Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold228
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: 4123243
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 9 of 27
Found at i:1230638 original size:3 final size:3
Alignment explanation
Indices: 1230630--1230675 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
1230620 CTACCTGCAA
1230630 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1230676 TTTTCGGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1240605 original size:21 final size:21
Alignment explanation
Indices: 1240581--1240639 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1240571 AATTTATGTT
*
1240581 AAATATAATTATAATAGATAA
1 AAATATAATTATAAAAGATAA
** *
1240602 AAATATAAAAATAAAATATAA
1 AAATATAATTATAAAAGATAA
*
1240623 ATATATGAATTATAAAA
1 AAATAT-AATTATAAAA
1240640 TCTAATTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (21 bp):
AAATATAATTATAAAAGATAA
Found at i:1241162 original size:5 final size:5
Alignment explanation
Indices: 1241152--1241184 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
1241142 ATTATCATTA
1241152 TTATT TTATTT TTATT TTATT TTATT TTATT TT
1 TTATT TTA-TT TTATT TTATT TTATT TTATT TT
1241185 TATAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTATT
Found at i:1243443 original size:26 final size:26
Alignment explanation
Indices: 1243414--1243480 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
1243404 TACTCCACTT
*
1243414 ATTAATATT-TATAAATATTTAATTAA
1 ATTAATATTATATAAAT-TTAAATTAA
1243440 ATTAATAATTATATAAATTTAAATTAA
1 ATTAAT-ATTATATAAATTTAAATTAA
*
1243467 ATT-ATATTAAATAA
1 ATTAATATTATATAA
1243481 TTATTATTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.22
26 8 0.22
27 14 0.38
28 7 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTAATATTATATAAATTTAAATTAA
Found at i:1243461 original size:22 final size:21
Alignment explanation
Indices: 1243428--1243478 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1243418 ATATTTATAA
*
1243428 ATATTTAA-TTAAATTAATAATT
1 ATATTAAATTTAAATT-A-AATT
1243450 ATA-TAAATTTAAATTAAATT
1 ATATTAAATTTAAATTAAATT
1243470 ATATTAAAT
1 ATATTAAAT
1243479 AATTATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 7 0.27
21 9 0.35
22 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATATTAAATTTAAATTAAATT
Found at i:1243526 original size:17 final size:18
Alignment explanation
Indices: 1243490--1243527 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
1243480 ATTATTATTT
* *
1243490 ATTTAAATATTTTTTGTA
1 ATTTAAATATTTTATATA
1243508 ATTTAAA-ATTTTATATA
1 ATTTAAATATTTTATATA
1243525 ATT
1 ATT
1243528 GAATTTAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTAAATATTTTATATA
Found at i:1244662 original size:8 final size:8
Alignment explanation
Indices: 1244633--1244687 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
1244623 TTCATTTTAA
1244633 ATATATTT
1 ATATATTT
*
1244641 ATAT-TTA
1 ATATATTT
1244648 ATA-ATTT
1 ATATATTT
1244655 ATATATTT
1 ATATATTT
1244663 ATATTATATT
1 ATA-TAT-TT
1244673 CATATATTT
1 -ATATATTT
*
1244682 TTATAT
1 ATATAT
1244688 ATCATAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
7 10 0.26
8 16 0.41
9 5 0.13
10 5 0.13
11 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
ATATATTT
Found at i:1244697 original size:29 final size:30
Alignment explanation
Indices: 1244633--1244712 Score: 82
Period size: 29 Copynumber: 2.8 Consensus size: 30
1244623 TTCATTTTAA
*
1244633 ATATAT-TTATATT--TAATA-ATTTATAT
1 ATATATATTATATTCATAATATTTTTATAT
*
1244659 ATTTATATTATATTCAT-ATATTTTTATAT
1 ATATATATTATATTCATAATATTTTTATAT
*
1244688 ATCATA-ATTATATTTATAATATTTT
1 AT-ATATATTATATTCATAATATTTT
1244713 AATTTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
26 5 0.11
27 7 0.16
28 3 0.07
29 20 0.45
30 9 0.20
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
ATATATATTATATTCATAATATTTTTATAT
Found at i:1244713 original size:29 final size:29
Alignment explanation
Indices: 1244626--1244713 Score: 82
Period size: 27 Copynumber: 3.2 Consensus size: 29
1244616 CTTGTAATTC
1244626 ATTTTA-A-ATATAT-TTATA-TT-TAAT
1 ATTTTATATATATATATTATATTTATAAT
* * *
1244650 AATTTATATATTTATATTATATTCAT-AT
1 ATTTTATATATATATATTATATTTATAAT
1244678 ATTTT-TATATATCATAATTATATTTATAAT
1 ATTTTATATATAT-AT-ATTATATTTATAAT
1244708 ATTTTA
1 ATTTTA
1244714 ATTTTTTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
24 5 0.10
25 1 0.02
26 5 0.10
27 11 0.22
28 9 0.18
29 11 0.22
30 7 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
ATTTTATATATATATATTATATTTATAAT
Found at i:1245125 original size:3 final size:3
Alignment explanation
Indices: 1245117--1245170 Score: 81
Period size: 3 Copynumber: 17.3 Consensus size: 3
1245107 TTATCAAAAT
*
1245117 ATA ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
1245163 ATCA ATA A
1 AT-A ATA A
1245171 AAAATTAATT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
3 41 0.87
4 6 0.13
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1250239 original size:22 final size:22
Alignment explanation
Indices: 1250202--1250287 Score: 77
Period size: 22 Copynumber: 3.8 Consensus size: 22
1250192 TAATGATAAT
1250202 TTTTTTAATTCT-TTAAATATTA
1 TTTTTTAATT-TATTAAATATTA
* * *
1250224 TTTTTTAATTTGTT-AATGTAAA
1 TTTTTTAATTTATTAAATAT-TA
1250246 TTTTTTAAAGTTTAATTAAATATTA
1 TTTTTT-AA-TTT-ATTAAATATTA
*
1250271 TTTTTTATTTTATTAAA
1 TTTTTTAATTTATTAAA
1250288 AATAATAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.10
22 25 0.48
23 5 0.10
24 4 0.08
25 9 0.17
26 4 0.08
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (22 bp):
TTTTTTAATTTATTAAATATTA
Found at i:1250328 original size:32 final size:33
Alignment explanation
Indices: 1250269--1250340 Score: 94
Period size: 32 Copynumber: 2.2 Consensus size: 33
1250259 AATTAAATAT
1250269 TATTTTTTATTTTATTAAAAATAATAATAAAAAA
1 TATTTTTTATTTTA-TAAAAATAATAATAAAAAA
**
1250303 TATTTTTTATCTTTA-AAAAAT-ATAATAATTAA
1 TATTTTTTAT-TTTATAAAAATAATAATAAAAAA
1250335 TATTTT
1 TATTTT
1250341 AATTTTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 15 0.43
33 6 0.17
34 10 0.29
35 4 0.11
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (33 bp):
TATTTTTTATTTTATAAAAATAATAATAAAAAA
Found at i:1250442 original size:132 final size:132
Alignment explanation
Indices: 1250304--1250557 Score: 377
Period size: 132 Copynumber: 1.9 Consensus size: 132
1250294 AATAAAAAAT
* * *
1250304 ATTTTTTATCTTTA-AAAAATATAATAATTAATATTTTAATTTTTTGATATAAATTTTTTAAACT
1 ATTTTTTATCTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATAT-AATTTTTTAAACT
* * *
1250368 TAATTAAATATTATTTTTTATTTTATT-AAAAATTATAATAAAAAACTTTTTTTATTTTTTATTT
65 TAATTAAATATTA-TTTTTAATTTATTAAAAAATAATAATAAAAAACCTTTTTTATTTTTTATTT
1250432 TAAA
129 TAAA
* * *
1250436 ATTTTTTGTTTTTATAAAAACATAATAATTGATATTTTAATTTGTTAATATAATTTTTTAAACTT
1 ATTTTTTATCTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATATAATTTTTTAAACTT
* *
1250501 TATTAAATATTATTTTTAATTTATTAAAAAATAATAATAATAAACCTTTTTTATTTT
66 AATTAAATATTATTTTTAATTTATTAAAAAATAATAATAAAAAACCTTTTTTATTTT
1250558 AAAAAATTAA
Statistics
Matches: 109, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
131 12 0.11
132 65 0.60
133 32 0.29
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.55
Consensus pattern (132 bp):
ATTTTTTATCTTTATAAAAACATAATAATTAATATTTTAATTTGTTAATATAATTTTTTAAACTT
AATTAAATATTATTTTTAATTTATTAAAAAATAATAATAAAAAACCTTTTTTATTTTTTATTTTA
AA
Found at i:1250496 original size:21 final size:21
Alignment explanation
Indices: 1250470--1250533 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
1250460 ATAATTGATA
*
1250470 TTTTAATTTGTTAATATAAT-T
1 TTTTAATTTATTAA-ATAATAT
*
1250491 TTTTAAACTTTATTAAATATTAT
1 TTTT-AA-TTTATTAAATAATAT
*
1250514 TTTTAATTTATTAAAAAATA
1 TTTTAATTTATTAAATAATA
1250534 ATAATAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 16 0.44
22 8 0.22
23 12 0.33
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTAATTTATTAAATAATAT
Found at i:1250520 original size:44 final size:44
Alignment explanation
Indices: 1250470--1250618 Score: 118
Period size: 54 Copynumber: 3.1 Consensus size: 44
1250460 ATAATTGATA
*
1250470 TTTTAATTTGTTAATATAATTTTTTAAACTTTATTAAATATTAT
1 TTTTAATTTATTAATATAATTTTTTAAACTTTATTAAATATTAT
* * ** *
1250514 TTTTAATTTATTAAAAAATAATAATAATAAACCTTTTTTATTTTAAAAAATTAAT
1 TTTTAATTTATT--AATATAAT-TTTTTAAA-C---TTTA--TT-AAATATT-AT
*
1250569 ATTTTAATTTATTAATATATATTTTTTAAACTTAATTAAATATTAT
1 -TTTTAATTTATTAATATA-ATTTTTTAAACTTTATTAAATATTAT
1250615 TTTT
1 TTTT
1250619 TAAAAAATAA
Statistics
Matches: 80, Mismatches: 12, Indels: 25
0.68 0.10 0.21
Matches are distributed among these distances:
44 11 0.14
45 4 0.05
46 9 0.11
47 11 0.14
48 3 0.04
50 3 0.04
51 4 0.05
53 3 0.04
54 16 0.20
55 4 0.05
56 12 0.15
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (44 bp):
TTTTAATTTATTAATATAATTTTTTAAACTTTATTAAATATTAT
Found at i:1250629 original size:25 final size:25
Alignment explanation
Indices: 1250582--1250629 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1250572 TTAATTTATT
**
1250582 AATATATATTTTTTAAACTTAATTA
1 AATATATATTTTTTAAAAATAATTA
1250607 AATAT-TATTTTTTAAAAAATAAT
1 AATATATATTTTTT-AAAAATAAT
1250630 AATTAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
AATATATATTTTTTAAAAATAATTA
Found at i:1250819 original size:3 final size:3
Alignment explanation
Indices: 1250805--1250838 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1250795 CTAACTGCAA
*
1250805 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1250839 TTTTCAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1255934 original size:24 final size:23
Alignment explanation
Indices: 1255886--1255934 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
1255876 TTTGAAGATA
**
1255886 AAGATAAAAAATTAATTTGTGAC
1 AAGATAAAAAATTAATTTGCAAC
1255909 AAGATAAAAAAATTAATCTT-CAAC
1 AAGAT-AAAAAATTAAT-TTGCAAC
1255933 AA
1 AA
1255935 CTTATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 5 0.23
24 15 0.68
25 2 0.09
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.27
Consensus pattern (23 bp):
AAGATAAAAAATTAATTTGCAAC
Found at i:1256247 original size:15 final size:17
Alignment explanation
Indices: 1256208--1256249 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
1256198 AAAATGACTT
1256208 AAAATTAAAATATTTCA
1 AAAATTAAAATATTTCA
*
1256225 AACA-TAAAA-ATTT-A
1 AAAATTAAAATATTTCA
1256239 AAAATTAAAAT
1 AAAATTAAAAT
1256250 GACTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
14 4 0.19
15 9 0.43
16 5 0.24
17 3 0.14
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATTAAAATATTTCA
Found at i:1257041 original size:2 final size:2
Alignment explanation
Indices: 1257034--1257076 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1257024 AAAGAACAAA
1257034 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
1257076 A
1 A
1257077 CACTGAATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1257122 original size:17 final size:17
Alignment explanation
Indices: 1257100--1257134 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1257090 AAATGTATAT
1257100 ATAAGGTTGTCACTTAC
1 ATAAGGTTGTCACTTAC
1257117 ATAAGGTTGTCACTTAC
1 ATAAGGTTGTCACTTAC
1257134 A
1 A
1257135 AAAGAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (17 bp):
ATAAGGTTGTCACTTAC
Found at i:1257151 original size:2 final size:2
Alignment explanation
Indices: 1257144--1257172 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1257134 AAAAGAACAA
1257144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1257173 CTGAATTGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1257781 original size:2 final size:2
Alignment explanation
Indices: 1257770--1257818 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
1257760 CTAATTTTTT
* * *
1257770 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1257812 TA TA TA T
1 TA TA TA T
1257819 TTAGATAGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1259417 original size:33 final size:33
Alignment explanation
Indices: 1259336--1259420 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 33
1259326 TGGTAAAAAC
*
1259336 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGAAACCTACCAAAT
* *
1259369 CTCCCATTTAGTCAACAATGGTAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-AAACCTACCAAAT
1259403 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
1259421 TCTCCCACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
33 16 0.36
34 25 0.56
35 4 0.09
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGAAACCTACCAAAT
Found at i:1263911 original size:33 final size:33
Alignment explanation
Indices: 1263830--1263912 Score: 114
Period size: 34 Copynumber: 2.5 Consensus size: 33
1263820 TGGTAAAAAC
*
1263830 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGAAACCTACCAAAT
* *
1263863 CTCCCATTTAGTCAACAATGGTAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-AAACCTACCAAAT
1263897 CACCATTTAATCAACA
1 CACCATTTAATCAACA
1263913 CTGTGGAGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
33 14 0.33
34 25 0.58
35 4 0.09
ACGTcount: A:0.41, C:0.30, G:0.06, T:0.23
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGAAACCTACCAAAT
Found at i:1265430 original size:27 final size:27
Alignment explanation
Indices: 1265389--1265443 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1265379 ACTTTGGACA
*
1265389 TGAAACTTGGAACTTCAAATTTAAGATT
1 TGAAACATGGAACTTCAAATTTAA-ATT
* *
1265417 TGAAACAT-GAACTTGAGATTTAAATT
1 TGAAACATGGAACTTCAAATTTAAATT
1265443 T
1 T
1265444 TTATTCTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.17
27 13 0.54
28 7 0.29
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (27 bp):
TGAAACATGGAACTTCAAATTTAAATT
Found at i:1265468 original size:21 final size:20
Alignment explanation
Indices: 1265444--1265529 Score: 77
Period size: 21 Copynumber: 4.2 Consensus size: 20
1265434 ATTTAAATTT
* *
1265444 TTATTCTTTTAAGATATATAA
1 TTATTATTTTAAAATA-ATAA
**
1265465 TTATTATTTTAAAATAATTT
1 TTATTATTTTAAAATAATAA
1265485 TTATT-TGTTTAAGAA-ATATAA
1 TTATTAT-TTTAA-AATA-ATAA
*
1265506 TTATTATTTTAAAATAATTA
1 TTATTATTTTAAAATAATAA
1265526 TTAT
1 TTAT
1265530 GCTTTAAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 22 0.42
21 29 0.55
22 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (20 bp):
TTATTATTTTAAAATAATAA
Found at i:1265483 original size:17 final size:17
Alignment explanation
Indices: 1265461--1265529 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 17
1265451 TTTAAGATAT
1265461 ATAATTATTATTTTAAA
1 ATAATTATTATTTTAAA
*
1265478 ATAATTTTTATTTGTTTAAGAAA
1 ATAATTATTA--T-TTT---AAA
1265501 TATAATTATTATTTTAAA
1 -ATAATTATTATTTTAAA
1265519 ATAATTATTAT
1 ATAATTATTAT
1265530 GCTTTAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
17 20 0.47
18 3 0.07
19 1 0.02
20 3 0.07
21 3 0.07
22 1 0.02
23 3 0.07
24 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
ATAATTATTATTTTAAA
Found at i:1265487 original size:41 final size:41
Alignment explanation
Indices: 1265439--1265534 Score: 149
Period size: 41 Copynumber: 2.3 Consensus size: 41
1265429 TTGAGATTTA
*
1265439 AATTTTTATTCTTTTAAGATATATAATTATTATTTTAAAAT
1 AATTTTTATTCTTTTAAGAAATATAATTATTATTTTAAAAT
1265480 AATTTTTATT-TGTTTAAGAAATATAATTATTATTTTAAAAT
1 AATTTTTATTCT-TTTAAGAAATATAATTATTATTTTAAAAT
* *
1265521 AATTATTATGCTTT
1 AATTTTTATTCTTT
1265535 AAATATGTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
40 1 0.02
41 48 0.96
42 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (41 bp):
AATTTTTATTCTTTTAAGAAATATAATTATTATTTTAAAAT
Found at i:1266093 original size:2 final size:2
Alignment explanation
Indices: 1266081--1266121 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
1266071 GGACCATTTT
* *
1266081 TA TA T- TA TA TA TA TA TA TA TG TA TA TA TA TA TA TT 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
1266122 CACCAATATG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1266730 original size:28 final size:28
Alignment explanation
Indices: 1266699--1266762 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
1266689 CATTTTTTAC
1266699 ATACAAA-AATAACCACCATATTTGACAA
1 ATACAAAGAA-AACCACCATATTTGACAA
*
1266727 ATACAAAGGAAACCACCATATTTGACAA
1 ATACAAAGAAAACCACCATATTTGACAA
1266755 ATACAAAG
1 ATACAAAG
1266763 GGTGGCATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.53, C:0.20, G:0.08, T:0.19
Consensus pattern (28 bp):
ATACAAAGAAAACCACCATATTTGACAA
Found at i:1266763 original size:28 final size:28
Alignment explanation
Indices: 1266709--1266763 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1266699 ATACAAAAAT
1266709 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
1266737 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
1266764 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:1271264 original size:24 final size:24
Alignment explanation
Indices: 1271236--1271281 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1271226 AATAAAAATT
1271236 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* * *
1271260 AGCCACCATTTTTTACATACAA
1 AGCCACCAATTTTGACAAACAA
1271282 AAATAACCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.28, G:0.07, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:1271307 original size:28 final size:28
Alignment explanation
Indices: 1271276--1271338 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 28
1271266 CATTTTTTAC
1271276 ATACAAA-AATAACCACCATATTTGACAA
1 ATACAAATAA-AACCACCATATTTGACAA
*
1271304 ATACAAATGAAACCACCATATTTGACAA
1 ATACAAATAAAACCACCATATTTGACAA
1271332 ATACAAA
1 ATACAAA
1271339 GGGTGGCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 32 0.97
29 1 0.03
ACGTcount: A:0.54, C:0.21, G:0.05, T:0.21
Consensus pattern (28 bp):
ATACAAATAAAACCACCATATTTGACAA
Found at i:1278620 original size:20 final size:21
Alignment explanation
Indices: 1278587--1278637 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
1278577 ATTTTTTAAG
* *
1278587 AAAATAAATGAATA-ATTTTA
1 AAAATAAGTAAATAGATTTTA
*
1278607 AAAATAAGTAAATAGTTTTTA
1 AAAATAAGTAAATAGATTTTA
*
1278628 AATATAAGTA
1 AAAATAAGTA
1278638 TTAGTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (21 bp):
AAAATAAGTAAATAGATTTTA
Found at i:1278645 original size:19 final size:21
Alignment explanation
Indices: 1278602--1278647 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1278592 AAATGAATAA
1278602 TTTTAAAAATAAGTAAATAGT
1 TTTTAAAAATAAGTAAATAGT
* *
1278623 TTTTAAATATAAGT-ATTAGT
1 TTTTAAAAATAAGTAAATAGT
1278643 TTTTA
1 TTTTA
1278648 TTAAGAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (21 bp):
TTTTAAAAATAAGTAAATAGT
Found at i:1281018 original size:164 final size:163
Alignment explanation
Indices: 1280794--1281093 Score: 403
Period size: 164 Copynumber: 1.8 Consensus size: 163
1280784 GAAATATATA
* *
1280794 AAAATGATTAATTTTATTTTAAAGGGTTAGATTGATTTTATTTTGATTATTATTTATTTAATTCT
1 AAAATGATTAACTTTATTTTAAAGGGTTAGATTGATTTTATTTT-ATCATTATTTATTTAATTCT
* * *
1280859 T-AAAAAAATCATTTCGTACCCGACAATAAATGGAGATAATACGAAAAA-TTTT-AAATATTTCT
65 TAAAAAAAATCATTACATACCCGACAA-AAATCGAGATAATAC-AAAAAGTTTTAAAATATTT-T
1280921 ATACCCTTAAGGATGACTATATGAATACTAGAAGTCT
127 ATACCCTTAAGGATGACTATATGAATACTAGAAGTCT
* *
1280958 AAAATTATTAACTTTATTTT-AAGAGGTTGGATTGATTTTATGCTTT-TCATTATTTATTTAATT
1 AAAATGATTAACTTTATTTTAAAG-GGTTAGATTGATTTTAT--TTTATCATTATTTATTTAATT
** *
1281021 CTTAAAAAAAATTGTTACATACCTGACAAAAATCGAGATAATACAAAAAGTTTTAAAATATTTTA
63 CTTAAAAAAAATCATTACATACCCGACAAAAATCGAGATAATACAAAAAGTTTTAAAATATTTTA
*
1281086 TACTCTTA
128 TACCCTTA
1281094 TAGAAGGCCA
Statistics
Matches: 119, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
163 8 0.07
164 80 0.67
165 28 0.24
166 3 0.03
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.41
Consensus pattern (163 bp):
AAAATGATTAACTTTATTTTAAAGGGTTAGATTGATTTTATTTTATCATTATTTATTTAATTCTT
AAAAAAAATCATTACATACCCGACAAAAATCGAGATAATACAAAAAGTTTTAAAATATTTTATAC
CCTTAAGGATGACTATATGAATACTAGAAGTCT
Found at i:1282211 original size:12 final size:11
Alignment explanation
Indices: 1282182--1282232 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
1282172 TAAAGCTTGG
1282182 TTTTTC-TATT
1 TTTTTCTTATT
1282192 TTTTTCTTATT
1 TTTTTCTTATT
*
1282203 TTCTTTCTTTCTT
1 TT-TTTC-TTATT
* *
1282216 TTTTTTTTCTT
1 TTTTTCTTATT
1282227 TTTTTC
1 TTTTTC
1282233 CCTCTATTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
10 6 0.17
11 16 0.46
12 7 0.20
13 6 0.17
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTATT
Found at i:1283178 original size:17 final size:17
Alignment explanation
Indices: 1283158--1283190 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1283148 AATTTCGTAA
1283158 TTCAA-AAATAAATGAAT
1 TTCAAGAAA-AAATGAAT
1283175 TTCAAGAAAAAATGAA
1 TTCAAGAAAAAATGAA
1283191 AAATGAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.61, C:0.06, G:0.09, T:0.24
Consensus pattern (17 bp):
TTCAAGAAAAAATGAAT
Found at i:1283884 original size:32 final size:32
Alignment explanation
Indices: 1283829--1283961 Score: 239
Period size: 32 Copynumber: 4.1 Consensus size: 32
1283819 TTCAACGATT
*
1283829 TGTATCGATACATAAAGTGTTGTATCGATAGAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1283862 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1283894 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1283926 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1283958 TGTA
1 TGTA
1283962 AGCTACCGCC
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
32 85 0.87
33 13 0.13
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1283886 original size:19 final size:18
Alignment explanation
Indices: 1283827--1283956 Score: 101
Period size: 19 Copynumber: 7.8 Consensus size: 18
1283817 ATTTCAACGA
1283827 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
*
1283846 TGTTGTATCGAT--AGAA-
1 T-TTGTATCGATACATAAG
1283862 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1283878 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1283894 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1283910 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1283926 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1283942 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1283957 ATGTAAGCTA
Statistics
Matches: 90, Mismatches: 2, Indels: 38
0.69 0.02 0.29
Matches are distributed among these distances:
13 31 0.34
15 7 0.08
17 6 0.07
18 1 0.01
19 35 0.39
20 10 0.11
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1283899 original size:13 final size:13
Alignment explanation
Indices: 1283881--1283937 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1283871 ACATAAGTGT
1283881 TGTATCGATACAA
1 TGTATCGATACAA
1283894 TGTATCGATACATAA
1 TGTATCGATAC--AA
1283909 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1283926 TGTATCGATACA
1 TGTATCGATACA
1283938 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1284017 original size:13 final size:13
Alignment explanation
Indices: 1283999--1284023 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1283989 ATTACTCAAA
1283999 TGTATCGATACAT
1 TGTATCGATACAT
1284012 TGTATCGATACA
1 TGTATCGATACA
1284024 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1284153 original size:52 final size:52
Alignment explanation
Indices: 1284032--1284160 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1284022 CACTGATCTT
** *
1284032 TGTATCGATACATGCAGAAAAATTTGCCCAGATATATCGATACACTATAAAC
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
* *
1284084 TGTATCGATATATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
1284136 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1284161 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCGATACACTATAAAA
Found at i:1288703 original size:30 final size:30
Alignment explanation
Indices: 1288669--1288737 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
1288659 TTATTAAATT
*
1288669 AAATTAAACCAATACAAAATCTACACTTTC
1 AAATTAAACCAATACAAAATCAACACTTTC
*
1288699 AAATTAAACCAATACAAATTCAACACTTTC
1 AAATTAAACCAATACAAAATCAACACTTTC
1288729 AAATTAAAC
1 AAATTAAAC
1288738 TTAACTAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (30 bp):
AAATTAAACCAATACAAAATCAACACTTTC
Found at i:1288731 original size:15 final size:15
Alignment explanation
Indices: 1288691--1288737 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1288681 TACAAAATCT
1288691 ACACTTTCAAATTAA
1 ACACTTTCAAATTAA
* * *
1288706 AC-CAATACAAATTCA
1 ACAC-TTTCAAATTAA
1288721 ACACTTTCAAATTAA
1 ACACTTTCAAATTAA
1288736 AC
1 AC
1288738 TTAACTAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (15 bp):
ACACTTTCAAATTAA
Found at i:1290783 original size:20 final size:20
Alignment explanation
Indices: 1290732--1290824 Score: 91
Period size: 20 Copynumber: 4.6 Consensus size: 20
1290722 ACCCTTAAAA
* *
1290732 GTATCGATACACAATT-CAAA
1 GTATCGATACA-TATTGCAAT
1290752 GTATCGATACATATTGCAAT
1 GTATCGATACATATTGCAAT
***
1290772 GTATCGATACATGA-AAAAGAT
1 GTATCGATACAT-ATTGCA-AT
*
1290793 GTATCGATACATGTTGCAAT
1 GTATCGATACATATTGCAAT
1290813 GTATCGATACAT
1 GTATCGATACAT
1290825 GAAAAAGATG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.05
20 41 0.68
21 16 0.27
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACATATTGCAAT
Found at i:1290796 original size:21 final size:21
Alignment explanation
Indices: 1290770--1290845 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1290760 ACATATTGCA
1290770 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1290791 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1290811 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1290832 ATGTATCGATACAT
1 ATGTATCGATACAT
1290846 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1290803 original size:41 final size:41
Alignment explanation
Indices: 1290752--1290845 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1290742 ACAATTCAAA
1290752 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
*
1290793 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
1290834 GTATCGATACAT
1 GTATCGATACAT
1290846 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
Found at i:1290825 original size:20 final size:20
Alignment explanation
Indices: 1290752--1290825 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1290742 ACAATTCAAA
*
1290752 GTATCGATACATATTGCAAT
1 GTATCGATACATGTTGCAAT
****
1290772 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1290793 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1290813 GTATCGATACATG
1 GTATCGATACATG
1290826 AAAAAGATGT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1290902 original size:13 final size:13
Alignment explanation
Indices: 1290884--1290909 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1290874 TACAGAAAGT
1290884 ATGTATCGATACA
1 ATGTATCGATACA
1290897 ATGTATCGATACA
1 ATGTATCGATACA
1290910 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1290907 original size:32 final size:33
Alignment explanation
Indices: 1290866--1290929 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1290856 TAGCCAAACT
* **
1290866 TGTATCGATACAGAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1290898 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1290930 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1293156 original size:21 final size:21
Alignment explanation
Indices: 1293123--1293167 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1293113 TTGCAAGTTG
*
1293123 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1293145 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1293165 AAA
1 AAA
1293168 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1297085 original size:20 final size:20
Alignment explanation
Indices: 1297006--1297085 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1296996 AATGTCCAAA
*
1297006 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1297026 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1297051 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1297071 TTGTATCGATACATT
1 ATGTATCGATACATT
1297086 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1297089 original size:13 final size:13
Alignment explanation
Indices: 1297071--1297135 Score: 112
Period size: 13 Copynumber: 5.0 Consensus size: 13
1297061 ACATTTTTCT
1297071 TTGTATCGATACA
1 TTGTATCGATACA
1297084 TTGTATCGATACA
1 TTGTATCGATACA
*
1297097 CTGTATCGATACA
1 TTGTATCGATACA
1297110 TTGTATCGATACA
1 TTGTATCGATACA
*
1297123 CTGTATCGATACA
1 TTGTATCGATACA
1297136 GGGTGATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.35
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1297108 original size:26 final size:26
Alignment explanation
Indices: 1297072--1297135 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
1297062 CATTTTTCTT
1297072 TGTATCGATACATTGTATCGATACAC
1 TGTATCGATACATTGTATCGATACAC
1297098 TGTATCGATACATTGTATCGATACAC
1 TGTATCGATACATTGTATCGATACAC
1297124 TGTATCGATACA
1 TGTATCGATACA
1297136 GGGTGATTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (26 bp):
TGTATCGATACATTGTATCGATACAC
Found at i:1299618 original size:20 final size:20
Alignment explanation
Indices: 1299567--1299659 Score: 91
Period size: 20 Copynumber: 4.6 Consensus size: 20
1299557 ACCCTTAAAA
* *
1299567 GTATCGATACACAATT-CAAA
1 GTATCGATACA-TATTGCAAT
1299587 GTATCGATACATATTGCAAT
1 GTATCGATACATATTGCAAT
***
1299607 GTATCGATACATGA-AAAAGAT
1 GTATCGATACAT-ATTGCA-AT
*
1299628 GTATCGATACATGTTGCAAT
1 GTATCGATACATATTGCAAT
1299648 GTATCGATACAT
1 GTATCGATACAT
1299660 GAAAAAGATG
Statistics
Matches: 60, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.05
20 41 0.68
21 16 0.27
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACATATTGCAAT
Found at i:1299631 original size:21 final size:21
Alignment explanation
Indices: 1299605--1299680 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1299595 ACATATTGCA
1299605 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
1299626 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
1299646 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
1299667 ATGTATCGATACAT
1 ATGTATCGATACAT
1299681 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:1299638 original size:41 final size:41
Alignment explanation
Indices: 1299587--1299680 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1299577 ACAATTCAAA
1299587 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
*
1299628 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
1299669 GTATCGATACAT
1 GTATCGATACAT
1299681 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATATTGCAATGTATCGATACATGAAAAAGAT
Found at i:1299660 original size:20 final size:20
Alignment explanation
Indices: 1299587--1299660 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1299577 ACAATTCAAA
*
1299587 GTATCGATACATATTGCAAT
1 GTATCGATACATGTTGCAAT
****
1299607 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
1299628 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1299648 GTATCGATACATG
1 GTATCGATACATG
1299661 AAAAAGATGT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1299737 original size:13 final size:13
Alignment explanation
Indices: 1299719--1299744 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1299709 TACAGCAAGT
1299719 ATGTATCGATACA
1 ATGTATCGATACA
1299732 ATGTATCGATACA
1 ATGTATCGATACA
1299745 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1302311 original size:25 final size:23
Alignment explanation
Indices: 1302246--1302314 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 23
1302236 AAAACTAATA
1302246 AAATGATTTTTTA-TATTAATATTT
1 AAAT-ATTTTTTATTATTAA-ATTT
* *
1302270 ATATA-TTTTTATAATTAAATTAT
1 AAATATTTTTTATTATTAAATT-T
1302293 GAAATATTTTTTATTATTAAAT
1 -AAATATTTTTTATTATTAAAT
1302315 AATAATTCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
22 9 0.24
23 7 0.19
24 7 0.19
25 14 0.38
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (23 bp):
AAATATTTTTTATTATTAAATTT
Found at i:1304628 original size:18 final size:19
Alignment explanation
Indices: 1304607--1304649 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1304597 ATTATATAAA
1304607 TTAATTAAATTA-AAATAT
1 TTAATTAAATTATAAATAT
**
1304625 TTAAAAAAATTATAAATAT
1 TTAATTAAATTATAAATAT
1304644 TTAATT
1 TTAATT
1304650 TACTGTCATA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAATTAAATTATAAATAT
Found at i:1310996 original size:5 final size:5
Alignment explanation
Indices: 1310986--1311032 Score: 58
Period size: 5 Copynumber: 9.0 Consensus size: 5
1310976 TCAAAAAAGA
**
1310986 ATTTT ATTTT ATTTT ATTTT ATTTT ACTTTAT AAATT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT A-TTT-T ATTTT ATTTT ATTTT
1311033 TAAGTGATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 30 0.83
6 4 0.11
7 2 0.06
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (5 bp):
ATTTT
Found at i:1312927 original size:13 final size:13
Alignment explanation
Indices: 1312909--1312934 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1312899 ACATACAAGA
1312909 TGTATCGATACAT
1 TGTATCGATACAT
1312922 TGTATCGATACAT
1 TGTATCGATACAT
1312935 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1312950 original size:33 final size:32
Alignment explanation
Indices: 1312889--1312955 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
1312879 CCTTAACTGT
1312889 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
1312921 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1312954 TT
1 TT
1312956 AGCTTGTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:1313010 original size:20 final size:20
Alignment explanation
Indices: 1312920--1313018 Score: 69
Period size: 20 Copynumber: 4.8 Consensus size: 20
1312910 GTATCGATAC
*
1312920 ATTGTATCGATACATGACCAA
1 ATTGTATCGATACAT-TCCAA
*
1312941 A-TGTATCGATACATT--AG
1 ATTGTATCGATACATTCCAA
* * * *
1312958 CTTGTAACGGCTACATTTTCAA
1 ATTGTATC-GATACA-TTCCAA
1312980 ATGCATGTATCGATACATTCCAA
1 AT---TGTATCGATACATTCCAA
1313003 ATTGTATCGATACATT
1 ATTGTATCGATACATT
1313019 GACACGGATT
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
17 1 0.02
18 5 0.08
19 5 0.08
20 29 0.48
21 1 0.02
22 2 0.03
23 7 0.12
24 5 0.08
25 5 0.08
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.34
Consensus pattern (20 bp):
ATTGTATCGATACATTCCAA
Found at i:1317895 original size:20 final size:20
Alignment explanation
Indices: 1317870--1317922 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
1317860 AATTCTAGAT
1317870 TGTATCGATACATGTTACAA
1 TGTATCGATACATGTTACAA
1317890 TGTATCGATACATGTTACAA
1 TGTATCGATACATGTTACAA
1317910 TGTATCGATACAT
1 TGTATCGATACAT
1317923 CTGGAAAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (20 bp):
TGTATCGATACATGTTACAA
Found at i:1319891 original size:185 final size:185
Alignment explanation
Indices: 1319579--1319952 Score: 748
Period size: 185 Copynumber: 2.0 Consensus size: 185
1319569 TAGGATTAGC
1319579 TTTCCTAGGAATTATTATGTTTGCTTGACTTCGTGTTTTTTTTTATCGTTTTTATTGTACTTTGA
1 TTTCCTAGGAATTATTATGTTTGCTTGACTTCGTGTTTTTTTTTATCGTTTTTATTGTACTTTGA
1319644 CTTTTTGATATATCATATGATGTTTGTTTCCATTATTGTCTTTTATGAAATATTTGCTTTATGAA
66 CTTTTTGATATATCATATGATGTTTGTTTCCATTATTGTCTTTTATGAAATATTTGCTTTATGAA
1319709 AATGATTGATTATCTTTTTTGTTCGCATTTTGCTATAACAAAAAGGGGGAGAGAA
131 AATGATTGATTATCTTTTTTGTTCGCATTTTGCTATAACAAAAAGGGGGAGAGAA
1319764 TTTCCTAGGAATTATTATGTTTGCTTGACTTCGTGTTTTTTTTTATCGTTTTTATTGTACTTTGA
1 TTTCCTAGGAATTATTATGTTTGCTTGACTTCGTGTTTTTTTTTATCGTTTTTATTGTACTTTGA
1319829 CTTTTTGATATATCATATGATGTTTGTTTCCATTATTGTCTTTTATGAAATATTTGCTTTATGAA
66 CTTTTTGATATATCATATGATGTTTGTTTCCATTATTGTCTTTTATGAAATATTTGCTTTATGAA
1319894 AATGATTGATTATCTTTTTTGTTCGCATTTTGCTATAACAAAAAGGGGGAGAGAA
131 AATGATTGATTATCTTTTTTGTTCGCATTTTGCTATAACAAAAAGGGGGAGAGAA
1319949 TTTC
1 TTTC
1319953 TGTAAATAAA
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
185 189 1.00
ACGTcount: A:0.24, C:0.10, G:0.16, T:0.51
Consensus pattern (185 bp):
TTTCCTAGGAATTATTATGTTTGCTTGACTTCGTGTTTTTTTTTATCGTTTTTATTGTACTTTGA
CTTTTTGATATATCATATGATGTTTGTTTCCATTATTGTCTTTTATGAAATATTTGCTTTATGAA
AATGATTGATTATCTTTTTTGTTCGCATTTTGCTATAACAAAAAGGGGGAGAGAA
Found at i:1320741 original size:19 final size:19
Alignment explanation
Indices: 1320717--1320780 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
1320707 CTTAACTGTT
1320717 TGTATCGATACATACAAGA
1 TGTATCGATACATACAAGA
1320736 TGTATCGATACAT------
1 TGTATCGATACATACAAGA
1320749 TGTATCGATACATACAAGA
1 TGTATCGATACATACAAGA
1320768 TGTATCGATACAT
1 TGTATCGATACAT
1320781 TGTATCGATA
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 13 0.33
19 26 0.67
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (19 bp):
TGTATCGATACATACAAGA
Found at i:1320754 original size:13 final size:13
Alignment explanation
Indices: 1320736--1320793 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
1320726 ACATACAAGA
1320736 TGTATCGATACAT
1 TGTATCGATACAT
1320749 TGTATCGATACAT
1 TGTATCGATACAT
1320762 ACAAGATGTATCGATACAT
1 ------TGTATCGATACAT
1320781 TGTATCGATACAT
1 TGTATCGATACAT
1320794 GACCAAATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 26 0.67
19 13 0.33
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1320757 original size:32 final size:32
Alignment explanation
Indices: 1320716--1320815 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
1320706 CCTTAACTGT
1320716 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
1320748 TTGTATCGATACATACAAGATGTATCGATACA
1 TTGTATCGATACATACAAGATGTATCGATACA
1320780 TTGTATCGATACATGACCAA-ATGTATCGATACA
1 TTGTATCGATACAT-A-CAAGATGTATCGATACA
1320813 TTG
1 TTG
1320816 GCTTGTAATG
Statistics
Matches: 66, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
32 46 0.70
33 17 0.26
34 3 0.05
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACATACAAGATGTATCGATACA
Found at i:1321872 original size:22 final size:24
Alignment explanation
Indices: 1321847--1321894 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1321837 TTTTATTATG
*
1321847 ATTTTTA-TG-TAAAAATGAAATA
1 ATTTTTATTGATAAAAATAAAATA
1321869 ATTTTTATTTGATAAAAATAAAATA
1 ATTTTTA-TTGATAAAAATAAAATA
1321894 A
1 A
1321895 GTTTATTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 7 0.32
24 2 0.09
25 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (24 bp):
ATTTTTATTGATAAAAATAAAATA
Found at i:1321981 original size:26 final size:27
Alignment explanation
Indices: 1321939--1321989 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1321929 TTTTATTATA
*
1321939 TAATTACTATAATTAATTAAA-AATAAG
1 TAATTACTATAAATAA-TAAATAATAAG
1321966 TAATTA-TATAAATAATAAATAATA
1 TAATTACTATAAATAATAAATAATA
1321990 TAAAATATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 4 0.18
26 12 0.55
27 6 0.27
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (27 bp):
TAATTACTATAAATAATAAATAATAAG
Found at i:1321999 original size:16 final size:16
Alignment explanation
Indices: 1321946--1322006 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 16
1321936 ATATAATTAC
*
1321946 TATAATTAAT-TAAAA
1 TATAAATAATATAAAA
*
1321961 -ATAAGTAATTATATAAA
1 TATAAATAA-TATA-AAA
1321978 TAATAAATAATATAAAA
1 T-ATAAATAATATAAAA
1321995 TATAAA-AATATA
1 TATAAATAATATA
1322007 TATTTTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 7 0.18
15 7 0.18
16 7 0.18
17 7 0.18
18 4 0.10
19 7 0.18
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
TATAAATAATATAAAA
Found at i:1323370 original size:87 final size:88
Alignment explanation
Indices: 1323221--1323446 Score: 266
Period size: 87 Copynumber: 2.6 Consensus size: 88
1323211 TAAAATTTTT
* * * * *
1323221 GAAATTATTTTAAAAAGATGGATTCTAAAGTTTGTGTTAAAAACCAGAGAAAAGTAGTTGGGTTT
1 GAAATTATTTTAAAAAGATGGATTCTAAAGTCTATGTTGAAAACCAAAGAAAAGTAGTTGGGTTA
*
1323286 GGGAGT-GGTTACATGTGATTTC
66 GGAAGTCGGTTACATGTGATTTC
* * *
1323308 -AGGATTATTTTAAAAAGATGGATTCTAAAGTCTACGTTGAAAACTAAAG-AAAGTGAGTTGGGT
1 GA-AATTATTTTAAAAAGATGGATTCTAAAGTCTATGTTGAAAACCAAAGAAAAGT-AGTTGGGT
* *
1323371 TAGGAAGTCGGTTACGTGTGCTTTC
64 TAGGAAGTCGGTTACATGTGATTTC
* *
1323396 GAAATTATTTTAGAAAA-ACGGATTCTAAAGTCTATGTTG--TACCAAAGAAAA
1 GAAATTATTTTA-AAAAGATGGATTCTAAAGTCTATGTTGAAAACCAAAGAAAA
1323447 TGAGTTGACT
Statistics
Matches: 117, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
86 12 0.10
87 57 0.49
88 43 0.37
89 5 0.04
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.32
Consensus pattern (88 bp):
GAAATTATTTTAAAAAGATGGATTCTAAAGTCTATGTTGAAAACCAAAGAAAAGTAGTTGGGTTA
GGAAGTCGGTTACATGTGATTTC
Found at i:1324707 original size:9 final size:9
Alignment explanation
Indices: 1324695--1324770 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 9
1324685 TAAATTTTAT
1324695 TTAATATAA
1 TTAATATAA
*
1324704 TTAAAATAA
1 TTAATATAA
* *
1324713 TT-TTATTA
1 TTAATATAA
*
1324721 -TAATAGAA
1 TTAATATAA
*
1324729 TAAAT-TAA
1 TTAATATAA
* *
1324737 TAAATATAT
1 TTAATATAA
1324746 TTATTATATAA
1 TTA--ATATAA
1324757 TTAATATAA
1 TTAATATAA
1324766 TTAAT
1 TTAAT
1324771 TAACAATAAG
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
7 1 0.02
8 13 0.26
9 28 0.56
11 8 0.16
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (9 bp):
TTAATATAA
Found at i:1324718 original size:24 final size:24
Alignment explanation
Indices: 1324665--1324767 Score: 77
Period size: 25 Copynumber: 4.1 Consensus size: 24
1324655 GCTTATTATG
1324665 ATTTTAATTTAA-A-AA-TAAAATAA
1 ATTTT-ATTTAATATAATTAAAAT-A
1324688 ATTTTATTTAATATAATTAAAATA
1 ATTTTATTTAATATAATTAAAATA
* *
1324712 ATTTTATTATAATAGAATAAATTAATA
1 ATTTTATT-TAATATAATTAA--AATA
* * *
1324739 AATATATTTATTATATAATTAATATA
1 ATTTTATTTA--ATATAATTAAAATA
1324765 ATT
1 ATT
1324768 AATTAACAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 13
0.75 0.09 0.15
Matches are distributed among these distances:
22 6 0.09
23 6 0.09
24 11 0.17
25 16 0.25
26 7 0.11
27 10 0.16
28 8 0.12
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (24 bp):
ATTTTATTTAATATAATTAAAATA
Found at i:1324768 original size:33 final size:31
Alignment explanation
Indices: 1324695--1324770 Score: 79
Period size: 33 Copynumber: 2.5 Consensus size: 31
1324685 TAAATTTTAT
1324695 TTAATATAATT-A-AAATAATTTTATTATAA
1 TTAATATAATTAATAAATAATTTTATTATAA
*
1324724 TAGAATA-AATTAATAAAT-ATATTTATTATATAA
1 T-TAATATAATTAATAAATAAT-TTTA-T-TATAA
1324757 TTAATATAATTAAT
1 TTAATATAATTAAT
1324771 TAACAATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
29 5 0.13
30 7 0.18
31 8 0.21
32 5 0.13
33 13 0.34
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (31 bp):
TTAATATAATTAATAAATAATTTTATTATAA
Found at i:1324806 original size:27 final size:27
Alignment explanation
Indices: 1324755--1324806 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
1324745 TTTATTATAT
* *
1324755 AATTAATATAATTAATTAACAATAAGC
1 AATTAATATAAATAATTAAAAATAAGC
1324782 AATT-ATATAAATAATTAAAATATAA
1 AATTAATATAAATAATTAAAA-ATAA
1324807 AAATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (27 bp):
AATTAATATAAATAATTAAAAATAAGC
Found at i:1324848 original size:15 final size:16
Alignment explanation
Indices: 1324830--1324862 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1324820 AATTTATCCA
1324830 TTTATT-ATTTATTTT
1 TTTATTAATTTATTTT
1324845 TTTATTAATTTATTTT
1 TTTATTAATTTATTTT
1324861 TT
1 TT
1324863 AGCATAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATTAATTTATTTT
Found at i:1329013 original size:49 final size:51
Alignment explanation
Indices: 1328901--1329014 Score: 187
Period size: 49 Copynumber: 2.3 Consensus size: 51
1328891 AATTAACTAG
*
1328901 ATGTATCGATACATTGAATAATGTATCGATACATCTGAGTAAAAAAACAGA
1 ATGTATCGATACATTGAATAATCTATCGATACATCTGAGTAAAAAAACAGA
* *
1328952 ATGTATCAATACATTGAA-AATCTATCGATACATCTGGGT-AAAAAACAGA
1 ATGTATCGATACATTGAATAATCTATCGATACATCTGAGTAAAAAAACAGA
1329001 ATGTATCGATACAT
1 ATGTATCGATACAT
1329015 GTACTGTTCA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
49 23 0.39
50 19 0.32
51 17 0.29
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (51 bp):
ATGTATCGATACATTGAATAATCTATCGATACATCTGAGTAAAAAAACAGA
Found at i:1332774 original size:52 final size:51
Alignment explanation
Indices: 1332710--1332892 Score: 188
Period size: 52 Copynumber: 3.5 Consensus size: 51
1332700 GAAATAATGA
* * * **
1332710 AGTTTGAGTATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATTGG
1 AGTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTGGAAATAAAACAGG
** * *
1332762 AGTTGGAGTATCCCCGATTAAAAGAAAATTGGTGTTTTGAAAATAAAACCAGG
1 AGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAA-CAGG
* * * * *
1332815 -GTTGGAGTATCCCCGATTGTGGAAAATTAATGTTTTAGAAATAAAACCGG
1 AGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACAGG
* *
1332865 GGTTGGAGTATCCCCGATTATGAGAAAT
1 AGTTGGAGTATCCCCGATTATGAAAAAT
1332893 CGGGGTTAGA
Statistics
Matches: 107, Mismatches: 21, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 3 0.03
51 44 0.41
52 49 0.46
53 11 0.10
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (51 bp):
AGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACAGG
Found at i:1332861 original size:51 final size:50
Alignment explanation
Indices: 1332715--1332883 Score: 187
Period size: 51 Copynumber: 3.3 Consensus size: 50
1332705 AATGAAGTTT
* * **
1332715 GAGTATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAA-TTGGAGTTG
1 GAGTATCCCCGATTGTGGAAAATTAGTG-TTTT-GAAATAAAACCAGG-GTTG
*** *
1332767 GAGTATCCCCGATTAAAAGAAAATTGGTGTTTTGAAAATAAAACCAGGGTTG
1 GAGTATCCCCGATT-GTGGAAAATTAGTGTTTTG-AAATAAAACCAGGGTTG
* *
1332819 GAGTATCCCCGATTGTGGAAAATTAATGTTTTAGAAATAAAACCGGGGTTG
1 GAGTATCCCCGATTGTGGAAAATTAGTGTTTT-GAAATAAAACCAGGGTTG
1332870 GAGTATCCCCGATT
1 GAGTATCCCCGATT
1332884 ATGAGAAATC
Statistics
Matches: 99, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
51 44 0.44
52 44 0.44
53 11 0.11
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (50 bp):
GAGTATCCCCGATTGTGGAAAATTAGTGTTTTGAAATAAAACCAGGGTTG
Found at i:1333276 original size:52 final size:51
Alignment explanation
Indices: 1333213--1333607 Score: 257
Period size: 52 Copynumber: 7.6 Consensus size: 51
1333203 GAAATAATGA
* * *
1333213 AGTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGG
1 AGTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTGGAAATAAAACCGG
** * *
1333265 AGTTGGAGTATCCCCGATTAAAAGAAAATTGGTGTTTTGAAAATAAAACCAGG
1 AGTTGGAGTATCCCCGATTATGA-AAAATTAGTGTTTTGGAAATAAAACC-GG
* * * * *
1333318 -GTTGGAGTATCCCCGATTGTGGAAAATTAATGTTTTAGAAATAAAATCGG
1 AGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * * * * *
1333368 GGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGG
1 AGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
* * *** * * *
1333419 GGTTGGAGTATCCCC--TTGGAGGTAACGGGGTTGGAGTATCCTCGATGAAAT--AA-C-G
1 AGTTGGAGTATCCCCGATT--ATG-AA--AAATT--AGTGT-TTTG--GAAATAAAACCGG
* * * *
1333474 AGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGG
1 A-GTTGGAGTATCCCCGATTATGAAAAATTAGTG-TTTTGGAAATAAAACCGG
* * * * *
1333527 AGTTAGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAACCGTG
1 AGTTGGAGTATCCCCGATT-ATGAAAAATTAGTGTTTTGGAAATAAAACCG-G
*
1333580 -GTTGGAGTATCCCCGATTATGAACAATT
1 AGTTGGAGTATCCCCGATTATGAAAAATT
1333608 GAGAAACTTA
Statistics
Matches: 264, Mismatches: 56, Indels: 47
0.72 0.15 0.13
Matches are distributed among these distances:
49 7 0.03
50 2 0.01
51 93 0.35
52 102 0.39
53 27 0.10
54 1 0.00
55 3 0.01
56 19 0.07
57 3 0.01
58 2 0.01
59 5 0.02
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
AGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
Found at i:1333340 original size:503 final size:503
Alignment explanation
Indices: 1332393--1333396 Score: 1972
Period size: 503 Copynumber: 2.0 Consensus size: 503
1332383 TTGGAGACGC
1332393 GGTTAGAATACATCCCCCGACGAGAAATTTAATATTTTGGAGATAATAACGGAGTTGGAGTATCC
1 GGTTAGAATACATCCCCCGACGAGAAATTTAATATTTTGGAGATAATAACGGAGTTGGAGTATCC
1332458 TCTCGAAAATAACGGGGTTGGAGAATTCCCGATTGTGAAAAATCGATGATTTAGAAATAAGACAA
66 TCTCGAAAATAACGGGGTTGGAGAATTCCCGATTGTGAAAAATCGATGATTTAGAAATAAGACAA
1332523 GGGTTGAAGTGTCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAGTCAGGATTGGAGTATCC
131 GGGTTGAAGTGTCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAGTCAGGATTGGAGTATCC
1332588 CCGTGAAAATAATAGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCG
196 CCGTGAAAATAATAGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCG
*
1332653 GGGTTGGAGTATCCCCTCGGAGGTAACGGGATTGGAGTATCCCCGATGAAATAATGAAGTTTGAG
261 GGGTTGGAGTATCCCCTCGGAGGTAACGGGATTGGAGTATCCCCGATGAAATAATGAAGTTGGAG
*
1332718 TATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATTGGAGTTGGAGTATCCCCGATTAA
326 TATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
1332783 AAGAAAATTGGTGTTTTGAAAATAAAACCAGGGTTGGAGTATCCCCGATTGTGGAAAATTAATGT
391 AAGAAAATTGGTGTTTTGAAAATAAAACCAGGGTTGGAGTATCCCCGATTGTGGAAAATTAATGT
1332848 TTTAGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAGAAATCGG
456 TTTAGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAGAAATCGG
*
1332896 GGTTAGAATACATCCCCCGACGAGAAATTTAATATTTTGGAGATAATAACGGGGTTGGAGTATCC
1 GGTTAGAATACATCCCCCGACGAGAAATTTAATATTTTGGAGATAATAACGGAGTTGGAGTATCC
1332961 TCTCGAAAATAACGGGGTTGGAGAATTCCCGATTGTGAAAAATCGATGATTTAGAAATAAGACAA
66 TCTCGAAAATAACGGGGTTGGAGAATTCCCGATTGTGAAAAATCGATGATTTAGAAATAAGACAA
1333026 GGGTTGAAGTGTCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAGTCAGGATTGGAGTATCC
131 GGGTTGAAGTGTCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAGTCAGGATTGGAGTATCC
1333091 CCGTGAAAATAATAGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCG
196 CCGTGAAAATAATAGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCG
1333156 GGGTTGGAGTATCCCCTCGGAGGTAACGGGATTGGAGTATCCCCGATGAAATAATGAAGTTGGAG
261 GGGTTGGAGTATCCCCTCGGAGGTAACGGGATTGGAGTATCCCCGATGAAATAATGAAGTTGGAG
1333221 TATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
326 TATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
1333286 AAGAAAATTGGTGTTTTGAAAATAAAACCAGGGTTGGAGTATCCCCGATTGTGGAAAATTAATGT
391 AAGAAAATTGGTGTTTTGAAAATAAAACCAGGGTTGGAGTATCCCCGATTGTGGAAAATTAATGT
*
1333351 TTTAGAAATAAAATCGGGGTTGGAGTATCCCCGATTATGAGAAATC
456 TTTAGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAGAAATC
1333397 AATATTTTGG
Statistics
Matches: 497, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
503 497 1.00
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (503 bp):
GGTTAGAATACATCCCCCGACGAGAAATTTAATATTTTGGAGATAATAACGGAGTTGGAGTATCC
TCTCGAAAATAACGGGGTTGGAGAATTCCCGATTGTGAAAAATCGATGATTTAGAAATAAGACAA
GGGTTGAAGTGTCCCCGATTATAGAAAATAGATGTTTCAAAAATAAAGTCAGGATTGGAGTATCC
CCGTGAAAATAATAGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCG
GGGTTGGAGTATCCCCTCGGAGGTAACGGGATTGGAGTATCCCCGATGAAATAATGAAGTTGGAG
TATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAA
AAGAAAATTGGTGTTTTGAAAATAAAACCAGGGTTGGAGTATCCCCGATTGTGGAAAATTAATGT
TTTAGAAATAAAACCGGGGTTGGAGTATCCCCGATTATGAGAAATCGG
Found at i:1333371 original size:51 final size:51
Alignment explanation
Indices: 1333214--1333433 Score: 244
Period size: 51 Copynumber: 4.3 Consensus size: 51
1333204 AAATAATGAA
* * * * * *
1333214 GTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATTAATG-TTTTGGAAATAAAACCGGG
** ** * *
1333266 GTTGGAGTATCCCCGATTAAAAGAAAATTGGTGTTTTGAAAATAAAACCAGG
1 GTTGGAGTATCCCCGATT-ATGGAAAATTAATGTTTTGGAAATAAAACCGGG
* * *
1333318 GTTGGAGTATCCCCGATTGTGGAAAATTAATGTTTTAGAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTATGGAAAATTAATGTTTTGGAAATAAAACCGGG
* * *
1333369 GTTGGAGTATCCCCGATTAT-GAGAAATCAATATTTTGGAAATAAAGCCGGG
1 GTTGGAGTATCCCCGATTATGGA-AAATTAATGTTTTGGAAATAAAACCGGG
1333420 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1333434 TTGGAGGTAA
Statistics
Matches: 141, Mismatches: 25, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
50 2 0.01
51 80 0.57
52 50 0.35
53 9 0.06
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATTAATGTTTTGGAAATAAAACCGGG
Found at i:1333394 original size:103 final size:103
Alignment explanation
Indices: 1333214--1333433 Score: 298
Period size: 103 Copynumber: 2.1 Consensus size: 103
1333204 AAATAATGAA
* * *
1333214 GTTGGAGTATCCTCGATTGTGAAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTTAGAAATAAAATCGGAGTTGGAGTATCCC
*** *
1333279 CGATTAAAAGAAAATTGGTGTTTTGAAAATAAAACCAGG
66 CGATTAAAAG-AAATCAATATTTTGAAAATAAAACCAGG
* *
1333318 GTTGGAGTATCCCCGATTGTGGAAAATTAATG-TTTTAGAAATAAAATCGGGGTTGGAGTATCCC
1 GTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTTAGAAATAAAATCGGAGTTGGAGTATCCC
** * * *
1333382 CGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGG
66 CGATTAAAAGAAATCAATATTTTGAAAATAAAACCAGG
1333420 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1333434 TTGGAGGTAA
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
102 35 0.34
103 38 0.37
104 29 0.28
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (103 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTAATGTTTTTAGAAATAAAATCGGAGTTGGAGTATCCC
CGATTAAAAGAAATCAATATTTTGAAAATAAAACCAGG
Found at i:1333438 original size:31 final size:28
Alignment explanation
Indices: 1333416--1333487 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
1333406 GAAATAAAGC
**
1333416 CGGGGTTGGAGTATCCCCTTGGAGGTAA
1 CGGGGTTGGAGTATCCCCTTGGAAATAA
**
1333444 CGGGGTTGGAGTATCCTCGAT-GAAATAA
1 CGGGGTTGGAGTATCC-CCTTGGAAATAA
*
1333472 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1333488 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.22, C:0.17, G:0.36, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTTGGAAATAA
Found at i:1333570 original size:262 final size:262
Alignment explanation
Indices: 1333105--1333597 Score: 880
Period size: 262 Copynumber: 1.9 Consensus size: 262
1333095 GAAAATAATA
*
1333105 GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCC
*
1333170 CCTCGGAGGTAACGGGATTGGAGTATCCCCGATGAAATAATGAAGTTGGAGTATCCTCGATTGTG
66 CCTCGGAGGTAACGGGATTGGAGTATCCCCGATGAAATAACGAAGTTGGAGTATCCTCGATTGTG
*
1333235 AAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAAGAAAATTGGTGT
131 AAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAAGAAAATTGGTGT
1333300 TTTGAAAATAAAACCAG-GGTTGGAGTATCCCCGATTGTGGAAAATTAATGTTTTAGAAATAAAA
196 TTTGAAAATAAAACC-GTGGTTGGAGTATCCCCGATTGTGGAAAATTAATGTTTTAGAAATAAAA
1333364 TCG
260 TCG
*
1333367 GGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCC
* * * *
1333432 CCTTGGAGGTAACGGGGTTGGAGTATCCTCGATGAAATAACGAGGTTGGAGTATCCTCGATTGTG
66 CCTCGGAGGTAACGGGATTGGAGTATCCCCGATGAAATAACGAAGTTGGAGTATCCTCGATTGTG
* *
1333497 AAAAATTGGTGTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAGGAAAATTGGTGT
131 AAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAAGAAAATTGGTGT
1333562 TTTGAAAATAAAACCGTGGTTGGAGTATCCCCGATT
196 TTTGAAAATAAAACCGTGGTTGGAGTATCCCCGATT
1333598 ATGAACAATT
Statistics
Matches: 220, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
261 1 0.00
262 219 1.00
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (262 bp):
GGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTGGAGTATCC
CCTCGGAGGTAACGGGATTGGAGTATCCCCGATGAAATAACGAAGTTGGAGTATCCTCGATTGTG
AAAAATTAGTGTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTAAAAGAAAATTGGTGT
TTTGAAAATAAAACCGTGGTTGGAGTATCCCCGATTGTGGAAAATTAATGTTTTAGAAATAAAAT
CG
Found at i:1335967 original size:13 final size:13
Alignment explanation
Indices: 1335949--1335974 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1335939 AACTTCCTAG
1335949 ATGTATCGATACA
1 ATGTATCGATACA
1335962 ATGTATCGATACA
1 ATGTATCGATACA
1335975 CTTCCTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1335987 original size:21 final size:21
Alignment explanation
Indices: 1335961--1336002 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1335951 GTATCGATAC
1335961 AATGTATCGATACACTTCCTT
1 AATGTATCGATACACTTCCTT
*
1335982 AATGTATCGATACATTTCCTT
1 AATGTATCGATACACTTCCTT
1336003 GGCAGTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (21 bp):
AATGTATCGATACACTTCCTT
Found at i:1336051 original size:19 final size:20
Alignment explanation
Indices: 1336027--1336080 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
1336017 AGTGGTACAT
*
1336027 TGTATCGATACAAAACT-TA
1 TGTATCGATACAAAACTGAA
**
1336046 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACTGAA
1336067 TGTATCGATACAAA
1 TGTATCGATACAAA
1336081 TTATTAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 12 0.43
20 3 0.11
21 13 0.46
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAAAACTGAA
Found at i:1339439 original size:82 final size:81
Alignment explanation
Indices: 1339385--1339567 Score: 269
Period size: 82 Copynumber: 2.2 Consensus size: 81
1339375 TCTTGTATGT
*
1339385 CATGTATG-TTGAAATATTTACTTTGTATTAATCTTTGAACATGTTTATGAGTTAAAACAACTTG
1 CATGTATGCTTGAAATATTTACTTTGTATTAATCTTTGAACATGTTTATGAGTTAAAACAAC-TA
*
1339449 ATTGAATCAACTTTGAA
65 ATTGAATCAACTATGAA
* * * *
1339466 CATGTATGCTTGAAATATTTACTTTGTTTTAATCTTTGAACATGTTTATGAGTTGAAACAGCTTG
1 CATGTATGCTTGAAATATTTACTTTGTATTAATCTTTGAACATGTTTATGAGTTAAAACAAC-TA
*
1339531 ATTGAATCAACTTTGAA
65 ATTGAATCAACTATGAA
*
1339548 TATGTATGCTTGAAATATTT
1 CATGTATGCTTGAAATATTT
1339568 TTTTAATTAA
Statistics
Matches: 97, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
81 8 0.08
82 89 0.92
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (81 bp):
CATGTATGCTTGAAATATTTACTTTGTATTAATCTTTGAACATGTTTATGAGTTAAAACAACTAA
TTGAATCAACTATGAA
Found at i:1339464 original size:42 final size:42
Alignment explanation
Indices: 1339417--1339552 Score: 122
Period size: 42 Copynumber: 3.3 Consensus size: 42
1339407 TTGTATTAAT
1339417 CTTTGAACATGTTTATGAGTTAAAACAACTTGATTGAATCAA
1 CTTTGAACATGTTTATGAGTTAAAACAACTTGATTGAATCAA
* ** * *
1339459 CTTTGAACATG--TATG-CTTGAAATATTTACTTTGTTTTAAT---
1 CTTTGAACATGTTTATGAGTT-AAA-A-CAAC-TTGATTGAATCAA
* *
1339499 CTTTGAACATGTTTATGAGTTGAAACAGCTTGATTGAATCAA
1 CTTTGAACATGTTTATGAGTTAAAACAACTTGATTGAATCAA
*
1339541 CTTTGAATATGT
1 CTTTGAACATGT
1339553 ATGCTTGAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 20
0.68 0.12 0.19
Matches are distributed among these distances:
39 10 0.14
40 19 0.27
41 2 0.03
42 30 0.42
43 10 0.14
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (42 bp):
CTTTGAACATGTTTATGAGTTAAAACAACTTGATTGAATCAA
Found at i:1339510 original size:40 final size:39
Alignment explanation
Indices: 1339385--1339510 Score: 107
Period size: 40 Copynumber: 3.1 Consensus size: 39
1339375 TCTTGTATGT
*
1339385 CATGTATGTTGAAATATTTACTTTGTATTAATCTTTGAA
1 CATGTATGTTGAAATATTTACTTTGTTTTAATCTTTGAA
** * *
1339424 CATGTTTATGAGTT-AAA-A-CAAC-TTGATTGAATCAACTTTGAA
1 CATG--TAT--GTTGAAATATTTACTTTGTTTTAAT---CTTTGAA
1339466 CATGTATGCTTGAAATATTTACTTTGTTTTAATCTTTGAA
1 CATGTATG-TTGAAATATTTACTTTGTTTTAATCTTTGAA
1339506 CATGT
1 CATGT
1339511 TTATGAGTTG
Statistics
Matches: 66, Mismatches: 9, Indels: 23
0.67 0.09 0.23
Matches are distributed among these distances:
38 1 0.02
39 13 0.20
40 20 0.30
41 5 0.08
42 16 0.24
43 11 0.17
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.44
Consensus pattern (39 bp):
CATGTATGTTGAAATATTTACTTTGTTTTAATCTTTGAA
Found at i:1342591 original size:22 final size:24
Alignment explanation
Indices: 1342563--1342621 Score: 70
Period size: 22 Copynumber: 2.6 Consensus size: 24
1342553 TTATAATAAT
*
1342563 AAAATTAAAAATAGAA-AAAA-TA
1 AAAATTAAAAATACAATAAAAGTA
*
1342585 AAAATTAAGAATACAATAAAAGTA
1 AAAATTAAAAATACAATAAAAGTA
*
1342609 AGAA-TAAAAATAC
1 AAAATTAAAAATAC
1342622 TTTCTTCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
22 14 0.45
23 12 0.39
24 5 0.16
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.19
Consensus pattern (24 bp):
AAAATTAAAAATACAATAAAAGTA
Found at i:1348916 original size:13 final size:13
Alignment explanation
Indices: 1348900--1348925 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1348890 TAGGGTAGCT
1348900 TTGTATCGATACA
1 TTGTATCGATACA
1348913 TTGTATCGATACA
1 TTGTATCGATACA
1348926 ACACTCATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1349837 original size:49 final size:48
Alignment explanation
Indices: 1349770--1350320 Score: 300
Period size: 49 Copynumber: 11.9 Consensus size: 48
1349760 GAAGTGTCAA
*
1349770 AGATGCCAATATGCTGATTCAAGGCCAATGATATCGGACTTAAAGATTG
1 AGATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGA-TG
* * * ** * *
1349819 AGATGCTAATGTGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGATG
1 AGATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATG
*
1349867 ACGATGCTAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATG
1 A-GATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATG
* * *
1349916 AAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGG-------GCT-
1 -AGATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATG
* * * ** * * * **
1349957 CG-TGCTAATGTGCTGATTCAAGGCCAGCGAGATTAGTCTTAAAGACA
1 AGATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATG
* *
1350004 AGATGCCAATATGCTGATTCAAGGCCAACGATATTGG-GTT-----T-
1 AGATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATG
* ** * ** * **
1350045 --ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAGAGACA
1 AGATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATG
* * *
1350091 AGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGGAC-TCAAGATGG
1 AGATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGAT-G
* * ***
1350139 TAAATGTGCCAATATGTTGATTCAATGGCCAGCAATATTGGACTT-AA-A-G
1 -AGA--TGCCAATATGCTGATTCAA-GGCCAATGATATTGGACTTAAAGATG
* **
1350188 -G-TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT--AGA-G
1 AGATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATG
* * ** * * *
1350231 -G-TACCAATGA-GCTGATTCAAGGCTAGCGACATT-GAGCTTAAAGGTA
1 AGATGCCAAT-ATGCTGATTCAAGGCCAATGATATTGGA-CTTAAAGATG
* * **
1350277 AGGTGCCAATATGCTGATCCAAGGCCAGCGATATTGGACTTAAA
1 AGATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAA
1350321 AGTGCCACAG
Statistics
Matches: 398, Mismatches: 68, Indels: 73
0.74 0.13 0.14
Matches are distributed among these distances:
39 61 0.15
40 3 0.01
42 5 0.01
43 51 0.13
44 17 0.04
45 2 0.01
46 1 0.00
47 9 0.02
48 95 0.24
49 116 0.29
50 1 0.00
51 19 0.05
52 17 0.04
53 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (48 bp):
AGATGCCAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATG
Found at i:1349897 original size:98 final size:98
Alignment explanation
Indices: 1349715--1349953 Score: 284
Period size: 98 Copynumber: 2.4 Consensus size: 98
1349705 TAGAATTGAA
* ** * * *
1349715 GAAGAATGCCAATGTGCTGAGACAAGGCCAGCGACATTGGGCTAAGAAG-TGTCAAAGATGCCAA
1 GAAG-ATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTA-AAGATG---ACGATGCCAA
1349779 TATGCTGATTCAAGGCCAATGATATCGGACTTAAAGATT
61 TATGCTGATTCAAGGCCAATGATATCGGACTTAAAGA-T
* * * *
1349818 G-AGATGCTAATGTGCTGATTTAAGGCCAGCGACATTGGTCTTAAAGATGACGATGCTAATATGC
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACGATGCCAATATGC
*
1349882 TGATTCAAGGCCAATGATATTGGACTTAAAGAT
66 TGATTCAAGGCCAATGATATCGGACTTAAAGAT
* * *
1349915 GAAGGTGCCAATATGCTGATTCAAGGCCAGTGATATTGG
1 GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGG
1349954 GCTCGTGCTA
Statistics
Matches: 119, Mismatches: 15, Indels: 9
0.83 0.10 0.06
Matches are distributed among these distances:
97 2 0.02
98 75 0.63
100 3 0.03
101 36 0.30
102 2 0.02
103 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (98 bp):
GAAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACGATGCCAATATGC
TGATTCAAGGCCAATGATATCGGACTTAAAGAT
Found at i:1350039 original size:87 final size:87
Alignment explanation
Indices: 1349870--1350313 Score: 369
Period size: 87 Copynumber: 5.0 Consensus size: 87
1349860 AAAGATGACG
* ** * * *
1349870 ATGCTAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATATGCTGAT
1 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGAT
1349935 TCAAGGCCAGTGATATTGGGCTC
65 TCAAGGCCAGTGATATTGGGCTC
* * * *
1349958 GTGCTAATGTGCTGATTCAAGGCCAGCGAGATTAGTCTTAAAGACAAGATGCCAATATGCTGATT
1 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
** * *
1350023 CAAGGCCAACGATATTGGGTTT
66 CAAGGCCAGTGATATTGGGCTC
* * *
1350045 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAGAGACAAGGTGCCAATATGCTGATT
1 ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
*
1350110 CAAGGCCAGTGATATTGGACTC
66 CAAGGCCAGTGATATTGGGCTC
* * * *
1350132 AAGATGGTAAATGTGCCAATATGTTGATTCAATGGCCAGCAATATTGGACTT----A-AAGGTGC
1 ---ATGCT-AATGTG-C-------TGATTCAA-GGCCAGCGACATTGGTCTTAAAGACAAGGTGC
* * * *
1350192 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAG
53 CAATATGCTGATTCAAGGCCAGTGATATTGGGC-T-C
* * * * **
1350229 AGGTACCAATGAGCTGATTCAAGGCTAGCGACATTGAG-CTTAAAGGTAAGGTGCCAATATGCTG
1 A--TGCTAATGTGCTGATTCAAGGCCAGCGACATTG-GTCTTAAAGACAAGGTGCCAATATGCTG
* *
1350293 ATCCAAGGCCAGCGATATTGG
63 ATTCAAGGCCAGTGATATTGG
1350314 ACTTAAAAGT
Statistics
Matches: 289, Mismatches: 44, Indels: 43
0.77 0.12 0.11
Matches are distributed among these distances:
86 14 0.05
87 121 0.42
88 37 0.13
90 3 0.01
91 42 0.15
92 1 0.00
94 2 0.01
95 43 0.15
96 3 0.01
99 8 0.03
100 15 0.05
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (87 bp):
ATGCTAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
CAAGGCCAGTGATATTGGGCTC
Found at i:1350060 original size:39 final size:39
Alignment explanation
Indices: 1350006--1350084 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
1349996 TAAAGACAAG
*
1350006 ATGCCAATATGCTGATTCAAGGCCAACGATATTGGGTTT
1 ATGCCAATATGCTGATTCAAGGCCAACGACATTGGGTTT
* * *
1350045 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTT
1 ATGCCAATATGCTGATTCAAGGCCAACGACATTGGGTTT
1350084 A
1 A
1350085 GAGACAAGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (39 bp):
ATGCCAATATGCTGATTCAAGGCCAACGACATTGGGTTT
Found at i:1350162 original size:186 final size:185
Alignment explanation
Indices: 1349970--1350316 Score: 443
Period size: 186 Copynumber: 1.9 Consensus size: 185
1349960 GCTAATGTGC
* *
1349970 TGATTCAA-GGCCAGCGAGATTAGTCTTAAAGACAAGATGCCAATATGCTGATTCAAGGCCAACG
1 TGATTCAATGGCCAGCAAGATTAGACTTAAAG----G-TGCCAATATGCTGATTCAAGGCCAACG
* * * * * *
1350034 ATATTGG-GTT-TA-TGCCAATGTGCTGATTCAAGGCCAGCGACATTG-GTTTTAGAGACAAGGT
61 ATATTGGACTTAGAGTACCAATGAGCTGATTCAAGGCCAGCGACATTGAG-CTTAAAGACAAGGT
* *
1350095 GCCAATATGCTGATTCAAGGCCAGTGATATTGGACTCAAGATGGTAAATGTGCCAATATGT
125 GCCAATATGCTGATCCAAGGCCAGCGATATTGGACTCAAGATGGTAAATGTGCCAATATGT
* * * *
1350156 TGATTCAATGGCCAGCAATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATT
1 TGATTCAATGGCCAGCAAGATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATT
* **
1350221 GGACTTAGAGGTACCAATGAGCTGATTCAAGGCTAGCGACATTGAGCTTAAAGGTAAGGTGCCAA
66 GGACTTAGA-GTACCAATGAGCTGATTCAAGGCCAGCGACATTGAGCTTAAAGACAAGGTGCCAA
1350286 TATGCTGATCCAAGGCCAGCGATATTGGACT
130 TATGCTGATCCAAGGCCAGCGATATTGGACT
1350317 TAAAAGTGCC
Statistics
Matches: 138, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
182 32 0.23
183 3 0.02
184 1 0.01
186 82 0.59
187 20 0.14
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (185 bp):
TGATTCAATGGCCAGCAAGATTAGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATT
GGACTTAGAGTACCAATGAGCTGATTCAAGGCCAGCGACATTGAGCTTAAAGACAAGGTGCCAAT
ATGCTGATCCAAGGCCAGCGATATTGGACTCAAGATGGTAAATGTGCCAATATGT
Found at i:1350197 original size:52 final size:51
Alignment explanation
Indices: 1350093--1350316 Score: 148
Period size: 43 Copynumber: 4.7 Consensus size: 51
1350083 TAGAGACAAG
**
1350093 GTGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTCAAGATGGTAAAT
1 GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTCAAGATGGTAAAT
* *
1350144 GTGCCAATATGTTGATTCAATGGCCAGCAATATTGGA--C----T--TAAAG
1 GTGCCAATATGCTGATTCAA-GGCCAGCAATATTGGACTCAAGATGGTAAAT
* * *
1350188 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACT-TAGA-GGT--A-
1 GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTCAAGATGGTAAAT
* * * * *
1350234 ---CCAATGA-GCTGATTCAAGGCTAGCGACATT-GAGCTTAA-A-GGT-AAG
1 GTGCCAAT-ATGCTGATTCAAGGCCAGCAATATTGGA-CTCAAGATGGTAAAT
* *
1350279 GTGCCAATATGCTGATCCAAGGCCAGCGATATTGGACT
1 GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACT
1350317 TAAAAGTGCC
Statistics
Matches: 140, Mismatches: 14, Indels: 41
0.72 0.07 0.21
Matches are distributed among these distances:
42 2 0.01
43 47 0.34
44 24 0.17
46 1 0.01
47 2 0.01
48 27 0.19
49 3 0.02
50 1 0.01
51 19 0.14
52 14 0.10
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (51 bp):
GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTCAAGATGGTAAAT
Found at i:1350224 original size:43 final size:43
Alignment explanation
Indices: 1350139--1350327 Score: 202
Period size: 43 Copynumber: 4.3 Consensus size: 43
1350129 CTCAAGATGG
* * *
1350139 TAAATGTGCCAATATGTTGATTCAATGGCCAGCAATATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAA-GGCCAGCGATATTGGACT
*
1350183 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
* * * *
1350226 TAGAGGTACCAATGA-GCTGATTCAAGGCTAGCGACATT-GAGCT
1 TAAAGGTGCCAAT-ATGCTGATTCAAGGCCAGCGATATTGGA-CT
*
1350269 TAAAGGTAAGGTGCCAATATGCTGATCCAAGGCCAGCGATATTGGACT
1 T--A---AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
*
1350317 TAAAAGTGCCA
1 TAAAGGTGCCA
1350328 CAGAGTTGTG
Statistics
Matches: 121, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
42 2 0.02
43 60 0.50
44 22 0.18
45 1 0.01
46 1 0.01
47 1 0.01
48 32 0.26
49 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
Found at i:1350320 original size:48 final size:47
Alignment explanation
Indices: 1350046--1350320 Score: 255
Period size: 48 Copynumber: 5.9 Consensus size: 47
1350036 ATTGGGTTTA
* * ** * *
1350046 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAGAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG-GAAGG
* * *
1350094 TGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTCAAGATGGTAAATG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAA-A-GG--AAGG
* *
1350145 TGCCAATATGTTGATTCAATGGCCAGCAATATTGGACTT--A--AAGG
1 TGCCAATATGCTGATTCAA-GGCCAGCGATATTGGACTTAAAGGAAGG
*
1350189 TGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT--A-G-AGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGAAGG
* * *
1350232 TACCAATGA-GCTGATTCAAGGCTAGCGACATT-GAGCTTAAAGGTAAGG
1 TGCCAAT-ATGCTGATTCAAGGCCAGCGATATTGGA-CTTAAAGG-AAGG
*
1350280 TGCCAATATGCTGATCCAAGGCCAGCGATATTGGACTTAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1350321 AGTGCCACAG
Statistics
Matches: 187, Mismatches: 25, Indels: 30
0.77 0.10 0.12
Matches are distributed among these distances:
42 2 0.01
43 52 0.28
44 20 0.11
45 1 0.01
46 1 0.01
47 1 0.01
48 68 0.36
49 4 0.02
50 1 0.01
51 21 0.11
52 16 0.09
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (47 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGAAGG
Found at i:1350441 original size:34 final size:34
Alignment explanation
Indices: 1350318--1351295 Score: 581
Period size: 33 Copynumber: 31.1 Consensus size: 34
1350308 TATTGGACTT
* *
1350318 AAAAGTGCCACAGAGTTGTGGACTT-ACAGGAAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* ** * *
1350351 GAGGGATGCCACGGAGGTGTGGGCTTAAAAGGAAA
1 AAAAG-TGCCACGGAGTTGTGGACTTAAAAGGAAA
* * * *
1350386 AAGA-TACCATGAAGTTGTGGACTTAAAAGGAAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
** *
1350419 AAAAGTGCCACGGAGTCATGGACTTAAAA--AGA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* * * *
1350451 AAAGGTGCCACAGAGTTGTGGACTTAAAAAGAAC
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* *
1350485 AAGA-TGCTACGGAGTTGTGGACTTAAAAGG-AA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* * * *
1350517 CAAGGTGCCACAGAGTTGTGGACTTAAAAGGGAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* ** * *
1350551 AAGAGTGCCATAGAGTCGTGGACTTAAAA--AGA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* * * *
1350583 AAAGGTGCCACAGAGTTGTGGACATAAAAGGAAC
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* *
1350617 AAGA-TGCCACAGAGTTGTGGACTTAAAAGG---
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
*
1350647 ----GTGCCACGGGGTTGTGGACTTAAAAGGAAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* * * *
1350677 AAGA-TGCCACAGATTTGTGGGCTTAAAAGG---
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
1350707 ----GTGCCACGGAGTTGTGGACTTAAAAGG---
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
1350734 ----GTGCCACGGAGTTGTGGACTTAAAAGGAAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* *
1350764 AAGAGTGCCACGGAGTTGTGGGCTTAAAAGG---
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* *
1350795 ----GTGCCACGGAGTTGCGGACTTAAAAGG-GA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* * *
1350824 CAAGGTGCCACAGAGTTGTGGACTTAAAAGG---
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
*
1350855 ----GTGCCACAGAGTTGTGGACTTAAAAGGAAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* * * * *
1350885 AAGAGTGTCATGGAGTTGTGGGCTTAAAAGGGAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* *
1350919 AAATGTGCCATGGAGTTGTGGACTTAAAAGGAAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* ** *
1350953 AAGA-TGCCATAGAGTTGTGGACTCAAAAGG---
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* **
1350983 ----GTGCCACGAAGTTGTGGACTT-ATTGGAAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* * * * *
1351012 AAAGGATGCCACAGAGGTCTAGG-CTTAAAAGGGAA
1 AAAAG-TGCCACGGAGTTGT-GGACTTAAAAGGAAA
** * *
1351047 AATGGTGCCACGGAGTCGTGGACTTAAAA--AGA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* * *
1351079 AAAGGTGCCACGGAGTTGTAGACTTAAAAGGAAC
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* *
1351113 AAGA-TGCCACGGAGTTGTGGA-TT--TA--AAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* * *
1351141 AAGA-TGTCACAGAGTTGTGGACTTAAAAGG---
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
1351171 ----GTGCCACGGAGTTGTGGACTTAAAA-G-AA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
* * *
1351199 ACAAGATGCCACGGAGTTGTGGGCTTAAAAGG-GA
1 AAAAG-TGCCACGGAGTTGTGGACTTAAAAGGAAA
* *
1351233 AAAGGTGCCACAGAGTTGTGGACTTAAAAGG---
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
*
1351264 ----GTGCCACGGAATTGTGGACTTAAAAGGAAA
1 AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
1351294 AA
1 AA
1351296 GGATGCCACG
Statistics
Matches: 748, Mismatches: 126, Indels: 143
0.74 0.12 0.14
Matches are distributed among these distances:
26 4 0.01
27 189 0.25
28 21 0.03
29 2 0.00
30 1 0.00
31 1 0.00
32 84 0.11
33 238 0.32
34 188 0.25
35 20 0.03
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.20
Consensus pattern (34 bp):
AAAAGTGCCACGGAGTTGTGGACTTAAAAGGAAA
Found at i:1350660 original size:27 final size:27
Alignment explanation
Indices: 1350621--1351290 Score: 343
Period size: 27 Copynumber: 22.0 Consensus size: 27
1350611 AGGAACAAGA
*
1350621 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
1350648 TGCCACGGGGTTGTGGACTTAAAAGGAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-----G
* * *
1350680 ATGCCACAGATTTGTGGGCTTAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
1350708 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
1350735 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAA-G-----G-G
*
1350769 TGCCACGGAGTTGTGGGCTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
1350796 TGCCACGGAGTTGCGGACTTAAAAGGGACAAGG
1 TGCCACGGAGTTGTGGACTTAAAA--G----GG
*
1350829 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
1350856 TGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGACTTAAAA-G-----G-G
* * *
1350890 TGTCATGGAGTTGTGGGCTTAAAAGGGAAAAATG
1 TGCCACGGAGTTGTGGACTTAAAA-GG------G
*
1350924 TGCCATGGAGTTGTGGACTTAAAAGGAAAAAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-----G
** *
1350956 ATGCCATAGAGTTGTGGACTCAAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGG
* *
1350984 TGCCACGAAGTTGTGGACTTATTGGAAAAAAGGA
1 TGCCACGGAGTTGTGGAC---TT----AAAAGGG
* * *
1351018 TGCCACAGAGGTCTAGG-CTTAAAAGGGAAAATGG
1 TGCCACGGAGTTGT-GGACTTAAAA--G-----GG
*
1351052 TGCCACGGAGTCGTGGACTTAAAAAGAAAAGG
1 TGCCACGGAGTTGTGGACTT-AAAAG----GG
*
1351084 TGCCACGGAGTTGTAGACTTAAAAGGAACAAG
1 TGCCACGGAGTTGTGGACTTAAAAGG-----G
* * *
1351116 ATGCCACGGAGTTGTGGATTTAAAAAAGA
1 -TGCCACGGAGTTGTGGACTT-AAAAGGG
* *
1351145 TGTCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
1351172 TGCCACGGAGTTGTGGACTTAAAAGAAACAAGA
1 TGCCACGGAGTTGTGGACTTAAAAG------GG
*
1351205 TGCCACGGAGTTGTGGGCTTAAAAGGGAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAA--G----GG
*
1351238 TGCCACAGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
*
1351265 TGCCACGGAATTGTGGACTTAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAGG
1351291 AAAAAGGATG
Statistics
Matches: 519, Mismatches: 60, Indels: 128
0.73 0.08 0.18
Matches are distributed among these distances:
27 195 0.38
28 22 0.04
29 3 0.01
30 1 0.00
31 9 0.02
32 30 0.06
33 146 0.28
34 106 0.20
35 7 0.01
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:1350671 original size:60 final size:60
Alignment explanation
Indices: 1350311--1351726 Score: 686
Period size: 60 Copynumber: 22.6 Consensus size: 60
1350301 CCAGCGATAT
* * *
1350311 TGGACTT-AAA-A-GTGCCACAGAGTTGTGGACTT-ACAGGAAAGAGGGATGCCACGGAGGTG
1 TGGACTTAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGGAAA-A--GATGCCACGGAGTTG
* * * * * *
1350370 TGGGCTTAAAAGGAAAAAGATACCATGAAGTTGTGGACTTAAAAGGAAAAAAAGTGCCACGGAGT
1 TGGACTTAAAA-G----AGGTGCCACGGAGTTGTGGACTTAAAAGG-AAAAGA-TGCCACGGAGT
**
1350435 CA
59 TG
* * *
1350437 TGGACTTAAAAAGAAAAGGTGCCACAGAGTTGTGGACTTAAAAAGAACAAGATGCTACGGAGTTG
1 TGGACTT-AAAAG---AGGTGCCACGGAGTTGTGGACTTAAAAGGAA-AAGATGCCACGGAGTTG
* **
1350502 TGGACTTAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTAAAAGGGAAAAGAGTGCCATAGAGT
1 TGGACTTAAAA-G----AGGTGCCACGGAGTTGTGGACTTAAAA-GGAAAAGA-TGCCACGGAGT
*
1350567 CG
59 TG
* * *
1350569 TGGACTTAAAAAGAAAAGGTGCCACAGAGTTGTGGACATAAAAGGAACAAGATGCCACAGAGTTG
1 TGGACTT-AAAAG---AGGTGCCACGGAGTTGTGGACTTAAAAGGAA-AAGATGCCACGGAGTTG
* * *
1350634 TGGACTTAAAAG-GGTGCCACGGGGTTGTGGACTTAAAAGGAAAAAGATGCCACAGATTTG
1 TGGACTTAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGG-AAAAGATGCCACGGAGTTG
*
1350694 TGGGCTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGG----G-TGCCACGGAGTTG
1 TGGACTTAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTTG
*
1350748 TGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG----G-TGCCACGGAGTT
1 TGGACTTAAAA-G----AG-GTGCCACGGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTT
1350808 G
60 G
* * *
1350809 CGGACTTAAAAGGGACAAGGTGCCACAGAGTTGTGGACTTAAAAGG----G-TGCCACAGAGTTG
1 TGGACTTAAAA--G---AGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTTG
* * * *
1350869 TGGACTTAAAAGGAAAAAGAGTGTCATGGAGTTGTGGGCTTAAAAGGGAAAA-ATGTGCCATGGA
1 TGGACTTAAAA-G----AG-GTGCCACGGAGTTGTGGACTTAAAA-GGAAAAGA--TGCCACGGA
1350933 GTTG
57 GTTG
* ** * *
1350937 TGGACTTAAAAGGAAAAAGATGCCATAGAGTTGTGGACTCAAAAGG----G-TGCCACGAAGTTG
1 TGGACTTAAAA-G----AGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTTG
* * * * *
1350997 TGGACTTATTGGAAAAAAGGATGCCACAGAGGTCTAGG-CTTAAAAGGGAAAATGGTGCCACGGA
1 TGGAC---TT--AAAAGAGG-TGCCACGGAGTTGT-GGACTTAAAA-GGAAAA-GATGCCACGGA
*
1351061 GTCG
57 GTTG
*
1351065 TGGACTTAAAAAGAAAAGGTGCCACGGAGTTGTAGACTTAAAAGGAACAAGATGCCACGGAGTTG
1 TGGACTT-AAAAG---AGGTGCCACGGAGTTGTGGACTTAAAAGGAA-AAGATGCCACGGAGTTG
* * * * *
1351130 TGGATTTAAAAAAGATGTCACAGAGTTGTGGACTTAAAAGG----G-TGCCACGGAGTTG
1 TGGACTTAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTTG
* * * *
1351185 TGGACTTAAAAGAAACAAGATGCCACGGAGTTGTGGGCTTAAAAGGGAAAAGGTGCCACAGAGTT
1 TGGACTTAAAAG-----AGGTGCCACGGAGTTGTGGACTTAAAA-GGAAAAGATGCCACGGAGTT
1351250 G
60 G
*
1351251 TGGACTTAAAAG-GGTGCCACGGAATTGTGGACTTAAAAGGAAAAAGGATGCCAC-GATGTTG
1 TGGACTTAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGG-AAAA-GATGCCACGGA-GTTG
* * ** * ** * * * **
1351312 TGGGCTTTAAAA-AGATGCCATTGAGTCGTGGACTT-TGA-GAAGAGATTACCACTGAGTCA
1 TGGAC-TTAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGA-TGCCACGGAGTTG
* * ** ** * *
1351371 TGGACTTTGAAGAAAAGATGCCACTAAGTTGTGGACTT-TGAGAAAAGAGATGCCACTGAGTTG
1 TGGAC-TT-AA-AAGAGGTGCCACGGAGTTGTGGACTTAAAAGGAAA-AGATGCCACGGAGTTG
* * * * * * * * ** *
1351434 TGGACTTTGAGAAGAGATGGCACTGAGTCGTGGATTTCGAGAA-G-AGAGATGCCATTGAGTCG
1 TGGAC-TT-AAAAGAGGTGCCACGGAGTTGTGGACTT--AAAAGGAAAAGATGCCACGGAGTTG
* * * ** ** **
1351496 TGGACTTTGAGAAGAGATTGCCACTGAGTTGTGGACTTGGAA-GAAAAGGATGCCACTAAGTCA
1 TGGAC-TT-AAAAGAG-GTGCCACGGAGTTGTGGACTTAAAAGGAAAA-GATGCCACGGAGTTG
* * * * *
1351559 TGGACTTAGAAAAGAGATGCCACTGAGTTGTGGACTATGAAAAGAAAAAGGTGCCACAGAGTTG
1 TGGACTT--AAAAGAGGTGCCACGGAGTTGTGGACT-T-AAAAGGAAAAGATGCCACGGAGTTG
* * *
1351623 TGGACTTAAGAGGAACAAGGTGCCACGGAGTTGTGGACATAAAAAGAAAAAGATGCCACGGAGTT
1 TGGACTT-A-A--AA-GAGGTGCCACGGAGTTGTGGAC-TTAAAAGGAAAAGATGCCACGGAGTT
1351688 G
60 G
**
1351689 TGGACTTAAAAG-GGTGCCACAAAGTTGTGGACTTAAAA
1 TGGACTTAAAAGAGGTGCCACGGAGTTGTGGACTTAAAA
1351727 AGGTGCCACG
Statistics
Matches: 1104, Mismatches: 157, Indels: 192
0.76 0.11 0.13
Matches are distributed among these distances:
54 21 0.02
55 25 0.02
56 1 0.00
58 2 0.00
59 32 0.03
60 229 0.21
61 143 0.13
62 130 0.12
63 68 0.06
64 41 0.04
65 79 0.07
66 174 0.16
67 96 0.09
68 60 0.05
69 3 0.00
ACGTcount: A:0.35, C:0.13, G:0.31, T:0.21
Consensus pattern (60 bp):
TGGACTTAAAAGAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGATGCCACGGAGTTG
Found at i:1351155 original size:28 final size:28
Alignment explanation
Indices: 1350417--1351749 Score: 361
Period size: 33 Copynumber: 43.0 Consensus size: 28
1350407 CTTAAAAGGA
**
1350417 AAAAAAG-TGCCACGGAGTCATGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
* *
1350444 AAAAAGAAAAGGTGCCACAGAGTTGTGGACTT
1 ---AA-AAAAGATGCCACGGAGTTGTGGACTT
*
1350476 AAAAAGAACAAGATGCTACGGAGTTGTGGACTT
1 ---AA-AA-AAGATGCCACGGAGTTGTGGACTT
* *
1350509 AAAAGGAACAAGGTGCCACAGAGTTGTGGACTT
1 --AA--AA-AAGATGCCACGGAGTTGTGGACTT
** *
1350542 AAAAGGGAAAAGAGTGCCATAGAGTCGTGGACTT
1 --AA---AAAAGA-TGCCACGGAGTTGTGGACTT
* * *
1350576 AAAAAGAAAAGGTGCCACAGAGTTGTGGACATAA
1 ---AA-AAAAGATGCCACGGAGTTGTGGAC-T-T
*
1350610 AAGGAACAAGATGCCACAGAGTTGTGGACTT
1 AA--AA-AAGATGCCACGGAGTTGTGGACTT
* * *
1350641 -AAAAGGGTGCCACGGGGTTGTGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
* * *
1350668 AAAAGGAAAAAGATGCCACAGATTTGTGGGCTT
1 ---A--AAAAAGATGCCACGGAGTTGTGGACTT
* *
1350701 -AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
* *
1350728 -AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
*
1350755 AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 ---A--AAAAAGA-TGCCACGGAGTTGTGGACTT
* * *
1350789 -AAAAGGGTGCCACGGAGTTGCGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
* *
1350816 AAAAGGGACAAGGTGCCACAGAGTTGTGGACTT
1 -AAA---A-AAGATGCCACGGAGTTGTGGACTT
* * *
1350849 -AAAAGGGTGCCACAGAGTTGTGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
* * *
1350876 AAAAGGAAAAAGAGTGTCATGGAGTTGTGGGCTT
1 ---A--AAAAAGA-TGCCACGGAGTTGTGGACTT
* *
1350910 AAAAGGGAAAAATGTGCCATGGAGTTGTGGACTT
1 -AAA---AAAGA--TGCCACGGAGTTGTGGACTT
**
1350944 AAAAGGAAAAAGATGCCATAGAGTTGTGGAC-T
1 ---A--AAAAAGATGCCACGGAGTTGTGGACTT
* * * *
1350976 CAAAAGGGTGCCACGAAGTTGTGGACTTATT
1 AAAAAAGATGCCACGGAGTTGTGGAC---TT
* * *
1351007 GGAAAAAAGGATGCCACAGAGGTCTAGG-CTT
1 --AAAAAA-GATGCCACGGAGTTGT-GGACTT
* *
1351038 AAAAGGGAAAATGGTGCCACGGAGTCGTGGACTT
1 --AA---AAAA-GATGCCACGGAGTTGTGGACTT
* *
1351072 AAAAAGAAAAGGTGCCACGGAGTTGTAGACTT
1 ---AA-AAAAGATGCCACGGAGTTGTGGACTT
*
1351104 AAAAGGAACAAGATGCCACGGAGTTGTGGATTT
1 --AA--AA-AAGATGCCACGGAGTTGTGGACTT
* *
1351137 AAAAAAGATGTCACAGAGTTGTGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
* *
1351165 -AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
*
1351192 AAAAGAAACAAGATGCCACGGAGTTGTGGGCTT
1 ---A-AAA-AAGATGCCACGGAGTTGTGGACTT
* *
1351225 AAAAGGGAAAAGGTGCCACAGAGTTGTGGACTT
1 --AA---AAAAGATGCCACGGAGTTGTGGACTT
* * *
1351258 -AAAAGGGTGCCACGGAATTGTGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
*
1351285 AAAAGGAAAAAGGATGCCAC-GATGTTGTGGGCTT
1 ---A--AAAAA-GATGCCACGGA-GTTGTGGACTT
* ** *
1351319 TAAAAAGATGCCATTGAGTCGTGGACTTT
1 AAAAAAGATGCCACGGAGTTGTGGAC-TT
* * * * **
1351348 GAGAAGAGATTACCACTGAGTCATGGACTTT
1 -AAAAAAGA-TGCCACGGAGTTGTGGAC-TT
**
1351379 GAAGAAAAGATGCCACTAAGTTGTGGACTTT
1 -AA-AAAAGATGCCACGGAGTTGTGGAC-TT
*
1351410 GAGAAAAGAGATGCCACTGAGTTGTGGACTTT
1 -A-AAAA-AGATGCCACGGAGTTGTGGAC-TT
* * * * * *
1351442 GAGAAGAGATGGCACTGAGTCGTGGATTT
1 -AAAAAAGATGCCACGGAGTTGTGGACTT
* ** *
1351471 CGAGAAGAGAGATGCCATTGAGTCGTGGACTTT
1 --A-AA-AAAGATGCCACGGAGTTGTGGAC-TT
* * *
1351504 GAGAAGAGATTGCCACTGAGTTGTGGACTT
1 -AAAAAAGA-TGCCACGGAGTTGTGGACTT
** **
1351534 GGAAGAAAAGGATGCCACTAAGTCATGGACTT
1 --AA-AAAA-GATGCCACGGAGTTGTGGACTT
*
1351566 AGAAAAGAGATGCCACTGAGTTGTGGACTAT
1 A-AAAA-AGATGCCACGGAGTTGTGGACT-T
* *
1351597 GAAAAGAAAAAGGTGCCACAGAGTTGTGGACTT
1 ----A-AAAAAGATGCCACGGAGTTGTGGACTT
* *
1351630 AAGAGGAACAAGGTGCCACGGAGTTGTGGACATAAAA
1 -A-A--AA-AAGATGCCACGGAGTTGTGGAC-T---T
1351667 AGAAAAAGATGCCACGGAGTTGTGGACTT
1 A-AAAAAGATGCCACGGAGTTGTGGACTT
* * **
1351696 -AAAAGGGTGCCACAAAGTTGTGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
* *
1351723 -AAAAAGGTGCCACGGAGTCGTGGACTT
1 AAAAAAGATGCCACGGAGTTGTGGACTT
1351750 TTGGAAAAGA
Statistics
Matches: 1045, Mismatches: 152, Indels: 215
0.74 0.11 0.15
Matches are distributed among these distances:
27 222 0.21
28 43 0.04
29 15 0.01
30 64 0.06
31 88 0.08
32 158 0.15
33 281 0.27
34 147 0.14
35 20 0.02
36 5 0.00
38 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.21
Consensus pattern (28 bp):
AAAAAAGATGCCACGGAGTTGTGGACTT
Found at i:1351313 original size:34 final size:35
Alignment explanation
Indices: 1351258--1351323 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 35
1351248 TTGTGGACTT
*
1351258 AAAAGGGTGCCACGGAATTGTGGAC-TTAAAAGGA
1 AAAAGGATGCCACGGAATTGTGGACTTTAAAAGGA
* *
1351292 AAAAGGATGCCAC-GATGTTGTGGGCTTTAAAA
1 AAAAGGATGCCACGGA-ATTGTGGACTTTAAAA
1351324 AGATGCCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 2 0.07
34 19 0.70
35 6 0.22
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.21
Consensus pattern (35 bp):
AAAAGGATGCCACGGAATTGTGGACTTTAAAAGGA
Found at i:1351417 original size:30 final size:30
Alignment explanation
Indices: 1351292--1351945 Score: 440
Period size: 30 Copynumber: 21.2 Consensus size: 30
1351282 CTTAAAAGGA
* *
1351292 AAAAGGATGCCAC-GATGTTGTGGGCTTT-A-
1 AAAA-GATGCCACTGA-GTCGTGGACTTTGAG
*
1351321 AAAAGATGCCATTGAGTCGTGGACTTTGAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
* * *
1351351 AAGAGATTACCACTGAGTCATGGACTTTGAAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTG-AG
* *
1351383 AAAAGATGCCACTAAGTTGTGGACTTTGAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
*
1351413 AAAAGAGATGCCACTGAGTTGTGGACTTTGAG
1 -AAA-AGATGCCACTGAGTCGTGGACTTTGAG
* *
1351445 AAGAGATGGCACTGAGTCGTGGA-TTTCGAG
1 AAAAGATGCCACTGAGTCGTGGACTTT-GAG
*
1351475 AAGAGAGATGCCATTGAGTCGTGGACTTTGAG
1 AA-A-AGATGCCACTGAGTCGTGGACTTTGAG
* * *
1351507 AAGAGATTGCCACTGAGTTGTGGACTTGGAAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTG-AG
* * *
1351539 AAAAGGATGCCACTAAGTCATGGACTTAGA-
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
* *
1351569 AAAGAGATGCCACTGAGTTGTGGACTATGAAAAG
1 AAA-AGATGCCACTGAGTCGTGGACTTTG---AG
* * * *
1351603 AAAAAGGTGCCACAGAGTTGTGGACTTAAGAGG
1 -AAAAGATGCCACTGAGTCGTGGACTT-TGA-G
* * * ***
1351636 AACAAGGTGCCACGGAGTTGTGGACATAAAAAG
1 AA-AAGATGCCACTGAGTCGTGGAC-T-TTGAG
* *
1351669 AAAAAGATGCCACGGAGTTGTGGAC-TT-A-
1 -AAAAGATGCCACTGAGTCGTGGACTTTGAG
* * ** *
1351697 AAAGGGTGCCACAAAGTTGTGGAC-TT-A-
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
* *
1351724 AAAAGGTGCCACGGAGTCGTGGACTTTTG-G
1 AAAAGATGCCACTGAGTCGTGGAC-TTTGAG
* *
1351754 AAAAGATGCCACTAAGTCATGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTG-AG
* * *
1351785 AAAAGGTTGCCACTAAGTCGTGGGC-TT-AG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
* * *
1351814 AAAAGAAATGCCACTGAGTCGTGGGC-TTAAA
1 AAAAG--ATGCCACTGAGTCGTGGACTTTGAG
*
1351845 AAAGAGATGCCACTGAGTCGTGAACTTTG-G
1 AAA-AGATGCCACTGAGTCGTGGACTTTGAG
* *
1351875 AAAGAGATGCCATTGAGTCGTGGACTTTAAAGAA
1 AAA-AGATGCCACTGAGTCGTGGACTTT---GAG
1351909 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTG-AG
1351940 AAAAGA
1 AAAAGA
1351946 GATTTGAAGA
Statistics
Matches: 512, Mismatches: 70, Indels: 84
0.77 0.11 0.13
Matches are distributed among these distances:
27 43 0.08
28 18 0.04
29 23 0.04
30 138 0.27
31 83 0.16
32 101 0.20
33 74 0.14
34 28 0.05
35 4 0.01
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAG
Found at i:1351575 original size:93 final size:90
Alignment explanation
Indices: 1351292--1351948 Score: 421
Period size: 93 Copynumber: 7.1 Consensus size: 90
1351282 CTTAAAAGGA
* * * * *
1351292 AAAAG-GATGCCAC-GATGTTGTGGGCTTT-A-AAAAGATGCCATTGAGTCGTGGACTTTGAGAA
1 AAAAGAGATGCCACTGA-GTCGTGGACTTTGAGAAGAGATGCCACTGAGTTGTGGAC-TTGAGAA
* * * *
1351353 GA-GATTACCACTGAGTCATGGACTTTG
64 AAGGA-TGCCACTGAGTCGTGGACTTAG
* * *
1351380 AAGAAAAGATGCCACTAAGTTGTGGACTTTGAGAAAAGAGATGCCACTGAGTTGTGGACTTTGAG
1 AA-AAGAGATGCCACTGAGTCGTGGACTTTGAG--AAGAGATGCCACTGAGTTGTGGAC-TTGAG
* * *
1351445 AAGA-GATGGCACTGAGTCGTGGATTTCGAG
62 AAAAGGATGCCACTGAGTCGTGGACTT--AG
* *
1351475 AAGAGAGATGCCATTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTTGTGGACTTGGAAGA
1 AAAAGAGATGCCACTGAGTCGTGGACTTTGAGAAGAGA-TGCCACTGAGTTGTGGACTT-G-AGA
* *
1351540 AAAGGATGCCACTAAGTCATGGACTTAG
63 AAAGGATGCCACTGAGTCGTGGACTTAG
* * * * *
1351568 AAAAGAGATGCCACTGAGTTGTGGACTATGAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAG
1 AAAAGAGATGCCACTGAGTCGTGGACTTTG---AG-AAGAGATGCCACTGAGTTGTGGACTT--G
* * *
1351633 AGGAACAAGG-TGCCACGGAGTTGTGGACATA-
60 A-GAA-AAGGATGCCACTGAGTCGTGGACTTAG
* * * * **
1351664 AAAAGAAAAAGATGCCACGGAGTTGTGGAC-TT-AAAAG-GGTGCCACAAAGTTGTGGACTT-A-
1 AAAAG----AGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTGAGTTGTGGACTTGAG
* *
1351724 AAAAGG-TGCCACGGAGTCGTGGACTTTTG
62 AAAAGGATGCCACTGAGTCGTGGAC-TTAG
* * * * * * * *
1351753 GAAA-AGATGCCACTAAGTCATGGACTTTGAAGAAAAGGTTGCCACTAAGTCGTGGGCTT-AGAA
1 AAAAGAGATGCCACTGAGTCGTGGACTTTG-AGAAGA-GATGCCACTGAGTTGTGGACTTGAGAA
* * *
1351816 AAGAAATGCCACTGAGTCGTGGGCTTAA
64 AAG-GATGCCACTGAGTCGTGGACTTAG
* * * *
1351844 AAAAGAGATGCCACTGAGTCGTGAACTTTG-GAAAGAGATGCCATTGAGTCGTGGACTTTAAAGA
1 AAAAGAGATGCCACTGAGTCGTGGACTTTGAG-AAGAGATGCCACTGAGTTGTGGAC-TT-GAG-
*
1351908 AAAAAGATGCCACTGAGTCGTGGACTTTGAAG
62 AAAAGGATGCCACTGAGTCGTGGAC-TT--AG
1351940 AAAAGAGAT
1 AAAAGAGAT
1351949 TTGAAGAATT
Statistics
Matches: 455, Mismatches: 71, Indels: 78
0.75 0.12 0.13
Matches are distributed among these distances:
84 17 0.04
85 2 0.00
87 24 0.05
88 5 0.01
89 24 0.05
90 42 0.09
91 12 0.03
92 46 0.10
93 104 0.23
94 71 0.16
95 22 0.05
96 37 0.08
97 24 0.05
98 4 0.01
99 1 0.00
100 20 0.04
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.23
Consensus pattern (90 bp):
AAAAGAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTGAGTTGTGGACTTGAGAAAA
GGATGCCACTGAGTCGTGGACTTAG
Found at i:1351858 original size:60 final size:63
Alignment explanation
Indices: 1351172--1351934 Score: 355
Period size: 62 Copynumber: 12.3 Consensus size: 63
1351162 CTTAAAAGGG
* * * * * * * * **
1351172 TGCCACGGAGTTGTGGACTTAAAAGAAACAAGATGCCACGGAGTTGTGGGCTTAAAAGGGAAAAG
1 TGCCACTGAGTCGTGGACTT-AGA-AAAGAA-ATGCCACTGAGTCGTGGACTTTAAAGAAAAAAG
*
1351237 G
63 A
* * ** * * * * *
1351238 TGCCACAGAGTTGTGGACTT--AAAAG-GGTGCCACGGAATTGTGGACTTAAAAGGAAAAAGGA
1 TGCCACTGAGTCGTGGACTTAGAAAAGAAATGCCACTGAGTCGTGGACTTTAAA-GAAAAAAGA
* * * * *
1351299 TGCCAC-GATGTTGTGGGCTTTA-AAAAG--ATGCCATTGAGTCGTGGACTTT---GAGAAGAGA
1 TGCCACTGA-GTCGTGGAC-TTAGAAAAGAAATGCCACTGAGTCGTGGACTTTAAAGAAAAAAGA
* * * * * * *
1351357 TTACCACTGAGTCATGGACTTTGAAGAA-AAGATGCCACTAAGTTGTGGACTTT-GAGAAAAGAG
1 -TGCCACTGAGTCGTGGACTTAGAA-AAGAA-ATGCCACTGAGTCGTGGACTTTAAAGAAAAAAG
1351420 A
63 A
* * * * * ** * *
1351421 TGCCACTGAGTTGTGGACTTTGAGAAGAGATGGCACTGAGTCGTGGA-TTTCGAGAAGAGAGA
1 TGCCACTGAGTCGTGGACTTAGAAAAGAAATGCCACTGAGTCGTGGACTTTAAAGAAAAAAGA
* * * * * ** *
1351483 TGCCATTGAGTCGTGGACTTTGAGAAGAGATTGCCACTGAGTTGTGGACTTGGAAG-AAAAGGA
1 TGCCACTGAGTCGTGGACTTAGAAAAGA-AATGCCACTGAGTCGTGGACTTTAAAGAAAAAAGA
* * * * * *
1351546 TGCCACTAAGTCATGGACTTAGAAAAGAGATGCCACTGAGTTGTGGACTATGAAA-AGAAAAAGG
1 TGCCACTGAGTCGTGGACTTAGAAAAGAAATGCCACTGAGTCGTGGACT-TTAAAGA-AAAAAGA
* * * * * * * * *
1351610 TGCCACAGAGTTGTGGACTTAAGAGGAACAAGGTGCCACGGAGTTGTGGAC-ATAAAAAGAAAAA
1 TGCCACTGAGTCGTGGACTT-AGA-AAAGAA-ATGCCACTGAGTCGTGGACTTTAAAGA-AAAAA
1351674 GA
62 GA
* * ** ** * *
1351676 TGCCACGGAGTTGTGGACTT--AAAAG-GGTGCCACAAAGTTGTGGAC-TT-----AAAAAGG
1 TGCCACTGAGTCGTGGACTTAGAAAAGAAATGCCACTGAGTCGTGGACTTTAAAGAAAAAAGA
* * * * * * *
1351730 TGCCACGGAGTCGTGGACTTTTGGAAAAG--ATGCCACTAAGTCATGGACTTTGAAG-AAAAGGT
1 TGCCACTGAGTCGTGGAC--TTAGAAAAGAAATGCCACTGAGTCGTGGACTTTAAAGAAAAAAGA
* * * *
1351792 TGCCACTAAGTCGTGGGCTTAGAAAAGAAATGCCACTGAGTCGTGGGC-TT-AA-AAAAGAGA
1 TGCCACTGAGTCGTGGACTTAGAAAAGAAATGCCACTGAGTCGTGGACTTTAAAGAAAAAAGA
* * * * *
1351852 TGCCACTGAGTCGTGAACTTTGGAAAGAGATGCCATTGAGTCGTGGACTTTAAAGAAAAAAGA
1 TGCCACTGAGTCGTGGACTTAGAAAAGAAATGCCACTGAGTCGTGGACTTTAAAGAAAAAAGA
1351915 TGCCACTGAGTCGTGGACTT
1 TGCCACTGAGTCGTGGACTT
1351935 TGAAGAAAAG
Statistics
Matches: 551, Mismatches: 107, Indels: 81
0.75 0.14 0.11
Matches are distributed among these distances:
54 23 0.04
56 2 0.00
57 15 0.03
58 15 0.03
59 13 0.02
60 100 0.18
61 26 0.05
62 152 0.28
63 100 0.18
64 33 0.06
65 6 0.01
66 49 0.09
67 17 0.03
ACGTcount: A:0.33, C:0.14, G:0.30, T:0.22
Consensus pattern (63 bp):
TGCCACTGAGTCGTGGACTTAGAAAAGAAATGCCACTGAGTCGTGGACTTTAAAGAAAAAAGA
Found at i:1353264 original size:24 final size:25
Alignment explanation
Indices: 1353237--1353283 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1353227 GCCTTTGCAC
1353237 TTTTTTTGTGTATT-TTTTTTTTGT
1 TTTTTTTGTGTATTCTTTTTTTTGT
* *
1353261 TTTTTTTGTTTCTTCTTTTTTTT
1 TTTTTTTGTGTATTCTTTTTTTT
1353284 TGTCTTAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (25 bp):
TTTTTTTGTGTATTCTTTTTTTTGT
Found at i:1360437 original size:13 final size:13
Alignment explanation
Indices: 1360419--1360444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1360409 AGGGTTGCTT
1360419 TGTATCGATACAA
1 TGTATCGATACAA
1360432 TGTATCGATACAA
1 TGTATCGATACAA
1360445 CACTCATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1364501 original size:20 final size:17
Alignment explanation
Indices: 1364458--1364510 Score: 79
Period size: 17 Copynumber: 2.9 Consensus size: 17
1364448 TAAAAAGACA
1364458 GAATGTATCGATACATT
1 GAATGTATCGATACATT
1364475 GAATGTATCGATACATT
1 GAATGTATCGATACATT
1364492 GAAAAATGTATCGATACAT
1 G---AATGTATCGATACAT
1364511 CTGGGTACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 18 0.55
20 15 0.45
ACGTcount: A:0.40, C:0.11, G:0.17, T:0.32
Consensus pattern (17 bp):
GAATGTATCGATACATT
Found at i:1364910 original size:10 final size:11
Alignment explanation
Indices: 1364893--1364921 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1364883 ATTTTTTCTC
1364893 TTTTTTTTTGT
1 TTTTTTTTTGT
1364904 TTTTTTTTTGT
1 TTTTTTTTTGT
1364915 TTTTTTT
1 TTTTTTT
1364922 AAAAAGTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:1365425 original size:16 final size:16
Alignment explanation
Indices: 1365395--1365437 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1365385 ATCTTAAAAG
1365395 AATATTAA-TAA--AA
1 AATATTAATTAATTAA
1365408 AATATTAATTAATTAA
1 AATATTAATTAATTAA
*
1365424 AAAATTAATTAATT
1 AATATTAATTAATT
1365438 CTACACGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.31
14 3 0.12
16 15 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATATTAATTAATTAA
Found at i:1367080 original size:2 final size:2
Alignment explanation
Indices: 1367068--1367113 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
1367058 TAGAGATTTG
1367068 TA TA GTA 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
1367111 TA T
1 TA T
1367114 TTAAAGGCCG
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Done.