Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 90 of 135
Found at i:30334490 original size:5 final size:5
Alignment explanation
Indices: 30334476--30334525 Score: 57
Period size: 5 Copynumber: 9.6 Consensus size: 5
30334466 TTTGCATTTC
*
30334476 TTTA- TTTAT TTTAT TTTAT CATTTAT TTTGTT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT --TTTAT TTT-AT TTTAT TTTAT TTTAT
30334523 TTT
1 TTT
30334526 GCTTTAGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
4 4 0.10
5 27 0.68
6 4 0.10
7 5 0.12
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:30335259 original size:74 final size:74
Alignment explanation
Indices: 30335138--30335289 Score: 279
Period size: 74 Copynumber: 2.1 Consensus size: 74
30335128 TTTAAGGGTG
*
30335138 CTAATCCTTCCTCATATGTAACCGACTCCTGAATCCACTTTTCTGATTTCGTAGGTCAAAAATCA
1 CTAATCCTTCCTCATACGTAACCGACTCCTGAATCCACTTTTCTGATTTCGTAGGTCAAAAATCA
30335203 TCATTTTAA
66 TCATTTTAA
*
30335212 CTAATCCTTCCTCATACGTAACCGACTCTTGAATCCACTTTTCTGATTTCGTAGGTCAAAAATCA
1 CTAATCCTTCCTCATACGTAACCGACTCCTGAATCCACTTTTCTGATTTCGTAGGTCAAAAATCA
30335277 TCATTTTAA
66 TCATTTTAA
30335286 -TAAT
1 CTAAT
30335290 TTTAACATTT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 4 0.05
74 72 0.95
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (74 bp):
CTAATCCTTCCTCATACGTAACCGACTCCTGAATCCACTTTTCTGATTTCGTAGGTCAAAAATCA
TCATTTTAA
Found at i:30337938 original size:12 final size:13
Alignment explanation
Indices: 30337912--30337944 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
30337902 CATATGCATG
30337912 AAAACTAAAACTA
1 AAAACTAAAACTA
*
30337925 AAAACTGAAA-TA
1 AAAACTAAAACTA
30337937 AAAACTAA
1 AAAACTAA
30337945 CTCAATTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.70, C:0.12, G:0.03, T:0.15
Consensus pattern (13 bp):
AAAACTAAAACTA
Found at i:30338001 original size:17 final size:18
Alignment explanation
Indices: 30337979--30338017 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
30337969 CATGATGTTT
30337979 TTTTCTT-CTTACACTTC
1 TTTTCTTCCTTACACTTC
* *
30337996 TTTTCTTCCTTGCAGTTC
1 TTTTCTTCCTTACACTTC
30338014 TTTT
1 TTTT
30338018 TATCTTTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.08, C:0.26, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTCTTCCTTACACTTC
Found at i:30346721 original size:20 final size:20
Alignment explanation
Indices: 30346690--30346741 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
30346680 AAATTAAAAA
30346690 AAAGGAAAAA-AGAGAAAAAGG
1 AAAGGAAAAAGA-AG-AAAAGG
*
30346711 AAAGGAAAAAGAAGAAAAGT
1 AAAGGAAAAAGAAGAAAAGG
*
30346731 AAAAGAAAAAG
1 AAAGGAAAAAG
30346742 GGGAGGTCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 15 0.54
21 12 0.43
22 1 0.04
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (20 bp):
AAAGGAAAAAGAAGAAAAGG
Found at i:30347845 original size:49 final size:49
Alignment explanation
Indices: 30347661--30347846 Score: 176
Period size: 49 Copynumber: 3.8 Consensus size: 49
30347651 ACAAATCTAA
* * * ***
30347661 TACCCTAGAGATATGAAGAGAAAGGTTGAAGTCGCAACGACAAACCTTG
1 TACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGTGAACCTTG
* * ** * * *
30347710 TACCTTAGGGACGTGATA-GGAAAGATTGAAGCTGCGACGGTGAATCTTG
1 TACCCTAGAGATATGA-AGGGAAAGATTGAAGCCGCAACGGTGAACCTTG
* * * *
30347759 TACCCTAGAGTTATGGAGGGAAAGGTTGAAGCTGCAACGGTGAACCTTG
1 TACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGTGAACCTTG
* **
30347808 TACCCTAGAGATGTGAAGGGAAAGATTGGGGCCGCAACG
1 TACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACG
30347847 ACGAATCTTA
Statistics
Matches: 106, Mismatches: 29, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
48 1 0.01
49 104 0.98
50 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.31, T:0.20
Consensus pattern (49 bp):
TACCCTAGAGATATGAAGGGAAAGATTGAAGCCGCAACGGTGAACCTTG
Found at i:30347853 original size:98 final size:98
Alignment explanation
Indices: 30347661--30347855 Score: 223
Period size: 98 Copynumber: 2.0 Consensus size: 98
30347651 ACAAATCTAA
* *
30347661 TACCCTAGAGATATGAAGAGAAAGGTTGAAGTCGCAACGACAAACCTTGTACCTTAGGGACGTGA
1 TACCCTAGAGATATGAAGAGAAAGGTTGAAGTCGCAACGACAAACCTTGTACCCTAGAGACGTGA
* * **
30347726 TAGGAAAGATTGAAGCTGCGACGGTGAATCTTG
66 TAGGAAAGATTGAAGCCGCAACGACGAATCTTG
* * * *** *
30347759 TACCCTAGAGTTATGGAGGGAAAGGTTGAAG-CTGCAACGGTGAACCTTGTACCCTAGAGATGTG
1 TACCCTAGAGATATGAAGAGAAAGGTTGAAGTC-GCAACGACAAACCTTGTACCCTAGAGACGTG
**
30347823 A-AGGGAAAGATTGGGGCCGCAACGACGAATCTT
65 ATA-GGAAAGATTGAAGCCGCAACGACGAATCTT
30347856 ACACCCTGAA
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
97 2 0.03
98 78 0.98
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (98 bp):
TACCCTAGAGATATGAAGAGAAAGGTTGAAGTCGCAACGACAAACCTTGTACCCTAGAGACGTGA
TAGGAAAGATTGAAGCCGCAACGACGAATCTTG
Found at i:30348195 original size:40 final size:40
Alignment explanation
Indices: 30348129--30348342 Score: 183
Period size: 40 Copynumber: 5.4 Consensus size: 40
30348119 AAGTTACAAT
**
30348129 CATCCAATCTTTTACCCTAATTAGAGGGCAGATTGAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
** * * *
30348169 CATCTGATCTTTTACCCTAACCAGAGGACAAATTAAAGAC
1 CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
* * *
30348209 CATCCAATCTCTTACCCTGATCATGA-GGCAGATTGAAG-C
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAGAC
* *
30348248 AATCCAATCTTTTACCC-AACCATGA-GGCAGATTTAAGTA-
1 CATCCAATCTTTTACCCTAACCA-GAGGGCAGATTGAAG-AC
* * * *
30348287 -ATTCAGATCTTTTTCCCTAACCAGAGGGTAGATTTAAGTA-
1 CATCCA-ATCTTTTACCCTAACCAGAGGGCAGATTGAAG-AC
30348327 -ATCCAATCTTTTACCC
1 CATCCAATCTTTTACCC
30348343 CTAAAGCTAT
Statistics
Matches: 143, Mismatches: 25, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
38 21 0.15
39 38 0.27
40 82 0.57
41 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.29
Consensus pattern (40 bp):
CATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGAC
Found at i:30348396 original size:50 final size:51
Alignment explanation
Indices: 30348342--30348468 Score: 179
Period size: 50 Copynumber: 2.5 Consensus size: 51
30348332 ATCTTTTACC
* * *
30348342 CCTAAAGCTATGGAGGTGCAGATTGAAA-CCGCAATGGCAAATCTCATAT-A
1 CCTAAAGCTGTAGAGGGGCAGATTGAAAGCCGCAATGGCAAATCTCAT-TCA
* *
30348392 CCTAAAGCTGTAGAGGGGTAGAAT-AAAGCCGCAATGGCAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAAGCCGCAATGGCAAATCTCATTCA
30348442 CCTAAAGCTGTAGAGGGGCAGATTGAA
1 CCTAAAGCTGTAGAGGGGCAGATTGAA
30348469 GTCACAAGGA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
49 4 0.06
50 61 0.91
51 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.20
Consensus pattern (51 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAAGCCGCAATGGCAAATCTCATTCA
Found at i:30348571 original size:40 final size:40
Alignment explanation
Indices: 30348523--30348853 Score: 304
Period size: 40 Copynumber: 8.4 Consensus size: 40
30348513 AGTTACAACC
* *
30348523 TCCAATCTCTTACACTAACCAGAGGGCAGATTGAAGACCA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * * *
30348563 TCCGATCTCTTACGCC-AATCATG-GGGCAGATTGAAAACTA
1 TCCAATCTCTTAC-CCTAACCA-GAGGGCAGATTGAAGACAA
* ** *
30348603 TCCAATCTTTTACCCTAATAAGAGGGCAGATTGAAGACCA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * *
30348643 TCCAATCAT-TTACCCTAATCAGAGGACAGATTGAAGGCAA
1 TCCAATC-TCTTACCCTAACCAGAGGGCAGATTGAAGACAA
*
30348683 TCCAATCTCTTACCCCAACCATG-GGGCAGATTGAA-ACAA
1 TCCAATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACAA
* * * *
30348722 CCCAATCTTTTA-CCTAACCAAAGGGTAGATTGAAG-CAA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
* * * * *
30348760 TCCAATCTTTTACCCTAGCCAGAGGGCAAATTAAAGACTA
1 TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
**
30348800 T-CAGATCTCTTACCCCGACCATG-GGGCAGATTGAA-ACAA
1 TCCA-ATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACAA
*
30348839 TCCAATCTTTTACCC
1 TCCAATCTCTTACCC
30348854 CTAAAGTTAT
Statistics
Matches: 239, Mismatches: 38, Indels: 29
0.78 0.12 0.09
Matches are distributed among these distances:
38 32 0.13
39 51 0.21
40 151 0.63
41 5 0.02
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACAA
Found at i:30348808 original size:117 final size:118
Alignment explanation
Indices: 30348523--30348852 Score: 423
Period size: 117 Copynumber: 2.8 Consensus size: 118
30348513 AGTTACAACC
* * * * * *
30348523 TCCAATCTCTTACACTAACCAGAGGGCAGATTGAAGACCATCCGATCTCTTACGCCAATCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCAGATCTCTTACCCCAACCATGGG
* * *
30348588 GCAGATTGAAAACTATCCAATCTTTTACCCTAATAAGAGGGCAGATTGAAGACCA
66 GCAGATTG-AAACAATCCAATCTTTTA-CCTAACAAGAGGGCAGATTGAAGACAA
* * * *
30348643 TCCAATCATTTACCCTAATCAGAGGACAGATTGAAGGCAATCCA-ATCTCTTACCCCAACCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAAT-CAGATCTCTTACCCCAACCATGG
* *
30348707 GGCAGATTGAAACAACCCAATCTTTTACCTAACCAA-AGGGTAGATTGAAG-CAA
65 GGCAGATTGAAACAATCCAATCTTTTACCTAA-CAAGAGGGCAGATTGAAGACAA
* * * * *
30348760 TCCAATCTTTTACCCTAGCCAGAGGGCAAATTAAAGACTATCAGATCTCTTACCCCGACCATGGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCAGATCTCTTACCCCAACCATGGG
30348825 GCAGATTGAAACAATCCAATCTTTTACC
66 GCAGATTGAAACAATCCAATCTTTTACC
30348853 CCTAAAGTTA
Statistics
Matches: 182, Mismatches: 25, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
116 2 0.01
117 82 0.45
118 18 0.10
119 18 0.10
120 61 0.34
121 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (118 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACAATCAGATCTCTTACCCCAACCATGGG
GCAGATTGAAACAATCCAATCTTTTACCTAACAAGAGGGCAGATTGAAGACAA
Found at i:30349139 original size:154 final size:154
Alignment explanation
Indices: 30348876--30349236 Score: 519
Period size: 154 Copynumber: 2.4 Consensus size: 154
30348866 AGGGGCAGAT
* * **
30348876 TAAAGCTACAAAAGCAAATCCTATACCCCTAAAGTTGTAGAGGGGTGGATTAAAACTCACAGTAG
1 TAAAGCTACAGAAGCAAATCCTATACCCCTAAAGTTATAGAGGGGCAGATTAAAACTCACAGTAG
* *
30348941 TAAACCTCAATCTTCACTGAAGTTGCAAAGAAATAGAGTAAAGCTATAAAGGCAAATCCTTATTT
66 TAAACCACAATCTTCACTGAAGTTGCAAAGAAATAGAGTAAAGCTATAAAGGCAAATCCTTATCT
*
30349006 CTCTGAAGTTACAGTAGAGCAAGA
131 CTCTAAAGTTACAGTAGAGCAAGA
*
30349030 TAAAGCTACAGAAGTAAATCCTATACCCCTAAAGTTATAGAGGGGCAGATTAAAACTCACAGTAG
1 TAAAGCTACAGAAGCAAATCCTATACCCCTAAAGTTATAGAGGGGCAGATTAAAACTCACAGTAG
* * * * * *
30349095 TAGACCACGATTTTCACTGAAGTTGCAAAGAAATAGAGTGAAGCTATGAAGGCGAATCCTTATCT
66 TAAACCACAATCTTCACTGAAGTTGCAAAGAAATAGAGTAAAGCTATAAAGGCAAATCCTTATCT
*
30349160 CTCTAAAGTTGCAGTAGAGCAAGA
131 CTCTAAAGTTACAGTAGAGCAAGA
* * * * *
30349184 TGAAGCTACAAGAA-CAAATCCTATACCCTTGAAGTTA-AGTGGGTCAGATTAAA
1 TAAAGCTAC-AGAAGCAAATCCTATACCCCTAAAGTTATAGAGGGGCAGATTAAA
30349237 GTCATTAACA
Statistics
Matches: 185, Mismatches: 21, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
153 14 0.08
154 167 0.90
155 4 0.02
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.24
Consensus pattern (154 bp):
TAAAGCTACAGAAGCAAATCCTATACCCCTAAAGTTATAGAGGGGCAGATTAAAACTCACAGTAG
TAAACCACAATCTTCACTGAAGTTGCAAAGAAATAGAGTAAAGCTATAAAGGCAAATCCTTATCT
CTCTAAAGTTACAGTAGAGCAAGA
Found at i:30372609 original size:15 final size:14
Alignment explanation
Indices: 30372573--30372651 Score: 83
Period size: 14 Copynumber: 5.7 Consensus size: 14
30372563 GATTTCACCC
30372573 AAAAG-AAAAAGAAG
1 AAAAGAAAAAAG-AG
*
30372587 ACAA-AAAAAAGAG
1 AAAAGAAAAAAGAG
*
30372600 AAAGATAAAAAAGA-
1 AAA-AGAAAAAAGAG
*
30372614 AAAAGAAAGAAGAG
1 AAAAGAAAAAAGAG
*
30372628 AAAAGAGAAAAGAG
1 AAAAGAAAAAAGAG
30372642 AAAAGAAAAA
1 AAAAGAAAAA
30372652 GAAAAAGGGA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
13 12 0.22
14 34 0.63
15 8 0.15
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (14 bp):
AAAAGAAAAAAGAG
Found at i:30372611 original size:19 final size:18
Alignment explanation
Indices: 30372573--30372658 Score: 59
Period size: 20 Copynumber: 4.6 Consensus size: 18
30372563 GATTTCACCC
*
30372573 AAAAGAAAAAGAAGACAAAA
1 AAAAGAGAAAGAA-A-AAAA
30372593 AAAAGAGAAAGATAAAAAA
1 AAAAGAGAAAGA-AAAAAA
* *
30372612 GAAAA-AGAAAGAAGAGAA
1 -AAAAGAGAAAGAAAAAAA
* *
30372630 AAGAGA-AAAGAGAAAAGA
1 AAAAGAGAAAGA-AAAAAA
*
30372648 AAAAGAAAAAG
1 AAAAGAGAAAG
30372659 GGAATGCTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
17 8 0.15
18 13 0.25
19 15 0.28
20 16 0.30
21 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.01
Consensus pattern (18 bp):
AAAAGAGAAAGAAAAAAA
Found at i:30372619 original size:35 final size:33
Alignment explanation
Indices: 30372573--30372654 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 33
30372563 GATTTCACCC
*
30372573 AAAAGAAAAAGAAGACAAAAAAAAGAGAAAGATAA
1 AAAAGAAAAAGAAGA-AAAAAAAAGAGAAA-AGAA
* * *
30372608 AAAAGAAAAAGAAAGAAGAGAAAAGAGAAAAGAG
1 AAAAGAAAAAG-AAGAAAAAAAAAGAGAAAAGAA
30372642 AAAAGAAAAAGAA
1 AAAAGAAAAAGAA
30372655 AAAGGGAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 2 0.05
34 13 0.31
35 23 0.55
36 4 0.10
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.01
Consensus pattern (33 bp):
AAAAGAAAAAGAAGAAAAAAAAAGAGAAAAGAA
Found at i:30372626 original size:7 final size:6
Alignment explanation
Indices: 30372573--30372658 Score: 73
Period size: 6 Copynumber: 12.8 Consensus size: 6
30372563 GATTTCACCC
* *
30372573 AAAAGA AAAAGA AGACAAAA AAAAGA GAAAGATAA AAAAGA AAAAGA AAGAAGA
1 AAAAGA AAAAGA A-A-AAGA AAAAGA -AAA-A-GA AAAAGA AAAAGA AA-AAGA
30372627 GAAAAGA GAAAAGA GAAAAGA AAAAGA AAAAG
1 -AAAAGA -AAAAGA -AAAAGA AAAAGA AAAAG
30372659 GGAATGCTTG
Statistics
Matches: 69, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
6 30 0.43
7 28 0.41
8 10 0.14
9 1 0.01
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:30373076 original size:100 final size:99
Alignment explanation
Indices: 30372957--30373830 Score: 790
Period size: 100 Copynumber: 8.7 Consensus size: 99
30372947 AGTAAAAACA
* * * *
30372957 AGTAGAAGATCTTAATCTCCACTGAAGTTGCAGTGGAATAGAGTGAAGCCACACCAAATCTTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* * *
30373022 TACTTGAAGATGCAGTGGATCAGATTAAAACTAAT
66 TCCTTAAAGATGCAGTGGATC-GATTAAAACTAAC
* * ** * * *
30373057 AGTAGCAAATCTCAATCTCCACTAAAGTTGCAAAGGAATTGAGTGAGGCCACACCAAATTCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* * *
30373122 TCCTTGAAGATGAAGTGGAACGCATTAAAACTAAC
66 TCCTTAAAGATGCAGTGGATCG-ATTAAAACTAAC
* * * *
30373157 AGTAGCAGATCTCAATCACCACTGGAGTTGCAATGGAATGGACTGAAGCCACACCAAATCCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* *
30373222 TCCTTGAAGATGCAGTGGATCAAATTAAAACTAAC
66 TCCTTAAAGATGCAGTGGATC-GATTAAAACTAAC
* * * * *
30373257 AGTAGTAGATCTCAATCTCAACTGAAGTGGTAGTGGAATAGAGTGAAGCCACACCAAATCCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* * *
30373322 -CCTTTAAAGTTATAG-AGAGG--CGAATTAGAATTAAC
66 TCC-TTAAAG--AT-GCAGTGGATCG-ATTAAAACTAAC
* *
30373357 AGTAGAAGATCTCAATCTCCATTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* * * * *
30373422 TCCCTAAAGTTGTAGTAGATCGAATTAAAACTAAT
66 TCCTTAAAGATGCAGTGGATCG-ATTAAAACTAAC
* * * * * * *
30373457 AGTAGCAGATCTCAATCTCAATTGAAGTTGCACTAGAATTGAGTGAAGCCATACAAAATCCTAT-
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* * * * * * * *
30373521 GCCTCTAAAGTTGTAGTGGGGTAGACTAAAGCTAAT
66 TCCT-TAAAGATGCAGT-GGATCGATTAAAACTAAC
** * * * * * **
30373557 AGTATTAGATCTTAATTTCCATTGAAGTTGTAGTGGAATGGAGTGAAGCCACACCAAGTATTATA
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
* * * * * * *
30373622 CCCCTAAAGTTGTAGAGGGGTGGATTAAAACTAAC
66 TCCTTAAAGATGCAG-TGGATCGATTAAAACTAAC
* * * *
30373657 AGTAGCAGATCTTAATCTCCACTAAAGTTACAGTAGAATGGAGTGAAGCCACAACCCCAAATCCT
1 AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCAC-A--CCAAATCCT
* * * *
30373722 ATATCCTTAAAGTTACAGTGGATTGGATTAAAACTCAC
63 ATATCCTTAAAGATGCAGTGGA-TCGATTAAAACTAAC
* * **
30373760 AGTAAC-GAATCTCAATCTCC-CTGAAGTTGTAGTGGAATGGAGTGAAGTTACAAGCCCAAATCC
1 AGTAGCAG-ATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCAC-A--CCAAATCC
30373823 TATATCCT
62 TATATCCT
30373831 AGAAGTTACA
Statistics
Matches: 639, Mismatches: 115, Indels: 38
0.81 0.15 0.05
Matches are distributed among these distances:
97 1 0.00
98 4 0.01
99 5 0.01
100 517 0.81
101 8 0.01
102 53 0.08
103 51 0.08
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (99 bp):
AGTAGCAGATCTCAATCTCCACTGAAGTTGCAGTGGAATGGAGTGAAGCCACACCAAATCCTATA
TCCTTAAAGATGCAGTGGATCGATTAAAACTAAC
Found at i:30375471 original size:23 final size:23
Alignment explanation
Indices: 30375444--30375603 Score: 125
Period size: 23 Copynumber: 7.0 Consensus size: 23
30375434 ATATTCCAGC
30375444 TGTTCCTGTATTAGATGATTTGT
1 TGTTCCTGTATTAGATGATTTGT
* * *
30375467 TGTTCTTGAAATT-GA-GACTTTAT
1 TGTTCCTG-TATTAGATGA-TTTGT
*
30375490 TGCTCCTGTATTAGATGATTTGT
1 TGTTCCTGTATTAGATGATTTGT
* * *
30375513 TGTTCTTGAAATT-GA-GACTTTAT
1 TGTTCCTG-TATTAGATGA-TTTGT
*
30375536 TATTCCTGTATTAGATGATTTGT
1 TGTTCCTGTATTAGATGATTTGT
* *
30375559 TGTTCTTGAGATT-GA-GACTTTGT
1 TGTTCCTG-TATTAGATGA-TTTGT
*
30375582 TGTTCATGTATTAGATGATTTG
1 TGTTCCTGTATTAGATGATTTG
30375604 CAGCCAGGGA
Statistics
Matches: 105, Mismatches: 20, Indels: 24
0.70 0.13 0.16
Matches are distributed among these distances:
22 15 0.14
23 75 0.71
24 15 0.14
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.49
Consensus pattern (23 bp):
TGTTCCTGTATTAGATGATTTGT
Found at i:30375514 original size:46 final size:46
Alignment explanation
Indices: 30375444--30375603 Score: 275
Period size: 46 Copynumber: 3.5 Consensus size: 46
30375434 ATATTCCAGC
30375444 TGTTCCTGTATTAGATGATTTGTTGTTCTTGAAATTGAGACTTTAT
1 TGTTCCTGTATTAGATGATTTGTTGTTCTTGAAATTGAGACTTTAT
*
30375490 TGCTCCTGTATTAGATGATTTGTTGTTCTTGAAATTGAGACTTTAT
1 TGTTCCTGTATTAGATGATTTGTTGTTCTTGAAATTGAGACTTTAT
* * *
30375536 TATTCCTGTATTAGATGATTTGTTGTTCTTGAGATTGAGACTTTGT
1 TGTTCCTGTATTAGATGATTTGTTGTTCTTGAAATTGAGACTTTAT
*
30375582 TGTTCATGTATTAGATGATTTG
1 TGTTCCTGTATTAGATGATTTG
30375604 CAGCCAGGGA
Statistics
Matches: 107, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 107 1.00
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.49
Consensus pattern (46 bp):
TGTTCCTGTATTAGATGATTTGTTGTTCTTGAAATTGAGACTTTAT
Found at i:30377142 original size:18 final size:19
Alignment explanation
Indices: 30377121--30377162 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
30377111 CAATTACCGA
*
30377121 TGTCAACG-CAACCAGTTT
1 TGTCAACGACAACCAGATT
*
30377139 TGTC-ACGACAACCTGATT
1 TGTCAACGACAACCAGATT
30377157 TGTCAA
1 TGTCAA
30377163 TACCTTTACC
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 3 0.15
18 16 0.80
19 1 0.05
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (19 bp):
TGTCAACGACAACCAGATT
Found at i:30379850 original size:18 final size:18
Alignment explanation
Indices: 30379827--30379863 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
30379817 ATGGCAAATA
30379827 ACATTCCCAACCTGATTC
1 ACATTCCCAACCTGATTC
30379845 ACATTCCCAACCTGATTC
1 ACATTCCCAACCTGATTC
30379863 A
1 A
30379864 AAGTCCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.38, G:0.05, T:0.27
Consensus pattern (18 bp):
ACATTCCCAACCTGATTC
Found at i:30386453 original size:108 final size:108
Alignment explanation
Indices: 30386264--30386483 Score: 413
Period size: 108 Copynumber: 2.0 Consensus size: 108
30386254 CTAAACTCAT
*
30386264 AATTACTCCTAATAATTATTTACGAACTCGATTTACTAAGATAGAGGCCCTATAACTCACTTTTT
1 AATTACTCCTAATAATTATTTACGAACTCGATTTACTAAGATAGAGGCCATATAACTCACTTTTT
*
30386329 CGGTGCCCGTGAATTTAGGTCATTACATTTCTCTCCCTTAATA
66 CGGTGCCCGTGAATTTAGGTCATTACATTTCTCTCCCATAATA
*
30386372 AATTACTCCTAATAATTATTTACGAACTCGATTTACTAAGATGGAGGCCATATAACTCACTTTTT
1 AATTACTCCTAATAATTATTTACGAACTCGATTTACTAAGATAGAGGCCATATAACTCACTTTTT
30386437 CGGTGCCCGTGAATTTAGGTCATTACATTTCTCTCCCATAATA
66 CGGTGCCCGTGAATTTAGGTCATTACATTTCTCTCCCATAATA
30386480 AATT
1 AATT
30386484 TCGTCCTCGA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (108 bp):
AATTACTCCTAATAATTATTTACGAACTCGATTTACTAAGATAGAGGCCATATAACTCACTTTTT
CGGTGCCCGTGAATTTAGGTCATTACATTTCTCTCCCATAATA
Found at i:30396442 original size:43 final size:44
Alignment explanation
Indices: 30396387--30396613 Score: 329
Period size: 43 Copynumber: 5.3 Consensus size: 44
30396377 TTATGCGAAA
** *
30396387 AAGCGCCGCTAAAGAACATGTTTTTTAGCGGCGCTTTTC-CCAC
1 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCTCCAC
* *
30396430 AAGCACCGCTAAAGGCCTTGTTCTTTAGCGGCGC-TTTCTCCAC
1 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCTCCAC
* *
30396473 AAGCGCTGCTAAAGGCCTTGTTCTTTAGCGGCGCTTTTC-CCAC
1 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCTCCAC
30396516 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGC-TTTCTCCAC
1 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCTCCAC
* *
30396559 AAACGCCGCTAAAGGCCATGTTCTTTAGCGGCGC-TTTCTCCAA
1 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCTCCAC
*
30396602 AAGTGCCGCTAA
1 AAGCGCCGCTAA
30396614 TATAACAGAT
Statistics
Matches: 168, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
42 8 0.05
43 156 0.93
44 4 0.02
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (44 bp):
AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGCTTTTCTCCAC
Found at i:30396702 original size:15 final size:15
Alignment explanation
Indices: 30396682--30396710 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
30396672 CCTGTAAATT
30396682 CAAATCCAACCAATG
1 CAAATCCAACCAATG
30396697 CAAATCCAACCAAT
1 CAAATCCAACCAAT
30396711 AACTTCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.34, G:0.03, T:0.14
Consensus pattern (15 bp):
CAAATCCAACCAATG
Found at i:30397075 original size:65 final size:66
Alignment explanation
Indices: 30396929--30397085 Score: 235
Period size: 65 Copynumber: 2.4 Consensus size: 66
30396919 CTTCGCTTGC
* * * *
30396929 CTCGCTGCTGCCTCCACTTTAAGTTGTAGGTGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTC
1 CTCGCTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTC
30396994 T
66 T
* * *
30396995 CTCACTGCAGCCTCCTCTTTAAGTTTTAGATGGAGTTCATCATA-TTTTTTTGAGCCTCTGCTTC
1 CTCGCTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTC
30397059 T
66 T
*
30397060 CTCGTTGCAGCCTCCTCTTTAAGTTG
1 CTCGCTGCAGCCTCCTCTTTAAGTTG
30397086 AGCAATTTGC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
65 43 0.53
66 38 0.47
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.43
Consensus pattern (66 bp):
CTCGCTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTGAGACTCTGCTTC
T
Found at i:30397659 original size:18 final size:19
Alignment explanation
Indices: 30397625--30397661 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
30397615 TCCTACATTA
30397625 TAGTAGGAAATATATTAAT
1 TAGTAGGAAATATATTAAT
30397644 TAGTA-GAAAGTA-ATTAAT
1 TAGTAGGAAA-TATATTAAT
30397662 ATTTGACACA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (19 bp):
TAGTAGGAAATATATTAAT
Found at i:30402472 original size:31 final size:33
Alignment explanation
Indices: 30402433--30402498 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
30402423 TTGATTTAAA
30402433 TTAAAA-ATATATATTAGTGACAAAATTTTACT
1 TTAAAATATATATATTAGTGACAAAATTTTACT
*
30402465 TTAAAATATATATATTAGTGACAACATTTTACT
1 TTAAAATATATATATTAGTGACAAAATTTTACT
30402498 T
1 T
30402499 AAATATTTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (33 bp):
TTAAAATATATATATTAGTGACAAAATTTTACT
Found at i:30402541 original size:19 final size:19
Alignment explanation
Indices: 30402517--30402580 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
30402507 TGGTTGTTTT
30402517 TATTAATTAAATAATTAAA
1 TATTAATTAAATAATTAAA
*
30402536 TATTAATTTAGTATAATTAAA
1 TATTAA-TTA-AATAATTAAA
*
30402557 TTATTAA-TAATTAATTAAA
1 -TATTAATTAAATAATTAAA
30402576 -ATTAA
1 TATTAA
30402581 ATAATTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
17 5 0.13
19 14 0.36
20 5 0.13
21 9 0.23
22 6 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TATTAATTAAATAATTAAA
Found at i:30402555 original size:29 final size:29
Alignment explanation
Indices: 30402520--30402650 Score: 87
Period size: 29 Copynumber: 4.5 Consensus size: 29
30402510 TTGTTTTTAT
30402520 TAATTAAATAATTAAATATTAATTTAGTA
1 TAATTAAATAATTAAATATTAATTTAGTA
*
30402549 TAATTAAATTATT-AATAATTAA-TTA--A
1 TAATTAAATAATTAAAT-ATTAATTTAGTA
* *
30402575 -AATTAAATAATTATATATATTTATTTAGGA
1 TAATTAAATAATTA-A-ATATTAATTTAGTA
* * * *
30402605 AATATTTAA-AATTATAATATTTTAATTAAATA
1 TA-ATTAAATAATTA-AATA--TTAATTTAGTA
30402637 TAATTAAAT-ATTAA
1 TAATTAAATAATTAA
30402651 TTTTGATATT
Statistics
Matches: 80, Mismatches: 10, Indels: 23
0.71 0.09 0.20
Matches are distributed among these distances:
25 11 0.14
26 1 0.01
27 5 0.06
28 11 0.14
29 17 0.21
30 5 0.06
31 17 0.21
32 13 0.16
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (29 bp):
TAATTAAATAATTAAATATTAATTTAGTA
Found at i:30402566 original size:15 final size:15
Alignment explanation
Indices: 30402520--30402570 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
30402510 TTGTTTTTAT
*
30402520 TAATTAAATAATTAA
1 TAATTAAATTATTAA
* *
30402535 -ATATTAATTTAGT-A
1 TA-ATTAAATTATTAA
30402549 TAATTAAATTATTAA
1 TAATTAAATTATTAA
30402564 TAATTAA
1 TAATTAA
30402571 TTAAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
TAATTAAATTATTAA
Found at i:30402786 original size:110 final size:110
Alignment explanation
Indices: 30402638--30402904 Score: 454
Period size: 110 Copynumber: 2.5 Consensus size: 110
30402628 AATTAAATAT
* *
30402638 AATTAAATA-TTAATT--TTGATATTGTTTACAATTAAATACATAATTAAACATAATTAA-T-AA
1 AATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACA-AATTAATTGAA
30402698 TTAATATAATTATTTACTTTAATATAATTAAATATTTAAATCTTTTA
65 TTAATATAA-TATTTACTTTAATATAATTAAATATTTAAATCTTTTA
*
30402745 AATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACAAATTAATTGATT
1 AATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACAAATTAATTGAAT
30402810 TAATATAATATTTACTTTAATATAATTAAATATTTAAATCTTTTA
66 TAATATAATATTTACTTTAATATAATTAAATATTTAAATCTTTTA
30402855 AATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAA
1 AATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAA
30402905 TCTTTTAAAT
Statistics
Matches: 152, Mismatches: 3, Indels: 7
0.94 0.02 0.04
Matches are distributed among these distances:
107 9 0.06
108 6 0.04
109 6 0.04
110 121 0.80
111 10 0.07
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (110 bp):
AATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACAAATTAATTGAAT
TAATATAATATTTACTTTAATATAATTAAATATTTAAATCTTTTA
Found at i:30402904 original size:32 final size:32
Alignment explanation
Indices: 30402866--30402960 Score: 98
Period size: 25 Copynumber: 3.2 Consensus size: 32
30402856 ATTAAATATT
30402866 TAATTAATTGATACTGTTTACAATTTAATACA
1 TAATTAATTGATACTGTTTACAATTTAATACA
* **
30402898 TAATT-A---AT-CT-TTTA-AATTAAATATT
1 TAATTAATTGATACTGTTTACAATTTAATACA
30402923 TAA-TAATTGATACTGTTTACAATTTAATACA
1 TAATTAATTGATACTGTTTACAATTTAATACA
*
30402954 TATTTAA
1 TAATTAA
30402961 ACATAATTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 16
0.68 0.10 0.23
Matches are distributed among these distances:
24 1 0.02
25 12 0.25
26 4 0.08
27 2 0.04
28 4 0.08
29 2 0.04
30 4 0.08
31 11 0.23
32 8 0.17
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (32 bp):
TAATTAATTGATACTGTTTACAATTTAATACA
Found at i:30402986 original size:18 final size:18
Alignment explanation
Indices: 30402963--30403228 Score: 69
Period size: 18 Copynumber: 14.4 Consensus size: 18
30402953 ATATTTAAAC
30402963 ATAATTAATTGATTTAAT
1 ATAATTAATTGATTTAAT
*
30402981 ATAATT-ATTTACTTTAAT
1 ATAATTAATTGA-TTTAAT
30402999 ATAATTAA-T-ATTTAAATCTT
1 ATAATTAATTGATTT-AA---T
* *
30403019 TTAAATTAAAT-ATTTAAT
1 AT-AATTAATTGATTTAAT
30403037 -TAATTAATATTG-TTTACAAT
1 ATAATT-A-ATTGATTT--AAT
* * * *
30403057 TTAA-TACA-TAATTAAAC
1 ATAATTA-ATTGATTTAAT
30403074 ATAATTAATTGATTTAAT
1 ATAATTAATTGATTTAAT
*
30403092 ATAATT-ATTTACTTTAAT
1 ATAATTAATTGA-TTTAAT
*
30403110 ATAATTAAAT-ATTTAAATCT
1 ATAATTAATTGATTT-AA--T
* *
30403130 TTAAATTAAAT-ATTTAAT
1 AT-AATTAATTGATTTAAT
30403148 -TAATTGATATTG-TTTACAAT
1 ATAATT-A-ATTGATTT--AAT
* * * *
30403168 TTAA-TACA-TAATTAAAC
1 ATAATTA-ATTGATTTAAT
30403185 ATAATTAATTGATTTAAT
1 ATAATTAATTGATTTAAT
* *
30403203 ATAA-TCATTTACTTTAAT
1 ATAATTAATTGA-TTTAAT
30403221 ATAATTAA
1 ATAATTAA
30403229 ATTATTAAAT
Statistics
Matches: 188, Mismatches: 26, Indels: 67
0.67 0.09 0.24
Matches are distributed among these distances:
16 11 0.06
17 35 0.19
18 84 0.45
19 13 0.07
20 14 0.07
21 26 0.14
22 5 0.03
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (18 bp):
ATAATTAATTGATTTAAT
Found at i:30403011 original size:167 final size:168
Alignment explanation
Indices: 30402736--30403404 Score: 688
Period size: 167 Copynumber: 4.0 Consensus size: 168
30402726 TAAATATTTA
30402736 AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACA-AA
1 AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATAA
*
30402800 TTAATTGATTTAATATAA-TATTTACTTTAATATAATTAAATATTTAAATCTTTTAAATTAAATA
66 TTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTT-AATTAAATA
30402864 TTTAATTAATTGATACTGTTTACAATTTAATACATAATT
130 TTTAATTAATTGATACTGTTTACAATTTAATACATAATT
*
30402903 AATCTTTTAAATTAAATATTTAA-TAATTGATACTGTTTACAATTTAATACATATTTAAACATAA
1 AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATAA
*
30402967 TTAATTGATTTAATATAATTATTTACTTTAATATAATT-AATATTTAAATCTTTTAAATTAAATA
66 TTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTT-AATTAAATA
* *
30403031 TTTAATTAATTAATATTGTTTACAATTTAATACATAATT
130 TTTAATTAATTGATACTGTTTACAATTTAATACATAATT
* * * * * *
30403070 AAAC--AT-AATTAATTGATTTAATATAATT-ATTTAC--TTT--AATATAATTAAATATTTAAA
1 AATCTTTTAAATTAAAT-ATTTAAT-TAATTGA--TACTGTTTACAATTTAA-TACATAATTAAA
* * * * *
30403127 TCTTTAAATTAAAT-ATTTAAT-TAATTGATATT-GTTTACAATTTAA-TACATAATTAAA-C--
61 -C-AT-AATTAATTGATTTAATATAATT-AT-TTACTTT--AATATAATTAAATAATTAAATCTT
* * * * * *
30403185 ATAATTAATTGATTTAATATAATCAT-TTAC--TTT--AATATAATTAAATTATT
119 TTAATTAAAT-ATTTAAT-TAAT--TGATACTGTTTACAATTTAA-TACATAATT
* * *
30403235 AAATATTTTAAATTAATTATTTAATTAATTGACACTGTTTACAATTTAATACATAATTAAACATA
1 -AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATA
* * *
30403300 ATTAA-TAATTTAATATAATTATTTAGTTTAATATAATTAAATAATTAAATCTATTTATTTAAAT
65 ATTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCT-TTTAATTAAAT
* * *
30403364 ATTTAATTAATTGGTACTGTTTATAA-TAAATACATAATT
129 ATTTAATTAATTGATACTGTTTACAATTTAATACATAATT
30403403 AA
1 AA
30403405 ACATAATTAA
Statistics
Matches: 420, Mismatches: 39, Indels: 86
0.77 0.07 0.16
Matches are distributed among these distances:
164 25 0.06
165 47 0.11
166 85 0.20
167 148 0.35
168 65 0.15
169 42 0.10
170 8 0.02
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (168 bp):
AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATAA
TTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATAATTAAATCTTTTAATTAAATAT
TTAATTAATTGATACTGTTTACAATTTAATACATAATT
Found at i:30403064 original size:111 final size:112
Alignment explanation
Indices: 30402903--30403515 Score: 909
Period size: 111 Copynumber: 5.5 Consensus size: 112
30402893 ATACATAATT
*
30402903 AATCTTTTAAATTAAATATTTAA-TAATTGATACTGTTTACAATTTAATACATATTTAAACATAA
1 AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATAA
30402967 TTAATTGATTTAATATAATTATTTACTTTAATATAATT-AATATTTA
66 TTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATATTTA
* *
30403013 AATCTTTTAAATTAAATATTTAATTAATTAATATTGTTTACAATTTAATACATAATTAAACATAA
1 AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATAA
30403078 TTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATATTTA
66 TTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATATTTA
*
30403125 AATC-TTTAAATTAAATATTTAATTAATTGATATTGTTTACAATTTAATACATAATTAAACATAA
1 AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATAA
*
30403189 TTAATTGATTTAATATAATCATTTACTTTAATATAATTAAAT-TATTA
66 TTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATAT-TTA
* * *
30403236 AATATTTTAAATTAATTATTTAATTAATTGACACTGTTTACAATTTAATACATAATTAAACATAA
1 AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATAA
* * *
30403301 TTAA-TAATTTAATATAATTATTTAGTTTAATATAATTAAATAATTA
66 TTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATATTTA
* * * *
30403347 AATCTATTT-ATTTAAATATTTAATTAATTGGTACTGTTTATAA-TAAATACATAATTAAACATA
1 AATCT-TTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATA
* * * * * *
30403410 ATTAAATAATTTAACATAATTATTTAGTTTAATATAATTAAAAAATTA
65 ATTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATATTTA
* * * * *
30403458 AACCTATTAAATTAAATATTTAATTAATTGGTACTGTTTATAA-TTAGATATATAATTA
1 AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTA-ATACATAATTA
30403516 TTTAATTATT
Statistics
Matches: 467, Mismatches: 27, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
110 50 0.11
111 331 0.71
112 86 0.18
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (112 bp):
AATCTTTTAAATTAAATATTTAATTAATTGATACTGTTTACAATTTAATACATAATTAAACATAA
TTAATTGATTTAATATAATTATTTACTTTAATATAATTAAATATTTA
Found at i:30403239 original size:18 final size:18
Alignment explanation
Indices: 30403178--30403249 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 18
30403168 TTAATACATA
*
30403178 ATTAAACATAATT-AATT
1 ATTAAATATAATTAAATT
* * *
30403195 GATTTAATATAA-TCATTT
1 -ATTAAATATAATTAAATT
*
30403213 ACTTTAATATAATTAAATT
1 A-TTAAATATAATTAAATT
*
30403232 ATTAAATAT-TTTAAATT
1 ATTAAATATAATTAAATT
30403249 A
1 A
30403250 ATTATTTAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
17 10 0.23
18 29 0.66
19 5 0.11
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (18 bp):
ATTAAATATAATTAAATT
Found at i:30403410 original size:10 final size:10
Alignment explanation
Indices: 30403395--30403431 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
30403385 TATAATAAAT
30403395 ACATAATTAA
1 ACATAATTAA
30403405 ACATAATT-A
1 ACATAATTAA
*
30403414 A-ATAATTTA
1 ACATAATTAA
30403423 ACATAATTA
1 ACATAATTA
30403432 TTTAGTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
8 6 0.25
9 4 0.17
10 14 0.58
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (10 bp):
ACATAATTAA
Found at i:30403418 original size:18 final size:18
Alignment explanation
Indices: 30403397--30403469 Score: 67
Period size: 18 Copynumber: 4.1 Consensus size: 18
30403387 TAATAAATAC
30403397 ATAATTAAACATAATTAA
1 ATAATTAAACATAATTAA
* *
30403415 ATAATTTAACATAATTAT
1 ATAATTAAACATAATTAA
* * * *
30403433 TTAGTTTAATATAATTAA
1 ATAATTAAACATAATTAA
* *
30403451 AAAATTAAACCT-ATTAA
1 ATAATTAAACATAATTAA
30403468 AT
1 AT
30403470 TAAATATTTA
Statistics
Matches: 42, Mismatches: 13, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
17 6 0.14
18 36 0.86
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.40
Consensus pattern (18 bp):
ATAATTAAACATAATTAA
Found at i:30405011 original size:15 final size:15
Alignment explanation
Indices: 30404991--30405021 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30404981 AACTTTTTCT
30404991 TTCAGGCTGGTTAGG
1 TTCAGGCTGGTTAGG
30405006 TTCAGGCTGGTTAGG
1 TTCAGGCTGGTTAGG
30405021 T
1 T
30405022 ATGTGTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.39, T:0.35
Consensus pattern (15 bp):
TTCAGGCTGGTTAGG
Found at i:30406817 original size:2 final size:2
Alignment explanation
Indices: 30406810--30406878 Score: 111
Period size: 2 Copynumber: 34.5 Consensus size: 2
30406800 AATATACATT
30406810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
30406852 TA TA TA TA TA TA TT TG TA TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
30406879 TGATAAATGA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30409086 original size:41 final size:41
Alignment explanation
Indices: 30408919--30409484 Score: 455
Period size: 41 Copynumber: 13.8 Consensus size: 41
30408909 TTTAAATAAA
*
30408919 TTAGCGGCGCTT-ATGGGAAAGCGCCGCTAATG-CAC-ACCT
1 TTAGCGGCGCTTGA-GGGAAAGCGCCGCTAATGACCCTACCT
* * * *
30408958 TTAGCGACGCTCACT-A-GAAAAGCGCCACTAATGACCCGACCT
1 TTAGCGGCGCT---TGAGGGAAAGCGCCGCTAATGACCCTACCT
* *** * * *
30409000 TTAGCGGCGCTTATATATAAAGCGCTGCTAATGACCCGACAT
1 TTAGCGGCGCTT-GAGGGAAAGCGCCGCTAATGACCCTACCT
* * *
30409042 TTAGCGGCGCTTGAGGGAAAGCGTCGCTAATGATCTTACCT
1 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCCTACCT
* *
30409083 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAAAGATCCTACCT
1 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCCTACCT
* * * *
30409124 TTAGCGACGCTTGAGGAAAAGCGCCGCTAAAGATCCTACCT
1 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCCTACCT
*
30409165 TTAGCGGCGCTTGAGGAAAAGCGCCGCTAATGATCCC-ACCT
1 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGA-CCCTACCT
****** * *
30409206 TTAGCGGCGCTTTCCCTCAAGCGCCGCTAATTACCCGACCT
1 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCCTACCT
* * * *
30409247 TTAGCGGCGCTTGTGGGAAAGCGCCACTAATTACCATACCT
1 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCCTACCT
* *** * * *
30409288 TTAGCGGCGCTTCACCCACAAGCGTCGCTAATTACCCGACCT
1 TTAGCGGCGCTTGAGGGA-AAGCGCCGCTAATGACCCTACCT
* * * *
30409330 TTAGCGGCGCTTGTGGGAAAGCGCCACTAATTACCATACCT
1 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCCTACCT
* *** *
30409371 TTAGCGGCGCTTCACCCACAAGCGCCGCTAATGA-CCTGACAT
1 TTAGCGGCGCTTGAGGGA-AAGCGCCGCTAATGACCCT-ACCT
* * *** * *
30409413 TTAGCAGCGCTTGTGATTAAGCGCCACTAATGACCCGACCT
1 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCCTACCT
***
30409454 TTAGCGGCGCTTG-GATTAAGCGCCGCTAATG
1 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATG
30409485 CTTTACCATT
Statistics
Matches: 430, Mismatches: 83, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
39 11 0.03
40 35 0.08
41 272 0.63
42 112 0.26
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.22
Consensus pattern (41 bp):
TTAGCGGCGCTTGAGGGAAAGCGCCGCTAATGACCCTACCT
Found at i:30409331 original size:83 final size:83
Alignment explanation
Indices: 30408919--30409465 Score: 516
Period size: 83 Copynumber: 6.6 Consensus size: 83
30408909 TTTAAATAAA
* * * ** *
30408919 TTAGCGGCGCTTATGGGAAAGCGCCGCTAATG--CACACCTTTAGCGACGC-TCACTAGAAAAGC
1 TTAGCGGCGCTTGTGGGAAAGCGCCGCTAATGACCATACCTTTAGCGGCGCTTCAC-CCACAAGC
*
30408981 GCCACTAATGACCCGACCT
65 GCCGCTAATGACCCGACCT
* *** * ** * * ***
30409000 TTAGCGGCGCTTATATATAAAGCGCTGCTAATGACCCGACATTTAGCGGCGCTTGAGGGA-AAGC
1 TTAGCGGCGCTTGT-GGGAAAGCGCCGCTAATGACCATACCTTTAGCGGCGCTTCACCCACAAGC
* * **
30409064 GTCGCTAATGATCTTACCT
65 GCCGCTAATGACCCGACCT
* * * * ** *
30409083 TTAGCGGCGCTTGAGGGAAAGCGCCGCTAAAGATCC-TACCTTTAGCGACGCTTGA-GGAAAAGC
1 TTAGCGGCGCTTGTGGGAAAGCGCCGCTAATGA-CCATACCTTTAGCGGCGCTTCACCCACAAGC
* * *
30409146 GCCGCTAAAGATCCTACCT
65 GCCGCTAATGACCCGACCT
* * * * *
30409165 TTAGCGGCGCTTGAGGAAAAGCGCCGCTAATGATCC-CACCTTTAGCGGCGCTT-TCCCTCAAGC
1 TTAGCGGCGCTTGTGGGAAAGCGCCGCTAATGA-CCATACCTTTAGCGGCGCTTCACCCACAAGC
*
30409228 GCCGCTAATTACCCGACCT
65 GCCGCTAATGACCCGACCT
* *
30409247 TTAGCGGCGCTTGTGGGAAAGCGCCACTAATTACCATACCTTTAGCGGCGCTTCACCCACAAGCG
1 TTAGCGGCGCTTGTGGGAAAGCGCCGCTAATGACCATACCTTTAGCGGCGCTTCACCCACAAGCG
* *
30409312 TCGCTAATTACCCGACCT
66 CCGCTAATGACCCGACCT
* *
30409330 TTAGCGGCGCTTGTGGGAAAGCGCCACTAATTACCATACCTTTAGCGGCGCTTCACCCACAAGCG
1 TTAGCGGCGCTTGTGGGAAAGCGCCGCTAATGACCATACCTTTAGCGGCGCTTCACCCACAAGCG
* *
30409395 CCGCTAATGACCTGACAT
66 CCGCTAATGACCCGACCT
* *** * **
30409413 TTAGCAGCGCTTGTGATTAAGCGCCACTAATGACCCGACCTTTAGCGGCGCTT
1 TTAGCGGCGCTTGTGGGAAAGCGCCGCTAATGACCATACCTTTAGCGGCGCTT
30409466 GGATTAAGCG
Statistics
Matches: 396, Mismatches: 61, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
81 19 0.05
82 177 0.45
83 183 0.46
84 15 0.04
85 2 0.01
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (83 bp):
TTAGCGGCGCTTGTGGGAAAGCGCCGCTAATGACCATACCTTTAGCGGCGCTTCACCCACAAGCG
CCGCTAATGACCCGACCT
Found at i:30410876 original size:27 final size:26
Alignment explanation
Indices: 30410835--30410966 Score: 140
Period size: 27 Copynumber: 4.9 Consensus size: 26
30410825 AAACACGAAA
*
30410835 TCTGAAAGAACTGCCTTTATGGCAAAC
1 TCTGAAAGAA-TGCCTTTGTGGCAAAC
30410862 TCTGAAAGGAATGCCTTTGTGGCGAAA-
1 TCTGAAA-GAATGCCTTTGTGGC-AAAC
* * *
30410889 TCTGGAAGAACTACCTTCGTGGCAAAC
1 TCTGAAAGAA-TGCCTTTGTGGCAAAC
*
30410916 TCTGAAATGAATGCCTATGTGGCAAAC
1 TCTGAAA-GAATGCCTTTGTGGCAAAC
* *
30410943 TTTAAAAGAAATGCCTTTGTGGCA
1 TCTGAAAG-AATGCCTTTGTGGCA
30410967 TGTCATAATA
Statistics
Matches: 88, Mismatches: 11, Indels: 12
0.79 0.10 0.11
Matches are distributed among these distances:
26 7 0.08
27 72 0.82
28 9 0.10
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (26 bp):
TCTGAAAGAATGCCTTTGTGGCAAAC
Found at i:30410952 original size:54 final size:54
Alignment explanation
Indices: 30410830--30410966 Score: 168
Period size: 54 Copynumber: 2.5 Consensus size: 54
30410820 ATCATAAACA
* * *
30410830 CGAAATCTGAAAGAACTGCCTTTATGGCAAACTCTGAAAGGAATGCCTTTGTGG
1 CGAAATCTAAAAGAACTGCCTTTGTGGCAAACTCTGAAAGGAATGCCTATGTGG
** * * *
30410884 CGAAATCTGGAAGAACTACCTTCGTGGCAAACTCTGAAATGAATGCCTATGTGG
1 CGAAATCTAAAAGAACTGCCTTTGTGGCAAACTCTGAAAGGAATGCCTATGTGG
* *
30410938 C-AAACTTTAAAAGAAATGCCTTTGTGGCA
1 CGAAA-TCTAAAAGAACTGCCTTTGTGGCA
30410967 TGTCATAATA
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
53 3 0.04
54 67 0.96
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (54 bp):
CGAAATCTAAAAGAACTGCCTTTGTGGCAAACTCTGAAAGGAATGCCTATGTGG
Found at i:30416940 original size:21 final size:21
Alignment explanation
Indices: 30416914--30416954 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
30416904 TATTTGGTTG
30416914 GTGAGAAAACTAAAGAAAATT
1 GTGAGAAAACTAAAGAAAATT
*
30416935 GTGAGAAAACTGAAGAAAAT
1 GTGAGAAAACTAAAGAAAAT
30416955 GGATTTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.56, C:0.05, G:0.22, T:0.17
Consensus pattern (21 bp):
GTGAGAAAACTAAAGAAAATT
Found at i:30417162 original size:73 final size:73
Alignment explanation
Indices: 30417059--30417351 Score: 478
Period size: 73 Copynumber: 4.0 Consensus size: 73
30417049 GGAGGCATTG
* *
30417059 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATATATTTGGAAAGAGAGAAACTCTGGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTGGGAAAGTG
30417124 TTGAGAAA
66 TTGAGAAA
* * *
30417132 AGAAAATCTGGAAAGAGAGAAAAAAATAAAGATGTATTTGGAAAGAGAGAAAATCTGGAAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTGGGAAAGTG
*
30417197 TTGATAAA
66 TTGAGAAA
* * *
30417205 AGAAAATATGAAAAGAAAGGAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTGGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTGGGAAAGTG
30417270 TTGAGAAA
66 TTGAGAAA
* * *
30417278 AGAAAATCTGGAAAGAGAGAAAAAACTAAAGATGTGTTTGGAAAGAGAGAAAATCTAGGAAAGTG
1 AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTGGGAAAGTG
30417343 TTGAGAAA
66 TTGAGAAA
30417351 A
1 A
30417352 AAATGTTTTA
Statistics
Matches: 201, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 201 1.00
ACGTcount: A:0.53, C:0.04, G:0.26, T:0.18
Consensus pattern (73 bp):
AGAAAATCTGGAAAGAAAGAAAAAACTAAAGATGTATTTGGAAAGAGAGAAAATCTGGGAAAGTG
TTGAGAAA
Found at i:30418209 original size:29 final size:27
Alignment explanation
Indices: 30418172--30418226 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
30418162 CAAGGGAAGA
*
30418172 GCCCAAACCGTCCACTAAGGGAAGGAGAG
1 GCCCAAACCATCCACT-AGGG-AGGAGAG
*
30418201 GCCCGAACCATCCACTAGGGAGGAGA
1 GCCCAAACCATCCACTAGGGAGGAGA
30418227 AGGGAGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 4 0.17
29 14 0.58
ACGTcount: A:0.33, C:0.29, G:0.31, T:0.07
Consensus pattern (27 bp):
GCCCAAACCATCCACTAGGGAGGAGAG
Found at i:30418960 original size:11 final size:11
Alignment explanation
Indices: 30418944--30418973 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
30418934 AAACACATCT
30418944 AAACATGCCAA
1 AAACATGCCAA
*
30418955 AAACATACCAA
1 AAACATGCCAA
30418966 AAACATGC
1 AAACATGC
30418974 AACCTATGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.27, G:0.07, T:0.10
Consensus pattern (11 bp):
AAACATGCCAA
Found at i:30419867 original size:13 final size:13
Alignment explanation
Indices: 30419851--30419906 Score: 80
Period size: 13 Copynumber: 4.3 Consensus size: 13
30419841 TCATCTAAAT
30419851 ATTTCATCTTAC-C
1 ATTTCAT-TTACAC
30419864 ATTTCATTTACAC
1 ATTTCATTTACAC
30419877 ATTTCATCTTAC-C
1 ATTTCAT-TTACAC
30419890 ATTTCATTTACAC
1 ATTTCATTTACAC
30419903 ATTT
1 ATTT
30419907 AACACATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.20
13 28 0.70
14 4 0.10
ACGTcount: A:0.27, C:0.25, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTCATTTACAC
Found at i:30419867 original size:26 final size:26
Alignment explanation
Indices: 30419838--30419906 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
30419828 TCGTATAACA
*
30419838 ATTTCATCTAAATATTTCATCTTACC
1 ATTTCATCTAAACATTTCATCTTACC
* *
30419864 ATTTCATTTACACATTTCATCTTACC
1 ATTTCATCTAAACATTTCATCTTACC
* *
30419890 ATTTCATTTACACATTT
1 ATTTCATCTAAACATTT
30419907 AACACATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTTCATCTAAACATTTCATCTTACC
Found at i:30427485 original size:70 final size:70
Alignment explanation
Indices: 30427379--30427509 Score: 208
Period size: 70 Copynumber: 1.9 Consensus size: 70
30427369 TGTTACGACG
*
30427379 TAGCTCCCCCTATATCGCGACAAACCTATCAGTTTTGAAATTTTAACAATTTGACCCCTTTGTTG
1 TAGCTCCCCCTATATCGCGACAAACCTATCAATTTTGAAATTTTAACAATTTGACCCCTTTGTTG
30427444 CCTCA
66 CCTCA
* * * * *
30427449 TAGCTCTCCCTGTGTCGCGGCAAACCTATCAATTTTGAAATTTTAACAGTTTGACCCCTTT
1 TAGCTCCCCCTATATCGCGACAAACCTATCAATTTTGAAATTTTAACAATTTGACCCCTTT
30427510 TTCGCAACAT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 55 1.00
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.35
Consensus pattern (70 bp):
TAGCTCCCCCTATATCGCGACAAACCTATCAATTTTGAAATTTTAACAATTTGACCCCTTTGTTG
CCTCA
Found at i:30436603 original size:12 final size:12
Alignment explanation
Indices: 30436586--30436613 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
30436576 TCTGTCGGAA
30436586 AAAATATAAAGT
1 AAAATATAAAGT
30436598 AAAATATAAAGT
1 AAAATATAAAGT
30436610 AAAA
1 AAAA
30436614 CCCTATTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (12 bp):
AAAATATAAAGT
Found at i:30439189 original size:21 final size:21
Alignment explanation
Indices: 30439164--30439203 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30439154 TTGCATTATG
*
30439164 TTTAATATTT-TGTATGAGTTA
1 TTTAAT-TTTATGCATGAGTTA
30439185 TTTAATTTTATGCATGAGT
1 TTTAATTTTATGCATGAGT
30439204 CGAGTTGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.55
Consensus pattern (21 bp):
TTTAATTTTATGCATGAGTTA
Found at i:30444595 original size:17 final size:17
Alignment explanation
Indices: 30444575--30444617 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
30444565 AAATGCAACT
*
30444575 ACAATGCAAATGTGTTG
1 ACAATGCAAATGTGATG
*
30444592 ACAAAT-AAAATGTGATG
1 AC-AATGCAAATGTGATG
30444609 ACAATGCAA
1 ACAATGCAA
30444618 TTATAACTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
16 3 0.14
17 15 0.71
18 3 0.14
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.23
Consensus pattern (17 bp):
ACAATGCAAATGTGATG
Found at i:30445062 original size:12 final size:12
Alignment explanation
Indices: 30445045--30445069 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30445035 TTCTCTCCTA
30445045 CTTCTTTTTCTT
1 CTTCTTTTTCTT
30445057 CTTCTTTTTCTT
1 CTTCTTTTTCTT
30445069 C
1 C
30445070 CTCGATACCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTCTTTTTCTT
Found at i:30451070 original size:18 final size:18
Alignment explanation
Indices: 30451049--30451091 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
30451039 GGCTGCATAC
*
30451049 GAGCATGTGATTGCATCT
1 GAGCATGTGACTGCATCT
30451067 GAGCATGTGACTGCATCT
1 GAGCATGTGACTGCATCT
*
30451085 GATCATG
1 GAGCATG
30451092 ATGTGCCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (18 bp):
GAGCATGTGACTGCATCT
Found at i:30455400 original size:26 final size:26
Alignment explanation
Indices: 30455364--30455490 Score: 96
Period size: 26 Copynumber: 4.9 Consensus size: 26
30455354 TAATGTCGTA
*
30455364 GCATGAGCATGTCTAGAATTGTCGCT
1 GCATGAACATGTCTAGAATTGTCGCT
* * **
30455390 GCA-GAAACATGTCCAGAGTTGTCATT
1 GCATG-AACATGTCTAGAATTGTCGCT
* * *
30455416 ACATGAGCATGTCTAGAATTGTCGTT
1 GCATGAACATGTCTAGAATTGTCGCT
* * * *
30455442 GCA-GAAACTTGACCAGAATTATCGCT
1 GCATG-AACATGTCTAGAATTGTCGCT
* *
30455468 GCATGAACATGTTTAGAGTTGTC
1 GCATGAACATGTCTAGAATTGTC
30455491 ACTATATGAG
Statistics
Matches: 74, Mismatches: 23, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
25 2 0.03
26 70 0.95
27 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (26 bp):
GCATGAACATGTCTAGAATTGTCGCT
Found at i:30455473 original size:52 final size:52
Alignment explanation
Indices: 30455364--30455490 Score: 155
Period size: 52 Copynumber: 2.4 Consensus size: 52
30455354 TAATGTCGTA
* * * *
30455364 GCATGAGCATGTCTAGAATTGTCGCTGCAGAAACATGTCCAGAGTTGTCATT
1 GCATGAGCATGTCTAGAATTGTCGCTGCAGAAACATGACCAGAATTATCACT
* * * *
30455416 ACATGAGCATGTCTAGAATTGTCGTTGCAGAAACTTGACCAGAATTATCGCT
1 GCATGAGCATGTCTAGAATTGTCGCTGCAGAAACATGACCAGAATTATCACT
* * *
30455468 GCATGAACATGTTTAGAGTTGTC
1 GCATGAGCATGTCTAGAATTGTC
30455491 ACTATATGAG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (52 bp):
GCATGAGCATGTCTAGAATTGTCGCTGCAGAAACATGACCAGAATTATCACT
Found at i:30478862 original size:15 final size:15
Alignment explanation
Indices: 30478836--30478882 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
30478826 TGTGGGTGTT
30478836 AAAGAGGAAGAAAAGA
1 AAAGA-GAAGAAAAGA
30478852 AAAGAGAAGAAGAA-A
1 AAAGAGAAGAA-AAGA
*
30478867 GAAGAGAAGAAAAGA
1 AAAGAGAAGAAAAGA
30478882 A
1 A
30478883 GAAAAGGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 2 0.07
15 18 0.67
16 7 0.26
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAAGAGAAGAAAAGA
Found at i:30478876 original size:20 final size:20
Alignment explanation
Indices: 30478848--30478886 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30478838 AGAGGAAGAA
*
30478848 AAGAAAAGAGAAGAAGAAAG
1 AAGAAAAGAAAAGAAGAAAG
*
30478868 AAGAGAAGAAAAGAAGAAA
1 AAGAAAAGAAAAGAAGAAA
30478887 AGGAAAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (20 bp):
AAGAAAAGAAAAGAAGAAAG
Found at i:30478893 original size:13 final size:13
Alignment explanation
Indices: 30478842--30478911 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
30478832 TGTTAAAGAG
30478842 GAAGAAAAGAAAA
1 GAAGAAAAGAAAA
30478855 G-AGAAGAAG-AAA
1 GAAGAA-AAGAAAA
*
30478867 GAAGAGAAGAAAA
1 GAAGAAAAGAAAA
*
30478880 GAAGAAAAGGAAA
1 GAAGAAAAGAAAA
* *
30478893 GGA-AAAAGACAAT
1 GAAGAAAAGA-AAA
30478906 GAAGAA
1 GAAGAA
30478912 GATTTTGTGC
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
12 16 0.36
13 27 0.60
14 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.29, T:0.01
Consensus pattern (13 bp):
GAAGAAAAGAAAA
Found at i:30484524 original size:17 final size:18
Alignment explanation
Indices: 30484502--30484539 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
30484492 TAAAGAGCAT
30484502 AAAATA-AAAGATAAAA-C
1 AAAATAGAAA-ATAAAATC
30484519 AAAATAGAAAATAAAATC
1 AAAATAGAAAATAAAATC
30484537 AAA
1 AAA
30484540 GGTTTGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.13
Consensus pattern (18 bp):
AAAATAGAAAATAAAATC
Found at i:30492961 original size:18 final size:18
Alignment explanation
Indices: 30492926--30492968 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
30492916 GGCTACATAC
**
30492926 GAGCATGTGATTGCATCT
1 GAGCATGTGACCGCATCT
*
30492944 GAGCATGTGACCGTATCT
1 GAGCATGTGACCGCATCT
*
30492962 GATCATG
1 GAGCATG
30492969 ATATGCCTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (18 bp):
GAGCATGTGACCGCATCT
Found at i:30497250 original size:26 final size:26
Alignment explanation
Indices: 30497215--30497364 Score: 106
Period size: 26 Copynumber: 5.8 Consensus size: 26
30497205 AATGTCGCTA
*
30497215 CATGAGCATGTCTAGAATTGTCACTG
1 CATGAACATGTCTAGAATTGTCACTG
* *
30497241 CA-GAAACATGTCCAGAGTTGTCACTG
1 CATG-AACATGTCTAGAATTGTCACTG
* ** *
30497267 CATGAGCATGTCTAGAATTGTCGTTT
1 CATGAACATGTCTAGAATTGTCACTG
* * * * *
30497293 CA-GAAACTTGACCAGAATTATCGCTG
1 CATG-AACATGTCTAGAATTGTCACTG
* *
30497319 CATGAACATGTTTAGAGTTGTCACTG
1 CATGAACATGTCTAGAATTGTCACTG
* * * *
30497345 TATGAGCTTGTCTAAAATTG
1 CATGAACATGTCTAGAATTG
30497365 CGCCCAGAAT
Statistics
Matches: 91, Mismatches: 29, Indels: 8
0.71 0.23 0.06
Matches are distributed among these distances:
25 2 0.02
26 87 0.96
27 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (26 bp):
CATGAACATGTCTAGAATTGTCACTG
Found at i:30497297 original size:52 final size:52
Alignment explanation
Indices: 30497215--30497344 Score: 161
Period size: 52 Copynumber: 2.5 Consensus size: 52
30497205 AATGTCGCTA
* * *
30497215 CATGAGCATGTCTAGAATTGTCACTGCAGAAACATGTCCAGAGTTGTCACTG
1 CATGAGCATGTCTAGAATTGTCACTGCAGAAACATGACCAGAATTATCACTG
** * * *
30497267 CATGAGCATGTCTAGAATTGTCGTTTCAGAAACTTGACCAGAATTATCGCTG
1 CATGAGCATGTCTAGAATTGTCACTGCAGAAACATGACCAGAATTATCACTG
* * *
30497319 CATGAACATGTTTAGAGTTGTCACTG
1 CATGAGCATGTCTAGAATTGTCACTG
30497345 TATGAGCTTG
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (52 bp):
CATGAGCATGTCTAGAATTGTCACTGCAGAAACATGACCAGAATTATCACTG
Found at i:30502945 original size:21 final size:21
Alignment explanation
Indices: 30502919--30502959 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
30502909 CCTCCTCTAT
30502919 GATGAC-TGTGTTATTCACAAA
1 GATGACAT-TGTTATTCACAAA
*
30502940 GATGACATTTTTATTCACAA
1 GATGACATTGTTATTCACAA
30502960 CCTTTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (21 bp):
GATGACATTGTTATTCACAAA
Found at i:30504885 original size:17 final size:17
Alignment explanation
Indices: 30504814--30504885 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 17
30504804 TATTAGTAAG
* *
30504814 CATTGTCATCACATTCC
1 CATTGTCATTACATTTC
30504831 CATTGTCATTACATTTC
1 CATTGTCATTACATTTC
* * * *
30504848 AATTGTCACTGCATTTG
1 CATTGTCATTACATTTC
*
30504865 CATTGTCATTGCATTTC
1 CATTGTCATTACATTTC
30504882 CATT
1 CATT
30504886 TGTTGTTGTA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 46 1.00
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.43
Consensus pattern (17 bp):
CATTGTCATTACATTTC
Found at i:30505464 original size:15 final size:16
Alignment explanation
Indices: 30505444--30505474 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
30505434 AGTCACATAA
30505444 AAAAGAA-AAAAAAGG
1 AAAAGAAGAAAAAAGG
30505459 AAAAGAAGAAAAAAGG
1 AAAAGAAGAAAAAAGG
30505475 TATATATATA
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:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (16 bp):
AAAAGAAGAAAAAAGG
Found at i:30505948 original size:26 final size:26
Alignment explanation
Indices: 30505926--30506040 Score: 117
Period size: 26 Copynumber: 4.4 Consensus size: 26
30505916 GAGCATGCCT
30505926 AGAATTGTCGCTGCAGAAACATGTCC
1 AGAATTGTCGCTGCAGAAACATGTCC
*
30505952 A-AAGTTGTCGCTGCAGAAACTTGTCC
1 AGAA-TTGTCGCTGCAGAAACATGTCC
*
30505978 AGAATTATCGCTGCATG-AACATGTCC
1 AGAATTGTCGCTGCA-GAAACATGTCC
* * * ** * *
30506004 AGAGTTGTTGCTGTATTAGCATGTCT
1 AGAATTGTCGCTGCAGAAACATGTCC
30506030 AGAATTGTCGC
1 AGAATTGTCGC
30506041 CACATCTGAT
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
25 2 0.03
26 68 0.93
27 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (26 bp):
AGAATTGTCGCTGCAGAAACATGTCC
Found at i:30506034 original size:52 final size:52
Alignment explanation
Indices: 30505917--30506040 Score: 142
Period size: 52 Copynumber: 2.4 Consensus size: 52
30505907 TCGCTACATG
*
30505917 AGCATGCCTAGAATTGTCGCTGCAGAAACATGTCCAAAGTTGTCGCTGCAGA
1 AGCATGTCTAGAATTGTCGCTGCAGAAACATGTCCAAAGTTGTCGCTGCAGA
* * * * * * * **
30505969 AACTTGTCCAGAATTATCGCTGCATG-AACATGTCCAGAGTTGTTGCTGTATT
1 AGCATGTCTAGAATTGTCGCTGCA-GAAACATGTCCAAAGTTGTCGCTGCAGA
30506021 AGCATGTCTAGAATTGTCGC
1 AGCATGTCTAGAATTGTCGC
30506041 CACATCTGAT
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
52 56 0.98
53 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (52 bp):
AGCATGTCTAGAATTGTCGCTGCAGAAACATGTCCAAAGTTGTCGCTGCAGA
Found at i:30522709 original size:15 final size:15
Alignment explanation
Indices: 30522683--30522727 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
30522673 TGTGGGTGTT
30522683 AAAGAGGAAGAAAAGA
1 AAAGA-GAAGAAAAGA
30522699 AAAGAGAAGAAGAA-A
1 AAAGAGAAGAA-AAGA
*
30522714 GAAGAGAAGAAAAG
1 AAAGAGAAGAAAAG
30522728 GAAGCAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 2 0.08
15 17 0.65
16 7 0.27
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (15 bp):
AAAGAGAAGAAAAGA
Found at i:30528380 original size:17 final size:18
Alignment explanation
Indices: 30528341--30528387 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
30528331 GAGTTTGTTG
30528341 TAAAGAGCATAAATAAAAGA
1 TAAA-AGCA-AAATAAAAGA
30528361 TAAAA-CAAAATAGAAA-A
1 TAAAAGCAAAATA-AAAGA
30528378 TAAAAGCAAA
1 TAAAAGCAAA
30528388 GGTTTGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.44
18 9 0.36
19 1 0.04
20 4 0.16
ACGTcount: A:0.70, C:0.06, G:0.11, T:0.13
Consensus pattern (18 bp):
TAAAAGCAAAATAAAAGA
Found at i:30549778 original size:21 final size:21
Alignment explanation
Indices: 30549752--30549814 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
30549742 CAAAAAATGA
*
30549752 CAAAAAGTGTCGATACCTTTT
1 CAAAAAGTATCGATACCTTTT
*
30549773 CAAAAAGTATCTATACCTTTT
1 CAAAAAGTATCGATACCTTTT
30549794 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTATCGATACCTTTT
30549815 ATTAGGTATC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (21 bp):
CAAAAAGTATCGATACCTTTT
Found at i:30553694 original size:28 final size:27
Alignment explanation
Indices: 30553619--30553699 Score: 126
Period size: 27 Copynumber: 3.0 Consensus size: 27
30553609 AGAGTGATAC
*
30553619 TCTGATATAGCTCAGGTAGAGCTTTGA
1 TCTGTTATAGCTCAGGTAGAGCTTTGA
*
30553646 TCTGTTATAGCTCAGGAAGAGCTTTGA
1 TCTGTTATAGCTCAGGTAGAGCTTTGA
*
30553673 TCTGTTTATAGCTCGGGTAGAGCTTTG
1 TCTG-TTATAGCTCAGGTAGAGCTTTG
30553700 GTTGGCTTAC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 29 0.59
28 20 0.41
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (27 bp):
TCTGTTATAGCTCAGGTAGAGCTTTGA
Found at i:30553737 original size:55 final size:55
Alignment explanation
Indices: 30553678--30553906 Score: 228
Period size: 55 Copynumber: 4.2 Consensus size: 55
30553668 TTTGATCTGT
** * * * *
30553678 TTATAGCTCGGGTAGAGCTTTGG-TTGGCTTACATCTCAGTTAGAGCCTAAAGATA
1 TTATAGCTCAAGTAAAGCTTTGGATT-GCTTACATCTCGGTTAGAGCGTAAAGCTA
* * * * *
30553733 TTATAGCACAAGTAAAACTTTGGATTGCTTACGTCTCGTTTAGAGTGTAAAGCTA
1 TTATAGCTCAAGTAAAGCTTTGGATTGCTTACATCTCGGTTAGAGCGTAAAGCTA
** * * * *
30553788 TTATAGCTCGGGTAAAGCTTTGGACTGCTTACGTCTCGGTTAAAGCGTAAAGCTT
1 TTATAGCTCAAGTAAAGCTTTGGATTGCTTACATCTCGGTTAGAGCGTAAAGCTA
* ** *
30553843 TTATAGCTCAAGTAGAGCTTTGG-TCTGCTTACATCTCGGTTAGAATGTAAATCTA
1 TTATAGCTCAAGTAAAGCTTTGGAT-TGCTTACATCTCGGTTAGAGCGTAAAGCTA
*
30553898 TTTTAGCTC
1 TTATAGCTC
30553907 GAGAGGAGCA
Statistics
Matches: 141, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
55 139 0.99
56 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (55 bp):
TTATAGCTCAAGTAAAGCTTTGGATTGCTTACATCTCGGTTAGAGCGTAAAGCTA
Found at i:30553807 original size:110 final size:110
Alignment explanation
Indices: 30553678--30553907 Score: 284
Period size: 110 Copynumber: 2.1 Consensus size: 110
30553668 TTTGATCTGT
* * *
30553678 TTATAGCTCGGGTAGAGCTTTGG-TTGGCTTACATCTCAGTTAGAGCCTAAAGATATTATAGCAC
1 TTATAGCTCGGGTAAAGCTTTGGACT-GCTTACATCTCAGTTAAAGCCTAAAGATATTATAGCAC
* * *
30553742 AAGTAAAACTTTGGAT-TGCTTACGTCTCGTTTAGAGTGTAAAGCTA
65 AAGTAAAACTTTGG-TCTGCTTACATCTCGGTTAGAATGTAAAGCTA
* * * * * *
30553788 TTATAGCTCGGGTAAAGCTTTGGACTGCTTACGTCTCGGTTAAAGCGTAAAGCTTTTATAGCTCA
1 TTATAGCTCGGGTAAAGCTTTGGACTGCTTACATCTCAGTTAAAGCCTAAAGATATTATAGCACA
* * *
30553853 AGTAGAGCTTTGGTCTGCTTACATCTCGGTTAGAATGTAAATCTA
66 AGTAAAACTTTGGTCTGCTTACATCTCGGTTAGAATGTAAAGCTA
*
30553898 TTTTAGCTCG
1 TTATAGCTCG
30553908 AGAGGAGCAT
Statistics
Matches: 102, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
109 1 0.01
110 100 0.98
111 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.35
Consensus pattern (110 bp):
TTATAGCTCGGGTAAAGCTTTGGACTGCTTACATCTCAGTTAAAGCCTAAAGATATTATAGCACA
AGTAAAACTTTGGTCTGCTTACATCTCGGTTAGAATGTAAAGCTA
Found at i:30567860 original size:9 final size:9
Alignment explanation
Indices: 30567846--30567871 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
30567836 CAAGATTTGG
30567846 TTTCTTGAT
1 TTTCTTGAT
30567855 TTTCTTGAT
1 TTTCTTGAT
30567864 TTTCTTGA
1 TTTCTTGA
30567872 AAACAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (9 bp):
TTTCTTGAT
Found at i:30572897 original size:23 final size:23
Alignment explanation
Indices: 30572849--30572900 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
30572839 CACCAACATA
** *
30572849 ATTAAGCTATGGTTAAATTTCTC
1 ATTAAGCTATGGTTAAATCACAC
30572872 ATTAAG-TCATGGTTAAATCACAC
1 ATTAAGCT-ATGGTTAAATCACAC
30572895 ATTAAG
1 ATTAAG
30572901 GATTTTGCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (23 bp):
ATTAAGCTATGGTTAAATCACAC
Found at i:30577565 original size:11 final size:11
Alignment explanation
Indices: 30577490--30577565 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
30577480 ATTCCAAAAA
*
30577490 TAATATTATTT
1 TAATATTAATT
30577501 TAATAGTTTAATAT
1 TAATA--TTAAT-T
30577515 TAA-ATTAAATT
1 TAATATT-AATT
*
30577526 TAATACTTATTT
1 TAATA-TTAATT
30577538 TAATATT-ATT
1 TAATATTAATT
30577548 T--TATTAATT
1 TAATATTAATT
30577557 TAATATTAA
1 TAATATTAA
30577566 AGTGATTATC
Statistics
Matches: 53, Mismatches: 3, Indels: 18
0.72 0.04 0.24
Matches are distributed among these distances:
8 4 0.08
9 4 0.08
10 3 0.06
11 19 0.36
12 12 0.23
13 7 0.13
14 4 0.08
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:30586022 original size:40 final size:40
Alignment explanation
Indices: 30585911--30586024 Score: 176
Period size: 40 Copynumber: 2.9 Consensus size: 40
30585901 TTTACAAATT
* *
30585911 CACCGGCTCATAGCCTGCTAAGTCGT-ACTTGAATCTTTA
1 CACCAGCTCATAGCCTGCTAAGTCGTAACTTGAATCTTAA
* *
30585950 CACCAGCTCATAGCCTGCTAAGCCGTAGCTTGAATCTTAA
1 CACCAGCTCATAGCCTGCTAAGTCGTAACTTGAATCTTAA
*
30585990 CACCAGCTCATAGCCTGCTAAGTCATAACTTGAAT
1 CACCAGCTCATAGCCTGCTAAGTCGTAACTTGAAT
30586025 TATATCGTAA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
39 24 0.36
40 43 0.64
ACGTcount: A:0.27, C:0.29, G:0.17, T:0.27
Consensus pattern (40 bp):
CACCAGCTCATAGCCTGCTAAGTCGTAACTTGAATCTTAA
Found at i:30588355 original size:25 final size:26
Alignment explanation
Indices: 30588307--30588355 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
30588297 TATAAAATAT
*
30588307 TAACAATTTAAAATAAATTAAAAAGC
1 TAACAATTTAAAACAAATTAAAAAGC
30588333 TAACAATTT-AAACAAATTAAAAA
1 TAACAATTTAAAACAAATTAAAAA
30588356 TTAGGAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (26 bp):
TAACAATTTAAAACAAATTAAAAAGC
Found at i:30599307 original size:51 final size:51
Alignment explanation
Indices: 30599230--30599458 Score: 327
Period size: 51 Copynumber: 4.5 Consensus size: 51
30599220 CTTTGTTCCG
* * * * **
30599230 CACGATGACA-TTGAGTCATC-GAACCTTTAATTCGTCATGCATTTGTTTACT
1 CACGATGACACTT-AGTCATCAG-ACCTTTAATCCGTAAAGGATTCATTTACT
* * *
30599281 CACAATGATACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATTTATT
1 CACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATTTACT
30599332 CACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATTTACT
1 CACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATTTACT
*
30599383 CATGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATTTACT
1 CACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATTTACT
*
30599434 CACGATGACACTTAGTCATCGGACC
1 CACGATGACACTTAGTCATCAGACC
30599459 CTTTCGTTTA
Statistics
Matches: 161, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
51 158 0.98
52 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
CACGATGACACTTAGTCATCAGACCTTTAATCCGTAAAGGATTCATTTACT
Found at i:30606631 original size:51 final size:51
Alignment explanation
Indices: 30606505--30606740 Score: 242
Period size: 51 Copynumber: 4.6 Consensus size: 51
30606495 TTTCATTTAA
* * ** * * *
30606505 TACTCACGAAGACA-TATAGTCATCGGACCGCTTTGTTTCGTATAGGAATTTATA
1 TACTCACGATGACACT-TAGTCATCAGA-C-CTTTAATTCGTAAAGG-ATTCATT
* * * * * * *
30606559 TACTTACGATGACACTGAGTCATCGGACCTTTAATTCGTCATGAATCCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATTCGTAAAGGATTCATT
* * *
30606610 TACTCACGATGATACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATTCGTAAAGGATTCATT
* *
30606661 TACTCACGATGACACTAAGTCATCAGACCTTTAA-TCTGTTAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCAGACCTTTAATTC-GTAAAGGATTCATT
30606712 TACTCACGATGACACTTAGTCATCAGACC
1 TACTCACGATGACACTTAGTCATCAGACC
30606741 CTTTCGTTTA
Statistics
Matches: 154, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
50 1 0.01
51 119 0.77
52 10 0.06
53 1 0.01
54 22 0.14
55 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCAGACCTTTAATTCGTAAAGGATTCATT
Found at i:30610790 original size:59 final size:59
Alignment explanation
Indices: 30610698--30610815 Score: 236
Period size: 59 Copynumber: 2.0 Consensus size: 59
30610688 TTTATACGGG
30610698 GAGAAGTGTCATATATTCACAGATCATAAAAGTTTAAGGTATCTGATGACTCAGAAGGA
1 GAGAAGTGTCATATATTCACAGATCATAAAAGTTTAAGGTATCTGATGACTCAGAAGGA
30610757 GAGAAGTGTCATATATTCACAGATCATAAAAGTTTAAGGTATCTGATGACTCAGAAGGA
1 GAGAAGTGTCATATATTCACAGATCATAAAAGTTTAAGGTATCTGATGACTCAGAAGGA
30610816 ACTGAATTTT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (59 bp):
GAGAAGTGTCATATATTCACAGATCATAAAAGTTTAAGGTATCTGATGACTCAGAAGGA
Found at i:30613693 original size:51 final size:51
Alignment explanation
Indices: 30613630--30613918 Score: 337
Period size: 51 Copynumber: 5.6 Consensus size: 51
30613620 CTATAAACGA
* * *
30613630 AAAGGTCTGATGACTAAGTGTCATCGTGAGGAAATGAATCATTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
30613681 AAAGGTCCGATGACTAAGTATTATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
30613732 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAGTCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * ** * *
30613783 AAATGTCCGATGTCTAAGTGTCATCGTGAGTAAATGACTCAATAATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* ** * * * **
30613834 AAGGGTCCGATGACTTTGTGTCATCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
*
30613886 AAGAGGTCCGATGACTATA-TGTCATTGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
30613919 TTAAATGAAA
Statistics
Matches: 201, Mismatches: 34, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
51 167 0.83
52 9 0.04
53 25 0.12
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.31
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:30616018 original size:17 final size:17
Alignment explanation
Indices: 30615998--30616074 Score: 120
Period size: 17 Copynumber: 4.6 Consensus size: 17
30615988 CCAAATAGAA
30615998 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
30616015 TTTAAGTTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
30616032 TTGAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
30616049 TTGAAATTTAAATTTA-
1 TTTAAATTTAAATTTAT
30616065 TTTAAATTTA
1 TTTAAATTTA
30616075 TTAATGTCCC
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
16 9 0.16
17 47 0.84
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:30616057 original size:7 final size:6
Alignment explanation
Indices: 30615996--30616074 Score: 73
Period size: 6 Copynumber: 14.0 Consensus size: 6
30615986 ACCCAAATAG
* *
30615996 AATTTA AATTTA AATTT- ATTTTA AGTTTA AATTT- -ATTTGA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA
30616042 AATTT- -ATTTGA AATTTA AATTT- -ATTTA AATTTA
1 AATTTA AATTT-A AATTTA AATTTA AATTTA AATTTA
30616075 TTAATGTCCC
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
4 12 0.20
5 4 0.07
6 37 0.61
7 8 0.13
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:30616067 original size:10 final size:10
Alignment explanation
Indices: 30616021--30616076 Score: 52
Period size: 10 Copynumber: 6.2 Consensus size: 10
30616011 TTATTTTAAG
30616021 TTTAAATTTA
1 TTTAAATTTA
*
30616031 TTTGAA---A
1 TTTAAATTTA
30616038 TTTAAATTTA
1 TTTAAATTTA
*
30616048 TTTGAA---A
1 TTTAAATTTA
30616055 TTTAAATTTA
1 TTTAAATTTA
30616065 TTTAAATTTA
1 TTTAAATTTA
30616075 TT
1 TT
30616077 AATGTCCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
7 12 0.33
10 24 0.67
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:30616148 original size:19 final size:20
Alignment explanation
Indices: 30616108--30616149 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
30616098 TGAGTCCAAA
*
30616108 CAATTACAAGTCCAATGGCC
1 CAATTACAAGACCAATGGCC
*
30616128 CAATTACATGACCAA-GGCC
1 CAATTACAAGACCAATGGCC
30616147 CAA
1 CAA
30616150 AAATACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.38, C:0.31, G:0.14, T:0.17
Consensus pattern (20 bp):
CAATTACAAGACCAATGGCC
Found at i:30616455 original size:15 final size:17
Alignment explanation
Indices: 30616432--30616464 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
30616422 AATCATTAGG
30616432 AAGCAAATC-AGTTTCC
1 AAGCAAATCAAGTTTCC
30616448 AAGC-AATCAAGTTTCC
1 AAGCAAATCAAGTTTCC
30616464 A
1 A
30616465 TTCAAGCGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (17 bp):
AAGCAAATCAAGTTTCC
Found at i:30617495 original size:30 final size:29
Alignment explanation
Indices: 30617461--30617784 Score: 222
Period size: 30 Copynumber: 10.9 Consensus size: 29
30617451 TTAACCCTCC
*
30617461 AACTTTGCAAAAATTACATTTTAACCCCTA
1 AACTTT-CTAAAATTACATTTTAACCCCTA
* * **
30617491 AACTTCACAAAAATTACATTTTAACCTTTA
1 AACTT-TCTAAAATTACATTTTAACCCCTA
** *
30617521 TATTTTTCTAAAATTACATTTTAACCCTTA
1 -AACTTTCTAAAATTACATTTTAACCCCTA
*
30617551 AACTTCTTTAAAATTACATTTTAACCCC-A
1 AACTT-TCTAAAATTACATTTTAACCCCTA
**
30617580 AACTTTCCTAAAACCACATTTTAACCCC-A
1 AACTTT-CTAAAATTACATTTTAACCCCTA
* *
30617609 AACTTTCTTAAAATCACATTTTTTACCCCTA
1 AACTTTC-TAAAATTACA-TTTTAACCCCTA
* * * *
30617640 CACTTTTTCAAAATTACATTTTAACCCTTG
1 AACTTTCT-AAAATTACATTTTAACCCCTA
* * * * * * * *
30617670 AACTTTTTTGAAAGTGCATTTTGATCTCAA
1 AAC-TTTCTAAAATTACATTTTAACCCCTA
* * *
30617700 TAATTTTCCAAAATTACATTTTGA-CCCTA
1 -AACTTTCTAAAATTACATTTTAACCCCTA
*
30617729 AACTTCTCTAAAATTACATTTTTACCCCTA
1 AACTT-TCTAAAATTACATTTTAACCCCTA
* * **
30617759 AGCTTTTCCAAAATTATGTTTTAACC
1 AAC-TTTCTAAAATTACATTTTAACC
30617785 TTGAATTCTC
Statistics
Matches: 232, Mismatches: 49, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
28 6 0.03
29 62 0.27
30 138 0.59
31 26 0.11
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (29 bp):
AACTTTCTAAAATTACATTTTAACCCCTA
Found at i:30617661 original size:119 final size:119
Alignment explanation
Indices: 30617476--30617784 Score: 306
Period size: 119 Copynumber: 2.6 Consensus size: 119
30617466 TGCAAAAATT
* * * * **
30617476 ACATTTTAACCCCTAAACTTCACAAAAATTACATTTTAACCTTTATA--TTTTTCTAAAATTACA
1 ACATTTTAACCCC-AAACTTCTCTAAAATCACATTTTTACCCCTA-AGCTTTTTC-AAAATTACA
* *
30617539 TTTTAACCCTTAAACTTCTTTAAAATTACATTTT-AACCCCA-AACTTTCCTAAAACC
63 TTTTAACCCTTAAACTTCTTTAAAAGTACATTTTGAACCCAATAACTTTCC-AAAACC
30617595 ACATTTTAACCCCAAACTT-TCTTAAAATCACATTTTTTACCCCTACA-CTTTTTCAAAATTACA
1 ACATTTTAACCCCAAACTTCTC-TAAAATCACA-TTTTTACCCCTA-AGCTTTTTCAAAATTACA
* * * * * * * **
30617658 TTTTAACCCTTGAACTTTTTTGAAAGTGCATTTTGATCTCAATAATTTTCCAAAATT
63 TTTTAACCCTTAAACTTCTTTAAAAGTACATTTTGAACCCAATAACTTTCCAAAACC
* * * * **
30617715 ACATTTTGACCCTAAACTTCTCTAAAATTACATTTTTACCCCTAAGCTTTTCCAAAATTATGTTT
1 ACATTTTAACCCCAAACTTCTCTAAAATCACATTTTTACCCCTAAGCTTTTTCAAAATTACATTT
30617780 TAACC
66 TAACC
30617785 TTGAATTCTC
Statistics
Matches: 159, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
117 1 0.01
118 15 0.09
119 94 0.59
120 40 0.25
121 9 0.06
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (119 bp):
ACATTTTAACCCCAAACTTCTCTAAAATCACATTTTTACCCCTAAGCTTTTTCAAAATTACATTT
TAACCCTTAAACTTCTTTAAAAGTACATTTTGAACCCAATAACTTTCCAAAACC
Found at i:30617663 original size:60 final size:58
Alignment explanation
Indices: 30617470--30617784 Score: 258
Period size: 60 Copynumber: 5.3 Consensus size: 58
30617460 CAACTTTGCA
** ** * *
30617470 AAAATTACATTTTAACCCCTAAACTTCACAAAAATTACATTTTAACCTTTATATTTTTCT
1 AAAATTACATTTTAA-CCCTAAACTTC-TTAAAATTACATTTTAACCCCTATACTTTTCC
*
30617530 AAAATTACATTTTAACCCTTAAACTTCTTTAAAATTACATTTTAACCCC-AAAC-TTTCC
1 AAAATTACATTTTAACCC-TAAACTTC-TTAAAATTACATTTTAACCCCTATACTTTTCC
** * * * * *
30617588 TAAAACCACATTTTAACCCCAAACTTTCTTAAAATCACATTTTTTACCCCTACACTTTTTC
1 -AAAATTACATTTTAACCCTAAAC-TTCTTAAAATTACA-TTTTAACCCCTATACTTTTCC
* * * * * * * * * *
30617649 AAAATTACATTTTAACCCTTGAACTTTTTTGAAAGTGCATTTTGATCTCAATAATTTTCC
1 AAAATTACATTTTAACCC-TAAAC-TTCTTAAAATTACATTTTAACCCCTATACTTTTCC
* *
30617709 AAAATTACATTTTGACCCTAAACTTCTCTAAAATTACATTTTTACCCCTA-AGCTTTTCC
1 AAAATTACATTTTAACCCTAAACTTCT-TAAAATTACATTTTAACCCCTATA-CTTTTCC
**
30617768 AAAATTATGTTTTAACC
1 AAAATTACATTTTAACC
30617785 TTGAATTCTC
Statistics
Matches: 201, Mismatches: 45, Indels: 19
0.76 0.17 0.07
Matches are distributed among these distances:
58 22 0.11
59 72 0.36
60 90 0.45
61 17 0.08
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (58 bp):
AAAATTACATTTTAACCCTAAACTTCTTAAAATTACATTTTAACCCCTATACTTTTCC
Found at i:30617883 original size:19 final size:19
Alignment explanation
Indices: 30617850--30617890 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
30617840 TGTATATAAA
30617850 TTTTAATTATTATCCTTTATT
1 TTTTAATTA-TATCCTTT-TT
30617871 TTTTAATTA-ATCCTTTTT
1 TTTTAATTATATCCTTTTT
30617889 TT
1 TT
30617891 ATTTTGATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 7 0.35
21 9 0.45
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTAATTATATCCTTTTT
Found at i:30617895 original size:21 final size:21
Alignment explanation
Indices: 30617849--30617895 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
30617839 TTGTATATAA
30617849 ATTTTAATTATTATCCTTTATT
1 ATTTTAATTA-TATCCTTTATT
*
30617871 -TTTTAATTA-ATCCTTTTTTT
1 ATTTTAATTATATCC-TTTATT
30617891 ATTTT
1 ATTTT
30617896 GATTCGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 4 0.18
20 5 0.23
21 13 0.59
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.68
Consensus pattern (21 bp):
ATTTTAATTATATCCTTTATT
Found at i:30629697 original size:39 final size:39
Alignment explanation
Indices: 30629646--30630608 Score: 376
Period size: 39 Copynumber: 24.7 Consensus size: 39
30629636 AAGATTTTGT
* * *
30629646 TCTCCTACCCCGATCATGGGGCAGATCACAGTCATCCGA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* * *
30629685 TCTTTTACCCCGAGCTTGGGGCAGATCACCA-TCAACCAA
1 TCTCTTACCCCGAGCATGGGGCAGATCA-CAGTCATCCAA
* * * * ** * * *
30629724 TCTCTTACCCCAAGCCTAGGGCAAATTGCAGCCATTCGA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* ** * * *
30629763 TCTTTTACCTTGAGCTTGGGGTAGATCACCA-TCAACCAA
1 TCTCTTACCCCGAGCATGGGGCAGATCA-CAGTCATCCAA
* ** * *
30629802 TCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* * * * *
30629841 TCTTTTACCTCAAGCCTGGGGCAGATCACCA-TCAACCAA
1 TCTCTTACCCCGAGCATGGGGCAGATCA-CAGTCATCCAA
* * * * ** * * *
30629880 TCTCTTACCCTGAGCTTAGGGTAGATTGCAGCCGTCCGA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* *
30629919 TCTCTTACCTCGAGCCTGGGGCAGATCACCA-TCAGT-CAA
1 TCTCTTACCCCGAGCATGGGGCAGATCA-CAGTCA-TCCAA
* * * * * * * *
30629958 TCTCTTACCCTGAGCCTGGGGAAGATTACA-ACTGTTCGA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTC-ATCCAA
* * * *
30629997 TCTCTTACCCCAAGCCTGCGGCAGATCATCA-TCAACCAA
1 TCTCTTACCCCGAGCATGGGGCAGATCA-CAGTCATCCAA
* * ** ** *
30630036 TCTCTTACCCCGAGCCTGGGGCATATTGCAACCATCCGA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* * * * ** * * *
30630075 TCTTTTACCTCGAGCTTAGGATAGATCACTA-TTAGCTAAA
1 TCTCTTACCCCGAGCATGGGGCAGATCAC-AGTCATC-CAA
* * ** *
30630115 TCTCTTACCCCGAGCTTAGGGCAGATTGCAG-C-TACTCGA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCAT-C-CAA
** * * *
30630154 TCTCTTACCCAAAGCCTAGGGCAGATCACCA-TCAACCAA
1 TCTCTTACCCCGAGCATGGGGCAGATCA-CAGTCATCCAA
* * * ** ** *
30630193 TCTCTTATCCCGAGCTTGGGGCAAATTGCAACCATCCGA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* * ** * * *
30630232 TCTTTTACCCCGATCATAAGGAAGATCACCGTCAACCAA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* ** ** *
30630271 TCTCTTACCCAAC-AACA-GGGGCAGATTGCAACCATCCGA
1 TCTCTTACCC--CGAGCATGGGGCAGATCACAGTCATCCAA
* * * * *
30630310 TCTTTTACCCCGATCATGGGGCAGATCACTGTCAGCTAA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* * * ** * *
30630349 TCTCTTACCCCGCAACA-GAGGCTGATTGCAGCCATCCGA
1 TCTCTTACCCCG-AGCATGGGGCAGATCACAGTCATCCAA
* * * * *
30630388 TCTTTTACCCCGATCATGGGGCAGATCACTGTCAGCTAA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* * * *
30630427 TCTCTTACCCC--GCAATAAGGGCAGATTATAGCCATCCAA
1 TCTCTTACCCCGAGC-AT-GGGGCAGATCACAGTCATCCAA
* ** * * *
30630466 TCTTTTACCCCGATTATGGGGCAGATCACCGTCAGCTAA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* ** * *
30630505 TCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
* * * * * * *
30630544 TCTTTTACCTCAAGCTTGGGACAGATCACCGTCAGCCAA
1 TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
*
30630583 TCTCTTACGCCGAGCCA-GGGGCAGAT
1 TCTCTTACCCCGAG-CATGGGGCAGAT
30630609 TACAACCCTC
Statistics
Matches: 649, Mismatches: 244, Indels: 62
0.68 0.26 0.06
Matches are distributed among these distances:
37 2 0.00
38 22 0.03
39 574 0.88
40 50 0.08
41 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (39 bp):
TCTCTTACCCCGAGCATGGGGCAGATCACAGTCATCCAA
Found at i:30629764 original size:78 final size:78
Alignment explanation
Indices: 30629646--30630609 Score: 850
Period size: 78 Copynumber: 12.3 Consensus size: 78
30629636 AAGATTTTGT
* * * * ** *
30629646 TCTCCTACCCCGATCATGGGGCAGATCACAGTCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
1 TCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
30629711 CACCATCAACCAA
66 CACCATCAACCAA
* * * ** *
30629724 TCTCTTACCCCAAGCCTAGGGCAAATTGCAGCCATTCGATCTTTTACCTTGAGCTTGGGGTAGAT
1 TCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
30629789 CACCATCAACCAA
66 CACCATCAACCAA
* * * * *
30629802 TCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCTCAAGCCTGGGGCAGAT
1 TCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
30629867 CACCATCAACCAA
66 CACCATCAACCAA
* * * * * * *
30629880 TCTCTTACCCTGAGCTTAGGGTAGATTGCAGCCGTCCGATCTCTTACCTCGAGCCTGGGGCAGAT
1 TCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
**
30629945 CACCATCAGTCAA
66 CACCATCAACCAA
* * * * * ** * * * * *
30629958 TCTCTTACCCTGAGCCTGGGGAAGATTACAACTGTTCGATCTCTTACCCCAAGCCTGCGGCAGAT
1 TCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
*
30630023 CATCATCAACCAA
66 CACCATCAACCAA
* * * * * **
30630036 TCTCTTACCCCGAGCCTGGGGCATATTGCAACCATCCGATCTTTTACCTCGAGCTTAGGATAGAT
1 TCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
* * * *
30630101 CACTATTAGCTAAA
66 CACCATCAAC-CAA
* * * ** * *
30630115 TCTCTTACCCCGAGCTTAGGGCAGATTGCAGCTA-CTCGATCTCTTACCCAAAGCCTAGGGCAGA
1 TCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATC-CGATCTTTTACCCCGAGCTTGGGGCAGA
30630179 TCACCATCAACCAA
65 TCACCATCAACCAA
* * * * * * * ** *
30630193 TCTCTTATCCCGAGCTTGGGGCAAATTGCAACCATCCGATCTTTTACCCCGATCATAAGGAAGAT
1 TCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
*
30630258 CACCGTCAACCAA
66 CACCATCAACCAA
* * * *
30630271 TCTCTTACCCAAC-A-AC-AGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGGCA
1 TCTCTTACCC--CGAGCCTA-GGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCA
** * *
30630333 GATCACTGTCAGCTAA
63 GATCACCATCAACCAA
* * * *
30630349 TCTCTTACCCCGCA-AC-AGAGGCTGATTGCAGCCATCCGATCTTTTACCCCGATCATGGGGCAG
1 TCTCTTACCCCG-AGCCTAG-GGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAG
** * *
30630412 ATCACTGTCAGCTAA
64 ATCACCATCAACCAA
* ** * *
30630427 TCTCTTACCCC--GCAATAAGGGCAGATTATAGCCATCCAATCTTTTACCCCGA-TTATGGGGCA
1 TCTCTTACCCCGAGC-CT-AGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCT-TGGGGCA
* * *
30630489 GATCACCGTCAGCTAA
63 GATCACCATCAACCAA
* * * * *
30630505 TCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCTCAAGCTTGGGACAGAT
1 TCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
* *
30630570 CACCGTCAGCCAA
66 CACCATCAACCAA
*
30630583 TCTCTTACGCCGAGCC-AGGGGCAGATT
1 TCTCTTACCCCGAGCCTA-GGGCAGATT
30630610 ACAACCCTCT
Statistics
Matches: 741, Mismatches: 127, Indels: 36
0.82 0.14 0.04
Matches are distributed among these distances:
76 1 0.00
77 1 0.00
78 670 0.90
79 66 0.09
80 3 0.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (78 bp):
TCTCTTACCCCGAGCCTAGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
CACCATCAACCAA
Found at i:30629939 original size:156 final size:156
Alignment explanation
Indices: 30629646--30630612 Score: 947
Period size: 156 Copynumber: 6.2 Consensus size: 156
30629636 AAGATTTTGT
* * * * * * *
30629646 TCTCCTACCCCGATCATGGGGCAGATCACAGTCATCCGATCTTTTACCCCGAGCTTGGGGCAGAT
1 TCTCTTACCCCGAGCTTGGGGCAGATTACAGCCATCCGATCTTTTACCCCAAGCCTGGGGCAGAT
* * * * *
30629711 CACCATCAACCAATCTCTTACCCCAAGCCTAGGGCAAATTGCAGCCATTCGATCTTTTACCTTGA
66 CACCATCAACCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACCTCGA
* *
30629776 GCTTGGGGTAGATCACCATCAACCAA
131 GCTTGGGGCAGATCACCATCAGCCAA
* *
30629802 TCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCTCAAGCCTGGGGCAGAT
1 TCTCTTACCCCGAGCTTGGGGCAGATTACAGCCATCCGATCTTTTACCCCAAGCCTGGGGCAGAT
* * * *
30629867 CACCATCAACCAATCTCTTACCCTGAGCTTAGGGTAGATTGCAGCCGTCCGATCTCTTACCTCGA
66 CACCATCAACCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACCTCGA
* *
30629932 GCCTGGGGCAGATCACCATCAGTCAA
131 GCTTGGGGCAGATCACCATCAGCCAA
* * * * ** * * *
30629958 TCTCTTACCCTGAGCCTGGGGAAGATTACAACTGTTCGATCTCTTACCCCAAGCCTGCGGCAGAT
1 TCTCTTACCCCGAGCTTGGGGCAGATTACAGCCATCCGATCTTTTACCCCAAGCCTGGGGCAGAT
* * * * *
30630023 CATCATCAACCAATCTCTTACCCCGAGCCTGGGGCATATTGCAACCATCCGATCTTTTACCTCGA
66 CACCATCAACCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACCTCGA
* ** * * *
30630088 GCTTAGGATAGATCACTATTAGCTAAA
131 GCTTGGGGCAGATCACCATCAGC-CAA
* * * * * *
30630115 TCTCTTACCCCGAGCTTAGGGCAGATTGCAGCTA-CTCGATCTCTTACCCAAAGCCTAGGGCAGA
1 TCTCTTACCCCGAGCTTGGGGCAGATTACAGCCATC-CGATCTTTTACCCCAAGCCTGGGGCAGA
* * * * *
30630179 TCACCATCAACCAATCTCTTATCCCGAGCTTGGGGCAAATTGCAACCATCCGATCTTTTACCCCG
65 TCACCATCAACCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACCTCG
* * ** * * *
30630244 ATCATAAGGAAGATCACCGTCAACCAA
130 AGCTTGGGGCAGATCACCATCAGCCAA
* * * * * * *
30630271 TCTCTTACCCAAC-AAC-AGGGGCAGATTGCAACCATCCGATCTTTTACCCCGATCATGGGGCAG
1 TCTCTTACCC--CGAGCTTGGGGCAGATTACAGCCATCCGATCTTTTACCCCAAGCCTGGGGCAG
** * * * *
30630334 ATCACTGTCAGCTAATCTCTTACCCCGCAAC--AGAGGCTGATTGCAGCCATCCGATCTTTTACC
64 ATCACCATCAACCAATCTCTTACCCCG-AGCTTAG-GGCAGATTGCAGCCATCCGATCTTTTACC
* * * ** *
30630397 CCGATCATGGGGCAGATCACTGTCAGCTAA
127 TCGAGCTTGGGGCAGATCACCATCAGCCAA
* ** * * * ***
30630427 TCTCTTACCCCGCA-ATAAGGGCAGATTATAGCCATCCAATCTTTTACCCCGATTATGGGGCAGA
1 TCTCTTACCCCG-AGCTTGGGGCAGATTACAGCCATCCGATCTTTTACCCCAAGCCTGGGGCAGA
* * * * *
30630491 TCACCGTCAGCTAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCTCA
65 TCACCATCAACCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACCTCG
* *
30630556 AGCTTGGGACAGATCACCGTCAGCCAA
130 AGCTTGGGGCAGATCACCATCAGCCAA
* **
30630583 TCTCTTACGCCGAGCCAGGGGCAGATTACA
1 TCTCTTACCCCGAGCTTGGGGCAGATTACA
30630613 ACCCTCTAAT
Statistics
Matches: 672, Mismatches: 126, Indels: 26
0.82 0.15 0.03
Matches are distributed among these distances:
154 1 0.00
155 4 0.01
156 531 0.79
157 135 0.20
158 1 0.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.24
Consensus pattern (156 bp):
TCTCTTACCCCGAGCTTGGGGCAGATTACAGCCATCCGATCTTTTACCCCAAGCCTGGGGCAGAT
CACCATCAACCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGCCATCCGATCTTTTACCTCGA
GCTTGGGGCAGATCACCATCAGCCAA
Found at i:30631108 original size:6 final size:6
Alignment explanation
Indices: 30631097--30631164 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
30631087 ACCCAAACAG
* * *
30631097 AATTTA AATTTA AATTT- ATTTTA AGTTGA AATTT- -ATTTGA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA
*
30631143 AGTTTA AATTT- -ATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA
30631165 TTAATGTCCC
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
4 8 0.16
5 4 0.08
6 33 0.67
7 4 0.08
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (6 bp):
AATTTA
Found at i:30631142 original size:23 final size:22
Alignment explanation
Indices: 30631116--30631164 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
30631106 TTAAATTTAT
30631116 TTTAAGTTGAAATTTATTTGAAA
1 TTTAAGTTGAAATTTATTT-AAA
*
30631139 TTTAAGTTTAAATTTATTTAAA
1 TTTAAGTTGAAATTTATTTAAA
30631161 TTTA
1 TTTA
30631165 TTAATGTCCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (22 bp):
TTTAAGTTGAAATTTATTTAAA
Found at i:30631148 original size:17 final size:16
Alignment explanation
Indices: 30631098--30631166 Score: 61
Period size: 17 Copynumber: 4.2 Consensus size: 16
30631088 CCCAAACAGA
30631098 ATTTAAATTTAAATTT
1 ATTTAAATTTAAATTT
* *
30631114 ATTTTAAGTTGAAATTT
1 A-TTTAAATTTAAATTT
*
30631131 ATTTGAAATTTAAGTTT
1 ATTT-AAATTTAAATTT
30631148 AAATTT--ATTTAAATTT
1 --ATTTAAATTTAAATTT
30631164 ATT
1 ATT
30631167 AATGTCCCTT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 3 0.07
16 13 0.30
17 23 0.53
19 4 0.09
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
ATTTAAATTTAAATTT
Found at i:30631160 original size:10 final size:10
Alignment explanation
Indices: 30631125--30631166 Score: 57
Period size: 10 Copynumber: 3.9 Consensus size: 10
30631115 TTTTAAGTTG
30631125 AAATTTATTT
1 AAATTTATTT
30631135 GAAATTTAAGTTT
1 -AAATTT-A-TTT
30631148 AAATTTATTT
1 AAATTTATTT
30631158 AAATTTATT
1 AAATTTATT
30631167 AATGTCCCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 12 0.41
11 7 0.24
12 7 0.24
13 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (10 bp):
AAATTTATTT
Found at i:30631223 original size:20 final size:19
Alignment explanation
Indices: 30631198--30631238 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
30631188 TGAGTCCAAA
*
30631198 CAATTACAAGCCCAATGGCC
1 CAATTACAAGACCAA-GGCC
*
30631218 CAATTACATGACCAAGGCC
1 CAATTACAAGACCAAGGCC
30631237 CA
1 CA
30631239 TAAGGCCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.37, C:0.34, G:0.15, T:0.15
Consensus pattern (19 bp):
CAATTACAAGACCAAGGCC
Found at i:30631543 original size:16 final size:16
Alignment explanation
Indices: 30631524--30631556 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30631514 ATCATCAGAG
30631524 AAGCAAATC-AGTTTCC
1 AAGC-AATCAAGTTTCC
30631540 AAGCAATCAAGTTTCC
1 AAGCAATCAAGTTTCC
30631556 A
1 A
30631557 TTCAAGCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (16 bp):
AAGCAATCAAGTTTCC
Found at i:30632722 original size:29 final size:29
Alignment explanation
Indices: 30632645--30632865 Score: 191
Period size: 29 Copynumber: 7.6 Consensus size: 29
30632635 GAACTTTGTA
* * *
30632645 AAAATTACATTTTGACCCTCAAA-TTTCAT
1 AAAACTACATTTTAACCCT-AAACTTTCCT
* * *
30632674 AAAAAATATATTTTGACCCTAAACTTTCCT
1 -AAAACTACATTTTAACCCTAAACTTTCCT
* * *
30632704 AAAACCACACTTTAACCCTAAACTTTCCC
1 AAAACTACATTTTAACCCTAAACTTTCCT
* *
30632733 AAAATTACATTTTAACCCCAAACTTT-CT
1 AAAACTACATTTTAACCCTAAACTTTCCT
* * *
30632761 CAAAACCACACTTTAACCCCAAACTTTCC-
1 -AAAACTACATTTTAACCCTAAACTTTCCT
*
30632790 AAAAGTACATTTTAACCCTAAAC-TTCTCT
1 AAAACTACATTTTAACCCTAAACTTTC-CT
* *
30632819 AAAATTACATTTTTACCCTTAAACTTTTCC-
1 AAAACTACATTTTAACCC-TAAAC-TTTCCT
*
30632849 AAAATTACATTTTAACC
1 AAAACTACATTTTAACC
30632866 TCAAATTCTC
Statistics
Matches: 159, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
27 3 0.02
28 21 0.13
29 87 0.55
30 44 0.28
31 1 0.01
32 3 0.02
ACGTcount: A:0.38, C:0.27, G:0.01, T:0.33
Consensus pattern (29 bp):
AAAACTACATTTTAACCCTAAACTTTCCT
Found at i:30632757 original size:58 final size:57
Alignment explanation
Indices: 30632683--30632870 Score: 227
Period size: 58 Copynumber: 3.2 Consensus size: 57
30632673 TAAAAAATAT
* *
30632683 ATTTTGACCCTAAACTTTCCTAAAACCACACTTTAACCCTAAACTTTCCCAAAATTAC
1 ATTTTAACCCCAAACTTTCCTAAAACCACACTTTAACCCTAAACTTT-CCAAAATTAC
* *
30632741 ATTTTAACCCCAAACTTT-CTCAAAACCACACTTTAACCCCAAACTTTCCAAAAGTAC
1 ATTTTAACCCCAAACTTTCCT-AAAACCACACTTTAACCCTAAACTTTCCAAAATTAC
* ** * *
30632798 ATTTTAACCCTAAAC-TTCTCTAAAATTACATTTTTACCCTTAAACTTTTCCAAAATTAC
1 ATTTTAACCCCAAACTTTC-CTAAAACCACACTTTAACCC-TAAAC-TTTCCAAAATTAC
*
30632857 ATTTTAACCTCAAA
1 ATTTTAACCCCAAA
30632871 TTCTCCGAAA
Statistics
Matches: 112, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
56 2 0.02
57 39 0.35
58 47 0.42
59 24 0.21
ACGTcount: A:0.37, C:0.29, G:0.01, T:0.33
Consensus pattern (57 bp):
ATTTTAACCCCAAACTTTCCTAAAACCACACTTTAACCCTAAACTTTCCAAAATTAC
Found at i:30632863 original size:87 final size:87
Alignment explanation
Indices: 30632645--30632870 Score: 226
Period size: 87 Copynumber: 2.6 Consensus size: 87
30632635 GAACTTTGTA
* * ** * * *
30632645 AAAATTACATTTTGACCCTCAAA-TTTCATAAAAAATATATTTTGACCCTAAACTTTCCTAAAAC
1 AAAATTACATTTTAACCC-CAAACTTTC-TCAAAACCACATTTTAACCCCAAACTTTCCTAAAAC
30632709 CACACTTTAACCCTAAACTTTCCC
64 CACACTTTAACCCTAAACTTTCCC
* **
30632733 AAAATTACATTTTAACCCCAAACTTTCTCAAAACCACACTTTAACCCCAAACTTTCC-AAAAGTA
1 AAAATTACATTTTAACCCCAAACTTTCTCAAAACCACATTTTAACCCCAAACTTTCCTAAAACCA
* *
30632797 CATTTTAACCCTAAAC-TTCTCT
66 CACTTTAACCCTAAACTTTC-CC
* * ** *
30632819 AAAATTACATTTTTACCCTTAAACTTT-TCCAAAATTACATTTTAACCTCAAA
1 AAAATTACATTTTAACCC-CAAACTTTCT-CAAAACCACATTTTAACCCCAAA
30632871 TTCTCCGAAA
Statistics
Matches: 116, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
85 3 0.03
86 39 0.34
87 53 0.46
88 21 0.18
ACGTcount: A:0.39, C:0.27, G:0.01, T:0.33
Consensus pattern (87 bp):
AAAATTACATTTTAACCCCAAACTTTCTCAAAACCACATTTTAACCCCAAACTTTCCTAAAACCA
CACTTTAACCCTAAACTTTCCC
Found at i:30632967 original size:20 final size:20
Alignment explanation
Indices: 30632933--30632978 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
30632923 TTGTATATAA
30632933 TTTTAATTATTATCCTTTGTTT
1 TTTTAATTA-TATCCTTT-TTT
30632955 TTTTAATTA-ATCCTTTTTT
1 TTTTAATTATATCCTTTTTT
30632974 TTTTA
1 TTTTA
30632979 TTTTGATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 8 0.33
20 7 0.29
22 9 0.38
ACGTcount: A:0.20, C:0.09, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTAATTATATCCTTTTTT
Found at i:30636989 original size:32 final size:32
Alignment explanation
Indices: 30636927--30636989 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
30636917 ACCGATGAAA
*
30636927 TTCGGTTCGATTATTTCGGTTACCCCTTAAAT
1 TTCGGTTCGATTATTTCGATTACCCCTTAAAT
* * * *
30636959 TTCGGTTCGGTTATTTTGATTATCCTTTAAA
1 TTCGGTTCGATTATTTCGATTACCCCTTAAA
30636990 ACTCAATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.19, C:0.17, G:0.16, T:0.48
Consensus pattern (32 bp):
TTCGGTTCGATTATTTCGATTACCCCTTAAAT
Found at i:30641166 original size:20 final size:20
Alignment explanation
Indices: 30641122--30641166 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
30641112 TTAATTCATT
***
30641122 CATATATACGTATATATGTT
1 CATATATACGTATATATAAA
*
30641142 TATATATACGTATATATAAA
1 CATATATACGTATATATAAA
30641162 CATAT
1 CATAT
30641167 CCTAATGGCA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (20 bp):
CATATATACGTATATATAAA
Found at i:30641513 original size:25 final size:25
Alignment explanation
Indices: 30641485--30641534 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
30641475 GACGTGACTA
30641485 ATGGAATAACCAAACAGTGATGCAT
1 ATGGAATAACCAAACAGTGATGCAT
*
30641510 ATGGATTAACCAAACAGTGATGCAT
1 ATGGAATAACCAAACAGTGATGCAT
30641535 GACTTGCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (25 bp):
ATGGAATAACCAAACAGTGATGCAT
Found at i:30644222 original size:17 final size:18
Alignment explanation
Indices: 30644200--30644240 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
30644190 ATTTAATTAG
30644200 TTAAATTAAATTT-TCAA
1 TTAAATTAAATTTCTCAA
30644217 TTAAA-TAAATTTCTCAA
1 TTAAATTAAATTTCTCAA
*
30644234 TTTAATT
1 TTAAATT
30644241 CTAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 7 0.33
17 13 0.62
18 1 0.05
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAAATTAAATTTCTCAA
Found at i:30645827 original size:80 final size:79
Alignment explanation
Indices: 30645688--30645840 Score: 252
Period size: 80 Copynumber: 1.9 Consensus size: 79
30645678 TACAAGCACT
* *
30645688 AATTTCATTTTAACTCTTGTAGGGAAACCAATGAGTCATGTCTCTTCCTTAGGATCTGATGTAGT
1 AATTTCATTTTAACCCTTGTAGGGAAACCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGT
30645753 TGAAAAGGAATGAC
66 TGAAAAGGAATGAC
* **
30645767 AATTTCGATTTTATCCCTTGTAGGGAAGTCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAG
1 AATTTC-ATTTTAACCCTTGTAGGGAAACCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAG
30645832 TTGAAAAGG
65 TTGAAAAGG
30645841 CATGGTATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 6 0.09
80 62 0.91
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (79 bp):
AATTTCATTTTAACCCTTGTAGGGAAACCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGT
TGAAAAGGAATGAC
Found at i:30647637 original size:28 final size:28
Alignment explanation
Indices: 30647603--30647713 Score: 152
Period size: 28 Copynumber: 4.0 Consensus size: 28
30647593 TAGTAACAGG
*
30647603 CATGACCTTTGGGTCAATAGGGAGTAAA
1 CATGACCTTTAGGTCAATAGGGAGTAAA
* *
30647631 CATGACCTTTGGGTCAATAGGGAGTAAG
1 CATGACCTTTAGGTCAATAGGGAGTAAA
* *
30647659 CATGACCTTTAGGTCAACAGGGAGTAAG
1 CATGACCTTTAGGTCAATAGGGAGTAAA
* *
30647687 TATGACCTTTAGGTCAA-AGAGAGTAAA
1 CATGACCTTTAGGTCAATAGGGAGTAAA
30647714 TCGGATATCG
Statistics
Matches: 77, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
27 8 0.10
28 69 0.90
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.24
Consensus pattern (28 bp):
CATGACCTTTAGGTCAATAGGGAGTAAA
Found at i:30659299 original size:30 final size:30
Alignment explanation
Indices: 30659258--30659434 Score: 205
Period size: 30 Copynumber: 5.9 Consensus size: 30
30659248 TTTGACCCAA
30659258 AACTTTCCAAAAATTACATTTTAACCCTCG
1 AACTTTCCAAAAATTACATTTTAACCCTCG
* *
30659288 AACTTTTCAAAAATTACATTTTAACCCTCT
1 AACTTTCCAAAAATTACATTTTAACCCTCG
* * *
30659318 AGC-TACCAAAAATTACATTTTAACCC-CC
1 AACTTTCCAAAAATTACATTTTAACCCTCG
** * *
30659346 AAAATTCCTAAAAATTACATTTTGACCCTCA
1 AACTTTCC-AAAAATTACATTTTAACCCTCG
* *
30659377 AAGTTTCCAAAAATTACATTTTTACCCTCG
1 AACTTTCCAAAAATTACATTTTAACCCTCG
* * *
30659407 AACTTTCCAAAAGTTACGTTTTGACCCT
1 AACTTTCCAAAAATTACATTTTAACCCT
30659435 TAAAATTCTC
Statistics
Matches: 125, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 24 0.19
30 92 0.74
31 7 0.06
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (30 bp):
AACTTTCCAAAAATTACATTTTAACCCTCG
Found at i:30659334 original size:59 final size:60
Alignment explanation
Indices: 30659239--30659434 Score: 222
Period size: 59 Copynumber: 3.3 Consensus size: 60
30659229 GTTTTATCTG
* * *
30659239 AAAATTACA-TTTGA-CC-CAAAACTTTCCAAAAATTACATTTTAACCCTCGAACTTTTCA
1 AAAATTACATTTTGACCCTCAAAGC-TACCAAAAATTACATTTTAACCCTCGAACTTTCCA
* * * **
30659297 AAAATTACATTTTAACCCTC-TAGCTACCAAAAATTACATTTTAACCC-CCAAAATTCCTA
1 AAAATTACATTTTGACCCTCAAAGCTACCAAAAATTACATTTTAACCCTCGAACTTTCC-A
* * *
30659356 AAAATTACATTTTGACCCTCAAAGTTTCCAAAAATTACATTTTTACCCTCGAACTTTCCA
1 AAAATTACATTTTGACCCTCAAAGCTACCAAAAATTACATTTTAACCCTCGAACTTTCCA
* *
30659416 AAAGTTACGTTTTGACCCT
1 AAAATTACATTTTGACCCT
30659435 TAAAATTCTC
Statistics
Matches: 114, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
58 15 0.13
59 46 0.40
60 45 0.39
61 8 0.07
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (60 bp):
AAAATTACATTTTGACCCTCAAAGCTACCAAAAATTACATTTTAACCCTCGAACTTTCCA
Found at i:30659459 original size:30 final size:30
Alignment explanation
Indices: 30659239--30659463 Score: 201
Period size: 30 Copynumber: 7.6 Consensus size: 30
30659229 GTTTTATCTG
30659239 AAAATTACA-TTTGA-CC-CAAAACTTTCCA
1 AAAATTACATTTTGACCCTCAAAA-TTTCCA
* * * *
30659267 AAAATTACATTTTAACCCTCGAACTTTTCA
1 AAAATTACATTTTGACCCTCAAAATTTCCA
* * ** *
30659297 AAAATTACATTTTAACCCTC-TAGCTACCA
1 AAAATTACATTTTGACCCTCAAAATTTCCA
* *
30659326 AAAATTACATTTTAACCCCCAAAA-TTCCTA
1 AAAATTACATTTTGACCCTCAAAATTTCC-A
*
30659356 AAAATTACATTTTGACCCTCAAAGTTTCCA
1 AAAATTACATTTTGACCCTCAAAATTTCCA
* * *
30659386 AAAATTACATTTTTACCCTCGAACTTTCCA
1 AAAATTACATTTTGACCCTCAAAATTTCCA
* * * *
30659416 AAAGTTACGTTTTGACCCTTAAAATTCTCTA
1 AAAATTACATTTTGACCCTCAAAATT-TCCA
*
30659447 AAACTT-CATTTTGACCC
1 AAAATTACATTTTGACCC
30659464 CGTTTTTTTT
Statistics
Matches: 162, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
28 9 0.06
29 30 0.19
30 108 0.67
31 15 0.09
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTGACCCTCAAAATTTCCA
Found at i:30662092 original size:13 final size:13
Alignment explanation
Indices: 30662076--30662116 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
30662066 GTAAACATTT
30662076 TTTTCTTCTTTTC
1 TTTTCTTCTTTTC
*
30662089 TTTTC-TCTTTTA
1 TTTTCTTCTTTTC
*
30662101 TTTTTTTC-TTTC
1 TTTTCTTCTTTTC
30662113 TTTT
1 TTTT
30662117 TCTCATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
12 17 0.71
13 7 0.29
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTCTTTTC
Found at i:30662110 original size:25 final size:27
Alignment explanation
Indices: 30662075--30662125 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
30662065 AGTAAACATT
30662075 TTTTTCTTCTTT-TCTTTTCTC-TTTTA
1 TTTTTCTTCTTTCT-TTTTCTCATTTTA
30662101 TTTTT-TTCTTTCTTTTTCTCATTTT
1 TTTTTCTTCTTTCTTTTTCTCATTTT
30662126 CCTTTTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (27 bp):
TTTTTCTTCTTTCTTTTTCTCATTTTA
Found at i:30681163 original size:23 final size:23
Alignment explanation
Indices: 30681137--30681181 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
30681127 AATTAAAGGA
*
30681137 TTAAAGAATAAATTTAACCCAAT
1 TTAAAGAATAAATTCAACCCAAT
** *
30681160 TTAATTAATTAATTCAACCCAA
1 TTAAAGAATAAATTCAACCCAA
30681182 ATTATTTAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (23 bp):
TTAAAGAATAAATTCAACCCAAT
Done.