Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015178.1 Kokia drynarioides strain JFW-HI SEQ_130222, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 270551
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 310 characters in sequence are not A, C, G, or T
Found at i:678 original size:21 final size:19
Alignment explanation
Indices: 634--683 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
624 AATATTTAAC
*
634 AAAATTTTAAGGTGAAAAT
1 AAAAGTTTAAGGTGAAAAT
*
653 AAAAGATTTAGAGGTGAAATT
1 AAAAG-TTTA-AGGTGAAAAT
*
674 CAAAGTTTAA
1 AAAAGTTTAA
684 AAAAAAAGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 5 0.19
20 8 0.31
21 13 0.50
ACGTcount: A:0.50, C:0.02, G:0.18, T:0.30
Consensus pattern (19 bp):
AAAAGTTTAAGGTGAAAAT
Found at i:10109 original size:17 final size:17
Alignment explanation
Indices: 10089--10219 Score: 64
Period size: 17 Copynumber: 7.4 Consensus size: 17
10079 AGAACGGGGG
10089 AAAAGGGAAATATATTA
1 AAAAGGGAAATATATTA
*****
10106 AAAAGGAAGAAATACGGGG
1 AAAAGG--GAAATATATTA
10125 AAAAGGGAAATATATTA
1 AAAAGGGAAATATATTA
*****
10142 AAAAGGAAGAAATACGGGG
1 AAAAGG--GAAATATATTA
*
10161 AAAAGGGAAATGTATTA
1 AAAAGGGAAATATATTA
****
10178 AAAAGGAAGAAATACGGGA
1 AAAAGG--GAAATATATTA
*
10197 AAAAGGGAAATGTATTA
1 AAAAGGGAAATATATTA
10214 AAAAGG
1 AAAAGG
10220 AAGAAATACG
Statistics
Matches: 77, Mismatches: 31, Indels: 12
0.64 0.26 0.10
Matches are distributed among these distances:
17 41 0.53
19 36 0.47
ACGTcount: A:0.56, C:0.02, G:0.27, T:0.15
Consensus pattern (17 bp):
AAAAGGGAAATATATTA
Found at i:10125 original size:36 final size:36
Alignment explanation
Indices: 10085--10237 Score: 270
Period size: 36 Copynumber: 4.2 Consensus size: 36
10075 AATGAGAACG
10085 GGGGAAAAGGGAAATATATTAAAAAGGAAGAAATAC
1 GGGGAAAAGGGAAATATATTAAAAAGGAAGAAATAC
10121 GGGGAAAAGGGAAATATATTAAAAAGGAAGAAATAC
1 GGGGAAAAGGGAAATATATTAAAAAGGAAGAAATAC
*
10157 GGGGAAAAGGGAAATGTATTAAAAAGGAAGAAATAC
1 GGGGAAAAGGGAAATATATTAAAAAGGAAGAAATAC
* *
10193 GGGAAAAAGGGAAATGTATTAAAAAGGAAGAAATAC
1 GGGGAAAAGGGAAATATATTAAAAAGGAAGAAATAC
*
10229 GGGAAAAAG
1 GGGGAAAAG
10238 CTTGGGCTAA
Statistics
Matches: 115, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 115 1.00
ACGTcount: A:0.55, C:0.03, G:0.29, T:0.13
Consensus pattern (36 bp):
GGGGAAAAGGGAAATATATTAAAAAGGAAGAAATAC
Found at i:10235 original size:19 final size:19
Alignment explanation
Indices: 10105--10237 Score: 80
Period size: 19 Copynumber: 7.3 Consensus size: 19
10095 GAAATATATT
10105 AAAAAGGAAGAAATACGGG
1 AAAAAGGAAGAAATACGGG
* ****
10124 GAAAAGG--GAAATATATT
1 AAAAAGGAAGAAATACGGG
10141 AAAAAGGAAGAAATACGGG
1 AAAAAGGAAGAAATACGGG
* *****
10160 GAAAAGG--GAAATGTATT
1 AAAAAGGAAGAAATACGGG
10177 AAAAAGGAAGAAATACGGG
1 AAAAAGGAAGAAATACGGG
*****
10196 AAAAAGG--GAAATGTATT
1 AAAAAGGAAGAAATACGGG
10213 AAAAAGGAAGAAATACGGG
1 AAAAAGGAAGAAATACGGG
10232 AAAAAG
1 AAAAAG
10238 CTTGGGCTAA
Statistics
Matches: 76, Mismatches: 32, Indels: 12
0.63 0.27 0.10
Matches are distributed among these distances:
17 35 0.46
19 41 0.54
ACGTcount: A:0.56, C:0.03, G:0.29, T:0.12
Consensus pattern (19 bp):
AAAAAGGAAGAAATACGGG
Found at i:10500 original size:34 final size:34
Alignment explanation
Indices: 10457--10524 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
10447 CTTATACCTT
10457 AATATATATATATATATATGTGTGTGTGTGTGTG
1 AATATATATATATATATATGTGTGTGTGTGTGTG
10491 AATATATATATATATATATGTGTGTGTGTGTGTG
1 AATATATATATATATATATGTGTGTGTGTGTGTG
10525 TGTGTGTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (34 bp):
AATATATATATATATATATGTGTGTGTGTGTGTG
Found at i:10514 original size:2 final size:2
Alignment explanation
Indices: 10509--10549 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
10499 TATATATATA
10509 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
10550 TTTAATTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:21986 original size:33 final size:34
Alignment explanation
Indices: 21941--22006 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
21931 ACAGCAATAT
21941 CAAAACAAT-AAAAAACAGCACCAAAACAACAAC
1 CAAAACAATAAAAAAACAGCACCAAAACAACAAC
*
21974 CAAAACATTAAAAAAACAGCACCAAAACAACAA
1 CAAAACAATAAAAAAACAGCACCAAAACAACAA
22007 TATAATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 8 0.26
34 23 0.74
ACGTcount: A:0.67, C:0.26, G:0.03, T:0.05
Consensus pattern (34 bp):
CAAAACAATAAAAAAACAGCACCAAAACAACAAC
Found at i:23095 original size:6 final size:6
Alignment explanation
Indices: 23084--23135 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
23074 TCTTGGCATA
23084 GCCAGT GCCAGT GCCAGT GCCAGT GCCAGT GCCAGT GCCAGT GCCAGT
1 GCCAGT GCCAGT GCCAGT GCCAGT GCCAGT GCCAGT GCCAGT GCCAGT
23132 GCCA
1 GCCA
23136 AGGCCAAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.17, C:0.35, G:0.33, T:0.15
Consensus pattern (6 bp):
GCCAGT
Found at i:33698 original size:42 final size:42
Alignment explanation
Indices: 33614--33742 Score: 152
Period size: 42 Copynumber: 3.0 Consensus size: 42
33604 TTATGCTCTA
* * * *
33614 CCGAGTCATAAGTCTTCGTTTTTAAACATAATCTCATGCTCATT
1 CCGAGTCATGAGTCTTC--CTTTAATCATAATCTCATTCTCATT
*
33658 CCGAGTCATGAGTCTTCCTTTAATCATAGTCTCATTCTCA-T
1 CCGAGTCATGAGTCTTCCTTTAATCATAATCTCATTCTCATT
* * *
33699 CCTGAGACATGAGTATTCCTTTAATCATATTCTCATTCTCATT
1 CC-GAGTCATGAGTCTTCCTTTAATCATAATCTCATTCTCATT
33742 C
1 C
33743 TCATATTGAG
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 3 0.04
42 54 0.72
43 2 0.03
44 16 0.21
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.40
Consensus pattern (42 bp):
CCGAGTCATGAGTCTTCCTTTAATCATAATCTCATTCTCATT
Found at i:38859 original size:15 final size:16
Alignment explanation
Indices: 38839--38869 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38829 ACTTCCCTAT
38839 ATTCTA-TTTCTTTTA
1 ATTCTATTTTCTTTTA
38854 ATTCTATTTTCTTTTA
1 ATTCTATTTTCTTTTA
38870 TCTTTAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.19, C:0.13, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTCTATTTTCTTTTA
Found at i:38860 original size:22 final size:22
Alignment explanation
Indices: 38835--38891 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
38825 TTCGACTTCC
*
38835 CTATATTCTATT-TCTTTTAATT
1 CTATATTCTTTTATC-TTTAATT
*
38857 CTATTTTCTTTTATCTTTAATT
1 CTATATTCTTTTATCTTTAATT
*
38879 CTGT-TTCTTTTAT
1 CTATATTCTTTTAT
38892 TTTTCCTCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.29
22 20 0.65
23 2 0.06
ACGTcount: A:0.18, C:0.14, G:0.02, T:0.67
Consensus pattern (22 bp):
CTATATTCTTTTATCTTTAATT
Found at i:38887 original size:21 final size:22
Alignment explanation
Indices: 38850--38891 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
38840 TTCTATTTCT
*
38850 TTTAATTCTATTTTCTTTTATC
1 TTTAATTCTAGTTTCTTTTATC
38872 TTTAATTCT-GTTTCTTTTAT
1 TTTAATTCTAGTTTCTTTTAT
38892 TTTTCCTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTAATTCTAGTTTCTTTTATC
Found at i:43922 original size:15 final size:16
Alignment explanation
Indices: 43902--43931 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43892 CTTCCTTATT
43902 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
43917 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
43932 TCTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:43924 original size:22 final size:22
Alignment explanation
Indices: 43898--43947 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
43888 TCGACTTCCT
*
43898 TATTTTCTATTTCT-TTTAATTC
1 TATTTTCT-TTTATCTTTAATTC
43920 TATTTTCTTTTATCTTTAATTC
1 TATTTTCTTTTATCTTTAATTC
*
43942 TGTTTT
1 TATTTT
43948 ATTTATTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (22 bp):
TATTTTCTTTTATCTTTAATTC
Found at i:50657 original size:12 final size:12
Alignment explanation
Indices: 50637--50670 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
50627 AAACATAAAT
*
50637 TTAAAATTAATA
1 TTAATATTAATA
50649 TTAATATTAATA
1 TTAATATTAATA
50661 TTAATATTAA
1 TTAATATTAA
50671 ATAAAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAATATTAATA
Found at i:50678 original size:18 final size:18
Alignment explanation
Indices: 50638--50675 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
50628 AACATAAATT
50638 TAAA-ATTAATATTAATA
1 TAAATATTAATATTAATA
*
50655 TTAATATTAATATTAA-A
1 TAAATATTAATATTAATA
50672 TAAA
1 TAAA
50676 ATAAAAATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAATATTAATATTAATA
Found at i:52451 original size:24 final size:24
Alignment explanation
Indices: 52419--52494 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
52409 CACAAATAAC
* *
52419 ATTAGCTCTCACGAGCCCGGAATG
1 ATTAGCTCTTACGAGCCCAGAATG
*
52443 GTTAGCTCTTACGAGCCCAGAATG
1 ATTAGCTCTTACGAGCCCAGAATG
*
52467 ATTAGATCTTACGAGCCCAGAATG
1 ATTAGCTCTTACGAGCCCAGAATG
52491 ATTA
1 ATTA
52495 ACCACTATAC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (24 bp):
ATTAGCTCTTACGAGCCCAGAATG
Found at i:53742 original size:16 final size:16
Alignment explanation
Indices: 53710--53743 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53700 CTATTTGATC
* *
53710 TTTCAATTATATTAAA
1 TTTCAATTAAATAAAA
53726 TTTCAATTAAATAAAA
1 TTTCAATTAAATAAAA
53742 TT
1 TT
53744 GTTTTCAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTCAATTAAATAAAA
Found at i:54320 original size:25 final size:24
Alignment explanation
Indices: 54287--54333 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
54277 GTAGGGATTT
*
54287 TTATTTTATTTAATATTAATATAA
1 TTATTTTATTTAATATAAATATAA
54311 TTATATTTATTTAATATAAATAT
1 TTAT-TTTATTTAATATAAATAT
54334 TAATATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTTTATTTAATATAAATATAA
Found at i:54324 original size:19 final size:18
Alignment explanation
Indices: 54296--54348 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
54286 TTTATTTTAT
54296 TTAATATTAATATAATTATA
1 TTAATATTAATATAA--ATA
*
54316 TTTAT-TTAATATAAATA
1 TTAATATTAATATAAATA
54333 TTAATATTAATATAAA
1 TTAATATTAATATAAA
54349 ATTTAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 7 0.23
18 10 0.33
19 9 0.30
20 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTAATATTAATATAAATA
Found at i:61499 original size:40 final size:40
Alignment explanation
Indices: 61443--61789 Score: 261
Period size: 40 Copynumber: 8.7 Consensus size: 40
61433 GATGGTTGCG
* *
61443 ATCTGCTCCATGATCGGGGTAAGAGATCGGATGGTTTTTA
1 ATCTGCCCCATAATCGGGGTAAGAGATCGGATGGTTTTTA
* * *
61483 ATCTGCCCTACAATCGGGGTAAGAGATTGGATGGTTTTTA
1 ATCTGCCCCATAATCGGGGTAAGAGATCGGATGGTTTTTA
* * * ** * *
61523 ATCTGCCTCATGATCGGGGTAAGAGATTGGAT-GACTATG
1 ATCTGCCCCATAATCGGGGTAAGAGATCGGATGGTTTTTA
*
61562 ATCTGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTTA
1 ATCTGCCCCATAATCGGGGTAAGAGATCGGATGGTTTTTA
* * * * * * ***
61602 GTCTACCCCATGATCGGGGTAAGAGATTGAATGG-CTACG
1 ATCTGCCCCATAATCGGGGTAAGAGATCGGATGGTTTTTA
* * * *
61641 ATTTGCCCCATAATCGGGGTAAGAGATCGAATGATTTTCA
1 ATCTGCCCCATAATCGGGGTAAGAGATCGGATGGTTTTTA
* * * * * *
61681 ATCTGCCCTATGATCGGGGTAAAAGATTGGCAAT-GTCTTCA
1 ATCTGCCCCATAATCGGGGTAAGAGATCGG--ATGGTTTTTA
* * * * *
61722 ATCTGTCCCATGATCGAGGTAAGAGATTGGCAAT-GTCTTTA
1 ATCTGCCCCATAATCGGGGTAAGAGATCGG--ATGGTTTTTA
* * * *
61763 ATCTGCCCTATGATCAGGGTAAAAGAT
1 ATCTGCCCCATAATCGGGGTAAGAGAT
61790 TGGCGATATC
Statistics
Matches: 249, Mismatches: 54, Indels: 7
0.80 0.17 0.02
Matches are distributed among these distances:
39 62 0.25
40 122 0.49
41 63 0.25
42 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (40 bp):
ATCTGCCCCATAATCGGGGTAAGAGATCGGATGGTTTTTA
Found at i:61516 original size:79 final size:77
Alignment explanation
Indices: 61443--61789 Score: 275
Period size: 79 Copynumber: 4.3 Consensus size: 77
61433 GATGGTTGCG
** * *
61443 ATCTGCTCCATGATCGGGGTAAGAGATCGGATGGTTTTTAATCTGCCCTACAATCGGGGTAAGAG
1 ATCTGC-CCATGATCGGGGTAAGAGATCGGAT-GACTATAATCTGCCCCACAATCGGGGTAAGAG
*
61508 ATTGGATGGTTTTTA
64 ATCGGATGG-TTTTA
* * **
61523 ATCTGCCTCATGATCGGGGTAAGAGATTGGATGACTATGATCTGCCCCATGATCGGGGTAAGAGA
1 ATCTGCC-CATGATCGGGGTAAGAGATCGGATGACTATAATCTGCCCCACAATCGGGGTAAGAGA
61588 TCGGATGGTTTTTA
65 TCGGATGG-TTTTA
* * * * * ** * *
61602 GTCTACCCCATGATCGGGGTAAGAGATTGAATGGCTACGATTTGCCCCATAATCGGGGTAAGAGA
1 ATCT-GCCCATGATCGGGGTAAGAGATCGGATGACTATAATCTGCCCCACAATCGGGGTAAGAGA
* *
61667 TCGAATGATTTTCA
65 TCGGATGGTTTT-A
* * * * ** *
61681 ATCTGCCCTATGATCGGGGTAAAAGATTGGCAATGTCT-TCAATCTGTCCCATGATCGAGGTAAG
1 ATCTGCCC-ATGATCGGGGTAAGAGATCGG--ATGACTAT-AATCTGCCCCACAATCGGGGTAAG
*
61745 AGATTGGCAAT-GTCTTTA
62 AGATCGG--ATGGT-TTTA
* *
61763 ATCTGCCCTATGATCAGGGTAAAAGAT
1 ATCTGCCC-ATGATCGGGGTAAGAGAT
61790 TGGCGATATC
Statistics
Matches: 224, Mismatches: 33, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
78 7 0.03
79 124 0.55
80 31 0.14
81 29 0.13
82 28 0.12
83 5 0.02
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.29
Consensus pattern (77 bp):
ATCTGCCCATGATCGGGGTAAGAGATCGGATGACTATAATCTGCCCCACAATCGGGGTAAGAGAT
CGGATGGTTTTA
Found at i:61735 original size:41 final size:40
Alignment explanation
Indices: 61443--62048 Score: 487
Period size: 41 Copynumber: 15.1 Consensus size: 40
61433 GATGGTTGCG
* * * *
61443 ATCTGCTCCATGATCGGGGTAAGAGATCGG-ATGGTTTTTA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGCAT-GTCTTCA
* ** * *
61483 ATCTGCCCTACAATCGGGGTAAGAGATTGG-ATGGTTTTTA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGCAT-GTCTTCA
* * *
61523 ATCTGCCTCATGATCGGGGTAAGAGATTGG-ATGACTAT-G
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGCATGTCT-TCA
* * *
61562 ATCTGCCCCATGATCGGGGTAAGAGATCGG-ATGGTTTTTA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGCAT-GTCTTCA
* * * * * *
61602 GTCTACCCCATGATCGGGGTAAGAGATT-GAATGGCTACG
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGCATGTCTTCA
* * * * *
61641 ATTTGCCCCATAATCGGGGTAAGAGA-TCGAATGATTTTCA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGCATG-TCTTCA
* *
61681 ATCTGCCCTATGATCGGGGTAAAAGATTGGCAATGTCTTCA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGC-ATGTCTTCA
* * *
61722 ATCTGTCCCATGATCGAGGTAAGAGATTGGCAATGTCTTTA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGC-ATGTCTTCA
* * * *
61763 ATCTGCCCTATGATCAGGGTAAAAGATTGGCGATATCTTCA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGC-ATGTCTTCA
* * * * *
61804 ATCTACCTCATGATTGGGGTAAGAGATTTG-ATGGCTTCA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGCATGTCTTCA
* * * **
61843 ATCTACCTCATGATCGAGGTAAGAGATTGGCGAAATCTTCA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGC-ATGTCTTCA
* ***
61884 ATCTGTCCCATGATCAATGTAAGAGATTGGCGATGTCTTCA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGC-ATGTCTTCA
* * *
61925 ATCTGCCCCATGATTGGGGTAAGAGATT-TCATGGT-TTTA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGCAT-GTCTTCA
* * **
61964 ATCTACCCTATGATCAAGGTAAGAGATTGGCGATGTCTTCA
1 ATCTGCCCCATGATCGGGGTAAGAGATTGGC-ATGTCTTCA
* * *
62005 ATCTACCCCATGATCGGGGGTAAGAGATTTG-ATGACTTCA
1 ATCTGCCCCATGATC-GGGGTAAGAGATTGGCATGTCTTCA
62045 ATCT
1 ATCT
62049 TCTTCATCAT
Statistics
Matches: 457, Mismatches: 94, Indels: 30
0.79 0.16 0.05
Matches are distributed among these distances:
38 1 0.00
39 125 0.27
40 135 0.30
41 181 0.40
42 15 0.03
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (40 bp):
ATCTGCCCCATGATCGGGGTAAGAGATTGGCATGTCTTCA
Found at i:61866 original size:121 final size:118
Alignment explanation
Indices: 61443--62033 Score: 450
Period size: 121 Copynumber: 4.9 Consensus size: 118
61433 GATGGTTGCG
* ** * * * ** *
61443 ATCTGCTCCATGATCGGGGTAAGAGATCGGATGGTTTTTAATCTGCCCTACAATCGGGGTAAGAG
1 ATCTGC-CCATGATTGGGGTAAGAGATTTGATGG-CTTCAATCTACCC-ATGATCGAGGTAAGAG
* * * *
61508 ATTGG--ATGGTTTTTAATCTGCCTCATGATCGGGGTAAGAGATT-G-GATGA-CTAT-G
63 ATTGGCAAT-GTCTTCAATCTGCC-CATGATCAGGGTAAGAGATTGGCGAT-ATCT-TCA
* ** * * * *
61562 ATCTGCCCCATGATCGGGGTAAGAGATCGGATGGTTTTTAGTCTACCCCATGATCGGGGTAAGAG
1 ATCTG-CCCATGATTGGGGTAAGAGATTTGATGG-CTTCAATCTA-CCCATGATCGAGGTAAGAG
* * * * * * *
61627 ATT-G-AATGGCTACGATTTGCCCCATAATCGGGGTAAGAGA-T--CGAATGATTTTCA
63 ATTGGCAATGTCTTCAATCTG-CCCATGATCAGGGTAAGAGATTGGCG-AT-ATCTTCA
* * * * *
61681 ATCTGCCCTATGATCGGGGTAAAAGATTGGCAATGTCTTCAATCTGTCCCATGATCGAGGTAAGA
1 ATCTGCCC-ATGATTGGGGTAAGAGATTTG--ATGGCTTCAATCT-ACCCATGATCGAGGTAAGA
* *
61746 GATTGGCAATGTCTTTAATCTGCCCTATGATCAGGGTAAAAGATTGGCGATATCTTCA
62 GATTGGCAATGTCTTCAATCTGCCC-ATGATCAGGGTAAGAGATTGGCGATATCTTCA
*
61804 ATCTACCTCATGATTGGGGTAAGAGATTTGATGGCTTCAATCTACCTCATGATCGAGGTAAGAGA
1 ATCTGCC-CATGATTGGGGTAAGAGATTTGATGGCTTCAATCTACC-CATGATCGAGGTAAGAGA
* ** *
61869 TTGGCGAA-ATCTTCAATCTGTCCCATGATCAATGTAAGAGATTGGCGATGTCTTCA
64 TTGGC-AATGTCTTCAATCTG-CCCATGATCAGGGTAAGAGATTGGCGATATCTTCA
* * * *
61925 ATCTGCCCCATGATTGGGGTAAGAGATTTCATGGTTTTAATCTACCCTATGATCAAGGTAAGAGA
1 ATCTG-CCCATGATTGGGGTAAGAGATTTGATGGCTTCAATCTACCC-ATGATCGAGGTAAGAGA
* * *
61990 TTGGCGATGTCTTCAATCTACCCCATGATCGGGGGTAAGAGATT
64 TTGGCAATGTCTTCAATCT-GCCCATGATC-AGGGTAAGAGATT
62034 TGATGACTTC
Statistics
Matches: 392, Mismatches: 53, Indels: 51
0.79 0.11 0.10
Matches are distributed among these distances:
117 2 0.01
118 32 0.08
119 87 0.22
120 35 0.09
121 159 0.41
122 41 0.10
123 31 0.08
124 3 0.01
125 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (118 bp):
ATCTGCCCATGATTGGGGTAAGAGATTTGATGGCTTCAATCTACCCATGATCGAGGTAAGAGATT
GGCAATGTCTTCAATCTGCCCATGATCAGGGTAAGAGATTGGCGATATCTTCA
Found at i:62006 original size:162 final size:161
Alignment explanation
Indices: 61677--62033 Score: 418
Period size: 162 Copynumber: 2.2 Consensus size: 161
61667 TCGAATGATT
* * * *
61677 TTCAATCTGCCCTATGATCGGGGTAAAAGATTGGCAATGTCTTCAATCTGTCCCATGATCGAGGT
1 TTCAATCTACCC-ATGATCGGGGTAAGAGATTGGCAATATCTTCAATCTGTCCCATGATCAAGGT
* *
61742 AAGAGATTGGCAATGTCTTTAATCTGCCCTATGATCAGGGTAAAAGATTGGCGATATCTTCAATC
65 AAGAGATTGGCAATGTCTTCAATCTGCCCCATGATCAGGGTAAAAGATTGGCGATATCTTCAATC
*** *
61807 TACCTCATGATTGGGGTAAGAGATTTGATGGC
130 TACCTCATGATCAAGGTAAGAGATTCGATGGC
* *
61839 TTCAATCTACCTCATGATCGAGGTAAGAGATTGGCGAA-ATCTTCAATCTGTCCCATGATCAATG
1 TTCAATCTACC-CATGATCGGGGTAAGAGATTGGC-AATATCTTCAATCTGTCCCATGATCAAGG
* ** * * * *
61903 TAAGAGATTGGCGATGTCTTCAATCTGCCCCATGATTGGGGTAAGAGATT-TC-ATGGT-TTTAA
64 TAAGAGATTGGCAATGTCTTCAATCTGCCCCATGATCAGGGTAAAAGATTGGCGAT-ATCTTCAA
*
61965 TCTACC-CTATGATCAAGGTAAGAGATTGGCGATGTC
128 TCTACCTC-ATGATCAAGGTAAGAGATT--CGATGGC
62001 TTCAATCTACCCCATGATCGGGGGTAAGAGATT
1 TTCAATCTA-CCCATGATC-GGGGTAAGAGATT
62034 TGATGACTTC
Statistics
Matches: 166, Mismatches: 21, Indels: 15
0.82 0.10 0.07
Matches are distributed among these distances:
159 1 0.01
160 28 0.17
161 2 0.01
162 118 0.71
163 17 0.10
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (161 bp):
TTCAATCTACCCATGATCGGGGTAAGAGATTGGCAATATCTTCAATCTGTCCCATGATCAAGGTA
AGAGATTGGCAATGTCTTCAATCTGCCCCATGATCAGGGTAAAAGATTGGCGATATCTTCAATCT
ACCTCATGATCAAGGTAAGAGATTCGATGGC
Found at i:62233 original size:100 final size:100
Alignment explanation
Indices: 62060--62253 Score: 250
Period size: 100 Copynumber: 1.9 Consensus size: 100
62050 CTTCATCATG
* **
62060 TTTCTAAGGTGCTAGGTTCGCCGTTGCAACGTCAACATTTCCCTTCCTATCTTCATGGTACTGGA
1 TTTCTAAGGTGCTAGGTTCGCCGTTGCAACCTCAACATTTCCCTTCAAATCTTCATGGTACTGGA
* * * *
62125 TTTACCGTTGTGGTCTTAATCTTTCCCATCATATC
66 TTCACCGTTGCGGACTTAACCTTTCCCATCATATC
* * *
62160 TTTCTAAGGT-ATCAGGTTCGCCGTTGCAGCCTCAACCTTT-CCTCTCAAATCTTCATGGTACTA
1 TTTCTAAGGTGCT-AGGTTCGCCGTTGCAACCTCAACATTTCCCT-TCAAATCTTCATGGTACT-
62223 GG-TTCACCGTTGCGGACTTAACCTTTCCCAT
63 GGATTCACCGTTGCGGACTTAACCTTTCCCAT
62254 TACATTTTAT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
99 4 0.05
100 75 0.93
101 2 0.02
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.37
Consensus pattern (100 bp):
TTTCTAAGGTGCTAGGTTCGCCGTTGCAACCTCAACATTTCCCTTCAAATCTTCATGGTACTGGA
TTCACCGTTGCGGACTTAACCTTTCCCATCATATC
Found at i:62246 original size:49 final size:49
Alignment explanation
Indices: 62108--62253 Score: 136
Period size: 49 Copynumber: 2.9 Consensus size: 49
62098 TTCCCTTCCT
* * * * *
62108 ATCTTCATGGTACT-GGATTTACCGTTGTGGTCTTAATCTTTCCCATCAT
1 ATCTTCATGGTACTAGG-TTCACCGTTGCGGACTTAACCTTTCCCATCAA
* * * * *
62157 ATCTTTCTAAGGTA-TCAGGTTCGCCGTTGCAGCCTCAACCTTTCCTC-TCAA
1 ATC-TTC-ATGGTACT-AGGTTCACCGTTGCGGACTTAACCTTTCC-CATCAA
62208 ATCTTCATGGTACTAGGTTCACCGTTGCGGACTTAACCTTTCCCAT
1 ATCTTCATGGTACTAGGTTCACCGTTGCGGACTTAACCTTTCCCAT
62254 TACATTTTAT
Statistics
Matches: 76, Mismatches: 14, Indels: 14
0.73 0.13 0.13
Matches are distributed among these distances:
48 1 0.01
49 34 0.45
50 8 0.11
51 30 0.39
52 3 0.04
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.37
Consensus pattern (49 bp):
ATCTTCATGGTACTAGGTTCACCGTTGCGGACTTAACCTTTCCCATCAA
Found at i:67994 original size:13 final size:14
Alignment explanation
Indices: 67965--67999 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
67955 TAAAGAAATA
67965 TAAAAAAAAATGGT
1 TAAAAAAAAATGGT
*
67979 TAAAAAAAAAT-TT
1 TAAAAAAAAATGGT
67992 TAAAAAAA
1 TAAAAAAA
68000 TCTAAGGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (14 bp):
TAAAAAAAAATGGT
Found at i:73611 original size:6 final size:6
Alignment explanation
Indices: 73600--73631 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
73590 CTATTGTACA
73600 ACACCC ACACCC ACACCC ACACCC ACACCC AC
1 ACACCC ACACCC ACACCC ACACCC ACACCC AC
73632 GCTGTTAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (6 bp):
ACACCC
Found at i:74137 original size:15 final size:15
Alignment explanation
Indices: 74117--74154 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
74107 TTTTATGTCA
74117 ATTTATTATA-AATAT
1 ATTTATTATATAAT-T
74132 ATTTATTATATAATT
1 ATTTATTATATAATT
74147 ATGTTATT
1 AT-TTATT
74155 TATTAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATTTATTATATAATT
Found at i:77227 original size:29 final size:28
Alignment explanation
Indices: 77169--77233 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
77159 TAAATGTCAA
*
77169 AATTATATATTAATTTTAATTTAATATGT
1 AATTATATATTAATTTTAATTT-AGATGT
*
77198 AATTATATACTTGAATTTTAATTT-GGTGT
1 AATTATATA-TT-AATTTTAATTTAGATGT
77227 AATTATA
1 AATTATA
77234 CACTCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 19 0.59
30 2 0.06
31 11 0.34
ACGTcount: A:0.38, C:0.02, G:0.08, T:0.52
Consensus pattern (28 bp):
AATTATATATTAATTTTAATTTAGATGT
Found at i:80328 original size:22 final size:22
Alignment explanation
Indices: 80241--80328 Score: 78
Period size: 22 Copynumber: 4.2 Consensus size: 22
80231 TTGGTCCTGT
*
80241 TTTTTTACTGTTTTGGTTGCTA
1 TTTTTTACTGTTTTGGTTGCTG
** *
80263 TTTTTTGTTGTTTTGG-TGTTG
1 TTTTTTACTGTTTTGGTTGCTG
*
80284 TATTTTTACTGTTTT-GAT--T-
1 T-TTTTTACTGTTTTGGTTGCTG
*
80303 TTTTTTATTGTTTTGGTTGCTG
1 TTTTTTACTGTTTTGGTTGCTG
80325 TTTT
1 TTTT
80329 GGTGCTATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
18 12 0.23
19 3 0.06
20 1 0.02
21 6 0.12
22 30 0.58
ACGTcount: A:0.07, C:0.05, G:0.19, T:0.69
Consensus pattern (22 bp):
TTTTTTACTGTTTTGGTTGCTG
Found at i:80351 original size:23 final size:22
Alignment explanation
Indices: 80325--80398 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
80315 TTGGTTGCTG
80325 TTTTGGTGCTATTTTTTTTACTA
1 TTTTGGTGCTATTTTTTTTA-TA
* *
80348 TTTTAGTGCTGTTTTTATTGT-TA
1 TTTTGGTGCTATTTTT-TT-TATA
* *
80371 TTTTTGTTACTATTTTTTTCTATA
1 -TTTTGGTGCTATTTTTTT-TATA
80395 TTTT
1 TTTT
80399 TGTTGCTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
23 23 0.57
24 16 0.40
25 1 0.03
ACGTcount: A:0.14, C:0.07, G:0.11, T:0.69
Consensus pattern (22 bp):
TTTTGGTGCTATTTTTTTTATA
Found at i:80410 original size:12 final size:12
Alignment explanation
Indices: 80325--80410 Score: 52
Period size: 12 Copynumber: 7.2 Consensus size: 12
80315 TTGGTTGCTG
*
80325 TTTTGGTGCTAT
1 TTTTGTTGCTAT
* *
80337 TTTTTTTACTAT
1 TTTTGTTGCTAT
* *
80349 TTTAG-TGCTGT
1 TTTTGTTGCTAT
* *
80360 TTTTATTGTTAT
1 TTTTGTTGCTAT
*
80372 TTTTGTTACTAT
1 TTTTGTTGCTAT
80384 TTTT-TT-CTATAT
1 TTTTGTTGC--TAT
*
80396 TTTTGTTGCTGT
1 TTTTGTTGCTAT
80408 TTT
1 TTT
80411 GGTCGTTATT
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
10 1 0.02
11 9 0.17
12 41 0.76
13 2 0.04
14 1 0.02
ACGTcount: A:0.12, C:0.07, G:0.13, T:0.69
Consensus pattern (12 bp):
TTTTGTTGCTAT
Found at i:80410 original size:23 final size:22
Alignment explanation
Indices: 80337--80410 Score: 60
Period size: 24 Copynumber: 3.2 Consensus size: 22
80327 TTGGTGCTAT
*
80337 TTTTTTTACTATTTTAG-TGCTG
1 TTTTTTTA-TATTTTTGTTGCTG
* * *
80359 TTTTTATTGTTATTTTTGTTACTAT
1 TTTTT-TT-ATATTTTTGTTGCT-G
80384 TTTTTTCTATATTTTTGTTGCTG
1 TTTTTT-TATATTTTTGTTGCTG
80407 TTTT
1 TTTT
80411 GGTCGTTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
22 5 0.12
23 13 0.32
24 16 0.40
25 6 0.15
ACGTcount: A:0.12, C:0.07, G:0.11, T:0.70
Consensus pattern (22 bp):
TTTTTTTATATTTTTGTTGCTG
Found at i:80420 original size:24 final size:24
Alignment explanation
Indices: 80367--80427 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
80357 TGTTTTTATT
* **
80367 GTTATTTTTGTTACTATTTTTTTC
1 GTTATTTTTGTTGCTATTTTGGTC
*
80391 -TATATTTTTGTTGCTGTTTTGGTC
1 GT-TATTTTTGTTGCTATTTTGGTC
*
80415 GTTATTTTGGTTG
1 GTTATTTTTGTTG
80428 TTTGGATGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.10, C:0.07, G:0.18, T:0.66
Consensus pattern (24 bp):
GTTATTTTTGTTGCTATTTTGGTC
Found at i:82839 original size:21 final size:22
Alignment explanation
Indices: 82801--82848 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
82791 TGTGACACTG
* *
82801 AATTCAATTATTAGTATA-AAT
1 AATTAAATTATAAGTATACAAT
*
82822 AATTAAATTATAATTATATCAAT
1 AATTAAATTATAAGTATA-CAAT
82845 AATT
1 AATT
82849 CAAAATAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 15 0.68
23 7 0.32
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (22 bp):
AATTAAATTATAAGTATACAAT
Found at i:93555 original size:19 final size:19
Alignment explanation
Indices: 93533--93577 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
93523 TTATATTAGG
93533 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
93552 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
93571 ATTTAAT
1 ATTTAAT
93578 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:101520 original size:22 final size:20
Alignment explanation
Indices: 101476--101564 Score: 76
Period size: 22 Copynumber: 4.3 Consensus size: 20
101466 ATTATATTAT
*
101476 TGTTTT-GTTGTTTTTTTTGC
1 TGTTTTGGTTG-TTTTTTTAC
101496 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGGTTG-T-TTTTTTAC
*
101518 TGTTTTGATGTTGTGTTTTTAC
1 TGTTTTG--GTTGTTTTTTTAC
*
101540 TGTTTTAG-T-TTTTTTTAC
1 TGTTTTGGTTGTTTTTTTAC
*
101558 TATTTTG
1 TGTTTTG
101565 ATTGCTGTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
18 13 0.22
19 1 0.02
20 7 0.12
21 5 0.09
22 27 0.47
23 1 0.02
24 4 0.07
ACGTcount: A:0.08, C:0.06, G:0.18, T:0.69
Consensus pattern (20 bp):
TGTTTTGGTTGTTTTTTTAC
Found at i:101615 original size:23 final size:24
Alignment explanation
Indices: 101585--101658 Score: 98
Period size: 23 Copynumber: 3.2 Consensus size: 24
101575 TGGTGCTATT
101585 TTTTTATTATTA-TTTTGTTGCTA
1 TTTTTATTATTATTTTTGTTGCTA
* *
101608 TTTTTATTGTTATTTTTGTTTCTA
1 TTTTTATTATTATTTTTGTTGCTA
* *
101632 TTTTT-CTATTATTTTTGCTGCTA
1 TTTTTATTATTATTTTTGTTGCTA
101655 TTTT
1 TTTT
101659 GGTTGTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 29 0.66
24 15 0.34
ACGTcount: A:0.14, C:0.07, G:0.08, T:0.72
Consensus pattern (24 bp):
TTTTTATTATTATTTTTGTTGCTA
Found at i:101656 original size:12 final size:12
Alignment explanation
Indices: 101597--101675 Score: 63
Period size: 12 Copynumber: 6.7 Consensus size: 12
101587 TTTATTATTA
101597 TTTTGTTGCTAT
1 TTTTGTTGCTAT
* *
101609 TTTTATTGTTAT
1 TTTTGTTGCTAT
*
101621 TTTTGTTTCTAT
1 TTTTGTTGCTAT
*
101633 TTTTCTAT--TAT
1 TTTTGT-TGCTAT
*
101644 TTTTGCTGCTAT
1 TTTTGTTGCTAT
* *
101656 TTTGGTTGTTAT
1 TTTTGTTGCTAT
*
101668 TTTGGTTG
1 TTTTGTTG
101676 TTTTGATGTT
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
10 1 0.02
11 7 0.13
12 44 0.83
13 1 0.02
ACGTcount: A:0.10, C:0.06, G:0.15, T:0.68
Consensus pattern (12 bp):
TTTTGTTGCTAT
Found at i:101670 original size:23 final size:22
Alignment explanation
Indices: 101572--101691 Score: 82
Period size: 23 Copynumber: 5.2 Consensus size: 22
101562 TTGATTGCTG
* *
101572 TTTTGGTGCTATTTTTTTATTATT
1 TTTTGTTGCTA-TTTTTTGTTA-T
101596 ATTTTGTTGCTATTTTTATTGTTAT
1 -TTTTGTTGCTA-TTTT-TTGTTAT
* *
101621 TTTTGTTTCTATTTTTCTATTAT
1 TTTTGTTGCTATTTTT-TGTTAT
*
101644 TTTTGCTGCTATTTTGGTTGTTAT
1 TTTTGTTGCTATTTT--TTGTTAT
* **
101668 TTTGGTTG-T-TTTGATGTTAT
1 TTTTGTTGCTATTTTTTGTTAT
101688 TTTT
1 TTTT
101692 ATGCGTTTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
20 9 0.11
22 4 0.05
23 23 0.29
24 21 0.27
25 17 0.22
26 5 0.06
ACGTcount: A:0.12, C:0.05, G:0.14, T:0.69
Consensus pattern (22 bp):
TTTTGTTGCTATTTTTTGTTAT
Found at i:112793 original size:31 final size:31
Alignment explanation
Indices: 112757--112824 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
112747 AAATCTATAA
*
112757 AAATTTCATGATTTTAGCTTTTTTACCTTAT
1 AAATTTCATGAATTTAGCTTTTTTACCTTAT
112788 AAATTTCATGAATTTAGCTTTTTTACCTTAT
1 AAATTTCATGAATTTAGCTTTTTTACCTTAT
112819 AAATTT
1 AAATTT
112825 TGGTGACCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (31 bp):
AAATTTCATGAATTTAGCTTTTTTACCTTAT
Found at i:119892 original size:12 final size:12
Alignment explanation
Indices: 119877--119901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
119867 TTAACGACCT
119877 AATTAAATAGAA
1 AATTAAATAGAA
119889 AATTAAATAGAA
1 AATTAAATAGAA
119901 A
1 A
119902 GGATAATTAT
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AATTAAATAGAA
Found at i:123848 original size:15 final size:17
Alignment explanation
Indices: 123828--123859 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
123818 TCATTTCATT
123828 TATAT-AATG-ATAAAA
1 TATATAAATGCATAAAA
123843 TATATAAATGCATAAAA
1 TATATAAATGCATAAAA
123860 AGATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
TATATAAATGCATAAAA
Found at i:125769 original size:24 final size:23
Alignment explanation
Indices: 125740--125810 Score: 85
Period size: 24 Copynumber: 3.1 Consensus size: 23
125730 AATTTCACTC
125740 AAACAAATAAACATAGTTTAATTG
1 AAACAAATAAACA-AGTTTAATTG
125764 AAACAAATAAAC-AG--TAATTG
1 AAACAAATAAACAAGTTTAATTG
* *
125784 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACA-AGTTTAATTG
125808 AAA
1 AAA
125811 GATTATTTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 17 0.41
22 4 0.10
24 20 0.49
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (23 bp):
AAACAAATAAACAAGTTTAATTG
Found at i:125783 original size:20 final size:20
Alignment explanation
Indices: 125758--125797 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
125748 AAACATAGTT
125758 TAATTGAAACAAATAAACAG
1 TAATTGAAACAAATAAACAG
*
125778 TAATTGAAACAATTAAACAG
1 TAATTGAAACAAATAAACAG
125798 AGTTTAACTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (20 bp):
TAATTGAAACAAATAAACAG
Found at i:127780 original size:24 final size:24
Alignment explanation
Indices: 127752--127802 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
127742 AGCTTGACTC
*
127752 AAACAAATAAACAGAT-TTTAATTG
1 AAACAAATAAACAG-TGTTTAACTG
*
127776 AAACAATTAAACAGTGTTTAACTG
1 AAACAAATAAACAGTGTTTAACTG
127800 AAA
1 AAA
127803 GATTATTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (24 bp):
AAACAAATAAACAGTGTTTAACTG
Found at i:128955 original size:30 final size:29
Alignment explanation
Indices: 128891--128956 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
128881 TTTAGTGTAA
* *
128891 TTTTAATTTTAAATTATCTCCTTCTTCTT
1 TTTTAATATTAAATAATCTCCTTCTTCTT
*
128920 TTTTAATATTAAATAATTTCCTTTCTT-TT
1 TTTTAATATTAAATAATCTCC-TTCTTCTT
128949 TCTTTAAT
1 T-TTTAAT
128957 CTTATTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTAATATTAAATAATCTCCTTCTTCTT
Found at i:129673 original size:11 final size:12
Alignment explanation
Indices: 129650--129679 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
129640 CAATCTAAAT
129650 TTTATTATTTTA
1 TTTATTATTTTA
129662 TTTATT-TTTTA
1 TTTATTATTTTA
129673 TTTATTA
1 TTTATTA
129680 AATAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:129704 original size:16 final size:16
Alignment explanation
Indices: 129676--129725 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
129666 TTTTTTATTT
129676 ATTAAATAAATAAACAA
1 ATTAAA-AAATAAACAA
129693 A-TAATAAAATAATA-AA
1 ATTAA-AAAATAA-ACAA
*
129709 ATTAAAAAATATACAA
1 ATTAAAAAATAAACAA
129725 A
1 A
129726 CTCAATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
15 1 0.04
16 21 0.75
17 6 0.21
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (16 bp):
ATTAAAAAATAAACAA
Found at i:130794 original size:30 final size:30
Alignment explanation
Indices: 130755--130924 Score: 181
Period size: 30 Copynumber: 5.7 Consensus size: 30
130745 ATCACCAAAG
*
130755 TTTTC-AAAAATTCAAATTTGACCCCTAAA
1 TTTTCTAAAAATTCAAATTTAACCCCTAAA
*
130784 TTTTCTAAAAATTCAAATTTCA-CCCTCAAA
1 TTTTCTAAAAATTCAAATTTAACCCCT-AAA
* *
130814 TTTTCCAAAAATTCAAATTTAATCTCC-AAA
1 TTTTCTAAAAATTCAAATTTAA-CCCCTAAA
130844 GTTTTC-AAAAATTCAAATTTAACCCCTTAAA
1 -TTTTCTAAAAATTCAAATTTAACCCC-TAAA
*
130875 TTTT-TCAAAAATTCAAATTTAACCCTTAAA
1 TTTTCT-AAAAATTCAAATTTAACCCCTAAA
* *
130905 GTTTT-TAAAATTTAAAATTT
1 -TTTTCTAAAAATTCAAATTT
130925 GACTCCATTT
Statistics
Matches: 123, Mismatches: 8, Indels: 19
0.82 0.05 0.13
Matches are distributed among these distances:
29 12 0.10
30 77 0.63
31 32 0.26
32 2 0.02
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.39
Consensus pattern (30 bp):
TTTTCTAAAAATTCAAATTTAACCCCTAAA
Found at i:130823 original size:60 final size:61
Alignment explanation
Indices: 130750--130924 Score: 216
Period size: 61 Copynumber: 2.9 Consensus size: 61
130740 TTTCGATCAC
* *
130750 CAAAGTTTTCAAAAATTCAAATTTGACCCCTAAA-TTTTCTAAAAATTCAAATTTCA-CCCT
1 CAAA-TTTTCAAAAATTCAAATTTAACCCCTAAAGTTTTCTAAAAATTCAAATTTAACCCCT
*
130810 CAAATTTTCCAAAAATTCAAATTTAATCTCC-AAAGTTTTC-AAAAATTCAAATTTAACCCCT
1 CAAATTTT-CAAAAATTCAAATTTAA-CCCCTAAAGTTTTCTAAAAATTCAAATTTAACCCCT
* * * *
130871 TAAATTTTTCAAAAATTCAAATTTAACCCTTAAAGTTTT-TAAAATTTAAAATTT
1 CAAA-TTTTCAAAAATTCAAATTTAACCCCTAAAGTTTTCTAAAAATTCAAATTT
130925 GACTCCATTT
Statistics
Matches: 100, Mismatches: 8, Indels: 13
0.83 0.07 0.11
Matches are distributed among these distances:
59 4 0.04
60 40 0.40
61 52 0.52
62 4 0.04
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (61 bp):
CAAATTTTCAAAAATTCAAATTTAACCCCTAAAGTTTTCTAAAAATTCAAATTTAACCCCT
Found at i:138176 original size:30 final size:30
Alignment explanation
Indices: 138140--138247 Score: 135
Period size: 30 Copynumber: 3.6 Consensus size: 30
138130 ACATATTCTC
* *
138140 AAATTTAAATTTGACCCCCGAATTTTTTAA
1 AAATTTAAATTTGACCCCCAAATTTTTCAA
* * *
138170 AAATTTAAATTTCACCCTCAAATTTTCCAA
1 AAATTTAAATTTGACCCCCAAATTTTTCAA
* * *
138200 AAATTTAAATTTAATCCCCAAAGTTTTCAA
1 AAATTTAAATTTGACCCCCAAATTTTTCAA
*
138230 AAATTAAAATTTGACCCC
1 AAATTTAAATTTGACCCC
138248 GTTTTAATGT
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (30 bp):
AAATTTAAATTTGACCCCCAAATTTTTCAA
Found at i:139903 original size:4 final size:4
Alignment explanation
Indices: 139896--139934 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
139886 CATCATATAT
139896 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
139935 CAAGTGAGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:142866 original size:21 final size:22
Alignment explanation
Indices: 142840--142898 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
142830 ATCTAATAAC
*
142840 AAATATTTAATAATTATA-TTT
1 AAATATTTAATAAATATAGTTT
142861 AAATATTTAA-AAATATAGTTT
1 AAATATTTAATAAATATAGTTT
*
142882 ATATATTCTAATTAAAT
1 AAATATT-TAA-TAAAT
142899 TTTATAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 6 0.19
21 19 0.59
22 3 0.09
24 4 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATATTTAATAAATATAGTTT
Found at i:145089 original size:25 final size:25
Alignment explanation
Indices: 145036--145086 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
145026 AATTTATTTT
*
145036 AATAAATAATTTAAAATGATTATAA
1 AATAAATAATTAAAAATGATTATAA
145061 AATAAATAA-TAAAAAT-ATTTATAA
1 AATAAATAATTAAAAATGA-TTATAA
145085 AA
1 AA
145087 ATATATGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 1 0.04
24 14 0.58
25 9 0.38
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (25 bp):
AATAAATAATTAAAAATGATTATAA
Found at i:145705 original size:60 final size:60
Alignment explanation
Indices: 145612--145802 Score: 240
Period size: 59 Copynumber: 3.2 Consensus size: 60
145602 TTAATATAAC
* * *
145612 ATTTGATATCTGAACTTGACACTTTTTTTTAATTTGATACCTAAACTTTTTTTTTACCCA
1 ATTTGATACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTTTGACCCA
* * * * *
145672 ATTTGGTACTTGAACTTGACACTTTTTCTTAATTTGGTACTTAAAC-TTTTTTGGACCCA
1 ATTTGATACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTTTGACCCA
* * * **
145731 ATTTGATACCTGAACTTGACATTTTTTCCTAATTTGATACCTAAGCTTTTTTTTAGATTCA
1 ATTTGATACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTTT-GACCCA
*
145792 ATTTGGTACCT
1 ATTTGATACCT
145803 AAATTTATTA
Statistics
Matches: 110, Mismatches: 19, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
59 50 0.45
60 46 0.42
61 14 0.13
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (60 bp):
ATTTGATACCTGAACTTGACACTTTTTCTTAATTTGATACCTAAACTTTTTTTTGACCCA
Found at i:157315 original size:129 final size:129
Alignment explanation
Indices: 157085--157341 Score: 406
Period size: 129 Copynumber: 2.0 Consensus size: 129
157075 TGAACCATTG
* * ** * *
157085 TGAATCATTCGTTAAATTTTGATGGTTCATATTAGTTTTTCTCTTCAAAATGATTCGTCCTCAAA
1 TGAATCATTCGTTAAATTCTGATGGTTCATATCAAATTTTCCCTTCAAAATGATTCATCCTCAAA
*
157150 TCTAAACCTGCATCAAAAGAAAATGGGGAAAGATTAGTGACACGTAAGGTGATACTAACACAAA
66 TCTAAACCTGCATCAAAAGAAAATGGGGAAAGATTAGTGACACGTAAGGTGACACTAACACAAA
*
157214 TGAATCATTCGTTGAATTCTGATGGTTCATATCAAATTTTCCCTTCAAAATGATTCATCCTCAAA
1 TGAATCATTCGTTAAATTCTGATGGTTCATATCAAATTTTCCCTTCAAAATGATTCATCCTCAAA
* * * *
157279 TCTGAACTTGCATCAAAAGACAATGGGGAAAGATTAGTGACACTTAAGGTGACACTAACACAA
66 TCTAAACCTGCATCAAAAGAAAATGGGGAAAGATTAGTGACACGTAAGGTGACACTAACACAA
157342 GATGCACCAA
Statistics
Matches: 116, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 116 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (129 bp):
TGAATCATTCGTTAAATTCTGATGGTTCATATCAAATTTTCCCTTCAAAATGATTCATCCTCAAA
TCTAAACCTGCATCAAAAGAAAATGGGGAAAGATTAGTGACACGTAAGGTGACACTAACACAAA
Found at i:157390 original size:129 final size:127
Alignment explanation
Indices: 157126--157372 Score: 293
Period size: 129 Copynumber: 1.9 Consensus size: 127
157116 TTAGTTTTTC
*
157126 TCTTCAAAATGATTCGTCCTCAAATCTAAACCTGCATCAAAAGAAAATGGGGAAAGATTAGTGAC
1 TCTTCAAAATGATTCATCCTCAAATCTAAACCTGCATCAAAAGAAAATGGGGAAAGATTAGTGAC
* * * * **** *
157191 ACGTAAGGTGATACTAACACAAATGAATCATTCGTTGAATTCTGATGGTTCATATCAAATTT
66 ACGTAAGGTGACACTAACACAAATGAACCATTAGTTGAATGCTGATGAAAAATATCAAATCT
* * *
157253 TCCCTTCAAAATGATTCATCCTCAAATCTGAACTTGCATCAAAAGACAATGGGGAAAGATTAGTG
1 T--CTTCAAAATGATTCATCCTCAAATCTAAACCTGCATCAAAAGAAAATGGGGAAAGATTAGTG
* *
157318 ACACTTAAGGTGACACTAACACAAGATGCACCAATTAGATT-AATGC-GAT-AAAAAT
64 ACACGTAAGGTGACACTAACACAA-ATGAACC-ATTAG-TTGAATGCTGATGAAAAAT
157373 TTTCATTAAT
Statistics
Matches: 101, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
127 1 0.01
129 82 0.81
130 8 0.08
131 8 0.08
132 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (127 bp):
TCTTCAAAATGATTCATCCTCAAATCTAAACCTGCATCAAAAGAAAATGGGGAAAGATTAGTGAC
ACGTAAGGTGACACTAACACAAATGAACCATTAGTTGAATGCTGATGAAAAATATCAAATCT
Found at i:159744 original size:78 final size:78
Alignment explanation
Indices: 159655--159852 Score: 315
Period size: 78 Copynumber: 2.5 Consensus size: 78
159645 ATGTAAGTTT
159655 TGAAATGTAAGATTTGAAACTAATAATAACACATATGAATACAATTTATTTAACTAATTTATCAA
1 TGAAATGTAAGATTTGAAACTAATAATAACACATATGAATACAATTTATTTAACTAATTTATCAA
* **
159720 AACACTTAAATAA
66 AAAACAAAAATAA
* * * *
159733 TGAAATGTAAGATTCGAAACTACTAATAGCACATATGAATACAATTTATTTAAGTAATTTATCAA
1 TGAAATGTAAGATTTGAAACTAATAATAACACATATGAATACAATTTATTTAACTAATTTATCAA
159798 AAAACAAAAATAA
66 AAAACAAAAATAA
*
159811 TAAAATGTAAGATTTGAAACTAATAATAACACATATGCAATA
1 TGAAATGTAAGATTTGAAACTAATAATAACACATATG-AATA
159853 TATAAGAAAT
Statistics
Matches: 108, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
78 104 0.96
79 4 0.04
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (78 bp):
TGAAATGTAAGATTTGAAACTAATAATAACACATATGAATACAATTTATTTAACTAATTTATCAA
AAAACAAAAATAA
Found at i:160472 original size:19 final size:18
Alignment explanation
Indices: 160448--160483 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
160438 AACCCAAAAT
160448 TCTCTCAAACTCACAAGAC
1 TCTCTCAAACTCA-AAGAC
*
160467 TCTCTCAATCTCAAAGA
1 TCTCTCAAACTCAAAGA
160484 TGGTAAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.36, C:0.33, G:0.06, T:0.25
Consensus pattern (18 bp):
TCTCTCAAACTCAAAGAC
Found at i:160718 original size:22 final size:22
Alignment explanation
Indices: 160692--160734 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
160682 TCGGGATGTC
160692 GTTTTCTTCTTT-TCGAGACATT
1 GTTTTCTT-TTTATCGAGACATT
*
160714 GTTTTCTTTTTATTGAGACAT
1 GTTTTCTTTTTATCGAGACAT
160735 CAGGTGTCGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.56
Consensus pattern (22 bp):
GTTTTCTTTTTATCGAGACATT
Found at i:168196 original size:17 final size:18
Alignment explanation
Indices: 168174--168208 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
168164 TTGAGAGTGT
168174 TTAAATT-TCGATTAAAA
1 TTAAATTATCGATTAAAA
168191 TTAAATTGATCGATTAAA
1 TTAAATT-ATCGATTAAA
168209 TTTTTAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (18 bp):
TTAAATTATCGATTAAAA
Found at i:168548 original size:20 final size:20
Alignment explanation
Indices: 168523--168569 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
168513 TCAAAAATTG
*
168523 TTATTTTCTTA-TTTTTGTTT
1 TTATTTT-TTATTTTTTATTT
168543 TTATTTTTTATTTTTTATTT
1 TTATTTTTTATTTTTTATTT
168563 TTATTTT
1 TTATTTT
168570 ATAAGTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (20 bp):
TTATTTTTTATTTTTTATTT
Found at i:168549 original size:6 final size:6
Alignment explanation
Indices: 168531--168569 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
168521 TGTTATTTTC
*
168531 TTATTT TTGTTT TTATTTT TTATTTT TTATTT TTATTT T
1 TTATTT TTATTT TTA-TTT TTA-TTT TTATTT TTATTT T
168570 ATAAGTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 17 0.57
7 13 0.43
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:168550 original size:7 final size:7
Alignment explanation
Indices: 168523--168569 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
168513 TCAAAAATTG
168523 TTATTTT
1 TTATTTT
168530 CTTA-TTT
1 -TTATTTT
*
168537 TT-GTTT
1 TTATTTT
168543 TTATTTT
1 TTATTTT
168550 TTATTTT
1 TTATTTT
168557 TTA-TTT
1 TTATTTT
168563 TTATTTT
1 TTATTTT
168570 ATAAGTTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
6 13 0.37
7 19 0.54
8 3 0.09
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (7 bp):
TTATTTT
Found at i:168556 original size:13 final size:13
Alignment explanation
Indices: 168523--168569 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
168513 TCAAAAATTG
168523 TTATTTTCTTATTT
1 TTATTTT-TTATTT
*
168537 TT-GTTTTTATTTT
1 TTATTTTTTA-TTT
168550 TTATTTTTTATTT
1 TTATTTTTTATTT
168563 TTATTTT
1 TTATTTT
168570 ATAAGTTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 3 0.10
13 18 0.62
14 8 0.28
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (13 bp):
TTATTTTTTATTT
Found at i:174521 original size:5 final size:5
Alignment explanation
Indices: 174511--174535 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
174501 GATTTATGTT
174511 TTACA TTACA TTACA TTACA TTACA
1 TTACA TTACA TTACA TTACA TTACA
174536 GCTCTCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
TTACA
Found at i:186774 original size:6 final size:6
Alignment explanation
Indices: 186763--186791 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
186753 ATAAAGACAA
186763 GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
186792 AGACCCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.34, T:0.14
Consensus pattern (6 bp):
GAAGAT
Found at i:197469 original size:16 final size:15
Alignment explanation
Indices: 197448--197498 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
197438 GGAATTAATT
197448 AAATTTTAAATATTAA
1 AAATTTTAAATA-TAA
*
197464 AAATTTAATAAATATAT
1 AAATTT--TAAATATAA
197481 AAATTATTAAATA-AA
1 AAATT-TTAAATATAA
197496 AAA
1 AAA
197499 AATAAAAGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 4 0.13
16 12 0.40
17 7 0.23
18 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTTTAAATATAA
Found at i:200864 original size:26 final size:26
Alignment explanation
Indices: 200829--200888 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
200819 GTTCTGAATA
*
200829 GAGAGAAGAAAAAAATGGAATTAAAAT
1 GAGAG-AGAAAAAAATGGAATCAAAAT
* *
200856 GAGAGAGAAACAGATGGAATCAAAAT
1 GAGAGAGAAAAAAATGGAATCAAAAT
*
200882 GAAAGAG
1 GAGAGAG
200889 TTGTTTGATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.58, C:0.03, G:0.27, T:0.12
Consensus pattern (26 bp):
GAGAGAGAAAAAAATGGAATCAAAAT
Found at i:214215 original size:13 final size:15
Alignment explanation
Indices: 214190--214225 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
214180 AGTATTTAAT
214190 ATTA-TTATCAAAAA
1 ATTATTTATCAAAAA
214204 A-TATTTAT-AAAAA
1 ATTATTTATCAAAAA
214217 ATTATTTAT
1 ATTATTTAT
214226 TTTTAATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
ATTATTTATCAAAAA
Found at i:214875 original size:20 final size:21
Alignment explanation
Indices: 214790--214876 Score: 79
Period size: 22 Copynumber: 4.1 Consensus size: 21
214780 AAAAAATATA
*
214790 TTACTGTTTTAGTGTTATTTTT
1 TTACTGTTTTAATG-TATTTTT
*
214812 TTACTGTTTTGAT-TACTATTTT
1 TTACTGTTTTAATGTA-T-TTTT
* * *
214834 TTATTGTTTTGATGT-TATTT
1 TTACTGTTTTAATGTATTTTT
*
214854 TTACTGTTTTAATGTTTTTTT
1 TTACTGTTTTAATGTATTTTT
214875 TT
1 TT
214877 TTTTGGTTGC
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
20 18 0.33
21 8 0.15
22 27 0.50
23 1 0.02
ACGTcount: A:0.15, C:0.05, G:0.11, T:0.69
Consensus pattern (21 bp):
TTACTGTTTTAATGTATTTTT
Found at i:214947 original size:12 final size:12
Alignment explanation
Indices: 214912--215005 Score: 70
Period size: 12 Copynumber: 8.0 Consensus size: 12
214902 ACTATTTTAG
214912 TATTGTTATTTT
1 TATTGTTATTTT
* *
214924 TGTT-TATGTTTT
1 TATTGT-TATTTT
*
214936 TATTGCTA-TTT
1 TATTGTTATTTT
214947 TACTT-TTATTTT
1 TA-TTGTTATTTT
* *
214959 TGTTGTTGTTTT
1 TATTGTTATTTT
214971 TATTGTTA-TTT
1 TATTGTTATTTT
* *
214982 TATTATTTTTTT
1 TATTGTTATTTT
*
214994 TGTTGTTATTTT
1 TATTGTTATTTT
215006 AGTTATTTGG
Statistics
Matches: 61, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
11 19 0.31
12 42 0.69
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.74
Consensus pattern (12 bp):
TATTGTTATTTT
Found at i:214956 original size:35 final size:35
Alignment explanation
Indices: 214912--215005 Score: 120
Period size: 35 Copynumber: 2.7 Consensus size: 35
214902 ACTATTTTAG
*
214912 TATTGTTATTTTTGTT-TATGTTTTTATTGCTATTT
1 TATTATTATTTTTGTTGT-TGTTTTTATTGCTATTT
*
214947 TACTT-TTATTTTTGTTGTTGTTTTTATTGTTATTT
1 TA-TTATTATTTTTGTTGTTGTTTTTATTGCTATTT
* *
214982 TATTATTTTTTTTGTTGTTATTTT
1 TATTATTATTTTTGTTGTTGTTTT
215006 AGTTATTTGG
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 2 0.04
35 48 0.91
36 3 0.06
ACGTcount: A:0.13, C:0.02, G:0.11, T:0.74
Consensus pattern (35 bp):
TATTATTATTTTTGTTGTTGTTTTTATTGCTATTT
Found at i:214982 original size:23 final size:23
Alignment explanation
Indices: 214904--215012 Score: 80
Period size: 23 Copynumber: 4.5 Consensus size: 23
214894 TTCTTTTTAC
*
214904 TATTTTAGTATTGTTATTT-TTGTT
1 TATTTTATTATTGTT-TTTATTG-T
214928 TATGTTT-TTATTGCTATTTTACTT-T
1 TAT-TTTATTATTG-T-TTTTA-TTGT
* *
214953 TATTTTTGTTGTTGTTTTTATTGT
1 TA-TTTTATTATTGTTTTTATTGT
* *
214977 TATTTTATTATTTTTTTTGTTGT
1 TATTTTATTATTGTTTTTATTGT
215000 TATTTTAGTTATT
1 TATTTTA-TTATT
215013 TGGATATTAT
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
23 26 0.37
24 21 0.30
25 14 0.20
26 7 0.10
27 2 0.03
ACGTcount: A:0.15, C:0.02, G:0.11, T:0.72
Consensus pattern (23 bp):
TATTTTATTATTGTTTTTATTGT
Found at i:215026 original size:32 final size:34
Alignment explanation
Indices: 214917--215026 Score: 86
Period size: 35 Copynumber: 3.2 Consensus size: 34
214907 TTTAGTATTG
* * *
214917 TTATTTTTGTT-TATGTTTTTATTGCTATTTTACTT-
1 TTATTTTTGTTGT-TGATTTTA-TGTTATTTGA-TTA
* *
214952 TTATTTTTGTTGTTGTTTTTATTGTTATTTTATTA
1 TTATTTTTGTTGTTGATTTTA-TGTTATTTGATTA
*
214987 TTTTTTTTGTTGTT-ATTTTA-GTTATTTGGA-TA
1 TTATTTTTGTTGTTGATTTTATGTTATTT-GATTA
215019 TTATTTTT
1 TTATTTTT
215027 ATATATTTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
32 16 0.24
33 1 0.01
34 7 0.10
35 42 0.63
36 1 0.01
ACGTcount: A:0.15, C:0.02, G:0.11, T:0.73
Consensus pattern (34 bp):
TTATTTTTGTTGTTGATTTTATGTTATTTGATTA
Found at i:215485 original size:27 final size:28
Alignment explanation
Indices: 215455--215517 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 28
215445 AAAGGGTTTT
* *
215455 TTACCTAAATAATAT-AAAAATA-ATTAA
1 TTACC-AAAAAATATGAAAAACATATTAA
215482 TTA-CAAAAAATATGAAAAACATATTAA
1 TTACCAAAAAATATGAAAAACATATTAA
215509 TTA-CAAAAA
1 TTACCAAAAA
215518 TAGGCATTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 8 0.25
26 7 0.22
27 17 0.53
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.29
Consensus pattern (28 bp):
TTACCAAAAAATATGAAAAACATATTAA
Found at i:215499 original size:25 final size:27
Alignment explanation
Indices: 215465--215517 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
215455 TTACCTAAAT
*
215465 AATAT-AAAAATA-ATTAATTACAAAA
1 AATATAAAAAACATATTAATTACAAAA
*
215490 AATATGAAAAACATATTAATTACAAAA
1 AATATAAAAAACATATTAATTACAAAA
215517 A
1 A
215518 TAGGCATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 5 0.20
26 6 0.24
27 14 0.56
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (27 bp):
AATATAAAAAACATATTAATTACAAAA
Found at i:216064 original size:18 final size:17
Alignment explanation
Indices: 216030--216065 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
216020 TATGTCAGAC
*
216030 ATTTTTTGAATAAAAAT
1 ATTTTTTGAAAAAAAAT
216047 ATTTTTTGAAAAATAAAT
1 ATTTTTTGAAAAA-AAAT
216065 A
1 A
216066 AAATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATTTTTTGAAAAAAAAT
Found at i:216345 original size:29 final size:28
Alignment explanation
Indices: 216296--216350 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
216286 CAAATACTTA
*
216296 TTTTTATAATTAATTTATTTTCTATACC
1 TTTTTATAATTAATATATTTTCTATACC
216324 TTTTTCATAATTAATA-ATTTTTCTATA
1 TTTTT-ATAATTAATATA-TTTTCTATA
216351 TTATTTAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTTATAATTAATATATTTTCTATACC
Found at i:217720 original size:23 final size:23
Alignment explanation
Indices: 217685--217738 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
217675 ACTCACAAGG
* **
217685 ACTAAAAATAAATGTTAAAATAA
1 ACTAAAAACAAATAATAAAATAA
* *
217708 ATTAAAAACAAATAATAAAATAC
1 ACTAAAAACAAATAATAAAATAA
217731 ACTAAAAA
1 ACTAAAAA
217739 TATTAAAATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (23 bp):
ACTAAAAACAAATAATAAAATAA
Found at i:218318 original size:23 final size:24
Alignment explanation
Indices: 218278--218323 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
218268 AACATAACTA
*
218278 TTTAAAAAACAAATAA-TTAAAAT
1 TTTAAAAAACAAAAAATTTAAAAT
218301 TTTAAAAAGA-AAAAAATTTAAAA
1 TTTAAAAA-ACAAAAAATTTAAAA
218324 AAAAAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (24 bp):
TTTAAAAAACAAAAAATTTAAAAT
Found at i:218334 original size:15 final size:16
Alignment explanation
Indices: 218296--218337 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
218286 ACAAATAATT
*
218296 AAAATTTTAAAAAGAA
1 AAAAATTTAAAAAGAA
218312 AAAAATTTAAAAA-AA
1 AAAAATTTAAAAAGAA
*
218327 AAACATTTAAA
1 AAAAATTTAAA
218338 CTTGCCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (16 bp):
AAAAATTTAAAAAGAA
Found at i:221522 original size:20 final size:22
Alignment explanation
Indices: 221497--221536 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
221487 TTTATATTAT
221497 TGTTTTGG-TGCT-TTTTTTAC
1 TGTTTTGGTTGCTATTTTTTAC
221517 TGTTTTGGTTGCTATTTTTT
1 TGTTTTGGTTGCTATTTTTT
221537 GTTGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 4 0.22
22 6 0.33
ACGTcount: A:0.05, C:0.07, G:0.20, T:0.68
Consensus pattern (22 bp):
TGTTTTGGTTGCTATTTTTTAC
Found at i:221534 original size:21 final size:20
Alignment explanation
Indices: 221497--221535 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
221487 TTTATATTAT
*
221497 TGTTTTGGTGCTTTTTTTAC
1 TGTTTTGGTGCTATTTTTAC
221517 TGTTTTGGTTGCTATTTTT
1 TGTTTTGG-TGCTATTTTT
221536 TGTTGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.05, C:0.08, G:0.21, T:0.67
Consensus pattern (20 bp):
TGTTTTGGTGCTATTTTTAC
Found at i:221542 original size:22 final size:20
Alignment explanation
Indices: 221493--221544 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 20
221483 AAAATTTATA
221493 TTATTGTTTTGGTGCTTTTT
1 TTATTGTTTTGGTGCTTTTT
*
221513 TTACTGTTTTGGTTGCTATTTT
1 TTATTGTTTTGG-TGCT-TTTT
*
221535 TTGTTGTTTT
1 TTATTGTTTT
221545 TTATTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 11 0.41
21 4 0.15
22 12 0.44
ACGTcount: A:0.06, C:0.06, G:0.19, T:0.69
Consensus pattern (20 bp):
TTATTGTTTTGGTGCTTTTT
Found at i:221597 original size:52 final size:52
Alignment explanation
Indices: 221493--221598 Score: 142
Period size: 52 Copynumber: 2.0 Consensus size: 52
221483 AAAATTTATA
* * *
221493 TTATTGTTTTGGTGCTTTTTTTACTGTTTTGGTTGCTATTTTTTGTTGTTTT
1 TTATTATTTTGGTGCTTTTTTTACTGTTTTGATTGCTATTTTGTGTTGTTTT
* * *
221545 TTATTATTTTGGTGC-TTTTTTACTGTTTTGATTGTTGTTTTCGTGTTTTTTT
1 TTATTATTTTGGTGCTTTTTTTACTGTTTTGATTGCTATTTT-GTGTTGTTTT
221597 TT
1 TT
221599 GCTGTTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
51 23 0.49
52 24 0.51
ACGTcount: A:0.07, C:0.06, G:0.18, T:0.70
Consensus pattern (52 bp):
TTATTATTTTGGTGCTTTTTTTACTGTTTTGATTGCTATTTTGTGTTGTTTT
Found at i:229425 original size:21 final size:21
Alignment explanation
Indices: 229399--229438 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
229389 AATTGAATTT
229399 TAAAATCA-AAAAAATAAAAAA
1 TAAAAT-ATAAAAAATAAAAAA
*
229420 TAAAATATTAAAAATAAAA
1 TAAAATATAAAAAATAAAA
229439 GTAGAAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAAATATAAAAAATAAAAAA
Found at i:243509 original size:119 final size:120
Alignment explanation
Indices: 243349--243582 Score: 314
Period size: 119 Copynumber: 2.0 Consensus size: 120
243339 AGTTTCTTCC
* *
243349 GATGATCCGACTGTAAGCAACGATGCTTCACAGACTAGACAAAGGTACCGAATTTCT-TTTTGTT
1 GATGATCCGACTGTAACCAACGATGATTCACAGACTAGACAAAGGTACCGAATTTCTGTTTT-TT
* * *
243413 TTGTCGTAAATTTCAATCCTTAAACCCTAATTCCCCCATG-TACTTAATTTCTTTG
65 TTCTCCTAAATTTCAATCCTTAAACCCTAATTCCCCAATGTTACTTAATTTCTTTG
* * * *
243468 GATG-TCCGCACTGTAACCAAC-AGTGATTCACAGCCTCGACAAAGTTATCGAATTTCTGTTTTT
1 GATGATCCG-ACTGTAACCAACGA-TGATTCACAGACTAGACAAAGGTACCGAATTTCTGTTTTT
* *
243531 TTTCTCCTAAATTTCAATTCTTAAACCCTAATTTCCCAATGTTACTTAATTT
64 TTTCTCCTAAATTTCAATCCTTAAACCCTAATTCCCCAATGTTACTTAATTT
243583 TTAAATTCAA
Statistics
Matches: 100, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
118 5 0.05
119 81 0.81
120 14 0.14
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.37
Consensus pattern (120 bp):
GATGATCCGACTGTAACCAACGATGATTCACAGACTAGACAAAGGTACCGAATTTCTGTTTTTTT
TCTCCTAAATTTCAATCCTTAAACCCTAATTCCCCAATGTTACTTAATTTCTTTG
Found at i:252962 original size:2 final size:2
Alignment explanation
Indices: 252955--252994 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
252945 TCTTACATAA
252955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
252995 TAACCATCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:256100 original size:14 final size:16
Alignment explanation
Indices: 256081--256113 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
256071 GGTTTTTTAC
256081 ATAAAT-AATAT-AAA
1 ATAAATAAATATGAAA
256095 ATAAATAAATATGAAA
1 ATAAATAAATATGAAA
256111 ATA
1 ATA
256114 GGGTAACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 5 0.29
16 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (16 bp):
ATAAATAAATATGAAA
Found at i:256711 original size:123 final size:124
Alignment explanation
Indices: 256572--256808 Score: 372
Period size: 125 Copynumber: 1.9 Consensus size: 124
256562 AAAATATTAA
*
256572 TTTTTTTTTTTAATTATAAAAGGGGATTGGTCT-C-AACCCCACACAACTTATTTCATCATTCAT
1 TTTTTTTTTTTAATTATAAAAGGGGATTGGTCTCCGAACCCCACACAAATTATTTCATCATTCAT
* *
256635 TTTGCCCTCAT-CACGTAAGTTCTTTTCTTCTCCTCTTACTTTGTTTTTTAATTAGGCTT
66 TTTGACCTCATCCACGTAAGTTC-ATTCTTCTCCTCTTACTTTGTTTTTTAATTAGGCTT
* *
256694 TTTTTTTTTTTAAATTATAAATGGGGATTGGTCTCCGAACCCCACACAAATTGTTTCATCATTCA
1 TTTTTTTTTTT-AATTATAAAAGGGGATTGGTCTCCGAACCCCACACAAATTATTTCATCATTCA
* *
256759 TTTTGACTTCATCCAGGTAAGTTCATTCTTCTCCTCTTACTTTGTTTTTT
65 TTTTGACCTCATCCACGTAAGTTCATTCTTCTCCTCTTACTTTGTTTTTT
256809 TTTAATTAAT
Statistics
Matches: 104, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
122 11 0.11
123 21 0.20
124 1 0.01
125 61 0.59
126 10 0.10
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.47
Consensus pattern (124 bp):
TTTTTTTTTTTAATTATAAAAGGGGATTGGTCTCCGAACCCCACACAAATTATTTCATCATTCAT
TTTGACCTCATCCACGTAAGTTCATTCTTCTCCTCTTACTTTGTTTTTTAATTAGGCTT
Found at i:257218 original size:20 final size:20
Alignment explanation
Indices: 257195--257263 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
257185 TAATGTAAAA
257195 ATTTGAAAAGTAATAATATT
1 ATTTGAAAAGTAATAATATT
* *
257215 ATTTTAAAA--AGTAA-ATT
1 ATTTGAAAAGTAATAATATT
* *
257232 -GTTGAAAAGCAAT-ATATT
1 ATTTGAAAAGTAATAATATT
257250 ATTTTGAAAAGTAA
1 A-TTTGAAAAGTAA
257264 AAAAAAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
16 6 0.16
17 4 0.11
18 9 0.24
20 18 0.49
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.38
Consensus pattern (20 bp):
ATTTGAAAAGTAATAATATT
Found at i:257260 original size:35 final size:36
Alignment explanation
Indices: 257197--257264 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
257187 ATGTAAAAAT
*
257197 TTGAAAAGTAATAATATTATTTTAAAAAGTAAATTG
1 TTGAAAAGCAATAATATTATTTTAAAAAGTAAATTG
*
257233 TTGAAAAGCAAT-ATATTATTTTGAAAAGTAAA
1 TTGAAAAGCAATAATATTATTTTAAAAAGTAAA
257265 AAAAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.50, C:0.01, G:0.12, T:0.37
Consensus pattern (36 bp):
TTGAAAAGCAATAATATTATTTTAAAAAGTAAATTG
Found at i:257833 original size:29 final size:31
Alignment explanation
Indices: 257776--257834 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
257766 ATCTCGAAAT
* *
257776 TATATATGAATTTTAATTTAATGTGTAATTG
1 TATACATGAATTTTAATTTAATGTATAATTG
257807 TATACATGAATTTTAATTT-A-GTATAATT
1 TATACATGAATTTTAATTTAATGTATAATT
257835 ATACACGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 7 0.27
30 1 0.04
31 18 0.69
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (31 bp):
TATACATGAATTTTAATTTAATGTATAATTG
Found at i:257845 original size:29 final size:31
Alignment explanation
Indices: 257781--257845 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
257771 GAAATTATAT
* * *
257781 ATGAATTTTAATTTAATGTGTAATTGTATAC
1 ATGAATTTTAATTTAATGTATAATTATACAC
257812 ATGAATTTTAATTT-A-GTATAATTATACAC
1 ATGAATTTTAATTTAATGTATAATTATACAC
*
257841 GTGAA
1 ATGAA
257846 AACTTTAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.50
30 1 0.03
31 14 0.47
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (31 bp):
ATGAATTTTAATTTAATGTATAATTATACAC
Found at i:258221 original size:17 final size:19
Alignment explanation
Indices: 258188--258229 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
258178 AGTGACGTTT
*
258188 TATTATATTTTTCATTTAA
1 TATTTTATTTTTCATTTAA
258207 T-TTTTATTTTT-ATTTAA
1 TATTTTATTTTTCATTTAA
258224 TATTTT
1 TATTTT
258230 TCTTTAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 7 0.33
18 13 0.62
19 1 0.05
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTATTTTTCATTTAA
Found at i:259451 original size:30 final size:29
Alignment explanation
Indices: 259224--259450 Score: 273
Period size: 30 Copynumber: 7.8 Consensus size: 29
259214 TTTGGGAAAA
*
259224 TTTGGGGTTAAAAATAGAATTTTTGGAAGT
1 TTTGGGG-TAAAAATGGAATTTTTGGAAGT
259254 TTT---G-AAAAATGGAATTTTTGGAAGT
1 TTTGGGGTAAAAATGGAATTTTTGGAAGT
* *
259279 TTAGGGGTAAAAATGGAATTTTTGGAAAT
1 TTTGGGGTAAAAATGGAATTTTTGGAAGT
* * *
259308 TTTGAGGTTAAAAAAGGAATTTTTGGAAAT
1 TTTG-GGGTAAAAATGGAATTTTTGGAAGT
* *
259338 TTTAGGGTTAAAAATGGAATTTTTAGAAGT
1 TTT-GGGGTAAAAATGGAATTTTTGGAAGT
*
259368 TTTGAGGTCAAAAATGGAATTTTTGGAAGT
1 TTTGGGGT-AAAAATGGAATTTTTGGAAGT
* *
259398 TTTGAGGTTAAAGATGGAATTTTTGGAAGT
1 TTTG-GGGTAAAAATGGAATTTTTGGAAGT
*
259428 TTTGGGGTCAAAATGGAATTTTT
1 TTTGGGGTAAAAATGGAATTTTT
259451 TAAAGTTTCG
Statistics
Matches: 171, Mismatches: 18, Indels: 17
0.83 0.09 0.08
Matches are distributed among these distances:
25 22 0.13
27 1 0.01
28 1 0.01
29 42 0.25
30 102 0.60
31 3 0.02
ACGTcount: A:0.34, C:0.01, G:0.26, T:0.39
Consensus pattern (29 bp):
TTTGGGGTAAAAATGGAATTTTTGGAAGT
Found at i:260569 original size:27 final size:28
Alignment explanation
Indices: 260511--260571 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
260501 AAAATGAGAG
*
260511 TTTTCGGATGCTCGGGGGCAAAATGGTAA
1 TTTT-GGATGCTCGGGGACAAAATGGTAA
* *
260540 TTTTGGATTCTC-GGGACAAAATGGTGA
1 TTTTGGATGCTCGGGGACAAAATGGTAA
260567 TTTTG
1 TTTTG
260572 AGAAAAATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 18 0.62
28 7 0.24
29 4 0.14
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.34
Consensus pattern (28 bp):
TTTTGGATGCTCGGGGACAAAATGGTAA
Found at i:260659 original size:29 final size:28
Alignment explanation
Indices: 260617--260806 Score: 87
Period size: 30 Copynumber: 6.4 Consensus size: 28
260607 TTCGAGGTCG
*
260617 AAATTGAAGTTTTTGGACATCCAGGGGCAA
1 AAATGGAA-TTTTTGGA-ATCCAGGGGCAA
*
260647 AAATGGAATTTTTGGAGGATCGA-GGGCAA
1 AAATGGAATTTTTGGA--ATCCAGGGGCAA
* *** *
260676 AAATGAGATTTTTTGGAAGTTTGGGGGTAA
1 AAATG-GAATTTTTGGAA-TCCAGGGGCAA
* * **
260706 AAATGGAATTTTTGGGAGTTTC-GAGATCAA
1 AAATGGAATTTTT-GGA-ATCCAG-GGGCAA
*** *
260736 AAATGGAATTTTTGGAAGTTTGGGGGTAA
1 AAATGGAATTTTTGGAA-TCCAGGGGCAA
* ** *
260765 AAATGGAAATTTTGGAAGTTTTAGGGTCAA
1 AAATGGAATTTTTGGAA--TCCAGGGGCAA
260795 AAATGGAATTTT
1 AAATGGAATTTT
260807 AGAAGTTTGA
Statistics
Matches: 125, Mismatches: 25, Indels: 20
0.74 0.15 0.12
Matches are distributed among these distances:
28 1 0.01
29 52 0.42
30 72 0.58
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (28 bp):
AAATGGAATTTTTGGAATCCAGGGGCAA
Found at i:260708 original size:59 final size:57
Alignment explanation
Indices: 260640--260981 Score: 328
Period size: 59 Copynumber: 5.8 Consensus size: 57
260630 TGGACATCCA
* * *
260640 GGGGCAAAAATGGAATTTTTGGAGGATCGAGGGCAAAAATGAGATTTTTTGGAAGTTTG
1 GGGGTAAAAATGGAATTTTTGGAGGTTCGAGGGCAAAAATG-GA-TTTTTAGAAGTTTG
* ** *
260699 GGGGTAAAAATGGAATTTTTGGGAGTTTCGAGATCAAAAATGGAATTTTTGGAAGTTTG
1 GGGGTAAAAATGGAATTTTT-GGAGGTTCGAGGGCAAAAATGG-ATTTTTAGAAGTTTG
* * ** *
260758 GGGGTAAAAATGGAAATTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTAGAAGTTTG
1 GGGGTAAAAATGGAATTTTTGGAGGTTCGAGGG-CAAAAATGGATTTTTAGAAGTTTG
* * * * *
260816 AGGGTAAAAATGGAATGTTTGGAAGTTTTG-GGGTCAAAAATGGGATTTTTAGAAGTTTA
1 GGGGTAAAAATGGAATTTTTGG-AGGTTCGAGGG-CAAAAAT-GGATTTTTAGAAGTTTG
* * * * *
260875 GGGGTGAAAATGGAATTTTTGCAAGTTTCGAGGTCAAAAATGGAATTTTTAGAAGTTTTT
1 GGGGTAAAAATGGAATTTTTG-GAGGTTCGAGGGCAAAAATGG-ATTTTTAGAAG-TTTG
* * * * *
260935 GGGTTAAAAATGGGATTTTTGGAAGTTCGAGGG-TAAAACGGATTTTT
1 GGGGTAAAAATGGAATTTTTGGAGGTTCGAGGGCAAAAATGGATTTTT
260982 TGGACAGTTT
Statistics
Matches: 236, Mismatches: 38, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
57 6 0.03
58 58 0.25
59 131 0.56
60 41 0.17
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (57 bp):
GGGGTAAAAATGGAATTTTTGGAGGTTCGAGGGCAAAAATGGATTTTTAGAAGTTTG
Found at i:260811 original size:29 final size:29
Alignment explanation
Indices: 260732--260953 Score: 211
Period size: 29 Copynumber: 7.6 Consensus size: 29
260722 AGTTTCGAGA
* **
260732 TCAAAAATGGAATTTTTGGAAGTTTGGGGG
1 TCAAAAATGGAA-TTTTAGAAGTTTTAGGG
*
260762 T-AAAAATGGAAATTTTGGAAGTTTTAGGG
1 TCAAAAATGG-AATTTTAGAAGTTTTAGGG
*
260791 TCAAAAATGGAATTTTAGAAGTTTGAGGG
1 TCAAAAATGGAATTTTAGAAGTTTTAGGG
* *
260820 T-AAAAATGGAATGTTTGGAAGTTTTGGGG
1 TCAAAAATGGAAT-TTTAGAAGTTTTAGGG
*
260849 TCAAAAATGGGATTTTTAGAAG-TTTAGGGG
1 TCAAAAAT-GGAATTTTAGAAGTTTTA-GGG
* * *
260879 T-GAAAATGGAATTTTTGCAAG-TTTCGAGG
1 TCAAAAATGGAATTTTAG-AAGTTTTAG-GG
*
260908 TCAAAAATGGAATTTTTAGAAGTTTTTGGG
1 TCAAAAATGGAA-TTTTAGAAGTTTTAGGG
* *
260938 TTAAAAATGGGATTTT
1 TCAAAAATGGAATTTT
260954 TGGAAGTTCG
Statistics
Matches: 162, Mismatches: 19, Indels: 23
0.79 0.09 0.11
Matches are distributed among these distances:
28 20 0.12
29 77 0.48
30 52 0.32
31 13 0.08
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
TCAAAAATGGAATTTTAGAAGTTTTAGGG
Found at i:260971 original size:29 final size:29
Alignment explanation
Indices: 260645--260995 Score: 338
Period size: 30 Copynumber: 12.0 Consensus size: 29
260635 ATCCAGGGGC
* * * *
260645 AAAAATGGAATTTTTGGAGGATCGAGGGC
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT
* *
260674 AAAAATGAGATTTTTTGGAAGTTTGGGGGT
1 AAAAATG-GAATTTTTGGAAGTTTGAGGGT
* *
260704 AAAAATGGAATTTTTGGGAGTTTCGA-GAT
1 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
*
260733 CAAAAATGGAATTTTTGGAAGTTTGGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGAGGGT
* *
260763 AAAAATGGAAATTTTGGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT
*
260792 CAAAAATGGAA-TTTTAGAAGTTTGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGAGGGT
*
260821 AAAAATGGAATGTTTGGAAGTTTTG-GGGT
1 AAAAATGGAATTTTTGGAAG-TTTGAGGGT
* *
260850 CAAAAATGGGATTTTTAGAAGTTT-AGGGGT
1 -AAAAATGGAATTTTTGGAAGTTTGA-GGGT
* *
260880 GAAAATGGAATTTTTGCAAGTTTCGA-GGT
1 AAAAATGGAATTTTTGGAAGTTT-GAGGGT
* **
260909 CAAAAATGGAATTTTTAGAAGTTTTTGGGTT
1 -AAAAATGGAATTTTTGGAAGTTTGAGGG-T
* *
260940 AAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTTGAGGGT
* *
260969 -AAAACGGATTTTTTGGACAGTTT-AGGG
1 AAAAATGGAATTTTTGGA-AGTTTGAGGG
260996 ACCTCCAAGG
Statistics
Matches: 265, Mismatches: 41, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
28 28 0.11
29 107 0.40
30 128 0.48
31 2 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTTGAGGGT
Found at i:262055 original size:3 final size:3
Alignment explanation
Indices: 262042--262110 Score: 59
Period size: 3 Copynumber: 22.0 Consensus size: 3
262032 GTTTCCCTTT
* *
262042 TTA TT- TTA TTA TTA ATA TTA TTA TTA TTTA TTAA ATA GTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA -TTA TTA TTA
* *
262089 TTA TTAA CTA TTA TTA CTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA
262111 ATGTTACTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
2 2 0.04
3 42 0.79
4 9 0.17
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:262102 original size:16 final size:16
Alignment explanation
Indices: 262081--262111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
262071 ATTAAATAGT
*
262081 TATTATTATTATTAAC
1 TATTATTACTATTAAC
262097 TATTATTACTATTAA
1 TATTATTACTATTAA
262112 TGTTACTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTATTACTATTAAC
Found at i:262876 original size:17 final size:17
Alignment explanation
Indices: 262851--262939 Score: 81
Period size: 17 Copynumber: 5.1 Consensus size: 17
262841 GTCTTTTTAA
* **
262851 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
262868 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
262885 TTAAA-TTTAAAGGAAAT
1 TTAAATTTTAAA-TAAAT
*
262902 TTAAATTTAAAAGATAAAT
1 TTAAATTT-TAA-ATAAAT
*
262921 TTAAATTTAAAATAAAT
1 TTAAATTTTAAATAAAT
262938 TT
1 TT
262940 GAATCAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
16 5 0.08
17 35 0.58
18 5 0.08
19 14 0.23
20 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:262880 original size:6 final size:6
Alignment explanation
Indices: 262866--262931 Score: 64
Period size: 6 Copynumber: 11.2 Consensus size: 6
262856 TTTTAAATCC
* **
262866 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GGAA ATTTAA ATTTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
**
262913 AGATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA A
262932 ATAAATTTGA
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
5 7 0.15
6 36 0.77
7 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:262922 original size:19 final size:18
Alignment explanation
Indices: 262866--262939 Score: 91
Period size: 17 Copynumber: 4.2 Consensus size: 18
262856 TTTTAAATCC
* *
262866 ATTTAAATTT-TAATTAA
1 ATTTAAATTTAAAAGTAA
*
262883 ATTTAAATTT-AAAGGAA
1 ATTTAAATTTAAAAGTAA
262900 ATTTAAATTTAAAAGATAA
1 ATTTAAATTTAAAAG-TAA
262919 ATTTAAATTTAAAA-TAA
1 ATTTAAATTTAAAAGTAA
262936 ATTT
1 ATTT
262940 GAATCAATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
17 31 0.61
18 4 0.08
19 16 0.31
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (18 bp):
ATTTAAATTTAAAAGTAA
Found at i:263774 original size:3 final size:3
Alignment explanation
Indices: 263766--263806 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
263756 GCATTAATAC
263766 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
263807 ACTATTTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:264724 original size:17 final size:17
Alignment explanation
Indices: 264702--264761 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
264692 ATTAATTTTA
264702 ATTAAAAAAATTTAAAT
1 ATTAAAAAAATTTAAAT
*
264719 ATTAAAAAAGAGTATAAAAT
1 ATTAAAAAA-A-T-TTAAAT
*
264739 ATTAAAAATAATATAAA-
1 ATTAAAAA-AATTTAAAT
264756 ATTAAA
1 ATTAAA
264762 TGAATTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
17 15 0.42
18 4 0.11
19 2 0.06
20 14 0.39
21 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
ATTAAAAAAATTTAAAT
Found at i:264753 original size:19 final size:18
Alignment explanation
Indices: 264702--264757 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 18
264692 ATTAATTTTA
*
264702 ATTAAAAAAAT-TTAAAT
1 ATTAAAAAAATATAAAAT
264719 ATTAAAAAAGAGTATAAAAT
1 ATTAAAAAA-A-TATAAAAT
264739 ATTAAAAATAATATAAAAT
1 ATTAAAAA-AATATAAAAT
264758 TAAATGAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 9 0.26
18 1 0.03
19 9 0.26
20 14 0.41
21 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (18 bp):
ATTAAAAAAATATAAAAT
Found at i:265034 original size:14 final size:15
Alignment explanation
Indices: 264998--265039 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
264988 TTAGATTATT
264998 ATTTTTTATATGCCTCA
1 ATTTTTTATAT--CTCA
*
265015 AGTTTTTATAT-TCA
1 ATTTTTTATATCTCA
265029 ATTTTTTATAT
1 ATTTTTTATAT
265040 ACCTCTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 13 0.57
17 10 0.43
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.60
Consensus pattern (15 bp):
ATTTTTTATATCTCA
Found at i:265488 original size:23 final size:21
Alignment explanation
Indices: 265440--265480 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 21
265430 ATCATCTTTT
265440 AATTAATAAATAT-ATTTTATA
1 AATT-ATAAATATAATTTTATA
265461 AATTATAAATATAATATTTA
1 AATTATAAATATAAT-TTTA
265481 ATGAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTATAAATATAATTTTATA
Done.