Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 102 of 199
Found at i:28813883 original size:119 final size:120
Alignment explanation
Indices: 28813682--28814115 Score: 791
Period size: 119 Copynumber: 3.6 Consensus size: 120
28813672 TTTAATAAAA
* *
28813682 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAACTTAAAATAATAATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
* *
28813747 AATATAATTTAACAAAAATATATAATTTAATAAAATTCTTAGTGTTAAATATTCT
66 AATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
28813802 TATATGAATTTACTAAAATCATAATATATAATACTAT-AAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
* *
28813866 AATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATGAAATATCCT
66 AATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
28813921 TATATGAATTTACT-AAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
28813985 AATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
66 AATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
*
28814040 TATATGAATTTACTAAAATTATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
1 TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
28814105 AATATAATTTA
66 AATATAATTTA
28814116 TAATCTACTT
Statistics
Matches: 303, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
118 22 0.07
119 184 0.61
120 97 0.32
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.42
Consensus pattern (120 bp):
TATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATTATTATTA
AATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATTAAATATTCT
Found at i:28818530 original size:23 final size:22
Alignment explanation
Indices: 28818456--28818547 Score: 100
Period size: 22 Copynumber: 4.2 Consensus size: 22
28818446 AAATTCAATA
* * *
28818456 TCAATTTCTTTCAAAAATTCTC
1 TCAATTCCCTTCAAAATTTCTC
28818478 TCAA-TCCCTTTCAAAATTTCTC
1 TCAATTCCC-TTCAAAATTTCTC
28818500 TCAATTCCCTTCAAAATTTC-C
1 TCAATTCCCTTCAAAATTTCTC
*
28818521 ATCAATTTCCTTCCAAAA-TTCTC
1 -TCAATTCCCTT-CAAAATTTCTC
28818544 TCAA
1 TCAA
28818548 ACTCTCAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 10
0.81 0.05 0.13
Matches are distributed among these distances:
21 3 0.05
22 48 0.79
23 10 0.16
ACGTcount: A:0.30, C:0.29, G:0.00, T:0.40
Consensus pattern (22 bp):
TCAATTCCCTTCAAAATTTCTC
Found at i:28818563 original size:52 final size:51
Alignment explanation
Indices: 28818497--28818599 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 51
28818487 TTCAAAATTT
* *
28818497 CTCTCAATTCCCTT-CAAAATTTCC-ATCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA--TCCTATCAATTTCCTTCAAAAAATCTC-CAAA
*
28818549 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
28818600 TCCATATTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
51 7 0.16
52 29 0.64
53 9 0.20
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTATCAATTTCCTTCAAAAAATCTCCAAA
Found at i:28818588 original size:21 final size:22
Alignment explanation
Indices: 28818549--28818590 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
28818539 TTCTCTCAAA
28818549 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
28818571 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
28818591 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:28818655 original size:26 final size:27
Alignment explanation
Indices: 28818625--28818683 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
28818615 TTTTTCCATT
28818625 AAATTTCAT-TTTTTTAAGA-AAATTTA
1 AAATTTCATATTTTTTAA-ATAAATTTA
** *
28818651 AAATTTTTTATTTTTTAAATAATTTTA
1 AAATTTCATATTTTTTAAATAAATTTA
28818678 AAATTT
1 AAATTT
28818684 TTAATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (27 bp):
AAATTTCATATTTTTTAAATAAATTTA
Found at i:28818686 original size:26 final size:27
Alignment explanation
Indices: 28818634--28818685 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
28818624 TAAATTTCAT
28818634 TTTTTTAAGAAAATTTAAAATTTTTTA
1 TTTTTTAAGAAAATTTAAAATTTTTTA
*
28818661 TTTTTTAA-ATAATTTTAAAATTTTT
1 TTTTTTAAGA-AAATTTAAAATTTTT
28818686 AATATTTTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTTTAAGAAAATTTAAAATTTTTTA
Found at i:28818839 original size:24 final size:23
Alignment explanation
Indices: 28818777--28818839 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
28818767 TAAATTTAAA
*
28818777 TTTTAAAT-TTTTTTTAAGATAT
1 TTTTATATATTTTTTTAAGATAT
*
28818799 TTTTATTTATGTATTTTT-AGATAT
1 TTTTATATAT-T-TTTTTAAGATAT
28818823 TTATTAATATATTTTTT
1 TT-TT-ATATATTTTTT
28818840 GTTATAAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 6 0.18
23 1 0.03
24 13 0.39
25 8 0.24
26 5 0.15
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (23 bp):
TTTTATATATTTTTTTAAGATAT
Found at i:28820992 original size:17 final size:18
Alignment explanation
Indices: 28820970--28821005 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
28820960 TAAAATCCCT
28820970 AAACCCT-ACTTAATTAA
1 AAACCCTAACTTAATTAA
*
28820987 AAACCCTAATTTAATTAA
1 AAACCCTAACTTAATTAA
28821005 A
1 A
28821006 TTAAAAACCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (18 bp):
AAACCCTAACTTAATTAA
Found at i:28821035 original size:23 final size:24
Alignment explanation
Indices: 28820958--28821047 Score: 105
Period size: 24 Copynumber: 3.8 Consensus size: 24
28820948 ACATCATTTG
*
28820958 ATTAAAATCCCTAAACCCTACTTA
1 ATTAAAAACCCTAAACCCTACTTA
** *
28820982 ATTAAAAACCCT-AA-TTTAATTAA
1 ATTAAAAACCCTAAACCCTACTT-A
28821005 ATTAAAAACCCTAAACCCTACTTA
1 ATTAAAAACCCTAAACCCTACTTA
*
28821029 ATTAAAAACTCT-AACCCTA
1 ATTAAAAACCCTAAACCCTA
28821048 ACCTAATTTA
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
22 4 0.07
23 22 0.40
24 25 0.45
25 4 0.07
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (24 bp):
ATTAAAAACCCTAAACCCTACTTA
Found at i:28821099 original size:28 final size:28
Alignment explanation
Indices: 28820998--28821560 Score: 411
Period size: 28 Copynumber: 20.8 Consensus size: 28
28820988 AACCCTAATT
* *
28820998 TAATTAAATTAAAAACCCTAA---ACCC
1 TAATTTAATTAAAAACCCTAACCTAACC
* *
28821023 T-ACTTAATTAAAAACTCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAA-CCTAACC
28821051 TAATTTAATTAAATTAAAACCCTAACCTAACC
1 TAATTTAATT--A--AAAACCCTAACCTAACC
28821083 TAATTTAATTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAA-CCTAACC
28821112 TAACCTACTTAAATTAAAAA--C---CCTAACC
1 TAA--T--TT-AATTAAAAACCCTAACCTAACC
28821140 TAATTTAATTAAAAACCCTAACCT-A-C
1 TAATTTAATTAAAAACCCTAACCTAACC
* * **
28821166 ---TTAAATTAAAAACCCTAACCTTATT
1 TAATTTAATTAAAAACCCTAACCTAACC
*
28821191 TAATTAAATTAAAAACCCTAACCT-A-C
1 TAATTTAATTAAAAACCCTAACCTAACC
* *
28821217 ---TTAAATTAAAAACCCTAACCCCT-ACT
1 TAATTTAATTAAAAACCCTAA--CCTAACC
* *
28821243 TAATTAAATTAAAAACCCTAA---ACCC
1 TAATTTAATTAAAAACCCTAACCTAACC
*
28821268 T-ACTTAATTAAAAACCCTAACCCTAACC
1 TAATTTAATTAAAAACCCTAA-CCTAACC
28821296 TAATTTAATTAAATTAAAAACCCTAACCTAACC
1 TAA--T--TT-AATTAAAAACCCTAACCTAACC
28821329 TAATTTAATTAAAAACCCTAACCT-A-C
1 TAATTTAATTAAAAACCCTAACCTAACC
*
28821355 ---TTAAATTAAAAACCCTAACCTAACC
1 TAATTTAATTAAAAACCCTAACCTAACC
*
28821380 TAATTAAATTAAAAACCCTAACCCTAACCTAACC
1 TAATTTAATT--AAA----AACCCTAACCTAACC
28821414 TAATTTAATTAAAAA--C---CCTAACC
1 TAATTTAATTAAAAACCCTAACCTAACC
* **
28821437 TAATTTAATTAAAAACCCTAACCTTATT
1 TAATTTAATTAAAAACCCTAACCTAACC
*
28821465 TAATTAAATTAAAAACCCT-A---AACC
1 TAATTTAATTAAAAACCCTAACCTAACC
28821489 TAATTTAATTAAAAACCCTAACCTAACC
1 TAATTTAATTAAAAACCCTAACCTAACC
*
28821517 TAATTAAATTAAAAACCCTAA-C---CC
1 TAATTTAATTAAAAACCCTAACCTAACC
28821541 T-ATTTAATTAAAAACCCTAA
1 TAATTTAATTAAAAACCCTAA
28821561 TTAAATTGTA
Statistics
Matches: 448, Mismatches: 28, Indels: 126
0.74 0.05 0.21
Matches are distributed among these distances:
23 107 0.24
24 59 0.13
25 11 0.02
26 4 0.01
27 5 0.01
28 125 0.28
29 38 0.08
30 4 0.01
31 3 0.01
32 21 0.05
33 23 0.05
34 48 0.11
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (28 bp):
TAATTTAATTAAAAACCCTAACCTAACC
Found at i:28821137 original size:23 final size:23
Alignment explanation
Indices: 28821110--28821289 Score: 209
Period size: 23 Copynumber: 7.3 Consensus size: 23
28821100 CTAACCCTAA
28821110 CCTAACCTACTTAAATTAAAAAC
1 CCTAACCTACTTAAATTAAAAAC
* *
28821133 CCTAACCTAATTTAATTAAAAAC
1 CCTAACCTACTTAAATTAAAAAC
28821156 CCTAACCTACTTAAATTAAAAAC
1 CCTAACCTACTTAAATTAAAAAC
*
28821179 CCTAACCTTATTTAATTAAATTAAAAAC
1 CCTAACC-----TACTTAAATTAAAAAC
28821207 CCTAACCTACTTAAATTAAAAAC
1 CCTAACCTACTTAAATTAAAAAC
28821230 CCTAACCCCTACTTAATTAAATTAAAAAC
1 CCTAA--CCTAC----TTAAATTAAAAAC
28821259 CCTAAACCCTACTT-AATTAAAAAC
1 CCT-AA-CCTACTTAAATTAAAAAC
28821283 CCTAACC
1 CCTAACC
28821290 CTAACCTAAT
Statistics
Matches: 139, Mismatches: 6, Indels: 25
0.82 0.04 0.15
Matches are distributed among these distances:
22 2 0.01
23 71 0.51
24 13 0.09
25 7 0.05
28 22 0.16
29 22 0.16
30 2 0.01
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (23 bp):
CCTAACCTACTTAAATTAAAAAC
Found at i:28821456 original size:18 final size:20
Alignment explanation
Indices: 28821411--28821472 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 20
28821401 CCCTAACCTA
28821411 ACCTAATTTAATTAAAAACCC
1 ACCTAATTTAATTAAAAA-CC
28821432 TAACCTAATTTAATTAAAAACCC
1 --ACCTAATTTAATTAAAAA-CC
*
28821455 TAACCTTATTTAATTAAA
1 --ACCTAATTTAATTAAA
28821473 TTAAAAACCC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.47, C:0.19, G:0.00, T:0.34
Consensus pattern (20 bp):
ACCTAATTTAATTAAAAACC
Found at i:28821549 original size:51 final size:52
Alignment explanation
Indices: 28820981--28821560 Score: 446
Period size: 51 Copynumber: 10.8 Consensus size: 52
28820971 AACCCTACTT
** * *
28820981 AATTAAAAACCCTAA-TTTAATTAAATTAAAAACCCTAAACCCT-ACTTAATTA
1 AATTAAAAACCCTAACCCTAATTTAATTAAAAACCCT-AA-CCTAACCTAATTA
* *
28821033 AA--AACTCTAACCCTAA-CCTAATTTAATTAAATTAAAACCCTAACCTAACCTAATTT
1 AATTAA---AAACCCTAACCCTAATTTAATT--A--AAAACCCTAACCTAACCTAATTA
28821089 AATTAAAAACCCTAACCCTAACCTAACCTACTTAAATTAAAAACCCTAACCTAA--T--TT-
1 AATTAAAAACCCTAA--C---CCTAA--T--TT-AATTAAAAACCCTAACCTAACCTAATTA
* * * **
28821146 AATTAAAAACCCTAA-CCTACTTAAATTAAAAACCCTAACCTTATTTAATTA
1 AATTAAAAACCCTAACCCTAATTTAATTAAAAACCCTAACCTAACCTAATTA
* * *
28821197 AATTAAAAACCCTAA-CCTACTTAAATTAAAAACCCTAACCCCT-ACTTAATTA
1 AATTAAAAACCCTAACCCTAATTTAATTAAAAACCCTAA--CCTAACCTAATTA
*
28821249 AATTAAAAACCCTAAACCCT-ACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTA
1 AATTAAAAACCCT-AACCCTAATTTAATTAAAAACCCTAA-CCTAACC-----TAATTA
28821307 AATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCT-A-C---TTA
1 AATTAAAAACCCTAA-C---CCTAATTTAATTAAAAACCCTAACCTAACCTAATTA
* *
28821358 AATTAAAAACCCTAACCTAACCTAATTAAATTAAAAACCCTAACCCTAACCTAACCTAATTT
1 AATTAAAAACCCTAA-C---CCTAATTTAATT--AAA----AACCCTAACCTAACCTAATTA
* **
28821420 AATTAAAAACCCTAA-CCTAATTTAATTAAAAACCCTAACCTTATTTAATTA
1 AATTAAAAACCCTAACCCTAATTTAATTAAAAACCCTAACCTAACCTAATTA
*
28821471 AATTAAAAACCCTAAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTA
1 AATTAAAAACCCTAACCCTAATTTAATTAAAAACCCTAACCTAACCTAATTA
28821523 AATTAAAAACCCTAACCCT-ATTTAATTAAAAACCCTAA
1 AATTAAAAACCCTAACCCTAATTTAATTAAAAACCCTAA
28821561 TTAAATTGTA
Statistics
Matches: 448, Mismatches: 27, Indels: 107
0.77 0.05 0.18
Matches are distributed among these distances:
46 19 0.04
47 1 0.00
48 1 0.00
49 1 0.00
50 4 0.01
51 127 0.28
52 78 0.17
53 43 0.10
54 3 0.01
55 15 0.03
56 11 0.02
57 47 0.10
58 25 0.06
59 2 0.00
60 2 0.00
61 11 0.02
62 50 0.11
63 1 0.00
64 1 0.00
65 2 0.00
66 4 0.01
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.28
Consensus pattern (52 bp):
AATTAAAAACCCTAACCCTAATTTAATTAAAAACCCTAACCTAACCTAATTA
Found at i:28824945 original size:124 final size:124
Alignment explanation
Indices: 28824725--28824979 Score: 361
Period size: 124 Copynumber: 2.1 Consensus size: 124
28824715 CCACGAGGGC
* *
28824725 GCGATTTGAGACTGTTTGCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
1 GCGATTTGAGACTATTTCCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
* * * * **
28824790 AAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
* *
28824849 GCGATTTTATACTATTTCCTCAGAAAACGTCAAAAAAAATTATTT-CTCACATGACC-ACTGTAG
1 GCGATTTGAGACTATTTCCTCAG-AAACGTCAAAAAAAATTATTTCCT-ACATGACCAACTGTAG
* * *
28824912 CGAAATCGCGTCCACGATGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTAGTAGAA
64 CGAAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
28824973 GCGATTT
1 GCGATTT
28824980 CTCACTATTT
Statistics
Matches: 116, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
124 87 0.75
125 29 0.25
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (124 bp):
GCGATTTGAGACTATTTCCTCAGAAACGTCAAAAAAAATTATTTCCTACATGACCAACTGTAGCG
AAATCGCGTCCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
Found at i:28825964 original size:11 final size:11
Alignment explanation
Indices: 28825934--28825966 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
28825924 AATTGTTTTA
28825934 TTTTATTATTT
1 TTTTATTATTT
*
28825945 CTTTA-TATTT
1 TTTTATTATTT
28825955 TTTTATTATTT
1 TTTTATTATTT
28825966 T
1 T
28825967 ACCTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTATTATTT
Found at i:28832064 original size:27 final size:28
Alignment explanation
Indices: 28832034--28832087 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
28832024 TCCAACAAGC
**
28832034 TTAAAACATA-ATCAGTATCTAACAAAT
1 TTAAAACATATATCAAAATCTAACAAAT
*
28832061 TTAAGACATATATCAAAATCTAACAAA
1 TTAAAACATATATCAAAATCTAACAAA
28832088 CTAAAATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.28
Consensus pattern (28 bp):
TTAAAACATATATCAAAATCTAACAAAT
Found at i:28833424 original size:24 final size:24
Alignment explanation
Indices: 28833392--28833439 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28833382 GGCAATGGTC
28833392 AACATTGCCCTTGTATTATATGTT
1 AACATTGCCCTTGTATTATATGTT
28833416 AACATTGCCCTTGTATTATATGTT
1 AACATTGCCCTTGTATTATATGTT
28833440 TTATAATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (24 bp):
AACATTGCCCTTGTATTATATGTT
Found at i:28836324 original size:18 final size:18
Alignment explanation
Indices: 28836303--28836337 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
28836293 CTGGGGTAGG
28836303 TTTGGG-TTTAAGTTTGGT
1 TTTGGGCTTT-AGTTTGGT
28836321 TTTGGGCTTTAGTTTGG
1 TTTGGGCTTTAGTTTGG
28836338 GTACTAGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.09, C:0.03, G:0.34, T:0.54
Consensus pattern (18 bp):
TTTGGGCTTTAGTTTGGT
Found at i:28838084 original size:41 final size:41
Alignment explanation
Indices: 28838039--28838164 Score: 114
Period size: 41 Copynumber: 3.1 Consensus size: 41
28838029 TTTATTATCA
* * *
28838039 GTGAAATAAT-TCAGACTTTATGTCTAGCAGGCTTGATGCCG
1 GTGAAATAATGT-AGACTATAAGTCTAGCAGGCTTAATGCCG
*
28838080 GTGAAATTATGTAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGAAATAATGTAGACTATAAGTCTAGCAGGCTTAATGCCG
* * * * * *
28838121 ATG--ATACATTTCGGACAATAAGTCTAGCAGGCTAAAAGCCG
1 GTGAAATA-ATGT-AGACTATAAGTCTAGCAGGCTTAATGCCG
28838162 GTG
1 GTG
28838165 TACCGATTCA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
39 2 0.03
40 3 0.04
41 64 0.91
42 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.28
Consensus pattern (41 bp):
GTGAAATAATGTAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:28838456 original size:32 final size:31
Alignment explanation
Indices: 28838398--28838462 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 31
28838388 CAATTATTAA
* * * *
28838398 ATATATATATATATGTGCATTCGGTATATGC
1 ATATATAAATATATATGCAATAGGTATATGC
28838429 ATATATTAAATATATATGCAATAGGTATATGC
1 ATATA-TAAATATATATGCAATAGGTATATGC
28838461 AT
1 AT
28838463 TTGCTAAGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 5 0.17
32 24 0.83
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (31 bp):
ATATATAAATATATATGCAATAGGTATATGC
Found at i:28839587 original size:15 final size:17
Alignment explanation
Indices: 28839567--28839606 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
28839557 CGATCCATCT
28839567 ACACAAAATA-ATG-TC
1 ACACAAAATATATGATC
28839582 ACAC-AAATATATGATC
1 ACACAAAATATATGATC
28839598 ACTACAAAA
1 AC-ACAAAA
28839607 AAGATGCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.24
15 7 0.33
16 4 0.19
17 2 0.10
18 3 0.14
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (17 bp):
ACACAAAATATATGATC
Found at i:28840253 original size:16 final size:16
Alignment explanation
Indices: 28840224--28840272 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
28840214 TTATAAATTT
28840224 TTATAATGTTTTTTAAA
1 TTATAAT-TTTTTTAAA
*
28840241 TTATAATTTTTTTATAG
1 TTATAATTTTTTTA-AA
*
28840258 TTCT-ATTTTTTTAAA
1 TTATAATTTTTTTAAA
28840273 ATAAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 1 0.04
16 16 0.57
17 11 0.39
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (16 bp):
TTATAATTTTTTTAAA
Found at i:28840370 original size:25 final size:25
Alignment explanation
Indices: 28840328--28840381 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
28840318 CTATTTTTTA
**
28840328 TAATTTTTTAAATTATAAAT-TGAT
1 TAATTTTTTAAAAAATAAATATGAT
28840352 TAATTTTTATAAAAAATAAATAATGAT
1 TAATTTTT-TAAAAAATAAAT-ATGAT
28840379 TAA
1 TAA
28840382 GTGCACTGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 8 0.32
25 10 0.40
27 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
TAATTTTTTAAAAAATAAATATGAT
Found at i:28843314 original size:21 final size:21
Alignment explanation
Indices: 28843289--28843330 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
28843279 AGGGCCTAGG
*
28843289 GTTTATGGG-TAGGGTTTTAGT
1 GTTTA-GGGTTAGGGTTATAGT
28843310 GTTTAGGGTTAGGGTTATAGT
1 GTTTAGGGTTAGGGTTATAGT
28843331 TTTTGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 3 0.16
21 16 0.84
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (21 bp):
GTTTAGGGTTAGGGTTATAGT
Found at i:28843349 original size:28 final size:28
Alignment explanation
Indices: 28843318--28843375 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
28843308 GTGTTTAGGG
*
28843318 TTAGGG-TTATAGTTTTTGAAAAAATAAA
1 TTAGGGTTTATAGATTTT-AAAAAATAAA
* *
28843346 TTAGGGTTTATGGATTTTAAAAATTAAA
1 TTAGGGTTTATAGATTTTAAAAAATAAA
28843374 TT
1 TT
28843376 TGAGTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (28 bp):
TTAGGGTTTATAGATTTTAAAAAATAAA
Found at i:28843390 original size:27 final size:28
Alignment explanation
Indices: 28843331--28843391 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
28843321 GGGTTATAGT
* *
28843331 TTTTGAAAAAATAAATTAGGGTTTATGGA
1 TTTT-AAAAAATAAATTAGAGTTTAAGGA
* *
28843360 TTTTAAAAATTAAATTTGAGTTTAAGG-
1 TTTTAAAAAATAAATTAGAGTTTAAGGA
28843387 TTTTA
1 TTTTA
28843392 GGATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.18
28 19 0.68
29 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.44
Consensus pattern (28 bp):
TTTTAAAAAATAAATTAGAGTTTAAGGA
Found at i:28858747 original size:25 final size:25
Alignment explanation
Indices: 28858609--28858747 Score: 127
Period size: 25 Copynumber: 5.6 Consensus size: 25
28858599 TGAGCATGTA
* * * *
28858609 ATCGAGAAGCTCTTCCGAGCTATAT
1 ATCGGGAAGCTCATGCGAGCTAAAT
* *
28858634 AACGGGAAGCTCATGTGAGCTAAAT
1 ATCGGGAAGCTCATGCGAGCTAAAT
* * ** **
28858659 AACGGGAAGCTTATATGAGCTGTAT
1 ATCGGGAAGCTCATGCGAGCTAAAT
* ** *
28858684 ATCGGGAAGCTTATAAGAGCTGAA-
1 ATCGGGAAGCTCATGCGAGCTAAAT
28858708 ATCGGGAAGCTCATGCGAGCTAAAT
1 ATCGGGAAGCTCATGCGAGCTAAAT
28858733 ATCGGGAAGCTCATG
1 ATCGGGAAGCTCATG
28858748 AGAAATGTGG
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
24 20 0.21
25 76 0.79
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.23
Consensus pattern (25 bp):
ATCGGGAAGCTCATGCGAGCTAAAT
Found at i:28860910 original size:33 final size:33
Alignment explanation
Indices: 28860843--28860910 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
28860833 TAATCACTCT
* *
28860843 AATATTAAATTTAATCTAATATTTATCTTGATA
1 AATATTAAATTAAATCTAATATTAATCTTGATA
* *
28860876 AATATTAGATTAAATTTAATATTAAATCTT-ATA
1 AATATTAAATTAAATCTAATATT-AATCTTGATA
28860909 AA
1 AA
28860911 AATAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (33 bp):
AATATTAAATTAAATCTAATATTAATCTTGATA
Found at i:28861035 original size:37 final size:39
Alignment explanation
Indices: 28860941--28861043 Score: 119
Period size: 37 Copynumber: 2.7 Consensus size: 39
28860931 AAAGATAAAC
*
28860941 ATTAAATTAA-ATTAAA-TATTAAGATAATTACTTTAAT
1 ATTAAATTAATATTAAACTATTAAGATAAGTACTTTAAT
*
28860978 ATTAAATTAATA-AAATACTATTAAGATAAGT-C-TTAA-
1 ATTAAATTAATATTAA-ACTATTAAGATAAGTACTTTAAT
*
28861014 ATTAAATTTAATATTAAACTATTAAAATAA
1 ATTAAA-TTAATATTAAACTATTAAGATAA
28861044 TATTATTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
36 6 0.11
37 34 0.60
38 5 0.09
39 12 0.21
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (39 bp):
ATTAAATTAATATTAAACTATTAAGATAAGTACTTTAAT
Found at i:28864297 original size:18 final size:18
Alignment explanation
Indices: 28864249--28864299 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
28864239 ACTTAATCAC
28864249 TTTAATATTAAA--TTAA
1 TTTAATATTAAATCTTAA
** **
28864265 GATAATATTTTATCTTAA
1 TTTAATATTAAATCTTAA
28864283 TTTAATATTAAATCTTA
1 TTTAATATTAAATCTTA
28864300 TTAAAATAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
16 8 0.32
18 17 0.68
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTAATATTAAATCTTAA
Found at i:28864380 original size:20 final size:18
Alignment explanation
Indices: 28864333--28864381 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
28864323 GTAGATAAAC
28864333 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
28864350 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
28864370 ATTAAATTAATA
1 ATTAAATTAATA
28864382 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:28869715 original size:53 final size:53
Alignment explanation
Indices: 28869653--28869761 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
28869643 AACCGTAGAG
28869653 AATCAAAATTATTTGTTTTAAGATTGATTGATTCTTATGAATGATTATTATAA
1 AATCAAAATTATTTGTTTTAAGATTGATTGATTCTTATGAATGATTATTATAA
28869706 AATCAAAATTATTTGTTTTAAGATTGATTGATTCTTATGAATGATTATTATAA
1 AATCAAAATTATTTGTTTTAAGATTGATTGATTCTTATGAATGATTATTATAA
28869759 AAT
1 AAT
28869762 TGCCATAGCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.47
Consensus pattern (53 bp):
AATCAAAATTATTTGTTTTAAGATTGATTGATTCTTATGAATGATTATTATAA
Found at i:28871126 original size:18 final size:18
Alignment explanation
Indices: 28871103--28871137 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28871093 CCCTCGTCCT
* *
28871103 CTAAGGGGAAACAGAAAG
1 CTAAGGGAAAAAAGAAAG
28871121 CTAAGGGAAAAAAGAAA
1 CTAAGGGAAAAAAGAAA
28871138 CCTACTAAGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.09, G:0.29, T:0.06
Consensus pattern (18 bp):
CTAAGGGAAAAAAGAAAG
Found at i:28872703 original size:6 final size:6
Alignment explanation
Indices: 28872687--28872752 Score: 77
Period size: 6 Copynumber: 11.3 Consensus size: 6
28872677 ATAAAAATTA
28872687 AATATTT AATATT AATATT AATATT AATATT AATATT AATA-- AATATTT
1 AATA-TT AATATT AATATT AATATT AATATT AATATT AATATT AATA-TT
*
28872735 AAT-TT AAT-CT AATATT AA
1 AATATT AATATT AATATT AA
28872753 ATTTGTTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
4 4 0.08
5 9 0.17
6 33 0.62
7 7 0.13
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:28878810 original size:14 final size:16
Alignment explanation
Indices: 28878779--28878811 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
28878769 ATAATGCATT
28878779 AAACCACATAACACCA
1 AAACCACATAACACCA
28878795 AAACCAC-TAA-ACCA
1 AAACCACATAACACCA
28878809 AAA
1 AAA
28878812 TGATATAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.61, C:0.33, G:0.00, T:0.06
Consensus pattern (16 bp):
AAACCACATAACACCA
Found at i:28879752 original size:9 final size:9
Alignment explanation
Indices: 28879735--28879810 Score: 125
Period size: 9 Copynumber: 8.4 Consensus size: 9
28879725 GTAGTGATTC
*
28879735 AATTTGGTT
1 AATTCGGTT
28879744 AATTCGGTT
1 AATTCGGTT
28879753 AATTCGGTT
1 AATTCGGTT
*
28879762 AATTCGGGT
1 AATTCGGTT
*
28879771 AATTCGGGT
1 AATTCGGTT
28879780 AATTCGGTT
1 AATTCGGTT
28879789 AATTCGGTT
1 AATTCGGTT
28879798 AATTCGGTT
1 AATTCGGTT
28879807 AATT
1 AATT
28879811 TTTAACCAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 64 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:28879991 original size:12 final size:12
Alignment explanation
Indices: 28879974--28879998 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28879964 TGTTATTTCG
28879974 GGTCGGTTAACC
1 GGTCGGTTAACC
28879986 GGTCGGTTAACC
1 GGTCGGTTAACC
28879998 G
1 G
28879999 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:28880091 original size:7 final size:8
Alignment explanation
Indices: 28880075--28880102 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
28880065 AAGTTGAATC
28880075 AAAATAAA
1 AAAATAAA
28880083 AAAATAAA
1 AAAATAAA
28880091 AAAATAAA
1 AAAATAAA
28880099 AAAA
1 AAAA
28880103 CATCAGCAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:28880198 original size:16 final size:16
Alignment explanation
Indices: 28880179--28880211 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28880169 AGAATTTATT
28880179 TTAAAAT-TTATTTAAA
1 TTAAAATATT-TTTAAA
28880195 TTAAAATATTTTTAAA
1 TTAAAATATTTTTAAA
28880211 T
1 T
28880212 GTATTTGACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.88
17 2 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAATATTTTTAAA
Found at i:28881865 original size:19 final size:19
Alignment explanation
Indices: 28881837--28881876 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
28881827 AGTTCTAATA
*
28881837 TTTTTTAATA-AATTTTCAC
1 TTTTTAAATATAATTTT-AC
28881856 TTTTTAAATATAATTTTAC
1 TTTTTAAATATAATTTTAC
28881875 TT
1 TT
28881877 ATATCTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTAAATATAATTTTAC
Found at i:28892266 original size:62 final size:62
Alignment explanation
Indices: 28892169--28892295 Score: 245
Period size: 62 Copynumber: 2.0 Consensus size: 62
28892159 ACTTAGTCGC
28892169 ATAAAGAGTTTCTAACATTTTCCACAAGGCAGATGAGGTATTCTCCATCAATACCTCCTAAA
1 ATAAAGAGTTTCTAACATTTTCCACAAGGCAGATGAGGTATTCTCCATCAATACCTCCTAAA
*
28892231 ATAAAGAGTTTCTAACATTTTCCACAAGGCAGATGAGGTATTCTCCATCAATACTTCCTAAA
1 ATAAAGAGTTTCTAACATTTTCCACAAGGCAGATGAGGTATTCTCCATCAATACCTCCTAAA
28892293 ATA
1 ATA
28892296 CCGTATCCAC
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (62 bp):
ATAAAGAGTTTCTAACATTTTCCACAAGGCAGATGAGGTATTCTCCATCAATACCTCCTAAA
Found at i:28892893 original size:24 final size:24
Alignment explanation
Indices: 28892865--28892916 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
28892855 TTAGTAAGTC
* *
28892865 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
28892889 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
28892913 AAAT
1 AAAT
28892917 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:28896532 original size:79 final size:82
Alignment explanation
Indices: 28896421--28896605 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 82
28896411 GCTACTCGTT
* * *
28896421 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGAACAAATGCCTTC-GGATCTTAACCC
* *
28896484 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
28896501 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGAACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGAACAAATGCCTTCGGATCTTAACCCG
* *
28896564 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
28896581 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
28896606 CATCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 54 0.59
80 34 0.37
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGAACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:28896605 original size:40 final size:40
Alignment explanation
Indices: 28896402--28896605 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
28896392 CGGAATTTAA
** *
28896402 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
28896442 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
28896482 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
28896521 CCGGA-ATTAGTATCTCGAACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
28896561 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
28896601 CCGGA
1 CCGGA
28896606 CATCATTCAA
Statistics
Matches: 139, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.01
39 32 0.23
40 94 0.68
41 11 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:28898562 original size:13 final size:13
Alignment explanation
Indices: 28898518--28898571 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
28898508 TAGAACACGG
*
28898518 AAAAAATTTTAAT
1 AAAAAATATTAAT
*
28898531 AAAAAA-ATT-CT
1 AAAAAATATTAAT
*
28898542 TAAAAATATTAAT
1 AAAAAATATTAAT
*
28898555 AAAAAATA-GAAT
1 AAAAAATATTAAT
28898567 AAAAA
1 AAAAA
28898572 TAGAATTTGG
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
11 6 0.18
12 13 0.39
13 14 0.42
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (13 bp):
AAAAAATATTAAT
Found at i:28898720 original size:20 final size:20
Alignment explanation
Indices: 28898695--28898734 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
28898685 TAAATTAGTA
28898695 GGTGGGGGCTTTATAGTTTC
1 GGTGGGGGCTTTATAGTTTC
28898715 GGTGGGGGCTTTATAGTTTC
1 GGTGGGGGCTTTATAGTTTC
28898735 TTTGTGACCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.10, G:0.40, T:0.40
Consensus pattern (20 bp):
GGTGGGGGCTTTATAGTTTC
Found at i:28899690 original size:125 final size:125
Alignment explanation
Indices: 28899466--28899937 Score: 687
Period size: 125 Copynumber: 3.8 Consensus size: 125
28899456 CGAGTTGACT
* * *
28899466 TTTCTG-GTCAAATAATATAAAATCGCTTCTACCA-AGATGCTATTTGAAAAGAAATTGTGAAAT
1 TTTCTGAG-CAAATAGTATAAAATCACTTCTACCAGA-ATGCTATTTGAGAAGAAATTGTGAAAT
* * *
28899529 CGCACTCTCGTGGACGCGATTTTGCTACAGTGGGTCATGTAAGAAATAATTTTTTTCTGATG
64 CGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCTGATG
** * *
28899591 TTTCTGAGCAAATAGTATAAAATCGTTTCTACGAGAATGCTACTTGAGAAGAAATTGTGAAATCG
1 TTTCTGAGCAAATAGTATAAAATCACTTCTACCAGAATGCTATTTGAGAAGAAATTGTGAAATCG
* * * * *
28899656 CGCCATCATGGACGCGATTTTGCTATAGTAGGTCATGTAAGAAATGATTTTTTTCTAATG
66 CGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCTGATG
* * * *
28899716 TTTCTGAGCAAATAGTATAAAATTATTTCTACGAGAATGCTATTTAAGAAGAAATTGTGAAATCG
1 TTTCTGAGCAAATAGTATAAAATCACTTCTACCAGAATGCTATTTGAGAAGAAATTGTGAAATCG
* * *
28899781 CGCCCTCGTGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTGTTGACG
66 CGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTT-CTGATG
* *
28899842 TTTCTGAGCAAATAGTATAAAATCACTTCTACCAGGATGCTATTTGAGAAGAAATTATGAAATCG
1 TTTCTGAGCAAATAGTATAAAATCACTTCTACCAGAATGCTATTTGAGAAGAAATTGTGAAATCG
28899907 CGCCCTCGTGGACGCGATTTTGCTACAGTAG
66 CGCCCTCGTGGACGCGATTTTGCTACAGTAG
28899938 CAAGTTTGGG
Statistics
Matches: 312, Mismatches: 32, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
125 218 0.70
126 94 0.30
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (125 bp):
TTTCTGAGCAAATAGTATAAAATCACTTCTACCAGAATGCTATTTGAGAAGAAATTGTGAAATCG
CGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTCTGATG
Found at i:28903065 original size:10 final size:10
Alignment explanation
Indices: 28903050--28903074 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28903040 CAAATCTAAC
28903050 ATTATGTAAA
1 ATTATGTAAA
28903060 ATTATGTAAA
1 ATTATGTAAA
28903070 ATTAT
1 ATTAT
28903075 TAAGCCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (10 bp):
ATTATGTAAA
Found at i:28903164 original size:21 final size:21
Alignment explanation
Indices: 28903140--28903202 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
28903130 ATTAAGTCAA
*
28903140 AAAATTGTGTTAATGGTTAGT
1 AAAATTGTATTAATGGTTAGT
*
28903161 AAAA-T-TATTAA--GTCA--
1 AAAATTGTATTAATGGTTAGT
28903176 AAAATTGTATTAATGGTTAGT
1 AAAATTGTATTAATGGTTAGT
28903197 AAAATT
1 AAAATT
28903203 TATGAAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 12
0.69 0.06 0.25
Matches are distributed among these distances:
15 4 0.12
16 1 0.03
17 9 0.27
19 8 0.24
20 1 0.03
21 10 0.30
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.40
Consensus pattern (21 bp):
AAAATTGTATTAATGGTTAGT
Found at i:28903189 original size:36 final size:37
Alignment explanation
Indices: 28903123--28903202 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 37
28903113 TCAAATAAAC
*
28903123 TAAAATTATTAAGTCAAAAAATTGTGTTAATGGTTAG
1 TAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAG
28903160 TAAAATTATTAAGTC-AAAAATTGTATTAATGGTTAG
1 TAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAG
28903196 TAAAATT
1 TAAAATT
28903203 TATGAAATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
36 27 0.64
37 15 0.36
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.39
Consensus pattern (37 bp):
TAAAATTATTAAGTCAAAAAATTGTATTAATGGTTAG
Found at i:28903195 original size:92 final size:93
Alignment explanation
Indices: 28903065--28903260 Score: 331
Period size: 92 Copynumber: 2.1 Consensus size: 93
28903055 GTAAAATTAT
*
28903065 GTAAAATTATTAAGCCAAAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAATAAACTAAAATT
1 GTAAAATTATTAAGCC-AAAAAATTGTATTAATGGTTAGTAAAATTTATCAAATAAACTAAAATT
28903130 ATTAAGTCAAAAAATTGTGTTAATGGTTA
65 ATTAAGTCAAAAAATTGTGTTAATGGTTA
* *
28903159 GTAAAATTATTAAGTC-AAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTA
1 GTAAAATTATTAAGCCAAAAAATTGTATTAATGGTTAGTAAAATTTATCAAATAAACTAAAATTA
* *
28903223 TTAAGTCCAGAAATTGTGTTAATGGTTA
66 TTAAGTCAAAAAATTGTGTTAATGGTTA
28903251 GTAAAATTAT
1 GTAAAATTAT
28903261 CAAAATATGT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 82 0.85
94 15 0.15
ACGTcount: A:0.46, C:0.05, G:0.13, T:0.36
Consensus pattern (93 bp):
GTAAAATTATTAAGCCAAAAAATTGTATTAATGGTTAGTAAAATTTATCAAATAAACTAAAATTA
TTAAGTCAAAAAATTGTGTTAATGGTTA
Found at i:28903248 original size:56 final size:56
Alignment explanation
Indices: 28903160--28903376 Score: 334
Period size: 56 Copynumber: 3.9 Consensus size: 56
28903150 TAATGGTTAG
*
28903160 TAAAATTATTAAGT-CAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAAC
1 TAAAATTATTAAGTCCAAAAATTGTATTAATGGTTAGTAAAATTTATCAAATAAAC
* * **
28903215 TAAAATTATTAAGTCCAGAAATTGTGTTAATGGTTAGTAAAA-TTATCAAA-ATATG
1 TAAAATTATTAAGTCCAAAAATTGTATTAATGGTTAGTAAAATTTATCAAATA-AAC
*
28903270 TAAAATTATTAAG-CCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAAC
1 TAAAATTATTAAGTCCAAAAATTGTATTAATGGTTAGTAAAATTTATCAAATAAAC
*
28903325 TAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAAT
1 TAAAATTATTAAGTCCAAAAATTGTATTAATGGTTAGTAAAATTTATCAAAT
28903377 TAAGTTAGGT
Statistics
Matches: 145, Mismatches: 12, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
54 27 0.19
55 56 0.39
56 62 0.43
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (56 bp):
TAAAATTATTAAGTCCAAAAATTGTATTAATGGTTAGTAAAATTTATCAAATAAAC
Found at i:28903281 original size:110 final size:111
Alignment explanation
Indices: 28903159--28903375 Score: 409
Period size: 110 Copynumber: 2.0 Consensus size: 111
28903149 TTAATGGTTA
*
28903159 GTAAAATTATTAAGTCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTAT
1 GTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTAT
*
28903224 TAAGTCCAGAAATTGTGTTAATGGTTAGTAAAA-TTATCAAAATAT
66 TAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAAATAT
28903269 GTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTAT
1 GTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTAT
28903334 TAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAA
66 TAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAA
28903376 TTAAGTTAGG
Statistics
Matches: 104, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
110 96 0.92
111 8 0.08
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.36
Consensus pattern (111 bp):
GTAAAATTATTAAGCCAAAAATTGTATTAATGGTTAGTAAAATTTATGAAATAAACTAAAATTAT
TAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTTATCAAAATAT
Found at i:28903413 original size:29 final size:29
Alignment explanation
Indices: 28903374--28903952 Score: 536
Period size: 29 Copynumber: 19.8 Consensus size: 29
28903364 AAATTTATCA
28903374 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
* *
28903403 AGTTAATTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
*
28903432 AATTAATTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
* * *
28903461 AATTAATTTATGTTAGGGTTGGGGTTTTTAGTT
1 AATTAAGTTAGGTTAGGGTTAGGG--TTT--TT
*
28903494 AATTTAGGTTAGGGTTAGGGTTAGGGTTTTT
1 AA-TTAAGTTA-GGTTAGGGTTAGGGTTTTT
*
28903525 AGTTAATTTAGGTTAGGGTTAGGGTTAGGGTTTTT
1 AATT-A---A-GTTA-GGTTAGGGTTAGGGTTTTT
28903560 AATTAAGTTAGGTTAGGGTTAGGG--TTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
28903587 --TT-AGTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
28903613 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
* *
28903642 AGTTAGGTTAGGTTAGGGTTAGGG---TT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
* *
28903668 AGGTTAGGTTAGAGTTAGGGTT----TTTAATT
1 A-ATTAAGTTAG-GTTAGGGTTAGGGTTT--TT
*
28903697 AATT--T--AGGTTAGGGTTAGGG-TTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
* *
28903721 AGTTAGGTTAGGGTTAGGGTT----TTTAATT
1 AATTAAGTTA-GGTTAGGGTTAGGGTTT--TT
* *
28903749 AATTTAGGTTAGGGTTAGAGTTAGGGTTTTT
1 AA-TTAAGTTA-GGTTAGGGTTAGGGTTTTT
28903780 AATTAAGTTAGGTTAGGGTTAGGGTTAGGGTTTTT
1 AATT-A---A-GTTA-GGTTAGGGTTAGGGTTTTT
** *
28903815 AATTAAGCAAGGTTAAGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
* *
28903844 AGTTAGGTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
* *
28903873 AATTAATTTAGGTTGGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
*
28903902 AATTAATTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTT
28903931 AATTAAGTTAGGTTA-GGTTAGG
1 AATTAAGTTAGGTTAGGGTTAGG
28903953 TTAGGTTAGG
Statistics
Matches: 469, Mismatches: 36, Indels: 91
0.79 0.06 0.15
Matches are distributed among these distances:
23 9 0.02
24 26 0.06
25 2 0.00
26 10 0.02
27 13 0.03
28 24 0.05
29 277 0.59
30 10 0.02
31 14 0.03
33 10 0.02
34 8 0.02
35 66 0.14
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.45
Consensus pattern (29 bp):
AATTAAGTTAGGTTAGGGTTAGGGTTTTT
Found at i:28903437 original size:58 final size:58
Alignment explanation
Indices: 28903374--28903952 Score: 620
Period size: 58 Copynumber: 9.9 Consensus size: 58
28903364 AAATTTATCA
*
28903374 AATTAAGTTAGGTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTT
* * *
28903432 AATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAATTTATGTTAGGGTTGGGGTTTTTAGTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGG--TTT--TT
* *
28903494 AATTTAGGTTAGGGTTAGGGTTAGGGTTTTTAGTTAATTTAGGTTAGGGTTAGGGTTAGGGTTTT
1 AA-TTAAGTTA-GGTTAGGGTTAGGGTTTTTAATTAA--T---TTA-GGTTAGGGTTAGGGTTTT
28903559 T
58 T
*
28903560 AATTAAGTTAGGTTAGGGTTAGGG--TTT--TT-AGTTAGGTTAGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTT
* **
28903613 AATTAAGTTAGGTTAGGGTTAGGGTTTTTAGTTAGGTTAGGTTAGGGTTAGGG-----
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTT
* *
28903666 --TTAGGTTAGGTTAGAGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGG---TT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTT
28903719 --TT-AGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGAGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTA--G---G-GTTAGGGTTTTT
*** *
28903780 AATTAAGTTAGGTTAGGGTTAGGGTTAGGGTTTTTAATTAAGCAAGGTTAAGGTTAGGGTTTTT
1 AATT-A---A-GTTA-GGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTT
* * *
28903844 AGTTAGGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTGGGGTTAGGGTTTTT
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTT
* *
28903902 AATTAATTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTA-GGTTAGG
1 AATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGG
28903953 TTAGGTTAGG
Statistics
Matches: 449, Mismatches: 35, Indels: 75
0.80 0.06 0.13
Matches are distributed among these distances:
51 46 0.10
52 37 0.08
53 45 0.10
54 4 0.01
55 3 0.01
57 10 0.02
58 156 0.35
59 5 0.01
60 5 0.01
61 2 0.00
62 7 0.02
63 9 0.02
64 53 0.12
65 8 0.02
66 5 0.01
68 4 0.01
69 7 0.02
70 43 0.10
ACGTcount: A:0.22, C:0.00, G:0.32, T:0.45
Consensus pattern (58 bp):
AATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGGGTTTTT
Found at i:28903634 original size:6 final size:6
Alignment explanation
Indices: 28903619--28903689 Score: 62
Period size: 6 Copynumber: 12.5 Consensus size: 6
28903609 TTTTAATTAA
***
28903619 GTTA-G GTTAGG GTTAGG GTTTTTA GTTA-G GTTA-G GTTAGG GTTAGG
1 GTTAGG GTTAGG GTTAGG G-TTAGG GTTAGG GTTAGG GTTAGG GTTAGG
*
28903665 GTTA-G GTTA-G GTTAGA GTTAGG GTT
1 GTTAGG GTTAGG GTTAGG GTTAGG GTT
28903690 TTTAATTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
5 23 0.42
6 29 0.53
7 3 0.05
ACGTcount: A:0.18, C:0.00, G:0.41, T:0.41
Consensus pattern (6 bp):
GTTAGG
Found at i:28903671 original size:22 final size:21
Alignment explanation
Indices: 28903643--28903738 Score: 79
Period size: 22 Copynumber: 4.3 Consensus size: 21
28903633 AGGGTTTTTA
28903643 GTTAGGTTAGGTTAGGGTTAGG
1 GTTAGGTTAGGTTA-GGTTAGG
28903665 GTTAGGTTAGGTTAGAGTTAGG
1 GTTAGGTTAGGTTAG-GTTAGG
* **
28903687 GTTTTTA-ATTAATTTAGGTTAGG
1 G---TTAGGTTAGGTTAGGTTAGG
28903710 GTTAGGGTTTTA-GTTAGGTTAGG
1 GTTA-GG--TTAGGTTAGGTTAGG
28903733 GTTAGG
1 GTTAGG
28903739 GTTTTTAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
20 3 0.05
21 1 0.02
22 23 0.38
23 21 0.34
24 10 0.16
25 3 0.05
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.42
Consensus pattern (21 bp):
GTTAGGTTAGGTTAGGTTAGG
Found at i:28903731 original size:17 final size:19
Alignment explanation
Indices: 28903699--28903735 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
28903689 TTTTAATTAA
28903699 TTTAGGTTAGGGTTAGGGT
1 TTTAGGTTAGGGTTAGGGT
28903718 TTTA-GTTA-GGTTAGGGT
1 TTTAGGTTAGGGTTAGGGT
28903735 T
1 T
28903736 AGGGTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 4 0.22
19 4 0.22
ACGTcount: A:0.16, C:0.00, G:0.38, T:0.46
Consensus pattern (19 bp):
TTTAGGTTAGGGTTAGGGT
Found at i:28903756 original size:103 final size:104
Alignment explanation
Indices: 28903566--28903773 Score: 283
Period size: 103 Copynumber: 2.0 Consensus size: 104
28903556 TTTTAATTAA
* * * ***
28903566 GTTAGGTTAGGGTTAGGGTTTTTAGTTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGG
1 GTTAGGTTAGAGTTAGGGTTTTTAATTAAGTTAGGGTTAGGGTTAGGAATTAAGTTAGGTTAGGG
* * *
28903631 TTAGGGTTTTTAGTTAGGTTAGGTTAGGGTTAGGGTTAG
66 TTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGAGTTAG
* ** *
28903670 GTTAGGTTAGAGTTAGGGTTTTTAATTAATTTA-GGTTAGGGTTAGGGTTTTAGTTAGGTTAGGG
1 GTTAGGTTAGAGTTAGGGTTTTTAATTAAGTTAGGGTTAGGGTTAGGAATTAAGTTAGGTTAGGG
*
28903734 TTAGGGTTTTTAATTAATTTAGGTTAGGGTTAGAGTTAG
66 TTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGAGTTAG
28903773 G
1 G
28903774 GTTTTTAATT
Statistics
Matches: 90, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
103 61 0.68
104 29 0.32
ACGTcount: A:0.21, C:0.00, G:0.35, T:0.44
Consensus pattern (104 bp):
GTTAGGTTAGAGTTAGGGTTTTTAATTAAGTTAGGGTTAGGGTTAGGAATTAAGTTAGGTTAGGG
TTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGAGTTAG
Found at i:28903947 original size:5 final size:5
Alignment explanation
Indices: 28903937--28903962 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28903927 TTTTAATTAA
28903937 GTTAG GTTAG GTTAG GTTAG GTTAG G
1 GTTAG GTTAG GTTAG GTTAG GTTAG G
28903963 GTTTTCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.38
Consensus pattern (5 bp):
GTTAG
Found at i:28905171 original size:7 final size:7
Alignment explanation
Indices: 28905161--28905192 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
28905151 TTATATACAT
28905161 AATACTA
1 AATACTA
28905168 AATACTA
1 AATACTA
28905175 AATACTA
1 AATACTA
28905182 AATACTA
1 AATACTA
28905189 AATA
1 AATA
28905193 TCAATCGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:28906539 original size:28 final size:28
Alignment explanation
Indices: 28906481--28906543 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
28906471 GCGATTTTCT
28906481 AAAAAATGGACCATTTCGATAAATAATA
1 AAAAAATGGACCATTTCGATAAATAATA
*
28906509 AAAAAATCGGCCCATTTCGATAAATTAA-A
1 AAAAAAT-GGACCATTTCGATAAA-TAATA
28906538 AAAAAA
1 AAAAAA
28906544 GGAATTTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 7 0.22
29 22 0.69
30 3 0.09
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.22
Consensus pattern (28 bp):
AAAAAATGGACCATTTCGATAAATAATA
Found at i:28909934 original size:21 final size:23
Alignment explanation
Indices: 28909886--28909934 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
28909876 AATTGTTTTC
* *
28909886 AGTTTTAACAAGTTTTTTATTTT
1 AGTTTTAACAAGTTTTATATGTT
*
28909909 TGTTTT-AC-AGTTTTATATGTT
1 AGTTTTAACAAGTTTTATATGTT
28909930 AGTTT
1 AGTTT
28909935 GCGCTTTGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.68
22 2 0.09
23 5 0.23
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.61
Consensus pattern (23 bp):
AGTTTTAACAAGTTTTATATGTT
Found at i:28918059 original size:17 final size:17
Alignment explanation
Indices: 28918037--28918069 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
28918027 ATATTTATTA
28918037 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
28918054 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
28918070 TAAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:28918980 original size:9 final size:9
Alignment explanation
Indices: 28918963--28918999 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28918953 TGAGTTTTCG
28918963 AATTCGAAT
1 AATTCGAAT
*
28918972 AACTCGAAT
1 AATTCGAAT
28918981 AATTCGAAT
1 AATTCGAAT
28918990 AATTCGAAT
1 AATTCGAAT
28918999 A
1 A
28919000 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28920081 original size:18 final size:20
Alignment explanation
Indices: 28920056--28920099 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
28920046 GGTATCATAT
*
28920056 ATTT-ATTCAT-ATTTTTC-
1 ATTTAATTCATAATTTTACG
28920073 ATTTAATTCATAATTTTACG
1 ATTTAATTCATAATTTTACG
28920093 ATTTAAT
1 ATTTAAT
28920100 CCATTTGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 6 0.26
19 6 0.26
20 7 0.30
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTAATTCATAATTTTACG
Found at i:28925113 original size:17 final size:18
Alignment explanation
Indices: 28925084--28925118 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28925074 AAAAAATCAC
28925084 ATTTTTTACATTTAATAT
1 ATTTTTTACATTTAATAT
*
28925102 ATTTTTTA-ATTTCATAT
1 ATTTTTTACATTTAATAT
28925119 TACATATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTTACATTTAATAT
Found at i:28936614 original size:26 final size:25
Alignment explanation
Indices: 28936558--28936633 Score: 91
Period size: 26 Copynumber: 3.0 Consensus size: 25
28936548 ATGAATTTTC
* * *
28936558 TCAAAATTTTATCAGGATAAAATCG
1 TCAAAATTTTATGAGGGTAAAATTG
*
28936583 TTAAAATTTTACTGAGGGTAAAATTG
1 TCAAAATTTTA-TGAGGGTAAAATTG
28936609 TCAAAATTTTATTG-GGGTAAAATTG
1 TCAAAATTTTA-TGAGGGTAAAATTG
28936634 GGATGAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
25 21 0.48
26 23 0.52
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (25 bp):
TCAAAATTTTATGAGGGTAAAATTG
Found at i:28936632 original size:25 final size:25
Alignment explanation
Indices: 28936558--28936633 Score: 89
Period size: 25 Copynumber: 3.0 Consensus size: 25
28936548 ATGAATTTTC
** * *
28936558 TCAAAATTTTATCAGGATAAAATCG
1 TCAAAATTTTATTGGGGTAAAATTG
* *
28936583 TTAAAATTTTACTGAGGGTAAAATTG
1 TCAAAATTTTATTG-GGGTAAAATTG
28936609 TCAAAATTTTATTGGGGTAAAATTG
1 TCAAAATTTTATTGGGGTAAAATTG
28936634 GGATGAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 21 0.50
26 21 0.50
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (25 bp):
TCAAAATTTTATTGGGGTAAAATTG
Found at i:28940072 original size:27 final size:27
Alignment explanation
Indices: 28940042--28940219 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
28940032 ATATCGAGTC
* * * *
28940042 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
28940069 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28940096 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28940124 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28940151 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28940178 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28940205 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28940220 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28940181 original size:82 final size:81
Alignment explanation
Indices: 28940063--28940218 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
28940053 TGCTATATAA
*
28940063 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28940128 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28940145 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28940209 CACTTAGTGC
65 CACTTAGTGC
28940219 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28948117 original size:27 final size:27
Alignment explanation
Indices: 28948087--28948264 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
28948077 ATATCGAGTC
* * * *
28948087 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
28948114 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28948141 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
28948169 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28948196 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28948223 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28948250 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28948265 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28948226 original size:82 final size:81
Alignment explanation
Indices: 28948108--28948263 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
28948098 TGCTATATAA
*
28948108 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
28948173 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28948190 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28948254 CACTTAGTGC
65 CACTTAGTGC
28948264 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28968381 original size:12 final size:12
Alignment explanation
Indices: 28968356--28968394 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
28968346 ACTCGCTTCT
* *
28968356 TTACTTACTCAC
1 TTACTTGCTTAC
*
28968368 TTACTTGTTTAC
1 TTACTTGCTTAC
28968380 TTACTTGCTTAC
1 TTACTTGCTTAC
28968392 TTA
1 TTA
28968395 AATAACTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:28968718 original size:50 final size:50
Alignment explanation
Indices: 28968642--28968834 Score: 224
Period size: 50 Copynumber: 3.7 Consensus size: 50
28968632 TTTTCTGTAT
* * * **
28968642 TGCCAATGTCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
28968692 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
28968742 TGCCAACGCCCTGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
28968798 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
28968835 TCTCATTCCC
Statistics
Matches: 119, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
50 81 0.68
53 2 0.02
56 36 0.30
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:28970371 original size:46 final size:47
Alignment explanation
Indices: 28970269--28970371 Score: 154
Period size: 47 Copynumber: 2.2 Consensus size: 47
28970259 ATTGTTTTCA
* *
28970269 AGTTATTGCATTGACAACCATCCTCACAATTTATCTTATTTATATCT
1 AGTTATTGCATCGACAACCATCCTCACAATTTATATTATTTATATCT
* * *
28970316 GGTTATTGCATCGATAACTATCCTCACAATTT-TATTATTTATATCT
1 AGTTATTGCATCGACAACCATCCTCACAATTTATATTATTTATATCT
28970362 AGTTATTGCA
1 AGTTATTGCA
28970372 CCAACATTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
46 22 0.44
47 28 0.56
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (47 bp):
AGTTATTGCATCGACAACCATCCTCACAATTTATATTATTTATATCT
Found at i:28972525 original size:22 final size:22
Alignment explanation
Indices: 28972485--28972530 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
28972475 GGACACATTA
*
28972485 AAGCAACTGCAGATAAACACTG
1 AAGCAACTGCAAATAAACACTG
* *
28972507 AAGCAACTGCAAATCAACATTG
1 AAGCAACTGCAAATAAACACTG
28972529 AA
1 AA
28972531 ACTATTCCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.48, C:0.22, G:0.15, T:0.15
Consensus pattern (22 bp):
AAGCAACTGCAAATAAACACTG
Found at i:28975182 original size:31 final size:31
Alignment explanation
Indices: 28975142--28975205 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
28975132 GGTACCTTTG
*
28975142 TCGATGCATTGAAATCTTACTGTCAACGCAT
1 TCGACGCATTGAAATCTTACTGTCAACGCAT
28975173 TCGACGCATTGAAATCTTACTGTCAACGCAT
1 TCGACGCATTGAAATCTTACTGTCAACGCAT
28975204 TC
1 TC
28975206 CTTAAGTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (31 bp):
TCGACGCATTGAAATCTTACTGTCAACGCAT
Found at i:28996108 original size:20 final size:20
Alignment explanation
Indices: 28996085--28996132 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
28996075 CATTAAAGAG
*
28996085 TGGCACAACGTATTATCTGA
1 TGGCACAACGTATTAACTGA
28996105 TGGCACAACGTATTAACTGA
1 TGGCACAACGTATTAACTGA
28996125 TGGCACAA
1 TGGCACAA
28996133 TCCCTATCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (20 bp):
TGGCACAACGTATTAACTGA
Found at i:29002520 original size:29 final size:27
Alignment explanation
Indices: 29002473--29002548 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
29002463 AAACCACCGT
*
29002473 ATAACATA-AATGC-AGAAAATCTGTCGA
1 ATAACATATAATGCGATAAAAT-TGTC-A
29002500 ATAACATATAATGCGATAAAATTGTCA
1 ATAACATATAATGCGATAAAATTGTCA
* *
29002527 GTATCATATAATGCGATAAAAT
1 ATAACATATAATGCGATAAAAT
29002549 GCCAATCCCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 29 0.66
28 9 0.20
29 6 0.14
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (27 bp):
ATAACATATAATGCGATAAAATTGTCA
Found at i:29004215 original size:25 final size:25
Alignment explanation
Indices: 29004181--29004252 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
29004171 ACGAATTTTC
29004181 TCAAAATTTTACTAGGATAAAATCA
1 TCAAAATTTTACTAGGATAAAATCA
* * **
29004206 TCAAAATTTTACAAAGAATAAAATTG
1 TCAAAATTTTAC-TAGGATAAAATCA
*
29004232 TCAAAAGTTTACTAGGATAAA
1 TCAAAATTTTACTAGGATAAA
29004253 GTTGGTGTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 19 0.49
26 20 0.51
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.31
Consensus pattern (25 bp):
TCAAAATTTTACTAGGATAAAATCA
Found at i:29005413 original size:11 final size:11
Alignment explanation
Indices: 29005399--29005437 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
29005389 TTTTTTGCTG
29005399 TTATTTTGTTA
1 TTATTTTGTTA
* **
29005410 TTATATTACTA
1 TTATTTTGTTA
29005421 TTATTTTGTTA
1 TTATTTTGTTA
29005432 TTATTT
1 TTATTT
29005438 GGATATTATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.05, T:0.69
Consensus pattern (11 bp):
TTATTTTGTTA
Found at i:29005436 original size:33 final size:33
Alignment explanation
Indices: 29005399--29005473 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
29005389 TTTTTTGCTG
* *
29005399 TTATTTTGTTATTATATTACTATTATTTTGTTA
1 TTATTTTGTTATTATATAACTATTATTTTATTA
* * *
29005432 TTATTTGGATATTATATAACTCTTATTTTATTA
1 TTATTTTGTTATTATATAACTATTATTTTATTA
*
29005465 TTAATTTGT
1 TTATTTTGT
29005474 CTACTATTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.04, G:0.07, T:0.63
Consensus pattern (33 bp):
TTATTTTGTTATTATATAACTATTATTTTATTA
Found at i:29005552 original size:17 final size:18
Alignment explanation
Indices: 29005532--29005565 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29005522 TATTTAAGTA
29005532 TAAATACTT-TTTTAATG
1 TAAATACTTATTTTAATG
*
29005549 TAAATATTTATTTTAAT
1 TAAATACTTATTTTAAT
29005566 ATTTTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TAAATACTTATTTTAATG
Found at i:29005579 original size:23 final size:22
Alignment explanation
Indices: 29005552--29005613 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 22
29005542 TTTAATGTAA
*
29005552 ATATTTATTTTAATATTTTTAAT
1 ATATTTATTTTAATATATTT-AT
* * *
29005575 ATATTTAATTTATTATATTTCT
1 ATATTTATTTTAATATATTTAT
* *
29005597 AAATTTATTTTTATATA
1 ATATTTATTTTAATATA
29005614 AAAAATTAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (22 bp):
ATATTTATTTTAATATATTTAT
Found at i:29010343 original size:21 final size:21
Alignment explanation
Indices: 29010302--29010345 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
29010292 ATGTAATGAT
*
29010302 AAAATTATATTTTAATCTTTTA
1 AAAATTATAATTTAA-CTTTTA
29010324 AAAATTTATAATTTAA-TTTTA
1 AAAA-TTATAATTTAACTTTTA
29010345 A
1 A
29010346 CTTCTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 4 0.20
23 10 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AAAATTATAATTTAACTTTTA
Found at i:29011248 original size:19 final size:20
Alignment explanation
Indices: 29011215--29011265 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
29011205 ATAAAACCAT
*
29011215 AAAAATAAAATAAATATTTTAA
1 AAAAAT-AAA-AATTATTTTAA
*
29011237 AAAAATAAAAATTATTTTTA
1 AAAAATAAAAATTATTTTAA
29011257 AAAAATAAA
1 AAAAATAAA
29011266 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 18 0.67
21 3 0.11
22 6 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAATAAAAATTATTTTAA
Found at i:29011571 original size:16 final size:17
Alignment explanation
Indices: 29011542--29011579 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
29011532 CGGTTCAAAT
* *
29011542 AAAATAAATTATTTTTA
1 AAAATAAATAATTTATA
29011559 AAAATAAA-AATTTATA
1 AAAATAAATAATTTATA
29011575 AAAAT
1 AAAAT
29011580 CGATTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATAAATAATTTATA
Found at i:29011829 original size:26 final size:25
Alignment explanation
Indices: 29011788--29011838 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 25
29011778 AATATATGGG
29011788 AAAAAAATCTTTAAAAT-TCAAAAAT
1 AAAAAAATCTTTAAAATAT-AAAAAT
29011813 AAAAAATAT-TTTAAAAATATAAAAAT
1 AAAAAA-ATCTTT-AAAATATAAAAAT
29011839 TTCAAAATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
25 9 0.39
26 13 0.57
27 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAAAAATCTTTAAAATATAAAAAT
Found at i:29011840 original size:17 final size:18
Alignment explanation
Indices: 29011804--29011845 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29011794 ATCTTTAAAA
29011804 TTCAAAAATAAAAAATAT
1 TTCAAAAATAAAAAATAT
* *
29011822 TTTAAAAATATAAAA-AT
1 TTCAAAAATAAAAAATAT
29011839 TTCAAAA
1 TTCAAAA
29011846 TTCAATGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (18 bp):
TTCAAAAATAAAAAATAT
Found at i:29012014 original size:15 final size:16
Alignment explanation
Indices: 29011989--29012019 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
29011979 AGTTGAATCA
29011989 ATTTTTATAATTTTTT
1 ATTTTTATAATTTTTT
29012005 ATTTTT-TAATTTTTT
1 ATTTTTATAATTTTTT
29012020 TCTGCTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
ATTTTTATAATTTTTT
Found at i:29013303 original size:20 final size:20
Alignment explanation
Indices: 29013275--29013327 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
29013265 AAGGTTTTTC
* *
29013275 TTTTCTTCTTTCCGATTCGG
1 TTTTTTTCTTTCCGATTCCG
*
29013295 TTTTTTTCTTT-CGATTCCT
1 TTTTTTTCTTTCCGATTCCG
29013314 TTTTTCTTCTTTCC
1 TTTTT-TTCTTTCC
29013328 TTTTTGTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 11 0.39
20 16 0.57
21 1 0.04
ACGTcount: A:0.04, C:0.25, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTTTTTCTTTCCGATTCCG
Found at i:29015865 original size:27 final size:27
Alignment explanation
Indices: 29015825--29015876 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
29015815 AAGATAGTCT
**
29015825 GACGGGACGTTAAACACGAGGTAGTTC
1 GACGGGACACTAAACACGAGGTAGTTC
**
29015852 GACGGGACACTAAACGTGAGGTAGT
1 GACGGGACACTAAACACGAGGTAGT
29015877 CCACCTTGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.31, C:0.17, G:0.35, T:0.17
Consensus pattern (27 bp):
GACGGGACACTAAACACGAGGTAGTTC
Found at i:29020113 original size:31 final size:30
Alignment explanation
Indices: 29020077--29020148 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
29020067 ATTATATACG
29020077 AATTTTAATTTAATGTGCAATATCACACAT-A
1 AATTTTAATTTAATGT--AATATCACACATGA
* * * * *
29020108 AATTTTGATTTTATGTAATTTTATACATGA
1 AATTTTAATTTAATGTAATATCACACATGA
29020138 AATTTTAATTT
1 AATTTTAATTT
29020149 GATTTAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 9 0.26
30 11 0.32
31 14 0.41
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (30 bp):
AATTTTAATTTAATGTAATATCACACATGA
Found at i:29020142 original size:30 final size:29
Alignment explanation
Indices: 29020103--29020159 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
29020093 GCAATATCAC
* *
29020103 ACATAAATTTTGATTTTATGTAATTTTAT
1 ACATAAATTTTAATTTGATGTAATTTTAT
*
29020132 ACATGAAATTTTAATTTGATTTAATTTT
1 ACAT-AAATTTTAATTTGATGTAATTTT
29020160 CAAAAATCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (29 bp):
ACATAAATTTTAATTTGATGTAATTTTAT
Found at i:29026612 original size:21 final size:21
Alignment explanation
Indices: 29026597--29026645 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
29026587 TTTATTTATT
29026597 AAAATAATAATTTTATAAATA
1 AAAATAATAATTTTATAAATA
*
29026618 AAAATAATAGTTTTATAAAT-
1 AAAATAATAATTTTATAAATA
29026638 AAAATAAT
1 AAAATAAT
29026646 TTAAGGGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 8 0.30
21 19 0.70
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAATAATAATTTTATAAATA
Found at i:29027171 original size:16 final size:15
Alignment explanation
Indices: 29027135--29027178 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
29027125 TGTTTGTGAG
*
29027135 TTTTTTATAAAAATAT
1 TTTTTTAT-AAATTAT
29027151 TTTTTTATAAATTAT
1 TTTTTTATAAATTAT
*
29027166 TATTTTAATAAAT
1 T-TTTTTATAAAT
29027179 AAATTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.28
16 18 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTTATAAATTAT
Found at i:29027666 original size:14 final size:14
Alignment explanation
Indices: 29027639--29027677 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
29027629 CCTTACTTTT
29027639 TTTATTTAATTTATA
1 TTTATTT-ATTTATA
*
29027654 TTTATTTATTTATT
1 TTTATTTATTTATA
*
29027668 TTTATCTATT
1 TTTATTTATT
29027678 AAACAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTATTTATTTATA
Found at i:29028578 original size:26 final size:26
Alignment explanation
Indices: 29028546--29028599 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
29028536 CAAGTTGTTT
* * *
29028546 AAAATATTATAATGGATTCTTTAAAA
1 AAAATATTAGAATGAATTATTTAAAA
*
29028572 AAAATATTAGAATTAATTATTTAAAA
1 AAAATATTAGAATGAATTATTTAAAA
29028598 AA
1 AA
29028600 TCAAGATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.37
Consensus pattern (26 bp):
AAAATATTAGAATGAATTATTTAAAA
Found at i:29030567 original size:23 final size:21
Alignment explanation
Indices: 29030507--29030567 Score: 52
Period size: 23 Copynumber: 2.8 Consensus size: 21
29030497 ATCAGTATAT
29030507 GACACATAAGTGCCT-AAAAC
1 GACACATAAGTGCCTGAAAAC
* * * *
29030527 AACACACGAGGTGTCTGAAATAC
1 GACACA-TAAGTGCCTGAAA-AC
29030550 GACACATAAAGTGCCTGA
1 GACACAT-AAGTGCCTGA
29030568 TCGGCAAAGC
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
20 5 0.17
21 6 0.21
22 3 0.10
23 15 0.52
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (21 bp):
GACACATAAGTGCCTGAAAAC
Found at i:29031677 original size:18 final size:19
Alignment explanation
Indices: 29031656--29031691 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
29031646 ATTATTTATC
29031656 TAATAAATATCT-TTTAAA
1 TAATAAATATCTATTTAAA
29031674 TAATAAATATCTATTTAA
1 TAATAAATATCTATTTAA
29031692 TATACAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (19 bp):
TAATAAATATCTATTTAAA
Found at i:29031700 original size:19 final size:18
Alignment explanation
Indices: 29031660--29031702 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
29031650 TTTATCTAAT
*
29031660 AAATATCTTTTAAATAAT
1 AAATATCTTTTAAATAAC
29031678 AAATATCTATTT-AATATAC
1 AAATATCT-TTTAAATA-AC
29031697 AAATAT
1 AAATAT
29031703 AAATATTGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATCTTTTAAATAAC
Found at i:29041941 original size:19 final size:19
Alignment explanation
Indices: 29041914--29041969 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
29041904 GGAAAGTTCA
29041914 ATATTATTATTTTTAATAT
1 ATATTATTATTTTTAATAT
* *
29041933 ATATAATTATATATTAA-AT
1 ATATTATTAT-TTTTAATAT
*
29041952 ATATTATTATATTTAATA
1 ATATTATTATTTTTAATA
29041970 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 4 0.13
19 21 0.70
20 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATATTATTATTTTTAATAT
Found at i:29048159 original size:16 final size:16
Alignment explanation
Indices: 29048138--29048176 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
29048128 AATAATAGAA
29048138 ATATATAAAAACATGT
1 ATATATAAAAACATGT
* **
29048154 ATATATGAAAGTATGT
1 ATATATAAAAACATGT
29048170 ATATATA
1 ATATATA
29048177 TAAATTAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:29049130 original size:17 final size:17
Alignment explanation
Indices: 29049090--29049131 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
29049080 TCAGAAAAGG
29049090 TTTTTTTTTCTCTCTTT
1 TTTTTTTTTCTCTCTTT
* * *
29049107 ATATTTTTTCTTTCTTT
1 TTTTTTTTTCTCTCTTT
29049124 TTTTTTTT
1 TTTTTTTT
29049132 GCAAATGTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.05, C:0.12, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTCTCTCTTT
Found at i:29052755 original size:22 final size:21
Alignment explanation
Indices: 29052716--29052761 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 21
29052706 TAAACTTATT
*
29052716 TTTTATTATCTAAATTTAATA
1 TTTTATTATCTAAATTTAAAA
29052737 TTTT-TTATCTAAACCTTTAAAA
1 TTTTATTATCTAAA--TTTAAAA
29052759 TTT
1 TTT
29052762 CGAGCAGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 4 0.18
22 9 0.41
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATTATCTAAATTTAAAA
Found at i:29056200 original size:65 final size:65
Alignment explanation
Indices: 29056120--29056249 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
29056110 TTATTTTCCC
29056120 AAGGCCTGCGACATACCTGTGGGTTCTCTATAACTTATCATAGTTAATCCTCAATAAGAAACTTA
1 AAGGCCTGCGACATACCTGTGGGTTCTCTATAACTTATCATAGTTAATCCTCAATAAGAAACTTA
29056185 AAGGCCTGCGACATACCTGTGGGTTCTCTATAACTTATCATAGTTAATCCTCAATAAGAAACTTA
1 AAGGCCTGCGACATACCTGTGGGTTCTCTATAACTTATCATAGTTAATCCTCAATAAGAAACTTA
29056250 CTTACAACTT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (65 bp):
AAGGCCTGCGACATACCTGTGGGTTCTCTATAACTTATCATAGTTAATCCTCAATAAGAAACTTA
Found at i:29057963 original size:23 final size:23
Alignment explanation
Indices: 29057928--29057972 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29057918 TGGAGTATAA
* *
29057928 AAGTTTTATATTTTTATATGTAC
1 AAGTTTTATATTTATACATGTAC
29057951 AAGTTTTGA-ATTTATACATGTA
1 AAGTTTT-ATATTTATACATGTA
29057973 TATACAAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (23 bp):
AAGTTTTATATTTATACATGTAC
Found at i:29058597 original size:42 final size:42
Alignment explanation
Indices: 29058550--29058680 Score: 217
Period size: 42 Copynumber: 3.1 Consensus size: 42
29058540 AGTGCCTATC
* * *
29058550 AGGCTTAATGCCGGTGAAATAATTTCAGACTTTACGTCTAGT
1 AGGCTTAATACCGGTGAAACAATATCAGACTTTACGTCTAGT
29058592 AGGCTTAATACCGGTGAAACAATATCAGACTTTACGTCTAGT
1 AGGCTTAATACCGGTGAAACAATATCAGACTTTACGTCTAGT
* *
29058634 AGGCTTAATACCGGTGAAACAATATCAGACTTTACATCTAGC
1 AGGCTTAATACCGGTGAAACAATATCAGACTTTACGTCTAGT
29058676 AGGCT
1 AGGCT
29058681 AAGTGCCGGT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (42 bp):
AGGCTTAATACCGGTGAAACAATATCAGACTTTACGTCTAGT
Found at i:29068417 original size:6 final size:6
Alignment explanation
Indices: 29068379--29068408 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
29068369 AATTTTTCAA
29068379 AAAAAG AAAAAG AAAAAG AAAAAG CAAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG -AAAAA
29068409 AAGAAAAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:29069768 original size:42 final size:41
Alignment explanation
Indices: 29069720--29069854 Score: 126
Period size: 42 Copynumber: 3.1 Consensus size: 41
29069710 TTGCAGATCT
29069720 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCC-AGCC
* * * * * * ** *
29069762 TATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCT
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGTCCCAG--CC
*
29069806 TATCTCCCTAAGCAGTAGTGGAGCATATCGAAGTCCCAAGCC
1 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCC-AGCC
29069848 TTATCTC
1 -TATCTC
29069855 TCTGAGTAGC
Statistics
Matches: 69, Mismatches: 19, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
42 28 0.41
43 14 0.20
44 27 0.39
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (41 bp):
TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCAGCC
Found at i:29069848 original size:86 final size:87
Alignment explanation
Indices: 29069703--29069928 Score: 319
Period size: 86 Copynumber: 2.6 Consensus size: 87
29069693 GCAAAGCAGA
* *
29069703 TTGAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAGCC-TATCT
1 TTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCAAGCCTTATCT
**
29069767 CCCTGAGCAGCAGTGGAGTAGG
66 CCCTGAGCAGCAGCAGAGTAGG
* *
29069789 TTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCGAAGTCCCAAGCCTTATCT
1 TTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCAAGCCTTATCT
* *
29069854 CTCTGAGTAGCAGCAGAGTAGG
66 CCCTGAGCAGCAGCAGAGTAGG
* *
29069876 TTAAAAAAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAA
1 TT----GAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAA
29069929 AACACTAGCC
Statistics
Matches: 123, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
86 55 0.45
87 25 0.20
91 43 0.35
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
TTGAAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCAAGCCTTATCT
CCCTGAGCAGCAGCAGAGTAGG
Found at i:29070127 original size:218 final size:218
Alignment explanation
Indices: 29069883--29070454 Score: 966
Period size: 218 Copynumber: 2.6 Consensus size: 218
29069873 AGGTTAAAAA
* * * *
29069883 AAAATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAAACACTAGCCTTGCCTCCC
1 AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCTCCC
* *
29069948 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATCTTGCCTCCCTGTACTAACAGTGAAGCAGAT
66 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATATTGCCTCCCTGTACTGACAGTGAAGCAGAT
*
29070013 TGAAAAAACCAATCTTATCTCCCTGGTCAGCAGTGAAATAAGTTGAGGATTGAGAATCCTATCTC
131 CGAAAAAACCAATCTTATCTCCCTGGTCAGCAGTGAAATAAGTTGAGGATTGAGAATCCTATCTC
29070078 CCTGGACAGTAGTGGAATAGGTT
196 CCTGGACAGTAGTGGAATAGGTT
29070101 AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCTCCC
1 AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCTCCC
* * * *
29070166 TCGGTGGTAGCGGAGCAGGCTAAAGATAGTAGATTTTGCCTCCCTATACTGACAGTGAAGCAGAT
66 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATATTGCCTCCCTGTACTGACAGTGAAGCAGAT
* * *
29070231 CGAAAAAACCAATCTTATCTCCCTGGTCAGTAGTGGAATAATTTGAGGATTGAGAATCCTATCTC
131 CGAAAAAACCAATCTTATCTCCCTGGTCAGCAGTGAAATAAGTTGAGGATTGAGAATCCTATCTC
29070296 CCTGGACAGTAGTGGAATAGGTT
196 CCTGGACAGTAGTGGAATAGGTT
* * *
29070319 AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACATTAACCTTGCCTCTC
1 AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCTCCC
* *
29070384 TCGGTGGCAGCGGAGCAGGTTAAAGATAGCAGATATTGCCTTCCTGTACTGACAGTGAAGCAGAT
66 TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATATTGCCTCCCTGTACTGACAGTGAAGCAGAT
29070449 C-AAAAA
131 CGAAAAA
29070455 TTGTGAATCC
Statistics
Matches: 332, Mismatches: 22, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
217 5 0.02
218 327 0.98
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (218 bp):
AAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACACTAGCCTTGCCTCCC
TCGGTGGCAGCGGAGCAGGCTAAAGATAGCAGATATTGCCTCCCTGTACTGACAGTGAAGCAGAT
CGAAAAAACCAATCTTATCTCCCTGGTCAGCAGTGAAATAAGTTGAGGATTGAGAATCCTATCTC
CCTGGACAGTAGTGGAATAGGTT
Found at i:29070588 original size:176 final size:175
Alignment explanation
Indices: 29070279--29070625 Score: 514
Period size: 176 Copynumber: 2.0 Consensus size: 175
29070269 TAATTTGAGG
*
29070279 ATTGAGAATCCTATCTCCCTGGACAGTAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAA
1 ATTGAGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAA
* ** * **
29070344 GCAGTAGCGGAGCAGATCGAAGACATTAACCTTGCCTCTCTCGGTGGCAGCGGAGCAGGTTAAAG
66 GCAGTAGCAGAGCAGATCGAAGACACCAACCTTGCCTCCCTCGGTCACAGCGGAGCAGGTTAAAG
*
29070409 ATAGCAGATATTGCCTTCCTGTACTGACAGTGAAGCAGATCAAAA
131 ATAGCAGATATTGCCTTCCTGTACCGACAGTGAAGCAGATCAAAA
* *
29070454 ATTGTGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAAATTACATATCTTATCTCCCTA
1 ATTGAGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTT-AAAATTACAGATCTTATCTCCCTA
* * * * * * * *
29070519 AGCAGTAGCAGAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTCATAGTGGATCATGTTGAA
65 AGCAGTAGCAGAGCAGATCGAAGACACCAACCTTGCCTCCCTCGGTCACAGCGGAGCAGGTTAAA
*
29070584 GATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATC
130 GATAGCAGATATTGCCTTCCTGTACCGACAGTGAAGCAGATC
29070626 GAAGATACCA
Statistics
Matches: 152, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
175 38 0.25
176 114 0.75
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (175 bp):
ATTGAGAATCCTATCTCCCTGGACAGCAGTGGAATAGGTTAAAATTACAGATCTTATCTCCCTAA
GCAGTAGCAGAGCAGATCGAAGACACCAACCTTGCCTCCCTCGGTCACAGCGGAGCAGGTTAAAG
ATAGCAGATATTGCCTTCCTGTACCGACAGTGAAGCAGATCAAAA
Found at i:29070632 original size:45 final size:45
Alignment explanation
Indices: 29070530--29070812 Score: 170
Period size: 44 Copynumber: 6.4 Consensus size: 45
29070520 GCAGTAGCAG
* * * * *
29070530 AGCAGATCGAAGATACCAG-CCTTGCCTCCCTGG-GTCATAGTGG
1 AGCAGATCGAAGATACCAGATCTTGCCTTCCTGGACTGATAGTGA
* * * * * *
29070573 ATCATG-TTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGTGA
1 AGCA-GATCGAAGATACCAGATCTTGCCTTCCTGGACTGATAGTGA
* * * ** *
29070618 AGCAGATCGAAGATACCAG-GCTTACCTCCCTGGGTTG-TAGTGG
1 AGCAGATCGAAGATACCAGATCTTGCCTTCCTGGACTGATAGTGA
* * * * * *
29070661 AGCAGGTTGAAGATAACAAATCTTGCCTTCCTGTACCGATAGTGA
1 AGCAGATCGAAGATACCAGATCTTGCCTTCCTGGACTGATAGTGA
* ** *
29070706 AGCAGATCGAAGATACCAG-CCTTGCC-TCCTTGGGTTG-TAGTGG
1 AGCAGATCGAAGATACCAGATCTTGCCTTCC-TGGACTGATAGTGA
* * ** *
29070749 AGCAGGTTGAAGATAGCCA-ATCTTGCCTTCCTACACTGACAGTGA
1 AGCAGATCGAAGATA-CCAGATCTTGCCTTCCTGGACTGATAGTGA
* *
29070794 AGCAGATCAAAGACACCAG
1 AGCAGATCGAAGATACCAG
29070813 CCTTGCTTCC
Statistics
Matches: 170, Mismatches: 58, Indels: 22
0.68 0.23 0.09
Matches are distributed among these distances:
43 54 0.32
44 59 0.35
45 57 0.34
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (45 bp):
AGCAGATCGAAGATACCAGATCTTGCCTTCCTGGACTGATAGTGA
Found at i:29070636 original size:88 final size:87
Alignment explanation
Indices: 29070530--29070871 Score: 459
Period size: 88 Copynumber: 3.9 Consensus size: 87
29070520 GCAGTAGCAG
** * *
29070530 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTCATAGTGGATCATGTTGAAGATAGCAGATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCA-ATC
29070595 TTGCCTTCCTGTACCGACAGTGA
65 TTGCCTTCCTGTACCGACAGTGA
* * *
29070618 AGCAGATCGAAGATACCAGGCTTACCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAACAAATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGC-AATC
*
29070683 TTGCCTTCCTGTACCGATAGTGA
65 TTGCCTTCCTGTACCGACAGTGA
*
29070706 AGCAGATCGAAGATACCAGCCTTGCCTCCTTGGGTTGTAGTGGAGCAGGTTGAAGATAGCCAATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAG-CAATC
** *
29070771 TTGCCTTCCTACACTGACAGTGA
65 TTGCCTTCCTGTACCGACAGTGA
* * * ** * *
29070794 AGCAGATCAAAGACACCAGCCTTGCTTCCCTGGGTTGTAACGGAGCAGGCTGAAGATAGTAGATC
1 AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCA-ATC
* *
29070859 TTGTCTTCATGTA
65 TTGCCTTCCTGTA
29070872 TTAGCATGAA
Statistics
Matches: 223, Mismatches: 28, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
87 1 0.00
88 220 0.99
89 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (87 bp):
AGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGCAATCT
TGCCTTCCTGTACCGACAGTGA
Found at i:29070909 original size:44 final size:44
Alignment explanation
Indices: 29070854--29071087 Score: 294
Period size: 44 Copynumber: 5.3 Consensus size: 44
29070844 TGAAGATAGT
*
29070854 AGATCTTGTCTTCATGTATTAGCATGAAGTAGATCAAAGATAAC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
** **
29070898 AGATCTTGTCTTTCCA--TATTGGTGGTGAAGTAGATTGAAGA-AAGC
1 AGATCTTGTC-TT-CATGTATTGG-CATGAAGTAGATCAAAGATAA-C
* * *
29070943 AGATCTTGTTTTCATGTATTGGCATGAAGTAGATCAAAGGTAGC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
* * * *
29070987 AGATCTTGTCTTCACGTATTGGCGTGAAGTAGATCGAAGATGAC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
*
29071031 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGC
1 AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
29071075 AGATCTTGTCTTC
1 AGATCTTGTCTTC
29071088 CCATACTGGT
Statistics
Matches: 159, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
43 2 0.01
44 122 0.77
45 33 0.21
46 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.33
Consensus pattern (44 bp):
AGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAAC
Found at i:29071051 original size:88 final size:89
Alignment explanation
Indices: 29070845--29071116 Score: 399
Period size: 89 Copynumber: 3.1 Consensus size: 89
29070835 GGAGCAGGCT
* * *
29070845 GAAGAT-AGTAGATCTTGTCTTCATGTATTAGCATGAAGTAGATCAAAGATAACAGATCTTGTCT
1 GAAGATAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTC-
*
29070909 TTCCATATTGGTGGTGAAGTAGATT
65 TTCCATATTGGTGGTGAAGTAGATC
* *
29070934 GAAGA-AAGCAGATCTTGTTTTCATGTATTGGCATGAAGTAGATCAAAGGTAGCAGATCTTGTCT
1 GAAGATAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCT
* *
29070998 TCACGTATTGG-CGTGAAGTAGATC
66 TC-CATATTGGTGGTGAAGTAGATC
*
29071022 GAAGATGA-CAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCT
1 GAAGATAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCT
*
29071086 TCCCATACTGGTGGTGAAGTAGATC
66 T-CCATATTGGTGGTGAAGTAGATC
29071111 GAAGAT
1 GAAGAT
29071117 CGCATCTAGT
Statistics
Matches: 164, Mismatches: 14, Indels: 10
0.87 0.07 0.05
Matches are distributed among these distances:
88 80 0.49
89 84 0.51
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.32
Consensus pattern (89 bp):
GAAGATAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGATCAAAGATAGCAGATCTTGTCT
TCCATATTGGTGGTGAAGTAGATC
Found at i:29075533 original size:21 final size:21
Alignment explanation
Indices: 29075507--29075549 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29075497 AAACTAACAA
* *
29075507 TATACCTTGTGGACCTCACAG
1 TATACCTTGCGAACCTCACAG
29075528 TATACCTTGCGAACCTCACAG
1 TATACCTTGCGAACCTCACAG
29075549 T
1 T
29075550 GTAACCATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (21 bp):
TATACCTTGCGAACCTCACAG
Found at i:29076799 original size:90 final size:90
Alignment explanation
Indices: 29076643--29076813 Score: 243
Period size: 90 Copynumber: 1.9 Consensus size: 90
29076633 TTATCTATTG
* ** * * *
29076643 ATTATTGAACGTAGCTAAAGACGATGATGGGCCATCGAGAGGGAAAAGAAAGGCAAGATTCGTTG
1 ATTATCGAACGTAGCTAAAGACGATGATGCACCATCGAAAGGGAAAAGAAAGGCAAGAGTCATTG
29076708 ACGAGCAACTGTGATTTGTGTTTGT
66 ACGAGCAACTGTGATTTGTGTTTGT
* ** *
29076733 ATTATCGAACGTAGCTAAAGACGATGCTGCACTGTCGAAAGGGAAAAGAAAGGCGAGAGTCATTG
1 ATTATCGAACGTAGCTAAAGACGATGATGCACCATCGAAAGGGAAAAGAAAGGCAAGAGTCATTG
*
29076798 ACGAGTAACTGTGATT
66 ACGAGCAACTGTGATT
29076814 CCAATTTGCA
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.23
Consensus pattern (90 bp):
ATTATCGAACGTAGCTAAAGACGATGATGCACCATCGAAAGGGAAAAGAAAGGCAAGAGTCATTG
ACGAGCAACTGTGATTTGTGTTTGT
Done.