Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 124 of 290
Found at i:42156741 original size:32 final size:32
Alignment explanation
Indices: 42156705--42156765 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
42156695 CTTCATTGAG
*
42156705 TCTCTACTCTCATAATATTTTGGCATACTGAA
1 TCTCTACTCTCATAATAGTTTGGCATACTGAA
42156737 TCTCTACTCTCATAATAGTTTGGCATACT
1 TCTCTACTCTCATAATAGTTTGGCATACT
42156766 TATAGCAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (32 bp):
TCTCTACTCTCATAATAGTTTGGCATACTGAA
Found at i:42157606 original size:27 final size:27
Alignment explanation
Indices: 42157576--42157627 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
42157566 CTTGTTTAAG
* *
42157576 GTCCCTACGAACTACCCCGTGTTTATT
1 GTCCCGACAAACTACCCCGTGTTTATT
* *
42157603 GTCCCGATAAACTACCCTGTGTTTA
1 GTCCCGACAAACTACCCCGTGTTTA
42157628 CTCTTTTTGT
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:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (27 bp):
GTCCCGACAAACTACCCCGTGTTTATT
Found at i:42157649 original size:54 final size:54
Alignment explanation
Indices: 42157586--42157688 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
42157576 GTCCCTACGA
* * * * *
42157586 ACTACCCCGTGTTTATTGTCCCGATAAACTACCCTGTGTTTACTCTTTTTGTGG
1 ACTAACCCGTGTTTACTGTCCCAATAAACTACCCTATGTTTACTATTTTTGTGG
*
42157640 ACTAACCCGTGTTTACTGTCCCAATAGACTACCCTATGTTTACTATTTT
1 ACTAACCCGTGTTTACTGTCCCAATAAACTACCCTATGTTTACTATTTT
42157689 GGCAGACTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (54 bp):
ACTAACCCGTGTTTACTGTCCCAATAAACTACCCTATGTTTACTATTTTTGTGG
Found at i:42162363 original size:99 final size:96
Alignment explanation
Indices: 42162188--42162366 Score: 243
Period size: 96 Copynumber: 1.8 Consensus size: 96
42162178 AGGATATAAT
* * * *
42162188 GCCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCATCCATCAAGTTGATGCTATATCCCAA
1 GCCGACGCCATGTCCCAGACATGGTCTTACACTAGCTCATCCATCAAGTTGATGCCATATCCCAA
42162253 ACATGGTCTTACACTGACTATCGAAATCGAG
66 ACATGGTCTTACACTGACTATCGAAATCGAG
* ** *
42162284 GCCGACGCCATGTCTCAGACATGGTCTTACACTAGCTC-TCACATATCCGTGTTGATGCCATGTC
1 GCCGACGCCATGTCCCAGACATGGTCTTACACTAGCTCATC-C--AT-CAAGTTGATGCCATATC
42162348 CCAAACATGGTCTTACACT
62 CCAAACATGGTCTTACACT
42162367 AACACATCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
95 2 0.03
96 35 0.49
98 2 0.03
99 32 0.45
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.27
Consensus pattern (96 bp):
GCCGACGCCATGTCCCAGACATGGTCTTACACTAGCTCATCCATCAAGTTGATGCCATATCCCAA
ACATGGTCTTACACTGACTATCGAAATCGAG
Found at i:42164871 original size:49 final size:49
Alignment explanation
Indices: 42164818--42164998 Score: 247
Period size: 49 Copynumber: 3.7 Consensus size: 49
42164808 CTGGTACGCA
*
42164818 TAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
* * * *
42164867 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-CCAA-TTATCCGGTACACG
* * * *
42164918 TAGTAGCCTGCACTTAGTA-TACACATGCGACCAATTATTCAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
*
42164966 TAGTAGCTTGCACTTAGTACTACACACGTGACC
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC
42164999 TGACAATAGA
Statistics
Matches: 113, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
48 27 0.24
49 44 0.39
50 12 0.11
51 30 0.27
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:42164978 original size:99 final size:100
Alignment explanation
Indices: 42164805--42164996 Score: 332
Period size: 99 Copynumber: 1.9 Consensus size: 100
42164795 CAGCCAAAGC
* * *
42164805 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGTGACCAATTATCCGGTACACGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAG
42164870 TAGCCTGCACTTAGTACTACACACGTGATCGAAGT
66 TAGCCTGCACTTAGTACTACACACGTGATCGAAGT
*
42164905 TATCGGGTACGCATAGTAGCCTGCACTTAGTA-TACACATGCGACCAATTATTCAGTACACGTAG
1 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAG
*
42164969 TAGCTTGCACTTAGTACTACACACGTGA
66 TAGCCTGCACTTAGTACTACACACGTGA
42164997 CCTGACAATA
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
99 56 0.64
100 31 0.36
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (100 bp):
TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCCAGTACACGTAG
TAGCCTGCACTTAGTACTACACACGTGATCGAAGT
Found at i:42170015 original size:20 final size:18
Alignment explanation
Indices: 42169978--42170016 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
42169968 ATTAATAAAA
*
42169978 TTAATAAAATTTATTATT
1 TTAATAAAATTTAATATT
42169996 TTAATAAATTATTTAATATT
1 TTAATAAA--ATTTAATATT
42170016 T
1 T
42170017 CAATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATAAAATTTAATATT
Found at i:42170714 original size:16 final size:16
Alignment explanation
Indices: 42170693--42170728 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42170683 TAGTATGTAT
42170693 AATTTTTGGATGATTA
1 AATTTTTGGATGATTA
**
42170709 AATTTTTTTATGATTA
1 AATTTTTGGATGATTA
42170725 AATT
1 AATT
42170729 ATTGTTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (16 bp):
AATTTTTGGATGATTA
Found at i:42170774 original size:22 final size:24
Alignment explanation
Indices: 42170722--42170775 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
42170712 TTTTTTATGA
* *
42170722 TTAAATTATTGTTATTAAATATGTT
1 TTAAATTATAGTTATT-AATATCTT
*
42170747 TGAAATTATAG-TATT-ATATCTT
1 TTAAATTATAGTTATTAATATCTT
42170769 TTAAATT
1 TTAAATT
42170776 GAATTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 12 0.48
24 4 0.16
25 9 0.36
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (24 bp):
TTAAATTATAGTTATTAATATCTT
Found at i:42172391 original size:94 final size:94
Alignment explanation
Indices: 42172270--42172535 Score: 326
Period size: 94 Copynumber: 2.9 Consensus size: 94
42172260 GTTATGTGAG
* * *
42172270 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCTGCATTGAGATGAGGGCTAGTGTAAGGCATG
1 AGCCAGTGTAAGACCATGTCTGAGACATGGCATC-GCATTGAGATGAGTGCTAGTGTAAGACATG
* *
42172335 TCTGGGACATGCATCTGCCAC-ATTATGAT
65 TCTGGGACATGCATCAGCCACAATGATGAT
* * * *
42172364 AGCCAGTGTAAGACCATATCTGAGACATGGCATCGACATAGAGACGAGTGCTATTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTGAGACATGGCATCG-CATTGAGATGAGTGCTAGTGTAAGACATG
* *
42172429 TCTGGGACATGCATCAGCCTCAATGATGCT
65 TCTGGGACATGCATCAGCCACAATGATGAT
* * * **
42172459 AGCCAGTGTAAGA-CGTGTCTGAGACAT-GCATCGGC--TAAGCTTCGTGCTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTGAGACATGGCATC-GCATTGAGATGAGTGCTAGTGTAAGACATG
42172520 TCTGGGACATGCATCA
65 TCTGGGACATGCATCA
42172536 ACACGTATAC
Statistics
Matches: 149, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
91 35 0.23
93 7 0.05
94 88 0.59
95 19 0.13
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (94 bp):
AGCCAGTGTAAGACCATGTCTGAGACATGGCATCGCATTGAGATGAGTGCTAGTGTAAGACATGT
CTGGGACATGCATCAGCCACAATGATGAT
Found at i:42172469 original size:47 final size:44
Alignment explanation
Indices: 42172270--42172634 Score: 180
Period size: 47 Copynumber: 7.8 Consensus size: 44
42172260 GTTATGTGAG
* * *
42172270 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCTGCATTGAGATGAG
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC-GC-CTAAGATGAT
* * * *
42172318 GGCTAGTGTAAGGCATGTCTGGGACATGCATCTGCC-ACATTATGAT
1 AGCCAGTGTAAGACATGTCTGGGACATGCATC-GCCTA-A-GATGAT
* * * *
42172364 AGCCAGTGTAAGACCATATCTGAGACATGGCATCGACATAGAGACGAGT
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG-CCTA-AGATGA-T
* * *
42172413 -GCTATTGTAAGACATGTCTGGGACATGCATCAGCCTCAATGATGCT
1 AGCCAGTGTAAGACATGTCTGGGACATGCATC-GCCT-AA-GATGAT
* * * *
42172459 AGCCAGTGTAAGACGTGTCTGAGACATGCATCGGCTAAGCTTCG-T
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGCCTAAG-AT-GAT
* * * ** *
42172504 -GCTAGTGTAAGACATGTCTGGGACATGCATCAACACGTATACACAAG
1 AGCCAGTGTAAGACATGTCTGGGACATGCATC-GC-C-TA-AGATGAT
* * * *
42172551 AGCTAGTGTAAGACCATGTCTGGGACATGGTATCGACCTCGATGAAGAT
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG-CCT--AAGATGAT
* *
42172600 AACCAGTGTAAGACCATGTCTGAGACATGGCATCG
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
42172635 GCAACTTAAC
Statistics
Matches: 243, Mismatches: 50, Indels: 47
0.71 0.15 0.14
Matches are distributed among these distances:
44 29 0.12
45 5 0.02
46 36 0.15
47 73 0.30
48 43 0.18
49 51 0.21
50 6 0.02
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.24
Consensus pattern (44 bp):
AGCCAGTGTAAGACATGTCTGGGACATGCATCGCCTAAGATGAT
Found at i:42177232 original size:21 final size:21
Alignment explanation
Indices: 42177206--42177331 Score: 132
Period size: 21 Copynumber: 6.1 Consensus size: 21
42177196 TGAATACACC
*
42177206 AATAGAAGCT-AGTAAGAGCTG
1 AATAGAAGCTCA-TAAGAGTTG
42177227 AATAGAAGCTCATAAGAGTTG
1 AATAGAAGCTCATAAGAGTTG
*
42177248 AATAGAAGCTC-GAA-AGTTG
1 AATAGAAGCTCATAAGAGTTG
* ** * *
42177267 AACAGAAGCTCGCAAGAGCTA
1 AATAGAAGCTCATAAGAGTTG
*
42177288 AATAGAAACTCATAAGAGTTG
1 AATAGAAGCTCATAAGAGTTG
* *
42177309 AACAGAAGCTCATAAGAGATG
1 AATAGAAGCTCATAAGAGTTG
42177330 AA
1 AA
42177332 CATAAAGTAA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
19 15 0.17
20 4 0.05
21 67 0.77
22 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.18
Consensus pattern (21 bp):
AATAGAAGCTCATAAGAGTTG
Found at i:42178516 original size:13 final size:13
Alignment explanation
Indices: 42178498--42178522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42178488 ATAATACTCC
42178498 AAAAATATTTATA
1 AAAAATATTTATA
42178511 AAAAATATTTAT
1 AAAAATATTTAT
42178523 GACTCGGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAAATATTTATA
Found at i:42189721 original size:31 final size:31
Alignment explanation
Indices: 42189686--42189753 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
42189676 GCACTGTTCC
*
42189686 AATTAGAGAAGAAATTTATTTTGATAAATCG
1 AATTACAGAAGAAATTTATTTTGATAAATCG
*
42189717 AATTACTGAAGAAATTTATTTTGATAAATCG
1 AATTACAGAAGAAATTTATTTTGATAAATCG
42189748 AATTAC
1 AATTAC
42189754 TAAGGTACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (31 bp):
AATTACAGAAGAAATTTATTTTGATAAATCG
Found at i:42189754 original size:31 final size:31
Alignment explanation
Indices: 42189693--42189754 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
42189683 TCCAATTAGA
42189693 GAAGAAATTTATTTTGATAAATCGAATTACT
1 GAAGAAATTTATTTTGATAAATCGAATTACT
42189724 GAAGAAATTTATTTTGATAAATCGAATTACT
1 GAAGAAATTTATTTTGATAAATCGAATTACT
42189755 AAGGTACAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (31 bp):
GAAGAAATTTATTTTGATAAATCGAATTACT
Found at i:42192112 original size:28 final size:28
Alignment explanation
Indices: 42192080--42192163 Score: 83
Period size: 28 Copynumber: 3.2 Consensus size: 28
42192070 AACTGTGATC
42192080 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
* * *
42192108 ACGTGTATCAG-A-T-GGT-TAGG-T-C-
1 ACGTGTGT-AGTACTAAGTGCAGGCTACT
42192130 ACGTGTGTAGTACTAAGTGCAGGCTACT
1 ACGTGTGTAGTACTAAGTGCAGGCTACT
42192158 ACGTGT
1 ACGTGT
42192164 ACCGGATAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
21 2 0.05
22 8 0.19
23 2 0.05
24 3 0.07
25 6 0.14
26 3 0.07
27 2 0.05
28 14 0.33
29 2 0.05
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
ACGTGTGTAGTACTAAGTGCAGGCTACT
Found at i:42192149 original size:50 final size:49
Alignment explanation
Indices: 42192032--42192220 Score: 216
Period size: 50 Copynumber: 3.8 Consensus size: 49
42192022 TGAGGTCGCA
* * * * * *
42192032 TGTGTAGTACTAAGTGTAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAA-T-TGGTCACG
* **
42192083 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACG
* * *
42192133 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
* * *
42192182 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
42192221 GCTTTGGCTA
Statistics
Matches: 118, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 41 0.35
50 45 0.38
51 32 0.27
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACG
Found at i:42194493 original size:19 final size:18
Alignment explanation
Indices: 42194469--42194510 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
42194459 TGACCACATG
42194469 TTCATTGAACGGTTTTAAT
1 TTCATT-AACGGTTTTAAT
* *
42194488 TTCATTTACGGTTTTTAT
1 TTCATTAACGGTTTTAAT
42194506 TTCAT
1 TTCAT
42194511 ATTCTTTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (18 bp):
TTCATTAACGGTTTTAAT
Found at i:42195960 original size:27 final size:27
Alignment explanation
Indices: 42195922--42195984 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
42195912 TATCGAAAAA
42195922 TATAA-TATAATTA-TAAAATAATTAAAT
1 TATAATTA-AATTATTAAAAT-ATTAAAT
* *
42195949 TATACTTAAATTATTAACATATTAAAT
1 TATAATTAAATTATTAAAATATTAAAT
42195976 TATAATTAA
1 TATAATTAA
42195985 TTTTATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (27 bp):
TATAATTAAATTATTAAAATATTAAAT
Found at i:42198618 original size:29 final size:29
Alignment explanation
Indices: 42198576--42198639 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
42198566 TGGCTAGCAT
42198576 GTGTGCCCTAAAAAAGGCCACTCACGCTC
1 GTGTGCCCTAAAAAAGGCCACTCACGCTC
*
42198605 GTGTGCCCTAAAAAAGGCCACTCACGTTC
1 GTGTGCCCTAAAAAAGGCCACTCACGCTC
42198634 GTGTGC
1 GTGTGC
42198640 TAGGCCGTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.25, C:0.31, G:0.23, T:0.20
Consensus pattern (29 bp):
GTGTGCCCTAAAAAAGGCCACTCACGCTC
Found at i:42208684 original size:85 final size:85
Alignment explanation
Indices: 42208541--42209469 Score: 1858
Period size: 85 Copynumber: 10.9 Consensus size: 85
42208531 AAAGACCTTA
42208541 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42208606 ATTTAGTCTTTTTTTAATTC
66 ATTTAGTCTTTTTTTAATTC
42208626 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42208691 ATTTAGTCTTTTTTTAATTC
66 ATTTAGTCTTTTTTTAATTC
42208711 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42208776 ATTTAGTCTTTTTTTAATTC
66 ATTTAGTCTTTTTTTAATTC
42208796 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42208861 ATTTAGTCTTTTTTTAATTC
66 ATTTAGTCTTTTTTTAATTC
42208881 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42208946 ATTTAGTCTTTTTTTAATTC
66 ATTTAGTCTTTTTTTAATTC
42208966 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42209031 ATTTAGTCTTTTTTTAATTC
66 ATTTAGTCTTTTTTTAATTC
42209051 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42209116 ATTTAGTCTTTTTTTAATTC
66 ATTTAGTCTTTTTTTAATTC
42209136 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42209201 ATTTAGTCTTTTTTTAATTC
66 ATTTAGTCTTTTTTTAATTC
42209221 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42209286 ATTTAGTCTTTTTTTAATTC
66 ATTTAGTCTTTTTTTAATTC
42209306 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42209371 ATTTAGTCTTTTTTTAATTC
66 ATTTAGTCTTTTTTTAATTC
42209391 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
1 AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
42209456 ATTTAGTCTTTTTT
66 ATTTAGTCTTTTTT
42209470 ACCGAATTAA
Statistics
Matches: 844, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 844 1.00
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.45
Consensus pattern (85 bp):
AATTTAAGGTTCTATAGCTATTAGATACTTTTAGCTAATAGAACTCCACTTTTACACTTTACGCA
ATTTAGTCTTTTTTTAATTC
Found at i:42211395 original size:48 final size:48
Alignment explanation
Indices: 42211324--42211420 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
42211314 CCACAATGTT
42211324 GACGAAGTTTTATGAAGCACTTCACCATAAAGTTACCATCTTCAACCA
1 GACGAAGTTTTATGAAGCACTTCACCATAAAGTTACCATCTTCAACCA
42211372 GACGAAGTTTTATGAAGCACTTCACCATAAAGTTACCATCTTCAACCA
1 GACGAAGTTTTATGAAGCACTTCACCATAAAGTTACCATCTTCAACCA
42211420 G
1 G
42211421 TCTAATTCTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (48 bp):
GACGAAGTTTTATGAAGCACTTCACCATAAAGTTACCATCTTCAACCA
Found at i:42211405 original size:25 final size:25
Alignment explanation
Indices: 42211328--42211405 Score: 60
Period size: 25 Copynumber: 3.2 Consensus size: 25
42211318 AATGTTGACG
42211328 AAGTTTTATGAAGCACTTCACCATA
1 AAGTTTTATGAAGCACTTCACCATA
* *
42211353 AAG---T-T--ACCATCTTCAACCAGA
1 AAGTTTTATGAAGCA-CTTC-ACCATA
42211374 CGAAGTTTTATGAAGCACTTCACCATA
1 --AAGTTTTATGAAGCACTTCACCATA
42211401 AAGTT
1 AAGTT
42211406 ACCATCTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 20
0.62 0.06 0.32
Matches are distributed among these distances:
19 3 0.08
20 4 0.10
21 6 0.15
22 1 0.03
23 3 0.08
25 8 0.21
26 1 0.03
27 6 0.15
28 4 0.10
29 3 0.08
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (25 bp):
AAGTTTTATGAAGCACTTCACCATA
Found at i:42214253 original size:69 final size:68
Alignment explanation
Indices: 42214176--42214386 Score: 211
Period size: 69 Copynumber: 3.2 Consensus size: 68
42214166 CGAGTATAAG
* * *
42214176 AACCAATAGAGTCTGTTGGGATAGTAAACATGGGGATTATAAGGTGTAAGAACATAGCTCGGCTA
1 AACCAATAGAGTCCGCTGGGACAGTAAACATGGGGATTATAAGGTGTAAGAACATAGCTC-GCTA
42214241 TGAC
65 TGAC
* * * ** *
42214245 AACCAATAGAGTCCACAGAGACAGTAAACACAGGGATTATAAGGTGTAAG-----A-CTCACTAT
1 AACCAATAGAGTCCGCTGGGACAGTAAACATGGGGATTATAAGGTGTAAGAACATAGCTCGCTAT
*
42214304 GAA
66 GAC
* * * *
42214307 AACTAATAGAGTCCGCTGGAACAGTAAATATGAGGATTATAAGGTGTAA-AACCATAGCTCAGCT
1 AACCAATAGAGTCCGCTGGGACAGTAAACATGGGGATTATAAGGTGTAAGAA-CATAGCTC-GCT
*
42214371 ATGGC
64 ATGAC
42214376 AACCAATAGAG
1 AACCAATAGAG
42214387 ACCACCAGGA
Statistics
Matches: 111, Mismatches: 23, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
62 46 0.41
63 3 0.03
64 1 0.01
67 1 0.01
68 3 0.03
69 57 0.51
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (68 bp):
AACCAATAGAGTCCGCTGGGACAGTAAACATGGGGATTATAAGGTGTAAGAACATAGCTCGCTAT
GAC
Found at i:42214984 original size:34 final size:34
Alignment explanation
Indices: 42214945--42215009 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
42214935 AGTTAGAACC
*
42214945 CATTGACAAGAAGAGGTACTAAGAAGGATAAACT
1 CATTGACAAGAAGAGGTACTAAGAAGCATAAACT
* * *
42214979 CATTGATAGGAAGAGGTGCTAAGAAGCATAA
1 CATTGACAAGAAGAGGTACTAAGAAGCATAA
42215010 TCTAGGTGAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.45, C:0.11, G:0.26, T:0.18
Consensus pattern (34 bp):
CATTGACAAGAAGAGGTACTAAGAAGCATAAACT
Found at i:42216352 original size:17 final size:17
Alignment explanation
Indices: 42216330--42216363 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42216320 GATGAGTGAA
42216330 TATTTATGTCACTTCAT
1 TATTTATGTCACTTCAT
*
42216347 TATTTATGTTACTTCAT
1 TATTTATGTCACTTCAT
42216364 CCCTTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.06, T:0.56
Consensus pattern (17 bp):
TATTTATGTCACTTCAT
Found at i:42227113 original size:33 final size:34
Alignment explanation
Indices: 42227055--42227121 Score: 127
Period size: 33 Copynumber: 2.0 Consensus size: 34
42227045 TATGTGTCAA
42227055 AATTTTGTGAGTTAATTTTATCGATTGGTTGGTT
1 AATTTTGTGAGTTAATTTTATCGATTGGTTGGTT
42227089 AATTTTGTGAGTTAA-TTTATCGATTGGTTGGTT
1 AATTTTGTGAGTTAATTTTATCGATTGGTTGGTT
42227122 TATTAAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 18 0.55
34 15 0.45
ACGTcount: A:0.21, C:0.03, G:0.24, T:0.52
Consensus pattern (34 bp):
AATTTTGTGAGTTAATTTTATCGATTGGTTGGTT
Found at i:42228080 original size:40 final size:40
Alignment explanation
Indices: 42228036--42228149 Score: 183
Period size: 40 Copynumber: 2.9 Consensus size: 40
42228026 GTTATTTGTA
* *
42228036 GCACTTAGTGTGCGATACGACATAGCTTCGGCTATATATG
1 GCACTTAGTGTGCGATTCGAGATAGCTTCGGCTATATATG
42228076 GCACTTAGTGTGCGATTCGAGATAGCTTCGGCTATATATG
1 GCACTTAGTGTGCGATTCGAGATAGCTTCGGCTATATATG
* * *
42228116 GTACTTAGTGTGCCATTTGAGATAGCTTCGGCTA
1 GCACTTAGTGTGCGATTCGAGATAGCTTCGGCTA
42228150 CGTACGACAC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (40 bp):
GCACTTAGTGTGCGATTCGAGATAGCTTCGGCTATATATG
Found at i:42228189 original size:28 final size:28
Alignment explanation
Indices: 42228157--42228210 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
42228147 CTACGTACGA
* * *
42228157 CACTTTGCGTGTGAGATATTGAGTATGG
1 CACTTAGCGTGCGAGACATTGAGTATGG
*
42228185 CACTTAGTGTGCGAGACATTGAGTAT
1 CACTTAGCGTGCGAGACATTGAGTAT
42228211 TCGACAGTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.30, T:0.33
Consensus pattern (28 bp):
CACTTAGCGTGCGAGACATTGAGTATGG
Found at i:42238304 original size:14 final size:14
Alignment explanation
Indices: 42238285--42238318 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42238275 TTGTTTCACT
42238285 GAAAATGACTTCCG
1 GAAAATGACTTCCG
* *
42238299 GAAAATGATTTCTG
1 GAAAATGACTTCCG
42238313 GAAAAT
1 GAAAAT
42238319 AATTTATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (14 bp):
GAAAATGACTTCCG
Found at i:42238790 original size:15 final size:15
Alignment explanation
Indices: 42238770--42238821 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
42238760 ACTATAAAAC
42238770 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
42238785 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
42238804 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
42238819 ATT
1 ATT
42238822 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:42238879 original size:15 final size:16
Alignment explanation
Indices: 42238859--42238889 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42238849 AACAATATCA
42238859 TTTAAAA-TTATTATT
1 TTTAAAATTTATTATT
42238874 TTTAAAATTTATTATT
1 TTTAAAATTTATTATT
42238890 AAAATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTTATTATT
Found at i:42238914 original size:18 final size:18
Alignment explanation
Indices: 42238876--42238911 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42238866 TTATTATTTT
*
42238876 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
42238894 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
42238912 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:42239455 original size:29 final size:29
Alignment explanation
Indices: 42239413--42239472 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
42239403 TCTCTAGCTA
*
42239413 GTAGAGTCTTGGCAAAACAAATCCCCAGG
1 GTAGAGTCTCGGCAAAACAAATCCCCAGG
* * *
42239442 GTAGAGTCTCGGCATAACACATCCCTAGG
1 GTAGAGTCTCGGCAAAACAAATCCCCAGG
42239471 GT
1 GT
42239473 TTGTCCTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (29 bp):
GTAGAGTCTCGGCAAAACAAATCCCCAGG
Found at i:42255557 original size:18 final size:18
Alignment explanation
Indices: 42255520--42255557 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
42255510 TAAATGATGA
42255520 ATTTAAAATATTAGTTGTT
1 ATTTAAAATATTA-TTGTT
42255539 ATTTAAAAATATT-TTGTT
1 ATTT-AAAATATTATTGTT
42255557 A
1 A
42255558 AGTAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
ATTTAAAATATTATTGTT
Found at i:42256250 original size:20 final size:20
Alignment explanation
Indices: 42256190--42256331 Score: 113
Period size: 20 Copynumber: 7.1 Consensus size: 20
42256180 TCGATACCCT
*
42256190 TGTTTGCACATCAATGCCCC
1 TGTTTGCACATCAGTGCCCC
* * * * **
42256210 TATTTGTACTTCGGTAACCC
1 TGTTTGCACATCAGTGCCCC
42256230 TGTTTGCACATCAGTGCCCC
1 TGTTTGCACATCAGTGCCCC
* * * *
42256250 TGATTGTACATCGGTACCCC
1 TGTTTGCACATCAGTGCCCC
* * *
42256270 TGTTTGCACCTCGGTGCCCT
1 TGTTTGCACATCAGTGCCCC
* * * * *
42256290 TGATTGTACTTCAATACCCC
1 TGTTTGCACATCAGTGCCCC
42256310 TGTTTGCACATCAGTGCCCC
1 TGTTTGCACATCAGTGCCCC
42256330 TG
1 TG
42256332 ATTGTACCTC
Statistics
Matches: 88, Mismatches: 34, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
20 88 1.00
ACGTcount: A:0.17, C:0.32, G:0.18, T:0.33
Consensus pattern (20 bp):
TGTTTGCACATCAGTGCCCC
Found at i:42256349 original size:20 final size:20
Alignment explanation
Indices: 42256166--42256350 Score: 88
Period size: 20 Copynumber: 9.2 Consensus size: 20
42256156 TGAAGAAGTG
* *
42256166 CCCCTAATTGTACTTCGATA
1 CCCCTGATTGTACATCGATA
* * * * *
42256186 CCCTTGTTTGCACATCAATG
1 CCCCTGATTGTACATCGATA
* *
42256206 CCCCT-ATTTGTACTTCGGTA
1 CCCCTGA-TTGTACATCGATA
* * * *
42256226 ACCCTGTTTGCACATC-AGTG
1 CCCCTGATTGTACATCGA-TA
*
42256246 CCCCTGATTGTACATCGGTA
1 CCCCTGATTGTACATCGATA
* * * * *
42256266 CCCCTGTTTGCACCTCGGTG
1 CCCCTGATTGTACATCGATA
* * *
42256286 CCCTTGATTGTACTTCAATA
1 CCCCTGATTGTACATCGATA
* * *
42256306 CCCCTGTTTGCACATC-AGTG
1 CCCCTGATTGTACATCGA-TA
*
42256326 CCCCTGATTGTACCTCGATA
1 CCCCTGATTGTACATCGATA
42256346 CCCCT
1 CCCCT
42256351 AAATGCACAT
Statistics
Matches: 114, Mismatches: 45, Indels: 12
0.67 0.26 0.07
Matches are distributed among these distances:
19 1 0.01
20 112 0.98
21 1 0.01
ACGTcount: A:0.18, C:0.33, G:0.16, T:0.33
Consensus pattern (20 bp):
CCCCTGATTGTACATCGATA
Found at i:42256360 original size:40 final size:40
Alignment explanation
Indices: 42256162--42256350 Score: 254
Period size: 40 Copynumber: 4.7 Consensus size: 40
42256152 GAAATGAAGA
* *
42256162 AGTGCCCCTAATTGTACTTCGATACCCTTGTTTGCACATC
1 AGTGCCCCTGATTGTACTTCGATACCCCTGTTTGCACATC
* * *
42256202 AATGCCCCT-ATTTGTACTTCGGTAACCCTGTTTGCACATC
1 AGTGCCCCTGA-TTGTACTTCGATACCCCTGTTTGCACATC
* * *
42256242 AGTGCCCCTGATTGTACATCGGTACCCCTGTTTGCACCTC
1 AGTGCCCCTGATTGTACTTCGATACCCCTGTTTGCACATC
* * *
42256282 GGTGCCCTTGATTGTACTTCAATACCCCTGTTTGCACATC
1 AGTGCCCCTGATTGTACTTCGATACCCCTGTTTGCACATC
*
42256322 AGTGCCCCTGATTGTACCTCGATACCCCT
1 AGTGCCCCTGATTGTACTTCGATACCCCT
42256351 AAATGCACAT
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 127 0.98
41 1 0.01
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (40 bp):
AGTGCCCCTGATTGTACTTCGATACCCCTGTTTGCACATC
Found at i:42256368 original size:40 final size:40
Alignment explanation
Indices: 42256194--42256371 Score: 108
Period size: 40 Copynumber: 4.5 Consensus size: 40
42256184 TACCCTTGTT
* ** * ***
42256194 TGCACATCAATGCCCCT-ATTTGTACTTCGGTAACCCTGTT
1 TGCACATCAATGCCCCTGA-TTGTACCTCAATACCCCTAAA
* * ** ***
42256234 TGCACATCAGTGCCCCTGATTGTACATCGGTACCCCTGTT
1 TGCACATCAATGCCCCTGATTGTACCTCAATACCCCTAAA
* ** * * ***
42256274 TGCACCTCGGTGCCCTTGATTGTACTTCAATACCCCTGTT
1 TGCACATCAATGCCCCTGATTGTACCTCAATACCCCTAAA
* *
42256314 TGCACATCAGTGCCCCTGATTGTACCTCGATACCCCTAAA
1 TGCACATCAATGCCCCTGATTGTACCTCAATACCCCTAAA
42256354 TGCACAT-ATATGCCCCTG
1 TGCACATCA-ATGCCCCTG
42256372 TTTGCACTTC
Statistics
Matches: 118, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 1 0.01
40 116 0.98
41 1 0.01
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.31
Consensus pattern (40 bp):
TGCACATCAATGCCCCTGATTGTACCTCAATACCCCTAAA
Found at i:42256391 original size:80 final size:79
Alignment explanation
Indices: 42256162--42256415 Score: 258
Period size: 80 Copynumber: 3.2 Consensus size: 79
42256152 GAAATGAAGA
* * * *
42256162 AGTGCCCCTAATTGTACTTCGATACCCTTGTTTGCACATCAATGCCCCTATTTGTACTTCGGTAA
1 AGTGCCCCTGATTGTACATCGATACCCCTGTTTGCACAT-AATGCCCCTGTTTGTACTTCGGTAA
42256227 CCCTGTTTGCACATC
65 CCCTGTTTGCACATC
* * ** * * ** *
42256242 AGTGCCCCTGATTGTACATCGGTACCCCTGTTTGCACCTCGGTGCCCTTGATTGTACTTCAATAC
1 AGTGCCCCTGATTGTACATCGATACCCCTGTTTGCACAT-AATGCCCCTGTTTGTACTTCGGTAA
42256307 CCCTGTTTGCACATC
65 CCCTGTTTGCACATC
* *** * **
42256322 AGTGCCCCTGATTGTACCTCGATACCCCTAAATGCACATATATGCCCCTGTTTGCACTTCGGTGT
1 AGTGCCCCTGATTGTACATCGATACCCCTGTTTGCACATA-ATGCCCCTGTTTGTACTTCGGTAA
* *
42256387 CCCTGATCGCACATTC
65 CCCTGTTTGCACA-TC
*
42256403 -GTGCTCCTGATTG
1 AGTGCCCCTGATTG
42256416 CACTTTGATG
Statistics
Matches: 141, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
80 139 0.99
81 2 0.01
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.33
Consensus pattern (79 bp):
AGTGCCCCTGATTGTACATCGATACCCCTGTTTGCACATAATGCCCCTGTTTGTACTTCGGTAAC
CCTGTTTGCACATC
Found at i:42258922 original size:20 final size:21
Alignment explanation
Indices: 42258874--42258923 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
42258864 AATAATTCAT
42258874 GCAAATTTTGAGTATTTTAATA
1 GCAAATTTTGAG-ATTTTAATA
*
42258896 GCAAATTTTGTAG-TTTTATTA
1 GCAAATTTTG-AGATTTTAATA
42258917 -CAAATTT
1 GCAAATTT
42258924 GTACAATAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.27
21 7 0.27
22 10 0.38
23 2 0.08
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (21 bp):
GCAAATTTTGAGATTTTAATA
Found at i:42261697 original size:15 final size:15
Alignment explanation
Indices: 42261677--42261745 Score: 75
Period size: 15 Copynumber: 4.6 Consensus size: 15
42261667 GTATCTTGGG
42261677 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
42261692 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* * *
42261707 TTTCTGTATTCTGGG
1 TTTCTTTATCCTGGA
* *
42261722 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
42261737 TTTCTTTAT
1 TTTCTTTAT
42261746 TCAGTTTTCT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.12, C:0.17, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:42261737 original size:30 final size:30
Alignment explanation
Indices: 42261668--42261747 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 30
42261658 CATAGTATCG
* * *
42261668 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATCTCTC
* * *
42261698 TAT-TCTGGATTTCTGTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATCTCTC
42261728 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
42261748 AGTTTTCTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.02
30 39 0.95
31 1 0.02
ACGTcount: A:0.11, C:0.17, G:0.16, T:0.55
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATCTCTC
Found at i:42268076 original size:5 final size:5
Alignment explanation
Indices: 42268049--42268088 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
42268039 CTAATTTAAC
* *
42268049 ATAAA ATTAA ATAAA AAATAA ATAAA ATAAA ATAAA ATAA
1 ATAAA ATAAA ATAAA ATA-AA ATAAA ATAAA ATAAA ATAA
42268089 GATTTATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
ATAAA
Found at i:42281224 original size:26 final size:25
Alignment explanation
Indices: 42281185--42281282 Score: 99
Period size: 26 Copynumber: 3.8 Consensus size: 25
42281175 TCTCATCCCC
* *
42281185 ATTTTACTCTGGTAAAATTTTGACG
1 ATTTTACCCTGGTAAAATTTCGACG
* *
42281210 ATTTTATCGCTGGTAAAATTTCGACA
1 ATTTTA-CCCTGGTAAAATTTCGACG
* *
42281236 ATTGTACCCTCGGTAAAATTTCAACG
1 ATTTTACCCT-GGTAAAATTTCGACG
42281262 ATTTTATCCCCT-GTAAAATTT
1 ATTTTA--CCCTGGTAAAATTT
42281283 TGAGAAAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
25 9 0.15
26 48 0.79
28 4 0.07
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (25 bp):
ATTTTACCCTGGTAAAATTTCGACG
Found at i:42299441 original size:20 final size:20
Alignment explanation
Indices: 42299385--42299441 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
42299375 ACATGGTTGA
*
42299385 TATGATATGCACATGACATG
1 TATGATATGCACATGATATG
42299405 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
*
42299425 TATGAAATGCACATGAT
1 TATGATATGCACATGAT
42299442 GTATTCATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:42299527 original size:26 final size:26
Alignment explanation
Indices: 42299491--42299625 Score: 181
Period size: 26 Copynumber: 5.3 Consensus size: 26
42299481 GAGGAAGTGC
*
42299491 AAAAGGGCTTACGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
42299517 AAAAGGGCTTATGCCCCAATTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
42299543 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* *
42299569 AAAAGGGCTT-TGCCCCAATTTA-TC
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
42299593 AAGAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
42299616 AAAAGAGGCT
1 AAAAG-GGCT
42299626 AGGCCTCCAG
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
23 7 0.07
24 22 0.22
25 11 0.11
26 59 0.60
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:42306502 original size:19 final size:19
Alignment explanation
Indices: 42306480--42306517 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
42306470 ATGCTTGGAG
42306480 TTTAATTTGATCCTTGATT
1 TTTAATTTGATCCTTGATT
42306499 TTTAATTTGATCCTTGATT
1 TTTAATTTGATCCTTGATT
42306518 ACTCCTTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.58
Consensus pattern (19 bp):
TTTAATTTGATCCTTGATT
Found at i:42309972 original size:30 final size:31
Alignment explanation
Indices: 42309897--42309972 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
42309887 AATATAACAT
* *
42309897 TTGGTACCTGAACTTGACACTTTTTCCTAAT
1 TTGGTACCTAAACTTGACACTTTTTCCTAAG
* * *
42309928 TTGGCACCTAAACTTGAGACTTTTT-TTAAG
1 TTGGTACCTAAACTTGACACTTTTTCCTAAG
*
42309958 TTGGTACTTAAACTT
1 TTGGTACCTAAACTT
42309973 TTTGGCGTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 16 0.42
31 22 0.58
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.42
Consensus pattern (31 bp):
TTGGTACCTAAACTTGACACTTTTTCCTAAG
Found at i:42310266 original size:31 final size:32
Alignment explanation
Indices: 42310207--42310279 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
42310197 AAAAGCTTAA
*
42310207 GTACCAAATTAGGAAAAAAAATGCCAAGTTTAG
1 GTACCAAATTAGG-AAAAAAATGCCAAGTTCAG
* *
42310240 GTACCAAATTAGG-AAAAAGTGTCAAGTTCAG
1 GTACCAAATTAGGAAAAAAATGCCAAGTTCAG
42310271 GTACCAAAT
1 GTACCAAAT
42310280 ATTATATTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 24 0.65
33 13 0.35
ACGTcount: A:0.45, C:0.14, G:0.19, T:0.22
Consensus pattern (32 bp):
GTACCAAATTAGGAAAAAAATGCCAAGTTCAG
Found at i:42312284 original size:30 final size:28
Alignment explanation
Indices: 42312206--42312285 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 28
42312196 AACTTTGATT
* *
42312206 AAAATAACAATACAGACACTAAATTTAGA
1 AAAATAACAA-CCAGTCACTAAATTTAGA
* * *
42312235 AAAGTGACAACTCAATCACTAAAGTTTAGA
1 AAAATAACAAC-CAGTCACTAAA-TTTAGA
42312265 AAAATAACAAGCCAGTCACTA
1 AAAATAACAA-CCAGTCACTA
42312286 GTAATCATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
29 17 0.43
30 22 0.55
31 1 0.03
ACGTcount: A:0.53, C:0.17, G:0.10, T:0.20
Consensus pattern (28 bp):
AAAATAACAACCAGTCACTAAATTTAGA
Found at i:42313072 original size:3 final size:3
Alignment explanation
Indices: 42313064--42313095 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
42313054 TTCATGGAAT
42313064 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
42313096 TTGGGTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:42314140 original size:1 final size:1
Alignment explanation
Indices: 42314134--42314207 Score: 103
Period size: 1 Copynumber: 74.0 Consensus size: 1
42314124 AGCACCCCAT
* * * **
42314134 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCACCCCCCCCCACCCCCCCCATCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
42314199 CCCCCCCCC
1 CCCCCCCCC
42314208 GCACCCACTT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.04, C:0.93, G:0.00, T:0.03
Consensus pattern (1 bp):
C
Found at i:42314188 original size:37 final size:37
Alignment explanation
Indices: 42314137--42314213 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
42314127 ACCCCATCCC
* * *
42314137 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTCA
1 CCCCCCCCCACCCCCCCCACCCCCCCCCCCCCCCGCA
*
42314174 CCCCCCCCCACCCCCCCCATCCCCCCCCCCCCCCGCA
1 CCCCCCCCCACCCCCCCCACCCCCCCCCCCCCCCGCA
42314211 CCC
1 CCC
42314214 ACTTCGCCCC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.05, C:0.91, G:0.01, T:0.03
Consensus pattern (37 bp):
CCCCCCCCCACCCCCCCCACCCCCCCCCCCCCCCGCA
Found at i:42314614 original size:20 final size:21
Alignment explanation
Indices: 42314592--42314646 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
42314582 CCTATTCAAT
42314592 TATTAAAATAATAATTTAATTA
1 TATTAAAATAATAATTTAA-TA
*
42314614 TATTATAAAT--TAATTTAATG
1 TATTA-AAATAATAATTTAATA
42314634 TATTTAAAATAAT
1 TA-TTAAAATAAT
42314647 TGCAAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
20 7 0.25
21 11 0.39
22 6 0.21
23 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TATTAAAATAATAATTTAATA
Found at i:42317705 original size:41 final size:41
Alignment explanation
Indices: 42317648--42317731 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
42317638 GTAAACACTC
42317648 AATTTTGCTTACAACCTTAAGTTGTGTCCTAGACTTATTAA
1 AATTTTGCTTACAACCTTAAGTTGTGTCCTAGACTTATTAA
*
42317689 AATTTTGCTTACAACCTTAAGTTGTGTCCTAGATTTATTAA
1 AATTTTGCTTACAACCTTAAGTTGTGTCCTAGACTTATTAA
42317730 AA
1 AA
42317732 CACCTGGCTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (41 bp):
AATTTTGCTTACAACCTTAAGTTGTGTCCTAGACTTATTAA
Found at i:42321012 original size:27 final size:26
Alignment explanation
Indices: 42320951--42321013 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
42320941 ACTCCATTTT
42320951 ATTTATATTAGGATAATTAATATTAAG
1 ATTT-TATTAGGATAATTAATATTAAG
* * * *
42320978 ATCATTATTAGGATCATTTAATTTTAGG
1 AT-TTTATTAGGAT-AATTAATATTAAG
42321006 ATTTTATT
1 ATTTTATT
42321014 TTATTTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
27 16 0.55
28 13 0.45
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:42321026 original size:10 final size:10
Alignment explanation
Indices: 42321008--42321055 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
42320998 ATTTTAGGAT
42321008 TTTAT-TTTA
1 TTTATCTTTA
42321017 TTTATCTTTA
1 TTTATCTTTA
42321027 TTTATCTTTA
1 TTTATCTTTA
* ** *
42321037 ATTAAATGTA
1 TTTATCTTTA
42321047 TTTATCTTT
1 TTTATCTTT
42321056 TTAGAATTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
9 5 0.17
10 25 0.83
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:42324541 original size:21 final size:20
Alignment explanation
Indices: 42324512--42324551 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
42324502 CATGTATTTT
42324512 AATGATTGATGATAGATTATG
1 AATGATTGATGATAG-TTATG
*
42324533 AATGTTTGATGATAGTTAT
1 AATGATTGATGATAGTTAT
42324552 ACAAGTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (20 bp):
AATGATTGATGATAGTTATG
Found at i:42324559 original size:20 final size:21
Alignment explanation
Indices: 42324517--42324559 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42324507 ATTTTAATGA
*
42324517 TTGATGATAGATTATGAATGT
1 TTGATGATAGATTATGAAAGT
42324538 TTGATGATAG-TTAT-ACAAGT
1 TTGATGATAGATTATGA-AAGT
42324558 TT
1 TT
42324560 TGTTAAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 9 0.45
21 10 0.50
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (21 bp):
TTGATGATAGATTATGAAAGT
Found at i:42333990 original size:47 final size:47
Alignment explanation
Indices: 42333938--42334104 Score: 228
Period size: 47 Copynumber: 3.6 Consensus size: 47
42333928 GATAATTGTG
* * *
42333938 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGGTGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
42333985 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
42334032 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
*
42334079 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
42334105 TCCCGAAGGG
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
46 2 0.02
47 103 0.96
48 2 0.02
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:42336688 original size:29 final size:29
Alignment explanation
Indices: 42336655--42336756 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 29
42336645 TGAATATGAC
*
42336655 TGGGCCTAACGGGCCATATAAATGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* *
42336684 TGGGCCTAATGGGCCATATATAGGTGATT
1 TGGGCCTAATGGGCCATATAAATGTGATT
* * *
42336713 TGGGCCTCATGGGCCATATGAATATGA-T
1 TGGGCCTAATGGGCCATATAAATGTGATT
42336741 TGGG-CTCAATGGGCCA
1 TGGGCCT-AATGGGCCA
42336757 GATACAGGTA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
27 2 0.03
28 13 0.21
29 48 0.76
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (29 bp):
TGGGCCTAATGGGCCATATAAATGTGATT
Found at i:42336727 original size:58 final size:57
Alignment explanation
Indices: 42336655--42336765 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 57
42336645 TGAATATGAC
* * *
42336655 TGGGCCTAACGGGCCATATAAATGTGATTTGGGC-CTAATGGGCCATATATAGGTGATT
1 TGGGCCTAACGGGCCATATAAATATGA-TTGGGCTC-AATGGGCCAGATACAGGTGATT
* * *
42336713 TGGGCCTCATGGGCCATATGAATATGATTGGGCTCAATGGGCCAGATACAGGT
1 TGGGCCTAACGGGCCATATAAATATGATTGGGCTCAATGGGCCAGATACAGGT
42336766 ATGTGAGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
57 22 0.48
58 24 0.52
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (57 bp):
TGGGCCTAACGGGCCATATAAATATGATTGGGCTCAATGGGCCAGATACAGGTGATT
Found at i:42348827 original size:12 final size:12
Alignment explanation
Indices: 42348810--42348838 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
42348800 TGTCAAAGTA
42348810 AATTTTTTTAAT
1 AATTTTTTTAAT
42348822 AA-TTTTTTAAT
1 AATTTTTTTAAT
42348833 AATTTT
1 AATTTT
42348839 AAATTTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
AATTTTTTTAAT
Found at i:42348829 original size:11 final size:11
Alignment explanation
Indices: 42348813--42348838 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42348803 CAAAGTAAAT
42348813 TTTTTTAATAA
1 TTTTTTAATAA
42348824 TTTTTTAATAA
1 TTTTTTAATAA
42348835 TTTT
1 TTTT
42348839 AAATTTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTAATAA
Found at i:42357042 original size:12 final size:12
Alignment explanation
Indices: 42357009--42357043 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
42356999 TGAGACAAGA
42357009 TATTCTTTAAAT
1 TATTCTTTAAAT
*
42357021 TACTCTTTTAAAT
1 TATTC-TTTAAAT
42357034 TATTCTTTAA
1 TATTCTTTAA
42357044 GTAACCTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (12 bp):
TATTCTTTAAAT
Found at i:42357501 original size:16 final size:16
Alignment explanation
Indices: 42357448--42357511 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 16
42357438 AATTAAATTA
* *
42357448 CTATTATAATTTTATT
1 CTATTACAATTCTATT
* * *
42357464 TTATTACAACTCTACT
1 CTATTACAATTCTATT
* * *
42357480 CCATTATAATTTTATT
1 CTATTACAATTCTATT
42357496 CTATTACAATTCTATT
1 CTATTACAATTCTATT
42357512 ATATATTTTT
Statistics
Matches: 34, Mismatches: 14, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.31, C:0.16, G:0.00, T:0.53
Consensus pattern (16 bp):
CTATTACAATTCTATT
Found at i:42357512 original size:27 final size:28
Alignment explanation
Indices: 42357439--42357520 Score: 96
Period size: 32 Copynumber: 2.8 Consensus size: 28
42357429 CAATCAAATA
*
42357439 ATTA-AATTACTATTATAATTTTATTTT
1 ATTACAATTACTATTATAATTTTATTCT
42357466 ATTACAACTCTACTCCATTATAATTTTATTCT
1 ATTACAA-T-TACT--ATTATAATTTTATTCT
42357498 ATTACAATT-CTATTATATATTTT
1 ATTACAATTACTATTATA-ATTTT
42357521 TTTTCTCTTG
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
27 10 0.21
28 7 0.15
29 3 0.06
30 5 0.10
31 1 0.02
32 22 0.46
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.54
Consensus pattern (28 bp):
ATTACAATTACTATTATAATTTTATTCT
Found at i:42361947 original size:43 final size:43
Alignment explanation
Indices: 42361886--42361973 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
42361876 AAGTTCATTG
42361886 TAGCCCTGATATTCTGACACTTGCTTGCTTAATATGTGATTTT
1 TAGCCCTGATATTCTGACACTTGCTTGCTTAATATGTGATTTT
42361929 TAGCCCTGATATTCTGACACTTGCTTGCTTAATATGTGATTTT
1 TAGCCCTGATATTCTGACACTTGCTTGCTTAATATGTGATTTT
42361972 TA
1 TA
42361974 CTTGTGAATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (43 bp):
TAGCCCTGATATTCTGACACTTGCTTGCTTAATATGTGATTTT
Found at i:42373434 original size:21 final size:21
Alignment explanation
Indices: 42373393--42373434 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42373383 GATGCTTTGA
*
42373393 CATGTTTTGAGCTTGTTTAAT
1 CATGTTTTGAGCTTGTATAAT
42373414 CATGTTTTGAG-TTGGTATAAT
1 CATGTTTTGAGCTT-GTATAAT
42373435 TGATGGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.50
Consensus pattern (21 bp):
CATGTTTTGAGCTTGTATAAT
Found at i:42373768 original size:21 final size:21
Alignment explanation
Indices: 42373744--42373789 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
42373734 CTGTTAGTGT
* *
42373744 ACACAGATGTGTGAAGTAGTC
1 ACACAGACGTGTGAAGTAGCC
* *
42373765 ACACGGGCGTGTGAAGTAGCC
1 ACACAGACGTGTGAAGTAGCC
42373786 ACAC
1 ACAC
42373790 CGCCATGTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.17
Consensus pattern (21 bp):
ACACAGACGTGTGAAGTAGCC
Found at i:42376379 original size:21 final size:21
Alignment explanation
Indices: 42376338--42376380 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42376328 ATGATTTATT
* **
42376338 TGAAGTAGCCACACGGGCATG
1 TGAAGTAGCAACACGAACATG
42376359 TGAAGTAGCAACACGAACATG
1 TGAAGTAGCAACACGAACATG
42376380 T
1 T
42376381 CTTGAGCCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.21, G:0.28, T:0.16
Consensus pattern (21 bp):
TGAAGTAGCAACACGAACATG
Found at i:42377032 original size:7 final size:7
Alignment explanation
Indices: 42377020--42377057 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
42377010 TTACATTTCT
42377020 ACCCTAA
1 ACCCTAA
42377027 ACCCTAA
1 ACCCTAA
**
42377034 ACTTTAA
1 ACCCTAA
42377041 ACCCTAA
1 ACCCTAA
42377048 ACCCTAA
1 ACCCTAA
42377055 ACC
1 ACC
42377058 AAATCATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.42, C:0.39, G:0.00, T:0.18
Consensus pattern (7 bp):
ACCCTAA
Found at i:42377297 original size:27 final size:27
Alignment explanation
Indices: 42377257--42377326 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 27
42377247 CATTTTATCT
* *
42377257 CATGTTTAACGTCCTAACAGACTACAC
1 CATGTTTAATGTCCTAACAAACTACAC
* * * *
42377284 CGTGTTTGATGTCCCAACAAACTACTC
1 CATGTTTAATGTCCTAACAAACTACAC
42377311 CATGTTTAATGTCCTA
1 CATGTTTAATGTCCTA
42377327 GTGGACTACC
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (27 bp):
CATGTTTAATGTCCTAACAAACTACAC
Found at i:42382285 original size:13 final size:13
Alignment explanation
Indices: 42382253--42382278 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42382243 GCTTTAATGA
42382253 AGCTTAGTAAGTT
1 AGCTTAGTAAGTT
42382266 AGCTTAGTAAGTT
1 AGCTTAGTAAGTT
42382279 CGTTTAGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.23, T:0.38
Consensus pattern (13 bp):
AGCTTAGTAAGTT
Found at i:42382535 original size:37 final size:37
Alignment explanation
Indices: 42382492--42382563 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
42382482 GATTTACTCA
*
42382492 ATTGAGCATT-ATTCAATATAATAGTATGAATTGGTCG
1 ATTGAGC-TTCATTCAATATAATAGTAAGAATTGGTCG
* * *
42382529 ATTGAGCTTCATTCAGTATAGTAGTAAGATTTGGT
1 ATTGAGCTTCATTCAATATAATAGTAAGAATTGGT
42382564 TCAAAAGAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 2 0.07
37 28 0.93
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (37 bp):
ATTGAGCTTCATTCAATATAATAGTAAGAATTGGTCG
Found at i:42383253 original size:18 final size:18
Alignment explanation
Indices: 42383230--42383264 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
42383220 GGAGTTTGAT
42383230 TTTCTAGTTGAAATAAAA
1 TTTCTAGTTGAAATAAAA
42383248 TTTCTAGTTGAAATAAA
1 TTTCTAGTTGAAATAAA
42383265 CTTCTACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (18 bp):
TTTCTAGTTGAAATAAAA
Found at i:42389832 original size:42 final size:42
Alignment explanation
Indices: 42389785--42389935 Score: 142
Period size: 42 Copynumber: 3.6 Consensus size: 42
42389775 TGAGTTATCA
*
42389785 TGTAAGACCATATCTGGGATATGGCGTTGATATGAGATTTCG
1 TGTAAGACCATATCTGGGATATGGCGTCGATATGAGATTTCG
* * * * *
42389827 TGTAAGACCATGTCCGAGATATAGG-GTCGAAATGAGAATTCG
1 TGTAAGACCATATCTGGGATAT-GGCGTCGATATGAGATTTCG
** * * * ** *
42389869 TAAAAGACCATATCTGGGATATGGCATCAATGTGAGATCCCA
1 TGTAAGACCATATCTGGGATATGGCGTCGATATGAGATTTCG
* *
42389911 TGTAAGACCATGTCTGGGACATGGC
1 TGTAAGACCATATCTGGGATATGGC
42389936 ATTGGCATCT
Statistics
Matches: 84, Mismatches: 23, Indels: 4
0.76 0.21 0.04
Matches are distributed among these distances:
41 2 0.02
42 80 0.95
43 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (42 bp):
TGTAAGACCATATCTGGGATATGGCGTCGATATGAGATTTCG
Found at i:42400843 original size:71 final size:71
Alignment explanation
Indices: 42400737--42400986 Score: 500
Period size: 71 Copynumber: 3.5 Consensus size: 71
42400727 TTTCAATGCC
42400737 GTATATATATAACCTCTAAAAATACTACTAGCTGCATTGGTATTCATGGAGATCAGCTAGTGTTT
1 GTATATATATAACCTCTAAAAATACTACTAGCTGCATTGGTATTCATGGAGATCAGCTAGTGTTT
42400802 TTGACT
66 TTGACT
42400808 GTATATATATAACCTCTAAAAATACTACTAGCTGCATTGGTATTCATGGAGATCAGCTAGTGTTT
1 GTATATATATAACCTCTAAAAATACTACTAGCTGCATTGGTATTCATGGAGATCAGCTAGTGTTT
42400873 TTGACT
66 TTGACT
42400879 GTATATATATAACCTCTAAAAATACTACTAGCTGCATTGGTATTCATGGAGATCAGCTAGTGTTT
1 GTATATATATAACCTCTAAAAATACTACTAGCTGCATTGGTATTCATGGAGATCAGCTAGTGTTT
42400944 TTGACT
66 TTGACT
42400950 GTATATATATAACCTCTAAAAATACTACTAGCTGCAT
1 GTATATATATAACCTCTAAAAATACTACTAGCTGCAT
42400987 ACATATCAGA
Statistics
Matches: 179, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 179 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (71 bp):
GTATATATATAACCTCTAAAAATACTACTAGCTGCATTGGTATTCATGGAGATCAGCTAGTGTTT
TTGACT
Found at i:42402993 original size:59 final size:59
Alignment explanation
Indices: 42402928--42403115 Score: 150
Period size: 59 Copynumber: 3.2 Consensus size: 59
42402918 ATTTTATTAA
42402928 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
* * ** * * * ** * * * *
42402987 ATCATATATTATGATTTTAGTA-AATTCATA-TAAGAATATTGATTATTAGAATTTTATTA-A
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCA-AATTA-TATTTTA-TAGT
* * * *
42403047 ATTATATATTTTAATTAAAATATATTTAATAATT-ATTATTTTAATTTATATTTTACAGT
1 ATCATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTCAAATTATATTTTATAGT
42403106 ATCATATATT
1 ATCATATATT
42403116 ATGATTTGAG
Statistics
Matches: 91, Mismatches: 30, Indels: 16
0.66 0.22 0.12
Matches are distributed among these distances:
57 5 0.05
58 10 0.11
59 36 0.40
60 25 0.27
61 10 0.11
62 4 0.04
63 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.52
Consensus pattern (59 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTTATAGT
Found at i:42403042 original size:119 final size:120
Alignment explanation
Indices: 42402917--42403205 Score: 492
Period size: 119 Copynumber: 2.4 Consensus size: 120
42402907 AATTATTTTA
*
42402917 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
* * *
42402982 ATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AG
66 ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
42403036 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATT-ATTATTTTAATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAAT-ATTAATTATTTCAAATTATATTT
42403100 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
42403156 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTAT
42403206 GTTNNNNNNN
Statistics
Matches: 160, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
119 109 0.68
120 51 0.32
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:42403063 original size:18 final size:18
Alignment explanation
Indices: 42403037--42403092 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 18
42403027 GATTATTAGA
42403037 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAATTATAT
42403054 ATTTTAATTAAA--ATAT
1 ATTTTAATTAAATTATAT
42403070 A-TTTAA-T-AATTAT-T
1 ATTTTAATTAAATTATAT
42403084 ATTTTAATT
1 ATTTTAATT
42403093 TATATTTTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.06
14 3 0.09
15 12 0.35
16 6 0.18
17 5 0.15
18 6 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTTAATTAAATTATAT
Found at i:42403173 original size:59 final size:58
Alignment explanation
Indices: 42402991--42403173 Score: 146
Period size: 56 Copynumber: 3.1 Consensus size: 58
42402981 TATAGTATCA
*
42402991 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATT-AGAATTTTATTAAAT
1 TATATTATGATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
* * * * * *
42403049 TATA-TAT--TTTAATTAAAATAT-ATTTAATAATTATTATT-TTAATTTATATTTTA-CAGTAT
1 TATATTATGATTTAAGT-AAAT-TCATATAAGAA-TATTATTATTAA--GA-ATTTTATTA-AAT
*
42403108 CATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTTAAGTAAATTCATATAAGAATATT-ATTATTAAGAATTTTATTAAAT
42403169 TATAT
1 TATAT
42403174 ATTTTAATTA
Statistics
Matches: 94, Mismatches: 14, Indels: 33
0.67 0.10 0.23
Matches are distributed among these distances:
55 7 0.07
56 15 0.16
57 8 0.09
58 6 0.06
59 13 0.14
61 12 0.13
62 10 0.11
63 14 0.15
64 9 0.10
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (58 bp):
TATATTATGATTTAAGTAAATTCATATAAGAATATTATTATTAAGAATTTTATTAAAT
Found at i:42403185 original size:18 final size:17
Alignment explanation
Indices: 42403157--42403191 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42403147 ATTATTAAGA
*
42403157 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
42403174 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
42403192 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:42411738 original size:39 final size:39
Alignment explanation
Indices: 42411694--42411813 Score: 204
Period size: 39 Copynumber: 3.1 Consensus size: 39
42411684 ATTATATTAT
* **
42411694 CAGCACAAAGCCTGCGGGACTTTAACCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
42411733 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
1 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
*
42411772 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATATATTTC
1 CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
42411811 CAG
1 CAG
42411814 TGTCTTGCAT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.23, C:0.30, G:0.26, T:0.21
Consensus pattern (39 bp):
CAGCACGAAGCCTGCGGGACTTTGGCCCGGATACATTTC
Found at i:42416490 original size:17 final size:17
Alignment explanation
Indices: 42416452--42416496 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
42416442 AATGAATGAA
*
42416452 AAATTGAGA-ACTAAAT
1 AAATTGAGAGAATAAAT
*
42416468 -AGTTGAGAGAATAAAT
1 AAATTGAGAGAATAAAT
42416484 AAATTGAGAGAAT
1 AAATTGAGAGAAT
42416497 TAGGAGAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 7 0.29
16 6 0.25
17 11 0.46
ACGTcount: A:0.53, C:0.02, G:0.20, T:0.24
Consensus pattern (17 bp):
AAATTGAGAGAATAAAT
Found at i:42416710 original size:23 final size:23
Alignment explanation
Indices: 42416657--42416711 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
42416647 AGAAACTTTT
* *
42416657 CTATTTCACTCTCTAGAATTAGA
1 CTATTTCCCCCTCTAGAATTAGA
42416680 CTATTTCCCCCTCTAGAATTAGA
1 CTATTTCCCCCTCTAGAATTAGA
42416703 CTATTTCCC
1 CTATTTCCC
42416712 TAAATATCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.25, C:0.29, G:0.07, T:0.38
Consensus pattern (23 bp):
CTATTTCCCCCTCTAGAATTAGA
Found at i:42417350 original size:19 final size:20
Alignment explanation
Indices: 42417328--42417365 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
42417318 GCAAAAAAAT
*
42417328 TACTTAATACAT-AAAATAC
1 TACTTAAAACATGAAAATAC
42417347 TACTTAAAACATGAAAATA
1 TACTTAAAACATGAAAATA
42417366 TTTTAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (20 bp):
TACTTAAAACATGAAAATAC
Found at i:42417363 original size:72 final size:71
Alignment explanation
Indices: 42417281--42417426 Score: 231
Period size: 72 Copynumber: 2.0 Consensus size: 71
42417271 TTAATACATC
* * *
42417281 AAACGTGAAAATGTTTTTAAAGTAATTAATAAAACTTGCAAAAAAATTACTTAATACATAAAATA
1 AAACATGAAAATATTTTAAAAGTAATTAATAAAACTTG--AAAAAATTACTTAATACATAAAATA
42417346 CTACTT-A
64 CTACTTCA
*
42417353 AAACATGAAAATATTTTAAAAGTAATTAATAAAACTTGAAAAAATTACTTAATACATAAAATATT
1 AAACATGAAAATATTTTAAAAGTAATTAATAAAACTTGAAAAAATTACTTAATACATAAAATACT
42417418 ACTTCA
66 ACTTCA
42417424 AAA
1 AAA
42417427 AAATGTTTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
70 30 0.43
71 4 0.06
72 35 0.51
ACGTcount: A:0.54, C:0.09, G:0.05, T:0.32
Consensus pattern (71 bp):
AAACATGAAAATATTTTAAAAGTAATTAATAAAACTTGAAAAAATTACTTAATACATAAAATACT
ACTTCA
Found at i:42419366 original size:20 final size:20
Alignment explanation
Indices: 42419341--42419378 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
42419331 AGCAGGCTGA
42419341 GGGCCAGATCTCTAATTTGC
1 GGGCCAGATCTCTAATTTGC
42419361 GGGCCAGATCTCTAATTT
1 GGGCCAGATCTCTAATTT
42419379 ATTAGGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
GGGCCAGATCTCTAATTTGC
Found at i:42428411 original size:41 final size:41
Alignment explanation
Indices: 42428354--42428435 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
42428344 TTGTTTTCTG
42428354 CTAAATCGGGTATATGTTTATCCAAGTAATAAAATGTGTCA
1 CTAAATCGGGTATATGTTTATCCAAGTAATAAAATGTGTCA
42428395 CTAAATCGGGTATATGTTTATCCAAGTAATAAAATGTGTCA
1 CTAAATCGGGTATATGTTTATCCAAGTAATAAAATGTGTCA
42428436 AACAGAGCAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (41 bp):
CTAAATCGGGTATATGTTTATCCAAGTAATAAAATGTGTCA
Found at i:42434714 original size:16 final size:17
Alignment explanation
Indices: 42434671--42434731 Score: 65
Period size: 16 Copynumber: 3.6 Consensus size: 17
42434661 ATTATTTTAT
*
42434671 TTTTATTTTTAATAT--
1 TTTTAATTTTAATATAA
42434686 TTTATAAATTTTAATATAA
1 TTT-T-AATTTTAATATAA
*
42434705 TTTT-ATTTTAATATAT
1 TTTTAATTTTAATATAA
42434721 TTTTAATTTTA
1 TTTTAATTTTA
42434732 CCAAATTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 3 0.08
16 16 0.41
17 16 0.41
18 1 0.03
19 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTAATTTTAATATAA
Found at i:42440710 original size:17 final size:17
Alignment explanation
Indices: 42440688--42440723 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
42440678 TAAATACATT
* *
42440688 ATCCGCCAAATATCTGA
1 ATCCGCAAAAAATCTGA
42440705 ATCCGCAAAAAATCTGA
1 ATCCGCAAAAAATCTGA
42440722 AT
1 AT
42440724 TTAACATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.22
Consensus pattern (17 bp):
ATCCGCAAAAAATCTGA
Found at i:42440836 original size:22 final size:21
Alignment explanation
Indices: 42440799--42440840 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
42440789 CTAAAATTTT
42440799 AAAAATAATATAAAATCAAATA
1 AAAAATAATATAAAAT-AAATA
* *
42440821 AAAAATAATTTTAAATAAAT
1 AAAAATAATATAAAATAAAT
42440841 TTTATTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATAATATAAAATAAATA
Found at i:42447555 original size:9 final size:9
Alignment explanation
Indices: 42447543--42447572 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
42447533 AACCTCTCAA
42447543 ACCATCACC
1 ACCATCACC
42447552 ACCATCACC
1 ACCATCACC
*
42447561 ACCACCACC
1 ACCATCACC
42447570 ACC
1 ACC
42447573 GTCTCTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.33, C:0.60, G:0.00, T:0.07
Consensus pattern (9 bp):
ACCATCACC
Found at i:42448342 original size:6 final size:6
Alignment explanation
Indices: 42448333--42448386 Score: 67
Period size: 6 Copynumber: 9.2 Consensus size: 6
42448323 TTTAAATGTT
* *
42448333 ATATTA ATATTA ATATTA ATATTA ATATTA A-ATAA ATA-TA ATTTTTA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA A-TATTA
42448380 ATATTA A
1 ATATTA A
42448387 ATAAAATAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 6 0.15
6 32 0.78
7 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATATTA
Found at i:42449365 original size:19 final size:19
Alignment explanation
Indices: 42449341--42449379 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
42449331 ACAAAATGAT
42449341 TATGGATGAATGGTTGTGA
1 TATGGATGAATGGTTGTGA
42449360 TATGGATGAATGGTTGTGA
1 TATGGATGAATGGTTGTGA
42449379 T
1 T
42449380 GAGGTGGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.36, T:0.38
Consensus pattern (19 bp):
TATGGATGAATGGTTGTGA
Found at i:42449478 original size:3 final size:3
Alignment explanation
Indices: 42449470--42449494 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42449460 CATTTTCCTC
42449470 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
42449495 TGTGGGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:42454510 original size:17 final size:17
Alignment explanation
Indices: 42454490--42454523 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42454480 ACCTAACCCC
42454490 AGAAAAAAAAAGAAAAA
1 AGAAAAAAAAAGAAAAA
*
42454507 AGAAGAAAAAAGAAAAA
1 AGAAAAAAAAAGAAAAA
42454524 CCTAACCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAGAAAAA
Found at i:42454518 original size:10 final size:10
Alignment explanation
Indices: 42454490--42454520 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
42454480 ACCTAACCCC
*
42454490 AGAAAAAAAA
1 AGAAAAAAGA
42454500 AGAAAAAAGA
1 AGAAAAAAGA
42454510 AGAAAAAAGA
1 AGAAAAAAGA
42454520 A
1 A
42454521 AAACCTAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (10 bp):
AGAAAAAAGA
Found at i:42455592 original size:65 final size:66
Alignment explanation
Indices: 42455519--42455648 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 66
42455509 TATTCTAGTA
42455519 TTCCATGTTAATATTTTTCATTAATGATATCA-TTTTTTTGCATCTTTTATCTATTTTTAATTTC
1 TTCCATGTTAATATTTTTCATTAATGATATCATTTTTTTTGCATCTTTTATCTATTTTTAATTTC
42455583 G
66 G
42455584 TTCCATGTTAATATTTTTCATTAATGATATCATTTTTTTTGCATCTTTTATCTATTTTTAATTTC
1 TTCCATGTTAATATTTTTCATTAATGATATCATTTTTTTTGCATCTTTTATCTATTTTTAATTTC
42455649 TCACTTTAGG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
65 32 0.50
66 32 0.50
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.59
Consensus pattern (66 bp):
TTCCATGTTAATATTTTTCATTAATGATATCATTTTTTTTGCATCTTTTATCTATTTTTAATTTC
G
Found at i:42455667 original size:66 final size:64
Alignment explanation
Indices: 42455520--42455648 Score: 240
Period size: 66 Copynumber: 2.0 Consensus size: 64
42455510 ATTCTAGTAT
42455520 TCCATGTTAATATTTTTCATTAATGATATCATTTTTTTGCATCTTTTATCTATTTTTAATTTCG
1 TCCATGTTAATATTTTTCATTAATGATATCATTTTTTTGCATCTTTTATCTATTTTTAATTTCG
42455584 TTCCATGTTAATATTTTTCATTAATGATATCATTTTTTTTGCATCTTTTATCTATTTTTAATTTC
1 -TCCATGTTAATATTTTTCATTAATGATATCA-TTTTTTTGCATCTTTTATCTATTTTTAATTTC
42455649 TCACTTTAGG
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
65 31 0.49
66 32 0.51
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.59
Consensus pattern (64 bp):
TCCATGTTAATATTTTTCATTAATGATATCATTTTTTTGCATCTTTTATCTATTTTTAATTTCG
Found at i:42456785 original size:14 final size:14
Alignment explanation
Indices: 42456754--42456795 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
42456744 ACACAAAAAA
* *
42456754 TATTCTTTTTTTAG
1 TATTCTTTTTCTAT
42456768 TATTCTTTTTCTAT
1 TATTCTTTTTCTAT
*
42456782 TATT-TTTGTCTAT
1 TATTCTTTTTCTAT
42456795 T
1 T
42456796 TTATTACCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
13 9 0.36
14 16 0.64
ACGTcount: A:0.14, C:0.10, G:0.05, T:0.71
Consensus pattern (14 bp):
TATTCTTTTTCTAT
Found at i:42456845 original size:14 final size:14
Alignment explanation
Indices: 42456808--42456846 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
42456798 ATTACCATTT
*
42456808 TACTATTATATTAC
1 TACTATTATTTTAC
*
42456822 TACTATTATTTTAT
1 TACTATTATTTTAC
*
42456836 TATTATTATTT
1 TACTATTATTT
42456847 GAATATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (14 bp):
TACTATTATTTTAC
Found at i:42457431 original size:47 final size:47
Alignment explanation
Indices: 42457380--42457473 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
42457370 ATATTAGCCT
*
42457380 AATCAATAATCCCCCCATTATTTCAAAGACTTCAACTCCCCCCCCCC
1 AATCAATAATCCCCCCATTATTTCAAAGACTTCAAATCCCCCCCCCC
42457427 AATCAATAATCCCCCCATTATTTCAAAGACTTCAAATCCCCCCCCCC
1 AATCAATAATCCCCCCATTATTTCAAAGACTTCAAATCCCCCCCCCC
42457474 TTTTTATTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.31, C:0.44, G:0.02, T:0.23
Consensus pattern (47 bp):
AATCAATAATCCCCCCATTATTTCAAAGACTTCAAATCCCCCCCCCC
Found at i:42465936 original size:44 final size:41
Alignment explanation
Indices: 42465873--42466023 Score: 117
Period size: 44 Copynumber: 3.6 Consensus size: 41
42465863 ATATGTGTTA
* ** *
42465873 TCGTGTAAGACTACGTCTGGGACGTTGACATCA-ATTTGTTATT
1 TCGTGTAAGACCATATCTGGGACATTGACATCATA-TTG--ATT
* *
42465916 TACGTGTAAGACCATATCTGGGACATTGGCATCATATTGGTT
1 T-CGTGTAAGACCATATCTGGGACATTGACATCATATTGATT
* * *
42465958 TCGTGTAAGACCCTATCTGGGACAGTGGCATCGATACTTG-TT
1 TCGTGTAAGACCATATCTGGGACATTGACATC-ATA-TTGATT
* **
42466000 TACATGTAAGACCACGTCTGGGAC
1 T-CGTGTAAGACCATATCTGGGAC
42466024 GTTGGCATTG
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
41 29 0.32
42 9 0.10
43 22 0.24
44 30 0.33
45 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (41 bp):
TCGTGTAAGACCATATCTGGGACATTGACATCATATTGATT
Found at i:42465975 original size:41 final size:43
Alignment explanation
Indices: 42465914--42466031 Score: 145
Period size: 41 Copynumber: 2.8 Consensus size: 43
42465904 CAATTTGTTA
*
42465914 TTTACGTGTAAGACCATATCTGGGACATTGGCATC-ATA-TTGG
1 TTTACGTGTAAGACCCTATCTGGGACATTGGCATCGATACTT-G
*
42465956 TTT-CGTGTAAGACCCTATCTGGGACAGTGGCATCGATACTTG
1 TTTACGTGTAAGACCCTATCTGGGACATTGGCATCGATACTTG
* * *
42465998 TTTACATGTAAGACCAC-GTCTGGGACGTTGGCAT
1 TTTACGTGTAAGACC-CTATCTGGGACATTGGCAT
42466032 TGTATGAGCT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
41 29 0.44
42 10 0.15
43 26 0.39
44 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.31
Consensus pattern (43 bp):
TTTACGTGTAAGACCCTATCTGGGACATTGGCATCGATACTTG
Found at i:42471152 original size:20 final size:20
Alignment explanation
Indices: 42471127--42471166 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
42471117 GTTAACTTGG
*
42471127 AGTTGGAGGTTCAATATGAA
1 AGTTGGAGGTTCAAGATGAA
42471147 AGTTGGAGGTTCAAGATGAA
1 AGTTGGAGGTTCAAGATGAA
42471167 TTGGAAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.33, T:0.28
Consensus pattern (20 bp):
AGTTGGAGGTTCAAGATGAA
Found at i:42474280 original size:4 final size:4
Alignment explanation
Indices: 42474271--42474298 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
42474261 ATTCACAATG
42474271 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
42474299 GGATCATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:42474725 original size:26 final size:27
Alignment explanation
Indices: 42474660--42474717 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
42474650 GTTTACAATG
*
42474660 TAAAAA-AATAT--ATATATATTGTTA
1 TAAAAATAATATAAATACATATTGTTA
*
42474684 TAAAATTAATATAAATACATATT-TTA
1 TAAAAATAATATAAATACATATTGTTA
42474710 TAAAAATA
1 TAAAAATA
42474718 CTGTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 5 0.18
25 5 0.18
26 10 0.36
27 8 0.29
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (27 bp):
TAAAAATAATATAAATACATATTGTTA
Found at i:42480386 original size:52 final size:53
Alignment explanation
Indices: 42480329--42480495 Score: 164
Period size: 52 Copynumber: 3.1 Consensus size: 53
42480319 ATAGAAATTG
42480329 TGAAAATGGAGAAATGAGAAAT-ATTTGAAAATGATTATGGTTTTCTCCAAAA
1 TGAAAATGGAGAAATGAGAAATCATTTGAAAATGATTATGGTTTTCTCCAAAA
* * * *
42480381 TGAAAAT--AAAAATGAAGAAATGAAATCATTTGGAAATAATTATGGTTTTTTTCCAAAA
1 TGAAAATGGAGAAAT---G--A-GAAATCATTTGAAAATGATTATGG-TTTTCTCCAAAA
* * * *
42480439 TGAAAATGGAGAAAT--GAAATCATTTAAAAATGAATGTAGTTTTCTCCAAAA
1 TGAAAATGGAGAAATGAGAAATCATTTGAAAATGATTATGGTTTTCTCCAAAA
42480490 TGAAAA
1 TGAAAA
42480496 AGACCTGGAA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
50 5 0.05
51 17 0.18
52 25 0.27
53 1 0.01
55 1 0.01
56 5 0.05
57 16 0.17
58 18 0.19
60 5 0.05
ACGTcount: A:0.47, C:0.06, G:0.16, T:0.31
Consensus pattern (53 bp):
TGAAAATGGAGAAATGAGAAATCATTTGAAAATGATTATGGTTTTCTCCAAAA
Found at i:42480427 original size:57 final size:58
Alignment explanation
Indices: 42480331--42480445 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 58
42480321 AGAAATTGTG
* *
42480331 AAAATGGAGAAATGAGAAATATTTGAAAATGATTATGG-TTTTCTCCAAAATGAAAATA
1 AAAATGAAGAAAT-AGAAATATTTGAAAATAATTATGGTTTTTCTCCAAAATGAAAATA
* *
42480389 AAAATGAAGAAAT-GAAATCATTTGGAAATAATTATGGTTTTTTTCCAAAATGAAAAT
1 AAAATGAAGAAATAGAAAT-ATTTGAAAATAATTATGGTTTTTCTCCAAAATGAAAAT
42480446 GGAGAAATGA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
56 5 0.10
57 16 0.31
58 30 0.59
ACGTcount: A:0.48, C:0.05, G:0.16, T:0.31
Consensus pattern (58 bp):
AAAATGAAGAAATAGAAATATTTGAAAATAATTATGGTTTTTCTCCAAAATGAAAATA
Found at i:42480458 original size:57 final size:55
Alignment explanation
Indices: 42480329--42480458 Score: 144
Period size: 57 Copynumber: 2.4 Consensus size: 55
42480319 ATAGAAATTG
*
42480329 TGAAAATGGAGAAATG--A-GAAATATTTGAAAATGATTATGGTTTTCTCCAAAA
1 TGAAAATGGAGAAATGAAATGAAATATTTGAAAATAATTATGGTTTTCTCCAAAA
* * *
42480381 TGAAAAT--AAAAATGAAGAAATGAAATCATTTGGAAATAATTATGGTTTTTTTCCAAAA
1 TGAAAATGGAGAAAT---GAAATGAAAT-ATTTGAAAATAATTATGG-TTTTCTCCAAAA
42480439 TGAAAATGGAGAAATGAAAT
1 TGAAAATGGAGAAATGAAAT
42480459 CATTTAAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
50 5 0.08
52 7 0.11
53 1 0.02
55 1 0.02
56 5 0.08
57 21 0.33
58 18 0.29
60 5 0.08
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.30
Consensus pattern (55 bp):
TGAAAATGGAGAAATGAAATGAAATATTTGAAAATAATTATGGTTTTCTCCAAAA
Found at i:42496215 original size:2 final size:2
Alignment explanation
Indices: 42496208--42496265 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
42496198 TACTATTTTC
42496208 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
42496250 CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA
42496266 TATATCGTTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:42496520 original size:39 final size:39
Alignment explanation
Indices: 42496477--42496608 Score: 201
Period size: 39 Copynumber: 3.4 Consensus size: 39
42496467 GGTCTTTAAC
* ** *
42496477 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATATTTCCAGCATATAGCCTGCGGACCTCATGT
* *
42496516 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATATTTCCAGCATATAGCCTGCGGACCTCATGT
*
42496555 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATATTTCCAGCATATAGCCTGCGGACCTCATGT
42496594 CCGGATATATTTCCA
1 CCGGATATATTTCCA
42496609 ATCTCATATA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 83 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.30
Consensus pattern (39 bp):
CCGGATATATTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:42504155 original size:2 final size:2
Alignment explanation
Indices: 42504148--42504173 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42504138 CGAACTCATT
42504148 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
42504174 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:42504445 original size:39 final size:39
Alignment explanation
Indices: 42504397--42504522 Score: 173
Period size: 39 Copynumber: 3.2 Consensus size: 39
42504387 TTTAACCCGT
* ** *
42504397 ATATTTTTCTAGCACGTAGCCTGCGGACCTCAAGTCCGG
1 ATATATTTCTAGCATATAGCCTGCGGACCTCATGTCCGG
* *
42504436 ATATATTTCTAGCATATAGTCTGCGGATCTCATGTCCGG
1 ATATATTTCTAGCATATAGCCTGCGGACCTCATGTCCGG
*
42504475 ATAT-TTTTTCAGCATATAGCCTGCGGACCTCATGTCCGG
1 ATATATTTCT-AGCATATAGCCTGCGGACCTCATGTCCGG
42504514 ATATATTTC
1 ATATATTTC
42504523 CAATCTCATA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
38 4 0.05
39 68 0.91
40 3 0.04
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (39 bp):
ATATATTTCTAGCATATAGCCTGCGGACCTCATGTCCGG
Found at i:42513075 original size:10 final size:10
Alignment explanation
Indices: 42513049--42513080 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
42513039 GATCAAGTAA
42513049 AATT-AAATT
1 AATTAAAATT
42513058 AA-TAAAATT
1 AATTAAAATT
42513067 AATTAAAATT
1 AATTAAAATT
42513077 AATT
1 AATT
42513081 TTTAAGTCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 1 0.05
9 9 0.43
10 11 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
AATTAAAATT
Found at i:42516864 original size:18 final size:18
Alignment explanation
Indices: 42516841--42516878 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
42516831 CACAGCTGAG
42516841 ACACGCGCCCGTGTCTCT
1 ACACGCGCCCGTGTCTCT
42516859 ACACGCGCCCGTGTCTCT
1 ACACGCGCCCGTGTCTCT
42516877 AC
1 AC
42516879 CCTTGTGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.45, G:0.21, T:0.21
Consensus pattern (18 bp):
ACACGCGCCCGTGTCTCT
Found at i:42521661 original size:12 final size:12
Alignment explanation
Indices: 42521627--42521671 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
42521617 TCAAAGGTTT
42521627 GAGCAGTTGCAA
1 GAGCAGTTGCAA
* *
42521639 AAGGA-TATGCAA
1 GAGCAGT-TGCAA
42521651 GAGCAGTTGCAA
1 GAGCAGTTGCAA
42521663 GAGCAGTTG
1 GAGCAGTTG
42521672 GCTAAGATGC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 1 0.04
12 25 0.93
13 1 0.04
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (12 bp):
GAGCAGTTGCAA
Done.