Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000422.1 Hibiscus syriacus cultivar Beakdansim tig00000773_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2457469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1355761 original size:2 final size:2
Alignment explanation
Indices: 1355754--1355780 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1355744 ATCAAAATTG
1355754 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1355781 TAATTGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1358628 original size:21 final size:21
Alignment explanation
Indices: 1358603--1358659 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
1358593 GTAATTTACA
1358603 CCGAAGTG-CCACATAATTGTC
1 CCGAA-TGACCACATAATTGTC
1358624 CCGAATGACCACATAATTGTC
1 CCGAATGACCACATAATTGTC
*
1358645 CC-AAAGAACCACATA
1 CCGAATG-ACCACATA
1358660 GAACCCTCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 5 0.15
21 28 0.85
ACGTcount: A:0.37, C:0.30, G:0.14, T:0.19
Consensus pattern (21 bp):
CCGAATGACCACATAATTGTC
Found at i:1365150 original size:21 final size:21
Alignment explanation
Indices: 1365126--1365182 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
1365116 ACCGTTTGCA
1365126 CCGAAGTGCCACATAATTATC
1 CCGAAGTGCCACATAATTATC
* *
1365147 CCGAAGGGCCACATAATTGTC
1 CCGAAGTGCCACATAATTATC
1365168 CCGAA-TGACCACATA
1 CCGAAGTG-CCACATA
1365183 GAACCCTCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.33, C:0.30, G:0.18, T:0.19
Consensus pattern (21 bp):
CCGAAGTGCCACATAATTATC
Found at i:1370721 original size:3 final size:3
Alignment explanation
Indices: 1370706--1370750 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
1370696 CCAAAGTTTA
* *
1370706 ATT ATT GTT ATT ATT ATAT ATT ATT ATT ATT ATT AAT ATT ATT AT
1 ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT AT
1370751 CCCGTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1370886 original size:18 final size:20
Alignment explanation
Indices: 1370860--1370896 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1370850 AAAGGCCCAG
1370860 CAAGGAA-CCG-ACCCGATT
1 CAAGGAACCCGTACCCGATT
*
1370878 CAAGTAACCCGTACCCGAT
1 CAAGGAACCCGTACCCGAT
1370897 CTAACAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 6 0.38
19 3 0.19
20 7 0.44
ACGTcount: A:0.32, C:0.35, G:0.19, T:0.14
Consensus pattern (20 bp):
CAAGGAACCCGTACCCGATT
Found at i:1372217 original size:15 final size:16
Alignment explanation
Indices: 1372197--1372229 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1372187 TAAATTCCTT
1372197 TTAAATAATT-TTTGA
1 TTAAATAATTGTTTGA
*
1372212 TTAAATATTTGTTTGA
1 TTAAATAATTGTTTGA
1372228 TT
1 TT
1372230 TTTATTATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (16 bp):
TTAAATAATTGTTTGA
Found at i:1377640 original size:9 final size:9
Alignment explanation
Indices: 1377626--1377658 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
1377616 ATCCAGACAT
1377626 GGTGAGTAA
1 GGTGAGTAA
1377635 GGTGAGTAA
1 GGTGAGTAA
1377644 GGTGAGTAA
1 GGTGAGTAA
1377653 GGTGAG
1 GGTGAG
1377659 ATGTTCGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.48, T:0.21
Consensus pattern (9 bp):
GGTGAGTAA
Found at i:1382587 original size:14 final size:14
Alignment explanation
Indices: 1382565--1382617 Score: 69
Period size: 14 Copynumber: 4.1 Consensus size: 14
1382555 TCGATTATAT
*
1382565 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
1382579 GTTCATTTATG-T-
1 GTTCATTTATGTTC
1382591 -TT-ATTTATGTTC
1 GTTCATTTATGTTC
1382603 GTTCATTTATGTTC
1 GTTCATTTATGTTC
1382617 G
1 G
1382618 AGCAGATGGC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 7 0.21
11 3 0.09
13 3 0.09
14 21 0.62
ACGTcount: A:0.13, C:0.11, G:0.17, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:1382597 original size:24 final size:24
Alignment explanation
Indices: 1382570--1382615 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
1382560 TATATGTTCG
1382570 TTTATGTTCGTTCATTTATGTTTA
1 TTTATGTTCGTTCATTTATGTTTA
1382594 TTTATGTTCGTTCATTTATGTT
1 TTTATGTTCGTTCATTTATGTT
1382616 CGAGCAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.09, G:0.13, T:0.63
Consensus pattern (24 bp):
TTTATGTTCGTTCATTTATGTTTA
Found at i:1382911 original size:14 final size:13
Alignment explanation
Indices: 1382870--1382918 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
1382860 TTTTTTGTGT
*
1382870 GTTTGTGTTGTTC
1 GTTTATGTTGTTC
1382883 GTTTAT-TGTGTTC
1 GTTTATGT-TGTTC
1382896 GTTTATGTTCGTTC
1 GTTTATGTT-GTTC
*
1382910 GTTTGTGTT
1 GTTTATGTT
1382919 TGTTTACGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 1 0.03
13 17 0.55
14 13 0.42
ACGTcount: A:0.04, C:0.08, G:0.27, T:0.61
Consensus pattern (13 bp):
GTTTATGTTGTTC
Found at i:1383022 original size:16 final size:16
Alignment explanation
Indices: 1383001--1383033 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1382991 AAAAAAAATT
1383001 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1383017 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1383033 T
1 T
1383034 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1384536 original size:11 final size:11
Alignment explanation
Indices: 1384520--1384544 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1384510 GAATTTAAAC
1384520 TTTAATTTTTA
1 TTTAATTTTTA
1384531 TTTAATTTTTA
1 TTTAATTTTTA
1384542 TTT
1 TTT
1384545 TATTCATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTAATTTTTA
Found at i:1384572 original size:15 final size:15
Alignment explanation
Indices: 1384552--1384586 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1384542 TTTTATTCAT
*
1384552 AATTTAAGTAATTTA
1 AATTTAAGCAATTTA
*
1384567 AATTTATGCAATTTA
1 AATTTAAGCAATTTA
1384582 AATTT
1 AATTT
1384587 TACGTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (15 bp):
AATTTAAGCAATTTA
Found at i:1384781 original size:2 final size:2
Alignment explanation
Indices: 1384774--1384798 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1384764 TTGGTTAAAT
1384774 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1384799 CATTTTCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1388019 original size:37 final size:37
Alignment explanation
Indices: 1387964--1388071 Score: 171
Period size: 37 Copynumber: 2.9 Consensus size: 37
1387954 AATACGGGTA
* * *
1387964 GTAAATATAAAATAATATATGTTTATAGATAATTGAG
1 GTAAGTATAAAATAATATATTTTTAAAGATAATTGAG
1388001 GTAAGTATAAAATAATATATTTTTAAAGATAATTGAG
1 GTAAGTATAAAATAATATATTTTTAAAGATAATTGAG
* *
1388038 GTAAGTATAAGATAATATATTTTTAAAGGTAATT
1 GTAAGTATAAAATAATATATTTTTAAAGATAATT
1388072 TTATATTATT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (37 bp):
GTAAGTATAAAATAATATATTTTTAAAGATAATTGAG
Found at i:1389044 original size:15 final size:15
Alignment explanation
Indices: 1389024--1389057 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1389014 TCTTCCACTT
1389024 TCCTTCTTCTTCCTC
1 TCCTTCTTCTTCCTC
1389039 TCCTTCTTCTTCCTC
1 TCCTTCTTCTTCCTC
1389054 TCCT
1 TCCT
1389058 GTCCGAGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (15 bp):
TCCTTCTTCTTCCTC
Found at i:1389506 original size:19 final size:20
Alignment explanation
Indices: 1389482--1389521 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1389472 TGATTTTGGG
*
1389482 CAAGG-AGTATCGATATTGC
1 CAAGGAAGTATCGATACTGC
1389501 CAAGGAAGTATCGATACTGC
1 CAAGGAAGTATCGATACTGC
1389521 C
1 C
1389522 CCTTCTGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.23
Consensus pattern (20 bp):
CAAGGAAGTATCGATACTGC
Found at i:1392265 original size:6 final size:6
Alignment explanation
Indices: 1392254--1392278 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1392244 GGTCAGGTTA
1392254 TTGATG TTGATG TTGATG TTGATG T
1 TTGATG TTGATG TTGATG TTGATG T
1392279 CGGAGATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TTGATG
Found at i:1395306 original size:97 final size:97
Alignment explanation
Indices: 1395140--1395334 Score: 354
Period size: 97 Copynumber: 2.0 Consensus size: 97
1395130 CTGGTTGAAG
1395140 AATATGCATGGGCTATAGGAAACTAAATAAAACAACGAGGAAAGACCACTTTCCATTGCCCTTCA
1 AATATGCATGGGCTATAGGAAACTAAATAAAACAACGAGGAAAGACCACTTTCCATTGCCCTTCA
1395205 TAGATCAAATGTTAGATCAACTTGCGGGCAAT
66 TAGATCAAATGTTAGATCAACTTGCGGGCAAT
* *
1395237 AATATGCCTGGGCTATAGGAAACTAAATAAAACAACGAGGAAATACCACTTTCCATTGCCCTTCA
1 AATATGCATGGGCTATAGGAAACTAAATAAAACAACGAGGAAAGACCACTTTCCATTGCCCTTCA
* *
1395302 TAGATCAAATGTTAGATCGACTTGTGGGCAAT
66 TAGATCAAATGTTAGATCAACTTGCGGGCAAT
1395334 A
1 A
1395335 TTTTTTTATT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 94 1.00
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.25
Consensus pattern (97 bp):
AATATGCATGGGCTATAGGAAACTAAATAAAACAACGAGGAAAGACCACTTTCCATTGCCCTTCA
TAGATCAAATGTTAGATCAACTTGCGGGCAAT
Found at i:1397936 original size:7 final size:7
Alignment explanation
Indices: 1397924--1397956 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
1397914 TCCACCTTAG
1397924 AATTTTA
1 AATTTTA
1397931 AATTTTA
1 AATTTTA
1397938 AATTTTA
1 AATTTTA
1397945 AATTTTA
1 AATTTTA
1397952 AATTT
1 AATTT
1397957 ATGTTATCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:1400387 original size:45 final size:43
Alignment explanation
Indices: 1400323--1400425 Score: 143
Period size: 45 Copynumber: 2.3 Consensus size: 43
1400313 GAGAGACTTG
* * *
1400323 GGAAATAAGTTGGGTAATGCTAGTAATAGCTCTAACATAGTCTTA
1 GGAAATAAGTTGGATAATGCTAGTAATAGCTCCAACATAG--TGA
*
1400368 GGAAATAAGTTGGATAATGCTGGTAATAGCTCCAACATAGTGA
1 GGAAATAAGTTGGATAATGCTAGTAATAGCTCCAACATAGTGA
1400411 GAGAAATAAGTTGGA
1 G-GAAATAAGTTGGA
1400426 ATTTCAACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
43 3 0.06
44 13 0.25
45 37 0.70
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (43 bp):
GGAAATAAGTTGGATAATGCTAGTAATAGCTCCAACATAGTGA
Found at i:1405807 original size:19 final size:19
Alignment explanation
Indices: 1405779--1405826 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1405769 TAAATAAGTG
1405779 AATAAAAATAAAAAAATAA
1 AATAAAAATAAAAAAATAA
* *
1405798 AATAAGAATAAAAGAATAA
1 AATAAAAATAAAAAAATAA
*
1405817 AATGAAAATA
1 AATAAAAATA
1405827 GTAAATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (19 bp):
AATAAAAATAAAAAAATAA
Found at i:1405915 original size:55 final size:60
Alignment explanation
Indices: 1405784--1405915 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 60
1405774 AAGTGAATAA
1405784 AAATAAAA-AAATAAAATAAGAATAAAAGAATAAAATGAAAATAGTAAATATATATATGT
1 AAATAAAATAAATAAAATAAGAATAAAAGAATAAAATGAAAATAGTAAATATATATATGT
* * * *
1405843 AAATAATATCGATAATAAAA-AAGAA-AGAAATAAT-AAAT-AATATA-TATATATATATAT-T
1 AAATAAAAT--A-AATAAAATAAGAATA-AAAGAATAAAATGAAAATAGTAAATATATATATGT
1405901 AAATAAAATAAATAA
1 AAATAAAATAAATAA
1405916 GGGAAAGGGA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
55 5 0.08
56 1 0.02
58 9 0.14
59 19 0.30
60 5 0.08
61 5 0.08
62 12 0.19
63 7 0.11
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.27
Consensus pattern (60 bp):
AAATAAAATAAATAAAATAAGAATAAAAGAATAAAATGAAAATAGTAAATATATATATGT
Found at i:1407335 original size:15 final size:13
Alignment explanation
Indices: 1407251--1407337 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 13
1407241 TTGGGCCCTG
*
1407251 TAAAAATATA-AA
1 TAAAATTATATAA
*
1407263 TAAAGTTA-ATAA
1 TAAAATTATATAA
1407275 TATATATATTATATAGA
1 TA-A-A-ATTATATA-A
1407292 TGAATATATTATATAA
1 T-AA-A-ATTATATAA
1407308 TAAAATT-TATAA
1 TAAAATTATATAA
1407320 TATAAATATATATAA
1 TA-AAAT-TATATAA
1407335 TAA
1 TAA
1407338 TGTGGAACAA
Statistics
Matches: 62, Mismatches: 3, Indels: 18
0.75 0.04 0.22
Matches are distributed among these distances:
11 1 0.02
12 17 0.27
13 8 0.13
14 4 0.06
15 12 0.19
16 5 0.08
17 14 0.23
18 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (13 bp):
TAAAATTATATAA
Found at i:1407808 original size:106 final size:106
Alignment explanation
Indices: 1407620--1408391 Score: 1215
Period size: 106 Copynumber: 7.3 Consensus size: 106
1407610 CCAAAGATAA
* * *
1407620 TTCGTTGTGAAGTTGAAACTGGCTTTGAAATTGGGAAGTTGTTTATTGACAACCAGCAGTCCCTT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTT
* *
1407685 CGTCATGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCC
66 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
* * * * *
1407726 TTTGTTGTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACTAGCGGTCCCTT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTT
*
1407791 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCTAATATCC
66 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
*
1407832 TTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTT
* *
1407897 CGTCGTAAAGTCGAACTTGCGTTGTCTGGAGTCCAATATCC
66 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
*
1407938 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTT
*
1408003 CGTCATGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
66 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
* *
1408044 TTCGTTGTAAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTT
* *
1408109 TGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCC
66 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
** * *
1408150 TTCACTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGATAACCAGCGGTCCCTT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTT
*
1408214 CGTCGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCC
66 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
** * *
1408255 TTCACTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTG-TTGTTGACAACCAGCGGTCCCTT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTT
1408319 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
66 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
*** * * *
1408360 TTAACTATAAAGTTGAAATTGGCTCCGAAATT
1 TTCGTTGTGAAGTTGAAATTGGCTCTGAAATT
1408392 TTTTGTTGAC
Statistics
Matches: 620, Mismatches: 46, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
105 190 0.31
106 430 0.69
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (106 bp):
TTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTT
CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
Found at i:1419839 original size:2 final size:2
Alignment explanation
Indices: 1419832--1419869 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1419822 ATAATAAATA
1419832 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
1419870 TAAATAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1420018 original size:17 final size:18
Alignment explanation
Indices: 1419998--1420034 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1419988 AAAAAACTAG
1419998 AAAATAAAAGAAATA-AT
1 AAAATAAAAGAAATATAT
*
1420015 AAAATAAAATAAATATAT
1 AAAATAAAAGAAATATAT
1420033 AA
1 AA
1420035 TAAGGGACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (18 bp):
AAAATAAAAGAAATATAT
Found at i:1421112 original size:9 final size:9
Alignment explanation
Indices: 1421098--1421123 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1421088 GAAATCGGTT
1421098 AATTAACCG
1 AATTAACCG
1421107 AATTAACCG
1 AATTAACCG
1421116 AATTAACC
1 AATTAACC
1421124 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:1421269 original size:17 final size:17
Alignment explanation
Indices: 1421247--1421285 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
1421237 TGAATCAAAT
1421247 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1421264 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
1421281 -AATTA
1 TAATTA
1421286 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:1421455 original size:30 final size:31
Alignment explanation
Indices: 1421395--1421456 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
1421385 AATACTTTAA
*
1421395 AAAAAAAAGTTCGGTTCGATTAACGGTTAAGG
1 AAAAAAAAGTTCGGTTCAATT-ACGGTTAAGG
1421427 AAAAAAAAGTTCGGTT-AATT-CGGTTTAAGG
1 AAAAAAAAGTTCGGTTCAATTACGG-TTAAGG
1421457 TATTTCGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 3 0.11
30 6 0.21
31 3 0.11
32 16 0.57
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.27
Consensus pattern (31 bp):
AAAAAAAAGTTCGGTTCAATTACGGTTAAGG
Found at i:1422938 original size:12 final size:13
Alignment explanation
Indices: 1422915--1422940 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1422905 GATTTTGATA
1422915 TTTGATTTTTTTT
1 TTTGATTTTTTTT
1422928 TTTGATTTTTTTT
1 TTTGATTTTTTTT
1422941 AATATTATCT
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:0.08, C:0.00, G:0.08, T:0.85
Consensus pattern (13 bp):
TTTGATTTTTTTT
Found at i:1423199 original size:60 final size:59
Alignment explanation
Indices: 1423090--1423235 Score: 145
Period size: 60 Copynumber: 2.4 Consensus size: 59
1423080 GTTGATTCGT
* * * *
1423090 AAACTTTAAATATTCTAATTTCATCCTCAAACTATGATACTTATGCTAAATTAGTCCTC
1 AAACTTTAAACATTCCAATTTCATCCTCAAACTATGACACTCATGCTAAATTAGTCCTC
* * * *
1423149 AAACTTTAGAACATTCCAGTTTTATCCTCAAACTATGACCCTCA-GTCTAAATTGGTCC-C
1 AAACTTTA-AACATTCCAATTTCATCCTCAAACTATGACACTCATG-CTAAATTAGTCCTC
*
1423208 TAACCTTTTAAATC-TTCCAATTTCATCC
1 -AAAC-TTTAAA-CATTCCAATTTCATCC
1423236 CTAAATTCAT
Statistics
Matches: 71, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
59 10 0.14
60 56 0.79
61 5 0.07
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (59 bp):
AAACTTTAAACATTCCAATTTCATCCTCAAACTATGACACTCATGCTAAATTAGTCCTC
Found at i:1425239 original size:2 final size:2
Alignment explanation
Indices: 1425227--1425282 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
1425217 TGTCAATGAC
* * ** *
1425227 AT AT AT TT AT AT AT AT A- AT AT AT CT AT AT CG AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1425268 AG AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1425283 CACAAACAAC
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1427029 original size:36 final size:36
Alignment explanation
Indices: 1426996--1427063 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
1426986 TACAAATTGT
*
1426996 AAAATATTTCTAT-ATTTTCTTTA-AAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTACAAAATTAAATTC
*
1427031 ATAATATTTATATAATTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTACAAAATTAAA
1427064 AATATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 15 0.52
36 14 0.48
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (36 bp):
AAAATATTTATATAATTTTTTTACAAAATTAAATTC
Found at i:1428699 original size:16 final size:16
Alignment explanation
Indices: 1428678--1428731 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
1428668 GTATTACCCA
1428678 ACCTGTTTTCAACCTG
1 ACCTGTTTTCAACCTG
* *
1428694 ACCTGTTATGAACCTG
1 ACCTGTTTTCAACCTG
*
1428710 ACATGTTTTCAACCTG
1 ACCTGTTTTCAACCTG
1428726 ACCTGT
1 ACCTGT
1428732 AAATGATCTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (16 bp):
ACCTGTTTTCAACCTG
Found at i:1429291 original size:33 final size:37
Alignment explanation
Indices: 1429248--1429331 Score: 113
Period size: 33 Copynumber: 2.4 Consensus size: 37
1429238 AAAATAAAAT
* *
1429248 AAAAACATAAAAAT-AAAA-ATT-AATGAATCAAAG-
1 AAAAAAATAAAAATAAAAATATTAAATAAATCAAAGA
1429281 AAAAAAATAAAAATAAAAATATTAAATAAATCAAAGA
1 AAAAAAATAAAAATAAAAATATTAAATAAATCAAAGA
1429318 AGAAAAAATAAAAA
1 A-AAAAAATAAAAA
1429332 AGTTAAATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
33 13 0.30
34 4 0.09
35 3 0.07
36 11 0.25
37 1 0.02
38 12 0.27
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.17
Consensus pattern (37 bp):
AAAAAAATAAAAATAAAAATATTAAATAAATCAAAGA
Found at i:1429298 original size:5 final size:6
Alignment explanation
Indices: 1429237--1429301 Score: 53
Period size: 6 Copynumber: 10.2 Consensus size: 6
1429227 AATCAAAGGG
*
1429237 AAAAAT -AAAAT AAAAACAT AAAAAT AAAAATT AATGAAT CAAAGAA-
1 AAAAAT AAAAAT -AAAA-AT AAAAAT AAAAA-T AA-AAAT -AAA-AAT
1429283 AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT A
1429302 TTAAATAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
5 7 0.14
6 23 0.47
7 11 0.22
8 8 0.16
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:1430691 original size:28 final size:30
Alignment explanation
Indices: 1430659--1430727 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
1430649 AAATCAAATA
*
1430659 AAAAAGAAAA-TATTAATAAAATA-ATAAAT
1 AAAAATAAAAGTATTAATAAAATATAT-AAT
*
1430688 AAAAATAAATAGTATTAATATAATATATAAT
1 AAAAATAAA-AGTATTAATAAAATATATAAT
1430719 -AAAATAAAA
1 AAAAATAAAA
1430728 ATCAATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 9 0.26
30 9 0.26
31 15 0.43
32 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (30 bp):
AAAAATAAAAGTATTAATAAAATATATAAT
Found at i:1430707 original size:31 final size:30
Alignment explanation
Indices: 1430669--1430726 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
1430659 AAAAAGAAAA
1430669 TATTAATAAAATA-ATAAATAAAAATAAATAG
1 TATTAATAAAATATAT-AAT-AAAATAAATAG
*
1430700 TATTAATATAATATATAATAAAATAAA
1 TATTAATAAAATATATAATAAAATAAA
1430727 AATCAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 15 0.60
32 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (30 bp):
TATTAATAAAATATATAATAAAATAAATAG
Found at i:1430863 original size:37 final size:37
Alignment explanation
Indices: 1430742--1431093 Score: 285
Period size: 38 Copynumber: 9.4 Consensus size: 37
1430732 ATTTTAAAAC
* * *
1430742 TATATTATATACGT-TTTTGAAAATTGTTTTCAAAACCA
1 TATATTATATA--TATTTTCAAAAATGTTTTCAAAACAA
* *
1430780 TATAATA-ATATATTTTCAAAATTTAT-TTTTTAAAAC--
1 TATATTATATATATTTTCAAAA---ATGTTTTCAAAACAA
* * *
1430816 TACATAATATATATTTTCAAAAATATTTTCAAAACAA
1 TATATTATATATATTTTCAAAAATGTTTTCAAAACAA
* * *
1430853 TATATTATATATAATTTTTAAAAATGTTTTTAAAACTA
1 TATATTATATAT-ATTTTCAAAAATGTTTTCAAAACAA
* * * *
1430891 TATATTATATATAGTTTTTAAAACTGTTCTCAAAACTA
1 TATATTATATATA-TTTTCAAAAATGTTTTCAAAACAA
* * *
1430929 TATA-T-TATATAGTTTCAAAAATATTTTCAAAACCA
1 TATATTATATATATTTTCAAAAATGTTTTCAAAACAA
*
1430964 TATATTATATATATTTTC-AAAATATTTTCAAAAACTATATA
1 TATATTATATATATTTTCAAAAATGTTTTC-AAAAC---A-A
*
1431005 TTATATTATATATATTTTC-AAAATGTTTTCAAAAAAA
1 -TATATTATATATATTTTCAAAAATGTTTTCAAAACAA
* *
1431042 CTATATTTTATATATTTTTTC-AAAATGTTTTCAAAA-AC
1 -TATA--TTATATATATTTTCAAAAATGTTTTCAAAACAA
1431080 TATATTATATATAT
1 TATATTATATATAT
1431094 ATATATATAT
Statistics
Matches: 263, Mismatches: 31, Indels: 43
0.78 0.09 0.13
Matches are distributed among these distances:
34 2 0.01
35 41 0.16
36 30 0.11
37 53 0.20
38 75 0.29
39 29 0.11
41 5 0.02
42 28 0.11
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATTATATATATTTTCAAAAATGTTTTCAAAACAA
Found at i:1430888 original size:111 final size:110
Alignment explanation
Indices: 1430742--1431038 Score: 305
Period size: 111 Copynumber: 2.7 Consensus size: 110
1430732 ATTTTAAAAC
** * *
1430742 TATATTATATACGTTTTTGAAAATTGTTTTCAAAACCATATAATA-ATATA-TTTTCAAAATTTA
1 TATATTATATATATTTTT-AAAAATGTTTTCAAAACCATATAATATATATAGTTTTCAAAA-CT-
* * * *
1430805 TTTTTTAAAACTACATAATATATATTTTCAAAAATATTTTCAAAACAA
63 GTTCTCAAAACTACATAATATATAGTTTCAAAAATATTTTCAAAACAA
* * * *
1430853 TATATTATATATAATTTTTAAAAATGTTTTTAAAACTATATATTATATATAGTTTTTAAAACTGT
1 TATATTATATAT-ATTTTTAAAAATGTTTTCAAAACCATATAATATATATAGTTTTCAAAACTGT
* * *
1430918 TCTCAAAACTATATATTATATAGTTTCAAAAATATTTTCAAAACCA
65 TCTCAAAACTACATAATATATAGTTTCAAAAATATTTTCAAAACAA
* * * *
1430964 TATATTATATATA-TTTTCAAAATATTTTCAAAAACTATATATTATATTATATATATTTTCAAAA
1 TATATTATATATATTTTTAAAAATGTTTTC-AAAACCATATA--ATA-TATATA-GTTTTCAAAA
*
1431028 -TGTTTTCAAAA
61 CTGTTCTCAAAA
1431039 AAACTATATT
Statistics
Matches: 156, Mismatches: 22, Indels: 14
0.81 0.11 0.07
Matches are distributed among these distances:
109 13 0.08
110 12 0.08
111 86 0.55
112 13 0.08
113 24 0.15
114 8 0.05
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (110 bp):
TATATTATATATATTTTTAAAAATGTTTTCAAAACCATATAATATATATAGTTTTCAAAACTGTT
CTCAAAACTACATAATATATAGTTTCAAAAATATTTTCAAAACAA
Found at i:1431010 original size:42 final size:42
Alignment explanation
Indices: 1430964--1431103 Score: 191
Period size: 42 Copynumber: 3.3 Consensus size: 42
1430954 TTCAAAACCA
*
1430964 TATATTATATATATTTTCAAAATATTTTCAAAAACTATATAT
1 TATATTATATATATTTTCAAAATGTTTTCAAAAACTATATAT
1431006 TATATTATATATATTTTCAAAATGTTTTCAAAAAAACTATAT-T
1 TATATTATATATATTTTCAAAATGTTTTC--AAAAACTATATAT
1431049 T-TA-TATAT-T-TTTTCAAAATGTTTTCAAAAACTATATTAT
1 TATATTATATATATTTTCAAAATGTTTTCAAAAACTATA-TAT
1431088 ATATATATATATATAT
1 -TATAT-TATATATAT
1431104 ATATATATAT
Statistics
Matches: 87, Mismatches: 1, Indels: 17
0.83 0.01 0.16
Matches are distributed among these distances:
37 10 0.11
38 1 0.01
39 17 0.20
40 2 0.02
41 7 0.08
42 30 0.34
43 7 0.08
44 12 0.14
45 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (42 bp):
TATATTATATATATTTTCAAAATGTTTTCAAAAACTATATAT
Found at i:1431092 original size:2 final size:2
Alignment explanation
Indices: 1431080--1431117 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1431070 TTTCAAAAAC
1431080 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1431118 CAAAATGTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1431328 original size:18 final size:18
Alignment explanation
Indices: 1431268--1431330 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
1431258 TTATAATAAA
*
1431268 ATATTAATTATGATAATT
1 ATATTAATTATGATTATT
* *
1431286 AAATTAATGAATAGATTTATT
1 ATATTAAT-TAT-GA-TTATT
*
1431307 ATATTAATTATGATTCTT
1 ATATTAATTATGATTATT
1431325 ATATTA
1 ATATTA
1431331 TGATTCTTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
18 17 0.47
19 4 0.11
20 4 0.11
21 11 0.31
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (18 bp):
ATATTAATTATGATTATT
Found at i:1431366 original size:14 final size:14
Alignment explanation
Indices: 1431313--1431359 Score: 85
Period size: 14 Copynumber: 3.4 Consensus size: 14
1431303 TATTATATTA
1431313 ATTATGATTCTTAT
1 ATTATGATTCTTAT
1431327 ATTATGATTCTTAT
1 ATTATGATTCTTAT
1431341 ATTATGATTCTTAT
1 ATTATGATTCTTAT
*
1431355 GTTAT
1 ATTAT
1431360 AAATCTTCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (14 bp):
ATTATGATTCTTAT
Found at i:1431366 original size:28 final size:28
Alignment explanation
Indices: 1431313--1431366 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1431303 TATTATATTA
* *
1431313 ATTATGATTCTTATATTATGATTCTTAT
1 ATTATGATTCTTATATTATAAATCTTAT
*
1431341 ATTATGATTCTTATGTTATAAATCTT
1 ATTATGATTCTTATATTATAAATCTT
1431367 CAATATAATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (28 bp):
ATTATGATTCTTATATTATAAATCTTAT
Found at i:1432027 original size:15 final size:15
Alignment explanation
Indices: 1431990--1432028 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
1431980 TAATAGTTGC
*
1431990 ATTGCATATCATATA
1 ATTGCATATCAAATA
* *
1432005 GTTTCATATCAAATA
1 ATTGCATATCAAATA
1432020 ATTGCATAT
1 ATTGCATAT
1432029 TATATTTGAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (15 bp):
ATTGCATATCAAATA
Found at i:1432956 original size:29 final size:29
Alignment explanation
Indices: 1432910--1432965 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1432900 TATATTTAAT
**
1432910 TAGTTTATATGTAAAATATATAGTATATA
1 TAGTTTATATACAAAATATATAGTATATA
* *
1432939 TAGTTTATATACATAATATATGGTATA
1 TAGTTTATATACAAAATATATAGTATA
1432966 CAAATATCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.45
Consensus pattern (29 bp):
TAGTTTATATACAAAATATATAGTATATA
Found at i:1433015 original size:13 final size:13
Alignment explanation
Indices: 1432999--1433234 Score: 88
Period size: 13 Copynumber: 17.3 Consensus size: 13
1432989 AAATATAAAC
1432999 TATAGTTTATATA
1 TATAGTTTATATA
*
1433012 TATAGTATATATA
1 TATAGTTTATATA
*
1433025 TATAGTATATACTA
1 TATAGTTTATA-TA
*
1433039 TATAAATATT-T-TA
1 TAT-AGT-TTATATA
*
1433052 TATAGTTCAT-TA
1 TATAGTTTATATA
**
1433064 -ATAAATTATATA
1 TATAGTTTATATA
*
1433076 TATAGTTTATATG
1 TATAGTTTATATA
* *
1433089 TAAATTATATATATTA
1 TATAGT-T-TATA-TA
* *
1433105 TATAGTATATAAA
1 TATAGTTTATATA
**
1433118 TATCA-ACTATAATA
1 TAT-AGTTTAT-ATA
*
1433132 TATAGCTTAAATATAAA
1 TATAG-TT---TATATA
*
1433149 CTATAGCTTATATA
1 -TATAGTTTATATA
1433163 TATAGTTT-TATA
1 TATAGTTTATATA
* *
1433175 TATAGTTCATATG
1 TATAGTTTATATA
* *
1433188 TAAACTATATAGTATA
1 TATAGT-T-TA-TATA
1433204 TATAGTTTATATA
1 TATAGTTTATATA
* *
1433217 TGTAGTATATACTA
1 TATAGTTTATA-TA
1433231 TATA
1 TATA
1433235 AATAGTTTAT
Statistics
Matches: 163, Mismatches: 38, Indels: 43
0.67 0.16 0.18
Matches are distributed among these distances:
11 7 0.04
12 18 0.11
13 76 0.47
14 29 0.18
15 9 0.06
16 13 0.08
17 3 0.02
18 8 0.05
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:1433024 original size:22 final size:21
Alignment explanation
Indices: 1432925--1433055 Score: 74
Period size: 22 Copynumber: 6.1 Consensus size: 21
1432915 TATATGTAAA
1432925 ATATATAGTATATATAGTTTAT
1 ATATATA-TATATATAGTTTAT
* * * *
1432947 ATACATA-ATATATGGTATAC
1 ATATATATATATATAGTTTAT
*
1432967 AAATATCA-ACTATATAG--TAT
1 ATATAT-ATA-TATATAGTTTAT
* *
1432987 ATAAATATAAACTATAGTTTAT
1 ATATATATATA-TATAGTTTAT
*
1433009 ATATATAGTATATATA-TATAGT
1 ATATATA-TATATATAGTTTA-T
* *
1433031 ATATACTATATAAATATTTTAT
1 ATATA-TATATATATAGTTTAT
1433053 ATA
1 ATA
1433056 GTTCATTAAT
Statistics
Matches: 83, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
19 2 0.02
20 26 0.31
21 5 0.06
22 42 0.51
23 8 0.10
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (21 bp):
ATATATATATATATAGTTTAT
Found at i:1433033 original size:20 final size:20
Alignment explanation
Indices: 1432885--1433551 Score: 120
Period size: 20 Copynumber: 33.0 Consensus size: 20
1432875 AACTTTATTT
*
1432885 TATATAGTTTATA-TATATA
1 TATATAGTATATAGTATATA
* * *
1432904 TTTAATTAGTTTATATGTA-AAA
1 TAT-A-TAGTATATA-GTATATA
*
1432926 TATATAGTATATATAGTTTATA
1 TATATAG--TATATAGTATATA
* * * *
1432948 TACATAATATATGGTATACA
1 TATATAGTATATAGTATATA
* *
1432968 AATATCAACTATATAGTATATA
1 TATAT--AGTATATAGTATATA
* * *
1432990 AATATA-AACTATAGTTTATA
1 TATATAGTA-TATAGTATATA
1433010 TATATAGTATATA-TATATA
1 TATATAGTATATAGTATATA
* * *
1433029 GTATATACTATATA-AATATTT
1 -TATATAGTATATAGTATA-TA
*
1433050 TATATAGTTCATTAATA-AATTATA
1 TATATAG-T-A-T-ATAGTA-TATA
* *
1433074 TATATAGTTTATATGTAAATTA
1 TATATAGTATATA-GTATA-TA
*
1433096 TATATATTATATAGTATATA
1 TATATAGTATATAGTATATA
* *
1433116 AATATCA--ACTATAATATATA
1 TATAT-AGTA-TATAGTATATA
* * * **
1433136 GCT-TA-AATATAAACTATAGC
1 --TATATAGTATATAGTATATA
*
1433156 T-TATA-TATATAGT-TTTA
1 TATATAGTATATAGTATATA
*
1433173 TATATAGT-TCATATGTAAACTA
1 TATATAGTAT-ATA-GTATA-TA
*
1433195 TATAGTA-TATATAGTTTATA
1 TATA-TAGTATATAGTATATA
* *
1433215 TATGTAGTATATACTATATA
1 TATATAGTATATAGTATATA
* *
1433235 -A-ATAGTTTATTAAT-TA-A
1 TATATAGTATA-TAGTATATA
* *
1433252 TGTACTCAACTATATAGTATTCATA
1 TATA-T--AGTATATAGTA-T-ATA
* *
1433277 TATATAATATATACGT-TGAATT
1 TATATAGTATATA-GTAT--ATA
1433299 TATATAGTATA-A--AT-TA
1 TATATAGTATATAGTATATA
*
1433315 TATA-AGTATGA-ACTATAT-
1 TATATAGTAT-ATAGTATATA
*
1433333 TATATAGTATATA-AATATCA
1 TATATAGTATATAGTATAT-A
1433353 -ACTATAGTATATAGTATATA
1 TA-TATAGTATATAGTATATA
* *
1433373 AATATCAAT-TATAGTATATA
1 TATAT-AGTATATAGTATATA
1433393 GT-T-TA-TATATA-TATATA
1 -TATATAGTATATAGTATATA
* *
1433410 TATATAGTTTTTA-TATATA
1 TATATAGTATATAGTATATA
*
1433429 GT-TCATATGTAAACTA-TATAGTA
1 -TAT-ATA-GTATA-TAGTATA-TA
* *
1433452 TATCTAGTTTATA-TATATAA
1 TATATAGTATATAGTATAT-A
*
1433472 TATATAGTATATA-AATATCA
1 TATATAGTATATAGTATAT-A
* *
1433492 -ACTATAATATATATTATATA
1 TA-TATAGTATATAGTATATA
* * *
1433512 AATATA-AACTATAGTTTATA
1 TATATAGTA-TATAGTATATA
*
1433532 TATATAGTATATACTATATA
1 TATATAGTATATAGTATATA
1433552 AATAGTTTAT
Statistics
Matches: 480, Mismatches: 89, Indels: 157
0.66 0.12 0.22
Matches are distributed among these distances:
15 5 0.01
16 8 0.02
17 11 0.02
18 40 0.08
19 46 0.10
20 195 0.41
21 51 0.11
22 90 0.19
23 13 0.03
24 15 0.03
25 6 0.01
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (20 bp):
TATATAGTATATAGTATATA
Found at i:1433331 original size:27 final size:27
Alignment explanation
Indices: 1433301--1433537 Score: 155
Period size: 27 Copynumber: 8.7 Consensus size: 27
1433291 GTTGAATTTA
* * * *
1433301 TATAGTATAAATTATATAAGTATGAAC
1 TATAGTATATAGTATATAAATATCAAC
*
1433328 TATATTATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
*
1433355 TATAGTATATAGTATATAAATATCAAT
1 TATAGTATATAGTATATAAATATCAAC
* *
1433382 TATAGTATATAGTTTATATATAT--A-
1 TATAGTATATAGTATATAAATATCAAC
* * *
1433406 TATA-TATATAGTTTTTATATATAGTTCATATG
1 TATAGTATATAG--TATATAAATA--TCA-A-C
* * **
1433438 TAAACTATATAGTATATCTAGTTTAT-ATA-
1 TATAGTATATAGTATA--TA-AATATCA-AC
*
1433467 TATAATATATAGTATATAAATATCAAC
1 TATAGTATATAGTATATAAATATCAAC
* * *
1433494 TATAATATATATTATATAAATATAAAC
1 TATAGTATATAGTATATAAATATCAAC
*
1433521 TATAGTTTATA-TATATA
1 TATAGTATATAGTATATA
1433538 GTATATACTA
Statistics
Matches: 175, Mismatches: 20, Indels: 31
0.77 0.09 0.14
Matches are distributed among these distances:
23 7 0.04
24 4 0.02
25 11 0.06
26 10 0.06
27 106 0.61
29 14 0.08
30 1 0.01
31 6 0.03
32 4 0.02
33 9 0.05
34 3 0.02
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (27 bp):
TATAGTATATAGTATATAAATATCAAC
Found at i:1433345 original size:2 final size:2
Alignment explanation
Indices: 1433328--1433699 Score: 96
Period size: 2 Copynumber: 178.5 Consensus size: 2
1433318 AAGTATGAAC
*
1433328 TA TA T- TA TA TA GTA TA TA AA TA TCA -A CTA TA GTA TA TA GTA TA
1 TA TA TA TA TA TA -TA TA TA TA TA T-A TA -TA TA -TA TA TA -TA TA
* *
1433371 TA AA TA TCA -A T- TA TA GTA TA TA GTT TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * *
1433412 TA TA GTT TT TA TA TA TA GT- TCA TA TG TA AA CTA TA TA GTA TA TC
1 TA TA -TA TA TA TA TA TA -TA T-A TA TA TA TA -TA TA TA -TA TA TA
* *
1433456 TA GTT TA TA TA TA TA -A TA TA TA GTA TA TA AA TA TCA -A CTA TA
1 TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T-A TA -TA TA
* * *
1433498 -A TA TA TA T- TA TA TA AA TA TA AA CTA TA GTT TA TA TA TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA -TA
* * *
1433541 TA TA CTA TA TA AA TA GTT TA TA TA TA CTA -A TGA -A CTA TA TA GTT
1 TA TA -TA TA TA TA TA -TA TA TA TA TA -TA TA T-A TA -TA TA TA -TA
* * *
1433585 TA T- TA -A TA TA -A T- TA TA TA AA CTA TA TA CTT TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA
* * * *
1433624 T- TA -A TA TA AA CTA TA TA TA TG TA TA TA AA TA TA AA CTA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
1433666 TT TCA TA TA TA CA CTA TA TA TA TA TA TA TA -A TA T
1 TA T-A TA TA TA TA -TA TA TA TA TA TA TA TA TA TA T
1433700 TTTAAGAATT
Statistics
Matches: 271, Mismatches: 48, Indels: 102
0.64 0.11 0.24
Matches are distributed among these distances:
1 18 0.07
2 211 0.78
3 42 0.15
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1433403 original size:13 final size:13
Alignment explanation
Indices: 1433381--1433484 Score: 70
Period size: 13 Copynumber: 7.8 Consensus size: 13
1433371 TAAATATCAA
1433381 TTATAGTATATAGT
1 TTATA-TATATAGT
1433395 TTATATATATA--
1 TTATATATATAGT
1433406 -TATATATATAGT
1 TTATATATATAGT
*
1433418 TTTTATATATAGT
1 TTATATATATAGT
* * * *
1433431 TCATATGTAAACT
1 TTATATATATAGT
*
1433444 ATATAGTATATCTAGT
1 -T-TA-TATATATAGT
*
1433460 TTATATATATAAT
1 TTATATATATAGT
*
1433473 ATATAGTATATA
1 TTATA-TATATA
1433485 AATATCAACT
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
10 10 0.14
13 37 0.54
14 14 0.20
15 2 0.03
16 6 0.09
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (13 bp):
TTATATATATAGT
Found at i:1433454 original size:29 final size:29
Alignment explanation
Indices: 1433421--1433484 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1433411 ATATAGTTTT
*
1433421 TATATATAGTTCATATGTA-AACTATATAG
1 TATATATAGTTCATATATATAA-TATATAG
* *
1433450 TATATCTAGTTTATATATATAATATATAG
1 TATATATAGTTCATATATATAATATATAG
1433479 TATATA
1 TATATA
1433485 AATATCAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (29 bp):
TATATATAGTTCATATATATAATATATAG
Found at i:1433551 original size:9 final size:8
Alignment explanation
Indices: 1433328--1433699 Score: 96
Period size: 9 Copynumber: 44.6 Consensus size: 8
1433318 AAGTATGAAC
1433328 TATAT-TA
1 TATATATA
1433335 TATAGTATA
1 TATA-TATA
*
1433344 TAAATATCA
1 TATATAT-A
1433353 -ACTATAGTA
1 TA-TATA-TA
1433362 TATAGTATA
1 TATA-TATA
*
1433371 TAAATATCA
1 TATATAT-A
1433380 -AT-TATA
1 TATATATA
*
1433386 GTATATAGTT
1 -TATATA-TA
1433396 TATATATA
1 TATATATA
1433404 TATATATA
1 TATATATA
* *
1433412 TATAGTTTT
1 TATA-TATA
1433421 TATATATA
1 TATATATA
*
1433429 GT-TCATATG
1 -TAT-ATATA
*
1433438 TAAACTATA
1 TATA-TATA
*
1433447 TAGTATATC
1 TA-TATATA
*
1433456 TAGTTTATA
1 TA-TATATA
1433465 TATATA-A
1 TATATATA
1433472 TATATAGTA
1 TATATA-TA
*
1433481 TATAAATA
1 TATATATA
1433489 TCA-ACTATA
1 T-ATA-TATA
1433498 -ATATATA
1 TATATATA
1433505 T-TATATA
1 TATATATA
* *
1433512 AATATAAA
1 TATATATA
*
1433520 CTATAGTTTA
1 -TATA-TATA
1433530 TATATATA
1 TATATATA
1433538 GTATATACTA
1 -TATATA-TA
*
1433548 TATAAATA
1 TATATATA
*
1433556 GTTTATATA
1 -TATATATA
1433565 TACTA-ATGA
1 TA-TATAT-A
1433574 -ACTATATA
1 TA-TATATA
*
1433582 GTTTAT-TA
1 -TATATATA
1433590 -ATATA-A
1 TATATATA
1433596 T-TATATA
1 TATATATA
*
1433603 AACTATATA
1 TA-TATATA
* *
1433612 CTTTATAGTT
1 -TATATA-TA
1433622 TAT-TA-A
1 TATATATA
*
1433628 TATAAACTA
1 TATATA-TA
*
1433637 TATATATG
1 TATATATA
*
1433645 TATATAAA
1 TATATATA
*
1433653 TATAAACTA
1 TATATA-TA
*
1433662 TATATTTCA
1 TATATAT-A
*
1433671 TATATACA
1 TATATATA
1433679 CTATATATA
1 -TATATATA
1433688 TATATATA
1 TATATATA
1433696 -ATAT
1 TATAT
1433700 TTTAAGAATT
Statistics
Matches: 267, Mismatches: 50, Indels: 96
0.65 0.12 0.23
Matches are distributed among these distances:
6 12 0.04
7 31 0.12
8 81 0.30
9 132 0.49
10 11 0.04
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (8 bp):
TATATATA
Found at i:1433738 original size:24 final size:22
Alignment explanation
Indices: 1433712--1433833 Score: 71
Period size: 22 Copynumber: 5.7 Consensus size: 22
1433702 TAAGAATTTT
1433712 TATT-TTTATATTATT-AAAATA
1 TATTATTTA-ATTATTAAAAATA
1433733 TATTATTTAATTATTAAAAATA
1 TATTATTTAATTATTAAAAATA
**
1433755 TA--A-AAAATTATTATAAAATA
1 TATTATTTAATTATTA-AAAATA
* * *
1433775 TATTAGTATAATCT-TTTAAAATC
1 TATTA-TTTAAT-TATTAAAAATA
* **
1433798 TAATAAATAATTA-T-AAAATA
1 TATTATTTAATTATTAAAAATA
1433818 TATTATTTTAATTATT
1 TATTA-TTTAATTATT
1433834 TTAAAATACT
Statistics
Matches: 79, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
19 8 0.10
20 18 0.23
21 18 0.23
22 19 0.24
23 9 0.11
24 6 0.08
25 1 0.01
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (22 bp):
TATTATTTAATTATTAAAAATA
Found at i:1433767 original size:43 final size:43
Alignment explanation
Indices: 1433720--1433833 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 43
1433710 TTTATTTTTA
1433720 TATTATTAAAATATATTA-TTTAATTATTAAAAATATAAAAAAT
1 TATTA-TAAAATATATTAGTTTAATTATTAAAAATATAAAAAAT
* * * *
1433763 TATTATAAAATATATTAGTATAATCT-TTTAAAATCTAATAAAT
1 TATTATAAAATATATTAGTTTAAT-TATTAAAAATATAAAAAAT
* *
1433806 AATTATAAAATATATTATTTTAATTATT
1 TATTATAAAATATATTAGTTTAATTATT
1433834 TTAAAATACT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
42 13 0.21
43 47 0.77
44 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (43 bp):
TATTATAAAATATATTAGTTTAATTATTAAAAATATAAAAAAT
Found at i:1434770 original size:51 final size:51
Alignment explanation
Indices: 1434708--1434939 Score: 256
Period size: 51 Copynumber: 4.5 Consensus size: 51
1434698 TATTTACATA
* *
1434708 GGTGTAAGTATGTGTTAAGTGCTA-TCTTTTTTTATTTTATTTACTTTCAC
1 GGTGTAAGTATGTGTTAAGTGCTATTCTTTTTTTATTTTATTCACTTACAC
* *
1434758 AGTTGTAAGTATGTGTTAAGTGCTACATTTCTTTATTTTATTTTATTCACTAACACC
1 -GGTGTAAGTATGTGTTAAGTGCT--A-TTCTTT-TTTTATTTTATTCACTTACA-C
** * *
1434815 GGTGT-AGTATGTGTTAAGTGCTACACTTTTTTTGTTTTATTCACTTGCATC
1 GGTGTAAGTATGTGTTAAGTGCTATTCTTTTTTTATTTTATTCACTTACA-C
** *
1434866 GGTGTAAGTATGTGTTAAGTGCTACAC-TTGTTTATTTTATTCACTTACAC
1 GGTGTAAGTATGTGTTAAGTGCTATTCTTTTTTTATTTTATTCACTTACAC
*
1434916 TGGTGT-AGTAAGTGTTAAGTGCTA
1 -GGTGTAAGTATGTGTTAAGTGCTA
1434940 CACTCTTTTC
Statistics
Matches: 158, Mismatches: 15, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
50 18 0.11
51 69 0.44
52 25 0.16
53 2 0.01
55 22 0.14
56 21 0.13
57 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (51 bp):
GGTGTAAGTATGTGTTAAGTGCTATTCTTTTTTTATTTTATTCACTTACAC
Found at i:1434872 original size:107 final size:102
Alignment explanation
Indices: 1434708--1434953 Score: 316
Period size: 107 Copynumber: 2.3 Consensus size: 102
1434698 TATTTACATA
* * * * *
1434708 GGTGTAAGTATGTGTTAAGTGCTA-TCTTTTTTTATTTTATTTACTTTCACAGTTGTAAGTATGT
1 GGTGT-AGTATGTGTTAAGTGCTACACTTTTTTTGTTTTATTCACTTGCACAGGTGTAAGTATGT
*
1434772 GTTAAGTGCTACATTTCTTTATTTTATTTTATTCACTAACACC
65 GTTAAGTGCTACA---C-TT-GTTTATTTTATTCACTAACACC
1434815 GGTGTAGTATGTGTTAAGTGCTACACTTTTTTTGTTTTATTCACTTGCATC-GGTGTAAGTATGT
1 GGTGTAGTATGTGTTAAGTGCTACACTTTTTTTGTTTTATTCACTTGCA-CAGGTGTAAGTATGT
* *
1434879 GTTAAGTGCTACACTTGTTTATTTTATTCACTTACACT
65 GTTAAGTGCTACACTTGTTTATTTTATTCACTAACACC
*
1434917 GGTGTAGTAAGTGTTAAGTGCTACACTCTTTTCTTGT
1 GGTGTAGTATGTGTTAAGTGCTACACT-TTTT-TTGT
1434954 GTTTGATTGC
Statistics
Matches: 126, Mismatches: 9, Indels: 11
0.86 0.06 0.08
Matches are distributed among these distances:
102 45 0.36
103 6 0.05
104 5 0.04
106 18 0.14
107 51 0.40
108 1 0.01
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (102 bp):
GGTGTAGTATGTGTTAAGTGCTACACTTTTTTTGTTTTATTCACTTGCACAGGTGTAAGTATGTG
TTAAGTGCTACACTTGTTTATTTTATTCACTAACACC
Found at i:1435215 original size:20 final size:21
Alignment explanation
Indices: 1435177--1435216 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1435167 AGTCGTTGGG
*
1435177 GCCTGATGGTATCGTTACTAT
1 GCCTGATGGTATCGATACTAT
*
1435198 GCCT-ATGGTATTGATACTA
1 GCCTGATGGTATCGATACTA
1435217 CTATACAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.38
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:1441015 original size:27 final size:27
Alignment explanation
Indices: 1440977--1441041 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
1440967 GAGCAGTTTG
1440977 AACTCGACTTGGTTAAAATTCAATAAA
1 AACTCGACTTGGTTAAAATTCAATAAA
*
1441004 AACTCGACTTGGTTAAAATTTAATAAA
1 AACTCGACTTGGTTAAAATTCAATAAA
1441031 AACTCGACTTG
1 AACTCGACTTG
1441042 AGACCTTAAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (27 bp):
AACTCGACTTGGTTAAAATTCAATAAA
Found at i:1442644 original size:20 final size:20
Alignment explanation
Indices: 1442619--1442685 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 20
1442609 TTTTCCCAAT
1442619 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
1442639 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
1442659 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
1442680 TCGCAA
1 TCGCAA
1442686 CGCAAATTGG
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:1442661 original size:41 final size:41
Alignment explanation
Indices: 1442616--1442711 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
1442606 CGATTTTCCC
*
1442616 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGA
1442657 AATTCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGA
*
1442698 AAATCGCAATGCGA
1 AATTCGCAATGCGA
1442712 TACTGACTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGA
Found at i:1442665 original size:21 final size:20
Alignment explanation
Indices: 1442619--1442711 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
1442609 TTTTCCCAAT
*
1442619 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
1442639 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
1442659 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* * **
1442680 TCGCAACGCAAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
1442701 TCGCAATGCGA
1 TCGCAATGCGA
1442712 TACTGACTAT
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 28 0.50
21 28 0.50
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:1442725 original size:20 final size:20
Alignment explanation
Indices: 1442700--1442793 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
1442690 AATTGGGAAA
*
1442700 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
1442720 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
1442741 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
1442761 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
*
1442781 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1442794 TTACTTAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1442774 original size:41 final size:41
Alignment explanation
Indices: 1442697--1442774 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1442687 GCAAATTGGG
* * **
1442697 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
* *
1442738 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
1442775 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAA
Found at i:1443060 original size:27 final size:27
Alignment explanation
Indices: 1443004--1443063 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1442994 ATCGCCGGCG
* *
1443004 AAATCCCTCACAACCATTCACAGTCAA
1 AAATCCCTCACAACCATTCAAAATCAA
* *
1443031 AAATCCCTCACAATCATTCAGAAATGAA
1 AAATCCCTCACAACCATTCA-AAATCAA
1443059 AAATC
1 AAATC
1443064 AACCTCCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.45, C:0.30, G:0.05, T:0.20
Consensus pattern (27 bp):
AAATCCCTCACAACCATTCAAAATCAA
Found at i:1443371 original size:19 final size:19
Alignment explanation
Indices: 1443347--1443391 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1443337 GCAACGAGAT
*
1443347 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
1443366 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
1443385 AATCGCA
1 AATCGCA
1443392 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:1443409 original size:19 final size:19
Alignment explanation
Indices: 1443387--1443571 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
1443377 GAAACCAAAA
*
1443387 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1443406 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1443425 TCGCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
1443444 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1443464 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1443480 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1443497 TCGCGTTGTGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1443511 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1443530 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1443550 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1443570 TC
1 TC
1443572 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1443464 original size:39 final size:38
Alignment explanation
Indices: 1443387--1443476 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
1443377 GAAACCAAAA
* *
1443387 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
1443425 TCGCGTTGCGATTTTAATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTAATTTCGC-GTTGCGATTTTCATT
1443464 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1443477 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTAATTTCGCGTTGCGATTTTCATT
Found at i:1443496 original size:33 final size:33
Alignment explanation
Indices: 1443459--1443546 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
1443449 GTTGCGATTT
* *
1443459 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
* *
1443492 TCATTTCGCGTTGTGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1443525 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1443547 ATTATCTCGT
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.11, C:0.24, G:0.25, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1443548 original size:20 final size:20
Alignment explanation
Indices: 1443514--1443571 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
1443504 GTGATTCTCT
**
1443514 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
1443534 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
1443554 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
1443572 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:1445630 original size:42 final size:42
Alignment explanation
Indices: 1445570--1445692 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
1445560 GCCCGACTCG
* * *
1445570 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1445612 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
1445654 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
1445693 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1445650 original size:21 final size:21
Alignment explanation
Indices: 1445626--1445692 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1445616 TCATTCCTCG
1445626 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1445647 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1445668 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1445689 AGAG
1 AGAG
1445693 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1447068 original size:14 final size:14
Alignment explanation
Indices: 1447049--1447084 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1447039 ATTGTTTAAT
1447049 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1447063 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1447077 TGATTTGT
1 TGATTTGT
1447085 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1447285 original size:19 final size:19
Alignment explanation
Indices: 1447263--1447380 Score: 76
Period size: 19 Copynumber: 6.7 Consensus size: 19
1447253 CGAAATTAAA
1447263 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1447282 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1447297 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1447315 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1447330 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1447348 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1447367 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1447381 GGACATTAAG
Statistics
Matches: 73, Mismatches: 15, Indels: 21
0.67 0.14 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1447309 original size:33 final size:33
Alignment explanation
Indices: 1447267--1447360 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
1447257 ATTAAATTCG
1447267 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1447300 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1447333 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1447361 AGTAATTTCC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1449665 original size:12 final size:12
Alignment explanation
Indices: 1449648--1449672 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1449638 TCTTCGGGGA
1449648 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1449660 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1449672 C
1 C
1449673 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1451169 original size:14 final size:14
Alignment explanation
Indices: 1451150--1451186 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1451140 CATCAATTAA
1451150 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1451164 ACAAATCATCTTTT
1 ACAAATCAACATTT
1451178 ACAAATCAA
1 ACAAATCAA
1451187 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1451576 original size:20 final size:20
Alignment explanation
Indices: 1451551--1451601 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1451541 ATTCATTTGA
1451551 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
1451571 CTATCGCAACGTGAAAATGG
1 CTATCGCAACGTGAAAATGG
*
1451591 TTATCGCAACG
1 CTATCGCAACG
1451602 AGAATATCGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (20 bp):
CTATCGCAACGTGAAAATGG
Found at i:1451651 original size:14 final size:15
Alignment explanation
Indices: 1451631--1451703 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
1451621 TGAAAATCGC
1451631 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
1451646 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
1451663 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
1451681 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
1451697 -TTGCGAT
1 ATTGCGAT
1451704 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:1451668 original size:19 final size:19
Alignment explanation
Indices: 1451627--1451693 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
1451617 GAAATGAAAA
1451627 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
1451643 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1451660 TCGCATTGCGA-TTTCATT
1 TCGCATTGCGATTTTCATT
1451678 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1451694 TCGTTGCGAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
18 18 0.40
19 10 0.22
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1451829 original size:14 final size:14
Alignment explanation
Indices: 1451810--1451846 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1451800 CATCAATTAA
1451810 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1451824 ACAAATCATCTTTT
1 ACAAATCAACATTT
1451838 ACAAATCAA
1 ACAAATCAA
1451847 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1453734 original size:20 final size:19
Alignment explanation
Indices: 1453699--1453765 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1453689 CGAACTTAAA
1453699 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1453718 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
1453738 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
1453757 ATCGCAACG
1 ATCGCAACG
1453766 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1453773 original size:14 final size:14
Alignment explanation
Indices: 1453754--1453811 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1453744 ATGCGAAATG
1453754 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1453768 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1453784 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1453800 AAAATCGCAACG
1 AAAATCGCAACG
1453812 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1453796 original size:32 final size:33
Alignment explanation
Indices: 1453738--1453816 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1453728 GGAAATGGCT
*
1453738 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1453771 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1453803 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1453817 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1453849 original size:18 final size:18
Alignment explanation
Indices: 1453823--1453916 Score: 80
Period size: 18 Copynumber: 5.7 Consensus size: 18
1453813 GAAACACAAA
*
1453823 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
1453841 TCGCGTTGCGA-TT--TG
1 TCGCGTTGCGATTTCATT
1453856 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
1453872 TCGCGTTGCGATTT--TG
1 TCGCGTTGCGATTTCATT
1453888 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
*
1453905 TCGCATTGCGAT
1 TCGCGTTGCGAT
1453917 AGCCATTTCC
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
13 8 0.13
14 10 0.17
15 5 0.08
16 4 0.07
17 4 0.07
18 22 0.37
19 7 0.12
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:1453860 original size:13 final size:14
Alignment explanation
Indices: 1453844--1453900 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1453834 TTTCATTTCG
1453844 CGTTGCGA-TTTGT
1 CGTTGCGATTTTGT
*
1453857 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1453873 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1453889 CGTTGCGATTTT
1 CGTTGCGATTTT
1453901 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
13 8 0.22
14 14 0.38
16 4 0.11
18 11 0.30
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1453866 original size:31 final size:31
Alignment explanation
Indices: 1453828--1453916 Score: 151
Period size: 31 Copynumber: 2.8 Consensus size: 31
1453818 ACAAATCGCA
1453828 TTGCGATTTCATTTCGCGTTGCGATTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTTGTCG
1453859 TTGCGATTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCGTTGCGA-TTTGTCG
*
1453891 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGA-TTTCATTTCGCGTTGCGAT
1453917 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
31 24 0.44
32 14 0.25
33 17 0.31
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (31 bp):
TTGCGATTTCATTTCGCGTTGCGATTTGTCG
Found at i:1453955 original size:20 final size:20
Alignment explanation
Indices: 1453901--1453944 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1453891 TTGCGATTTT
1453901 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
1453920 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
1453940 CATTT
1 CATTT
1453945 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:1454451 original size:18 final size:18
Alignment explanation
Indices: 1454425--1454469 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1454415 GTCGATCAGA
*
1454425 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
1454443 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
1454461 TGATGGCTC
1 TGATGGCTC
1454470 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:1456102 original size:22 final size:22
Alignment explanation
Indices: 1456077--1456120 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1456067 GATTTAGATA
1456077 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1456099 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1456121 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1456333 original size:20 final size:20
Alignment explanation
Indices: 1456308--1456401 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
1456298 GATTATGTAT
1456308 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1456328 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
1456348 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
1456369 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1456389 TATCGCATTGCGA
1 TATCGCGTTGCGA
1456402 TTTACTTATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1456402 original size:20 final size:20
Alignment explanation
Indices: 1456288--1456402 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1456278 CGCTTTGAAA
*
1456288 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1456309 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1456329 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
1456349 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1456370 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1456390 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1456403 TTACTTATTC
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1456433 original size:21 final size:20
Alignment explanation
Indices: 1456391--1456462 Score: 99
Period size: 20 Copynumber: 3.5 Consensus size: 20
1456381 ATAGTCAGTA
1456391 TCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
1456411 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
1456432 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
1456452 TCGCATTGCGA
1 TCGCATTGCGA
1456463 ATTGGGAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 27 0.63
21 16 0.37
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:1460142 original size:15 final size:15
Alignment explanation
Indices: 1460119--1460148 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1460109 TTATTGTATT
1460119 ATACCACACTTTACC
1 ATACCACACTTTACC
*
1460134 ATACTACACTTTACC
1 ATACCACACTTTACC
1460149 CCTTTGCATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (15 bp):
ATACCACACTTTACC
Found at i:1466244 original size:190 final size:190
Alignment explanation
Indices: 1465921--1466302 Score: 764
Period size: 190 Copynumber: 2.0 Consensus size: 190
1465911 AAATCAAGGA
1465921 TGGAAGCCAGTCTCGCCGAGAGTCATGATCGTCTTGAATTGGAACTATTGAGGGCTTCAAACCCT
1 TGGAAGCCAGTCTCGCCGAGAGTCATGATCGTCTTGAATTGGAACTATTGAGGGCTTCAAACCCT
1465986 TAAACATTTCATGCTCTTAGGCATTATATCGCCTTTAAAGGACCTCGTGTAATATTCTCGCACAA
66 TAAACATTTCATGCTCTTAGGCATTATATCGCCTTTAAAGGACCTCGTGTAATATTCTCGCACAA
1466051 GGGTCAACTCCGACGACAATGTTACCGATGTTAATATTCGAACGAACGCGAATAGAAGCG
131 GGGTCAACTCCGACGACAATGTTACCGATGTTAATATTCGAACGAACGCGAATAGAAGCG
1466111 TGGAAGCCAGTCTCGCCGAGAGTCATGATCGTCTTGAATTGGAACTATTGAGGGCTTCAAACCCT
1 TGGAAGCCAGTCTCGCCGAGAGTCATGATCGTCTTGAATTGGAACTATTGAGGGCTTCAAACCCT
1466176 TAAACATTTCATGCTCTTAGGCATTATATCGCCTTTAAAGGACCTCGTGTAATATTCTCGCACAA
66 TAAACATTTCATGCTCTTAGGCATTATATCGCCTTTAAAGGACCTCGTGTAATATTCTCGCACAA
1466241 GGGTCAACTCCGACGACAATGTTACCGATGTTAATATTCGAACGAACGCGAATAGAAGCG
131 GGGTCAACTCCGACGACAATGTTACCGATGTTAATATTCGAACGAACGCGAATAGAAGCG
1466301 TG
1 TG
1466303 TTTGATTTGT
Statistics
Matches: 192, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
190 192 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (190 bp):
TGGAAGCCAGTCTCGCCGAGAGTCATGATCGTCTTGAATTGGAACTATTGAGGGCTTCAAACCCT
TAAACATTTCATGCTCTTAGGCATTATATCGCCTTTAAAGGACCTCGTGTAATATTCTCGCACAA
GGGTCAACTCCGACGACAATGTTACCGATGTTAATATTCGAACGAACGCGAATAGAAGCG
Found at i:1469366 original size:19 final size:20
Alignment explanation
Indices: 1469344--1469384 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1469334 GAATCCTTCG
1469344 TCGTGAA-TTGAAATCGAAC
1 TCGTGAAGTTGAAATCGAAC
1469363 TCGTGAAGTTGAAATCGAAC
1 TCGTGAAGTTGAAATCGAAC
1469383 TC
1 TC
1469385 AAGTTCTGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (20 bp):
TCGTGAAGTTGAAATCGAAC
Found at i:1469533 original size:23 final size:24
Alignment explanation
Indices: 1469499--1469550 Score: 97
Period size: 23 Copynumber: 2.2 Consensus size: 24
1469489 GTTGAACTTG
1469499 CGTTGCCTGGAGTCCAATATCCTT
1 CGTTGCCTGGAGTCCAATATCCTT
1469523 CGTTG-CTGGAGTCCAATATCCTT
1 CGTTGCCTGGAGTCCAATATCCTT
1469546 CGTTG
1 CGTTG
1469551 TGAAGTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35
Consensus pattern (24 bp):
CGTTGCCTGGAGTCCAATATCCTT
Found at i:1469711 original size:105 final size:105
Alignment explanation
Indices: 1469523--1470093 Score: 1058
Period size: 105 Copynumber: 5.5 Consensus size: 105
1469513 CAATATCCTT
*
1469523 CGTTG-CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTT
1 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
1469587 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
* * *
1469627 CGTTGTTTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAATTTGAGAAATGTTT
1 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
*
1469692 GTTGACAACCAGCGGTCCCTTCGTCTTGAAGTTGAACTTG
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
*
1469732 TGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
1 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
1469797 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
*
1469837 CGTTGTATGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
1 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
1469902 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1469942 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
1 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
1470007 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
66 GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
1470047 CGTTGTCTGGAGTCCAATATCCTTCGTT-TGAAGTTGAAATT-GCTCTG
1 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1470094 GGTAAAACCT
Statistics
Matches: 455, Mismatches: 11, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
103 6 0.01
104 18 0.04
105 431 0.95
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (105 bp):
CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTT
GTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
Found at i:1470902 original size:7 final size:7
Alignment explanation
Indices: 1470890--1470946 Score: 82
Period size: 7 Copynumber: 8.1 Consensus size: 7
1470880 ACGTTTTTTC
1470890 TTTCTTT
1 TTTCTTT
1470897 TTTCTTT
1 TTTCTTT
1470904 TTTCTTT
1 TTTCTTT
1470911 TTTCTTT
1 TTTCTTT
1470918 TTT-TTT
1 TTTCTTT
1470924 CTTTCTTT
1 -TTTCTTT
1470932 TTTCATTT
1 TTTC-TTT
1470940 TTT-TTT
1 TTTCTTT
1470946 T
1 T
1470947 CAACTTAGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
6 7 0.15
7 31 0.66
8 9 0.19
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTCTTT
Found at i:1480036 original size:16 final size:16
Alignment explanation
Indices: 1479996--1480041 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
1479986 AATGGTTAGT
*
1479996 AAAATAAAAATAAATG
1 AAAATAAAAATAAAAG
1480012 AAAATAAAAATAACAAG
1 AAAATAAAAATAA-AAG
1480029 AAAA-AAAACATAA
1 AAAATAAAA-ATAA
1480042 GAAAAAACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.13
Consensus pattern (16 bp):
AAAATAAAAATAAAAG
Found at i:1482851 original size:12 final size:12
Alignment explanation
Indices: 1482825--1482867 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1482815 AGAAAAAATG
1482825 TAATA-AATATA
1 TAATATAATATA
*
1482836 TAATATAATTTA
1 TAATATAATATA
1482848 TAATATAA-ATA
1 TAATATAATATA
1482859 TATATATAA
1 TA-ATATAA
1482868 GGACGAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TAATATAATATA
Found at i:1485313 original size:18 final size:18
Alignment explanation
Indices: 1485292--1485343 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
1485282 TTTTTTAAAA
1485292 TCATATTTAATTTTT-ATT
1 TCATATTTAATTTTTCA-T
1485310 TCAT-TTTAATATTTTCAT
1 TCATATTTAAT-TTTTCAT
*
1485328 TCAAAATTTAATTTTT
1 TC-ATATTTAATTTTT
1485344 TAATTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 6 0.21
18 11 0.38
19 6 0.21
20 6 0.21
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (18 bp):
TCATATTTAATTTTTCAT
Found at i:1485353 original size:14 final size:14
Alignment explanation
Indices: 1485334--1485360 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1485324 TCATTCAAAA
1485334 TTTAATTTTTTAAT
1 TTTAATTTTTTAAT
1485348 TTTAATTTTTTAA
1 TTTAATTTTTTAA
1485361 AATTTAGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAATTTTTTAAT
Found at i:1491020 original size:20 final size:21
Alignment explanation
Indices: 1490995--1491034 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1490985 CTTCACATAG
1490995 TAGTATCGATACCAT-AGGCT
1 TAGTATCGATACCATCAGGCT
1491015 TAGTATCGATACCATCAGGC
1 TAGTATCGATACCATCAGGC
1491035 CCAACGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATCAGGCT
Found at i:1497071 original size:18 final size:18
Alignment explanation
Indices: 1497025--1497098 Score: 85
Period size: 19 Copynumber: 4.0 Consensus size: 18
1497015 ATGAACTTGA
*
1497025 AAAATAAGCTATGAATCT
1 AAAATAAGTTATGAATCT
1497043 AAAATTAAGTTATGAATCT
1 AAAA-TAAGTTATGAATCT
*
1497062 AAAATAAGTTATGAGTCT
1 AAAATAAGTTATGAATCT
* * *
1497080 GGAAACAAGTTTTGAATCT
1 -AAAATAAGTTATGAATCT
1497099 GAGAATGAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
18 17 0.35
19 31 0.65
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (18 bp):
AAAATAAGTTATGAATCT
Found at i:1497265 original size:39 final size:39
Alignment explanation
Indices: 1497220--1497302 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
1497210 AAAAAGAAAA
*
1497220 TGATATGACTATTACGTATGATATTATTCATTATGGCTT
1 TGATATGACTATTACGTATGATATTATTCATCATGGCTT
** * * *
1497259 TGATATGACTATTTTGTATGATATTGTTTATCATGGTTT
1 TGATATGACTATTACGTATGATATTATTCATCATGGCTT
1497298 TGATA
1 TGATA
1497303 AAATCATGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.27, C:0.07, G:0.17, T:0.49
Consensus pattern (39 bp):
TGATATGACTATTACGTATGATATTATTCATCATGGCTT
Found at i:1501309 original size:32 final size:31
Alignment explanation
Indices: 1501207--1501324 Score: 157
Period size: 31 Copynumber: 3.8 Consensus size: 31
1501197 CCTAACATTT
*
1501207 ACTTTTTGTTTCATTTTAGTACATGTCGTCA
1 ACTTTTTGTTTCATTTTAGTACCTGTCGTCA
1501238 ACTTTTTGTTTCATTTTAGTACCTGTCGTCA
1 ACTTTTTGTTTCATTTTAGTACCTGTCGTCA
* * *
1501269 ACTTTTTGTTTCATTTTAATACCCT-ACTGTTA
1 ACTTTTTGTTTCATTTTAGTA-CCTGTC-GTCA
* *
1501301 ACTTTTTGTTTTATTTTATTACCT
1 ACTTTTTGTTTCATTTTAGTACCT
1501325 AAATTTTTAA
Statistics
Matches: 79, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
31 54 0.68
32 25 0.32
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (31 bp):
ACTTTTTGTTTCATTTTAGTACCTGTCGTCA
Found at i:1501324 original size:63 final size:62
Alignment explanation
Indices: 1501207--1501324 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 62
1501197 CCTAACATTT
* *
1501207 ACTTTTTGTTTCATTTTAGTACATGTCGTCAACTTTTTGTTTCATTTTAGTACCTGTCGTCA
1 ACTTTTTGTTTCATTTTAATACATCTCGTCAACTTTTTGTTTCATTTTAGTACCTGTCGTCA
* * * *
1501269 ACTTTTTGTTTCATTTTAATAC-CCTACTGTTAACTTTTTGTTTTATTTTATTACCT
1 ACTTTTTGTTTCATTTTAATACATCT-C-GTCAACTTTTTGTTTCATTTTAGTACCT
1501325 AAATTTTTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
61 1 0.02
62 22 0.46
63 25 0.52
ACGTcount: A:0.19, C:0.17, G:0.09, T:0.55
Consensus pattern (62 bp):
ACTTTTTGTTTCATTTTAATACATCTCGTCAACTTTTTGTTTCATTTTAGTACCTGTCGTCA
Found at i:1504652 original size:20 final size:19
Alignment explanation
Indices: 1504621--1504660 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1504611 TTATCACACC
*
1504621 AAATTTTCTCAAATTCTCT
1 AAATTTTCTCAAATACTCT
1504640 AAATTTCTCTCAAATACTCT
1 AAATTT-TCTCAAATACTCT
1504660 A
1 A
1504661 TCTTTTTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATTTTCTCAAATACTCT
Found at i:1504927 original size:111 final size:111
Alignment explanation
Indices: 1504786--1505118 Score: 587
Period size: 111 Copynumber: 3.0 Consensus size: 111
1504776 TGTAAATCAT
* *
1504786 ATATCTCTACACTTTGCTGATACGGA-AACATTTTAACTTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCGACACTTTGCTGATAC-GATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
*
1504850 ATATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
65 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1504897 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1504962 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
1505008 ATATCTTGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
1505073 TAATTAGTTGATTTATTTAATGTATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1505119 TTTTTGTAAT
Statistics
Matches: 214, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
110 2 0.01
111 212 0.99
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1510629 original size:12 final size:12
Alignment explanation
Indices: 1510612--1510648 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1510602 ATTTATAAGA
1510612 GAGGAGAGATGC
1 GAGGAGAGATGC
*
1510624 GA-G-GAGATGT
1 GAGGAGAGATGC
1510634 GAGGAGAGATGC
1 GAGGAGAGATGC
1510646 GAG
1 GAG
1510649 AACCGGAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.11
Consensus pattern (12 bp):
GAGGAGAGATGC
Found at i:1510866 original size:51 final size:51
Alignment explanation
Indices: 1510811--1510922 Score: 118
Period size: 51 Copynumber: 2.2 Consensus size: 51
1510801 AGCGCGAAGG
* * * *
1510811 AGGGGGCGCGATATAC-CCAACGTGTAACCCAGCCAGCGTATAGCGCGGTAC
1 AGGGGGCGCGATATACTCC-ACGTGGAACCAAACCAGCATATAGCGCGGTAC
* * ** * *
1510862 AGGGGGCGTGCTATACTCCACGTGGCGCCAAATCAGCATATAGCGCGGTTC
1 AGGGGGCGCGATATACTCCACGTGGAACCAAACCAGCATATAGCGCGGTAC
1510913 AGGGGGCGCG
1 AGGGGGCGCG
1510923 CTTTACTGCT
Statistics
Matches: 49, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
51 47 0.96
52 2 0.04
ACGTcount: A:0.22, C:0.28, G:0.35, T:0.15
Consensus pattern (51 bp):
AGGGGGCGCGATATACTCCACGTGGAACCAAACCAGCATATAGCGCGGTAC
Found at i:1525841 original size:15 final size:15
Alignment explanation
Indices: 1525823--1525856 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1525813 AAAATAAAAT
1525823 ATCCTAAAATTCTTA
1 ATCCTAAAATTCTTA
1525838 ATCCTAAAATTCTTA
1 ATCCTAAAATTCTTA
1525853 ATCC
1 ATCC
1525857 CTTCCCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (15 bp):
ATCCTAAAATTCTTA
Found at i:1528092 original size:42 final size:42
Alignment explanation
Indices: 1528032--1528523 Score: 379
Period size: 42 Copynumber: 11.9 Consensus size: 42
1528022 ATGTACTTTA
* * *
1528032 GTGGCGTTTTAAGCACAAACGCCGCTAATTTCACGTAC-TTC
1 GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTACATAC
* * * * *
1528073 AGTGGTGTTTAACGTACAAACGCCGCTAATTACACGCACTATA-
1 -GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTAC-ATAC
* * * * * * *
1528116 GTGGCATTTT-TGTATAAACACCGATAAATAC-TGTACATAC
1 GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTACATAC
* *
1528156 GTGGCGTTTTAT--ACAAACGCCGCTAGTTACACGTACATGC
1 GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTACATAC
*
1528196 GTGGCGTTTTAAGCACAAACGCCGCTAATTACACGTACATAC
1 GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTACATAC
* *
1528238 GTGGTGTTTTATGCACAAACGCCACTAATTACACGTACATAC
1 GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTACATAC
*
1528280 GTGGCGTTTTATGCACAAACGCCACTAATTACACGTACATAC
1 GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTACATAC
* * * * *
1528322 GTGGCGTTTTATGTACAAACGCCACGAATTACATGCACTATA-
1 GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTAC-ATAC
* * * * * * *
1528364 GTGGTGTTTTTAT--ATAAACGTCGATAAATA-ATGTACTTTA-
1 GTGGCG-TTTTATGCACAAACGCCGCTAATTACACGTAC-ATAC
* * *
1528404 GTGGCGTTTTTAT--ACAAACGCCGCTAA--AGGACTTACTTTA-
1 GTGGCG-TTTTATGCACAAACGCCGCTAATTA-CACGTAC-ATAC
* ** * * *
1528444 GTGGCGTTTTAAGTGCAAATGCCGCTAATTACACGTTCTTTA-
1 GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTAC-ATAC
* * *
1528486 GTGGCATTTTATGCAAAAATGCCGCTAATTACACGTAC
1 GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTAC
1528524 TCTAGTTGCA
Statistics
Matches: 372, Mismatches: 63, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
38 1 0.00
39 21 0.06
40 75 0.20
41 40 0.11
42 224 0.60
43 10 0.03
44 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (42 bp):
GTGGCGTTTTATGCACAAACGCCGCTAATTACACGTACATAC
Found at i:1528470 original size:248 final size:247
Alignment explanation
Indices: 1528032--1528523 Score: 605
Period size: 248 Copynumber: 2.0 Consensus size: 247
1528022 ATGTACTTTA
* * * *
1528032 GTGGCGTTTTAAGCACAAACGCCGCTAATTTCACGTACTTCAGTGGTGTTTAACGTACAAACGCC
1 GTGGCGTTTTAAGCACAAACGCCACTAATTACACGTACTACAGTGGCGTTTAACGTACAAACGCC
* * * *
1528097 GCTAATTACACGCACTATAGTGGCATTTTTGTATAAACACCGATAAATACTGTACATACGTGGCG
66 ACGAATTACACGCACTATAGTGGCATTTTTATATAAACACCGATAAATAATGTACATACGTGGCG
* *
1528162 TTTTATACAAACGCCGCTAGTTACACGTACATGCGTGGCGTTTTAAGCACAAACGCCGCTAATTA
131 TTTTATACAAACGCCGCTAG-AACACGTACATGAGTGGCGTTTTAAGCACAAACGCCGCTAATTA
** *
1528227 CACGTAC-ATACGTGGTGTTTTATGCACAAACGCCACTAATTACACGTACATAC
195 CACGTACTATA-GTGGCATTTTATGCAAAAACGCCACTAATTACACGTACATAC
* * *
1528280 GTGGCGTTTTATGCACAAACGCCACTAATTACACGTACATAC-GTGGCGTTTTATGTACAAACGC
1 GTGGCGTTTTAAGCACAAACGCCACTAATTACACGTAC-TACAGTGGCGTTTAACGTACAAACGC
* ** ** *
1528344 CACGAATTACATGCACTATAGTGGTGTTTTTATATAAACGTCGATAAATAATGTACTTTA-GTGG
65 CACGAATTACACGCACTATAGTGGCATTTTTATATAAACACCGATAAATAATGTAC-ATACGTGG
* * * * ** *
1528408 CGTTTTTATACAAACGCCGCTA-AAGGACTTACTTTAGTGGCGTTTTAAGTGCAAATGCCGCTAA
129 CG-TTTTATACAAACGCCGCTAGAA-CACGTACATGAGTGGCGTTTTAAGCACAAACGCCGCTAA
* * * *
1528472 TTACACGTTCTTTAGTGGCATTTTATGCAAAAATGCCGCTAATTACACGTAC
192 TTACACGTACTATAGTGGCATTTTATGCAAAAACGCCACTAATTACACGTAC
1528524 TCTAGTTGCA
Statistics
Matches: 206, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
247 1 0.00
248 180 0.87
249 25 0.12
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (247 bp):
GTGGCGTTTTAAGCACAAACGCCACTAATTACACGTACTACAGTGGCGTTTAACGTACAAACGCC
ACGAATTACACGCACTATAGTGGCATTTTTATATAAACACCGATAAATAATGTACATACGTGGCG
TTTTATACAAACGCCGCTAGAACACGTACATGAGTGGCGTTTTAAGCACAAACGCCGCTAATTAC
ACGTACTATAGTGGCATTTTATGCAAAAACGCCACTAATTACACGTACATAC
Found at i:1528476 original size:164 final size:163
Alignment explanation
Indices: 1528280--1528763 Score: 563
Period size: 164 Copynumber: 2.9 Consensus size: 163
1528270 ACGTACATAC
* * * * * * * *
1528280 GTGGCGTTTTATGCACAAACGCCACTAATTACACGTACATACGTGGCGTTTTATGTACAAACGCC
1 GTGGCGTTTTAAGCACAAATGCCGCTAATTACACGTTCTTA-GTGGCATTTTATGCACAAATGCC
* * * * * *
1528345 ACGAATTACATGCACTATAGTGGTGTTTTTATATAAACGTCGATAAATAATGTACTTTAGTGGCG
65 GCTAATTACACGTACTATAGTGGCGTTTTTATATAAACGCCGATAAATAATGTACTTTAGTGGCG
*
1528410 TTTTTATACAAACGCCGCTAAAGGACTTACTTTA
130 TTTTTATACAAACGCCGCTAAAGGACGTACTTTA
** *
1528444 GTGGCGTTTTAAGTGCAAATGCCGCTAATTACACGTTCTTTAGTGGCATTTTATGCAAAAATGCC
1 GTGGCGTTTTAAGCACAAATGCCGCTAATTACACGTTC-TTAGTGGCATTTTATGCACAAATGCC
* * * * * * *
1528509 GCTAATTACACGTACTCTAGTTGCATTTTTATATAAACACCGAGAAATATTGTACTTTAGTGGCA
65 GCTAATTACACGTACTATAGTGGCGTTTTTATATAAACGCCGATAAATAATGTACTTTAGTGGCG
*
1528574 TTTTTATACAAACGCCGCTAAAGGTCGTACTTTA
130 TTTTTATACAAACGCCGCTAAAGGACGTACTTTA
** * * * **
1528608 GTGGCGTTGCAAGCACAAATGCCGCTAATTACACATTTTTTTGTGGCATTTTACACACAAATGCC
1 GTGGCGTTTTAAGCACAAATGCCGCTAATTACAC-GTTCTTAGTGGCATTTTATGCACAAATGCC
* * * * *
1528673 GCTAATTACACATACTTTAGTGGCGTTTTTAACATAAACGCCGCTAAATACTAGTACTTTAGTGG
65 GCTAATTACACGTACTATAGTGGCGTTTTT-ATATAAACGCCGATAAATAAT-GTACTTTAGTGG
* *
1528738 CGTTTTTAGAAAAACGCCGCTAAAGG
128 CGTTTTTATACAAACGCCGCTAAAGG
1528764 TCGTCTTGAT
Statistics
Matches: 268, Mismatches: 48, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
164 213 0.79
165 20 0.07
166 35 0.13
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (163 bp):
GTGGCGTTTTAAGCACAAATGCCGCTAATTACACGTTCTTAGTGGCATTTTATGCACAAATGCCG
CTAATTACACGTACTATAGTGGCGTTTTTATATAAACGCCGATAAATAATGTACTTTAGTGGCGT
TTTTATACAAACGCCGCTAAAGGACGTACTTTA
Found at i:1528696 original size:42 final size:41
Alignment explanation
Indices: 1528024--1528743 Score: 264
Period size: 42 Copynumber: 17.4 Consensus size: 41
1528014 GGAAAATAAT
* * *
1528024 GTACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTTCAC
1 GTACTTTAGTGGCATTTTAA-CACAAATGCCGCTAATTACAC
* *
1528066 GTACTTCAGTGG--TGTTTAACGTACAAACGCCGCTAATTACAC
1 GTACTTTAGTGGCAT-TTTAAC--ACAAATGCCGCTAATTACAC
* * *** * ** * * *
1528108 GCACTATAGTGGCATTTTTGTATAAACACCGATAAATAC-T
1 GTACTTTAGTGGCATTTTAACACAAATGCCGCTAATTACAC
* * * * *
1528148 GTAC-ATACGTGGCGTTTT-ATACAAACGCCGCTAGTTACAC
1 GTACTTTA-GTGGCATTTTAACACAAATGCCGCTAATTACAC
* ** * *
1528188 GTACATGCGTGGCGTTTTAAGCACAAACGCCGCTAATTACAC
1 GTACTTTAGTGGCATTTTAA-CACAAATGCCGCTAATTACAC
* ** * * *
1528230 GTAC-ATACGTGGTGTTTTATGCACAAACGCCACTAATTACAC
1 GTACTTTA-GTGGCATTTTA-ACACAAATGCCGCTAATTACAC
* * * * *
1528272 GTAC-ATACGTGGCGTTTTATGCACAAACGCCACTAATTACAC
1 GTACTTTA-GTGGCATTTTA-ACACAAATGCCGCTAATTACAC
* * ** * * * *
1528314 GTAC-ATACGTGGCGTTTTATGTACAAACGCCACGAATTACAT
1 GTACTTTA-GTGGCATTTTA-ACACAAATGCCGCTAATTACAC
* * ** * * * * * * * *
1528356 GCACTATAGTGGTGTTTTTATATAAACGTCGATAAATA-AT
1 GTACTTTAGTGGCATTTTAACACAAATGCCGCTAATTACAC
* * * * *
1528396 GTACTTTAGTGGCGTTTTTATACAAACGCCGCTAA--AGGAC
1 GTACTTTAGTGGCATTTTAACACAAATGCCGCTAATTA-CAC
* * **
1528436 TTACTTTAGTGGCGTTTTAAGTGCAAATGCCGCTAATTACAC
1 GTACTTTAGTGGCATTTTAA-CACAAATGCCGCTAATTACAC
* * *
1528478 GTTCTTTAGTGGCATTTTATGCAAAAATGCCGCTAATTACAC
1 GTACTTTAGTGGCATTTTA-ACACAAATGCCGCTAATTACAC
* * * * * ** ** * **
1528520 GTACTCTAGTTGCATTTTTATATAAACACCGAGAAATA-TT
1 GTACTTTAGTGGCATTTTAACACAAATGCCGCTAATTACAC
* * * **
1528560 GTACTTTAGTGGCATTTTTATACAAACGCCGCTAA--AGGTC
1 GTACTTTAGTGGCATTTTAACACAAATGCCGCTAATTA-CAC
* **
1528600 GTACTTTAGTGGCGTTGCAAGCACAAATGCCGCTAATTACAC
1 GTACTTTAGTGGCATTTTAA-CACAAATGCCGCTAATTACAC
* ** *
1528642 ATTTTTTTGTGGCATTTTACACACAAATGCCGCTAATTACAC
1 GTACTTTAGTGGCATTTTA-ACACAAATGCCGCTAATTACAC
* * * * *
1528684 ATACTTTAGTGGCGTTTTTAACATAAACGCCGCTAAATACTA-
1 GTACTTTAGTGGC-ATTTTAACACAAATGCCGCTAATTAC-AC
*
1528726 GTACTTTAGTGGCGTTTT
1 GTACTTTAGTGGCATTTT
1528744 TAGAAAAACG
Statistics
Matches: 540, Mismatches: 111, Indels: 55
0.76 0.16 0.08
Matches are distributed among these distances:
38 2 0.00
39 17 0.03
40 124 0.23
41 73 0.14
42 308 0.57
43 15 0.03
44 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (41 bp):
GTACTTTAGTGGCATTTTAACACAAATGCCGCTAATTACAC
Done.