-TTATTATTTCAATATAT
565070 TTTA--A-TATGT-TTATTTCAATATAT
1 TTTATTATTAT-TATTATTTCAATATAT
565094 TTTATTATTATTATTATT
1 TTTATTATTATTATTATT
565112 ATTTAGTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
24 18 0.51
25 3 0.09
26 2 0.06
27 12 0.34
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (27 bp):
TTTATTATTATTATTATTTCAATATAT
Found at i:584264 original size:47 final size:45
Alignment explanation
Indices: 584185--584401 Score: 249
Period size: 47 Copynumber: 4.8 Consensus size: 45
584175 TATAAAATCT
* ** * *
584185 CTTACCATTTATCCCATAAGCTTGTAATCTTATTTTACCAACATA
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAATATA
* *
584230 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCATAAGCTTATTTTACCAATATA
* *
584277 TTTACCATTTGTTCCATAAGCTC-TAAGCTTATTTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCATAAGCTTA-TTTTACCAATATA
* * **
584322 TTTACCATTTAATACCATAAGCTCATAAGCTTATTTTTTCAATATA
1 CTTACCATTT-ATTCCATAAGCTCATAAGCTTATTTTACCAATATA
* *
584368 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCATAAGCTTATTT
584402 GCATGGTTAC
Statistics
Matches: 151, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
44 31 0.21
45 46 0.30
46 27 0.18
47 47 0.31
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAATATA
Found at i:584367 original size:91 final size:92
Alignment explanation
Indices: 584185--584401 Score: 287
Period size: 91 Copynumber: 2.4 Consensus size: 92
584175 TATAAAATCT
* * * *
584185 CTTACCATTTATCCCATAAGCTTGTAATCTTA-TTTTACCAACATACTTACCATTTAAATTCCAT
1 CTTACCATTTATTCCATAAGC-TCTAAGCTTATTTTTACCAACATACTTACCATTTAAATACCAT
*
584249 AAGCTCGTAAGCTTATTTTATCAATATA
65 AAGCTCATAAGCTTATTTTATCAATATA
* * * *
584277 TTTACCATTTGTTCCATAAGCTCTAAGCTTATTTTTACCAATATATTTACCATTT-AATACCATA
1 CTTACCATTTATTCCATAAGCTCTAAGCTTATTTTTACCAACATACTTACCATTTAAATACCATA
*
584341 AGCTCATAAGCTTATTTTTTCAATATA
66 AGCTCATAAGCTTATTTTATCAATATA
* *
584368 CTTGCCA-TTATTCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTC-TAAGCTTATTT
584402 GCATGGTTAC
Statistics
Matches: 109, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
90 13 0.12
91 57 0.52
92 39 0.36
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (92 bp):
CTTACCATTTATTCCATAAGCTCTAAGCTTATTTTTACCAACATACTTACCATTTAAATACCATA
AGCTCATAAGCTTATTTTATCAATATA
Found at i:585270 original size:2 final size:2
Alignment explanation
Indices: 585263--585303 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
585253 TGTATGTATG
585263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
585304 GTGTGTGTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:586547 original size:9 final size:9
Alignment explanation
Indices: 586533--586557 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
586523 AAAAAAGGTT
586533 GAGAGTTTG
1 GAGAGTTTG
586542 GAGAGTTTG
1 GAGAGTTTG
586551 GAGAGTT
1 GAGAGTT
586558 GAGGAGCGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (9 bp):
GAGAGTTTG
Found at i:589690 original size:55 final size:55
Alignment explanation
Indices: 589598--589730 Score: 140
Period size: 55 Copynumber: 2.4 Consensus size: 55
589588 TGATCTATGT
* * * * * * * *
589598 AGAAGGACATCCTATAAATGAATAAATTTGAACCTGATTGAAGAACGATTCACGA
1 AGAAAGACATCCGATGAATGAAGAAATGTGAAACTGATTAAAGAACGATCCACGA
* * ** *
589653 AGATAGACATCCGATGAATGAAGACATGTGAAACTGATTAAAGATTGATCCATGA
1 AGAAAGACATCCGATGAATGAAGAAATGTGAAACTGATTAAAGAACGATCCACGA
*
589708 AGAAATACATCCGATGAATGAAG
1 AGAAAGACATCCGATGAATGAAG
589731 TTTGAAGTTG
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
55 63 1.00
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.23
Consensus pattern (55 bp):
AGAAAGACATCCGATGAATGAAGAAATGTGAAACTGATTAAAGAACGATCCACGA
Found at i:595857 original size:34 final size:34
Alignment explanation
Indices: 595759--595894 Score: 209
Period size: 34 Copynumber: 3.9 Consensus size: 34
595749 AGCAAAGTCA
* *
595759 ATCTTAAGCCTTCACAGGAGAGTAGTGAAGCAATC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-ACC
595794 ATCTTAAGCCTTCACAAGAAGAGTAGTGAAGCACC
1 ATCTTAAGCCTTCAC-AGAAGAGTAGTGAAGCACC
* *
595829 ATCTTAAGCCTCCACAGAGGAGTAGTGAAGCACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCACC
*
595863 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCA
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCA
595895 AATCCATCCA
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
34 47 0.51
35 31 0.33
36 15 0.16
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.21
Consensus pattern (34 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCACC
Found at i:596703 original size:215 final size:216
Alignment explanation
Indices: 595898--596767 Score: 1481
Period size: 215 Copynumber: 4.0 Consensus size: 216
595888 TGAAGCAAAT
* * *
595898 CCATCCATAAGACCTTCGGGTAGGATATTTTCACATGAATTTGAAAATGAAAAAAATTATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTT
* *
595963 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCATAATGTATAAGTCCTTC
66 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTC
* * *
596028 GGGCTATCAGTAAGTCTTTCGAGCATGATGCTTAAATCTTTCGGGTCATCTGTAAGCCTTTAGAG
131 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTAGAG
* *
596093 CAAGATAATAAGTCCTTCAGG
196 CAAGATGATAAGTCCTTCGGG
*
596114 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACAAGAATTTGAAAATGATAAAAAAATGATGTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATG--AAAAAAATGATGTT
* * *
596179 TTAAGAAGATGGAATTTTTTAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCAT
64 TTAAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCT
*
596244 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAAATCCTTCAGGTAATCTGTAAGCCTTTA
129 TCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTT-AAATCCTTCAGGTCATCTGTAAGCCTTTA
596309 GAGCAAGATGATAAGTCCTTCGGG
193 GAGCAAGATGATAAGTCCTTCGGG
596333 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTT
*
596398 AAGAAGATGGAATTTTTGAAAACGAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCCTTC
66 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTC
* *
596463 GGGCCATCAGTAAGTCTTTCGAGCATTATGCTTAAATCCTTCAGGTCATCAGTAAGCCTTTAGAG
131 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTAGAG
596528 CAAGATGATAAGTCCTTCGGG
196 CAAGATGATAAGTCCTTCGGG
*
596549 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTCGAAAATG-AAAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTT
* * *
596613 AAGAAGATGAAATTTTTAAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTC
66 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTC
* * *
596678 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAACCCTTCGGGTCATCTGTAAGCCTTTTGAG
131 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTAGAG
596743 CAAGATGATAAGTCCTTCGGG
196 CAAGATGATAAGTCCTTCGGG
596764 CCAT
1 CCAT
596768 TTTAAGTCTC
Statistics
Matches: 618, Mismatches: 33, Indels: 7
0.94 0.05 0.01
Matches are distributed among these distances:
215 161 0.26
216 145 0.23
217 109 0.18
218 107 0.17
219 96 0.16
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (216 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAAAATGATGTTTT
AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTC
GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTGTAAGCCTTTAGAG
CAAGATGATAAGTCCTTCGGG
Found at i:597167 original size:2 final size:2
Alignment explanation
Indices: 597160--597210 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
597150 TTTACTCCAT
597160 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
597202 TA TA TA TA T
1 TA TA TA TA T
597211 TGTGTGTGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:598525 original size:15 final size:15
Alignment explanation
Indices: 598505--598542 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
598495 CTCGGTTGTT
598505 AAGGTTGAACGAAAA
1 AAGGTTGAACGAAAA
*
598520 AAGGTTGAACGGAAA
1 AAGGTTGAACGAAAA
598535 AAGGTTGA
1 AAGGTTGA
598543 GGGTTTGGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.47, C:0.05, G:0.32, T:0.16
Consensus pattern (15 bp):
AAGGTTGAACGAAAA
Found at i:603774 original size:20 final size:20
Alignment explanation
Indices: 603749--603823 Score: 75
Period size: 20 Copynumber: 3.9 Consensus size: 20
603739 CATGAATGCC
603749 CACAATGCACCAAAGTGCTA
1 CACAATGCACCAAAGTGCTA
*
603769 CACAATGC-CCAAAGT-C-C
1 CACAATGCACCAAAGTGCTA
* * *
603786 CACAATACACCGAAGTGTTA
1 CACAATGCACCAAAGTGCTA
* *
603806 CAAAATGCACCGAAGTGC
1 CACAATGCACCAAAGTGC
603824 CATAATGAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
17 7 0.16
18 7 0.16
19 7 0.16
20 23 0.52
ACGTcount: A:0.39, C:0.31, G:0.16, T:0.15
Consensus pattern (20 bp):
CACAATGCACCAAAGTGCTA
Found at i:604983 original size:2 final size:2
Alignment explanation
Indices: 604978--605003 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
604968 ATTAACATTA
604978 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
605004 GTGTTTGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:607443 original size:21 final size:21
Alignment explanation
Indices: 607417--607461 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
607407 TCTTTCTGAA
*
607417 GCATCAGGAGGTGGTGATGGT
1 GCATCAAGAGGTGGTGATGGT
607438 GCATCAAGAGGTGGTGATGGT
1 GCATCAAGAGGTGGTGATGGT
607459 GCA
1 GCA
607462 GCAGTAGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.22, C:0.11, G:0.44, T:0.22
Consensus pattern (21 bp):
GCATCAAGAGGTGGTGATGGT
Found at i:621216 original size:24 final size:24
Alignment explanation
Indices: 621184--621245 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
621174 GTGGTGGCTG
621184 ATGAGTGGTCCAAGCGGCGGTGGA
1 ATGAGTGGTCCAAGCGGCGGTGGA
* *
621208 ATGAGTGGT-CACTGCGGCGGTGGC
1 ATGAGTGGTCCA-AGCGGCGGTGGA
621232 ATGAGTGGTCCAAG
1 ATGAGTGGTCCAAG
621246 TGGTGGCAGC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 2 0.06
24 29 0.88
25 2 0.06
ACGTcount: A:0.19, C:0.18, G:0.44, T:0.19
Consensus pattern (24 bp):
ATGAGTGGTCCAAGCGGCGGTGGA
Found at i:621476 original size:18 final size:18
Alignment explanation
Indices: 621449--621490 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
621439 TAAATCTGTA
621449 AAATAA-AAT-ATAATTAT
1 AAATAATAATAATAA-TAT
621466 AAATAATAATAATAATAT
1 AAATAATAATAATAATAT
621484 AAATAAT
1 AAATAAT
621491 GACGGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAATAATAATAATAT
Found at i:625223 original size:16 final size:17
Alignment explanation
Indices: 625186--625224 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
625176 CGCAGATCAA
625186 TTTTTATCTTAAAAATG
1 TTTTTATCTTAAAAATG
* *
625203 ATTTT-TCTTAAAATTG
1 TTTTTATCTTAAAAATG
625219 TTTTTA
1 TTTTTA
625225 AAAGACGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 2
0.78 0.13 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (17 bp):
TTTTTATCTTAAAAATG
Found at i:630974 original size:1 final size:1
Alignment explanation
Indices: 630968--631074 Score: 52
Period size: 1 Copynumber: 107.0 Consensus size: 1
630958 CATCTATCAG
* * * ** * * * * * *
630968 AAAAAAAAAAGATAAAGAAAAAGGAAAAAGAGAAAAAAAAAGAAAAAAAGAAAAAAAGAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
631033 GAAAAAGAAAAAAAAAGAAAAGAAAAGAAAAGAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
631075 TGAACCAAGA
Statistics
Matches: 72, Mismatches: 34, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (1 bp):
A
Found at i:630984 original size:6 final size:6
Alignment explanation
Indices: 630966--631063 Score: 86
Period size: 6 Copynumber: 17.0 Consensus size: 6
630956 CTCATCTATC
*
630966 AGAAAA A-AAAA AGATAA AGAAAA AGGAAAA AGAGAAA A-AAAA AGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA A-GAAAA AGA-AAA AGAAAA AGAAAA
*
631014 A-AAGA A-AAAA AGAAAA AGAGAAA A-AGAAA A-AAAA AG-AAA AG-AAA
1 AGAAAA AGAAAA AGAAAA AGA-AAA AGA-AAA AGAAAA AGAAAA AGAAAA
631058 AGAAAA
1 AGAAAA
631064 GAAGAAAAAA
Statistics
Matches: 80, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
5 31 0.39
6 35 0.44
7 14 0.17
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (6 bp):
AGAAAA
Found at i:631002 original size:8 final size:8
Alignment explanation
Indices: 630966--631074 Score: 98
Period size: 8 Copynumber: 13.1 Consensus size: 8
630956 CTCATCTATC
630966 AGAAAAAA
1 AGAAAAAA
630974 A-AAAGATAA
1 AGAAA-A-AA
630983 AG-AAAAA
1 AGAAAAAA
*
630990 GGAAAAAGA
1 AGAAAAA-A
*
630999 GAAAAAAAA
1 -AGAAAAAA
631008 AGAAAAAA
1 AGAAAAAA
631016 AGAAAAAA
1 AGAAAAAA
*
631024 AGAAAAAG
1 AGAAAAAA
631032 AGAAAAAGA
1 AGAAAAA-A
631041 A-AAAAAA
1 AGAAAAAA
631048 AGAAAAGAAA
1 AG-AAA-AAA
*
631058 AGAAAAGA
1 AGAAAAAA
631066 AGAAAAAA
1 AGAAAAAA
631074 A
1 A
631075 TGAACCAAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
7 8 0.10
8 51 0.61
9 14 0.17
10 10 0.12
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.01
Consensus pattern (8 bp):
AGAAAAAA
Found at i:631013 original size:42 final size:40
Alignment explanation
Indices: 630966--631066 Score: 136
Period size: 41 Copynumber: 2.5 Consensus size: 40
630956 CTCATCTATC
630966 AGAAAAAAAAAAGATAAAGAAAAAG-GAAAAAGAGAAAAAAAA
1 AGAAAAAAAAAAGA-AAAGAAAAAGAG-AAAA-AGAAAAAAAA
631008 AGAAAAAAAGAAA-AAAAGAAAAAGAGAAAAAGAAAAAAAA
1 AGAAAAAAA-AAAGAAAAGAAAAAGAGAAAAAGAAAAAAAA
*
631048 AG-AAAAGAAAAGAAAAGAA
1 AGAAAAAAAAAAGAAAAGAA
631067 GAAAAAAATG
Statistics
Matches: 55, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
38 3 0.05
39 12 0.22
40 12 0.22
41 14 0.25
42 11 0.20
43 3 0.05
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (40 bp):
AGAAAAAAAAAAGAAAAGAAAAAGAGAAAAAGAAAAAAAA
Found at i:631022 original size:50 final size:50
Alignment explanation
Indices: 630966--631074 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 50
630956 CTCATCTATC
* *
630966 AGAAAAAAA-AAAGATAAAGAAAAAG-GAAAAAGAGAAAAAAAAAGAAAAAA
1 AGAAAAAAAGAAA-A-AAAGAAAAAGAAAAAAAAAGAAAAAAAAAGAAAAAA
* * *
631016 AGAAAAAAAGAAAAAGAGAAAAAGAAAAAAAAAGAAAAGAAAAGAAAAGA
1 AGAAAAAAAGAAAAAAAGAAAAAGAAAAAAAAAGAAAAAAAAAGAAAAAA
631066 AGAAAAAAA
1 AGAAAAAAA
631075 TGAACCAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
49 9 0.17
50 40 0.77
51 3 0.06
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.01
Consensus pattern (50 bp):
AGAAAAAAAGAAAAAAAGAAAAAGAAAAAAAAAGAAAAAAAAAGAAAAAA
Found at i:631023 original size:34 final size:32
Alignment explanation
Indices: 630966--631074 Score: 123
Period size: 34 Copynumber: 3.3 Consensus size: 32
630956 CTCATCTATC
* * *
630966 AGAAAAAAAAAAGATAAAGAAAAAGGAAAAAG
1 AGAAAAAAAAAAAAAAAAGAAAAAAGAAAAAG
630998 AGAAAAAAAAAGAAAAAAAGAAAAAAAGAAAAAG
1 AGAAAAAAAAA-AAAAAAAG-AAAAAAGAAAAAG
631032 AGAAAAAGAAAAAAAAAGAA-AAGAAAAG-AAAAG
1 AGAAAAA-AAAAAAAAA-AAGAA-AAAAGAAAAAG
631065 AAGAAAAAAA
1 -AGAAAAAAA
631075 TGAACCAAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.16
33 15 0.22
34 36 0.53
35 6 0.09
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.01
Consensus pattern (32 bp):
AGAAAAAAAAAAAAAAAAGAAAAAAGAAAAAG
Found at i:631069 original size:42 final size:41
Alignment explanation
Indices: 630966--631072 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 41
630956 CTCATCTATC
630966 AGAAAAAAA-AAAGATAAAGAAAAAGGAAAAAGAGAAAAAAAA
1 AGAAAAAAAGAAA-A-AAAGAAAAAGGAAAAAGAGAAAAAAAA
631008 AGAAAAAAAGAAAAAAAGAAAAA-GAGAAAA-AGAAAAAAAA
1 AGAAAAAAAGAAAAAAAGAAAAAGGA-AAAAGAGAAAAAAAA
*
631048 AGAAAAGAAAAGAAAAGAAGAAAAA
1 AG-AAA-AAAAGAAAAAAAGAAAAA
631073 AATGAACCAA
Statistics
Matches: 60, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
40 14 0.23
41 16 0.27
42 27 0.45
43 3 0.05
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.01
Consensus pattern (41 bp):
AGAAAAAAAGAAAAAAAGAAAAAGGAAAAAGAGAAAAAAAA
Found at i:632443 original size:52 final size:52
Alignment explanation
Indices: 632365--632556 Score: 181
Period size: 52 Copynumber: 3.7 Consensus size: 52
632355 TATATTATCT
* * * *
632365 ATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAAATAAAGAAGTAATCC
1 ATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGAAAGAAGTAATCC
* * * * * * *
632417 ATGTGAGGCATCTGGAAGGTTCACATCAGCAT-AAAAGGACATAATTAATCT
1 ATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGAAAGAAGTAATCC
* *
632468 ATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGACAGATA-TTATCC
1 ATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGAAAGA-AGTAATCC
* * * * * * *
632520 ATATGGGGCATCTTGGAGGCTCACACCAACATGAAAA
1 ATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAA
632557 GGTTGGGATA
Statistics
Matches: 115, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
51 43 0.37
52 71 0.62
53 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (52 bp):
ATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGAAAGAAGTAATCC
Found at i:632486 original size:51 final size:52
Alignment explanation
Indices: 632361--632511 Score: 196
Period size: 51 Copynumber: 2.9 Consensus size: 52
632351 GGTCTATATT
* * * * *
632361 ATCTATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAAATAAAGAAGTA
1 ATCTATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGACAGAAGTA
* * * * * *
632413 ATCCATGTGAGGCATCTGGAAGGTTCACATCAGCAT-AAAAGGACATAATTA
1 ATCTATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGACAGAAGTA
632464 ATCTATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGACAGA
1 ATCTATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGACAGA
632512 TATTATCCAT
Statistics
Matches: 83, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
51 43 0.52
52 40 0.48
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (52 bp):
ATCTATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGACAGAAGTA
Found at i:632544 original size:103 final size:104
Alignment explanation
Indices: 632361--632558 Score: 258
Period size: 103 Copynumber: 1.9 Consensus size: 104
632351 GGTCTATATT
* * * *
632361 ATCTATGTGGGGTATCTTGAAGGCTCACATCAGCATGAAAAATAAAGAAGTAATCCATGTGAGGC
1 ATCTATGTGAGGAATCTTGAAGGCTCACATCAGCATGAAAAAGAAAGAAGTAATCCATATGAGGC
* * *
632426 ATCTGGAAGGTTCACATCAGCAT-AAAAGGACATAATTA
66 ATCTGGAAGGCTCACACCAACATGAAAAGGACATAATTA
* * * *
632464 ATCTATGTGAGGAATCTTGAAGGTTCACATCAGCATGAAAAAGACAGATA-TTATCCATATGGGG
1 ATCTATGTGAGGAATCTTGAAGGCTCACATCAGCATGAAAAAGAAAGA-AGTAATCCATATGAGG
632528 CATCTTGG-AGGCTCACACCAACATGAAAAGG
65 CATC-TGGAAGGCTCACACCAACATGAAAAGG
632559 TTGGGATATT
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
103 71 0.88
104 10 0.12
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.24
Consensus pattern (104 bp):
ATCTATGTGAGGAATCTTGAAGGCTCACATCAGCATGAAAAAGAAAGAAGTAATCCATATGAGGC
ATCTGGAAGGCTCACACCAACATGAAAAGGACATAATTA
Found at i:634183 original size:117 final size:117
Alignment explanation
Indices: 634033--634458 Score: 653
Period size: 117 Copynumber: 3.6 Consensus size: 117
634023 AATATTTCCA
634033 GAAGAGTTCATAATGAGAAGAACTCATCGAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 GAAGAGTTCATAATGAGAAGAACTCATCGAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
634098 TTCAACCTTGGTTTGATTCCATCACAAAAAGAGGTGGATCAACATTTTCAGT
66 TTCAACCTTGGTTTGATTCCATCACAAAAAGAGGTGGATCAACATTTTCAGT
* * *
634150 AAAGAGTTCATAATGAGAAGAACTCAT-GCAATGAGGAAGAAAAAGTTCATAATGAGAAGAAATT
1 GAAGAGTTCATAATGAGAAGAACTCATCG-AATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
*
634214 GTTCAACCTTGGTTTGATTCCATCA-AAGAAAGAGGTGGATCAACATTTCCAGT
65 GTTCAACCTTGGTTTGATTCCATCACAA-AAAGAGGTGGATCAACATTTTCAGT
* * *
634267 GGAA-AGCTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTCATAATGAGAAAAACTT
1 -GAAGAGTTCATAATGAGAAGAACTCATCGAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * *
634331 ATTCAACCTTGGTTTGATTCCATCACAGAAGGAGGTGGATCAACA-TTTCTAGT
65 GTTCAACCTTGGTTTGATTCCATCACAAAAAGAGGTGGATCAACATTTTC-AGT
* * * * *
634384 GAAGAGTTCATAATGAGAAGAACTCATCTAACGAGGAAGAAGAAGTTCTTAATGAGACGAACTCG
1 GAAGAGTTCATAATGAGAAGAACTCATCGAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
634449 TTCAACCTTG
66 TTCAACCTTG
634459 CATTAACATT
Statistics
Matches: 280, Mismatches: 22, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
116 9 0.03
117 268 0.96
118 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (117 bp):
GAAGAGTTCATAATGAGAAGAACTCATCGAATGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTGGTTTGATTCCATCACAAAAAGAGGTGGATCAACATTTTCAGT
Found at i:634490 original size:91 final size:91
Alignment explanation
Indices: 634372--634544 Score: 240
Period size: 91 Copynumber: 1.9 Consensus size: 91
634362 GAGGTGGATC
* * * ** *
634372 AACATTTCTAGTGAAGAGTTCATAATGAGAAGAACTCATCTAACGAG-GAAGAAGAAGTTCTTAA
1 AACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAAAAAGAG-AGAAGAAGTTCATAA
*
634436 TGAGACGAACTCGTTCAACCTTGCATT
65 TGAGAAGAACTCGTTCAACCTTGCATT
* *
634463 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAAAAAGAGAGAATAAGTTCATAAT
1 AACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAAAAAGAGAGAAGAAGTTCATAAT
*
634528 GAGAAGAACTTGTTCAA
66 GAGAAGAACTCGTTCAA
634545 TTCAACACTT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
91 70 0.99
92 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (91 bp):
AACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCAAAAAGAGAGAAGAAGTTCATAAT
GAGAAGAACTCGTTCAACCTTGCATT
Found at i:634542 original size:20 final size:20
Alignment explanation
Indices: 634479--634543 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
634469 TCCAATGGAG
634479 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* * *
634499 CA-TCCAAAAAGAG-AGAA-T
1 -AGTTCATAATGAGAAGAACT
634517 AAGTTCATAATGAGAAGAACT
1 -AGTTCATAATGAGAAGAACT
*
634538 TGTTCA
1 AGTTCA
634544 ATTCAACACT
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
18 2 0.06
19 12 0.36
20 17 0.52
21 2 0.06
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.23
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:634904 original size:129 final size:128
Alignment explanation
Indices: 634754--635143 Score: 331
Period size: 129 Copynumber: 3.0 Consensus size: 128
634744 CGTAGGAACC
* *
634754 GTGTTATCACCTATAGATGGCCTTCCA-TCCTCATCACGTAGGAACCGTGTCATCACCCGACCT-
1 GTGTTATCACCTATAGATGGCC-ACAACTCCTCATCACGTAGGAACCGTGTCATCACCCGA-CTA
* * *
634817 GATCTCCTTATTATGTAGGAGCTGTGTCAATCCTTGATAACCAGAACTCTTCATCACGTATGAGT
64 GATCTCCTCATTATGTAGGAGCTATGTCAA-CCTAGATAACCAGAACTCTTCATCACGTATGAGT
634882 T
128 T
* * * * *
634883 GTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCACCCGACTAGA
1 GTGTTATCACCTATAGATGGCCACAACTCCTCATCACGTAGGAACCGTGTCATCACCCGACTAGA
* * * * ***
634948 TTTCCTCATTATGTAGGAGCTATGTCAACCTAGATAACCAG-CCGTCCTCATCACGTAGGAACC
66 TCTCCTCATTATGTAGGAGCTATGTCAACCTAGATAACCAGAAC-TCTTCATCACGTATGAGTT
* * ** * * * * * *
635011 GAGTTATCACTCTTCCTAAAGATGGAAAAGAACTCTTCATCACGTATGAGCAGTGTCATC-CCAT
1 GTGTTATCA-----CCTATAGATGG-CCACAACTCCTCATCACGTAGGAACCGTGTCATCACC-C
* * ** * *
635075 GACTAAATCTCCTCATTATGTAGGAGTCT-TGTCACCCTTAGACGACCAGAACTCTTCAGCACAT
59 GACTAGATCTCCTCATTATGTAGGAG-CTATGTCAACC-TAGATAACCAGAACTCTTCATCACGT
635139 ATGAG
122 ATGAG
635144 CAGCGTCGTC
Statistics
Matches: 213, Mismatches: 35, Indels: 20
0.79 0.13 0.07
Matches are distributed among these distances:
127 1 0.00
128 37 0.17
129 78 0.37
133 11 0.05
134 62 0.29
135 23 0.11
136 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.29
Consensus pattern (128 bp):
GTGTTATCACCTATAGATGGCCACAACTCCTCATCACGTAGGAACCGTGTCATCACCCGACTAGA
TCTCCTCATTATGTAGGAGCTATGTCAACCTAGATAACCAGAACTCTTCATCACGTATGAGTT
Found at i:643913 original size:19 final size:19
Alignment explanation
Indices: 643891--643935 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
643881 AGCATACGAA
643891 GTCAAATATTTCATAAAAT
1 GTCAAATATTTCATAAAAT
643910 GTCAAATATTTCATAAAAT
1 GTCAAATATTTCATAAAAT
643929 GTCAAAT
1 GTCAAAT
643936 TTTACACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (19 bp):
GTCAAATATTTCATAAAAT
Found at i:646824 original size:25 final size:24
Alignment explanation
Indices: 646770--646824 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
646760 CTTTTGTGTT
* * **
646770 TTTTTTTTCTTTGAAATCTCTCTG
1 TTTTTTTGCTTTAAAATCTCTCCC
646794 TCTTTTTTGCTTTAAAATCTCTCACC
1 T-TTTTTTGCTTTAAAATCTCTC-CC
646820 TTTTT
1 TTTTT
646825 CCTTTGATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 23 0.92
26 1 0.04
ACGTcount: A:0.15, C:0.20, G:0.05, T:0.60
Consensus pattern (24 bp):
TTTTTTTGCTTTAAAATCTCTCCC
Found at i:647579 original size:137 final size:134
Alignment explanation
Indices: 647266--647657 Score: 479
Period size: 131 Copynumber: 2.9 Consensus size: 134
647256 ATCAGATCTC
* * * *
647266 GAAAA-ATTTGATTCACATCGCTGCTCTTCAGGGAAGGTTGAATCGAACTTGAATTGCTTCACTG
1 GAAAACATTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTG
* * *
647330 CTCTTCAAGAAGACCAAATTTGAAA-GAAGAAGAATCTGCTCTACTACTCTTT-AGGG-GACAGA
66 CTCTTCAGGAAGACCAAATCTGAAAGGAA-AAGAATCTGCTCCACTACTCTTTAAGGGAGACAGA
647392 CTCGA
130 CTCGA
* * ** * * *
647397 GAAAAC-TTTGATTCACTTCATTGTTCTTCAGAAAATATTGAATCGAACTTGATTTGCTTCGCTT
1 GAAAACATTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTG
*
647461 CTCTTCAGGAAGACCAAATCCTGAAAGGAAAAGAATCTACTCCACTACTCTTTAAGGGAGATCAG
66 CTCTTCAGGAAGACCAAAT-CTGAAAGGAAAAGAATCTGCTCCACTACTCTTTAAGGGAGA-CAG
*
647526 ACTTGAA
129 ACTCG-A
* * *
647533 GAAAACATTTGATCCACTTCACTGCTCTTCAGGGAAGATTAAATCGAATTTGATTTGCTTCACTG
1 GAAAACATTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTG
* * * * *
647598 CTCTTCAGGAAGACCAAATCTAAAAATGAAAAAGAATTTGCTCCACTACTTTTTAGGGGA
66 CTCTTCAGGAAGACCAAATCT-GAAA-GGAAAAGAATCTGCTCCACTACTCTTTAAGGGA
647658 AACCAGATCT
Statistics
Matches: 219, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
131 70 0.32
132 26 0.12
133 7 0.03
134 2 0.01
135 7 0.03
136 9 0.04
137 70 0.32
138 28 0.13
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.30
Consensus pattern (134 bp):
GAAAACATTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAACTTGATTTGCTTCACTG
CTCTTCAGGAAGACCAAATCTGAAAGGAAAAGAATCTGCTCCACTACTCTTTAAGGGAGACAGAC
TCGA
Found at i:651448 original size:2 final size:2
Alignment explanation
Indices: 651441--651473 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
651431 AACTTTATTG
651441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
651474 ATCACCTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:654595 original size:80 final size:80
Alignment explanation
Indices: 654470--654677 Score: 310
Period size: 80 Copynumber: 2.6 Consensus size: 80
654460 CAGCAAAAAG
* ** *
654470 GGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAATGACATCCTTAGATCTGTAGGGTTACC
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAA-GATATCCTTAGATCTGTAGGGTTACC
* *
654534 TTAAGCACACAGCTAA
65 TTAAGCACACAACAAA
*
654550 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCTGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGATCTGTAGGGTTACCT
*
654615 TATGCACACAACAAA
66 TAAGCACACAACAAA
* *
654630 GGGAACCATCCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCTTA
1 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTA
654678 AGTCCGTAAT
Statistics
Matches: 117, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
80 107 0.91
81 10 0.09
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGATCTGTAGGGTTACCT
TAAGCACACAACAAA
Found at i:657565 original size:16 final size:17
Alignment explanation
Indices: 657534--657568 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
657524 TTACTATTAC
657534 TTCACTCCAGACTTTCT
1 TTCACTCCAGACTTTCT
*
657551 TTCAC-CCATACTTTCT
1 TTCACTCCAGACTTTCT
657567 TT
1 TT
657569 ACTTGTTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.17, C:0.34, G:0.03, T:0.46
Consensus pattern (17 bp):
TTCACTCCAGACTTTCT
Found at i:657721 original size:21 final size:21
Alignment explanation
Indices: 657695--657743 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
657685 ATCATTTTCA
**
657695 TTCTCAATTGCTTCCCATGTT
1 TTCTCAATTGCTTCCCATGCC
*
657716 TTCTCAATTGCTTCTCATGCC
1 TTCTCAATTGCTTCCCATGCC
657737 TTCTCAA
1 TTCTCAA
657744 CCGCAGAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.31, G:0.08, T:0.45
Consensus pattern (21 bp):
TTCTCAATTGCTTCCCATGCC
Found at i:661513 original size:17 final size:17
Alignment explanation
Indices: 661491--661529 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
661481 GCATATAACG
*
661491 TATTTAATAATAGAAAA
1 TATTTAATAACAGAAAA
*
661508 TATTT-ATAACATAAAA
1 TATTTAATAACAGAAAA
661524 TATTTA
1 TATTTA
661530 TACTGGACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (17 bp):
TATTTAATAACAGAAAA
Found at i:661519 original size:58 final size:58
Alignment explanation
Indices: 661457--661645 Score: 163
Period size: 58 Copynumber: 3.1 Consensus size: 58
661447 CTGGATACAA
661457 AACATATAAAATTTAATAACCATGGCATATAACGTATTTAATAATAGAAAATATTTAT
1 AACATATAAAATTTAATAACCATGGCATATAACGTATTTAATAATAGAAAATATTTAT
* * * *
661515 AACATA-AAATATTT-AT-A-C-TGGACACACACACATATATATATATATCATACACAAATACTG
1 AACATATAAA-ATTTAATAACCATGG-CATATA-ACGTAT-T-TA-ATA--ATAGA-AAATA-T-
* *
661575 GATACAA
55 --T-TAT
661582 AACATATAAAATTTAATAACCATGGCATATAACGTATTTAATAATAGAAAATATTTAT
1 AACATATAAAATTTAATAACCATGGCATATAACGTATTTAATAATAGAAAATATTTAT
661640 AACATA
1 AACATA
661646 AAAGGAACTA
Statistics
Matches: 100, Mismatches: 12, Indels: 38
0.67 0.08 0.25
Matches are distributed among these distances:
54 3 0.03
55 5 0.05
56 6 0.06
57 6 0.06
58 19 0.19
59 4 0.04
61 4 0.04
62 6 0.06
63 6 0.06
64 4 0.04
66 4 0.04
67 13 0.13
68 6 0.06
69 6 0.06
70 5 0.05
71 3 0.03
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.31
Consensus pattern (58 bp):
AACATATAAAATTTAATAACCATGGCATATAACGTATTTAATAATAGAAAATATTTAT
Found at i:661523 original size:56 final size:56
Alignment explanation
Indices: 661462--661648 Score: 146
Period size: 56 Copynumber: 3.1 Consensus size: 56
661452 TACAAAACAT
661462 ATAAAATTTAATAACCATGGCATATAACGTATTTAATAATAGAAAATATTTATAAC
1 ATAAAATTTAATAACCATGGCATATAACGTATTTAATAATAGAAAATATTTATAAC
* * * * * *
661518 ATAAAATATTTAT-A-C-TGGACACACACACATATATATATATATCATACACAAATACTGGATAC
1 ATAAAAT-TTAATAACCATGG-CATATA-ACGTAT-T-TA-ATA--ATAGA-AAATA-T---T-T
*
661580 AAAAC
52 ATAAC
661585 ATATAAAATTTAATAACCATGGCATATAACGTATTTAATAATAGAAAATATTTATAAC
1 --ATAAAATTTAATAACCATGGCATATAACGTATTTAATAATAGAAAATATTTATAAC
661643 ATAAAA
1 ATAAAA
661649 GGAACTAAAA
Statistics
Matches: 98, Mismatches: 14, Indels: 38
0.65 0.09 0.25
Matches are distributed among these distances:
54 3 0.03
55 5 0.05
56 19 0.19
57 5 0.05
58 6 0.06
59 4 0.04
61 4 0.04
62 6 0.06
63 6 0.06
64 4 0.04
66 4 0.04
67 6 0.06
68 5 0.05
69 13 0.13
70 5 0.05
71 3 0.03
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (56 bp):
ATAAAATTTAATAACCATGGCATATAACGTATTTAATAATAGAAAATATTTATAAC
Found at i:661540 original size:125 final size:125
Alignment explanation
Indices: 661411--661648 Score: 449
Period size: 125 Copynumber: 1.9 Consensus size: 125
661401 TTGATATTTA
*
661411 ACACACGCAAACATATATATATATCATACACAAATACTGGATACAAAACATATAAAATTTAATAA
1 ACACACACAAACATATATATATATCATACACAAATACTGGATACAAAACATATAAAATTTAATAA
661476 CCATGGCATATAACGTATTTAATAATAGAAAATATTTATAACATAAAATATTTATACTGG
66 CCATGGCATATAACGTATTTAATAATAGAAAATATTTATAACATAAAATATTTATACTGG
* *
661536 ACACACACACATATATATATATATCATACACAAATACTGGATACAAAACATATAAAATTTAATAA
1 ACACACACAAACATATATATATATCATACACAAATACTGGATACAAAACATATAAAATTTAATAA
661601 CCATGGCATATAACGTATTTAATAATAGAAAATATTTATAACATAAAA
66 CCATGGCATATAACGTATTTAATAATAGAAAATATTTATAACATAAAA
661649 GGAACTAAAA
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 110 1.00
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (125 bp):
ACACACACAAACATATATATATATCATACACAAATACTGGATACAAAACATATAAAATTTAATAA
CCATGGCATATAACGTATTTAATAATAGAAAATATTTATAACATAAAATATTTATACTGG
Found at i:662504 original size:25 final size:26
Alignment explanation
Indices: 662450--662513 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
662440 CCCCTTTTTT
* * *
662450 TTTTTTGCTTTGAAATCTCTGTGTCA
1 TTTTTTCCTTTGAAATCTCTCTGCCA
*
662476 TTTTTTCCTTTGAAATCTCTCT-CCC
1 TTTTTTCCTTTGAAATCTCTCTGCCA
*
662501 TTTTCTCCTTTGA
1 TTTTTTCCTTTGA
662514 TTTGTAGATG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 13 0.39
26 20 0.61
ACGTcount: A:0.12, C:0.23, G:0.09, T:0.55
Consensus pattern (26 bp):
TTTTTTCCTTTGAAATCTCTCTGCCA
Found at i:663448 original size:21 final size:21
Alignment explanation
Indices: 663391--663437 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
663381 GGAAGTCGAA
663391 GAGTTTAGGTCGTTTTCGGGT
1 GAGTTTAGGTCGTTTTCGGGT
663412 GAGTTTAGGTCGTTTTCGGGT
1 GAGTTTAGGTCGTTTTCGGGT
663433 G-GTTT
1 GAGTTT
663438 TAGGGCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.09, C:0.09, G:0.38, T:0.45
Consensus pattern (21 bp):
GAGTTTAGGTCGTTTTCGGGT
Found at i:664278 original size:21 final size:21
Alignment explanation
Indices: 664230--664279 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
664220 TTTTTCTTAT
*
664230 TTTTTATTATTTATTTTTACA
1 TTTTTATTATTTATTTTTAAA
* *
664251 TGTTTATTGTTTA-TTTTAAA
1 TTTTTATTATTTATTTTTAAA
664271 TTTGTTATT
1 TTT-TTATT
664280 TTAGTTCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (21 bp):
TTTTTATTATTTATTTTTAAA
Found at i:670725 original size:23 final size:21
Alignment explanation
Indices: 670680--670722 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
670670 TTCTTTAAAT
670680 TTTTTATAAAAAGTTAATATA
1 TTTTTATAAAAAGTTAATATA
**
670701 TTTTTATAAAATTTTAATATA
1 TTTTTATAAAAAGTTAATATA
670722 T
1 T
670723 ATTATATTTT
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:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TTTTTATAAAAAGTTAATATA
Found at i:671143 original size:17 final size:17
Alignment explanation
Indices: 671111--671175 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
671101 CTTAAAGAAA
671111 ATATTAAAAT-TATTAAT
1 ATATTAAAATAT-TTAAT
*
671128 ATATTAAAATATTTAAA
1 ATATTAAAATATTTAAT
* * *
671145 ACATTTAAATTTTTAAAT
1 ATATTAAAATATTT-AAT
*
671163 AAATTAAAA-ATTT
1 ATATTAAAATATTT
671176 TAAAACTTAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 28 0.74
18 10 0.26
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATTAAAATATTTAAT
Found at i:671289 original size:2 final size:2
Alignment explanation
Indices: 671282--671313 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
671272 AAAAATTTAA
671282 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
671314 GAACTTTATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:676084 original size:13 final size:12
Alignment explanation
Indices: 676057--676096 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
676047 TAATATTGAT
676057 AAATATATATTA
1 AAATATATATTA
*
676069 AAATATGATTTTA
1 AAATAT-ATATTA
676082 AAATAATATATTA
1 AAAT-ATATATTA
676095 AA
1 AA
676097 TTTATAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 6 0.25
13 16 0.67
14 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (12 bp):
AAATATATATTA
Found at i:676135 original size:33 final size:33
Alignment explanation
Indices: 676055--676135 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
676045 CTTAATATTG
* * *
676055 ATAAATATATATTA-AAATATGATTTTAAAATA
1 ATAAATAAATATTATAAAGAGGATTTTAAAATA
*
676087 ATATATTAAAT-TTATAAAGAGGATTTTAATAA-A
1 ATA-AATAAATATTATAAAGAGGATTTTAA-AATA
676120 ATAAATAAATATTATA
1 ATAAATAAATATTATA
676136 TATATATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
32 12 0.30
33 26 0.65
34 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (33 bp):
ATAAATAAATATTATAAAGAGGATTTTAAAATA
Found at i:676164 original size:3 final size:3
Alignment explanation
Indices: 676156--676185 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
676146 TACATGACTA
*
676156 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
676186 TAAATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:677811 original size:3 final size:3
Alignment explanation
Indices: 677805--677889 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
677795 ATTTATTATT
* * * * * *
677805 TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAT TAT TAA TAT TAT TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
677853 TAT TAA TAA TAA TAA T-A TAA TAA -AA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
677890 ATTAAAAAAT
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
2 4 0.06
3 68 0.94
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:677886 original size:22 final size:21
Alignment explanation
Indices: 677856--677901 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
677846 TTATTATTAT
677856 TAATAATAAT-AATATAATAAAA
1 TAATAATAATAAAT-TAA-AAAA
*
677878 TAATTATAATAAATTAAAAAA
1 TAATAATAATAAATTAAAAAA
677899 TAA
1 TAA
677902 AACACAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 12 0.55
23 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATAATAATAAATTAAAAAA
Found at i:678391 original size:123 final size:123
Alignment explanation
Indices: 678105--678761 Score: 530
Period size: 112 Copynumber: 5.6 Consensus size: 123
678095 GATGTAATGT
* * *
678105 AACAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTTCTCTTCAGATGAGTTCTTCTC
1 AACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTC
* ** * * *
678170 GTTATGAAC-ACTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCA
66 ATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCA
** * *
678227 TGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTT
1 AACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTC
*
678292 ATTATGAACTTTTTCTGGAAAAGTTGCTGCTGATTCTATCTCCTTCTGTGATAGAATCA
66 ATTATGAACTTTTTCTGGAAAAGTTGATGCTGA-TCTATCTCCTTCTGTGATAGAATCA
*
678351 AAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTG
1 AACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTC
**
678415 ATTATGAACTTTTTCTGGAAAAGTTGA---T--TC-A--T-C--AAGTGAT-GAATTCA
66 ATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAA-TCA
* * * * * *
678462 AGA-AAAACGTTGAACAAGCTCTTCTCATTTTGAATTTTTTCTTCTTTTTCAGATGAGTTCTTCT
1 A-ACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCT
* ** * * ***
678526 CATTATGAACTCTACCT-TAAAA--TG-T--T-A---ATC-CATTGAATGAT-GAATTCA
65 CATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAA-TCA
*** ** * *
678574 AGTGAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCT
1 AACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCT
** * * **
678639 CATTATGAA-TTCTACCTGG-CAA-TT--T--TGATCCA--T-C--AAGTGAT-GAATTCA
65 CATTATGAACTT-TTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAA-TCA
* * * * *
678687 AGCAAAATGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCTTTTTCAGATGAGTTCTTCTC
1 AACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTC
678752 ATTATGAACT
66 ATTATGAACT
678762 CTTCCAAAAA
Statistics
Matches: 453, Mismatches: 59, Indels: 55
0.80 0.10 0.10
Matches are distributed among these distances:
108 1 0.00
109 3 0.01
110 3 0.01
111 13 0.03
112 143 0.32
113 88 0.19
114 3 0.01
116 1 0.00
117 3 0.01
120 1 0.00
122 66 0.15
123 103 0.23
124 25 0.06
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (123 bp):
AACAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAATCA
Found at i:678682 original size:113 final size:112
Alignment explanation
Indices: 678354--678791 Score: 549
Period size: 112 Copynumber: 3.9 Consensus size: 112
678344 AGAATCAAAC
* * *
678354 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTGATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
** * *
678419 TGAACTT-TTTCTGGAAAAGTTGATTCATCAAGTGATGAATTCAAGAA
66 TGAA-TTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGAA
* * * *
678466 AAACGTTGAACAAGCTCTTCTCATTTTGAATTTTTTCTTCTTTTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
* ** * * **
678531 TGAACTCTACCTTAAAATGTTAATCCATTGAA-TGATGAATTCAAGTG
66 TGAATTCTACCTGGAAATGTTGATCCA-TCAAGTGATGAATTCAAGAA
** *
678578 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATT
* * *
678643 ATGAATTCTACCTGGCAATTTTGATCCATCAAGTGATGAATTCAAGCA
65 ATGAATTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGAA
* *
678691 AAATGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
* * ** *
678756 TGAACTCTTCC-AAAAATGTTGATCCATCGAGTGATG
66 TGAATTCTACCTGGAAATGTTGATCCATCAAGTGATG
678792 GGTTAAAATC
Statistics
Matches: 276, Mismatches: 46, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
111 21 0.08
112 158 0.57
113 97 0.35
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (112 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAATTTCTTCTTCTTCTTCAGATGAGTTCTTCTCATTA
TGAATTCTACCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGAA
Found at i:678701 original size:225 final size:223
Alignment explanation
Indices: 678354--678791 Score: 662
Period size: 225 Copynumber: 2.0 Consensus size: 223
678344 AGAATCAAAC
* * *
678354 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTGATTA
1 AAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTCATTA
** *
678419 TGAACTTTTTCTGGAAAAGTTGATTCATCAAGTGATGAATTCAAGAAAAACGTTGAACAAGCTCT
66 TGAACTTTACCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAGAAAAACGTTGAACAAGCTCT
* * *
678484 TCTCATTTTGAATTTTTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTCTACCTTAAAAT
131 TCTCATTATGAATTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTCTACC-AAAAAT
*
678549 GTTAATCCATTGAATGATGAATTCAAGTG
195 GTTAATCCATCGAATGATGAATTCAAGTG
* *
678578 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATT
1 AAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGACGAGTTCTTCTCATT
* ** * *
678643 ATGAA-TTCTACCTGGCAATTTTGATCCATCAAGTGATGAATTCAAGCAAAATGTTGAACAAGCT
65 ATGAACTT-TACCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAGAAAAACGTTGAACAAGCT
*
678707 CTTCTCATTATGAATTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTCTTCCAAAAA
129 CTTCTCATTATGAATTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTCTACCAAAAA
* *
678772 TGTTGATCCATCGAGTGATG
194 TGTTAATCCATCGAATGATG
678792 GGTTAAAATC
Statistics
Matches: 192, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
224 61 0.32
225 131 0.68
ACGTcount: A:0.28, C:0.18, G:0.14, T:0.39
Consensus pattern (223 bp):
AAAGGTTGAACAAACTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGACGAGTTCTTCTCATTA
TGAACTTTACCTGGAAAAGTTGATCCATCAAGTGATGAATTCAAGAAAAACGTTGAACAAGCTCT
TCTCATTATGAATTTCTTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTCTACCAAAAATG
TTAATCCATCGAATGATGAATTCAAGTG
Found at i:680333 original size:2 final size:2
Alignment explanation
Indices: 680326--680384 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
680316 CCTCATTTTC
680326 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
680368 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
680385 TCATCATTTT
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:680420 original size:17 final size:17
Alignment explanation
Indices: 680398--680453 Score: 78
Period size: 18 Copynumber: 3.3 Consensus size: 17
680388 TCATTTTTCC
*
680398 TTTTCATTTTTTCTTCA
1 TTTTCATTTTTTCTTCT
*
680415 TTTTCATTTTTTCCTTTT
1 TTTTCATTTTTT-CTTCT
680433 TTTTCATTTTTT-TTCT
1 TTTTCATTTTTTCTTCT
680449 TTTTC
1 TTTTC
680454 TTCAAGCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.23
17 12 0.34
18 15 0.43
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTTCATTTTTTCTTCT
Found at i:686445 original size:188 final size:187
Alignment explanation
Indices: 686098--686473 Score: 743
Period size: 187 Copynumber: 2.0 Consensus size: 187
686088 TTCCTTCCAT
686098 TCTCTTCCTGGATTGCGTTCACGTTTTTATCTCCATGATTTGGCAGCGAATGATTTGATGTAGCT
1 TCTCTTCCTGGATTGCGTTCACGTTTTTATCTCCATGATTTGGCAGCGAATGATTTGATGTAGCT
686163 AGTGAATTGAATTCCAGCTTTCTTGTATTAATCAAATTTTGGATCACCCTTTGAATGCCAAACAG
66 AGTGAATTGAATTCCAGCTTTCTTGTATTAATCAAATTTTGGATCACCCTTTGAATGCCAAACAG
686228 TTTTCAATGGAGTGACCCATAATTCCGTCATGATAAACACATTATGCTTTCACATCA
131 TTTTCAATGGAGTGACCCATAATTCCGTCATGATAAACACATTATGCTTTCACATCA
686285 TCTCTTCCTGGATTGCGTTCACGTTTTTATCTCCATGATTTGGCAGCGAATGATTTGATGTAGCT
1 TCTCTTCCTGGATTGCGTTCACGTTTTTATCTCCATGATTTGGCAGCGAATGATTTGATGTAGCT
686350 AGTGAATTGAATTCCAGCTTTCTTGTATTAATCAAATTTTGGATCACCCTTTTGAATGCCAAACA
66 AGTGAATTGAATTCCAGCTTTCTTGTATTAATCAAATTTTGGATCACCC-TTTGAATGCCAAACA
686415 GTTTTCAATGGAGTGACCCATAATTCCGTCATGATAAACACATTATGCTTTCACATCA
130 GTTTTCAATGGAGTGACCCATAATTCCGTCATGATAAACACATTATGCTTTCACATCA
686473 T
1 T
686474 ACCATGGAGG
Statistics
Matches: 188, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
187 114 0.61
188 74 0.39
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.37
Consensus pattern (187 bp):
TCTCTTCCTGGATTGCGTTCACGTTTTTATCTCCATGATTTGGCAGCGAATGATTTGATGTAGCT
AGTGAATTGAATTCCAGCTTTCTTGTATTAATCAAATTTTGGATCACCCTTTGAATGCCAAACAG
TTTTCAATGGAGTGACCCATAATTCCGTCATGATAAACACATTATGCTTTCACATCA
Found at i:691303 original size:2 final size:2
Alignment explanation
Indices: 691296--691364 Score: 131
Period size: 2 Copynumber: 35.0 Consensus size: 2
691286 GATATTAATA
691296 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
691338 AT AT AT AT AT AT -T AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
691365 GAAAATAAGT
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 65 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:692205 original size:33 final size:33
Alignment explanation
Indices: 692125--692205 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
692115 CTTAATATTG
* *
692125 ATAAATATATATTA-AAATATGATTTAAAAATA
1 ATAAATAAATATTATAAATAGGATTTAAAAATA
* *
692157 ATATATTAAAT-TTATAAATAGGATTTTAATAA-A
1 ATA-AATAAATATTATAAATAGGA-TTTAAAAATA
692190 ATAAATAAATATTATA
1 ATAAATAAATATTATA
692206 TATATATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
32 12 0.30
33 21 0.52
34 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (33 bp):
ATAAATAAATATTATAAATAGGATTTAAAAATA
Found at i:693489 original size:22 final size:22
Alignment explanation
Indices: 693463--693522 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
693453 GAATGAATTT
*
693463 TGGTGAGTCACCATAGTTATGG
1 TGGTGACTCACCATAGTTATGG
693485 TGGTGACTCACCATAGTTATGG
1 TGGTGACTCACCATAGTTATGG
693507 TGGTGACTCACCATAG
1 TGGTGACTCACCATAG
693523 AGCTCGACGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (22 bp):
TGGTGACTCACCATAGTTATGG
Found at i:693915 original size:3 final size:3
Alignment explanation
Indices: 693909--693994 Score: 140
Period size: 3 Copynumber: 29.0 Consensus size: 3
693899 ATTTATTATT
693909 TAA TAA TAA TAA 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
*
693957 TAA TAA TAA -AA TAA TATA TAA TAA -AA TAA TTA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
693995 ATCAAAAAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
2 4 0.05
3 71 0.91
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:697976 original size:84 final size:78
Alignment explanation
Indices: 697776--697978 Score: 241
Period size: 77 Copynumber: 2.6 Consensus size: 78
697766 AGATGCTCAA
* *
697776 TTAGGTTGGC-TCC-CTTTGCTGTGTGCTTAGGGCAAGCTCTATGGACTTACGGACTTAAGGATA
1 TTAGGTTGGCTTCCTCTTTGCTGTGTGCTTAGGGTAAGCCCTATGGACTTACGGACTTAAGGATA
* *
697839 CATGCTCCAATCC
66 CAGGCCCCAATCC
* *
697852 TTAGGTTGGCTCCCT-TTTACTGTGTGCTTAGGGTAAGCCCTATGGACTTACGGACTTAAGGATA
1 TTAGGTTGGCTTCCTCTTTGCTGTGTGCTTAGGGTAAGCCCTATGGACTTACGGACTTAAGGATA
*
697916 TAGGCCCCAAAGCCTATCC
66 CAGGCCCC--A----ATCC
* * *
697935 TTAGGTTGGCTTCCTCTTTGCTATGAGCTTAAGGTAAGCCCTAT
1 TTAGGTTGGCTTCCTCTTTGCTGTGTGCTTAGGGTAAGCCCTAT
697979 AGACGCAGTT
Statistics
Matches: 106, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
76 10 0.09
77 53 0.50
79 1 0.01
83 18 0.17
84 24 0.23
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (78 bp):
TTAGGTTGGCTTCCTCTTTGCTGTGTGCTTAGGGTAAGCCCTATGGACTTACGGACTTAAGGATA
CAGGCCCCAATCC
Found at i:698206 original size:22 final size:22
Alignment explanation
Indices: 698115--698203 Score: 151
Period size: 22 Copynumber: 4.0 Consensus size: 22
698105 GATTTTATTG
698115 TACTGTTGGAACACACTAGACA
1 TACTGTTGGAACACACTAGACA
*
698137 TACTATTGGAACACACTAGACA
1 TACTGTTGGAACACACTAGACA
*
698159 TATTGTTGGAACACACTAGACA
1 TACTGTTGGAACACACTAGACA
*
698181 TCCTGTTGGAACACACTAGACA
1 TACTGTTGGAACACACTAGACA
698203 T
1 T
698204 CCTATTTGAT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 62 1.00
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (22 bp):
TACTGTTGGAACACACTAGACA
Found at i:698731 original size:14 final size:14
Alignment explanation
Indices: 698708--698758 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 14
698698 TAACTGAAAT
* *
698708 TATTAAATATTTAA
1 TATTATATATATAA
698722 TATTATATATAT-A
1 TATTATATATATAA
698735 TA-TATATATAT-A
1 TATTATATATATAA
698747 TA-TATATATATA
1 TATTATATATATA
698759 TTATACATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 21 0.62
13 3 0.09
14 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTATATATATAA
Found at i:698732 original size:2 final size:2
Alignment explanation
Indices: 698721--698763 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
698711 TAAATATTTA
698721 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
698761 AT A
1 AT A
698764 CATTATTTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:700509 original size:18 final size:18
Alignment explanation
Indices: 700486--700528 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
700476 TGCAGTAAAA
700486 TCTACTTTAACAAAGTTT
1 TCTACTTTAACAAAGTTT
700504 TCTACTTTAACAAAGTTT
1 TCTACTTTAACAAAGTTT
700522 TCTACTT
1 TCTACTT
700529 CTAATCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (18 bp):
TCTACTTTAACAAAGTTT
Found at i:703838 original size:21 final size:21
Alignment explanation
Indices: 703793--703849 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
703783 ATATATAATT
* *
703793 TGTCCCAAAAGA-CAGATAGA
1 TGTCCCAAAGGACCACATAGA
*
703813 TGTCCCAAAGGACCACATATA
1 TGTCCCAAAGGACCACATAGA
*
703834 TGTCCCGAAGGACCAC
1 TGTCCCAAAGGACCAC
703850 TCCTTAAGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 11 0.34
21 21 0.66
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.16
Consensus pattern (21 bp):
TGTCCCAAAGGACCACATAGA
Done.