Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008274.1 Hibiscus syriacus cultivar Beakdansim tig00110931_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: 1661830
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 6
Found at i:1193269 original size:22 final size:22
Alignment explanation
Indices: 1193220--1193268 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1193210 ATAAATTATT
* **
1193220 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATACATATAA
1193242 TAAAATAAATCAATACATACTAA
1 TAAAATAAATCAATACATA-TAA
1193265 TAAA
1 TAAA
1193269 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATACATATAA
Found at i:1193328 original size:22 final size:22
Alignment explanation
Indices: 1193303--1193362 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
1193293 CAACTACAAT
1193303 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
*
1193325 AATAAATCAATACATATTTTAA
1 AATAAATCAATCCATATTTTAA
1193347 AATAAATCAATCCATA
1 AATAAATCAATCCATA
1193363 CTAATAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:1193371 original size:22 final size:22
Alignment explanation
Indices: 1193274--1193370 Score: 95
Period size: 22 Copynumber: 4.2 Consensus size: 22
1193264 ATAAATTATT
*
1193274 TAAAATAAATCAATCCATACAA
1 TAAAATAAATCAATCCATATAA
**
1193296 CTACAATAATAAATCAATCCATATTT
1 -T--AA-AATAAATCAATCCATATAA
* **
1193322 TAAAATAAATCAATACATATTT
1 TAAAATAAATCAATCCATATAA
1193344 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
1193367 TAAA
1 TAAA
1193371 TTATTTAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
22 36 0.57
23 8 0.13
25 3 0.05
26 16 0.25
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:1193381 original size:32 final size:32
Alignment explanation
Indices: 1193342--1193439 Score: 126
Period size: 32 Copynumber: 3.4 Consensus size: 32
1193332 CAATACATAT
1193342 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1193374 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1193396 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
1193428 TTTAAAATAAAT
1 TTTAAAATAAAT
1193440 TATTTTAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
22 16 0.29
23 2 0.04
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 2 0.04
32 28 0.50
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:1193400 original size:22 final size:22
Alignment explanation
Indices: 1193374--1193474 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
1193364 TAATAAATTA
1193374 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
1193396 TTTAAAATAAATCAATCCATACT
1 TTTAAAATAAATCAATCCATA-T
** * ** * **
1193419 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATCCA-TAT
1193443 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
1193465 TTTATAATAA
1 TTTAAAATAA
1193475 TTTATTTTAA
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
22 33 0.56
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:1193448 original size:15 final size:15
Alignment explanation
Indices: 1193419--1193648 Score: 246
Period size: 15 Copynumber: 14.5 Consensus size: 15
1193409 AATCCATACT
1193419 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
1193433 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1193448 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
1193470 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
1193485 AGTAAATTATTTTAA
1 AATAAATTATTTTAA
1193500 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1193515 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
1193537 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
1193552 AGTAAATTATTTTAA
1 AATAAATTATTTTAA
*
1193567 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1193582 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1193597 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1193612 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1193627 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1193642 AATAAAT
1 AATAAAT
1193649 AACCTTATTA
Statistics
Matches: 184, Mismatches: 17, Indels: 29
0.80 0.07 0.13
Matches are distributed among these distances:
14 9 0.05
15 141 0.77
17 2 0.01
18 4 0.02
19 6 0.03
20 2 0.01
22 20 0.11
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1193506 original size:52 final size:47
Alignment explanation
Indices: 1193339--1193671 Score: 220
Period size: 45 Copynumber: 6.9 Consensus size: 47
1193329 AATCAATACA
*
1193339 TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAAT--A--AAT
*
1193390 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT
1 ---TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAAT
* *
1193440 TATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAGTAAAT
1 TATTTTAAAATAAATCAATCCATA----ATAATAAATTA-TTTAAAATAAAT
* * ** * * * *
1193492 TATTTTAAAATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATT
1 TATTTTAAAATAAATCAATCCATAAT-AATAAAT---TA-TTTAAAATAAAT
* * ** *
1193544 TATTTTAAAGTAAAT-TAT-TTTAA-AATAAATTATTTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAATTA-TTTAAAATAAAT
* * *
1193589 TATTTTAAAATAAAT-TAT--TTTATAATAAATTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAATTA-TTTAAAATAAAT
* *
1193634 TATTTTATAATAAAT-AA-CC-T--TATTAAATTATTTAAAAT
1 TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAAT
1193672 TATTTTAATA
Statistics
Matches: 241, Mismatches: 26, Indels: 36
0.80 0.09 0.12
Matches are distributed among these distances:
42 8 0.03
43 9 0.04
44 3 0.01
45 68 0.28
47 24 0.10
48 8 0.03
49 5 0.02
50 6 0.02
51 10 0.04
52 57 0.24
54 43 0.18
ACGTcount: A:0.50, C:0.06, G:0.01, T:0.44
Consensus pattern (47 bp):
TATTTTAAAATAAATCAATCCATAATAATAAATTATTTAAAATAAAT
Found at i:1193525 original size:67 final size:67
Alignment explanation
Indices: 1193365--1193648 Score: 365
Period size: 67 Copynumber: 4.3 Consensus size: 67
1193355 AATCCATACT
** **
1193365 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAAT-AATTTAT-TTTA-TAATAAATTAT
1193428 TTTAA
63 TTTAA
*
1193433 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTA-AAGTAAATTATTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATTTATTTTATAA-TAAATTATTT
1193497 TAA
65 TAA
*
1193500 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTA-AAGTAAATTATTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATTTATTTTATAA-TAAATTATTT
1193564 TAA
65 TAA
* *
1193567 AATAAATTATTTT---AT-AATAAAT---TATTTTAAAATAAATTATTTTATAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATTTATTTTATAATAAATTATTTT
1193625 AA
66 AA
*
1193627 AATAAATTATTTTATAATAAAT
1 AATAAATTATTTTAAAATAAAT
1193649 AACCTTATTA
Statistics
Matches: 200, Mismatches: 8, Indels: 20
0.88 0.04 0.09
Matches are distributed among these distances:
60 46 0.23
61 2 0.01
63 8 0.04
64 5 0.03
65 2 0.01
66 7 0.04
67 87 0.44
68 14 0.07
69 29 0.14
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.45
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATTTATTTTATAATAAATTATTTT
AA
Found at i:1194316 original size:16 final size:16
Alignment explanation
Indices: 1194295--1194326 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1194285 TACAAAATCT
1194295 AATAATTCATAATATA
1 AATAATTCATAATATA
*
1194311 AATAATTCATTATATA
1 AATAATTCATAATATA
1194327 TATATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
AATAATTCATAATATA
Found at i:1202429 original size:15 final size:15
Alignment explanation
Indices: 1202409--1202447 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1202399 GAGTTGCTGC
1202409 TGTTATATCACTTGT
1 TGTTATATCACTTGT
*
1202424 TGTTATATTACTTGT
1 TGTTATATCACTTGT
1202439 TGTTATATC
1 TGTTATATC
1202448 TCAAATTGCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.21, C:0.10, G:0.13, T:0.56
Consensus pattern (15 bp):
TGTTATATCACTTGT
Found at i:1207353 original size:60 final size:59
Alignment explanation
Indices: 1207231--1207368 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
1207221 CAACAGGCTG
** * *
1207231 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* ** * *
1207290 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATTGGTGGACACGACCTTATGTTT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGA-TGGTGGACACGACCTTATGTGT
*
1207350 CATACTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
1207369 CGGTGCTTAT
Statistics
Matches: 63, Mismatches: 14, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
59 31 0.49
60 32 0.51
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:1207490 original size:44 final size:43
Alignment explanation
Indices: 1207441--1207539 Score: 117
Period size: 44 Copynumber: 2.2 Consensus size: 43
1207431 TGGTATATGG
* * *
1207441 TTATGGAATAATGGAAAGTGTATTGGTAAAATAAGTTTACGAGA
1 TTATGG-ATAATGGAAAGTATATTAGTAAAATAAGCTTACGAGA
* * *
1207485 TTATGGATAAATGGTAAGTATATTAGTAAAATAAGCTTATGAGC
1 TTATGGAT-AATGGAAAGTATATTAGTAAAATAAGCTTACGAGA
1207529 TTATGGGATAA
1 TTAT-GGATAA
1207540 ATGGTAAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
43 2 0.04
44 41 0.87
45 4 0.09
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.33
Consensus pattern (43 bp):
TTATGGATAATGGAAAGTATATTAGTAAAATAAGCTTACGAGA
Found at i:1212277 original size:18 final size:18
Alignment explanation
Indices: 1212254--1212288 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1212244 TTCCATCCGG
*
1212254 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1212272 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1212289 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1213417 original size:15 final size:16
Alignment explanation
Indices: 1213387--1213420 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1213377 GGTCAACATT
1213387 GGTCAACGTCGGTCAAC
1 GGTCAACG-CGGTCAAC
1213404 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
1213419 GG
1 GG
1213421 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.26, G:0.35, T:0.15
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:1213441 original size:18 final size:18
Alignment explanation
Indices: 1213418--1213499 Score: 119
Period size: 18 Copynumber: 4.6 Consensus size: 18
1213408 AACGGGTCAA
* *
1213418 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGTAAACGGGT
* *
1213436 CGGGTCGGGTCAACTGGT
1 CGGGTCGGGTAAACGGGT
*
1213454 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTAAACGGGT
1213472 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
1213490 CGGGTCGGGT
1 CGGGTCGGGT
1213500 TGTGACCGGT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 59 1.00
ACGTcount: A:0.13, C:0.18, G:0.49, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:1213459 original size:13 final size:13
Alignment explanation
Indices: 1213410--1213441 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1213400 CAACGGTCAA
*
1213410 CGGGTCAACGGGT
1 CGGGTCAACAGGT
1213423 CGGGTCAACAGGT
1 CGGGTCAACAGGT
1213436 CGGGTC
1 CGGGTC
1213442 GGGTCAACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.25, G:0.44, T:0.16
Consensus pattern (13 bp):
CGGGTCAACAGGT
Found at i:1217090 original size:17 final size:16
Alignment explanation
Indices: 1217064--1217110 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1217054 AATAAAAATA
*
1217064 TTTATAATTTATATGTAT
1 TTTAT-ATTTATAT-AAT
1217082 TTTATATTTATGATAAT
1 TTTATATTTAT-ATAAT
1217099 TTTATA-TTATAT
1 TTTATATTTATAT
1217111 TAAATCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 2 0.07
16 4 0.15
17 14 0.52
18 7 0.26
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (16 bp):
TTTATATTTATATAAT
Found at i:1225847 original size:3 final size:3
Alignment explanation
Indices: 1225839--1225870 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1225829 ACTTAACCAC
*
1225839 ATT ATT ATT ATT ATT ATT ATT AAT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1225871 ATTTAGATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1229783 original size:39 final size:39
Alignment explanation
Indices: 1229729--1229809 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
1229719 GGGCGACCAT
* *
1229729 AGTCTTTAGATTTCAATTAACCTCATCCTTTGGCAAGCA
1 AGTCTTTAGATTTCAATTAACCTCATACTTTGACAAGCA
1229768 AGTCTTTAGATTTCAATTAACCTCATACTTTGACAAGCA
1 AGTCTTTAGATTTCAATTAACCTCATACTTTGACAAGCA
1229807 AGT
1 AGT
1229810 TATATTCAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (39 bp):
AGTCTTTAGATTTCAATTAACCTCATACTTTGACAAGCA
Found at i:1232562 original size:54 final size:49
Alignment explanation
Indices: 1232503--1232603 Score: 123
Period size: 49 Copynumber: 2.0 Consensus size: 49
1232493 AAAACTTATA
1232503 AGCTTAAAATTATCAAGTTCAAATCGAACTCGAAAT-AAAAAATTAAAGCTCGCG
1 AGCTTAAAATTATCAAG--C---TCG-ACTCGAAATAAAAAAATTAAAGCTCGCG
* *
1232557 AGCTTAAAATTTTCAAGCTCGACTCGAAATAAAAAAATTGAAGCTCG
1 AGCTTAAAATTATCAAGCTCGACTCGAAATAAAAAAATTAAAGCTCG
1232604 ACTCAAGCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
48 9 0.20
49 18 0.41
52 1 0.02
54 16 0.36
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.25
Consensus pattern (49 bp):
AGCTTAAAATTATCAAGCTCGACTCGAAATAAAAAAATTAAAGCTCGCG
Found at i:1233174 original size:60 final size:60
Alignment explanation
Indices: 1233101--1233330 Score: 262
Period size: 60 Copynumber: 3.8 Consensus size: 60
1233091 TAATGAATAG
* *
1233101 TCGAGTGACCATTTTATAACTTTTAATTGTCGAGGGACCCAATAAAGCAACTCCCTATAA
1 TCGAGTGACCATCTAATAACTTTTAATTGTCGAGGGACCCAATAAAGCAACTCCCTATAA
* * * *
1233161 TCGAGTAACCATTTAATAAATTTTAATTGTCGAGGGACCTAATAAAGCAACTCCCTATAA
1 TCGAGTGACCATCTAATAACTTTTAATTGTCGAGGGACCCAATAAAGCAACTCCCTATAA
* * * * * *
1233221 TCTAGTGATCATCTAATAAATTTTTAATTGCCGAGGGACTCAATAAAGCAACTCCCTATAG
1 TCGAGTGACCATCTAAT-AACTTTTAATTGTCGAGGGACCCAATAAAGCAACTCCCTATAA
* * * ** * * * *
1233282 TTGAGGGATCATCTTGTAACTTTTAATGGTCGAGAGACTCAACAAAGCA
1 TCGAGTGACCATCTAATAACTTTTAATTGTCGAGGGACCCAATAAAGCA
1233331 GTATCATATA
Statistics
Matches: 146, Mismatches: 23, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
60 96 0.66
61 50 0.34
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (60 bp):
TCGAGTGACCATCTAATAACTTTTAATTGTCGAGGGACCCAATAAAGCAACTCCCTATAA
Found at i:1237413 original size:29 final size:29
Alignment explanation
Indices: 1237371--1237428 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
1237361 ATCGTATATC
1237371 GAATGTATATATTAAGGAAAGATAGAGCT
1 GAATGTATATATTAAGGAAAGATAGAGCT
1237400 GAATGTATATATTAAGGAAAGATAGAGCT
1 GAATGTATATATTAAGGAAAGATAGAGCT
1237429 TTTGCTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.24, T:0.28
Consensus pattern (29 bp):
GAATGTATATATTAAGGAAAGATAGAGCT
Found at i:1240931 original size:2 final size:2
Alignment explanation
Indices: 1240919--1240950 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1240909 TTAAATTAAC
1240919 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1240951 ATTAAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1241209 original size:20 final size:19
Alignment explanation
Indices: 1241184--1241228 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
1241174 ACATGTATTC
1241184 ATTTTTTT-CTTCTCTTAAAT
1 ATTTTTTTACTT-T-TTAAAT
*
1241204 ATTTTTTTACTTTTTTAAT
1 ATTTTTTTACTTTTTAAAT
1241223 ATTTTT
1 ATTTTT
1241229 AAATTACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 11 0.48
20 9 0.39
21 3 0.13
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTTTTTACTTTTTAAAT
Found at i:1241839 original size:156 final size:155
Alignment explanation
Indices: 1241645--1241965 Score: 579
Period size: 155 Copynumber: 2.1 Consensus size: 155
1241635 ACATAGGTTA
* *
1241645 ATTATAATTTAGTTACTCTATTATTTATGTGGTTCTGTTTGAGTAATCTAATTTTATTTTTCAAA
1 ATTAT-ATTTAGTTACTCTACTATTTATGCGGTTCTGTTTGAGTAATCTAATTTTATTTTTCAAA
1241710 ATTATCACTAAACTTTAGTTTTTGTTACGTTTTGGTCACCCAATTTGATTTAATTTACTTTTTAA
65 ATTATCACTAAACTTTAG-TTTTGTTACGTTTTGGTCACCCAATTTGATTTAATTTACTTTTTAA
*
1241775 ATTTTTAATATATAAGAATTCATTTAT
129 AATTTTAATATATAAGAATTCATTTAT
*
1241802 ATTATATTTAGTTACTCTACTATTTATGCGGTTCTGTTTGAGTTATCTAATTTTATTTTTCAAAA
1 ATTATATTTAGTTACTCTACTATTTATGCGGTTCTGTTTGAGTAATCTAATTTTATTTTTCAAAA
1241867 TTATCACTAAACTTTAGTTTTGTTACGTTTTGGTCACCCAATTTGATTTAATTTACTTTTTAAAA
66 TTATCACTAAACTTTAGTTTTGTTACGTTTTGGTCACCCAATTTGATTTAATTTACTTTTTAAAA
*
1241932 TTTTAATGTATAAGAATTCATTTAT
131 TTTTAATATATAAGAATTCATTTAT
1241957 ATTATATTT
1 ATTATATTT
1241966 TTTACTCAAC
Statistics
Matches: 159, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
155 80 0.50
156 74 0.47
157 5 0.03
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (155 bp):
ATTATATTTAGTTACTCTACTATTTATGCGGTTCTGTTTGAGTAATCTAATTTTATTTTTCAAAA
TTATCACTAAACTTTAGTTTTGTTACGTTTTGGTCACCCAATTTGATTTAATTTACTTTTTAAAA
TTTTAATATATAAGAATTCATTTAT
Found at i:1242014 original size:17 final size:17
Alignment explanation
Indices: 1241994--1242026 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1241984 TTAAAATAAA
1241994 TATAAAATAAATAATAT
1 TATAAAATAAATAATAT
*
1242011 TATAAGATAAATAATA
1 TATAAAATAAATAATA
1242027 AATAACATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TATAAAATAAATAATAT
Found at i:1252745 original size:31 final size:31
Alignment explanation
Indices: 1252685--1252754 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 31
1252675 GAAGAATCAC
1252685 GATTAAATGAGCTCTTATTTAAAAAAATTAT
1 GATTAAATGAGCTCTTATTTAAAAAAATTAT
*
1252716 AGATTAAATGAG-TCATTATTT-GAAAAATTAT
1 -GATTAAATGAGCTC-TTATTTAAAAAAATTAT
*
1252747 GATCAAAT
1 GATTAAAT
1252755 TTGTGCTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 7 0.20
31 11 0.31
32 17 0.49
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.37
Consensus pattern (31 bp):
GATTAAATGAGCTCTTATTTAAAAAAATTAT
Found at i:1253200 original size:2 final size:2
Alignment explanation
Indices: 1253193--1253247 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1253183 CAGCGTCGTT
1253193 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1253235 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
1253248 ATATATATAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1253252 original size:2 final size:2
Alignment explanation
Indices: 1253247--1253272 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1253237 TCTCTCTCTC
1253247 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
1253273 CACCCAAGAA
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):
TA
Found at i:1253909 original size:150 final size:143
Alignment explanation
Indices: 1253660--1254076 Score: 545
Period size: 150 Copynumber: 2.9 Consensus size: 143
1253650 TTCAGAAAAA
* * * * * * **
1253660 GGAATTTTGCTTTTCATTCTTTGATTTTAGTGTATTATCTGTT--TTTT-ATATGTGCTCTCAAC
1 GGAATTTTGC-TTTAATTCTTTAATATTGGTGTATTATATGTTGCTTTTGAGATGTGCTCTTGAC
* *** * *
1253722 ATTAATCATTAATTTCTAGGGTTTATGAAGTAAAACCTATTATCGGAGATTTGATGATAAAAATT
65 ATTAACCCCCAATATCTAGGGTTTATGAAGTAAAACCTATTATTGGAGATTTGATGATAAAAATT
1253787 TCTGTTTCAGCTAT
130 TCTGTTTCAGCTAT
* *
1253801 GGAATTTTTCTTTAATTCTTTAATATTTGTGTATTATATGTTGCTTTTGAGATGTGCTCTTGAGT
1 GGAATTTTGCTTTAATTCTTTAATATTGGTGTATTATATGTTGCTTTTGAGATGTG--C-----T
1253866 CTTGACATTAACCCCCAATATCTAGGGTTTATGAAGTAAAACCTATTATTGGAGATTTGATGATA
59 CTTGACATTAACCCCCAATATCTAGGGTTTATGAAGTAAAACCTATTATTGGAGATTTGATGATA
1253931 AAAATTTCTGTTTCAGCTAT
124 AAAATTTCTGTTTCAGCTAT
1253951 GGAATTTTGCTTTAATTCTTTAATATTGGTGTATTATATGTTGCTTTTGAGATGTGCTCTTGACA
1 GGAATTTTGCTTTAATTCTTTAATATTGGTGTATTATATGTTGCTTTTGAGATGTGCTCTTGACA
* * **
1254016 TTAACCCCCAATATCTAGGGTTTATTAAGTAAAATCC-ATTATTGAAGACCTGATGATAAAA
66 TTAACCCCCAATATCTAGGGTTTATGAAGTAAAA-CCTATTATTGGAGATTTGATGATAAAA
1254077 TTTTAAGAGA
Statistics
Matches: 244, Mismatches: 21, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
140 27 0.11
141 9 0.04
142 4 0.02
143 68 0.28
144 2 0.01
145 1 0.00
148 1 0.00
150 132 0.54
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (143 bp):
GGAATTTTGCTTTAATTCTTTAATATTGGTGTATTATATGTTGCTTTTGAGATGTGCTCTTGACA
TTAACCCCCAATATCTAGGGTTTATGAAGTAAAACCTATTATTGGAGATTTGATGATAAAAATTT
CTGTTTCAGCTAT
Found at i:1255467 original size:16 final size:16
Alignment explanation
Indices: 1255446--1255477 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1255436 GGTAAGTTTT
1255446 CACGCGCATACATACA
1 CACGCGCATACATACA
1255462 CACGCGCATACATACA
1 CACGCGCATACATACA
1255478 TATACATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.38, G:0.12, T:0.12
Consensus pattern (16 bp):
CACGCGCATACATACA
Found at i:1259389 original size:14 final size:13
Alignment explanation
Indices: 1259372--1259402 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
1259362 ATTTATATAA
1259372 AAATAAATCAAAAT
1 AAATAAATC-AAAT
1259386 AAATAAATCAAAT
1 AAATAAATCAAAT
1259399 AAAT
1 AAAT
1259403 CAAAAAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (13 bp):
AAATAAATCAAAT
Found at i:1259485 original size:2 final size:2
Alignment explanation
Indices: 1259478--1259511 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1259468 AAAATAGAAA
1259478 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
1259512 CAAAGAAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1260685 original size:3 final size:3
Alignment explanation
Indices: 1260679--1260714 Score: 63
Period size: 3 Copynumber: 11.7 Consensus size: 3
1260669 AAAAATTAAA
1260679 AAT AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AA
1260715 ATAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1260718 original size:16 final size:16
Alignment explanation
Indices: 1260678--1260711 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1260668 AAAAAATTAA
1260678 AAATAATAATAATAAT
1 AAATAATAATAATAAT
1260694 AAATAATAATAATAAT
1 AAATAATAATAATAAT
1260710 AA
1 AA
1260712 TAAATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAATAATAATAATAAT
Found at i:1260730 original size:19 final size:19
Alignment explanation
Indices: 1260675--1260718 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1260665 GAAAAAAAAT
1260675 TAAA-AATAATAATAATAA
1 TAAATAATAATAATAATAA
1260693 TAAATAATAATAATAATAA
1 TAAATAATAATAATAATAA
1260712 TAAATAA
1 TAAATAA
1260719 ATAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
TAAATAATAATAATAATAA
Found at i:1260731 original size:12 final size:10
Alignment explanation
Indices: 1260675--1260730 Score: 73
Period size: 9 Copynumber: 5.7 Consensus size: 10
1260665 GAAAAAAAAT
1260675 TAAA-AATAA
1 TAAATAATAA
1260684 T-AATAATAA
1 TAAATAATAA
1260693 TAAATAATAA
1 TAAATAATAA
1260703 T-AATAATAA
1 TAAATAATAA
1260712 TAAATAAATAAA
1 TAAAT-AAT-AA
1260724 TAAATAA
1 TAAATAA
1260731 AAAGTATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
8 2 0.05
9 16 0.38
10 12 0.29
11 5 0.12
12 7 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
TAAATAATAA
Found at i:1260849 original size:18 final size:18
Alignment explanation
Indices: 1260826--1260889 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
1260816 AAAAATGTTT
1260826 TTTTCAAAAACTATATAA
1 TTTTCAAAAACTATATAA
* * **
1260844 TTTTCAAAAA-TGTTTTT
1 TTTTCAAAAACTATATAA
* *
1260861 TTTTCTAAAAACCATATAC
1 TTTTC-AAAAACTATATAA
1260880 TTTTCAAAAA
1 TTTTCAAAAA
1260890 TGTTTTTTTT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
17 8 0.23
18 20 0.57
19 7 0.20
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTTCAAAAACTATATAA
Found at i:1260871 original size:36 final size:35
Alignment explanation
Indices: 1260801--1260900 Score: 132
Period size: 36 Copynumber: 2.8 Consensus size: 35
1260791 ACTATATACT
*
1260801 CTATATAAATTTTTAAAAAATG--TTTTTTTCAAAAA
1 CTATAT-AA-TTTTCAAAAATGTTTTTTTTTCAAAAA
1260836 CTATATAATTTTCAAAAATGTTTTTTTTTCTAAAAA
1 CTATATAATTTTCAAAAATGTTTTTTTTTC-AAAAA
* *
1260872 CCATATACTTTTCAAAAATGTTTTTTTTT
1 CTATATAATTTTCAAAAATGTTTTTTTTT
1260901 TATAAAAAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
33 11 0.19
34 2 0.03
35 14 0.24
36 32 0.54
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (35 bp):
CTATATAATTTTCAAAAATGTTTTTTTTTCAAAAA
Found at i:1261020 original size:37 final size:36
Alignment explanation
Indices: 1260906--1261111 Score: 256
Period size: 37 Copynumber: 5.5 Consensus size: 36
1260896 TTTTTTATAA
* *
1260906 AAAAATTATATATTATATAGGTTTTTAAAAAATGTTTT
1 AAAAACTATATATTATATAAGTTTTT--AAAATGTTTT
*
1260944 CAAAAACTATATACTATATAAGTTTTTCAAAATGTTTTT
1 -AAAAACTATATATTATATAAGTTTTT-AAAATG-TTTT
*
1260983 AAAAACTATATATTATATAAATTTTCTAAAATGTTTT
1 AAAAACTATATATTATATAAGTTTT-TAAAATGTTTT
1261020 AAAAACTATATATTATAT-AGTTTTTAAAAGTGTTTT
1 AAAAACTATATATTATATAAGTTTTTAAAA-TGTTTT
*
1261056 AAAAACTATATATTATATACA-TTTTCAAAATGTTTTT
1 AAAAACTATATATTATATA-AGTTTTTAAAATG-TTTT
1261093 AGAAAA-TATATATTATATA
1 A-AAAACTATATATTATATA
1261112 TGTATTCTCA
Statistics
Matches: 152, Mismatches: 8, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
35 5 0.03
36 31 0.20
37 48 0.32
38 40 0.26
39 28 0.18
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (36 bp):
AAAAACTATATATTATATAAGTTTTTAAAATGTTTT
Found at i:1261074 original size:73 final size:74
Alignment explanation
Indices: 1260906--1261111 Score: 269
Period size: 73 Copynumber: 2.8 Consensus size: 74
1260896 TTTTTTATAA
* ** *
1260906 AAAAATTATATATTATATAGGTTTT-TAAAAAATGTTTTCAAAAACTATATACTATATAAGTTTT
1 AAAAACTATATATTATATAAATTTTCT--AAAATGTTTT-AAAAACTATATATTATAT-AGTTTT
1260970 TCAAAATGTTTTT
62 TCAAAATGTTTTT
1260983 AAAAACTATATATTATATAAATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTTTTT-AA
1 AAAAACTATATATTATATAAATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTTTTTCAA
1261047 AA-GTGTTTT
66 AATGT-TTTT
*
1261056 AAAAACTATATATTATATACATTTTC-AAAATGTTTTTAGAAAA-TATATATTATATA
1 AAAAACTATATATTATATAAATTTTCTAAAATG-TTTTA-AAAACTATATATTATATA
1261112 TGTATTCTCA
Statistics
Matches: 120, Mismatches: 5, Indels: 12
0.88 0.04 0.09
Matches are distributed among these distances:
72 8 0.07
73 51 0.43
74 11 0.09
75 17 0.14
76 10 0.08
77 22 0.18
78 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (74 bp):
AAAAACTATATATTATATAAATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTTTTTCAA
AATGTTTTT
Found at i:1262038 original size:166 final size:166
Alignment explanation
Indices: 1261702--1262813 Score: 1590
Period size: 165 Copynumber: 6.7 Consensus size: 166
1261692 TTATTGACAA
* * ** * * *
1261702 ATAGCCCTTCTTGCCTTGTGCTATGTTGCAAATGATGTGCCTTAGAGCTAATCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTC
* * * *
1261767 AAAGGTCTTCTGG-TGACAGATAACCCTTCTAGCATTGAGTTATCCTGTAAATGATGTGCCCTCG
66 AAAGGTCTTCTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCG
* * * *
1261831 AAGTTGAGTGTAATCGAACTTGAGCGTCTTTTGGTAG
131 AAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGGCAG
*
1261868 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTAAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTC
1261933 AAAGGTCTTCTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCG
66 AAAGGTCTTCTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCG
* *
1261998 GAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGCAG
131 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* *
1262034 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTAAGCGTAGTCTAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTC
* * * * * *
1262099 AAAGGTCTT-TGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCG
66 AAAGGTCTTCTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCG
* * *
1262163 AAGCTGAATATAATCGAACTCG-GGGTTTTTGGCAG
131 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* * *
1262198 ATAGCCCTTCTCGACTTAAGCTATGCTACAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTC
* * * ** * * * *
1262263 AAAGGT-TTTTGGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTACAAATGATGTGCCCTCG
66 AAAGGTCTTCTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCG
1262327 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
131 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* * * *
1262363 ATAGCCCTTCTCGACTTAAGTTATACTACAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTC
* *
1262428 AAAGGTCTT-TGGTT-ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCG
66 AAAGGTCTTCTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCG
* *
1262491 AAGTTGAGTGTAATCAAACTCGAGGGTCTTTTGGCAG
131 AAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGGCAG
*
1262528 ATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTC
* *
1262593 AAAGGTCTTCTGGTTGATAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTTG
66 AAAGGTCTTCTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCG
* * *
1262658 GAGCTAAGTGTAATCGAACTCGGGGGTCTTTGGCAG
131 AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
* * * *
1262694 ATAGCCCTTCTCGACTTAAGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTC
* * * *
1262759 GAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGAT
66 AAAGGTCTTCTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGAT
1262814 GTCTTAAAAA
Statistics
Matches: 863, Mismatches: 76, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
163 2 0.00
164 218 0.25
165 267 0.31
166 238 0.28
167 138 0.16
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.30
Consensus pattern (166 bp):
ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTC
AAAGGTCTTCTGGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCG
AAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAG
Found at i:1267901 original size:22 final size:22
Alignment explanation
Indices: 1267876--1267963 Score: 74
Period size: 22 Copynumber: 3.9 Consensus size: 22
1267866 AAAAAACTAC
*
1267876 ATAAATAAAATAAAAAATAATG
1 ATAAATAAAATAAAAAATAATA
* *
1267898 ATAAATCAAAAGGAAAAAATATTTA
1 ATAAAT-AAAA-TAAAAAATA-ATA
*
1267923 TATAAA-AAAAT-AAAAATAAAA
1 -ATAAATAAAATAAAAAATAATA
1267944 ATAAAT-AAATAAATAAATAA
1 ATAAATAAAATAAA-AAATAA
1267964 ATCTAAAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
20 9 0.17
21 3 0.06
22 19 0.36
23 4 0.08
24 12 0.23
25 1 0.02
26 5 0.09
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (22 bp):
ATAAATAAAATAAAAAATAATA
Found at i:1267951 original size:4 final size:4
Alignment explanation
Indices: 1267924--1267965 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
1267914 AAATATTTAT
* *
1267924 ATAA AAAA ATAA A-AA TAAAA ATAA ATAA ATAA ATAA ATAA AT
1 ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATAA ATAA ATAA AT
1267966 CTAAAAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
3 2 0.06
4 29 0.88
5 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
ATAA
Found at i:1267965 original size:12 final size:12
Alignment explanation
Indices: 1267924--1267964 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1267914 AAATATTTAT
1267924 ATAAAAAAATAA
1 ATAAAAAAATAA
1267936 A-AATAAAAATAA
1 ATAA-AAAAATAA
*
1267948 ATAAATAAATAA
1 ATAAAAAAATAA
1267960 ATAAA
1 ATAAA
1267965 TCTAAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 2 0.08
12 22 0.85
13 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
ATAAAAAAATAA
Found at i:1268045 original size:2 final size:2
Alignment explanation
Indices: 1268038--1268073 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1268028 TAAAAATAGA
1268038 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
1268074 CAAAGAAAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1269291 original size:43 final size:38
Alignment explanation
Indices: 1269209--1269317 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 38
1269199 ATAAATAAAT
1269209 AATATTTTTTTTAAAAAACTATATAATATAAAATTTTAA
1 AATA-TTTTTTTAAAAAACTATATAATATAAAATTTTAA
*
1269248 AATTATTTCTTTT-AAAAACTATATACTCTATATAAATTTTTAA
1 AA-TATTT-TTTTAAAAAACTATATA----ATATAAAATTTTAA
* *
1269291 AAAATGTTTTTTCAAAAACTATATAAT
1 AATAT-TTTTTTAAAAAACTATATAAT
1269318 TTTCAAAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
39 19 0.32
40 6 0.10
42 6 0.10
43 29 0.48
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (38 bp):
AATATTTTTTTAAAAAACTATATAATATAAAATTTTAA
Found at i:1269313 original size:34 final size:33
Alignment explanation
Indices: 1269275--1269370 Score: 113
Period size: 36 Copynumber: 2.8 Consensus size: 33
1269265 ACTATATACT
*
1269275 CTATATAAATTTTTAAAAAATGTTTTTTC-AAAAA
1 CTATAT-AA-TTTTCAAAAATGTTTTTTCTAAAAA
1269309 CTATATAATTTTCAAAAATGCTTTTTTTTCTAAAAA
1 CTATATAATTTTCAAAAATG---TTTTTTCTAAAAA
* *
1269345 CCATATACTTTTCAAAAATGTTTTTT
1 CTATATAATTTTCAAAAATGTTTTTT
1269371 TATAAAAAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
32 11 0.20
33 8 0.15
34 6 0.11
35 7 0.13
36 23 0.42
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (33 bp):
CTATATAATTTTCAAAAATGTTTTTTCTAAAAA
Found at i:1269344 original size:36 final size:34
Alignment explanation
Indices: 1269285--1269371 Score: 115
Period size: 36 Copynumber: 2.6 Consensus size: 34
1269275 CTATATAAAT
* *
1269285 TTTTAAAAAATG--TTTTTTCAAAAACTATATAA
1 TTTTCAAAAATGTTTTTTTTCAAAAACCATATAA
*
1269317 TTTTCAAAAATGCTTTTTTTTCTAAAAACCATATAC
1 TTTTCAAAAATG-TTTTTTTTC-AAAAACCATATAA
1269353 TTTTCAAAAATGTTTTTTT
1 TTTTCAAAAATGTTTTTTT
1269372 ATAAAAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
32 11 0.23
35 14 0.29
36 23 0.48
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.48
Consensus pattern (34 bp):
TTTTCAAAAATGTTTTTTTTCAAAAACCATATAA
Found at i:1269361 original size:18 final size:18
Alignment explanation
Indices: 1269299--1269362 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
1269289 AAAAAATGTT
*
1269299 TTTTCAAAAACTATATAA
1 TTTTCAAAAACCATATAA
* **
1269317 TTTTCAAAAATGC-T-TTT
1 TTTTCAAAAA-CCATATAA
*
1269334 TTTTCTAAAAACCATATAC
1 TTTTC-AAAAACCATATAA
1269353 TTTTCAAAAA
1 TTTTCAAAAA
1269363 TGTTTTTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
17 7 0.20
18 22 0.63
19 6 0.17
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (18 bp):
TTTTCAAAAACCATATAA
Found at i:1269456 original size:37 final size:37
Alignment explanation
Indices: 1269382--1269580 Score: 246
Period size: 37 Copynumber: 5.4 Consensus size: 37
1269372 ATAAAAAATT
*
1269382 TATATATTATATAGGTTTTTAAAAAATGTTTTCAAAAAC
1 TATATATTATATAAGTTTTT-AAAAATGTTTT-AAAAAC
*
1269421 TATATACTATATAAGTTTTTAAAAATGTTTTAAAAAC
1 TATATATTATATAAGTTTTTAAAAATGTTTTAAAAAC
*
1269458 TATATATTATATAAATTTTCT-AAAATGTTTTAAAAAC
1 TATATATTATATAAGTTTT-TAAAAATGTTTTAAAAAC
* *
1269495 TATATATTATAT-AGTTTTTAAAAGTATTTTAAAAAC
1 TATATATTATATAAGTTTTTAAAAATGTTTTAAAAAC
**
1269531 TATATATTATATACA--TTTTCGAAATGTTTTTAGAAAA-
1 TATATATTATATA-AGTTTTTAAAAATG-TTTTA-AAAAC
1269568 TATATATTATATA
1 TATATATTATATA
1269581 CGTATTCTCA
Statistics
Matches: 143, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
35 1 0.01
36 38 0.27
37 69 0.48
38 17 0.12
39 18 0.13
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (37 bp):
TATATATTATATAAGTTTTTAAAAATGTTTTAAAAAC
Found at i:1269532 original size:73 final size:73
Alignment explanation
Indices: 1269382--1269580 Score: 260
Period size: 73 Copynumber: 2.7 Consensus size: 73
1269372 ATAAAAAATT
** *
1269382 TATATATTATATAGGTTTT-TAAAAAATGTTTTCAAAAACTATATACTATATAAGTTTTTAAAAA
1 TATATATTATATAAATTTTCT--AAAATGTTTT-AAAAACTATATATTATAT-AGTTTTTAAAAA
*
1269446 TGTTTTAAAAAC
62 TATTTTAAAAAC
*
1269458 TATATATTATATAAATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTTTTTAAAAGTATT
1 TATATATTATATAAATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTTTTTAAAAATATT
1269523 TTAAAAAC
66 TTAAAAAC
* *
1269531 TATATATTATATACATTTTC-GAAATGTTTTTAGAAAA-TATATATTATATA
1 TATATATTATATAAATTTTCTAAAATG-TTTTA-AAAACTATATATTATATA
1269581 CGTATTCTCA
Statistics
Matches: 113, Mismatches: 7, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
72 5 0.04
73 59 0.52
74 21 0.19
75 10 0.09
76 17 0.15
77 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (73 bp):
TATATATTATATAAATTTTCTAAAATGTTTTAAAAACTATATATTATATAGTTTTTAAAAATATT
TTAAAAAC
Found at i:1293840 original size:21 final size:20
Alignment explanation
Indices: 1293811--1293849 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1293801 TCATCCATTG
1293811 ATCTCTTCTCCAT-TTGTTCC
1 ATCTCTTCT-CATGTTGTTCC
1293831 ATCTGCTTCTCATGTTGTT
1 ATCT-CTTCTCATGTTGTT
1293850 TGCTAAGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.10, C:0.28, G:0.10, T:0.51
Consensus pattern (20 bp):
ATCTCTTCTCATGTTGTTCC
Found at i:1296002 original size:2 final size:2
Alignment explanation
Indices: 1295995--1296020 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1295985 GGAAATCAAA
1295995 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1296021 GAAGTGGCAT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1299724 original size:30 final size:30
Alignment explanation
Indices: 1299690--1299752 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
1299680 AAATTAAAGA
1299690 ACATGCAATCTTAGATGCAAGGCAGCAAGC
1 ACATGCAATCTTAGATGCAAGGCAGCAAGC
1299720 ACATGCAATCTTAGATGCAAGGCAGCAAGC
1 ACATGCAATCTTAGATGCAAGGCAGCAAGC
1299750 ACA
1 ACA
1299753 CCTATAGAGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (30 bp):
ACATGCAATCTTAGATGCAAGGCAGCAAGC
Found at i:1304930 original size:31 final size:31
Alignment explanation
Indices: 1304880--1304950 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
1304870 ATGATTCAAT
*
1304880 GATCAAATTGATATCTTATCTAAAATTTAGG
1 GATCAAATTAATATCTTATCTAAAATTTAGG
* * *
1304911 GATCAACTTAATATTTTATCTAAAATTTAGA
1 GATCAAATTAATATCTTATCTAAAATTTAGG
1304942 G-TCAAATTA
1 GATCAAATTA
1304951 GTAGTATATC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 7 0.20
31 28 0.80
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (31 bp):
GATCAAATTAATATCTTATCTAAAATTTAGG
Found at i:1304967 original size:31 final size:31
Alignment explanation
Indices: 1304896--1304965 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
1304886 ATTGATATCT
* * * *
1304896 TATCTAAAATTTAGGGATCAACTTAATATTT
1 TATCTAAAATTTAGAGATCAAATTAATAGTA
*
1304927 TATCTAAAATTTAGAG-TCAAATTAGTAGTA
1 TATCTAAAATTTAGAGATCAAATTAATAGTA
1304957 TATCTAAAA
1 TATCTAAAA
1304966 ATATAAGGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 19 0.56
31 15 0.44
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.39
Consensus pattern (31 bp):
TATCTAAAATTTAGAGATCAAATTAATAGTA
Found at i:1308516 original size:27 final size:25
Alignment explanation
Indices: 1308474--1308531 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
1308464 AATTATCTTG
* **
1308474 TCAAAAAAATATAAAACCTCAAAAA
1 TCAAAAAAATAAAAAAAATCAAAAA
1308499 TCAAAAAATATGAAAAAAAATCAAAAA
1 TCAAAAAA-AT-AAAAAAAATCAAAAA
1308526 T-AAAAA
1 TCAAAAA
1308532 TTAATCAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 8 0.29
26 7 0.25
27 13 0.46
ACGTcount: A:0.72, C:0.10, G:0.02, T:0.16
Consensus pattern (25 bp):
TCAAAAAAATAAAAAAAATCAAAAA
Found at i:1312351 original size:189 final size:192
Alignment explanation
Indices: 1312025--1312405 Score: 700
Period size: 189 Copynumber: 2.0 Consensus size: 192
1312015 ACTCTTGGCA
1312025 TCAATGCCTTCCTCCATGTTGACCAAGCAAATGGTCTTGGATCCTATTACAAGTGTTCAAATCAG
1 TCAATGCCTTCCTCCATGTTGACCAAGCAAATGGTCTTGGATCCTATTACAAGTGTTCAAATCAG
1312090 GAGAAATAAAGAGCTAATGTCCAGAGAATTGCATCTTAGTAACATATCTAATATTGCCTTAAACT
66 GAGAAATAAAGAGCTAATGTCCAGAGAATTGCATCTTAGTAACATATCTAATATTGCCTTAAACT
*
1312155 TGACAGAAAGGAGGAATCACAAATAAATCAGCAAAATACACATTGTAGG-A-GTTGAAAGGG
131 TGACAGAAAGGAGGAATCACAAAAAAATCAGCAAAATACACATTGTAGGAATGTTGAAAGGG
1312215 TCAATG-CTTCCTCCATGTTGACCAAGCAAATGGTCTTGGATCCTATATTACAAGTGTTCAAATC
1 TCAATGCCTTCCTCCATGTTGACCAAGCAAATGGTCTTGGATCC--TATTACAAGTGTTCAAATC
1312279 AGGAGAAATAAAGAGCTAATGTCCAGAG-ATTGCATCTTAGTAACATATCTAATATTGCCTTAAA
64 AGGAGAAATAAAGAGCTAATGTCCAGAGAATTGCATCTTAGTAACATATCTAATATTGCCTTAAA
1312343 C-TGACAGAAAGGAGGAATCACAAAAAAATCAGCAAAATACACATTGTAGGAATGTTGAAAGGG
129 CTTGACAGAAAGGAGGAATCACAAAAAAATCAGCAAAATACACATTGTAGGAATGTTGAAAGGG
1312406 AAAAAAACAA
Statistics
Matches: 186, Mismatches: 1, Indels: 7
0.96 0.01 0.04
Matches are distributed among these distances:
189 85 0.46
190 44 0.24
191 57 0.31
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (192 bp):
TCAATGCCTTCCTCCATGTTGACCAAGCAAATGGTCTTGGATCCTATTACAAGTGTTCAAATCAG
GAGAAATAAAGAGCTAATGTCCAGAGAATTGCATCTTAGTAACATATCTAATATTGCCTTAAACT
TGACAGAAAGGAGGAATCACAAAAAAATCAGCAAAATACACATTGTAGGAATGTTGAAAGGG
Found at i:1316298 original size:169 final size:168
Alignment explanation
Indices: 1315974--1316310 Score: 649
Period size: 169 Copynumber: 2.0 Consensus size: 168
1315964 ATTCGATACT
1315974 ATTATTAATAACTATGAGGTACTCTTTTCTTCCTTCCAATGTTCGTTAACATACTTTTAGTATGT
1 ATTATTAATAACTATGAGGTACTCTTTTCTTCCTTCCAATGTTCGTTAACATACTTTTAGTATGT
1316039 GGACGAATACGAAGGGAGTTTTTTAATGAGGCCTCCAACTCTATAAAAAAAATGTTAGAATTTCA
66 GGACGAATACGAAGGGAGTTTTTTAATGAGGCCTCCAACTCTATAAAAAAAATGTTAGAATTTCA
1316104 GGGCTCTCATTGTTAATCTAAAACTTTCCACTTATAAA
131 GGGCTCTCATTGTTAATCTAAAACTTTCCACTTATAAA
1316142 ATTATTAATAACTATGAGGTACTCTTTTCTTCCTTCCAATGTTCGTTAACATACTTTTTAGTATG
1 ATTATTAATAACTATGAGGTACTCTTTTCTTCCTTCCAATGTTCGTTAACATAC-TTTTAGTATG
1316207 TGGACGAATACGAAGGGAG-TTTTTAATGAGGCCTCCAACTTCTATAAAAAAAATGTTAGAATTT
65 TGGACGAATACGAAGGGAGTTTTTTAATGAGGCCTCCAAC-TCTATAAAAAAAATGTTAGAATTT
1316271 CAGGGCTCTCATTGTTAATCTAAAACTTTCCACTTATAAA
129 CAGGGCTCTCATTGTTAATCTAAAACTTTCCACTTATAAA
1316311 TGTAGCATAA
Statistics
Matches: 167, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
168 74 0.44
169 93 0.56
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (168 bp):
ATTATTAATAACTATGAGGTACTCTTTTCTTCCTTCCAATGTTCGTTAACATACTTTTAGTATGT
GGACGAATACGAAGGGAGTTTTTTAATGAGGCCTCCAACTCTATAAAAAAAATGTTAGAATTTCA
GGGCTCTCATTGTTAATCTAAAACTTTCCACTTATAAA
Found at i:1317826 original size:14 final size:14
Alignment explanation
Indices: 1317807--1317843 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1317797 GGGAATCAGT
1317807 GAGTTAGGGATAAC
1 GAGTTAGGGATAAC
1317821 GAGTTAGGGATAAC
1 GAGTTAGGGATAAC
1317835 GAGTTAGGG
1 GAGTTAGGG
1317844 TTTTAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.32, C:0.05, G:0.41, T:0.22
Consensus pattern (14 bp):
GAGTTAGGGATAAC
Found at i:1318589 original size:20 final size:21
Alignment explanation
Indices: 1318564--1318615 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1318554 TTTTCCCAAT
*
1318564 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1318584 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1318605 TCGCAATGCGA
1 TCGCAATGCGA
1318616 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1318671 original size:20 final size:20
Alignment explanation
Indices: 1318646--1318698 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1318636 TAATACAAAA
*
1318646 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATACTGACTT
* *
1318666 TCGCAACGCGATTCTGATTT
1 TCGCAACGCGATACTGACTT
1318686 TCGCAACGCGATA
1 TCGCAACGCGATA
1318699 ATACATAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:1318913 original size:22 final size:22
Alignment explanation
Indices: 1318886--1318929 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1318876 CACTCTCTCA
1318886 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
1318908 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGGCGAAATCCGTC
1318930 TATCTCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.45, G:0.18, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGGCGAAATCCGTC
Found at i:1319197 original size:20 final size:20
Alignment explanation
Indices: 1319172--1319209 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1319162 CGATTCTCTC
1319172 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1319192 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1319210 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1319400 original size:25 final size:24
Alignment explanation
Indices: 1319346--1319400 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1319336 TGTTTATTAT
* *
1319346 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1319370 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1319396 TGTTT
1 TGTTT
1319401 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1320549 original size:18 final size:18
Alignment explanation
Indices: 1320528--1320572 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1320518 TCCACTTCGG
*
1320528 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1320546 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1320564 GAGCCATCA
1 GAGCCATCA
1320573 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1321111 original size:19 final size:20
Alignment explanation
Indices: 1321059--1321111 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1321049 TTTACTTTCG
*
1321059 CAACACGAAAATGACTATCA
1 CAACGCGAAAATGACTATCA
* *
1321079 CAACGCGGAAATGACTATCG
1 CAACGCGAAAATGACTATCA
*
1321099 CAATGC-AAAATGA
1 CAACGCGAAAATGA
1321112 AAATCGCAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
CAACGCGAAAATGACTATCA
Found at i:1321117 original size:19 final size:19
Alignment explanation
Indices: 1321095--1321176 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
1321085 GGAAATGACT
*
1321095 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1321114 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
1321128 ATCGCAATGCGAAAT-AAA
1 ATCGCAATGCGAAATGAAA
*
1321146 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1321165 ATCGCAATGCGA
1 ATCGCAATGCGA
1321177 TTTGTGTTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 1 0.02
18 18 0.34
19 21 0.40
ACGTcount: A:0.48, C:0.21, G:0.18, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1321170 original size:37 final size:38
Alignment explanation
Indices: 1321079--1321176 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 38
1321069 ATGACTATCA
** *
1321079 CAACGCGGAAATGACTATCGCAATGCAAAATGAAAATCG
1 CAACGC-GAAATGAAAATCGCAATGCGAAATGAAAATCG
*
1321118 CAA--CG--A-CAAAATCGCAATGCGAAAT-AAAATCG
1 CAACGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
1321150 CAACGCGAAATGAAAATCGCAATGCGA
1 CAACGCGAAATGAAAATCGCAATGCGA
1321177 TTTGTGTTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
32 10 0.20
33 15 0.31
34 3 0.06
36 2 0.04
37 16 0.33
39 3 0.06
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.13
Consensus pattern (38 bp):
CAACGCGAAATGAAAATCGCAATGCGAAATGAAAATCG
Found at i:1321207 original size:14 final size:14
Alignment explanation
Indices: 1321188--1321245 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1321178 TTGTGTTTCG
1321188 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1321202 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1321218 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1321234 CGTTGCGATTTT
1 CGTTGCGATTTT
1321246 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1321226 original size:32 final size:33
Alignment explanation
Indices: 1321183--1321261 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1321173 GCGATTTGTG
*
1321183 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1321215 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1321248 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1321262 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1321280 original size:20 final size:19
Alignment explanation
Indices: 1321246--1321301 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
1321236 TTGCGATTTT
*
1321246 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1321265 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
1321285 CATTTTCGTGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1321302 TTTAAGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 24 0.75
21 3 0.09
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1323187 original size:14 final size:14
Alignment explanation
Indices: 1323168--1323203 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1323158 ATTGTTTAAT
1323168 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1323182 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1323196 TGATTTGT
1 TGATTTGT
1323204 TTAATTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1323213 original size:13 final size:14
Alignment explanation
Indices: 1323155--1323216 Score: 51
Period size: 13 Copynumber: 4.6 Consensus size: 14
1323145 TTATTATTTT
*
1323155 TTGA-TTGTTTAA-
1 TTGATTTGTTAAAG
*
1323167 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
*
1323181 ATGATTTG-TAAATG
1 TTGATTTGTTAAA-G
*
1323195 TTGATTTGTTTAA-
1 TTGATTTGTTAAAG
1323208 TTGATTTGT
1 TTGATTTGT
1323217 AAAACTGACT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
12 4 0.10
13 18 0.45
14 15 0.38
15 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.53
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:1323292 original size:19 final size:19
Alignment explanation
Indices: 1323240--1323285 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1323230 GTAACGAGAG
1323240 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1323259 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1323278 AATCGCAA
1 AATCGCAA
1323286 CGAGAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.48, C:0.17, G:0.20, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1323324 original size:19 final size:19
Alignment explanation
Indices: 1323300--1323336 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1323290 AAAATCGCAA
1323300 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
1323319 ATTTCGCATTGCGATTTT
1 ATTTCGCATTGCGATTTT
1323337 GTCGTTGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:1324377 original size:24 final size:24
Alignment explanation
Indices: 1324350--1324403 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1324340 GTATTCGAAA
*
1324350 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1324374 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1324398 TTTGAT
1 TTTGAT
1324404 GATGTTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1324595 original size:12 final size:12
Alignment explanation
Indices: 1324578--1324602 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1324568 ATATAATCCT
1324578 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1324590 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1324602 G
1 G
1324603 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1326797 original size:32 final size:32
Alignment explanation
Indices: 1326739--1326861 Score: 173
Period size: 32 Copynumber: 3.9 Consensus size: 32
1326729 GGAAATTACT
1326739 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACG-GAGA
*
1326772 ATCGCAATGCGAAATG-AAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACG-GAGA
*
1326803 TTTCGCAATGCGAAATGAAAATCGC-AC-GAGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGGAGA
1326834 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1326862 CGAATTTAAT
Statistics
Matches: 80, Mismatches: 5, Indels: 11
0.83 0.05 0.11
Matches are distributed among these distances:
30 24 0.30
31 4 0.05
32 29 0.36
33 23 0.29
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.15
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAAATCGCAACGGAGA
Found at i:1326897 original size:14 final size:14
Alignment explanation
Indices: 1326878--1326932 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1326868 TAATTTCGCA
1326878 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
1326892 TTGCGATTTTCATTTCGCG
1 TTGCGA--TTC---TCTCG
1326911 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
1326925 TTGCGATT
1 TTGCGATT
1326933 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:1326914 original size:19 final size:19
Alignment explanation
Indices: 1326890--1326950 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1326880 GCGATTCTCT
1326890 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1326909 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
1326923 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
1326942 CATTGCGAT
1 CGTTGCGAT
1326951 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:1326915 original size:33 final size:33
Alignment explanation
Indices: 1326861--1326950 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
1326851 AAATCGCAAC
* *
1326861 GCGAATTTAATTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
*
1326894 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1326927 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCATTGCGAT
1326951 AGTACTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.14, C:0.22, G:0.20, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
Found at i:1328475 original size:42 final size:41
Alignment explanation
Indices: 1328416--1328621 Score: 155
Period size: 42 Copynumber: 4.9 Consensus size: 41
1328406 TGTGAATCGG
* *
1328416 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
1328458 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * * *
1328500 CTCTTCAATGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
* * * *
1328542 CTCTTGAACGGTGGGAGGGGACT-ATCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
1328584 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAG
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAG
1328622 GCGAGTCGGG
Statistics
Matches: 124, Mismatches: 32, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
41 9 0.07
42 104 0.84
43 11 0.09
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:1328482 original size:21 final size:21
Alignment explanation
Indices: 1328416--1328482 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1328406 TGTGAATCGG
*
1328416 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1328436 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1328458 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1328479 CTCT
1 CTCT
1328483 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1328557 original size:84 final size:84
Alignment explanation
Indices: 1328446--1328621 Score: 334
Period size: 84 Copynumber: 2.1 Consensus size: 84
1328436 CCTCTTCAAC
* *
1328446 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAATGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTATCGAGGAATGATAGGGGCCTCTTCAACGA
1328511 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1328530 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTATCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTATCGAGGAATGATAGGGGCCTCTTCAACGA
1328595 TAGGAGTGGACTCTTGAGG
66 TAGGAGTGGACTCTTGAGG
1328614 GATGACAG
1 GATGACAG
1328622 GCGAGTCGGG
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (84 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTATCGAGGAATGATAGGGGCCTCTTCAACGA
TAGGAGTGGACTCTTGAGG
Found at i:1329236 original size:62 final size:63
Alignment explanation
Indices: 1329167--1329296 Score: 244
Period size: 62 Copynumber: 2.1 Consensus size: 63
1329157 TAAAGTAGAC
*
1329167 ACCTCCACACGCCATGCACCATTGTTATCGCGTAGAGTACCGATCTCCTCAC-CAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1329229 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1329292 ACCTC
1 ACCTC
1329297 ATCACGTACT
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
62 51 0.77
63 15 0.23
ACGTcount: A:0.24, C:0.37, G:0.18, T:0.22
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:1330751 original size:38 final size:38
Alignment explanation
Indices: 1330709--1330837 Score: 164
Period size: 38 Copynumber: 3.6 Consensus size: 38
1330699 TCTTTTGGTT
1330709 GAAATG-AAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGA-AATGAGAATCGCAACGC
**
1330747 GAAATGACTATCGC-AC--G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAAATGAGAATCGCAACGC
* *
1330779 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAAATGAGAATCGCAACGC
1330817 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
1330838 GACCAACGCG
Statistics
Matches: 78, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
32 26 0.33
33 3 0.04
35 1 0.01
36 1 0.01
37 1 0.01
38 41 0.53
39 5 0.06
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGAGAAATGAGAATCGCAACGC
Found at i:1330752 original size:19 final size:19
Alignment explanation
Indices: 1330709--1330834 Score: 149
Period size: 19 Copynumber: 6.9 Consensus size: 19
1330699 TCTTTTGGTT
*
1330709 GAAATG-AAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1330727 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1330747 GAAATGACTATCGC-A--C
1 GAAATGAAAATCGCAACGC
*
1330763 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1330779 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1330798 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1330817 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
1330835 AGAGACCAAC
Statistics
Matches: 93, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
13 7 0.08
14 2 0.02
16 4 0.04
18 4 0.04
19 64 0.69
20 12 0.13
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1330769 original size:32 final size:33
Alignment explanation
Indices: 1330733--1330862 Score: 160
Period size: 38 Copynumber: 3.9 Consensus size: 33
1330723 ACGAGATAAT
**
1330733 GAGAATCGCAACGCGAAATGACTATCGC-ACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1330765 GAGAATCGCAACGCGAAATGAAAATCGCAACGCGAAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA--CG--A
*
1330802 TGAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 -GAGAATCGCAACGCGAAATGAAAATCGCAACGA
1330836 GAG-A-C-CAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAAAATCGCAA
1330863 TGCGATTTTG
Statistics
Matches: 88, Mismatches: 4, Indels: 14
0.83 0.04 0.13
Matches are distributed among these distances:
30 22 0.25
31 1 0.01
32 27 0.31
33 3 0.03
34 1 0.01
35 2 0.02
36 2 0.02
37 1 0.01
38 29 0.33
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.10
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:1330822 original size:70 final size:69
Alignment explanation
Indices: 1330709--1330868 Score: 227
Period size: 70 Copynumber: 2.3 Consensus size: 69
1330699 TCTTTTGGTT
* * **
1330709 GAAATG-AAATCGCAACGAGATAATGAGAATCGCAACGCGAAATGACTATCGC-ACGAGAGAATC
1 GAAATGAAAATCGCAACGCGATAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG-A-C
1330772 GCAACGC
64 -CAACGC
1330779 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGACCA
1 GAAATGAAAATCGCAACGCGATAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGACCA
1330843 ACGC
66 ACGC
*
1330847 GAAATGAAAATCGCAATGCGAT
1 GAAATGAAAATCGCAACGCGAT
1330869 TTTGGTTTCG
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
68 26 0.32
69 1 0.01
70 35 0.43
71 20 0.24
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (69 bp):
GAAATGAAAATCGCAACGCGATAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAGACCA
ACGC
Found at i:1331532 original size:41 final size:41
Alignment explanation
Indices: 1331440--1331534 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
1331430 CGCTATGTAA
* * * * ** *
1331440 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
1331481 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
1331523 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
1331535 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:1345869 original size:209 final size:212
Alignment explanation
Indices: 1345509--1345929 Score: 821
Period size: 209 Copynumber: 2.0 Consensus size: 212
1345499 TGAAGAAATT
1345509 GAGGCTCATAATTAGCGATGGACATGTGTCGAGTCGAATAAGTTTTTGACATATTTAAATTTAAT
1 GAGGCTCATAATTAGCGATGGACATGTGTCGAGTCGAATAAGTTTTTGACATATTTAAATTTAAT
1345574 CAAAGTATAATACTTTTTCATTTGTCATTCGATTTGAGGTTAAGAAAAGTTTATCTTAACTCATT
66 CAAAGTATAATACTTTTTCATTTGTCATTCGATTTGAGGTTAAGAAAAGTTTATCTTAACTCATT
1345639 TTTAAGGTAAAAACTCGTATTCGACCTAAT-AAAATAAAAATAT-AA-ATAAAAATTTTATTTTT
131 TTTAAGGTAAAAACTCGTATTCGACCTAATAAAAATAAAAATATAAATATAAAAATTTTATTTTT
1345701 GTTAGATGAAATACATA
196 GTTAGATGAAATACATA
1345718 GAGGCTCATAATTAGCGATGGACATGTGTCGAGTCGAATAAGTTTTTGACATATTTAAATTTAAT
1 GAGGCTCATAATTAGCGATGGACATGTGTCGAGTCGAATAAGTTTTTGACATATTTAAATTTAAT
1345783 CAAAGTATAATACTTTTTCATTTGTCATTCGATTTGAGGTTAAGAAAAGTTTATCTTAACTCATT
66 CAAAGTATAATACTTTTTCATTTGTCATTCGATTTGAGGTTAAGAAAAGTTTATCTTAACTCATT
1345848 TTTAAGGTAAAAACTCGTATTCGACCTAATAAAAATAAAAATATAAATATAAAAATTTTATTTTT
131 TTTAAGGTAAAAACTCGTATTCGACCTAATAAAAATAAAAATATAAATATAAAAATTTTATTTTT
1345913 GTTAGATGAAATACATA
196 GTTAGATGAAATACATA
1345930 TTTAATTAAA
Statistics
Matches: 209, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
209 160 0.77
210 13 0.06
211 2 0.01
212 34 0.16
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (212 bp):
GAGGCTCATAATTAGCGATGGACATGTGTCGAGTCGAATAAGTTTTTGACATATTTAAATTTAAT
CAAAGTATAATACTTTTTCATTTGTCATTCGATTTGAGGTTAAGAAAAGTTTATCTTAACTCATT
TTTAAGGTAAAAACTCGTATTCGACCTAATAAAAATAAAAATATAAATATAAAAATTTTATTTTT
GTTAGATGAAATACATA
Found at i:1354293 original size:21 final size:21
Alignment explanation
Indices: 1354269--1354316 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1354259 ATCAAAAATA
*
1354269 TTATTATTTCTA-TCGGTTTTG
1 TTATTATTTCTACT-GATTTTG
*
1354290 TTATTTTTTTCTACTGATTTTG
1 TTA-TTATTTCTACTGATTTTG
1354312 TTATT
1 TTATT
1354317 GTTAGAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 5 0.22
22 17 0.74
23 1 0.04
ACGTcount: A:0.15, C:0.08, G:0.10, T:0.67
Consensus pattern (21 bp):
TTATTATTTCTACTGATTTTG
Found at i:1355167 original size:14 final size:14
Alignment explanation
Indices: 1355142--1355176 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
1355132 GAAAGCTACA
1355142 GCAACAAGCCTTGAT
1 GCAAC-AGCCTTGAT
1355157 GCAACAGCCTTGAT
1 GCAACAGCCTTGAT
1355171 GCAACA
1 GCAACA
1355177 TCAGTCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.17
Consensus pattern (14 bp):
GCAACAGCCTTGAT
Found at i:1362272 original size:2 final size:2
Alignment explanation
Indices: 1362253--1362300 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
1362243 GAGGCAATAC
* *
1362253 AT AT AC AT AT AC 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
1362295 AT AT AT
1 AT AT AT
1362301 TGCTCAAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1364160 original size:3 final size:3
Alignment explanation
Indices: 1364152--1364241 Score: 155
Period size: 3 Copynumber: 30.3 Consensus size: 3
1364142 GGCCAAAAAC
* *
1364152 TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA T-A TAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1364199 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1364242 TTTTGTATGT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
2 2 0.02
3 80 0.98
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1375606 original size:12 final size:13
Alignment explanation
Indices: 1375589--1375617 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1375579 CGAAATTATA
1375589 ATATTAT-TTTTT
1 ATATTATATTTTT
1375601 ATATTATATTTTT
1 ATATTATATTTTT
1375614 ATAT
1 ATAT
1375618 AAATAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATTATATTTTT
Found at i:1376179 original size:23 final size:25
Alignment explanation
Indices: 1376153--1376198 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
1376143 GAATATTGAT
1376153 ATTAACTTTT-TT-AAAA-AGAAATC
1 ATTAA-TTTTATTCAAAATAGAAATC
1376176 ATTAATTTTATTCAAAATAGAAA
1 ATTAATTTTATTCAAAATAGAAA
1376199 ACGGCCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 4 0.20
25 5 0.25
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (25 bp):
ATTAATTTTATTCAAAATAGAAATC
Found at i:1377738 original size:2 final size:2
Alignment explanation
Indices: 1377679--1377722 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1377669 CATATACAAC
1377679 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
1377721 AT
1 AT
1377723 TATTTTCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1377750 original size:23 final size:23
Alignment explanation
Indices: 1377685--1377750 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
1377675 CAACATATAT
* *
1377685 ATATATATATATATAT-ATATAT-
1 ATATATATACATATATCAT-TTTC
* *
1377707 ATATATATATATATATTATTTTC
1 ATATATATACATATATCATTTTC
*
1377730 ATATATATACATGTATCATTT
1 ATATATATACATATATCATTT
1377751 GAGAGTTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 18 0.47
23 20 0.53
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (23 bp):
ATATATATACATATATCATTTTC
Found at i:1385362 original size:23 final size:25
Alignment explanation
Indices: 1385336--1385381 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
1385326 GAATATTGAT
1385336 ATTAACTTTT-TT-AAAA-AGAAATC
1 ATTAA-TTTTATTCAAAATAGAAATC
1385359 ATTAATTTTATTCAAAATAGAAA
1 ATTAATTTTATTCAAAATAGAAA
1385382 ACGGCCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 4 0.20
25 5 0.25
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (25 bp):
ATTAATTTTATTCAAAATAGAAATC
Found at i:1394791 original size:23 final size:25
Alignment explanation
Indices: 1394765--1394810 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
1394755 GAATATTGAT
1394765 ATTAACTTTT-TT-AAAA-AGAAATC
1 ATTAA-TTTTATTCAAAATAGAAATC
1394788 ATTAATTTTATTCAAAATAGAAA
1 ATTAATTTTATTCAAAATAGAAA
1394811 ACGGCCAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 4 0.20
25 5 0.25
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (25 bp):
ATTAATTTTATTCAAAATAGAAATC
Found at i:1403821 original size:23 final size:22
Alignment explanation
Indices: 1403780--1403822 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1403770 ATCAAGCGAG
*
1403780 TTTAATTAGCTTAATCTTTATC
1 TTTAATTAGCTTAAGCTTTATC
*
1403802 TTTAATTGAGCTTGAGCTTTA
1 TTTAATT-AGCTTAAGCTTTA
1403823 AATGTGAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (22 bp):
TTTAATTAGCTTAAGCTTTATC
Found at i:1415081 original size:29 final size:29
Alignment explanation
Indices: 1415047--1415105 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1415037 CCTAAATTAA
1415047 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
*
1415076 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
1415105 T
1 T
1415106 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:1422441 original size:13 final size:13
Alignment explanation
Indices: 1422416--1422507 Score: 55
Period size: 14 Copynumber: 6.8 Consensus size: 13
1422406 AGAATTTCAG
1422416 ATAAAGATAAAA-A
1 ATAAA-ATAAAATA
1422429 TATAAGAATAAAATA
1 -ATAA-AATAAAATA
1422444 ATAAAAT-AAATA
1 ATAAAATAAAATA
*
1422456 ATTAAATATAAATA
1 ATAAAATA-AAATA
* **
1422470 GTTTAAAATGGAAT-
1 --ATAAAATAAAATA
*
1422484 ATAAGGATAAAATA
1 ATAA-AATAAAATA
1422498 ATAAAATAAA
1 ATAAAATAAA
1422508 TAAATAATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
12 14 0.23
13 13 0.22
14 23 0.38
15 5 0.08
16 5 0.08
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (13 bp):
ATAAAATAAAATA
Found at i:1425863 original size:89 final size:90
Alignment explanation
Indices: 1425750--1425967 Score: 386
Period size: 89 Copynumber: 2.4 Consensus size: 90
1425740 GAAGGACCTA
* * *
1425750 TCCAGAGGTCACAAAGA-CCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
1425814 AGGTCATAAAGATCCTCGGTAACTG
66 AGGTCATAAAGATCCTCGGTAACTG
1425839 TCCAGAGGTC-TAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
1425903 AGGTCATAAAGATCCTCGGTAACTG
66 AGGTCATAAAGATCCTCGGTAACTG
*
1425928 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTC
1 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTC
1425968 CCGAAGAACC
Statistics
Matches: 123, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
88 5 0.04
89 90 0.73
90 28 0.23
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (90 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
AGGTCATAAAGATCCTCGGTAACTG
Found at i:1425960 original size:119 final size:118
Alignment explanation
Indices: 1425750--1425967 Score: 391
Period size: 119 Copynumber: 1.8 Consensus size: 118
1425740 GAAGGACCTA
1425750 TCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGA
1 TCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGA
1425815 GGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCTAAAGATCCTCGGTAACTG
66 GGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCTAAAGATCCTCGGTAACTG
* * *
1425868 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
1 TCCAGAGGTCACAAAGA-CCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
*
1425933 AGGTCATAAAGATCCTCGGTAACTGTCCATAGGTC
65 AGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTC
1425968 CCGAAGAACC
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
118 16 0.17
119 79 0.83
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (118 bp):
TCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGA
GGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCTAAAGATCCTCGGTAACTG
Found at i:1425984 original size:30 final size:30
Alignment explanation
Indices: 1425750--1425967 Score: 386
Period size: 30 Copynumber: 7.3 Consensus size: 30
1425740 GAAGGACCTA
* * *
1425750 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1425779 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1425809 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1425839 TCCAGAGGTC-TAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1425868 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1425898 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1425928 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1425958 TCCATAGGTC
1 TCCAGAGGTC
1425968 CCGAAGAACC
Statistics
Matches: 183, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
29 45 0.25
30 138 0.75
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1427114 original size:21 final size:21
Alignment explanation
Indices: 1427084--1427128 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1427074 ATTCTGTCGT
* *
1427084 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1427105 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1427126 TTG
1 TTG
1427129 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1430833 original size:30 final size:30
Alignment explanation
Indices: 1430777--1430994 Score: 386
Period size: 30 Copynumber: 7.3 Consensus size: 30
1430767 GAAGGACCTA
* * *
1430777 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1430806 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1430836 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1430866 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1430896 TCCAGAGGTCATAAAGATCCTCGGTAA-TG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1430925 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1430955 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
1430985 TCCATAGGTC
1 TCCAGAGGTC
1430995 CCGAAGAACT
Statistics
Matches: 183, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
29 45 0.25
30 138 0.75
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1430934 original size:89 final size:90
Alignment explanation
Indices: 1430777--1430994 Score: 386
Period size: 89 Copynumber: 2.4 Consensus size: 90
1430767 GAAGGACCTA
* * *
1430777 TCCAGAGGTCACAAAGA-CCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
1430841 AGGTCATAAAGATCCTCGGTAACTG
66 AGGTCATAAAGATCCTCGGTAACTG
1430866 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAA-TGTCCAG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
1430930 AGGTCATAAAGATCCTCGGTAACTG
66 AGGTCATAAAGATCCTCGGTAACTG
*
1430955 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTC
1 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTC
1430995 CCGAAGAACT
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
89 87 0.70
90 37 0.30
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (90 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
AGGTCATAAAGATCCTCGGTAACTG
Found at i:1430968 original size:119 final size:119
Alignment explanation
Indices: 1430777--1430994 Score: 384
Period size: 119 Copynumber: 1.8 Consensus size: 119
1430767 GAAGGACCTA
1430777 TCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGA
1 TCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGA
1430842 GGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
66 GGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
* * *
1430896 TCCAGAGGTCATAAAGATCCTCGGTAA-TGTCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
1 TCCAGAGGTCACAAAGA-CCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAG
*
1430960 AGGTCATAAAGATCCTCGGTAACTGTCCATAGGTC
65 AGGTCATAAAGATCCTCGGTAACTGTCCAGAGGTC
1430995 CCGAAGAACT
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
119 86 0.91
120 8 0.09
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.22
Consensus pattern (119 bp):
TCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAACTGTCCAGA
GGTCATAAAGATCCTCGGTAACTGTCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:1431019 original size:30 final size:31
Alignment explanation
Indices: 1430980--1431043 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
1430970 GATCCTCGGT
1430980 AACTGTCCATAGGTCCCG-AAGA-ACTAGGTA
1 AACTGTCCATAGGTCCCGAAAGACA-TAGGTA
* * *
1431010 AACTTTCCATATGTCTCGAAAGACATAGGTA
1 AACTGTCCATAGGTCCCGAAAGACATAGGTA
1431041 AAC
1 AAC
1431044 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 15 0.52
31 13 0.45
32 1 0.03
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAAGACATAGGTA
Found at i:1432060 original size:20 final size:20
Alignment explanation
Indices: 1432031--1432068 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1432021 TTTTCCTTTA
1432031 GGGGGAATCGGTTCCCCTGT
1 GGGGGAATCGGTTCCCCTGT
*
1432051 GGGGGTATCGGTTCCCCT
1 GGGGGAATCGGTTCCCCT
1432069 CTGGCATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.26, G:0.39, T:0.26
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCCTGT
Found at i:1437889 original size:35 final size:35
Alignment explanation
Indices: 1437796--1437896 Score: 114
Period size: 35 Copynumber: 2.9 Consensus size: 35
1437786 AACACAATCA
* **
1437796 TCAATTACATTCTAAACCCCAAAATCCAAAATGTT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
* **
1437831 TTAATTACATTCTAAACATCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATACT
* **
1437866 TCAATTACATGCCCAACCCCAAATT-CAAAAT
1 TCAATTACATTCTAAACCCCAAATTCCAAAAT
1437897 CAAATCTCAA
Statistics
Matches: 54, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
34 6 0.11
35 48 0.89
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.29
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATACT
Found at i:1438347 original size:146 final size:146
Alignment explanation
Indices: 1438054--1438348 Score: 441
Period size: 146 Copynumber: 2.0 Consensus size: 146
1438044 CTCAATTCAA
* **** *
1438054 TTTATAAAATAGTTGACTCGAATTTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATT
1 TTTATAAAATAGTTGACTCAAAAAAATTTCGATTTGAATTTATAAAATTTAAATCAAGTCGAATT
* *
1438119 GAATTGATTTTCGAGTTTCTATTTAAATTTAATTATAATATTTATCATATTATAATATTATTTTA
66 GAATTGATTTTCGAGTTTCTATTTAAATTTAATTATAATATTTATCATACTATAATATTATTTGA
**
1438184 TTCTAATTCAGTTTAG
131 TTCTAATTCAGAATAG
1438200 TTTATAAAATAGTTGACTCAAAAAAATTTCGATTTGAATTTATAAAATTTAAATCAAGTCGAATT
1 TTTATAAAATAGTTGACTCAAAAAAATTTCGATTTGAATTTATAAAATTTAAATCAAGTCGAATT
* * *
1438265 GAATTGAATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATTATACTATAATATTATTT
66 GAATTG-ATTTTCGAGTTTCTATTTAAATTTAATTAT-AATATTTATCATACTATAATATTATTT
1438330 GATTCTAA-TCA-AATAG
129 GATTCTAATTCAGAATAG
1438346 TTT
1 TTT
1438349 TTAACCATAT
Statistics
Matches: 134, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
146 71 0.53
147 31 0.23
148 32 0.24
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.47
Consensus pattern (146 bp):
TTTATAAAATAGTTGACTCAAAAAAATTTCGATTTGAATTTATAAAATTTAAATCAAGTCGAATT
GAATTGATTTTCGAGTTTCTATTTAAATTTAATTATAATATTTATCATACTATAATATTATTTGA
TTCTAATTCAGAATAG
Found at i:1438885 original size:35 final size:36
Alignment explanation
Indices: 1438824--1438904 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 36
1438814 GGGGTTGGTC
* * *
1438824 ATGTAATTGAATTATTTTTGGAATTTGCTGTTTAGA
1 ATGTAATTGAAATATTTTTGAAATTTGCGGTTTAGA
*
1438860 ATGTAATTGAAATA-TTTTGAAATTTGGGGTTTAGA
1 ATGTAATTGAAATATTTTTGAAATTTGCGGTTTAGA
1438895 ATGTAATTGA
1 ATGTAATTGA
1438905 TGGCTGTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 28 0.68
36 13 0.32
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (36 bp):
ATGTAATTGAAATATTTTTGAAATTTGCGGTTTAGA
Found at i:1454234 original size:24 final size:24
Alignment explanation
Indices: 1454202--1454253 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
1454192 GTGTGATGAG
1454202 TGTTCTAAATTGAGAACATTTACT
1 TGTTCTAAATTGAGAACATTTACT
1454226 TGTTCTAAATTGAGAACATTTACT
1 TGTTCTAAATTGAGAACATTTACT
1454250 TGTT
1 TGTT
1454254 AATTATTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.44
Consensus pattern (24 bp):
TGTTCTAAATTGAGAACATTTACT
Found at i:1460919 original size:23 final size:23
Alignment explanation
Indices: 1460893--1460940 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
1460883 ATAAAGTACA
* *
1460893 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
**
1460916 ATAATGTAATAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
1460939 AT
1 AT
1460941 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Done.